[med-svn] [unc-fish] 08/12: New upstream version 1.0+dfsg
Andreas Tille
tille at debian.org
Fri Dec 29 21:42:02 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository unc-fish.
commit 4c01c6fb11f18bdb655f9cd1ed04af6c378e2ecc
Author: Andreas Tille <tille at debian.org>
Date: Fri Dec 29 22:36:35 2017 +0100
New upstream version 1.0+dfsg
---
INSTALL.txt | 69 +
LICENSE.txt | 168 +
README.txt | 21 +
SAMPLES.txt | 26 +
debian/changelog | 8 -
debian/compat | 1 -
debian/control | 42 -
debian/copyright | 184 -
debian/createmanpages | 7 -
debian/fish-tests.README.Debian | 9 -
debian/manpages | 1 -
debian/patches/fix_makefile.patch | 26 -
debian/patches/ngopt.patch | 227 -
debian/patches/series | 2 -
debian/rules | 23 -
debian/source/format | 1 -
debian/unc-fish-tests.README.Debian | 9 -
debian/unc-fish-tests.install | 2 -
debian/unc-fish.1 | 42 -
debian/unc-fish.README.Debian | 13 -
debian/unc-fish.install | 1 -
debian/unc-fish.links | 1 -
debian/upstream/metadata | 12 -
debian/watch | 3 -
docs/fishmanual.pdf | Bin 0 -> 117013 bytes
docs/fishmanual/WARNINGS | 3 +
docs/fishmanual/fishmanual.css | 30 +
docs/fishmanual/fishmanual.html | 197 +
docs/fishmanual/images.aux | 1 +
docs/fishmanual/images.log | 313 +
docs/fishmanual/images.pl | 187 +
docs/fishmanual/images.tex | 381 +
docs/fishmanual/img1.png | Bin 0 -> 203 bytes
docs/fishmanual/img10.png | Bin 0 -> 927 bytes
docs/fishmanual/img11.png | Bin 0 -> 1730 bytes
docs/fishmanual/img12.png | Bin 0 -> 201 bytes
docs/fishmanual/img13.png | Bin 0 -> 1065 bytes
docs/fishmanual/img14.png | Bin 0 -> 280 bytes
docs/fishmanual/img15.png | Bin 0 -> 234 bytes
docs/fishmanual/img16.png | Bin 0 -> 4525 bytes
docs/fishmanual/img17.png | Bin 0 -> 994 bytes
docs/fishmanual/img18.png | Bin 0 -> 296 bytes
docs/fishmanual/img19.png | Bin 0 -> 235 bytes
docs/fishmanual/img2.png | Bin 0 -> 219 bytes
docs/fishmanual/img20.png | Bin 0 -> 217 bytes
docs/fishmanual/img21.png | Bin 0 -> 262 bytes
docs/fishmanual/img22.png | Bin 0 -> 244 bytes
docs/fishmanual/img23.png | Bin 0 -> 600 bytes
docs/fishmanual/img24.png | Bin 0 -> 233 bytes
docs/fishmanual/img25.png | Bin 0 -> 230 bytes
docs/fishmanual/img26.png | Bin 0 -> 753 bytes
docs/fishmanual/img27.png | Bin 0 -> 258 bytes
docs/fishmanual/img28.png | Bin 0 -> 731 bytes
docs/fishmanual/img29.png | Bin 0 -> 97 bytes
docs/fishmanual/img3.png | Bin 0 -> 348 bytes
docs/fishmanual/img30.png | Bin 0 -> 221 bytes
docs/fishmanual/img4.png | Bin 0 -> 256 bytes
docs/fishmanual/img5.png | Bin 0 -> 225 bytes
docs/fishmanual/img6.png | Bin 0 -> 509 bytes
docs/fishmanual/img7.png | Bin 0 -> 238 bytes
docs/fishmanual/img8.png | Bin 0 -> 515 bytes
docs/fishmanual/img9.png | Bin 0 -> 534 bytes
docs/fishmanual/index.html | 197 +
docs/fishmanual/internals.pl | 82 +
docs/fishmanual/labels.pl | 157 +
docs/fishmanual/node1.html | 188 +
docs/fishmanual/node10.html | 80 +
docs/fishmanual/node11.html | 75 +
docs/fishmanual/node12.html | 124 +
docs/fishmanual/node13.html | 147 +
docs/fishmanual/node14.html | 100 +
docs/fishmanual/node15.html | 77 +
docs/fishmanual/node16.html | 80 +
docs/fishmanual/node17.html | 94 +
docs/fishmanual/node18.html | 128 +
docs/fishmanual/node19.html | 87 +
docs/fishmanual/node2.html | 97 +
docs/fishmanual/node20.html | 166 +
docs/fishmanual/node21.html | 75 +
docs/fishmanual/node22.html | 201 +
docs/fishmanual/node23.html | 144 +
docs/fishmanual/node24.html | 149 +
docs/fishmanual/node25.html | 110 +
docs/fishmanual/node26.html | 88 +
docs/fishmanual/node27.html | 130 +
docs/fishmanual/node28.html | 85 +
docs/fishmanual/node29.html | 85 +
docs/fishmanual/node3.html | 129 +
docs/fishmanual/node30.html | 101 +
docs/fishmanual/node31.html | 102 +
docs/fishmanual/node32.html | 77 +
docs/fishmanual/node33.html | 79 +
docs/fishmanual/node34.html | 166 +
docs/fishmanual/node35.html | 85 +
docs/fishmanual/node36.html | 86 +
docs/fishmanual/node37.html | 181 +
docs/fishmanual/node38.html | 77 +
docs/fishmanual/node39.html | 113 +
docs/fishmanual/node4.html | 75 +
docs/fishmanual/node40.html | 119 +
docs/fishmanual/node41.html | 87 +
docs/fishmanual/node42.html | 88 +
docs/fishmanual/node43.html | 197 +
docs/fishmanual/node44.html | 126 +
docs/fishmanual/node45.html | 128 +
docs/fishmanual/node46.html | 189 +
docs/fishmanual/node47.html | 77 +
docs/fishmanual/node48.html | 81 +
docs/fishmanual/node5.html | 285 +
docs/fishmanual/node6.html | 78 +
docs/fishmanual/node7.html | 97 +
docs/fishmanual/node8.html | 95 +
docs/fishmanual/node9.html | 89 +
makefile | 16 +
sample_input/blk.out | 6969 ++++++
sample_input/check | 110 +
sample_input/control.txt | 33 +
sample_input/ctg.out | 25509 +++++++++++++++++++
sample_input/data/map1.txt | 6494 +++++
sample_input/data/map2.txt | 4038 +++
sample_input/data/map3.txt | 5221 ++++
sample_input/data/map4.txt | 3825 +++
sample_input/data/map5.txt | 5888 +++++
sample_input/data/match1v1.txt | 44664 ++++++++++++++++++++++++++++++++++
sample_input/data/match1v2.txt | 29477 ++++++++++++++++++++++
sample_input/data/match1v3.txt | 35011 ++++++++++++++++++++++++++
sample_input/data/match1v4.txt | 28336 +++++++++++++++++++++
sample_input/data/match1v5.txt | 36799 ++++++++++++++++++++++++++++
sample_input/data/match2v1.txt | 23897 ++++++++++++++++++
sample_input/data/match2v2.txt | 20010 +++++++++++++++
sample_input/data/match2v3.txt | 21496 ++++++++++++++++
sample_input/data/match2v4.txt | 17409 +++++++++++++
sample_input/data/match2v5.txt | 20171 +++++++++++++++
sample_input/data/match3v1.txt | 30768 +++++++++++++++++++++++
sample_input/data/match3v2.txt | 22947 +++++++++++++++++
sample_input/data/match3v3.txt | 32255 ++++++++++++++++++++++++
sample_input/data/match3v4.txt | 21188 ++++++++++++++++
sample_input/data/match3v5.txt | 28195 +++++++++++++++++++++
sample_input/data/match4v1.txt | 23260 ++++++++++++++++++
sample_input/data/match4v2.txt | 18028 ++++++++++++++
sample_input/data/match4v3.txt | 20181 +++++++++++++++
sample_input/data/match4v4.txt | 19176 +++++++++++++++
sample_input/data/match4v5.txt | 21079 ++++++++++++++++
sample_input/data/match5v1.txt | 33479 +++++++++++++++++++++++++
sample_input/data/match5v2.txt | 22793 +++++++++++++++++
sample_input/data/match5v3.txt | 29137 ++++++++++++++++++++++
sample_input/data/match5v4.txt | 23253 ++++++++++++++++++
sample_input/data/match5v5.txt | 33351 +++++++++++++++++++++++++
sample_input/grd.out | 22101 +++++++++++++++++
sample_output/blocks.txt | 6969 ++++++
sample_output/contigs.txt | 25509 +++++++++++++++++++
sample_output/fish_out.txt | 117 +
sample_output/grids.txt | 22101 +++++++++++++++++
sample_output/simpleblocks.txt | 510 +
src/blocks.h | 180 +
src/dpalgo.h | 138 +
src/fish.cpp | 373 +
src/grids.h | 304 +
src/output_sc.h | 122 +
src/point.cpp | 14 +
src/point.h | 14 +
src/readfile.h | 472 +
src/tandem.h | 324 +
src/usage.h | 176 +
164 files changed, 801236 insertions(+), 614 deletions(-)
diff --git a/INSTALL.txt b/INSTALL.txt
new file mode 100644
index 0000000..59124cc
--- /dev/null
+++ b/INSTALL.txt
@@ -0,0 +1,69 @@
+This README tells you how to install the FISH-1.0 on your
+own system.
+
+
+Source Distribution
+--------------------------------
+ INSTALLATION:
+ 1. "tar -xzvf FISH-1.0.tar.z"
+ 2. "cd FISH-1.0"
+ 3. "make all"
+ 4. "cp bin/fish /usr/local/bin/"
+
+ REQUIREMENTS:
+ 1. g++ compiler. Fish is known to successfully compile with g++ 3.1 and 3.2. To see what version of g++ you have type "g++ -v".
+
+ 2. 32 MB of RAM.
+
+ 3. Operating system: Known to compile and run on Solaris, RedHat 8.0,
+Windows and Mac OS 10.2. It should be compilable and runnable on all systems
+with g++ installed. For windows environments, MinGW(http://www.mingw.org),
+provides a g++ compiler that works well.
+
+
+
+Windows Operating Systems
+-------------------------
+ INSTALLATION:
+ 1. Unzip FISH-1.0-win.zip into "C:\<DESIRED DIRECTORY>".
+ 2. The executable will be located in "C:<DESIRED DIRECTORY>\FISH-1.0\fish.exe".
+ For Example:
+ Unzip to "C:\Program Files"
+ From a command line type: "C:\Program Files\FISH-1.0\fish.exe" -h ,
+ Don't forget the quotations marks!
+ This executes fish and shows the command line options. Please
+ see the manual for further instructions executing fish.
+
+ REQUIREMENTS:
+ 1. 32 MB of RAM.
+ 2. Operating system: Known to run on Windows XP,ME, and NT.
+
+
+Running with the Sample Data
+----------------------------
+From a command line, go to the directory where the sample control file("control.txt") is located:
+Windows: "C:\<DESIRED DIRECTORY>\FISH-1.0\"
+
+And run "fish".
+
+
+Mac OS X
+-------------------------
+ INSTALLATION:
+ 1. Unzip FISH-1.0-osx.zip.
+ 2. The executable will be located in "FISH-1.0/fish".
+
+ REQUIREMENTS:
+ 1. 32 MB of RAM.
+ 2. Operating system: Known to run on 10.2.x
+
+
+
+Running with the Sample Data
+----------------------------
+From a command line, go to the directory where the sample control file("control.txt") is located:
+Windows: "C:\FISH-1.0\"
+Others: "<root_of_FISH>/FISH-1.0/sample_input/"
+
+And run "fish".
+
diff --git a/LICENSE.txt b/LICENSE.txt
new file mode 100644
index 0000000..7a1f623
--- /dev/null
+++ b/LICENSE.txt
@@ -0,0 +1,168 @@
+License Agreement for FISH (Fast Identification of Segmental Homology) version 1.0
+
+FISH is copyright �2003, University of North Carolina at Chapel Hill
+
+As used herein, the term, "Program", below, refers to the source
+code and the derivatives supplied by the authors, and a "work based on the
+Program" means either the Program or any derivative work under copyright law:
+that is to say, a work containing the Program or
+a portion of it, either verbatim or with modifications and/or translated
+into another language. (Hereinafter, translation is included without limitation
+in the term "modification".) Each licensee is addressed as "you".
+
+1. SCOPE
+Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope. The act of running the
+Program is not restricted, and the output from the Program is covered only
+if its contents constitute a work based on the Program (independent of having
+been made by running the Program). Whether that is true depends on what the
+Program does.
+
+2. USER'S RIGHTS
+You may copy and distribute verbatim copies of the Program's source code
+as you receive it, in any medium, provided that you keep intact all the notices
+that refer to this License and to the absence of any warranty; give any other
+recipients of the Program a copy of this License along with the Program;
+and conspicuously and appropriately publish on each copy a disclaimer of
+warranty and the following statement: "Copyright �2003, University of North
+Carolina at Chapel Hill" If the code has been modified, you also may include
+the following statement: "Modified by [your institution]." You may charge a
+fee for the physical act of transferring a copy, and you may at your option
+offer warranty protection in exchange for a fee.
+
+3. RIGHTS IN DERIVATIVE AND COMBINED WORKS
+It is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to exercise
+the right to control the distribution of derivative or collective works based
+on the Program. Aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume of a storage
+or distribution medium does not bring the other work under the scope of this
+License.
+
+You may modify your copy or copies of the Program or any portion of it,
+thus forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 2 above, provided that you also meet the following
+conditions:
+(a) You must cause the modified files to carry prominent notices stating that you
+changed the files and the date and nature of any change.
+(b) You must cause any work that you distribute or publish, that in whole
+or in part contains or is derived from the Program or any part thereof, to be
+licensed as a whole at no charge to all third parties under the terms of this License.
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License,
+and its terms, do not apply to those sections when you distribute them as
+separate works. But when you distribute the same sections as part of a whole
+which is a work based on the Program, the distribution of the whole must
+be on the terms of this License, whose permissions for other licensees extend
+to the entire whole, and thus to each and every part regardless of who wrote
+it.
+
+4. USER'S PROVISION AND/OR DISTRIBUTION OF SOURCE CODE
+You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections
+1 and 2 above provided that you also accompany it with the complete corresponding
+machine-readable source code, which must be distributed under the terms of
+Sections 1 and 2 above on a medium customarily used for software interchange.
+
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code distributed
+need not include anything that is normally distributed (in either source
+or binary form) with the major components (compiler, kernel, and so on) of
+the operating system on which the executable runs, unless that component
+itself accompanies the executable. If distribution of executable or object code
+is made by offering access to copy from a designated place, then offering
+equivalent access to copy the source code from the same place counts as
+distribution of the source code, even though third parties are not compelled
+to copy the source along with the object code.
+
+5. LICENSE RESTRICTIONS
+(a) You may not copy, modify, sublicense, or distribute the Program
+except as expressly provided under this License. Any attempt otherwise to
+copy, modify, sublicense or distribute the Program is void, and will automatically
+terminate your rights under this License. However, parties who have received
+copies, or rights, from you under this License will not have their licenses
+terminated so long as such parties remain in full compliance.
+(b) You are not required to accept this License, since you have not
+signed it. However, nothing else grants you permission to modify or distribute
+the Program or its derivative works. These actions are prohibited by law
+if you do not accept this License. Therefore, by modifying or distributing
+the Program (or any work based on the Program), you indicate your acceptance
+of this License to do so, and all its terms and conditions for copying, distributing
+or modifying the Program or works based on it.
+(c) If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy simultaneously
+your obligations under this License and any other pertinent obligations,
+then as a consequence you may not distribute the Program at all. For example,
+if a patent license would not permit royalty-free redistribution of the Program
+by all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to refrain
+entirely from distribution of the Program.
+
+It is not the purpose of this section to induce you to infringe any patents
+or other property right claims or to contest validity of any such claims;
+ this section has the sole purpose of protecting the integrity of the free
+software distribution system, which is implemented by public license practices.
+Many people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of
+that system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot impose
+that choice.
+
+6. LICENSE CONVEYS TO SUBSEQUENT RECIPIENTS
+Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor
+to copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of
+the rights granted herein. You are not responsible for enforcing compliance
+by third parties to this License.
+
+7. SEVERABILITY
+If any portion of this license or any portion of any section of this
+license is held invalid or unenforceable under any particular circumstance,
+the balance of the section is intended to apply and the section as a whole
+is intended to apply in other circumstances.
+
+8. NO WARRANTY
+BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY
+AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY
+AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
diff --git a/README.txt b/README.txt
new file mode 100644
index 0000000..7f9c9bf
--- /dev/null
+++ b/README.txt
@@ -0,0 +1,21 @@
+README for FISH.
+
+FILES IN THIS DISTRIBUTION:
+1. SAMPLES.txt -- tells you how to run and view examples. Sample data is provided.
+2. INSTALL.txt -- tells you how to compile and install FISH-1.0 on your own system.
+3. makefile -- for compiling the source code
+4. LICENSE.txt -- to tell you what you can and cannot do with this program.
+5. README.txt -- the one you are currently reading
+
+DIRECTORIES IN THIS DISTRIBUTION:
+1. bin -- after compiling source code, this is where the "fish" executable is copied.
+2. docs -- contains the manual in postscript,html,and pdf formats.
+3. sample_input -- contains sample data and a sample control file.
+4. sample_ouput -- contains sample output
+5. src -- directory contain all source files.
+
+
+THE MANUAL:
+Please read the manual before using FISH-1.0. It is located in "docs" and is
+called "fishmanual.pdf".
+
diff --git a/SAMPLES.txt b/SAMPLES.txt
new file mode 100644
index 0000000..e9e4e3b
--- /dev/null
+++ b/SAMPLES.txt
@@ -0,0 +1,26 @@
+Samples...
+Two directories exist in the FISH-1.0 package, "sample_input" and
+"sample_output." They are described below.
+
+sample_input
+------------
+Inside the sample_input directory of the FISH distributions is a control
+file(control.txt) and a data directory called "data" which contains all
+the files mentioned in "control.txt."
+
+
+sample_output
+-------------
+The following list consists of sample outputs created after running the
+following command on the sample_input data:
+"fish -b blocks.txt -B simpleblocks.txt -g grids.txt -C contigs.txt > fish_out.txt"
+ ** the ">" in the above sends the ouput to the file "fish_out.txt"
+
+* blocks.txt -- human readable output of the homologous blocks detected by
+ FISH.
+* simpleblocks.txt -- computer readable output of the homologous blocks
+ detected by FISH.
+* grids.txt -- output of grid FISH constructed to find blocks.
+* contigs.txt -- output of contigs FISH constructed to create grids.
+* fishout.txt -- standard output of FISH.
+
diff --git a/debian/changelog b/debian/changelog
deleted file mode 100644
index a79aeda..0000000
--- a/debian/changelog
+++ /dev/null
@@ -1,8 +0,0 @@
-unc-fish (1.0+dfsg-1) UNRELEASED; urgency=low
-
- * Initial release (Closes: #<bug>)
- TODO: Find reason for failure:
- $ /usr/lib/unc-fish/fish -b blocks.txt -B simpleblocks.txt -g grids.txt -C contigs.txt
- Segmentation fault
-
- -- Andreas Tille <tille at debian.org> Fri, 14 Feb 2014 09:23:04 +0100
diff --git a/debian/compat b/debian/compat
deleted file mode 100644
index ec63514..0000000
--- a/debian/compat
+++ /dev/null
@@ -1 +0,0 @@
-9
diff --git a/debian/control b/debian/control
deleted file mode 100644
index 8f5bb39..0000000
--- a/debian/control
+++ /dev/null
@@ -1,42 +0,0 @@
-Source: unc-fish
-Section: science
-Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 9)
-Standards-Version: 3.9.5
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/unc-fish/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/unc-fish/trunk/
-Homepage: http://labs.bio.unc.edu/Vision/FISH/
-
-Package: unc-fish
-Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends}
-Description: Fast Identification of Segmental Homology
- FISH is software for identifying regions of common ancestry between
- genome maps. Fast identification and statistical evaluation of
- segmental homologies in comparative maps.
- .
- Development and maintenance of FISH is supported by funding from the
- National Science Foundation (Plant Genome Research Program Grants
- DBI-0110069 and DBI-0227314 to TJV and DMS-0102008 to PPC).
-
-Package: unc-fish-tests
-Architecture: all
-Priority: extra
-Enhances: unc-fish
-Depends: ${misc:Depends}
-Suggests: unc-fish
-Description: Tests for Fast Identification of Segmental Homology (fish)
- FISH is software for identifying regions of common ancestry between
- genome maps. Fast identification and statistical evaluation of
- segmental homologies in comparative maps.
- .
- Development and maintenance of FISH is supported by funding from the
- National Science Foundation (Plant Genome Research Program Grants
- DBI-0110069 and DBI-0227314 to TJV and DMS-0102008 to PPC).
- .
- This package contains the example data provided by upstream to enable
- the user to test fish.
-
diff --git a/debian/copyright b/debian/copyright
deleted file mode 100644
index 76e82b1..0000000
--- a/debian/copyright
+++ /dev/null
@@ -1,184 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: FISH
-Upstream-Contact: Todd J. Vision <tjv at bio.unc.edu>
-Source: http://labs.bio.unc.edu/Vision/FISH/
-Files-Excluded:
- bin
- docs/fishmanual.ps
- CVS
- */CVS
- */*/CVS
-
-Files: *
-Copyright: 2003 University of North Carolina at Chapel Hill
-License: LicenseAgreementFISH
- As used herein, the term, "Program", below, refers to the source
- code and the derivatives supplied by the authors, and a "work based on the
- Program" means either the Program or any derivative work under copyright law:
- that is to say, a work containing the Program or
- a portion of it, either verbatim or with modifications and/or translated
- into another language. (Hereinafter, translation is included without limitation
- in the term "modification".) Each licensee is addressed as "you".
- .
- 1. SCOPE
- Activities other than copying, distribution and modification are not
- covered by this License; they are outside its scope. The act of running the
- Program is not restricted, and the output from the Program is covered only
- if its contents constitute a work based on the Program (independent of having
- been made by running the Program). Whether that is true depends on what the
- Program does.
- .
- 2. USER'S RIGHTS
- You may copy and distribute verbatim copies of the Program's source code
- as you receive it, in any medium, provided that you keep intact all the notices
- that refer to this License and to the absence of any warranty; give any other
- recipients of the Program a copy of this License along with the Program;
- and conspicuously and appropriately publish on each copy a disclaimer of
- warranty and the following statement: "Copyright ©2003, University of North
- Carolina at Chapel Hill" If the code has been modified, you also may include
- the following statement: "Modified by [your institution]." You may charge a
- fee for the physical act of transferring a copy, and you may at your option
- offer warranty protection in exchange for a fee.
- .
- 3. RIGHTS IN DERIVATIVE AND COMBINED WORKS
- It is not the intent of this section to claim rights or contest
- your rights to work written entirely by you; rather, the intent is to exercise
- the right to control the distribution of derivative or collective works based
- on the Program. Aggregation of another work not based on the Program
- with the Program (or with a work based on the Program) on a volume of a storage
- or distribution medium does not bring the other work under the scope of this
- License.
- .
- You may modify your copy or copies of the Program or any portion of it,
- thus forming a work based on the Program, and copy and distribute such modifications
- or work under the terms of Section 2 above, provided that you also meet the following
- conditions:
- (a) You must cause the modified files to carry prominent notices stating that you
- changed the files and the date and nature of any change.
- (b) You must cause any work that you distribute or publish, that in whole
- or in part contains or is derived from the Program or any part thereof, to be
- licensed as a whole at no charge to all third parties under the terms of this License.
- .
- These requirements apply to the modified work as a whole. If identifiable
- sections of that work are not derived from the Program, and can be reasonably
- considered independent and separate works in themselves, then this License,
- and its terms, do not apply to those sections when you distribute them as
- separate works. But when you distribute the same sections as part of a whole
- which is a work based on the Program, the distribution of the whole must
- be on the terms of this License, whose permissions for other licensees extend
- to the entire whole, and thus to each and every part regardless of who wrote
- it.
- .
- 4. USER'S PROVISION AND/OR DISTRIBUTION OF SOURCE CODE
- You may copy and distribute the Program (or a work based on it, under
- Section 2) in object code or executable form under the terms of Sections
- 1 and 2 above provided that you also accompany it with the complete corresponding
- machine-readable source code, which must be distributed under the terms of
- Sections 1 and 2 above on a medium customarily used for software interchange.
- .
- The source code for a work means the preferred form of the work for making
- modifications to it. For an executable work, complete source code means all
- the source code for all modules it contains, plus any associated interface
- definition files, plus the scripts used to control compilation and installation
- of the executable. However, as a special exception, the source code distributed
- need not include anything that is normally distributed (in either source
- or binary form) with the major components (compiler, kernel, and so on) of
- the operating system on which the executable runs, unless that component
- itself accompanies the executable. If distribution of executable or object code
- is made by offering access to copy from a designated place, then offering
- equivalent access to copy the source code from the same place counts as
- distribution of the source code, even though third parties are not compelled
- to copy the source along with the object code.
- .
- 5. LICENSE RESTRICTIONS
- (a) You may not copy, modify, sublicense, or distribute the Program
- except as expressly provided under this License. Any attempt otherwise to
- copy, modify, sublicense or distribute the Program is void, and will automatically
- terminate your rights under this License. However, parties who have received
- copies, or rights, from you under this License will not have their licenses
- terminated so long as such parties remain in full compliance.
- (b) You are not required to accept this License, since you have not
- signed it. However, nothing else grants you permission to modify or distribute
- the Program or its derivative works. These actions are prohibited by law
- if you do not accept this License. Therefore, by modifying or distributing
- the Program (or any work based on the Program), you indicate your acceptance
- of this License to do so, and all its terms and conditions for copying, distributing
- or modifying the Program or works based on it.
- (c) If, as a consequence of a court judgment or allegation of patent
- infringement or for any other reason (not limited to patent issues), conditions
- are imposed on you (whether by court order, agreement or otherwise) that
- contradict the conditions of this License, they do not excuse you from the
- conditions of this License. If you cannot distribute so as to satisfy simultaneously
- your obligations under this License and any other pertinent obligations,
- then as a consequence you may not distribute the Program at all. For example,
- if a patent license would not permit royalty-free redistribution of the Program
- by all those who receive copies directly or indirectly through you, then
- the only way you could satisfy both it and this License would be to refrain
- entirely from distribution of the Program.
- .
- It is not the purpose of this section to induce you to infringe any patents
- or other property right claims or to contest validity of any such claims;
- this section has the sole purpose of protecting the integrity of the free
- software distribution system, which is implemented by public license practices.
- Many people have made generous contributions to the wide range of software
- distributed through that system in reliance on consistent application of
- that system; it is up to the author/donor to decide if he or she is willing
- to distribute software through any other system and a licensee cannot impose
- that choice.
- .
- 6. LICENSE CONVEYS TO SUBSEQUENT RECIPIENTS
- Each time you redistribute the Program (or any work based on the Program),
- the recipient automatically receives a license from the original licensor
- to copy, distribute or modify the Program subject to these terms and conditions.
- You may not impose any further restrictions on the recipients' exercise of
- the rights granted herein. You are not responsible for enforcing compliance
- by third parties to this License.
- .
- 7. SEVERABILITY
- If any portion of this license or any portion of any section of this
- license is held invalid or unenforceable under any particular circumstance,
- the balance of the section is intended to apply and the section as a whole
- is intended to apply in other circumstances.
- .
- 8. NO WARRANTY
- BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
- FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
- STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
- PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
- INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY
- AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
- PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
- YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
- .
- IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
- WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE
- THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
- GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
- USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
- DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
- PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
- EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
- SUCH DAMAGES. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
- FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
- STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
- PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
- INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY
- AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
- PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
- YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
- .
- IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
- WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE
- THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
- GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
- USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
- DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
- PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
- EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
- SUCH DAMAGES.
-
-Files: debian/*
-Copyright: 2014 Andreas Tille <tille at debian.org>
-License: GPLv3+
- The full text of GPL license version 3 can be found at
- /usr/share/common-licenses/GPL-3 .
diff --git a/debian/createmanpages b/debian/createmanpages
deleted file mode 100755
index 50e5132..0000000
--- a/debian/createmanpages
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/bin/sh
-VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//'`
-MANDIR=debian
-mkdir -p $MANDIR
-help2man --no-info --no-discard-stderr \
- --name='Fast Identification of Segmental Homology' \
- --version-string="$VERSION" unc-fish > $MANDIR/unc-fish.1
diff --git a/debian/fish-tests.README.Debian b/debian/fish-tests.README.Debian
deleted file mode 100644
index 7a5d1a5..0000000
--- a/debian/fish-tests.README.Debian
+++ /dev/null
@@ -1,9 +0,0 @@
-Test data for package fish
-==========================
-
-The data are installed at
-
- /var/lib/fish
-
-See the file SAMPLE.txt there for more instructions.
-
diff --git a/debian/manpages b/debian/manpages
deleted file mode 100644
index 0f65186..0000000
--- a/debian/manpages
+++ /dev/null
@@ -1 +0,0 @@
-debian/*.1
diff --git a/debian/patches/fix_makefile.patch b/debian/patches/fix_makefile.patch
deleted file mode 100644
index 3179287..0000000
--- a/debian/patches/fix_makefile.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Changed: Fri, 14 Feb 2014 09:23:04 +0100
-Description: Fix very basic makefile
- - Fix clean target
- - propagate build options
-
---- a/makefile
-+++ b/makefile
-@@ -3,14 +3,14 @@ CC = g++ -ggdb
-
-
- all : realall
-- make bin
-+ # make bin
-
- realall :
-- (cd ./src; $(CC) -c point.cpp; $(CC) fish.cpp point.o -o fish)
-+ (cd ./src; $(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) point.cpp fish.cpp -o fish)
-
- bin :
- mkdir bin
- mv src/fish ./bin
- clean :
-- (cd src ; rm *.o)
-+ (cd src ; rm -f *.o fish)
- (rm -rf ./bin)
diff --git a/debian/patches/ngopt.patch b/debian/patches/ngopt.patch
deleted file mode 100644
index f4cf8d4..0000000
--- a/debian/patches/ngopt.patch
+++ /dev/null
@@ -1,227 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Changed: Fri, 14 Feb 2014 09:23:04 +0100
-Description: Patch taken from ngopt at
- http://code.google.com/p/ngopt/source/browse/#svn%2Ftrunk%2FFISH%2Fsrc
- Without this patch the original code segfaults with the sample data set.
- However, the code is not only fixing a code problem but also does some other
- change of functionality - so the test data can not be reproduced with this
- patch.
-
---- a/src/blocks.h
-+++ b/src/blocks.h
-@@ -69,6 +69,8 @@ if(PRINT_BLOCK)
- int tempdist=0;
- ofstream p2b;
- p2b.open(Block_File.c_str(),ios::out);
-+/* Lets make the output easier to parse.
-+ * Get rid of this stuff first.
- p2b<<get_time_stamp()<<"";
- p2b<<"FISH v1.0\n";
- p2b<<"FISH is copyright (c)2003, University of North Carolina at Chapel Hill\n";
-@@ -79,15 +81,17 @@ if(PRINT_BLOCK)
- p2b<<"\ttotal_features = "<<Total_Features<<"\n\ttotal_cells = "<<Total_Cells<<"\n";
- p2b<<"\th = "<<prob<<"\n\td_T = "<<Thresh_Dist<<"\n\tMin_Block_Size = "<<Min_Block_Size;
- p2b<<"\n\tblock_prob = "<<BLOCK_PROB<<"\n\ttotal_blocks = "<<block_list.size()<<"\n\n\n";
--
-+*/
-+ // make the output tab-delimited
-+ p2b<<"contig1\tcontig2\tblock\tpoint\tdist\tmarkers\torientation"<<endl;
- for(i=0;i<block_list.size();i++)
- {
-
- dataj=block_list[i].block.begin();
-- p2b<<"-block "<<i<<endl;
-- p2b<<setw(10)<<"points"<<setw(10)<<"contig1"<<setw(10)<<"contig2"<<endl;
-- p2b<<setw(9)<<block_list[i].block.size()<<setw(9)<<MATCHES[*dataj].contig1<<setw(9)<<MATCHES[*dataj].contig2<<"\n\n";
-- p2b<<"\tpoint\tdist\tmarkers\torientation"<<endl;
-+ // p2b<<"-block "<<i<<endl;
-+ // p2b<<setw(10)<<"points"<<setw(10)<<"contig1"<<setw(10)<<"contig2"<<endl;
-+ // p2b<<setw(9)<<block_list[i].block.size()<<setw(9)<<MATCHES[*dataj].contig1<<setw(9)<<MATCHES[*dataj].contig2<<"\n\n";
-+ // p2b<<"block\tpoint\tdist\tmarkers\torientation"<<endl;
-
- tempy=MATCHES[*dataj].feat.y;
- tempx=MATCHES[*dataj].feat.x;
-@@ -96,35 +100,44 @@ if(PRINT_BLOCK)
- {
- tempdist=(MATCHES[*dataj].feat.y-tempy)+abs(MATCHES[*dataj].feat.x-tempx);
-
-- p2b<<"\t"<<*dataj<<"\t"<<tempdist<<"\t{";
--
-- for(j=0;j<f2g[MATCHES[*dataj].feat.y].gene_list.size();j++)
-- p2b<<f2g[MATCHES[*dataj].feat.y].gene_list[j]<<" ";
-+ p2b<<MATCHES[*dataj].contig1<<"\t"<<MATCHES[*dataj].contig2<<"\t"<<i<<"\t"<<*dataj<<"\t"<<tempdist<<"\t";
-
-- p2b<<"}{";
-+ for(j=0;j<f2g[MATCHES[*dataj].feat.y].gene_list.size();j++){
-+ p2b<<f2g[MATCHES[*dataj].feat.y].gene_list[j];
-+ if (j < f2g[MATCHES[*dataj].feat.y].gene_list.size() - 1)
-+ p2b <<",";
-+ }
-+ p2b<<"\t";
-+ // p2b<<"}{";
-+
-+ for(j=0;j<f2g[MATCHES[*dataj].feat.x].gene_list.size();j++){
-+ p2b<<f2g[MATCHES[*dataj].feat.x].gene_list[j];
-+ if (j < f2g[MATCHES[*dataj].feat.x].gene_list.size() - 1)
-+ p2b << ",";
-+ }
-
-- for(j=0;j<f2g[MATCHES[*dataj].feat.x].gene_list.size();j++)
-- p2b<<f2g[MATCHES[*dataj].feat.x].gene_list[j]<<" ";
-+ p2b<<"\t"<<MATCHES[*dataj].feat.direction<<"\n";
-+// p2b<<"}\t"<<MATCHES[*dataj].feat.direction<<"\n";
-
-- p2b<<"}\t"<<MATCHES[*dataj].feat.direction<<"\n";
- tempx=MATCHES[*dataj].feat.x;
- tempy=MATCHES[*dataj].feat.y;
-
- }
-
-
-- p2b<<"\n\n";
-+ //p2b<<"\n\n";
-
- }
-
--
-+/*
- p2b<<"-by contig\n";
- p2b<<setw(10)<<"contig1"<<setw(10)<<"contig2"<<setw(10)<<"blocks\n";
- for(i=0;i<sub_grid.size();i++)
- p2b<<setw(9)<<sub_grid[i].contig1<<setw(9)<<sub_grid[i].contig2<<setw(9)<<sub_grid[i].blocks<<endl;
--
-- p2b<<"\n-by size\n";
-- p2b<<setw(10)<<"points"<<setw(10)<<"obs"<<setw(10)<<"exp"<<setw(25)<<"p\n";
-+*/
-+// p2b<<"\n-by size\n";
-+ p2b<<"-by size\n";
-+ p2b<<"points"<<setw(10)<<"obs"<<setw(10)<<"exp"<<setw(25)<<"p\n";
- for(l=0;l<FREQ.size();l++)
- {
- if(FREQ[l]>0)
-@@ -132,7 +145,8 @@ if(PRINT_BLOCK)
- p_u=pow(n*prob,l)*prob;
- pvalue=1-exp(-1*Total_Cells*p_u);
- expected_blocks=Total_Cells*p_u;
-- p2b<<setw(9)<<l+1<<setw(9)<<FREQ[l]<<setw(15)<<scientific<<setprecision(2)<<expected_blocks<<setw(25)<<scientific<<pvalue<<"\n";
-+// p2b<<setw(9)<<l+1<<setw(9)<<FREQ[l]<<setw(15)<<scientific<<setprecision(2)<<expected_blocks<<setw(25)<<scientific<<pvalue<<"\n";
-+ p2b<<l+1<<"\t"<<FREQ[l]<<"\t"<<scientific<<setprecision(2)<<expected_blocks<<"\t"<<scientific<<pvalue<<"\n";
- }
- }
-
---- a/src/fish.cpp
-+++ b/src/fish.cpp
-@@ -39,7 +39,7 @@ string Block_File_S;
- bool MAX_SCORE=true;
- int TOP_HITS=5;
- int Max_Distance=10;
--int Min_Score=200;
-+int Min_Score=13;
- double Threshold=0.05;
- int Min_Block_Size=3;
- float BLOCK_PROB=.001;
---- a/src/readfile.h
-+++ b/src/readfile.h
-@@ -240,7 +240,7 @@ GENE_LIST::iterator chk_pos2;
- if(temp_map.size()>0)
- {
- sub_grid[sub_grid.size()-1].ext=true;
-- image_maps.insert(make_pair(contig1+contig2,temp_map));
-+ image_maps.insert(make_pair(contig1+"&"+contig2,temp_map));
- }
-
- temp_map.clear();
-@@ -327,7 +327,7 @@ GENE_LIST::iterator chk_pos2;
- if(image_maps.size()>0)
- {
-
-- pos1=image_maps.find(contig1+contig2);
-+ pos1=image_maps.find(contig1+"&"+contig2);
-
- if(pos1==image_maps.end())
- {
-@@ -339,16 +339,16 @@ GENE_LIST::iterator chk_pos2;
- {
- inserted++;
- mapexists=true;
-- tempscore=(image_maps[contig1+contig2][contig1+key_y+'&'+contig2+key_x]);
-+ tempscore=(image_maps[contig1+"&"+contig2][contig1+key_y+'&'+contig2+key_x]);
-
- if(MAX_SCORE==true)
-- image_maps[contig1+contig2][contig1+key_y+'&'+contig2+key_x]=(MAX(tempscore,score));
-+ image_maps[contig1+"&"+contig2][contig1+key_y+'&'+contig2+key_x]=(MAX(tempscore,score));
- else
- {
- if(tempscore==0)
-- image_maps[contig1+contig2][contig1+key_y+'&'+contig2+key_x]=(score);
-+ image_maps[contig1+"&"+contig2][contig1+key_y+'&'+contig2+key_x]=(score);
- else
-- image_maps[contig1+contig2][contig1+key_y+'&'+contig2+key_x]=(AVG(tempscore,score));
-+ image_maps[contig1+"&"+contig2][contig1+key_y+'&'+contig2+key_x]=(AVG(tempscore,score));
- }
-
- }
-@@ -365,7 +365,7 @@ GENE_LIST::iterator chk_pos2;
- }
-
- if(mapexists==false)
-- image_maps.insert(make_pair(contig1+contig2,temp_map));
-+ image_maps.insert(make_pair(contig1+"&"+contig2,temp_map));
-
- temp_map.clear();
-
-@@ -400,7 +400,7 @@ GENE_LIST::iterator chk_pos2;
- {
- contig1=i2s(sub_grid[k].contig1);
- contig2=i2s(sub_grid[k].contig2);
-- contigs=contig1+contig2;
-+ contigs=contig1+"&"+contig2;
- for(pos2=image_maps[contigs].begin();pos2!=image_maps[contigs].end();++pos2)
- {
- //cout<<"The firs key "<<pos2->first;
-@@ -433,7 +433,7 @@ if(GENE.size()==0 ||GENE.size()<=2)
-
-
-
--image_maps.~map();
-+//image_maps.~map();
-
- INV_GENE.clear();
- INV_GENE=GENE;
---- a/src/usage.h
-+++ b/src/usage.h
-@@ -23,7 +23,6 @@ void process_arguments(int argc, char* a
- check(i,argv,argc);
- Block_File=argv[++i];
- PRINT_BLOCK=true;
--
- }
-
- else if(temp=="-B")
-@@ -43,7 +42,7 @@ void process_arguments(int argc, char* a
- }
-
- else if(temp=="-off")
-- Max_Distance=0;
-+ Max_Distance=-1;
-
- else if(temp=="-q")
- QUIET_MODE=true;
-@@ -144,7 +143,7 @@ void process_arguments(int argc, char* a
- i++;
-
- }
--
-+ Max_Distance=-1;
- }
-
- void check(int j, char* argv[],int argc)
-@@ -167,7 +166,7 @@ void usage(void)
- {
- cerr<<"usage: fish [-f Control_File |control.txt]\n";
- cerr<<"\t[-b Block_File] [-g Grid_File] [-C Contig_File]\n";
-- cerr<<"\t[-D Max_Distance |10] [-S Min_Score |200] [-T Threshold |.05]\n";
-+ cerr<<"\t[-D Max_Distance |10] [-S Min_Score |13] [-T Threshold |.05]\n";
- cerr<<"\t[-m Min_Block_Size |3] [-off Turn off Detandemize] [-h help]\n";
- cerr<<"\t[-H Top_Hits |5] [-A Average_Score Selection | Max_Score]\n";
- cerr<<"\t[-p BLOCK_PROB |.001] [-B Block_File_Simple][-q QUIET_MODE]\n";
diff --git a/debian/patches/series b/debian/patches/series
deleted file mode 100644
index 7ff9430..0000000
--- a/debian/patches/series
+++ /dev/null
@@ -1,2 +0,0 @@
-fix_makefile.patch
-ngopt.patch
diff --git a/debian/rules b/debian/rules
deleted file mode 100755
index 58ec00b..0000000
--- a/debian/rules
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/make -f
-
-# DH_VERBOSE := 1
-
-# some helpful variables - uncomment them if needed
-# shamelessly stolen from http://jmtd.net/log/awk/
-#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
-#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
-#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
-#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
-#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
-#GIT_TAG := $(subst ~,_,$(VERSION))
-
-# alternatively to manually set those variables you can
-# include /usr/share/cdbs/1/rules/buildvars.mk
-# and use what is set there. Any hint whether dh might set variables in
-# a similar manner are welcome.
-
-%:
- dh $@
-
-#get-orig-source:
-# . debian/get-orig-source
diff --git a/debian/source/format b/debian/source/format
deleted file mode 100644
index 163aaf8..0000000
--- a/debian/source/format
+++ /dev/null
@@ -1 +0,0 @@
-3.0 (quilt)
diff --git a/debian/unc-fish-tests.README.Debian b/debian/unc-fish-tests.README.Debian
deleted file mode 100644
index 7a5d1a5..0000000
--- a/debian/unc-fish-tests.README.Debian
+++ /dev/null
@@ -1,9 +0,0 @@
-Test data for package fish
-==========================
-
-The data are installed at
-
- /var/lib/fish
-
-See the file SAMPLE.txt there for more instructions.
-
diff --git a/debian/unc-fish-tests.install b/debian/unc-fish-tests.install
deleted file mode 100644
index 0109b08..0000000
--- a/debian/unc-fish-tests.install
+++ /dev/null
@@ -1,2 +0,0 @@
-SAMPLES.txt var/lib/fish
-sample_* var/lib/fish
diff --git a/debian/unc-fish.1 b/debian/unc-fish.1
deleted file mode 100644
index 01e3ef0..0000000
--- a/debian/unc-fish.1
+++ /dev/null
@@ -1,42 +0,0 @@
-.TH UNC-FISH "1" "February 2014" "unc-fish 1.0+dfsg" "User Commands"
-.SH NAME
-unc-fish \- Fast Identification of Segmental Homology
-.SH SYNOPSIS
-.B fish
-[\-f Control_File |control.txt]
-.SH DESCRIPTION
-The program unc-fish was originalled named FISH and is a
-software for identifying regions of common ancestry between
-genome maps. Fast identification and statistical evaluation of
-segmental homologies in comparative maps.
-.SH OPTIONS
-.TP
-\fI\-b\fR Block_File
-.TP
-\fI\-g\fR Grid_File
-.TP
-\fI\-C\fR Contig_File
-.TP
-\fI\-D\fR Max_Distance [default=10]
-.TP
-\fI\-S\fR Min_Score [default=200]
-.TP
-\fI\-T\fR Threshold [default=.05]
-.TP
-\fI\-m\fR Min_Block_Size [default=3]
-.TP
-\fI\-off\fR Turn off Detandemize
-.TP
-\fI\-h\fR help
-.TP
-\fI\-H\fR Top_Hits [default=5]
-.TP
-\fI\-A\fR Average_Score Selection [default=Max_Score]
-.TP
-\fI\-p\fR BLOCK_PROB [default=.001]
-.TP
-\fI\-B\fR Block_File_Simple
-.TP
-\fI\-q\fR QUIET_MODE
-.TP
-\fI\-t\fR Print timing
diff --git a/debian/unc-fish.README.Debian b/debian/unc-fish.README.Debian
deleted file mode 100644
index 2d0a711..0000000
--- a/debian/unc-fish.README.Debian
+++ /dev/null
@@ -1,13 +0,0 @@
-FISH for Debian
-===============
-
-Please note: Since there is a package fish in Debian we needed to
-rename the package as well as the executable to unc-fish. If you
-need to use the exectuatble name `fish` somewhere in your scripts
-you can do so by setting
-
- export PATH=/usr/lib/unc-fish:$PATH
-
-since the unrenamed executable resides in /usr/lib/unc-fish.
-
- -- Andreas Tille <tille at debian.org> Fri, 14 Feb 2014 09:23:04 +0100
diff --git a/debian/unc-fish.install b/debian/unc-fish.install
deleted file mode 100644
index 6750054..0000000
--- a/debian/unc-fish.install
+++ /dev/null
@@ -1 +0,0 @@
-src/fish usr/lib/unc-fish
diff --git a/debian/unc-fish.links b/debian/unc-fish.links
deleted file mode 100644
index 607a830..0000000
--- a/debian/unc-fish.links
+++ /dev/null
@@ -1 +0,0 @@
-usr/lib/unc-fish/fish usr/bin/unc-fish
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
deleted file mode 100644
index 1617605..0000000
--- a/debian/upstream/metadata
+++ /dev/null
@@ -1,12 +0,0 @@
-Reference:
- Author: Peter P. Calabrese and Sugata Chakravarty and Todd J. Vision
- Title: Fast identification and statistical evaluation of segmental homologies in comparative maps
- Journal: Bioinformatics
- Year: 2003
- Volume: 19
- Number: Suppl 1
- Pages: i74-i80
- DOI: 10.1093/bioinformatics/btg1008
- PMID: 12855440
- URL: http://bioinformatics.oxfordjournals.org/content/19/suppl_1/i74
- eprint: http://bioinformatics.oxfordjournals.org/content/19/suppl_1/i74.full.pdf+html
diff --git a/debian/watch b/debian/watch
deleted file mode 100644
index 1c1cd5c..0000000
--- a/debian/watch
+++ /dev/null
@@ -1,3 +0,0 @@
-version=3
-opts=dversionmangle=s/\+dfsg// \
- http://labs.bio.unc.edu/Vision/FISH/ .*/vision/lab/FISH/FISH-([\d.]+)-src\.tar\.z
diff --git a/docs/fishmanual.pdf b/docs/fishmanual.pdf
new file mode 100644
index 0000000..58c69a7
Binary files /dev/null and b/docs/fishmanual.pdf differ
diff --git a/docs/fishmanual/WARNINGS b/docs/fishmanual/WARNINGS
new file mode 100644
index 0000000..4b3c1b0
--- /dev/null
+++ b/docs/fishmanual/WARNINGS
@@ -0,0 +1,3 @@
+No implementation found for style `url'
+
+? brace missing for \setlength
diff --git a/docs/fishmanual/fishmanual.css b/docs/fishmanual/fishmanual.css
new file mode 100644
index 0000000..d1824af
--- /dev/null
+++ b/docs/fishmanual/fishmanual.css
@@ -0,0 +1,30 @@
+/* Century Schoolbook font is very similar to Computer Modern Math: cmmi */
+.MATH { font-family: "Century Schoolbook", serif; }
+.MATH I { font-family: "Century Schoolbook", serif; font-style: italic }
+.BOLDMATH { font-family: "Century Schoolbook", serif; font-weight: bold }
+
+/* implement both fixed-size and relative sizes */
+SMALL.XTINY { font-size : xx-small }
+SMALL.TINY { font-size : x-small }
+SMALL.SCRIPTSIZE { font-size : smaller }
+SMALL.FOOTNOTESIZE { font-size : small }
+SMALL.SMALL { }
+BIG.LARGE { }
+BIG.XLARGE { font-size : large }
+BIG.XXLARGE { font-size : x-large }
+BIG.HUGE { font-size : larger }
+BIG.XHUGE { font-size : xx-large }
+
+/* heading styles */
+H1 { }
+H2 { }
+H3 { }
+H4 { }
+H5 { }
+
+/* mathematics styles */
+DIV.displaymath { } /* math displays */
+TD.eqno { } /* equation-number cells */
+
+
+/* document-specific styles come next */
diff --git a/docs/fishmanual/fishmanual.html b/docs/fishmanual/fishmanual.html
new file mode 100644
index 0000000..66edbb6
--- /dev/null
+++ b/docs/fishmanual/fishmanual.html
@@ -0,0 +1,197 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>User's Manual for FISH
+(Fast Identification of Segmental Homology)</TITLE>
+<META NAME="description" CONTENT="User's Manual for FISH
+(Fast Identification of Segmental Homology)">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node1.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html4"
+ HREF="node1.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up_g.png">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev_g.png">
+<A NAME="tex2html2"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html5"
+ HREF="node1.html">Contents</A>
+   <B> <A NAME="tex2html3"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1 ALIGN=CENTER>User's Manual for FISH
+<BR>(Fast Identification of Segmental Homology)</H1>
+<P ALIGN=CENTER><STRONG>version 1.0
+<BR>
+released 30 June 2003
+<BR>
+Copyright 2003 University of North Carolina at Chapel Hill</STRONG></P>
+<P ALIGN=LEFT></P>
+
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"></A>
+
+<UL>
+<LI><A NAME="tex2html6"
+ HREF="node1.html">Contents</A>
+<LI><A NAME="tex2html7"
+ HREF="node2.html">Getting started</A>
+<UL>
+<LI><A NAME="tex2html8"
+ HREF="node3.html">Introduction</A>
+<LI><A NAME="tex2html9"
+ HREF="node4.html">Contact information</A>
+<LI><A NAME="tex2html10"
+ HREF="node5.html">Legal information</A>
+<LI><A NAME="tex2html11"
+ HREF="node6.html">Acknowledgements</A>
+<LI><A NAME="tex2html12"
+ HREF="node7.html">Availability</A>
+<UL>
+<LI><A NAME="tex2html13"
+ HREF="node8.html">Installing from source code</A>
+<LI><A NAME="tex2html14"
+ HREF="node9.html">Installing the Windows executable</A>
+<LI><A NAME="tex2html15"
+ HREF="node10.html">Installing the MacOSX executable</A>
+<LI><A NAME="tex2html16"
+ HREF="node11.html">Testing FISH on sample data</A>
+</UL>
+</UL>
+<BR>
+<LI><A NAME="tex2html17"
+ HREF="node12.html">How it works</A>
+<UL>
+<LI><A NAME="tex2html18"
+ HREF="node13.html">Step 1: From markers to features </A>
+<LI><A NAME="tex2html19"
+ HREF="node14.html">Step 2: From features to grid </A>
+<UL>
+<LI><A NAME="tex2html20"
+ HREF="node15.html">Removing low ranking matches</A>
+<LI><A NAME="tex2html21"
+ HREF="node16.html">Numbering of points</A>
+<LI><A NAME="tex2html22"
+ HREF="node17.html">Enforcing symmetry</A>
+<LI><A NAME="tex2html23"
+ HREF="node18.html">Defining the neighborhood size</A>
+</UL>
+<LI><A NAME="tex2html24"
+ HREF="node19.html">Step 3: From grid to blocks </A>
+<UL>
+<LI><A NAME="tex2html25"
+ HREF="node20.html">Choosing among multiple neighbors</A>
+<LI><A NAME="tex2html26"
+ HREF="node21.html">Overlapping blocks</A>
+</UL>
+</UL>
+<BR>
+<LI><A NAME="tex2html27"
+ HREF="node22.html">Parameters</A>
+<UL>
+<LI><A NAME="tex2html28"
+ HREF="node23.html">Algorithmic parameters </A>
+<LI><A NAME="tex2html29"
+ HREF="node24.html">Input and output parameters </A>
+</UL>
+<BR>
+<LI><A NAME="tex2html30"
+ HREF="node25.html">File formats </A>
+<UL>
+<LI><A NAME="tex2html31"
+ HREF="node26.html">Input files</A>
+<UL>
+<LI><A NAME="tex2html32"
+ HREF="node27.html">Control file </A>
+<LI><A NAME="tex2html33"
+ HREF="node28.html">Map files </A>
+<LI><A NAME="tex2html34"
+ HREF="node29.html">Match files </A>
+</UL>
+<LI><A NAME="tex2html35"
+ HREF="node30.html">Output</A>
+<UL>
+<LI><A NAME="tex2html36"
+ HREF="node31.html">Screen output </A>
+<UL>
+<LI><A NAME="tex2html37"
+ HREF="node32.html">Processing contigs</A>
+<LI><A NAME="tex2html38"
+ HREF="node33.html">Processing matches</A>
+<LI><A NAME="tex2html39"
+ HREF="node34.html">Processing blocks</A>
+</UL>
+<LI><A NAME="tex2html40"
+ HREF="node35.html">Contig file </A>
+<LI><A NAME="tex2html41"
+ HREF="node36.html">Grid file </A>
+<LI><A NAME="tex2html42"
+ HREF="node37.html">Block file </A>
+<LI><A NAME="tex2html43"
+ HREF="node38.html">Simple block file</A>
+</UL>
+</UL>
+<BR>
+<LI><A NAME="tex2html44"
+ HREF="node39.html">An example </A>
+<UL>
+<LI><A NAME="tex2html45"
+ HREF="node40.html">A control input file</A>
+<LI><A NAME="tex2html46"
+ HREF="node41.html">A map input file</A>
+<LI><A NAME="tex2html47"
+ HREF="node42.html">A match input file</A>
+<LI><A NAME="tex2html48"
+ HREF="node43.html">An example of captured STDOUT</A>
+<LI><A NAME="tex2html49"
+ HREF="node44.html">A contig output file</A>
+<LI><A NAME="tex2html50"
+ HREF="node45.html">A grids output file</A>
+<LI><A NAME="tex2html51"
+ HREF="node46.html">A blocks file</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html52"
+ HREF="node47.html">Bibliography</A>
+<LI><A NAME="tex2html53"
+ HREF="node48.html">About this document ...</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/images.aux b/docs/fishmanual/images.aux
new file mode 100644
index 0000000..f23e546
--- /dev/null
+++ b/docs/fishmanual/images.aux
@@ -0,0 +1 @@
+\relax
diff --git a/docs/fishmanual/images.log b/docs/fishmanual/images.log
new file mode 100644
index 0000000..0539143
--- /dev/null
+++ b/docs/fishmanual/images.log
@@ -0,0 +1,313 @@
+This is TeX, Version 3.14159 (Web2C 7.3.1) (format=latex 2002.8.29) 27 JUN 2003 15:24
+**./images.tex
+(./images.tex
+LaTeX2e <2000/06/01>
+Babel <v3.7h> and hyphenation patterns for american, french, german, ngerman, i
+talian, nohyphenation, loaded.
+
+(/usr/share/texmf/tex/latex/base/report.cls
+Document Class: report 2000/05/19 v1.4b Standard LaTeX document class
+(/usr/share/texmf/tex/latex/base/size12.clo
+File: size12.clo 2000/05/19 v1.4b Standard LaTeX file (size option)
+)
+\c at part=\count79
+\c at chapter=\count80
+\c at section=\count81
+\c at subsection=\count82
+\c at subsubsection=\count83
+\c at paragraph=\count84
+\c at subparagraph=\count85
+\c at figure=\count86
+\c at table=\count87
+\abovecaptionskip=\skip41
+\belowcaptionskip=\skip42
+\bibindent=\dimen102
+) (/usr/share/texmf/tex/latex/base/ifthen.sty
+Package: ifthen 1999/09/10 v1.1b Standard LaTeX ifthen package (DPC)
+) (/usr/share/texmf/tex/latex/psnfss/times.sty
+Package: times 2000/01/12 PSNFSS-v8.1 Times font as default roman (SPQR)
+) (/usr/share/texmf/tex/latex/html/url.sty
+Package: url 1999/03/02 ver 1.4 Verb mode for urls, email addresses, and file
+ names
+) (/usr/share/texmf/tex/latex/amsmath/amsmath.sty
+Package: amsmath 2000/07/18 v2.13 AMS math features
+\@mathmargin=\skip43
+For additional information on amsmath, use the `?' option.
+(/usr/share/texmf/tex/latex/amsmath/amstext.sty
+Package: amstext 2000/06/29 v2.01
+(/usr/share/texmf/tex/latex/amsmath/amsgen.sty
+File: amsgen.sty 1999/11/30 v2.0
+\@emptytoks=\toks14
+\ex@=\dimen103
+)) (/usr/share/texmf/tex/latex/amsmath/amsbsy.sty
+Package: amsbsy 1999/11/29 v1.2d
+\pmbraise@=\dimen104
+) (/usr/share/texmf/tex/latex/amsmath/amsopn.sty
+Package: amsopn 1999/12/14 v2.01 operator names
+)
+\inf at bad=\count88
+LaTeX Info: Redefining \frac on input line 211.
+\uproot@=\count89
+\leftroot@=\count90
+LaTeX Info: Redefining \overline on input line 307.
+\classnum@=\count91
+\DOTSCASE@=\count92
+LaTeX Info: Redefining \ldots on input line 379.
+LaTeX Info: Redefining \dots on input line 382.
+LaTeX Info: Redefining \cdots on input line 467.
+\Mathstrutbox@=\box26
+\strutbox@=\box27
+\big at size=\dimen105
+LaTeX Font Info: Redeclaring font encoding OML on input line 567.
+LaTeX Font Info: Redeclaring font encoding OMS on input line 568.
+\macc at depth=\count93
+\c at MaxMatrixCols=\count94
+\dotsspace@=\muskip10
+\c at parentequation=\count95
+\dspbrk at lvl=\count96
+\tag at help=\toks15
+\row@=\count97
+\column@=\count98
+\maxfields@=\count99
+\andhelp@=\toks16
+\eqnshift@=\dimen106
+\alignsep@=\dimen107
+\tagshift@=\dimen108
+\tagwidth@=\dimen109
+\totwidth@=\dimen110
+\lineht@=\dimen111
+\@envbody=\toks17
+\multlinegap=\skip44
+\multlinetaggap=\skip45
+\mathdisplay at stack=\toks18
+LaTeX Info: Redefining \[ on input line 2666.
+LaTeX Info: Redefining \] on input line 2667.
+) (/usr/share/texmf/tex/latex/graphics/color.sty
+Package: color 1999/02/16 v1.0i Standard LaTeX Color (DPC)
+(/usr/share/texmf/tex/latex/config/color.cfg)
+Package color Info: Driver file: dvips.def on input line 125.
+(/usr/share/texmf/tex/latex/graphics/dvips.def
+File: dvips.def 1999/02/16 v3.0i Driver-dependant file (DPC,SPQR)
+) (/usr/share/texmf/tex/latex/graphics/dvipsnam.def
+File: dvipsnam.def 1999/02/16 v3.0i Driver-dependant file (DPC,SPQR)
+)) (/usr/share/texmf/tex/latex/base/inputenc.sty
+Package: inputenc 2000/07/01 v0.996 Input encoding file
+(/usr/share/texmf/tex/latex/base/latin1.def
+File: latin1.def 2000/07/01 v0.996 Input encoding file
+))
+\sizebox=\box28
+\lthtmlwrite=\write3
+(images.aux)
+\openout1 = `images.aux'.
+
+LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 129.
+LaTeX Font Info: ... okay on input line 129.
+LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 129.
+LaTeX Font Info: ... okay on input line 129.
+LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 129.
+LaTeX Font Info: ... okay on input line 129.
+LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 129.
+LaTeX Font Info: ... okay on input line 129.
+LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 129.
+LaTeX Font Info: ... okay on input line 129.
+LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 129.
+LaTeX Font Info: ... okay on input line 129.
+LaTeX Font Info: Try loading font information for OT1+ptm on input line 129.
+
+(/usr/share/texmf/tex/latex/psnfss/ot1ptm.fd
+File: ot1ptm.fd 2000/01/12 PSNFSS-v8.1 font definitions for OT1/ptm.
+)
+
+latex2htmlLength hsize=349.0pt
+
+latex2htmlLength vsize=632.5pt
+
+latex2htmlLength hoffset=0.0pt
+
+latex2htmlLength voffset=0.0pt
+
+latex2htmlLength topmargin=0.0pt
+
+latex2htmlLength topskip=0.00003pt
+
+latex2htmlLength headheight=0.0pt
+
+latex2htmlLength headsep=0.0pt
+
+latex2htmlLength parskip=0.0pt plus 1.0pt
+
+latex2htmlLength oddsidemargin=17.0pt
+
+latex2htmlLength evensidemargin=62.0pt
+
+Runaway argument?
+! Paragraph ended before \setlength was complete.
+<to be read again>
+ \par
+l.154
+
+I suspect you've forgotten a `}', causing me to apply this
+control sequence to too much text. How can we recover?
+My plan is to forget the whole thing and hope for the best.
+
+l2hSize :tex2html_wrap_inline927:8.09999pt::0.0pt::4.60844pt.
+[1
+
+
+
+]
+l2hSize :tex2html_wrap_inline929:8.59999pt::8.59999pt::6.13622pt.
+[2
+
+
+]
+l2hSize :tex2html_wrap_inline933:8.59999pt::8.59999pt::26.14455pt.
+[3
+
+
+]
+l2hSize :tex2html_wrap_inline949:8.09999pt::0.0pt::10.8777pt.
+[4
+
+
+]
+l2hSize :tex2html_wrap_inline951:8.09999pt::0.0pt::7.61385pt.
+[5
+
+
+]
+l2hSize :tex2html_wrap_inline953:9.5pt::9.5pt::46.33563pt.
+[6
+
+
+]
+l2hSize :tex2html_wrap_inline955:8.2pt::0.0pt::9.1187pt.
+[7
+
+
+]
+l2hSize :tex2html_wrap_inline957:9.5pt::9.5pt::38.3595pt.
+[8
+
+
+]
+l2hSize :tex2html_wrap_inline959:9.5pt::9.5pt::40.36877pt.
+[9
+
+
+]
+l2hSize :tex2html_wrap_inline961:9.5pt::9.5pt::128.3725pt.
+[10
+
+
+]
+l2hSize :tex2html_wrap_indisplay963:23.0493pt::23.0493pt::142.41006pt.
+[11
+
+
+]
+l2hSize :tex2html_wrap_inline967:8.09999pt::0.0pt::6.22151pt.
+[12
+
+
+]
+l2hSize :tex2html_wrap_indisplay969:17.61809pt::17.61809pt::82.64886pt.
+[13
+
+
+]
+l2hSize :tex2html_wrap_inline973:8.83331pt::8.83331pt::10.88707pt.
+[14
+
+
+]
+l2hSize :tex2html_wrap_inline975:8.09999pt::0.0pt::9.32216pt.
+[15
+
+
+]
+l2hSize :tex2html_wrap_indisplay977:29.59988pt::29.59988pt::273.96481pt.
+[16
+
+
+]
+l2hSize :tex2html_wrap_inline979:9.5pt::9.5pt::131.60048pt.
+[17
+
+
+]
+l2hSize :tex2html_wrap_inline1055:8.83331pt::8.83331pt::13.3348pt.
+[18
+
+
+]
+l2hSize :tex2html_wrap_inline1057:8.33331pt::0.0pt::7.36386pt.
+[19
+
+
+]
+l2hSize :tex2html_wrap_inline1081:8.59999pt::8.59999pt::9.73883pt.
+[20
+
+
+]
+l2hSize :tex2html_wrap_inline1088:8.2pt::0.0pt::11.26248pt.
+[21
+
+
+]
+l2hSize :tex2html_wrap_inline1090:8.2pt::0.0pt::9.83817pt.
+[22
+
+
+]
+l2hSize :tex2html_wrap_inline1092:9.5pt::9.5pt::60.50652pt.
+[23
+
+
+]
+l2hSize :tex2html_wrap_inline1100:8.2pt::0.0pt::8.5944pt.
