Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 205 of 205
Found at i:60796872 original size:17 final size:19
Alignment explanation
Indices: 60796850--60796887 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
60796840 AAGAATTATT
60796850 TTAAAA-AAT-AAAAAATA
1 TTAAAATAATAAAAAAATA
*
60796867 TTAAAATTATAAAAAAATA
1 TTAAAATAATAAAAAAATA
60796886 TT
1 TT
60796888 TTTAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 2 0.11
19 10 0.56
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TTAAAATAATAAAAAAATA
Found at i:60798132 original size:17 final size:17
Alignment explanation
Indices: 60798110--60798142 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
60798100 TTCCAGATTT
*
60798110 TGATACCTATATCTTTC
1 TGATACCCATATCTTTC
60798127 TGATACCCATATCTTT
1 TGATACCCATATCTTT
60798143 GACTTTCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:60801639 original size:17 final size:17
Alignment explanation
Indices: 60801617--60801649 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
60801607 TCCCAGATTT
*
60801617 TGATACCCATATCTTTC
1 TGATACCAATATCTTTC
60801634 TGATACCAATATCTTT
1 TGATACCAATATCTTT
60801650 GACTTTCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.24, G:0.06, T:0.42
Consensus pattern (17 bp):
TGATACCAATATCTTTC
Found at i:60806371 original size:113 final size:113
Alignment explanation
Indices: 60806173--60806626 Score: 899
Period size: 113 Copynumber: 4.0 Consensus size: 113
60806163 CTTCAATCAT
60806173 GGCACAACATACTGATAGTAATCATATATTGTATTAAGAACTGTAATATATGCTACCTGGACTCT
1 GGCACAACATACTGATAGTAATCATATATTGTATTAAGAACTGTAATATATGCTACCTGGACTCT
60806238 TGTTTTACCGTAAATTACATGTTTCGGCATATATTTGGAATAGGTATG
66 TGTTTTACCGTAAATTACATGTTTCGGCATATATTTGGAATAGGTATG
60806286 GGCACAACATACTGATAGTAATCATATATTGTATTAAGAACTGTAATATATGCTACCTGGACTCT
1 GGCACAACATACTGATAGTAATCATATATTGTATTAAGAACTGTAATATATGCTACCTGGACTCT
60806351 TGTTTTACCGTAAATTACATGTTTCGGCATATATTTGGAATAGGTATG
66 TGTTTTACCGTAAATTACATGTTTCGGCATATATTTGGAATAGGTATG
60806399 GGCACAACATACTGATAGTAATCATATATTGTATTAAGAACTGTAATATATGCTACCTGGACTCT
1 GGCACAACATACTGATAGTAATCATATATTGTATTAAGAACTGTAATATATGCTACCTGGACTCT
60806464 TGTTTTACCGTAAATTACATGTTTCGGCATATATTTGGAATAGGTATG
66 TGTTTTACCGTAAATTACATGTTTCGGCATATATTTGGAATAGGTATG
60806512 GGCACAACATACTGATAGTAATCATATATTGTATTAAGAACTGTAATATATGCTACCTGGACTCT
1 GGCACAACATACTGATAGTAATCATATATTGTATTAAGAACTGTAATATATGCTACCTGGACTCT
*
60806577 TGTTTTACCGTAAATTACATCTTTCGGCATATATTTGGAATAGGTATG
66 TGTTTTACCGTAAATTACATGTTTCGGCATATATTTGGAATAGGTATG
60806625 GG
1 GG
60806627 GATATAGTCT
Statistics
Matches: 340, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 340 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (113 bp):
GGCACAACATACTGATAGTAATCATATATTGTATTAAGAACTGTAATATATGCTACCTGGACTCT
TGTTTTACCGTAAATTACATGTTTCGGCATATATTTGGAATAGGTATG
Found at i:60807242 original size:21 final size:21
Alignment explanation
Indices: 60807216--60807262 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
60807206 TTCTAATTTT
*
60807216 ACCGCTACAGTATCCAATCTC
1 ACCGCTACAGTAACCAATCTC
*
60807237 ACCGCTACAGTAACTAATCTC
1 ACCGCTACAGTAACCAATCTC
60807258 ACCGC
1 ACCGC
60807263 CACCGCTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.38, G:0.11, T:0.21
Consensus pattern (21 bp):
ACCGCTACAGTAACCAATCTC
Found at i:60808141 original size:23 final size:22
Alignment explanation
Indices: 60808111--60808155 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
60808101 TATAATTTTA
60808111 ATAAATTATATGATAAAA-TAAAT
1 ATAAATTATA-GA-AAAATTAAAT
60808134 ATAAATTATAGAAAAATTAAAT
1 ATAAATTATAGAAAAATTAAAT
60808156 CTCTATTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 7 0.33
23 10 0.48
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
ATAAATTATAGAAAAATTAAAT
Found at i:60809106 original size:12 final size:12
Alignment explanation
Indices: 60809086--60809128 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
60809076 GTTAGACTGG
*
60809086 AATAGAAATAGA
1 AATAAAAATAGA
60809098 AATAAAAATAGA
1 AATAAAAATAGA
*
60809110 AATAAAAAATAAA
1 AAT-AAAAATAGA
60809123 AATAAA
1 AATAAA
60809129 TGGGTTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (12 bp):
AATAAAAATAGA
Found at i:60809109 original size:18 final size:19
Alignment explanation
Indices: 60809086--60809126 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
60809076 GTTAGACTGG
*
60809086 AATAGAAAT-AGAAATAAA
1 AATAGAAATAAAAAATAAA
60809104 AATAGAAATAAAAAATAAA
1 AATAGAAATAAAAAATAAA
60809123 AATA
1 AATA
60809127 AATGGGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (19 bp):
AATAGAAATAAAAAATAAA
Found at i:60809123 original size:6 final size:6
Alignment explanation
Indices: 60809086--60809128 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
60809076 GTTAGACTGG
* * *
60809086 AATAGA AATAGA AATAAA AATAGA AATAAAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AAT-AAA AATAAA AATAAA
60809129 TGGGTTTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
6 28 0.85
7 5 0.15
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:60821635 original size:13 final size:13
Alignment explanation
Indices: 60821619--60821643 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60821609 TCCTAAATTT
60821619 TATAAAAATAAAG
1 TATAAAAATAAAG
60821632 TATAAAAATAAA
1 TATAAAAATAAA
60821644 ATAATTGTTT
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:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
TATAAAAATAAAG
Found at i:60825252 original size:54 final size:55
Alignment explanation
Indices: 60825168--60825286 Score: 177
Period size: 54 Copynumber: 2.2 Consensus size: 55
60825158 ATTTTCCTTG
* *
60825168 TTGAAACAAAAACTAGTGGATTTTTTGCACAAATAAATGGAAAACTTGCTCTCAAA
1 TTGAAA-AAAAACAAGTGGAATTTTTGCACAAATAAATGGAAAACTTGCTCTCAAA
* * *
60825224 TTGAAAAAAAA-AAGTGGAATTTTTGCACAAATAATTGTAAAACTTGCTCTCAAG
1 TTGAAAAAAAACAAGTGGAATTTTTGCACAAATAAATGGAAAACTTGCTCTCAAA
60825278 TTGAAAAAA
1 TTGAAAAAA
60825287 GGTGGATTCT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 47 0.81
55 5 0.09
56 6 0.10
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (55 bp):
TTGAAAAAAAACAAGTGGAATTTTTGCACAAATAAATGGAAAACTTGCTCTCAAA
Found at i:60825323 original size:51 final size:50
Alignment explanation
Indices: 60825182--60825327 Score: 159
Period size: 54 Copynumber: 2.8 Consensus size: 50
60825172 AACAAAAACT
60825182 AGTGGATTTTTTGCACAAATAAATGGAAAACTTGCTCTCAAATTGAAAAAAAAA
1 AGTGGA-TTTTTGCACAAATAAAT-GAAAACTTGCTCTCAAATTG--AAAAAAA
* *
60825236 AGTGGAATTTTTGCACAAATAATTGTAAAACTTGCTCTCAAGTTG-AAAAAA
1 AGTGG-ATTTTTGCACAAATAAATG-AAAACTTGCTCTCAAATTGAAAAAAA
* * * *
60825287 GGTGGATTCTTTGCTCAAATAAATGAATATCATGCTCTCAA
1 AGTGGATT-TTTGCACAAATAAATGAA-AACTTGCTCTCAA
60825328 CTTATTTTTA
Statistics
Matches: 81, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
50 5 0.06
51 35 0.43
53 1 0.01
54 39 0.48
55 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (50 bp):
AGTGGATTTTTGCACAAATAAATGAAAACTTGCTCTCAAATTGAAAAAAA
