Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold415
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: 1242643
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 4 of 8
Found at i:519599 original size:6 final size:6
Alignment explanation
Indices: 519590--519617 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
519580 TTTTTTATTT
519590 TAAATA TAAATA TAAATA TAAATA TAAA
1 TAAATA TAAATA TAAATA TAAATA TAAA
519618 AATATAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
TAAATA
Found at i:519629 original size:18 final size:17
Alignment explanation
Indices: 519589--519629 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
519579 TTTTTTTATT
*
519589 TTAAATATAAATATAAA
1 TTAAATATAAAAATAAA
519606 TATAAATATAAAAATATAA
1 T-TAAATATAAAAATA-AA
519625 TTAAA
1 TTAAA
519630 AGTAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 17 0.81
19 3 0.14
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TTAAATATAAAAATAAA
Found at i:522903 original size:12 final size:12
Alignment explanation
Indices: 522882--522913 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
522872 CTAACACTAA
522882 ATGAACATGTTC
1 ATGAACATGTTC
*
522894 ATGAATATGTTC
1 ATGAACATGTTC
522906 ATGAACAT
1 ATGAACAT
522914 ATAATCGAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (12 bp):
ATGAACATGTTC
Found at i:523148 original size:23 final size:24
Alignment explanation
Indices: 523097--523151 Score: 85
Period size: 23 Copynumber: 2.3 Consensus size: 24
523087 ATAAACGGGT
* *
523097 TTTAAACAATTTATTTGAACGAGC
1 TTTAAACAATTTATTTAAACAAGC
523121 TTTAAACAATTTA-TTAAACAAGC
1 TTTAAACAATTTATTTAAACAAGC
523144 TTTAAACA
1 TTTAAACA
523152 TATTATGTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (24 bp):
TTTAAACAATTTATTTAAACAAGC
Found at i:530352 original size:15 final size:17
Alignment explanation
Indices: 530322--530353 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
530312 ACATTTTTCT
530322 AAATGAAAATTTGAAAA
1 AAATGAAAATTTGAAAA
530339 AAAT-AAAA-TTGAAAA
1 AAATGAAAATTTGAAAA
530354 TTTCCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (17 bp):
AAATGAAAATTTGAAAA
Found at i:530603 original size:40 final size:36
Alignment explanation
Indices: 530555--530645 Score: 101
Period size: 40 Copynumber: 2.4 Consensus size: 36
530545 AGGAATTGAG
530555 GAGATAGAAGGGAGGAAGGGAAGGGAAGGGAAAGGGAAGA
1 GAGATAGAAGGGAGGAAGGG-AGGG-AGGG-AAGGGAA-A
* * *
530595 GAGATAGAAGGAAGGGAGGGAGGGAGGGAGGGGAAA
1 GAGATAGAAGGGAGGAAGGGAGGGAGGGAAGGGAAA
**
530631 GAGAGGGAAGGGAGG
1 GAGATAGAAGGGAGG
530646 GGATGATGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
36 13 0.29
37 6 0.13
38 4 0.09
39 4 0.09
40 18 0.40
ACGTcount: A:0.41, C:0.00, G:0.57, T:0.02
Consensus pattern (36 bp):
GAGATAGAAGGGAGGAAGGGAGGGAGGGAAGGGAAA
Found at i:533533 original size:14 final size:15
Alignment explanation
Indices: 533498--533536 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
533488 CATGTAATTC
*
533498 TTTATAACAAAGCTA
1 TTTATATCAAAGCTA
*
533513 GTTATATCAAAG-TA
1 TTTATATCAAAGCTA
533527 TTTATATCAA
1 TTTATATCAA
533537 CAATATAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (15 bp):
TTTATATCAAAGCTA
Found at i:543063 original size:181 final size:178
Alignment explanation
Indices: 542728--543226 Score: 639
Period size: 181 Copynumber: 2.8 Consensus size: 178
542718 AGTGTGTTCC
* * * * * **
542728 TGTTGAGTTCACTTCCTCTGCTTCGTTATTACTGTTTCTCTTATAATATTTTGGTATTGGCTTCA
1 TGTTGAGTTCACTT-C-CT-CTTAGTTGTTACTATTTCTCTTAT-A-ATTTGGGTCTTGGCTTTG
** * * * * * * * *
542793 ATTTATTTACTTATTTA--T-GCT-TGTTTTCTACTGTGGTGTGCCTTTTACTTTCTAATGTCTT
61 ATTTATTTACTTATTTATTTATTTATTTTTTCTATTGTAGCGTGTCTTTTACTTTATCATGTTTT
* * *
542854 TTGAGATA-GGGTGTGTCCATTTTCAGTCTTATTTACTCTCGGCTTCCATCCG
126 TTGAGATAGGGGTGTGTCCATTTTCAGTCTTATTTACCCTCGGCCTCCATCCA
*
542906 TGTTGAGTTCACTTTCTCTTAGTTGTTACTATTTCTCTTATAATTTGGGTCTTGGCTTTGATTTA
1 TGTTGAGTTCACTTCCTCTTAGTTGTTACTATTTCTCTTATAATTTGGGTCTTGGCTTTGATTTA
* * * * *
542971 TTTACTTATGTTTTTTTTTTTTTTTTTTCATATTGTAGGGTGTCTTTTGCTTTATCATGTTTTTT
66 TTTACTTA--TTTATTTATTTATTTTTTC-TATTGTAGCGTGTCTTTTACTTTATCATGTTTTTT
543036 GAGATAGGGGTGTGTCCATTTTCAGTCTTATTTACCCTCGGCCTCCATCCA
128 GAGATAGGGGTGTGTCCATTTTCAGTCTTATTTACCCTCGGCCTCCATCCA
543087 TGTTGAGTTCACTTCCTCTTAGTTGTTACTATTTCTCTTATAATTTGGGTCTTGGCTTTGATTTA
1 TGTTGAGTTCACTTCCTCTTAGTTGTTACTATTTCTCTTATAATTTGGGTCTTGGCTTTGATTTA
* *
543152 TTTAGTTATTTATTTATTTATTTTTTCTATTGTAGCGTGTCTTTTACTTTATCATGTTTTGTGAG
66 TTTACTTATTTATTTATTTATTTTTTCTATTGTAGCGTGTCTTTTACTTTATCATGTTTTTTGAG
543217 ATAGGGGTGT
131 ATAGGGGTGT
543227 CTGCTTTATG
Statistics
Matches: 282, Mismatches: 31, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
173 27 0.10
174 1 0.00
175 24 0.09
176 2 0.01
177 1 0.00
178 60 0.21
179 22 0.08
180 33 0.12
181 112 0.40
ACGTcount: A:0.15, C:0.15, G:0.17, T:0.53
Consensus pattern (178 bp):
TGTTGAGTTCACTTCCTCTTAGTTGTTACTATTTCTCTTATAATTTGGGTCTTGGCTTTGATTTA
TTTACTTATTTATTTATTTATTTTTTCTATTGTAGCGTGTCTTTTACTTTATCATGTTTTTTGAG
ATAGGGGTGTGTCCATTTTCAGTCTTATTTACCCTCGGCCTCCATCCA
Found at i:543348 original size:178 final size:177
Alignment explanation
Indices: 542834--543348 Score: 553
Period size: 181 Copynumber: 2.9 Consensus size: 177
542824 TGTGGTGTGC
* * * * *
542834 CTTTTACTTTCTAATGTCTTT-TGAGATA-GGGTGTGTCCATTTTCAGTCTTATTTACTCTCGGC
1 CTTTTACTTTATCATGT-TTTGTGAGATAGGGGTGTCTCCATTTT-AGTCTTATTTACCCTAGGC
* * *
542897 TTCCATCCGTGTTGAGTTCACTTTCTCTTAGTTGTTACTATTTCTCTTATAATTTGGGTCTTGGC
64 ATCCA-CC-AGTTGAGTTCACTTCCTCTTAGTTGTTACTATTTCTCTTATAATTTGGGTCTTGGC
* * * *
542962 TTTGATTTATTTACTTATGTTTTTTTTTTTTTTTTTTCATATTGTAGGGTGT
127 TTTGATTTATTTACTTAT-TTATTTTATTTATTTTTTCATATTGTAGCGTGT
* * * * *
543014 CTTTTGCTTTATCATGTTTTTTGAGATAGGGGTGTGTCCATTTTCAGTCTTATTTACCCTCGGCC
1 CTTTTACTTTATCATGTTTTGTGAGATAGGGGTGTCTCCATTTT-AGTCTTATTTACCCTAGGCA
543079 TCCATCCATGTTGAGTTCACTTCCTCTTAGTTGTTACTATTTCTCTTATAATTTGGGTCTTGGCT
65 TCCA-CCA-GTTGAGTTCACTTCCTCTTAGTTGTTACTATTTCTCTTATAATTTGGGTCTTGGCT
*
543144 TTGATTTATTTAGTTATTTA-TTTATTTATTTTTTC-TATTGTAGCGTGT
128 TTGATTTATTTACTTATTTATTTTATTTATTTTTTCATATTGTAGCGTGT
* * * *
543192 CTTTTACTTTATCATGTTTTGTGAGATAGGGGTGTCTGC--TTTATGTCTTATTTGCTTTCTATG
1 CTTTTACTTTATCATGTTTTGTGAGATAGGGGTGTCTCCATTTTA-GTCTTATTTAC--CCTAGG
* * * * ** * * *
543255 TATGC-CCA-TTGAGTTCACTTCCTC-TACATTGTTACTGTTTTCTCTTATAAAAATGGTTATCG
63 CATCCACCAGTTGAGTTCACTTCCTCTTA-GTTGTTACT-ATTTCTCTTAT-AATTTGGGTCTTG
543317 GCTTTGATTTATTTACTTATTTATGTTTATTT
125 GCTTTGATTTATTTACTTATTTAT-TTTATTT
543349 TCTTTCCCCA
Statistics
Matches: 293, Mismatches: 31, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
173 2 0.01
174 24 0.08
175 11 0.04
176 46 0.16
178 59 0.20
179 16 0.05
180 23 0.08
181 112 0.38
ACGTcount: A:0.16, C:0.15, G:0.16, T:0.53
Consensus pattern (177 bp):
CTTTTACTTTATCATGTTTTGTGAGATAGGGGTGTCTCCATTTTAGTCTTATTTACCCTAGGCAT
CCACCAGTTGAGTTCACTTCCTCTTAGTTGTTACTATTTCTCTTATAATTTGGGTCTTGGCTTTG
ATTTATTTACTTATTTATTTTATTTATTTTTTCATATTGTAGCGTGT
Found at i:543726 original size:2 final size:2
Alignment explanation
Indices: 543719--543746 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
543709 TTCTGATTGA
543719 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
543747 AGAAGACGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:544526 original size:2 final size:2
Alignment explanation
Indices: 544519--544559 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
544509 CTTTTCTTAC
544519 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
544560 CACCTAACCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:545123 original size:3 final size:3
Alignment explanation
Indices: 545115--545154 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
545105 TGTTTTTTGA
545115 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
545155 AAAAATCTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:546603 original size:2 final size:2
Alignment explanation
Indices: 546596--546635 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
546586 AATATTTTGA
546596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
546636 GGATACTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:548369 original size:29 final size:29
Alignment explanation
Indices: 548314--548390 Score: 127
Period size: 29 Copynumber: 2.6 Consensus size: 29
548304 GCTATGAAAT
548314 TCTTGATTTTTTCCTCTTTTTCACATGATTTC
1 TCTTGA-TTTTT--TCTTTTTCACATGATTTC
548346 TCTTGATTTTTTCTTTTTCACATGATTTC
1 TCTTGATTTTTTCTTTTTCACATGATTTC
548375 TCTTGATTTTTTCTTT
1 TCTTGATTTTTTCTTT
548391 CTAATTAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
29 34 0.76
31 5 0.11
32 6 0.13
ACGTcount: A:0.12, C:0.18, G:0.06, T:0.64
Consensus pattern (29 bp):
TCTTGATTTTTTCTTTTTCACATGATTTC
Found at i:550477 original size:19 final size:17
Alignment explanation
Indices: 550453--550515 Score: 62
Period size: 19 Copynumber: 3.7 Consensus size: 17
550443 AAACAGAAAA
550453 TGTATCGATACATAAGGGT
1 TGTATCGATACATAA--GT
550472 TGTATCGATAC--AA--
1 TGTATCGATACATAAGT
550485 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG--T
550504 TGTATCGATACA
1 TGTATCGATACA
550516 ATGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (17 bp):
TGTATCGATACATAAGT
Found at i:550490 original size:13 final size:13
Alignment explanation
Indices: 550472--550536 Score: 76
Period size: 13 Copynumber: 4.5 Consensus size: 13
550462 ACATAAGGGT
550472 TGTATCGATACAA
1 TGTATCGATACAA
550485 TGTATCGATACATAA
1 TGTATCGATAC--AA
550500 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
550517 TGTATCGATACAA
1 TGTATCGATACAA
550530 TGTATCG
1 TGTATCG
550537 CTACGAAGCT
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
13 31 0.67
15 2 0.04
17 2 0.04
19 11 0.24
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:550492 original size:32 final size:32
Alignment explanation
Indices: 550451--550528 Score: 138
Period size: 32 Copynumber: 2.4 Consensus size: 32
550441 ACAAACAGAA
550451 AATGTATCGATACATAAGGGTTGTATCGATAC
1 AATGTATCGATACATAAGGGTTGTATCGATAC
**
550483 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGGGTTGTATCGATAC
550515 AATGTATCGATACA
1 AATGTATCGATACA
550529 ATGTATCGCT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (32 bp):
AATGTATCGATACATAAGGGTTGTATCGATAC
Found at i:550586 original size:21 final size:21
Alignment explanation
Indices: 550556--550595 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
550546 TACTGCCAAA
550556 GAAATATATCGAAACATTAAG
1 GAAATATATCGAAACATTAAG
* *
550577 GAAATGTATCGATACATTA
1 GAAATATATCGAAACATTA
550596 TATCGATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (21 bp):
GAAATATATCGAAACATTAAG
Found at i:553013 original size:52 final size:52
Alignment explanation
Indices: 552955--553079 Score: 162
Period size: 52 Copynumber: 2.4 Consensus size: 52
552945 TCAATTGTTT
*
552955 ATAATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACAAATTTTCC
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACAAATTTTCC
* * * * *
553006 TTTAATCGGGGATACTCCAACTCTGATTTTATTTTCAAAAACACCAATTTTTC
1 -ATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACAAATTTTCC
* *
553059 ACAATCGAGGATACTCCAACC
1 ATAATCGGGGATACTCCAACC
553080 TTATTTCATC
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
52 48 0.77
53 14 0.23
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (52 bp):
ATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACAAATTTTCC
Found at i:553137 original size:28 final size:28
Alignment explanation
Indices: 553062--553168 Score: 141
Period size: 28 Copynumber: 3.9 Consensus size: 28
553052 ATTTTTCACA
*
553062 ATCGAGGATACTCCAA--CC-TTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
553087 ATCGGGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
553115 ATCGGGGATACTCCAACCCCGTTACCTTC
1 ATCGGGGATACTCCAACCCCGTTA-TTTC
*
553144 A-AGGGGATACTCCAACCCCGTTATT
1 ATCGGGGATACTCCAACCCCGTTATT
553169 ATCTCCAAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
25 15 0.21
27 2 0.03
28 51 0.71
29 4 0.06
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:558574 original size:140 final size:138
Alignment explanation
Indices: 558320--558588 Score: 421
Period size: 140 Copynumber: 1.9 Consensus size: 138
558310 TCTTTGTTAT
*
558320 TTATCTTATTTATCATTTACTTTTTAGCTTTTAGTAATTCATTTGACTAAATTGAAGTTATTTAT
1 TTATCTTATTTATCATTTACTTTTTAACTTTTAGTAATTCATTTGACTAAATTGAAGTTATTTAT
558385 CGGTAACATTAAACTCAGTCAAACACTTTAATAATAAAATAAATATAGATCTCCTTTTAAAAAAT
66 CGGTAACATTAAACTCAGTCAAACACTTTAATAATAAAATAAATATAGATCT--TTTTAAAAAAT
558450 AACTAGTCAC
129 AACTAGTCAC