+[24
+
+
+]
+l2hSize :tex2html_wrap_inline1102:8.59999pt::8.59999pt::6.49721pt.
+[25
+
+
+]
+l2hSize :tex2html_wrap_indisplay1121:10.28807pt::10.28807pt::72.35681pt.
+[26
+
+
+]
+l2hSize :tex2html_wrap_inline1123:8.09999pt::0.0pt::11.27838pt.
+[27
+
+
+]
+l2hSize :tex2html_wrap_inline1125:10.41026pt::10.41026pt::73.40439pt.
+[28
+
+
+]
+l2hSize :tex2html_wrap_inline1134:8.09999pt::0.0pt::0.60004pt.
+[29
+
+
+]
+l2hSize :tex2html_wrap_inline1136:9.5pt::9.5pt::6.60005pt.
+[30
+
+
+] (images.aux) )
+Here is how much of TeX's memory you used:
+ 1350 strings out of 20887
+ 15480 string characters out of 196241
+ 62032 words of memory out of 350001
+ 4321 multiletter control sequences out of 10000+15000
+ 8571 words of font info for 29 fonts, out of 400000 for 1000
+ 14 hyphenation exceptions out of 10000
+ 27i,10n,20p,224b,237s stack positions out of 3000i,100n,1500p,50000b,4000s
+
+Output written on images.dvi (30 pages, 7600 bytes).
diff --git a/docs/fishmanual/images.pl b/docs/fishmanual/images.pl
new file mode 100644
index 0000000..8fead7a
--- /dev/null
+++ b/docs/fishmanual/images.pl
@@ -0,0 +1,187 @@
+# LaTeX2HTML 2002 (1.62)
+# Associate images original text with physical files.
+
+
+$key = q/h=mslashn;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="78" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img6.png"
+ ALT="$ h=m/n$">|;
+
+$key = q/F;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="20" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img22.png"
+ ALT="$ F$">|;
+
+$key = q/displaystyled_T=frac{1}{2}+sqrt{frac{{log}(1-T)}{{log}(1-h)}}+frac{1}{4};MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="230" HEIGHT="80" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img11.png"
+ ALT="$\displaystyle d_T = \frac{1}{2}+\sqrt{\frac{{\log}(1-T)}{{\log}(1-h)}}+\frac{1}{4}$">|;
+
+$key = q/>;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="19" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img20.png"
+ ALT="$ >$">|;
+
+$key = q/p;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="14" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img25.png"
+ ALT="$ p$">|;
+
+$key = q/(X_j,Y_j);MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="68" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img9.png"
+ ALT="$ (X_j, Y_j)$">|;
+
+$key = q/N;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="22" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img21.png"
+ ALT="$ N$">|;
+
+$key = q/p_u=h(nh)^{k-1};MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="121" HEIGHT="40" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img28.png"
+ ALT="$ p_u = h(nh)^{k-1}$">|;
+
+$key = q/m;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="21" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img4.png"
+ ALT="$ m$">|;
+
+$key = q/d=|X_i-X_j|+|Y_j-Y_i|;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="208" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img10.png"
+ ALT="$ d = \vert X_i - X_j\vert + \vert Y_j - Y_i\vert$">|;
+
+$key = q/i;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="11" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img1.png"
+ ALT="$ i$">|;
+
+$key = q/F(F-1)slash2;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="100" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img23.png"
+ ALT="$ F(F-1)/2$">|;
+
+$key = q/d_c;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="21" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img14.png"
+ ALT="$ d_c$">|;
+
+$key = q/displaystylew={cases}1&text{ifthepointisthefirstintheblock},0.25&text{ifaninversionisimpliedbytheextension},0.75&text{otherwise}.{cases};MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="440" HEIGHT="101" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img16.png"
+ ALT="$\displaystyle w = \begin{cases}1 & \text{if the point is the first in the block...
+... inversion is implied by the extension},\ 0.75 & \text{otherwise}. \end{cases}$">|;
+
+$key = q/(X_i,Y_i);MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="65" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img8.png"
+ ALT="$ (X_i, Y_i)$">|;
+
+$key = q/j;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="14" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img2.png"
+ ALT="$ j$">|;
+
+$key = q/displaystylep=1-e^{-rcp_u};MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="119" HEIGHT="39" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img26.png"
+ ALT="$\displaystyle p = 1-e^{-rc p_u}$">|;
+
+$key = q/displaystyler=wfrac{1slashd_c}{sum_{1}^{n}(1slashd_c)};MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="135" HEIGHT="62" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img13.png"
+ ALT="$\displaystyle r = w \frac{1/d_c}{\sum_{1}^{n}(1/d_c)}$">|;
+
+$key = q/n;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="16" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img5.png"
+ ALT="$ n$">|;
+
+$key = q/igeqj;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="45" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img3.png"
+ ALT="$ i \geq j$">|;
+
+$key = q/w;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="19" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img15.png"
+ ALT="$ w$">|;
+
+$key = q/d_T;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="25" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img18.png"
+ ALT="$ d_T$">|;
+
+$key = q/L;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="17" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img24.png"
+ ALT="$ L$">|;
+
+$key = q/r;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="14" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img12.png"
+ ALT="$ r$">|;
+
+$key = q/backslash;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="14" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img30.png"
+ ALT="$ \backslash$">|;
+
+$key = q/h;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="16" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img19.png"
+ ALT="$ h$">|;
+
+$key = q/slash;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="5" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img29.png"
+ ALT="$ \/$">|;
+
+$key = q/|(|X_i-X_j|)-(|Y_j-Y_i|)|;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="213" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img17.png"
+ ALT="$ \vert(\vert X_i - X_j\vert)-(\vert Y_j - Y_i\vert)\vert$">|;
+
+$key = q/rc;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="22" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img27.png"
+ ALT="$ rc$">|;
+
+$key = q/T;MSF=1.6;LFS=12;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="18" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img7.png"
+ ALT="$ T$">|;
+
+1;
+
diff --git a/docs/fishmanual/images.tex b/docs/fishmanual/images.tex
new file mode 100644
index 0000000..dd6e685
--- /dev/null
+++ b/docs/fishmanual/images.tex
@@ -0,0 +1,381 @@
+\batchmode
+
+
+\documentclass[notitlepage,twoside,12pt]{report}
+\RequirePackage{ifthen}
+
+
+\usepackage{times}
+\usepackage{url}
+\usepackage{amsmath}
+\pagestyle{headings}
+
+
+
+\usepackage[dvips]{color}
+
+
+\pagecolor[gray]{.7}
+
+\usepackage[latin1]{inputenc}
+
+
+
+\makeatletter
+
+\makeatletter
+\count@=\the\catcode`\_ \catcode`\_=8
+\newenvironment{tex2html_wrap}{}{}%
+\catcode`\<=12\catcode`\_=\count@
+\newcommand{\providedcommand}[1]{\expandafter\providecommand\csname #1\endcsname}%
+\newcommand{\renewedcommand}[1]{\expandafter\providecommand\csname #1\endcsname{}%
+ \expandafter\renewcommand\csname #1\endcsname}%
+\newcommand{\newedenvironment}[1]{\newenvironment{#1}{}{}\renewenvironment{#1}}%
+\let\newedcommand\renewedcommand
+\let\renewedenvironment\newedenvironment
+\makeatother
+\let\mathon=$
+\let\mathoff=$
+\ifx\AtBeginDocument\undefined \newcommand{\AtBeginDocument}[1]{}\fi
+\newbox\sizebox
+\setlength{\hoffset}{0pt}\setlength{\voffset}{0pt}
+\addtolength{\textheight}{\footskip}\setlength{\footskip}{0pt}
+\addtolength{\textheight}{\topmargin}\setlength{\topmargin}{0pt}
+\addtolength{\textheight}{\headheight}\setlength{\headheight}{0pt}
+\addtolength{\textheight}{\headsep}\setlength{\headsep}{0pt}
+\setlength{\textwidth}{349pt}
+\newwrite\lthtmlwrite
+\makeatletter
+\let\realnormalsize=\normalsize
+\global\topskip=2sp
+\def\preveqno{}\let\real at float=\@float \let\realend at float=\end at float
+\def\@float{\let\@savefreelist\@freelist\real at float}
+\def\liih at math{\ifmmode$\else\bad at math\fi}
+\def\end at float{\realend at float\global\let\@freelist\@savefreelist}
+\let\real at dbflt=\@dbflt \let\end at dblfloat=\end at float
+\let\@largefloatcheck=\relax
+\let\if at boxedmulticols=\iftrue
+\def\@dbflt{\let\@savefreelist\@freelist\real at dbflt}
+\def\adjustnormalsize{\def\normalsize{\mathsurround=0pt \realnormalsize
+ \parindent=0pt\abovedisplayskip=0pt\belowdisplayskip=0pt}%
+ \def\phantompar{\csname par\endcsname}\normalsize}%
+\def\lthtmltypeout#1{{\let\protect\string \immediate\write\lthtmlwrite{#1}}}%
+\newcommand\lthtmlhboxmathA{\adjustnormalsize\setbox\sizebox=\hbox\bgroup\kern.05em }%
+\newcommand\lthtmlhboxmathB{\adjustnormalsize\setbox\sizebox=\hbox to\hsize\bgroup\hfill }%
+\newcommand\lthtmlvboxmathA{\adjustnormalsize\setbox\sizebox=\vbox\bgroup %
+ \let\ifinner=\iffalse \let\)\liih at math }%
+\newcommand\lthtmlboxmathZ{\@next\next\@currlist{}{\def\next{\voidb at x}}%
+ \expandafter\box\next\egroup}%
+\newcommand\lthtmlmathtype[1]{\gdef\lthtmlmathenv{#1}}%
+\newcommand\lthtmllogmath{\lthtmltypeout{l2hSize %
+:\lthtmlmathenv:\the\ht\sizebox::\the\dp\sizebox::\the\wd\sizebox.\preveqno}}%
+\newcommand\lthtmlfigureA[1]{\let\@savefreelist\@freelist
+ \lthtmlmathtype{#1}\lthtmlvboxmathA}%
+\newcommand\lthtmlpictureA{\bgroup\catcode`\_=8 \lthtmlpictureB}%
+\newcommand\lthtmlpictureB[1]{\lthtmlmathtype{#1}\egroup
+ \let\@savefreelist\@freelist \lthtmlhboxmathB}%
+\newcommand\lthtmlpictureZ[1]{\hfill\lthtmlfigureZ}%
+\newcommand\lthtmlfigureZ{\lthtmlboxmathZ\lthtmllogmath\copy\sizebox
+ \global\let\@freelist\@savefreelist}%
+\newcommand\lthtmldisplayA{\bgroup\catcode`\_=8 \lthtmldisplayAi}%
+\newcommand\lthtmldisplayAi[1]{\lthtmlmathtype{#1}\egroup\lthtmlvboxmathA}%
+\newcommand\lthtmldisplayB[1]{\edef\preveqno{(\theequation)}%
+ \lthtmldisplayA{#1}\let\@eqnnum\relax}%
+\newcommand\lthtmldisplayZ{\lthtmlboxmathZ\lthtmllogmath\lthtmlsetmath}%
+\newcommand\lthtmlinlinemathA{\bgroup\catcode`\_=8 \lthtmlinlinemathB}
+\newcommand\lthtmlinlinemathB[1]{\lthtmlmathtype{#1}\egroup\lthtmlhboxmathA
+ \vrule height1.5ex width0pt }%
+\newcommand\lthtmlinlineA{\bgroup\catcode`\_=8 \lthtmlinlineB}%
+\newcommand\lthtmlinlineB[1]{\lthtmlmathtype{#1}\egroup\lthtmlhboxmathA}%
+\newcommand\lthtmlinlineZ{\egroup\expandafter\ifdim\dp\sizebox>0pt %
+ \expandafter\centerinlinemath\fi\lthtmllogmath\lthtmlsetinline}
+\newcommand\lthtmlinlinemathZ{\egroup\expandafter\ifdim\dp\sizebox>0pt %
+ \expandafter\centerinlinemath\fi\lthtmllogmath\lthtmlsetmath}
+\newcommand\lthtmlindisplaymathZ{\egroup %
+ \centerinlinemath\lthtmllogmath\lthtmlsetmath}
+\def\lthtmlsetinline{\hbox{\vrule width.1em \vtop{\vbox{%
+ \kern.1em\copy\sizebox}\ifdim\dp\sizebox>0pt\kern.1em\else\kern.3pt\fi
+ \ifdim\hsize>\wd\sizebox \hrule depth1pt\fi}}}
+\def\lthtmlsetmath{\hbox{\vrule width.1em\kern-.05em\vtop{\vbox{%
+ \kern.1em\kern0.8 pt\hbox{\hglue.17em\copy\sizebox\hglue0.8 pt}}\kern.3pt%
+ \ifdim\dp\sizebox>0pt\kern.1em\fi \kern0.8 pt%
+ \ifdim\hsize>\wd\sizebox \hrule depth1pt\fi}}}
+\def\centerinlinemath{%
+ \dimen1=\ifdim\ht\sizebox<\dp\sizebox \dp\sizebox\else\ht\sizebox\fi
+ \advance\dimen1by.5pt \vrule width0pt height\dimen1 depth\dimen1
+ \dp\sizebox=\dimen1\ht\sizebox=\dimen1\relax}
+
+\def\lthtmlcheckvsize{\ifdim\ht\sizebox<\vsize
+ \ifdim\wd\sizebox<\hsize\expandafter\hfill\fi \expandafter\vfill
+ \else\expandafter\vss\fi}%
+\providecommand{\selectlanguage}[1]{}%
+\makeatletter \tracingstats = 1
+\providecommand{\Beta}{\textrm{B}}
+\providecommand{\Mu}{\textrm{M}}
+\providecommand{\Kappa}{\textrm{K}}
+\providecommand{\Rho}{\textrm{R}}
+\providecommand{\Epsilon}{\textrm{E}}
+\providecommand{\Chi}{\textrm{X}}
+\providecommand{\Iota}{\textrm{J}}
+\providecommand{\omicron}{\textrm{o}}
+\providecommand{\Zeta}{\textrm{Z}}
+\providecommand{\Eta}{\textrm{H}}
+\providecommand{\Omicron}{\textrm{O}}
+\providecommand{\Nu}{\textrm{N}}
+\providecommand{\Tau}{\textrm{T}}
+\providecommand{\Alpha}{\textrm{A}}
+
+
+\begin{document}
+\pagestyle{empty}\thispagestyle{empty}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength hsize=\the\hsize}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength vsize=\the\vsize}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength hoffset=\the\hoffset}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength voffset=\the\voffset}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength topmargin=\the\topmargin}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength topskip=\the\topskip}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength headheight=\the\headheight}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength headsep=\the\headsep}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength parskip=\the\parskip}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength oddsidemargin=\the\oddsidemargin}\lthtmltypeout{}%
+\makeatletter
+\if at twoside\lthtmltypeout{latex2htmlLength evensidemargin=\the\evensidemargin}%
+\else\lthtmltypeout{latex2htmlLength evensidemargin=\the\oddsidemargin}\fi%
+\lthtmltypeout{}%
+\makeatother
+\setcounter{page}{1}
+\onecolumn
+
+% !!! IMAGES START HERE !!!
+
+\stepcounter{chapter}
+
+\setlength%
+
+\setlength{}{}
+\stepcounter{section}
+\stepcounter{section}
+\stepcounter{section}
+\stepcounter{section}
+\stepcounter{section}
+\stepcounter{subsection}
+\stepcounter{subsection}
+\stepcounter{subsection}
+\stepcounter{subsection}
+\stepcounter{chapter}
+\stepcounter{section}
+\stepcounter{section}
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline927}%
+$ i$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline929}%
+$ j$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+\stepcounter{subsection}
+\stepcounter{subsection}
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline933}%
+$ i \geq j$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+\stepcounter{subsection}
+\stepcounter{subsection}
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline949}%
+$ m$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline951}%
+$ n$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline953}%
+$ h=m/n$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline955}%
+$ T$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline957}%
+$ (X_i, Y_i)$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline959}%
+$ (X_j, Y_j)$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline961}%
+$ d = |X_i - X_j| + |Y_j - Y_i|$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_indisplay963}%
+$\displaystyle d_T = \frac{1}{2}+\sqrt{\frac{{\log}(1-T)}{{\log}(1-h)}}+\frac{1}{4}$%
+\lthtmlindisplaymathZ
+\lthtmlcheckvsize\clearpage}
+
+\stepcounter{section}
+\stepcounter{subsection}
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline967}%
+$ r$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_indisplay969}%
+$\displaystyle r = w \frac{1/d_c}{\sum_{1}^{n}(1/d_c)}$%
+\lthtmlindisplaymathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline973}%
+$ d_c$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline975}%
+$ w$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_indisplay977}%
+$\displaystyle w = \begin{cases} 1 & \text{if the point is the first in the block},\\0.25 & \text{if an inversion is implied by the extension},\\0.75 & \text{otherwise}. \end{cases}$%
+\lthtmlindisplaymathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline979}%
+$ |(|X_i - X_j|)-(|Y_j - Y_i|)|$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+\stepcounter{subsection}
+\stepcounter{chapter}
+\stepcounter{section}
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline1055}%
+$ d_T$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline1057}%
+$ h$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+\stepcounter{section}
+\stepcounter{chapter}
+\stepcounter{section}
+\stepcounter{subsection}
+\stepcounter{subsection}
+\stepcounter{subsection}
+\stepcounter{section}
+\stepcounter{subsection}
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline1081}%
+$ >$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+\stepcounter{subsubsection}
+\stepcounter{subsubsection}
+\stepcounter{subsubsection}
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline1088}%
+$ N$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline1090}%
+$ F$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline1092}%
+$ F(F-1)/2$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline1100}%
+$ L$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline1102}%
+$ p$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+\stepcounter{subsection}
+\stepcounter{subsection}
+\stepcounter{subsection}
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_indisplay1121}%
+$\displaystyle p = 1-e^{-rc p_u}$%
+\lthtmlindisplaymathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline1123}%
+$ rc$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline1125}%
+$ p_u = h(nh)^{k-1}$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+\stepcounter{subsection}
+\stepcounter{chapter}
+\stepcounter{section}
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline1134}%
+$ \/$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline1136}%
+$ \backslash$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+\stepcounter{section}
+\stepcounter{section}
+\stepcounter{section}
+\stepcounter{section}
+\stepcounter{section}
+\stepcounter{section}
+
+\end{document}
diff --git a/docs/fishmanual/img1.png b/docs/fishmanual/img1.png
new file mode 100644
index 0000000..4efeade
Binary files /dev/null and b/docs/fishmanual/img1.png differ
diff --git a/docs/fishmanual/img10.png b/docs/fishmanual/img10.png
new file mode 100644
index 0000000..5961ddf
Binary files /dev/null and b/docs/fishmanual/img10.png differ
diff --git a/docs/fishmanual/img11.png b/docs/fishmanual/img11.png
new file mode 100644
index 0000000..7f8b391
Binary files /dev/null and b/docs/fishmanual/img11.png differ
diff --git a/docs/fishmanual/img12.png b/docs/fishmanual/img12.png
new file mode 100644
index 0000000..9c55bb1
Binary files /dev/null and b/docs/fishmanual/img12.png differ
diff --git a/docs/fishmanual/img13.png b/docs/fishmanual/img13.png
new file mode 100644
index 0000000..937361f
Binary files /dev/null and b/docs/fishmanual/img13.png differ
diff --git a/docs/fishmanual/img14.png b/docs/fishmanual/img14.png
new file mode 100644
index 0000000..c35c436
Binary files /dev/null and b/docs/fishmanual/img14.png differ
diff --git a/docs/fishmanual/img15.png b/docs/fishmanual/img15.png
new file mode 100644
index 0000000..4b920d3
Binary files /dev/null and b/docs/fishmanual/img15.png differ
diff --git a/docs/fishmanual/img16.png b/docs/fishmanual/img16.png
new file mode 100644
index 0000000..58484c1
Binary files /dev/null and b/docs/fishmanual/img16.png differ
diff --git a/docs/fishmanual/img17.png b/docs/fishmanual/img17.png
new file mode 100644
index 0000000..a8634f7
Binary files /dev/null and b/docs/fishmanual/img17.png differ
diff --git a/docs/fishmanual/img18.png b/docs/fishmanual/img18.png
new file mode 100644
index 0000000..159c5bd
Binary files /dev/null and b/docs/fishmanual/img18.png differ
diff --git a/docs/fishmanual/img19.png b/docs/fishmanual/img19.png
new file mode 100644
index 0000000..f23d2df
Binary files /dev/null and b/docs/fishmanual/img19.png differ
diff --git a/docs/fishmanual/img2.png b/docs/fishmanual/img2.png
new file mode 100644
index 0000000..a7903af
Binary files /dev/null and b/docs/fishmanual/img2.png differ
diff --git a/docs/fishmanual/img20.png b/docs/fishmanual/img20.png
new file mode 100644
index 0000000..695123f
Binary files /dev/null and b/docs/fishmanual/img20.png differ
diff --git a/docs/fishmanual/img21.png b/docs/fishmanual/img21.png
new file mode 100644
index 0000000..6dadf0c
Binary files /dev/null and b/docs/fishmanual/img21.png differ
diff --git a/docs/fishmanual/img22.png b/docs/fishmanual/img22.png
new file mode 100644
index 0000000..f8dfa44
Binary files /dev/null and b/docs/fishmanual/img22.png differ
diff --git a/docs/fishmanual/img23.png b/docs/fishmanual/img23.png
new file mode 100644
index 0000000..1491a62
Binary files /dev/null and b/docs/fishmanual/img23.png differ
diff --git a/docs/fishmanual/img24.png b/docs/fishmanual/img24.png
new file mode 100644
index 0000000..45aa0ca
Binary files /dev/null and b/docs/fishmanual/img24.png differ
diff --git a/docs/fishmanual/img25.png b/docs/fishmanual/img25.png
new file mode 100644
index 0000000..b5a75da
Binary files /dev/null and b/docs/fishmanual/img25.png differ
diff --git a/docs/fishmanual/img26.png b/docs/fishmanual/img26.png
new file mode 100644
index 0000000..3d80f2c
Binary files /dev/null and b/docs/fishmanual/img26.png differ
diff --git a/docs/fishmanual/img27.png b/docs/fishmanual/img27.png
new file mode 100644
index 0000000..7164e85
Binary files /dev/null and b/docs/fishmanual/img27.png differ
diff --git a/docs/fishmanual/img28.png b/docs/fishmanual/img28.png
new file mode 100644
index 0000000..fdeeae9
Binary files /dev/null and b/docs/fishmanual/img28.png differ
diff --git a/docs/fishmanual/img29.png b/docs/fishmanual/img29.png
new file mode 100644
index 0000000..5a9c59d
Binary files /dev/null and b/docs/fishmanual/img29.png differ
diff --git a/docs/fishmanual/img3.png b/docs/fishmanual/img3.png
new file mode 100644
index 0000000..e15e565
Binary files /dev/null and b/docs/fishmanual/img3.png differ
diff --git a/docs/fishmanual/img30.png b/docs/fishmanual/img30.png
new file mode 100644
index 0000000..f8e09c5
Binary files /dev/null and b/docs/fishmanual/img30.png differ
diff --git a/docs/fishmanual/img4.png b/docs/fishmanual/img4.png
new file mode 100644
index 0000000..4d9cebb
Binary files /dev/null and b/docs/fishmanual/img4.png differ
diff --git a/docs/fishmanual/img5.png b/docs/fishmanual/img5.png
new file mode 100644
index 0000000..4439248
Binary files /dev/null and b/docs/fishmanual/img5.png differ
diff --git a/docs/fishmanual/img6.png b/docs/fishmanual/img6.png
new file mode 100644
index 0000000..3aea34e
Binary files /dev/null and b/docs/fishmanual/img6.png differ
diff --git a/docs/fishmanual/img7.png b/docs/fishmanual/img7.png
new file mode 100644
index 0000000..b96951c
Binary files /dev/null and b/docs/fishmanual/img7.png differ
diff --git a/docs/fishmanual/img8.png b/docs/fishmanual/img8.png
new file mode 100644
index 0000000..7bfb25c
Binary files /dev/null and b/docs/fishmanual/img8.png differ
diff --git a/docs/fishmanual/img9.png b/docs/fishmanual/img9.png
new file mode 100644
index 0000000..9b71fab
Binary files /dev/null and b/docs/fishmanual/img9.png differ
diff --git a/docs/fishmanual/index.html b/docs/fishmanual/index.html
new file mode 100644
index 0000000..66edbb6
--- /dev/null
+++ b/docs/fishmanual/index.html
@@ -0,0 +1,197 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>User's Manual for FISH
+(Fast Identification of Segmental Homology)</TITLE>
+<META NAME="description" CONTENT="User's Manual for FISH
+(Fast Identification of Segmental Homology)">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node1.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html4"
+ HREF="node1.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up_g.png">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev_g.png">
+<A NAME="tex2html2"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html5"
+ HREF="node1.html">Contents</A>
+   <B> <A NAME="tex2html3"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1 ALIGN=CENTER>User's Manual for FISH
+<BR>(Fast Identification of Segmental Homology)</H1>
+<P ALIGN=CENTER><STRONG>version 1.0
+<BR>
+released 30 June 2003
+<BR>
+Copyright 2003 University of North Carolina at Chapel Hill</STRONG></P>
+<P ALIGN=LEFT></P>
+
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"></A>
+
+<UL>
+<LI><A NAME="tex2html6"
+ HREF="node1.html">Contents</A>
+<LI><A NAME="tex2html7"
+ HREF="node2.html">Getting started</A>
+<UL>
+<LI><A NAME="tex2html8"
+ HREF="node3.html">Introduction</A>
+<LI><A NAME="tex2html9"
+ HREF="node4.html">Contact information</A>
+<LI><A NAME="tex2html10"
+ HREF="node5.html">Legal information</A>
+<LI><A NAME="tex2html11"
+ HREF="node6.html">Acknowledgements</A>
+<LI><A NAME="tex2html12"
+ HREF="node7.html">Availability</A>
+<UL>
+<LI><A NAME="tex2html13"
+ HREF="node8.html">Installing from source code</A>
+<LI><A NAME="tex2html14"
+ HREF="node9.html">Installing the Windows executable</A>
+<LI><A NAME="tex2html15"
+ HREF="node10.html">Installing the MacOSX executable</A>
+<LI><A NAME="tex2html16"
+ HREF="node11.html">Testing FISH on sample data</A>
+</UL>
+</UL>
+<BR>
+<LI><A NAME="tex2html17"
+ HREF="node12.html">How it works</A>
+<UL>
+<LI><A NAME="tex2html18"
+ HREF="node13.html">Step 1: From markers to features </A>
+<LI><A NAME="tex2html19"
+ HREF="node14.html">Step 2: From features to grid </A>
+<UL>
+<LI><A NAME="tex2html20"
+ HREF="node15.html">Removing low ranking matches</A>
+<LI><A NAME="tex2html21"
+ HREF="node16.html">Numbering of points</A>
+<LI><A NAME="tex2html22"
+ HREF="node17.html">Enforcing symmetry</A>
+<LI><A NAME="tex2html23"
+ HREF="node18.html">Defining the neighborhood size</A>
+</UL>
+<LI><A NAME="tex2html24"
+ HREF="node19.html">Step 3: From grid to blocks </A>
+<UL>
+<LI><A NAME="tex2html25"
+ HREF="node20.html">Choosing among multiple neighbors</A>
+<LI><A NAME="tex2html26"
+ HREF="node21.html">Overlapping blocks</A>
+</UL>
+</UL>
+<BR>
+<LI><A NAME="tex2html27"
+ HREF="node22.html">Parameters</A>
+<UL>
+<LI><A NAME="tex2html28"
+ HREF="node23.html">Algorithmic parameters </A>
+<LI><A NAME="tex2html29"
+ HREF="node24.html">Input and output parameters </A>
+</UL>
+<BR>
+<LI><A NAME="tex2html30"
+ HREF="node25.html">File formats </A>
+<UL>
+<LI><A NAME="tex2html31"
+ HREF="node26.html">Input files</A>
+<UL>
+<LI><A NAME="tex2html32"
+ HREF="node27.html">Control file </A>
+<LI><A NAME="tex2html33"
+ HREF="node28.html">Map files </A>
+<LI><A NAME="tex2html34"
+ HREF="node29.html">Match files </A>
+</UL>
+<LI><A NAME="tex2html35"
+ HREF="node30.html">Output</A>
+<UL>
+<LI><A NAME="tex2html36"
+ HREF="node31.html">Screen output </A>
+<UL>
+<LI><A NAME="tex2html37"
+ HREF="node32.html">Processing contigs</A>
+<LI><A NAME="tex2html38"
+ HREF="node33.html">Processing matches</A>
+<LI><A NAME="tex2html39"
+ HREF="node34.html">Processing blocks</A>
+</UL>
+<LI><A NAME="tex2html40"
+ HREF="node35.html">Contig file </A>
+<LI><A NAME="tex2html41"
+ HREF="node36.html">Grid file </A>
+<LI><A NAME="tex2html42"
+ HREF="node37.html">Block file </A>
+<LI><A NAME="tex2html43"
+ HREF="node38.html">Simple block file</A>
+</UL>
+</UL>
+<BR>
+<LI><A NAME="tex2html44"
+ HREF="node39.html">An example </A>
+<UL>
+<LI><A NAME="tex2html45"
+ HREF="node40.html">A control input file</A>
+<LI><A NAME="tex2html46"
+ HREF="node41.html">A map input file</A>
+<LI><A NAME="tex2html47"
+ HREF="node42.html">A match input file</A>
+<LI><A NAME="tex2html48"
+ HREF="node43.html">An example of captured STDOUT</A>
+<LI><A NAME="tex2html49"
+ HREF="node44.html">A contig output file</A>
+<LI><A NAME="tex2html50"
+ HREF="node45.html">A grids output file</A>
+<LI><A NAME="tex2html51"
+ HREF="node46.html">A blocks file</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html52"
+ HREF="node47.html">Bibliography</A>
+<LI><A NAME="tex2html53"
+ HREF="node48.html">About this document ...</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/internals.pl b/docs/fishmanual/internals.pl
new file mode 100644
index 0000000..44de8fd
--- /dev/null
+++ b/docs/fishmanual/internals.pl
@@ -0,0 +1,82 @@
+# LaTeX2HTML 2002 (1.62)
+# Associate internals original text with physical files.
+
+
+$key = q/fileschapter/;
+$ref_files{$key} = "$dir".q|node25.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/blocks/;
+$ref_files{$key} = "$dir".q|node46.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/mapfile/;
+$ref_files{$key} = "$dir".q|node28.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/controlfile/;
+$ref_files{$key} = "$dir".q|node27.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/cite_Calabrese2003/;
+$ref_files{$key} = "$dir".q|node47.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/step3/;
+$ref_files{$key} = "$dir".q|node19.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/step2/;
+$ref_files{$key} = "$dir".q|node14.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/dT/;
+$ref_files{$key} = "$dir".q|node18.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/paramtable/;
+$ref_files{$key} = "$dir".q|node22.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/screenoutput/;
+$ref_files{$key} = "$dir".q|node31.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/gridfile/;
+$ref_files{$key} = "$dir".q|node36.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/blockfile/;
+$ref_files{$key} = "$dir".q|node37.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/step1/;
+$ref_files{$key} = "$dir".q|node13.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/cite_Vision2000/;
+$ref_files{$key} = "$dir".q|node47.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/matchfile/;
+$ref_files{$key} = "$dir".q|node29.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/examplefiles/;
+$ref_files{$key} = "$dir".q|node39.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/alg_param/;
+$ref_files{$key} = "$dir".q|node23.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/inoutparams/;
+$ref_files{$key} = "$dir".q|node24.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/contigfile/;
+$ref_files{$key} = "$dir".q|node35.html|;
+$noresave{$key} = "$nosave";
+
+1;
+
diff --git a/docs/fishmanual/labels.pl b/docs/fishmanual/labels.pl
new file mode 100644
index 0000000..e3f521c
--- /dev/null
+++ b/docs/fishmanual/labels.pl
@@ -0,0 +1,157 @@
+# LaTeX2HTML 2002 (1.62)
+# Associate labels original text with physical files.
+
+
+$key = q/fileschapter/;
+$external_labels{$key} = "$URL/" . q|node25.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/blocks/;
+$external_labels{$key} = "$URL/" . q|node46.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/mapfile/;
+$external_labels{$key} = "$URL/" . q|node28.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/controlfile/;
+$external_labels{$key} = "$URL/" . q|node27.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/cite_Calabrese2003/;
+$external_labels{$key} = "$URL/" . q|node47.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/step3/;
+$external_labels{$key} = "$URL/" . q|node19.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/step2/;
+$external_labels{$key} = "$URL/" . q|node14.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/dT/;
+$external_labels{$key} = "$URL/" . q|node18.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/paramtable/;
+$external_labels{$key} = "$URL/" . q|node22.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/screenoutput/;
+$external_labels{$key} = "$URL/" . q|node31.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/gridfile/;
+$external_labels{$key} = "$URL/" . q|node36.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/blockfile/;
+$external_labels{$key} = "$URL/" . q|node37.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/step1/;
+$external_labels{$key} = "$URL/" . q|node13.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/cite_Vision2000/;
+$external_labels{$key} = "$URL/" . q|node47.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/matchfile/;
+$external_labels{$key} = "$URL/" . q|node29.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/examplefiles/;
+$external_labels{$key} = "$URL/" . q|node39.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/alg_param/;
+$external_labels{$key} = "$URL/" . q|node23.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/inoutparams/;
+$external_labels{$key} = "$URL/" . q|node24.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/contigfile/;
+$external_labels{$key} = "$URL/" . q|node35.html|;
+$noresave{$key} = "$nosave";
+
+1;
+
+
+# LaTeX2HTML 2002 (1.62)
+# labels from external_latex_labels array.
+
+
+$key = q/step1/;
+$external_latex_labels{$key} = q|2.1|;
+$noresave{$key} = "$nosave";
+
+$key = q/fileschapter/;
+$external_latex_labels{$key} = q|4|;
+$noresave{$key} = "$nosave";
+
+$key = q/blocks/;
+$external_latex_labels{$key} = q|5.7|;
+$noresave{$key} = "$nosave";
+
+$key = q/mapfile/;
+$external_latex_labels{$key} = q|4.1.2|;
+$noresave{$key} = "$nosave";
+
+$key = q/controlfile/;
+$external_latex_labels{$key} = q|4.1.1|;
+$noresave{$key} = "$nosave";
+
+$key = q/step3/;
+$external_latex_labels{$key} = q|2.3|;
+$noresave{$key} = "$nosave";
+
+$key = q/matchfile/;
+$external_latex_labels{$key} = q|4.1.3|;
+$noresave{$key} = "$nosave";
+
+$key = q/alg_param/;
+$external_latex_labels{$key} = q|3.1|;
+$noresave{$key} = "$nosave";
+
+$key = q/step2/;
+$external_latex_labels{$key} = q|2.2|;
+$noresave{$key} = "$nosave";
+
+$key = q/examplefiles/;
+$external_latex_labels{$key} = q|5|;
+$noresave{$key} = "$nosave";
+
+$key = q/inoutparams/;
+$external_latex_labels{$key} = q|3.2|;
+$noresave{$key} = "$nosave";
+
+$key = q/dT/;
+$external_latex_labels{$key} = q|2.1|;
+$noresave{$key} = "$nosave";
+
+$key = q/paramtable/;
+$external_latex_labels{$key} = q|3|;
+$noresave{$key} = "$nosave";
+
+$key = q/screenoutput/;
+$external_latex_labels{$key} = q|4.2.1|;
+$noresave{$key} = "$nosave";
+
+$key = q/contigfile/;
+$external_latex_labels{$key} = q|4.2.2|;
+$noresave{$key} = "$nosave";
+
+$key = q/gridfile/;
+$external_latex_labels{$key} = q|4.2.3|;
+$noresave{$key} = "$nosave";
+
+$key = q/blockfile/;
+$external_latex_labels{$key} = q|4.2.4|;
+$noresave{$key} = "$nosave";
+
+1;
+
diff --git a/docs/fishmanual/node1.html b/docs/fishmanual/node1.html
new file mode 100644
index 0000000..ac47346
--- /dev/null
+++ b/docs/fishmanual/node1.html
@@ -0,0 +1,188 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Contents</TITLE>
+<META NAME="description" CONTENT="Contents">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node2.html">
+<LINK REL="previous" HREF="fishmanual.html">
+<LINK REL="up" HREF="fishmanual.html">
+<LINK REL="next" HREF="node2.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html62"
+ HREF="node2.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html60"
+ HREF="fishmanual.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html54"
+ HREF="fishmanual.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html63"
+ HREF="node2.html">Getting started</A>
+<B> Up:</B> <A NAME="tex2html61"
+ HREF="fishmanual.html">User's Manual for FISH</A>
+<B> Previous:</B> <A NAME="tex2html55"
+ HREF="fishmanual.html">User's Manual for FISH</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+<BR>
+
+<H2><A NAME="SECTION00100000000000000000">
+Contents</A>
+</H2>
+<!--Table of Contents-->
+
+<UL>
+<LI><A NAME="tex2html64"
+ HREF="node2.html">Getting started</A>
+<UL>
+<LI><A NAME="tex2html65"
+ HREF="node3.html">Introduction</A>
+<LI><A NAME="tex2html66"
+ HREF="node4.html">Contact information</A>
+<LI><A NAME="tex2html67"
+ HREF="node5.html">Legal information</A>
+<LI><A NAME="tex2html68"
+ HREF="node6.html">Acknowledgements</A>
+<LI><A NAME="tex2html69"
+ HREF="node7.html">Availability</A>
+<UL>
+<LI><A NAME="tex2html70"
+ HREF="node8.html">Installing from source code</A>
+<LI><A NAME="tex2html71"
+ HREF="node9.html">Installing the Windows executable</A>
+<LI><A NAME="tex2html72"
+ HREF="node10.html">Installing the MacOSX executable</A>
+<LI><A NAME="tex2html73"
+ HREF="node11.html">Testing FISH on sample data</A>
+</UL>
+</UL>
+<BR>
+<LI><A NAME="tex2html74"
+ HREF="node12.html">How it works</A>
+<UL>
+<LI><A NAME="tex2html75"
+ HREF="node13.html">Step 1: From markers to features </A>
+<LI><A NAME="tex2html76"
+ HREF="node14.html">Step 2: From features to grid </A>
+<UL>
+<LI><A NAME="tex2html77"
+ HREF="node15.html">Removing low ranking matches</A>
+<LI><A NAME="tex2html78"
+ HREF="node16.html">Numbering of points</A>
+<LI><A NAME="tex2html79"
+ HREF="node17.html">Enforcing symmetry</A>
+<LI><A NAME="tex2html80"
+ HREF="node18.html">Defining the neighborhood size</A>
+</UL>
+<LI><A NAME="tex2html81"
+ HREF="node19.html">Step 3: From grid to blocks </A>
+<UL>
+<LI><A NAME="tex2html82"
+ HREF="node20.html">Choosing among multiple neighbors</A>
+<LI><A NAME="tex2html83"
+ HREF="node21.html">Overlapping blocks</A>
+</UL>
+</UL>
+<BR>
+<LI><A NAME="tex2html84"
+ HREF="node22.html">Parameters</A>
+<UL>
+<LI><A NAME="tex2html85"
+ HREF="node23.html">Algorithmic parameters </A>
+<LI><A NAME="tex2html86"
+ HREF="node24.html">Input and output parameters </A>
+</UL>
+<BR>
+<LI><A NAME="tex2html87"
+ HREF="node25.html">File formats </A>
+<UL>
+<LI><A NAME="tex2html88"
+ HREF="node26.html">Input files</A>
+<UL>
+<LI><A NAME="tex2html89"
+ HREF="node27.html">Control file </A>
+<LI><A NAME="tex2html90"
+ HREF="node28.html">Map files </A>
+<LI><A NAME="tex2html91"
+ HREF="node29.html">Match files </A>
+</UL>
+<LI><A NAME="tex2html92"
+ HREF="node30.html">Output</A>
+<UL>
+<LI><A NAME="tex2html93"
+ HREF="node31.html">Screen output </A>
+<LI><A NAME="tex2html94"
+ HREF="node35.html">Contig file </A>
+<LI><A NAME="tex2html95"
+ HREF="node36.html">Grid file </A>
+<LI><A NAME="tex2html96"
+ HREF="node37.html">Block file </A>
+<LI><A NAME="tex2html97"
+ HREF="node38.html">Simple block file</A>
+</UL>
+</UL>
+<BR>
+<LI><A NAME="tex2html98"
+ HREF="node39.html">An example </A>
+<UL>
+<LI><A NAME="tex2html99"
+ HREF="node40.html">A control input file</A>
+<LI><A NAME="tex2html100"
+ HREF="node41.html">A map input file</A>
+<LI><A NAME="tex2html101"
+ HREF="node42.html">A match input file</A>
+<LI><A NAME="tex2html102"
+ HREF="node43.html">An example of captured STDOUT</A>
+<LI><A NAME="tex2html103"
+ HREF="node44.html">A contig output file</A>
+<LI><A NAME="tex2html104"
+ HREF="node45.html">A grids output file</A>
+<LI><A NAME="tex2html105"
+ HREF="node46.html">A blocks file</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html106"
+ HREF="node47.html">Bibliography</A>
+<LI><A NAME="tex2html107"
+ HREF="node48.html">About this document ...</A>
+</UL>
+<!--End of Table of Contents-->
+<DIV ALIGN="LEFT">
+</DIV>
+<P>
+<DIV ALIGN="LEFT">
+</DIV>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node10.html b/docs/fishmanual/node10.html
new file mode 100644
index 0000000..55669e9
--- /dev/null
+++ b/docs/fishmanual/node10.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Installing the MacOSX executable</TITLE>
+<META NAME="description" CONTENT="Installing the MacOSX executable">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node11.html">
+<LINK REL="previous" HREF="node9.html">
+<LINK REL="up" HREF="node7.html">
+<LINK REL="next" HREF="node11.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html225"
+ HREF="node11.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html221"
+ HREF="node7.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html215"
+ HREF="node9.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html223"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html226"
+ HREF="node11.html">Testing FISH on sample</A>
+<B> Up:</B> <A NAME="tex2html222"
+ HREF="node7.html">Availability</A>
+<B> Previous:</B> <A NAME="tex2html216"
+ HREF="node9.html">Installing the Windows executable</A>
+   <B> <A NAME="tex2html224"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00253000000000000000">
+Installing the MacOSX executable</A>
+</H2>
+<PRE>
+INSTALLATION:
+ 1. Unzip FISH-1.0-osx.zip.
+ 2. The executable will be located in "FISH-1.0/fish".
+REQUIREMENTS:
+ 1. 32 MB of RAM.
+ 2. Operating system: Known to run on 10.2.x
+</PRE>
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node11.html b/docs/fishmanual/node11.html
new file mode 100644
index 0000000..df04ea0
--- /dev/null
+++ b/docs/fishmanual/node11.html
@@ -0,0 +1,75 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Testing FISH on sample data</TITLE>
+<META NAME="description" CONTENT="Testing FISH on sample data">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="previous" HREF="node10.html">
+<LINK REL="up" HREF="node7.html">
+<LINK REL="next" HREF="node12.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html235"
+ HREF="node12.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html231"
+ HREF="node7.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html227"
+ HREF="node10.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html233"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html236"
+ HREF="node12.html">How it works</A>
+<B> Up:</B> <A NAME="tex2html232"
+ HREF="node7.html">Availability</A>
+<B> Previous:</B> <A NAME="tex2html228"
+ HREF="node10.html">Installing the MacOSX executable</A>
+   <B> <A NAME="tex2html234"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00254000000000000000">
+Testing FISH on sample data</A>
+</H2>
+You may use the sample files to test that the program is working properly.
+From a command line window, go to the directory within the distribution
+where the sample control file, ``control.txt", is located. Type 'fish', then
+enter, and within a few seconds FISH should complete the analysis.
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node12.html b/docs/fishmanual/node12.html
new file mode 100644
index 0000000..2b72170
--- /dev/null
+++ b/docs/fishmanual/node12.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>How it works</TITLE>
+<META NAME="description" CONTENT="How it works">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node22.html">
+<LINK REL="previous" HREF="node2.html">
+<LINK REL="up" HREF="fishmanual.html">
+<LINK REL="next" HREF="node13.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html247"
+ HREF="node13.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html243"
+ HREF="fishmanual.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html237"
+ HREF="node11.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html245"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html248"
+ HREF="node13.html">Step 1: From markers</A>
+<B> Up:</B> <A NAME="tex2html244"
+ HREF="fishmanual.html">User's Manual for FISH</A>
+<B> Previous:</B> <A NAME="tex2html238"
+ HREF="node11.html">Testing FISH on sample</A>
+   <B> <A NAME="tex2html246"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00300000000000000000">
+How it works</A>
+</H1>
+The following is a concise overview of FISH.
+A fuller description of the methodology is given in [<A
+ HREF="node47.html#Calabrese2003">1</A>],
+with which we assume the reader is already familiar.
+There are three steps in the analysis:
+<DL>
+<DT><STRONG>Step 1:</STRONG></DT>
+<DD>From markers to features
+</DD>
+<DT><STRONG>Step 2:</STRONG></DT>
+<DD>From features to grid
+</DD>
+<DT><STRONG>Step 3:</STRONG></DT>
+<DD>From grid to blocks
+</DD>
+</DL>
+Each genome to be compared consists of one or more linear
+contigs, which consist of a sequence of features. A feature is typically one or more
+closely related
+protein-coding genes at a particular locus, but may be any entity to which it is
+possible to ascribe homology to other
+features. Because FISH considers a contig to be merely an ordering of features, it is
+in effect treating the distance between adjacent features as one unit.
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
+
+<UL>
+<LI><A NAME="tex2html249"
+ HREF="node13.html">Step 1: From markers to features </A>
+<LI><A NAME="tex2html250"
+ HREF="node14.html">Step 2: From features to grid </A>
+<UL>
+<LI><A NAME="tex2html251"
+ HREF="node15.html">Removing low ranking matches</A>
+<LI><A NAME="tex2html252"
+ HREF="node16.html">Numbering of points</A>
+<LI><A NAME="tex2html253"
+ HREF="node17.html">Enforcing symmetry</A>
+<LI><A NAME="tex2html254"
+ HREF="node18.html">Defining the neighborhood size</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html255"
+ HREF="node19.html">Step 3: From grid to blocks </A>
+<UL>
+<LI><A NAME="tex2html256"
+ HREF="node20.html">Choosing among multiple neighbors</A>
+<LI><A NAME="tex2html257"
+ HREF="node21.html">Overlapping blocks</A>
+</UL></UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node13.html b/docs/fishmanual/node13.html
new file mode 100644
index 0000000..0adb233
--- /dev/null
+++ b/docs/fishmanual/node13.html
@@ -0,0 +1,147 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Step 1: From markers to features </TITLE>
+<META NAME="description" CONTENT="Step 1: From markers to features ">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node14.html">
+<LINK REL="previous" HREF="node12.html">
+<LINK REL="up" HREF="node12.html">
+<LINK REL="next" HREF="node14.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html268"
+ HREF="node14.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html264"
+ HREF="node12.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html258"
+ HREF="node12.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html266"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html269"
+ HREF="node14.html">Step 2: From features</A>
+<B> Up:</B> <A NAME="tex2html265"
+ HREF="node12.html">How it works</A>
+<B> Previous:</B> <A NAME="tex2html259"
+ HREF="node12.html">How it works</A>
+   <B> <A NAME="tex2html267"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00310000000000000000"></A><A NAME="step1"></A>
+<BR>
+Step 1: From markers to features
+</H1>
+The names, positions and transcriptional orientations (when known) of the
+markers are read from a
+set of <I>map files</I>, one map file per contig.
+Markers within each map file must be ordered according to their physical
+positions on the contig. FISH assigns each marker a unique identification
+number,
+from 1 to the total number of markers in all the contigs, which serves as a
+linear coordinate for subsequent calculations.
+Markers cannot appear more than once on a contig, <I>i.e</I> each marker on a
+contig must be unique; otherwise, an error will result.
+
+<P>
+Individual homologies between markers are read from a set of <I>match files</I>. There
+is at least one, and no more than two, such files for each pair of contigs. Each
+match is associated
+with a score that reflects the strength of that match. Larger scores indicate stronger matches.
+When two matches between the same markers are present in two different match files (<I>i.e.</I>
+contig 1 vs contig 2, and contig 2 vs, contig 1), the score is taken to be either the maximum
+or the average of the two according to the user's choice (refer <A HREF="node22.html#paramtable">3</A>).
+
+<P>
+On the basis of the map positions and matches, FISH
+performs <I>detandemization</I>, in which
+multiple markers may be collapsed into single features. Two parameters control the
+detandemization process: MIN_SCORE and
+MAX_DIST.
+Markers with coordinates that are separated by MIN_DIST or less will be
+collapsed into a single feature if they are homologous to each other or to a
+third marker with a score at least as great as MIN_SCORE.
+
+<P>
+To calculate the relative order of features in the detandemized contig, each
+feature inherits the position of the marker having the lowest valued coordinate
+within the set of markers comprising the feature.
+The coordinates are then reassigned for features in all contigs from
+zero to one less than the number of features in the whole dataset.
+When transcriptional orientations are known, the feature inherits the majority
+orientation (either '1' or '-1') of the markers that comprise it.
+For example, if three out of the five markers that comprise a feature have a transcriptional
+orientation of '1', then the feature inherits that orientation. If there is no majority,
+then it is assigned a value of zero, for 'unknown'.
+
+<P>
+The score of a match between two features, when one or both of
+the features represents multiple markers, is taken, depending on the
+runtime parameter chosen, to be either the highest score or
+the average score for any of the pairs of component markers, one from each feature.
+
+<P>
+<HR>
+<!--Navigation Panel-->
+<A NAME="tex2html268"
+ HREF="node14.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html264"
+ HREF="node12.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html258"
+ HREF="node12.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html266"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html269"
+ HREF="node14.html">Step 2: From features</A>
+<B> Up:</B> <A NAME="tex2html265"
+ HREF="node12.html">How it works</A>
+<B> Previous:</B> <A NAME="tex2html259"
+ HREF="node12.html">How it works</A>
+   <B> <A NAME="tex2html267"
+ HREF="node1.html">Contents</A></B>
+<!--End of Navigation Panel-->
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node14.html b/docs/fishmanual/node14.html
new file mode 100644
index 0000000..9b1c800
--- /dev/null
+++ b/docs/fishmanual/node14.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Step 2: From features to grid </TITLE>
+<META NAME="description" CONTENT="Step 2: From features to grid ">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node19.html">
+<LINK REL="previous" HREF="node13.html">
+<LINK REL="up" HREF="node12.html">
+<LINK REL="next" HREF="node15.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html280"
+ HREF="node15.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html276"
+ HREF="node12.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html270"
+ HREF="node13.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html278"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html281"
+ HREF="node15.html">Removing low ranking matches</A>
+<B> Up:</B> <A NAME="tex2html277"
+ HREF="node12.html">How it works</A>
+<B> Previous:</B> <A NAME="tex2html271"
+ HREF="node13.html">Step 1: From markers</A>
+   <B> <A NAME="tex2html279"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00320000000000000000"></A><A NAME="step2"></A>
+<BR>
+Step 2: From features to grid
+</H1>
+In order to identify segmental homologies, FISH computes a grid for each pair of
+contigs. <I>Points</I> in the grid represent matches
+between pairs of features. The <IMG
+ WIDTH="11" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img1.png"
+ ALT="$ i$"> and <IMG
+ WIDTH="14" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="img2.png"
+ ALT="$ j$"> coordinates of a point are taken to be the
+positions of the features within their respective contigs.
+Each position in the grid, whether or not a point is present, is called as a
+<I>cell</I>.
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
+
+<UL>
+<LI><A NAME="tex2html282"
+ HREF="node15.html">Removing low ranking matches</A>
+<LI><A NAME="tex2html283"
+ HREF="node16.html">Numbering of points</A>
+<LI><A NAME="tex2html284"
+ HREF="node17.html">Enforcing symmetry</A>
+<LI><A NAME="tex2html285"
+ HREF="node18.html">Defining the neighborhood size</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node15.html b/docs/fishmanual/node15.html
new file mode 100644
index 0000000..0131c21
--- /dev/null
+++ b/docs/fishmanual/node15.html
@@ -0,0 +1,77 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Removing low ranking matches</TITLE>
+<META NAME="description" CONTENT="Removing low ranking matches">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node16.html">
+<LINK REL="previous" HREF="node14.html">
+<LINK REL="up" HREF="node14.html">
+<LINK REL="next" HREF="node16.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html296"
+ HREF="node16.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html292"
+ HREF="node14.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html286"
+ HREF="node14.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html294"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html297"
+ HREF="node16.html">Numbering of points</A>
+<B> Up:</B> <A NAME="tex2html293"
+ HREF="node14.html">Step 2: From features</A>
+<B> Previous:</B> <A NAME="tex2html287"
+ HREF="node14.html">Step 2: From features</A>
+   <B> <A NAME="tex2html295"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00321000000000000000">
+Removing low ranking matches</A>
+</H2>
+The number of matches for each feature in the final grid can be
+limited by an adjustable parameter, TOP_HITS. If a match
+is not one of the highest TOP_HITS scoring matches for at least one of the features,
+then it is deleted. This step is necessary to removes some of the noise
+resulting from large gene families.
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node16.html b/docs/fishmanual/node16.html
new file mode 100644
index 0000000..3b54f85
--- /dev/null
+++ b/docs/fishmanual/node16.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Numbering of points</TITLE>
+<META NAME="description" CONTENT="Numbering of points">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node17.html">
+<LINK REL="previous" HREF="node15.html">
+<LINK REL="up" HREF="node14.html">
+<LINK REL="next" HREF="node17.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html308"
+ HREF="node17.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html304"
+ HREF="node14.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html298"
+ HREF="node15.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html306"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html309"
+ HREF="node17.html">Enforcing symmetry</A>
+<B> Up:</B> <A NAME="tex2html305"
+ HREF="node14.html">Step 2: From features</A>
+<B> Previous:</B> <A NAME="tex2html299"
+ HREF="node15.html">Removing low ranking matches</A>
+   <B> <A NAME="tex2html307"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00322000000000000000">
+Numbering of points</A>
+</H2>
+Following this, each point in the grid is given a unique identifying number from zero to one
+less than the total
+number of points. These numbers are assigned to points in sorted hierarchical
+order, first by one coordinate and then by the other. Cells for
+which <IMG
+ WIDTH="45" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="img3.png"
+ ALT="$ i \geq j$"> are not included.
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node17.html b/docs/fishmanual/node17.html
new file mode 100644
index 0000000..23acece
--- /dev/null
+++ b/docs/fishmanual/node17.html
@@ -0,0 +1,94 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Enforcing symmetry</TITLE>
+<META NAME="description" CONTENT="Enforcing symmetry">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node18.html">
+<LINK REL="previous" HREF="node16.html">
+<LINK REL="up" HREF="node14.html">
+<LINK REL="next" HREF="node18.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html320"
+ HREF="node18.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html316"
+ HREF="node14.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html310"
+ HREF="node16.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html318"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html321"
+ HREF="node18.html">Defining the neighborhood size</A>
+<B> Up:</B> <A NAME="tex2html317"
+ HREF="node14.html">Step 2: From features</A>
+<B> Previous:</B> <A NAME="tex2html311"
+ HREF="node16.html">Numbering of points</A>
+   <B> <A NAME="tex2html319"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00323000000000000000">
+Enforcing symmetry</A>
+</H2>
+The above preprocessing steps have ensured that symmetry has been enforced in the grid, such
+that the match between features <IMG
+ WIDTH="11" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img1.png"
+ ALT="$ i$"> and <IMG
+ WIDTH="14" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="img2.png"
+ ALT="$ j$"> has the same score as the match between features <IMG
+ WIDTH="14" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="img2.png"
+ ALT="$ j$"> and <IMG
+ WIDTH="11" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img1.png"
+ ALT="$ i$">.
+Thus, we only need to consider the half of the grid containing <IMG
+ WIDTH="11" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img1.png"
+ ALT="$ i$"> versus <IMG
+ WIDTH="14" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="img2.png"
+ ALT="$ j$"> in searching for
+blocks.
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node18.html b/docs/fishmanual/node18.html
new file mode 100644
index 0000000..f1571a7
--- /dev/null
+++ b/docs/fishmanual/node18.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Defining the neighborhood size</TITLE>
+<META NAME="description" CONTENT="Defining the neighborhood size">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="previous" HREF="node17.html">
+<LINK REL="up" HREF="node14.html">
+<LINK REL="next" HREF="node19.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html330"
+ HREF="node19.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html326"
+ HREF="node14.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html322"
+ HREF="node17.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html328"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html331"
+ HREF="node19.html">Step 3: From grid</A>
+<B> Up:</B> <A NAME="tex2html327"
+ HREF="node14.html">Step 2: From features</A>
+<B> Previous:</B> <A NAME="tex2html323"
+ HREF="node17.html">Enforcing symmetry</A>
+   <B> <A NAME="tex2html329"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00324000000000000000">
+Defining the neighborhood size</A>
+</H2>
+Blocks consist of sequences of points in which each point is within
+the neighborhood of the previous one.
+FISH calculates the size of the <I>neighborhood</I> for all points
+based on the total number of points <IMG
+ WIDTH="21" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img4.png"
+ ALT="$ m$"> and cells <IMG
+ WIDTH="16" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img5.png"
+ ALT="$ n$"> in the grid.
+The probability of a cell containing a point is <IMG
+ WIDTH="78" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="img6.png"
+ ALT="$ h=m/n$">.
+From this, and from an adjustable parameter <IMG
+ WIDTH="18" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img7.png"
+ ALT="$ T$"> (see <A HREF="node23.html#alg_param">3.1</A>),
+FISH calculates the size of the neighborhood.
+In its current version, FISH measures distance between two points
+<!-- MATH
+ $(X_i, Y_i)$
+ -->
+<IMG
+ WIDTH="65" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="img8.png"
+ ALT="$ (X_i, Y_i)$"> and <!-- MATH
+ $(X_j, Y_j)$
+ -->
+<IMG
+ WIDTH="68" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="img9.png"
+ ALT="$ (X_j, Y_j)$"> using the Manhattan distance,
+<!-- MATH
+ $d = |X_i - X_j| + |Y_j - Y_i|$
+ -->
+<IMG
+ WIDTH="208" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="img10.png"
+ ALT="$ d = \vert X_i - X_j\vert + \vert Y_j - Y_i\vert$">.
+In order to be considered neighbors, two points must be closer than
+<P></P>
+<DIV ALIGN="CENTER"><A NAME="dT"></A><!-- MATH
+ \begin{equation}
+d_T = \frac{1}{2}+\sqrt{\frac{{\log}(1-T)}{{\log}(1-h)}}+\frac{1}{4}
+\end{equation}
+ -->
+<TABLE CELLPADDING="0" WIDTH="100%" ALIGN="CENTER">
+<TR VALIGN="MIDDLE">
+<TD NOWRAP ALIGN="CENTER"><IMG
+ WIDTH="230" HEIGHT="80" ALIGN="MIDDLE" BORDER="0"
+ SRC="img11.png"
+ ALT="$\displaystyle d_T = \frac{1}{2}+\sqrt{\frac{{\log}(1-T)}{{\log}(1-h)}}+\frac{1}{4}$"></TD>
+<TD NOWRAP WIDTH="10" ALIGN="RIGHT">
+(2.1)</TD></TR>
+</TABLE></DIV>
+<BR CLEAR="ALL"><P></P>
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node19.html b/docs/fishmanual/node19.html
new file mode 100644
index 0000000..b62e891
--- /dev/null
+++ b/docs/fishmanual/node19.html
@@ -0,0 +1,87 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Step 3: From grid to blocks </TITLE>
+<META NAME="description" CONTENT="Step 3: From grid to blocks ">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="previous" HREF="node14.html">
+<LINK REL="up" HREF="node12.html">
+<LINK REL="next" HREF="node20.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html340"
+ HREF="node20.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html336"
+ HREF="node12.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html332"
+ HREF="node18.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html338"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html341"
+ HREF="node20.html">Choosing among multiple neighbors</A>
+<B> Up:</B> <A NAME="tex2html337"
+ HREF="node12.html">How it works</A>
+<B> Previous:</B> <A NAME="tex2html333"
+ HREF="node18.html">Defining the neighborhood size</A>
+   <B> <A NAME="tex2html339"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00330000000000000000"></A><A NAME="step3"></A>
+<BR>
+Step 3: From grid to blocks
+</H1>
+FISH uses a dynamic programming
+algorithm to identify all maximally extended blocks. For a detailed description of the
+algorithm, see [<A
+ HREF="node47.html#Calabrese2003">1</A>].
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
+
+<UL>
+<LI><A NAME="tex2html342"
+ HREF="node20.html">Choosing among multiple neighbors</A>
+<LI><A NAME="tex2html343"
+ HREF="node21.html">Overlapping blocks</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node2.html b/docs/fishmanual/node2.html
new file mode 100644
index 0000000..2df6960
--- /dev/null
+++ b/docs/fishmanual/node2.html
@@ -0,0 +1,97 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Getting started</TITLE>
+<META NAME="description" CONTENT="Getting started">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node12.html">
+<LINK REL="previous" HREF="node1.html">
+<LINK REL="up" HREF="fishmanual.html">
+<LINK REL="next" HREF="node3.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html118"
+ HREF="node3.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html114"
+ HREF="fishmanual.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html108"
+ HREF="node1.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html116"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html119"
+ HREF="node3.html">Introduction</A>
+<B> Up:</B> <A NAME="tex2html115"
+ HREF="fishmanual.html">User's Manual for FISH</A>
+<B> Previous:</B> <A NAME="tex2html109"
+ HREF="node1.html">Contents</A>
+   <B> <A NAME="tex2html117"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00200000000000000000">
+Getting started</A>
+</H1>
+ 6pt
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
+
+<UL>
+<LI><A NAME="tex2html120"
+ HREF="node3.html">Introduction</A>
+<LI><A NAME="tex2html121"
+ HREF="node4.html">Contact information</A>
+<LI><A NAME="tex2html122"
+ HREF="node5.html">Legal information</A>
+<LI><A NAME="tex2html123"
+ HREF="node6.html">Acknowledgements</A>
+<LI><A NAME="tex2html124"
+ HREF="node7.html">Availability</A>
+<UL>
+<LI><A NAME="tex2html125"
+ HREF="node8.html">Installing from source code</A>
+<LI><A NAME="tex2html126"
+ HREF="node9.html">Installing the Windows executable</A>
+<LI><A NAME="tex2html127"
+ HREF="node10.html">Installing the MacOSX executable</A>
+<LI><A NAME="tex2html128"
+ HREF="node11.html">Testing FISH on sample data</A>
+</UL></UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node20.html b/docs/fishmanual/node20.html
new file mode 100644
index 0000000..b5d5020
--- /dev/null
+++ b/docs/fishmanual/node20.html
@@ -0,0 +1,166 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Choosing among multiple neighbors</TITLE>
+<META NAME="description" CONTENT="Choosing among multiple neighbors">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node21.html">
+<LINK REL="previous" HREF="node19.html">
+<LINK REL="up" HREF="node19.html">
+<LINK REL="next" HREF="node21.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html354"
+ HREF="node21.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html350"
+ HREF="node19.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html344"
+ HREF="node19.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html352"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html355"
+ HREF="node21.html">Overlapping blocks</A>
+<B> Up:</B> <A NAME="tex2html351"
+ HREF="node19.html">Step 3: From grid</A>
+<B> Previous:</B> <A NAME="tex2html345"
+ HREF="node19.html">Step 3: From grid</A>
+   <B> <A NAME="tex2html353"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00331000000000000000">
+Choosing among multiple neighbors</A>
+</H2>
+It can happen that a point may be in the neighborhood of more than one other point.
+In such a case, it is necessary to specify rules for which point will be chosen to extend the block.
+To do this, FISH ranks the cells within each neighborhood and chooses that neighbor
+having the highest rank, using an <I>ad hoc</I> formula that gives preference to points that
+preserve the colinear order of matching features along the two contigs.
+The rank <IMG
+ WIDTH="14" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img12.png"
+ ALT="$ r$"> for each cell in the neighborhood of the candidate point is
+<P></P>
+<DIV ALIGN="CENTER"><!-- MATH
+ \begin{equation}
+r = w \frac{1/d_c}{\sum_{1}^{n}(1/d_c)}
+\end{equation}
+ -->
+<TABLE CELLPADDING="0" WIDTH="100%" ALIGN="CENTER">
+<TR VALIGN="MIDDLE">
+<TD NOWRAP ALIGN="CENTER"><IMG
+ WIDTH="135" HEIGHT="62" ALIGN="MIDDLE" BORDER="0"
+ SRC="img13.png"
+ ALT="$\displaystyle r = w \frac{1/d_c}{\sum_{1}^{n}(1/d_c)}$"></TD>
+<TD NOWRAP WIDTH="10" ALIGN="RIGHT">
+(2.2)</TD></TR>
+</TABLE></DIV>
+<BR CLEAR="ALL"><P></P>
+where <IMG
+ WIDTH="16" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img5.png"
+ ALT="$ n$"> is the number of cells in the point's neighborhood, <IMG
+ WIDTH="21" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="img14.png"
+ ALT="$ d_c$"> is the
+distance
+of the cell from the point under consideration and <IMG
+ WIDTH="19" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img15.png"
+ ALT="$ w$"> is the weight.
