Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1017
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1024007
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.32
Warning! 32449 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:329721 original size:17 final size:17
Alignment explanation
Indices: 329699--329737 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
329689 TTTTGTTACT
329699 TTTTCCATCTGAAATTG
1 TTTTCCATCTGAAATTG
329716 TTTTCCATCTGAAATTG
1 TTTTCCATCTGAAATTG
329733 TTTTC
1 TTTTC
329738 TACCTCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.21, C:0.18, G:0.10, T:0.51
Consensus pattern (17 bp):
TTTTCCATCTGAAATTG
Found at i:334860 original size:165 final size:163
Alignment explanation
Indices: 334398--335549 Score: 1599
Period size: 165 Copynumber: 7.0 Consensus size: 163
334388 TGGCTGATTA
* * * *
334398 GTTTCTGAAAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAGTTTGTTTGACCC
1 GTTTCTGAGAAGAAG-TTTTTAAAGATTTACTCTATATGTTCCTATGTAAAACTTTG---AACCC
* * *
334463 CCCATCCATTGTGGCCCCACCCTACTCCCGGGGTTGTCATTATTTTCACAACTTTGAATTTACAG
62 CCC--CCATTGTGGCCCCACCCTACCCCCGGGG--GTCATGATTTTCACAACTTTGAATCTACAG
*
334528 TACCCGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATT
123 TACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGC----T
* * *
334573 AGTTTCTGAGAAGAAGATCTTTAAAGATTTACTCTATATGTTCCTATGTACAACTTT-AACACCC
1 -GTTTCTGAGAAGAAG-TTTTTAAAGATTTACTCTATATGTTCCTATGTAAAACTTTGAACCCCC
* *
334637 CCCA-TGTGGCCCCACCTTACCCCCGGTGGTCATGATTTTCACAACTTTGAATCTACAGTACCTG
64 CCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTACAGTACCTG
* *
334701 AGGATGCTTCTACACAAGTTTCAGCATTCCTGGCT
129 AGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCT
* * * * *
334736 GTTTCTGAGAAGAAGTTTTTAAAAGATTTACTCAATATGTTTCTTTGTAAAACTTCGACCCCCCC
1 GTTTCTGAGAAGAAGTTTTT-AAAGATTTACTCTATATGTTCCTATGTAAAACTTTGA-ACCCCC
*
334801 CCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAACCTACAGTACCTG
64 CCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTACAGTACCTG
* * *
334866 GGGATGCTTCCACACAAGTTTCAGATTTCATGGCT
129 AGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCT
* * * *
334901 GTTTCTGAGAAGAAGTTTTTAAAGATTCACTCAATATATTCCTATGTTAAACTTTGACACCCCCC
1 GTTTCTGAGAAGAAGTTTTTAAAGATTTACTCTATATGTTCCTATGTAAAACTTTGA-ACCCCCC
*
334966 CCATTGTAGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTACAGTACCTGA
65 CCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTACAGTACCTGA
335031 GGATGCTTCCACACAAGTTTCAGCTTTCCTGGCT
130 GGATGCTTCCACACAAGTTTCAGCTTTCCTGGCT
* * *
335065 GTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTACATATTCCTATGTTAAACTTTG-A---CCC
1 GTTTCTGAGAAGAAG-TTTTTAAAGATTTACTCTATATGTTCCTATGTAAAACTTTGAACCCCCC
* *
335126 CCATTGTGGCCCCACCCTACCCCCGGGGGTCAAGATTTTCACAACATTGAATCTACAGTACCTGA
65 CCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTACAGTACCTGA
*
335191 GGATGCTTTCACACAAGTTTCAGCTTTCCTGGCCGATT
130 GGATGCTTCCACACAAGTTTCAGCTTTCCTGG-C---T
*
335229 AGTTTCTGAGAAGAAGTTTTTAAAAGATTTACTCTATATGTTCCTATGTAAAACTTT-AACACCC
1 -GTTTCTGAGAAGAAGTTTTT-AAAGATTTACTCTATATGTTCCTATGTAAAACTTTGAACCCCC
* * *
335293 CCCA-TGTGTCCCAACCCAACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTACAGTACCTG
64 CCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTACAGTACCTG
335357 AGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCT
129 AGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCT
* * *
335392 GTTTCTGAGAAGAAACTTTTTAAAGATTTACTCTACATGTTCCTATGTTAAACTTTG-A---CCC
1 GTTTCTGAGAAG-AAGTTTTTAAAGATTTACTCTATATGTTCCTATGTAAAACTTTGAACCCCCC
*
335453 CCATTGTGGCCCCACCCTACCCCCGGTGGTCATGATTTTCACAACTTTGAATCTACAGTACCTGA
65 CCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTACAGTACCTGA
*
335518 GGATGCTTCCACACAAGCTTCAGCTTTCCTGG
130 GGATGCTTCCACACAAGTTTCAGCTTTCCTGG
335550 TCTTATGGTT
Statistics
Matches: 891, Mismatches: 67, Indels: 52
0.88 0.07 0.05
Matches are distributed among these distances:
159 6 0.01
160 184 0.21
161 5 0.01
162 91 0.10
163 11 0.01
164 161 0.18
165 193 0.22
166 1 0.00
167 152 0.17
168 6 0.01
169 21 0.02
170 3 0.00
172 6 0.01
176 51 0.06
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.32
Consensus pattern (163 bp):
GTTTCTGAGAAGAAGTTTTTAAAGATTTACTCTATATGTTCCTATGTAAAACTTTGAACCCCCCC
CATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTACAGTACCTGAG
GATGCTTCCACACAAGTTTCAGCTTTCCTGGCT
Found at i:335391 original size:327 final size:327
Alignment explanation
Indices: 334398--335549 Score: 1676
Period size: 327 Copynumber: 3.5 Consensus size: 327
334388 TGGCTGATTA
* * *
334398 GTTTCTGAAAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAGTTTGTTTGACCC
1 GTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTACATATTCCTATGTAAAA----CTTTGA--C
* * *
334463 CCCATCCATTGTGGCCCCACCCTACTCCCGGGGTTGTCATTATTTTCACAACTTTGAATTTACAG
60 CCC--CCATTGTGGCCCCACCCTACCCCCGGGG--GTCATGATTTTCACAACTTTGAATCTACAG
* * *
334528 TACCCGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATCT
121 TACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCCGATTAGTTTCTGAGAAGAAG-TTT
* * *
334593 TTAAAGATTTACTCTATATGTTCCTATGTACAACTTTAACACCCCCCATGTGGCCCCACCTTACC
185 TTAAAGATTTACTCTATATGTTCCTATGTAAAACTTTAACACCCCCCATGTGTCCCCACCCTACC
* *
334658 CCCGGTGGTCATGATTTTCACAACTTTGAATCTACAGTACCTGAGGATGCTTCTACACAAGTTTC
250 CCCGGGGGTCATGATTTTCACAACTTTGAATCTACAGTACCTGAGGATGCTTCCACACAAGTTTC
*
334723 AGCATTCCTGGCT
315 AGCTTTCCTGGCT
* * * * * *
334736 GTTTCTGAGAAGAAG-TTTTTAAAAGATTTACTCAATATGTTTCTTTGTAAAACTTCGACCCCCC
1 GTTTCTGAGAAGAAGATTTTT-AAAGATTTACTCTACATATTCCTATGTAAAACTTTGA----CC
*
334800 CCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAACCTACAGTACCT
61 CCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTACAGTACCT
* * *
334865 GGGGATGCTTCCACACAAGTTTCAGATTTCATGG-C---T-GTTTCTGAGAAGAAGTTTTTAAAG
126 GAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCCGATTAGTTTCTGAGAAGAAGTTTTTAAAG
* * * * *
334925 ATTCACTCAATATATTCCTATGTTAAACTTTGACACCCCCCCCAT-TGTAGCCCCACCCTACCCC
191 ATTTACTCTATATGTTCCTATGTAAAACTTT-A-ACACCCCCCATGTGT--CCCCACCCTACCCC
334989 CGGGGGTCATGATTTTCACAACTTTGAATCTACAGTACCTGAGGATGCTTCCACACAAGTTTCAG
252 CGGGGGTCATGATTTTCACAACTTTGAATCTACAGTACCTGAGGATGCTTCCACACAAGTTTCAG
335054 CTTTCCTGGCT
317 CTTTCCTGGCT
*
335065 GTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTACATATTCCTATGTTAAACTTTGA-CCCCCA
1 GTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTACATATTCCTATGTAAAACTTTGACCCCCCA
* *
335129 TTGTGGCCCCACCCTACCCCCGGGGGTCAAGATTTTCACAACATTGAATCTACAGTACCTGAGGA
66 TTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTACAGTACCTGAGGA
*
335194 TGCTTTCACACAAGTTTCAGCTTTCCTGGCCGATTAGTTTCTGAGAAGAAGTTTTTAAAAGATTT
131 TGCTTCCACACAAGTTTCAGCTTTCCTGGCCGATTAGTTTCTGAGAAGAAGTTTTT-AAAGATTT
* *
335259 ACTCTATATGTTCCTATGTAAAACTTTAACACCCCCCATGTGTCCCAACCCAACCCCCGGGGGTC
195 ACTCTATATGTTCCTATGTAAAACTTTAACACCCCCCATGTGTCCCCACCCTACCCCCGGGGGTC
335324 ATGATTTTCACAACTTTGAATCTACAGTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
260 ATGATTTTCACAACTTTGAATCTACAGTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTG
335389 GCT
325 GCT
* *
335392 GTTTCTGAGAAGAA-ACTTTTTAAAGATTTACTCTACATGTTCCTATGTTAAACTTTGA-CCCCC
1 GTTTCTGAGAAGAAGA-TTTTTAAAGATTTACTCTACATATTCCTATGTAAAACTTTGACCCCCC
*
335455 ATTGTGGCCCCACCCTACCCCCGGTGGTCATGATTTTCACAACTTTGAATCTACAGTACCTGAGG
65 ATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTACAGTACCTGAGG
*
335520 ATGCTTCCACACAAGCTTCAGCTTTCCTGG
130 ATGCTTCCACACAAGTTTCAGCTTTCCTGG
335550 TCTTATGGTT
Statistics
Matches: 743, Mismatches: 55, Indels: 43
0.88 0.07 0.05
Matches are distributed among these distances:
324 93 0.13
325 1 0.00
326 35 0.05
327 256 0.34
328 22 0.03
329 155 0.21
330 36 0.05
332 62 0.08
334 31 0.04
336 6 0.01
337 5 0.01
338 41 0.06
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.32
Consensus pattern (327 bp):
GTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTACATATTCCTATGTAAAACTTTGACCCCCCA
TTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTACAGTACCTGAGGA
TGCTTCCACACAAGTTTCAGCTTTCCTGGCCGATTAGTTTCTGAGAAGAAGTTTTTAAAGATTTA
CTCTATATGTTCCTATGTAAAACTTTAACACCCCCCATGTGTCCCCACCCTACCCCCGGGGGTCA
TGATTTTCACAACTTTGAATCTACAGTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGG
CT
Found at i:341004 original size:2 final size:2
Alignment explanation
Indices: 340997--341032 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
340987 TTTTTGTCTG
340997 CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
341033 GTTTCAAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:345924 original size:21 final size:21
Alignment explanation
Indices: 345885--345924 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
345875 CTTTCTAAGA
*
345885 TCAACTTACAGTCATCCACCT
1 TCAACTTACAGTCAACCACCT
* *
345906 TCAACTTTCAGTTAACCAC
1 TCAACTTACAGTCAACCAC
345925 GGTTCTCGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (21 bp):
TCAACTTACAGTCAACCACCT
Found at i:349044 original size:2 final size:2
Alignment explanation
Indices: 348949--349025 Score: 102
Period size: 2 Copynumber: 38.5 Consensus size: 2
348939 GTCTAGACAG
348949 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * *
348991 TC TT TC TC T- TGC CC TC AC TC TC TC TG TC TC TC TC T
1 TC TC TC TC TC T-C TC TC TC TC TC TC TC TC TC TC TC T
349026 TGGTCTTGCT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.01, C:0.47, G:0.03, T:0.49
Consensus pattern (2 bp):
TC
Found at i:356057 original size:1 final size:1
Alignment explanation
Indices: 356051--356075 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
356041 ATATAAATGT
356051 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
356076 AAAAAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:357749 original size:2 final size:2
Alignment explanation
Indices: 357742--357776 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
357732 AAGTAATTGT
357742 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
357777 CAGTTTGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:360108 original size:2 final size:2
Alignment explanation
Indices: 360101--360132 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
360091 AAAAATGATG
360101 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
360133 ATGAAGTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:366995 original size:17 final size:17
Alignment explanation
Indices: 366970--367011 Score: 75
Period size: 18 Copynumber: 2.4 Consensus size: 17
366960 GGTGGTAGCT
366970 GTTATTTTTTGGTTTCAA
1 GTTATTTTTTGGTTT-AA
366988 GTTATTTTTTGGTTTAA
1 GTTATTTTTTGGTTTAA
367005 GTTATTT
1 GTTATTT
367012 CTCCTTTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.17, C:0.02, G:0.17, T:0.64
Consensus pattern (17 bp):
GTTATTTTTTGGTTTAA
Found at i:372591 original size:23 final size:23
Alignment explanation
Indices: 372565--372608 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
372555 ATAAAATTCG
* *
372565 AACTATTAATTTTTTAAATGATA
1 AACTATTAAATTTATAAATGATA
*
372588 AACTTTTAAATTTATAAATGA
1 AACTATTAAATTTATAAATGA
372609 CTACACAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (23 bp):
AACTATTAAATTTATAAATGATA
Found at i:385304 original size:19 final size:19
Alignment explanation
Indices: 385276--385317 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
385266 ATCAAAGGGC
*
385276 ACCTGCTCCAAAAACTTTA
1 ACCTGCTCCAAAAACCTTA
*
385295 ACCTGGTCCAAAAACCTTA
1 ACCTGCTCCAAAAACCTTA
385314 ACCT
1 ACCT
385318 CCTTCAGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.33, G:0.07, T:0.24
Consensus pattern (19 bp):
ACCTGCTCCAAAAACCTTA
Found at i:388212 original size:30 final size:30
Alignment explanation
Indices: 388176--388237 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
388166 GACCACGTAT
*
388176 TGGGATACGGTAGGTTGACCAGAGGTTGAC
1 TGGGATACGATAGGTTGACCAGAGGTTGAC
388206 TGGGATACGATAGGTTGACCAGAGGTTGAC
1 TGGGATACGATAGGTTGACCAGAGGTTGAC
388236 TG
1 TG
388238 AGACCTTGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.13, G:0.39, T:0.24
Consensus pattern (30 bp):
TGGGATACGATAGGTTGACCAGAGGTTGAC
Found at i:388672 original size:2 final size:2
Alignment explanation
Indices: 388665--388711 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
388655 TGCTTGCTTG
388665 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
388707 CT CT C
1 CT CT C
388712 ATAACATCCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:390096 original size:21 final size:21
Alignment explanation
Indices: 390048--390097 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
390038 AGCAAGACAC
390048 ATTACAGTCTGTTACAAAATA
1 ATTACAGTCTGTTACAAAATA
* * * * *
390069 ATAACAGTGTGTTAGAAATTG
1 ATTACAGTCTGTTACAAAATA
390090 ATTACAGT
1 ATTACAGT
390098 ATATTTATGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (21 bp):
ATTACAGTCTGTTACAAAATA
Found at i:390160 original size:38 final size:39
Alignment explanation
Indices: 390106--390180 Score: 107
Period size: 38 Copynumber: 1.9 Consensus size: 39
390096 GTATATTTAT
* * *
390106 GTATATGTAGTGATTACAGCATGGTACAGATTGATTACA
1 GTATATGTAGTGATTACAGCATAGTACAAAATGATTACA
*
390145 GTATAT-TAGTTATTACAGCATAGTACAAAATGATTA
