Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 10 of 185
Found at i:2830510 original size:123 final size:123
Alignment explanation
Indices: 2830286--2830532 Score: 359
Period size: 123 Copynumber: 2.0 Consensus size: 123
2830276 AAAAGCTGTA
* * *
2830286 GATATTGATGAAAGTGATGAAGATGATGTTAAAGATTTGAAGTCTCCTGTAAAGCCAGGTGGAAA
1 GATATTGACGAAAGTGATGAAGAGGATATTAAAGATTTGAAGTCTCCTGTAAAGCCAGGTGGAAA
* * *
2830351 GGTTCGTGGTGGCAGGGGTGCATCAAAAGGCCCAGCTGGCGGAAGAGGCAGAGGTGGT
66 GGCTCGTGGTGGCAGGGGTGCATCAAAAGGACCAGCTAGCGGAAGAGGCAGAGGTGGT
* * * * *
2830409 GATATTGACGAAAGTGATGAAGAGGATATTAAAGATTTGGAGTCTCCTGTGAAGTCTGGTGGAAG
1 GATATTGACGAAAGTGATGAAGAGGATATTAAAGATTTGAAGTCTCCTGTAAAGCCAGGTGGAAA
* * * *
2830474 GGCTCGTGGTGGTAGGGGTGCATCAACAGGATCAGCTAGTGGAAGAGGCAGAGGTGGT
66 GGCTCGTGGTGGCAGGGGTGCATCAAAAGGACCAGCTAGCGGAAGAGGCAGAGGTGGT
2830532 G
1 G
2830533 GACGGGGTGG
Statistics
Matches: 109, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
123 109 1.00
ACGTcount: A:0.28, C:0.11, G:0.38, T:0.23
Consensus pattern (123 bp):
GATATTGACGAAAGTGATGAAGAGGATATTAAAGATTTGAAGTCTCCTGTAAAGCCAGGTGGAAA
GGCTCGTGGTGGCAGGGGTGCATCAAAAGGACCAGCTAGCGGAAGAGGCAGAGGTGGT
Found at i:2846298 original size:110 final size:110
Alignment explanation
Indices: 2846105--2846325 Score: 307
Period size: 110 Copynumber: 2.0 Consensus size: 110
2846095 GCCTTTTGAA
* * * *
2846105 CCACTTCACATACTAGAACAGGGGAAACTCCCTTTAATCTAATGTTTGAAAGAGAGGTCGTGGTC
1 CCACTTCACATACTAGAACAAGGGAAACTCCCTTTAATCTAATATTTGAAACAGAGATCGTGGTC
* * * *
2846170 TCCACTGAAATCATAATCATCTCTTTTAAAACTGCATACTATGAG
66 CCCACTGAAATCATAATCAGCTCCTTTAAAACTGCACACTATGAG
* * * * *
2846215 CCACTTCACATACTGGAACAATGGAAACTCCTTTTGATCTAATATTTGGAACAGAGATCGTGGTC
1 CCACTTCACATACTAGAACAAGGGAAACTCCCTTTAATCTAATATTTGAAACAGAGATCGTGGTC
* *
2846280 CCCACTGAAATCATAATCAGCTCCTTTAGAACTGCGCACTATGAG
66 CCCACTGAAATCATAATCAGCTCCTTTAAAACTGCACACTATGAG
2846325 C
1 C
2846326 GTGGTCTCAA
Statistics
Matches: 96, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
110 96 1.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.28
Consensus pattern (110 bp):
CCACTTCACATACTAGAACAAGGGAAACTCCCTTTAATCTAATATTTGAAACAGAGATCGTGGTC
CCCACTGAAATCATAATCAGCTCCTTTAAAACTGCACACTATGAG
Found at i:2856982 original size:28 final size:28
Alignment explanation
Indices: 2856950--2857006 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
2856940 GTTTTTATTT
*
2856950 TGACAGTTGTACCTGTTTCTGAATAGTG
1 TGACAGTTATACCTGTTTCTGAATAGTG
2856978 TGACAGTTATACCTGTTTCTGAATAGTG
1 TGACAGTTATACCTGTTTCTGAATAGTG
2857006 T
1 T
2857007 TTGATTGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.40
Consensus pattern (28 bp):
TGACAGTTATACCTGTTTCTGAATAGTG
Found at i:2858408 original size:56 final size:55
Alignment explanation
Indices: 2858312--2858452 Score: 212
Period size: 56 Copynumber: 2.5 Consensus size: 55
2858302 CCTTTTATGT
* * *
2858312 GTATACTCTGTACATGTGTA-TCTATCATAAACTTTTGTCTATGTCAATTGTTGG
1 GTATACTCTGTACATGTGTACTCTATTATAAAATTTTGTCTATGTCAATTGTTGC
*
2858366 GTATACTCTGTATATGTGTACCTCTATTATAAAATTTTGTCTATGTCAATTGTTGC
1 GTATACTCTGTACATGTGTA-CTCTATTATAAAATTTTGTCTATGTCAATTGTTGC
*
2858422 ATATACTCTGTACATGTGTAGCTCTATTATA
1 GTATACTCTGTACATGTGTA-CTCTATTATA
2858453 CTCTGTAGAG
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 19 0.24
56 59 0.76
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.45
Consensus pattern (55 bp):
GTATACTCTGTACATGTGTACTCTATTATAAAATTTTGTCTATGTCAATTGTTGC
Found at i:2859376 original size:7 final size:7
Alignment explanation
Indices: 2859361--2859407 Score: 76
Period size: 7 Copynumber: 6.7 Consensus size: 7
2859351 TGCAAGAATG
*
2859361 AATAATC
1 AATACTC
2859368 AATACTC
1 AATACTC
*
2859375 AACACTC
1 AATACTC
2859382 AATACTC
1 AATACTC
2859389 AATACTC
1 AATACTC
2859396 AATACTC
1 AATACTC
2859403 AATAC
1 AATAC
2859408 ATACATATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.26
Consensus pattern (7 bp):
AATACTC
Found at i:2883370 original size:23 final size:23
Alignment explanation
Indices: 2883344--2883393 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
2883334 TTCATAACTG
2883344 AAAAAAAATTATAAAAATTGTAT
1 AAAAAAAATTATAAAAATTGTAT
**
2883367 AAAACTAATTATAAAAATTGTAT
1 AAAAAAAATTATAAAAATTGTAT
2883390 AAAA
1 AAAA
2883394 CTAATAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (23 bp):
AAAAAAAATTATAAAAATTGTAT
Found at i:2883394 original size:23 final size:23
Alignment explanation
Indices: 2883350--2883398 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
2883340 ACTGAAAAAA
2883350 AATTATAAAAATTGTATAAAACT
1 AATTATAAAAATTGTATAAAACT
2883373 AATTATAAAAATTGTATAAAACT
1 AATTATAAAAATTGTATAAAACT
2883396 AAT
1 AAT
2883399 AAAATTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTATAAAAATTGTATAAAACT
Found at i:2887576 original size:13 final size:13
Alignment explanation
Indices: 2887558--2887582 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2887548 GAAAGGCCAA
2887558 TTTGTTATGTATG
1 TTTGTTATGTATG
2887571 TTTGTTATGTAT
1 TTTGTTATGTAT
2887583 ATTATTATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.20, T:0.64
Consensus pattern (13 bp):
TTTGTTATGTATG
Found at i:2898812 original size:20 final size:20
Alignment explanation
Indices: 2898781--2898856 Score: 67
Period size: 19 Copynumber: 4.2 Consensus size: 20
2898771 AAAATTATAA
2898781 AAAAATTC-AAAATATTTAT
1 AAAAATTCTAAAATATTTAT
*
2898800 AAAAATTCT-AAA-ATCTAT
1 AAAAATTCTAAAATATTTAT
*
2898818 ---ATTTCTAAAATA-TTAT
1 AAAAATTCTAAAATATTTAT
* *
2898834 AAAAATTCTAAAAAATATAT
1 AAAAATTCTAAAATATTTAT
2898854 AAA
1 AAA
2898857 TGAAGTTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
15 5 0.11
16 6 0.14
17 1 0.02
18 5 0.11
19 21 0.48
20 6 0.14
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAATTCTAAAATATTTAT
Found at i:2902030 original size:40 final size:39
Alignment explanation
Indices: 2901986--2902119 Score: 103
Period size: 40 Copynumber: 3.4 Consensus size: 39
2901976 CCAGTTTAGC
*
2901986 ACCCAGTGCCTCATCGGATAATTCGAAGTAATAAGTTGAT
1 ACCCAGTGCCTCATCGGATAATCCGAAGTAATAA-TTGAT
* * ** *
2902026 ACCCAATGTCTCATCGG-CCATGCCGAAGT-A-AATTGGT
1 ACCCAGTGCCTCATCGGATAAT-CCGAAGTAATAATTGAT
* * * * *
2902063 ACCCAGTACCTCATCGAATTTATCCGAAGTAATAATTTAAC
1 ACCCAGTGCCTCATCGGA-TAATCCGAAGTAATAA-TTGAT
*
2902104 ACCCAGTGTCTCATCG
1 ACCCAGTGCCTCATCG
2902120 ACTCGAAGTC
Statistics
Matches: 71, Mismatches: 17, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
37 17 0.24
38 9 0.13
39 6 0.08
40 23 0.32
41 16 0.23
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (39 bp):
ACCCAGTGCCTCATCGGATAATCCGAAGTAATAATTGAT
Found at i:2902265 original size:11 final size:11
Alignment explanation
Indices: 2902249--2902273 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2902239 TTCAATTCAA
2902249 ATAATCAATAT
1 ATAATCAATAT
2902260 ATAATCAATAT
1 ATAATCAATAT
2902271 ATA
1 ATA
2902274 TACAAATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATCAATAT
Found at i:2903005 original size:19 final size:20
Alignment explanation
Indices: 2902981--2903032 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
2902971 CTAATTTCTC
2902981 CTTTCTTTCTT-TCCCT-TTT
1 CTTTCTTT-TTCTCCCTGTTT
2903000 CTTTCTTTTTCTCCCTGTTT
1 CTTTCTTTTTCTCCCTGTTT
*
2903020 CGTTTCTATTTCT
1 C-TTTCTTTTTCT
2903033 TTTTGTTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 2 0.07
19 13 0.45
20 4 0.14
21 10 0.34
ACGTcount: A:0.02, C:0.29, G:0.04, T:0.65
Consensus pattern (20 bp):
CTTTCTTTTTCTCCCTGTTT
Found at i:2903092 original size:30 final size:31
Alignment explanation
Indices: 2903052--2903130 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 31
2903042 TTTTATTTAT
*
2903052 TATATTTACTTATTATAATATATA-ATATAA
1 TATATATACTTATTATAATATATAGATATAA
2903082 TATATATACTTA--ATAAT-TA-AGATATAA
1 TATATATACTTATTATAATATATAGATATAA
*
2903109 TAT-TATA-GTATTATAATATATA
1 TATATATACTTATTATAATATATA
2903131 TTTTTAACTT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
25 2 0.05
26 5 0.12
27 16 0.38
28 7 0.17
29 1 0.02
30 11 0.26
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (31 bp):
TATATATACTTATTATAATATATAGATATAA
Found at i:2904795 original size:7 final size:7
Alignment explanation
Indices: 2904783--2904824 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
2904773 ATCTCGAACC