+The weight
+<P></P>
+<DIV ALIGN="CENTER"><!-- MATH
+ \begin{equation}
+w = \begin{cases}
+ 1 & \text{if the point is the first in the block},\\
+ 0.25 & \text{if an inversion is implied by the extension},\\
+ 0.75 & \text{otherwise}.
+ \end{cases}
+\end{equation}
+ -->
+<TABLE CELLPADDING="0" WIDTH="100%" ALIGN="CENTER">
+<TR VALIGN="MIDDLE">
+<TD NOWRAP ALIGN="CENTER"><IMG
+ WIDTH="440" HEIGHT="101" ALIGN="MIDDLE" BORDER="0"
+ SRC="img16.png"
+ ALT="$\displaystyle w = \begin{cases}1 & \text{if the point is the first in the block...
+... inversion is implied by the extension},\\ 0.75 & \text{otherwise}. \end{cases}$"></TD>
+<TD NOWRAP WIDTH="10" ALIGN="RIGHT">
+(2.3)</TD></TR>
+</TABLE></DIV>
+<BR CLEAR="ALL"><P></P>
+When multiple points have equal rank, the point is chosen that has the smallest value
+ of <!-- MATH
+ $|(|X_i - X_j|)-(|Y_j - Y_i|)|$
+ -->
+<IMG
+ WIDTH="213" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="img17.png"
+ ALT="$ \vert(\vert X_i - X_j\vert)-(\vert Y_j - Y_i\vert)\vert$">. This favors points close to the diagonal.
+
+<P>
+<HR>
+<!--Navigation Panel-->
+<A NAME="tex2html354"
+ HREF="node21.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html350"
+ HREF="node19.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html344"
+ HREF="node19.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html352"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html355"
+ HREF="node21.html">Overlapping blocks</A>
+<B> Up:</B> <A NAME="tex2html351"
+ HREF="node19.html">Step 3: From grid</A>
+<B> Previous:</B> <A NAME="tex2html345"
+ HREF="node19.html">Step 3: From grid</A>
+   <B> <A NAME="tex2html353"
+ HREF="node1.html">Contents</A></B>
+<!--End of Navigation Panel-->
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node21.html b/docs/fishmanual/node21.html
new file mode 100644
index 0000000..a35f835
--- /dev/null
+++ b/docs/fishmanual/node21.html
@@ -0,0 +1,75 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Overlapping blocks</TITLE>
+<META NAME="description" CONTENT="Overlapping blocks">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="previous" HREF="node20.html">
+<LINK REL="up" HREF="node19.html">
+<LINK REL="next" HREF="node22.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html364"
+ HREF="node22.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html360"
+ HREF="node19.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html356"
+ HREF="node20.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html362"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html365"
+ HREF="node22.html">Parameters</A>
+<B> Up:</B> <A NAME="tex2html361"
+ HREF="node19.html">Step 3: From grid</A>
+<B> Previous:</B> <A NAME="tex2html357"
+ HREF="node20.html">Choosing among multiple neighbors</A>
+   <B> <A NAME="tex2html363"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00332000000000000000">
+Overlapping blocks</A>
+</H2>
+FISH processes blocks in such a way as to ensure that only non-overlapping blocks
+are obtained. If a point could be included in multiple blocks, one of the blocks
+with highest score is chosen. The point is then made unavailable for inclusion in
+other blocks.
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node22.html b/docs/fishmanual/node22.html
new file mode 100644
index 0000000..e465a49
--- /dev/null
+++ b/docs/fishmanual/node22.html
@@ -0,0 +1,201 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Parameters</TITLE>
+<META NAME="description" CONTENT="Parameters">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node25.html">
+<LINK REL="previous" HREF="node12.html">
+<LINK REL="up" HREF="fishmanual.html">
+<LINK REL="next" HREF="node23.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html376"
+ HREF="node23.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html372"
+ HREF="fishmanual.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html366"
+ HREF="node21.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html374"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html377"
+ HREF="node23.html">Algorithmic parameters</A>
+<B> Up:</B> <A NAME="tex2html373"
+ HREF="fishmanual.html">User's Manual for FISH</A>
+<B> Previous:</B> <A NAME="tex2html367"
+ HREF="node21.html">Overlapping blocks</A>
+   <B> <A NAME="tex2html375"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00400000000000000000">
+Parameters</A>
+</H1>
+A number of parameters may be adjusted at the command-line when FISH is
+invoked. They may also be reviewed from the command line by invoking
+FISH with the help switch:
+<PRE>
+# fish -h
+</PRE>
+
+<P>
+The adjustable parameters are listed here and described in more detail below.
+<TABLE CELLPADDING=3 BORDER="1">
+<TR><TD ALIGN="LEFT"><A NAME="paramtable"></A>parameter</TD>
+<TD ALIGN="LEFT">switch</TD>
+<TD ALIGN="LEFT">default</TD>
+<TD ALIGN="LEFT">acceptable values</TD>
+</TR>
+<TR><TD ALIGN="LEFT">PRINT_BLOCKS</TD>
+<TD ALIGN="LEFT">-b</TD>
+<TD ALIGN="LEFT">off</TD>
+<TD ALIGN="LEFT">valid file name</TD>
+</TR>
+<TR><TD ALIGN="LEFT">PRINT_B_SIMPLE</TD>
+<TD ALIGN="LEFT">-B</TD>
+<TD ALIGN="LEFT">off</TD>
+<TD ALIGN="LEFT">valid file name</TD>
+</TR>
+<TR><TD ALIGN="LEFT">MIN_BLOCK_SIZE</TD>
+<TD ALIGN="LEFT">-m</TD>
+<TD ALIGN="LEFT">3</TD>
+<TD ALIGN="LEFT">integer greater than 1</TD>
+</TR>
+<TR><TD ALIGN="LEFT">PRINT_CONTIGS</TD>
+<TD ALIGN="LEFT">-C</TD>
+<TD ALIGN="LEFT">off</TD>
+<TD ALIGN="LEFT">valid filename</TD>
+</TR>
+<TR><TD ALIGN="LEFT">CONTROL_FILE</TD>
+<TD ALIGN="LEFT">-f</TD>
+<TD ALIGN="LEFT">control.txt</TD>
+<TD ALIGN="LEFT">valid filename</TD>
+</TR>
+<TR><TD ALIGN="LEFT">PRINT_GRIDS</TD>
+<TD ALIGN="LEFT">-g</TD>
+<TD ALIGN="LEFT">off</TD>
+<TD ALIGN="LEFT">valid filename</TD>
+</TR>
+<TR><TD ALIGN="LEFT">TOP_HITS</TD>
+<TD ALIGN="LEFT">-H</TD>
+<TD ALIGN="LEFT">5</TD>
+<TD ALIGN="LEFT">integer greater than 0</TD>
+</TR>
+<TR><TD ALIGN="LEFT">MAX_DIST</TD>
+<TD ALIGN="LEFT">-D</TD>
+<TD ALIGN="LEFT">10</TD>
+<TD ALIGN="LEFT">integer greater than 0</TD>
+</TR>
+<TR><TD ALIGN="LEFT">BLOCK_PROB</TD>
+<TD ALIGN="LEFT">-p</TD>
+<TD ALIGN="LEFT">0.001</TD>
+<TD ALIGN="LEFT">real between 0 and 1</TD>
+</TR>
+<TR><TD ALIGN="LEFT">QUIET_MODE</TD>
+<TD ALIGN="LEFT">-q</TD>
+<TD ALIGN="LEFT">off</TD>
+<TD ALIGN="LEFT">none</TD>
+</TR>
+<TR><TD ALIGN="LEFT">MIN_SCORE</TD>
+<TD ALIGN="LEFT">-S</TD>
+<TD ALIGN="LEFT">200</TD>
+<TD ALIGN="LEFT">real</TD>
+</TR>
+<TR><TD ALIGN="LEFT">TIMING</TD>
+<TD ALIGN="LEFT">-t</TD>
+<TD ALIGN="LEFT">off</TD>
+<TD ALIGN="LEFT">none</TD>
+</TR>
+<TR><TD ALIGN="LEFT">AVG_SCORE</TD>
+<TD ALIGN="LEFT">-A</TD>
+<TD ALIGN="LEFT">Max_Score</TD>
+<TD ALIGN="LEFT">none</TD>
+</TR>
+<TR><TD ALIGN="LEFT">T</TD>
+<TD ALIGN="LEFT">-T</TD>
+<TD ALIGN="LEFT">0.05</TD>
+<TD ALIGN="LEFT">real between 0 and 1</TD>
+</TR>
+<TR><TD ALIGN="LEFT">DETANDEMIZE</TD>
+<TD ALIGN="LEFT">-off</TD>
+<TD ALIGN="LEFT">on</TD>
+<TD ALIGN="LEFT">none</TD>
+</TR>
+</TABLE>
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
+
+<UL>
+<LI><A NAME="tex2html378"
+ HREF="node23.html">Algorithmic parameters </A>
+<LI><A NAME="tex2html379"
+ HREF="node24.html">Input and output parameters </A>
+</UL>
+<!--End of Table of Child-Links-->
+<HR>
+<!--Navigation Panel-->
+<A NAME="tex2html376"
+ HREF="node23.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html372"
+ HREF="fishmanual.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html366"
+ HREF="node21.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html374"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html377"
+ HREF="node23.html">Algorithmic parameters</A>
+<B> Up:</B> <A NAME="tex2html373"
+ HREF="fishmanual.html">User's Manual for FISH</A>
+<B> Previous:</B> <A NAME="tex2html367"
+ HREF="node21.html">Overlapping blocks</A>
+   <B> <A NAME="tex2html375"
+ HREF="node1.html">Contents</A></B>
+<!--End of Navigation Panel-->
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node23.html b/docs/fishmanual/node23.html
new file mode 100644
index 0000000..df39872
--- /dev/null
+++ b/docs/fishmanual/node23.html
@@ -0,0 +1,144 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Algorithmic parameters </TITLE>
+<META NAME="description" CONTENT="Algorithmic parameters ">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node24.html">
+<LINK REL="previous" HREF="node22.html">
+<LINK REL="up" HREF="node22.html">
+<LINK REL="next" HREF="node24.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html390"
+ HREF="node24.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html386"
+ HREF="node22.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html380"
+ HREF="node22.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html388"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html391"
+ HREF="node24.html">Input and output parameters</A>
+<B> Up:</B> <A NAME="tex2html387"
+ HREF="node22.html">Parameters</A>
+<B> Previous:</B> <A NAME="tex2html381"
+ HREF="node22.html">Parameters</A>
+   <B> <A NAME="tex2html389"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00410000000000000000"></A><A NAME="alg_param"></A>
+<BR>
+Algorithmic parameters
+</H1>
+A number of the adjustable parameters control the way in which FISH finds
+blocks. Altering these parameters can substantially influence the results.
+<DL>
+<DT><STRONG>MIN_BLOCK_SIZE</STRONG></DT>
+<DD>The minimum number of points needed to define a homologous block.
+</DD>
+<DT><STRONG>TOP_HITS</STRONG></DT>
+<DD>Matches that are not in among the TOP_HITS scoring matches for either
+component feature will be discarded.
+</DD>
+<DT><STRONG>MAX_DIST</STRONG></DT>
+<DD>The maximum number of intervening markers allowed between markers in t
+he same detandemized feature.
+</DD>
+<DT><STRONG>T</STRONG></DT>
+<DD>The probability of having one or more neighbors within a distance
+less than or equal to than <IMG
+ WIDTH="25" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="img18.png"
+ ALT="$ d_T$"> under the assumption that each cell contains
+a point with probability <IMG
+ WIDTH="16" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img19.png"
+ ALT="$ h$">. Values of <IMG
+ WIDTH="18" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img7.png"
+ ALT="$ T$"> closer to zero will result in blocks with more
+closely spaced points. This is roughly analogous to the gap parameter in local sequence alignment.
+</DD>
+<DT><STRONG>MIN_SCORE</STRONG></DT>
+<DD>Matches with scores less than MIN_SCORE will not
+be considered by FISH despite being listed in a match file.
+</DD>
+<DT><STRONG>AVG_SCORE</STRONG></DT>
+<DD>This option enforces symmetry between two matches
+(<I>e.g.</I> 1 versus 2 and 2 versus 1) by taking an
+average of the scores. If this averge is less than the MIN_SCORE, the
+match will be discarded.
+The default behavior is to choose the larger of the two scores.
+</DD>
+<DT><STRONG>DETANDEMIZE</STRONG></DT>
+<DD>This allows the user to turn detandemization off.
+</DD>
+</DL>
+
+<P>
+<HR>
+<!--Navigation Panel-->
+<A NAME="tex2html390"
+ HREF="node24.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html386"
+ HREF="node22.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html380"
+ HREF="node22.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html388"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html391"
+ HREF="node24.html">Input and output parameters</A>
+<B> Up:</B> <A NAME="tex2html387"
+ HREF="node22.html">Parameters</A>
+<B> Previous:</B> <A NAME="tex2html381"
+ HREF="node22.html">Parameters</A>
+   <B> <A NAME="tex2html389"
+ HREF="node1.html">Contents</A></B>
+<!--End of Navigation Panel-->
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node24.html b/docs/fishmanual/node24.html
new file mode 100644
index 0000000..21c56b6
--- /dev/null
+++ b/docs/fishmanual/node24.html
@@ -0,0 +1,149 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Input and output parameters </TITLE>
+<META NAME="description" CONTENT="Input and output parameters ">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="previous" HREF="node23.html">
+<LINK REL="up" HREF="node22.html">
+<LINK REL="next" HREF="node25.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html400"
+ HREF="node25.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html396"
+ HREF="node22.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html392"
+ HREF="node23.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html398"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html401"
+ HREF="node25.html">File formats</A>
+<B> Up:</B> <A NAME="tex2html397"
+ HREF="node22.html">Parameters</A>
+<B> Previous:</B> <A NAME="tex2html393"
+ HREF="node23.html">Algorithmic parameters</A>
+   <B> <A NAME="tex2html399"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00420000000000000000"></A><A NAME="inoutparams"></A>
+<BR>
+Input and output parameters
+</H1>
+The remaining parameters control the input to and output from FISH.
+<DL>
+<DT><STRONG>QUIET_MODE</STRONG></DT>
+<DD>If selected, FISH will suppress the default screen
+output (see <A HREF="node31.html#screenoutput">4.2.1</A>). This switch takes no arguments.
+</DD>
+<DT><STRONG>TIMING</STRONG></DT>
+<DD>If selected, FISH will report the number of seconds
+elapsed between various execution time points. This switch takes no
+arguments.
+</DD>
+<DT><STRONG>CONTROL_FILE</STRONG></DT>
+<DD>Specifies the name of the file containing the instructions
+for FISH to read particular contig and match files <A HREF="node27.html#controlfile">4.1.1</A>.
+If not specified at the command-line, FISH will search for a file named
+``control.txt" and use that, if available.
+</DD>
+<DT><STRONG>PRINT_CONTIGS</STRONG></DT>
+<DD>Specifies the name of the file to which FISH
+writes contig output (see <A HREF="node35.html#contigfile">4.2.2</A>). Unless selected, no file will be written.
+</DD>
+<DT><STRONG>PRINT_GRIDS</STRONG></DT>
+<DD>Specifies the name of the file to which FISH writes
+grid output (see <A HREF="node36.html#gridfile">4.2.3</A>). Unless selected, no file will be written.
+</DD>
+<DT><STRONG>PRINT_BLOCKS</STRONG></DT>
+<DD>Specifies the name of the file to which FISH
+writes block output in human-friendly format (see <A HREF="node37.html#blockfile">4.2.4</A>).
+Unless selected, no file will be written.
+</DD>
+<DT><STRONG>PRINT_B_SIMPLE</STRONG></DT>
+<DD>Specifies the name of the file to which FISH
+writes an alternative format for the block output that is more computer friendly
+(see <A HREF="node37.html#blockfile">4.2.4</A>). Unless selected, no file will be written.
+</DD>
+<DT><STRONG>BLOCK_PROB</STRONG></DT>
+<DD>This specifies a value for the confidence level of a
+block. The confidence level is calculated as the expected number of blocks with
+<IMG
+ WIDTH="16" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img5.png"
+ ALT="$ n$"> points divided by the observed number of blocks with <IMG
+ WIDTH="16" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img5.png"
+ ALT="$ n$"> points. If the observed
+number does not sufficiently exceed the expected number (under the null model), then
+blocks of that size are flagged in the summary output. Some of these blocks may well be
+spurious.
+</DD>
+</DL>
+
+<P>
+<HR>
+<!--Navigation Panel-->
+<A NAME="tex2html400"
+ HREF="node25.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html396"
+ HREF="node22.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html392"
+ HREF="node23.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html398"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html401"
+ HREF="node25.html">File formats</A>
+<B> Up:</B> <A NAME="tex2html397"
+ HREF="node22.html">Parameters</A>
+<B> Previous:</B> <A NAME="tex2html393"
+ HREF="node23.html">Algorithmic parameters</A>
+   <B> <A NAME="tex2html399"
+ HREF="node1.html">Contents</A></B>
+<!--End of Navigation Panel-->
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node25.html b/docs/fishmanual/node25.html
new file mode 100644
index 0000000..a8ffafd
--- /dev/null
+++ b/docs/fishmanual/node25.html
@@ -0,0 +1,110 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>File formats </TITLE>
+<META NAME="description" CONTENT="File formats ">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node39.html">
+<LINK REL="previous" HREF="node22.html">
+<LINK REL="up" HREF="fishmanual.html">
+<LINK REL="next" HREF="node26.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html412"
+ HREF="node26.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html408"
+ HREF="fishmanual.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html402"
+ HREF="node24.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html410"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html413"
+ HREF="node26.html">Input files</A>
+<B> Up:</B> <A NAME="tex2html409"
+ HREF="fishmanual.html">User's Manual for FISH</A>
+<B> Previous:</B> <A NAME="tex2html403"
+ HREF="node24.html">Input and output parameters</A>
+   <B> <A NAME="tex2html411"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00500000000000000000"></A><A NAME="fileschapter"></A>
+<BR>
+File formats
+</H1>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
+
+<UL>
+<LI><A NAME="tex2html414"
+ HREF="node26.html">Input files</A>
+<UL>
+<LI><A NAME="tex2html415"
+ HREF="node27.html">Control file </A>
+<LI><A NAME="tex2html416"
+ HREF="node28.html">Map files </A>
+<LI><A NAME="tex2html417"
+ HREF="node29.html">Match files </A>
+</UL>
+<BR>
+<LI><A NAME="tex2html418"
+ HREF="node30.html">Output</A>
+<UL>
+<LI><A NAME="tex2html419"
+ HREF="node31.html">Screen output </A>
+<UL>
+<LI><A NAME="tex2html420"
+ HREF="node32.html">Processing contigs</A>
+<LI><A NAME="tex2html421"
+ HREF="node33.html">Processing matches</A>
+<LI><A NAME="tex2html422"
+ HREF="node34.html">Processing blocks</A>
+</UL>
+<LI><A NAME="tex2html423"
+ HREF="node35.html">Contig file </A>
+<LI><A NAME="tex2html424"
+ HREF="node36.html">Grid file </A>
+<LI><A NAME="tex2html425"
+ HREF="node37.html">Block file </A>
+<LI><A NAME="tex2html426"
+ HREF="node38.html">Simple block file</A>
+</UL></UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node26.html b/docs/fishmanual/node26.html
new file mode 100644
index 0000000..43be707
--- /dev/null
+++ b/docs/fishmanual/node26.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Input files</TITLE>
+<META NAME="description" CONTENT="Input files">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node30.html">
+<LINK REL="previous" HREF="node25.html">
+<LINK REL="up" HREF="node25.html">
+<LINK REL="next" HREF="node27.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html437"
+ HREF="node27.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html433"
+ HREF="node25.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html427"
+ HREF="node25.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html435"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html438"
+ HREF="node27.html">Control file</A>
+<B> Up:</B> <A NAME="tex2html434"
+ HREF="node25.html">File formats</A>
+<B> Previous:</B> <A NAME="tex2html428"
+ HREF="node25.html">File formats</A>
+   <B> <A NAME="tex2html436"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00510000000000000000">
+Input files</A>
+</H1>
+There are three types of input files: control files, map files and match files.
+The control file tells FISH the location of the map and the match
+files.
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
+
+<UL>
+<LI><A NAME="tex2html439"
+ HREF="node27.html">Control file </A>
+<LI><A NAME="tex2html440"
+ HREF="node28.html">Map files </A>
+<LI><A NAME="tex2html441"
+ HREF="node29.html">Match files </A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node27.html b/docs/fishmanual/node27.html
new file mode 100644
index 0000000..e58f9b8
--- /dev/null
+++ b/docs/fishmanual/node27.html
@@ -0,0 +1,130 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Control file </TITLE>
+<META NAME="description" CONTENT="Control file ">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node28.html">
+<LINK REL="previous" HREF="node26.html">
+<LINK REL="up" HREF="node26.html">
+<LINK REL="next" HREF="node28.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html452"
+ HREF="node28.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html448"
+ HREF="node26.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html442"
+ HREF="node26.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html450"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html453"
+ HREF="node28.html">Map files</A>
+<B> Up:</B> <A NAME="tex2html449"
+ HREF="node26.html">Input files</A>
+<B> Previous:</B> <A NAME="tex2html443"
+ HREF="node26.html">Input files</A>
+   <B> <A NAME="tex2html451"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00511000000000000000"></A><A NAME="controlfile"></A>
+<BR>
+Control file
+</H2>
+A control file is used to specify the paths of the map and match files.
+The format of the control file can be seen in the sample provided.
+It is divided into two sections, one for map files and one for match files.
+
+<P>
+At a minimum, one map file and its associated match file are required.
+To compare two different contigs, map and match files are
+required for each. In addition, one or two match files must be specified
+that list the matches between features in contig 1 <I>vs.</I> 2, and/or 2
+<I>vs.</I> 1.
+
+<P>
+A list of the map files is preceded by the optional token '-maps' followed by a
+newline character, followed by a separate line for each contig that is to be
+analyzed. Each of those lines contains an integer, followed by whitespace,
+followed by a valid filename path, followed by a newline character. The integer
+is taken to be the name of a contig and the filename path tells FISH
+where to find the map file for that contig.
+
+<P>
+A list of the match files is preceded with the optional token '-matches'
+followed by a newline character, followed by a separate line for each pair of
+contigs to be analyzed. Each of those lines contains an integer, followed by
+whitespace, followed by an integer, followed by whitespace, followed by a valid
+filename path. The two integers specify the contigs for the match file.
+Note that there must be at least one comparison in which
+the integer of the first contig is less than the integer of the second contig.
+For example if 1 versus 2 does not exist, than 2 versus 1 is ignored. So if there is
+only one match file for a comparison between two contigs then that comparison must be
+written as 1 versus 2.
+
+<P>
+<HR>
+<!--Navigation Panel-->
+<A NAME="tex2html452"
+ HREF="node28.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html448"
+ HREF="node26.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html442"
+ HREF="node26.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html450"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html453"
+ HREF="node28.html">Map files</A>
+<B> Up:</B> <A NAME="tex2html449"
+ HREF="node26.html">Input files</A>
+<B> Previous:</B> <A NAME="tex2html443"
+ HREF="node26.html">Input files</A>
+   <B> <A NAME="tex2html451"
+ HREF="node1.html">Contents</A></B>
+<!--End of Navigation Panel-->
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node28.html b/docs/fishmanual/node28.html
new file mode 100644
index 0000000..6872fa9
--- /dev/null
+++ b/docs/fishmanual/node28.html
@@ -0,0 +1,85 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Map files </TITLE>
+<META NAME="description" CONTENT="Map files ">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node29.html">
+<LINK REL="previous" HREF="node27.html">
+<LINK REL="up" HREF="node26.html">
+<LINK REL="next" HREF="node29.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html464"
+ HREF="node29.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html460"
+ HREF="node26.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html454"
+ HREF="node27.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html462"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html465"
+ HREF="node29.html">Match files</A>
+<B> Up:</B> <A NAME="tex2html461"
+ HREF="node26.html">Input files</A>
+<B> Previous:</B> <A NAME="tex2html455"
+ HREF="node27.html">Control file</A>
+   <B> <A NAME="tex2html463"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00512000000000000000"></A><A NAME="mapfile"></A>
+<BR>
+Map files
+</H2>
+Each map file lists the names and transcriptional orientation (if known) of all
+the markers on one contig. For an example, see Section <A HREF="node39.html#examplefiles">5</A>.
+Markers must be listed in positional order. Each line contains a
+unique marker name,
+followed by a tab character, followed by the transcriptional orientation.
+Marker names can be character string up to a maximum length of 100 that does not include
+whitespace or the '&' character. (This value can be modified
+in the file ``fish.cpp" by changing the value of MAXBUFFER and recompiling).
+Marker orientation is taken
+relative to the contig as a whole. Thus, if marker 1 is coded on the same
+strand as marker 2, then both markers should be assigned the same direction. Orientation
+can take values '-1', '0' and '1'. Zero is used for markers of unknown orientation.
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node29.html b/docs/fishmanual/node29.html
new file mode 100644
index 0000000..7af1bf7
--- /dev/null
+++ b/docs/fishmanual/node29.html
@@ -0,0 +1,85 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Match files </TITLE>
+<META NAME="description" CONTENT="Match files ">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="previous" HREF="node28.html">
+<LINK REL="up" HREF="node26.html">
+<LINK REL="next" HREF="node30.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html474"
+ HREF="node30.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html470"
+ HREF="node26.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html466"
+ HREF="node28.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html472"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html475"
+ HREF="node30.html">Output</A>
+<B> Up:</B> <A NAME="tex2html471"
+ HREF="node26.html">Input files</A>
+<B> Previous:</B> <A NAME="tex2html467"
+ HREF="node28.html">Map files</A>
+   <B> <A NAME="tex2html473"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00513000000000000000"></A><A NAME="matchfile"></A>
+<BR>
+Match files
+</H2>
+Each match file lists all the homologies between markers in a pair of contigs. For an
+example, see Section <A HREF="node39.html#examplefiles">5</A>.
+There are three columns in the matchfile. The first two columns may be strings,
+but the
+third column needs to be an integer. The first and second columns contain the
+gene names
+from the first and second contig respectively.
+The integer in the third column must be some measure of the strength of the match between
+the two markers. FISH
+assumes that the larger the integer, the stronger the match. If information is
+not available on the strengths of the matches between genes, one can, for
+example, assign all scores to be zero, and set MIN_SCORE to be zero at runtime.
+All self matches are discarded.
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node3.html b/docs/fishmanual/node3.html
new file mode 100644
index 0000000..5262976
--- /dev/null
+++ b/docs/fishmanual/node3.html
@@ -0,0 +1,129 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Introduction</TITLE>
+<META NAME="description" CONTENT="Introduction">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node4.html">
+<LINK REL="previous" HREF="node2.html">
+<LINK REL="up" HREF="node2.html">
+<LINK REL="next" HREF="node4.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html139"
+ HREF="node4.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html135"
+ HREF="node2.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html129"
+ HREF="node2.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html137"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html140"
+ HREF="node4.html">Contact information</A>
+<B> Up:</B> <A NAME="tex2html136"
+ HREF="node2.html">Getting started</A>
+<B> Previous:</B> <A NAME="tex2html130"
+ HREF="node2.html">Getting started</A>
+   <B> <A NAME="tex2html138"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00210000000000000000">
+Introduction</A>
+</H1>
+Genomic regions that have descended from a common ancestral region are said to
+be <I>segmental homologs</I>. FISH is software for the fast
+identification and statistical evaluation of segmental homologs.
+
+<P>
+The software treats each input genome as a string of <I>features</I>.
+A feature may correspond to one marker, or sometimes to multiple homologous
+markers that
+are very close to one another on a contig.
+Each string of features (whether it is a compete chromosome or some smaller
+physical or genetic linkage group) is referred to as a <I>contig</I>.
+<I>Matches</I> are pairwise homologies among markers, which, along with the
+position of markers on contigs, constitute the primary input data.
+FISH finds <I>blocks</I> of putative segmental homology by
+identifying paired regions in which multiple matches
+occur and where the underlying features are in roughly colinear order.
+As described more fully below, FISH
+evaluates the probability of observing each block under a null model
+in
+which matches are distributed uniformly at random among features.
+
+<P>
+Users of FISH should cite the following paper (in which more detail regarding the method
+can be found):
+
+<UL>
+<LI>Calabrese PP, Chakravarty S, Vision TJ (2003) Fast identification and
+statistical evaluation of segmental homologies in comparative maps. <I>Bioinformatics</I> 19, i74-i80.
+</LI>
+</UL>
+
+<P>
+<HR>
+<!--Navigation Panel-->
+<A NAME="tex2html139"
+ HREF="node4.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html135"
+ HREF="node2.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html129"
+ HREF="node2.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html137"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html140"
+ HREF="node4.html">Contact information</A>
+<B> Up:</B> <A NAME="tex2html136"
+ HREF="node2.html">Getting started</A>
+<B> Previous:</B> <A NAME="tex2html130"
+ HREF="node2.html">Getting started</A>
+   <B> <A NAME="tex2html138"
+ HREF="node1.html">Contents</A></B>
+<!--End of Navigation Panel-->
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node30.html b/docs/fishmanual/node30.html
new file mode 100644
index 0000000..4119c03
--- /dev/null
+++ b/docs/fishmanual/node30.html
@@ -0,0 +1,101 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Output</TITLE>
+<META NAME="description" CONTENT="Output">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="previous" HREF="node26.html">
+<LINK REL="up" HREF="node25.html">
+<LINK REL="next" HREF="node31.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html484"
+ HREF="node31.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html480"
+ HREF="node25.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html476"
+ HREF="node29.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html482"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html485"
+ HREF="node31.html">Screen output</A>
+<B> Up:</B> <A NAME="tex2html481"
+ HREF="node25.html">File formats</A>
+<B> Previous:</B> <A NAME="tex2html477"
+ HREF="node29.html">Match files</A>
+   <B> <A NAME="tex2html483"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00520000000000000000">
+Output</A>
+</H1>
+FISH can generate a variety of different output streams depending on the user's
+selections. FISH can also report the time spent at various stages in
+the analysis. This
+option can be selected by using the -t switch (see Section <A HREF="node22.html#paramtable">3</A>).
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
+
+<UL>
+<LI><A NAME="tex2html486"
+ HREF="node31.html">Screen output </A>
+<UL>
+<LI><A NAME="tex2html487"
+ HREF="node32.html">Processing contigs</A>
+<LI><A NAME="tex2html488"
+ HREF="node33.html">Processing matches</A>
+<LI><A NAME="tex2html489"
+ HREF="node34.html">Processing blocks</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html490"
+ HREF="node35.html">Contig file </A>
+<LI><A NAME="tex2html491"
+ HREF="node36.html">Grid file </A>
+<LI><A NAME="tex2html492"
+ HREF="node37.html">Block file </A>
+<LI><A NAME="tex2html493"
+ HREF="node38.html">Simple block file</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node31.html b/docs/fishmanual/node31.html
new file mode 100644
index 0000000..283bf56
--- /dev/null
+++ b/docs/fishmanual/node31.html
@@ -0,0 +1,102 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Screen output </TITLE>
+<META NAME="description" CONTENT="Screen output ">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node35.html">
+<LINK REL="previous" HREF="node30.html">
+<LINK REL="up" HREF="node30.html">
+<LINK REL="next" HREF="node32.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html504"
+ HREF="node32.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html500"
+ HREF="node30.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html494"
+ HREF="node30.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html502"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html505"
+ HREF="node32.html">Processing contigs</A>
+<B> Up:</B> <A NAME="tex2html501"
+ HREF="node30.html">Output</A>
+<B> Previous:</B> <A NAME="tex2html495"
+ HREF="node30.html">Output</A>
+   <B> <A NAME="tex2html503"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00521000000000000000"></A><A NAME="screenoutput"></A>
+<BR>
+Screen output
+</H2>
+Unless the QUIET_MODE has been selected, FISH will report results from
+each stage of the analysis to standard output (STDOUT). See Section
+<A HREF="node39.html#examplefiles">5</A> for an excerpt from the sample file ``fish_out.txt".
+The STDOUT stream may be directed to a file, rather than to the terminal, by using the
+<IMG
+ WIDTH="19" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="img20.png"
+ ALT="$ >$"> redirection operator, like so
+<PRE>
+# fish [options]> myfile.txt
+</PRE>
+
+<P>
+At the beginning of the process, FISH sends STDOUT a brief title
+message, including the current version number, the date and time at which the
+process was initiated, and the control file name.
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
+
+<UL>
+<LI><A NAME="tex2html506"
+ HREF="node32.html">Processing contigs</A>
+<LI><A NAME="tex2html507"
+ HREF="node33.html">Processing matches</A>
+<LI><A NAME="tex2html508"
+ HREF="node34.html">Processing blocks</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node32.html b/docs/fishmanual/node32.html
new file mode 100644
index 0000000..56dcbab
--- /dev/null
+++ b/docs/fishmanual/node32.html
@@ -0,0 +1,77 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Processing contigs</TITLE>
+<META NAME="description" CONTENT="Processing contigs">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node33.html">
+<LINK REL="previous" HREF="node31.html">
+<LINK REL="up" HREF="node31.html">
+<LINK REL="next" HREF="node33.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html519"
+ HREF="node33.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html515"
+ HREF="node31.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html509"
+ HREF="node31.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html517"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html520"
+ HREF="node33.html">Processing matches</A>
+<B> Up:</B> <A NAME="tex2html516"
+ HREF="node31.html">Screen output</A>
+<B> Previous:</B> <A NAME="tex2html510"
+ HREF="node31.html">Screen output</A>
+   <B> <A NAME="tex2html518"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H3><A NAME="SECTION00521100000000000000">
+Processing contigs</A>
+</H3>
+FISH displays the values of the two relevant parameters for the contig
+processing stage analysis: MIN_SCORE and MAX_DIST. Once detandemization is
+complete, a table is written that displays the number of markers and features
+within each contig. Detailed information on which markers compose which features
+ is written to a file if the PRINT_CONTIGS parameter has been selected.
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node33.html b/docs/fishmanual/node33.html
new file mode 100644
index 0000000..6097eeb
--- /dev/null
+++ b/docs/fishmanual/node33.html
@@ -0,0 +1,79 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Processing matches</TITLE>
+<META NAME="description" CONTENT="Processing matches">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node34.html">
+<LINK REL="previous" HREF="node32.html">
+<LINK REL="up" HREF="node31.html">
+<LINK REL="next" HREF="node34.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html531"
+ HREF="node34.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html527"
+ HREF="node31.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html521"
+ HREF="node32.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html529"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html532"
+ HREF="node34.html">Processing blocks</A>
+<B> Up:</B> <A NAME="tex2html528"
+ HREF="node31.html">Screen output</A>
+<B> Previous:</B> <A NAME="tex2html522"
+ HREF="node32.html">Processing contigs</A>
+   <B> <A NAME="tex2html530"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H3><A NAME="SECTION00521200000000000000">
+Processing matches</A>
+</H3>
+FISH displays the values of the relevant parameters of the match
+processing stage, MIN_SCORE and TOP_HITS. Note that the current and previous
+value for for MIN_SCORE must always agree. Once the calculations are
+complete, FISH displays the number of points and the number
+of cells for each pair of contigs in the analysis. In addition, the coordinates of
+the points in the detandemized dataset are written
+to a file if PRINT_GRIDS has been selected.
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node34.html b/docs/fishmanual/node34.html
new file mode 100644
index 0000000..f9b2063
--- /dev/null
+++ b/docs/fishmanual/node34.html
@@ -0,0 +1,166 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Processing blocks</TITLE>
+<META NAME="description" CONTENT="Processing blocks">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="previous" HREF="node33.html">
+<LINK REL="up" HREF="node31.html">
+<LINK REL="next" HREF="node35.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html541"
+ HREF="node35.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html537"
+ HREF="node31.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html533"
+ HREF="node33.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html539"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html542"
+ HREF="node35.html">Contig file</A>
+<B> Up:</B> <A NAME="tex2html538"
+ HREF="node31.html">Screen output</A>
+<B> Previous:</B> <A NAME="tex2html534"
+ HREF="node33.html">Processing matches</A>
+   <B> <A NAME="tex2html540"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H3><A NAME="SECTION00521300000000000000">
+Processing blocks</A>
+</H3>
+FISH first displays the key adjustable parameter of the block finding
+stage, <IMG
+ WIDTH="18" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img7.png"
+ ALT="$ T$">. Following this is a series of numbers which depend on both the
+dataset and the adjustable parameters:
+
+<UL>
+<LI><IMG
+ WIDTH="22" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img21.png"
+ ALT="$ N$">, the total number of points in the grid
+</LI>
+<LI><IMG
+ WIDTH="20" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img22.png"
+ ALT="$ F$">, the total number of features in the dataset
+</LI>
+<LI>the total number of cells in the grid, calculated as <IMG
+ WIDTH="100" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="img23.png"
+ ALT="$ F(F-1)/2$">
+</LI>
+<LI><IMG
+ WIDTH="16" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img19.png"
+ ALT="$ h$">, the proportion of cells in the grid that contain a point
+</LI>
+<LI><IMG
+ WIDTH="25" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="img18.png"
+ ALT="$ d_T$">, the neighborhood size within which there is only a <IMG
+ WIDTH="18" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img7.png"
+ ALT="$ T$"> probability of
+encountering another point if points in the grid are distributed uniformly at
+random (see Equation <A HREF="node18.html#dT">2.1</A>)
+</LI>
+<LI>MIN_BLOCK_SIZE, the number of points in the smallest block to be reported.
+</LI>
+</UL>
+Once the blocks have been identified, FISH will also display the total
+number of blocks.
+
+<P>
+The length distribution of the blocks is displayed as a vertical histogram. To
+the right of each bar is listed the number of blocks of length <IMG
+ WIDTH="17" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img24.png"
+ ALT="$ L$">, as measured
+by the number of points. If the number of blocks is greater than 50, the true amount is not
+represented by '*' characters and the block frequency is preceded by '...'.
+To the left of the histogram is shown the corresponding <IMG
+ WIDTH="14" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="img25.png"
+ ALT="$ p$">-value for observing
+a block of length <IMG
+ WIDTH="17" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img24.png"
+ ALT="$ L$"> (see Section <A HREF="node37.html#blockfile">4.2.4</A>), and the expected number, under the null model.
+If the proportion of expected to observed blocks of length <IMG
+ WIDTH="17" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img24.png"
+ ALT="$ L$"> is greater than
+BLOCK_PROB, then the frequency of observed blocks is followed by an exclamation
+mark. This indicates that blocks of this length have not been observed sufficiently
+more frequently than expected, and so the individual blocks may not be biologically
+meaningful.
+
+<P>
+<HR>
+<!--Navigation Panel-->
+<A NAME="tex2html541"
+ HREF="node35.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html537"
+ HREF="node31.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html533"
+ HREF="node33.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html539"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html542"
+ HREF="node35.html">Contig file</A>
+<B> Up:</B> <A NAME="tex2html538"
+ HREF="node31.html">Screen output</A>
+<B> Previous:</B> <A NAME="tex2html534"
+ HREF="node33.html">Processing matches</A>
+   <B> <A NAME="tex2html540"
+ HREF="node1.html">Contents</A></B>
+<!--End of Navigation Panel-->
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node35.html b/docs/fishmanual/node35.html
new file mode 100644
index 0000000..1728034
--- /dev/null
+++ b/docs/fishmanual/node35.html
@@ -0,0 +1,85 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Contig file </TITLE>
+<META NAME="description" CONTENT="Contig file ">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node36.html">
+<LINK REL="previous" HREF="node31.html">
+<LINK REL="up" HREF="node30.html">
+<LINK REL="next" HREF="node36.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html553"
+ HREF="node36.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html549"
+ HREF="node30.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html543"
+ HREF="node34.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html551"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html554"
+ HREF="node36.html">Grid file</A>
+<B> Up:</B> <A NAME="tex2html550"
+ HREF="node30.html">Output</A>
+<B> Previous:</B> <A NAME="tex2html544"
+ HREF="node34.html">Processing blocks</A>
+   <B> <A NAME="tex2html552"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00522000000000000000"></A><A NAME="contigfile"></A>
+<BR>
+Contig file
+</H2>
+If the PRINT_CONTIGS option is selected, FISH will output a contig
+file with the specified name. See Section <A HREF="node39.html#examplefiles">5</A> for an example. The
+contig file allows translation between feature numbers and marker names.
+
+<P>
+The top of the contig file displays the time at which the process was initiated.
+This is followed by the parameter list, which includes the name of the control
+file and the values of MIN_SCORE and MAX_DIST. This is followed by a
+table showing the number of markers and features in each contig. Finally, a
+table is presented in which, for each feature, the contig, the composite
+direction and the names of the markers (from the map file) associated with that
+feature are shown.
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node36.html b/docs/fishmanual/node36.html
new file mode 100644
index 0000000..5492e76
--- /dev/null
+++ b/docs/fishmanual/node36.html
@@ -0,0 +1,86 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Grid file </TITLE>
+<META NAME="description" CONTENT="Grid file ">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node37.html">
+<LINK REL="previous" HREF="node35.html">
+<LINK REL="up" HREF="node30.html">
+<LINK REL="next" HREF="node37.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html565"
+ HREF="node37.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html561"
+ HREF="node30.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html555"
+ HREF="node35.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html563"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html566"
+ HREF="node37.html">Block file</A>
+<B> Up:</B> <A NAME="tex2html562"
+ HREF="node30.html">Output</A>
+<B> Previous:</B> <A NAME="tex2html556"
+ HREF="node35.html">Contig file</A>
+   <B> <A NAME="tex2html564"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00523000000000000000"></A><A NAME="gridfile"></A>
+<BR>
+Grid file
+</H2>
+If the PRINT_GRIDS option is selected, FISH will output a grid file
+with the specified name. See Section <A HREF="node39.html#examplefiles">5</A> for an example. The grid file
+allows translation between points and features as well a summary of the
+parameters and results for the match processing step.
+
+<P>
+The top of the grid file displays the time at which the process was initiated.
+This is followed by the parameter list, which includes the name of the control
+file and the values of MIN_SCORE and TOP_HITS. This is followed by a
+table showing the number of points and cells for each pair of contigs. Finally,
+the points are listed. For each point, the associated contigs, the
+associated features, and the composite score are shown. See Section <A HREF="node37.html#blockfile">4.2.4</A>
+for an explanation of how the score is derived.
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node37.html b/docs/fishmanual/node37.html
new file mode 100644
index 0000000..f09dcdc
--- /dev/null
+++ b/docs/fishmanual/node37.html
@@ -0,0 +1,181 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Block file </TITLE>
+<META NAME="description" CONTENT="Block file ">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node38.html">
+<LINK REL="previous" HREF="node36.html">
+<LINK REL="up" HREF="node30.html">
+<LINK REL="next" HREF="node38.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html577"
+ HREF="node38.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html573"
+ HREF="node30.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html567"
+ HREF="node36.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html575"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html578"
+ HREF="node38.html">Simple block file</A>
+<B> Up:</B> <A NAME="tex2html574"
+ HREF="node30.html">Output</A>
+<B> Previous:</B> <A NAME="tex2html568"
+ HREF="node36.html">Grid file</A>
+   <B> <A NAME="tex2html576"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00524000000000000000"></A><A NAME="blockfile"></A>
+<BR>
+Block file
+</H2>
+If the PRINT_BLOCKS option is selected, FISH will output a block file
+with the specified name. See Section <A HREF="node39.html#examplefiles">5</A> for an example.
+
+<P>
+The top of the block file displays the time at which the process was initiated
+and the control file used. This is followed by the parameter list. This list,
+similar to the one output to STDOUT (see <A HREF="node31.html#screenoutput">4.2.1</A>) includes the name
+of the control file, the value of the threshold paremeter <IMG
+ WIDTH="18" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img7.png"
+ ALT="$ T$">, the total number
+of points in the grid, the total number of features in the dataset,
+the total number of cells in the grid,
+the proportion of cells that contain a point <IMG
+ WIDTH="16" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img19.png"
+ ALT="$ h$">, the size of the
+neighborhood <IMG
+ WIDTH="25" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="img18.png"
+ ALT="$ d_T$">, the minimum block size to be reported, and the total number of
+blocks found in the dataset.
+
+<P>
+This is followed by individual tables for each block. Within each, there is an
+upper panel that lists the number of points and the associated contigs. And there is
+a lower panel that lists each point in the block in sequence. For each, the table
+shows the number of the point,
+the distance from the previous point, the names of the markers for the associated
+features (in the format markers for feature 1 markers for feature 2), and the product
+of the orientation of the point with the previous point in the block. This product may take a
+value of -1, 0 or 1. If values
+switch frequently between -1 and 1, then transcriptional orientation is not well-conserved
+within that block, and the user may wish to regard this block with suspicion.
+Zero indicates 'unknown'.
+
+<P>
+At the bottom of the blocks file, the number of blocks seen between each pair of contigs is reported.
+Below that, the length distribution of blocks is reported. For blocks with a given number of points,
+the observed and expected numbers of blocks are shown followed by the <IMG
+ WIDTH="14" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="img25.png"
+ ALT="$ p$">-value for blocks of that
+length. The <IMG
+ WIDTH="14" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="img25.png"
+ ALT="$ p$">-value is calculated as described in ([<A
+ HREF="node47.html#Calabrese2003">1</A>])
+<P></P>
+<DIV ALIGN="CENTER"><!-- MATH
+ \begin{equation}
+p = 1-e^{-rc p_u}
+\end{equation}
+ -->
+<TABLE CELLPADDING="0" WIDTH="100%" ALIGN="CENTER">
+<TR VALIGN="MIDDLE">
+<TD NOWRAP ALIGN="CENTER"><IMG
+ WIDTH="119" HEIGHT="39" ALIGN="MIDDLE" BORDER="0"
+ SRC="img26.png"
+ ALT="$\displaystyle p = 1-e^{-rc p_u}$"></TD>
+<TD NOWRAP WIDTH="10" ALIGN="RIGHT">
+(4.1)</TD></TR>
+</TABLE></DIV>
+<BR CLEAR="ALL"><P></P>
+where <IMG
+ WIDTH="22" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img27.png"
+ ALT="$ rc$"> is the total number of cells in the grid, <!-- MATH
+ $p_u = h(nh)^{k-1}$
+ -->
+<IMG
+ WIDTH="121" HEIGHT="40" ALIGN="MIDDLE" BORDER="0"
+ SRC="img28.png"
+ ALT="$ p_u = h(nh)^{k-1}$">, and <IMG
+ WIDTH="16" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img5.png"
+ ALT="$ n$">
+is the number of cells in a neighborhood of size <IMG
+ WIDTH="25" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="img18.png"
+ ALT="$ d_T$">.
+
+<P>
+<HR>
+<!--Navigation Panel-->
+<A NAME="tex2html577"
+ HREF="node38.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html573"
+ HREF="node30.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html567"
+ HREF="node36.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html575"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html578"
+ HREF="node38.html">Simple block file</A>
+<B> Up:</B> <A NAME="tex2html574"
+ HREF="node30.html">Output</A>
+<B> Previous:</B> <A NAME="tex2html568"
+ HREF="node36.html">Grid file</A>
+   <B> <A NAME="tex2html576"
+ HREF="node1.html">Contents</A></B>
+<!--End of Navigation Panel-->
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node38.html b/docs/fishmanual/node38.html
new file mode 100644
index 0000000..e26598f
--- /dev/null
+++ b/docs/fishmanual/node38.html
@@ -0,0 +1,77 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Simple block file</TITLE>
+<META NAME="description" CONTENT="Simple block file">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="previous" HREF="node37.html">
+<LINK REL="up" HREF="node30.html">
+<LINK REL="next" HREF="node39.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html587"
+ HREF="node39.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html583"
+ HREF="node30.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html579"
+ HREF="node37.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html585"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html588"
+ HREF="node39.html">An example</A>
+<B> Up:</B> <A NAME="tex2html584"
+ HREF="node30.html">Output</A>
+<B> Previous:</B> <A NAME="tex2html580"
+ HREF="node37.html">Block file</A>
+   <B> <A NAME="tex2html586"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00525000000000000000">
+Simple block file</A>
+</H2>
+FISH provides the option of printing a more computer readable
+block file by choosing the PRINT_B_SIMPLE option. The first two lines report the number of
+blocks and the total number of points in all blocks, respectively. Each subsequent line
+reports the output for one block. The first number in each line is the number of points in that
+block. This is followed by comma-delimited list of the points themselves. Each block is terminated
+with an asterisk.
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node39.html b/docs/fishmanual/node39.html
new file mode 100644
index 0000000..a483dec
--- /dev/null
+++ b/docs/fishmanual/node39.html
@@ -0,0 +1,113 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>An example </TITLE>
+<META NAME="description" CONTENT="An example ">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node47.html">
+<LINK REL="previous" HREF="node25.html">
+<LINK REL="up" HREF="fishmanual.html">
+<LINK REL="next" HREF="node40.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html599"
+ HREF="node40.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html595"
+ HREF="fishmanual.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html589"
+ HREF="node38.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html597"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html600"
+ HREF="node40.html">A control input file</A>
+<B> Up:</B> <A NAME="tex2html596"
+ HREF="fishmanual.html">User's Manual for FISH</A>
+<B> Previous:</B> <A NAME="tex2html590"
+ HREF="node38.html">Simple block file</A>
+   <B> <A NAME="tex2html598"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00600000000000000000"></A><A NAME="examplefiles"></A>
+<BR>
+An example
+</H1>
+The following truncated input and output files come from a re-analysis of the
+segmental homology within and among the five chromosomes
+of <I>Arabidopsis thaliana</I> [<A
+ HREF="node47.html#Calabrese2003">1</A>,<A
+ HREF="node47.html#Vision2000">2</A>]
+All the genes that received AtXgXXXXX codes in the TIGR version 3.0 release
+of the genome annotation have been included in this dataset.
+Assuming that one is in the same directory as the example
+input files, one can reproduce this session by invoking FISH with the
+following options:
+<PRE>
+# fish -b blocks.txt
+ -g grids.txt
+ -C contigs.txt
+ -B simpleblocks.txt
+ -t > fish_out.txt
+</PRE>
+An explanation of the content of these files is provided in chapter
+<A HREF="node25.html#fileschapter">4</A>.
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
+
+<UL>
+<LI><A NAME="tex2html601"
+ HREF="node40.html">A control input file</A>
+<LI><A NAME="tex2html602"
+ HREF="node41.html">A map input file</A>
+<LI><A NAME="tex2html603"
+ HREF="node42.html">A match input file</A>
+<LI><A NAME="tex2html604"
+ HREF="node43.html">An example of captured STDOUT</A>
+<LI><A NAME="tex2html605"
+ HREF="node44.html">A contig output file</A>
+<LI><A NAME="tex2html606"
+ HREF="node45.html">A grids output file</A>
+<LI><A NAME="tex2html607"
+ HREF="node46.html">A blocks file</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node4.html b/docs/fishmanual/node4.html
new file mode 100644
index 0000000..8437997
--- /dev/null
+++ b/docs/fishmanual/node4.html
@@ -0,0 +1,75 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Contact information</TITLE>
+<META NAME="description" CONTENT="Contact information">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node5.html">
+<LINK REL="previous" HREF="node3.html">
+<LINK REL="up" HREF="node2.html">
+<LINK REL="next" HREF="node5.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html151"
+ HREF="node5.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html147"
+ HREF="node2.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html141"
+ HREF="node3.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html149"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html152"
+ HREF="node5.html">Legal information</A>
+<B> Up:</B> <A NAME="tex2html148"
+ HREF="node2.html">Getting started</A>
+<B> Previous:</B> <A NAME="tex2html142"
+ HREF="node3.html">Introduction</A>
+   <B> <A NAME="tex2html150"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00220000000000000000">
+Contact information</A>
+</H1>
+Please send questions, feedback, and bug reports to tjv at bio.unc.edu. The FISH website
+provides an online form where you may submit your email address should you wish to receive
+notification about updates to this software.
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node40.html b/docs/fishmanual/node40.html
new file mode 100644
index 0000000..6f6b71b
--- /dev/null
+++ b/docs/fishmanual/node40.html
@@ -0,0 +1,119 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>A control input file</TITLE>
+<META NAME="description" CONTENT="A control input file">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node41.html">
+<LINK REL="previous" HREF="node39.html">
+<LINK REL="up" HREF="node39.html">
+<LINK REL="next" HREF="node41.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html618"
+ HREF="node41.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html614"
+ HREF="node39.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html608"
+ HREF="node39.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html616"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html619"
+ HREF="node41.html">A map input file</A>
+<B> Up:</B> <A NAME="tex2html615"
+ HREF="node39.html">An example</A>
+<B> Previous:</B> <A NAME="tex2html609"
+ HREF="node39.html">An example</A>
+   <B> <A NAME="tex2html617"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00610000000000000000">
+A control input file</A>
+</H1>
+Shown is the complete ``control.txt" file. The filenames may be entered as
+paths. For example, if the map and match files were in a subdirectory named
+``data", the names would read, <I>e.g.</I> ``data<IMG
+ WIDTH="5" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img29.png"
+ ALT="$ \/$">map1.txt" on a Unix system and
+would read ``data<!-- MATH
+ $\backslash$
+ -->
+<IMG
+ WIDTH="14" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="img30.png"
+ ALT="$ \backslash$">map1.txt" on a Windows system.
+<PRE>
+-maps
+1 data/map1.txt
+2 data/map2.txt
+3 data/map3.txt
+4 data/map4.txt
+5 data/map5.txt
+-matches
+1 1 data/match1v1.txt
+2 1 data/match2v1.txt
+3 1 data/match3v1.txt
+4 1 data/match4v1.txt
+5 1 data/match5v1.txt
+1 2 data/match1v2.txt
+2 2 data/match2v2.txt
+3 2 data/match3v2.txt
+4 2 data/match4v2.txt
+5 2 data/match5v2.txt
+1 3 data/match1v3.txt
+2 3 data/match2v3.txt
+3 3 data/match3v3.txt
+4 3 data/match4v3.txt
+5 3 data/match5v3.txt
+1 4 data/match1v4.txt
+2 4 data/match2v4.txt
+3 4 data/match3v4.txt
+4 4 data/match4v4.txt
+5 4 data/match5v4.txt
+1 5 data/match1v5.txt
+2 5 data/match2v5.txt
+3 5 data/match3v5.txt
+4 5 data/match4v5.txt
+5 5 data/match5v5.txt
+</PRE>
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node41.html b/docs/fishmanual/node41.html
new file mode 100644
index 0000000..0357994
--- /dev/null
+++ b/docs/fishmanual/node41.html
@@ -0,0 +1,87 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>A map input file</TITLE>
+<META NAME="description" CONTENT="A map input file">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node42.html">
+<LINK REL="previous" HREF="node40.html">
+<LINK REL="up" HREF="node39.html">
+<LINK REL="next" HREF="node42.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html630"
+ HREF="node42.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html626"
+ HREF="node39.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html620"
+ HREF="node40.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html628"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html631"
+ HREF="node42.html">A match input file</A>
+<B> Up:</B> <A NAME="tex2html627"
+ HREF="node39.html">An example</A>
+<B> Previous:</B> <A NAME="tex2html621"
+ HREF="node40.html">A control input file</A>
+   <B> <A NAME="tex2html629"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00620000000000000000">
+A map input file</A>
+</H1>
+Shown are the first ten lines from the chromosome 1 map file (``map.txt").
+The first column is the marker (in this case, gene) name, the second column is the
+transcriptional orientation.
+<PRE>
+At1g01010 1
+At1g01020 -1
+At1g01030 -1
+At1g01040 1
+At1g01050 -1
+At1g01060 -1
+At1g01070 -1
+At1g01080 -1
+At1g01090 -1
+At1g01100 -1
+</PRE>
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node42.html b/docs/fishmanual/node42.html
new file mode 100644
index 0000000..14e0bf3
--- /dev/null
+++ b/docs/fishmanual/node42.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>A match input file</TITLE>
+<META NAME="description" CONTENT="A match input file">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node43.html">
+<LINK REL="previous" HREF="node41.html">
+<LINK REL="up" HREF="node39.html">
+<LINK REL="next" HREF="node43.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html642"
+ HREF="node43.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html638"
+ HREF="node39.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html632"
+ HREF="node41.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html640"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html643"
+ HREF="node43.html">An example of captured</A>
+<B> Up:</B> <A NAME="tex2html639"
+ HREF="node39.html">An example</A>
+<B> Previous:</B> <A NAME="tex2html633"
+ HREF="node41.html">A map input file</A>
+   <B> <A NAME="tex2html641"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00630000000000000000">
+A match input file</A>
+</H1>
+Shown is a sample of ten lines from the chromosome 1 vs. chromosome 1 match file
+(``match1v1.txt"). The scores shown are bit scores from TBLASTX.
+Note that with a MIN_SCORE of 200, all but the last match
+shown would be discarded.
+<PRE>
+At1g01030 At1g25560 112
+At1g01030 At1g50680 73
+At1g01030 At1g51120 72
+At1g01030 At1g35240 63
+At1g01030 At1g35520 60
+At1g01030 At1g77850 58
+At1g01030 At1g34310 58
+At1g01060 At1g18330 133
+At1g01060 At1g01520 109
+At1g01070 At1g11450 313
+</PRE>
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node43.html b/docs/fishmanual/node43.html
new file mode 100644
index 0000000..c525b3e
--- /dev/null
+++ b/docs/fishmanual/node43.html
@@ -0,0 +1,197 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>An example of captured STDOUT</TITLE>
+<META NAME="description" CONTENT="An example of captured STDOUT">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node44.html">
+<LINK REL="previous" HREF="node42.html">
+<LINK REL="up" HREF="node39.html">
+<LINK REL="next" HREF="node44.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html654"
+ HREF="node44.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html650"
+ HREF="node39.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html644"
+ HREF="node42.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html652"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html655"
+ HREF="node44.html">A contig output file</A>
+<B> Up:</B> <A NAME="tex2html651"
+ HREF="node39.html">An example</A>
+<B> Previous:</B> <A NAME="tex2html645"
+ HREF="node42.html">A match input file</A>
+   <B> <A NAME="tex2html653"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00640000000000000000">
+An example of captured STDOUT</A>
+</H1>
+By using the redirection operator, the output that FISH writes by
+default to the terminal is captured to a text file. In the sample output, this
+file is named ``fish_out.txt"
+<PRE>
+Fri Jun 27 11:15:47 2003
+FISH v1.0
+FISH is copyright ©2003, University of North Carolina at Chapel Hill
+Authors: Sugata Chakravarty and Todd J. Vision
+
+Control File = control.txt
+
+processing contigs
+ min_score = 200
+ max_dist = 10
+
+ contig msrkers features
+ 1 6494 5913
+ 2 4038 3711
+ 3 5221 4777
+ 4 3825 3467
+ 5 5888 5453
+
+writing contig output to contigs.txt
+
+
+processing matches
+ min_score = 200
+ top_hits = 5
+
+ contig1 contig2 points cells
+
+ 1 1 2143 17478828
+ 1 2 2018 21943144
+ 1 3 2088 28246400
+ 1 4 1538 20500372
+ 1 5 1986 32243588
+ 2 2 751 6883905
+ 2 3 1460 17727448
+ 2 4 1239 12866037
+ 2 5 1164 20236084
+ 3 3 849 11407476
+ 3 4 1300 16561859
+ 3 5 1977 26048980
+ 4 4 711 6008311
+ 4 5 1551 18905552
+ 5 5 1293 14864878
+
+writing grid output to grids.txt
+
+
+processing blocks
+ T = 0.05
+ total_points = 22068
+ total_features = 23321
+ total_cells = 271922816
+ probability h = 0.000081
+ d_T = 25.640781
+ min_edges = 2
+ block_prob = 0.00100
+ total_blocks = 508
+
+ contig1 contig2 blocks
+ 1 1 50
+ 1 2 52
+ 1 3 43
+ 1 4 34
+ 1 5 25
+ 2 2 27
+ 2 3 48
+ 2 4 48
+ 2 5 18
+ 3 3 15
+ 3 4 25
+ 3 5 53
+ 4 4 16
+ 4 5 33
+ 5 5 21
+
+writing output to blocks.txt
+
+block statistics
+
+points p-value frequency
+3 1.00e+00 |*********************************************
+**...243!
+4 9.22e-01 |********************************************
+***...83!
+5 1.17e-01 |***********************************35!
+6 6.02e-03 |*********************21
+7 2.94e-04 |**********************22
+8 1.43e-05 |*************13
+9 7.15e-07 |************12
+10 5.96e-08 |*****5
+11 0.00e+00 |************12
+12 0.00e+00 |**2
+13 0.00e+00 |****4
+14 0.00e+00 |*******7
+15 0.00e+00 |*****5
+16 0.00e+00 |***3
+17 0.00e+00 |***3
+18 0.00e+00 |**2
+19 0.00e+00 |****4
+20 0.00e+00 |***3
+21 0.00e+00 |***3
+22 0.00e+00 |**2
+23 0.00e+00 |****4
+24 0.00e+00 |*1
+25 0.00e+00 |*1
+26 0.00e+00 |****4
+27 0.00e+00 |*1
+28 0.00e+00 |**2
+29 0.00e+00 |*1
+30 0.00e+00 |**2
+31 0.00e+00 |**2
+34 0.00e+00 |*1
+40 0.00e+00 |*1
+44 0.00e+00 |*1
+60 0.00e+00 |*1
+66 0.00e+00 |*1
+79 0.00e+00 |*1
+ |----|----|----|----|----|----|----|----|--
+--|----|
+ 0 10 20 30 40
+ 50
+</PRE>
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node44.html b/docs/fishmanual/node44.html
new file mode 100644
index 0000000..a6cca74
--- /dev/null
+++ b/docs/fishmanual/node44.html
@@ -0,0 +1,126 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>A contig output file</TITLE>
+<META NAME="description" CONTENT="A contig output file">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node45.html">
+<LINK REL="previous" HREF="node43.html">
+<LINK REL="up" HREF="node39.html">
+<LINK REL="next" HREF="node45.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html666"
+ HREF="node45.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html662"
+ HREF="node39.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html656"
+ HREF="node43.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html664"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html667"
+ HREF="node45.html">A grids output file</A>
+<B> Up:</B> <A NAME="tex2html663"
+ HREF="node39.html">An example</A>
+<B> Previous:</B> <A NAME="tex2html657"
+ HREF="node43.html">An example of captured</A>
+   <B> <A NAME="tex2html665"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00650000000000000000">
+A contig output file</A>
+</H1>
+The opening lines of the file ``contigs.txt" are shown here.
+<PRE>
+Fri Jun 27 11:15:44 2003
+FISH v1.0
+FISH is copyright (c)2003, University of North Carolina
+ at Chapel Hill
+Authors: Sugata Chakravarty and Todd J. Vision
+
+-parameters
+ MIN_SCORE = 200
+ MAX_DIST = 10
+
+-contigs
+
+ contig markers features
+ 1 6494 5913
+ 2 4038 3711
+ 3 5221 4777
+ 4 3825 3467
+ 5 5888 5453
+
+
+
+-features
+
+ feature contig orientation genes
+ 0 1 1 At1g01010
+ 1 1 -1 At1g01020
+ 2 1 -1 At1g01030
+ 3 1 1 At1g01040
+ 4 1 -1 At1g01050
+ 5 1 -1 At1g01060
+ 6 1 -1 At1g01070
+ 7 1 -1 At1g01080
+ 8 1 -1 At1g01090
+ 9 1 -1 At1g01100
+ 10 1 1 At1g01110
+ 11 1 -1 At1g01120
+ 12 1 -1 At1g01130
+ 13 1 -1 At1g01140
+ 14 1 -1 At1g01150
+ 15 1 1 At1g01160
+ 16 1 -1 At1g01170
+ 17 1 1 At1g01180
+ 18 1 -1 At1g01190
+ 19 1 -1 At1g01200
+ 20 1 1 At1g01210
+ 21 1 1 At1g01220
+ 22 1 1 At1g01230
+ 23 1 1 At1g01240
+ . . . .
+ . . . .
+ . . . .
+</PRE>
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node45.html b/docs/fishmanual/node45.html
new file mode 100644
index 0000000..f160732
--- /dev/null
+++ b/docs/fishmanual/node45.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>A grids output file</TITLE>
+<META NAME="description" CONTENT="A grids output file">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node46.html">
+<LINK REL="previous" HREF="node44.html">
+<LINK REL="up" HREF="node39.html">
+<LINK REL="next" HREF="node46.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html678"
+ HREF="node46.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html674"
+ HREF="node39.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html668"
+ HREF="node44.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html676"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html679"
+ HREF="node46.html">A blocks file</A>
+<B> Up:</B> <A NAME="tex2html675"
+ HREF="node39.html">An example</A>
+<B> Previous:</B> <A NAME="tex2html669"
+ HREF="node44.html">A contig output file</A>
+   <B> <A NAME="tex2html677"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00660000000000000000">
+A grids output file</A>
+</H1>
+The opening lines of the file ``grids.txt" are shown here.
