Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold60
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: 3815296
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 18690 characters in sequence are not A, C, G, or T
File 10 of 21
Found at i:1337840 original size:17 final size:18
Alignment explanation
Indices: 1337815--1337848 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1337805 TTTAATACAT
*
1337815 TTAATATTTTAAAAAATA
1 TTAATATTTAAAAAAATA
1337833 TTAA-ATTTAAAAAAAT
1 TTAATATTTAAAAAAAT
1337849 TGAATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TTAATATTTAAAAAAATA
Found at i:1337926 original size:26 final size:28
Alignment explanation
Indices: 1337895--1337956 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 28
1337885 ATTGATGTTA
1337895 ATATAATTTATTTTT-TATTT-TATAATT
1 ATATAATTTATTTTTATATTTATAT-ATT
1337922 -TATAA--TATTTTTATATTTATATATT
1 ATATAATTTATTTTTATATTTATATATT
1337947 ATATAATTTA
1 ATATAATTTA
1337957 AAATTAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
24 7 0.23
25 8 0.27
26 13 0.43
28 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
ATATAATTTATTTTTATATTTATATATT
Found at i:1337928 original size:31 final size:34
Alignment explanation
Indices: 1337893--1337964 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 34
1337883 AGATTGATGT
*
1337893 TAATATAATTTAT-TTT-T-TATTTTATAATTTA
1 TAATATAATTTATATTTATATATTATATAATTTA
*
1337924 TAATAT-TTTTATATTTATATATTATATAATTTA
1 TAATATAATTTATATTTATATATTATATAATTTA
*
1337957 AAAT-TAAT
1 TAATATAAT
1337965 ATTTGATGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 5 0.15
31 9 0.27
32 2 0.06
33 17 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TAATATAATTTATATTTATATATTATATAATTTA
Found at i:1337955 original size:24 final size:23
Alignment explanation
Indices: 1337906--1337953 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
1337896 TATAATTTAT
1337906 TTTTTATTTTATAATTTATAATA
1 TTTTTATTTTATAATTTATAATA
1337929 TTTTTATATTTATATATTATATAAT
1 TTTTTAT-TTTATA-ATT-TATAAT
1337954 TTAAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.32
24 6 0.27
25 3 0.14
26 6 0.27
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTTATTTTATAATTTATAATA
Found at i:1337966 original size:29 final size:28
Alignment explanation
Indices: 1337934--1337989 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
1337924 TAATATTTTT
*
1337934 ATATTT-ATATATTATATAATTTAAAATTA
1 ATATTTGATATATTA-ATAA-ATAAAATTA
*
1337963 ATATTTGATGTATTAATAAATAAAATT
1 ATATTTGATATATTAATAAATAAAATT
1337990 TTTAACTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.29
29 10 0.42
30 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (28 bp):
ATATTTGATATATTAATAAATAAAATTA
Found at i:1338059 original size:16 final size:17
Alignment explanation
Indices: 1338029--1338062 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1338019 TTATGTATAT
*
1338029 ATTTTTATTTTTAATTA
1 ATTTTTATTTATAATTA
1338046 ATTTTTA-TTATAATTA
1 ATTTTTATTTATAATTA
1338062 A
1 A
1338063 AAAATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTTATTTATAATTA
Found at i:1338205 original size:16 final size:16
Alignment explanation
Indices: 1338184--1338214 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1338174 AATATAAATA
*
1338184 TTAAATTTATTTTAAC
1 TTAAATATATTTTAAC
1338200 TTAAATATATTTTAA
1 TTAAATATATTTTAA
1338215 AATTTAATAA
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:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAAATATATTTTAAC
Found at i:1338228 original size:23 final size:23
Alignment explanation
Indices: 1338202--1338245 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1338192 ATTTTAACTT
*
1338202 AAATATATT-TTAAAATTTAATAA
1 AAATA-ATTATTAAAAATTAATAA
1338225 AAATAATTATTAAAAATTAAT
1 AAATAATTATTAAAAATTAAT
1338246 TTTCCATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATAATTATTAAAAATTAATAA
Found at i:1338646 original size:25 final size:26
Alignment explanation
Indices: 1338617--1338672 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
1338607 AATATAATAT
1338617 ATTTAATATT-TATATTA-AATATTAA
1 ATTTAAT-TTATATATTATAATATTAA
*
1338642 ATTT-ATTTATATATTATATTATTAA
1 ATTTAATTTATATATTATAATATTAA
1338667 ATTTAA
1 ATTTAA
1338673 ATAAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 2 0.07
24 9 0.33
25 15 0.56
26 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTTAATTTATATATTATAATATTAA
Found at i:1338733 original size:42 final size:41
Alignment explanation
Indices: 1338680--1338803 Score: 111
Period size: 41 Copynumber: 3.1 Consensus size: 41
1338670 TAAATAAAAA
*
1338680 TTTTAA-TAATTTAAATTATTTTATAAATAATAAAAATTAT
1 TTTTAATTAATTTAAATTATTTTATAAATAATAAAAATAAT
* ** *
1338720 TTTTATTTAAATTT-AATTATAAATATTAAT-ATAAAAATAAT
1 TTTTAATT-AATTTAAATTAT-TTTATAAATAATAAAAATAAT
*
1338761 TTTTAATT--TTTATATTA-TTT-TAAATAAT-AAAATAAAT
1 TTTTAATTAATTTAAATTATTTTATAAATAATAAAAAT-AAT
1338798 TTTTAA
1 TTTTAA
1338804 ATCGACTTAA
Statistics
Matches: 68, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
36 9 0.13
37 12 0.18
38 3 0.04
39 4 0.06
40 5 0.07
41 24 0.35
42 11 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (41 bp):
TTTTAATTAATTTAAATTATTTTATAAATAATAAAAATAAT
Found at i:1339733 original size:28 final size:27
Alignment explanation
Indices: 1339673--1339743 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
1339663 AACATGCCAT
*
1339673 CATTTTTGACAAATAAAAAGAAACCAC
1 CATTTTTGACAAACAAAAAGAAACCAC
*
1339700 CATTTTTGACAAACACAAAA-TAACCAC
1 CATTTTTGACAAACA-AAAAGAAACCAC
*
1339727 CATTTTTGATAAACAAA
1 CATTTTTGACAAACAAA
1339744 GGGTGACTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 2 0.05
27 34 0.85
28 4 0.10
ACGTcount: A:0.49, C:0.20, G:0.06, T:0.25
Consensus pattern (27 bp):
CATTTTTGACAAACAAAAAGAAACCAC
Found at i:1345631 original size:2 final size:2
Alignment explanation
Indices: 1345624--1345654 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1345614 GTAATGGAAT
1345624 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1345655 TATCGAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1345754 original size:2 final size:2
Alignment explanation
Indices: 1345747--1345779 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1345737 TTGATTAATG
1345747 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 A
1345780 AGTATCAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1350656 original size:316 final size:315
Alignment explanation
Indices: 1350047--1350683 Score: 1150
Period size: 316 Copynumber: 2.0 Consensus size: 315
1350037 TGTTGAGGAT
* *
1350047 TCAAA-TCCAATATTGTTCTATTCTACTGAACCAACCATTGCTATAGCTATTCCATTCCACTCTA
1 TCAAACTCCAATATTGTTCTATACTACTAAACCAACCATTGCTATAGCTATTCCATTCCACTCTA
1350111 GCCTTATGCCATTCTCATAGAATGATTATTCCATTACAGCTCTATTCCACTCTAGTGAACCAAGC
66 GCCTTATGCCATTCTCATAGAATGATTATTCCATTACAGCTCTATTCCACTCTAGTGAACCAAGC
* *
1350176 ATATCGTAAATAGACCTGTCAATCTATTCCAAAGTAGACCAGAATCTTTGAAGATTCTCCAGATG
131 ATATCGTAAATAGACCTGTCAATCCACTCCAAAGTAGACCAGAATCTTTGAAGATTCTCCAGATG
* *
1350241 CTGGATACAAAGGGAAAACTCCTAAGTACTACCAAATGGTATAATAGGCCATGGCACCAAAAGTG
