Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 132 of 433
Found at i:40693841 original size:15 final size:15
Alignment explanation
Indices: 40693808--40693840 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
40693798 GCTGATTTCC
40693808 TTTTCTTTTTTTCTT
1 TTTTCTTTTTTTCTT
40693823 TTTTCTTTTTTT-TT
1 TTTTCTTTTTTTCTT
40693837 TTTT
1 TTTT
40693841 TTAAGGTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (15 bp):
TTTTCTTTTTTTCTT
Found at i:40693842 original size:8 final size:8
Alignment explanation
Indices: 40693808--40693841 Score: 54
Period size: 7 Copynumber: 4.5 Consensus size: 8
40693798 GCTGATTTCC
40693808 TTTTCTTT
1 TTTTCTTT
40693816 TTTTC-TT
1 TTTTCTTT
40693823 TTTTCTTT
1 TTTTCTTT
40693831 TTTT-TTT
1 TTTTCTTT
40693838 TTTT
1 TTTT
40693842 TAAGGTATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 14 0.56
8 11 0.44
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (8 bp):
TTTTCTTT
Found at i:40695535 original size:31 final size:31
Alignment explanation
Indices: 40695499--40695586 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 31
40695489 AATGTTTATG
*
40695499 ATTGAATCAATATCAAAGTTTCATATATATA
1 ATTGAATCAAAATCAAAGTTTCATATATATA
* * * *
40695530 ATTGAATTAAAATCAAATTTTCATGTGTATA
1 ATTGAATCAAAATCAAAGTTTCATATATATA
* *
40695561 A-TAATATC-ACATCAAAG-TTCATATAT
1 ATTGA-ATCAAAATCAAAGTTTCATATAT
40695587 TACAATGTAC
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
29 7 0.16
30 9 0.20
31 29 0.64
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (31 bp):
ATTGAATCAAAATCAAAGTTTCATATATATA
Found at i:40697811 original size:2 final size:2
Alignment explanation
Indices: 40697806--40697836 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
40697796 CTAACGGAAA
40697806 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40697837 TTATCTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40698914 original size:31 final size:31
Alignment explanation
Indices: 40698838--40698936 Score: 80
Period size: 29 Copynumber: 3.3 Consensus size: 31
40698828 ATTATTTACA
* * *
40698838 TAAGGGTCAAAAATTTTAAAA--TGATCAAA
1 TAAGGGCCAAAACTTTTAAAATGTGATCAAG
*** *
40698867 TAAGGATTAAATCTTTTAAAATGTGATCAAG
1 TAAGGGCCAAAACTTTTAAAATGTGATCAAG
* *
40698898 TAAGGGCCAAAACTTTTTAAATG-G-TTAAG
1 TAAGGGCCAAAACTTTTAAAATGTGATCAAG
*
40698927 TAAGAGCCAA
1 TAAGGGCCAA
40698937 TTTTTTTTTC
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
29 30 0.54
30 1 0.02
31 25 0.45
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.29
Consensus pattern (31 bp):
TAAGGGCCAAAACTTTTAAAATGTGATCAAG
Found at i:40704658 original size:20 final size:20
Alignment explanation
Indices: 40704633--40704674 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
40704623 AATCTCAAAT
40704633 ATTGAGATTAAAAAAATTAA
1 ATTGAGATTAAAAAAATTAA
40704653 ATTGAGATTAAAAAAATTAA
1 ATTGAGATTAAAAAAATTAA
40704673 AT
1 AT
40704675 ATCAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.31
Consensus pattern (20 bp):
ATTGAGATTAAAAAAATTAA
Found at i:40704683 original size:21 final size:20
Alignment explanation
Indices: 40704639--40704685 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
40704629 AAATATTGAG
* *
40704639 ATTAAAAAAATTAAATTGAG
1 ATTAAAAAAATTAAATTCAA
40704659 ATTAAAAAAATTAAATATCAA
1 ATTAAAAAAATTAAAT-TCAA
40704680 ATTAAA
1 ATTAAA
40704686 GAACAAGTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (20 bp):
ATTAAAAAAATTAAATTCAA
Found at i:40718732 original size:89 final size:89
Alignment explanation
Indices: 40718520--40718733 Score: 248
Period size: 89 Copynumber: 2.4 Consensus size: 89
40718510 GAAGACCGTG
* * * *
40718520 GTACAGACATGCAGTATTAATTGCCAGATCAGATATTTTACACAGCAAAGCTAGCGTATAAGTTG
1 GTACAGACATGCAGTATAAACTGCCAGATCAGATATATTACACAGCAAAGCTAGCGTATAAGCTG
* * * *
40718585 TACTGTGCAATGCGGTAGACCGCG
66 TACTATACAATGCGGTAAACCGCA
* * * * * *** * *
40718609 GTACAAACATGCAGTATGAACTGGCAAATTAGATATATTGTGCAGTAAGGCTAGCGTATAAGCTG
1 GTACAGACATGCAGTATAAACTGCCAGATCAGATATATTACACAGCAAAGCTAGCGTATAAGCTG
*
40718674 TACTATACAATGCGGTAAACTGCA
66 TACTATACAATGCGGTAAACCGCA
*
40718698 GTACAGACATGTAGTATAAACTGCCAGATCAGATAT
1 GTACAGACATGCAGTATAAACTGCCAGATCAGATAT
40718734 TGGCACGTAG
Statistics
Matches: 101, Mismatches: 24, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
89 101 1.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (89 bp):
GTACAGACATGCAGTATAAACTGCCAGATCAGATATATTACACAGCAAAGCTAGCGTATAAGCTG
TACTATACAATGCGGTAAACCGCA
Found at i:40720127 original size:6 final size:6
Alignment explanation
Indices: 40720116--40720171 Score: 67
Period size: 6 Copynumber: 9.0 Consensus size: 6
40720106 AAGGAAGAAG
* * *
40720116 AATAAA AATAAAA AATAAA AATAAA AGTAAA AATAAA TAATAAT AATAAT
1 AATAAA AAT-AAA AATAAA AATAAA AATAAA AATAAA -AATAAA AATAAA
40720166 AATAAA
1 AATAAA
40720172 CAAATAAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
6 33 0.75
7 11 0.25
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (6 bp):
AATAAA
Found at i:40720134 original size:13 final size:13
Alignment explanation
Indices: 40720116--40720164 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
40720106 AAGGAAGAAG
40720116 AATAAAAATAAAA
1 AATAAAAATAAAA
40720129 AATAAAAAT-AAA
1 AATAAAAATAAAA
* *
40720141 AGTAAAAATAAAT
1 AATAAAAATAAAA
*
40720154 AATAATAATAA
1 AATAAAAATAA
40720165 TAATAAACAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
12 11 0.35
13 20 0.65
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (13 bp):
AATAAAAATAAAA
Found at i:40720140 original size:19 final size:19
Alignment explanation
Indices: 40720116--40720179 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
40720106 AAGGAAGAAG
40720116 AATAAAAATAAAAA-ATAAA
1 AATAAAAATAAAAATA-AAA
* *
40720135 AATAAAAGTAAAAATAAAT
1 AATAAAAATAAAAATAAAA
* *
40720154 AATAATAATAATAATAAACA
1 AATAAAAATAAAAATAAA-A
40720174 AATAAA
1 AATAAA
40720180 CAAAATAAGT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
19 30 0.83
20 6 0.17
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAA
Found at i:40720171 original size:25 final size:24
Alignment explanation
Indices: 40720116--40720171 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 24
40720106 AAGGAAGAAG
40720116 AATAAAAATAAAAAATAAAAATAA
1 AATAAAAATAAAAAATAAAAATAA
* *
40720140 AAGTAAAAATAAATAATAATAATAA
1 AA-TAAAAATAAAAAATAAAAATAA
40720165 TAATAAA
1 -AATAAA
40720172 CAAATAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 2 0.07
25 24 0.86
26 2 0.07
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (24 bp):
AATAAAAATAAAAAATAAAAATAA
Found at i:40722401 original size:89 final size:88
Alignment explanation
Indices: 40722248--40722442 Score: 219
Period size: 89 Copynumber: 2.2 Consensus size: 88
40722238 GGGCTATCAG
* * * * *
40722248 TAAGCTGTACGGTGTCAAGCGGAAGACTACGATACAGACATGCAGTATGAACTGCCAGACCAGAT
1 TAAGCTGTACTGTG-CAAACGGAAGACCACGATACAGACATGCAATATAAACTGCCAGACCAGAT
*
40722313 ATATTACGTAGTAAGGCCAACGTA
65 ATATTACGTAGCAAGGCCAACGTA
* * * * * *
40722337 TAAGCTGTACTGTGCAATACGGAAGACCGCGGTATAGACATGCAATATAAATTGGCAGATCAGAT
1 TAAGCTGTACTGTGCAA-ACGGAAGACCACGATACAGACATGCAATATAAACTGCCAGACCAGAT
* *
40722402 ATATTACGTAGCAAGGCTAGCGTA
65 ATATTACGTAGCAAGGCCAACGTA
* * *
40722426 TATGTTGTACTATGCAA
1 TAAGCTGTACTGTGCAA
40722443 CGCGGTAAAT
Statistics
Matches: 88, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
88 3 0.03
89 85 0.97
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (88 bp):
TAAGCTGTACTGTGCAAACGGAAGACCACGATACAGACATGCAATATAAACTGCCAGACCAGATA
TATTACGTAGCAAGGCCAACGTA
Found at i:40723945 original size:16 final size:16
Alignment explanation
Indices: 40723924--40723955 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40723914 ATTTTACTAT
40723924 ATAGTGGTTCATAAAA
1 ATAGTGGTTCATAAAA
40723940 ATAGTGGTTCATAAAA
1 ATAGTGGTTCATAAAA
40723956 GGTTGTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATAGTGGTTCATAAAA
Found at i:40728729 original size:5 final size:5
Alignment explanation
Indices: 40728719--40728788 Score: 63
Period size: 5 Copynumber: 14.0 Consensus size: 5
40728709 AAGATGACTT
* * * * *
40728719 TATAA TATAA TATAA TATAA -AAAA TAAAA AATTA T-TAAA TATTAA CATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT-AA TA-TAA TATAA
40728769 TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA
40728789 ATAGTTTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
4 4 0.08
5 45 0.85
6 3 0.06
7 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (5 bp):