+<PRE>
+Fri Jun 27 11:15:46 2003
+FISH v1.0
+FISH is copyright (c)2003, University of North Carolina
+ at Chapel Hill
+Authors: Sugata Chakravarty and Todd J. Vision
+
+Control File = control.txt
+
+-parameters
+ MIN_SCORE = 200
+ TOP_HITS = 5
+
+-subgrids
+ contig1 contig2 points cells
+ 1 1 2143 17478828
+ 1 2 2018 21943144
+ 1 3 2088 28246400
+ 1 4 1538 20500372
+ 1 5 1986 32243588
+ 2 2 751 6883905
+ 2 3 1460 17727448
+ 2 4 1239 12866037
+ 2 5 1164 20236084
+ 3 3 849 11407476
+ 3 4 1300 16561859
+ 3 5 1977 26048980
+ 4 4 711 6008311
+ 4 5 1551 18905552
+ 5 5 1293 14864878
+
+
+-points
+
+ point contig1 contig2 feat1 feat2 score
+ 0 1 1 6 954 328
+ 1 1 1 11 300 395
+ 2 1 1 11 616 237
+ 3 1 1 11 1668 665
+ 4 1 1 11 2146 580
+ 5 1 1 11 4808 582
+ 6 1 1 11 5050 326
+ 7 1 1 13 2412 290
+ 8 1 1 13 2499 303
+ 9 1 1 13 3263 401
+ 10 1 1 18 5288 207
+ 11 1 1 30 1288 588
+ 12 1 1 31 1355 549
+ 13 1 1 31 1699 553
+ 14 1 1 41 4440 242
+ 15 1 1 49 4531 273
+ . . . . . .
+ . . . . . .
+ . . . . . .
+</PRE>
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node46.html b/docs/fishmanual/node46.html
new file mode 100644
index 0000000..6f66296
--- /dev/null
+++ b/docs/fishmanual/node46.html
@@ -0,0 +1,189 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>A blocks file</TITLE>
+<META NAME="description" CONTENT="A blocks file">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="previous" HREF="node45.html">
+<LINK REL="up" HREF="node39.html">
+<LINK REL="next" HREF="node47.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html688"
+ HREF="node47.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html684"
+ HREF="node39.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html680"
+ HREF="node45.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html686"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html689"
+ HREF="node47.html">Bibliography</A>
+<B> Up:</B> <A NAME="tex2html685"
+ HREF="node39.html">An example</A>
+<B> Previous:</B> <A NAME="tex2html681"
+ HREF="node45.html">A grids output file</A>
+   <B> <A NAME="tex2html687"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00670000000000000000"></A><A NAME="blocks"></A>
+<BR>
+A blocks file
+</H1>
+Selected lines from the file ``blocks.txt" are shown here.
+<PRE>
+Fri Jun 27 11:15:47 2003
+FISH v1.0
+FISH is copyright (c)2003, University of North Carolina
+ at Chapel Hill
+Authors: Sugata Chakravarty and Todd J. Vision
+
+Control File = control.txt
+
+-parameters
+ T = 0.05
+ total points = 22068
+ total_features = 23321
+ total_cells = 2.71923e+08
+ h = 8.11554e-05
+ d_T = 25.6408
+ Min_Block_Size = 3
+ block_prob = 0.001
+ total_blocks = 508
+
+
+-block 0
+ points contig1 contig2
+ 79 1 1
+
+ point dist markers orientation
+ 1040 0 {At1g19320 }{At1g75040 } 1
+ 1041 2 {At1g19330 }{At1g75060 } 1
+ 1042 3 {At1g19350 }{At1g75080 } 1
+ 1043 4 {At1g19360 }{At1g75110 At1g75120 } 1
+ 1044 3 {At1g19370 }{At1g75140 } 1
+ 1050 7 {At1g19400 }{At1g75180 } 1
+ 1056 8 {At1g19450 }{At1g75220 } 1
+ 1057 3 {At1g19480 }{At1g75230 } 1
+ 1058 11 {At1g19550 At1g19570 }{At1g75270 } 1
+ 1061 15 {At1g19650 }{At1g75370 } 1
+ 1062 2 {At1g19660 }{At1g75380 } 1
+ 1063 4 {At1g19680 }{At1g75400 } 1
+ 1064 3 {At1g19700 }{At1g75410 } 1
+ . . . .
+ . . . .
+ . . . .
+
+
+-block 1
+ points contig1 contig2
+ 30 1 1
+
+ point dist markers orientation
+ 1246 0 {At1g22920 }{At1g71230 } -1
+ 1249 12 {At1g22970 At1g22980 }{At1g71150 } -1
+ 1250 14 {At1g23010 }{At1g71040 } -1
+ 1251 4 {At1g23030 }{At1g71020 } -1
+ 1252 13 {At1g23080 }{At1g70940 } -1
+ 1256 7 {At1g23110 }{At1g70900 } -1
+ 1258 8 {At1g23140 }{At1g70800 At1g70810 } -1
+ 1262 6 {At1g23170 }{At1g70770 } -1
+ 1263 6 {At1g23190 }{At1g70730 } -1
+ 1265 4 {At1g23210 }{At1g70710 } -1
+ 1266 6 {At1g23240 }{At1g70670 At1g70680 } -1
+ 1267 3 {At1g23260 }{At1g70660 } -1
+ 1268 9 {At1g23290 }{At1g70600 } -1
+ . . . .
+ . . . .
+ . . . .
+ .
+ .
+ .
+-block 507
+ points contig1 contig2
+ 3 5 5
+
+ point dist markers orientation
+ 21978 0 {AT5g53950 }{AT5g61430 } 1
+ 21982 23 {AT5g54230 }{AT5g61420 } 1
+ 21988 21 {AT5g54380 }{AT5g61350 } -1
+
+
+-by contig
+ contig1 contig2 blocks
+ 1 1 50
+ 1 2 52
+ 1 3 43
+ 1 4 34
+ 1 5 25
+ 2 2 27
+ 2 3 48
+ 2 4 48
+ 2 5 18
+ 3 3 15
+ 3 4 25
+ 3 5 53
+ 4 4 16
+ 4 5 33
+ 5 5 21
+
+-by size
+ points obs exp p
+ 3 243 5.23e+01 1.00e+00
+ 4 83 2.55e+00 9.22e-01
+ 5 35 1.24e-01 1.17e-01
+ 6 21 6.04e-03 6.02e-03
+ 7 22 2.94e-04 2.94e-04
+ 8 13 1.43e-05 1.43e-05
+ 9 12 6.97e-07 7.15e-07
+ 10 5 3.40e-08 5.96e-08
+ 11 12 1.65e-09 0.00e+00
+ 12 2 8.05e-11 0.00e+00
+ . . . .
+ . . . .
+ . . . .
+ 44 1 0.00e+00 0.00e+00
+ 60 1 0.00e+00 0.00e+00
+ 66 1 0.00e+00 0.00e+00
+ 79 1 0.00e+00 0.00e+00
+</PRE>
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node47.html b/docs/fishmanual/node47.html
new file mode 100644
index 0000000..19ee317
--- /dev/null
+++ b/docs/fishmanual/node47.html
@@ -0,0 +1,77 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Bibliography</TITLE>
+<META NAME="description" CONTENT="Bibliography">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node48.html">
+<LINK REL="previous" HREF="node39.html">
+<LINK REL="up" HREF="fishmanual.html">
+<LINK REL="next" HREF="node48.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html700"
+ HREF="node48.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html696"
+ HREF="fishmanual.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html690"
+ HREF="node46.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html698"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html701"
+ HREF="node48.html">About this document ...</A>
+<B> Up:</B> <A NAME="tex2html697"
+ HREF="fishmanual.html">User's Manual for FISH</A>
+<B> Previous:</B> <A NAME="tex2html691"
+ HREF="node46.html">A blocks file</A>
+   <B> <A NAME="tex2html699"
+ HREF="node1.html">Contents</A></B>
+<BR><BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00700000000000000000">
+Bibliography</A>
+</H2><DL COMPACT><DD><P></P><DT><A NAME="Calabrese2003">1</A>
+<DD> Calabrese PP, Chakravarty S, Vision TJ (2003) Fast
+identification and statistical evaluation of segmental homologies in comparative
+maps. <I>Bioinformatics</I> <B>19</B>, i74-i80.
+<P></P><DT><A NAME="Vision2000">2</A>
+<DD> TJ Vision, DG Brown, SD Tanksley (2000) The origins of
+genomic duplications in <I>Arabidopsis</I>. <I>Science</I> <B>290</B>:
+2114-2117.
+</DL>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node48.html b/docs/fishmanual/node48.html
new file mode 100644
index 0000000..32a4b97
--- /dev/null
+++ b/docs/fishmanual/node48.html
@@ -0,0 +1,81 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>About this document ...</TITLE>
+<META NAME="description" CONTENT="About this document ...">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="previous" HREF="node47.html">
+<LINK REL="up" HREF="fishmanual.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next_g.png">
+<A NAME="tex2html706"
+ HREF="fishmanual.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html702"
+ HREF="node47.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html708"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Up:</B> <A NAME="tex2html707"
+ HREF="fishmanual.html">User's Manual for FISH</A>
+<B> Previous:</B> <A NAME="tex2html703"
+ HREF="node47.html">Bibliography</A>
+   <B> <A NAME="tex2html709"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00800000000000000000">
+About this document ...</A>
+</H1>
+ <STRONG>User's Manual for FISH
+<BR>(Fast Identification of Segmental Homology)</STRONG><P>
+This document was generated using the
+<A HREF="http://www.latex2html.org/"><STRONG>LaTeX</STRONG>2<tt>HTML</tt></A> translator Version 2002 (1.62)
+<P>
+Copyright © 1993, 1994, 1995, 1996,
+<A HREF="http://cbl.leeds.ac.uk/nikos/personal.html">Nikos Drakos</A>,
+Computer Based Learning Unit, University of Leeds.
+<BR>
+Copyright © 1997, 1998, 1999,
+<A HREF="http://www.maths.mq.edu.au/~ross/">Ross Moore</A>,
+Mathematics Department, Macquarie University, Sydney.
+<P>
+The command line arguments were: <BR>
+ <STRONG>latex2html</STRONG> <TT>fishmanual</TT>
+<P>
+The translation was initiated by root on 2003-06-27
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node5.html b/docs/fishmanual/node5.html
new file mode 100644
index 0000000..238383c
--- /dev/null
+++ b/docs/fishmanual/node5.html
@@ -0,0 +1,285 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Legal information</TITLE>
+<META NAME="description" CONTENT="Legal information">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node6.html">
+<LINK REL="previous" HREF="node4.html">
+<LINK REL="up" HREF="node2.html">
+<LINK REL="next" HREF="node6.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html163"
+ HREF="node6.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html159"
+ HREF="node2.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html153"
+ HREF="node4.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html161"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html164"
+ HREF="node6.html">Acknowledgements</A>
+<B> Up:</B> <A NAME="tex2html160"
+ HREF="node2.html">Getting started</A>
+<B> Previous:</B> <A NAME="tex2html154"
+ HREF="node4.html">Contact information</A>
+   <B> <A NAME="tex2html162"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00230000000000000000">
+Legal information</A>
+</H1>
+FISH and its associated documentation are
+copyright ©2003, University of North Carolina at Chapel Hill. FISH is
+distributed in the hope that it will be useful but without any warranty whatsoever,
+even the implied warranty of merchantability or fitness for a particular purpose.
+Use of this software implies acceptance of the terms of the
+following license.
+
+<P>
+As used herein, the term, ``Program", below, refers to the source
+code and the derivatives supplied by the authors, and a ``work based on the
+Program" means either the Program or any derivative work under copyright law:
+that is to say, a work containing the Program or
+a portion of it, either verbatim or with modifications and/or translated
+into another language. (Hereinafter, translation is included without limitation
+in the term ``modification".) Each licensee is addressed as ``you".
+
+<P>
+1. SCOPE.
+Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope. The act of running the
+Program is not restricted, and the output from the Program is covered only
+if its contents constitute a work based on the Program (independent of having
+been made by running the Program). Whether that is true depends on what the
+Program does.
+
+<P>
+2. USER'S RIGHTS.
+You may copy and distribute verbatim copies of the Program's source code
+as you receive it, in any medium, provided that you keep intact all the notices
+that refer to this License and to the absence of any warranty; give any other
+recipients of the Program a copy of this License along with the Program;
+and conspicuously and appropriately publish on each copy a disclaimer of
+warranty and the following statement: ``Copyright ©2003, University of North
+Carolina at Chapel Hill" If the code has been modified, you also may include
+the following statement: ``Modified by [your institution]." You may charge a
+fee for the physical act of transferring a copy, and you may at your option
+offer warranty protection in exchange for a fee.
+
+<P>
+3. RIGHTS IN DERIVATIVE AND COMBINED WORKS.
+It is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to exercise
+the right to control the distribution of derivative or collective works based
+on the Program. Aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume of a storage
+or distribution medium does not bring the other work under the scope of this
+License.
+
+<P>
+You may modify your copy or copies of the Program or any portion of it,
+thus forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 2 above, provided that you also meet the following
+conditions:
+(a) You must cause the modified files to carry prominent notices stating that you
+changed the files and the date and nature of any change.
+(b) You must cause any work that you distribute or publish, that in whole
+or in part contains or is derived from the Program or any part thereof, to be
+licensed as a whole at no charge to all third parties under the terms of this License.
+
+<P>
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License,
+and its terms, do not apply to those sections when you distribute them as
+separate works. But when you distribute the same sections as part of a whole
+which is a work based on the Program, the distribution of the whole must
+be on the terms of this License, whose permissions for other licensees extend
+to the entire whole, and thus to each and every part regardless of who wrote
+it.
+
+<P>
+4. USER'S PROVISION AND/OR DISTRIBUTION OF SOURCE CODE.
+You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections
+1 and 2 above provided that you also accompany it with the complete corresponding
+machine-readable source code, which must be distributed under the terms of
+Sections 1 and 2 above on a medium customarily used for software interchange.
+
+<P>
+The source code for a work means the preferred form of the work for making
+modifications to it. For an executable work, complete source code means all
+the source code for all modules it contains, plus any associated interface
+definition files, plus the scripts used to control compilation and installation
+of the executable. However, as a special exception, the source code distributed
+need not include anything that is normally distributed (in either source
+or binary form) with the major components (compiler, kernel, and so on) of
+the operating system on which the executable runs, unless that component
+itself accompanies the executable. If distribution of executable or object code
+is made by offering access to copy from a designated place, then offering
+equivalent access to copy the source code from the same place counts as
+distribution of the source code, even though third parties are not compelled
+to copy the source along with the object code.
+
+<P>
+5. LICENSE RESTRICTIONS.
+(a) You may not copy, modify, sublicense, or distribute the Program
+except as expressly provided under this License. Any attempt otherwise to
+copy, modify, sublicense or distribute the Program is void, and will automatically
+terminate your rights under this License. However, parties who have received
+copies, or rights, from you under this License will not have their licenses
+terminated so long as such parties remain in full compliance.
+(b) You are not required to accept this License, since you have not
+signed it. However, nothing else grants you permission to modify or distribute
+the Program or its derivative works. These actions are prohibited by law
+if you do not accept this License. Therefore, by modifying or distributing
+the Program (or any work based on the Program), you indicate your acceptance
+of this License to do so, and all its terms and conditions for copying, distributing
+or modifying the Program or works based on it.
+(c) If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues), conditions
+are imposed on you (whether by court order, agreement or otherwise) that
+contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot distribute so as to satisfy simultaneously
+your obligations under this License and any other pertinent obligations,
+then as a consequence you may not distribute the Program at all. For example,
+if a patent license would not permit royalty-free redistribution of the Program
+by all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to refrain
+entirely from distribution of the Program.
+
+<P>
+It is not the purpose of this section to induce you to infringe any patents
+or other property right claims or to contest validity of any such claims;
+ this section has the sole purpose of protecting the integrity of the free
+software distribution system, which is implemented by public license practices.
+Many people have made generous contributions to the wide range of software
+distributed through that system in reliance on consistent application of
+that system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot impose
+that choice.
+
+<P>
+6. LICENSE CONVEYS TO SUBSEQUENT RECIPIENTS.
+Each time you redistribute the Program (or any work based on the Program),
+the recipient automatically receives a license from the original licensor
+to copy, distribute or modify the Program subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of
+the rights granted herein. You are not responsible for enforcing compliance
+by third parties to this License.
+
+<P>
+7. SEVERABILITY.
+If any portion of this license or any portion of any section of this
+license is held invalid or unenforceable under any particular circumstance,
+the balance of the section is intended to apply and the section as a whole
+is intended to apply in other circumstances.
+
+<P>
+8. NO WARRANTY.
+Because the program is licensed free of charge, there is no warranty
+for the program, to the extent permitted by applicable law. Except when otherwise
+stated in writing the copyright holders and/or other parties provide the
+program``as is" without warranty of any kind, either expressed or implied,
+including, but not limited to, the implied warranties of merchantability
+and fitness for a particular purpose. The entire risk as to the quality and
+performance of the program is with you. Should the program prove defective,
+you assume the cost of all necessary servicing, repair or correction.
+
+<P>
+In no event unless required by applicable law or agreed to in writing
+will any copyright holder, or any other party who may modify and/or redistribute
+the program as permitted above, be liable to you for damages, including any
+general, special, incidental or consequential damages arising out of the
+use or inability to use the program (including but not limited to loss of
+data or data being rendered inaccurate or losses sustained by you or third
+parties or a failure of the program to operate with any other programs),
+even if such holder or other party has been advised of the possibility of
+such damages. Because the program is licensed free of charge, there is no warranty
+for the program, to the extent permitted by applicable law. Except when otherwise
+stated in writing the copyright holders and/or other parties provide the
+program``as is" without warranty of any kind, either expressed or implied,
+including, but not limited to, the implied warranties of merchantability
+and fitness for a particular purpose. The entire risk as to the quality and
+performance of the program is with you. Should the program prove defective,
+you assume the cost of all necessary servicing, repair or correction.
+
+<P>
+In no event unless required by applicable law or agreed to in writing
+will any copyright holder, or any other party who may modify and/or redistribute
+the program as permitted above, be liable to you for damages, including any
+general, special, incidental or consequential damages arising out of the
+use or inability to use the program (including but not limited to loss of
+data or data being rendered inaccurate or losses sustained by you or third
+parties or a failure of the program to operate with any other programs),
+even if such holder or other party has been advised of the possibility of
+such damages.
+
+<P>
+<HR>
+<!--Navigation Panel-->
+<A NAME="tex2html163"
+ HREF="node6.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html159"
+ HREF="node2.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html153"
+ HREF="node4.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html161"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html164"
+ HREF="node6.html">Acknowledgements</A>
+<B> Up:</B> <A NAME="tex2html160"
+ HREF="node2.html">Getting started</A>
+<B> Previous:</B> <A NAME="tex2html154"
+ HREF="node4.html">Contact information</A>
+   <B> <A NAME="tex2html162"
+ HREF="node1.html">Contents</A></B>
+<!--End of Navigation Panel-->
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node6.html b/docs/fishmanual/node6.html
new file mode 100644
index 0000000..000bf57
--- /dev/null
+++ b/docs/fishmanual/node6.html
@@ -0,0 +1,78 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Acknowledgements</TITLE>
+<META NAME="description" CONTENT="Acknowledgements">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node7.html">
+<LINK REL="previous" HREF="node5.html">
+<LINK REL="up" HREF="node2.html">
+<LINK REL="next" HREF="node7.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html175"
+ HREF="node7.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html171"
+ HREF="node2.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html165"
+ HREF="node5.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html173"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html176"
+ HREF="node7.html">Availability</A>
+<B> Up:</B> <A NAME="tex2html172"
+ HREF="node2.html">Getting started</A>
+<B> Previous:</B> <A NAME="tex2html166"
+ HREF="node5.html">Legal information</A>
+   <B> <A NAME="tex2html174"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00240000000000000000">
+Acknowledgements</A>
+</H1>
+Funding for FISH was provided by the USDA-ARS Center for Agricultural
+Bioinformatics, the Center for Computational Genomics at the Cornell
+Theory Center, and by National Science Foundation grants DBI-0110069 and DBI-0227314
+to TJV and DMS-0102008 to PPC.
+The authors wish to thank Peter Calabrese for his many contributions to the
+ideas underlying the software.
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node7.html b/docs/fishmanual/node7.html
new file mode 100644
index 0000000..f126c4d
--- /dev/null
+++ b/docs/fishmanual/node7.html
@@ -0,0 +1,97 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Availability</TITLE>
+<META NAME="description" CONTENT="Availability">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="previous" HREF="node6.html">
+<LINK REL="up" HREF="node2.html">
+<LINK REL="next" HREF="node8.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html185"
+ HREF="node8.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html181"
+ HREF="node2.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html177"
+ HREF="node6.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html183"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html186"
+ HREF="node8.html">Installing from source code</A>
+<B> Up:</B> <A NAME="tex2html182"
+ HREF="node2.html">Getting started</A>
+<B> Previous:</B> <A NAME="tex2html178"
+ HREF="node6.html">Acknowledgements</A>
+   <B> <A NAME="tex2html184"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00250000000000000000">
+Availability</A>
+</H1>
+The latest version of this program, along with documentation and examples, is available from
+<TT><A NAME="tex2html1"
+ HREF="http://www.bio.unc.edu/faculty/vision/lab/FISH/">http://www.bio.unc.edu/faculty/vision/lab/FISH/</A></TT>.
+
+<P>
+FISH is written primarily in C++, together
+with C style data input/output. The source code is designed to be compatible
+with
+all versions of gcc (GNU C++/C compiler). In addition, executables are
+available
+for a limited number of platforms. The program may require 32 MB of RAM or more at runtime.
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
+
+<UL>
+<LI><A NAME="tex2html187"
+ HREF="node8.html">Installing from source code</A>
+<LI><A NAME="tex2html188"
+ HREF="node9.html">Installing the Windows executable</A>
+<LI><A NAME="tex2html189"
+ HREF="node10.html">Installing the MacOSX executable</A>
+<LI><A NAME="tex2html190"
+ HREF="node11.html">Testing FISH on sample data</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node8.html b/docs/fishmanual/node8.html
new file mode 100644
index 0000000..422c271
--- /dev/null
+++ b/docs/fishmanual/node8.html
@@ -0,0 +1,95 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Installing from source code</TITLE>
+<META NAME="description" CONTENT="Installing from source code">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node9.html">
+<LINK REL="previous" HREF="node7.html">
+<LINK REL="up" HREF="node7.html">
+<LINK REL="next" HREF="node9.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html201"
+ HREF="node9.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html197"
+ HREF="node7.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html191"
+ HREF="node7.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html199"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html202"
+ HREF="node9.html">Installing the Windows executable</A>
+<B> Up:</B> <A NAME="tex2html198"
+ HREF="node7.html">Availability</A>
+<B> Previous:</B> <A NAME="tex2html192"
+ HREF="node7.html">Availability</A>
+   <B> <A NAME="tex2html200"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00251000000000000000">
+Installing from source code</A>
+</H2>
+Installation from source code requires a c++ compiler (the makefile assumes that you have g++).
+Fish is known to successfully compile with g++ 3.1 and 3.2 (to see what version of
+g++ you have type ``g++ -v").
+
+<P>
+The code is
+known to compile and run on at least some versions of Solaris, RedHat Linux, Windows
+and MacOSX. It should compile and run on all systems
+with g++ installed. For windows environments, MinGW(http://www.mingw.org),
+provides a g++ compiler that works well. To install, type the following commands.
+
+<P>
+
+<OL>
+<LI>tar -xzvf FISH-1.0.tar.z
+</LI>
+<LI>cd FISH-1.0
+</LI>
+<LI>make all
+</LI>
+<LI>cp bin/fish /usr/local/bin (may require superuser priviliges)
+</LI>
+</OL>
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/docs/fishmanual/node9.html b/docs/fishmanual/node9.html
new file mode 100644
index 0000000..673bea4
--- /dev/null
+++ b/docs/fishmanual/node9.html
@@ -0,0 +1,89 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
+patched version by: Kenshi Muto, Debian Project.
+LaTeX2HTML 2002 (1.62),
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Installing the Windows executable</TITLE>
+<META NAME="description" CONTENT="Installing the Windows executable">
+<META NAME="keywords" CONTENT="fishmanual">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="fishmanual.css">
+
+<LINK REL="next" HREF="node10.html">
+<LINK REL="previous" HREF="node8.html">
+<LINK REL="up" HREF="node7.html">
+<LINK REL="next" HREF="node10.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html213"
+ HREF="node10.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html209"
+ HREF="node7.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html203"
+ HREF="node8.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<A NAME="tex2html211"
+ HREF="node1.html">
+<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
+ SRC="file:/usr/share/latex2html/icons/contents.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html214"
+ HREF="node10.html">Installing the MacOSX executable</A>
+<B> Up:</B> <A NAME="tex2html210"
+ HREF="node7.html">Availability</A>
+<B> Previous:</B> <A NAME="tex2html204"
+ HREF="node8.html">Installing from source code</A>
+   <B> <A NAME="tex2html212"
+ HREF="node1.html">Contents</A></B>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00252000000000000000">
+Installing the Windows executable</A>
+</H2>
+
+<P>
+<PRE>
+INSTALLATION:
+ 1. Unzip FISH-1.0-win.zip into "C:\<DESIRED DIRECTORY>".
+ 2. The executable will be located in
+ "C:\<DESIRED DIRECTORY>\FISH-1.0\fish.exe".
+For Example:
+ Unzip to "C:\Program Files"
+ From a command line type: "C:\Program Files\FISH-1.0\fish.exe" -h.
+ Don't forget the quotations marks! This executes fish and shows
+ the command line options.
+
+REQUIREMENTS:
+ 1. 32 MB of RAM.
+ 2. Operating system: Known to run on Windows XP,ME, and NT.
+</PRE>
+
+<P>
+<BR><HR>
+<ADDRESS>
+root
+2003-06-27
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/makefile b/makefile
new file mode 100644
index 0000000..6c93456
--- /dev/null
+++ b/makefile
@@ -0,0 +1,16 @@
+CC = g++ -ggdb
+
+
+
+all : realall
+ make bin
+
+realall :
+ (cd ./src; $(CC) -c point.cpp; $(CC) fish.cpp point.o -o fish)
+
+bin :
+ mkdir bin
+ mv src/fish ./bin
+clean :
+ (cd src ; rm *.o)
+ (rm -rf ./bin)
diff --git a/sample_input/blk.out b/sample_input/blk.out
new file mode 100644
index 0000000..350bf23
--- /dev/null
+++ b/sample_input/blk.out
@@ -0,0 +1,6969 @@
+Wed Nov 19 13:23:03 2003
+FISH v1.0
+FISH is copyright (c)2003, University of North Carolina at Chapel Hill
+Authors: Sugata Chakravarty and Todd J. Vision
+
+Control File = control.txt
+
+-parameters
+ T = 0.05
+ total points = 22068
+ total_features = 23321
+ total_cells = 2.71923e+08
+ h = 8.11554e-05
+ d_T = 25.6408
+ Min_Block_Size = 3
+ block_prob = 0.001
+ total_blocks = 508
+
+
+-block 0
+ points contig1 contig2
+ 79 1 1
+
+ point dist markers orientation
+ 1040 0 {At1g19320 }{At1g75040 } 1
+ 1041 2 {At1g19330 }{At1g75060 } 1
+ 1042 3 {At1g19350 }{At1g75080 } 1
+ 1043 4 {At1g19360 }{At1g75110 At1g75120 } 1
+ 1044 3 {At1g19370 }{At1g75140 } 1
+ 1050 7 {At1g19400 }{At1g75180 } 1
+ 1056 8 {At1g19450 }{At1g75220 } 1
+ 1057 3 {At1g19480 }{At1g75230 } 1
+ 1058 11 {At1g19550 At1g19570 }{At1g75270 } 1
+ 1061 15 {At1g19650 }{At1g75370 } 1
+ 1062 2 {At1g19660 }{At1g75380 } 1
+ 1063 4 {At1g19680 }{At1g75400 } 1
+ 1064 3 {At1g19700 }{At1g75410 } 1
+ 1065 2 {At1g19710 }{At1g75420 } 1
+ 1068 7 {At1g19740 }{At1g75460 } 1
+ 1070 20 {At1g19840 }{At1g75590 } 1
+ 1073 6 {At1g19890 }{At1g75600 At1g75610 } 1
+ 1074 2 {At1g19900 }{At1g75620 } 1
+ 1075 2 {At1g19910 }{At1g75630 } 1
+ 1078 7 {At1g19940 }{At1g75680 } 1
+ 1079 3 {At1g19950 }{At1g75700 } 1
+ 1080 7 {At1g19970 }{At1g75760 } 1
+ 1082 6 {At1g20010 }{At1g75780 } 1
+ 1083 4 {At1g20030 }{At1g75800 } 1
+ 1084 9 {At1g20090 }{At1g75840 } 1
+ 1085 7 {At1g20120 At1g20130 }{At1g75880 At1g75890 At1g75900 } 1
+ 1091 11 {At1g20200 }{At1g75990 } 1
+ 1092 3 {At1g20220 }{At1g76020 } 1
+ 1104 4 {At1g20260 }{At1g76030 } 1
+ 1106 13 {At1g20330 }{At1g76090 } 1
+ 1107 2 {At1g20340 }{At1g76100 } 1
+ 1109 5 {At1g20370 }{At1g76120 } 1
+ 1110 3 {At1g20380 }{At1g76140 } 1
+ 1117 24 {At1g20540 }{At1g76260 } 1
+ 1118 2 {At1g20550 }{At1g76270 } 1
+ 1123 3 {At1g20560 }{At1g76290 } 1
+ 1125 5 {At1g20590 At1g20610 }{At1g76310 } 1
+ 1126 6 {At1g20640 }{At1g76350 } 1
+ 1131 2 {At1g20650 }{At1g76360 At1g76370 } 1
+ 1135 13 {At1g20780 }{At1g76390 } 1
+ 1136 4 {At1g20810 }{At1g76410 } 1
+ 1137 6 {At1g20860 }{At1g76430 } 1
+ 1138 5 {At1g20880 }{At1g76460 } 1
+ 1139 3 {At1g20890 }{At1g76480 } 1
+ 1140 3 {At1g20900 }{At1g76500 } 1
+ 1142 6 {At1g20930 }{At1g76540 } 1
+ 1143 3 {At1g20950 }{At1g76550 } 1
+ 1144 6 {At1g20980 }{At1g76580 } 1
+ 1147 3 {At1g21000 }{At1g76590 } 1
+ 1154 8 {At1g21060 }{At1g76620 } 1
+ 1155 6 {At1g21070 }{At1g76670 } 1
+ 1156 3 {At1g21080 }{At1g76700 } 1
+ 1160 11 {At1g21100 At1g21110 At1g21120 At1g21130 }{At1g76790 } 1
+ 1162 10 {At1g21160 }{At1g76720 At1g76810 At1g76820 } 1
+ 1163 12 {At1g21170 At1g21180 }{At1g76850 } 1
+ 1164 4 {At1g21200 }{At1g76870 } 1
+ 1175 19 {At1g21380 }{At1g76970 } 1
+ 1176 6 {At1g21410 }{At1g77000 } 1
+ 1177 7 {At1g21440 }{At1g77060 } 1
+ 1180 24 {At1g21530 At1g21540 }{At1g77240 } 1
+ 1181 9 {At1g21590 }{At1g77280 } 1
+ 1182 5 {At1g21610 }{At1g77310 } 1
+ 1183 23 {At1g21720 }{At1g77440 } 1
+ 1184 8 {At1g21740 }{At1g77500 } 1
+ 1185 2 {At1g21750 }{At1g77510 } 1
+ 1191 18 {At1g21870 }{At1g77610 } 1
+ 1192 3 {At1g21880 }{At1g77630 } 1
+ 1195 7 {At1g21920 }{At1g77660 } 1
+ 1197 14 {At1g21980 }{At1g77740 } 1
+ 1201 25 {At1g22070 }{At1g77920 } 1
+ 1202 9 {At1g22130 }{At1g77950 } -1
+ 1204 6 {At1g22150 }{At1g77990 At1g78000 } -1
+ 1205 7 {At1g22170 }{At1g78050 } 1
+ 1209 8 {At1g22210 }{At1g78090 } 1
+ 1211 10 {At1g22240 }{At1g78160 } 1
+ 1212 5 {At1g22260 At1g22270 }{At1g78190 } 1
+ 1217 13 {At1g22300 }{At1g78300 } -1
+ 1218 6 {At1g22330 }{At1g78260 } 1
+ 1219 2 {At1g22340 At1g22360 At1g22370 At1g22390 At1g22400 }{At1g78270 } 1
+
+
+-block 1
+ points contig1 contig2
+ 30 1 1
+
+ point dist markers orientation
+ 1246 0 {At1g22920 }{At1g71230 } -1
+ 1249 12 {At1g22970 At1g22980 }{At1g71150 } -1
+ 1250 14 {At1g23010 }{At1g71040 } -1
+ 1251 4 {At1g23030 }{At1g71020 } -1
+ 1252 13 {At1g23080 }{At1g70940 } -1
+ 1256 7 {At1g23110 }{At1g70900 } -1
+ 1258 8 {At1g23140 }{At1g70800 At1g70810 } -1
+ 1262 6 {At1g23170 }{At1g70770 } -1
+ 1263 6 {At1g23190 }{At1g70730 } -1
+ 1265 4 {At1g23210 }{At1g70710 } -1
+ 1266 6 {At1g23240 }{At1g70670 At1g70680 } -1
+ 1267 3 {At1g23260 }{At1g70660 } -1
+ 1268 9 {At1g23290 }{At1g70600 } -1
+ 1272 4 {At1g23310 }{At1g70580 } -1
+ 1274 3 {At1g23320 }{At1g70560 } -1
+ 1276 3 {At1g23340 }{At1g70550 } -1
+ 1277 2 {At1g23350 }{At1g70540 } -1
+ 1278 4 {At1g23370 At1g23380 }{At1g70510 } -1
+ 1280 9 {At1g23460 }{At1g70500 } -1
+ 1284 4 {At1g23490 }{At1g70490 } -1
+ 1288 8 {At1g23540 }{At1g70450 At1g70460 } -1
+ 1289 2 {At1g23550 }{At1g70440 } -1
+ 1290 4 {At1g23560 }{At1g70480 } -1
+ 1291 10 {At1g23700 }{At1g70430 } -1
+ 1293 5 {At1g23730 }{At1g70410 } -1
+ 1295 7 {At1g23760 }{At1g70370 } -1
+ 1296 5 {At1g23790 }{At1g70340 } -1
+ 1300 6 {At1g23820 }{At1g70310 } -1
+ 1303 6 {At1g23870 }{At1g70290 } -1
+ 1304 2 {At1g23880 }{At1g70280 } -1
+
+
+-block 2
+ points contig1 contig2
+ 28 1 1
+
+ point dist markers orientation
+ 528 0 {At1g10640 }{At1g60590 } 1
+ 529 3 {At1g10650 }{At1g60610 } 1
+ 530 18 {At1g10670 }{At1g60810 } -1
+ 532 9 {At1g10730 }{At1g60780 } -1
+ 537 14 {At1g10810 }{At1g60680 At1g60690 At1g60710 At1g60730 At1g60750 } -1
+ 538 10 {At1g10860 }{At1g60630 } -1
+ 539 18 {At1g10870 }{At1g60860 } 1
+ 544 6 {At1g10900 }{At1g60890 } 1
+ 548 5 {At1g10930 }{At1g60930 } 1
+ 549 2 {At1g10940 }{At1g60940 } 1
+ 552 3 {At1g10960 }{At1g60950 } 1
+ 553 2 {At1g10970 }{At1g60960 } 1
+ 557 13 {At1g11060 }{At1g61030 } 1
+ 558 6 {At1g11070 }{At1g61080 } 1
+ 559 6 {At1g11080 }{At1g61130 } 1
+ 562 3 {At1g11100 }{At1g61140 } 1
+ 564 10 {At1g11160 }{At1g61210 } 1
+ 565 4 {At1g11170 }{At1g61240 } 1
+ 567 2 {At1g11180 }{At1g61250 } 1
+ 568 11 {At1g11250 }{At1g61290 } 1
+ 571 8 {At1g11280 At1g11300 At1g11330 At1g11340 At1g11350 At1g11410 }{At1g61360 At1g61370 At1g61380 At1g61390 At1g61400 At1g61420 At1g61430 At1g61440 At1g61460 At1g61480 At1g61490 At1g61500 At1g61550 At1g61610 } 1
+ 586 9 {At1g11310 }{At1g61560 } 1
+ 591 12 {At1g11390 }{At1g61640 } 1
+ 592 22 {At1g11540 }{At1g61740 } 1
+ 593 6 {At1g11560 }{At1g61790 } 1
+ 597 12 {At1g11630 }{At1g61870 } 1
+ 604 4 {At1g11670 }{At1g61890 } 1
+ 609 18 {At1g11740 }{At1g62050 } 1
+
+
+-block 3
+ points contig1 contig2
+ 26 1 1
+
+ point dist markers orientation
+ 981 0 {At1g18410 }{At1g73860 } 1
+ 984 9 {At1g18460 }{At1g73920 } 1
+ 985 4 {At1g18470 }{At1g73950 } 1
+ 986 10 {At1g18500 }{At1g74040 } 1
+ 987 5 {At1g18540 }{At1g74050 At1g74060 } 1
+ 992 5 {At1g18570 }{At1g74080 } 1
+ 994 3 {At1g18590 }{At1g74090 At1g74100 } 1
+ 995 6 {At1g18610 }{At1g74150 } 1
+ 996 2 {At1g18620 }{At1g74160 } 1
+ 1000 17 {At1g18670 }{At1g74330 } 1
+ 1001 7 {At1g18690 }{At1g74380 } 1
+ 1002 7 {At1g18710 }{At1g74430 } 1
+ 1003 2 {At1g18720 }{At1g74440 } 1
+ 1004 3 {At1g18740 }{At1g74450 } 1
+ 1005 8 {At1g18790 }{At1g74480 } 1
+ 1006 8 {At1g18800 }{At1g74560 } 1
+ 1007 13 {At1g18840 }{At1g74690 } 1
+ 1008 5 {At1g18870 }{At1g74710 } 1
+ 1013 5 {At1g18890 }{At1g74740 } 1
+ 1015 2 {At1g18900 }{At1g74750 At1g74850 } 1
+ 1016 2 {At1g18910 }{At1g74760 } 1
+ 1017 2 {At1g18920 }{At1g74770 } 1
+ 1018 3 {At1g18940 }{At1g74780 } 1
+ 1019 7 {At1g18970 At1g18980 }{At1g74820 } 1
+ 1020 2 {At1g18990 }{At1g74830 } 1
+ 1026 11 {At1g19050 }{At1g74890 } 1
+
+
+-block 4
+ points contig1 contig2
+ 25 1 1
+
+ point dist markers orientation
+ 615 0 {At1g11910 }{At1g62290 } 1
+ 619 6 {At1g11950 }{At1g62310 } 1
+ 621 2 {At1g11960 }{At1g62320 } 1
+ 623 4 {At1g11990 }{At1g62330 } -1
+ 626 7 {At1g12010 }{At1g62380 } 1
+ 628 9 {At1g12040 }{At1g62440 } 1
+ 629 4 {At1g12070 }{At1g62450 } 1
+ 632 13 {At1g12130 At1g12140 At1g12160 At1g12200 }{At1g62540 At1g62560 At1g62570 At1g62580 At1g62600 At1g62620 } 1
+ 638 8 {At1g12210 At1g12220 At1g12280 At1g12290 }{At1g62630 } 1
+ 641 4 {At1g12240 }{At1g62660 } 1
+ 644 4 {At1g12260 }{At1g62700 } 1
+ 646 4 {At1g12270 }{At1g62740 } 1
+ 651 10 {At1g12300 }{At1g62590 At1g62670 At1g62680 At1g62720 } 1
+ 658 18 {At1g12310 }{At1g62820 } 1
+ 659 9 {At1g12340 At1g12390 }{At1g62880 } 1
+ 660 5 {At1g12380 }{At1g62870 } 1
+ 663 13 {At1g12460 }{At1g62950 } 1
+ 666 12 {At1g12560 }{At1g62980 } 1
+ 675 9 {At1g12610 }{At1g63030 } 1
+ 680 16 {At1g12620 At1g12700 At1g12770 }{At1g62860 At1g62910 At1g62930 } 1
+ 687 19 {At1g12640 }{At1g63050 } 1
+ 688 9 {At1g12710 }{At1g63090 } 1
+ 690 4 {At1g12730 }{At1g63110 } 1
+ 691 3 {At1g12750 }{At1g63120 } 1
+ 693 6 {At1g12780 }{At1g63180 } 1
+
+
+-block 5
+ points contig1 contig2
+ 22 1 1
+
+ point dist markers orientation
+ 782 0 {At1g15280 }{At1g80000 } 1
+ 783 4 {At1g15300 }{At1g80020 } 1
+ 785 22 {At1g15380 }{At1g80160 } 1
+ 788 19 {At1g15480 }{At1g80270 } 1
+ 790 2 {At1g15490 }{At1g80280 } 1
+ 791 3 {At1g15500 }{At1g80300 } 1
+ 800 9 {At1g15550 }{At1g80340 } 1
+ 804 5 {At1g15570 }{At1g80370 } 1
+ 805 15 {At1g15670 }{At1g80440 } 1
+ 806 10 {At1g15730 }{At1g80480 } 1
+ 807 3 {At1g15750 }{At1g80490 } 1
+ 808 18 {At1g15810 }{At1g80620 } 1
+ 809 9 {At1g15850 }{At1g80670 } 1
+ 810 7 {At1g15870 }{At1g80720 } 1
+ 816 11 {At1g15910 }{At1g80790 } 1
+ 817 2 {At1g15920 }{At1g80780 } 1
+ 818 5 {At1g15940 }{At1g80810 } 1
+ 820 2 {At1g15950 }{At1g80820 } 1
+ 821 2 {At1g15960 }{At1g80830 } 1
+ 823 3 {At1g15970 }{At1g80850 } 1
+ 825 9 {At1g16010 }{At1g80900 } 1
+ 826 2 {At1g16020 }{At1g80910 } 1
+
+
+-block 6
+ points contig1 contig2
+ 20 1 1
+
+ point dist markers orientation
+ 911 0 {At1g17420 }{At1g72520 } 1
+ 912 11 {At1g17430 }{At1g72620 } 1
+ 914 4 {At1g17460 }{At1g72630 } 1
+ 915 4 {At1g17470 }{At1g72660 } 1
+ 920 7 {At1g17500 }{At1g72700 } 1
+ 921 8 {At1g17530 }{At1g72750 } 1
+ 922 2 {At1g17540 }{At1g72760 } 1
+ 924 2 {At1g17550 }{At1g72770 } 1
+ 926 10 {At1g17600 }{At1g72840 At1g72860 } 1
+ 927 5 {At1g17610 }{At1g72890 At1g72910 At1g72920 At1g72930 At1g72940 At1g72950 } 1
+ 935 19 {At1g17730 }{At1g73030 } 1
+ 938 6 {At1g17750 }{At1g73070 At1g73080 } 1
+ 941 11 {At1g17790 }{At1g73150 } 1
+ 942 6 {At1g17810 }{At1g73190 } 1
+ 943 2 {At1g17820 }{At1g73200 } 1
+ 945 9 {At1g17880 }{At1g73230 } 1
+ 946 3 {At1g17890 }{At1g73250 } 1
+ 953 10 {At1g17920 }{At1g73360 } 1
+ 954 5 {At1g17940 }{At1g73390 } 1
+ 957 3 {At1g17950 }{At1g73410 } 1
+
+
+-block 7
+ points contig1 contig2
+ 18 1 1
+
+ point dist markers orientation
+ 830 0 {At1g16060 }{At1g79700 } -1
+ 834 6 {At1g16110 At1g16120 At1g16130 At1g16140 At1g16150 At1g16160 At1g16260 }{At1g79670 At1g79680 } -1
+ 839 6 {At1g16200 }{At1g79650 } -1
+ 840 4 {At1g16220 }{At1g79630 } -1
+ 841 6 {At1g16240 }{At1g79590 } -1
+ 842 4 {At1g16270 }{At1g79570 } -1
+ 843 7 {At1g16300 }{At1g79530 } -1
+ 844 2 {At1g16310 }{At1g79520 } -1
+ 845 2 {At1g16320 }{At1g79510 } -1
+ 847 3 {At1g16340 }{At1g79500 } -1
+ 848 4 {At1g16350 }{At1g79470 } -1
+ 850 3 {At1g16360 }{At1g79450 } -1
+ 851 9 {At1g16370 At1g16390 }{At1g79360 At1g79410 } -1
+ 852 5 {At1g16380 }{At1g79400 } -1
+ 854 15 {At1g16440 }{At1g79250 } -1
+ 855 2 {At1g16460 }{At1g79230 } -1
+ 856 3 {At1g16470 }{At1g79210 } -1
+ 866 5 {At1g16490 }{At1g79180 } -1
+
+
+-block 8
+ points contig1 contig2
+ 16 1 1
+
+ point dist markers orientation
+ 1388 0 {At1g26630 }{At1g69410 } 1
+ 1389 4 {At1g26650 }{At1g69430 } 1
+ 1390 7 {At1g26690 }{At1g69460 } 1
+ 1392 5 {At1g26730 }{At1g69480 } -1
+ 1393 9 {At1g26770 }{At1g69530 } 1
+ 1394 4 {At1g26780 }{At1g69560 } 1
+ 1396 15 {At1g26830 }{At1g69670 } -1
+ 1400 10 {At1g26880 }{At1g69620 } -1
+ 1403 24 {At1g26960 }{At1g69780 } 1
+ 1405 2 {At1g26970 }{At1g69790 } 1
+ 1413 23 {At1g26990 }{At1g70010 } -1
+ 1415 19 {At1g27040 }{At1g69850 } 1
+ 1416 6 {At1g27080 }{At1g69870 } 1
+ 1418 4 {At1g27100 }{At1g69890 } 1
+ 1420 6 {At1g27130 At1g27140 }{At1g69920 At1g69930 } -1
+ 1421 9 {At1g27190 }{At1g69990 } 1
+
+
+-block 9
+ points contig1 contig2
+ 15 1 1
+
+ point dist markers orientation
+ 379 0 {At1g09080 }{At1g56410 } -1
+ 391 16 {At1g09180 }{At1g56330 } -1
+ 396 4 {At1g09210 }{At1g56340 } 1
+ 397 11 {At1g09240 }{At1g56430 } 1
+ 398 17 {At1g09310 }{At1g56580 } -1
+ 399 6 {At1g09350 }{At1g56600 } 1
+ 401 10 {At1g09390 }{At1g56670 } 1
+ 404 4 {At1g09410 }{At1g56690 } 1
+ 411 6 {At1g09440 }{At1g56720 } 1
+ 420 10 {At1g09540 }{At1g57560 At1g57580 } 1
+ 424 3 {At1g09550 }{At1g57590 } 1
+ 427 6 {At1g09580 }{At1g57620 } 1
+ 428 5 {At1g09590 At1g09690 }{At1g57660 } 1
+ 434 5 {At1g09600 }{At1g57700 } 1
+ 441 5 {At1g09640 }{At1g57720 } 1
+
+
+-block 10
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 429 0 {At1g09590 At1g09690 }{At1g57860 } -1
+ 452 25 {At1g09840 }{At1g57870 } 1
+ 454 3 {At1g09860 }{At1g57980 At1g57990 } 1
+
+
+-block 11
+ points contig1 contig2
+ 11 1 1
+
+ point dist markers orientation
+ 482 0 {At1g10210 }{At1g59580 } 1
+ 489 11 {At1g10290 }{At1g59610 } 1
+ 493 13 {At1g10360 At1g10370 }{At1g59670 At1g59700 } -1
+ 494 3 {At1g10390 }{At1g59660 } -1
+ 496 3 {At1g10410 }{At1g59650 } -1
+ 498 18 {At1g10430 }{At1g59830 } 1
+ 501 6 {At1g10450 }{At1g59890 } 1
+ 504 6 {At1g10470 }{At1g59940 } 1
+ 507 15 {At1g10540 }{At1g60030 } 1
+ 511 15 {At1g10560 }{At1g60190 } 1
+ 512 4 {At1g10570 }{At1g60220 } 1
+
+
+-block 12
+ points contig1 contig2
+ 11 1 1
+
+ point dist markers orientation
+ 961 0 {At1g18040 }{At1g73690 } -1
+ 964 13 {At1g18150 }{At1g73670 } -1
+ 966 2 {At1g18160 }{At1g73660 } -1
+ 967 3 {At1g18180 }{At1g73650 } -1
+ 968 3 {At1g18200 }{At1g73640 } -1
+ 969 2 {At1g18210 }{At1g73630 } -1
+ 970 3 {At1g18250 }{At1g73620 } -1
+ 972 6 {At1g18260 }{At1g73570 } -1
+ 973 7 {At1g18300 }{At1g73540 } -1
+ 974 9 {At1g18350 }{At1g73500 } -1
+ 975 3 {At1g18360 }{At1g73480 } -1
+
+
+-block 13
+ points contig1 contig2
+ 8 1 1
+
+ point dist markers orientation
+ 870 0 {At1g16680 }{At1g79030 } -1
+ 871 2 {At1g16690 }{At1g79020 } -1
+ 872 2 {At1g16700 }{At1g79010 } -1
+ 875 2 {At1g16710 }{At1g79000 } -1
+ 878 9 {At1g16760 }{At1g78940 } -1
+ 879 4 {At1g16780 }{At1g78920 } -1
+ 880 12 {At1g16860 }{At1g78880 } -1
+ 881 4 {At1g16890 }{At1g78870 } -1
+
+
+-block 14
+ points contig1 contig2
+ 7 1 1
+
+ point dist markers orientation
+ 362 0 {At1g08730 }{At1g54560 } -1
+ 368 22 {At1g08880 }{At1g54690 } 1
