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 133 of 205
Found at i:40336455 original size:18 final size:19
Alignment explanation
Indices: 40336411--40336459 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
40336401 AGGCATTTTC
40336411 CAACCTTAACATACAAAAT
1 CAACCTTAACATACAAAAT
* *
40336430 AAATCTTAACATAC-AAAT
1 CAACCTTAACATACAAAAT
40336448 CAACCTTAACAT
1 CAACCTTAACAT
40336460 TCATCACATG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (19 bp):
CAACCTTAACATACAAAAT
Found at i:40344788 original size:52 final size:52
Alignment explanation
Indices: 40344726--40344826 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
40344716 CATGCACATA
* *
40344726 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGTTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCCATTATTG
40344778 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCCATTA
40344827 CTTTTCCTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.34
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCCATTATTG
Found at i:40347461 original size:102 final size:102
Alignment explanation
Indices: 40347289--40347799 Score: 1004
Period size: 102 Copynumber: 5.0 Consensus size: 102
40347279 CACGTAATTA
*
40347289 CCCGATCGTCAACGAGGAATAGTTGAGTTATCGGGAAATAGGATGAAATAAGGCTAAAGATGATG
1 CCCGATCGTCGACGAGGAATAGTTGAGTTATC-GGAAATAGGATGAAATAAGGCTAAAGATGATG
40347354 TGATCTGGCTCAGTTGATTGAGTCGATTCACTTGATTG
65 TGATCTGGCTCAGTTGATTGAGTCGATTCACTTGATTG
40347392 CCCGATCGTCGACGAGGAATAGTTGAGTTATCGGAAATAGGATGAAATAAGGCTAAAGATGATGT
1 CCCGATCGTCGACGAGGAATAGTTGAGTTATCGGAAATAGGATGAAATAAGGCTAAAGATGATGT
40347457 GATCTGGCTCAGTTGATTGAGTCGATTCACTTGATTG
66 GATCTGGCTCAGTTGATTGAGTCGATTCACTTGATTG
40347494 CCCGATCGTCGACGAGGAATAGTTGAGTTATCGGAAATAGGATGAAATAAGGCTAAAGATGATGT
1 CCCGATCGTCGACGAGGAATAGTTGAGTTATCGGAAATAGGATGAAATAAGGCTAAAGATGATGT
40347559 GATCTGGCTCAGTTGATTGAGTCGATTCACTTGATTG
66 GATCTGGCTCAGTTGATTGAGTCGATTCACTTGATTG
40347596 CCCGATCGTCGACGAGGAATAGTTGAGTTATCGGAAATAGGATGAAATAAGGCTAAAGATGATGT
1 CCCGATCGTCGACGAGGAATAGTTGAGTTATCGGAAATAGGATGAAATAAGGCTAAAGATGATGT
40347661 GATCTGGCTCAGTTGATTGAGTCGATTCACTTGATTG
66 GATCTGGCTCAGTTGATTGAGTCGATTCACTTGATTG
40347698 CCCGATCGTCGACGAGGAATAGTTGAGTTATCGGAAATAGGATGAAATAAGGCTAAAGATGATGT
1 CCCGATCGTCGACGAGGAATAGTTGAGTTATCGGAAATAGGATGAAATAAGGCTAAAGATGATGT
40347763 GATCTGGCTCAGTTGATTGAGTCGATTCACTTGATTG
66 GATCTGGCTCAGTTGATTGAGTCGATTCACTTGATTG
40347800 NNNNNNNNNN
Statistics
Matches: 407, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
102 376 0.92
103 31 0.08
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (102 bp):
CCCGATCGTCGACGAGGAATAGTTGAGTTATCGGAAATAGGATGAAATAAGGCTAAAGATGATGT
GATCTGGCTCAGTTGATTGAGTCGATTCACTTGATTG
Found at i:40350640 original size:37 final size:37
Alignment explanation
Indices: 40350594--40350668 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
40350584 ATTACCCGAA
*
40350594 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
* *
40350631 TTGAATCACTACATAATTAAAAACATTACGTAATTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
40350668 T
1 T
40350669 GAAATTAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:40350682 original size:37 final size:37
Alignment explanation
Indices: 40350594--40350685 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 37
40350584 ATTACCCGAA
* *
40350594 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATAACTACATAATTAAAAACATTACATAAGTCT
* * *
40350631 TTGAATCACTACATAATTAAAAACATTACGTAATTC-
1 TTGAATAACTACATAATTAAAAACATTACATAAGTCT
40350667 TTGAAATTAAC-ACATAATT
1 TTG-AA-TAACTACATAATT
40350686 GAAATGTAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
36 3 0.06
37 43 0.88
38 3 0.06
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.35
Consensus pattern (37 bp):
TTGAATAACTACATAATTAAAAACATTACATAAGTCT
Found at i:40350972 original size:41 final size:41
Alignment explanation
Indices: 40350915--40350996 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
40350905 TTACGGACGC
40350915 AATCCTCATTTTCTCTGCTTCAACGCCGATTTCTAATCCCT
1 AATCCTCATTTTCTCTGCTTCAACGCCGATTTCTAATCCCT
*
40350956 AATCCTCATTTTCTCTGCTTCAACGCCTATTTCTAATCCCT
1 AATCCTCATTTTCTCTGCTTCAACGCCGATTTCTAATCCCT
40350997 TCCAAAAGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.20, C:0.34, G:0.06, T:0.40
Consensus pattern (41 bp):
AATCCTCATTTTCTCTGCTTCAACGCCGATTTCTAATCCCT
Found at i:40353777 original size:133 final size:134
Alignment explanation
Indices: 40353606--40353982 Score: 487
Period size: 133 Copynumber: 2.8 Consensus size: 134
40353596 GCGGCAAACA
* ** * *
40353606 ATTGGAATATAGCGGCGTTTTTTTAGAAACGCCGGTAAAGATAACGAATTTGAGGAAAAAATCTG
1 ATTGGAATATAGCGGCGTTATTGGAGAAACGCCGGTAAAGATAACTAATTTGAGGAAAAAATTTG
40353671 AGCAAAACAGTACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCGCATTGTAAAAAACACCGG
66 AGCAAAACAGTACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCGCATTGTAAAAAACACC-G
40353736 AAAAG
130 AAAAG
40353741 ATT-GAAT-TAGCGGCGTT-TTCAGG-GAAACGCCGGTAAAGATAACTAATTTGAGGAAAAAATT
1 ATTGGAATATAGCGGCGTTATT--GGAGAAACGCCGGTAAAGATAACTAATTTGAGGAAAAAATT
* * * * * *
40353802 TG-GACAAAACACTACCGTTTTATTGCTTCATTTTATTTCTTTAGTGGCTCATTGTAAAAGACGC
64 TGAG-CAAAACAGTACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCGCATTGTAAAAAACAC
* *
40353866 CGCAAAT
128 CGAAAAG
* * * * *
40353873 ATTGGGATATAGTGGTGTTATTGGAGAAACGCCGGTAAAGATATCTAATTTGAGGAAAAATTTTG
1 ATTGGAATATAGCGGCGTTATTGGAGAAACGCCGGTAAAGATAACTAATTTGAGGAAAAAATTTG
* *
40353938 AGCAAAACAGTACCGTTTTGTTGTTTCCTTTT-TATGCTTTAGTGG
66 AGCAAAACAGTACCGTTTTGTTGTTTCATTTTAT-TTCTTTAGTGG
40353983 TGAAATGTTA
Statistics
Matches: 211, Mismatches: 22, Indels: 19
0.84 0.09 0.08
Matches are distributed among these distances:
132 10 0.05
133 109 0.52
134 86 0.41
135 6 0.03
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (134 bp):
ATTGGAATATAGCGGCGTTATTGGAGAAACGCCGGTAAAGATAACTAATTTGAGGAAAAAATTTG
AGCAAAACAGTACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCGCATTGTAAAAAACACCGA
AAAG
Found at i:40354388 original size:21 final size:20
Alignment explanation
Indices: 40354354--40354405 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
40354344 TTGTGTTCTA
40354354 GGCTTAGAGTTGAGGTTTAG
1 GGCTTAGAGTTGAGGTTTAG
* *
40354374 GGCTTGGAGATTGAGGTTTAA
1 GGCTTAGAG-TTGAGGTTTAG
*
40354395 GGTTTAGAGTT
1 GGCTTAGAGTT
40354406 TATATTTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.21, C:0.04, G:0.38, T:0.37
Consensus pattern (20 bp):
GGCTTAGAGTTGAGGTTTAG
Found at i:40354733 original size:93 final size:93
Alignment explanation
Indices: 40354622--40354792 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
40354612 CATTCATTTG
* * *
40354622 TTTGCTAAAAATAGAGCATAAA-TTTATAATTGTAAGACATTATTGGAATAGTGTGAATACTTAA
1 TTTGCTAAAAAGAGAGCATAAAGTTGA-AATTGTAAGACATTATTGGAATAGTGTGAATAATTAA
40354686 TAAATTTGAATGTTGGAGCGTTATCCATA
65 TAAATTTGAATGTTGGAGCGTTATCCATA
40354715 TTTGCTAAAAAGAGAGCATAAAGTTGAAATTGTAAGACATTATTGGAATAGTGTGAATAATTAAT
1 TTTGCTAAAAAGAGAGCATAAAGTTGAAATTGTAAGACATTATTGGAATAGTGTGAATAATTAAT
40354780 AAATTTGAATGTT
66 AAATTTGAATGTT
40354793 TATAGTATTT
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
93 71 0.96
94 3 0.04
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (93 bp):
TTTGCTAAAAAGAGAGCATAAAGTTGAAATTGTAAGACATTATTGGAATAGTGTGAATAATTAAT
AAATTTGAATGTTGGAGCGTTATCCATA
Found at i:40354817 original size:93 final size:93
Alignment explanation
Indices: 40354626--40354818 Score: 237
Period size: 93 Copynumber: 2.1 Consensus size: 93
40354616 CATTTGTTTG
* * *
40354626 CTAAAAATAGAGCATAAATTTATAATTGTAAGACATTATTGGAATAGTGTGAATACTTAATAAAT
1 CTAAAAAGAGAGCATAAATTGATAATTGTAAGACATTATTGGAATAGTGTGAATAATTAATAAAT
* ** * * *
40354691 TTGAATGTTGGAGCGTTATCCATATTTG
66 TTGAATGTTGGAGAGTTATAAAAATCTA
40354719 CTAAAAAGAGAGCATAAAGTTGA-AATTGTAAGACATTATTGGAATAGTGTGAATAATTAATAAA
1 CTAAAAAGAGAGCATAAA-TTGATAATTGTAAGACATTATTGGAATAGTGTGAATAATTAATAAA
* * *
40354783 TTTGAATGTT-TATAGTATTTAAAAATCTA
65 TTTGAATGTTGGAGAGT-TATAAAAATCTA
*
40354812 TTAAAAA
1 CTAAAAA
40354819 TAAAAATACT
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
92 3 0.04
93 79 0.93
94 3 0.04
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (93 bp):
CTAAAAAGAGAGCATAAATTGATAATTGTAAGACATTATTGGAATAGTGTGAATAATTAATAAAT
TTGAATGTTGGAGAGTTATAAAAATCTA
Found at i:40355479 original size:7 final size:7
Alignment explanation
Indices: 40355460--40355490 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
40355450 GTTTATAGCA
40355460 TTTAGGG
1 TTTAGGG
40355467 TTTAGGG
1 TTTAGGG
*
40355474 TTTAGGA
1 TTTAGGG
40355481 TTTAGGG
1 TTTAGGG
40355488 TTT
1 TTT
40355491 CAGTGTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:40355485 original size:21 final size:22
Alignment explanation
Indices: 40355459--40355499 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
40355449 AGTTTATAGC
40355459 ATTTAGGGTTT-AGGGTTTAGG
1 ATTTAGGGTTTCAGGGTTTAGG
*
40355480 ATTTAGGGTTTCAGTGTTTA
1 ATTTAGGGTTTCAGGGTTTA
40355500 ATTACTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.46
Consensus pattern (22 bp):
ATTTAGGGTTTCAGGGTTTAGG
Found at i:40357999 original size:521 final size:510
Alignment explanation
Indices: 40357029--40358059 Score: 1767
Period size: 521 Copynumber: 2.0 Consensus size: 510
40357019 AACATCTTAA
*
40357029 GGTTCGAATGTCCGATTCTTCGTATTTATAGATTGGGTTTTGTCGTATTTTTAATTTTGATTTTG
1 GGTTCGAATGTCCGATTCTTCGTATTTATACATTGGGTTTTGTCGTATTTTTAATTTTGATTTTG
*** * *
40357094 CTTTCTTATTGGTTTAGGGTTTTCTGTGTGTTCTCTGTGTTTATGGTTTTCGGTGTGTTCGACCG
66 CTTTCTTATTGGTTTAGGGTTAAATGTGTATTCTCTGTGTTTAGGGTTTTCGGTGTGTTCGACCG
*
40357159 TTTTGTTCATCCTCGTGAAGGTAAATTACTGCTTCTATTGTTCATTACTGTTTTTGTGAATGGTT
131 TTTTGTTCATCCTCGTGAAGGTAAATTACTGCTTCTATTGTTCATTAATGTTTTTGTGAATGGTT
40357224 TAATTTGTTAGGAACTGATTTTAACTTATGTTTTTTTCTCCAGTTTTTGGTCAATCCATTTCATT
196 TAATTTGTTAGGAACTGATTTTAACTTATGTTTTTTTCTCCAGTTTTTGGTCAATCCATTTCATT
40357289 GCTCGTATTTCAGTTTTCTTCATCGTTCTGAAGGTACAGAACACATGCTTTGTTACTGTTTATTT
261 GCTCGTATTTCAGTTTTCTTCATCGTTCTGAAGGTACAGAACACATGCTTTGTTACTGTTTATTT
40357354 GTTGAACTCATTTGGTACTGTTTTTAAAGTATGGAACTTTGATGTCTAGTTTAGGGTTTAATTTA
326 GTTGAACTCATTTGGTACTGTTTTTAAAGTATGGAACTTTGATGTCTAGTTTAGGGTTTAATTTA
*
40357419 TTAGGTTATAAAACCGTTCTATTAAATGTGGTGCAGCCGATTACATTTCCAGGTAATGAAATGGA
391 TTAGGTTATAAAACCGTTCTATTAAATGTGGTGCAGCCGATTACATTTCCAAGTAATGAAATGGA
*
40357484 TTTTTAAGTTGAATTTTATTAAGCCATGTTGTTTTTTAGTATGATTTTTAAGTTC
456 TTTTTAAGTTGAATTTTATTAAGCCATGTTGTTTTTTAGTATGATTTCTAAGTTC
* * *
40357539 GGTTCGAATGTTCGATTCTTTGTATTTATACATTGGGTTTTTTCGTATTTTTAATTTTGATTTTG
1 GGTTCGAATGTCCGATTCTTCGTATTTATACATTGGGTTTTGTCGTATTTTTAATTTTGATTTTG
* * *
40357604 CTTTCTTATTGGTTGGTGATATTGGGATTAAAAAAT-TTTATTCTTTGTGTTTAGGGTTTTTGGT
66 CTTTCTTATTGG-T--T--TA--GGG-TT---AAATGTGTATTCTCTGTGTTTAGGGTTTTCGGT
*
40357668 GTGTTCGACTGTTTTGTTCATCCTCGTGAAGGTAAATTACTGCTTCTATTGTTCATTAATGTTTT
120 GTGTTCGACCGTTTTGTTCATCCTCGTGAAGGTAAATTACTGCTTCTATTGTTCATTAATGTTTT
40357733 TGTGAATGGTTTAATTTGTTAGGAACTGATTTTAACTTATGTTTTTTTTCTCCAGTTTTTGGTCA
185 TGTGAATGGTTTAATTTGTTAGGAACTGATTTTAACTTATG-TTTTTTTCTCCAGTTTTTGGTCA
*
40357798 ATCCATTTCATTGCTCGTATTTCAGTTTTCTTCATCGTTTTGAAGGTACAGAACACATGCTTTGT
