[med-svn] [Git][med-team/last-align][upstream] New upstream version 1268
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Sat Feb 26 18:35:44 GMT 2022
Nilesh Patra pushed to branch upstream at Debian Med / last-align
Commits:
8452e4ce by Nilesh Patra at 2022-02-26T23:50:43+05:30
New upstream version 1268
- - - - -
5 changed files:
- bin/maf-convert
- doc/maf-convert.rst
- src/makefile
- test/maf-convert-test.out
- test/maf-convert-test.sh
Changes:
=====================================
bin/maf-convert
=====================================
@@ -92,7 +92,10 @@ def symbolSize(symbol, letterSize):
def insertSize(row, letterSize):
"""Get the length of sequence included in the row."""
- return (len(row) - row.count("-")) * letterSize - 4 * row.count("/") - 2 * row.count("\\")
+ x = len(row) - row.count("-")
+ if letterSize:
+ return x * letterSize - 4 * row.count("/") - 2 * row.count("\\")
+ return x // 3 # assume it's divisible by 3
def matchAndInsertSizes(alignmentColumns, letterSizes):
"""Get sizes of gapless blocks, and of the inserts between them."""
@@ -127,8 +130,8 @@ def matchAndInsertSizes(alignmentColumns, letterSizes):
##### Routines for reading MAF format: #####
-def updateEvalueParameters(opts, line):
- for field in line.split():
+def updateEvalueParameters(opts, fields):
+ for field in fields:
try:
k, v = field.split("=")
x = float(v)
@@ -149,6 +152,8 @@ def scoreAndEvalue(aLine):
return score, evalue
def mafInput(opts, lines):
+ opts.scoreMatrix = {}
+ matrixColumnNames = []
aLine = ""
sLines = []
qLines = []
@@ -181,7 +186,14 @@ def mafInput(opts, lines):
qLines = []
pLines = []
elif line[0] == "#":
- updateEvalueParameters(opts, line)
+ fields = line.split()
+ updateEvalueParameters(opts, fields)
+ if len(fields) == 65 and all(len(i) == 3 for i in fields[1:]):
+ matrixColumnNames = [i.upper() for i in fields[1:]]
+ if len(fields) == 66 and len(fields[1]) == 1:
+ r = fields[1].upper()
+ for c, x in zip(matrixColumnNames, fields[2:]):
+ opts.scoreMatrix[r, c] = int(x)
if opts.isKeepComments:
print(line, end="")
if sLines: yield aLine, sLines, qLines, pLines
@@ -695,11 +707,43 @@ def mafConvertToSam(opts, lines):
##### Routines for converting to BLAST-like format: #####
-def pairwiseMatchSymbol(alignmentColumn):
- if isMatch(alignmentColumn):
- return "|"
- else:
- return " "
+def codonMatchSymbols(opts, geneticCode, aaSeq, ntSeq):
+ scoreSymbols = " ", "...", ":::"
+ seqLen = len(aaSeq)
+ i = 0
+ while i < seqLen:
+ if aaSeq[i] == "-":
+ yield " "
+ i += 1
+ else:
+ j = i + 3
+ a = aminoAcidCodes.get(aaSeq[i:j], "X")
+ b = ntSeq[i:j]
+ if geneticCode.get(b, "X") == a:
+ yield "|||"
+ else:
+ score = opts.scoreMatrix.get((a, b), -1)
+ yield scoreSymbols[(score >= 0) + (score > 0)]
+ i = j
+
+def translatedSeq(codon2triplet, aaSeq, ntSeq):
+ seqLen = len(aaSeq)
+ i = 0
+ while i < seqLen:
+ if aaSeq[i] == "-":
+ j = i + 1
+ while j < seqLen and aaSeq[j] == "-":
+ j += 1
+ if (j - i) % 3 == 0:
+ for b in range(i, j, 3):
+ e = b + 3
+ yield codon2triplet.get(ntSeq[b:e], " ")
+ else:
+ yield " " * (j - i)
+ else:
+ j = i + 3
+ yield codon2triplet.get(ntSeq[i:j], " ")
+ i = j
def strandText(strand):
if strand == "+":
@@ -738,11 +782,27 @@ def blastChunker(sLines, lineSize, alignmentColumns):
ends = list(map(blastEndCoordinate, coords, strands, seqLens))
yield chunkCols, chunkRows, begs, ends
-def writeBlast(opts, maf, oldQueryName):
+def blastDataFromMafFields(fields):
+ seqName, seqLen, strand, letterSize, beg, end, row = fields
+ maxPos = end
+ if strand == "-":
+ beg -= seqLen
+ maxPos = -beg
+ return seqName, seqLen, strand, letterSize, beg, maxPos, row, row.upper()
+
+def blastLineData(letterSize, beg, line):
+ end = beg + insertSize(line, letterSize)
+ begStr = str(beg + 1 if beg >= 0 else -beg)
+ endStr = str(end if end > 0 else 1 - end)
+ return begStr, line, endStr, end
+
+def writeBlast(opts, geneticCode, codon2triplet, maf, oldQueryName):
aLine, sLines, qLines, pLines = maf
fieldsA, fieldsB = pairOrDie(sLines, "Blast")
- seqNameA, seqLenA, strandA, letterSizeA, begA, endA, rowA = fieldsA
- seqNameB, seqLenB, strandB, letterSizeB, begB, endB, rowB = fieldsB
+ dataA = blastDataFromMafFields(fieldsA)
+ dataB = blastDataFromMafFields(fieldsB)
+ seqNameA, seqLenA, strandA, letterSizeA, begA, maxPosA, rowA, upA = dataA
+ seqNameB, seqLenB, strandB, letterSizeB, begB, maxPosB, rowB, upB = dataB
if seqNameB != oldQueryName:
print("Query= " + seqNameB)
@@ -766,13 +826,23 @@ def writeBlast(opts, maf, oldQueryName):
print(scoreLine)
- alignmentColumns = list(zip(rowA, rowB))
+ if letterSizeA * letterSizeB < 1:
+ c = codonMatchCounts(geneticCode, letterSizeA, letterSizeB, upA, upB)
+ matches, mismatches, gaps, dangles = c
+ alnSize = matches + mismatches + gaps
+ (aaSeq, ntSeq) = (upA, upB) if letterSizeB else (upB, upA)
+ sySeq = "".join(codonMatchSymbols(opts, geneticCode, aaSeq, ntSeq))
+ txSeq = "".join(translatedSeq(codon2triplet, aaSeq, ntSeq))
+ lineSize = max(opts.linesize, 3)
+ else:
+ sySeq = "".join(" |"[x == y] for x, y in zip(upA, upB))
+ matches = sySeq.count("|")
+ gaps = upA.count("-") + upB.count("-")
+ alnSize = len(sySeq)
+ lineSize = opts.linesize
- alnSize = len(alignmentColumns)
- matches = sum(x.upper() == y.upper() for x, y in alignmentColumns)
matchPercent = 100 * matches // alnSize # round down, like BLAST
identLine = " Identities = %s/%s (%s%%)" % (matches, alnSize, matchPercent)
- gaps = rowA.count("-") + rowB.count("-")
if gaps:
gapPercent = 100 * gaps // alnSize # round down, like BLAST
identLine += ", Gaps = %s/%s (%s%%)" % (gaps, alnSize, gapPercent)
@@ -781,23 +851,39 @@ def writeBlast(opts, maf, oldQueryName):
print(" Strand = %s / %s" % (strandText(strandB), strandText(strandA)))
print()
- for chunk in blastChunker(sLines, opts.linesize, alignmentColumns):
- cols, rows, begs, ends = chunk
- begWidth = maxlen(begs)
- matchSymbols = ''.join(map(pairwiseMatchSymbol, cols))
- print("Query: %-*s %s %s" % (begWidth, begs[1], rows[1], ends[1]))
- print(" %-*s %s" % (begWidth, " ", matchSymbols))
- print("Sbjct: %-*s %s %s" % (begWidth, begs[0], rows[0], ends[0]))
+ begWidth = len(str(max(maxPosA, maxPosB)))
+ pad = " " * (begWidth + 7)
+
+ numOfColumns = len(sySeq)
+ i = 0
+ while i < numOfColumns:
+ j = min(i + lineSize, numOfColumns)
+ rem = 0
+ if letterSizeA * letterSizeB < 1 and j < numOfColumns:
+ rem = (j - i - aaSeq.count("-", i, j)) % 3
+ j -= rem
+ bA, lineA, eA, begA = blastLineData(letterSizeA, begA, rowA[i:j])
+ bB, lineB, eB, begB = blastLineData(letterSizeB, begB, rowB[i:j])
+ if letterSizeA == 0: print(pad, txSeq[i:j])
+ print("Query: %-*s" % (begWidth, bB), lineB + " " * rem, eB)
+ print(pad, sySeq[i:j])
+ print("Sbjct: %-*s" % (begWidth, bA), lineA + " " * rem, eA)
+ if letterSizeB == 0: print(pad, txSeq[i:j])
print()
+ i = j
def mafConvertToBlast(opts, lines):
+ geneticCode = standardGeneticCode()
+ aa2triplet = dict((j, i.title()) for i, j in aminoAcidCodes.items())
+ codon2triplet = dict((i, aa2triplet[j]) for i, j in geneticCode.items())
+
oldQueryName = ""
for maf in mafInput(opts, lines):
- writeBlast(opts, maf, oldQueryName)
+ writeBlast(opts, geneticCode, codon2triplet, maf, oldQueryName)
sLines = maf[1]
oldQueryName = sLines[1][0]
-def blastDataFromMafFields(fields):
+def btabDataFromMafFields(fields):
seqName, seqLen, strand, letterSize, beg, end, row = fields
if strand == "+":
beg += 1
@@ -807,8 +893,6 @@ def blastDataFromMafFields(fields):
return seqName, letterSize, str(beg), str(end), row.upper()
def codonMatchCounts(geneticCode, letterSizeA, letterSizeB, rowA, rowB):
- letterSpanA = 3 - letterSizeA * 2
- letterSpanB = 3 - letterSizeB * 2
codeA = geneticCode if letterSizeA else aminoAcidCodes
codeB = geneticCode if letterSizeB else aminoAcidCodes
loopEnd = len(rowA)
@@ -843,8 +927,8 @@ def codonMatchCounts(geneticCode, letterSizeA, letterSizeB, rowA, rowB):
def writeBlastTab(opts, geneticCode, maf):
aLine, sLines, qLines, pLines = maf
fieldsA, fieldsB = pairOrDie(sLines, "BlastTab")
- seqNameA, letterSizeA, begA, endA, rowA = blastDataFromMafFields(fieldsA)
- seqNameB, letterSizeB, begB, endB, rowB = blastDataFromMafFields(fieldsB)
+ seqNameA, letterSizeA, begA, endA, rowA = btabDataFromMafFields(fieldsA)
+ seqNameB, letterSizeB, begB, endB, rowB = btabDataFromMafFields(fieldsB)
gapOpens = gapRunCount(rowA) + gapRunCount(rowB)
if letterSizeA * letterSizeB < 1:
=====================================
doc/maf-convert.rst
=====================================
@@ -72,6 +72,27 @@ Options
Write CHARS characters per line. This affects blast and html
formats only.