2904783 CTAAACT
1 CTAAACT
*
2904790 CTAAACC
1 CTAAACT
2904797 CTAAA-T
1 CTAAACT
2904803 CTAAACT
1 CTAAACT
2904810 CTAAAC-
1 CTAAACT
2904816 CTCAAACT
1 CT-AAACT
2904824 C
1 C
2904825 AGACCTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
6 7 0.23
7 22 0.73
8 1 0.03
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (7 bp):
CTAAACT
Found at i:2904807 original size:13 final size:14
Alignment explanation
Indices: 2904779--2904815 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
2904769 CTGAATCTCG
2904779 AACCCTAAACTCTA
1 AACCCTAAACTCTA
2904793 AACCCTAAA-TCTA
1 AACCCTAAACTCTA
*
2904806 AACTCTAAAC
1 AACCCTAAAC
2904816 CTCAAACTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (14 bp):
AACCCTAAACTCTA
Found at i:2908388 original size:39 final size:40
Alignment explanation
Indices: 2908343--2908474 Score: 176
Period size: 40 Copynumber: 3.3 Consensus size: 40
2908333 GCTCCTCGTT
* * * *
2908343 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
*
2908383 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
* * *
2908422 CGAATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
*
2908462 CAAAGGCCTTCGG
1 CAAATGCCTTCGG
2908475 ATCTTAGTCC
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
39 34 0.42
40 47 0.58
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
Found at i:2908487 original size:40 final size:40
Alignment explanation
Indices: 2908343--2908527 Score: 144
Period size: 40 Copynumber: 4.7 Consensus size: 40
2908333 GCTCCTCGTT
* * * * ** *
2908343 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
* *
2908383 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
* * * *
2908422 CGAATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
** * * *
2908462 CAAAGGCCTTC-GGATCTTAGTCCGGATATATTC-ACTTAGCA
1 CAAAGGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCA
*
2908503 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAAGGCCTTCGGGACTTAACCCGGA
2908528 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
39 37 0.30
40 74 0.61
41 11 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAAGGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
Found at i:2908536 original size:41 final size:41
Alignment explanation
Indices: 2908459--2908536 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
2908449 TTAATATCTC
* * *
2908459 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
2908500 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
2908537 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:2916250 original size:39 final size:40
Alignment explanation
Indices: 2916205--2916336 Score: 176
Period size: 40 Copynumber: 3.3 Consensus size: 40
2916195 GCTCCTCGTT
* * * *
2916205 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
*
2916245 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
* * *
2916284 CGAATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
*
2916324 CAAAGGCCTTCGG
1 CAAATGCCTTCGG
2916337 ATCTTAGTCC
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
39 34 0.42
40 47 0.58
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
Found at i:2916349 original size:40 final size:40
Alignment explanation
Indices: 2916205--2916389 Score: 144
Period size: 40 Copynumber: 4.7 Consensus size: 40
2916195 GCTCCTCGTT
* * * * ** *
2916205 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
* *
2916245 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
* * * *
2916284 CGAATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
** * * *
2916324 CAAAGGCCTTC-GGATCTTAGTCCGGATATATTC-ACTTAGCA
1 CAAAGGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCA
*
2916365 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAAGGCCTTCGGGACTTAACCCGGA
2916390 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
39 37 0.30
40 74 0.61
41 11 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAAGGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
Found at i:2916398 original size:41 final size:41
Alignment explanation
Indices: 2916321--2916398 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
2916311 TTAATATCTC
* * *
2916321 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
2916362 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
2916399 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:2919433 original size:22 final size:22
Alignment explanation
Indices: 2919408--2919498 Score: 83
Period size: 22 Copynumber: 4.1 Consensus size: 22
2919398 TTAGCATAAG
*
2919408 GGTTCGCATAAAAATTCATATA
1 GGTTCGCATAATAATTCATATA
* * *
2919430 GGTTCGCATAGTACTTCATCTA
1 GGTTCGCATAATAATTCATATA
* *
2919452 GGATTTGCATAATAATTCTTATA
1 GG-TTCGCATAATAATTCATATA
* * * *
2919475 GGTTTGTATAATACTTCATCTA
1 GGTTCGCATAATAATTCATATA
2919497 GG
1 GG
2919499 GTTTACACAT
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
22 38 0.69
23 17 0.31
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.38
Consensus pattern (22 bp):
GGTTCGCATAATAATTCATATA
Found at i:2919469 original size:45 final size:45
Alignment explanation
Indices: 2919413--2919498 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
2919403 ATAAGGGTTC
*
2919413 GCATAAAAATTCATATAGGTTCGCATAGTACTTCATCTAGGATTT
1 GCATAAAAATTCATATAGGTTCGCATAATACTTCATCTAGGATTT
* * * *
2919458 GCATAATAATTCTTATAGGTTTGTATAATACTTCATCTAGG
1 GCATAAAAATTCATATAGGTTCGCATAATACTTCATCTAGG
2919499 GTTTACACAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (45 bp):
GCATAAAAATTCATATAGGTTCGCATAATACTTCATCTAGGATTT
Found at i:2919717 original size:16 final size:16
Alignment explanation
Indices: 2919698--2919733 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2919688 CTAGGGTTTG
2919698 CATACATAAGGGTTCA
1 CATACATAAGGGTTCA
**
2919714 CATACATGGGGGTTCA
1 CATACATAAGGGTTCA
2919730 CATA
1 CATA
2919734 ACAAATTACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (16 bp):
CATACATAAGGGTTCA
Found at i:2922004 original size:8 final size:8
Alignment explanation
Indices: 2921986--2922027 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
2921976 ATTACTCTTC
2921986 TTTTTTCT
1 TTTTTTCT
*
2921994 TTTTCT-T
1 TTTTTTCT
2922001 TTTTTTCT
1 TTTTTTCT
2922009 TTTTTTCT
1 TTTTTTCT
2922017 TTTTTT-T
1 TTTTTTCT
2922024 TTTT
1 TTTT
2922028 GCGTCTGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
7 11 0.35
8 20 0.65
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTCT
Found at i:2922007 original size:9 final size:9
Alignment explanation
Indices: 2921993--2922027 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
2921983 TTCTTTTTTC
2921993 TTTTTCTTT
1 TTTTTCTTT
2922002 TTTTTC-TT
1 TTTTTCTTT
2922010 TTTTTCTTT
1 TTTTTCTTT
2922019 TTTTT-TTT
1 TTTTTCTTT
2922027 T
1 T
2922028 GCGTCTGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 12 0.48
9 13 0.52
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:2922027 original size:15 final size:16
Alignment explanation
Indices: 2921986--2922027 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
2921976 ATTACTCTTC
2921986 TTTTTTCTTTTTCT-T
1 TTTTTTCTTTTTCTCT
*
2922001 TTTTTTCTTTTTTTCT
1 TTTTTTCTTTTTCTCT
2922017 TTTTTT-TTTTT
1 TTTTTTCTTTTT
2922028 GCGTCTGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (16 bp):
TTTTTTCTTTTTCTCT
Found at i:2930746 original size:16 final size:18
Alignment explanation
Indices: 2930711--2930748 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
2930701 GTTACTGATA
*
2930711 ATTCATTCCAAGTATTTT
1 ATTCATTCCAACTATTTT
2930729 ATTCA-TCCAACT-TTTT
1 ATTCATTCCAACTATTTT
2930745 ATTC
1 ATTC
2930749 TCTCTCCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.26, C:0.21, G:0.03, T:0.50
Consensus pattern (18 bp):
ATTCATTCCAACTATTTT
Found at i:2934349 original size:42 final size:42
Alignment explanation
Indices: 2934285--2934383 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 42
2934275 TATATGAACA
2934285 GCACTAAGTGTGCGAAACTAAAAT-GACGAGGTTGAATAAAGG
1 GCACTAAGTGTGCGAAACTAAAATGGA-GAGGTTGAATAAAGG
* * * *
2934327 GCACTAAATGTGCGAAATTAAAATGGAGATGTTGAATAACGG
1 GCACTAAGTGTGCGAAACTAAAATGGAGAGGTTGAATAAAGG
2934369 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
2934384 TACCGAGAGC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 49 0.96
43 2 0.04
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.21
