Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 107 of 193
Found at i:34372014 original size:4 final size:4
Alignment explanation
Indices: 34371997--34372067 Score: 58
Period size: 4 Copynumber: 18.0 Consensus size: 4
34371987 ATAACATAAG
* * *
34371997 AATA AAT- AACA AATA AATA AATA AAAA CAATA AATA AATA AA-A ATTA
1 AATA AATA AATA AATA AATA AATA AATA -AATA AATA AATA AATA AATA
* *
34372044 AAT- ACTAA AATA AATG AATA AATA
1 AATA AAT-A AATA AATA AATA AATA
34372068 CAAATAATAA
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
3 6 0.12
4 41 0.79
5 5 0.10
ACGTcount: A:0.72, C:0.04, G:0.01, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:34372017 original size:31 final size:30
Alignment explanation
Indices: 34371982--34372083 Score: 81
Period size: 28 Copynumber: 3.3 Consensus size: 30
34371972 AGGTCAAAAT
34371982 ATAAAATAACATAAGAATAAATAACAAATAA
1 ATAAAATAA-ATAAGAATAAATAACAAATAA
*
34372013 AT-AAATAAA-AACAATAAATAA-ATAA-AA
1 ATAAAATAAATAAGAATAAATAACA-AATAA
34372040 ATTAAATACTAAAATAAATGAATAAAT-ACAAAT-A
1 A-TAAA-A-T-AAAT-AA-GAATAAATAACAAATAA
34372074 ATAAAATAAA
1 ATAAAATAAA
34372084 AGGGACTAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 23
0.70 0.02 0.28
Matches are distributed among these distances:
27 4 0.07
28 14 0.24
29 3 0.05
30 10 0.17
31 4 0.07
32 4 0.07
33 4 0.07
34 7 0.12
35 8 0.14
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.22
Consensus pattern (30 bp):
ATAAAATAAATAAGAATAAATAACAAATAA
Found at i:34372028 original size:17 final size:18
Alignment explanation
Indices: 34371997--34372040 Score: 72
Period size: 17 Copynumber: 2.4 Consensus size: 18
34371987 ATAACATAAG
34371997 AATAAATAACAAATAAATA
1 AATAAA-AACAAATAAATA
34372016 AATAAAAAC-AATAAATA
1 AATAAAAACAAATAAATA
34372033 AATAAAAA
1 AATAAAAA
34372041 TTAAATACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 16 0.64
18 3 0.12
19 6 0.24
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (18 bp):
AATAAAAACAAATAAATA
Found at i:34372065 original size:13 final size:12
Alignment explanation
Indices: 34371992--34372083 Score: 68
Period size: 11 Copynumber: 7.8 Consensus size: 12
34371982 ATAAAATAAC
34371992 ATAAGAATAAATA
1 ATAA-AATAAATA
*
34372005 A-CAAATAAATA
1 ATAAAATAAATA
* *
34372016 A-ATAA-AAACA
1 ATAAAATAAATA
34372026 AT-AAATAAATA
1 ATAAAATAAATA
*
34372037 A-AAATTAAATA
1 ATAAAATAAATA
*
34372048 CTAAAATAAATGA
1 ATAAAATAAAT-A
*
34372061 ATAAATACAAATA
1 ATAAA-ATAAATA
34372074 ATAAAATAAA
1 ATAAAATAAA
34372084 AGGGACTAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
10 7 0.11
11 24 0.39
12 13 0.21
13 12 0.20
14 5 0.08
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (12 bp):
ATAAAATAAATA
Found at i:34372084 original size:31 final size:31
Alignment explanation
Indices: 34371978--34372084 Score: 93
Period size: 31 Copynumber: 3.5 Consensus size: 31
34371968 TAAAAGGTCA
*
34371978 AAAT-ATAAAATAACAT-AA-GAATAAATAAC
1 AAATAATAAAATAAAATAAATGAATAAAT-AC
*
34372007 AAATAA-ATAAATAAAA-ACAATAAATAAATA-
1 AAATAATA-AAATAAAATA-AATGAATAAATAC
*
34372037 AAA-ATTAAATACTAAAATAAATGAATAAATAC
1 AAATAATAAA-A-TAAAATAAATGAATAAATAC
34372069 AAATAATAAAATAAAA
1 AAATAATAAAATAAAA
34372085 GGGACTAAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
29 8 0.13
30 13 0.21
31 24 0.39
32 12 0.19
33 5 0.08
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (31 bp):
AAATAATAAAATAAAATAAATGAATAAATAC
Found at i:34373400 original size:18 final size:18
Alignment explanation
Indices: 34373377--34373413 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
34373367 ATAAGTGAAA
*
34373377 TTATTTTTGGTTTTATTT
1 TTATTTTAGGTTTTATTT
34373395 TTATTTTAGGTTTTATTT
1 TTATTTTAGGTTTTATTT
34373413 T
1 T
34373414 AAAATAGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.76
Consensus pattern (18 bp):
TTATTTTAGGTTTTATTT
Found at i:34374868 original size:85 final size:85
Alignment explanation
Indices: 34374735--34374904 Score: 340
Period size: 85 Copynumber: 2.0 Consensus size: 85
34374725 TAAATGCTGC
34374735 ATTTCCTGTTCTCTTTAAGTGGTGTTTGGATTATGTTGGTGGGTTGGTGTTGATATTGGAGAATT
1 ATTTCCTGTTCTCTTTAAGTGGTGTTTGGATTATGTTGGTGGGTTGGTGTTGATATTGGAGAATT
34374800 TGATAAATAATAAATAGATG
66 TGATAAATAATAAATAGATG
34374820 ATTTCCTGTTCTCTTTAAGTGGTGTTTGGATTATGTTGGTGGGTTGGTGTTGATATTGGAGAATT
1 ATTTCCTGTTCTCTTTAAGTGGTGTTTGGATTATGTTGGTGGGTTGGTGTTGATATTGGAGAATT
34374885 TGATAAATAATAAATAGATG
66 TGATAAATAATAAATAGATG
34374905 TATCATTGTA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.25, C:0.05, G:0.27, T:0.44
Consensus pattern (85 bp):
ATTTCCTGTTCTCTTTAAGTGGTGTTTGGATTATGTTGGTGGGTTGGTGTTGATATTGGAGAATT
TGATAAATAATAAATAGATG
Found at i:34386381 original size:30 final size:30
Alignment explanation
Indices: 34386315--34386381 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
34386305 TTTAATAACT
34386315 TATAA-TTTTATAATTTTTAAAAGATTAAA
1 TATAATTTTTATAATTTTTAAAAGATTAAA
34386344 T-TAAATTTTTATTAA-TTTTAAAAGATTAAA
1 TAT-AATTTTTA-TAATTTTTAAAAGATTAAA
34386374 TATAATTT
1 TATAATTT
34386382 CATCGTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
28 1 0.03
29 3 0.09
30 26 0.76
31 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (30 bp):
TATAATTTTTATAATTTTTAAAAGATTAAA
Found at i:34400907 original size:28 final size:28
Alignment explanation
Indices: 34400848--34400909 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
34400838 CAAAATCCCC
* *
34400848 ATTCTATTAAAGGAAGCCTTTGTGGCTG
1 ATTCTATTAAAAGAAGCCTTTGTAGCTG
* * *
34400876 ATTCTGTTAAAAGAAGCCTTTGTAGTTT
1 ATTCTATTAAAAGAAGCCTTTGTAGCTG
34400904 ATTCTA
1 ATTCTA
34400910 AAAATGGAGC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.40
Consensus pattern (28 bp):
ATTCTATTAAAAGAAGCCTTTGTAGCTG
Found at i:34401068 original size:28 final size:28
Alignment explanation
Indices: 34401024--34401077 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
34401014 TGATGAAAAA
* * *
34401024 CCTTTGTGGCTATCTTTGTTTAAGGATG
1 CCTTTGTGGATACCTTTATTTAAGGATG
*
34401052 CCTTTGTGGATACCTTTATTTGAGGA
1 CCTTTGTGGATACCTTTATTTAAGGA
34401078 CGTATATGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.17, C:0.15, G:0.24, T:0.44
Consensus pattern (28 bp):
CCTTTGTGGATACCTTTATTTAAGGATG
Found at i:34422624 original size:19 final size:19
Alignment explanation
Indices: 34422600--34422637 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
34422590 CACATCCTAT
*
34422600 TTTTTAAGTAGTTAATTAA
1 TTTTTAAGTAATTAATTAA
*
34422619 TTTTTAATTAATTAATTAA
1 TTTTTAAGTAATTAATTAA
34422638 GTTAGTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTTTAAGTAATTAATTAA
Found at i:34423467 original size:17 final size:18
Alignment explanation
Indices: 34423428--34423467 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
34423418 GTGACCATTT
*
34423428 TTCTTC-CTTTTGATTTA
1 TTCTTCTCTTTTGATTGA
34423445 TT-TTCTCTTTTG-TTGA
1 TTCTTCTCTTTTGATTGA
34423461 TTCTTCT
1 TTCTTCT
34423468 AAGGATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.07, C:0.17, G:0.07, T:0.68
Consensus pattern (18 bp):
TTCTTCTCTTTTGATTGA
Found at i:34424119 original size:21 final size:21
Alignment explanation
Indices: 34424094--34424144 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
34424084 GTGAAAATCG
34424094 TGATATGTGTTATGTGATCTA
1 TGATATGTGTTATGTGATCTA
* *
34424115 TGATAAGTGTTATGTGATGTA
1 TGATATGTGTTATGTGATCTA
34424136 TGATATGTG
1 TGATATGTG
34424145 ATTTCATCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.02, G:0.27, T:0.45
Consensus pattern (21 bp):
TGATATGTGTTATGTGATCTA
Found at i:34424886 original size:18 final size:19
Alignment explanation
Indices: 34424845--34424886 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
34424835 TGATGTGAAT
*
34424845 ATTATATGTGTTTATTGTC
1 ATTATATGTGTTTATAGTC
*
34424864 A-TATATGTGTTTA-AGTG
1 ATTATATGTGTTTATAGTC
34424881 ATTATA
1 ATTATA
34424887 GTGGGAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 3 0.15
18 16 0.80
19 1 0.05
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (19 bp):
ATTATATGTGTTTATAGTC
Found at i:34427506 original size:7 final size:8
Alignment explanation
Indices: 34427485--34427514 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
34427475 TTTTTAAAAC
34427485 TATTTTTA
1 TATTTTTA
34427493 TATTTTTA
1 TATTTTTA
34427501 TATTTTTA
1 TATTTTTA
34427509 -ATTTTT
1 TATTTTT
34427515 TTAAAACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TATTTTTA
Found at i:34433769 original size:2 final size:2
Alignment explanation
Indices: 34433762--34433788 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
34433752 AGCCTTTGGA
34433762 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
34433789 TTGAATGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:34440210 original size:16 final size:17
Alignment explanation
Indices: 34440179--34440211 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
34440169 AACCTGAGGC
34440179 TTTGTTTGCTAGGATGAG
1 TTTGTTTGC-AGGATGAG
34440197 TTTGTTTG-AGGATGA
1 TTTGTTTGCAGGATGA
34440212 CAGTCTCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.18, C:0.03, G:0.33, T:0.45
Consensus pattern (17 bp):
TTTGTTTGCAGGATGAG
Found at i:34442593 original size:23 final size:23
Alignment explanation
Indices: 34442562--34442617 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
34442552 ACTCGAATTA
* *
34442562 GACCCGACCCATTGATTTTGACC
1 GACCCGACCCATTAACTTTGACC
* *
34442585 GACCTGACCGATTAACTTTGACC
1 GACCCGACCCATTAACTTTGACC
* *
34442608 AACCCAACCC
1 GACCCGACCC
34442618 GACCTATTGA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.38, G:0.14, T:0.21
Consensus pattern (23 bp):
GACCCGACCCATTAACTTTGACC
Found at i:34442645 original size:28 final size:28
Alignment explanation
Indices: 34442583--34442646 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
34442573 TTGATTTTGA
*
34442583 CCGACCTGACCGATTAACTTTGACCAAC
1 CCGACCCGACCGATTAACTTTGACCAAC
* * * **
34442611 CCAACCCGACCTATTGACTTTGATTAAC
1 CCGACCCGACCGATTAACTTTGACCAAC
34442639 CCGACCCG
1 CCGACCCG
34442647 TTGACTTTGA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.27, C:0.38, G:0.14, T:0.22
Consensus pattern (28 bp):
CCGACCCGACCGATTAACTTTGACCAAC
Found at i:34442666 original size:23 final size:23
Alignment explanation
Indices: 34442611--34442673 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
34442601 TTTGACCAAC
**
34442611 CCAACCCGACCTATTGACTTTGA
1 CCAACCCGACCCGTTGACTTTGA
**
34442634 TTAACCCGACCCGTTGACTTTGA
1 CCAACCCGACCCGTTGACTTTGA
* *
34442657 CCAACTCGACTCGTTGA
1 CCAACCCGACCCGTTGA
34442674 TTGTTAACTT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (23 bp):
CCAACCCGACCCGTTGACTTTGA
Found at i:34447452 original size:22 final size:22
Alignment explanation
Indices: 34447425--34447480 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
34447415 GCAATACATT
*
34447425 AAATAATTTCTAATAAT-AAAAA
