Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 3 of 141
Found at i:499549 original size:15 final size:15
Alignment explanation
Indices: 499526--499555 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
499516 AAAAGGAAGG
*
499526 AAAATAAAGAAAGAA
1 AAAAGAAAGAAAGAA
499541 AAAAGAAAGAAAGAA
1 AAAAGAAAGAAAGAA
499556 GGGAAATAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (15 bp):
AAAAGAAAGAAAGAA
Found at i:503885 original size:28 final size:28
Alignment explanation
Indices: 503844--503922 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 28
503834 CTGAATCTCG
* * **
503844 AACCTCGAACCTCGAACCTTGAATTATA
1 AACCTCAAATCTCGAACCTTGAACCATA
* * * *
503872 AATCTTAAATCTCGAATCTTGAACCCTA
1 AACCTCAAATCTCGAACCTTGAACCATA
503900 AACCTCAAATC-CGAACCTTGAAC
1 AACCTCAAATCTCGAACCTTGAAC
503923 TCCGAATACT
Statistics
Matches: 40, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
27 11 0.28
28 29 0.73
ACGTcount: A:0.37, C:0.29, G:0.09, T:0.25
Consensus pattern (28 bp):
AACCTCAAATCTCGAACCTTGAACCATA
Found at i:504684 original size:37 final size:36
Alignment explanation
Indices: 504612--504716 Score: 128
Period size: 37 Copynumber: 2.9 Consensus size: 36
504602 TTTCTTTTTT
* *
504612 TTTTA-AAACACGAATTTTTTTTAAATACA--AGAA
1 TTTTAGAAACACGAATTTTTTTTAAAAACACGAAAA
504645 TTTTAGAAACACGAATTTTTTTTAAAAAACACGAAAA
1 TTTTAGAAACACGAATTTTTTTT-AAAAACACGAAAA
*
504682 TTTT-GAAACACGAGATTTTTTTTTGAAAACACGAA
1 TTTTAGAAACACGA-A-TTTTTTTTAAAAACACGAA
504717 TTTTCCTTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
33 5 0.08
34 17 0.27
35 6 0.10
36 9 0.14
37 18 0.29
38 8 0.13
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (36 bp):
TTTTAGAAACACGAATTTTTTTTAAAAACACGAAAA
Found at i:504707 original size:20 final size:20
Alignment explanation
Indices: 504682--504736 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
504672 AACACGAAAA
*
504682 TTTTGAAACACGAGATTTT-T
1 TTTTGAAACACGA-ATTTTCC
504702 TTTTGAAAACACGAATTTTCC
1 TTTTG-AAACACGAATTTTCC
*
504723 TTTTGAAGCACGAA
1 TTTTGAAACACGAA
504737 AATTTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
TTTTGAAACACGAATTTTCC
Found at i:504713 original size:21 final size:21
Alignment explanation
Indices: 504682--504729 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
504672 AACACGAAAA
*
504682 TTTTG-AAACACGAGATTTT-T
1 TTTTGAAAACACGA-ATTTTCC
504702 TTTTGAAAACACGAATTTTCC
1 TTTTGAAAACACGAATTTTCC
504723 TTTTGAA
1 TTTTGAA
504730 GCACGAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (21 bp):
TTTTGAAAACACGAATTTTCC
Found at i:504720 original size:57 final size:57
Alignment explanation
Indices: 504651--504770 Score: 145
Period size: 58 Copynumber: 2.1 Consensus size: 57
504641 AGAATTTTAG
* * * *
504651 AAACACGAATTTT-TTTTAAAAAACACGAAAA-TTTTGAAACACGAGATTTTTTTTTGA
1 AAACACGAATTTTCTTTT--AAAACACGAAAATTTTTAAAACACAAAATTTGTTTTTGA
* *
504708 AAACACGAATTTTCCTTTTGAAGCACGAAAATTTTTAAAACACAAAATTTGTTTTTGA
1 AAACACGAATTTT-CTTTTAAAACACGAAAATTTTTAAAACACAAAATTTGTTTTTGA
504766 AAACA
1 AAACA
504771 TAAAAATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
57 23 0.43
58 27 0.50
59 4 0.07
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (57 bp):
AAACACGAATTTTCTTTTAAAACACGAAAATTTTTAAAACACAAAATTTGTTTTTGA
Found at i:504779 original size:22 final size:20
Alignment explanation
Indices: 504739--504779 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
504729 AGCACGAAAA
*
504739 TTTTTAAAACACAAAATTTG
1 TTTTTAAAACAAAAAATTTG
504759 TTTTTGAAAACATAAAAATTT
1 TTTTT-AAAACA-AAAAATTT
504780 TGATAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (20 bp):
TTTTTAAAACAAAAAATTTG
Found at i:504860 original size:18 final size:18
Alignment explanation
Indices: 504806--505109 Score: 171
Period size: 18 Copynumber: 16.8 Consensus size: 18
504796 ATGAGGGTTT
*
504806 TTTTTG-AAACACAAAAA
1 TTTTTGAAAACACGAAAA
* **
504823 TTTATG-AAACACGGTCAA
1 TTTTTGAAAACAC-GAAAA
*
504841 TTTTTGAAAACACAAAAA
1 TTTTTGAAAACACGAAAA
* * *
504859 TTTTTGAAAGAC-GGGAAT
1 TTTTTGAAA-ACACGAAAA
504877 TTTTTGAAAACACTG-AAA
1 TTTTTGAAAACAC-GAAAA
*
504895 TTTATG-AAACACGGAAAA
1 TTTTTGAAAACAC-GAAAA
*
504913 TTTTTTTTGAAAACAAGAAAA
1 ---TTTTTGAAAACACGAAAA
* **
504934 TTTTTG-AAATACGGGAA
1 TTTTTGAAAACACGAAAA
*
504951 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
*
504969 TTTTTG-AAACACTG-GAA
1 TTTTTGAAAACAC-GAAAA
* *
504986 -TGTTGAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
* *
505003 TTTTTG-AAACATGAGAA
1 TTTTTGAAAACACGAAAA
**
505020 TTTTTGAAAACACGAATTT
1 TTTTTGAAAACACGAA-AA
* * *
505039 TTTTTTAAAACACGGAAG
1 TTTTTGAAAACACGAAAA
* **
505057 TTTTTGAAACACAAGAATTTT
1 TTTTTGAAA-ACACGAA--AA
*
505078 TTTTTAAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
505096 TTTTTG-AAACACGA
1 TTTTTGAAAACACGA
505110 TTTTTTTTAG
Statistics
Matches: 214, Mismatches: 53, Indels: 40
0.70 0.17 0.13
Matches are distributed among these distances:
16 5 0.02
17 69 0.32
18 83 0.39
19 28 0.13
20 6 0.03
21 18 0.08
22 5 0.02
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:504878 original size:35 final size:35
Alignment explanation
Indices: 504806--505078 Score: 232
Period size: 36 Copynumber: 7.7 Consensus size: 35
504796 ATGAGGGTTT
* *
504806 TTTTTG-AAACACAAAAATTTATGAAACACGGTCAA
1 TTTTTGAAAACACAAAAATTTTTGAAACACGG-GAA
*
504841 TTTTTGAAAACACAAAAATTTTTGAAAGACGGGAA
1 TTTTTGAAAACACAAAAATTTTTGAAACACGGGAA
** * *
504876 TTTTTTGAAAACACTGAAATTTATGAAACACGGAAAA
1 -TTTTTGAAAACACAAAAATTTTTGAAACACGG-GAA
*
504913 TTTTTTTTGAAAACA-AGAAAATTTTTGAAATACGGGAA
1 ---TTTTTGAAAACACA-AAAATTTTTGAAACACGGGAA
** *
504951 TTTTTGAAAACATGAAAATTTTTGAAACACTGGAA
1 TTTTTGAAAACACAAAAATTTTTGAAACACGGGAA
* * * * *
504986 -TGTTGAAAACACGAAGATTTTTGAAACATGAGAA
1 TTTTTGAAAACACAAAAATTTTTGAAACACGGGAA
*** *
505020 TTTTTGAAAACACGAATTTTTTTTTAAAACAC-GGAA
1 TTTTTGAAAACAC-AA-AAATTTTTGAAACACGGGAA
*
505056 GTTTTTG-AAACACAAGAATTTTT
1 -TTTTTGAAAACACAAAAATTTTT
505079 TTTTAAAAAC
Statistics
Matches: 194, Mismatches: 33, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
34 33 0.17
35 52 0.27
36 61 0.31
37 18 0.09
38 2 0.01
39 28 0.14
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.33
Consensus pattern (35 bp):
TTTTTGAAAACACAAAAATTTTTGAAACACGGGAA
Found at i:505084 original size:38 final size:37
Alignment explanation
Indices: 505003--505107 Score: 131
Period size: 37 Copynumber: 2.8 Consensus size: 37
504993 AACACGAAGA
* * *
505003 TTTTTGAAACATGAGAATTTTTGAAA-ACACGAATTTT
1 TTTTTAAAACACG-GAATTTTTGAAACACAAGAATTTT
505040 TTTTTAAAACACGGAAGTTTTTGAAACACAAGAATTTT
1 TTTTTAAAACACGGAA-TTTTTGAAACACAAGAATTTT
*
505078 TTTTTAAAAACACGAAAATTTTTGAAACAC
1 TTTTT-AAAACACG-GAATTTTTGAAACAC
505108 GATTTTTTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
36 3 0.05
37 20 0.33
38 15 0.25
39 20 0.33
40 2 0.03
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.37
Consensus pattern (37 bp):
TTTTTAAAACACGGAATTTTTGAAACACAAGAATTTT
Found at i:505105 original size:17 final size:17
Alignment explanation
Indices: 504806--505109 Score: 157
Period size: 17 Copynumber: 16.8 Consensus size: 17
504796 ATGAGGGTTT
*
504806 TTTTTGAAACACAAAAA
1 TTTTTGAAACACGAAAA
* **
504823 TTTATGAAACACGGTCAA
1 TTTTTGAAACAC-GAAAA
*
504841 TTTTTGAAAACACAAAAA
1 TTTTTG-AAACACGAAAA
* * *
504859 TTTTTGAAAGACGGGAAT
1 TTTTTGAAACAC-GAAAA
504877 TTTTTGAAAACACTG-AAA
1 TTTTTG-AAACAC-GAAAA
*
504895 TTTATGAAACACGGAAAA
1 TTTTTGAAACAC-GAAAA
*
504913 TTTTTTTTGAAAACAAGAAAA
1 ---TTTTTG-AAACACGAAAA
* **
504934 TTTTTGAAATACGGGAA
1 TTTTTGAAACACGAAAA
*
504951 TTTTTGAAAACATGAAAA
1 TTTTTG-AAACACGAAAA
*
504969 TTTTTGAAACACTG-GAA
1 TTTTTGAAACAC-GAAAA
* *
504986 -TGTTGAAAACACGAAGA
1 TTTTTG-AAACACGAAAA
* *
505003 TTTTTGAAACATGAGAA
1 TTTTTGAAACACGAAAA
**
505020 TTTTTGAAAACACGAATTTT
1 TTTTTG-AAACACGAA--AA
* * *
505040 TTTTTAAAACACGGAAG
1 TTTTTGAAACACGAAAA
505057 TTTTTGAAACAC-AAGAA
1 TTTTTGAAACACGAA-AA
*
505074 TTTTTTTTTAAAAACACGAAAA
1 ----TTTTT-GAAACACGAAAA
505096 TTTTTGAAACACGA
1 TTTTTGAAACACGA
505110 TTTTTTTTAG
Statistics
Matches: 214, Mismatches: 49, Indels: 48
0.69 0.16 0.15
Matches are distributed among these distances:
16 6 0.03
17 84 0.39
18 69 0.32
19 20 0.09
20 5 0.02
21 15 0.07
22 13 0.06
23 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:505117 original size:39 final size:36
Alignment explanation
Indices: 505003--505117 Score: 142
Period size: 39 Copynumber: 3.1 Consensus size: 36
504993 AACACGAAGA
* * *
505003 TTTTTGAAACATGAGAATTTTTGAAAACACGAATTTT
1 TTTTTAAAACACGAAAATTTTTG-AAACACGAATTTT
* *
505040 TTTTTAAAACACGGAAGTTTTTGAAACACAAGAATTTT
1 TTTTTAAAACACGAAAATTTTTGAAACAC--GAATTTT
505078 TTTTTAAAAACACGAAAATTTTTGAAACACG-ATTTT
1 TTTTT-AAAACACGAAAATTTTTGAAACACGAATTTT
505114 TTTT
1 TTTT
505118 AGAAGTACCG
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
36 15 0.22
37 19 0.28
38 12 0.18
39 22 0.32
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (36 bp):
TTTTTAAAACACGAAAATTTTTGAAACACGAATTTT
Found at i:505828 original size:4 final size:4
Alignment explanation
Indices: 505821--505877 Score: 53
Period size: 4 Copynumber: 13.8 Consensus size: 4
505811 TTTTTTTTCC
* * *
505821 CTTT CTTT CTTCCC CTTT CTTTT CTTT CTTT ATTT CTTT -TTT CTTC CTTT
1 CTTT CTTT CTT--T CTTT C-TTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
505871 CTTT CTT
1 CTTT CTT
505878 CCCCGATCAG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
3 3 0.07
4 33 0.77
5 4 0.09
6 3 0.07
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:505862 original size:19 final size:19
Alignment explanation
Indices: 505840--505877 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
505830 TTCCCCTTTC
*
505840 TTTTCTTTCTTTATTTCTT
1 TTTTCTTCCTTTATTTCTT
*
505859 TTTTCTTCCTTTCTTTCTT
1 TTTTCTTCCTTTATTTCTT
505878 CCCCGATCAG
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:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTCTTCCTTTATTTCTT
Found at i:506032 original size:28 final size:28
Alignment explanation
Indices: 505981--506042 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
505971 CCCCCTTTTT
**
505981 CTTTTTTATTCTTTGCTCTTTTTTCTTC
1 CTTTTTTATTCTTTGCTCGCTTTTCTTC
* * * *
506009 TTTTTTTCTTTTTTGCTCGCTTTTTTTC
1 CTTTTTTATTCTTTGCTCGCTTTTCTTC
506037 CTTTTT
1 CTTTTT
506043 CTTGCCTCTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.02, C:0.19, G:0.05, T:0.74
Consensus pattern (28 bp):
CTTTTTTATTCTTTGCTCGCTTTTCTTC
Found at i:506441 original size:29 final size:29
Alignment explanation
Indices: 506408--506560 Score: 98
Period size: 30 Copynumber: 5.2 Consensus size: 29
506398 GCAAAAATGA
*
506408 AATTTTAGGAAAATATAGGGCTAAAGTGT
1 AATTTTAGAAAAATATAGGGCTAAAGTGT
* *
506437 AATTTATAG-AAAGTTTAGGGGCCT-AAGTGT
1 AATTT-TAGAAAAATATA-GGG-CTAAAGTGT
* * *
506467 AA-TTTA-CAAAATATTAGGGGTCAAGATGT
1 AATTTTAGAAAAATA-TAGGGCTAAAG-TGT
* * *
506496 AATTTTTGAAAAATTTAGAGGCTAAAATGT
1 AATTTTAGAAAAATATAG-GGCTAAAGTGT
* * * *
506526 AATTTTTGAAAAATTCTGGGGCTAAAATGT
1 AATTTTAGAAAAA-TATAGGGCTAAAGTGT
506556 AATTT
1 AATTT
506561 ATTTTTTGTA
Statistics
Matches: 100, Mismatches: 13, Indels: 21
0.75 0.10 0.16
Matches are distributed among these distances:
27 1 0.01