+DNA-versus-protein blast output
+-------------------------------
+
+If the input has protein-versus-DNA alignments like this::
+
+ GluTrpThrAlaLeuIleAsnLeuLysAsnArg--AspLeuValIleLysAlaAlaAsp
+ GAATAGTCCGGTTGAAAAAATGTACAAAAACATAAGAGAACATTACAAAACTTGCAGTC
+
+then the blast-format output will look like this::
+
+ Glu***SerGly***LysAsnValGlnLysHis GluAsnIleThrLysLeuAlaVal
+ GAATAGTCCGGTTGAAAAAATGTACAAAAACATAAGAGAACATTACAAAACTTGCAGTC
+ |||:::::: |||...:::...::: ::: :::...||| |||
+ GluTrpThrAlaLeuIleAsnLeuLysAsnArg--AspLeuValIleLysAlaAlaAsp
+
+The DNA's translation (assuming the standard genetic code) is shown
+above it. ``|||`` indicates a match, ``:::`` a positive alignment
+score, and ``...`` an alignment score of 0. ``:::`` and ``...`` are
+shown only for alignments preceded by a substitution score matrix of
+the sort in lastal's output header.
+
Hints for sam/bam
-----------------
=====================================
src/makefile
=====================================
@@ -143,7 +143,7 @@ ScoreMatrixData.hh: ../data/*.mat
../build/mat-inc.sh ../data/*.mat > $@
VERSION1 = git describe --dirty
-VERSION2 = echo ' (HEAD -> main, tag: 1260) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
+VERSION2 = echo ' (HEAD -> main, tag: 1268) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
VERSION = \"`test -e ../.git && $(VERSION1) || $(VERSION2)`\"
=====================================
test/maf-convert-test.out
=====================================
@@ -6755,9 +6755,9 @@ Query= 21
Identities = 69/87 (79%)
Strand = Plus / Plus
-Query: 1 GATAGTATTGCGAGACGTTGGAGTCGGAGTATTCTATGTCGTAGTATTTGTTTTTGATTT 60
- ||||| ||||||||||| ||||| ||||| | |||||||| ||||| ||| |||||||
-Sbjct: 81 GATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC 140
+Query: 1 GATAGTATTGCGAGACGTTGGAGTCGGAGTATTCTATGTCGTAGTATTTGTTTTTGATTT 60
+ ||||| ||||||||||| ||||| ||||| | |||||||| ||||| ||| |||||||
+Sbjct: 81 GATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC 140
Query: 61 TTGTTTTATTTTATTATTTATCGTATT 87
|| | ||| |||||||||||| |
@@ -6881,13 +6881,13 @@ Query= 28
Identities = 66/87 (75%)
Strand = Plus / Plus
-Query: 1 TAAGTTAATAGAAGTCGGCGTAAAGAGTGTTTTAGATTATTTTTTTTTTAATAAAGTTAA 60
- |||| |||||||| |||||||||||||||||||||| | | ||||||| |||
-Sbjct: 919 CAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAA 978
+Query: 1 TAAGTTAATAGAAGTCGGCGTAAAGAGTGTTTTAGATTATTTTTTTTTTAATAAAGTTAA 60
+ |||| |||||||| |||||||||||||||||||||| | | ||||||| |||
+Sbjct: 919 CAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAA 978
-Query: 61 AATTTATTTGAGTTGTAAAAAATTTTA 87
- || | | |||||||||||||| | |
-Sbjct: 979 AACTCACCTGAGTTGTAAAAAACTCCA 1005
+Query: 61 AATTTATTTGAGTTGTAAAAAATTTTA 87
+ || | | |||||||||||||| | |
+Sbjct: 979 AACTCACCTGAGTTGTAAAAAACTCCA 1005
Query= 29
(87 letters)
@@ -7409,13 +7409,13 @@ Query= 55
Identities = 74/87 (85%)
Strand = Plus / Plus
-Query: 1 AGCTTTTTATGTATTTGGTATTTTCGTTTGGGGGGTGTGTACGCGATAGTATTGCGAGAC 60
- |||| | ||| ||||||||||||||| ||||||||||| ||||||||| ||||||||||
-Sbjct: 37 AGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGAC 96
+Query: 1 AGCTTTTTATGTATTTGGTATTTTCGTTTGGGGGGTGTGTACGCGATAGTATTGCGAGAC 60
+ |||| | ||| ||||||||||||||| ||||||||||| ||||||||| ||||||||||
+Sbjct: 37 AGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGAC 96
-Query: 61 GTTGGAGTCGGAGTAATCTATGTCGTA 87
- | ||||| ||||| | |||||||| |
-Sbjct: 97 GCTGGAGCCGGAGCACCCTATGTCGCA 123
+Query: 61 GTTGGAGTCGGAGTAATCTATGTCGTA 87
+ | ||||| ||||| | |||||||| |
+Sbjct: 97 GCTGGAGCCGGAGCACCCTATGTCGCA 123
Query= 56
(87 letters)
@@ -8209,6 +8209,474 @@ Query: 27 TACGCCTAACCGATAATATTATTACAA 1
|||||||||||| ||| |||| | ||
Sbjct: 9000 TACGCCTAACCGCTAACATTACTGCAG 9026
+Query= chrUn_KI270748v1
+ (93321 letters)
+
+>UN-L1MA6_pol#LINE/L1
+ Length = 1275
+
+ Score = 1.08e+03 bits (3177.2), Expect = 0
+ Identities = 404/633 (63%), Gaps = 35/633 (5%)
+ Strand = Plus / Plus
+
+ GlnGlyCysProLeuSerGluLeuLeuPheAsnIleValLeuAspValLeuAlaArgAlaIleArgGlnLysLysGluIleLysGlyMetLysIleGlyLysGluGluValLysLeuPhe
+Query: 13905 CAAGGGTGCCCACTCTCAGAACTTCTATTCAACATAGTACTGGATGTCCTAGCCAGAGCAATTAGGCAAAAGAAAGaaaTAAAAGGCATGAAAATTGGAAAGGAAGAAGTTAAATTGTTT 14024
+ |||||||||||||||||| |||||||||||||||||||||:::||||||||||||||||||||||||:::|||||||||||||||::: ||||||||||||||||||||||||...
