Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 153 of 214
Found at i:45539827 original size:2 final size:2
Alignment explanation
Indices: 45539820--45539856 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
45539810 GGGCATTTCT
45539820 TC TC TC TC TC 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 TC TC TC TC TC T
45539857 TTTATCTGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:45550126 original size:24 final size:24
Alignment explanation
Indices: 45550099--45550150 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
45550089 TTAGTAAGTC
*
45550099 AAATAAATTATACTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
45550123 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
45550147 AAAT
1 AAAT
45550151 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:45552095 original size:24 final size:24
Alignment explanation
Indices: 45552068--45552119 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
45552058 TTAGTAAGTC
45552068 AAATAAACTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
* *
45552092 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
45552116 AAAT
1 AAAT
45552120 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:45568756 original size:22 final size:24
Alignment explanation
Indices: 45568713--45568756 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
45568703 AAATATGTAT
**
45568713 ATAATCTAGAAAAATATTATAAAA
1 ATAATCTAGAAAAATACGATAAAA
45568737 ATAAT-TA-AAAAATACGATAA
1 ATAATCTAGAAAAATACGATAA
45568757 TTGAAAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.61
23 2 0.11
24 5 0.28
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (24 bp):
ATAATCTAGAAAAATACGATAAAA
Found at i:45568998 original size:18 final size:18
Alignment explanation
Indices: 45568954--45569003 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
45568944 CATTATCTTG
* *
45568954 ACTTTTTAA-ATTTTATA
1 ACTTTTTAATTTTTTAAA
45568971 A-TTTTATAATTTTTTAAA
1 ACTTTT-TAATTTTTTAAA
45568989 ACTTTTTAATTTTTT
1 ACTTTTTAATTTTTT
45569004 TATATATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 4 0.14
17 4 0.14
18 16 0.57
19 4 0.14
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (18 bp):
ACTTTTTAATTTTTTAAA
Found at i:45576994 original size:28 final size:28
Alignment explanation
Indices: 45576954--45577012 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
45576944 ACTAAACCTT
45576954 AACCACTTTAGAATTCTAACTCCACCCA
1 AACCACTTTAGAATTCTAACTCCACCCA
45576982 AACCACTTTAGAATTCTAACTCCACCCA
1 AACCACTTTAGAATTCTAACTCCACCCA
45577010 AAC
1 AAC
45577013 ACTCTCAGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.37, C:0.36, G:0.03, T:0.24
Consensus pattern (28 bp):
AACCACTTTAGAATTCTAACTCCACCCA
Found at i:45577752 original size:16 final size:16
Alignment explanation
Indices: 45577727--45577768 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
45577717 GTTAGAAAGT
*
45577727 TATAAATATATTTAAA
1 TATAATTATATTTAAA
*
45577743 TATAATTATAATTAAA
1 TATAATTATATTTAAA
*
45577759 -ATAATAATAT
1 TATAATTATAT
45577769 AAACATGGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATAATTATATTTAAA
Found at i:45587843 original size:27 final size:28
Alignment explanation
Indices: 45587794--45587846 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
45587784 CTCATTATAA
**
45587794 TAATTAAAAATACAATATTTATAAAAAC
1 TAATTAAAAATACAATACGTATAAAAAC
*
45587822 TAATTAAAAATTCAA-ACGTATAAAA
1 TAATTAAAAATACAATACGTATAAAA
45587847 TCACATACGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (28 bp):
TAATTAAAAATACAATACGTATAAAAAC
Found at i:45589410 original size:42 final size:43
Alignment explanation
Indices: 45589306--45589430 Score: 198
Period size: 43 Copynumber: 2.9 Consensus size: 43
45589296 GCATTTACAG
*
45589306 AAAAAAATGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAAC
1 AAAAAAATGCCGCTAAAGATCATGTTCTTTAGCAGCGCTTAAC
*
45589349 AAAAAAATGCCGCTAAAGATCATGTTCTTTAACAGCGCTTAA-
1 AAAAAAATGCCGCTAAAGATCATGTTCTTTAGCAGCGCTTAAC
* * *
45589391 AGAAAAACGCCGCTAAAGATCATATTCTTTAGCAGCGCTT
1 AAAAAAATGCCGCTAAAGATCATGTTCTTTAGCAGCGCTT
45589431 GGTAAAAAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
42 36 0.47
43 40 0.53
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.26
Consensus pattern (43 bp):
AAAAAAATGCCGCTAAAGATCATGTTCTTTAGCAGCGCTTAAC
Found at i:45589457 original size:44 final size:42
Alignment explanation
Indices: 45589308--45589464 Score: 154
Period size: 43 Copynumber: 3.7 Consensus size: 42
45589298 ATTTACAGAA
* * * * *
45589308 AAAAATGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAACAA
1 AAAAACGCCGCTAAACATCATGTTCTTTAACAGCGCTTAA-AG
* *
45589351 AAAAATGCCGCTAAAGATCATGTTCTTTAACAGCGCTTAAAG
1 AAAAACGCCGCTAAACATCATGTTCTTTAACAGCGCTTAAAG
* * *
45589393 AAAAACGCCGCTAAAGATCATATTCTTTAGCAGCGCTTGGTAAA-
1 AAAAACGCCGCTAAACATCATGTTCTTTAACAGCGC-T--TAAAG
** *
45589437 AAAAACGTTGCTATACATCATGTTCTTT
1 AAAAACGCCGCTAAACATCATGTTCTTT
45589465 TGGGATTTTT
Statistics
Matches: 100, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
42 34 0.34
43 39 0.39
44 23 0.23
45 4 0.04
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (42 bp):
AAAAACGCCGCTAAACATCATGTTCTTTAACAGCGCTTAAAG
Found at i:45589872 original size:21 final size:21
Alignment explanation
Indices: 45589848--45589893 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
45589838 TCTCTCACTA
*
45589848 CTTCTCGCGCTGCAGCCTCTG
1 CTTCTCGCACTGCAGCCTCTG
* *
45589869 CTTCTCTCACTGCAGCCTCTT
1 CTTCTCGCACTGCAGCCTCTG
45589890 CTTC
1 CTTC
45589894 CCTCGTTGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.07, C:0.43, G:0.15, T:0.35
Consensus pattern (21 bp):
CTTCTCGCACTGCAGCCTCTG
Found at i:45594727 original size:9 final size:9
Alignment explanation
Indices: 45594711--45594788 Score: 65
Period size: 9 Copynumber: 9.1 Consensus size: 9
45594701 CTAACAGCAT
45594711 TGTAAGTTA
1 TGTAAGTTA
*
45594720 TTTAAGTTA
1 TGTAAGTTA
**
45594729 TGTAAGTGG
1 TGTAAGTTA
45594738 TGT-A-TTA
1 TGTAAGTTA
45594745 TGTAAGTTA
1 TGTAAGTTA
*
45594754 AGTAAGTTA
1 TGTAAGTTA
* *
45594763 TGTAGGCTA
1 TGTAAGTTA
45594772 TGT-A-TTA
1 TGTAAGTTA
*
45594779 TGCAAGTTA
1 TGTAAGTTA
45594788 T
1 T
45594789 TTAACCTATG
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
7 8 0.15
8 3 0.06
9 41 0.79
ACGTcount: A:0.31, C:0.03, G:0.23, T:0.44
Consensus pattern (9 bp):
TGTAAGTTA
Found at i:45594766 original size:25 final size:25
Alignment explanation
Indices: 45594717--45594766 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
45594707 GCATTGTAAG
* * *
45594717 TTATTTAAGTTATGTAAGTGGTGTA
1 TTATGTAAGTTAAGTAAGTGATGTA
*
45594742 TTATGTAAGTTAAGTAAGTTATGTA
1 TTATGTAAGTTAAGTAAGTGATGTA
45594767 GGCTATGTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (25 bp):
TTATGTAAGTTAAGTAAGTGATGTA
Found at i:45594776 original size:34 final size:34
Alignment explanation
Indices: 45594711--45594787 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
45594701 CTAACAGCAT
** *
45594711 TGTAAGTTATTTAAGTTATGTAAGTGGTGTATTA
1 TGTAAGTTAAGTAAGTTATGTAAGTGATGTATTA
*
45594745 TGTAAGTTAAGTAAGTTATGTAGGCT-ATGTATTA
1 TGTAAGTTAAGTAAGTTATGTAAG-TGATGTATTA
*
45594779 TGCAAGTTA
1 TGTAAGTTA
45594788 TTTAACCTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 36 0.97
35 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.23, T:0.43
Consensus pattern (34 bp):
TGTAAGTTAAGTAAGTTATGTAAGTGATGTATTA
Found at i:45596447 original size:19 final size:19
Alignment explanation
Indices: 45596423--45596473 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
45596413 TAACTAATAT
45596423 TTATAAATTTTAGATAAAA
1 TTATAAATTTTAGATAAAA
45596442 TTATAAATTTTAGATAAAA
1 TTATAAATTTTAGATAAAA
45596461 TTATAAATTTTAG
1 TTATAAATTTTAG
45596474 TGTTTTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (19 bp):
TTATAAATTTTAGATAAAA
Found at i:45596652 original size:25 final size:26
Alignment explanation
Indices: 45596614--45596662 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
45596604 TAAAATTAAC
*
45596614 ATTTTTAGTGTTTTAATTTCATTTTT
1 ATTTTTAGTATTTTAATTTCATTTTT
*
45596640 ATTTTTA-TATTTTAATTTTATTT
1 ATTTTTAGTATTTTAATTTCATTT
45596663 ATTAATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.71
Consensus pattern (26 bp):
ATTTTTAGTATTTTAATTTCATTTTT
Found at i:45596658 original size:13 final size:12
Alignment explanation
Indices: 45596624--45596669 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
45596614 ATTTTTAGTG
*
45596624 TTTTAATTTCAT
1 TTTTAATTTTAT
*
45596636 TTTTATTTTTAT
1 TTTTAATTTTAT
45596648 ATTTTAATTTTAT
1 -TTTTAATTTTAT
45596661 TTATTAATT
1 TT-TTAATT
45596670 AATAAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 12 0.41
13 17 0.59
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTAATTTTAT
Found at i:45597383 original size:38 final size:38
Alignment explanation
Indices: 45597341--45597417 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
45597331 TAAAATTAAC
45597341 TTATTTATTAATTCTATTTAAGCTAATATTTAAATATA
1 TTATTTATTAATTCTATTTAAGCTAATATTTAAATATA
45597379 TTATTTATTAATTCTATTTAAGCTAATATTTAAATATA
1 TTATTTATTAATTCTATTTAAGCTAATATTTAAATATA
45597417 T
1 T
45597418 CAAATTGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (38 bp):
TTATTTATTAATTCTATTTAAGCTAATATTTAAATATA
Found at i:45598105 original size:15 final size:15
Alignment explanation
Indices: 45598081--45598111 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
45598071 AACCCCTAAT
45598081 CCATAATCCCTAAAC
1 CCATAATCCCTAAAC
*
45598096 CCATACTCCCTAAAC
1 CCATAATCCCTAAAC
45598111 C
1 C
45598112 TTAAAATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.45, G:0.00, T:0.19
Consensus pattern (15 bp):
CCATAATCCCTAAAC
Found at i:45598644 original size:74 final size:73
Alignment explanation
Indices: 45598499--45598746 Score: 363
Period size: 73 Copynumber: 3.4 Consensus size: 73
