Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008238.1 Hibiscus syriacus cultivar Beakdansim tig00110885_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 622934
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 3 of 3
Found at i:514108 original size:64 final size:64
Alignment explanation
Indices: 513981--514100 Score: 204
Period size: 64 Copynumber: 1.9 Consensus size: 64
513971 TATGTTATAT
*
513981 CATTTAACCGGAAATATTATCAAGCAGAATAACATATTAGGTAGCACTTATATAATAAAATAGG
1 CATTTAACCGGAAATATTATCAAGCAGAATAACAAATTAGGTAGCACTTATATAATAAAATAGG
* * *
514045 CATTTAACCGGAAATATTATCAAGTATAATAACAAATTAGGTAGCGCTTATATAAT
1 CATTTAACCGGAAATATTATCAAGCAGAATAACAAATTAGGTAGCACTTATATAAT
514101 GTAATAGGTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.30
Consensus pattern (64 bp):
CATTTAACCGGAAATATTATCAAGCAGAATAACAAATTAGGTAGCACTTATATAATAAAATAGG
Found at i:516779 original size:26 final size:26
Alignment explanation
Indices: 516750--516802 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
516740 CCCAGTTTTG
516750 TTGATTTGATGTGCCTCCAGAAATAA
1 TTGATTTGATGTGCCTCCAGAAATAA
516776 TTGATTTGATGTGCCTCCAGAAATAA
1 TTGATTTGATGTGCCTCCAGAAATAA
516802 T
1 T
516803 GCAAATGGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (26 bp):
TTGATTTGATGTGCCTCCAGAAATAA
Found at i:517901 original size:176 final size:183
Alignment explanation
Indices: 517607--518354 Score: 574
Period size: 176 Copynumber: 3.9 Consensus size: 183
517597 CTCATAAAAT
* * * *
517607 CGGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTCGATGTTTTTAGGATCGACAC
1 CGGTTACATTGTTATGTTACCTATTACATTATAATTAC-GGTTTCGATGTTTTTGGGATCGACAC
* * * *
517672 TTTTTCTAAATGTATCGACATTTTTTCATGAACTTGTTTGGAAAATCTATTATGGACATAAAGTG
65 TTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATCTATTATGGACATAAAGTG
* ** ***
517737 TCGATAC-AT-TAT-GTATACTTTTTTTTA-ATA-ACC-GGT-AT--ATTTAGAC
130 TCGACACAATGTATAGTAT-CGATACATTATATATACCTGGTAATAAATTTAGAC
517783 CGGTTACATTGTTATGTTACCTATTACATTATAATTACGAGTTTCGATGTTTTTGGGATCGACAC
1 CGGTTACATTGTTATGTTACCTATTACATTATAATTACG-GTTTCGATGTTTTTGGGATCGACAC
*
517848 TTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTG
65 TTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATCTATTATGGACATAAAGTG
* **
517913 TCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTTAATAACCGGTATATTTA
130 TCGACAC-AATGTAT--AGTATCGATACATTATATATACC----TGGTAAT-A-----A-ATTTA
517978 GAC
181 GAC
*
517981 CGGTTACATTGTTATGTTACCTA-TACATTATAATTACTGGTTTCGATGTTTTTGGGATCTACAC
1 CGGTTACATTGTTATGTTACCTATTACATTATAATTAC-GGTTTCGATGTTTTTGGGATCGACAC
* *
518045 TTGTTATAAATGTATCAACACTTTTTCGTGAACTTGTTTGG-AAATAC-ATTCTGG--ATAACAT
65 TTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAAT-CTATTATGGACATAA-A-
* * * * ** **
518106 GTATCGACACAAATGAATAAAGTGTCGATACATATTGTAGACCTATTTTCTCATAAAATCGGTAA
127 GTGTCGACAC-AATG--TATAGTATCGATAC--A-T-TATA--TA-TACCTGGT--AA----TAA
*
518171 ATTTAAAC
176 ATTTAGAC
* * * *
518179 CGGTTACATTGTAAAGTGACCTATTACATTATAGTTACGGGTTTCGATGTTTTTGGGATCGACAC
1 CGGTTACATTGTTATGTTACCTATTACATTATAATTAC-GGTTTCGATGTTTTTGGGATCGACAC
* * *
518244 TTGATATAAATGTATCAACACTTATTT-GTGAACTTTTTTTGGTTGGAAAATAC-ATTATGGACA
65 TTGTTATAAATGTATCGACACTT-TTTCGTGAAC-----TTGTTTGGAAAAT-CTATTATGGACA
* * ** *
518307 CAAAGTATCGACACAAATGTATAAAGTGCCGATACATTATGTATACCT
123 TAAAGTGTCGACAC-AATGTAT--AGTATCGATACATTATATATACCT
518355 CTTTTCTCAT
Statistics
Matches: 469, Mismatches: 48, Indels: 88
0.78 0.08 0.15
Matches are distributed among these distances:
175 1 0.00
176 125 0.27
178 2 0.00
179 3 0.01
181 5 0.01
182 6 0.01
183 3 0.01
188 1 0.00
189 2 0.00
194 4 0.01
195 1 0.00
196 34 0.07
197 78 0.17
198 65 0.14
199 72 0.15
200 5 0.01
201 4 0.01
202 3 0.01
203 5 0.01
204 8 0.02
205 38 0.08
206 1 0.00
207 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (183 bp):
CGGTTACATTGTTATGTTACCTATTACATTATAATTACGGTTTCGATGTTTTTGGGATCGACACT
TGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATCTATTATGGACATAAAGTGT
CGACACAATGTATAGTATCGATACATTATATATACCTGGTAATAAATTTAGAC
Found at i:518010 original size:197 final size:197
Alignment explanation
Indices: 517729--518375 Score: 878
Period size: 197 Copynumber: 3.2 Consensus size: 197
517719 TATTATGGAC
517729 ATAAAGTGTCGATACATTATGTATA-CTTTTTTTTAATAACCGGTATATTTAGACCGGTTACATT
1 ATAAAGTGTCGATACATTATGTATACCTTTTTTTTAATAACCGGTATATTTAGACCGGTTACATT
517793 GTTATGTTACCTATTACATTATAATTACGAGTTTCGATGTTTTTGGGATCGACACTTGTTATAAA
66 GTTATGTTACCTATTACATTATAATTACG-GTTTCGATGTTTTTGGGATCGACACTTGTTATAAA
* ** *
517858 TGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTCGACACAAA
130 TGTATCAACACTTTTTCGTGAACTTGTTTGGAAAATACATTATGGACATAAAGTATCGACACAAA
517923 TGT
195 TGT
*
517926 ATAAAGTATCGATACATTATGTATACCTTTTTTTTAATAACCGGTATATTTAGACCGGTTACATT
1 ATAAAGTGTCGATACATTATGTATACCTTTTTTTTAATAACCGGTATATTTAGACCGGTTACATT
*
517991 GTTATGTTACCTA-TACATTATAATTACTGGTTTCGATGTTTTTGGGATCTACACTTGTTATAAA
66 GTTATGTTACCTATTACATTATAATTAC-GGTTTCGATGTTTTTGGGATCGACACTTGTTATAAA
*
518055 TGTATCAACACTTTTTCGTGAACTTGTTTGG-AAATACATTCTGG--ATAACATGTATCGACACA
130 TGTATCAACACTTTTTCGTGAACTTGTTTGGAAAATACATTATGGACATAA-A-GTATCGACACA
*
518117 AATGA
193 AATGT
* * * * *
518122 ATAAAGTGTCGATACA-TATTGTAGACCTATTTTCTCATAA-AATCGGTAAATTTAAACCGGTTA
1 ATAAAGTGTCGATACATTA-TGTATACCT-TTTT-T-TTAATAACCGGTATATTTAGACCGGTTA
* * * * *
518185 CATTGTAAAGTGACCTATTACATTATAGTTACGGGTTTCGATGTTTTTGGGATCGACACTTGATA
62 CATTGTTATGTTACCTATTACATTATAATTAC-GGTTTCGATGTTTTTGGGATCGACACTTGTTA
* *
518250 TAAATGTATCAACACTTATTT-GTGAACTTTTTTTGGTTGGAAAATACATTATGGACACAAAGTA
126 TAAATGTATCAACACTT-TTTCGTGAAC-----TTGTTTGGAAAATACATTATGGACATAAAGTA
518314 TCGACACAAATGT
185 TCGACACAAATGT
* * * *
518327 ATAAAGTGCCGATACATTATGTATACCTCTTTTCTCATAAACCGGTATA
1 ATAAAGTGTCGATACATTATGTATACCTTTTTTTTAAT-AACCGGTATA
518376 ATTATGTTTG
Statistics
Matches: 397, Mismatches: 32, Indels: 35
0.86 0.07 0.08
Matches are distributed among these distances:
194 4 0.01
195 3 0.01
196 47 0.12
197 106 0.27
198 88 0.22
199 69 0.17
200 3 0.01
202 2 0.01
203 1 0.00
204 18 0.05
205 50 0.13
206 3 0.01
207 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (197 bp):
ATAAAGTGTCGATACATTATGTATACCTTTTTTTTAATAACCGGTATATTTAGACCGGTTACATT
GTTATGTTACCTATTACATTATAATTACGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAAT
GTATCAACACTTTTTCGTGAACTTGTTTGGAAAATACATTATGGACATAAAGTATCGACACAAAT
GT
Found at i:523501 original size:15 final size:15
Alignment explanation
Indices: 523477--523526 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
523467 ATTTACTCAA
*
523477 AAGAGCTGGGTTGAG
1 AAGAGATGGGTTGAG
*
523492 AAGAGGTGGGTTGAG
1 AAGAGATGGGTTGAG
523507 AAGAGATGGGTTGAG
1 AAGAGATGGGTTGAG
523522 AAGAG
1 AAGAG
523527 CCCCGATTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.32, C:0.02, G:0.48, T:0.18
Consensus pattern (15 bp):
AAGAGATGGGTTGAG
Found at i:524410 original size:198 final size:198
Alignment explanation
Indices: 524072--524693 Score: 1120
Period size: 198 Copynumber: 3.1 Consensus size: 198
524062 TCTCATAAAA
*
524072 CGGTTAGATTCATAATTTACCTATTACATTATAATTATGGATCTCGATGTTTTTGGGATCGATAC
1 CGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTGGGATCGATAC
*
524137 TTGTTATAAATGTATCGACACATTTCCATGCACTTGGTAAGGAAATCATTCTGGACACAAAGTAT
66 TTTTTATAAATGTATCGACACATTTCCATGCACTTGGTAAGGAAATCATTCTGGACACAAAGTAT
*
524202 CGACACAAATTCAACAAGTGTCAATACTTTATGTACACCTGTTTTCTCATAAACTGGTGTATTTA
131 CGACACAAATTCAACAAGTGTCGATACTTTATGTACACCTGTTTTCTCATAAACTGGTGTATTTA
524267 GAC
196 GAC
*
524270 CGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTGGGATTGATAC
1 CGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTGGGATCGATAC
*
524335 TTTTTATAAATGTATCGACACATTTCCATGCACTTGGTAAGGAAATCATTTTGGACACAAAGTAT
66 TTTTTATAAATGTATCGACACATTTCCATGCACTTGGTAAGGAAATCATTCTGGACACAAAGTAT
*
524400 CGACACAAATTCAACAAGTGTTGATACTTTATGTACACCTGTTTTCTCATAAA-TCGGTGTATTT
131 CGACACAAATTCAACAAGTGTCGATACTTTATGTACACCTGTTTTCTCATAAACT-GGTGTATTT
524464 AGAC
195 AGAC
524468 CGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTGGGATCGATAC
1 CGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTGGGATCGATAC
**
524533 TTTTTATAAATGTATCGACACATTTCCATGCACTTGGTAAGGAAATTGTTCTGGACACAAAGTAT
66 TTTTTATAAATGTATCGACACATTTCCATGCACTTGGTAAGGAAATCATTCTGGACACAAAGTAT
* * *
524598 CGACACAAATTCAATAAGTGTCGATACTTTATGTACACTTGTTTTCTCATAAACCGGTGTATTTA
131 CGACACAAATTCAACAAGTGTCGATACTTTATGTACACCTGTTTTCTCATAAACTGGTGTATTTA
*
524663 GAT
196 GAC
524666 CGGTTAGATTCATAATTTACCTATTACA
1 CGGTTAGATTCATAATTTACCTATTACA
524694 CATTATAAAT
Statistics
Matches: 407, Mismatches: 15, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
197 1 0.00
198 406 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (198 bp):
CGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTGGGATCGATAC
TTTTTATAAATGTATCGACACATTTCCATGCACTTGGTAAGGAAATCATTCTGGACACAAAGTAT
CGACACAAATTCAACAAGTGTCGATACTTTATGTACACCTGTTTTCTCATAAACTGGTGTATTTA
GAC
Found at i:525046 original size:19 final size:19
Alignment explanation
Indices: 525022--525071 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