Found at i:60835554 original size:28 final size:28
Alignment explanation
Indices: 60835521--60835581 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
60835511 ACTTAGTTCA
60835521 TCAACAA-CAGCAATTATCTAAGAATGTT
1 TCAACAACCA-CAATTATCTAAGAATGTT
60835549 TCAACAACCACAATTATCTAAGAATGTT
1 TCAACAACCACAATTATCTAAGAATGTT
60835577 TCAAC
1 TCAAC
60835582 TGGACCATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 30 0.94
29 2 0.06
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (28 bp):
TCAACAACCACAATTATCTAAGAATGTT
Found at i:60843622 original size:75 final size:76
Alignment explanation
Indices: 60843498--60843648 Score: 286
Period size: 75 Copynumber: 2.0 Consensus size: 76
60843488 TGAAACTCCT
*
60843498 CTATTTGATATTTGCAGCCACCCTATTTCCCCCTTTTATAGAAATTTATTCTCTTTTCATATCTT
1 CTATTTGATATTTGCAGCCACCCTATTTCCCCATTTTATAGAAATTTATTCTCTTTTCATATCTT
60843563 GAATTCACATA
66 GAATTCACATA
60843574 CTATTTGATATTTGCAGCCA-CCTATTTCCCCATTTTATAGAAATTTATTCTCTTTTCATATCTT
1 CTATTTGATATTTGCAGCCACCCTATTTCCCCATTTTATAGAAATTTATTCTCTTTTCATATCTT
60843638 GAATTCACATA
66 GAATTCACATA
60843649 TGCCAATCTG
Statistics
Matches: 74, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
75 54 0.73
76 20 0.27
ACGTcount: A:0.26, C:0.23, G:0.07, T:0.45
Consensus pattern (76 bp):
CTATTTGATATTTGCAGCCACCCTATTTCCCCATTTTATAGAAATTTATTCTCTTTTCATATCTT
GAATTCACATA
Found at i:60855352 original size:4 final size:4
Alignment explanation
Indices: 60855345--60855386 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
60855335 TCTTGAATGA
60855345 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
60855387 ATACATGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:60862686 original size:15 final size:15
Alignment explanation
Indices: 60862666--60862697 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
60862656 CTCTTCATTA
60862666 AAAATTGTATAGTTT
1 AAAATTGTATAGTTT
60862681 AAAATTGTATAGTTT
1 AAAATTGTATAGTTT
60862696 AA
1 AA
60862698 TTGGGTGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (15 bp):
AAAATTGTATAGTTT
Found at i:60862912 original size:23 final size:23
Alignment explanation
Indices: 60862851--60862913 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
60862841 AATATTCACG
* *
60862851 AACATGTTCATTTAAC-TTAATCA
1 AACATGTTCA-TAAACATTAAACA
**
60862874 AACATGTTCACGAACATTAAACA
1 AACATGTTCATAAACATTAAACA
60862897 AACATGTTCATAAACAT
1 AACATGTTCATAAACAT
60862914 ATAATTGAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 3 0.09
23 31 0.91
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.30
Consensus pattern (23 bp):
AACATGTTCATAAACATTAAACA
Found at i:60863107 original size:15 final size:16
Alignment explanation
Indices: 60863073--60863111 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
60863063 CATTTGGTTC
60863073 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
60863089 GCTGTAATGGAAT-GA
1 GCTGTAATGGAATAGA
60863104 GCTGTAAT
1 GCTGTAAT
60863112 AATAATTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:60863408 original size:55 final size:54
Alignment explanation
Indices: 60863310--60863415 Score: 124
Period size: 55 Copynumber: 1.9 Consensus size: 54
60863300 TAAATAATAA
* * *
60863310 ATAATTTAATCATATTTTAACATAATTATTATTAAATATAATTTAATAAAAAGAT
1 ATAATTTAATAAAATTTTAACATAATCATTATT-AATATAATTTAATAAAAAGAT
* * *
60863365 ATAATTTAATAAAATTCTTAATATAATCATTCTT-ATATGAATTTACTAAAA
1 ATAATTTAATAAAATT-TTAACATAATCATTATTAATAT-AATTTAATAAAA
60863416 TCATAATATA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
54 4 0.09
55 25 0.58
56 14 0.33
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (54 bp):
ATAATTTAATAAAATTTTAACATAATCATTATTAATATAATTTAATAAAAAGAT
Found at i:60863519 original size:25 final size:21
Alignment explanation
Indices: 60863467--60863510 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
60863457 ACACAAACGG
60863467 AAAACATCAACTTAATACAGA
1 AAAACATCAACTTAATACAGA
*
60863488 AAAACATCAACTTAATATAGA
1 AAAACATCAACTTAATACAGA
60863509 AA
1 AA
60863511 CCAAAACATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.59, C:0.16, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAACATCAACTTAATACAGA
Found at i:60864483 original size:16 final size:16
Alignment explanation
Indices: 60864462--60864493 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
60864452 AGCTGCTGAG
60864462 GGAATAAGCAAGGAAT
1 GGAATAAGCAAGGAAT
*
60864478 GGAATAGGCAAGGAAT
1 GGAATAAGCAAGGAAT
60864494 CGGTAAACGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.34, T:0.12
Consensus pattern (16 bp):
GGAATAAGCAAGGAAT
Found at i:60884253 original size:19 final size:17
Alignment explanation
Indices: 60884202--60884249 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
60884192 TTGTCTAATT
60884202 TTAA-ATTTTAAATCTAG
1 TTAACATTTTAAAT-TAG
60884219 TTAACATTTTAAATTAG
1 TTAACATTTTAAATTAG
60884236 TATAACATTTTAAA
1 T-TAACATTTTAAA
60884250 ATTAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.28
18 21 0.72
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (17 bp):
TTAACATTTTAAATTAG
Found at i:60885703 original size:138 final size:138
Alignment explanation
Indices: 60885534--60885807 Score: 422
Period size: 138 Copynumber: 2.0 Consensus size: 138
60885524 TCTTTTCTTC
* * * * *
60885534 GATGTAAACTTATCACTCGCAGTTGCTAAAGTAATGGCTTCATTGATCTTCAGTTTATGATGATT
1 GATGTAAAATTATCACTCGCAGTTGCCAAAGTAAGGGCTTCATTGATATTCAGTTTATAATGATT
* *
60885599 GTTACGTTCACCAACTTCAACCCCTGGGGGTTTATTCATTGAAAGAGACCATTCTAACGAGCTAT
66 GTTACGTTCACCAACTTCAACCCCTGGGGGTTTATTCATTGAAAGAGACAATTCTAACGAGATAT
*
60885664 CGGCATTG
131 CAGCATTG
*
60885672 GATGTAAAATTATCACTCGTAGTTGCCAAAGTAAGGGCTTCATTGATATTCAGTTTATAATGATT
1 GATGTAAAATTATCACTCGCAGTTGCCAAAGTAAGGGCTTCATTGATATTCAGTTTATAATGATT
* * * * *
60885737 GTTACGTTCACCGACTTCAACCCTTTGGGGTTTGTTCATTGAAAGATACAATTCTAACGAGATAT
66 GTTACGTTCACCAACTTCAACCCCTGGGGGTTTATTCATTGAAAGAGACAATTCTAACGAGATAT
60885802 CAGCAT
131 CAGCAT
60885808 CGGTAGCGTC
Statistics
Matches: 122, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
138 122 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (138 bp):
GATGTAAAATTATCACTCGCAGTTGCCAAAGTAAGGGCTTCATTGATATTCAGTTTATAATGATT
GTTACGTTCACCAACTTCAACCCCTGGGGGTTTATTCATTGAAAGAGACAATTCTAACGAGATAT
CAGCATTG
Found at i:60888222 original size:14 final size:14
Alignment explanation
Indices: 60888205--60888234 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
60888195 TTATGGGAGG
*
60888205 AATGTTTGTGTTTA
1 AATGTTTATGTTTA
60888219 AATGTTTATGTTTA
1 AATGTTTATGTTTA
60888233 AA
1 AA
60888235 ACCTTGTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
AATGTTTATGTTTA
Found at i:60893124 original size:27 final size:28
Alignment explanation
Indices: 60893093--60893147 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
60893083 GACAAATCAA
*
60893093 AATATTTTA-ATTTTTTTGTAAA-ATTTT
1 AATATTTTATATTTATTT-TAAAGATTTT
60893120 AATATTTTATATTTATTTTAAAGATTTT
1 AATATTTTATATTTATTTTAAAGATTTT