Consensus pattern (42 bp):
GCACTAAGTGTGCGAAACTAAAATGGAGAGGTTGAATAAAGG
Found at i:2938183 original size:15 final size:15
Alignment explanation
Indices: 2938135--2938177 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
2938125 ATGACCTTGC
*
2938135 GAGGTCGATGAGCAA
1 GAGGTCAATGAGCAA
**
2938150 CCGGTCAATGAGCAA
1 GAGGTCAATGAGCAA
2938165 GAGGTCAATGAGC
1 GAGGTCAATGAGC
2938178 CGGAGGATGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.35, T:0.14
Consensus pattern (15 bp):
GAGGTCAATGAGCAA
Found at i:2939171 original size:3 final size:3
Alignment explanation
Indices: 2939163--2939197 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2939153 ATTATGTAGT
2939163 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2939198 GTTTATTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2957037 original size:20 final size:19
Alignment explanation
Indices: 2957012--2957052 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
2957002 ATAGAAATTA
*
2957012 TTATTCCCAGAAAATATAAT
1 TTATTCCAAGAAAATA-AAT
2957032 TTATTCCAAGAAAATAAAT
1 TTATTCCAAGAAAATAAAT
2957051 TT
1 TT
2957053 CCACTACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (19 bp):
TTATTCCAAGAAAATAAAT
Found at i:2961746 original size:18 final size:19
Alignment explanation
Indices: 2961715--2961751 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2961705 ATTGTAGTTC
*
2961715 AAAATTACTAAACATTTAA
1 AAAATCACTAAACATTTAA
2961734 AAAATCACT-AACATTTAA
1 AAAATCACTAAACATTTAA
2961752 CTATCTAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAATCACTAAACATTTAA
Found at i:2961853 original size:51 final size:51
Alignment explanation
Indices: 2961777--2961878 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
2961767 AACTAATTAT
2961777 ATTAAAAAAGTCAGAAAATACAACTTAAAGGAAAGCGCGTCCTGCTGGGTG
1 ATTAAAAAAGTCAGAAAATACAACTTAAAGGAAAGCGCGTCCTGCTGGGTG
2961828 ATTAAAAAAGTCAGAAAATACAACTTAAAGGAAAGCGCGTCCTGCTGGGTG
1 ATTAAAAAAGTCAGAAAATACAACTTAAAGGAAAGCGCGTCCTGCTGGGTG
2961879 CGCTTTCCCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.20
Consensus pattern (51 bp):
ATTAAAAAAGTCAGAAAATACAACTTAAAGGAAAGCGCGTCCTGCTGGGTG
Found at i:2962346 original size:17 final size:18
Alignment explanation
Indices: 2962311--2962355 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
2962301 ATTAATTTTT
2962311 ATCATATTTA-AAATAAA
1 ATCATATTTATAAATAAA
*
2962328 ATCATATTTATATAT-AA
1 ATCATATTTATAAATAAA
*
2962345 ATTATATTTAT
1 ATCATATTTAT
2962356 TTAGTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 22 0.88
18 3 0.12
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (18 bp):
ATCATATTTATAAATAAA
Found at i:2963230 original size:4 final size:4
Alignment explanation
Indices: 2963221--2963262 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
2963211 TTCAAACTCG
2963221 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG-A TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
2963263 GAAGTTGTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.08
4 34 0.92
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:2965665 original size:2 final size:2
Alignment explanation
Indices: 2965658--2965725 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
2965648 TGCCTTTGAA
2965658 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2965700 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
2965726 GTATGCAGTG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2966151 original size:27 final size:27
Alignment explanation
Indices: 2966111--2966164 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
2966101 TTCATATTAA
*
2966111 TATTTTAATAATAAAATTAATCTTTTT
1 TATTTTAATAATAAAATCAATCTTTTT
* *
2966138 TATTTTAATTATAAAATCACTCTTTTT
1 TATTTTAATAATAAAATCAATCTTTTT
2966165 AATATATAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (27 bp):
TATTTTAATAATAAAATCAATCTTTTT
Found at i:2966948 original size:20 final size:20
Alignment explanation
Indices: 2966918--2966967 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
2966908 ATGTTCAAGA
2966918 TTTTGGGTTC-AGAGTTTAGGG
1 TTTT-GGTTCAAG-GTTTAGGG
2966939 TTTTGGTTCAAGGTTTAGGG
1 TTTTGGTTCAAGGTTTAGGG
2966959 TTTTGGTTC
1 TTTTGGTTC
2966968 GGGGGTCAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 22 0.79
21 6 0.21
ACGTcount: A:0.12, C:0.06, G:0.34, T:0.48
Consensus pattern (20 bp):
TTTTGGTTCAAGGTTTAGGG
Found at i:2966978 original size:20 final size:20
Alignment explanation
Indices: 2966935--2966979 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2966925 TTCAGAGTTT
* *
2966935 AGGGTTTTGGTTCAAGGTTT
1 AGGGTTTTGGTTCAAGGGTC
**
2966955 AGGGTTTTGGTTCGGGGGTC
1 AGGGTTTTGGTTCAAGGGTC
2966975 AGGGT
1 AGGGT
2966980 AAAAAAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.07, G:0.44, T:0.38
Consensus pattern (20 bp):
AGGGTTTTGGTTCAAGGGTC
Found at i:2967552 original size:30 final size:30
Alignment explanation
Indices: 2967508--2967570 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
2967498 ACTTAACAAG
2967508 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
2967538 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
2967568 CAA
1 CAA
2967571 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:2973860 original size:25 final size:25
Alignment explanation
Indices: 2973831--2973880 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
2973821 ATATCAAGTG
2973831 AGTTTAGAGCTTTAATTTTGTTGTA
1 AGTTTAGAGCTTTAATTTTGTTGTA
2973856 AGTTTAGAGCTTTAATTTTGTTGTA
1 AGTTTAGAGCTTTAATTTTGTTGTA
2973881 TGATGAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.04, G:0.20, T:0.52
Consensus pattern (25 bp):
AGTTTAGAGCTTTAATTTTGTTGTA
Found at i:2974051 original size:17 final size:17
Alignment explanation
Indices: 2974004--2974051 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
2973994 AGCCTAAAAT
*
2974004 ATTTGGATAAATTATTG
1 ATTTAGATAAATTATTG
2974021 ATTTAGA-AATATTAGTTG
1 ATTTAGATAA-ATTA-TTG
2974039 ATTT-GATAAATTA
1 ATTTAGATAAATTA
2974052 ATTAGTTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 2 0.07
17 16 0.59
18 9 0.33
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.46
Consensus pattern (17 bp):
ATTTAGATAAATTATTG
Found at i:2974524 original size:24 final size:25
Alignment explanation
Indices: 2974471--2974518 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
2974461 TTAGCCCTCT
*
2974471 CGAGCTTCCCGTTATATAGTTCTTG
1 CGAGCTTCCCGTTATATAGCTCTTG
*
2974496 CGAGCTTCCTGTTA-ATAGCTCTT
1 CGAGCTTCCCGTTATATAGCTCTT
2974519 CGGAGCATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.40
Consensus pattern (25 bp):
CGAGCTTCCCGTTATATAGCTCTTG
Found at i:2974612 original size:26 final size:25
Alignment explanation
Indices: 2974582--2974673 Score: 89
Period size: 26 Copynumber: 3.6 Consensus size: 25
2974572 CTTATAAGTG
2974582 TCCCGATATATGGCTCTTCGTGAGCT
1 TCCCGATAT-TGGCTCTTCGTGAGCT
* *
2974608 TCCCGTTGATTGGCTCTTTGTGAGCT
1 TCCCGAT-ATTGGCTCTTCGTGAGCT
* *
2974634 TCCTC-ATTAATGGCTCTCCG-GAGCT
1 TCC-CGA-TATTGGCTCTTCGTGAGCT
*
2974659 TCTCGATATTGGCTC
1 TCCCGATATTGGCTC
2974674 GCTTGAACTT
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
24 9 0.17
25 8 0.15
26 33 0.61
27 4 0.07
ACGTcount: A:0.13, C:0.27, G:0.23, T:0.37
Consensus pattern (25 bp):
TCCCGATATTGGCTCTTCGTGAGCT
Found at i:2975264 original size:20 final size:20
Alignment explanation
Indices: 2975239--2975288 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2975229 CGAAAATTTT
2975239 GAAACACGAGATTTT-TTTAG
1 GAAACACGA-ATTTTCTTTAG
**
2975259 GAAACACGAATTTTCTTTTT
1 GAAACACGAATTTTCTTTAG
2975279 GAAACACGAA
1 GAAACACGAA
2975289 AATTTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
GAAACACGAATTTTCTTTAG
Found at i:2975318 original size:19 final size:19
Alignment explanation
Indices: 2975274--2975330 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
2975264 ACGAATTTTC
2975274 TTTTTG-AAACACGAAAA--
1 TTTTTGAAAACAC-AAAATT
2975291 TTTTT-AAAACACAAAATT
1 TTTTTGAAAACACAAAATT
*
2975309 TTTTTGAAAACATAAAATT
1 TTTTTGAAAACACAAAATT
2975328 TTT
1 TTT
2975331 GATAAAATAC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
16 4 0.11
17 11 0.31
18 5 0.14
19 15 0.43
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (19 bp):
TTTTTGAAAACACAAAATT
Found at i:2975331 original size:17 final size:17