TATAA
Found at i:40733200 original size:17 final size:17
Alignment explanation
Indices: 40733174--40733212 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
40733164 GATTGTGTAT
40733174 ACTGAAACTGTAGT-AAA
1 ACTGAAACTGTA-TCAAA
*
40733191 ACTGAGACTGTATCAAA
1 ACTGAAACTGTATCAAA
40733208 ACTGA
1 ACTGA
40733213 TAGAGACTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.23
Consensus pattern (17 bp):
ACTGAAACTGTATCAAA
Found at i:40738350 original size:18 final size:18
Alignment explanation
Indices: 40738327--40738417 Score: 96
Period size: 18 Copynumber: 4.9 Consensus size: 18
40738317 CGAGGACTTC
*
40738327 AAAAATGTGAAGAACATT
1 AAAAATGTAAAGAACATT
40738345 AAAAATGTAAAGAACATT
1 AAAAATGTAAAGAACATT
* *
40738363 AAATCAA-GCTACGAGGAC-TT
1 AAA--AATG-TA-AAGAACATT
40738383 CAAAAATGTAAAGAACATT
1 -AAAAATGTAAAGAACATT
40738402 AAAAATGTAAAGAACA
1 AAAAATGTAAAGAACA
40738418 CTTACAATCA
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
18 40 0.66
19 7 0.11
20 7 0.11
21 7 0.11
ACGTcount: A:0.56, C:0.10, G:0.14, T:0.20
Consensus pattern (18 bp):
AAAAATGTAAAGAACATT
Found at i:40738377 original size:57 final size:58
Alignment explanation
Indices: 40738305--40738431 Score: 229
Period size: 57 Copynumber: 2.2 Consensus size: 58
40738295 TGAAAATAGG
*
40738305 TAAATCAAGCTACGAGGACTTCAAAAATGTGAAGAACATTAAAAATGTAAAGAACA-T
1 TAAATCAAGCTACGAGGACTTCAAAAATGTAAAGAACATTAAAAATGTAAAGAACACT
40738362 TAAATCAAGCTACGAGGACTTCAAAAATGTAAAGAACATTAAAAATGTAAAGAACACT
1 TAAATCAAGCTACGAGGACTTCAAAAATGTAAAGAACATTAAAAATGTAAAGAACACT
40738420 TACAATCAAGCT
1 TA-AATCAAGCT
40738432 TGAAAGTTGA
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
57 55 0.82
58 3 0.04
59 9 0.13
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (58 bp):
TAAATCAAGCTACGAGGACTTCAAAAATGTAAAGAACATTAAAAATGTAAAGAACACT
Found at i:40741685 original size:12 final size:12
Alignment explanation
Indices: 40741658--40741701 Score: 51
Period size: 10 Copynumber: 4.0 Consensus size: 12
40741648 CAAATCTATT
40741658 CAAAATTAA-T-
1 CAAAATTAATTA
*
40741668 CAAAATTTATTA
1 CAAAATTAATTA
40741680 CAAAATTAATT-
1 CAAAATTAATTA
40741691 -AAAATTAATTA
1 CAAAATTAATTA
40741702 TGTTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
10 18 0.62
11 1 0.03
12 10 0.34
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (12 bp):
CAAAATTAATTA
Found at i:40741686 original size:22 final size:22
Alignment explanation
Indices: 40741649--40741701 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
40741639 CCATTTGTGC
*
40741649 AAATCTATT-CAAAATTAATCA
1 AAATTTATTACAAAATTAATCA
*
40741670 AAATTTATTACAAAATTAATTA
1 AAATTTATTACAAAATTAATCA
*
40741692 AAATTAATTA
1 AAATTTATTA
40741702 TGTTAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATTTATTACAAAATTAATCA
Found at i:40746837 original size:29 final size:29
Alignment explanation
Indices: 40746804--40746964 Score: 191
Period size: 29 Copynumber: 5.6 Consensus size: 29
40746794 GTGACGAGAT
40746804 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
40746833 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
40746862 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * ***
40746891 TGGCACTAAGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * **
40746920 TGGCACTATGTGTGCAG-GCT-TAAATCGCA
1 TGGCACTAAGTGTGC-GTGCTGGAAAT-ATA
40746949 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
40746965 AAATCGAGTA
Statistics
Matches: 117, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
28 3 0.03
29 113 0.97
30 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:40746952 original size:87 final size:87
Alignment explanation
Indices: 40746804--40746963 Score: 214
Period size: 87 Copynumber: 1.8 Consensus size: 87
40746794 GTGACGAGAT
* * * * *
40746804 TGGCACTAAGTGTGCGTGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACT
1 TGGCACTAAGTGTGCGAGCTCGAAAGATATGGCACTAAGTGTGCAGGCTGGAAATACATGGCACT
40746869 AAGTGTGCATGCTGGAAATATA
66 AAGTGTGCATGCTGGAAATATA
* * * * *
40746891 TGGCACTAAGTGTGCGAGCTCGAAGGGTATGGCACTATGTGTGCAGGCT-TAAATCGCATGGCAC
1 TGGCACTAAGTGTGCGAGCTCGAAAGATATGGCACTAAGTGTGCAGGCTGGAAAT-ACATGGCAC
40746955 TAAGTGTGC
65 TAAGTGTGC
40746964 GAAATCGAGT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
86 4 0.06
87 58 0.94
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (87 bp):
TGGCACTAAGTGTGCGAGCTCGAAAGATATGGCACTAAGTGTGCAGGCTGGAAATACATGGCACT
AAGTGTGCATGCTGGAAATATA
Found at i:40754594 original size:29 final size:29
Alignment explanation
Indices: 40754561--40754721 Score: 216
Period size: 29 Copynumber: 5.6 Consensus size: 29
40754551 GTGACGAGAT
40754561 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
40754590 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
40754619 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * ***
40754648 TGGCACTAAGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * * **
40754677 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ATA
40754706 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
40754722 AAATCGAGTA
Statistics
Matches: 119, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
28 2 0.02
29 117 0.98
ACGTcount: A:0.25, C:0.16, G:0.33, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:40755205 original size:22 final size:22
Alignment explanation
Indices: 40755166--40755224 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
40755156 GTTTTAAGAA
*
40755166 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
40755187 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
40755209 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
40755225 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:40755241 original size:26 final size:24
Alignment explanation
Indices: 40755195--40755254 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
40755185 ATTTGTTTTA
*
40755195 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
40755219 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
* *
40755245 TTTTTTATTT
1 ATATTTATTT
40755255 AATAAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:40762471 original size:2 final size:2
Alignment explanation
Indices: 40762464--40762500 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
40762454 ATGATTACTG
* *
40762464 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40762501 CGTATGACTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40762481 original size:12 final size:12
Alignment explanation
Indices: 40762464--40762500 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
40762454 ATGATTACTG
*
40762464 ATATATATATAT
1 ATATATATGTAT
40762476 ATATATATGTAT
1 ATATATATGTAT
40762488 ATATATATGTAT
1 ATATATATGTAT
40762500 A
1 A
40762501 CGTATGACTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (12 bp):
ATATATATGTAT
Found at i:40769697 original size:35 final size:35
Alignment explanation
Indices: 40769651--40769720 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
40769641 AACAAATTAG
40769651 TGAATTTGAGAAAATATTTAACTGTGAAAAACTAA
1 TGAATTTGAGAAAATATTTAACTGTGAAAAACTAA
40769686 TGAATTTGAGAAAATATTTAACTGTGAAAAACTAA
1 TGAATTTGAGAAAATATTTAACTGTGAAAAACTAA
40769721 GGTAGTAGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (35 bp):
TGAATTTGAGAAAATATTTAACTGTGAAAAACTAA
Found at i:40770063 original size:16 final size:16
Alignment explanation
Indices: 40770042--40770074 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
40770032 CACAATGACA
40770042 TTACTTTCAATTAGAG
1 TTACTTTCAATTAGAG
40770058 TTACTTTCAATTAGAG
1 TTACTTTCAATTAGAG
40770074 T
1 T
40770075 ATTAACTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (16 bp):
TTACTTTCAATTAGAG
Found at i:40780323 original size:30 final size:30
Alignment explanation
Indices: 40780283--40780342 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
40780273 ATAGGCAGTG
40780283 TTTGCAAGTCAACCATAGCCCTTGGCACAT
1 TTTGCAAGTCAACCATAGCCCTTGGCACAT
*
40780313 TTTGCCAGTCAACCATAGCCCTTGGCACAT
1 TTTGCAAGTCAACCATAGCCCTTGGCACAT
40780343 ACTCTTGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.27
Consensus pattern (30 bp):
TTTGCAAGTCAACCATAGCCCTTGGCACAT
Found at i:40781969 original size:21 final size:21
Alignment explanation
Indices: 40781940--40781980 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40781930 TTTCCAAAGA
* *
40781940 TATGTATTGGATTGAATTGAG
1 TATGAATTGGATTAAATTGAG
*
40781961 TATGAATTGTATTAAATTGA
1 TATGAATTGGATTAAATTGA