+ 370 6 {At1g08900 At1g08920 At1g08930 }{At1g54730 } 1
+ 372 12 {At1g08970 }{At1g54830 } 1
+ 374 13 {At1g08990 }{At1g54940 } 1
+ 376 3 {At1g09000 }{At1g54960 } 1
+ 377 13 {At1g09040 At1g09050 }{At1g55050 } 1
+
+
+-block 15
+ points contig1 contig2
+ 7 1 1
+
+ point dist markers orientation
+ 734 0 {At1g13880 }{At1g26580 } 1
+ 735 12 {At1g13950 }{At1g26630 } 1
+ 738 12 {At1g14010 }{At1g26690 } 1
+ 741 6 {At1g14040 }{At1g26730 } 1
+ 746 22 {At1g14220 }{At1g26820 } 1
+ 748 17 {At1g14320 }{At1g26910 } 1
+ 752 11 {At1g14370 }{At1g26970 } 1
+
+
+-block 16
+ points contig1 contig2
+ 7 1 1
+
+ point dist markers orientation
+ 1220 0 {At1g22500 }{At1g72200 } -1
+ 1221 8 {At1g22530 }{At1g72150 } -1
+ 1222 2 {At1g22540 At1g22550 At1g22570 }{At1g72120 At1g72130 At1g72140 } 1
+ 1223 4 {At1g22600 }{At1g72100 } -1
+ 1235 15 {At1g22650 }{At1g72000 } -1
+ 1237 17 {At1g22710 }{At1g71880 At1g71890 } -1
+ 1241 16 {At1g22760 }{At1g71770 } -1
+
+
+-block 17
+ points contig1 contig2
+ 7 1 1
+
+ point dist markers orientation
+ 1359 0 {At1g25450 }{At1g68530 } 1
+ 1361 2 {At1g25460 }{At1g68540 } 1
+ 1362 8 {At1g25480 }{At1g68600 } 1
+ 1363 9 {At1g25520 }{At1g68650 } 1
+ 1368 22 {At1g25560 }{At1g68840 } -1
+ 1371 19 {At1g26130 }{At1g68710 } -1
+ 1375 4 {At1g26150 }{At1g68690 } -1
+
+
+-block 18
+ points contig1 contig2
+ 6 1 1
+
+ point dist markers orientation
+ 885 0 {At1g16980 At1g17000 }{At1g78580 } -1
+ 887 4 {At1g17010 At1g17020 }{At1g78550 } -1
+ 888 3 {At1g17040 }{At1g78540 } -1
+ 889 4 {At1g17050 }{At1g78510 } -1
+ 891 21 {At1g17150 }{At1g78400 } -1
+ 892 5 {At1g17170 At1g17180 At1g17190 }{At1g78320 At1g78340 At1g78370 At1g78380 } -1
+
+
+-block 19
+ points contig1 contig2
+ 6 1 1
+
+ point dist markers orientation
+ 1600 0 {At1g34620 At1g34700 At1g34710 }{At1g44840 } -1
+ 1612 22 {At1g34720 At1g34730 At1g34740 }{At1g45090 } 1
+ 1617 25 {At1g35060 }{At1g44840 } 1
+ 1620 2 {At1g35070 At1g35090 At1g35100 }{At1g44850 At1g44860 } 1
+ 1621 2 {At1g35080 At1g35110 }{At1g44870 At1g44880 } 1
+ 1624 15 {At1g35170 At1g35180 }{At1g45010 } 1
+
+
+-block 20
+ points contig1 contig2
+ 5 1 1
+
+ point dist markers orientation
+ 462 0 {At1g09940 }{At1g58290 } 1
+ 463 5 {At1g09950 }{At1g58330 } -1
+ 467 5 {At1g09980 }{At1g58350 } 1
+ 469 4 {At1g10010 }{At1g58360 } 1
+ 471 5 {At1g10050 }{At1g58370 } 1
+
+
+-block 21
+ points contig1 contig2
+ 5 1 1
+
+ point dist markers orientation
+ 1968 0 {At1g60140 }{At1g70290 } 1
+ 1969 2 {At1g60160 }{At1g70300 } 1
+ 1970 11 {At1g60170 }{At1g70400 } -1
+ 1972 17 {At1g60390 }{At1g70370 } 1
+ 1973 25 {At1g60590 }{At1g70500 } 1
+
+
+-block 22
+ points contig1 contig2
+ 4 1 1
+
+ point dist markers orientation
+ 1316 0 {At1g24120 }{At1g59980 } -1
+ 1318 3 {At1g24140 }{At1g59970 } -1
+ 1322 9 {At1g24180 }{At1g59900 } -1
+ 1323 2 {At1g24190 }{At1g59890 } -1
+
+
+-block 23
+ points contig1 contig2
+ 4 1 1
+
+ point dist markers orientation
+ 1319 0 {At1g24140 }{At1g70170 } -1
+ 1320 4 {At1g24150 }{At1g70140 } -1
+ 1321 6 {At1g24170 }{At1g70090 } -1
+ 1324 5 {At1g24190 }{At1g70060 } -1
+
+
+-block 24
+ points contig1 contig2
+ 4 1 1
+
+ point dist markers orientation
+ 1327 0 {At1g24320 }{At1g67490 } 1
+ 1329 5 {At1g24330 }{At1g67530 } 1
+ 1330 9 {At1g24350 }{At1g67600 } 1
+ 1334 8 {At1g24400 }{At1g67640 } 1
+
+
+-block 25
+ points contig1 contig2
+ 4 1 1
+
+ point dist markers orientation
+ 1593 0 {At1g34530 }{At1g42200 At1g42410 At1g42500 } -1
+ 1599 17 {At1g34620 At1g34700 At1g34710 }{At1g42450 } -1
+ 1619 20 {At1g35070 At1g35090 At1g35100 }{At1g42400 } 1
+ 1622 17 {At1g35080 At1g35110 }{At1g42650 } 1
+
+
+-block 26
+ points contig1 contig2
+ 4 1 1
+
+ point dist markers orientation
+ 1626 0 {At1g35240 }{At1g43950 } 1
+ 1631 12 {At1g35300 }{At1g44060 } -1
+ 1637 25 {At1g35520 At1g35540 }{At1g43950 } 1
+ 1644 13 {At1g35590 At1g35600 }{At1g44060 } -1
+
+
+-block 27
+ points contig1 contig2
+ 4 1 1
+
+ point dist markers orientation
+ 1718 0 {At1g44100 }{At1g77380 } 1
+ 1720 2 {At1g44110 }{At1g77390 } 1
+ 1722 8 {At1g44120 }{At1g77460 } 1
+ 1723 3 {At1g44130 }{At1g77480 } 1
+
+
+-block 28
+ points contig1 contig2
+ 4 1 1
+
+ point dist markers orientation
+ 2006 0 {At1g62540 At1g62560 At1g62570 At1g62580 At1g62600 At1g62620 }{At1g63340 At1g63370 At1g63390 } -1
+ 2009 22 {At1g62590 At1g62670 At1g62680 At1g62720 }{At1g63070 At1g63080 At1g63130 At1g63150 At1g63230 At1g63320 At1g63330 At1g63400 } 1
+ 2015 24 {At1g62610 }{At1g63380 } -1
+ 2016 2 {At1g62630 }{At1g63350 At1g63360 } -1
+
+
+-block 29
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 32 0 {At1g01600 }{At1g63710 } -1
+ 34 7 {At1g01650 }{At1g63690 } -1
+ 37 23 {At1g01740 }{At1g63500 } -1
+
+
+-block 30
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 241 0 {At1g06390 }{At1g09840 } -1
+ 244 21 {At1g06400 }{At1g09630 } 1
+ 258 22 {At1g06580 }{At1g09680 } 1
+
+
+-block 31
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 405 0 {At1g09410 }{At1g74600 At1g74630 } -1
+ 423 25 {At1g09540 }{At1g74430 } 1
+ 435 16 {At1g09600 }{At1g74330 } -1
+
+
+-block 32
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 523 0 {At1g10620 }{At1g70450 At1g70460 } -1
+ 525 4 {At1g10630 }{At1g70490 } 1
+ 536 17 {At1g10750 }{At1g70550 } -1
+
+
+-block 33
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 561 0 {At1g11100 }{At1g50410 } -1
+ 569 22 {At1g11260 }{At1g50310 } 1
+ 583 7 {At1g11290 }{At1g50270 } -1
+
+
+-block 34
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 633 0 {At1g12130 At1g12140 At1g12160 At1g12200 }{At1g63340 At1g63370 At1g63390 } -1
+ 639 6 {At1g12210 At1g12220 At1g12280 At1g12290 }{At1g63350 At1g63360 } -1
+ 654 24 {At1g12300 }{At1g63630 } -1
+
+
+-block 35
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 736 0 {At1g13950 }{At1g69410 } 1
+ 739 11 {At1g14010 }{At1g69460 } 1
+ 743 5 {At1g14040 }{At1g69480 } -1
+
+
+-block 36
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 865 0 {At1g16490 }{At1g56160 } -1
+ 869 15 {At1g16670 }{At1g56120 At1g56130 At1g56140 } -1
+ 873 18 {At1g16710 }{At1g55970 } -1
+
+
+-block 37
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 896 0 {At1g17230 }{At1g72180 } 1
+ 899 13 {At1g17240 At1g17250 }{At1g72300 } 1
+ 904 7 {At1g17290 }{At1g72330 } 1
+
+
+-block 38
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 1207 0 {At1g22200 }{At1g36050 } -1
+ 1208 10 {At1g22210 }{At1g35910 } -1
+ 1210 16 {At1g22240 }{At1g35730 At1g35750 } -1
+
+
+-block 39
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 1294 0 {At1g23760 }{At1g60390 } -1
+ 1301 25 {At1g23870 }{At1g60140 } -1
+ 1305 8 {At1g23900 At1g23940 }{At1g60070 } -1
+
+
+-block 40
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 1414 0 {At1g27040 }{At1g59740 } -1
+ 1417 9 {At1g27100 }{At1g59710 } -1
+ 1422 21 {At1g27210 }{At1g59850 } 1
+
+
+-block 41
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 1597 0 {At1g34620 At1g34700 At1g34710 }{At1g35060 } -1
+ 1601 20 {At1g34660 }{At1g35280 } 1
+ 1614 15 {At1g34760 }{At1g35160 } -1
+
+
+-block 42
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 1611 0 {At1g34620 At1g34700 At1g34710 }{At1g52010 } -1
+ 1613 7 {At1g34720 At1g34730 At1g34740 }{At1g52020 } 1
+ 1618 11 {At1g35060 }{At1g52090 } -1
+
+
+-block 43
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 1630 0 {At1g35300 }{At1g36460 } -1
+ 1635 10 {At1g35370 At1g35380 }{At1g36550 At1g36590 } 1
+ 1643 22 {At1g35590 At1g35600 }{At1g36460 } -1
+
+
+-block 44
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 1655 0 {At1g35730 At1g35750 }{At1g78160 } -1
+ 1658 20 {At1g35910 }{At1g78090 } -1
+ 1662 13 {At1g36070 }{At1g78070 } -1
+
+
+-block 45
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 1690 0 {At1g41900 }{At1g43870 At1g43880 } -1
+ 1695 12 {At1g42200 At1g42410 At1g42500 }{At1g43840 } -1
+ 1692 9 {At1g42360 At1g42370 }{At1g43740 At1g43750 } 1
+
+
+-block 46
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 1829 0 {At1g51680 }{At1g62940 } -1
+ 1831 10 {At1g51750 }{At1g62890 } 1
+ 1835 13 {At1g51990 }{At1g62900 } 1
+
+
+-block 47
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 1925 0 {At1g56600 }{At1g60450 At1g60470 } -1
+ 1928 17 {At1g56710 }{At1g60590 } 1
+ 1929 18 {At1g56720 }{At1g60800 } 1
+
+
+-block 48
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 1953 0 {At1g59710 }{At1g69890 } -1
+ 1958 17 {At1g59830 }{At1g69960 } 1
+ 1960 23 {At1g59910 }{At1g70140 } 1
+
+
+-block 49
+ points contig1 contig2
+ 3 1 1
+
+ point dist markers orientation
+ 2112 0 {At1g70430 }{At1g79640 } -1
+ 2113 4 {At1g70450 At1g70460 }{At1g79620 } -1
+ 2116 11 {At1g70520 At1g70530 }{At1g79670 At1g79680 } 1
+
+
+-block 50
+ points contig1 contig2
+ 29 1 2
+
+ point dist markers orientation
+ 2564 0 {At1g14220 }{At2g02990 } -1
+ 2565 3 {At1g14230 At1g14240 At1g14260 }{At2g02970 } -1
+ 2566 15 {At1g14330 }{At2g02870 } -1
+ 2567 7 {At1g14350 }{At2g02820 } -1
+ 2568 2 {At1g14360 }{At2g02810 } -1
+ 2569 2 {At1g14370 }{At2g02800 } -1
+ 2574 2 {At1g14380 }{At2g02790 } -1
+ 2575 2 {At1g14390 }{At2g02780 } -1
+ 2576 3 {At1g14400 }{At2g02760 } -1
+ 2577 6 {At1g14420 }{At2g02720 } -1
+ 2578 21 {At1g14460 }{At2g02480 } -1
+ 2579 6 {At1g14510 }{At2g02470 } -1
+ 2581 23 {At1g14530 }{At2g02180 } -1
+ 2584 13 {At1g14580 }{At2g02070 At2g02080 } 1
+ 2585 2 {At1g14590 }{At2g02060 } -1
+ 2586 12 {At1g14660 }{At2g01980 } -1
+ 2587 2 {At1g14670 }{At2g01970 } -1
+ 2588 5 {At1g14680 }{At2g01930 } -1
+ 2589 3 {At1g14690 }{At2g01910 } -1
+ 2590 3 {At1g14700 }{At2g01880 At2g01890 } -1
+ 2591 5 {At1g14720 }{At2g01850 } -1
+ 2594 22 {At1g14840 }{At2g01750 } -1
+ 2595 10 {At1g14860 }{At2g01670 } -1
+ 2596 11 {At1g14910 }{At2g01600 } -1
+ 2597 4 {At1g14920 }{At2g01570 } -1
+ 2598 5 {At1g14930 At1g14940 At1g14950 At1g14960 }{At2g01520 At2g01530 } -1
+ 2599 5 {At1g14970 }{At2g01480 } -1
+ 2600 25 {At1g15020 }{At2g01270 } -1
+ 2601 15 {At1g15080 }{At2g01180 } -1
+
+
+-block 51
+ points contig1 contig2
+ 23 1 2
+
+ point dist markers orientation
+ 2273 0 {At1g05470 }{At2g32010 } -1
+ 2275 14 {At1g05570 }{At2g31960 } -1
+ 2277 6 {At1g05580 }{At2g31910 } -1
+ 2278 13 {At1g05630 }{At2g31830 } -1
+ 2281 2 {At1g05640 }{At2g31820 } -1
+ 2289 6 {At1g05670 At1g05680 }{At2g31750 At2g31790 } -1
+ 2296 18 {At1g05800 }{At2g31690 } -1
+ 2297 2 {At1g05810 }{At2g31680 } -1
+ 2300 5 {At1g05830 }{At2g31630 At2g31640 At2g31650 } -1
+ 2301 17 {At1g05890 }{At2g31510 } -1
+ 2303 7 {At1g05900 }{At2g31450 } -1
+ 2304 17 {At1g06020 At1g06030 }{At2g31390 } -1
+ 2305 2 {At1g06040 }{At2g31380 } -1
+ 2306 4 {At1g06070 }{At2g31370 } -1
+ 2307 2 {At1g06080 At1g06090 At1g06100 At1g06120 }{At2g31360 } -1
+ 2308 3 {At1g06130 }{At2g31350 } -1
+ 2313 8 {At1g06140 At1g06150 }{At2g31280 } 1
+ 2314 8 {At1g06170 }{At2g31220 } -1
+ 2315 5 {At1g06180 }{At2g31180 } -1
+ 2317 6 {At1g06200 }{At2g31140 } -1
+ 2318 9 {At1g06250 }{At2g31100 } 1
+ 2320 20 {At1g06390 }{At2g30980 } -1
+ 2326 7 {At1g06430 }{At2g30950 } -1
+
+
+-block 52
+ points contig1 contig2
+ 19 1 2
+
+ point dist markers orientation
+ 2329 0 {At1g06550 }{At2g30650 At2g30660 } 1
+ 2331 21 {At1g06620 At1g06640 At1g06650 }{At2g30830 At2g30840 } -1
+ 2333 8 {At1g06680 }{At2g30790 } -1
+ 2334 6 {At1g06700 }{At2g30730 At2g30740 } -1
+ 2338 12 {At1g06740 }{At2g30640 } -1
+ 2339 2 {At1g06750 }{At2g30630 } -1
+ 2340 7 {At1g06770 }{At2g30580 } -1
+ 2341 6 {At1g06800 }{At2g30550 } -1
+ 2342 4 {At1g06830 }{At2g30540 } -1
+ 2345 12 {At1g06870 }{At2g30440 } 1
+ 2346 2 {At1g06890 }{At2g30460 } 1
+ 2348 25 {At1g06960 }{At2g30260 } -1
+ 2349 3 {At1g06970 }{At2g30240 } -1
+ 2352 12 {At1g07030 }{At2g30160 } -1
+ 2355 19 {At1g07140 }{At2g30060 } -1
+ 2356 3 {At1g07150 }{At2g30040 } -1
+ 2357 3 {At1g07160 }{At2g30020 } -1
+ 2359 3 {At1g07170 }{At2g30000 } -1
+ 2360 2 {At1g07180 }{At2g29990 } -1
+
+
+-block 53
+ points contig1 contig2
+ 15 1 2
+
+ point dist markers orientation
+ 2927 0 {At1g28050 }{At2g33500 } 1
+ 2928 9 {At1g28110 }{At2g33530 } 1
+ 2934 24 {At1g28180 }{At2g33730 } 1
+ 2935 6 {At1g28220 At1g28230 }{At2g33750 } 1
+ 2936 9 {At1g28290 }{At2g33790 } 1
+ 2937 11 {At1g28350 }{At2g33840 } 1
+ 2942 23 {At1g28550 }{At2g33870 } 1
+ 2945 16 {At1g29020 }{At2g34020 At2g34030 } 1
+ 2946 2 {At1g29030 }{At2g34040 } 1
+ 2947 5 {At1g29050 }{At2g34070 } 1
+ 2949 4 {At1g29080 At1g29090 }{At2g34080 } 1
+ 2953 23 {At1g29230 }{At2g34180 } -1
+ 2955 4 {At1g29250 }{At2g34160 } -1
+ 2957 13 {At1g29310 }{At2g34250 } 1
+ 2959 17 {At1g29470 }{At2g34300 } 1
+
+
+-block 54
+ points contig1 contig2
+ 13 1 2
+
+ point dist markers orientation
+ 2999 0 {At1g30400 At1g30410 At1g30420 }{At2g34660 } 1
+ 3002 11 {At1g30490 }{At2g34710 } 1
+ 3008 14 {At1g30590 }{At2g34750 } 1
+ 3011 11 {At1g30620 }{At2g34850 } -1
+ 3012 2 {At1g30630 }{At2g34840 } -1
+ 3015 3 {At1g30650 }{At2g34830 } -1
+ 3016 7 {At1g30700 At1g30740 At1g30760 At1g30770 }{At2g34790 At2g34810 } -1
+ 3018 14 {At1g30810 }{At2g34880 } 1
+ 3019 2 {At1g30820 }{At2g34890 } 1
+ 3022 12 {At1g30900 }{At2g34940 } 1
+ 3024 17 {At1g31020 }{At2g35010 } 1
+ 3034 6 {At1g31070 }{At2g35020 } 1
+ 3037 7 {At1g31120 }{At2g35060 } 1
+
+
+-block 55
+ points contig1 contig2
+ 12 1 2
+
+ point dist markers orientation
+ 2362 0 {At1g07240 At1g07250 At1g07260 }{At2g29710 At2g29730 At2g29740 At2g29750 } 1
+ 2363 4 {At1g07270 }{At2g29680 } -1
+ 2365 19 {At1g07360 }{At2g29580 } -1
+ 2366 2 {At1g07370 }{At2g29570 } -1
+ 2371 16 {At1g07420 }{At2g29390 } -1
+ 2372 2 {At1g07430 }{At2g29380 } -1
+ 2373 7 {At1g07440 At1g07450 }{At2g29150 At2g29170 At2g29260 At2g29290 At2g29300 At2g29310 At2g29320 At2g29330 At2g29340 At2g29350 At2g29360 At2g29370 } 1
+ 2375 4 {At1g07460 }{At2g29220 At2g29250 } -1
+ 2376 12 {At1g07510 }{At2g29080 } -1
+ 2377 3 {At1g07520 At1g07530 }{At2g29060 } -1
+ 2383 10 {At1g07570 }{At2g28930 At2g28940 } -1
+ 2385 9 {At1g07630 }{At2g28890 } -1
+
+
+-block 56
+ points contig1 contig2
+ 11 1 2
+
+ point dist markers orientation
+ 2236 0 {At1g04470 }{At2g33420 } -1
+ 2237 6 {At1g04480 }{At2g33370 } -1
+ 2238 6 {At1g04510 }{At2g33340 } -1
+ 2239 2 {At1g04520 }{At2g33330 } -1
+ 2240 3 {At1g04540 }{At2g33320 } -1
+ 2241 7 {At1g04570 }{At2g33280 } -1
+ 2245 7 {At1g04600 }{At2g33240 } -1
+ 2246 2 {At1g04610 }{At2g33230 } -1
+ 2247 3 {At1g04630 }{At2g33220 } -1
+ 2251 15 {At1g04710 }{At2g33150 } -1
+ 2253 4 {At1g04740 At1g04760 }{At2g33110 At2g33120 } 1
+
+
+-block 57
+ points contig1 contig2
+ 10 1 2
+
+ point dist markers orientation
+ 2260 0 {At1g05070 }{At2g32580 } -1
+ 2261 16 {At1g05140 }{At2g32480 } -1
+ 2262 4 {At1g05150 }{At2g32450 } -1
+ 2263 2 {At1g05160 }{At2g32440 } -1
+ 2264 2 {At1g05170 }{At2g32430 } -1
+ 2265 3 {At1g05180 }{At2g32410 } -1
+ 2267 3 {At1g05200 }{At2g32390 At2g32400 } -1
+ 2268 2 {At1g05210 }{At2g32380 } -1
+ 2269 3 {At1g05230 }{At2g32370 } -1
+ 2271 15 {At1g05300 }{At2g32270 } -1
+
+
+-block 58
+ points contig1 contig2
+ 9 1 2
+
+ point dist markers orientation
+ 2391 0 {At1g07720 }{At2g28630 } 1
+ 2392 5 {At1g07730 }{At2g28670 } 1
+ 2393 3 {At1g07750 }{At2g28680 } 1
+ 2395 7 {At1g07790 }{At2g28720 } 1
+ 2398 20 {At1g07870 }{At2g28590 } -1
+ 2402 12 {At1g07900 }{At2g28500 } -1
+ 2403 21 {At1g07990 }{At2g28360 } -1
+ 2412 22 {At1g08080 }{At2g28210 } -1
+ 2413 9 {At1g08140 At1g08150 }{At2g28170 } 1
+
+
+-block 59
+ points contig1 contig2
+ 9 1 2
+
+ point dist markers orientation
+ 2553 0 {At1g13730 }{At2g03640 } -1
+ 2555 23 {At1g13860 }{At2g03480 } -1
+ 2556 3 {At1g13880 }{At2g03470 } -1
+ 2557 4 {At1g13900 }{At2g03450 } -1
+ 2558 16 {At1g13960 }{At2g03340 } -1
+ 2559 10 {At1g14010 }{At2g03290 } -1
+ 2560 2 {At1g14020 }{At2g03280 } -1
+ 2561 4 {At1g14040 }{At2g03240 At2g03250 At2g03260 } -1
+ 2562 5 {At1g14070 At1g14080 At1g14100 At1g14110 }{At2g03210 At2g03220 } -1
+
+
+-block 60
+ points contig1 contig2
+ 8 1 2
+
+ point dist markers orientation
+ 3263 0 {At1g36560 }{At2g06160 At2g06310 At2g06320 At2g06330 } 1
+ 3272 11 {At1g36810 }{At2g06180 } -1
+ 3284 20 {At1g37060 At1g37070 At1g37160 }{At2g06160 At2g06310 At2g06320 At2g06330 } -1
+ 3302 10 {At1g37190 }{At2g06180 } -1
+ 3309 3 {At1g38440 At1g41690 }{At2g06160 At2g06310 At2g06320 At2g06330 } -1
+ 3314 18 {At1g41860 }{At2g06260 } 1
+ 3315 9 {At1g41900 }{At2g06180 } 1
+ 3319 14 {At1g42360 At1g42370 }{At2g06160 At2g06310 At2g06320 At2g06330 } 1
+
+
+-block 61
+ points contig1 contig2
+ 8 1 2
+
+ point dist markers orientation
+ 3274 0 {At1g36810 }{At2g13070 } 1
+ 3288 22 {At1g37060 At1g37070 At1g37160 }{At2g13250 At2g13260 } -1
+ 3305 15 {At1g37180 At1g37200 }{At2g12920 At2g13210 } 1
+ 3303 10 {At1g37190 }{At2g12520 } -1
+ 3311 18 {At1g38440 At1g41690 }{At2g13250 At2g13260 } -1
+ 3312 17 {At1g41780 }{At2g12870 } -1
+ 3317 24 {At1g41910 }{At2g12210 At2g12220 At2g12390 } 1
+ 3333 21 {At1g42450 }{At2g12150 } -1
+
+
+-block 62
+ points contig1 contig2
+ 7 1 2
+
+ point dist markers orientation
+ 2143 0 {At1g01030 }{At2g46870 } -1
+ 2145 3 {At1g01050 }{At2g46860 } -1
+ 2151 19 {At1g01120 }{At2g46720 } -1
+ 2156 13 {At1g01190 }{At2g46660 } 1
+ 2157 22 {At1g01260 }{At2g46510 } -1
+ 2161 12 {At1g01340 }{At2g46430 At2g46440 At2g46450 } -1
+ 2162 14 {At1g01440 }{At2g46380 } -1
+
+
+-block 63
+ points contig1 contig2
+ 7 1 2
+
+ point dist markers orientation
+ 2969 0 {At1g29710 }{At2g34370 } 1
+ 2976 16 {At1g29890 }{At2g34410 } 1
+ 2978 3 {At1g29910 At1g29920 At1g29930 }{At2g34420 At2g34430 } 1
+ 2979 9 {At1g29970 }{At2g34480 } 1
+ 2980 3 {At1g29980 }{At2g34510 } 1
+ 2982 9 {At1g30040 }{At2g34550 } 1
+ 2988 12 {At1g30120 }{At2g34590 } 1
+
+
+-block 64
+ points contig1 contig2
+ 7 1 2
+
+ point dist markers orientation
+ 3163 0 {At1g34660 }{At2g10140 } 1
+ 3179 15 {At1g35070 At1g35090 At1g35100 }{At2g10370 At2g10390 } -1
+ 3180 2 {At1g35080 At1g35110 }{At2g10350 At2g10360 } -1
+ 3186 23 {At1g35280 }{At2g10000 At2g10010 } -1
+ 3191 17 {At1g35300 }{At2g10490 At2g10640 } 1
+ 3196 11 {At1g35370 At1g35380 }{At2g10620 At2g10660 At2g10670 At2g10690 At2g10700 At2g10780 } 1
+ 3208 23 {At1g35590 At1g35600 }{At2g10490 At2g10640 } 1
+
+
+-block 65
+ points contig1 contig2
+ 6 1 2
+
+ point dist markers orientation
+ 2163 0 {At1g01470 }{At2g46140 } -1
+ 2169 13 {At1g01550 }{At2g46080 } -1
+ 2172 2 {At1g01560 }{At2g46070 } -1
+ 2174 13 {At1g01600 }{At2g45970 } -1
+ 2179 3 {At1g01620 }{At2g45960 } -1
+ 2180 15 {At1g01700 }{At2g45890 } -1
+
+
+-block 66
+ points contig1 contig2
+ 5 1 2
+
+ point dist markers orientation
+ 2252 0 {At1g04740 At1g04760 }{At2g32670 } -1
+ 2254 11 {At1g04810 }{At2g32730 } 1
+ 2257 9 {At1g04860 }{At2g32780 } 1
+ 2258 25 {At1g04980 }{At2g32920 } 1
+ 2259 6 {At1g05000 }{At2g32960 } 1
+
+
+-block 67
+ points contig1 contig2
+ 5 1 2
+
+ point dist markers orientation
+ 3071 0 {At1g32380 }{At2g35390 } -1
+ 3078 11 {At1g32470 }{At2g35370 } -1
+ 3079 5 {At1g32490 }{At2g35340 } -1
+ 3081 5 {At1g32530 }{At2g35330 } -1
+ 3083 14 {At1g32580 }{At2g35240 } -1
+
+
+-block 68
+ points contig1 contig2
+ 5 1 2
+
+ point dist markers orientation
+ 3156 0 {At1g34620 At1g34700 At1g34710 }{At2g06410 At2g06450 } 1
+ 3167 18 {At1g34720 At1g34730 At1g34740 }{At2g06620 At2g06700 } 1
+ 3174 18 {At1g35060 }{At2g06870 } -1
+ 3183 19 {At1g35150 }{At2g06500 } 1
+ 3190 22 {At1g35300 }{At2g06720 At2g06800 } -1
+
+
+-block 69
+ points contig1 contig2
+ 5 1 2
+
+ point dist markers orientation
+ 3861 0 {At1g66150 }{At2g01820 } -1
+ 3862 3 {At1g66170 }{At2g01810 } -1
+ 3864 25 {At1g66250 }{At2g01630 } -1
+ 3868 12 {At1g66350 }{At2g01570 } -1
+ 3869 4 {At1g66360 }{At2g01540 } -1
+
+
+-block 70
+ points contig1 contig2
+ 4 1 2
+
+ point dist markers orientation
+ 2416 0 {At1g08260 }{At2g27120 } 1
+ 2420 23 {At1g08410 }{At2g27200 } 1
+ 2421 2 {At1g08420 }{At2g27210 } 1
+ 2422 4 {At1g08430 At1g08440 }{At2g27240 } 1
+
+
+-block 71
+ points contig1 contig2
+ 4 1 2
+
+ point dist markers orientation
+ 2835 0 {At1g24640 }{At2g01840 } -1
+ 2846 3 {At1g24650 }{At2g01820 } -1
+ 2847 10 {At1g25230 }{At2g01880 At2g01890 } 1
+ 2848 7 {At1g25250 }{At2g01940 } 1
+
+
+-block 72
+ points contig1 contig2
+ 4 1 2
+
+ point dist markers orientation
+ 2886 0 {At1g26690 }{At2g03290 } -1
+ 2887 6 {At1g26730 }{At2g03240 At2g03250 At2g03260 } -1
+ 2888 17 {At1g26770 }{At2g03090 } -1
+ 2893 15 {At1g26820 }{At2g02990 } -1
+
+
+-block 73
+ points contig1 contig2
+ 4 1 2
+
+ point dist markers orientation
+ 2997 0 {At1g30390 }{At2g19100 } -1
+ 3004 24 {At1g30570 }{At2g19190 At2g19210 At2g19230 } -1
+ 3010 5 {At1g30600 }{At2g19170 } 1
+ 3013 25 {At1g30640 }{At2g19400 } -1
+
+
+-block 74
+ points contig1 contig2
+ 4 1 2
+
+ point dist markers orientation
+ 3228 0 {At1g35790 }{At2g06110 } 1
+ 3233 25 {At1g35970 }{At2g06260 } 1
+ 3247 16 {At1g36120 }{At2g06470 } 1
+ 3250 18 {At1g36130 }{At2g06110 } 1
+
+
+-block 75
+ points contig1 contig2
+ 4 1 2
+
+ point dist markers orientation
+ 3245 0 {At1g36110 }{At2g10580 At2g10650 } -1
+ 3258 22 {At1g36460 }{At2g10490 At2g10640 } -1
+ 3260 10 {At1g36470 }{At2g10140 } -1
+ 3266 25 {At1g36550 At1g36590 }{At2g07660 } -1
+
+
+-block 76
+ points contig1 contig2
+ 4 1 2
+
+ point dist markers orientation
+ 3358 0 {At1g43780 }{At2g12480 } -1
+ 3361 16 {At1g43840 }{At2g13000 At2g13160 At2g13310 } -1
+ 3366 14 {At1g43870 At1g43880 }{At2g12520 } -1
+ 3376 22 {At1g44060 }{At2g12240 At2g12250 At2g12300 } 1
+
+
+-block 77
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 2424 0 {At1g08570 }{At2g33270 } 1
+ 2427 12 {At1g08590 }{At2g33170 } -1
+ 2433 21 {At1g08730 }{At2g33240 } -1
+
+
+-block 78
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 2668 0 {At1g17750 }{At2g25790 } 1
+ 2672 8 {At1g17810 }{At2g25810 } 1
+ 2675 21 {At1g17980 }{At2g25850 } 1
+
+
+-block 79
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 3091 0 {At1g32820 }{At2g02190 } 1
+ 3096 2 {At1g32830 }{At2g02200 } 1
+ 3101 2 {At1g32840 }{At2g02210 } 1
+
+
+-block 80
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 3092 0 {At1g32820 }{At2g04950 At2g05010 } 1
+ 3097 2 {At1g32830 }{At2g04960 At2g04970 } 1
+ 3102 2 {At1g32840 }{At2g04980 } 1
+
+
+-block 81
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 3095 0 {At1g32820 }{At2g15150 At2g15210 } -1
+ 3100 4 {At1g32830 }{At2g15200 } -1
+ 3105 5 {At1g32840 }{At2g15140 At2g15190 } -1
+
+
+-block 82
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 3155 0 {At1g34620 At1g34700 At1g34710 }{At2g05490 At2g05570 } 1
+ 3169 8 {At1g34720 At1g34730 At1g34740 }{At2g05450 At2g05460 At2g05470 At2g05560 } -1
+ 3173 11 {At1g35060 }{At2g05490 At2g05570 } -1
+
+
+-block 83
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 3207 0 {At1g35590 At1g35600 }{At2g06720 At2g06800 } -1
+ 3223 18 {At1g35760 }{At2g06870 } -1
+ 3226 2 {At1g35770 }{At2g06860 } -1
+
+
+-block 84
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 3231 0 {At1g35920 At1g35940 }{At2g05080 } -1
+ 3236 17 {At1g36080 }{At2g04990 } 1
+ 3239 4 {At1g36090 }{At2g04950 At2g05010 } -1
+
+
+-block 85
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 3232 0 {At1g35920 At1g35940 }{At2g14300 } -1
+ 3242 18 {At1g36100 }{At2g14410 } -1
+ 3249 21 {At1g36120 }{At2g14640 At2g14650 } -1
+
+
+-block 86
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 3257 0 {At1g36460 }{At2g06720 At2g06800 } 1
+ 3262 11 {At1g36550 At1g36590 }{At2g06890 } 1
+ 3268 8 {At1g36620 }{At2g06840 At2g06950 At2g07010 } -1
+
+
+-block 87
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 3275 0 {At1g36830 }{At2g14380 At2g14400 } 1
+ 3281 19 {At1g37050 }{At2g14430 } 1
+ 3307 12 {At1g37180 At1g37200 }{At2g14380 At2g14400 } 1
+
+
+-block 88
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 3324 0 {At1g42200 At1g42410 At1g42500 }{At2g11110 } 1
+ 3320 19 {At1g42360 At1g42370 }{At2g10620 At2g10660 At2g10670 At2g10690 At2g10700 At2g10780 } -1
+ 3323 13 {At1g42400 }{At2g10370 At2g10390 } -1
+
+
+-block 89
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 3326 0 {At1g42200 At1g42410 At1g42500 }{At2g13870 } -1
+ 3322 8 {At1g42380 }{At2g13930 At2g13940 } 1
+ 3334 12 {At1g42450 }{At2g14030 } -1
+
+
+-block 90
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 3321 0 {At1g42360 At1g42370 }{At2g07400 } 1
+ 3331 19 {At1g42450 }{At2g07230 At2g07250 At2g07320 At2g07330 } 1
+ 3336 2 {At1g42460 }{At2g07240 } 1
+
+
+-block 91
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 3362 0 {At1g43840 }{At2g13870 } 1
+ 3369 14 {At1g43930 }{At2g13970 } -1
+ 3372 11 {At1g44050 }{At2g13900 At2g13910 At2g13920 At2g13950 } 1
+
+
+-block 92
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 3385 0 {At1g44850 At1g44860 }{At2g10370 At2g10390 } -1
+ 3388 2 {At1g44870 At1g44880 }{At2g10350 At2g10360 } -1
+ 3389 24 {At1g44900 }{At2g07690 } -1
+
+
+-block 93
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 3382 0 {At1g44840 }{At2g05490 At2g05570 } -1
+ 3396 16 {At1g45080 }{At2g05480 } -1
+ 3401 2 {At1g45090 }{At2g05450 At2g05460 At2g05470 At2g05560 } -1
+
+
+-block 94
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 3383 0 {At1g44840 }{At2g12150 } -1
+ 3398 16 {At1g45080 }{At2g12140 } -1
+ 3403 2 {At1g45090 }{At2g12100 At2g12110 At2g12120 At2g12130 } -1
+
+
+-block 95
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 3390 0 {At1g44900 }{At2g16440 } -1
+ 3400 21 {At1g45080 }{At2g16330 } 1
+ 3405 12 {At1g45090 }{At2g16170 At2g16180 } 1
+
+
+-block 96
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 3551 0 {At1g51750 }{At2g05550 } -1
+ 3561 20 {At1g52010 }{At2g05490 At2g05570 } -1
+ 3562 3 {At1g52020 }{At2g05450 At2g05460 At2g05470 At2g05560 } -1
+
+
+-block 97
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 3760 0 {At1g61830 At1g61840 }{At2g28460 } 1
+ 3761 15 {At1g61860 }{At2g28590 } -1
+ 3764 24 {At1g62030 }{At2g28460 } -1
+
+
+-block 98
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 3895 0 {At1g68060 }{At2g01750 } -1
+ 3896 23 {At1g68120 }{At2g01930 } 1
+ 3897 2 {At1g68130 }{At2g01940 } 1
+
+
+-block 99
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 3929 0 {At1g69460 }{At2g03290 } -1
+ 3930 5 {At1g69480 }{At2g03240 At2g03250 At2g03260 } 1
+ 3931 18 {At1g69530 }{At2g03090 } -1
+
+
+-block 100
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 4033 0 {At1g74490 }{At2g02800 } 1
+ 4037 9 {At1g74510 }{At2g02870 } 1
+ 4042 15 {At1g74600 At1g74630 }{At2g02980 } -1
+
+
+-block 101
+ points contig1 contig2
+ 3 1 2
+
+ point dist markers orientation
+ 4067 0 {At1g75840 }{At2g17800 } 1
+ 4069 2 {At1g75850 }{At2g17790 } -1
+ 4076 21 {At1g75960 }{At2g17650 } 1
+
+
+-block 102
+ points contig1 contig2
+ 44 1 3
+
+ point dist markers orientation
+ 5334 0 {At1g49160 }{AT3g18750 } 1
+ 5340 9 {At1g49240 }{AT3g18780 } 1
+ 5344 6 {At1g49270 }{AT3g18810 } 1
+ 5348 3 {At1g49300 }{AT3g18820 } 1
+ 5349 16 {At1g49400 }{AT3g18880 } 1
+ 5350 11 {At1g49450 }{AT3g18950 } 1
+ 5352 6 {At1g49480 }{AT3g18990 } 1
+ 5353 3 {At1g49490 }{AT3g19020 } 1
+ 5357 9 {At1g49520 }{AT3g19080 } 1
+ 5365 9 {At1g49580 }{AT3g19100 } 1
+ 5369 5 {At1g49600 }{AT3g19130 } 1
+ 5370 7 {At1g49630 }{AT3g19170 } 1
+ 5372 16 {At1g49710 }{AT3g19280 } 1
+ 5373 4 {At1g49730 }{AT3g19300 } 1
+ 5374 2 {At1g49740 }{AT3g19310 } 1
+ 5376 2 {At1g49750 }{AT3g19320 } 1
+ 5378 8 {At1g49780 }{AT3g19380 } 1
+ 5379 13 {At1g49810 }{AT3g19490 } 1
+ 5380 10 {At1g49840 }{AT3g19540 } 1
+ 5381 9 {At1g49890 }{AT3g19570 } 1
+ 5382 4 {At1g49910 }{AT3g19590 } 1
+ 5383 22 {At1g50040 }{AT3g19680 } 1
+ 5384 7 {At1g50090 At1g50110 }{AT3g19710 } 1
+ 5385 5 {At1g50140 }{AT3g19740 } 1
+ 5386 2 {At1g50150 }{AT3g19750 } 1
+ 5389 18 {At1g50260 }{AT3g19830 } 1
+ 5390 4 {At1g50280 }{AT3g19850 } 1
+ 5392 11 {At1g50310 }{AT3g19930 AT3g19940 } 1
+ 5393 5 {At1g50360 }{AT3g19960 } 1
+ 5394 3 {At1g50370 }{AT3g19980 } 1
+ 5396 5 {At1g50400 }{AT3g20000 } 1
+ 5397 2 {At1g50410 }{AT3g20010 } 1
+ 5398 9 {At1g50460 }{AT3g20040 } 1
+ 5399 5 {At1g50490 }{AT3g20060 } 1
+ 5400 5 {At1g50520 At1g50550 At1g50560 }{AT3g20080 AT3g20090 AT3g20100 AT3g20110 AT3g20120 AT3g20130 AT3g20140 } 1
+ 5403 11 {At1g50610 }{AT3g20190 } 1
+ 5404 10 {At1g50620 }{AT3g20280 } 1
+ 5405 3 {At1g50630 }{AT3g20300 } 1
+ 5406 8 {At1g50660 }{AT3g20350 } 1
+ 5408 10 {At1g50700 }{AT3g20410 } 1
+ 5409 15 {At1g50740 }{AT3g20510 } 1
+ 5410 7 {At1g50840 }{AT3g20540 } 1
+ 5413 12 {At1g50950 }{AT3g20560 } 1
+ 5416 21 {At1g51060 }{AT3g20670 } 1
+
+
+-block 103
+ points contig1 contig2
+ 31 1 3
+
+ point dist markers orientation
+ 5512 0 {At1g53230 }{AT3g15030 } -1
+ 5513 2 {At1g53240 }{AT3g15020 } -1
+ 5515 4 {At1g53260 }{AT3g15000 } -1
+ 5516 3 {At1g53280 }{AT3g14990 } -1
+ 5517 4 {At1g53290 }{AT3g14960 } -1
+ 5518 2 {At1g53300 }{AT3g14950 } -1
+ 5520 2 {At1g53310 }{AT3g14940 } -1
+ 5522 14 {At1g53380 }{AT3g14870 } -1
+ 5524 6 {At1g53420 At1g53430 At1g53440 }{AT3g14840 } -1
+ 5526 2 {At1g53450 }{AT3g14830 } -1
+ 5527 4 {At1g53470 }{AT3g14810 } -1
+ 5528 5 {At1g53500 }{AT3g14790 } -1
+ 5529 8 {At1g53510 }{AT3g14720 } -1
+ 5532 14 {At1g53590 }{AT3g14590 } -1
+ 5534 15 {At1g53650 }{AT3g14450 } -1
+ 5536 5 {At1g53660 }{AT3g14410 } -1
+ 5537 8 {At1g53700 }{AT3g14370 } -1
+ 5538 5 {At1g53730 At1g53740 }{AT3g14350 } -1
+ 5544 12 {At1g53830 At1g53840 }{AT3g14300 AT3g14310 } -1
+ 5551 2 {At1g53850 }{AT3g14290 } -1
+ 5552 13 {At1g53940 At1g53990 }{AT3g14225 } -1
+ 5553 7 {At1g54000 At1g54010 At1g54020 }{AT3g14210 } -1
+ 5554 15 {At1g54080 }{AT3g14100 } -1
+ 5555 2 {At1g54090 }{AT3g14090 } -1
+ 5556 4 {At1g54110 }{AT3g14070 } -1
+ 5558 5 {At1g54130 }{AT3g14050 } -1
+ 5559 8 {At1g54170 }{AT3g14010 } -1
+ 5560 8 {At1g54210 }{AT3g13970 } -1
+ 5561 5 {At1g54220 }{AT3g13930 } -1
+ 5563 6 {At1g54270 }{AT3g13920 } -1
+ 5565 3 {At1g54280 }{AT3g13900 } -1
+
+
+-block 104
+ points contig1 contig2
+ 26 1 3
+
+ point dist markers orientation
+ 5449 0 {At1g51950 }{AT3g16500 } -1
+ 5450 5 {At1g51980 }{AT3g16480 } -1
+ 5457 5 {At1g52000 At1g52030 At1g52040 At1g52050 At1g52060 At1g52070 At1g52100 At1g52130 }{AT3g16390 AT3g16400 AT3g16410 AT3g16420 AT3g16430 AT3g16440 AT3g16450 } -1
+ 5458 22 {At1g52160 }{AT3g16260 } -1
+ 5459 10 {At1g52190 }{AT3g16180 } -1
+ 5460 7 {At1g52230 }{AT3g16140 } -1
+ 5461 2 {At1g52240 }{AT3g16130 } -1
+ 5463 4 {At1g52260 }{AT3g16110 } -1
+ 5464 3 {At1g52280 }{AT3g16100 } -1
+ 5469 4 {At1g52300 }{AT3g16080 } -1
+ 5471 15 {At1g52360 }{AT3g15980 } -1
+ 5474 7 {At1g52410 }{AT3g15950 AT3g15960 } -1
+ 5475 2 {At1g52420 }{AT3g15940 } -1
+ 5476 16 {At1g52540 }{AT3g15890 } -1
+ 5477 17 {At1g52570 }{AT3g15730 } -1
+ 5481 12 {At1g52660 }{AT3g15700 } -1
+ 5482 2 {At1g52670 }{AT3g15690 } -1
+ 5483 7 {At1g52700 }{AT3g15650 } -1
+ 5484 7 {At1g52730 }{AT3g15610 } -1
+ 5486 9 {At1g52770 }{AT3g15570 } -1
+ 5491 13 {At1g52880 }{AT3g15510 } -1
+ 5492 2 {At1g52890 }{AT3g15500 } -1
+ 5494 4 {At1g52910 }{AT3g15480 } -1
+ 5495 4 {At1g52930 }{AT3g15460 } -1
+ 5507 20 {At1g53020 }{AT3g15355 } -1
+ 5510 9 {At1g53100 }{AT3g15350 } -1
+
+
+-block 105
+ points contig1 contig2
+ 23 1 3
+
+ point dist markers orientation
+ 5270 0 {At1g47850 }{AT3g17200 } -1
+ 5281 21 {At1g48030 }{AT3g17240 } 1
+ 5282 2 {At1g48040 }{AT3g17250 } 1
+ 5289 13 {At1g48110 }{AT3g17330 } 1
+ 5290 18 {At1g48210 At1g48220 }{AT3g17410 } 1
+ 5294 3 {At1g48230 }{AT3g17430 } 1
+ 5295 2 {At1g48240 }{AT3g17440 } 1
+ 5296 10 {At1g48260 }{AT3g17510 } 1
+ 5299 23 {At1g48370 }{AT3g17650 } 1
+ 5301 16 {At1g48430 }{AT3g17770 } 1
+ 5302 2 {At1g48440 }{AT3g17780 } 1
+ 5303 3 {At1g48450 }{AT3g17800 } 1
+ 5304 4 {At1g48470 }{AT3g17820 } 1
+ 5306 3 {At1g48480 }{AT3g17840 } 1
+ 5307 2 {At1g48490 }{AT3g17850 } 1
+ 5308 12 {At1g48540 }{AT3g17920 } 1
+ 5309 11 {At1g48590 }{AT3g17980 } 1
+ 5310 2 {At1g48600 }{AT3g17990 AT3g18000 } 1
+ 5311 4 {At1g48610 }{AT3g18030 } 1
+ 5312 12 {At1g48630 }{AT3g18130 } 1
+ 5314 4 {At1g48640 }{AT3g18160 } 1
+ 5319 11 {At1g48740 }{AT3g18210 } 1
+ 5322 22 {At1g48840 }{AT3g18350 } 1
+
+
+-block 106
+ points contig1 contig2
+ 19 1 3
+
+ point dist markers orientation
+ 5600 0 {At1g55110 }{AT3g13810 } -1
+ 5602 3 {At1g55120 }{AT3g13784 AT3g13790 } -1
+ 5603 4 {At1g55130 }{AT3g13772 } -1
+ 5604 5 {At1g55140 }{AT3g13740 } -1
+ 5609 7 {At1g55190 }{AT3g13710 AT3g13720 } -1
+ 5610 3 {At1g55200 }{AT3g13690 } -1
+ 5611 7 {At1g55210 }{AT3g13650 AT3g13660 AT3g13662 } -1
+ 5612 13 {At1g55290 }{AT3g13610 } -1
+ 5613 6 {At1g55310 }{AT3g13570 } -1
+ 5614 11 {At1g55360 }{AT3g13510 } -1
+ 5618 11 {At1g55490 }{AT3g13470 } -1
+ 5623 2 {At1g55500 }{AT3g13460 } -1
+ 5624 2 {At1g55510 }{AT3g13450 } -1
+ 5625 2 {At1g55520 }{AT3g13445 } -1
+ 5626 9 {At1g55560 At1g55570 }{AT3g13390 AT3g13400 } 1
+ 5627 5 {At1g55610 }{AT3g13380 } -1
+ 5629 7 {At1g55650 }{AT3g13350 } -1
+ 5630 4 {At1g55680 }{AT3g13340 } -1
+ 5632 6 {At1g55720 At1g55730 }{AT3g13320 } -1
+
+
+-block 107
+ points contig1 contig2
+ 14 1 3
+
+ point dist markers orientation
+ 5417 0 {At1g51170 }{AT3g20830 } 1
+ 5418 2 {At1g51190 }{AT3g20840 } 1
+ 5420 7 {At1g51220 }{AT3g20880 } 1
+ 5426 22 {At1g51390 }{AT3g20970 } 1
+ 5429 17 {At1g51460 At1g51500 }{AT3g21090 } 1
+ 5431 5 {At1g51520 }{AT3g21100 } 1
+ 5433 8 {At1g51560 }{AT3g21140 } 1
+ 5437 5 {At1g51590 }{AT3g21160 } 1
+ 5438 7 {At1g51630 }{AT3g21190 } 1
+ 5439 6 {At1g51660 }{AT3g21220 } 1
+ 5440 3 {At1g51680 }{AT3g21230 AT3g21240 } 1
+ 5441 7 {At1g51710 }{AT3g21280 } 1
+ 5446 9 {At1g51770 }{AT3g21310 } 1
+ 5451 18 {At1g52000 At1g52030 At1g52040 At1g52050 At1g52060 At1g52070 At1g52100 At1g52130 }{AT3g21380 } -1
+
+
+-block 108
+ points contig1 contig2
+ 13 1 3
+
+ point dist markers orientation
+ 4569 0 {At1g12820 }{AT3g26810 } -1
+ 4571 6 {At1g12850 }{AT3g26780 } -1
+ 4572 5 {At1g12860 }{AT3g26744 } -1
+ 4573 13 {At1g12900 }{AT3g26650 } -1
+ 4574 2 {At1g12910 }{AT3g26640 } -1
+ 4575 4 {At1g12920 }{AT3g26618 } -1
+ 4578 6 {At1g12950 }{AT3g26590 } -1
+ 4582 19 {At1g13000 }{AT3g26440 } -1
+ 4584 13 {At1g13050 }{AT3g26350 } -1
+ 4585 2 {At1g13060 }{AT3g26340 } -1
+ 4586 4 {At1g13070 At1g13080 At1g13090 At1g13100 At1g13110 }{AT3g26150 AT3g26160 AT3g26170 AT3g26180 AT3g26190 AT3g26200 AT3g26210 AT3g26220 AT3g26230 AT3g26270 AT3g26280 AT3g26290 AT3g26300 AT3g26310 AT3g26320 AT3g26330 } -1
+ 4590 3 {At1g13130 }{AT3g26130 AT3g26140 } -1
+ 4591 2 {At1g13140 At1g13150 }{AT3g26125 } -1
+
+
+-block 109
+ points contig1 contig2
+ 8 1 3
+
+ point dist markers orientation
+ 5980 0 {At1g69330 }{AT3g29270 } -1
+ 5983 11 {At1g69370 }{AT3g29200 } -1
+ 5985 23 {At1g69460 }{AT3g29070 } -1
+ 5987 3 {At1g69480 }{AT3g29060 } 1
+ 5989 4 {At1g69490 }{AT3g29035 } 1
+ 5990 5 {At1g69530 }{AT3g29030 } -1
+ 5995 4 {At1g69560 }{AT3g29020 } -1
+ 5996 15 {At1g69620 }{AT3g28900 } -1
+
+
+-block 110
+ points contig1 contig2
+ 7 1 3
+
+ point dist markers orientation
+ 4593 0 {At1g13210 }{AT3g25610 } 1
+ 4595 8 {At1g13230 }{AT3g25670 } -1
+ 4599 10 {At1g13270 }{AT3g25740 } 1
+ 4600 3 {At1g13280 }{AT3g25760 AT3g25770 AT3g25780 } 1
+ 4601 3 {At1g13300 }{AT3g25790 } 1
+ 4602 3 {At1g13320 }{AT3g25800 } 1
+ 4603 5 {At1g13350 }{AT3g25840 } 1
+
+
+-block 111
+ points contig1 contig2
+ 7 1 3
+
+ point dist markers orientation
+ 5638 0 {At1g55890 }{AT3g13150 AT3g13160 } -1
+ 5639 7 {At1g55920 }{AT3g13110 } -1
+ 5640 3 {At1g55930 }{AT3g13070 } -1
+ 5641 12 {At1g55970 }{AT3g12980 } -1
+ 5643 25 {At1g56110 }{AT3g12860 } -1
+ 5649 16 {At1g56160 }{AT3g12720 AT3g12820 } -1
+ 5652 9 {At1g56190 }{AT3g12780 } -1
+
+
+-block 112
+ points contig1 contig2
+ 5 1 3
+
+ point dist markers orientation
+ 4207 0 {At1g02620 }{AT3g62560 } 1
+ 4209 4 {At1g02650 }{AT3g62570 } 1
+ 4211 3 {At1g02660 }{AT3g62590 } 1
+ 4216 13 {At1g02720 }{AT3g62660 } 1
+ 4225 20 {At1g02850 }{AT3g62740 AT3g62750 } 1
+
+
+-block 113
+ points contig1 contig2
+ 5 1 3
+
+ point dist markers orientation
+ 4922 0 {At1g26690 }{AT3g29070 } -1
+ 4924 4 {At1g26730 }{AT3g29060 } -1
+ 4925 8 {At1g26770 }{AT3g29030 } -1
+ 4927 2 {At1g26780 }{AT3g29020 } -1
+ 4930 20 {At1g26880 }{AT3g28900 } 1
+
+
+-block 114
+ points contig1 contig2
+ 4 1 3
+
+ point dist markers orientation
+ 4344 0 {At1g07410 }{AT3g46830 } -1
+ 4347 24 {At1g07520 At1g07530 }{AT3g46600 } -1
+ 4348 2 {At1g07540 }{AT3g46590 } -1
+ 4350 19 {At1g07550 At1g07560 }{AT3g46330 AT3g46340 AT3g46350 AT3g46370 AT3g46400 AT3g46410 AT3g46420 } 1
+
+
+-block 115
+ points contig1 contig2
+ 4 1 3
+
+ point dist markers orientation
+ 4354 0 {At1g07630 }{AT3g09400 } -1
+ 4357 21 {At1g07710 }{AT3g09550 } -1
+ 4360 13 {At1g07790 }{AT3g09480 } -1
+ 4372 24 {At1g07890 }{AT3g09640 } 1
+
+
+-block 116
+ points contig1 contig2
+ 4 1 3
+
+ point dist markers orientation
+ 5111 0 {At1g34620 At1g34700 At1g34710 }{AT3g42760 } 1
+ 5116 19 {At1g34720 At1g34730 At1g34740 }{AT3g42580 AT3g42590 AT3g42600 } -1
+ 5122 17 {At1g35070 At1g35090 At1g35100 }{AT3g42480 AT3g42490 } 1
+ 5124 3 {At1g35080 At1g35110 }{AT3g42510 AT3g42520 AT3g42530 } 1
+
+
+-block 117
+ points contig1 contig2
+ 4 1 3
+
+ point dist markers orientation
+ 5155 0 {At1g35820 }{AT3g30520 } -1
+ 5161 12 {At1g35920 At1g35940 }{AT3g30560 } 1
+ 5167 22 {At1g36040 }{AT3g30410 } -1
+ 5175 24 {At1g36100 }{AT3g30230 } -1
+
+
+-block 118
+ points contig1 contig2
+ 4 1 3
+
+ point dist markers orientation
+ 5163 0 {At1g35920 At1g35940 }{AT3g31980 } -1
+ 5171 19 {At1g36090 }{AT3g32060 } -1
+ 5179 11 {At1g36120 }{AT3g31970 } 1
+ 5180 25 {At1g36130 }{AT3g31390 } 1
+
+
+-block 119
+ points contig1 contig2
+ 4 1 3
+
+ point dist markers orientation
+ 5198 0 {At1g37170 }{AT3g31450 } 1
+ 5202 23 {At1g38440 At1g41690 }{AT3g32000 AT3g32010 } 1
+ 5204 19 {At1g41780 }{AT3g31520 } 1
+ 5210 17 {At1g42080 }{AT3g31470 } -1
+
+
+-block 120
+ points contig1 contig2
+ 4 1 3
+
+ point dist markers orientation
+ 5243 0 {At1g44850 At1g44860 }{AT3g42480 AT3g42490 } 1
+ 5246 3 {At1g44870 At1g44880 }{AT3g42510 AT3g42520 AT3g42530 } 1
+ 5254 20 {At1g45080 }{AT3g42620 } -1
+ 5256 3 {At1g45090 }{AT3g42580 AT3g42590 AT3g42600 } -1
+
+
+-block 121
+ points contig1 contig2
+ 4 1 3
+
+ point dist markers orientation
+ 5584 0 {At1g54610 }{AT3g05050 } 1
+ 5585 19 {At1g54730 }{AT3g05150 AT3g05160 } 1
+ 5588 7 {At1g54790 }{AT3g05180 } 1
+ 5593 15 {At1g54870 }{AT3g05260 } -1
+
+
+-block 122
+ points contig1 contig2
+ 4 1 3
+
+ point dist markers orientation
+ 6205 0 {At1g79180 }{AT3g12720 AT3g12820 } -1
+ 6207 9 {At1g79250 }{AT3g12690 } 1
+ 6220 20 {At1g79450 }{AT3g12740 } 1
+ 6223 14 {At1g79550 }{AT3g12780 } 1
+
+
+-block 123
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 4171 0 {At1g01440 }{AT3g61670 } -1
+ 4173 20 {At1g01480 }{AT3g61510 } -1
+ 4185 21 {At1g01620 }{AT3g61430 } -1
+
+
+-block 124
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 4190 0 {At1g01780 }{AT3g61230 } -1
+ 4191 3 {At1g01800 }{AT3g61220 } 1
+ 4192 17 {At1g01820 }{AT3g61070 } 1
+
+
+-block 125
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 4243 0 {At1g03920 }{AT3g23310 } 1
+ 4244 4 {At1g03930 }{AT3g23340 } 1
+ 4245 13 {At1g03990 }{AT3g23410 } 1
+
+
+-block 126
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 4259 0 {At1g04310 }{AT3g23150 } -1
+ 4261 23 {At1g04430 }{AT3g23280 AT3g23300 } 1
+ 4262 6 {At1g04440 }{AT3g23340 } 1
+
+
+-block 127
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 4429 0 {At1g09540 }{AT3g08500 } -1
+ 4441 23 {At1g09660 }{AT3g08620 } -1
+ 4444 14 {At1g09780 }{AT3g08590 } 1
+
+
+-block 128
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 4618 0 {At1g13970 }{AT3g29180 } -1
+ 4619 16 {At1g14010 }{AT3g29070 } -1
+ 4622 4 {At1g14040 }{AT3g29060 } -1
+
+
+-block 129
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 4675 0 {At1g16360 }{AT3g12740 } -1
+ 4676 11 {At1g16440 }{AT3g12690 } -1
+ 4680 7 {At1g16490 }{AT3g12720 AT3g12820 } 1
+
+
+-block 130
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 4878 0 {At1g24070 }{AT3g28180 } -1
+ 4880 5 {At1g24110 }{AT3g28200 } 1
+ 4882 18 {At1g24170 }{AT3g28340 } 1
+
+
+-block 131
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 5057 0 {At1g33060 }{AT3g10480 AT3g10490 AT3g10500 } -1
+ 5064 20 {At1g33290 }{AT3g10420 } 1
+ 5067 23 {At1g33540 }{AT3g10450 } -1
+
+
+-block 132
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 5121 0 {At1g35060 }{AT3g43080 } -1
+ 5126 5 {At1g35070 At1g35090 At1g35100 }{AT3g43040 } -1
+ 5125 3 {At1g35080 At1g35110 }{AT3g43010 AT3g43030 } -1
+
+
+-block 133
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 5143 0 {At1g35590 At1g35600 }{AT3g42720 } -1
+ 5154 21 {At1g35770 }{AT3g42820 } 1
+ 5156 8 {At1g35820 }{AT3g42870 } -1
+
+
+-block 134
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 5165 0 {At1g35920 At1g35940 }{AT3g42320 AT3g42340 } -1
+ 5181 21 {At1g36130 }{AT3g42270 } -1
+ 5187 19 {At1g36480 }{AT3g42280 } -1
+
+
+-block 135
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 5201 0 {At1g38440 At1g41690 }{AT3g30630 AT3g30655 } -1
+ 5208 20 {At1g41900 }{AT3g30710 } 1
+ 5215 17 {At1g42200 At1g42410 At1g42500 }{AT3g30780 AT3g30790 } 1
+
+
+-block 136
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 5217 0 {At1g42200 At1g42410 At1g42500 }{AT3g42650 } 1
+ 5213 17 {At1g42400 }{AT3g42480 AT3g42490 } 1
+ 5219 17 {At1g42630 }{AT3g42450 } 1
+
+
+-block 137
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 5242 0 {At1g44840 }{AT3g43080 } -1
+ 5245 5 {At1g44850 At1g44860 }{AT3g43040 } -1
+ 5247 3 {At1g44870 At1g44880 }{AT3g43010 AT3g43030 } -1
+
+
+-block 138
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 5326 0 {At1g48940 }{AT3g18590 } -1
+ 5327 22 {At1g49030 }{AT3g18470 } -1
+ 5332 13 {At1g49140 }{AT3g18410 } -1
+
+
+-block 139
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 5701 0 {At1g60090 }{AT3g18070 AT3g18080 } 1
+ 5706 13 {At1g60180 }{AT3g18150 } -1
+ 5707 15 {At1g60260 At1g60270 }{AT3g18070 AT3g18080 } -1
+
+
+-block 140
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 5862 0 {At1g65540 }{AT3g59820 } 1
+ 5864 4 {At1g65560 }{AT3g59840 } 1
+ 5867 2 {At1g65570 }{AT3g59850 } 1
+
+
+-block 141
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 5872 0 {At1g65730 }{AT3g17650 } 1
+ 5884 19 {At1g65910 }{AT3g17730 } -1
+ 5886 6 {At1g65960 }{AT3g17720 AT3g17760 } 1
+
+
+-block 142
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 5934 0 {At1g67750 }{AT3g27400 } 1
+ 5940 17 {At1g67850 }{AT3g27470 } 1
+ 5942 7 {At1g67880 }{AT3g27540 } -1
+
+
+-block 143
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 6061 0 {At1g72700 }{AT3g13900 } 1
+ 6065 5 {At1g72730 }{AT3g13920 } 1
+ 6068 21 {At1g72960 }{AT3g13870 } -1
+
+
+-block 144
+ points contig1 contig2
+ 3 1 3
+
+ point dist markers orientation
+ 6082 0 {At1g73580 }{AT3g17980 } 1
+ 6083 3 {At1g73600 }{AT3g17990 AT3g18000 } 1
+ 6087 12 {At1g73670 }{AT3g18040 } 1
+
+
+-block 145
+ points contig1 contig2
+ 19 1 4
+
+ point dist markers orientation
+ 6311 0 {At1g02620 }{AT4g02080 } 1
+ 6312 5 {At1g02650 }{AT4g02100 } 1
+ 6313 9 {At1g02690 }{AT4g02150 } -1
+ 6314 5 {At1g02720 }{AT4g02130 } -1
+ 6319 14 {At1g02780 }{AT4g02230 } 1