1 AAATAATTTATAA-AATAAAAAA
* *
34447447 ATATAATTAATAAAATAAAAAA
1 AAATAATTTATAAAATAAAAAA
34447469 AAATAATTTATA
1 AAATAATTTATA
34447481 TAACATTCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
AAATAATTTATAAAATAAAAAA
Found at i:34448259 original size:21 final size:21
Alignment explanation
Indices: 34448235--34448275 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
34448225 AACGTATTTT
34448235 AATCTATAAA-ATAAATATGAA
1 AATCT-TAAATATAAATATGAA
34448256 AATCTTAAATATAAATATGA
1 AATCTTAAATATAAATATGA
34448276 TAGACACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (21 bp):
AATCTTAAATATAAATATGAA
Found at i:34448437 original size:27 final size:26
Alignment explanation
Indices: 34448407--34448469 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 26
34448397 TTTATCGAGG
34448407 TTATTAATTTATCGATAAATAAATATT
1 TTATTAATTTATCGATAAATAAATA-T
*
34448434 TTATTAATTTATCGATAAATTAATAT
1 TTATTAATTTATCGATAAATAAATAT
34448460 TTATT-ATTTA
1 TTATTAATTTA
34448470 GAGAATATGT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 5 0.14
26 6 0.17
27 24 0.69
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (26 bp):
TTATTAATTTATCGATAAATAAATAT
Found at i:34449795 original size:12 final size:11
Alignment explanation
Indices: 34449779--34449817 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
34449769 CGACCTTTCC
34449779 TTTTCTTTTTT
1 TTTTCTTTTTT
*
34449790 CTTTTCATCTTTT
1 -TTTTC-TTTTTT
34449803 TTTTCTTTTTT
1 TTTTCTTTTTT
34449814 TTTT
1 TTTT
34449818 GTGAAATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 9 0.38
12 10 0.42
13 5 0.21
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:34458692 original size:27 final size:28
Alignment explanation
Indices: 34458662--34458720 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
34458652 ACAGATTATC
*
34458662 GCTCC-CACGAGCCAGAAACAGAATAAT
1 GCTCCTCACAAGCCAGAAACAGAATAAT
** *
34458689 GCTCCTTTCAAGCCAGAAATAGAATAAT
1 GCTCCTCACAAGCCAGAAACAGAATAAT
34458717 GCTC
1 GCTC
34458721 TTTTTGAGCC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.19
Consensus pattern (28 bp):
GCTCCTCACAAGCCAGAAACAGAATAAT
Found at i:34458712 original size:28 final size:28
Alignment explanation
Indices: 34458669--34458817 Score: 165
Period size: 28 Copynumber: 5.3 Consensus size: 28
34458659 ATCGCTCCCA
*
34458669 CGAGCCAGAAACAGAATAATGCTCCTTT
1 CGAGCCAGAAACAGAATAATGCTCTTTT
* *
34458697 CAAGCCAGAAATAGAATAATGCTCTTTT
1 CGAGCCAGAAACAGAATAATGCTCTTTT
* * *
34458725 TGAGCCAGAAACAAAATGATGCTCTTTT
1 CGAGCCAGAAACAGAATAATGCTCTTTT
* * *
34458753 CGAGCCAGAGACAGGATAATGTTCTTTT
1 CGAGCCAGAAACAGAATAATGCTCTTTT
** * *
34458781 CGAGCCAGAGTCTAGAATATTGCTC-TTA
1 CGAGCCAGAAAC-AGAATAATGCTCTTTT
34458809 CGAGCCAGA
1 CGAGCCAGA
34458818 GTCCACCAAC
Statistics
Matches: 101, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
28 92 0.91
29 9 0.09
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (28 bp):
CGAGCCAGAAACAGAATAATGCTCTTTT
Found at i:34466847 original size:74 final size:74
Alignment explanation
Indices: 34466766--34467000 Score: 398
Period size: 74 Copynumber: 3.2 Consensus size: 74
34466756 CATTCATATT
* *
34466766 CATCAACTCAACTGAATAAGTTCATTGTCATTTCAAAATACATGCCAATCATTCAAGCCACAATA
1 CATCAACTCAACTGAATAAGTTCATTGCCATTTCAAAATACATGCCAATCATTCAAGCCACAACA
34466831 AGCATTCAA
66 AGCATTCAA
* * *
34466840 CATCAACTCAATTGAATAAGTTCGTTGCCATTTCAAAATACATGTCAATCATTCAAGCCACAACA
1 CATCAACTCAACTGAATAAGTTCATTGCCATTTCAAAATACATGCCAATCATTCAAGCCACAACA
*
34466905 AGCATTTAA
66 AGCATTCAA
*
34466914 CATCAACTCAACTGAATAAGTTCATTGCCATTTCAAAATACATGCCAATCATTTAAGCCACAACA
1 CATCAACTCAACTGAATAAGTTCATTGCCATTTCAAAATACATGCCAATCATTCAAGCCACAACA
34466979 AGCATTCAA
66 AGCATTCAA
*
34466988 CATCAACTTAACT
1 CATCAACTCAACT
34467001 TCATTCTCCT
Statistics
Matches: 149, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 149 1.00
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.27
Consensus pattern (74 bp):
CATCAACTCAACTGAATAAGTTCATTGCCATTTCAAAATACATGCCAATCATTCAAGCCACAACA
AGCATTCAA
Found at i:34468545 original size:31 final size:29
Alignment explanation
Indices: 34468510--34468583 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 29
34468500 ATAATGGCTC
34468510 AGTGACTAAAATGTTACAACA-TTATAACGTA
1 AGTGACTAAAATGTT--AACATTTA-AACGTA
* * *
34468541 AGTGAGTAAAACG-TAACATTTCAAACTTA
1 AGTGACTAAAATGTTAACATTT-AAACGTA
34468570 AGTGACTAAAATGT
1 AGTGACTAAAATGT
34468584 AACCCAAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
28 4 0.11
29 18 0.51
30 2 0.06
31 11 0.31
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (29 bp):
AGTGACTAAAATGTTAACATTTAAACGTA
Found at i:34468651 original size:28 final size:29
Alignment explanation
Indices: 34468597--34468656 Score: 104
Period size: 28 Copynumber: 2.1 Consensus size: 29
34468587 CCAAGATAAA
34468597 TAAAAGTGACTATTTTGAGAATCTACCCT
1 TAAAAGTGACTATTTTGAGAATCTACCCT
*
34468626 TAAAAGTGACTA-TTTGAGAATTTACCCT
1 TAAAAGTGACTATTTTGAGAATCTACCCT
34468654 TAA
1 TAA
34468657 TTATATTGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (29 bp):
TAAAAGTGACTATTTTGAGAATCTACCCT
Found at i:34469099 original size:27 final size:25
Alignment explanation
Indices: 34469047--34469099 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
34469037 TTATTTATTT
* * *
34469047 TATATTTTAAATATTTTTTTATATA
1 TATATATTAAATATTTTTTAAAATA
*
34469072 TATATATTAAATATTTTTTAAAAAA
1 TATATATTAAATATTTTTTAAAATA
34469097 TAT
1 TAT
34469100 TGAAAAATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TATATATTAAATATTTTTTAAAATA
Found at i:34480628 original size:13 final size:13
Alignment explanation
Indices: 34480610--34480635 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34480600 ACTGCTATTA
34480610 TAGTTATCTTCTT
1 TAGTTATCTTCTT
34480623 TAGTTATCTTCTT
1 TAGTTATCTTCTT
34480636 GTATCAGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.08, T:0.62
Consensus pattern (13 bp):
TAGTTATCTTCTT
Found at i:34485997 original size:30 final size:30
Alignment explanation
Indices: 34485961--34486031 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
34485951 TTACTTCTAG
*
34485961 TATGAATATTGCTAAAAGTATTGCACTTGA
1 TATGAATATAGCTAAAAGTATTGCACTTGA
*
34485991 TATGAATATAGTTAAAAGTATTGCACTTGA
1 TATGAATATAGCTAAAAGTATTGCACTTGA
34486021 TATGAATATAG
1 TATGAATATAG
34486032 AGTGTATACT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (30 bp):
TATGAATATAGCTAAAAGTATTGCACTTGA
Found at i:34487144 original size:15 final size:16
Alignment explanation
Indices: 34487109--34487143 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
34487099 CAATAATTTG
*
34487109 AAATATTATCAGTAAAA
1 AAATATTATAAG-AAAA
34487126 AAATATTATAAGAAAA
1 AAATATTATAAGAAAA
34487142 AA
1 AA
34487144 TGAAATACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.26
Consensus pattern (16 bp):
AAATATTATAAGAAAA
Found at i:34487241 original size:24 final size:26
Alignment explanation
Indices: 34487199--34487262 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 26
34487189 TTGTCTCCAA
*
34487199 TTTTTTCATTCTATCTGTAAGTTTTC
1 TTTTTTCTTTCTATCTGTAAGTTTTC
*
34487225 TTTTTTCTTTCT-T-TGTAATTTTTC
1 TTTTTTCTTTCTATCTGTAAGTTTTC
*
34487249 -TGTTTCTTTCTATC
1 TTTTTTCTTTCTATC
34487263 AGACTAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 10 0.30
24 11 0.33
25 1 0.03
26 11 0.33
ACGTcount: A:0.11, C:0.16, G:0.06, T:0.67
Consensus pattern (26 bp):
TTTTTTCTTTCTATCTGTAAGTTTTC
Found at i:34487254 original size:23 final size:24
Alignment explanation
Indices: 34487214--34487259 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
34487204 TCATTCTATC
*
34487214 TGTAAGTTTTCTTTTTTCTTTCTT
1 TGTAAGTTTTCTTGTTTCTTTCTT
*
34487238 TGTAATTTTTC-TGTTTCTTTCT
1 TGTAAGTTTTCTTGTTTCTTTCT
34487260 ATCAGACTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.09, C:0.13, G:0.09, T:0.70
Consensus pattern (24 bp):
TGTAAGTTTTCTTGTTTCTTTCTT
Found at i:34488311 original size:2 final size:2
Alignment explanation
Indices: 34488304--34488336 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
34488294 TTTAGGATAA
*
34488304 AT AT AT AT AC 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
34488337 CTATTATCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:34495713 original size:8 final size:8
Alignment explanation
Indices: 34495702--34495733 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
34495692 ATTTATATTC
34495702 ATAAAATA
1 ATAAAATA
34495710 AT-AAATA
1 ATAAAATA
34495717 ATAAAATA
1 ATAAAATA
34495725 ATAAAATA
1 ATAAAATA
34495733 A
1 A
34495734 AATTAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
ATAAAATA
Found at i:34495722 original size:15 final size:14
Alignment explanation
Indices: 34495702--34495741 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
34495692 ATTTATATTC
34495702 ATAAAATAATAAATA
1 ATAAAATAATAAA-A
34495717 ATAAAATAAT-AAA
1 ATAAAATAATAAAA
34495730 ATAAAATTAATA
1 ATAAAA-TAATA
34495742 TTATTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.30
14 6 0.26
15 10 0.43
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAAAATAATAAAA
Found at i:34495754 original size:63 final size:64
Alignment explanation
Indices: 34495641--34495803 Score: 210
Period size: 67 Copynumber: 2.5 Consensus size: 64
34495631 TTATTTATTT
*
34495641 ATAATAATAAATAAATAATAAAACAAAATTAATATTATTTTACATTTATTTATTTATATTCAT-A
1 ATAATAATAAATAAATAATAAAATAAAATTAATATTATTTTA-A-TTATTTATTT-TATTCATAA
34495705 AA
63 AA
*
34495707 ATAATAA-ATAATAAAATAATAAAATAAAATTAATATTATTTT-A-TATTTATTTTGTTCATAAA
1 ATAATAATA-AAT-AAATAATAAAATAAAATTAATATTATTTTAATTATTTATTTTATTCATAAA
34495769 A
64 A
*
34495770 ATAATAATAAATAAATAA-ATAAATAAAAATAATA
1 ATAATAATAAATAAATAATA-AAATAAAATTAATA
34495804 AGAAAAATGG
Statistics
Matches: 89, Mismatches: 3, Indels: 14
0.84 0.03 0.13
Matches are distributed among these distances:
61 1 0.01
62 25 0.28
63 22 0.25
64 1 0.01
65 2 0.02
66 10 0.11
67 28 0.31
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (64 bp):
ATAATAATAAATAAATAATAAAATAAAATTAATATTATTTTAATTATTTATTTTATTCATAAAA
Found at i:34495811 original size:22 final size:22
Alignment explanation
Indices: 34495768--34495811 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
34495758 TTGTTCATAA
* *
34495768 AAATAATAATAAATAAATAAAT
1 AAATAAAAATAAATAAAAAAAT
34495790 AAATAAAAAT-AATAAGAAAAAT
1 AAATAAAAATAAATAA-AAAAAT
34495812 GGAATTGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (22 bp):
AAATAAAAATAAATAAAAAAAT
Found at i:34496393 original size:40 final size:39
Alignment explanation
Indices: 34496331--34497303 Score: 459
Period size: 39 Copynumber: 24.3 Consensus size: 39
34496321 TAACTTTAGG
* *
34496331 GGTAAAAGATTAGATTGT-TTCAA-CTTGCCCCATGGTCGA
1 GGTAAAAGATT-GATGGTCTTCAATC-TGCCCCATGATCGA
* * * *
34496370 GGTAAGAGATCTGATGGTCTTCAATCTGCCCTTCTATAACTTTAGG
1 GGTAAAAGAT-TGATGGTCTTCAATCTGCCC--C-ATGA---TCGA
