Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 40 of 203
Found at i:13234493 original size:29 final size:29
Alignment explanation
Indices: 13234431--13234493 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
13234421 CCCCCAATTT
**
13234431 AAAAATAAATTAAAAAAAGTATTAATTTT
1 AAAAATAAATTAAAAAAAGTATTAATTGG
* **
13234460 TAAAATAAATTTTAAAAAGTATTAATTGG
1 AAAAATAAATTAAAAAAAGTATTAATTGG
13234489 AAAAA
1 AAAAA
13234494 AAGTTGTGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.33
Consensus pattern (29 bp):
AAAAATAAATTAAAAAAAGTATTAATTGG
Found at i:13234674 original size:30 final size:30
Alignment explanation
Indices: 13234640--13234701 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
13234630 AGAGTGGAGT
13234640 AAGAAATTTTATTTAGAAGATGGAGATAAA
1 AAGAAATTTTATTTAGAAGATGGAGATAAA
13234670 AAGAAATTTTATTTAGAAGATGGAGATAAA
1 AAGAAATTTTATTTAGAAGATGGAGATAAA
13234700 AA
1 AA
13234702 AATAACTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.52, C:0.00, G:0.19, T:0.29
Consensus pattern (30 bp):
AAGAAATTTTATTTAGAAGATGGAGATAAA
Found at i:13245788 original size:53 final size:53
Alignment explanation
Indices: 13245730--13245836 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
13245720 TAATATTGTG
*
13245730 AAAATTTTACTCGAGATTAAATTCGATTCTAAATTTAATTAAGATTTAATGTA
1 AAAATTTTACTCGAGATTAAATTCGATTCTAAATTTAATTAAGATGTAATGTA
13245783 AAAATTTTACTCGAGATTAAATTCGATTCTAAATTTAATTAAGATGTAATGTA
1 AAAATTTTACTCGAGATTAAATTCGATTCTAAATTTAATTAAGATGTAATGTA
13245836 A
1 A
13245837 TTATAATTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.40
Consensus pattern (53 bp):
AAAATTTTACTCGAGATTAAATTCGATTCTAAATTTAATTAAGATGTAATGTA
Found at i:13248237 original size:15 final size:15
Alignment explanation
Indices: 13248217--13248268 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
13248207 ACTACAAAAC
13248217 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
13248232 ATTTATAATTATAATAAAT
1 ATTTATTA-T-TAAT--AT
*
13248251 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
13248266 ATT
1 ATT
13248269 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:13248254 original size:19 final size:19
Alignment explanation
Indices: 13248230--13248266 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
13248220 TATTATTAAT
*
13248230 ATATTTATAATTATAATAA
1 ATATTTATAATTAAAATAA
*
13248249 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
13248267 TTAATATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:13248389 original size:22 final size:22
Alignment explanation
Indices: 13248349--13248404 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
13248339 AATAAAATTG
*
13248349 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
13248369 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
13248391 TATTAATAATTTAT
1 AAATAATAAATTAT
13248405 TATATGACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:13252326 original size:23 final size:22
Alignment explanation
Indices: 13252274--13252348 Score: 93
Period size: 21 Copynumber: 3.5 Consensus size: 22
13252264 CCTGATCAGT
*
13252274 ATACGACACA-GAAAGTGCCT-A
1 ATACGACACACG-AGGTGCCTGA
*
13252295 AAACGACACACGAGGTGCCTG-
1 ATACGACACACGAGGTGCCTGA
13252316 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACGAGGTGCCTG-A
13252339 ATACGACACA
1 ATACGACACA
13252349 TAAAGTGCCT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
21 36 0.77
22 1 0.02
23 10 0.21
ACGTcount: A:0.39, C:0.27, G:0.23, T:0.12
Consensus pattern (22 bp):
ATACGACACACGAGGTGCCTGA
Found at i:13252356 original size:23 final size:23
Alignment explanation
Indices: 13252274--13252360 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
13252264 CCTGATCAGT
*
13252274 ATACGACACAGAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
13252296 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
13252316 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
13252339 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
13252361 TCAATAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.14
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:13252360 original size:44 final size:42
Alignment explanation
Indices: 13252274--13252361 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 42
13252264 CCTGATCAGT
* *
13252274 ATACGACACAGAAAGTGCCTAAAACGACACACGAGGTGCCTG
1 ATACGACACAGAAAGTGCCTAAAACGACACACAAAGTGCCTG
* *
13252316 ATACGACACACG-AGGTGCCTGAAATACGACACATAAAGTGCCTG
1 ATACGACACA-GAAAGTGCCT-AAA-ACGACACACAAAGTGCCTG
13252360 AT
1 AT
13252362 CAATAAAGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
42 17 0.44
43 4 0.10
44 18 0.46
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.15
Consensus pattern (42 bp):
ATACGACACAGAAAGTGCCTAAAACGACACACAAAGTGCCTG
Found at i:13252756 original size:15 final size:15
Alignment explanation
Indices: 13252731--13252773 Score: 77
Period size: 15 Copynumber: 2.8 Consensus size: 15
13252721 TCATATATAT
13252731 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
13252747 TATAAATTCAATCAA
1 TATAAATTCAATCAA
13252762 TATAAATTCAAT
1 TATAAATTCAAT
13252774 AAATTCATCG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 23 0.85
16 4 0.15
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:13254056 original size:5 final size:5
Alignment explanation
Indices: 13254043--13254074 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
13254033 TTCTTTAGTT
13254043 TATATA TATAA TATAA TATAA TATAA TATAA T
1 TATA-A TATAA TATAA TATAA TATAA TATAA T
13254075 TAAAACATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TATAA
Found at i:13254110 original size:8 final size:8
Alignment explanation
Indices: 13254097--13254125 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
13254087 TATCTTTATT
13254097 ATATAATA
1 ATATAATA
13254105 ATATAATA
1 ATATAATA
13254113 ATATAATA
1 ATATAATA
13254121 ATATA
1 ATATA
13254126 CTAAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:13259648 original size:31 final size:32
Alignment explanation
Indices: 13259592--13259654 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
13259582 CACACTTGTC
*
13259592 ATAATTTAATATATTTATTACATAAAAATCTT
1 ATAATATAATATATTTATTACATAAAAATCTT
*
13259624 ATAATATAA-ATATTTAATTA-ATAAATATCTT
1 ATAATATAATATATTT-ATTACATAAAAATCTT
13259655 TTATAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (32 bp):
ATAATATAATATATTTATTACATAAAAATCTT
Found at i:13274728 original size:11 final size:11
Alignment explanation
Indices: 13274714--13274750 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
13274704 AAACTGTGAT
13274714 AAAACAACAAG
1 AAAACAACAAG
* *
13274725 AAAATAACAAC
1 AAAACAACAAG
13274736 AAAACAACAAG
1 AAAACAACAAG
13274747 AAAA
1 AAAA
13274751 TGGTAAATTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.76, C:0.16, G:0.05, T:0.03
Consensus pattern (11 bp):
AAAACAACAAG
Found at i:13280042 original size:25 final size:25
Alignment explanation
Indices: 13279997--13280045 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
13279987 AAGGTTTGTA
*
13279997 ATACGTGAAAGAATTTCTTAAAACT
1 ATACGTGAAAGAATTTATTAAAACT
*
13280022 ATACGTGAAA-ATTTTAATTAAAAC
1 ATACGTGAAAGAATTT-ATTAAAAC
13280046 ATGAAACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (25 bp):
ATACGTGAAAGAATTTATTAAAACT
Found at i:13280647 original size:28 final size:27
Alignment explanation
Indices: 13280580--13280647 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 27
13280570 AATATAAAAT
*
13280580 ATTTATTTTTATATAAAAATTAAAATTA
1 ATTTA-TTTTAAATAAAAATTAAAATTA
*
13280608 ATTATATATTAAATAAAAA-TAAAATTTA
1 ATT-TATTTTAAATAAAAATTAAAA-TTA
*
13280636 GTTTAGTTTTAA
1 ATTTA-TTTTAA
13280648 GTAACCACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 7 0.21
28 24 0.73
29 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (27 bp):
ATTTATTTTAAATAAAAATTAAAATTA
Found at i:13284017 original size:3 final size:3
Alignment explanation
Indices: 13284009--13284093 Score: 50
Period size: 3 Copynumber: 28.0 Consensus size: 3
13283999 TTTTTTATAT
* * * *
13284009 TTA TTA TTA TTA -TG TTA TTTA TTG TTA TTA TTA -CA TTT TTA TGTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * *
13284054 TATA ATA TT- TATA TTA TTA CTA CTA TTA TTA TTA TTA TTA
1 T-TA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13284094 GCATATTTCT
Statistics
Matches: 63, Mismatches: 13, Indels: 12
0.72 0.15 0.14
Matches are distributed among these distances:
2 3 0.05
3 51 0.81
4 9 0.14
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:13284133 original size:18 final size:18
Alignment explanation
Indices: 13284110--13284148 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
13284100 TTCTCAATTA
13284110 ATACTTACATATATATAT
1 ATACTTACATATATATAT
* *
13284128 ATACTTTCATATATATTT
1 ATACTTACATATATATAT
13284146 ATA
1 ATA
13284149 GTTGTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (18 bp):
ATACTTACATATATATAT
Found at i:13284313 original size:24 final size:25
Alignment explanation
Indices: 13284286--13284347 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
13284276 ATATATCATC
13284286 TTATGTATATATTCTTAAATA-C-TA
1 TTATGTATATATT-TTAAATACCATA
* *
13284310 TTATATATATATTTTTAATACCATA
1 TTATGTATATATTTTAAATACCATA
*
13284335 TTGTGTATATATT
