Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2411
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: 206453
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
File 1 of 2
Found at i:1837 original size:2 final size:2
Alignment explanation
Indices: 1832--1866 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1822 TATGTGTGTG
* *
1832 TA TA TA TA TA CA TA TA TA TA TA TA CA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1867 TTTTATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1849 original size:14 final size:14
Alignment explanation
Indices: 1832--1866 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1822 TATGTGTGTG
1832 TATATATATACATA
1 TATATATATACATA
1846 TATATATATACATA
1 TATATATATACATA
1860 TATATAT
1 TATATAT
1867 TTTTATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (14 bp):
TATATATATACATA
Found at i:6562 original size:46 final size:46
Alignment explanation
Indices: 6512--6602 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
6502 AGGCATTCCC
* *
6512 CTTAGGATTA-TTCAGGTATTCAATTAATTCAATGAAGTTTAGGATT
1 CTTAGGAATATTTC-GGTATTCAATTAATTCAATGAAATTTAGGATT
*
6558 CTTAGGAATATTTCGGTATTTAATTAATTCAATGAAATTTAGGAT
1 CTTAGGAATATTTCGGTATTCAATTAATTCAATGAAATTTAGGAT
6603 ATTAGTTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 38 0.93
47 3 0.07
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (46 bp):
CTTAGGAATATTTCGGTATTCAATTAATTCAATGAAATTTAGGATT
Found at i:9528 original size:29 final size:28
Alignment explanation
Indices: 9495--9585 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 28
9485 TTTTTCACAG
* *
9495 GTTATGAATGATAAATCTAATTTTTAAAA
1 GTTAT-AATAATAAATATAATTTTTAAAA
*
9524 GTTATAAACAATAAATATAATTTTT-AAA
1 GTTAT-AATAATAAATATAATTTTTAAAA
*
9552 GATTATAGATAAATAAAATGTAATTTTTAAAA
1 G-TTATA-AT-AAT-AAATATAATTTTTAAAA
9584 GT
1 GT
9586 ATTGGTGAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
28 5 0.10
29 26 0.51
30 3 0.06
31 13 0.25
32 4 0.08
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (28 bp):
GTTATAATAATAAATATAATTTTTAAAA
Found at i:9579 original size:31 final size:29
Alignment explanation
Indices: 9505--9585 Score: 94
Period size: 29 Copynumber: 2.7 Consensus size: 29
9495 GTTATGAATG
*
9505 ATAAATCTAATTTTTAAAAGTTATAAACA
1 ATAAATATAATTTTTAAAAGTTATAAACA
9534 ATAAATATAATTTTT-AAAGATTATAGATA-A
1 ATAAATATAATTTTTAAAAG-TTATA-A-ACA
*
9564 ATAAAATGTAATTTTTAAAAGT
1 AT-AAATATAATTTTTAAAAGT
9586 ATTGGTGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
28 4 0.09
29 19 0.42
30 4 0.09
31 14 0.31
32 4 0.09
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (29 bp):
ATAAATATAATTTTTAAAAGTTATAAACA
Found at i:11079 original size:5 final size:5
Alignment explanation
Indices: 11064--11097 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
11054 CAAATTTCTT
*
11064 TTTTCC TTTTC TTTTC TTTTC TTTTT TTTTC TTT
1 TTTT-C TTTTC TTTTC TTTTC TTTTC TTTTC TTT
11098 CAATAAATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:13406 original size:2 final size:2
Alignment explanation
Indices: 13399--13430 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
13389 TCAAGCTTGC
13399 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13431 TAAAATCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15068 original size:11 final size:11
Alignment explanation
Indices: 15052--15076 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
15042 ATTTATCTTT
15052 TAAAATAAAAA
1 TAAAATAAAAA
15063 TAAAATAAAAA
1 TAAAATAAAAA
15074 TAA
1 TAA
15077 GAACTAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
TAAAATAAAAA
Found at i:15324 original size:40 final size:40
Alignment explanation
Indices: 15247--15324 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
15237 AAATTATATT
* * *
15247 TAATGATAACTTTTGTTATTATGAATTCTTATAATATACA
1 TAATGATAAATTTAGTTATTATAAATTCTTATAATATACA
* * *
15287 TAATGATAAATTTAGTTGTTATAAATTTTTATTATATA
1 TAATGATAAATTTAGTTATTATAAATTCTTATAATATA
15325 TATATATATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (40 bp):
TAATGATAAATTTAGTTATTATAAATTCTTATAATATACA
Found at i:15866 original size:71 final size:71
Alignment explanation
Indices: 15789--15920 Score: 183
Period size: 71 Copynumber: 1.9 Consensus size: 71
15779 CGAATCTCAT
* * * * ** *
15789 TTAACATTATTAATAATTTTTCTTATTTGTTTTAATCTTAAATGTGTAAGGATGAAAATACCGAA
1 TTAACATCATTAATAATTTTCCTTATTTGCTCTAATCTTAAATGAATAAAGATGAAAATACCGAA
15854 CTTTGC
66 CTTTGC
* *
15860 TTAACATCATTAATAATTTTCCTTGTTTGCTCTAATTTTAAATGAATAAAGATGAAAATAC
1 TTAACATCATTAATAATTTTCCTTATTTGCTCTAATCTTAAATGAATAAAGATGAAAATAC
15921 TTAGTTTAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
71 52 1.00
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (71 bp):
TTAACATCATTAATAATTTTCCTTATTTGCTCTAATCTTAAATGAATAAAGATGAAAATACCGAA
CTTTGC
Found at i:16719 original size:20 final size:20
Alignment explanation
Indices: 16671--16712 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
16661 TATTCATATA
* *
16671 ATAAGTGAATGTATCGATAC
1 ATAAATGAATGTATCAATAC
16691 ATAAATGAATGTATCAATAC
1 ATAAATGAATGTATCAATAC
16711 AT
1 AT
16713 GGCTGAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (20 bp):
ATAAATGAATGTATCAATAC
Found at i:16822 original size:51 final size:52
Alignment explanation
Indices: 16766--16877 Score: 181
Period size: 51 Copynumber: 2.2 Consensus size: 52
16756 TCTAAAAAGA
*
16766 AAATGTATCAATACATTTCTCCTTGTATCGATACATTTTGGG-TTTTGACCC
1 AAATGTATCAATACATTTCTCATTGTATCGATACATTTTGGGTTTTTGACCC
* * *
16817 AAATGTATCGATACATTTTTTATTGTATCGATACATTTTGGGTTTTTGACCC
1 AAATGTATCAATACATTTCTCATTGTATCGATACATTTTGGGTTTTTGACCC
16869 AAATGTATC
1 AAATGTATC
16878 GATATATGCA
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
51 38 0.68
52 18 0.32
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (52 bp):
AAATGTATCAATACATTTCTCATTGTATCGATACATTTTGGGTTTTTGACCC
Found at i:19044 original size:29 final size:31
Alignment explanation
Indices: 19012--19081 Score: 117
Period size: 29 Copynumber: 2.3 Consensus size: 31
19002 TAGATGATAA
*
19012 AATTTTTAAAGGTTATAAAT-GAT-AAATAT
1 AATTTTTAAAGGTTATAAATAAATAAAATAT
19041 AATTTTTAAAGGTTATAAATAAATAAAATAT
1 AATTTTTAAAGGTTATAAATAAATAAAATAT
19072 AATTTTTAAA
1 AATTTTTAAA
19082 AGTATTGAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 20 0.53
30 2 0.05
31 16 0.42
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (31 bp):
AATTTTTAAAGGTTATAAATAAATAAAATAT
Found at i:20393 original size:46 final size:46
Alignment explanation
Indices: 20336--20425 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
20326 GGCATTCCCC
* *
20336 TTAGGATTATTTGGGTATTCAATTAATTCAATGAAATTTGGGATTT
1 TTAGGAATATTTAGGTATTCAATTAATTCAATGAAATTTGGGATTT
* * *
20382 TTAGGAATATTTAGGTATTTAATTAATTTACTGAAATTTGGGAT
1 TTAGGAATATTTAGGTATTCAATTAATTCAATGAAATTTGGGAT
20426 ATTAATTTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (46 bp):
TTAGGAATATTTAGGTATTCAATTAATTCAATGAAATTTGGGATTT
Found at i:21724 original size:17 final size:17
Alignment explanation
Indices: 21702--21753 Score: 95
Period size: 17 Copynumber: 3.1 Consensus size: 17