40781981 TGTTAAATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (21 bp):
TATGAATTGGATTAAATTGAG
Found at i:40782489 original size:27 final size:25
Alignment explanation
Indices: 40782459--40782513 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
40782449 GGAGCTTTTT
* *
40782459 GATTAAAGGCTTTTTCATGAGCTTCCC
1 GATTAAAGGCTCTCT-A-GAGCTTCCC
*
40782486 GATTAATGGCTCTCTAGAGCTTCCC
1 GATTAAAGGCTCTCTAGAGCTTCCC
40782511 GAT
1 GAT
40782514 ATTGGCTTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 12 0.48
26 1 0.04
27 12 0.48
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.35
Consensus pattern (25 bp):
GATTAAAGGCTCTCTAGAGCTTCCC
Found at i:40782511 original size:25 final size:24
Alignment explanation
Indices: 40782477--40782619 Score: 103
Period size: 24 Copynumber: 5.8 Consensus size: 24
40782467 GCTTTTTCAT
40782477 GAGCTTCCCGATTAATGGCTCTCTA
1 GAGCTTCCCG-TTAATGGCTCTCTA
* * *
40782502 GAGCTTCCCGATATTGGCT-TGCTT
1 GAGCTTCCCGTTAATGGCTCT-CTA
* * * *
40782526 GAACTTCCCGATATTGGCTC-GTA
1 GAGCTTCCCGTTAATGGCTCTCTA
* *
40782549 TGAGCTTCTCGTTAATGGCTCTCCA
1 -GAGCTTCCCGTTAATGGCTCTCTA
* *
40782574 GAGCTTCTCGTTACATGGCTCACGT-
1 GAGCTTCCCGTTA-ATGGCTCTC-TA
*
40782599 GAGCTTCCTGTTATATGGCTC
1 GAGCTTCCCGTTA-ATGGCTC
40782620 AAAAGAGCTT
Statistics
Matches: 95, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
23 2 0.02
24 56 0.59
25 37 0.39
ACGTcount: A:0.17, C:0.27, G:0.22, T:0.34
Consensus pattern (24 bp):
GAGCTTCCCGTTAATGGCTCTCTA
Found at i:40782652 original size:25 final size:25
Alignment explanation
Indices: 40782540--40782652 Score: 92
Period size: 25 Copynumber: 4.6 Consensus size: 25
40782530 TTCCCGATAT
*
40782540 TGGCTCGTATGAGCTTCTCGTTA-A
1 TGGCTCATATGAGCTTCTCGTTATA
*
40782564 TGGCTC-TCCA-GAGCTTCTCGTTACA
1 TGGCTCAT--ATGAGCTTCTCGTTATA
**
40782589 TGGCTCACGTGAGCTTC-CTGTTATA
1 TGGCTCATATGAGCTTCTC-GTTATA
* *
40782614 TGGCTCAAAAGAGCTTCTCGTT-TA
1 TGGCTCATATGAGCTTCTCGTTATA
*
40782638 TGTGCTCGTATGAGC
1 TG-GCTCATATGAGC
40782653 AATCCTGAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
23 1 0.01
24 24 0.33
25 46 0.64
26 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.35
Consensus pattern (25 bp):
TGGCTCATATGAGCTTCTCGTTATA
Found at i:40782652 original size:50 final size:49
Alignment explanation
Indices: 40782540--40782652 Score: 122
Period size: 50 Copynumber: 2.3 Consensus size: 49
40782530 TTCCCGATAT
***
40782540 TGGCTCGTATGAGCTTCTCGTTAATGGCTCTCCAGAGCTTCTCGTTACA
1 TGGCTCGTATGAGCTTCTCGTTAATGGCTCAAAAGAGCTTCTCGTTACA
*** *
40782589 TGGCTCACGTGAGCTTC-CTGTTATATGGCTCAAAAGAGCTTCTCGTT-TA
1 TGGCTCGTATGAGCTTCTC-GTTA-ATGGCTCAAAAGAGCTTCTCGTTACA
40782638 TGTGCTCGTATGAGC
1 TG-GCTCGTATGAGC
40782653 AATCCTGAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
48 1 0.02
49 21 0.41
50 29 0.57
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.35
Consensus pattern (49 bp):
TGGCTCGTATGAGCTTCTCGTTAATGGCTCAAAAGAGCTTCTCGTTACA
Found at i:40787054 original size:43 final size:42
Alignment explanation
Indices: 40786989--40787111 Score: 142
Period size: 43 Copynumber: 2.9 Consensus size: 42
40786979 TATTGAGATG
* * * *
40786989 TGATTACATGTAAGACCTTGTGTGGGACAGTGGCATTGTATTA
1 TGATTACGTGTAAGACCATGTGTGGGACAGTGGCATCGT-TAA
*
40787032 TGATTACGTGTAAGACCATGTGTGGGACA-TCGACATCGTTAA
1 TGATTACGTGTAAGACCATGTGTGGGACAGT-GGCATCGTTAA
*
40787074 TCGACTT-CGTGTAAGACCCTGTGTGGGACAGTGGCATC
1 T-GA-TTACGTGTAAGACCATGTGTGGGACAGTGGCATC
40787112 AATAAGTGTT
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
42 4 0.06
43 62 0.90
44 3 0.04
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (42 bp):
TGATTACGTGTAAGACCATGTGTGGGACAGTGGCATCGTTAA
Found at i:40788018 original size:21 final size:21
Alignment explanation
Indices: 40787992--40788033 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
40787982 TGAAGTCTGC
40787992 ACCTTAATTTTGGAATTTTAT
1 ACCTTAATTTTGGAATTTTAT
40788013 ACCTTAATTTTGGAATTTTAT
1 ACCTTAATTTTGGAATTTTAT
40788034 TTGCCACACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (21 bp):
ACCTTAATTTTGGAATTTTAT
Found at i:40790022 original size:40 final size:40
Alignment explanation
Indices: 40789937--40790087 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
40789927 AATTGAATGA
* * *
40789937 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
40789977 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
40790018 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
40790057 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
40790088 ACGTGATTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:40790101 original size:40 final size:40
Alignment explanation
Indices: 40789973--40790103 Score: 156
Period size: 40 Copynumber: 3.3 Consensus size: 40
40789963 TATGCTGGAA
* * *
40789973 ATTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG
** * * **
40790013 GCTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGAC
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG
*
40790053 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTG
40790093 ATTATATCCGG
1 ATTATATCCGG
40790104 TTATATTCCG
Statistics
Matches: 73, Mismatches: 17, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
39 1 0.01
40 72 0.99
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG
Found at i:40798110 original size:40 final size:40
Alignment explanation
Indices: 40797982--40798112 Score: 147
Period size: 40 Copynumber: 3.3 Consensus size: 40
40797972 TATGCTGGAA
* * * *
40797982 ATTATATCCGGGTTAAGACCCGAAGGCAATTGCGCTAGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG
** * * **
40798022 GCTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGAC
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG
*
40798062 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTG
40798102 ATTATATCCGG
1 ATTATATCCGG
40798113 TTATATTCCG
Statistics
Matches: 72, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
39 1 0.01
40 71 0.99
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG
Found at i:40805902 original size:43 final size:43
Alignment explanation
Indices: 40805764--40805906 Score: 125
Period size: 43 Copynumber: 3.3 Consensus size: 43
40805754 TGAGATGTGA
* * *
40805764 TTACATGCAAGACCCTGTATGGGACAGTGGCATTGTATTACG-A
1 TTACATGTAAGACCCTGTGTGGGACAGTGGCATTG-ATTACGTG
* * * **
40805807 TTACATTTAAGACCATGTGTGGGACA-TCGGCA-TCATTAATTG
1 TTACATGTAAGACCCTGTGTGGGACAGT-GGCATTGATTACGTG
*
40805849 ACTT-CGTGTAAGACCCTGTGTGGGACAGTGGCATTGA-TACGTG
1 --TTACATGTAAGACCCTGTGTGGGACAGTGGCATTGATTACGTG
40805892 TTAACATGTAAGACC
1 TT-ACATGTAAGACC
40805907 ATATCAAGGA
Statistics
Matches: 77, Mismatches: 15, Indels: 16
0.71 0.14 0.15
Matches are distributed among these distances:
41 6 0.08
42 2 0.03
43 64 0.83
44 5 0.06
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (43 bp):
TTACATGTAAGACCCTGTGTGGGACAGTGGCATTGATTACGTG
Found at i:40810728 original size:28 final size:25
Alignment explanation
Indices: 40810697--40810755 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 25
40810687 AAAATCAACT
40810697 TTTTTTAATTAATTTGTATATTATATCA
1 TTTTTTAATTAATTT-T-T-TTATATCA
* * *
40810725 TTTTGTATTTAATTTTTTTATATTA
1 TTTTTTAATTAATTTTTTTATATCA
40810750 TTTTTT
1 TTTTTT
40810756 TATAAAAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 12 0.44
26 1 0.04
27 1 0.04
28 13 0.48
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.69
Consensus pattern (25 bp):
TTTTTTAATTAATTTTTTTATATCA
Found at i:40817258 original size:2 final size:2
Alignment explanation
Indices: 40817251--40817275 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40817241 CCAAATATTT
40817251 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
40817276 TAAAAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40818775 original size:4 final size:4
Alignment explanation
Indices: 40818766--40818804 Score: 69
Period size: 4 Copynumber: 9.5 Consensus size: 4
40818756 GTTTTTTATG
40818766 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TT
40818805 ATTAAATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 30 0.88
5 4 0.12
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:40818791 original size:21 final size:22
Alignment explanation
Indices: 40818760--40818804 Score: 83
Period size: 21 Copynumber: 2.1 Consensus size: 22
40818750 TGTTTTGTTT
40818760 TTTATGTTTATTTATTTATTTA
1 TTTATGTTTATTTATTTATTTA
40818782 TTTAT-TTTATTTATTTATTTA
1 TTTATGTTTATTTATTTATTTA
40818803 TT
1 TT
