Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 109 of 221
Found at i:33450578 original size:87 final size:87
Alignment explanation
Indices: 33450342--33450605 Score: 339
Period size: 87 Copynumber: 3.0 Consensus size: 87
33450332 GACTATCGAC
*
33450342 TATGAAAAGGGATGGTGACGACCATCAAATATGAAAAGGGATAGTTTCGACTATCGACTATGAAA
1 TATGAAAAGGGATGGTGATGACCATCAAATATGAAAAGGGATAGTTTCGACTATCGACTATGAAA
*
33450407 AGGGATGGTAACGACCATCAAA
66 AGGGATGGTGACGACCATCAAA
* * ** * * *
33450429 TATGAATAGGGATGGTGATGACCATCAAATATGAAAAGGGATGGTGACGACCAGCAACTATGAAA
1 TATGAAAAGGGATGGTGATGACCATCAAATATGAAAAGGGATAGTTTCGACTATCGACTATGAAA
* *
33450494 AGGGATGGTGACGATCATTAAA
66 AGGGATGGTGACGACCATCAAA
* ** * * * * **
33450516 TATGAAAAGGGATAGTTTTGACTATCAATTATGAAAAGGGATAGTTTTGACTATTGGTTATGAAA
1 TATGAAAAGGGATGGTGATGACCATCAAATATGAAAAGGGATAGTTTCGACTATCGACTATGAAA
*
33450581 GGGGATGGTGACGACCATCAAA
66 AGGGATGGTGACGACCATCAAA
33450603 TAT
1 TAT
33450606 AAATGCACTA
Statistics
Matches: 147, Mismatches: 30, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
87 147 1.00
ACGTcount: A:0.38, C:0.11, G:0.27, T:0.24
Consensus pattern (87 bp):
TATGAAAAGGGATGGTGATGACCATCAAATATGAAAAGGGATAGTTTCGACTATCGACTATGAAA
AGGGATGGTGACGACCATCAAA
Found at i:33452381 original size:20 final size:20
Alignment explanation
Indices: 33452358--33452396 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
33452348 TTCTTTCTTC
33452358 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
33452378 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
33452397 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:33452748 original size:49 final size:50
Alignment explanation
Indices: 33452672--33452791 Score: 116
Period size: 49 Copynumber: 2.4 Consensus size: 50
33452662 CCAGATATGG
* ** * ** *
33452672 TCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCTAAACATGA
1 TCTTACAGGGGAACTCTCATATCGGTGCCAACACCATGTCCCAAACATGA
* * * *
33452722 TCTTAC-GGGGAACTCTCATCTTGGTGCCAACACCATGTCCCAGACATGG
1 TCTTACAGGGGAACTCTCATATCGGTGCCAACACCATGTCCCAAACATGA
* *
33452771 TCTTACATGGGACCTCTCATA
1 TCTTACAGGGGAACTCTCATA
33452792 ACCTCAATAA
Statistics
Matches: 55, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
49 38 0.69
50 17 0.31
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (50 bp):
TCTTACAGGGGAACTCTCATATCGGTGCCAACACCATGTCCCAAACATGA
Found at i:33453216 original size:30 final size:30
Alignment explanation
Indices: 33453180--33453238 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
33453170 TCCTTGACTC
33453180 AAACTTTGGCATAATTACAATTTTGCCCCT
1 AAACTTTGGCATAATTACAATTTTGCCCCT
* * * *
33453210 AAACTTTTGCATATTTACACTTTTTCCCC
1 AAACTTTGGCATAATTACAATTTTGCCCC
33453239 AAATCTCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.27, C:0.25, G:0.07, T:0.41
Consensus pattern (30 bp):
AAACTTTGGCATAATTACAATTTTGCCCCT
Found at i:33461846 original size:129 final size:130
Alignment explanation
Indices: 33461677--33461938 Score: 456
Period size: 129 Copynumber: 2.0 Consensus size: 130
33461667 TTTGTGATCG
*
33461677 AGGTAAGTTTGTATGTTTAAATAGTGTTTTAATGTATTTGAGCTAAATGTTATTACGTTAATTAT
1 AGGTAAGATTGTATGTTTAAATAGTGTTTTAATGTATTTGAGCTAAATGTTATTACGTTAATTAT
* *
33461742 CATATGATGCTTCAACAGAAAAATCCAATGACGTTACGA-TGACTATCGAGCCCCATTTGAACCT
66 CATATGATGCTCCAACAGAAAAATCCAATGACGTTACAACT-ACTATCGAGCCCCATTTGAACCT
33461806 T
130 T
*
33461807 AGGTAAGATTGTATGTTT-AATAGTGTTTTAATGTGTTTGAGCTAAATGTTATTACGTTAATTAT
1 AGGTAAGATTGTATGTTTAAATAGTGTTTTAATGTATTTGAGCTAAATGTTATTACGTTAATTAT
*
33461871 CATATGATGCTCCAACAGAAAAATCCAATGATGTTACAACTACTATCGAGCCCCATTTGAACCTT
66 CATATGATGCTCCAACAGAAAAATCCAATGACGTTACAACTACTATCGAGCCCCATTTGAACCTT
33461936 AGG
1 AGG
33461939 AATATATAGG
Statistics
Matches: 126, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
129 108 0.86
130 18 0.14
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.36
Consensus pattern (130 bp):
AGGTAAGATTGTATGTTTAAATAGTGTTTTAATGTATTTGAGCTAAATGTTATTACGTTAATTAT
CATATGATGCTCCAACAGAAAAATCCAATGACGTTACAACTACTATCGAGCCCCATTTGAACCTT
Found at i:33475052 original size:14 final size:14
Alignment explanation
Indices: 33475033--33475059 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
33475023 TTGAGTTGAA
33475033 TCGAGTTAAATTAT
1 TCGAGTTAAATTAT
33475047 TCGAGTTAAATTA
1 TCGAGTTAAATTA
33475060 AAAAATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (14 bp):
TCGAGTTAAATTAT
Found at i:33475552 original size:23 final size:23
Alignment explanation
Indices: 33475502--33475552 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
33475492 CTCAACTCGA
*
33475502 AACTCGAATTACTTATTCAAGTT
1 AACTCGAATAACTTATTCAAGTT
* *
33475525 GACTCGAATAACTTAATTCGA-TT
1 AACTCGAATAACTT-ATTCAAGTT
33475548 AACTC
1 AACTC
33475553 AAAATTCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (23 bp):
AACTCGAATAACTTATTCAAGTT
Found at i:33483171 original size:96 final size:96
Alignment explanation
Indices: 33483054--33483237 Score: 233
Period size: 96 Copynumber: 1.9 Consensus size: 96
33483044 ATGTCATTAG
* * * * * *
33483054 GGTTACCATGTTTCAGGTGCTGGCCCTAAATGTCTTACCAATGGTTGAGTTCTGACATTTGTTGC
1 GGTTACCATGTTTCAGGTGCTGGCCCTAAATGTCCTACCAATGGCTAAGGTCCGACATTAGTTGC
* *
33483119 AAATACTCGTCAGCTTGTGTGAGCAGACCTA
66 AAATACTCATCAGCTTGTATGAGCAGACCTA
* * * ** *
33483150 GGTTACCATGTTTCGGGTGCTGGTCCTGAATGTCCTACTGATGGCTAAGGTCCGGCATTAGTTGC
1 GGTTACCATGTTTCAGGTGCTGGCCCTAAATGTCCTACCAATGGCTAAGGTCCGACATTAGTTGC
*
33483215 AAATACTTATCAGCTTGTATGAG
66 AAATACTCATCAGCTTGTATGAG
33483238 TAGCATTGTG
Statistics
Matches: 73, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
96 73 1.00
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (96 bp):
GGTTACCATGTTTCAGGTGCTGGCCCTAAATGTCCTACCAATGGCTAAGGTCCGACATTAGTTGC
AAATACTCATCAGCTTGTATGAGCAGACCTA
Found at i:33496837 original size:19 final size:20
Alignment explanation
Indices: 33496799--33496838 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
33496789 AAACAAGCTT
*
33496799 ATTGAGCTGGAAATGAGCTGA
1 ATTGAGCT-GAAACGAGCTGA
33496820 ATTGAGCT-AAACGAGCTGA
1 ATTGAGCTGAAACGAGCTGA
33496839 GATTAAGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.35, C:0.12, G:0.30, T:0.23
Consensus pattern (20 bp):
ATTGAGCTGAAACGAGCTGA
Found at i:33505937 original size:18 final size:18
Alignment explanation
Indices: 33505916--33505950 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33505906 TAAAAAATTA
33505916 TAAAAAACATAAAAAACG
1 TAAAAAACATAAAAAACG
* *
33505934 TAAAAAAGATGAAAAAC
1 TAAAAAACATAAAAAAC
33505951 AAAAAGAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.09, G:0.09, T:0.11
Consensus pattern (18 bp):
TAAAAAACATAAAAAACG
Found at i:33520610 original size:20 final size:20
Alignment explanation
Indices: 33520587--33520633 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33520577 GGGTTAAGAT
*
33520587 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
33520607 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
33520627 TGAGCTG
1 TGAGCTG
33520634 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:33521824 original size:48 final size:48
Alignment explanation
Indices: 33521769--33521874 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
33521759 TTGTCTTTTC
*
33521769 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
33521817 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
33521865 TTTCTTTTTC
1 TTTCTTTTTC
33521875 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:33524474 original size:20 final size:20
Alignment explanation
Indices: 33524451--33524497 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33524441 GGGTTAAGAT
*
33524451 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
33524471 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
33524491 TGAGCTG
1 TGAGCTG
33524498 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:33525688 original size:48 final size:48
Alignment explanation