1 GTATATGTAGTGATTACAGCATAGTACAAAATGATTA
390181 TAGTTTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 26 0.81
39 6 0.19
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (39 bp):
GTATATGTAGTGATTACAGCATAGTACAAAATGATTACA
Found at i:390944 original size:22 final size:22
Alignment explanation
Indices: 390919--391094 Score: 90
Period size: 22 Copynumber: 7.9 Consensus size: 22
390909 TGTTGTAAAG
*
390919 GAATTTTATGTACTGCTGTACA
1 GAATTTAATGTACTGCTGTACA
* *
390941 GAATTTAATGTTCTCCTGTACA
1 GAATTTAATGTACTGCTGTACA
* * *
390963 -ATATCATT-GTATACTGCTGTTCA
1 GA-AT--TTAATGTACTGCTGTACA
* *
390986 GCGA-TTAATGTACTCCTGTACA
1 G-AATTTAATGTACTGCTGTACA
* *
391008 GCATTTAATGTACTGTTGTACA
1 GAATTTAATGTACTGCTGTACA
* * * *
391030 AAATCATT-GTGTACTGCTCTGCA
1 GAAT--TTAATGTACTGCTGTACA
* * *
391053 GCATTTAAAGTACTGCTATACA
1 GAATTTAATGTACTGCTGTACA
* * *
391075 GCATTTAATGTGCTCCTGTA
1 GAATTTAATGTACTGCTGTA
391095 AAATATTATT
Statistics
Matches: 112, Mismatches: 32, Indels: 20
0.68 0.20 0.12
Matches are distributed among these distances:
21 6 0.05
22 78 0.70
23 23 0.21
24 5 0.04
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.38
Consensus pattern (22 bp):
GAATTTAATGTACTGCTGTACA
Found at i:391036 original size:67 final size:67
Alignment explanation
Indices: 390921--391094 Score: 215
Period size: 67 Copynumber: 2.6 Consensus size: 67
390911 TTGTAAAGGA
* * * * * *
390921 ATTTTATGTACTGCTGTACAGAATTTAATGTTCTCCTGTACAATATCATTGTATACTGCTGTTCA
1 ATTTAATGTACTGCTGTACAGCATTTAATGTACTCCTGTACAAAATCATTGTATACTGCTCTGCA
390986 GC
66 GC
* ** *
390988 GA-TTAATGTACTCCTGTACAGCATTTAATGTACTGTTGTACAAAATCATTGTGTACTGCTCTGC
1 -ATTTAATGTACTGCTGTACAGCATTTAATGTACTCCTGTACAAAATCATTGTATACTGCTCTGC
391052 AGC
65 AGC
* * *
391055 ATTTAAAGTACTGCTATACAGCATTTAATGTGCTCCTGTA
1 ATTTAATGTACTGCTGTACAGCATTTAATGTACTCCTGTA
391095 AAATATTATT
Statistics
Matches: 89, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
66 1 0.01
67 87 0.98
68 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (67 bp):
ATTTAATGTACTGCTGTACAGCATTTAATGTACTCCTGTACAAAATCATTGTATACTGCTCTGCA
GC
Found at i:394266 original size:172 final size:172
Alignment explanation
Indices: 393879--394420 Score: 796
Period size: 172 Copynumber: 3.2 Consensus size: 172
393869 AGAAATTTTC
*
393879 AAAAATCTTCTTCTCA-AGAACCAGAA-AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCCCA
1 AAAAATCTTCTTCTCAGA-AACTA-AACAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCCCA
* * * *
393942 GGCAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCT-GGGGTAGGGTGGGGCCACAAT---G
64 GGCAGTGTAGATTCAAAGTTGTGAAAATCATGA-TCCCTGGGGGTAGGGTGAGGCCACATTGGGG
394003 GGGGGGTCG---AAGTTTTACATAGGAATATATAGAGTAAATCTTT
128 GGGGGGT-GTTAAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* *
394046 AAAAATCTTCTTCTCAGAAACTAAACAGCCAGCAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAAACAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCCCAGG
*
394111 TAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGAGGCCACATTGGGGGGG
66 CAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGAGGCCACATTGGGGGGG
* *
394176 GGGTGTTAAAATTTTACATAGGGATATATAGAGTAAATCTTT
131 GGGTGTTAAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* *
394218 AAAAATCTTCTTTTCAGAAAATAAACAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCCCAGG
1 AAAAATCTTCTTCTCAGAAACTAAACAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCCCAGG
*
394283 CAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGAGGTCACATTGGGGGGG
66 CAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGAGGCCACATT--GGGGG
* * *
394348 GGGGGGGTTAAAGTTTTACATAGGAATAAATAGAGTAAATCTTC
129 GGGGGTGTTAAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* * *
394392 AGAAATCTCCTTCTCAGAAACTAATCAGC
1 AAAAATCTTCTTCTCAGAAACTAAACAGC
394421 AAGATGATTC
Statistics
Matches: 338, Mismatches: 26, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
166 6 0.02
167 105 0.31
168 1 0.00
169 1 0.00
170 8 0.02
172 149 0.44
174 68 0.20
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (172 bp):
AAAAATCTTCTTCTCAGAAACTAAACAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCCCAGG
CAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGAGGCCACATTGGGGGGG
GGGTGTTAAAGTTTTACATAGGAATATATAGAGTAAATCTTT
Found at i:417508 original size:2 final size:2
Alignment explanation
Indices: 417503--417578 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
417493 ATATTTTTTA
417503 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
417545 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
417579 ATTCCAGATA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:427060 original size:2 final size:2
Alignment explanation
Indices: 427053--427113 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
427043 ATGCAAATAG
427053 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
427094 GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA
427114 ATTATGCTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:427573 original size:28 final size:28
Alignment explanation
Indices: 427534--427593 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
427524 ACCAGTACAA
*
427534 CCCCCCCCCCCTTTCCAAAAAAAAANAC
1 CCCCCCCCCCCTTTCCAAAAAAAAAAAC
427562 CCCCCCCCCCCTTTCCAAAAAAAAAAAC
1 CCCCCCCCCCCTTTCCAAAAAAAAAAAC
427590 CCCC
1 CCCC
427594 GGGTATTTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.35, C:0.53, G:0.00, T:0.10
Consensus pattern (28 bp):
CCCCCCCCCCCTTTCCAAAAAAAAAAAC
Found at i:433175 original size:2 final size:2
Alignment explanation
Indices: 433168--433219 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
433158 TAAATTCCAC
433168 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
433210 AA AG AG AG AG
1 AG AG AG AG AG
433220 TGGGATGATC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:433464 original size:21 final size:21
Alignment explanation
Indices: 433438--433500 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
433428 ACAGGTAGGT
* *
433438 CCAGCAGTGTTCATTTATGGC
1 CCAGCAGTGTCCATTAATGGC
433459 CCAGCAGTGTCCATTAATGGC
1 CCAGCAGTGTCCATTAATGGC
433480 CCAGCAGTGTCCATTAATGGC
1 CCAGCAGTGTCCATTAATGGC
433501 TGTCTGATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (21 bp):
CCAGCAGTGTCCATTAATGGC
Found at i:434369 original size:12 final size:12
Alignment explanation
Indices: 434344--434377 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
434334 GTTGTCCGCC
*
434344 GTCCGTCCGTCT
1 GTCCGTCTGTCT
*
434356 GTCTGTCTGTCT
1 GTCCGTCTGTCT
434368 GTCCGTCTGT
1 GTCCGTCTGT
434378 AAACTTTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.26, T:0.41
Consensus pattern (12 bp):
GTCCGTCTGTCT
Found at i:436415 original size:167 final size:166
Alignment explanation
Indices: 436163--436501 Score: 538
Period size: 167 Copynumber: 2.0 Consensus size: 166
436153 AGAACCAGAA
*
436163 AGCCAGGAAAGCTGAAACTTTTGTGGAAGCATCCCCAGGTAGTGTAGATTCAAAGTTGTGAAATT
1 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCCCAGGTAGTGTAGATTCAAAGTTGTGAAATT
*
436228 CATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGGTCGAAGTTTTACATAGGAATATATAG
66 CATGACCCCCGGAGGTAGGGTGGGGCCACAAT-GGGGGGTCGAAGTTTTACATAGGAATATATAG
* * *
436293 AGTAAA-CATTTAAAAATCTTCTTCTTAGAAACTAATC
130 AGGAAATC-TTTAAAAATATTCTTCTCAGAAACTAATC
*
436330 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA-GTCAGTGTAGATTCAAAGTTGTGAAAT
1 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCCCAGGT-AGTGTAGATTCAAAGTTGTGAAAT
* * **
436394 TCATGACCCCTGGATGTAGGGTGGGGCTTCAATGGGGGGTCGAAGTTTTACATAGGAATATATAG
65 TCATGACCCCCGGAGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATATAG
*
436459 AGGAAATCTTTAAGAATATTCTTCTCAGAAACTAATC
130 AGGAAATCTTTAAAAATATTCTTCTCAGAAACTAATC
436496 AGCCAG
1 AGCCAG
436502 ATGATTCTTT
Statistics
Matches: 159, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
166 71 0.45
167 88 0.55
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (166 bp):
AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCCCAGGTAGTGTAGATTCAAAGTTGTGAAATT
CATGACCCCCGGAGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATATAGA
GGAAATCTTTAAAAATATTCTTCTCAGAAACTAATC
Found at i:442488 original size:1 final size:1
Alignment explanation
Indices: 442482--442507 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
442472 NNNNNNNGTG
442482 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
442508 GTAAAATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:446113 original size:48 final size:49
Alignment explanation
Indices: 446049--446182 Score: 177
Period size: 48 Copynumber: 2.8 Consensus size: 49
446039 AGCCGTACAG
*
446049 ACAGACTTACAGAAATACAAGCACTTAGAGAAGGTAGTTCTACA-AAAAT
1 ACAGACTTACAGAAATACAAGCATTTAGAGAAGGTAGTTCTA-ATAAAAT
*
446098 ACAGACTT-CAGAAATACAAGCATTTAGAGAA-GTA-TTCTAATATAAT
1 ACAGACTTACAGAAATACAAGCATTTAGAGAAGGTAGTTCTAATAAAAT
* * *
446144 TCACACTTACAGAAATACAAGCATTTAAAGAAAGGTAGT
1 ACAGACTTACAGAAATACAAGCATTTAGAG-AAGGTAGT
446183 GTTTAATACT
Statistics
Matches: 75, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
45 1 0.01
46 15 0.20
47 23 0.31
48 24 0.32
49 11 0.15
50 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (49 bp):
ACAGACTTACAGAAATACAAGCATTTAGAGAAGGTAGTTCTAATAAAAT
Found at i:453616 original size:26 final size:25
Alignment explanation
Indices: 453577--453672 Score: 70
Period size: 26 Copynumber: 3.7 Consensus size: 25
453567 AATTATCGCA
* *
453577 AATTGGTGATCAGTCTAAATGTCTTG
1 AATTGGTAAACAGTC-AAATGTCTTG
* *
453603 AATTGGTAAACAGTCCAAGA-GTCGTA
1 AATTGGTAAACAGT-CAA-ATGTCTTG
* *
453629 AATTGGTGAACAGTCCAATAGT-TATG
1 AATTGGTAAACAGTCAAAT-GTCT-TG
*
453655 CATTGGTAAACAGTCAAA
1 AATTGGTAAACAGTCAAA
453673 CAATCGTATA
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
24 1 0.02
25 2 0.04
26 49 0.91
27 2 0.04
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (25 bp):
AATTGGTAAACAGTCAAATGTCTTG
Found at i:453634 original size:52 final size:52
Alignment explanation
Indices: 453556--454122 Score: 301
Period size: 52 Copynumber: 10.8 Consensus size: 52
453546 TCCAAGAGCC
* * * *
453556 GTAAACAGTCCAATTA-TCGCAAATTGGTGATCAGTCTAAAT-GTCTTGAATTG
1 GTAAACAGTCCAA-GAGTCGTAAATTGGTGAACAGTC-AAATAGTCTTAAATTG
* **
453608 GTAAACAGTCCAAGAGTCGTAAATTGGTGAACAGTCCAATAGT-TATGCATTG
1 GTAAACAGTCCAAGAGTCGTAAATTGGTGAACAGTCAAATAGTCT-TAAATTG
* * * * * * *
453660 GTAAACAGTCAAACAATCGTATATTGGTGAACAGTCCAATAATCGTAAATTG
1 GTAAACAGTCCAAGAGTCGTAAATTGGTGAACAGTCAAATAGTCTTAAATTG
* * ** * * * *
453712 GTCAACAGTCCAATAGTTATACATTGGTAAACAGTCCAACAGTCTTAAATTG
1 GTAAACAGTCCAAGAGTCGTAAATTGGTGAACAGTCAAATAGTCTTAAATTG
*** * * * * *
453764 GCGGACAGTCCAAGAGTTGTACATTGGTGAACATTAAAAATTTAAAAAAGT-TAAAAATTG
1 GTAAACAGTCCAAGAGTCGTAAATTGGTGAACAGT-CAAA--T-----AGTCT-TAAATTG
* * * *
453824 GTTAACATTCCAAAAGTTGTAAATTGGTGAACAGTTC-AATAGT-TGTAAATTG
1 GTAAACAGTCCAAGAGTCGTAAATTGGTGAACAG-TCAAATAGTCT-TAAATTG
** * * * * * *
453876 GGGAACAGTCCAATAGTTGTAAATTGGTGAACAGACCAATAAT-TGAAAATTG
1 GTAAACAGTCCAAGAGTCGTAAATTGGTGAACAGTCAAATAGTCT-TAAATTG
** * * * * * * *
453928 GGGAACAGTCCAAAAGTTGTTAATTGCTGAACAGTCTAATAATCGTAAATTG
1 GTAAACAGTCCAAGAGTCGTAAATTGGTGAACAGTCAAATAGTCTTAAATTG
* * * *
453980 GTGAACAGTCCAATAGTTGTAAATTGGTGAACAGTCCAATAGT-TGTAAATTG
1 GTAAACAGTCCAAGAGTCGTAAATTGGTGAACAGTCAAATAGTCT-TAAATTG
* * * * * * *
454032 ATGAACAGTTCAAAAGTTGTAGATTGGGGAACAGTCCAAA-AGT-TGTATAA-TG
1 GTAAACAGTCCAAGAGTCGTAAATTGGTGAACAGT-CAAATAGTCT-TA-AATTG
* * *
454084 GTGAACAGTCCAAAAATCGTAAATTGGTGAACAGTCAAA
1 GTAAACAGTCCAAGAGTCGTAAATTGGTGAACAGTCAAA
454123 CAGTTGTAAA
Statistics
Matches: 418, Mismatches: 78, Indels: 39
0.78 0.15 0.07
Matches are distributed among these distances:
51 10 0.02
52 360 0.86
53 7 0.02
57 1 0.00
59 3 0.01
60 36 0.09
61 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (52 bp):
GTAAACAGTCCAAGAGTCGTAAATTGGTGAACAGTCAAATAGTCTTAAATTG
Found at i:453669 original size:78 final size:75
Alignment explanation
Indices: 453587--454119 Score: 282
Period size: 78 Copynumber: 6.7 Consensus size: 75
453577 AATTGGTGAT
*
453587 CAGTCTAAATGTCTTGAATTGGTAAACAGTCCAAGAGTCGTAAATTGGTGAACAGTCCAATAGTT
1 CAGTC-AAA-GTCTT-AATTGGTGAACAGTCCAAGAGTCGTAAATTGGTGAACAGTCCAATAGTT
*
453652 ATGCATTGGTAAA
63 ATACATTGGTAAA
* * * * *
453665 CAGTCAAACAATCGTATATTGGTGAACAGTCCAATAATCGTAAATTGGTCAACAGTCCAATAGTT
1 CAGTC-AA-AGTCTTA-ATTGGTGAACAGTCCAAGAGTCGTAAATTGGTGAACAGTCCAATAGTT
453730 ATACATTGGTAAA
63 ATACATTGGTAAA
* * * * * **
453743 CAGTCCAACAGTCTTAAATTGGCGGACAGTCCAAGAGTTGTACATTGGTGAACATTAAAAATTTA
1 CAGT-CAA-AGTCTT-AATTGGTGAACAGTCCAAGAGTCGTAAATTGGTGAACAGT-CCAA--T-
* * *
453808 AAAAAGTTAAAAATTGGTTAA
59 ----AGTTATACATTGGTAAA
* * * * *
453829 CATTCCAAAAGT-TGTAAATTGGTGAACAGTTCAATAGTTGTAAATTGGGGAACAGTCCAATAGT
1 CAGT-C-AAAGTCT-T-AATTGGTGAACAGTCCAAGAGTCGTAAATTGGTGAACAGTCCAATAGT
* * *
453893 TGTAAATTGGTGAA
62 TATACATTGGTAAA
* * * * * * * * * *
453907 CAGACCAATAAT-TGAAAATTGGGGAACAGTCCAAAAGTTGTTAATTGCTGAACAGTCTAATAAT
1 CAG-TCAA-AGTCT--TAATTGGTGAACAGTCCAAGAGTCGTAAATTGGTGAACAGTCCAATAGT
** * *
453971 CGTAAATTGGTGAA
62 TATACATTGGTAAA
* * * * *
453985 CAGTCCAATAGT-TGTAAATTGGTGAACAGTCCAATAGTTGTAAATTGATGAACAGTTCAAAAGT
1 CAGT-CAA-AGTCT-T-AATTGGTGAACAGTCCAAGAGTCGTAAATTGGTGAACAGTCCAATAGT