1 TTATGTATATATT
13284348 ATTATTATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 6 0.19
24 13 0.41
25 13 0.41
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.53
Consensus pattern (25 bp):
TTATGTATATATTTTAAATACCATA
Found at i:13284363 original size:13 final size:13
Alignment explanation
Indices: 13284345--13284369 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13284335 TTGTGTATAT
13284345 ATTATTATTATTA
1 ATTATTATTATTA
13284358 ATTATTATTATT
1 ATTATTATTATT
13284370 GCTAGTATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTATTATTATTA
Found at i:13284523 original size:16 final size:17
Alignment explanation
Indices: 13284483--13284526 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
13284473 GCTTTTGTAT
13284483 TTTA-ATATTATTATTA
1 TTTATATATTATTATTA
13284499 TTTAT-TATTATT-TT-
1 TTTATATATTATTATTA
13284513 TTGTATATATTATT
1 TT-TATATATTATT
13284527 CATACTATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.08
15 5 0.20
16 18 0.72
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (17 bp):
TTTATATATTATTATTA
Found at i:13284726 original size:17 final size:17
Alignment explanation
Indices: 13284704--13284753 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 17
13284694 CTATTATTAC
13284704 ATATTATTTTATTTTTA
1 ATATTATTTTATTTTTA
*
13284721 ATATTATTAAATTATTTTTT
1 ATATTATT---TTATTTTTA
*
13284741 ATATTCTTTTATT
1 ATATTATTTTATT
13284754 ATCATTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 13 0.46
20 15 0.54
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (17 bp):
ATATTATTTTATTTTTA
Found at i:13284740 original size:27 final size:27
Alignment explanation
Indices: 13284688--13284742 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
13284678 ATATTTACCC
* *
13284688 TTTTTACTATTATTACATATTATTTTA
1 TTTTTAATATTATTAAATATTATTTTA
13284715 TTTTTAATATTATTAAATTATT-TTTTA
1 TTTTTAATATTATTAAA-TATTATTTTA
13284742 T
1 T
13284743 ATTCTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTTTAATATTATTAAATATTATTTTA
Found at i:13284823 original size:28 final size:27
Alignment explanation
Indices: 13284791--13284863 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 27
13284781 ATACATATAC
13284791 ATATATATTTTTTGTACATATCATTATTTT
1 ATATATA-TTTTTGTACATAT-ATT-TTTT
*
13284821 ATAT-TATTGTTGTA-A-ATATTTTTT
1 ATATATATTTTTGTACATATATTTTTT
13284845 ATATATATTTTATGTACAT
1 ATATATATTTT-TGTACAT
13284864 CTCCTAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
24 8 0.22
25 8 0.22
26 6 0.16
27 2 0.05
28 7 0.19
29 2 0.05
30 4 0.11
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.59
Consensus pattern (27 bp):
ATATATATTTTTGTACATATATTTTTT
Found at i:13286246 original size:34 final size:34
Alignment explanation
Indices: 13286203--13286270 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
13286193 TCAGCAAAGG
13286203 ACTTAATAAATAGTATAGATAAAAATAATTTATT
1 ACTTAATAAATAGTATAGATAAAAATAATTTATT
13286237 ACTTAATAAATAGTATAGATAAAAATAATTTATT
1 ACTTAATAAATAGTATAGATAAAAATAATTTATT
13286271 TCTTTTGAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (34 bp):
ACTTAATAAATAGTATAGATAAAAATAATTTATT
Found at i:13288693 original size:38 final size:38
Alignment explanation
Indices: 13288641--13288717 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
13288631 CGAATGGAGT
13288641 TAAGCTCGCAAGAGCTAACAGCTATTGTAGTTAATCAG
1 TAAGCTCGCAAGAGCTAACAGCTATTGTAGTTAATCAG
*
13288679 TAAGCTCGCGAGAGCTAACAGCTATTGTAGTTAATCAG
1 TAAGCTCGCAAGAGCTAACAGCTATTGTAGTTAATCAG
13288717 T
1 T
13288718 GCGGGATCGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27
Consensus pattern (38 bp):
TAAGCTCGCAAGAGCTAACAGCTATTGTAGTTAATCAG
Found at i:13294010 original size:21 final size:20
Alignment explanation
Indices: 13293986--13294025 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
13293976 ATAAAAGAAT
*
13293986 AATATATTAATATTTTATTAA
1 AATATATTAA-AATTTATTAA
*
13294007 AATATTTTAAAATTTATTA
1 AATATATTAAAATTTATTA
13294026 CATTTTTATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATATATTAAAATTTATTAA
Found at i:13298698 original size:19 final size:19
Alignment explanation
Indices: 13298676--13298715 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
13298666 ATCAAATGAC
*
13298676 TTTAAATT-ATTGCTTGAAT
1 TTTAAATTGATT-CTTAAAT
13298695 TTTAAATTGATTCTTAAAT
1 TTTAAATTGATTCTTAAAT
13298714 TT
1 TT
13298716 CAAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (19 bp):
TTTAAATTGATTCTTAAAT
Found at i:13299550 original size:62 final size:60
Alignment explanation
Indices: 13299445--13299566 Score: 181
Period size: 62 Copynumber: 2.0 Consensus size: 60
13299435 AAAGTATAAT
* * *
13299445 TTTACAGAAAATAATTTGTAATTTTATCAGGAGACTGAGAAACAAAGTTCCAGGCTGTGC
1 TTTACAGAAAATAATTTGTAATATTATCAGGAAACTGAAAAACAAAGTTCCAGGCTGTGC
* *
13299505 TTTACAGAAAATAATATTTTTAATATTATCGGGAAACTGAAAAACAAAGTTCCAGGCTGTGC
1 TTTACAGAAAAT-A-ATTTGTAATATTATCAGGAAACTGAAAAACAAAGTTCCAGGCTGTGC
13299567 CCAAAATCAC
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 12 0.22
61 1 0.02
62 42 0.76
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (60 bp):
TTTACAGAAAATAATTTGTAATATTATCAGGAAACTGAAAAACAAAGTTCCAGGCTGTGC
Found at i:13299710 original size:7 final size:7
Alignment explanation
Indices: 13299674--13299709 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
13299664 CTCGCCTAAT
13299674 CCGCATG
1 CCGCATG
13299681 CCGCATG
1 CCGCATG
13299688 CCGCATG
1 CCGCATG
13299695 CCGCATG
1 CCGCATG
*
13299702 CTGCATG
1 CCGCATG
13299709 C
1 C
13299710 TCTATATAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.42, G:0.28, T:0.17
Consensus pattern (7 bp):
CCGCATG
Found at i:13311771 original size:15 final size:15
Alignment explanation
Indices: 13311751--13311781 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13311741 TTCTGCTTTT
13311751 TTCTTCGTCGTCTTC
1 TTCTTCGTCGTCTTC
*
13311766 TTCTTCGTCTTCTTC
1 TTCTTCGTCGTCTTC
13311781 T
1 T
13311782 CTTGCCTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.32, G:0.10, T:0.58
Consensus pattern (15 bp):
TTCTTCGTCGTCTTC
Found at i:13311781 original size:12 final size:12
Alignment explanation
Indices: 13311751--13311781 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
13311741 TTCTGCTTTT
*
13311751 TTCTTCGTCGTC
1 TTCTTCTTCGTC
13311763 TTCTTCTTCGTC
1 TTCTTCTTCGTC
13311775 TTCTTCT
1 TTCTTCT
13311782 CTTGCCTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.32, G:0.10, T:0.58
Consensus pattern (12 bp):
TTCTTCTTCGTC
Found at i:13312603 original size:60 final size:60
Alignment explanation
Indices: 13312492--13312605 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
13312482 ATGTTTTTTT
* * * *
13312492 TTTCTTTTTTGGTCGCTCGACAATGAAAAATTATAAAATAGTCATCCAACTATTAGTAAA
1 TTTCTTTTTTGGTCCCTCAACAATGAAAAATTATAAAACAATCATCCAACTATTAGTAAA
*
13312552 TTTCTTTTTTGGTCACCT-AACTATGAAAAATTATAAAACAATCA-CCAAACTATT
1 TTTCTTTTTTGGTC-CCTCAACAATGAAAAATTATAAAACAATCATCC-AACTATT
13312606 CAAATTTGTC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 2 0.04
60 43 0.91
61 2 0.04
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.37
Consensus pattern (60 bp):
TTTCTTTTTTGGTCCCTCAACAATGAAAAATTATAAAACAATCATCCAACTATTAGTAAA
Found at i:13312618 original size:60 final size:59
Alignment explanation
Indices: 13312514--13312628 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 59
13312504 TCGCTCGACA
* * **
13312514 ATGAAAAATTATAAAATAGTCATCCAACTATTAGTAAATTTCTTTTTTGGTCACCTAACT
1 ATGAAAAATTATAAAACAATCATCCAACTATTAG-AAATTTCTTTTAGGGTCACCTAACT
*
13312574 ATGAAAAATTATAAAACAATCA-CCAAACTATTCA-AATTTGTCTTTTAGGGTCACC
1 ATGAAAAATTATAAAACAATCATCC-AACTATT-AGAAATT-TCTTTTAGGGTCACC
13312629 AATTGGCTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
59 6 0.13
60 40 0.85
61 1 0.02
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.35
Consensus pattern (59 bp):
ATGAAAAATTATAAAACAATCATCCAACTATTAGAAATTTCTTTTAGGGTCACCTAACT
Found at i:13313397 original size:17 final size:17
Alignment explanation
Indices: 13313354--13313398 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
13313344 TTGAATTTAC
*
13313354 AAAATTATTATAAATTT
1 AAAATAATTATAAATTT
*
13313371 AAAATTATTATAAATTT
1 AAAATAATTATAAATTT
*
13313388 AAAGTAATTAT
1 AAAATAATTAT
13313399 GTTAAATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
AAAATAATTATAAATTT
Found at i:13313398 original size:20 final size:17
Alignment explanation
Indices: 13313354--13313390 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
13313344 TTGAATTTAC
13313354 AAAATTATTATAAATTT
1 AAAATTATTATAAATTT
13313371 AAAATTATTATAAATTT
1 AAAATTATTATAAATTT
13313388 AAA
1 AAA
13313391 GTAATTATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATTATTATAAATTT
Found at i:13317370 original size:25 final size:25
Alignment explanation
Indices: 13317342--13317394 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
13317332 ACAAGTAATG
13317342 AAGACTCCAAACATTTTTGTTCAAC
1 AAGACTCCAAACATTTTTGTTCAAC
13317367 AAGACTCCAAACATTTTTGTTCAAC
1 AAGACTCCAAACATTTTTGTTCAAC
13317392 AAG
1 AAG
13317395 TACTTAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.30
Consensus pattern (25 bp):
AAGACTCCAAACATTTTTGTTCAAC
Found at i:13319918 original size:20 final size:19
Alignment explanation
