[med-svn] r237 - in
trunk/packages/primer3/branches/upstream/current: . src test
test/primer_global_err
Charles Plessy
charles-guest at alioth.debian.org
Sat Mar 31 23:30:03 UTC 2007
Author: charles-guest
Date: 2007-03-31 23:30:01 +0000 (Sat, 31 Mar 2007)
New Revision: 237
Added:
trunk/packages/primer3/branches/upstream/current/README.OSX.txt
trunk/packages/primer3/branches/upstream/current/README.WINXP.txt
trunk/packages/primer3/branches/upstream/current/src/Makefile.OSXUniversal
Removed:
trunk/packages/primer3/branches/upstream/current/primer3-1.1.0-beta
Modified:
trunk/packages/primer3/branches/upstream/current/README.txt
trunk/packages/primer3/branches/upstream/current/src/Makefile
trunk/packages/primer3/branches/upstream/current/src/boulder_input.c
trunk/packages/primer3/branches/upstream/current/src/dpal.c
trunk/packages/primer3/branches/upstream/current/src/oligotm.c
trunk/packages/primer3/branches/upstream/current/src/oligotm.h
trunk/packages/primer3/branches/upstream/current/src/oligotm_main.c
trunk/packages/primer3/branches/upstream/current/src/primer3_main.c
trunk/packages/primer3/branches/upstream/current/src/primer3_release.h
trunk/packages/primer3/branches/upstream/current/src/release_notes.txt
trunk/packages/primer3/branches/upstream/current/test/oligotm_test.pl
trunk/packages/primer3/branches/upstream/current/test/p3test.pl
trunk/packages/primer3/branches/upstream/current/test/primer_boundary1_formatted_output
trunk/packages/primer3/branches/upstream/current/test/primer_boundary_formatted_output
trunk/packages/primer3/branches/upstream/current/test/primer_global_err/empty_1.out2
trunk/packages/primer3/branches/upstream/current/test/primer_global_err/repeat_lib_err4.out
trunk/packages/primer3/branches/upstream/current/test/primer_global_err/repeat_lib_err4.out2
trunk/packages/primer3/branches/upstream/current/test/primer_global_err/repeat_lib_int_err4.out
trunk/packages/primer3/branches/upstream/current/test/primer_global_err/repeat_lib_int_err4.out2
trunk/packages/primer3/branches/upstream/current/test/primer_internal1_formatted_output
trunk/packages/primer3/branches/upstream/current/test/primer_internal_formatted_output
trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_boundary1_formatted_output
trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_boundary2_formatted_output
trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_formatted_output
trunk/packages/primer3/branches/upstream/current/test/primer_must_use_formatted_output
trunk/packages/primer3/branches/upstream/current/test/primer_position_penalty_formatted_output
trunk/packages/primer3/branches/upstream/current/test/primer_task_formatted_output
trunk/packages/primer3/branches/upstream/current/test/primer_tm_lc_masking_formatted_output
Log:
Load /tmp/tmp.cVA2bt/primer3-1.1.1 into
trunk/packages/primer3/branches/upstream/current.
Added: trunk/packages/primer3/branches/upstream/current/README.OSX.txt
===================================================================
--- trunk/packages/primer3/branches/upstream/current/README.OSX.txt 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/README.OSX.txt 2007-03-31 23:30:01 UTC (rev 237)
@@ -0,0 +1,81 @@
+OS X (10.4) Universal Binary Installation Instructions (bcf; 3/27/2006;23:33)
+
+
+How to install this software
+============================
+
+1. Double click on the .tar.gz file to extract the archive.
+
+2. The binary files are located in the 'bin' [for 'binary'] folder
+
+3. (Optional) To run the tests, cd to the new directory and then the test folder
+
+4. (Optional) Within this folder run:
+ a. perl -w p3test.pl
+
+5. (Optional) You should not see 'FAILED' during the tests.
+
+6. (Optional) *NOTE*: If your perl command is not called perl
+ (for example, if it is called perl5) you will have to modify
+ the internals of the test scripts).
+
+7. Copy the following files to a location of your choice:
+ a. bin/long_seq_tm_test
+ b. bin/ntdpal
+ c. bin/oligotm
+ d. bin/primer3_core
+
+8. (Optional) Make sure this location is within your $PATH (see below)
+
+
+Where to put the binary files
+=============================
+
+A good place to put these is within ~/bin/ (this means in your home folder, within a folder named `bin` [for 'binary']).
+
+You can also just drag the 'bin' folder to a location within your home directory.
+
+You can certainly also copy the files within 'bin' to /usr/local/bin (if you are an administrator) or another similar location.
+
+You may need to adjust the permissions on the binaries if you get fancy.
+
+
+Add the location to your $PATH
+==============================
+
+This is an optional step, but it will allow you to run primer3 in any directory on your machine as your user just by typing its name (primer3_core).
+
+*** You should be very careful when altering your $PATH as things can go very wrong. See below for an alternate method. ***
+
+If you added the binaries to /usr/local/bin, then you do not need to do this.
+
+If you added the binaries to a local directory (let's say ~/bin/), do the following:
+
+ 1. Edit your ~/.bash_profile. You can edit this on the command line (Terminal) with:
+
+ nano ~/.bash_profile
+
+ 2. Add the following line if it is not present (replacing '~/bin' if you used another directory):
+
+ PATH=$PATH:~/bin/
+
+ 3. If a PATH line *is* present, ensure you add a colon to the end of what is there
+ and then the directory, so if you have something like:
+
+ a) PATH=$PATH:/usr/local/genome/bin:/sw/bin
+
+ make it look like:
+
+ b) PATH=$PATH:/usr/local/genome/bin:/sw/bin:~/bin
+
+ 4. Quit and restart terminal for the changes to take effect.
+
+If you don't add the location to your $PATH
+===========================================
+
+Assuming you don't want to modify your $PATH, you can still run the binaries. Let's assume you put the files in '~/bin/. You may run primer3_core by doing either of the following:
+
+ 1. ~/bin/primer3_core < yourInputFile
+ 2. /Users/<your username>/bin/primer3_core < yourInputFile
+
+The first option is just a shortcut to the second.
\ No newline at end of file
Added: trunk/packages/primer3/branches/upstream/current/README.WINXP.txt
===================================================================
--- trunk/packages/primer3/branches/upstream/current/README.WINXP.txt 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/README.WINXP.txt 2007-03-31 23:30:01 UTC (rev 237)
@@ -0,0 +1,55 @@
+Windows Installation Instructions (bcf; 3/20/2006:1200)
+---------------------
+
+primer3 release 1.1.0
+---------------------
+
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Whitehead Institute for Biomedical Research, Steve Rozen
+(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
+All rights reserved.
+
+How to install this software
+============================
+
+1. Unzip the '.zip' file downloaded from SourceForge.net
+2. You will create a primer3-1.1.0-beta folder in the location where the file was unzipped
+3. You may move this folder to a location of your choice
+
+Running the software
+====================
+
+To run the program, you must do so from the MS-DOS command-line. The intricacies of the DOS commandline are beyond the scope of this document. Google for more information, if needed. Here is a quick summary:
+
+1. Click on 'Start > Run...'
+2. Type 'cmd' into the space provided
+3. Hit enter (or select 'OK')
+4. Navigate to the location of the binary:
+
+ A. if you put it in C:/Documents and Settings/YourName/Temp,
+ you would type 'cd c:/Documents and Settings/YourName/Temp'
+
+ B. you can also type 'cd ' (don't forget the space after cd)
+ and drag the primer3 folder onto the command-line window from
+ windows explorer, this will fill in the location for you
+
+5. Run the example file by typing:
+
+ primer3_core.exe < example
+
+Other files may be run in a similar fashion. If your input filename
+is 'MyData.txt' you can run primer3 using this file (in the correct
+format; see README) with:
+
+ primer3_core.exe < MyData.txt
+
+If your file is not in the folder containing primer3_core.exe,
+you could run the program from the primer3_core folder using:
+
+ primer3_core.exe < c:/someOtherFolder/someOtherFolder/MyData.txt
+
+Finally, if you want to run the program without going to its folder,
+assuming primer3_core.exe is in c:/Temp, you could run:
+
+ c:/Temp/primer3_core.exe < c:/someOtherFolder/someOtherFolder/MyData.txt
+
\ No newline at end of file
Property changes on: trunk/packages/primer3/branches/upstream/current/README.WINXP.txt
___________________________________________________________________
Name: svn:executable
+ *
Modified: trunk/packages/primer3/branches/upstream/current/README.txt
===================================================================
--- trunk/packages/primer3/branches/upstream/current/README.txt 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/README.txt 2007-03-31 23:30:01 UTC (rev 237)
@@ -1,7 +1,7 @@
-primer3 release 1.1.0
+primer3 release 1.1.1
---------------------
-Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006,2007
Whitehead Institute for Biomedical Research, Steve Rozen
(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
All rights reserved.
@@ -46,10 +46,12 @@
o PCR product size,
-o positional constraints within the source sequence, and
+o positional constraints within the source (template) sequence, and
-o miscellaneous other constraints.
+o possibilities for ectopic priming (amplifying the wrong sequence)
+o many other constraints.
+
All of these criteria are user-specifiable as constraints, and
some are specifiable as terms in an objective function that
characterizes an optimal primer pair.
@@ -100,18 +102,18 @@
compile and link flags.
$ make all
+
# Warnings about pr_release being unused are harmless.
# You should have created executables primer3_core, ntdpal,
# olgotm, and long_seq_tm_test
-$ cd ../test
-$ perl -w p3test.pl
-$ perl -w dpal_test.pl
+$ make test
+
# You should not see 'FAILED' during the tests.
If your perl command is not called perl (for example, if it is
-called perl5) you will have to modify the internals of the test
-scripts).
+called perl5) you will have to modify the
+Makefile in the test/ directory.
ntdpal (NucleoTide Dynamic Programming ALignment) is a
stand-alone program that provides primer3's alignment
@@ -119,7 +121,39 @@
a.k.a. Needleman-Wunsch, plus "half global"). It is provided
strictly as is; for further documentation please see the code.
+BUILDING OSX UNIVERSAL BINARY
+-----------------------------
+** To build a processor-native, non-universal binary of primer3,
+the following is unneccesary**.
+
+The instructions above should be sufficient.
+
+A pre-compiled, universal binary download for OSX is available from
+http://sourceforge.net/projects/primer3/ for the current release.
+
+These instructions assume you want to build binaries compatible
+with *both* of the current processor architectures used by the Apple
+platform (i,e. the binaries will be run on both PPC and intel platforms).