196 CTGGATACAAAGGGAAAACTCCTAAGTACTACCAAATGGAATAATAGGCAATGGCACCAAAAGTG
* * *
1350306 ATTTGAAGCAAAATGGAACTATATGGGGTTCAGAAGTGTTGAAACAAATACCTCC
261 ATTTGAAGCAAAATGGAACTATATAGGGTTCAGAAGTGTTAAAAAAAATACCTCC
* *
1350361 TCAAACTCCCATATTGTTCTATACTACTAAACCAAACTATTGCTATAGCTATTCCATTCCACTCT
1 TCAAACTCCAATATTGTTCTATACTACTAAACC-AACCATTGCTATAGCTATTCCATTCCACTCT
1350426 AGCCTTATGCCATTCTCATAGAATGATTATTCCATTACAGCTCTATTCCACTCTAGTGAACCAAG
65 AGCCTTATGCCATTCTCATAGAATGATTATTCCATTACAGCTCTATTCCACTCTAGTGAACCAAG
*
1350491 CATATCGTAAATAGACCTGTCAATCCACTCCAAAGTAGACCCGAATCTTTGAAGATTCTCCAGAT
130 CATATCGTAAATAGACCTGTCAATCCACTCCAAAGTAGACCAGAATCTTTGAAGATTCTCCAGAT
1350556 GCTGGATACAAAGGGAAAACTCCTAAGTACTACCAAATGGAATAATAGGCAATGGCACCAAAAGT
195 GCTGGATACAAAGGGAAAACTCCTAAGTACTACCAAATGGAATAATAGGCAATGGCACCAAAAGT
1350621 GATTTGAAGCAAAATGGAACTATATAGGGTTCAGAAGTGTTAAAAAAAATACCTCC
260 GATTTGAAGCAAAATGGAACTATATAGGGTTCAGAAGTGTTAAAAAAAATACCTCC
1350677 TCAAACT
1 TCAAACT
1350684 GTTGTATCAA
Statistics
Matches: 309, Mismatches: 12, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
314 5 0.02
315 24 0.08
316 280 0.91
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (315 bp):
TCAAACTCCAATATTGTTCTATACTACTAAACCAACCATTGCTATAGCTATTCCATTCCACTCTA
GCCTTATGCCATTCTCATAGAATGATTATTCCATTACAGCTCTATTCCACTCTAGTGAACCAAGC
ATATCGTAAATAGACCTGTCAATCCACTCCAAAGTAGACCAGAATCTTTGAAGATTCTCCAGATG
CTGGATACAAAGGGAAAACTCCTAAGTACTACCAAATGGAATAATAGGCAATGGCACCAAAAGTG
ATTTGAAGCAAAATGGAACTATATAGGGTTCAGAAGTGTTAAAAAAAATACCTCC
Found at i:1351065 original size:14 final size:14
Alignment explanation
Indices: 1351043--1351072 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1351033 ATAGAGATAT
1351043 ATGGCGTATTAAGG
1 ATGGCGTATTAAGG
*
1351057 ATGGTGTATTAAGG
1 ATGGCGTATTAAGG
1351071 AT
1 AT
1351073 CTCAGAACAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (14 bp):
ATGGCGTATTAAGG
Found at i:1353725 original size:14 final size:14
Alignment explanation
Indices: 1353698--1353737 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1353688 TAATAAATAT
* *
1353698 TAATAAATTTAAAA
1 TAATATATTAAAAA
1353712 TAATATATTAAAAA
1 TAATATATTAAAAA
1353726 TAATAATATTAA
1 TAAT-ATATTAA
1353738 TATTGATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAATATATTAAAAA
Found at i:1355031 original size:22 final size:21
Alignment explanation
Indices: 1354979--1355031 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
1354969 TTTACTCGAT
**
1354979 ATTTATAAATATTAATTAAAA
1 ATTTATATTTATTAATTAAAA
* *
1355000 ATTATTTATTTATTATTTAAAAA
1 ATT-TATATTTATTAATT-AAAA
1355023 ATTTATATT
1 ATTTATATT
1355032 AATACATCAC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 3 0.12
22 15 0.60
23 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTATATTTATTAATTAAAA
Found at i:1355637 original size:23 final size:25
Alignment explanation
Indices: 1355594--1355648 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 25
1355584 AAAATATAGA
1355594 TATT-ATAATTTTTATAATAAA-ATTT
1 TATTAATAATTTTTAT-ATAAATA-TT
1355619 TATTAATAATTTTT-T-TAAATATT
1 TATTAATAATTTTTATATAAATATT
1355642 TATTAAT
1 TATTAAT
1355649 TTAAATCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 13 0.46
24 1 0.04
25 5 0.18
26 9 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTAATAATTTTTATATAAATATT
Found at i:1357955 original size:21 final size:20
Alignment explanation
Indices: 1357884--1357961 Score: 59
Period size: 21 Copynumber: 3.6 Consensus size: 20
1357874 AAGTAAGAAA
*
1357884 AAAATTATAAAAATTAAGATT
1 AAAATTATAAATATTAA-ATT
*
1357905 AAAATCT-TAAATTTATTTAAATG
1 AAAAT-TATAAA--TA-TTAAATT
1357928 AAGAATTATAAATATTAATATT
1 AA-AATTATAAATATTAA-ATT
*
1357950 AAAATTTTAAAT
1 AAAATTATAAAT
1357962 TTGATGACTA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
21 22 0.48
22 7 0.15
23 6 0.13
24 11 0.24
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (20 bp):
AAAATTATAAATATTAAATT
Found at i:1362134 original size:71 final size:70
Alignment explanation
Indices: 1362060--1362194 Score: 157
Period size: 71 Copynumber: 1.9 Consensus size: 70
1362050 TTATTTGATT
* * * *
1362060 TTTTTAAAATT-TAATTAGAATTTAAGTT-ATTAAAAATTTTATTTTATTATTTAAAATAAATTA
1 TTTTT-AAATTATAATTAAAATTAAAATTAAATAAAAA-TTTATTTTATTATTTAAAATAAATTA
1362123 AAATATA
64 AAATATA
* * * *
1362130 TTTTTATATTAATATTTAAAATTAAAATTAAATAAAAATTTATTTTATTATTTAAATTAATTTAA
1 TTTTTAAATT-ATAATTAAAATTAAAATTAAATAAAAATTTATTTTATTATTTAAAATAAATTAA
1362195 TTTAATTTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
69 4 0.07
70 5 0.09
71 38 0.70
72 7 0.13
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (70 bp):
TTTTTAAATTATAATTAAAATTAAAATTAAATAAAAATTTATTTTATTATTTAAAATAAATTAAA
ATATA
Found at i:1362172 original size:36 final size:37
Alignment explanation
Indices: 1362090--1362189 Score: 118
Period size: 35 Copynumber: 2.8 Consensus size: 37
1362080 TTTAAGTTAT
1362090 TAAAAATTTTATTTTATTATTTAAAA-T-AAATTAAAA
1 TAAAAA-TTTATTTTATTATTTAAAATTAAAATTAAAA
* ** * *
1362126 TATATTTTTATATTAATATTTAAAATTAAAATT-AAA
1 TAAAAATTTATTTTATTATTTAAAATTAAAATTAAAA
1362162 TAAAAATTTATTTTATTATTT-AAATTAA
1 TAAAAATTTATTTTATTATTTAAAATTAA
1362190 TTTAATTTAA
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
35 24 0.46
36 23 0.44
37 5 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (37 bp):
TAAAAATTTATTTTATTATTTAAAATTAAAATTAAAA
Found at i:1362199 original size:15 final size:15
Alignment explanation
Indices: 1362179--1362221 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1362169 TTATTTTATT
1362179 ATTTAAATTAATTTA
1 ATTTAAATTAATTTA
* *
1362194 ATTTAATTTAATATA
1 ATTTAAATTAATTTA
* *
1362209 AATTAAATAAATT
1 ATTTAAATTAATT
1362222 ATTTTACGAG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTAAATTAATTTA
Found at i:1362688 original size:2 final size:2
Alignment explanation
Indices: 1362681--1362711 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1362671 GACCATTTAC
1362681 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 A
1362712 ATCAGATATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1364639 original size:2 final size:2
Alignment explanation
Indices: 1364632--1364667 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1364622 CCTATAATTA
*
1364632 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1364668 TATGAGATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1365376 original size:20 final size:20
Alignment explanation
Indices: 1365351--1365388 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1365341 AACCTAAAGT
1365351 AAAAGTACAATTCCATAATA
1 AAAAGTACAATTCCATAATA
*
1365371 AAAAGTACAATTGCATAA
1 AAAAGTACAATTCCATAA
1365389 GGCAAATCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.08, T:0.24
Consensus pattern (20 bp):
AAAAGTACAATTCCATAATA
Found at i:1368006 original size:24 final size:23
Alignment explanation
Indices: 1367962--1368006 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
1367952 AAAAAATATT
* *
1367962 ATTTATTTTAATTAACGAAATAC
1 ATTTATTTTAATGAACAAAATAC
*
1367985 ATTTATTATTAATGAATAAAAT
1 ATTTATT-TTAATGAACAAAAT
1368007 GCTGGAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (23 bp):
ATTTATTTTAATGAACAAAATAC