Indices: 33525633--33525738 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
33525623 TTGTCTTTTC
*
33525633 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
33525681 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
33525729 TTTCTTTTTC
1 TTTCTTTTTC
33525739 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:33528183 original size:20 final size:20
Alignment explanation
Indices: 33528160--33528206 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33528150 GGGTTAAGAT
*
33528160 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
33528180 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
33528200 TGAGCTG
1 TGAGCTG
33528207 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:33528416 original size:18 final size:18
Alignment explanation
Indices: 33528395--33528429 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33528385 TATTCTTTTT
33528395 GTTTTTCATCTTTTTTAC
1 GTTTTTCATCTTTTTTAC
* *
33528413 GTTTTTTATGTTTTTTA
1 GTTTTTCATCTTTTTTA
33528430 TAATTTTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.09, G:0.09, T:0.71
Consensus pattern (18 bp):
GTTTTTCATCTTTTTTAC
Found at i:33531160 original size:13 final size:14
Alignment explanation
Indices: 33531142--33531170 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
33531132 AAAATTGCTT
33531142 AAAAATCAAG-CAA
1 AAAAATCAAGTCAA
33531155 AAAAATCAAGTCAA
1 AAAAATCAAGTCAA
33531169 AA
1 AA
33531171 GCCACTAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.69, C:0.14, G:0.07, T:0.10
Consensus pattern (14 bp):
AAAAATCAAGTCAA
Found at i:33531530 original size:20 final size:21
Alignment explanation
Indices: 33531486--33531532 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
33531476 TTAGCTTGGT
* *
33531486 TCAGCTCACATAAGTTTTAAT
1 TCAGCTCACATAAGTCTTAAC
*
33531507 TCAGCTCACATGAG-CTTAAC
1 TCAGCTCACATAAGTCTTAAC
33531527 TCAGCT
1 TCAGCT
33531533 TGTTTGAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.32
Consensus pattern (21 bp):
TCAGCTCACATAAGTCTTAAC
Found at i:33532966 original size:39 final size:39
Alignment explanation
Indices: 33532912--33532989 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
33532902 TGTTTCTATC
*
33532912 CTTAGCCGAGCCATCACCAATCCTATCC-CTAAAACACTT
1 CTTAGCCGAACCATCACCAATCCTATCCTC-AAAACACTT
* *
33532951 CTTAGCCGAACCATCACCTATCCTATTCTCAAAACACTT
1 CTTAGCCGAACCATCACCAATCCTATCCTCAAAACACTT
33532990 TGCAAACCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 34 0.97
40 1 0.03
ACGTcount: A:0.31, C:0.37, G:0.06, T:0.26
Consensus pattern (39 bp):
CTTAGCCGAACCATCACCAATCCTATCCTCAAAACACTT
Found at i:33545197 original size:23 final size:22
Alignment explanation
Indices: 33545145--33545197 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
33545135 TCCACGTCTT
*
33545145 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
33545167 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
33545190 TTTCTTTT
1 TTTCTTTT
33545198 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:33548143 original size:23 final size:22
Alignment explanation
Indices: 33548108--33548154 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
33548098 AGAAGTGAGC
*
33548108 AAAAAAAGAAAAAAAAAGTAAA
1 AAAAAAACAAAAAAAAAGTAAA
*
33548130 AAAAAGAACAAAAAAAAAGTTAA
1 AAAAA-AACAAAAAAAAAGTAAA
33548153 AA
1 AA
33548155 GTCTTGTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.83, C:0.02, G:0.09, T:0.06
Consensus pattern (22 bp):
AAAAAAACAAAAAAAAAGTAAA
Found at i:33548154 original size:10 final size:10
Alignment explanation
Indices: 33548108--33548145 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
33548098 AGAAGTGAGC
33548108 AAAAAAAGAA
1 AAAAAAAGAA
*
33548118 AAAAAAAGTA
1 AAAAAAAGAA
33548128 AAAAAAAGAA
1 AAAAAAAGAA
33548138 CAAAAAAA
1 -AAAAAAA
33548146 AAGTTAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.87, C:0.03, G:0.08, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:33551015 original size:20 final size:20
Alignment explanation
Indices: 33550969--33551015 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
33550959 AGCTCGTTTC
*
33550969 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
33550989 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
33551009 CAGCTCA
1 CAGCTCA
33551016 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:33554617 original size:21 final size:23
Alignment explanation
Indices: 33554572--33554618 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
33554562 TCACCTGCAA
* *
33554572 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
33554595 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
33554616 TAA
1 TAA
33554619 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:33556747 original size:46 final size:46
Alignment explanation
Indices: 33556695--33556783 Score: 153
Period size: 46 Copynumber: 1.9 Consensus size: 46
33556685 ATAGTGTGGC
*
33556695 GTTCATCATATACCAAGGTTCTTATCA-TCATTGATAGTGGGTCAAG
1 GTTCATCATATACCAAGGTTCCTATCATTC-TTGATAGTGGGTCAAG
33556741 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTC
1 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTC
33556784 GAGTGATGTG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
46 39 0.95
47 2 0.05
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (46 bp):
GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCAAG
Found at i:33559334 original size:11 final size:12
Alignment explanation
Indices: 33559317--33559363 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
33559307 TAGTTTCTCG
33559317 AAAAAAAAACTC
1 AAAAAAAAACTC
*
33559329 AAAAAAAAAATTC
1 -AAAAAAAAACTC
*
33559342 -AAAAAAAATTC
1 AAAAAAAAACTC
*
33559353 GAAAAAAAACT
1 AAAAAAAAACT
33559364 AGTTTCATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
11 11 0.35
12 9 0.29
13 11 0.35
ACGTcount: A:0.74, C:0.11, G:0.02, T:0.13
Consensus pattern (12 bp):
AAAAAAAAACTC
Found at i:33559358 original size:13 final size:13
Alignment explanation
Indices: 33559314--33559361 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
33559304 TAGTAGTTTC
*
33559314 TCGAAAAAAAAAC
1 TCGAAAAAAAAAT
*
33559327 TCAAAAAAAAAAT
1 TCGAAAAAAAAAT
33559340 TC--AAAAAAAAT
1 TCGAAAAAAAAAT
33559351 TCGAAAAAAAA
1 TCGAAAAAAAA
33559362 CTAGTTTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 11 0.35
13 20 0.65
ACGTcount: A:0.73, C:0.10, G:0.04, T:0.12
Consensus pattern (13 bp):
TCGAAAAAAAAAT
Found at i:33559420 original size:13 final size:13
Alignment explanation
Indices: 33559402--33559446 Score: 83
Period size: 13 Copynumber: 3.5 Consensus size: 13
33559392 ATCAAGTTGT
33559402 AAAAAAATT-TGA
1 AAAAAAATTGTGA
33559414 AAAAAAATTGTGA
1 AAAAAAATTGTGA
33559427 AAAAAAATTGTGA
1 AAAAAAATTGTGA
33559440 AAAAAAA
1 AAAAAAA
33559447 GAGAGCTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 9 0.28
13 23 0.72
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.20
Consensus pattern (13 bp):
AAAAAAATTGTGA
Found at i:33565062 original size:11 final size:11
Alignment explanation
Indices: 33565046--33565082 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 11
33565036 AAAGGAAACC
33565046 AATTTTTTTTG
1 AATTTTTTTTG
33565057 AATTTTTTTTTCG
1 AA-TTTTTTTT-G
33565070 AATTTTTTTTG
1 AATTTTTTTTG
33565081 AA
1 AA
33565083 GAAACTACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.21
12 16 0.67
13 3 0.12
ACGTcount: A:0.22, C:0.03, G:0.08, T:0.68
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:33565066 original size:13 final size:13
Alignment explanation
Indices: 33565048--33565079 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
33565038 AGGAAACCAA
33565048 TTTTTTTT-GAAT
1 TTTTTTTTCGAAT
33565060 TTTTTTTTCGAAT
1 TTTTTTTTCGAAT
33565073 TTTTTTT
1 TTTTTTT
33565080 GAAGAAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.12, C:0.03, G:0.06, T:0.78
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:33569574 original size:22 final size:22
Alignment explanation