45598489 CTGAGCGTTA
* *
45598499 GCGGCGCTTTCTTAGAAACGCCGCTAAATCCCCCGAAAGCTCAGAAAACGGCGTCGTTGTGCTTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAT-CCCCGAAAGCTCAGAAAACGGCGTCGTTGTGCTTA
45598564 GGTTTTTTT
65 GGTTTTTTT
* * * * *
45598573 GCGACGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACAGCGTAGTTGGGCTTAG
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGTGCTTAG
45598638 G-TTTTTT
66 GTTTTTTT
*** * *
45598645 GCGGCGCTTTCTTGGAAACGCTGCTAAATCTCCCGAAAGCTCAGAAAACGGCGTCGTTGTGTTTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATC-CCCGAAAGCTCAGAAAACGGCGTCGTTGTGCTTA
45598710 GGTTTTTTT
65 GGTTTTTTT
45598719 GCGGCGCTTTCTCAAAAACGCCGCTAAA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAA
45598747 GCCCTGAGCA
Statistics
Matches: 151, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
72 31 0.21
73 64 0.42
74 56 0.37
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.27
Consensus pattern (73 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGTGCTTAG
GTTTTTTT
Found at i:45598846 original size:114 final size:114
Alignment explanation
Indices: 45598645--45599087 Score: 647
Period size: 114 Copynumber: 3.9 Consensus size: 114
45598635 TAGGTTTTTT
** * * * *
45598645 GCGGCGCTTTCTTGGAAACGCTGCTAAATCTCCCGAAAGCTCAGAAAACGGCGTCGTTGTGTTTA
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATC-CCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTA
45598710 GGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
65 GGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* *
45598760 GCGGCGTTTTCTTAAAAACGCCGCTAGATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAG
45598825 GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
66 GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * * * ** *
45598874 GCGGCGCTTGCCTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAATGGCGTCGTTGGGCAAAT
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAG
* * *
45598939 GTTTTTTTGCGGCGTTTTCTCAGAATCGCCGCTAAAGCCCTGA--ATTA
66 GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * *
45598986 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCTCAAAAAACAGCGTCGTTAGGCTTAT
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTA-
* *
45599051 GTTTTTTTTGCGGCGCTTTCTTAAAAACGCCGCTAAA
65 GGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAA
45599088 TCCCCGAAAG
Statistics
Matches: 292, Mismatches: 35, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
112 59 0.20
113 31 0.11
114 177 0.61
115 25 0.09
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (114 bp):
GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAG
GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:45599107 original size:74 final size:74
Alignment explanation
Indices: 45598986--45599130 Score: 218
Period size: 74 Copynumber: 2.0 Consensus size: 74
45598976 CCCTGAATTA
*
45598986 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCTCAAAAAACAGCGTCGTTAGGCTTAT
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCTCAAAAAACAGCGTCGTTAGGCTTAG
45599051 GTTTTTTTT
66 GTTTTTTTT
* *** * * *
45599060 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTTGTAAAACGGGGTCGTTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCTCAAAAAACAGCGTCGTTAGGCTTAG
45599125 GTTTTT
66 GTTTTT
45599131 GCGGCACTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 63 1.00
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (74 bp):
GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCTCAAAAAACAGCGTCGTTAGGCTTAG
GTTTTTTTT
Found at i:45602084 original size:47 final size:47
Alignment explanation
Indices: 45602033--45602129 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
45602023 TGTCATATAA
45602033 TAAGAGGGATAAAACTTGATTCGATTTTAAAAAATAAAAAATATATT
1 TAAGAGGGATAAAACTTGATTCGATTTTAAAAAATAAAAAATATATT
45602080 TAAGAGGGATAAAACTTGATTCGATTTTAAAAAATAAAAAATATATT
1 TAAGAGGGATAAAACTTGATTCGATTTTAAAAAATAAAAAATATATT
45602127 TAA
1 TAA
45602130 ATTTTGAGTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.32
Consensus pattern (47 bp):
TAAGAGGGATAAAACTTGATTCGATTTTAAAAAATAAAAAATATATT
Found at i:45611222 original size:21 final size:21
Alignment explanation
Indices: 45611168--45611225 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
45611158 AATTTCTATT
45611168 TTAATATTTTAATAATAAATA
1 TTAATATTTTAATAATAAATA
*
45611189 -TAGAT-TTTATAAT-TTAACATA
1 TTA-ATATTT-TAATAATAA-ATA
45611210 TTAATATTTTAATAAT
1 TTAATATTTTAATAAT
45611226 TAAAACATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 11
0.69 0.05 0.26
Matches are distributed among these distances:
20 8 0.28
21 15 0.52
22 6 0.21
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
TTAATATTTTAATAATAAATA
Found at i:45615914 original size:6 final size:6
Alignment explanation
Indices: 45615874--45615912 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
45615864 TGCTGCTTCA
*
45615874 GCCCCT GCCCCT GCCCCT GCCCCT GCCCCT GCCTCT GCC
1 GCCCCT GCCCCT GCCCCT GCCCCT GCCCCT GCCCCT GCC
45615913 TCCTCTCTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.64, G:0.18, T:0.18
Consensus pattern (6 bp):
GCCCCT
Found at i:45620510 original size:2 final size:2
Alignment explanation
Indices: 45620503--45620527 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45620493 AGAAACAGAA
45620503 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
45620528 CATAAATCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:45623008 original size:127 final size:128
Alignment explanation
Indices: 45622750--45622978 Score: 286
Period size: 126 Copynumber: 1.8 Consensus size: 128
45622740 TAATATGCTA
*
45622750 AAAATATTAATTAAAAAAAGAAGAAACTTGAAGCAACATGAAATACAAAATACAAATATGAGTAG
1 AAAATATTAATTAAAAAAAGAAGAAACTTGAAGCAACATGAAATACAAAATACAAATATAAGTAG
** ***
45622815 GAGAGAAATTAAACTCAAGACTCAAAGATATAATTGCAACTATCTAACCATCTAACCGTTTAT
66 GAGAGAAATTAAACTCAAGACTCAAAGATATAAAAGCAACTATCTAACCATCTAACCGAAAAT
*** * * *
45622878 AAAA-ATTAATTAAAAATTTAA-AAAGCTTGAAGCAATATGAAATA-AAAATACAAGTGTAAGTA
1 AAAATATTAATTAAAAAAAGAAGAAA-CTTGAAGCAACATGAAATACAAAATACAAATATAAGTA
* * *
45622940 GGAGAGAAATTGAACTCGAGACTCAAGGATA-AAAAGCAA
65 GGAGAGAAATTAAACTCAAGACTCAAAGATATAAAAGCAA
45622979 TAACATTTAA
Statistics
Matches: 88, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
125 6 0.07
126 46 0.52
127 32 0.36
128 4 0.05
ACGTcount: A:0.53, C:0.11, G:0.14, T:0.22
Consensus pattern (128 bp):
AAAATATTAATTAAAAAAAGAAGAAACTTGAAGCAACATGAAATACAAAATACAAATATAAGTAG
GAGAGAAATTAAACTCAAGACTCAAAGATATAAAAGCAACTATCTAACCATCTAACCGAAAAT
Found at i:45624164 original size:19 final size:19
Alignment explanation
Indices: 45624126--45624166 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
45624116 ATTCAATTAA
* *
45624126 ATAAAAAATTTTAATTTTT
1 ATAAAAAATGTTAATATTT
*
45624145 ATAAAAAATGTTACTATTT
1 ATAAAAAATGTTAATATTT
45624164 ATA
1 ATA
45624167 TTTTGTAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
ATAAAAAATGTTAATATTT
Found at i:45624679 original size:21 final size:20
Alignment explanation
Indices: 45624639--45624680 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
45624629 AATCTTGATT
*
45624639 TTAAAAAAAGTAAATATAAA
1 TTAAAAAAAGTAAAAATAAA
*
45624659 TTAAAAAAATTAAAAAGTAAA
1 TTAAAAAAAGTAAAAA-TAAA
45624680 T
1 T
45624681 ATAAGAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (20 bp):
TTAAAAAAAGTAAAAATAAA
Found at i:45625111 original size:7 final size:7
Alignment explanation
Indices: 45625099--45625123 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
45625089 TGAGAAAAAG
45625099 TAAATTT
1 TAAATTT
45625106 TAAATTT
1 TAAATTT
45625113 TAAATTT
1 TAAATTT
45625120 TAAA
1 TAAA
45625124 AAGTAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TAAATTT
Found at i:45625130 original size:14 final size:14
Alignment explanation
Indices: 45625093--45625131 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
45625083 GGTTGATGAG
45625093 AAAAAGTAAATTTT
1 AAAAAGTAAATTTT
***
45625107 AAATTTTAAATTTT
1 AAAAAGTAAATTTT
45625121 AAAAAGTAAAT
1 AAAAAGTAAAT
45625132 ATAAAAATAT
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (14 bp):
AAAAAGTAAATTTT
Found at i:45632530 original size:16 final size:16
Alignment explanation
Indices: 45632511--45632559 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
45632501 GAAGAGAATG
*
45632511 GAAATTAAAGAAAAAA
1 GAAATAAAAGAAAAAA
* **
45632527 GAAAGAAAAGTTAAAA
1 GAAATAAAAGAAAAAA
45632543 GAATATAAAAGAAAAAA
1 GAA-ATAAAAGAAAAAA
45632560 ATTAAATTGC
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.12
Consensus pattern (16 bp):
GAAATAAAAGAAAAAA
Found at i:45633379 original size:16 final size:18
Alignment explanation
Indices: 45633358--45633395 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
45633348 TTCTATATGG
45633358 ATTTTACT-TT-TATTTT
1 ATTTTACTATTGTATTTT
45633374 ATTTTACTATTGTATTTT
1 ATTTTACTATTGTATTTT
45633392 ATTT
1 ATTT
45633396 AAATAAGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (18 bp):
ATTTTACTATTGTATTTT
Found at i:45638082 original size:17 final size:18
Alignment explanation
Indices: 45638060--45638098 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
45638050 GATTTGACAA
45638060 AAAAAAGTT-TAAAACTT
1 AAAAAAGTTGTAAAACTT
45638077 AAAAAAGTTGTAAAACTT
1 AAAAAAGTTGTAAAACTT
45638095 AAAA
1 AAAA
45638099 GCCTCTTGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.26
Consensus pattern (18 bp):
AAAAAAGTTGTAAAACTT
Found at i:45638082 original size:18 final size:19
Alignment explanation
Indices: 45638059--45638098 Score: 66
Period size: 17 Copynumber: 2.2 Consensus size: 19
45638049 TGATTTGACA
45638059 AAAAAAAGTT-TAAAACTT
1 AAAAAAAGTTGTAAAACTT
45638077 -AAAAAAGTTGTAAAACTT
1 AAAAAAAGTTGTAAAACTT
45638095 AAAA
1 AAAA
45638099 GCCTCTTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 8 0.40
19 3 0.15