28 12 0.12
29 20 0.20
30 52 0.52
31 15 0.15
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.35
Consensus pattern (29 bp):
AATTTTAGAAAAATATAGGGCTAAAGTGT
Found at i:506513 original size:59 final size:57
Alignment explanation
Indices: 506417--506530 Score: 124
Period size: 59 Copynumber: 2.0 Consensus size: 57
506407 AAATTTTAGG
* * *
506417 AAAATATAGGGCTAAAGTGTAATTTATAGAAAGTTTAGGGGCCT-AAGTGTAATTTAC
1 AAAATATAGGGCTAAAGTGTAATTTATAGAAAATTTAGAGG-CTAAAATGTAATTTAC
* * *
506474 AAAATATTAGGGGTCAAGATGTAATTT-TTGAAAAATTTAGAGGCTAAAATGTAATTT
1 AAAATA-TAGGGCTAAAG-TGTAATTTATAG-AAAATTTAGAGGCTAAAATGTAATTT
506531 TTGAAAAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
57 6 0.13
58 13 0.28
59 28 0.60
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.33
Consensus pattern (57 bp):
AAAATATAGGGCTAAAGTGTAATTTATAGAAAATTTAGAGGCTAAAATGTAATTTAC
Found at i:506528 original size:30 final size:30
Alignment explanation
Indices: 506492--506560 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
506482 AGGGGTCAAG
506492 ATGTAATTTTTGAAAAATT-TAGAGGCTAAA
1 ATGTAATTTTTGAAAAATTCT-GAGGCTAAA
*
506522 ATGTAATTTTTGAAAAATTCTGGGGCTAAA
1 ATGTAATTTTTGAAAAATTCTGAGGCTAAA
506552 ATGTAATTT
1 ATGTAATTT
506561 ATTTTTTGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
30 36 0.97
31 1 0.03
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.39
Consensus pattern (30 bp):
ATGTAATTTTTGAAAAATTCTGAGGCTAAA
Found at i:508760 original size:55 final size:56
Alignment explanation
Indices: 508668--508779 Score: 181
Period size: 55 Copynumber: 2.0 Consensus size: 56
508658 GTAAGGTTCC
* * * *
508668 AAATCTATAATTCTAATTATTTTATGAGTTCATAATCCAAATATGTTATGTGAAAA
1 AAATCTATAATTCTAAGTAATTTATGAATTCACAATCCAAATATGTTATGTGAAAA
508724 AAAT-TATAATTCTAAGTAATTTATGAATTCACAATCCAAATATGTTATGTGAAAA
1 AAATCTATAATTCTAAGTAATTTATGAATTCACAATCCAAATATGTTATGTGAAAA
508779 A
1 A
508780 GAAAACAACA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
55 48 0.92
56 4 0.08
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (56 bp):
AAATCTATAATTCTAAGTAATTTATGAATTCACAATCCAAATATGTTATGTGAAAA
Found at i:510888 original size:17 final size:16
Alignment explanation
Indices: 510868--510917 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
510858 GGAAGAGCCA
510868 TTATTGAGGAACAACTC
1 TTATTGA-GAACAACTC
*
510885 TTATTTAGAACAACCTC
1 TTATTGAGAACAA-CTC
*
510902 TACATTGAGAACAACT
1 T-TATTGAGAACAACT
510918 ATGTTGAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 6 0.21
17 12 0.43
18 10 0.36
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (16 bp):
TTATTGAGAACAACTC
Found at i:510914 original size:18 final size:17
Alignment explanation
Indices: 510870--510916 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
510860 AAGAGCCATT
*
510870 ATTGAGGAACAA-CTCTT
1 ATTGA-GAACAACCTCTC
*
510887 ATTTAGAACAACCTCTAC
1 ATTGAGAACAACCTCT-C
510905 ATTGAGAACAAC
1 ATTGAGAACAAC
510917 TATGTTGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 6 0.24
17 8 0.32
18 11 0.44
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (17 bp):
ATTGAGAACAACCTCTC
Found at i:511568 original size:12 final size:12
Alignment explanation
Indices: 511537--511568 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
511527 CAGATTTGCA
511537 TTTCTTT-TTAT
1 TTTCTTTATTAT
511548 TTT-TTTATTAT
1 TTTCTTTATTAT
511559 TTTCTTTATT
1 TTTCTTTATT
511569 TTGTATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.16
11 10 0.53
12 6 0.32
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTCTTTATTAT
Found at i:512194 original size:3 final size:3
Alignment explanation
Indices: 512186--512235 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
512176 ACAAATTTCA
512186 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
512234 TA
1 TA
512236 GTTTTATTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:516375 original size:8 final size:8
Alignment explanation
Indices: 516362--516400 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
516352 AAAAGAGAAG
516362 AAAAAAAT
1 AAAAAAAT
516370 AAAAAAAT
1 AAAAAAAT
*
516378 CAAAAAAT
1 AAAAAAAT
*
516386 CAAAAAA-
1 AAAAAAAT
516393 AAAAAAAT
1 AAAAAAAT
516401 CAATCAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.85, C:0.05, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:516420 original size:23 final size:23
Alignment explanation
Indices: 516363--516412 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
516353 AAAGAGAAGA
516363 AAAAAATAAAAAAATCAAAAAATC
1 AAAAAA-AAAAAAATCAAAAAATC
**
516387 AAAAAAAAAAAAATCAATCAATC
1 AAAAAAAAAAAAATCAAAAAATC
516410 AAA
1 AAA
516413 GCCAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (23 bp):
AAAAAAAAAAAAATCAAAAAATC
Found at i:519163 original size:46 final size:46
Alignment explanation
Indices: 519111--520245 Score: 813
Period size: 46 Copynumber: 25.6 Consensus size: 46
519101 TCACACCAGG
*
519111 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCAGA
* ** *
519157 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGAC-AT-A-A
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCAGA
* * * * * ** * **
519200 TCCTATCTCCTTGAGATTACAGTAGAGCGGA-TTAA-A-ATAAAGGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCA-GA
* * * * * *
519244 TCTTATCTCTCTGAAGTTACAGTAGAGCAGATCG--CAC---CAGG
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCAGA
* *
519285 TCTTATCTCCCTGAGGTTACAGTAGAGTAGACCGAAGACTTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCAGA
* * * *
519331 TCTTATCTCCTTGAGGTTACAGCGGAGCAGATCGAAGAC-AT-A-A
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCAGA
* * * ** * **
519374 TCCTATCTCCCTGAAGTTACAGTGGAGCGGA-TTAA-A-ATAAAGGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCA-GA
* * * * * * *
519418 TCTTATCTCTCTGAAGTTACGGTAGAGCAGATCG--CAC---CAGG
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCAGA
* * *
519459 TCTTATCTCCTTGAGGTTACAGTAGAGTAGACCGAAGACTTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCAGA
** * *
519505 TCTTATCTCCCTGAGGTTACAGCAGAGCAGATCGAAGAC-AT-A-A
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCAGA
* * * ** * **
519548 TCCTATCTCCCTGAAGTTACAGTGGAGCGGA-TTAA-A-ATAAAGGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCA-GA
* *
519592 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAAACTTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCAGA
* ** *
519638 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGAC-AT-A-A
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCAGA
* * * * ** * **
519681 TCCTATCTCCCTGAAGTTACAGTGGCGCGGA-TTAA-A-ATAAAGGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCA-GA
* * *
519725 TCTTAACTCCCTGAGGTTACAGTGGAGTAGACCGAAAACTTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCAGA
* *
519771 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAAACTTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCAGA
* *
519817 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAAACTTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCAGA
* *
519863 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAAACTTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCAGA
* *
519909 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAAACTTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCAGA
* *
519955 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAAACTTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCAGA
* ** *
520001 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGAC-AT-A-A
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCAGA
* * * * ** * **
520044 TCCTATCTCCCTGAAGTTACAGTGGCGCGGA-TTAA-A-ATAAAGGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCA-GA
* * * * * *
520088 TCTTATCTCTCTGAAGTTACAGTAGAGCAGATC--ACAC---CAGG
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCAGA
* ** * *
520129 TCTTATCTTCCTGATATTACAGTGGAGCAGA-GGAAGAATTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCAGA
* * ** *
520174 TCTTATCTCCCTGA-GATATCAGCGGAGCAGATTGAAGA-TAGT-A-A
1 TCTTATCTCCCTGAGGTTA-CAGTGGAGCAGACCGAAGACT-TTCAGA
* *
520218 TCCTATCTCCCTGAGATTACAGTGGAGC
1 TCTTATCTCCCTGAGGTTACAGTGGAGC
520246 GGATTAAAAT
Statistics
Matches: 883, Mismatches: 152, Indels: 110
0.77 0.13 0.10
Matches are distributed among these distances:
41 92 0.10
42 23 0.03
43 139 0.16
44 166 0.19
45 40 0.05
46 419 0.47
47 4 0.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (46 bp):
TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGACTTTCAGA
Found at i:519284 original size:174 final size:174
Alignment explanation
Indices: 518991--519935 Score: 1173
Period size: 174 Copynumber: 5.4 Consensus size: 174
518981 NNNNNNNNNN
518991 CCCTGAGGTTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTACAGTGGAGCGG
1 CCCTGAGGTTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTACAGTGGAGCGG
* *
519056 ATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGGTCACACCAGGTCTTATCTCC
66 ATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGGTCTTATCTCC
519121 CTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGATCTTATCT
131 CTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGATCTTATCT
* * *
519165 CCCTGAGGTTACAGCGGAGCAGATTGAAGACATAATCCTATCTCCTTG-AGATTACAGTAGAGCG
1 CCCTGAGGTTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAG-TTACAGTGGAGCG
*
519229 GATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCACCAGGTCTTATCTC
65 GATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGGTCTTATCTC
*
519294 CCTGAGGTTACAGTAGAGTAGACCGAAGACTTTCAGATCTTATCT
130 CCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGATCTTATCT
*
519339 CCTTGAGGTTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTACAGTGGAGCGG
1 CCCTGAGGTTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTACAGTGGAGCGG
* *
519404 ATTAAAATAAAGGATCTTATCTCTCTGAAGTTACGGTAGAGCAGATCGCACCAGGTCTTATCTCC
66 ATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGGTCTTATCTCC
* *
519469 TTGAGGTTACAGTAGAGTAGACCGAAGACTTTCAGATCTTATCT
131 CTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGATCTTATCT
*
519513 CCCTGAGGTTACAGCAGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTACAGTGGAGCGG
1 CCCTGAGGTTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTACAGTGGAGCGG
* * * * * *
519578 ATTAAAATAAAGGATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAAACTTTCAGATCTTA
66 ATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG--CAC---CAGGTCTTA
* * ** * *
519643 TCTCCCTGAGGTTACAGCGGAGCAGATTGAAGAC-AT-A-ATCCTATCT
126 TCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGATCTTATCT
* * * * * * * * * * * *
519689 CCCTGAAGTTACAGTGGCGCGGAT-TAAAATAAAGGATCTTAACTCCCTGAGGTTACAGTGGAGT
1 CCCTGAGGTTACAGCGGAGCAGATCGAAGACATA--ATCCTATCTCCCTGAAGTTACAGTGGAGC
* ** ** * * * * * *
519753 AGACCGAAAACTTTCA-GATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAAACTTTCAGA
64 GGA-TTAAAA--TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG--CAC---CAGG
*
519817 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAAACTTTCAGATCTTATCT
121 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGATCTTATCT
* * * * * * *
519871 CCCTGAGGTTACAGTGGAGTAGACCGAAAACTTTCAGATCTTATCTCCCTGAGGTTACAGTGGAG