Indices: 33569519--33569582 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
33569509 TATTTGGGAA
*
33569519 TTGGTACGAAATGGTAAAGGAT
1 TTGGTACGAAATGGTAATGGAT
* ** *
33569541 GTGACACAAAATGGTAATGGAT
1 TTGGTACGAAATGGTAATGGAT
33569563 TTGGTACGAAATGGTAATGG
1 TTGGTACGAAATGGTAATGG
33569583 TTCAAAAAGG
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.36, C:0.06, G:0.31, T:0.27
Consensus pattern (22 bp):
TTGGTACGAAATGGTAATGGAT
Found at i:33573430 original size:14 final size:14
Alignment explanation
Indices: 33573411--33573447 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
33573401 GACTCACCTG
33573411 TTTTAAAATAAATA
1 TTTTAAAATAAATA
33573425 TTTTAAAATAAATA
1 TTTTAAAATAAATA
*
33573439 TTTCAAAAT
1 TTTTAAAAT
33573448 TGTTTCAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTTAAAATAAATA
Found at i:33578939 original size:20 final size:20
Alignment explanation
Indices: 33578914--33578953 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
33578904 AATGAAATTG
33578914 AAAAAG-AAAATGAAAAAGAA
1 AAAAAGTAAAA-GAAAAAGAA
*
33578934 AAAAAGTGAAAGAAAAAGAA
1 AAAAAGTAAAAGAAAAAGAA
33578954 GATGAGTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (20 bp):
AAAAAGTAAAAGAAAAAGAA
Found at i:33579200 original size:20 final size:21
Alignment explanation
Indices: 33579165--33579203 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
33579155 CAGCTCGTTG
33579165 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
33579186 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
33579204 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:33580755 original size:21 final size:21
Alignment explanation
Indices: 33580729--33580778 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
33580719 GTAAGTGATT
* *
33580729 AAAAAAATTTAAAAAAA-TAA
1 AAAAAAAATAAAAAAAAGTAA
33580749 AAAAAAAATAAAAAAAAGTAA
1 AAAAAAAATAAAAAAAAGTAA
33580770 AAGAAAAAA
1 AA-AAAAAA
33580779 ATTCGTGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 15 0.58
21 5 0.19
22 6 0.23
ACGTcount: A:0.84, C:0.00, G:0.04, T:0.12
Consensus pattern (21 bp):
AAAAAAAATAAAAAAAAGTAA
Found at i:33580765 original size:10 final size:10
Alignment explanation
Indices: 33580729--33580777 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
33580719 GTAAGTGATT
**
33580729 AAAAAAATTT
1 AAAAAAATAA
33580739 AAAAAAATAAA
1 AAAAAAAT-AA
33580750 AAAAAAATAA
1 AAAAAAATAA
*
33580760 AAAAAAGTAA
1 AAAAAAATAA
33580770 AAGAAAAA
1 AA-AAAAA
33580778 AATTCGTGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 21 0.64
11 12 0.36
ACGTcount: A:0.84, C:0.00, G:0.04, T:0.12
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:33581750 original size:18 final size:18
Alignment explanation
Indices: 33581729--33581820 Score: 84
Period size: 18 Copynumber: 5.3 Consensus size: 18
33581719 AATGAATTCA
*
33581729 AAAAAGAAAGTGAAAAAG
1 AAAAAGAAAATGAAAAAG
*
33581747 AAAAAGAAAACGAAAAAG
1 AAAAAGAAAATGAAAAAG
* * ** *
33581765 AAAACGAAAAAGTGAGAG
1 AAAAAGAAAATGAAAAAG
33581783 AAAAAGAAAATG---AA-
1 AAAAAGAAAATGAAAAAG
33581797 AAAAAGAAAATTGAAAAAG
1 AAAAAGAAAA-TGAAAAAG
33581816 AAAAA
1 AAAAA
33581821 TATGAAAATG
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
14 10 0.17
15 3 0.05
18 41 0.69
19 5 0.08
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.05
Consensus pattern (18 bp):
AAAAAGAAAATGAAAAAG
Found at i:33581799 original size:13 final size:14
Alignment explanation
Indices: 33581783--33581819 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
33581773 AAAGTGAGAG
33581783 AAAAAGAAAA-TGAA
1 AAAAAGAAAATTG-A
33581797 AAAAAGAAAATTG-
1 AAAAAGAAAATTGA
33581810 AAAAAGAAAA
1 AAAAAGAAAA
33581820 ATATGAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.45
14 10 0.45
15 2 0.09
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (14 bp):
AAAAAGAAAATTGA
Found at i:33581811 original size:15 final size:15
Alignment explanation
Indices: 33581783--33581828 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
33581773 AAAGTGAGAG
33581783 AAAAAGAAAA-TGAA
1 AAAAAGAAAATTGAA
33581797 AAAAAGAAAATTGAA
1 AAAAAGAAAATTGAA
*
33581812 AAAGA-AAAATATGAA
1 AAAAAGAAAAT-TGAA
33581827 AA
1 AA
33581829 TGAGATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 15 0.52
15 14 0.48
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (15 bp):
AAAAAGAAAATTGAA
Found at i:33581831 original size:6 final size:6
Alignment explanation
Indices: 33581729--33581820 Score: 76
Period size: 6 Copynumber: 14.8 Consensus size: 6
33581719 AATGAATTCA
** * *
33581729 AAAAAG AAAGTG AAAAAG AAAAAG AAAACG AAAAAG AAAACG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
** * * *
33581777 TGAGAG AAAAAG AAAATGAA AAAAAG AAAATTG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAA--AG AAAAAG AAAA-AG AAAAAG AAAAA
33581821 TATGAAAATG
Statistics
Matches: 65, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
6 55 0.85
7 5 0.08
8 5 0.08
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.05
Consensus pattern (6 bp):
AAAAAG
Found at i:33581863 original size:17 final size:18
Alignment explanation
Indices: 33581838--33581877 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
33581828 ATGAGATTTC
33581838 AAAAACAAAA-GAGAGTG
1 AAAAACAAAATGAGAGTG
* *
33581855 AAAAGCAAAATGAGATTG
1 AAAAACAAAATGAGAGTG
33581873 AAAAA
1 AAAAA
33581878 GAAAGAGAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.65, C:0.05, G:0.20, T:0.10
Consensus pattern (18 bp):
AAAAACAAAATGAGAGTG
Found at i:33581869 original size:18 final size:17
Alignment explanation
Indices: 33581838--33581887 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
33581828 ATGAGATTTC
33581838 AAAAACAAAAGAGAGTG
1 AAAAACAAAAGAGAGTG
* *
33581855 AAAAGCAAAATGAGATTG
1 AAAAACAAAA-GAGAGTG
*
33581873 AAAAA-GAAAGAGAGT
1 AAAAACAAAAGAGAGT
33581888 TTGAAAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 5 0.19
17 12 0.44
18 10 0.37
ACGTcount: A:0.62, C:0.04, G:0.24, T:0.10
Consensus pattern (17 bp):
AAAAACAAAAGAGAGTG
Found at i:33582686 original size:45 final size:45
Alignment explanation
Indices: 33582581--33582767 Score: 313
Period size: 45 Copynumber: 4.2 Consensus size: 45
33582571 CATGAAATTA
*
33582581 AGGAAGCATTTGACCAACATCATGCATAATTCATGGGAGAA-TTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
33582625 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
33582670 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
* * * *
33582715 AGGAAGCATTTGGCCAACATCATGCATAATTTATGGAACAAATTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
33582760 AGGAAGCA
1 AGGAAGCA
33582768 CCATGGCCGA
Statistics
Matches: 135, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
44 40 0.30
45 95 0.70
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.25
Consensus pattern (45 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
Found at i:33584791 original size:45 final size:45
Alignment explanation
Indices: 33584553--33584783 Score: 401
Period size: 45 Copynumber: 5.2 Consensus size: 45
33584543 CATGAAATTA
33584553 AGGAAGCATTTGACCAACATCATGCATAATTCATGG-AGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
33584597 AGGAAGCATTTCACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
33584642 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
33584687 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
* * * *
33584732 AGGAAGCATTTGGCCAACATCATGCATAATTTATGGAACAAATTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
33584777 AGGAAGC
1 AGGAAGC
33584784 CCATGGCCGA
Statistics
Matches: 178, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
44 35 0.20
45 143 0.80
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (45 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
Found at i:33591008 original size:45 final size:45
Alignment explanation
Indices: 33590944--33591175 Score: 394
Period size: 45 Copynumber: 5.2 Consensus size: 45
33590934 CATGAAATTA
*