** * * *
558460 TTATCTTATTTATTGTTTACTTTTTAACTTTTAGTAATTTATTTGACTAAGTTGAAGTTATTTGT
1 TTATCTTATTTATCATTTACTTTTTAACTTTTAGTAATTCATTTGACTAAATTGAAGTTATTTAT
* * * * *
558525 TGGTAACATTAAACTTAGTCAAATACTTTAATAATAGAATAAATGTAGATCTTTTTAAAAAATA
66 CGGTAACATTAAACTCAGTCAAACACTTTAATAATAAAATAAATATAGATCTTTTTAAAAAATA
558589 TATATAACTA
Statistics
Matches: 118, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
138 12 0.10
140 106 0.90
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.44
Consensus pattern (138 bp):
TTATCTTATTTATCATTTACTTTTTAACTTTTAGTAATTCATTTGACTAAATTGAAGTTATTTAT
CGGTAACATTAAACTCAGTCAAACACTTTAATAATAAAATAAATATAGATCTTTTTAAAAAATAA
CTAGTCAC
Found at i:559580 original size:16 final size:16
Alignment explanation
Indices: 559547--559581 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
559537 TAAATATAAA
*
559547 ATAAATAATTTCATTT
1 ATAAATAATTTCAATT
*
559563 ATAAATAATTTTAATT
1 ATAAATAATTTCAATT
559579 ATA
1 ATA
559582 TTATAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAAATAATTTCAATT
Found at i:560043 original size:2 final size:2
Alignment explanation
Indices: 560036--560070 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
560026 TGCGTTGTCT
560036 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
560071 GCTGCCTCTT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:565755 original size:162 final size:163
Alignment explanation
Indices: 565580--565904 Score: 564
Period size: 162 Copynumber: 2.0 Consensus size: 163
565570 CAATGGTAAA
565580 AATAAAATTTAAAATAATATTAATATAATATTAATTTTTATCGATAAAAATATGATAATAAAAAC
1 AATAAAATTTAAAATAATATTAATATAATATTAATTTTTATCGATAAAAATATGATAATAAAAAC
* * *
565645 ATATCAATAATATTATATTATCAATTTTTAAAAAATATTTAAATTAAAAAAT-AAAATATTCATG
66 ATATCAATAATATTATATTATCAATTTTTAAAAAATAGTTAAATTAAAAAATAAAAAAATTCATA
565709 AAGATTTTTATTGA-AAAGAATTAACACATTAGT
131 AAGATTTTTATTGATAAA-AATTAACACATTAGT
* * *
565742 AATAAAATTTAAAATAATATTAATATGATATTAATTTTTATCGATAAAATTATGATAATAACAAC
1 AATAAAATTTAAAATAATATTAATATAATATTAATTTTTATCGATAAAAATATGATAATAAAAAC
565807 ATATCAATAATATTATATTATCAATTTTTAAAAAATAGTTAAATTAAAAAATAAAAAAATTCATA
66 ATATCAATAATATTATATTATCAATTTTTAAAAAATAGTTAAATTAAAAAATAAAAAAATTCATA
*
565872 AAGATTTTTATTGATAAAAATTGACACATTAGT
131 AAGATTTTTATTGATAAAAATTAACACATTAGT
565905 TTTATTAAAT
Statistics
Matches: 154, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
162 113 0.73
163 38 0.25
164 3 0.02
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (163 bp):
AATAAAATTTAAAATAATATTAATATAATATTAATTTTTATCGATAAAAATATGATAATAAAAAC
ATATCAATAATATTATATTATCAATTTTTAAAAAATAGTTAAATTAAAAAATAAAAAAATTCATA
AAGATTTTTATTGATAAAAATTAACACATTAGT
Found at i:566842 original size:18 final size:19
Alignment explanation
Indices: 566819--566854 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
566809 AAGTTAAATT
*
566819 ATTTATTTGA-ATTTAAAA
1 ATTTATTTAATATTTAAAA
566837 ATTTATTTAATATTTAAA
1 ATTTATTTAATATTTAAA
566855 TAAAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
ATTTATTTAATATTTAAAA
Found at i:567057 original size:17 final size:19
Alignment explanation
Indices: 567022--567067 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
567012 TATTATATTA
*
567022 AAAAAATGAGATTGGATTT
1 AAAAAATAAGATTGGATTT
*
567041 -AAAAATAAGATT-TATTT
1 AAAAAATAAGATTGGATTT
567058 AAAAAATAAG
1 AAAAAATAAG
567068 TTAAGCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (19 bp):
AAAAAATAAGATTGGATTT
Found at i:567213 original size:18 final size:19
Alignment explanation
Indices: 567168--567207 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
567158 ATGTAATTTT
*
567168 TATCATATATAAAAATATA
1 TATCATATATAAAAATAAA
567187 TATCATATA-AAAAATAAA
1 TATCATATATAAAAATAAA
567205 TAT
1 TAT
567208 ATTATATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
TATCATATATAAAAATAAA
Found at i:567219 original size:25 final size:24
Alignment explanation
Indices: 567176--567237 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 24
567166 TTTATCATAT
567176 ATAAAAATATATATCATATAAAAA
1 ATAAAAATATATATCATATAAAAA
* * *
567200 ATAAATATATTATATTATATAAACA
1 ATAAAAATA-TATATCATATAAAAA
*
567225 TTAAAAA-ATATAT
1 ATAAAAATATATAT
567238 TAAACTAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
23 5 0.16
24 9 0.28
25 18 0.56
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (24 bp):
ATAAAAATATATATCATATAAAAA
Found at i:570689 original size:20 final size:18
Alignment explanation
Indices: 570664--570727 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 18
570654 CATTTCATAC
*
570664 TTGCATCCACGTTACATGCT
1 TTGCAT-CACATT-CATGCT
570684 TTGCATCATCATTTCATGCT
1 TTGCATCA-CA-TTCATGCT
* *
570704 TT-CATAACCTTCATGCT
1 TTGCATCACATTCATGCT
570721 TTGCATC
1 TTGCATC
570728 CTTTTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 10 0.27
18 4 0.11
19 6 0.16
20 15 0.41
21 2 0.05
ACGTcount: A:0.20, C:0.28, G:0.11, T:0.41
Consensus pattern (18 bp):
TTGCATCACATTCATGCT
Found at i:570694 original size:39 final size:37
Alignment explanation
Indices: 570651--570727 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 37
570641 TTGTTTGCTG
* *
570651 CATCATTTCATACTTGCATCCACGTTACATGCTTTGCAT
1 CATCATTTCATACTTGCAT-AACCTT-CATGCTTTGCAT
* *
570690 CATCATTTCATGCTTTCATAACCTTCATGCTTTGCAT
1 CATCATTTCATACTTGCATAACCTTCATGCTTTGCAT
570727 C
1 C
570728 CTTTTTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 13 0.38
38 4 0.12
39 17 0.50
ACGTcount: A:0.22, C:0.29, G:0.09, T:0.40
Consensus pattern (37 bp):
CATCATTTCATACTTGCATAACCTTCATGCTTTGCAT
Found at i:570764 original size:22 final size:22
Alignment explanation
Indices: 570739--570780 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
570729 TTTTTTATTT
570739 TTGATAATTTTGATTTTTTTGA
1 TTGATAATTTTGATTTTTTTGA
**
570761 TTGATTTTTTTGATTTTTTT
1 TTGATAATTTTGATTTTTTT
570781 AATTTCTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.12, T:0.71
Consensus pattern (22 bp):
TTGATAATTTTGATTTTTTTGA
Found at i:570766 original size:13 final size:13
Alignment explanation
Indices: 570748--570775 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
570738 TTTGATAATT
570748 TTGATTTTTTTGA
1 TTGATTTTTTTGA
570761 TTGATTTTTTTGA
1 TTGATTTTTTTGA
570774 TT
1 TT
570776 TTTTTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (13 bp):
TTGATTTTTTTGA
Found at i:570796 original size:15 final size:15
Alignment explanation
Indices: 570776--570811 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
570766 TTTTTTGATT
570776 TTTTTAATTTCTTGA
1 TTTTTAATTTCTTGA
* *
570791 TTTTTAATTTTTTTA
1 TTTTTAATTTCTTGA
570806 TTTTTA
1 TTTTTA
570812 TCATTATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (15 bp):
TTTTTAATTTCTTGA
Found at i:571860 original size:48 final size:47
Alignment explanation
Indices: 571802--571941 Score: 139
Period size: 48 Copynumber: 3.0 Consensus size: 47
571792 GGTAAACTTA
*
571802 AGGGTGAAAAAGTCTCTAGGGTCAAAGCCGATAGGCAGACTTTAGATG
1 AGGGT-AAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTTTAGATG
* * * * *
571850 AGGGTAAAAAATTCTCCAGGGTCAAAGCGGACAAGCAGAC-TGAGGAT-
1 AGGGT-AAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTTTA-GATG
* *
571897 A-GG---AAAGTCTCTAGGGTCAAAGCCAACAGGTAGACTTTAGATG
1 AGGGTAAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTTTAGATG
571940 AG
1 AG
571942 TCGGTCTCCA
Statistics
Matches: 74, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
42 29 0.39
43 3 0.04
46 2 0.03
47 3 0.04
48 37 0.50
ACGTcount: A:0.36, C:0.16, G:0.30, T:0.19
Consensus pattern (47 bp):
AGGGTAAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTTTAGATG
Found at i:571909 original size:90 final size:84
Alignment explanation
Indices: 571809--572279 Score: 233
Period size: 84 Copynumber: 5.5 Consensus size: 84
571799 TTAAGGGTGA
* * *
571809 AAAAGTCTCTAGGGTCAAAGCCGATAGGCAGACTTTAGATGAGGGTAAAAAATTCTCCAGGGTCA
1 AAAAGTCTCTAGGGTCAAAGCCAACAGGCAGACTTTAGATGA--GT----AAGTCTCCAGGGTCA
571874 AAG-CGGACAAGCAGACTGAGGATAG
60 AAGTC-GACAAGCAGACTGAGGATAG
* * **
571899 GAAAGTCTCTAGGGTCAAAGCCAACAGGTAGACTTTAGATGAGTCGGTCTCCAGGGTCAAAGTCG
1 AAAAGTCTCTAGGGTCAAAGCCAACAGGCAGACTTTAGATGAGTAAGTCTCCAGGGTCAAAGTCG
* * *
571964 ACAGGCATACTGAGGGTAG
66 ACAAGCAGACTGAGGATAG
* * ** * * * *
571983 AAAAGTCTCTAGGGTCAAAGTCGACAGATAGAC-TGAG-GGAAGGAAAGTCTCCA-GGTCAAAGC
1 AAAAGTCTCTAGGGTCAAAGCCAACAGGCAGACTTTAGATG-A-GTAAGTCTCCAGGGTCAAAGT
* ** * *
572045 CCACTGGCAGACCTTA-AATA-
64 CGACAAGCAGA-CTGAGGATAG
** * * * ** * ** * *
572065 AGGCAGTCTCCAGAGTTAAAGCTGACGGGCAGACTTTAGATGAG-GCGATCTCCAAGGTCAAAGC
1 A-AAAGTCTCTAGGGTCAAAGCCAACAGGCAGACTTTAGATGAGTAAG-TCTCCAGGGTCAAAGT
* * * *
572129 CTATAGGTAGACTGAAGGATA-
64 CGACAAGCAGACTG-AGGATAG
* *** * ** *
572150 AGAAAGTCTCCA-GGTCAAAGTTGACAAGCAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCT
1 A-AAAGTCTCTAGGGTCAAAGCCAACAGGCAGACTTTAGATGAGTAAGTCTCCAGGGTCAAAG-T
*
572214 TGAC-AGACAGACTGGAGGATAG
64 CGACAAG-CAGACT-GAGGATAG
* * * * *
572236 GAAAGTCTCCAAGGTCAAAGCCGATCAGGTAGACTTTAGATGAG
1 AAAAGTCTCTAGGGTCAAAGCC-AACAGGCAGACTTTAGATGAG
572280 GCAGTCTCTA
Statistics
Matches: 293, Mismatches: 70, Indels: 39
0.73 0.17 0.10
Matches are distributed among these distances:
82 3 0.01
83 53 0.18
84 133 0.45
85 38 0.13
86 9 0.03
87 17 0.06
88 2 0.01
90 38 0.13
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.19
Consensus pattern (84 bp):
AAAAGTCTCTAGGGTCAAAGCCAACAGGCAGACTTTAGATGAGTAAGTCTCCAGGGTCAAAGTCG
ACAAGCAGACTGAGGATAG
Found at i:572020 original size:126 final size:125
Alignment explanation
Indices: 571848--572397 Score: 403
Period size: 126 Copynumber: 4.3 Consensus size: 125
571838 AGACTTTAGA
* * * * *
571848 TGAGGGTAAAAAATTCTCCAGGGTCAAAGCGGACA-AGCAGACTGAGGATAGGAAAGTCTCTAGG
1 TGAGGATAGAAAAGTCTCCAGGGTCAAAGCCGACAGA-TAGACTGAGGATAGGAAAGTCTCTA-G
* * * * *
571912 GTCAAAGCCAACAGGTAGACTTTAGATGAGTCGGTCTCCAGGGTCAAAGTCGACAGGCATAC
64 GTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGTCGACAGGCAGAC
* * * *
571974 TGAGGGTAGAAAAGTCTCTAGGGTCAAAGTCGACAGATAGACTGAGGGA-AGGAAAGTCTCCAGG
1 TGAGGATAGAAAAGTCTCCAGGGTCAAAGCCGACAGATAGACTGA-GGATAGGAAAGTCTCTAGG
* * * * * * * *
572038 TCAAAGCCCACTGGCAGACCTTAAATAAGGCAGTCTCCAGAGTTAAAG-CTGACGGGCAGAC
65 TCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGTC-GACAGGCAGAC
* *** * * * * * *
572099 TTTA-GAT-GAGGCGATCTCCAAGGTCAAAGCCTATAGGTAGACTGAAGGATAAGAAAGTCTCCA
1 -TGAGGATAGAAAAG-TCTCCAGGGTCAAAGCCGACAGATAGACTG-AGGATAGGAAAGTCTCTA
** * * * *
572162 GGTCAAAGTTGACAAGCAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCTTGACAGACAGAC
63 GGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAG-TCGACAGGCAGAC
* * * * *
572226 TGGAGGATAGGAAAGTCTCCAAGGTCAAAGCCGATCAGGTAGACTTTA-GATGAGG-CAGTCTCT
1 T-GAGGATAGAAAAGTCTCCAGGGTCAAAGCCGA-CAGATAGAC-TGAGGAT-AGGAAAGTCTCT
* * * * * * * * * * *
572289 AAAGTCAAAACTGATAGGTAGACTTTAGATGAGGCAATCTCTATGGTCAAAGCCGATAGGTAGAC
62 -AGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGTCGACAGGCAGAC
* * * *
572354 TAAAGGATAGAAAAGTCTCTAGGGTCAAAGCCGATAGACAGACT
1 T-GAGGATAGAAAAGTCTCCAGGGTCAAAGCCGACAGATAGACT
572398 TCAGATAAGG
Statistics
Matches: 331, Mismatches: 77, Indels: 32
0.75 0.17 0.07
Matches are distributed among these distances:
124 4 0.01
125 78 0.24
126 105 0.32
127 20 0.06
128 67 0.20
129 56 0.17
130 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (125 bp):
TGAGGATAGAAAAGTCTCCAGGGTCAAAGCCGACAGATAGACTGAGGATAGGAAAGTCTCTAGGT
CAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGTCGACAGGCAGAC
Found at i:572225 original size:43 final size:42
Alignment explanation
Indices: 571812--572424 Score: 208
Period size: 42 Copynumber: 14.4 Consensus size: 42
571802 AGGGTGAAAA
* * *
571812 AGTCTCTAGGGTCAAAGCCGATAGGCAGACTTTAGATGAGGGTAAAAA
1 AGTCTCTAGGGTCAAAGCCGACAGACAGACTTTAGATGA-GG-----C
* * * * *
571860 ATTCTCCAGGGTCAAAGCGGACA-AGCAGAC-TGAGGAT-AGGAA
1 AGTCTCTAGGGTCAAAGCCGACAGA-CAGACTTTA-GATGAGG-C
* ** *
571902 AGTCTCTAGGGTCAAAGCCAACAGGTAGACTTTAGATGAGTC
1 AGTCTCTAGGGTCAAAGCCGACAGACAGACTTTAGATGAGGC
* * * * * * * **
571944 GGTCTCCAGGGTCAAAGTCGACAGGCATAC-TGAG-GGTAGAAA
1 AGTCTCTAGGGTCAAAGCCGACAGACAGACTTTAGATG-AG-GC
* * * * *
571986 AGTCTCTAGGGTCAAAGTCGACAGATAGAC-TGAG-GGAAGGAA
1 AGTCTCTAGGGTCAAAGCCGACAGACAGACTTTAGATG-AGG-C
* * * * * * *
572028 AGTCTCCA-GGTCAAAGCCCACTGGCAGACCTTAAATAAGGC
1 AGTCTCTAGGGTCAAAGCCGACAGACAGACTTTAGATGAGGC
* * * * * *
572069 AGTCTCCAGAGTTAAAGCTGACGGGCAGACTTTAGATGAGGC
1 AGTCTCTAGGGTCAAAGCCGACAGACAGACTTTAGATGAGGC
* * * * ** ** * **
572111 -GATCTCCAAGGTCAAAGCCTATAGGTAGACTGAAGGATAAGAA
1 AG-TCTCTAGGGTCAAAGCCGACAGACAGACTTTA-GATGAGGC
* **
572154 AGTCTCCA-GGTCAAAGTTGACA-AGCAGACTTTAGATGAGGC