1 CCCTGAGGTTACAGCGGAGCAGATCGAAGAC-AT-A-ATCCTATCTCCCTGAAGTTACAGTGGAG
519936 TAGACCGAAA
Statistics
Matches: 687, Mismatches: 66, Indels: 26
0.88 0.08 0.03
Matches are distributed among these distances:
173 2 0.00
174 434 0.63
175 7 0.01
176 29 0.04
177 28 0.04
178 5 0.01
179 118 0.17
180 3 0.00
181 1 0.00
182 27 0.04
183 4 0.01
184 28 0.04
185 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (174 bp):
CCCTGAGGTTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTACAGTGGAGCGG
ATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGGTCTTATCTCC
CTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGATCTTATCT
Found at i:519443 original size:133 final size:134
Alignment explanation
Indices: 519285--520245 Score: 802
Period size: 133 Copynumber: 7.2 Consensus size: 134
519275 TCGCACCAGG
* * * *
519285 TCTTATCTCCCTGAGGTTACAGTAGAGTAGACCGAAGACTTTCAGATCTTATCTCCTTGAGGTTA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACCGAA-ACTTTCAGATCTTATCTCCCTGAGGTTA
* * * * * * * * *
519350 CAGCGGAGCAGATCGAAGAC-AT-A-ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAT
65 CAGTGGAGTAGACCGAAAACTTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATGAAAAT
519412 AAAGGA
130 AAA-GA
* * * * * * *
519418 TCTTATCTCTCTGAAGTTACGGTAGAGCAGATCG-CAC---CAGGTCTTATCTCCTTGAGGTTAC
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACCGAAACTTTCAGATCTTATCTCCCTGAGGTTAC
* * ** * *
519479 AGTAGAGTAGACCGAAGACTTTCAGATCTTATCTCCCTGAGGTTACAGCAGAGCAGATCGAAGAC
66 AGTGGAGTAGACCGAAAACTTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGAT-GAAAAT
*
519544 ATA-A
130 AAAGA
* * ** * **
519548 TCCTATCTCCCTGAAGTTACAGTGGAGCGGA-TTAAA-ATAAAGGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACCGAAACTTTCA-GATCTTATCTCCCTGAGGTTA
* *
519611 CAGTGGAGTAGACCGAAAACTTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGA
65 CAGTGGAGTAGACCGAAAACTTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGA-TGAAAA
* *
519676 CATA-A
129 TAAAGA
* * * ** * ** *
519681 TCCTATCTCCCTGAAGTTACAGTGGCGCGGA-TTAAA-ATAAAGGATCTTAACTCCCTGAGGTTA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACCGAAACTTTCA-GATCTTATCTCCCTGAGGTTA
* *
519744 CAGTGGAGTAGACCGAAAACTTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAAA
65 CAGTGGAGTAGACCGAAAACTTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGA-TGAAAA
**
519809 CTTTCAGA
129 --TAAAGA
* *
519817 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAAACTTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACCG-AAACTTTCAGATCTTATCTCCCTGAGGTTA
* *
519882 CAGTGGAGTAGACCGAAAACTTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAAA
65 CAGTGGAGTAGACCGAAAACTTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGA-TGAAAA
**
519947 CTTTCAGA
129 --TAAAGA
* *
519955 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAAACTTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACCG-AAACTTTCAGATCTTATCTCCCTGAGGTTA
* * ** * * * * * * *
520020 CAGCGGAGCAGATTGAAGAC-AT-A-ATCCTATCTCCCTGAAGTTACAGTGGCGCGGATTAAAAT
65 CAGTGGAGTAGACCGAAAACTTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATGAAAAT
520082 AAAGGA
130 AAA-GA
* * * * * * **
520088 TCTTATCTCTCTGAAGTTACAGTAGAGCAGATC-ACAC---CAGGTCTTATCTTCCTGATATTAC
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACCGAAACTTTCAGATCTTATCTCCCTGAGGTTAC
* * * * *
520149 AGTGGAGCAGA-GGAAGAA-TTTCAGATCTTATCTCCCTGA-GATATCAGCGGAGCAGATTGAAG
66 AGTGGAGTAGACCGAA-AACTTTCAGATCTTATCTCCCTGAGGTTA-CAGTGGAGCAGA-TGAAA
*
520211 ATAGTA-A
128 ATA-AAGA
*
520218 TCCTATCTCCCTG-AGATTACAGTGGAGC
1 TCTTATCTCCCTGAAG-TTACAGTGGAGC
520246 GGATTAAAAT
Statistics
Matches: 707, Mismatches: 96, Indels: 53
0.83 0.11 0.06
Matches are distributed among these distances:
127 3 0.00
128 70 0.10
129 7 0.01
130 75 0.11
131 39 0.06
132 9 0.01
133 264 0.37
134 5 0.01
135 28 0.04
136 28 0.04
137 1 0.00
138 176 0.25
139 2 0.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (134 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCAGACCGAAACTTTCAGATCTTATCTCCCTGAGGTTAC
AGTGGAGTAGACCGAAAACTTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATGAAAATA
AAGA
Found at i:520391 original size:140 final size:140
Alignment explanation
Indices: 520179--520493 Score: 431
Period size: 140 Copynumber: 2.2 Consensus size: 140
520169 TCAGATCTTA
520179 TCTCCCTGAGATATCAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACAGTGGA
1 TCTCCCTGAGATATCAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACAGTGGA
* * *
520244 GCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATTACATCAGATTGAAG
66 GCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCACATTGAAG
520309 CCAGAGATCT
131 CCAGAGATCT
* * * * * *
520319 TCTCTCTGAGAT-TACAGTGGAGTAGATTTAAGCTAGTAATCCTATCTCTCTGA-AGTTACAGTG
1 TCTCCCTGAGATAT-CAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGA-TTACAGTG
*
520382 GAGTGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCACATTGA
64 GAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCACATTGA
520447 AGCCAGTA-ATTCT
129 AGCCAG-AGA-TCT
* * **
520460 ATCTCCCTG-GATAGCAGTGGAATAGATTGAAGAT
1 -TCTCCCTGAGATATCAGCGGAGCAGATTGAAGAT
520494 TGCAGATCTT
Statistics
Matches: 154, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
139 2 0.01
140 121 0.79
141 24 0.16
142 7 0.05
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (140 bp):
TCTCCCTGAGATATCAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACAGTGGA
GCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCACATTGAAG
CCAGAGATCT
Found at i:521897 original size:3 final size:3
Alignment explanation
Indices: 521889--521938 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
521879 ACAAATTTCA
521889 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
521937 TA
1 TA
521939 GTTTTATTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:523145 original size:3 final size:3
Alignment explanation
Indices: 523137--523186 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
523127 ACAAATTTCA
523137 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
523185 TA
1 TA
523187 GTTTTATTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:523861 original size:110 final size:112
Alignment explanation
Indices: 523643--523861 Score: 347
Period size: 110 Copynumber: 2.0 Consensus size: 112
523633 GTTATGCATA
*
523643 TTAATATCCTTAAAAAATATATTTCAAAATAAGGAAATGTTTTGCGTTTGGAAATTCGAGAAAAC
1 TTAATATCCTTAAAAAATATATTTCAAAATAAGGAAATGTTTTGCATTTGGAAATTCGAGAAAAC
523708 ATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATGGC
66 ATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATGGC
* * *
523755 TTAATATCCTTTTAAAAA-AT-TTT-AAAATAA-GACAATGTTTTGTATTTGGAAATTTGAGAAA
1 TTAATATCC-TTAAAAAATATATTTCAAAATAAGGA-AATGTTTTGCATTTGGAAATTCGAGAAA
*
523816 ACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTTAACCAAAT
64 ACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAAT
523862 TGTCAGATAT
Statistics
Matches: 100, Mismatches: 5, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
109 2 0.02
110 77 0.77
111 3 0.03
112 11 0.11
113 7 0.07
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (112 bp):
TTAATATCCTTAAAAAATATATTTCAAAATAAGGAAATGTTTTGCATTTGGAAATTCGAGAAAAC
ATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATGGC
Found at i:523905 original size:110 final size:108
Alignment explanation
Indices: 523678--523886 Score: 287
Period size: 110 Copynumber: 1.9 Consensus size: 108
523668 AAAATAAGGA
**
523678 AATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTT
1 AATGTTTTGTATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTT
* * *
523743 CAACCAAATGGCTTAATATCCTTTTAAAAAATTTTAAAATAAGAC
66 CAACCAAATGGCTCAATATCCTCTT--AAAATTTTAAAACAAGAC
*
523788 AATGTTTTGTATTTGGAAATTTGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTT
1 AATGTTTTGTATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTT
* * * *
523853 TAACCAAATTG-TCAGATATTCTCTT-GAATTTTAA
66 CAACCAAATGGCTCA-ATATCCTCTTAAAATTTTAA
523887 TCCATGCCAT
Statistics
Matches: 89, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
107 8 0.09
109 2 0.02
110 79 0.89
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (108 bp):
AATGTTTTGTATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTT
CAACCAAATGGCTCAATATCCTCTTAAAATTTTAAAACAAGAC
Found at i:528539 original size:17 final size:17
Alignment explanation
Indices: 528513--528546 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
528503 ACGGAAATGA
* *
528513 TTTGTTAGATTCTAAAT
1 TTTGTAAGATTCCAAAT
528530 TTTGTAAGATTCCAAAT
1 TTTGTAAGATTCCAAAT
528547 CTATGATTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (17 bp):
TTTGTAAGATTCCAAAT
Found at i:531815 original size:3 final size:3
Alignment explanation
Indices: 531786--531840 Score: 71
Period size: 3 Copynumber: 18.7 Consensus size: 3
531776 TTTACTCCTC
531786 ATT ATT A-T ATT A-T ATT AATGT -TT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT -AT-T ATT ATT ATT ATT ATT ATT ATT ATT
531830 ATT ATT ATT AT
1 ATT ATT ATT AT
531841 CATCATATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
2 5 0.11
3 39 0.83
4 2 0.04
5 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:535738 original size:12 final size:12
Alignment explanation
Indices: 535721--535750 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
535711 GTGGTTGAGT
535721 ATTCAAAACAAA
1 ATTCAAAACAAA
535733 ATTCAAAACAAA
1 ATTCAAAACAAA
535745 A-TCAAA
1 ATTCAAA
535751 CTTTGCAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (12 bp):
ATTCAAAACAAA
Found at i:536705 original size:5 final size:5
Alignment explanation
Indices: 536695--536722 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
536685 GTGAGCATTC
536695 AATCG AATCG AATCG AATCG AATCG AAT
1 AATCG AATCG AATCG AATCG AATCG AAT
536723 AAAAATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (5 bp):
AATCG
Found at i:537609 original size:9 final size:9
Alignment explanation
Indices: 537595--537631 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
537585 TATAGTTTGA
537595 TATTCGAAT
1 TATTCGAAT
537604 TATTCGAAT
1 TATTCGAAT
* *
537613 TATTTGAGT
1 TATTCGAAT
537622 TATTCGAAT
1 TATTCGAAT
537631 T
1 T
537632 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:540162 original size:3 final size:3
Alignment explanation
Indices: 540154--540229 Score: 152
Period size: 3 Copynumber: 25.3 Consensus size: 3
540144 NNNNNNNTAT
540154 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
540202 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
540230 AGTCATAGTA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:541483 original size:23 final size:24
Alignment explanation
Indices: 541442--541488 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
541432 CAGATGTATA
541442 GGAACTGGTGCTTCAATCTACTCC
1 GGAACTGGTGCTTCAATCTACTCC
541466 GGAACTGGTG-TTCAATCTACTCC
1 GGAACTGGTGCTTCAATCTACTCC
541489 ACTGCAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (24 bp):
GGAACTGGTGCTTCAATCTACTCC
Found at i:541821 original size:44 final size:44
Alignment explanation
Indices: 541768--541956 Score: 333
Period size: 44 Copynumber: 4.3 Consensus size: 44