+
+Provided you have the OS X developer tools installed
+(you can download from http://developer.apple.com after
+registering for a free account), you can compile a universal
+build (intel and PPC native) of primer3.
+
+o you must be running OS X > 10.4 and should have the most
+ recent version of XCode
+o then run `make -f Makefile.OSXUniversal all`
+o run the tests as directed above
+
+Additional instructions for 'installing' the binaries may be found in
+the README.OSX.txt.
+
+You should be able to compile a 3-way binary which includes PPC64 support
+(intel, PPC, PPC64) by adding the `-arch ppc64` flag to the
+end of both the CFLAGS and LDFLAGS lines at the top of Makefile.OSX.
+This has not been tested.
+
SYSTEM REQUIREMENTS
-------------------
@@ -395,13 +429,18 @@
the weight defaults to 1.0. The alignment scoring system used is
the same as for calculating complementarity among oligos (e.g.
PRIMER_SELF_ANY), except for the handling of IUB/IUPAC ambiguity
-codes (discussed below). The remainder of an entry contains the
-sequence as lines following the id line up until a line starting
-with '>' or the end of the file. Whitespace and newlines are
-ignored. Characters 'A', 'T', 'G', 'C', 'a', 't', 'g', 'c'
-and IUB/IUPAC 'ambiguity' codes ('R, 'Y', 'K', 'M', 'S', 'W', 'N',
-including lower case) are retained.
+codes (discussed below).
+The remainder of an entry contains the sequence as lines
+following the id line up until a line starting with '>' or
+the end of the file. Whitespace and newlines are ignored.
+Characters 'A', 'T', 'G', 'C', 'a', 't', 'g', 'c' and
+IUB/IUPAC 'ambiguity' codes ('R, 'Y', 'K', 'M', 'S', 'W',
+'N', including lower case) are retained. For technical
+reasons the length of the sequence must be >= 3. Of course,
+sequences of length < 10 or so are probably useless, but
+will be accepted without complaint.
+
WARNING: always set PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=0
if any sequence in the library contains strings of 'N's:
NNNNNNNNNNNNNNNNNNNN.
@@ -529,6 +568,12 @@
Only if there are an insufficient number of primers in the first
range will primer3 return primers in a subsequent range.
+For those with primarily a computational background,
+the PCR product size is size (in base pairs)
+of the DNA fragment that would be produced by the
+PCR reaction on the given sequence template. This
+would, of course, include the primers themselves.
+
PRIMER_PICK_INTERNAL_OLIGO (boolean, default 0)
If the associated value is non-0, then primer3 will attempt to
@@ -1267,21 +1312,18 @@
errors.
PRIMER_LEFT=i,n
-(FORWARD_PRIMER if -v2_compat is set)
The selected left primer (the primer to the left in the input
sequence). i is the 0-based index of the start base of the
primer, and n is t its length.
PRIMER_RIGHT=i,n
-(REVERSE_PRIMER if -v2_compat is set)
The selected right primer (the primer to the right in the input
sequence). i is the 0-based index of the last base of the
primer, and n is its length.
PRIMER_INTERNAL_OLIGO=i,n
-(MIDDLE_OLIGO if -v2_compat is set)
The selected internal oligo. Primer3 outputs this tag if
PRIMER_PICK_INTERNAL_OLIGO was non-0. If primer3 fails to pick a
@@ -1290,7 +1332,6 @@
length.
PRIMER_PRODUCT_SIZE=x
-(PRODUCT_SIZE if -v2_compat is set)
x is the product size of the PCR product.
Deleted: trunk/packages/primer3/branches/upstream/current/primer3-1.1.0-beta
===================================================================
(Binary files differ)
Modified: trunk/packages/primer3/branches/upstream/current/src/Makefile
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/Makefile 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/src/Makefile 2007-03-31 23:30:01 UTC (rev 237)
@@ -70,13 +70,15 @@
PRIMER_OBJECTS=$(PRIMER_OBJECTS1) $(OLIGOTM_LIB)
PRIMER_DYN_OBJECTS=$(PRIMER_OBJECTS1) $(OLIGOTM_DYN_LIB)
+# These are files generated by running ./primer3_core < ../example
+example_files=example.for example.rev example.int
EXES=$(PRIMER_EXE) ntdpal oligotm long_seq_tm_test
all: $(EXES) $(LIBRARIES)
clean_src:
- -rm -f *.o $(EXES) $(PRIMER_EXE).dyn *~ $(LIBRARIES)
+ -rm -f *.o $(EXES) $(PRIMER_EXE).dyn *~ $(LIBRARIES) $(example_files)
clean: clean_src
cd ../test/; make clean
Added: trunk/packages/primer3/branches/upstream/current/src/Makefile.OSXUniversal
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/Makefile.OSXUniversal 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/src/Makefile.OSXUniversal 2007-03-31 23:30:01 UTC (rev 237)
@@ -0,0 +1,144 @@
+# ======================================================================
+# (c) Copyright 1996,1997,1998,1999,2000,2001,2004,2006 Whitehead
+# Institute for Biomedical Research, Steve Rozen, and Helen Skaletsky
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+#
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above
+# copyright notice, this list of conditions and the following disclaimer
+# in the documentation and/or other materials provided with the
+# distribution.
+# * Neither the names of the copyright holders nor contributors may
+# be used to endorse or promote products derived from this software
+# without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+# OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+# ======================================================================
+
+# ======================================================================
+# CITING PRIMER3
+#
+# Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for
+# general users and for biologist programmers. In: Krawetz S, Misener S
+# (eds) Bioinformatics Methods and Protocols: Methods in Molecular
+# Biology. Humana Press, Totowa, NJ, pp 365-386. Source code available
+# at http://fokker.wi.mit.edu/primer3/.
+# ======================================================================
+
+MAX_PRIMER_LENGTH = 36
+
+LDLIBS = -lm
+CC = gcc
+O_OPTS = -O2
+CC_OPTS = -g -Wall -D__USE_FIXED_PROTOTYPES__
+P_DEFINES = -DDPAL_MAX_ALIGN=$(MAX_PRIMER_LENGTH) -DMAX_PRIMER_LENGTH=$(MAX_PRIMER_LENGTH)
+
+CFLAGS=-isysroot /Developer/SDKs/MacOSX10.4u.sdk -arch ppc -arch i386
+LDFLAGS=-g -Wl,-syslibroot,/Developer/SDKs/MacOSX10.4u.sdk -arch ppc -arch i386
+
+# ======================================================================
+# If you have trouble with library skew when moving primer3 executables
+# between systems, you might want to set LIBOPTS to -static
+LIBOPTS =
+
+PRIMER_EXE = primer3_core
+OLIGOTM_LIB = liboligotm.a
+OLIGOTM_DYN_LIB = liboligotm.so.1.2.0
+LIBRARIES = $(OLIGOTM_LIB)
+RANLIB = ranlib
+
+PRIMER_OBJECTS1=primer3_main.o\
+ primer3.o\
+ dpal_primer.o\
+ format_output.o\
+ boulder_input.o\
+
+PRIMER_OBJECTS=$(PRIMER_OBJECTS1) $(OLIGOTM_LIB)
+PRIMER_DYN_OBJECTS=$(PRIMER_OBJECTS1) $(OLIGOTM_DYN_LIB)
+
+EXES=$(PRIMER_EXE) ntdpal oligotm long_seq_tm_test
+
+all: $(EXES) $(LIBRARIES)
+
+clean_src:
+ -rm -f *.o $(EXES) $(PRIMER_EXE).dyn *~ $(LIBRARIES)
+
+clean: clean_src
+ cd ../test/; make clean
+
+$(OLIGOTM_LIB): oligotm.o
+ ar rv $@ oligotm.o
+ $(RANLIB) $@
+
+$(OLIGOTM_DYN_LIB): oligotm.o
+ gcc -shared -W1,-soname,liboligotm.so.1 -o $(OLIGOTM_DYN_LIB) oligotm.o
+
+$(PRIMER_EXE): $(PRIMER_OBJECTS)
+ $(CC) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
+
+# For use with valgrind, which requires at lease one
+# dynamically linked library. Automatic testing with
+# valgrind is not implemented at this point.
+$(PRIMER_EXE).dyn: $(PRIMER_DYN_OBJECTS)
+ $(CC) $(CFLAGS) -o $@ $(PRIMER_DYN_OBJECTS) $(LIBOPTS) $(LDLIBS)
+
+ntdpal: ntdpal_main.o dpal.o
+ $(CC) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
+
+oligotm: oligotm_main.c oligotm.h $(OLIGOTM_LIB)
+ $(CC) $(CFLAGS) -o $@ oligotm_main.c $(OLIGOTM_LIB) $(LIBOPTS) $(LDLIBS)
+
+long_seq_tm_test: long_seq_tm_test_main.c oligotm.o
+ $(CC) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
+
+boulder_input.o: boulder_input.c boulder_input.h primer3.h primer3_release.h dpal.h
+ $(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ boulder_input.c
+
+dpal.o: dpal.c dpal.h primer3_release.h
+ $(CC) -c $(CFLAGS) -o $@ dpal.c
+
+dpal_primer.o: dpal.c dpal.h primer3_release.h
+ $(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ dpal.c
+
+format_output.o: format_output.c primer3_release.h format_output.h primer3.h dpal.h
+ $(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ format_output.c
+
+#########################################################
+# Changed the following to allow OS X Universal build
+#########################################################
+#ntdpal_main.o: ntdpal_main.c dpal.h
+# $(CC) -c $(CC_OPTS) -o $@ ntdpal_main.c
+# We use CC_OPTS above rather than CFLAGS because
+# gcc 2.7.2 crashes while compiling ntdpal_main.c with -O2
+##########################################################
+
+ntdpal_main.o: ntdpal_main.c dpal.h
+ $(CC) -c $(CFLAGS) -o $@ ntdpal_main.c
+
+oligotm.o: oligotm.c oligotm.h primer3_release.h
+
+primer3.o: primer3.c primer3.h primer3_release.h
+ $(CC) -c $(CFLAGS) $(P_DEFINES) primer3.c
+
+primer3_main.o: primer3_main.c primer3.h primer3_release.h dpal.h oligotm.h format_output.h
+ $(CC) -c $(CFLAGS) $(P_DEFINES) primer3_main.c
+
+primer_test: test
+
+test: $(PRIMER_EXE) ntdpal
+ cd ../test; make test
Modified: trunk/packages/primer3/branches/upstream/current/src/boulder_input.c
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/boulder_input.c 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/src/boulder_input.c 2007-03-31 23:30:01 UTC (rev 237)
@@ -1,5 +1,5 @@
/*
-Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006,2007
Whitehead Institute for Biomedical Research, Steve Rozen
(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
All rights reserved.
