Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 43 of 199
Found at i:12448069 original size:25 final size:23
Alignment explanation
Indices: 12448032--12448078 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
12448022 TGTCAAATAA
*
12448032 TATTTCTAATATTTTATAATTTTT
1 TATTTCTAATATTATAT-ATTTTT
*
12448056 TATTTTTACATATTATATATTTT
1 TATTTCTA-ATATTATATATTTT
12448079 AAATTTCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (23 bp):
TATTTCTAATATTATATATTTTT
Found at i:12449346 original size:29 final size:29
Alignment explanation
Indices: 12449299--12449362 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
12449289 AAACCCTGAA
*
12449299 TATATTATGTTATAAAATTATTA-TATTAAT
1 TATA-TATGTTATAAAATTATAATTA-TAAT
12449329 TATATATGTTA-AATAATTATAATTATAAT
1 TATATATGTTATAA-AATTATAATTATAAT
12449358 TATAT
1 TATAT
12449363 TAAATTACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 2 0.06
29 23 0.74
30 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (29 bp):
TATATATGTTATAAAATTATAATTATAAT
Found at i:12449549 original size:39 final size:39
Alignment explanation
Indices: 12449469--12449541 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
12449459 AAAAATTATA
*
12449469 TTTAATACAATAAAATATTTATAATATTTATTTGTATTT
1 TTTAATACAATAAAATATTTATAATATTTATTGGTATTT
*
12449508 TTTAATACAATAAAAT-TTTATTATATTTA-TGGTA
1 TTTAATACAATAAAATATTTATAATATTTATTGGTA
12449542 GTGTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 4 0.12
38 12 0.38
39 16 0.50
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (39 bp):
TTTAATACAATAAAATATTTATAATATTTATTGGTATTT
Found at i:12451672 original size:24 final size:24
Alignment explanation
Indices: 12451651--12451711 Score: 95
Period size: 25 Copynumber: 2.5 Consensus size: 24
12451641 AGTAAAATTT
*
12451651 TATTTTGGTTTTACAGGGAAATAA
1 TATTTTAGTTTTACAGGGAAATAA
*
12451675 TATTTTATTTTTTACAGGGAAATAA
1 TATTTTA-GTTTTACAGGGAAATAA
12451700 TATTTTAGTTTT
1 TATTTTAGTTTT
12451712 TTTCATGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 10 0.30
25 23 0.70
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.51
Consensus pattern (24 bp):
TATTTTAGTTTTACAGGGAAATAA
Found at i:12451693 original size:25 final size:26
Alignment explanation
Indices: 12451659--12451713 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 26
12451649 TTTATTTTGG
12451659 TTTTACAGGGAAATAATATTTTA-TT
1 TTTTACAGGGAAATAATATTTTAGTT
12451684 TTTTACAGGGAAATAATATTTTAGTT
1 TTTTACAGGGAAATAATATTTTAGTT
12451710 TTTT
1 TTTT
12451714 TCATGTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 23 0.79
26 6 0.21
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.51
Consensus pattern (26 bp):
TTTTACAGGGAAATAATATTTTAGTT
Found at i:12452966 original size:15 final size:15
Alignment explanation
Indices: 12452948--12452996 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
12452938 ATAATTATTT
12452948 TTATTTTATTTTAAA
1 TTATTTTATTTTAAA
* *
12452963 TTATATTATATTAAA
1 TTATTTTATTTTAAA
* *
12452978 ATATTTAATTTTAAA
1 TTATTTTATTTTAAA
12452993 TTAT
1 TTAT
12452997 ATTTTGAAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATTTTATTTTAAA
Found at i:12453015 original size:32 final size:30
Alignment explanation
Indices: 12452949--12453037 Score: 106
Period size: 30 Copynumber: 2.9 Consensus size: 30
12452939 TAATTATTTT
* *
12452949 TATTTTATTTTAAATTATATTATATTAAAA
1 TATTTTATTTTAAATTATATTTTAATAAAA
*
12452979 TATTTAATTTTAAATTATATTTTGAAATAAAA
1 TATTTTATTTTAAATTATATTTT--AATAAAA
* * *
12453011 TATTTTGTATTAAATTATATTTAAATA
1 TATTTTATTTTAAATTATATTTTAATA
12453038 TTTTATTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
30 25 0.50
32 25 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (30 bp):
TATTTTATTTTAAATTATATTTTAATAAAA
Found at i:12453581 original size:57 final size:57
Alignment explanation
Indices: 12453493--12453606 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
12453483 AAAAGAATGA
*
12453493 ATAATATTAAAAAGACTTATTCTCATAGCTATTAGAATTTCTACCTTACCCTGATAG
1 ATAATATTAAAAAGACTTATTCTCATAGCTATTAGAATTACTACCTTACCCTGATAG
12453550 ATAATATTAAAAAGACTTATTCTCATAGCTATTAGAATTACTACCTTACCCTGATAG
1 ATAATATTAAAAAGACTTATTCTCATAGCTATTAGAATTACTACCTTACCCTGATAG
12453607 GGATTCCTAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (57 bp):
ATAATATTAAAAAGACTTATTCTCATAGCTATTAGAATTACTACCTTACCCTGATAG
Found at i:12453618 original size:57 final size:57
Alignment explanation
Indices: 12453495--12453621 Score: 191
Period size: 57 Copynumber: 2.2 Consensus size: 57
12453485 AAGAATGAAT
* * *
12453495 AATATTAAAAAGACTTATTCTCATAGCTATTAGAATTTCTACCTTACCCTGATAGAT
1 AATACTAAAAAGACTTATTCTCATAGCTATTAGAATTACTACCTTACCCTGATAGAG
* *
12453552 AATATTAAAAAGACTTATTCTCATAGCTATTAGAATTACTACCTTACCCTGATAGGG
1 AATACTAAAAAGACTTATTCTCATAGCTATTAGAATTACTACCTTACCCTGATAGAG
* *
12453609 ATTCCTAAAAAGA
1 AATACTAAAAAGA
12453622 ATTTATAGTC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 64 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (57 bp):
AATACTAAAAAGACTTATTCTCATAGCTATTAGAATTACTACCTTACCCTGATAGAG
Found at i:12454127 original size:5 final size:5
Alignment explanation
Indices: 12454113--12454151 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
12454103 TCTGCATTTG
*
12454113 TTTAT CTTAT TTTAT TTTAT TTTAT TTTATT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT TTT
12454152 TATCTTTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:12455179 original size:32 final size:32
Alignment explanation
Indices: 12455132--12455205 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
12455122 TTACACATAC
* * * *
12455132 ATATATATATCTATATCCATC-ATACATTTTT
1 ATATATATATATATATACATCTATAAATTTAT
*
12455163 ATAATATATATATATATACGTCTATAAATTTAT
1 AT-ATATATATATATATACATCTATAAATTTAT
12455196 ATATATATAT
1 ATATATATAT
12455206 GTACATAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
31 2 0.06
32 24 0.67
33 10 0.28
ACGTcount: A:0.42, C:0.09, G:0.01, T:0.47
Consensus pattern (32 bp):
ATATATATATATATATACATCTATAAATTTAT
Found at i:12455463 original size:36 final size:35
Alignment explanation
Indices: 12455414--12455490 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 35
12455404 CCTTTTATAA
*
12455414 ATATATTTTTATTTATATAAATAT-ATATACATATTT
1 ATATTTTTTTATTT-TATAAATATCATATACAT-TTT
* *
12455450 ATATTTTTTTATTTTATAATTTTCATATACATTTT
1 ATATTTTTTTATTTTATAAATATCATATACATTTT
12455485 -TATTTT
1 ATATTTT
12455491 CATATAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 6 0.16
35 10 0.27
36 21 0.57
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (35 bp):
ATATTTTTTTATTTTATAAATATCATATACATTTT
Found at i:12455504 original size:27 final size:26
Alignment explanation
Indices: 12455455--12455505 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
12455445 TATTTATATT
*
12455455 TTTTTATTTTATAATTTTCATATACA
1 TTTTTATTTTATAAATTTCATATACA
12455481 TTTTTATTTTCATATAATTT-ATATA
1 TTTTTATTTT-ATA-AATTTCATATA
12455506 TATACCTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 10 0.45
27 8 0.36
28 4 0.18
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTTTATTTTATAAATTTCATATACA
Found at i:12482145 original size:6 final size:6
Alignment explanation
Indices: 12482136--12482190 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
12482126 TTTATTTTAT
* * *
12482136 TTAATA TTAAT- TTAATTA TT-TTA TTTTATA TTAGTA TTAATA TTAATA
1 TTAATA TTAATA TTAA-TA TTAATA -TTAATA TTAATA TTAATA TTAATA
12482184 TTAATA T
1 TTAATA T
12482191 AAAAATTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
5 6 0.15
6 30 0.75
7 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (6 bp):
TTAATA
Found at i:12485766 original size:14 final size:14
Alignment explanation
Indices: 12485747--12485777 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
12485737 ATACTAATGC
12485747 TAGCAGTGAAATAA
1 TAGCAGTGAAATAA
12485761 TAGCAGTGAAATAA
1 TAGCAGTGAAATAA
12485775 TAG
1 TAG
12485778 ACTAAGTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.06, G:0.23, T:0.23
Consensus pattern (14 bp):
TAGCAGTGAAATAA
Found at i:12488061 original size:22 final size:22
Alignment explanation
Indices: 12488006--12488048 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
12487996 TTTATTGTTC
12488006 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
12488028 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
12488049 TAGCCATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:12490428 original size:21 final size:19
Alignment explanation
Indices: 12490387--12490429 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
12490377 TGATTATATG
* *
12490387 TATTAATTAAAATATACTA
1 TATTAATTAAAATAAAATA
12490406 TATTATATTATAAATAAAATA
1 TATTA-ATTA-AAATAAAATA
12490427 TAT
1 TAT
12490430 AAGGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 4 0.20
21 11 0.55
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TATTAATTAAAATAAAATA
Found at i:12490710 original size:19 final size:19
Alignment explanation
Indices: 12490688--12490726 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
12490678 AAAGAAAGGT
12490688 AAAGTACAACAACAAAACA
1 AAAGTACAACAACAAAACA
* * *
12490707 AAAGTAGACCAACAAGACA
1 AAAGTACAACAACAAAACA
12490726 A
1 A
12490727 CAACAAAGGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.64, C:0.21, G:0.10, T:0.05
Consensus pattern (19 bp):
AAAGTACAACAACAAAACA
Found at i:12494304 original size:4 final size:4
Alignment explanation
Indices: 12494280--12494332 Score: 63
Period size: 4 Copynumber: 13.2 Consensus size: 4
12494270 AACTTGAGCC
* * *
12494280 TTTA TTTA CTTA ATTA CTTA TTTA TTTA TTT- TTTA TTTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA
12494328 TTTA T
1 TTTA T
12494333 GTACAAGCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 3 0.07
4 36 0.84
5 4 0.09
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:12494993 original size:28 final size:28
Alignment explanation
Indices: 12494953--12495009 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
12494943 TATCCATACT
12494953 ATATGCACATGTTAAGGATGAGAAATCG
1 ATATGCACATGTTAAGGATGAGAAATCG
12494981 ATATGCACATGTTAAGGATGAGAAATCG
1 ATATGCACATGTTAAGGATGAGAAATCG
12495009 A
1 A
12495010 CTTCAGAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.25
Consensus pattern (28 bp):
ATATGCACATGTTAAGGATGAGAAATCG
Found at i:12496820 original size:20 final size:20