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.25
Consensus pattern (19 bp):
AAAAAAAGTTGTAAAACTT
Found at i:45644034 original size:12 final size:12
Alignment explanation
Indices: 45644017--45644046 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
45644007 GATCTCTTTT
45644017 AACAAAAATTAC
1 AACAAAAATTAC
45644029 AACAAAAATTAC
1 AACAAAAATTAC
45644041 AA-AAAA
1 AACAAAA
45644047 GATTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.73, C:0.13, G:0.00, T:0.13
Consensus pattern (12 bp):
AACAAAAATTAC
Found at i:45646380 original size:15 final size:15
Alignment explanation
Indices: 45646362--45646394 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
45646352 ATTTCTCTAA
45646362 TTTTTTGAACAAGGT
1 TTTTTTGAACAAGGT
45646377 TTTTTTGAACAAGGT
1 TTTTTTGAACAAGGT
45646392 TTT
1 TTT
45646395 AACAATGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.52
Consensus pattern (15 bp):
TTTTTTGAACAAGGT
Found at i:45646692 original size:13 final size:15
Alignment explanation
Indices: 45646663--45646694 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
45646653 TATGTTATTG
45646663 TTAATATAATATTTA
1 TTAATATAATATTTA
45646678 TTAAT-TAAT-TTTA
1 TTAATATAATATTTA
45646691 TTAA
1 TTAA
45646695 AAGCAATCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 4 0.24
15 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTAATATAATATTTA
Found at i:45651389 original size:56 final size:57
Alignment explanation
Indices: 45651266--45651389 Score: 214
Period size: 57 Copynumber: 2.2 Consensus size: 57
45651256 TGCAGGATGT
45651266 GGAGAAGATAATCTTGGGATGTTAGTTTTTATCCTAGAAAAAAAGAATTTAAAAAGA
1 GGAGAAGATAATCTTGGGATGTTAGTTTTTATCCTAGAAAAAAAGAATTTAAAAAGA
* *
45651323 GGAGAAGATAATTTTGGGATGTTGGTTTTTATCCTA-AAAAAAAGAATTTAAAAAGA
1 GGAGAAGATAATCTTGGGATGTTAGTTTTTATCCTAGAAAAAAAGAATTTAAAAAGA
*
45651379 GTAGAAGATAA
1 GGAGAAGATAA
45651390 AAATGGGTTG
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
56 30 0.47
57 34 0.53
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.30
Consensus pattern (57 bp):
GGAGAAGATAATCTTGGGATGTTAGTTTTTATCCTAGAAAAAAAGAATTTAAAAAGA
Found at i:45651402 original size:56 final size:57
Alignment explanation
Indices: 45651266--45651403 Score: 188
Period size: 56 Copynumber: 2.4 Consensus size: 57
45651256 TGCAGGATGT
*** *
45651266 GGAGAAGATAATCTTGGGATGTTAGTTTTTATCCTAGAAAAAAAGAATTTAAAAAGA
1 GGAGAAGATAAAAATGGGATGTTGGTTTTTATCCTAGAAAAAAAGAATTTAAAAAGA
***
45651323 GGAGAAGATAATTTTGGGATGTTGGTTTTTATCCTA-AAAAAAAGAATTTAAAAAGA
1 GGAGAAGATAAAAATGGGATGTTGGTTTTTATCCTAGAAAAAAAGAATTTAAAAAGA
* *
45651379 GTAGAAGATAAAAATGGGTTGTTGG
1 GGAGAAGATAAAAATGGGATGTTGG
45651404 ATTTACCCTA
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
56 40 0.54
57 34 0.46
ACGTcount: A:0.42, C:0.04, G:0.24, T:0.30
Consensus pattern (57 bp):
GGAGAAGATAAAAATGGGATGTTGGTTTTTATCCTAGAAAAAAAGAATTTAAAAAGA
Found at i:45665534 original size:23 final size:26
Alignment explanation
Indices: 45665494--45665540 Score: 64
Period size: 23 Copynumber: 1.9 Consensus size: 26
45665484 ATATTTATGT
*
45665494 TCAATATAGGAAGTAATT-CTAATAA
1 TCAATATAGGAAGAAATTACTAATAA
45665519 TCAAT-TA-GAAGAAATTACTAAT
1 TCAATATAGGAAGAAATTACTAAT
45665541 TTTAAAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 7 0.35
25 5 0.25
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.32
Consensus pattern (26 bp):
TCAATATAGGAAGAAATTACTAATAA
Found at i:45676766 original size:210 final size:211
Alignment explanation
Indices: 45676403--45676826 Score: 665
Period size: 210 Copynumber: 2.0 Consensus size: 211
45676393 CAAGAAGTTT
* * *
45676403 ATAGTCTTGATTGCTGGTTCAGTTTCCTGATAATAGTTGGGGTCAAGAAATAACATTTTGAGAGA
1 ATAGTCTTGATTGCTGGTTCAGTTTCCTGATAATAGTAGGGCTCAAGAAATAACATTGTGAGAGA
* * *
45676468 TGAGGGTGGTGCATATGATTCTTAACAAACCAGCCAGTATACTGCACCAAATCAAGATGAAAATT
66 CGAGGGTGGTGCATATGATTCCTAACAAACCAACCAGTATACTGCACCAAATCAAGATGAAAATT
* ** * *
45676533 CGATATTGGAACTAACGAATTTTCATATGATGTCCTGGTTTACTAAATACAGAAGAGTAGGTTTA
131 CGATATTGGAACTAAAGAATTTTCATATGATACCCTAGTTTACTAAAGACAGAAGAGTAGGTTTA
45676598 ATATGGTTCAACTTCC
196 ATATGGTTCAACTTCC
* *
45676614 ATAGTCTTGATTGCTGGTTCAGTTTTCC-GATATTGGTAGGGCTCAAGAAATAACATTGT-AGAG
1 ATAGTCTTGATTGCTGGTTCAG-TTTCCTGATAATAGTAGGGCTCAAGAAATAACATTGTGAGAG
*
45676677 ACGAGGGTGGTGCATATGATTCCTAACAAACCAACCAGTATACTGCACCAAATCAAGGTGAAAAT
65 ACGAGGGTGGTGCATATGATTCCTAACAAACCAACCAGTATACTGCACCAAATCAAGATGAAAAT
* *
45676742 TTGATATTGTG-ACTAAAGAATTTTCATATGATACCCTAGTTTACTAAAGACGGAAGAGTAGGTT
130 TCGATATTG-GAACTAAAGAATTTTCATATGATACCCTAGTTTACTAAAGACAGAAGAGTAGGTT
45676806 TAATATGGTTCAACTTCC
194 TAATATGGTTCAACTTCC
45676824 ATA
1 ATA
45676827 AAGAAGCCTG
Statistics
Matches: 195, Mismatches: 16, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
210 141 0.72
211 49 0.25
212 5 0.03
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (211 bp):
ATAGTCTTGATTGCTGGTTCAGTTTCCTGATAATAGTAGGGCTCAAGAAATAACATTGTGAGAGA
CGAGGGTGGTGCATATGATTCCTAACAAACCAACCAGTATACTGCACCAAATCAAGATGAAAATT
CGATATTGGAACTAAAGAATTTTCATATGATACCCTAGTTTACTAAAGACAGAAGAGTAGGTTTA
ATATGGTTCAACTTCC
Found at i:45680102 original size:18 final size:18
Alignment explanation
Indices: 45680076--45680111 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
45680066 ATTGAATCGA
*
45680076 TTGTTATGTTGAAATATT
1 TTGTCATGTTGAAATATT
*
45680094 TTGTCATGTTGGAATATT
1 TTGTCATGTTGAAATATT
45680112 GCTTCTTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (18 bp):
TTGTCATGTTGAAATATT
Found at i:45680253 original size:55 final size:55
Alignment explanation
Indices: 45680113--45680430 Score: 286
Period size: 55 Copynumber: 5.8 Consensus size: 55
45680103 TGGAATATTG
* * * * *
45680113 CTTCTTTTGAATCGGTTGTTTATATGTTTAAAAT-AATTGTTAGGTAGGAATACTA
1 CTTCTTTTGAATAGATTGTTTATATGTTT-AAATCGATTGTTATGTAAGAATACTA
* * * * * *
45680168 -TT-TTTTTAATTGACTGTTTACATGTGTAAATCGATTGTTATGTAAGAATGCTA
1 CTTCTTTTGAATAGATTGTTTATATGTTTAAATCGATTGTTATGTAAGAATACTA
* * * * *
45680221 CTTCTTTTGAATCA-ATTGTTTATACGGTTAAATCGATTGTTCTGGTGAA-ATATTGCTT
1 CTTCTTTTGAAT-AGATTGTTTATATGTTTAAATCGATTGTTAT-GT-AAGA-A-TACTA
* **
45680279 CTTCTTTTGAATAGATTGTTTATATGTTTAAATCGATTATTATGTTGGAATACTA
1 CTTCTTTTGAATAGATTGTTTATATGTTTAAATCGATTGTTATGTAAGAATACTA
* ** * **
45680334 CTTCTTTTGAATAGATTGTTTATATATTTAAATTAATTGTTATATCGGAATACTA
1 CTTCTTTTGAATAGATTGTTTATATGTTTAAATCGATTGTTATGTAAGAATACTA
* * **
45680389 CTTCTTTTGAGTTGATTGTTTATATGTTTAAATTAATTGTTA
1 CTTCTTTTGAATAGATTGTTTATATGTTTAAATCGATTGTTA
45680431 AAAAGCAAGT
Statistics
Matches: 217, Mismatches: 36, Indels: 20
0.79 0.13 0.07
Matches are distributed among these distances:
52 4 0.02
53 36 0.17
54 4 0.02
55 121 0.56
56 4 0.02
57 7 0.03
58 41 0.19
ACGTcount: A:0.28, C:0.08, G:0.15, T:0.49
Consensus pattern (55 bp):
CTTCTTTTGAATAGATTGTTTATATGTTTAAATCGATTGTTATGTAAGAATACTA
Found at i:45680299 original size:58 final size:57
Alignment explanation
Indices: 45680194--45680357 Score: 187
Period size: 58 Copynumber: 2.9 Consensus size: 57
45680184 TTTACATGTG
*
45680194 TAAATCGATTGTTAT-GT-AAGA-ATGCTACTTCTTTTGAATCA-ATTGTTTATACGGT
1 TAAATCGATTATTATGGTGAA-ATATGCTACTTCTTTTGAAT-AGATTGTTTATACGGT
* * * * *
45680249 TAAATCGATTGTTCTGGTGAAATATTGCTTCTTCTTTTGAATAGATTGTTTATATGTT
1 TAAATCGATTATTATGGTGAAATA-TGCTACTTCTTTTGAATAGATTGTTTATACGGT
* *
45680307 TAAATCGATTATTATGTTGGAATA--CTACTTCTTTTGAATAGATTGTTTATA
1 TAAATCGATTATTATGGTGAAATATGCTACTTCTTTTGAATAGATTGTTTATA
45680358 TATTTAAATT
Statistics
Matches: 95, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
55 40 0.42
56 3 0.03
57 4 0.04
58 48 0.51
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.47
Consensus pattern (57 bp):
TAAATCGATTATTATGGTGAAATATGCTACTTCTTTTGAATAGATTGTTTATACGGT
Found at i:45680393 original size:113 final size:110
Alignment explanation
Indices: 45680099--45680421 Score: 334
Period size: 113 Copynumber: 2.9 Consensus size: 110
45680089 ATATTTTGTC
* * * * * *
45680099 ATGTTGGAATATTGCTTCTTTTGAATCGGTTGTTTATATGTTTAAAATAATTGTTAGGTAGGAAT
1 ATGTTGGAATACTACTTCTTTTGAATAGATTGTTTATATGTTTAAATTAATTGTTATGT-GGAAT
* * * *
45680164 ACTAT-TT-TTTT-AATTGACTGTTTACATGTGTAAATCGATTGTT
65 ACTATCTTCTTTTGAATTGATTGTTTATATGTTTAAATCGATTATT
** * * * ** * *
45680207 ATGTAAGAATGCTACTTCTTTTGAATCA-ATTGTTTATACGGTTAAATCGATTGTTCTGGTGAAA
1 ATGTTGGAATACTACTTCTTTTGAAT-AGATTGTTTATATGTTTAAATTAATTGTTAT-GTGGAA
*
45680271 TATTGCT-TCTTCTTTTGAATAGATTGTTTATATGTTTAAATCGATTATT
64 TA---CTATCTTCTTTTGAATTGATTGTTTATATGTTTAAATCGATTATT
* *
45680320 ATGTTGGAATACTACTTCTTTTGAATAGATTGTTTATATATTTAAATTAATTGTTATATCGGAAT
1 ATGTTGGAATACTACTTCTTTTGAATAGATTGTTTATATGTTTAAATTAATTGTTATGT-GGAAT
*
45680385 ACTA-CTTCTTTTGAGTTGATTGTTTATATGTTTAAAT
65 ACTATCTTCTTTTGAATTGATTGTTTATATGTTTAAAT
45680422 TAATTGTTAA
Statistics
Matches: 171, Mismatches: 33, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
108 47 0.27
109 2 0.01
110 34 0.20
111 4 0.02
112 6 0.04
113 78 0.46
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (110 bp):
ATGTTGGAATACTACTTCTTTTGAATAGATTGTTTATATGTTTAAATTAATTGTTATGTGGAATA
CTATCTTCTTTTGAATTGATTGTTTATATGTTTAAATCGATTATT
Found at i:45681770 original size:31 final size:29
Alignment explanation
Indices: 45681705--45681770 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 29
45681695 GTTAGTGATT
45681705 TAATATAAATATATAATTATTATTTAACA
1 TAATATAAATATATAATTATTATTTAACA
* *
45681734 T-ATATAATTAATATAA-TATTTTTAATAACA
1 TAATATAAAT-ATATAATTATTATT--TAACA
45681764 TAATATA
1 TAATATA
45681771 TTCGGGCTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
28 13 0.42
29 7 0.23
30 6 0.19
31 5 0.16
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (29 bp):
TAATATAAATATATAATTATTATTTAACA
Found at i:45685928 original size:15 final size:14
Alignment explanation
Indices: 45685908--45685942 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
45685898 TAATCCTTAG
*