541758 AAGACTTGTA
* * * *
541768 TCTTCGATCTACTTCACGCTAATACATGAAGACAAGACCTGCTA
1 TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
541812 TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
1 TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
*
541856 TCTTTGATCTACTTCACGCCAATACATAAAGACAAGATCTGCTT
1 TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
541900 TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
1 TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
541944 TCTTTGATCTACT
1 TCTTTGATCTACT
541957 GCCGACCAGG
Statistics
Matches: 139, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 139 1.00
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (44 bp):
TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
Found at i:542274 original size:44 final size:43
Alignment explanation
Indices: 541964--542407 Score: 150
Period size: 44 Copynumber: 10.1 Consensus size: 43
541954 ACTGCCGACC
* *
541964 AGGGAGATAGAATTACTGGCTTCAATATACTCCACTGTAACCTC
1 AGGGAGATAGAATTACTGGCTTCAATCTACTCCACTGT-ACCTT
* * *** * *
542008 AGGGAGGTAAAATCTACCATCTTCGATCTACTCCAC--TACTGTCT
1 AGGGAGATAGAAT-TACTGGCTTCAATCTACTCCACTGTAC-CT-T
* * * *
542052 GGGGAGATAAGATCTGTAAT--CTTCAATCTATTCCACTGCTA-C--
1 AGGGAGAT-AGA-AT-TACTGGCTTCAATCTACTCCACTG-TACCTT
* *
542094 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTC
1 AGGGAGATAGAATTACTGGCTTCAATCTACTCCACTGT-ACCTT
* * * *** ** * *
542138 AGGGAGGTAAAATCCACCATCTTTGATTTGCTCCAC--TACTGCTT
1 AGGGAGATAGAAT-TACTGGCTTCAATCTACTCCACTGTAC--CTT
* * * * *
542182 AGGGAGATAAGATATGTAAT--CTTCAATCTATTCCGCTGCTGCC-C
1 AGGGAGAT-AGA-AT-TACTGGCTTCAATCTACTCCACTG-TACCTT
*
542226 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTT
1 AGGGAGATAGAATTACTGGCTTCAATCTACTCCACTGT-ACCTT
* * *** * *
542270 AGGGAGGTAAAATCTACCATCTTCGATCTGCTCCAC--TACTGCTT
1 AGGGAGATAGAAT-TACTGGCTTCAATCTACTCCACTGTAC--CTT
* * *
542314 AGGGAGATA-AGA-T-CTGTGAACTTTAATCTATTCCACTGCTACC-C
1 AGGGAGATAGA-ATTACTG-G--CTTCAATCTACTCCACTG-TACCTT
*
542358 AGGGAGATAGAATTACTGGCTTCAATATACTCCACTGTAACCTT
1 AGGGAGATAGAATTACTGGCTTCAATCTACTCCACTGT-ACCTT
542402 AGGGAG
1 AGGGAG
542408 GTAAAATCCG
Statistics
Matches: 283, Mismatches: 76, Indels: 82
0.64 0.17 0.19
Matches are distributed among these distances:
39 3 0.01
40 2 0.01
41 24 0.08
42 19 0.07
43 43 0.15
44 120 0.42
45 56 0.20
46 9 0.03
47 7 0.02
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (43 bp):
AGGGAGATAGAATTACTGGCTTCAATCTACTCCACTGTACCTT
Found at i:542281 original size:132 final size:131
Alignment explanation
Indices: 541962--542422 Score: 730
Period size: 132 Copynumber: 3.5 Consensus size: 131
541952 CTACTGCCGA
*
541962 CCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTGTAACCTCAGGGAGGTAAAATCTACCA
1 CCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTGTAACCTCAGGGAGGTAAAATCCACCA
* *
542027 TCTTCGATCTACTCCACTACTG-TCTGGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGC
66 TCTTCGATCTGCTCCACTACTGCT-TAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGC
542091 T-
130 TC
* *
542092 ACAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCA
1 CCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTGTAACCTCAGGGAGGTAAAATCCACCA
* * * *
542157 TCTTTGATTTGCTCCACTACTGCTTAGGGAGATAAGATATGTAATCTTCAATCTATTCCGCTGCT
66 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCT
542222 GC
131 -C
* * *
542224 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTTAGGGAGGTAAAATCTACCA
1 CCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTGTAACCTCAGGGAGGTAAAATCCACCA
*
542289 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGAA-CTTTAATCTATTCCACTGC
66 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT-AATCTTCAATCTATTCCACTGC
542353 TAC
130 T-C
* *
542356 CCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTGTAACCTTAGGGAGGTAAAATCCGCCA
1 CCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTGTAACCTCAGGGAGGTAAAATCCACCA
542421 TC
66 TC
542423 AACCTGCTCC
Statistics
Matches: 306, Mismatches: 21, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
130 119 0.39
131 1 0.00
132 184 0.60
133 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (131 bp):
CCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTGTAACCTCAGGGAGGTAAAATCCACCA
TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCT
C
Found at i:542510 original size:45 final size:45
Alignment explanation
Indices: 542459--542596 Score: 126
Period size: 45 Copynumber: 3.1 Consensus size: 45
542449 GTAAGGCTGG
542459 TATCTTTAATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATTTGC
1 TATCTTTAATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATTTGC
* * * * * **
542504 TATCTTTAA-CTTGCTCCACCG-CAACT-AAGGGAGGCAAGGCTT--
1 TATCTTTAATC-TGCTTCGCTGTCAA-TGTAGGAAGGCAAGATTTGC
* *
542546 TAT-TTTCGATCTGCTTCGCTGTCGATGTAGGAAGGCAAGATTTGC
1 TATCTTT-AATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATTTGC
542591 TATCTT
1 TATCTT
542597 CACTGATCTA
Statistics
Matches: 68, Mismatches: 16, Indels: 17
0.67 0.16 0.17
Matches are distributed among these distances:
41 3 0.04
42 12 0.18
43 15 0.22
44 16 0.24
45 20 0.29
46 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (45 bp):
TATCTTTAATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATTTGC
Found at i:546971 original size:73 final size:74
Alignment explanation
Indices: 546851--546999 Score: 291
Period size: 73 Copynumber: 2.0 Consensus size: 74
546841 CTCCTTTTTG
546851 TTTGATCTAGGTCGTAAATCTTTACTCATTCACGTTCATTAGCTTCTTTATGAGATTGGGACCTT
1 TTTGATCTAGGTCGTAAATCTTTACTCATTCACGTTCATTAGCTTCTTTATGAGATTGGGACCTT
546916 TGATGACTT
66 TGATGACTT
546925 TTTGATCTA-GTCGTAAATCTTTACTCATTCACGTTCATTAGCTTCTTTATGAGATTGGGACCTT
1 TTTGATCTAGGTCGTAAATCTTTACTCATTCACGTTCATTAGCTTCTTTATGAGATTGGGACCTT
546989 TGATGACTT
66 TGATGACTT
546998 TT
1 TT
547000 GAATAAATTT
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 66 0.88
74 9 0.12
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.44
Consensus pattern (74 bp):
TTTGATCTAGGTCGTAAATCTTTACTCATTCACGTTCATTAGCTTCTTTATGAGATTGGGACCTT
TGATGACTT
Found at i:548346 original size:17 final size:17
Alignment explanation
Indices: 548326--548363 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
548316 TTTGATTATA
548326 AAATATGA-AAAATGTAT
1 AAATATGATAAAA-GTAT
*
548343 AAATATTATAAAAGTAT
1 AAATATGATAAAAGTAT
548360 AAAT
1 AAAT
548364 GTACATACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (17 bp):
AAATATGATAAAAGTAT
Found at i:548510 original size:3 final size:3
Alignment explanation
Indices: 548502--548553 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
548492 ATATGTAAGT
*
548502 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
548550 ATA A
1 ATA A
548554 AGTCATAGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:549713 original size:16 final size:16
Alignment explanation
Indices: 549688--549718 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
549678 TAAATAAAAA
549688 ACATAGATATATATAC
1 ACATAGATATATATAC
*
549704 ACATATATATATATA
1 ACATAGATATATATA
549719 AATATAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (16 bp):
ACATAGATATATATAC
Found at i:549802 original size:27 final size:29
Alignment explanation
Indices: 549734--549802 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 29
549724 AAAAATATTC
549734 ATTAAAAAAATATATACATGTACATATATAA
1 ATTAAAAAAATATATACA-GTA-ATATATAA
*
549765 A-GAAAATAAATATATACA-T-ATATATAA
1 ATTAAAA-AAATATATACAGTAATATATAA
549792 ATTAAAAAAAT
1 ATTAAAAAAAT
549803 TAATTACATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
27 13 0.38
28 4 0.12
29 1 0.03
30 4 0.12
31 12 0.35
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.30
Consensus pattern (29 bp):
ATTAAAAAAATATATACAGTAATATATAA
Found at i:549802 original size:31 final size:31
Alignment explanation
Indices: 549737--549802 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
549727 AATATTCATT
* *
549737 AAAA-AAATATATACATGTACATATATAAAG
1 AAAATAAATATATACATATACATAAATAAAG
*
549767 AAAATAAATATATACATATATATAAATTAAA-
1 AAAATAAATATATACATATACATAAA-TAAAG
549798 AAAAT
1 AAAAT
549803 TAATTACATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 4 0.13
31 23 0.74
32 4 0.13
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.29
Consensus pattern (31 bp):
AAAATAAATATATACATATACATAAATAAAG
Found at i:554819 original size:43 final size:43
Alignment explanation
Indices: 554674--554834 Score: 159
Period size: 43 Copynumber: 3.8 Consensus size: 43
554664 CTTTCTTGAG
* * *
554674 TCTGCTCCACTGCAAATTCAG-GAAGATAAGACCTAATAC---AA
1 TCTGCTCCACTGCAACTTCAGAG-AGATAAGA-TTACTACTTTAA
* * * *
554715 TCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTATTTTAA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGAT-TACTACTTTAA
* * *
554759 TCCGCTCCACTGCAACTTCAGAGAGATAGGATTACTGCTTTAA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGATTACTACTTTAA
* *
554802 TCTGCTCCACTGTAACTTCAGGGAGATAAGATT
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGATT
554835 CGCCATATTA
Statistics
Matches: 98, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
41 30 0.31
42 1 0.01
43 37 0.38
44 30 0.31
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTCAGAGAGATAAGATTACTACTTTAA
Found at i:556018 original size:25 final size:26
Alignment explanation
Indices: 555990--556038 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
555980 GTGTCTTGAA
555990 AAGAA-AAAGGTATT-CAAGAACAACG
1 AAGAATAAA-GTATTGCAAGAACAACG
556015 AAGAATAAAGTATTGCAAGAACAA
1 AAGAATAAAGTATTGCAAGAACAA
556039 ACAAATTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.57, C:0.10, G:0.18, T:0.14
Consensus pattern (26 bp):
AAGAATAAAGTATTGCAAGAACAACG
Found at i:567578 original size:29 final size:31
Alignment explanation
Indices: 567514--567579 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 31
567504 AAATATTCAT
* * *
567514 TAAA-AAATATATACATGTACATATATAAAG
1 TAAATAAACATATACATATACATATATAAAC
*
567544 AAAATAAACATATACATATA-A-ATATAAAC
1 TAAATAAACATATACATATACATATATAAAC
567573 TAAATAA
1 TAAATAA
567580 TAATAATTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 13 0.43
30 4 0.13
31 13 0.43
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.27
Consensus pattern (31 bp):
TAAATAAACATATACATATACATATATAAAC
Found at i:567599 original size:20 final size:20
Alignment explanation
Indices: 567574--567611 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
567564 AATATAAACT
567574 AAATAATAATAATTACATAC
1 AAATAATAATAATTACATAC
567594 AAATAATAATAATTACAT
1 AAATAATAATAATTACAT
567612 TATTTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATAATAATAATTACATAC
Found at i:568077 original size:310 final size:314
Alignment explanation
Indices: 567603--568228 Score: 1046
Period size: 310 Copynumber: 2.0 Consensus size: 314
567593 CAAATAATAA
* * *
567603 TAATTACATTATTTAATTAATTTAAAAATAAAATAAAAAAGACTAAATCGAATTGCAGATAAAAA
1 TAATGACATTATTTAATTAATTTAAAAAT--AATAAAAAAGACTAAATCGAACTACAGATAAAAA
* *
567668 AACTGGGGCAAATCCGTAAATAAGTGAAGATAAAAGCACTAAATTGAACACGCAAACAACAGAGA
64 AACTGGGCCAAATCCGCAAATAAGTGAAGATAAAAGCACTAAATTGAACACGCAAACAACAGAGA
* *