Alignment explanation
Indices: 12496795--12496832 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
12496785 GAGAAAAAAG
12496795 GGTATGCCCACAGTGCATAC
1 GGTATGCCCACAGTGCATAC
12496815 GGTATGCCCACAGTGCAT
1 GGTATGCCCACAGTGCAT
12496833 CATTGAGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.26, T:0.21
Consensus pattern (20 bp):
GGTATGCCCACAGTGCATAC
Found at i:12505948 original size:14 final size:14
Alignment explanation
Indices: 12505925--12505963 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
12505915 ATATGCGGAA
12505925 ACAT-GAAATTAGG
1 ACATAGAAATTAGG
12505938 ACATAGAAATTAGG
1 ACATAGAAATTAGG
*
12505952 ACAAAGAAATTA
1 ACATAGAAATTA
12505964 TTAAAATGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.54, C:0.08, G:0.18, T:0.21
Consensus pattern (14 bp):
ACATAGAAATTAGG
Found at i:12517891 original size:13 final size:13
Alignment explanation
Indices: 12517873--12517901 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
12517863 CCATTCAATG
12517873 AGGAGGTCTTCAT
1 AGGAGGTCTTCAT
12517886 AGGAGGTCTTCAT
1 AGGAGGTCTTCAT
12517899 AGG
1 AGG
12517902 TCAACAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.14, G:0.34, T:0.28
Consensus pattern (13 bp):
AGGAGGTCTTCAT
Found at i:12528434 original size:16 final size:16
Alignment explanation
Indices: 12528415--12528445 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12528405 GCATTTTCAG
*
12528415 AAAACCTTGTTTTAGT
1 AAAACCATGTTTTAGT
12528431 AAAACCATGTTTTAG
1 AAAACCATGTTTTAG
12528446 CTAACGGTCG
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:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (16 bp):
AAAACCATGTTTTAGT
Found at i:12532870 original size:29 final size:27
Alignment explanation
Indices: 12532804--12532870 Score: 71
Period size: 31 Copynumber: 2.3 Consensus size: 27
12532794 GAGTTTCACG
* *
12532804 TGTATAATTACACCAAATTAAAGTTTA
1 TGTATAATTACACCAAATCAAAGTTCA
*
12532831 TGTATACAATTACACATTAAATCAAAGTTCA
1 TGTAT--AATTACAC--CAAATCAAAGTTCA
12532862 TGTATAATT
1 TGTATAATT
12532871 TTGAGATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 5 0.15
29 12 0.36
31 16 0.48
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.37
Consensus pattern (27 bp):
TGTATAATTACACCAAATCAAAGTTCA
Found at i:12533666 original size:11 final size:11
Alignment explanation
Indices: 12533650--12533679 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12533640 GACTCGGTTT
12533650 CCACTTATATG
1 CCACTTATATG
12533661 CCACTTATATG
1 CCACTTATATG
*
12533672 CCAATTAT
1 CCACTTAT
12533680 CATACTCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.37
Consensus pattern (11 bp):
CCACTTATATG
Found at i:12534726 original size:110 final size:110
Alignment explanation
Indices: 12534491--12535235 Score: 948
Period size: 110 Copynumber: 6.7 Consensus size: 110
12534481 GATACATAAT
**
12534491 TTCATGTATCGTGATCTT-TCATTTCAATTCATACACTATCGAAGGCTACACCATGAATATAAGA
1 TTCATGTATCGTGATCTTCT-ATTTTGATTCATACACTATCGAAGGCTACACCATGAATATAA-A
* * *
12534555 TA-GA-CATATCATGCCATGGGTCTTAACCATATGGTCTTAGACACA
64 TACAAGCATATCATGCCATGGGTCTTAACCACATGGTCTTACACACA
* * *
12534600 TTCATTTATCGTGATCTTCTATTTCGATTCATACACTATCAAAGGCTACACCATGAATATAAATA
1 TTCATGTATCGTGATCTTCTATTTTGATTCATACACTATCGAAGGCTACACCATGAATATAAATA
* * **
12534665 CAAGCATATCATGCTATGGTTCTTAACCACATGGTCTTACATGCA
66 CAAGCATATCATGCCATGGGTCTTAACCACATGGTCTTACACACA
* * *
12534710 TTCATGTATCATGATCTACTATTTTGATTCATACACTATCGAAGGCTACACCATGAATATAAGTA
1 TTCATGTATCGTGATCTTCTATTTTGATTCATACACTATCGAAGGCTACACCATGAATATAAATA
* * * *
12534775 CAAACATATCATGCCATGGGTCTTAACCATATGGTGTTGCACACA
66 CAAGCATATCATGCCATGGGTCTTAACCACATGGTCTTACACACA
* * * *
12534820 TTCATTTATCGTGATCTTCCATTTTGATTCATACACTACCAAAGGCTACACCATGAATATAAATA
1 TTCATGTATCGTGATCTTCTATTTTGATTCATACACTATCGAAGGCTACACCATGAATATAAATA
* * * * *
12534885 TGAA-CATATGATGCTATGGCTCTTAAACACATGGTCTTACACACA
66 -CAAGCATATCATGCCATGGGTCTTAACCACATGGTCTTACACACA
* * *
12534930 TTCATGTATTGTGATCTACTATTTTGATTCATACACTATCGAAGGCTACACCATAAATATAAATA
1 TTCATGTATCGTGATCTTCTATTTTGATTCATACACTATCGAAGGCTACACCATGAATATAAATA
* * * *
12534995 CAAACATATCATGACATGGGTTTTAAACACATGGTCTTACACACA
66 CAAGCATATCATGCCATGGGTCTTAACCACATGGTCTTACACACA
*
12535040 TTCATGTATCGTGATCTATC-ATTTCGATTCATACACTATCGAAGGCTACACCATGAATATAAAT
1 TTCATGTATCGTGATCT-TCTATTTTGATTCATACACTATCGAAGGCTACACCATGAATATAAAT
12535104 A-AAGACATATCATGCCATGGGTCTTAATCC-CATGGTCTTACACACA
65 ACAAG-CATATCATGCCATGGGTCTTAA-CCACATGGTCTTACACACA
* * * *
12535150 TTCAAGTATCATGATCTGAC-ATTTTGATTCATACACTATCGAATCGAAGGTTACACCATGAATA
1 TTCATGTATCGTGATCT-TCTATTTTGATTCATACAC--T---ATCGAAGGCTACACCATGAATA
* *
12535214 CAAATACAGGCATATCATGCCA
60 TAAATACAAGCATATCATGCCA
12535236 ATATGGTTAG
Statistics
Matches: 554, Mismatches: 68, Indels: 22
0.86 0.11 0.03
Matches are distributed among these distances:
108 3 0.01
109 62 0.11
110 444 0.80
111 4 0.01
112 1 0.00
115 38 0.07
116 2 0.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (110 bp):
TTCATGTATCGTGATCTTCTATTTTGATTCATACACTATCGAAGGCTACACCATGAATATAAATA
CAAGCATATCATGCCATGGGTCTTAACCACATGGTCTTACACACA
Found at i:12536310 original size:21 final size:21
Alignment explanation
Indices: 12536271--12536310 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12536261 GCACTTGTAT
*
12536271 TGCTTTTTTTTTTCCTTTTTA
1 TGCTTTTTTTTTACCTTTTTA
12536292 TGCTTTTTTTTTA-CTTTTT
1 TGCTTTTTTTTTACCTTTTT
12536311 CACTTCTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.05, C:0.12, G:0.05, T:0.78
Consensus pattern (21 bp):
TGCTTTTTTTTTACCTTTTTA
Found at i:12537349 original size:11 final size:12
Alignment explanation
Indices: 12537335--12537370 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
12537325 TTTTAAATTG
12537335 TTAAATTTAT-A
1 TTAAATTTATAA
12537346 TT-AATTTATAA
1 TTAAATTTATAA
12537357 TTAAATTT-TAA
1 TTAAATTTATAA
12537368 TTA
1 TTA
12537371 TTTTAACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 7 0.30
11 11 0.48
12 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TTAAATTTATAA
Found at i:12549884 original size:22 final size:21
Alignment explanation
Indices: 12549818--12549884 Score: 50
Period size: 22 Copynumber: 3.1 Consensus size: 21
12549808 TAATTTAGTC
12549818 ATTTTTATTTT-TTTAATATTT
1 ATTTTTATTTTGTTTAAT-TTT
* *
12549839 TTATTTTA-ATTG-TTACATTTTT
1 AT-TTTTATTTTGTTTA-A-TTTT
12549861 ATTTTTATTTTGTTTAATTCTT
1 ATTTTTATTTTGTTTAATT-TT
12549883 AT
1 AT
12549885 AGGTTCTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 13
0.67 0.08 0.25
Matches are distributed among these distances:
21 13 0.37
22 18 0.51
23 4 0.11
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (21 bp):
ATTTTTATTTTGTTTAATTTT
Found at i:12553347 original size:28 final size:28
Alignment explanation
Indices: 12553303--12553380 Score: 81
Period size: 27 Copynumber: 2.8 Consensus size: 28
12553293 TATTTAGATT
* * *
12553303 TTATTTAGTTTTCTTTTTCTTTTTC-TTC
1 TTATTT-GTTTTATTTTTATTTTTCATAC
12553331 TTATTTGTATTTA-TTTTATTTTTCATAC
1 TTATTTGT-TTTATTTTTATTTTTCATAC
*
12553359 TTATATGTTTTA-TTTTATTTTT
1 TTATTTGTTTTATTTTTATTTTT
12553381 ATTTTGAACT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
27 26 0.59
28 18 0.41
ACGTcount: A:0.15, C:0.08, G:0.04, T:0.73
Consensus pattern (28 bp):
TTATTTGTTTTATTTTTATTTTTCATAC
Found at i:12553370 original size:27 final size:27
Alignment explanation
Indices: 12553317--12553380 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
12553307 TTAGTTTTCT
* * *
12553317 TTTTCTTTTTCTTCTTATTTGTATTTA
1 TTTTATTTTTCTACTTATATGTATTTA
12553344 TTTTATTTTTCATACTTATATGT-TTTA
1 TTTTATTTTTC-TACTTATATGTATTTA
12553371 TTTTATTTTT
1 TTTTATTTTT
12553381 ATTTTGAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 24 0.73
28 9 0.27
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.73
Consensus pattern (27 bp):
TTTTATTTTTCTACTTATATGTATTTA
Found at i:12555789 original size:49 final size:49
Alignment explanation
Indices: 12555706--12555800 Score: 145
Period size: 49 Copynumber: 1.9 Consensus size: 49
12555696 ATTTATTTAT
* *
12555706 AGGTTGAAAAACCTTATTCTAATCAATGTCAAATAGAAGTAGTGTAGTA
1 AGGTTGAAAAACCTTATTCTAATCAATATCAAATAGAAGAAGTGTAGTA
* * *
12555755 AGGTTGAAACACCTTATTCTAATTAATATTAAATAGAAGAAGTGTA
1 AGGTTGAAAAACCTTATTCTAATCAATATCAAATAGAAGAAGTGTA
12555801 CTTCTATATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (49 bp):
AGGTTGAAAAACCTTATTCTAATCAATATCAAATAGAAGAAGTGTAGTA
Found at i:12558802 original size:15 final size:15
Alignment explanation
Indices: 12558782--12558812 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12558772 GTTATGTAAG
12558782 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
*
12558797 TGAAAGGTTAAGAGT
1 TGAAAGGTCAAGAGT
12558812 T
1 T
12558813 ATGTTGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.32, T:0.26
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:12561319 original size:30 final size:30
Alignment explanation
Indices: 12561283--12561343 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
12561273 CAGATTTTAG
* * *
12561283 GAGCCACACGGGTTGGACACATGCCCATGT
1 GAGCCACACGAGCTGGACACACGCCCATGT
* *
12561313 GAGCCACATGAGCTGGACACACGGCCATGT
1 GAGCCACACGAGCTGGACACACGCCCATGT
12561343 G
1 G
12561344 CAAGCCCGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.25, C:0.30, G:0.31, T:0.15
Consensus pattern (30 bp):
GAGCCACACGAGCTGGACACACGCCCATGT
Found at i:12565887 original size:26 final size:26
Alignment explanation
Indices: 12565858--12565993 Score: 146
Period size: 26 Copynumber: 5.2 Consensus size: 26
12565848 GCCAACATAC
**
12565858 CAATATCGCAGCAAAACTGCCAGTAA
1 CAATATCGCAGCAAGGCTGCCAGTAA
* *
12565884 CAATATTGCAGCAAGGTTGCCAGTAA
1 CAATATCGCAGCAAGGCTGCCAGTAA
* * *
12565910 CAGTATCACAGTAAGGCTGCCAGTAA
1 CAATATCGCAGCAAGGCTGCCAGTAA
* * **
12565936 TAGTATCGCAGCAAGGCTGCCAAAAA
1 CAATATCGCAGCAAGGCTGCCAGTAA
* * *
12565962 CAGTATCACAGCAAAGCTGCCAGTAA
1 CAATATCGCAGCAAGGCTGCCAGTAA
12565988 CAATAT
1 CAATAT
12565994 ACTTCCTCCA
Statistics
Matches: 90, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 90 1.00
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (26 bp):
CAATATCGCAGCAAGGCTGCCAGTAA
Found at i:12565957 original size:52 final size:52
Alignment explanation
Indices: 12565861--12565993 Score: 176
Period size: 52 Copynumber: 2.6 Consensus size: 52
12565851 AACATACCAA
* * * * **