45685908 TAATTATCTTAATA
1 TAATTATCCTAATA
45685922 TTAATTATCCTAATA
1 -TAATTATCCTAATA
45685937 TAATTA
1 TAATTA
45685943 AAGTAGAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (14 bp):
TAATTATCCTAATA
Found at i:45686861 original size:27 final size:26
Alignment explanation
Indices: 45686831--45686895 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 26
45686821 GTACATAATT
*
45686831 GGGAAGCCTTCTCTCGAGCCATATAAC
1 GGGAAGCCTTATCT-GAGCCATATAAC
* *
45686858 GGGAAG-CTTATGTGAGCCATGTAAC
1 GGGAAGCCTTATCTGAGCCATATAAC
*
45686883 GGGAAGCTTTATC
1 GGGAAGCCTTATC
45686896 CAGGCTGTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
25 17 0.53
26 9 0.28
27 6 0.19
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (26 bp):
GGGAAGCCTTATCTGAGCCATATAAC
Found at i:45687110 original size:26 final size:26
Alignment explanation
Indices: 45687031--45687110 Score: 83
Period size: 26 Copynumber: 3.1 Consensus size: 26
45687021 AGCCATATTA
* * *
45687031 GGAAGCTC-CGGAGAGCTATTAATCA
1 GGAAGCTCACGAAGAGCCATTAATCG
** *
45687056 GGAAGCTCAAAAAGAGCCTTTAATCG
1 GGAAGCTCACGAAGAGCCATTAATCG
45687082 GGAAGCTCACGAAGAGCCATATAAT-G
1 GGAAGCTCACGAAGAGCCAT-TAATCG
45687108 GGA
1 GGA
45687111 CACTTATAAG
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
25 8 0.18
26 32 0.73
27 4 0.09
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.17
Consensus pattern (26 bp):
GGAAGCTCACGAAGAGCCATTAATCG
Found at i:45687263 original size:24 final size:25
Alignment explanation
Indices: 45687203--45687265 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
45687193 ATTGCAAGAA
*
45687203 CCATATAACGGGAAGCTCAATAAGG
1 CCATATAACGGGATGCTCAATAAGG
*
45687228 CCATATACCGGGATGCTC-ATAAGAG
1 CCATATAACGGGATGCTCAATAAG-G
*
45687253 CTA-ATAACGGGAT
1 CCATATAACGGGAT
45687266 ACTCTTTCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 14 0.42
25 19 0.58
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.19
Consensus pattern (25 bp):
CCATATAACGGGATGCTCAATAAGG
Found at i:45689447 original size:18 final size:18
Alignment explanation
Indices: 45689416--45689460 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
45689406 ATTCCCACTC
45689416 ATAATAATAATAATACTA
1 ATAATAATAATAATACTA
* *
45689434 ATAATTATATTAATACTA
1 ATAATAATAATAATACTA
*
45689452 ATATTAATA
1 ATAATAATA
45689461 CTTACTTCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAATAATAATAATACTA
Found at i:45689462 original size:12 final size:12
Alignment explanation
Indices: 45689420--45689460 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
45689410 CCACTCATAA
*
45689420 TAATAATAATAC
1 TAATAATAATAT
*
45689432 TAATAATTATAT
1 TAATAATAATAT
*
45689444 TAATACTAATAT
1 TAATAATAATAT
45689456 TAATA
1 TAATA
45689461 CTTACTTCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:45690227 original size:19 final size:19
Alignment explanation
Indices: 45690182--45690221 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
45690172 TTTGTTTTGT
*
45690182 TTTTATTT-CTTTACTTTC
1 TTTTATTTACTTTACTTTA
45690200 TTTTATTTACTTTACTTTA
1 TTTTATTTACTTTACTTTA
45690219 TTT
1 TTT
45690222 CTTTTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTATTTACTTTACTTTA
Found at i:45690381 original size:5 final size:5
Alignment explanation
Indices: 45690373--45690432 Score: 54
Period size: 5 Copynumber: 12.2 Consensus size: 5
45690363 TATTTAATTT
* * *
45690373 ATATA ATATA ATACA ATATA ATATA TTATATT ATATT ATATA ATA-A A-ATA
1 ATATA ATATA ATATA ATATA ATATA --ATATA ATATA ATATA ATATA ATATA
45690423 ATAT- ATATA A
1 ATATA ATATA A
45690433 AACATAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
3 1 0.02
4 8 0.17
5 33 0.72
7 4 0.09
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:45694205 original size:24 final size:24
Alignment explanation
Indices: 45694164--45694275 Score: 74
Period size: 24 Copynumber: 4.8 Consensus size: 24
45694154 AATTTATTTA
* *
45694164 AATA-TATATTTAATTTTAAATCT
1 AATATTATTTTTAAATTTAAATCT
** *
45694187 AATATTATTTTTATGTTT-AAGCTT
1 AATATTATTTTTAAATTTAAATC-T
* *
45694211 AATGTTATTTTTAAATTTATCATC-
1 AATATTATTTTTAAATTTA-AATCT
*
45694235 AATATTA-TTTT-AATTTACAATGT
1 AATATTATTTTTAAATTTA-AATCT
*
45694258 ATTATTA-TTTTAAATTTA
1 AATATTATTTTTAAATTTA
45694276 TCATGTATTT
Statistics
Matches: 69, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
22 8 0.12
23 21 0.30
24 38 0.55
26 2 0.03
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (24 bp):
AATATTATTTTTAAATTTAAATCT
Found at i:45694281 original size:24 final size:24
Alignment explanation
Indices: 45694219--45694284 Score: 84
Period size: 23 Copynumber: 2.8 Consensus size: 24
45694209 TTAATGTTAT
* *
45694219 TTTTAAATTTATCAT-CAATATTA
1 TTTTAAATTTATCATGTATTATTA
45694242 TTTT-AATTTA-CAATGTATTATTA
1 TTTTAAATTTATC-ATGTATTATTA
45694265 TTTTAAATTTATCATGTATT
1 TTTTAAATTTATCATGTATT
45694285 TGTTTATCGT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
21 1 0.03
22 8 0.22
23 14 0.38
24 13 0.35
25 1 0.03
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (24 bp):
TTTTAAATTTATCATGTATTATTA
Found at i:45694354 original size:24 final size:24
Alignment explanation
Indices: 45694299--45694355 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
45694289 TATCGTGTAC
* *
45694299 TATTATTTTAAGTTTATCACGTAT
1 TATTATTTTAAGTTTATCAAGGAT
45694323 T-TTCATTTTGAA-TTTATCAAGGAT
1 TATT-ATTTT-AAGTTTATCAAGGAT
45694347 TATTATTTT
1 TATTATTTT
45694356 TTAACTTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 2 0.07
24 22 0.79
25 4 0.14
ACGTcount: A:0.28, C:0.07, G:0.09, T:0.56
Consensus pattern (24 bp):
TATTATTTTAAGTTTATCAAGGAT
Found at i:45695061 original size:18 final size:17
Alignment explanation
Indices: 45695034--45695068 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
45695024 GATTATTGCT
45695034 CTTATGTGTATTGTATTG
1 CTTATGTGTATT-TATTG
*
45695052 CTTATTTGTATTTATTG
1 CTTATGTGTATTTATTG
45695069 ATTTGTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.17, C:0.06, G:0.17, T:0.60
Consensus pattern (17 bp):
CTTATGTGTATTTATTG
Found at i:45703164 original size:17 final size:16
Alignment explanation
Indices: 45703142--45703175 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
45703132 ATTTTTGAAT
45703142 TTTTATATTTTATATAA
1 TTTT-TATTTTATATAA
45703159 -TTTTATTTTATATAA
1 TTTTTATTTTATATAA
45703174 TT
1 TT
45703176 GATATATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTATTTTATATAA
Found at i:45703165 original size:15 final size:15
Alignment explanation
Indices: 45703147--45703175 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
45703137 TGAATTTTTA
45703147 TATTTTATATAATTT
1 TATTTTATATAATTT
45703162 TATTTTATATAATT
1 TATTTTATATAATT
45703176 GATATATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TATTTTATATAATTT
Found at i:45704555 original size:43 final size:42
Alignment explanation
Indices: 45704365--45704613 Score: 292
Period size: 42 Copynumber: 5.9 Consensus size: 42
45704355 CTAAGAAAAT
*
45704365 AAACGCCGCTAAAGATCATGTTCTTTAGCAGCGCTTATGAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTATGAAA
*
45704407 AAACGCAGCTAAAGATCATGTTCTTTAGCGGCGCTTATGAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTATGAAA
* * *
45704449 AAGCGCCGCTAAAGATCACGTTCTTTAGCGACGCTT-TGGAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAT-GAAA
* *
45704491 AAACGCCGCTAAAGATCATGTTCTTTAACGGCGCTT-TGGGAGA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAT--GAAA
* * * **
45704534 AAACGCCGCTAAA-ACTAATGTTCTATAGCGGCGCTTGTTCAA
1 AAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTATGAAA
*
45704576 AAACGCCGCTAATAG-T-AGTGTTATTTAGCGGCGCTTAT
1 AAACGCCGCTAA-AGATCA-TGTTCTTTAGCGGCGCTTAT
45704614 TTCACAAACG
Statistics
Matches: 180, Mismatches: 20, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
41 2 0.01
42 141 0.78
43 36 0.20
44 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (42 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTATGAAA
Found at i:45710629 original size:7 final size:7
Alignment explanation
Indices: 45710619--45710664 Score: 56
Period size: 7 Copynumber: 6.0 Consensus size: 7
45710609 TGATATATTT
45710619 TTATGTA
1 TTATGTA
45710626 TTATGTAA
1 TTATGT-A
45710634 GTTATGTAA
1 -TTATGT-A
45710643 GTTATGTA
1 -TTATGTA
45710651 TTATGTA
1 TTATGTA
45710658 TTATGTA
1 TTATGTA
45710665 AGTACTGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 20 0.54
8 2 0.05
9 15 0.41
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.52
Consensus pattern (7 bp):
TTATGTA
Found at i:45710640 original size:9 final size:9
Alignment explanation
Indices: 45710626--45710766 Score: 113
Period size: 9 Copynumber: 16.4 Consensus size: 9
45710616 TTTTTATGTA
45710626 TTATGTAAG
1 TTATGTAAG
45710635 TTATGTAAG
1 TTATGTAAG
45710644 TTATGT-A-
1 TTATGTAAG
45710651 TTATGT-A-
1 TTATGTAAG
45710658 TTATGTAAG
1 TTATGTAAG
45710667 -TACTGTAAG
1 TTA-TGTAAG
*
45710676 TAATGTAAG
1 TTATGTAAG
45710685 TTATGTAAAG
1 TTATGT-AAG
*
45710695 TAATGT-A-
1 TTATGTAAG
*
45710702 TAATGTAAG
1 TTATGTAAG
*
45710711 TTAAG-AAGG
1 TTATGTAA-G
45710720 TTATGT-A-
1 TTATGTAAG
*
45710727 TAATGTAAG
1 TTATGTAAG
*
45710736 TCATGTAAG
1 TTATGTAAG
* *
45710745 TTATTTAAT
1 TTATGTAAG
45710754 TTATGTAAG
1 TTATGTAAG
45710763 TTAT
1 TTAT
45710767 TTATGTAAGT
Statistics
Matches: 108, Mismatches: 13, Indels: 22
0.76 0.09 0.15
Matches are distributed among these distances:
7 24 0.22
8 9 0.08
9 66 0.61
10 9 0.08
ACGTcount: A:0.36, C:0.01, G:0.19, T:0.43
Consensus pattern (9 bp):
TTATGTAAG
Found at i:45710655 original size:32 final size:33
Alignment explanation
Indices: 45710619--45710748 Score: 124
Period size: 32 Copynumber: 3.9 Consensus size: 33
45710609 TGATATATTT
45710619 TTATGTATTATGTAAGTTATGTAAGTTATGTA-
1 TTATGTATTATGTAAGTTATGTAAGTTATGTAG
*
45710651 TTATGTATTATGTAAG-TACTGTAAGTAATGTAAG
1 TTATGTATTATGTAAGTTA-TGTAAGTTATGT-AG