+Sbjct: 658 GlnGlyCysProLeuSerProLeuLeuPheAsnIleValLeuGluValLeuAlaArgAlaIleArgGlnGluLysGluIleLysGlyIleGlnIleGlyLysGluGluValLysLeuSer 697
+
+ LeuPheAlaValAspMetIleLeuTyrIleGluAsnThrAsnAsnSerAlaLysLys LeuGluPheIleAsnGluPheSerLysValAlaGlyTyrAsnValAsnIleGlnAsn
+Query: 14025 CTGTTTGCAGTTGACATGATCTTATATATAGAAAACACCAATAACTCTGCCAAAAAA---TTTAGAATTCATAAATGAATTTAGTAAAGTTGCAGGATACAATGTGAACATACAAAAT 14139
+ ||||||||| |||||||||||||||||||||||| ::::::|||:::|||||| ||||||:::||||||||||||||||||||||||||||||::::::|||||||||:::
+Sbjct: 698 LeuPheAlaAspAspMetIleLeuTyrIleGluAsnProLysAspSerThrLysLysLeu-LeuGluLeuIleAsnGluPheSerLysValAlaGlyTyrLysIleAsnIleGlnLys 736
+
+ SerValAlaPheLeuHisIleAsnAsnLysLeu ThrLysLysGluIleLysLysThrIleLeuPheIleIleAlaThrLys TyrLeuAspValAsnLeuAsnLysGlu
+Query: 14140 TCAGTAGCATTTCTACACATCAACAACAAACTATACAAAAAAagaaatcaagaaaacaATCCTATTTATAATAGCAACAAAA---------AATACTTAGATGTAAATTTAAACAAAGAG 14250
+ |||||||||||||||::: |||...:::||| ...:::|||||||||||||||||||||:::|||:::|||||||||||| ||||||::::::|||||| ||||||
+Sbjct: 737 SerValAlaPheLeuTyrAlaAsnSerGluLeu-SerGluLysGluIleLyslysthrilepropheThrIleAlaThrLysLysIleLys--TyrLeuGlyIleAsnLeuThrLysGlu 775
+
+ ValAsnAspLeuTyrThrGluAsnTyrLysThrLeuMetLysThrIleGluGluAlaThrAsnLysTrpLysAspIleSerCysSerTrpIleGlyLysSerAsnMetPheGluMetSer
+Query: 14251 GTGAATGATCTTTACACTGAAAACTACAAAACATTGATGAAAACAATTGAAGAAGCCACAAATAAATGGAAAGATATCTCATGTTCATGGATTGGAAAAAGTAATATGTTTGAAATGTCC 14370
+ |||:::|||||||||...|||||||||||||||||||||||| ||||||||| |||||||||||||||||||||:::|||||||||||||||::: |||::: ||||||
+Sbjct: 776 ValLysAspLeuTyrXaaGluAsnTyrLysThrLeuMetLysGluIleGluGluAspThrAsnLysTrpLysAspIleProCysSerTrpIleGlyArgIleAsnIleValLysMetSer 815
+
+ IleLeuSerLysValMetTyrIleLeuAsnAlaIleSerIleLysIleProMetThrPheSerHisArgAsnArgLysThrThrLeuLysSerValTrpAsnHisLysLysLeu***Lys
+Query: 14371 ATACTATCCAAAGTGATGTACATATTGAATGCAATCTCTATCAAAATTCCTATGACATTTTCCCACAGAAATAGAAAAACAACTCTCAAATCTGTATGGAATCACAAAAAACTCTGAAAA 14490
+ ||||||:::|||::::::||| :::|||||||||:::|||||||||||||||||||||::: ||||||:::||||||:::|||||||||||||||:::::::::
+Sbjct: 816 IleLeuProLysAlaIleTyrArgPheAsnAlaIleProIleLysIleProMetThrPhePheThrGluIleGluLysThrIleLeuLysPheValTrpAsnHisLysArgProArgIle 855
+
+ AlaLysIleIleLeuIleGluLysSerLysAlaGlyAspIleThrLeuProAspPheLysLeuTyrTyrIleAlaIleAlaIleGluThrProTrpTyrTrpHisLysArgArgHisIle
+Query: 14491 GCCAAAATAATCTTGATCGAAAAAAGCAAGGCAGGAGATATCACATTACCTGACTTCAAATTATACTACATAGCTATAGCAATCGAAACACCATGGTACTGGCATAAACGCAGACACATA 14610
+ |||||| |||||| |||:::|||||||||:::|||||||||||||||||||||...|||||| ||||||:::::: ||| ||||||||||||||| |||||||||
+Sbjct: 856 AlaLysAlaIleLeuSerLysLysAsnLysAlaGlyGlyIleThrLeuProAspPheLysIleTyrTyrLysAlaIleValThrLysThrAlaTrpTyrTrpHisLysAsnArgHisIle 895
+
+ AspGlnLeuHisArgIleLysSerPro***IleAsnLeuHis TyrSerGlnLeuThrPheAsnLysGlyAlaArgAsnThr TrpGlyLysAsnSerLeuPheLysLys
+Query: 14611 GACCAATTACACAGAATAAAGAGCCCATAAATAAATCTACAT---ATTATAGTCAATTGACTTTCAACAAAGGTGCCAGGAACACA---CATGGGGAAAGAACAGTCTCTTCAAAAAA 14722
+ |||||| :::||||||:::||||||:::||||||:::... ||||||||||||:::|||:::|||||||||:::|||||| |||||||||:::|||||||||...|||
+Sbjct: 896 AspGlnTrpAsnArgIleGluSerProGluIleAsnProArgIle--TyrSerGlnLeuIlePheAspLysGlyAlaLysAsnThrGln--TrpGlyLysAspSerLeuPheAsnLys 933
+
+ TrpCys***GluAsn***MetSerThr ArgLeuIleLeuGlyProTyrPheIleProTyrLysAsnIleAsnSerLys***Val AspLeuAsnValArgProSerThr
+Query: 14723 TGGTGTTGAGAAAACTGAATGTCCACA------AGATTGATCTTAGGCCCTTATTTCATACCATATAAAAATATAAATTCAAAATAAGTT---AGACTTAAATGTAAGACCTAGCACT 14831
+ ||||||:::||||||::::::|||||| |||::: |||:::||||||::: |||||| :::||||||||||||:::::: |||||||||||||||||| |||
+Sbjct: 934 TrpCysTrpGluAsnTrpIleSerThrCysArgArgMetLysLeuAspProTyrLeuSerProTyrThrLysIleAsnSerLysTrpIleLys-AspLeuAsnValArgProGluThr 972
+
+ IleGluLeuLeuGluGluAsn GlyGlu***LeuGlnAspIleGlyLeuGlyAsnAsnIleLeu***TyrAspSerLysAlaGlnAlaArgLysAlaThrLysHisLysTrpAsn
+Query: 14832 ATAGAACTCCTAGAAGAAAAC---AGGGGAATAACTCCAAGACATTGGTCTGGGCAATAATATTTTATGATATGACTCTAAAGCACAGGCAAGAAAAGCAACAAAACACAAATGGAAT 14946
+ ::: ||||||||||||||| |||||| |||:::|||||||||||||||:::::: ||| ||||||||||||||| |||||| :::||||||:::
+Sbjct: 973 MetLysLeuLeuGluGluAsnIle-GlyGluMetLeuHisAspIleGlyLeuGlyLysAspPheLeuAspLysThrSerLysAlaGlnAlaThrLysAlaLysIleAspLysTrpAsp 1011
+
+ SerIleAsnLeuLysSerPheCysAlaAlaLysGlu ValAsnArgValLys******ProThrLysTrpGluGluLeuSerAlaAsnTyrThrPheAspLysArgLeuMetSer
+Query: 14947 AGCATCAACCTAAAAAGCTTCTGCGCAGCAAAAGAA---AGTCAACAGAGTGAAGTGATAACCTACAAAATGGGAGGAATTATCTGCAAACTATACATTTGATAAGAGGCTAATGTCC 15061
+ |||:::|||||||||||||||:::||||||||| :::||||||||||||::::::||||||:::|||||| ...:::|||||||||:::...||||||:::|||:::|||
+Sbjct: 1012 TyrIleLysLeuLysSerPheCysThrAlaLysGluThr-IleAsnArgValLysArgGlnProThrGluTrpGluLysIlePheAlaAsnTyrAlaSerAspLysGlyLeuIleSer 1050
+
+ LysIleSer***GluLeuLysGlnHisAsnAsnLysLysThrArgAsnProAsnGluLysLeuThrLysAspLeuAsnArgHisPheSerLysGluAspIleGlnMetAlaAsnArgTyr
+Query: 15062 AAAATATCTTAGGAACTCAAACAACACAataataagaaAACAAGGAACCCTAATGAAAAATTGACAAAGGATCTAAATAGACATTTCTCAAAAGAAGACATACAAATGGCCAACAGATAT 15181
+ :::|||... |||||||||||| ||| ||||||||| |||||| ...|||::::::||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Sbjct: 1051 ArgIleTyrLysGluLeuLysGlnLeuAsnSerLysLysThrAsnAsnProIleXaaLysTrpAlaLysAspLeuAsnArgHisPheSerLysGluAspIleGlnMetAlaAsnArgTyr 1090
+
+ Ile LysCys***LeuSerLeuIleIleArgGluMetHisIleLysThrThrIleLysCysHisPheThrSerValArgMetAlaValThrGluLysAlaGluAspThrLysCys
+Query: 15182 ATA---AAAATGCTAATTATCACTGATCATCAGAGAAATGCATATTAAAACTACAATAAAATGCCATTTCACATCCGTTAGAATGGCTGTTACAGAAAAGGCAGAAGATACCAAGTGT 15296
+ ::: |||||| |||||||||||||||||||||:::||||||||||||:::::::::|||:::|||:::||||||||||||:::::: |||::: |||:::||||||
+Sbjct: 1091 MetLys-LysCysSerThrSerLeuIleIleArgGluMetGlnIleLysThrThrMetArgTyrHisLeuThrProValArgMetAlaIleIleLysLysThrLysAspAsnLysCys 1129
+
+ TrpArgGlyCysGlyGluLysGluAsnLeuVal Cys***GluCysLysLeuPheGlnProLeu***LysThrVal***ValIleLeu LysIleGluLeu