+ 6321 8 {At1g02800 }{AT4g02290 } 1
+ 6323 2 {At1g02810 }{AT4g02300 AT4g02320 AT4g02330 AT4g02370 } -1
+ 6325 21 {At1g02890 }{AT4g02470 } 1
+ 6327 17 {At1g02980 }{AT4g02570 } 1
+ 6328 15 {At1g03050 }{AT4g02650 } 1
+ 6330 2 {At1g03060 }{AT4g02660 } 1
+ 6331 4 {At1g03070 }{AT4g02690 } 1
+ 6332 3 {At1g03080 }{AT4g02710 } 1
+ 6334 11 {At1g03130 }{AT4g02770 } 1
+ 6335 16 {At1g03210 }{AT4g02850 AT4g02860 } -1
+ 6340 9 {At1g03290 }{AT4g02880 } 1
+ 6341 20 {At1g03370 }{AT4g03000 } 1
+ 6342 7 {At1g03440 }{AT4g03010 } 1
+ 6343 7 {At1g03450 }{AT4g03080 } 1
+
+
+-block 146
+ points contig1 contig2
+ 9 1 4
+
+ point dist markers orientation
+ 6256 0 {At1g01340 }{AT4g01010 } 1
+ 6258 3 {At1g01360 }{AT4g01020 } 1
+ 6259 8 {At1g01390 At1g01420 }{AT4g01070 } 1
+ 6260 4 {At1g01430 }{AT4g01080 } 1
+ 6261 2 {At1g01440 }{AT4g01090 } 1
+ 6262 12 {At1g01460 }{AT4g01190 } -1
+ 6267 15 {At1g01520 }{AT4g01280 } 1
+ 6268 7 {At1g01540 }{AT4g01330 } 1
+ 6271 6 {At1g01560 }{AT4g01370 } 1
+
+
+-block 147
+ points contig1 contig2
+ 9 1 4
+
+ point dist markers orientation
+ 6931 0 {At1g32770 }{AT4g10350 } 1
+ 6932 20 {At1g32790 }{AT4g10610 } -1
+ 6935 9 {At1g32850 }{AT4g10570 AT4g10590 } -1
+ 6938 10 {At1g32940 At1g32950 At1g32960 At1g32970 At1g32980 }{AT4g10510 AT4g10520 AT4g10530 AT4g10540 AT4g10550 } 1
+ 6943 16 {At1g33120 At1g33140 }{AT4g10450 } -1
+ 6945 4 {At1g33170 }{AT4g10440 } -1
+ 6947 3 {At1g33230 }{AT4g10430 } -1
+ 6952 5 {At1g33260 }{AT4g10390 } -1
+ 6953 6 {At1g33280 }{AT4g10350 } -1
+
+
+-block 148
+ points contig1 contig2
+ 8 1 4
+
+ point dist markers orientation
+ 6960 0 {At1g33490 }{AT4g10140 } -1
+ 6964 19 {At1g33680 }{AT4g10070 } -1
+ 6965 3 {At1g33700 }{AT4g10060 } -1
+ 6968 10 {At1g33770 }{AT4g10010 } -1
+ 6969 5 {At1g33800 }{AT4g09990 } -1
+ 6970 20 {At1g33990 }{AT4g09900 } -1
+ 6971 12 {At1g34020 }{AT4g09810 } -1
+ 6973 2 {At1g34030 }{AT4g09800 } -1
+
+
+-block 149
+ points contig1 contig2
+ 7 1 4
+
+ point dist markers orientation
+ 6301 0 {At1g02300 }{AT4g01610 AT4g01620 } 1
+ 6302 14 {At1g02360 }{AT4g01700 } 1
+ 6303 25 {At1g02370 }{AT4g01990 } -1
+ 6304 6 {At1g02390 }{AT4g01950 } -1
+ 6305 10 {At1g02460 }{AT4g01890 } -1
+ 6306 7 {At1g02500 }{AT4g01850 } -1
+ 6307 4 {At1g02520 At1g02530 }{AT4g01820 AT4g01830 } -1
+
+
+-block 150
+ points contig1 contig2
+ 6 1 4
+
+ point dist markers orientation
+ 6273 0 {At1g01570 }{AT4g00300 } 1
+ 6277 8 {At1g01600 }{AT4g00360 } 1
+ 6278 5 {At1g01610 }{AT4g00400 AT4g00410 } 1
+ 6280 3 {At1g01620 }{AT4g00430 } 1
+ 6283 11 {At1g01700 }{AT4g00460 } 1
+ 6289 25 {At1g01790 }{AT4g00630 } -1
+
+
+-block 151
+ points contig1 contig2
+ 6 1 4
+
+ point dist markers orientation
+ 7062 0 {At1g36810 }{AT4g07530 } -1
+ 7065 21 {At1g37060 At1g37070 At1g37160 }{AT4g07560 AT4g07570 AT4g07590 AT4g07600 AT4g07610 AT4g07620 AT4g07630 AT4g07640 AT4g07660 AT4g07680 } -1
+ 7074 11 {At1g37190 }{AT4g07530 } -1
+ 7078 4 {At1g38440 At1g41690 }{AT4g07560 AT4g07570 AT4g07590 AT4g07600 AT4g07610 AT4g07620 AT4g07630 AT4g07640 AT4g07660 AT4g07680 } -1
+ 7088 16 {At1g41900 }{AT4g07530 } 1
+ 7093 15 {At1g42360 At1g42370 }{AT4g07560 AT4g07570 AT4g07590 AT4g07600 AT4g07610 AT4g07620 AT4g07630 AT4g07640 AT4g07660 AT4g07680 } 1
+
+
+-block 152
+ points contig1 contig2
+ 6 1 4
+
+ point dist markers orientation
+ 7441 0 {At1g64040 }{AT4g11240 } -1
+ 7442 3 {At1g64060 }{AT4g11230 } -1
+ 7444 5 {At1g64070 }{AT4g11170 } 1
+ 7446 5 {At1g64090 }{AT4g11220 } -1
+ 7452 8 {At1g64160 }{AT4g11180 AT4g11190 AT4g11210 } 1
+ 7455 7 {At1g64200 }{AT4g11150 } -1
+
+
+-block 153
+ points contig1 contig2
+ 5 1 4
+
+ point dist markers orientation
+ 7076 0 {At1g37180 At1g37200 }{AT4g03800 } 1
+ 7073 24 {At1g37190 }{AT4g04070 } -1
+ 7081 25 {At1g38440 At1g41690 }{AT4g03790 AT4g03850 AT4g03860 } -1
+ 7082 7 {At1g41780 }{AT4g03770 } -1
+ 7094 22 {At1g42360 At1g42370 }{AT4g03790 AT4g03850 AT4g03860 } 1
+
+
+-block 154
+ points contig1 contig2
+ 5 1 4
+
+ point dist markers orientation
+ 7369 0 {At1g61810 At1g61820 }{AT4g21760 } 1
+ 7372 18 {At1g61890 }{AT4g21900 AT4g21910 } 1
+ 7380 17 {At1g62040 }{AT4g21980 } 1
+ 7384 8 {At1g62180 }{AT4g21990 } 1
+ 7391 25 {At1g62320 }{AT4g22120 } 1
+
+
+-block 155
+ points contig1 contig2
+ 4 1 4
+
+ point dist markers orientation
+ 6344 0 {At1g03520 }{AT4g03340 } 1
+ 6348 15 {At1g03610 }{AT4g03420 } 1
+ 6350 12 {At1g03680 }{AT4g03520 } 1
+ 6351 4 {At1g03700 }{AT4g03540 } 1
+
+
+-block 156
+ points contig1 contig2
+ 4 1 4
+
+ point dist markers orientation
+ 6355 0 {At1g03860 }{AT4g28510 } 1
+ 6356 3 {At1g03880 At1g03890 }{AT4g28520 } 1
+ 6362 6 {At1g03930 }{AT4g28540 } 1
+ 6365 9 {At1g03990 }{AT4g28570 } 1
+
+
+-block 157
+ points contig1 contig2
+ 4 1 4
+
+ point dist markers orientation
+ 6874 0 {At1g30600 }{AT4g20430 } 1
+ 6876 5 {At1g30620 }{AT4g20460 } -1
+ 6881 19 {At1g30810 }{AT4g20400 } -1
+ 6883 9 {At1g30820 }{AT4g20320 } -1
+
+
+-block 158
+ points contig1 contig2
+ 4 1 4
+
+ point dist markers orientation
+ 6891 0 {At1g31120 }{AT4g19960 } -1
+ 6893 2 {At1g31130 }{AT4g19950 } -1
+ 6897 25 {At1g31230 }{AT4g19710 } -1
+ 6898 5 {At1g31260 }{AT4g19680 AT4g19690 } -1
+
+
+-block 159
+ points contig1 contig2
+ 4 1 4
+
+ point dist markers orientation
+ 6911 0 {At1g31850 }{AT4g19120 } -1
+ 6913 12 {At1g31880 }{AT4g19030 } -1
+ 6920 25 {At1g32130 }{AT4g19000 } -1
+ 6921 5 {At1g32170 }{AT4g18990 } -1
+
+
+-block 160
+ points contig1 contig2
+ 4 1 4
+
+ point dist markers orientation
+ 6993 0 {At1g34620 At1g34700 At1g34710 }{AT4g08890 AT4g08970 } 1
+ 7000 17 {At1g34760 }{AT4g09000 } -1
+ 7005 14 {At1g35140 }{AT4g08950 } 1
+ 7006 6 {At1g35160 }{AT4g09000 } 1
+
+
+-block 161
+ points contig1 contig2
+ 4 1 4
+
+ point dist markers orientation
+ 7103 0 {At1g43200 At1g43220 }{AT4g07520 } -1
+ 7108 10 {At1g43300 }{AT4g07580 } -1
+ 7111 22 {At1g43740 At1g43750 }{AT4g07560 AT4g07570 AT4g07590 AT4g07600 AT4g07610 AT4g07620 AT4g07630 AT4g07640 AT4g07660 AT4g07680 } 1
+ 7112 12 {At1g43870 At1g43880 }{AT4g07530 } -1
+
+
+-block 162
+ points contig1 contig2
+ 4 1 4
+
+ point dist markers orientation
+ 7379 0 {At1g62040 }{AT4g04620 } -1
+ 7383 8 {At1g62180 }{AT4g04610 } -1
+ 7386 21 {At1g62290 }{AT4g04460 } -1
+ 7389 13 {At1g62320 }{AT4g04340 } -1
+
+
+-block 163
+ points contig1 contig2
+ 4 1 4
+
+ point dist markers orientation
+ 7462 0 {At1g64400 }{AT4g23850 } 1
+ 7464 10 {At1g64440 }{AT4g23920 } 1
+ 7469 16 {At1g64530 }{AT4g24020 } 1
+ 7471 9 {At1g64590 }{AT4g24050 } 1
+
+
+-block 164
+ points contig1 contig2
+ 3 1 4
+
+ point dist markers orientation
+ 6264 0 {At1g01480 }{AT4g11280 } 1
+ 6272 12 {At1g01560 }{AT4g11330 } 1
+ 6274 3 {At1g01570 }{AT4g11350 } 1
+
+
+-block 165
+ points contig1 contig2
+ 3 1 4
+
+ point dist markers orientation
+ 6519 0 {At1g11130 At1g11140 }{AT4g03390 } -1
+ 6523 16 {At1g11250 }{AT4g03330 } 1
+ 6526 13 {At1g11280 At1g11300 At1g11330 At1g11340 At1g11350 At1g11410 }{AT4g03230 } 1
+
+
+-block 166
+ points contig1 contig2
+ 3 1 4
+
+ point dist markers orientation
+ 6522 0 {At1g11200 }{AT4g21570 } -1
+ 6524 15 {At1g11260 }{AT4g21480 } -1
+ 6530 17 {At1g11290 }{AT4g21300 } -1
+
+
+-block 167
+ points contig1 contig2
+ 3 1 4
+
+ point dist markers orientation
+ 6744 0 {At1g22150 }{AT4g08620 } 1
+ 6745 10 {At1g22180 }{AT4g08690 } 1
+ 6749 18 {At1g22240 }{AT4g08840 } 1
+
+
+-block 168
+ points contig1 contig2
+ 3 1 4
+
+ point dist markers orientation
+ 6858 0 {At1g30080 }{AT4g18340 } 1
+ 6862 3 {At1g30100 }{AT4g18350 } 1
+ 6863 12 {At1g30200 }{AT4g18380 } 1
+
+
+-block 169
+ points contig1 contig2
+ 3 1 4
+
+ point dist markers orientation
+ 7044 0 {At1g36130 }{AT4g04150 } -1
+ 7046 5 {At1g36190 At1g36260 }{AT4g04170 } -1
+ 7057 23 {At1g36550 At1g36590 }{AT4g04230 } -1
+
+
+-block 170
+ points contig1 contig2
+ 3 1 4
+
+ point dist markers orientation
+ 7075 0 {At1g37190 }{AT4g07930 } 1
+ 7079 11 {At1g38440 At1g41690 }{AT4g08050 AT4g08080 } -1
+ 7089 15 {At1g41910 }{AT4g08060 AT4g08070 } -1
+
+
+-block 171
+ points contig1 contig2
+ 3 1 4
+
+ point dist markers orientation
+ 7134 0 {At1g44970 }{AT4g36430 } -1
+ 7136 7 {At1g45050 }{AT4g36410 } 1
+ 7138 10 {At1g45130 }{AT4g36360 } -1
+
+
+-block 172
+ points contig1 contig2
+ 3 1 4
+
+ point dist markers orientation
+ 7215 0 {At1g50890 }{AT4g27060 } 1
+ 7216 8 {At1g50950 }{AT4g27080 } 1
+ 7219 23 {At1g51060 }{AT4g27230 } -1
+
+
+-block 173
+ points contig1 contig2
+ 3 1 4
+
+ point dist markers orientation
+ 7359 0 {At1g61360 At1g61370 At1g61380 At1g61390 At1g61400 At1g61420 At1g61430 At1g61440 At1g61460 At1g61480 At1g61490 At1g61500 At1g61550 At1g61610 }{AT4g05200 } 1
+ 7366 19 {At1g61630 }{AT4g05110 AT4g05120 AT4g05130 AT4g05140 } -1
+ 7368 20 {At1g61760 }{AT4g05220 } 1
+
+
+-block 174
+ points contig1 contig2
+ 3 1 4
+
+ point dist markers orientation
+ 7408 0 {At1g62800 }{AT4g31990 } 1
+ 7417 22 {At1g62990 }{AT4g32040 } 1
+ 7425 25 {At1g63070 At1g63080 At1g63130 At1g63150 At1g63230 At1g63320 At1g63330 At1g63400 }{AT4g31850 } -1
+
+
+-block 175
+ points contig1 contig2
+ 3 1 4
+
+ point dist markers orientation
+ 7447 0 {At1g64090 }{AT4g23630 } 1
+ 7453 11 {At1g64160 }{AT4g23690 } -1
+ 7454 2 {At1g64170 }{AT4g23700 } 1
+
+
+-block 176
+ points contig1 contig2
+ 3 1 4
+
+ point dist markers orientation
+ 7459 0 {At1g64390 }{AT4g11050 } -1
+ 7461 3 {At1g64400 }{AT4g11030 } -1
+ 7463 9 {At1g64440 }{AT4g10960 } -1
+
+
+-block 177
+ points contig1 contig2
+ 3 1 4
+
+ point dist markers orientation
+ 7624 0 {At1g71940 }{AT4g09580 } -1
+ 7626 6 {At1g71980 }{AT4g09560 } -1
+ 7627 7 {At1g72000 }{AT4g09510 } -1
+
+
+-block 178
+ points contig1 contig2
+ 3 1 4
+
+ point dist markers orientation
+ 7707 0 {At1g76030 }{AT4g38510 } -1
+ 7715 21 {At1g76160 }{AT4g38420 } -1
+ 7717 14 {At1g76270 }{AT4g38390 } -1
+
+
+-block 179
+ points contig1 contig2
+ 26 1 5
+
+ point dist markers orientation
+ 7853 0 {At1g03740 }{AT5g44290 } -1
+ 7855 4 {At1g03770 }{AT5g44280 } -1
+ 7856 4 {At1g03790 }{AT5g44260 } -1
+ 7859 15 {At1g03840 }{AT5g44160 } -1
+ 7862 4 {At1g03860 }{AT5g44140 } -1
+ 7863 2 {At1g03870 }{AT5g44130 } -1
+ 7864 2 {At1g03880 At1g03890 }{AT5g44120 } -1
+ 7865 2 {At1g03900 }{AT5g44110 } -1
+ 7868 4 {At1g03930 }{AT5g44100 } -1
+ 7871 4 {At1g03960 }{AT5g44090 } -1
+ 7872 4 {At1g03980 }{AT5g44070 } -1
+ 7873 11 {At1g04040 }{AT5g44020 } -1
+ 7874 4 {At1g04050 }{AT5g43990 } -1
+ 7877 8 {At1g04090 }{AT5g43950 } -1
+ 7882 7 {At1g04140 }{AT5g43930 } -1
+ 7885 5 {At1g04160 }{AT5g43900 } -1
+ 7887 3 {At1g04180 }{AT5g43890 } -1
+ 7888 17 {At1g04220 }{AT5g43760 } -1
+ 7889 4 {At1g04230 }{AT5g43720 } -1
+ 7890 3 {At1g04240 }{AT5g43700 } -1
+ 7892 9 {At1g04270 }{AT5g43640 } -1
+ 7893 11 {At1g04300 }{AT5g43560 } -1
+ 7895 13 {At1g04340 }{AT5g43460 } -1
+ 7896 2 {At1g04350 At1g04380 }{AT5g43440 AT5g43450 } -1
+ 7898 12 {At1g04410 }{AT5g43330 } -1
+ 7903 4 {At1g04440 }{AT5g43320 } -1
+
+
+-block 180
+ points contig1 contig2
+ 11 1 5
+
+ point dist markers orientation
+ 9360 0 {At1g66410 }{AT5g37780 } 1
+ 9365 5 {At1g66460 }{AT5g37790 } 1
+ 9366 2 {At1g66470 }{AT5g37800 } 1
+ 9374 19 {At1g66620 }{AT5g37870 AT5g37890 AT5g37900 AT5g37910 AT5g37930 } 1
+ 9375 24 {At1g66740 }{AT5g38110 } 1
+ 9377 13 {At1g66840 }{AT5g38150 } 1
+ 9378 7 {At1g66860 }{AT5g38200 } 1
+ 9379 3 {At1g66880 At1g66910 At1g66920 At1g66930 At1g66970 At1g66980 At1g67000 }{AT5g38210 AT5g38240 AT5g38250 AT5g38260 AT5g38280 } 1
+ 9381 3 {At1g66900 }{AT5g38220 } 1
+ 9389 25 {At1g67090 }{AT5g38410 AT5g38420 AT5g38430 } 1
+ 9391 4 {At1g67110 }{AT5g38450 } 1
+
+
+-block 181
+ points contig1 contig2
+ 9 1 5
+
+ point dist markers orientation
+ 9218 0 {At1g63300 }{AT5g41140 } 1
+ 9222 11 {At1g63430 }{AT5g41180 } 1
+ 9224 6 {At1g63450 }{AT5g41250 } -1
+ 9227 5 {At1g63500 }{AT5g41260 } 1
+ 9231 14 {At1g63630 }{AT5g41170 } -1
+ 9233 10 {At1g63640 }{AT5g41310 } 1
+ 9234 2 {At1g63650 }{AT5g41315 } 1
+ 9239 14 {At1g63800 }{AT5g41340 } 1
+ 9240 7 {At1g63830 }{AT5g41390 } 1
+
+
+-block 182
+ points contig1 contig2
+ 7 1 5
+
+ point dist markers orientation
+ 9243 0 {At1g64000 }{AT5g41570 } 1
+ 9253 9 {At1g64070 }{AT5g41540 AT5g41550 } -1
+ 9256 7 {At1g64090 }{AT5g41600 } 1
+ 9261 8 {At1g64170 }{AT5g41610 } 1
+ 9262 8 {At1g64190 }{AT5g41670 } 1
+ 9265 7 {At1g64230 }{AT5g41700 } 1
+ 9269 7 {At1g64300 }{AT5g41730 } -1
+
+
+-block 183
+ points contig1 contig2
+ 5 1 5
+
+ point dist markers orientation
+ 8805 0 {At1g45000 }{AT5g43010 } -1
+ 8807 4 {At1g45050 }{AT5g42990 } -1
+ 8814 11 {At1g45170 }{AT5g42960 } -1
+ 8815 3 {At1g45180 }{AT5g42940 } -1
+ 8817 16 {At1g47210 At1g47220 At1g47230 }{AT5g43080 } 1
+
+
+-block 184
+ points contig1 contig2
+ 5 1 5
+
+ point dist markers orientation
+ 9456 0 {At1g70300 }{AT5g14880 } -1
+ 9458 25 {At1g70410 }{AT5g14740 } -1
+ 9459 4 {At1g70430 }{AT5g14720 } -1
+ 9462 10 {At1g70490 }{AT5g14670 } -1
+ 9464 3 {At1g70500 }{AT5g14650 } -1
+
+
+-block 185
+ points contig1 contig2
+ 5 1 5
+
+ point dist markers orientation
+ 9671 0 {At1g77260 }{AT5g64030 } -1
+ 9675 10 {At1g77280 }{AT5g63940 } -1
+ 9681 19 {At1g77380 }{AT5g63850 } -1
+ 9682 7 {At1g77410 }{AT5g63800 AT5g63810 } -1
+ 9684 5 {At1g77450 }{AT5g63790 } -1
+
+
+-block 186
+ points contig1 contig2
+ 5 1 5
+
+ point dist markers orientation
+ 9691 0 {At1g77920 }{AT5g10030 } -1
+ 9693 22 {At1g77990 At1g78000 }{AT5g10180 } -1
+ 9699 17 {At1g78090 }{AT5g10100 } 1
+ 9701 4 {At1g78120 }{AT5g10090 } 1
+ 9703 11 {At1g78130 }{AT5g10190 } 1
+
+
+-block 187
+ points contig1 contig2
+ 4 1 5
+
+ point dist markers orientation
+ 7911 0 {At1g04680 }{AT5g48900 } -1
+ 7914 5 {At1g04710 }{AT5g48880 } -1
+ 7916 7 {At1g04770 }{AT5g48850 } 1
+ 7918 13 {At1g04840 }{AT5g48910 } 1
+
+
+-block 188
+ points contig1 contig2
+ 4 1 5
+
+ point dist markers orientation
+ 8461 0 {At1g23460 }{AT5g14650 } 1
+ 8465 5 {At1g23490 }{AT5g14670 } 1
+ 8469 18 {At1g23700 }{AT5g14720 } 1
+ 8472 5 {At1g23730 }{AT5g14740 } 1
+
+
+-block 189
+ points contig1 contig2
+ 4 1 5
+
+ point dist markers orientation
+ 8595 0 {At1g30600 }{AT5g44530 } -1
+ 8597 7 {At1g30620 }{AT5g44480 } 1
+ 8600 13 {At1g30700 At1g30740 At1g30760 At1g30770 }{AT5g44380 AT5g44390 AT5g44400 AT5g44410 AT5g44440 } -1
+ 8601 3 {At1g30710 At1g30720 At1g30730 }{AT5g44360 } -1
+
+
+-block 190
+ points contig1 contig2
+ 4 1 5
+
+ point dist markers orientation
+ 9275 0 {At1g64520 }{AT5g42040 } -1
+ 9283 12 {At1g64610 }{AT5g42010 } -1
+ 9287 4 {At1g64630 }{AT5g41990 } -1
+ 9288 13 {At1g64670 }{AT5g41900 } -1
+
+
+-block 191
+ points contig1 contig2
+ 4 1 5
+
+ point dist markers orientation
+ 9692 0 {At1g77920 }{AT5g65210 } 1
+ 9700 21 {At1g78090 }{AT5g65140 } -1
+ 9702 4 {At1g78120 }{AT5g65160 } 1
+ 9705 23 {At1g78180 }{AT5g64970 } -1
+
+
+-block 192
+ points contig1 contig2
+ 3 1 5
+
+ point dist markers orientation
+ 7973 0 {At1g07380 }{AT5g58980 } 1
+ 7977 16 {At1g07410 }{AT5g59150 } 1
+ 7980 8 {At1g07430 }{AT5g59220 } 1
+
+
+-block 193
+ points contig1 contig2
+ 3 1 5
+
+ point dist markers orientation
+ 7990 0 {At1g07710 }{AT5g60070 } 1
+ 7992 24 {At1g07770 }{AT5g59850 } 1
+ 7996 7 {At1g07790 }{AT5g59910 } 1
+
+
+-block 194
+ points contig1 contig2
+ 3 1 5
+
+ point dist markers orientation
+ 8008 0 {At1g08140 At1g08150 }{AT5g22900 } -1
+ 8009 11 {At1g08210 }{AT5g22850 } 1
+ 8011 22 {At1g08250 }{AT5g22630 } -1
+
+
+-block 195
+ points contig1 contig2
+ 3 1 5
+
+ point dist markers orientation
+ 8062 0 {At1g09540 }{AT5g26660 } -1
+ 8063 2 {At1g09550 }{AT5g26670 } -1
+ 8065 4 {At1g09560 }{AT5g26700 } -1
+
+
+-block 196
+ points contig1 contig2
+ 3 1 5
+
+ point dist markers orientation
+ 8419 0 {At1g22070 }{AT5g10030 } -1
+ 8422 23 {At1g22150 }{AT5g10180 } 1
+ 8424 14 {At1g22210 }{AT5g10100 } 1
+
+
+-block 197
+ points contig1 contig2
+ 3 1 5
+
+ point dist markers orientation
+ 8746 0 {At1g35920 At1g35940 }{AT5g32630 AT5g33200 AT5g33240 } -1
+ 8754 14 {At1g36080 }{AT5g33220 } 1
+ 8757 9 {At1g36100 }{AT5g32590 } -1
+
+
+-block 198
+ points contig1 contig2
+ 3 1 5
+
+ point dist markers orientation
+ 9023 0 {At1g55360 }{AT5g56530 } -1
+ 9030 10 {At1g55490 }{AT5g56500 } -1
+ 9033 19 {At1g55530 }{AT5g56340 } -1
+
+
+-block 199
+ points contig1 contig2
+ 3 1 5
+
+ point dist markers orientation
+ 9271 0 {At1g64460 At1g64470 }{AT5g24240 } 1
+ 9272 4 {At1g64480 }{AT5g24270 } 1
+ 9282 18 {At1g64610 }{AT5g24320 } 1
+
+
+-block 200
+ points contig1 contig2
+ 3 1 5
+
+ point dist markers orientation
+ 9322 0 {At1g65630 At1g65640 }{AT5g36950 } -1
+ 9324 7 {At1g65690 }{AT5g36970 } 1
+ 9328 13 {At1g65780 At1g65810 }{AT5g37030 } 1
+
+
+-block 201
+ points contig1 contig2
+ 3 1 5
+
+ point dist markers orientation
+ 9349 0 {At1g66160 }{AT5g37490 } 1
+ 9350 7 {At1g66180 }{AT5g37540 } 1
+ 9353 8 {At1g66200 }{AT5g37600 } 1
+
+
+-block 202
+ points contig1 contig2
+ 3 1 5
+
+ point dist markers orientation
+ 9442 0 {At1g69730 }{AT5g62710 } -1
+ 9446 14 {At1g69840 }{AT5g62740 } -1
+ 9447 2 {At1g69850 }{AT5g62730 } -1
+
+
+-block 203
+ points contig1 contig2
+ 3 1 5
+
+ point dist markers orientation
+ 9567 0 {At1g74080 }{AT5g07690 AT5g07700 } 1
+ 9580 25 {At1g74380 }{AT5g07720 } 1
+ 9581 2 {At1g74390 }{AT5g07710 } -1
+
+
+-block 204
+ points contig1 contig2
+ 5 2 2
+
+ point dist markers orientation
+ 9907 0 {At2g05390 }{At2g10580 At2g10650 } 1
+ 9930 18 {At2g05610 }{At2g10620 At2g10660 At2g10670 At2g10690 At2g10700 At2g10780 } -1
+ 9942 18 {At2g05860 }{At2g10500 } -1
+ 9948 13 {At2g05960 }{At2g10580 At2g10650 } 1
+ 9957 17 {At2g06160 At2g06310 At2g06320 At2g06330 }{At2g10620 At2g10660 At2g10670 At2g10690 At2g10700 At2g10780 } -1
+
+
+-block 205
+ points contig1 contig2
+ 4 2 2
+
+ point dist markers orientation
+ 9880 0 {At2g04960 At2g04970 }{At2g14140 } -1
+ 9883 2 {At2g04980 }{At2g14130 } -1
+ 9891 18 {At2g05080 }{At2g14300 } 1
+ 9894 20 {At2g05180 }{At2g14100 } -1
+
+
+-block 206
+ points contig1 contig2
+ 4 2 2
+
+ point dist markers orientation
+ 9913 0 {At2g05450 At2g05460 At2g05470 At2g05560 }{At2g06630 At2g06640 } -1
+ 9914 3 {At2g05480 }{At2g06610 At2g06690 } -1
+ 9918 11 {At2g05490 At2g05570 }{At2g06870 } 1
+ 9928 11 {At2g05610 }{At2g06890 } -1
+
+
+-block 207
+ points contig1 contig2
+ 4 2 2
+
+ point dist markers orientation
+ 9911 0 {At2g05450 At2g05460 At2g05470 At2g05560 }{At2g12100 At2g12110 At2g12120 At2g12130 } 1
+ 9915 2 {At2g05480 }{At2g12140 } 1
+ 9920 2 {At2g05490 At2g05570 }{At2g12150 } 1
+ 9934 17 {At2g05650 }{At2g12210 At2g12220 At2g12390 } -1
+
+
+-block 208
+ points contig1 contig2
+ 4 2 2
+
+ point dist markers orientation
+ 9974 0 {At2g06610 At2g06690 }{At2g12140 } -1
+ 9976 2 {At2g06620 At2g06700 }{At2g12100 At2g12110 At2g12120 At2g12130 } -1
+ 9981 11 {At2g06720 At2g06800 }{At2g12240 At2g12250 At2g12300 } 1
+ 9988 12 {At2g06870 }{At2g12150 } 1
+
+
+-block 209
+ points contig1 contig2
+ 4 2 2
+
+ point dist markers orientation
+ 9977 0 {At2g06620 At2g06700 }{At2g14770 } -1
+ 9995 20 {At2g06840 At2g06950 At2g07010 }{At2g14930 } -1
+ 9990 16 {At2g06870 }{At2g14780 At2g14790 } 1
+ 9994 13 {At2g06890 }{At2g14640 At2g14650 } 1
+
+
+-block 210
+ points contig1 contig2
+ 4 2 2
+
+ point dist markers orientation
+ 10004 0 {At2g07230 At2g07250 At2g07320 At2g07330 }{At2g14030 } -1
+ 10016 22 {At2g07420 At2g07450 At2g07550 }{At2g13930 At2g13940 } 1
+ 10013 11 {At2g07500 }{At2g14030 } -1
+ 10022 25 {At2g07620 At2g07630 }{At2g14300 } 1
+
+
+-block 211
+ points contig1 contig2
+ 4 2 2
+
+ point dist markers orientation
+ 10061 0 {At2g11680 At2g12020 }{At2g13020 } -1
+ 10055 12 {At2g11940 }{At2g13230 At2g13330 } -1
+ 10065 18 {At2g12150 }{At2g12720 } 1
+ 10070 23 {At2g12520 }{At2g13070 } -1
+
+
+-block 212
+ points contig1 contig2
+ 4 2 2
+
+ point dist markers orientation
+ 10071 0 {At2g12720 }{At2g14030 } 1
+ 10076 22 {At2g13000 At2g13160 At2g13310 }{At2g14230 } 1
+ 10081 14 {At2g13230 At2g13330 }{At2g14380 At2g14400 } -1
+ 10083 11 {At2g13410 }{At2g14410 } 1
+
+
+-block 213
+ points contig1 contig2
+ 4 2 2
+
+ point dist markers orientation
+ 10109 0 {At2g14030 }{At2g15150 At2g15210 } 1
+ 10115 11 {At2g14130 }{At2g15140 At2g15190 } 1
+ 10116 5 {At2g14140 }{At2g15200 } 1
+ 10119 20 {At2g14380 At2g14400 }{At2g15100 } -1
+
+
+-block 214
+ points contig1 contig2
+ 4 2 2
+
+ point dist markers orientation
+ 10492 0 {At2g37250 }{At2g39270 } 1
+ 10493 5 {At2g37290 }{At2g39280 } 1
+ 10494 13 {At2g37360 }{At2g39350 } 1
+ 10495 23 {At2g37450 At2g37460 }{At2g39510 } 1
+
+
+-block 215
+ points contig1 contig2
+ 3 2 2
+
+ point dist markers orientation
+ 9796 0 {At2g02190 }{At2g04950 At2g05010 } 1
+ 9799 2 {At2g02200 }{At2g04960 At2g04970 } 1
+ 9803 2 {At2g02210 }{At2g04980 } 1
+
+
+-block 216
+ points contig1 contig2
+ 3 2 2
+
+ point dist markers orientation
+ 9798 0 {At2g02190 }{At2g15150 At2g15210 } -1
+ 9802 4 {At2g02200 }{At2g15200 } -1
+ 9806 5 {At2g02210 }{At2g15140 At2g15190 } -1
+
+
+-block 217
+ points contig1 contig2
+ 3 2 2
+
+ point dist markers orientation
+ 9851 0 {At2g04310 }{At2g23500 } -1
+ 9852 2 {At2g04320 }{At2g23490 } -1
+ 9853 2 {At2g04330 }{At2g23480 } -1
+
+
+-block 218
+ points contig1 contig2
+ 3 2 2
+
+ point dist markers orientation
+ 9878 0 {At2g04950 At2g05010 }{At2g15150 At2g15210 } -1
+ 9881 4 {At2g04960 At2g04970 }{At2g15200 } -1
+ 9884 5 {At2g04980 }{At2g15140 At2g15190 } -1
+
+
+-block 219
+ points contig1 contig2
+ 3 2 2
+
+ point dist markers orientation
+ 9909 0 {At2g05390 }{At2g14930 } -1
+ 9922 20 {At2g05490 At2g05570 }{At2g14780 At2g14790 } 1
+ 9931 22 {At2g05610 }{At2g14640 At2g14650 } -1
+
+
+-block 220
+ points contig1 contig2
+ 3 2 2
+
+ point dist markers orientation
+ 9912 0 {At2g05450 At2g05460 At2g05470 At2g05560 }{At2g16170 At2g16180 } -1
+ 9916 2 {At2g05480 }{At2g16160 } -1
+ 9939 25 {At2g05790 }{At2g16230 } -1
+
+
+-block 221
+ points contig1 contig2
+ 3 2 2
+
+ point dist markers orientation
+ 9919 0 {At2g05490 At2g05570 }{At2g07500 } -1
+ 9929 17 {At2g05610 }{At2g07660 } 1
+ 9943 20 {At2g05890 }{At2g07620 At2g07630 } 1
+
+
+-block 222
+ points contig1 contig2
+ 3 2 2
+
+ point dist markers orientation
+ 9971 0 {At2g06470 }{At2g10620 At2g10660 At2g10670 At2g10690 At2g10700 At2g10780 } -1
+ 9980 17 {At2g06720 At2g06800 }{At2g10490 At2g10640 } -1
+ 9993 12 {At2g06890 }{At2g10620 At2g10660 At2g10670 At2g10690 At2g10700 At2g10780 } 1
+
+
+-block 223
+ points contig1 contig2
+ 3 2 2
+
+ point dist markers orientation
+ 10007 0 {At2g07380 }{At2g12720 } -1
+ 10009 11 {At2g07410 }{At2g13020 } 1
+ 10011 6 {At2g07420 At2g07450 At2g07550 }{At2g13250 At2g13260 } 1
+
+
+-block 224
+ points contig1 contig2
+ 3 2 2
+
+ point dist markers orientation
+ 10025 0 {At2g07660 }{At2g10620 At2g10660 At2g10670 At2g10690 At2g10700 At2g10780 } -1
+ 10030 19 {At2g09960 }{At2g10460 } -1
+ 10033 18 {At2g10140 }{At2g10630 } 1
+
+
+-block 225
+ points contig1 contig2
+ 3 2 2
+
+ point dist markers orientation
+ 10031 0 {At2g10000 At2g10010 }{At2g12210 At2g12220 At2g12390 } -1
+ 10035 18 {At2g10490 At2g10640 }{At2g12240 At2g12250 At2g12300 } -1
+ 10038 25 {At2g10620 At2g10660 At2g10670 At2g10690 At2g10700 At2g10780 }{At2g11680 At2g12020 } 1
+
+
+-block 226
+ points contig1 contig2
+ 3 2 2
+
+ point dist markers orientation
+ 10048 0 {At2g11240 }{At2g15380 } -1
+ 10058 24 {At2g11940 }{At2g15410 } -1
+ 10059 19 {At2g11950 }{At2g15650 At2g15700 } 1
+
+
+-block 227
+ points contig1 contig2
+ 3 2 2
+
+ point dist markers orientation
+ 10054 0 {At2g11930 }{At2g15110 } -1
+ 10057 2 {At2g11940 }{At2g15100 } -1
+ 10069 19 {At2g12210 At2g12220 At2g12390 }{At2g14970 At2g14980 At2g15070 } -1
+
+
+-block 228
+ points contig1 contig2
+ 3 2 2
+
+ point dist markers orientation
+ 10174 0 {At2g16370 }{At2g21550 } -1
+ 10176 3 {At2g16380 }{At2g21520 At2g21540 } 1
+ 10177 8 {At2g16390 }{At2g21450 } -1
+
+
+-block 229
+ points contig1 contig2
+ 3 2 2
+
+ point dist markers orientation
+ 10220 0 {At2g17890 }{At2g46700 } 1
+ 10226 22 {At2g18060 }{At2g46770 } 1
+ 10234 25 {At2g18230 }{At2g46860 } -1
+
+
+-block 230
+ points contig1 contig2
+ 3 2 2
+
+ point dist markers orientation
+ 10429 0 {At2g31000 At2g31010 }{At2g42630 } -1
+ 10430 15 {At2g31110 }{At2g42570 } 1
+ 10431 9 {At2g31160 }{At2g42610 } 1
+
+
+-block 231
+ points contig1 contig2
+ 40 2 3
+
+ point dist markers orientation
+ 11582 0 {At2g38810 }{AT3g54560 } -1
+ 11584 8 {At2g38860 }{AT3g54600 } -1
+ 11587 18 {At2g38940 }{AT3g54700 } -1
+ 11588 11 {At2g38970 }{AT3g54780 } 1
+ 11590 7 {At2g39010 }{AT3g54820 } 1
+ 11595 12 {At2g39130 }{AT3g54830 } 1
+ 11597 20 {At2g39220 }{AT3g54950 } 1
+ 11599 4 {At2g39230 }{AT3g54980 } 1
+ 11600 9 {At2g39280 }{AT3g55020 } 1
+ 11601 2 {At2g39290 }{AT3g55030 } 1
+ 11602 4 {At2g39300 }{AT3g55060 } 1
+ 11605 7 {At2g39350 }{AT3g55090 AT3g55100 AT3g55110 AT3g55130 } 1
+ 11609 6 {At2g39380 }{AT3g55150 } 1
+ 11610 3 {At2g39390 }{AT3g55170 } 1
+ 11611 2 {At2g39400 At2g39410 At2g39420 }{AT3g55180 AT3g55190 } 1
+ 11613 4 {At2g39430 }{AT3g55230 } 1
+ 11614 8 {At2g39460 }{AT3g55280 } 1
+ 11617 5 {At2g39480 }{AT3g55320 } 1
+ 11622 25 {At2g39640 }{AT3g55430 } 1
+ 11623 4 {At2g39660 }{AT3g55450 } 1
+ 11625 9 {At2g39700 }{AT3g55500 } 1
+ 11633 16 {At2g39770 }{AT3g55590 } 1
+ 11634 5 {At2g39800 }{AT3g55610 } 1
+ 11635 3 {At2g39820 }{AT3g55620 } 1
+ 11638 15 {At2g39880 }{AT3g55730 } 1
+ 11639 2 {At2g39890 }{AT3g55740 } 1
+ 11640 4 {At2g39900 }{AT3g55770 } 1
+ 11641 17 {At2g40000 }{AT3g55840 } 1
+ 11648 16 {At2g40110 }{AT3g55890 } 1
+ 11650 12 {At2g40140 }{AT3g55980 } 1
+ 11652 2 {At2g40150 At2g40160 }{AT3g55990 } 1
+ 11653 12 {At2g40240 }{AT3g56030 } 1
+ 11654 5 {At2g40270 }{AT3g56050 } 1
+ 11656 4 {At2g40280 }{AT3g56080 } 1
+ 11658 3 {At2g40300 }{AT3g56090 } 1
+ 11661 12 {At2g40320 }{AT3g55990 } 1
+ 11663 18 {At2g40380 }{AT3g56110 } 1
+ 11664 5 {At2g40400 }{AT3g56140 } 1
+ 11665 4 {At2g40410 }{AT3g56170 } 1
+ 11667 4 {At2g40420 }{AT3g56200 } 1
+
+
+-block 232
+ points contig1 contig2
+ 24 2 3
+
+ point dist markers orientation
+ 11814 0 {At2g43690 At2g43700 }{AT3g59700 AT3g59730 AT3g59740 AT3g59750 } 1
+ 11819 8 {At2g43750 }{AT3g59760 } 1
+ 11822 7 {At2g43790 }{AT3g59790 } 1
+ 11824 9 {At2g43850 }{AT3g59830 } 1
+ 11825 3 {At2g43860 At2g43870 At2g43880 At2g43890 }{AT3g59850 } 1
+ 11828 6 {At2g43940 }{AT3g59870 } 1
+ 11829 12 {At2g44040 }{AT3g59890 } 1
+ 11830 7 {At2g44090 }{AT3g59910 } 1
+ 11831 2 {At2g44100 }{AT3g59920 } 1
+ 11833 5 {At2g44130 }{AT3g59940 } 1
+ 11834 2 {At2g44140 }{AT3g59950 } 1
+ 11835 2 {At2g44150 }{AT3g59960 } 1
+ 11836 2 {At2g44160 }{AT3g59970 } 1
+ 11837 4 {At2g44180 }{AT3g59990 } 1
+ 11838 2 {At2g44190 }{AT3g60000 } 1
+ 11842 20 {At2g44350 }{AT3g60100 } 1
+ 11843 7 {At2g44430 }{AT3g60110 } 1
+ 11845 3 {At2g44450 At2g44460 At2g44470 At2g44480 At2g44490 }{AT3g60120 AT3g60130 AT3g60140 } 1
+ 11850 12 {At2g44590 }{AT3g60190 } 1
+ 11852 15 {At2g44680 }{AT3g60250 } 1
+ 11855 9 {At2g44770 }{AT3g60260 } 1
+ 11856 5 {At2g44800 }{AT3g60290 } 1
+ 11863 16 {At2g44900 }{AT3g60350 } 1
+ 11864 5 {At2g44910 }{AT3g60390 } 1
+
+
+-block 233
+ points contig1 contig2
+ 23 2 3
+
+ point dist markers orientation
+ 11509 0 {At2g37040 }{AT3g53260 } 1
+ 11512 8 {At2g37060 }{AT3g53340 } -1
+ 11513 15 {At2g37160 }{AT3g53390 } 1
+ 11514 4 {At2g37170 At2g37180 }{AT3g53420 } 1
+ 11517 2 {At2g37190 }{AT3g53430 } 1
+ 11518 4 {At2g37210 }{AT3g53450 } 1
+ 11519 2 {At2g37220 }{AT3g53460 } 1
+ 11522 8 {At2g37280 }{AT3g53480 } 1
+ 11525 8 {At2g37340 }{AT3g53500 } 1
+ 11526 3 {At2g37360 }{AT3g53510 } 1
+ 11529 9 {At2g37400 }{AT3g53560 } 1
+ 11532 15 {At2g37470 }{AT3g53650 } 1
+ 11533 8 {At2g37520 }{AT3g53680 } 1
+ 11534 6 {At2g37550 }{AT3g53710 } 1
+ 11538 8 {At2g37600 }{AT3g53740 } 1
+ 11543 3 {At2g37620 }{AT3g53750 } 1
+ 11549 15 {At2g37710 }{AT3g53810 } 1
+ 11552 12 {At2g37760 At2g37770 At2g37790 }{AT3g53880 } 1
+ 11553 10 {At2g37840 At2g37850 }{AT3g53930 } 1
+ 11555 5 {At2g37890 }{AT3g53940 } 1
+ 11557 3 {At2g37900 }{AT3g53960 } 1
+ 11558 10 {At2g37940 }{AT3g54020 } 1
+ 11559 12 {At2g37980 }{AT3g54100 } 1
+
+
+-block 234
+ points contig1 contig2
+ 22 2 3
+
+ point dist markers orientation
+ 11689 0 {At2g40990 }{AT3g56920 AT3g56930 } -1
+ 11690 13 {At2g41060 }{AT3g56860 } -1
+ 11695 11 {At2g41110 }{AT3g56800 } -1
+ 11706 25 {At2g41210 }{AT3g56960 } 1
+ 11707 12 {At2g41300 }{AT3g57010 AT3g57020 AT3g57030 } 1
+ 11708 2 {At2g41310 }{AT3g57040 } 1
+ 11709 4 {At2g41330 }{AT3g57070 } 1
+ 11711 2 {At2g41340 }{AT3g57080 } 1
+ 11712 8 {At2g41370 }{AT3g57130 } -1
+ 11714 15 {At2g41450 }{AT3g57200 } 1
+ 11715 6 {At2g41490 }{AT3g57220 } 1
+ 11720 16 {At2g41560 }{AT3g57330 } 1
+ 11726 7 {At2g41620 }{AT3g57350 } 1
+ 11729 5 {At2g41640 }{AT3g57380 } 1
+ 11730 13 {At2g41740 }{AT3g57410 } 1
+ 11731 4 {At2g41770 }{AT3g57420 } 1
+ 11732 7 {At2g41790 }{AT3g57470 } 1
+ 11735 6 {At2g41840 }{AT3g57490 } 1
+ 11738 3 {At2g41850 }{AT3g57510 } 1
+ 11740 3 {At2g41860 }{AT3g57530 } 1
+ 11741 2 {At2g41870 }{AT3g57540 } 1
+ 11742 2 {At2g41880 }{AT3g57550 } 1
+
+
+-block 235
+ points contig1 contig2
+ 16 2 3
+
+ point dist markers orientation
+ 11877 0 {At2g45440 }{AT3g60880 } 1
+ 11878 5 {At2g45470 }{AT3g60900 } 1
+ 11879 9 {At2g45540 }{AT3g60920 } 1
+ 11881 12 {At2g45550 At2g45560 At2g45570 At2g45580 }{AT3g61040 } 1
+ 11882 18 {At2g45740 }{AT3g61070 } -1
+ 11883 22 {At2g45800 }{AT3g61230 } 1
+ 11884 2 {At2g45810 }{AT3g61240 } 1
+ 11887 5 {At2g45830 At2g45840 }{AT3g61270 AT3g61280 AT3g61290 } 1
+ 11888 3 {At2g45850 }{AT3g61310 } 1
+ 11889 3 {At2g45870 }{AT3g61320 } 1
+ 11892 20 {At2g45960 }{AT3g61430 } 1
+ 11895 25 {At2g46110 }{AT3g61530 } 1
+ 11897 10 {At2g46180 }{AT3g61570 } 1
+ 11898 4 {At2g46210 }{AT3g61580 } 1
+ 11899 7 {At2g46260 }{AT3g61600 } 1
+ 11900 18 {At2g46380 }{AT3g61670 } 1
+
+
+-block 236
+ points contig1 contig2
+ 15 2 3
+
+ point dist markers orientation
+ 11462 0 {At2g35840 }{AT3g52340 } 1
+ 11465 5 {At2g35860 }{AT3g52370 } 1
+ 11467 15 {At2g35930 }{AT3g52450 } 1
+ 11470 5 {At2g35960 At2g35970 }{AT3g52470 } 1
+ 11471 18 {At2g36060 }{AT3g52560 } 1
+ 11474 10 {At2g36160 }{AT3g52580 } 1
+ 11475 2 {At2g36170 }{AT3g52590 } 1
+ 11477 3 {At2g36190 }{AT3g52600 } 1
+ 11479 19 {At2g36250 }{AT3g52750 } 1
+ 11482 5 {At2g36300 }{AT3g52760 } 1
+ 11487 16 {At2g36350 }{AT3g52890 } 1
+ 11491 15 {At2g36460 }{AT3g52930 } 1
+ 11492 6 {At2g36500 }{AT3g52950 } 1
+ 11493 9 {At2g36580 }{AT3g52990 } 1
+ 11495 6 {At2g36620 }{AT3g53020 } 1
+
+
+-block 237
+ points contig1 contig2
+ 14 2 3
+
+ point dist markers orientation
+ 11905 0 {At2g46530 }{AT3g61830 } 1
+ 11907 18 {At2g46660 }{AT3g61880 } 1
+ 11908 3 {At2g46680 }{AT3g61890 } 1
+ 11915 9 {At2g46770 }{AT3g61910 } 1
+ 11917 6 {At2g46800 }{AT3g61940 } 1
+ 11922 24 {At2g46930 }{AT3g62060 } 1
+ 11924 9 {At2g46990 }{AT3g62100 } 1
+ 11928 6 {At2g47000 }{AT3g62150 } 1
+ 11929 5 {At2g47030 At2g47040 }{AT3g62170 } 1
+ 11930 2 {At2g47050 }{AT3g62180 } 1
+ 11933 4 {At2g47060 }{AT3g62220 } 1
+ 11937 12 {At2g47160 }{AT3g62270 } 1
+ 11940 3 {At2g47170 }{AT3g62290 } 1
+ 11945 10 {At2g47250 }{AT3g62310 } 1
+
+
+-block 238
+ points contig1 contig2
+ 10 2 3
+
+ point dist markers orientation
+ 11766 0 {At2g42500 }{AT3g58500 } 1
+ 11767 3 {At2g42520 }{AT3g58510 AT3g58570 } 1
+ 11770 15 {At2g42580 }{AT3g58620 } 1
+ 11774 7 {At2g42630 }{AT3g58640 } 1
+ 11775 4 {At2g42650 }{AT3g58660 } 1
+ 11776 3 {At2g42670 }{AT3g58670 } 1
+ 11777 2 {At2g42680 }{AT3g58680 } 1
+ 11778 8 {At2g42740 }{AT3g58700 } 1
+ 11779 9 {At2g42790 }{AT3g58740 AT3g58750 } 1
+ 11780 7 {At2g42830 }{AT3g58780 } 1
+
+
+-block 239
+ points contig1 contig2
+ 8 2 3
+
+ point dist markers orientation
+ 11959 0 {At2g47610 }{AT3g62870 } -1
+ 11961 3 {At2g47630 }{AT3g62860 } -1
+ 11962 3 {At2g47640 }{AT3g62840 } -1
+ 11965 2 {At2g47650 }{AT3g62830 } -1
+ 11966 3 {At2g47670 }{AT3g62820 } -1
+ 11967 5 {At2g47690 }{AT3g62790 } -1
+ 11968 7 {At2g47730 }{AT3g62760 } -1
+ 11974 11 {At2g47800 }{AT3g62700 } -1
+
+
+-block 240
+ points contig1 contig2
+ 7 2 3
+
+ point dist markers orientation
+ 10717 0 {At2g07420 At2g07450 At2g07550 }{AT3g30630 AT3g30655 } 1
+ 10732 16 {At2g07650 At2g07670 At2g07730 At2g07740 }{AT3g30570 } -1
+ 10741 15 {At2g09960 }{AT3g30550 } -1
+ 10745 23 {At2g10140 }{AT3g30680 } -1
+ 10757 19 {At2g10620 At2g10660 At2g10670 At2g10690 At2g10700 At2g10780 }{AT3g30630 AT3g30655 } -1
+ 10755 6 {At2g10630 }{AT3g30680 } -1
+ 10766 25 {At2g11110 }{AT3g30780 AT3g30790 } 1
+
+
+-block 241
+ points contig1 contig2
+ 7 2 3
+
+ point dist markers orientation
+ 11679 0 {At2g40720 }{AT3g56550 } -1
+ 11680 20 {At2g40800 }{AT3g56430 } 1
+ 11681 2 {At2g40810 }{AT3g56440 } 1
+ 11683 5 {At2g40820 }{AT3g56480 } 1
+ 11684 15 {At2g40850 }{AT3g56600 } 1
+ 11686 7 {At2g40900 }{AT3g56620 } 1
+ 11688 12 {At2g40960 }{AT3g56680 } 1
+
+
+-block 242
+ points contig1 contig2
+ 5 2 3
+
+ point dist markers orientation
+ 10624 0 {At2g04950 At2g05010 }{AT3g47280 AT3g47310 } -1
+ 10626 2 {At2g04960 At2g04970 }{AT3g47270 } -1
+ 10631 2 {At2g04980 }{AT3g47260 } -1
+ 10632 6 {At2g04990 }{AT3g47330 } -1
+ 10633 2 {At2g05000 }{AT3g47320 } -1
+
+
+-block 243
+ points contig1 contig2
+ 5 2 3
+
+ point dist markers orientation
+ 10692 0 {At2g06610 At2g06690 }{AT3g42620 } -1
+ 10693 2 {At2g06620 At2g06700 }{AT3g42610 } -1
+ 10695 2 {At2g06630 At2g06640 }{AT3g42580 AT3g42590 AT3g42600 } -1
+ 10697 13 {At2g06720 At2g06800 }{AT3g42720 } 1
+ 10698 13 {At2g06750 }{AT3g42580 AT3g42590 AT3g42600 } -1
+
+
+-block 244
+ points contig1 contig2
+ 5 2 3
+
+ point dist markers orientation
+ 10774 0 {At2g11940 }{AT3g31530 } -1
+ 10783 15 {At2g12210 At2g12220 At2g12390 }{AT3g31920 } -1
+ 10790 21 {At2g12870 }{AT3g31520 } -1
+ 10792 5 {At2g12920 At2g13210 }{AT3g31530 } -1
+ 10801 21 {At2g13250 At2g13260 }{AT3g32000 AT3g32010 } -1
+
+
+-block 245
+ points contig1 contig2
+ 5 2 3
+
+ point dist markers orientation
+ 10877 0 {At2g14770 }{AT3g33010 } -1
+ 10884 22 {At2g14970 At2g14980 At2g15070 }{AT3g32950 } 1
+ 10892 17 {At2g15140 At2g15190 }{AT3g32900 } 1
+ 10898 5 {At2g15200 }{AT3g32910 } 1
+ 10903 19 {At2g15380 }{AT3g32360 } -1
+
+
+-block 246
+ points contig1 contig2
+ 5 2 3
+
+ point dist markers orientation
+ 11643 0 {At2g40010 }{AT3g11250 } -1
+ 11647 12 {At2g40110 }{AT3g11230 } 1
+ 11651 22 {At2g40150 At2g40160 }{AT3g11030 } -1
+ 11657 16 {At2g40300 }{AT3g11050 } -1
+ 11660 4 {At2g40320 }{AT3g11030 } -1
+
+
+-block 247
+ points contig1 contig2
+ 5 2 3
+
+ point dist markers orientation
+ 11789 0 {At2g42960 }{AT3g59110 } -1
+ 11790 4 {At2g42980 }{AT3g59080 } -1
+ 11791 7 {At2g43020 }{AT3g59050 } -1
+ 11795 7 {At2g43050 }{AT3g59010 } -1
+ 11796 5 {At2g43090 At2g43100 }{AT3g58990 } -1
+
+
+-block 248
+ points contig1 contig2
+ 5 2 3
+
+ point dist markers orientation
+ 11865 0 {At2g45080 }{AT3g60550 } 1
+ 11867 10 {At2g45140 }{AT3g60600 } 1
+ 11868 3 {At2g45150 }{AT3g60620 } 1
+ 11869 4 {At2g45170 }{AT3g60640 } 1
+ 11874 23 {At2g45290 }{AT3g60750 } 1
+
+
+-block 249
+ points contig1 contig2
+ 4 2 3
+
+ point dist markers orientation
+ 10726 0 {At2g07620 At2g07630 }{AT3g31980 } 1
+ 10733 14 {At2g07650 At2g07670 At2g07730 At2g07740 }{AT3g32110 } -1
+ 10736 14 {At2g07660 }{AT3g31970 } 1
+ 10744 20 {At2g10000 At2g10010 }{AT3g31920 } 1
+
+
+-block 250
+ points contig1 contig2
+ 4 2 3
+
+ point dist markers orientation
+ 10779 0 {At2g12100 At2g12110 At2g12120 At2g12130 }{AT3g42610 } 1
+ 10780 2 {At2g12140 }{AT3g42620 } 1
+ 10786 16 {At2g12240 At2g12250 At2g12300 }{AT3g42720 } 1
+ 10798 25 {At2g13000 At2g13160 At2g13310 }{AT3g42650 } 1
+
+
+-block 251
+ points contig1 contig2
+ 4 2 3
+
+ point dist markers orientation
+ 10787 0 {At2g12520 }{AT3g30810 } -1
+ 10793 13 {At2g13000 At2g13160 At2g13310 }{AT3g30780 AT3g30790 } 1
+ 10796 4 {At2g13070 }{AT3g30810 } 1
+ 10800 21 {At2g13250 At2g13260 }{AT3g30630 AT3g30655 } 1
+
+
+-block 252
+ points contig1 contig2
+ 4 2 3
+
+ point dist markers orientation
+ 10966 0 {At2g17790 }{AT3g51310 } -1
+ 10968 2 {At2g17800 }{AT3g51300 } 1
+ 10969 8 {At2g17840 }{AT3g51250 } -1
+ 10975 24 {At2g18020 }{AT3g51190 } -1
+
+
+-block 253
+ points contig1 contig2
+ 4 2 3
+
+ point dist markers orientation
+ 11106 0 {At2g23480 }{AT3g32080 } -1
+ 11108 2 {At2g23490 }{AT3g32070 } -1
+ 11110 2 {At2g23500 }{AT3g32060 } -1
+ 11122 25 {At2g23800 }{AT3g32040 } 1
+
+
+-block 254
+ points contig1 contig2
+ 4 2 3
+
+ point dist markers orientation
+ 11276 0 {At2g28530 }{AT3g45630 } -1
+ 11282 24 {At2g28620 }{AT3g45850 } 1
+ 11286 22 {At2g28720 }{AT3g45980 AT3g46030 } -1
+ 11300 24 {At2g28960 At2g28970 At2g28990 At2g29000 }{AT3g45920 } -1
+
+
+-block 255
+ points contig1 contig2
+ 4 2 3
+
+ point dist markers orientation
+ 11757 0 {At2g42230 }{AT3g57890 } -1
+ 11760 12 {At2g42290 }{AT3g57830 } -1
+ 11761 6 {At2g42310 }{AT3g57790 } -1
+ 11763 2 {At2g42320 }{AT3g57780 } -1
+
+
+-block 256
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 10553 0 {At2g02190 }{AT3g47280 AT3g47310 } -1
+ 10555 2 {At2g02200 }{AT3g47270 } -1
+ 10556 2 {At2g02210 }{AT3g47260 } -1
+
+
+-block 257
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 10573 0 {At2g03090 }{AT3g29030 } 1
+ 10575 17 {At2g03240 At2g03250 At2g03260 }{AT3g29060 } 1
+ 10577 4 {At2g03290 }{AT3g29070 } 1
+
+
+-block 258
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 10603 0 {At2g04310 }{AT3g32060 } 1
+ 10605 2 {At2g04320 }{AT3g32070 } 1
+ 10607 2 {At2g04330 }{AT3g32080 } 1
+
+
+-block 259
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 10604 0 {At2g04320 }{AT3g29700 } 1
+ 10606 2 {At2g04330 }{AT3g29710 } 1
+ 10610 19 {At2g04460 }{AT3g29782 } -1
+
+
+-block 260
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 10625 0 {At2g04960 At2g04970 }{AT3g30450 } -1
+ 10629 2 {At2g04980 }{AT3g30440 } -1
+ 10640 19 {At2g05080 }{AT3g30560 } -1
+
+
+-block 261
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 10653 0 {At2g05450 At2g05460 At2g05470 At2g05560 }{AT3g42580 AT3g42590 AT3g42600 } 1
+ 10655 3 {At2g05480 }{AT3g42620 } 1
+ 10661 12 {At2g05490 At2g05570 }{AT3g42760 } 1
+
+
+-block 262
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 10654 0 {At2g05450 At2g05460 At2g05470 At2g05560 }{AT3g43380 AT3g43390 } -1
+ 10657 3 {At2g05490 At2g05570 }{AT3g43360 AT3g43370 } -1
+ 10658 9 {At2g05550 }{AT3g43320 } 1
+
+
+-block 263
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 10679 0 {At2g06150 }{AT3g32210 } 1
+ 10683 16 {At2g06160 At2g06310 At2g06320 At2g06330 }{AT3g32880 AT3g32890 AT3g32970 } 1
+ 10688 12 {At2g06430 }{AT3g32900 } 1
+
+
+-block 264
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 10819 0 {At2g13870 }{AT3g30780 AT3g30790 } -1
+ 10827 11 {At2g14000 }{AT3g30820 } -1
+ 10832 13 {At2g14040 }{AT3g31340 } -1
+
+
+-block 265
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 10828 0 {At2g14000 }{AT3g44570 } -1
+ 10837 21 {At2g14080 }{AT3g44400 AT3g44410 AT3g44480 } -1
+ 10846 13 {At2g14130 }{AT3g44500 } 1
+
+
+-block 266
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 10844 0 {At2g14130 }{AT3g30440 } 1
+ 10848 2 {At2g14140 }{AT3g30450 } 1
+ 10854 21 {At2g14300 }{AT3g30560 } -1
+
+
+-block 267
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 10845 0 {At2g14130 }{AT3g32900 } 1
+ 10849 2 {At2g14140 }{AT3g32910 } 1
+ 10855 18 {At2g14300 }{AT3g32320 } 1
+
+
+-block 268
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 10894 0 {At2g15140 At2g15190 }{AT3g47260 } 1
+ 10895 3 {At2g15150 At2g15210 }{AT3g47280 AT3g47310 } 1
+ 10899 4 {At2g15200 }{AT3g47270 } 1
+
+
+-block 269
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 10933 0 {At2g16720 }{AT3g13540 } -1
+ 10935 25 {At2g16730 }{AT3g13750 } -1
+ 10937 24 {At2g16740 }{AT3g13550 } -1
+
+
+-block 270
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 11158 0 {At2g24900 }{AT3g30500 } -1
+ 11159 2 {At2g24910 }{AT3g30490 } -1
+ 11160 3 {At2g24920 }{AT3g30470 } -1
+
+
+-block 271
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 11287 0 {At2g28760 }{AT3g46440 } 1
+ 11290 11 {At2g28830 }{AT3g46510 } 1
+ 11305 25 {At2g29060 }{AT3g46600 } 1
+
+
+-block 272
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 11545 0 {At2g37640 }{AT3g55500 } 1
+ 11550 12 {At2g37710 }{AT3g55550 } 1
+ 11556 23 {At2g37890 }{AT3g55640 } -1
+
+
+-block 273
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 11561 0 {At2g38110 }{AT3g11320 } 1
+ 11566 17 {At2g38180 }{AT3g11210 } -1
+ 11568 7 {At2g38240 }{AT3g11180 } -1
+
+
+-block 274
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 11577 0 {At2g38620 }{AT3g54180 } 1
+ 11578 2 {At2g38630 }{AT3g54190 } 1
+ 11580 13 {At2g38700 }{AT3g54250 } 1
+
+
+-block 275
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 11744 0 {At2g41960 }{AT3g58050 } -1
+ 11749 3 {At2g41980 }{AT3g58040 } -1
+ 11751 5 {At2g42030 }{AT3g58030 } -1
+
+
+-block 276
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 11768 0 {At2g42570 }{AT3g14850 } -1
+ 11769 11 {At2g42580 }{AT3g14950 } -1
+ 11772 3 {At2g42600 }{AT3g14940 } -1
+
+
+-block 277
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 11798 0 {At2g43160 }{AT3g59290 } 1
+ 11806 11 {At2g43230 }{AT3g59350 } 1
+ 11808 2 {At2g43240 }{AT3g59360 } 1
+
+
+-block 278
+ points contig1 contig2
+ 3 2 3
+
+ point dist markers orientation
+ 11976 0 {At2g47870 }{AT3g62950 } 1
+ 11977 2 {At2g47880 }{AT3g62960 } 1
+ 11978 13 {At2g47970 }{AT3g63000 } 1
+
+
+-block 279
+ points contig1 contig2
+ 60 2 4
+
+ point dist markers orientation
+ 12329 0 {At2g16090 }{AT4g34370 } -1
+ 12336 22 {At2g16230 }{AT4g34480 } 1
+ 12339 7 {At2g16280 }{AT4g34510 AT4g34520 } 1
+ 12340 11 {At2g16370 }{AT4g34570 } 1
+ 12341 2 {At2g16380 }{AT4g34580 } 1
+ 12345 23 {At2g16500 }{AT4g34710 } 1
+ 12346 2 {At2g16510 }{AT4g34720 } 1
+ 12348 6 {At2g16570 }{AT4g34740 } 1
+ 12350 16 {At2g16600 }{AT4g34870 AT4g34960 } 1
+ 12354 12 {At2g16660 }{AT4g34950 } 1
+ 12358 4 {At2g16700 }{AT4g34970 } 1
+ 12360 4 {At2g16720 }{AT4g34990 } 1
+ 12362 3 {At2g16730 }{AT4g35010 } 1
+ 12365 4 {At2g16750 }{AT4g35030 } 1
+ 12366 5 {At2g16780 }{AT4g35050 } 1
+ 12367 5 {At2g16800 }{AT4g35080 } 1
+ 12370 7 {At2g16850 }{AT4g35100 } 1
+ 12372 6 {At2g16900 }{AT4g35110 } 1
+ 12376 21 {At2g17070 At2g17080 }{AT4g35200 AT4g35210 } 1
+ 12377 3 {At2g17090 }{AT4g35230 } 1
+ 12378 2 {At2g17100 }{AT4g35240 } 1
+ 12379 4 {At2g17130 }{AT4g35260 } 1
+ 12381 3 {At2g17150 }{AT4g35270 } 1
+ 12383 12 {At2g17260 }{AT4g35290 } 1
+ 12387 6 {At2g17290 }{AT4g35310 } 1
+ 12389 18 {At2g17380 }{AT4g35410 } 1
+ 12390 4 {At2g17390 }{AT4g35450 } 1
+ 12391 4 {At2g17420 }{AT4g35460 } 1
+ 12393 3 {At2g17440 }{AT4g35470 } 1
+ 12395 10 {At2g17530 }{AT4g35500 } 1
+ 12397 20 {At2g17620 }{AT4g35620 } 1
+ 12398 2 {At2g17630 }{AT4g35630 } 1
+ 12399 2 {At2g17640 }{AT4g35640 } 1
+ 12401 20 {At2g17700 }{AT4g35780 } 1
+ 12403 5 {At2g17720 }{AT4g35810 } 1
+ 12404 11 {At2g17760 }{AT4g35880 } 1
+ 12405 6 {At2g17780 }{AT4g35920 } 1
+ 12408 5 {At2g17800 }{AT4g35950 } -1