60893148 TTTTAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (28 bp):
AATATTTTATATTTATTTTAAAGATTTT
Found at i:60894629 original size:32 final size:32
Alignment explanation
Indices: 60894576--60894651 Score: 145
Period size: 32 Copynumber: 2.4 Consensus size: 32
60894566 TAGTAGGAAG
60894576 CAACTATAGATG-TTTTTTTATTTATTTTTCA
1 CAACTATAGATGTTTTTTTTATTTATTTTTCA
60894607 CAACTATAGATGTTTTTTTTATTTATTTTTCA
1 CAACTATAGATGTTTTTTTTATTTATTTTTCA
60894639 CAACTATAGATGT
1 CAACTATAGATGT
60894652 AGTTGAAAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 12 0.27
32 32 0.73
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.54
Consensus pattern (32 bp):
CAACTATAGATGTTTTTTTTATTTATTTTTCA
Found at i:60915660 original size:30 final size:29
Alignment explanation
Indices: 60915583--60915661 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 29
60915573 AATTATAAAA
60915583 AATAAAAATCAATAAA-AAATATTAAATTTT
1 AATAAAAAT--ATAAAGAAATATTAAATTTT
*
60915613 AATAGAAATGATAAAGAAATATTAAAATTTT
1 AATAAAAAT-ATAAAGAAATATT-AAATTTT
*
60915644 ATTAAAAAT-TAGAAGAAA
1 AATAAAAATATA-AAGAAA
60915662 AAAATTATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
29 7 0.17
30 21 0.50
31 14 0.33
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.30
Consensus pattern (29 bp):
AATAAAAATATAAAGAAATATTAAATTTT
Found at i:60915903 original size:9 final size:9
Alignment explanation
Indices: 60915889--60916052 Score: 63
Period size: 9 Copynumber: 18.0 Consensus size: 9
60915879 TTTTAGTACG
60915889 ATAATTTTT
1 ATAATTTTT
60915898 ATAATTTTTTT
1 ATAA--TTTTT
* *
60915909 ACAAATTTT
1 ATAATTTTT
*
60915918 ATATTTCTTT
1 ATAATT-TTT
* *
60915928 ACATTTTTT
1 ATAATTTTT
60915937 ATAATTTTCTT
1 ATAA-TTT-TT
* *
60915948 ATGA-CTTT
1 ATAATTTTT
*
60915956 ATAAAATTTT
1 AT-AATTTTT
60915966 ATAA-TTTT
1 ATAATTTTT
*
60915974 -T--TTTCT
1 ATAATTTTT
*
60915980 AT-ATTTCT
1 ATAATTTTT
60915988 AT-ATATTTT
1 ATAAT-TTTT
60915997 ATAATTTTT
1 ATAATTTTT
*
60916006 ATGATTTTT
1 ATAATTTTT
*
60916015 ATAAAATTTT
1 AT-AATTTTT
*
60916025 ACAATTTTTT
1 ATAA-TTTTT
* *
60916035 GTGATTTTT
1 ATAATTTTT
60916044 ATAATTTTT
1 ATAATTTTT
60916053 TCTTATAATT
Statistics
Matches: 117, Mismatches: 24, Indels: 28
0.69 0.14 0.17
Matches are distributed among these distances:
6 3 0.03
7 2 0.02
8 17 0.15
9 53 0.45
10 29 0.25
11 13 0.11
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (9 bp):
ATAATTTTT
Found at i:60915936 original size:19 final size:19
Alignment explanation
Indices: 60915891--60915939 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
60915881 TTAGTACGAT
*
60915891 AATTTTTATAATTTTTTTAC
1 AATTTTTAT-ATTTCTTTAC
*
60915911 AAATTTTATATTTCTTTAC
1 AATTTTTATATTTCTTTAC
*
60915930 ATTTTTTATA
1 AATTTTTATA
60915940 ATTTTCTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (19 bp):
AATTTTTATATTTCTTTAC
Found at i:60915967 original size:29 final size:27
Alignment explanation
Indices: 60915933--60916051 Score: 89
Period size: 29 Copynumber: 4.1 Consensus size: 27
60915923 TCTTTACATT
60915933 TTTTATAATTTTCTTATGACTTTATAAAA
1 TTTTATAATTTT-TTATGA-TTTATAAAA
* *
60915962 TTTTATAATTTTTTTTCTAT-ATTTCTATATA
1 TTTTATAA---TTTTT-TATGATTTATA-AAA
60915993 TTTTATAA-TTTTTATGATTTTTATAAAA
1 TTTTATAATTTTTTATGA--TTTATAAAA
* * * *
60916021 TTTTACAATTTTTTGTGATTTTTATAA
1 TTTTATAATTTTTTATGATTTATAAAA
60916048 TTTT
1 TTTT
60916052 TTCTTATAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
26 3 0.04
27 16 0.22
28 9 0.12
29 21 0.29
30 5 0.07
31 12 0.16
32 7 0.10
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.63
Consensus pattern (27 bp):
TTTTATAATTTTTTATGATTTATAAAA
Found at i:60916066 original size:22 final size:22
Alignment explanation
Indices: 60916038--60916097 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
60916028 ATTTTTTGTG
* *
60916038 ATTTTTATAAT-TTTTTCTTATA
1 ATTTTTA-AATATTTTTATTAAA
60916060 ATTTTTAAATATTTTTATTAAA
1 ATTTTTAAATATTTTTATTAAA
*
60916082 A--TTTAATTATTTTTAT
1 ATTTTTAAATATTTTTAT
60916098 AACTTTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 14 0.41
21 3 0.09
22 17 0.50
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTTTTAAATATTTTTATTAAA
Found at i:60921137 original size:17 final size:19
Alignment explanation
Indices: 60921101--60921137 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
60921091 TTATAACAAA
*
60921101 AAAAAATTATTTAAATCTT
1 AAAAAATTATCTAAATCTT
60921120 AAAAAATT-TCTAAA-CTT
1 AAAAAATTATCTAAATCTT
60921137 A
1 A
60921138 TGGAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.24
18 5 0.29
19 8 0.47
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAAATTATCTAAATCTT
Found at i:60923643 original size:22 final size:22
Alignment explanation
Indices: 60923616--60923666 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
60923606 TTTGTTTTTC
*
60923616 TATTATTTTGCTACCATTTCAT
1 TATTATTTTGCTACCATTTCAA
* * *
60923638 TATTATGTTGCTACTATTTTAA
1 TATTATTTTGCTACCATTTCAA
60923660 TATTATT
1 TATTATT
60923667 GTTCTTGTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.25, C:0.12, G:0.06, T:0.57
Consensus pattern (22 bp):
TATTATTTTGCTACCATTTCAA
Found at i:60925537 original size:19 final size:19
Alignment explanation
Indices: 60925498--60925537 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
60925488 GTTCTTTCTC
*
60925498 TTCTACTTCTCCTTCTATT
1 TTCTACTTCTCCATCTATT
* *
60925517 TTCTTCTTCTCCATCTCTT
1 TTCTACTTCTCCATCTATT
60925536 TT
1 TT
60925538 AACATAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.07, C:0.33, G:0.00, T:0.60
Consensus pattern (19 bp):
TTCTACTTCTCCATCTATT
Found at i:60926936 original size:4 final size:4
Alignment explanation
Indices: 60926927--60926953 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
60926917 ATTTTAAAAA
60926927 AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AAT
60926954 GTTTAATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:60938930 original size:11 final size:10
Alignment explanation
Indices: 60938866--60938935 Score: 54
Period size: 10 Copynumber: 7.1 Consensus size: 10
60938856 GAAACATTAT
60938866 AAAAAATA-A
1 AAAAAATATA
*
60938875 ATAAATATATA
1 A-AAAAATATA
*
60938886 AAAAAATTTA
1 AAAAAATATA
* *
60938896 GAAAAGTATA
1 AAAAAATATA
* *
60938906 TATAAAT-TA
1 AAAAAATATA
*
60938915 AAAAATTATA
1 AAAAAATATA
60938925 AAAAAATATA
1 AAAAAATATA
60938935 A
1 A
60938936 TTCATACACA
Statistics
Matches: 45, Mismatches: 13, Indels: 5
0.71 0.21 0.08
Matches are distributed among these distances:
9 7 0.16
10 36 0.80
11 2 0.04
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (10 bp):
AAAAAATATA
Found at i:60938931 original size:19 final size:19
Alignment explanation
Indices: 60938861--60938931 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
60938851 AGGTTGAAAC
60938861 ATTAT-AAAAAA-TAAATAA
1 ATTATAAAAAAATTAAA-AA
*
60938879 ATATATAAAAAAATTTAGAAA
1 AT-TATAAAAAAA-TTAAAAA
* * *
60938900 AGTATATATAAATTAAAAA
1 ATTATAAAAAAATTAAAAA
60938919 ATTATAAAAAAAT
1 ATTATAAAAAAAT