21692 CATTCATACT
21702 TTTTTATCTATATTTCA
1 TTTTTATCTATATTTCA
21719 TTTTTATCTATATTTCA
1 TTTTTATCTATATTTCA
*
21736 TTTTTATCTATAATTCA
1 TTTTTATCTATATTTCA
21753 T
1 T
21754 AAAAGTTGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTTATCTATATTTCA
Found at i:22615 original size:20 final size:21
Alignment explanation
Indices: 22590--22642 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
22580 TTCTACAATT
*
22590 TGTATCGATACATAAGTG-AA
1 TGTATCGATACATAACTGAAA
* **
22610 TGTATCGATATATGTCTGAAA
1 TGTATCGATACATAACTGAAA
22631 TGTATCGATACA
1 TGTATCGATACA
22643 AGACCATGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (21 bp):
TGTATCGATACATAACTGAAA
Found at i:22786 original size:52 final size:50
Alignment explanation
Indices: 22679--22796 Score: 119
Period size: 50 Copynumber: 2.3 Consensus size: 50
22669 TTTAGAAAGA
* * * *
22679 AAATATATCGATACATTTCTCATTGTATCATACATTATGGGTTTTGACCT
1 AAATGTATCGATACATTTCTCATTATATCATACATTAGGGGTTTTGACCC
* * * * * *
22729 AAATGTGTCGATACATTTTTTATTATATCGATATATTCGGGGTTTTTGGCCC
1 AAATGTATCGATACATTTCTCATTATATC-ATACATTAGGGG-TTTTGACCC
*
22781 AAATGTACCGATACAT
1 AAATGTATCGATACAT
22797 GCAAGTAATT
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
50 24 0.44
51 9 0.17
52 21 0.39
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (50 bp):
AAATGTATCGATACATTTCTCATTATATCATACATTAGGGGTTTTGACCC
Found at i:23817 original size:20 final size:21
Alignment explanation
Indices: 23787--23830 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
23777 TTATGAAATA
23787 TTTGTTTCAATAG-TGATATTT
1 TTTGTTTCAATAGTTGAT-TTT
23808 TTTG-TTCAATAGTTGATTTT
1 TTTGTTTCAATAGTTGATTTT
23828 TTT
1 TTT
23831 CAATAATTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.20, C:0.05, G:0.14, T:0.61
Consensus pattern (21 bp):
TTTGTTTCAATAGTTGATTTT
Found at i:24422 original size:12 final size:12
Alignment explanation
Indices: 24407--24432 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
24397 TATTAATATA
24407 AAAATATTTTTT
1 AAAATATTTTTT
24419 AAAATATTTTTT
1 AAAATATTTTTT
24431 AA
1 AA
24433 GAGTAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
AAAATATTTTTT
Found at i:25065 original size:3 final size:3
Alignment explanation
Indices: 25057--25095 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
25047 GGCCTCAGTA
25057 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
25096 GACAATGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:25662 original size:6 final size:6
Alignment explanation
Indices: 25651--25703 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
25641 GAATTAGCAA
* * * * *
25651 AATGAT AATGAT AAAGAT AATAAT AATGAT GATGAT GATGAT GAT-AT
1 AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT
25698 AATGAT
1 AATGAT
25704 TTAAAATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
5 4 0.10
6 36 0.90
ACGTcount: A:0.49, C:0.00, G:0.19, T:0.32
Consensus pattern (6 bp):
AATGAT
Found at i:28213 original size:14 final size:14
Alignment explanation
Indices: 28172--28221 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
28162 AAAAATTATT
28172 TTTTAAA-TAATAA
1 TTTTAAATTAATAA
* * *
28185 -TATAAAATAAAAA
1 TTTTAAATTAATAA
28198 TTTTAAATTAATAA
1 TTTTAAATTAATAA
28212 TTTT-AATTAA
1 TTTTAAATTAA
28222 ATATTAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
12 5 0.17
13 11 0.37
14 14 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTTAAATTAATAA
Found at i:29046 original size:15 final size:15
Alignment explanation
Indices: 29026--29057 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
29016 AAAGTTGGGT
29026 TAATTGGTGTGCATA
1 TAATTGGTGTGCATA
29041 TAATTGGTGTGCATA
1 TAATTGGTGTGCATA
29056 TA
1 TA
29058 TACGTATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.41
Consensus pattern (15 bp):
TAATTGGTGTGCATA
Found at i:33160 original size:13 final size:12
Alignment explanation
Indices: 33139--33172 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
33129 TTCCACATAT
33139 TTTTCTTTTTT-
1 TTTTCTTTTTTG
33150 TTTTCATTTTTTG
1 TTTTC-TTTTTTG
33163 TTTTCTTTTT
1 TTTTCTTTTT
33173 CCTAAAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.24
12 11 0.52
13 5 0.24
ACGTcount: A:0.03, C:0.09, G:0.03, T:0.85
Consensus pattern (12 bp):
TTTTCTTTTTTG
Found at i:35603 original size:30 final size:32
Alignment explanation
Indices: 35567--35637 Score: 110
Period size: 30 Copynumber: 2.3 Consensus size: 32
35557 GATGATAAAA
*
35567 TTTTTAAAGGTTATAAAT-GAT-AAATATAAT
1 TTTTTAAAGGTTATAAATAAATAAAATATAAT
35597 TTTTTAAAGGTTATAAATAAATAAAATATAAT
1 TTTTTAAAGGTTATAAATAAATAAAATATAAT
*
35629 TTTTAAAAG
1 TTTTTAAAG
35638 TATTGAATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 18 0.49
31 2 0.05
32 17 0.46
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.42
Consensus pattern (32 bp):
TTTTTAAAGGTTATAAATAAATAAAATATAAT
Found at i:35629 original size:32 final size:30
Alignment explanation
Indices: 35549--35637 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 30
35539 TTTTGACTAA
* *
35549 AAATAATAGATGATAAAATTTTTAAAGGTTAT
1 AAATAATAAAT-AT-AATTTTTTAAAGGTTAT
*
35581 AAATGATAAATATAATTTTTTAAAGGTTAT
1 AAATAATAAATATAATTTTTTAAAGGTTAT
*
35611 AAATAAATAAAATATAATTTTTAAAAG
1 AAAT-AAT-AAATATAATTTTTTAAAG
35638 TATTGAATGA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
30 20 0.40
31 4 0.08
32 26 0.52
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (30 bp):
AAATAATAAATATAATTTTTTAAAGGTTAT
Found at i:37732 original size:46 final size:46
Alignment explanation
Indices: 37676--37764 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
37666 ACATTCCTCT
* *
37676 TAGGATTATTTAGGTATTCAATTAATTCAATGAAATTTGGGATTCG
1 TAGGAATATTTAGATATTCAATTAATTCAATGAAATTTGGGATTCG
* * *
37722 TAGGAATATTTAGATATTTAATTAATTTACTGAAATTTGGGAT
1 TAGGAATATTTAGATATTCAATTAATTCAATGAAATTTGGGAT
37765 ATTAATTTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.35, C:0.04, G:0.18, T:0.43
Consensus pattern (46 bp):
TAGGAATATTTAGATATTCAATTAATTCAATGAAATTTGGGATTCG
Found at i:38650 original size:17 final size:17
Alignment explanation
Indices: 38617--38651 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
38607 CATTCATAAT
*
38617 TTTTTATCTACATTTCA
1 TTTTTATCTACAATTCA
*
38634 TTTTTATCTATAATTCA
1 TTTTTATCTACAATTCA
38651 T
1 T
38652 AAAAGTTGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTTATCTACAATTCA
Found at i:44025 original size:20 final size:21
Alignment explanation
Indices: 44000--44052 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
43990 TTCTACAATT
*
44000 TGTATCGATACATAAGTG-AA
1 TGTATCGATACATAACTGAAA
* **
44020 TGTATCGATATATGTCTGAAA
1 TGTATCGATACATAACTGAAA
44041 TGTATCGATACA
1 TGTATCGATACA
44053 AGACCATGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (21 bp):
TGTATCGATACATAACTGAAA
Found at i:44195 original size:52 final size:50
Alignment explanation
Indices: 44089--44206 Score: 128
Period size: 50 Copynumber: 2.3 Consensus size: 50
44079 TTTAGAAAGA
* * * *
44089 AAATATATCGATACATTTCTCATTGTATCATACATTATGGGTTTTGACCT
1 AAATGTATCGATACATTTCTCATTATATCATACATTAGGGGTTTTGACCC