Found at i:1371492 original size:20 final size:20
Alignment explanation
Indices: 1371450--1371492 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1371440 TTTTATATTT
* *
1371450 TTTTATATATTATAATCTCA
1 TTTTAAATATTATAATATCA
1371470 TTTTAAATATTATATATAT-A
1 TTTTAAATATTATA-ATATCA
1371490 TTT
1 TTT
1371493 ATATAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTAAATATTATAATATCA
Found at i:1371497 original size:10 final size:10
Alignment explanation
Indices: 1371476--1371592 Score: 54
Period size: 10 Copynumber: 11.6 Consensus size: 10
1371466 CTCATTTTAA
1371476 ATATTATATAT
1 ATATT-TATAT
1371487 ATATTTATAT
1 ATATTTATAT
*
1371497 AAATTTA-AGT
1 ATATTTATA-T
1371507 ATATTTATAAT
1 ATATTTAT-AT
*
1371518 TTATGGTTA-AT
1 ATAT--TTATAT
1371529 GA-ATTT-TGAT
1 -ATATTTAT-AT
1371539 ATA-TT-TAT
1 ATATTTATAT
1371547 ATATTTATAT
1 ATATTTATAT
*
1371557 -TATAT-TAT
1 ATATTTATAT
1371565 AT-TTTATATT
1 ATATTTATA-T
1371575 ATATTTATTAAT
1 ATATTTA-T-AT
1371587 ATATTT
1 ATATTT
1371593 GTGCCGTATA
Statistics
Matches: 83, Mismatches: 6, Indels: 33
0.68 0.05 0.27
Matches are distributed among these distances:
8 10 0.12
9 16 0.19
10 27 0.33
11 17 0.20
12 9 0.11
13 4 0.05
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (10 bp):
ATATTTATAT
Found at i:1371515 original size:32 final size:33
Alignment explanation
Indices: 1371479--1371561 Score: 75
Period size: 32 Copynumber: 2.6 Consensus size: 33
1371469 ATTTTAAATA
1371479 TTATATATATAT-TTATATAAATTTAAGTATAT
1 TTATATATATATGTTATATAAATTTAAGTATAT
* * *
1371511 TTATA-ATTTATGGTTA-ATGAATTT-TGATATAT
1 TTATATATATAT-GTTATATAAATTTAAG-TATAT
* *
1371543 TTATATATTTATATTATAT
1 TTATATATATATGTTATAT
1371562 TATATTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
31 6 0.14
32 25 0.60
33 11 0.26
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (33 bp):
TTATATATATATGTTATATAAATTTAAGTATAT
Found at i:1371572 original size:17 final size:17
Alignment explanation
Indices: 1371538--1371583 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 17
1371528 TGAATTTTGA
1371538 TATATTTATATATTTATAT
1 TATA-TTATAT-TTTATAT
1371557 TATATTATATTTTATAT
1 TATATTATATTTTATAT
1371574 TATATT-TATT
1 TATATTATATT
1371584 AATATATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.15
17 13 0.48
18 6 0.22
19 4 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATATTATATTTTATAT
Found at i:1371589 original size:17 final size:17
Alignment explanation
Indices: 1371538--1371591 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
1371528 TGAATTTTGA
1371538 TATATTTATATATTTATAT
1 TATATTTAT-TA-TTATAT
1371557 TATATTATATT-TTATAT
1 TATATT-TATTATTATAT
*
1371574 TATATTTATTAATATAT
1 TATATTTATTATTATAT
1371591 T
1 T
1371592 TGTGCCGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 4 0.12
17 18 0.56
19 7 0.22
20 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATATTTATTATTATAT
Found at i:1371875 original size:21 final size:23
Alignment explanation
Indices: 1371836--1371878 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1371826 TATAAAGTAA
*
1371836 ATTACAAATTTTTTAAATTAAAT
1 ATTACAAATATTTTAAATTAAAT
1371859 ATTA-AAATATTTT-AATTAAA
1 ATTACAAATATTTTAAATTAAA
1371879 CTCAACTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 8 0.42
23 4 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTACAAATATTTTAAATTAAAT
Found at i:1372706 original size:16 final size:15
Alignment explanation
Indices: 1372685--1372736 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
1372675 ATTTGAATAA
1372685 AAAATAACTTAAATTT
1 AAAATAA-TTAAATTT
* * *
1372701 AAAATAATTTAACTG
1 AAAATAATTAAATTT
1372716 AAAATAATTTAAATTT
1 AAAATAA-TTAAATTT
1372732 AAAAT
1 AAAAT
1372737 GATTCGAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (15 bp):
AAAATAATTAAATTT
Found at i:1373821 original size:2 final size:2
Alignment explanation
Indices: 1373814--1373838 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1373804 AAATCGAATC
1373814 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 A
1373839 CTTACAGCTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1374257 original size:21 final size:21
Alignment explanation
Indices: 1374233--1374280 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1374223 TAAGTATAAA
*
1374233 TATTAAATATAAATATATATT
1 TATTAAAAATAAATATATATT
* *
1374254 TATTAAAAATATATATTTATT
1 TATTAAAAATAAATATATATT
*
1374275 TTTTAA
1 TATTAA
1374281 TTTTTTTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTAAAAATAAATATATATT
Found at i:1374909 original size:13 final size:12
Alignment explanation
Indices: 1374891--1374932 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
1374881 AAGTTAGAAG
1374891 TTTATTATATATT
1 TTTATTATAT-TT
*
1374904 TTTATTTTATTAT
1 TTTATTATATT-T
1374917 TTTATTA-ATTT
1 TTTATTATATTT
1374928 TTTAT
1 TTTAT
1374933 AATACATTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 6 0.23
12 4 0.15
13 16 0.62
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATTATATTT
Found at i:1382718 original size:3 final size:3
Alignment explanation
Indices: 1382710--1382735 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1382700 CATTGAATGA
1382710 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
1382736 GTAAATTAAT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1383204 original size:22 final size:20
Alignment explanation
Indices: 1383146--1383208 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
1383136 AAATATTATG
*
1383146 AAATATAAATTTTTAATAAAA-
1 AAATTTAAATTTTT--TAAAAT
1383167 AAATTTAAATTTTTTAAAAT
1 AAATTTAAATTTTTTAAAAT
*
1383187 AATTTTATAATTTATTTAAAAT
1 AAATTTA-AATTT-TTTAAAAT
1383209 TAAAATAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.14
20 6 0.16
21 18 0.49
22 8 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AAATTTAAATTTTTTAAAAT
Found at i:1383984 original size:3 final size:3
Alignment explanation
Indices: 1383976--1384001 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1383966 GTGCGTACTC
1383976 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1384002 TTGACGATAA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1384052 original size:47 final size:48
Alignment explanation
Indices: 1383981--1384083 Score: 154
Period size: 47 Copynumber: 2.1 Consensus size: 48
1383971 TACTCTTATT
* *
1383981 ATTATTATTATTATTATTATTTTGACGATAAATATTAAAAAAAATTCAA
1 ATTA-TATTATTATTAGTATTTTGACGATAAAGATTAAAAAAAATTCAA
* *
1384030 ATTATATTTTTATTAGT-TTTTGACGATGAAGATTAAAAAAAATTCAA
1 ATTATATTATTATTAGTATTTTGACGATAAAGATTAAAAAAAATTCAA
1384077 ATTATAT
1 ATTATAT
1384084 GATCAAATTG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 35 0.70
48 11 0.22
49 4 0.08
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (48 bp):
ATTATATTATTATTAGTATTTTGACGATAAAGATTAAAAAAAATTCAA
Found at i:1385239 original size:85 final size:85
Alignment explanation
Indices: 1385092--1385251 Score: 223
Period size: 85 Copynumber: 1.9 Consensus size: 85
1385082 ACTTAGCCAT
* * * * * *
1385092 TATGGCCTTATTGTTATATGATGGTTTTTCTGTTGTATTCATGCATATGTTCTTATTCGCAGATG
1 TATGGCCTTATTGTTATATAATGGTTTCTATGCTGTATTCAAGCATATATTCTTATTCGCAGATG
1385157 CTTACAAATTATGTTAGTTA