567733 GGGACTGGAAGGGAAATTTTCCCTTCTCCTCTAAAACGGCGTCGTTCAAGTAGGTCTAAATTTAA
129 GGGACTGGAAGGGAAATTTTCCCTTCTCCTCTAAAACGGCGTCGTTCAAGTAGGGCTAAATTGAA
*
567798 ATTCAAAATAAATTAAAGGGCGAATTAAAAAAATAAAAAAACC-AATTATAAAAATATTAAAAAG
194 ATTCAAAATAAATTAAAGGGCAAATTAAAAAAATAAAAAAACCTAATTATAAAAATATTAAAAAG
*
567862 GCGGAGGGGCTAAAAGCGCAATTTACCCCTCCGA-TCAAAAACACGCGGATCCTAGG
259 GCAGAGGGGCTAAAAGCGCAATTTACCCCTCC-ACTCAAAAACACGCGGATCCTAGG
567918 TAATGACATTATTTAATTAATTTAAAAAT-A-AAAAAAGACTAAATCGAACTACAGAT-AAAAAA
1 TAATGACATTATTTAATTAATTTAAAAATAATAAAAAAGACTAAATCGAACTACAGATAAAAAAA
* * *
567980 TTTGGCCAAATTCGCAAATAAGTGAAGATAAAAGCACTAAATTGAACACGCAAACAACAGAGAGG
66 CTGGGCCAAATCCGCAAATAAGTGAAGATAAAAGCACTAAATTGAACACGCAAACAACAGAGAGG
*
568045 GACTGGAAGGGAAATTTTCCCTTCTCCTCTAAAACGGCGTTGTTCAAGTAGGGCTAAATTGAAAT
131 GACTGGAAGGGAAATTTTCCCTTCTCCTCTAAAACGGCGTCGTTCAAGTAGGGCTAAATTGAAAT
* *
568110 TCAAAATAAATTAAAGGGCAAATTAAAAAAATAAAAAAACCTAATTGTAAAAATATTAAAAAGGT
196 TCAAAATAAATTAAAGGGCAAATTAAAAAAATAAAAAAACCTAATTATAAAAATATTAAAAAGGC
*
568175 AGATGGGCTAAAAGCGCAATTTACCCCTCCACTCAAAAACACGCGGATCCTAGG
261 AGAGGGGCTAAAAGCGCAATTTACCCCTCCACTCAAAAACACGCGGATCCTAGG
568229 CCAGGTCGGG
Statistics
Matches: 293, Mismatches: 16, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
310 169 0.58
311 95 0.32
312 1 0.00
315 28 0.10
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.23
Consensus pattern (314 bp):
TAATGACATTATTTAATTAATTTAAAAATAATAAAAAAGACTAAATCGAACTACAGATAAAAAAA
CTGGGCCAAATCCGCAAATAAGTGAAGATAAAAGCACTAAATTGAACACGCAAACAACAGAGAGG
GACTGGAAGGGAAATTTTCCCTTCTCCTCTAAAACGGCGTCGTTCAAGTAGGGCTAAATTGAAAT
TCAAAATAAATTAAAGGGCAAATTAAAAAAATAAAAAAACCTAATTATAAAAATATTAAAAAGGC
AGAGGGGCTAAAAGCGCAATTTACCCCTCCACTCAAAAACACGCGGATCCTAGG
Found at i:569163 original size:25 final size:25
Alignment explanation
Indices: 569129--569177 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
569119 GGAATAAAAC
569129 TGTATTATTATTGTAATTATATTTT
1 TGTATTATTATTGTAATTATATTTT
*
569154 TGTATTATTATTGTCATTATATTT
1 TGTATTATTATTGTAATTATATTT
569178 CTATTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (25 bp):
TGTATTATTATTGTAATTATATTTT
Found at i:569186 original size:25 final size:25
Alignment explanation
Indices: 569131--569187 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
569121 AATAAAACTG
* *
569131 TATTATTATTGTAATTATATTTTTG
1 TATTATTATTGTAATTATATTTCTA
*
569156 TATTATTATTGTCATTATATTTCTA
1 TATTATTATTGTAATTATATTTCTA
*
569181 TTTTATT
1 TATTATT
569188 TATTTATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.26, C:0.04, G:0.05, T:0.65
Consensus pattern (25 bp):
TATTATTATTGTAATTATATTTCTA
Found at i:569234 original size:3 final size:3
Alignment explanation
Indices: 569226--569266 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
569216 TCTTTTAACC
569226 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
569267 TTGTTNNNNN
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:569437 original size:4 final size:4
Alignment explanation
Indices: 569428--569454 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
569418 TTTTTATAAT
569428 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
569455 TTCATTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:571695 original size:6 final size:6
Alignment explanation
Indices: 571678--571707 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
571668 TCTTCACTAT
*
571678 TCACCA TTACCA TCACCA TCACCA TCACCA
1 TCACCA TCACCA TCACCA TCACCA TCACCA
571708 ACAAAAACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.47, G:0.00, T:0.20
Consensus pattern (6 bp):
TCACCA
Found at i:576631 original size:13 final size:13
Alignment explanation
Indices: 576615--576640 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
576605 GCTAGGTTTT
576615 GAGGAAGAAGAAG
1 GAGGAAGAAGAAG
576628 GAGGAAGAAGAAG
1 GAGGAAGAAGAAG
576641 AAGAAAGAAA
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:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (13 bp):
GAGGAAGAAGAAG
Found at i:576648 original size:13 final size:13
Alignment explanation
Indices: 576619--576661 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
576609 GGTTTTGAGG
* *
576619 AAGAAGAAGGAGG
1 AAGAAGAAGAAGA
576632 AAGAAGAAGAAGA
1 AAGAAGAAGAAGA
*
576645 AAGAA-AAGAAAA
1 AAGAAGAAGAAGA
576657 AAGAA
1 AAGAA
576662 AAAAACGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 11 0.41
13 16 0.59
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (13 bp):
AAGAAGAAGAAGA
Found at i:576660 original size:16 final size:16
Alignment explanation
Indices: 576641--576680 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
576631 GAAGAAGAAG
576641 AAGAAAGAAAA-GAAAA
1 AAGAAA-AAAACGAAAA
576657 AAGAAAAAAACGAAAA
1 AAGAAAAAAACGAAAA
*
576673 AATAAAAA
1 AAGAAAAA
576681 TAATAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (16 bp):
AAGAAAAAAACGAAAA
Found at i:576856 original size:21 final size:23
Alignment explanation
Indices: 576806--576859 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
576796 AATCCAGCGT
* *
576806 AGGCCCAGTGCAGCAGCAGGCTCC
1 AGGCCCAGCGCAGCAGCAAGC-CC
576830 AGGCCCAGCGCAGCAGCAAG-CC
1 AGGCCCAGCGCAGCAGCAAGCCC
576852 A-GCCCAGC
1 AGGCCCAGC
576860 AGGCCCACAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 7 0.25
22 3 0.11
24 18 0.64
ACGTcount: A:0.24, C:0.41, G:0.31, T:0.04
Consensus pattern (23 bp):
AGGCCCAGCGCAGCAGCAAGCCC
Found at i:583292 original size:80 final size:80
Alignment explanation
Indices: 583109--584207 Score: 1376
Period size: 80 Copynumber: 13.8 Consensus size: 80
583099 TTTTTTTTTT
* * * * *
583109 AAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTTGGGCACACGCCGAGGTATTTC--TT-AAT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
***
583171 TTCTGTTTTTTTCAA
66 TTCTGTTTTTCAAAA
*
583186 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAAC-CATGCCGAGGTATTTCTTTTAAAT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
583250 TTCTGTTTTTCAAAAA
66 TTCTGTTTTTC-AAAA
* *
583266 AAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTTGGAC-CATGCCGAGGTATTTCTTTTAAAT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
* *
583330 TTCTATTTTTCCAAA
66 TTCTGTTTTTCAAAA
* * * * *
583345 AAATCAACTCATATTGTGAAAGGTAAGTTGAGCCTCGGGTCACATACCGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACATGCCGAGGTATTTCTTTTAAA
*
583410 TTTTTGTTTTTC-AAA
65 TTTCTGTTTTTCAAAA
*
583425 AAATCAACTCATATTGCGAG-GGTGAGTTGAGCCTCAGACACATGCCGAGGTATTTCTTTTAAAT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
* *
583489 TTTTATTTTTC--AA
66 TTCTGTTTTTCAAAA
* * * * * * *
583502 AAAGCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGATATTT-TTTAAAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACATGCCGAGGTATTTCTTT-TAA
*
583566 ATTTCTATTTTTTTTCAAAAA
64 ATTTC---TGTTTTTC-AAAA
583587 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGAC-CATGCCGAGGTATTTCTTTTAAAT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
583651 TTCTGTTTTTCAAAA
66 TTCTGTTTTTCAAAA
* * *
583666 AAATCAACTCATATTGCGAAAGATGAGTTGAGCCTCGGACACATACCGAGGTATTTCTTTTAAAT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
*
583731 TTCTATTTTTCAAAA
66 TTCTGTTTTTCAAAA
* * * * *
583746 AAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCACATACCAAGGTGTTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACATGCCGAGGTATTTCTTTTAAA
*
583811 TTTCTATTTTTCAAAA
65 TTTCTGTTTTTCAAAA
*
583827 AAATCAACTCATATTGCGAGA---G-G-T-AGCCTCGGACACATACCGAGGTATTTCTTTTAAAT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
583886 TTCTGTTTTTC--AA
66 TTCTGTTTTTCAAAA
** * * ** *
583899 AAATCAACTCATATTGTTAAAGGTGAGTTGAGCCTCAGGTCACATGTTGAGGTATTT-TTTAAAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACATGCCGAGGTATTTCTTTTAAA
*
583963 TTTCTATTTTTTTTCAAAA
65 TTTC---TGTTTTTCAAAA
583982 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGAC-CATGCCGAGGTATTTCTTTTAAAT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
*
584046 TTTTGTTTTTCAAAAA
66 TTCTGTTTTTC-AAAA
* * *
584062 AAATCAACTCATATTGCGAGAGGGGAGTTGAGCCTCAGACACATACCGAGGTATTTCTTTTAAAT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
*
584127 TTTTGTTTTTTTTTCAAAA
66 TTCTG----TTTTTCAAAA
***
584146 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATAATGAGGTATTTCTTTTA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTA
584208 CATTAATCAA
Statistics
Matches: 897, Mismatches: 88, Indels: 67
0.85 0.08 0.06
Matches are distributed among these distances:
72 20 0.02
74 36 0.04
75 7 0.01
76 17 0.02
77 57 0.06
78 73 0.08
79 147 0.16
80 216 0.24
81 141 0.16
82 19 0.02
83 54 0.06
84 68 0.08
85 42 0.05
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (80 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
TTCTGTTTTTCAAAA
Found at i:584525 original size:30 final size:30
Alignment explanation
Indices: 584418--584514 Score: 140
Period size: 30 Copynumber: 3.2 Consensus size: 30
584408 TTGTGTTAAA
* *
584418 AAAATTGCATTTTAACCCTTAAACTTTTTC
1 AAAATTACATTTTAACCCTTAAACTTTCTC
* *
584448 AAAATTACATTTTAACCCCTAAACTTTCTT
1 AAAATTACATTTTAACCCTTAAACTTTCTC
* *
584478 AAAATTACATTTTGACCCTTGAACTTTCTC
1 AAAATTACATTTTAACCCTTAAACTTTCTC
584508 AAAATTA
1 AAAATTA
584515 TCTTTTGACC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (30 bp):
AAAATTACATTTTAACCCTTAAACTTTCTC
Found at i:584526 original size:60 final size:60
Alignment explanation
Indices: 584418--584555 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 60
584408 TTGTGTTAAA
* * *
584418 AAAATTGCATTTTAACCCTTAAACTTTTTCAAAATTACATTTTAACCCCTAAACTTTCTT-
1 AAAATTACATTTTGACCCTTAAACTTTCTCAAAATTACATTTTAACCCC-AAACTTTCTTC
* * ** *
584478 AAAATTACATTTTGACCCTTGAACTTTCTCAAAATTATC-TTTTGACCCCAATTTTTTTTC
1 AAAATTACATTTTGACCCTTAAACTTTCTCAAAATTA-CATTTTAACCCCAAACTTTCTTC
*
584538 AAAATTACGTTTTGACCC
1 AAAATTACATTTTGACCC
584556 CAAAATTTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 7 0.10
60 59 0.88
61 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.04, T:0.42
Consensus pattern (60 bp):
AAAATTACATTTTGACCCTTAAACTTTCTCAAAATTACATTTTAACCCCAAACTTTCTTC
Found at i:584565 original size:30 final size:30
Alignment explanation
Indices: 584418--584565 Score: 120
Period size: 30 Copynumber: 4.9 Consensus size: 30
584408 TTGTGTTAAA
* * ** *
584418 AAAATTGCATTTTAACCCTTAAACTTTTTC
1 AAAATTACATTTTGACCCCAAAATTTTTTC
* * *
584448 AAAATTACATTTTAACCCCTAAACTTTCTT-
1 AAAATTACATTTTGACCCC-AAAATTTTTTC
*** * *
584478 AAAATTACATTTTGACCCTTGAACTTTCTC
1 AAAATTACATTTTGACCCCAAAATTTTTTC
**
584508 AAAATTATC-TTTTGACCCCAATTTTTTTTC
1 AAAATTA-CATTTTGACCCCAAAATTTTTTC
*
584538 AAAATTACGTTTTGACCCCAAAATTTTT
1 AAAATTACATTTTGACCCCAAAATTTTT
584566 ACTACGCTTA
Statistics
Matches: 91, Mismatches: 23, Indels: 8
0.75 0.19 0.07
Matches are distributed among these distances:
29 5 0.05
30 79 0.87
31 7 0.08
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.43
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAATTTTTTC
Found at i:584921 original size:3 final size:3
Alignment explanation
Indices: 584913--584968 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
584903 TTTGAGGAGA
*
584913 AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