+Query: 15297 TGGAGAGGATGTGGAGAAAAGGAAAACCTTGTA------ATTGTTGAGAATGTAAACTATTTCAGCCATTGTAAAAGACAGTATAAGTGATTCTG---------TAAAAATAGAATTA 15399
+ |||||||||||||||||||||::: |||... ::::::|||||||||||| |||||||||:::|||||||||::: ||| ||||||||||||
+Sbjct: 1130 TrpArgGlyCysGlyGluLysGlyThrLeuThrHisCys--TrpTrpGluCysLysLeuValGlnProLeuTrpLysThrValTrpArgPheLeuLysLysLeu--LysIleGluLeu 1167
+
+ ProTyrAspSerValMetLeuPheLeuGlyIleTyr***LysAspIleLysSerValCysGln***ValIleCysThrProIlePheIleValAlaLeuPheThrThrAlaLysMetTrp
+Query: 15400 CCATATGATTCAGTAATGCTATTTCTGGGCATATATTAAAAAGATATCAAATCAGTGTGTCAATGAGTTATCTGTACTCCCATATTTATTGTAGCATTATTCACAACAGCCAAGATGTGG 15519
+ |||||||||:::::::::::::::|||||||||||| |||::::::||||||||||||:::::: ||||||||||||:::||||||:::||||||||||||:::||||||:::|||
+Sbjct: 1168 ProTyrAspProAlaIleProLeuLeuGlyIleTyrProLysGluMetLysSerValCysArgArgAspIleCysThrProMetPheIleAlaAlaLeuPheThrIleAlaLysIleTrp 1207
+
+ Asn***LeuLysTyrProSerThrHisGluTrpMetLysLysMetTrpTyrThrTyrThrIleGlu***TyrThrThrLeuLysAsnLysLys ValSerPheValThrThr***
+Query: 15520 AATTAACTTAAGTATCCATCGACACATGAGTGGATGAAGAAAATGTGGTACACATACACAATAGAATAGTATACAACCTTAaaaaataaaaaa---aGTATCATTTGTGACAACATGA 15634
+ |||::::::|||:::|||||||||...||||||:::|||||||||||||||:::||||||:::|||:::|||...:::...|||:::...::: ...||||||:::||||||:::
+Sbjct: 1208 AsnGlnProLysCysProSerThrAspGluTrpIleLysLysMetTrpTyrIleTyrThrMetGluTyrTyrSerAlaIleLysLysAsnGluIle-LeuSerPheAlaThrThrTrp 1246
+
+ MetAsnArgGluAspIleIleLeuSerLysIleIleGlnAlaGlnLysAlaArgTyrCysIleIleSerLeuValCysGly
+Query: 15635 ATGAACCGGGAGGACATTATACTGAGTAAAATAATCCAGGCACAGAAAGCCAGATACTGCATAATCTCACTTGTATGTGGA 15715
+ |||||| |||||||||:::||||||:::||| |||||||||||| :::|||::::::|||||||||:::||||||
+Sbjct: 1247 MetAsnLeuGluAspIleMetLeuSerGluIleSerGlnAlaGlnLysAspLysTyrArgMetIleSerLeuIleCysGly 1273
+
+>UN-L1PA2_pol#LINE/L1
+ Length = 1276
+
+ Score = 603 bits (1775.7), Expect = 1.5e-169
+ Identities = 212/227 (93%)
+ Strand = Plus / Plus
+
+ LeuIleSerGlyIleTyrAsnGluProLysGlnIleTyrLysLysLysThrAsnAsnProIleLysLysTrpAlaLysAspMetAsnArgHisPheSerLysGluAspIleTyrAlaAla
+Query: 3860 CTAATATCCGGAATCTACAATGAACCCAAACAAATTTACAAGAAaaaaacaaacaaCCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCC 3979
+ |||||||||:::|||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Sbjct: 1049 LeuIleSerArgIleTyrAsnGluLeuLysGlnIleTyrLysLysLysThrAsnAsnProIleLysLysTrpAlaLysAspMetAsnArgHisPheSerLysGluAspIleTyrAlaAla 1088
+
+ LysLysHisMetLysLysCysSerLeuSerLeuAlaIleArgGluMetGlnIleLysThrThrMetArgTyrHisLeuThrProValArgMetAlaIleIleLysLysSerGlyAsnAsn
+Query: 3980 AAAAAACACATGAAAAAATGCTCACTATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTTACACCAGTTAGAATGGCCATCATTAAAAAGTCAGGAAACAAC 4099
+ |||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Sbjct: 1089 LysLysHisMetLysLysCysSerSerSerLeuAlaIleArgGluMetGlnIleLysThrThrMetArgTyrHisLeuThrProValArgMetAlaIleIleLysLysSerGlyAsnAsn 1128
+
+ ArgCysTrpArgGlyCysGlyGluIleGlyThrPheLeuHisCysTrpTrpAspCysLysLeuValGlnProLeuTrpLysThrValTrp***PheArgArgAspLeuGluLeuGluIle
+Query: 4100 AGGTGCTGGAGAGGATGTGGAGAAATAGGAACATTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGACAGTGTGGTGATTCCGCAGGGATCTAGAACTAGAAATA 4219
+ |||||||||||||||||||||||||||||||||:::|||||||||||||||||||||||||||||||||||||||||||||...||||||:::|||...|||||||||||||||||||||
+Sbjct: 1129 ArgCysTrpArgGlyCysGlyGluIleGlyThrLeuLeuHiscystrptrpaspcyslysLeuValGlnProLeuTrpLysSerValTrpArgPheLeuArgAspLeuGluLeuGluIle 1168
+
+ ProPheAspProAlaIleProLeuLeuGlyIleTyrProLysAspTyrLysSerCysCysTyrLysAspThrCysThrArgMetPheThrValAlaLeuPheThrIleAlaLysThrTrp
+Query: 4220 CCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTACTGTGGCACTATTCACAATAGCAAAGACTTGG 4339
+ |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||::::::|||||||||||||||||||||||||||
+Sbjct: 1169 ProPheAspProAlaIleProLeuLeuGlyIleTyrProLysAspTyrLysSerCysCysTyrLysAspThrCysThrArgMetPheIleAlaAlaLeuPheThrIleAlaLysThrTrp 1208
+
+ AsnGlnSerLysCysProThrMetIleAspTrpIleLysLysThrTrpHisIleTyrThrMetGluTyrTyrAlaAlaIleLysAsnAspGluPheMetSerPheValGlyThrTrpMet
+Query: 4340 AACCAATCCAAATGTCCAACAATGATAGACTGGATTAAGAAAACGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTAGGGACATGGATG 4459
+ ||||||:::|||||||||||||||||||||||||||||||||:::|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Sbjct: 1209 AsnGlnProLysCysProThrMetIleAspTrpIleLysLysMetTrpHisIleTyrThrMetGluTyrTyrAlaAlaIleLysAsnAspGluPheMetSerPheValGlyThrTrpMet 1248
+
+ LysLeuGluThrIleIleLeuSerLysGlnSerGlnGlyGlnLysThrLysHisArgMetPheSerLeuIleGlyGlyAsn
+Query: 4460 AAGCTGGAAACCATCATTCTCAGCAAACAATCACAAGGACAAAAAACCAAACACCGCATGTTCTCACTCATAGGTGGGAAT 4540
+ |||||||||:::||||||||||||||| ||||||:::||||||||||||||||||:::|||||||||||||||||||||
+Sbjct: 1249 LysLeuGluIleIleIleLeuSerLysLeuSerGlnGluGlnLysThrLysHisArgIlePheSerLeuIleGlyGlyAsn 1275
+
+>UN-L1MA6_pol#LINE/L1
+ Length = 1275
+
+ Score = 546 bits (1607.4), Expect = 2.5e-152
+ Identities = 240/386 (62%), Gaps = 39/386 (10%)
+ Strand = Minus / Plus
+
+ LysAlaAsnLysAspThrIleArgLysVal GlyGlnProIleSerLeuMetAsnThrAspThrLysValLeuLysLys ValLeuAlaAsnArgIle***GlnHisIleArg
+Query: 3661 aaggcaaacaAGGACACTATAAGAAAAGTA---TGGGCCAACCAATATCCCTGATGAACACAGATACAAAAGTCCTCAAAAAAAAGTACTAGCAAACAGAATTTAACAACATATTAGG 3547
+ ||| :::|||||||||::::::||| :::||||||||||||||||||:::|||:::|||:::|||...||| :::|||||||||||||||:::|||||||||:::
+Sbjct: 518 LysProAspLysAspThrThrLysLysGluAsn--TyrArgProIleSerLeuMetAsnIleAspAlaLysIleLeuAsnLys--IleLeuAlaAsnArgIleGlnGlnHisIleLys 555
+
+ Arg IleTyrHisAspLys GlyPheIleLeu ArgCysPheSerLysHisLysSer AsnValIleAsnHisIleAsnArgMetLysAspLysLys
+Query: 3546 AGA---ACATTTACCATGATAAA---GTGGATTTATCCTC---------CAGATGTTTCAGCAAACACAAATCA---AATGTGATAAACCACATTAACAGAATGAAGGATAAAAAA--- 3449
+ ::: |||:::|||||| |||||||||::: ::::::|||::: :::|||||| |||||||||...||||||||||||||||||||||||...