249 ATCCATTTCATTGCTCGTATTTCAGTTTTCTTCATCGTTCTGAAGGTACAGAACACATGCTTTGT
40357863 TACTGTTTATTTGTTGAACTCATTTGGTACTGTTTTTAAAGTATGGAACTTTGATGTCTAGTTTA
314 TACTGTTTATTTGTTGAACTCATTTGGTACTGTTTTTAAAGTATGGAACTTTGATGTCTAGTTTA
* * *
40357928 GGGTTTAATTTATTAGGTTATAAAACTGTTTTGTTAAATGTGGTGCAGCCGATTACATTTCCAAG
379 GGGTTTAATTTATTAGGTTATAAAACCGTTCTATTAAATGTGGTGCAGCCGATTACATTTCCAAG
40357993 TAATGAAATGGATTTTTAAGTTGAATTTTATTAAGCCATGTTGTTTTTTAGTATGATTTCTAAGT
444 TAATGAAATGGATTTTTAAGTTGAATTTTATTAAGCCATGTTGTTTTTTAGTATGATTTCTAAGT
40358058 TC
509 TC
40358060 AAAATATATA
Statistics
Matches: 489, Mismatches: 20, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
510 73 0.15
511 1 0.00
513 1 0.00
515 2 0.00
517 3 0.01
518 2 0.00
520 127 0.26
521 280 0.57
ACGTcount: A:0.21, C:0.11, G:0.19, T:0.48
Consensus pattern (510 bp):
GGTTCGAATGTCCGATTCTTCGTATTTATACATTGGGTTTTGTCGTATTTTTAATTTTGATTTTG
CTTTCTTATTGGTTTAGGGTTAAATGTGTATTCTCTGTGTTTAGGGTTTTCGGTGTGTTCGACCG
TTTTGTTCATCCTCGTGAAGGTAAATTACTGCTTCTATTGTTCATTAATGTTTTTGTGAATGGTT
TAATTTGTTAGGAACTGATTTTAACTTATGTTTTTTTCTCCAGTTTTTGGTCAATCCATTTCATT
GCTCGTATTTCAGTTTTCTTCATCGTTCTGAAGGTACAGAACACATGCTTTGTTACTGTTTATTT
GTTGAACTCATTTGGTACTGTTTTTAAAGTATGGAACTTTGATGTCTAGTTTAGGGTTTAATTTA
TTAGGTTATAAAACCGTTCTATTAAATGTGGTGCAGCCGATTACATTTCCAAGTAATGAAATGGA
TTTTTAAGTTGAATTTTATTAAGCCATGTTGTTTTTTAGTATGATTTCTAAGTTC
Found at i:40358969 original size:21 final size:21
Alignment explanation
Indices: 40358943--40358989 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
40358933 CTACAACTTA
*
40358943 AAGCAGATGCGGCAGCGATG-G
1 AAGCAGAGGCGGCAGCGA-GAG
*
40358964 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
40358985 AAGCA
1 AAGCA
40358990 AAGGTTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.34, C:0.19, G:0.40, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:40359881 original size:658 final size:658
Alignment explanation
Indices: 40358625--40359945 Score: 2588
Period size: 658 Copynumber: 2.0 Consensus size: 658
40358615 CTAACTATGT
40358625 GATTTATTTTTTAGGAAAAACTAAAGGATAAAAAGGCGGAGCACGCAGCGATTGTTTCTAGTGAT
1 GATTTATTTTTTAGGAAAAACTAAAGGATAAAAAGGCGGAGCACGCAGCGATTGTTTCTAGTGAT
40358690 AGTTCTGTTCATCCTGAAGACATTGATAACCGGATTATTACTGAAGTTTTGGGTCCTGAAAGGTA
66 AGTTCTGTTCATCCTGAAGACATTGATAACCGGATTATTACTGAAGTTTTGGGTCCTGAAAGGTA
40358755 TGGTCGGGTTCGATTTCAAGGATCTTTTGTTAGCCTAACCCAATATTTTGGATCCAGCTCGCAGC
131 TGGTCGGGTTCGATTTCAAGGATCTTTTGTTAGCCTAACCCAATATTTTGGATCCAGCTCGCAGC
40358820 AATACATGGCTTCGGGGACTCAGGCTCAAGCTGAAGTTCAGAGGTTAAAAGACCAGATGACTCAG
196 AATACATGGCTTCGGGGACTCAGGCTCAAGCTGAAGTTCAGAGGTTAAAAGACCAGATGACTCAG
40358885 ATGCAAGCGACCACAGTTGAGGTTCAAAGGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGA
261 ATGCAAGCGACCACAGTTGAGGTTCAAAGGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGA
* *
40358950 TGCGGCAGCGATGGAAGCAGAGGCTGCAGCGAGAGAAGCAAAGGTTCAAAAGAAATATGAAGAAC
326 TGCGGCAGCGAGGGAAACAGAGGCTGCAGCGAGAGAAGCAAAGGTTCAAAAGAAATATGAAGAAC
40359015 TGCAGCTAAAACTTAAAGCAGAGGCTGCAGCGAGAGAAGCAGAGCAGAGAAGAAAGTACAACGAA
391 TGCAGCTAAAACTTAAAGCAGAGGCTGCAGCGAGAGAAGCAGAGCAGAGAAGAAAGTACAACGAA
40359080 CTCCAGCAGCAGCTTGAGAGTATGATGAAGATGTTTCAGTCGCATCTTCTACCGTCATAGTGTAT
456 CTCCAGCAGCAGCTTGAGAGTATGATGAAGATGTTTCAGTCGCATCTTCTACCGTCATAGTGTAT
40359145 TGCATTAATATTTTTATCATTTTAACTTTTAACATTTTTGCAAAAATAGTATGAATTCACTTTTA
521 TGCATTAATATTTTTATCATTTTAACTTTTAACATTTTTGCAAAAATAGTATGAATTCACTTTTA
*
40359210 TTTATTGATATTAATATTATTTTATTCGTTTAATTTGAAATATTATATAAATTTATTACTTTTGG
586 TTTATTGATATTAATATTATTTTAGTCGTTTAATTTGAAATATTATATAAATTTATTACTTTTGG
40359275 CTGGTTTA
651 CTGGTTTA
40359283 GATTTATTTTTTAGGAAAAACTAAAGGATAAAAAGGCGGAGCACGCAGCGATTGTTTCTAGTGAT
1 GATTTATTTTTTAGGAAAAACTAAAGGATAAAAAGGCGGAGCACGCAGCGATTGTTTCTAGTGAT
40359348 AGTTCTGTTCATCCTGAAGACATTGATAACCGGATTATTACTGAAGTTTTGGGTCCTGAAAGGTA
66 AGTTCTGTTCATCCTGAAGACATTGATAACCGGATTATTACTGAAGTTTTGGGTCCTGAAAGGTA
40359413 TGGTCGGGTTCGATTTCAAGGATCTTTTGTTAGCCTAACCCAATATTTTGGATCCAGCTCGCAGC
131 TGGTCGGGTTCGATTTCAAGGATCTTTTGTTAGCCTAACCCAATATTTTGGATCCAGCTCGCAGC
40359478 AATACATGGCTTCGGGGACTCAGGCTCAAGCTGAAGTTCAGAGGTTAAAAGACCAGATGACTCAG
196 AATACATGGCTTCGGGGACTCAGGCTCAAGCTGAAGTTCAGAGGTTAAAAGACCAGATGACTCAG
*
40359543 ATGCAAGCGACCACAGTTGAGGTTCAAAGGAAATCTGAAGAACTCCAGCTACAACTTAAAGCAGA
261 ATGCAAGCGACCACAGTTGAGGTTCAAAGGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGA
40359608 TGCGGCAGCGAGGGAAACAGAGGCTGCAGCGAGAGAAGCAAAGGTTCAAAAGAAATATGAAGAAC
326 TGCGGCAGCGAGGGAAACAGAGGCTGCAGCGAGAGAAGCAAAGGTTCAAAAGAAATATGAAGAAC
*
40359673 TGCAGCTAAAACTTAAAGCAGAGGCTGCAGCGAGAGAAGCAGAGCAGAGCAGAAAGTACAACGAA
391 TGCAGCTAAAACTTAAAGCAGAGGCTGCAGCGAGAGAAGCAGAGCAGAGAAGAAAGTACAACGAA
*
40359738 CTCCAGCAGCAGCTTGAGAGTATGATGAAGATGTTTCAGTCGCATCTTCTGCCGTCATAGTGTAT
456 CTCCAGCAGCAGCTTGAGAGTATGATGAAGATGTTTCAGTCGCATCTTCTACCGTCATAGTGTAT
40359803 TGCATTAATATTTTTATCATTTTAACTTTTAACATTTTTGCAAAAATAGTATGAATTCACTTTTA
521 TGCATTAATATTTTTATCATTTTAACTTTTAACATTTTTGCAAAAATAGTATGAATTCACTTTTA
40359868 TTTATTGATATTAATATTATTTTAGTCGTTTAATTTGAAATATTATATAAATTTATTACTTTTGG
586 TTTATTGATATTAATATTATTTTAGTCGTTTAATTTGAAATATTATATAAATTTATTACTTTTGG
40359933 CTGGTTTA
651 CTGGTTTA
40359941 GATTT
1 GATTT
40359946 GGTTGTTTTT
Statistics
Matches: 657, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
658 657 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (658 bp):
GATTTATTTTTTAGGAAAAACTAAAGGATAAAAAGGCGGAGCACGCAGCGATTGTTTCTAGTGAT
AGTTCTGTTCATCCTGAAGACATTGATAACCGGATTATTACTGAAGTTTTGGGTCCTGAAAGGTA
TGGTCGGGTTCGATTTCAAGGATCTTTTGTTAGCCTAACCCAATATTTTGGATCCAGCTCGCAGC
AATACATGGCTTCGGGGACTCAGGCTCAAGCTGAAGTTCAGAGGTTAAAAGACCAGATGACTCAG
ATGCAAGCGACCACAGTTGAGGTTCAAAGGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGA
TGCGGCAGCGAGGGAAACAGAGGCTGCAGCGAGAGAAGCAAAGGTTCAAAAGAAATATGAAGAAC
TGCAGCTAAAACTTAAAGCAGAGGCTGCAGCGAGAGAAGCAGAGCAGAGAAGAAAGTACAACGAA
CTCCAGCAGCAGCTTGAGAGTATGATGAAGATGTTTCAGTCGCATCTTCTACCGTCATAGTGTAT
TGCATTAATATTTTTATCATTTTAACTTTTAACATTTTTGCAAAAATAGTATGAATTCACTTTTA
TTTATTGATATTAATATTATTTTAGTCGTTTAATTTGAAATATTATATAAATTTATTACTTTTGG
CTGGTTTA
Found at i:40360132 original size:42 final size:42
Alignment explanation
Indices: 40360032--40360191 Score: 243
Period size: 42 Copynumber: 3.8 Consensus size: 42
40360022 CGTTTTTGTA
*
40360032 AAAAAGCGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAA--
1 AAAAA-CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAGG
* *
40360073 AAAAATGCCGCTAAAGAACATGTTCTTTAGTGGCGCTTAAGG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAGG
* *
40360115 AAAAACGCCGCTAAAGAACATGTTTTTTAGCGACGCTTAAGG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAGG
*
40360157 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG
40360192 TTTTTAGTTG
Statistics
Matches: 108, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
40 33 0.31
41 5 0.05
42 70 0.65
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAGG
Found at i:40360179 original size:84 final size:83
Alignment explanation
Indices: 40360032--40360191 Score: 241
Period size: 82 Copynumber: 1.9 Consensus size: 83
40360022 CGTTTTTGTA
* *
40360032 AAAAAGCGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAAAAAAATGCCGCTAAAGAACATGTT
1 AAAAAGCGCCGCTAAAGAACATGTTCTTTAGAGACGCTTAAAAAAACGCCGCTAAAGAACATGTT
*
40360097 CTTTAGTGGCGCTTAAGG
66 CTTTAGCGGCGCTTAAGG
* * *
40360115 AAAAA-CGCCGCTAAAGAACATGTTTTTTAGCGACGCTTAAGGAAAAACGCCGCTAAAGATCATG
1 AAAAAGCGCCGCTAAAGAACATGTTCTTTAGAGACGCTTAA--AAAAACGCCGCTAAAGAACATG
40360179 TTCTTTAGCGGCG
64 TTCTTTAGCGGCG
40360192 TTTTTAGTTG
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
82 32 0.46
83 5 0.07
84 32 0.46
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (83 bp):
AAAAAGCGCCGCTAAAGAACATGTTCTTTAGAGACGCTTAAAAAAACGCCGCTAAAGAACATGTT
CTTTAGCGGCGCTTAAGG
Found at i:40360813 original size:21 final size:21
Alignment explanation
Indices: 40360772--40360814 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
40360762 AATAAAGTAG
*
40360772 ATTATAAATTATTTTTATAGT
1 ATTATAAATTATATTTATAGT
*
40360793 ATTATATATTATGATTT-TAGT
1 ATTATAAATTAT-ATTTATAGT
40360814 A
1 A
40360815 AATTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (21 bp):
ATTATAAATTATATTTATAGT
Found at i:40360851 original size:15 final size:16
Alignment explanation
Indices: 40360823--40360852 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40360813 TAAATTCATA
40360823 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
40360839 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
40360853 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:40360872 original size:18 final size:18
Alignment explanation
Indices: 40360844--40360978 Score: 94
Period size: 18 Copynumber: 8.0 Consensus size: 18
40360834 ATTATTAAGA
40360844 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
40360861 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
*
40360877 A-TTTAA-T-AATAAT-T
1 ATTTTAATTAAATTATAT
* *
40360891 ATTTCAAATTATATTATAT
1 ATTT-TAATTAAATTATAT
* * * *
40360910 AGTATAA-TATATTAT-G
1 ATTTTAATTAAATTATAT
*
40360926 ATTTT-AGTAAATTCATAT
1 ATTTTAATTAAATT-ATAT
40360944 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
*
40360961 ATTTTTATTAAATTATAT
1 ATTTTAATTAAATTATAT
40360979 TTAATAATAA
Statistics
Matches: 94, Mismatches: 12, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
13 2 0.02
14 3 0.03
15 10 0.11
16 15 0.16
17 25 0.27
18 36 0.38
19 3 0.03
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:40361203 original size:44 final size:46
Alignment explanation
Indices: 40361140--40361228 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
40361130 ACCTCTATTA
* * *
40361140 CATTCAATCAAACACAAGAA-TATC-ATTACGCCTCTATTCCATTC
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTC
40361184 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATT
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATT
40361229 ACGCATCTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 18 0.45
45 3 0.08
46 19 0.47
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.29
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTC
Found at i:40361231 original size:16 final size:16
Alignment explanation
Indices: 40361210--40361274 Score: 94
Period size: 16 Copynumber: 4.1 Consensus size: 16
40361200 AGAATTACCT
*
40361210 ATTACGCCTCTATTCC
1 ATTACGCATCTATTCC
40361226 ATTACGCATCTATTCC
1 ATTACGCATCTATTCC
*
40361242 ATTAAGCATCTATTCC
1 ATTACGCATCTATTCC
* *
40361258 ATTACACCTCTATTCC
1 ATTACGCATCTATTCC
40361274 A
1 A
40361275 ATACAGCGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.26, C:0.32, G:0.05, T:0.37
Consensus pattern (16 bp):
ATTACGCATCTATTCC
Found at i:40361380 original size:39 final size:39
Alignment explanation
Indices: 40361298--40361406 Score: 184
Period size: 39 Copynumber: 2.8 Consensus size: 39
40361288 AACGTGCTGT
*
40361298 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
* *
40361336 TAGACTTTAATTTTAGTTTTATTGAGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
40361375 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGT
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGT
40361407 GTAGTAACTA
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
38 25 0.38
39 40 0.62