12565861 TATCGCAGCAAAACTGCCAGTAACAATATTGCAGCAAGGTTGCCAGTAACAG
1 TATCACAGCAAAGCTGCCAGTAACAATATCGCAGCAAGGCTGCCAAAAACAG
* * * *
12565913 TATCACAGTAAGGCTGCCAGTAATAGTATCGCAGCAAGGCTGCCAAAAACAG
1 TATCACAGCAAAGCTGCCAGTAACAATATCGCAGCAAGGCTGCCAAAAACAG
12565965 TATCACAGCAAAGCTGCCAGTAACAATAT
1 TATCACAGCAAAGCTGCCAGTAACAATAT
12565994 ACTTCCTCCA
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (52 bp):
TATCACAGCAAAGCTGCCAGTAACAATATCGCAGCAAGGCTGCCAAAAACAG
Found at i:12578834 original size:29 final size:31
Alignment explanation
Indices: 12578782--12578843 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
12578772 GCTTTTTGAA
12578782 AATATTTACAAAAAGAGGCATCT-AATTTTT
1 AATATTTACAAAAAGAGGCATCTAAATTTTT
12578812 AATATTTACAAAAAGA-GCATCTAAATTTTT
1 AATATTTACAAAAAGAGGCATCTAAATTTTT
12578842 AA
1 AA
12578844 AAATATTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 6 0.19
30 25 0.81
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (31 bp):
AATATTTACAAAAAGAGGCATCTAAATTTTT
Found at i:12592151 original size:25 final size:26
Alignment explanation
Indices: 12592111--12592159 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
12592101 TGAATTTGTT
12592111 TGTTCTTCAAATACTTTATTCTTTGC
1 TGTTCTTCAAATACTTTATTCTTTGC
* *
12592137 TGTTCTT-GAATACTTTTTTCTTT
1 TGTTCTTCAAATACTTTATTCTTT
12592160 TCAAGACACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.59
Consensus pattern (26 bp):
TGTTCTTCAAATACTTTATTCTTTGC
Found at i:12593383 original size:117 final size:117
Alignment explanation
Indices: 12593203--12593478 Score: 437
Period size: 117 Copynumber: 2.4 Consensus size: 117
12593193 CATTCTAACA
*
12593203 GAGCAGATTGAAGCCACGACGGCGAATCTTATCTCCCTGGCGTTAAGGCTTGGATTAGCTGAAGT
1 GAGCAGATTGAAGCCACGACGGCGAATCGTATCTCCCTGGCGTTAAGGCTTGGATTAGCTGAAGT
*
12593268 GGAGTGAATTGAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTACAGCG
66 GGAGCGAATTGAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTACAGCG
* * *
12593320 GAGCAGATTGAAGCCACGACGGCGAATCGTATCTCCTTGGCGTTAAGGTTTGGATTAGTTGAAGT
1 GAGCAGATTGAAGCCACGACGGCGAATCGTATCTCCCTGGCGTTAAGGCTTGGATTAGCTGAAGT
* * *
12593385 GGAGCGGATTGAAGCTGTGGGCAGCGAGTCCTATCTCTTTGGCATTACAGTG
66 GGAGCGAATTGAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTACAGCG
* * *
12593437 GAGCAGATTGAAACCACGACGGTGAATCTTA-CTCCCCTGGCG
1 GAGCAGATTGAAGCCACGACGGCGAATCGTATCT-CCCTGGCG
12593479 GAGTAGTGGA
Statistics
Matches: 146, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
116 2 0.01
117 144 0.99
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (117 bp):
GAGCAGATTGAAGCCACGACGGCGAATCGTATCTCCCTGGCGTTAAGGCTTGGATTAGCTGAAGT
GGAGCGAATTGAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTACAGCG
Found at i:12593644 original size:50 final size:50
Alignment explanation
Indices: 12593491--12594021 Score: 196
Period size: 50 Copynumber: 10.6 Consensus size: 50
12593481 GTAGTGGAAC
* * ** *
12593491 AGATTGAAGGTACGACGGTGAATCTTGTTTCCCCAACATTACAATTAAAA
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGTAATGAAAA
* ** ** ** * * *
12593541 TGATTGAAG-T-CGCAACGGCG-ATCTT-ACTCCCCTGGCGGTGTAGTGGAAC
1 AGATTGAAGCTACG--ACGGCGAATCTTGTTTCCCC-AACATTGTAATGAAAA
* *
12593590 AGATTGAAGCTACGACGGTGAATCTTGTTTCCCCAACATTGTAATTAAAA
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGTAATGAAAA
** * * ** ** ** * * *
12593640 AGATTGAAGCCGCAACGGTGAATCTT-ACTCCCCTGGCGGTGTAGTGGAAT
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCC-AACATTGTAATGAAAA
* * * *
12593690 AGATTGAAGCTACGACAGCGAATCTTGTTTCCCTAACATTGCAATTAAAA
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGTAATGAAAA
* * * * ** ** ** * * *
12593740 ATATTGAAGCCACAATGGCGAATCTT-ACTCCCCTGGCGGTGTAGTGGAAT
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCC-AACATTGTAATGAAAA
* ** ** *
12593790 TGATTGAAGCTACGACGG-GAAATCTCATTTCCCCAACATTACAATTAAAA
1 AGATTGAAGCTACGACGGCG-AATCTTGTTTCCCCAACATTGTAATGAAAA
** * ** ** * * * *
12593840 AGATTGAAGCCGCAACGGCGAATCTT-ACTCCCCTGGCAATGTAGTGGAAT
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCC-AACATTGTAATGAAAA
* * *
12593890 AGATTGAAGCTACGACGGCGAATCTTGTTTCTCCAACATTGCAATTAAAA
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGTAATGAAAA
** * * ** **** * * * * *
12593940 AGATTGAAGCCGCAACGGTGAATCTTACTTCCTTGGCAGTATAGTGGAAC
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGTAATGAAAA
*
12593990 AGATTGAAGCTACGACGGTGAATCTTGTTTCC
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCC
12594022 TGACATATCA
Statistics
Matches: 322, Mismatches: 144, Indels: 30
0.65 0.29 0.06
Matches are distributed among these distances:
48 7 0.02
49 40 0.12
50 254 0.79
51 21 0.07
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (50 bp):
AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGTAATGAAAA
Found at i:12593718 original size:100 final size:100
Alignment explanation
Indices: 12593441--12594021 Score: 842
Period size: 100 Copynumber: 5.8 Consensus size: 100
12593431 ACAGTGGAGC
* * * * * *
12593441 AGATTGAAACCACGACGGTGAATCTTACTCCCCTGGCGGAGTAGTGGAACAGATTGAAGGTACGA
1 AGATTGAAGCCGCAACGGCGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
*
12593506 CGGTGAATCTTGTTTCCCCAACATTACAATTAAAA
66 CGGTGAATCTTGTTTCCCCAACATTGCAATTAAAA
* *
12593541 TGATTGAAGTCGCAACGGCG-ATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
1 AGATTGAAGCCGCAACGGCGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
*
12593605 CGGTGAATCTTGTTTCCCCAACATTGTAATTAAAA
66 CGGTGAATCTTGTTTCCCCAACATTGCAATTAAAA
* *
12593640 AGATTGAAGCCGCAACGGTGAATCTTACTCCCCTGGCGGTGTAGTGGAATAGATTGAAGCTACGA
1 AGATTGAAGCCGCAACGGCGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
* * *
12593705 CAGCGAATCTTGTTTCCCTAACATTGCAATTAAAA
66 CGGTGAATCTTGTTTCCCCAACATTGCAATTAAAA
* * * **
12593740 ATATTGAAGCCACAATGGCGAATCTTACTCCCCTGGCGGTGTAGTGGAATTGATTGAAGCTACGA
1 AGATTGAAGCCGCAACGGCGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
** *
12593805 CGG-GAAATCTCATTTCCCCAACATTACAATTAAAA
66 CGGTG-AATCTTGTTTCCCCAACATTGCAATTAAAA
** *
12593840 AGATTGAAGCCGCAACGGCGAATCTTACTCCCCTGGCAATGTAGTGGAATAGATTGAAGCTACGA
1 AGATTGAAGCCGCAACGGCGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
* *
12593905 CGGCGAATCTTGTTTCTCCAACATTGCAATTAAAA
66 CGGTGAATCTTGTTTCCCCAACATTGCAATTAAAA
* * * * *
12593940 AGATTGAAGCCGCAACGGTGAATCTTACTTCCTTGGCAGTATAGTGGAACAGATTGAAGCTACGA
1 AGATTGAAGCCGCAACGGCGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
12594005 CGGTGAATCTTGTTTCC
66 CGGTGAATCTTGTTTCC
12594022 TGACATATCA
Statistics
Matches: 432, Mismatches: 46, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
99 93 0.22
100 338 0.78
101 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (100 bp):
AGATTGAAGCCGCAACGGCGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
CGGTGAATCTTGTTTCCCCAACATTGCAATTAAAA
Found at i:12594277 original size:45 final size:45
Alignment explanation
Indices: 12594227--12594349 Score: 124
Period size: 45 Copynumber: 2.7 Consensus size: 45
12594217 GTCATATCAG
**
12594227 GTCTTATCACCCT-AAAGTTACAGAGGAGCAGACCCAAGAAAGTGA
1 GTCTTATCACCCTGAAA-TTACAGAGGAGCAGACCCAAGAAAGCAA
* * * *
12594272 GTCTTATCTCCCTGAAATTGCAGTGGAGCAGACTCAAGAAAGCAA
1 GTCTTATCACCCTGAAATTACAGAGGAGCAGACCCAAGAAAGCAA
* * * *
12594317 GTCTTAGC-CTCCTGAAATTGCAGTGGGGCAGAC
1 GTCTTATCAC-CCTGAAATTACAGAGGAGCAGAC
12594350 TGAATAAACA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
44 1 0.01
45 64 0.94
46 3 0.04
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (45 bp):
GTCTTATCACCCTGAAATTACAGAGGAGCAGACCCAAGAAAGCAA
Found at i:12594350 original size:45 final size:45
Alignment explanation
Indices: 12594251--12594350 Score: 139
Period size: 45 Copynumber: 2.2 Consensus size: 45
12594241 AAGTTACAGA
* ** *
12594251 GGAGCAGACCCAAGAAAGTGAGTCTTATCTCCCTGAAATTGCAGT
1 GGAGCAGACTCAAGAAAGCAAGTCTTACCTCCCTGAAATTGCAGT
12594296 GGAGCAGACTCAAGAAAGCAAGTCTTAGCCT-CCTGAAATTGCAGT
1 GGAGCAGACTCAAGAAAGCAAGTCTTA-CCTCCCTGAAATTGCAGT
*
12594341 GGGGCAGACT
1 GGAGCAGACT
12594351 GAATAAACAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
45 47 0.96
46 2 0.04
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (45 bp):
GGAGCAGACTCAAGAAAGCAAGTCTTACCTCCCTGAAATTGCAGT
Found at i:12605746 original size:33 final size:33
Alignment explanation
Indices: 12605709--12605775 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
12605699 ATCAGTTAGA
12605709 AGTAAAGGCTTACACTACTGTGACTGATGAATC
1 AGTAAAGGCTTACACTACTGTGACTGATGAATC
12605742 AGTAAAGGCTTACACTACTGTGACTGATGAATC
1 AGTAAAGGCTTACACTACTGTGACTGATGAATC
12605775 A
1 A
12605776 TGTTTATGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (33 bp):
AGTAAAGGCTTACACTACTGTGACTGATGAATC
Found at i:12609980 original size:30 final size:30
Alignment explanation
Indices: 12609939--12610006 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
12609929 ATTTTGGGCA
12609939 GATAC-TTTTATTCCTATAGAAACTTGGCG
1 GATACTTTTTATTCCTATAGAAACTTGGCG
12609968 GATACTTTTTATTCCTATAGAAACTTGGCG
1 GATACTTTTTATTCCTATAGAAACTTGGCG
12609998 GATACTTTT
1 GATACTTTT
12610007 AATTTCGGGC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 5 0.13
30 33 0.87
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.41
Consensus pattern (30 bp):
GATACTTTTTATTCCTATAGAAACTTGGCG
Found at i:12617304 original size:9 final size:10
Alignment explanation
Indices: 12617288--12617340 Score: 61
Period size: 10 Copynumber: 5.1 Consensus size: 10
12617278 CGTGTGAACC
12617288 ATTTTTTTCA
1 ATTTTTTTCA
*
12617298 ATTTTTTTCT
1 ATTTTTTTCA
12617308 ATTTTTTTCAAA
1 ATTTTTTTC--A
**
12617320 AGATTTTTCA
1 ATTTTTTTCA
12617330 ATTTTTTTCA
1 ATTTTTTTCA
12617340 A
1 A
12617341 ACGTTATTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
10 28 0.80
12 7 0.20
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (10 bp):
ATTTTTTTCA
Found at i:12617349 original size:24 final size:22
Alignment explanation
Indices: 12617300--12617360 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 22
12617290 TTTTTTCAAT
12617300 TTTTTTCTATTTTTTTCAAAAGA
1 TTTTTTC-ATTTTTTTCAAAAGA
*
12617323 -TTTTTCAATTTTTTTCAAACGTTA
1 TTTTTTC-ATTTTTTTCAAAAG--A
12617347 TTTTTTCATTTTTT
1 TTTTTTCATTTTTT
12617361 AATATAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 19 0.58
24 8 0.24
25 6 0.18
ACGTcount: A:0.21, C:0.10, G:0.03, T:0.66
Consensus pattern (22 bp):
TTTTTTCATTTTTTTCAAAAGA