* * *
34496416 GGTAAAAGATTAGATTGT-TTCAA-CTTGACCCATGGTCGA
1 GGTAAAAGATT-GATGGTCTTCAATC-TGCCCCATGATCGA
* ** * *
34496455 GGTAAGAGATTTGATGGTCTTCAATCTGCCCTTTGGT-TA
1 GGTAAAAGA-TTGATGGTCTTCAATCTGCCCCATGATCGA
* * *
34496494 GGGTAAAAGATTGGAT-TTCTTCAATATGCCCCATGATCGG
1 -GGTAAAAGATT-GATGGTCTTCAATCTGCCCCATGATCGA
* * *
34496534 GGTAAAAGATCGGATGGTCTTCAATCTTCCCTC-TGAT-TA
1 GGTAAAAGAT-TGATGGTCTTCAATCTGCCC-CATGATCGA
* *
34496573 GGGTAAAAGATTGGAT-TTCTTCAATCTGCCCCATGATCGG
1 -GGTAAAAGATT-GATGGTCTTCAATCTGCCCCATGATCGA
* * * *
34496613 GGTAAAAGATCGGATGGTCTTCAATCTTGTCCTC-TAGTTAG-
1 GGTAAAAGAT-TGATGGTCTTCAATC-TG-CCCCAT-GATCGA
* *
34496654 GGTAAAAGATTGGAT-TTCTTCAATCTGCCCCATGATCGG
1 GGTAAAAGATT-GATGGTCTTCAATCTGCCCCATGATCGA
* * * * * *
34496693 GGTAAAAGATCGGATGGTCTTTAATCTTTCCTC-TAGTTAG-
1 GGTAAAAGAT-TGATGGTCTTCAATC-TGCCCCAT-GATCGA
* * * *
34496733 GGTAAAAGATTAAAT-TTCTTCTATCTGCCCCATGATCGG
1 GGTAAAAGATT-GATGGTCTTCAATCTGCCCCATGATCGA
* * * *
34496772 GGTAAAAGATCGGATGGTCTTCAATCTTCTCTC-TGAT-TA
1 GGTAAAAGAT-TGATGGTCTTCAATCTGC-CCCATGATCGA
* * *
34496811 GGGTAAAAGATTGGAT-TTCTTCAATCTGCCCTATGATCGG
1 -GGTAAAAGATT-GATGGTCTTCAATCTGCCCCATGATCGA
* * *
34496851 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTC-TAGTTAG-
1 GGTAAAAGAT-TGATGGTCTTCAATC-TGCCC-CAT-GATCGA
* *
34496892 GGTAAAAGATTGGAT-TTCTTCAATCTGCCCCATGATCGG
1 GGTAAAAGATT-GATGGTCTTCAATCTGCCCCATGATCGA
* * *
34496931 GGTAAAAGATCGGATAGTCTTCAATCTTGCCCTC-TGAT-TA
1 GGTAAAAGAT-TGATGGTCTTCAATC-TGCCC-CATGATCGA
* *
34496971 GGGTAAAAGATTGGAT-TTCTTCAATCTGCCCCATGATCGG
1 -GGTAAAAGATT-GATGGTCTTCAATCTGCCCCATGATCGA
* * * *
34497011 GGTAAAAGATCGGATGGGCTTCAATCTTGCCCTC-TGGT-TA
1 GGTAAAAGAT-TGATGGTCTTCAATC-TGCCC-CATGATCGA
* *
34497051 GGGTAAAAGATTGAAT-TTCTTCAATCTGCCCCATGATCGG
1 -GGTAAAAGATTG-ATGGTCTTCAATCTGCCCCATGATCGA
* * *
34497091 GGTAAAAGATCGGATGGTCTTCAATCTTGCCCTC-TAGTTAG-
1 GGTAAAAGAT-TGATGGTCTTCAATC-TGCCC-CAT-GATCGA
* * * *
34497132 GGTAAAAGATTGGAT-TTCTTTAATCTGCCCTATGATCGG
1 GGTAAAAGATT-GATGGTCTTCAATCTGCCCCATGATCGA
* * * * *
34497171 GGTAAAAGATCGGATGGTCTTCAATCTTATCCTC-TGGT-TA
1 GGTAAAAGAT-TGATGGTCTTCAATC-T-GCCCCATGATCGA
* * *
34497211 GGGTAAAAGATTGGAT-TTCTTCAATCTGCCCCATGATGGG
1 -GGTAAAAGATT-GATGGTCTTCAATCTGCCCCATGATCGA
* *
34497251 GGTAAAAGATCGAATGGTCTTCAATCTTGCCCTC-TGGT-GA
1 GGTAAAAGATTG-ATGGTCTTCAATC-TGCCC-CATGATCGA
34497291 GGGTAAAAGATTG
1 -GGTAAAAGATTG
34497304 GAGGTTGTAA
Statistics
Matches: 704, Mismatches: 139, Indels: 180
0.69 0.14 0.18
Matches are distributed among these distances:
38 28 0.04
39 251 0.36
40 230 0.33
41 144 0.20
42 21 0.03
43 3 0.00
44 1 0.00
45 10 0.01
46 16 0.02
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (39 bp):
GGTAAAAGATTGATGGTCTTCAATCTGCCCCATGATCGA
Found at i:34496550 original size:79 final size:80
Alignment explanation
Indices: 34496330--34497305 Score: 1430
Period size: 80 Copynumber: 12.2 Consensus size: 80
34496320 ATAACTTTAG
* * * * *
34496330 GGGTAAAAGATTAGATTGT-TTCAA-CTTGCCCCATGGTCGAGGTAAGAGATCTGATGGTCTTCA
1 GGGTAAAAGATTGGATT-TCTTCAATC-TGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCA
**
34496393 ATC-TGCCCTTCTATAACTTTA
64 ATCTTGCCC-TC--T--GGTTA
* * * * * **
34496414 GGGGTAAAAGATTAGATTGT-TTCAA-CTTGACCCATGGTCGAGGTAAGAGATTTGATGGTCTTC
1 -GGGTAAAAGATTGGATT-TCTTCAATC-TGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
*
34496477 AATC-TGCCCTTTGGTTA
63 AATCTTGCCCTCTGGTTA
*
34496494 GGGTAAAAGATTGGATTTCTTCAATATGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
34496559 CTT-CCCTCTGATTA
66 CTTGCCCTCTGGTTA
34496573 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
* *
34496638 CTTGTCCTCTAGTTA
66 CTTGCCCTCTGGTTA
*
34496653 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTTAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
* *
34496718 CTT-TCCTCTAGTTA
66 CTTGCCCTCTGGTTA
** *
34496732 GGGTAAAAGATTAAATTTCTTCTATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
* *
34496797 CTT-CTCTCTGATTA
66 CTTGCCCTCTGGTTA
*
34496811 GGGTAAAAGATTGGATTTCTTCAATCTGCCCTATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
34496876 CTTGCCCTCTAGTTA
66 CTTGCCCTCTGGTTA
*
34496891 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATAGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
34496956 CTTGCCCTCTGATTA
66 CTTGCCCTCTGGTTA
*
34496971 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGGCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
34497036 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
*
34497051 GGGTAAAAGATTGAATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
34497116 CTTGCCCTCTAGTTA
66 CTTGCCCTCTGGTTA
* *
34497131 GGGTAAAAGATTGGATTTCTTTAATCTGCCCTATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
**
34497196 CTTATCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* *
34497211 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATGGGGGTAAAAGATCGAATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
34497276 CTTGCCCTCTGGTGA
66 CTTGCCCTCTGGTTA
34497291 GGGTAAAAGATTGGA
1 GGGTAAAAGATTGGA
34497306 GGTTGTAATT
Statistics
Matches: 828, Mismatches: 58, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
78 1 0.00
79 277 0.33
80 479 0.58
82 1 0.00
84 1 0.00
85 69 0.08
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (80 bp):
GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
CTTGCCCTCTGGTTA
Found at i:34497432 original size:50 final size:50
Alignment explanation
Indices: 34497359--34497484 Score: 119
Period size: 50 Copynumber: 2.5 Consensus size: 50
34497349 GTCCTTATGA
* * * * *
34497359 CTTCAATCTTCTCTTCTATAGCTTTAAATG-ACTGAGATTTGCCATTACAG
1 CTTCAATCTGCACCTCTACAGCTTTAAATGTA-TGAGATTTACCATTACAG
* * * ** *
34497409 CTTCATTTTGCCCCTCTACAGCTTTAGGTGTATGAGATTTACCATTGCAG
1 CTTCAATCTGCACCTCTACAGCTTTAAATGTATGAGATTTACCATTACAG
* *
34497459 TTTCAATCTGCACCTCTACCGCTTTA
1 CTTCAATCTGCACCTCTACAGCTTTA
34497485 GGGGTAAAAG
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
50 59 0.98
51 1 0.02
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.39
Consensus pattern (50 bp):
CTTCAATCTGCACCTCTACAGCTTTAAATGTATGAGATTTACCATTACAG
Found at i:34497485 original size:50 final size:50
Alignment explanation
Indices: 34497391--34497486 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 50
34497381 TTTAAATGAC
* * * *
34497391 TGAGATTTGCCATTACAGCTTCATTTTGCCCCTCTACAGCTTTAGGTGTA
1 TGAGATTTACCATTACAGCTTCAATCTGCACCTCTACAGCTTTAGGTGTA
* * *
34497441 TGAGATTTACCATTGCAGTTTCAATCTGCACCTCTACCGCTTTAGG
1 TGAGATTTACCATTACAGCTTCAATCTGCACCTCTACAGCTTTAGG
34497487 GGTAAAAGAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (50 bp):
TGAGATTTACCATTACAGCTTCAATCTGCACCTCTACAGCTTTAGGTGTA
Found at i:34497497 original size:50 final size:50
Alignment explanation
Indices: 34497393--34497498 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 50
34497383 TAAATGACTG
* * * * * **
34497393 AGATTTGCCATTACAGCTTCATTTTGCCCCTCTACAGCTTTAGGTGTATG
1 AGATTTACCATTACAGCTTCAATCTGCACCTCTACAGCTTTAGGGGTAAA
* * *
34497443 AGATTTACCATTGCAGTTTCAATCTGCACCTCTACCGCTTTAGGGGTAAA
1 AGATTTACCATTACAGCTTCAATCTGCACCTCTACAGCTTTAGGGGTAAA
34497493 AGATTT
1 AGATTT
34497499 GTTGTTCTAT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.36
Consensus pattern (50 bp):
AGATTTACCATTACAGCTTCAATCTGCACCTCTACAGCTTTAGGGGTAAA
Found at i:34498434 original size:21 final size:21
Alignment explanation
Indices: 34498409--34498467 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
34498399 CTCGACCTCC
34498409 CCTTTTTCTTTTTCTTTTCTT
1 CCTTTTTCTTTTTCTTTTCTT
*
34498430 CC-TTTTCCTTTTCTTTGTCTT
1 CCTTTTTCTTTTTCTTT-TCTT
34498451 --TTTTTCTTTTTTCTTTT
1 CCTTTTTC-TTTTTCTTTT
34498468 TTTAATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (21 bp):
CCTTTTTCTTTTTCTTTTCTT
Found at i:34498441 original size:26 final size:26
Alignment explanation
Indices: 34498412--34498467 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
34498402 GACCTCCCCT
*
34498412 TTTTCTTTTTCTTTTCTTCCTTTTCC
1 TTTTCTTTGTCTTTTCTTCCTTTTCC
* * *
34498438 TTTTCTTTGTCTTTTTTTCTTTTTTC
1 TTTTCTTTGTCTTTTCTTCCTTTTCC
34498464 TTTT
1 TTTT
34498468 TTTAATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (26 bp):
TTTTCTTTGTCTTTTCTTCCTTTTCC
Found at i:34498460 original size:8 final size:8
Alignment explanation
Indices: 34498447--34498492 Score: 51
Period size: 9 Copynumber: 5.8 Consensus size: 8
34498437 CTTTTCTTTG
34498447 TCTTTTTT
1 TCTTTTTT
34498455 TC-TTTTT
1 TCTTTTTT
34498462 TCTTTTTT
1 TCTTTTTT
*
34498470 TAATTTTTT
1 T-CTTTTTT
34498479 ATCTTTTTT
1 -TCTTTTTT
34498488 T-TTTT
1 TCTTTT
34498493 GAAATTTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
7 11 0.33
8 9 0.27
9 12 0.36
10 1 0.03
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.85
Consensus pattern (8 bp):
TCTTTTTT
Found at i:34498467 original size:15 final size:15
Alignment explanation
Indices: 34498438--34498492 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
34498428 TTCCTTTTCC
*
34498438 TTTTC-TTTGTCTTT
1 TTTTCTTTTTTCTTT
34498452 TTTTCTTTTTTCTTT
1 TTTTCTTTTTTCTTT
*
34498467 TTTTAATTTTTTATCTTT
1 TTTT--CTTTTT-TCTTT
34498485 TTTT-TTTT
1 TTTTCTTTT
34498493 GAAATTTCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
14 5 0.14
15 16 0.46
17 5 0.14
18 9 0.26
ACGTcount: A:0.05, C:0.09, G:0.02, T:0.84
Consensus pattern (15 bp):
TTTTCTTTTTTCTTT
Found at i:34498498 original size:24 final size:24
Alignment explanation
Indices: 34498449--34498499 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
34498439 TTTCTTTGTC
**
34498449 TTTTTTTCTTTTTTCTTTTTTTAA
1 TTTTTTTCTTTTTTCTTTTTGAAA
34498473 TTTTTTATCTTTTTT-TTTTTGAAA
1 TTTTTT-TCTTTTTTCTTTTTGAAA
34498497 TTT
1 TTT
34498500 CTTCCTCACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.80
Consensus pattern (24 bp):
TTTTTTTCTTTTTTCTTTTTGAAA
Found at i:34501451 original size:16 final size:15
Alignment explanation
Indices: 34501430--34501471 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 15
34501420 ATATGGTCGT
34501430 GCCTTAATGTTCAAAA
1 GCCTTAAT-TTCAAAA
34501446 GCCTTAA--TCAAAA
1 GCCTTAATTTCAAAA
34501459 GCCTTAATCTTCA
1 GCCTTAAT-TTCA
34501472 TAGGAAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 13 0.57
16 10 0.43
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.31
Consensus pattern (15 bp):
GCCTTAATTTCAAAA
Found at i:34501458 original size:13 final size:13
Alignment explanation
Indices: 34501440--34501467 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
34501430 GCCTTAATGT
34501440 TCAAAAGCCTTAA
1 TCAAAAGCCTTAA
34501453 TCAAAAGCCTTAA
1 TCAAAAGCCTTAA
34501466 TC
1 TC
34501468 TTCATAGGAA
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:0.43, C:0.25, G:0.07, T:0.25
Consensus pattern (13 bp):
TCAAAAGCCTTAA
Found at i:34503564 original size:63 final size:64
Alignment explanation
Indices: 34503485--34503633 Score: 223