66 CTTACAAATTATGTTAGTTA
* *
1385177 TATGGCCTTA-TGTTTATATAATGGTTTCTATGCTGTATTCAAGCATCTATTCTTATTTGCAGAT
1 TATGGCCTTATTG-TTATATAATGGTTTCTATGCTGTATTCAAGCATATATTCTTATTCGCAGAT
*
1385241 GCTTGCAAATT
65 GCTTACAAATT
1385252 TAGTTATATA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
84 2 0.03
85 63 0.97
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (85 bp):
TATGGCCTTATTGTTATATAATGGTTTCTATGCTGTATTCAAGCATATATTCTTATTCGCAGATG
CTTACAAATTATGTTAGTTA
Found at i:1385990 original size:2 final size:2
Alignment explanation
Indices: 1385983--1386055 Score: 103
Period size: 2 Copynumber: 37.0 Consensus size: 2
1385973 TTAAGGTTCT
1385983 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
* * * *
1386025 TA TA TC TA TA TA T- TT TA GA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1386056 CCATGAAAGG
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1390352 original size:13 final size:13
Alignment explanation
Indices: 1390334--1390361 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1390324 ATATGTATCG
1390334 AATATAAATATTA
1 AATATAAATATTA
1390347 AATATAAATATTA
1 AATATAAATATTA
1390360 AA
1 AA
1390362 AAAAATCCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATATAAATATTA
Found at i:1390528 original size:14 final size:15
Alignment explanation
Indices: 1390509--1390538 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1390499 AACGATCTGG
1390509 AAAATTAAAAA-AAA
1 AAAATTAAAAATAAA
1390523 AAAATTAAAAATAAA
1 AAAATTAAAAATAAA
1390538 A
1 A
1390539 CCAGACAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAATTAAAAATAAA
Found at i:1392173 original size:2 final size:2
Alignment explanation
Indices: 1392166--1392205 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1392156 TTTTCTTTAC
*
1392166 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1392206 TTAAATTAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1392700 original size:18 final size:17
Alignment explanation
Indices: 1392669--1392720 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 17
1392659 AATATTTATT
1392669 TAAATTTAATTATAAAAA
1 TAAATTTAA-TATAAAAA
*
1392687 TAAATATTAATATAAAAG
1 TAAAT-TTAATATAAAAA
1392705 TAATATTTTAATATAA
1 TAA-A-TTTAATATAA
1392721 TTTTTAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 15 0.50
19 14 0.47
20 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
TAAATTTAATATAAAAA
Found at i:1392715 original size:19 final size:18
Alignment explanation
Indices: 1392669--1392720 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
1392659 AATATTTATT
1392669 TAAA-TTTAATTATAAAAA
1 TAAATTTTAA-TATAAAAA
* *
1392687 TAAATATTAATATAAAAG
1 TAAATTTTAATATAAAAA
1392705 TAATATTTTAATATAA
1 TAA-ATTTTAATATAA
1392721 TTTTTAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
TAAATTTTAATATAAAAA
Found at i:1392743 original size:27 final size:27
Alignment explanation
Indices: 1392713--1392776 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
1392703 AGTAATATTT
* *
1392713 TAATATAATTTTTAAAAAATTAAATTA
1 TAATTTAATTTTAAAAAAATTAAATTA
1392740 TAATTTAATTTTAAAAAAATTAAATTA
1 TAATTTAATTTTAAAAAAATTAAATTA
1392767 TAATTTAATT
1 TAATTTAATT
1392777 CACCTTATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TAATTTAATTTTAAAAAAATTAAATTA
Found at i:1395431 original size:28 final size:28
Alignment explanation
Indices: 1395400--1395457 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
1395390 AATTATTAAT
*
1395400 AATTTTATAATTT-ATTGATAAAATATTA
1 AATTTT-TAATTTCATTAATAAAATATTA
* *
1395428 AATTTTTTATTTCATTAATGAAATATTA
1 AATTTTTAATTTCATTAATAAAATATTA
1395456 AA
1 AA
1395458 GTCTTATTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (28 bp):
AATTTTTAATTTCATTAATAAAATATTA
Found at i:1399356 original size:2 final size:2
Alignment explanation
Indices: 1399351--1399380 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1399341 TTTCTATTTT
1399351 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
1399381 ATTTTTTTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1405893 original size:2 final size:2
Alignment explanation
Indices: 1405886--1405913 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1405876 TGGTCATGGC
1405886 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1405914 GCACGCTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1407240 original size:2 final size:2
Alignment explanation
Indices: 1407233--1407263 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1407223 AAAGCTTTCC
1407233 TA TA TA 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 TA TA TA T
1407264 TCAATTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1407657 original size:23 final size:23
Alignment explanation
Indices: 1407631--1407674 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
1407621 AGCTAAAGAT
1407631 TATTTTAATTTTT-TTATATTTAA
1 TATTTTAATTTTTATTA-ATTTAA
1407654 TATTTTAATTTTTATTAATTT
1 TATTTTAATTTTTATTAATTT
1407675 TTAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TATTTTAATTTTTATTAATTTAA
Found at i:1408040 original size:20 final size:20
Alignment explanation
Indices: 1408017--1408056 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1408007 TTATTATATT
1408017 TAAAATATTATAAATTAATA
1 TAAAATATTATAAATTAATA
* * *
1408037 TAAATTTTTATATATTAATA
1 TAAAATATTATAAATTAATA
1408057 ATTTATTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAAATATTATAAATTAATA
Found at i:1408065 original size:20 final size:20
Alignment explanation
Indices: 1408042--1408107 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
1408032 TAATATAAAT
1408042 TTTTATATATTAATAATTTA
1 TTTTATATATTAATAATTTA
1408062 TTTTATATATTTAATATATTTA
1 TTTTATATA-TTAATA-ATTTA
* *
1408084 -TATATTTATTAAT-ATTTA
1 TTTTATATATTAATAATTTA
*
1408102 TATTAT
1 TTTTAT
1408108 TTTATAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 5 0.13
19 3 0.08
20 14 0.36
21 12 0.31
22 5 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTATATATTAATAATTTA
Found at i:1408076 original size:18 final size:18
Alignment explanation
Indices: 1408042--1408109 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
1408032 TAATATAAAT
1408042 TTTTATATATTAATAATTTA
1 TTTTATATATT--TAATTTA
*
1408062 TTTTATATATTTAATATA
1 TTTTATATATTTAATTTA
*
1408080 -TTTATATATTT-ATTAA
1 TTTTATATATTTAATTTA
1408096 TATTTATATTATTT
1 T-TTTATA-TATTT
1408110 TATAATATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
16 3 0.07
17 11 0.26
18 12 0.29
19 5 0.12
20 11 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTATATATTTAATTTA
Found at i:1408078 original size:9 final size:9
Alignment explanation
Indices: 1408055--1408119 Score: 53
Period size: 9 Copynumber: 7.1 Consensus size: 9
1408045 TATATATTAA
*
1408055 TAATTTATT
1 TAATATATT
*
1408064 TTATATATT
1 TAATATATT
1408073 TAATATATT
1 TAATATATT
1408082 T-ATATATT
1 TAATATATT
*
1408090 TATTAATATT
1 TAAT-ATATT
1408100 T-ATATTATT
1 TAATA-TATT
*
1408109 TTATAATATT
1 TAAT-ATATT
1408119 T
1 T
1408120 TAGATTTAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
8 9 0.20
9 23 0.50
10 13 0.28
11 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TAATATATT