Found at i:12618922 original size:27 final size:27
Alignment explanation
Indices: 12618864--12619042 Score: 207
Period size: 27 Copynumber: 6.7 Consensus size: 27
12618854 GGGTATAACA
* * *
12618864 GTCATTTTATCCTAT-GAGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
*
12618890 GACATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
12618917 GTCATTCTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
12618944 GTCATTTTATCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
12618971 ATCATCTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
12618998 GTCAATTTACCATATGAGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
12619025 GTTATTTTATCCTATGGG
1 GTCATTTTACCCTATGGG
12619043 CTATTTTAGT
Statistics
Matches: 126, Mismatches: 26, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
26 13 0.10
27 113 0.90
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:12618958 original size:54 final size:52
Alignment explanation
Indices: 12618864--12619064 Score: 188
Period size: 54 Copynumber: 3.8 Consensus size: 52
12618854 GGGTATAACA
* * * * *
12618864 GTCATTTTATCCTATGAGGTATTTCAGACATTTTACCCTATGGGGGTATTTCG
1 GTCATTCTACCCTATGGGGTATTTCGGTCATTTTA-CCTATGGGGGTATTTCG
12618917 GTCATTCTACCCTATAGGGGTATTTCGGTCATTTTATCCTATGGGGGTATTTCG
1 GTCATTCTACCCTAT-GGGGTATTTCGGTCATTTTA-CCTATGGGGGTATTTCG
* * * * *
12618971 ATCA-TCTTACCCTATGGGGGTATTTTGGTCAATTTACCATATGAGGGTATTTCA
1 GTCATTC-TACCCTAT-GGGGTATTTCGGTCATTTTACC-TATGGGGGTATTTCG
* * * * ** *
12619025 GTTATTTTATCCTATGGGCTATTTTAGTTATTTTACCTAT
1 GTCATTCTACCCTATGGGGTATTTCGGTCATTTTACCTAT
12619065 TTTAGGGTTT
Statistics
Matches: 124, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
52 3 0.02
53 35 0.28
54 85 0.69
55 1 0.01
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.43
Consensus pattern (52 bp):
GTCATTCTACCCTATGGGGTATTTCGGTCATTTTACCTATGGGGGTATTTCG
Found at i:12619001 original size:81 final size:81
Alignment explanation
Indices: 12618862--12619042 Score: 253
Period size: 81 Copynumber: 2.2 Consensus size: 81
12618852 AGGGGTATAA
* *
12618862 CAGTCATTTTATCCTAT-GAGGTATTTCAGACATTTTACCCTATGGGGGTATTTCGGTC-ATTCT
1 CAGTCATTTTATCCTATGGGGGTATTTCAGACATCTTACCCTATGGGGGTATTTCGGTCAATT-T
*
12618925 ACCCTAT-AGGGGTATTT
65 ACCATATGA-GGGTATTT
* *
12618942 CGGTCATTTTATCCTATGGGGGTATTTC-GATCATCTTACCCTATGGGGGTATTTTGGTCAATTT
1 CAGTCATTTTATCCTATGGGGGTATTTCAGA-CATCTTACCCTATGGGGGTATTTCGGTCAATTT
12619006 ACCATATGAGGGTATTT
65 ACCATATGAGGGTATTT
*
12619023 CAGTTATTTTATCCTATGGG
1 CAGTCATTTTATCCTATGGG
12619043 CTATTTTAGT
Statistics
Matches: 90, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
80 18 0.20
81 68 0.76
82 4 0.04
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (81 bp):
CAGTCATTTTATCCTATGGGGGTATTTCAGACATCTTACCCTATGGGGGTATTTCGGTCAATTTA
CCATATGAGGGTATTT
Found at i:12622480 original size:27 final size:27
Alignment explanation
Indices: 12622450--12622663 Score: 243
Period size: 27 Copynumber: 7.9 Consensus size: 27
12622440 GGTATAACAG
*
12622450 TCATTTTATCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
*
12622477 TCATTTTACCCTATGGGAGTATTTC-A
1 TCATTTTACCCTATGGGGGTATTTCGA
* *
12622503 GTCATTCTACCTTATGGGGGTATTTCGA
1 -TCATTTTACCCTATGGGGGTATTTCGA
* *
12622531 TCATTTTATCCTATGGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGA
*
12622558 TTATTTTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
** * *
12622585 TCATTTTACTTTATGAGTGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
** *
12622612 TCATTTTACCCTATAAGGGTATTT-TA
1 TCATTTTACCCTATGGGGGTATTTCGA
* * *
12622638 GTCATTTTACCGTATAGGGATATTTC
1 -TCATTTTACCCTATGGGGGTATTTC
12622664 AGTTATTTTA
Statistics
Matches: 158, Mismatches: 25, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
26 2 0.01
27 155 0.98
28 1 0.01
ACGTcount: A:0.21, C:0.15, G:0.20, T:0.44
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGA
Found at i:12622540 original size:81 final size:81
Alignment explanation
Indices: 12622450--12622676 Score: 289
Period size: 81 Copynumber: 2.8 Consensus size: 81
12622440 GGTATAACAG
*
12622450 TCATTTTATCCTATGGGGGTATTTCGATCATTTTACCCTATGGGAGTATTTCAGTCATTCTACCT
1 TCATTTTATCCTATGGGGGTATTTCGATCATTTTACCCTATGGGAGTATTTCAGTCATTTTACCT
*
12622515 TATGGGGGTATTTCGA
66 TATGAGGGTATTTCGA
* * * *
12622531 TCATTTTATCCTATGGGGGTATTTCGGTTATTTTACCCTATGGGGGTATTTC-GATCATTTTACT
1 TCATTTTATCCTATGGGGGTATTTCGATCATTTTACCCTATGGGAGTATTTCAG-TCATTTTACC
*
12622595 TTATGAGTGTATTTCGA
65 TTATGAGGGTATTTCGA
* ** * * *
12622612 TCATTTTACCCTATAAGGGTATTT-TAGTCATTTTACCGTATAGGGA-TATTTCAGTTATTTTAC
1 TCATTTTATCCTATGGGGGTATTTCGA-TCATTTTACCCTAT-GGGAGTATTTCAGTCATTTTAC
12622675 CT
64 CT
12622677 ATTTTGGGGT
Statistics
Matches: 125, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
80 1 0.01
81 120 0.96
82 4 0.03
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.45
Consensus pattern (81 bp):
TCATTTTATCCTATGGGGGTATTTCGATCATTTTACCCTATGGGAGTATTTCAGTCATTTTACCT
TATGAGGGTATTTCGA
Found at i:12628939 original size:76 final size:78
Alignment explanation
Indices: 12628811--12628953 Score: 200
Period size: 76 Copynumber: 1.9 Consensus size: 78
12628801 TTGGACTTGG
* * *
12628811 TTAAAGGTGTGAATGTTATATATATGTATATGTGAGTTGGAACATATATGTATATACATGAATAA
1 TTAAAGGTATGAATGTTATATATATGTATATGTAAGTTCGAACATATATGTATATACATGAATAA
12628876 GTCTTGAATATAT
66 GTCTTGAATATAT
* * * * *
12628889 TTAAAGGTATGAATG-T-TATGTATGTATATGTAATTTCGAATATGTATGTATATACATGTATAA
1 TTAAAGGTATGAATGTTATATATATGTATATGTAAGTTCGAACATATATGTATATACATGAATAA
12628952 GT
66 GT
12628954 TTTTGTATTG
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 42 0.74
77 1 0.02
78 14 0.25
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.41
Consensus pattern (78 bp):
TTAAAGGTATGAATGTTATATATATGTATATGTAAGTTCGAACATATATGTATATACATGAATAA
GTCTTGAATATAT
Found at i:12640471 original size:40 final size:41
Alignment explanation
Indices: 12640427--12640518 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 41
12640417 TCCTTGAGAG
** *
12640427 CGCGATTTCCTTCCACATCAGCCT-C-TCGCGCTGACGTGGA
1 CGCGATTTCCTGACACAT-ACCCTACATCGCGCTGACGTGGA
* *
12640467 CGCGATTTCCTGACGCGTACCCTGACATCGCGCTGACGTGGA
1 CGCGATTTCCTGACACATACCCT-ACATCGCGCTGACGTGGA
12640509 CGCGATTTCC
1 CGCGATTTCC
12640519 CGGAAAAAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
39 4 0.09
40 14 0.32
41 1 0.02
42 25 0.57
ACGTcount: A:0.15, C:0.36, G:0.25, T:0.24
Consensus pattern (41 bp):
CGCGATTTCCTGACACATACCCTACATCGCGCTGACGTGGA
Found at i:12641114 original size:12 final size:12
Alignment explanation
Indices: 12641097--12641122 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12641087 CAAAACAGGC
12641097 TTTTAGCGGCGT
1 TTTTAGCGGCGT
12641109 TTTTAGCGGCGT
1 TTTTAGCGGCGT
12641121 TT
1 TT
12641123 AGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:12641381 original size:115 final size:114
Alignment explanation
Indices: 12641191--12641748 Score: 748
Period size: 114 Copynumber: 4.9 Consensus size: 114
12641181 AAAATAAGCA
* * * * * *
12641191 TTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAAGCCTACCGACGTCATTTCCCGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCAAACGACGCCGTTTTCTGAGCTT
* * *
12641255 TCGGGGATTTAGCGGCGTTTCTAAGAAAGCGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAAGGCT
* * * *
12641304 TTAGCGACG-TTTTCAGGAAAGCGCCGCAAAAAAAACCTAAGCCAAACGACGCCGTTTTCTTATC
1 TTAGCGGCGTTTTTGA-GAAAGCGCCGC-AAAAAAACCTAAGCCAAACGACGCCGTTTTCTGAGC
* * *
12641368 TTTCGGGGGTTTAGCGGCGTTTTTACGGAAGCGCCGCTAATGCTCAGGGCT
64 TTTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAAGGCT
* * * * *
12641419 TTAGCGGCGTTTTCGGGAAAGCGCCGCAAAAAAACCTAAGCCAAACGACGTCGTTTTCTCATCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCAAACGACGCCGTTTTCTGAGCTT
* *
12641484 TCGGGGGTTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAAGGAT
66 TCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAAGGCT
* * *
12641533 TTAGCGGCGTTTTTGATAAAGCGCCGCAAAAAAACCTAAGCCCAACGATGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCAAACGACGCCGTTTTCTGAGCTT
**
12641598 TCGGGGATTTAGCGGCGTTTTTAAGGAAGCGTTGCTAATGCTCAAGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAAGGCT
* * * *
12641647 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACTTAAGCCCAACGATGCC-TTTTTTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCAAACGACGCCGTTTTCTGAGCTT
*
12641711 TCGGGGATATAGCGGCGTTTTT--GGAAAAGCGCCGCTAA
66 TCGGGGATTTAGCGGCGTTTTTAAGG--AAGCGCCGCTAA
12641749 AAATATTTTA
Statistics
Matches: 398, Mismatches: 41, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
111 2 0.01
112 5 0.01
113 61 0.15
114 234 0.59
115 93 0.23
116 3 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCAAACGACGCCGTTTTCTGAGCTT
TCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAAGGCT
Found at i:12642016 original size:15 final size:15
Alignment explanation
Indices: 12641996--12642026 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12641986 TACATTTTAA
12641996 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
12642011 GGTTTAGGGATTATG
1 GGTTTAGGGAGTATG
12642026 G
1 G
12642027 ATTAGGGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.35
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:12642285 original size:15 final size:15
Alignment explanation
Indices: 12642265--12642311 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
12642255 TATTTTAAGG
*
12642265 TTTAGGGAGTATGGA
1 TTTAGGGATTATGGA
12642280 TTTAGGGATTAT-GA
1 TTTAGGGATTATGGA
*
12642294 ATTAGGGATTATGG-
1 TTTAGGGATTATGGA
12642308 TTTA
1 TTTA
12642312 AGGGTTGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.28, C:0.00, G:0.32, T:0.40
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:12642340 original size:7 final size:7
Alignment explanation
Indices: 12642330--12642368 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
12642320 AATTTAAGGT
12642330 TTAGGGG
1 TTAGGGG
12642337 TTAGGGG
1 TTAGGGG
12642344 TTTAGGGG
1 -TTAGGGG
**
12642352 TTAGATG
1 TTAGGGG
12642359 TTAGGGG
1 TTAGGGG
12642366 TTA
1 TTA
12642369 AGATCAGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.18, C:0.00, G:0.46, T:0.36
Consensus pattern (7 bp):
TTAGGGG
Found at i:12642347 original size:15 final size:15
Alignment explanation
Indices: 12642326--12642368 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
12642316 TTGGAATTTA