ACGTcount: A:0.19, C:0.03, G:0.27, T:0.51
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:40362484 original size:16 final size:17
Alignment explanation
Indices: 40362454--40362491 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
40362444 TTAAATTTAA
40362454 TATTAGTTTGCTATTAT
1 TATTAGTTTGCTATTAT
*
40362471 TATTA-TTTGTTATTAT
1 TATTAGTTTGCTATTAT
40362487 TATTA
1 TATTA
40362492 ATCTTGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.63
Consensus pattern (17 bp):
TATTAGTTTGCTATTAT
Found at i:40363819 original size:17 final size:17
Alignment explanation
Indices: 40363797--40363838 Score: 75
Period size: 17 Copynumber: 2.4 Consensus size: 17
40363787 TTCGACATTG
40363797 GGTAATTGGGTTGGGTT
1 GGTAATTGGGTTGGGTT
40363814 GGTAATTGGGTTGGGTT
1 GGTAATTGGGTTGGGTT
40363831 GGATAATT
1 GG-TAATT
40363839 TTATTTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (17 bp):
GGTAATTGGGTTGGGTT
Found at i:40365147 original size:27 final size:27
Alignment explanation
Indices: 40365116--40365171 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
40365106 TAAACTCTGC
40365116 CAGTAAATAACTATTCATATTCTGATT
1 CAGTAAATAACTATTCATATTCTGATT
40365143 CAGTAAATAACTATTCATATTCTGATT
1 CAGTAAATAACTATTCATATTCTGATT
40365170 CA
1 CA
40365172 TTTTAGAGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (27 bp):
CAGTAAATAACTATTCATATTCTGATT
Found at i:40368544 original size:88 final size:87
Alignment explanation
Indices: 40368427--40368628 Score: 262
Period size: 90 Copynumber: 2.3 Consensus size: 87
40368417 AAATTTTTTT
* * * ** *
40368427 AAAAAAGTAATTAAGCTCCTGCTTTTTTTT-CACTCGTTTGGGTACTTGAACTTTTAAAATGCAT
1 AAAAAAGTAATTAAACCCCTACTTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCAT
* *
40368491 CAAAAAGGCCCTCAAACCTTTTCA
66 CAAAAAGACCCTCAAA-C-TTTAA
* * *
40368515 AAAAAAGCAATTAATCCCCTACTTTTTTTTTGCACTTAATTGGGTACTTGAACTTTCAAAATGCA
1 AAAAAAGTAATTAAACCCCTAC-TTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCA
40368580 TCAAAAAGACCCTCAAACTTTAA
65 TCAAAAAGACCCTCAAACTTTAA
*
40368603 AAAAAAATAATTAAACCCCTACTTTT
1 AAAAAAGTAATTAAACCCCTACTTTT
40368629 ATTAAAAATT
Statistics
Matches: 99, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
87 4 0.04
88 41 0.41
89 9 0.09
90 45 0.45
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (87 bp):
AAAAAAGTAATTAAACCCCTACTTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCAT
CAAAAAGACCCTCAAACTTTAA
Found at i:40368800 original size:19 final size:19
Alignment explanation
Indices: 40368704--40368799 Score: 93
Period size: 21 Copynumber: 4.7 Consensus size: 19
40368694 TTCAAATATT
40368704 AAAAATTTATTAAAAATTAGAA
1 AAAAATTTA-TAAAAATT-G-A
* *
40368726 AAAAAATTATAAAAATCATAA
1 AAAAATTTATAAAAAT--TGA
* *
40368747 AAAAATATATAAAAATTGT
1 AAAAATTTATAAAAATTGA
*
40368766 AAAATTTTATAAAAATTGCA
1 AAAAATTTATAAAAATTG-A
40368786 AAAAATTTATAAAA
1 AAAAATTTATAAAA
40368800 TATATAGAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
19 17 0.28
20 13 0.21
21 22 0.36
22 8 0.13
23 1 0.02
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (19 bp):
AAAAATTTATAAAAATTGA
Found at i:40368827 original size:9 final size:9
Alignment explanation
Indices: 40368748--40368834 Score: 52
Period size: 9 Copynumber: 9.3 Consensus size: 9
40368738 AAATCATAAA
*
40368748 AAAATATAT
1 AAAATTTAT
* *
40368757 AAAAATTGT
1 AAAATTTAT
40368766 AAAATTTTAT
1 AAAA-TTTAT
* *
40368776 AAAAATTGCAA
1 -AAAATT-TAT
40368787 AAAATTTAT
1 AAAATTTAT
*
40368796 AAAATATAT
1 AAAATTTAT
*
40368805 AGAAA--TAA
1 A-AAATTTAT
40368813 AAAATTTAT
1 AAAATTTAT
40368822 AAAATTTTAT
1 AAAA-TTTAT
40368832 AAA
1 AAA
40368835 GTCATAAGAA
Statistics
Matches: 59, Mismatches: 12, Indels: 13
0.70 0.14 0.15
Matches are distributed among these distances:
7 3 0.05
8 3 0.05
9 26 0.44
10 22 0.37
11 5 0.08
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (9 bp):
AAAATTTAT
Found at i:40368830 original size:10 final size:10
Alignment explanation
Indices: 40368703--40368834 Score: 78
Period size: 10 Copynumber: 13.4 Consensus size: 10
40368693 ATTCAAATAT
40368703 TAAAAATTTA
1 TAAAAATTTA
*
40368713 TTAAAAATTAGA
1 -TAAAAATT-TA
* *
40368725 AAAAAAATTA
1 TAAAAATTTA
*
40368735 TAAAAATCATA
1 TAAAAAT-TTA
* *
40368746 AAAAAATATA
1 TAAAAATTTA
*
40368756 TAAAAA-TTG
1 TAAAAATTTA
*
40368765 TAAAATTTTA
1 TAAAAATTTA
*
40368775 TAAAAATTGCA
1 TAAAAATT-TA
40368786 -AAAAATTTA
1 TAAAAATTTA
*
40368795 T-AAAATATA
1 TAAAAATTTA
*
40368804 TAGAAA--TA
1 TAAAAATTTA
40368812 -AAAAATTTA
1 TAAAAATTTA
*
40368821 TAAAATTTTA
1 TAAAAATTTA
40368831 TAAA
1 TAAA
40368835 GTCATAAGAA
Statistics
Matches: 92, Mismatches: 20, Indels: 19
0.70 0.15 0.15
Matches are distributed among these distances:
7 4 0.04
8 2 0.02
9 17 0.18
10 45 0.49
11 23 0.25
12 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.33
Consensus pattern (10 bp):
TAAAAATTTA
Found at i:40369110 original size:10 final size:10
Alignment explanation
Indices: 40369097--40369175 Score: 55
Period size: 10 Copynumber: 8.4 Consensus size: 10
40369087 ATAAAAAATT
40369097 ATAATTTTTA
1 ATAATTTTTA
40369107 ATAATTTTT-
1 ATAATTTTTA
40369116 AT-ATTTTT-
1 ATAATTTTTA
*
40369124 ATATTTTATTA
1 ATAATTT-TTA
40369135 A-AA--TTTA
1 ATAATTTTTA
*
40369142 AT-ATTTTTT
1 ATAATTTTTA
*
40369151 ATAATTTTTTT
1 ATAA-TTTTTA
*
40369162 CTAATTTTTA
1 ATAATTTTTA
40369172 ATAA
1 ATAA
40369176 GAGCAGAGGC
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
7 5 0.09
8 9 0.16
9 10 0.18
10 21 0.38
11 10 0.18
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:40369123 original size:8 final size:9
Alignment explanation
Indices: 40369037--40369159 Score: 72
Period size: 9 Copynumber: 13.6 Consensus size: 9
40369027 TCGTTAGGTT
*
40369037 TTTTTATGA
1 TTTTTATAA
40369046 TTTTTATAA
1 TTTTTATAA
* *
40369055 ATTTTACAA
1 TTTTTATAA
*
40369064 TTTTTA-ATT
1 TTTTTATA-A
*
40369073 TTTTTACAA
1 TTTTTATAA
*
40369082 TTGTTATAAA
1 TTTTTAT-AA
***
40369092 AAATTATAA
1 TTTTTATAA
40369101 TTTTTAATAA
1 TTTTT-ATAA
40369111 TTTTTAT-A
1 TTTTTATAA
*
40369119 TTTTTATAT
1 TTTTTATAA
40369128 TTTATTA-AA
1 TTT-TTATAA
* * *
40369137 ATTTAATAT
1 TTTTTATAA
40369146 TTTTTATAA
1 TTTTTATAA
40369155 TTTTT
1 TTTTT
40369160 TTCTAATTTT
Statistics
Matches: 85, Mismatches: 22, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
8 11 0.13
9 55 0.65
10 19 0.22
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:40369126 original size:37 final size:36
Alignment explanation
Indices: 40369037--40369126 Score: 92
Period size: 37 Copynumber: 2.4 Consensus size: 36
40369027 TCGTTAGGTT
** *
40369037 TTTTTATGATTTTTAT-AAATTTTACAATTTTTAATT
1 TTTTTAT-ATTTTTATAAAAAATTACAATTTTTAATA
* * *
40369073 TTTTTACAATTGTTATAAAAAATTATAATTTTTAATAA
1 TTTTTA-TATTTTTATAAAAAATTACAATTTTTAAT-A
40369111 TTTTTATATTTTTATA
1 TTTTTATATTTTTATA
40369127 TTTTATTAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
36 13 0.30
37 24 0.56
38 6 0.14
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (36 bp):
TTTTTATATTTTTATAAAAAATTACAATTTTTAATA
Found at i:40369141 original size:17 final size:17
Alignment explanation
Indices: 40369103--40369157 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
40369093 AATTATAATT
* * *
40369103 TTTAATAATTTTTATAT
1 TTTAATATTTTTTAAAA
*
40369120 TTTTATATTTTATTAAAA
1 TTTAATATTTT-TTAAAA
*
40369138 TTTAATATTTTTTATAA
1 TTTAATATTTTTTAAAA
40369155 TTT
1 TTT
40369158 TTTTCTAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 17 0.55
18 14 0.45
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTAATATTTTTTAAAA
Found at i:40369157 original size:44 final size:47
Alignment explanation
Indices: 40369056--40369159 Score: 117
Period size: 44 Copynumber: 2.3 Consensus size: 47
40369046 TTTTTATAAA
* *
40369056 TTTTACAATTTTTAATTTTTTTACAATTGTTATAAAAAATTATAATT
1 TTTTATAATTTTTAATATTTTTACAATTGTTATAAAAAATTATAATT
* * * *
40369103 TTTAATAATTTTT-ATATTTTTA-TATT-TTATTAAAATTTA-ATATT
1 TTTTATAATTTTTAATATTTTTACAATTGTTATAAAAAATTATA-ATT
40369147 TTTTATAATTTTT
1 TTTTATAATTTTT
40369160 TTCTAATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
43 1 0.02
44 26 0.53
45 3 0.06
46 8 0.16
47 11 0.22
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.62
Consensus pattern (47 bp):
TTTTATAATTTTTAATATTTTTACAATTGTTATAAAAAATTATAATT
Found at i:40369278 original size:89 final size:90
Alignment explanation
Indices: 40369183--40369355 Score: 210
Period size: 90 Copynumber: 1.9 Consensus size: 90
40369173 TAAGAGCAGA
* *
40369183 GGCTTAATTAC-TTTTTTGAAAAA-TGTTAAGGGTCTTTCTGAT-ACATTTTGAAAGTTCAAGTA
1 GGCTTAATTACTTTTTTTGAAAAAGT-TTAAGGGCCTTTCTGATGA-ATTTTGAAAATTCAAGT-
40369245 CCT-AATTGAGTGAAAAAAAAAAGAAGG
63 CCTCAATTGAGTGAAAAAAAAAAGAAGG
* * * * **
40369272 GGCTTAATTGCTTTTTTTGAAGAAGTTTGAGGGCCTTTTTGATGAATTTTGAAAATTCAAGTGTT
1 GGCTTAATTACTTTTTTTGAAAAAGTTTAAGGGCCTTTCTGATGAATTTTGAAAATTCAAGTCCT
*
40369337 CAATTGAGTGCAAAAAAAA
66 CAATTGAGTGAAAAAAAAA
40369356 GGGGCTTAAT
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
89 11 0.15
90 58 0.82
91 2 0.03
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.36
Consensus pattern (90 bp):
GGCTTAATTACTTTTTTTGAAAAAGTTTAAGGGCCTTTCTGATGAATTTTGAAAATTCAAGTCCT
CAATTGAGTGAAAAAAAAAAGAAGG
Found at i:40379176 original size:19 final size:19
Alignment explanation
Indices: 40379152--40379214 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
40379142 TCTAATTAAG
*
40379152 TAATAACTCTATTTCACTT
1 TAATAACTCTATTTAACTT
* * * ***
40379171 TAATAAGTTTATTAAAAAG
1 TAATAACTCTATTTAACTT
*
40379190 TAATAACTCTATTTTACTT
1 TAATAACTCTATTTAACTT
40379209 TAATAA
1 TAATAA
40379215 ACTATTGCTT
Statistics
Matches: 30, Mismatches: 14, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.44
Consensus pattern (19 bp):
TAATAACTCTATTTAACTT
Found at i:40379278 original size:18 final size:17
Alignment explanation
Indices: 40379249--40379283 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
40379239 GTAATGTTTC
*
40379249 AAAAAATGTTTTTAGGA
1 AAAAAATGTTTTAAGGA
40379266 AAAAAATGTTTTTAAGGA
1 AAAAAATG-TTTTAAGGA
40379284 GAAGGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (17 bp):
AAAAAATGTTTTAAGGA
Found at i:40380640 original size:27 final size:27
Alignment explanation
Indices: 40380597--40380686 Score: 128
Period size: 27 Copynumber: 3.3 Consensus size: 27
40380587 TTTTAGTCCT
* *
40380597 GTGCTGCCAATCTCTTTGACACCTTTG
1 GTGCCGCCAATCTCTTTGGCACCTTTG
*
40380624 GT-CAGGCCAATCTCTTTGGCACCTTTG
1 GTGC-CGCCAATCTCTTTGGCACCTTTG
*
40380651 GTGCCGCCAATCACTTTGGCACCTTTG
1 GTGCCGCCAATCTCTTTGGCACCTTTG
40380678 GTGCCGCCA
1 GTGCCGCCA
40380687 CAGGTTTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
26 1 0.02
27 55 0.96
28 1 0.02
ACGTcount: A:0.14, C:0.32, G:0.22, T:0.31
Consensus pattern (27 bp):
GTGCCGCCAATCTCTTTGGCACCTTTG
Found at i:40380707 original size:15 final size:16
Alignment explanation
Indices: 40380687--40380716 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40380677 GGTGCCGCCA
40380687 CAGGTTTTT-TTTTTG
1 CAGGTTTTTGTTTTTG
40380702 CAGGTTTTTGTTTTT
1 CAGGTTTTTGTTTTT
40380717 TTTGGTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.07, C:0.07, G:0.20, T:0.67
Consensus pattern (16 bp):
CAGGTTTTTGTTTTTG
Found at i:40382708 original size:16 final size:17