Found at i:1408120 original size:10 final size:9
Alignment explanation
Indices: 1408060--1408121 Score: 58
Period size: 10 Copynumber: 6.8 Consensus size: 9
1408050 ATTAATAATT
1408060 TATTTTATA
1 TATTTTATA
*
1408069 TATTTAATA
1 TATTTTATA
1408078 TA-TTTATA
1 TATTTTATA
1408086 TA-TTTAT-
1 TATTTTATA
1408093 TAATATTTATA
1 T-AT-TTTATA
1408104 TTATTTTATAA
1 -TATTTTAT-A
1408115 TATTTTA
1 TATTTTA
1408122 GATTTAATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
7 1 0.02
8 13 0.29
9 10 0.22
10 17 0.38
11 3 0.07
12 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTTATA
Found at i:1408610 original size:20 final size:19
Alignment explanation
Indices: 1408567--1408610 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1408557 TTGAATAAAA
* *
1408567 ATTTTATTTTAAATTATTT
1 ATTTTATTTTAAATAATAT
*
1408586 TTTTTATTTTTAAATAATAT
1 ATTTTA-TTTTAAATAATAT
1408606 ATTTT
1 ATTTT
1408611 GAAAAATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTTATTTTAAATAATAT
Found at i:1409800 original size:27 final size:28
Alignment explanation
Indices: 1409753--1409805 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
1409743 TTTATTTTTA
1409753 TTTAATTAAAATTTTAATAA-TAAAATT
1 TTTAATTAAAATTTTAATAATTAAAATT
* *
1409780 TTTAATT-AATTTTTATCTAATTAAAA
1 TTTAATTAAAATTTTA-ATAATTAAAA
1409806 ATTCAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 7 0.32
27 10 0.45
28 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTAATTAAAATTTTAATAATTAAAATT
Found at i:1410403 original size:3 final size:3
Alignment explanation
Indices: 1410395--1410433 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1410385 ATTAAAAACC
1410395 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1410434 CTATACGTCG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1410737 original size:24 final size:22
Alignment explanation
Indices: 1410693--1410738 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1410683 GTATCAACAT
*
1410693 TTATATAAAAAATTAACTATAA
1 TTATATAAAAAATTAAATATAA
1410715 TTATAATAAAAAATATAAATATAA
1 TTAT-ATAAAAAAT-TAAATATAA
1410739 GATAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.19
23 9 0.43
24 8 0.38
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
TTATATAAAAAATTAAATATAA
Found at i:1410743 original size:23 final size:23
Alignment explanation
Indices: 1410697--1410743 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1410687 CAACATTTAT
* *
1410697 ATAAAAAATTAACTATAATTATA
1 ATAAAAAATTAAATATAATGATA
1410720 ATAAAAAATATAAATATAA-GATA
1 ATAAAAAAT-TAAATATAATGATA
1410743 A
1 A
1410744 ATATATGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
ATAAAAAATTAAATATAATGATA
Found at i:1410746 original size:24 final size:23
Alignment explanation
Indices: 1410697--1410746 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
1410687 CAACATTTAT
* *
1410697 ATAAAAAATTAACTATAATTATA
1 ATAAAAAATTAAATATAAATATA
1410720 ATAAAAAATATAAATATAAGATA-A
1 ATAAAAAAT-TAAATATAA-ATATA
1410744 ATA
1 ATA
1410747 TATGAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 9 0.39
24 12 0.52
25 2 0.09
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
ATAAAAAATTAAATATAAATATA
Found at i:1410957 original size:2 final size:2
Alignment explanation
Indices: 1410950--1410986 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1410940 GTGGATCATC
1410950 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1410987 TAATTAAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1420730 original size:2 final size:2
Alignment explanation
Indices: 1420725--1420752 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1420715 ACAAATTTCG
1420725 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
1420753 ATTAAACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1421114 original size:2 final size:2
Alignment explanation
Indices: 1421107--1421140 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1421097 ACTCAAGTGG
1421107 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1421141 TATTTTATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1421365 original size:15 final size:14
Alignment explanation
Indices: 1421342--1421464 Score: 57
Period size: 14 Copynumber: 9.1 Consensus size: 14
1421332 CTTTTAGATT
1421342 TAATAATATTAAATA
1 TAATAATA-TAAATA
*
1421357 TAATCATAT-AA-A
1 TAATAATATAAATA
1421369 T-ATAATATAAATA
1 TAATAATATAAATA
*
1421382 AAATAAT-TAAAATA
1 TAATAATAT-AAATA
*
1421396 TAATACAATATGAATA
1 TAAT--AATATAAATA
* *
1421412 T-ATATTTTAAAATA
1 TAATAATAT-AAATA
**
1421426 TTTTAA-ATAAA-A
1 TAATAATATAAATA
*
1421438 TTATAATAT-AATA
1 TAATAATATAAATA
*
1421451 AAAT-ATATAAATA
1 TAATAATATAAATA
1421464 T
1 T
1421465 GATGTGAATA
Statistics
Matches: 81, Mismatches: 15, Indels: 26
0.66 0.12 0.21
Matches are distributed among these distances:
11 6 0.07
12 16 0.20
13 19 0.23
14 20 0.25
15 11 0.14
16 8 0.10
17 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (14 bp):
TAATAATATAAATA
Found at i:1421394 original size:25 final size:26
Alignment explanation
Indices: 1421344--1421400 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
1421334 TTTAGATTTA
* *
1421344 ATAATATTAAATATAATCATATAAAT
1 ATAATATTAAATAAAATAATATAAAT
1421370 ATAATA-TAAATAAAATAAT-TAAAAT
1 ATAATATTAAATAAAATAATAT-AAAT
1421395 ATAATA
1 ATAATA
1421401 CAATATGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 1 0.04
25 21 0.75
26 6 0.21
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
ATAATATTAAATAAAATAATATAAAT
Found at i:1431109 original size:2 final size:2
Alignment explanation
Indices: 1431102--1431136 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1431092 ACGAAAACAC
1431102 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1431137 AGGCAAAGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1434967 original size:17 final size:17
Alignment explanation
Indices: 1434945--1434979 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1434935 TGCATAATCA
1434945 AAACCATGTCTAAGAAT
1 AAACCATGTCTAAGAAT
1434962 AAACCATGTCTAAGAAT
1 AAACCATGTCTAAGAAT
1434979 A
1 A
1434980 GACAGGCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.17, G:0.11, T:0.23
Consensus pattern (17 bp):
AAACCATGTCTAAGAAT
Found at i:1441151 original size:2 final size:2
Alignment explanation
Indices: 1441146--1441183 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1441136 ATATATATAT
1441146 AG AG AG AG AG AG AG AG AG AG A- AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1441184 AATATATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1442458 original size:19 final size:20
Alignment explanation
Indices: 1442430--1442468 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1442420 ATCAAAATAT
* *
1442430 TATTTGTATATTTATAATTA
1 TATTTGTATAATTAAAATTA
1442450 TATTT-TATAATTAAAATTA
1 TATTTGTATAATTAAAATTA
1442469 AATAATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TATTTGTATAATTAAAATTA
Found at i:1442473 original size:27 final size:23
Alignment explanation
Indices: 1442443--1442501 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 23
1442433 TTGTATATTT
1442443 ATAATTATATTTTATAATTAAAATTAA
1 ATAATTA-ATTTT-TAATT-AAA-TAA