1 AGTCTCTAGGGTCAAAGCCGACAGA-CAGACTTTAGATGAGGC
* ** *
572195 AGTCTCTAGGGTCAAAGCTTGACAGACAGACTGGAGGAT-AGGAA
1 AGTCTCTAGGGTCAAAGC-CGACAGACAGACTTTA-GATGAGG-C
* * **
572239 AGTCTCCAAGGTCAAAGCCGATCAGGTAGACTTTAGATGAGGC
1 AGTCTCTAGGGTCAAAGCCGA-CAGACAGACTTTAGATGAGGC
** * * * **
572282 AGTCTCTAAAGTCAAAACTGATAGGTAGACTTTAGATGAGGC
1 AGTCTCTAGGGTCAAAGCCGACAGACAGACTTTAGATGAGGC
* * * ** ** **
572324 AATCTCTATGGTCAAAGCCGATAGGTAGACTAAAGGAT-AGAAA
1 AGTCTCTAGGGTCAAAGCCGACAGACAGACTTTA-GATGAG-GC
* * * *
572367 AGTCTCTAGGGTCAAAGCCGATAGACAGACTTCAGATAAGGT
1 AGTCTCTAGGGTCAAAGCCGACAGACAGACTTTAGATGAGGC
572409 AGTCTCTAGGGTCAAA
1 AGTCTCTAGGGTCAAA
572425 ATCGACTAAG
Statistics
Matches: 430, Mismatches: 110, Indels: 56
0.72 0.18 0.09
Matches are distributed among these distances:
40 1 0.00
41 42 0.10
42 237 0.55
43 85 0.20
44 33 0.08
46 2 0.00
47 3 0.01
48 27 0.06
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (42 bp):
AGTCTCTAGGGTCAAAGCCGACAGACAGACTTTAGATGAGGC
Found at i:572296 original size:87 final size:84
Alignment explanation
Indices: 572069--572297 Score: 253
Period size: 84 Copynumber: 2.7 Consensus size: 84
572059 TAAATAAGGC
* * ** * *
572069 AGTCTCCAGAGTTAAAGCTGACGGGCAGACTTTAGATGAGGC-GATCTCCAAGGTCAAAGCCTAT
1 AGTCTCCAG-GTCAAAGCCGACAAGCAGACTTTAGATGAGGCAG-TCTCTAAGGTCAAAGCCTAC
**
572133 AGGTAGACTGAAGGATAAGAA
64 AGACAGACTGAAGGATAAGAA
** * *
572154 AGTCTCCAGGTCAAAGTTGACAAGCAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCTTGACA
1 AGTCTCCAGGTCAAAGCCGACAAGCAGACTTTAGATGAGGCAGTCTCTAAGGTCAAAGCCT-ACA
* *
572219 GACAGACTGGAGGATAGGAA
65 GACAGACTGAAGGATAAGAA
* * *
572239 AGTCTCCAAGGTCAAAGCCGATCAGGTAGACTTTAGATGAGGCAGTCTCTAAAGTCAAA
1 AGTCTCC-AGGTCAAAGCCGA-CAAGCAGACTTTAGATGAGGCAGTCTCTAAGGTCAAA
572298 ACTGATAGGT
Statistics
Matches: 122, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
84 43 0.35
85 35 0.29
86 11 0.09
87 33 0.27
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.21
Consensus pattern (84 bp):
AGTCTCCAGGTCAAAGCCGACAAGCAGACTTTAGATGAGGCAGTCTCTAAGGTCAAAGCCTACAG
ACAGACTGAAGGATAAGAA
Found at i:572315 original size:42 final size:42
Alignment explanation
Indices: 572095--572424 Score: 218
Period size: 42 Copynumber: 7.8 Consensus size: 42
572085 GCTGACGGGC
* *
572095 AGACTTTAGATGAGGC-GATCTCCAAGGTCAAAGCCTATAGGT
1 AGACTTTAGATGAGGCAG-TCTCTAAGGTCAAAGCCGATAGGT
** * ** * ** * * *
572137 AGACTGAAGGATAAGAAAGTCTC-CAGGTCAAAGTTGACAAGC
1 AGACTTTA-GATGAGGCAGTCTCTAAGGTCAAAGCCGATAGGT
* * * **
572179 AGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCTTGACAGAC
1 AGACTTTAGATGAGGCAGTCTCTAAGGTCAAAGC-CGATAGGT
** * *
572222 AGACTGGAGGAT-AGGAAAGTCTCCAAGGTCAAAGCCGATCAGGT
1 AGACTTTA-GATGAGG-CAGTCTCTAAGGTCAAAGCCGAT-AGGT
* * *
572266 AGACTTTAGATGAGGCAGTCTCTAAAGTCAAAACTGATAGGT
1 AGACTTTAGATGAGGCAGTCTCTAAGGTCAAAGCCGATAGGT
* *
572308 AGACTTTAGATGAGGCAATCTCTATGGTCAAAGCCGATAGGT
1 AGACTTTAGATGAGGCAGTCTCTAAGGTCAAAGCCGATAGGT
** ** * **
572350 AGACTAAAGGAT-AGAAAAGTCTCTAGGGTCAAAGCCGATAGAC
1 AGACTTTA-GATGAG-GCAGTCTCTAAGGTCAAAGCCGATAGGT
* * * *
572393 AGACTTCAGATAAGGTAGTCTCTAGGGTCAAA
1 AGACTTTAGATGAGGCAGTCTCTAAGGTCAAA
572425 ATCGACTAAG
Statistics
Matches: 222, Mismatches: 55, Indels: 22
0.74 0.18 0.07
Matches are distributed among these distances:
41 11 0.05
42 100 0.45
43 80 0.36
44 31 0.14
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.22
Consensus pattern (42 bp):
AGACTTTAGATGAGGCAGTCTCTAAGGTCAAAGCCGATAGGT
Found at i:572341 original size:213 final size:210
Alignment explanation
Indices: 571986--572430 Score: 547
Period size: 213 Copynumber: 2.1 Consensus size: 210
571976 AGGGTAGAAA
* *
571986 AGTCTCTAGGGTCAAAGTCGACAGATAGACTGAGGGAAGGAAAGTCTCCAGGTCAAAGCCCACTG
1 AGTCTCTAGGGTCAAAGTCGACAGACAGACTGAGGGAAGGAAAGTCTCCAGGTCAAAGCCCACAG
* * * * *
572051 GCAGACCTTAAATAAGGCAGTCTCCAGAGTTAAAGCTGACGGGCAGACTTTAGATGAGGCGATCT
66 GCAGACCTTAAATAAGGCAGTCTCCAAAGTCAAAACTGACAGGCAGACTTTAGATGAGGCAATCT
* * **
572116 CCAAGGTCAAAGCCTATAGGTAGACTGAAGGATA-AGAAAGTCTCCA-GGTCAAAGTTGACAAG-
131 CCAAGGTCAAAGCCGATAGGTAGACTAAAGGATAGA-AAAGTCTCCAGGGTCAAAGCCGA-AAGA
* *
572178 CAGACTTTAGATGAGGC
194 CAGACTTCAGATAAGGC
* *
572195 AGTCTCTAGGGTCAAAGCTTGACAGACAGACTG-GAGGATAGGAAAGTCTCCAAGGTCAAAGCCG
1 AGTCTCTAGGGTCAAAG-TCGACAGACAGACTGAG-GGA-AGGAAAGTCTCC-AGGTCAAAGCCC
* * * * * * *
572259 ATCAGGTAGACTTTAGATGAGGCAGTCTCTAAAGTCAAAACTGATAGGTAGACTTTAGATGAGGC
62 A-CAGGCAGACCTTAAATAAGGCAGTCTCCAAAGTCAAAACTGACAGGCAGACTTTAGATGAGGC
* * * *
572324 AATCTCTATGGTCAAAGCCGATAGGTAGACTAAAGGATAGAAAAGTCTCTAGGGTCAAAGCCGAT
126 AATCTCCAAGGTCAAAGCCGATAGGTAGACTAAAGGATAGAAAAGTCTCCAGGGTCAAAGCCGAA
*
572389 AGACAGACTTCAGATAAGGT
191 AGACAGACTTCAGATAAGGC
*
572409 AGTCTCTAGGGTCAAAATCGAC
1 AGTCTCTAGGGTCAAAGTCGAC
572431 TAAGCGGACT
Statistics
Matches: 199, Mismatches: 29, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
209 18 0.09
210 16 0.08
211 12 0.06
212 12 0.06
213 100 0.50
214 41 0.21
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.20
Consensus pattern (210 bp):
AGTCTCTAGGGTCAAAGTCGACAGACAGACTGAGGGAAGGAAAGTCTCCAGGTCAAAGCCCACAG
GCAGACCTTAAATAAGGCAGTCTCCAAAGTCAAAACTGACAGGCAGACTTTAGATGAGGCAATCT
CCAAGGTCAAAGCCGATAGGTAGACTAAAGGATAGAAAAGTCTCCAGGGTCAAAGCCGAAAGACA
GACTTCAGATAAGGC
Found at i:572397 original size:85 final size:84
Alignment explanation
Indices: 572186--572424 Score: 203
Period size: 85 Copynumber: 2.8 Consensus size: 84
572176 AGCAGACTTT
** * ** *
572186 AGATGAGGCAGTCTCTAGGGTCAAAGCTTGACAGACAGACTGGAGGATAGGAAAGTCTCCAAGGT
1 AGATGAGAAAGTCTCTAGGGTCAAAGC-TGATAGACAGACTTCA-GATAGGAAA-TCTCTAAGGT
**
572251 CAAAGCCGATCAGGTAGACTTT
63 CAAAGCCGATCAGGTAGACTAA
** ** * ** * * *
572273 AGATGAGGCAGTCTCTAAAGTCAAAACTGATAGGTAGACTTTAGATGAGGCAATCTCTATGGTCA
1 AGATGAGAAAGTCTCTAGGGTCAAAGCTGATAGACAGACTTCAGAT-AGGAAATCTCTAAGGTCA
572338 AAGCCGAT-AGGTAGACTAA
65 AAGCCGATCAGGTAGACTAA
* * * *
572357 AGGAT-AGAAAAGTCTCTAGGGTCAAAGCCGATAGACAGACTTCAGATAAGGTAGTCTCTAGGGT
1 A-GATGAG-AAAGTCTCTAGGGTCAAAGCTGATAGACAGACTTCAGAT-AGGAAATCTCTAAGGT
572421 CAAA
63 CAAA
572425 ATCGACTAAG
Statistics
Matches: 123, Mismatches: 26, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
84 12 0.10
85 71 0.58
86 16 0.13
87 24 0.20
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (84 bp):
AGATGAGAAAGTCTCTAGGGTCAAAGCTGATAGACAGACTTCAGATAGGAAATCTCTAAGGTCAA
AGCCGATCAGGTAGACTAA
Found at i:580814 original size:22 final size:23
Alignment explanation
Indices: 580789--580833 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
580779 ATTCTTATTA
*
580789 ATTAAGCAAATAATG-ATGAATG
1 ATTAAGAAAATAATGTATGAATG
* *
580811 ATTATGAAAATGATGTATGAATG
1 ATTAAGAAAATAATGTATGAATG
580834 CCATGAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.47, C:0.02, G:0.20, T:0.31
Consensus pattern (23 bp):
ATTAAGAAAATAATGTATGAATG
Found at i:585975 original size:2 final size:2
Alignment explanation
Indices: 585968--586000 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
585958 AAACAAACAA
585968 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
586001 ATCAACTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:586968 original size:17 final size:17
Alignment explanation
Indices: 586948--586983 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
586938 TTTTTGATAA
*
586948 TTTTGATTTTCTTGATT
1 TTTTGAATTTCTTGATT
*
586965 TTTTTAATTTCTTGATT
1 TTTTGAATTTCTTGATT
586982 TT
1 TT
586984 CAATTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (17 bp):
TTTTGAATTTCTTGATT
Found at i:592234 original size:21 final size:21
Alignment explanation
Indices: 592210--592259 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
592200 ATTAACCCCA
*
592210 TAGACTATGGGCTATTTAATC
1 TAGACTACGGGCTATTTAATC
592231 TAGACTACGGGCTATTTAATC
1 TAGACTACGGGCTATTTAATC
592252 TAGACTAC
1 TAGACTAC
592260 TTACTTTAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (21 bp):
TAGACTACGGGCTATTTAATC
Found at i:599471 original size:10 final size:10
Alignment explanation
Indices: 599458--599491 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
599448 TAGAATACCG
*
599458 TAGAAGGCTC
1 TAGAAGGTTC
*
599468 TAGAAGATTC
1 TAGAAGGTTC
599478 TAGAAGGTTC
1 TAGAAGGTTC
599488 TAGA
1 TAGA
599492 TGTTGTGGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.26
Consensus pattern (10 bp):
TAGAAGGTTC
Found at i:599547 original size:20 final size:20
Alignment explanation
Indices: 599518--599559 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
599508 GAACATTTTC
599518 GAAGGATCTGGAATAATGTG
1 GAAGGATCTGGAATAATGTG
* *
599538 GAAGGTTCTGGAATATTGTG
1 GAAGGATCTGGAATAATGTG
599558 GA
1 GA
599560 GGCTTATGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.36, T:0.29
Consensus pattern (20 bp):
GAAGGATCTGGAATAATGTG
Found at i:599569 original size:20 final size:20
Alignment explanation
Indices: 599526--599571 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
599516 TCGAAGGATC
*
599526 TGGAATAATGTGGAAGGTTC
1 TGGAATAATGTGGAAGGTTA
*
599546 TGGAATATTGTGG-AGGCTTA
1 TGGAATAATGTGGAAGG-TTA
599566 TGGAAT
1 TGGAAT
599572 GTTCTAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.33
Consensus pattern (20 bp):
TGGAATAATGTGGAAGGTTA
Found at i:601817 original size:155 final size:153
Alignment explanation
Indices: 601561--602288 Score: 577
Period size: 155 Copynumber: 4.7 Consensus size: 153
601551 CTAAGTTTGA
* * * ** * *
601561 AAAAAATAACGAAAATACCCTTAGTGGATACCTTCAACGTGGAAGTACCCGA-TACCCCTAAAGG
1 AAAAAATTACGAAAATACCC-TAGAGGATACCTTCGACGTAAAAGTATCCTAGTACCCCTAAAGG
* * * * *** *
601625 ACTTAAAAATGACTGTAACAAGGATGATCCTATCCTAAATACCCACCTTCGGCATAAAAATGGAT
65 AC-TAAAAAAGACTATAA-AAGGATGAACCTAACCTAAATACCCACCTTCGGCATAAAAGCAGAC
* *
601690 CCGGTTATAACTTAGGACTCAATTCT
128 CCGGTGATAACTTAGGACTCGATTCT
* *
601716 AAAAAATTATGAAAATACCCTAGAGGATACCTTCGACGTAAAAGTATTCTAGTACCCCTAAAGGA
1 AAAAAATTACGAAAATACCCTAGAGGATACCTTCGACGTAAAAGTATCCTAGTACCCCTAAAGGA
* * *
601781 CATAAAAAAGACTATAAAAGGGGTGAACTTAACCTAAATACCTACCTTCGGCATAAAAGCAGACC
66 C-TAAAAAAGACTATAAAA-GGATGAACCTAACCTAAATACCCACCTTCGGCATAAAAGCAGACC
* *
601846 CGGTGATCACTTAAGACTCGATTCT
129 CGGTGATAACTTAGGACTCGATTCT
** * * * * *
601871 AAAAAATTACGAAAATGTTCCTAAAAGATACTTTCGACGTAAAAGTAT-CTCCGTACCCTTAAAG
1 AAAAAATTACGAAAAT-ACCCTAGAGGATACCTTCGACGTAAAAGTATCCT-AGTACCCCTAAAG
* * * * *
601935 GACTTAGAAAGACCTATAAACAGGATTAACCT-ATCTAAATACCCACATTCGG-ATAAAAGCAGA
64 GACTAAAAAAGA-CTATAAA-AGGATGAACCTAACCTAAATACCCACCTTCGGCATAAAAGCAGA
*
601998 CCCGGTGATAACTTAGGACTCGATTTT
127 CCCGGTGATAACTTAGGACTCGATTCT
* * * * *
602025 AAAAAAATTACGAAAATACCTCTA-AGGGATGCCTTTGACTTAAAAGTATCCTAATACCCTTAAA
1 -AAAAAATTACGAAAATACC-CTAGA-GGATACCTTCGACGTAAAAGTATCCTAGTACCCCTAAA
* * * ** * * * * * *
602089 AGACTTAAAAAGAATTATATATTGGGTGAACCTATCTTAAATACCCACCTTTGACATAAAAGCGG
63 GGACTAAAAAAG-ACTATA-AAAGGATGAACCTAACCTAAATACCCACCTTCGGCATAAAAGCAG
* * * * * * *
602154 ACCTGATGATGACCTAGGAATTGGTTCT
126 ACCCGGTGATAACTTAGGACTCGATTCT
* * * * * * * * * *
602182 AAGAAATTACCAAAATGCCCCTATAGGTATACTTTCGACGTGAAAGTCT-TTCGATATCCCTAAA
1 AAAAAATTACGAAAAT-ACCCTAGAGG-ATACCTTCGACGTAAAAGTATCCTAG-TACCCCTAAA
* * * *
602246 GGACTTAAAAAGGATTATAGAAGGGATGAACCTATCCTAAATA
63 GGAC-TAAAAAAGACTATA-AAAGGATGAACCTAACCTAAATA
602289 TCTACTTTTG
Statistics
Matches: 457, Mismatches: 97, Indels: 36
0.77 0.16 0.06
Matches are distributed among these distances:
154 63 0.14
155 212 0.46
156 92 0.20
157 84 0.18
158 6 0.01
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (153 bp):
AAAAAATTACGAAAATACCCTAGAGGATACCTTCGACGTAAAAGTATCCTAGTACCCCTAAAGGA
CTAAAAAAGACTATAAAAGGATGAACCTAACCTAAATACCCACCTTCGGCATAAAAGCAGACCCG
GTGATAACTTAGGACTCGATTCT
Found at i:602151 original size:311 final size:312
Alignment explanation
Indices: 601613--602288 Score: 731
Period size: 311 Copynumber: 2.2 Consensus size: 312
601603 AAGTACCCGA
* * *
601613 TACCCCTAAAGGACTTAAAAATGACTGTAACAAGGATGATCCTATCCTAAATACCCACCTTCGGC
1 TACCCCTAAAGGACTTAAAAATGACTATAACAAGGATGAACCTATCCTAAATACCCACATTCGGC
** * * *
601678 ATAAAAATGGATCCGGTTATAACTTAGGACTCAATTCTAAAAAATTATGAAAATACCCTAGAGGA
66 ATAAAAACAGACCCGGTGATAACTTAGGACTCAATTCTAAAAAATTACGAAAATACCCTAGAGGA
* * *
601743 TACCTTCGACGTAAAAGTATTCTAGTACCCCTAAAGGACATAAAAAAGACTATAAAAGGGGTGAA
131 TACCTTCGACGTAAAAGTATCCTAATACCCCTAAAAGACATAAAAAAGACTATAAAAGGGGTGAA
* * * * * *
601808 CTTAACCTAAATACCTACCTTCGGCATAAAAGCAGACCCGGTGATCACTTAAGACTCGATTCTAA
196 CCTAACCTAAATACCCACCTTCGACATAAAAGCAGACCCGATGATCACCTAAGAATCGATTCTAA
* **
601873 AAAATTACGAAAATGTTCCTAAAAG-ATACTTTCGACGTAAAAGTATCTCCG
261 AAAATTACCAAAATGCCCCTAAAAGTATACTTTCGACGTAAAAGTATCTCCG
* * *
601924 TACCCTTAAAGGACTTAGAAA-GACCTATAA-ACAGGATTAACCTAT-CTAAATACCCACATTCG