525012 TTACATTCTC
*
525022 ATACAAAATTATAAATCGT
1 ATACAAAATTAAAAATCGT
*
525041 ATACAAAATTAAAAATCTT
1 ATACAAAATTAAAAATCGT
525060 ATACAAAATTAA
1 ATACAAAATTAA
525072 CCCTACATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.30
Consensus pattern (19 bp):
ATACAAAATTAAAAATCGT
Found at i:526234 original size:17 final size:17
Alignment explanation
Indices: 526212--526247 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
526202 GAATCATTAG
*
526212 GATTAATATTTTTTCAT
1 GATTAATATATTTTCAT
526229 GATTAATATATTTTCAT
1 GATTAATATATTTTCAT
526246 GA
1 GA
526248 AATATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (17 bp):
GATTAATATATTTTCAT
Found at i:526568 original size:18 final size:18
Alignment explanation
Indices: 526545--526579 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
526535 TTCTCCTCAT
526545 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
526563 TTCCTCCATCTTTTCTT
1 TTCCTCCATCTTTTCTT
526580 TTCAAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.06, C:0.37, G:0.00, T:0.57
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:527059 original size:14 final size:14
Alignment explanation
Indices: 527040--527067 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
527030 TTAATTTTTT
527040 CTTAATATTATTTA
1 CTTAATATTATTTA
527054 CTTAATATTATTTA
1 CTTAATATTATTTA
527068 ATTTCATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
CTTAATATTATTTA
Found at i:527085 original size:23 final size:24
Alignment explanation
Indices: 527041--527085 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
527031 TAATTTTTTC
527041 TTAATATTATTTACTTAATATTAT
1 TTAATATTATTTACTTAATATTAT
527065 TTAAT-TTCATTTA-TTAATATT
1 TTAATATT-ATTTACTTAATATT
527086 TCTAGCTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (24 bp):
TTAATATTATTTACTTAATATTAT
Found at i:530366 original size:21 final size:21
Alignment explanation
Indices: 530340--530392 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
530330 GTTTCCAGAT
530340 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
530361 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
530382 TCGCAATGCGA
1 TCGCAACGCGA
530393 TTTTCCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:530484 original size:51 final size:54
Alignment explanation
Indices: 530396--530498 Score: 176
Period size: 52 Copynumber: 2.0 Consensus size: 54
530386 AATGCGATTT
530396 TCCAAATTCGTTGCGATTAGTACAAGTTCGCGTTGCGA-TTATTCCAAATTCTA
1 TCCAAATTCGTTGCGATTAGTACAAGTTCGCGTTGCGATTTATTCCAAATTCTA
*
530449 TCCAAGTTCGTTGCGA-TAGT-CAAGTTCGCGTTGCGATTTATTCCAAATTC
1 TCCAAATTCGTTGCGATTAGTACAAGTTCGCGTTGCGATTTATTCCAAATTC
530499 GTTGCGATAG
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
51 16 0.33
52 17 0.35
53 15 0.31
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.36
Consensus pattern (54 bp):
TCCAAATTCGTTGCGATTAGTACAAGTTCGCGTTGCGATTTATTCCAAATTCTA
Found at i:531354 original size:19 final size:19
Alignment explanation
Indices: 531330--531468 Score: 116
Period size: 19 Copynumber: 6.9 Consensus size: 19
531320 TTGTTGCGAT
*
531330 TTTGGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
531349 TTTGGAATAAATCGCAACGCGAA
1 TTTGGAAT--ATCGCAA--CGAA
* *
531372 CTTGGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
* ** *
531391 TTTGTAATAAAGCAACAAA
1 TTTGGAATATCGCAACGAA
531410 TTTGGAATAAATCGCAACGCGAA
1 TTTGGAAT--ATCGCAA--CGAA
* *
531433 CTTGGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
*
531452 TTTGGAAAATCGCAACG
1 TTTGGAATATCGCAACG
531469 CGAACTTCGA
Statistics
Matches: 94, Mismatches: 18, Indels: 16
0.73 0.14 0.12
Matches are distributed among these distances:
19 49 0.52
21 26 0.28
23 19 0.20
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.23
Consensus pattern (19 bp):
TTTGGAATATCGCAACGAA
Found at i:531436 original size:61 final size:61
Alignment explanation
Indices: 531341--531455 Score: 221
Period size: 61 Copynumber: 1.9 Consensus size: 61
531331 TTGGACTATC
*
531341 GCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGTAATAAA
1 GCAACAAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGTAATAAA
531402 GCAACAAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTG
1 GCAACAAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTG
531456 GAAAATCGCA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (61 bp):
GCAACAAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGTAATAAA
Found at i:531462 original size:40 final size:42
Alignment explanation
Indices: 531402--531487 Score: 140
Period size: 40 Copynumber: 2.1 Consensus size: 42
531392 TTGTAATAAA
*
531402 GCAACAAATTTGGAATAAATCGCAACGCGAACTTGGACTATC
1 GCAACAAATTTGGAATAAATCGCAACGCGAACTTCGACTATC
*
531444 GCAACGAATTTGG-A-AAATCGCAACGCGAACTTCGACTATC
1 GCAACAAATTTGGAATAAATCGCAACGCGAACTTCGACTATC
531484 GCAA
1 GCAA
531488 TGCGAATCGC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
40 29 0.69
41 1 0.02
42 12 0.29
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (42 bp):
GCAACAAATTTGGAATAAATCGCAACGCGAACTTCGACTATC
Found at i:531467 original size:61 final size:62
Alignment explanation
Indices: 531330--531467 Score: 219
Period size: 61 Copynumber: 2.3 Consensus size: 62
531320 TTGTTGCGAT
* *
531330 TTTGGACT-ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAA
1 TTTGGAATAATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAA
* *
531391 TTTGTAATAA-AGCAACAAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAA
1 TTTGGAATAATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAA
531452 TTTGGAA-AATCGCAAC
1 TTTGGAATAATCGCAAC
531468 GCGAACTTCG
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
60 2 0.03
61 66 0.96
62 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (62 bp):
TTTGGAATAATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAA
Found at i:531484 original size:21 final size:21
Alignment explanation
Indices: 531331--531493 Score: 99
Period size: 19 Copynumber: 8.0 Consensus size: 21
531321 TGTTGCGATT
*
531331 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
531350 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
531373 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* * ** * *
531392 TTGTAATAAAGCAA--CAAAT
1 TTGGACTATCGCAACGCGAAC
*
531411 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
531434 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
**
531453 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
* *
531474 TTCGACTATCGCAATGCGAA
1 TTGGACTATCGCAACGCGAA
531494 TCGCAGCACG
Statistics
Matches: 111, Mismatches: 23, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
19 46 0.41
21 46 0.41
23 19 0.17
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:531506 original size:33 final size:33
Alignment explanation
Indices: 531459--531527 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
531449 GAATTTGGAA
*
531459 AATCGCAACGCGAACTTCGACTATCGCAATGCG
1 AATCGCAACACGAACTTCGACTATCGCAATGCG
*
531492 AATCGCAGCACGAACTTCGACTATCGCAATGCG
1 AATCGCAACACGAACTTCGACTATCGCAATGCG
531525 AAT
1 AAT
531528 ATGTAAATCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.19
Consensus pattern (33 bp):
AATCGCAACACGAACTTCGACTATCGCAATGCG
Found at i:532932 original size:3 final size:3
Alignment explanation
Indices: 532924--532948 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
532914 TAATTTATAC
532924 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
532949 AATCAACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:535176 original size:165 final size:166
Alignment explanation
Indices: 534980--535314 Score: 654
Period size: 166 Copynumber: 2.0 Consensus size: 166
534970 TATTTTAAAT
534980 TAAATAATTTAAAATTTCTTTTTCCCTTTTTAAAATTAATGTCAAGATGACCCAGATTTTAGTAT
1 TAAATAATTTAAAATTTCTTTTTCCCTTTTTAAAATTAATGTCAAGATGACCCAGATTTTAGTAT
535045 TGCAACAACGCAGAATAA-AACACCTCCATTTAAGTCCCATGAGCTTCAAAACCCAATTAAGATA
66 TGCAACAACGCAGAATAACAACACCTCCATTTAAGTCCCATGAGCTTCAAAACCCAATTAAGATA
535109 ATATTAAGAGAACAAAATTCCCTTTAATTAATTACA
131 ATATTAAGAGAACAAAATTCCCTTTAATTAATTACA
535145 TAAATAATTTAAAATTTCTTTTTCCCTTTTTAAAATTAATGTCAAGATGACCCAGATTTTAGTAT
1 TAAATAATTTAAAATTTCTTTTTCCCTTTTTAAAATTAATGTCAAGATGACCCAGATTTTAGTAT
*
535210 TGCAACAACGCAGAATAACAACACCTCCATTTAATTCCCATGAGCTTCAAAACCCAATTAAGATA
66 TGCAACAACGCAGAATAACAACACCTCCATTTAAGTCCCATGAGCTTCAAAACCCAATTAAGATA
535275 ATATTAAGAGAACAAAATTCCCTTTAATTAATTACA
131 ATATTAAGAGAACAAAATTCCCTTTAATTAATTACA
535311 TAAA
1 TAAA
535315 AGTAGTCATT
Statistics
Matches: 168, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
165 83 0.49
166 85 0.51
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (166 bp):
TAAATAATTTAAAATTTCTTTTTCCCTTTTTAAAATTAATGTCAAGATGACCCAGATTTTAGTAT
TGCAACAACGCAGAATAACAACACCTCCATTTAAGTCCCATGAGCTTCAAAACCCAATTAAGATA
ATATTAAGAGAACAAAATTCCCTTTAATTAATTACA
Found at i:537215 original size:22 final size:21
Alignment explanation
Indices: 537171--537212 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
537161 TTGTTGTATA
537171 ATTATATTTTTAATTTAAAAAT
1 ATTATATTTTT-ATTTAAAAAT
537193 ATTATAATTTTT-TTTAAAAA