60938932 ATAATTCATA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
18 2 0.05
19 19 0.46
20 14 0.34
21 3 0.07
22 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (19 bp):
ATTATAAAAAAATTAAAAA
Found at i:60948411 original size:16 final size:16
Alignment explanation
Indices: 60948386--60948416 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
60948376 CTTAAATGGA
60948386 TTATAAATTTTAAAAG
1 TTATAAATTTTAAAAG
*
60948402 TTATATATTTTAAAA
1 TTATAAATTTTAAAA
60948417 AATAAAATCT
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TTATAAATTTTAAAAG
Found at i:60948877 original size:21 final size:21
Alignment explanation
Indices: 60948844--60948886 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
60948834 TTTATTTTTT
60948844 AAAAATATATTTTT-TTTAAA
1 AAAAATATATTTTTGTTTAAA
*
60948864 AAAAATTATGTTTTTGTTTAAA
1 AAAAA-TATATTTTTGTTTAAA
60948886 A
1 A
60948887 TAAGAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 8 0.40
22 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
AAAAATATATTTTTGTTTAAA
Found at i:60954228 original size:13 final size:13
Alignment explanation
Indices: 60954210--60954234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60954200 TATTTTAATA
60954210 TTATTTTGTGTGT
1 TTATTTTGTGTGT
60954223 TTATTTTGTGTG
1 TTATTTTGTGTG
60954235 CATTCGATGG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:60955974 original size:41 final size:41
Alignment explanation
Indices: 60955767--60955963 Score: 317
Period size: 41 Copynumber: 4.8 Consensus size: 41
60955757 TTTATCGTTA
* * * *
60955767 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
60955808 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
60955849 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
60955890 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
60955931 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
60955964 AAGAGCCGGT
Statistics
Matches: 148, Mismatches: 4, Indels: 8
0.93 0.03 0.05
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 143 0.97
42 2 0.01
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:60956236 original size:33 final size:32
Alignment explanation
Indices: 60956180--60956243 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
60956170 AGATATGTAT
60956180 ATATATATATATGTTGCATTCGGCATAGGTGG
1 ATATATATATATGTTGCATTCGGCATAGGTGG
* *
60956212 ATATATTTATGTGTATGCATTCGGCATAGGTG
1 ATATATATATATGT-TGCATTCGGCATAGGTG
60956244 AAAATAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (32 bp):
ATATATATATATGTTGCATTCGGCATAGGTGG
Found at i:60956260 original size:33 final size:33
Alignment explanation
Indices: 60956187--60956260 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
60956177 TATATATATA
* * **
60956187 TATATGT-TGCATTCGGCATAGGTGGATATATT
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
60956219 TATGTGTATGCATTCGGCATAGGTGAAAATAAG
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
60956252 TGTATGTAT
1 TATATGTAT
60956261 CTATGCATTC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (33 bp):
TATATGTATGCATTCGGCATAGGTGAAAATAAG
Found at i:60959288 original size:3 final size:3
Alignment explanation
Indices: 60959280--60959307 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
60959270 AGTCCAAATC
60959280 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
60959308 GTTGTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:60960455 original size:48 final size:48
Alignment explanation
Indices: 60960384--60960479 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
60960374 ATAGGAAAAA
60960384 TTTCAAATCATAATCAAGTAACATTGACAAGTCTTTGATTTGTAATCT
1 TTTCAAATCATAATCAAGTAACATTGACAAGTCTTTGATTTGTAATCT
60960432 TTTCAAATCATAATCAAGTAACATTGACAAGTCTTTGATTTGTAATCT
1 TTTCAAATCATAATCAAGTAACATTGACAAGTCTTTGATTTGTAATCT
60960480 GTTTTTTCCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (48 bp):
TTTCAAATCATAATCAAGTAACATTGACAAGTCTTTGATTTGTAATCT
Found at i:60961241 original size:25 final size:25
Alignment explanation
Indices: 60961185--60961245 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
60961175 ATGGATTAGC
*
60961185 TTGTTATTATGTTTTTTTTGTATAAT
1 TTGTTATTAT-TTTTTGTTGTATAAT
*
60961211 TT-TTATTATTTTTTGTTGT-TAGT
1 TTGTTATTATTTTTTGTTGTATAAT
60961234 TTAGTTATTATT
1 TT-GTTATTATT
60961246 GTTAGTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 5 0.16
24 9 0.29
25 15 0.48
26 2 0.06
ACGTcount: A:0.18, C:0.00, G:0.11, T:0.70
Consensus pattern (25 bp):
TTGTTATTATTTTTTGTTGTATAAT
Found at i:60961479 original size:37 final size:38
Alignment explanation
Indices: 60961437--60961523 Score: 115
Period size: 40 Copynumber: 2.3 Consensus size: 38
60961427 TTTTACATTA
* **
60961437 TATTATTGTTAG-T-TATTATTTTTAGTAAAACCCTAAT
1 TATTATTGTTAGTTATATTATTTTGAGTAAAAAACT-AT
60961474 TATTATTGTTAGTTAGTATTATTTTGAGTAAAAAACTAT
1 TATTATTGTTAGTTA-TATTATTTTGAGTAAAAAACTAT
60961513 TATTATTGTTA
1 TATTATTGTTA
60961524 TTGTGTTAGT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
37 12 0.27
38 1 0.02
39 13 0.30
40 18 0.41
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.52
Consensus pattern (38 bp):
TATTATTGTTAGTTATATTATTTTGAGTAAAAAACTAT
Found at i:60961482 original size:60 final size:62
Alignment explanation
Indices: 60961370--60961487 Score: 161
Period size: 60 Copynumber: 1.9 Consensus size: 62
60961360 AAAAACTAAT
60961370 ATTATTATTATGGTTAGTTATTAGGATTATAGTAAAAACCCTAATATGATTGTTAGTTTTTAC
1 ATTATTATTATGGTTAGTTATTA-GATTATAGTAAAAACCCTAATATGATTGTTAGTTTTTAC
* * * *
60961433 ATTA-TATTATTGTTAGTTATTA-TTTTTAGT-AAAACCCTAATTATTATTGTTAGTT
1 ATTATTATTATGGTTAGTTATTAGATTATAGTAAAAACCCTAA-TATGATTGTTAGTT
60961488 AGTATTATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
59 10 0.20
60 19 0.38
62 17 0.34
63 4 0.08
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.50
Consensus pattern (62 bp):
ATTATTATTATGGTTAGTTATTAGATTATAGTAAAAACCCTAATATGATTGTTAGTTTTTAC
Found at i:60966579 original size:156 final size:157
Alignment explanation
Indices: 60966379--60967044 Score: 901
Period size: 156 Copynumber: 4.3 Consensus size: 157
60966369 ACTTTAAAAA
* * * * *
60966379 AAATTTAGTAAAA-AACACTTATTTCGGACTTTTGTTCGTATTTTTTTCCCGGATTTTATTACTT
1 AAATTTAGAAAAATAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGGATTTTATTACTT
* *
60966443 T-AA-AAAAATATACTATTTTC-TAATTTTATTACTTTACATTATTTTAGTACATTATGTTTGAA
66 TCAATAAAAATATATTATTTTCAT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAA
60966505 AT-TCATTAATTCAGTGTGTTTTTTTAAAT
130 ATGT-ATTAATT-AGTGTGTTTTTTTAAAT
* * *
60966534 AAATTTAGAAAAATAACCTTTATTTCGGCTCTTTGCTCGTATTTTTTTCCCGGATTTTATTATTT
1 AAATTTAGAAAAATAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGGATTTTATTACTT
60966599 TCAAT-AAAATATATTATTTTCATATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
66 TCAATAAAAATATATTATTTTCATATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
*
60966663 TTTATTAATTTAGTGTG-TTTTTTAAAT
131 TGTATTAA-TTAGTGTGTTTTTTTAAAT
*** * *
60966690 AAATTTTTTTAAAA-AACCATTATTTCGGCCCTTTACTCGTATTTTTTTCCCGGATTTTATTACT