33590944 AGGAAGCATTTGACCAACATCATGCATAATTCATGGGAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
33590989 AGGAAGCATTTCACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
33591034 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
33591079 AGGAAGCATTTGA-CAACATCATGCATAATTCATGGAAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
* * * *
33591123 AGGAAGCATTTGGCCAACATCATGCATAATTTATGGAACAAATTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
33591168 AGGAAGCA
1 AGGAAGCA
33591176 CCATGGCTGA
Statistics
Matches: 177, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
44 42 0.24
45 135 0.76
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (45 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
Found at i:33591148 original size:89 final size:90
Alignment explanation
Indices: 33590941--33591175 Score: 400
Period size: 89 Copynumber: 2.6 Consensus size: 90
33590931 TGGCATGAAA
*
33590941 TTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGGAGAATTTGAGGAAGCATTTCACCAA
1 TTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTCACCAA
33591006 CATCATGCATAATTCATGGAAGAAT
66 CATCATGCATAATTCATGGAAGAAT
* *
33591031 TTGAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGA-CAA
1 TTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTCACCAA
33591095 CATCATGCATAATTCATGGAAGAAT
66 CATCATGCATAATTCATGGAAGAAT
* * * *
33591120 TTAAGGAAGCATTTGGCCAACATCATGCATAATTTATGGAACAAATTGAGGAAGCA
1 TTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCA
33591176 CCATGGCTGA
Statistics
Matches: 137, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 79 0.58
90 58 0.42
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.26
Consensus pattern (90 bp):
TTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTCACCAA
CATCATGCATAATTCATGGAAGAAT
Found at i:33591591 original size:20 final size:20
Alignment explanation
Indices: 33591545--33591591 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
33591535 AGCTCGTTTC
* *
33591545 CAGCTGACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
33591565 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
33591585 CAGCTCA
1 CAGCTCA
33591592 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.15, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:33594288 original size:48 final size:47
Alignment explanation
Indices: 33594209--33594314 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
33594199 GAGTGTCATG
*
33594209 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
33594257 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
33594305 GAAAAAGAAA
1 GAAAAAGAAA
33594315 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:33596031 original size:20 final size:20
Alignment explanation
Indices: 33595985--33596031 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33595975 AGCTCGTTTC
*
33595985 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
33596005 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
33596025 CAGCTCA
1 CAGCTCA
33596032 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:33597758 original size:10 final size:10
Alignment explanation
Indices: 33597743--33597804 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
33597733 TTTGAACCAT
*
33597743 TACCAATTCG
1 TACCAATTCA
*
33597753 TACCAAATACCA
1 TACC-AAT-TCA
*
33597765 TACCATTTCA
1 TACCAATTCA
33597775 TACCAATTCCA
1 TACCAATT-CA
* *
33597786 TACCATTTCG
1 TACCAATTCA
33597796 TACCAATTC
1 TACCAATTC
33597805 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:33597788 original size:21 final size:21
Alignment explanation
Indices: 33597743--33597805 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
33597733 TTTGAACCAT
* *
33597743 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
33597765 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
33597786 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
33597806 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:33598861 original size:15 final size:15
Alignment explanation
Indices: 33598829--33598862 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
33598819 GTTCAACGAA
*
33598829 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
33598844 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
33598859 GAGG
1 GAGG
33598863 GAGGTTCGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:33602614 original size:10 final size:10
Alignment explanation
Indices: 33602599--33602660 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
33602589 TTTGAACCAT
*
33602599 TACCAATTCG
1 TACCAATTCA
*
33602609 TACCAAATACCA
1 TACC-AAT-TCA
*
33602621 TACCATTTCA
1 TACCAATTCA
33602631 TACCAATTCCA
1 TACCAATT-CA
* *
33602642 TACCATTTCG
1 TACCAATTCA
33602652 TACCAATTC
1 TACCAATTC
33602661 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:33602644 original size:21 final size:21
Alignment explanation
Indices: 33602599--33602661 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
33602589 TTTGAACCAT
* *
33602599 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
33602621 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
33602642 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
33602662 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:33604364 original size:20 final size:21
Alignment explanation
Indices: 33604329--33604367 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
33604319 CAGCTCGTTG
33604329 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
33604350 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
33604368 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:33610061 original size:32 final size:32
Alignment explanation
Indices: 33610025--33610162 Score: 107
Period size: 39 Copynumber: 3.9 Consensus size: 32
33610015 ATTTACATCG
* *
33610025 TAATCACATTTACATTTAAGCATATA-CACATA
1 TAATCACA-TAACATTCAAGCATATATCACATA
33610057 TAATCACATAACATTCAAGCATATATCACAATACTCA
1 TAATCACATAACATTCAAGCATATATCAC---A-T-A
* *
33610094 TAAAATGACATAACATTCAAGCATATTTCACAATACTCA
1 T--AATCACATAACATTCAAGCATATATCAC---A-T-A
*
33610133 TAATCACATAACATTCAAGTATATATCACA
1 TAATCACATAACATTCAAGCATATATCACA
33610163 ATACTCAAAA
Statistics
Matches: 91, Mismatches: 7, Indels: 14
0.81 0.06 0.12
Matches are distributed among these distances:
31 15 0.16
32 11 0.12
34 1 0.01
35 1 0.01
36 1 0.01
37 27 0.30
39 35 0.38
ACGTcount: A:0.46, C:0.21, G:0.04, T:0.30
Consensus pattern (32 bp):
TAATCACATAACATTCAAGCATATATCACATA
Found at i:33610105 original size:39 final size:39
Alignment explanation
Indices: 33610048--33610173 Score: 186
Period size: 39 Copynumber: 3.3 Consensus size: 39
33610038 ATTTAAGCAT
* *
33610048 ATACACATATAATCACATAACATTCAAGCATATATCACA
1 ATACTCATAAAATCACATAACATTCAAGCATATATCACA
* *
33610087 ATACTCATAAAATGACATAACATTCAAGCATATTTCACA
1 ATACTCATAAAATCACATAACATTCAAGCATATATCACA
*
33610126 ATACTCAT--AATCACATAACATTCAAGTATATATCACA
1 ATACTCATAAAATCACATAACATTCAAGCATATATCACA
33610163 ATACTCA-AAAA
1 ATACTCATAAAA
33610174 CATGTTTAGA
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
37 33 0.42
38 2 0.03
39 43 0.55
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.27
Consensus pattern (39 bp):
ATACTCATAAAATCACATAACATTCAAGCATATATCACA
Found at i:33610151 original size:37 final size:37
Alignment explanation
Indices: 33610056--33610169 Score: 183
Period size: 37 Copynumber: 3.0 Consensus size: 37
33610046 ATATACACAT
33610056 ATAATCACATAACATTCAAGCATATATCACAATACTC
1 ATAATCACATAACATTCAAGCATATATCACAATACTC
* *
33610093 ATAAAATGACATAACATTCAAGCATATTTCACAATACTC
1 AT--AATCACATAACATTCAAGCATATATCACAATACTC
*
33610132 ATAATCACATAACATTCAAGTATATATCACAATACTC
1 ATAATCACATAACATTCAAGCATATATCACAATACTC
33610169 A
1 A
33610170 AAAACATGTT
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
37 35 0.50
39 35 0.50
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (37 bp):
ATAATCACATAACATTCAAGCATATATCACAATACTC
Found at i:33610802 original size:18 final size:18