1 ATTAT-ATTTTTATTTAAAAA
537213 ATAATGTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 5 0.26
23 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTATATTTTTATTTAAAAAT
Found at i:538705 original size:20 final size:20
Alignment explanation
Indices: 538682--538724 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
538672 AACGCGATCC
538682 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
538702 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
538722 CCA
1 CCA
538725 AAAGCGCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:538732 original size:20 final size:20
Alignment explanation
Indices: 538689--538733 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
538679 TCCCCAGAAT
* *
538689 CGCAAATCAGTTTCCAGAAT
1 CGCAAATCAGTTTCCAAAAG
538709 CGCAAATCAGTTTCCAAAAG
1 CGCAAATCAGTTTCCAAAAG
538729 CGCAA
1 CGCAA
538734 CGCGATTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.20
Consensus pattern (20 bp):
CGCAAATCAGTTTCCAAAAG
Found at i:538753 original size:21 final size:20
Alignment explanation
Indices: 538723--538821 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
538713 AATCAGTTTC
*
538723 CAAAAGCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
538744 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
538765 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
538785 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
538806 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
538822 ACACATAAAT
Statistics
Matches: 60, Mismatches: 16, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
20 16 0.27
21 44 0.73
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:538850 original size:20 final size:20
Alignment explanation
Indices: 538788--538981 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
538778 CGATTTTCCA
* ** *
538788 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
538808 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
538828 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
538848 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
538868 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
538888 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
538908 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
538928 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
538948 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
538969 AAATCGCAACGCG
1 AAATCGCAACGCG
538982 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:538872 original size:60 final size:60
Alignment explanation
Indices: 538788--538981 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
538778 CGATTTTCCA
* ** * *
538788 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
538848 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
538908 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
538969 AAATCGCAACGCG
1 AAATCGCAACGCG
538982 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:539398 original size:33 final size:33
Alignment explanation
Indices: 539359--539429 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
539349 TTCACTTAGA
*
539359 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
539392 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
539425 TTTCA
1 TTTCA
539430 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:539568 original size:14 final size:14
Alignment explanation
Indices: 539549--539603 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
539539 AGAATGACTG
539549 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
539563 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
539582 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
539596 TCGCAACG
1 TCGCAACG
539604 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:539616 original size:33 final size:33
Alignment explanation
Indices: 539549--539619 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
539539 AGAATGACTG
***
539549 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
539582 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
539615 TCGCA
1 TCGCA
539620 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:539637 original size:19 final size:19
Alignment explanation
Indices: 539615--539712 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
539605 GAAACCAAAA
*
539615 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
539634 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
539648 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
539667 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
539681 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
539700 TCGCGTTGCGATT
1 TCGCGTTGCGATT
539713 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:539656 original size:14 final size:14
Alignment explanation
Indices: 539637--539726 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
539627 TTTCATTTCG
539637 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
539651 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
539670 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
539684 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
539701 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
539717 CGTTGCGATT
1 CGTTGCGATT
539727 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:539662 original size:33 final size:33
Alignment explanation
Indices: 539620--539734 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
539610 CAAAATCGCA
539620 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
539653 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
539686 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
539719 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
539735 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:545721 original size:10 final size:10
Alignment explanation
Indices: 545690--545714 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
545680 TATTTTTATT
545690 AATTTAAATA
1 AATTTAAATA
545700 AATTTAAATA
1 AATTTAAATA
545710 AATTT
1 AATTT
545715 TATTAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AATTTAAATA
Found at i:550155 original size:29 final size:29
Alignment explanation
Indices: 550121--550234 Score: 174
Period size: 29 Copynumber: 3.9 Consensus size: 29
550111 TCCCTAAGCA
550121 TAGGTCGCCATGCAATCCGGGCGACCTTG
1 TAGGTCGCCATGCAATCCGGGCGACCTTG
*
550150 TAGGTCGCCATGCAATCCTGGCGACCTTG
1 TAGGTCGCCATGCAATCCGGGCGACCTTG
* * *
550179 TAGGTCGCCATGCACTCCTGGCGACCTTA
1 TAGGTCGCCATGCAATCCGGGCGACCTTG
* *
550208 TAGGTCGTCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCAATCCGGGCGACCT
550235 ACCTTGCTCG
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 80 1.00
ACGTcount: A:0.17, C:0.32, G:0.28, T:0.23
Consensus pattern (29 bp):
TAGGTCGCCATGCAATCCGGGCGACCTTG
Found at i:550323 original size:14 final size:14
Alignment explanation
Indices: 550302--550347 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
550292 CTCACATAAT
550302 TCGGTCGGATGCCC
1 TCGGTCGGATGCCC
* *
550316 TTGGTCGGATGGCC
1 TCGGTCGGATGCCC
*
550330 TCGGTCGGATGGCC
1 TCGGTCGGATGCCC
550344 TCGG
1 TCGG
550348 ATGCCCACCG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.07, C:0.28, G:0.41, T:0.24
Consensus pattern (14 bp):
TCGGTCGGATGCCC
Found at i:550600 original size:34 final size:35
Alignment explanation
Indices: 550542--550625 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 35
550532 CTTTTGCCAA
* * * *
550542 TCCTTTCACTATATTATTCTTTTTTTTGTA-TCAT
1 TCCTTTCACTGTATTACTCCTTTTTTTATATTCAT
* *
550576 TCCTTTCACTGTATTGCTCCTTTTTTTATATTGAT
1 TCCTTTCACTGTATTACTCCTTTTTTTATATTCAT
*
550611 TTCTTT-ACTGTATTA
1 TCCTTTCACTGTATTA
550626 TTTCTTTTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
34 33 0.80
35 8 0.20
ACGTcount: A:0.17, C:0.18, G:0.06, T:0.60
Consensus pattern (35 bp):
TCCTTTCACTGTATTACTCCTTTTTTTATATTCAT
Found at i:551000 original size:65 final size:64
Alignment explanation
Indices: 550859--551097 Score: 272
Period size: 65 Copynumber: 3.8 Consensus size: 64
550849 ATTATATAGT
* * * * * *
550859 CACTCCACCTTATGCACCACAAAGGTACACAAGTTCGT-TAAATGATTTTGT--AGTATTCAATT
1 CACTCCACCTCATGCACCACAAAGGTACACGAG-TCATATGAGTGA-TCTGTACAGTATTCAATT
550921 A
64 A
* * *
550922 TCACTCCACCTCATGCACCACAATGGTACATGAGTCATATGAGTGATTTGTACAGTATTCAATTA
1 -CACTCCACCTCATGCACCACAAAGGTACACGAGTCATATGAGTGATCTGTACAGTATTCAATTA
* * * *
550987 GCACTCCAGCTCATGCACCACAAAGGTACACGAGTTATATGAGTGATCTGTGCAATATTCAATTA
1 -CACTCCACCTCATGCACCACAAAGGTACACGAGTCATATGAGTGATCTGTACAGTATTCAATTA
* *
551052 -TCT-CACCTCATGTACCACAAAGGTACACGAGTCATATGAGTGATCT
1 CACTCCACCTCATGCACCACAAAGGTACACGAGTCATATGAGTGATCT
551098 ATACTGGTGC
Statistics
Matches: 153, Mismatches: 19, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
62 40 0.26
63 10 0.07
64 34 0.22
65 69 0.45
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (64 bp):
CACTCCACCTCATGCACCACAAAGGTACACGAGTCATATGAGTGATCTGTACAGTATTCAATTA
Found at i:551088 original size:127 final size:128
Alignment explanation
Indices: 550859--551095 Score: 318