40818805 ATTAAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTATGTTTATTTATTTATTTA
Found at i:40818895 original size:34 final size:38
Alignment explanation
Indices: 40818826--40818899 Score: 111
Period size: 34 Copynumber: 2.1 Consensus size: 38
40818816 AAAATTTATA
*
40818826 ATATATTATTAATATATATATTTTTCTAAATTTTAAAT
1 ATATATTATTAAAATATATATTTTTCTAAATTTTAAAT
40818864 ATATATT-TTAAAAT-TA-ATTTTT-TAAATTTTAAAT
1 ATATATTATTAAAATATATATTTTTCTAAATTTTAAAT
40818898 AT
1 AT
40818900 TAAATATATT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
34 14 0.40
35 6 0.17
36 2 0.06
37 6 0.17
38 7 0.20
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (38 bp):
ATATATTATTAAAATATATATTTTTCTAAATTTTAAAT
Found at i:40819503 original size:2 final size:2
Alignment explanation
Indices: 40819496--40819540 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
40819486 AATATGATTC
40819496 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40819538 TA T
1 TA T
40819541 TATGCATGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40820045 original size:22 final size:24
Alignment explanation
Indices: 40820014--40820071 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 24
40820004 TAAAAAACCC
40820014 TTTTA-AATATTATTTAATT-TG-
1 TTTTATAATATTATTTAATTATGA
*
40820035 TTTTATAATATT-TTAAATTATGA
1 TTTTATAATATTATTTAATTATGA
40820058 TTTT-TAA-ATTATTT
1 TTTTATAATATTATTT
40820072 TTAAAGATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
21 14 0.45
22 13 0.42
23 4 0.13
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (24 bp):
TTTTATAATATTATTTAATTATGA
Found at i:40820366 original size:17 final size:17
Alignment explanation
Indices: 40820344--40820410 Score: 62
Period size: 18 Copynumber: 3.8 Consensus size: 17
40820334 AATTAAAAAA
*
40820344 TAAAAAAATATATTTGT
1 TAAAAAAATATATTTAT
*
40820361 TAAAAAAGATTTATTTAT
1 TAAAAAA-ATATATTTAT
* * *
40820379 TGAAAAACTAAATTTATT
1 TAAAAAAATATATTTA-T
*
40820397 TAAAAATATATATT
1 TAAAAAAATATATT
40820411 AAAAATTTAA
Statistics
Matches: 38, Mismatches: 10, Indels: 3
0.75 0.20 0.06
Matches are distributed among these distances:
17 13 0.34
18 25 0.66
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.42
Consensus pattern (17 bp):
TAAAAAAATATATTTAT
Found at i:40820414 original size:13 final size:13
Alignment explanation
Indices: 40820396--40820444 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
40820386 CTAAATTTAT
40820396 TTAAAAATATATA
1 TTAAAAATATATA
* *
40820409 TTAAAAATTTAAAA
1 TTAAAAATAT-ATA
*
40820423 TTAAAAATACATA
1 TTAAAAATATATA
40820436 TTATAAAAT
1 TTA-AAAAT
40820445 TACATCATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 14 0.48
14 15 0.52
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
TTAAAAATATATA
Found at i:40820924 original size:40 final size:41
Alignment explanation
Indices: 40820879--40820963 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 41
40820869 GTGTTGGTTA
* * *
40820879 TAATTTTTTAATTTTAATACACATTTATGAATTTATATA-T
1 TAATTTTTAAATTTTAATACACATTCATAAATTTATATACT
* *
40820919 TAATTTTTAAATTTTAGTACACATTCATAAATTTATGTACT
1 TAATTTTTAAATTTTAATACACATTCATAAATTTATATACT
40820960 TAAT
1 TAAT
40820964 ATATATTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 34 0.87
41 5 0.13
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.52
Consensus pattern (41 bp):
TAATTTTTAAATTTTAATACACATTCATAAATTTATATACT
Found at i:40820974 original size:40 final size:40
Alignment explanation
Indices: 40820888--40820977 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
40820878 ATAATTTTTT
* * * *
40820888 AATTTTAATACACATTTATGAATTTATATATTAATTTTTA
1 AATTTTAATACACATTCATAAATTTATATATTAATATATA
* *
40820928 AATTTTAGTACACATTCATAAATTTATGTACTTAATATAT-
1 AATTTTAATACACATTCATAAATTTATATA-TTAATATATA
*
40820968 ATTTTTAATA
1 AATTTTAATA
40820978 GGTAAAGCCA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
40 34 0.83
41 7 0.17
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (40 bp):
AATTTTAATACACATTCATAAATTTATATATTAATATATA
Found at i:40821138 original size:71 final size:72
Alignment explanation
Indices: 40821026--40821178 Score: 254
Period size: 71 Copynumber: 2.1 Consensus size: 72
40821016 TTTTAAAAAC
*
40821026 TTAAAGAAATTAAATATATTAAAAAAATGTTAAGCATAACCAATTTTAAAATTTTAATATATTTA
1 TTAAA-AAATTAAATATATTAAAAAAATGTTAAGCATAACCAATTTTAAAATTTTAATATATTCA
40821091 ATATAGTT
65 ATATAGTT
*
40821099 TTAAAAAATTAAATATATT-AAAAAATGTTAAGTATAACCAATTTTAAAATTTTAATATATTCAA
1 TTAAAAAATTAAATATATTAAAAAAATGTTAAGCATAACCAATTTTAAAATTTTAATATATTCAA
*
40821163 TATATTT
66 TATAGTT
*
40821170 TTTAAAAAT
1 TTAAAAAAT
40821179 ATATTTTAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
71 57 0.75
72 14 0.18
73 5 0.07
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (72 bp):
TTAAAAAATTAAATATATTAAAAAAATGTTAAGCATAACCAATTTTAAAATTTTAATATATTCAA
TATAGTT
Found at i:40821291 original size:16 final size:17
Alignment explanation
Indices: 40821269--40821306 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
40821259 AAAAACGTAA
*
40821269 AAAAATTTAAATATATT
1 AAAATTTTAAATATATT
*
40821286 AAAATTTTAAATATGTT
1 AAAATTTTAAATATATT
40821303 AAAA
1 AAAA
40821307 GAAAATGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AAAATTTTAAATATATT
Found at i:40824432 original size:13 final size:14
Alignment explanation
Indices: 40824411--40824439 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
40824401 AGAAAAATAG
40824411 ATTAGAAAATATTT
1 ATTAGAAAATATTT
40824425 ATTA-AAAATATTT
1 ATTAGAAAATATTT
40824438 AT
1 AT
40824440 GAAGTTAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
ATTAGAAAATATTT
Found at i:40824915 original size:23 final size:23
Alignment explanation
Indices: 40824889--40824939 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
40824879 TGTATGGTAT
*
40824889 GTATA-ATGACATGTGTAATATTA
1 GTATACAT-ACATGTGTAAAATTA
*
40824912 GTATACATACATTTGTAAAATTA
1 GTATACATACATGTGTAAAATTA
*
40824935 ATATA
1 GTATA
40824940 TGTTTACTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (23 bp):
GTATACATACATGTGTAAAATTA
Found at i:40825449 original size:15 final size:15
Alignment explanation
Indices: 40825426--40825473 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
40825416 TATCAAATTT
40825426 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
40825441 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
40825456 ATATTGATTGAAAT-
1 ATATTGATTGAAATC
40825470 ATAT
1 ATAT
40825474 AATATATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:40825694 original size:18 final size:20
Alignment explanation
Indices: 40825671--40825711 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
40825661 TTGAATTGAA
40825671 TGAAAATGTATG-ATAT-TG
1 TGAAAATGTATGAATATATG
*
40825689 TGAAAATGTGTGAATATATG
1 TGAAAATGTATGAATATATG
40825709 TGA
1 TGA
40825712 TTATTAGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 4 0.20
20 5 0.25
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (20 bp):
TGAAAATGTATGAATATATG
Found at i:40826012 original size:21 final size:23
Alignment explanation
Indices: 40825970--40826012 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
40825960 TAATATTCCG
*
40825970 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTAGGATATTCT
40825993 GGTGTGTTTGGG-AGGA-ATTC
1 GGTGTGTTTGGGTAGGATATTC
40826013 GCGTATCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 3 0.16
23 12 0.63
ACGTcount: A:0.12, C:0.05, G:0.42, T:0.42
Consensus pattern (23 bp):
GGTGTGTTTGGGTAGGATATTCT
Found at i:40826130 original size:18 final size:19
Alignment explanation
Indices: 40826109--40826149 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
40826099 AATGAAATGA
40826109 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
40826127 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
40826146 GAAA
1 GAAA
40826150 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:40827820 original size:21 final size:22
Alignment explanation
Indices: 40827780--40827820 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
40827770 CTCCACCAAA
40827780 TAAAATATTAAATATTAATTCT
1 TAAAATATTAAATATTAATTCT
*
40827802 TAAAATTTTAAAT-TTAATT
1 TAAAATATTAAATATTAATT
40827821 TAAAAAACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TAAAATATTAAATATTAATTCT
Found at i:40827827 original size:21 final size:22
Alignment explanation
Indices: 40827781--40827826 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
40827771 TCCACCAAAT
*