* * **
454049 TGTAGATTGGGGAA
62 TATACATTGGTAAA
* * *
454063 CAGTCCAAAAGT-TGTATAATGGTGAACAGTCCAAAAATCGTAAATTGGTGAACAGTC
1 CAGT-C-AAAGTCT-TA-ATTGGTGAACAGTCCAAGAGTCGTAAATTGGTGAACAGTC
454120 AAACAGTTGT
Statistics
Matches: 363, Mismatches: 71, Indels: 42
0.76 0.15 0.09
Matches are distributed among these distances:
77 4 0.01
78 288 0.79
79 7 0.02
81 1 0.00
83 1 0.00
85 3 0.01
86 57 0.16
87 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (75 bp):
CAGTCAAAGTCTTAATTGGTGAACAGTCCAAGAGTCGTAAATTGGTGAACAGTCCAATAGTTATA
CATTGGTAAA
Found at i:453685 original size:26 final size:26
Alignment explanation
Indices: 453603--453764 Score: 135
Period size: 26 Copynumber: 6.2 Consensus size: 26
453593 AAATGTCTTG
* *
453603 AATTGGTAAACAGTCCAAGAGTCGTA
1 AATTGGTAAACAGTCCAACAATCGTA
* * * ** *
453629 AATTGGTGAACAGTCCAATAGTTATG
1 AATTGGTAAACAGTCCAACAATCGTA
* *
453655 CATTGGTAAACAGTCAAACAATCGTA
1 AATTGGTAAACAGTCCAACAATCGTA
* * *
453681 TATTGGTGAACAGTCCAATAATCGTA
1 AATTGGTAAACAGTCCAACAATCGTA
* * * **
453707 AATTGGTCAACAGTCCAATAGTTATA
1 AATTGGTAAACAGTCCAACAATCGTA
* * *
453733 CATTGGTAAACAGTCCAACAGTCTTA
1 AATTGGTAAACAGTCCAACAATCGTA
453759 AATTGG
1 AATTGG
453765 CGGACAGTCC
Statistics
Matches: 108, Mismatches: 28, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 108 1.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (26 bp):
AATTGGTAAACAGTCCAACAATCGTA
Found at i:453789 original size:26 final size:25
Alignment explanation
Indices: 453715--453790 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 25
453705 TAAATTGGTC
* *
453715 AACAGTCCAATAGTTATACATTGGTA
1 AACAGTCCAACAGTT-TACATTGGCA
* *
453741 AACAGTCCAACAGTCTTAAATTGGCG
1 AACAGTCCAACAGT-TTACATTGGCA
* *
453767 GACAGTCCAAGAGTTGTACATTGG
1 AACAGTCCAACAGTT-TACATTGG
453791 TGAACATTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
25 1 0.02
26 39 0.95
27 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (25 bp):
AACAGTCCAACAGTTTACATTGGCA
Found at i:453838 original size:26 final size:26
Alignment explanation
Indices: 453818--454132 Score: 377
Period size: 26 Copynumber: 12.1 Consensus size: 26
453808 AAAAAGTTAA
* *
453818 AAATTGGTTAACATTCCAAAAGTTGT
1 AAATTGGTGAACAGTCCAAAAGTTGT
* *
453844 AAATTGGTGAACAGTTCAATAGTTGT
1 AAATTGGTGAACAGTCCAAAAGTTGT
* *
453870 AAATTGGGGAACAGTCCAATAGTTGT
1 AAATTGGTGAACAGTCCAAAAGTTGT
* *
453896 AAATTGGTGAACAGACCAATAA-TTGA
1 AAATTGGTGAACAGTCCAA-AAGTTGT
*
453922 AAATTGGGGAACAGTCCAAAAGTTGT
1 AAATTGGTGAACAGTCCAAAAGTTGT
* * * *
453948 TAATTGCTGAACAGTCTAATAA-TCGT
1 AAATTGGTGAACAGTCCAA-AAGTTGT
*
453974 AAATTGGTGAACAGTCCAATAGTTGT
1 AAATTGGTGAACAGTCCAAAAGTTGT
*
454000 AAATTGGTGAACAGTCCAATAGTTGT
1 AAATTGGTGAACAGTCCAAAAGTTGT
* *
454026 AAATTGATGAACAGTTCAAAAGTTGT
1 AAATTGGTGAACAGTCCAAAAGTTGT
* *
454052 AGATTGGGGAACAGTCCAAAAGTTGT
1 AAATTGGTGAACAGTCCAAAAGTTGT
* *
454078 ATAA-TGGTGAACAGTCCAAAAATCGT
1 A-AATTGGTGAACAGTCCAAAAGTTGT
454104 AAATTGGTGAACAGT-CAAACAGTTGT
1 AAATTGGTGAACAGTCCAAA-AGTTGT
454130 AAA
1 AAA
454133 AGGGTTGAAA
Statistics
Matches: 246, Mismatches: 36, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
25 9 0.04
26 233 0.95
27 4 0.02
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.28
Consensus pattern (26 bp):
AAATTGGTGAACAGTCCAAAAGTTGT
Found at i:455689 original size:167 final size:163
Alignment explanation
Indices: 454965--456251 Score: 1188
Period size: 165 Copynumber: 7.8 Consensus size: 163
454955 TCTCAATATA
* * * *
454965 TAAAAATTTATCCCACATTGTGG-CCCAGCCCTACCCCCCAGGGACCATGATTTGAAAAAAAACT
1 TAAAAATTCATCCCCCATTGTGGCCCCA--CCTA--CCCCGGGGACCATGATTTG--AACAAACT
* * * ** * **
455029 TGAATCCACACTATCTAAGGATGCTTACACGC-CA----AGCTTTTCTGGCCAAATAGTTTTAAA
60 TGAATCTACACTATCTGAGGATGCTTCCATTCAAATTTGAGCTTTTCTGGCCAAATAGTTTTTGA
*
455089 GAAAAAGATTTTTAAAGATGTTCTCTATATATTCCTATG
125 GAAAAAGATTTTTAAAGATTTTCTCTATATATTCCTATG
** * * * *
455128 TAAAAATTCCCCCCCCCCCCCATTTTGGCCTCACTGTACCCC-GGGACTATGATTTGAACAAACT
1 TAAAAATT-----CATCCCCCATTGTGGCCCCAC-CTACCCCGGGGACCATGATTTGAACAAACT
* * * * * * * *
455192 TGAATCTATA-TGATCTGGGGATGCTTCCACTCAAATTTGGGCTTTCCTGGCCTAATA-ATTTTC
60 TGAATCTACACT-ATCTGAGGATGCTTCCATTCAAATTTGAGCTTTTCTGGCCAAATAGTTTTTG
** * *
455255 ATCAGAAGATTTTTAAAGATTTTCTC--GATA----TA--
124 AGAAAAAGATTTTTAAAGATTTTCTCTATATATTCCTATG
* * * *
455287 TAAAAATTTATCCCCCATTGTGGCCCCGCCCTACCCCCAGGGACCCTGATTTGAACAAACTTGAA
1 TAAAAATTCATCCCCCATTGTGGCCCC-ACCTA-CCCCGGGGACCATGATTTGAACAAACTTGAA
* * * ** * * *
455352 TCCACACTATCTAAGGATGCTTACACGCCAATTTGAGCTTTCCTGGCCTAATAG---TT-A-AAA
64 TCTACACTATCTGAGGATGCTTCCATTCAAATTTGAGCTTTTCTGGCCAAATAGTTTTTGAGAAA
* * * *
455412 AA-ATTGTTT-AAGATTTTCTCTTTATATTTCTGTA
129 AAGATT-TTTAAAGATTTTCTCTATATATTCCTATG
* * *
455446 TAAAAATTCATACCCCAATTGTGGCCCCACCTAGCCCCGGGCATCATGATTTGAACAAACTTGAA
1 TAAAAATTCAT-CCCCCATTGTGGCCCCACCTA-CCCCGGGGACCATGATTTGAACAAACTTGAA
* * *
455511 TCTACACTATCTGAGGATGCCTCCAGTCAAATTTGAGCTTTTCTGGCCTAATAGTTTTTGAGAAA
64 TCTACACTATCTGAGGATGCTTCCATTCAAATTTGAGCTTTTCTGGCCAAATAGTTTTTGAGAAA
455576 AAGATTTTTAAAGATTTTTCTCTATATATTCCTATG
129 AAGATTTTTAAAGA-TTTTCTCTATATATTCCTATG
* * *
455612 TAAAAATCCATTCCCCCATTGTGGCCCCGCCGTACCTCCGGGGACCATGATTTGAAGAAACTTGA
1 TAAAAATTCA-TCCCCCATTGTGGCCCCACC-TACC-CCGGGGACCATGATTTGAACAAACTTGA
** **
455677 ATCTTTACTATCTGAGGATGCTTCCATTTTAATTTGAGCTTTTCTGGCCAAATAGTTTTTGAGAA
63 ATCTACACTATCTGAGGATGCTTCCATTCAAATTTGAGCTTTTCTGGCCAAATAGTTTTTGAGAA
* *
455742 GAAGATTTTTAAACATTTTCTCTATATACATGTATTCCTATG
128 AAAGATTTTTAAAGATTTTCTC--TAT--A--TATTCCTATG
* * * *
455784 TAAAAATCCATTCCCCCATTGTGGCCCCGCCATAACCCCAGGGACTATGATTTGAACAAACTTGA
1 TAAAAATTCA-TCCCCCATTGTGGCCCCACC-T-ACCCCGGGGACCATGATTTGAACAAACTTGA
* * * ** * *
455849 GT-T-CACTATCTGAGGTTGCTTTCATTTTAATTTGAGCTTATCTGGCCTAATAGTTTTTGAGAA
63 ATCTACACTATCTGAGGATGCTTCCATTCAAATTTGAGCTTTTCTGGCCAAATAGTTTTTGAGAA
* *
455912 GAAGATTTTTAAAGATTTTCTCTAAATATTCCTATG
128 AAAGATTTTTAAAGATTTTCTCTATATATTCCTATG
* * * * * **
455948 TAAAACTTTATCCCCCTGTTGTGACACCACCCTATGCCGGGGACCATGATTTGAACAAACTTGAA
1 TAAAAATTCATCCCCC-ATTGTGGCCCCA-CCTACCCCGGGGACCATGATTTGAACAAACTTGAA
* * ** *
456013 TCTACACAACCTGAGGATGCTTCCATTTTAATTTGAGCTTATCTGGCCAAATAGTTTTTGAGAAA
64 TCTACACTATCTGAGGATGCTTCCATTCAAATTTGAGCTTTTCTGGCCAAATAGTTTTTGAGAAA
456078 AAGATTTTTAAAGATTTTCTCTATATATTCCTATG
129 AAGATTTTTAAAGATTTTCTCTATATATTCCTATG
* * *
456113 -AAAAACTTGATCCCCCTATTGTGGCCCCACCTACCCACGGTGATCATGATTTGAACAAACTTGA
1 TAAAAA-TTCATCCCCC-ATTGTGGCCCCACCTACCC-CGGGGACCATGATTTGAACAAACTTGA
* * ** * *
456177 ATCTACACTACCTGAGGATGCCTCCACACAAGTTTAAGCTTTTCTGGCCAAATAGTTTTTGAGAA
63 ATCTACACTATCTGAGGATGCTTCCATTCAAATTTGAGCTTTTCTGGCCAAATAGTTTTTGAGAA
*
456242 GAAGATTTTT
128 AAAGATTTTT
456252 GAAAAATACC
Statistics
Matches: 939, Mismatches: 133, Indels: 102
0.80 0.11 0.09
Matches are distributed among these distances:
151 14 0.01
152 6 0.01
153 4 0.00
154 18 0.02
155 5 0.01
156 67 0.07
157 2 0.00
159 95 0.10
160 15 0.02
161 2 0.00
162 3 0.00
163 74 0.08
164 45 0.05
165 223 0.24
166 57 0.06
167 125 0.13
168 32 0.03
169 3 0.00
170 77 0.08
171 1 0.00
172 68 0.07
173 3 0.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (163 bp):
TAAAAATTCATCCCCCATTGTGGCCCCACCTACCCCGGGGACCATGATTTGAACAAACTTGAATC
TACACTATCTGAGGATGCTTCCATTCAAATTTGAGCTTTTCTGGCCAAATAGTTTTTGAGAAAAA
GATTTTTAAAGATTTTCTCTATATATTCCTATG
Found at i:456619 original size:127 final size:130
Alignment explanation
Indices: 456383--456643 Score: 440
Period size: 127 Copynumber: 2.0 Consensus size: 130
456373 AAATCTGCCC
456383 AGTGGTTCTGGAGAAGAAGAAGAAAATAGGAAAAGTTTACAACGACAACGCCGCCAACGCCAACG
1 AGTGGTTCTGGAGAAGAAGAAGAAAATAGGAAAAGTTTACAACGACAA--CCGCC-ACGCCAACG
*
456448 CCGACGACAGACAACTGACAAATTTTGATCAGAAAAGCTCACTTGAGCTTTCAGCTCAGGTGAGC
63 CCGACGACAGACAACGGACAAATTTTGATCAGAAAAGCTCACTTGAGCTTTCAGCTCAGGTGAGC
456513 TAA
128 TAA
*
456516 AGTGGTTCTGGAGAGGAAGAAGAAAAT-GTGAAAAGTTTACAACGACAA-CG-C-CGCCAACGCC
1 AGTGGTTCTGGAGAAGAAGAAGAAAATAG-GAAAAGTTTACAACGACAACCGCCACGCCAACGCC
456577 GACGACAGACAACGGACAAATTTTGATCAGAAAAGCTCACTTGAGCTTTCAGCTCAGGTGAGCTA
65 GACGACAGACAACGGACAAATTTTGATCAGAAAAGCTCACTTGAGCTTTCAGCTCAGGTGAGCTA
456642 A
130 A
456643 A
1 A
456644 AAAAAACTAT
Statistics
Matches: 125, Mismatches: 2, Indels: 8
0.93 0.01 0.06
Matches are distributed among these distances:
127 76 0.61
129 1 0.01
130 2 0.02
132 1 0.01
133 45 0.36
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (130 bp):
AGTGGTTCTGGAGAAGAAGAAGAAAATAGGAAAAGTTTACAACGACAACCGCCACGCCAACGCCG
ACGACAGACAACGGACAAATTTTGATCAGAAAAGCTCACTTGAGCTTTCAGCTCAGGTGAGCTAA
Found at i:460080 original size:12 final size:12
Alignment explanation
Indices: 460063--460095 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
460053 TGAAAAGTTT
460063 ACAGACGGACGG
1 ACAGACGGACGG
*
460075 ACAGACAGACGG
1 ACAGACGGACGG
460087 AC-GACGGAC
1 ACAGACGGAC
460096 AAAATGTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.36, C:0.27, G:0.36, T:0.00
Consensus pattern (12 bp):
ACAGACGGACGG
Found at i:464469 original size:4 final size:4
Alignment explanation
Indices: 464460--464506 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
464450 AAAGTTTACG
* * * *
464460 GACA GACA GACA GACG GACG GACA GACG GACA GACG GAC- GACA GACA
1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA
464507 AAATGTAATC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 3 0.08
4 34 0.92
ACGTcount: A:0.40, C:0.26, G:0.34, T:0.00
Consensus pattern (4 bp):
GACA
Found at i:464482 original size:20 final size:20
Alignment explanation
Indices: 464457--464506 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
464447 TGAAAAGTTT
464457 ACGGACAGACAGACAGACGG
1 ACGGACAGACAGACAGACGG
*
464477 ACGGACAGACGGACAGACGG
1 ACGGACAGACAGACAGACGG
464497 AC-GACAGACA
1 ACGGACAGACA
464507 AAATGTAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 7 0.25
20 21 0.75
ACGTcount: A:0.40, C:0.26, G:0.34, T:0.00
Consensus pattern (20 bp):
ACGGACAGACAGACAGACGG
Found at i:468399 original size:35 final size:34
Alignment explanation
Indices: 468369--469276 Score: 1077
Period size: 35 Copynumber: 26.0 Consensus size: 34
468359 GTTAACTTTA
*
468369 GACACATAATAAGATGTGGCTCGACCTTAACTTAG
1 GACACATAATAAGATGTGG-TCGACCATAACTTAG
* *
468404 GACACATAATAAGATGAAGGACGACCATAACTTAG
1 GACACATAATAAGATG-TGGTCGACCATAACTTAG
* * *
468439 GACACAGTGATAAGATGTAGCTCGACCATAAGTTAG
1 GACACA-TAATAAGATGT-GGTCGACCATAACTTAG
* * *
468475 GACACATAATAAGATGAAGGACGACCATAACTTAA
1 GACACATAATAAGATG-TGGTCGACCATAACTTAG
* * *
468510 GACACATAATAAGATGAAGGACGACCATATCTTAG
1 GACACATAATAAGATG-TGGTCGACCATAACTTAG
* * *
468545 GACACATACTAAGATGTAGGACGACCATAACATAG
1 GACACATAATAAGATGT-GGTCGACCATAACTTAG
* *
468580 GACACATAAAAAGATGTAGCTCGACCATAACTTAG
1 GACACATAATAAGATGT-GGTCGACCATAACTTAG
* *
468615 GACACATAATAAGATGAAGGACGACCATAACTTAG
1 GACACATAATAAGATG-TGGTCGACCATAACTTAG
** *
468650 GACA-ATTAATAAGATGTAGCCCGACCATAAATTAG
1 GACACA-TAATAAGATGT-GGTCGACCATAACTTAG
*
468685 GACACAATGATAAGATGTAGGTCGACCATAACTTAG
1 GACAC-ATAATAAGATGT-GGTCGACCATAACTTAG
* *
468721 GACACATAATAAGATGAAGGACGACCATAACTTAG
1 GACACATAATAAGATG-TGGTCGACCATAACTTAG
*
468756 GACACATAATAAGATGTTGGTCGACCATAACTCAG
1 GACACATAATAAGATG-TGGTCGACCATAACTTAG
468791 GACACATAATAAGATGTTGGTCGACCATAACTTAG
1 GACACATAATAAGATG-TGGTCGACCATAACTTAG
*
468826 GACACATAATAAGATGTTGGTCGACCATAACTCAG
1 GACACATAATAAGATG-TGGTCGACCATAACTTAG
468861 GACACATAATAAGATGTTGGTCGACCATAACTTAG
1 GACACATAATAAGATG-TGGTCGACCATAACTTAG
* *
468896 GACACATAATAAGATGAAGGACGACCATAACTTAG
1 GACACATAATAAGATG-TGGTCGACCATAACTTAG
* * *
468931 GACACATAATATGATGTAGATCGACCATATCTTAG
1 GACACATAATAAGATGT-GGTCGACCATAACTTAG
*
468966 GACACATTA-AAGATGTAGGTCGACCATAACTTAG
1 GACACATAATAAGATGT-GGTCGACCATAACTTAG
* *
469000 GACACATAATAAGATGTAGCTCGACCTTAACTTAG
1 GACACATAATAAGATGT-GGTCGACCATAACTTAG
* *
469035 GACACATAATAAGATGTAGCTCGACCTTAACTTAG
1 GACACATAATAAGATGT-GGTCGACCATAACTTAG
* *
469070 GACACATAATAAGATGTAGCTCGACCTTAACTTAG
1 GACACATAATAAGATGT-GGTCGACCATAACTTAG
* * *
469105 GATATATAATAAGATGTAGCTCGACCATAACTTA-
1 GACACATAATAAGATGT-GGTCGACCATAACTTAG
*
469139 GACACATTA-AAGATGTAGGTCGACCATAACTTAG
1 GACACATAATAAGATGT-GGTCGACCATAACTTAG
* *
469173 GACACCTAATAAGATGTAGGTCGACCTTAACTTAG
1 GACACATAATAAGATGT-GGTCGACCATAACTTAG
* * *
469208 GACACCTAATAAGATGTAGGTCGACCTTAACTTAA
1 GACACATAATAAGATGT-GGTCGACCATAACTTAG
* *
469243 GACACATAGTAAGATGTAGCTCGACCATAACTTA
1 GACACATAATAAGATGT-GGTCGACCATAACTTA
469277 TGTGTTGTCT
Statistics
Matches: 781, Mismatches: 77, Indels: 30
0.88 0.09 0.03
Matches are distributed among these distances:
33 23 0.03
34 44 0.06
35 652 0.83
36 61 0.08
37 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (34 bp):
GACACATAATAAGATGTGGTCGACCATAACTTAG
Found at i:468566 original size:70 final size:70
Alignment explanation
Indices: 468369--469276 Score: 1259
Period size: 70 Copynumber: 13.0 Consensus size: 70
468359 GTTAACTTTA
* * *
468369 GACACATAATAAGATGT-GGCTCGACCTTAACTTAGGACACATAATAAGATGAAGGACGACCATA
1 GACACATAATAAGATGTAGG-TCGACCATAACTTAGGACACATAATAAGATGTAGGTCGACCATA
468433 ACTTAG
65 ACTTAG
* * * * *
468439 GACACAGTGATAAGATGTAGCTCGACCATAAGTTAGGACACATAATAAGATGAAGGACGACCATA
1 GACACA-TAATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGTAGGTCGACCATA
*
468504 ACTTAA
65 ACTTAG
* * * * *
468510 GACACATAATAAGATGAAGGACGACCATATCTTAGGACACATACTAAGATGTAGGACGACCATAA
1 GACACATAATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGTAGGTCGACCATAA
*
468575 CATAG
66 CTTAG
* * * *
468580 GACACATAAAAAGATGTAGCTCGACCATAACTTAGGACACATAATAAGATGAAGGACGACCATAA
1 GACACATAATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGTAGGTCGACCATAA
468645 CTTAG
66 CTTAG
** * *
468650 GACA-ATTAATAAGATGTAGCCCGACCATAAATTAGGACACAATGATAAGATGTAGGTCGACCAT
1 GACACA-TAATAAGATGTAGGTCGACCATAACTTAGGACAC-ATAATAAGATGTAGGTCGACCAT
468714 AACTTAG
64 AACTTAG
* * *
468721 GACACATAATAAGATGAAGGACGACCATAACTTAGGACACATAATAAGATGTTGGTCGACCATAA
1 GACACATAATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGTAGGTCGACCATAA
*
468786 CTCAG
66 CTTAG
* *
468791 GACACATAATAAGATGTTGGTCGACCATAACTTAGGACACATAATAAGATGTTGGTCGACCATAA
1 GACACATAATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGTAGGTCGACCATAA
*
468856 CTCAG
66 CTTAG
* * *
468861 GACACATAATAAGATGTTGGTCGACCATAACTTAGGACACATAATAAGATGAAGGACGACCATAA
1 GACACATAATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGTAGGTCGACCATAA
468926 CTTAG
66 CTTAG
* * * *
468931 GACACATAATATGATGTAGATCGACCATATCTTAGGACACATTA-AAGATGTAGGTCGACCATAA
1 GACACATAATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGTAGGTCGACCATAA
468995 CTTAG
66 CTTAG
* * * *
469000 GACACATAATAAGATGTAGCTCGACCTTAACTTAGGACACATAATAAGATGTAGCTCGACCTTAA
1 GACACATAATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGTAGGTCGACCATAA
469065 CTTAG
66 CTTAG
* * * * *
469070 GACACATAATAAGATGTAGCTCGACCTTAACTTAGGATATATAATAAGATGTAGCTCGACCATAA
1 GACACATAATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGTAGGTCGACCATAA
469135 CTTA-
66 CTTAG
* * *
469139 GACACATTA-AAGATGTAGGTCGACCATAACTTAGGACACCTAATAAGATGTAGGTCGACCTTAA
1 GACACATAATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGTAGGTCGACCATAA
469203 CTTAG
66 CTTAG
* * * * *
469208 GACACCTAATAAGATGTAGGTCGACCTTAACTTAAGACACATAGTAAGATGTAGCTCGACCATAA
1 GACACATAATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGTAGGTCGACCATAA
469273 CTTA
66 CTTA
469277 TGTGTTGTCT
Statistics
Matches: 754, Mismatches: 76, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
68 52 0.07
69 78 0.10
70 498 0.66
71 124 0.16
72 2 0.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (70 bp):
GACACATAATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGTAGGTCGACCATAA
CTTAG
Found at i:468610 original size:105 final size:105
Alignment explanation
Indices: 468369--469276 Score: 1252
Period size: 105 Copynumber: 8.7 Consensus size: 105
468359 GTTAACTTTA
* *
468369 GACACATAATAAGATGT-GGCTCGACCTTAACTTAGGACACATAATAAGATGAAGGACGACCATA
1 GACACATAATAAGATGTAGG-TCGACCATAACTTAGGACACATAATAAGATGTAGGACGACCATA
* * *
468433 ACTTAGGACACAGTGATAAGATGTAGCTCGACCATAAGTTAG
65 ACTTAGGACACA-TAATAAGATGTAGGTCGACCATAACTTAG
* * * * *
468475 GACACATAATAAGATGAAGGACGACCATAACTTAAGACACATAATAAGATGAAGGACGACCATAT
1 GACACATAATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGTAGGACGACCATAA
* * *
468540 CTTAGGACACATACTAAGATGTAGGACGACCATAACATAG
66 CTTAGGACACATAATAAGATGTAGGTCGACCATAACTTAG
* * *
468580 GACACATAAAAAGATGTAGCTCGACCATAACTTAGGACACATAATAAGATGAAGGACGACCATAA
1 GACACATAATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGTAGGACGACCATAA
** *
468645 CTTAGGACA-ATTAATAAGATGTAGCCCGACCATAAATTAG
66 CTTAGGACACA-TAATAAGATGTAGGTCGACCATAACTTAG
* *
468685 GACACAATGATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGAAGGACGACCATA
1 GACAC-ATAATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGTAGGACGACCATA
* *
468750 ACTTAGGACACATAATAAGATGTTGGTCGACCATAACTCAG
65 ACTTAGGACACATAATAAGATGTAGGTCGACCATAACTTAG
* * *
468791 GACACATAATAAGATGTTGGTCGACCATAACTTAGGACACATAATAAGATGTTGGTCGACCATAA
1 GACACATAATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGTAGGACGACCATAA
* *
468856 CTCAGGACACATAATAAGATGTTGGTCGACCATAACTTAG
66 CTTAGGACACATAATAAGATGTAGGTCGACCATAACTTAG
* * *
468896 GACACATAATAAGATGAAGGACGACCATAACTTAGGACACATAATATGATGTA-GATCGACCATA
1 GACACATAATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGTAGGA-CGACCATA
* *
468960 TCTTAGGACACATTA-AAGATGTAGGTCGACCATAACTTAG
65 ACTTAGGACACATAATAAGATGTAGGTCGACCATAACTTAG
* * ** *
469000 GACACATAATAAGATGTAGCTCGACCTTAACTTAGGACACATAATAAGATGTAGCTCGACCTTAA
1 GACACATAATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGTAGGACGACCATAA
* *
469065 CTTAGGACACATAATAAGATGTAGCTCGACCTTAACTTAG
66 CTTAGGACACATAATAAGATGTAGGTCGACCATAACTTAG
* * * * *
469105 GATATATAATAAGATGTAGCTCGACCATAACTTA-GACACATTA-AAGATGTAGGTCGACCATAA
1 GACACATAATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGTAGGACGACCATAA
* *
469168 CTTAGGACACCTAATAAGATGTAGGTCGACCTTAACTTAG
66 CTTAGGACACATAATAAGATGTAGGTCGACCATAACTTAG
* * * * **
469208 GACACCTAATAAGATGTAGGTCGACCTTAACTTAAGACACATAGTAAGATGTAGCTCGACCATAA
1 GACACATAATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGTAGGACGACCATAA
469273 CTTA
66 CTTA
469277 TGTGTTGTCT
Statistics
Matches: 718, Mismatches: 75, Indels: 19
0.88 0.09 0.02
Matches are distributed among these distances:
103 85 0.12
104 109 0.15
105 358 0.50
106 163 0.23
107 3 0.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (105 bp):
GACACATAATAAGATGTAGGTCGACCATAACTTAGGACACATAATAAGATGTAGGACGACCATAA
CTTAGGACACATAATAAGATGTAGGTCGACCATAACTTAG
Found at i:469905 original size:17 final size:17
Alignment explanation
Indices: 469883--469918 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
469873 TATAACGTGT
469883 GAGTACCCATTATTGCC
1 GAGTACCCATTATTGCC
469900 GAGTACCCATTATTGCC
1 GAGTACCCATTATTGCC
469917 GA
1 GA
469919 TTGTTATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (17 bp):
GAGTACCCATTATTGCC
Found at i:471384 original size:32 final size:33
Alignment explanation
Indices: 471339--471422 Score: 107
Period size: 35 Copynumber: 2.5 Consensus size: 33
471329 TTTTTCCCCC
471339 ATAGTAGCTTTTCCCCCC-GGAAAACCTACTAT
1 ATAGTAGCTTTTCCCCCCGGGAAAACCTACTAT
* * *
471371 ATAGTAGCCTTTCCCCCCGGGGGGAAAGCTACTAT
1 ATAGTAGCTTTTCCCCCC--GGGAAAACCTACTAT
*
471406 ATAGCAGCTTTTCCCCC
1 ATAGTAGCTTTTCCCCC
471423 ATAGTAGGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
32 17 0.39
35 27 0.61
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (33 bp):
ATAGTAGCTTTTCCCCCCGGGAAAACCTACTAT
Found at i:473312 original size:183 final size:184
Alignment explanation
Indices: 472998--473353 Score: 669
Period size: 183 Copynumber: 1.9 Consensus size: 184
472988 AATGGAGTAC
472998 CCTACATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGAATTTTTTTCCATAAATTAT
1 CCTACATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGAATTTTTTTCCATAAATTAT
*
473063 CGGAAATCAAAATCCTAGCAATATGCATACCTCTAATATAAGTACAATTGATCTGCAAAAGAACA
66 CGGAAATCAAAATCCTAGCAATATGCACACCTCTAATATAAGTACAATTGATCTGCAAAAGAACA
473128 ACTTATTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGTCAGAGGGTAT
131 ACTTATTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGTCAGAGGGTAT
* *
473182 CCTATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGATTTTTTT-CATAAATTAT
1 CCTACATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGAATTTTTTTCCATAAATTAT
473246 CGGAAATCAAAATCCTAGCAATATGCACACCTCTAATATAAGTACAATTGATCTGCAAAAGAACA
66 CGGAAATCAAAATCCTAGCAATATGCACACCTCTAATATAAGTACAATTGATCTGCAAAAGAACA
*
473311 ACTTCTTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATG
131 ACTTATTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATG
473354 AGAGTACCCT
Statistics
Matches: 168, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
183 116 0.69
184 52 0.31
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.30
Consensus pattern (184 bp):
CCTACATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGAATTTTTTTCCATAAATTAT
CGGAAATCAAAATCCTAGCAATATGCACACCTCTAATATAAGTACAATTGATCTGCAAAAGAACA
ACTTATTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGTCAGAGGGTAT
Found at i:475446 original size:30 final size:30
Alignment explanation
Indices: 475412--475547 Score: 139
Period size: 30 Copynumber: 4.5 Consensus size: 30
475402 AGAATCCTGC
*
475412 GAATCCTCACATTTACTAGTGGATTC-CCGT
1 GAATCCTCACATTTACTGGTGGATTCTCC-T
*
475442 GAATCCTCGCATTTACTGGTGGATTCTCCT
1 GAATCCTCACATTTACTGGTGGATTCTCCT
* * ***
475472 GAGTCCTCAAATTTACTGGTGGATTCTGGA
1 GAATCCTCACATTTACTGGTGGATTCTCCT
* * * *
475502 GAGTCCTCAAATTTACTGATGGATTCTCCA
1 GAATCCTCACATTTACTGGTGGATTCTCCT
* *
475532 GAGTCCTCAAATTTAC
1 GAATCCTCACATTTAC
475548 CAATAGATTC
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
30 92 0.98
31 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.34
Consensus pattern (30 bp):
GAATCCTCACATTTACTGGTGGATTCTCCT
Found at i:475509 original size:60 final size:60
Alignment explanation
Indices: 475415--475547 Score: 176
Period size: 60 Copynumber: 2.2 Consensus size: 60
475405 ATCCTGCGAA
* * ** * *
475415 TCCTCACATTTACTAGTGGATTCCCGTGAATCCTCGCATTTACTGGTGGATTCTCCTGAG
1 TCCTCAAATTTACTAGTGGATTCCCGAGAATCCTCAAATTTACTGATGGATTCTCCAGAG
* ** *
475475 TCCTCAAATTTACTGGTGGATTCTGGAGAGTCCTCAAATTTACTGATGGATTCTCCAGAG
1 TCCTCAAATTTACTAGTGGATTCCCGAGAATCCTCAAATTTACTGATGGATTCTCCAGAG
475535 TCCTCAAATTTAC
1 TCCTCAAATTTAC
475548 CAATAGATTC
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (60 bp):
TCCTCAAATTTACTAGTGGATTCCCGAGAATCCTCAAATTTACTGATGGATTCTCCAGAG
Found at i:475557 original size:60 final size:60
Alignment explanation
Indices: 475452--475576 Score: 169
Period size: 60 Copynumber: 2.1 Consensus size: 60
475442 GAATCCTCGC
* * *** *
475452 ATTTACTGGTGGATTCTCCTGAGTCCTCAAATTTACTGGTGGATTCTGGAGAGTCCTCAA
1 ATTTACTGATGGATTCTCCAGAGTCCTCAAATTTACCAATAGATTCTGGAGAGTCCTCAA
* * *
475512 ATTTACTGATGGATTCTCCAGAGTCCTCAAATTTACCAATAGATTCTTGCGAGTCCTCAC
1 ATTTACTGATGGATTCTCCAGAGTCCTCAAATTTACCAATAGATTCTGGAGAGTCCTCAA
475572 ATTTA
1 ATTTA
475577 TTCATTGATT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (60 bp):
ATTTACTGATGGATTCTCCAGAGTCCTCAAATTTACCAATAGATTCTGGAGAGTCCTCAA
Found at i:475558 original size:30 final size:30
Alignment explanation
Indices: 475452--475547 Score: 147
Period size: 30 Copynumber: 3.2 Consensus size: 30
475442 GAATCCTCGC
* *
475452 ATTTACTGGTGGATTCTCCTGAGTCCTCAA
1 ATTTACTGATGGATTCTCCAGAGTCCTCAA
* **
475482 ATTTACTGGTGGATTCTGGAGAGTCCTCAA
1 ATTTACTGATGGATTCTCCAGAGTCCTCAA
475512 ATTTACTGATGGATTCTCCAGAGTCCTCAA
1 ATTTACTGATGGATTCTCCAGAGTCCTCAA
475542 ATTTAC
1 ATTTAC
475548 CAATAGATTC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (30 bp):
ATTTACTGATGGATTCTCCAGAGTCCTCAA
Found at i:475566 original size:30 final size:30
Alignment explanation
Indices: 475452--475576 Score: 128
Period size: 30 Copynumber: 4.2 Consensus size: 30
475442 GAATCCTCGC
* *
475452 ATTTACTGGTGGATTC-TCCTGAGTCCTCAA
1 ATTTACTGATGGATTCTTGC-GAGTCCTCAA
* * *
475482 ATTTACTGGTGGATTCTGGAGAGTCCTCAA
1 ATTTACTGATGGATTCTTGCGAGTCCTCAA
*
475512 ATTTACTGATGGATTC-TCCAGAGTCCTCAA
1 ATTTACTGATGGATTCTTGC-GAGTCCTCAA
** * *
475542 ATTTACCAATAGATTCTTGCGAGTCCTCAC
1 ATTTACTGATGGATTCTTGCGAGTCCTCAA
475572 ATTTA
1 ATTTA
475577 TTCATTGATT
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
30 78 0.98
31 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (30 bp):
ATTTACTGATGGATTCTTGCGAGTCCTCAA
Found at i:476330 original size:3 final size:3
Alignment explanation
Indices: 476317--476350 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
476307 ACCTGACACA
* *
476317 GTG GGG GTG GTG GTG GTG GTG GTG GAG GTG GTG G
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG G
476351 GGGACGGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.00, G:0.71, T:0.26
Consensus pattern (3 bp):
GTG
Found at i:480872 original size:3 final size:3
Alignment explanation
Indices: 480864--480919 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
480854 TCTCAATATC
* * *
480864 TGA TGA TGA TGA TGA TGA TGA TGA CGA -GA T-A TCA TCA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
* *
480910 CGG TGA TGA T
1 TGA TGA TGA T
480920 TTCTATGCGA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.32, C:0.07, G:0.30, T:0.30
Consensus pattern (3 bp):
TGA
Found at i:493467 original size:253 final size:252
Alignment explanation
Indices: 493019--493523 Score: 1001
Period size: 253 Copynumber: 2.0 Consensus size: 252
493009 NNNNNNNNNC
493019 CCCCCCCCGATGCTACGTGCCTGAATAACCAAAAGAGCTTCTATCTTAGTTGTAAAATACATGGC
1 CCCCCCCCGATGCTACGTGCCTGAATAACCAAAAGAGCTTCTATCTTAGTTGTAAAATACATGGC
493084 CCCCAAATCAGGCGTTCGTGTGCTATTAGAGAGATCTTACGATAAATGCATTTAATGTTTTGAAA
66 CCCCAAATCAGGCGTTCGTGTGCTATTAGAGAGATCTTACGATAAATGCATTTAATGTTTTGAAA
493149 TCCTCTCTTCATCCAAGCAATAAGCAAACTGATTAATTTATATTTACATGTTCAACTTTCTTTGT
131 TCCTCTCTTCATCCAAGCAATAAGCAAACTGATTAATTTATATTTACATGTTCAACTTTCTTTGT
493214 CTGTGATAACATTACGAATCAATTATAAAAGATGAGCGACACAAAATGGGCGTGTCT
196 CTGTGATAACATTACGAATCAATTATAAAAGATGAGCGACACAAAATGGGCGTGTCT
493271 NCCCCCCCCGATGCTACGTGCCTGAATAACCAAAAGAGCTTCTATCTTAGTTGTAAAATACATGG
1 -CCCCCCCCGATGCTACGTGCCTGAATAACCAAAAGAGCTTCTATCTTAGTTGTAAAATACATGG
493336 CCCCCAAATCAGGCGTTCGTGTGCTATTAGAGAGATCTTACGATAAATGCATTTAATGTTTTGAA
65 CCCCCAAATCAGGCGTTCGTGTGCTATTAGAGAGATCTTACGATAAATGCATTTAATGTTTTGAA
493401 ATCCTCTCTTCATCCAAGCAATAAGCAAACTGATTAATTTATATTTACATGTTCAACTTTCTTTG