Period size: 63 Copynumber: 2.3 Consensus size: 64
34503475 TTATTTATTT
34503485 ATAATATAAATAAATAATAAAACAAAATTAAT-ATTATTTTACATTTATTTATATTCAT-AAAAT
1 ATAA-ATAAATAAATAATAAAACAAAATTAATAATTATTTT-CATTTATTTATATTCATAAAAAT
34503548 A
64 A
* * *
34503549 ATAAATAAATAAATAATAAAATAAAATTAATAATTATTTTTATTTATTTATGTTCATAAAAATA
1 ATAAATAAATAAATAATAAAACAAAATTAATAATTATTTTCATTTATTTATATTCATAAAAATA
34503613 AT-AATAAATAAATAAATAAAA
1 ATAAATAAATAAAT-AATAAAA
34503634 ATAATAAGAA
Statistics
Matches: 79, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
63 52 0.66
64 27 0.34
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.39
Consensus pattern (64 bp):
ATAAATAAATAAATAATAAAACAAAATTAATAATTATTTTCATTTATTTATATTCATAAAAATA
Found at i:34503647 original size:18 final size:18
Alignment explanation
Indices: 34503606--34503647 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
34503596 TTATGTTCAT
*
34503606 AAAAATAATAATAAATAA
1 AAAAATAAAAATAAATAA
*
34503624 ATAAATAAAAAT-AATAA
1 AAAAATAAAAATAAATAA
34503641 GAAAAAT
1 -AAAAAT
34503648 GAAATTGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (18 bp):
AAAAATAAAAATAAATAA
Found at i:34509597 original size:18 final size:18
Alignment explanation
Indices: 34509574--34509611 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
34509564 TAATATAGTT
34509574 TTATTCG-GTTTATTCGAA
1 TTATTCGAG-TTATTCGAA
34509592 TTATTCGAGTTATTCGAA
1 TTATTCGAGTTATTCGAA
34509610 TT
1 TT
34509612 TGAAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.50
Consensus pattern (18 bp):
TTATTCGAGTTATTCGAA
Found at i:34510232 original size:15 final size:16
Alignment explanation
Indices: 34510212--34510242 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
34510202 TTTTTCCAGA
34510212 TTTTTTATTTT-TAAT
1 TTTTTTATTTTCTAAT
34510227 TTTTTTATTTTCTAAT
1 TTTTTTATTTTCTAAT
34510243 ATTTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTATTTTCTAAT
Found at i:34510551 original size:19 final size:20
Alignment explanation
Indices: 34510517--34510564 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
34510507 ATTTTCGAAA
34510517 AATAATTTT-TATAAAAT-T
1 AATAATTTTCTATAAAATGT
34510535 ATATAATTTTCTA-AAAATGT
1 A-ATAATTTTCTATAAAATGT
34510555 AAT-ATTTTCT
1 AATAATTTTCT
34510565 GACATTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 8 0.30
19 15 0.56
20 4 0.15
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (20 bp):
AATAATTTTCTATAAAATGT
Found at i:34514699 original size:3 final size:3
Alignment explanation
Indices: 34514691--34514718 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
34514681 AAACTAAAAC
34514691 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
34514719 AACAAATAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:34516453 original size:29 final size:29
Alignment explanation
Indices: 34516421--34516485 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
34516411 GAAAATGTGA
** *
34516421 TTTTGGAAATTTGGGAGCAAAATGGTAAT
1 TTTTGGAAATTCAGGAGCAAAATAGTAAT
** *
34516450 TTTTGGATGTTCAGGAGTAAAATAGTAAT
1 TTTTGGAAATTCAGGAGCAAAATAGTAAT
34516479 TTTTGGA
1 TTTTGGA
34516486 TGTTCGAGGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.03, G:0.26, T:0.38
Consensus pattern (29 bp):
TTTTGGAAATTCAGGAGCAAAATAGTAAT
Found at i:34516511 original size:29 final size:29
Alignment explanation
Indices: 34516434--34516510 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
34516424 TGGAAATTTG
*
34516434 GGAGCAAAATGGTAATTTTTGGATGTTCA
1 GGAGCAAAATAGTAATTTTTGGATGTTCA
*
34516463 GGAGTAAAATAGTAATTTTTGGATGTTC-
1 GGAGCAAAATAGTAATTTTTGGATGTTCA
34516491 -GAGGCAAAATCA-TAATTTTT
1 GGA-GCAAAAT-AGTAATTTTT
34516511 TTAGAAGTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 2 0.05
28 14 0.33
29 27 0.63
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.36
Consensus pattern (29 bp):
GGAGCAAAATAGTAATTTTTGGATGTTCA
Found at i:34516582 original size:60 final size:59
Alignment explanation
Indices: 34516515--34516830 Score: 264
Period size: 60 Copynumber: 5.3 Consensus size: 59
34516505 ATTTTTTTAG
**
34516515 AAGTTTGGGGTTTAAAATGGGATTTTGAAGAAGTTTGGAGGTTAAAATGTAATTTTGGAA
1 AAGTTTGGGG-TTAAAATGTAATTTTGAAGAAGTTTGGAGGTTAAAATGTAATTTTGGAA
* * * * * *
34516575 GACTTTGGGGGTTAAAATATAATCTTGGAA-AATTTTAGG-GGTTAAAATGTAATTTTGGAG
1 AAGTTT-GGGGTTAAAATGTAAT-TTTGAAGAAGTTT-GGAGGTTAAAATGTAATTTTGGAA
* * * * * *
34516635 AAGTTTAGGAGTCAAAATGTAATTTTAGAA-AAG-CTCGAGGATCAAAATGTAATTTTAGAA
1 AAGTTT-GGGGTTAAAATGTAATTTT-GAAGAAGTTTGGAGG-TTAAAATGTAATTTTGGAA
* * * * * *
34516695 AAGTTCAGAGGTTAAAATATAATTTTGGAGAAGTTTGGGGGTTAAAATGTATTTTTGGAA
1 AAGTT-TGGGGTTAAAATGTAATTTTGAAGAAGTTTGGAGGTTAAAATGTAATTTTGGAA
* * * * * * *
34516755 AAGTTTGAGGATAAAATGTAATTTTAAAGAAG-TTCGAGGTTAAAATATAATTTTAGAG
1 AAGTTTGGGGTTAAAATGTAATTTTGAAGAAGTTTGGAGGTTAAAATGTAATTTTGGAA
*
34516813 AAGTTTATGGGTTAAAAT
1 AAGTTT-GGGGTTAAAAT
34516831 ATGATTTTTG
Statistics
Matches: 199, Mismatches: 47, Indels: 21
0.75 0.18 0.08
Matches are distributed among these distances:
58 27 0.14
59 37 0.19
60 120 0.60
61 15 0.08
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.35
Consensus pattern (59 bp):
AAGTTTGGGGTTAAAATGTAATTTTGAAGAAGTTTGGAGGTTAAAATGTAATTTTGGAA
Found at i:34516623 original size:90 final size:90
Alignment explanation
Indices: 34516521--34516844 Score: 291
Period size: 90 Copynumber: 3.6 Consensus size: 90
34516511 TTAGAAGTTT
** * * * *
34516521 GGGGTTTAAAATGGGATTTTGAAGAAGTTTGGAGGTTAAAATGTAATTTTGGAAGA-CTTTGGGG
1 GGGG-TTAAAATGTAATTTTGGAGAAGTTTGGAGGTTAAAATGTAATTTTGGAAAAGC-TCGAGG
* * * * *
34516585 GTTAAAATATAATCTTGGAAAATTTTA
64 ATCAAAATATAATCTTAGAAAAGTTCA
* *
34516612 GGGGTTAAAATGTAATTTTGGAGAAGTTTAGGA-GTCAAAATGTAATTTTAGAAAAGCTCGAGGA
1 GGGGTTAAAATGTAATTTTGGAGAAGTTT-GGAGGTTAAAATGTAATTTTGGAAAAGCTCGAGGA
* *
34516676 TCAAAATGTAATTTTAGAAAAGTTCA
65 TCAAAATATAATCTTAGAAAAGTTCA
* * * * * *
34516702 GAGGTTAAAATATAATTTTGGAGAAGTTTGGGGGTTAAAATGTATTTTTGGAAAAGTTTGAGGAT
1 GGGGTTAAAATGTAATTTTGGAGAAGTTTGGAGGTTAAAATGTAATTTTGGAAAAGCTCGAGGAT
* *
34516767 -AAAATGTAATTTTA-AAGAAGTTC-
66 CAAAATATAATCTTAGAA-AAGTTCA
* * * * * *
34516790 GAGGTTAAAATATAATTTTAGAGAAGTTTATG-GGTTAAAATATGATTTTTGGAAA
1 GGGGTTAAAATGTAATTTTGGAGAAGTTT-GGAGGTTAAAATGT-AATTTTGGAAA
34516845 GTTTAAGGAC
Statistics
Matches: 201, Mismatches: 26, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
88 40 0.20
89 34 0.17
90 119 0.59
91 8 0.04
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (90 bp):
GGGGTTAAAATGTAATTTTGGAGAAGTTTGGAGGTTAAAATGTAATTTTGGAAAAGCTCGAGGAT
CAAAATATAATCTTAGAAAAGTTCA
Found at i:34516831 original size:30 final size:29
Alignment explanation
Indices: 34516515--34516849 Score: 219
Period size: 30 Copynumber: 11.2 Consensus size: 29
34516505 ATTTTTTTAG
* **
34516515 AAGTTTGGGGTTTAAAATGGGATTTT-GAA
1 AAGTTTAGGG-TTAAAATGTAATTTTAGAA
* *
34516544 GAAGTTTGGAGGTTAAAATGTAATTTTGGAA
1 -AAGTTTAG-GGTTAAAATGTAATTTTAGAA
* * * * * *
34516575 GACTTTGGGGGTTAAAATATAATCTTGGAA
1 AAGTTT-AGGGTTAAAATGTAATTTTAGAA
* * *
34516605 AATTTTAGGGGTTAAAATGTAATTTTGGAG
1 AAGTTTA-GGGTTAAAATGTAATTTTAGAA
*
34516635 AAGTTTAGGAGTCAAAATGTAATTTTAGAA
1 AAGTTTAGG-GTTAAAATGTAATTTTAGAA
** * *
34516665 AAGCTCGAGGATCAAAATGTAATTTTAGAA
1 AAG-TTTAGGGTTAAAATGTAATTTTAGAA
* * * *
34516695 AAGTTCAGAGGTTAAAATATAATTTTGGAG
1 AAGTTTAG-GGTTAAAATGTAATTTTAGAA
* * *
34516725 AAGTTTGGGGGTTAAAATGTATTTTTGGAA
1 AAGTTT-AGGGTTAAAATGTAATTTTAGAA
*
34516755 AAGTTT-GAGGATAAAATGTAATTTTA-AA
1 AAGTTTAG-GGTTAAAATGTAATTTTAGAA
* * *
34516783 GAAG-TTCGAGGTTAAAATATAATTTTAGAG
1 -AAGTTTAG-GGTTAAAATGTAATTTTAGAA
* * * *
34516813 AAGTTTATGGGTTAAAATATGATTTTTGGA
1 AAGTTTA-GGGTTAAAATGTAATTTTAGAA
34516843 AAGTTTA
1 AAGTTTA
34516850 AGGACCTACT
Statistics
Matches: 249, Mismatches: 42, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
28 5 0.02
29 44 0.18
30 187 0.75
31 13 0.05
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.36
Consensus pattern (29 bp):
AAGTTTAGGGTTAAAATGTAATTTTAGAA
Found at i:34521995 original size:29 final size:28
Alignment explanation
Indices: 34521963--34522022 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
34521953 GAAAATATGA
*
34521963 TTTTGGAAATTTGGGGGCAAAACGGTAAT
1 TTTTGGAAATTCGGGGGC-AAACGGTAAT
** *
34521992 TTTTGGACGTTCGGGGGCAAATGGTAAT
1 TTTTGGAAATTCGGGGGCAAACGGTAAT
34522020 TTT
1 TTT
34522023 GGACGTTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.25, C:0.08, G:0.32, T:0.35
Consensus pattern (28 bp):
TTTTGGAAATTCGGGGGCAAACGGTAAT
Found at i:34522030 original size:27 final size:29
Alignment explanation
Indices: 34521975--34522030 Score: 89
Period size: 27 Copynumber: 2.0 Consensus size: 29
34521965 TTGGAAATTT
34521975 GGGGGCAAAACGGTAATTTTTGGACGTTC
1 GGGGGCAAAACGGTAATTTTTGGACGTTC
*
34522004 GGGGGC-AAATGGTAA-TTTTGGACGTTC
1 GGGGGCAAAACGGTAATTTTTGGACGTTC
34522031 AAGGCAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 12 0.46
28 8 0.31
29 6 0.23
ACGTcount: A:0.23, C:0.12, G:0.36, T:0.29
Consensus pattern (29 bp):
GGGGGCAAAACGGTAATTTTTGGACGTTC
Found at i:34522040 original size:27 final size:28
Alignment explanation
Indices: 34521978--34522052 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 28
34521968 GAAATTTGGG
* **
34521978 GGCAAAACGGTAATTTTTGGACGTTCGGG
1 GGCAAAATGGTAA-TTTTGGACGTTCGAA
34522007 GGC-AAATGGTAATTTTGGACGTTC-AA
1 GGCAAAATGGTAATTTTGGACGTTCGAA
**
34522033 GGCAAAATTATAATTTTGGA
1 GGCAAAATGGTAATTTTGGA
34522053 GAAGTTTAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 3 0.08
27 26 0.65
28 8 0.20
29 3 0.08
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.31
Consensus pattern (28 bp):
GGCAAAATGGTAATTTTGGACGTTCGAA
Found at i:34522095 original size:30 final size:30
Alignment explanation
Indices: 34522043--34522316 Score: 245
Period size: 30 Copynumber: 9.2 Consensus size: 30
34522033 GGCAAAATTA
* *
34522043 TAATTTTGGAGAAGTTTA-AGGTTAAAATG
1 TAATTTTAGAAAAGTTTAGAGGTTAAAATG
* *
34522072 -AGATTTTATATAAGTTTAGAGGTTAAAATG
1 TA-ATTTTAGAAAAGTTTAGAGGTTAAAATG
* * * *
34522102 TAATTTTGGAGAAGTTTGGAGGTCAAAATG
1 TAATTTTAGAAAAGTTTAGAGGTTAAAATG
* * * * *
34522132 TAATTTTGGAAGAGTTTAGGGGTCAAAATA
1 TAATTTTAGAAAAGTTTAGAGGTTAAAATG
* * * *
34522162 TAATTTTATATAAGTTTGGTGGTTAAAATG
1 TAATTTTAGAAAAGTTTAGAGGTTAAAATG
*
34522192 TAATTTTAGAAAAGCTT-GAGGGTTAAAATG
1 TAATTTTAGAAAAGTTTAGA-GGTTAAAATG
*
34522222 TAATTTTGGAAAAGTTT-GAGGGTTAAAATG
1 TAATTTTAGAAAAGTTTAGA-GGTTAAAATG
* * *
34522252 TAATTTTGGAGAAGTTT-GGGGTTAAAATG
1 TAATTTTAGAAAAGTTTAGAGGTTAAAATG
* * *
34522281 TATTTTTGGAAAAGTTTA-AGGGTTAAAATA
1 TAATTTTAGAAAAGTTTAGA-GGTTAAAATG
34522311 TAATTT
1 TAATTT
34522317 CAAAGAAGTT
Statistics
Matches: 205, Mismatches: 34, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
28 1 0.00
29 39 0.19
30 164 0.80
31 1 0.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.38
Consensus pattern (30 bp):