40827781 AAAATATTAAATATTAATTCTT
1 AAAATATTAAATATTAATTCTA
*
40827803 AAAATTTTAAAT-TTAATT-TA
1 AAAATATTAAATATTAATTCTA
40827823 AAAA
1 AAAA
40827827 ACGTTTGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 6 0.27
22 11 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAATATTAAATATTAATTCTA
Found at i:40828032 original size:32 final size:32
Alignment explanation
Indices: 40827990--40828070 Score: 96
Period size: 32 Copynumber: 2.5 Consensus size: 32
40827980 TGAAATGTAT
40827990 ATTTGAAATATT-TTAT-AATATATATTTTT-TAA
1 ATTTGAAATATTATT-TGAA-AT-TATTTTTATAA
*
40828022 ATTTTAAATATATATTTGAAATTATTTTTATAA
1 ATTTGAAATAT-TATTTGAAATTATTTTTATAA
40828055 ATTTGAAATATTATTT
1 ATTTGAAATATTATTT
40828071 TTTAATATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
32 22 0.51
33 17 0.40
34 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (32 bp):
ATTTGAAATATTATTTGAAATTATTTTTATAA
Found at i:40828034 original size:20 final size:20
Alignment explanation
Indices: 40828009--40828117 Score: 65
Period size: 20 Copynumber: 5.7 Consensus size: 20
40827999 ATTTTATAAT
40828009 ATATATTTTTTAAATTTTAA
1 ATATATTTTTTAAATTTTAA
*
40828029 ATATA-----T--ATTTGAA
1 ATATATTTTTTAAATTTTAA
*
40828042 AT-TATTTTTATAAATTTGAA
1 ATATATTTTT-TAAATTTTAA
*
40828062 ATATTATTTTTTAATATTTTTA
1 ATA-TATTTTTTAA-ATTTTAA
* *
40828084 AT-TTTATTTTTAAATATTAA
1 ATATAT-TTTTTAAATTTTAA
40828104 ATATATATTTTTAA
1 ATATAT-TTTTTAA
40828118 TAATATAAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 25
0.68 0.07 0.25
Matches are distributed among these distances:
12 2 0.03
13 8 0.12
15 1 0.01
18 1 0.01
20 23 0.33
21 20 0.29
22 14 0.20
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
ATATATTTTTTAAATTTTAA
Found at i:40828048 original size:23 final size:22
Alignment explanation
Indices: 40827982--40828066 Score: 79
Period size: 23 Copynumber: 3.9 Consensus size: 22
40827972 AAAAATCTTG
*
40827982 AAATGTATATTTGAAATATTTT
1 AAATATATATTTGAAATATTTT
**
40828004 ATAATATATATTTTTTAA-ATTTT
1 A-AATATATA-TTTGAAATATTTT
40828027 AAATATATATTTGAAATTATTTT
1 AAATATATATTTGAAA-TATTTT
*
40828050 ---TATAAATTTGAAATATT
1 AAATATATATTTGAAATATT
40828067 ATTTTTTAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
19 4 0.08
20 12 0.23
21 5 0.09
22 9 0.17
23 18 0.34
24 5 0.09
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (22 bp):
AAATATATATTTGAAATATTTT
Found at i:40828070 original size:22 final size:22
Alignment explanation
Indices: 40828030--40828116 Score: 69
Period size: 22 Copynumber: 4.1 Consensus size: 22
40828020 AAATTTTAAA
*
40828030 TATATATTTG-AA-ATTATTTT
1 TATAAATTTGAAATATTATTTT
40828050 TATAAATTTGAAATATTATTTT
1 TATAAATTTGAAATATTATTTT
** *
40828072 T-TAATATTTTTAATTTTA-TTT
1 TATAA-ATTTGAAATATTATTTT
40828093 T-TAAATATT-AAATATATATTTT
1 TATAAAT-TTGAAATAT-TATTTT
40828115 TA
1 TA
40828117 ATAATATAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
20 15 0.28
21 16 0.30
22 23 0.43
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TATAAATTTGAAATATTATTTT
Found at i:40828083 original size:32 final size:32
Alignment explanation
Indices: 40828011--40828070 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
40828001 TTTATAATAT
*
40828011 ATATTTTT-TAAATTTTAAATATATATTTGAA
1 ATATTTTTATAAATTTGAAATATATATTTGAA
40828042 ATTATTTTTATAAATTTGAAATAT-TATTT
1 A-TATTTTTATAAATTTGAAATATATATTT
40828071 TTTAATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 1 0.04
32 12 0.46
33 13 0.50
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (32 bp):
ATATTTTTATAAATTTGAAATATATATTTGAA
Found at i:40828095 original size:21 final size:22
Alignment explanation
Indices: 40828060--40828130 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 22
40828050 TATAAATTTG
*
40828060 AAATAT-TATTTTTTAATATTTT
1 AAATATATA-TTTTTAATATATT
* *
40828082 TAAT-TTTATTTTTAA-ATATT
1 AAATATATATTTTTAATATATT
*
40828102 AAATATATATTTTTAATAATATA
1 AAATATATATTTTTAAT-ATATT
40828125 AAATAT
1 AAATAT
40828131 TTAAATATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
20 7 0.17
21 18 0.45
22 5 0.12
23 10 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AAATATATATTTTTAATATATT
Found at i:40828128 original size:23 final size:21
Alignment explanation
Indices: 40828088--40828148 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 21
40828078 TTTTTAATTT
*
40828088 TATTTTTAAATATTAAATATA
1 TATTTTTAAATATAAAATATA
40828109 TATTTTTAATAATATAAAATATTTA
1 TATTTTT-A-AATATAAAATA--TA
*
40828134 AATATTTTAAATATA
1 TAT-TTTTAAATATA
40828149 TGACCTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
21 7 0.21
22 1 0.03
23 10 0.30
24 6 0.18
25 5 0.15
26 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATTTTTAAATATAAAATATA
Found at i:40828206 original size:21 final size:22
Alignment explanation
Indices: 40828181--40828243 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 22
40828171 ATTTTATAAT
*
40828181 ATTTTAAATATTATTTAATT-TG
1 ATTTTAAATATT-TTAAATTATG
40828203 -TTTTATAATATTTTAAATTATG
1 ATTTTA-AATATTTTAAATTATG
40828225 ATTTTAAATTATCTTTAAA
1 ATTTTAAA-TAT-TTTAAA
40828244 ATTTAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
21 11 0.31
22 10 0.29
23 8 0.23
24 6 0.17
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (22 bp):
ATTTTAAATATTTTAAATTATG
Found at i:40828230 original size:13 final size:13
Alignment explanation
Indices: 40828212--40828236 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40828202 GTTTTATAAT
40828212 ATTTTAAATTATG
1 ATTTTAAATTATG
40828225 ATTTTAAATTAT
1 ATTTTAAATTAT
40828237 CTTTAAAATT
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:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
ATTTTAAATTATG
Found at i:40828310 original size:5 final size:5
Alignment explanation
Indices: 40828295--40828332 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
40828285 TTAATCATAA
40828295 AAAAT -AAAT AAAAT AAAAT AAAAT -AAAT AAAGAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AAAA
40828333 GACAAAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 8 0.27
5 17 0.57
6 5 0.17
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:40828312 original size:14 final size:15
Alignment explanation
Indices: 40828295--40828332 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
40828285 TTAATCATAA
40828295 AAAAT-AAATAAAAT
1 AAAATAAAATAAAAT
40828309 AAAATAAAAT-AAAT
1 AAAATAAAATAAAAT
40828323 AAAGATAAAA
1 AAA-ATAAAA
40828333 GACAAAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (15 bp):
AAAATAAAATAAAAT
Found at i:40828504 original size:14 final size:15
Alignment explanation
Indices: 40828485--40828548 Score: 69
Period size: 15 Copynumber: 4.3 Consensus size: 15
40828475 ATCTTTAAAA
40828485 ATAATTTAAAA-ATT
1 ATAATTTAAAATATT
40828499 ATAATTTAAAATATT
1 ATAATTTAAAATATT
* * *
40828514 ATAAATTAAATTA-A
1 ATAATTTAAAATATT
40828528 ATAATATTTAAAATATT
1 AT-A-ATTTAAAATATT
40828545 ATAA
1 ATAA
40828549 AAATAATAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
14 13 0.32
15 16 0.40
16 9 0.22
17 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATTTAAAATATT
Found at i:40828533 original size:22 final size:23
Alignment explanation
Indices: 40828483--40828556 Score: 68
Period size: 22 Copynumber: 3.3 Consensus size: 23
40828473 ATATCTTTAA
*
40828483 AAATAAT-TTAAAAATTATAATT
1 AAATAATATTATAAATTATAATT
*
40828505 TAA-AATATTATAAATTA-AATT
1 AAATAATATTATAAATTATAATT
*
40828526 AAATAATATTTAAAATATTATAA--
1 AAATAATA-TTATAA-ATTATAATT
40828549 AAATAATA
1 AAATAATA
40828557 ACAAATTTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
21 9 0.21
22 15 0.35
23 13 0.30
24 4 0.09
25 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATAATATTATAAATTATAATT
Found at i:40828607 original size:20 final size:20
Alignment explanation
Indices: 40828597--40828692 Score: 87
Period size: 21 Copynumber: 5.0 Consensus size: 20
40828587 TTTTATATTA
40828597 TTAAAAAATATATTTAATAT
1 TTAAAAAATATATTTAATAT
*
40828617 TTAAAAAATAATATTTAAAAT
1 TTAAAAAAT-ATATTTAATAT
*
40828638 TT--AAAA-A-A-GTAAT-T
1 TTAAAAAATATATTTAATAT
* *
40828652 TCAAAAAATATATTTAAAAT
1 TTAAAAAATATATTTAATAT
40828672 TTAGAAAAATATATATTAATA
1 TTA-AAAAATATAT-TTAATA
40828693 AAATATTCTA
Statistics
Matches: 59, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
14 2 0.03
15 3 0.05
16 5 0.08
17 2 0.03
18 1 0.02
19 7 0.12
20 12 0.20
21 22 0.37
22 5 0.08
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (20 bp):
TTAAAAAATATATTTAATAT