584961 AAG AAG AA
1 AAG AAG AA
584969 ATGAAAAATG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:585835 original size:19 final size:19
Alignment explanation
Indices: 585811--586102 Score: 123
Period size: 19 Copynumber: 15.6 Consensus size: 19
585801 AAAATTCCCG
585811 TGTTTT-AAAAAATATTCA
1 TGTTTTCAAAAAATATTCA
* *
585829 TGTTTTTTAAAAAA-ATTCC
1 TG-TTTTCAAAAAATATTCA
* *
585848 CGTGTTTCAAAAAATATTCG
1 TGT-TTTCAAAAAATATTCA
*
585868 TGTTTTCAAAAAAAATTC-
1 TGTTTTCAAAAAATATTCA
585886 TCGTGTTTCAAAAAATATTCA
1 T-GT-TTTCAAAAAATATTCA
* *
585907 TGTTTTCAAAAAAAATTCC
1 TGTTTTCAAAAAATATTCA
* * *
585926 CGTGTTTC-AAAAATTTTCG
1 TGT-TTTCAAAAAATATTCA
* * *
585945 TGTTTTC-AGAAAT-TCCCG
1 TGTTTTCAAAAAATAT-TCA
* **
585963 TGTTTT--AAAAATTTTTG
1 TGTTTTCAAAAAATATTCA
*
585980 TGTTTTCAAAAAAT-TTCCC
1 TGTTTTCAAAAAATATT-CA
*
585999 T-TGTTTC-AAAAAT-TTCCG
1 TGT-TTTCAAAAAATATT-CA
* *
586017 TGTTTTCAAAAAAAATTTCG
1 TGTTTTCAAAAAATA-TTCA
586037 TG-TTTCAAAAAAT-TCTCA
1 TGTTTTCAAAAAATAT-TCA
* * *
586055 T-ATTTC-AAAAATTTTCG
1 TGTTTTCAAAAAATATTCA
* *
586072 CGTTTTCAAAAATTATT-A
1 TGTTTTCAAAAAATATTCA
586090 TTGTGTTTCAAAA
1 -TGT-TTTCAAAA
586103 TTCTCGTGTT
Statistics
Matches: 217, Mismatches: 32, Indels: 48
0.73 0.11 0.16
Matches are distributed among these distances:
17 22 0.10
18 52 0.24
19 96 0.44
20 44 0.20
21 3 0.01
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.42
Consensus pattern (19 bp):
TGTTTTCAAAAAATATTCA
Found at i:586065 original size:37 final size:38
Alignment explanation
Indices: 585800--586050 Score: 298
Period size: 39 Copynumber: 6.7 Consensus size: 38
585790 TTCTTGTTTC
* * **
585800 AAAAATTCCCGTGTTTTAAAAAATATTCATGTTTTTTAA
1 AAAAATTCCCGTGTTTCAAAAAAT-TTCGTGTTTTCAAA
585839 AAAAATTCCCGTGTTTCAAAAAATATTCGTGTTTTCAAA
1 AAAAATTCCCGTGTTTCAAAAAAT-TTCGTGTTTTCAAA
* *
585878 AAAAATTCTCGTGTTTCAAAAAATATTCATGTTTTCAAA
1 AAAAATTCCCGTGTTTCAAAAAAT-TTCGTGTTTTCAAA
*
585917 AAAAATTCCCGTGTTTCAAAAATTTTCGTGTTTTC---
1 AAAAATTCCCGTGTTTCAAAAAATTTCGTGTTTTCAAA
* * * *
585952 AGAAATTCCCGTGTTTTAAAAATTTTTGTGTTTTC-AA
1 AAAAATTCCCGTGTTTCAAAAAATTTCGTGTTTTCAAA
* *
585989 AAAATTTCCCTTGTTTC-AAAAATTTCCGTGTTTTCAAA
1 AAAAATTCCCGTGTTTCAAAAAATTT-CGTGTTTTCAAA
*
586027 AAAAATT-TCGTGTTTCAAAAAATT
1 AAAAATTCCCGTGTTTCAAAAAATT
586051 CTCATATTTC
Statistics
Matches: 186, Mismatches: 21, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
35 32 0.17
36 7 0.04
37 28 0.15
38 25 0.13
39 94 0.51
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41
Consensus pattern (38 bp):
AAAAATTCCCGTGTTTCAAAAAATTTCGTGTTTTCAAA
Found at i:586078 original size:18 final size:18
Alignment explanation
Indices: 585796--586119 Score: 162
Period size: 18 Copynumber: 17.5 Consensus size: 18
585786 AAAATTCTTG
**
585796 TTTCAAAAATTCCCGTGT
1 TTTCAAAAATTTTCGTGT
* * *
585814 TTTAAAAAATATTCATGTTT
1 TTTCAAAAATTTTC--GTGT
* **
585834 TTTAAAAAAATTCCCGTG-
1 TTT-CAAAAATTTTCGTGT
*
585852 TTTCAAAAAATATTCGTGT
1 TTTC-AAAAATTTTCGTGT
*
585871 TTTCAAAAAAAATTCTCGTG-
1 TTTC---AAAAATTTTCGTGT
* *
585891 TTTCAAAAAATATTCATGT
1 TTTC-AAAAATTTTCGTGT
**
585910 TTTCAAAAAAAATTCCCGTG-
1 TTTC---AAAAATTTTCGTGT
585930 TTTCAAAAATTTTCGTGT
1 TTTCAAAAATTTTCGTGT
* **
585948 TTTCAGAAATTCCCGTGT
1 TTTCAAAAATTTTCGTGT
*
585966 TTT-AAAAATTTTTGTGT
1 TTTCAAAAATTTTCGTGT
* *
585983 TTTCAAAAAATTTCCCT-T
1 TTTC-AAAAATTTTCGTGT
*
586001 GTTTCAAAAATTTCCGTGT
1 -TTTCAAAAATTTTCGTGT
*
586020 TTTCAAAAAAAATTTCGTG-
1 TTTC--AAAAATTTTCGTGT
* * *
586039 TTTCAAAAAATTCTCAT-A
1 TTTC-AAAAATTTTCGTGT
*
586057 TTTCAAAAATTTTCGCGT
1 TTTCAAAAATTTTCGTGT
**
586075 TTTCAAAAATTATTATTGT
1 TTTCAAAAATT-TTCGTGT
*
586094 GTTTC-AAAATTCTCGTGT
1 -TTTCAAAAATTTTCGTGT
586112 TTT-AAAAA
1 TTTCAAAAA
586120 AAATCATGCT
Statistics
Matches: 234, Mismatches: 50, Indels: 45
0.71 0.15 0.14
Matches are distributed among these distances:
17 40 0.17
18 97 0.41
19 38 0.16
20 29 0.12
21 30 0.13
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (18 bp):
TTTCAAAAATTTTCGTGT
Found at i:598248 original size:3 final size:3
Alignment explanation
Indices: 598240--598295 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
598230 TTTGAGGAGA
*
598240 AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
598288 AAG AAG AA
1 AAG AAG AA
598296 ATGAAAAATG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:599142 original size:39 final size:38
Alignment explanation
Indices: 599099--599277 Score: 166
Period size: 38 Copynumber: 4.7 Consensus size: 38
599089 CGATACGTCC
* *
599099 TTAAAAAAAATCGCTTGTTTCAAAAAATATTCATGTTTT
1 TTAAAAAAAATC-CGTGTTTCAAAAAATATTCGTGTTTT
*
599138 TTAAAAAAATTCCAGTGTTTCAAAAAATATTCGTG-TTT
1 TTAAAAAAAATCC-GTGTTTCAAAAAATATTCGTGTTTT
* * *
599176 TCAAAAAAACTCCCGTGTTTCAAAAAATATTCGTTTTTT
1 TTAAAAAAAAT-CCGTGTTTCAAAAAATATTCGTGTTTT
** ** * *
599215 TTTTAAAATTTCTCGTGTTTC-AAAAATTTTTGTG-TTT
1 TTAAAAAAAATC-CGTGTTTCAAAAAATATTCGTGTTTT
* *
599252 TCAAAAAAATTCCCGTGTTTCAAAAA
1 TTAAAAAAAAT-CCGTGTTTCAAAAA
599278 TTTCATTATT
Statistics
Matches: 116, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
37 18 0.16
38 49 0.42
39 49 0.42
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (38 bp):
TTAAAAAAAATCCGTGTTTCAAAAAATATTCGTGTTTT
Found at i:599143 original size:20 final size:20
Alignment explanation
Indices: 599116--599207 Score: 84
Period size: 19 Copynumber: 4.8 Consensus size: 20
599106 AAATCGCTTG
599116 TTTCAAAAAATATTCATGTT
1 TTTCAAAAAATATTCATGTT
* *
599136 TTTTAAAAAA-ATTCCA-GTG
1 TTTCAAAAAATATT-CATGTT
*
599155 TTTCAAAAAATATTCGTG-T
1 TTTCAAAAAATATTCATGTT
* ** *
599174 TTTCAAAAAA-ACTCCCGTG
1 TTTCAAAAAATATTCATGTT
599193 TTTCAAAAAATATTC
1 TTTCAAAAAATATTC
599208 GTTTTTTTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
18 4 0.07
19 35 0.61
20 18 0.32
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (20 bp):
TTTCAAAAAATATTCATGTT
Found at i:599242 original size:18 final size:18
Alignment explanation
Indices: 599219--599347 Score: 122
Period size: 18 Copynumber: 7.2 Consensus size: 18
599209 TTTTTTTTTT
599219 AAAATTTCTCGTGTTTCA
1 AAAATTTCTCGTGTTTCA
*
599237 AAAATTT-TTGTGTTTTCAA
1 AAAATTTCTCGTG-TTTC-A
* *
599256 AAAAATTCCCGTGTTTCA
1 AAAATTTCTCGTGTTTCA
**
599274 AAAATTTCATTAT-TTTCA
1 AAAATTTC-TCGTGTTTCA
599292 AAAATTT-TCGTGTTTCA
1 AAAATTTCTCGTGTTTCA
* * *
599309 AAAAATTCTCTTATTTCA
1 AAAATTTCTCGTGTTTCA
*
599327 AAAATTTC-CGTGTTTTA
1 AAAATTTCTCGTGTTTCA
599344 AAAA
1 AAAA
599348 AATTATTATT
Statistics
Matches: 88, Mismatches: 17, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
16 2 0.02
17 25 0.28
18 46 0.52
19 12 0.14
20 3 0.03
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (18 bp):
AAAATTTCTCGTGTTTCA
Found at i:599304 original size:35 final size:34
Alignment explanation
Indices: 599136--599347 Score: 147
Period size: 38 Copynumber: 5.8 Consensus size: 34
599126 TATTCATGTT
* * * *
599136 TTTTAAAAAAATTCCAGTGTTTCAAAAAATATTCGTG
1 TTTTCAAAAATTTCC-GTGTTTC-AAAAAT-TTCTTA
* * *
599173 TTTTCAAAAAAACTCCCGTGTTTCAAAAAATATTCGTTTT
1 TTTTC--AAAAATTTCCGTGTTTC-AAAAAT-TTC--TTA
** * *
599213 TTTTTTAAAATTTCTCGTGTTTCAAAAATTTTTGTG
1 TTTTCAAAAATTTC-CGTGTTTCAAAAATTTCT-TA
*
599249 TTTTCAAAAAAATTCCCGTGTTTCAAAAATTTCATTA
1 TTTTC--AAAAATTTCCGTGTTTCAAAAATTTC-TTA
*
599286 TTTTCAAAAATTTTCGTGTTTCAAAAAATTCTCTTA
1 TTTTCAAAAATTTCCGTGTTTC-AAAAATT-TCTTA
*
599322 -TTTCAAAAATTTCCGTGTTTTAAAAA
1 TTTTCAAAAATTTCCGTGTTTCAAAAA
599348 AATTATTATT
Statistics
Matches: 144, Mismatches: 20, Indels: 25
0.76 0.11 0.13
Matches are distributed among these distances:
34 5 0.03
35 35 0.24
36 15 0.10
37 30 0.21
38 38 0.26
39 16 0.11
40 5 0.03
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (34 bp):
TTTTCAAAAATTTCCGTGTTTCAAAAATTTCTTA
Found at i:599348 original size:35 final size:36
Alignment explanation
Indices: 599114--599357 Score: 124
Period size: 35 Copynumber: 6.6 Consensus size: 36
599104 AAAAATCGCT
* * * *
599114 TGTTTCAAAAAATATTCATGTTTTTTAAAAAAATTCCAG
1 TGTTTTAAAAAAT-TTCAT-TATTTTCAAAAATTTCC-G
* * * * *
599153 TGTTTCAAAAAATATTC-GTGTTTTCAAAAAAACTCCCG
1 TGTTTTAAAAAAT-TTCATTATTTTC--AAAAATTTCCG
* * * **
599191 TGTTTCAAAAAATATTCGTTTTTTTTTTAAAATTTCTCG
1 TGTTTTAAAAAAT-TTC-ATTATTTTCAAAAATTTC-CG
* * * *
599230 TG-TTTCAAAAATTT-TTGTGTTTTCAAAAAAATTCCCG
1 TGTTTTAAAAAATTTCAT-TATTTTC--AAAAATTTCCG
* *
599267 TG-TTTCAAAAATTTCATTATTTTCAAAAATTTTCG
1 TGTTTTAAAAAATTTCATTATTTTCAAAAATTTCCG
*
599302 TGTTTCAAAAAATTCTC-TTA-TTTCAAAAATTTCCG
1 TGTTTTAAAAAATT-TCATTATTTTCAAAAATTTCCG
*
599337 TGTTTTAAAAAAATT-ATTATT
1 TGTTTTAAAAAATTTCATTATT
599358 GTGCTTCAAA
Statistics
Matches: 166, Mismatches: 26, Indels: 30
0.75 0.12 0.14
Matches are distributed among these distances:
34 4 0.02
35 40 0.24
36 17 0.10
37 31 0.19
38 40 0.24
39 29 0.17
40 5 0.03
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (36 bp):
TGTTTTAAAAAATTTCATTATTTTCAAAAATTTCCG
Found at i:599351 original size:19 final size:18
Alignment explanation
Indices: 599136--599348 Score: 89
Period size: 18 Copynumber: 11.6 Consensus size: 18
599126 TATTCATGTT
*
599136 TTTTAAAAAAATTCCAGTG
1 TTTTAAAAAATTTCC-GTG
*
599155 TTTCAAAAAATATT-CGTG
1 TTTTAAAAAAT-TTCCGTG
* *
599173 TTTTCAAAAAAACTCCCGTG
1 TTTT--AAAAAATTTCCGTG
* *
599193 TTTCAAAAAATATT-CGTTTT
1 TTTTAAAAAAT-TTCCG--TG
**
599213 TTTTTTAAAATTTCTCGTG
1 TTTTAAAAAATTTC-CGTG
* **
599232 -TTTCAAAAATTTTTGTG
1 TTTTAAAAAATTTCCGTG
*
599249 TTTTCAAAAAAATTCCCGTG
1 TTTT--AAAAAATTTCCGTG
* ** *
599269 -TTTCAAAAATTTCATTA
1 TTTTAAAAAATTTCCGTG
* *
599286 TTTTCAAAAATTTTCGTG
1 TTTTAAAAAATTTCCGTG
*
599304 TTTCAAAAAA-TTCTC-T-
1 TTTTAAAAAATTTC-CGTG
*
599320 TATTTCAAAAATTTCCGTG
1 T-TTTAAAAAATTTCCGTG
599339 TTTTAAAAAA
1 TTTTAAAAAA
599349 ATTATTATTG
Statistics
Matches: 140, Mismatches: 36, Indels: 37
0.66 0.17 0.17
Matches are distributed among these distances:
16 1 0.01
17 23 0.16
18 61 0.44
19 19 0.14
20 34 0.24
21 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (18 bp):
TTTTAAAAAATTTCCGTG
Found at i:599849 original size:27 final size:26
Alignment explanation
Indices: 599770--599922 Score: 108
Period size: 26 Copynumber: 5.7 Consensus size: 26
599760 AATTTTAAGC
* * * *
599770 AATTTAAAATAAACATTACATAAAAT
1 AATTTAAAATAAATAATATATAAAAA
* * * *
599796 AGTTTAAAAGAAATGATATGTAAAAAA
1 AATTTAAAATAAATAATATAT-AAAAA
*
599823 AATCTAAAATAAATAATATATATAAAA
1 AATTTAAAATAAATAATATATA-AAAA
* * * **
599850 CAGTTTAAGATAAAATAATATAGAAAGT
1 -AATTTAAAAT-AAATAATATATAAAAA
* * *
599878 AATTCAAAATAAATAATATATGAAAC
1 AATTTAAAATAAATAATATATAAAAA
*
599904 AATTTAAAATAGATAATAT
1 AATTTAAAATAAATAATAT
599923 CAAACAGCTT
Statistics
Matches: 95, Mismatches: 28, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
26 44 0.46
27 31 0.33
28 9 0.09
29 11 0.12
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (26 bp):
AATTTAAAATAAATAATATATAAAAA
Found at i:600793 original size:1 final size:1
Alignment explanation
Indices: 600787--600813 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
600777 GGTTTCTTTG
600787 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
600814 GATATGTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:605319 original size:23 final size:23
Alignment explanation