1 TACCCCTAAAGGACTTAAAAATGA-CTATAACA-AGGATGAACCTATCCTAAATACCCACATTCG
* * *
601986 G-ATAAAAGCAGACCCGGTGATAACTTAGGACTCGATTTTAAAAAAATTACGAAAATACCTCTA-
64 GCATAAAAACAGACCCGGTGATAACTTAGGACTCAATTCT-AAAAAATTACGAAAATACC-CTAG
* * * * * * * **
602049 AGGGATGCCTTTGACTTAAAAGTATCCTAATACCCTTAAAAGAC-TTAAAAAGAATTATATATTG
127 A-GGATACCTTCGACGTAAAAGTATCCTAATACCCCTAAAAGACATAAAAAAG-ACTATAAAAGG
* * * * * * * * *
602113 GGTGAACCTATCTTAAATACCCACCTTTGACATAAAAGCGGACCTGATGATGACCTAGGAATTGG
190 GGTGAACCTAACCTAAATACCCACCTTCGACATAAAAGCAGACCCGATGATCACCTAAGAATCGA
* * * * * *
602178 TTCTAAGAAATTACCAAAATGCCCCTATAGGTATACTTTCGACGTGAAAGTCT-TTCG
255 TTCTAAAAAATTACCAAAATGCCCCTAAAAGTATACTTTCGACGTAAAAGTATCTCCG
* * * *
602235 ATATCCCTAAAGGACTTAAAAAGGATTATAGA-AGGGATGAACCTATCCTAAATA
1 -TACCCCTAAAGGACTTAAAAATGACTATA-ACAAGGATGAACCTATCCTAAATA
602289 TCTACTTTTG
Statistics
Matches: 298, Mismatches: 56, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
309 31 0.10
310 46 0.15
311 158 0.53
312 52 0.17
313 11 0.04
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.26
Consensus pattern (312 bp):
TACCCCTAAAGGACTTAAAAATGACTATAACAAGGATGAACCTATCCTAAATACCCACATTCGGC
ATAAAAACAGACCCGGTGATAACTTAGGACTCAATTCTAAAAAATTACGAAAATACCCTAGAGGA
TACCTTCGACGTAAAAGTATCCTAATACCCCTAAAAGACATAAAAAAGACTATAAAAGGGGTGAA
CCTAACCTAAATACCCACCTTCGACATAAAAGCAGACCCGATGATCACCTAAGAATCGATTCTAA
AAAATTACCAAAATGCCCCTAAAAGTATACTTTCGACGTAAAAGTATCTCCG
Found at i:604001 original size:11 final size:11
Alignment explanation
Indices: 603981--604028 Score: 71
Period size: 11 Copynumber: 4.4 Consensus size: 11
603971 TTTTTCTTAA
603981 TTTT-TCTCTT
1 TTTTCTCTCTT
*
603991 TTTTCTTTCTT
1 TTTTCTCTCTT
604002 TTTTCTCTCTTT
1 TTTTCTCTC-TT
604014 TTTTCTCTCTT
1 TTTTCTCTCTT
604025 TTTT
1 TTTT
604029 TTCAGCTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
10 4 0.12
11 19 0.56
12 11 0.32
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTCTCTCTT
Found at i:604003 original size:19 final size:19
Alignment explanation
Indices: 603971--604019 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
603961 AATCCAACTA
**
603971 TTTTTCTTAATTTTTCTCT
1 TTTTTCTTTCTTTTTCTCT
603990 TTTTTCTTTCTTTTTTCTCT
1 TTTTTCTTTC-TTTTTCTCT
*
604010 CTTTT-TTTCT
1 TTTTTCTTTCT
604020 CTCTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 1 0.04
19 12 0.46
20 13 0.50
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTCTTTCTTTTTCTCT
Found at i:604004 original size:12 final size:12
Alignment explanation
Indices: 603981--604029 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
603971 TTTTTCTTAA
603981 TTTT-TCTC-TT
1 TTTTCTCTCTTT
*
603991 TTTTCTTTC-TT
1 TTTTCTCTCTTT
604002 TTTTCTCTCTTT
1 TTTTCTCTCTTT
604014 TTTTCTCTCTTT
1 TTTTCTCTCTTT
604026 TTTT
1 TTTT
604030 TCAGCTCAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
10 4 0.11
11 13 0.37
12 18 0.51
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTCTCTCTTT
Found at i:604004 original size:20 final size:19
Alignment explanation
Indices: 603981--604019 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
603971 TTTTTCTTAA
*
603981 TTTTTCTCTTTTTTCTTTCT
1 TTTTTCTCTCTTTT-TTTCT
604001 TTTTTCTCTCTTTTTTTCT
1 TTTTTCTCTCTTTTTTTCT
604020 CTCTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTCTCTCTTTTTTTCT
Found at i:605065 original size:167 final size:166
Alignment explanation
Indices: 604655--605240 Score: 645
Period size: 167 Copynumber: 3.5 Consensus size: 166
604645 AAATTTGAAC
* * * * *
604655 AAAAAATCCAAAACAT-ATGAAAATGAATTAATTTTTTAAAAATGAATTAATAT-GAATCAAATA
1 AAAAAATCAAAAAC-TCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATAAAAT-AAATA
* * * *
604718 ATTATGT-TTTG-TGAATTATAAAATTTGAAAACCAAGAAAAATCTCCTCGAAAAAATTTACGAA
64 A-TA-GTATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTAGGAA
* * *
604781 GTAAAAAACA-TAGTGTTTTAGAAAAAAAAAAGGAATTTCAAGTA
127 -TAGAAAACACT-GTATTTTAG--AAAAATAA-GAATTTCAAGTA
* *
604825 AAAAAATAAAAAACTCATGACAATGAATGAATTTTTGAAAACTGAATTAATATAAAATAAATAAT
1 AAAAAATCAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATAAAATAAATAAT
*
604890 -GATATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTTGAAAAAAATTTATGGAAT
66 AG-TATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCG-AAAAAATTTA-GGAAT
* *
604954 AGAAAACACTGTAATTCAGAAAAATAAGAATTTCAAGTA
128 AGAAAACACTGTATTTTAGAAAAATAAGAATTTCAAGTA
* *
604993 AAAAAATCAAAAACTCATGAAAATGAATCAA-TTTTGAAAACTAAATTAATATAAAATAAATAAT
1 AAAAAATCAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATAAAATAAATAAT
* * ** * *
605057 AGTATTTGATGAATTTCAAAAGTCAAAAACCAAGAAAAGT-CCCTCCGAAAAAATTTAAGGAGTA
66 AGTATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCT-CGAAAAAATTT-AGGAATA
* * *
605121 GAAAACTCCGTATTTTTAAAAAAAT-AGAAATTTCAAG-A
129 GAAAACACTGTA-TTTTAGAAAAATAAG-AATTTCAAGTA
* * * *
605159 AAAAAACTC-AAAATTCATGGAAACGAATGAATTTTTGAAAACTGAATTAATACAAAATAAATAA
1 AAAAAA-TCAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATAAAATAAATAA
*
605223 TAATATTTGATGAATTTT
65 TAGTATTTGATGAATTTT
605241 GATGTTTGAA
Statistics
Matches: 360, Mismatches: 41, Indels: 33
0.83 0.09 0.08
Matches are distributed among these distances:
166 55 0.15
167 134 0.37
168 42 0.12
169 13 0.04
170 85 0.24
171 27 0.08
172 4 0.01
ACGTcount: A:0.53, C:0.09, G:0.10, T:0.28
Consensus pattern (166 bp):
AAAAAATCAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATAAAATAAATAAT
AGTATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTAGGAATAGA
AAACACTGTATTTTAGAAAAATAAGAATTTCAAGTA
Found at i:605330 original size:42 final size:43
Alignment explanation
Indices: 605269--605360 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 43
605259 AAATTTTACC
*
605269 AAAAATTTTACATACAAAGAAAAAGTCGTGTTTTGTTCCC-GA
1 AAAAATTTTACATACAAAGAAAAAGTCGTGCTTTGTTCCCGGA
** * *
605311 AAAAATTTTATGTATAAAGAAAAAGTCGTGCTTTGTTCCCGGG
1 AAAAATTTTACATACAAAGAAAAAGTCGTGCTTTGTTCCCGGA
605354 AAAAATT
1 AAAAATT
605361 CAAGATTTGC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 36 0.82
43 8 0.18
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (43 bp):
AAAAATTTTACATACAAAGAAAAAGTCGTGCTTTGTTCCCGGA
Found at i:608198 original size:27 final size:28
Alignment explanation
Indices: 608145--608198 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 28
608135 TATCCAAATG
* *
608145 TATTAAATTTTGTATATAAAATGTTTTC
1 TATTAAATGTTGTATATAAAATATTTTC
* *
608173 TATT-AATGTTGTATATATATTATTTT
1 TATTAAATGTTGTATATAAAATATTTT
608199 ATTATCTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (28 bp):
TATTAAATGTTGTATATAAAATATTTTC
Found at i:612909 original size:15 final size:15
Alignment explanation
Indices: 612889--612919 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
612879 ATGCTTTCCA
612889 TATTCTATTTTCTTT
1 TATTCTATTTTCTTT
*
612904 TATTCTCTTTTCTTT
1 TATTCTATTTTCTTT
612919 T
1 T
612920 CTTTTCCTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTCTATTTTCTTT
Found at i:612930 original size:20 final size:20
Alignment explanation
Indices: 612891--612937 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
612881 GCTTTCCATA
* *
612891 TTCTATTTTCTTTTATTCTC
1 TTCTCTTTTCTTTTACTCTC
* *
612911 TTTTCTTTTCTTTTCCTCTC
1 TTCTCTTTTCTTTTACTCTC
612931 TTCTCTT
1 TTCTCTT
612938 CACTTCTATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.04, C:0.26, G:0.00, T:0.70
Consensus pattern (20 bp):
TTCTCTTTTCTTTTACTCTC
Found at i:617596 original size:19 final size:19
Alignment explanation
Indices: 617549--617597 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
617539 AAGTTATAAA
617549 TTAAAAT-TAAAAAAGAAC
1 TTAAAATATAAAAAAGAAC
*
617567 TTAACAA-ATAAAAAA-ATAG
1 TTAA-AATATAAAAAAGA-AC
617586 TTAAAATATAAA
1 TTAAAATATAAA
617598 TAATTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.24
Consensus pattern (19 bp):
TTAAAATATAAAAAAGAAC
Found at i:619376 original size:2 final size:2
Alignment explanation
Indices: 619363--619398 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
619353 AGGGAGAAAG
*
619363 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
619399 GCGGAATGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:619441 original size:12 final size:12
Alignment explanation
Indices: 619424--619472 Score: 62
Period size: 12 Copynumber: 3.8 Consensus size: 12
619414 AAGTGATAGG
619424 AGAAGAAAAGGA
1 AGAAGAAAAGGA
*
619436 AGAAGAAAAGAA
1 AGAAGAAAAGGA
619448 AGAAGGAAAAAGGA
1 AGAA-G-AAAAGGA
619462 AGAAAGAAAAG
1 AG-AAGAAAAG
619473 AAGGAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 15 0.47
13 6 0.19
14 9 0.28
15 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (12 bp):
AGAAGAAAAGGA
Found at i:619472 original size:23 final size:23
Alignment explanation
Indices: 619437--619481 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
619427 AGAAAAGGAA
619437 GAAGAAAAGAAAGAAGGAAAAAG
1 GAAGAAAAGAAAGAAGGAAAAAG
619460 GAAG-AAAGAAAAGAAGGAAAAA
1 GAAGAAAAG-AAAGAAGGAAAAA
619482 AATCTTAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (23 bp):
GAAGAAAAGAAAGAAGGAAAAAG
Found at i:619483 original size:26 final size:26
Alignment explanation
Indices: 619424--619483 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
619414 AAGTGATAGG
619424 AGAAGAAAAGGAAGAAGAAAAGAAAGA
1 AGAA-AAAAGGAAGAAGAAAAGAAAGA
* *
619451 AGGAAAAAGGAAGAAAGAAAAGAAGGA
1 AGAAAAAAGGAAG-AAGAAAAGAAAGA
619478 A-AAAAA
1 AGAAAAA
619484 TCTTAGTCTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 13 0.45
27 16 0.55
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (26 bp):
AGAAAAAAGGAAGAAGAAAAGAAAGA
Found at i:620092 original size:16 final size:17
Alignment explanation
Indices: 620071--620103 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
620061 AGGGGTGAGT
*
620071 GAAGAA-GAAAAGAAAG
1 GAAGAAGGAAAAAAAAG
620087 GAAGAAGGAAAAAAAAG
1 GAAGAAGGAAAAAAAAG
620104 AGTGGGTCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
GAAGAAGGAAAAAAAAG
Found at i:620153 original size:46 final size:44
Alignment explanation
Indices: 620073--620190 Score: 139
Period size: 46 Copynumber: 2.6 Consensus size: 44
620063 GGGTGAGTGA
* *
620073 AGAAGAAAAGAAAGGAAGAAGGAAAAAAAAGAGTGGGTCAGGTAGG
1 AGAAGAAAAGAAAGGAAGAA--AAAAAAAAGAGTGGGCCAGGCAGG
* *
620119 AGAGGAAAAGAAAGGAAGAAAAAAAGAAATGAGTGGGCCTGGCAGG
1 AGAAGAAAAGAAAGGAAGAAAAAAA-AAA-GAGTGGGCCAGGCAGG
* *
620165 AGAAGAAAAG-AACGAAGGAAAAAAAA
1 AGAAGAAAAGAAAGGAAGAAAAAAAAA
620191 GTTTTAGTCT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
44 7 0.11
45 15 0.24
46 41 0.65
ACGTcount: A:0.57, C:0.04, G:0.34, T:0.05
Consensus pattern (44 bp):
AGAAGAAAAGAAAGGAAGAAAAAAAAAAGAGTGGGCCAGGCAGG
Found at i:621256 original size:42 final size:42
Alignment explanation
Indices: 621197--621283 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
621187 GTTAATTTTT
621197 TAATTACTTGGTGGTCTTAATGGTACTTACTTTTGTTGGCAA
1 TAATTACTTGGTGGTCTTAATGGTACTTACTTTTGTTGGCAA
* *
621239 TAATTACTTTGTGGTCTTAATGGTACTTATTTTTGTTGGCAA
1 TAATTACTTGGTGGTCTTAATGGTACTTACTTTTGTTGGCAA
621281 TAA
1 TAA
621284 CTGTTGAAGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.23, C:0.10, G:0.20, T:0.47
Consensus pattern (42 bp):
TAATTACTTGGTGGTCTTAATGGTACTTACTTTTGTTGGCAA
Found at i:631506 original size:2 final size:2
Alignment explanation
Indices: 631499--631527 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
631489 TACTTATTGT
631499 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
631528 TTTCTTTCCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:637430 original size:24 final size:23
Alignment explanation
Indices: 637403--637459 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
637393 CAGATCTTGG
* *
637403 TATGAAATTTTTTATCGAATCTGC
1 TATGAAATTTTTGAT-GAATCTAC
** *
637427 TATGAAAACTTTGATGGATCTAC
1 TATGAAATTTTTGATGAATCTAC
637450 TATGAAATTT
1 TATGAAATTT
637460 ATAAATCTGA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (23 bp):
TATGAAATTTTTGATGAATCTAC
Found at i:643748 original size:22 final size:22
Alignment explanation
Indices: 643707--643749 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
643697 ATTTAGATAG
* **
643707 TTTTTTAATTTATTTTATTTTA
1 TTTTCTAATTTATTAAATTTTA
643729 TTTTCTAATTTATTAAATTTT
1 TTTTCTAATTTATTAAATTTT
643750 TATTATTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTCTAATTTATTAAATTTTA
Found at i:647177 original size:28 final size:27
Alignment explanation
Indices: 647146--647217 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 27
647136 CTATTTCAGA
*
647146 CATTGTCTTATTAAGACAAATTTATCCT
1 CATTGTCTTATTAAGACAAACTTAT-CT
* *
647174 CATTATCTTATTAAGACAAGCTTATCT
1 CATTGTCTTATTAAGACAAACTTATCT
*