Indices: 13319888--13319925 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
13319878 GATTTATAAA
13319888 ATTAAAATTAATAAAAATC
1 ATTAAAATTAATAAAAATC
*
13319907 ATTAATAATTAATTAAAAT
1 ATTAA-AATTAATAAAAAT
13319926 ATAATTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTAAAATTAATAAAAATC
Found at i:13319931 original size:15 final size:16
Alignment explanation
Indices: 13319910--13319945 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
13319900 AAAAATCATT
13319910 AATAATTA-ATTAAAA
1 AATAATTATATTAAAA
*
13319925 TATAATTATATTAAAA
1 AATAATTATATTAAAA
13319941 AATAA
1 AATAA
13319946 AATCCAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AATAATTATATTAAAA
Found at i:13320940 original size:57 final size:57
Alignment explanation
Indices: 13320844--13320952 Score: 132
Period size: 57 Copynumber: 1.9 Consensus size: 57
13320834 ATCAAACTGA
* * * *
13320844 AAAAAAACTCACATACCAATTTGAATATTGAAGTCAAACTCAAGTATTAAATTAAGG
1 AAAAAAACTCACATACCAAATTGAACATTGAACTCAAACTCAAGTACTAAATTAAGG
* *
13320901 AAAAAAGCTCA-AGTACCAAATTGAACATTGAAACT-AAACTTAAGTACTAAAT
1 AAAAAAACTCACA-TACCAAATTGAACATTG-AACTCAAACTCAAGTACTAAAT
13320953 AGGATATTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
56 1 0.02
57 40 0.91
58 3 0.07
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (57 bp):
AAAAAAACTCACATACCAAATTGAACATTGAACTCAAACTCAAGTACTAAATTAAGG
Found at i:13321999 original size:18 final size:18
Alignment explanation
Indices: 13321972--13322064 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
13321962 TACGACCGTT
13321972 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
13321990 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
13322008 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
13322026 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
13322044 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
13322062 TAC
1 TAC
13322065 AGTAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:13327622 original size:29 final size:30
Alignment explanation
Indices: 13327590--13327647 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
13327580 TTCAACTGAG
13327590 TTTTTA-TATTTAATAATTTT-TTAAAATAT
1 TTTTTATTATTTAA-AATTTTATTAAAATAT
*
13327619 TTTTTATTTTTTAAAATTTTATTAAAATA
1 TTTTTATTATTTAAAATTTTATTAAAATA
13327648 ATATGTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTTTATTATTTAAAATTTTATTAAAATAT
Found at i:13331423 original size:30 final size:31
Alignment explanation
Indices: 13331373--13331433 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
13331363 CTAACACGGT
13331373 TAAATTATGATCTCAAA-TTTTAAAATATTC
1 TAAATTATGATCTCAAATTTTTAAAATATTC
* *
13331403 TAAATT-TGATCTACATATTTTTAATATATTC
1 TAAATTATGATCT-CAAATTTTTAAAATATTC
13331434 AATATTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 6 0.22
30 9 0.33
31 12 0.44
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.48
Consensus pattern (31 bp):
TAAATTATGATCTCAAATTTTTAAAATATTC
Found at i:13343344 original size:52 final size:52
Alignment explanation
Indices: 13343273--13343470 Score: 309
Period size: 52 Copynumber: 3.9 Consensus size: 52
13343263 ATCAAGTGAC
*
13343273 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
*
13343325 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC------
1 AAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
*
13343371 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
* *
13343423 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGAGACAA
1 AAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
13343471 AGTGATAAGT
Statistics
Matches: 133, Mismatches: 7, Indels: 12
0.88 0.05 0.08
Matches are distributed among these distances:
46 44 0.33
52 89 0.67
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (52 bp):
AAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
Found at i:13343378 original size:98 final size:98
Alignment explanation
Indices: 13343259--13343481 Score: 437
Period size: 98 Copynumber: 2.3 Consensus size: 98
13343249 TTTGAGTACT
13343259 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
13343324 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
13343357 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
13343422 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
*
13343455 TCTGATCAAGAGACAAAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
13343482 GCTACACTTA
Statistics
Matches: 124, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 124 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:13343388 original size:46 final size:46
Alignment explanation
Indices: 13343325--13343480 Score: 231
Period size: 46 Copynumber: 3.3 Consensus size: 46
13343315 TGACAAGTGG
13343325 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC
* *
13343371 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC
*
13343417 AAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 ------AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC
13343469 AAAGTGATAAGT
1 AAAGTGATAAGT
13343481 GGCTACACTT
Statistics
Matches: 99, Mismatches: 5, Indels: 12
0.85 0.04 0.10
Matches are distributed among these distances:
46 56 0.57
52 43 0.43
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (46 bp):
AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC
Found at i:13343494 original size:37 final size:37
Alignment explanation
Indices: 13343444--13343553 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
13343434 TAATAGCTTC
*
13343444 GGCTATACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
* *
13343481 GGCTACACTTATCTGATCAAGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
*
13343518 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
13343553 G
1 G
13343554 ATCATACGTA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.25
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
Found at i:13345559 original size:22 final size:23
Alignment explanation
Indices: 13345495--13345559 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 23
13345485 ATTATATGTG
*
13345495 TATATATTATGTAAAACGTTTTAA
1 TATATATTATG-AAAATGTTTTAA
*
13345519 TATTATATTAT-ATATATGTTTT-A
1 TA-TATATTATGA-AAATGTTTTAA
*
13345542 TATATATTATGAACATGT
1 TATATATTATGAAAATGT
13345560 ATTTTCAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
22 13 0.37
23 5 0.14
24 9 0.26
25 8 0.23
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (23 bp):
TATATATTATGAAAATGTTTTAA
Found at i:13349577 original size:126 final size:126
Alignment explanation
Indices: 13349352--13349859 Score: 588
Period size: 126 Copynumber: 3.9 Consensus size: 126
13349342 AGACATACTA
** * * * *
13349352 TTGGACAAAGCTAACTCTTATTTAAGTGTTGCCTTAGGCATGCATATACCATCTCTTATACAAAG
1 TTGGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTATACAAAG
13349417 AGTTGGCCAAAGCATATGTTGACAAGTCTATCCCAACACTTAGGAAAGTGTTGGCATAGTC
66 AGTTGGCCAAAGCATATGTTGACAAGTCTATCCCAACACTTAGGAAAGTGTTGGCATAGTC
* **
13349478 TTGGACAAAACCGACTCTTATTTAAAAGTTGCCTTAGGCATGCATATCCCAACCCTTATACAAAG
1 TTGGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTATACAAAG
** *
13349543 AGTTGGCCAAAGTGTATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTTGACCCAAATGTGT
66 AGTTGGCCAAAGCATATGTTGACAAGTCTATCCCAACACTTAGGAAA-----G-------TGT-T
*
13349608 AGGCATAGTG
118 -GGCATAGTC
* * *
13349618 TTCGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAAGCATGCATATCCCAACCCTTATACAAAA
1 TTGGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTATACAAAG
* * * * * * * *
13349683 AGTTGACCAAA-AAGTATGTCGACAAGTCTATCCCAACACTTAGGAAAATGTCGTCTTAGGAC
66 AGTTGGCCAAAGCA-TATGTTGACAAGTCTATCCCAACACTTAGGAAAGTGTTGGCATA-GTC
* * * * *
13349745 -TGGACAAAGCCAACTCTTATTTAAGCGTTGTCTTAGGCATACATATCGCAACCCTTATGCAAAG
1 TTGGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTATACAAAG
*
13349809 AGTTGGCCAAAGCATATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGT
66 AGTTGGCCAAAGCATATGTTGACAAGTCTATCCCAACACTTAGGAAAGTGT
13349860 CGCCCCAAAA
Statistics
Matches: 323, Mismatches: 42, Indels: 34
0.81 0.11 0.09
Matches are distributed among these distances:
126 205 0.63
127 2 0.01
128 3 0.01
131 1 0.00
138 3 0.01
139 1 0.00
140 108 0.33
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.28
Consensus pattern (126 bp):
TTGGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTATACAAAG
AGTTGGCCAAAGCATATGTTGACAAGTCTATCCCAACACTTAGGAAAGTGTTGGCATAGTC
Found at i:13349721 original size:140 final size:138
Alignment explanation
Indices: 13349464--13349960 Score: 509
Period size: 140 Copynumber: 3.6 Consensus size: 138
13349454 ACTTAGGAAA
* * * * ** *
13349464 GTGTTGGCATAGTCTTGGACAAAACCGACTCTTATTTAAAAGTTGCCTTAGGCATGCATATCCCA
1 GTGTAGGCATAGTGTT-GACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATACATATCCCA
**
13349529 ACCCTTATACAAAGAGTTGGCCAAAGTGTATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGT
65 ACCCTTATACAAAGAGTTGGCCAAAAAGTATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGT
13349594 TGACCCAAAT
130 TG-CCCAAAT
* * *
13349604 GTGTAGGCATAGTGTTCGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAAGCATGCATATCCCA
1 GTGTAGGCATAGTGTT-GACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATACATATCCCA
* * * * *
13349669 ACCCTTATACAAAAAGTTGACCAAAAAGTATGTCGACAAGTCTATCCCAACACTTAGGAAAATG-