Indices: 605288--605338 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
605278 TTAATAAGAT
605288 TATTATTAAATATAA-T-TTTTTAA
1 TATTATT-AATATAAGTATTTTT-A
*
605311 TATTTTTAATATAAGTATTTTTA
1 TATTATTAATATAAGTATTTTTA
605334 TATTA
1 TATTA
605339 AATCATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 7 0.29
23 12 0.50
24 5 0.21
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TATTATTAATATAAGTATTTTTA
Found at i:607306 original size:29 final size:29
Alignment explanation
Indices: 607195--607299 Score: 113
Period size: 29 Copynumber: 3.6 Consensus size: 29
607185 TCGTTTTTTT
* *
607195 AATTATATTTTAACCCCTCAACTTTTTAA
1 AATTGTATTTTAACCCCTAAACTTTTTAA
* *
607224 AATTGTA-TTTGACCCCTAAAATTTTTAAA
1 AATTGTATTTTAACCCCTAAACTTTTT-AA
* * * *
607253 AATTGCATTTTGACCCTTAAACTTTTTTA
1 AATTGTATTTTAACCCCTAAACTTTTTAA
*
607282 AATTTTATTTTAACCCCT
1 AATTGTATTTTAACCCCT
607300 GGACTTTCTT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
28 16 0.26
29 29 0.47
30 17 0.27
ACGTcount: A:0.32, C:0.18, G:0.04, T:0.46
Consensus pattern (29 bp):
AATTGTATTTTAACCCCTAAACTTTTTAA
Found at i:607586 original size:20 final size:20
Alignment explanation
Indices: 607563--607622 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 20
607553 AAAAACTTGC
607563 GAAAAAGAGAAAAAGAAGAG
1 GAAAAAGAGAAAAAGAAGAG
*
607583 GAAAAAAGAGAGAAAG-AGAG
1 G-AAAAAGAGAAAAAGAAGAG
* *
607603 GAGAAAG-G-AGAAGAAGAG
1 GAAAAAGAGAAAAAGAAGAG
607621 GA
1 GA
607623 GAGGGTCCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 3 0.09
18 7 0.21
19 5 0.15
20 6 0.18
21 13 0.38
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (20 bp):
GAAAAAGAGAAAAAGAAGAG
Found at i:607588 original size:21 final size:21
Alignment explanation
Indices: 607564--607619 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
607554 AAAACTTGCG
607564 AAAAAGAGAAAAAGAAGAGGA
1 AAAAAGAGAAAAAGAAGAGGA
*
607585 AAAAAGAGAGAAAG-AGAGGA
1 AAAAAGAGAAAAAGAAGAGGA
* * *
607605 GAAAGGAGAAGAAGA
1 AAAAAGAGAAAAAGA
607620 GGAGAGGGTC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (21 bp):
AAAAAGAGAAAAAGAAGAGGA
Found at i:607613 original size:18 final size:19
Alignment explanation
Indices: 607575--607624 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
607565 AAAAGAGAAA
*
607575 AAGAAGAGGAAAAAAGAGAG
1 AAGAAGAGG-AGAAAGAGAG
607595 AA-AGAGAGGAGAAAG-GAG
1 AAGA-AGAGGAGAAAGAGAG
607613 AAGAAGAGGAGA
1 AAGAAGAGGAGA
607625 GGGTCCTACG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 13 0.48
19 7 0.26
20 7 0.26
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (19 bp):
AAGAAGAGGAGAAAGAGAG
Found at i:608016 original size:11 final size:10
Alignment explanation
Indices: 607999--608041 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
607989 AGTAGAGAAA
607999 AAAGAAAAAG
1 AAAGAAAAAG
608009 AGAAGAAAAAAG
1 A-AAG-AAAAAG
608021 AAAAGAAAAAG
1 -AAAGAAAAAG
*
608032 AAAAAAAAAG
1 AAAGAAAAAG
608042 GGGTTTCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
10 10 0.34
11 9 0.31
12 9 0.31
13 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:608017 original size:18 final size:18
Alignment explanation
Indices: 607994--608037 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
607984 GGCCCAGTAG
*
607994 AGAAAAAAGAAAA-AGAGA
1 AGAAAAAAGAAAAGA-AAA
608012 AGAAAAAAGAAAAGAAAA
1 AGAAAAAAGAAAAGAAAA
608030 AGAAAAAA
1 AGAAAAAA
608038 AAAGGGGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 23 0.96
19 1 0.04
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AGAAAAAAGAAAAGAAAA
Found at i:608026 original size:23 final size:21
Alignment explanation
Indices: 607998--608041 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 21
607988 CAGTAGAGAA
607998 AAAAGAAAAAGAGAAGAAAAAAG
1 AAAAGAAAAAGA-AA-AAAAAAG
608021 AAAAGAAAAAGAAAAAAAAAG
1 AAAAGAAAAAGAAAAAAAAAG
608042 GGGTTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.33
22 2 0.10
23 12 0.57
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (21 bp):
AAAAGAAAAAGAAAAAAAAAG
Found at i:608209 original size:17 final size:18
Alignment explanation
Indices: 608183--608223 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
608173 ATTTTTTTGT
608183 ATTTATATTTTTAATTTA
1 ATTTATATTTTTAATTTA
*
608201 ATTTA-ATTTTTATTTTA
1 ATTTATATTTTTAATTTA
*
608218 TTTTAT
1 ATTTAT
608224 TTAAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTATATTTTTAATTTA
Found at i:608232 original size:25 final size:30
Alignment explanation
Indices: 608177--608235 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 30
608167 TTATGCATTT
*
608177 TTTTGTATTTATATTTTTAATTTAATTTAA
1 TTTTGTATTTATATTTTTAATTTAATATAA
608207 TTTT-TATTT-TA-TTTT-ATTTAA-ATAA
1 TTTTGTATTTATATTTTTAATTTAATATAA
608232 TTTT
1 TTTT
608236 AATAAATAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 7 0.25
26 6 0.21
27 4 0.14
28 2 0.07
29 5 0.18
30 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (30 bp):
TTTTGTATTTATATTTTTAATTTAATATAA
Found at i:608455 original size:38 final size:38
Alignment explanation
Indices: 608354--608456 Score: 102
Period size: 38 Copynumber: 2.7 Consensus size: 38
608344 ATCAAAAAAA
* * * *
608354 TTCAAAAAAAATTCGTGTTTTCAAAAAAATTCTTGAGT
1 TTCAGAAAATATTCGTGTTTTAAAAAAAATTCTCGAGT
* ** *
608392 TTC-G-AAATTTTCGTGTCTTTAAAAAATTTTTCTCGTGT
1 TTCAGAAAATATTCGTGT-TTTAAAAAA-AATTCTCGAGT
608430 TTCAGAAAATATTCGTGTTTTAAAAAA
1 TTCAGAAAATATTCGTGTTTTAAAAAA
608457 TAAGGCAACG
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
36 10 0.19
37 8 0.15
38 13 0.25
39 10 0.19
40 11 0.21
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.42
Consensus pattern (38 bp):
TTCAGAAAATATTCGTGTTTTAAAAAAAATTCTCGAGT
Found at i:608456 original size:18 final size:18
Alignment explanation
Indices: 608357--608458 Score: 55
Period size: 18 Copynumber: 5.4 Consensus size: 18
608347 AAAAAAATTC
*
608357 AAAAAAAATTCGTGTTTT
1 AAAAAATATTCGTGTTTT
* *
608375 CAAAAAA-ATTCTTGAGTTT
1 -AAAAAATATTCGTG-TTTT
** *
608394 -CGAAATTTTCGTGTCTTT
1 AAAAAATATTCGTGT-TTT
* *
608412 AAAAAATTTTTCTCGTGTTTC
1 AAAAAA--TAT-TCGTGTTTT
*
608433 AGAAAATATTCGTGTTTT
1 AAAAAATATTCGTGTTTT
608451 AAAAAATA
1 AAAAAATA
608459 AGGCAACGAA
Statistics
Matches: 62, Mismatches: 14, Indels: 15
0.68 0.15 0.16
Matches are distributed among these distances:
17 3 0.05
18 29 0.47
19 14 0.23
21 10 0.16
22 6 0.10
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (18 bp):
AAAAAATATTCGTGTTTT
Found at i:608587 original size:18 final size:18
Alignment explanation
Indices: 608564--608806 Score: 252
Period size: 17 Copynumber: 13.9 Consensus size: 18
608554 AAAAGAATCG
*
608564 AAAATTTTCATGTTTTCA
1 AAAATTTTCGTGTTTTCA
*
608582 AAAATTCTCGTGTTTT-A
1 AAAATTTTCGTGTTTTCA
*
608599 AAAATTTCCGTGTTTTCA
1 AAAATTTTCGTGTTTTCA
608617 AAAATTTTCGTG-TTTCA
1 AAAATTTTCGTGTTTTCA
*
608634 AAAATTTTTGTGTTTTCA
1 AAAATTTTCGTGTTTTCA
* * *
608652 ACAATTCTCGTGTTTTAAA
1 AAAATTTTCGTGTTTT-CA
* *
608671 AAAATTTTGGTGTTTTGA
1 AAAATTTTCGTGTTTTCA
*
608689 CAAAATTCTCGTG-TTTCA
1 -AAAATTTTCGTGTTTTCA
*
608707 AAAATTATCGTG-TTTCA
1 AAAATTTTCGTGTTTTCA
*
608724 AAAA-TTTCGTGTTTTTA
1 AAAATTTTCGTGTTTTCA
*
608741 AAAA-TAT-GTGTTTTCA
1 AAAATTTTCGTGTTTTCA
* *
608757 AAAATTCTCGTATTTTCA
1 AAAATTTTCGTGTTTTCA
*
608775 AAAATTCTCGTG-TTTCA
1 AAAATTTTCGTGTTTTCA
*
608792 AAAACTTTCGT-TTTT
1 AAAATTTTCGTGTTTT
608807 TTTATTTTTC
Statistics
Matches: 190, Mismatches: 27, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
16 18 0.09
17 80 0.42
18 68 0.36
19 24 0.13
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (18 bp):
AAAATTTTCGTGTTTTCA
Found at i:608613 original size:35 final size:35
Alignment explanation
Indices: 608564--608795 Score: 267
Period size: 35 Copynumber: 6.6 Consensus size: 35
608554 AAAAGAATCG
*
608564 AAAATTTTCATGTTTTCAAAAATTCTCGTGTTTTA
1 AAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTTA
* * *
608599 AAAATTTCCGTGTTTTCAAAAATTTTCGTGTTTCA
1 AAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTTA
* *
608634 AAAATTTTTGTGTTTTCAACAATTCTCGTGTTTTAAA
1 AAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTT--A
* * *
608671 AAAATTTTGGTGTTTTGACAAAATTCTCGTGTTTCA
1 AAAATTTTCGTGTTTTCA-AAAATTCTCGTGTTTTA
*
608707 AAAATTATCGTG-TTTCAAAAATT-TCGTGTTTTTA
1 AAAATTTTCGTGTTTTCAAAAATTCTCGTG-TTTTA
* *
608741 AAAA-TAT-GTGTTTTCAAAAATTCTCGTATTTTCA
1 AAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTT-A
*
608775 AAAATTCTCGTG-TTTCAAAAA
1 AAAATTTTCGTGTTTTCAAAAA
608796 CTTTCGTTTT
Statistics
Matches: 169, Mismatches: 19, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
32 3 0.02
33 23 0.14
34 23 0.14
35 75 0.44
36 14 0.08
37 17 0.10
38 14 0.08
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (35 bp):
AAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTTA
Found at i:611803 original size:23 final size:23
Alignment explanation
Indices: 611777--611822 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
611767 TGAGCAAGGT
611777 AAACAAATTATTCAAAATTTCAA
1 AAACAAATTATTCAAAATTTCAA
*
611800 AAACAAGTTATTCAAAATTTCAA
1 AAACAAATTATTCAAAATTTCAA
611823 CTCGAGATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.30
Consensus pattern (23 bp):
AAACAAATTATTCAAAATTTCAA
Found at i:612101 original size:19 final size:20
Alignment explanation
Indices: 612060--612101 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
612050 TTGGTTGCAT
* *
612060 TTTTTTGGAGTCTTGTACTC
1 TTTTTTGGAGCCTTGCACTC
*
612080 TTTTTTGGTGCCTTGCAC-C
1 TTTTTTGGAGCCTTGCACTC
612099 TTT
1 TTT
612102 ATTAATATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.07, C:0.19, G:0.19, T:0.55
Consensus pattern (20 bp):
TTTTTTGGAGCCTTGCACTC
Found at i:618592 original size:20 final size:20
Alignment explanation
Indices: 618567--618606 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
618557 GGCATTTATA
618567 CAATTC-ACATATACAACATT
1 CAATTCAACATATA-AACATT
618587 CAATTCAAACATATAAACAT
1 CAATTC-AACATATAAACAT
618607 ACACAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.28
Consensus pattern (20 bp):
CAATTCAACATATAAACATT
Found at i:621993 original size:36 final size:37
Alignment explanation
Indices: 621912--621993 Score: 96
Period size: 36 Copynumber: 2.2 Consensus size: 37
621902 TACTTCATGC
* * *
621912 TAATTTTTTTTATTTTTTATATTATTTTTTTGAATTT
1 TAATTTATTTTATTTTTTATAATATTTTTATGAATTT
* *
621949 TGAGTTATTTTATTTTTTA-AATATTTTTAT-AATTAT
1 TAATTTATTTTATTTTTTATAATATTTTTATGAATT-T
621985 TAATTTATT
1 TAATTTATT
621994 GTTGGCGTGG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
35 4 0.11
36 17 0.46
37 16 0.43
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.70
Consensus pattern (37 bp):
TAATTTATTTTATTTTTTATAATATTTTTATGAATTT
Found at i:627350 original size:6 final size:6
Alignment explanation
Indices: 627334--627386 Score: 81
Period size: 6 Copynumber: 9.0 Consensus size: 6
627324 CTGTGAGTTA
* *
627334 CTGTT- CTGTTG CTGTTG CTGTTG CTGTTG CTGTTG CAGTTG CTGCTG
1 CTGTTG CTGTTG CTGTTG CTGTTG CTGTTG CTGTTG CTGTTG CTGTTG
627381 CTGTTG
1 CTGTTG
627387 ATGCAACTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
5 5 0.12
6 38 0.88
ACGTcount: A:0.02, C:0.19, G:0.32, T:0.47
Consensus pattern (6 bp):
CTGTTG
Found at i:628030 original size:30 final size:30