Alignment explanation
Indices: 40382682--40382715 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
40382672 ACATATGACA
40382682 AAAAAATTATAAAAAAT
1 AAAAAATTATAAAAAAT
40382699 AAAAAA-TATAAAAAAT
1 AAAAAATTATAAAAAAT
40382715 A
1 A
40382716 TTAAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAAATTATAAAAAAT
Found at i:40382731 original size:19 final size:20
Alignment explanation
Indices: 40382709--40382753 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
40382699 AAAAAATATA
40382709 AAAAATATTAAAT-TTTAAT
1 AAAAATATTAAATATTTAAT
*
40382728 AAAAATATTAAATATTTATT
1 AAAAATATTAAATATTTAAT
40382748 AAAAAT
1 AAAAAT
40382754 TAAAAAATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAATATTAAATATTTAAT
Found at i:40382874 original size:9 final size:9
Alignment explanation
Indices: 40382683--40382879 Score: 59
Period size: 9 Copynumber: 21.0 Consensus size: 9
40382673 CATATGACAA
40382683 AAAAATTAT
1 AAAAATTAT
40382692 AAAAA--AT
1 AAAAATTAT
*
40382699 AAAAAATAT
1 AAAAATTAT
*
40382708 AAAAAATATT
1 AAAAATTA-T
**
40382718 AAATTTTAAT
1 AAAAATT-AT
40382728 AAAAA-TATT
1 AAAAATTA-T
*
40382737 AAATATTTATT
1 AAA-AATTA-T
40382748 AAAAATTA-
1 AAAAATTAT
**
40382756 AAAAATCGT
1 AAAAATTAT
*
40382765 AAAATATTGT
1 AAAA-ATTAT
40382775 -AAAATATAT
1 AAAAAT-TAT
* *
40382784 AGAAATATAG
1 AAAAAT-TAT
*
40382794 AAAAAATAT
1 AAAAATTAT
*
40382803 -AAAATTTT
1 AAAAATTAT
*
40382811 ATAAAGTCGTA-
1 A-AAAAT--TAT
40382822 AGAAAATTAT
1 A-AAAATTAT
*
40382832 AAAAAATAT
1 AAAAATTAT
*
40382841 AAAGAAATAT
1 AAA-AATTAT
40382851 -AAAATTCAT
1 AAAAATT-AT
40382860 AAAAAAATTAT
1 --AAAAATTAT
40382871 AAAAATTAT
1 AAAAATTAT
40382880 CTACCAAAAG
Statistics
Matches: 143, Mismatches: 24, Indels: 42
0.68 0.11 0.20
Matches are distributed among these distances:
7 7 0.05
8 18 0.13
9 56 0.39
10 40 0.28
11 15 0.10
12 7 0.05
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:40383080 original size:19 final size:19
Alignment explanation
Indices: 40383058--40383210 Score: 90
Period size: 19 Copynumber: 8.2 Consensus size: 19
40383048 TTTTTATGCA
40383058 TTTT-ATAATTTTTAATAAT
1 TTTTAATAATTTTT-ATAAT
* *
40383077 TTTT-ATAGAATTTTACAAT
1 TTTTAATA-ATTTTTATAAT
* * *
40383096 TTTTTATATTTTTTATGAT
1 TTTTAATAATTTTTATAAT
*
40383115 TTTTAAT--TTTTTTTAA-
1 TTTTAATAATTTTTATAAT
40383131 TTTTAATAAAATTTTTAT-AT
1 TTTTAAT--AATTTTTATAAT
*
40383151 TTTT-AT-ATTTTTATTAAA
1 TTTTAATAATTTTTA-TAAT
* *
40383169 ATTTAATAATTTTTTATAAA
1 TTTTAATAA-TTTTTATAAT
* *
40383189 TTTTATTGA-TTTTATAAT
1 TTTTAATAATTTTTATAAT
40383207 TTTT
1 TTTT
40383211 TTGCCACATG
Statistics
Matches: 106, Mismatches: 16, Indels: 25
0.72 0.11 0.17
Matches are distributed among these distances:
16 14 0.13
17 8 0.08
18 16 0.15
19 33 0.31
20 29 0.27
21 6 0.06
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTAATAATTTTTATAAT
Found at i:40383106 original size:28 final size:29
Alignment explanation
Indices: 40383048--40383211 Score: 155
Period size: 28 Copynumber: 5.9 Consensus size: 29
40383038 TAAATGACAT
* *
40383048 TTTTTAT-GCATTTTATAATTTTTAATAA
1 TTTTTATAGAATTTTATAATTTTTTATAA
* *
40383076 TTTTTATAGAATTTTACAATTTTTTATAT
1 TTTTTATAGAATTTTATAATTTTTTATAA
*
40383105 TTTTTAT-G-ATTTT-TAATTTTTTTTAA
1 TTTTTATAGAATTTTATAATTTTTTATAA
* *
40383131 TTTTAATAAAATTTT-T-ATATTTTTAT-A
1 TTTTTATAGAATTTTATAAT-TTTTTATAA
* *
40383158 TTTTTATTAAAATTTAATAATTTTTTATAA
1 TTTTTA-TAGAATTTTATAATTTTTTATAA
* *
40383188 ATTTTATTG-ATTTTATAATTTTTT
1 TTTTTATAGAATTTTATAATTTTTT
40383212 TGCCACATGT
Statistics
Matches: 112, Mismatches: 16, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
26 16 0.14
27 13 0.12
28 42 0.38
29 33 0.29
30 8 0.07
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (29 bp):
TTTTTATAGAATTTTATAATTTTTTATAA
Found at i:40383107 original size:8 final size:8
Alignment explanation
Indices: 40383096--40383164 Score: 50
Period size: 8 Copynumber: 7.9 Consensus size: 8
40383086 ATTTTACAAT
40383096 TTTTTATA
1 TTTTTATA
40383104 TTTTTTATGA
1 -TTTTTAT-A
40383114 TTTTTA-A
1 TTTTTATA
*
40383121 TTTTTTTTAA
1 -TTTTTAT-A
*
40383131 TTTTAATAAAA
1 TTTT--T-ATA
40383142 TTTTTATA
1 TTTTTATA
40383150 TTTTTATA
1 TTTTTATA
40383158 TTTTTAT
1 TTTTTAT
40383165 TAAAATTTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
7 1 0.02
8 22 0.45
9 18 0.37
10 2 0.04
11 6 0.12
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (8 bp):
TTTTTATA
Found at i:40383161 original size:37 final size:36
Alignment explanation
Indices: 40383105--40383186 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 36
40383095 TTTTTTATAT
* *
40383105 TTTTTATGATTTTTAATTTTT-TTTAATTTTAATAAAA
1 TTTTTAT-ATTTTTAATTTTTATTAAAATTTAAT-AAA
*
40383142 TTTTTATATTTTTATATTTTTATTAAAATTTAATAAT
1 TTTTTATATTTTTA-ATTTTTATTAAAATTTAATAAA
40383179 TTTTTATA
1 TTTTTATA
40383187 AATTTTATTG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
36 7 0.17
37 23 0.57
38 10 0.25
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (36 bp):
TTTTTATATTTTTAATTTTTATTAAAATTTAATAAA
Found at i:40383211 original size:10 final size:9
Alignment explanation
Indices: 40383058--40383210 Score: 98
Period size: 9 Copynumber: 16.4 Consensus size: 9
40383048 TTTTTATGCA
40383058 TTTTATAAT
1 TTTTATAAT
40383067 TTTTAATAAT
1 TTTT-ATAAT
*
40383077 TTTTATAGAA
1 TTTTATA-AT
*
40383087 TTTTACAATT
1 TTTTATAA-T
*
40383097 TTTTATATT
1 TTTTATAAT
*
40383106 TTTTATGAT
1 TTTTATAAT
*
40383115 TTTTA-ATT
1 TTTTATAAT
*
40383123 TTTTTTAAT
1 TTTTATAAT
*
40383132 TTTAATAAAAT
1 TTT--TATAAT
40383143 TTTTAT-AT
1 TTTTATAAT
40383151 TTTTAT-AT
1 TTTTATAAT
*
40383159 TTTTATTAAAA
1 TTTTA-T-AAT
*
40383170 TTTAATAATT
1 TTTTATAA-T
*
40383180 TTTTATAAA
1 TTTTATAAT
*
40383189 TTTTATTGA-
1 TTTTA-TAAT
40383198 TTTTATAAT
1 TTTTATAAT
40383207 TTTT
1 TTTT
40383211 TTGCCACATG
Statistics
Matches: 111, Mismatches: 21, Indels: 24
0.71 0.13 0.15
Matches are distributed among these distances:
8 22 0.20
9 45 0.41
10 32 0.29
11 12 0.11
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:40383479 original size:88 final size:88
Alignment explanation
Indices: 40383285--40383598 Score: 337
Period size: 89 Copynumber: 3.5 Consensus size: 88
40383275 TCAAAGGGGT
** * * *
40383285 TTTTTTAATGCATTTTGGCAGTTTAAGTATC-CAATTAAGTGTAAAAAAAAGTAGGGGCTTAATT
1 TTTTTT-ATGCATTTTGAAAGTTCAAGTA-CACAATTGAGTGTAAAAAAAAGTAGGGGATTAATT
*
40383349 TCTTTTCTTGAAAAAGTTTGAGGGCA
64 ACTTTT-TTGAAAAAGTTTGAGGGCA
* * **
40383375 TTTTTTATGTATTTTGAAAGTTCAAGTACACAATTGAGTGTAAAAAAAAG-GGGGGATTAATGGC
1 TTTTTTATGCATTTTGAAAGTTCAAGTACACAATTGAGTGTAAAAAAAAGTAGGGGATTAATTAC
***
40383439 TTTTTT-TTTAAGTTTGAGGGCA
66 TTTTTTGAAAAAGTTTGAGGGCA
* * * * * *
40383461 TTTTTTTTATGCATTTTGAAATTTTAAGTACACAATTGACTGGAAAAAAAAGTAAGGGTTTAATT
1 --TTTTTTATGCATTTTGAAAGTTCAAGTACACAATTGAGTGTAAAAAAAAGTAGGGGATTAATT
40383526 ACTTTTTATGAAAAAGTTTGAGGGCA
64 ACTTTTT-TGAAAAAGTTTGAGGGCA
* ** * *
40383552 TTTTTGATAAATTTTGAAAGTTCAAGTACTCAATTGAGTGCAAAAAA
1 TTTTTTATGCATTTTGAAAGTTCAAGTACACAATTGAGTGTAAAAAA
40383599 CAAAAACAAA
Statistics
Matches: 185, Mismatches: 33, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
86 13 0.07
87 2 0.01
88 60 0.32
89 90 0.49
90 7 0.04
91 13 0.07
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.39
Consensus pattern (88 bp):
TTTTTTATGCATTTTGAAAGTTCAAGTACACAATTGAGTGTAAAAAAAAGTAGGGGATTAATTAC
TTTTTTGAAAAAGTTTGAGGGCA
Found at i:40384444 original size:16 final size:16
Alignment explanation
Indices: 40384423--40384454 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40384413 ATCACCAAAA
40384423 TATTTTTTCGCTGCGC
1 TATTTTTTCGCTGCGC
40384439 TATTTTTTCGCTGCGC
1 TATTTTTTCGCTGCGC
40384455 CATGGGGCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TATTTTTTCGCTGCGC
Found at i:40386451 original size:13 final size:13
Alignment explanation
Indices: 40386433--40386457 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40386423 AAATTCAATG
40386433 TCAATTTCATATA
1 TCAATTTCATATA
40386446 TCAATTTCATAT
1 TCAATTTCATAT
40386458 CTAAACATGT
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:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (13 bp):
TCAATTTCATATA
Found at i:40387137 original size:7 final size:8
Alignment explanation
Indices: 40387118--40387176 Score: 52
Period size: 8 Copynumber: 7.4 Consensus size: 8
40387108 ATTCCTTAAG
40387118 TCATATAA
1 TCATATAA
40387126 TCATAT-A
1 TCATATAA
*
40387133 TCATAAAA
1 TCATATAA
40387141 TCA-ATCCAA
1 TCATAT--AA
40387150 GTCATATAA
1 -TCATATAA
40387159 TCATAT-A
1 TCATATAA
*
40387166 TCATAAAA
1 TCATATAA
40387174 TCA
1 TCA
40387177 ATCCAAGTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
7 13 0.31
8 20 0.48
9 4 0.10
10 3 0.07
11 2 0.05
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (8 bp):
TCATATAA
Found at i:40387142 original size:15 final size:15
Alignment explanation
Indices: 40387118--40387176 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 15
40387108 ATTCCTTAAG
*
40387118 TCATATAATCATATA
1 TCATAAAATCATATA
40387133 TCATAAAATCA-ATCCAA
1 TCATAAAATCATAT---A
*
40387150 GTCATATAATCATATA
1 -TCATAAAATCATATA
40387166 TCATAAAATCA
1 TCATAAAATCA
40387177 ATCCAAGTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
14 2 0.06
15 20 0.56
16 1 0.03
17 1 0.03
18 10 0.28
19 2 0.06
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (15 bp):
TCATAAAATCATATA
Found at i:40387157 original size:33 final size:33
Alignment explanation
Indices: 40387115--40387190 Score: 152
Period size: 33 Copynumber: 2.3 Consensus size: 33
40387105 TTCATTCCTT
40387115 AAGTCATATAATCATATATCATAAAATCAATCC
1 AAGTCATATAATCATATATCATAAAATCAATCC
40387148 AAGTCATATAATCATATATCATAAAATCAATCC
1 AAGTCATATAATCATATATCATAAAATCAATCC
40387181 AAGTCATATA
1 AAGTCATATA
40387191 GCTAAATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.49, C:0.17, G:0.04, T:0.30
Consensus pattern (33 bp):
AAGTCATATAATCATATATCATAAAATCAATCC
Found at i:40387160 original size:18 final size:18
Alignment explanation
Indices: 40387133--40387188 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
40387123 TAATCATATA
40387133 TCATAAAATCAATCCAAG
1 TCATAAAATCAATCCAAG
*
40387151 TCATATAATC-AT--ATA-
1 TCATAAAATCAATCCA-AG
40387166 TCATAAAATCAATCCAAG
1 TCATAAAATCAATCCAAG
40387184 TCATA
1 TCATA
40387189 TAGCTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
15 10 0.32
16 3 0.10
17 3 0.10
18 15 0.48
ACGTcount: A:0.48, C:0.20, G:0.04, T:0.29
Consensus pattern (18 bp):
TCATAAAATCAATCCAAG
Found at i:40387573 original size:22 final size:22
Alignment explanation
Indices: 40387547--40387637 Score: 105
Period size: 23 Copynumber: 4.0 Consensus size: 22
40387537 TTGAGCAGGT
40387547 AAACGGTAAGCTCTATCA-AGCTG
1 AAACGGTAAGCTC-AT-AGAGCTG
*
40387570 -AACGGTAAGCTCCGTAGAGCTG
1 AAACGGTAAGCT-CATAGAGCTG
*
40387592 AAACAGTAAGCTCATAAGAGCTG
1 AAACGGTAAGCTCAT-AGAGCTG
40387615 AAACGGTAAGCTCATACGAGCTG
1 AAACGGTAAGCTCATA-GAGCTG
40387638 TGGTGAGTCC
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
21 1 0.02
22 20 0.34
23 38 0.64
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (22 bp):
AAACGGTAAGCTCATAGAGCTG
Found at i:40387636 original size:46 final size:45
Alignment explanation
Indices: 40387547--40387637 Score: 114