Alignment explanation
Indices: 33610779--33610814 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
33610769 TAGGTATGAG
33610779 AAAGCTAACACTCCGAAT
1 AAAGCTAACACTCCGAAT
*
33610797 AAAGCTTACACTCCGAAT
1 AAAGCTAACACTCCGAAT
33610815 TTAGAGTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.28, G:0.11, T:0.19
Consensus pattern (18 bp):
AAAGCTAACACTCCGAAT
Found at i:33612203 original size:269 final size:269
Alignment explanation
Indices: 33611724--33612250 Score: 1000
Period size: 269 Copynumber: 2.0 Consensus size: 269
33611714 GGGGAAGAGA
*
33611724 TGATGTGATCCGGCTCGGTTGATTGAGCCGATTCACTTGGTTGCCCGATCGTCGACGAGAAGTTT
1 TGATGTGATCCGGCTCGGTTGATTGAGCCGATTCACTTGATTGCCCGATCGTCGACGAGAAGTTT
33611789 GTTCGATTTTGTAGATAGATGGAGTTAGATGATTTTTTATAGCGGAAGTTGAGAAAATGGGTTCA
66 GTTCGATTTTGTAGATAGATGGAGTTAGATGATTTTTTATAGCGGAAGTTGAGAAAATGGGTTCA
33611854 AAAGATGGTTTGGGTAGATGTTTGATAGGCTCGGTGAAATAAAGAAATATTCTTTATAATTTAAT
131 AAAGATGGTTTGGGTAGATGTTTGATAGGCTCGGTGAAATAAAGAAATATTCTTTATAATTTAAT
33611919 AGTTAAAATGGAATGGAAAAATAGAACTCAAGCGAAGAACGATTCAATACTATATGAAGTATTGC
196 AGTTAAAATGGAATGGAAAAATAGAACTCAAGCGAAGAACGATTCAATACTATATGAAGTATTGC
33611984 CCCAGGACT
261 CCCAGGACT
* * *
33611993 TGATGTGATTCGGCTCGGTTGATTGAGTCGATTCACTTGATTTCCCGATCGTCGACGAGAAGTTT
1 TGATGTGATCCGGCTCGGTTGATTGAGCCGATTCACTTGATTGCCCGATCGTCGACGAGAAGTTT
33612058 GTTCGATTTTGTAGATAGATGGAGTTAGATGATTTTTTATAGCGGAAGTTGAGAAAATGGGTTCA
66 GTTCGATTTTGTAGATAGATGGAGTTAGATGATTTTTTATAGCGGAAGTTGAGAAAATGGGTTCA
* *
33612123 AAAGATGGTTTGGGTAGATGTTTGATAGGCTCGGTGAAATAAAGAAATGTTGTTTATAATTTAAT
131 AAAGATGGTTTGGGTAGATGTTTGATAGGCTCGGTGAAATAAAGAAATATTCTTTATAATTTAAT
33612188 AGTTAAAATGGAATGGAAAAATAGAACTCAAGCGAAGAACGATTCAATACTATATGAAGTATT
196 AGTTAAAATGGAATGGAAAAATAGAACTCAAGCGAAGAACGATTCAATACTATATGAAGTATT
33612251 ACCCAGGGAC
Statistics
Matches: 252, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
269 252 1.00
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (269 bp):
TGATGTGATCCGGCTCGGTTGATTGAGCCGATTCACTTGATTGCCCGATCGTCGACGAGAAGTTT
GTTCGATTTTGTAGATAGATGGAGTTAGATGATTTTTTATAGCGGAAGTTGAGAAAATGGGTTCA
AAAGATGGTTTGGGTAGATGTTTGATAGGCTCGGTGAAATAAAGAAATATTCTTTATAATTTAAT
AGTTAAAATGGAATGGAAAAATAGAACTCAAGCGAAGAACGATTCAATACTATATGAAGTATTGC
CCCAGGACT
Found at i:33613343 original size:20 final size:20
Alignment explanation
Indices: 33613320--33613366 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
33613310 GGGTTAAGAT
33613320 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTTGAG
* *
33613340 TGAGTTGACTTGAGCTTGAG
1 TGAGCTGAATTGAGCTTGAG
33613360 TGAGCTG
1 TGAGCTG
33613367 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.11, G:0.36, T:0.32
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTTGAG
Found at i:33616372 original size:20 final size:20
Alignment explanation
Indices: 33616349--33616395 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33616339 GGGTTAAGAT
*
33616349 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
33616369 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
33616389 TGAGCTG
1 TGAGCTG
33616396 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:33619351 original size:12 final size:12
Alignment explanation
Indices: 33619336--33619391 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 12
33619326 TTTTTTTCAC
33619336 TTTTTTTGAATT
1 TTTTTTTGAATT
*
33619348 TTTTTTTCAATCAAAT
1 TTTTTTTGAAT----T
*
33619364 TTTTTTCGAATT
1 TTTTTTTGAATT
33619376 TTTTTTTG-ATT
1 TTTTTTTGAATT
33619387 TTTTT
1 TTTTT
33619392 GTTACTCCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
11 8 0.22
12 18 0.50
16 10 0.28
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (12 bp):
TTTTTTTGAATT
Found at i:33620893 original size:20 final size:20
Alignment explanation
Indices: 33620870--33620916 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33620860 GGGTTAAGAT
*
33620870 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
33620890 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
33620910 TGAGCTG
1 TGAGCTG
33620917 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:33623796 original size:20 final size:20
Alignment explanation
Indices: 33623773--33623819 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33623763 GGGTTAAGAT
*
33623773 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
33623793 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
33623813 TGAGCTG
1 TGAGCTG
33623820 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:33628166 original size:23 final size:22
Alignment explanation
Indices: 33628115--33628166 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
33628105 CCTCGTCTTT
*
33628115 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
33628137 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
33628160 TTCTTTT
1 TTCTTTT
33628167 TCAAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:33633684 original size:6 final size:6
Alignment explanation
Indices: 33633673--33633697 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
33633663 AGTTGTAAAG
33633673 TTTTAT TTTTAT TTTTAT TTTTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT T
33633698 AATTTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:33634908 original size:13 final size:13
Alignment explanation
Indices: 33634892--33634953 Score: 63
Period size: 13 Copynumber: 4.6 Consensus size: 13
33634882 ACAAAAAAAT
33634892 AAAAAAAAATTCG
1 AAAAAAAAATTCG
*
33634905 AAAAAAAAATTTG
1 AAAAAAAAATTCG
*
33634918 ATTGAAAAAAAATTCA
1 A---AAAAAAAATTCG
*
33634934 AAAAAAAAAGT-G
1 AAAAAAAAATTCG
33634946 AAAAAAAA
1 AAAAAAAA
33634954 TCGAGCAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
12 8 0.20
13 22 0.54
16 11 0.27
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (13 bp):
AAAAAAAAATTCG
Found at i:33634965 original size:29 final size:27
Alignment explanation
Indices: 33634932--33634997 Score: 71
Period size: 29 Copynumber: 2.4 Consensus size: 27
33634922 AAAAAAAATT
**
33634932 CAAAAAAAAAAGTGAAAAAAAA-TCGAG
1 CAAAAAAAAAAAAGAAAAAAAAGT-GAG
*
33634959 CAAAAAAAAGGAAAGAAAAAAAAGGTGAG
1 CAAAAAAAA-AAAAGAAAAAAAA-GTGAG
33634988 CAAAAAAAAA
1 CAAAAAAAAA
33634998 TCAAGTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
27 9 0.28
28 10 0.31
29 12 0.38
30 1 0.03
ACGTcount: A:0.73, C:0.06, G:0.17, T:0.05
Consensus pattern (27 bp):
CAAAAAAAAAAAAGAAAAAAAAGTGAG
Found at i:33636010 original size:6 final size:6
Alignment explanation
Indices: 33635978--33636084 Score: 58
Period size: 6 Copynumber: 17.7 Consensus size: 6
33635968 AAAGAAATTG
* * ** *
33635978 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
33636025 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTG-A
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
33636075 AAAGAA AAAG
1 AAAGAA AAAG
33636085 CGAAAAAAGA
Statistics
Matches: 73, Mismatches: 22, Indels: 13
0.68 0.20 0.12
Matches are distributed among these distances:
5 5 0.07
6 60 0.82
7 4 0.05
8 4 0.05
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:33636039 original size:18 final size:18
Alignment explanation
Indices: 33635982--33636040 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
33635972 AAATTGAAAG
* *
33635982 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAATCGA
* *
33636000 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATCGA
*
33636018 AAAAGAAAAAGAAATCAA
1 AAAAGAAAAAGAAATCGA
33636036 AAAAG
1 AAAAG
33636041 TGAGAGAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.75, C:0.07, G:0.14, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCGA
Found at i:33644589 original size:12 final size:13
Alignment explanation
Indices: 33644557--33644589 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
33644547 TAGTTTCTCG
33644557 AAAAAAAATTCGA
1 AAAAAAAATTCGA
33644570 AAAAAAAATTC-A
1 AAAAAAAATTCGA
33644582 AAAAAAAA
1 AAAAAAAA
33644590 CTAGTTTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:33644650 original size:12 final size:13