65 ACCCTTATACAAAGAGTTGGCCAAAAAGTATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGT
*
13349733 T---C--GT
130 TGCCCAAAT
* * * *
13349737 CT-TAGG---ACTG--GACAAAGCCAACTCTTATTTAAGCGTTGTCTTAGGCATACATATCGCAA
1 GTGTAGGCATAGTGTTGACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATACATATCCCAA
* *
13349796 CCCTTATGCAAAGAGTTGGCCAAAGCA-TATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGT
66 CCCTTATACAAAGAGTTGGCCAAA-AAGTATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGT
* *
13349860 CGCCCCAAAA
130 TG-CCCAAAT
* * * * * * * *
13349870 ATGTCGTCTTAG-GACTAGACAAAAGCCAACTCTTATTTAAGCGTTGTCTTAGGTATACATATCA
1 GTGTAGGCATAGTG--TTGAC-AAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATACATATCC
*
13349934 CAACCCTTATGCAAAGAGTTGGCCAAA
63 CAACCCTTATACAAAGAGTTGGCCAAA
13349961 GCATACAACA
Statistics
Matches: 302, Mismatches: 38, Indels: 33
0.81 0.10 0.09
Matches are distributed among these distances:
126 98 0.32
127 1 0.00
129 3 0.01
131 1 0.00
132 4 0.01
133 3 0.01
134 2 0.01
135 1 0.00
136 1 0.00
137 1 0.00
139 1 0.00
140 118 0.39
141 68 0.23
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (138 bp):
GTGTAGGCATAGTGTTGACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATACATATCCCAA
CCCTTATACAAAGAGTTGGCCAAAAAGTATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTT
GCCCAAAT
Found at i:13349829 original size:266 final size:265
Alignment explanation
Indices: 13349355--13350249 Score: 881
Period size: 266 Copynumber: 3.4 Consensus size: 265
13349345 CATACTATTG
* * * * *
13349355 GACAAAGCTAACTCTTATTTAAGTGTTGCCTTAGGCATGCATATACCATCTCTTATACAAAGAGT
1 GACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTATACAAAGAGT
* * * * * *
13349420 TGGCCAAAGCA-TATGTTGACAAGTCTATCCCAACACTTAGGAAAGTGTTGGCATA-GTCTTGGA
66 TGGCCAAA-AAGTATG-TGACAAGTCTATCCCAACACTTAGGAAAATGTCGTCTTAGGAC-TGGA
* * ** * * * *
13349483 CAAAACCGACTCTTATTTAAAAGTTGCCTTAGGCATGCATATCCCAACCCTTATACAAAGAGTTG
128 CAAAGCCAACTCTTATTTAAGCGTTGTCTTAGGCATACATATCACAACCCTTATGCAAAGAGTTG
** * **
13349548 GCCAAAGTGTATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTTGACCCAAATGTGTAGGCA
193 GCCAAAGCATATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGACCCAAAAATGTAGGCA
* *
13349613 TAGTG-TTC
258 TAG-GACTA
* * *
13349621 GACAAAGCCGACTCTTATTTAAGCGTTGCCTTAAGCATGCATATCCCAACCCTTATACAAAAAGT
1 GACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTATACAAAGAGT
*
13349686 TGACCAAAAAGTATGTCGACAAGTCTATCCCAACACTTAGGAAAATGTCGTCTTAGGACTGGACA
66 TGGCCAAAAAGTATGT-GACAAGTCTATCCCAACACTTAGGAAAATGTCGTCTTAGGACTGGACA
*
13349751 AAGCCAACTCTTATTTAAGCGTTGTCTTAGGCATACATATCGCAACCCTTATGCAAAGAGTTGGC
130 AAGCCAACTCTTATTTAAGCGTTGTCTTAGGCATACATATCACAACCCTTATGCAAAGAGTTGGC
* * * *
13349816 CAAAGCATATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGCCCCAAAAATGTCGTCTTA
195 CAAAGCATATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGACCCAAAAATGTAGGCATA
13349881 GGACTA
260 GGACTA
* * * * *
13349887 GACAAAAGCCAACTCTTATTTAAGCGTTGTCTTAGGTATACATATCACAACCCTTATGCAAAGAG
1 GAC-AAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTATACAAAGAG
* ** *** * * *
13349952 TTGGCC--AAAGCA--T-ACAACACT-TAGGAA-AGTGTCGCCCCAAAAGTGTCGTCTTAGGACT
65 TTGGCCAAAAAGTATGTGACAAGTCTATCCCAACACT-TAG---GAAAA-TGTCGTCTTAGGACT
** *
13350010 ACACAAAAGCCAACTCTTATTTAAGCGTTGTCTTAGGTATACATATCACAACCCTTATGCAAAGA
125 GGAC-AAAGCCAACTCTTATTTAAGCGTTGTCTTAGGCATACATATCACAACCCTTATGCAAAGA
* * *
13350075 GTTGGCC--A--A-A-----GC-A---TA---CAACACTTAGGAAAGTGTCGCCCCAAAAGTGTC
189 GTTGGCCAAAGCATATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGACCCAAAAATGTA
* *
13350123 GTCTTAGGACTA
254 GGCATAGGACTA
* * * *
13350135 GACAAAGCCAACTCTTATTTAAGCGTTGTCTTAGTCATGCATATCCCAACCTTTATACAAATAGT
1 GACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTATACAAAGAGT
** * * * *
13350200 TGGCCAAAGCGTATATTGGCCAGTCTATCCCAACACTTAGGAAAGTGTCG
66 TGGCCAAAAAGTAT-GTGACAAGTCTATCCCAACACTTAGGAAAATGTCG
13350250 CCACAAAAGT
Statistics
Matches: 532, Mismatches: 78, Indels: 54
0.80 0.12 0.08
Matches are distributed among these distances:
247 60 0.11
248 47 0.09
249 3 0.01
250 5 0.01
251 5 0.01
252 1 0.00
253 4 0.01
254 6 0.01
255 4 0.01
259 2 0.00
260 6 0.01
261 7 0.01
263 6 0.01
264 17 0.03
265 73 0.14
266 226 0.42
267 60 0.11
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (265 bp):
GACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTATACAAAGAGT
TGGCCAAAAAGTATGTGACAAGTCTATCCCAACACTTAGGAAAATGTCGTCTTAGGACTGGACAA
AGCCAACTCTTATTTAAGCGTTGTCTTAGGCATACATATCACAACCCTTATGCAAAGAGTTGGCC
AAAGCATATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGACCCAAAAATGTAGGCATAG
GACTA
Found at i:13349861 original size:126 final size:126
Alignment explanation
Indices: 13349621--13350249 Score: 558
Period size: 124 Copynumber: 4.9 Consensus size: 126
13349611 CATAGTGTTC
* * * * * * *
13349621 GACAAAGCCGACTCTTATTTAAGCGTTGCCTTAAGCATGCATATCCCAACCCTTATACAAAAAGT
1 GACAAAGCCAACTCTTATTTAAGCGTTGTCTTAGGCATACATATCACAACCCTTATGCAAAGAGT
* * * * * * *
13349686 TGACCAAA-AAGTATGTCGACAAGTCTATCCCAACACTTAGGAAAATGTCGTCTTAGGACTG
66 TGGCCAAAGCA-TATCTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGTCTTAGGACTA
*
13349747 GACAAAGCCAACTCTTATTTAAGCGTTGTCTTAGGCATACATATCGCAACCCTTATGCAAAGAGT
1 GACAAAGCCAACTCTTATTTAAGCGTTGTCTTAGGCATACATATCACAACCCTTATGCAAAGAGT
*
13349812 TGGCCAAAGCATATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGCCCCAAAAATGTCGT
66 TGGCCAAAGCATATCTTGGCAAGTCTATCCCAACACTTAGGAAA-----G---------TGTCGT
13349877 CTTAGGACTA
117 CTTAGGACTA
*
13349887 GACAAAAGCCAACTCTTATTTAAGCGTTGTCTTAGGTATACATATCACAACCCTTATGCAAAGAG
1 GAC-AAAGCCAACTCTTATTTAAGCGTTGTCTTAGGCATACATATCACAACCCTTATGCAAAGAG
* * *
13349952 TTGGCCAAAGCATACAACACTTAGGAAAG--TGTCGCC--C-C--A--AAAGTGTCGTCTTAGGA
65 TTGGCCAAAGCAT---A-TCTT-GGCAAGTCTATC-CCAACACTTAGGAAAGTGTCGTCTTAGGA
13350008 CTA
124 CTA
* *
13350011 CACAAAAGCCAACTCTTATTTAAGCGTTGTCTTAGGTATACATATCACAACCCTTATGCAAAGAG
1 GAC-AAAGCCAACTCTTATTTAAGCGTTGTCTTAGGCATACATATCACAACCCTTATGCAAAGAG
* * *
13350076 TTGGCCAAAGCATACAACACTTAGGAAAG--TGTCGCC--C-C--A--AAAGTGTCGTCTTAGGA
65 TTGGCCAAAGCAT---A-TCTT-GGCAAGTCTATC-CCAACACTTAGGAAAGTGTCGTCTTAGGA
13350132 CTA
124 CTA
* * * * * *
13350135 GACAAAGCCAACTCTTATTTAAGCGTTGTCTTAGTCATGCATATCCCAACCTTTATACAAATAGT
1 GACAAAGCCAACTCTTATTTAAGCGTTGTCTTAGGCATACATATCACAACCCTTATGCAAAGAGT
* * *
13350200 TGGCCAAAGCGTATATTGGCCAGTCTATCCCAACACTTAGGAAAGTGTCG
66 TGGCCAAAGCATATCTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTCG
13350250 CCACAAAAGT
Statistics
Matches: 438, Mismatches: 34, Indels: 62
0.82 0.06 0.12
Matches are distributed among these distances:
118 4 0.01
119 4 0.01
120 4 0.01
121 1 0.00
122 1 0.00
123 66 0.15
124 142 0.32
126 105 0.24
127 1 0.00
133 1 0.00
138 3 0.01
140 19 0.04
141 72 0.16
142 1 0.00
143 1 0.00
144 4 0.01
145 4 0.01
146 5 0.01
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (126 bp):
GACAAAGCCAACTCTTATTTAAGCGTTGTCTTAGGCATACATATCACAACCCTTATGCAAAGAGT
TGGCCAAAGCATATCTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGTCTTAGGACTA
Found at i:13350062 original size:124 final size:124
Alignment explanation
Indices: 13349842--13350209 Score: 650
Period size: 124 Copynumber: 3.0 Consensus size: 124
13349832 AAGTCTATCC
*
13349842 CAACACTTAGGAAAGTGTCGCCCCAAAAATGTCGTCTTAGGACTAGACAAAAGCCAACTCTTATT
1 CAACACTTAGGAAAGTGTCGCCCCAAAAGTGTCGTCTTAGGACTAGACAAAAGCCAACTCTTATT
13349907 TAAGCGTTGTCTTAGGTATACATATCACAACCCTTATGCAAAGAGTTGGCCAAAGCATA
66 TAAGCGTTGTCTTAGGTATACATATCACAACCCTTATGCAAAGAGTTGGCCAAAGCATA
*
13349966 CAACACTTAGGAAAGTGTCGCCCCAAAAGTGTCGTCTTAGGACTACACAAAAGCCAACTCTTATT
1 CAACACTTAGGAAAGTGTCGCCCCAAAAGTGTCGTCTTAGGACTAGACAAAAGCCAACTCTTATT
13350031 TAAGCGTTGTCTTAGGTATACATATCACAACCCTTATGCAAAGAGTTGGCCAAAGCATA
66 TAAGCGTTGTCTTAGGTATACATATCACAACCCTTATGCAAAGAGTTGGCCAAAGCATA
13350090 CAACACTTAGGAAAGTGTCGCCCCAAAAGTGTCGTCTTAGGACTAGAC-AAAGCCAACTCTTATT
1 CAACACTTAGGAAAGTGTCGCCCCAAAAGTGTCGTCTTAGGACTAGACAAAAGCCAACTCTTATT
* * * * *
13350154 TAAGCGTTGTCTTA-GTCATGCATATCCCAACCTTTATACAAATAGTTGGCCAAAGC
66 TAAGCGTTGTCTTAGGT-ATACATATCACAACCCTTATGCAAAGAGTTGGCCAAAGC
13350210 GTATATTGGC
Statistics
Matches: 235, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
122 2 0.01
123 64 0.27
124 169 0.72
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (124 bp):
CAACACTTAGGAAAGTGTCGCCCCAAAAGTGTCGTCTTAGGACTAGACAAAAGCCAACTCTTATT
TAAGCGTTGTCTTAGGTATACATATCACAACCCTTATGCAAAGAGTTGGCCAAAGCATA
Found at i:13355346 original size:91 final size:91
Alignment explanation
Indices: 13354731--13355373 Score: 304
Period size: 93 Copynumber: 7.1 Consensus size: 91
13354721 TTTTTTAAAT
* * *
13354731 ATAATAATTTTCATAATTA-TCTTGAAAA-ATTAAAAAAAATATTTTTGCA-CTACCATACTCAA
1 ATAATAATTTTTATAATTATTC-CGAAAATATT-AAAAATATA-TTTTG-AGC-ACCATACTCAA
** * * *
13354793 GCTAAAGTGTTCC-AAAGATAAAATATTATAA
61 GCCCAAGTCTCCCGAAA-ATAAAATATAATAA
* * * * * * *
13354824 ACAATAATTTTTACAACTATTCCAAAAAAAAATT-AAAATAT-TCTT-AGGCATCATACTCAAAG
1 ATAATAATTTTTATAATTATTCC--GAAAATATTAAAAATATATTTTGA-GCACCATACTC-AAG
* * ** * *
13354886 TCCAAGTGTCCCGAAAATGGAACATAACAA
62 CCCAAGTCTCCCGAAAATAAAATATAATAA
* *** * *
13354916 ATAATAATTTTTACAATTA-TCTTTAAA-A--AAAAATAT-TTTTGCACCACCATACTCAAGGAC