1 AAA-TTTAGAAAAATAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGGATTTTATTACT
* *
60966754 TTTAATAAAAATATATTATTTTCATATTTTATTATTTTATATTATTTTAGTACATTATGTTTGAA
65 TTCAATAAAAATATATTATTTTCATATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAA
*
60966819 ATGTATTAATTAAT-T-TTGTTTTTAAAT
130 ATGTATTAATTAGTGTGTT-TTTTTAAAT
* * **
60966846 AAATTTAGAAAAATAACCCTTATTTTGGCCCTTTTCTCGT-GCTTTTTCCCGGATTTTATTACTT
1 AAATTTAGAAAAATAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGGATTTTATTACTT
**
60966910 TCAATAAAAATATATTATTTTTGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
66 TCAATAAAAATATATTATTTTCATATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
* *
60966975 TGTATTAATTAATTCTGTTTTTTTAAA-
131 TGTATTAATT-AGTGTGTTTTTTTAAAT
* * *
60967002 ATATTTAG-TAAAT-ACCCTTATTTCGGCCCTTTGTTCGTATTTT
1 AAATTTAGAAAAATAACCCTTATTTCGGCCCTTTGCTCGTATTTT
60967045 ATTACTTTCG
Statistics
Matches: 455, Mismatches: 41, Indels: 30
0.87 0.08 0.06
Matches are distributed among these distances:
154 22 0.05
155 120 0.26
156 157 0.35
157 150 0.33
158 6 0.01
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (157 bp):
AAATTTAGAAAAATAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGGATTTTATTACTT
TCAATAAAAATATATTATTTTCATATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
TGTATTAATTAGTGTGTTTTTTTAAAT
Found at i:60966788 original size:16 final size:15
Alignment explanation
Indices: 60966767--60966796 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
60966757 AATAAAAATA
60966767 TATTATTTTCATATTT
1 TATTATTTT-ATATTT
60966783 TATTATTTTATATT
1 TATTATTTTATATT
60966797 ATTTTAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTTATATTT
Found at i:60967053 original size:142 final size:148
Alignment explanation
Indices: 60966427--60967032 Score: 638
Period size: 157 Copynumber: 3.9 Consensus size: 148
60966417 TATTTTTTTC
* *
60966427 CCGGATTTTATTACTTT-AA-AAAAATATACTATTTTC-TAATTTTATTACTTTACATTATTTTA
1 CCGGATTTTATTACTTTCAATAAAAATATATTATTTTCAT-ATTTTATTATTTTACATTATTTTA
*
60966489 GTACATTATGTTTGAAAT-TCATTAATTCAGTGTGTT-TTTTTAAATAAATTTAGAAAAATAACC
65 GTACATTATGTTTGAAATGT-ATTAATT-AAT-T-TTGTTTTTAAATAAATTTAGAAAAATAACC
* * *
60966552 TTTATTTCGGCTCTTTGCTCGTATTTTTTT
126 CTTATTTCGGC-CCTT-CTC-----TGTTT
*
60966582 CCCGGATTTTATTATTTTCAAT-AAAATATATTATTTTCATATTTTATTATTTTACATTATTTTA
1 -CCGGATTTTATTACTTTCAATAAAAATATATTATTTTCATATTTTATTATTTTACATTATTTTA
* * * * *** *
60966646 GTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATAAATTTTTTTAAAA-AACCAT
65 GTACATTATGTTTGAAATGTATTAATTAATTTTG-TTTTTAAATAAA-TTTAGAAAAATAACCCT
*
60966710 TATTTCGGCCCTTTACTCGTATTTTTTT
128 TATTTCGGCCC-TT-CTC-----TGTTT
* *
60966738 CCCGGATTTTATTACTTTTAATAAAAATATATTATTTTCATATTTTATTATTTTATATTATTTTA
1 -CCGGATTTTATTACTTTCAATAAAAATATATTATTTTCATATTTTATTATTTTACATTATTTTA
60966803 GTACATTATGTTTGAAATGTATTAATTAATTTTGTTTTTAAATAAATTTAGAAAAATAACCCTTA
65 GTACATTATGTTTGAAATGTATTAATTAATTTTGTTTTTAAATAAATTTAGAAAAATAACCCTTA
*
60966868 TTTTGGCCCTTTTCTCGTGCTTTTT
130 TTTCGGCCC--TTCTC-TG---TTT
**
60966893 CCCGGATTTTATTACTTTCAATAAAAATATATTATTTTTGTATTTTATTATTTTACATTATTTTA
1 -CCGGATTTTATTACTTTCAATAAAAATATATTATTTTCATATTTTATTATTTTACATTATTTTA
* * *
60966958 GTACATTATGTTTGAAATGTATTAATTAATTCTGTTTTTTTAAA-ATATTTAG-TAAAT-ACCCT
65 GTACATTATGTTTGAAATGTATTAATTAATT-T-TGTTTTTAAATAAATTTAGAAAAATAACCCT
60967020 TATTTCGGCCCTT
128 TATTTCGGCCCTT
60967033 TGTTCGTATT
Statistics
Matches: 399, Mismatches: 35, Indels: 36
0.85 0.07 0.08
Matches are distributed among these distances:
152 3 0.01
154 16 0.04
155 108 0.27
156 115 0.29
157 155 0.39
158 2 0.01
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (148 bp):
CCGGATTTTATTACTTTCAATAAAAATATATTATTTTCATATTTTATTATTTTACATTATTTTAG
TACATTATGTTTGAAATGTATTAATTAATTTTGTTTTTAAATAAATTTAGAAAAATAACCCTTAT
TTCGGCCCTTCTCTGTTT
Found at i:60967411 original size:33 final size:30
Alignment explanation
Indices: 60967374--60967434 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 30
60967364 TTTCTTTCTT
60967374 TTTCCTTCCTTTGGTCTTCTTCTTCTCCTTTCC
1 TTTCCTTCCTTT-GTC-T-TTCTTCTCCTTTCC
* *
60967407 TTTCCTTTCTTTTTCTTTCTTCTCCTTT
1 TTTCCTTCCTTTGTCTTTCTTCTCCTTT
60967435 ACTAACACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 1 0.04
32 2 0.08
33 11 0.42
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.64
Consensus pattern (30 bp):
TTTCCTTCCTTTGTCTTTCTTCTCCTTTCC
Found at i:60967434 original size:10 final size:10
Alignment explanation
Indices: 60967393--60967434 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
60967383 TTTGGTCTTC
60967393 TTCTTCTCCT
1 TTCTTCTCCT
60967403 TTCCTT-TCCT
1 TT-CTTCTCCT
* *
60967413 TTCTTTTTCT
1 TTCTTCTCCT
60967423 TTCTTCTCCT
1 TTCTTCTCCT
60967433 TT
1 TT
60967435 ACTAACACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (10 bp):
TTCTTCTCCT
Found at i:60987295 original size:18 final size:18
Alignment explanation
Indices: 60987274--60987310 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
60987264 TAAGTTTTCG
60987274 AATTCGAA-AAACTCGAAT
1 AATTCGAATAAA-TCGAAT
60987292 AATTCGAATAAATCGAAT
1 AATTCGAATAAATCGAAT
60987310 A
1 A
60987311 TCAAACTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.24
Consensus pattern (18 bp):
AATTCGAATAAATCGAAT
Found at i:60989071 original size:13 final size:13
Alignment explanation
Indices: 60989048--60989139 Score: 132
Period size: 13 Copynumber: 7.0 Consensus size: 13
60989038 TGAGTTCGGT
60989048 TATATTGTTTTAA
1 TATATTGTTTTAA
60989061 TATACTT-TTTTAA
1 TATA-TTGTTTTAA
60989074 TATATTGTTTTAA
1 TATATTGTTTTAA
60989087 TATATTGTTTTAA
1 TATATTGTTTTAA
* *
60989100 TATACTGTTATAA
1 TATATTGTTTTAA
60989113 TTATATTGTTTTAA
1 -TATATTGTTTTAA
*
60989127 TATAATGTTTTAA
1 TATATTGTTTTAA
60989140 CTTTTAAATT
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
12 2 0.03
13 56 0.79
14 13 0.18
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.59
Consensus pattern (13 bp):
TATATTGTTTTAA
Found at i:60989117 original size:27 final size:27
Alignment explanation
Indices: 60989068--60989171 Score: 104
Period size: 27 Copynumber: 3.9 Consensus size: 27
60989058 TAATATACTT
* *
60989068 TTTTAATATATTGTTTTAA-TATATTG
1 TTTTAATATACTGTTATAATTATATTG
60989094 TTTTAATATACTGTTATAATTATATTG
1 TTTTAATATACTGTTATAATTATATTG
* * * **
60989121 TTTTAATATAATGTTTTAACTTTTA-AA
1 TTTTAATATACTGTTATAA-TTATATTG
* *
60989148 TTTTAGTATACTGTTATAAATATA
1 TTTTAATATACTGTTATAATTATA
60989172 CATTTAATTT
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
26 20 0.31
27 40 0.62
28 4 0.06
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.56
Consensus pattern (27 bp):
TTTTAATATACTGTTATAATTATATTG
Found at i:60989129 original size:40 final size:39
Alignment explanation
Indices: 60989048--60989139 Score: 148
Period size: 40 Copynumber: 2.3 Consensus size: 39
60989038 TGAGTTCGGT
* *
60989048 TATATTGTTTTAATATACTTTTTTAATATATTGTTTTAA
1 TATATTGTTTTAATATACTGTTATAATATATTGTTTTAA