Period size: 127 Copynumber: 1.9 Consensus size: 128
550849 ATTATATAGT
* * * * *
550859 CACTCCACCTTATGCACCACAAAGGTACACAAGTTCGTTAAATGATTTTGTAGTATTCAATTATC
1 CACTCCACCTCATGCACCACAAAGGTACACAAGTTCATTAAATGATTGTGCAATATTCAATTAT-
* *
550924 ACTCCACCTCATGCACCACAATGGTACATGAGTCATATGAGTGATTTGTACAGTATTCAATTAG
65 ACTCCACCTCATGCACCACAAAGGTACACGAGTCATATGAGTGATTTGTACAGTATTCAATTAG
* * * *
550988 CACTCCAGCTCATGCACCACAAAGGTACACGAGTT-ATATGAGTGATCTGTGCAATATTCAATTA
1 CACTCCACCTCATGCACCACAAAGGTACACAAGTTCAT-TAAATGAT-TGTGCAATATTCAATTA
*
551052 T-CT-CACCTCATGTACCACAAAGGTACACGAGTCATATGAGTGAT
64 TACTCCACCTCATGCACCACAAAGGTACACGAGTCATATGAGTGAT
551096 CTATACTGGT
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
127 38 0.40
128 3 0.03
129 38 0.40
130 15 0.16
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (128 bp):
CACTCCACCTCATGCACCACAAAGGTACACAAGTTCATTAAATGATTGTGCAATATTCAATTATA
CTCCACCTCATGCACCACAAAGGTACACGAGTCATATGAGTGATTTGTACAGTATTCAATTAG
Found at i:552628 original size:29 final size:29
Alignment explanation
Indices: 552586--552657 Score: 135
Period size: 29 Copynumber: 2.5 Consensus size: 29
552576 CTACAGTGGT
552586 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
*
552615 CTTGGAGGTCGCCATGGCATCTGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
552644 CTTGGAGGTCGCCA
1 CTTGGAGGTCGCCA
552658 AGGTCGCCAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.14, C:0.29, G:0.38, T:0.19
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGGGCGAC
Found at i:552745 original size:17 final size:16
Alignment explanation
Indices: 552723--552793 Score: 90
Period size: 17 Copynumber: 4.4 Consensus size: 16
552713 ATGCAATCAA
552723 CATGGGACGTGGGAATG
1 CATGGG-CGTGGGAATG
* * *
552740 CATGGGGGAGGGGATG
1 CATGGGCGTGGGAATG
552756 CATGGGACGTGGGAATG
1 CATGGG-CGTGGGAATG
552773 CATGGG-GTGGGAATG
1 CATGGGCGTGGGAATG
552788 CATGGG
1 CATGGG
552794 GGAGGGGATG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
15 15 0.32
16 13 0.28
17 19 0.40
ACGTcount: A:0.21, C:0.10, G:0.52, T:0.17
Consensus pattern (16 bp):
CATGGGCGTGGGAATG
Found at i:552758 original size:16 final size:16
Alignment explanation
Indices: 552733--552799 Score: 82
Period size: 16 Copynumber: 4.2 Consensus size: 16
552723 CATGGGACGT
552733 GGGAATGCATGGGGGA
1 GGGAATGCATGGGGGA
* * *
552749 GGGGATGCATGGGACGT
1 GGGAATGCATGGG-GGA
*
552766 GGGAATGCAT-GGGGT
1 GGGAATGCATGGGGGA
552781 GGGAATGCATGGGGGA
1 GGGAATGCATGGGGGA
552797 GGG
1 GGG
552800 GATGGTGCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
15 12 0.28
16 21 0.49
17 10 0.23
ACGTcount: A:0.21, C:0.07, G:0.57, T:0.15
Consensus pattern (16 bp):
GGGAATGCATGGGGGA
Found at i:552760 original size:33 final size:32
Alignment explanation
Indices: 552723--552793 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 32
552713 ATGCAATCAA
*
552723 CATGGGACGTGGGAATGCATGGGGGAGGGGATG
1 CATGGGACGTGGGAATGCAT-GGGGAGGGAATG
*
552756 CATGGGACGTGGGAATGCATGGGGTGGGAATG
1 CATGGGACGTGGGAATGCATGGGGAGGGAATG
552788 CATGGG
1 CATGGG
552794 GGAGGGGATG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 16 0.44
33 20 0.56
ACGTcount: A:0.21, C:0.10, G:0.52, T:0.17
Consensus pattern (32 bp):
CATGGGACGTGGGAATGCATGGGGAGGGAATG
Found at i:552784 original size:15 final size:15
Alignment explanation
Indices: 552731--552794 Score: 83
Period size: 15 Copynumber: 4.1 Consensus size: 15
552721 AACATGGGAC
552731 GTGGGAATGCATGGGG
1 GTGGGAATGCAT-GGG
* *
552747 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
552762 ACGTGGGAATGCATGGG
1 --GTGGGAATGCATGGG
552779 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
552794 G
1 G
552795 GAGGGGATGG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
15 19 0.45
16 10 0.24
17 13 0.31
ACGTcount: A:0.20, C:0.08, G:0.55, T:0.17
Consensus pattern (15 bp):
GTGGGAATGCATGGG
Found at i:553284 original size:21 final size:21
Alignment explanation
Indices: 553259--553302 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
553249 AATCTAGTTA
553259 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
553280 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
553301 AT
1 AT
553303 ATATATTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:554166 original size:26 final size:25
Alignment explanation
Indices: 554137--554195 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
554127 AAATCATATT
*
554137 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
554163 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
554189 ATTATTA
1 ATTATTA
554196 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:557009 original size:11 final size:11
Alignment explanation
Indices: 556974--557322 Score: 70
Period size: 11 Copynumber: 28.9 Consensus size: 11
556964 ATTTCTATGT
* *
556974 ATTTATTAATC
1 ATTTAATAATG
*
556985 ATTATAAAAATG
1 ATT-TAATAATG
556997 ATTTAATAATG
1 ATTTAATAATG
557008 ATTT-A-AAT-
1 ATTTAATAATG
557016 ATTTAATGATTTGATG
1 ATTTAAT-A----ATG
*
557032 ATTTAGTAATG
1 ATTTAATAATG
*
557043 ATTTGATAATAATC
1 A-TT--TAATAATG
*
557057 ATTATAGTAATG
1 ATT-TAATAATG
557069 ATTTGATAATAAT-
1 A-TT--TAATAATG
557082 ATTATAATAATG
1 ATT-TAATAATG
*
557094 ATTTAGTAATAATC
1 A-TT--TAATAATG
*
557108 ATTATAAAAATG
1 ATT-TAATAATG
557120 ATTTAATAATG
1 ATTTAATAATG
557131 ATTT-A-AAT-
1 ATTTAATAATG
* *
557139 TTTTAATGATTTG
1 ATTTAAT-A-ATG
*
557152 ATGATTAGTAATG
1 AT--TTAATAATG
* *
557165 ATTTGATAATA
1 ATTTAATAATG
*
557176 ATCATTATGTAATG
1 AT--TTA-ATAATG
* *
557190 ATTTGATAAAATC
1 ATTT-A-ATAATG
557203 ATTATAATAATG
1 ATT-TAATAATG
*
557215 ATTTAGTAATAATC
1 A-TT--TAATAATG
*
557229 ATTATAAAAATG
1 ATT-TAATAATG
557241 ATTTAATAATG
1 ATTTAATAATG
557252 ATTT-A-AAT-
1 ATTTAATAATG
557260 ATTTAATGATTTGATG
1 ATTTAAT-A----ATG
*
557276 ATTTAGTAATG
1 ATTTAATAATG
*
557287 ATTTGATAATAATC
1 A-TT--TAATAATG
557301 ATTATAATAATG
1 ATT-TAATAATG
*
557313 ATTTTATAAT
1 ATTTAATAAT
557323 AATTATTAGT
Statistics
Matches: 253, Mismatches: 43, Indels: 84
0.67 0.11 0.22
Matches are distributed among these distances:
8 11 0.04
9 12 0.05
10 3 0.01
11 69 0.27
12 60 0.24
13 31 0.12
14 45 0.18
15 10 0.04
16 12 0.05
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (11 bp):
ATTTAATAATG
Found at i:557241 original size:121 final size:123
Alignment explanation
Indices: 556980--557330 Score: 636
Period size: 121 Copynumber: 2.9 Consensus size: 123
556970 ATGTATTTAT
556980 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
557045 TTGATAATAATCATTATAGTAATGATTTGATAATAATATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATATTATAATAATGATTTAGTAA
*
557103 TAATCATTATAAAAATGATTTAATAATGATTTAAATTTTTAATGATTTGATGA-TTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
557167 TTGATAATAATCATTAT-GTAATGATTTGATAA-AATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAAT-ATTATAATAATGATTTAGTAA
557224 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* *
557289 TTGATAATAATCATTATAATAATGATTTTATAATAATTATTA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAA-TATTA
557331 GTTATTATTT
Statistics
Matches: 219, Mismatches: 4, Indels: 9
0.94 0.02 0.04
Matches are distributed among these distances:
120 3 0.01
121 88 0.40
122 56 0.26
123 65 0.30
124 6 0.03
125 1 0.00
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (123 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATATTATAATAATGATTTAGTAA
Found at i:557250 original size:26 final size:26
Alignment explanation
Indices: 557038--557330 Score: 203
Period size: 26 Copynumber: 11.9 Consensus size: 26
557028 GATGATTTAG
* *
557038 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTAATAATAATCATTATAA
*
557064 TAATGATTTGATAATAAT-ATTATAA
1 TAATGATTTAATAATAATCATTATAA
*
557089 TAATGATTTAGTAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
* *
557115 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTAATAATAATCATTATAA
* * * *
557138 T--T--TTTAATGATTTGATGA-T-TAG
1 TAATGATTTAAT-A-ATAATCATTATAA
* *
557160 TAATGATTTGATAATAATCATTAT-G
1 TAATGATTTAATAATAATCATTATAA
*
557185 TAATGATTTGATAA-AATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
*
557210 TAATGATTTAGTAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
* *
557236 AAATGA-TT--TAATAATGATT-T-A
1 TAATGATTTAATAATAATCATTATAA
* * * *
557257 -AAT-ATTTAATGATTTGATGATT-TAG
1 TAATGATTTAAT-A-ATAATCATTATAA
*
557282 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
* *
557308 TAATGATTTTATAATAATTATTA
1 TAATGATTTAATAATAATCATTA
557331 GTTATTATTT
Statistics
Matches: 216, Mismatches: 28, Indels: 46
0.74 0.10 0.16
Matches are distributed among these distances:
19 7 0.03
20 6 0.03
21 6 0.03
22 5 0.02
23 13 0.06
24 25 0.12
25 59 0.27
26 89 0.41
27 6 0.03
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (26 bp):
TAATGATTTAATAATAATCATTATAA
Found at i:557536 original size:23 final size:21
Alignment explanation
Indices: 557475--557541 Score: 59
Period size: 23 Copynumber: 3.1 Consensus size: 21
557465 GGATTATTGT
557475 TAATA-TTAATTATTGA-TAC
1 TAATATTTAATTATTGATTAC
*
557494 TAATGATTTAAAATAGTTGATTTAC
1 TAAT-ATTT-AATTA-TTGA-TTAC