1 ATAATAATTTTTATAATTATTCCGAAAATATTAAAAATATATTTTG-AGCACCATACTCAA-GCC
*
13354976 C---T-T---GAAAAT-GAATATAATAA
64 CAAGTCTCCCGAAAATAAAATATAATAA
* * * *
13354996 ATAAT-TTTTTTATAATTATTCCGAAAA-ATTAAGAATATATTTTGTA-CTACTATACTCAAACC
1 ATAATAATTTTTATAATTATTCCGAAAATATTAAAAATATATTTTG-AGC-ACCATACTCAAGCC
* *
13355058 CAAGTATCCCGAAAATGAAATATAATAA
64 CAAGTCTCCCGAAAATAAAATATAATAA
* * *
13355086 ATAATAATTTTTACAATTATCTCC-AAAA-ATTTAAAATATATGTTCAT-AGCATCATACTCAAG
1 ATAATAATTTTTATAATTAT-TCCGAAAATATTAAAAATATAT-TT--TGAGCACCATACTCAAG
* ** * * *
13355148 TCCAAGTGCT-TTGAAAAATGATATATAGTAA
62 CCCAAGT-CTCCCG-AAAATAAAATATAATAA
* * * * * * *
13355179 ACAATAATTTTCATAATTATCCCGAAAA-AGTAAAAAAAATATTTTTGCACCACCATACTCAAGT
1 ATAATAATTTTTATAATTATTCCGAAAATA-TTAAAAATATA-TTTTG-AGCACCATACTCAAGC
** * * *
13355243 TAAAAT-TACCCGAAGATAAAATATTATAA
63 CCAAGTCT-CCCGAAAATAAAATATAATAA
* * *
13355272 ATAATAATTTTTATAATTATTCTGAAAATTTTAAAAATAT-TTTTCGGGCACCATACTCAAGCCC
1 ATAATAATTTTTATAATTATTCCGAAAATATTAAAAATATATTTT-GAGCACCATACTCAAGCCC
* *
13355336 AAGTCTCCCGAAAATAAAATGTAAAAA
65 AAGTCTCCCGAAAATAAAATATAATAA
13355363 ATAA-AATTTTT
1 ATAATAATTTTT
13355374 TATATATAGT
Statistics
Matches: 418, Mismatches: 89, Indels: 89
0.70 0.15 0.15
Matches are distributed among these distances:
79 11 0.03
80 20 0.05
81 6 0.01
82 10 0.02
83 16 0.04
84 1 0.00
85 2 0.00
86 1 0.00
87 12 0.03
88 13 0.03
89 10 0.02
90 23 0.06
91 78 0.19
92 69 0.17
93 101 0.24
94 37 0.09
95 5 0.01
96 3 0.01
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (91 bp):
ATAATAATTTTTATAATTATTCCGAAAATATTAAAAATATATTTTGAGCACCATACTCAAGCCCA
AGTCTCCCGAAAATAAAATATAATAA
Found at i:13355977 original size:19 final size:19
Alignment explanation
Indices: 13355950--13355986 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
13355940 TCTTCATTGA
*
13355950 ATTTATAAAAATATTTAAT
1 ATTTATAAAAAAATTTAAT
*
13355969 ATTTGTAAAAAAATTTAA
1 ATTTATAAAAAAATTTAA
13355987 AGTAGAAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (19 bp):
ATTTATAAAAAAATTTAAT
Found at i:13361442 original size:22 final size:22
Alignment explanation
Indices: 13361394--13361439 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
13361384 AAATGAGAGG
*
13361394 TTTAATTAAAATTTTTGAGAAA
1 TTTAATGAAAATTTTTGAGAAA
*
13361416 ATTAATGAAAATTTTTGA-AAA
1 TTTAATGAAAATTTTTGAGAAA
13361437 TTT
1 TTT
13361440 TAAAGGGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (22 bp):
TTTAATGAAAATTTTTGAGAAA
Found at i:13365846 original size:21 final size:21
Alignment explanation
Indices: 13365822--13365861 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13365812 TAATATTTAT
*
13365822 ATATTTTATAATAA-AATTAGA
1 ATATATTATAA-AATAATTAGA
13365843 ATATATTATAAAATAATTA
1 ATATATTATAAAATAATTA
13365862 TTTAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
ATATATTATAAAATAATTAGA
Found at i:13373015 original size:2 final size:2
Alignment explanation
Indices: 13373008--13373039 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
13372998 AATAGTAAAA
13373008 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
13373040 GAAGTCCTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13375831 original size:23 final size:24
Alignment explanation
Indices: 13375786--13375833 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
13375776 TAATTTTATT
* *
13375786 ATTTAAAAAAATTTAAAGGGATTA
1 ATTTAAAAAAATTAAAAGAGATTA
*
13375810 ATTT-AAAAAATTAAAATAGATTA
1 ATTTAAAAAAATTAAAAGAGATTA
13375833 A
1 A
13375834 AAATAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (24 bp):
ATTTAAAAAAATTAAAAGAGATTA
Found at i:13377269 original size:122 final size:118
Alignment explanation
Indices: 13377066--13377286 Score: 327
Period size: 122 Copynumber: 1.8 Consensus size: 118
13377056 CCATTTTTGG
*
13377066 GTGATTGAATTAAAGGGGTTTTTTTTTTGAGCTTTAAGGATTTGATTTTTTGTTTTTACACTTAA
1 GTGATTGAATTAAAGGGATTTTTTTTTTGAGCTTTAAGGATTTGATTTTTTGTTTTTACACTTAA
*
13377131 ATGATTATTACCTGTATGCCAATGGAAATGTATGGACTAAAAACCATTTTCAT
66 ATGATTATTACATGTATGCCAATGGAAATGTATGGACTAAAAACCATTTTCAT
* *
13377184 GTGATTGAATTGAAGGGATTTTTTTTTCTGAGCTTTTAAGGTTTTGATTTTTTTGTTTTTTACAC
1 GTGATTGAATTAAAGGGATTTTTTTTT-TGAGC-TTTAAGGATTTGA-TTTTTTG-TTTTTACAC
* * *
13377249 TTTTAA-GATTATTGCATGTATGCCATTGGAAATGTATG
62 -TTAAATGATTATTACATGTATGCCAATGGAAATGTATG
13377287 AACAACCTTT
Statistics
Matches: 91, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
118 25 0.27
119 5 0.05
120 12 0.13
121 7 0.08
122 38 0.42
123 4 0.04
ACGTcount: A:0.26, C:0.08, G:0.19, T:0.47
Consensus pattern (118 bp):
GTGATTGAATTAAAGGGATTTTTTTTTTGAGCTTTAAGGATTTGATTTTTTGTTTTTACACTTAA
ATGATTATTACATGTATGCCAATGGAAATGTATGGACTAAAAACCATTTTCAT
Found at i:13383413 original size:10 final size:10
Alignment explanation
Indices: 13383398--13383423 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
13383388 TGGAATTGGG
13383398 AAAAAAAAAC
1 AAAAAAAAAC
13383408 AAAAAAAAAC
1 AAAAAAAAAC
13383418 AAAAAA
1 AAAAAA
13383424 CAAAACAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:13386313 original size:4 final size:4
Alignment explanation
Indices: 13386304--13386344 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
13386294 AATAAGTAAC
13386304 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
13386345 AATTTGAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (4 bp):
ATTA
Found at i:13398095 original size:42 final size:42
Alignment explanation
Indices: 13398037--13398132 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
13398027 GGCTACTTAT
** *
13398037 TGCAA-CCCATTTCAATATCACAT-ATAATGTCAATGGATGTA
1 TGCAAGCCCATTTCAATATCACATGA-AATACCAATGAATGTA
*
13398078 TGCAAGCCCATTTCAATATCATATGAAATACCAATGAATGTA
1 TGCAAGCCCATTTCAATATCACATGAAATACCAATGAATGTA
13398120 TGCAAGCCCATTT
1 TGCAAGCCCATTT
13398133 GGGGAGACTA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
41 5 0.10
42 43 0.88
43 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.30
Consensus pattern (42 bp):
TGCAAGCCCATTTCAATATCACATGAAATACCAATGAATGTA
Found at i:13398348 original size:26 final size:26
Alignment explanation
Indices: 13398264--13398399 Score: 190
Period size: 26 Copynumber: 5.3 Consensus size: 26
13398254 CTGGAGGCCT
13398264 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
**
13398288 AGCCCTTTTCGGTAAACTGGGGCA-A
1 AGCCCTTTTCAATAAACTGGGGCATA
13398313 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
**
13398339 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
13398365 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
*
13398391 AGCTCTTTT
1 AGCCCTTTT
13398400 GCACTTCCTC
Statistics
Matches: 100, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.05
24 5 0.05
25 33 0.33
26 57 0.57
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:13398388 original size:52 final size:51
Alignment explanation
Indices: 13398264--13398399 Score: 224
Period size: 52 Copynumber: 2.7 Consensus size: 51
13398254 CTGGAGGCCT
13398264 AGCCTCTTTT-AAT-AACTGGGGCA-AAGCCCTTTTCGGTAAACTGGGGCAA
1 AGCC-CTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCAA
13398313 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCA-A
*
13398365 AGCCCTTTTCAATAAACTGGGGCATAAGCTCTTTT
1 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTT
13398400 GCACTTCCTC
Statistics
Matches: 82, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
48 5 0.06
49 7 0.09
50 10 0.12
51 25 0.30
52 35 0.43
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (51 bp):
AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCAA
Found at i:13398499 original size:5 final size:5
Alignment explanation
Indices: 13398489--13398515 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
13398479 GTGAGCATTC
13398489 AATCG AATCG AATCG AATCG AATCG AA
1 AATCG AATCG AATCG AATCG AATCG AA
13398516 AATTTTCGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
AATCG
Found at i:13400806 original size:27 final size:27
Alignment explanation
Indices: 13400776--13400971 Score: 141
Period size: 27 Copynumber: 7.3 Consensus size: 27
13400766 TTTCATCCTG
* * *
13400776 CAAGGGTGTTTTGGTAAATCTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
**
13400803 CAAGGGTATTTCT-GTAATTTTGTAAAT
1 CAAGGGTATTT-TGGTAATTTTACAAAT
* *
13400830 CAGGGGTATTTTGGTAACTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
** *
13400857 TGAGGGTATTTCGGTAATTTTACAAA-
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
13400883 CCAGTGGTATTTTGGTAATTTTACAAA-
1 CAAG-GGTATTTTGGTAATTTTACAAAT
* * * * **
13400910 CTAGGGGTGTTATGGTAATTCTACCCTAT
1 C-AAGGGTATTTTGGTAATTTTA-CAAAT
* **
13400939 -AGGGGTATTTCAGTAATTTTAC-AAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
13400964 CAAGGGTA
1 CAAGGGTA
13400972 AAACAGTAAT
Statistics
Matches: 131, Mismatches: 31, Indels: 15
0.74 0.18 0.08
Matches are distributed among these distances:
25 2 0.02
26 10 0.08
27 115 0.88
28 4 0.03
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.38
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAT
Found at i:13400854 original size:54 final size:54
Alignment explanation
Indices: 13400779--13400909 Score: 163
Period size: 54 Copynumber: 2.4 Consensus size: 54
13400769 CATCCTGCAA
* * * ** *
13400779 GGGTGTTTTGGTAAATCTACAAATCAAGGGTATTTCTGTAATTTTGTAAATCAG