60989087 TATATTGTTTTAATATACTGTTATAATTATATTGTTTTAA
1 TATATTGTTTTAATATACTGTTATAA-TATATTGTTTTAA
*
60989127 TATAATGTTTTAA
1 TATATTGTTTTAA
60989140 CTTTTAAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 24 0.49
40 25 0.51
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.59
Consensus pattern (39 bp):
TATATTGTTTTAATATACTGTTATAATATATTGTTTTAA
Found at i:60989195 original size:15 final size:15
Alignment explanation
Indices: 60989175--60989208 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
60989165 AAATATACAT
*
60989175 TTAATTTGTAACACA
1 TTAATTTCTAACACA
60989190 TTAATTTCTAACACA
1 TTAATTTCTAACACA
60989205 TTAA
1 TTAA
60989209 ATTTTAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (15 bp):
TTAATTTCTAACACA
Found at i:60989351 original size:13 final size:13
Alignment explanation
Indices: 60989335--60989431 Score: 85
Period size: 13 Copynumber: 7.6 Consensus size: 13
60989325 TACTGTTTTA
60989335 ATAATATATTGTT
1 ATAATATATTGTT
60989348 ATAA-A-A-T-TT
1 ATAATATATTGTT
*
60989357 ATAATATAATGTT
1 ATAATATATTGTT
* * *
60989370 TTAATATACTATT
1 ATAATATATTGTT
60989383 ATAAATATATTGTT
1 AT-AATATATTGTT
* *
60989397 TTAATATACTGTT
1 ATAATATATTGTT
60989410 ATAATTATATTGTT
1 ATAA-TATATTGTT
*
60989424 TTAATATA
1 ATAATATA
60989432 ATTTTTTAAC
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
9 6 0.09
10 2 0.03
11 2 0.03
12 2 0.03
13 34 0.51
14 21 0.31
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (13 bp):
ATAATATATTGTT
Found at i:60989377 original size:27 final size:27
Alignment explanation
Indices: 60989347--60989432 Score: 88
Period size: 27 Copynumber: 3.2 Consensus size: 27
60989337 AATATATTGT
*
60989347 TATAAAATTTATAATATAATGTTTTAA
1 TATAAAATTTATAATATATTGTTTTAA
**
60989374 TATACTA-TTATAAATATATTGTTTTAA
1 TATAAAATTTAT-AATATATTGTTTTAA
*
60989401 TAT--ACTGTTATAATTATATTGTTTTAA
1 TATAAAAT-TTATAA-TATATTGTTTTAA
60989428 TATAA
1 TATAA
60989433 TTTTTTAACT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
26 6 0.12
27 42 0.88
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (27 bp):
TATAAAATTTATAATATATTGTTTTAA
Found at i:60989438 original size:13 final size:13
Alignment explanation
Indices: 60989358--60989440 Score: 53
Period size: 13 Copynumber: 6.2 Consensus size: 13
60989348 ATAAAATTTA
*
60989358 TAATATAATGTTT
1 TAATATAATTTTT
* * *
60989371 TAATATACTATTA
1 TAATATAATTTTT
60989384 TAA-ATATATTGTTT
1 TAATATA-ATT-TTT
* * *
60989398 TAATATACTGTTA
1 TAATATAATTTTT
60989411 TAAT-TATATTGTTT
1 TAATATA-ATT-TTT
60989425 TAATATAATTTTT
1 TAATATAATTTTT
60989438 TAA
1 TAA
60989441 CTTTTAAATT
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
12 5 0.10
13 27 0.52
14 15 0.29
15 5 0.10
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (13 bp):
TAATATAATTTTT
Found at i:60989640 original size:25 final size:25
Alignment explanation
Indices: 60989611--60989658 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
60989601 TTAAGATTTG
*
60989611 ATTGTTTGTAATTAAATTTAAATTA
1 ATTGTTTGTAATTAAATTCAAATTA
60989636 ATTGTTTGTAATTAAATTCAAAT
1 ATTGTTTGTAATTAAATTCAAAT
60989659 AAGTAATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (25 bp):
ATTGTTTGTAATTAAATTCAAATTA
Found at i:60989750 original size:16 final size:16
Alignment explanation
Indices: 60989729--60989762 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
60989719 ATATAAATTC
60989729 AATAACAATTACTTTT
1 AATAACAATTACTTTT
*
60989745 AATAACAATTAGTTTT
1 AATAACAATTACTTTT
60989761 AA
1 AA
60989763 CTTTTAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (16 bp):
AATAACAATTACTTTT
Found at i:60997555 original size:165 final size:164
Alignment explanation
Indices: 60997273--60997655 Score: 644
Period size: 165 Copynumber: 2.3 Consensus size: 164
60997263 AGTATAGCGG
*
60997273 TGGATCACCGGTGTTCTCCCTCTTCTCTTCGGTAAACAAAAATGTAAAATAGAAACAACAAAACT
1 TGGATCATC-GTGTTCTCCCTCTTCTCTTCGGTAAACAAAAATGTAAAATAGAAACAACAAAACT
60997338 CAACGCCGTCTGTGGGAATCGAACCCACGACCACGTGGTTAAAAGCCACGCGCTCTACCGGCTGA
65 CAACGCCGTCTGTGGGAATCGAACCCACGACCACGTGGTTAAAAGCCACGCGCTCTACCGGCTGA
* *
60997403 GCTAAGACGGCTATTGATAGACAGTGGCATAGTGC
130 GCTAAGACGGCTACTGATAGACAGTGACATAGTGC
*
60997438 T-GACTCATCAGTGTTCTCCCTCTTCTCTTCGGTAAACAAAAATGTAAAATAGTAACAACAAAAC
1 TGGA-TCATC-GTGTTCTCCCTCTTCTCTTCGGTAAACAAAAATGTAAAATAGAAACAACAAAAC
60997502 TCAACGCCGTCTGTGGGAATCGAACCCACGACCACGTGGTTAAAAGCCACGCGCTCTACCGGCTG
64 TCAACGCCGTCTGTGGGAATCGAACCCACGACCACGTGGTTAAAAGCCACGCGCTCTACCGGCTG
* *
60997567 AGCTAAGACGGCTACTGATGGACAGTGACATAGTGG
129 AGCTAAGACGGCTACTGATAGACAGTGACATAGTGC
*
60997603 TGGATCATCG-GATTCTCCATCTTCTCTTCGGTAAACAAAAATGTAAAAGTAGA
1 TGGATCATCGTG-TTCTCCCTCTTCTCTTCGGTAAACAAAAATGTAAAA-TAGA
60997656 GGTTATTAGG
Statistics
Matches: 205, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
163 1 0.00
164 38 0.19
165 164 0.80
166 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (164 bp):
TGGATCATCGTGTTCTCCCTCTTCTCTTCGGTAAACAAAAATGTAAAATAGAAACAACAAAACTC
AACGCCGTCTGTGGGAATCGAACCCACGACCACGTGGTTAAAAGCCACGCGCTCTACCGGCTGAG
CTAAGACGGCTACTGATAGACAGTGACATAGTGC
Found at i:60998792 original size:165 final size:163
Alignment explanation
Indices: 60998510--60998984 Score: 765
Period size: 165 Copynumber: 2.9 Consensus size: 163
60998500 AGTATAGCGG
*
60998510 TGGATCACCGGTGTTCTCCCTCTTCTCTTCGGTAAACAAAAATGTAAAATAGAAACAACAAAACT
1 TGGATCATC-GTGTTCTCCCTCTTCTCTTCGGTAAACAAAAATGTAAAATAG-AACAACAAAACT
60998575 CAACGCCGTCTGTGGGAATCGAACCCACGACCACGTGGTTAAAAGCCACGCGCTCTACCGGCTGA
64 CAACGCCGTCTGTGGGAATCGAACCCACGACCACGTGGTTAAAAGCCACGCGCTCTACCGGCTGA
* *
60998640 GCTAAGACGGCTATTGATAGACAGTGGCATAGTGC
129 GCTAAGACGGCTACTGATAGACAGTGACATAGTGC
60998675 T-GACTCATCAGTGTTCTCCCTCTTCTCTTCGGTAAACAAAAATGTAAAATAGTAACAACAAAAC
1 TGGA-TCATC-GTGTTCTCCCTCTTCTCTTCGGTAAACAAAAATGTAAAATAG-AACAACAAAAC
60998739 TCAACGCCGTCTGTGGGAATCGAACCCACGACCACGTGGTTAAAAGCCACGCGCTCTACCGGCTG
63 TCAACGCCGTCTGTGGGAATCGAACCCACGACCACGTGGTTAAAAGCCACGCGCTCTACCGGCTG
* *
60998804 AGCTAAGACGGCTACTGATGGACAGTGACATAGTGG
128 AGCTAAGACGGCTACTGATAGACAGTGACATAGTGC
* *** *
60998840 TGGATCATCG-GATTCTCCATCTTCTCTTCGGTAAACAAAAATGTAAAAGTAGAGGTTACAAAAA
1 TGGATCATCGTG-TTCTCCCTCTTCTCTTCGGTAAACAAAAATGTAAAA-TAGA-ACAACAAAAC
*
60998904 TCGACGCCGTCTGTGGGAATCGAACCCACGACCACGTGGTTAAAAGCCACGCGCTCTACCGGCTG
63 TCAACGCCGTCTGTGGGAATCGAACCCACGACCACGTGGTTAAAAGCCACGCGCTCTACCGGCTG
60998969 AGCTAAGACGGCTACT
128 AGCTAAGACGGCTACT
60998985 AATGACAAGC
Statistics
Matches: 292, Mismatches: 13, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
163 1 0.00
164 39 0.13
165 250 0.86
166 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (163 bp):
TGGATCATCGTGTTCTCCCTCTTCTCTTCGGTAAACAAAAATGTAAAATAGAACAACAAAACTCA
ACGCCGTCTGTGGGAATCGAACCCACGACCACGTGGTTAAAAGCCACGCGCTCTACCGGCTGAGC
TAAGACGGCTACTGATAGACAGTGACATAGTGC
Found at i:61005963 original size:20 final size:20
Alignment explanation
Indices: 61005934--61005981 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
61005924 ATTGTTAAAA
*