647201 CTTTTGTCTTATTAAGA
1 C-ATTGTCTTATTAAGA
647218 TATCAGACAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 3 0.08
28 35 0.92
ACGTcount: A:0.31, C:0.17, G:0.08, T:0.44
Consensus pattern (27 bp):
CATTGTCTTATTAAGACAAACTTATCT
Found at i:647373 original size:84 final size:83
Alignment explanation
Indices: 647284--647501 Score: 242
Period size: 84 Copynumber: 2.6 Consensus size: 83
647274 GTTTATTCAC
* * * * * * *
647284 ATTGTCCTGTTAAGACAAGCTTATCCATTTTGTTTTAACATATTTTTACTTTAGACACTT-TCTT
1 ATTGTCTTATTAAGACAAGCTTATCCATTTTGTCTTAACACATGTCTACTTTAGACA-TTATATT
*
647348 GTTAAGAAAAGCTTATCTAT
65 GTTAAGAAAACCTTATC-AT
* * * ** * *
647368 ATTGTCTTATTAAAATAAGCTTATCTATTTTGTCTTATTACATGTCTATTTTAGATATTATATTG
1 ATTGTCTTATTAAGACAAGCTTATCCATTTTGTCTTAACACATGTCTACTTTAGACATTATATTG
*
647433 TTAAGACAACCTTATCAT
66 TTAAGAAAACCTTATCAT
* *
647451 CTTGTCTTATTAAGACAAACTTATCCATTTTGTCTTAA-ACATGTCTACTTT
1 ATTGTCTTATTAAGACAAGCTTATCCATTTTGTCTTAACACATGTCTACTTT
647502 GAATAATGTT
Statistics
Matches: 110, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
82 12 0.11
83 36 0.33
84 62 0.56
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.46
Consensus pattern (83 bp):
ATTGTCTTATTAAGACAAGCTTATCCATTTTGTCTTAACACATGTCTACTTTAGACATTATATTG
TTAAGAAAACCTTATCAT
Found at i:647473 original size:27 final size:28
Alignment explanation
Indices: 647433--647487 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
647423 TATTATATTG
*
647433 TTAAGACAACCTTAT-CATCTTGTCTTA
1 TTAAGACAAACTTATCCATCTTGTCTTA
*
647460 TTAAGACAAACTTATCCATTTTGTCTTA
1 TTAAGACAAACTTATCCATCTTGTCTTA
647488 AACATGTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (28 bp):
TTAAGACAAACTTATCCATCTTGTCTTA
Found at i:647542 original size:83 final size:83
Alignment explanation
Indices: 647349--647530 Score: 188
Period size: 83 Copynumber: 2.2 Consensus size: 83
647339 CACTTTCTTG
* * * * * * * * *
647349 TTAAGAAAAGCTTATCTATATTGTCTTATTAAAATAAGCTTATCTATTTTGTCTTATTACATGTC
1 TTAAGACAACCTTATC-ATCTTATCTTATTAAGACAAACTTATCCATTTTGTCTTATAACATGTC
* * *
647414 TATTTTAGATATTATATTG
65 TATTTGAGATAATATATTA
*
647433 TTAAGACAACCTTATCATCTTGTCTTATTAAGACAAACTTATCCATTTTGTCTTA-AACATGTCT
1 TTAAGACAACCTTATCATCTTATCTTATTAAGACAAACTTATCCATTTTGTCTTATAACATGTCT
* *
647497 ACTTTGA-ATAATGTTTTA
66 A-TTTGAGATAATATATTA
*
647515 TTAAGATAACCTTATC
1 TTAAGACAACCTTATC
647531 CACTTTATCT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
82 31 0.37
83 38 0.46
84 14 0.17
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (83 bp):
TTAAGACAACCTTATCATCTTATCTTATTAAGACAAACTTATCCATTTTGTCTTATAACATGTCT
ATTTGAGATAATATATTA
Found at i:654817 original size:60 final size:60
Alignment explanation
Indices: 654720--654904 Score: 203
Period size: 60 Copynumber: 3.1 Consensus size: 60
654710 TATAACACAA
* * ** * * *
654720 AATACTAAGAATCAAAATCC-AGACTTTAAAGAATCCCTATTAGAATTGATTTCAACCCAG
1 AATACTAAGAATCACAA-CCTAGAATCCAAACAATCCCTATTAAAATTGATTTCAACCTAG
* ***
654780 AATACT-AGAAATCACACCCTAGAATTTGAACAATCCCTATTAAAATTGATTTCAACCTAG
1 AATACTAAG-AATCACAACCTAGAATCCAAACAATCCCTATTAAAATTGATTTCAACCTAG
* * * *
654840 AATAGTAAGAATCACAACCTTGAATCCAAAGAATCCCTATTAAAACTGATTTCAACCTAG
1 AATACTAAGAATCACAACCTAGAATCCAAACAATCCCTATTAAAATTGATTTCAACCTAG
654900 AATAC
1 AATAC
654905 CATGAATGAC
Statistics
Matches: 106, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
59 4 0.04
60 100 0.94
61 2 0.02
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.26
Consensus pattern (60 bp):
AATACTAAGAATCACAACCTAGAATCCAAACAATCCCTATTAAAATTGATTTCAACCTAG
Found at i:654940 original size:60 final size:58
Alignment explanation
Indices: 654751--654944 Score: 210
Period size: 60 Copynumber: 3.2 Consensus size: 58
654741 GACTTTAAAG
* * * *
654751 AATCCCTATTAGAATTGATTTCAACCCAGAATACTAGAAATCACACCCTAGAATTTGAAC
1 AATCCCTATTAAAATTGATTTCAACCTAGAATACTAG-AATCACA-CCTAGAATCTGAAA
* * *
654811 AATCCCTATTAAAATTGATTTCAACCTAGAATAGTAAGAATCACAACCTTGAATC-CAAA
1 AATCCCTATTAAAATTGATTTCAACCTAGAATACT-AGAATCAC-ACCTAGAATCTGAAA
* * *
654870 GAATCCCTATTAAAACTGATTTCAACCTAGAATACCATGAATGACACCTAAGAATCTGAAA
1 -AATCCCTATTAAAATTGATTTCAACCTAGAATACTA-GAATCACACCT-AGAATCTGAAA
**
654931 AATTGCTATTAAAA
1 AATCCCTATTAAAA
654945 AGGTATTTCA
Statistics
Matches: 113, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
59 7 0.06
60 100 0.88
61 6 0.05
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.27
Consensus pattern (58 bp):
AATCCCTATTAAAATTGATTTCAACCTAGAATACTAGAATCACACCTAGAATCTGAAA
Found at i:656967 original size:28 final size:28
Alignment explanation
Indices: 656932--657000 Score: 120
Period size: 28 Copynumber: 2.5 Consensus size: 28
656922 AATAAAATCA
*
656932 GGGTTGGAGTATCCCCTCAAAAATAACG
1 GGGTTGGAGTATCCCCGCAAAAATAACG
*
656960 GGGTTGGAGTATCCCCGCGAAAATAACG
1 GGGTTGGAGTATCCCCGCAAAAATAACG
656988 GGGTTGGAGTATC
1 GGGTTGGAGTATC
657001 TCCGATTGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.28, C:0.19, G:0.32, T:0.22
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGCAAAAATAACG
Found at i:657049 original size:51 final size:51
Alignment explanation
Indices: 656986--657105 Score: 195
Period size: 51 Copynumber: 2.4 Consensus size: 51
656976 GCGAAAATAA
* *
656986 CGGGGTTGGAGTATCTCCGATTGTGAGAAATCAATATTTTAGGAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGGAATAAAAC
*
657037 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGGAATAAAGC
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGGAATAAAAC
**
657088 CGGGGTTCAAGTATCCCC
1 CGGGGTTGGAGTATCCCC
657106 TCGGAAATAA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGGAATAAAAC
Found at i:657128 original size:28 final size:27
Alignment explanation
Indices: 657088--657162 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
657078 GGAATAAAGC
** **
657088 CGGGGTTCAAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGAGG-AATAA
* * *
657116 CGGGGTTGGAGTATTCCCGATGATTAA
1 CGGGGTTGGAGTATCCCCGAGGAATAA
657143 CGGGGTTGGAGTATCCCCGA
1 CGGGGTTGGAGTATCCCCGA
657163 TTATAAAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 23 0.59
28 16 0.41
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGAGGAATAA
Found at i:657191 original size:158 final size:157
Alignment explanation
Indices: 656939--657223 Score: 367
Period size: 158 Copynumber: 1.8 Consensus size: 157
656929 TCAGGGTTGG
*
656939 AGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGCGAAAATAACGGGGTTGGAGTATCTCC
1 AGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGCGAAAATAACGGGGTTGGAGTATCCCC
* * * * * *
657004 GATTGTGAGAAATCAATATTTTAGGAATAAAACCGGGGTTGGAGTATCCCCGATTATGAGAAATC
66 GATTATAAAAAATCAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCCAATTAT-AGAAATC
657069 AATATTTTAGGAATAAAGCCGGGGTTCA
130 AATATTTTAGGAATAAAGCCGGGGTTCA
** * * *
657097 AGTATCCCCTCGGAAATAACGGGGTTGGAGTAT-TCC-CGATGATTAACGGGGTTGGAGTATCCC
1 AGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGCGA-AAATAACGGGGTTGGAGTATCCC
*** * * *
657160 CGATTATAAAAAATTGGTGTTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCAATTATAGAAA
65 CGATTATAAAAAATCAATATTTTAG-AAATAAAACCGGAGTTGGAGTATCCCCAATTATAGAAA
657224 ATTGGTGTTT
Statistics
Matches: 107, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
156 3 0.03
157 44 0.41
158 60 0.56
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.27
Consensus pattern (157 bp):
AGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGCGAAAATAACGGGGTTGGAGTATCCCC
GATTATAAAAAATCAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCCAATTATAGAAATCA
ATATTTTAGGAATAAAGCCGGGGTTCA
Found at i:657242 original size:158 final size:158
Alignment explanation
Indices: 656939--657263 Score: 352
Period size: 158 Copynumber: 2.1 Consensus size: 158
656929 TCAGGGTTGG
*
656939 AGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGCGAAAATAACGGGGTTGGAGTATCTCC
1 AGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGCGAAAATAACGGGGTTGGAGTATCCCC
* * * * * *
657004 GATTGTGAGAAATCAATATTTTAGGAATAAAACCGGGGTTGGAGTATCCCCGATTATGAGAAATC
66 GATTATAAAAAATCAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCCAATTATGAGAAATC
* *
657069 AATATTTTAGGAATAAAGCCGGGGTTCA
131 AATATTTTAGGAATAAAACCGGAGTTCA
** * * *
657097 AGTATCCCCTCGGAAATAACGGGGTTGGAGTAT-TCC-CGATGATTAACGGGGTTGGAGTATCCC
1 AGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGCGA-AAATAACGGGGTTGGAGTATCCC
*** * * *
657160 CGATTATAAAAAATTGGTGTTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCAATTAT-AGAAA
65 CGATTATAAAAAATCAATATTTTAG-AAATAAAACCGGAGTTGGAGTATCCCCAATTATGAG-AA
*** * * *
657224 ATTGGTGTTTT-GGAAATAAAATCGGAGTTGA
128 ATCAATATTTTAGG-AATAAAACCGGAGTTCA
657255 AGTATCCCC
1 AGTATCCCC
657264 GATTATAGAA
Statistics
Matches: 137, Mismatches: 26, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
156 3 0.02
157 43 0.31
158 91 0.66
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.27
Consensus pattern (158 bp):
AGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGCGAAAATAACGGGGTTGGAGTATCCCC
GATTATAAAAAATCAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCCAATTATGAGAAATC
AATATTTTAGGAATAAAACCGGAGTTCA
Found at i:657259 original size:51 final size:51
Alignment explanation
Indices: 657147--657427 Score: 361
Period size: 51 Copynumber: 5.5 Consensus size: 51
657137 GATTAACGGG
* *
657147 GTTGGAGTATCCCCGATTATAAAAAATTGGTGTTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCAATTATAGAAAATTGGTG-TTTTGAAAATAAAATCGGA
*
657199 GTTGGAGTATCCCCAATTATAGAAAATTGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCAATTATAGAAAATTGGTGTTTTGAAAATAAAATCGGA
* * *
657250 GTTGAAGTATCCCCGATTATAGAAAATTGGTGTTTTGAAAATAAAATCGGG
1 GTTGGAGTATCCCCAATTATAGAAAATTGGTGTTTTGAAAATAAAATCGGA
* * *
657301 GTTGGAGTATCCCCAGTTATGGAAAATTGGTGTTTTGAAAATAAAATCGAA
1 GTTGGAGTATCCCCAATTATAGAAAATTGGTGTTTTGAAAATAAAATCGGA
* * * * * * *
657352 GTTTGAGTATCCCCGATTGT-GAAAAATTAGTATTTT-AGAAATAAAACCGGG
1 GTTGGAGTATCCCCAATTATAG-AAAATTGGTGTTTTGA-AAATAAAATCGGA
*
657403 GTTGGAGTACCCCCAATTAT-GAAAA
1 GTTGGAGTATCCCCAATTATAGAAAA
657428 ATTGAGAAAC
Statistics
Matches: 201, Mismatches: 26, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
50 6 0.03
51 165 0.82
52 30 0.15
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCAATTATAGAAAATTGGTGTTTTGAAAATAAAATCGGA
Found at i:657431 original size:153 final size:154
Alignment explanation
Indices: 657143--657427 Score: 398
Period size: 153 Copynumber: 1.9 Consensus size: 154
657133 CGATGATTAA
*
657143 CGGGGTTGGAGTATCCCCGATTATAAAAAATTGGTGTTTTTGAAAATAAAATCGGAGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTATAAAAAATTGGTGTTTTTGAAAATAAAATCGAAGTTGGAGTA
* * * * * *
657208 TCCCCAATTATAGAAAATTGGTGTTTTGGAAATAAAATCGGAGTTGAAGTATCCCCGATTATAGA
66 TCCCCAATTATAGAAAATTAGTATTTTAGAAATAAAACCGGAGTTGAAGTACCCCCAATTATAGA
657273 AAATTGGTGTTTTGAAAATAAAAT
131 AAATTGGTGTTTTGAAAATAAAAT
** *
657297 CGGGGTTGGAGTATCCCC-AGTTATGGAAAATTGGTG-TTTTGAAAATAAAATCGAAGTTTGAGT
1 CGGGGTTGGAGTATCCCCGA-TTATAAAAAATTGGTGTTTTTGAAAATAAAATCGAAGTTGGAGT
* * * *
657360 ATCCCCGATTGT-GAAAAATTAGTATTTTAGAAATAAAACCGGGGTTGGAGTACCCCCAATTAT-
65 ATCCCCAATTATAG-AAAATTAGTATTTTAGAAATAAAACCGGAGTTGAAGTACCCCCAATTATA
657423 GAAAA
129 GAAAA
657428 ATTGAGAAAC
Statistics
Matches: 115, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
152 6 0.05
153 77 0.67
154 32 0.28
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (154 bp):
CGGGGTTGGAGTATCCCCGATTATAAAAAATTGGTGTTTTTGAAAATAAAATCGAAGTTGGAGTA
TCCCCAATTATAGAAAATTAGTATTTTAGAAATAAAACCGGAGTTGAAGTACCCCCAATTATAGA
AAATTGGTGTTTTGAAAATAAAAT
Found at i:659853 original size:19 final size:21
Alignment explanation
Indices: 659829--659880 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
659819 AGCGATACAC
*
659829 TGTATCGATACA-TTACT-TA
1 TGTATCGATACATTTACTGAA
659848 TGTATCGATACATTTACTGAA
1 TGTATCGATACATTTACTGAA
659869 TGTATCGATACA
1 TGTATCGATACA
659881 AATTATTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.40
20 5 0.17
21 13 0.43
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTACTGAA
Found at i:661060 original size:12 final size:12
Alignment explanation
Indices: 661043--661067 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
661033 CTAATATGCT
661043 CACCTAACACAC
1 CACCTAACACAC
661055 CACCTAACACAC
1 CACCTAACACAC
661067 C
1 C
661068 TAATATGCTC
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:0.40, C:0.52, G:0.00, T:0.08
Consensus pattern (12 bp):
CACCTAACACAC
Found at i:661060 original size:34 final size:34
Alignment explanation
Indices: 661022--661088 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
661012 CTAACAAATT
661022 ACCTAACACACCTAATATGCTCACCTAACACACC