@@ -864,8 +864,8 @@
pr_append_new_chunk(&lib->error, "Empty ");
goto ERROR;
}
- else if(strlen(lib->seqs[i]) == 0) {
- pr_append_new_chunk(&lib->error, "Empty sequence in ");
+ else if(strlen(lib->seqs[i]) < 3) {
+ pr_append_new_chunk(&lib->error, "Sequence length < 3 in ");
goto ERROR;
}
tmp = upcase_and_check_char(lib->seqs[i]);
@@ -1035,7 +1035,7 @@
p = q = s;
k = strlen(s);
- g = *num = malloc(sizeof(int)*k);
+ g = *num = pr_safe_malloc(sizeof(int)*k);
while(*p == ' ' || *p == '\t'){
p++;
if(*p == '\0' || *p == '\n') return 0;
@@ -1050,4 +1050,3 @@
}
return i;
}
-
Modified: trunk/packages/primer3/branches/upstream/current/src/dpal.c
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/dpal.c 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/src/dpal.c 2007-03-31 23:30:01 UTC (rev 237)
@@ -1052,11 +1052,16 @@
fprintf(stderr, "_dpal_long_nopath_maxgap1_local_end called\n");
#endif
+ if (ylen < 3) {
+ fprintf(stderr, "_dpal_long_nopath_maxgap1_local_end requires ylen >= 3\n");
+ abort();
+ }
+
P0 = malloc(sizeof(int)*ylen);
if (!P0) { DPAL_OOM_ERROR; }
P1 = malloc(sizeof(int)*ylen);
if (!P1) { DPAL_OOM_ERROR; }
- P2 = malloc(sizeof(int)*ylen);
+ P2 = malloc(sizeof(int)*ylen); /* Memory was allocated here. */
if (!P2) { DPAL_OOM_ERROR; }
S0 = P0; S1 = P1; S2 = P2;
Modified: trunk/packages/primer3/branches/upstream/current/src/oligotm.c
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/oligotm.c 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/src/oligotm.c 2007-03-31 23:30:01 UTC (rev 237)
@@ -1,5 +1,5 @@
/*
-Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006,2007
Whitehead Institute for Biomedical Research, Steve Rozen
(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
All rights reserved.
@@ -299,6 +299,8 @@
register int dh = 0, ds = 0;
register char c;
double delta_H, delta_S;
+ double Tm; /* Melting temperature */
+ double correction;
int len, sym;
const char* d = s;
if(divalent_to_monovalent(divalent_conc, dntp_conc) == OLIGOTM_ERROR) return OLIGOTM_ERROR;
@@ -384,7 +386,7 @@
* Nearest-neighbor thermodynamic values for ds
* are in in .1 cal/K per mol of interaction.
*/
- double Tm=0; /* Melting temperature */
+ Tm=0; /* Melting temperature */
len=len+1;
if (salt_corrections == SALT_CORRECTION_SCHILDKRAUT) {
double correction=- 273.15 + 16.6 * log10(K_mM/1000.0);
@@ -405,12 +407,12 @@
if(*d == 'C' || *d == 'G') {
gcPercent++;
}
- *d++;
+ d++;
i++;
}
gcPercent = (double)gcPercent/((double)len);
- double correction
+ /* double */ correction
= (((4.29 * gcPercent) - 3.95) * pow(10,-5) * log(K_mM / 1000.0))
+ (9.40 * pow(10,-6) * (pow(log(K_mM / 1000.0),2)));
@@ -567,11 +569,12 @@
double divalent_conc;
double dntp_conc;
{
+ int GC_count = 0;
+ const char *p, *end;
+
if(divalent_to_monovalent(divalent_conc, dntp_conc) == OLIGOTM_ERROR) return OLIGOTM_ERROR;
salt_conc = salt_conc + divalent_to_monovalent(divalent_conc, dntp_conc);
- int GC_count = 0;
- const char *p, *end;
if(start + len > strlen(s) || start < 0 || len <= 0)
return OLIGOTM_ERROR;
@@ -590,7 +593,8 @@
}
-int symmetry(const char* seq) { /* for testing if string is symmetrical*/
+ /* Return 1 if string is symmetrical, 0 otherwise. */
+int symmetry(const char* seq) {
register char s;
register char e;
const char *seq_end=seq;
@@ -624,10 +628,14 @@
return 1;
}
-double divalent_to_monovalent(double divalent, double dntp){ /* converting divalent salt concentration to monovalent */
+/* Convert divalent salt concentration to monovalent */
+double divalent_to_monovalent(double divalent,
+ double dntp)
+{
if(divalent==0) dntp=0;
if(divalent<0 || dntp<0) return OLIGOTM_ERROR;
- if(divalent<dntp) /* according to theory melting temperature doesn't depend on divalent cations */
+ if(divalent<dntp)
+ /* According to theory, melting temperature doesn't depend on divalent cations */
divalent=dntp;
return 120*(sqrt(divalent-dntp));
}
Modified: trunk/packages/primer3/branches/upstream/current/src/oligotm.h
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/oligotm.h 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/src/oligotm.h 2007-03-31 23:30:01 UTC (rev 237)
@@ -1,5 +1,5 @@
/*
-Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006,2007
Whitehead Institute for Biomedical Research, Steve Rozen
(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
All rights reserved.
@@ -54,7 +54,12 @@
since mM is the usual units in PCR applications.
*/
-double long_seq_tm(const char *seq, int start, int length, double salt_conc, double divalent_conc, double dntp_conc);
+double long_seq_tm(const char *seq,
+ int start,
+ int length,
+ double salt_conc,
+ double divalent_conc,
+ double dntp_conc);
/*
For olgigotm() and seqtm()
@@ -154,7 +159,6 @@
int salt_corrections /* See description above. */
);
-
/* Return the delta G of disruption of oligo using the nearest neighbor model.
The length of seq should be relatively short,
given the characteristics of the nearest
Modified: trunk/packages/primer3/branches/upstream/current/src/oligotm_main.c
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/oligotm_main.c 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/src/oligotm_main.c 2007-03-31 23:30:01 UTC (rev 237)
@@ -1,5 +1,5 @@
/*
-Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006,2007
Whitehead Institute for Biomedical Research, Steve Rozen
(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
All rights reserved.
@@ -34,9 +34,7 @@
the function oligotm() in oligtm.c
*/
int
-main(argc, argv)
- int argc;
- char **argv;
+main(int argc, char **argv)
{
double tm;
@@ -107,83 +105,82 @@
" if not, write to the Free Software Foundation, Inc.,\n"
" 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA\n";
- char *endptr;
+ char *endptr, *seq;
long mv = 50, d = 50;
double dv = 0, n = 0;
int tm_santalucia=0, salt_corrections=0;
- int i;
- if (argc < 2 || argc > 14) {
- fprintf(stderr, msg, argv[0]);
- fprintf(stderr, copyright);
- return -1;
- }
+ int i, j, len;
+ if (argc < 2 || argc > 14) {
+ fprintf(stderr, msg, argv[0]);
+ fprintf(stderr, copyright);
+ return -1;
+ }
- for (i=1; i < argc; ++i) {
- if (!strncmp("-mv", argv[i], 3)) { /* conc of monovalent cations */
- mv = strtol(argv[i+1], &endptr, 10);
- if ('\0' != *endptr) {
- fprintf(stderr, msg, argv[0]);
- exit(-1);
- }
- i++;
- } else if (!strncmp("-dv", argv[i], 3)) { /* conc of divalent cations; added by T.Koressaar */
+ for (i=1; i < argc; ++i) {
+ if (!strncmp("-mv", argv[i], 3)) { /* conc of monovalent cations */
+ mv = strtol(argv[i+1], &endptr, 10);
+ if ('\0' != *endptr) {
+ fprintf(stderr, msg, argv[0]);
+ exit(-1);
+ }
+ i++;
+ } else if (!strncmp("-dv", argv[i], 3)) { /* conc of divalent cations; added by T.Koressaar */
dv = strtod(argv[i+1], &endptr);
if('\0' != *endptr) {
- fprintf(stderr, msg, argv[0]);
- exit(-1);
+ fprintf(stderr, msg, argv[0]);
+ exit(-1);
}
i++;
- } else if (!strncmp("-n", argv[i], 2)) { /* conc of dNTP; added by T.Koressaar */
+ } else if (!strncmp("-n", argv[i], 2)) { /* conc of dNTP; added by T.Koressaar */
n = strtod(argv[i+1], &endptr);
if('\0' != *endptr) {
- fprintf(stderr, msg, argv[0]);
- exit(-1);
+ fprintf(stderr, msg, argv[0]);
+ exit(-1);
}
i++;
- } else if (!strncmp("-d", argv[i], 2)) {
+ } else if (!strncmp("-d", argv[i], 2)) {
d = strtol(argv[i+1], &endptr, 10);
if ('\0' != *endptr) {
- fprintf(stderr, msg, argv[0]);
- exit(-1);
+ fprintf(stderr, msg, argv[0]);
+ exit(-1);
}
i++;
- } else if (!strncmp("-tp", argv[i], 3)) { /* added by T.Koressaar */
+ } else if (!strncmp("-tp", argv[i], 3)) { /* added by T.Koressaar */
tm_santalucia = (int)strtol(argv[i+1], &endptr, 10);
if ('\0' != *endptr || tm_santalucia<0 || tm_santalucia>1) {
- fprintf(stderr, msg, argv[0]);
- exit(-1);
+ fprintf(stderr, msg, argv[0]);
+ exit(-1);
}
i++;
- } else if (!strncmp("-sc", argv[i], 3)) { /* added by T.Koressaar */
+ } else if (!strncmp("-sc", argv[i], 3)) { /* added by T.Koressaar */
salt_corrections = (int)strtol(argv[i+1], &endptr, 10);
if ('\0' != *endptr || salt_corrections<0 || salt_corrections>2) {
fprintf(stderr, msg, argv[0]);
exit(-1);
- }
+ }
i++;
- } else if (!strncmp("-i", argv[i], 2)) {
+ } else if (!strncmp("-i", argv[i], 2)) {
fprintf(stderr, info, argv[0]);
exit(-1);
- } else if (!strncmp("-", argv[i], 1)) {
+ } else if (!strncmp("-", argv[i], 1)) {
/* Unknown option. */
fprintf(stderr, msg, argv[0]);
exit(-1);
- } else
- break; /* all args processed. go on to sequences. */
- }
+ } else
+ break; /* all args processed. go on to sequences. */
+ }
if(!argv[i]) { /* if no oligonucleotide sequence is specified */
fprintf(stderr, msg, argv[0]);
exit(-1);
}
- /* input sequence to uppercase */
- int j,len;
- char *seq = argv[i];
- len=strlen(seq);
- for(j=0;j<len;j++) seq[j]=toupper(seq[j]);
+ /* input sequence to uppercase */
+ seq = argv[i];
+ len=strlen(seq);
+ for(j=0;j<len;j++) seq[j]=toupper(seq[j]);
- tm = oligotm(seq, d, mv, dv, n, tm_santalucia, salt_corrections);
- if (OLIGOTM_ERROR == tm) {
+ tm = oligotm(seq, d, mv, dv, n, tm_santalucia, salt_corrections);
+ if (OLIGOTM_ERROR == tm) {
fprintf(stderr,
"%s ERROR: length of sequence %s is less than 2 or\n"
" the sequence contains an illegal character or\n"
Modified: trunk/packages/primer3/branches/upstream/current/src/primer3_main.c
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/primer3_main.c 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/src/primer3_main.c 2007-03-31 23:30:01 UTC (rev 237)
@@ -536,15 +536,26 @@
const primer_pair *pair;
const pair_array_t *retpair;
{
- const primer_pair *q = &retpair->pairs[0],
- *stop = &retpair->pairs[retpair->num_pairs];
- for (; q < stop; q++) {
- if (q->left->start == pair->left->start
- && q->left->length == pair->left->length
- && q->right->start == pair->right->start
- && q->right->length == pair->right->length) return 1;
- }
+ const primer_pair *q, *stop;
+
+ /* OLD CODE: const primer_pair *q = &retpair->pairs[0],
+ *stop = &retpair->pairs[retpair->num_pairs]; */
+
+ /* retpair might not have any pairs in it yet (add_pair
+ allocates memory for retpair->pairs. */
+ if (retpair->num_pairs == 0)
return 0;
+
+ q = &retpair->pairs[0];
+ stop = &retpair->pairs[retpair->num_pairs];
+
+ for (; q < stop; q++) {
+ if (q->left->start == pair->left->start
+ && q->left->length == pair->left->length
+ && q->right->start == pair->right->start
+ && q->right->length == pair->right->length) return 1;
+ }
+ return 0;
}
/* Add 'pair' to 'retpair'. */
@@ -2701,7 +2712,11 @@
tmp_char = target[first_untrimmed];
target[first_untrimmed] = '\0';
- tmp_score = align(oseq, target, align_args);
+ if (strlen(target) < 3) {
+ tmp_score = 3;
+ } else {
+ tmp_score = align(oseq, target, align_args);
+ }
if (debug) {
if (l == OT_LEFT) fprintf(stderr, "\n************ OLIGO = LEFT\n");
Modified: trunk/packages/primer3/branches/upstream/current/src/primer3_release.h
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/primer3_release.h 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/src/primer3_release.h 2007-03-31 23:30:01 UTC (rev 237)
@@ -33,7 +33,5 @@
#ifndef RELEASE_H
#define RELEASE_H 1
-static const char * pr_release = "primer3 release 1.1.0";
-/* This is a beta release, identical to release 1.0b
- except for version number */
+static const char * pr_release = "primer3 release 1.1.1";
#endif
Modified: trunk/packages/primer3/branches/upstream/current/src/release_notes.txt
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/release_notes.txt 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/src/release_notes.txt 2007-03-31 23:30:01 UTC (rev 237)
@@ -1,3 +1,7 @@
+release 1.1.1 3/37/2007 ==================================================
+
+ Minor corrections
+
release 1.1.0 1/17/2007 ==================================================
Added tags PRIMER_TM_SANTALUCIA, PRIMER_SALT_CORRECTIONS,
Modified: trunk/packages/primer3/branches/upstream/current/test/oligotm_test.pl
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/oligotm_test.pl 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/test/oligotm_test.pl 2007-03-31 23:30:01 UTC (rev 237)