130 ATCCTCTCTTCATCCAAGCAATAAGCAAACTGATTAATTTATATTTACATGTTCAACTTTCTTTG
493466 TCTGTGATAACATTACGAATCAATTATAAAAGATGAGCGACACAAAATGGGCGTGTCT
195 TCTGTGATAACATTACGAATCAATTATAAAAGATGAGCGACACAAAATGGGCGTGTCT
493524 TTTGGCATAA
Statistics
Matches: 252, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
253 252 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (252 bp):
CCCCCCCCGATGCTACGTGCCTGAATAACCAAAAGAGCTTCTATCTTAGTTGTAAAATACATGGC
CCCCAAATCAGGCGTTCGTGTGCTATTAGAGAGATCTTACGATAAATGCATTTAATGTTTTGAAA
TCCTCTCTTCATCCAAGCAATAAGCAAACTGATTAATTTATATTTACATGTTCAACTTTCTTTGT
CTGTGATAACATTACGAATCAATTATAAAAGATGAGCGACACAAAATGGGCGTGTCT
Found at i:499784 original size:28 final size:28
Alignment explanation
Indices: 499753--499821 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
499743 GGAATGTTGT
* *
499753 TGTACATGGATATAGAATGAGAAGATGA
1 TGTACATGGATATAAAAGGAGAAGATGA
* * *
499781 TGTATATGGATATAAAAGGAGATGATGT
1 TGTACATGGATATAAAAGGAGAAGATGA
*
499809 TGTACATGTATAT
1 TGTACATGGATAT
499822 GGATATTGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (28 bp):
TGTACATGGATATAAAAGGAGAAGATGA
Found at i:499809 original size:59 final size:57
Alignment explanation
Indices: 499746--499862 Score: 128
Period size: 59 Copynumber: 2.0 Consensus size: 57
499736 AGTGAAGGGA
*
499746 ATGTTGT-TGTACATGGATATAGAATGAGAAGATGATGTATATGGATATAAAAGGAGATG
1 ATGTTGTATGTACATGGATATAGAA-G-GAA-ATGATGCATATGGATATAAAAGGAGATG
* * * **
499805 ATGTTGTACATGTATATGGATATTGAAGGAAATGCTGCATATGGATATGGAAGGAGAT
1 ATGTTGT--ATGTACATGGATATAGAAGGAAATGATGCATATGGATATAAAAGGAGAT
499863 TGTTATCTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
59 30 0.61
60 3 0.06
61 1 0.02
62 15 0.31
ACGTcount: A:0.37, C:0.03, G:0.29, T:0.31
Consensus pattern (57 bp):
ATGTTGTATGTACATGGATATAGAAGGAAATGATGCATATGGATATAAAAGGAGATG
Found at i:499955 original size:17 final size:17
Alignment explanation
Indices: 499933--499965 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
499923 TGAATATAGA
499933 TTTATACTTGTAATATT
1 TTTATACTTGTAATATT
499950 TTTATACTTGTAATAT
1 TTTATACTTGTAATAT
499966 ATTGGACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (17 bp):
TTTATACTTGTAATATT
Found at i:504934 original size:133 final size:134
Alignment explanation
Indices: 504777--505043 Score: 509
Period size: 133 Copynumber: 2.0 Consensus size: 134
504767 GCAGTTAGCT
*
504777 CAAGAATTTGGTTCTCAGTTCATTTTTCAAATAAGATTTTAAAAAAACCTCTATTTGTGTACAAT
1 CAAGAATTAGGTTCTCAGTTCATTTTTCAAATAAGATTTTAAAAAAACCTCTATTTGTGTACAAT
504842 GTATCTAGCATTAATTTTGATAAATTAGTTTTTGCTTAATTATGATTATGTTGAGTTGAAAAA-T
66 GTATCTAGCATTAATTTTGATAAATTAGTTTTTGCTTAATTATGATTATGTTGAGTTGAAAAATT
504906 AAAA
131 AAAA
*
504910 CAAGAATTAGGTTCTCAGTTCATTTTTCAAATAAGATTTTAAAAAACCCTCTATTTGTGTACAAT
1 CAAGAATTAGGTTCTCAGTTCATTTTTCAAATAAGATTTTAAAAAAACCTCTATTTGTGTACAAT
504975 GTATCTAGCATTAATTTTGATAAATTAGTTTTTGCTTAATTATGATTATGTTGAGTTGAAAAATT
66 GTATCTAGCATTAATTTTGATAAATTAGTTTTTGCTTAATTATGATTATGTTGAGTTGAAAAATT
505040 AAAA
131 AAAA
505044 AGCCCATAAA
Statistics
Matches: 131, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
133 126 0.96
134 5 0.04
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (134 bp):
CAAGAATTAGGTTCTCAGTTCATTTTTCAAATAAGATTTTAAAAAAACCTCTATTTGTGTACAAT
GTATCTAGCATTAATTTTGATAAATTAGTTTTTGCTTAATTATGATTATGTTGAGTTGAAAAATT
AAAA
Found at i:505379 original size:11 final size:11
Alignment explanation
Indices: 505363--505389 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
505353 TTTACAGTCG
505363 TAATTATTCAT
1 TAATTATTCAT
505374 TAATTATTCAT
1 TAATTATTCAT
505385 TAATT
1 TAATT
505390 TCACATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (11 bp):
TAATTATTCAT
Found at i:506910 original size:2 final size:2
Alignment explanation
Indices: 506903--506972 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
506893 AGAGCGTAAC
*
506903 GA GA GA GA GA GA GA GA TA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
506945 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
506973 TATGTTGATG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.49, T:0.01
Consensus pattern (2 bp):
GA
Found at i:508381 original size:36 final size:37
Alignment explanation
Indices: 508330--508423 Score: 103
Period size: 36 Copynumber: 2.7 Consensus size: 37
508320 ATCGTTGGTA
*
508330 AGATTTGGGGATGTCAT-TGTTACAGTAG-CTGTTATT
1 AGATTTGGGGATGTCATATGATACAGT-GCCTGTTATT
508366 AGATTTGGGTG-TGTCATATGATACAGTGCCTG---TT
1 AGATTTGGG-GATGTCATATGATACAGTGCCTGTTATT
*
508400 AGATTT-GGGATGTCATATAATACA
1 AGATTTGGGGATGTCATATGATACA
508424 ATAGTTGTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
32 1 0.02
33 15 0.29
34 8 0.15
36 16 0.31
37 12 0.23
ACGTcount: A:0.26, C:0.10, G:0.27, T:0.38
Consensus pattern (37 bp):
AGATTTGGGGATGTCATATGATACAGTGCCTGTTATT
Found at i:508400 original size:37 final size:33
Alignment explanation
Indices: 508330--508433 Score: 95
Period size: 33 Copynumber: 3.0 Consensus size: 33
508320 ATCGTTGGTA
*
508330 AGATTTGGGGATGTCAT-TGTTACAGTAGCTGTTATT
1 AGATTTGGGG-TGTCATATGATACAGTAGCTG---TT
508366 AGATTTGGGTGTGTCATATGATACAGT-GCCTGTT
1 AGATTTGGG-GTGTCATATGATACAGTAG-CTGTT
* * * *
508400 AGATTTGGGATGTCATATAATACAATAGTTGTT
1 AGATTTGGGGTGTCATATGATACAGTAGCTGTT
508433 A
1 A
508434 TAATTGACAC
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
33 19 0.32
34 12 0.20
36 16 0.27
37 12 0.20
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (33 bp):
AGATTTGGGGTGTCATATGATACAGTAGCTGTT
Found at i:516764 original size:72 final size:72
Alignment explanation
Indices: 516644--516927 Score: 489
Period size: 72 Copynumber: 3.9 Consensus size: 72
516634 GATCATTAGA
*
516644 ACTAAATTTTGACCCTAATTGTAAACTATACAGTGT-TATGAGATAGTTTATGGAACAAACATTA
1 ACTAAATTTTGACCCTAA-TGTAAACTATACAGAGTAT-TGAGATAGTTTATGGAACAAACATTA
516708 CTCATTGGG
64 CTCATTGGG
*
516717 ACTAAATTTTGACCCTAATGTAAACTTTACAGAGTATTGAGATAGTTTATGGAACAAACATTACT
1 ACTAAATTTTGACCCTAATGTAAACTATACAGAGTATTGAGATAGTTTATGGAACAAACATTACT
516782 CATTGGG
66 CATTGGG
* *
516789 ACTTAATTTTGACCCTAATGTAAACTTTACAGAGTATTGAGATAGTTTATGGAACAAACATTACT
1 ACTAAATTTTGACCCTAATGTAAACTATACAGAGTATTGAGATAGTTTATGGAACAAACATTACT
516854 CATTGGG
66 CATTGGG
* *
516861 ACTAAATTTTGACCCTAATGTAAACTATACAGAGTATTGAGATAGCTTATGGAACAAACATTGCT
1 ACTAAATTTTGACCCTAATGTAAACTATACAGAGTATTGAGATAGTTTATGGAACAAACATTACT
516926 CA
66 CA
516928 ATAAATCCTG
Statistics
Matches: 203, Mismatches: 7, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
72 184 0.91
73 19 0.09
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (72 bp):
ACTAAATTTTGACCCTAATGTAAACTATACAGAGTATTGAGATAGTTTATGGAACAAACATTACT
CATTGGG
Found at i:519586 original size:44 final size:47
Alignment explanation
Indices: 519526--519643 Score: 134
Period size: 52 Copynumber: 2.5 Consensus size: 47
519516 AGCTTATTTA
*
519526 TAAGCATACATTTACAT-TA-A-TATATATGTCCCAAAAGGCTTATT
1 TAAGCATACATGTACATATATATTATATATGTCCCAAAAGGCTTATT
*
519570 TAAGCATACATGTACATATATATATATTTATATATGTTCCAAAAGGCTTATT
1 TAAGCATACATGTAC----ATATATA-TTATATATGTCCCAAAAGGCTTATT
* *
519622 TTAGCATACATGTACAAATATA
1 TAAGCATACATGTACATATATA
519644 CATCCCAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
44 14 0.23
48 8 0.13
49 2 0.03
50 1 0.02
52 37 0.60
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (47 bp):
TAAGCATACATGTACATATATATTATATATGTCCCAAAAGGCTTATT
Found at i:524134 original size:23 final size:23
Alignment explanation
Indices: 524039--524135 Score: 56
Period size: 23 Copynumber: 4.2 Consensus size: 23
524029 GTTACATTAT
524039 AGTTATAGATAT-AGGCACATTTG
1 AGTTATA-ATATAAGGCACATTTG
* * * * *
524062 AGTTACATTTTAAGGTACATTAG
1 AGTTATAATATAAGGCACATTTG
* * * **
524085 AGTTATACTTTGAGTTACATTAT-
1 AGTTATAATATAAGGCACATT-TG
524108 AGTTATAGATAT-AGGCACATTTG
1 AGTTATA-ATATAAGGCACATTTG
524131 AGTTA
1 AGTTA
524136 CATTTTAAGG
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
22 3 0.05
23 51 0.91
24 2 0.04
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (23 bp):
AGTTATAATATAAGGCACATTTG
Found at i:524150 original size:23 final size:23
Alignment explanation
Indices: 524055--524151 Score: 81
Period size: 23 Copynumber: 4.2 Consensus size: 23
524045 AGATATAGGC
524055 ACATTTGAGTTACATTTTAAGGT
1 ACATTTGAGTTACATTTTAAGGT
* * * * *
524078 ACATTAGAGTTATACTTTGAGTT
1 ACATTTGAGTTACATTTTAAGGT
* ** *
524101 ACATTAT-AGTTATA-GATATAGGC
1 ACATT-TGAGTTACATTTTA-AGGT
524124 ACATTTGAGTTACATTTTAAGGT
1 ACATTTGAGTTACATTTTAAGGT
524147 ACATT
1 ACATT
524152 ANNNNNNNNN
Statistics
Matches: 55, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
22 2 0.04
23 51 0.93
24 2 0.04
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.41
Consensus pattern (23 bp):
ACATTTGAGTTACATTTTAAGGT
Found at i:524151 original size:69 final size:69
Alignment explanation
Indices: 523970--524152 Score: 287
Period size: 69 Copynumber: 2.7 Consensus size: 69
523960 GGTATACTTA
* * * * *
523970 AGTTATACATTTAGGCACATATT-AGTTATATTTTTAGGTACATCAGAGTTATACAATGAGTTAC
1 AGTTATAGATATAGGCACAT-TTGAGTTACATTTTAAGGTACATTAGAGTTATACAATGAGTTAC
524034 ATTAT
65 ATTAT
**
524039 AGTTATAGATATAGGCACATTTGAGTTACATTTTAAGGTACATTAGAGTTATACTTTGAGTTACA
1 AGTTATAGATATAGGCACATTTGAGTTACATTTTAAGGTACATTAGAGTTATACAATGAGTTACA
524104 TTAT
66 TTAT
524108 AGTTATAGATATAGGCACATTTGAGTTACATTTTAAGGTACATTA
1 AGTTATAGATATAGGCACATTTGAGTTACATTTTAAGGTACATTA
524153 NNNNNNNNNN
Statistics
Matches: 106, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
68 2 0.02
69 104 0.98
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.40
Consensus pattern (69 bp):
AGTTATAGATATAGGCACATTTGAGTTACATTTTAAGGTACATTAGAGTTATACAATGAGTTACA
TTAT
Found at i:527548 original size:83 final size:82
Alignment explanation
Indices: 527436--527682 Score: 327
Period size: 83 Copynumber: 3.0 Consensus size: 82
527426 AAACATTTAA
* * * * *
527436 AAATGACAAAGTCCAAATTAGTTACAAAAAAGTTATACTGAAAAATTCTAAGTCTGA-ATAAGGC
1 AAATGACAAAGTCCAAATTAGGTACAAAAAAGTTATAGTGAAAATTTCTAAGTGTGATAT-AGGT
527500 ACAGTTTAGTTATACTAAG
65 ACA-TTTAGTTATACTAAG
527519 AAATGACAAAGTCCAAA-TAGGTACAAAAAAGTTATAGTGAAAATTTTCTAAGTGTGATATAGGT
1 AAATGACAAAGTCCAAATTAGGTACAAAAAAGTTATAGTGAAAA-TTTCTAAGTGTGATATAGGT
**
527583 ACATTTCAGTTATACTTTG
65 ACATTT-AGTTATACTAAG
* * * *
527602 AAATGACTAAGTTCAAATTAGGCACAGAAAAGTTATAGTGAAAATTGTCTAAGTGTGATATAGGT
1 AAATGACAAAGTCCAAATTAGGTACAAAAAAGTTATAGTGAAAATT-TCTAAGTGTGATATAGGT
527667 ACATTTTAGTTATACT
65 ACA-TTTAGTTATACT
527683 TCAAAACGAC
Statistics
Matches: 147, Mismatches: 11, Indels: 11
0.87 0.07 0.07
Matches are distributed among these distances:
82 27 0.18
83 61 0.41
84 56 0.38
85 3 0.02
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (82 bp):
AAATGACAAAGTCCAAATTAGGTACAAAAAAGTTATAGTGAAAATTTCTAAGTGTGATATAGGTA
CATTTAGTTATACTAAG
Found at i:527552 original size:41 final size:41
Alignment explanation
Indices: 527434--527561 Score: 116
Period size: 41 Copynumber: 3.1 Consensus size: 41
527424 ACAAACATTT
*
527434 AAAAATGACAAAGTCCAAATTAGTTACAAAAAAGTTATACTG
1 AAAAATGACAAAGTCCAAA-TAGGTACAAAAAAGTTATACTG
* * ** * ****
527476 AAAAAT-TCTAAGTCTGAATAAGGCACAGTTTAGTTATACT-
1 AAAAATGACAAAGTCCAAAT-AGGTACAAAAAAGTTATACTG
*
527516 AAGAAATGACAAAGTCCAAATAGGTACAAAAAAGTTATAGTG
1 AA-AAATGACAAAGTCCAAATAGGTACAAAAAAGTTATACTG
527558 AAAA
1 AAAA
527562 TTTTCTAAGT
Statistics
Matches: 62, Mismatches: 20, Indels: 9
0.68 0.22 0.10
Matches are distributed among these distances:
40 3 0.05
41 42 0.68
42 17 0.27
ACGTcount: A:0.50, C:0.11, G:0.15, T:0.24
Consensus pattern (41 bp):
AAAAATGACAAAGTCCAAATAGGTACAAAAAAGTTATACTG
Found at i:527583 original size:42 final size:42
Alignment explanation
Indices: 527535--527669 Score: 123
Period size: 42 Copynumber: 3.2 Consensus size: 42
527525 CAAAGTCCAA
*
527535 ATAGGTACAAAAAAGTTATAGTGAAAATTTTCTAAGTGTGAT
1 ATAGGTACAAAAAAGTTATAGTGAAAATTGTCTAAGTGTGAT
**** * * * *
527577 ATAGGTACATTTCAGTTATACTTTG-AAA-TGACTAAGT-TCAA
1 ATAGGTACAAAAAAGTTATA--GTGAAAATTGTCTAAGTGTGAT
* *
527618 ATTAGGCACAGAAAAGTTATAGTGAAAATTGTCTAAGTGTGAT
1 A-TAGGTACAAAAAAGTTATAGTGAAAATTGTCTAAGTGTGAT
527661 ATAGGTACA
1 ATAGGTACA
527670 TTTTAGTTAT
Statistics
Matches: 68, Mismatches: 19, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
40 2 0.03
41 6 0.09
42 52 0.76
43 6 0.09
44 2 0.03
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (42 bp):
ATAGGTACAAAAAAGTTATAGTGAAAATTGTCTAAGTGTGAT
Found at i:527654 original size:84 final size:82
Alignment explanation
Indices: 527436--527713 Score: 330
Period size: 84 Copynumber: 3.3 Consensus size: 82
527426 AAACATTTAA
* * * * *
527436 AAATGACAAAGTCCAAATTAGTTACAAAAAAGTTATACTGAAAAATTCTAAGTCTGA-ATAAGGC
1 AAATGACAAAGTCCAAATTAGGTACAAAAAAGTTATAGTGAAAATTTCTAAGTGTGATAT-AGGT
*
527500 ACAGTTTAGTTATACTAAG
65 ACA-TTTAGTTATACTTAG
527519 AAATGACAAAGTCCAAA-TAGGTACAAAAAAGTTATAGTGAAAATTTTCTAAGTGTGATATAGGT
1 AAATGACAAAGTCCAAATTAGGTACAAAAAAGTTATAGTGAAAA-TTTCTAAGTGTGATATAGGT
*
527583 ACATTTCAGTTATACTTTG
65 ACATTT-AGTTATACTTAG
* * * *
527602 AAATGACTAAGTTCAAATTAGGCACAGAAAAGTTATAGTGAAAATTGTCTAAGTGTGATATAGGT
1 AAATGACAAAGTCCAAATTAGGTACAAAAAAGTTATAGTGAAAATT-TCTAAGTGTGATATAGGT
527667 ACATTTTAGTTATACTTCA-
65 ACA-TTTAGTTATACTT-AG
* * *