1 ACCTAACACACCTAATATGCTCACCTAACACACC
661056 ACCTAACACACCTAATATGCTCACCTAACACAC
1 ACCTAACACACCTAATATGCTCACCTAACACAC
661089 TTAATATGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.39, C:0.40, G:0.03, T:0.18
Consensus pattern (34 bp):
ACCTAACACACCTAATATGCTCACCTAACACACC
Found at i:661083 original size:22 final size:22
Alignment explanation
Indices: 661055--661107 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
661045 CCTAACACAC
661055 CACCTAACACACCTAATATGCT
1 CACCTAACACACCTAATATGCT
* *
661077 CACCTAACACACTTAATATGTT
1 CACCTAACACACCTAATATGCT
*
661099 TACCTAACA
1 CACCTAACA
661108 TACCACATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.32, G:0.04, T:0.26
Consensus pattern (22 bp):
CACCTAACACACCTAATATGCT
Found at i:670053 original size:20 final size:20
Alignment explanation
Indices: 670006--670080 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
669996 AAAAAGACAT
*
670006 AATGTATCGATACATTGA-A
1 AATGTATCGATACATTCATA
*
670025 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
670046 CATGTATCGATATATTAAAA
1 AATGTATCGATACATTCATA
670066 AATGTATCGATACAT
1 AATGTATCGATACAT
670081 CTGGGTTAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 44 0.98
21 1 0.02
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:670074 original size:40 final size:39
Alignment explanation
Indices: 670003--670080 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
669993 GGTAAAAAGA
* *
670003 CATAATGTATCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTAAAAAATATATCGATACATT
* *
670042 CATACATGTATCGATATATTAAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTAAAAAATATATCGATACAT
670081 CTGGGTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTAAAAAATATATCGATACATT
Found at i:670974 original size:117 final size:117
Alignment explanation
Indices: 670641--671865 Score: 1196
Period size: 117 Copynumber: 10.5 Consensus size: 117
670631 AAAAAAAATG
* * * *
670641 GTGCCACTAACTTGTGTGGACTTTGAAAAGAGTTGCCACCAACTCGTGTGGGCTTTGAAAAGAGT
1 GTGCCACTGACTTGTG-GG-CTTTG-AAAGGGTTGCCACCGACT--TGTGGGCTTTGAAAGGA-T
* *
670706 GCCACTGACTTGTGGGCTTTG-AAAGGG-TGCCACTGACT-TGTGGGCTTTGAAAGGA
60 GCCACTGACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCTGTGGGCTTTGAAAAGA
* *
670761 -TGCCACTGACTTGTGAGCTTTGAAAAGGGTTGCCACCGACTCATGTGGCCTTTGAAAGGATGCC
1 GTGCCACTGACTTGTGGGCTTTG-AAAGGGTTGCCACCGACT--TGTGGGCTTTGAAAGGATGCC
* *
670825 ACTGA-TTGTGTGGACTTTGAAAAGAGTTGCCACCAACTCGTGTGGGCTTTGAAAAGA
63 ACTGACTTGTG-GG-CTTTGAAAAGGGTTGCCACCGACTC-TGTGGGCTTTGAAAAGA
* * * * *
670882 GTGCCACTGACTTGTAGACTTTAAAAAGG-TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACT
1 GTGCCACTGACTTGTGGGCTTTGAAAGGGTTGCCACCGACTTGTGGGCTTTGAAAGGATGCCACT
* * *
670946 AACTTGTGGTCTTTGAAAAGGGTTGCCACCGACTCATGTGGGCTTTG-AAAGG
66 GACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTC-TGTGGGCTTTGAAAAGA
* * *
670998 GTGCCACTGACTTGTGGGCTTTGAAAAGTGTTACCACCGACTCGTGGGCTTTGAAAGGATGCCAC
1 GTGCCACTGACTTGTGGGCTTTG-AAAGGGTTGCCACCGACTTGTGGGCTTTGAAAGGATGCCAC
* *
671063 TGACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAAA
65 TGACTTGTGGGCTTTGAAAAGGGTTGCCACCGAC-TCTGTGGGCTTTGAAAAGA
**
671117 GTGCCACTGACTTGTGGGCTTTGAAAGGG-TGCCACTTACTTGTGGGCTTTGAAAGGATGCCACT
1 GTGCCACTGACTTGTGGGCTTTGAAAGGGTTGCCACCGACTTGTGGGCTTTGAAAGGATGCCACT
* * *
671181 GACTTGTGGGCTTTGAAAAGTGTTGCCACCAACTC-GTGGGCTTTGAAAGGA
66 GACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCTGTGGGCTTTGAAAAGA
* *
671232 -TGCCACTAACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTGC
1 GTGCCACTGACTTGTGGGCTTTG-AAAGGGTTGCCACCGACT--TGTGGGCTTTGAAAGGA-TGC
* * *
671296 CA-TCGACTTGTGGGCTTTG-AAAGGG-TGCCACTGACT-TATGGGCTTTGAAAGGA
62 CACT-GACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCTGTGGGCTTTGAAAAGA
* *
671349 -TGCCACTGACTTGTGGGCTTTGAAAAGTGTTGCCACCGACTCGTGGGCTTTGAAAGGATGCCAC
1 GTGCCACTGACTTGTGGGCTTTG-AAAGGGTTGCCACCGACTTGTGGGCTTTGAAAGGATGCCAC
*
671413 TAACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCGTGTGGGCTTTGAAAAGA
65 TGACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTC-TGTGGGCTTTGAAAAGA
* * *
671467 GTGCCA-TCGACTTGTGGGCTTTGAAAGGG-TGCCACTGATTTGTGGGCTTTAAAATGG-TGCCA
1 GTGCCACT-GACTTGTGGGCTTTGAAAGGGTTGCCACCGACTTGTGGGCTTTGAAA-GGATGCCA
* * * *
671529 CTGACTTGTGGG-TTTG-AAAGGG-TGCCACTGA-TTTGTGGGCTTTGAAATGG
64 CTGACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCTGTGGGCTTTGAAAAGA
* *
671579 GTTGCCACCGACTTGTGTGGGCTTTCAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATAGG
1 G-TGCCACTGAC-T-TGTGGGCTTTGAAA-GGGTTGCCACCGAC-T-TGTGGGCTTTG-AA-AGG
* * * *
671644 TTGCCACCGACTTGTGTGGGCTTT-AAAAGGG-TGCCACTGACT-TGTGGGC-TTAAAAAG-
58 ATGCCACTGAC-T-TGTGGGCTTTGAAAAGGGTTGCCACCGACTCTGTGGGCTTTGAAAAGA
* ** * * * * * *
671701 GATGCCAC-GAAGTTGTGAAC-TTAAAAGGG-TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCA
1 G-TGCCACTG-ACTTGTGGGCTTTGAAAGGGTTGCCACCGACTTGTGGGCTTTGAAAGGATGCCA
* * * * * * *
671763 CGGAGTTGTGGACTTT--AAA-GGATGCCACGGAGT-TGTGGAC-TT-AAAACGA
64 CTGACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCTGTGGGCTTTGAAAA-GA
* * * * * * *
671812 -TGCCACGGAGTTGTGGACTTTAAAAGGG-TGCCACGGAGTTGTGGACTTT-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGGGTTGCCACCGACTTGTGGGCTTTGAAAGG
671866 GTACCACGAA
Statistics
Matches: 958, Mismatches: 98, Indels: 109
0.82 0.08 0.09
Matches are distributed among these distances:
109 26 0.03
110 52 0.05
111 9 0.01
112 17 0.02
113 20 0.02
114 51 0.05
115 75 0.08
116 63 0.07
117 259 0.27
118 159 0.17
119 110 0.11
120 19 0.02
121 33 0.03
122 27 0.03
123 12 0.01
124 25 0.03
125 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (117 bp):
GTGCCACTGACTTGTGGGCTTTGAAAGGGTTGCCACCGACTTGTGGGCTTTGAAAGGATGCCACT
GACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCTGTGGGCTTTGAAAAGA
Found at i:671180 original size:175 final size:175
Alignment explanation
Indices: 670642--671708 Score: 1351
Period size: 175 Copynumber: 6.0 Consensus size: 175
670632 AAAAAAATGG
* * *
670642 TGCCACTAACTTGTGTGGACTTTGAAAAGAGTTGCCACCAACTCGTGTGGGCTTTGAAAAGAGTG
1 TGCCACTGACTTGTG-GG-CTTTGAAAAGTGTTGCCACCAACTC--GTGGGCTTTGAAAGGA-TG
* *
670707 CCACTGACTTGTGGGCTTTG-AAAGGG-TGCCACTGAC-T-TGTGGGCTTTGAAAGGA-TGCCAC
61 CCACTGACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGAGTGCCAC
* * *
670767 TGACTTGTGAGCTTTGAAAAGGGTTGCCACCGACTCATGTGGCCTTTGAAAGGA
126 TGACTTGTGGGCTTTG-AAAGGG-TGCCACTGACT--TGTGGGCTTTGAAAGGA
* *
670821 TGCCACTGA-TTGTGTGGACTTTGAAAAGAGTTGCCACCAACTCGTGTGGGCTTTGAAAAGAGTG
1 TGCCACTGACTTGTG-GG-CTTTGAAAAGTGTTGCCACCAACTC--GTGGGCTTTGAAAGGA-TG
* * * * *
670885 CCACTGACTTGTAGACTTT-AAAAAGG-TGCCACTGAC-T-TGTGGGCTTTGAAAGGA-TGCCAC
61 CCACTGACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGAGTGCCAC
* * * *
670945 TAACTTGTGGTCTTTGAAAAGGGTTGCCACCGACTCATGTGGGCTTTGAAAGGG
126 TGACTTGTGGGCTTTG-AAAGGG-TGCCACTGACT--TGTGGGCTTTGAAAGGA
* *
670999 TGCCACTGACTTGTGGGCTTTGAAAAGTGTTACCACCGACTCGTGGGCTTTGAAAGGATGCCACT
1 TGCCACTGACTTGTGGGCTTTGAAAAGTGTTGCCACCAACTCGTGGGCTTTGAAAGGATGCCACT
*
671064 GACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAAAGTGCCACTGACT
66 GACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGAGTGCCACTGACT
*
671129 TGTGGGCTTTGAAAGGGTGCCACTTACTTGTGGGCTTTGAAAGGA
131 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
671174 TGCCACTGACTTGTGGGCTTTGAAAAGTGTTGCCACCAACTCGTGGGCTTTGAAAGGATGCCACT
1 TGCCACTGACTTGTGGGCTTTGAAAAGTGTTGCCACCAACTCGTGGGCTTTGAAAGGATGCCACT
* *
671239 AACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTGCCA-TCGAC
66 GACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGAGTGCCACT-GAC
*
671303 TTGTGGGCTTTGAAAGGGTGCCACTGACTTATGGGCTTTGAAAGGA
130 TTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
*
671349 TGCCACTGACTTGTGGGCTTTGAAAAGTGTTGCCACCGACTCGTGGGCTTTGAAAGGATGCCACT
1 TGCCACTGACTTGTGGGCTTTGAAAAGTGTTGCCACCAACTCGTGGGCTTTGAAAGGATGCCACT
* *
671414 AACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTGCCA-TCGAC
66 GACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGAGTGCCACT-GAC
* *
671478 TTGTGGGCTTTGAAAGGGTGCCACTGATTTGTGGGCTTTAAAATGG-
130 TTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAA-GGA
* ** * * *
671524 TGCCACTGACTTGTGGG-TTTG-AAAG-GGTGCCACTGATTTGTGGGCTTTGAAATGGGTTGCCA
1 TGCCACTGACTTGTGGGCTTTGAAAAGTGTTGCCACCAACTCGTGGGCTTTGAAA--GGATGCCA
* * *
671586 CCGACTTGTGTGGGCTTTCAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATAG-GTTGCCA
64 CTGAC-T-TGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAA-AGAG-TGCCA
* * **
671650 CCGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTAAAAAGGA
125 CTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
671703 TGCCAC
1 TGCCAC
671709 GAAGTTGTGA
Statistics
Matches: 820, Mismatches: 49, Indels: 38
0.90 0.05 0.04
Matches are distributed among these distances:
172 23 0.03
173 4 0.00
174 34 0.04
175 389 0.47
176 55 0.07
177 42 0.05
178 195 0.24
179 78 0.10
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (175 bp):
TGCCACTGACTTGTGGGCTTTGAAAAGTGTTGCCACCAACTCGTGGGCTTTGAAAGGATGCCACT
GACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGAGTGCCACTGACT
TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
Found at i:671808 original size:82 final size:82
Alignment explanation
Indices: 670687--672623 Score: 1283
Period size: 82 Copynumber: 22.8 Consensus size: 82
670677 CACCAACTCG
* * * * * * * *
670687 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
1 TGTGGACTTT-AAAAGGGTGCCACGGAGTTGTGGACTTT-AAAGGGTGCCACGGAGTTGTGGAC-
* * *
670752 TTGAAAGGATGCCACTGACT
63 TTAAAAGGATGCCACGGAGT
* * * * * *
670772 TGT-GAGCTTTGAAAAGGGTTGCCACCGACTCATGTGGCCTTTGAAAGGATGCCACTGATTGTGT
1 TGTGGA-CTTT-AAAAGGG-TGCCACGGAGT--TGTGGACTTT-AAAGGGTGCCACGGAGT-TGT
* ** *
670836 GGACTTTGAAAAGAGTTGCCACCAACT
59 GGAC-TT-AAAAG-GATGCCACGGAGT
* * * * * * * * *
670863 CGTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTAGACTTTAAAAAGGTGCCACTGACTTGTGGG
1 --TGTGGACTTT-AAAAGGGTGCCACGGAGTTGTGGACTTT-AAAGGGTGCCACGGAGTTGTGGA
* ** *
670928 CTTTGAAAGGATGCCACTAACT
62 C-TTAAAAGGATGCCACGGAGT
* * * * * *
670950 TGTGGTCTTTGAAAAGGGTTGCCACCGACTCATGTGGGCTTTGAAAGGGTGCCACTGACTTGTGG
1 TGTGGACTTT-AAAAGGG-TGCCACGGAGT--TGTGGACTTT-AAAGGGTGCCACGGAGTTGTGG
* * * * *
671015 GCTTTGAAAAGTGTTACCACCGACT
61 AC-TT-AAAAG-GATGCCACGGAGT
* * * * * * * * *
671040 CGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGG
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT--AAAGGG-TGCCACGGA-GT-TGTGG
* * * *
671105 GCTTTGAAAA-AAGTGCCACTGACT
61 AC-TT-AAAAGGA-TGCCACGGAGT
* * ** * * * * * *
671129 TGTGGGCTTTGAAAGGGTGCCACTTACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAGGGTGCCACGGAGTTGTGGAC-T
* ** *
671194 TGAAAAGTGTTGCCACCAACT
64 T-AAAAG-GATGCCACGGAGT
* * * * ** * * * *
671215 CGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCGTGTGG
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT--AAAGGG-TGCCACGGAGT--TGTGG
* *
671280 GCTTTGAAAA-GAGTGCCATC-GACT
61 AC-TT-AAAAGGA-TGCCA-CGGAGT
* * * * * * * * * *
671304 TGTGGGCTTTGAAAGGGTGCCACTGACTTATGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAGGGTGCCACGGAGTTGTGGAC-T
* * *
671369 TGAAAAGTGTTGCCACCGACT
64 T-AAAAG-GATGCCACGGAGT
* * * * ** * * * *
671390 CGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCGTGTGG
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT--AAAGGG-TGCCACGGAGT--TGTGG
* *
671455 GCTTTGAAAA-GAGTGCCATC-GACT
61 AC-TT-AAAAGGA-TGCCA-CGGAGT
* * * * * * * * **
671479 TGTGGGCTTTGAAAGGGTGCCACTGATTTGTGGGCTTTAAAATGGTGCCACTGACTTGTGGGTTT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAGGGTGCCACGGAGTTGTGGACTT
* * * *
671544 GAAAGGGTGCCACTGATT
65 AAAAGGATGCCACGGAGT
* * * * * * *
671562 TGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTCAAATGGGTTGCCACCGACTTGT
1 TGTGGACTTT-AAAAGGG-TGCCACGGA-GT-TGTGGACTTT-AAA-GGG-TGCCACGGA-GT-T
* * * *
671627 GTGGGCTTTGAAATAGGTTGCCACCGACTT
57 GTGGAC-TT-AAA-AGGATGCCACGGA-GT
* * * * * * * *
671657 GTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTAAAAAGGATGCCACGAAGTTGTGAACT
1 -TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT-TAAAGGGTGCCACGGAGTTGTGGACT
*
671722 TAAAAGGGTGCCACGGAGT
64 TAAAAGGATGCCACGGAGT
*
671741 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGATGCCACGGAGTTGTGGACTTA
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGACTTA
*
671806 AAACGATGCCACGGAGT
66 AAAGGATGCCACGGAGT
* *
671823 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTACCACGAAGTTGTGGACTTA
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGACTTA
* *
671888 AAATGATACCACGGAGT
66 AAAGGATGCCACGGAGT
*