* * *
45710685 TTATGTA--AAGTAATGTATAATGTAAGTTAAGAAGG
1 TTATGTATTATGTAA-GT-T-ATGTAAGTTATGTA-G
* *
45710720 TTATGTATAATGTAAGTCATGTAAGTTAT
1 TTATGTATTATGTAAGTTATGTAAGTTAT
45710749 TTAATTTATG
Statistics
Matches: 80, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
31 2 0.03
32 32 0.40
33 2 0.03
34 18 0.22
35 18 0.22
36 3 0.04
37 5 0.06
ACGTcount: A:0.36, C:0.02, G:0.20, T:0.42
Consensus pattern (33 bp):
TTATGTATTATGTAAGTTATGTAAGTTATGTAG
Found at i:45710770 original size:13 final size:13
Alignment explanation
Indices: 45710752--45710777 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45710742 AAGTTATTTA
45710752 ATTTATGTAAGTT
1 ATTTATGTAAGTT
45710765 ATTTATGTAAGTT
1 ATTTATGTAAGTT
45710778 GTCTTGGCTT
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:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
ATTTATGTAAGTT
Found at i:45711032 original size:16 final size:16
Alignment explanation
Indices: 45711013--45711048 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
45711003 CTGTAAGTGC
*
45711013 TGTATTATATAAGTTA
1 TGTATTATATAAGATA
*
45711029 TGTATTATGTAAGATA
1 TGTATTATATAAGATA
45711045 TGTA
1 TGTA
45711049 AGTTGTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (16 bp):
TGTATTATATAAGATA
Found at i:45711050 original size:25 final size:25
Alignment explanation
Indices: 45711022--45711105 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 25
45711012 CTGTATTATA
45711022 TAAGTTATGTATTATGTAAGATATG
1 TAAGTTATGTATTATGTAAGATATG
* * * *
45711047 TAAGTTGTATTTTATGTAAGTTATG
1 TAAGTTATGTATTATGTAAGATATG
* * *
45711072 TAAGTAACG-AGTTATGTAAGCTATG
1 TAAGTTATGTA-TTATGTAAGATATG
45711097 TAAGTTATG
1 TAAGTTATG
45711106 CAAGATTATA
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.43
Consensus pattern (25 bp):
TAAGTTATGTATTATGTAAGATATG
Found at i:45711070 original size:9 final size:9
Alignment explanation
Indices: 45710949--45711105 Score: 82
Period size: 9 Copynumber: 18.6 Consensus size: 9
45710939 AAGTTGTATT
*
45710949 TTATGAAAG
1 TTATGTAAG
*
45710958 TTATATAAG
1 TTATGTAAG
*
45710967 TTATGTAGG
1 TTATGTAAG
* *
45710976 CTATGT--T
1 TTATGTAAG
*
45710983 TTATGCAAG
1 TTATGTAAG
* *
45710992 TTATTTAAT
1 TTATGTAAG
*
45711001 TTCTGTAAG
1 TTATGTAAG
**
45711010 TGCTGT-A-
1 TTATGTAAG
*
45711017 TTATATAAG
1 TTATGTAAG
45711026 TTATGT-A-
1 TTATGTAAG
45711033 TTATGTAAG
1 TTATGTAAG
*
45711042 ATATGTAAG
1 TTATGTAAG
**
45711051 -T-TGTATT
1 TTATGTAAG
45711058 TTATGTAAG
1 TTATGTAAG
45711067 TTATGTAAG
1 TTATGTAAG
* *
45711076 TAACG--AG
1 TTATGTAAG
45711083 TTATGTAAG
1 TTATGTAAG
*
45711092 CTATGTAAG
1 TTATGTAAG
45711101 TTATG
1 TTATG
45711106 CAAGATTATA
Statistics
Matches: 107, Mismatches: 31, Indels: 20
0.68 0.20 0.13
Matches are distributed among these distances:
7 22 0.21
8 6 0.06
9 79 0.74
ACGTcount: A:0.32, C:0.04, G:0.20, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:45711141 original size:8 final size:7
Alignment explanation
Indices: 45711123--45711168 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
45711113 ATAATATAAG
45711123 TTATGTA
1 TTATGTA
45711130 TTATGTTA
1 TTATG-TA
45711138 TTATGTA
1 TTATGTA
45711145 TTATGTA
1 TTATGTA
*
45711152 --ATTTA
1 TTATGTA
45711157 TTATGTTA
1 TTATG-TA
45711165 TTAT
1 TTAT
45711169 ATATAAGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
5 4 0.12
7 16 0.48
8 13 0.39
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (7 bp):
TTATGTA
Found at i:45711141 original size:27 final size:26
Alignment explanation
Indices: 45711110--45711239 Score: 89
Period size: 27 Copynumber: 5.2 Consensus size: 26
45711100 GTTATGCAAG
45711110 ATTATAATATAAGTTATGTATTATGTT
1 ATTAT-ATATAAGTTATGTATTATGTT
* * * *
45711137 ATTATGTATTATGTAATTTATTATGTT
1 ATTATATA-TAAGTTATGTATTATGTT
* *
45711164 ATTATATATAAGTTA--TATGGAAGTT
1 ATTATATATAAGTTATGTAT-TATGTT
*
45711189 A-T-TATATAAGTTATGCA--A-GCTT
1 ATTATATATAAGTTATGTATTATG-TT
*
45711211 A-TA-AAATAAGTTATGTATTATGTT
1 ATTATATATAAGTTATGTATTATGTT
45711235 ATTAT
1 ATTAT
45711240 GTATTATGTA
Statistics
Matches: 80, Mismatches: 12, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
21 1 0.01
22 17 0.21
23 11 0.14
24 8 0.10
25 9 0.11
26 7 0.09
27 27 0.34
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (26 bp):
ATTATATATAAGTTATGTATTATGTT
Found at i:45711143 original size:15 final size:15
Alignment explanation
Indices: 45711123--45711168 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
45711113 ATAATATAAG
45711123 TTATGTATTATGTTA
1 TTATGTATTATGTTA
45711138 TTATGTATTATG-TA
1 TTATGTATTATGTTA
*
45711152 --ATTTATTATGTTA
1 TTATGTATTATGTTA
45711165 TTAT
1 TTAT
45711169 ATATAAGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 9 0.33
13 2 0.07
14 2 0.07
15 14 0.52
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (15 bp):
TTATGTATTATGTTA
Found at i:45711860 original size:33 final size:33
Alignment explanation
Indices: 45711822--45711925 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 33
45711812 CTAGGGTTAA
45711822 TAAATTTAAAGTATATTAAATATAAGTTAATGG
1 TAAATTTAAAGTATATTAAATATAAGTTAATGG
* * ** * ** **
45711855 TAAA-TTCAATTATATT-TTTCTCTGCAACATGG
1 TAAATTTAAAGTATATTAAATATAAGTTA-ATGG
45711887 TAAATTTAAAGTATATTAAATATAAGTTAATGG
1 TAAATTTAAAGTATATTAAATATAAGTTAATGG
45711920 TAAATT
1 TAAATT
45711926 AAGGTCTGAT
Statistics
Matches: 50, Mismatches: 18, Indels: 6
0.68 0.24 0.08
Matches are distributed among these distances:
31 4 0.08
32 18 0.36
33 24 0.48
34 4 0.08
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (33 bp):
TAAATTTAAAGTATATTAAATATAAGTTAATGG
Found at i:45711870 original size:32 final size:32
Alignment explanation
Indices: 45711822--45711927 Score: 97
Period size: 32 Copynumber: 3.2 Consensus size: 32
45711812 CTAGGGTTAA
45711822 TAAATTTAAAGTATATTAAATATAAGTTAATGG
1 TAAA-TTAAAGTATATTAAATATAAGTTAATGG
* * ** * ** **
45711855 TAAATTCAATTATATT-TTTCTCTGCAACATGG
1 TAAATTAAAGTATATTAAATATAAGTTA-ATGG
45711887 TAAATTTAAAGTATATTAAATATAAGTTAATGG
1 TAAA-TTAAAGTATATTAAATATAAGTTAATGG
45711920 TAAATTAA
1 TAAATTAA
45711928 GGTCTGATTT
Statistics
Matches: 52, Mismatches: 18, Indels: 7
0.68 0.23 0.09
Matches are distributed among these distances:
31 4 0.08
32 22 0.42
33 22 0.42
34 4 0.08
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (32 bp):
TAAATTAAAGTATATTAAATATAAGTTAATGG
Found at i:45714308 original size:17 final size:17
Alignment explanation
Indices: 45714286--45714334 Score: 75
Period size: 16 Copynumber: 3.0 Consensus size: 17
45714276 TATCCTATTT
45714286 CCTACATTATATAATAA
1 CCTACATTATATAATAA
45714303 CCTACATTATAT-ATAA
1 CCTACATTATATAATAA
*
45714319 ACTACA-TATATAATAA
1 CCTACATTATATAATAA
45714335 TCTAGCGGCG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 5 0.17
16 13 0.43
17 12 0.40
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (17 bp):
CCTACATTATATAATAA
Found at i:45714537 original size:113 final size:110
Alignment explanation
Indices: 45714362--45714706 Score: 377
Period size: 113 Copynumber: 3.0 Consensus size: 110
45714352 CAACGCGCTG
* * * * *
45714362 CTAATAATATGTTTTAGCGGCATTTTACCATAAGCGCCAC-AACTGCTAGTATACATCAAGACCA
1 CTAATACTATGCTTTAGCGGCGTTTTA-AATAAGCGCCACTAA-TGCTAATATACATCAAGACCA
*
45714426 ATGCGTTGCGTTTTGGTTAATATTTTGCGGCGCTTTACAATAAGCGCCT
64 A-GC-TTGCGTTTTGGTTAATATTTTGCGGCGCTTTACAATAAGCGCCA
* * *
45714475 CTAATACTATGCTTTAGCGGCGTTTTCAAATAAGCGCCACTAATCCTAATGTACCTCAAGACCAA
1 CTAATACTATGCTTTAGCGGCGTTTT-AAATAAGCGCCACTAATGCTAATATACATCAAGACCAA
* * * * * ** *
45714540 ACTCTGCGTTTTGGTTAAGAAATATTGCGGCGCTTTTCAGTACTCGCCG
65 GCT-TGCGTTTTGGTT-A-ATATTTTGCGGCGCTTTACAATAAGCGCCA
* * *
45714589 CTAATACTATTCTTTAGCGGCGTTTTAATATAAGCGCCACTAAGGCTACTATACATCAAGACCAA
1 CTAATACTATGCTTTAGCGGCGTTTTAA-ATAAGCGCCACTAATGCTAATATACATCAAGACC-A
* * *
45714654 AGCACTGCGTTTTGGTTAATATTTTGCGGCGTTTTCCAATAAGCGCCA
64 AGC-TTGCGTTTTGGTTAATATTTTGCGGCGCTTTACAATAAGCGCCA
45714702 CTAAT
1 CTAAT
45714707 CTTAATATAC
Statistics
Matches: 192, Mismatches: 32, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
111 1 0.01
112 13 0.07
113 82 0.43
114 81 0.42
115 15 0.08
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (110 bp):
CTAATACTATGCTTTAGCGGCGTTTTAAATAAGCGCCACTAATGCTAATATACATCAAGACCAAG
CTTGCGTTTTGGTTAATATTTTGCGGCGCTTTACAATAAGCGCCA
Found at i:45714727 original size:74 final size:73
Alignment explanation
Indices: 45714605--45714745 Score: 178
Period size: 74 Copynumber: 1.9 Consensus size: 73
45714595 CTATTCTTTA
* *
45714605 GCGGCGTTTTAATATAAGCGCCACTAAGGCTACTATACATCAAGACCAAAGCACTGCGTTTTGGT
1 GCGGCGTTTTAATATAAGCGCCACTAAGGCTAATATACAGCAAGACCAAA-CACTGCGTTTTGGT
45714670 TAATATTTT
65 TAATATTTT
* * * * *
45714679 GCGGCGTTTTCCA-ATAAGCGCCACTAA-TCTTAATATACCGCAATACCAAACTCTGCGTTTTGG
1 GCGGCGTTTT-AATATAAGCGCCACTAAGGC-TAATATACAGCAAGACCAAACACTGCGTTTTGG
45714742 TTAA
64 TTAA
45714746 GAAATATTGC
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
73 17 0.29
74 40 0.69
75 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (73 bp):
GCGGCGTTTTAATATAAGCGCCACTAAGGCTAATATACAGCAAGACCAAACACTGCGTTTTGGTT
AATATTTT
Found at i:45714808 original size:188 final size:188
Alignment explanation
Indices: 45714491--45715082 Score: 986
Period size: 188 Copynumber: 3.1 Consensus size: 188
45714481 CTATGCTTTA
* * *
45714491 GCGGCGTTTTCAAATAAGCGCCACTAATCCTAATGTACCTCAAGACCAAACTCTGCGTTTTGGTT
1 GCGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGTT
* *
45714556 AAGAAATATTGCGGCGCTTTTCAGTACTCGCCGCTAATACTATTCTTTAGCGGCGTTTTAATATA
66 AAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATA
** * *
45714621 AGCGCCACTAAGGCTACTATACATCAAGACCAAAGCACTGCGTTTTGGTTAATATTTT
131 AGCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTT
* *
45714679 GCGGCGTTTTCCAATAAGCGCCACTAATCTTAATATACCGCAATACCAAACTCTGCGTTTTGGTT
1 GCGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGTT
* *
45714744 AAGAAATATTGCGGCGCTTTTCACTACTTGCCGCTAATACTATTCTTTAGCAGCATTTTAATATA
66 AAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATA
45714809 AGCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTT
131 AGCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTT
* *
45714867 GCAGCATTTTCCAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGTT
1 GCGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGTT
*
45714932 AAGAAATCTTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATA
66 AAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATA
* *
45714997 AGCGCCACTACTGCTAGTATATATCAAGACCAAAGCGTTGCGTTTTGGTTAATATTTT
131 AGCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTT
* * * *
45715055 GCGGCGCTTTACAATAAGCACCGCTAAT
1 GCGGCGTTTTCCAATAAGCGCCACTAAT
45715083 AATATGTTTT
Statistics
Matches: 376, Mismatches: 28, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
188 376 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (188 bp):
GCGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGTT
AAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATA
AGCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTT
Found at i:45714914 original size:74 final size:73
Alignment explanation
Indices: 45714793--45714933 Score: 194
Period size: 74 Copynumber: 1.9 Consensus size: 73
45714783 CTATTCTTTA
* * * *
45714793 GCAGCATTTTAATATAAGCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGT
1 GCAGCATTTTAATATAAGCGCCACTAATCCTAATATACAGCAAGACCAAA-CGCTGCGTTTTGGT
45714858 TAATATTTT
65 TAATATTTT
* * *
45714867 GCAGCATTTTCCA-ATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGT
1 GCAGCATTTT-AATATAAGCGCCACTAATCCTAATATACAGCAAGACCAAACGCTGCGTTTTGGT
45714931 TAA
65 TAA
45714934 GAAATCTTGC
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
73 16 0.27
74 42 0.71
75 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (73 bp):
GCAGCATTTTAATATAAGCGCCACTAATCCTAATATACAGCAAGACCAAACGCTGCGTTTTGGTT
AATATTTT
Found at i:45715101 original size:113 final size:113
Alignment explanation
Indices: 45714880--45715402 Score: 588
Period size: 113 Copynumber: 4.6 Consensus size: 113
45714870 GCATTTTCCA
* ** *
45714880 ATAAGCGCCACTAATCCTAATATACCGCAAGACCAAA-C-TCTGCGTTTTGGTTAAGAAATCTTG
1 ATAAGCGCCACTAATGCTAATATACATCAAGACCAAAGCGT-TGCGTTTTGGTT-A-AAATTTTG
* * ** * *
45714943 CGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAAT
63 CGGCGCTTTACAATAAGCGCCGCTAATACTATGCTTTAGCGGCGTTTTAAT
* * * *
45714994 ATAAGCGCCACTACTGCTAGTATATATCAAGACCAAAGCGTTGCGTTTTGGTTAATATTTTGCGG
1 ATAAGCGCCACTAATGCTAATATACATCAAGACCAAAGCGTTGCGTTTTGGTTAAAATTTTGCGG
* * * **
45715059 CGCTTTACAATAAGCACCGCTAATAATATGTTTTAGCGGCGTTTTACC
66 CGCTTTACAATAAGCGCCGCTAATACTATGCTTTAGCGGCGTTTTAAT
* * * * * * *
45715107 ATAAGTGCCACAAATGCTAGTATACATCGAGACCAATGTGTTGCGTTTTGGTTAATATTTTGCGG
1 ATAAGCGCCACTAATGCTAATATACATCAAGACCAAAGCGTTGCGTTTTGGTTAAAATTTTGCGG
45715172 CGCTTTACAATAAGCGCCGCTAATACTATGCTTTAGCGGCGTTTTCAA-
66 CGCTTTACAATAAGCGCCGCTAATACTATGCTTTAGCGGCGTTTT-AAT
* * *
45715220 ATAAGCGCCACTAATCCTAATATACCTCAAGACCAAA-C-TATGCGTTTTGGTTAAGAAATATTG
1 ATAAGCGCCACTAATGCTAATATACATCAAGACCAAAGCGT-TGCGTTTTGGTT-A-AAATTTTG
* * ** *
45715283 CGGCGCTTTTCAGTACTCGCCGCTAATACTATACTTTAGCGGCGTTTTAAT
63 CGGCGCTTTACAATAAGCGCCGCTAATACTATGCTTTAGCGGCGTTTTAAT
* * * *
45715334 ATAAGCACCACTAAGGCTAATATACATCAAGACCAAAGCGCTGCGTTTTGGTTAAGAGCTTTTGC
1 ATAAGCGCCACTAATGCTAATATACATCAAGACCAAAGCGTTGCGTTTTGGTTAA-A-ATTTTGC
45715399 GGCG
64 GGCG
45715403 TTTGTTCAGA
Statistics
Matches: 346, Mismatches: 52, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
111 1 0.00
112 12 0.03
113 180 0.52
114 117 0.34
115 35 0.10
116 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (113 bp):
ATAAGCGCCACTAATGCTAATATACATCAAGACCAAAGCGTTGCGTTTTGGTTAAAATTTTGCGG
CGCTTTACAATAAGCGCCGCTAATACTATGCTTTAGCGGCGTTTTAAT
Found at i:45717056 original size:15 final size:16
Alignment explanation
Indices: 45717036--45717074 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
45717026 AGTTCAGTCC
45717036 AAAACCCAAA-TAAAT
1 AAAACCCAAACTAAAT
*
45717051 AAAACCCAAACTCAAT
1 AAAACCCAAACTAAAT
45717067 -AAACCCAA
1 AAAACCCAA
45717075 CAAACCCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.62, C:0.28, G:0.00, T:0.10
Consensus pattern (16 bp):
AAAACCCAAACTAAAT
Found at i:45718205 original size:3 final size:3
Alignment explanation
Indices: 45718197--45718227 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
45718187 GTTAATCTGT
*
45718197 TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
45718228 ATCCGTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:45718360 original size:3 final size:3
Alignment explanation
Indices: 45718354--45718440 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
45718344 TCACATTTTA
* * * * * * *
45718354 TAT TAT TAT TGT TAT TAT TAT AAT AAT TAT TAT TGT TAC TAT CAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
45718402 TAT TAT TAT TAT TAT TAT TAG TAT TAG TAT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
45718441 ATATCAATTT
Statistics
Matches: 66, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:45726405 original size:202 final size:197
Alignment explanation
Indices: 45726061--45726425 Score: 428
Period size: 202 Copynumber: 1.8 Consensus size: 197
45726051 TTTTACTCAT
* * *
45726061 AAGTTAATCTATTTTTTTAATTTTAATATCGTACATATTTAATGTTTTATTATTAATTAGTTTCA
1 AAGTTAATCTATATTTTTAATTTTAACATCGTACATATTTAATGTTTTATTAATAATTAGTTTCA
** * * * * * * * *
45726126 AATTATACATTTTATCATTTATTGTATTTTATTTTAAACTAACATCTGGGTTCTAAGTGCATTGT
66 AAACAAACATTTCATCATTTACTGTATATTATTTTAAACTAACATCTAGGTTCTAAATACATAGT
*
45726191 TTCTACACACATACACATGTGATAAAATTTTTAATATTGATAATGTTGTTGATTGAGTTAGTGTC
131 TTCTAAACACATACACATGTGATAAAATTTTTAATATTGATAATGTTGTTGATTGAGTTAGTGTC
45726256 AC
196 AC
* * *
45726258 AAGTTAATCTAATATTTTTCATTTTAGCATCGTACATATTTAATGCGTTATTATTAATACTTAGT
1 AAGTTAATCT-ATATTTTTAATTTTAACATCGTACATATTTAAT--GTT-TTATTAATAATTAGT
* * *
45726323 TTCAAAACAAATATTTCATTATTTACTGTATATTATTTTTAAAC--ACGACTCTATGTTCTAAAT
62 TTCAAAACAAACATTTCATCATTTACTGTATATTA-TTTTAAACTAAC-A-TCTAGGTTCTAAAT
* ** * *
45726386 ACATAGTTTTTAAACACATATGCGTGTGATAGAATTTTTA
124 ACATAGTTTCTAAACACATACACATGTGATAAAATTTTTA
45726426 GTATCATATC
Statistics
Matches: 136, Mismatches: 25, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
197 10 0.07
198 29 0.21
200 5 0.04
201 41 0.30
202 51 0.38
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.47
Consensus pattern (197 bp):
AAGTTAATCTATATTTTTAATTTTAACATCGTACATATTTAATGTTTTATTAATAATTAGTTTCA
AAACAAACATTTCATCATTTACTGTATATTATTTTAAACTAACATCTAGGTTCTAAATACATAGT
TTCTAAACACATACACATGTGATAAAATTTTTAATATTGATAATGTTGTTGATTGAGTTAGTGTC
AC
Found at i:45726831 original size:16 final size:17
Alignment explanation
Indices: 45726801--45726833 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
45726791 TATACAAGAG
*
45726801 AAAATTATTACTTCAAA
1 AAAATTAATACTTCAAA
45726818 AAAATTAATA-TTCAAA
1 AAAATTAATACTTCAAA
45726834 TATGATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTAATACTTCAAA
Found at i:45737705 original size:31 final size:31
Alignment explanation
Indices: 45737638--45737717 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
45737628 AAGTTTAAAT
** * *
45737638 TTTAATATGAAAATAATTGTCAAGTTGATGA
1 TTTAATATGAAAATAATTAACAAATTGAGGA
45737669 TTTAATATGAAAATAATTAACAAATTGAAGGA
1 TTTAATATGAAAATAATTAACAAATTG-AGGA
45737701 -TTAATATGGATAAATAA
1 TTTAATAT-GA-AAATAA
45737718 AATTTAAGCC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 31 0.74
32 5 0.12
33 6 0.14
ACGTcount: A:0.49, C:0.03, G:0.14, T:0.35
Consensus pattern (31 bp):
TTTAATATGAAAATAATTAACAAATTGAGGA
Found at i:45752764 original size:15 final size:15
Alignment explanation
Indices: 45752739--45752773 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
45752729 GACTCTATTT
*
45752739 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
45752753 TAATTAATATTAAGA
1 TAATTAATATTAAGA
45752768 TAATTA
1 TAATTA
45752774 TTAAGGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:45756650 original size:7 final size:7
Alignment explanation
Indices: 45756634--45756710 Score: 72
Period size: 7 Copynumber: 11.0 Consensus size: 7
45756624 CAACACAATT
45756634 TTTATT-
1 TTTATTA
45756640 TTTATTA
1 TTTATTA
45756647 TTTATTA
1 TTTATTA
45756654 TTTATTA
1 TTTATTA
45756661 TTTATT-
1 TTTATTA
* *
45756667 TTTCTTTC
1 TTT-ATTA
45756675 TTTACTTTA
1 TTTA--TTA
45756684 TTTATTA
1 TTTATTA
45756691 CTTTA-T-
1 -TTTATTA
45756697 TTTATTA
1 TTTATTA
45756704 TTTATTA
1 TTTATTA
45756711 CTGATTTGGA
Statistics
Matches: 60, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
5 4 0.07
6 10 0.17
7 33 0.55
8 7 0.12
9 6 0.10
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTATTA
Found at i:45756693 original size:12 final size:12
Alignment explanation
Indices: 45756676--45756709 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
45756666 TTTTCTTTCT
45756676 TTACTTTATTTA
1 TTACTTTATTTA
45756688 TTACTTTATTTTA
1 TTACTTTA-TTTA
45756701 TTA-TTTATT
1 TTACTTTATT
45756710 ACTGATTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 12 0.57
13 7 0.33
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (12 bp):
TTACTTTATTTA
Found at i:45757599 original size:101 final size:101
Alignment explanation
Indices: 45757414--45757605 Score: 228
Period size: 101 Copynumber: 1.9 Consensus size: 101
45757404 AAACGTGACT
* * * * *
45757414 GACTGAGTAATCGGGGTAGGGTGCTTGAGTTGTCATCCTATTTCGCGTCAAAAGGTTCAATGTGT
1 GACTGAGTAACCGAGGTAGGGTGCTTGAGCTGTCATCCTATTTCGCGTCAAAAGGTTCAATATAT
*
45757479 TCTTAAGAAAAAATTATAATAAATAAGGAATCCGCTG
66 TCTAAAGAAAAAA-TATAATAAATAAGGAATCCGCTG
* * * *
45757516 GACTGAGTAACCGAGGTGGGGTGCTTG-GCTGTTATCTCTCTTT-GCGTCAAAAGGTTCAGTATA
1 GACTGAGTAACCGAGGTAGGGTGCTTGAGCTGTCATC-CTATTTCGCGTCAAAAGGTTCAATATA