Alignment explanation
Indices: 33644627--33644666 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
33644617 GGATATCAAG
33644627 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
*
33644640 TTTTGAAAAAAAAA
1 TTGTG-AAAAAAAA
33644654 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
33644667 GAGAGCTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:33644651 original size:14 final size:14
Alignment explanation
Indices: 33644627--33644666 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
33644617 GGATATCAAG
33644627 TTGTG-AAAAAAAA
1 TTGTGAAAAAAAAA
*
33644640 TTTTGAAAAAAAAA
1 TTGTGAAAAAAAAA
33644654 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
33644667 GAGAGCTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:33646446 original size:20 final size:20
Alignment explanation
Indices: 33646399--33646446 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
33646389 AGTAAGCTCG
33646399 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
33646419 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
33646439 GTTGAGCT
1 GTTGAGCT
33646447 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:33648105 original size:27 final size:27
Alignment explanation
Indices: 33648074--33648149 Score: 68
Period size: 27 Copynumber: 2.8 Consensus size: 27
33648064 TTACTTTCTC
33648074 CTTTTTCACTCTTCTCTTTTTCAA-ATT
1 CTTTTTCACT-TTCTCTTTTTCAATATT
* * *
33648101 CTTTTTTCGCTTTTTCTTTTTCAATTTT
1 C-TTTTTCACTTTCTCTTTTTCAATATT
33648129 CTTTTCTTCA-TTT-TCTTTTTC
1 C-TTT-TTCACTTTCTCTTTTTC
33648150 TCTCACTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
27 21 0.50
28 18 0.43
29 3 0.07
ACGTcount: A:0.09, C:0.22, G:0.01, T:0.67
Consensus pattern (27 bp):
CTTTTTCACTTTCTCTTTTTCAATATT
Found at i:33648128 original size:13 final size:12
Alignment explanation
Indices: 33648112--33648231 Score: 63
Period size: 12 Copynumber: 10.0 Consensus size: 12
33648102 TTTTTTCGCT
33648112 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
33648125 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
33648139 TTTTCTTTTTC-
1 TTTTCTTTTTCA
** *
33648150 TCTCACTTTTTTGA
1 T-TTTC-TTTTTCA
33648164 -TTTCTTTTTC-
1 TTTTCTTTTTCA
** *
33648174 TTTTGCAATTTCT
1 TTTT-CTTTTTCA
*
33648187 TTTTCTTTTTCG
1 TTTTCTTTTTCA
*
33648199 TTTTCTTTTT-G
1 TTTTCTTTTTCA
33648210 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
33648220 ATTTCTTTTTCA
1 TTTTCTTTTTCA
33648232 ATCTCTTTCT
Statistics
Matches: 83, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 15 0.18
12 32 0.39
13 17 0.20
14 9 0.11
15 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.71
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:33648128 original size:14 final size:14
Alignment explanation
Indices: 33648068--33648133 Score: 55
Period size: 13 Copynumber: 4.7 Consensus size: 14
33648058 GCTCGATTAC
*
33648068 TTTCTCCTTTTTCAC
1 TTTCT-CTTTTTCAA
33648083 TCTTCTCTTTTTCAA
1 T-TTCTCTTTTTCAA
* **
33648098 ATTCT-TTTTTCGC
1 TTTCTCTTTTTCAA
*
33648111 TTTTTCTTTTTCAA
1 TTTCTCTTTTTCAA
33648125 TTT-TCTTTT
1 TTTCTCTTTT
33648134 CTTCATTTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
13 15 0.37
14 13 0.32
15 9 0.22
16 4 0.10
ACGTcount: A:0.09, C:0.23, G:0.02, T:0.67
Consensus pattern (14 bp):
TTTCTCTTTTTCAA
Found at i:33648141 original size:14 final size:14
Alignment explanation
Indices: 33648075--33648148 Score: 55
Period size: 14 Copynumber: 5.3 Consensus size: 14
33648065 TACTTTCTCC
* *
33648075 TTTTTCACTCTTCT
1 TTTTTCAATTTTCT
*
33648089 CTTTTTCAA-ATTCT
1 -TTTTTCAATTTTCT
**
33648103 TTTTTCGCTTTT-T
1 TTTTTCAATTTTCT
33648116 CTTTTTCAATTTTCT
1 -TTTTTCAATTTTCT
33648131 TTTCTTC-ATTTTCT
1 TTT-TTCAATTTTCT
33648145 TTTT
1 TTTT
33648149 CTCTCACTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
13 8 0.17
14 29 0.60
15 11 0.23
ACGTcount: A:0.09, C:0.20, G:0.01, T:0.69
Consensus pattern (14 bp):
TTTTTCAATTTTCT
Found at i:33648230 original size:6 final size:6
Alignment explanation
Indices: 33648110--33648217 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
33648100 TCTTTTTTCG
* * * **
33648110 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* * ** *
33648161 -TGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
33648209 -GTTTT CTTT
1 CTTTTT CTTT
33648218 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 23, Indels: 10
0.69 0.21 0.09
Matches are distributed among these distances:
5 5 0.07
6 56 0.76
7 10 0.14
8 3 0.04
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:33649303 original size:12 final size:12
Alignment explanation
Indices: 33649299--33649323 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33649289 TTTTTTTCAA
33649299 TTTTTTTGAATT
1 TTTTTTTGAATT
33649311 TTTTTTTGAATT
1 TTTTTTTGAATT
33649323 T
1 T
33649324 CTTCTCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTTTTTGAATT
Found at i:33650886 original size:20 final size:20
Alignment explanation
Indices: 33650839--33650886 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
33650829 AGTAATCTCG
33650839 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
33650859 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
33650879 GTTGAGCT
1 GTTGAGCT
33650887 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:33655523 original size:10 final size:10
Alignment explanation
Indices: 33655507--33655564 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
33655497 CAACTCCGAC
33655507 CAGCTCAATT
1 CAGCTCAATT
* *
33655517 GAGCTCATTT
1 CAGCTCAATT
33655527 CAGCTCAA-T
1 CAGCTCAATT
33655536 CGAGCTCAATT
1 C-AGCTCAATT
*
33655547 TAGCTACAATT
1 CAGCT-CAATT
33655558 CAGCTCA
1 CAGCTCA
33655565 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:33655530 original size:20 final size:20
Alignment explanation
Indices: 33655507--33655567 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
33655497 CAACTCCGAC
33655507 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
33655527 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
33655548 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
33655568 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:33656931 original size:11 final size:11
Alignment explanation
Indices: 33656915--33656987 Score: 56
Period size: 11 Copynumber: 6.1 Consensus size: 11
33656905 ATTGGAGTAA
33656915 CAAAAAAAAAT
1 CAAAAAAAAAT
*
33656926 CAAAAAAAATT
1 CAAAAAAAAAT
33656937 CGAAAAAAAATTGATT
1 C-AAAAAAAA---A-T
* *
33656953 GAAAAAAAATT
1 CAAAAAAAAAT
33656964 CAAAAAAAAAGT
1 CAAAAAAAAA-T
*
33656976 GAAAAAAAAAT
1 CAAAAAAAAAT
33656987 C
1 C
33656988 GAGCAAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
11 21 0.44
12 18 0.38
15 8 0.17
16 1 0.02
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.15
Consensus pattern (11 bp):
CAAAAAAAAAT
Found at i:33656984 original size:27 final size:27
Alignment explanation
Indices: 33656927--33656985 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
33656917 AAAAAAAATC
* * ***
33656927 AAAAAAAATTCGAAAAAAAATTGATTG
1 AAAAAAAATTCAAAAAAAAAGTGAAAA
33656954 AAAAAAAATTCAAAAAAAAAGTGAAAA
1 AAAAAAAATTCAAAAAAAAAGTGAAAA
33656981 AAAAA
1 AAAAA
33656986 TCGAGCAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.15
Consensus pattern (27 bp):
AAAAAAAATTCAAAAAAAAAGTGAAAA
Found at i:33656994 original size:27 final size:28
Alignment explanation
Indices: 33656963--33657037 Score: 89
Period size: 27 Copynumber: 2.6 Consensus size: 28
33656953 GAAAAAAAAT
*
33656963 TCAAAAAAAAAGTGAAAAAAAAATCGAG
1 TCAAAAAAAAAGTGAAAAAAAAATCAAG
* *
33656991 -CAAAAAAAAGGTGACCAAAAAAATCAAG
1 TCAAAAAAAAAGTGA-AAAAAAAATCAAG
*
33657019 TTAAAAAAAAAAGTGAAAA
1 -TCAAAAAAAAAGTGAAAA
33657038 GTCTTGCGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 13 0.34
28 11 0.29
29 2 0.05
30 12 0.32
ACGTcount: A:0.68, C:0.08, G:0.13, T:0.11
Consensus pattern (28 bp):
TCAAAAAAAAAGTGAAAAAAAAATCAAG