Period size: 45 Copynumber: 2.0 Consensus size: 45
40387537 TTGAGCAGGT
* * *
40387547 AAACGGTAAGCTCTATCAAGCTGAACGGTAAGCTCCGTAGAGCTG
1 AAACAGTAAGCTCTATAAAGCTGAACGGTAAGCTCCATAGAGCTG
40387592 AAACAGTAAGCTC-ATAAGAGCTGAAACGGTAAGCT-CATACGAGCTG
1 AAACAGTAAGCTCTATAA-AGCTG-AACGGTAAGCTCCATA-GAGCTG
40387638 TGGTGAGTCC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
44 3 0.08
45 20 0.50
46 17 0.43
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (45 bp):
AAACAGTAAGCTCTATAAAGCTGAACGGTAAGCTCCATAGAGCTG
Found at i:40391066 original size:14 final size:12
Alignment explanation
Indices: 40391042--40391075 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
40391032 CAAACTTATA
40391042 AAAAGTATTTTT
1 AAAAGTATTTTT
40391054 CAAAAGTACTTTTT
1 -AAAAGTA-TTTTT
40391068 AAAAGTAT
1 AAAAGTAT
40391076 ACTAAATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 1 0.05
13 14 0.70
14 5 0.25
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (12 bp):
AAAAGTATTTTT
Found at i:40396059 original size:28 final size:28
Alignment explanation
Indices: 40396030--40396100 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 28
40396020 TATAAAAAAT
40396030 AAAATTATTAAAAATGAT-ATAAATTCATA
1 AAAATTA-TAAAAAT-ATAATAAATTCATA
*
40396059 AAAATTATAAAAATATAATAAATT-TTA
1 AAAATTATAAAAATATAATAAATTCATA
40396086 ACAAATTATAAAAAT
1 A-AAATTATAAAAAT
40396101 TACAAAAGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 5 0.13
28 27 0.69
29 7 0.18
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (28 bp):
AAAATTATAAAAATATAATAAATTCATA
Found at i:40396063 original size:10 final size:9
Alignment explanation
Indices: 40396000--40396107 Score: 84
Period size: 10 Copynumber: 12.0 Consensus size: 9
40395990 TTAATTTAAT
40396000 ATTA-AAAA
1 ATTATAAAA
40396008 ATTA-AAAA
1 ATTATAAAA
40396016 TATTTATAAAA
1 -A-TTATAAAA
40396027 A--AT-AAA
1 ATTATAAAA
40396033 ATTATTAAAA
1 ATTA-TAAAA
* *
40396043 ATGATATAA
1 ATTATAAAA
40396052 ATTCATAAAA
1 ATT-ATAAAA
40396062 ATTATAAAA
1 ATTATAAAA
40396071 A-TATAATAA
1 ATTATAA-AA
*
40396080 ATTTTAACAA
1 ATTATAA-AA
40396090 ATTATAAAA
1 ATTATAAAA
*
40396099 ATTACAAAA
1 ATTATAAAA
40396108 GTAACAAAGC
Statistics
Matches: 82, Mismatches: 8, Indels: 19
0.75 0.07 0.17
Matches are distributed among these distances:
6 4 0.05
7 2 0.02
8 14 0.17
9 28 0.34
10 30 0.37
11 4 0.05
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (9 bp):
ATTATAAAA
Found at i:40396072 original size:19 final size:18
Alignment explanation
Indices: 40396000--40396107 Score: 84
Period size: 19 Copynumber: 6.0 Consensus size: 18
40395990 TTAATTTAAT
40396000 ATTA-AAAAATTA-AAAA
1 ATTATAAAAATTATAAAA
40396016 TATTTATAAAAA--AT-AAA
1 -A-TTATAAAAATTATAAAA
* *
40396033 ATTATTAAAAATGATATAA
1 ATTA-TAAAAATTATAAAA
40396052 ATTCATAAAAATTATAAAA
1 ATT-ATAAAAATTATAAAA
*
40396071 A-TATAATAAATTTTAACAA
1 ATTATAA-AAATTATAA-AA
*
40396090 ATTATAAAAATTACAAAA
1 ATTATAAAAATTATAAAA
40396108 GTAACAAAGC
Statistics
Matches: 74, Mismatches: 6, Indels: 21
0.73 0.06 0.21
Matches are distributed among these distances:
15 3 0.04
16 7 0.09
17 9 0.12
18 16 0.22
19 33 0.45
20 6 0.08
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (18 bp):
ATTATAAAAATTATAAAA
Found at i:40396576 original size:10 final size:9
Alignment explanation
Indices: 40396558--40396732 Score: 67
Period size: 10 Copynumber: 18.6 Consensus size: 9
40396548 TTTATGTTTA
40396558 TTTATAATT
1 TTTATAATT
40396567 TTTATAAATT
1 TTTAT-AATT
*
40396577 TATATTAATT
1 TTTA-TAATT
* *
40396587 TTAAT-TTT
1 TTTATAATT
40396595 TTTAATAATTT
1 TTT-ATAA-TT
*
40396606 TTTACAATT
1 TTTATAATT
40396615 TTT-TAAAGTT
1 TTTAT-AA-TT
* * *
40396625 CTAATACGTT
1 TTTATA-ATT
*
40396635 TTT-TTA-T
1 TTTATAATT
40396642 TTTA-AATAT
1 TTTATAAT-T
40396651 TTTATTAA-T
1 TTTA-TAATT
40396660 TTTATAACTT
1 TTTATAA-TT
40396670 TTTATAATT
1 TTTATAATT
* *
40396679 TATTAGATTT
1 T-TTATAATT
40396689 TTTAT-ATT
1 TTTATAATT
40396697 TTTGATAATT
1 TTT-ATAATT
*
40396707 TTTATAGTTTT
1 TTTATA--ATT
40396718 TTTATGAATT
1 TTTAT-AATT
40396728 TTTAT
1 TTTAT
40396733 TTTTAATATT
Statistics
Matches: 122, Mismatches: 22, Indels: 43
0.65 0.12 0.23
Matches are distributed among these distances:
7 5 0.04
8 12 0.10
9 37 0.30
10 51 0.42
11 16 0.13
12 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTATAATT
Found at i:40396677 original size:18 final size:17
Alignment explanation
Indices: 40396640--40396717 Score: 61
Period size: 18 Copynumber: 4.3 Consensus size: 17
40396630 ACGTTTTTTT
40396640 ATTTTA-AATATTTTATTA
1 ATTTTATAAT-TTTTA-TA
40396658 ATTTTATAACTTTTTATA
1 ATTTTATAA-TTTTTATA
40396676 A-TTTATTAGATTTTTTATA
1 ATTTTA-TA-A-TTTTTATA
*
40396695 TTTTTGATAATTTTTATA
1 ATTTT-ATAATTTTTATA
*
40396713 GTTTT
1 ATTTT
40396718 TTTATGAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
17 4 0.08
18 23 0.45
19 17 0.33
20 6 0.12
21 1 0.02
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (17 bp):
ATTTTATAATTTTTATA
Found at i:40396718 original size:29 final size:29
Alignment explanation
Indices: 40396659--40396722 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
40396649 ATTTTATTAA
*
40396659 TTTTATAACTTTTTATAATTTATTAGATT
1 TTTTATAACTTTTGATAATTTATTAGATT
* * *
40396688 TTTTAT-ATTTTTGATAATTTTTATAGTTT
1 TTTTATAACTTTTGATAATTTAT-TAGATT
40396717 TTTTAT
1 TTTTAT
40396723 GAATTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 13 0.43
29 17 0.57
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (29 bp):
TTTTATAACTTTTGATAATTTATTAGATT
Found at i:40396727 original size:21 final size:18
Alignment explanation
Indices: 40396687--40396736 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
40396677 TTTATTAGAT
40396687 TTTTTATATTTTTGATAA
1 TTTTTATATTTTTGATAA
*
40396705 TTTTTATAGTTTTTTTATGAA
1 TTTTTATA--TTTTTGAT-AA
40396726 TTTTTAT-TTTT
1 TTTTTATATTTT
40396737 AATATTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 12 0.43
20 7 0.25
21 9 0.32
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (18 bp):
TTTTTATATTTTTGATAA
Found at i:40396808 original size:24 final size:22
Alignment explanation
Indices: 40396764--40396815 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
40396754 ATATTTTTTG
40396764 ATAATTTTTCTGATACCTTATT
1 ATAATTTTTCTGATACCTTATT
* *
40396786 ATAATTTTTTTGATATCTT-TT
1 ATAATTTTTCTGATACCTTATT
*
40396807 ATGATTTTT
1 ATAATTTTT
40396816 ATAATTAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.62
Consensus pattern (22 bp):
ATAATTTTTCTGATACCTTATT
Found at i:40402625 original size:27 final size:27
Alignment explanation
Indices: 40402571--40402626 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
40402561 CTAGGCCAAA
* * **
40402571 AATTTTAATTAATTATGTAAATGTCCT
1 AATTTTAATAAAATATGTAAATAACCT
40402598 AATTTTAATAAAATATGTAAATAACCT
1 AATTTTAATAAAATATGTAAATAACCT
40402625 AA
1 AA
40402627 AATCTAGAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (27 bp):
AATTTTAATAAAATATGTAAATAACCT
Found at i:40403769 original size:27 final size:27
Alignment explanation
Indices: 40403730--40403782 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
40403720 AAATCAAAAA
40403730 AATTAAAAGGACATTTTTAA-AGAAAG
1 AATTAAAAGGACATTTTTAATAGAAAG
*
40403756 AATTATAATGGACATTTTTAATAGAAA
1 AATTA-AAAGGACATTTTTAATAGAAA
40403783 TAAAAAAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 5 0.21
27 14 0.58
28 5 0.21
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.32
Consensus pattern (27 bp):
AATTAAAAGGACATTTTTAATAGAAAG
Found at i:40404331 original size:7 final size:7
Alignment explanation
Indices: 40404321--40404365 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
40404311 TTTTAAAATA
40404321 CATTTCC
1 CATTTCC
*
40404328 CATTAACC
1 CATT-TCC
40404336 CATTTCCC
1 CATTT-CC
40404344 CATTTCC
1 CATTTCC
*
40404351 CATTCCC
1 CATTTCC
40404358 CATTTCC
1 CATTTCC
40404365 C
1 C
40404366 CTCTTCCACG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 19 0.59
8 13 0.41
ACGTcount: A:0.18, C:0.47, G:0.00, T:0.36
Consensus pattern (7 bp):
CATTTCC
Found at i:40404345 original size:8 final size:8
Alignment explanation
Indices: 40404321--40404366 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
40404311 TTTTAAAATA
40404321 CATTT-CC
1 CATTTCCC
**
40404328 CATTAACC
1 CATTTCCC
40404336 CATTTCCC
1 CATTTCCC
40404344 CATTT-CC
1 CATTTCCC
40404351 CA-TTCCC
1 CATTTCCC
40404358 CATTTCCC
1 CATTTCCC
40404366 C
1 C
40404367 TCTTCCACGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
6 2 0.06
7 12 0.36
8 19 0.58
ACGTcount: A:0.17, C:0.48, G:0.00, T:0.35
Consensus pattern (8 bp):
CATTTCCC
Found at i:40404372 original size:22 final size:23
Alignment explanation
Indices: 40404321--40404366 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
40404311 TTTTAAAATA
40404321 CATTTCCCATTAACCCATTTCCC
1 CATTTCCCATTAACCCATTTCCC
*
40404344 CATTTCCCATT-CCCCATTTCCC
1 CATTTCCCATTAACCCATTTCCC
40404366 C
1 C
40404367 TCTTCCACGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.17, C:0.48, G:0.00, T:0.35
Consensus pattern (23 bp):
CATTTCCCATTAACCCATTTCCC
Found at i:40406879 original size:18 final size:18
Alignment explanation
Indices: 40406850--40406895 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
40406840 TCTACAAATT
*
40406850 CACCATAAAAAAGAATGTA
1 CACCA-AAAAAAAAATGTA
40406869 CACCAAAAAAAAAATGTA
1 CACCAAAAAAAAAATGTA
40406887 CACCAAAAA
1 CACCAAAAA
40406896 TACCGTGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.63, C:0.20, G:0.07, T:0.11
Consensus pattern (18 bp):
CACCAAAAAAAAAATGTA
Found at i:40407106 original size:22 final size:23
Alignment explanation
Indices: 40407061--40407124 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
40407051 TAAAAAACAC
* *
40407061 ATTTTAAAAAAAAAATTTAAATTT
1 ATTTTTAAAAAAAAA-GTAAATTT
*
40407085 -TTTTTAAAAAAAAAGTAGATTT
1 ATTTTTAAAAAAAAAGTAAATTT
40407107 ATTTTATAAAAATAAAAG
1 ATTTT-TAAAAA-AAAAG
40407125 CCTTGAAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 6 0.18
23 17 0.50
24 6 0.18
25 5 0.15
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (23 bp):
ATTTTTAAAAAAAAAGTAAATTT
Found at i:40412641 original size:56 final size:56
Alignment explanation
Indices: 40412560--40412672 Score: 145
Period size: 56 Copynumber: 2.0 Consensus size: 56
40412550 GATTGAGACA
* * **
40412560 AATTTGATGAGGCTTTATTTATTTCTTTGTTTAGGATGGAGTTGACCCTTGATTAT
1 AATTTGATGAGACTTTATTTATTTCTTTCTTTAGGATGGAGTCAACCCTTGATTAT
* * * * *
40412616 AATTTGATGAGATTTTGTTTCTTTCTTTCTTTAGGATTGAGTCAATCCTTGATTAT
1 AATTTGATGAGACTTTATTTATTTCTTTCTTTAGGATGGAGTCAACCCTTGATTAT
40412672 A
1 A
40412673 GGGATTCTTC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.22, C:0.10, G:0.19, T:0.50
Consensus pattern (56 bp):
AATTTGATGAGACTTTATTTATTTCTTTCTTTAGGATGGAGTCAACCCTTGATTAT
Found at i:40413610 original size:56 final size:56
Alignment explanation
Indices: 40413529--40413641 Score: 145
Period size: 56 Copynumber: 2.0 Consensus size: 56
40413519 GATTGAGACA
* * **
40413529 AATTTGATGAGGCTTTATTTATTTCTTTGTTTAGGATGGAGTTGACCCTTGATTAT
1 AATTTGATGAGACTTTATTTATTTCTTTCTTTAGGATGGAGTCAACCCTTGATTAT
* * * * *
40413585 AATTTGATGAGATTTTGTTTCTTTCTTTCTTTAGGATTGAGTCAATCCTTGATTAT