1442470 ATAA-TAATTTTTAATTAAATAA
1 ATAATTAATTTTTAATTAAATAA
1442492 ATAA-TAATTT
1 ATAATTAATTT
1442502 AAAATTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 13 0.41
23 3 0.09
24 5 0.16
25 5 0.16
26 2 0.06
27 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAATTAATTTTTAATTAAATAA
Found at i:1443267 original size:2 final size:2
Alignment explanation
Indices: 1443260--1443295 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1443250 TATAAAATTC
* *
1443260 AT AT AT AT AT AT AT AT AC AT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1443296 GAAATTCTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1444531 original size:16 final size:16
Alignment explanation
Indices: 1444512--1444545 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1444502 TAATTAATTT
1444512 TAAAAATAATATTTAA
1 TAAAAATAATATTTAA
**
1444528 TAAATTTAATATTTAA
1 TAAAAATAATATTTAA
1444544 TA
1 TA
1444546 TTTATAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAAATAATATTTAA
Found at i:1444533 original size:23 final size:24
Alignment explanation
Indices: 1444502--1444557 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
1444492 TTAATTCATA
*
1444502 TAATTAATTTTAA-AAATAATATT
1 TAATAAATTTTAATAAATAATATT
**
1444525 TAATAAA-TTTAATATTTAATATT
1 TAATAAATTTTAATAAATAATATT
1444548 T-ATAAATTTT
1 TAATAAATTTT
1444558 TATTATCCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TAATAAATTTTAATAAATAATATT
Found at i:1451017 original size:16 final size:16
Alignment explanation
Indices: 1450996--1451028 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1450986 TTTAATCATA
1450996 TTAAA-TTAAATCAAAT
1 TTAAATTTAAAT-AAAT
1451012 TTAAATTTAAATAAAT
1 TTAAATTTAAATAAAT
1451028 T
1 T
1451029 ACTTATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAAATTTAAATAAAT
Found at i:1456195 original size:3 final size:3
Alignment explanation
Indices: 1456187--1456218 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1456177 GAAGCTTTTC
*
1456187 TCT TCT TCT TCT TCT TCT TCT TCT TCC TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1456219 CTTGCGTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:1458991 original size:9 final size:9
Alignment explanation
Indices: 1458977--1459004 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1458967 AGTCATTTAC
1458977 ATTAATAAG
1 ATTAATAAG
1458986 ATTAATAAG
1 ATTAATAAG
1458995 ATTAATAAG
1 ATTAATAAG
1459004 A
1 A
1459005 AACTGCACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (9 bp):
ATTAATAAG
Found at i:1461749 original size:22 final size:21
Alignment explanation
Indices: 1461724--1461782 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 21
1461714 TAAATATAAA
* *
1461724 TAAATATTAATATAAAATATTT
1 TAAATAATAAAATAAAAT-TTT
1461746 TAAATAATAAAATAAAATTTT
1 TAAATAATAAAATAAAATTTT
1461767 TAATATAA-AAAATAAA
1 TAA-ATAATAAAATAAA
1461783 GTTGAATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 14 0.41
22 20 0.59
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAATAATAAAATAAAATTTT
Found at i:1462154 original size:16 final size:15
Alignment explanation
Indices: 1462115--1462228 Score: 56
Period size: 16 Copynumber: 7.5 Consensus size: 15
1462105 AAATGATTTG
*
1462115 AATTCAAAATAACTTA
1 AATTTAAAATAA-TTA
*
1462131 AATATAAAATAATTAA
1 AATTTAAAATAATT-A
* **
1462147 AATTTAAAATGACTCG
1 AATTTAAAAT-AATTA
* * * *
1462163 TACTCAAAAAAATTTA
1 AATTTAAAATAA-TTA
1462179 AATTT--A-TAATTA
1 AATTTAAAATAATTA
* *
1462191 AATTAAAAAT-TTTAA
1 AATTTAAAATAATT-A
1462206 AATTTAAAATAATTA
1 AATTTAAAATAATTA
1462221 AATTTAAA
1 AATTTAAA
1462229 TTAACCTTAT
Statistics
Matches: 69, Mismatches: 21, Indels: 17
0.64 0.20 0.16
Matches are distributed among these distances:
12 7 0.10
13 2 0.03
14 4 0.06
15 23 0.33
16 31 0.45
17 2 0.03
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (15 bp):
AATTTAAAATAATTA
Found at i:1462198 original size:25 final size:23
Alignment explanation
Indices: 1462170--1462230 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 23
1462160 TCGTACTCAA
*
1462170 AAAAATTTAAATTTATAATTAAATT
1 AAAAATTTAAATTTA-AAAT-AATT
1462195 AAAAATTTTAAAATTTAAAATAATT
1 AAAAA-TTT-AAATTTAAAATAATT
1462220 --AAATTTAAATT
1 AAAAATTTAAATT
1462231 AACCTTATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 5 0.15
22 3 0.09
23 3 0.09
25 9 0.27
26 6 0.18
27 7 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAAATTTAAATTTAAAATAATT
Found at i:1462214 original size:15 final size:15
Alignment explanation
Indices: 1462184--1462228 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
1462174 ATTTAAATTT
*
1462184 ATAATTAAATTAAAA
1 ATAATTAAATTTAAA
*
1462199 AT-TTTAAAATTTAAA
1 ATAATT-AAATTTAAA
1462214 ATAATTAAATTTAAA
1 ATAATTAAATTTAAA
1462229 TTAACCTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 21 0.84
16 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAATTAAATTTAAA
Found at i:1463884 original size:13 final size:13
Alignment explanation
Indices: 1463866--1463890 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1463856 TATATTAATT
1463866 TTTTAATAAGTAA
1 TTTTAATAAGTAA
1463879 TTTTAATAAGTA
1 TTTTAATAAGTA
1463891 TTAAAGTTGG
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TTTTAATAAGTAA
Found at i:1464830 original size:23 final size:22
Alignment explanation
Indices: 1464804--1464853 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
1464794 GTCTATTTAA
1464804 AATATTATTTTTAT-ATTAATATT
1 AATATT-TTTTTATAATTAA-ATT
1464827 AATATTTTTTTATAATTAAATT
1 AATATTTTTTTATAATTAAATT
*
1464849 TATAT
1 AATAT
1464854 AAAAATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
AATATTTTTTTATAATTAAATT
Found at i:1466316 original size:2 final size:2
Alignment explanation
Indices: 1466303--1466336 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1466293 GGTTTAAGTT
* *
1466303 TA TA TA TT TA TA TA TA TT 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
1466337 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:1466318 original size:10 final size:10
Alignment explanation
Indices: 1466303--1466336 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
1466293 GGTTTAAGTT
1466303 TATATATTTA
1 TATATATTTA
1466313 TATATATTTA
1 TATATATTTA
*
1466323 TATATATATA
1 TATATATTTA
1466333 TATA
1 TATA
1466337 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TATATATTTA
Found at i:1467863 original size:20 final size:19
Alignment explanation
Indices: 1467839--1467883 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1467829 GTAAAATAAA
*
1467839 AAAATAAAATTTAAAAATG
1 AAAATAAAATATAAAAATG
* *
1467858 ATAAATAATATATAAATATG
1 A-AAATAAAATATAAAAATG
1467878 AAAATA
1 AAAATA
1467884 TTTAATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (19 bp):
AAAATAAAATATAAAAATG
Found at i:1474473 original size:2 final size:2
Alignment explanation
Indices: 1474466--1474500 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1474456 ATATGCATGA
1474466 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1474501 ACCGAAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1474687 original size:12 final size:12
Alignment explanation