12642326 AGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
12642341 GGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
12642356 ATG-TTAGGGGTTA
1 AGGTTTAGGGGTTA
12642369 AGATCAGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.19, C:0.00, G:0.47, T:0.35
Consensus pattern (15 bp):
AGGTTTAGGGGTTAG
Found at i:12643373 original size:146 final size:147
Alignment explanation
Indices: 12642960--12643848 Score: 1408
Period size: 153 Copynumber: 5.9 Consensus size: 147
12642950 ATTTTATAAA
* * * * * *
12642960 AAATCAATTTATAAAAAATAAAATAAAAAAATTTTGGCATAGCAAATCGGCGTCGTTTTGTTTAA
1 AAATCAATTTATAAAAAAT-AAAT---TAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAA
*
12643025 AATGAAAAAAATTTTGCGGCGTTTTATGAAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGT
62 AATGAAAAAAAATTTGCGGCGTTTTATGAAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGT
12643090 TATAAAAACGCCGCAAAAAAT
127 TATAAAAACGCCGCAAAAAAT
*
12643111 TAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG
1 AAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG
12643176 AAAAAAAATTTGCGGCGTTTTATGAAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGTTATA
66 AAAAAAAATTTGCGGCGTTTTATGAAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGTTATA
*
12643241 AAAACGCTGCAAAAAAT
131 AAAACGCCGCAAAAAAT
12643258 AAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAAT-
1 AAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG
12643322 AAAAAAAATTTGCGGCGTTTTATGAAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGTTATA
66 AAAAAAAATTTGCGGCGTTTTATGAAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGTTATA
12643387 AAAACGCCGCAAAAAAT
131 AAAACGCCGCAAAAAAT
12643404 AAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG
1 AAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG
*
12643469 AAAAAATA-TTGCGGCGTTTTTCATAAAAGCAAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTT
66 AAAAAAAATTTGCGGCG-TTTT-AT----G-AAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTT
12643533 TGTTATAAAAACGCCGCAAAAAAT
124 TGTTATAAAAACGCCGCAAAAAAT
12643557 AAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG
1 AAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG
*
12643622 AAAAAATA-TTGCGGCGCTTTTCATAAAAGCAAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTT
66 AAAAAAAATTTGCGGCG-TTTT-AT----G-AAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTT
12643686 TGTTATAAAAACGCCGCAAAAAAT
124 TGTTATAAAAACGCCGCAAAAAAT
* * *
12643710 AAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGTTGTTTTATTTAAAATG
1 AAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG
* * * * *
12643775 AAAAAAATTTTACAGCGTTTTATGAAAAGCGCCGCTAAAGGTAGGCAATAGGGGCGTTT-TTGTA
66 AAAAAAAATTTGCGGCGTTTTATGAAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGTTAT-
12643839 AAAAACGCCG
130 AAAAACGCCG
12643849 AAATCCCAAC
Statistics
Matches: 706, Mismatches: 22, Indels: 24
0.94 0.03 0.03
Matches are distributed among these distances:
146 156 0.22
147 234 0.33
148 3 0.00
150 4 0.01
151 18 0.03
152 3 0.00
153 282 0.40
154 6 0.01
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.28
Consensus pattern (147 bp):
AAATCAATTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG
AAAAAAAATTTGCGGCGTTTTATGAAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGTTATA
AAAACGCCGCAAAAAAT
Found at i:12648553 original size:20 final size:20
Alignment explanation
Indices: 12648509--12648566 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
12648499 AAAAATAAAA
12648509 TAAAATAAA-A-TATTTATCAT
1 TAAAATAAATATTATTTA--AT
*
12648529 AAAAATAAATATTATTTAAT
1 TAAAATAAATATTATTTAAT
*
12648549 TAAAATATATATT-TTTAA
1 TAAAATAAATATTATTTAA
12648567 AGGTTATGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 5 0.15
20 21 0.64
21 1 0.03
22 6 0.18
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAAATAAATATTATTTAAT
Found at i:12648684 original size:43 final size:43
Alignment explanation
Indices: 12648564--12648825 Score: 221
Period size: 43 Copynumber: 6.1 Consensus size: 43
12648554 TATATATTTT
* * * * * *
12648564 TAAAGGTTAT-GTTTTTAGCGGCGTTTCTGCGACAAGCGCTGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGTGAAAAGCGCCGC
* * * *
12648606 TAAAGGTTTAT--TCTTTAGTGGCATTTGTGAT-AAAAGCGTCGC
1 TAAAGG-TCATGGTCTTTAGCGGCGTTTGTG-TGAAAAGCGCCGC
12648648 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGTGAAAAGCGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGTGAAAAGCGCCGC
* * * * *
12648691 TAAATGTCAGGGTCTATAGCGGCGTTTGTGGGAGAAGCGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGTGAAAAGCGCCGC
* * * * * *
12648734 TAAATGTCAGGGTCTATAGCGGCGTTT-TTTGGATAAGCGCCAC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGT-GAAAAGCGCCGC
* * *
12648777 TAAAGGTCATGATCTTTAGCGGCGTTTATTTCTGAAAA-CGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCG-TT-TGTGTGAAAAGCGCCGC
12648821 TAAAG
1 TAAAG
12648826 TTAGCGACGC
Statistics
Matches: 183, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
41 3 0.02
42 36 0.20
43 125 0.68
44 12 0.07
45 5 0.03
46 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.31
Consensus pattern (43 bp):
TAAAGGTCATGGTCTTTAGCGGCGTTTGTGTGAAAAGCGCCGC
Found at i:12649266 original size:15 final size:14
Alignment explanation
Indices: 12649234--12649269 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
12649224 GCACAAGTAG
12649234 ATTATA-TATATTA
1 ATTATATTATATTA
12649247 ATTATATTATATTAA
1 ATTATATTATATT-A
12649262 ATTATATT
1 ATTATATT
12649270 TTTTTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.29
14 6 0.29
15 9 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTATATTATATTA
Found at i:12649547 original size:22 final size:23
Alignment explanation
Indices: 12649519--12649581 Score: 83
Period size: 22 Copynumber: 2.7 Consensus size: 23
12649509 AATAATTATG
12649519 TTAATTTAATCATTTTC-TTTTT
1 TTAATTTAATCATTTTCATTTTT
12649541 TTAATTTAATCATTTTCATTTTT
1 TTAATTTAATCATTTTCATTTTT
* *
12649564 CTAAGCATTAATCATTTT
1 TTAA--TTTAATCATTTT
12649582 ATTAGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 17 0.47
23 8 0.22
25 11 0.31
ACGTcount: A:0.27, C:0.11, G:0.02, T:0.60
Consensus pattern (23 bp):
TTAATTTAATCATTTTCATTTTT
Found at i:12650493 original size:9 final size:9
Alignment explanation
Indices: 12650480--12650513 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
12650470 GAATAGCATT
12650480 ACAAAATAA
1 ACAAAATAA
*
12650489 TCAAAATAA
1 ACAAAATAA
*
12650498 ACAAAAGAA
1 ACAAAATAA
12650507 ACAAAAT
1 ACAAAAT
12650514 GAGTAAGTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.74, C:0.12, G:0.03, T:0.12
Consensus pattern (9 bp):
ACAAAATAA
Found at i:12652149 original size:21 final size:21
Alignment explanation
Indices: 12652125--12652164 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
12652115 TGGGCATTTC
12652125 CACACGGGC-AGGCCACACATT
1 CACACGGGCTA-GCCACACATT
12652146 CACACGGGCTAGCCACACA
1 CACACGGGCTAGCCACACA
12652165 CCCATGTGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.40, G:0.23, T:0.07
Consensus pattern (21 bp):
CACACGGGCTAGCCACACATT
Found at i:12652313 original size:23 final size:24
Alignment explanation
Indices: 12652261--12652313 Score: 56
Period size: 23 Copynumber: 2.2 Consensus size: 24
12652251 GTCTATAAAT
* *
12652261 ATCAATTAGAAGAAGATCTAAGGA
1 ATCACTTAGAAGAAGATCTAAGAA
*
12652285 AGCACTTAG-AGAAGAT-TGAAGAA
1 ATCACTTAGAAGAAGATCT-AAGAA
12652308 ATCACT
1 ATCACT
12652314 CGAAGAACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 1 0.04
23 16 0.67
24 7 0.29
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (24 bp):
ATCACTTAGAAGAAGATCTAAGAA
Found at i:12653015 original size:14 final size:14
Alignment explanation
Indices: 12652996--12653025 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12652986 GTTGCGTTCA
12652996 TAGTTAAATTAGAT
1 TAGTTAAATTAGAT
*
12653010 TAGTTAATTTAGAT
1 TAGTTAAATTAGAT
12653024 TA
1 TA
12653026 AAAATAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
TAGTTAAATTAGAT
Found at i:12655650 original size:21 final size:21
Alignment explanation
Indices: 12655626--12655668 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
12655616 AACAAGCTAA
12655626 CAAATCTCCCTAGGACTTAGT
1 CAAATCTCCCTAGGACTTAGT
*
12655647 CAAATCTCCCTAGGTCTTAGT
1 CAAATCTCCCTAGGACTTAGT
12655668 C
1 C
12655669 TTATTACTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.30
Consensus pattern (21 bp):
CAAATCTCCCTAGGACTTAGT
Found at i:12666470 original size:45 final size:45
Alignment explanation
Indices: 12666406--12666496 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
12666396 TGCAATATGG
12666406 ATATGAAATTTTAGAAACTTGGATGCCCAAAACATGGAAAAAAGA
1 ATATGAAATTTTAGAAACTTGGATGCCCAAAACATGGAAAAAAGA
12666451 ATATGAAATTTTAGAAACTTGGATGCCCAAAACATGGAAAAAAGA
1 ATATGAAATTTTAGAAACTTGGATGCCCAAAACATGGAAAAAAGA
12666496 A
1 A
12666497 AAAAAAAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.49, C:0.11, G:0.18, T:0.22
Consensus pattern (45 bp):
ATATGAAATTTTAGAAACTTGGATGCCCAAAACATGGAAAAAAGA
Found at i:12671867 original size:4 final size:4
Alignment explanation
Indices: 12671858--12671906 Score: 80
Period size: 4 Copynumber: 12.2 Consensus size: 4
12671848 AAGATGAAGG
* *
12671858 TTTA TTTA TTTA TATA TTTA TATA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
12671906 T
1 T
12671907 AATCAATTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:12672945 original size:21 final size:21
Alignment explanation
Indices: 12672919--12672958 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12672909 TTAGTTTTAA
12672919 GTTTGATCA-AATAATATTTGG
1 GTTTGA-CATAATAATATTTGG
*
12672940 GTTTGACATAATATTATTT
1 GTTTGACATAATAATATTT
12672959 CTAATATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (21 bp):
GTTTGACATAATAATATTTGG
Found at i:12677397 original size:3 final size:3
Alignment explanation
Indices: 12677389--12677414 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12677379 TGACTAACAT
12677389 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
12677415 TAAAAAGAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12679479 original size:11 final size:11
Alignment explanation
Indices: 12679463--12679489 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
12679453 GAAAGAATCT
12679463 ACCTAGACTTC
1 ACCTAGACTTC
12679474 ACCTAGACTTC
1 ACCTAGACTTC
12679485 ACCTA