557519 TAAATATTTAATTATTGA-TAC
1 T-AATATTTAATTATTGATTAC
557540 TA
1 TA
557542 GTAATGATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
19 4 0.10
20 2 0.05
21 6 0.15
22 4 0.10
23 8 0.21
24 4 0.10
25 8 0.21
26 3 0.08
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.46
Consensus pattern (21 bp):
TAATATTTAATTATTGATTAC
Found at i:558830 original size:95 final size:97
Alignment explanation
Indices: 558671--558860 Score: 366
Period size: 95 Copynumber: 2.0 Consensus size: 97
558661 CAAAATAATA
558671 TTTAATTAATATTTTATATTAAAATAGAGGATTCATATTACCTTCCGGCAAGTGGAAAGTCAACC
1 TTTAATTAATATTTTATATTAAAATAGAGGATTCATATTACCTTCCGGCAAGTGGAAAGTCAACC
558736 GCAGTCTGACTAATCGGTGTCAAAAACGGATT
66 GCAGTCTGACTAATCGGTGTCAAAAACGGATT
558768 TTTAATTAATATTTTATA-TAAAATAGAGGATTCATATTACCTT-CGGCAAGTGGAAAGTCAACC
1 TTTAATTAATATTTTATATTAAAATAGAGGATTCATATTACCTTCCGGCAAGTGGAAAGTCAACC
558831 GCAGTCTGACTAATCGGTGTCAAAAACGGA
66 GCAGTCTGACTAATCGGTGTCAAAAACGGA
558861 AGTTATGCCA
Statistics
Matches: 93, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
95 50 0.54
96 25 0.27
97 18 0.19
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (97 bp):
TTTAATTAATATTTTATATTAAAATAGAGGATTCATATTACCTTCCGGCAAGTGGAAAGTCAACC
GCAGTCTGACTAATCGGTGTCAAAAACGGATT
Found at i:559727 original size:15 final size:14
Alignment explanation
Indices: 559704--559734 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
559694 TACAACACTA
559704 AACTTTAATATAAT
1 AACTTTAATATAAT
559718 AACTTATAATATAAT
1 AACTT-TAATATAAT
559733 AA
1 AA
559735 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:559742 original size:16 final size:16
Alignment explanation
Indices: 559709--559755 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
559699 CACTAAACTT
*
559709 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
559724 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
559740 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
559756 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:560148 original size:4 final size:4
Alignment explanation
Indices: 560131--560186 Score: 55
Period size: 4 Copynumber: 14.5 Consensus size: 4
560121 ACCTTATCTC
** *
560131 CTTT C-TT C-TT CTTT CTTT CCTTT CTCC CTTT CTTT CTTT C-TC CTTT
1 CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT CTTT
560177 CTTT CTTT CT
1 CTTT CTTT CT
560187 CGGCTGCAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
3 8 0.19
4 31 0.72
5 4 0.09
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (4 bp):
CTTT
Found at i:560160 original size:27 final size:22
Alignment explanation
Indices: 560127--560178 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 22
560117 ATTTACCTTA
*
560127 TCTCCTTTCTTC-TTCTTTC-T
1 TCTCCTTTCTCCTTTCTTTCTT
560147 T-TCCTTTCTCCCTTTCTTTCTT
1 TCTCCTTTCT-CCTTTCTTTCTT
560169 TCTCCTTTCT
1 TCTCCTTTCT
560179 TTCTTTCTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 8 0.30
20 2 0.07
21 7 0.26
22 2 0.07
23 8 0.30
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (22 bp):
TCTCCTTTCTCCTTTCTTTCTT
Found at i:560177 original size:15 final size:15
Alignment explanation
Indices: 560131--560187 Score: 80
Period size: 15 Copynumber: 3.7 Consensus size: 15
560121 ACCTTATCTC
*
560131 CTTTC-TTCTTCTTT
1 CTTTCTTTCTCCTTT
560145 CTTTCCTTTCTCCCTTT
1 CTTT-CTTTCT-CCTTT
560162 CTTTCTTTCTCCTTT
1 CTTTCTTTCTCCTTT
560177 CTTTCTTTCTC
1 CTTTCTTTCTC
560188 GGCTGCAATC
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
14 4 0.10
15 17 0.44
16 10 0.26
17 8 0.21
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (15 bp):
CTTTCTTTCTCCTTT
Found at i:560220 original size:23 final size:23
Alignment explanation
Indices: 560190--560235 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
560180 TCTTTCTCGG
560190 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
560213 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
560236 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.39, G:0.04, T:0.48
Consensus pattern (23 bp):
CTGCAATCTCTTCTCCCTTTCTT
Found at i:560288 original size:22 final size:23
Alignment explanation
Indices: 560248--560292 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
560238 TTTCTTTTAT
560248 AACCGGCTGCCTAATTATTTCAC
1 AACCGGCTGCCTAATTATTTCAC
560271 AACCGGCTGCC-AATTATTTCAC
1 AACCGGCTGCCTAATTATTTCAC
560293 CAATAATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.29
Consensus pattern (23 bp):
AACCGGCTGCCTAATTATTTCAC
Found at i:560549 original size:29 final size:29
Alignment explanation
Indices: 560482--560552 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
560472 ATGGGAATTG
*
560482 CGCCGGGACAACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
560511 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
560540 CGCCGGGACTACA
1 CGCCGGGACTACA
560553 ACCTACAAGG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.25, C:0.32, G:0.31, T:0.11
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTACAAGGT
Found at i:560553 original size:17 final size:17
Alignment explanation
Indices: 560502--560553 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
560492 ACATGGCGAC
560502 CTACAAGGTCGCCGGGA
1 CTACAAGGTCGCCGGGA
* *
560519 CTACATGG-CGAC----
1 CTACAAGGTCGCCGGGA
560531 CTACAAGGTCGCCGGGA
1 CTACAAGGTCGCCGGGA
560548 CTACAA
1 CTACAA
560554 CCTACAAGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 10
0.65 0.10 0.25
Matches are distributed among these distances:
12 7 0.27
13 3 0.12
16 3 0.12
17 13 0.50
ACGTcount: A:0.27, C:0.31, G:0.29, T:0.13
Consensus pattern (17 bp):
CTACAAGGTCGCCGGGA
Found at i:560561 original size:24 final size:25
Alignment explanation
Indices: 560499--560567 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 25
560489 ACAACATGGC
560499 GACCTACAAGGTCGCCGGGACTACA
1 GACCTACAAGGTCGCCGGGACTACA
560524 TGGCGACCTACAAGGTCGCCGGGACTACA
1 ----GACCTACAAGGTCGCCGGGACTACA
560553 -ACCTACAAGGTCGCC
1 GACCTACAAGGTCGCC
560568 TAGGCTGCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
24 15 0.38
29 25 0.62
ACGTcount: A:0.26, C:0.33, G:0.28, T:0.13
Consensus pattern (25 bp):
GACCTACAAGGTCGCCGGGACTACA
Found at i:560659 original size:31 final size:31
Alignment explanation
Indices: 560624--560703 Score: 115
Period size: 35 Copynumber: 2.5 Consensus size: 31
560614 TGGGGAGAAC
560624 GCTCGTATGGCTCGCATGGGGAGAACCATTG
1 GCTCGTATGGCTCGCATGGGGAGAACCATTG
560655 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
1 GCTCGTATGGCTC----GCATGGGGAGAACCATTG
*
560690 GCTCGTATAGCTCG
1 GCTCGTATGGCTCG
560704 TATGTCACCC
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
31 14 0.32
35 30 0.68
ACGTcount: A:0.19, C:0.23, G:0.34, T:0.25
Consensus pattern (31 bp):
GCTCGTATGGCTCGCATGGGGAGAACCATTG
Found at i:560683 original size:35 final size:35
Alignment explanation
Indices: 560637--560707 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
560627 CGTATGGCTC
*
560637 GCATGGGGAGAACCATTGGCTCGTATGGCTCGTAT
1 GCATGGGGAGAACCATTGGCTCGTATAGCTCGTAT
560672 GCATGGGGAGAACCATTGGCTCGTATAGCTCGTAT
1 GCATGGGGAGAACCATTGGCTCGTATAGCTCGTAT
560707 G
1 G
560708 TCACCCCGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.21, C:0.20, G:0.34, T:0.25
Consensus pattern (35 bp):
GCATGGGGAGAACCATTGGCTCGTATAGCTCGTAT
Found at i:560719 original size:12 final size:12
Alignment explanation
Indices: 560702--560743 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
560692 TCGTATAGCT
560702 CGTATGTCACCC
1 CGTATGTCACCC
*
560714 CGTATGTCAACC
1 CGTATGTCACCC
560726 CGTATGTCACCC
1 CGTATGTCACCC
560738 CGTATG
1 CGTATG
560744 GCCACCTCGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.26
Consensus pattern (12 bp):
CGTATGTCACCC
Found at i:560801 original size:26 final size:26
Alignment explanation
Indices: 560772--560834 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
560762 AACGCTCGTA
*
560772 TGGCTCGTATGCATGGGGAGAACCAT
1 TGGCTCGTATGCATAGGGAGAACCAT
560798 TGGCTCGTATGCATAGGGAGAACCAT
1 TGGCTCGTATGCATAGGGAGAACCAT
560824 TGGCTCGTATG
1 TGGCTCGTATG
560835 GCTCGTATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.25
Consensus pattern (26 bp):
TGGCTCGTATGCATAGGGAGAACCAT
Found at i:560805 original size:35 final size:32
Alignment explanation
Indices: 560765--560843 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 32
560755 TGGGGAGAAC
560765 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
1 GCTCGTATGGCTCGTATG-A--GGGAGAACCATTG
560800 GCTCGTAT-G--C--AT-AGGGAGAACCATTG
1 GCTCGTATGGCTCGTATGAGGGAGAACCATTG
560826 GCTCGTATGGCTCGTATG
1 GCTCGTATGGCTCGTATG
560844 TCACCCCGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 15
0.72 0.00 0.28
Matches are distributed among these distances:
26 21 0.55
27 1 0.03
28 1 0.03
29 1 0.03
30 2 0.05
31 2 0.05
32 1 0.03
34 1 0.03
35 8 0.21
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.27
Consensus pattern (32 bp):
GCTCGTATGGCTCGTATGAGGGAGAACCATTG
Found at i:561919 original size:19 final size:20
Alignment explanation
Indices: 561877--561919 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
561867 AACATAATCC