Alignment explanation
Indices: 627994--628051 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
627984 ATCACATTAT
* *
627994 TTAGATTCCAAATATACAAGTAATATGAAC
1 TTAGATTCCAAATAAACAAGTAAAATGAAC
*
628024 TTAGATTCCAAATAAATAAGTAAAATGA
1 TTAGATTCCAAATAAACAAGTAAAATGA
628052 CCCGAGTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.29
Consensus pattern (30 bp):
TTAGATTCCAAATAAACAAGTAAAATGAAC
Found at i:629096 original size:27 final size:27
Alignment explanation
Indices: 629066--629225 Score: 158
Period size: 27 Copynumber: 5.8 Consensus size: 27
629056 TGCTGTGGTG
*
629066 GCTGCTGCTGCTGTTGCTGTTGTTGCT
1 GCTGCTGCTGCTGTTGCTGTTGCTGCT
* * * *
629093 GCTGTTGTTGCTGTTGCTGTTGTTGTTGTT
1 GCTGCTGCTGCTGTTGC---TGTTGCTGCT
* * *
629123 GTTGCTGTTGCTGTTGCTGTTGCTGTT
1 GCTGCTGCTGCTGTTGCTGTTGCTGCT
*
629150 GCTGCTGTTGCTGTTGCTGTTGCTGCT
1 GCTGCTGCTGCTGTTGCTGTTGCTGCT
* * *
629177 GCTGTTGCTGCTGCTGTTGTTGCTGCT
1 GCTGCTGCTGCTGTTGCTGTTGCTGCT
* * *
629204 GTTGTTGCTGCTGTTGTTGTTG
1 GCTGCTGCTGCTGTTGCTGTTG
629226 TTGGGCATGC
Statistics
Matches: 116, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
27 92 0.79
30 24 0.21
ACGTcount: A:0.00, C:0.17, G:0.34, T:0.49
Consensus pattern (27 bp):
GCTGCTGCTGCTGTTGCTGTTGCTGCT
Found at i:629220 original size:12 final size:12
Alignment explanation
Indices: 629055--629222 Score: 183
Period size: 12 Copynumber: 14.0 Consensus size: 12
629045 CCTGCTGGGA
* *
629055 CTGCTGTGGTGG
1 CTGCTGTTGTTG
* *
629067 CTGCTGCTGCTG
1 CTGCTGTTGTTG
*
629079 TTGCTGTTGTTG
1 CTGCTGTTGTTG
629091 CTGCTGTTGTTG
1 CTGCTGTTGTTG
* *
629103 CTGTTGCTGTTG
1 CTGCTGTTGTTG
* *
629115 TTGTTGTTGTTG
1 CTGCTGTTGTTG
* *
629127 CTGTTGCTGTTG
1 CTGCTGTTGTTG
* *
629139 CTGTTGCTGTTG
1 CTGCTGTTGTTG
*
629151 CTGCTGTTGCTG
1 CTGCTGTTGTTG
* *
629163 TTGCTGTTGCTG
1 CTGCTGTTGTTG
*
629175 CTGCTGTTGCTG
1 CTGCTGTTGTTG
629187 CTGCTGTTGTTG
1 CTGCTGTTGTTG
629199 CTGCTGTTGTTG
1 CTGCTGTTGTTG
629211 CTGCTGTTGTTG
1 CTGCTGTTGTTG
629223 TTGTTGGGCA
Statistics
Matches: 136, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 136 1.00
ACGTcount: A:0.00, C:0.17, G:0.35, T:0.48
Consensus pattern (12 bp):
CTGCTGTTGTTG
Found at i:629226 original size:6 final size:6
Alignment explanation
Indices: 629077--629228 Score: 97
Period size: 6 Copynumber: 25.3 Consensus size: 6
629067 CTGCTGCTGC
* * * * *
629077 TGTTGC TGTTGT TGCTGC TGTTGT TGCTGT TGCTGT TGTTGT TGTTGT
1 TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT
* * * * * * * * *
629125 TGCTGT TGCTGT TGCTGT TGCTGT TGCTGC TGTTGC TGTTGC TGTTGC
1 TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT
* * * * * * * * *
629173 TGCTGC TGTTGC TGCTGC TGTTGT TGCTGC TGTTGT TGCTGC TGTTGT
1 TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT
629221 TGTTGT TG
1 TGTTGT TG
629229 GGCATGCCTC
Statistics
Matches: 123, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 123 1.00
ACGTcount: A:0.00, C:0.15, G:0.34, T:0.51
Consensus pattern (6 bp):
TGTTGT
Found at i:629328 original size:12 final size:12
Alignment explanation
Indices: 629266--629329 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
629256 CATCTGCAGT
629266 TGTTGCTGCTGC
1 TGTTGCTGCTGC
* *
629278 TGTTGCTGTTGA
1 TGTTGCTGCTGC
* *
629290 TGTTGAGGCTGTTGA
1 TGTT---GCTGCTGC
*
629305 GGTTGCTGCTGC
1 TGTTGCTGCTGC
629317 TGTTGCTGCTGC
1 TGTTGCTGCTGC
629329 T
1 T
629330 CCCGTGCTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
12 32 0.74
15 11 0.26
ACGTcount: A:0.05, C:0.17, G:0.36, T:0.42
Consensus pattern (12 bp):
TGTTGCTGCTGC
Found at i:631289 original size:1 final size:1
Alignment explanation
Indices: 631285--631329 Score: 54
Period size: 1 Copynumber: 45.0 Consensus size: 1
631275 TTTTGAGAGC
* * * *
631285 TTTTTTTTTCTTTTTCTTTTTCTTTTTTTTCTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
631330 GGTGTATGTG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:631329 original size:15 final size:15
Alignment explanation
Indices: 631284--631329 Score: 74
Period size: 15 Copynumber: 3.0 Consensus size: 15
631274 TTTTTGAGAG
631284 CTTTTTTTTTCTTTTT
1 CTTTTTTTTT-TTTTT
*
631300 CTTTTTCTTTTTTTT
1 CTTTTTTTTTTTTTT
631315 CTTTTTTTTTTTTTT
1 CTTTTTTTTTTTTTT
631330 GGTGTATGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
15 19 0.68
16 9 0.32
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (15 bp):
CTTTTTTTTTTTTTT
Found at i:635052 original size:31 final size:31
Alignment explanation
Indices: 635012--635134 Score: 101
Period size: 31 Copynumber: 4.0 Consensus size: 31
635002 TTAAAATGAG
*
635012 TATAATTGAATCAAC-ATTAAAGTTTCATGTA
1 TATAATTGAA-CAACAATCAAAGTTTCATGTA
* * *
635043 TATATTTGAACCACAATCAAAGTTTCATGTG
1 TATAATTGAACAACAATCAAAGTTTCATGTA
* * * *
635074 CACAATTGCACCA-AATCAAAG-TTCATGTA
1 TATAATTGAACAACAATCAAAGTTTCATGTA
* * *
635103 TCTAATTGCACATTCAATCAAAG-TTCATGTA
1 TATAATTGAACA-ACAATCAAAGTTTCATGTA
635134 T
1 T
635135 CATTTTGAGA
Statistics
Matches: 75, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
29 15 0.20
30 11 0.15
31 49 0.65
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (31 bp):
TATAATTGAACAACAATCAAAGTTTCATGTA
Found at i:636513 original size:31 final size:31
Alignment explanation
Indices: 636473--636595 Score: 101
Period size: 31 Copynumber: 4.0 Consensus size: 31
636463 TTAAAATGAG
*
636473 TATAATTGAATCAAC-ATTAAAGTTTCATGTA
1 TATAATTGAA-CAACAATCAAAGTTTCATGTA
* * *
636504 TATATTTGAACCACAATCAAAGTTTCATGTG
1 TATAATTGAACAACAATCAAAGTTTCATGTA
* * * *
636535 CACAATTGCACCA-AATCAAAG-TTCATGTA
1 TATAATTGAACAACAATCAAAGTTTCATGTA
* * *
636564 TCTAATTGCACATTCAATCAAAG-TTCATGTA
1 TATAATTGAACA-ACAATCAAAGTTTCATGTA
636595 T
1 T
636596 CATTTTGAGA
Statistics
Matches: 75, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
29 15 0.20
30 11 0.15
31 49 0.65
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (31 bp):
TATAATTGAACAACAATCAAAGTTTCATGTA
Found at i:643427 original size:19 final size:18
Alignment explanation
Indices: 643379--643417 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
643369 ATTTTACAAC
*
643379 AAATTTAATTGTTATAAT
1 AAATTTAATTATTATAAT
643397 AAATTTAATTATTATAAT
1 AAATTTAATTATTATAAT
643415 AAA
1 AAA
643418 ATGTTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
AAATTTAATTATTATAAT
Found at i:646603 original size:17 final size:17
Alignment explanation
Indices: 646581--646613 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
646571 GCATAATTTA
*
646581 AAATAAATATTTTAAAG
1 AAATAAATATTGTAAAG
646598 AAATAAATATTGTAAA
1 AAATAAATATTGTAAA
646614 AATATTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (17 bp):
AAATAAATATTGTAAAG
Found at i:662045 original size:21 final size:21
Alignment explanation
Indices: 662003--662090 Score: 108
Period size: 21 Copynumber: 4.2 Consensus size: 21
661993 TAGATTAGAA
*
662003 TTTTGTATGAATATTTTAAATT
1 TTTTGTATGAATATTGT-AATT
662025 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
*
662046 TTTTTTATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
* *
662065 TGTTGTCTGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
662086 ATTTT
1 -TTTT
662091 ATAATTAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
19 16 0.28
21 22 0.39
22 19 0.33
ACGTcount: A:0.28, C:0.01, G:0.12, T:0.58
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:662267 original size:19 final size:19
Alignment explanation
Indices: 662194--662251 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 19
662184 TGAATATTGT
*
662194 AATATTATAATTTTGTATG
1 AATATTGTAATTTTGTATG
*
662213 AATATTGCAATTTTTTTGTATG
1 AATATTGTAA---TTTTGTATG
*
662235 AATATTGTAATATTGTA
1 AATATTGTAATTTTGTA
662252 ATTTTGTATG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
19 14 0.44
22 18 0.56
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (19 bp):
AATATTGTAATTTTGTATG
Found at i:665926 original size:2 final size:2
Alignment explanation
Indices: 665919--665943 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
665909 TTAGGATAGA
665919 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
665944 AAGTGGATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:674838 original size:101 final size:101
Alignment explanation
Indices: 674666--674848 Score: 242
Period size: 101 Copynumber: 1.8 Consensus size: 101
674656 AATTGAGAAT
* * * * * *
674666 TGTGGAGTACTAGATGTTGGATCTTGTGAGATCATCCTTATGATACGAAATCTTTAGATTCCAAC
1 TGTGGAGTACAAAAGGTTGGATCTTATGAGAACATCCTTATGATACAAAATCTTTAGATTCCAAC
*
674731 CGTGTGAGT-TCTTATTAACTAAGTCAGGTTGAGGAC
66 AGTGTGA-TATCTTATTAACTAAGTCAGGTTGAGGAC
* * * *
674767 TGTGGAGTACAAAAGGTTGGGTCTTATGATAACATTCTTATGATACAAAATCTTTAGATTTCAAC
1 TGTGGAGTACAAAAGGTTGGATCTTATGAGAACATCCTTATGATACAAAATCTTTAGATTCCAAC
*
674832 ATTGTGATATCTTATTA
66 AGTGTGATATCTTATTA
674849 TTTTGTTGTT
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
100 1 0.01
101 68 0.99
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.37
Consensus pattern (101 bp):
TGTGGAGTACAAAAGGTTGGATCTTATGAGAACATCCTTATGATACAAAATCTTTAGATTCCAAC
AGTGTGATATCTTATTAACTAAGTCAGGTTGAGGAC
Found at i:676488 original size:19 final size:19
Alignment explanation
Indices: 676451--676488 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
676441 TACGGTAAAA
*
676451 TTAGGTTTTTCTCTGATAT
1 TTAGGTTTTTCTCTCATAT
676470 TTAGG-TTTTCTCATCATAT
1 TTAGGTTTTTCTC-TCATAT
676489 ATGTATTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.18, C:0.13, G:0.13, T:0.55
Consensus pattern (19 bp):
TTAGGTTTTTCTCTCATAT
Found at i:681170 original size:22 final size:23
Alignment explanation
Indices: 681145--681188 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
681135 TTAAAAATAA
*
681145 AAAAATAAAATAAAAT-TATTTT
1 AAAAATAAAAAAAAATATATTTT
*
681167 AAAATTAAAAAAAAATATATTT
1 AAAAATAAAAAAAAATATATTT
681189 ATTATATTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
AAAAATAAAAAAAAATATATTTT
Found at i:681329 original size:6 final size:6
Alignment explanation
Indices: 681307--681350 Score: 63
Period size: 6 Copynumber: 7.3 Consensus size: 6
681297 TAAAGTATTT
*
681307 TAAAAA T-AAAT TAAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA T-AAAAA TAAAAA TAAAAA TAAAAA TAAAAA TA
681351 TATATTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 4 0.12
6 26 0.76
7 4 0.12
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:687565 original size:25 final size:25
Alignment explanation
Indices: 687531--687578 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
687521 AAAGAATAAA
*
687531 ATATATAATAAAAATTAAAAATTGT
1 ATATATAATAAAAAGTAAAAATTGT
*
687556 ATATATAATAAATAGTAAAAATT
1 ATATATAATAAAAAGTAAAAATT
687579 AAAAAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATATAATAAAAAGTAAAAATTGT
Found at i:690104 original size:23 final size:22
Alignment explanation
Indices: 690061--690105 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
690051 AGATTAAAGG
690061 GAGAGAAAAAAAATTAAAAAAAA
1 GAGAGAAAAAAAA-TAAAAAAAA
*
690084 GAGAGGAAAAAAAA-AACAAAAA
1 GAGA-GAAAAAAAATAAAAAAAA
690106 TCACAGTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 9 0.45
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (22 bp):
GAGAGAAAAAAAATAAAAAAAA
Done.