*
45757579 TTCCTAAAGCATAAAA-ATAATAAATAA
65 TT-CTAAAG-AAAAAATATAATAAATAA
45757606 ATAAAAATCA
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
101 37 0.49
102 34 0.45
103 5 0.07
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (101 bp):
GACTGAGTAACCGAGGTAGGGTGCTTGAGCTGTCATCCTATTTCGCGTCAAAAGGTTCAATATAT
TCTAAAGAAAAAATATAATAAATAAGGAATCCGCTG
Found at i:45757606 original size:4 final size:4
Alignment explanation
Indices: 45757593--45757638 Score: 53
Period size: 4 Copynumber: 11.8 Consensus size: 4
45757583 TAAAGCATAA
45757593 AAAT -AAT AAAT AAAT -AA- AAAT CAAAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT --AAAT AAAT AAAT AAAT AAAT AAA
45757639 AAGAAAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
3 7 0.19
4 26 0.70
6 4 0.11
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:45757610 original size:24 final size:24
Alignment explanation
Indices: 45757589--45757634 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
45757579 TTCCTAAAGC
45757589 ATAAAAAT-AATAAATAAATAAAA
1 ATAAAAATAAATAAATAAATAAAA
*
45757612 ATCAAAATAAATAAATAAATAAA
1 ATAAAAATAAATAAATAAATAAA
45757635 TAAAAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (24 bp):
ATAAAAATAAATAAATAAATAAAA
Found at i:45757611 original size:16 final size:17
Alignment explanation
Indices: 45757589--45757638 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 17
45757579 TTCCTAAAGC
45757589 ATAAAAATAATAAATAA
1 ATAAAAATAATAAATAA
*
45757606 ATAAAAATCA-AAATAA
1 ATAAAAATAATAAATAA
*
45757622 ATAAATA-AATAAATAA
1 ATAAAAATAATAAATAA
45757638 A
1 A
45757639 AAGAAAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 1 0.03
16 19 0.66
17 9 0.31
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (17 bp):
ATAAAAATAATAAATAA
Found at i:45757646 original size:28 final size:27
Alignment explanation
Indices: 45757593--45757655 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
45757583 TAAAGCATAA
**
45757593 AAATAATAAATAAATAAAAATCAAAAT
1 AAATAATAAATAAATAAAAAGAAAAAT
*
45757620 AAATAAATAAATAAATAAAAAGAAAAAG
1 AAAT-AATAAATAAATAAAAAGAAAAAT
45757648 AATATAAT
1 AA-ATAAT
45757656 TTGGTGACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 4 0.13
28 25 0.81
29 2 0.06
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.21
Consensus pattern (27 bp):
AAATAATAAATAAATAAAAAGAAAAAT
Found at i:45762442 original size:23 final size:23
Alignment explanation
Indices: 45762394--45762448 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
45762384 ATTTTATGCA
* *
45762394 TGCAAGTGTTAGTGGCACTACGG
1 TGCAAGTGATAGTGGCACTACAG
**
45762417 TGCAAGTGATAGTGGCACTTTAG
1 TGCAAGTGATAGTGGCACTACAG
45762440 TGCAAGTGA
1 TGCAAGTGA
45762449 CAGAAGCACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (23 bp):
TGCAAGTGATAGTGGCACTACAG
Found at i:45766292 original size:18 final size:18
Alignment explanation
Indices: 45766271--45766305 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
45766261 ATTCTGTAAT
45766271 TAGTTTAAATTTAATTTC
1 TAGTTTAAATTTAATTTC
*
45766289 TAGTTTAAATTTGATTT
1 TAGTTTAAATTTAATTT
45766306 TTAAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.57
Consensus pattern (18 bp):
TAGTTTAAATTTAATTTC
Found at i:45768894 original size:28 final size:29
Alignment explanation
Indices: 45768833--45768890 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
45768823 AAATATTTTT
* * *
45768833 AATTAATAATTCCTTTATTTATATAAATA
1 AATTAATAATTCATATAATTATATAAATA
45768862 AATTAATAATT-ATATAATTATAT-AATA
1 AATTAATAATTCATATAATTATATAAATA
45768889 AA
1 AA
45768891 ATTATATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 6 0.23
28 9 0.35
29 11 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (29 bp):
AATTAATAATTCATATAATTATATAAATA
Found at i:45768895 original size:13 final size:14
Alignment explanation
Indices: 45768851--45768898 Score: 57
Period size: 13 Copynumber: 3.5 Consensus size: 14
45768841 ATTCCTTTAT
45768851 TTATATAA-ATAAA
1 TTATATAATATAAA
45768864 TTA-ATAATTATATAA
1 TTATATAA-TATA-AA
45768879 TTATATAATA-AAA
1 TTATATAATATAAA
45768892 TTATATA
1 TTATATA
45768899 TTTTTTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 4 0.13
13 12 0.39
14 4 0.13
15 7 0.23
16 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTATATAATATAAA
Found at i:45817225 original size:17 final size:17
Alignment explanation
Indices: 45817199--45817246 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
45817189 AAATATTTTT
*
45817199 AGTATCATAATTATATA
1 AGTATAATAATTATATA
* *
45817216 TGTATAATAAATATATA
1 AGTATAATAATTATATA
45817233 AG-ATTAATAATTAT
1 AGTA-TAATAATTAT
45817247 TAAAATTTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 1 0.04
17 24 0.96
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (17 bp):
AGTATAATAATTATATA
Found at i:45832169 original size:44 final size:44
Alignment explanation
Indices: 45832077--45832169 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
45832067 ATCTCAAGGT
* *
45832077 CCATATTTATAACATAGCAATTAAAGAAGAATTGACAGAAAAGT
1 CCATGTTTATAACATAGCAATTAAAGAAGAATTGACAGAAAAGA
* * *
45832121 CCATGTTTATAACATGGCAATT-AAGAAAGAATTGACGGAACAGA
1 CCATGTTTATAACATAGCAATTAAAG-AAGAATTGACAGAAAAGA
45832165 CCATG
1 CCATG
45832170 GTTGGACCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 3 0.07
44 40 0.93
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (44 bp):
CCATGTTTATAACATAGCAATTAAAGAAGAATTGACAGAAAAGA
Found at i:45832181 original size:44 final size:44
Alignment explanation
Indices: 45832087--45832183 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 44
45832077 CCATATTTAT
* * * *
45832087 AACATAGCAATTAAAGAAGAATTGACAGAAAAGTCCATGTTTAT
1 AACATGGCAATTAAAGAAGAATTGACAGAAAAGACCATGGTTAG
* * *
45832131 AACATGGCAATT-AAGAAAGAATTGACGGAACAGACCATGGTTGG
1 AACATGGCAATTAAAG-AAGAATTGACAGAAAAGACCATGGTTAG
*
45832175 ACCATGGCA
1 AACATGGCA
45832184 GTAAGTGTGC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 3 0.07
44 41 0.93
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21
Consensus pattern (44 bp):
AACATGGCAATTAAAGAAGAATTGACAGAAAAGACCATGGTTAG
Found at i:45832251 original size:50 final size:51
Alignment explanation
Indices: 45832190--45832421 Score: 253
Period size: 50 Copynumber: 4.7 Consensus size: 51
45832180 GGCAGTAAGT
*
45832190 GTGCCAATGTAAGACCATATCTGGGACATGGCATCGGCACAGACCGA-GGA
1 GTGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCACAGACCGATGGA
* * *
45832240 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGACC-ATCGA
1 GTGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCACAGACCGATGGA
* * * *
45832290 GTGCTAGTGTAAGACCATATCTGGGACATGGCATCGGCACGGACAGA-GAA
1 GTGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCACAGACCGATGGA
* * * * * * *
45832340 GAGTCAGTGTAAGACCATGTATGGGACATGGCATCGACACCGA--TATGTGA
1 GTGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCACAGACCGATG-GA
* *
45832390 -TCCCA-TGTAAGACCATATCTGGGATATGGCAT
1 GTGCCAGTGTAAGACCATATCTGGGACATGGCAT
45832422 TGGCGTCCTA
Statistics
Matches: 152, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
48 25 0.16
49 4 0.03
50 122 0.80
51 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (51 bp):
GTGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCACAGACCGATGGA
Found at i:45834058 original size:16 final size:17
Alignment explanation
Indices: 45834037--45834087 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
45834027 TTATTCTTAT
45834037 TTTTC-TCTTTTTTCCC
1 TTTTCATCTTTTTTCCC
*
45834053 TTTTCTTCTTCTTTT--C
1 TTTTCATCTT-TTTTCCC
45834069 TTTTCATCTTTTTTCCC
1 TTTTCATCTTTTTTCCC
45834086 TT
1 TT
45834088 CCAAACAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.13
16 15 0.50
17 7 0.23
18 4 0.13
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTCATCTTTTTTCCC
Found at i:45835311 original size:6 final size:6
Alignment explanation
Indices: 45835300--45835335 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
45835290 GATTTTCTCC
45835300 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
45835336 GAGAAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:45849694 original size:17 final size:16
Alignment explanation
Indices: 45849663--45849706 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
45849653 GATTTATTTA
45849663 ATAATATAATATCATT
1 ATAATATAATATCATT
*
45849679 ATAATTTAATTATCATT
1 ATAATATAA-TATCATT
*
45849696 AATTATATAAT
1 -ATAATATAAT
45849707 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATATAATATCATT
Found at i:45855581 original size:46 final size:44
Alignment explanation
Indices: 45855477--45855584 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
45855467 TGTCTTTAAC
** * * *
45855477 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
45855521 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
45855567 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
45855585 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:45861948 original size:46 final size:44
Alignment explanation
Indices: 45861844--45861951 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
45861834 TGTCTTTAAC
** * * *
45861844 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
45861888 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
45861934 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
45861952 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:45871071 original size:42 final size:42
Alignment explanation
Indices: 45870972--45871081 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
45870962 TCTCATAAGC
* * * * * *
45870972 TTCAGTTAA-CTCATATGAGTTTCTGTTTAACCCTATTGGTT
1 TTCAGTTAAGCACTTATGAGCTTCTGTTCAACCCTATCGGGT
*
45871013 TTCAGTTAAGCTCTTATGAGCTTCTGTTCAACCCT-TACGGGT
1 TTCAGTTAAGCACTTATGAGCTTCTGTTCAACCCTAT-CGGGT
* * *
45871055 TTCCGTTTAGCACTTATGTGCTTCTGT
1 TTCAGTTAAGCACTTATGAGCTTCTGT
45871082 GTAGCCTTCG