+Sbjct: 556 LysIle--IleHisHisAspGlnVal--GlyPheIleProGlyMetGln-GlyTrpPheAsnIleArgLysSerIleAsnValIleHisHisIleAsnArgMetLysAspLysAsnHis 593
+
+ IleAlaIleSerIleTyrAlaGluLysAlaPheAsp***IleGlnAsnProLeuMetThrLysProLeuAsnLysLeuGlyIleGluGlyMetTyrLeuAsnThrLysGlnAspIleTyr
+Query: 3448 ATAGCTATCTCTATATATGCAGAAAAAGCATTTGACTAAATTCAAAATCCTCTCATGACTAAACCTCTCAACAAATTGGGCATAGAAGGCATGTACCTTAACACAAAACAGGACATATAT 3329
+ ::: |||||||||...||||||||||||||||||:::||||||...|||:::|||:::||| ||||||||||||||||||||||||:::|||||||||||| ||||||
+Sbjct: 594 MetIleIleSerIleAspAlaGluLysAlaPheAspLysIleGlnHisProPheMetIleLysThrLeuAsnLysLeuGlyIleGluGlyThrTyrLeuAsnThrIleLysAlaIleTyr 633
+
+ AsnLysLeuThrAlaHisIleIleProAsnAsnGluLysValLysSerPheLeuLeuArgSerLysThrArgGlnGlyTyrLeuPheSerLeuLeuLeuPheAsnLeuPheLeuGluVal
+Query: 3328 AACAAGCTCACAGCTCACATCATACCCAACAATGAAAAAGTGAAATCTTTTCTGCTAAGATCAAAAACAAGACAAGGATATTTATTCTCACTACTTCTATTCAACTTATTTCTGGAAGTC 3209
+ :::|||:::||||||:::|||||| ||| ||||||...|||:::|||:::||||||||| ||||||||||||::: :::|||:::||||||||||||... |||||||||
+Sbjct: 634 AspLysProThrAlaAsnIleIleLeuAsnGlyGluLysLeuLysAlaPheProLeuArgSerGlyThrArgGlnGlyCysProLeuSerProLeuLeuPheAsnIleValLeuGluVal 673
+
+ LeuAlaArgAlaIleLysProAsnLysGluIleLys IleGlnIleGluLysGluGluValLysLeuSerLeuPheAspAsp IleLeuTyrIleGlyAsnProLysAsn
+Query: 3208 CTAGCCAGAGCAATTAAGCCAAATAAAGAAATAAAA---TATTCAAATTGAAAAGGaagaagtaaaaTTGTCTCTGTTTGATGAC------ATATTATATATAGGAAACCCTAAAAAC 3100
+ |||||||||||||||:::... |||||||||||| |||||||||:::||||||||||||||||||||||||||| ||| ||||||||||||:::|||||||||:::
+Sbjct: 674 LeuAlaArgAlaIleArgGlnGluLysGluIleLysGly-IleGlnIleGlyLysGluGluValLysLeuSerLeuPheAlaAspAspMetIleLeuTyrIleGluAsnProLysAsp 712
+
+ SerThrLysLysLeuLeuGluMetIleAsnGluPheAsnLysIleSerGluPheLysIleAsnValGlnAsnSerVal PheLeuTyrThrHisAsnLysLeuTyrAspLys
+Query: 3099 TCCACCAAAAAGCTATTAGAAATGATAAATGAATTCAATAAAATTTCAGAATTCAAAATCAATGTACAAAACTCAGTA---GTTTCTTTACACTCACAACAAACTATATGACAAA---A 2987
+ |||||||||||||||||||||:::|||||||||||| |||::::::::::::|||||||||:::|||:::|||||| |||||||||::::::...:::||| :::|||
+Sbjct: 713 SerThrLysLysLeuLeuGluLeuIleAsnGluPheSerLysValAlaGlyTyrLysIleAsnIleGlnLysSerValAla-PheLeuTyrAlaAsnSerGluLeuSerGluLysGlu- 751
+
+ IleLysLysSerIleSerPheThrValAlaSerLysLysThrTyrPhePheCysLeuGlyAlaHisLeuGly***TyrLeuGlyValHisLeuThrLysGluValLysAspLeuTyrSer
+Query: 2986 ATAAAGAAATCAATCTCATTCACAGTAGCATCAAaaaaaacgtattttttttGTTTAGGAGCACATTTAGGATAGTACttaggagtacatttaACCAAGGAGGTGAAAGATCTGTATTCT 2867
+ |||||||||:::|||:::||||||:::|||:::||||||::: |||||||||::::::|||||||||||||||||||||||||||...
+Sbjct: 752 IleLyslysthrilepropheThrIleAlaThrLysLysIle------------------------------LysTyrLeuGlyIleAsnLeuThrLysGluValLysAspLeuTyrXaa 781
+
+ GluHisTyrLysThrLeuMetLys IleValAspAspThrAsnThrTrpLysAspIleLeuCysSerTrpValGlyArgIleAsnIleLeuLysMetSerLeuLeuProLysAla
+Query: 2866 GAACACTATAAAACATTGATGAAA---AATTGTAGATGACACAAATACATGGAAAGATATTTTATGTTCATGGGTAGGAAGAATTAATATTCTTAAAATGTCCTTACTGCCCAAAGCG 2752
+ |||:::|||||||||||||||||| ||| :::||||||||| |||||||||||| |||||||||:::||||||||||||||| |||||||||...||||||||||||
+Sbjct: 782 GluAsnTyrLysThrLeuMetLysGlu-IleGluGluAspThrAsnLysTrpLysAspIleProCysSerTrpIleGlyArgIleAsnIleValLysMetSerIleLeuProLysAla 820
+
+ IleTyrArgPheAsnAlaIlePheIleLysIleSerMetSerPhePheThrGluIleGluLysThrIle***LysPheIleTrpAsnHisLysGlySer***IleThrLysGlyLeuLeu
+Query: 2751 ATTTATAGGTTTAATGCAATATTTATCAAAATTTCAATGTCATTCTTCACAGAAATAGAAAAAACAATTTGAAAATTTATATGGAACCACAAAGGATCCTGAATAACTAAAGGACTCTTG 2632
+ ||||||||||||||||||||| |||||||||:::|||:::||||||||||||||||||||||||||| ||||||:::||||||||||||:::::::::|||:::||| |||
+Sbjct: 821 IleTyrArgPheAsnAlaIleProIleLysIleProMetThrPhePheThrGluIleGluLysThrIleLeuLysPheValTrpAsnHisLysArgProArgIleAlaLysAlaIleLeu 860
+
+ SerAsnLysAsnLysAlaGluGlyLeuThr SerAspPheLysThrTyrTyrArg
+Query: 2631 AGCAATAAGAACAAAGCTGAAGGCCTCACA---ATCTGACTTCAAAACATATTACAGG 2577
+ |||:::||||||||||||:::||| ||| :::|||||||||:::||||||:::
+Sbjct: 861 SerLysLysAsnLysAlaGlyGlyIleThrLeu-ProAspPheLysIleTyrTyrLys 879
+
+>UN-L1MA6_pol#LINE/L1
+ Length = 1275
+
+ Score = 530 bits (1559.7), Expect = 2e-147
+ Identities = 180/292 (61%), Gaps = 23/292 (7%)
+ Strand = Minus / Plus
+
+ ***SerAlaTrp***SerArg AsnArgHisIleAspGlnTrpAsnArgIleGluAsnProAspIleAsnProHisIleTyrSerGlnLeuIlePheSerLysGlyThrAsnAsn
+Query: 90089 TaatcagcctggtaatcaCGT---AAAACAGACACATAGACCAGTGGAACAGAATAGAGAACCCAGATATAAATCCACACATTTACAGCCAGCTCATCTTCAGCAAAGGCACCAACAAC 89974
+ ::::::||||||::: ::: |||||||||||||||||||||||||||||||||...|||:::|||||||||:::|||||||||||||||||||||...||||||::::::|||
+Sbjct: 884 LysThrAlaTrpTyrTrpHisLys--AsnArgHisIleAspGlnTrpAsnArgIleGluSerProGluIleAsnProArgIleTyrSerGlnLeuIlePheAspLysGlyAlaLysAsn 922
+
+ IleArg ArgLysAspGlyLeuPheHisLysTrpCysArgGlyAsn***IleLysIleCysArgArgMetLysLeuAspProSerLeuLeuProTyrThrGluIleLysSerGlu
+Query: 89973 ATACGA---GCGAAAGGACGGTCTCTTCCATAAGTGGTGCAGGGGAAACTAGATAAAGATATGCAGAAGAATGAAACTAGACCCGTCTCTCTTACCATACACAGAAATCAAATCAGAA 89859
+ :::::: ...|||||| ||||||:::|||||||||::::::|||:::||| :::||||||||||||||||||||||||...|||:::||||||||| |||...|||
+Sbjct: 923 ThrGlnTrp-GlyLysAspSerLeuPheAsnLysTrpCysTrpGluAsnTrpIleSerThrCysArgArgMetLysLeuAspProTyrLeuSerProTyrThrLysIleAsnSerLys 961
+
+ TrpIleLysGly LysLeuArgProGluSerIleLysLeuLeuGluGluAsnIleArgGluValLeuGlnAspIleValLeuSerLysAspPhePheSerArgAlaProLysAla
+Query: 89858 TGGATTAAAGGT---AAAACTGAGACCTGAAAGTATAAAACTACTGGAAGAAAACATTAGGGAAGTGCTCCAGGACATTGTTCTCAGCAAAGACTTTTTCAGTAGGGCCCCAAAAGCA 89744
+ |||||||||::: ... |||||||||...:::|||||||||||||||||||||:::|||:::|||:::|||||| |||:::|||||||||::::::::::::...||||||