1 ACCTA
12679490 TTATCCTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.37, G:0.07, T:0.26
Consensus pattern (11 bp):
ACCTAGACTTC
Found at i:12686532 original size:12 final size:12
Alignment explanation
Indices: 12686515--12686560 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
12686505 ACTCATCTCC
12686515 TTATAATTTTTA
1 TTATAATTTTTA
12686527 TTATAATTGTTTA
1 TTATAATT-TTTA
* *
12686540 TAAT-ATTTATA
1 TTATAATTTTTA
12686551 TTATAATTTT
1 TTATAATTTT
12686561 GATATATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 6 0.21
12 15 0.54
13 7 0.25
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (12 bp):
TTATAATTTTTA
Found at i:12686543 original size:22 final size:24
Alignment explanation
Indices: 12686515--12686558 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
12686505 ACTCATCTCC
12686515 TTATAAT-TTT-TATTATAATTGT
1 TTATAATATTTATATTATAATTGT
12686537 TTATAATATTTATATTATAATT
1 TTATAATATTTATATTATAATT
12686559 TTGATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 3 0.15
24 10 0.50
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
TTATAATATTTATATTATAATTGT
Found at i:12686569 original size:24 final size:25
Alignment explanation
Indices: 12686516--12686569 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
12686506 CTCATCTCCT
* *
12686516 TATA-ATTTTTATTATAATTGTTTA
1 TATATATTTATATTATAATTGTTGA
12686540 TA-ATATTTATATTATAATT-TTGA
1 TATATATTTATATTATAATTGTTGA
12686563 TATATAT
1 TATATAT
12686570 ATGTATGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (25 bp):
TATATATTTATATTATAATTGTTGA
Found at i:12695966 original size:24 final size:24
Alignment explanation
Indices: 12695938--12696054 Score: 83
Period size: 25 Copynumber: 4.7 Consensus size: 24
12695928 AAGTTCATGC
*
12695938 GAGCCAATATCGGGTAGCTTCG-AA
1 GAGCCAATATCGGGAAGC-TCGTAA
*
12695962 GAGCCATTAATCGGGAAGCTCGTAA
1 GAGCCAAT-ATCGGGAAGCTCGTAA
* * *
12695987 GAGCCATATATTGGGATGCTCATAA
1 GAGCCA-ATATCGGGAAGCTCGTAA
* * * * *
12696012 TAGCTAAATAACGAGAAGCTCGTGA
1 GAGC-CAATATCGGGAAGCTCGTAA
*
12696037 GAGCCAAATATCAGGAAG
1 GAGCC-AATATCGGGAAG
12696055 GTCAAGAGTG
Statistics
Matches: 69, Mismatches: 19, Indels: 9
0.71 0.20 0.09
Matches are distributed among these distances:
24 10 0.14
25 57 0.83
26 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (24 bp):
GAGCCAATATCGGGAAGCTCGTAA
Found at i:12696054 original size:25 final size:24
Alignment explanation
Indices: 12695902--12696089 Score: 78
Period size: 25 Copynumber: 7.7 Consensus size: 24
12695892 CCACGTAATG
* *
12695902 GGAAGCTCATAAGA-TCAATAATCA
1 GGAAGCTCATGAGAGCCAAT-ATCA
* * *
12695926 GGAAGTTCATGCGAGCCAATATCG
1 GGAAGCTCATGAGAGCCAATATCA
* * *
12695950 GGTAGCT--TCGAAGAGCCATTAATCG
1 GGAAGCTCAT-G-AGAGCCAAT-ATCA
* * **
12695975 GGAAGCTCGTAAGAGCCATATATTG
1 GGAAGCTCATGAGAGCCA-ATATCA
* * * * *
12696000 GGATGCTCATAATAGCTAA-ATAA
1 GGAAGCTCATGAGAGCCAATATCA
*
12696023 CGAGAAGCTCGTGAGAGCCAAATATCA
1 -G-GAAGCTCATGAGAGCC-AATATCA
* * *
12696050 GGAAGGTCAAGAGTGCCAATATCA
1 GGAAGCTCATGAGAGCCAATATCA
*
12696074 GGATGCTCATGAGAGC
1 GGAAGCTCATGAGAGC
12696090 TAATTACTGG
Statistics
Matches: 120, Mismatches: 33, Indels: 22
0.69 0.19 0.13
Matches are distributed among these distances:
22 1 0.01
23 3 0.03
24 47 0.39
25 61 0.51
26 4 0.03
27 4 0.03
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (24 bp):
GGAAGCTCATGAGAGCCAATATCA
Found at i:12703793 original size:50 final size:49
Alignment explanation
Indices: 12703639--12703824 Score: 168
Period size: 50 Copynumber: 3.8 Consensus size: 49
12703629 ATGTAACGAA
* * *
12703639 AAGCTCATAAGAGTC-ATAATCGGGAAGCTCATGCGAGCC-AATATTGGG
1 AAGCTCATAAGAGCCAATAATCGGGAAGCTCATGAGAGCCAAATA-TCGG
* * * * *
12703687 TAGCTC-TGAAGAGCCATTAATCGGGAAGCTCATAAGAGCCATATGTCGAG
1 AAGCTCAT-AAGAGCCAATAATCGGGAAGCTCATGAGAGCCAAATATCG-G
* *
12703737 ATGCTCATAAGAGCTAAATAA-CGGGAAGCTCATGAGAGCCAAATATCAGG
1 AAGCTCATAAGAGC-CAATAATCGGGAAGCTCATGAGAGCCAAATATC-GG
* *
12703787 AAGCTCA-AGAGAGCCAAT-ATCAGGATGCTCATGAGAGC
1 AAGCTCATA-AGAGCCAATAATCGGGAAGCTCATGAGAGC
12703825 TACTAATAGG
Statistics
Matches: 110, Mismatches: 19, Indels: 17
0.75 0.13 0.12
Matches are distributed among these distances:
47 1 0.01
48 12 0.11
49 43 0.39
50 48 0.44
51 6 0.05
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (49 bp):
AAGCTCATAAGAGCCAATAATCGGGAAGCTCATGAGAGCCAAATATCGG
Found at i:12703810 original size:24 final size:25
Alignment explanation
Indices: 12703639--12703824 Score: 123
Period size: 25 Copynumber: 7.6 Consensus size: 25
12703629 ATGTAACGAA
* * * *
12703639 AAGCTCATAAGAGTCATA-ATCGGG
1 AAGCTCATGAGAGCCAAATATCAGG
* **
12703663 AAGCTCATGCGAGCC-AATATTGGG
1 AAGCTCATGAGAGCCAAATATCAGG
* * *
12703687 TAGCTC-TGAAGAGCC-ATTAATCGGG
1 AAGCTCATG-AGAGCCAAAT-ATCAGG
* * *
12703712 AAGCTCATAAGAGCCATATGTC-GAG
1 AAGCTCATGAGAGCCAAATATCAG-G
* * * * *
12703737 ATGCTCATAAGAGCTAAATAACGGG
1 AAGCTCATGAGAGCCAAATATCAGG
12703762 AAGCTCATGAGAGCCAAATATCAGG
1 AAGCTCATGAGAGCCAAATATCAGG
*
12703787 AAGCTCAAGAGAGCC-AATATCAGG
1 AAGCTCATGAGAGCCAAATATCAGG
*
12703811 ATGCTCATGAGAGC
1 AAGCTCATGAGAGC
12703825 TACTAATAGG
Statistics
Matches: 128, Mismatches: 27, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
23 3 0.02
24 51 0.40
25 71 0.55
26 3 0.02
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (25 bp):
AAGCTCATGAGAGCCAAATATCAGG
Found at i:12707261 original size:18 final size:19
Alignment explanation
Indices: 12707238--12707275 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
12707228 TGGTGTGAAG
12707238 AAAAGGAAAAGAAA-AGAA
1 AAAAGGAAAAGAAATAGAA
*
12707256 AAAAGGAGAAGAAATAGAA
1 AAAAGGAAAAGAAATAGAA
12707275 A
1 A
12707276 GAGGAGGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (19 bp):
AAAAGGAAAAGAAATAGAA
Found at i:12718505 original size:74 final size:75
Alignment explanation
Indices: 12718374--12718538 Score: 242
Period size: 74 Copynumber: 2.2 Consensus size: 75
12718364 CAAAACACAC
* * *
12718374 TTTTAGCGGCGTTTTCGAGAAAGCGCCGCAAAAAAAACATATGCCCAACGATACCGTTTTCGTGA
1 TTTT-GCGGCATTTTTGAGAAAGCGCAGCAAAAAAAACATATGCCCAACGATACCGTTTTCGTGA
*
12718439 GCTTTCGGGGA
65 GCTTCCGGGGA
* * *
12718450 TTTTGCGGCATTTTTGAGAAAGCGCAGC-AAAGAAACATATGCCCAACGATGCCGTTTTTGTGAG
1 TTTTGCGGCATTTTTGAGAAAGCGCAGCAAAAAAAACATATGCCCAACGATACCGTTTTCGTGAG
12718514 CTTCCGGGGA
66 CTTCCGGGGA
*
12718524 TTTTGCAGCATTTTT
1 TTTTGCGGCATTTTT
12718539 AGGAAAACAC
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
74 56 0.69
75 21 0.26
76 4 0.05
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (75 bp):
TTTTGCGGCATTTTTGAGAAAGCGCAGCAAAAAAAACATATGCCCAACGATACCGTTTTCGTGAG
CTTCCGGGGA
Found at i:12719003 original size:15 final size:15
Alignment explanation
Indices: 12718930--12719015 Score: 63
Period size: 15 Copynumber: 5.9 Consensus size: 15
12718920 CATATTTTAA
*
12718930 GGTTTAGGGAG-TATG
1 GGTTTAGGG-GTTAGG
* *
12718945 GGTTTAGGGATTA-T
1 GGTTTAGGGGTTAGG
*
12718959 GGATTAGGGGTT-GG
1 GGTTTAGGGGTTAGG
* * *
12718973 GATTTAAGGTTTAGG
1 GGTTTAGGGGTTAGG
12718988 GG-TTAGAGGGTTAGG
1 GGTTTAG-GGGTTAGG
12719003 GGTTTAGGGGTTA
1 GGTTTAGGGGTTA
12719016 AACGTGCTAG
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
14 21 0.39
15 29 0.54
16 4 0.07
ACGTcount: A:0.20, C:0.00, G:0.45, T:0.35
Consensus pattern (15 bp):
GGTTTAGGGGTTAGG
Found at i:12720257 original size:25 final size:25
Alignment explanation
Indices: 12720190--12720251 Score: 117
Period size: 24 Copynumber: 2.5 Consensus size: 25
12720180 CCTTAAATAC
12720190 AATTAATAAATAAGTTAATTTTATT
1 AATTAATAAATAAGTTAATTTTATT
12720215 AATTAATAAATAAGTTAA-TTTATT
1 AATTAATAAATAAGTTAATTTTATT
12720239 AATTAATAAATAA
1 AATTAATAAATAA
12720252 AATTAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 19 0.51
25 18 0.49
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (25 bp):
AATTAATAAATAAGTTAATTTTATT
Found at i:12722261 original size:12 final size:12
Alignment explanation
Indices: 12722246--12722279 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12722236 TAACCTACAT
12722246 AACTTACATAGA
1 AACTTACATAGA
*
12722258 AACTTATATAGA
1 AACTTACATAGA
*
12722270 AACTTGCATA
1 AACTTACATA
12722280 ACTTACATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (12 bp):
AACTTACATAGA
Found at i:12722338 original size:16 final size:16
Alignment explanation
Indices: 12722319--12722491 Score: 101
Period size: 16 Copynumber: 11.0 Consensus size: 16
12722309 ATACATAGCC
12722319 TACATAACTTACATAA
1 TACATAACTTACATAA
**
12722335 TACACCACTTAC---A
1 TACATAACTTACATAA
*
12722348 TA-ATAACTTGCATAA
1 TACATAACTTACATAA
**
12722363 TACACCACTTACAT-A
1 TACATAACTTACATAA
*
12722378 -A-ATAACTTGCATAA
1 TACATAACTTACATAA
* * *
12722392 TACATAGCCTACGTAA
1 TACATAACTTACATAA
*
12722408 CTTACTTAACTTACATAA
1 --TACATAACTTACATAA
** *
12722426 TACACCACTTACGTAA
1 TACATAACTTACATAA
*
12722442 CTTAAATAACTTACATAA
1 --TACATAACTTACATAA
*
12722460 TACTTAACTTTA-ATAA
1 TACATAAC-TTACATAA
*
12722476 TACACAACTTACATAA
1 TACATAACTTACATAA
12722492 CTTAATTACA
Statistics
Matches: 113, Mismatches: 31, Indels: 26
0.66 0.18 0.15
Matches are distributed among these distances:
12 6 0.05
13 11 0.10
14 2 0.02
15 8 0.07
16 59 0.52
17 3 0.03
18 24 0.21
ACGTcount: A:0.44, C:0.23, G:0.03, T:0.31
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:12722362 original size:28 final size:29
Alignment explanation
Indices: 12722322--12722395 Score: 132
Period size: 28 Copynumber: 2.6 Consensus size: 29
12722312 CATAGCCTAC
*
12722322 ATAACTTACATAATACACCACTTACAT-A
1 ATAACTTGCATAATACACCACTTACATAA
12722350 ATAACTTGCATAATACACCACTTACATAA
1 ATAACTTGCATAATACACCACTTACATAA
12722379 ATAACTTGCATAATACA
1 ATAACTTGCATAATACA
12722396 TAGCCTACGT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 26 0.59
29 18 0.41
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.28
Consensus pattern (29 bp):
ATAACTTGCATAATACACCACTTACATAA
Found at i:12722419 original size:34 final size:34
Alignment explanation
Indices: 12722322--12722462 Score: 117
Period size: 34 Copynumber: 4.5 Consensus size: 34
12722312 CATAGCCTAC
*
12722322 ATAACTTACATAATACACCA-CT---T-ACAT-A
1 ATAACTTACATAATACACCACCTACGTAACTTAA
* *
12722350 ATAACTTGCATAATACACCA-CT---T-ACATAA
1 ATAACTTACATAATACACCACCTACGTAACTTAA
* * *
12722379 ATAACTTGCATAATACA-TAGCCTACGTAACTTAC
1 ATAACTTACATAATACACCA-CCTACGTAACTTAA
* *