* * * * *
44139 AAATGTGTCGATACATTTTTTATTATATCGATATATTCGGGGTTTTTGACCC
1 AAATGTATCGATACATTTCTCATTATATC-ATACATTAGGGG-TTTTGACCC
*
44191 AAATGTACCGATACAT
1 AAATGTATCGATACAT
44207 GCAAGTAATT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
50 24 0.44
51 9 0.16
52 22 0.40
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (50 bp):
AAATGTATCGATACATTTCTCATTATATCATACATTAGGGGTTTTGACCC
Found at i:45238 original size:19 final size:21
Alignment explanation
Indices: 45197--45239 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
45187 TTATGAAATA
45197 TTTGTTTCAATAGTGATATTT
1 TTTGTTTCAATAGTGATATTT
*
45218 TTTG-TTCAATAGTTA-ATTT
1 TTTGTTTCAATAGTGATATTT
45237 TTT
1 TTT
45240 TCAATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 10 0.48
21 4 0.19
ACGTcount: A:0.23, C:0.05, G:0.12, T:0.60
Consensus pattern (21 bp):
TTTGTTTCAATAGTGATATTT
Found at i:45242 original size:17 final size:17
Alignment explanation
Indices: 45196--45250 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
45186 TTTATGAAAT
*
45196 ATTTGTTTCAATAGTGATA
1 ATTTTTTTCAATAGT--TA
*
45215 TTTTTTGTTCAATAGTTA
1 ATTTTT-TTCAATAGTTA
*
45233 ATTTTTTTCAATAATTA
1 ATTTTTTTCAATAGTTA
45250 A
1 A
45251 GACTTATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 11 0.35
18 7 0.23
19 4 0.13
20 9 0.29
ACGTcount: A:0.31, C:0.05, G:0.09, T:0.55
Consensus pattern (17 bp):
ATTTTTTTCAATAGTTA
Found at i:46869 original size:19 final size:19
Alignment explanation
Indices: 46845--46882 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
46835 TAGAGGAAAA
46845 AACCCAACAATACCCTTGG
1 AACCCAACAATACCCTTGG
46864 AACCCAACAATACCCTTGG
1 AACCCAACAATACCCTTGG
46883 TTTATCTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.37, G:0.11, T:0.16
Consensus pattern (19 bp):
AACCCAACAATACCCTTGG
Found at i:47583 original size:22 final size:22
Alignment explanation
Indices: 47539--47582 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 22
47529 ATATGAAATA
47539 TTTGTTTCAATAGTGATGATTT
1 TTTGTTTCAATAGTGATGATTT
47561 TTTG-TTCAATAGT--TGATTT
1 TTTGTTTCAATAGTGATGATTT
47580 TTT
1 TTT
47583 TCAATAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.41
21 9 0.41
22 4 0.18
ACGTcount: A:0.20, C:0.05, G:0.16, T:0.59
Consensus pattern (22 bp):
TTTGTTTCAATAGTGATGATTT
Found at i:47997 original size:3 final size:3
Alignment explanation
Indices: 47989--48027 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
47979 GACCTCAGTA
47989 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
48028 GAAAGTCTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:49868 original size:2 final size:2
Alignment explanation
Indices: 49861--49896 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
49851 CATCACATAC
49861 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49897 CACCGTAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50284 original size:6 final size:6
Alignment explanation
Indices: 50273--50311 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
50263 TAGCAAAATA
* * *
50273 ATAATG ATAATG ATAACG ATAATA ATAATG ATGATG ATA
1 ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG ATA
50312 TAATGATTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.51, C:0.03, G:0.15, T:0.31
Consensus pattern (6 bp):
ATAATG
Found at i:52380 original size:2 final size:2
Alignment explanation
Indices: 52375--52411 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
52365 TATATGTGTG
* *
52375 TA TA TA TA TA CA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52412 TTTTATTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:53691 original size:6 final size:7
Alignment explanation
Indices: 53673--53702 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
53663 AAAAATAGAA
53673 GAAAAAT
1 GAAAAAT
53680 GAAAAAT
1 GAAAAAT
53687 GAAAAAT
1 GAAAAAT
53694 GAAAAAT
1 GAAAAAT
53701 GA
1 GA
53703 TGGTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (7 bp):
GAAAAAT
Found at i:57134 original size:46 final size:46
Alignment explanation
Indices: 57084--57171 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 46
57074 AGGCATTCCC
* *
57084 CTTAGGATTATTCAGGTATTCAATTAATTCAATGAAGTTTAGGATT
1 CTTAGGAATATTCAGGTATTCAATTAATTCAATGAAATTTAGGATT
** *
57130 CTTAGGAATATTTGGGTATTTAATTAATTCAATGAAATTTAG
1 CTTAGGAATATTCAGGTATTCAATTAATTCAATGAAATTTAG
57172 AATATTAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (46 bp):
CTTAGGAATATTCAGGTATTCAATTAATTCAATGAAATTTAGGATT
Found at i:59968 original size:29 final size:28
Alignment explanation
Indices: 59935--60025 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 28
59925 TTTTTCACAG
* *
59935 GTTATGAATGATAAATCTAATTTTTAAAA
1 GTTAT-AATAATAAATATAATTTTTAAAA
*
59964 GTTATAAACAATAAATATAATTTTT-AAA
1 GTTAT-AATAATAAATATAATTTTTAAAA
*
59992 GATTATAGATAAATAAAATGTAATTTTTAAAA
1 G-TTATA-AT-AAT-AAATATAATTTTTAAAA
60024 GT
1 GT
60026 ATTGGTGAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
28 5 0.10
29 26 0.51
30 3 0.06
31 13 0.25
32 4 0.08
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (28 bp):
GTTATAATAATAAATATAATTTTTAAAA
Found at i:60019 original size:31 final size:29
Alignment explanation
Indices: 59945--60025 Score: 94
Period size: 29 Copynumber: 2.7 Consensus size: 29
59935 GTTATGAATG
*
59945 ATAAATCTAATTTTTAAAAGTTATAAACA
1 ATAAATATAATTTTTAAAAGTTATAAACA
59974 ATAAATATAATTTTT-AAAGATTATAGATA-A
1 ATAAATATAATTTTTAAAAG-TTATA-A-ACA
*
60004 ATAAAATGTAATTTTTAAAAGT
1 AT-AAATATAATTTTTAAAAGT
60026 ATTGGTGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
28 4 0.09
29 19 0.42
30 4 0.09
31 14 0.31
32 4 0.09
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (29 bp):
ATAAATATAATTTTTAAAAGTTATAAACA
Found at i:61821 original size:50 final size:50
Alignment explanation
Indices: 61752--61984 Score: 358
Period size: 50 Copynumber: 4.6 Consensus size: 50
61742 AGTTGTTGCC
* * ***
61752 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAGAGAGGTGGTTGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
61802 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
61852 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* * * *
61902 ATTGTTGACGATTTTTCACCAACCTTTGACAAATGGAGAAAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGAC-AATAGAGAGAGGTGGCCATA
*
61953 ATTGTTGACGATTCTTCACGAACCTTTGACAA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAA
61985 ATGTGGCCAT
Statistics
Matches: 169, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
50 124 0.73
51 45 0.27
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:66473 original size:50 final size:50
Alignment explanation
Indices: 66398--66630 Score: 358
Period size: 50 Copynumber: 4.6 Consensus size: 50
66388 AGTTGTTGCC
* * * *
66398 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
** *
66448 ATTGTTGACGATTCTTCAATAACCTTTGACAATAGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
66498 ATTGTTGACGATTCTTCACTAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* *
66548 ATTGTTGACGATTCTTCACCAACCTTTGACAAATGGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGAC-AATAGAGAGAGGTGGCCATA