Alignment explanation
Indices: 2975274--2975332 Score: 68
Period size: 17 Copynumber: 3.4 Consensus size: 17
2975264 ACGAATTTTC
2975274 TTTTTG-AAACACGAAAA
1 TTTTTGAAAACAC-AAAA
2975291 TTTTT-AAAACACAAAA
1 TTTTTGAAAACACAAAA
*
2975307 TTTTTTTGAAAACATAAAA
1 --TTTTTGAAAACACAAAA
2975326 TTTTTGA
1 TTTTTGA
2975333 TAAAATACGA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
16 4 0.11
17 18 0.49
18 5 0.14
19 10 0.27
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (17 bp):
TTTTTGAAAACACAAAA
Found at i:2975337 original size:19 final size:18
Alignment explanation
Indices: 2975280--2975337 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
2975270 TTTCTTTTTG
2975280 AAACACGAAAA-TTTT-TA
1 AAACAC-AAAATTTTTATA
*
2975297 AAACACAAAATTTTTTTGA
1 AAACACAAAATTTTTAT-A
*
2975316 AAACATAAAATTTTTGATA
1 AAACACAAAATTTTT-ATA
2975335 AAA
1 AAA
2975338 TACGAAACAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 4 0.11
17 10 0.29
18 1 0.03
19 19 0.54
20 1 0.03
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33
Consensus pattern (18 bp):
AAACACAAAATTTTTATA
Found at i:2975364 original size:18 final size:18
Alignment explanation
Indices: 2975341--2975590 Score: 89
Period size: 17 Copynumber: 14.0 Consensus size: 18
2975331 GATAAAATAC
*
2975341 GAAACACGAGGATTTTTT
1 GAAACACGAGAATTTTTT
* *
2975359 GAAACACGA-AAATTTAT
1 GAAACACGAGAATTTTTT
2975376 GAAACACG-GTCAATTTTTGT
1 GAAACACGAG--AATTTTT-T
*
2975396 GAAAACACGA-AAATTTTT
1 G-AAACACGAGAATTTTTT
* *
2975414 GAAAGACG-GGATTTTTT
1 GAAACACGAGAATTTTTT
* * *
2975431 GAAAACATG-GAAATTTAT
1 G-AAACACGAGAATTTTTT
2975449 GAAACACG-GAATTTTTTT
1 GAAACACGAGAA-TTTTTT
* * *
2975467 GAAA-ACAAGAAAATTTTC
1 GAAACACGAG-AATTTTTT
* * * *
2975485 GGAATACG-GGA-CTTTT
1 GAAACACGAGAATTTTTT
* *
2975501 GAAAACAAGGAAAATTTTTT
1 G-AAAC-ACGAGAATTTTTT
*
2975521 GAAAACACGACAA-TTTTT
1 G-AAACACGAGAATTTTTT
2975539 GAAACACTG-GAA--TTTT
1 GAAACAC-GAGAATTTTTT
2975555 GAAAACACGA-AGATTTTTT
1 G-AAACACGAGA-ATTTTTT
* *
2975574 -AAACACAAAAATTTTTT
1 GAAACACGAGAATTTTTT
2975591 TTAAAACATG
Statistics
Matches: 174, Mismatches: 35, Indels: 47
0.68 0.14 0.18
Matches are distributed among these distances:
16 11 0.06
17 69 0.40
18 50 0.29
19 25 0.14
20 12 0.07
21 7 0.04
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (18 bp):
GAAACACGAGAATTTTTT
Found at i:2975428 original size:36 final size:35
Alignment explanation
Indices: 2975341--2975589 Score: 179
Period size: 35 Copynumber: 7.0 Consensus size: 35
2975331 GATAAAATAC
*
2975341 GAAACACGAGGATTTTTTG-AAACACGAAAATTTAT
1 GAAACACG-GGATTTTTTGAAAACACGAAAATTTTT
*
2975376 GAAACACGGTCAATTTTTGTGAAAACACGAAAATTTTT
1 GAAACACGG--GATTTTT-TGAAAACACGAAAATTTTT
* * * *
2975414 GAAAGACGGGATTTTTTGAAAACATGGAAATTTAT
1 GAAACACGGGATTTTTTGAAAACACGAAAATTTTT
* * *
2975449 GAAACACGGAATTTTTTTGAAAACAAGAAAATTTTC
1 GAAACACGGGA-TTTTTTGAAAACACGAAAATTTTT
* * * *
2975485 GGAATACGGGA-CTTTTGAAAACAAGGAAAATTTTTT
1 GAAACACGGGATTTTTTGAAAAC-ACGAAAA-TTTTT
** * *
2975521 GAAAACACGACAATTTTTG-AAACACTG-GAA-TTTT
1 G-AAACACGGGATTTTTTGAAAACAC-GAAAATTTTT
* *
2975555 GAAAACACGAAGATTTTTT--AAACACAAAAATTTTT
1 G-AAACACG-GGATTTTTTGAAAACACGAAAATTTTT
2975590 TTTAAAACAT
Statistics
Matches: 171, Mismatches: 30, Indels: 26
0.75 0.13 0.11
Matches are distributed among these distances:
34 32 0.19
35 50 0.29
36 48 0.28
37 13 0.08
38 28 0.16
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (35 bp):
GAAACACGGGATTTTTTGAAAACACGAAAATTTTT
Found at i:2975451 original size:73 final size:72
Alignment explanation
Indices: 2975340--2975539 Score: 226
Period size: 73 Copynumber: 2.8 Consensus size: 72
2975330 TGATAAAATA
* * *
2975340 CGAAACACGAGGATTTTTTG-AAACACGAAAATTTATGAAACACGGTCAATTTTTGTGAAAACAC
1 CGAAACACG-GGATTTTTTGAAAACAAGGAAATTTATGAAACACGG-CAATTTTTGTGAAAACAA
2975404 GAAAATTTT
64 GAAAATTTT
* * * *
2975413 TGAAAGACGGGATTTTTTGAAAACATGGAAATTTATGAAACACGG-AATTTTTTTGAAAACAAGA
1 CGAAACACGGGATTTTTTGAAAACAAGGAAATTTATGAAACACGGCAATTTTTGTGAAAACAAGA
2975477 AAATTTT
66 AAATTTT
* * * * *
2975484 CGGAATACGGGA-CTTTTGAAAACAAGGAAAATTTTTTGAAAACACGACAATTTTTG
1 CGAAACACGGGATTTTTTGAAAACAAGG-AAA-TTTATG-AAACACGGCAATTTTTG
2975540 AAACACTGGA
Statistics
Matches: 108, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
70 13 0.12
71 36 0.33
72 15 0.14
73 37 0.34
74 7 0.06
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (72 bp):
CGAAACACGGGATTTTTTGAAAACAAGGAAATTTATGAAACACGGCAATTTTTGTGAAAACAAGA
AAATTTT
Found at i:2975516 original size:71 final size:73
Alignment explanation
Indices: 2975340--2975539 Score: 221
Period size: 71 Copynumber: 2.8 Consensus size: 73
2975330 TGATAAAATA
* * *
2975340 CGAAACACGAGGATTTTTTG-AAAC-ACGAAAATTTATGAAACACGGTCAATTTTTGTGAAAACA
1 CGAAAGACG-GGATCTTTTGAAAACAAGGAAAATTTATGAAACACGG-CAATTTTTGTGAAAACA
*
2975403 CGAAAATTTT
64 AGAAAATTTT
* * * *
2975413 TGAAAGACGGGATTTTTTGAAAACATGG-AAATTTATGAAACACGG-AATTTTTTTGAAAACAAG
1 CGAAAGACGGGATCTTTTGAAAACAAGGAAAATTTATGAAACACGGCAATTTTTGTGAAAACAAG
2975476 AAAATTTT
66 AAAATTTT
* * * *
2975484 CGGAATACGGGA-CTTTTGAAAACAAGGAAAATTTTTTGAAAACACGACAATTTTTG
1 CGAAAGACGGGATCTTTTGAAAACAAGGAAAA-TTTATG-AAACACGGCAATTTTTG
2975540 AAACACTGGA
Statistics
Matches: 107, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
70 13 0.12
71 36 0.34
72 15 0.14
73 35 0.33
74 8 0.07
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (73 bp):
CGAAAGACGGGATCTTTTGAAAACAAGGAAAATTTATGAAACACGGCAATTTTTGTGAAAACAAG
AAAATTTT
Found at i:2975538 original size:20 final size:20
Alignment explanation
Indices: 2975497--2975542 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2975487 AATACGGGAC
*
2975497 TTTTGAAAACAAGGAAAATT
1 TTTTGAAAACAACGAAAATT
*
2975517 TTTTGAAAAC-ACGACAA-T
1 TTTTGAAAACAACGAAAATT
2975535 TTTTGAAA
1 TTTTGAAA
2975543 CACTGGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.38
19 5 0.21
20 10 0.42
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.33
Consensus pattern (20 bp):
TTTTGAAAACAACGAAAATT
Found at i:2976307 original size:14 final size:14
Alignment explanation
Indices: 2976288--2976325 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
2976278 GAAAATGGGC
2976288 CTTTTCTCTTTTTT
1 CTTTTCTCTTTTTT
2976302 CTTTTCT-TTTTTT
1 CTTTTCTCTTTTTT
2976315 CTTTT-TCTTTT
1 CTTTTCTCTTTT
2976326 CTGCAGATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.04
13 15 0.65
14 7 0.30
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
CTTTTCTCTTTTTT
Found at i:2976441 original size:19 final size:19
Alignment explanation
Indices: 2976417--2976464 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
2976407 TGCTGTTCTG
*
2976417 GGCTTGCTGGACTGGGTCA
1 GGCTTGCTGGACTGGGACA
* * *
2976436 GGCTTGTTGGGCTTGGACA
1 GGCTTGCTGGACTGGGACA
*
2976455 GGCCTGCTGG
1 GGCTTGCTGG
2976465 CCTTTTTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.08, C:0.21, G:0.44, T:0.27
Consensus pattern (19 bp):
GGCTTGCTGGACTGGGACA
Found at i:2976649 original size:11 final size:11
Alignment explanation
Indices: 2976635--2976688 Score: 65
Period size: 13 Copynumber: 4.7 Consensus size: 11
2976625 TTATTTTTTG
2976635 TTCTTTTTTCT
1 TTCTTTTTTCT
2976646 TTCTCTTTTTCT
1 TTCT-TTTTTCT
2976658 TCTCTCTTTTTCT
1 T-TCT-TTTTTCT
*
2976671 TCCTTTTTT-T
1 TTCTTTTTTCT
2976681 TTCTTTTT
1 TTCTTTTT
2976689 CTTCTTCTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
10 8 0.21
11 9 0.23
12 10 0.26
13 12 0.31
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTCTTTTTTCT
Found at i:2976654 original size:13 final size:13
Alignment explanation
Indices: 2976636--2976694 Score: 58
Period size: 11 Copynumber: 4.8 Consensus size: 13
2976626 TATTTTTTGT
2976636 TCTTTTTTCTTTC
1 TCTTTTTTCTTTC
2976649 TC-TTTTTC-TTC
1 TCTTTTTTCTTTC
2976660 TCTCTTTTTC-TTC
1 TCT-TTTTTCTTTC
2976673 -CTTTTTT-TTTC
1 TCTTTTTTCTTTC
2976684 T-TTTTCTTCTT
1 TCTTTT-TTCTT
2976695 CTTCCTCGGG
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
11 17 0.43
12 10 0.25
13 13 0.32
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TCTTTTTTCTTTC
Found at i:2976658 original size:6 final size:6
Alignment explanation
Indices: 2976639--2976697 Score: 55
Period size: 6 Copynumber: 9.3 Consensus size: 6
2976629 TTTTTGTTCT
* * *