* **
561877 AAAATCAAAGAAAAAGGACT
1 AAAATCAAAGAAAAAAGAAA
561897 AAAAT-AAAGAAAAAAGAAA
1 AAAATCAAAGAAAAAAGAAA
561916 AAAA
1 AAAA
561920 ACATACATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.77, C:0.05, G:0.12, T:0.07
Consensus pattern (20 bp):
AAAATCAAAGAAAAAAGAAA
Found at i:566837 original size:3 final size:3
Alignment explanation
Indices: 566829--566858 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
566819 CGAGGGCTAC
566829 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
566859 TGAAAAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:576736 original size:439 final size:439
Alignment explanation
Indices: 575918--576795 Score: 1747
Period size: 439 Copynumber: 2.0 Consensus size: 439
575908 TTTTTTAATA
575918 AGTTGGAAAATATTTATATGTTTTCTTTAAAAAAATTAAATTCATAAAATTCAAATAATTTTTTT
1 AGTTGGAAAATATTTATATGTTTTCTTTAAAAAAATTAAATTCATAAAATTCAAATAATTTTTTT
575983 ACAAAATTGAAAATGTAAAAAGGTTTAATGAAATGGTAAAATTTTATTTTAACCCCTGAACTTCA
66 ACAAAATTGAAAATGTAAAAAGGTTTAATGAAATGGTAAAATTTTATTTTAACCCCTGAACTTCA
576048 TATAAAATTTTAATTATAGATTTTTTTTGTAAATCTAAAATAGTTTAAGGATAAATTTGTAATTT
131 TATAAAATTTTAATTATAGATTTTTTTTGTAAATCTAAAATAGTTTAAGGATAAATTTGTAATTT
576113 AACATTCGTAGAATTTTTATTATTTAATGACAGAATAAAGATATTTTTGAAAGAAATTTTTTTAA
196 AACATTCGTAGAATTTTTATTATTTAATGACAGAATAAAGATATTTTTGAAAGAAATTTTTTTAA
576178 GAGCTTTTTAGTCCAAAACGCCGGTAATCCAACAATACGTAAGGGAAGGGAGGTAATGACATTCC
261 GAGCTTTTTAGTCCAAAACGCCGGTAATCCAACAATACGTAAGGGAAGGGAGGTAATGACATTCC
576243 CGATAATATATCCCAAAAAATCTACTATTGGTAATGTAAGATTAACGAGAATAATATTCCCGACC
326 CGATAATATATCCCAAAAAATCTACTATTGGTAATGTAAGATTAACGAGAATAATATTCCCGACC
576308 AACCAAATAGGGGAATGTGGATTTCATTCCCATGGGAATCTCACATTCC
391 AACCAAATAGGGGAATGTGGATTTCATTCCCATGGGAATCTCACATTCC
576357 AGTTGGAAAATATTTATATGTTTTCTTTAAAAAAATTAAATTCATAAAATTCAAATAATTTTTTT
1 AGTTGGAAAATATTTATATGTTTTCTTTAAAAAAATTAAATTCATAAAATTCAAATAATTTTTTT
576422 ACAAAATTGAAAATGTAAAAAGGTTTAATGAAATGGTAAAATTTTATTTTAACCCCTGAACTTCA
66 ACAAAATTGAAAATGTAAAAAGGTTTAATGAAATGGTAAAATTTTATTTTAACCCCTGAACTTCA
576487 TATAAAATTTTAATTATAGATTTTTTTTGTAAATCTAAAATAGTTTAAGGATAAATTTGTAATTT
131 TATAAAATTTTAATTATAGATTTTTTTTGTAAATCTAAAATAGTTTAAGGATAAATTTGTAATTT
*
576552 AACATTCGTAGAATTTTTATTATTTAATGACAGAATAAGGATATTTTTGAAAGAAATTTTTTTAA
196 AACATTCGTAGAATTTTTATTATTTAATGACAGAATAAAGATATTTTTGAAAGAAATTTTTTTAA
576617 GAGCTTTTTAGTCCAAAACGCCGGTAATCCAACAATACGTAAGGGAAGGGAGGTAATGACATTCC
261 GAGCTTTTTAGTCCAAAACGCCGGTAATCCAACAATACGTAAGGGAAGGGAGGTAATGACATTCC
576682 CGATAATATATCCCAAAAAATCTACTATTGGTAATGTAAGATTAACGAGAATAATATTCCCGACC
326 CGATAATATATCCCAAAAAATCTACTATTGGTAATGTAAGATTAACGAGAATAATATTCCCGACC
576747 AACCAAATAGGGGAATGTGGATTTCATTCCCATGGGAATCTCACATTCC
391 AACCAAATAGGGGAATGTGGATTTCATTCCCATGGGAATCTCACATTCC
576796 CCCAACCAAA
Statistics
Matches: 438, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
439 438 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.36
Consensus pattern (439 bp):
AGTTGGAAAATATTTATATGTTTTCTTTAAAAAAATTAAATTCATAAAATTCAAATAATTTTTTT
ACAAAATTGAAAATGTAAAAAGGTTTAATGAAATGGTAAAATTTTATTTTAACCCCTGAACTTCA
TATAAAATTTTAATTATAGATTTTTTTTGTAAATCTAAAATAGTTTAAGGATAAATTTGTAATTT
AACATTCGTAGAATTTTTATTATTTAATGACAGAATAAAGATATTTTTGAAAGAAATTTTTTTAA
GAGCTTTTTAGTCCAAAACGCCGGTAATCCAACAATACGTAAGGGAAGGGAGGTAATGACATTCC
CGATAATATATCCCAAAAAATCTACTATTGGTAATGTAAGATTAACGAGAATAATATTCCCGACC
AACCAAATAGGGGAATGTGGATTTCATTCCCATGGGAATCTCACATTCC
Found at i:577833 original size:15 final size:17
Alignment explanation
Indices: 577804--577841 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
577794 AAGGGTAAAT
577804 TATTTTTTCACCACTCA
1 TATTTTTTCACCACTCA
*
577821 -ATTTTTTC-TCACTCA
1 TATTTTTTCACCACTCA
577836 TATTTT
1 TATTTT
577842 GATAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTTTTTCACCACTCA
Found at i:588078 original size:22 final size:22
Alignment explanation
Indices: 588050--588100 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
588040 CCTTCTTTTT
588050 TCGCCGGCAGTCACAGCCTCCA
1 TCGCCGGCAGTCACAGCCTCCA
*
588072 TCGCCGGCAGTCACAGCTTCCA
1 TCGCCGGCAGTCACAGCCTCCA
588094 TCGCCGG
1 TCGCCGG
588101 GCGCTAACAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.16, C:0.43, G:0.25, T:0.16
Consensus pattern (22 bp):
TCGCCGGCAGTCACAGCCTCCA
Found at i:593972 original size:21 final size:21
Alignment explanation
Indices: 593948--593989 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
593938 TAAATTAAAT
*
593948 ATTAGATAGGATCAGTTTTTA
1 ATTAGATAGAATCAGTTTTTA
593969 ATTAGATAGAATCAGTTTTTA
1 ATTAGATAGAATCAGTTTTTA
593990 TTCTATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.43
Consensus pattern (21 bp):
ATTAGATAGAATCAGTTTTTA
Found at i:594026 original size:20 final size:21
Alignment explanation
Indices: 594001--594040 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
593991 TCTATTAGTT
*
594001 ATTAGATAGGATCA-TTTTTA
1 ATTAGATAGAATCAGTTTTTA
594021 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTT
594041 TTATTCTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (21 bp):
ATTAGATAGAATCAGTTTTTA
Found at i:594041 original size:53 final size:53
Alignment explanation
Indices: 593947--594074 Score: 213
Period size: 54 Copynumber: 2.4 Consensus size: 53
593937 CTAAATTAAA
593947 TATTAGATAGGATCAGTTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
1 TATTAGATAGGATCA-TTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
594000 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTTATTCTATTAGT
* *
594054 TATTAGATAGAATAATTTTTA
1 TATTAGATAGGATCATTTTTA
594075 TTCTGTTGCT
Statistics
Matches: 71, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
52 21 0.30
53 15 0.21
54 35 0.49
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48
Consensus pattern (53 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
Found at i:598650 original size:21 final size:21
Alignment explanation
Indices: 598626--598667 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
598616 TAAATTAAAT
*
598626 ATTAGATAGGATCAGTTTTTA
1 ATTAGATAGAATCAGTTTTTA
598647 ATTAGATAGAATCAGTTTTTA
1 ATTAGATAGAATCAGTTTTTA
598668 TTCTATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.43
Consensus pattern (21 bp):
ATTAGATAGAATCAGTTTTTA
Found at i:598704 original size:20 final size:21
Alignment explanation
Indices: 598679--598718 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
598669 TCTATTAGTT
*
598679 ATTAGATAGGATCA-TTTTTA
1 ATTAGATAGAATCAGTTTTTA
598699 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTT
598719 TATTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (21 bp):
ATTAGATAGAATCAGTTTTTA
Found at i:598707 original size:52 final size:53
Alignment explanation
Indices: 598625--598751 Score: 229
Period size: 53 Copynumber: 2.4 Consensus size: 53
598615 CTAAATTAAA
598625 TATTAGATAGGATCAGTTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
1 TATTAGATAGGATCA-TTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
598678 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
*
598731 TATTAGATAGAATCATTTTTA
1 TATTAGATAGGATCATTTTTA
598752 TTCTATTAGT
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
52 21 0.29
53 51 0.71
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (53 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
Found at i:598753 original size:31 final size:31
Alignment explanation
Indices: 598699--598786 Score: 158
Period size: 31 Copynumber: 2.8 Consensus size: 31
598689 ATCATTTTTA
598699 ATTAGATAGAATCAGTTTTTTATTCTATTAGTT
1 ATTAGATAGAATCA--TTTTTATTCTATTAGTT
598732 ATTAGATAGAATCATTTTTATTCTATTAGTT
1 ATTAGATAGAATCATTTTTATTCTATTAGTT
598763 ATTAGATAGAATCATTTTTATTCT
1 ATTAGATAGAATCATTTTTATTCT
598787 GTTGCTAATT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
31 41 0.75
33 14 0.25
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (31 bp):
ATTAGATAGAATCATTTTTATTCTATTAGTT
Found at i:603859 original size:23 final size:23
Alignment explanation
Indices: 603832--603884 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
603822 TTATGGAATA
603832 CAAGTGCAAAGTAGTGGAAGTTT
1 CAAGTGCAAAGTAGTGGAAGTTT
*
603855 CAAGTGCTAAGTAGTGGAAGTTT
1 CAAGTGCAAAGTAGTGGAAGTTT
603878 CAAGTGC
1 CAAGTGC
603885 CTTGTTCTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.26
Consensus pattern (23 bp):
CAAGTGCAAAGTAGTGGAAGTTT
Found at i:608956 original size:48 final size:47
Alignment explanation
Indices: 608904--609204 Score: 257
Period size: 48 Copynumber: 6.3 Consensus size: 47
608894 CGGATTGGAT
* *
608904 GTGGTGGAGACTTATAGACATAGGAAGGGGGTCAGAAGTGAACTGGTG
1 GTGGTGGAGACTTATAGACATAGGAACGAGGTC-GAAGTGAACTGGTG
* * *
608952 GTGGTGGAGACTTATAGATATAGGGACGAGGTTC-ATAGTGGAA-TGGAG
1 GTGGTGGAGACTTATAGACATAGGAACGAGG-TCGA-AGT-GAACTGGTG
* * * **
609000 GTGGTGGAGACCTATAAACATAGGGACGAGGTCGAAAGTGGGCTGGTG
1 GTGGTGGAGACTTATAGACATAGGAACGAGGTCG-AAGTGAACTGGTG
* * * *
609048 GTGGTGGAGACTTAT-GTACATAGGGACGAGGTCGGGAGTGAAATGGAG
1 GTGGTGGAGACTTATAG-ACATAGGAACGAGGTC-GAAGTGAACTGGTG
* * * * *
609096 GTGGTGGAGACTTATAAACATAGGGACTAAGTCGAGAGTGGACTGGTG