Indices: 1474670--1474694 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1474660 TACTTGCTTG
1474670 CAATTGCAATTC
1 CAATTGCAATTC
1474682 CAATTGCAATTC
1 CAATTGCAATTC
1474694 C
1 C
1474695 CTTTTCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (12 bp):
CAATTGCAATTC
Found at i:1477560 original size:2 final size:2
Alignment explanation
Indices: 1477553--1477586 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1477543 AGGAAAAACC
1477553 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1477587 GGGAAATAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1478821 original size:31 final size:32
Alignment explanation
Indices: 1478769--1478835 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
1478759 TATTTTTATT
1478769 TAAATTTAATTTATAAATATTAATATAAAT-A
1 TAAATTTAATTTATAAATATTAATATAAATAA
* * * * *
1478800 TAAATTTAATTTTTTATTATTATTTTAAATAA
1 TAAATTTAATTTATAAATATTAATATAAATAA
1478832 TAAA
1 TAAA
1478836 AAAAATTACA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TAAATTTAATTTATAAATATTAATATAAATAA
Found at i:1478882 original size:20 final size:20
Alignment explanation
Indices: 1478832--1478890 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
1478822 TTTTAAATAA
*
1478832 TAAAAAAAATTACATTA-ATT
1 TAAAAAAATTTA-ATTATATT
**
1478852 TAAACTTAATTTAATTATATT
1 TAAA-AAAATTTAATTATATT
*
1478873 TAAAAAAATTAAATTATA
1 TAAAAAAATTTAATTATA
1478891 AATTCAATTC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAAAAATTTAATTATATT
Found at i:1483814 original size:11 final size:12
Alignment explanation
Indices: 1483793--1483847 Score: 58
Period size: 12 Copynumber: 4.5 Consensus size: 12
1483783 TTTTTTTATG
1483793 TATTATATTTTA
1 TATTATATTTTA
*
1483805 -ATTATTTTTTA
1 TATTATATTTTA
*
1483816 TATTATATTAATA
1 TATTATATT-TTA
*
1483829 TAATTATATTTAA
1 T-ATTATATTTTA
1483842 TATTAT
1 TATTAT
1483848 CACATCCCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
11 10 0.29
12 12 0.34
13 5 0.14
14 8 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTATATTTTA
Found at i:1483819 original size:23 final size:25
Alignment explanation
Indices: 1483749--1483847 Score: 70
Period size: 26 Copynumber: 4.2 Consensus size: 25
1483739 AATTAATAAT
* *
1483749 TTATATTATATAA--ATATTTAATA
1 TTATATTATATAATTATTTTTTATA
*
1483772 -TAT-TTACAT-ATT-TTTTTTATGTA
1 TTATATTATATAATTATTTTTTA--TA
1483795 TTATATT-T-TAATTATTTTTTATA
1 TTATATTATATAATTATTTTTTATA
* *
1483818 TTATATTAATATAATTATATTTAATA
1 TTATATT-ATATAATTATTTTTTATA
1483844 TTAT
1 TTAT
1483848 CACATCCCTT
Statistics
Matches: 59, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
20 1 0.02
21 10 0.17
22 3 0.05
23 12 0.20
24 6 0.10
25 10 0.17
26 17 0.29
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (25 bp):
TTATATTATATAATTATTTTTTATA
Found at i:1486275 original size:16 final size:13
Alignment explanation
Indices: 1486244--1486296 Score: 65
Period size: 14 Copynumber: 4.1 Consensus size: 13
1486234 TTAACAAAAT
1486244 ATAAATATATTTA
1 ATAAATATATTTA
1486257 ATAAAGTATATTT-
1 ATAAA-TATATTTA
*
1486270 A-AAATACATTTA
1 ATAAATATATTTA
1486282 ATAAAATATATTTA
1 AT-AAATATATTTA
1486296 A
1 A
1486297 AATCGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
11 6 0.18
12 4 0.12
13 6 0.18
14 18 0.53
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (13 bp):
ATAAATATATTTA
Found at i:1486275 original size:25 final size:24
Alignment explanation
Indices: 1486221--1486299 Score: 94
Period size: 25 Copynumber: 3.4 Consensus size: 24
1486211 TTGAATTAAA
*
1486221 ATTTAAAATATATTTAACAAA-AT
1 ATTTAAAATATATTTAATAAATAT
1486244 A--T-AAATATATTTAATAAAGTAT
1 ATTTAAAATATATTTAATAAA-TAT
*
1486266 ATTTAAAATACATTTAATAAAATAT
1 ATTTAAAATATATTTAAT-AAATAT
1486291 ATTTAAAAT
1 ATTTAAAAT
1486300 CGAAAAAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
20 15 0.31
21 1 0.02
22 3 0.06
23 1 0.02
24 1 0.02
25 24 0.50
26 3 0.06
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.41
Consensus pattern (24 bp):
ATTTAAAATATATTTAATAAATAT
Found at i:1494527 original size:14 final size:14
Alignment explanation
Indices: 1494510--1494593 Score: 54
Period size: 14 Copynumber: 6.4 Consensus size: 14
1494500 ACGATAGATA
1494510 AATATAATATATTT
1 AATATAATATATTT
1494524 AATA-AATATA---
1 AATATAATATATTT
* * *
1494534 AAAATAATATAATA
1 AATATAATATATTT
*
1494548 AATATAATATGATAT
1 AATATAATAT-ATTT
* *
1494563 -GTTTAA-ATATTT
1 AATATAATATATTT
*
1494575 AATTTAATATATTT
1 AATATAATATATTT
1494589 AATAT
1 AATAT
1494594 GAGTATTGTA
Statistics
Matches: 53, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
10 3 0.06
11 6 0.11
12 3 0.06
13 13 0.25
14 27 0.51
15 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
AATATAATATATTT
Found at i:1494553 original size:9 final size:9
Alignment explanation
Indices: 1494507--1494556 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
1494497 AACACGATAG
1494507 ATAAATATA
1 ATAAATATA
* *
1494516 ATATATTTA
1 ATAAATATA
1494525 ATAAATATAA
1 ATAAATAT-A
*
1494535 AAATAATATA
1 ATA-AATATA
1494545 ATAAATATA
1 ATAAATATA
1494554 ATA
1 ATA
1494557 TGATATGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 22 0.67
10 6 0.18
11 5 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
ATAAATATA
Found at i:1496148 original size:17 final size:17
Alignment explanation
Indices: 1496096--1496148 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
1496086 ATTTTTATTG
1496096 AATTT-AATAA-AAATA
1 AATTTAAATAATAAATA
*
1496111 ATATATTAAAT-ATAAAAA
1 A-AT-TTAAATAATAAATA
1496129 AATTTAAATAATAAATA
1 AATTTAAATAATAAATA
1496146 AAT
1 AAT
1496149 AATACTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 1 0.03
16 8 0.26
17 14 0.45
18 8 0.26
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATTTAAATAATAAATA
Found at i:1496404 original size:23 final size:22
Alignment explanation
Indices: 1496372--1496415 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1496362 TATTTTTATT
1496372 TAAATTTAA-TTATAAAATAATA
1 TAAATTTAATTTA-AAAATAATA
1496394 TAAATATTAATTTAAAAATAAT
1 TAAAT-TTAATTTAAAAATAAT
1496416 TTTTTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 12 0.60
24 3 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAATTTAATTTAAAAATAATA
Found at i:1497222 original size:29 final size:30
Alignment explanation
Indices: 1497190--1497254 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 30
1497180 AAGGGTTAGC
* *
1497190 TTTAATATATTTTAATTA-ATTAAAT-TTTT
1 TTTAATATAATTTAATTATA-AAAATATTTT
1497219 TTT-ATA-AATTTAATTATAAAAATATTTT
1 TTTAATATAATTTAATTATAAAAATATTTT
1497247 TTTAATAT
1 TTTAATAT
1497255 TTTAATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
27 13 0.43
28 11 0.37
29 6 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
TTTAATATAATTTAATTATAAAAATATTTT
Found at i:1497229 original size:28 final size:28
Alignment explanation
Indices: 1497198--1497260 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
1497188 GCTTTAATAT
*
1497198 ATTTTAATTA-ATTAAAT-TTTTTTTATAA
1 ATTTTAATTATA-AAAATATTTTTTTA-AA
*
1497226 A-TTTAATTATAAAAATATTTTTTTAAT
1 ATTTTAATTATAAAAATATTTTTTTAAA
1497253 ATTTTAAT
1 ATTTTAAT
1497261 ATATTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