671905 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAGAAGGGTGCCATGGAGTTGTGGACTT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTA-AAGGGTGCCACGGAGTTGTGGACTT
* *
671970 TAAAGGGTGCCACGGAGT
65 AAAAGGATGCCACGGAGT
* * * * * * * * *
671988 TGTAGAC-TTAAAAGGGTACCATGAAGTTGT-G--TTAAAATGATGCCATGAAGTTGTGGACTTT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGAC-TT
*
672049 AAAAGGGTGCCACGGAGT
65 AAAAGGATGCCACGGAGT
* *
672067 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTATGGATTTA
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGACTTA
*
672132 AAATGATGCCACGGAGT
66 AAAGGATGCCACGGAGT
*
672149 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGTACTTTAAAAGGGTGCCACGGAGTTGTGGACTT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAGGGTGCCACGGAGTTGTGGACTT
* *
672214 TAAAGGGTGCCACGGAGT
65 AAAAGGATGCCACGGAGT
* * * * * * *
672232 TGTGGAC-TTAAAAGGGTACCACGAAGTTGTGGACTTAAAATGATACCACGAAGTTGTGGACTTT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGAC-TT
*
672296 AAAAGGGTGCCACGGAGT
65 AAAAGGATGCCACGGAGT
672314 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGACTTA
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGACTTA
*
672379 AAACGATGCCACGGAGT
66 AAAGGATGCCACGGAGT
* * ** * *
672396 TATGGACTTTAAAAGGGTGCCACGGGGTTGTGGACTTTAAAGGGTATCATGGAGTTATGGACTTA
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGACTTA
* *
672461 AAACGATGCCACAGAGT
66 AAAGGATGCCACGGAGT
* *
672478 TGTGGACTTTAAAAGGGTGCCATGGAGTTATGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAGGGTGCCACGGAGTTGTGGAC-T
672543 TAAAAGGATGCCACGGAGT
64 TAAAAGGATGCCACGGAGT
* * * * * * *
672562 TGTGGAC-TTAAAAAGATGCCACAGAGTCGTGGACTTTGAAA-AG-GCCACTGAGTCGTGGACTT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAGGGTGCCACGGAGTTGTGGACTT
672624 TGAAAAGGTC
Statistics
Matches: 1577, Mismatches: 211, Indels: 133
0.82 0.11 0.07
Matches are distributed among these distances:
78 20 0.01
79 28 0.02
80 22 0.01
81 37 0.02
82 412 0.26
83 256 0.16
84 35 0.02
85 86 0.05
86 123 0.08
87 71 0.05
88 126 0.08
89 166 0.11
90 98 0.06
91 18 0.01
92 24 0.02
93 17 0.01
94 20 0.01
95 8 0.01
96 10 0.01
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.27
Consensus pattern (82 bp):
TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGACTTA
AAAGGATGCCACGGAGT
Found at i:671835 original size:110 final size:110
Alignment explanation
Indices: 670687--672631 Score: 1343
Period size: 110 Copynumber: 17.1 Consensus size: 110
670677 CACCAACTCG
* * * * * * * *
670687 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCT
1 TGTGGACTTT-AAAAGGGTGCCACGGAGTTGTGGACTTT-AAAGGGTGCCACGGAGTTGTGGAC-
* * * * *
670752 TTGAAAGGATGCCACTGACTTGT-GAGCTTTGAAAAGGGTTGCCACCGACT
63 TTAAAAGGATGCCACGGAGTTGTGGA-CTTT-AAAAGGG-TGCCACGGAGT
* * * * * * ** *
670802 CATGTGGCCTTTGAAAGGATGCCACTGATTGTGTGGACTTTGAAAAGAGTTGCCACCAACTCGTG
1 --TGTGGACTTTAAAAGGGTGCCACGGAGT-TGTGGACTTT--AAAG-GGTGCCACGGAGT--TG
* * * * * * *
670867 TGGGCTTTGAAAA-GAGTGCCACTGACTTGTAGACTTTAAAAAGGTGCCACTGACT
58 TGGAC-TT-AAAAGGA-TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
* * * ** * * * *
670922 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGGTCTTTGAAAAGGGTTGCCACCGACTCATGTGG
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT--AAAGGG-TGCCACGGAGT--TGTGG
* * * * * * * * * *
670987 GCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGTGTTACCACCGACT
61 AC-TTAAAAGGATGCCACGGAGTTGTGGACTTT-AAAAG-GGTGCCACGGAGT
* * * * * * * * *
671040 CGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGG
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT--AAAGGG-TGCCACGGA-GT-TGTGG
* * * * * * ** *
671105 GCTTTGAAAA-AAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTTACT
61 AC-TT-AAAAGGA-TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
* * * * * * * ** * * *
671157 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGTGTTGCCACCAACTCGTGGGC
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT--AAAG-GGTGCCACGGAGTTGTGGAC
* ** * * * *
671222 TTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGGTTGCCACCGACT
63 -TTAAAAGGATGCCACGGAGTTGTGGACTTT-AAAAGGG-TGCCACGGAGT
* * * * * * *
671273 CGTGTGGGCTTTGAAAAGAGTGCCATC-GACTTGTGGGCTTTGAAAGGGTGCCACTGACTTATGG
1 --TGTGGACTTT-AAAAGGGTGCCA-CGGAGTTGTGGACTTT-AAAGGGTGCCACGGAGTTGTGG
* * * * * * * *
671337 GCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGTGTTGCCACCGACT
61 AC-TTAAAAGGATGCCACGGAGTTGTGGACTTT-AAAAG-GGTGCCACGGAGT
* * * * ** * * * *
671390 CGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCGTGTGG
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT--AAAGGG-TGCCACGGAGT--TGTGG
* * * * * *
671455 GCTTTGAAAA-GAGTGCCATC-GACTTGTGGGCTTTGAAAGGGTGCCACTGATT
61 AC-TT-AAAAGGA-TGCCA-CGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
* * * * * * * *
671507 TGTGGGCTTTAAAATGGTGCCACTGACTTGTGG-GTTTGAAAGGGTGCCACTGATTTGTGGGCTT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAGGGTGCCACGGAGTTGTGGAC-T
* * * * * * * *
671571 TGAAATGGGTTGCCACCGACTTGTGTGGGCTTTCAAATGGGTTGCCACCGACTT
64 T-AAA-AGGATGCCACGGA-GT-TGTGGACTTT-AAAAGGG-TGCCACGGA-GT
* * * * * * *
671625 GTGTGGGCTTTGAAATAGGTTGCCACCGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTG
1 -TGTGGACTTT-AAA-AGGGTGCCACGGA-GT-TGTGGACTTT-AAAGGGTGCCACGGAGTTGTG
* * *
671690 GGCTTAAAAAGGATGCCACGAAGTTGTGAAC-TTAAAAGGGTGCCACGGAGT
60 GACTT-AAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
*
671741 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGATGCCACGGAGTTGTGGACTTA
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGACTTA
*
671806 AAACGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
66 AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
* * * * * *
671851 TGTGGACTTT-AAAGGGTACCACGAAGTTGTGGACTTAAAATGATACCACGGAGTTGTGGACTTT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGAC-TT
* * *
671915 AAAAGGGTGCCACGGAGTTGTGGACTTTAGAAGGGTGCCATGGAGT
65 AAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
* * * * *
671961 TGTGGACTTT-AAAGGGTGCCACGGAGTTGTAGACTTAAAAGGGTACCATGAAGTTGT-G--TTA
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGACTTA
* * *
672022 AAATGATGCCATGAAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
66 AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
* *
672067 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTATGGATTTA
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGACTTA
*
672132 AAATGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
66 AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
*
672177 TGTGTACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGACTTA
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGACTTA
* * * * * * *
672242 AAAGGGTACCACGAAGTTGTGGAC-TTAAAATGATACCACGAAGT
66 AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
672286 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAGGGTGCCACGGAGTTGTGGACTT
* * * *
672351 TAAAGGGTGCCACGGAGTTGTGGAC-TTAAAACGATGCCACGGAGT
65 AAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
* * ** * *
672396 TATGGACTTTAAAAGGGTGCCACGGGGTTGTGGACTTTAAAGGGTATCATGGAGTTATGGACTTA
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGACTTA
* * *
672461 AAACGATGCCACAGAGTTGTGGACTTTAAAAGGGTGCCATGGAGT
66 AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
* *
672506 TATGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAGGGTGCCACGGAGTTGTGGACTT
* * * *
672571 AAAAAGATGCCACAGAGTCGTGGACTTTGAAAA--G-GCCACTGAGT
65 AAAAGGATGCCACGGAGTTGTGGACTTT-AAAAGGGTGCCACGGAGT
*
672615 CGTGGACTTTGAAAAGG
1 TGTGGACTTT-AAAAGG
672632 TCACAGTACT
Statistics
Matches: 1577, Mismatches: 194, Indels: 121
0.83 0.10 0.06
Matches are distributed among these distances:
106 52 0.03
107 41 0.03
108 1 0.00
109 181 0.11
110 436 0.28
111 56 0.04
112 20 0.01
113 19 0.01
114 59 0.04
115 56 0.04
116 66 0.04
117 235 0.15
118 145 0.09
119 92 0.06
120 20 0.01
121 29 0.02
122 31 0.02
123 12 0.01
124 26 0.02
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.27
Consensus pattern (110 bp):
TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGACTTA
AAAGGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGT
Found at i:672567 original size:28 final size:28
Alignment explanation
Indices: 670687--672631 Score: 1426
Period size: 28 Copynumber: 68.6 Consensus size: 28
670677 CACCAACTCG
* * * *
670687 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGACTTT-AAAAGGGTGCCACGGAGT
* * * *
670716 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * * * *
670744 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* *
670772 TGT-GAGCTTTGAAAAGGGTTGCCACCGACT
1 TGTGGA-CTTT-AAAAGGG-TGCCACGGAGT
* * * * *
670802 CATGTGGCCTTTGAAAGGATGCCACTGATT
1 --TGTGGACTTTAAAAGGGTGCCACGGAGT
* ** *
670832 GTGTGGACTTTGAAAAGAGTTGCCACCAACT
1 -TGTGGACTTT-AAAAG-GGTGCCACGGAGT
* * * *
670863 CGTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 --TGTGGACTTT-AAAAGGGTGCCACGGAGT
* * * *
670894 TGTAGACTTTAAAAAGGTGCCACTGACT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * * ** *
670922 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * *
670950 TGTGGTCTTTGAAAAGGGTTGCCACCGACT
1 TGTGGACTTT-AAAAGGG-TGCCACGGAGT
* * * *
670980 CATGTGGGCTTTGAAAGGGTGCCACTGACT
1 --TGTGGACTTTAAAAGGGTGCCACGGAGT
* * * * *
671010 TGTGGGCTTTGAAAAGTGTTACCACCGACT
1 TGTGGACTTT-AAAAG-GGTGCCACGGAGT
* * * * * *
671040 CGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * *
671068 TGTGGGCTTTGAAAAGGGTTGCCACCGACTT
1 TGTGGACTTT-AAAAGGG-TGCCACGGA-GT
* ** * *
671099 GTGTGGGCTTTGAAAAAAGTGCCACTGACT
1 -TGTGGACTTT-AAAAGGGTGCCACGGAGT
* * ** *
671129 TGTGGGCTTTGAAAGGGTGCCACTTACT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * * * *
671157 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * ** *
671185 TGTGGGCTTTGAAAAGTGTTGCCACCAACT
1 TGTGGACTTT-AAAAG-GGTGCCACGGAGT
* * * * ** *
671215 CGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * *
671243 TGTGGGCTTTGAAAAGGGTTGCCACCGACT
1 TGTGGACTTT-AAAAGGG-TGCCACGGAGT
* * *
671273 CGTGTGGGCTTTGAAAAGAGTGCCATC-GACT
1 --TGTGGACTTT-AAAAGGGTGCCA-CGGAGT
* * * *
671304 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * * * * *
671332 TATGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * * *
671360 TGTGGGCTTTGAAAAGTGTTGCCACCGACT
1 TGTGGACTTT-AAAAG-GGTGCCACGGAGT
* * * * ** *
671390 CGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * *
671418 TGTGGGCTTTGAAAAGGGTTGCCACCGACT
1 TGTGGACTTT-AAAAGGG-TGCCACGGAGT
* * *
671448 CGTGTGGGCTTTGAAAAGAGTGCCATC-GACT
1 --TGTGGACTTT-AAAAGGGTGCCA-CGGAGT
* * * *
671479 TGTGGGCTTTGAAAGGGTGCCACTGATT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * * *
671507 TGTGGGCTTTAAAATGGTGCCACTGACT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * * *
671535 TGTGG-GTTTGAAAGGGTGCCACTGATT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * * *
671562 TGTGGGCTTTGAAATGGGTTGCCACCGACTT
1 TGTGGACTTT-AAAAGGG-TGCCACGGA-GT
* * * *
671593 GTGTGGGCTTTCAAATGGGTTGCCACCGACTT
1 -TGTGGACTTT-AAAAGGG-TGCCACGGA-GT
* * * *
671625 GTGTGGGCTTTGAAATAGGTTGCCACCGACTT
1 -TGTGGACTTT-AAA-AGGGTGCCACGGA-GT
* * *
671657 GTGTGGGCTTTAAAAGGGTGCCACTGACT
1 -TGTGGACTTTAAAAGGGTGCCACGGAGT
* * * *
671686 TGTGGGCTTAAAAAGGATGCCACGAAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
*
671714 TGTGAAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
671741 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
*
671769 TGTGGACTTT-AAAGGATGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* *
671796 TGTGGAC-TTAAAACGATGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
671823 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* *
671851 TGTGGACTTT-AAAGGGTACCACGAAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * *
671878 TGTGGAC-TTAAAATGATACCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
671905 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* *
671933 TGTGGACTTTAGAAGGGTGCCATGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
671961 TGTGGACTTT-AAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * * *
671988 TGTAGAC-TTAAAAGGGTACCATGAAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * * *
672015 TGT-G---TTAAAATGATGCCATGAAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
672039 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
672067 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
672095 TGTGGACTTT-AAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * *
672122 TATGGA-TTTAAAATGATGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
672149 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
*