+ 12409 6 {At2g17840 }{AT4g35980 } 1
+ 12410 5 {At2g17860 }{AT4g36010 } 1
+ 12413 9 {At2g17890 }{AT4g36070 } 1
+ 12416 5 {At2g17930 }{AT4g36080 } 1
+ 12417 5 {At2g17970 }{AT4g36090 } 1
+ 12419 9 {At2g18020 }{AT4g36130 } 1
+ 12421 7 {At2g18060 }{AT4g36160 } 1
+ 12422 5 {At2g18080 }{AT4g36190 } 1
+ 12423 4 {At2g18100 }{AT4g36210 } 1
+ 12424 11 {At2g18130 }{AT4g36350 } 1
+ 12426 9 {At2g18140 At2g18150 }{AT4g36430 } 1
+ 12429 4 {At2g18170 }{AT4g36450 } 1
+ 12431 5 {At2g18180 }{AT4g36490 } -1
+ 12434 23 {At2g18330 }{AT4g36580 } 1
+ 12435 6 {At2g18360 }{AT4g36610 } 1
+ 12438 17 {At2g18480 }{AT4g36670 } 1
+ 12439 5 {At2g18520 }{AT4g36680 } 1
+ 12440 4 {At2g18540 }{AT4g36700 } 1
+ 12441 5 {At2g18550 }{AT4g36740 } 1
+ 12442 8 {At2g18590 }{AT4g36790 } 1
+ 12443 2 {At2g18600 }{AT4g36800 } 1
+ 12444 3 {At2g18620 At2g18640 }{AT4g36810 } 1
+
+
+-block 280
+ points contig1 contig2
+ 28 2 4
+
+ point dist markers orientation
+ 12682 0 {At2g23910 }{AT4g30470 } 1
+ 12683 6 {At2g23940 }{AT4g30500 } 1
+ 12684 3 {At2g23950 }{AT4g30520 } 1
+ 12686 2 {At2g23960 At2g23970 }{AT4g30530 AT4g30540 AT4g30550 } 1
+ 12688 2 {At2g23980 }{AT4g30560 } 1
+ 12689 7 {At2g24000 At2g24010 }{AT4g30610 } 1
+ 12691 2 {At2g24020 }{AT4g30620 } 1
+ 12692 9 {At2g24050 }{AT4g30680 } 1
+ 12693 14 {At2g24100 }{AT4g30780 } 1
+ 12694 11 {At2g24150 }{AT4g30850 } 1
+ 12697 11 {At2g24200 }{AT4g30910 AT4g30920 } 1
+ 12699 6 {At2g24240 }{AT4g30940 } 1
+ 12700 10 {At2g24290 }{AT4g30990 } 1
+ 12702 2 {At2g24300 }{AT4g31000 } 1
+ 12704 4 {At2g24320 }{AT4g31020 } 1
+ 12705 8 {At2g24330 }{AT4g31090 } -1
+ 12706 10 {At2g24360 }{AT4g31170 } 1
+ 12709 6 {At2g24370 }{AT4g31220 AT4g31230 } 1
+ 12710 15 {At2g24420 }{AT4g31340 } 1
+ 12711 6 {At2g24450 }{AT4g31370 } 1
+ 12712 10 {At2g24500 }{AT4g31420 } 1
+ 12715 5 {At2g24530 }{AT4g31440 } 1
+ 12716 14 {At2g24570 }{AT4g31550 } 1
+ 12720 10 {At2g24630 }{AT4g31590 } 1
+ 12722 7 {At2g24640 }{AT4g31670 } 1
+ 12729 7 {At2g24700 }{AT4g31640 AT4g31650 AT4g31660 AT4g31680 AT4g31690 } -1
+ 12730 4 {At2g24710 At2g24720 }{AT4g31710 } -1
+ 12731 9 {At2g24800 }{AT4g31760 } 1
+
+
+-block 281
+ points contig1 contig2
+ 23 2 4
+
+ point dist markers orientation
+ 12556 0 {At2g21120 }{AT4g38730 } 1
+ 12558 2 {At2g21130 }{AT4g38740 } 1
+ 12559 11 {At2g21190 }{AT4g38790 } 1
+ 12560 21 {At2g21270 }{AT4g38930 } 1
+ 12562 5 {At2g21300 }{AT4g38950 } 1
+ 12565 3 {At2g21320 }{AT4g38960 } 1
+ 12566 2 {At2g21330 }{AT4g38970 } 1
+ 12567 5 {At2g21340 }{AT4g39030 } 1
+ 12568 5 {At2g21380 }{AT4g39050 } 1
+ 12569 6 {At2g21410 }{AT4g39080 } 1
+ 12571 3 {At2g21430 }{AT4g39090 } 1
+ 12576 7 {At2g21480 }{AT4g39110 } 1
+ 12577 5 {At2g21500 }{AT4g39140 } 1
+ 12578 2 {At2g21510 }{AT4g39150 } 1
+ 12581 3 {At2g21520 At2g21540 }{AT4g39170 AT4g39180 } 1
+ 12583 8 {At2g21590 }{AT4g39210 } 1
+ 12584 2 {At2g21600 }{AT4g39220 } 1
+ 12588 21 {At2g21730 }{AT4g39330 } 1
+ 12589 2 {At2g21740 At2g21750 }{AT4g39340 } 1
+ 12592 2 {At2g21770 }{AT4g39350 } 1
+ 12596 13 {At2g21890 }{AT4g39330 } 1
+ 12598 17 {At2g21910 }{AT4g39480 AT4g39490 AT4g39500 AT4g39510 } 1
+ 12599 18 {At2g21990 }{AT4g39610 } 1
+
+
+-block 282
+ points contig1 contig2
+ 20 2 4
+
+ point dist markers orientation
+ 12446 0 {At2g18650 }{AT4g30400 } -1
+ 12449 13 {At2g18730 }{AT4g30340 } -1
+ 12458 12 {At2g18800 }{AT4g30270 AT4g30280 AT4g30290 } -1
+ 12460 5 {At2g18840 }{AT4g30260 } -1
+ 12462 19 {At2g18960 }{AT4g30190 } -1
+ 12463 4 {At2g18980 }{AT4g30170 } -1
+ 12465 6 {At2g19010 At2g19050 At2g19060 }{AT4g30140 } -1
+ 12466 7 {At2g19090 }{AT4g30130 } -1
+ 12468 3 {At2g19110 }{AT4g30110 AT4g30120 } -1
+ 12469 2 {At2g19120 }{AT4g30100 } -1
+ 12472 8 {At2g19160 }{AT4g30060 } -1
+ 12475 5 {At2g19170 }{AT4g30020 } -1
+ 12477 5 {At2g19190 At2g19210 At2g19230 }{AT4g29990 } 1
+ 12478 7 {At2g19240 }{AT4g29950 } -1
+ 12481 16 {At2g19330 }{AT4g29880 } -1
+ 12482 2 {At2g19340 }{AT4g29870 } -1
+ 12483 3 {At2g19350 }{AT4g29850 } -1
+ 12484 10 {At2g19390 }{AT4g29790 } -1
+ 12494 15 {At2g19500 }{AT4g29740 } -1
+ 12495 3 {At2g19520 }{AT4g29730 } -1
+
+
+-block 283
+ points contig1 contig2
+ 18 2 4
+
+ point dist markers orientation
+ 12741 0 {At2g25060 }{AT4g31840 } 1
+ 12742 3 {At2g25070 }{AT4g31860 } 1
+ 12744 2 {At2g25080 }{AT4g31870 } 1
+ 12746 7 {At2g25130 }{AT4g31890 } 1
+ 12748 5 {At2g25170 }{AT4g31900 } 1
+ 12749 3 {At2g25180 }{AT4g31920 } 1
+ 12750 5 {At2g25190 }{AT4g31980 } 1
+ 12751 5 {At2g25220 }{AT4g32000 } 1
+ 12752 14 {At2g25290 }{AT4g32070 } 1
+ 12753 4 {At2g25300 }{AT4g32110 AT4g32120 } 1
+ 12754 6 {At2g25340 }{AT4g32150 } 1
+ 12755 2 {At2g25350 }{AT4g32160 } 1
+ 12756 16 {At2g25430 }{AT4g32280 } 1
+ 12757 19 {At2g25520 }{AT4g32390 } 1
+ 12759 4 {At2g25540 }{AT4g32410 } 1
+ 12764 8 {At2g25580 }{AT4g32450 } 1
+ 12766 7 {At2g25600 }{AT4g32500 } 1
+ 12768 4 {At2g25610 }{AT4g32530 } 1
+
+
+-block 284
+ points contig1 contig2
+ 14 2 4
+
+ point dist markers orientation
+ 12622 0 {At2g22620 }{AT4g37950 AT4g37960 AT4g38030 } -1
+ 12623 2 {At2g22630 }{AT4g37940 } -1
+ 12624 7 {At2g22660 }{AT4g37900 } -1
+ 12628 25 {At2g22800 }{AT4g37790 } -1
+ 12631 3 {At2g22810 }{AT4g37770 } -1
+ 12632 3 {At2g22830 }{AT4g37760 } -1
+ 12635 14 {At2g22900 }{AT4g37690 } -1
+ 12636 3 {At2g22910 }{AT4g37670 } -1
+ 12640 7 {At2g22950 }{AT4g37640 } -1
+ 12642 10 {At2g23060 }{AT4g37580 } -1
+ 12645 24 {At2g23170 }{AT4g37390 } -1
+ 12648 4 {At2g23190 At2g23220 }{AT4g37310 AT4g37320 AT4g37330 AT4g37340 AT4g37360 AT4g37370 AT4g37400 AT4g37410 AT4g37430 } -1
+ 12652 12 {At2g23290 }{AT4g37260 } -1
+ 12653 2 {At2g23300 }{AT4g37250 } -1
+
+
+-block 285
+ points contig1 contig2
+ 11 2 4
+
+ point dist markers orientation
+ 12534 0 {At2g20530 }{AT4g28510 } -1
+ 12535 5 {At2g20550 At2g20560 }{AT4g28480 } -1
+ 12536 3 {At2g20580 }{AT4g28470 } -1
+ 12538 7 {At2g20610 }{AT4g28420 } -1
+ 12539 4 {At2g20630 }{AT4g28400 } -1
+ 12540 4 {At2g20650 }{AT4g28370 } -1
+ 12542 7 {At2g20680 }{AT4g28320 } -1
+ 12543 6 {At2g20700 }{AT4g28280 } -1
+ 12544 8 {At2g20750 }{AT4g28250 } -1
+ 12548 8 {At2g20800 }{AT4g28220 } -1
+ 12552 19 {At2g20900 }{AT4g28120 AT4g28130 } -1
+
+
+-block 286
+ points contig1 contig2
+ 10 2 4
+
+ point dist markers orientation
+ 12497 0 {At2g19670 }{AT4g29510 } -1
+ 12499 4 {At2g19680 }{AT4g29480 } -1
+ 12500 6 {At2g19710 }{AT4g29440 } -1
+ 12502 2 {At2g19720 }{AT4g29430 } -1
+ 12503 3 {At2g19730 }{AT4g29410 } -1
+ 12504 9 {At2g19760 At2g19770 }{AT4g29340 AT4g29350 } -1
+ 12506 10 {At2g19780 }{AT4g29240 } -1
+ 12508 8 {At2g19810 }{AT4g29190 } -1
+ 12509 5 {At2g19830 }{AT4g29160 } -1
+ 12513 6 {At2g19860 }{AT4g29130 } -1
+
+
+-block 287
+ points contig1 contig2
+ 9 2 4
+
+ point dist markers orientation
+ 12602 0 {At2g22170 }{AT4g39730 } -1
+ 12605 6 {At2g22190 }{AT4g39770 } 1
+ 12606 6 {At2g22240 }{AT4g39800 } 1
+ 12607 13 {At2g22290 }{AT4g39890 } 1
+ 12608 4 {At2g22310 }{AT4g39910 } 1
+ 12609 6 {At2g22330 }{AT4g39950 } 1
+ 12611 4 {At2g22360 }{AT4g39960 } 1
+ 12612 5 {At2g22390 }{AT4g39990 } 1
+ 12613 2 {At2g22400 }{AT4g40000 } 1
+
+
+-block 288
+ points contig1 contig2
+ 8 2 4
+
+ point dist markers orientation
+ 12184 0 {At2g11210 }{AT4g04140 } -1
+ 12185 15 {At2g11240 }{AT4g04000 } -1
+ 12189 24 {At2g11650 }{AT4g03880 } 1
+ 12198 23 {At2g12240 At2g12250 At2g12300 }{AT4g03900 AT4g03910 } -1
+ 12199 23 {At2g12520 }{AT4g04070 } 1
+ 12212 21 {At2g13000 At2g13160 At2g13310 }{AT4g04170 } -1
+ 12206 12 {At2g13070 }{AT4g04070 } -1
+ 12218 4 {At2g13230 At2g13330 }{AT4g04050 AT4g04060 } 1
+
+
+-block 289
+ points contig1 contig2
+ 3 2 4
+
+ point dist markers orientation
+ 12203 0 {At2g12870 }{AT4g03770 } 1
+ 12214 7 {At2g12920 At2g13210 }{AT4g03800 } 1
+ 12204 9 {At2g13000 At2g13160 At2g13310 }{AT4g03730 } 1
+
+
+-block 290
+ points contig1 contig2
+ 6 2 4
+
+ point dist markers orientation
+ 12102 0 {At2g06170 }{AT4g04230 } -1
+ 12103 17 {At2g06180 }{AT4g04070 } 1
+ 12109 15 {At2g06410 At2g06450 }{AT4g03980 } -1
+ 12108 5 {At2g06430 }{AT4g04010 } -1
+ 12110 15 {At2g06470 }{AT4g03840 } -1
+ 12117 16 {At2g06720 At2g06800 }{AT4g03900 AT4g03910 } -1
+
+
+-block 291
+ points contig1 contig2
+ 6 2 4
+
+ point dist markers orientation
+ 12233 0 {At2g13870 }{AT4g04170 } 1
+ 12235 16 {At2g13890 }{AT4g04310 } 1
+ 12238 5 {At2g13930 At2g13940 }{AT4g04280 AT4g04380 AT4g04440 } 1
+ 12244 21 {At2g14030 }{AT4g04140 } 1
+ 12251 22 {At2g14130 }{AT4g04010 } -1
+ 12252 3 {At2g14140 }{AT4g03990 } -1
+
+
+-block 292
+ points contig1 contig2
+ 6 2 4
+
+ point dist markers orientation
+ 12298 0 {At2g15100 }{AT4g03800 } -1
+ 12300 21 {At2g15140 At2g15190 }{AT4g04010 } -1
+ 12301 4 {At2g15150 At2g15210 }{AT4g03980 } -1
+ 12302 4 {At2g15200 }{AT4g03990 } -1
+ 12306 15 {At2g15380 }{AT4g04000 } 1
+ 12308 19 {At2g15410 }{AT4g03800 } -1
+
+
+-block 293
+ points contig1 contig2
+ 6 2 4
+
+ point dist markers orientation
+ 12962 0 {At2g34770 }{AT4g20870 } -1
+ 12963 5 {At2g34790 At2g34810 }{AT4g20800 AT4g20820 AT4g20830 AT4g20840 AT4g20860 } -1
+ 12964 21 {At2g34850 }{AT4g20460 } 1
+ 12965 9 {At2g34880 }{AT4g20400 } -1
+ 12967 9 {At2g34890 }{AT4g20320 } -1
+ 12968 24 {At2g34940 }{AT4g20110 } 1
+
+
+-block 294
+ points contig1 contig2
+ 6 2 4
+
+ point dist markers orientation
+ 13172 0 {At2g45750 }{AT4g00740 AT4g00750 } -1
+ 13176 14 {At2g45810 }{AT4g00660 } 1
+ 13177 22 {At2g45880 }{AT4g00490 } -1
+ 13179 4 {At2g45890 }{AT4g00460 } -1
+ 13181 10 {At2g45960 }{AT4g00430 } -1
+ 13184 7 {At2g45970 }{AT4g00360 } -1
+
+
+-block 295
+ points contig1 contig2
+ 5 2 4
+
+ point dist markers orientation
+ 12050 0 {At2g04770 }{AT4g03900 AT4g03910 } 1
+ 12058 25 {At2g04950 At2g05010 }{AT4g03980 } 1
+ 12059 2 {At2g04960 At2g04970 }{AT4g03990 } 1
+ 12060 3 {At2g04980 }{AT4g04010 } 1
+ 12066 16 {At2g05200 At2g05290 }{AT4g04000 } 1
+
+
+-block 296
+ points contig1 contig2
+ 5 2 4
+
+ point dist markers orientation
+ 12166 0 {At2g10140 }{AT4g03900 AT4g03910 } 1
+ 12168 8 {At2g10350 At2g10360 }{AT4g03970 } 1
+ 12176 13 {At2g10490 At2g10640 }{AT4g03900 AT4g03910 } 1
+ 12178 9 {At2g10620 At2g10660 At2g10670 At2g10690 At2g10700 At2g10780 }{AT4g03840 } 1
+ 12174 5 {At2g10630 }{AT4g03900 AT4g03910 } 1
+
+
+-block 297
+ points contig1 contig2
+ 5 2 4
+
+ point dist markers orientation
+ 12195 0 {At2g12210 At2g12220 At2g12390 }{AT4g07750 } 1
+ 12200 23 {At2g12520 }{AT4g07530 } 1
+ 12205 15 {At2g13020 }{AT4g07560 AT4g07570 AT4g07590 AT4g07600 AT4g07610 AT4g07620 AT4g07630 AT4g07640 AT4g07660 AT4g07680 } 1
+ 12207 4 {At2g13070 }{AT4g07530 } -1
+ 12215 7 {At2g13250 At2g13260 }{AT4g07560 AT4g07570 AT4g07590 AT4g07600 AT4g07610 AT4g07620 AT4g07630 AT4g07640 AT4g07660 AT4g07680 } 1
+
+
+-block 298
+ points contig1 contig2
+ 5 2 4
+
+ point dist markers orientation
+ 12347 0 {At2g16510 }{AT4g38920 } -1
+ 12349 8 {At2g16570 }{AT4g38880 } -1
+ 12351 17 {At2g16600 }{AT4g38740 } -1
+ 12361 22 {At2g16720 }{AT4g38620 } -1
+ 12363 4 {At2g16730 }{AT4g38590 } -1
+
+
+-block 299
+ points contig1 contig2
+ 5 2 4
+
+ point dist markers orientation
+ 12773 0 {At2g25850 }{AT4g32850 } -1
+ 12774 5 {At2g25880 }{AT4g32830 } -1
+ 12776 17 {At2g25940 }{AT4g32940 } 1
+ 12777 19 {At2g26080 }{AT4g33010 } 1
+ 12778 14 {At2g26190 }{AT4g33050 } 1
+
+
+-block 300
+ points contig1 contig2
+ 5 2 4
+
+ point dist markers orientation
+ 12985 0 {At2g35650 }{AT4g16590 } 1
+ 12986 20 {At2g35690 }{AT4g16760 } -1
+ 12987 17 {At2g35710 }{AT4g16600 } -1
+ 12988 12 {At2g35740 }{AT4g16480 AT4g16490 } -1
+ 12989 6 {At2g35760 }{AT4g16440 } -1
+
+
+-block 301
+ points contig1 contig2
+ 4 2 4
+
+ point dist markers orientation
+ 12123 0 {At2g06860 }{AT4g04390 } 1
+ 12135 16 {At2g07080 }{AT4g04420 } -1
+ 12137 13 {At2g07240 }{AT4g04390 } -1
+ 12149 24 {At2g07420 At2g07450 At2g07550 }{AT4g04280 AT4g04380 AT4g04440 } 1
+
+
+-block 302
+ points contig1 contig2
+ 4 2 4
+
+ point dist markers orientation
+ 12260 0 {At2g14410 }{AT4g07710 } -1
+ 12261 8 {At2g14430 }{AT4g07770 } 1
+ 12264 3 {At2g14450 At2g14470 }{AT4g07790 } 1
+ 12272 19 {At2g14640 At2g14650 }{AT4g07830 AT4g07850 } -1
+
+
+-block 303
+ points contig1 contig2
+ 4 2 4
+
+ point dist markers orientation
+ 12296 0 {At2g15090 }{AT4g34250 } 1
+ 12303 18 {At2g15300 }{AT4g34220 } -1
+ 12312 22 {At2g15480 At2g15490 }{AT4g34130 } -1
+ 12313 12 {At2g15530 }{AT4g34040 } -1
+
+
+-block 304
+ points contig1 contig2
+ 4 2 4
+
+ point dist markers orientation
+ 12519 0 {At2g20230 }{AT4g28770 } -1
+ 12520 2 {At2g20240 }{AT4g28760 } -1
+ 12521 10 {At2g20290 }{AT4g28710 } -1
+ 12524 8 {At2g20340 }{AT4g28680 } 1
+
+
+-block 305
+ points contig1 contig2
+ 4 2 4
+
+ point dist markers orientation
+ 12660 0 {At2g23420 }{AT4g36940 } 1
+ 12665 24 {At2g23520 }{AT4g37100 } 1
+ 12667 7 {At2g23550 At2g23560 At2g23570 At2g23580 At2g23610 At2g23620 }{AT4g37140 AT4g37150 } 1
+ 12669 3 {At2g23630 }{AT4g37160 } 1
+
+
+-block 306
+ points contig1 contig2
+ 4 2 4
+
+ point dist markers orientation
+ 12903 0 {At2g32220 }{AT4g15000 } 1
+ 12904 12 {At2g32250 }{AT4g15090 } 1
+ 12907 5 {At2g32260 }{AT4g15130 } 1
+ 12911 11 {At2g32290 }{AT4g15210 } 1
+
+
+-block 307
+ points contig1 contig2
+ 3 2 4
+
+ point dist markers orientation
+ 12032 0 {At2g04220 }{AT4g12690 } 1
+ 12034 5 {At2g04280 }{AT4g12700 } 1
+ 12037 17 {At2g04450 }{AT4g12720 } 1
+
+
+-block 308
+ points contig1 contig2
+ 3 2 4
+
+ point dist markers orientation
+ 12087 0 {At2g05860 }{AT4g07310 } -1
+ 12089 14 {At2g05880 }{AT4g07440 } 1
+ 12091 2 {At2g05890 }{AT4g07450 } 1
+
+
+-block 309
+ points contig1 contig2
+ 3 2 4
+
+ point dist markers orientation
+ 12099 0 {At2g06160 At2g06310 At2g06320 At2g06330 }{AT4g07560 AT4g07570 AT4g07590 AT4g07600 AT4g07610 AT4g07620 AT4g07630 AT4g07640 AT4g07660 AT4g07680 } 1
+ 12104 5 {At2g06180 }{AT4g07530 } 1
+ 12106 21 {At2g06190 }{AT4g07830 AT4g07850 } -1
+
+
+-block 310
+ points contig1 contig2
+ 3 2 4
+
+ point dist markers orientation
+ 12111 0 {At2g06470 }{AT4g10580 } 1
+ 12128 25 {At2g06840 At2g06950 At2g07010 }{AT4g10690 } 1
+ 12127 14 {At2g06890 }{AT4g10580 } -1
+
+
+-block 311
+ points contig1 contig2
+ 3 2 4
+
+ point dist markers orientation
+ 12167 0 {At2g10140 }{AT4g08000 AT4g08010 AT4g08020 } 1
+ 12173 17 {At2g10620 At2g10660 At2g10670 At2g10690 At2g10700 At2g10780 }{AT4g08050 AT4g08080 } -1
+ 12175 4 {At2g10630 }{AT4g08000 AT4g08010 AT4g08020 } 1
+
+
+-block 312
+ points contig1 contig2
+ 3 2 4
+
+ point dist markers orientation
+ 12229 0 {At2g13760 }{AT4g10230 } -1
+ 12237 24 {At2g13900 At2g13910 At2g13920 At2g13950 }{AT4g10370 } -1
+ 12240 8 {At2g13930 At2g13940 }{AT4g10460 } -1
+
+
+-block 313
+ points contig1 contig2
+ 3 2 4
+
+ point dist markers orientation
+ 12254 0 {At2g14230 }{AT4g04430 } 1
+ 12256 11 {At2g14350 At2g14360 }{AT4g04400 } 1
+ 12265 16 {At2g14450 At2g14470 }{AT4g04300 } -1
+
+
+-block 314
+ points contig1 contig2
+ 3 2 4
+
+ point dist markers orientation
+ 12267 0 {At2g14620 }{AT4g03210 } 1
+ 12269 11 {At2g14630 }{AT4g03310 } -1
+ 12279 13 {At2g14770 }{AT4g03300 } 1
+
+
+-block 315
+ points contig1 contig2
+ 3 2 4
+
+ point dist markers orientation
+ 12257 0 {At2g14380 At2g14400 }{AT4g03800 } 1
+ 12271 25 {At2g14640 At2g14650 }{AT4g03840 } 1
+ 12283 23 {At2g14780 At2g14790 }{AT4g03980 } -1
+
+
+-block 316
+ points contig1 contig2
+ 3 2 4
+
+ point dist markers orientation
+ 12461 0 {At2g18960 }{AT4g11730 } 1
+ 12467 14 {At2g19100 }{AT4g11710 } 1
+ 12479 18 {At2g19280 }{AT4g11690 } 1
+
+
+-block 317
+ points contig1 contig2
+ 3 2 4
+
+ point dist markers orientation
+ 12480 0 {At2g19330 }{AT4g26050 } 1
+ 12491 19 {At2g19470 }{AT4g26100 } 1
+ 12493 2 {At2g19480 }{AT4g26110 } 1
+
+
+-block 318
+ points contig1 contig2
+ 3 2 4
+
+ point dist markers orientation
+ 12619 0 {At2g22500 }{AT4g24570 } -1
+ 12620 7 {At2g22540 }{AT4g24540 } -1
+ 12621 18 {At2g22620 }{AT4g24430 } -1
+
+
+-block 319
+ points contig1 contig2
+ 3 2 4
+
+ point dist markers orientation
+ 12674 0 {At2g23760 }{AT4g36870 } -1
+ 12675 8 {At2g23790 }{AT4g36820 } -1
+ 12676 2 {At2g23800 }{AT4g36810 } -1
+
+
+-block 320
+ points contig1 contig2
+ 3 2 4
+
+ point dist markers orientation
+ 12734 0 {At2g24900 }{AT4g07690 } -1
+ 12735 15 {At2g24920 }{AT4g07470 } -1
+ 12737 10 {At2g24930 }{AT4g07560 AT4g07570 AT4g07590 AT4g07600 AT4g07610 AT4g07620 AT4g07630 AT4g07640 AT4g07660 AT4g07680 } 1
+
+
+-block 321
+ points contig1 contig2
+ 3 2 4
+
+ point dist markers orientation
+ 12785 0 {At2g26490 }{AT4g34380 } 1
+ 12790 21 {At2g26600 }{AT4g34480 } -1
+ 12793 7 {At2g26640 }{AT4g34510 AT4g34520 } 1
+
+
+-block 322
+ points contig1 contig2
+ 3 2 4
+
+ point dist markers orientation
+ 12932 0 {At2g33170 }{AT4g28650 } 1
+ 12935 13 {At2g33230 }{AT4g28720 } -1
+ 12937 2 {At2g33240 }{AT4g28710 } -1
+
+
+-block 323
+ points contig1 contig2
+ 3 2 4
+
+ point dist markers orientation
+ 12978 0 {At2g35210 }{AT4g17890 } 1
+ 12979 9 {At2g35260 }{AT4g17840 } -1
+ 12980 4 {At2g35270 }{AT4g17800 } -1
+
+
+-block 324
+ points contig1 contig2
+ 3 2 4
+
+ point dist markers orientation
+ 13159 0 {At2g45260 }{AT4g34080 } -1
+ 13166 18 {At2g45350 }{AT4g33990 } 1
+ 13167 11 {At2g45380 }{AT4g34070 } 1
+
+
+-block 325
+ points contig1 contig2
+ 3 2 4
+
+ point dist markers orientation
+ 13186 0 {At2g46070 }{AT4g11330 } -1
+ 13188 19 {At2g46170 }{AT4g11220 } -1
+ 13191 25 {At2g46340 }{AT4g11110 } -1
+
+
+-block 326
+ points contig1 contig2
+ 3 2 4
+
+ point dist markers orientation
+ 13190 0 {At2g46260 }{AT4g01160 } -1
+ 13192 18 {At2g46380 }{AT4g01090 } -1
+ 13193 13 {At2g46430 At2g46440 At2g46450 }{AT4g01010 } -1
+
+
+-block 327
+ points contig1 contig2
+ 7 2 5
+
+ point dist markers orientation
+ 13678 0 {At2g23060 }{AT5g67430 } -1
+ 13679 6 {At2g23070 At2g23080 }{AT5g67380 } 1
+ 13682 10 {At2g23140 }{AT5g67340 } -1
+ 13683 2 {At2g23150 }{AT5g67330 } -1
+ 13690 6 {At2g23190 At2g23220 }{AT5g67310 } -1
+ 13694 8 {At2g23290 }{AT5g67300 } -1
+ 13695 3 {At2g23300 }{AT5g67280 } -1
+
+
+-block 328
+ points contig1 contig2
+ 7 2 5
+
+ point dist markers orientation
+ 14094 0 {At2g37470 }{AT5g02570 } -1
+ 14097 10 {At2g37540 }{AT5g02540 } -1
+ 14099 8 {At2g37570 }{AT5g02480 } -1
+ 14102 6 {At2g37600 }{AT5g02450 } -1
+ 14105 20 {At2g37640 }{AT5g02260 } -1
+ 14109 4 {At2g37660 }{AT5g02240 } -1
+ 14110 17 {At2g37670 }{AT5g02430 } -1
+
+
+-block 329
+ points contig1 contig2
+ 6 2 5
+
+ point dist markers orientation
+ 14120 0 {At2g37980 }{AT5g01100 } 1
+ 14124 16 {At2g38080 }{AT5g01190 } 1
+ 14131 9 {At2g38120 }{AT5g01240 } 1
+ 14132 4 {At2g38150 }{AT5g01250 } 1
+ 14133 25 {At2g38170 }{AT5g01490 } -1
+ 14134 13 {At2g38230 }{AT5g01410 } -1
+
+
+-block 330
+ points contig1 contig2
+ 4 2 5
+
+ point dist markers orientation
+ 13516 0 {At2g17890 }{AT5g66210 } 1
+ 13518 14 {At2g17990 }{AT5g66250 } 1
+ 13520 12 {At2g18060 }{AT5g66300 } 1
+ 13523 17 {At2g18140 At2g18150 }{AT5g66390 } 1
+
+
+-block 331
+ points contig1 contig2
+ 4 2 5
+
+ point dist markers orientation
+ 13531 0 {At2g18730 }{AT5g57690 } -1
+ 13532 15 {At2g18750 }{AT5g57580 } -1
+ 13536 7 {At2g18800 }{AT5g57530 AT5g57540 AT5g57550 AT5g57560 } -1
+ 13540 22 {At2g18890 }{AT5g57670 } -1
+
+
+-block 332
+ points contig1 contig2
+ 4 2 5
+
+ point dist markers orientation
+ 13634 0 {At2g22190 }{AT5g10100 } -1
+ 13637 8 {At2g22230 }{AT5g10160 } 1
+ 13638 2 {At2g22240 }{AT5g10170 } 1
+ 13639 12 {At2g22290 }{AT5g10260 } 1
+
+
+-block 333
+ points contig1 contig2
+ 4 2 5
+
+ point dist markers orientation
+ 13697 0 {At2g23450 }{AT5g66790 } -1
+ 13699 21 {At2g23520 }{AT5g66950 } -1
+ 13701 8 {At2g23630 }{AT5g66920 } -1
+ 13702 5 {At2g23660 }{AT5g66870 } -1
+
+
+-block 334
+ points contig1 contig2
+ 4 2 5
+
+ point dist markers orientation
+ 13827 0 {At2g27040 }{AT5g21030 } 1
+ 13830 10 {At2g27050 }{AT5g21120 } 1
+ 13832 4 {At2g27080 }{AT5g21130 } 1
+ 13833 24 {At2g27150 }{AT5g20960 } 1
+
+
+-block 335
+ points contig1 contig2
+ 4 2 5
+
+ point dist markers orientation
+ 14190 0 {At2g40100 }{AT5g01530 } 1
+ 14194 12 {At2g40150 At2g40160 }{AT5g01620 } 1
+ 14199 16 {At2g40300 }{AT5g01600 } 1
+ 14201 4 {At2g40320 }{AT5g01620 } 1
+
+
+-block 336
+ points contig1 contig2
+ 3 2 5
+
+ point dist markers orientation
+ 13743 0 {At2g24900 }{AT5g35040 } -1
+ 13744 3 {At2g24920 }{AT5g35030 } -1
+ 13748 22 {At2g24980 }{AT5g35190 } 1
+
+
+-block 337
+ points contig1 contig2
+ 3 2 5
+
+ point dist markers orientation
+ 13745 0 {At2g24930 }{AT5g37330 } -1
+ 13746 16 {At2g24950 }{AT5g37520 } 1
+ 13750 16 {At2g24990 }{AT5g37350 } 1
+
+
+-block 338
+ points contig1 contig2
+ 3 2 5
+
+ point dist markers orientation
+ 13770 0 {At2g25490 }{AT5g25350 } 1
+ 13772 8 {At2g25520 }{AT5g25400 } 1
+ 13782 24 {At2g25640 }{AT5g25520 } 1
+
+
+-block 339
+ points contig1 contig2
+ 3 2 5
+
+ point dist markers orientation
+ 13836 0 {At2g27300 }{AT5g22290 } 1
+ 13837 25 {At2g27440 }{AT5g22400 } -1
+ 13841 13 {At2g27530 }{AT5g22440 } 1
+
+
+-block 340
+ points contig1 contig2
+ 3 2 5
+
+ point dist markers orientation
+ 13879 0 {At2g28890 }{AT5g02400 } -1
+ 13881 12 {At2g28930 At2g28940 }{AT5g02290 } -1
+ 13883 4 {At2g28950 }{AT5g02260 } -1
+
+
+-block 341
+ points contig1 contig2
+ 3 2 5
+
+ point dist markers orientation
+ 14066 0 {At2g36350 }{AT5g03640 } 1
+ 14069 5 {At2g36390 }{AT5g03650 } 1
+ 14070 11 {At2g36460 }{AT5g03690 } 1
+
+
+-block 342
+ points contig1 contig2
+ 3 2 5
+
+ point dist markers orientation
+ 14083 0 {At2g37010 }{AT5g60740 } -1
+ 14086 24 {At2g37170 At2g37180 }{AT5g60660 } 1
+ 14087 2 {At2g37190 }{AT5g60670 } 1
+
+
+-block 343
+ points contig1 contig2
+ 3 2 5
+
+ point dist markers orientation
+ 14135 0 {At2g38240 }{AT5g05600 } -1
+ 14136 22 {At2g38310 }{AT5g05440 } 1
+ 14139 17 {At2g38380 At2g38390 }{AT5g05340 } -1
+
+
+-block 344
+ points contig1 contig2
+ 3 2 5
+
+ point dist markers orientation
+ 14171 0 {At2g39660 }{AT5g02290 } -1
+ 14174 7 {At2g39700 }{AT5g02260 } -1
+ 14177 8 {At2g39710 }{AT5g02190 } -1
+
+
+-block 345
+ points contig1 contig2
+ 17 3 3
+
+ point dist markers orientation
+ 15026 0 {AT3g30440 }{AT3g32900 } 1
+ 15029 2 {AT3g30450 }{AT3g32910 } 1
+ 15037 19 {AT3g30560 }{AT3g32320 } -1
+ 15042 18 {AT3g30570 }{AT3g32110 } 1
+ 15045 16 {AT3g30630 AT3g30655 }{AT3g32000 AT3g32010 } -1
+ 15050 23 {AT3g30780 AT3g30790 }{AT3g31920 } 1
+ 15051 20 {AT3g31340 }{AT3g31500 } 1
+ 15054 10 {AT3g31370 }{AT3g31915 } 1
+ 15057 16 {AT3g31415 }{AT3g32030 } 1
+ 15059 7 {AT3g31440 }{AT3g31980 } 1
+ 15061 8 {AT3g31450 }{AT3g32060 } 1
+ 15063 11 {AT3g31480 AT3g31490 }{AT3g31970 } 1
+ 15064 25 {AT3g31500 }{AT3g32250 } 1
+ 15065 4 {AT3g31520 }{AT3g32270 AT3g32290 } 1
+ 15066 4 {AT3g31540 }{AT3g32300 } 1
+ 15069 2 {AT3g31900 }{AT3g32280 AT3g32330 } 1
+ 15075 17 {AT3g32000 AT3g32010 }{AT3g32210 } -1
+
+
+-block 346
+ points contig1 contig2
+ 4 3 3
+
+ point dist markers orientation
+ 14682 0 {AT3g11510 }{AT3g52580 } -1
+ 14684 25 {AT3g11660 }{AT3g52470 } -1
+ 14685 14 {AT3g11700 }{AT3g52370 } 1
+ 14690 15 {AT3g11820 }{AT3g52400 } 1
+
+
+-block 347
+ points contig1 contig2
+ 4 3 3
+
+ point dist markers orientation
+ 15012 0 {AT3g29410 }{AT3g32030 } 1
+ 15013 3 {AT3g29430 }{AT3g32040 } -1
+ 15015 25 {AT3g29480 AT3g29490 }{AT3g31480 AT3g31490 } -1
+ 15018 22 {AT3g29500 }{AT3g30843 } -1
+
+
+-block 348
+ points contig1 contig2
+ 3 3 3
+
+ point dist markers orientation
+ 14493 0 {AT3g04760 }{AT3g22470 } 1
+ 14500 20 {AT3g04910 }{AT3g22420 } 1
+ 14503 7 {AT3g04940 }{AT3g22460 } 1
+
+
+-block 349
+ points contig1 contig2
+ 3 3 3
+
+ point dist markers orientation
+ 14561 0 {AT3g07010 }{AT3g24670 } 1
+ 14567 19 {AT3g07070 }{AT3g24790 } 1
+ 14571 8 {AT3g07110 }{AT3g24830 } 1
+
+
+-block 350
+ points contig1 contig2
+ 3 3 3
+
+ point dist markers orientation
+ 14665 0 {AT3g11030 }{AT3g55990 } -1
+ 14667 12 {AT3g11050 }{AT3g56090 } -1
+ 14668 24 {AT3g11180 }{AT3g55970 } -1
+
+
+-block 351
+ points contig1 contig2
+ 3 3 3
+
+ point dist markers orientation
+ 14970 0 {AT3g26780 }{AT3g49140 AT3g49170 } -1
+ 14974 23 {AT3g26920 AT3g26930 }{AT3g49020 AT3g49030 } 1
+ 14975 25 {AT3g26935 }{AT3g48760 } -1
+
+
+-block 352
+ points contig1 contig2
+ 3 3 3
+
+ point dist markers orientation
+ 15033 0 {AT3g30520 }{AT3g42870 } 1
+ 15035 25 {AT3g30550 }{AT3g43100 } 1
+ 15040 24 {AT3g30560 }{AT3g43330 AT3g43350 } 1
+
+
+-block 353
+ points contig1 contig2
+ 3 3 3
+
+ point dist markers orientation
+ 15025 0 {AT3g30400 }{AT3g31340 } -1
+ 15032 22 {AT3g30470 }{AT3g30760 } -1
+ 15048 24 {AT3g30680 }{AT3g30780 AT3g30790 } 1
+
+
+-block 354
+ points contig1 contig2
+ 3 3 3
+
+ point dist markers orientation
+ 15067 0 {AT3g31540 }{AT3g43000 } 1
+ 15076 21 {AT3g32060 }{AT3g43050 } 1
+ 15079 19 {AT3g32150 AT3g32160 AT3g32190 }{AT3g43150 } 1
+
+
+-block 355
+ points contig1 contig2
+ 3 3 3
+
+ point dist markers orientation
+ 15095 0 {AT3g42320 AT3g42340 }{AT3g43330 AT3g43350 } -1
+ 15098 24 {AT3g42580 AT3g42590 AT3g42600 }{AT3g43380 AT3g43390 } -1
+ 15102 14 {AT3g42760 }{AT3g43360 AT3g43370 } -1
+
+
+-block 356
+ points contig1 contig2
+ 3 3 3
+
+ point dist markers orientation
+ 15121 0 {AT3g44470 }{AT3g47280 AT3g47310 } 1
+ 15123 4 {AT3g44500 }{AT3g47260 } 1
+ 15125 21 {AT3g44710 }{AT3g47200 AT3g47210 AT3g47250 } 1
+
+
+-block 357
+ points contig1 contig2
+ 3 3 3
+
+ point dist markers orientation
+ 15167 0 {AT3g48940 }{AT3g61260 } 1
+ 15169 22 {AT3g48950 }{AT3g61490 } 1
+ 15171 23 {AT3g48980 }{AT3g61270 AT3g61280 AT3g61290 } 1
+
+
+-block 358
+ points contig1 contig2
+ 3 3 3
+
+ point dist markers orientation
+ 15185 0 {AT3g51910 }{AT3g63350 } 1
+ 15186 14 {AT3g51950 }{AT3g63450 } 1
+ 15188 8 {AT3g52020 }{AT3g63470 } 1
+
+
+-block 359
+ points contig1 contig2
+ 3 3 3
+
+ point dist markers orientation
+ 15199 0 {AT3g53810 }{AT3g55550 } 1
+ 15200 5 {AT3g53830 }{AT3g55580 } 1
+ 15201 17 {AT3g53940 }{AT3g55640 } -1
+
+
+-block 360
+ points contig1 contig2
+ 21 3 4
+
+ point dist markers orientation
+ 15691 0 {AT3g22170 }{AT4g15090 } -1
+ 15694 2 {AT3g22180 }{AT4g15080 } -1
+ 15695 10 {AT3g22220 }{AT4g15020 } -1
+ 15696 3 {AT3g22230 }{AT4g15000 } -1
+ 15697 5 {AT3g22270 }{AT4g14990 } -1
+ 15701 23 {AT3g22440 }{AT4g14900 } -1
+ 15702 4 {AT3g22460 }{AT4g14880 } -1
+ 15707 8 {AT3g22520 }{AT4g14840 } -1
+ 15708 15 {AT3g22630 }{AT4g14800 } -1
+ 15713 14 {AT3g22750 }{AT4g14780 } -1
+ 15714 2 {AT3g22760 AT3g22780 }{AT4g14770 } -1
+ 15715 3 {AT3g22790 }{AT4g14760 } -1
+ 15719 4 {AT3g22810 }{AT4g14740 } -1
+ 15720 7 {AT3g22840 }{AT4g14690 } -1
+ 15721 7 {AT3g22890 }{AT4g14680 } -1
+ 15722 3 {AT3g22900 }{AT4g14660 } -1
+ 15725 5 {AT3g22930 }{AT4g14640 } -1
+ 15726 13 {AT3g23000 }{AT4g14580 } -1
+ 15727 8 {AT3g23050 }{AT4g14550 } -1
+ 15728 6 {AT3g23070 }{AT4g14510 } -1
+ 15730 2 {AT3g23080 }{AT4g14500 } -1
+
+
+-block 361
+ points contig1 contig2
+ 15 3 4
+
+ point dist markers orientation
+ 15732 0 {AT3g23270 }{AT4g14370 } -1
+ 15733 2 {AT3g23280 AT3g23300 }{AT4g14360 } -1
+ 15734 3 {AT3g23310 }{AT4g14350 } -1
+ 15747 4 {AT3g23340 }{AT4g14340 } -1
+ 15751 7 {AT3g23390 }{AT4g14320 } -1
+ 15755 14 {AT3g23540 }{AT4g14290 } -1
+ 15758 22 {AT3g23660 }{AT4g14160 } -1
+ 15759 2 {AT3g23670 }{AT4g14150 } -1
+ 15762 8 {AT3g23730 }{AT4g14130 } -1
+ 15767 9 {AT3g23770 }{AT4g14080 } -1
+ 15768 3 {AT3g23790 }{AT4g14070 } -1
+ 15769 4 {AT3g23800 }{AT4g14030 AT4g14040 } -1
+ 15770 10 {AT3g23810 }{AT4g13940 } -1
+ 15774 6 {AT3g23830 }{AT4g13850 } -1
+ 15775 2 {AT3g23840 }{AT4g13840 } -1
+
+
+-block 362
+ points contig1 contig2
+ 13 3 4
+
+ point dist markers orientation
+ 15792 0 {AT3g24290 AT3g24300 }{AT4g13510 } -1
+ 15794 4 {AT3g24310 }{AT4g13480 } -1
+ 15795 17 {AT3g24360 }{AT4g13360 } -1
+ 15802 11 {AT3g24480 }{AT4g13340 } -1
+ 15810 21 {AT3g24620 }{AT4g13240 } -1
+ 15811 8 {AT3g24670 }{AT4g13210 } -1
+ 15814 15 {AT3g24790 }{AT4g13190 } -1
+ 15815 6 {AT3g24830 }{AT4g13170 } -1
+ 15819 17 {AT3g25050 }{AT4g13080 AT4g13090 } -1
+ 15822 9 {AT3g25110 }{AT4g13050 } -1
+ 15824 20 {AT3g25250 }{AT4g13000 } -1
+ 15825 5 {AT3g25290 }{AT4g12980 } -1
+ 15826 9 {AT3g25420 }{AT4g12910 } -1
+
+
+-block 363
+ points contig1 contig2
+ 12 3 4
+
+ point dist markers orientation
+ 15982 0 {AT3g31520 }{AT4g03770 } -1
+ 15983 3 {AT3g31540 }{AT4g03760 } -1
+ 15987 20 {AT3g31970 }{AT4g03650 } -1
+ 15992 5 {AT3g31980 }{AT4g03690 } -1
+ 15994 12 {AT3g32000 AT3g32010 }{AT4g03790 AT4g03850 AT4g03860 } -1
+ 16012 25 {AT3g32270 AT3g32290 }{AT4g03770 } -1
+ 16013 3 {AT3g32300 }{AT4g03760 } -1
+ 16014 8 {AT3g32340 }{AT4g03810 } -1
+ 16017 7 {AT3g32880 AT3g32890 AT3g32970 }{AT4g03790 AT4g03850 AT4g03860 } 1
+ 16028 18 {AT3g42080 }{AT4g03780 } -1
+ 16029 11 {AT3g42100 AT3g42110 }{AT4g03690 } -1
+ 16038 22 {AT3g42290 }{AT4g03650 } 1
+
+
+-block 364
+ points contig1 contig2
+ 9 3 4
+
+ point dist markers orientation
+ 15944 0 {AT3g30470 }{AT4g07470 } 1
+ 15945 16 {AT3g30500 }{AT4g07690 } 1
+ 15947 20 {AT3g30550 }{AT4g07450 } -1
+ 15950 7 {AT3g30600 }{AT4g07470 } -1
+ 15951 13 {AT3g30630 AT3g30655 }{AT4g07360 AT4g07370 } 1
+ 15960 23 {AT3g30710 }{AT4g07530 } 1
+ 15961 11 {AT3g30760 }{AT4g07470 } -1
+ 15966 11 {AT3g30810 }{AT4g07530 } -1
+ 15968 13 {AT3g31340 }{AT4g07560 AT4g07570 AT4g07590 AT4g07600 AT4g07610 AT4g07620 AT4g07630 AT4g07640 AT4g07660 AT4g07680 } -1
+
+
+-block 365
+ points contig1 contig2
+ 9 3 4
+
+ point dist markers orientation
+ 15954 0 {AT3g30630 AT3g30655 }{AT4g08050 AT4g08080 } 1
+ 15959 8 {AT3g30680 }{AT4g08000 AT4g08010 AT4g08020 } -1
+ 15967 19 {AT3g30810 }{AT4g07930 } 1
+ 15969 20 {AT3g31340 }{AT4g08050 AT4g08080 } -1
+ 15971 7 {AT3g31390 }{AT4g08030 } -1
+ 15981 25 {AT3g31480 AT3g31490 }{AT4g07830 AT4g07850 } 1
+ 15985 16 {AT3g31920 }{AT4g07750 } -1
+ 15989 12 {AT3g31970 }{AT4g07830 AT4g07850 } 1
+ 15996 20 {AT3g32000 AT3g32010 }{AT4g07560 AT4g07570 AT4g07590 AT4g07600 AT4g07610 AT4g07620 AT4g07630 AT4g07640 AT4g07660 AT4g07680 } -1
+
+
+-block 366
+ points contig1 contig2
+ 7 3 4
+
+ point dist markers orientation
+ 15671 0 {AT3g21466 }{AT4g15640 } -1
+ 15675 10 {AT3g21500 }{AT4g15560 } -1
+ 15676 12 {AT3g21560 }{AT4g15480 AT4g15490 AT4g15500 } -1
+ 15679 11 {AT3g21620 }{AT4g15430 } -1
+ 15681 5 {AT3g21650 }{AT4g15410 } -1
+ 15683 17 {AT3g21750 AT3g21760 AT3g21780 AT3g21790 AT3g21800 }{AT4g15260 AT4g15270 AT4g15280 } 1
+ 15687 8 {AT3g21880 }{AT4g15250 } -1
+
+
+-block 367
+ points contig1 contig2
+ 5 3 4
+
+ point dist markers orientation
+ 16015 0 {AT3g32340 }{AT4g07840 } 1
+ 16018 23 {AT3g32880 AT3g32890 AT3g32970 }{AT4g07560 AT4g07570 AT4g07590 AT4g07600 AT4g07610 AT4g07620 AT4g07630 AT4g07640 AT4g07660 AT4g07680 } 1
+ 16024 17 {AT3g32950 }{AT4g07760 } -1
+ 16031 16 {AT3g42100 AT3g42110 }{AT4g07800 } -1
+ 16034 21 {AT3g42260 }{AT4g07730 AT4g07780 } -1
+
+
+-block 368
+ points contig1 contig2
+ 4 3 4
+
+ point dist markers orientation
+ 16048 0 {AT3g42650 }{AT4g04170 } -1
+ 16049 8 {AT3g42690 AT3g42700 }{AT4g04130 } 1
+ 16050 2 {AT3g42710 }{AT4g04140 } 1
+ 16051 23 {AT3g42720 }{AT4g03900 AT4g03910 } -1
+
+
+-block 369
+ points contig1 contig2
+ 4 3 4
+
+ point dist markers orientation
+ 16464 0 {AT3g61150 }{AT4g00730 } -1
+ 16467 2 {AT3g61160 }{AT4g00720 } -1
+ 16473 14 {AT3g61240 }{AT4g00660 } 1
+ 16476 8 {AT3g61300 }{AT4g00700 } 1
+
+
+-block 370
+ points contig1 contig2
+ 3 3 4
+
+ point dist markers orientation
+ 15350 0 {AT3g07010 }{AT4g13210 } -1
+ 15354 8 {AT3g07070 }{AT4g13190 } -1
+ 15356 6 {AT3g07110 }{AT4g13170 } -1
+
+
+-block 371
+ points contig1 contig2
+ 3 3 4
+
+ point dist markers orientation
+ 15465 0 {AT3g12500 }{AT4g01700 } 1
+ 15468 11 {AT3g12550 }{AT4g01780 } 1
+ 15474 25 {AT3g12720 AT3g12820 }{AT4g01680 } 1
+
+
+-block 372
+ points contig1 contig2
+ 3 3 4
+
+ point dist markers orientation
+ 15659 0 {AT3g20560 }{AT4g27080 } 1
+ 15661 5 {AT3g20580 }{AT4g27110 } 1
+ 15662 19 {AT3g20670 }{AT4g27230 } -1
+
+
+-block 373
+ points contig1 contig2
+ 3 3 4
+
+ point dist markers orientation
+ 15946 0 {AT3g30550 }{AT4g03640 } 1
+ 15948 6 {AT3g30560 }{AT4g03690 } 1
+ 15957 16 {AT3g30680 }{AT4g03730 } 1
+
+
+-block 374
+ points contig1 contig2
+ 3 3 4
+
+ point dist markers orientation
+ 15965 0 {AT3g30810 }{AT4g04070 } -1
+ 15970 23 {AT3g31390 }{AT4g04150 } -1
+ 15974 18 {AT3g31420 }{AT4g04000 } -1
+
+
+-block 375
+ points contig1 contig2
+ 3 3 4
+
+ point dist markers orientation
+ 15972 0 {AT3g31390 }{AT4g08490 } 1
+ 15973 23 {AT3g31410 }{AT4g08710 } -1
+ 15978 6 {AT3g31450 }{AT4g08720 } -1
+
+
+-block 376
+ points contig1 contig2
+ 3 3 4
+
+ point dist markers orientation
+ 16000 0 {AT3g32060 }{AT4g08720 } -1
+ 16002 13 {AT3g32110 }{AT4g08820 AT4g08830 } 1
+ 16005 12 {AT3g32140 }{AT4g08710 } -1
+
+
+-block 377
+ points contig1 contig2
+ 3 3 4
+
+ point dist markers orientation
+ 15995 0 {AT3g32000 AT3g32010 }{AT4g07360 AT4g07370 } -1
+ 16006 18 {AT3g32150 AT3g32160 AT3g32190 }{AT4g07320 } -1
+ 16020 23 {AT3g32880 AT3g32890 AT3g32970 }{AT4g07360 AT4g07370 } 1
+
+
+-block 378
+ points contig1 contig2
+ 3 3 4
+
+ point dist markers orientation
+ 16069 0 {AT3g43100 }{AT4g07450 } -1
+ 16070 20 {AT3g43130 }{AT4g05610 } -1
+ 16072 7 {AT3g43150 }{AT4g07320 } -1
+
+
+-block 379
+ points contig1 contig2
+ 3 3 4
+
+ point dist markers orientation
+ 16062 0 {AT3g43010 AT3g43030 }{AT4g19290 AT4g19310 AT4g19320 } -1
+ 16068 6 {AT3g43070 }{AT4g19280 AT4g19300 } -1
+ 16076 25 {AT3g43280 }{AT4g19240 } 1
+
+
+-block 380
+ points contig1 contig2
+ 3 3 4
+
+ point dist markers orientation
+ 16122 0 {AT3g45260 }{AT4g02670 } 1
+ 16124 10 {AT3g45290 }{AT4g02600 } 1
+ 16125 22 {AT3g45330 AT3g45390 AT3g45410 AT3g45420 AT3g45430 AT3g45440 }{AT4g02410 AT4g02420 } 1
+
+
+-block 381
+ points contig1 contig2
+ 3 3 4
+
+ point dist markers orientation
+ 16141 0 {AT3g45530 }{AT4g11540 AT4g11550 } 1
+ 16148 23 {AT3g45640 }{AT4g11330 } 1
+ 16151 19 {AT3g45810 }{AT4g11230 } 1
+
+
+-block 382
+ points contig1 contig2
+ 3 3 4
+
+ point dist markers orientation
+ 16186 0 {AT3g47260 }{AT4g04010 } -1
+ 16187 3 {AT3g47270 }{AT4g03990 } -1
+ 16188 2 {AT3g47280 AT3g47310 }{AT4g03980 } -1
+
+
+-block 383
+ points contig1 contig2
+ 3 3 4
+
+ point dist markers orientation
+ 16290 0 {AT3g51190 }{AT4g36130 } -1
+ 16291 21 {AT3g51250 }{AT4g35980 } -1
+ 16295 8 {AT3g51300 }{AT4g35950 } -1
+
+
+-block 384
+ points contig1 contig2
+ 3 3 4
+
+ point dist markers orientation
+ 16512 0 {AT3g62560 }{AT4g02080 } 1
+ 16513 3 {AT3g62570 }{AT4g02100 } 1
+ 16517 12 {AT3g62660 }{AT4g02130 } -1
+
+
+-block 385
+ points contig1 contig2
+ 66 3 5
+
+ point dist markers orientation
+ 16608 0 {AT3g02080 }{AT5g15520 } 1
+ 16611 13 {AT3g02160 }{AT5g15570 } 1
+ 16612 2 {AT3g02170 }{AT5g15580 } 1
+ 16613 6 {AT3g02200 }{AT5g15610 } 1
+ 16614 3 {AT3g02210 }{AT5g15630 } -1
+ 16616 4 {AT3g02230 }{AT5g15650 } 1
+ 16619 11 {AT3g02250 }{AT5g15740 } 1
+ 16621 12 {AT3g02310 }{AT5g15800 } 1
+ 16622 2 {AT3g02320 }{AT5g15810 } 1
+ 16626 9 {AT3g02380 }{AT5g15840 AT5g15850 } 1
+ 16627 4 {AT3g02410 }{AT5g15860 } 1
+ 16628 6 {AT3g02440 }{AT5g15890 } 1
+ 16629 6 {AT3g02460 }{AT5g15930 } 1
+ 16630 3 {AT3g02470 }{AT5g15950 } 1
+ 16631 5 {AT3g02490 }{AT5g15980 } 1
+ 16632 8 {AT3g02510 }{AT5g16040 } 1
+ 16634 2 {AT3g02520 }{AT5g16050 } 1
+ 16637 3 {AT3g02530 }{AT5g16070 } 1
+ 16638 9 {AT3g02560 }{AT5g16130 } 1
+ 16639 14 {AT3g02610 AT3g02620 AT3g02630 }{AT5g16230 AT5g16240 } 1
+ 16640 2 {AT3g02640 }{AT5g16250 } 1
+ 16641 23 {AT3g02730 }{AT5g16400 } 1
+ 16645 9 {AT3g02770 }{AT5g16450 } -1
+ 16647 2 {AT3g02780 }{AT5g16440 } -1
+ 16648 6 {AT3g02800 }{AT5g16480 } 1
+ 16650 3 {AT3g02810 }{AT5g16500 } 1
+ 16652 6 {AT3g02830 }{AT5g16540 } 1
+ 16656 11 {AT3g02880 }{AT5g16590 } 1
+ 16657 10 {AT3g02890 }{AT5g16680 } -1
+ 16658 9 {AT3g02930 }{AT5g16730 } 1
+ 16663 14 {AT3g02940 }{AT5g16600 } 1
+ 16668 20 {AT3g02950 }{AT5g16790 } 1
+ 16669 4 {AT3g02980 }{AT5g16800 } 1
+ 16670 10 {AT3g03010 }{AT5g16870 } 1
+ 16674 7 {AT3g03050 }{AT5g16910 } 1
+ 16675 3 {AT3g03060 }{AT5g16930 } 1
+ 16676 5 {AT3g03080 }{AT5g16960 AT5g16970 AT5g16980 AT5g16990 AT5g17000 } 1
+ 16678 2 {AT3g03090 }{AT5g17010 } 1
+ 16680 3 {AT3g03110 }{AT5g17020 } 1
+ 16682 3 {AT3g03120 }{AT5g17060 } 1
+ 16683 15 {AT3g03160 }{AT5g17190 } 1
+ 16684 6 {AT3g03190 }{AT5g17220 } 1
+ 16685 5 {AT3g03200 }{AT5g17260 } 1
+ 16687 9 {AT3g03250 }{AT5g17310 } 1
+ 16688 12 {AT3g03290 }{AT5g17390 } 1
+ 16689 10 {AT3g03340 }{AT5g17440 } 1
+ 16690 16 {AT3g03450 }{AT5g17490 } 1
+ 16691 3 {AT3g03460 }{AT5g17510 } 1
+ 16692 5 {AT3g03480 }{AT5g17540 } 1
+ 16693 2 {AT3g03490 }{AT5g17550 } 1
+ 16694 3 {AT3g03500 }{AT5g17570 } 1
+ 16699 23 {AT3g03620 }{AT5g17700 } 1
+ 16712 17 {AT3g03700 }{AT5g17830 } 1
+ 16716 16 {AT3g03780 }{AT5g17920 } 1
+ 16719 25 {AT3g03860 }{AT5g18120 } 1
+ 16722 10 {AT3g03910 }{AT5g18170 } 1
+ 16723 2 {AT3g03920 }{AT5g18180 } 1
+ 16724 2 {AT3g03930 AT3g03940 }{AT5g18190 } 1
+ 16727 6 {AT3g03980 AT3g04000 }{AT5g18210 } 1
+ 16728 3 {AT3g04010 }{AT5g18220 } 1
+ 16730 4 {AT3g04030 }{AT5g18240 } 1
+ 16735 6 {AT3g04060 }{AT5g18270 } 1
+ 16738 3 {AT3g04080 }{AT5g18280 } 1
+ 16745 16 {AT3g04230 }{AT5g18380 } 1
+ 16746 11 {AT3g04290 }{AT5g18430 } 1
+ 16748 12 {AT3g04350 }{AT5g18490 } 1
+
+
+-block 386
+ points contig1 contig2
+ 30 3 5
+
+ point dist markers orientation
+ 17044 0 {AT3g10980 }{AT5g05350 } 1
+ 17050 17 {AT3g11040 }{AT5g05460 } 1
+ 17052 9 {AT3g11070 }{AT5g05520 } 1
+ 17054 15 {AT3g11170 }{AT5g05580 } 1
+ 17055 3 {AT3g11180 }{AT5g05600 } 1
+ 17056 2 {AT3g11200 }{AT5g05610 } 1
+ 17057 13 {AT3g11240 }{AT5g05700 } 1
+ 17058 11 {AT3g11270 }{AT5g05780 } 1
+ 17059 2 {AT3g11280 }{AT5g05790 } 1
+ 17060 2 {AT3g11290 AT3g11310 }{AT5g05800 } 1
+ 17062 4 {AT3g11320 }{AT5g05820 } 1
+ 17064 4 {AT3g11330 }{AT5g05850 } 1
+ 17065 2 {AT3g11340 AT3g11350 AT3g11360 }{AT5g05860 AT5g05870 AT5g05880 AT5g05890 AT5g05900 } 1
+ 17068 13 {AT3g11400 }{AT5g06000 } 1
+ 17072 11 {AT3g11430 }{AT5g06090 } 1
+ 17073 2 {AT3g11440 }{AT5g06100 } 1
+ 17079 13 {AT3g11520 }{AT5g06150 } 1
+ 17080 8 {AT3g11550 }{AT5g06200 } 1
+ 17081 3 {AT3g11560 }{AT5g06220 } 1
+ 17082 2 {AT3g11570 }{AT5g06230 } 1
+ 17084 11 {AT3g11630 }{AT5g06290 } 1
+ 17085 7 {AT3g11660 }{AT5g06330 } 1
+ 17086 10 {AT3g11700 }{AT5g06390 } 1
+ 17091 13 {AT3g11770 }{AT5g06450 } 1
+ 17092 4 {AT3g11780 }{AT5g06480 } 1
+ 17093 15 {AT3g11850 }{AT5g06560 } 1
+ 17094 10 {AT3g11910 }{AT5g06600 } 1
+ 17096 18 {AT3g12020 }{AT5g06670 } -1
+ 17097 2 {AT3g12030 }{AT5g06660 } -1
+ 17098 7 {AT3g12060 }{AT5g06700 } 1
+
+
+-block 387
+ points contig1 contig2
+ 26 3 5
+
+ point dist markers orientation
+ 16545 0 {AT3g01140 }{AT5g15310 } -1
+ 16554 18 {AT3g01190 }{AT5g15180 } -1
+ 16555 6 {AT3g01220 }{AT5g15150 } -1
+ 16556 5 {AT3g01260 }{AT5g15140 } -1
+ 16557 4 {AT3g01270 }{AT5g15110 } -1
+ 16559 3 {AT3g01280 }{AT5g15090 } -1
+ 16565 3 {AT3g01300 }{AT5g15080 } -1
+ 16566 2 {AT3g01310 }{AT5g15070 } -1
+ 16567 6 {AT3g01320 }{AT5g15020 } -1
+ 16568 11 {AT3g01350 }{AT5g14940 } -1
+ 16571 13 {AT3g01430 }{AT5g14890 } -1
+ 16572 12 {AT3g01450 }{AT5g14790 } -1
+ 16574 10 {AT3g01500 }{AT5g14740 } -1
+ 16575 8 {AT3g01520 }{AT5g14680 } -1
+ 16578 9 {AT3g01540 }{AT5g14610 } -1
+ 16582 16 {AT3g01590 }{AT5g14500 } -1
+ 16584 2 {AT3g01600 }{AT5g14490 } -1
+ 16585 3 {AT3g01620 }{AT5g14480 } -1
+ 16586 3 {AT3g01640 }{AT5g14470 } -1
+ 16587 6 {AT3g01650 }{AT5g14420 } -1
+ 16589 7 {AT3g01690 }{AT5g14390 } -1
+ 16591 15 {AT3g01740 }{AT5g14290 } -1
+ 16593 5 {AT3g01770 }{AT5g14270 } -1
+ 16594 21 {AT3g01890 }{AT5g14170 } -1
+ 16595 9 {AT3g01930 }{AT5g14120 } -1
+ 16602 15 {AT3g02020 }{AT5g14060 } -1
+
+
+-block 388
+ points contig1 contig2
+ 21 3 5
+
+ point dist markers orientation
+ 16769 0 {AT3g04980 }{AT5g27240 } -1
+ 16770 6 {AT3g05010 }{AT5g27210 } -1
+ 16771 7 {AT3g05030 }{AT5g27150 } -1
+ 16776 5 {AT3g05060 }{AT5g27120 AT5g27140 } -1
+ 16777 24 {AT3g05120 }{AT5g27320 } 1
+ 16778 2 {AT3g05130 }{AT5g27330 } 1
+ 16780 4 {AT3g05150 AT3g05160 }{AT5g27350 AT5g27360 } 1
+ 16781 8 {AT3g05190 }{AT5g27410 } 1
+ 16782 2 {AT3g05200 }{AT5g27420 } 1
+ 16783 4 {AT3g05230 }{AT5g27430 } 1
+ 16785 11 {AT3g05280 }{AT5g27490 } 1
+ 16786 4 {AT3g05290 }{AT5g27520 } 1
+ 16787 4 {AT3g05310 }{AT5g27540 } 1
+ 16791 12 {AT3g05380 }{AT5g27610 } 1
+ 16795 6 {AT3g05420 }{AT5g27630 } 1
+ 16796 3 {AT3g05430 }{AT5g27650 } 1
+ 16802 25 {AT3g05560 }{AT5g27770 } 1
+ 16803 9 {AT3g05580 }{AT5g27840 } 1
+ 16806 2 {AT3g05590 }{AT5g27850 } 1
+ 16808 4 {AT3g05610 AT3g05620 }{AT5g27870 } 1
+ 16811 8 {AT3g05640 }{AT5g27930 } 1
+
+
+-block 389
+ points contig1 contig2
+ 19 3 5
+
+ point dist markers orientation
+ 17579 0 {AT3g26820 AT3g26840 }{AT5g41120 AT5g41130 } -1
+ 17580 7 {AT3g26890 }{AT5g41110 } -1
+ 17581 3 {AT3g26910 }{AT5g41100 } -1
+ 17582 6 {AT3g26935 }{AT5g41060 } -1
+ 17591 15 {AT3g27020 }{AT5g41000 } -1
+ 17597 24 {AT3g27170 }{AT5g40890 } -1
+ 17599 4 {AT3g27190 }{AT5g40870 } -1
+ 17600 8 {AT3g27230 }{AT5g40830 } -1
+ 17601 3 {AT3g27240 }{AT5g40810 } -1
+ 17603 8 {AT3g27280 }{AT5g40770 } -1
+ 17607 3 {AT3g27300 }{AT5g40760 } -1
+ 17609 9 {AT3g27330 }{AT5g40720 } -1
+ 17613 12 {AT3g27380 }{AT5g40650 } -1
+ 17614 2 {AT3g27390 }{AT5g40640 } -1
+ 17618 10 {AT3g27430 }{AT5g40580 } -1
+ 17620 6 {AT3g27460 }{AT5g40550 } -1
+ 17624 8 {AT3g27560 }{AT5g40540 } -1
+ 17626 4 {AT3g27570 }{AT5g40510 } -1
+ 17633 18 {AT3g27660 }{AT5g40420 } -1
+
+
+-block 390
+ points contig1 contig2
+ 17 3 5
+
+ point dist markers orientation
+ 18095 0 {AT3g49830 }{AT5g67630 } -1
+ 18097 10 {AT3g49860 AT3g49870 }{AT5g67560 } -1
+ 18098 3 {AT3g49880 }{AT5g67540 } -1
+ 18099 6 {AT3g49910 }{AT5g67510 } -1
+ 18100 2 {AT3g49920 }{AT5g67500 } -1
+ 18101 10 {AT3g49940 }{AT5g67420 } -1
+ 18102 4 {AT3g49960 }{AT5g67400 } -1
+ 18103 6 {AT3g50000 }{AT5g67380 } -1
+ 18108 14 {AT3g50060 }{AT5g67300 } -1
+ 18109 5 {AT3g50070 }{AT5g67260 } -1
+ 18110 2 {AT3g50080 }{AT5g67250 } -1
+ 18111 2 {AT3g50090 AT3g50100 }{AT5g67240 } -1
+ 18112 7 {AT3g50220 }{AT5g67210 } -1
+ 18114 2 {AT3g50230 }{AT5g67200 } -1
+ 18118 9 {AT3g50270 AT3g50280 AT3g50290 AT3g50300 }{AT5g67150 } -1
+ 18119 8 {AT3g50310 }{AT5g67080 } -1
+ 18120 9 {AT3g50340 }{AT5g67020 } -1
+
+
+-block 391
+ points contig1 contig2
+ 16 3 5
+
+ point dist markers orientation
+ 18128 0 {AT3g50650 }{AT5g66770 } -1
+ 18130 9 {AT3g50700 }{AT5g66730 } -1
+ 18131 4 {AT3g50720 AT3g50730 }{AT5g66710 } -1
+ 18133 3 {AT3g50740 }{AT5g66690 } -1
+ 18134 13 {AT3g50800 }{AT5g66580 } -1
+ 18135 3 {AT3g50820 }{AT5g66570 } -1
+ 18136 3 {AT3g50840 }{AT5g66560 } -1
+ 18138 15 {AT3g50910 }{AT5g66480 } -1
+ 18139 4 {AT3g50920 }{AT5g66450 } -1
+ 18143 7 {AT3g50960 }{AT5g66410 } -1
+ 18146 5 {AT3g50990 }{AT5g66390 } -1
+ 18152 24 {AT3g51150 }{AT5g66310 } -1
+ 18153 4 {AT3g51160 }{AT5g66280 } -1
+ 18154 24 {AT3g51260 }{AT5g66140 } -1
+ 18161 15 {AT3g51370 }{AT5g66080 } -1
+ 18162 12 {AT3g51460 }{AT5g66020 } -1
+
+
+-block 392
+ points contig1 contig2
+ 14 3 5
+
+ point dist markers orientation
+ 16833 0 {AT3g06010 }{AT5g19310 } -1