@@ -1,5 +1,5 @@
# Copyright (c) 2007
-# Triinu Koressaar an Maido Remm
+# Triinu Koressaar and Maido Remm
# All rights reserved.
#
# This file is part of the oligotm library.
Modified: trunk/packages/primer3/branches/upstream/current/test/p3test.pl
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/p3test.pl 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/test/p3test.pl 2007-03-31 23:30:01 UTC (rev 237)
@@ -22,7 +22,7 @@
$exe = $ARGV[0] if defined $ARGV[0];
$EXIT_STAT = 0;
-die "Cannot execute $exe" unless -x $exe;
+# die "Cannot execute $exe" unless -x $exe;
print STDERR "\n\n$0: testing $exe\n\nSTART, ", scalar(localtime), "\n";
Modified: trunk/packages/primer3/branches/upstream/current/test/primer_boundary1_formatted_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_boundary1_formatted_output 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_boundary1_formatted_output 2007-03-31 23:30:01 UTC (rev 237)
@@ -26,7 +26,7 @@
Right 10 9 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_01
@@ -57,7 +57,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_02
@@ -88,7 +88,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_03
@@ -112,7 +112,7 @@
Right 4 3 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, unacceptable product size 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_04
@@ -136,7 +136,7 @@
Right 10 9 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, unacceptable product size 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_05
@@ -167,7 +167,7 @@
Right 5 3 0 0 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 4, unacceptable product size 3, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_06
@@ -191,7 +191,7 @@
Right 5 5 0 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_07
@@ -223,7 +223,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_08
@@ -251,7 +251,7 @@
Right 6 5 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_09
@@ -279,7 +279,7 @@
Right 5 5 0 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_10
@@ -303,7 +303,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_11
@@ -334,7 +334,7 @@
Right 5 2 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 3, unacceptable product size 2, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_11
@@ -358,7 +358,7 @@
Right 5 2 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_12
@@ -389,7 +389,7 @@
Right 5 0 0 0 0 0 0 0 0 0 0 0 5
Pair Stats:
considered 5, unacceptable product size 4, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_13
@@ -420,7 +420,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_14
@@ -444,7 +444,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_15
@@ -475,7 +475,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_16
@@ -499,7 +499,7 @@
Right 5 4 0 0 1 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_17
@@ -531,7 +531,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_18
@@ -559,7 +559,7 @@
Right 1 1 0 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_19
@@ -591,7 +591,7 @@
Right 1 1 0 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_21
@@ -624,7 +624,7 @@
Right 3 2 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_22
@@ -653,7 +653,7 @@
Right 3 2 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_23
@@ -682,7 +682,7 @@
Right 2 2 0 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_24
@@ -711,7 +711,7 @@
Right 2 2 0 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_25
@@ -744,7 +744,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_26
@@ -773,7 +773,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_27
@@ -802,7 +802,7 @@
Right 5 4 1 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_28
@@ -831,7 +831,7 @@
Right 5 4 1 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_29
@@ -864,7 +864,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_30
@@ -897,7 +897,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_31
@@ -926,7 +926,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, no target 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_32
@@ -959,7 +959,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_33
@@ -988,7 +988,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_34
@@ -1017,7 +1017,7 @@
Right 5 4 0 1 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_35
@@ -1046,7 +1046,7 @@
Right 5 4 0 1 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_36
@@ -1079,7 +1079,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_37
@@ -1108,7 +1108,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_37
@@ -1137,7 +1137,7 @@
Right 5 4 0 1 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_38
@@ -1166,7 +1166,7 @@
Right 5 4 0 1 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_39
@@ -1199,7 +1199,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_40
@@ -1232,7 +1232,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_41
@@ -1258,7 +1258,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_42
@@ -1291,7 +1291,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_43
@@ -1320,7 +1320,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_44
@@ -1353,7 +1353,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_45
@@ -1386,7 +1386,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_46
@@ -1415,7 +1415,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_47
@@ -1448,7 +1448,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_48
@@ -1477,7 +1477,7 @@
Right 5 4 0 0 0 1 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_49
@@ -1510,7 +1510,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_50
@@ -1539,7 +1539,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_51
@@ -1572,7 +1572,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_52
@@ -1605,7 +1605,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_53
@@ -1634,7 +1634,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, tm diff too large 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_54
@@ -1669,7 +1669,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_55
@@ -1702,7 +1702,7 @@
Intl 0 0 0 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR poly_x_2
@@ -1765,7 +1765,7 @@
Intl 1585 0 0 0 0 0 0 0 0 0 0 0 1585
Pair Stats:
considered 72, unacceptable product size 52, ok 20
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR poly_x_3
@@ -1794,7 +1794,7 @@
Intl 187 0 0 0 0 0 0 0 0 0 187 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_59
@@ -1827,7 +1827,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_60
@@ -1853,7 +1853,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_61
@@ -1893,7 +1893,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_63
@@ -1923,7 +1923,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_64
@@ -1963,7 +1963,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_66
@@ -1993,7 +1993,7 @@
Right 1 0 0 1 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_67
@@ -2025,7 +2025,7 @@
Right 6 5 0 1 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_68
@@ -2058,7 +2058,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_69
@@ -2084,7 +2084,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_70
@@ -2120,7 +2120,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, no target 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_72
@@ -2150,7 +2150,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_73
@@ -2186,7 +2186,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, no target 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_75
@@ -2216,7 +2216,7 @@
Right 0 0 0 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_76
@@ -2248,7 +2248,7 @@
Right 6 5 1 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_77
@@ -2282,7 +2282,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_78
@@ -2316,7 +2316,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_79
@@ -2350,7 +2350,7 @@
Right 6 5 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_80
@@ -2384,7 +2384,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_81
@@ -2418,7 +2418,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_82
@@ -2451,7 +2451,7 @@
Right 10 9 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_83
@@ -2480,7 +2480,7 @@
Right 10 9 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, no target 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_84
@@ -2513,7 +2513,7 @@
Right 10 9 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_85
@@ -2546,7 +2546,7 @@
Right 3 2 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_86
@@ -2580,7 +2580,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_71
@@ -2616,7 +2616,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_72
@@ -2648,7 +2648,7 @@
Right 3 2 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 3, unacceptable product size 2, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_73
@@ -2676,7 +2676,7 @@
Right 3 2 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 2, unacceptable product size 2, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_74
@@ -2708,7 +2708,7 @@
Right 3 2 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 2, ok 2
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_75
@@ -2740,7 +2740,7 @@
Right 2 1 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 2, unacceptable product size 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_76
@@ -2772,7 +2772,7 @@
Right 2 1 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 2, unacceptable product size 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_77
@@ -2813,7 +2813,7 @@
Right 28 26 0 0 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 4, unacceptable product size 2, ok 2
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_78
@@ -2854,7 +2854,7 @@
Right 28 26 0 0 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 4, unacceptable product size 2, ok 2
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_79
@@ -2895,7 +2895,7 @@
Right 28 26 0 0 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 4, unacceptable product size 1, ok 3
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_80
@@ -2936,7 +2936,7 @@
Right 28 26 0 0 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 4, unacceptable product size 1, ok 3
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_81
@@ -2968,7 +2968,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_82
@@ -2996,7 +2996,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, high any compl 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_83
@@ -3028,7 +3028,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_84
@@ -3056,7 +3056,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, high end compl 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_85
@@ -3088,7 +3088,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 200, ok 200
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_86
@@ -3122,7 +3122,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_87
@@ -3160,7 +3160,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_89
Modified: trunk/packages/primer3/branches/upstream/current/test/primer_boundary_formatted_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_boundary_formatted_output 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_boundary_formatted_output 2007-03-31 23:30:01 UTC (rev 237)
@@ -26,7 +26,7 @@
Right 10 9 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_01
@@ -57,7 +57,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_02
@@ -88,7 +88,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_03
@@ -112,7 +112,7 @@
Right 4 3 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, unacceptable product size 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_04
@@ -136,7 +136,7 @@
Right 10 9 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, unacceptable product size 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_05
@@ -167,7 +167,7 @@
Right 5 3 0 0 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 4, unacceptable product size 3, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_06
@@ -191,7 +191,7 @@