Found at i:40828623 original size:21 final size:21
Alignment explanation
Indices: 40828583--40828650 Score: 84
Period size: 21 Copynumber: 3.1 Consensus size: 21
40828573 AAAATATCTA
*
40828583 AATATTTTATATTATTAAAAAAT
1 AATATTTAATA-T-TTAAAAAAT
40828606 -ATATTTAATATTTAAAAAAT
1 AATATTTAATATTTAAAAAAT
*
40828626 AATATTTAAAATTTAAAAAAGT
1 AATATTTAATATTTAAAAAA-T
40828648 AAT
1 AAT
40828651 TTCAAAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
20 9 0.22
21 19 0.46
22 13 0.32
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (21 bp):
AATATTTAATATTTAAAAAAT
Found at i:40828658 original size:34 final size:35
Alignment explanation
Indices: 40828615--40828698 Score: 102
Period size: 34 Copynumber: 2.4 Consensus size: 35
40828605 TATATTTAAT
40828615 ATTT-AAAAAATAATATTTAAAATTTA-AAAAAGTA
1 ATTTAAAAAAAT-ATATTTAAAATTTAGAAAAAGTA
*
40828649 ATTTCAAAAAATATATTTAAAATTTAGAAAAA-TA
1 ATTTAAAAAAATATATTTAAAATTTAGAAAAAGTA
*
40828683 TATATTAATAAAATAT
1 -AT-TTAAAAAAATAT
40828699 TCTAAATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
34 20 0.45
35 14 0.32
36 10 0.23
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (35 bp):
ATTTAAAAAAATATATTTAAAATTTAGAAAAAGTA
Found at i:40828803 original size:9 final size:9
Alignment explanation
Indices: 40828770--40828803 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
40828760 AAAACATAAG
40828770 AAAAAAAGT
1 AAAAAAAGT
*
40828779 CAAAAAAGT
1 AAAAAAAGT
40828788 AAAAAAAGT
1 AAAAAAAGT
40828797 AAAAAAA
1 AAAAAAA
40828804 AAAAAGAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.79, C:0.03, G:0.09, T:0.09
Consensus pattern (9 bp):
AAAAAAAGT
Found at i:40828969 original size:10 final size:10
Alignment explanation
Indices: 40828954--40829002 Score: 57
Period size: 10 Copynumber: 4.8 Consensus size: 10
40828944 AAAATCATAA
40828954 TATAAAATAT
1 TATAAAATAT
40828964 TATAAAATAAAT
1 TATAAAAT--AT
40828976 TA-AATAATAT
1 TATAA-AATAT
40828986 T-TAAAATAT
1 TATAAAATAT
40828995 TATAAAAT
1 TATAAAAT
40829003 TAATAACAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
9 6 0.18
10 19 0.56
11 2 0.06
12 7 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TATAAAATAT
Found at i:40829062 original size:22 final size:21
Alignment explanation
Indices: 40829034--40829100 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
40829024 AAAATATTTA
*
40829034 AATATTTTATATTATTAAAAAAT
1 AATATTTAATA-T-TTAAAAAAT
40829057 -ATATTTAATATTTAAAAAAT
1 AATATTTAATATTTAAAAAAT
* * *
40829077 AATATTTAAAATTTTAAAAGT
1 AATATTTAATATTTAAAAAAT
40829098 AAT
1 AAT
40829101 TTAAAAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.23
21 21 0.54
22 9 0.23
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (21 bp):
AATATTTAATATTTAAAAAAT
Found at i:40829074 original size:21 final size:22
Alignment explanation
Indices: 40829034--40829095 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
40829024 AAAATATTTA
*
40829034 AATATTTTATATTATTAAAAAAT
1 AATATTTAATATT-TTAAAAAAT
40829057 -ATATTTAATA-TTTAAAAAAT
1 AATATTTAATATTTTAAAAAAT
*
40829077 AATATTTAAAATTTTAAAA
1 AATATTTAATATTTTAAAA
40829096 GTAATTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 9 0.26
21 10 0.29
22 16 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATATTTAATATTTTAAAAAAT
Found at i:40829100 original size:21 final size:21
Alignment explanation
Indices: 40829048--40829114 Score: 75
Period size: 20 Copynumber: 3.3 Consensus size: 21
40829038 TTTTATATTA
*
40829048 TTAAAAAAT-ATATTTAATAT
1 TTAAAAAATAATATTTAAAAT
40829068 TTAAAAAATAATATTTAAAAT
1 TTAAAAAATAATATTTAAAAT
* * *
40829089 TTTAAAAGTAAT-TTAAAAAT
1 TTAAAAAATAATATTTAAAAT
*
40829109 ATAAAA
1 TTAAAA
40829115 TTAAAATTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
20 20 0.50
21 20 0.50
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (21 bp):
TTAAAAAATAATATTTAAAAT
Found at i:40832237 original size:17 final size:18
Alignment explanation
Indices: 40832212--40832248 Score: 51
Period size: 16 Copynumber: 2.1 Consensus size: 18
40832202 ATTTTAGTGC
40832212 ATTATATTTTTAAA-AAAA
1 ATTATA-TTTTAAATAAAA
40832230 ATTA-ATTTTAAATAAAA
1 ATTATATTTTAAATAAAA
40832247 AT
1 AT
40832249 AATCTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
17 7 0.39
18 4 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTATATTTTAAATAAAA
Found at i:40837574 original size:4 final size:4
Alignment explanation
Indices: 40837565--40837597 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
40837555 TTTTCCTTAT
40837565 TTTA TTTA TTTA TTTA TTTA -TTA -TTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
40837598 CATATTATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 6 0.21
4 22 0.79
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:40837603 original size:14 final size:13
Alignment explanation
Indices: 40837565--40837605 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
40837555 TTTTCCTTAT
40837565 TTTATTTAT-TTA
1 TTTATTTATATTA
40837577 TTTATTTATTATTA
1 TTTATTTA-TATTA
40837591 TTTATTTCATATTA
1 TTTATTT-ATATTA
40837605 T
1 T
40837606 GAAAAATGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.31
13 1 0.04
14 16 0.62
15 1 0.04
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATTTATATTA
Found at i:40838101 original size:32 final size:30
Alignment explanation
Indices: 40838065--40838126 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 30
40838055 AAACATAAAG
*
40838065 ACTAAAATTGAT-AAATTCAAAACCTACAAAAA
1 ACTAAAATTAATCAAATT-AAAA--TACAAAAA
40838097 ACTAAAATTAATCAAATTAAAATACAAAAA
1 ACTAAAATTAATCAAATTAAAATACAAAAA
40838127 TTAAATTCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 8 0.29
32 15 0.54
33 5 0.18
ACGTcount: A:0.63, C:0.13, G:0.02, T:0.23
Consensus pattern (30 bp):
ACTAAAATTAATCAAATTAAAATACAAAAA
Found at i:40838355 original size:28 final size:28
Alignment explanation
Indices: 40838315--40838371 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
40838305 TCTCAAAGTT
*
40838315 AGACAACTTTTCTCAATTTGTTTCATGA
1 AGACAACTTTTCTCAATTTGTTCCATGA
40838343 AGACAACTTTTCTCAATTTGTTCCATGA
1 AGACAACTTTTCTCAATTTGTTCCATGA
40838371 A
1 A
40838372 CTTGAATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (28 bp):
AGACAACTTTTCTCAATTTGTTCCATGA
Found at i:40843018 original size:29 final size:28
Alignment explanation
Indices: 40842984--40843086 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
40842974 TACTCAATCA
*
40842984 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
40843013 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
* *
40843042 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
40843071 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
40843087 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:40845692 original size:6 final size:6
Alignment explanation
Indices: 40845677--40845720 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
40845667 GAAGGAAGAA
* *
40845677 ATGAAG ATGAAT ATGAAG ATGAAG GTGGAAG -TGAAG ATGAAG AT
1 ATGAAG ATGAAG ATGAAG ATGAAG AT-GAAG ATGAAG ATGAAG AT
40845721 AAAAAAGATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 4 0.12
6 25 0.76
7 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.34, T:0.20
Consensus pattern (6 bp):
ATGAAG
Found at i:40846112 original size:76 final size:74
Alignment explanation
Indices: 40845934--40846147 Score: 206
Period size: 76 Copynumber: 2.9 Consensus size: 74
40845924 TCATAAAATT
* **
40845934 TATTTTAT-TGTATTTTACATCAATA-ATATATTTATTTACAATCTA-GAAAAAATTTAAAAATT
1 TATTTT-TCTGTATTTTACATCAATATATATACTTATTTACAATCTATGAAAAAATAGAAAAATT
*
40845996 ATTTGTATTG
65 ATTTATATTG
* * * * *
40846006 TATTCTACTGTATTTCATATAAATAATATATACTTATTTACAATCTATGAAAAAATAAGAAAAAT
1 TATTTTTCTGTATTTTACATCAAT-ATATATACTTATTTACAATCTATGAAAAAAT-AGAAAAAT
40846071 T-TCTTATATTG
64 TAT-TTATATTG
* *
40846082 TATTTTTCTGTATTTTACATCAATAGTATAT-CAATATTTACAATTTACT-AAAAAATTAGAAGA
1 TATTTTTCTGTATTTTACATCAATA-TATATAC-TTATTTACAATCTA-TGAAAAAA-TAGAA-A
40846145 AAT
61 AAT
40846148 GAAAAAAATG
Statistics
Matches: 115, Mismatches: 16, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
72 18 0.16
73 1 0.01
74 19 0.17
75 11 0.10
76 60 0.52
77 6 0.05
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (74 bp):
TATTTTTCTGTATTTTACATCAATATATATACTTATTTACAATCTATGAAAAAATAGAAAAATTA
TTTATATTG
Found at i:40848641 original size:18 final size:18
Alignment explanation
Indices: 40848615--40848649 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40848605 GTTCGATTAA