61005934 AAAATATAAGATAATCT-TTT
1 AAAATTTAAGATAA-CTATTT
* *
61005954 AAAATTTAAGTTTACTATTT
1 AAAATTTAAGATAACTATTT
61005974 AAAATTTA
1 AAAATTTA
61005982 TGATCTAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (20 bp):
AAAATTTAAGATAACTATTT
Found at i:61006008 original size:14 final size:14
Alignment explanation
Indices: 61005964--61006009 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
61005954 AAAATTTAAG
*
61005964 TTTACTATTTAAAA
1 TTTATTATTTAAAA
* * *
61005978 TTTATGATCTAAGA
1 TTTATTATTTAAAA
61005992 TTTATTATTTAAAA
1 TTTATTATTTAAAA
61006006 TTTA
1 TTTA
61006010 AAATTTTATT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (14 bp):
TTTATTATTTAAAA
Found at i:61008902 original size:24 final size:24
Alignment explanation
Indices: 61008857--61008903 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
61008847 ATACATAATA
**
61008857 AAATTATATTTAAATTTTCAACAG
1 AAATTATATTTAAATTCCCAACAG
61008881 AAATTATAATTT-AATTCCCAACA
1 AAATTAT-ATTTAAATTCCCAACA
61008904 TACTAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.47, C:0.13, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATTATATTTAAATTCCCAACAG
Found at i:61011375 original size:18 final size:20
Alignment explanation
Indices: 61011335--61011376 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
61011325 TCCCTCAACA
*
61011335 AAAATTACAAAATAATTTTT
1 AAAATTACAAAATAATTTAT
61011355 AAAATT-CAAAAT-ATTTAT
1 AAAATTACAAAATAATTTAT
61011373 AAAA
1 AAAA
61011377 ATTTCTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 6 0.29
20 6 0.29
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATTACAAAATAATTTAT
Found at i:61011377 original size:19 final size:20
Alignment explanation
Indices: 61011334--61011379 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
61011324 ATCCCTCAAC
61011334 AAAAATTACAAAATAATTTT
1 AAAAATTACAAAATAATTTT
*
61011354 TAAAATT-CAAAAT-ATTTAT
1 AAAAATTACAAAATAATTT-T
61011373 AAAAATT
1 AAAAATT
61011380 TCTTAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 4 0.17
19 13 0.57
20 6 0.26
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAATTACAAAATAATTTT
Found at i:61017863 original size:90 final size:90
Alignment explanation
Indices: 61017710--61017982 Score: 465
Period size: 90 Copynumber: 3.0 Consensus size: 90
61017700 TCTCCAGGTC
*
61017710 TTTGGCTGCTATTCCCCTTGCTGAATGATGTAGACTTCACATTTATCTCCTTTGAGCTCATAGCT
1 TTTGGCTGCTATTCCCCTTGCTGAATGATGTAGACTTCACATTTATCTCCTTTGAGATCATAGCT
61017775 GAGCCCTCTTTCCTGGTGACCTGTT
66 GAGCCCTCTTTCCTGGTGACCTGTT
* *
61017800 TTTGGCAGCTATTCCCCTTGCTGGATGATGTAGACTTCACATTTATCTCCTTTGAGATCATAGCT
1 TTTGGCTGCTATTCCCCTTGCTGAATGATGTAGACTTCACATTTATCTCCTTTGAGATCATAGCT
*
61017865 GAGCCCTCTTTCCGGGTGACCTGTT
66 GAGCCCTCTTTCCTGGTGACCTGTT
* * * * *
61017890 TTTGGTTGCTATTCTCCTTGCTGAATGATGCAGACTTCACATTCATCTCCTTTGACATCATAGCT
1 TTTGGCTGCTATTCCCCTTGCTGAATGATGTAGACTTCACATTTATCTCCTTTGAGATCATAGCT
61017955 GAGCCCTCTTTCCTGGTGACCTGTT
66 GAGCCCTCTTTCCTGGTGACCTGTT
61017980 TTT
1 TTT
61017983 TATCCCTAAA
Statistics
Matches: 171, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 171 1.00
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.39
Consensus pattern (90 bp):
TTTGGCTGCTATTCCCCTTGCTGAATGATGTAGACTTCACATTTATCTCCTTTGAGATCATAGCT
GAGCCCTCTTTCCTGGTGACCTGTT
Found at i:61039913 original size:94 final size:95
Alignment explanation
Indices: 61039814--61040046 Score: 269
Period size: 94 Copynumber: 2.5 Consensus size: 95
61039804 CACTTGAGGT
* * * *
61039814 ACTTAGCTAAAATTTACAAAGTTATAAAGTAAACACCTCAAAGTGA-AAATTGTTC-GCTAAGTC
1 ACTTAGCTAAATTTTACAAAGTTATAAAGTAAACACCTCAAAGTGAGAAACTATTCATC-AAGTC
* * * * *
61039877 CATAGCTA-AAACATTACTAGCCTTTTAAGGC
65 AATAGC-AGAAAAACTACTAGCCTCTCAAGGC
*
61039908 ACTTAGCTAAATTTTACAAAGTTATAAAGCAAACA-CTCTAAAGT-AGAAACTATTCATCAAGTC
1 ACTTAGCTAAATTTTACAAAGTTATAAAGTAAACACCTC-AAAGTGAGAAACTATTCATCAAGTC
*
61039971 AATAGCAGAAAAACTACTAGCCTCTCAATGC
65 AATAGCAGAAAAACTACTAGCCTCTCAAGGC
* * * *
61040002 ACTCAGTTAAATTTTACAAAGTTATAAAGTAGACACCCCAAAGTG
1 ACTTAGCTAAATTTTACAAAGTTATAAAGTAAACACCTCAAAGTG
61040047 GATATTACTT
Statistics
Matches: 117, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
93 5 0.04
94 109 0.93
95 3 0.03
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (95 bp):
ACTTAGCTAAATTTTACAAAGTTATAAAGTAAACACCTCAAAGTGAGAAACTATTCATCAAGTCA
ATAGCAGAAAAACTACTAGCCTCTCAAGGC
Found at i:61040069 original size:94 final size:92
Alignment explanation
Indices: 61039818--61040074 Score: 262
Period size: 94 Copynumber: 2.7 Consensus size: 92
61039808 TGAGGTACTT
* * * * ** *
61039818 AGCTAAAATTTACAAAGTTATAAAGTAAACACCTCAAAGTGAAAATTGTTCGCTAAGTCCATAGC
1 AGCTAAATTTTACAAAGTTATAAAGTAAACACCCCAAAGTGGAAATTATT-AATAAGTCAATAGC
* * * * *
61039883 TAAAACATTACTAGCCTTTTAAGGCACTT
65 -AAAAAACTACTAGCCTCTCAAGGCACTC
* * * * * *
61039912 AGCTAAATTTTACAAAGTTATAAAGCAAACACTCTAAAGTAGAAACTATTCATCAAGTCAATAGC
1 AGCTAAATTTTACAAAGTTATAAAGTAAACACCCCAAAGTGGAAATTATTAAT-AAGTCAATAGC
*
61039977 AGAAAAACTACTAGCCTCTCAATGCACTC
65 A-AAAAACTACTAGCCTCTCAAGGCACTC
* * * *
61040006 AGTTAAATTTTACAAAGTTATAAAGTAGACACCCCAAAGTGGATATTACTTAATAAGTTAATAGC
1 AGCTAAATTTTACAAAGTTATAAAGTAAACACCCCAAAGTGGAAATTA-TTAATAAGTCAATAGC
61040071 AAAA
65 AAAA
61040075 TCGTTGCTAG
Statistics
Matches: 132, Mismatches: 28, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
93 5 0.04
94 123 0.93
95 4 0.03
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (92 bp):
AGCTAAATTTTACAAAGTTATAAAGTAAACACCCCAAAGTGGAAATTATTAATAAGTCAATAGCA
AAAAACTACTAGCCTCTCAAGGCACTC
Found at i:61041742 original size:5 final size:5
Alignment explanation
Indices: 61041727--61041757 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
61041717 AAGTAAATAG
61041727 ATATT -TATT ATATT ATATT ATATT ATATT AT
1 ATATT ATATT ATATT ATATT ATATT ATATT AT
61041758 TATTGTTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATATT
Found at i:61059216 original size:18 final size:19
Alignment explanation
Indices: 61059195--61059239 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
61059185 CATCAAAAGC
*
61059195 TTAATATAAAGTTAATT-A
1 TTAATATAAAGATAATTCA
*
61059213 TTAATATATAGATAATTCA
1 TTAATATAAAGATAATTCA
*
61059232 TAAATATA
1 TTAATATA
61059240 TAATTCACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.42
Consensus pattern (19 bp):
TTAATATAAAGATAATTCA
Found at i:61071269 original size:18 final size:17
Alignment explanation
Indices: 61071236--61071269 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
61071226 ATATGACTAT
*
61071236 ATAAAAATTTTCAATAA
1 ATAAAAATTTTAAATAA
61071253 ATAAAAATTATTAAATA
1 ATAAAAATT-TTAAATA
61071270 TTAATATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAAAAATTTTAAATAA
Found at i:61075140 original size:30 final size:31
Alignment explanation
Indices: 61075077--61075144 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
61075067 GGGCCCTCTA
*
61075077 AATTTTTTGAAAACTTTAGTTAAGTTTTCTT
1 AATTTTTTGAAAACTTTAGTTAAGCTTTCTT
* *
61075108 AATTTTTTGAAAATTTTCA-TTATGCTTT-TT