*
66599 ATTGTTGACGATTCTTCACGAACCTTTGACAA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAA
66631 ATGTGGCCAT
Statistics
Matches: 169, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
50 122 0.72
51 47 0.28
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:67267 original size:9 final size:9
Alignment explanation
Indices: 67253--67280 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
67243 GATTTCTCTC
67253 TTGATAATT
1 TTGATAATT
67262 TTGATAATT
1 TTGATAATT
67271 TTGATAATT
1 TTGATAATT
67280 T
1 T
67281 CTTTCCCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TTGATAATT
Found at i:67615 original size:12 final size:12
Alignment explanation
Indices: 67594--67628 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
67584 TTTTAACATG
67594 AAAAGAAGAAGAA
1 AAAAG-AGAAGAA
67607 AAAAGAGAAGAA
1 AAAAGAGAAGAA
67619 AAAA-AGAAGA
1 AAAAGAGAAGA
67629 TGAAGGTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 6 0.27
12 11 0.50
13 5 0.23
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAAGAGAAGAA
Found at i:69009 original size:2 final size:2
Alignment explanation
Indices: 69002--69045 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
68992 TCAAGCTTGC
69002 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69044 AT
1 AT
69046 TAAATCTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70011 original size:55 final size:55
Alignment explanation
Indices: 69952--70070 Score: 125
Period size: 55 Copynumber: 2.2 Consensus size: 55
69942 AATAGTTGAA
** *
69952 TTTTCATGAAAAAAATATTTACTT-TAAAAGTGATGA-TTTTCTTCTAATAATTAAT
1 TTTTCAT-AAAAAAATA-TTACTTCTAAAAGTGATGATTTTTCAACCAATAATTAAT
* *** * *
70007 TTTTCCTAAAGGGATATTATTTCTAAAAGTTATGATTTTTCAACCAATAATTAAT
1 TTTTCATAAAAAAATATTACTTCTAAAAGTGATGATTTTTCAACCAATAATTAAT
70062 TTTTCATAA
1 TTTTCATAA
70071 CAAATTGTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
53 5 0.10
54 17 0.33
55 30 0.58
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (55 bp):
TTTTCATAAAAAAATATTACTTCTAAAAGTGATGATTTTTCAACCAATAATTAAT
Found at i:70460 original size:3 final size:3
Alignment explanation
Indices: 70452--70512 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
70442 CATCACTAAA
70452 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
70500 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
70513 TTGCACCCCA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:71433 original size:11 final size:11
Alignment explanation
Indices: 71417--71441 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
71407 ATTTATCTTT
71417 TAAAATAAAAA
1 TAAAATAAAAA
71428 TAAAATAAAAA
1 TAAAATAAAAA
71439 TAA
1 TAA
71442 GAACTAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
TAAAATAAAAA
Found at i:71690 original size:40 final size:40
Alignment explanation
Indices: 71613--71690 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
71603 AAATTATATT
* * *
71613 TAATGATAACTTTTGTTATTATGAATTCTTATAATATAGA
1 TAATGATAAATTTAGTTATTATAAATTCTTATAATATAGA
* * *
71653 TAATGATAAATTTAGTTGTTATAAATTTTTATTATATA
1 TAATGATAAATTTAGTTATTATAAATTCTTATAATATA
71691 TATATATATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (40 bp):
TAATGATAAATTTAGTTATTATAAATTCTTATAATATAGA
Found at i:72234 original size:71 final size:71
Alignment explanation
Indices: 72159--72290 Score: 174
Period size: 71 Copynumber: 1.9 Consensus size: 71
72149 CGAATCTCAT
* ** * * ** *
72159 TTAACATTATTAATAATTTTTTTTATTTGTTTTAATCTTAAATGTGTAAGGATGAAAATACCAAA
1 TTAACATCATTAATAATTTTCCTTATTTGCTCTAATCTTAAATGAATAAAGATGAAAATACCAAA
72224 CTTTGC
66 CTTTGC
* *
72230 TTAACATCATTAATAATTTTCCTTGTTTGCTCTAATTTTAAATGAATAAAGATGAAAATAC
1 TTAACATCATTAATAATTTTCCTTATTTGCTCTAATCTTAAATGAATAAAGATGAAAATAC
72291 TTAGTTTAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
71 51 1.00
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.44
Consensus pattern (71 bp):
TTAACATCATTAATAATTTTCCTTATTTGCTCTAATCTTAAATGAATAAAGATGAAAATACCAAA
CTTTGC
Found at i:73089 original size:20 final size:20
Alignment explanation
Indices: 73041--73082 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
73031 TATTCATATA
* *
73041 ATAAGTGAATGTATCGATAC
1 ATAAATGAATGTATCAATAC
73061 ATAAATGAATGTATCAATAC
1 ATAAATGAATGTATCAATAC
73081 AT
1 AT
73083 GGCTGAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (20 bp):
ATAAATGAATGTATCAATAC
Found at i:73192 original size:51 final size:52
Alignment explanation
Indices: 73136--73247 Score: 181
Period size: 51 Copynumber: 2.2 Consensus size: 52
73126 TCTAAAAAGA
*
73136 AAATGTATCAATACATTTCTCCTTGTATCGATACATTTTGGG-TTTTGACCC
1 AAATGTATCAATACATTTCTCATTGTATCGATACATTTTGGGTTTTTGACCC
* * *
73187 AAATGTATCGATACATTTTTTATTGTATCGATACATTTTGGGTTTTTGACCC
1 AAATGTATCAATACATTTCTCATTGTATCGATACATTTTGGGTTTTTGACCC
73239 AAATGTATC
1 AAATGTATC
73248 GATATATGCA
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
51 38 0.68
52 18 0.32
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (52 bp):
AAATGTATCAATACATTTCTCATTGTATCGATACATTTTGGGTTTTTGACCC
Found at i:75415 original size:29 final size:31
Alignment explanation
Indices: 75383--75452 Score: 117
Period size: 29 Copynumber: 2.3 Consensus size: 31
75373 TAGATGATAA
*
75383 AATTTTTAAAGGTTATAAAT-GAT-AAATAT
1 AATTTTTAAAGGTTATAAATAAATAAAATAT
75412 AATTTTTAAAGGTTATAAATAAATAAAATAT
1 AATTTTTAAAGGTTATAAATAAATAAAATAT
75443 AATTTTTAAA
1 AATTTTTAAA
75453 AGTATTGAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 20 0.53
30 2 0.05
31 16 0.42
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (31 bp):
AATTTTTAAAGGTTATAAATAAATAAAATAT
Found at i:76730 original size:46 final size:46
Alignment explanation
Indices: 76673--76762 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
76663 GGCATTCCCC
* *
76673 TTAGGATTATTTGGGTATTCAATTAATTCAATGAAATTTGGGATTT
1 TTAGGAATATTTAGGTATTCAATTAATTCAATGAAATTTGGGATTT
* * *
76719 TTAGGAATATTTAGGTATTTAATTAATTTACTGAAATTTGGGAT
1 TTAGGAATATTTAGGTATTCAATTAATTCAATGAAATTTGGGAT
76763 ATTAATTTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (46 bp):
TTAGGAATATTTAGGTATTCAATTAATTCAATGAAATTTGGGATTT
Found at i:78067 original size:17 final size:17
Alignment explanation
Indices: 78045--78096 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
78035 CTTGTTTGTT
*
78045 TTTTTATCTATAGTTCA
1 TTTTTATCTAGAGTTCA
* *
78062 TTTTTATCTAGATTTCC
1 TTTTTATCTAGAGTTCA
*
78079 TTTTTATCTAGAATTCA
1 TTTTTATCTAGAGTTCA
78096 T
1 T
78097 AAAGTTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.23, C:0.13, G:0.06, T:0.58
Consensus pattern (17 bp):
TTTTTATCTAGAGTTCA
Found at i:78973 original size:20 final size:21
Alignment explanation
Indices: 78948--79000 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
78938 TTCTACAATT
*
78948 TGTATCGATACATAAGTG-AA
1 TGTATCGATACATAACTGAAA
* **
78968 TGTATCGATATATGTCTGAAA
1 TGTATCGATACATAACTGAAA
78989 TGTATCGATACA
1 TGTATCGATACA
79001 AGACCATGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (21 bp):
TGTATCGATACATAACTGAAA
Found at i:80177 original size:20 final size:21
Alignment explanation