* *
40848615 CCAATTAACCTGTTTCAT
1 CCAAATAACCTATTTCAT
40848633 CCAAATAACCTATTTCA
1 CCAAATAACCTATTTCA
40848650 CATATTTAAA
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:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (18 bp):
CCAAATAACCTATTTCAT
Found at i:40856143 original size:20 final size:20
Alignment explanation
Indices: 40856106--40856144 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40856096 GTGAGTTGGT
*
40856106 ATATTTTGACATGTTTTGAC
1 ATATTTTGACATGGTTTGAC
40856126 ATATTTTGA-ATAGGTTTGA
1 ATATTTTGACAT-GGTTTGA
40856145 ATGTTGGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.28, C:0.05, G:0.18, T:0.49
Consensus pattern (20 bp):
ATATTTTGACATGGTTTGAC
Found at i:40859187 original size:33 final size:30
Alignment explanation
Indices: 40859134--40859196 Score: 74
Period size: 33 Copynumber: 2.0 Consensus size: 30
40859124 TGTCATTTTG
40859134 TTGTTGTTTTGTTACAATTTCACT-ACTATT
1 TTGTTGTTTTGTTACAATTTCA-TAACTATT
*
40859164 TTGTTGTTATTGTTTAGATATTTCATAACTATT
1 TTGTTGTT-TTG-TTACA-ATTTCATAACTATT
40859197 ATTTTATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 8 0.29
31 3 0.11
32 5 0.18
33 12 0.43
ACGTcount: A:0.22, C:0.10, G:0.11, T:0.57
Consensus pattern (30 bp):
TTGTTGTTTTGTTACAATTTCATAACTATT
Found at i:40865200 original size:14 final size:14
Alignment explanation
Indices: 40865181--40865215 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
40865171 TTGTTTGACT
40865181 GAAAATGATTTCCG
1 GAAAATGATTTCCG
*
40865195 GAAAATGATTTCTG
1 GAAAATGATTTCCG
40865209 GAAAATG
1 GAAAATG
40865216 GCTTACTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.29
Consensus pattern (14 bp):
GAAAATGATTTCCG
Found at i:40866280 original size:29 final size:29
Alignment explanation
Indices: 40866238--40866298 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
40866228 TTTCAAAATA
* *
40866238 CATGCAATATCAATAAACATATGTAAGCC
1 CATGCAACATCAATAAACATATGCAAGCC
40866267 CATGCAACATCAATAAACATATGCAAGCC
1 CATGCAACATCAATAAACATATGCAAGCC
40866296 CAT
1 CAT
40866299 TTGGGGAGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.25, G:0.10, T:0.21
Consensus pattern (29 bp):
CATGCAACATCAATAAACATATGCAAGCC
Found at i:40866579 original size:26 final size:26
Alignment explanation
Indices: 40866550--40866602 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
40866540 TCAAACATGC
40866550 ATTTAGGTCAATTTA-CTCCTAGGGGT
1 ATTTAGGT-AATTTATCTCCTAGGGGT
* *
40866576 ATTTCGGTACTTTATCTCCTAGGGGT
1 ATTTAGGTAATTTATCTCCTAGGGGT
40866602 A
1 A
40866603 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.40
Consensus pattern (26 bp):
ATTTAGGTAATTTATCTCCTAGGGGT
Found at i:40867871 original size:12 final size:12
Alignment explanation
Indices: 40867854--40867972 Score: 64
Period size: 12 Copynumber: 9.9 Consensus size: 12
40867844 GCCAACTCCT
*
40867854 GCTCCTTGATCA
1 GCTCCTTAATCA
* *
40867866 GCTCCTAAATCT
1 GCTCCTTAATCA
* *
40867878 TCTCCTTTATCA
1 GCTCCTTAATCA
* *
40867890 GCTCCTAAATCC
1 GCTCCTTAATCA
*
40867902 TCTCCCTT-ATCA
1 GCT-CCTTAATCA
* *
40867914 GCTCCTAAATCC
1 GCTCCTTAATCA
*
40867926 TCTCCCTT-ATCA
1 GCT-CCTTAATCA
*
40867938 GCTCCTAAATCA
1 GCTCCTTAATCA
*
40867950 TCTCCCTT-ATCA
1 GCT-CCTTAATCA
*
40867962 GCTCCTAAATC
1 GCTCCTTAATC
40867973 CTTTCCCTTA
Statistics
Matches: 75, Mismatches: 26, Indels: 12
0.66 0.23 0.11
Matches are distributed among these distances:
11 9 0.12
12 57 0.76
13 9 0.12
ACGTcount: A:0.22, C:0.38, G:0.06, T:0.34
Consensus pattern (12 bp):
GCTCCTTAATCA
Found at i:40867889 original size:24 final size:24
Alignment explanation
Indices: 40867857--40868002 Score: 231
Period size: 24 Copynumber: 6.0 Consensus size: 24
40867847 AACTCCTGCT
40867857 CCTTGATCAGCTCCTAAATCTTCTC
1 CCTT-ATCAGCTCCTAAATCTTCTC
* *
40867882 CTTTATCAGCTCCTAAATCCTCTC
1 CCTTATCAGCTCCTAAATCTTCTC
*
40867906 CCTTATCAGCTCCTAAATCCTCTC
1 CCTTATCAGCTCCTAAATCTTCTC
*
40867930 CCTTATCAGCTCCTAAATCATCTC
1 CCTTATCAGCTCCTAAATCTTCTC
40867954 CCTTATCAGCTCCTAAATCCTT-TC
1 CCTTATCAGCTCCTAAAT-CTTCTC
40867978 CCTTATCAGCTCCTAAATCTTCTC
1 CCTTATCAGCTCCTAAATCTTCTC
40868002 C
1 C
40868003 TGACAGCCTT
Statistics
Matches: 114, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 3 0.03
24 106 0.93
25 5 0.04
ACGTcount: A:0.21, C:0.38, G:0.05, T:0.36
Consensus pattern (24 bp):
CCTTATCAGCTCCTAAATCTTCTC
Found at i:40870930 original size:14 final size:14
Alignment explanation
Indices: 40870911--40870938 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40870901 AAAAAGTAAG
40870911 AATATCAGAATTCC
1 AATATCAGAATTCC
40870925 AATATCAGAATTCC
1 AATATCAGAATTCC
40870939 GTTCAACTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (14 bp):
AATATCAGAATTCC
Found at i:40871511 original size:6 final size:6
Alignment explanation
Indices: 40871495--40871544 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
40871485 GGGATGCAAT
* * *
40871495 GAAGG- GAAGGA GAAGGA TAAGGA GAAGGA GAAGGA AAAGGG GAAGGA
1 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA
40871542 GAA
1 GAA
40871545 AGCGTTTCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (6 bp):
GAAGGA
Found at i:40871733 original size:14 final size:14
Alignment explanation
Indices: 40871714--40871740 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40871704 AGAAAATGCT
40871714 GAAAAGCTTTTACG
1 GAAAAGCTTTTACG
40871728 GAAAAGCTTTTAC
1 GAAAAGCTTTTAC
40871741 AGGTAAACAA
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:0.15, G:0.19, T:0.30
Consensus pattern (14 bp):
GAAAAGCTTTTACG
Found at i:40875746 original size:30 final size:30
Alignment explanation
Indices: 40875710--40875769 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
40875700 ACGGTTTATG
*
40875710 TACATAACTGTACCATCTTGTATCAATCTC
1 TACATAACTGTACCATCTCGTATCAATCTC
40875740 TACATAACTGTACCATCTCGTATCAATCTC
1 TACATAACTGTACCATCTCGTATCAATCTC
40875770 ATACTCAACC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (30 bp):
TACATAACTGTACCATCTCGTATCAATCTC
Found at i:40884458 original size:33 final size:32
Alignment explanation
Indices: 40884421--40884536 Score: 108
Period size: 33 Copynumber: 3.6 Consensus size: 32
40884411 ATGGACCTTT
* *
40884421 CCTTTTCTAGTTGTACACCCAAGGTGCACATTC
1 CCTTTTCAAGTTGTACACCCAA-GTGCACATAC
* * * *
40884454 CCTTTTCAAGTGGTACAGACGAAGTGTACATAC
1 CCTTTTCAAGTTGTACA-CCCAAGTGCACATAC
* * * *
40884487 CCTTTTCAAATTGTACACACAAAGTGCACGTAA
1 CCTTTTCAAGTTGTACAC-CCAAGTGCACATAC
40884520 CCTTTTCAAG-TGTACAC
1 CCTTTTCAAGTTGTACAC
40884537 ATATAGTGTA
Statistics
Matches: 67, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
32 7 0.10
33 57 0.85
34 3 0.04
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (32 bp):
CCTTTTCAAGTTGTACACCCAAGTGCACATAC
Found at i:40884556 original size:98 final size:98
Alignment explanation
Indices: 40884448--40884626 Score: 232
Period size: 98 Copynumber: 1.8 Consensus size: 98
40884438 CCCAAGGTGC
* * * * *
40884448 ACATTCCCTTTTCAAGTGGTACAGACGAAGTGTACATACCCTTTTCAAATTGTACACACAAAGTG
1 ACATTCCCTTTTCAAGTGGTACACACAAAGTATACATACCCTTTTCAAATGGTACACACAAAGTA
*
40884513 CACGTAACCTTTTCAAGTGTACACATATAGTGT
66 CACCTAACCTTTTCAAGTGTACACATATAGTGT
* * * ** * *
40884546 ACATTTCCTTTTCAAGTGGTATACACAAAGTATACCTTTCCTTTTCATATGGTATACACAAAGTA
1 ACATTCCCTTTTCAAGTGGTACACACAAAGTATACATACCCTTTTCAAATGGTACACACAAAGTA
*
40884611 TACCTAACCTTTTCAA
66 CACCTAACCTTTTCAA
40884627 ATTGTACCAT
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
98 67 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (98 bp):
ACATTCCCTTTTCAAGTGGTACACACAAAGTATACATACCCTTTTCAAATGGTACACACAAAGTA
CACCTAACCTTTTCAAGTGTACACATATAGTGT
Found at i:40884572 original size:65 final size:66
Alignment explanation
Indices: 40884418--40884576 Score: 178
Period size: 66 Copynumber: 2.4 Consensus size: 66
40884408 TCGATGGACC
* * * ** *
40884418 TTTCCTTTTCTAGTTGTACACCCAAGGTGCACATTCCCTTTTCAAGTGGTACAGACGAAGTGTAC
1 TTTCCTTTTCAAGTTGTACACACAAAGTGCACATAACCTTTTCAAGTGGTACACACGAAGTGTAC
40884483 A
66 A
** * * *
40884484 TACCCTTTTCAAATTGTACACACAAAGTGCACGTAACCTTTTCAAGT-GTACACA-TATAGTGTA
1 TTTCCTTTTCAAGTTGTACACACAAAGTGCACATAACCTTTTCAAGTGGTACACACGA-AGTGTA
40884547 CA
65 CA
* *
40884549 TTTCCTTTTCAAGTGGTATACACAAAGT
1 TTTCCTTTTCAAGTTGTACACACAAAGT
40884577 ATACCTTTCC
Statistics
Matches: 76, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
64 1 0.01
65 37 0.49
66 38 0.50
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (66 bp):