27 14 0.47
28 16 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
ATTTTAATTATAAAAATATTTTTTTAAA
Found at i:1497263 original size:27 final size:26
Alignment explanation
Indices: 1497195--1497263 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 26
1497185 TTAGCTTTAA
1497195 TATATTTTAAT-TAATTAAATTTTTTT
1 TATATTTTAATATAA-TAAATTTTTTT
*
1497221 TATAAATTTAATTATAA-AAATATTTTTT
1 TAT-ATTTTAA-TATAATAAAT-TTTTTT
1497249 TAATATTTTAATATA
1 T-ATATTTTAATATA
1497264 TTTTAAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
26 3 0.08
27 14 0.39
28 14 0.39
29 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TATATTTTAATATAATAAATTTTTTT
Found at i:1497989 original size:17 final size:17
Alignment explanation
Indices: 1497944--1497980 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1497934 AGATATTTAG
*
1497944 TTTTTAAAATTAATTAA
1 TTTTAAAAATTAATTAA
1497961 TTTTAAAAATTAATTAA
1 TTTTAAAAATTAATTAA
1497978 TTT
1 TTT
1497981 AATTAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTAAAAATTAATTAA
Found at i:1498100 original size:40 final size:41
Alignment explanation
Indices: 1498046--1498122 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 41
1498036 TTATTTTTAT
1498046 TTTTAATTATATTATACATAATATAA-ATAAAATTATATAA
1 TTTTAATTATATTATACATAATATAATATAAAATTATATAA
* * * *
1498086 TTTTATTTATATTATATATCATATAATATACAATTAT
1 TTTTAATTATATTATACATAATATAATATAAAATTAT
1498123 TTTTTTAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 23 0.72
41 9 0.28
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (41 bp):
TTTTAATTATATTATACATAATATAATATAAAATTATATAA
Found at i:1500101 original size:24 final size:23
Alignment explanation
Indices: 1500038--1500109 Score: 60
Period size: 24 Copynumber: 3.2 Consensus size: 23
1500028 ATAATTCAAA
* * *
1500038 AAATATATATATATATAATATTTT
1 AAATATAAATATATA-AATAATAT
*
1500062 AAATAT-AAT-TAAAAATAATAT
1 AAATATAAATATATAAATAATAT
*
1500083 ATAATATAAATATATAAATTAT-T
1 A-AATATAAATATATAAATAATAT
1500106 AAAT
1 AAAT
1500110 TGATGACTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
21 7 0.18
22 11 0.28
23 7 0.18
24 14 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATATAAATATATAAATAATAT
Found at i:1503293 original size:11 final size:11
Alignment explanation
Indices: 1503277--1503307 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1503267 TATATTTGGG
*
1503277 GGGGGGGGGGA
1 GGGGGGGGGAA
1503288 GGGGGGGGGAA
1 GGGGGGGGGAA
1503299 GGGGGGGGG
1 GGGGGGGGG
1503308 CTTGATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.90, T:0.00
Consensus pattern (11 bp):
GGGGGGGGGAA
Found at i:1508773 original size:2 final size:2
Alignment explanation
Indices: 1508766--1508790 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1508756 TTTATTTATT
1508766 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
1508791 TTATTTATTT
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:1509208 original size:1 final size:1
Alignment explanation
Indices: 1509204--1509228 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1509194 CTTTTTTTGT
1509204 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
1509229 TTTAACCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1509587 original size:2 final size:2
Alignment explanation
Indices: 1509580--1509614 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1509570 ACAGATTTAC
1509580 TA TA TA TA TA 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 TA TA TA TA TA T
1509615 CTGTATGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1519435 original size:2 final size:2
Alignment explanation
Indices: 1519430--1519455 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1519420 TATATATATA
1519430 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
1519456 CGCGTGTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1521762 original size:2 final size:2
Alignment explanation
Indices: 1521755--1521797 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
1521745 GGAGACTCTG
* * * *
1521755 AT AT AT AT AT AC AT AC AC AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1521797 A
1 A
1521798 CATAGAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1523007 original size:43 final size:41
Alignment explanation
Indices: 1522914--1523013 Score: 103
Period size: 42 Copynumber: 2.3 Consensus size: 41
1522904 CATGATATAA
* *
1522914 TTATATAATATAAAAATAATTAAAATATATAATATAAAATT
1 TTATAAAATATAAAAATAATTAAAATATATAATATAAAAAT
* *
1522955 TTACATAAAATA-AAAAATAATTTAAATATTTAAATACATAAAAAT
1 TT--ATAAAATATAAAAATAATTAAAATATAT-AAT--ATAAAAAT
*
1523000 TTATAAAAAATAAA
1 TTATAAAATATAAA
1523014 TTATTAATAT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
41 2 0.04
42 17 0.35
43 17 0.35
44 3 0.06
45 9 0.19
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (41 bp):
TTATAAAATATAAAAATAATTAAAATATATAATATAAAAAT
Found at i:1523085 original size:21 final size:22
Alignment explanation
Indices: 1523051--1523092 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1523041 ATCATATTTT
**
1523051 AAATATAATTATAAT-AAATAA
1 AAATATAAAAATAATGAAATAA
1523072 AAATATAAAAATAATGAAATA
1 AAATATAAAAATAATGAAATA
1523093 TACAAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
AAATATAAAAATAATGAAATAA
Found at i:1523497 original size:23 final size:24
Alignment explanation
Indices: 1523439--1523500 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
1523429 AAACTTTATT
*
1523439 TATATATATATTTTTTAAAATAAAA
1 TATATA-ATATTTTTAAAAATAAAA
* *
1523464 AATAATTATATTTTTAAAAAT-AAA
1 TAT-ATAATATTTTTAAAAATAAAA
1523488 TATATAATATTTT
1 TATATAATATTTT
1523501 AAAGTAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
23 9 0.29
24 5 0.16
25 15 0.48
26 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TATATAATATTTTTAAAAATAAAA
Found at i:1523666 original size:16 final size:16
Alignment explanation
Indices: 1523641--1523677 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1523631 AGTTAAAAAC
*
1523641 TTAAAATTAAAATAAT
1 TTAAAATTAAAATAAA
*
1523657 TTAAATTTAAAATAAA
1 TTAAAATTAAAATAAA
1523673 TTAAA
1 TTAAA
1523678 CGTAAACCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAAATTAAAATAAA
Found at i:1526053 original size:12 final size:12
Alignment explanation
Indices: 1526036--1526060 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1526026 AATTTTTATA
1526036 TTTTTTTAATTT
1 TTTTTTTAATTT
1526048 TTTTTTTAATTT
1 TTTTTTTAATTT
1526060 T
1 T
1526061 CAAATCTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTAATTT
Found at i:1526473 original size:20 final size:19
Alignment explanation
Indices: 1526413--1526473 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 19
1526403 TTTTTAACAC
*
1526413 AAAATATATTAAAATTTAT
1 AAAATATATTATAATTTAT
*
1526432 ATAA-ATA-TATAATATT-T
1 AAAATATATTATAAT-TTAT
*
1526449 CAAATATAATTATAATTTAT
1 AAAATAT-ATTATAATTTAT
1526469 AAAAT
1 AAAAT
1526474 TTATCTATCT
Statistics
Matches: 32, Mismatches: 5, Indels: 9
0.70 0.11 0.20
Matches are distributed among these distances:
17 8 0.25
18 7 0.22
19 6 0.19
20 11 0.34
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAATATATTATAATTTAT
Done.