TAATTTTAGAAAAGTTTAGAGGTTAAAATG
Found at i:34522168 original size:90 final size:89
Alignment explanation
Indices: 34522043--34522316 Score: 295
Period size: 90 Copynumber: 3.1 Consensus size: 89
34522033 GGCAAAATTA
* * * *
34522043 TAATTTTGGAGAAGTTT-AAGGTTAAAATGA-GATTTTATATAAGTTTAGAGGTTAAAATGTAAT
1 TAATTTTGGAAAAGTTTGAGGGTCAAAAT-ATAATTTTATATAAGTTT-GAGGTTAAAATGTAAT
*
34522106 TTTGGAGAAGTTTG-GAGGTCAAAATG
64 TTTGGAAAAGTTTGAG-GGTCAAAATG
* *
34522132 TAATTTTGGAAGAGTTT-AGGGGTCAAAATATAATTTTATATAAGTTTGGTGGTTAAAATGTAAT
1 TAATTTTGGAAAAGTTTGA-GGGTCAAAATATAATTTTATATAAGTTT-GAGGTTAAAATGTAAT
* * *
34522196 TTTAGAAAAGCTTGAGGGTTAAAATG
64 TTTGGAAAAGTTTGAGGGTCAAAATG
* * ** * * *
34522222 TAATTTTGGAAAAGTTTGAGGGTTAAAATGTAATTTTGGAGAAGTTTGGGGTTAAAATGTATTTT
1 TAATTTTGGAAAAGTTTGAGGGTCAAAATATAATTTTATATAAGTTTGAGGTTAAAATGTAATTT
* * *
34522287 TGGAAAAGTTTAAGGGTTAAAATA
66 TGGAAAAGTTTGAGGGTCAAAATG
34522311 TAATTT
1 TAATTT
34522317 CAAAGAAGTT
Statistics
Matches: 158, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
89 59 0.37
90 97 0.61
91 2 0.01
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.38
Consensus pattern (89 bp):
TAATTTTGGAAAAGTTTGAGGGTCAAAATATAATTTTATATAAGTTTGAGGTTAAAATGTAATTT
TGGAAAAGTTTGAGGGTCAAAATG
Found at i:34522744 original size:12 final size:12
Alignment explanation
Indices: 34522727--34522760 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
34522717 GCTGGCCATG
34522727 GCTCCGTCGTAC
1 GCTCCGTCGTAC
34522739 GCTCCGTCGTAC
1 GCTCCGTCGTAC
34522751 GCTCCGTCGT
1 GCTCCGTCGT
34522761 CCACGACGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.06, C:0.41, G:0.26, T:0.26
Consensus pattern (12 bp):
GCTCCGTCGTAC
Found at i:34523372 original size:10 final size:10
Alignment explanation
Indices: 34523340--34523374 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
34523330 GTGTAAAAAA
34523340 TAATATATAT
1 TAATATATAT
34523350 ATATATATATAT
1 -TA-ATATATAT
34523362 TAATATATAT
1 TAATATATAT
34523372 TAA
1 TAA
34523375 GAATAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 11 0.48
11 4 0.17
12 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
TAATATATAT
Found at i:34526687 original size:18 final size:17
Alignment explanation
Indices: 34526655--34526690 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
34526645 TAAATGAGTT
*
34526655 AATTAGGATTAAATTGG
1 AATTAAGATTAAATTGG
34526672 AATTAAGATATAAATTGG
1 AATTAAGAT-TAAATTGG
34526690 A
1 A
34526691 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.33
Consensus pattern (17 bp):
AATTAAGATTAAATTGG
Found at i:34535036 original size:13 final size:13
Alignment explanation
Indices: 34535020--34535049 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
34535010 TCAGTTATTA
34535020 TATTATTATCATT
1 TATTATTATCATT
*
34535033 TATTATTTTCATT
1 TATTATTATCATT
34535046 TATT
1 TATT
34535050 TCGAAAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTATTATCATT
Found at i:34536047 original size:29 final size:28
Alignment explanation
Indices: 34536013--34536297 Score: 168
Period size: 29 Copynumber: 9.8 Consensus size: 28
34536003 TGAACTTTTT
34536013 CAAAATCACATTTTAACCTCAAACTTTC
1 CAAAATCACATTTTAACCTCAAACTTTC
* * * *
34536041 CTAAAATTACATTTGACCCTTAAACTTTTTC
1 C-AAAATCACATTTTAACCTCAAAC--TTTC
* * * **
34536072 AAAAATTATATTTT-TGCTGCAAACTTCTC
1 CAAAATCACATTTTAACCT-CAAACTT-TC
* *
34536101 CAAAAATCACTTTTTAACCCTC-AACTTTT
1 C-AAAATCACATTTTAA-CCTCAAACTTTC
*
34536130 TAAAATCACATTTTAATCC-CTAAACTTTC
1 CAAAATCACATTTTAA-CCTC-AAACTTTC
* *
34536159 CAAAATTACATTTTAACCTTCATACTTTCC
1 CAAAATCACATTTTAACC-TCAAACTTT-C
* *
34536189 CAAAATCACATTTTGACC-CTAAACTTTTA
1 CAAAATCACATTTTAACCTC-AAAC-TTTC
* *
34536218 CAAAACCATATTTTAACC-CTAAACTTTC
1 CAAAATCACATTTTAACCTC-AAACTTTC
* * *
34536246 CTAAAATTACCTTTTTACC-CTAAACTTTC
1 C-AAAATCACATTTTAACCTC-AAACTTTC
* * *
34536275 CAAAATTACATTTTGACCCCAAA
1 CAAAATCACATTTTAACCTCAAA
34536298 TTCTTCGAAA
Statistics
Matches: 201, Mismatches: 39, Indels: 34
0.73 0.14 0.12
Matches are distributed among these distances:
27 1 0.00
28 44 0.22
29 98 0.49
30 51 0.25
31 5 0.02
32 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (28 bp):
CAAAATCACATTTTAACCTCAAACTTTC
Found at i:34536070 original size:58 final size:57
Alignment explanation
Indices: 34535999--34536287 Score: 214
Period size: 58 Copynumber: 5.0 Consensus size: 57
34535989 CATAAAAAGG
* *
34535999 CCCTTGAACTTTTTCAAAATCACATTTTAA-CCTCAAACTTTCCTAAAATTACATTTGA
1 CCCTTAAACTTTTTCAAAATCACATTTTAACCCT-AAACTTTCC-AAAATTACATTTAA
* * ** * * *
34536057 CCCTTAAACTTTTTCAAAAATTATATTTTTGCTGC-AAACTTCTCCAAAAATCACTTTTTAA
1 CCCTTAAACTTTTTC-AAAATCACATTTTAAC-CCTAAACTT-TCC-AAAATTAC-ATTTAA
*
34536118 CCC-TCAACTTTTT-AAAATCACATTTTAATCCCTAAACTTTCCAAAATTACATTTTAA
1 CCCTTAAACTTTTTCAAAATCACATTTTAA-CCCTAAACTTTCCAAAATTACA-TTTAA
* ** * * ** *
34536175 -CCTTCATACTTTCCCAAAATCACATTTTGACCCTAAACTTTTACAAAACCATATTTTAA
1 CCCTT-AAACTTTTTCAAAATCACATTTTAACCCTAAAC-TTTCCAAAATTACA-TTTAA
* * * *
34536234 CCC-TAAAC-TTTCCTAAAATTACCTTTTTACCCTAAACTTTCCAAAATTACATTT
1 CCCTTAAACTTTTTC-AAAATCACATTTTAACCCTAAACTTTCCAAAATTACATTT
34536288 TGACCCCAAA
Statistics
Matches: 181, Mismatches: 36, Indels: 30
0.73 0.15 0.12
Matches are distributed among these distances:
56 5 0.03
57 27 0.15
58 65 0.36
59 55 0.30
60 21 0.12
61 8 0.04
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (57 bp):
CCCTTAAACTTTTTCAAAATCACATTTTAACCCTAAACTTTCCAAAATTACATTTAA
Found at i:34536208 original size:87 final size:87
Alignment explanation
Indices: 34536092--34536293 Score: 248
Period size: 87 Copynumber: 2.3 Consensus size: 87
34536082 TTTTTGCTGC
* * * * * *
34536092 AAACTTCTCCAAAAATCACTTTTTAACCCTCAACTTTT-TAAAATCACATTTTAATCCCTAAACT
1 AAACTT-TCCCAAAATCACATTTTGACCCTAAACTTTTACAAAACCACATTTTAA-CCCTAAACT
*
34536156 TTCC-AAAATTACATTTTAACCTT
64 TTCCTAAAATTACATTTTAACCCT
* *
34536179 CATACTTTCCCAAAATCACATTTTGACCCTAAACTTTTACAAAACCATATTTTAACCCTAAACTT
1 -AAACTTTCCCAAAATCACATTTTGACCCTAAACTTTTACAAAACCACATTTTAACCCTAAACTT
* *
34536244 TCCTAAAATTACCTTTTTACCCT
65 TCCTAAAATTACATTTTAACCCT
*
34536267 AAACTTT-CCAAAATTACATTTTGACCC
1 AAACTTTCCCAAAATCACATTTTGACCC
34536294 CAAATTCTTC
Statistics
Matches: 99, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
86 19 0.19
87 46 0.46
88 34 0.34
ACGTcount: A:0.36, C:0.27, G:0.01, T:0.37
Consensus pattern (87 bp):
AAACTTTCCCAAAATCACATTTTGACCCTAAACTTTTACAAAACCACATTTTAACCCTAAACTTT
CCTAAAATTACATTTTAACCCT
Found at i:34543647 original size:39 final size:39
Alignment explanation
Indices: 34543591--34543710 Score: 132
Period size: 39 Copynumber: 2.9 Consensus size: 39
34543581 ATATTTTGCC
* *
34543591 TAAAAAATGGATTGAGATGAAAACTCGTAAAGGGCGTCT
1 TAAAAAAAGGATTGAGATGAAAACTCATAAAGGGCGTCT
* * *
34543630 TAAAAAAAGGATCGAGATGAAAACCCATAAAGGGCATCT
1 TAAAAAAAGGATTGAGATGAAAACTCATAAAGGGCGTCT
*
34543669 TGAAACCAAAAAGGATTTTGAGTTGAAAACTCATAAAGGGCG
1 T--AA--AAAAAGGA--TTGAGATGAAAACTCATAAAGGGCG
34543711 GCTCAAATTC
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
39 35 0.53
41 2 0.03
43 8 0.12
45 21 0.32
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.20
Consensus pattern (39 bp):
TAAAAAAAGGATTGAGATGAAAACTCATAAAGGGCGTCT
Found at i:34544571 original size:49 final size:48
Alignment explanation
Indices: 34544452--34544614 Score: 150
Period size: 49 Copynumber: 3.3 Consensus size: 48
34544442 AATACTTTGG
* * *
34544452 AGATATGAAGAGAAAGGTTGAGGCCGCAACGGCGAACCCGATACC-T-T
1 AGATATGAAG-GGAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGA
* * * **
34544499 AGAATATGTAATGGAAACGTTGAGGCCGCAATGATGAACCCGGTACCATGA
1 AG-ATATG-AA-GGGAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGA
* * * *
34544550 AGATTTGAAGGGAAGGATTGAGGCCACAACGGTGAATCCGGTACCATGA
1 AGATATGAAGGGAAGG-TTGAGGCCGCAACGGCGAACCCGGTACCATGA
*
34544599 AGATTTGAAGGGAAGG
1 AGATATGAAGGGAAGG
34544615 AAGGAAGAAG
Statistics
Matches: 97, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
47 2 0.02
48 10 0.10
49 77 0.79
50 6 0.06
51 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.18
Consensus pattern (48 bp):
AGATATGAAGGGAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGA
Found at i:34544615 original size:49 final size:49
Alignment explanation
Indices: 34544538--34544818 Score: 251
Period size: 49 Copynumber: 5.5 Consensus size: 49
34544528 AATGATGAAC
*
34544538 CCGGTACCATGAAGATTTGAAGGGAAGGATTGAGGCCACAACGGTGAAT
1 CCGGTACCATGAAGATTTGAAGGGAAGGATTGAGGCCACAACGGCGAAT
* * *
34544587 CCGGTACCATGAAGATTTGAAGGGAAGGAAGGAAGAAGGATAGGAGGCCGCGACGGCGAAT
1 CCGGTACCATGAAGATTT---------GAAGG--GAAGGAT-TGAGGCCACAACGGCGAAT
* *
34544648 CCGGTACCATGAAGATTTGAAGGGAAGAATTGAGGCCGA-AACGGCGAAC
1 CCGGTACCATGAAGATTTGAAGGGAAGGATTGAGGCC-ACAACGGCGAAT
* * * ** *
34544697 CCAGTACCATAAAGATTTGAAGGGAAGGATTGAGGCTATGACGGTGAAT
1 CCGGTACCATGAAGATTTGAAGGGAAGGATTGAGGCCACAACGGCGAAT
* * * **
34544746 CCGGTACCTTAGAAGATGTGATAGGAAAGG-TTGAGGCTGCAACGGCGAAT
1 CCGGTACCAT-GAAGATTTGA-AGGGAAGGATTGAGGCCACAACGGCGAAT
*
34544796 CCGGTACCATGAAGATATGAAGG
1 CCGGTACCATGAAGATTTGAAGG
34544819 AAAAAGTTGA
Statistics
Matches: 189, Mismatches: 27, Indels: 33
0.76 0.11 0.13
Matches are distributed among these distances:
48 4 0.02
49 89 0.47
50 39 0.21
51 7 0.04
52 5 0.03
58 5 0.03
60 7 0.04
61 33 0.17
ACGTcount: A:0.33, C:0.16, G:0.34, T:0.17
Consensus pattern (49 bp):
CCGGTACCATGAAGATTTGAAGGGAAGGATTGAGGCCACAACGGCGAAT
Found at i:34544648 original size:61 final size:60
Alignment explanation
Indices: 34544561--34544674 Score: 183
Period size: 61 Copynumber: 1.9 Consensus size: 60
34544551 GATTTGAAGG
* *
34544561 GAAGGATTGAGGCCACAACGGTGAATCCGGTACCATGAAGATTTGAAGGGAAGGAAGGAA
1 GAAGGATGGAGGCCACAACGGCGAATCCGGTACCATGAAGATTTGAAGGGAAGGAAGGAA
* *
34544621 GAAGGATAGGAGGCCGCGACGGCGAATCCGGTACCATGAAGATTTGAAGGGAAG
1 GAAGGAT-GGAGGCCACAACGGCGAATCCGGTACCATGAAGATTTGAAGGGAAG
34544675 AATTGAGGCC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
60 7 0.14
61 42 0.86
ACGTcount: A:0.34, C:0.15, G:0.37, T:0.14
Consensus pattern (60 bp):
GAAGGATGGAGGCCACAACGGCGAATCCGGTACCATGAAGATTTGAAGGGAAGGAAGGAA
Found at i:34544792 original size:99 final size:98
Alignment explanation
Indices: 34544638--34544818 Score: 238
Period size: 99 Copynumber: 1.8 Consensus size: 98
34544628 AGGAGGCCGC
* *
34544638 GACGGCGAATCCGGTACCATGAAGATTTGAAGGGAAGAATTGAGGCCGAAACGGCGAACCCAGTA
1 GACGGCGAATCCGGTACCATGAAGATGTGAAGGAAAGAATTGAGGCCGAAACGGCGAACCCAGTA
*
34544703 CCATAAAGATTTGAAGGGAAGGATTGAGGCTAT
66 CCATAAAGATATGAAGGGAAGGATTGAGGCTAT
* * * * * * *
34544736 GACGGTGAATCCGGTACCTTAGAAGATGTGATAGGAAAG-GTTGAGGCTGCAACGGCGAATCCGG
1 GACGGCGAATCCGGTACCAT-GAAGATGTGA-AGGAAAGAATTGAGGCCGAAACGGCGAACCCAG
*
34544800 TACCATGAAGATATGAAGG
64 TACCATAAAGATATGAAGG
34544819 AAAAAGTTGA
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
98 18 0.26
99 46 0.66
100 6 0.09