1 GGGTATTTTGGTAAATTTACAAATCAAGGGTATTTCGGTAATTTTACAAACCAG
* **
13400833 GGGTATTTTGGTAACTTTACAAATTGAGGGTATTTCGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAAATTTACAAATCAAGGGTATTTCGGTAATTTTACAAACCAG
* *
13400887 TGGTATTTTGGTAATTTTACAAA
1 GGGTATTTTGGTAAATTTACAAA
13400910 CTAGGGGTGT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 66 1.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (54 bp):
GGGTATTTTGGTAAATTTACAAATCAAGGGTATTTCGGTAATTTTACAAACCAG
Found at i:13400991 original size:27 final size:27
Alignment explanation
Indices: 13400949--13401052 Score: 149
Period size: 27 Copynumber: 3.9 Consensus size: 27
13400939 AGGGGTATTT
13400949 CAGTAA-TTT-TACAATCAAGGGTAAAA
1 CAGTAATTTTGTA-AATCAAGGGTAAAA
13400975 CAGTAATTTTGTAAATCAAGGGTAAAA
1 CAGTAATTTTGTAAATCAAGGGTAAAA
*
13401002 CAGTAATTTTGTAAATCGAGGGTAAAA
1 CAGTAATTTTGTAAATCAAGGGTAAAA
* * *
13401029 TAGTAATTTTATAAATCGAGGGTA
1 CAGTAATTTTGTAAATCAAGGGTA
13401053 GAACGCCCCC
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
26 6 0.08
27 65 0.89
28 2 0.03
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (27 bp):
CAGTAATTTTGTAAATCAAGGGTAAAA
Found at i:13401368 original size:27 final size:27
Alignment explanation
Indices: 13401338--13401593 Score: 140
Period size: 27 Copynumber: 9.4 Consensus size: 27
13401328 GTAATTTCAC
**
13401338 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACAGTAATTTTGTA
* *
13401365 AATCAAGTGTAAAACAGTAATTTTGTA
1 AATCGAGGGTAAAACAGTAATTTTGTA
* *
13401392 AATCGAGGGTAAAACAGTAATTCTATA
1 AATCGAGGGTAAAACAGTAATTTTGTA
*****
13401419 AATCGAGGGTACTTTGGTAATTTT-TA
1 AATCGAGGGTAAAACAGTAATTTTGTA
* *** **
13401445 CAAGTCGAGTGTATTTCAGTAATTTTACA
1 -AA-TCGAGGGTAAAACAGTAATTTTGTA
**** **
13401474 AATC-ATGGGGTATTTTAGTAATTTTACA
1 AATCGA--GGGTAAAACAGTAATTTTGTA
* ****
13401502 AA-CCAGGGGTATTTTAGTAATTTTGTA
1 AATCGA-GGGTAAAACAGTAATTTTGTA
* *
13401529 AATCGAGGGTAAAACAGTAATTCTATA
1 AATCGAGGGTAAAACAGTAATTTTGTA
* * *
13401556 AATCGAGGGTAGAACGGTAATTCTGTA
1 AATCGAGGGTAAAACAGTAATTTTGTA
*
13401583 AATCGGGGGTA
1 AATCGAGGGTA
13401594 CTTTGGTAAA
Statistics
Matches: 188, Mismatches: 34, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
26 3 0.02
27 140 0.74
28 44 0.23
29 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.34
Consensus pattern (27 bp):
AATCGAGGGTAAAACAGTAATTTTGTA
Found at i:13401477 original size:55 final size:54
Alignment explanation
Indices: 13401406--13401539 Score: 137
Period size: 55 Copynumber: 2.4 Consensus size: 54
13401396 GAGGGTAAAA
* * ** *
13401406 CAGTAATTCTATAAATCGAGGGTACTTTGGTAATTTTTACAAGTC-GAGTGTATTT
1 CAGTAATTTTATAAATCGAGGGTACTTTAGTAA-TTTTACAAACCAG-GGGTATTT
* *
13401461 CAGTAATTTTACAAATC-ATGGGGTATTTTAGTAATTTTACAAACCAGGGGTATTT
1 CAGTAATTTTATAAATCGA--GGGTACTTTAGTAATTTTACAAACCAGGGGTATTT
* *
13401516 TAGTAATTTTGTAAATCGAGGGTA
1 CAGTAATTTTATAAATCGAGGGTA
13401540 AAACAGTAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
54 6 0.09
55 45 0.69
56 14 0.22
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (54 bp):
CAGTAATTTTATAAATCGAGGGTACTTTAGTAATTTTACAAACCAGGGGTATTT
Found at i:13401486 original size:28 final size:27
Alignment explanation
Indices: 13401455--13401525 Score: 115
Period size: 28 Copynumber: 2.6 Consensus size: 27
13401445 CAAGTCGAGT
* *
13401455 GTATTTCAGTAATTTTACAAATCATGGG
1 GTATTTTAGTAATTTTACAAACCA-GGG
13401483 GTATTTTAGTAATTTTACAAACCAGGG
1 GTATTTTAGTAATTTTACAAACCAGGG
13401510 GTATTTTAGTAATTTT
1 GTATTTTAGTAATTTT
13401526 GTAAATCGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 19 0.46
28 22 0.54
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (27 bp):
GTATTTTAGTAATTTTACAAACCAGGG
Found at i:13404950 original size:27 final size:29
Alignment explanation
Indices: 13404885--13404955 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 29
13404875 TAATTATTTG
13404885 AAAGTTTTTATTTAAGTCATTGAACTATT
1 AAAGTTTTTATTTAAGTCATTGAACTATT
*
13404914 CAAAAGTTTTTATTTAAGTCACTTG-GCTATT
1 --AAAGTTTTTATTTAAGTCA-TTGAACTATT
13404945 -AA-TTTTTATTT
1 AAAGTTTTTATTT
13404956 TTTTTTAAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
27 9 0.24
28 2 0.05
31 24 0.63
32 3 0.08
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (29 bp):
AAAGTTTTTATTTAAGTCATTGAACTATT
Found at i:13406829 original size:22 final size:23
Alignment explanation
Indices: 13406794--13406836 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
13406784 AAATTGAGAC
*
13406794 AAAAAAATCACAAGTATCAAACT
1 AAAAAAATCACAAGTACCAAACT
*
13406817 AAAAAAAT-TCAAGTACCAAA
1 AAAAAAATCACAAGTACCAAA
13406837 ATGAATACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.63, C:0.16, G:0.05, T:0.16
Consensus pattern (23 bp):
AAAAAAATCACAAGTACCAAACT
Found at i:13407501 original size:41 final size:41
Alignment explanation
Indices: 13407440--13407523 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
13407430 TTAACCTTCT
* *
13407440 ATTTAAGGATCTAACTCAACTCGACTTCTGATATAATCAAA
1 ATTTAAAGATCTAACCCAACTCGACTTCTGATATAATCAAA
*
13407481 ATTTAAAGATCTAACCCAACTCGTCTTCTGATATAATCAAA
1 ATTTAAAGATCTAACCCAACTCGACTTCTGATATAATCAAA
13407522 AT
1 AT
13407524 CCAATATCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.32
Consensus pattern (41 bp):
ATTTAAAGATCTAACCCAACTCGACTTCTGATATAATCAAA
Found at i:13415538 original size:17 final size:17
Alignment explanation
Indices: 13415516--13415548 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
13415506 TTTGGATAGA
13415516 AAATAACAAA-GAAAATC
1 AAATAA-AAAGGAAAATC
13415533 AAATAAAAAGGAAAAT
1 AAATAAAAAGGAAAAT
13415549 AGTGAAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.73, C:0.06, G:0.09, T:0.12
Consensus pattern (17 bp):
AAATAAAAAGGAAAATC
Found at i:13426100 original size:46 final size:44
Alignment explanation
Indices: 13426003--13426101 Score: 112
Period size: 45 Copynumber: 2.2 Consensus size: 44
13425993 ATAAATTATG
*
13426003 ATATAAAACTTAATTCAGTTTATTAAAATTTAATTAAAATATAAA
1 ATAT-AAACTTAATTCAGTTTATTAAAATTTAAATAAAATATAAA
*
13426048 ATTATAAACTTAATTCAGTTT-TT-AAATTATAAAATATAAATAATAGA
1 A-TATAAACTTAATTCAGTTTATTAAAATT-T-AAATA-AAAT-ATAAA
13426095 ATATAAA
1 ATATAAA
13426102 TTGTTCAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
43 5 0.11
44 3 0.06
45 21 0.45
46 13 0.28
47 5 0.11
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (44 bp):
ATATAAACTTAATTCAGTTTATTAAAATTTAAATAAAATATAAA
Found at i:13429558 original size:26 final size:26
Alignment explanation
Indices: 13429512--13429561 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
13429502 TTCGCTCTTT
13429512 TATATAATATAAACAATAATATATCG
1 TATATAATATAAACAATAATATATCG
13429538 TATATAA-ATAAGAC-ATAAATATAT
1 TATATAATATAA-ACAAT-AATATAT
13429562 TATCATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.34
Consensus pattern (26 bp):
TATATAATATAAACAATAATATATCG
Found at i:13429754 original size:21 final size:21
Alignment explanation
Indices: 13429711--13429754 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
13429701 ATATATTATG
* * * *
13429711 TATAAATAGTATAAATTACTA
1 TATAAATAATAAAAAATAATA
13429732 TATAAATAATAAAAAATAATA
1 TATAAATAATAAAAAATAATA
13429753 TA
1 TA
13429755 CATTATTATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (21 bp):
TATAAATAATAAAAAATAATA
Found at i:13431352 original size:3 final size:3
Alignment explanation
Indices: 13431344--13431375 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
13431334 TCTTAACAAT
13431344 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
13431376 TTACATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:13431607 original size:19 final size:20
Alignment explanation
Indices: 13431572--13431610 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
13431562 AATAAATAAT
13431572 TTAAAAATTATAAAATTTTA
1 TTAAAAATTATAAAATTTTA
13431592 TTAAAAATT-TAAAATTTTA
1 TTAAAAATTATAAAATTTTA
13431611 ACCATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAAAAATTATAAAATTTTA
Found at i:13433878 original size:15 final size:15
Alignment explanation
Indices: 13433858--13433887 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13433848 ATTTTAAGTA
*
13433858 ACTTTAGTTTTTTTT
1 ACTTTACTTTTTTTT
13433873 ACTTTACTTTTTTTT
1 ACTTTACTTTTTTTT
13433888 TGTTGTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.03, T:0.73
Consensus pattern (15 bp):
ACTTTACTTTTTTTT
Found at i:13433964 original size:11 final size:12
Alignment explanation
Indices: 13433936--13433964 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
13433926 TTTATTAATA
13433936 TAATTTAGTTCT
1 TAATTTAGTTCT
13433948 TAATTTAGTTC-
1 TAATTTAGTTCT
13433959 TAATTT
1 TAATTT
13433965 GTTTCAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.59
Consensus pattern (12 bp):
TAATTTAGTTCT
Found at i:13434107 original size:25 final size:22
Alignment explanation
Indices: 13434055--13434115 Score: 63
Period size: 25 Copynumber: 2.7 Consensus size: 22
13434045 CATTTTTTAT
*
13434055 TTTATTTTGTTTT-AATATTTG
1 TTTATTATGTTTTAAATATTTG
13434076 TTT-TTATGTTTTAAATGCATTTG
1 TTTATTATGTTTTAAAT--ATTTG
*
13434099 ATTTATTATATTTTAAA
1 -TTTATTATGTTTTAAA
13434116 CTTTTTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 8 0.24
21 6 0.18
23 5 0.15
24 3 0.09
25 11 0.33
ACGTcount: A:0.26, C:0.02, G:0.08, T:0.64
Consensus pattern (22 bp):