Found at i:33663269 original size:40 final size:40
Alignment explanation
Indices: 33663178--33663347 Score: 198
Period size: 40 Copynumber: 4.3 Consensus size: 40
33663168 TCCTCGTTCA
* * * * *
33663178 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
33663217 CATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
33663257 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * *
33663297 AATGCCCTCGGGACTTAACTCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
33663337 AAGGCCTTCGG
1 AATGCCTTCGG
33663348 ATCTTAGTCC
Statistics
Matches: 111, Mismatches: 19, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
39 32 0.29
40 79 0.71
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:33667779 original size:10 final size:10
Alignment explanation
Indices: 33667763--33667820 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
33667753 CAACTCCGAC
33667763 CAGCTCAATT
1 CAGCTCAATT
* *
33667773 GAGCTCATTT
1 CAGCTCAATT
33667783 CAGCTCAA-T
1 CAGCTCAATT
33667792 CGAGCTCAATT
1 C-AGCTCAATT
*
33667803 TAGCTACAATT
1 CAGCT-CAATT
33667814 CAGCTCA
1 CAGCTCA
33667821 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:33667786 original size:20 final size:20
Alignment explanation
Indices: 33667763--33667823 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
33667753 CAACTCCGAC
33667763 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
33667783 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
33667804 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
33667824 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:33671059 original size:11 final size:11
Alignment explanation
Indices: 33671043--33671093 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
33671033 ACAAATAAAC
33671043 TTTTTTTTTAA
1 TTTTTTTTTAA
*
33671054 TTTTTTTTCAAA
1 TTTTTTTT-TAA
* *
33671066 ATTTTTTTTGA
1 TTTTTTTTTAA
*
33671077 TTTTTTTTGAA
1 TTTTTTTTTAA
33671088 TTTTTT
1 TTTTTT
33671094 CTCATAATGA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
11 23 0.72
12 9 0.28
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (11 bp):
TTTTTTTTTAA
Found at i:33676508 original size:13 final size:13
Alignment explanation
Indices: 33676490--33676514 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33676480 GTATTGATCA
33676490 TGTGTTCACACCT
1 TGTGTTCACACCT
33676503 TGTGTTCACACC
1 TGTGTTCACACC
33676515 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:33677874 original size:17 final size:18
Alignment explanation
Indices: 33677842--33677875 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33677832 AAAAGAGAGT
*
33677842 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
33677860 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
33677876 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:33679771 original size:13 final size:13
Alignment explanation
Indices: 33679753--33679777 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33679743 GTATTGATCA
33679753 TGTGTTCACACCT
1 TGTGTTCACACCT
33679766 TGTGTTCACACC
1 TGTGTTCACACC
33679778 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:33682526 original size:15 final size:13
Alignment explanation
Indices: 33682506--33682553 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
33682496 ACTCTCCTCA
33682506 TTCTTTTCTTTCTTT
1 TTCTTTTC--TCTTT
*
33682521 TTCTTTTCACTCTT
1 TTCTTTTCTCT-TT
33682535 TT-TTTTCTCTTT
1 TTCTTTTCTCTTT
33682547 TTCTTTT
1 TTCTTTT
33682554 TCTCGCTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 4 0.14
13 13 0.45
14 4 0.14
15 8 0.28
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (13 bp):
TTCTTTTCTCTTT
Found at i:33685523 original size:12 final size:12
Alignment explanation
Indices: 33685508--33685584 Score: 52
Period size: 12 Copynumber: 6.4 Consensus size: 12
33685498 GGTGAAAAGA
33685508 AAAAAGAGATTG
1 AAAAAGAGATTG
*
33685520 AAAAAGAAATTG
1 AAAAAGAGATTG
*
33685532 --AAAGAGA-AG
1 AAAAAGAGATTG
*
33685541 AAAAAGAAAGAGTGG
1 AAAAAG--AGA-TTG
*
33685556 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
33685568 AAAGAGAGCTTG
1 AAAAAGAGATTG
33685580 AAAAA
1 AAAAA
33685585 AAATCGAGTG
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
9 1 0.02
10 6 0.12
11 4 0.08
12 26 0.53
13 5 0.10
15 7 0.14
ACGTcount: A:0.62, C:0.01, G:0.25, T:0.12
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:33685549 original size:15 final size:15
Alignment explanation
Indices: 33685531--33685564 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
33685521 AAAAGAAATT
33685531 GAAAGAGAAGAAAAA
1 GAAAGAGAAGAAAAA
**
33685546 GAAAGAGTGGAAAAA
1 GAAAGAGAAGAAAAA
33685561 GAAA
1 GAAA
33685565 TTGAAAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (15 bp):
GAAAGAGAAGAAAAA
Found at i:33695859 original size:10 final size:10
Alignment explanation
Indices: 33695846--33695883 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
33695836 TTGTAGCTAA
33695846 ATTGAGCTCG
1 ATTGAGCTCG
33695856 ATTGAGCT-G
1 ATTGAGCTCG
33695865 ACTTGAGCTCG
1 A-TTGAGCTCG
*
33695876 AGTGAGCT
1 ATTGAGCT
33695884 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:33695863 original size:20 final size:20
Alignment explanation
Indices: 33695823--33695883 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
33695813 ACCAATAAAA
33695823 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
33695843 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
33695863 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
33695883 T
1 T
33695884 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:33695884 original size:20 final size:20
Alignment explanation
Indices: 33695847--33695884 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
33695837 TGTAGCTAAA
*
33695847 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
33695867 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
33695885 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:33703330 original size:24 final size:24
Alignment explanation
Indices: 33703298--33703430 Score: 153
Period size: 24 Copynumber: 5.5 Consensus size: 24
33703288 CCCTCAAGGT
*
33703298 TAAATGATTGATTTGTCTGTGATG
1 TAAATGACTGATTTGTCTGTGATG
* *
33703322 TAAATGATTGATTTGTCCGTGATG
1 TAAATGACTGATTTGTCTGTGATG
*
33703346 TAAATGACTGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATG
*
33703370 TAAATGACTAATTTGTCTGTGATTGG
1 TAAATGACTGATTTGTCTGTGA-T-G
* *
33703396 T--ATGACTGATTTTTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATG
**
33703418 TGTATGACTGATT
1 TAAATGACTGATT
33703431 CTGAGCATGG
Statistics
Matches: 96, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
22 1 0.01
23 1 0.01
24 92 0.96
25 1 0.01
26 1 0.01
ACGTcount: A:0.24, C:0.08, G:0.23, T:0.46
Consensus pattern (24 bp):
TAAATGACTGATTTGTCTGTGATG
Found at i:33708333 original size:23 final size:22
Alignment explanation
Indices: 33708282--33708333 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
33708272 CCTCGTCTTT
*
33708282 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
33708304 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
33708327 TTCTTTT
1 TTCTTTT
33708334 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:33709669 original size:9 final size:9
Alignment explanation
Indices: 33709655--33709688 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
33709645 TAATTTCATA
*
33709655 TTTTTTGAT
1 TTTTTTGAC
33709664 TTTTTTGAC
1 TTTTTTGAC
33709673 TTTTTTGAC
1 TTTTTTGAC
33709682 TGTTTTT
1 T-TTTTT
33709689 TTGCGGGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.09, C:0.06, G:0.12, T:0.74
Consensus pattern (9 bp):
TTTTTTGAC
Found at i:33724027 original size:11 final size:11
Alignment explanation
Indices: 33724011--33724040 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
33724001 TGTAGATTCA
33724011 AAAAAAAATCG
1 AAAAAAAATCG
33724022 AAAAAAAATCG
1 AAAAAAAATCG
33724033 AAAAAAAA
1 AAAAAAAA