2976639 TTTTTC TTTCTC TTTTTC TTCTCTC TTTTTC TTCCTTTT TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TT-TTTC TTTTTC TT--TTTC TTTTTC TTTTTC
*
2976690 TTCTTC TT
1 TTTTTC TT
2976698 CCTCGGGCCG
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
6 33 0.77
7 5 0.12
8 5 0.12
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:2976804 original size:14 final size:15
Alignment explanation
Indices: 2976776--2976824 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 15
2976766 GCGCGCCTCC
*
2976776 TCTTCTCTTCCTCTCT
1 TCTT-TCTTTCTCTCT
2976792 TCTTTCTTT-TCTCT
1 TCTTTCTTTCTCTCT
2976806 TCTTT-TTTCTCTCT
1 TCTTTCTTTCTCTCT
2976820 T-TTTC
1 TCTTTC
2976825 CTTTGGGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 6 0.20
14 16 0.53
15 4 0.13
16 4 0.13
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (15 bp):
TCTTTCTTTCTCTCT
Found at i:2977361 original size:29 final size:29
Alignment explanation
Indices: 2977277--2977403 Score: 132
Period size: 29 Copynumber: 4.3 Consensus size: 29
2977267 TGGGGCTAAT
*
2977277 ATGTAATTTAT-AGAAAGTTTAGGGG-TCAA
1 ATGTAATTT-TGA-AAAGTTTAGGGGTTGAA
* *
2977306 AGTGAAATTTTGAAAAAGTTTAAGGGTTGAA
1 A-TGTAATTTTG-AAAAGTTTAGGGGTTGAA
2977337 ATGTAATTTTGAAAAGTTTAGGGGTTGAA
1 ATGTAATTTTGAAAAGTTTAGGGGTTGAA
* * ***
2977366 ATGTAATTTAGAAAAGTTTTGGGGCCAAA
1 ATGTAATTTTGAAAAGTTTAGGGGTTGAA
2977395 ATGTAATTT
1 ATGTAATTT
2977404 ATATTTTTTG
Statistics
Matches: 84, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
29 52 0.62
30 27 0.32
31 5 0.06
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.35
Consensus pattern (29 bp):
ATGTAATTTTGAAAAGTTTAGGGGTTGAA
Found at i:2977949 original size:15 final size:15
Alignment explanation
Indices: 2977931--2977978 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
2977921 AATGTACATG
*
2977931 GAAATAATGGTATAT
1 GAAATAATGATATAT
*
2977946 GAAATATTGATATAAT
1 GAAATAATGATAT-AT
2977962 GAAATGAATGATATAT
1 GAAAT-AATGATATAT
2977978 G
1 G
2977979 TTTATGAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.39
16 10 0.36
17 7 0.25
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (15 bp):
GAAATAATGATATAT
Found at i:2979632 original size:20 final size:20
Alignment explanation
Indices: 2979607--2979644 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2979597 TGTTGAGTCA
2979607 GGAATCACTTCTTGGATGCT
1 GGAATCACTTCTTGGATGCT
2979627 GGAATCACTTCTTGGATG
1 GGAATCACTTCTTGGATG
2979645 TAACACCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.34
Consensus pattern (20 bp):
GGAATCACTTCTTGGATGCT
Found at i:2981971 original size:23 final size:25
Alignment explanation
Indices: 2981945--2981991 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2981935 AATTTAATTA
2981945 TTAATT-TTTGA-ATATATTATTTT
1 TTAATTCTTTGACATATATTATTTT
* *
2981968 TTAATTCTTTTACTTATATTATTT
1 TTAATTCTTTGACATATATTATTT
2981992 ATATAACCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 4 0.20
25 10 0.50
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (25 bp):
TTAATTCTTTGACATATATTATTTT
Found at i:2982002 original size:25 final size:25
Alignment explanation
Indices: 2981957--2982004 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
2981947 AATTTTTGAA
* *
2981957 TATATTATTTTTTAATTCTTTTACT
1 TATATTATTTTATAATCCTTTTACT
2981982 TATATTATTTATATAA-CCTTTTA
1 TATATTATTT-TATAATCCTTTTA
2982005 AATTGAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.62
Consensus pattern (25 bp):
TATATTATTTTATAATCCTTTTACT
Found at i:2987508 original size:21 final size:21
Alignment explanation
Indices: 2987484--2987533 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
2987474 GAGCTTACAA
2987484 GAGCAAATACAAGTGATGAAG
1 GAGCAAATACAAGTGATGAAG
2987505 GAGCAAATACAAGTGATGAAG
1 GAGCAAATACAAGTGATGAAG
2987526 GAGCAAAT
1 GAGCAAAT
2987534 GGCATAGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.48, C:0.10, G:0.28, T:0.14
Consensus pattern (21 bp):
GAGCAAATACAAGTGATGAAG
Found at i:2996191 original size:31 final size:31
Alignment explanation
Indices: 2996153--2996222 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
2996143 AAATACGTTG
2996153 ACATGGCATTATAAACAAATAGTATGGTGAT
1 ACATGGCATTATAAACAAATAGTATGGTGAT
* *
2996184 ACATGGCATTATCAACCAATAGTATGGTGAT
1 ACATGGCATTATAAACAAATAGTATGGTGAT
2996215 ACATGGCA
1 ACATGGCA
2996223 ACGTCATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (31 bp):
ACATGGCATTATAAACAAATAGTATGGTGAT
Found at i:2996500 original size:27 final size:28
Alignment explanation
Indices: 2996452--2996509 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
2996442 TTCGAAATTT
*
2996452 AAAATATATAATATTCTAAAAA-CTTAA
1 AAAATATATAATATTCTAAAAATATTAA
2996479 AAAATATATAA-ATT-TATTAAAATATTAA
1 AAAATATATAATATTCTA--AAAATATTAA
2996507 AAA
1 AAA
2996510 TATTAGTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 2 0.07
26 3 0.11
27 15 0.56
28 7 0.26
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (28 bp):
AAAATATATAATATTCTAAAAATATTAA
Found at i:2996753 original size:23 final size:24
Alignment explanation
Indices: 2996714--2996780 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 24
2996704 TTATACATTT
*
2996714 TATATATTTTA-ACAAAT-ATATTG
1 TATATATTTTATA-AAATAAGATTG
*
2996737 TATATATTTTATAAAATGCAAGATTT
1 TATATATTTTATAAAAT--AAGATTG
2996763 TATATATATTTATAAAAT
1 TATATAT-TTTATAAAAT
2996781 CTTATTGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
23 15 0.41
24 1 0.03
26 11 0.30
27 10 0.27
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (24 bp):
TATATATTTTATAAAATAAGATTG
Found at i:2997249 original size:18 final size:20
Alignment explanation
Indices: 2997206--2997242 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2997196 TTAACCCAAA
2997206 AAAATATAAAGTAAAAAATC
1 AAAATATAAAGTAAAAAATC
*
2997226 AAAATATATA-TAAAAAA
1 AAAATATAAAGTAAAAAA
2997243 GAAAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (20 bp):
AAAATATAAAGTAAAAAATC
Found at i:3001774 original size:93 final size:92
Alignment explanation
Indices: 3001614--3001891 Score: 344
Period size: 93 Copynumber: 3.0 Consensus size: 92
3001604 TGATGACAAT
* * * *
3001614 TTATGGTTTTGGTGCTTTTATTATATCTAGATTTGGGATTTAGTCCTTAAAATTTAATTTGACAT
1 TTATGGTTTTGGT-CTTTTATTATA-CCAGATTTGAGATTTAGTCCCTATAATTTAATTTGACAT
3001679 AATTTTTCTAT-TACTTTTATAATATCAAA
64 AATTTTTC-ATCTACTTTTATAATATCAAA
*
3001708 TTATGGTTTTGGTCTTTTTATTATACCGGAATTTGAGA-TTAGTCCCTATAATTTAATTTGACAT
1 TTATGGTTTTGGTC-TTTTATTATACCAG-ATTTGAGATTTAGTCCCTATAATTTAATTTGACAT
* *
3001772 AATTTTTCATCAACTTTTATGATATCAAA
64 AATTTTTCATCTACTTTTATAATATCAAA
* * * * *
3001801 TTGTGATTTTGGTCCTTTTATTATACTCATATATGAGATTTAGTCCCTATCATTTAATTTGACAC
1 TTATGGTTTTGGT-CTTTTATTATAC-CAGATTTGAGATTTAGTCCCTATAATTTAATTTGACA-
* *
3001866 AAACTTTTCATCTACTTTTATAATAT
63 TAATTTTTCATCTACTTTTATAATAT
3001892 AATTAGTTGC
Statistics
Matches: 160, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
92 2 0.01
93 80 0.50
94 56 0.35
95 22 0.14
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49
Consensus pattern (92 bp):
TTATGGTTTTGGTCTTTTATTATACCAGATTTGAGATTTAGTCCCTATAATTTAATTTGACATAA
TTTTTCATCTACTTTTATAATATCAAA
Found at i:3002169 original size:90 final size:90
Alignment explanation
Indices: 3002012--3002180 Score: 252
Period size: 90 Copynumber: 1.9 Consensus size: 90
3002002 CGATTAAACC
*
3002012 ATGATTTAGTTAGTCCAAATAATTACCATGGTTAATAATTTCGATTAAAGCGTTGAAGTGGAATT
1 ATGATTTAGTTAGTCCAAATAATTACCATGATTAATAATTTCGATTAAAGCGTTGAAGTGGAATT
*
3002077 TTCCTTAAACATACACGGTTAAGCA
66 TTCCGTAAACATACACGGTTAAGCA
* ** *
3002102 ATGATTTAGTTAGTCCAAATAATTATCATGATTAATAATTTC-AGTTAAATTGTTGAGGT-GAAT
1 ATGATTTAGTTAGTCCAAATAATTACCATGATTAATAATTTCGA-TTAAAGCGTTGAAGTGGAA-
3002165 TTTTCCGTAAACATAC
64 TTTTCCGTAAACATAC
3002181 TTATTCTGAT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
89 4 0.06
90 67 0.94
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (90 bp):
ATGATTTAGTTAGTCCAAATAATTACCATGATTAATAATTTCGATTAAAGCGTTGAAGTGGAATT
TTCCGTAAACATACACGGTTAAGCA
Found at i:3002513 original size:19 final size:19
Alignment explanation
Indices: 3002458--3002494 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3002448 TAATAAACAT
3002458 TAAAAAATTATTTTAAAAA
1 TAAAAAATTATTTTAAAAA
3002477 TAAAAAATTATTTTAAAA
1 TAAAAAATTATTTTAAAA
3002495 GTATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAAATTATTTTAAAAA
Found at i:3002524 original size:30 final size:30