TTTATTATGTTTTAAATATTTG
Found at i:13434521 original size:16 final size:16
Alignment explanation
Indices: 13434478--13434521 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
13434468 CGAGAAAAAT
13434478 ATAATAATTATACTTA
1 ATAATAATTATACTTA
*
13434494 ATAATTAATTATATTTAA
1 ATAA-TAATTATACTT-A
13434512 ATAA-AATTAT
1 ATAATAATTAT
13434522 TAGTATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 10 0.40
17 10 0.40
18 5 0.20
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAATAATTATACTTA
Found at i:13438644 original size:30 final size:30
Alignment explanation
Indices: 13438610--13438683 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 30
13438600 ATTTAATAAA
13438610 TTAATAATATAATTAATA--TAATTATTTATT
1 TTAATAATATAATTAATATTTAA-T-TTTATT
*
13438640 TTAATAA-ATTATTTAATATTTCAATTTTATT
1 TTAATAATA-TAATTAATATTT-AATTTTATT
13438671 TTAATAATA-AATT
1 TTAATAATATAATT
13438684 TTAAAATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
29 1 0.03
30 18 0.49
31 13 0.35
32 3 0.08
33 2 0.05
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (30 bp):
TTAATAATATAATTAATATTTAATTTTATT
Found at i:13438693 original size:15 final size:14
Alignment explanation
Indices: 13438668--13438707 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
13438658 TTTCAATTTT
13438668 ATTTT-AATAATAA
1 ATTTTAAATAATAA
13438681 ATTTTAAAATAAT-A
1 ATTTT-AAATAATAA
13438695 ATTTTAAATAATA
1 ATTTTAAATAATA
13438708 TTCTTCACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 12 0.50
14 6 0.25
15 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAAATAATAA
Found at i:13439256 original size:20 final size:21
Alignment explanation
Indices: 13439230--13439280 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
13439220 TGTAAGAAAG
* *
13439230 TTATAAAAAATGTTAAAGAAA
1 TTATAAAAAATGTAAAAAAAA
**
13439251 -TATAAAAGTTGTAAAAAAAA
1 TTATAAAAAATGTAAAAAAAA
13439271 TTATAAAAAA
1 TTATAAAAAA
13439281 CTATTGTACC
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (21 bp):
TTATAAAAAATGTAAAAAAAA
Found at i:13439484 original size:22 final size:22
Alignment explanation
Indices: 13439458--13439504 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
13439448 TCAAAGCGTC
*
13439458 TTTTTGATGCA-TTTTATAAATT
1 TTTTTGATG-ATTTTTATAAAAT
*
13439480 TTTTTTATGATTTTTATAAAAT
1 TTTTTGATGATTTTTATAAAAT
13439502 TTT
1 TTT
13439505 ACAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (22 bp):
TTTTTGATGATTTTTATAAAAT
Found at i:13439542 original size:19 final size:19
Alignment explanation
Indices: 13439489--13439532 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
13439479 TTTTTTTATG
13439489 ATTTTTATAAAATTTTACA
1 ATTTTTATAAAATTTTACA
13439508 ATTTTTATAAAATTTTACA
1 ATTTTTATAAAATTTTACA
13439527 ATTTTT
1 ATTTTT
13439533 TTATATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTTATAAAATTTTACA
Found at i:13439586 original size:27 final size:28
Alignment explanation
Indices: 13439508--13439610 Score: 77
Period size: 28 Copynumber: 3.6 Consensus size: 28
13439498 AAATTTTACA
* *
13439508 ATTTTT-ATAAAATTTTACAATTTTTTTAT
1 ATTTTTAATAAAA-TTTA-AATATTTCTAT
* **
13439537 ATTTTT-TTACTATTTATACATATTTCTA-
1 ATTTTTAATAAAATTTA-A-ATATTTCTAT
* *
13439565 ATTTTTAATGAAATTTAAATATTTTTAT
1 ATTTTTAATAAAATTTAAATATTTCTAT
*
13439593 ATTTTTATTAAAATTTAA
1 ATTTTTAATAAAATTTAA
13439611 TAATTTTTTT
Statistics
Matches: 58, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
27 8 0.14
28 28 0.48
29 22 0.38
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (28 bp):
ATTTTTAATAAAATTTAAATATTTCTAT
Found at i:13439596 original size:28 final size:26
Alignment explanation
Indices: 13439556--13439618 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 26
13439546 CTATTTATAC
* *
13439556 ATATTTCTAATTTTTAATGAAATTTAA
1 ATATTTTTAATTTTTAATAAAATTT-A
*
13439583 ATATTTTTATATTTTTATTAAAATTTA
1 ATATTTTTA-ATTTTTAATAAAATTTA
13439610 ATAATTTTT
1 AT-ATTTTT
13439619 TTAACTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 11 0.35
28 20 0.65
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (26 bp):
ATATTTTTAATTTTTAATAAAATTTA
Found at i:13439628 original size:57 final size:57
Alignment explanation
Indices: 13439521--13439628 Score: 130
Period size: 57 Copynumber: 1.9 Consensus size: 57
13439511 TTTATAAAAT
* ** *
13439521 TTTACAATTTTTTTATATTTTTTTACTATTTATACATATTTCTAATTTTTAATGAAA
1 TTTACAATATTTTTATATTTTTTTAAAATTTATACATATTTCTAACTTTTAATGAAA
* *
13439578 TTTA-AATATTTTTATATTTTTATTAAAATTTAATA-ATTTTTTTAACTTTTA
1 TTTACAATATTTTTATATTTTT-TTAAAATTT-ATACATATTTCTAACTTTTA
13439629 TTTTTTATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
56 16 0.37
57 24 0.56
58 3 0.07
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (57 bp):
TTTACAATATTTTTATATTTTTTTAAAATTTATACATATTTCTAACTTTTAATGAAA
Found at i:13439630 original size:29 final size:30
Alignment explanation
Indices: 13439508--13439630 Score: 98
Period size: 29 Copynumber: 4.3 Consensus size: 30
13439498 AAATTTTACA
* * *
13439508 ATTTTTA-TAAAATTTTACAATTTTTTTAT
1 ATTTTTATTAAAATTTAATAATATTTTTAT
** *
13439537 ATTTTT-TTACTATTT-ATACATATTTCTA-
1 ATTTTTATTAAAATTTAATA-ATATTTTTAT
* *
13439565 ATTTTTAATGAAATTT-A-AATATTTTTAT
1 ATTTTTATTAAAATTTAATAATATTTTTAT
*
13439593 ATTTTTATTAAAATTTAATAATTTTTTTA-
1 ATTTTTATTAAAATTTAATAATATTTTTAT
*
13439622 ACTTTTATT
1 ATTTTTATT
13439631 TTTTATATTT
Statistics
Matches: 74, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
27 8 0.11
28 23 0.31
29 34 0.46
30 9 0.12
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (30 bp):
ATTTTTATTAAAATTTAATAATATTTTTAT
Found at i:13440064 original size:22 final size:22
Alignment explanation
Indices: 13440021--13440072 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
13440011 GATTTTATTT
* *
13440021 AAAAATATAATTTTCTAAAACAG
1 AAAAA-ATAATTTTATAAAACAC
**
13440044 AAAAAATAATTTTATTCAACAC
1 AAAAAATAATTTTATAAAACAC
13440066 AAAAAAT
1 AAAAAAT
13440073 TTGAATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAAAATAATTTTATAAAACAC
Found at i:13440890 original size:21 final size:20
Alignment explanation
Indices: 13440856--13440894 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
13440846 ATAATAAAAT
*
13440856 ATTTATATATTTTATAATTAA
1 ATTTATATAATTTA-AATTAA
*
13440877 ATTTATTTAATTTAAATT
1 ATTTATATAATTTAAATT
13440895 GAAGTCCTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTATATAATTTAAATTAA
Found at i:13441017 original size:25 final size:25
Alignment explanation
Indices: 13440989--13441040 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
13440979 TTGAGCTGGG
13440989 AATGGATCTAATCGTCACTAAATAT
1 AATGGATCTAATCGTCACTAAATAT
13441014 AATGGATCTAATCGTCACTAAATAT
1 AATGGATCTAATCGTCACTAAATAT
13441039 AA
1 AA
13441041 GATATACTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (25 bp):
AATGGATCTAATCGTCACTAAATAT
Found at i:13442000 original size:26 final size:26
Alignment explanation
Indices: 13441954--13442007 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
13441944 ACTATTTAAT
13441954 TAACTAATTATATTATAAAATTAAAG
1 TAACTAATTATATTATAAAATTAAAG
* *
13441980 TAACTAA-TATATATATTAAATTAGAG
1 TAACTAATTATAT-TATAAAATTAAAG
13442006 TA
1 TA
13442008 TATAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.39
Consensus pattern (26 bp):
TAACTAATTATATTATAAAATTAAAG
Found at i:13450430 original size:107 final size:107
Alignment explanation
Indices: 13450295--13450508 Score: 392
Period size: 107 Copynumber: 2.0 Consensus size: 107
13450285 TTGAGCTTAT
*
13450295 AAGTAAATAAGTAAATGGTGAAATTATACTAACCCTTTTAAAAATTATAAAAATATAAATTAATA
1 AAGTAAATAAGTAAATGGTCAAATTATACTAACCCTTTTAAAAATTATAAAAATATAAATTAATA
*
13450360 TAATAACGAAATTACATTTTGACTCTCATAAAAATACTAATA
66 CAATAACGAAATTACATTTTGACTCTCATAAAAATACTAATA
*
13450402 AAGTAAATAAGTAAATGTTCAAATTATACTAACCCTTTTAAAAATTATAAAAATATAAATTAATA
1 AAGTAAATAAGTAAATGGTCAAATTATACTAACCCTTTTAAAAATTATAAAAATATAAATTAATA
*
13450467 CAATAACGAAATTACATTTTGACTCTTATAAAAATACTAATA
66 CAATAACGAAATTACATTTTGACTCTCATAAAAATACTAATA
13450509 TAATCTCGAC
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 103 1.00
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.33
Consensus pattern (107 bp):
AAGTAAATAAGTAAATGGTCAAATTATACTAACCCTTTTAAAAATTATAAAAATATAAATTAATA
CAATAACGAAATTACATTTTGACTCTCATAAAAATACTAATA
Found at i:13453035 original size:22 final size:22
Alignment explanation
Indices: 13453010--13453052 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
13453000 ATATTTAAAT
13453010 AATAACAATAAAATAGTAGCAA
1 AATAACAATAAAATAGTAGCAA
* *
13453032 AATAACAGTAAATTAGTAGCA
1 AATAACAATAAAATAGTAGCA
13453053 TGGAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (22 bp):
AATAACAATAAAATAGTAGCAA
Found at i:13458197 original size:31 final size:30
Alignment explanation
Indices: 13458162--13458259 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 30
13458152 TTAATACACC
*
13458162 ATTTGGTACCTGAGTTTGGCTTCAATACTCA
1 ATTTGGTACCTGAATTT-GCTTCAATACTCA
* ** *
13458193 ATTTGGTACATGAATTT--TT-TGT-CCCA
1 ATTTGGTACCTGAATTTGCTTCAATACTCA
* *
13458219 ATTTAGTACCTGAATTTAGCTTCAATATTCA
1 ATTTGGTACCTGAATTT-GCTTCAATACTCA
13458250 ATTTGGTACC
1 ATTTGGTACC
13458260 CAGACTAAAC
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
26 18 0.36