Right 5 5 0 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_07
@@ -223,7 +223,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_08
@@ -251,7 +251,7 @@
Right 6 5 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_09
@@ -279,7 +279,7 @@
Right 5 5 0 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_10
@@ -303,7 +303,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_11
@@ -334,7 +334,7 @@
Right 5 2 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 3, unacceptable product size 2, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_11
@@ -358,7 +358,7 @@
Right 5 2 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_12
@@ -389,7 +389,7 @@
Right 5 0 0 0 0 0 0 0 0 0 0 0 5
Pair Stats:
considered 5, unacceptable product size 4, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_13
@@ -420,7 +420,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_14
@@ -444,7 +444,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_15
@@ -475,7 +475,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_16
@@ -499,7 +499,7 @@
Right 5 4 0 0 1 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_17
@@ -531,7 +531,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_18
@@ -559,7 +559,7 @@
Right 1 1 0 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_19
@@ -591,7 +591,7 @@
Right 1 1 0 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_21
@@ -624,7 +624,7 @@
Right 3 2 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_22
@@ -653,7 +653,7 @@
Right 3 2 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_23
@@ -682,7 +682,7 @@
Right 2 2 0 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_24
@@ -711,7 +711,7 @@
Right 2 2 0 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_25
@@ -744,7 +744,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_26
@@ -773,7 +773,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_27
@@ -802,7 +802,7 @@
Right 5 4 1 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_28
@@ -831,7 +831,7 @@
Right 5 4 1 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_29
@@ -864,7 +864,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_30
@@ -897,7 +897,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_31
@@ -926,7 +926,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, no target 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_32
@@ -959,7 +959,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_33
@@ -988,7 +988,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_34
@@ -1017,7 +1017,7 @@
Right 5 4 0 1 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_35
@@ -1046,7 +1046,7 @@
Right 5 4 0 1 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_36
@@ -1079,7 +1079,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_37
@@ -1108,7 +1108,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_37
@@ -1137,7 +1137,7 @@
Right 5 4 0 1 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_38
@@ -1166,7 +1166,7 @@
Right 5 4 0 1 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_39
@@ -1199,7 +1199,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_40
@@ -1232,7 +1232,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_41
@@ -1258,7 +1258,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_42
@@ -1291,7 +1291,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_43
@@ -1320,7 +1320,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_44
@@ -1353,7 +1353,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_45
@@ -1386,7 +1386,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_46
@@ -1415,7 +1415,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_47
@@ -1448,7 +1448,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_48
@@ -1477,7 +1477,7 @@
Right 5 4 0 0 0 1 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_49
@@ -1510,7 +1510,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_50
@@ -1539,7 +1539,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_51
@@ -1572,7 +1572,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_52
@@ -1605,7 +1605,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_53
@@ -1634,7 +1634,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, tm diff too large 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_54
@@ -1669,7 +1669,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_55
@@ -1702,7 +1702,7 @@
Intl 0 0 0 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR poly_x_2
@@ -1765,7 +1765,7 @@
Intl 1585 0 0 0 0 0 0 0 0 0 0 0 1585
Pair Stats:
considered 72, unacceptable product size 52, ok 20
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR poly_x_3
@@ -1794,7 +1794,7 @@
Intl 187 0 0 0 0 0 0 0 0 0 187 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_59
@@ -1827,7 +1827,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_60
@@ -1853,7 +1853,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_61
@@ -1893,7 +1893,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_63
@@ -1923,7 +1923,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_64
@@ -1963,7 +1963,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_66
@@ -1993,7 +1993,7 @@
Right 1 0 0 1 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_67
@@ -2025,7 +2025,7 @@
Right 6 5 0 1 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_68
@@ -2058,7 +2058,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_69
@@ -2084,7 +2084,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_70
@@ -2120,7 +2120,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, no target 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_72
@@ -2150,7 +2150,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_73
@@ -2186,7 +2186,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, no target 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_75
@@ -2216,7 +2216,7 @@
Right 0 0 0 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_76
@@ -2248,7 +2248,7 @@
Right 6 5 1 0 0 0 0 0 0 0 0 0 0
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_77
@@ -2282,7 +2282,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_78
@@ -2316,7 +2316,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_79
@@ -2350,7 +2350,7 @@
Right 6 5 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_80
@@ -2384,7 +2384,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_81
@@ -2418,7 +2418,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_82
@@ -2451,7 +2451,7 @@
Right 10 9 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_83
@@ -2480,7 +2480,7 @@
Right 10 9 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, no target 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_84
@@ -2513,7 +2513,7 @@
Right 10 9 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_85
@@ -2546,7 +2546,7 @@
Right 3 2 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_86
@@ -2580,7 +2580,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_71
@@ -2616,7 +2616,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_72
@@ -2648,7 +2648,7 @@
Right 3 2 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 3, unacceptable product size 2, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_73
@@ -2676,7 +2676,7 @@
Right 3 2 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 2, unacceptable product size 2, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_74
@@ -2708,7 +2708,7 @@
Right 3 2 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 2, ok 2
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_75
@@ -2740,7 +2740,7 @@
Right 2 1 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 2, unacceptable product size 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_76
@@ -2772,7 +2772,7 @@
Right 2 1 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 2, unacceptable product size 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_77
@@ -2813,7 +2813,7 @@
Right 28 26 0 0 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 4, unacceptable product size 2, ok 2
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_78
@@ -2854,7 +2854,7 @@
Right 28 26 0 0 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 4, unacceptable product size 2, ok 2
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_79
@@ -2895,7 +2895,7 @@
Right 28 26 0 0 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 4, unacceptable product size 1, ok 3
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_80
@@ -2936,7 +2936,7 @@
Right 28 26 0 0 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 4, unacceptable product size 1, ok 3
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_81
@@ -2968,7 +2968,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_82
@@ -2996,7 +2996,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, high any compl 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_83
@@ -3028,7 +3028,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_84
@@ -3056,7 +3056,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, high end compl 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_85
@@ -3088,7 +3088,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 200, ok 200
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_86
@@ -3122,7 +3122,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_87
@@ -3160,7 +3160,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_89
@@ -3195,7 +3195,7 @@
Right 10 9 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_91
@@ -3219,7 +3219,7 @@
Right 10 9 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 0, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_92
@@ -3254,7 +3254,7 @@
Right 5 2 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 9, unacceptable product size 8, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_93
@@ -3289,7 +3289,7 @@
Right 5 0 0 0 0 0 0 0 0 0 0 0 5
Pair Stats:
considered 5, unacceptable product size 4, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_94
@@ -3324,7 +3324,7 @@
Right 5 0 0 0 0 0 0 0 0 0 0 0 5
Pair Stats:
considered 5, unacceptable product size 4, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_95
@@ -3359,7 +3359,7 @@
Right 5 4 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 5, unacceptable product size 4, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_96
@@ -3394,7 +3394,7 @@
Right 5 0 0 0 0 0 0 0 0 0 0 0 5
Pair Stats:
considered 5, unacceptable product size 4, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_97
@@ -3429,7 +3429,7 @@
Right 5 0 0 0 0 0 0 0 0 0 0 0 5
Pair Stats:
considered 5, unacceptable product size 4, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR test_098
@@ -3461,7 +3461,7 @@
Right 5 0 0 0 0 0 0 0 0 0 0 0 5
Pair Stats:
considered 5, unacceptable product size 4, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR test_099
@@ -3485,7 +3485,7 @@
Right 5 0 0 0 0 0 0 0 0 0 0 0 5
Pair Stats:
considered 5, unacceptable product size 4, high product Tm 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR test_100
@@ -3516,7 +3516,7 @@
Right 5 0 0 0 0 0 0 0 0 0 0 0 5
Pair Stats:
considered 5, unacceptable product size 4, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR test_101
@@ -3548,7 +3548,7 @@
Right 5 0 0 0 0 0 0 0 0 0 0 0 5
Pair Stats:
considered 5, unacceptable product size 4, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR test_102
@@ -3572,7 +3572,7 @@
Right 5 0 0 0 0 0 0 0 0 0 0 0 5
Pair Stats:
considered 5, unacceptable product size 4, low product Tm 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR test_103
@@ -3603,6 +3603,6 @@
Right 5 0 0 0 0 0 0 0 0 0 0 0 5
Pair Stats:
considered 5, unacceptable product size 4, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
Modified: trunk/packages/primer3/branches/upstream/current/test/primer_global_err/empty_1.out2
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_global_err/empty_1.out2 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_global_err/empty_1.out2 2007-03-31 23:30:01 UTC (rev 237)
@@ -32,7 +32,7 @@
USAGE: ../src/primer3_core [-format_output] [-2x_compat] [-strict_tags]
-This is primer3 (primer3 release 1.1.0)
+This is primer3 (primer3 release 1.1.1)
Input must be provided on standard input.