+Sbjct: 962 TrpIleLysAspLeu-AsnValArgProGluThrMetLysLeuLeuGluGluAsnIleGlyGluMetLeuHisAspIleGlyLeuGlyLysAspPheLeuAspLysThrSerLysAla 1000
+
+ GlnAlaThrLysAlaLysThrAspLys***AsnHisThrLysLeuArgThrLeuCysArgProLysGluLysValAsnLysLeuLysArgGlnProThrGluTrpGluLysIleLeuAla
+Query: 89743 CAGGCAACCAAAGCAAAAACAGACAAGTGAAATCACACCAAGCTAAGAACCCTCTGCAGACCAAAGGAAAAAGTCAACAAACTGAAGAGACAACCCACAGAATGGGAGAAAATACTTGCA 89624
+ ||||||||||||||||||:::||||||::::::::::::||||||:::::::::||| |||||| :::|||::: ||||||||||||||||||||||||||||||:::|||
+Sbjct: 1001 GlnAlaThrLysAlaLysIleAspLysTrpAspTyrIleLysLeuLysSerPheCysThrAlaLysGluThrIleAsnArgValLysArgGlnProThrGluTrpGluLysIlePheAla 1040
+
+ SerTyrProProAspLysGlyPheIleThr GluLeuLysGln ***GlnThrIleAsnArgIleLeuLysTrpAlaArgAspLeuSerArgHisPhe
+Query: 89623 AGCTACCCACCTGACAAGGGATTCATAACC------------AGGAGCTCAAACAA---------TAGCAAACAATTAATCGAATTTTAAAATGGGCAAGAGACCTGAGTAGACATTTC 89526
+ :::||| :::|||||||||:::|||::: |||||||||||| ...||| |||:::|||...|||||||||:::||||||:::|||||||||
+Sbjct: 1041 AsnTyrAlaSerAspLysGlyLeuIleSerArgIleTyrLys--GluLeuLysGlnLeuAsnSerLysLysThrAsnAsnProIleXaaLysTrpAlaLysAspLeuAsnArgHisPhe 1079
+
+ SerLysGluAspValGlnMetAlaSerArgTyrMetLysLysCysSerThrSerLeuIleIleArgGluThrGlnIle LysThrAlaMetArgSerSerLeuThrSerValLysMet
+Query: 89525 TCAAAAGAAGATGTACAAATGGCCAGCAGGTACATGAAAAAATGCTCAACATCACTAATCATCAGAGAAACGCAAATAAAAAACTGCAATGAGGTCTTCTCTCACCTCAGTTAAAATG 89408
+ ||||||||||||:::|||||||||:::||||||||||||||||||||||||||||||||||||||||||:::|||||| ||||||:::||||||... ||||||:::|||:::|||
+Sbjct: 1080 SerLysGluAspIleGlnMetAlaAsnArgTyrMetLysLysCysSerThrSerLeuIleIleArgGluMetGlnIle-LysThrThrMetArgTyrHisLeuThrProValArgMet 1118
+
+ AlaPheValLysAsnAlaGlyAsnLysGlyCysTrpArgGlyCysGlyGluArgGlyThrLeuThrHisCys TrpGluArg***LeuValGlnProLeuTrpLysThr
+Query: 89407 GCTTTCGTCAAAAACGCAGGGAATAAGGGATGCTGGCGAGGATGTGGAGAAAGGGGGACCCTCACACACTGT---TGTGGGAACGTTGATTAGTACAACCACTATGGAAAACA---GA 89296
+ ||| :::|||:::::: :::::: |||||||||||||||||||||:::|||||||||||||||||| ||||||::: ||||||||||||||||||||||||
+Sbjct: 1119 AlaIleIleLysLysThrLysAspAsnLysCysTrpArgGlyCysGlyGluLysGlyThrLeuThrHisCysTrp--TrpGluCysLysLeuValGlnProLeuTrpLysThrVal-- 1156
+
+ TrpArgLeuLeuLysLysProLys
+Query: 89295 TGGAGGCTCCTCAaaaaaccaaaa 89272
+ ||||||:::||||||||| |||
+Sbjct: 1157 TrpArgPheLeuLysLysLeuLys 1164
+
+>UN-L1PA16_pol#LINE/L1
+ Length = 1276
+
+ Score = 512 bits (1508.0), Expect = 3.8e-142
+ Identities = 230/359 (64%), Gaps = 33/359 (9%)
+ Strand = Plus / Plus
+
+ LysGluAsnTyrLysSerLeuSerLeuIleAsnThrAspValLysIleLeuAsnLysIleLeuAlaAsn***Ser***GlnHisIleLysLysIleIleHisHisAspGlnValGlyPhe
+Query: 17572 AAAGAAAACTACAAATCCTTATCCCTGATCAACACAGATGTAAAAATACTCAACAAAATTCTAGCAAACTGAAGCTAACAACACATCAAAAAGATAATTCATCATGATCAAGTGGGCTTT 17691
+ ||||||||||||::::::...||||||:::|||:::|||:::|||||||||||||||||||||||||||::: :::|||||||||||||||...||||||||||||||||||||||||
+Sbjct: 527 LysGluAsnTyrArgProIleSerLeuMetAsnIleAspAlaLysIleLeuAsnLysIleLeuAlaAsnArgIleGlnGlnHisIleLysLysLeuIleHisHisAspGlnValGlyPhe 566
+
+ IleProGlyValLeuGluTrpPheLysIleAspLysSerIleAsnMetIleHisHisIleAsnGlyThrGluAsnLysAsnProMetIleIleSerLeuAspAlaGlu***AlaPheAsp
+Query: 17692 ATTCCAGGGGTGCTTGAATGGTTCAAAATAGACAAATCAATAAACATGATTCACCACATAAATGGAACTGAGAACAAAAACCCTATGATCATCTCATTAGATGCAGAATaagcatttgat 17811
+ |||||||||::: :::||||||...||| ||||||||||||:::|||||||||||||||::::::...|||||||||...||||||||||||...|||||||||:::|||||||||
+Sbjct: 567 IleProGlyMetGlnGlyTrpPheAsnIleArgLysSerIleAsnValIleHisHisIleAsnArgIleLysAsnLysAsnHisMetIleIleSerIleAspAlaGluLysAlaPheAsp 606
+
+ LysIleGlnHisLeuPheMetIleLysThrLeuAsnAsnIleGlyIleAspGlyValTyrLeuLys Lys***ValIleTyrAspLysAlaThrAlaAsnIleIleLeuAspGlyGln
+Query: 17812 aaaatccaacatctgtttatgataaaaaccctcaACAATATAGGTATAGATGGAGTATACCTCAAA---AAATGAGTCATCTATGACAAAGCCACAGCCAACATCATCCTGGATGGGCAA 17928
+ ||||||||||||:::||||||||||||||||||...:::...||||||:::|||...||||||||| ::::::||||||||||||...||||||||||||||||||:::||||||
+Sbjct: 607 LysIleGlnHisProPheMetIleLysThrLeuXaaLysLeuGlyIleGluGlyThrTyrLeuLysIleIleArgAlaIleTyrAspLysProThrAlaAsnIleIleLeuAsnGlyGln 646
+
+ LysLeuGluValLeuLeuLeuGluThrGlyLysLysGlnGlyCysSerProSerSerPheLeuPheAsnThrValLeuGluValLeuAlaArgThrIleArgLysGluLysGluIleLys
+Query: 17929 AAGTTAGAAGTGTTGCTTCTAGAAACTGGAAAAAAGCAAGGATGTTCACCTTCATCATTCCTATTCAATACAGTACTGGAAGTGCTAGCCAGAACTATCAGAAAGGAGAAAGAAATAAAA 18048
+ |||||||||:::::::::||| |||||| :::|||||||||::: |||::::::|||||||||:::|||||||||||||||||||||:::||||||...|||||||||||||||
+Sbjct: 647 LysLeuGluAlaPheProLeuArgThrGlyThrArgGlnGlyCysProLeuSerProLeuLeuPheAsnIleValLeuGluValLeuAlaArgAlaIleArgGlnGluLysGluIleLys 686
+
+ GlyIleGlnIleArgLys GluValLys***SerLeuLeuThrAspAspMetThrValGlyLeuGluAsnProLysValPhe ArgArgLeuLeuAspLeuIleHisAspPheSer
+Query: 18049 GGTATACAAATTAGAAAA---GAAGTCAAATGATCTCTGCTCACTGATGACATGACTGTAGGCCTAGAAAACCCTAAAGTCTTC---AGAAGACTCCTAGACTTGATACACGACTTCAGT 18162
+ ||||||||||||:::||| ||||||||| ||||||::::::|||||||||:::... |||||||||||||||...... :::|||||||||:::||||||:::|||||||||
+Sbjct: 687 GlyIleGlnIleGlyLysGluGluValLysLeuSerLeuPheAlaAspAspMetIleLeuTyrLeuGluAsnProLysAspSerAlaLysArgLeuLeuGluLeuIleAsnAspPheSer 726
+
+ LysValLeuGly***ThrSer GlnLysSerValValPheLeuTyrThrLysTyrIleGlnAla GluAsnGlnIleLysAsn
+Query: 18163 AAAGTCTTGGGATAAACAAGC------CACAAAAATCAGTTGTATTTCTATACACCAAATACATTCAAGCTGTTTGAATGTTTGTTGAGATTAATTtgttgAGAACCAAATTAAGAAC 18274
+ ||||||:::|||::: ||||||||||||:::||||||||||||... :::|||||| |||...||||||||||||
+Sbjct: 727 LysValSerGlyTyrLysIleAsnVal--GlnLysSerValAlaPheLeuTyrThrAsnAsnValGlnAla-----------------------------GluSerGlnIleLysAsn 755
+