Indices: 80147--80190 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
80137 TTATGAAATA
80147 TTTGTTTCAATAG-TGATATTT
1 TTTGTTTCAATAGTTGAT-TTT
80168 TTTG-TTCAATAGTTGATTTT
1 TTTGTTTCAATAGTTGATTTT
80188 TTT
1 TTT
80191 CAATAATTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.20, C:0.05, G:0.14, T:0.61
Consensus pattern (21 bp):
TTTGTTTCAATAGTTGATTTT
Found at i:80788 original size:12 final size:12
Alignment explanation
Indices: 80773--80798 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
80763 TATTAATATA
80773 AAAATATTTTTT
1 AAAATATTTTTT
80785 AAAATATTTTTT
1 AAAATATTTTTT
80797 AA
1 AA
80799 GGAGTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
AAAATATTTTTT
Found at i:81434 original size:3 final size:3
Alignment explanation
Indices: 81426--81455 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
81416 GGCCTTAGTA
81426 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
81456 GACAATGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:82018 original size:6 final size:6
Alignment explanation
Indices: 82007--82059 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
81997 GAATTAGCAA
* * * * *
82007 AATGAT AATGAT AAAGAT AATAAT AATGAT GATGAT GATGAT GAT-AT
1 AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT
82054 AATGAT
1 AATGAT
82060 TTAAAATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
5 4 0.10
6 36 0.90
ACGTcount: A:0.49, C:0.00, G:0.19, T:0.32
Consensus pattern (6 bp):
AATGAT
Found at i:85394 original size:15 final size:15
Alignment explanation
Indices: 85374--85405 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
85364 AAAGTTGGGT
85374 TAATTGGTGTGCATA
1 TAATTGGTGTGCATA
85389 TAATTGGTGTGCATA
1 TAATTGGTGTGCATA
85404 TA
1 TA
85406 TACGTATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.41
Consensus pattern (15 bp):
TAATTGGTGTGCATA
Found at i:89505 original size:13 final size:13
Alignment explanation
Indices: 89489--89525 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
89479 TTTCCACATA
89489 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
*
89502 TTTTTCATTTTTT
1 TTTTTCTTTTTTT
*
89515 GTTTTCTTTTT
1 TTTTTCTTTTT
89526 CCTAAAATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.86
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:91969 original size:29 final size:31
Alignment explanation
Indices: 91937--92006 Score: 108
Period size: 29 Copynumber: 2.3 Consensus size: 31
91927 TAGATGATAA
*
91937 AATTTTTAAAGGATATAAAT-GAT-AAATAT
1 AATTTTTAAAGGATATAAATAAATAAAATAT
*
91966 AATTTTTAAAGGTTATAAATAAATAAAATAT
1 AATTTTTAAAGGATATAAATAAATAAAATAT
91997 AATTTTTAAA
1 AATTTTTAAA
92007 AGTATTGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTTTTAAAGGATATAAATAAATAAAATAT
Found at i:93348 original size:70 final size:71
Alignment explanation
Indices: 93274--93405 Score: 203
Period size: 71 Copynumber: 1.9 Consensus size: 71
93264 ATAAATTTCG
* * * *
93274 TTTAACACTATTAATAATTTT-TTTATTTGTTCTAATTTCAAATTTATAATGATGAAAATACCGA
1 TTTAACACCATTAATAATTTTCCTTATTTGTTCTAATTTCAAATGTATAAAGATGAAAATACCGA
93338 ATTTTA
66 ATTTTA
* *
93344 TTTAACACCATTAATAGTTTTCCTTATTTGTTCTAATTTGAAATGTATAAAGATGAAAATAC
1 TTTAACACCATTAATAATTTTCCTTATTTGTTCTAATTTCAAATGTATAAAGATGAAAATAC
93406 TTAGTTTAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
70 19 0.35
71 36 0.65
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (71 bp):
TTTAACACCATTAATAATTTTCCTTATTTGTTCTAATTTCAAATGTATAAAGATGAAAATACCGA
ATTTTA
Found at i:95330 original size:26 final size:27
Alignment explanation
Indices: 95301--95369 Score: 68
Period size: 32 Copynumber: 2.4 Consensus size: 27
95291 ATAATCGTAT
95301 TTAAAATATTTTTAT-TTATATAAATA
1 TTAAAATATTTTTATATTATATAAATA
* *
95327 TTAATATATTAATAATTTATATTATATAAATT
1 TTAA-A-A-T-AT-TTTTATATTATATAAATA
95359 TTAAAATATTT
1 TTAAAATATTT
95370 ATTCATATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 11
0.71 0.06 0.23
Matches are distributed among these distances:
26 4 0.12
27 2 0.06
28 3 0.09
29 2 0.06
30 3 0.09
31 6 0.18
32 14 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTAAAATATTTTTATATTATATAAATA
Found at i:99269 original size:15 final size:15
Alignment explanation
Indices: 99249--99278 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
99239 TTATCATTCT
99249 ATTACTTGTTAACAA
1 ATTACTTGTTAACAA
99264 ATTACTTGTTAACAA
1 ATTACTTGTTAACAA
99279 TAACGTACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (15 bp):
ATTACTTGTTAACAA
Found at i:99478 original size:84 final size:84
Alignment explanation
Indices: 99360--99551 Score: 217
Period size: 84 Copynumber: 2.3 Consensus size: 84
99350 TATTGTGACA
** * * *
99360 AAGAAGAAGCTGTTCCAGTTGTGGGCAGACGAGTTTGGAGATCATACGCAGCTAT-CTCTTGCTG
1 AAGAAGAAGCTGTTGGAGTTATGGGCAGACGAGTTTGGAGATCAGACGCACCTATAC-CTTGCTG
* *
99424 ATTCCGAACGTTTCGTGATG
65 ATTCCGAACATTTCGTCATG
* * * * *
99444 AAGAAGAAGCTGTTGGAGTTATGTGCAG-CGGAGTTTGGTGATGAGGCGCACCTATACGTTGCTG
1 AAGAAGAAGCTGTTGGAGTTATGGGCAGAC-GAGTTTGGAGATCAGACGCACCTATACCTTGCTG
**
99508 ATTCCGTCCATTTCGTCATG
65 ATTCCGAACATTTCGTCATG
*
99528 AAGAAGAAGCTGTTGGAATTATGG
1 AAGAAGAAGCTGTTGGAGTTATGG
99552 ACGGAGGAGC
Statistics
Matches: 90, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
83 1 0.01
84 88 0.98
85 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (84 bp):
AAGAAGAAGCTGTTGGAGTTATGGGCAGACGAGTTTGGAGATCAGACGCACCTATACCTTGCTGA
TTCCGAACATTTCGTCATG
Found at i:99668 original size:2 final size:2
Alignment explanation
Indices: 99661--99692 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
99651 TTTATTTCCC
99661 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
99693 GTGGTTGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:99748 original size:2 final size:2
Alignment explanation
Indices: 99741--99795 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
99731 TTGTCTTACT
99741 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
99783 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
99796 GTGGTTGTGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:99881 original size:3 final size:3
Alignment explanation
Indices: 99873--99922 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
99863 TAATTAAGTA
99873 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
99921 AT
1 AT
99923 CATCCTTTTT
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):
ATT
Found at i:101046 original size:2 final size:2
Alignment explanation
Indices: 101039--101063 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
101029 CTTATTAAAT
101039 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
101064 CAATCTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:101144 original size:89 final size:89
Alignment explanation
Indices: 100993--101174 Score: 346
Period size: 89 Copynumber: 2.0 Consensus size: 89
100983 AACAAGAAGC
*
100993 ACATGAGATTTATTGGTTCACACACAAATGTAATTTCTTATTAAATTATATATATATATATATAT
1 ACATGAGATTTATTGGTTCACACACAAATGTAATTTCTTATTAAATGATATATATATATATATAT
101058 ATATATCAATCTAATTTCTTTTCA
66 ATATATCAATCTAATTTCTTTTCA
*
101082 ACATGAGATTTATTGGTTCACACACAAATGTAATTTCTTATTAAATGATATGTATATATATATAT