1 AATTTTTTGAAAACTTT-AGTTAAGCTTTCTT
61075138 AATTTTT
1 AATTTTT
61075145 AAAAAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 9 0.27
31 23 0.70
32 1 0.03
ACGTcount: A:0.28, C:0.06, G:0.07, T:0.59
Consensus pattern (31 bp):
AATTTTTTGAAAACTTTAGTTAAGCTTTCTT
Found at i:61081578 original size:146 final size:143
Alignment explanation
Indices: 61081222--61081722 Score: 711
Period size: 146 Copynumber: 3.4 Consensus size: 143
61081212 AGGCGGCACC
* * ** *
61081222 CCCTTTGTTCGTATTTTTTCTTCAAATTTTATTATTTTTAAAAAATATACTTTTTTATTTTTT-A
1 CCCTATGTTCGTATTTTTTC-CCGGATTTTATTACTTTTAAAAAATATAC-----TATTTTTTAA
* * * *
61081286 TTTTACATTATTTTAATACATTATATTTGAAATGTATTAATTTAATGAGTTTTTAAATAAATTTT
60 TTTTACATTATTTTAGTATATTATATTTGAAATGTATTAATTTAGTGTGTTTTTAAATAAATTTT
61081351 AAAAAAACCCTTATTTCGG
125 AAAAAAACCCTTATTTCGG
* * * * *
61081370 CCCTATGTTCATATTTTTCCCCCGATTTTATTACTTTTAAAAAATATATTATTTTTTAATTTTAT
1 CCCTATGTTCGTATTTTTTCCCGGATTTTATTACTTTTAAAAAATATACTATTTTTTAATTTTAC
*
61081435 ATTATTTTAGTATATTACATTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTTTTAAAA
66 ATTATTTTAGTATATTATATTTGAAATGTATTAATTTAGTGTG-TTTTTAAATAAA-TTTTAAAA
61081500 AAACCCTTATTTCGG
129 AAACCCTTATTTCGG
*
61081515 CCCTATGTTCGTATTTTTTTCTCGGATTTTATTACTTTTAAAAAATATACTATTTTTTAATTTTA
1 CCCTATGTTCGTA-TTTTTTCCCGGATTTTATTACTTTTAAAAAATATACTATTTTTTAATTTTA
61081580 CATTATTTTAGTATATTATATTTGAAATGTATTAATTTAGTGTGCTTTTTAAATAAA-TTT-AAA
65 CATTATTTTAGTATATTATATTTGAAATGTATTAATTTAGTGTG-TTTTTAAATAAATTTTAAAA
*
61081643 AAACCCTTATTTTGG
129 AAACCCTTATTTCGG
61081658 CCCTATGTTCGTATTTATTTTCCCGGATTTTATTACTTTTAAAAAATATACTATTTTTTTAATTT
1 CCCTATGTTCGTA-TT-TTTTCCCGGATTTTATTACTTTTAAAAAATATACTA-TTTTTTAATTT
61081723 AGAGTTCTAC
Statistics
Matches: 323, Mismatches: 24, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
142 8 0.02
143 77 0.24
144 50 0.15
145 46 0.14
146 101 0.31
147 24 0.07
148 17 0.05
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (143 bp):
CCCTATGTTCGTATTTTTTCCCGGATTTTATTACTTTTAAAAAATATACTATTTTTTAATTTTAC
ATTATTTTAGTATATTATATTTGAAATGTATTAATTTAGTGTGTTTTTAAATAAATTTTAAAAAA
ACCCTTATTTCGG
Found at i:61083400 original size:31 final size:31
Alignment explanation
Indices: 61083358--61083423 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
61083348 TCAATATTCG
* **
61083358 AAAAAACACAAGGACGAAAATTTATCAAATC
1 AAAAAACACAAGAACGAAAATGAATCAAATC
* * *
61083389 AAAAAATACAAGAACTAAAATGAATCAAATT
1 AAAAAACACAAGAACGAAAATGAATCAAATC
61083420 AAAA
1 AAAA
61083424 CATTAAGACT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.64, C:0.12, G:0.08, T:0.17
Consensus pattern (31 bp):
AAAAAACACAAGAACGAAAATGAATCAAATC
Found at i:61083866 original size:22 final size:23
Alignment explanation
Indices: 61083831--61083873 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
61083821 ATGCAGCTTT
61083831 AAAAAAAAACTTTGAAATTTCGG
1 AAAAAAAAACTTTGAAATTTCGG
*
61083854 AAAACAAAA-TTTGAAATTTC
1 AAAAAAAAACTTTGAAATTTC
61083874 TATTTCCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.28
Consensus pattern (23 bp):
AAAAAAAAACTTTGAAATTTCGG
Found at i:61085974 original size:27 final size:28
Alignment explanation
Indices: 61085916--61085976 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
61085906 AATTAATAAT
*
61085916 TTTTTAATATATAGTTTAATATATTATA
1 TTTTTAATATATAGTTTAATATATTAAA
*
61085944 -TTTTAATAT-TA-TTTGATATAATTAAA
1 TTTTTAATATATAGTTTAATAT-ATTAAA
61085970 TTTTTAA
1 TTTTTAA
61085977 GTAATATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 7 0.24
26 7 0.24
27 15 0.52
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.57
Consensus pattern (28 bp):
TTTTTAATATATAGTTTAATATATTAAA
Found at i:61087391 original size:19 final size:20
Alignment explanation
Indices: 61087367--61087404 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
61087357 AAATATGTTA
61087367 ATATTATA-ATTATAATTTT
1 ATATTATATATTATAATTTT
*
61087386 ATATTATATGTTATAATTT
1 ATATTATATATTATAATTT
61087405 AAGCAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
ATATTATATATTATAATTTT
Found at i:61092729 original size:22 final size:21
Alignment explanation
Indices: 61092695--61092741 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
61092685 TTTTACTATT
61092695 TAAAATTATTTAA-ATATAATTA
1 TAAAATTATTTAATAT-TAA-TA
61092717 TAAAA-TATGTTAATATTAATA
1 TAAAATTAT-TTAATATTAATA
61092738 TAAA
1 TAAA
61092742 GTTAATTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 9 0.39
22 12 0.52
23 2 0.09
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TAAAATTATTTAATATTAATA
Found at i:61094263 original size:15 final size:16
Alignment explanation
Indices: 61094233--61094264 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
61094223 GGTTTGCATT
*
61094233 TTAAATTTTAAAAAAA
1 TTAAATTCTAAAAAAA
61094249 TTAAATTCTAAAAAAA
1 TTAAATTCTAAAAAAA
61094265 AAGCAGTCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (16 bp):
TTAAATTCTAAAAAAA
Found at i:61103902 original size:6 final size:6
Alignment explanation
Indices: 61103893--61103923 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
61103883 TTACCCAAAT
61103893 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA T
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA T
61103924 ATTGTTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTAA
Found at i:61106633 original size:88 final size:88
Alignment explanation
Indices: 61106482--61106657 Score: 334
Period size: 88 Copynumber: 2.0 Consensus size: 88
61106472 TTGGGTTGTA
*
61106482 ATGGCTTTCTTCCGGATTTTCTGTTACCATTGGCGTTGAGCAATAATTGCTGATCATTACTCTCT
1 ATGGCTTTCTTCCCGATTTTCTGTTACCATTGGCGTTGAGCAATAATTGCTGATCATTACTCTCT
61106547 ACTTTTGATATGAACATGCATGG
66 ACTTTTGATATGAACATGCATGG
*
61106570 ATGGCTTTCTTCCCGATTTTCTGTTACCATTGGCGTTGAGCAATAATTGCTGATCATTGCTCTCT
1 ATGGCTTTCTTCCCGATTTTCTGTTACCATTGGCGTTGAGCAATAATTGCTGATCATTACTCTCT
61106635 ACTTTTGATATGAACATGCATGG
66 ACTTTTGATATGAACATGCATGG
61106658 GATGTTTCAA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (88 bp):
ATGGCTTTCTTCCCGATTTTCTGTTACCATTGGCGTTGAGCAATAATTGCTGATCATTACTCTCT
ACTTTTGATATGAACATGCATGG
Found at i:61117776 original size:16 final size:16
Alignment explanation
Indices: 61117755--61117785 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
61117745 AGGAGAATTT
61117755 ATTAAATGTTTTAATC
1 ATTAAATGTTTTAATC
61117771 ATTAAATGTTTTAAT
1 ATTAAATGTTTTAAT
61117786 TATATATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (16 bp):
ATTAAATGTTTTAATC
Found at i:61118297 original size:22 final size:24
Alignment explanation
Indices: 61118251--61118298 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
61118241 TTTAATATTT
**
61118251 TAAAATATTTTTATCATATTGATA
1 TAAAATATTTTTATCATATAAATA
61118275 TAAAATATTTTT-T-ATATAAATA
1 TAAAATATTTTTATCATATAAATA
61118297 TA
1 TA
61118299 TATTTAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 9 0.41
23 1 0.05
24 12 0.55
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
TAAAATATTTTTATCATATAAATA
Done.