+ SerThrGluPheThrIleAlaMet LysTyrLeuGlyMetHis ThrIle***MetLysAspLeuTyrLysGluAsnTyrLysIleLeuMetLysGluIleIleAsp
+Query: 18275 TCAACTGAATTTACAATAGCCATG---------AAAAATACCTAGGAATGCAT---AACTATATAAATGAAAGATCTCTACAAGGAGAACTACAAAATACTAATGAAAGAAATTATAGAT 18382
+ :::::: ||||||||||||::: ||||||||||||:::||| ||| ::::::|||||||||||||||||||||||||||:::|||:::|||||||||||||||
+Sbjct: 756 AlaIleProPheThrIleAlaThrLysLysIle--LysTyrLeuGlyIleHisLeu-ThrLysGluValLysAspLeuTyrLysGluAsnTyrLysThrLeuLeuLysGluIleIleAsp 794
+
+ AspIleAsnLysTrpLysAsnIleProCysSerTrpIleArgLysIleAsn AlaLysValThrIleSerPro ThrIleTyrArgValAsnAlaIleProIleLysLeuPro
+Query: 18383 GACATAAACAAATGGAAAAACATCCCATGCTCATGGATTAGAAAAATCAAT---AGCTAAAGTGACCATATCACCC---ATACAATCTATAGAGTTAATGCAATTCCCATCAAATTACCA 18496
+ |||:::|||||||||||||||||||||||||||||||||::::::|||||| :::|||::::::||| ||| :::||||||||| ||||||||||||||||||||||||
+Sbjct: 795 AspThrAsnLysTrpLysAsnIleProCysSerTrpIleGlyArgIleAsnIle-ValLysMetAlaIleLeuProLys--AlaIleTyrArgPheAsnAlaIleProIleLysLeuPro 833
+
+ ThrLeuPheLeuThrLysLeuLysLys IleLeuLysPheThrTrpSerGln LysArgSerLeuIleAlaLysAlaLeuLeuSerLysLys
+Query: 18497 ACGTTATTTCTCACAaaattaaaaaaa---aaTCCTAAAGTTCACATGGAGCCAAAAAAAGATCCCTAATAGCCAAAGCACTTCTAAGCAAAAAa 18588
+ ::::::|||:::|||:::|||:::||| ||||||||||||:::|||:::||| ||||||::: |||||||||||| ||||||||||||
+Sbjct: 834 MetSerPhePheThrGluLeuGluLysThr-IleLeuLysPheIleTrpAsnGln-LysArgAlaGlnIleAlaLysAlaIleLeuSerLysLys 864
+
+Query= UN-L1MA6_pol#LINE/L1
+ (1275 letters)
+
+>chrUn_KI270748v1
+ Length = 93321
+
+ Score = 1559.7, Expect = 2e-147
+ Identities = 180/292 (61%), Gaps = 23/292 (7%)
+ Strand = Plus / Minus
+
+Query: 884 LysThrAlaTrpTyrTrpHisLys--AsnArgHisIleAspGlnTrpAsnArgIleGlu 902
+ |||||| |||||||||||||||||||||||||||||||||
+Sbjct: 90089 TaatcagcctggtaatcaCGT---AAAACAGACACATAGACCAGTGGAACAGAATAGAG 90034
+ ***SerAlaTrp***SerArg AsnArgHisIleAspGlnTrpAsnArgIleGlu
+
+Query: 903 SerProGluIleAsnProArgIleTyrSerGlnLeuIlePheAspLysGlyAlaLysAsn 922
+ ||| ||||||||| ||||||||||||||||||||| |||||| |||
+Sbjct: 90033 AACCCAGATATAAATCCACACATTTACAGCCAGCTCATCTTCAGCAAAGGCACCAACAAC 89974
+ AsnProAspIleAsnProHisIleTyrSerGlnLeuIlePheSerLysGlyThrAsnAsn
+
+Query: 923 ThrGlnTrp-GlyLysAspSerLeuPheAsnLysTrpCysTrpGluAsnTrpIleSer 941
+ |||||| |||||| ||||||||| ||| |||
+Sbjct: 89973 ATACGA---GCGAAAGGACGGTCTCTTCCATAAGTGGTGCAGGGGAAACTAGATAAAG 89919
+ IleArg ArgLysAspGlyLeuPheHisLysTrpCysArgGlyAsn***IleLys
+
+Query: 942 ThrCysArgArgMetLysLeuAspProTyrLeuSerProTyrThrLysIleAsnSerLys 961
+ |||||||||||||||||||||||| ||| ||||||||| ||| |||
+Sbjct: 89918 ATATGCAGAAGAATGAAACTAGACCCGTCTCTCTTACCATACACAGAAATCAAATCAGAA 89859
+ IleCysArgArgMetLysLeuAspProSerLeuLeuProTyrThrGluIleLysSerGlu
+
+Query: 962 TrpIleLysAspLeu-AsnValArgProGluThrMetLysLeuLeuGluGluAsnIle 980
+ ||||||||| ||||||||| |||||||||||||||||||||
+Sbjct: 89858 TGGATTAAAGGT---AAAACTGAGACCTGAAAGTATAAAACTACTGGAAGAAAACATT 89804
+ TrpIleLysGly LysLeuArgProGluSerIleLysLeuLeuGluGluAsnIle
+
+Query: 981 GlyGluMetLeuHisAspIleGlyLeuGlyLysAspPheLeuAspLysThrSerLysAla 1000
+ ||| ||| |||||| ||| ||||||||| ||||||
+Sbjct: 89803 AGGGAAGTGCTCCAGGACATTGTTCTCAGCAAAGACTTTTTCAGTAGGGCCCCAAAAGCA 89744
+ ArgGluValLeuGlnAspIleValLeuSerLysAspPhePheSerArgAlaProLysAla
+
+Query: 1001 GlnAlaThrLysAlaLysIleAspLysTrpAspTyrIleLysLeuLysSerPheCysThr 1020
+ |||||||||||||||||| |||||| |||||| |||
+Sbjct: 89743 CAGGCAACCAAAGCAAAAACAGACAAGTGAAATCACACCAAGCTAAGAACCCTCTGCAGA 89684
+ GlnAlaThrLysAlaLysThrAspLys***AsnHisThrLysLeuArgThrLeuCysArg
+
+Query: 1021 AlaLysGluThrIleAsnArgValLysArgGlnProThrGluTrpGluLysIlePheAla 1040
+ |||||| ||| |||||||||||||||||||||||||||||| |||
+Sbjct: 89683 CCAAAGGAAAAAGTCAACAAACTGAAGAGACAACCCACAGAATGGGAGAAAATACTTGCA 89624
+ ProLysGluLysValAsnLysLeuLysArgGlnProThrGluTrpGluLysIleLeuAla
+
+Query: 1041 AsnTyrAlaSerAspLysGlyLeuIleSerArgIleTyrLys--GluLeuLysGlnLeu 1059
+ ||| ||||||||| ||| ||||||||||||
+Sbjct: 89623 AGCTACCCACCTGACAAGGGATTCATAACC------------AGGAGCTCAAACAA--- 89580
+ SerTyrProProAspLysGlyPheIleThr GluLeuLysGln
+
+Query: 1060 AsnSerLysLysThrAsnAsnProIleXaaLysTrpAlaLysAspLeuAsnArgHisPhe 1079
+ ||| ||| ||| ||||||||| |||||| |||||||||
+Sbjct: 89579 ------TAGCAAACAATTAATCGAATTTTAAAATGGGCAAGAGACCTGAGTAGACATTTC 89526
+ ***GlnThrIleAsnArgIleLeuLysTrpAlaArgAspLeuSerArgHisPhe
+
+Query: 1080 SerLysGluAspIleGlnMetAlaAsnArgTyrMetLysLysCysSerThrSerLeuIle 1099
+ |||||||||||| ||||||||| |||||||||||||||||||||||||||||||||
+Sbjct: 89525 TCAAAAGAAGATGTACAAATGGCCAGCAGGTACATGAAAAAATGCTCAACATCACTAATC 89466
+ SerLysGluAspValGlnMetAlaSerArgTyrMetLysLysCysSerThrSerLeuIle
+
+Query: 1100 IleArgGluMetGlnIle-LysThrThrMetArgTyrHisLeuThrProValArgMet 1118
+ ||||||||| |||||| |||||| |||||| |||||| ||| |||
+Sbjct: 89465 ATCAGAGAAACGCAAATAAAAAACTGCAATGAGGTCTTCTCTCACCTCAGTTAAAATG 89408
+ IleArgGluThrGlnIle LysThrAlaMetArgSerSerLeuThrSerValLysMet
+
+Query: 1119 AlaIleIleLysLysThrLysAspAsnLysCysTrpArgGlyCysGlyGluLysGlyThr 1138
+ ||| ||| ||||||||||||||||||||| ||||||
+Sbjct: 89407 GCTTTCGTCAAAAACGCAGGGAATAAGGGATGCTGGCGAGGATGTGGAGAAAGGGGGACC 89348
+ AlaPheValLysAsnAlaGlyAsnLysGlyCysTrpArgGlyCysGlyGluArgGlyThr
+
+Query: 1139 LeuThrHisCysTrp--TrpGluCysLysLeuValGlnProLeuTrpLysThrVal-- 1156
+ |||||||||||| |||||| ||||||||||||||||||||||||
+Sbjct: 89347 CTCACACACTGT---TGTGGGAACGTTGATTAGTACAACCACTATGGAAAACA---GA 89296
+ LeuThrHisCys TrpGluArg***LeuValGlnProLeuTrpLysThr
+
+Query: 1157 TrpArgPheLeuLysLysLeuLys 1164
+ |||||| ||||||||| |||
+Sbjct: 89295 TGGAGGCTCCTCAaaaaaccaaaa 89272
+ TrpArgLeuLeuLysLysProLys
+
+Query= UN-L1PA16_pol#LINE/L1
+ (1276 letters)
+
+>chrUn_KI270748v1
+ Length = 93321
+
+ Score = 1508.0, Expect = 3.8e-142