1 AATTTGATGAGACTTTATTTATTTCTTTCTTTAGGATGGAGTCAACCCTTGATTAT
40413641 A
1 A
40413642 GGGATTCTTC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.22, C:0.10, G:0.19, T:0.50
Consensus pattern (56 bp):
AATTTGATGAGACTTTATTTATTTCTTTCTTTAGGATGGAGTCAACCCTTGATTAT
Found at i:40413683 original size:969 final size:969
Alignment explanation
Indices: 40411801--40413743 Score: 3877
Period size: 969 Copynumber: 2.0 Consensus size: 969
40411791 GACTACTCCC
*
40411801 ATTGAACAAAATCTTAAGTTATATTACTATTAAGGTGAATCTCCAACTGACAAAGTAAGATATCA
1 ATTGTACAAAATCTTAAGTTATATTACTATTAAGGTGAATCTCCAACTGACAAAGTAAGATATCA
40411866 AAAACTTGTGGGAAAATTTATTTATTTATCTCACACTAGACCTGATATTGCTTATGTAGTAAATG
66 AAAACTTGTGGGAAAATTTATTTATTTATCTCACACTAGACCTGATATTGCTTATGTAGTAAATG
40411931 TGATGAGTCAATTTATGCATGATCCTCGAAAGTCACATATGGAGGCTGTTGAACGCATATTGAAT
131 TGATGAGTCAATTTATGCATGATCCTCGAAAGTCACATATGGAGGCTGTTGAACGCATATTGAAT
40411996 TATTTAAAAGATGCTCCAAGAAAAGATTAATTTTTAAGAAACATGATCATCTAATAATAGAGGGT
196 TATTTAAAAGATGCTCCAAGAAAAGATTAATTTTTAAGAAACATGATCATCTAATAATAGAGGGT
40412061 TATAGTGATGCAGATTGGGCACGATCAGCTGATGATAGAAGGTCGACTTCAGGTTATTTCACTTT
261 TATAGTGATGCAGATTGGGCACGATCAGCTGATGATAGAAGGTCGACTTCAGGTTATTTCACTTT
40412126 CGTTGGAGGAAACCTTATAACTTGGAGAAGTAAGAAAGAACCAATCGTTGCAAGGTTAAGTGCAG
326 CGTTGGAGGAAACCTTATAACTTGGAGAAGTAAGAAAGAACCAATCGTTGCAAGGTTAAGTGCAG
40412191 AGGCAAAATACAGAGGCATGGTTTTTGGAGTATGTGAATTGTTGTGGTTGAAGAAATTGCTTGAA
391 AGGCAAAATACAGAGGCATGGTTTTTGGAGTATGTGAATTGTTGTGGTTGAAGAAATTGCTTGAA
40412256 GAATTAGACATTAATCTTCAAGGGTCAATGAACCTATATTGTGATAATACTTCGGCGATTGAGAT
456 GAATTAGACATTAATCTTCAAGGGTCAATGAACCTATATTGTGATAATACTTCGGCGATTGAGAT
40412321 TGCTTGCAACCTAGTTCAATATAATTGTACAAAGAATATAGAAGTTGATAGACACTTTATAAAAG
521 TGCTTGCAACCTAGTTCAATATAATTGTACAAAGAATATAGAAGTTGATAGACACTTTATAAAAG
40412386 AAAAACTTGAAGCTGAAACCATTTCATTGCCTTTGTTAAGTACGAAGATCAACTCGCTGACATAC
586 AAAAACTTGAAGCTGAAACCATTTCATTGCCTTTGTTAAGTACGAAGATCAACTCGCTGACATAC
40412451 TTACCAAGGCTGTTTCTAGCAATGATAAAGCTTTATACAAGTTAGGCATGTATGATATCCATGCC
651 TTACCAAGGCTGTTTCTAGCAATGATAAAGCTTTATACAAGTTAGGCATGTATGATATCCATGCC
40412516 CAACTTGAGGGGGAATGATAAAAATCAATGAGTTGATTGAGACAAATTTGATGAGGCTTTATTTA
716 CAACTTGAGGGGGAATGATAAAAATCAATGAGTTGATTGAGACAAATTTGATGAGGCTTTATTTA
40412581 TTTCTTTGTTTAGGATGGAGTTGACCCTTGATTATAATTTGATGAGATTTTGTTTCTTTCTTTCT
781 TTTCTTTGTTTAGGATGGAGTTGACCCTTGATTATAATTTGATGAGATTTTGTTTCTTTCTTTCT
40412646 TTAGGATTGAGTCAATCCTTGATTATAGGGATTCTTCAACTATTTCCTTGAAAAACTTCATGTGT
846 TTAGGATTGAGTCAATCCTTGATTATAGGGATTCTTCAACTATTTCCTTGAAAAACTTCATGTGT
40412711 TGTAGGTTATATATACTATTAACTCTTCTATTTTTGAAATATATAAAAATTCTTTCATA
911 TGTAGGTTATATATACTATTAACTCTTCTATTTTTGAAATATATAAAAATTCTTTCATA
40412770 ATTGTACAAAATCTTAAGTTATATTACTATTAAGGTGAATCTCCAACTGACAAAGTAAGATATCA
1 ATTGTACAAAATCTTAAGTTATATTACTATTAAGGTGAATCTCCAACTGACAAAGTAAGATATCA
40412835 AAAACTTGTGGGAAAATTTATTTATTTATCTCACACTAGACCTGATATTGCTTATGTAGTAAATG
66 AAAACTTGTGGGAAAATTTATTTATTTATCTCACACTAGACCTGATATTGCTTATGTAGTAAATG
40412900 TGATGAGTCAATTTATGCATGATCCTCGAAAGTCACATATGGAGGCTGTTGAACGCATATTGAAT
131 TGATGAGTCAATTTATGCATGATCCTCGAAAGTCACATATGGAGGCTGTTGAACGCATATTGAAT
40412965 TATTTAAAAGATGCTCCAAGAAAAGATTAATTTTTAAGAAACATGATCATCTAATAATAGAGGGT
196 TATTTAAAAGATGCTCCAAGAAAAGATTAATTTTTAAGAAACATGATCATCTAATAATAGAGGGT
40413030 TATAGTGATGCAGATTGGGCACGATCAGCTGATGATAGAAGGTCGACTTCAGGTTATTTCACTTT
261 TATAGTGATGCAGATTGGGCACGATCAGCTGATGATAGAAGGTCGACTTCAGGTTATTTCACTTT
40413095 CGTTGGAGGAAACCTTATAACTTGGAGAAGTAAGAAAGAACCAATCGTTGCAAGGTTAAGTGCAG
326 CGTTGGAGGAAACCTTATAACTTGGAGAAGTAAGAAAGAACCAATCGTTGCAAGGTTAAGTGCAG
40413160 AGGCAAAATACAGAGGCATGGTTTTTGGAGTATGTGAATTGTTGTGGTTGAAGAAATTGCTTGAA
391 AGGCAAAATACAGAGGCATGGTTTTTGGAGTATGTGAATTGTTGTGGTTGAAGAAATTGCTTGAA
40413225 GAATTAGACATTAATCTTCAAGGGTCAATGAACCTATATTGTGATAATACTTCGGCGATTGAGAT
456 GAATTAGACATTAATCTTCAAGGGTCAATGAACCTATATTGTGATAATACTTCGGCGATTGAGAT
40413290 TGCTTGCAACCTAGTTCAATATAATTGTACAAAGAATATAGAAGTTGATAGACACTTTATAAAAG
521 TGCTTGCAACCTAGTTCAATATAATTGTACAAAGAATATAGAAGTTGATAGACACTTTATAAAAG
40413355 AAAAACTTGAAGCTGAAACCATTTCATTGCCTTTGTTAAGTACGAAGATCAACTCGCTGACATAC
586 AAAAACTTGAAGCTGAAACCATTTCATTGCCTTTGTTAAGTACGAAGATCAACTCGCTGACATAC
40413420 TTACCAAGGCTGTTTCTAGCAATGATAAAGCTTTATACAAGTTAGGCATGTATGATATCCATGCC
651 TTACCAAGGCTGTTTCTAGCAATGATAAAGCTTTATACAAGTTAGGCATGTATGATATCCATGCC
40413485 CAACTTGAGGGGGAATGATAAAAATCAATGAGTTGATTGAGACAAATTTGATGAGGCTTTATTTA
716 CAACTTGAGGGGGAATGATAAAAATCAATGAGTTGATTGAGACAAATTTGATGAGGCTTTATTTA
40413550 TTTCTTTGTTTAGGATGGAGTTGACCCTTGATTATAATTTGATGAGATTTTGTTTCTTTCTTTCT
781 TTTCTTTGTTTAGGATGGAGTTGACCCTTGATTATAATTTGATGAGATTTTGTTTCTTTCTTTCT
40413615 TTAGGATTGAGTCAATCCTTGATTATAGGGATTCTTCAACTATTTCCTTGAAAAACTTCATGTGT
846 TTAGGATTGAGTCAATCCTTGATTATAGGGATTCTTCAACTATTTCCTTGAAAAACTTCATGTGT
40413680 TGTAGGTTATATATACTATTAACTCTTCTATTTTTGAAATATATAAAAATTCTTTCATA
911 TGTAGGTTATATATACTATTAACTCTTCTATTTTTGAAATATATAAAAATTCTTTCATA
40413739 ATTGT
1 ATTGT
40413744 GTATTTTTAC
Statistics
Matches: 973, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
969 973 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (969 bp):
ATTGTACAAAATCTTAAGTTATATTACTATTAAGGTGAATCTCCAACTGACAAAGTAAGATATCA
AAAACTTGTGGGAAAATTTATTTATTTATCTCACACTAGACCTGATATTGCTTATGTAGTAAATG
TGATGAGTCAATTTATGCATGATCCTCGAAAGTCACATATGGAGGCTGTTGAACGCATATTGAAT
TATTTAAAAGATGCTCCAAGAAAAGATTAATTTTTAAGAAACATGATCATCTAATAATAGAGGGT
TATAGTGATGCAGATTGGGCACGATCAGCTGATGATAGAAGGTCGACTTCAGGTTATTTCACTTT
CGTTGGAGGAAACCTTATAACTTGGAGAAGTAAGAAAGAACCAATCGTTGCAAGGTTAAGTGCAG
AGGCAAAATACAGAGGCATGGTTTTTGGAGTATGTGAATTGTTGTGGTTGAAGAAATTGCTTGAA
GAATTAGACATTAATCTTCAAGGGTCAATGAACCTATATTGTGATAATACTTCGGCGATTGAGAT
TGCTTGCAACCTAGTTCAATATAATTGTACAAAGAATATAGAAGTTGATAGACACTTTATAAAAG
AAAAACTTGAAGCTGAAACCATTTCATTGCCTTTGTTAAGTACGAAGATCAACTCGCTGACATAC
TTACCAAGGCTGTTTCTAGCAATGATAAAGCTTTATACAAGTTAGGCATGTATGATATCCATGCC
CAACTTGAGGGGGAATGATAAAAATCAATGAGTTGATTGAGACAAATTTGATGAGGCTTTATTTA
TTTCTTTGTTTAGGATGGAGTTGACCCTTGATTATAATTTGATGAGATTTTGTTTCTTTCTTTCT
TTAGGATTGAGTCAATCCTTGATTATAGGGATTCTTCAACTATTTCCTTGAAAAACTTCATGTGT
TGTAGGTTATATATACTATTAACTCTTCTATTTTTGAAATATATAAAAATTCTTTCATA
Found at i:40413841 original size:16 final size:16
Alignment explanation
Indices: 40413822--40413852 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40413812 AATTTTCTAA
40413822 AATTTTAAAAAGTTAG
1 AATTTTAAAAAGTTAG
*
40413838 AATTTTCAAAAGTTA
1 AATTTTAAAAAGTTA
40413853 ATTAAAAAAT
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:0.03, G:0.10, T:0.39
Consensus pattern (16 bp):
AATTTTAAAAAGTTAG
Found at i:40414035 original size:25 final size:27
Alignment explanation
Indices: 40413996--40414064 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 27
40413986 AAAAATTGGA
* *
40413996 AAAAAAGTATA-AAAATTTAAATT-TT
1 AAAAAACTATATAAAATTTAAATTATC
* *
40414021 AAAAAA-TATTTAAAATATAAATTATC
1 AAAAAACTATATAAAATTTAAATTATC
40414047 AAAAAACTATATAAAATT
1 AAAAAACTATATAAAATT
40414065 ATGAAAAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 3 0.08
25 17 0.47
26 7 0.19
27 9 0.25
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.33
Consensus pattern (27 bp):
AAAAAACTATATAAAATTTAAATTATC
Found at i:40423038 original size:24 final size:24
Alignment explanation
Indices: 40423011--40423062 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
40423001 TTAGTAAGTC
*
40423011 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
40423035 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
40423059 AAAT
1 AAAT
40423063 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:40425004 original size:24 final size:24
Alignment explanation
Indices: 40424977--40425028 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
40424967 TTAGTAAGTC
*
40424977 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
40425001 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
40425025 AAAT
1 AAAT
40425029 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:40432631 original size:24 final size:25
Alignment explanation
Indices: 40432584--40432745 Score: 83
Period size: 26 Copynumber: 6.6 Consensus size: 25
40432574 AAGCTCATGC
40432584 GAGCCA-ATAACGGGTAA-CTCCGAA
1 GAGCCATATAACGGG-AAGCTCCGAA
* *
40432608 GAGCTAT-TAACGGGAAGCTTCGAA
1 GAGCCATATAACGGGAAGCTCCGAA
* * *
40432632 TAGCCATATATCGGGAAG-TTC-AA
1 GAGCCATATAACGGGAAGCTCCGAA
*
40432655 GCGAGCCATAT--CGGGAAGCT-CTATA
1 --GAGCCATATAACGGGAAGCTCCGA-A
* *
40432680 GAGCCAT-TAATCAGGAAGCTCACAAA
1 GAGCCATATAA-CGGGAAGCTC-CGAA
* * *
40432706 GAGCC-TTTAATCGAGAAGCTCACAAA
1 GAGCCATATAA-CGGGAAGCTC-CGAA
40432732 GAGCCATATAACGG
1 GAGCCATATAACGG
40432746 AACGCTCATA
Statistics
Matches: 111, Mismatches: 12, Indels: 28
0.74 0.08 0.19
Matches are distributed among these distances:
22 1 0.01
23 19 0.17
24 28 0.25
25 27 0.24
26 30 0.27
27 6 0.05
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.19
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCCGAA
Found at i:40432752 original size:26 final size:25
Alignment explanation
Indices: 40432679--40432753 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 25
40432669 GAAGCTCTAT
40432679 AGAGCCATTAATCAGGAAGCTCACAA
1 AGAGCCATTAATC-GGAAGCTCACAA
*
40432705 AGAGCCTTTAATCGAGAAGCTCACAA
1 AGAGCCATTAATCG-GAAGCTCACAA
40432731 AGAGCCATATAA-CGGAACGCTCA
1 AGAGCCAT-TAATCGGAA-GCTCA
40432754 TAAGGGCTGT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.09
26 37 0.84
27 3 0.07
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (25 bp):
AGAGCCATTAATCGGAAGCTCACAA
Found at i:40437308 original size:5 final size:5
Alignment explanation
Indices: 40437279--40437317 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
40437269 TAACTTTAGC
* *
40437279 TCAAT TTAAT ACAAT TCATAT TCAAT TCAAT TCAAT TCA
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCA
40437318 CGTCCTAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
TCAAT
Found at i:40439499 original size:7 final size:7
Alignment explanation
Indices: 40439477--40439520 Score: 70
Period size: 7 Copynumber: 6.0 Consensus size: 7
40439467 TAAGAATATC
40439477 AAAAAACG
1 AAAAAA-G
40439485 ACAAAAAG
1 A-AAAAAG
40439493 AAAAAAG
1 AAAAAAG
40439500 AAAAAAG
1 AAAAAAG
40439507 AAAAAAG
1 AAAAAAG
40439514 AAAAAAG
1 AAAAAAG
40439521 GAAGAGTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
7 27 0.77
8 3 0.09
9 5 0.14
ACGTcount: A:0.82, C:0.05, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:40441593 original size:22 final size:22
Alignment explanation
Indices: 40441565--40441609 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
40441555 TTAACTTGTT
40441565 AACTGAGTTCGAGTAAATGAGA
1 AACTGAGTTCGAGTAAATGAGA
40441587 AACTGAGTTCGAGTAAATGAGA
1 AACTGAGTTCGAGTAAATGAGA
40441609 A
1 A
40441610 TTGTGCTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.27, T:0.22
Consensus pattern (22 bp):
AACTGAGTTCGAGTAAATGAGA
Found at i:40450869 original size:13 final size:13
Alignment explanation
Indices: 40450847--40450879 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
40450837 CTGGGATAAT
40450847 TCCC-TTTTTTTC
1 TCCCTTTTTTTTC
*
40450859 TCCCTTTTTTTTT
1 TCCCTTTTTTTTC
40450872 TCCCTTTT
1 TCCCTTTT
40450880 CTATTGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (13 bp):