1 ACATGAGATTTATTGGTTCACACACAAATGTAATTTCTTATTAAATGATATATATATATATATAT
101147 ATATATCAATCTAATTTCTTTTCA
66 ATATATCAATCTAATTTCTTTTCA
101171 ACAT
1 ACAT
101175 CTTTTGCGAA
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 91 1.00
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.44
Consensus pattern (89 bp):
ACATGAGATTTATTGGTTCACACACAAATGTAATTTCTTATTAAATGATATATATATATATATAT
ATATATCAATCTAATTTCTTTTCA
Found at i:101829 original size:24 final size:24
Alignment explanation
Indices: 101797--101843 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
101787 TAAAAAATAA
*
101797 TTTAAATA-TATATATATATTAAAT
1 TTTAAATATTATAAAT-TATTAAAT
*
101821 TTTATATATTATAAATTATTAAA
1 TTTAAATATTATAAATTATTAAA
101844 AATATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTAAATATTATAAATTATTAAAT
Found at i:102129 original size:18 final size:19
Alignment explanation
Indices: 102108--102143 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
102098 TTTTCTTTTG
*
102108 AATTTTT-TTTGTTTTTAA
1 AATTTTTATTTATTTTTAA
102126 AATTTTTATTTATTTTTA
1 AATTTTTATTTATTTTTA
102144 TATAAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (19 bp):
AATTTTTATTTATTTTTAA
Found at i:102487 original size:17 final size:16
Alignment explanation
Indices: 102467--102498 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
102457 TACAAAATAA
102467 TTATTTTAATATAATTT
1 TTATTTTAATA-AATTT
102484 TTATTTTAATAAATT
1 TTATTTTAATAAATT
102499 AAAAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATTTTAATAAATTT
Found at i:102606 original size:18 final size:18
Alignment explanation
Indices: 102585--102619 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
102575 ATTTAAAATA
* *
102585 TTTAATTAATTTTTTTAT
1 TTTAAATAATTATTTTAT
102603 TTTAAATAATTATTTTA
1 TTTAAATAATTATTTTA
102620 GAGTGTTGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTAAATAATTATTTTAT
Found at i:104274 original size:2 final size:2
Alignment explanation
Indices: 104267--104302 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
104257 TTCAGAGTTT
104267 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
104303 AAACATATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:104278 original size:27 final size:25
Alignment explanation
Indices: 104227--104276 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
104217 AATGGATCTG
104227 GGTTTTTCAGAGTTATATATATATA
1 GGTTTTTCAGAGTTATATATATATA
*
104252 GGTTTTTCAGAGTTTTATATATATA
1 GGTTTTTCAGAGTTATATATATATA
104277 TATATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.16, T:0.50
Consensus pattern (25 bp):
GGTTTTTCAGAGTTATATATATATA
Found at i:104869 original size:2 final size:2
Alignment explanation
Indices: 104862--104886 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
104852 TTTAATTTAA
104862 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
104887 ATTGAAGTTG
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:106463 original size:16 final size:16
Alignment explanation
Indices: 106442--106485 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 16
106432 TTTATGAATA
106442 AAAATTATATTTATTG
1 AAAATTATATTTATTG
106458 AAAA-T-TA--TATTG
1 AAAATTATATTTATTG
106470 AAAATTATATTTATTG
1 AAAATTATATTTATTG
106486 TATACTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
12 9 0.38
13 1 0.04
14 4 0.17
15 1 0.04
16 9 0.38
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (16 bp):
AAAATTATATTTATTG
Found at i:107007 original size:34 final size:34
Alignment explanation
Indices: 106961--107178 Score: 282
Period size: 34 Copynumber: 6.5 Consensus size: 34
106951 GTAAAAACCA
*
106961 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
106995 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
107029 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
107063 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
107096 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
107130 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
107163 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
107179 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 45 0.28
34 115 0.71
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:107075 original size:68 final size:67
Alignment explanation
Indices: 106959--107178 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
106949 TGGTAAAAAC
* * *
106959 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
107024 AT
66 AT
* * *
107026 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
107091 AAT
65 AAT
* * * * * *
107094 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
107159 AT
66 AT
107161 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
107179 TCTCCCACTT
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:111274 original size:19 final size:19
Alignment explanation
Indices: 111252--111288 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
111242 ACAGTAACCG
*
111252 TATACTTGAATAGTACCTA
1 TATACGTGAATAGTACCTA
111271 TATACGTGAATAGTACCT
1 TATACGTGAATAGTACCT
111289 CGACAACCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (19 bp):
TATACGTGAATAGTACCTA
Found at i:111639 original size:34 final size:34
Alignment explanation
Indices: 111593--111808 Score: 278
Period size: 34 Copynumber: 6.4 Consensus size: 34
111583 GTAAAAACCA
*
111593 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
111627 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
111661 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
111695 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
111728 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
111762 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
111795 CCATTTAATCAACA
1 CCATTTAATCAACA
111809 GTTTTCTCTT
Statistics
Matches: 160, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 43 0.27
34 115 0.72
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:111707 original size:68 final size:67
Alignment explanation
Indices: 111591--111808 Score: 319
Period size: 67 Copynumber: 3.2 Consensus size: 67
111581 TGGTAAAAAC
* * *
111591 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
111656 AT
66 AT
* * *
111658 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
111723 AAT
65 AAT
* * * * * *
111726 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
111791 AT
66 AT
111793 CACCATTTAATCAACA
1 CACCATTTAATCAACA
111809 GTTTTCTCTT
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 73 0.54
68 61 0.46
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:112992 original size:3 final size:3
Alignment explanation
Indices: 112978--113021 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
112968 ATTTATATGC
*
112978 TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT T
113022 GCATATTAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:113238 original size:2 final size:2
Alignment explanation
Indices: 113233--113286 Score: 54
Period size: 2 Copynumber: 27.0 Consensus size: 2
113223 ACATACATAC
* * * * *