+ Identities = 230/359 (64%), Gaps = 33/359 (9%)
+ Strand = Plus / Plus
+
+Query: 527 LysGluAsnTyrArgProIleSerLeuMetAsnIleAspAlaLysIleLeuAsnLysIle 546
+ |||||||||||| |||||| ||| ||| ||||||||||||||||||
+Sbjct: 17572 AAAGAAAACTACAAATCCTTATCCCTGATCAACACAGATGTAAAAATACTCAACAAAATT 17631
+ LysGluAsnTyrLysSerLeuSerLeuIleAsnThrAspValLysIleLeuAsnLysIle
+
+Query: 547 LeuAlaAsnArgIleGlnGlnHisIleLysLysLeuIleHisHisAspGlnValGlyPhe 566
+ ||||||||| ||||||||||||||| ||||||||||||||||||||||||
+Sbjct: 17632 CTAGCAAACTGAAGCTAACAACACATCAAAAAGATAATTCATCATGATCAAGTGGGCTTT 17691
+ LeuAlaAsn***Ser***GlnHisIleLysLysIleIleHisHisAspGlnValGlyPhe
+
+Query: 567 IleProGlyMetGlnGlyTrpPheAsnIleArgLysSerIleAsnValIleHisHisIle 586
+ ||||||||| |||||| ||| |||||||||||| ||||||||||||
+Sbjct: 17692 ATTCCAGGGGTGCTTGAATGGTTCAAAATAGACAAATCAATAAACATGATTCACCACATA 17751
+ IleProGlyValLeuGluTrpPheLysIleAspLysSerIleAsnMetIleHisHisIle
+
+Query: 587 AsnArgIleLysAsnLysAsnHisMetIleIleSerIleAspAlaGluLysAlaPheAsp 606
+ ||| ||||||||| |||||||||||| ||||||||| |||||||||
+Sbjct: 17752 AATGGAACTGAGAACAAAAACCCTATGATCATCTCATTAGATGCAGAATaagcatttgat 17811
+ AsnGlyThrGluAsnLysAsnProMetIleIleSerLeuAspAlaGlu***AlaPheAsp
+
+Query: 607 LysIleGlnHisProPheMetIleLysThrLeuXaaLysLeuGlyIleGluGlyThrTyr 626
+ |||||||||||| |||||||||||||||||| |||||| ||| |||
+Sbjct: 17812 aaaatccaacatctgtttatgataaaaaccctcaACAATATAGGTATAGATGGAGTATAC 17871
+ LysIleGlnHisLeuPheMetIleLysThrLeuAsnAsnIleGlyIleAspGlyValTyr
+
+Query: 627 LeuLysIleIleArgAlaIleTyrAspLysProThrAlaAsnIleIleLeuAsnGlyGln 646
+ |||||| |||||||||||| |||||||||||||||||| ||||||
+Sbjct: 17872 CTCAAA---AAATGAGTCATCTATGACAAAGCCACAGCCAACATCATCCTGGATGGGCAA 17928
+ LeuLys Lys***ValIleTyrAspLysAlaThrAlaAsnIleIleLeuAspGlyGln
+
+Query: 647 LysLeuGluAlaPheProLeuArgThrGlyThrArgGlnGlyCysProLeuSerProLeu 666
+ ||||||||| ||| |||||| ||||||||| |||
+Sbjct: 17929 AAGTTAGAAGTGTTGCTTCTAGAAACTGGAAAAAAGCAAGGATGTTCACCTTCATCATTC 17988
+ LysLeuGluValLeuLeuLeuGluThrGlyLysLysGlnGlyCysSerProSerSerPhe
+
+Query: 667 LeuPheAsnIleValLeuGluValLeuAlaArgAlaIleArgGlnGluLysGluIleLys 686
+ ||||||||| ||||||||||||||||||||| |||||| |||||||||||||||
+Sbjct: 17989 CTATTCAATACAGTACTGGAAGTGCTAGCCAGAACTATCAGAAAGGAGAAAGAAATAAAA 18048
+ LeuPheAsnThrValLeuGluValLeuAlaArgThrIleArgLysGluLysGluIleLys
+
+Query: 687 GlyIleGlnIleGlyLysGluGluValLysLeuSerLeuPheAlaAspAspMetIleLeu 706
+ |||||||||||| ||| ||||||||| |||||| |||||||||
+Sbjct: 18049 GGTATACAAATTAGAAAA---GAAGTCAAATGATCTCTGCTCACTGATGACATGACTGTA 18105
+ GlyIleGlnIleArgLys GluValLys***SerLeuLeuThrAspAspMetThrVal
+
+Query: 707 TyrLeuGluAsnProLysAspSerAlaLysArgLeuLeuGluLeuIleAsnAspPheSer 726
+ ||||||||||||||| ||||||||| |||||| |||||||||
+Sbjct: 18106 GGCCTAGAAAACCCTAAAGTCTTC---AGAAGACTCCTAGACTTGATACACGACTTCAGT 18162
+ GlyLeuGluAsnProLysValPhe ArgArgLeuLeuAspLeuIleHisAspPheSer
+
+Query: 727 LysValSerGlyTyrLysIleAsnVal--GlnLysSerValAlaPheLeuTyrThrAsn 745
+ |||||| ||| |||||||||||| ||||||||||||
+Sbjct: 18163 AAAGTCTTGGGATAAACAAGC------CACAAAAATCAGTTGTATTTCTATACACCAAA 18215
+ LysValLeuGly***ThrSer GlnLysSerValValPheLeuTyrThrLys
+
+Query: 746 AsnValGlnAla-----------------------------GluSerGlnIleLysAsn 755
+ |||||| ||| ||||||||||||
+Sbjct: 18216 TACATTCAAGCTGTTTGAATGTTTGTTGAGATTAATTtgttgAGAACCAAATTAAGAAC 18274
+ TyrIleGlnAla GluAsnGlnIleLysAsn
+
+Query: 756 AlaIleProPheThrIleAlaThrLysLysIle--LysTyrLeuGlyIleHisLeu-Thr 774
+ |||||||||||| |||||||||||| ||| |||
+Sbjct: 18275 TCAACTGAATTTACAATAGCCATG---------AAAAATACCTAGGAATGCAT---AACT 18322
+ SerThrGluPheThrIleAlaMet LysTyrLeuGlyMetHis Thr
+
+Query: 775 LysGluValLysAspLeuTyrLysGluAsnTyrLysThrLeuLeuLysGluIleIleAsp 794
+ ||||||||||||||||||||||||||| ||| |||||||||||||||
+Sbjct: 18323 ATATAAATGAAAGATCTCTACAAGGAGAACTACAAAATACTAATGAAAGAAATTATAGAT 18382
+ Ile***MetLysAspLeuTyrLysGluAsnTyrLysIleLeuMetLysGluIleIleAsp
+
+Query: 795 AspThrAsnLysTrpLysAsnIleProCysSerTrpIleGlyArgIleAsnIle-Val 813
+ ||| ||||||||||||||||||||||||||||||||| ||||||
+Sbjct: 18383 GACATAAACAAATGGAAAAACATCCCATGCTCATGGATTAGAAAAATCAAT---AGCT 18437
+ AspIleAsnLysTrpLysAsnIleProCysSerTrpIleArgLysIleAsn Ala
+
+Query: 814 LysMetAlaIleLeuProLys--AlaIleTyrArgPheAsnAlaIleProIleLysLeu 832
+ ||| ||| ||| ||||||||| |||||||||||||||||||||
+Sbjct: 18438 AAAGTGACCATATCACCC---ATACAATCTATAGAGTTAATGCAATTCCCATCAAATTA 18493
+ LysValThrIleSerPro ThrIleTyrArgValAsnAlaIleProIleLysLeu
+
+Query: 833 ProMetSerPhePheThrGluLeuGluLysThr-IleLeuLysPheIleTrpAsnGln- 851
+ ||| ||| ||| ||| ||| |||||||||||| ||| |||
+Sbjct: 18494 CCAACGTTATTTCTCACAaaattaaaaaaa---aaTCCTAAAGTTCACATGGAGCCAAA 18549
+ ProThrLeuPheLeuThrLysLeuLysLys IleLeuLysPheThrTrpSerGln
+
+Query: 852 LysArgAlaGlnIleAlaLysAlaIleLeuSerLysLys 864
+ |||||| |||||||||||| ||||||||||||
+Sbjct: 18550 AAAAGATCCCTAATAGCCAAAGCACTTCTAAGCAAAAAa 18588
+ LysArgSerLeuIleAlaLysAlaLeuLeuSerLysLys
+
0 chrM 93.10 87 6 0 87 1 13914 14000
1 chrM 85.06 87 13 0 1 87 1544 1630
10 chrM 61.67 60 23 0 1 60 3291 3350
=====================================
test/maf-convert-test.sh
=====================================
@@ -17,6 +17,8 @@ maf2=bs100.maf
head -n999 $maf1 | $r blast
head -n999 $maf1 | $r -l100 blast
$r blast $maf2
+ $r -l120 blast frameshift-new.maf
+ tail -n8 frameshift-new.maf | maf-swap | $r blast
$r blasttab $maf2
$r blasttab frameshift-new.maf
head -n999 $maf1 | $r chain
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/commit/8452e4ce09ce0738f89abf342efe95f6fdcaf056
--
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/commit/8452e4ce09ce0738f89abf342efe95f6fdcaf056
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