1 GTGGTGGAGACTTATAGACATAGGAACGAGGTCGA-AGTGAACTGGTG
* * * * * * *
609144 GTGGTGGAGACTTATACACATAAGAAGGAGATGGGGAGTGAATTGGTG
1 GTGGTGGAGACTTATAGACATAGGAACGAGGT-CGAAGTGAACTGGTG
*
609192 GCGGTGGAGACTT
1 GTGGTGGAGACTT
609205 GTAAATGTAA
Statistics
Matches: 205, Mismatches: 37, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
47 5 0.02
48 192 0.94
49 8 0.04
ACGTcount: A:0.28, C:0.09, G:0.41, T:0.22
Consensus pattern (47 bp):
GTGGTGGAGACTTATAGACATAGGAACGAGGTCGAAGTGAACTGGTG
Found at i:609088 original size:144 final size:144
Alignment explanation
Indices: 608904--609165 Score: 348
Period size: 144 Copynumber: 1.8 Consensus size: 144
608894 CGGATTGGAT
* * * * *
608904 GTGGTGGAGACTTATAGACATAGGAAGGGGGTCAGAAGTGAACTGGTGGTGGTGGAGACTTATAG
1 GTGGTGGAGACTTATAGACATAGGAACGAGGTCAGAAGTGAAATGGAGGTGGTGGAGACTTATAA
* * *
608969 ATATAGGGACGAGGTTC-ATAGTGGAATGGAGGTGGTGGAGACCTATAAACATAGGGACGAGGTC
66 ACATAGGGACGAAG-TCGAGAGTGGAATGGAGGTGGTGGAGACCTATAAACATAGGGACGAGGTC
609033 GAAAGTGGGCTGGTG
130 GAAAGTGGGCTGGTG
* * *
609048 GTGGTGGAGACTTAT-GTACATAGGGACGAGGTCGGGAGTGAAATGGAGGTGGTGGAGACTTATA
1 GTGGTGGAGACTTATAG-ACATAGGAACGAGGTCAGAAGTGAAATGGAGGTGGTGGAGACTTATA
* * * * *
609112 AACATAGGGACTAAGTCGAGAGTGGACTGGTGGTGGTGGAGACTTATACACATA
65 AACATAGGGACGAAGTCGAGAGTGGAATGGAGGTGGTGGAGACCTATAAACATA
609166 AGAAGGAGAT
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
143 3 0.03
144 97 0.97
ACGTcount: A:0.29, C:0.10, G:0.40, T:0.22
Consensus pattern (144 bp):
GTGGTGGAGACTTATAGACATAGGAACGAGGTCAGAAGTGAAATGGAGGTGGTGGAGACTTATAA
ACATAGGGACGAAGTCGAGAGTGGAATGGAGGTGGTGGAGACCTATAAACATAGGGACGAGGTCG
AAAGTGGGCTGGTG
Found at i:609165 original size:96 final size:96
Alignment explanation
Indices: 608899--609209 Score: 347
Period size: 96 Copynumber: 3.2 Consensus size: 96
608889 GTGAGCGGAT
* * * * * *
608899 TGGATGTGGTGGAGACTTATAGACATAGGAAGGGGGTC-AGAAGTGAACTGGTGGTGGTGGAGAC
1 TGGAGGTGGTGGAGACTTATAAACATAGGGACGAGGTCGAG-AGTGGACTGGTGGTGGTGGAGAC
* * ** *
608963 TTATAGATATAGGGACGAGGTTC-ATAGTGGAA
65 TTATACACATAGGGACGAGG-TCGGGAGTGAAA
* * *
608995 TGGAGGTGGTGGAGACCTATAAACATAGGGACGAGGTCGAAAGTGGGCTGGTGGTGGTGGAGACT
1 TGGAGGTGGTGGAGACTTATAAACATAGGGACGAGGTCGAGAGTGGACTGGTGGTGGTGGAGACT
**
609060 TATGTACATAGGGACGAGGTCGGGAGTGAAA
66 TATACACATAGGGACGAGGTCGGGAGTGAAA
* *
609091 TGGAGGTGGTGGAGACTTATAAACATAGGGACTAAGTCGAGAGTGGACTGGTGGTGGTGGAGACT
1 TGGAGGTGGTGGAGACTTATAAACATAGGGACGAGGTCGAGAGTGGACTGGTGGTGGTGGAGACT
* * * * * *
609156 TATACACATAAGAAGGAGATGGGGAGTGAAT
66 TATACACATAGGGACGAGGTCGGGAGTGAAA
* * *
609187 TGGTGGCGGTGGAGACTTGTAAA
1 TGGAGGTGGTGGAGACTTATAAA
609210 TGTAAGGAGG
Statistics
Matches: 182, Mismatches: 31, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
95 2 0.01
96 179 0.98
97 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.41, T:0.22
Consensus pattern (96 bp):
TGGAGGTGGTGGAGACTTATAAACATAGGGACGAGGTCGAGAGTGGACTGGTGGTGGTGGAGACT
TATACACATAGGGACGAGGTCGGGAGTGAAA
Found at i:609191 original size:144 final size:144
Alignment explanation
Indices: 608904--609204 Score: 327
Period size: 144 Copynumber: 2.1 Consensus size: 144
608894 CGGATTGGAT
* * * * *
608904 GTGGTGGAGACTTATAGACATAGGAAGGGGGTCAGAAGTGAACTGGTGGTGGTGGAGACTTATAG
1 GTGGTGGAGACTTATAGACATAGGAACGAGGTCAGAAGTGAAATGGAGGTGGTGGAGACTTATAA
* * * * * *
608969 ATATAGGGACGAGGTTCATAGTGGAATGGAGGTGGTGGAGACCTATAAACATAGGGACGAGGTCG
66 ACATAGGGACGAAGTTCAGAGTGGAATGGAGGTGGTGGAGACCTATAAACATAAGAACGAGATCG
**
609034 AAAGTGGGCTGGTG
131 AAAGTGAACTGGTG
* * *
609048 GTGGTGGAGACTTAT-GTACATAGGGACGAGGTCGGGAGTGAAATGGAGGTGGTGGAGACTTATA
1 GTGGTGGAGACTTATAG-ACATAGGAACGAGGTCAGAAGTGAAATGGAGGTGGTGGAGACTTATA
* * * * * *
609112 AACATAGGGACTAAG-TCGAGAGTGGACTGGTGGTGGTGGAGACTTATACACATAAGAAGGAGAT
65 AACATAGGGACGAAGTTC-AGAGTGGAATGGAGGTGGTGGAGACCTATAAACATAAGAACGAGAT
* ** *
609176 GGGGAGTGAATTGGTG
129 CGAAAGTGAACTGGTG
*
609192 GCGGTGGAGACTT
1 GTGGTGGAGACTT
609205 GTAAATGTAA
Statistics
Matches: 128, Mismatches: 27, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
143 3 0.02
144 125 0.98
ACGTcount: A:0.28, C:0.09, G:0.41, T:0.22
Consensus pattern (144 bp):
GTGGTGGAGACTTATAGACATAGGAACGAGGTCAGAAGTGAAATGGAGGTGGTGGAGACTTATAA
ACATAGGGACGAAGTTCAGAGTGGAATGGAGGTGGTGGAGACCTATAAACATAAGAACGAGATCG
AAAGTGAACTGGTG
Found at i:609300 original size:48 final size:48
Alignment explanation
Indices: 609194--610396 Score: 862
Period size: 48 Copynumber: 25.2 Consensus size: 48
609184 AATTGGTGGC
** * * * * * *
609194 GGTGGAGACTTGTAAATGTAAGGAGGAGGTGGTGGAT-GTGATCGTGGA
1 GGTGGAGACTTGTAAACATAAGTAGGTGGGGGT-GATGGTGATGGAGGT
* * * * * * *
609242 GGAGGGGACTTGTAGACATAACTAGGAGGAGGTGATGGAGATGGAGGT
1 GGTGGAGACTTGTAAACATAAGTAGGTGGGGGTGATGGTGATGGAGGT
* * * * * * * *
609290 GGTGGAGACTTGTAGATATATGGAGGTGGTGGTGAGGGTGTTGGTGGT
1 GGTGGAGACTTGTAAACATAAGTAGGTGGGGGTGATGGTGATGGAGGT
* * * * *
609338 GGAGGAGATTTATAAACGTAAGGT-GGTGGGGGAGATGGTGATGGAGGT
1 GGTGGAGACTTGTAAACATAA-GTAGGTGGGGGTGATGGTGATGGAGGT
* * *
609386 GGTGGAGACTTGTAAA-AT-A--AGGAGGGGGTGAAGGTGATGGTGGT
1 GGTGGAGACTTGTAAACATAAGTAGGTGGGGGTGATGGTGATGGAGGT
* * * * *
609430 GGAGGAGATTTATAAACGTAAGGT-GGTGGGGGAGATGGTGATGGAGGT
1 GGTGGAGACTTGTAAACATAA-GTAGGTGGGGGTGATGGTGATGGAGGT
* * * * *
609478 GGTGGAGACTTGTAAACATATGGAGG-AGGGGTGAAGGTGATGGTGGT
1 GGTGGAGACTTGTAAACATAAGTAGGTGGGGGTGATGGTGATGGAGGT
* * * *
609525 GGAGGAGATTTGTAAACGTAAGGT-GGT-GGGGAGATGGTGATGGAGGT
1 GGTGGAGACTTGTAAACATAA-GTAGGTGGGGGTGATGGTGATGGAGGT
* * * * * *
609572 GGTGGAGACTTGTAGACATATGGAGGTGGTGGTGAAGGTGATGGTGGT
1 GGTGGAGACTTGTAAACATAAGTAGGTGGGGGTGATGGTGATGGAGGT
* * * * ** *
609620 GGAGGAGATTTATAAACGTAAGGT-GGTGGGGAAGATGGTGATAGAGGT
1 GGTGGAGACTTGTAAACATAA-GTAGGTGGGGGTGATGGTGATGGAGGT
* * * * *
609668 GGTGGAGACTTGTAAACATATGGAGGAGGGGGTGAAGGTGATGGTGGT
1 GGTGGAGACTTGTAAACATAAGTAGGTGGGGGTGATGGTGATGGAGGT
* * * *
609716 GGAGGAGATTTATAAACATAAGGT-GGTGGAGG-GATGGTGATGGAGGT
1 GGTGGAGACTTGTAAACATAA-GTAGGTGGGGGTGATGGTGATGGAGGT
* * * * * * * *
609763 GGTGGAGAATTGTAGACATATGGAGGTGGTGGTGAAGGTAATGGTGGT
1 GGTGGAGACTTGTAAACATAAGTAGGTGGGGGTGATGGTGATGGAGGT
* * * * *
609811 GGAGGAGATTTATAAACGTAAGGT-GGTGGGGGAGATGGTGATGGAGGT
1 GGTGGAGACTTGTAAACATAA-GTAGGTGGGGGTGATGGTGATGGAGGT
* * * * *
609859 GGTGGAGACTTGTAAAAATAAGGAGGAGGGGGTGAAGGTGATGGTGGT
1 GGTGGAGACTTGTAAACATAAGTAGGTGGGGGTGATGGTGATGGAGGT
* * * * *
609907 GGAGGAGATTTATAAACGTAAGGT-GGTGGGGGAGATGGTGATGGAGGT
1 GGTGGAGACTTGTAAACATAA-GTAGGTGGGGGTGATGGTGATGGAGGT
* * * * *
609955 GGTGGAGACTTGTAAACATATGGAGG-AGGGGTGAAGGTGATGGTGGT
1 GGTGGAGACTTGTAAACATAAGTAGGTGGGGGTGATGGTGATGGAGGT
* * * *
610002 GGAGGAGATTTGTAAACGTAAGGT-GGTGGGGGAGATGGTGATGGAGGT
1 GGTGGAGACTTGTAAACATAA-GTAGGTGGGGGTGATGGTGATGGAGGT
* * * * * *
610050 GGTGGAGACTTGTAGACATATGGAGGTGGTGGTGAAGGTGATGGTGGT
1 GGTGGAGACTTGTAAACATAAGTAGGTGGGGGTGATGGTGATGGAGGT
* * * * ** *
610098 GGAGGAGATTTATAAACGTAAGGT-GGTGGGGAAGATGGTGATAGAGGT
1 GGTGGAGACTTGTAAACATAA-GTAGGTGGGGGTGATGGTGATGGAGGT
* * * * *
610146 GGTGGAGACTTGTAAACATATGGAGGAGGGGGTGAAGGTGATGGTGGT
1 GGTGGAGACTTGTAAACATAAGTAGGTGGGGGTGATGGTGATGGAGGT
* * * * *
610194 GGAGGAGATTTGTAAACGTAAGGT-GGTGGGGGAGATGATGATGGAGGT
1 GGTGGAGACTTGTAAACATAA-GTAGGTGGGGGTGATGGTGATGGAGGT
* * * * * *
610242 GGTGGAGACTTGTAGACATATGGAGGTGGTGGTGAAGGTGATGGTGGT
1 GGTGGAGACTTGTAAACATAAGTAGGTGGGGGTGATGGTGATGGAGGT
* * * * * * * *
610290 GGTGGAGACTTGTAGACATATGGAGGAGGTGGTGAAGGTGATGGTGGC
1 GGTGGAGACTTGTAAACATAAGTAGGTGGGGGTGATGGTGATGGAGGT
* * * * * ** *
610338 GGCGGTGATTTATAAACGTAAGGT-GGTGACGGAGATGGTGATGGAGGT
1 GGTGGAGACTTGTAAACATAA-GTAGGTGGGGGTGATGGTGATGGAGGT
610386 GGTGGAGACTT
1 GGTGGAGACTT
610397 ATAGATATAG
Statistics
Matches: 873, Mismatches: 252, Indels: 60
0.74 0.21 0.05
Matches are distributed among these distances:
44 33 0.04
45 1 0.00
46 4 0.00
47 155 0.18
48 672 0.77
49 8 0.01
ACGTcount: A:0.26, C:0.03, G:0.47, T:0.24
Consensus pattern (48 bp):
GGTGGAGACTTGTAAACATAAGTAGGTGGGGGTGATGGTGATGGAGGT
Found at i:609801 original size:191 final size:190
Alignment explanation
Indices: 609275--610297 Score: 1669
Period size: 191 Copynumber: 5.4 Consensus size: 190
609265 AGGAGGAGGT
* * * * * * *
609275 GATGGAGATGGAGGTGGTGGAGACTTGTAGATATATGGAGGTGGTGGTGAGGGTGTTGGTGGTGG
1 GATGGTGATGGAGGTGGTGGAGACTTGTAAACATATGGAGGAGGGGGTGAAGGTGATGGTGGTGG
609340 AGGAGATTTATAAACGTAAGGTGGTGGGGGAGATGGTGATGGAGGTGGTGGAGACTTGTAAA-AT
66 AGGAGATTTATAAACGTAAGGTGGT-GGGGAGATGGTGATGGAGGTGGTGGAGACTTGTAAACAT
*
609404 AAGGA-G-GGGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAACGTAAGGTGGTGGGGGA
130 ATGGAGGAGGGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAACGTAAGGTGGTGGGGGA
609463 GATGGTGATGGAGGTGGTGGAGACTTGTAAACATATGGAGGA-GGGGTGAAGGTGATGGTGGTGG
1 GATGGTGATGGAGGTGGTGGAGACTTGTAAACATATGGAGGAGGGGGTGAAGGTGATGGTGGTGG
* *
609527 AGGAGATTTGTAAACGTAAGGTGGTGGGGAGATGGTGATGGAGGTGGTGGAGACTTGTAGACATA
66 AGGAGATTTATAAACGTAAGGTGGTGGGGAGATGGTGATGGAGGTGGTGGAGACTTGTAAACATA
* *
609592 TGGAGGTGGTGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAACGTAAGGTGGTGGGGAA
131 TGGAGGAGG-GGTGAAGGTGATGGTGGTGGAGGAGATTTATAAACGTAAGGTGGTGGGGGA
*
609653 GATGGTGATAGAGGTGGTGGAGACTTGTAAACATATGGAGGAGGGGGTGAAGGTGATGGTGGTGG