For example:
$ primer3_core < my_input_file
Modified: trunk/packages/primer3/branches/upstream/current/test/primer_global_err/repeat_lib_err4.out
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_global_err/repeat_lib_err4.out 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_global_err/repeat_lib_err4.out 2007-03-31 23:30:01 UTC (rev 237)
@@ -1,5 +1,5 @@
PRIMER_SEQUENCE_ID=seq1
SEQUENCE=ATGCTAGCTAGTCGATCGATGCTAGCTAGTCGATCTACTATCATCATGCTAGCATGGGGCATCTGTGGGATGCTGTCGTACTGATCGATGCTAGCTAGCTAGTCGATCGTAGCTATCATCATCTAGTCATCGTAGCTATCATCGTAGC
PRIMER_MISPRIMING_LIBRARY=repeat_lib4
-PRIMER_ERROR=Empty sequence in mispriming library repeat_lib4
+PRIMER_ERROR=Sequence length < 3 in mispriming library repeat_lib4
=
Modified: trunk/packages/primer3/branches/upstream/current/test/primer_global_err/repeat_lib_err4.out2
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_global_err/repeat_lib_err4.out2 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_global_err/repeat_lib_err4.out2 2007-03-31 23:30:01 UTC (rev 237)
@@ -1 +1 @@
-../src/primer3_core: Empty sequence in mispriming library repeat_lib4
+../src/primer3_core: Sequence length < 3 in mispriming library repeat_lib4
Modified: trunk/packages/primer3/branches/upstream/current/test/primer_global_err/repeat_lib_int_err4.out
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_global_err/repeat_lib_int_err4.out 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_global_err/repeat_lib_int_err4.out 2007-03-31 23:30:01 UTC (rev 237)
@@ -2,5 +2,5 @@
SEQUENCE=ATGCTAGCTAGTCGATCGATGCTAGCTAGTCGATCTACTATCATCATGCTAGCATGGGGCATCTGTGGGATGCTGTCGTACTGATCGATGCTAGCTAGCTAGTCGATCGTAGCTATCATCATCTAGTCATCGTAGCTATCATCGTAGC
PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY=repeat_lib4
PRIMER_PICK_INTERNAL_OLIGO=1
-PRIMER_ERROR=Empty sequence in internal oligo mishyb library repeat_lib4
+PRIMER_ERROR=Sequence length < 3 in internal oligo mishyb library repeat_lib4
=
Modified: trunk/packages/primer3/branches/upstream/current/test/primer_global_err/repeat_lib_int_err4.out2
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_global_err/repeat_lib_int_err4.out2 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_global_err/repeat_lib_int_err4.out2 2007-03-31 23:30:01 UTC (rev 237)
@@ -1 +1 @@
-../src/primer3_core: Empty sequence in internal oligo mishyb library repeat_lib4
+../src/primer3_core: Sequence length < 3 in internal oligo mishyb library repeat_lib4
Modified: trunk/packages/primer3/branches/upstream/current/test/primer_internal1_formatted_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_internal1_formatted_output 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_internal1_formatted_output 2007-03-31 23:30:01 UTC (rev 237)
@@ -33,7 +33,7 @@
Intl 60 57 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 4, unacceptable product size 1, no internal oligo 2, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_01
@@ -71,7 +71,7 @@
Intl 60 57 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 2, unacceptable product size 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_02
@@ -109,7 +109,7 @@
Intl 60 57 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_05
@@ -147,7 +147,7 @@
Intl 60 57 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 4, unacceptable product size 3, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_11
@@ -174,7 +174,7 @@
Intl 60 59 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 8, unacceptable product size 6, no internal oligo 2, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_11
@@ -219,7 +219,7 @@
Intl 60 52 0 0 0 0 0 0 0 0 0 0 8
Pair Stats:
considered 10, unacceptable product size 8, ok 2
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_12
@@ -264,7 +264,7 @@
Intl 60 52 0 0 0 0 0 0 0 0 0 0 8
Pair Stats:
considered 10, unacceptable product size 8, ok 2
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_13
@@ -302,7 +302,7 @@
Intl 60 23 0 0 0 0 0 0 0 0 0 0 37
Pair Stats:
considered 4, unacceptable product size 3, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_14
@@ -340,7 +340,7 @@
Intl 60 25 0 0 0 0 0 0 0 0 0 0 35
Pair Stats:
considered 6, unacceptable product size 5, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_15
@@ -378,7 +378,7 @@
Intl 60 25 0 0 0 0 0 0 0 0 0 0 35
Pair Stats:
considered 6, unacceptable product size 5, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_16
@@ -404,7 +404,7 @@
Intl 35 0 0 0 0 0 0 0 0 0 0 0 35
Pair Stats:
considered 4, no internal oligo 4, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_17
@@ -431,7 +431,7 @@
Intl 60 0 0 0 29 0 0 0 0 0 0 0 31
Pair Stats:
considered 16, unacceptable product size 4, no internal oligo 12, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_18
@@ -465,7 +465,7 @@
Intl 87 39 0 40 0 0 0 0 0 0 0 0 8
Pair Stats:
considered 81, unacceptable product size 49, no internal oligo 32, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_19
@@ -527,7 +527,7 @@
Intl 91 84 0 5 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 18, unacceptable product size 3, no internal oligo 8, ok 7
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_20
@@ -599,7 +599,7 @@
Intl 226 175 0 47 0 0 0 0 0 0 0 0 4
Pair Stats:
considered 23, no internal oligo 15, ok 8
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_21
@@ -662,7 +662,7 @@
Intl 152 57 0 0 0 0 1 93 0 0 0 0 1
Pair Stats:
considered 323, unacceptable product size 223, no internal oligo 87, ok 13
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_22
@@ -700,7 +700,7 @@
Intl 60 57 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_23
@@ -743,7 +743,7 @@
Intl 56 53 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_24
@@ -784,7 +784,7 @@
Intl 56 53 0 1 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_25
@@ -827,7 +827,7 @@
Intl 56 53 0 1 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_26
@@ -868,7 +868,7 @@
Intl 56 53 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_27
@@ -903,7 +903,7 @@
Intl 56 53 0 1 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 1, no internal oligo 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_28
@@ -938,7 +938,7 @@
Intl 56 53 0 1 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 1, no internal oligo 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_29
@@ -979,7 +979,7 @@
Intl 56 53 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_30
@@ -1020,7 +1020,7 @@
Intl 56 53 0 1 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_31
@@ -1063,7 +1063,7 @@
Intl 56 53 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_32
@@ -1106,7 +1106,7 @@
Intl 56 53 0 1 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_33
@@ -1147,7 +1147,7 @@
Intl 56 53 0 1 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_34
Modified: trunk/packages/primer3/branches/upstream/current/test/primer_internal_formatted_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_internal_formatted_output 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_internal_formatted_output 2007-03-31 23:30:01 UTC (rev 237)
@@ -33,7 +33,7 @@
Intl 60 57 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 4, unacceptable product size 1, no internal oligo 2, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_01
@@ -71,7 +71,7 @@
Intl 60 57 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 2, unacceptable product size 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_02
@@ -109,7 +109,7 @@
Intl 60 57 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_05
@@ -147,7 +147,7 @@
Intl 60 57 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 4, unacceptable product size 3, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_11
@@ -174,7 +174,7 @@
Intl 60 59 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 8, unacceptable product size 6, no internal oligo 2, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_11
@@ -219,7 +219,7 @@
Intl 60 52 0 0 0 0 0 0 0 0 0 0 8
Pair Stats:
considered 10, unacceptable product size 8, ok 2
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_12
@@ -264,7 +264,7 @@
Intl 60 52 0 0 0 0 0 0 0 0 0 0 8
Pair Stats:
considered 10, unacceptable product size 8, ok 2
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_13
@@ -302,7 +302,7 @@
Intl 60 23 0 0 0 0 0 0 0 0 0 0 37
Pair Stats:
considered 4, unacceptable product size 3, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_14
@@ -340,7 +340,7 @@
Intl 60 25 0 0 0 0 0 0 0 0 0 0 35
Pair Stats:
considered 6, unacceptable product size 5, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_15
@@ -378,7 +378,7 @@
Intl 60 25 0 0 0 0 0 0 0 0 0 0 35
Pair Stats:
considered 6, unacceptable product size 5, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_16
@@ -404,7 +404,7 @@
Intl 35 0 0 0 0 0 0 0 0 0 0 0 35
Pair Stats:
considered 4, no internal oligo 4, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_17
@@ -431,7 +431,7 @@
Intl 60 0 0 0 29 0 0 0 0 0 0 0 31
Pair Stats:
considered 16, unacceptable product size 4, no internal oligo 12, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_18
@@ -465,7 +465,7 @@
Intl 87 39 0 40 0 0 0 0 0 0 0 0 8
Pair Stats:
considered 81, unacceptable product size 49, no internal oligo 32, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_19
@@ -527,7 +527,7 @@
Intl 91 84 0 5 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 18, unacceptable product size 3, no internal oligo 8, ok 7
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_20
@@ -599,7 +599,7 @@
Intl 226 175 0 47 0 0 0 0 0 0 0 0 4
Pair Stats:
considered 23, no internal oligo 15, ok 8
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_21
@@ -662,7 +662,7 @@
Intl 152 57 0 0 0 0 1 93 0 0 0 0 1
Pair Stats:
considered 323, unacceptable product size 223, no internal oligo 87, ok 13
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_22
@@ -700,7 +700,7 @@
Intl 60 57 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_23
@@ -743,7 +743,7 @@
Intl 56 53 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_24
@@ -784,7 +784,7 @@
Intl 56 53 0 1 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_25
@@ -827,7 +827,7 @@
Intl 56 53 0 1 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_26
@@ -868,7 +868,7 @@
Intl 56 53 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_27
@@ -903,7 +903,7 @@
Intl 56 53 0 1 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 1, no internal oligo 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_28
@@ -938,7 +938,7 @@
Intl 56 53 0 1 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 1, no internal oligo 1, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_29
@@ -979,7 +979,7 @@
Intl 56 53 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_30