527686 AAACGACAAAG-ACAAATATAGTTACAAA
1 AAATGACAAAGTCCAAAT-TAGGTACAAA
527714 TCAGTCATAA
Statistics
Matches: 169, Mismatches: 18, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
82 27 0.16
83 66 0.39
84 73 0.43
85 3 0.02
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (82 bp):
AAATGACAAAGTCCAAATTAGGTACAAAAAAGTTATAGTGAAAATTTCTAAGTGTGATATAGGTA
CATTTAGTTATACTTAG
Found at i:536819 original size:21 final size:19
Alignment explanation
Indices: 536770--536807 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
536760 CACATATATT
*
536770 CATTTATGTTAACATGCAA
1 CATTCATGTTAACATGCAA
536789 CATTCATGTTAACATGCAA
1 CATTCATGTTAACATGCAA
536808 TGTATTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (19 bp):
CATTCATGTTAACATGCAA
Found at i:537390 original size:21 final size:21
Alignment explanation
Indices: 537366--537483 Score: 123
Period size: 21 Copynumber: 5.6 Consensus size: 21
537356 TATTTAAGAA
537366 AACATGCAAGATATTTATGTC
1 AACATGCAAGATATTTATGTC
**
537387 AACATGCAAGATAACTATGTC
1 AACATGCAAGATATTTATGTC
*
537408 AACATGCAATATATTTATGTC
1 AACATGCAAGATATTTATGTC
537429 AACATGCAAGATGA-TTATGTTC
1 AACATGCAAGAT-ATTTATG-TC
* * * **
537451 -AGATGCAAGTTACTTATAAC
1 AACATGCAAGATATTTATGTC
*
537471 AACATGCCAGATA
1 AACATGCAAGATA
537484 ACTTGCATGT
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
20 2 0.03
21 75 0.94
22 3 0.04
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (21 bp):
AACATGCAAGATATTTATGTC
Found at i:537395 original size:42 final size:42
Alignment explanation
Indices: 537348--537437 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 42
537338 TAGATGTAAG
**
537348 ATGCAACATATTTAAGAAAACATGCAAGATATTTATGTCAAC
1 ATGCAACATAACTAAGAAAACATGCAAGATATTTATGTCAAC
* * ** *
537390 ATGCAAGATAACTATGTCAACATGCAATATATTTATGTCAAC
1 ATGCAACATAACTAAGAAAACATGCAAGATATTTATGTCAAC
537432 ATGCAA
1 ATGCAA
537438 GATGATTATG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (42 bp):
ATGCAACATAACTAAGAAAACATGCAAGATATTTATGTCAAC
Found at i:537448 original size:42 final size:42
Alignment explanation
Indices: 537366--537486 Score: 145
Period size: 42 Copynumber: 2.9 Consensus size: 42
537356 TATTTAAGAA
537366 AACATGCAAGATATTTATGTCAACATGCAAGATAACTATGTC
1 AACATGCAAGATATTTATGTCAACATGCAAGATAACTATGTC
* * *
537408 AACATGCAATATATTTATGTCAACATGCAAGATGATTATGTTC
1 AACATGCAAGATATTTATGTCAACATGCAAGATAACTATG-TC
* * * ** *
537451 -AGATGCAAGTTACTTATAACAACATGCCAGATAACT
1 AACATGCAAGATATTTATGTCAACATGCAAGATAACT
537487 TGCATGTTAA
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 64 0.97
43 2 0.03
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.30
Consensus pattern (42 bp):
AACATGCAAGATATTTATGTCAACATGCAAGATAACTATGTC
Found at i:537556 original size:21 final size:21
Alignment explanation
Indices: 537532--537585 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
537522 TTTCACTCGT
537532 ATGTCAACATAAACAAGTTGC
1 ATGTCAACATAAACAAGTTGC
** * **
537553 ATGTTGATATAAATGAGTTGC
1 ATGTCAACATAAACAAGTTGC
*
537574 ATGCCAACATAA
1 ATGTCAACATAA
537586 TTATAACTCA
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
ATGTCAACATAAACAAGTTGC
Found at i:537929 original size:21 final size:21
Alignment explanation
Indices: 537850--537951 Score: 105
Period size: 21 Copynumber: 4.8 Consensus size: 21
537840 TAGCACATCA
* * * *
537850 ACATAATAACCTTGCACGAAG
1 ACATAATTATCTTGCATGATG
* *
537871 ACATAATTATCTTGCACGAAG
1 ACATAATTATCTTGCATGATG
*
537892 ACATAATTATCTTGCATGCTG
1 ACATAATTATCTTGCATGATG
* *
537913 ACATAATTTTCTTGCATGTTG
1 ACATAATTATCTTGCATGATG
*
537934 ACATAAGTTATCCTGCAT
1 ACATAA-TTATCTTGCAT
537952 ATAGGGCAGA
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
21 62 0.87
22 9 0.13
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (21 bp):
ACATAATTATCTTGCATGATG
Found at i:538050 original size:22 final size:21
Alignment explanation
Indices: 538002--538058 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 21
537992 ATGCAAGTTG
* *
538002 CTTATTTATGTCAATATGCGA
1 CTTATTTATGTTAATATGCAA
*
538023 CATATTTATGTTATATATGCAA
1 CTTATTTATGTTA-ATATGCAA
538045 CTTATTTATGTTAA
1 CTTATTTATGTTAA
538059 CATTGATAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 12 0.39
22 19 0.61
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (21 bp):
CTTATTTATGTTAATATGCAA
Found at i:547847 original size:112 final size:112
Alignment explanation
Indices: 547650--547992 Score: 616
Period size: 112 Copynumber: 3.1 Consensus size: 112
547640 TTCGCGCATG
* *
547650 TAACAATTCGTAATGTTTCCCGTTGCTAAGTGCGTTGCTAACGCTGAGGGTAATAGAACAGATTA
1 TAACAATTTGTAATGTTACCCGTTGCTAAGTGCGTTGCTAACGCTGAGGGTAATAGAACAGATTA
*
547715 TGAAGTGCGTCTAAACCAATCAGATTTCAGTATTTAACATGAAAGTA
66 TGAACTGCGTCTAAACCAATCAGATTTCAGTATTTAACATGAAAGTA
547762 TAACAATTTGTAATGTTACCCGTTGCTAAGTGCGTTGCTAACGCTGAGGGTAATAGAACAGATTA
1 TAACAATTTGTAATGTTACCCGTTGCTAAGTGCGTTGCTAACGCTGAGGGTAATAGAACAGATTA
547827 TGAACTGCGTCTAAACCAATCAGATTTCAGTATTTAACATGAAAGTA
66 TGAACTGCGTCTAAACCAATCAGATTTCAGTATTTAACATGAAAGTA
* *
547874 TAACAATTTGTAATGTTACCCGTTGCTAAGTGCGTTGCTTACGCTGAGGGTAATAGAACGGATTA
1 TAACAATTTGTAATGTTACCCGTTGCTAAGTGCGTTGCTAACGCTGAGGGTAATAGAACAGATTA
*
547939 TGAACTGCGTCTTAACCAATCAGATTTCAGGT-TTTAACATGAAAGTA
66 TGAACTGCGTCTAAACCAATCAGATTTCA-GTATTTAACATGAAAGTA
547986 TAACAAT
1 TAACAAT
547993 ATTGATTGTC
Statistics
Matches: 224, Mismatches: 6, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
112 222 0.99
113 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (112 bp):
TAACAATTTGTAATGTTACCCGTTGCTAAGTGCGTTGCTAACGCTGAGGGTAATAGAACAGATTA
TGAACTGCGTCTAAACCAATCAGATTTCAGTATTTAACATGAAAGTA
Found at i:550532 original size:2 final size:2
Alignment explanation
Indices: 550525--550579 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
550515 TCCGCCCCTG
550525 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
550567 CT CT CT CT CT CT C
1 CT CT CT CT CT CT C
550580 ATATAACAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:557842 original size:30 final size:30
Alignment explanation
Indices: 557806--557882 Score: 127
Period size: 30 Copynumber: 2.6 Consensus size: 30
557796 CGGGGACGTG
*
557806 TGCTGTCATAGTCACAGAAAAATACAGGTA
1 TGCTGTCATAGTCACAGAAAAATACAGATA
* *
557836 TGCTGTCATAGTAACAGAAATATACAGATA
1 TGCTGTCATAGTCACAGAAAAATACAGATA
557866 TGCTGTCATAGTCACAG
1 TGCTGTCATAGTCACAG
557883 GTATGTTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (30 bp):
TGCTGTCATAGTCACAGAAAAATACAGATA
Found at i:570673 original size:24 final size:26
Alignment explanation
Indices: 570627--570678 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
570617 CTAATTCCTG
*
570627 TTGCTAATTTTTATTTTGAATG-ATA
1 TTGCTAATTTTTATTTTAAATGAATA
570652 TTGCTAA-TTTT-TTTTAACATGAATA
1 TTGCTAATTTTTATTTTAA-ATGAATA
570677 TT
1 TT
570679 ATGATGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 5 0.21
24 7 0.29
25 12 0.50
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.56
Consensus pattern (26 bp):
TTGCTAATTTTTATTTTAAATGAATA
Found at i:576432 original size:31 final size:31
Alignment explanation
Indices: 576397--576459 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
576387 AAAATGACAA
*
576397 TGAAAAATAACATATACATGTGTTTAAACAC
1 TGAAAAATAACATATACATGTGTTAAAACAC
576428 TGAAAAATAACATATACATGTGTTAAAACAC
1 TGAAAAATAACATATACATGTGTTAAAACAC
576459 T
1 T
576460 ATGTGTCCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.29
Consensus pattern (31 bp):
TGAAAAATAACATATACATGTGTTAAAACAC
Found at i:578706 original size:12 final size:12
Alignment explanation
Indices: 578689--578713 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
578679 AGTGGATTGA
578689 AACAGTCAGTCC
1 AACAGTCAGTCC
578701 AACAGTCAGTCC
1 AACAGTCAGTCC
578713 A
1 A
578714 CAGAAAGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.32, G:0.16, T:0.16
Consensus pattern (12 bp):
AACAGTCAGTCC
Found at i:590703 original size:18 final size:18
Alignment explanation
Indices: 590653--590708 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
590643 ATATCATGAC
590653 ATTATTATTATTATGGCT
1 ATTATTATTATTATGGCT
* ***
590671 ATCATTATGGCTATGGCT
1 ATTATTATTATTATGGCT
590689 ATTATTATTATTATGGCT
1 ATTATTATTATTATGGCT
590707 AT
1 AT
590709 CTGATAAAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (18 bp):
ATTATTATTATTATGGCT
Found at i:591988 original size:2 final size:2
Alignment explanation
Indices: 591981--592009 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
591971 GAACTACCAC
591981 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
592010 TAAATCGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:592086 original size:23 final size:23
Alignment explanation
Indices: 592060--592145 Score: 118
Period size: 23 Copynumber: 3.6 Consensus size: 23
592050 TATGAAAGAT
592060 TGTATTACAACTGTGAATGCAAA
1 TGTATTACAACTGTGAATGCAAA
592083 TGTATTACAACTGTGAATGCAAA
1 TGTATTACAACTGTGAATGCAAA
*
592106 TGTATTATAAGTAACTGTGAATGCAAA
1 TGTA-T-T-A-CAACTGTGAATGCAAA
*
592133 TGTATTGCAACTG
1 TGTATTACAACTG
592146 AATTAGAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
23 32 0.57
24 1 0.02
25 2 0.04
26 2 0.04
27 19 0.34
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
TGTATTACAACTGTGAATGCAAA
Found at i:596352 original size:56 final size:56
Alignment explanation
Indices: 596265--596386 Score: 192
Period size: 56 Copynumber: 2.2 Consensus size: 56
596255 AGGTTTTTTC
596265 TTTCTTTCTTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTG-TAATG
1 TTTCTTT-TTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGCT-ATG
* * *
596322 TTTCTTTTTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTTTG
1 TTTCTTTTTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGCTATG
596378 TTTCTTTTT
1 TTTCTTTTT
596387 CCCTTTTATT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
56 53 0.87
57 8 0.13
ACGTcount: A:0.19, C:0.17, G:0.16, T:0.48
Consensus pattern (56 bp):
TTTCTTTTTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGCTATG
Found at i:600057 original size:440 final size:438
Alignment explanation
Indices: 598935--600445 Score: 2331
Period size: 437 Copynumber: 3.4 Consensus size: 438
598925 GACCTTTCGG
* * * *
598935 TTGATATCAGGAAAAAGGGGCTGGCCCCTCAA-ATAA--GGGACCTAGAA-AGCTCTAAAGTCTT
1 TTGATATCAAGAAAAAGGGGCTGGCCCCT-AATAAAATGGGGACC-A-AAGGGCTCTAAAATCTT
* * ** * * * * * * *
598996 TTACCCATAGCTCTTCACCGAGGGATATTTTGT-AATAGATTATAGAAGCAAATATGTTTATCTC
63 TAATCTGTAGCCCTTTACTGAGAGATATTTTGTGAA-ATATTATAGAAGCAAATGTGTTTATCTT
* * *
599060 ACAGTTATATATTCAAGCAATGTAATGATTTTATGATATGTTACGTAATTAAGGGTTTTTAGGGG
127 ATAGTTATATATTCAAGCAATGTAATGATTTTATCATGTGTTACGTAATTAAGGGTTTTTAGGGG
* * * *
599125 CCAAAAGTCCAAAATTTCGATCACCCATATCTCACAAAGGAAAAATATTTTGTAATGCAATACAG
192 CCAAAAGTCAAAAAATTCGATCACCCATATCTCAGAAAGGAAAAATATTTTGTAATGCAGTACAG
*
599190 AAGAAAAGTTGTTCAAAATGATGTT-CCTAACAAAATGCAACCGTCAAAATTTCGTTGAACGGCC
257 AAGAAAAGTTGTTCAAAATGATGTTGTC-AACAAAATGCAACCGTCAAAATTTCGTTGAACGGCC
* *
599254 CCTAAAAGGAGAAAAAGGACCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAAAACGGTAACG
321 CCTAAAAGGAGATAAGGGACCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAAAACGGTAACG
* * *
599319 AATTTTTAAACACT-TGTTGAATAAGATTTGTGTAGAATTAAATGACCTTTTAT
386 AATTTCTAAACA-TATGTTGAACAAAATTTGTGTAGAATTAAATGACCTTTTAT
* * * *
599372 TTGATATTAAGAAAAAGGAGCTGGCCCCT--CAAATTAGGGGACCAAAGGGCTCTAAAATCTTTA
1 TTGATATCAAGAAAAAGGGGCTGGCCCCTAATAAAAT-GGGGACCAAAGGGCTCTAAAATCTTTA
*
599435 ATCTGTAGCCCTTTACTGAGAGATATTTTGTGAAATATTACAGAAGCAAATGTGTTTATCTTATA
65 ATCTGTAGCCCTTTACTGAGAGATATTTTGTGAAATATTATAGAAGCAAATGTGTTTATCTTATA
* *
599500 GTTCTGTATTCAAGCAATGTAATGATTTTATCATGTGTTACGTAATTAAGGGTTTTTAGGGGCCA
130 GTTATATATTCAAGCAATGTAATGATTTTATCATGTGTTACGTAATTAAGGGTTTTTAGGGGCCA
* *
599565 AAAGTCAAAAAATTTGAACACCCATATCTCAGAAAGGAAAAATATTTTGTAATGCAGTACAGAAG
195 AAAGTCAAAAAATTCGATCACCCATATCTCAGAAAGGAAAAATATTTTGTAATGCAGTACAGAAG
* *
599630 AAAAGTTGTTCAAAATGATGTTGTCAACAAACTGCAACCGTCAAAATTTCGTTGAACAGCCCCTA
260 AAAAGTTGTTCAAAATGATGTTGTCAACAAAATGCAACCGTCAAAATTTCGTTGAACGGCCCCTA
599695 AAAGGAGATAAGGGACCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAAAACGGTAACGAATT
325 AAAGGAGATAAGGGACCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAAAACGGTAACGAATT
599760 TCTAAACATATGTTGAACAAAATTTGTGTAGAATTAAATGACCTTTTAT
390 TCTAAACATATGTTGAACAAAATTTGTGTAGAATTAAATGACCTTTTAT
*
599809 TTGAAATCAAGAAAAAGGGGCTGGCCCCTAATAAAATGGGAGGACCAAAGGGCTCTAAAATCTTT
1 TTGATATCAAGAAAAAGGGGCTGGCCCCTAATAAAAT-GG-GGACCAAAGGGCTCTAAAATCTTT
*
599874 AATCTGTAGCCCTTTACTGAGAGATATATTGTGAAATATTATAGAAGCAAATGTGTTTATCTTAT
64 AATCTGTAGCCCTTTACTGAGAGATATTTTGTGAAATATTATAGAAGCAAATGTGTTTATCTTAT
* *
599939 AGTTTTGTATTCAAGCAATGTAATGATTTTATCATGTGTTACGTAATTAAGGGTTTTTAGGGGCC
129 AGTTATATATTCAAGCAATGTAATGATTTTATCATGTGTTACGTAATTAAGGGTTTTTAGGGGCC
* * *
600004 AAAAGTAAAAAAATTCGATCACCCATATCTCAGAAAGGAAAAATATTTTGTAATGCAGTATAAAA
194 AAAAGTCAAAAAATTCGATCACCCATATCTCAGAAAGGAAAAATATTTTGTAATGCAGTACAGAA
*
600069 GAAAAGTTGTTCAAAATGATGTTGTCAACAAATTGCAACCGTCAAAATTTCGTTGAACGGCCCCT
259 GAAAAGTTGTTCAAAATGATGTTGTCAACAAAATGCAACCGTCAAAATTTCGTTGAACGGCCCCT
600134 AAAAGGAGATAAGGGACCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAAAACGGTAACGAAT
324 AAAAGGAGATAAGGGACCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAAAACGGTAACGAAT
* * *
600199 TTCTAAACATATGTTGAACAAAAATTTGTTTAGAATTTAATGACCTTTCAT
389 TTCTAAACATATGTTGAAC-AAAATTTGTGTAGAATTAAATGACCTTTTAT
** *
600250 TCCATATCAAGAAAAAGGGGCTGGCCCCTAATAAAAT-GGGACCAAAGGGCTCTAAAGTCTTTAA
1 TTGATATCAAGAAAAAGGGGCTGGCCCCTAATAAAATGGGGACCAAAGGGCTCTAAAATCTTTAA
* * *
600314 TCTGTATCCCTTTACTGAGAAATATTTTGTGAAATGTTATAGAAGCAAATGTGTTTATCTTATAG
66 TCTGTAGCCCTTTACTGAGAGATATTTTGTGAAATATTATAGAAGCAAATGTGTTTATCTTATAG
* * *
600379 TTATATATTAAAGCAATGTAATGATTTTATCACGTGTCACGTAATTAAGGGTTTTTAGGGGCCAA
131 TTATATATTCAAGCAATGTAATGATTTTATCATGTGTTACGTAATTAAGGGTTTTTAGGGGCCAA
600444 AA
196 AA
600446 ATTTTCTAAA
Statistics
Matches: 992, Mismatches: 70, Indels: 23
0.91 0.06 0.02
Matches are distributed among these distances:
435 2 0.00
436 3 0.00
437 403 0.41
438 157 0.16
439 7 0.01
440 358 0.36
441 62 0.06
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (438 bp):
TTGATATCAAGAAAAAGGGGCTGGCCCCTAATAAAATGGGGACCAAAGGGCTCTAAAATCTTTAA
TCTGTAGCCCTTTACTGAGAGATATTTTGTGAAATATTATAGAAGCAAATGTGTTTATCTTATAG
TTATATATTCAAGCAATGTAATGATTTTATCATGTGTTACGTAATTAAGGGTTTTTAGGGGCCAA
AAGTCAAAAAATTCGATCACCCATATCTCAGAAAGGAAAAATATTTTGTAATGCAGTACAGAAGA
AAAGTTGTTCAAAATGATGTTGTCAACAAAATGCAACCGTCAAAATTTCGTTGAACGGCCCCTAA
AAGGAGATAAGGGACCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAAAACGGTAACGAATTT
CTAAACATATGTTGAACAAAATTTGTGTAGAATTAAATGACCTTTTAT
Found at i:607632 original size:14 final size:14
Alignment explanation
Indices: 607613--607687 Score: 60
Period size: 16 Copynumber: 4.9 Consensus size: 14
607603 TTTTAAATAT
*
607613 GAGAGAGAGACAGA
1 GAGAGACAGACAGA
607627 GAGAGACAGACAGACA
1 GAGAGACAGACAG--A
*
607643 GACAGACAGACAGACA
1 GAGAGACAGACAG--A
*
607659 GACAGACAGACAGACA
1 GAGAGACAGACAG--A
*
607675 GACAGACAGACAG
1 GAGAGACAGACAG
607688 GCTTTGGTTA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
14 12 0.21
16 45 0.79
ACGTcount: A:0.49, C:0.20, G:0.31, T:0.00
Consensus pattern (14 bp):
GAGAGACAGACAGA
Found at i:607637 original size:4 final size:4
Alignment explanation
Indices: 607630--607687 Score: 116
Period size: 4 Copynumber: 14.5 Consensus size: 4
607620 AGACAGAGAG
607630 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC
607678 AGAC AGAC AG
1 AGAC AGAC AG
607688 GCTTTGGTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.50, C:0.24, G:0.26, T:0.00
Consensus pattern (4 bp):
AGAC
Found at i:609612 original size:87 final size:87
Alignment explanation
Indices: 609466--609642 Score: 318
Period size: 87 Copynumber: 2.0 Consensus size: 87
609456 TTTAAAGTTA
*
609466 TTTGATAATATTCACTCGCAGACCAGTGCATATTTATTAACATACAAATAATACTAGTTCATAAA
1 TTTGATAATATTCACTCGCAGACCAGTGCATATTAATTAACATACAAATAATACTAGTTCATAAA
*
609531 AAGGGCATATGCCAACAAAGTG
66 AAGGGCATATGCCAACAAAGCG
* *
609553 TTTGATAATATTTACTCGCAGACCAGTGCATATTAATTAACATACAAATAATACTAGTTCATTAA
1 TTTGATAATATTCACTCGCAGACCAGTGCATATTAATTAACATACAAATAATACTAGTTCATAAA
609618 AAGGGCATATGCCAACAAAGCG
66 AAGGGCATATGCCAACAAAGCG
609640 TTT
1 TTT
609643 TAATTACAAC
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.30
Consensus pattern (87 bp):
TTTGATAATATTCACTCGCAGACCAGTGCATATTAATTAACATACAAATAATACTAGTTCATAAA
AAGGGCATATGCCAACAAAGCG
Found at i:612038 original size:15 final size:15
Alignment explanation
Indices: 612020--612048 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
612010 AAATGTTTCC
612020 AAAAAAAAAAAGAAA
1 AAAAAAAAAAAGAAA
612035 AAAAAAAAAAAGAA
1 AAAAAAAAAAAGAA
612049 GAGAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAGAAA
Found at i:616442 original size:2 final size:2
Alignment explanation
Indices: 616435--616490 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
616425 TCAGTGCCTT
*
616435 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TA TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
616477 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
616491 AATATTTGAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.02, C:0.48, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:624035 original size:9 final size:9
Alignment explanation
Indices: 624021--624060 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
624011 AACTGTTGCA
624021 CATGAGCCT
1 CATGAGCCT
*
624030 CATGAGTCT
1 CATGAGCCT
*
624039 CATAAGCCT
1 CATGAGCCT
624048 CATGAGCCT
1 CATGAGCCT
624057 CATG
1 CATG
624061 TGAGCAAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (9 bp):
CATGAGCCT
Found at i:624341 original size:21 final size:21
Alignment explanation
Indices: 624315--624359 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
624305 TTCTCAACTC
*
624315 TCAGGAATTGTAAGCGAGATT
1 TCAGGAAATGTAAGCGAGATT
624336 TCAGGAAATGTAAGCGAGATT
1 TCAGGAAATGTAAGCGAGATT
624357 TCA
1 TCA
624360 AAATCTGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.27
Consensus pattern (21 bp):
TCAGGAAATGTAAGCGAGATT
Found at i:624781 original size:4 final size:4
Alignment explanation
Indices: 624759--624808 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
624749 ATCACATTTT
* * *
624759 GTCC GT-C GTCC GTCT GTCC GTCC GTCT GTCC GTCT GTCC GTCC GTCC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC
624806 GTC
1 GTC
624809 TGTAAACTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 3 0.08
4 36 0.92
ACGTcount: A:0.00, C:0.42, G:0.26, T:0.32
Consensus pattern (4 bp):
GTCC
Found at i:624782 original size:12 final size:12
Alignment explanation
Indices: 624765--624811 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
624755 TTTTGTCCGT
624765 CGTCCGTCTGTC
1 CGTCCGTCTGTC
624777 CGTCCGTCTGTC
1 CGTCCGTCTGTC
* *
624789 CGTCTGTCCGTC
1 CGTCCGTCTGTC
624801 CGTCCGTCTGT
1 CGTCCGTCTGT
624812 AAACTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.00, C:0.40, G:0.26, T:0.34
Consensus pattern (12 bp):
CGTCCGTCTGTC
Found at i:626454 original size:167 final size:166
Alignment explanation
Indices: 626022--627266 Score: 1624
Period size: 166 Copynumber: 7.5 Consensus size: 166
626012 AGCTCACCTG
*
626022 AGGGTGGGGCCACGATGGGGGGTCGAAGTTTAACATAGGAA-A-ATAGAGTAAATCTTTAAAAAT
1 AGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAAT
* * * **
626085 CTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAACCTTGTGTGAAAGCATCATCAGGTAAAGT
66 CTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGT
* * * *
626150 AGATACACATTTGTGAAAATCAA-GACCCCCGGAGGT
131 AGATTCAAAGTTGTGAAAAT-AATGACCCCCGGGGGT
** * * *
626186 AGGGTGGGGCCACAATGAAGGATCGAAGTTTTACATAGGAATATATAGAGTAAATCTATAAAAAT
1 AGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAAT
* * * * *
626251 CTTCTTCTCAGAAACTAATCGGCAAGGATAGCTGACACTTGTGTGGAAGCATTCC-CATGTAGTG
66 CTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCA-TCCTCAGGTAGTG
*
626315 TAGAATCAAAGTTGTGAAAATAATGACCCCCGGGGGT
130 TAGATTCAAAGTTGTGAAAATAATGACCCCCGGGGGT
* * * *
626352 AGGGTGGGGCCACAATGGGGGGGTCAAAGTTTAACATATGAATGTATAAAGTAAATCTTTAAAAA
1 AGGGTGGGGCCACAAT-GGGGGGTCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAA
* * * *
626417 TCTTCTTCTCAGAAACTAATCGGCCAGGAAAGCTGACACTTGTGT-G--G-AT--GCAGGTGGTG
65 TCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTG
* * *
626476 TCA-ATTCAAAGTCGTGAAAATCATGA-CCCCTGGGGT
130 T-AGATTCAAAGTTGTGAAAATAATGACCCCCGGGGGT
* * ** * * *
626512 ACGGTGGGGTCACAATGGTTGGTTGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAGAT
1 AGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAAT
*
626577 CTTCTTCTCAGAAACTAATCGGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGT
66 CTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGT
* * *
626642 AGATTCATAGTTGTGAAAATCATGACCCCCGCGGGT
131 AGATTCAAAGTTGTGAAAATAATGACCCCCGGGGGT
* * *
626678 AGGGTGGGGCCACAATGGGGGGATCGATGTTTAACATAGGAGTTATATAGAGTAAATCTTAAAAA
1 AGGGTGGGGCCACAATGGGGGG-TCGAAGTTTAACATAGGA-ATATATAGAGTAAATCTTTAAAA
* *
626743 ATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGACACTTGTGTGGATGCATCCTCAGGTAGT
64 ATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGT
* * *
626808 GTAAATTTCAAAGTTGTGCAAATCATGACCCCCGGGGGT
129 GTAGA-TTCAAAGTTGTGAAAATAATGACCCCCGGGGGT
* *
626847 AGGGTGGGGCCACAATGGGAGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAAT
1 AGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAAT
* *
626912 CTTCTTCTCAGAAACTAATCAG-CTGGCAATGCTGAAACTTGT-TCGGAAGCATCCTCAGGTAGT
66 CTTCTTCTCAGAAACTAATCAGCCAGG-AAAGCTGAAACTTGTGT-GGAAGCATCCTCAGGTAGT
* **
626975 GTAGATTCAAAGTTGTGAAAATAATAACCCCTTGGGGT
129 GTAGATTCAAAGTTGTGAAAATAATGACCCCCGGGGGT
*** * * * * *
627013 AAAATGGGGCCACAATGGGAGGTCGATGTTTTACATAGGAATACACAGAGTAAATCTTTAAAAAT
1 AGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAAT
* * *
627078 CTTCTTCTCAGAAACTTATCAACCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGT
66 CTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGT
*
627143 AGATTCAAAGTTGTGAAAATAATGACCCCCAGGGGT
131 AGATTCAAAGTTGTGAAAATAATGACCCCCGGGGGT
* * * *
627179 AGGGTGAGGCCACAATGGGGGGTCAAAGTTTAACAAAGGAATATATAGGGTAAATCTTTAAAAA-
1 AGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAAT
627243 --TCTTCTCAGAAACTAATCAGCCAG
66 CTTCTTCTCAGAAACTAATCAGCCAG
627267 ATGATTCTTT
Statistics
Matches: 941, Mismatches: 118, Indels: 45
0.85 0.11 0.04
Matches are distributed among these distances:
159 83 0.09
160 24 0.03
161 28 0.03
162 3 0.00
163 25 0.03
164 38 0.04
165 33 0.04
166 371 0.39
167 183 0.19
168 103 0.11
169 50 0.05
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (166 bp):
AGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAAT
CTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGT
AGATTCAAAGTTGTGAAAATAATGACCCCCGGGGGT
Found at i:626669 original size:326 final size:328
Alignment explanation
Indices: 626022--627266 Score: 1568
Period size: 326 Copynumber: 3.8 Consensus size: 328
626012 AGCTCACCTG
* * *
626022 AGGGTGGGGCCACGATGGGGGGTCGAAGTTTAACATAGGAA-AATAGAGTAAATCTTTAAAAATC
1 AGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACATAGGAATTATAAAGTAAATCTTTAAAAATC
* **
626086 TTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGA-ACCTTGTGTGAAAGCATCATCAGGTAAAGT
66 TTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGACA-CTTGTGTG--AGCATC-GCAGGTAGTGT
* * * * *
626150 AGATACACATTTGTGAAAATCAAGACCCCC-GGAGGTAGGGTGGGGCCACAAT-GAAGGATCGAA
127 AGATTCAAAGTTGTGAAAATCATGACCCCCAGG-GGTAGGGTGGGGCCACAATGGGAGG-TCGAA
* * * *
626213 GTTTTACATAGGAATATATAGAGTAAATCTATAAAAATCTTCTTCTCAGAAACTAATCGGCAAGG
190 GTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGG
* * * *
626278 ATAGCTGACACTTGTGTGGAAGCATTCC-CATGTAGTGTAGAATCAAAGTTGTGAAAATAATGAC
255 AAAGCTGAAACTTGTGTGGAAGCA-TCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATAATGAC
626342 CCCCGGGGGT
319 CCCCGGGGGT
* *
626352 AGGGTGGGGCCACAATGGGGGGGTCAAAGTTTAACATATGAATGTATAAAGTAAATCTTTAAAAA
1 AGGGTGGGGCCACAAT-GGGGGGTCGAAGTTTAACATAGGAAT-TATAAAGTAAATCTTTAAAAA
* *
626417 TCTTCTTCTCAGAAACTAATCGGCCAGGAAAGCTGACACTTGTGTG-G-AT-GCAGGTGGTGTCA
64 TCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGACACTTGTGTGAGCATCGCAGGTAGTGT-A
* * * * ** *
626479 -ATTCAAAGTCGTGAAAATCATGA-CCCCTGGGGTACGGTGGGGTCACAATGGTTGGTTGAAGTT
128 GATTCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGGGTGGGGCCACAATGGGAGGTCGAAGTT
* * *
626542 TTACATAGGAATATATAGAGTAAATCTTTAAAGATCTTCTTCTCAGAAACTAATCGGCCAGGAAA
193 TAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAA
* *
626607 GCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCATAGTTGTGAAAATCATGACCCCC
258 GCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATAATGACCCCC
*
626672 GCGGGT
323 GGGGGT
* * *
626678 AGGGTGGGGCCACAATGGGGGGATCGATGTTTAACATAGGAGTTATATAGAGTAAATCTTAAAAA
1 AGGGTGGGGCCACAATGGGGGG-TCGAAGTTTAACATAGGAATTATA-A-AGTAAATCTTTAAAA
*
626743 ATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGACACTTGTGTGGATGCATCCTCAGGTAGT
63 ATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGACACTTGTGT-GA-GCAT-CGCAGGTAGT
* * * *
626808 GTAAATTTCAAAGTTGTGCAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGAGATCGA
125 GTAGA-TTCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGGGTGGGGCCACAATGGGAGGTCGA
*
626873 AGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG-CTG
189 AGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAG
* *
626937 GCAATGCTGAAACTTGT-TCGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATAATA
254 G-AAAGCTGAAACTTGTGT-GGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATAATG
**
627001 ACCCCTTGGGGT
317 ACCCCCGGGGGT
*** * * * *
627013 AAAATGGGGCCACAATGGGAGGTCGATGTTTTACATAGGAA-TACACAGAGTAAATCTTTAAAAA
1 AGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACATAGGAATTATA-A-AGTAAATCTTTAAAAA
* * * *
627077 TCTTCTTCTCAGAAACTTATCAACCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTG
64 TCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGACACTTGTGTG--AGCAT-CGCAGGTAGTG
* * * *
627142 TAGATTCAAAGTTGTGAAAATAATGACCCCCAGGGGTAGGGTGAGGCCACAATGGGGGGTCAAAG
126 TAGATTCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGGGTGGGGCCACAATGGGAGGTCGAAG
* *
627207 TTTAACAAAGGAATATATAGGGTAAATCTTTAAAAA---TCTTCTCAGAAACTAATCAGCCAG
191 TTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAG
627267 ATGATTCTTT
Statistics