Alignment explanation
Indices: 3002461--3002524 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
3002451 TAAACATTAA
* * ***
3002461 AAAATTATTTTAAAAATAAAAAATTATTTT
1 AAAAGTATTTTAAAAATAAAAAATAAAAAT
*
3002491 AAAAGTATTTTAAAATTAAAAAATAAAAAT
1 AAAAGTATTTTAAAAATAAAAAATAAAAAT
3002521 AAAA
1 AAAA
3002525 ATATATATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (30 bp):
AAAAGTATTTTAAAAATAAAAAATAAAAAT
Found at i:3004757 original size:22 final size:22
Alignment explanation
Indices: 3004732--3004776 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3004722 GGTGAAATTG
3004732 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
3004754 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
3004776 T
1 T
3004777 CTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:3008536 original size:22 final size:22
Alignment explanation
Indices: 3008508--3008552 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3008498 AGGGGGAGTG
3008508 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
3008530 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
3008552 T
1 T
3008553 CTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:3009778 original size:16 final size:17
Alignment explanation
Indices: 3009747--3009780 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3009737 GTATAAAATT
3009747 AAATATTAATTTTTAAA
1 AAATATTAATTTTTAAA
*
3009764 AAATATTTA-TTTTAAA
1 AAATATTAATTTTTAAA
3009780 A
1 A
3009781 TCTAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATATTAATTTTTAAA
Found at i:3009860 original size:20 final size:20
Alignment explanation
Indices: 3009835--3009876 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
3009825 TGGATGAAAA
3009835 ATAAATATGATGATTTCAGT
1 ATAAATATGATGATTTCAGT
*
3009855 ATAAATATGATGATTTGAGT
1 ATAAATATGATGATTTCAGT
3009875 AT
1 AT
3009877 CTCCTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.17, T:0.40
Consensus pattern (20 bp):
ATAAATATGATGATTTCAGT
Found at i:3010095 original size:21 final size:21
Alignment explanation
Indices: 3010071--3010114 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3010061 TTGGCCCGGG
3010071 CCCGGCCCGGTCCGACCCAGC
1 CCCGGCCCGGTCCGACCCAGC
3010092 CCCGGCCCGGTCCGACCCAGC
1 CCCGGCCCGGTCCGACCCAGC
3010113 CC
1 CC
3010115 GAATATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.59, G:0.27, T:0.05
Consensus pattern (21 bp):
CCCGGCCCGGTCCGACCCAGC
Found at i:3010150 original size:17 final size:18
Alignment explanation
Indices: 3010124--3010164 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
3010114 CGAATATAAT
3010124 AAATATTTTTTAATTTTA
1 AAATATTTTTTAATTTTA
*
3010142 AAATATTTTTTATTTTTA
1 AAATATTTTTTAATTTTA
3010160 AAATA
1 AAATA
3010165 AGTTTTTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AAATATTTTTTAATTTTA
Found at i:3010170 original size:18 final size:18
Alignment explanation
Indices: 3010131--3010170 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3010121 AATAAATATT
**
3010131 TTTTAATTTTAAAATATT
1 TTTTAATTTTAAAATAAG
*
3010149 TTTTATTTTTAAAATAAG
1 TTTTAATTTTAAAATAAG
3010167 TTTT
1 TTTT
3010171 TGGTGTTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTAATTTTAAAATAAG
Found at i:3013253 original size:9 final size:9
Alignment explanation
Indices: 3013239--3013305 Score: 82
Period size: 9 Copynumber: 7.4 Consensus size: 9
3013229 TTTGGTTAAA
3013239 AATTAACCG
1 AATTAACCG
*
3013248 AATTAAACG
1 AATTAACCG
*
3013257 AATTAACTG
1 AATTAACCG
*
3013266 AATTACCCG
1 AATTAACCG
3013275 AATTAACCG
1 AATTAACCG
3013284 AATT-ACTCG
1 AATTAAC-CG
*
3013293 AATTAATCG
1 AATTAACCG
3013302 AATT
1 AATT
3013306 GAATCACTAC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
8 2 0.04
9 46 0.94
10 1 0.02
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:3013275 original size:27 final size:27
Alignment explanation
Indices: 3013239--3013305 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
3013229 TTTGGTTAAA
3013239 AATTAACCGAATTAAACGAATTAACT-G
1 AATTAACCGAATTAAACGAATT-ACTCG
* *
3013266 AATTACCCGAATTAACCGAATTACTCG
1 AATTAACCGAATTAAACGAATTACTCG
*
3013293 AATTAATCGAATT
1 AATTAACCGAATT
3013306 GAATCACTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 3 0.09
27 32 0.91
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.28
Consensus pattern (27 bp):
AATTAACCGAATTAAACGAATTACTCG
Found at i:3014273 original size:20 final size:20
Alignment explanation
Indices: 3014248--3014293 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
3014238 TAAACACAAC
*
3014248 AAAAAAA-AATTTAGAAATTA
1 AAAAAAATAATTTA-AAAATA
*
3014268 AAAAAAATATTTTAAAAATA
1 AAAAAAATAATTTAAAAATA
3014288 AAAAAA
1 AAAAAA
3014294 TTTTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAAAAATAATTTAAAAATA
Found at i:3014294 original size:19 final size:17
Alignment explanation
Indices: 3014269--3014302 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
3014259 TAGAAATTAA
3014269 AAAAAATATTTTAAAAAT
1 AAAAAA-ATTTTAAAAAT
3014287 AAAAAAATTTTAAAAA
1 AAAAAAATTTTAAAAA
3014303 AGTATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAAAATTTTAAAAAT
Found at i:3014303 original size:18 final size:19
Alignment explanation
Indices: 3014248--3014303 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
3014238 TAAACACAAC
* * *
3014248 AAAAAAAAATTTAGAAATT
1 AAAAAAAATTTTAAAAAAT
*
3014267 AAAAAAAATATTTTAAAAAT
1 AAAAAAAAT-TTTAAAAAAT
3014287 -AAAAAAATTTTAAAAAA
1 AAAAAAAATTTTAAAAAA
3014304 GTATTTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 8 0.26
19 16 0.52
20 7 0.23
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAAAAAATTTTAAAAAAT
Found at i:3016715 original size:138 final size:138
Alignment explanation
Indices: 3016467--3016744 Score: 511
Period size: 138 Copynumber: 2.0 Consensus size: 138
3016457 GAGGCTTAAA
* *
3016467 AACGTATGGATGCTTTGAGGAGTCCCTGTTTTGAATTTTAGAATCATATGTAATTTCTTTAAAAA
1 AACGTATGGATGCTTTCAGGAGTCCCTGTTTTGAATTTTAGAACCATATGTAATTTCTTTAAAAA
3016532 TTGGCATTAAATTGTTTTTAGGTTTTATAATAACATTTCTCTTTGTTATGTTATTATGCAACTTA
66 TTGGCATTAAATTGTTTTTAGGTTTTATAATAACATTTCTCTTTGTTATGTTATTATGCAACTTA
3016597 TTTGATTT
131 TTTGATTT
* *
3016605 AACGTCTGGATGCTTTCAGGAGTCCCTGTTTTGAATTTTAGAACCATATGTAATTTCTTTAGAAA
1 AACGTATGGATGCTTTCAGGAGTCCCTGTTTTGAATTTTAGAACCATATGTAATTTCTTTAAAAA
*
3016670 TTGGCATTAAATTGTTTTTAGGTTTTATATTAACATTTCTCTTTGTTATGTTATTATGCAACTTA
66 TTGGCATTAAATTGTTTTTAGGTTTTATAATAACATTTCTCTTTGTTATGTTATTATGCAACTTA
3016735 TTTGATTT
131 TTTGATTT
3016743 AA
1 AA
3016745 AATTTTACAA
Statistics
Matches: 135, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
138 135 1.00
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.47
Consensus pattern (138 bp):
AACGTATGGATGCTTTCAGGAGTCCCTGTTTTGAATTTTAGAACCATATGTAATTTCTTTAAAAA
TTGGCATTAAATTGTTTTTAGGTTTTATAATAACATTTCTCTTTGTTATGTTATTATGCAACTTA
TTTGATTT
Found at i:3027811 original size:26 final size:26
Alignment explanation
Indices: 3027762--3027811 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3027752 TGGTTTCCTT
*
3027762 AACTATAGTTTCTTATTCTTCAAGTA
1 AACTATAGTTTCTTATTCTACAAGTA
*
3027788 AACTTTAGTTTCTTAGTT-TACAAG
1 AACTATAGTTTCTTA-TTCTACAAG
3027812 AATAAAACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (26 bp):
AACTATAGTTTCTTATTCTACAAGTA
Found at i:3027974 original size:29 final size:29
Alignment explanation
Indices: 3027916--3027975 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
3027906 TTCTAATGAG
** *
3027916 TCTAAGGTTAGGAGCTCCATTTGACTAGT
1 TCTAAGGTTAGGAGCTCCATTCAACGAGT
*
3027945 TCTAAGGTTAGGAGCTCCCTTCAACGAGT
1 TCTAAGGTTAGGAGCTCCATTCAACGAGT
3027974 TC
1 TC
3027976 CATACGTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (29 bp):
TCTAAGGTTAGGAGCTCCATTCAACGAGT
Found at i:3055643 original size:11 final size:12
Alignment explanation
Indices: 3055626--3055654 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
3055616 ATCATTAATA
3055626 AATAAATGAGTC
1 AATAAATGAGTC
3055638 -ATAAATGAGTC
1 AATAAATGAGTC
3055649 AATAAA
1 AATAAA
3055655 CAAGCTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (12 bp):
AATAAATGAGTC
Found at i:3066584 original size:50 final size:50
Alignment explanation
Indices: 3066461--3066645 Score: 225
Period size: 50 Copynumber: 3.7 Consensus size: 50
3066451 GATAATAACA
* *