1 GATGGTGATGGAGGTGGTGGAGACTTGTAAACATATGGAGGAGGGGGTGAAGGTGATGGTGGTGG
* * *
609718 AGGAGATTTATAAACATAAGGTGGTGGAGG-GATGGTGATGGAGGTGGTGGAGAATTGTAGACAT
66 AGGAGATTTATAAACGTAAGGTGGTGG-GGAGATGGTGATGGAGGTGGTGGAGACTTGTAAACAT
* *
609782 ATGGAGGTGGTGGTGAAGGTAATGGTGGTGGAGGAGATTTATAAACGTAAGGTGGTGGGGGA
130 ATGGAGGAGG-GGTGAAGGTGATGGTGGTGGAGGAGATTTATAAACGTAAGGTGGTGGGGGA
* *
609844 GATGGTGATGGAGGTGGTGGAGACTTGTAAAAATAAGGAGGAGGGGGTGAAGGTGATGGTGGTGG
1 GATGGTGATGGAGGTGGTGGAGACTTGTAAACATATGGAGGAGGGGGTGAAGGTGATGGTGGTGG
609909 AGGAGATTTATAAACGTAAGGTGGTGGGGGAGATGGTGATGGAGGTGGTGGAGACTTGTAAACAT
66 AGGAGATTTATAAACGTAAGGTGGT-GGGGAGATGGTGATGGAGGTGGTGGAGACTTGTAAACAT
*
609974 ATGGAGGAGGGGTGAAGGTGATGGTGGTGGAGGAGATTTGTAAACGTAAGGTGGTGGGGGA
130 ATGGAGGAGGGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAACGTAAGGTGGTGGGGGA
* * *
610035 GATGGTGATGGAGGTGGTGGAGACTTGTAGACATATGGAGGTGGTGGTGAAGGTGATGGTGGTGG
1 GATGGTGATGGAGGTGGTGGAGACTTGTAAACATATGGAGGAGGGGGTGAAGGTGATGGTGGTGG
*
610100 AGGAGATTTATAAACGTAAGGTGGTGGGGAAGATGGTGATAGAGGTGGTGGAGACTTGTAAACAT
66 AGGAGATTTATAAACGTAAGGTGGTGGGG-AGATGGTGATGGAGGTGGTGGAGACTTGTAAACAT
*
610165 ATGGAGGAGGGGGTGAAGGTGATGGTGGTGGAGGAGATTTGTAAACGTAAGGTGGTGGGGGA
130 ATGGAGGA-GGGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAACGTAAGGTGGTGGGGGA
* * * *
610227 GATGATGATGGAGGTGGTGGAGACTTGTAGACATATGGAGGTGGTGGTGAAGGTGATGGTGGTGG
1 GATGGTGATGGAGGTGGTGGAGACTTGTAAACATATGGAGGAGGGGGTGAAGGTGATGGTGGTGG
*
610292 TGGAGA
66 AGGAGA
610298 CTTGTAGACA
Statistics
Matches: 791, Mismatches: 34, Indels: 16
0.94 0.04 0.02
Matches are distributed among these distances:
186 35 0.04
187 49 0.06
188 39 0.05
189 2 0.00
190 95 0.12
191 404 0.51
192 167 0.21
ACGTcount: A:0.26, C:0.03, G:0.48, T:0.24
Consensus pattern (190 bp):
GATGGTGATGGAGGTGGTGGAGACTTGTAAACATATGGAGGAGGGGGTGAAGGTGATGGTGGTGG
AGGAGATTTATAAACGTAAGGTGGTGGGGAGATGGTGATGGAGGTGGTGGAGACTTGTAAACATA
TGGAGGAGGGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAACGTAAGGTGGTGGGGGA
Found at i:610264 original size:27 final size:27
Alignment explanation
Indices: 610234--610321 Score: 89
Period size: 27 Copynumber: 3.5 Consensus size: 27
610224 GGAGATGATG
610234 ATGGAGGTGGTGGAGACTTGTAGACAT
1 ATGGAGGTGGTGGAGACTTGTAGACAT
* **
610261 ATGGAGGTGGTGGTGA-AGGT-G----
1 ATGGAGGTGGTGGAGACTTGTAGACAT
*
610282 ATGGTGGTGGTGGAGACTTGTAGACAT
1 ATGGAGGTGGTGGAGACTTGTAGACAT
*
610309 ATGGAGGAGGTGG
1 ATGGAGGTGGTGG
610322 TGAAGGTGAT
Statistics
Matches: 46, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
21 14 0.30
22 2 0.04
23 1 0.02
25 1 0.02
26 2 0.04
27 26 0.57
ACGTcount: A:0.23, C:0.05, G:0.48, T:0.25
Consensus pattern (27 bp):
ATGGAGGTGGTGGAGACTTGTAGACAT
Found at i:610333 original size:96 final size:96
Alignment explanation
Indices: 609194--610297 Score: 1695
Period size: 96 Copynumber: 11.6 Consensus size: 96
609184 AATTGGTGGC
** * * * * * * * * *
609194 GGTGGAGACTTGTAAATGTAAGGAGGAGGTGGTGGATGTGATCGTGGAGGAGGGGACTTGTAGAC
1 GGTGGAGACTTGTAAACATATGGAGGAGGTGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAAC
* * * * * *
609259 ATAA-CTAGGAGGAGGTGATGGAGATGGAGGT
66 GTAAGGT-GGTGGGGGAGATGGTGATGGAGGT
* * * * *
609290 GGTGGAGACTTGTAGATATATGGAGGTGGTGGTGAGGGTGTTGGTGGTGGAGGAGATTTATAAAC
1 GGTGGAGACTTGTAAACATATGGAGGAGGTGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAAC
609355 GTAAGGTGGTGGGGGAGATGGTGATGGAGGT
66 GTAAGGTGGTGGGGGAGATGGTGATGGAGGT
*
609386 GGTGGAGACTTGTAAA-ATA---AGGAGGGGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAAC
1 GGTGGAGACTTGTAAACATATGGAGGAGGTGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAAC
609447 GTAAGGTGGTGGGGGAGATGGTGATGGAGGT
66 GTAAGGTGGTGGGGGAGATGGTGATGGAGGT
*
609478 GGTGGAGACTTGTAAACATATGGAGGAGG-GGTGAAGGTGATGGTGGTGGAGGAGATTTGTAAAC
1 GGTGGAGACTTGTAAACATATGGAGGAGGTGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAAC
609542 GTAAGGTGGT-GGGGAGATGGTGATGGAGGT
66 GTAAGGTGGTGGGGGAGATGGTGATGGAGGT
* *
609572 GGTGGAGACTTGTAGACATATGGAGGTGGTGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAAC
1 GGTGGAGACTTGTAAACATATGGAGGAGGTGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAAC
* *
609637 GTAAGGTGGTGGGGAAGATGGTGATAGAGGT
66 GTAAGGTGGTGGGGGAGATGGTGATGGAGGT
*
609668 GGTGGAGACTTGTAAACATATGGAGGAGGGGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAAC
1 GGTGGAGACTTGTAAACATATGGAGGAGGTGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAAC
* *
609733 ATAAGGTGGTGGAGG-GATGGTGATGGAGGT
66 GTAAGGTGGTGGGGGAGATGGTGATGGAGGT
* * * *
609763 GGTGGAGAATTGTAGACATATGGAGGTGGTGGTGAAGGTAATGGTGGTGGAGGAGATTTATAAAC
1 GGTGGAGACTTGTAAACATATGGAGGAGGTGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAAC
609828 GTAAGGTGGTGGGGGAGATGGTGATGGAGGT
66 GTAAGGTGGTGGGGGAGATGGTGATGGAGGT
* * *
609859 GGTGGAGACTTGTAAAAATAAGGAGGAGGGGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAAC
1 GGTGGAGACTTGTAAACATATGGAGGAGGTGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAAC
609924 GTAAGGTGGTGGGGGAGATGGTGATGGAGGT
66 GTAAGGTGGTGGGGGAGATGGTGATGGAGGT
*
609955 GGTGGAGACTTGTAAACATATGGAGGAGG-GGTGAAGGTGATGGTGGTGGAGGAGATTTGTAAAC
1 GGTGGAGACTTGTAAACATATGGAGGAGGTGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAAC
610019 GTAAGGTGGTGGGGGAGATGGTGATGGAGGT
66 GTAAGGTGGTGGGGGAGATGGTGATGGAGGT
* *
610050 GGTGGAGACTTGTAGACATATGGAGGTGGTGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAAC
1 GGTGGAGACTTGTAAACATATGGAGGAGGTGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAAC
* *
610115 GTAAGGTGGTGGGGAAGATGGTGATAGAGGT
66 GTAAGGTGGTGGGGGAGATGGTGATGGAGGT
* *
610146 GGTGGAGACTTGTAAACATATGGAGGAGGGGGTGAAGGTGATGGTGGTGGAGGAGATTTGTAAAC
1 GGTGGAGACTTGTAAACATATGGAGGAGGTGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAAC
*
610211 GTAAGGTGGTGGGGGAGATGATGATGGAGGT
66 GTAAGGTGGTGGGGGAGATGGTGATGGAGGT
* * *
610242 GGTGGAGACTTGTAGACATATGGAGGTGGTGGTGAAGGTGATGGTGGTGGTGGAGA
1 GGTGGAGACTTGTAAACATATGGAGGAGGTGGTGAAGGTGATGGTGGTGGAGGAGA
610298 CTTGTAGACA
Statistics
Matches: 928, Mismatches: 71, Indels: 18
0.91 0.07 0.02
Matches are distributed among these distances:
92 85 0.09
93 3 0.00
94 47 0.05
95 270 0.29
96 522 0.56
97 1 0.00
ACGTcount: A:0.26, C:0.03, G:0.47, T:0.24
Consensus pattern (96 bp):
GGTGGAGACTTGTAAACATATGGAGGAGGTGGTGAAGGTGATGGTGGTGGAGGAGATTTATAAAC
GTAAGGTGGTGGGGGAGATGGTGATGGAGGT
Found at i:610446 original size:71 final size:72
Alignment explanation
Indices: 610371--610509 Score: 199
Period size: 71 Copynumber: 1.9 Consensus size: 72
610361 TGGTGACGGA
* * * * *
610371 GATGGTGATGGAGGTGGTGGAGACTTATAGATATAGGGAGGA-AGTGTGAAGGTGATGGTGGTGG
1 GATGGTGATGGAGGTGGTGGAGACTTATAAACATAAGGAGGAGAGGGTGAAGGTGATGGTGGAGG
610435 TGGTGGG
66 TGGTGGG
* * *
610442 GATGGTGATGGGGGTGGTGGAGACTTGTAAACATAAGGAGGAGGGGGTGAAGGTGATGGTGGAGG
1 GATGGTGATGGAGGTGGTGGAGACTTATAAACATAAGGAGGAGAGGGTGAAGGTGATGGTGGAGG
610507 TGG
66 TGG
610510 AGAAGATTCA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
71 37 0.63
72 22 0.37
ACGTcount: A:0.23, C:0.02, G:0.52, T:0.23
Consensus pattern (72 bp):
GATGGTGATGGAGGTGGTGGAGACTTATAAACATAAGGAGGAGAGGGTGAAGGTGATGGTGGAGG
TGGTGGG
Found at i:610447 original size:18 final size:18
Alignment explanation
Indices: 610424--610458 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
610414 GTGTGAAGGT
* *
610424 GATGGTGGTGGTGGTGGG
1 GATGGTGATGGGGGTGGG
610442 GATGGTGATGGGGGTGG
1 GATGGTGATGGGGGTGG
610459 TGGAGACTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.00, G:0.66, T:0.26
Consensus pattern (18 bp):
GATGGTGATGGGGGTGGG
Found at i:612438 original size:93 final size:92
Alignment explanation
Indices: 612334--612515 Score: 355
Period size: 92 Copynumber: 2.0 Consensus size: 92
612324 ACAGGGGGGG
612334 AAAAAAAAGAGGAGACCATCTTGTAATCAGAGGAAAAAAAACGATTCCTTCAACATCTATTTTTC
1 AAAAAAAAGAGGAGACCATCTTGTAATCAGAGG-AAAAAAACGATTCCTTCAACATCTATTTTTC
612399 AACAAATAAAAAACAAATTTCAGAAAGA
65 AACAAATAAAAAACAAATTTCAGAAAGA
612427 AAAAAAAAGAGGAGACCATCTTGTAATCAGAGGAAAAAAACGATTCCTTCAACATCTATTTTTCA
1 AAAAAAAAGAGGAGACCATCTTGTAATCAGAGGAAAAAAACGATTCCTTCAACATCTATTTTTCA
612492 ACAAATAAAAAACAAATTTCAGAA
66 ACAAATAAAAAACAAATTTCAGAA
612516 GCAATTAGAT
Statistics
Matches: 89, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
92 56 0.63
93 33 0.37
ACGTcount: A:0.51, C:0.15, G:0.12, T:0.22
Consensus pattern (92 bp):
AAAAAAAAGAGGAGACCATCTTGTAATCAGAGGAAAAAAACGATTCCTTCAACATCTATTTTTCA
ACAAATAAAAAACAAATTTCAGAAAGA
Found at i:615378 original size:44 final size:47
Alignment explanation
Indices: 615302--615399 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 47
615292 TTTCGTTTTT
* *
615302 TTTTTCGAATAAATGCATGCGAACTAGGTATCATGCGGTTAGG-TTTA
1 TTTTT-GAATAAATGCATGCAAACTAGATATCATGCGGTTAGGATTTA
* *
615349 TTTTTGAAT-AA-GCATGCAAATTAGATATCATGCGGTTAGGATTTC
1 TTTTTGAATAAATGCATGCAAACTAGATATCATGCGGTTAGGATTTA
615394 TTTTTG
1 TTTTTG
615400 TAGATAACAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
44 26 0.57
45 11 0.24
46 4 0.09
47 5 0.11
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (47 bp):
TTTTTGAATAAATGCATGCAAACTAGATATCATGCGGTTAGGATTTA
Done.