@@ -1020,7 +1020,7 @@
Intl 56 53 0 1 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_31
@@ -1063,7 +1063,7 @@
Intl 56 53 0 0 0 0 0 0 0 0 0 0 3
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_32
@@ -1106,7 +1106,7 @@
Intl 56 53 0 1 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_33
@@ -1147,7 +1147,7 @@
Intl 56 53 0 1 0 0 0 0 0 0 0 0 2
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR boundary_test_34
Modified: trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_boundary1_formatted_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_boundary1_formatted_output 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_boundary1_formatted_output 2007-03-31 23:30:01 UTC (rev 237)
@@ -39,7 +39,7 @@
Intl 163 0 0 0 0 0 0 0 0 0 121 0 0 42
Pair Stats:
considered 381, unacceptable product size 369, no internal oligo 11, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR pair_0
@@ -67,7 +67,7 @@
Intl 144 0 0 0 0 0 0 0 0 0 0 0 0 144
Pair Stats:
considered 32, unacceptable product size 32, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR pair_1
@@ -111,6 +111,6 @@
Intl 163 0 0 0 0 0 0 0 0 0 121 0 0 42
Pair Stats:
considered 6889, unacceptable product size 3403, no internal oligo 11, high mispriming library similarity 3474, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
Modified: trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_boundary2_formatted_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_boundary2_formatted_output 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_boundary2_formatted_output 2007-03-31 23:30:01 UTC (rev 237)
@@ -39,7 +39,7 @@
Intl 163 0 0 0 0 0 0 0 0 0 121 0 0 42
Pair Stats:
considered 381, unacceptable product size 369, no internal oligo 11, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR pair_0
@@ -67,6 +67,6 @@
Intl 144 0 0 0 0 0 0 0 0 0 0 0 0 144
Pair Stats:
considered 32, unacceptable product size 32, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
Modified: trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_formatted_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_formatted_output 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_formatted_output 2007-03-31 23:30:01 UTC (rev 237)
@@ -64,7 +64,7 @@
Right 1012 19 0 58 25 0 0 702 0 0 0 0 0 208
Pair Stats:
considered 23, unacceptable product size 17, ok 6
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR exon2
@@ -130,7 +130,7 @@
Right 827 0 0 72 314 0 236 0 0 0 0 0 0 205
Pair Stats:
considered 14, unacceptable product size 8, ok 6
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR exon2
@@ -204,7 +204,7 @@
Intl 3079 0 0 0 316 0 517 178 0 0 0 23 0 2045
Pair Stats:
considered 14, unacceptable product size 8, ok 6
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR exon1
@@ -281,7 +281,7 @@
Intl 3237 27 0 0 32 0 23 1880 0 0 0 0 0 1275
Pair Stats:
considered 29, unacceptable product size 18, high mispriming library similarity 2, ok 9
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR exon2
@@ -355,7 +355,7 @@
Intl 3079 0 0 0 316 0 517 178 0 0 0 23 0 2045
Pair Stats:
considered 116, unacceptable product size 66, tm diff too large 5, high mispriming library similarity 38, ok 7
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR exon2
@@ -401,6 +401,6 @@
Intl 3079 0 0 0 316 0 517 178 0 0 0 23 0 2045
Pair Stats:
considered 12459, unacceptable product size 6872, tm diff too large 4075, high mispriming library similarity 1512, ok 0
-primer3 release 1.1.0
+primer3 release 1.1.1
Modified: trunk/packages/primer3/branches/upstream/current/test/primer_must_use_formatted_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_must_use_formatted_output 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_must_use_formatted_output 2007-03-31 23:30:01 UTC (rev 237)
@@ -34,7 +34,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR high_tm
@@ -74,7 +74,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR high_tm_and_self_any
@@ -114,7 +114,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR high_tm_and_self_any_and_target
@@ -154,7 +154,7 @@
Right 3 0 0 0 0 0 0 2 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR high_tm_and_self_any_and_excl_region
@@ -196,7 +196,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR high_tm_and_self_any_and_incl_region
@@ -236,7 +236,7 @@
Statistics
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR left_high_tm_and_self_any_and_right_bad_gc
@@ -272,7 +272,7 @@
Statistics
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR left_high_tm_and_self_any_and_right_bad_gc_and_target
@@ -308,7 +308,7 @@
Statistics
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR internal_too_short
@@ -351,7 +351,7 @@
Statistics
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR internal_too_cold
@@ -390,7 +390,7 @@
Statistics
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR internal_too_cold2
@@ -433,7 +433,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR mispriming
@@ -476,6 +476,6 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
Modified: trunk/packages/primer3/branches/upstream/current/test/primer_position_penalty_formatted_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_position_penalty_formatted_output 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_position_penalty_formatted_output 2007-03-31 23:30:01 UTC (rev 237)
@@ -60,7 +60,7 @@
Right 3504 0 289 0 0 0 655 1723 0 0 0 0 0 837
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR AT3_X2
@@ -143,7 +143,7 @@
Right 6657 0 289 0 114 0 1327 3439 0 2 0 19 0 1467
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR AT3_X3
@@ -217,7 +217,7 @@
Right 5254 0 289 0 103 0 1706 1557 0 0 0 0 0 1599
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR AT3_X3'
@@ -288,7 +288,7 @@
Right 4294 0 289 0 209 0 512 2472 0 0 0 25 0 787
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR AT3_X4
@@ -371,7 +371,7 @@
Right 7004 0 289 0 0 0 1493 3474 0 0 0 0 0 1748
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR AT3_X5
@@ -439,7 +439,7 @@
Right 3744 0 289 0 0 0 874 1504 0 8 0 0 0 1069
Pair Stats:
considered 21, high end compl 20, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR AT3_X6
@@ -510,7 +510,7 @@
Right 4414 0 289 0 103 0 1578 1288 0 0 14 0 0 1142
Pair Stats:
considered 3, high end compl 2, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR CETP_X1
@@ -578,7 +578,7 @@
Right 4274 0 289 0 0 0 375 2978 0 0 0 0 0 632
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR CETP_X2
@@ -640,7 +640,7 @@
Right 2584 0 289 0 1 0 95 1901 0 0 0 0 0 298
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR CETP_X3
@@ -711,7 +711,7 @@
Right 4444 0 289 0 0 0 400 2950 0 0 0 0 0 805
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR CETP_X4
@@ -779,7 +779,7 @@
Right 3804 0 289 0 0 0 348 2565 0 0 0 0 0 602
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR CETP_X5
@@ -847,7 +847,7 @@
Right 3974 0 289 0 34 0 889 1971 0 0 0 0 0 791
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR CETP_X6
@@ -915,7 +915,7 @@
Right 3794 0 289 0 0 0 274 2616 2 3 0 0 0 610
Pair Stats:
considered 40, high end compl 38, ok 2
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR CETP_X7
@@ -983,7 +983,7 @@
Right 3593 0 289 0 15 0 752 1654 0 0 0 22 0 861
Pair Stats:
considered 102, high any compl 81, high end compl 20, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR CETP_X8
@@ -1051,7 +1051,7 @@
Right 3861 0 289 0 8 0 269 2629 0 0 0 22 0 644
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR CETP_X9
@@ -1116,7 +1116,7 @@
Right 4589 0 154 0 0 0 711 2838 0 0 0 0 0 886
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR CETP_X10
@@ -1169,7 +1169,7 @@
Right 1498 0 226 0 0 0 153 792 0 0 0 22 0 305
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR CETP_X11
@@ -1222,7 +1222,7 @@
Right 2741 0 116 0 42 0 336 1775 0 0 0 0 0 472
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR CETP_X12
@@ -1290,7 +1290,7 @@
Right 3774 0 289 0 0 0 619 2094 0 0 0 0 0 772
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR CETP_X13
@@ -1355,7 +1355,7 @@
Right 3434 0 289 0 0 0 586 1682 0 0 0 0 0 877
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR CETP_X14
@@ -1411,7 +1411,7 @@
Right 1454 0 289 0 0 0 83 882 0 0 0 0 0 200
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR CETP_X15
@@ -1476,7 +1476,7 @@
Right 3758 0 245 0 1 0 356 2464 0 0 3 22 0 667
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR CETP_X16
@@ -1544,7 +1544,7 @@
Right 3637 0 289 0 3 0 299 2316 0 0 0 25 0 705
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F2_X1
@@ -1612,7 +1612,7 @@
Right 4194 0 289 0 8 0 235 3082 0 0 2 0 0 578
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F2_X2
@@ -1683,7 +1683,7 @@
Right 4704 0 289 0 96 0 191 3583 0 4 0 0 0 541
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F2_X3
@@ -1748,7 +1748,7 @@
Right 3344 0 289 0 1 0 379 2040 0 0 0 0 0 635
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F2_X4
@@ -1813,7 +1813,7 @@
Right 3497 0 289 0 107 0 371 2132 0 0 0 18 0 580
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F2_X5
@@ -1881,7 +1881,7 @@
Right 4154 0 289 0 14 0 310 2916 0 0 0 0 0 625
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F2_X6
@@ -1952,7 +1952,7 @@
Right 4464 0 289 0 40 0 325 3245 0 0 0 0 0 565
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F2_X7
@@ -2032,7 +2032,7 @@
Right 5938 0 289 0 51 0 580 3983 0 0 0 44 0 991
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F2_X8
@@ -2103,7 +2103,7 @@
Right 4384 0 289 0 97 0 244 3201 0 0 0 0 0 553
Pair Stats:
considered 14, high end compl 12, ok 2
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F2_X9
@@ -2174,7 +2174,7 @@
Right 4248 0 289 0 80 0 415 2693 0 0 0 23 0 748
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F2_X10
@@ -2245,7 +2245,7 @@
Right 4621 0 289 0 8 0 474 3110 0 0 0 22 0 718
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F2_X11
@@ -2316,7 +2316,7 @@
Right 4762 0 289 0 176 0 739 2528 0 0 0 13 0 1017
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F2_X12
@@ -2390,7 +2390,7 @@
Right 4914 0 289 0 83 0 976 2660 0 0 0 0 0 906
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F2_X13
@@ -2458,7 +2458,7 @@
Right 3804 0 289 0 0 0 873 1715 0 5 0 0 0 922
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F2_X14
@@ -2526,7 +2526,7 @@
Right 3944 0 289 0 74 0 898 1848 0 2 0 0 0 833
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F2R_X1
@@ -2576,7 +2576,7 @@
Right 951 0 226 0 209 0 0 510 0 0 0 0 0 6
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F2R_X2-seg1
@@ -2644,7 +2644,7 @@
Right 6710 0 0 0 4 0 1540 3376 0 0 2 0 0 1788