12722413 TTAACTTACATAATACACCACTTACGTAACTTAA
1 ATAACTTACATAATACACCACCTACGTAACTTAA
12722447 ATAACTTACATAATAC
1 ATAACTTACATAATAC
12722463 TTAACTTTAA
Statistics
Matches: 95, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
28 27 0.28
29 18 0.19
30 2 0.02
33 1 0.01
34 46 0.48
35 1 0.01
ACGTcount: A:0.43, C:0.23, G:0.04, T:0.30
Consensus pattern (34 bp):
ATAACTTACATAATACACCACCTACGTAACTTAA
Found at i:12722437 original size:25 final size:24
Alignment explanation
Indices: 12722406--12722497 Score: 89
Period size: 25 Copynumber: 3.7 Consensus size: 24
12722396 TAGCCTACGT
12722406 AACTTACTTAACTTACATAATACAC
1 AACTTACTTAACTTA-ATAATACAC
* * *
12722431 CACTTACGTAACTTAAATAACTTACAT
1 AACTTACTTAACTT-AATAA--TACAC
12722458 AA--TACTTAACTTTAATAATACAC
1 AACTTACTTAAC-TTAATAATACAC
*
12722481 AACTTACATAACTTAAT
1 AACTTACTTAACTTAAT
12722498 TACATTATAC
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
23 6 0.11
24 5 0.09
25 35 0.65
26 3 0.06
27 5 0.09
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.34
Consensus pattern (24 bp):
AACTTACTTAACTTAATAATACAC
Found at i:12722493 original size:9 final size:9
Alignment explanation
Indices: 12722379--12722495 Score: 63
Period size: 9 Copynumber: 13.9 Consensus size: 9
12722369 ACTTACATAA
*
12722379 ATAACTTGC
1 ATAACTTAC
12722388 ATAA--TAC
1 ATAACTTAC
* *
12722395 ATAGCCTAC
1 ATAACTTAC
*
12722404 GTAACTTAC
1 ATAACTTAC
*
12722413 TTAACTTAC
1 ATAACTTAC
12722422 ATAA--TAC
1 ATAACTTAC
**
12722429 ACCACTTAC
1 ATAACTTAC
* *
12722438 GTAACTTAA
1 ATAACTTAC
12722447 ATAACTTAC
1 ATAACTTAC
12722456 ATAA--TAC
1 ATAACTTAC
*
12722463 TTAACTTTA-
1 ATAAC-TTAC
12722472 ATAA--TAC
1 ATAACTTAC
*
12722479 ACAACTTAC
1 ATAACTTAC
12722488 ATAACTTA
1 ATAACTTA
12722496 ATTACATTAT
Statistics
Matches: 79, Mismatches: 19, Indels: 20
0.67 0.16 0.17
Matches are distributed among these distances:
6 2 0.03
7 19 0.24
9 56 0.71
10 2 0.03
ACGTcount: A:0.43, C:0.21, G:0.03, T:0.32
Consensus pattern (9 bp):
ATAACTTAC
Found at i:12724649 original size:43 final size:43
Alignment explanation
Indices: 12724602--12724828 Score: 276
Period size: 43 Copynumber: 5.3 Consensus size: 43
12724592 TCTGCTAAAA
* *
12724602 TTAGTGGCGTTTGTGAAAAAAGCGCCGCTAAAGAACATGACCT
1 TTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGACCT
* * * *
12724645 TTAGTGACATTTGTGGAAAAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGACCT
* * * *
12724688 GTAGCAGCGTTTGTGGAAAATGTGCCGCTAAAGAACATGATCC-
1 TTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGA-CCT
** **
12724731 TTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGTTCT
1 TTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGACCT
* * * *
12724774 TTAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAGACCCTGACCT
1 TTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGACCT
12724817 TTAGCGGCGTTT
1 TTAGCGGCGTTT
12724829 TTTTCGTATC
Statistics
Matches: 155, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
42 1 0.01
43 153 0.99
44 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGACCT
Found at i:12735052 original size:16 final size:16
Alignment explanation
Indices: 12735031--12735067 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
12735021 AAAAAGCCTA
12735031 AGAATCTAAATCAAAC
1 AGAATCTAAATCAAAC
12735047 AGAATCTAAATCAAAC
1 AGAATCTAAATCAAAC
12735063 AGAAT
1 AGAAT
12735068 GGGAAGAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.57, C:0.16, G:0.08, T:0.19
Consensus pattern (16 bp):
AGAATCTAAATCAAAC
Found at i:12757016 original size:14 final size:15
Alignment explanation
Indices: 12756994--12757070 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
12756984 CAATCAAACA
12756994 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
12757008 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
12757023 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
12757043 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
12757057 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
12757071 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:12757035 original size:20 final size:20
Alignment explanation
Indices: 12757010--12757049 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12757000 AATATTTTCC
*
12757010 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
12757030 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
12757050 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:12757055 original size:34 final size:35
Alignment explanation
Indices: 12756998--12757064 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
12756988 CAAACACCAG
*
12756998 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
12757033 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
12757065 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:12757800 original size:25 final size:25
Alignment explanation
Indices: 12757766--12757813 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
12757756 TTGTCTAGAA
12757766 GGTTTTGATCTTTCAAGAAAATATT
1 GGTTTTGATCTTTCAAGAAAATATT
*
12757791 GGTTTTGATCTTTCAAGTAAATA
1 GGTTTTGATCTTTCAAGAAAATA
12757814 GTTTTTCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (25 bp):
GGTTTTGATCTTTCAAGAAAATATT
Found at i:12765314 original size:37 final size:37
Alignment explanation
Indices: 12765259--12765390 Score: 160
Period size: 37 Copynumber: 3.6 Consensus size: 37
12765249 CTTAGTGTCG
* *
12765259 TGGCGTGTTATCGATTGGATTAGCTCTTTTGAGCGAT
1 TGGCGTGTTATCGGTTGGATTAGCTCTTATGAGCGAT
* * *
12765296 TGGCGTGTTATTGGTTGGATTATCTCTTATGAGCGTT
1 TGGCGTGTTATCGGTTGGATTAGCTCTTATGAGCGAT
* *
12765333 TGGCGTGTTAGCGGGTGGATTAGCAT-TTATGAGCGAT
1 TGGCGTGTTATCGGTTGGATTAGC-TCTTATGAGCGAT
* *
12765370 TTGCGTGTT-TTGGTTGGATTA
1 TGGCGTGTTATCGGTTGGATTA
12765391 CTTGTGTACT
Statistics
Matches: 80, Mismatches: 14, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
36 9 0.11
37 70 0.88
38 1 0.01
ACGTcount: A:0.15, C:0.11, G:0.33, T:0.42
Consensus pattern (37 bp):
TGGCGTGTTATCGGTTGGATTAGCTCTTATGAGCGAT
Found at i:12768121 original size:25 final size:25
Alignment explanation
Indices: 12768067--12768121 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
12768057 AAACATTAAA
*
12768067 TTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAATATTAAGAAAATCAC
*
12768092 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATCAC
12768116 TATTAA
1 T-TTAA
12768122 GATAAGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATCAC
Found at i:12768605 original size:9 final size:9
Alignment explanation
Indices: 12768581--12768635 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
12768571 AAAATATCAT
12768581 ATTAATTTTA
1 ATTAA-TTTA
*
12768591 ATTAATTTG
1 ATTAATTTA
12768600 ATTAATTTA
1 ATTAATTTA
* * *
12768609 ATTTTACTTG
1 A-TTAATTTA
12768619 ATTAATTTA
1 ATTAATTTA
12768628 ATTAATTT
1 ATTAATTT
12768636 TTCGAGAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
9 25 0.69
10 11 0.31
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (9 bp):
ATTAATTTA
Found at i:12768605 original size:19 final size:18
Alignment explanation
Indices: 12768581--12768635 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 18
12768571 AAAATATCAT
12768581 ATTAATTTTAATTAATTTG
1 ATTAA-TTTAATTAATTTG
* *
12768600 ATTAATTTAATTTTACTTG
1 ATTAATTTAA-TTAATTTG
12768619 ATTAATTTAATTAATTT
1 ATTAATTTAATTAATTT
12768636 TTCGAGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 10 0.32
19 21 0.68
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (18 bp):
ATTAATTTAATTAATTTG
Found at i:12769751 original size:14 final size:15
Alignment explanation
Indices: 12769727--12769755 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12769717 CTATGCATGC
12769727 AAAATATCAAAGACA
1 AAAATATCAAAGACA
12769742 AAAATA-CAAAGACA
1 AAAATATCAAAGACA
12769756 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.69, C:0.14, G:0.07, T:0.10
Consensus pattern (15 bp):
AAAATATCAAAGACA
Found at i:12773648 original size:2 final size:2
Alignment explanation
Indices: 12773641--12773693 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
12773631 AAAGTGATAA
12773641 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
12773682 AA AT AT AT AT AT
1 AT AT AT AT AT AT
12773694 TGTAATCTCT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12774530 original size:22 final size:22
Alignment explanation
Indices: 12774505--12774573 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
12774495 AGTCAAGCTG
12774505 CCAGAAATATGTGGACAAGCCA
1 CCAGAAATATGTGGACAAGCCA
* **** *
12774527 CCAGTAAT-TGCATTCAAGCTA
1 CCAGAAATATGTGGACAAGCCA
* *
12774548 CCAGGAATATGTGGACAAACCA
1 CCAGAAATATGTGGACAAGCCA
12774570 CCAG
1 CCAG
12774574 TAATTACAAA
Statistics
Matches: 33, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
21 15 0.45
22 18 0.55
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (22 bp):
CCAGAAATATGTGGACAAGCCA
Found at i:12774532 original size:43 final size:43
Alignment explanation
Indices: 12774471--12774578 Score: 171
Period size: 43 Copynumber: 2.5 Consensus size: 43
12774461 CACACCATTT
* *
12774471 TGTGGACAAACTACCAGTAATTGCAGTCAAGCTGCCAGAAATA
1 TGTGGACAAACCACCAGTAATTGCAGTCAAGCTACCAGAAATA
* * *
12774514 TGTGGACAAGCCACCAGTAATTGCATTCAAGCTACCAGGAATA
1 TGTGGACAAACCACCAGTAATTGCAGTCAAGCTACCAGAAATA
12774557 TGTGGACAAACCACCAGTAATT
1 TGTGGACAAACCACCAGTAATT
12774579 ACAAATAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.21
Consensus pattern (43 bp):
TGTGGACAAACCACCAGTAATTGCAGTCAAGCTACCAGAAATA
Found at i:12774550 original size:21 final size:21
Alignment explanation
Indices: 12774481--12774551 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
12774471 TGTGGACAAA
12774481 CTACCAGTAATTGCAGTCAAG
1 CTACCAGTAATTGCAGTCAAG
* * ** *
12774502 CTGCCAGAAATATGTGGACAAG
1 CTACCAGTAAT-TGCAGTCAAG
* *
12774524 CCACCAGTAATTGCATTCAAG
1 CTACCAGTAATTGCAGTCAAG
12774545 CTACCAG
1 CTACCAG
12774552 GAATATGTGG
Statistics
Matches: 36, Mismatches: 13, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
21 21 0.58
22 15 0.42
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (21 bp):
CTACCAGTAATTGCAGTCAAG
Found at i:12774639 original size:40 final size:41
Alignment explanation
Indices: 12774510--12774667 Score: 146
Period size: 40 Copynumber: 3.9 Consensus size: 41
12774500 AGCTGCCAGA