Matches: 809, Mismatches: 81, Indels: 50
0.86 0.09 0.05
Matches are distributed among these distances:
325 13 0.02
326 183 0.23
327 89 0.11
328 2 0.00
329 22 0.03
330 19 0.02
331 25 0.03
332 90 0.11
333 153 0.19
334 43 0.05
335 170 0.21
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (328 bp):
AGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACATAGGAATTATAAAGTAAATCTTTAAAAATC
TTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGACACTTGTGTGAGCATCGCAGGTAGTGTAGAT
TCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGGGTGGGGCCACAATGGGAGGTCGAAGTTTAA
CATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCT
GAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATAATGACCCCCGGG
GGT
Found at i:629885 original size:11 final size:11
Alignment explanation
Indices: 629869--629909 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
629859 TATTTAACAC
629869 ATGTTTTACAT
1 ATGTTTTACAT
*
629880 ATGTTTTACGT
1 ATGTTTTACAT
*
629891 ATGTTTAACAT
1 ATGTTTTACAT
629902 ATGGTTTT
1 AT-GTTTT
629910 TATTTTAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 21 0.84
12 4 0.16
ACGTcount: A:0.24, C:0.07, G:0.15, T:0.54
Consensus pattern (11 bp):
ATGTTTTACAT
Found at i:631400 original size:13 final size:15
Alignment explanation
Indices: 631382--631413 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
631372 TTAATGTGTG
631382 ATTTAACT-ACT-GT
1 ATTTAACTCACTGGT
631395 ATTTAACTCACTGGT
1 ATTTAACTCACTGGT
631410 ATTT
1 ATTT
631414 CATTTACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 3 0.18
15 6 0.35
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (15 bp):
ATTTAACTCACTGGT
Found at i:632088 original size:13 final size:11
Alignment explanation
Indices: 632056--632091 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
632046 TAAAAAAACC
*
632056 ACACATGAATA
1 ACACATGTATA
632067 ACACATGTATA
1 ACACATGTATA
*
632078 ACACATGTGTA
1 ACACATGTATA
632089 ACA
1 ACA
632092 TATGGGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.22
Consensus pattern (11 bp):
ACACATGTATA
Found at i:635052 original size:14 final size:14
Alignment explanation
Indices: 635033--635061 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
635023 CCCCCCCCCC
635033 AAAAAAAAAAGAAG
1 AAAAAAAAAAGAAG
635047 AAAAAAAAAAGAAG
1 AAAAAAAAAAGAAG
635061 A
1 A
635062 GAAATTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGAAG
Found at i:635054 original size:16 final size:16
Alignment explanation
Indices: 635033--635065 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
635023 CCCCCCCCCC
635033 AAAAAAAAAAG-A-AG
1 AAAAAAAAAAGAAGAG
635047 AAAAAAAAAAGAAGAG
1 AAAAAAAAAAGAAGAG
635063 AAA
1 AAA
635066 TTACTAACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 11 0.65
15 1 0.06
16 5 0.29
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAGAAGAG
Found at i:637346 original size:2 final size:2
Alignment explanation
Indices: 637339--637400 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
637329 AGTTGATTTT
*
637339 GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
637381 GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA
637401 TTATGCAGGT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:643586 original size:21 final size:21
Alignment explanation
Indices: 643560--643651 Score: 114
Period size: 21 Copynumber: 4.4 Consensus size: 21
643550 TTCTGCCATC
* *
643560 ACTTGTCAGATAATCATGTCG
1 ACTTGTCAGATCATTATGTCG
643581 ACTTGTCAGATC-TTGATGTCG
1 ACTTGTCAGATCATT-ATGTCG
* *
643602 ACTTGTCAGATGATTATGTTG
1 ACTTGTCAGATCATTATGTCG
*
643623 ACTTGTCAGATCTTTATGTCG
1 ACTTGTCAGATCATTATGTCG
*
643644 AATTGTCA
1 ACTTGTCA
643652 CTTATTCACA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
20 1 0.02
21 58 0.95
22 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (21 bp):
ACTTGTCAGATCATTATGTCG
Found at i:643626 original size:42 final size:42
Alignment explanation
Indices: 643560--643651 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
643550 TTCTGCCATC
643560 ACTTGTCAGATAATCATGTCGACTTGTCAGATCTTGATGTCG
1 ACTTGTCAGATAATCATGTCGACTTGTCAGATCTTGATGTCG
* * * *
643602 ACTTGTCAGATGATTATGTTGACTTGTCAGATCTTTATGTCG
1 ACTTGTCAGATAATCATGTCGACTTGTCAGATCTTGATGTCG
*
643644 AATTGTCA
1 ACTTGTCA
643652 CTTATTCACA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (42 bp):
ACTTGTCAGATAATCATGTCGACTTGTCAGATCTTGATGTCG
Found at i:643755 original size:21 final size:21
Alignment explanation
Indices: 643729--643887 Score: 171
Period size: 21 Copynumber: 7.7 Consensus size: 21
643719 CAATTTTTCT
643729 TCTGACAAGTCGACAT-ATGTA
1 TCTGACAAGTCGACATCAT-TA
* *
643750 TCTGACAAGTCGACATTATCA
1 TCTGACAAGTCGACATCATTA
*
643771 TCTGTCAAGTCGACATCATT-
1 TCTGACAAGTCGACATCATTA
* * *
643791 TTTGACATGTCGACATAATTA
1 TCTGACAAGTCGACATCATTA
*
643812 TCTGACAAGTCAACATCATTA
1 TCTGACAAGTCGACATCATTA
* * *
643833 TTTGACAAGACGACAT-AATA
1 TCTGACAAGTCGACATCATTA
* * *
643853 TCCGAAAAGTCAACATCATTA
1 TCTGACAAGTCGACATCATTA
643874 TCTGACAAGTCGAC
1 TCTGACAAGTCGAC
643888 TTATAATATG
Statistics
Matches: 110, Mismatches: 25, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
20 30 0.27
21 78 0.71
22 2 0.02
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.29
Consensus pattern (21 bp):
TCTGACAAGTCGACATCATTA
Found at i:643804 original size:41 final size:41
Alignment explanation
Indices: 643729--643896 Score: 187
Period size: 41 Copynumber: 4.0 Consensus size: 41
643719 CAATTTTTCT
* *
643729 TCTGACAAGTCGACAT-ATGTATCTGACAAGTCGACATTATCA
1 TCTGACAAGTCAACATCAT-TATCTGACAAGTCGACATAAT-A
* * * *
643771 TCTGTCAAGTCGACATCATT-TTTGACATGTCGACATAATTA
1 TCTGACAAGTCAACATCATTATCTGACAAGTCGACATAA-TA
* *
643812 TCTGACAAGTCAACATCATTATTTGACAAGACGACATAATA
1 TCTGACAAGTCAACATCATTATCTGACAAGTCGACATAATA
* *
643853 TCCGAAAAGTCAACATCATTATCTGACAAGTCGACTTATAATA
1 TCTGACAAGTCAACATCATTATCTGACAAGTCGAC--ATAATA
643896 T
1 T
643897 GAATGATAAT
Statistics
Matches: 109, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
41 67 0.61
42 33 0.30
43 9 0.08
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (41 bp):
TCTGACAAGTCAACATCATTATCTGACAAGTCGACATAATA
Found at i:643847 original size:62 final size:61
Alignment explanation
Indices: 643729--643884 Score: 168
Period size: 62 Copynumber: 2.5 Consensus size: 61
643719 CAATTTTTCT
* * * * * *
643729 TCTGACAAGTCGACATATGTATCTGACAAGTCGACATTATCATCTGTCAAGTCGACATCATT
1 TCTGACAAGTCGACATAT-TATCTGACAAGTCAACATCATCATCTGACAAGACGACATAATA
* * * *
643791 TTTGACATGTCGACATAATTATCTGACAAGTCAACATCATTATTTGACAAGACGACATAATA
1 TCTGACAAGTCGACAT-ATTATCTGACAAGTCAACATCATCATCTGACAAGACGACATAATA
* * *
643853 TCCGAAAAGTCAACATCATTATCTGACAAGTC
1 TCTGACAAGTCGACAT-ATTATCTGACAAGTC
643885 GACTTATAAT
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
62 75 0.97
63 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.29
Consensus pattern (61 bp):
TCTGACAAGTCGACATATTATCTGACAAGTCAACATCATCATCTGACAAGACGACATAATA
Found at i:643962 original size:21 final size:21
Alignment explanation
Indices: 643938--644025 Score: 160
Period size: 21 Copynumber: 4.2 Consensus size: 21
643928 CTGTCAAATC
*
643938 ATTATGTCGACTTGTCATATG
1 ATTATGTCGACTTGTCAGATG
643959 ATTATGTCGACTTGTCAGATG
1 ATTATGTCGACTTGTCAGATG
643980 ATTATGTCGACTTGTCAGATG
1 ATTATGTCGACTTGTCAGATG
644001 ATTATGTCGACTTGTCAGAT-
1 ATTATGTCGACTTGTCAGATG
644021 ATTAT
1 ATTAT
644026 AATGACAAGT
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
20 5 0.08
21 61 0.92
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (21 bp):
ATTATGTCGACTTGTCAGATG
Found at i:644131 original size:21 final size:21
Alignment explanation
Indices: 644105--644198 Score: 82
Period size: 21 Copynumber: 4.5 Consensus size: 21
644095 ATGATAATTT
* *
644105 TCTGACAAGTCAACGTAAAGA
1 TCTGACAAGTCAACATAAATA
** *
644126 TCTGACAAGTTGATATAAATA
1 TCTGACAAGTCAACATAAATA
*
644147 TCTGACAAGTCGACAT-AATCA
1 TCTGACAAGTCAACATAAAT-A
* * * *
644168 TTTGACAAGTCAGCTTAATTA
1 TCTGACAAGTCAACATAAATA
644189 TCTGACAAGT
1 TCTGACAAGT
644199 GGTGGCAGAT
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
20 3 0.05
21 53 0.91
22 2 0.03
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (21 bp):
TCTGACAAGTCAACATAAATA
Found at i:645729 original size:65 final size:64
Alignment explanation
Indices: 645647--646295 Score: 927
Period size: 65 Copynumber: 10.1 Consensus size: 64
645637 GAAGTGATAA
*
645647 TATGATCTGACACTCCAGATCACCACACTGTGGATTACTTCTCTCTGTTCCTGATGACATGATGG
1 TATGATCTGACACTCCAGATCACCACTCTGTGG-TTACTTCTCTCTGTTCCTGATGACATGATGG
**
645712 TATGATCTGACACTCCAGATCACCACTCTGTGGCTTAGATCTCTCTGTTCCTGATGACATGATGG
1 TATGATCTGACACTCCAGATCACCACTCTGTGG-TTACTTCTCTCTGTTCCTGATGACATGATGG
* *
645777 TATGATCTGACACTCCAGATCACCACTCTGTGGTTAACTTATCTCTGTTCCTGATGACATGATAG
1 TATGATCTGACACTCCAGATCACCACTCTGTGGTT-ACTTCTCTCTGTTCCTGATGACATGATGG
* *
645842 TATGATCTGACACTCCAGATCACCACACTGTGGATTACTTATCTCTGTTCCTGATGACATGATGG
1 TATGATCTGACACTCCAGATCACCACTCTGTGG-TTACTTCTCTCTGTTCCTGATGACATGATGG
* * * *
645907 TATGAACTGACACTCCAGATCACCACTCTGCGGATTACTTATCTCTGTTCCTGATGACCTGATGG
1 TATGATCTGACACTCCAGATCACCACTCTGTGG-TTACTTCTCTCTGTTCCTGATGACATGATGG
* *
645972 TATGAGCTGACACTCCAGATCACCACTCTGTGGTT--TACTCTCTGTTCCTGATGACATGATGG
1 TATGATCTGACACTCCAGATCACCACTCTGTGGTTACTTCTCTCTGTTCCTGATGACATGATGG
* * * *
646034 TATGAACTGACACTCCAGATCACCACACTGTGGCTTACTTCTATCTGTTCAT-ATGACATGATGG
1 TATGATCTGACACTCCAGATCACCACTCTGTGG-TTACTTCTCTCTGTTCCTGATGACATGATGG
* *
646098 TATGAACTGACACTCCAGATCACCACTCTGTGGTT--TACTCTCTGTTCCTGATGACATGATGG
1 TATGATCTGACACTCCAGATCACCACTCTGTGGTTACTTCTCTCTGTTCCTGATGACATGATGG
* * * *
646160 TATGAACTGACACTCCAGATCAACACTCTGTGGTTAACTTATTTCTGTTCCTGATGACATGATGG
1 TATGATCTGACACTCCAGATCACCACTCTGTGGTT-ACTTCTCTCTGTTCCTGATGACATGATGG
* * *
646225 TATAATCTGACACTCCAGATCACCATTCTGTGGTTTAC-TCTCT-T-TTACTGATGACATGATGG
1 TATGATCTGACACTCCAGATCACCACTCTGTGG-TTACTTCTCTCTGTTCCTGATGACATGATGG
*
646287 TATAATCTG
1 TATGATCTG
646296 TCTATATGAT
Statistics
Matches: 535, Mismatches: 39, Indels: 23
0.90 0.07 0.04
Matches are distributed among these distances:
61 11 0.02
62 127 0.24
63 5 0.01
64 51 0.10
65 337 0.63
66 4 0.01
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (64 bp):
TATGATCTGACACTCCAGATCACCACTCTGTGGTTACTTCTCTCTGTTCCTGATGACATGATGG
Found at i:651143 original size:2 final size:2
Alignment explanation
Indices: 651136--651181 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
651126 TTAGTAAAGT
651136 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
651178 GA GA
1 GA GA
651182 NNNNNNNNNN
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:651855 original size:19 final size:19
Alignment explanation
Indices: 651831--651874 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
651821 GAGAGAGAGA
651831 GAGAGAGAGAAGAACCAGG
1 GAGAGAGAGAAGAACCAGG
* **
651850 GAGAGAGGGAAGGGCCAGG
1 GAGAGAGAGAAGAACCAGG
651869 GAGAGA
1 GAGAGA
651875 AAAAGAAGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.50, T:0.00
Consensus pattern (19 bp):
GAGAGAGAGAAGAACCAGG
Found at i:651856 original size:2 final size:2
Alignment explanation
Indices: 651811--651840 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
651801 NNNNNNNNNN
651811 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
651841 AGAACCAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:656470 original size:18 final size:18
Alignment explanation
Indices: 656447--656482 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
656437 GTCCCACTCT
656447 GCGGGTGCCCTATAGTGA
1 GCGGGTGCCCTATAGTGA
*
656465 GCGGGTTCCCTATAGTGA
1 GCGGGTGCCCTATAGTGA
656483 TCAGTCTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.22, G:0.36, T:0.25
Consensus pattern (18 bp):
GCGGGTGCCCTATAGTGA
Found at i:659593 original size:43 final size:43
Alignment explanation
Indices: 659532--659623 Score: 166
Period size: 43 Copynumber: 2.1 Consensus size: 43
659522 AGCGAAGATG
*
659532 AGTAAATGATGGTTGAATGACATCTTAGAATAGACCCCCACAC
1 AGTAAAAGATGGTTGAATGACATCTTAGAATAGACCCCCACAC
*
659575 AGTAAAAGATGGTTGAATGACATCTTAGAATAGACCCCCTCAC
1 AGTAAAAGATGGTTGAATGACATCTTAGAATAGACCCCCACAC
659618 AGTAAA
1 AGTAAA
659624 TGCGGTACTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (43 bp):
AGTAAAAGATGGTTGAATGACATCTTAGAATAGACCCCCACAC
Found at i:661349 original size:1 final size:1
Alignment explanation
Indices: 661345--661393 Score: 62
Period size: 1 Copynumber: 49.0 Consensus size: 1
661335 AATAAATTAT
* * * *
661345 AAAAAAACAAAAAATAAAAAAAAAAATAAAAAAAAAATAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
661394 GTCCCACTTG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.92, C:0.02, G:0.00, T:0.06
Consensus pattern (1 bp):
A
Found at i:661359 original size:18 final size:17
Alignment explanation
Indices: 661328--661381 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 17
661318 TTGTTCCTTG
*
661328 AAAAAGAAATAAATTATAA
1 AAAAACAAATAAA-TA-AA
661347 AAAAACAAA-AAATAAA
1 AAAAACAAATAAATAAA
661363 AAAAA-AAATAAA-AAA
1 AAAAACAAATAAATAAA
661378 AAAA
1 AAAA
661382 TAAAAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 10 0.30
16 10 0.30
17 2 0.06
18 3 0.09
19 8 0.24
ACGTcount: A:0.85, C:0.02, G:0.02, T:0.11
Consensus pattern (17 bp):
AAAAACAAATAAATAAA
Done.