TTTCCTTTTCAAGTTGTACACACAAAGTGCACATAACCTTTTCAAGTGGTACACACGAAGTGTAC
A
Found at i:40884591 original size:33 final size:33
Alignment explanation
Indices: 40884520--40884626 Score: 128
Period size: 33 Copynumber: 3.3 Consensus size: 33
40884510 GTGCACGTAA
* * * * *
40884520 CCTTTTCAAGT-GTACACATATAGTGTACATTT
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
40884552 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
**
40884585 CCTTTTCATA-TGGTATACACAAAGTATACCTAA
1 CCTTTTCA-AGTGGTATACACAAAGTATACCTTT
40884618 CCTTTTCAA
1 CCTTTTCAA
40884627 ATTGTACCAT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
32 12 0.18
33 53 0.80
34 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.37
Consensus pattern (33 bp):
CCTTTTCAAGTGGTATACACAAAGTATACCTTT
Found at i:40891970 original size:38 final size:40
Alignment explanation
Indices: 40891888--40891981 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 40
40891878 CGGTACTTTT
* *
40891888 TGGTGTGTAGGGTT-GAATGGGTTGATTATATCCCCATACT
1 TGGTGTGTAGGGTTAGAATGGGTCGATTATATCCCCA-ACA
* * *
40891928 TGGTGTATAGGGTTAG-GTGGGTCGATTCTATCCCC-ACA
1 TGGTGTGTAGGGTTAGAATGGGTCGATTATATCCCCAACA
*
40891966 TGGTGTGTTGGGTTAG
1 TGGTGTGTAGGGTTAG
40891982 TCAGAGATGG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
38 16 0.35
40 29 0.63
41 1 0.02
ACGTcount: A:0.17, C:0.13, G:0.34, T:0.36
Consensus pattern (40 bp):
TGGTGTGTAGGGTTAGAATGGGTCGATTATATCCCCAACA
Found at i:40899955 original size:29 final size:29
Alignment explanation
Indices: 40899923--40900040 Score: 122
Period size: 29 Copynumber: 4.2 Consensus size: 29
40899913 CTATAAAGAT
40899923 TATCTGATATGTGGAAAGTTTGCCAGAAC
1 TATCTGATATGTGGAAAGTTTGCCAGAAC
* *
40899952 TATCTGATATGTGGAAAGTATGCCAGGAC
1 TATCTGATATGTGGAAAGTTTGCCAGAAC
*
40899981 TATCT--TATGTGG-AAGTCTATG--AGGAC
1 TATCTGATATGTGGAAAGT-T-TGCCAGAAC
* *
40900007 TATATGATATGTGGAAAGTCTGCCA-AGAC
1 TATCTGATATGTGGAAAGTTTGCCAGA-AC
40900036 TATCT
1 TATCT
40900041 TAATATGAGA
Statistics
Matches: 74, Mismatches: 7, Indels: 16
0.76 0.07 0.16
Matches are distributed among these distances:
26 13 0.18
27 9 0.12
28 9 0.12
29 43 0.58
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.31
Consensus pattern (29 bp):
TATCTGATATGTGGAAAGTTTGCCAGAAC
Found at i:40900017 original size:84 final size:84
Alignment explanation
Indices: 40899876--40900040 Score: 224
Period size: 84 Copynumber: 2.0 Consensus size: 84
40899866 AACATAGGAA
* * *
40899876 ATGTGGAAAGTCCACCAAGACTATCTTATGTCGAAGTCTATAAAGATTATCTGATATGTGGAAAG
1 ATGTGGAAAGTACACCAAGACTATCTTATGTCGAAGTCTATAAAGACTATATGATATGTGGAAAG
*
40899941 TTTGCC-AGAACTATCTGAT
66 TCTGCCAAG-ACTATCTGAT
** * * * *
40899960 ATGTGGAAAGTATGCCAGGACTATCTTATGTGGAAGTCTATGAGGACTATATGATATGTGGAAAG
1 ATGTGGAAAGTACACCAAGACTATCTTATGTCGAAGTCTATAAAGACTATATGATATGTGGAAAG
40900025 TCTGCCAAGACTATCT
66 TCTGCCAAGACTATCT
40900041 TAATATGAGA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
84 68 0.97
85 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (84 bp):
ATGTGGAAAGTACACCAAGACTATCTTATGTCGAAGTCTATAAAGACTATATGATATGTGGAAAG
TCTGCCAAGACTATCTGAT
Found at i:40902097 original size:62 final size:62
Alignment explanation
Indices: 40901987--40902115 Score: 179
Period size: 62 Copynumber: 2.1 Consensus size: 62
40901977 TGGTTCAGAA
*
40901987 GGTCTCAGAAAGTTACACAACCTAGAGACTTGACCATTGGACCACATTTCAAATATTCACAC
1 GGTCTCAGAAAGTTACACAACCTAGAGACATGACCATTGGACCACATTTCAAATATTCACAC
* * * ** *
40902049 GGTCTCAGAAAGTTACACGATCTAGAGACATGACC-GTGTGACTTCATTTCGAATATTCACAC
1 GGTCTCAGAAAGTTACACAACCTAGAGACATGACCATTG-GACCACATTTCAAATATTCACAC
40902111 GGTCT
1 GGTCT
40902116 AAGACATAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
61 2 0.03
62 57 0.97
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (62 bp):
GGTCTCAGAAAGTTACACAACCTAGAGACATGACCATTGGACCACATTTCAAATATTCACAC
Found at i:40905362 original size:22 final size:22
Alignment explanation
Indices: 40905334--40905384 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
40905324 GGCAATGATA
40905334 GCATATTCAATTAGCCTTTGTG
1 GCATATTCAATTAGCCTTTGTG
*
40905356 GCATATTCTATTAGCCTTTGTG
1 GCATATTCAATTAGCCTTTGTG
*
40905378 GCGTATT
1 GCATATT
40905385 TCATATGTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.43
Consensus pattern (22 bp):
GCATATTCAATTAGCCTTTGTG
Found at i:40909887 original size:27 final size:27
Alignment explanation
Indices: 40909857--40909922 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
40909847 ACATTTAACA
* * * *
40909857 TCCTAATGGACTATCCTATTTTTAATG
1 TCCTAATGAACTATCCCATGTTAAATG
**
40909884 TCCTGGTGAACTATCCCATGTTAAATG
1 TCCTAATGAACTATCCCATGTTAAATG
*
40909911 TCCTGATGAACT
1 TCCTAATGAACT
40909923 GTTTATACTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (27 bp):
TCCTAATGAACTATCCCATGTTAAATG
Found at i:40914994 original size:131 final size:131
Alignment explanation
Indices: 40914754--40915021 Score: 414
Period size: 131 Copynumber: 2.0 Consensus size: 131
40914744 AGTTTTGTAA
* * *
40914754 TCATGTCTTTAAAAATTCTTTAAAACGAAAGCAATGTTTGATGTTTGGCAATTCGGGGAATCGTG
1 TCATGTCTTTAAAAATCCTTTAAAACGAAAGCAATGTTCGATGTTAGGCAATTCGGGGAATCGTG
* * *
40914819 CCCAATCGTGCTGGGTTGCAATTCCCTGTTTGTTCAAAATAATCGAATATTCCTTTGGAATTTCA
66 CCCAATCGTGCTAGGTTGCAATTCCCTGTTTGTTCAAAACAATCGAATATTCCTTTAGAATTTCA
40914884 C
131 C
* * *
40914885 TCATTTCTTTAAAAATCCTTTAAAAC-AAAGGCAGTGTTCGATGTTAGGCAATTCGGGGAATTGT
1 TCATGTCTTTAAAAATCCTTTAAAACGAAA-GCAATGTTCGATGTTAGGCAATTCGGGGAATCGT
*
40914949 GCCCTATCGTGCTAGGTTGCAATTTCCC-GTTTGTTCAAAACAATCGAATATTCCTTTAGAATTT
65 GCCCAATCGTGCTAGGTTGCAA-TTCCCTGTTTGTTCAAAACAATCGAATATTCCTTTAGAATTT
40915013 CAC
129 CAC
40915016 TCATGT
1 TCATGT
40915022 TTTCTAAATT
Statistics
Matches: 124, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
130 3 0.02
131 116 0.94
132 5 0.04
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (131 bp):
TCATGTCTTTAAAAATCCTTTAAAACGAAAGCAATGTTCGATGTTAGGCAATTCGGGGAATCGTG
CCCAATCGTGCTAGGTTGCAATTCCCTGTTTGTTCAAAACAATCGAATATTCCTTTAGAATTTCA
C
Found at i:40926868 original size:18 final size:18
Alignment explanation
Indices: 40926847--40926883 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
40926837 ACAATTATTA
40926847 TCACTTTCAATTTCAATT
1 TCACTTTCAATTTCAATT
*
40926865 TCACTTTCACTTTCAATT
1 TCACTTTCAATTTCAATT
40926883 T
1 T
40926884 TGATCACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (18 bp):
TCACTTTCAATTTCAATT
Found at i:40933869 original size:18 final size:18
Alignment explanation
Indices: 40933846--40933882 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
40933836 TCTGTGAACA
40933846 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
*
40933864 AAATTGAAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
40933882 A
1 A
40933883 TAAGAATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:40933871 original size:12 final size:12
Alignment explanation
Indices: 40933846--40933882 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
40933836 TCTGTGAACA
40933846 AAATTGAAAGTG
1 AAATTGAAAGTG
* *
40933858 AAAGTGAAATTG
1 AAATTGAAAGTG
40933870 AAATTGAAAGTG
1 AAATTGAAAGTG
40933882 A
1 A
40933883 TAAGAATTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (12 bp):
AAATTGAAAGTG
Found at i:40943862 original size:21 final size:21
Alignment explanation
Indices: 40943838--40943885 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
40943828 AATCAATAAG
40943838 GTTAAACTGAAACCCATACGA
1 GTTAAACTGAAACCCATACGA
* *
40943859 GTT-AACTGAAACTCATATGA
1 GTTAAACTGAAACCCATACGA
*
40943879 GCTAAAC
1 GTTAAAC
40943886 GGGAAGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.23
Consensus pattern (21 bp):
GTTAAACTGAAACCCATACGA
Found at i:40946266 original size:19 final size:19
Alignment explanation
Indices: 40946242--40946283 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
40946232 GTTACGAATA
40946242 TTGTCGACATATATATTAT
1 TTGTCGACATATATATTAT
40946261 TTGTCGACATATATATTAT
1 TTGTCGACATATATATTAT
40946280 TTGT
1 TTGT
40946284 GACTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.50
Consensus pattern (19 bp):
TTGTCGACATATATATTAT
Found at i:40946607 original size:13 final size:11
Alignment explanation
Indices: 40946571--40946601 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
40946561 CCGCCCGTGT
40946571 TAATTTTTATA
1 TAATTTTTATA
*
40946582 TTATTTTTATA
1 TAATTTTTATA
40946593 TAATTTTTA
1 TAATTTTTA
40946602 AATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTTATA
Done.