** *
12774510 AATA-TGTGGACAAGCCACCAGTAATTGCAT-TCAAGCTACC
1 AATATTGTGGACAAGCCACCAGTAATTGCATAT-AAATTGCC
* * * **
12774550 AGGA-ATATGTGGACAAACCACCAGTAATTACAAATAAATTGAT
1 A--ATAT-TGTGGACAAGCCACCAGTAATTGCATATAAATTGCC
*
12774593 AGTATTGTGGACAAGCCACCAGT-ATTGCATATAAATTGCC
1 AATATTGTGGACAAGCCACCAGTAATTGCATATAAATTGCC
* *
12774633 AATATTGTGGATAAGCCACCAGT-ATTGCAGATAAA
1 AATATTGTGGACAAGCCACCAGTAATTGCATATAAA
12774668 CTGTCAGTAC
Statistics
Matches: 95, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
40 46 0.48
41 18 0.19
42 3 0.03
43 27 0.28
44 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (41 bp):
AATATTGTGGACAAGCCACCAGTAATTGCATATAAATTGCC
Found at i:12774658 original size:20 final size:20
Alignment explanation
Indices: 12774593--12774659 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 20
12774583 ATAAATTGAT
*
12774593 AGTATTGTGGACAAGCCACC
1 AGTATTGTGGATAAGCCACC
*** ****
12774613 AGTATTGCATATAAATTGCC
1 AGTATTGTGGATAAGCCACC
*
12774633 AATATTGTGGATAAGCCACC
1 AGTATTGTGGATAAGCCACC
12774653 AGTATTG
1 AGTATTG
12774660 CAGATAAACT
Statistics
Matches: 30, Mismatches: 17, Indels: 0
0.64 0.36 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (20 bp):
AGTATTGTGGATAAGCCACC
Found at i:12774665 original size:20 final size:20
Alignment explanation
Indices: 12774605--12774666 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 20
12774595 TATTGTGGAC
*
12774605 AAGCCACCAGTATTGCATAT
1 AAGCCACCAGTATTGCAGAT
**** * **
12774625 AAATTGCCAATATTGTGGAT
1 AAGCCACCAGTATTGCAGAT
12774645 AAGCCACCAGTATTGCAGAT
1 AAGCCACCAGTATTGCAGAT
12774665 AA
1 AA
12774667 ACTGTCAGTA
Statistics
Matches: 27, Mismatches: 15, Indels: 0
0.64 0.36 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (20 bp):
AAGCCACCAGTATTGCAGAT
Found at i:12774927 original size:20 final size:21
Alignment explanation
Indices: 12774890--12774933 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
12774880 TCACACTCTA
12774890 ATATCACCAAACATGCTATTC
1 ATATCACCAAACATGCTATTC
*
12774911 ATATCATCAAA-ATGCTATTC
1 ATATCACCAAACATGCTATTC
12774931 ATA
1 ATA
12774934 ACAAAACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.32
Consensus pattern (21 bp):
ATATCACCAAACATGCTATTC
Found at i:12781242 original size:44 final size:43
Alignment explanation
Indices: 12781193--12781449 Score: 219
Period size: 44 Copynumber: 5.7 Consensus size: 43
12781183 CATAGCAAAC
* ** *
12781193 CTTATCTCCCTGAAGTTGTAGTGGAGTAGGTTGAAGTTACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGTTACAA-T
* * * * *
12781237 CTTATCTCCCTGAAGTTGCAATGGAACAAACTGAAGATAATGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAG-TTA-CAAT
* * *
12781282 CTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATCAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAG-T-T--A-CAAT
* * *
12781330 CTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAAGTTACAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGTTAC-AAT
* * * * *
12781374 TTTATCTACCTGAAGTTTCAGTGGAACAGACTGAA-TAAACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGT-TA-CAAT
*
12781418 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATT
12781450 AAAATGATGG
Statistics
Matches: 168, Mismatches: 37, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
43 2 0.01
44 91 0.54
45 36 0.21
46 3 0.02
47 1 0.01
48 35 0.21
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (43 bp):
CTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGTTACAAT
Found at i:12781348 original size:137 final size:136
Alignment explanation
Indices: 12781190--12781452 Score: 409
Period size: 137 Copynumber: 1.9 Consensus size: 136
12781180 GATCATAGCA
* * *
12781190 AACCTTATCTCCCTGAAGTTGTAGTGGAGTAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTG
1 AACCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAAGTTACAAATCTTATCTACCTGAAGTTG
** *
12781255 CAATGGAACAAACTGAAGATAATGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCT
66 CAATGGAACAAACTGAAGA-AACCAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCT
12781320 ATAAATC
130 ATAAATC
* *
12781327 AACCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAAGTTACAAATTTTATCTACCTGAAGTTT
1 AACCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAAGTTACAAATCTTATCTACCTGAAGTTG
* * * *
12781392 CAGTGGAACAGACTGAATAAACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
66 CAATGGAACAAACTGAAGAAACCAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAA
12781453 ATGATGGATC
Statistics
Matches: 114, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
136 38 0.33
137 76 0.67
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (136 bp):
AACCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAAGTTACAAATCTTATCTACCTGAAGTTG
CAATGGAACAAACTGAAGAAACCAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTA
TAAATC
Found at i:12781464 original size:44 final size:44
Alignment explanation
Indices: 12781193--12781479 Score: 202
Period size: 44 Copynumber: 6.4 Consensus size: 44
12781183 CATAGCAAAC
* ** * * * *
12781193 CTTATCTCCCTGAAGTTGTAGTGGAGTAGGTTGAAGTTA-CAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAATAATCAA-T
* * * * *
12781237 CTTATCTCCCTGAAGTTGCAATGGAACAAACTGAAGATAATGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGA-TTAAAATAATCAAT
* *
12781282 CTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATCAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAA---AT-AATCAAT
* * * * * *
12781330 CTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAAGTTA-CAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAATAATC-AAT
* * * * * *
12781374 TTTATCTACCTGAAGTTTCAGTGGAACAGACT-GAATAAACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAT-AATCAAT
* * **
12781418 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATGGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAATAATCAAT
*
12781462 CTTATCTCTCTGAAGTTG
1 CTTATCTCCCTGAAGTTG
12781480 TAGTAGAGGA
Statistics
Matches: 185, Mismatches: 48, Indels: 20
0.73 0.19 0.08
Matches are distributed among these distances:
43 3 0.02
44 106 0.57
45 37 0.20
46 2 0.01
47 2 0.01
48 35 0.19
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAATAATCAAT
Found at i:12781467 original size:88 final size:89
Alignment explanation
Indices: 12781236--12781479 Score: 231
Period size: 88 Copynumber: 2.7 Consensus size: 89
12781226 AAGTTACAAG
* * * * * *
12781236 TCTTATCTCCCTGAAGTTGCAATGGAACAAACTGAAGATAATGAATCTTATTTCCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAATAATGAATCTTATCT-CCTGAAGTTGC
* * *
12781301 AGTGGAACAGATTAAAGCTATAAATCAA
64 AGTGGAACAGACT--AGCAATAAACCAA
* * * * * * ** * *
12781329 CCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAAGTTACAAATTTTATCTACCTGAAGTTTCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAATGAATCTTATCT-CCTGAAGTTGCA
12781394 GTGGAACAGACT-G-AATAAACCAA
65 GTGGAACAGACTAGCAATAAACCAA
* *
12781417 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATGGATCTTATCTCTCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAATGAATCTTATCTC-CTGAAGTTG
12781480 TAGTAGAGGA
Statistics
Matches: 119, Mismatches: 31, Indels: 7
0.76 0.20 0.04
Matches are distributed among these distances:
87 1 0.01
88 58 0.49
89 1 0.01
92 34 0.29
93 25 0.21
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (89 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAATGAATCTTATCTCCTGAAGTTGCAG
TGGAACAGACTAGCAATAAACCAA
Found at i:12782996 original size:3 final size:3
Alignment explanation
Indices: 12782988--12783038 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
12782978 CTATTAATTA
* * *
12782988 ATT ATT ATT ATT GTT ATT ATT ACT ATTT ATT ATT GTT ATT GA-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT -ATT ATT
12783034 ATT AT
1 ATT AT
12783039 ATTTGGTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 1 0.03
3 35 0.90
4 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:12783026 original size:28 final size:27
Alignment explanation
Indices: 12782979--12783042 Score: 85
Period size: 28 Copynumber: 2.4 Consensus size: 27
12782969 ATATTTTTGC
* *
12782979 TATTA-ATTAATTATTATTATTGTTAT
1 TATTATATTTATTATTATTATTGATAT
*
12783005 TATTACTATTTATTATTGTTATTGATAT
1 TATTA-TATTTATTATTATTATTGATAT
12783033 TATTATATTT
1 TATTATATTT
12783043 GGTTATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.15
27 5 0.15
28 23 0.70
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (27 bp):
TATTATATTTATTATTATTATTGATAT
Found at i:12794512 original size:44 final size:45
Alignment explanation
Indices: 12794357--12794657 Score: 220
Period size: 44 Copynumber: 6.7 Consensus size: 45
12794347 CATAGCAAAC
* * * * *
12794357 CTTATCTCCCTGAAGTTGCAGTGGAGCTGACTAAAG-ATAGCGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTA-AACCAAT
* * * * ** *
12794402 CTTATTTCCCTGAAGTTGTAGTGGAACAGATTAAAGCTATAAATTAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG---TAAACCAAT
* *
12794450 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGT-TA-CAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAAACCAA-T
* * * *
12794494 CTTATCTACCTGAAGTTGCAGTGGAACAAACTGAA-TAAACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAAACCAAT
*
12794538 CTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAG-AAACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAAACCAAT
* * * * * * * * ***
12794582 CCTATCTCTCTAAAGTTGTAGTGGAGCTGATTAAAAT-GATGGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAAACCAAT
* *
12794626 C-TATCTCTCTGAAGTTGCAGTAGAGCAGATTG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG
12794658 CATCAGACCT
Statistics
Matches: 202, Mismatches: 45, Indels: 20
0.76 0.17 0.07
Matches are distributed among these distances:
43 29 0.14
44 103 0.51
45 35 0.17
48 34 0.17
49 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (45 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAAACCAAT
Found at i:12796190 original size:3 final size:3
Alignment explanation
Indices: 12796182--12796232 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
12796172 CTATTAATTA
* * *
12796182 ATT ATT ATT ATT GTT ATT ATT ACT ATTT ATT ATT GTT ATT GA-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT -ATT ATT
12796228 ATT AT
1 ATT AT
12796233 ATTTGGTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 1 0.03
3 35 0.90
4 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (3 bp):
ATT
Done.