27 1 0.02
28 2 0.04
29 2 0.04
30 1 0.02
31 26 0.52
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (30 bp):
ATTTGGTACCTGAATTTGCTTCAATACTCA
Found at i:13458594 original size:23 final size:22
Alignment explanation
Indices: 13458568--13458610 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
13458558 ACTTAGGTAC
*
13458568 TTAACTGGAAAATAACTCAAGCA
1 TTAAATGGAAAA-AACTCAAGCA
*
13458591 TTAAATTGAAAAAACTCAAG
1 TTAAATGGAAAAAACTCAAG
13458611 TAAGACAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (22 bp):
TTAAATGGAAAAAACTCAAGCA
Found at i:13458639 original size:31 final size:31
Alignment explanation
Indices: 13458595--13458665 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 31
13458585 CAAGCATTAA
* * *
13458595 ATTGAAA--AAACTCAAGTAAGACAGTGAAC
1 ATTGAAACCAAACTCAAGCAACAAAGTGAAC
* *
13458624 ATTGAAACCAAACTCAAGCACCAAATTGAAC
1 ATTGAAACCAAACTCAAGCAACAAAGTGAAC
13458655 ATTGAAACCAA
1 ATTGAAACCAA
13458666 GCTTAGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 7 0.20
31 28 0.80
ACGTcount: A:0.51, C:0.20, G:0.13, T:0.17
Consensus pattern (31 bp):
ATTGAAACCAAACTCAAGCAACAAAGTGAAC
Found at i:13464318 original size:57 final size:56
Alignment explanation
Indices: 13464251--13464361 Score: 195
Period size: 57 Copynumber: 2.0 Consensus size: 56
13464241 CATGTTTCTG
* *
13464251 TAAAATGTTTAATTTCAATGCATATTAACATCATTTGGTCATTTTCTAATTTATTTC
1 TAAAATGTTTAATTTCAATGCATATTAACAT-AATTAGTCATTTTCTAATTTATTTC
13464308 TAAAATGTTTAATTTCAATGCATATTAACATAATTAGTCATTTTCTAATTTATT
1 TAAAATGTTTAATTTCAATGCATATTAACATAATTAGTCATTTTCTAATTTATT
13464362 GGAAGTACCA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
56 21 0.40
57 31 0.60
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (56 bp):
TAAAATGTTTAATTTCAATGCATATTAACATAATTAGTCATTTTCTAATTTATTTC
Found at i:13464582 original size:19 final size:20
Alignment explanation
Indices: 13464558--13464595 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13464548 ATTGATATTT
13464558 AAATT-ATATATATTTTTTA
1 AAATTAATATATATTTTTTA
*
13464577 AAATTAATATTTATTTTTT
1 AAATTAATATATATTTTTT
13464596 TTATATAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
AAATTAATATATATTTTTTA
Found at i:13465667 original size:11 final size:11
Alignment explanation
Indices: 13465651--13465676 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
13465641 TAATCAGAAT
13465651 TAAAAAATATA
1 TAAAAAATATA
13465662 TAAAAAATATA
1 TAAAAAATATA
13465673 TAAA
1 TAAA
13465677 TATCTATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAAAAATATA
Found at i:13471880 original size:11 final size:11
Alignment explanation
Indices: 13471864--13471894 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
13471854 AAGTATGGGT
13471864 AGGTATGGGAA
1 AGGTATGGGAA
*
13471875 AGGTATGGGCA
1 AGGTATGGGAA
13471886 AGGTATGGG
1 AGGTATGGG
13471895 GTATGGGTAT
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:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:13475971 original size:18 final size:18
Alignment explanation
Indices: 13475948--13476040 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
13475938 CCCAACTACT
*
13475948 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
13475966 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
13475984 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
*
13476002 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
13476020 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
13476038 GTA
1 GTA
13476041 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:13476000 original size:36 final size:36
Alignment explanation
Indices: 13475948--13476040 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
13475938 CCCAACTACT
*
13475948 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
*
13475984 GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
13476020 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
13476041 AACGGTCGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:13476602 original size:11 final size:11
Alignment explanation
Indices: 13476575--13476617 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
13476565 TGACCTTTCC
13476575 AAGGTATGGG-
1 AAGGTATGGGA
*
13476585 TAGGTATGGGA
1 AAGGTATGGGA
*
13476596 AAGGTATGGGC
1 AAGGTATGGGA
13476607 AAGGTATGGGA
1 AAGGTATGGGA
13476618 TATATTCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:13476614 original size:22 final size:21
Alignment explanation
Indices: 13476575--13476617 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
13476565 TGACCTTTCC
*
13476575 AAGGTATGGGTAGGTATGGGA
1 AAGGTATGGGAAGGTATGGGA
13476596 AAGGTATGGGCAAGGTATGGGA
1 AAGGTATGGG-AAGGTATGGGA
13476618 TATATTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (21 bp):
AAGGTATGGGAAGGTATGGGA
Found at i:13478291 original size:16 final size:16
Alignment explanation
Indices: 13478230--13478292 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
13478220 CAATTAATTC
13478230 AATTTTATTTATTTAA
1 AATTTTATTTATTTAA
* *
13478246 TATTATATTATATTATAAA
1 AATTTTATT-TATT-T-AA
*
13478265 AACTTTA--TATTTAA
1 AATTTTATTTATTTAA
13478279 AATTTTATTTATTT
1 AATTTTATTTATTT
13478293 TTAGAAACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
14 8 0.22
15 1 0.03
16 16 0.44
17 4 0.11
18 1 0.03
19 6 0.17
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
AATTTTATTTATTTAA
Found at i:13479269 original size:17 final size:17
Alignment explanation
Indices: 13479243--13479279 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
13479233 ATCGTAACAA
*
13479243 ATATATGGTAAAATATT
1 ATATAAGGTAAAATATT
*
13479260 ATATAAGGTAATATATT
1 ATATAAGGTAAAATATT
13479277 ATA
1 ATA
13479280 ATATATATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.41
Consensus pattern (17 bp):
ATATAAGGTAAAATATT
Found at i:13483783 original size:17 final size:17
Alignment explanation
Indices: 13483761--13483794 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
13483751 ATCCACTAAT
*
13483761 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
13483778 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
13483795 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:13488422 original size:17 final size:17
Alignment explanation
Indices: 13488400--13488433 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
13488390 ATCCACTAAT
*
13488400 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
13488417 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
13488434 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:13493548 original size:4 final size:4
Alignment explanation
Indices: 13493539--13493650 Score: 224
Period size: 4 Copynumber: 28.0 Consensus size: 4
13493529 GCAAACGTGG
13493539 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
13493587 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
13493635 GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA
13493651 TAGAAAAGGG
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 108 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:13495919 original size:69 final size:68
Alignment explanation
Indices: 13495829--13495983 Score: 274
Period size: 69 Copynumber: 2.2 Consensus size: 68
13495819 TTAGTAAATT
* *
13495829 AATACAAAGTAGTATCTATTATCTAAATATAAATTTGATGAAAATAAAGTTAAATAATTACAATA
1 AATATAAA-TAGTATCTATTATCTAAATATAAATCTGATGAAAATAAAGTTAAATAATTACAATA
13495894 TTTAA
65 TTT-A
13495899 AATATAAATAGTATCTATTATCTAAATATAAATCTGATGAAAATAAAGTTAAATAATTACAATAT
1 AATATAAATAGTATCTATTATCTAAATATAAATCTGATGAAAATAAAGTTAAATAATTACAATAT
13495964 TTA
66 TTA
13495967 AATATAAATAGTATCTA
1 AATATAAATAGTATCTA
13495984 AATTCTAATT
Statistics
Matches: 83, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
68 18 0.22
69 58 0.70
70 7 0.08
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (68 bp):
AATATAAATAGTATCTATTATCTAAATATAAATCTGATGAAAATAAAGTTAAATAATTACAATAT
TTA
Found at i:13497310 original size:14 final size:15
Alignment explanation
Indices: 13497291--13497320 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13497281 TTTTTAAATA
13497291 TATATTA-TATAATT
1 TATATTATTATAATT
13497305 TATATTATTATAATT
1 TATATTATTATAATT
13497320 T
1 T
13497321 TTCTAGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATATTATTATAATT
Found at i:13498646 original size:33 final size:33
Alignment explanation
Indices: 13498609--13498672 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
13498599 ATGTTGAGTT
*
13498609 ACAAAGTTATAAATACGAAAAAATTATCAATTA
1 ACAAAATTATAAATACGAAAAAATTATCAATTA
*
13498642 ACAAAATTATAAATACTAAAAAATTATCAAT
1 ACAAAATTATAAATACGAAAAAATTATCAAT
13498673 GATAATAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.28
Consensus pattern (33 bp):
ACAAAATTATAAATACGAAAAAATTATCAATTA
Found at i:13498647 original size:17 final size:17
Alignment explanation
Indices: 13498626--13498672 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
13498616 TATAAATACG
13498626 AAAAAATTATCAATTA-
1 AAAAAATTATCAATTAC
* *
13498642 ACAAAATTAT-AAATAC
1 AAAAAATTATCAATTAC
13498658 TAAAAAATTATCAAT
1 -AAAAAATTATCAAT
13498673 GATAATAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
15 4 0.17
16 9 0.38
17 9 0.38
18 2 0.08
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAAAATTATCAATTAC
Done.