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
41 10 0.17
42 48 0.83
ACGTcount: A:0.18, C:0.21, G:0.17, T:0.44
Consensus pattern (42 bp):
TTCAGTTAAGCACTTATGAGCTTCTGTTCAACCCTATCGGGT
Found at i:45882084 original size:29 final size:30
Alignment explanation
Indices: 45882026--45882084 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
45882016 AATTTAGATT
* * *
45882026 AAATCAAAATTTCATGTATAAATTTGCACA
1 AAATCAAAATTTCATATATAAAATTACACA
*
45882056 AAATCAAAGTTT-ATATATAAAATTACACA
1 AAATCAAAATTTCATATATAAAATTACACA
45882085 TCAAACCAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTCATATATAAAATTACACA
Found at i:45888075 original size:3 final size:3
Alignment explanation
Indices: 45888067--45888101 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
45888057 AAAATGCACA
*
45888067 AAT AAT AAT AAT AAT AAT AAT TAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
45888102 AAGGAAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:45889715 original size:39 final size:40
Alignment explanation
Indices: 45889651--45889739 Score: 119
Period size: 39 Copynumber: 2.2 Consensus size: 40
45889641 TAAAAAATAT
* * *
45889651 TTATATTAAAAAAATAATCATAAATATAATAAATGTTTTA
1 TTATATTAAAAAAAAAATCATAAATAAAATAAATATTTTA
45889691 TTATATTAAAAAATAAAAT-A-AAATAAAATAAATATTTTA
1 TTATATTAAAAAA-AAAATCATAAATAAAATAAATATTTTA
*
45889730 TTGTATTAAA
1 TTATATTAAA
45889740 TATAATATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
39 26 0.59
40 14 0.32
41 4 0.09
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.39
Consensus pattern (40 bp):
TTATATTAAAAAAAAAATCATAAATAAAATAAATATTTTA
Found at i:45891196 original size:27 final size:27
Alignment explanation
Indices: 45891139--45891202 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
45891129 GGTCTGCCAT
* * ** *
45891139 AGGCGGCACCAAAGGTGCCAGTGGCAG
1 AGGCGACACCAAAGGTGCCACTACCAC
*
45891166 AGGCGACACCAAAGGTGCCTCTACCAC
1 AGGCGACACCAAAGGTGCCACTACCAC
45891193 AGGCGACACC
1 AGGCGACACC
45891203 TGTGCCATGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.28, C:0.33, G:0.31, T:0.08
Consensus pattern (27 bp):
AGGCGACACCAAAGGTGCCACTACCAC
Found at i:45891404 original size:20 final size:19
Alignment explanation
Indices: 45891344--45891405 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
45891334 GGTGCCAAAA
45891344 AAAGA-AAAGAAAAAGAGAG
1 AAAGAGAAAGAAAAAGA-AG
*
45891363 AAAGAGAATAGAGAATAG-AG
1 AAAGAGAA-AGA-AAAAGAAG
*
45891383 AAAGGAGAAAGAAAGAGAAG
1 AAA-GAGAAAGAAAAAGAAG
45891403 AAA
1 AAA
45891406 AAAAATAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
19 9 0.25
20 15 0.42
21 8 0.22
22 4 0.11
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (19 bp):
AAAGAGAAAGAAAAAGAAG
Found at i:45891758 original size:37 final size:38
Alignment explanation
Indices: 45891716--45891814 Score: 119
Period size: 40 Copynumber: 2.5 Consensus size: 38
45891706 TTTTACACTA
**
45891716 TATTATTGTTAGTTATTATTTTTAGTAAAACCCTA-AT
1 TATTATTGTTAGTTATTATTTTTAGTAAAAAACTATAT
45891753 TATTATTGTTAGTTAGTATTATTTTTAGTAAAAAACTATTAT
1 TATTATTGTTAG-T--TATTATTTTTAGTAAAAAACTA-TAT
45891795 TATTATTTTGTTAGTTATTA
1 TATTA--TTGTTAGTTATTA
45891815 GGATTAGTGG
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
37 12 0.23
38 1 0.02
40 20 0.38
41 5 0.09
42 7 0.13
43 1 0.02
44 7 0.13
ACGTcount: A:0.32, C:0.04, G:0.09, T:0.55
Consensus pattern (38 bp):
TATTATTGTTAGTTATTATTTTTAGTAAAAAACTATAT
Found at i:45891796 original size:76 final size:78
Alignment explanation
Indices: 45891591--45891822 Score: 229
Period size: 76 Copynumber: 2.9 Consensus size: 78
45891581 GTTTAGTTAT
* *
45891591 TAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAAACTAATATTATTATTCTGGTTAGTTAT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAAC---TATTATTA-T-TGGTTAGTTAT
45891656 TAGGATTAGTAAAAACCC
61 TAGGATTAGTAAAAACCC
* * *** * **
45891674 TAATTATAATT-TTAGTTAGTATGATTGTTAGTTTTTACACTA-TATTATT-GTTAGTTATTATT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAG-TAAAAAACTATTATTATTGGTTAGTTATTAGG
*
45891736 TTTAGT-AAAACCC
65 ATTAGTAAAAACCC
* *
45891749 TAATTATTATTGTTAGTTAGTATTATTTTTAGTAAAAAACTATTATTATTATTTTGTTAGTTATT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAAC---TATTATTA-TTGGTTAGTTATT
45891814 AGGATTAGT
62 AGGATTAGT
45891823 GGTTAAATGT
Statistics
Matches: 120, Mismatches: 21, Indels: 18
0.75 0.13 0.11
Matches are distributed among these distances:
75 21 0.17
76 34 0.28
77 1 0.01
78 3 0.03
79 10 0.08
80 4 0.03
81 16 0.13
82 18 0.15
83 13 0.11
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.50
Consensus pattern (78 bp):
TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAACTATTATTATTGGTTAGTTATTAGGA
TTAGTAAAAACCC
Found at i:45896925 original size:157 final size:157
Alignment explanation
Indices: 45896564--45897419 Score: 1297
Period size: 157 Copynumber: 5.4 Consensus size: 157
45896554 TTTTTTTATT
* * * * * *
45896564 TTCGGATTTATCTTATTTTTGAATTTTATTGCTTTCAAAAAATATATTATTTTTGTATTTTATTA
1 TTCGTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTA
*
45896629 TTTTATATTATTTTAGTACATAA-AGTTTGAAATGTATTAATTTAGTGTATTTTTTTATATAAAT
66 TTTTATATTATTTTAGTACATAATA-TTTGAAATGTATTATTTTAGTG--TTTTTTTATATAAAT
* *
45896693 TTAGTAAAAAACCCTTATTTTGACCATTTG
128 TTAGTAAAAAACCCTTATTTTGGCCCTTTG
* *
45896723 TTCGTATTTTTCTTATTTTC-AGATTTTACTACTTTCAAAAAATATATTATTTTCGTATTTTATT
1 TTCGTATTTTTCTTATTTTCGA-ATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATT
45896787 ATTTTATATTATTTTAGTACATAATATTTGAAATGTATTATTTTAGTGTTTTTTTATATAAATTT
65 ATTTTATATTATTTTAGTACATAATATTTGAAATGTATTATTTTAGTGTTTTTTTATATAAATTT
* *
45896852 AGTAAAAAACTCTTATTTTGGTCCTTTG
130 AGTAAAAAACCCTTATTTTGGCCCTTTG
* * *
45896880 TTCATATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTA
1 TTCGTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTA
*
45896945 TTTTATATTATTTTAGTACATAA-AGTTTGAAATGTATTAATTTAGTGTGTGTGTTTTTTATATA
66 TTTTATATTATTTTAGTACATAATA-TTTGAAATGTATT-ATTT--T-AGTGT-TTTTTTATATA
* *
45897009 AATTTAGTAAAAAAACTCTTATTTTGGCCATTTG
125 AATTTAGT-AAAAAACCCTTATTTTGGCCCTTTG
*
45897043 TTCATATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTA
1 TTCGTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTA
*
45897108 TTTTATATTATTTTAGTACATAATATTTGAAATGTATTATTTTAGTGTGTTTTTATATAAATTTA
66 TTTTATATTATTTTAGTACATAATATTTGAAATGTATTATTTTAGTGTTTTTTTATATAAATTTA
*
45897173 GT-AAAAACCCCTATTTTGGCCCTTTG
131 GTAAAAAACCCTTATTTTGGCCCTTTG
*
45897199 TTCGTATTTTTCTTATTTTCGAATTTTATTACTTTTAAAAAATATACTATTTTCGTATTTTATTA
1 TTCGTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTA
* * *
45897264 TTTTATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTATTTTTATAAAAATTTA
66 TTTTATATTATTTTAGTACATAATATTTGAAATGTATTATTTTAGTGTTTTTTTATATAAATTTA
*
45897329 GTAAAAAACCATTATTTTGGCCCTTTG
131 GTAAAAAACCCTTATTTTGGCCCTTTG
* ** * *
45897356 TTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAGTAAATATACTATTTTTGTTTTTTATT
1 TTCGTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATT
45897420 TCTTTTCGTA
Statistics
Matches: 648, Mismatches: 37, Indels: 26
0.91 0.05 0.04
Matches are distributed among these distances:
156 149 0.23
157 218 0.34
158 23 0.04
159 105 0.16
160 3 0.00
161 4 0.01
162 23 0.04
163 122 0.19
164 1 0.00
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.54
Consensus pattern (157 bp):
TTCGTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTA
TTTTATATTATTTTAGTACATAATATTTGAAATGTATTATTTTAGTGTTTTTTTATATAAATTTA
GTAAAAAACCCTTATTTTGGCCCTTTG
Found at i:45897624 original size:14 final size:14
Alignment explanation
Indices: 45897572--45897634 Score: 67
Period size: 14 Copynumber: 4.5 Consensus size: 14
45897562 AAATTAATTA
*
45897572 AATAAAATA-AAAT
1 AATAAAACATAAAT
45897585 AATAAAACATAGAAT
1 AATAAAACATA-AAT
* *
45897600 -GTACTAACATAAAT
1 AATA-AAACATAAAT
45897614 AATAAAACATAAAT
1 AATAAAACATAAAT
45897628 AATAAAA
1 AATAAAA
45897635 TAATAAGACA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
13 8 0.20
14 22 0.54
15 11 0.27
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.22
Consensus pattern (14 bp):
AATAAAACATAAAT
Found at i:45897638 original size:51 final size:52
Alignment explanation
Indices: 45897577--45897676 Score: 175
Period size: 51 Copynumber: 1.9 Consensus size: 52
45897567 AATTAAATAA
45897577 AATAAAATAATAAAACATAGAATGTAC-TAACATAAATAATAAAACATAAAT
1 AATAAAATAATAAAACATAGAATGTACATAACATAAATAATAAAACATAAAT
* *
45897628 AATAAAATAATAAGACATAGTATGTACATAACATAAATAATAAAACATA
1 AATAAAATAATAAAACATAGAATGTACATAACATAAATAATAAAACATA
45897677 GAATGTACAT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 25 0.54
52 21 0.46
ACGTcount: A:0.63, C:0.08, G:0.05, T:0.24
Consensus pattern (52 bp):
AATAAAATAATAAAACATAGAATGTACATAACATAAATAATAAAACATAAAT
Found at i:45897668 original size:30 final size:30
Alignment explanation
Indices: 45897632--45897702 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
45897622 ATAAATAATA
* *
45897632 AAATAATAAGACATAGTATGTACATAACAT
1 AAATAATAAAACATAGAATGTACATAACAT
45897662 AAATAATAAAACATAGAATGTACATAACAT
1 AAATAATAAAACATAGAATGTACATAACAT
45897692 AAA-AATTAAAA
1 AAATAA-TAAAA
45897703 TTAAATTATG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 2 0.05
30 36 0.95
ACGTcount: A:0.61, C:0.08, G:0.07, T:0.24
Consensus pattern (30 bp):
AAATAATAAAACATAGAATGTACATAACAT
Found at i:45897692 original size:16 final size:16
Alignment explanation
Indices: 45897642--45897692 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
45897632 AAATAATAAG
*
45897642 ACATAGTATGTACATA
1 ACATAGAATGTACATA
*
45897658 ACATA-AATAATA-A-A
1 ACATAGAAT-GTACATA
45897672 ACATAGAATGTACATA
1 ACATAGAATGTACATA
45897688 ACATA
1 ACATA
45897693 AAAATTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
14 8 0.29
15 7 0.25
16 13 0.46
ACGTcount: A:0.55, C:0.12, G:0.08, T:0.25
Consensus pattern (16 bp):
ACATAGAATGTACATA
Done.