33724041 ATTTGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.80, C:0.07, G:0.07, T:0.07
Consensus pattern (11 bp):
AAAAAAAATCG
Found at i:33724029 original size:14 final size:13
Alignment explanation
Indices: 33724010--33724070 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
33724000 TTGTAGATTC
33724010 AAAAAAAAATCG-
1 AAAAAAAAATCGA
33724022 -AAAAAAAATCGA
1 AAAAAAAAATCGA
* *
33724034 AAAAAAAATTTGA
1 AAAAAAAAATCGA
*
33724047 AAAAAAAAATTTGA
1 AAAAAAAAA-TCGA
33724061 AAAAAAAAAT
1 AAAAAAAAAT
33724071 TGCATACGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
11 11 0.26
13 19 0.44
14 13 0.30
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (13 bp):
AAAAAAAAATCGA
Found at i:33724071 original size:14 final size:14
Alignment explanation
Indices: 33724033--33724071 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
33724023 AAAAAAATCG
33724033 AAAAAAAAATTTGA
1 AAAAAAAAATTTGA
33724047 AAAAAAAAATTTGA
1 AAAAAAAAATTTGA
33724061 AAAAAAAAATT
1 AAAAAAAAATT
33724072 GCATACGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (14 bp):
AAAAAAAAATTTGA
Found at i:33730864 original size:13 final size:13
Alignment explanation
Indices: 33730846--33730870 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33730836 TGGTCATCAT
33730846 GGTGTGAACACAA
1 GGTGTGAACACAA
33730859 GGTGTGAACACA
1 GGTGTGAACACA
33730871 TGATCAATAC
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:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:33733106 original size:18 final size:18
Alignment explanation
Indices: 33733085--33733119 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
33733075 TTTTTCTTTT
33733085 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
33733103 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
33733120 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:33734067 original size:13 final size:14
Alignment explanation
Indices: 33734050--33734116 Score: 66
Period size: 13 Copynumber: 4.7 Consensus size: 14
33734040 TTTTTGCTCG
33734050 ATTTTTTTTTTC-A
1 ATTTTTTTTTTCAA
* *
33734063 CTTTTTTTTTT-GA
1 ATTTTTTTTTTCAA
33734076 ATTTTTTTTTTCAATCA
1 ATTTTTTTTTTC-A--A
*
33734093 ATTTTTTTTTTCGA
1 ATTTTTTTTTTCAA
33734107 ATTTTTTTTT
1 ATTTTTTTTT
33734117 GATTTTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
13 21 0.47
14 11 0.24
17 13 0.29
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (14 bp):
ATTTTTTTTTTCAA
Found at i:33734068 original size:14 final size:13
Alignment explanation
Indices: 33734036--33734116 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 13
33734026 GGTCACCTTT
*
33734036 TTTTTTTTTGCTCGA
1 TTTTTTTTT--TCAA
*
33734051 TTTTTTTTTTCAC
1 TTTTTTTTTTCAA
*
33734064 TTTTTTTTTTGAA
1 TTTTTTTTTTCAA
33734077 TTTTTTTTTTCAATCAA
1 -TTTTTTTTT---TCAA
33734094 TTTTTTTTTTCGAA
1 TTTTTTTTTTC-AA
33734108 TTTTTTTTT
1 TTTTTTTTT
33734117 GATTTTTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
13 15 0.27
14 20 0.36
15 9 0.16
16 9 0.16
17 3 0.05
ACGTcount: A:0.12, C:0.09, G:0.05, T:0.74
Consensus pattern (13 bp):
TTTTTTTTTTCAA
Found at i:33734121 original size:11 final size:12
Alignment explanation
Indices: 33734095--33734128 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
33734085 TTCAATCAAT
33734095 TTTTTTTTTCGAA
1 TTTTTTTTT-GAA
33734108 TTTTTTTTTG-A
1 TTTTTTTTTGAA
33734119 TTTTTTTTTG
1 TTTTTTTTTG
33734129 TTACTCCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 1 0.05
13 9 0.43
ACGTcount: A:0.09, C:0.03, G:0.09, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:33734124 original size:13 final size:13
Alignment explanation
Indices: 33734051--33734127 Score: 57
Period size: 13 Copynumber: 5.6 Consensus size: 13
33734041 TTTTGCTCGA
* *
33734051 TTTTTTTTTTCAC
1 TTTTTTTTTTGAT
33734064 TTTTTTTTTTGAAT
1 TTTTTTTTTTG-AT
*
33734078 TTTTTTTTTCAATCAAT
1 TTTTTTTTT---T-GAT
*
33734095 TTTTTTTTTCGA-
1 TTTTTTTTTTGAT
*
33734107 ATTTTTTTTTGAT
1 TTTTTTTTTTGAT
33734120 TTTTTTTT
1 TTTTTTTT
33734128 GTTACTCCAA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
12 10 0.20
13 18 0.36
14 10 0.20
17 12 0.24
ACGTcount: A:0.13, C:0.06, G:0.04, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTTGAT
Found at i:33735177 original size:13 final size:13
Alignment explanation
Indices: 33735159--33735183 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33735149 TGGTCATCAT
33735159 GGTGTGAACACAA
1 GGTGTGAACACAA
33735172 GGTGTGAACACA
1 GGTGTGAACACA
33735184 TGATCAATAC
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:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:33740100 original size:20 final size:20
Alignment explanation
Indices: 33740077--33740123 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33740067 GGGTTAATAT
*
33740077 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
33740097 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
33740117 TGAGCTG
1 TGAGCTG
33740124 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:33741849 original size:48 final size:48
Alignment explanation
Indices: 33741794--33741899 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
33741784 TTGTCTTTTC
*
33741794 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
33741842 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
33741890 TTTCTTTTTC
1 TTTCTTTTTC
33741900 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:33741992 original size:21 final size:21
Alignment explanation
Indices: 33741963--33742018 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
33741953 CAAGCTCTCT
*
33741963 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
33741984 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
33742005 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
33742019 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:33742011 original size:14 final size:14
Alignment explanation
Indices: 33741962--33742018 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
33741952 TCAAGCTCTC
33741962 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
33741975 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
33741989 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
33742003 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
33742017 TT
1 TT
33742019 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:33742046 original size:18 final size:18
Alignment explanation
Indices: 33742025--33742083 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
33742015 TTTTCTCTCA
33742025 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
33742043 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
33742061 CTTCTTCGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
33742079 GTTTT
1 CTTTT
33742084 CTTTCAATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.05, C:0.17, G:0.07, T:0.71
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:33742100 original size:6 final size:6
Alignment explanation
Indices: 33741980--33742087 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
33741970 TCTTTTTTCG
* * * **
33741980 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** * *
33742031 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTCTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
33742079 -GTTTT CTTT
1 CTTTTT CTTT
33742088 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 27, Indels: 6
0.69 0.26 0.06
Matches are distributed among these distances:
5 4 0.06
6 56 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:33743184 original size:10 final size:10
Alignment explanation
Indices: 33743156--33743189 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
33743146 TTTTTTTTCC
*
33743156 TTTTTTTCGAT
1 TTTTTTT-GAA
33743167 TTTTTTTGAA
1 TTTTTTTGAA
33743177 TTTTTTTGAA
1 TTTTTTTGAA
33743187 TTT
1 TTT
33743190 CTTCTCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.68
11 7 0.32
ACGTcount: A:0.15, C:0.03, G:0.09, T:0.74
Consensus pattern (10 bp):
TTTTTTTGAA
Done.