3066461 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-CGG
* *
3066510 -GCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
* ** ** *
3066559 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
*
3066609 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
3066646 TCTCTTTACC
Statistics
Matches: 116, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
47 4 0.03
48 38 0.33
50 74 0.64
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
Found at i:3069002 original size:18 final size:20
Alignment explanation
Indices: 3068983--3069021 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3068973 GAGCAGACCA
3068983 TGCAGCTAGAGCC-ATGCATGT
1 TGCAGCTAGAGCCTATGCA--T
3069004 TGCAGCTAGAGCCTATGC
1 TGCAGCTAGAGCCTATGC
3069022 TACTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (20 bp):
TGCAGCTAGAGCCTATGCAT
Found at i:3074677 original size:14 final size:14
Alignment explanation
Indices: 3074633--3074716 Score: 62
Period size: 14 Copynumber: 5.9 Consensus size: 14
3074623 GTAATTTGTA
3074633 TATGTGAACCCCCTG
1 TATGTGAA-CCCCTG
* ** *
3074648 TACGTGAGTCCATG
1 TATGTGAACCCCTG
3074662 TATGTGAACCCCTG
1 TATGTGAACCCCTG
* *
3074676 TATGCGAACCAC-G
1 TATGTGAACCCCTG
* *
3074689 ATAGGCGAACCTCCTG
1 -TATGTGAACC-CCTG
3074705 TATGTGAACCCC
1 TATGTGAACCCC
3074717 CATATATGTG
Statistics
Matches: 52, Mismatches: 14, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
13 1 0.02
14 35 0.67
15 15 0.29
16 1 0.02
ACGTcount: A:0.24, C:0.30, G:0.23, T:0.24
Consensus pattern (14 bp):
TATGTGAACCCCTG
Found at i:3074866 original size:15 final size:15
Alignment explanation
Indices: 3074824--3074889 Score: 80
Period size: 15 Copynumber: 4.5 Consensus size: 15
3074814 ATGTGATTTA
*
3074824 ATATGTGAGAACCC-
1 ATATGTGCGAACCCT
**
3074838 ATACATGCGAACCCT
1 ATATGTGCGAACCCT
*
3074853 ATATGTGTGAACCCT
1 ATATGTGCGAACCCT
*
3074868 ATATGTGCGAACCTT
1 ATATGTGCGAACCCT
3074883 ATATGTG
1 ATATGTG
3074890 AACCTATTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
14 11 0.26
15 32 0.74
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (15 bp):
ATATGTGCGAACCCT
Found at i:3074866 original size:29 final size:30
Alignment explanation
Indices: 3074824--3074890 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
3074814 ATGTGATTTA
3074824 ATATGTGAGAACCC-ATACATGCGAACCCT
1 ATATGTGAGAACCCTATACATGCGAACCCT
* ** *
3074853 ATATGTGTGAACCCTATATGTGCGAACCTT
1 ATATGTGAGAACCCTATACATGCGAACCCT
3074883 ATATGTGA
1 ATATGTGA
3074891 ACCTATTATG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 13 0.41
30 19 0.59
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (30 bp):
ATATGTGAGAACCCTATACATGCGAACCCT
Found at i:3077533 original size:16 final size:16
Alignment explanation
Indices: 3077512--3077542 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3077502 AAAACTTTTT
3077512 TTATAAATGTTATATC
1 TTATAAATGTTATATC
*
3077528 TTATAAATTTTATAT
1 TTATAAATGTTATAT
3077543 TATTATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (16 bp):
TTATAAATGTTATATC
Found at i:3083552 original size:21 final size:20
Alignment explanation
Indices: 3083528--3083567 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3083518 AATATTATAA
3083528 TATAAATATTGAAAAAAATAT
1 TATAAA-ATTGAAAAAAATAT
* *
3083549 TATAAAATTTAATAAAATA
1 TATAAAATTGAAAAAAATA
3083568 AATATATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
TATAAAATTGAAAAAAATAT
Found at i:3083573 original size:21 final size:21
Alignment explanation
Indices: 3083524--3083578 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
3083514 ATATAATATT
3083524 ATAATATAAATATTGAAAAAA
1 ATAATATAAATATTGAAAAAA
* * *
3083545 ATATTATAAA-ATTTAATAAA
1 ATAATATAAATATTGAAAAAA
*
3083565 ATAAATATATATAT
1 AT-AATATAAATAT
3083579 GTTTAATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 10 0.37
21 15 0.56
22 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
ATAATATAAATATTGAAAAAA
Found at i:3088382 original size:12 final size:12
Alignment explanation
Indices: 3088367--3088391 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3088357 GATGAAAATG
3088367 TAAATAAAGAAA
1 TAAATAAAGAAA
3088379 TAAATAAAGAAA
1 TAAATAAAGAAA
3088391 T
1 T
3088392 GAACAAGGTT
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:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (12 bp):
TAAATAAAGAAA
Found at i:3090511 original size:44 final size:44
Alignment explanation
Indices: 3090397--3090513 Score: 123
Period size: 44 Copynumber: 2.7 Consensus size: 44
3090387 TTTTAACCCA
* * ** * *
3090397 CTCCACTGTAACTTCAGGGAGATAGGAT-AGTGTCTTCGATCTG
1 CTCCACTGTAACTTCAGGGGGATAAGATCTCTGGCTTCAATCTG
*
3090440 CTCCGCTGTAA-TCTC-GGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAACT-TCAGGGG-GATAAGATCTCTGGCTTCAATCTG
*
3090484 CTCCACTGTAACTTCAGGGGGACAAGATCT
1 CTCCACTGTAACTTCAGGGGGATAAGATCT
3090514 GTAATTTCCA
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
42 4 0.07
43 19 0.32
44 32 0.53
45 5 0.08
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (44 bp):
CTCCACTGTAACTTCAGGGGGATAAGATCTCTGGCTTCAATCTG
Found at i:3090940 original size:88 final size:88
Alignment explanation
Indices: 3090651--3091517 Score: 1279
Period size: 88 Copynumber: 9.9 Consensus size: 88
3090641 TGTAACCTTT
* * * *
3090651 AACCAGCTCCAAT-GCAACCGATG-GAGGCAAGGCTTTGT-T-TTTGATCTGCTTCGCTGTTAAT
1 AACCAGCTCC-ATCACAACCGA-GAGAGGCAAGG-TTTGTGTCTTCGACCTGCTTCGCTGTCAAT
** *
3090712 GCAGGAAGGCAAGATCTGCT-TCTTT
63 GCAGGAAGGCAAGATCTTTTGTCTTC
* * * * * *
3090737 AACTAGCTCCA-CTGCAATCGATG-GATGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAAT
1 AACCAGCTCCATC-ACAACCGA-GAGAGGCAAGG-TTTGTGTCTTCGACCTGCTTCGCTGTCAAT
* ** *
3090798 GTAGGAAGGCAAGATCTGCT-TCTTT
63 GCAGGAAGGCAAGATCTTTTGTCTTC
**
3090823 AACCAGCTCCA-CTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCATTGTCAATGC
1 AACCAGCTCCATC-ACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGC
*
3090887 AGGAAGGCAAGATATTTTGTCTTC
65 AGGAAGGCAAGATCTTTTGTCTTC
* * *
3090911 AACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1 AACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCA
* *
3090976 GAAAGGCAAGATCCTTTGTCTTC
66 GGAAGGCAAGATCTTTTGTCTTC
* * * *
3090999 AACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTATCAATGCA
1 AACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCA
*
3091064 GAAAGGCAAGATCTTTTGTCTTC
66 GGAAGGCAAGATCTTTTGTCTTC
3091087 AACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCA
1 AACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCA
3091152 GGAAGGCAAGATCTTTTGTCTTC
66 GGAAGGCAAGATCTTTTGTCTTC
*
3091175 AACCAGCTCCATCATAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCA
1 AACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCA
3091240 GGAAGGCAAGATCTTTTGTCTTC
66 GGAAGGCAAGATCTTTTGTCTTC
*
3091263 AACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCTTCGCTGTCAATGCA
1 AACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCA
3091328 GGAAGGCAAGATCTTTTGTCTTC
66 GGAAGGCAAGATCTTTTGTCTTC
*
3091351 AACCAGCTCCATCATAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCA
1 AACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCA
3091416 GGAAGGCAAGATCTTTTGTCTTC
66 GGAAGGCAAGATCTTTTGTCTTC
*
3091439 AACCAGCTCCATCATAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCA
1 AACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCA
*
3091504 GGAAGGCAAAATCT
66 GGAAGGCAAGATCT
3091518 GCAACTTCAT
Statistics
Matches: 735, Mismatches: 39, Indels: 12
0.94 0.05 0.02
Matches are distributed among these distances:
85 7 0.01
86 105 0.14
87 34 0.05
88 588 0.80
89 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (88 bp):
AACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCA
GGAAGGCAAGATCTTTTGTCTTC
Found at i:3092606 original size:21 final size:21
Alignment explanation
Indices: 3092580--3092626 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3092570 GGTATAGCAG
3092580 GATCACCACATGCCCCAATCT
1 GATCACCACATGCCCCAATCT
** *
3092601 GATCACTTCATGCCCCATTCT
1 GATCACCACATGCCCCAATCT
3092622 GATCA
1 GATCA
3092627 ATATTTGAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.38, G:0.11, T:0.26
Consensus pattern (21 bp):
GATCACCACATGCCCCAATCT
Found at i:3097675 original size:12 final size:12
Alignment explanation