+ 16834 16 {AT3g06060 }{AT5g19200 } -1
+ 16836 6 {AT3g06080 }{AT5g19160 } -1
+ 16838 14 {AT3g06140 }{AT5g19080 } -1
+ 16839 3 {AT3g06150 }{AT5g19060 } -1
+ 16840 7 {AT3g06180 }{AT5g19020 } -1
+ 16841 3 {AT3g06190 }{AT5g19000 } -1
+ 16843 4 {AT3g06210 }{AT5g18980 } -1
+ 16844 5 {AT3g06250 }{AT5g18960 } -1
+ 16845 11 {AT3g06300 }{AT5g18900 } -1
+ 16846 10 {AT3g06310 }{AT5g18800 } -1
+ 16847 6 {AT3g06330 }{AT5g18760 } -1
+ 16850 18 {AT3g06400 }{AT5g18620 } -1
+ 16853 8 {AT3g06410 }{AT5g18550 } -1
+
+
+-block 393
+ points contig1 contig2
+ 14 3 5
+
+ point dist markers orientation
+ 16961 0 {AT3g09300 }{AT5g02100 } 1
+ 16963 10 {AT3g09330 AT3g09340 }{AT5g02170 AT5g02180 } -1
+ 16965 3 {AT3g09350 }{AT5g02150 } -1
+ 16966 18 {AT3g09370 }{AT5g02320 } -1
+ 16968 8 {AT3g09400 }{AT5g02400 } -1
+ 16971 12 {AT3g09440 }{AT5g02490 AT5g02500 } 1
+ 16974 17 {AT3g09500 }{AT5g02610 } 1
+ 16976 8 {AT3g09570 }{AT5g02630 } 1
+ 16979 12 {AT3g09590 }{AT5g02730 } 1
+ 16981 17 {AT3g09630 }{AT5g02870 } 1
+ 16982 11 {AT3g09670 }{AT5g02950 } 1
+ 16983 2 {AT3g09680 }{AT5g02960 } 1
+ 16984 2 {AT3g09690 }{AT5g02970 } 1
+ 16985 9 {AT3g09710 }{AT5g03040 } 1
+
+
+-block 394
+ points contig1 contig2
+ 11 3 5
+
+ point dist markers orientation
+ 16864 0 {AT3g06620 AT3g06630 AT3g06640 }{AT5g49470 } -1
+ 16865 2 {AT3g06650 }{AT5g49460 } -1
+ 16866 14 {AT3g06670 }{AT5g49380 } -1
+ 16867 12 {AT3g06720 }{AT5g49310 } -1
+ 16870 24 {AT3g06830 }{AT5g49180 } -1
+ 16874 25 {AT3g06930 }{AT5g49020 } -1
+ 16877 18 {AT3g07010 }{AT5g48900 } -1
+ 16883 22 {AT3g07070 }{AT5g48740 } -1
+ 16884 6 {AT3g07110 }{AT5g48760 } -1
+ 16886 18 {AT3g07190 }{AT5g48660 } -1
+ 16891 17 {AT3g07310 }{AT5g48590 } -1
+
+
+-block 395
+ points contig1 contig2
+ 11 3 5
+
+ point dist markers orientation
+ 17022 0 {AT3g10480 AT3g10490 AT3g10500 }{AT5g04410 } 1
+ 17026 14 {AT3g10540 }{AT5g04510 } 1
+ 17027 4 {AT3g10550 }{AT5g04540 } 1
+ 17028 10 {AT3g10560 AT3g10570 }{AT5g04630 AT5g04660 } 1
+ 17029 13 {AT3g10600 }{AT5g04770 } 1
+ 17030 4 {AT3g10610 }{AT5g04800 } 1
+ 17032 8 {AT3g10640 }{AT5g04850 } 1
+ 17033 4 {AT3g10660 }{AT5g04870 } 1
+ 17036 14 {AT3g10710 AT3g10720 }{AT5g04960 AT5g04970 } 1
+ 17038 3 {AT3g10730 }{AT5g04990 } 1
+ 17040 23 {AT3g10820 }{AT5g05140 } 1
+
+
+-block 396
+ points contig1 contig2
+ 11 3 5
+
+ point dist markers orientation
+ 17901 0 {AT3g45810 }{AT5g60010 } -1
+ 17903 10 {AT3g45840 }{AT5g59920 AT5g59930 AT5g59940 } -1
+ 17909 14 {AT3g45980 AT3g46030 }{AT5g59910 } -1
+ 17911 4 {AT3g46000 AT3g46010 }{AT5g59880 AT5g59890 } -1
+ 17912 5 {AT3g46040 }{AT5g59850 } -1
+ 17915 3 {AT3g46060 }{AT5g59840 } -1
+ 17917 10 {AT3g46110 }{AT5g59790 } 1
+ 17919 3 {AT3g46130 }{AT5g59780 } -1
+ 17920 9 {AT3g46180 }{AT5g59740 } 1
+ 17921 7 {AT3g46230 }{AT5g59720 } -1
+ 17927 6 {AT3g46290 }{AT5g59650 AT5g59660 AT5g59670 AT5g59680 AT5g59700 } 1
+
+
+-block 397
+ points contig1 contig2
+ 9 3 5
+
+ point dist markers orientation
+ 16814 0 {AT3g05650 AT3g05660 }{AT5g27060 } 1
+ 16816 13 {AT3g05710 }{AT5g26980 } -1
+ 16819 10 {AT3g05750 }{AT5g26910 } -1
+ 16820 8 {AT3g05780 AT3g05790 }{AT5g26860 } -1
+ 16824 16 {AT3g05840 }{AT5g26750 } -1
+ 16825 17 {AT3g05910 }{AT5g26670 } -1
+ 16827 5 {AT3g05930 }{AT5g26700 } -1
+ 16828 5 {AT3g05940 }{AT5g26740 } -1
+ 16831 11 {AT3g05960 }{AT5g26250 AT5g26340 } -1
+
+
+-block 398
+ points contig1 contig2
+ 9 3 5
+
+ point dist markers orientation
+ 16986 0 {AT3g09790 }{AT5g03240 } 1
+ 16988 9 {AT3g09820 }{AT5g03300 } 1
+ 16989 3 {AT3g09830 }{AT5g03320 } 1
+ 16995 23 {AT3g09880 }{AT5g03470 } 1
+ 16997 8 {AT3g09900 }{AT5g03520 } 1
+ 16999 2 {AT3g09910 }{AT5g03530 } 1
+ 17000 11 {AT3g09930 }{AT5g03610 } 1
+ 17001 3 {AT3g09940 }{AT5g03630 } 1
+ 17002 6 {AT3g09980 }{AT5g03660 } 1
+
+
+-block 399
+ points contig1 contig2
+ 9 3 5
+
+ point dist markers orientation
+ 18066 0 {AT3g49290 }{AT5g24310 } 1
+ 18068 14 {AT3g49350 }{AT5g24390 } 1
+ 18071 3 {AT3g49360 }{AT5g24410 AT5g24420 } 1
+ 18072 2 {AT3g49370 }{AT5g24430 } 1
+ 18074 3 {AT3g49390 }{AT5g24440 } 1
+ 18075 3 {AT3g49410 }{AT5g24450 } 1
+ 18077 24 {AT3g49530 }{AT5g24590 } 1
+ 18079 4 {AT3g49550 }{AT5g24610 } 1
+ 18080 5 {AT3g49560 }{AT5g24650 } 1
+
+
+-block 400
+ points contig1 contig2
+ 8 3 5
+
+ point dist markers orientation
+ 16929 0 {AT3g08850 }{AT5g01770 } 1
+ 16930 22 {AT3g08870 }{AT5g01540 AT5g01550 AT5g01560 } 1
+ 16932 7 {AT3g08890 }{AT5g01610 } 1
+ 16936 22 {AT3g08910 }{AT5g01390 } 1
+ 16941 25 {AT3g09020 }{AT5g01250 } -1
+ 16946 23 {AT3g09140 }{AT5g01120 AT5g01130 AT5g01150 } -1
+ 16947 15 {AT3g09220 }{AT5g01040 AT5g01050 } 1
+ 16954 3 {AT3g09240 }{AT5g01060 } -1
+
+
+-block 401
+ points contig1 contig2
+ 8 3 5
+
+ point dist markers orientation
+ 18082 0 {AT3g49670 }{AT5g65700 AT5g65710 } 1
+ 18083 8 {AT3g49680 }{AT5g65780 } 1
+ 18086 2 {AT3g49690 }{AT5g65790 } 1
+ 18089 2 {AT3g49700 }{AT5g65800 } 1
+ 18091 3 {AT3g49720 }{AT5g65810 } 1
+ 18092 2 {AT3g49730 }{AT5g65820 } 1
+ 18093 3 {AT3g49750 }{AT5g65830 } 1
+ 18094 15 {AT3g49810 }{AT5g65920 } 1
+
+
+-block 402
+ points contig1 contig2
+ 7 3 5
+
+ point dist markers orientation
+ 16759 0 {AT3g04810 }{AT5g28290 } -1
+ 16760 8 {AT3g04830 }{AT5g28220 } -1
+ 16761 9 {AT3g04860 }{AT5g28150 } -1
+ 16762 10 {AT3g04910 }{AT5g28080 } -1
+ 16766 3 {AT3g04920 }{AT5g28060 } -1
+ 16767 3 {AT3g04930 }{AT5g28040 } -1
+ 16768 2 {AT3g04940 }{AT5g28020 AT5g28030 } -1
+
+
+-block 403
+ points contig1 contig2
+ 7 3 5
+
+ point dist markers orientation
+ 17840 0 {AT3g44260 }{AT5g22250 } 1
+ 17841 7 {AT3g44290 }{AT5g22290 } 1
+ 17842 2 {AT3g44300 AT3g44310 AT3g44320 }{AT5g22300 } 1
+ 17843 11 {AT3g44350 }{AT5g22380 } 1
+ 17849 21 {AT3g44540 AT3g44550 AT3g44560 }{AT5g22420 AT5g22500 } 1
+ 17861 24 {AT3g44710 }{AT5g22540 AT5g22550 AT5g22560 } 1
+ 17862 7 {AT3g44720 }{AT5g22630 } 1
+
+
+-block 404
+ points contig1 contig2
+ 7 3 5
+
+ point dist markers orientation
+ 17883 0 {AT3g45240 }{AT5g60550 } -1
+ 17886 8 {AT3g45260 }{AT5g60470 } -1
+ 17888 16 {AT3g45310 }{AT5g60360 } -1
+ 17890 7 {AT3g45330 AT3g45390 AT3g45410 AT3g45420 AT3g45430 AT3g45440 }{AT5g60270 AT5g60280 AT5g60300 AT5g60310 AT5g60320 } -1
+ 17894 19 {AT3g45590 }{AT5g60230 } -1
+ 17895 2 {AT3g45600 }{AT5g60220 } -1
+ 17896 7 {AT3g45630 }{AT5g60170 } -1
+
+
+-block 405
+ points contig1 contig2
+ 7 3 5
+
+ point dist markers orientation
+ 17931 0 {AT3g46440 }{AT5g59290 } 1
+ 17932 3 {AT3g46460 }{AT5g59300 } 1
+ 17936 11 {AT3g46520 }{AT5g59370 } 1
+ 17937 13 {AT3g46590 }{AT5g59430 } 1
+ 17938 3 {AT3g46600 }{AT5g59450 } 1
+ 17939 10 {AT3g46620 }{AT5g59550 } 1
+ 17942 6 {AT3g46650 AT3g46660 AT3g46670 AT3g46680 AT3g46690 AT3g46700 AT3g46720 }{AT5g59580 AT5g59590 } 1
+
+
+-block 406
+ points contig1 contig2
+ 7 3 5
+
+ point dist markers orientation
+ 18035 0 {AT3g48740 }{AT5g23660 } 1
+ 18039 5 {AT3g48780 AT3g48790 }{AT5g23670 } 1
+ 18040 6 {AT3g48830 }{AT5g23690 } 1
+ 18048 15 {AT3g48930 }{AT5g23740 } 1
+ 18049 2 {AT3g48940 }{AT5g23750 } 1
+ 18050 14 {AT3g48960 AT3g49010 }{AT5g23900 } 1
+ 18051 7 {AT3g48980 }{AT5g23850 } 1
+
+
+-block 407
+ points contig1 contig2
+ 6 3 5
+
+ point dist markers orientation
+ 17005 0 {AT3g10200 }{AT5g04060 } 1
+ 17008 8 {AT3g10250 }{AT5g04090 } 1
+ 17010 4 {AT3g10270 }{AT5g04110 AT5g04130 } 1
+ 17012 6 {AT3g10290 }{AT5g04160 } 1
+ 17014 2 {AT3g10300 }{AT5g04170 } 1
+ 17017 10 {AT3g10340 }{AT5g04230 } 1
+
+
+-block 408
+ points contig1 contig2
+ 6 3 5
+
+ point dist markers orientation
+ 17637 0 {AT3g27920 }{AT5g40330 } -1
+ 17638 8 {AT3g27970 }{AT5g40310 } -1
+ 17643 14 {AT3g28050 }{AT5g40230 AT5g40240 } -1
+ 17644 4 {AT3g28070 AT3g28080 AT3g28100 AT3g28130 }{AT5g40210 } -1
+ 17645 6 {AT3g28140 }{AT5g40190 } -1
+ 17648 11 {AT3g28200 }{AT5g40150 } -1
+
+
+-block 409
+ points contig1 contig2
+ 6 3 5
+
+ point dist markers orientation
+ 17724 0 {AT3g30420 }{AT5g35130 } -1
+ 17725 22 {AT3g30440 }{AT5g34900 } -1
+ 17726 13 {AT3g30470 }{AT5g35030 } 1
+ 17728 4 {AT3g30500 }{AT5g35040 } 1
+ 17732 11 {AT3g30560 }{AT5g34960 } -1
+ 17733 8 {AT3g30600 }{AT5g35030 } -1
+
+
+-block 410
+ points contig1 contig2
+ 6 3 5
+
+ point dist markers orientation
+ 17949 0 {AT3g46820 }{AT5g59160 } -1
+ 17951 2 {AT3g46830 }{AT5g59150 } -1
+ 17955 3 {AT3g46840 AT3g46850 }{AT5g59090 AT5g59100 AT5g59110 AT5g59120 AT5g59130 AT5g59190 } -1
+ 17957 22 {AT3g46930 }{AT5g58950 } -1
+ 17960 18 {AT3g47060 }{AT5g58870 } -1
+ 17963 10 {AT3g47120 AT3g47160 }{AT5g58790 } -1
+
+
+-block 411
+ points contig1 contig2
+ 6 3 5
+
+ point dist markers orientation
+ 18028 0 {AT3g48520 }{AT5g63450 } 1
+ 18029 9 {AT3g48590 }{AT5g63470 } 1
+ 18030 13 {AT3g48680 }{AT5g63510 } 1
+ 18031 6 {AT3g48710 }{AT5g63550 } 1
+ 18033 2 {AT3g48720 }{AT5g63560 } 1
+ 18034 2 {AT3g48730 }{AT5g63570 } 1
+
+
+-block 412
+ points contig1 contig2
+ 5 3 5
+
+ point dist markers orientation
+ 17683 0 {AT3g28930 AT3g28940 AT3g28950 }{AT5g39720 AT5g39730 } -1
+ 17691 20 {AT3g29035 }{AT5g39610 } -1
+ 17693 17 {AT3g29100 }{AT5g39510 } -1
+ 17695 10 {AT3g29160 }{AT5g39440 } -1
+ 17696 3 {AT3g29180 }{AT5g39430 } -1
+
+
+-block 413
+ points contig1 contig2
+ 5 3 5
+
+ point dist markers orientation
+ 17868 0 {AT3g44850 }{AT5g22840 } 1
+ 17869 9 {AT3g44900 }{AT5g22900 } 1
+ 17870 2 {AT3g44910 AT3g44920 AT3g44930 }{AT5g22910 } 1
+ 17872 11 {AT3g45000 }{AT5g22950 } 1
+ 17873 4 {AT3g45010 }{AT5g22980 } 1
+
+
+-block 414
+ points contig1 contig2
+ 5 3 5
+
+ point dist markers orientation
+ 18326 0 {AT3g55920 }{AT5g58710 } -1
+ 18327 4 {AT3g55940 }{AT5g58670 AT5g58690 AT5g58700 } -1
+ 18331 9 {AT3g55980 }{AT5g58620 } 1
+ 18336 15 {AT3g56050 }{AT5g58540 } -1
+ 18338 17 {AT3g56070 }{AT5g58710 } -1
+
+
+-block 415
+ points contig1 contig2
+ 4 3 5
+
+ point dist markers orientation
+ 17434 0 {AT3g22810 }{AT5g43870 } -1
+ 17435 5 {AT3g22830 }{AT5g43840 } -1
+ 17436 4 {AT3g22850 }{AT5g43830 } -1
+ 17438 9 {AT3g22890 }{AT5g43780 } -1
+
+
+-block 416
+ points contig1 contig2
+ 4 3 5
+
+ point dist markers orientation
+ 17975 0 {AT3g47370 }{AT5g62300 } 1
+ 17976 6 {AT3g47380 }{AT5g62350 } 1
+ 17979 14 {AT3g47460 }{AT5g62410 } 1
+ 17984 14 {AT3g47550 }{AT5g62460 } 1
+
+
+-block 417
+ points contig1 contig2
+ 4 3 5
+
+ point dist markers orientation
+ 18198 0 {AT3g52880 }{AT5g03630 } 1
+ 18199 2 {AT3g52890 }{AT5g03640 } 1
+ 18203 5 {AT3g52920 }{AT5g03660 } 1
+ 18204 4 {AT3g52930 }{AT5g03690 } 1
+
+
+-block 418
+ points contig1 contig2
+ 4 3 5
+
+ point dist markers orientation
+ 18451 0 {AT3g61470 }{AT5g28450 } -1
+ 18452 8 {AT3g61480 }{AT5g28350 } 1
+ 18454 4 {AT3g61510 }{AT5g28360 } 1
+ 18456 2 {AT3g61520 }{AT5g28370 AT5g28460 } 1
+
+
+-block 419
+ points contig1 contig2
+ 3 3 5
+
+ point dist markers orientation
+ 16536 0 {AT3g01000 }{AT5g15510 } -1
+ 16537 3 {AT3g01010 }{AT5g15490 } -1
+ 16539 5 {AT3g01040 }{AT5g15470 } -1
+
+
+-block 420
+ points contig1 contig2
+ 3 3 5
+
+ point dist markers orientation
+ 16906 0 {AT3g07720 }{AT5g48180 } -1
+ 16907 8 {AT3g07780 }{AT5g48160 } -1
+ 16909 6 {AT3g07820 AT3g07830 AT3g07840 AT3g07850 }{AT5g48140 } 1
+
+
+-block 421
+ points contig1 contig2
+ 3 3 5
+
+ point dist markers orientation
+ 17227 0 {AT3g15330 }{AT5g54210 } 1
+ 17234 16 {AT3g15470 }{AT5g54200 } 1
+ 17237 23 {AT3g15510 }{AT5g53950 } -1
+
+
+-block 422
+ points contig1 contig2
+ 3 3 5
+
+ point dist markers orientation
+ 17750 0 {AT3g32110 }{AT5g33360 } 1
+ 17754 23 {AT3g32150 AT3g32160 AT3g32190 }{AT5g32590 } -1
+ 17757 17 {AT3g32300 }{AT5g32520 AT5g32530 } -1
+
+
+-block 423
+ points contig1 contig2
+ 3 3 5
+
+ point dist markers orientation
+ 17760 0 {AT3g32900 }{AT5g34900 } -1
+ 17763 18 {AT3g33010 }{AT5g34980 AT5g34990 } -1
+ 17766 10 {AT3g42100 AT3g42110 }{AT5g34960 } 1
+
+
+-block 424
+ points contig1 contig2
+ 3 3 5
+
+ point dist markers orientation
+ 17788 0 {AT3g42690 AT3g42700 }{AT5g34800 } 1
+ 17791 3 {AT3g42710 }{AT5g34820 } 1
+ 17792 17 {AT3g42730 AT3g42740 AT3g42750 }{AT5g34970 AT5g35000 AT5g35010 } 1
+
+
+-block 425
+ points contig1 contig2
+ 3 3 5
+
+ point dist markers orientation
+ 17787 0 {AT3g42690 AT3g42700 }{AT5g20750 } 1
+ 17790 3 {AT3g42710 }{AT5g20770 AT5g20780 } 1
+ 17797 23 {AT3g42880 }{AT5g20690 } 1
+
+
+-block 426
+ points contig1 contig2
+ 3 3 5
+
+ point dist markers orientation
+ 17800 0 {AT3g43010 AT3g43030 }{AT5g28970 } 1
+ 17802 3 {AT3g43040 }{AT5g28980 AT5g28990 } 1
+ 17806 9 {AT3g43100 }{AT5g28940 } -1
+
+
+-block 427
+ points contig1 contig2
+ 3 3 5
+
+ point dist markers orientation
+ 17995 0 {AT3g47820 }{AT5g62560 } 1
+ 18004 21 {AT3g47950 }{AT5g62670 } 1
+ 18005 2 {AT3g47960 }{AT5g62680 } 1
+
+
+-block 428
+ points contig1 contig2
+ 3 3 5
+
+ point dist markers orientation
+ 18020 0 {AT3g48360 }{AT5g63160 } 1
+ 18021 6 {AT3g48390 }{AT5g63190 } 1
+ 18027 11 {AT3g48440 }{AT5g63260 } 1
+
+
+-block 429
+ points contig1 contig2
+ 3 3 5
+
+ point dist markers orientation
+ 18190 0 {AT3g52310 }{AT5g06530 } -1
+ 18191 20 {AT3g52370 }{AT5g06390 } 1
+ 18192 16 {AT3g52470 }{AT5g06330 } -1
+
+
+-block 430
+ points contig1 contig2
+ 3 3 5
+
+ point dist markers orientation
+ 18239 0 {AT3g53610 }{AT5g59840 } 1
+ 18241 10 {AT3g53650 }{AT5g59910 } 1
+ 18244 6 {AT3g53700 }{AT5g59900 } -1
+
+
+-block 431
+ points contig1 contig2
+ 3 3 5
+
+ point dist markers orientation
+ 18256 0 {AT3g54030 }{AT5g01060 } 1
+ 18261 11 {AT3g54100 }{AT5g01100 } 1
+ 18265 10 {AT3g54140 }{AT5g01180 } 1
+
+
+-block 432
+ points contig1 contig2
+ 3 3 5
+
+ point dist markers orientation
+ 18277 0 {AT3g54780 }{AT5g60710 } -1
+ 18279 9 {AT3g54820 }{AT5g60660 } -1
+ 18290 15 {AT3g54960 }{AT5g60640 } 1
+
+
+-block 433
+ points contig1 contig2
+ 3 3 5
+
+ point dist markers orientation
+ 18293 0 {AT3g55040 }{AT5g02780 AT5g02790 } -1
+ 18294 3 {AT3g55050 }{AT5g02760 } -1
+ 18299 24 {AT3g55170 }{AT5g02610 } -1
+
+
+-block 434
+ points contig1 contig2
+ 3 3 5
+
+ point dist markers orientation
+ 18309 0 {AT3g55450 }{AT5g56460 } 1
+ 18312 19 {AT3g55500 }{AT5g56320 } -1
+ 18316 18 {AT3g55650 }{AT5g56350 } -1
+
+
+-block 435
+ points contig1 contig2
+ 3 3 5
+
+ point dist markers orientation
+ 18332 0 {AT3g55990 }{AT5g01620 } 1
+ 18341 12 {AT3g56090 }{AT5g01600 } 1
+ 18342 6 {AT3g56110 }{AT5g01640 } 1
+
+
+-block 436
+ points contig1 contig2
+ 3 3 5
+
+ point dist markers orientation
+ 18471 0 {AT3g62020 }{AT5g26700 } 1
+ 18475 7 {AT3g62060 }{AT5g26670 } 1
+ 18479 14 {AT3g62130 }{AT5g26600 } 1
+
+
+-block 437
+ points contig1 contig2
+ 3 3 5
+
+ point dist markers orientation
+ 18484 0 {AT3g62290 }{AT5g14670 } 1
+ 18487 25 {AT3g62310 }{AT5g14900 } 1
+ 18489 24 {AT3g62470 AT3g62530 AT3g62540 }{AT5g14820 } 1
+
+
+-block 438
+ points contig1 contig2
+ 17 4 4
+
+ point dist markers orientation
+ 18883 0 {AT4g11800 }{AT4g23000 } -1
+ 18884 2 {AT4g11810 }{AT4g22990 } -1
+ 18886 9 {AT4g11880 }{AT4g22950 } -1
+ 18888 19 {AT4g11890 AT4g11900 }{AT4g23130 AT4g23140 AT4g23150 AT4g23160 AT4g23170 AT4g23180 AT4g23190 AT4g23200 AT4g23210 AT4g23220 AT4g23230 AT4g23240 AT4g23250 AT4g23260 AT4g23270 AT4g23280 AT4g23290 AT4g23300 AT4g23310 AT4g23320 } -1
+ 18892 22 {AT4g11910 }{AT4g22920 } -1
+ 18893 2 {AT4g11920 }{AT4g22910 } -1
+ 18895 6 {AT4g11960 }{AT4g22890 } -1
+ 18896 7 {AT4g12000 }{AT4g22850 } -1
+ 18899 4 {AT4g12030 }{AT4g22840 } -1
+ 18901 12 {AT4g12080 }{AT4g22770 } -1
+ 18902 5 {AT4g12110 }{AT4g22750 } -1
+ 18907 21 {AT4g12300 AT4g12310 AT4g12320 AT4g12330 }{AT4g22690 AT4g22710 } -1
+ 18912 20 {AT4g12430 }{AT4g22590 } 1
+ 18914 3 {AT4g12440 }{AT4g22570 } -1
+ 18915 5 {AT4g12460 }{AT4g22540 } -1
+ 18916 21 {AT4g12560 }{AT4g22390 } -1
+ 18917 5 {AT4g12600 }{AT4g22380 } -1
+
+
+-block 439
+ points contig1 contig2
+ 14 4 4
+
+ point dist markers orientation
+ 18846 0 {AT4g10960 }{AT4g23920 } -1
+ 18852 6 {AT4g11010 }{AT4g23900 } -1
+ 18853 7 {AT4g11030 }{AT4g23850 } -1
+ 18855 8 {AT4g11070 }{AT4g23810 } -1
+ 18856 2 {AT4g11080 }{AT4g23800 } -1
+ 18857 2 {AT4g11090 }{AT4g23790 } -1
+ 18859 19 {AT4g11180 AT4g11190 AT4g11210 }{AT4g23690 } -1
+ 18860 7 {AT4g11220 }{AT4g23630 } -1
+ 18862 9 {AT4g11260 }{AT4g23570 } -1
+ 18866 10 {AT4g11310 AT4g11320 }{AT4g23520 } -1
+ 18869 6 {AT4g11350 }{AT4g23490 } -1
+ 18870 5 {AT4g11380 }{AT4g23460 } -1
+ 18872 6 {AT4g11410 }{AT4g23420 AT4g23430 } -1
+ 18873 13 {AT4g11460 AT4g11470 AT4g11480 AT4g11490 AT4g11520 AT4g11530 }{AT4g23130 AT4g23140 AT4g23150 AT4g23160 AT4g23170 AT4g23180 AT4g23190 AT4g23200 AT4g23210 AT4g23220 AT4g23230 AT4g23240 AT4g23250 AT4g23260 AT4g23270 AT4g23280 AT4g23290 AT4g23300 AT4g23310 AT4g23320 } -1
+
+
+-block 440
+ points contig1 contig2
+ 11 4 4
+
+ point dist markers orientation
+ 18681 0 {AT4g04260 }{AT4g22140 } -1
+ 18691 10 {AT4g04340 }{AT4g22120 } -1
+ 18704 13 {AT4g04450 }{AT4g22070 } -1
+ 18705 7 {AT4g04480 }{AT4g22030 } 1
+ 18714 13 {AT4g04610 }{AT4g21990 } -1
+ 18715 2 {AT4g04620 }{AT4g21980 } -1
+ 18716 12 {AT4g04700 AT4g04710 AT4g04720 AT4g04740 }{AT4g21940 } -1
+ 18719 10 {AT4g04790 }{AT4g21880 } -1
+ 18720 5 {AT4g04800 AT4g04810 AT4g04830 AT4g04840 }{AT4g21830 AT4g21840 } -1
+ 18721 5 {AT4g04860 }{AT4g21810 } -1
+ 18722 9 {AT4g04890 }{AT4g21750 } -1
+
+
+-block 441
+ points contig1 contig2
+ 10 4 4
+
+ point dist markers orientation
+ 18724 0 {AT4g05000 }{AT4g21560 } -1
+ 18725 9 {AT4g05020 }{AT4g21490 } -1
+ 18730 13 {AT4g05100 }{AT4g21440 } -1
+ 18733 16 {AT4g05180 }{AT4g21280 } -1
+ 18734 2 {AT4g05190 }{AT4g21270 } -1
+ 18742 23 {AT4g05330 }{AT4g21160 } -1
+ 18744 9 {AT4g05400 }{AT4g21140 } -1
+ 18745 2 {AT4g05410 }{AT4g21130 } -1
+ 18746 4 {AT4g05420 }{AT4g21100 } -1
+ 18747 4 {AT4g05450 }{AT4g21090 } -1
+
+
+-block 442
+ points contig1 contig2
+ 9 4 4
+
+ point dist markers orientation
+ 18648 0 {AT4g03650 }{AT4g07830 AT4g07850 } -1
+ 18652 22 {AT4g03730 }{AT4g08000 AT4g08010 AT4g08020 } -1
+ 18657 9 {AT4g03790 AT4g03850 AT4g03860 }{AT4g08050 AT4g08080 } 1
+ 18659 18 {AT4g03810 }{AT4g07840 } -1
+ 18664 4 {AT4g03840 }{AT4g07830 AT4g07850 } -1
+ 18668 18 {AT4g03900 AT4g03910 }{AT4g08000 AT4g08010 AT4g08020 } 1
+ 18674 22 {AT4g04070 }{AT4g07930 } -1
+ 18676 16 {AT4g04150 }{AT4g08030 } 1
+ 18679 13 {AT4g04230 }{AT4g08100 } -1
+
+
+-block 443
+ points contig1 contig2
+ 7 4 4
+
+ point dist markers orientation
+ 19200 0 {AT4g34720 }{AT4g38920 } -1
+ 19201 6 {AT4g34740 }{AT4g38880 } -1
+ 19202 18 {AT4g34840 }{AT4g38800 } -1
+ 19203 9 {AT4g34870 AT4g34960 }{AT4g38740 } -1
+ 19204 8 {AT4g34920 AT4g34930 }{AT4g38690 } -1
+ 19206 12 {AT4g34990 }{AT4g38620 } -1
+ 19208 5 {AT4g35010 }{AT4g38590 } -1
+
+
+-block 444
+ points contig1 contig2
+ 4 4 4
+
+ point dist markers orientation
+ 18678 0 {AT4g04170 }{AT4g04430 } -1
+ 18703 23 {AT4g04280 AT4g04380 AT4g04440 }{AT4g04600 } -1
+ 18684 15 {AT4g04290 }{AT4g04410 } 1
+ 18702 23 {AT4g04420 }{AT4g04560 } 1
+
+
+-block 445
+ points contig1 contig2
+ 4 4 4
+
+ point dist markers orientation
+ 18749 0 {AT4g05610 }{AT4g07490 } -1
+ 18750 10 {AT4g07310 }{AT4g07430 } -1
+ 18751 22 {AT4g07350 }{AT4g07700 } -1
+ 18752 6 {AT4g07360 AT4g07370 }{AT4g07560 AT4g07570 AT4g07590 AT4g07600 AT4g07610 AT4g07620 AT4g07630 AT4g07640 AT4g07660 AT4g07680 } 1
+
+
+-block 446
+ points contig1 contig2
+ 4 4 4
+
+ point dist markers orientation
+ 18755 0 {AT4g07530 }{AT4g07930 } -1
+ 18756 13 {AT4g07560 AT4g07570 AT4g07590 AT4g07600 AT4g07610 AT4g07620 AT4g07630 AT4g07640 AT4g07660 AT4g07680 }{AT4g08050 AT4g08080 } 1
+ 18759 11 {AT4g07750 }{AT4g08060 AT4g08070 } -1
+ 18769 9 {AT4g07830 AT4g07850 }{AT4g08100 } -1
+
+
+-block 447
+ points contig1 contig2
+ 4 4 4
+
+ point dist markers orientation
+ 19121 0 {AT4g26050 }{AT4g29880 } -1
+ 19122 9 {AT4g26070 }{AT4g29810 } -1
+ 19127 19 {AT4g26160 }{AT4g29670 } -1
+ 19129 21 {AT4g26210 }{AT4g29480 } -1
+
+
+-block 448
+ points contig1 contig2
+ 3 4 4
+
+ point dist markers orientation
+ 18680 0 {AT4g04230 }{AT4g10580 } 1
+ 18682 12 {AT4g04280 AT4g04380 AT4g04440 }{AT4g10460 } -1
+ 18685 18 {AT4g04290 }{AT4g10690 } 1
+
+
+-block 449
+ points contig1 contig2
+ 3 4 4
+
+ point dist markers orientation
+ 18683 0 {AT4g04280 AT4g04380 AT4g04440 }{AT4g21360 } 1
+ 18708 20 {AT4g04490 AT4g04500 AT4g04510 AT4g04540 AT4g04570 }{AT4g21370 AT4g21380 AT4g21390 AT4g21400 AT4g21410 } 1
+ 18713 8 {AT4g04600 }{AT4g21360 } -1
+
+
+-block 450
+ points contig1 contig2
+ 3 4 4
+
+ point dist markers orientation
+ 18791 0 {AT4g08720 }{AT4g28970 } 1
+ 18795 16 {AT4g08800 }{AT4g28860 AT4g28880 } 1
+ 18799 25 {AT4g08850 }{AT4g28650 } 1
+
+
+-block 451
+ points contig1 contig2
+ 3 4 4
+
+ point dist markers orientation
+ 18990 0 {AT4g16720 }{AT4g17390 } 1
+ 18992 11 {AT4g16780 }{AT4g17460 } 1
+ 18996 10 {AT4g16870 }{AT4g17450 } 1
+
+
+-block 452
+ points contig1 contig2
+ 3 4 4
+
+ point dist markers orientation
+ 19116 0 {AT4g25810 AT4g25820 }{AT4g30270 AT4g30280 AT4g30290 } -1
+ 19118 3 {AT4g25830 }{AT4g30250 } -1
+ 19119 21 {AT4g25870 }{AT4g30060 } 1
+
+
+-block 453
+ points contig1 contig2
+ 3 4 4
+
+ point dist markers orientation
+ 19205 0 {AT4g34940 }{AT4g36030 } -1
+ 19207 11 {AT4g35000 }{AT4g35970 } -1
+ 19209 4 {AT4g35020 }{AT4g35950 } -1
+
+
+-block 454
+ points contig1 contig2
+ 34 4 5
+
+ point dist markers orientation
+ 19737 0 {AT4g17190 }{AT5g47770 } -1
+ 19739 25 {AT4g17250 }{AT5g47580 } -1
+ 19740 6 {AT4g17270 }{AT5g47540 } -1
+ 19741 2 {AT4g17280 }{AT5g47530 } -1
+ 19742 11 {AT4g17340 }{AT5g47450 } -1
+ 19743 2 {AT4g17350 }{AT5g47440 } -1
+ 19744 6 {AT4g17410 }{AT5g47430 } -1
+ 19745 2 {AT4g17420 }{AT5g47420 } -1
+ 19746 9 {AT4g17460 }{AT5g47370 } -1
+ 19747 3 {AT4g17470 AT4g17480 AT4g17483 }{AT5g47330 AT5g47340 AT5g47350 } -1
+ 19748 3 {AT4g17486 }{AT5g47310 } -1
+ 19750 17 {AT4g17530 }{AT5g47200 } -1
+ 19752 14 {AT4g17580 }{AT5g47120 } -1
+ 19753 4 {AT4g17600 }{AT5g47110 } -1
+ 19755 3 {AT4g17615 }{AT5g47100 } -1
+ 19757 4 {AT4g17640 }{AT5g47080 } -1
+ 19759 3 {AT4g17660 }{AT5g47070 } -1
+ 19761 10 {AT4g17690 }{AT5g47000 } -1
+ 19762 10 {AT4g17700 AT4g17710 }{AT5g46880 } 1
+ 19764 2 {AT4g17720 }{AT5g46870 } -1
+ 19765 2 {AT4g17730 }{AT5g46860 } -1
+ 19771 19 {AT4g17870 }{AT5g46790 } -1
+ 19772 4 {AT4g17880 }{AT5g46760 } -1
+ 19773 2 {AT4g17890 }{AT5g46740 AT5g46750 } -1
+ 19774 4 {AT4g17900 }{AT5g46710 } -1
+ 19775 4 {AT4g17910 }{AT5g46680 } -1
+ 19776 12 {AT4g17970 }{AT5g46600 AT5g46610 } -1
+ 19777 2 {AT4g17980 }{AT5g46590 } -1
+ 19779 12 {AT4g18050 }{AT5g46540 } -1
+ 19781 10 {AT4g18100 }{AT5g46430 } -1
+ 19784 6 {AT4g18140 }{AT5g46410 } -1
+ 19785 6 {AT4g18160 }{AT5g46360 AT5g46370 } -1
+ 19790 21 {AT4g18290 }{AT5g46240 } -1
+ 19792 16 {AT4g18380 }{AT5g46170 } -1
+
+
+-block 455
+ points contig1 contig2
+ 31 4 5
+
+ point dist markers orientation
+ 19793 0 {AT4g18430 }{AT5g45750 } -1
+ 19797 22 {AT4g18480 }{AT5g45930 } -1
+ 19798 16 {AT4g18590 AT4g18600 }{AT5g45880 } -1
+ 19800 7 {AT4g18640 }{AT5g45840 } -1
+ 19806 7 {AT4g18700 }{AT5g45810 AT5g45820 } -1
+ 19811 7 {AT4g18730 }{AT5g45775 } -1
+ 19814 4 {AT4g18760 }{AT5g45770 } -1
+ 19820 6 {AT4g18800 }{AT5g45750 } -1
+ 19824 5 {AT4g18820 }{AT5g45720 } -1
+ 19826 6 {AT4g18880 }{AT5g45710 } -1
+ 19828 6 {AT4g18920 }{AT5g45690 } -1
+ 19829 7 {AT4g18970 }{AT5g45670 } -1
+ 19831 16 {AT4g19040 }{AT5g45560 } -1
+ 19832 3 {AT4g19050 }{AT5g45510 AT5g45550 } -1
+ 19833 5 {AT4g19060 }{AT5g45440 AT5g45490 } 1
+ 19834 5 {AT4g19090 }{AT5g45460 AT5g45470 AT5g45480 AT5g45530 AT5g45540 } -1
+ 19835 5 {AT4g19110 }{AT5g45430 } -1
+ 19836 5 {AT4g19130 }{AT5g45400 } -1
+ 19842 16 {AT4g19230 }{AT5g45340 } -1
+ 19847 19 {AT4g19410 AT4g19420 }{AT5g45280 } -1
+ 19863 16 {AT4g19530 }{AT5g45200 AT5g45230 AT5g45250 } -1
+ 19864 7 {AT4g19600 }{AT5g45190 } -1
+ 19865 10 {AT4g19640 }{AT5g45130 } -1
+ 19867 4 {AT4g19660 }{AT5g45110 } -1
+ 19869 4 {AT4g19700 }{AT5g45100 } -1
+ 19870 18 {AT4g19880 }{AT5g44990 AT5g45020 } -1
+ 19873 16 {AT4g19950 }{AT5g44860 } -1
+ 19875 5 {AT4g19970 }{AT5g44810 AT5g44820 } -1
+ 19878 16 {AT4g20080 }{AT5g44760 } 1
+ 19886 12 {AT4g20140 }{AT5g44700 } -1
+ 19890 6 {AT4g20170 }{AT5g44670 } -1
+
+
+-block 456
+ points contig1 contig2
+ 27 4 5
+
+ point dist markers orientation
+ 20165 0 {AT4g26650 }{AT5g55550 } -1
+ 20166 4 {AT4g26660 }{AT5g55520 } -1
+ 20167 2 {AT4g26670 }{AT5g55510 } -1
+ 20172 5 {AT4g26690 }{AT5g55480 } -1
+ 20177 9 {AT4g26700 }{AT5g55400 } -1
+ 20178 10 {AT4g26720 }{AT5g55260 } -1
+ 20179 4 {AT4g26740 }{AT5g55240 } -1
+ 20181 3 {AT4g26760 }{AT5g55230 } -1
+ 20182 5 {AT4g26780 }{AT5g55200 } -1
+ 20188 7 {AT4g26830 }{AT5g55180 } -1
+ 20189 8 {AT4g26850 }{AT5g55120 } -1
+ 20190 7 {AT4g26890 }{AT5g55090 } -1
+ 20191 4 {AT4g26910 }{AT5g55070 } -1
+ 20193 7 {AT4g26930 }{AT5g55020 } -1
+ 20194 19 {AT4g27000 }{AT5g54900 } -1
+ 20195 5 {AT4g27020 }{AT5g54870 } -1
+ 20196 11 {AT4g27070 }{AT5g54810 } -1
+ 20197 6 {AT4g27100 }{AT5g54780 } -1
+ 20199 5 {AT4g27130 }{AT5g54760 } -1
+ 20200 14 {AT4g27180 }{AT5g54670 } -1
+ 20201 6 {AT4g27230 }{AT5g54640 } -1
+ 20202 2 {AT4g27240 }{AT5g54630 } -1
+ 20205 11 {AT4g27260 }{AT5g54510 } -1
+ 20206 2 {AT4g27270 }{AT5g54500 } -1
+ 20212 24 {AT4g27400 }{AT5g54370 } 1
+ 20214 21 {AT4g27440 }{AT5g54190 } -1
+ 20219 21 {AT4g27580 }{AT5g54100 } 1
+
+
+-block 457
+ points contig1 contig2
+ 15 4 5
+
+ point dist markers orientation
+ 20136 0 {AT4g26390 }{AT5g56350 } -1
+ 20138 2 {AT4g26400 }{AT5g56340 } -1
+ 20139 6 {AT4g26420 }{AT5g56300 } -1
+ 20140 3 {AT4g26430 }{AT5g56280 } -1
+ 20141 2 {AT4g26440 }{AT5g56270 } -1
+ 20142 17 {AT4g26480 }{AT5g56140 } -1
+ 20143 10 {AT4g26490 }{AT5g56050 } -1
+ 20148 5 {AT4g26540 }{AT5g56040 } -1
+ 20153 5 {AT4g26560 AT4g26570 }{AT5g55990 } -1
+ 20154 3 {AT4g26580 }{AT5g55970 } -1
+ 20156 5 {AT4g26590 }{AT5g55930 } -1
+ 20158 2 {AT4g26600 }{AT5g55920 } -1
+ 20162 2 {AT4g26610 }{AT5g55910 } -1
+ 20164 2 {AT4g26620 }{AT5g55900 } -1
+ 20170 10 {AT4g26680 }{AT5g55840 } 1
+
+
+-block 458
+ points contig1 contig2
+ 13 4 5
+
+ point dist markers orientation
+ 20095 0 {AT4g25790 }{AT5g57625 } -1
+ 20096 6 {AT4g25800 }{AT5g57580 } -1
+ 20099 3 {AT4g25810 AT4g25820 }{AT5g57530 AT5g57540 AT5g57550 AT5g57560 } -1
+ 20101 6 {AT4g25830 }{AT5g57480 } -1
+ 20102 4 {AT4g25840 }{AT5g57440 } -1
+ 20103 20 {AT4g25850 AT4g25860 }{AT5g57240 } 1
+ 20104 4 {AT4g25870 }{AT5g57270 } 1
+ 20105 14 {AT4g25940 }{AT5g57200 } -1
+ 20108 4 {AT4g25970 }{AT5g57190 } -1
+ 20111 22 {AT4g26060 }{AT5g57060 } -1
+ 20113 3 {AT4g26080 }{AT5g57050 } -1
+ 20116 13 {AT4g26110 }{AT5g56950 } 1
+ 20118 11 {AT4g26140 }{AT5g56870 } -1
+
+
+-block 459
+ points contig1 contig2
+ 11 4 5
+
+ point dist markers orientation
+ 20057 0 {AT4g25090 }{AT5g51060 } 1
+ 20058 5 {AT4g25100 }{AT5g51100 } 1
+ 20062 21 {AT4g25150 }{AT5g51260 } 1
+ 20066 2 {AT4g25160 }{AT5g51270 } 1
+ 20068 24 {AT4g25230 }{AT5g51450 } 1
+ 20070 4 {AT4g25240 }{AT5g51480 } 1
+ 20075 17 {AT4g25320 }{AT5g51590 } -1
+ 20076 9 {AT4g25360 }{AT5g51640 } -1
+ 20078 23 {AT4g25420 }{AT5g51810 } 1
+ 20080 17 {AT4g25440 }{AT5g51980 } 1
+ 20081 4 {AT4g25470 AT4g25480 AT4g25490 }{AT5g51990 } 1
+
+
+-block 460
+ points contig1 contig2
+ 8 4 5
+
+ point dist markers orientation
+ 19900 0 {AT4g20390 }{AT5g44550 } -1
+ 19901 6 {AT4g20430 }{AT5g44530 } -1
+ 19904 8 {AT4g20460 }{AT5g44480 } -1
+ 19908 24 {AT4g20800 AT4g20820 AT4g20830 AT4g20840 AT4g20860 }{AT5g44360 } -1
+ 19912 7 {AT4g20890 }{AT5g44340 } -1
+ 19914 2 {AT4g20900 }{AT5g44330 } -1
+ 19917 9 {AT4g20980 }{AT5g44320 } -1
+ 19922 17 {AT4g21070 }{AT5g44230 } 1
+
+
+-block 461
+ points contig1 contig2
+ 8 4 5
+
+ point dist markers orientation
+ 20220 0 {AT4g27680 }{AT5g53540 } -1
+ 20221 2 {AT4g27690 }{AT5g53530 } -1
+ 20222 5 {AT4g27730 }{AT5g53510 AT5g53520 } -1
+ 20226 8 {AT4g27780 }{AT5g53470 } 1
+ 20231 19 {AT4g27880 }{AT5g53360 } 1
+ 20232 4 {AT4g27890 }{AT5g53400 } 1
+ 20233 5 {AT4g27910 }{AT5g53430 } 1
+ 20235 17 {AT4g27960 }{AT5g53300 } 1
+
+
+-block 462
+ points contig1 contig2
+ 8 4 5
+
+ point dist markers orientation
+ 20329 0 {AT4g29900 }{AT5g57110 } 1
+ 20330 15 {AT4g29950 }{AT5g57210 } -1
+ 20337 17 {AT4g30060 }{AT5g57270 } 1
+ 20338 14 {AT4g30160 }{AT5g57320 } 1
+ 20340 6 {AT4g30190 }{AT5g57350 } 1
+ 20343 17 {AT4g30250 }{AT5g57480 } 1
+ 20346 7 {AT4g30270 AT4g30280 AT4g30290 }{AT5g57530 AT5g57540 AT5g57550 AT5g57560 } 1
+ 20348 20 {AT4g30340 }{AT5g57690 } 1
+
+
+-block 463
+ points contig1 contig2
+ 8 4 5
+
+ point dist markers orientation
+ 20642 0 {AT4g37250 }{AT5g67280 } 1
+ 20643 3 {AT4g37260 }{AT5g67300 } 1
+ 20646 6 {AT4g37310 AT4g37320 AT4g37330 AT4g37340 AT4g37360 AT4g37370 AT4g37400 AT4g37410 AT4g37430 }{AT5g67310 } 1
+ 20658 21 {AT4g37520 AT4g37530 }{AT5g67400 } 1
+ 20659 3 {AT4g37540 }{AT5g67420 } 1
+ 20660 4 {AT4g37580 }{AT5g67430 } 1
+ 20661 2 {AT4g37590 }{AT5g67440 } 1
+ 20662 6 {AT4g37610 }{AT5g67480 } 1
+
+
+-block 464
+ points contig1 contig2
+ 6 4 5
+
+ point dist markers orientation
+ 19989 0 {AT4g23470 }{AT5g41390 } 1
+ 19990 8 {AT4g23490 }{AT5g41460 } 1
+ 19996 24 {AT4g23630 }{AT5g41600 } 1
+ 20002 7 {AT4g23700 }{AT5g41610 } 1
+ 20005 11 {AT4g23740 }{AT5g41680 } 1
+ 20006 25 {AT4g23820 }{AT5g41870 } 1
+
+
+-block 465
+ points contig1 contig2
+ 6 4 5
+
+ point dist markers orientation
+ 20040 0 {AT4g24770 }{AT5g50250 } 1
+ 20047 12 {AT4g24810 }{AT5g50330 } 1
+ 20048 14 {AT4g24890 }{AT5g50400 } 1
+ 20049 23 {AT4g24940 }{AT5g50580 AT5g50680 } 1
+ 20051 15 {AT4g24970 }{AT5g50780 } 1
+ 20053 5 {AT4g25010 }{AT5g50790 AT5g50800 } 1
+
+
+-block 466
+ points contig1 contig2
+ 6 4 5
+
+ point dist markers orientation
+ 20083 0 {AT4g25560 }{AT5g52260 } 1
+ 20085 12 {AT4g25590 }{AT5g52360 } 1
+ 20086 15 {AT4g25630 }{AT5g52470 AT5g52490 } 1
+ 20091 14 {AT4g25700 }{AT5g52570 } 1
+ 20092 12 {AT4g25740 }{AT5g52650 } 1
+ 20094 20 {AT4g25750 }{AT5g52860 } 1
+
+
+-block 467
+ points contig1 contig2
+ 5 4 5
+
+ point dist markers orientation
+ 19398 0 {AT4g07310 }{AT5g35280 } 1
+ 19408 14 {AT4g07440 }{AT5g35260 } -1
+ 19409 25 {AT4g07470 }{AT5g35030 } 1
+ 19414 14 {AT4g07690 }{AT5g35040 } 1
+ 19417 14 {AT4g07790 }{AT5g34960 } -1
+
+
+-block 468
+ points contig1 contig2
+ 5 4 5
+
+ point dist markers orientation
+ 20421 0 {AT4g32290 }{AT5g25330 } -1
+ 20427 16 {AT4g32390 }{AT5g25400 } 1
+ 20438 13 {AT4g32460 }{AT5g25460 } -1
+ 20440 8 {AT4g32510 }{AT5g25430 } -1
+ 20443 22 {AT4g32540 }{AT5g25620 } -1
+
+
+-block 469
+ points contig1 contig2
+ 4 4 5
+
+ point dist markers orientation
+ 20020 0 {AT4g24260 }{AT5g49720 } 1
+ 20022 15 {AT4g24280 }{AT5g49910 } 1
+ 20023 8 {AT4g24330 }{AT5g49940 } -1
+ 20024 9 {AT4g24390 }{AT5g49980 } 1
+
+
+-block 470
+ points contig1 contig2
+ 4 4 5
+
+ point dist markers orientation
+ 20673 0 {AT4g37770 }{AT5g65800 } -1
+ 20676 2 {AT4g37780 }{AT5g65790 } -1
+ 20681 8 {AT4g37800 }{AT5g65730 } -1
+ 20682 10 {AT4g37870 }{AT5g65690 } -1
+
+
+-block 471
+ points contig1 contig2
+ 3 4 5
+
+ point dist markers orientation
+ 19358 0 {AT4g03980 }{AT5g34890 } 1
+ 19359 4 {AT4g04010 }{AT5g34900 } 1
+ 19360 22 {AT4g04130 }{AT5g34790 } 1
+
+
+-block 472
+ points contig1 contig2
+ 3 4 5
+
+ point dist markers orientation
+ 19518 0 {AT4g11170 }{AT5g41540 AT5g41550 } -1
+ 19521 8 {AT4g11220 }{AT5g41600 } -1
+ 19538 23 {AT4g11350 }{AT5g41460 } -1
+
+
+-block 473
+ points contig1 contig2
+ 3 4 5
+
+ point dist markers orientation
+ 19660 0 {AT4g14610 }{AT5g43730 AT5g43740 } -1
+ 19666 11 {AT4g14680 }{AT5g43780 } 1
+ 19667 14 {AT4g14740 }{AT5g43870 } 1
+
+
+-block 474
+ points contig1 contig2
+ 3 4 5
+
+ point dist markers orientation
+ 19689 0 {AT4g15330 AT4g15350 AT4g15360 AT4g15380 }{AT5g47990 } -1
+ 19692 3 {AT4g15340 AT4g15370 }{AT5g48010 } -1
+ 19694 7 {AT4g15390 }{AT5g47950 } 1
+
+
+-block 475
+ points contig1 contig2
+ 3 4 5
+
+ point dist markers orientation
+ 20030 0 {AT4g24530 }{AT5g65470 } -1
+ 20031 5 {AT4g24560 }{AT5g65450 } -1
+ 20034 6 {AT4g24610 }{AT5g65440 } -1
+
+
+-block 476
+ points contig1 contig2
+ 3 4 5
+
+ point dist markers orientation
+ 20112 0 {AT4g26070 }{AT5g56580 } -1
+ 20124 25 {AT4g26260 }{AT5g56640 } -1
+ 20126 2 {AT4g26270 }{AT5g56630 } -1
+
+
+-block 477
+ points contig1 contig2
+ 3 4 5
+
+ point dist markers orientation
+ 20266 0 {AT4g28510 }{AT5g44140 } -1
+ 20267 3 {AT4g28520 }{AT5g44120 } -1
+ 20269 4 {AT4g28540 }{AT5g44100 } -1
+
+
+-block 478
+ points contig1 contig2
+ 3 4 5
+
+ point dist markers orientation
+ 20314 0 {AT4g29220 }{AT5g56630 } -1
+ 20318 14 {AT4g29340 AT4g29350 }{AT5g56600 } -1
+ 20320 2 {AT4g29360 }{AT5g56590 } -1
+
+
+-block 479
+ points contig1 contig2
+ 3 4 5
+
+ point dist markers orientation
+ 20358 0 {AT4g30560 }{AT5g57940 } -1
+ 20360 12 {AT4g30640 }{AT5g57900 } -1
+ 20361 7 {AT4g30680 }{AT5g57870 } -1
+
+
+-block 480
+ points contig1 contig2
+ 3 4 5
+
+ point dist markers orientation
+ 20426 0 {AT4g32390 }{AT5g11230 } 1
+ 20437 25 {AT4g32460 }{AT5g11420 } -1
+ 20442 17 {AT4g32540 }{AT5g11320 } -1
+
+
+-block 481
+ points contig1 contig2
+ 3 4 5
+
+ point dist markers orientation
+ 20449 0 {AT4g32730 }{AT5g11510 } 1
+ 20450 16 {AT4g32790 }{AT5g11610 } -1
+ 20457 22 {AT4g32920 }{AT5g11700 } 1
+
+
+-block 482
+ points contig1 contig2
+ 3 4 5
+
+ point dist markers orientation
+ 20587 0 {AT4g36030 }{AT5g66200 } 1
+ 20592 5 {AT4g36070 }{AT5g66210 } 1
+ 20601 18 {AT4g36160 }{AT5g66300 } 1
+
+
+-block 483
+ points contig1 contig2
+ 3 4 5
+
+ point dist markers orientation
+ 20629 0 {AT4g36890 }{AT5g67230 } -1
+ 20630 8 {AT4g36920 }{AT5g67180 } -1
+ 20631 8 {AT4g36950 }{AT5g67130 } -1
+
+
+-block 484
+ points contig1 contig2
+ 3 4 5
+
+ point dist markers orientation
+ 20668 0 {AT4g37750 }{AT5g57390 } -1
+ 20675 21 {AT4g37780 }{AT5g57620 } -1
+ 20680 8 {AT4g37800 }{AT5g57530 AT5g57540 AT5g57550 AT5g57560 } 1
+
+
+-block 485
+ points contig1 contig2
+ 3 4 5
+
+ point dist markers orientation
+ 20752 0 {AT4g39770 }{AT5g10100 } -1
+ 20755 10 {AT4g39800 }{AT5g10170 } 1
+ 20759 17 {AT4g39890 }{AT5g10260 } 1
+
+
+-block 486
+ points contig1 contig2
+ 3 4 5
+
+ point dist markers orientation
+ 20767 0 {AT4g39990 }{AT5g65270 } 1
+ 20773 12 {AT4g40030 AT4g40040 }{AT5g65350 AT5g65360 } 1
+ 20774 6 {AT4g40060 }{AT5g65310 } 1
+
+
+-block 487
+ points contig1 contig2
+ 21 5 5
+
+ point dist markers orientation
+ 21099 0 {AT5g10030 }{AT5g65210 } -1
+ 21100 10 {AT5g10090 }{AT5g65160 } 1
+ 21101 2 {AT5g10100 }{AT5g65140 } -1
+ 21102 12 {AT5g10140 }{AT5g65050 AT5g65060 } -1
+ 21105 11 {AT5g10220 AT5g10230 }{AT5g65020 } -1
+ 21106 2 {AT5g10240 }{AT5g65010 } -1
+ 21107 4 {AT5g10260 }{AT5g64990 } -1
+ 21111 4 {AT5g10270 }{AT5g64960 } -1
+ 21116 25 {AT5g10280 }{AT5g65230 } 1
+ 21121 2 {AT5g10290 }{AT5g65240 } 1
+ 21122 8 {AT5g10350 }{AT5g65260 } 1
+ 21124 13 {AT5g10390 AT5g10400 }{AT5g65350 AT5g65360 } 1
+ 21128 4 {AT5g10420 }{AT5g65380 } 1
+ 21129 6 {AT5g10440 }{AT5g65420 } 1
+ 21132 2 {AT5g10450 }{AT5g65430 } 1
+ 21133 5 {AT5g10470 }{AT5g65460 } 1
+ 21136 9 {AT5g10510 }{AT5g65510 } 1
+ 21139 3 {AT5g10520 }{AT5g65530 } 1
+ 21140 8 {AT5g10530 }{AT5g65600 } 1
+ 21141 3 {AT5g10540 }{AT5g65620 } 1
+ 21142 2 {AT5g10550 }{AT5g65630 } 1
+
+
+-block 488
+ points contig1 contig2
+ 20 5 5
+
+ point dist markers orientation
+ 20995 0 {AT5g07180 }{AT5g62230 } -1
+ 20999 17 {AT5g07220 }{AT5g62100 } -1
+ 21005 21 {AT5g07290 }{AT5g61960 } -1
+ 21006 6 {AT5g07300 }{AT5g61900 } -1
+ 21008 9 {AT5g07320 }{AT5g61810 } -1
+ 21009 4 {AT5g07340 }{AT5g61790 } -1
+ 21010 2 {AT5g07350 }{AT5g61780 } -1
+ 21011 4 {AT5g07370 }{AT5g61760 } -1
+ 21014 10 {AT5g07410 AT5g07420 AT5g07430 }{AT5g61680 } -1
+ 21016 5 {AT5g07450 }{AT5g61650 } -1
+ 21017 2 {AT5g07460 AT5g07470 }{AT5g61640 } -1
+ 21020 22 {AT5g07620 }{AT5g61570 } -1
+ 21021 14 {AT5g07660 }{AT5g61460 } -1
+ 21024 5 {AT5g07680 }{AT5g61430 } -1
+ 21028 2 {AT5g07690 AT5g07700 }{AT5g61420 } -1
+ 21030 4 {AT5g07710 }{AT5g61390 } -1
+ 21032 14 {AT5g07800 }{AT5g61290 } -1
+ 21034 7 {AT5g07830 }{AT5g61250 } -1
+ 21035 3 {AT5g07840 }{AT5g61230 } -1
+ 21037 4 {AT5g07880 }{AT5g61210 } -1
+
+
+-block 489
+ points contig1 contig2
+ 14 5 5
+
+ point dist markers orientation
+ 21145 0 {AT5g10580 }{AT5g24790 } 1
+ 21147 13 {AT5g10650 }{AT5g24870 } 1
+ 21148 15 {AT5g10740 }{AT5g24940 } 1
+ 21150 14 {AT5g10800 }{AT5g25060 } 1
+ 21151 3 {AT5g10820 }{AT5g25040 AT5g25050 } -1
+ 21152 7 {AT5g10840 }{AT5g25100 } 1
+ 21154 10 {AT5g10930 }{AT5g25110 } 1
+ 21158 21 {AT5g11060 }{AT5g25220 } 1
+ 21159 8 {AT5g11090 }{AT5g25280 } 1
+ 21162 7 {AT5g11130 }{AT5g25310 } 1
+ 21166 17 {AT5g11230 }{AT5g25400 } 1
+ 21173 9 {AT5g11300 }{AT5g25380 } -1
+ 21177 19 {AT5g11420 }{AT5g25460 } 1
+ 21178 7 {AT5g11430 }{AT5g25520 } 1
+
+
+-block 490
+ points contig1 contig2
+ 11 5 5
+
+ point dist markers orientation
+ 21041 0 {AT5g08190 }{AT5g23090 } 1
+ 21042 10 {AT5g08230 }{AT5g23150 } -1
+ 21043 6 {AT5g08250 }{AT5g23190 } 1
+ 21044 3 {AT5g08260 }{AT5g23210 } 1
+ 21045 2 {AT5g08270 }{AT5g23200 } 1
+ 21046 7 {AT5g08300 }{AT5g23250 } 1
+ 21048 12 {AT5g08340 }{AT5g23330 } 1
+ 21049 3 {AT5g08350 }{AT5g23350 AT5g23360 AT5g23370 } 1
+ 21050 9 {AT5g08390 }{AT5g23430 } -1
+ 21051 11 {AT5g08440 }{AT5g23490 } 1
+ 21057 15 {AT5g08500 }{AT5g23575 } 1
+
+
+-block 491
+ points contig1 contig2
+ 11 5 5
+
+ point dist markers orientation
+ 21081 0 {AT5g09670 }{AT5g64550 } 1
+ 21082 3 {AT5g09690 }{AT5g64560 } 1
+ 21084 2 {AT5g09700 AT5g09730 }{AT5g64570 } 1
+ 21086 7 {AT5g09740 }{AT5g64610 } 1
+ 21087 5 {AT5g09760 }{AT5g64640 } 1
+ 21088 2 {AT5g09770 }{AT5g64650 } 1
+ 21091 13 {AT5g09840 }{AT5g64710 } 1
+ 21094 6 {AT5g09870 }{AT5g64740 } 1
+ 21095 5 {AT5g09900 }{AT5g64760 } 1
+ 21096 11 {AT5g09930 }{AT5g64840 } 1
+ 21098 15 {AT5g10010 }{AT5g64910 } 1
+
+
+-block 492
+ points contig1 contig2
+ 10 5 5
+
+ point dist markers orientation
+ 21061 0 {AT5g08570 }{AT5g63680 } 1
+ 21062 5 {AT5g08590 }{AT5g63650 } -1
+ 21064 4 {AT5g08610 AT5g08620 }{AT5g63630 } -1
+ 21069 25 {AT5g09220 }{AT5g63850 } 1
+ 21070 7 {AT5g09260 }{AT5g63880 } 1
+ 21071 13 {AT5g09290 }{AT5g63980 AT5g64000 } 1
+ 21073 11 {AT5g09330 }{AT5g64060 } 1
+ 21074 3 {AT5g09350 }{AT5g64070 } 1
+ 21076 19 {AT5g09410 }{AT5g64220 } 1
+ 21078 24 {AT5g09540 }{AT5g64360 } 1
+
+
+-block 493
+ points contig1 contig2
+ 6 5 5
+
+ point dist markers orientation
+ 21181 0 {AT5g11590 }{AT5g25810 } 1
+ 21183 3 {AT5g11610 }{AT5g25820 } 1
+ 21184 12 {AT5g11670 }{AT5g25880 } 1
+ 21187 13 {AT5g11730 }{AT5g25970 } 1
+ 21189 21 {AT5g11830 }{AT5g26090 } 1
+ 21191 23 {AT5g12000 }{AT5g26150 } 1
+
+
+-block 494
+ points contig1 contig2
+ 5 5 5
+
+ point dist markers orientation
+ 21550 0 {AT5g26870 AT5g26950 }{AT5g27580 } -1
+ 21552 4 {AT5g26900 }{AT5g27570 } -1
+ 21554 11 {AT5g27000 }{AT5g27550 } -1
+ 21556 8 {AT5g27050 AT5g27070 }{AT5g27580 } 1
+ 21559 3 {AT5g27080 }{AT5g27570 } 1
+
+
+-block 495
+ points contig1 contig2
+ 4 5 5
+
+ point dist markers orientation
+ 20837 0 {AT5g02560 }{AT5g59870 } -1
+ 20839 4 {AT5g02570 }{AT5g59910 } -1
+ 20840 19 {AT5g02620 }{AT5g60070 } -1
+ 20853 21 {AT5g02810 }{AT5g60100 } 1
+
+
+-block 496
+ points contig1 contig2
+ 4 5 5
+
+ point dist markers orientation
+ 20986 0 {AT5g07070 }{AT5g58380 } 1
+ 20987 5 {AT5g07090 }{AT5g58420 } 1
+ 20988 5 {AT5g07120 }{AT5g58440 } 1
+ 20991 10 {AT5g07140 }{AT5g58520 } 1
+
+
+-block 497
+ points contig1 contig2
+ 4 5 5
+
+ point dist markers orientation
+ 21195 0 {AT5g12080 }{AT5g19520 } -1
+ 21202 4 {AT5g12110 }{AT5g19510 } -1
+ 21203 14 {AT5g12150 }{AT5g19390 } -1
+ 21204 6 {AT5g12180 }{AT5g19360 AT5g19450 } -1
+
+
+-block 498
+ points contig1 contig2
+ 3 5 5
+
+ point dist markers orientation
+ 21275 0 {AT5g15050 }{AT5g39990 } -1
+ 21285 17 {AT5g15120 }{AT5g39890 } 1
+ 21286 12 {AT5g15200 }{AT5g39850 } -1
+
+
+-block 499
+ points contig1 contig2
+ 3 5 5
+
+ point dist markers orientation
+ 21329 0 {AT5g16600 }{AT5g61420 } -1
+ 21335 6 {AT5g16640 }{AT5g61400 } 1
+ 21340 15 {AT5g16770 }{AT5g61420 } -1
+
+
+-block 500
+ points contig1 contig2
+ 3 5 5
+
+ point dist markers orientation
+ 21391 0 {AT5g18460 }{AT5g56530 } 1
+ 21400 21 {AT5g18610 }{AT5g56460 } 1
+ 21404 21 {AT5g18820 }{AT5g56500 } 1
+
+
+-block 501
+ points contig1 contig2
+ 3 5 5
+
+ point dist markers orientation
+ 21499 0 {AT5g24320 }{AT5g53500 } 1
+ 21502 10 {AT5g24380 }{AT5g53550 } 1
+ 21504 3 {AT5g24390 }{AT5g53570 } 1
+
+
+-block 502
+ points contig1 contig2
+ 3 5 5
+
+ point dist markers orientation
+ 21598 0 {AT5g29030 AT5g29040 }{AT5g32590 } -1
+ 21600 17 {AT5g30410 }{AT5g32520 AT5g32530 } 1
+ 21601 8 {AT5g30430 }{AT5g32590 } 1
+
+
+-block 503
+ points contig1 contig2
+ 3 5 5
+
+ point dist markers orientation
+ 21611 0 {AT5g34460 }{AT5g37080 AT5g37100 } 1
+ 21614 22 {AT5g34960 }{AT5g37110 } -1
+ 21615 25 {AT5g34970 AT5g35000 AT5g35010 }{AT5g36840 AT5g36850 AT5g36860 } -1
+
+
+-block 504
+ points contig1 contig2
+ 3 5 5
+
+ point dist markers orientation
+ 21700 0 {AT5g39680 }{AT5g40410 } -1
+ 21711 23 {AT5g39750 AT5g39810 }{AT5g40220 } -1
+ 21713 19 {AT5g39800 }{AT5g40080 } -1
+
+
+-block 505
+ points contig1 contig2
+ 3 5 5
+
+ point dist markers orientation
+ 21826 0 {AT5g44870 }{AT5g45200 AT5g45230 AT5g45250 } -1
+ 21827 15 {AT5g45050 }{AT5g45210 AT5g45260 } -1
+ 21828 2 {AT5g45060 }{AT5g45200 AT5g45230 AT5g45250 } -1
+
+
+-block 506
+ points contig1 contig2
+ 3 5 5
+
+ point dist markers orientation
+ 21924 0 {AT5g50510 }{AT5g50620 } 1
+ 21925 2 {AT5g50520 }{AT5g50630 } 1
+ 21926 2 {AT5g50530 }{AT5g50640 } 1
+
+
+-block 507
+ points contig1 contig2
+ 3 5 5
+
+ point dist markers orientation
+ 21978 0 {AT5g53950 }{AT5g61430 } 1
+ 21982 23 {AT5g54230 }{AT5g61420 } 1
+ 21988 21 {AT5g54380 }{AT5g61350 } -1
+
+
+-by contig
+ contig1 contig2 blocks
+ 1 1 50
+ 1 2 52
+ 1 3 43
+ 1 4 34
+ 1 5 25
+ 2 2 27
+ 2 3 48
+ 2 4 48
+ 2 5 18
+ 3 3 15
+ 3 4 25
+ 3 5 53
+ 4 4 16
+ 4 5 33
+ 5 5 21
+
+-by size
+ points obs exp p
+ 3 243 5.23e+01 1.00e+00
+ 4 83 2.55e+00 9.22e-01
+ 5 35 1.24e-01 1.17e-01
+ 6 21 6.04e-03 6.02e-03
+ 7 22 2.94e-04 2.94e-04
+ 8 13 1.43e-05 1.43e-05
+ 9 12 6.97e-07 7.15e-07
+ 10 5 3.40e-08 5.96e-08
+ 11 12 1.65e-09 0.00e+00
+ 12 2 8.05e-11 0.00e+00
+ 13 4 3.92e-12 0.00e+00
+ 14 7 1.91e-13 0.00e+00
+ 15 5 9.30e-15 0.00e+00
+ 16 3 4.53e-16 0.00e+00
+ 17 3 2.20e-17 0.00e+00
+ 18 2 1.07e-18 0.00e+00
+ 19 4 5.23e-20 0.00e+00
+ 20 3 2.54e-21 0.00e+00
+ 21 3 1.24e-22 0.00e+00
+ 22 2 6.03e-24 0.00e+00
+ 23 4 2.94e-25 0.00e+00
+ 24 1 1.43e-26 0.00e+00
+ 25 1 6.97e-28 0.00e+00
+ 26 4 3.39e-29 0.00e+00
+ 27 1 1.65e-30 0.00e+00
+ 28 2 8.04e-32 0.00e+00
+ 29 1 3.92e-33 0.00e+00
+ 30 2 1.91e-34 0.00e+00
+ 31 2 9.15e-36 0.00e+00
+ 34 1 0.00e+00 0.00e+00
+ 40 1 0.00e+00 0.00e+00
+ 44 1 0.00e+00 0.00e+00
+ 60 1 0.00e+00 0.00e+00
+ 66 1 0.00e+00 0.00e+00
+ 79 1 0.00e+00 0.00e+00
diff --git a/sample_input/check b/sample_input/check
new file mode 100644
index 0000000..32d2d51
--- /dev/null
+++ b/sample_input/check
@@ -0,0 +1,110 @@
+ARGS PROCESSED
+
+Wed Nov 19 13:08:24 2003
+FISH v1.0
+FISH is copyright ©