ACGTcount: A:0.33, C:0.16, G:0.33, T:0.18
Consensus pattern (98 bp):
GACGGCGAATCCGGTACCATGAAGATGTGAAGGAAAGAATTGAGGCCGAAACGGCGAACCCAGTA
CCATAAAGATATGAAGGGAAGGATTGAGGCTAT
Found at i:34544831 original size:49 final size:48
Alignment explanation
Indices: 34544630--34545133 Score: 255
Period size: 49 Copynumber: 10.3 Consensus size: 48
34544620 AGAAGGATAG
* * * *
34544630 GAGGCCGCGACGGCGAATCCGGTACCATGAAGATTTGAAGGGAAGAATT
1 GAGGCCGCAACGGCGAATCCGGTACCATGAAGATATGAAGGAAAG-GTT
* * * * * *
34544679 GAGGCCGAAACGGCGAACCCAGTACCATAAAGATTTGAAGGGAAGGATT
1 GAGGCCGCAACGGCGAATCCGGTACCATGAAGATATGAAGGAAAGG-TT
**** * * *
34544728 GAGGCTATGACGGTGAATCCGGTACCTTAGAAGATGTGATAGGAAAGGTT
1 GAGGCCGCAACGGCGAATCCGGTACCAT-GAAGATATGA-AGGAAAGGTT
* *
34544778 GAGGCTGCAACGGCGAATCCGGTACCATGAAGATATGAAGGAAAAAGTT
1 GAGGCCGCAACGGCGAATCCGGTACCATGAAGATATGAAGG-AAAGGTT
* * * *
34544827 GAGGCCGTAACGACG-AGCTCGATACCATGAAGATATGAAGAGAAAGGTT
1 GAGGCCGCAACGGCGAATC-CGGTACCATGAAGATATGAAG-GAAAGGTT
* * * * * * * *
34544876 GAGGTCGCAACGG-TAAACCTGATACTAAGAAGATGTGATAGGAAAAGTT
1 GAGGCCGCAACGGCGAATCC-GGTACCATGAAGATATGA-AGGAAAGGTT
* * ** * * * *
34544925 GAGGCCACAATGATG-AGCCCGTACCACGGAGATATGAAGGGAAAGGTT
1 GAGGCCGCAACGGCGAATCCGGTACCATGAAGATATGAA-GGAAAGGTT
* * * ** * *
34544973 GAGGCTGCAATGGCGAA-CCTGGTACTTAAAAAGATGTGATGGGAAAGGTT
1 GAGGCCGCAACGGCGAATCC-GGTAC-CATGAAGATATGA-AGGAAAGGTT
** * * * **
34545023 GAGGCCGCAACGGTAAACCCGATA-CTTAGAAGATGCGATAGG-AAGGATT
1 GAGGCCGCAACGGCGAATCCGGTACCAT-GAAGATATGA-AGGAAAGG-TT
** * * * * * *
34545072 GAGGTTGCCATGACGAATCCGATACTATGAAGATATGAAGGGGAAGGTT
1 GAGGCCGCAACGGCGAATCCGGTACCATGAAGATATGAA-GGAAAGGTT
*
34545121 GAGGCCGTAACGG
1 GAGGCCGCAACGG
34545134 GAAACCTAGC
Statistics
Matches: 342, Mismatches: 92, Indels: 42
0.72 0.19 0.09
Matches are distributed among these distances:
47 1 0.00
48 44 0.13
49 214 0.63
50 74 0.22
51 9 0.03
ACGTcount: A:0.34, C:0.16, G:0.32, T:0.18
Consensus pattern (48 bp):
GAGGCCGCAACGGCGAATCCGGTACCATGAAGATATGAAGGAAAGGTT
Found at i:34544992 original size:97 final size:98
Alignment explanation
Indices: 34544769--34545034 Score: 297
Period size: 98 Copynumber: 2.7 Consensus size: 98
34544759 AGATGTGATA
* * *
34544769 GGAAAGGTTGAGGCTGCAACGGCGAATCC-GGTACCATGAAGATATGA-AGGAAAAAGTTGAGGC
1 GGAAAGGTTGAGGCTGCAACGGCGAA-CCTGGTACTAAGAAGATGTGATAGG-AAAAGTTGAGGC
** * *
34544832 CGTAACGACGAGCTCGATACCATGAAGATATGAAG
64 CACAACGACGAGCCCGATACCACGAAGATATGAAG
* ** *
34544867 AGAAAGGTTGAGG-TCGCAACGGTAAACCTGATACTAAGAAGATGTGATAGGAAAAGTTGAGGCC
1 GGAAAGGTTGAGGCT-GCAACGGCGAACCTGGTACTAAGAAGATGTGATAGGAAAAGTTGAGGCC
* * *
34544931 ACAATGATGAGCCCG-TACCACGGAGATATGAAG
65 ACAACGACGAGCCCGATACCACGAAGATATGAAG
* * * *
34544964 GGAAAGGTTGAGGCTGCAATGGCGAACCTGGTACTTAAAAAGATGTGATGGGAAAGGTTGAGGCC
1 GGAAAGGTTGAGGCTGCAACGGCGAACCTGGTAC-TAAGAAGATGTGATAGGAAAAGTTGAGGCC
*
34545029 GCAACG
65 ACAACG
34545035 GTAAACCCGA
Statistics
Matches: 139, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
97 46 0.33
98 90 0.65
99 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.32, T:0.17
Consensus pattern (98 bp):
GGAAAGGTTGAGGCTGCAACGGCGAACCTGGTACTAAGAAGATGTGATAGGAAAAGTTGAGGCCA
CAACGACGAGCCCGATACCACGAAGATATGAAG
Found at i:34545160 original size:147 final size:147
Alignment explanation
Indices: 34544868--34545145 Score: 317
Period size: 147 Copynumber: 1.9 Consensus size: 147
34544858 GATATGAAGA
* * *
34544868 GAAAGGTTGAGGTCGCAACGGTAAACCTGATACTAAGAAGATGTGATAGGAAAAGTTGAGGCCAC
1 GAAAGGTTGAGGCCGCAACGGTAAACCCGATACTAAGAAGATGCGATAGGAAAAGTTGAGGCCAC
* * * * * * *
34544933 AATGATGAGCCCGTACCACGGAGATATGAAGGGAAAGGTTGAGGCTGCAATGGCGAACCTGGTAC
66 AATGACGAACCCGTACCACGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTAGCAC
*
34544998 TTAAAAAGATGTGATGG
131 TTAAAAAGACGTGATGG
* * ***
34545015 GAAAGGTTGAGGCCGCAACGGTAAACCCGATACTTAGAAGATGCGATAGG-AAGGATTGAGGTTG
1 GAAAGGTTGAGGCCGCAACGGTAAACCCGATACTAAGAAGATGCGATAGGAAAAG-TTGAGGCCA
* * * * * *
34545079 CCATGACGAATCCGATACTATGAAGATATGAAGGGGAAGGTTGAGGCCGTAACGG-GAAACCTAG
65 CAATGACGAACCCG-TACCACGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCG-AACCTAG
34545143 CAC
128 CAC
34545146 CTTAGAAACG
Statistics
Matches: 107, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
146 3 0.03
147 63 0.59
148 41 0.38
ACGTcount: A:0.34, C:0.15, G:0.32, T:0.18
Consensus pattern (147 bp):
GAAAGGTTGAGGCCGCAACGGTAAACCCGATACTAAGAAGATGCGATAGGAAAAGTTGAGGCCAC
AATGACGAACCCGTACCACGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTAGCAC
TTAAAAAGACGTGATGG
Found at i:34547325 original size:57 final size:58
Alignment explanation
Indices: 34547211--34547363 Score: 177
Period size: 57 Copynumber: 2.6 Consensus size: 58
34547201 TCCTCAAACA
* *
34547211 TTCCTAAAATCACATTTTACCCTAAACTTTCCCAAAATCACATTTTTTACCCTAAACTT
1 TTCC-AAAATTACATTTTACCCTAAACTTTTCCAAAATCACATTTTTTACCCTAAACTT
* * **
34547270 TT-CAAAATTACATTTTTCCCTAACCTTTTCCAAAATCACATTTTGATT-GTC-AAACTT
1 TTCCAAAATTACATTTTACCCTAAACTTTTCCAAAATCACATTTT--TTACCCTAAACTT
*
34547327 TTCCGAAATTACATTTTGACTCCTAAACTTTTCCAAA
1 TTCCAAAATTACATTTT-AC-CCTAAACTTTTCCAAA
34547364 TTTCATTTTA
Statistics
Matches: 80, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
57 45 0.56
58 15 0.19
59 5 0.06
60 15 0.19
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (58 bp):
TTCCAAAATTACATTTTACCCTAAACTTTTCCAAAATCACATTTTTTACCCTAAACTT
Found at i:34547328 original size:30 final size:30
Alignment explanation
Indices: 34547211--34547363 Score: 149
Period size: 30 Copynumber: 5.2 Consensus size: 30
34547201 TCCTCAAACA
34547211 TTCCTAAAATCACATTTT-AC-CCTAAACTT
1 TTCC-AAAATCACATTTTGACTCCTAAACTT
* *
34547240 TCCCAAAATCACATTTTTTAC-CCTAAACTT
1 TTCCAAAATCACA-TTTTGACTCCTAAACTT
* * *
34547270 TT-CAAAATTACATTTT-TC-CCTAACCTT
1 TTCCAAAATCACATTTTGACTCCTAAACTT
**
34547297 TTCCAAAATCACATTTTGA-TTGTCAAACTT
1 TTCCAAAATCACATTTTGACTCCT-AAACTT
* *
34547327 TTCCGAAATTACATTTTGACTCCTAAACTT
1 TTCCAAAATCACATTTTGACTCCTAAACTT
34547357 TTCCAAA
1 TTCCAAA
34547364 TTTCATTTTA
Statistics
Matches: 102, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
27 11 0.11
28 26 0.25
29 17 0.17
30 46 0.45
31 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (30 bp):
TTCCAAAATCACATTTTGACTCCTAAACTT
Found at i:34547478 original size:29 final size:29
Alignment explanation
Indices: 34547222--34547493 Score: 119
Period size: 29 Copynumber: 9.4 Consensus size: 29
34547212 TCCTAAAATC
34547222 ACATTTT-ACCCTAAACTTTCCCAAAA-T
1 ACATTTTAACCCTAAACTTTCCCAAAACT
* * *
34547249 CACATTTTTTACCCTAAACTTT-TCAAAATT
1 -ACA-TTTTAACCCTAAACTTTCCCAAAACT
* * *
34547279 ACATTTT-TCCCTAACCTTTTCCAAAA-T
1 ACATTTTAACCCTAAACTTTCCCAAAACT
* *** * * *
34547306 CACATTTTGATTGTCAAACTTTTCCGAAATT
1 -ACATTTTAACCCT-AAACTTTCCCAAAACT
* * *
34547337 ACATTTTGACTCCTAAACTTTTCC-AAATT
1 ACATTTTAAC-CCTAAACTTTCCCAAAACT
* *** **
34547366 TCATTTTAACCCCCGCACTTTCTTAAAA-T
1 ACATTTTAA-CCCTAAACTTTCCCAAAACT
* * * *
34547395 CATATTTTAACCC-CAAGTTTCCCAAAACC
1 -ACATTTTAACCCTAAACTTTCCCAAAACT
* * *
34547424 ATATTTTGACCTTAAACTTTCCCAAAACT
1 ACATTTTAACCCTAAACTTTCCCAAAACT
* * ** *
34547453 ACCTTTTTACCCTAAACTTTTTCAAAATT
1 ACATTTTAACCCTAAACTTTCCCAAAACT
34547482 ACATTTTAACCC
1 ACATTTTAACCC
34547494 AAATTCTTCG
Statistics
Matches: 187, Mismatches: 43, Indels: 27
0.73 0.17 0.11
Matches are distributed among these distances:
27 11 0.06
28 38 0.20
29 81 0.43
30 55 0.29
31 2 0.01
ACGTcount: A:0.32, C:0.27, G:0.03, T:0.39
Consensus pattern (29 bp):
ACATTTTAACCCTAAACTTTCCCAAAACT
Found at i:34549487 original size:45 final size:46
Alignment explanation
Indices: 34549438--34549534 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 46
34549428 TGTGGTTACT
* * *
34549438 AGATACCACGACATCAT-TTCTGTTATG-TATAAGACCGTGGTTGAG
1 AGATACCACGACATCATATT-TGATATGTTATAAGACCGTAGTTGAA
* * * *
34549483 AGATACTATGGCATCATATTTGATATGTTATAAGACCTTAGTTGAA
1 AGATACCACGACATCATATTTGATATGTTATAAGACCGTAGTTGAA
34549529 AGATAC
1 AGATAC
34549535 TTTGGCATCA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
45 20 0.47
46 23 0.53
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (46 bp):
AGATACCACGACATCATATTTGATATGTTATAAGACCGTAGTTGAA
Found at i:34549533 original size:46 final size:45
Alignment explanation
Indices: 34549293--34549547 Score: 132
Period size: 45 Copynumber: 5.6 Consensus size: 45
34549283 GTAAGACTCC
* ** *
34549293 AGTTGAAAGATACTATGACATCATACCTGAAATGT-TCAAGACCGT
1 AGTTGAAAGATACTATGGCATCATATTTGATATGTAT-AAGACCGT
* * *
34549338 AGTTGAAAGATACTATGGCAT--TATGTCGATTATG--CAAGACCAT
1 AGTTGAAAGATACTATGGCATCATAT-TTGA-TATGTATAAGACCGT
* * * * *
34549381 -GATTGAAAGATA-TCATGGCATTAATCTGGAATTGAAATGTATAAAACTGT
1 AG-TTGAAAGATACT-ATGGCA-TCA--T--ATTTGATATGTATAAGACCGT
* * * * * *
34549431 GGTT-ACTAGATACCACGACATCAT-TTCTGTTATGTATAAGACCGT
1 AGTTGA-AAGATACTATGGCATCATATT-TGATATGTATAAGACCGT
* * *
34549476 GGTTGAGAGATACTATGGCATCATATTTGATATGTTATAAGACCTT
1 AGTTGAAAGATACTATGGCATCATATTTGATATG-TATAAGACCGT
*
34549522 AGTTGAAAGATACTTTGGCATCATAT
1 AGTTGAAAGATACTATGGCATCATAT
34549548 CAATAACGAT
Statistics
Matches: 157, Mismatches: 33, Indels: 39
0.69 0.14 0.17
Matches are distributed among these distances:
42 2 0.01
43 25 0.16
44 4 0.03
45 61 0.39
46 36 0.23
47 1 0.01
48 4 0.03
49 6 0.04
50 17 0.11
51 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.32
Consensus pattern (45 bp):
AGTTGAAAGATACTATGGCATCATATTTGATATGTATAAGACCGT
Found at i:34553489 original size:20 final size:20
Alignment explanation
Indices: 34553464--34553505 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
34553454 TATTATCCAG
34553464 TAATCATTACTTGAAATACC
1 TAATCATTACTTGAAATACC
34553484 TAATCATTACTTGAAATACC
1 TAATCATTACTTGAAATACC
34553504 TA
1 TA
34553506 CTTAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (20 bp):
TAATCATTACTTGAAATACC
Found at i:34556544 original size:6 final size:6
Alignment explanation
Indices: 34556533--34556578 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
34556523 ACACCAACAT
34556533 AACACA AACACA AACACA AACACA AACACA AACACA AACACA AACA
1 AACACA AACACA AACACA AACACA AACACA AACACA AACACA AACA
34556579 AACCTTCTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (6 bp):
AACACA
Found at i:34558118 original size:46 final size:45
Alignment explanation
Indices: 34558068--34558269 Score: 187
Period size: 46 Copynumber: 4.5 Consensus size: 45
34558058 TCGCTAATGA
* *
34558068 AATCTGCCTTTGGTTGTGGATTACATAACAAATGACCCGCAGATGG
1 AATCTGCCTTTGGCTGTGGATTACACAACAAAT-ACCCGCAGATGG
* * * *
34558114 AATCTGCCTATGGCTGTGG-GTACACAACAAATATCTCGCTA-ATGA
1 AATCTGCCTTTGGCTGTGGATTACACAACAAATA-CCCGC-AGATGG
* * * *
34558159 AATCTACATTTGGCCGTGGATTACATAACAAATGACCCGCAGATGG
1 AATCTGCCTTTGGCTGTGGATTACACAACAAAT-ACCCGCAGATGG
* * * * *
34558205 AAGT-TGTCTTTGGATGTGGA-TACACAGCAAGTACCCGCAGGTGG
1 AA-TCTGCCTTTGGCTGTGGATTACACAACAAATACCCGCAGATGG
*
34558249 AATCTACCTTTGGCTGTGGAT