Indices: 3097660--3097684 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3097650 GATGAAAATG
3097660 TAAATAAAGAAA
1 TAAATAAAGAAA
3097672 TAAATAAAGAAA
1 TAAATAAAGAAA
3097684 T
1 T
3097685 GAACAAGGTT
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:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (12 bp):
TAAATAAAGAAA
Found at i:3103045 original size:12 final size:12
Alignment explanation
Indices: 3103012--3103038 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3103002 ATTCTTGACT
3103012 TCTTGTTCTTGC
1 TCTTGTTCTTGC
3103024 TCTTGTTCTTGC
1 TCTTGTTCTTGC
3103036 TCT
1 TCT
3103039 GTTTCTTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.26, G:0.15, T:0.59
Consensus pattern (12 bp):
TCTTGTTCTTGC
Found at i:3106761 original size:3 final size:3
Alignment explanation
Indices: 3106755--3106785 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3106745 CTTCTTCTTC
3106755 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3106786 ATTGTTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3107046 original size:49 final size:47
Alignment explanation
Indices: 3106945--3107056 Score: 131
Period size: 47 Copynumber: 2.3 Consensus size: 47
3106935 TTTTATAATT
3106945 CATACATACATACATTTTTTATATATATTTTATAATTTAAAACTATA
1 CATACATACATACATTTTTTATATATATTTTATAATTTAAAACTATA
* * *
3106992 TATACATACATATATTCTTTT-TATATATTTTATAGTCTTAAAAC-ATA
1 CATACATACATACATT-TTTTATATATATTTTATAAT-TTAAAACTATA
3107039 CGCATACAT-CTATACATT
1 --CATACATAC-ATACATT
3107057 GTTATAATAC
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
47 31 0.56
48 12 0.22
49 12 0.22
ACGTcount: A:0.39, C:0.13, G:0.02, T:0.46
Consensus pattern (47 bp):
CATACATACATACATTTTTTATATATATTTTATAATTTAAAACTATA
Found at i:3107088 original size:26 final size:24
Alignment explanation
Indices: 3107058--3107109 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
3107048 CTATACATTG
*
3107058 TTATAATACATATATGTACATATATT
1 TTATAAT--ATATATATACATATATT
*
3107084 TTATAATTTATATATACATATATT
1 TTATAATATATATATACATATATT
3107108 TT
1 TT
3107110 TGTTATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 17 0.71
26 7 0.29
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (24 bp):
TTATAATATATATATACATATATT
Found at i:3107187 original size:12 final size:13
Alignment explanation
Indices: 3107159--3107199 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 13
3107149 CATATTTTCA
*
3107159 TATTT-TTTATAG
1 TATTTATTTATTG
3107171 T-TTTATTTATT-
1 TATTTATTTATTG
3107182 TATTTATTTATTG
1 TATTTATTTATTG
3107195 TATTT
1 TATTT
3107200 TTGTTTTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 4 0.16
12 16 0.64
13 5 0.20
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (13 bp):
TATTTATTTATTG
Found at i:3109091 original size:17 final size:19
Alignment explanation
Indices: 3109057--3109091 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3109047 GCACCACACA
3109057 GCCGTGTGGAAGGGTCTAG
1 GCCGTGTGGAAGGGTCTAG
3109076 GCCGTGT-GAA-GGTCTA
1 GCCGTGTGGAAGGGTCTA
3109092 CACGGTCATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.17, C:0.17, G:0.43, T:0.23
Consensus pattern (19 bp):
GCCGTGTGGAAGGGTCTAG
Found at i:3109146 original size:25 final size:25
Alignment explanation
Indices: 3109111--3109174 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
3109101 GTGAAAGAGG
*
3109111 CACACGCCCGTG-AAAAAGAAGCACA
1 CACACGACCGTGTAAAAA-AAGCACA
3109136 CACACGACCGTGTAAAAAAAGCACA
1 CACACGACCGTGTAAAAAAAGCACA
*
3109161 CGCACGACCGTGTA
1 CACACGACCGTGTA
3109175 GTGAAGACAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 31 0.86
26 5 0.14
ACGTcount: A:0.41, C:0.31, G:0.20, T:0.08
Consensus pattern (25 bp):
CACACGACCGTGTAAAAAAAGCACA
Found at i:3109664 original size:28 final size:28
Alignment explanation
Indices: 3109633--3109689 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
3109623 GATAGATATG
3109633 CTTCAATTCCACCAATTCTGATTCTAAA
1 CTTCAATTCCACCAATTCTGATTCTAAA
3109661 CTTCAATTCCACCAATTCTGATTCTAAA
1 CTTCAATTCCACCAATTCTGATTCTAAA
3109689 C
1 C
3109690 CCCAATGAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.35
Consensus pattern (28 bp):
CTTCAATTCCACCAATTCTGATTCTAAA
Found at i:3114515 original size:16 final size:16
Alignment explanation
Indices: 3114475--3114516 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
3114465 ATAATATGTG
3114475 AATACTATTATTTAAA
1 AATACTATTATTTAAA
*
3114491 AATATTATT-TTTAAA
1 AATACTATTATTTAAA
*
3114506 ATTTACTATTA
1 A-ATACTATTA
3114517 AAATAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (16 bp):
AATACTATTATTTAAA
Found at i:3114540 original size:18 final size:18
Alignment explanation
Indices: 3114502--3114537 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3114492 ATATTATTTT
*
3114502 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
3114520 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
3114538 TAATTTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:3116142 original size:38 final size:39
Alignment explanation
Indices: 3116057--3116142 Score: 97
Period size: 38 Copynumber: 2.2 Consensus size: 39
3116047 AATATATATT
*
3116057 TTTATTTTTATTTTTTAATTTTAAAATACTCTTAAAATAA
1 TTTA-TTTTATTTTTTAATTTTAAAATAATCTTAAAATAA
* **
3116097 TTT-TTTTATTTTTT-ATTGTTAAAATAATTTTTTAAT-A
1 TTTATTTTATTTTTTAATT-TTAAAATAATCTTAAAATAA
3116134 TTTATTTTA
1 TTTATTTTA
3116143 AAAATAGGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
37 7 0.17
38 30 0.75
40 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (39 bp):
TTTATTTTATTTTTTAATTTTAAAATAATCTTAAAATAA
Found at i:3116148 original size:26 final size:27
Alignment explanation
Indices: 3116088--3116145 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
3116078 TAAAATACTC
* *
3116088 TTAAAATAATTTTTTTATTTTTTATTG
1 TTAAAATAATTTTTTTAATATTTATTG
3116115 TTAAAATAA-TTTTTTAATATTTATT-
1 TTAAAATAATTTTTTTAATATTTATTG
3116140 TTAAAA
1 TTAAAA
3116146 ATAGGCCGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 6 0.21
26 14 0.48
27 9 0.31
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
TTAAAATAATTTTTTTAATATTTATTG
Found at i:3116655 original size:29 final size:30
Alignment explanation
Indices: 3116590--3116659 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
3116580 ACTATCAAAA
* **
3116590 TAGTCACTTTTGTTTGACTTAGGTTACATTT
1 TAGTCACTTATGTTTGAAATA-GTTACATTT
3116621 TAGTCACTTATGTTTGAAATA-TTACATTT
1 TAGTCACTTATGTTTGAAATAGTTACATTT
3116650 TAGTCACTTA
1 TAGTCACTTA
3116660 CGTTATCGCG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 18 0.50
31 18 0.50
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.49
Consensus pattern (30 bp):
TAGTCACTTATGTTTGAAATAGTTACATTT
Found at i:3119418 original size:29 final size:29
Alignment explanation
Indices: 3119364--3119419 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
3119354 AATAAAACAT
*
3119364 AATAATTTAAAAAATATTTGTATTAAAAA
1 AATAATTTAAAAAATATTTATATTAAAAA
*
3119393 AATAATTT-AAAAATATGTTATTTTAAA
1 AATAATTTAAAAAATAT-TTATATTAAA
3119420 TTCCAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (29 bp):
AATAATTTAAAAAATATTTATATTAAAAA
Found at i:3122819 original size:15 final size:15
Alignment explanation
Indices: 3122786--3122818 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
3122776 GATTGACTTG
3122786 TTTTATATTTTAATA
1 TTTTATATTTTAATA
3122801 TTTTATATTTTAAT-
1 TTTTATATTTTAATA
3122815 TTTT
1 TTTT
3122819 TTCTTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTATATTTTAATA
Found at i:3123500 original size:19 final size:17
Alignment explanation
Indices: 3123485--3123518 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
3123475 TCAAGAAATG
3123485 AGAAAAAGAACAAGAAAA
1 AGAAAAA-AACAAGAAAA
3123503 AGAAAAAAA-AAGAAAA
1 AGAAAAAAACAAGAAAA
3123519 TTTCTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (17 bp):
AGAAAAAAACAAGAAAA
Found at i:3123514 original size:10 final size:11
Alignment explanation
Indices: 3123485--3123518 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
3123475 TCAAGAAATG
3123485 AGAAAAAGAACA
1 AGAAAAAGAA-A
3123497 AGAAAAAGAAA
1 AGAAAAAGAAA
3123508 A-AAAAAGAAA
1 AGAAAAAGAAA
3123518 A
1 A
3123519 TTTCTTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.45
11 2 0.09
12 10 0.45
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (11 bp):
AGAAAAAGAAA
Done.