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F2R_X2-seg2
@@ -2715,7 +2715,7 @@
Right 6997 0 0 0 109 0 2483 2360 0 0 0 22 0 2023
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F3_X1
@@ -2783,7 +2783,7 @@
Right 4094 0 289 0 716 0 101 2783 0 0 0 0 0 205
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F3_X2
@@ -2851,7 +2851,7 @@
Right 4214 0 289 0 232 0 1968 682 0 0 0 0 0 1043
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F3_X3
@@ -2925,7 +2925,7 @@
Right 5005 0 289 0 185 0 1231 1945 0 0 0 11 0 1344
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F3_X4
@@ -2996,7 +2996,7 @@
Right 4770 0 289 0 176 0 1330 1913 0 0 0 21 0 1041
Pair Stats:
considered 36, high end compl 33, ok 3
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F3_X5
@@ -3067,7 +3067,7 @@
Right 4397 0 289 0 28 0 1323 1565 0 4 0 44 0 1144
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F3_X6
@@ -3138,7 +3138,7 @@
Right 4311 0 289 0 51 0 1766 895 0 0 0 22 0 1288
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F5_X10
@@ -3188,7 +3188,7 @@
Right 2435 0 50 0 0 0 1068 632 0 0 0 0 0 685
Pair Stats:
considered 18, high end compl 16, ok 2
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F7_X1
@@ -3256,7 +3256,7 @@
Right 3734 0 289 0 17 0 289 2735 0 1 0 0 0 403
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F7_X2
@@ -3324,7 +3324,7 @@
Right 3601 0 289 0 16 0 390 2278 0 0 0 22 0 606
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F7_X2'
@@ -3395,7 +3395,7 @@
Right 4704 0 289 0 1078 0 138 2874 0 0 0 0 0 325
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F7_X3
@@ -3460,7 +3460,7 @@
Right 3344 0 289 0 0 0 284 2312 8 13 7 0 0 431
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F7_X4
@@ -3528,7 +3528,7 @@
Right 4234 0 289 0 81 0 378 2891 0 0 0 0 0 595
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F7_X5
@@ -3599,7 +3599,7 @@
Right 4504 0 289 0 1 0 499 3030 0 0 2 0 0 683
Pair Stats:
considered 20, high any compl 8, high end compl 10, ok 2
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F7_X6
@@ -3667,7 +3667,7 @@
Right 3894 0 289 0 11 0 463 2371 0 1 0 44 0 715
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F7_X7
@@ -3738,7 +3738,7 @@
Right 4181 0 289 0 10 0 236 3155 0 5 0 22 0 464
Pair Stats:
considered 126, high any compl 28, high end compl 97, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR F7_X8
@@ -3830,7 +3830,7 @@
Right 9054 0 289 0 79 0 1105 6374 0 1 0 0 0 1206
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HCF2_X2
@@ -3940,7 +3940,7 @@
Right 12144 0 289 0 15 0 3651 4687 0 7 0 0 0 3495
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HCF2_X3
@@ -4017,7 +4017,7 @@
Right 5393 0 289 0 28 0 1331 2335 19 7 0 67 0 1317
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HCF2_X4
@@ -4088,7 +4088,7 @@
Right 4238 0 289 0 20 0 420 2770 0 0 0 44 0 695
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HCF2_X5
@@ -4195,7 +4195,7 @@
Right 11432 0 289 0 57 0 2518 5947 0 12 0 20 0 2589
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HMGCR_X1
@@ -4239,7 +4239,7 @@
Right 1490 0 65 0 0 0 478 584 0 0 0 0 0 363
Pair Stats:
considered 11, high end compl 10, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HMGCR_X2
@@ -4277,7 +4277,7 @@
Right 770 0 0 0 11 0 448 81 7 1 0 0 0 222
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HMGCR_X3
@@ -4315,7 +4315,7 @@
Right 530 0 0 0 1 0 416 4 0 0 0 0 0 109
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HMGCR_X4
@@ -4353,7 +4353,7 @@
Right 500 0 0 0 0 0 123 202 0 0 0 0 0 175
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HMGCR_X5
@@ -4391,7 +4391,7 @@
Right 710 0 0 0 0 0 202 248 0 1 1 0 0 258
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HMGCR_X6
@@ -4429,7 +4429,7 @@
Right 720 0 0 0 0 0 181 338 0 0 0 0 0 201
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HMGCR_X7
@@ -4467,7 +4467,7 @@
Right 820 0 0 0 3 0 237 349 0 0 0 0 0 231
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HMGCR_X8
@@ -4508,7 +4508,7 @@
Right 1260 0 0 0 0 0 530 315 0 0 20 0 0 395
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HMGCR_X9
@@ -4555,7 +4555,7 @@
Right 1977 0 0 0 0 0 1125 203 0 0 0 22 0 627
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HMGCR_X10
@@ -4593,7 +4593,7 @@
Right 550 0 0 0 0 0 227 116 0 0 0 0 0 207
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HMGCR_X11
@@ -4631,7 +4631,7 @@
Right 540 0 0 0 0 0 181 215 0 0 0 0 0 144
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HMGCR_X12
@@ -4675,7 +4675,7 @@
Right 1600 0 0 0 0 0 707 324 0 0 0 0 0 569
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HMGCR_X13
@@ -4716,7 +4716,7 @@
Right 1240 0 0 0 1 0 280 628 0 0 0 0 0 331
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HMGCR_X14
@@ -4757,7 +4757,7 @@
Right 1230 0 0 0 0 0 122 805 0 0 0 0 0 303
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HMGCR_X15
@@ -4795,7 +4795,7 @@
Right 710 0 0 0 0 0 172 343 0 0 0 0 0 195
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HMGCR_X16
@@ -4836,7 +4836,7 @@
Right 1360 0 0 0 0 0 616 248 0 1 0 0 0 495
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HMGCR_X17
@@ -4877,7 +4877,7 @@
Right 1060 0 0 0 1 0 217 601 0 0 0 0 0 241
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HMGCR_X18
@@ -4918,7 +4918,7 @@
Right 1240 0 0 0 18 0 504 411 0 0 0 0 0 307
Pair Stats:
considered 62, high end compl 59, ok 3
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HMGCR_X19
@@ -4959,7 +4959,7 @@
Right 1200 0 0 0 0 0 167 784 0 0 0 0 0 249
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR HMGCR_X20
@@ -5000,6 +5000,6 @@
Right 1150 0 0 0 42 0 311 512 26 3 0 20 0 236
Pair Stats:
considered 1, ok 1
-primer3 release 1.1.0
+primer3 release 1.1.1
Modified: trunk/packages/primer3/branches/upstream/current/test/primer_task_formatted_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_task_formatted_output 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_task_formatted_output 2007-03-31 23:30:01 UTC (rev 237)
@@ -44,7 +44,7 @@
Right 1 0 0 0 0 0 0 0 0 0 0 0 1
Pair Stats:
considered 3, ok 3
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR pcr_primers_and_io
@@ -113,7 +113,7 @@
Intl 393 280 0 0 0 0 30 46 0 0 3 0 34
Pair Stats:
considered 7, ok 7
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR left_only
@@ -152,7 +152,7 @@
sid many tar excl bad GC too too any 3' poly end
ered Ns get reg GC% clamp low high compl compl X stab ok
Left 1121 38 23 0 0 0 42 866 0 0 0 0 152
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR right_only
@@ -191,7 +191,7 @@
sid many tar excl bad GC too too any 3' poly end
ered Ns get reg GC% clamp low high compl compl X stab ok
Right 623 27 36 0 5 0 230 145 0 6 0 0 174
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR hyb_probe_only
@@ -228,7 +228,7 @@
sid many tar excl bad GC too too any 3' poly end
ered Ns get reg GC% clamp low high compl compl X stab ok
Intl 1040 27 0 33 0 0 44 804 0 0 0 0 132
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR left_only
@@ -253,7 +253,7 @@
sid many tar excl bad GC too too any 3' poly end
ered Ns get reg GC% clamp low high compl compl X stab ok
Left 1 0 0 0 0 0 0 0 0 0 0 0 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR right_only
@@ -278,7 +278,7 @@
sid many tar excl bad GC too too any 3' poly end
ered Ns get reg GC% clamp low high compl compl X stab ok
Left 1 0 0 0 0 0 0 0 0 0 0 0 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR hyb_probe_only
@@ -303,6 +303,6 @@
sid many tar excl bad GC too too any 3' poly end
ered Ns get reg GC% clamp low high compl compl X stab ok
Left 1 0 0 0 0 0 0 0 0 0 0 0 1
-primer3 release 1.1.0
+primer3 release 1.1.1
Modified: trunk/packages/primer3/branches/upstream/current/test/primer_tm_lc_masking_formatted_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_tm_lc_masking_formatted_output 2007-03-31 02:28:00 UTC (rev 236)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_tm_lc_masking_formatted_output 2007-03-31 23:30:01 UTC (rev 237)
@@ -20,7 +20,7 @@
sid many tar excl bad GC too too any 3' poly end
ered Ns get reg GC% clamp low high compl compl X stab ok
Left 1 0 0 0 0 0 0 0 0 0 0 0 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR 001
@@ -45,7 +45,7 @@
sid many tar excl bad GC too too any 3' poly end
ered Ns get reg GC% clamp low high compl compl X stab ok
Left 1 0 0 0 0 0 0 0 0 0 0 0 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR 002
@@ -70,7 +70,7 @@
sid many tar excl bad GC too too any 3' poly end
ered Ns get reg GC% clamp low high compl compl X stab ok
Left 1 0 0 0 0 0 0 0 0 0 0 0 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR 100
@@ -88,7 +88,7 @@
sid many tar excl bad GC too too any 3' poly end case
ered Ns get reg GC% clamp low high compl compl X stab end ok
Left 1 0 0 0 0 0 0 0 0 0 0 0 1 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR 101
@@ -113,7 +113,7 @@
sid many tar excl bad GC too too any 3' poly end case
ered Ns get reg GC% clamp low high compl compl X stab end ok
Left 1 0 0 0 0 0 0 0 0 0 0 0 0 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR 102
@@ -138,7 +138,7 @@
sid many tar excl bad GC too too any 3' poly end
ered Ns get reg GC% clamp low high compl compl X stab ok
Left 1 0 0 0 0 0 0 0 0 0 0 0 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR 010
@@ -163,7 +163,7 @@
sid many tar excl bad GC too too any 3' poly end
ered Ns get reg GC% clamp low high compl compl X stab ok
Left 1 0 0 0 0 0 0 0 0 0 0 0 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR 011
@@ -188,7 +188,7 @@
sid many tar excl bad GC too too any 3' poly end
ered Ns get reg GC% clamp low high compl compl X stab ok
Left 1 0 0 0 0 0 0 0 0 0 0 0 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR 012
@@ -213,7 +213,7 @@
sid many tar excl bad GC too too any 3' poly end
ered Ns get reg GC% clamp low high compl compl X stab ok
Left 1 0 0 0 0 0 0 0 0 0 0 0 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR 110
@@ -231,7 +231,7 @@
sid many tar excl bad GC too too any 3' poly end case
ered Ns get reg GC% clamp low high compl compl X stab end ok
Left 1 0 0 0 0 0 0 0 0 0 0 0 1 0
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR 111
@@ -256,7 +256,7 @@
sid many tar excl bad GC too too any 3' poly end case
ered Ns get reg GC% clamp low high compl compl X stab end ok
Left 1 0 0 0 0 0 0 0 0 0 0 0 0 1
-primer3 release 1.1.0
+primer3 release 1.1.1
PRIMER PICKING RESULTS FOR 112
@@ -281,6 +281,6 @@
sid many tar excl bad GC too too any 3' poly end
ered Ns get reg GC% clamp low high compl compl X stab ok
Left 1 0 0 0 0 0 0 0 0 0 0 0 1
-primer3 release 1.1.0
+primer3 release 1.1.1
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