1 AATCTGCCTTTGGCTGTGGAT
34558270 GCATAGCAAA
Statistics
Matches: 122, Mismatches: 26, Indels: 17
0.74 0.16 0.10
Matches are distributed among these distances:
43 1 0.01
44 27 0.22
45 43 0.35
46 49 0.40
47 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (45 bp):
AATCTGCCTTTGGCTGTGGATTACACAACAAATACCCGCAGATGG
Found at i:34558178 original size:91 final size:91
Alignment explanation
Indices: 34558017--34558206 Score: 265
Period size: 91 Copynumber: 2.1 Consensus size: 91
34558007 TAGTCCCCAT
* * * * * * * *
34558017 AGATGGAATTTGCCTCTAGCTGTGGGTACATAGAAGATGTATCGCTAATGAAATCTGCCTTTGGT
1 AGATGGAATCTGCCTATAGCTGTGGGTACACAGAAAATATATCGCTAATGAAATCTACATTTGGC
*
34558082 TGTGGATTACATAACAAATGACCCGC
66 CGTGGATTACATAACAAATGACCCGC
* *
34558108 AGATGGAATCTGCCTATGGCTGTGGGTACACA-ACAAATATCTCGCTAATGAAATCTACATTTGG
1 AGATGGAATCTGCCTATAGCTGTGGGTACACAGA-AAATATATCGCTAATGAAATCTACATTTGG
34558172 CCGTGGATTACATAACAAATGACCCGC
65 CCGTGGATTACATAACAAATGACCCGC
34558199 AGATGGAA
1 AGATGGAA
34558207 GTTGTCTTTG
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
90 1 0.01
91 86 0.99
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (91 bp):
AGATGGAATCTGCCTATAGCTGTGGGTACACAGAAAATATATCGCTAATGAAATCTACATTTGGC
CGTGGATTACATAACAAATGACCCGC
Found at i:34558223 original size:91 final size:91
Alignment explanation
Indices: 34558058--34558230 Score: 258
Period size: 91 Copynumber: 1.9 Consensus size: 91
34558048 AGAAGATGTA
* * **
34558058 TCGCTAATGAAATCTGCCTTTGGTTGTGGATTACATAACAAATGACCCGCAGATGGAATCTGCCT
1 TCGCTAATGAAATCTACATTTGGCCGTGGATTACATAACAAATGACCCGCAGATGGAATCTGCCT
* *
34558123 ATGGCTGTGGGTACACAACAAATATC
66 ATGGATGTGGATACACAACAAATATC
*
34558149 TCGCTAATGAAATCTACATTTGGCCGTGGATTACATAACAAATGACCCGCAGATGGAAGT-TGTC
1 TCGCTAATGAAATCTACATTTGGCCGTGGATTACATAACAAATGACCCGCAGATGGAA-TCTGCC
*
34558213 TTTGGATGTGGATACACA
65 TATGGATGTGGATACACA
34558231 GCAAGTACCC
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
91 72 0.99
92 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (91 bp):
TCGCTAATGAAATCTACATTTGGCCGTGGATTACATAACAAATGACCCGCAGATGGAATCTGCCT
ATGGATGTGGATACACAACAAATATC
Found at i:34567391 original size:30 final size:30
Alignment explanation
Indices: 34567351--34567412 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
34567341 TTTTGGCCGC
34567351 TTGAGGTGTGTTTCTGTCCGTGCTACATAT
1 TTGAGGTGTGTTTCTGTCCGTGCTACATAT
* * * *
34567381 TTGATGTGTGTTTCTTTCTGTGTTACATAT
1 TTGAGGTGTGTTTCTGTCCGTGCTACATAT
34567411 TT
1 TT
34567413 ATTATGTGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.13, C:0.13, G:0.23, T:0.52
Consensus pattern (30 bp):
TTGAGGTGTGTTTCTGTCCGTGCTACATAT
Found at i:34568114 original size:29 final size:29
Alignment explanation
Indices: 34568066--34568123 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
34568056 AGTTTTTACC
*
34568066 TTGTGTGATATTATTATGTGTTGTGTTAT
1 TTGTGTGATATTAATATGTGTTGTGTTAT
* *
34568095 TTGTGTGATTTTAATCTGTGTTGTGTTAT
1 TTGTGTGATATTAATATGTGTTGTGTTAT
34568124 CGCATGTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.16, C:0.02, G:0.24, T:0.59
Consensus pattern (29 bp):
TTGTGTGATATTAATATGTGTTGTGTTAT
Found at i:34568670 original size:24 final size:24
Alignment explanation
Indices: 34568609--34568671 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
34568599 TAGAGTAATA
* *
34568609 AGAGTTTGACTCAAACAAAGAAAT
1 AGAGTTTAACTGAAACAAAGAAAT
* *
34568633 AGAGTTTAATTGAAACAAATAAAT
1 AGAGTTTAACTGAAACAAAGAAAT
34568657 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
34568672 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAAGAAAT
Found at i:34572484 original size:59 final size:59
Alignment explanation
Indices: 34572404--34572779 Score: 406
Period size: 59 Copynumber: 6.4 Consensus size: 59
34572394 TGGACTCGCG
* * * * *
34572404 GGGGTGAAATGATAATTTTTGGTGAAATCGAGATCAAAAAGAGAATTTTGGAAAATTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAGAGAATTTTGGAAAGTTCA
* * * * *
34572463 AGGGTAAAATAGTAATTTTTGGTTAAATCGGGGTTAAAAATG-GAATTTTGGAAAGTTCT
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAA-GAGAATTTTGGAAAGTTCA
* *
34572522 GGGGTAAAATGGTAATTTTTGGTGAAACCG-GGATTAAAAATGA-AATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGG-TTAAAAA-GAGAATTTTGGAAAGTTCA
* * * * * * * *
34572581 GCGATAAAATAGTAA-TTTTGGTTTAAATCG-GGTTAAAAATAAAATTTTAGAAAGTTCG
1 GGGGTAAAATGGTAATTTTTGG-TGAAATCGAGGTTAAAAAGAGAATTTTGGAAAGTTCA
* * *
34572639 GGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTTTAAAATGA-AATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGG-TTAAAAAGAGAATTTTGGAAAGTTCA
* * *
34572698 GGGGTAAAATGGTAATTTTTGGTGAAA-CTGAGGTTAAAAATAGAATTTTGAAAAGTTCGG
1 GGGGTAAAATGGTAATTTTTGGTGAAATC-GAGGTTAAAAAGAGAATTTTGGAAAGTTC-A
34572758 GGGGTAAAATGGTAATTTTTGG
1 GGGGTAAAATGGTAATTTTTGG
34572780 ACCATCCAAG
Statistics
Matches: 266, Mismatches: 40, Indels: 21
0.81 0.12 0.06
Matches are distributed among these distances:
57 1 0.00
58 55 0.21
59 180 0.68
60 30 0.11
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAGAGAATTTTGGAAAGTTCA
Found at i:34572501 original size:30 final size:29
Alignment explanation
Indices: 34572467--34572746 Score: 74
Period size: 29 Copynumber: 9.5 Consensus size: 29
34572457 AATTCAAGGG
34572467 TAAAATAGTAATTTTTGGTTAAATCGGGGT
1 TAAAATAGTAATTTTTGG-TAAATCGGGGT
*
34572497 TAAAA-ATGGAA-TTTTGG-AAAGTTCTGGGG-
1 TAAAATA-GTAATTTTTGGTAAA--TC-GGGGT
* * *
34572526 TAAAATGGTAATTTTTGGTGAAACCGGGAT
1 TAAAATAGTAATTTTTGGT-AAATCGGGGT
* ** * *
34572556 TAAAA-A-TGAAATTTTGG-AAAGTTTAGCGA
1 TAAAATAGT-AATTTTTGGTAAA--TCGGGGT
34572585 TAAAATAGTAA-TTTTGGTTTAAATC-GGGT
1 TAAAATAGTAATTTTTGG--TAAATCGGGGT
* * *
34572614 TAAAA-A-TAAAATTTTAG-AAAGTTCGGGGG
1 TAAAATAGT-AATTTTTGGTAAA--TCGGGGT
* *
34572643 TAAAATGGTAATTTTTGGTAAAATCGAGGTT
1 TAAAATAGTAATTTTTGGT-AAATCG-GGGT
* *
34572674 TAAAAT-G-AAATTTTGG-AAAGTTTAGGGG-
1 TAAAATAGTAATTTTTGGTAAA---TCGGGGT
* *
34572702 TAAAATGGTAATTTTTGGTGAAA-CTGAGGT
1 TAAAATAGTAATTTTTGGT-AAATC-GGGGT
34572732 TAAAAATAG-AATTTT
1 T-AAAATAGTAATTTT
34572747 GAAAAGTTCG
Statistics
Matches: 183, Mismatches: 30, Indels: 74
0.64 0.10 0.26
Matches are distributed among these distances:
26 3 0.02
27 10 0.05
28 12 0.07
29 74 0.40
30 56 0.31
31 16 0.09
32 12 0.07
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (29 bp):
TAAAATAGTAATTTTTGGTAAATCGGGGT
Found at i:34572591 original size:118 final size:117
Alignment explanation
Indices: 34572402--34572779 Score: 487
Period size: 117 Copynumber: 3.2 Consensus size: 117
34572392 TTTGGACTCG
* * * * * *
34572402 CGGGGGTGAAATGATAATTTTTGGTGAAATCGAGATCAAAAA-GAGAATTTTGGAAAATTCAAGG
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGATTAAAAATGA-AATTTTGGAAAGTT-TAGG
*
34572466 GTAAAATAGTAATTTTTGGTTAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
64 GTAAAATAGTAATTTTTGGTTAAATCGGGGTTAAAAATAGAATTTTGGAAAGTT
* * *
34572520 CTGGGGTAAAATGGTAATTTTTGGTGAAACCGGGATTAAAAATGAAATTTTGGAAAGTTTAGCGA
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGATTAAAAATGAAATTTTGGAAAGTTTAG-GG
* *
34572585 TAAAATAGTAA-TTTTGGTTTAAATC-GGGTTAAAAATAAAATTTTAGAAAGTT
65 TAAAATAGTAATTTTTGG-TTAAATCGGGGTTAAAAATAGAATTTTGGAAAGTT
* *
34572637 CGGGGGTAAAATGGTAATTTTTGGTAAAATCGAGG-TTTAAAATGAAATTTTGGAAAGTTTAGGG
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCG-GGATTAAAAATGAAATTTTGGAAAGTTTA-GG
* * * *
34572701 GTAAAATGGTAATTTTTGGTGAAA-CTGAGGTTAAAAATAGAATTTTGAAAAGTT
64 GTAAAATAGTAATTTTTGGTTAAATC-GGGGTTAAAAATAGAATTTTGGAAAGTT
34572755 CGGGGGGTAAAATGGTAATTTTTGG
1 C-GGGGGTAAAATGGTAATTTTTGG
34572780 ACCATCCAAG
Statistics
Matches: 228, Mismatches: 23, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
116 1 0.00
117 101 0.44
118 101 0.44
119 25 0.11
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (117 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGATTAAAAATGAAATTTTGGAAAGTTTAGGGT
AAAATAGTAATTTTTGGTTAAATCGGGGTTAAAAATAGAATTTTGGAAAGTT
Found at i:34572655 original size:29 final size:29
Alignment explanation
Indices: 34572623--34572776 Score: 93
Period size: 30 Copynumber: 5.2 Consensus size: 29
34572613 TTAAAAATAA
*
34572623 AATTTTAGAAAGTTCGGGGGTAAAATGGT
1 AATTTTGGAAAGTTCGGGGGTAAAATGGT
* ** *
34572652 AATTTTTGGTAAA-ATCGAGGTTTAAAAT-GA
1 AA-TTTTGG-AAAGTTCG-GGGGTAAAATGGT
**
34572682 AATTTTGGAAAGTTTAGGGGTAAAATGGT
1 AATTTTGGAAAGTTCGGGGGTAAAATGGT
* * * *
34572711 AATTTTTGGTGAAA-CT-GAGGTTAAAAATAG-
1 AA-TTTT-G-GAAAGTTCGGGGGT-AAAATGGT
*
34572741 AATTTTGAAAAGTTCGGGGGGTAAAATGGT
1 AATTTTGGAAAGTTC-GGGGGTAAAATGGT
34572771 AATTTT
1 AATTTT
34572777 TGGACCATCC
Statistics
Matches: 91, Mismatches: 21, Indels: 25
0.66 0.15 0.18
Matches are distributed among these distances:
27 3 0.03
28 13 0.14
29 22 0.24
30 30 0.33
31 19 0.21
32 4 0.04
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (29 bp):
AATTTTGGAAAGTTCGGGGGTAAAATGGT
Found at i:34573176 original size:161 final size:162
Alignment explanation
Indices: 34572927--34573327 Score: 644
Period size: 161 Copynumber: 2.5 Consensus size: 162
34572917 TTTAAGGATT
*
34572927 AAATTAAAAATGACAGGGACTAGATACATAAATAAGCCAAAAAGTGACATGTGGCAGCCTCTGGT
1 AAATTAAAAATGACAGGGACTAGATACATAAATAAGCCAAAAAGTGACACGTGGCAGCCTCTGGT
* * *
34572992 GCAGTCAAACAGTTAAAGGACTAATTTAAAAATCTCAAAAGATTCCTGGGTCAATTTTGTTATTA
66 GCAGTCAAACAGTCAAAGGACTAATTTAAAAATCTCAAAAAATTCCTGGGTCAATTTTGTAATTA
*
34573057 AGCAAAAGTTGATTTGAGGATTAAATTAAAAC
131 AGCAAAAGTTGATTTAAGGATTAAATTAAAAC
* *
34573089 AAATTAAAAATGACGGGGATTAGATACATAAATAAGCC-AAAAGTGACACGTGGCAGCCTCTGGT
1 AAATTAAAAATGACAGGGACTAGATACATAAATAAGCCAAAAAGTGACACGTGGCAGCCTCTGGT
*
34573153 ACAGTCAAACAGTCAAAGGACTAATTTAAAAATCTCAAAAAATTCCTGGGTCAATTTTGTAATTA
66 GCAGTCAAACAGTCAAAGGACTAATTTAAAAATCTCAAAAAATTCCTGGGTCAATTTTGTAATTA
*
34573218 AGCATAAGTTGATTTAAGGATTAAATTAAAAC
131 AGCAAAAGTTGATTTAAGGATTAAATTAAAAC
* * * * * *
34573250 AAATTAAACATAACAGGGACTAAATGCA-AAATAAGCCAAAAAAATGACACGTGGCCGCCTCTGG
1 AAATTAAAAATGACAGGGACTAGATACATAAATAAGCC-AAAAAGTGACACGTGGCAGCCTCTGG
34573314 TGCAGTCAAACAGT
65 TGCAGTCAAACAGT
34573328 TGAAGGATTA
Statistics
Matches: 219, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
160 9 0.04
161 138 0.63
162 72 0.33
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (162 bp):
AAATTAAAAATGACAGGGACTAGATACATAAATAAGCCAAAAAGTGACACGTGGCAGCCTCTGGT
GCAGTCAAACAGTCAAAGGACTAATTTAAAAATCTCAAAAAATTCCTGGGTCAATTTTGTAATTA
AGCAAAAGTTGATTTAAGGATTAAATTAAAAC
Found at i:34574900 original size:6 final size:6
Alignment explanation
Indices: 34574885--34574943 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
34574875 TTAAATTTGA
* * *
34574885 TTAAAC TTAAAT TTAAA- GTAAAT TTAAAT GAGTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
*
34574933 ATAAAT TTAAA
1 TTAAAT TTAAA
34574944 ACCTTTTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
8 5 0.12