672177 TGTGTACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
672205 TGTGGACTTT-AAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* *
672232 TGTGGAC-TTAAAAGGGTACCACGAAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * * *
672259 TGTGGAC-TTAAAATGATACCACGAAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
672286 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
672314 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
672342 TGTGGACTTT-AAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* *
672369 TGTGGAC-TTAAAACGATGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* *
672396 TATGGACTTTAAAAGGGTGCCACGGGGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
** *
672424 TGTGGACTTT-AAAGGGTATCATGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * * *
672451 TATGGAC-TTAAAACGATGCCACAGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
*
672478 TGTGGACTTTAAAAGGGTGCCATGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
*
672506 TATGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
*
672534 TGTGGACTTTAAAAGGATGCCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* * *
672562 TGTGGAC-TTAAAAAGATGCCACAGAGT
1 TGTGGACTTTAAAAGGGTGCCACGGAGT
* *
672589 CGTGGACTTTGAAAA--G-GCCACTGAGT
1 TGTGGACTTT-AAAAGGGTGCCACGGAGT
*
672615 CGTGGACTTTGAAAAGG
1 TGTGGACTTT-AAAAGG
672632 TCACAGTACT
Statistics
Matches: 1647, Mismatches: 206, Indels: 127
0.83 0.10 0.06
Matches are distributed among these distances:
24 20 0.01
25 1 0.00
26 40 0.02
27 394 0.24
28 715 0.43
29 116 0.07
30 146 0.09
31 61 0.04
32 151 0.09
33 3 0.00
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.27
Consensus pattern (28 bp):
TGTGGACTTTAAAAGGGTGCCACGGAGT
Found at i:681057 original size:20 final size:20
Alignment explanation
Indices: 681032--681083 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
681022 AAGACATAAC
* *
681032 GTATCGATACATTCATACAT
1 GTATCGATACATTCAAAAAT
* *
681052 GTATCGATATATTGAAAAAT
1 GTATCGATACATTCAAAAAT
681072 GTATCGATACAT
1 GTATCGATACAT
681084 CTGGGTAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (20 bp):
GTATCGATACATTCAAAAAT
Found at i:681647 original size:21 final size:21
Alignment explanation
Indices: 681623--681668 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
681613 TTCTTCTTCA
681623 ATGGTGGTTTTAATAGCAAAC
1 ATGGTGGTTTTAATAGCAAAC
681644 ATGGTGGTTTTAATAGCAAAC
1 ATGGTGGTTTTAATAGCAAAC
681665 ATGG
1 ATGG
681669 CTTTGCCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.33
Consensus pattern (21 bp):
ATGGTGGTTTTAATAGCAAAC
Found at i:682482 original size:12 final size:12
Alignment explanation
Indices: 682467--682491 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
682457 CATCTAACAC
682467 TTAATAAAAATA
1 TTAATAAAAATA
682479 TTAATAAAAATA
1 TTAATAAAAATA
682491 T
1 T
682492 ATATATATCT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TTAATAAAAATA
Found at i:682822 original size:2 final size:2
Alignment explanation
Indices: 682817--682844 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
682807 AAAAATATTT
682817 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
682845 CACGATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:686891 original size:17 final size:17
Alignment explanation
Indices: 686869--686902 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
686859 GTATTTATAT
686869 ATGGAAAACTTAATGGC
1 ATGGAAAACTTAATGGC
686886 ATGGAAAACTTAATGGC
1 ATGGAAAACTTAATGGC
686903 TGTTAGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (17 bp):
ATGGAAAACTTAATGGC
Found at i:689204 original size:2 final size:2
Alignment explanation
Indices: 689197--689229 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
689187 TGGTATAATA
689197 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
689230 GACCATTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:689244 original size:21 final size:21
Alignment explanation
Indices: 689220--689268 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
689210 TATATATATA
* * *
689220 TATATTATATGACCATTATGG
1 TATAATATATGACCATAACGG
*
689241 TATAATATGTGACCATAACGG
1 TATAATATATGACCATAACGG
689262 TATAATA
1 TATAATA
689269 ATATATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (21 bp):
TATAATATATGACCATAACGG
Found at i:689447 original size:2 final size:2
Alignment explanation
Indices: 689435--689481 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
689425 ACTTGGATCA
689435 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
689476 AT -T AT A
1 AT AT AT A
689482 AATGAGCTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:689600 original size:3 final size:3
Alignment explanation
Indices: 689594--689620 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
689584 GCTCTACTAC
689594 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
689621 CATCTCCTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:689670 original size:44 final size:42
Alignment explanation
Indices: 689607--689706 Score: 164
Period size: 44 Copynumber: 2.3 Consensus size: 42
689597 TATTATTATT
689607 ATTATTATTATTATCATCTCCTACCAAAGAAAAAAAAAACAAGG
1 ATTATTATTATTATCATCTCCTACCAAAG--AAAAAAAACAAGG
* *
689651 ATTATTATTATTATCATCTCTTACCAAAGAAAAAAATCAAGG
1 ATTATTATTATTATCATCTCCTACCAAAGAAAAAAAACAAGG
689693 ATTATTATTATTAT
1 ATTATTATTATTAT
689707 TATTATTATT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
42 26 0.48
44 28 0.52
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (42 bp):
ATTATTATTATTATCATCTCCTACCAAAGAAAAAAAACAAGG
Found at i:689699 original size:3 final size:3
Alignment explanation
Indices: 689693--689726 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
689683 AAAATCAAGG
689693 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
689727 CTCTTACCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:692394 original size:24 final size:24
Alignment explanation
Indices: 692336--692403 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
692326 TGTAACGTTC
*
692336 TTAATATTTTAA-ATATATATTATT
1 TTAATATTTTAATA-ATAAATTATT
* *
692360 TTAATATTTTACTGATAAATTATT
1 TTAATATTTTAATAATAAATTATT
*
692384 ATTATTA-TTTAATAATAAAT
1 -TTAATATTTTAATAATAAAT
692404 ATATAAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
24 31 0.86
25 5 0.14
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (24 bp):
TTAATATTTTAATAATAAATTATT
Found at i:693406 original size:19 final size:19
Alignment explanation
Indices: 693360--693406 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
693350 ATTTGAAGTG
*
693360 AAAAAAACAAAGAAAGAAAT
1 AAAAAAA-AAAAAAAGAAAT
**
693380 AACGAAAAAAAAAAGAAAT
1 AAAAAAAAAAAAAAGAAAT
693399 AAAAAAAA
1 AAAAAAAA
693407 GTTTATATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.83, C:0.04, G:0.09, T:0.04
Consensus pattern (19 bp):
AAAAAAAAAAAAAAGAAAT
Found at i:693834 original size:31 final size:32
Alignment explanation
Indices: 693799--693858 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
693789 GCCATGGGAG
693799 AGAAAAAGATG-GAAAGAAA-AAAAGAAAAGAA
1 AGAAAAAGA-GAGAAAGAAATAAAAGAAAAGAA
* *
693830 AGAAAAGGAGAGAAGGAAATAAAAGAAAA
1 AGAAAAAGAGAGAAAGAAATAAAAGAAAA
693859 TTTATTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.04
31 15 0.60
32 9 0.36
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (32 bp):
AGAAAAAGAGAGAAAGAAATAAAAGAAAAGAA
Found at i:693982 original size:23 final size:23
Alignment explanation
Indices: 693944--694002 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
693934 TATATCTATC
693944 TATTTTTATATT-ATGTTTTAAT
1 TATTTTTATATTCATGTTTTAAT
* *
693966 TATTTTTACATTCATGTTTTTAT
1 TATTTTTATATTCATGTTTTAAT
693989 T-TTTTATATATTCA
1 TATTTT-TATATTCA
694003 AAGTAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.66
Consensus pattern (23 bp):
TATTTTTATATTCATGTTTTAAT
Found at i:694504 original size:14 final size:14
Alignment explanation
Indices: 694478--694515 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
694468 TGCAAAGAAA
694478 AAAGAAA-AAAAGG
1 AAAGAAAGAAAAGG
694491 AAAGAAAGAAAAGG
1 AAAGAAAGAAAAGG
* *
694505 AGAGAGAGAAA
1 AAAGAAAGAAA
694516 TAAAAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (14 bp):
AAAGAAAGAAAAGG
Found at i:694858 original size:23 final size:22
Alignment explanation
Indices: 694832--694888 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 22
694822 TGTATTTAAA
*
694832 ATATTATATTTTATTTTTTTTAC
1 ATATTATATTTTATTTTATTT-C
*
694855 ATATTAATAATTTATTTTATTTC
1 ATATT-ATATTTTATTTTATTTC
694878 ATA-TATATTTT
1 ATATTATATTTT
694889 TATATGTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 6 0.20
22 1 0.03
23 9 0.30
24 14 0.47
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.65
Consensus pattern (22 bp):
ATATTATATTTTATTTTATTTC
Found at i:695695 original size:23 final size:22
Alignment explanation
Indices: 695649--695697 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
695639 CATGTTAACC
*
695649 ATTATTAGTAAATTTCAAATCA
1 ATTATTACTAAATTTCAAATCA
695671 ATTATTACTAAATAATT-AAATCA
1 ATTATTACTAAAT--TTCAAATCA
695694 ATTA
1 ATTA
695698 AAATATCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 12 0.50
23 10 0.42
24 2 0.08
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (22 bp):
ATTATTACTAAATTTCAAATCA
Found at i:696867 original size:2 final size:2
Alignment explanation
Indices: 696860--696902 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
696850 GCTTGATTCT
696860 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
696902 T
1 T
696903 TCCTTGAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:698591 original size:12 final size:12
Alignment explanation
Indices: 698574--698604 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
698564 TTTTAATGAT
698574 ACACACACAGAC
1 ACACACACAGAC
*
698586 ACACACACAGAG
1 ACACACACAGAC
698598 ACACACA
1 ACACACA
698605 TATATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.52, C:0.39, G:0.10, T:0.00
Consensus pattern (12 bp):
ACACACACAGAC
Found at i:698593 original size:14 final size:14
Alignment explanation
Indices: 698574--698604 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
698564 TTTTAATGAT
698574 ACACACACAGACAC
1 ACACACACAGACAC
*
698588 ACACACAGAGACAC
1 ACACACACAGACAC
698602 ACA
1 ACA
698605 TATATATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.39, G:0.10, T:0.00
Consensus pattern (14 bp):
ACACACACAGACAC
Found at i:709242 original size:18 final size:18
Alignment explanation
Indices: 709215--709251 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
709205 TTTAACCAAA
709215 AAATTATATATGT-ATAT
1 AAATTATATATGTAATAT
709232 AAATATATATATGTAATAT
1 AAAT-TATATATGTAATAT
709251 A
1 A
709252 CGGGTATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 9 0.50
19 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (18 bp):
AAATTATATATGTAATAT
Found at i:713638 original size:43 final size:43
Alignment explanation
Indices: 713577--713663 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
713567 AGCTTTTCTT
713577 AATAGGTGTAGTCAATGTCTAGGGCTGTTCAATTGGTTAACCA
1 AATAGGTGTAGTCAATGTCTAGGGCTGTTCAATTGGTTAACCA
713620 AATAGGTGTAGTCAATGTCTAGGGCTGTTCAATTGGTTAACCA
1 AATAGGTGTAGTCAATGTCTAGGGCTGTTCAATTGGTTAACCA
713663 A
1 A
713664 CTGACTGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (43 bp):
AATAGGTGTAGTCAATGTCTAGGGCTGTTCAATTGGTTAACCA
Found at i:714031 original size:20 final size:21
Alignment explanation
Indices: 713979--714033 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
713969 ATATTTTGAA
*
713979 TAATTAAATTTAAATTTTTTAAT
1 TAATCAAA-TTAAATTTTTT-AT
714002 TAATCAAATTAAATTTTATT-T
1 TAATCAAATTAAATTTT-TTAT
714023 TAATC-AATTAA
1 TAATCAAATTAA
714034 TTTAATTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.20
21 6 0.20
22 9 0.30
23 9 0.30
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATCAAATTAAATTTTTTAT
Found at i:714372 original size:6 final size:6
Alignment explanation
Indices: 714361--714397 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
714351 TTAAGTAAAT
*
714361 AAATTA AAATT- AATTTA AAATTA AAATTA AAATTA AA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AA
714398 TTATTATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
AAATTA
Found at i:714380 original size:11 final size:11
Alignment explanation
Indices: 714360--714400 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
714350 TTTAAGTAAA
714360 TAAATTAAAAT
1 TAAATTAAAAT
*
714371 TAATTTAAAAT
1 TAAATTAAAAT
714382 TAAAATTAAAAT
1 T-AAATTAAAAT
714394 TAAATTA
1 TAAATTA
714401 TTATAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAATTAAAAT
Done.