TCCCTTTTTTTTC
Found at i:40451654 original size:49 final size:48
Alignment explanation
Indices: 40451597--40451690 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 48
40451587 AGAGTTATGG
*
40451597 AAGGTAAAATAATAAAATTGCT-TCTAGACGCATGGGAGGAGGCTTACGA
1 AAGGTAAAATAATAAAATTGCTCT-TAGACGCACGGG-GGAGGCTTACGA
* **
40451646 AAGGTAAAATACTAACCTTGCTCTTAGACGCACGGGGGAGGCTTA
1 AAGGTAAAATAATAAAATTGCTCTTAGACGCACGGGGGAGGCTTA
40451691 TGGAAGGCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
48 9 0.22
49 30 0.75
50 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (48 bp):
AAGGTAAAATAATAAAATTGCTCTTAGACGCACGGGGGAGGCTTACGA
Found at i:40452393 original size:23 final size:23
Alignment explanation
Indices: 40452363--40452413 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
40452353 ACTTAATAGC
*
40452363 GATCATATAACC-AGAACGAAATA
1 GATCATAT-ACCTAGAACGAAACA
*
40452386 GATCATATACCTAGAACGATACA
1 GATCATATACCTAGAACGAAACA
40452409 GATCA
1 GATCA
40452414 AAATATCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.47, C:0.20, G:0.14, T:0.20
Consensus pattern (23 bp):
GATCATATACCTAGAACGAAACA
Found at i:40454358 original size:25 final size:25
Alignment explanation
Indices: 40454330--40454387 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
40454320 ATAGGAAGTT
*
40454330 CAAATGAGCC-ATATCAGGAAGCTCA
1 CAAA-GAGCCTATATCAAGAAGCTCA
*
40454355 CAAAGAGCCTATATCAAGACGCTCA
1 CAAAGAGCCTATATCAAGAAGCTCA
*
40454380 TAAAGAGC
1 CAAAGAGC
40454388 TGCCGTATGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 5 0.17
25 24 0.83
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (25 bp):
CAAAGAGCCTATATCAAGAAGCTCA
Found at i:40456285 original size:12 final size:12
Alignment explanation
Indices: 40456268--40456310 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
40456258 TTGAAGAACT
40456268 AATAAATAAATG
1 AATAAATAAATG
*
40456280 AATAAATAAAATA
1 AATAAAT-AAATG
40456293 AATAAACT-AATG
1 AATAAA-TAAATG
40456305 AATAAA
1 AATAAA
40456311 ACAATTTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 16 0.59
13 10 0.37
14 1 0.04
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (12 bp):
AATAAATAAATG
Found at i:40456292 original size:21 final size:21
Alignment explanation
Indices: 40456268--40456311 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
40456258 TTGAAGAACT
40456268 AATAAATAAA-TGAATAAATAA
1 AATAAATAAACT-AATAAATAA
*
40456289 AATAAATAAACTAATGAATAA
1 AATAAATAAACTAATAAATAA
40456310 AA
1 AA
40456312 CAATTTACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (21 bp):
AATAAATAAACTAATAAATAA
Found at i:40458037 original size:143 final size:142
Alignment explanation
Indices: 40457776--40458566 Score: 1106
Period size: 143 Copynumber: 5.5 Consensus size: 142
40457766 TCCGACCCGT
* *
40457776 TGCAACTTCAGAGAGATAAGGCTGGTGGCTTTAATCTGCTCCACTGCAACTTCAAGAAGATAAGA
1 TGCAACTTCAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGA
40457841 -TCGGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCT
66 TTC-GCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCT
40457905 TCAGTCTGCTCAGC
130 TCAGTCTGCTC-GC
* *
40457919 TGTAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCA-GAGAGATAAG
1 TGCAACTTCAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGA-AGATAAG
* * *
40457983 ATTCGCCATAATTTGTAGCTTTAATCCGTTCCACTGCAACGCCATGGAAATAAGATTCCCTGTCT
65 ATTCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCT
*
40458048 TCAGTCTACTTCGC
130 TCAGTCTGC-TCGC
*
40458062 TGCAACTTCTAG-GAGATAAGGCTGATGGCTTCAAT-TGCTCCACTGCAACTTCAGGAAGATAAG
1 TGCAACTTC-AGAGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAG
* * * * *
40458125 ATCCGCCATAACTTGCAGCTTTAATCTTGTTCCACTGCAATGCTAGGGAAATAAGATTCGCTGTC
65 ATTCGCCATAATTTGTAGCTTTAATC-TGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTC
*
40458190 TTCAGTCTACTCCGC
129 TTCAGTCTGCT-CGC
* * * * *
40458205 TGTAAGTTCAGGGAGATAAGGCTGGTTGCTTCAATCTGCTCCACTGTAACTTCAGGAAGATAAGA
1 TGCAACTTCAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGA
* * * * * **
40458270 TCCGCTATAACTTGTAGTTTTAATCTGTTCCACTGTAACGTTAGGGAAATAAGATTCGCTGTCTT
66 TTCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCTT
40458335 CAGTCTGCTCTGC
131 CAGTCTGCTC-GC
* * *
40458348 TGCAACTTCAGAGAGATAAAGTTGGTGGCTTCAATCTGCTCCACTGCAACTTCAAGAAGATAAGA
1 TGCAACTTCAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGA
* * * *
40458413 TTCGTCATAATTTGTAGCTTTAAT-TCGTTCCACTACAACGCCATGGAAATAAGATTTGCTGTCT
66 TTCGCCATAATTTGTAGCTTTAATCT-GTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCT
40458477 TCAGTCTGCTCGGC
130 TCAGTCTGCTC-GC
** * *
40458491 TGCAACTTCAGAGAGATAAGGCCAGTGGCTTCAATTTGCTTCACTGCAACTTCAGGAAGATAAGA
1 TGCAACTTCAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGA
*
40458556 TTTGCCATAAT
66 TTCGCCATAAT
40458567 GACTTCAATC
Statistics
Matches: 579, Mismatches: 58, Indels: 22
0.88 0.09 0.03
Matches are distributed among these distances:
142 55 0.09
143 468 0.81
144 56 0.10
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (142 bp):
TGCAACTTCAGAGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGA
TTCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCTT
CAGTCTGCTCGC
Found at i:40460358 original size:45 final size:45
Alignment explanation
Indices: 40460294--40460386 Score: 159
Period size: 45 Copynumber: 2.1 Consensus size: 45
40460284 ACAGATACTT
* *
40460294 GGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCC
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCC
*
40460339 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTTC
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCC
40460384 GGT
1 GGT
40460387 TCACATAGTA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (45 bp):
GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCC
Found at i:40460450 original size:51 final size:50
Alignment explanation
Indices: 40460383--40460578 Score: 223
Period size: 51 Copynumber: 3.9 Consensus size: 50
40460373 CAATGATGTT
* * * *
40460383 CGGTTCACATAGTAGCCTGCACATATTACTACACATGTGACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATC
* * * *
40460434 CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATC
* * * * * *
40460485 CGGCACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TC
*
40460535 CGGTACACGTAGTAGCCTGCACATAGTACTATACACGTGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
40460579 CACTTTCACT
Statistics
Matches: 118, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
49 2 0.02
50 39 0.33
51 75 0.64
52 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCATC
Found at i:40460571 original size:101 final size:101
Alignment explanation
Indices: 40460390--40460574 Score: 300
Period size: 101 Copynumber: 1.8 Consensus size: 101
40460380 GTTCGGTTCA
* *
40460390 CATAGTAGCCTGCACATATTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTGCA
40460455 CATAGTACTACACACGTGATCGAAACTATCCGGCACG
65 CATAGTACTACACACGTGATCGAAACTATCCGGCACG
* *
40460492 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCTGCA
*
40460556 CATAGTACTATACACGTGA
65 CATAGTACTACACACGTGA
40460575 CCATCACTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
100 4 0.05
101 40 0.52
102 33 0.43
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCCGGCACG
Found at i:40462836 original size:22 final size:22
Alignment explanation
Indices: 40462793--40462833 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
40462783 TGGTAGAGGT
40462793 TTTTGTTATTTTATTTTTTTTG
1 TTTTGTTATTTTATTTTTTTTG
40462815 TTTTG-T-TTTTATTTTTTTT
1 TTTTGTTATTTTATTTTTTTT
40462834 TTGCCTCCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.68
21 1 0.05
22 5 0.26
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.85
Consensus pattern (22 bp):
TTTTGTTATTTTATTTTTTTTG
Found at i:40467646 original size:20 final size:19
Alignment explanation
Indices: 40467621--40467668 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
40467611 GTAATAAATT
40467621 ATATAAATAATA-ATAGTAAA
1 ATATAAATAATACATA--AAA
*
40467641 ATATAAA-AGTACATAAAA
1 ATATAAATAATACATAAAA
40467659 ATATAAATAA
1 ATATAAATAA
40467669 ATGAACTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 10 0.42
19 4 0.17
20 10 0.42
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (19 bp):
ATATAAATAATACATAAAA
Found at i:40473678 original size:12 final size:12
Alignment explanation
Indices: 40473661--40473693 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
40473651 ACCATTTAAA
40473661 TACTAGGCCTTT
1 TACTAGGCCTTT
40473673 TACTAGGCCTTT
1 TACTAGGCCTTT
40473685 TACTAGGCC
1 TACTAGGCC
40473694 CGGGCCCGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.36
Consensus pattern (12 bp):
TACTAGGCCTTT
Found at i:40473833 original size:16 final size:16
Alignment explanation
Indices: 40473796--40473835 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
40473786 TCAATAAAAT
* *
40473796 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
40473812 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
40473828 TAAAATTA
1 TAAAATTA
40473836 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:40473914 original size:59 final size:61
Alignment explanation
Indices: 40473845--40474024 Score: 265
Period size: 68 Copynumber: 2.9 Consensus size: 61
40473835 ATCAAATTAT
*
40473845 TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC--A--A
40473910 TTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC-A
1 -TAA-T-TATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
*
40473973 -AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
40474025 ACAAACTTGA
Statistics
Matches: 110, Mismatches: 2, Indels: 11
0.89 0.02 0.09
Matches are distributed among these distances:
59 48 0.44
60 1 0.01
61 2 0.02
63 1 0.01
66 3 0.03
67 1 0.01
68 54 0.49
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (61 bp):
TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
Found at i:40473941 original size:9 final size:9
Alignment explanation
Indices: 40473908--40473935 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
40473898 TTTATCAAAT
40473908 TATTAATTG
1 TATTAATTG
40473917 TATTAATTG
1 TATTAATTG
40473926 TATTAATTG
1 TATTAATTG
40473935 T
1 T
40473936 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:40473945 original size:68 final size:68
Alignment explanation
Indices: 40473824--40473994 Score: 319
Period size: 68 Copynumber: 2.5 Consensus size: 68
40473814 AAATTAATTG
*
40473824 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
40473887 TGA
66 TGA
40473890 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
40473955 TGA
66 TGA
40473958 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
40473995 TGTAACAAAA
Statistics
Matches: 102, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
66 26 0.25
68 76 0.75
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:40474120 original size:24 final size:23
Alignment explanation
Indices: 40474091--40474135 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
40474081 AAATAAACTT
*
40474091 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAAATA-TATATTTTA
40474115 AAAATAAAAAAATATATATTT
1 AAAATAAAAAAATATATATTT
40474136 AATATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAATAAAAAAATATATATTTTA
Found at i:40480284 original size:14 final size:14
Alignment explanation
Indices: 40480267--40480317 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
40480257 AATAATAATC
40480267 AAATTTATTTAGTT
1 AAATTTATTTAGTT
*
40480281 AAATTTAATTA-TT
1 AAATTTATTTAGTT
40480294 AATCAATTTATTTAGTT
1 -A--AATTTATTTAGTT
40480311 AAATTTA
1 AAATTTA
40480318 ATTATTAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 2 0.06
14 17 0.55
16 10 0.32
17 2 0.06
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (14 bp):
AAATTTATTTAGTT
Found at i:40480304 original size:30 final size:30
Alignment explanation
Indices: 40480262--40480332 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
40480252 CAAATAATAA
40480262 TAATCAAATTTATTTAGTTAAATTTAATTAT
1 TAATC-AATTTATTTAGTTAAATTTAATTAT
40480293 TAATCAATTTATTTAGTTAAATTTAATTAT
1 TAATCAATTTATTTAGTTAAATTTAATTAT
40480323 TAATC-ATTTA
1 TAATCAATTTA
40480333 CTATAAGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 5 0.12
30 30 0.75
31 5 0.12
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (30 bp):
TAATCAATTTATTTAGTTAAATTTAATTAT
Found at i:40483938 original size:13 final size:13
Alignment explanation
Indices: 40483920--40483944 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40483910 TACGCATTTC
40483920 TTTTATTTTATTA
1 TTTTATTTTATTA
40483933 TTTTATTTTATT
1 TTTTATTTTATT
40483945 TCTAGATTTT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATTTTATTA
Found at i:40487327 original size:17 final size:17
Alignment explanation
Indices: 40487305--40487340 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
40487295 ACTAAAGAAC
40487305 AAGAAAGGAAAATAATT
1 AAGAAAGGAAAATAATT
40487322 AAGAAAGGAAAATAATT
1 AAGAAAGGAAAATAATT
40487339 AA
1 AA
40487341 AGTAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (17 bp):
AAGAAAGGAAAATAATT
Found at i:40489813 original size:23 final size:24
Alignment explanation
Indices: 40489785--40489829 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
40489775 GTAAAGTATT
*
40489785 AAAATAAAAACTAT-TATATTTTA
1 AAAATAAAAAATATATATATTTTA
40489808 AAAATAAAAAATATATATATTT
1 AAAATAAAAAATATATATATTT
40489830 AATATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
AAAATAAAAAATATATATATTTTA
Found at i:40490094 original size:27 final size:28
Alignment explanation
Indices: 40490043--40490096 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
40490033 ACATGAATTT
* *
40490043 TTTCATAAATTTTGTCATGCTAAATAAA
1 TTTCATAAAATTTATCATGCTAAATAAA
40490071 TTTCATAAAATTTAT-ATGCTAAATAA
1 TTTCATAAAATTTATCATGCTAAATAA
40490097 CATAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (28 bp):
TTTCATAAAATTTATCATGCTAAATAAA
Found at i:40490254 original size:10 final size:11
Alignment explanation
Indices: 40490213--40490288 Score: 63
Period size: 10 Copynumber: 7.1 Consensus size: 11
40490203 TTCCTCCCCT
40490213 CTTCTTC-TT-
1 CTTCTTCTTTC
*
40490222 CTTCTTTTTTTC
1 CTTC-TTCTTTC
*
40490234 TCTTCTCCTTTC
1 -CTTCTTCTTTC
40490246 CTT-TTCTTTC
1 CTTCTTCTTTC
40490256 CTTCTT-TTTC
1 CTTCTTCTTTC
*
40490266 TTTCTTTCTTT-
1 CTTC-TTCTTTC
40490277 CTTCTTCTTTC
1 CTTCTTCTTTC
40490288 C
1 C
40490289 CTCTCCTTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
9 4 0.08
10 24 0.45
11 13 0.25
12 8 0.15
13 4 0.08
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (11 bp):
CTTCTTCTTTC
Found at i:40490269 original size:18 final size:18
Alignment explanation
Indices: 40490216--40490287 Score: 72
Period size: 18 Copynumber: 3.8 Consensus size: 18
40490206 CTCCCCTCTT
*
40490216 CTTCTTCTTCTTTTTTTC
1 CTTCTTCTTCTTTCTTTC
*
40490234 TCTTCTCCTTTCCTTTTCTTTC
1 -CTTCTTC-TT-C-TTTCTTTC
*
40490256 CTTCTTTTTCTTTCTTTC
1 CTTCTTCTTCTTTCTTTC
*
40490274 TTTCTTCTTCTTTC
1 CTTCTTCTTCTTTC
40490288 CCTCTCCTTC
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
18 20 0.45
19 7 0.16
20 4 0.09
21 6 0.14
22 7 0.16
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (18 bp):
CTTCTTCTTCTTTCTTTC
Found at i:40490287 original size:14 final size:14
Alignment explanation
Indices: 40490217--40490287 Score: 60
Period size: 14 Copynumber: 5.2 Consensus size: 14
40490207 TCCCCTCTTC
*
40490217 TTCTTCTTCTTTTT
1 TTCTTCTTCTTTCT
*
40490231 TTC-TCTTC-TCCT
1 TTCTTCTTCTTTCT
*
40490243 TTCCTT-TTCTTTCC
1 TT-CTTCTTCTTTCT
*
40490257 TTCTTTTTCTTTCT
1 TTCTTCTTCTTTCT
40490271 TTCTTTCTTC-TTCT
1 TTC-TTCTTCTTTCT
40490285 TTC
1 TTC
40490288 CCTCTCCTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
12 4 0.09
13 12 0.26
14 25 0.54
15 5 0.11
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
TTCTTCTTCTTTCT
Found at i:40490287 original size:32 final size:32
Alignment explanation
Indices: 40490185--40490288 Score: 90
Period size: 32 Copynumber: 3.2 Consensus size: 32
40490175 AAATTACCTT
* * * * **
40490185 TTCTTTCTTTCTTTTTCCTTCCTCCCCTCTTC
1 TTCTTTCCTTCTTTTTCTTTCTTTCTTTCTTC
40490217 TTC-TT-CTTCTTTTT-TTCTCTTCTCCTTTCCTT-
1 TTCTTTCCTTCTTTTTCTT-TCTT-T-CTTT-CTTC
40490249 TTCTTTCCTTCTTTTTCTTTCTTTCTTTCTTC
1 TTCTTTCCTTCTTTTTCTTTCTTTCTTTCTTC
40490281 TTCTTTCC
1 TTCTTTCC
40490289 CTCTCCTTCT
Statistics
Matches: 58, Mismatches: 6, Indels: 16
0.73 0.08 0.20
Matches are distributed among these distances:
29 1 0.02
30 11 0.19
31 5 0.09
32 20 0.34
33 6 0.10
34 13 0.22
35 2 0.03
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (32 bp):
TTCTTTCCTTCTTTTTCTTTCTTTCTTTCTTC
Found at i:40491305 original size:17 final size:17
Alignment explanation
Indices: 40491279--40491312 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
40491269 TAATTTATCA
40491279 AAATTAATTATTTTAAAT
1 AAATTAATTA-TTTAAAT
40491297 AAATT-ATTATTTAAAT
1 AAATTAATTATTTAAAT
40491313 TTGAAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTAATTATTTAAAT
Found at i:40492258 original size:22 final size:22
Alignment explanation
Indices: 40492230--40492280 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
40492220 CTCTCTAATC
*
40492230 CTCTCAATTTCCTTCTAAAATT
1 CTCTCAATTTCCTTCCAAAATT
40492252 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
40492274 CTCTCAA
1 CTCTCAA
40492281 ACTCATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.41
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:40492364 original size:29 final size:31
Alignment explanation
Indices: 40492324--40492388 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 31
40492314 CTCTCAATCC
*
40492324 ATTTTTTTAAAATAATTAT-AA-TTTTTTAT
1 ATTTTTTAAAAATAATTATAAATTTTTTTAT
*
40492353 ATTTTTTAAAAATAATTTTAAATTTTTTTAT
1 ATTTTTTAAAAATAATTATAAATTTTTTTAT
40492384 ATTTT
1 ATTTT
40492389 CATCAATGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 17 0.53
30 2 0.06
31 13 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (31 bp):
ATTTTTTAAAAATAATTATAAATTTTTTTAT
Found at i:40492820 original size:73 final size:73
Alignment explanation
Indices: 40492701--40492846 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
40492691 GTTGATCGAG
40492701 AGGTGGAGACCCGAGACGCACACATTTCATCTTCCATGTGGAGAGTGCACTATCACTCTAGAAGA
1 AGGTGGAGACCCGAGACGCACACATTTCATCTTCCATGTGGAGAGTGCACTATCACTCTAGAAGA
40492766 TGTCAGCA
66 TGTCAGCA
*
40492774 AGGTGGAGACCCGAGACTCACACATTTCATCTTCCATGTGGAGAGTGCACTATCACTCTAGAAGA
1 AGGTGGAGACCCGAGACGCACACATTTCATCTTCCATGTGGAGAGTGCACTATCACTCTAGAAGA
40492839 TGTCAGCA
66 TGTCAGCA
40492847 TGCATTTGGG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.23
Consensus pattern (73 bp):
AGGTGGAGACCCGAGACGCACACATTTCATCTTCCATGTGGAGAGTGCACTATCACTCTAGAAGA
TGTCAGCA
Found at i:40493542 original size:7 final size:7
Alignment explanation
Indices: 40493530--40493554 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40493520 AGTTGATTGA
40493530 TATTTAG
1 TATTTAG
40493537 TATTTAG
1 TATTTAG
40493544 TATTTAG
1 TATTTAG
40493551 TATT
1 TATT
40493555 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:40494531 original size:24 final size:24
Alignment explanation
Indices: 40494498--40494553 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
40494488 ATGCGGAACC
*
40494498 GGAAGAACCACAACCACCACCGAA
1 GGAAGAACCACAACCACCACCAAA
* *
40494522 GGAAGGACCACAATCACCACCAAA
1 GGAAGAACCACAACCACCACCAAA
40494546 GGAAGAAC
1 GGAAGAAC
40494554 AATCGCCGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.46, C:0.32, G:0.20, T:0.02
Consensus pattern (24 bp):
GGAAGAACCACAACCACCACCAAA
Found at i:40494824 original size:28 final size:28
Alignment explanation
Indices: 40494790--40495675 Score: 1115
Period size: 28 Copynumber: 30.4 Consensus size: 28
40494780 TAACCTAACC
*
40494790 CTAACCTAAATTAATTAAAAAACCTAAT
1 CTAACCTAAATTAATTAAAAACCCTAAT
*
40494818 CTAACCTAAATTAACTAAAAACCCTAACCT
1 CTAACCTAAATTAATTAAAAACCCTAA--T
*
40494848 AACCCTAACCTAAATTAACTAAAAACCCTAAT
1 ----CTAACCTAAATTAATTAAAAACCCTAAT
40494880 CTAACCTAAATTAATTAAAAACCCTAAT
1 CTAACCTAAATTAATTAAAAACCCTAAT
*
40494908 CTAACCTAAATTAACTAAAAACCCTAACCT
1 CTAACCTAAATTAATTAAAAACCCTAA--T
* *
40494938 AACCCTAACCTAAATTAACTAAAAACTCTAATCTAACC
1 ----CTAACCTAAATTAATTAAAAAC-C----CTAA-T
* *
40494976 CTAACCTAAATTAACTAAAAATCCTAAT
1 CTAACCTAAATTAATTAAAAACCCTAAT
40495004 CTAACCTAAATTAATTAAAAACCCTAAT
1 CTAACCTAAATTAATTAAAAACCCTAAT
* *
40495032 CTAACCTAATTTAATTTAAAACCCTAAT
1 CTAACCTAAATTAATTAAAAACCCTAAT
* *
40495060 CTAACCTAAATTAATTTAAAACCCTAACC
1 CTAACCTAAATTAATTAAAAACCCTAA-T
* **
40495089 CTAACTTAAATTAATTAAAAAATCTAAT
1 CTAACCTAAATTAATTAAAAACCCTAAT
*
40495117 CTAACCTAAATTAACTAAAAACCCTAAT
1 CTAACCTAAATTAATTAAAAACCCTAAT
* *
40495145 CTAACCTAAATTAATTAAAAACTCTAAC
1 CTAACCTAAATTAATTAAAAACCCTAAT
* *
40495173 CTAACCTAAATTAACTAAAAACCTTAAT
1 CTAACCTAAATTAATTAAAAACCCTAAT
* *
40495201 CTAACCTAAATTAATTTAAAACCCTAACC
1 CTAACCTAAATTAATTAAAAACCCTAA-T
*
40495230 CTAACCTAAATTAATTAAAAAACCTAAT
1 CTAACCTAAATTAATTAAAAACCCTAAT
*
40495258 CTAACCTAAATTAACTAAAAACCCTAACCT
1 CTAACCTAAATTAATTAAAAACCCTAA--T
*
40495288 AACCCTAACCTAAATTAACTAAAAACCCTAAT
1 ----CTAACCTAAATTAATTAAAAACCCTAAT
*
40495320 CTAACCTAAATTAATTAAAAACCCTAAC
1 CTAACCTAAATTAATTAAAAACCCTAAT
*
40495348 CTAACCTAAATTAACTAAAAACCCTAAT
1 CTAACCTAAATTAATTAAAAACCCTAAT
*
40495376 CTAACCTAAATTAATTAAAAACCCTAAC
1 CTAACCTAAATTAATTAAAAACCCTAAT
*
40495404 CTAACCTAAATTAACTAAAAACCCTAAT
1 CTAACCTAAATTAATTAAAAACCCTAAT
*
40495432 CTAACCTAAATTAATTTAAAACCCTAAT
1 CTAACCTAAATTAATTAAAAACCCTAAT
*
40495460 CTAACCTAAATTAATTTAAAACCCTAAT
1 CTAACCTAAATTAATTAAAAACCCTAAT
* * *
40495488 CTAACCTAAATTAATTTAAAACCTTAACC
1 CTAACCTAAATTAATTAAAAACCCTAA-T
*
40495517 CTAACCTAAATTAATTAAAAAACCTAAT
1 CTAACCTAAATTAATTAAAAACCCTAAT
*
40495545 CTAACCTAAATTAACTAAAAACCCTAACCT
1 CTAACCTAAATTAATTAAAAACCCTAA--T
40495575 AACCCTAACCTAAATTAATTAAAAACCCTAAT
1 ----CTAACCTAAATTAATTAAAAACCCTAAT
*
40495607 CTAACCTAAATTAATTAAAAACCCTAAAC
1 CTAACCTAAATTAATTAAAAACCCT-AAT
* *
40495636 CTAACCTAAATTAATTAAAAACCCAAAA
1 CTAACCTAAATTAATTAAAAACCCTAAT
40495664 CTAACCTAAATT
1 CTAACCTAAATT
40495676 TTTTTGGCTT
Statistics
Matches: 765, Mismatches: 60, Indels: 66
0.86 0.07 0.07
Matches are distributed among these distances:
28 526 0.69
29 102 0.13
30 4 0.01
32 3 0.00
33 1 0.00
34 123 0.16
35 1 0.00
38 1 0.00
39 4 0.01
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (28 bp):
CTAACCTAAATTAATTAAAAACCCTAAT
Done.