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:34574920 original size:14 final size:14
Alignment explanation
Indices: 34574901--34574927 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
34574891 TTAAATTTAA
34574901 AGTAAATTTAAATG
1 AGTAAATTTAAATG
34574915 AGTAAATTTAAAT
1 AGTAAATTTAAAT
34574928 TTAAAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (14 bp):
AGTAAATTTAAATG
Found at i:34583536 original size:30 final size:29
Alignment explanation
Indices: 34583491--34583555 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
34583481 TTTCAAAAAA
*
34583491 TAATTAATTATGAGAAATCA-TATTTATAT
1 TAATTAATTATGAGAAAACACT-TTTATAT
*
34583520 TAATTATATTTTGAGAAAACACTTTTATAT
1 TAATTA-ATTATGAGAAAACACTTTTATAT
34583550 TAATTA
1 TAATTA
34583556 CGTTATAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 6 0.19
30 25 0.78
31 1 0.03
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (29 bp):
TAATTAATTATGAGAAAACACTTTTATAT
Found at i:34585593 original size:24 final size:23
Alignment explanation
Indices: 34585562--34585608 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
34585552 TTAGATGGTA
*
34585562 GTGTTTG-TCTATTTATATGATGT
1 GTGTTTGTTC-ATTGATATGATGT
34585585 GTGTATTGTTCATTGATATGATGT
1 GTGT-TTGTTCATTGATATGATGT
34585609 AATAGATAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 15 0.71
25 2 0.10
ACGTcount: A:0.19, C:0.04, G:0.23, T:0.53
Consensus pattern (23 bp):
GTGTTTGTTCATTGATATGATGT
Found at i:34585765 original size:12 final size:12
Alignment explanation
Indices: 34585748--34585775 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
34585738 TGAACCGATG
34585748 ATAACAAATATC
1 ATAACAAATATC
34585760 ATAACAAATATC
1 ATAACAAATATC
34585772 ATAA
1 ATAA
34585776 AATTGATCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.25
Consensus pattern (12 bp):
ATAACAAATATC
Found at i:34586549 original size:33 final size:32
Alignment explanation
Indices: 34586496--34586583 Score: 92
Period size: 33 Copynumber: 2.7 Consensus size: 32
34586486 CCTGGACATG
*
34586496 ATTTTTTAAATAATTA-TAAAACCA-TTAT-TGAA
1 ATTTTTTAAA-AATTATTAAAA--ATTTATAAGAA
*
34586528 ATTTATTTAAAAACTATTAAAAATTTATAAGAA
1 ATTT-TTTAAAAATTATTAAAAATTTATAAGAA
34586561 ATCTTTTTAAAAATTATTAAAAA
1 AT-TTTTTAAAAATTATTAAAAA
34586584 CAACTTTTAG
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
31 1 0.02
32 12 0.25
33 33 0.69
34 2 0.04
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (32 bp):
ATTTTTTAAAAATTATTAAAAATTTATAAGAA
Found at i:34599475 original size:52 final size:52
Alignment explanation
Indices: 34599393--34599621 Score: 239
Period size: 52 Copynumber: 4.4 Consensus size: 52
34599383 AAAAAGGGTT
* *
34599393 CGATGACTAAGTGTCATCGTGAGTAA-ATGAATCTTTTATAGATTATGAGGTC
1 CGATGACTAAGTGTCATCGTGAG-AATATGAATCCTTTATAGATTATAAGGTC
*
34599445 CAATGACTAAGTGTCATCGTGAGAATATGAAATCCTTTATAGATT-TAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGAATATG-AATCCTTTATAGATTAT-AAGGTC
* * * * *
34599498 CGATTACTAAGTGTCATCGTGAGTATATGGATCCTTTACAGATTAAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGAATATGAATCCTTTATAGATTATAAGGTC
** * * * ** * *
34599550 CGATGACTCTGTGTCATCGTGAGTATACGAATCCCTCGTGGATTATAAGGTT
1 CGATGACTAAGTGTCATCGTGAGAATATGAATCCTTTATAGATTATAAGGTC
*
34599602 CGACGACTATA-TGTCATCGT
1 CGATGACTA-AGTGTCATCGT
34599622 AAGTATTAAA
Statistics
Matches: 148, Mismatches: 24, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
51 2 0.01
52 101 0.68
53 45 0.30
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.33
Consensus pattern (52 bp):
CGATGACTAAGTGTCATCGTGAGAATATGAATCCTTTATAGATTATAAGGTC
Found at i:34604908 original size:14 final size:14
Alignment explanation
Indices: 34604891--34604918 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34604881 CTTTCGAGCT
34604891 TGGACAAATAACCC
1 TGGACAAATAACCC
34604905 TGGACAAATAACCC
1 TGGACAAATAACCC
34604919 GATTTATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.14, T:0.14
Consensus pattern (14 bp):
TGGACAAATAACCC
Found at i:34610104 original size:26 final size:26
Alignment explanation
Indices: 34610075--34610127 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
34610065 CCTGAAGTTA
34610075 AAATTATATTATATATTGAATATAAT
1 AAATTATATTATATATTGAATATAAT
34610101 AAATTATATTATATATTGAATATAAT
1 AAATTATATTATATATTGAATATAAT
34610127 A
1 A
34610128 CAAATATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (26 bp):
AAATTATATTATATATTGAATATAAT
Found at i:34611505 original size:25 final size:24
Alignment explanation
Indices: 34611465--34611511 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
34611455 GAAGATGAGA
34611465 GAATGAGAAATAAAGGGGTGAGATG
1 GAATGAGAAATAAAGGGG-GAGATG
* *
34611490 GAATGAGACATTAAGGGGGAGA
1 GAATGAGAAATAAAGGGGGAGA
34611512 ATAGGGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.43, C:0.02, G:0.40, T:0.15
Consensus pattern (24 bp):
GAATGAGAAATAAAGGGGGAGATG
Found at i:34618325 original size:4 final size:4
Alignment explanation
Indices: 34618316--34618343 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
34618306 GGCTGACTTT
34618316 GGAG GGAG GGAG GGAG GGAG GGAG GGAG
1 GGAG GGAG GGAG GGAG GGAG GGAG GGAG
34618344 AGAGAGAGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.75, T:0.00
Consensus pattern (4 bp):
GGAG
Found at i:34620029 original size:29 final size:30
Alignment explanation
Indices: 34619965--34620030 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
34619955 TGTTTACAAG
* *
34619965 AATTGGATCAAATCAAAATTTCATGTATAA
1 AATTGCATAAAATCAAAATTTCATGTATAA
* *
34619995 AATTGCATAAAATCAAAGTTT-ATGTATAC
1 AATTGCATAAAATCAAAATTTCATGTATAA
34620024 AATTGCA
1 AATTGCA
34620031 CATTCAACCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (30 bp):
AATTGCATAAAATCAAAATTTCATGTATAA
Found at i:34621381 original size:27 final size:26
Alignment explanation
Indices: 34621350--34621481 Score: 102
Period size: 27 Copynumber: 4.9 Consensus size: 26
34621340 AGTAGTTCGC
*
34621350 TGGGACAATGAACTCGGGGTAGTTTGT
1 TGGGACAAT-AACTCGGGGTAGTCTGT
* * * * **
34621377 CGGGATAGTAAACTCAGGGTAGTCCAT
1 TGGGACAAT-AACTCGGGGTAGTCTGT
34621404 TGGGACAATAAGCTCGGGGTAGTCTGT
1 TGGGACAATAA-CTCGGGGTAGTCTGT
* *
34621431 TGGGACAGTATACTCGGGGTAGTCCGT
1 TGGGACAATA-ACTCGGGGTAGTCTGT
* * * *
34621458 CGAGACAGTAAATACGGGGTAGTC
1 TGGGACAATAACT-CGGGGTAGTC
34621482 CACCGAGACA
Statistics
Matches: 83, Mismatches: 19, Indels: 6
0.77 0.18 0.06
Matches are distributed among these distances:
26 4 0.05
27 78 0.94
28 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (26 bp):
TGGGACAATAACTCGGGGTAGTCTGT
Found at i:34621420 original size:54 final size:54
Alignment explanation
Indices: 34621325--34621455 Score: 158
Period size: 54 Copynumber: 2.4 Consensus size: 54
34621315 GTAGTCCATT
* * ** *
34621325 GGGACAGTAAACTC-GAGTAGTTCGCTGGGACAATGAACTCGGGGTAGTTTGTC
1 GGGACAGTAAACTCAGGGTAGTCCATTGGGACAATGAACTCGGGGTAGTCTGTC
* *
34621378 GGGATAGTAAACTCAGGGTAGTCCATTGGGACAAT-AAGCTCGGGGTAGTCTGTT
1 GGGACAGTAAACTCAGGGTAGTCCATTGGGACAATGAA-CTCGGGGTAGTCTGTC
* *
34621432 GGGACAGTATACTCGGGGTAGTCC
1 GGGACAGTAAACTCAGGGTAGTCC
34621456 GTCGAGACAG
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
53 15 0.23
54 51 0.77
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.24
Consensus pattern (54 bp):
GGGACAGTAAACTCAGGGTAGTCCATTGGGACAATGAACTCGGGGTAGTCTGTC
Found at i:34621468 original size:81 final size:80
Alignment explanation
Indices: 34621307--34621497 Score: 201
Period size: 81 Copynumber: 2.4 Consensus size: 80
34621297 TCGACTATGG
*
34621307 AAACT-AGGGTAGTCCATTGGGACAGTAAACTCGAGTAGTTCGCTGGGACAATGAACTCGGGGTA
1 AAACTCAGGGTAGTCCATTGGGACAATAAACTCGAGTAGTTCGCTGGGACAATGAACTCGGGGTA
** * *
34621371 GTTTGTCGGGATAGT
66 GTCCGTCGAGACAGT
* * * *
34621386 AAACTCAGGGTAGTCCATTGGGACAATAAGCTCGGGGTAG-TCTGTTGGGACAGT-ATACTCGGG
1 AAACTCAGGGTAGTCCATTGGGACAATAAACTC-GAGTAGTTC-GCTGGGACAATGA-ACTCGGG
34621449 GTAGTCCGTCGAGACAGT
63 GTAGTCCGTCGAGACAGT
* ** *
34621467 AAA-TACGGGGTAGTCCACCGAGACAATAAAC
1 AAACT-CAGGGTAGTCCATTGGGACAATAAAC
34621498 ACAGTGTAAC
Statistics
Matches: 93, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
79 5 0.05
80 29 0.31
81 59 0.63
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (80 bp):
AAACTCAGGGTAGTCCATTGGGACAATAAACTCGAGTAGTTCGCTGGGACAATGAACTCGGGGTA
GTCCGTCGAGACAGT
Found at i:34621476 original size:54 final size:54
Alignment explanation
Indices: 34621363--34621481 Score: 132
Period size: 54 Copynumber: 2.2 Consensus size: 54
34621353 GACAATGAAC
* * * * *
34621363 TCGGGGTAGTTTGTCGGGATAGTAAACTCAGGGTAGTCCATTGGGACAATAAGC
1 TCGGGGTAGTCTGTCGGGACAGTAAACTCAGGGTAGTCCATCGAGACAATAAGA
* * * * *
34621417 TCGGGGTAGTCTGTTGGGACAGTATACTCGGGGTAGTCCGTCGAGACAGTAA-A
1 TCGGGGTAGTCTGTCGGGACAGTAAACTCAGGGTAGTCCATCGAGACAATAAGA
34621470 TACGGGGTAGTC
1 T-CGGGGTAGTC
34621482 CACCGAGACA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
53 1 0.02
54 53 0.98
ACGTcount: A:0.24, C:0.16, G:0.35, T:0.25
Consensus pattern (54 bp):
TCGGGGTAGTCTGTCGGGACAGTAAACTCAGGGTAGTCCATCGAGACAATAAGA
Found at i:34621482 original size:27 final size:26
Alignment explanation
Indices: 34621363--34621496 Score: 79
Period size: 27 Copynumber: 5.0 Consensus size: 26
34621353 GACAATGAAC
** * *
34621363 TCGGGGTAGTTTGTCGGGATAGTAAA
1 TCGGGGTAGTCCGTCGAGACAGTAAA
* * * * * *
34621389 CTCAGGGTAGTCCATTGGGACAATAAGC
1 -TCGGGGTAGTCCGTCGAGACAGTAA-A
* * * *
34621417 TCGGGGTAGTCTGTTGGGACAGTATAC
1 TCGGGGTAGTCCGTCGAGACAGTA-AA
34621444 TCGGGGTAGTCCGTCGAGACAGTAAA
1 TCGGGGTAGTCCGTCGAGACAGTAAA
** *
34621470 TACGGGGTAGTCCACCGAGACAATAAA
1 T-CGGGGTAGTCCGTCGAGACAGTAAA
34621497 CACAGTGTAA
Statistics
Matches: 85, Mismatches: 19, Indels: 6
0.77 0.17 0.05
Matches are distributed among these distances:
26 2 0.02
27 82 0.96
28 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.33, T:0.23
Consensus pattern (26 bp):
TCGGGGTAGTCCGTCGAGACAGTAAA
Found at i:34623296 original size:18 final size:18
Alignment explanation
Indices: 34623273--34623309 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
34623263 TTTGTGATCA
34623273 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
34623291 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
34623309 A
1 A
34623310 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:34626157 original size:37 final size:38
Alignment explanation
Indices: 34626088--34626168 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 38
34626078 CGGTGTCATT
** **
34626088 ACTTTACTTCGGATAGATTCGATGAGGTACTGGGTACC
1 ACTTTACTTCGGATAGAGCCGATGAGACACTGGGTACC
* **
34626126 ACTTTACTTCGGCTAG-GCCGATGAGACACTGGGTGTC
1 ACTTTACTTCGGATAGAGCCGATGAGACACTGGGTACC
34626163 ACTTTA
1 ACTTTA
34626169 TTGCTTCGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
37 21 0.58
38 15 0.42
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (38 bp):
ACTTTACTTCGGATAGAGCCGATGAGACACTGGGTACC
Done.