113233 AT AT AT AT AT AT AT AT AT AT AT AT AT GT GT GT GT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
113275 AT AT TT AT AT AT
1 AT AT AT AT AT AT
113287 TTCTTTATGC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (2 bp):
AT
Found at i:113556 original size:34 final size:34
Alignment explanation
Indices: 113492--113774 Score: 401
Period size: 34 Copynumber: 8.4 Consensus size: 34
113482 TGGTACTTGA
* *
113492 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
113525 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
113559 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * * *
113593 TATTGATTAAAT-GGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
113626 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
113659 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
113693 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
113727 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
113761 TGTTGATTAAATGG
1 TGTTGATTAAATGG
113775 TGGTTTTTAC
Statistics
Matches: 220, Mismatches: 28, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
33 66 0.30
34 154 0.70
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:113738 original size:134 final size:135
Alignment explanation
Indices: 113492--113774 Score: 462
Period size: 134 Copynumber: 2.1 Consensus size: 135
113482 TGGTACTTGA
* *
113492 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGAGATTTGGTAGCTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
* *
113557 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCATTATTGATTAAAT-GGTGATTTGGT-GGTT
66 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCATTATTGACTAAATGGGAGATTTGGTAGG-T
113620 TGCCAT
130 TGCCAT
* *
113626 TGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGAGATTTGGTAGCTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
* * *
113691 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
66 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCATTATTGACTAAATGGGAGATTTGGTAGGTT
113756 GCCAT
131 GCCAT
113761 TGTTGATTAAATGG
1 TGTTGATTAAATGG
113775 TGGTTTTTAC
Statistics
Matches: 137, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
134 105 0.77
135 30 0.22
136 2 0.01
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (135 bp):
TGTTGATTAAATGGAGATTTGGTAGCTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCATTATTGACTAAATGGGAGATTTGGTAGGTT
GCCAT
Found at i:118257 original size:34 final size:34
Alignment explanation
Indices: 118191--118475 Score: 405
Period size: 34 Copynumber: 8.5 Consensus size: 34
118181 AAGTGGGAGA
* *
118191 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
118224 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
118258 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * * *
118292 ATTATTGATTAAAT-GGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
118325 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
118358 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
118392 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
118426 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
118460 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
118476 TGGTTTTTAC
Statistics
Matches: 222, Mismatches: 28, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
33 68 0.31
34 154 0.69
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:118439 original size:134 final size:135
Alignment explanation
Indices: 118191--118475 Score: 466
Period size: 134 Copynumber: 2.1 Consensus size: 135
118181 AAGTGGGAGA
* *
118191 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGAGATTTGGTAGCTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
* *
118256 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACCATTATTGATTAAAT-GGTGATTTGGT-GG
66 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACCATTATTGACTAAATGGGAGATTTGGTAGG
118319 TTTGCC
131 -TTGCC
* *
118325 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGAGATTTGGTAGCTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
* * *
118390 CCATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGG
66 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACCATTATTGACTAAATGGGAGATTTGGTAGG
118455 TTGCC
131 TTGCC
118460 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
118476 TGGTTTTTAC
Statistics
Matches: 139, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
134 107 0.77
135 30 0.22
136 2 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (135 bp):
ATTGTTGATTAAATGGAGATTTGGTAGCTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACCATTATTGACTAAATGGGAGATTTGGTAGG
TTGCC
Found at i:120442 original size:13 final size:13
Alignment explanation
Indices: 120424--120448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
120414 TAACTCAAGC
120424 AATAGAAAAAACA
1 AATAGAAAAAACA
120437 AATAGAAAAAAC
1 AATAGAAAAAAC
120449 TTGGGCAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.08, G:0.08, T:0.08
Consensus pattern (13 bp):
AATAGAAAAAACA
Found at i:120882 original size:105 final size:105
Alignment explanation
Indices: 120732--121116 Score: 601
Period size: 105 Copynumber: 3.7 Consensus size: 105
120722 TTACGGTACT
* ** *
120732 TTGGGGTGAATTCGGCGCAGCGATATTTCGTGGAGTTCCCGCTGCCTGAGCATGTGGAGTAGGCG
1 TTGGGGTGAATTCGGCGCAGCGATATTTCGTGGAGTTCGCGCTGCCTGAGCATGTGGAGTTTGCC
* * **
120797 CTGCCCGAGAATTTCCTGAAGGAGCTGCGGACGGCAAAAT
66 CTGCCCAAGAATTTCCTGAAGGAGCTGCGGACGGCGAAGG
* *
120837 TTGGGGTGAATTCGGTGCAGCGATAAATT-GTGGAGTTCGCGCTGCCTGAGCATGTGGAGTTTGC
1 TTGGGGTGAATTCGGCGCAGCGAT-ATTTCGTGGAGTTCGCGCTGCCTGAGCATGTGGAGTTTGC
120901 CCTGCCCAAGAATTTCCTGAAGGAGCTGCGGACGGCGAAGG
65 CCTGCCCAAGAATTTCCTGAAGGAGCTGCGGACGGCGAAGG
* * *
120942 ATAGGTTGAATTCGGCGCAGCGATATTTCGTGGAGTTCGCGCTGCCTGAGCATGTGGAGTTTGCC
1 TTGGGGTGAATTCGGCGCAGCGATATTTCGTGGAGTTCGCGCTGCCTGAGCATGTGGAGTTTGCC
121007 CTGCCCAAGAATTTCCTGAAGGAGCTGCGGACGGCGAAGG
66 CTGCCCAAGAATTTCCTGAAGGAGCTGCGGACGGCGAAGG
* * * *
121047 TTGGGGTGAATTCGGTGCAGCGATATTTGGTGGAGTTCGCGGTGCCTGAGCATGTGGAGTTTGGC
1 TTGGGGTGAATTCGGCGCAGCGATATTTCGTGGAGTTCGCGCTGCCTGAGCATGTGGAGTTTGCC
121112 CTGCC
66 CTGCC
121117 GCACCTTGTC
Statistics
Matches: 256, Mismatches: 22, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
104 3 0.01
105 250 0.98
106 3 0.01
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.25
Consensus pattern (105 bp):
TTGGGGTGAATTCGGCGCAGCGATATTTCGTGGAGTTCGCGCTGCCTGAGCATGTGGAGTTTGCC
CTGCCCAAGAATTTCCTGAAGGAGCTGCGGACGGCGAAGG
Found at i:125700 original size:3 final size:3
Alignment explanation
Indices: 125692--125730 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
125682 ATGGGCACAA
125692 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
125731 TTACACCCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:128560 original size:20 final size:21
Alignment explanation
Indices: 128523--128561 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
128513 GCAATTATCT
* *
128523 TATTTTTAACACATTTTATTA
1 TATTTTTAACAAAATTTATTA
128544 TATTTTT-ACAAAATTTAT
1 TATTTTTAACAAAATTTAT
128562 CATAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTTTTAACAAAATTTATTA
Found at i:129082 original size:84 final size:84
Alignment explanation
Indices: 128994--129154 Score: 214
Period size: 84 Copynumber: 1.9 Consensus size: 84
128984 GTGAGCTGGC
* * *
128994 GAGTTTGGAGATCATACGCAGCTATCCCTTGCTGATTCCGAACATTTCGTGATGAAGAAGAAGCT
1 GAGTTCGGAGATCAGACGCAGCTATACCTTGCTGATTCCGAACATTTCGTGATGAAGAAGAAGCT
*
129059 CTTGGAGTTATGTGCGGCG
66 CTTGGAATTATGTGCGGCG
* * ** * **
129078 GAGTTCGGTGATGAGGTGCAGCTATACGTTGCTGATTCCGTCCATTTCGTGATGAAGAAGAAGCT
1 GAGTTCGGAGATCAGACGCAGCTATACCTTGCTGATTCCGAACATTTCGTGATGAAGAAGAAGCT
*
129143 GTTGGAATTATG
66 CTTGGAATTATG
129155 GACGGAGGAG
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
84 65 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (84 bp):
GAGTTCGGAGATCAGACGCAGCTATACCTTGCTGATTCCGAACATTTCGTGATGAAGAAGAAGCT
CTTGGAATTATGTGCGGCG
Found at i:129549 original size:3 final size:3
Alignment explanation
Indices: 129541--129566 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
129531 TAATTAAGTA
129541 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
129567 CTTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:131705 original size:3 final size:3
Alignment explanation
Indices: 131697--131737 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
131687 ACGATTTGAA
131697 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
131738 AGTTGTTGTT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:133957 original size:29 final size:28
Alignment explanation
Indices: 133877--133957 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
133867 GATGAAATTC
* *
133877 TTTTAAAGGTTAT-GATTAAAAAATATATT
1 TTTTAAA-GTTATAGA-TAATAAATATAAT
* * *
133906 TTTTAAAATTTATAAATAGTAAATATAAT
1 TTTT-AAAGTTATAGATAATAAATATAAT
133935 TTTTAAAGTTATAGATGAATAAA
1 TTTTAAAGTTATAGAT-AATAAA
133958 ATTTAACTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
28 10 0.24
29 27 0.66
30 4 0.10
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (28 bp):
TTTTAAAGTTATAGATAATAAATATAAT
Found at i:134573 original size:18 final size:20
Alignment explanation
Indices: 134550--134593 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
134540 AGTTAATATA
134550 AATATAAT-TTTTATT-TTT
1 AATATAATATTTTATTATTT
134568 AATAT-ATATTTTATTATTT
1 AATATAATATTTTATTATTT
134587 AATATAA
1 AATATAA
134594 ATATAACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.09
18 12 0.52
19 8 0.35
20 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
AATATAATATTTTATTATTT
Found at i:134611 original size:20 final size:19
Alignment explanation
Indices: 134586--134627 Score: 75
Period size: 20 Copynumber: 2.2 Consensus size: 19
134576 TTTTATTATT
134586 TAATATAAATATAACTTTAA
1 TAATATAAATATAA-TTTAA
134606 TAATATAAATATAATTTAA
1 TAATATAAATATAATTTAA
134625 TAA
1 TAA
134628 ATTTTAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAATATAAATATAATTTAA
Found at i:134618 original size:43 final size:43
Alignment explanation
Indices: 134537--134623 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
134527 TATTTTAATA
* * * * *
134537 ATTAGTTAATATAAATATAATTTTTATTTTTAATATATATTTT
1 ATTAGTTAATATAAATATAACTTTAATATATAATATATAATTT
*
134580 ATTATTTAATATAAATATAACTTTAATAATATAA-ATATAATTT
1 ATTAGTTAATATAAATATAACTTTAAT-ATATAATATATAATTT
134623 A
1 A
134624 ATAAATTTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
43 33 0.89
44 4 0.11
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (43 bp):
ATTAGTTAATATAAATATAACTTTAATATATAATATATAATTT
Found at i:134684 original size:35 final size:36
Alignment explanation
Indices: 134606--134702 Score: 97
Period size: 35 Copynumber: 2.7 Consensus size: 36
134596 ATAACTTTAA
* *
134606 TAATATAAATATAATTTAATAAATTTTAATTATTATT
1 TAATATAAATATAATTTTATAAATATT-ATTATTATT
** **
134643 CCATATAAATATAATTTTATTTATATT-TTATTATT
1 TAATATAAATATAATTTTATAAATATTATTATTATT
* *
134678 TAATATAAGTATATTTTTAATAAAT
1 TAATATAAATATAATTTT-ATAAAT
134703 TATCATATAT
Statistics
Matches: 47, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
35 22 0.47
36 4 0.09
37 21 0.45
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (36 bp):
TAATATAAATATAATTTTATAAATATTATTATTATT
Found at i:134837 original size:21 final size:21
Alignment explanation
Indices: 134811--134862 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
134801 ACTGTCAATT
134811 TTAATTTTA-ATGTTATAAT-A
1 TTAATTTTACA-GTTATAATAA
134831 TTAAATTTTACAGTTATAATAA
1 TT-AATTTTACAGTTATAATAA
134853 TTAATTTTAC
1 TTAATTTTAC
134863 CGTCACTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 2 0.07
21 23 0.79
22 4 0.14
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (21 bp):
TTAATTTTACAGTTATAATAA
Found at i:135275 original size:4 final size:4
Alignment explanation
Indices: 135266--135293 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
135256 TTCAGGAAAT
135266 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
135294 GGTTATAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:136617 original size:21 final size:20
Alignment explanation
Indices: 136579--136619 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
136569 ATTTAATTGC
* *
136579 TTTAAAATTATTTTTAATTA
1 TTTAAAATTAATTCTAATTA
136599 TTTAAAATTAAATTCTAATTA
1 TTTAAAATT-AATTCTAATTA
136620 AATTATACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTAAAATTAATTCTAATTA
Found at i:136989 original size:13 final size:13
Alignment explanation
Indices: 136968--136998 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
136958 AATTTTTTGA
136968 TTTTA-ATTAAGT
1 TTTTATATTAAGT
136980 TTTTATATTAAGT
1 TTTTATATTAAGT
136993 TTTTAT
1 TTTTAT
136999 CACTAAACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (13 bp):
TTTTATATTAAGT
Found at i:138110 original size:5 final size:5
Alignment explanation
Indices: 138095--138124 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
138085 TAAATTTCCT
138095 TTTTCC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTT-C TTTTC TTTTC TTTTC TTTTC TTTT
138125 AATAAATCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:139013 original size:9 final size:9
Alignment explanation
Indices: 138982--139017 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
138972 TTCAACATGG
138982 TAAGAAGAA
1 TAAGAAGAA
138991 TAAGGAAGAA
1 TAA-GAAGAA
139001 -AAGAAGAA
1 TAAGAAGAA
139009 TAAGAAGAA
1 TAAGAAGAA
139018 GAGGAGTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 6 0.24
9 13 0.52
10 6 0.24
ACGTcount: A:0.67, C:0.00, G:0.25, T:0.08
Consensus pattern (9 bp):
TAAGAAGAA
Found at i:139561 original size:34 final size:34
Alignment explanation
Indices: 139494--139811 Score: 419
Period size: 34 Copynumber: 9.4 Consensus size: 34
139484 TGACCCACAG
* * * *
139494 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTGGCTTACCAT
* * *
139527 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTGGCTTACCAT
* *
139561 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTGGCTTACCAT
* *
139594 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTGGCTTACCAT
*
139628 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTGGCTTACCAT
* *
139662 TGTTGACTAAATGGGAGATTTGGTAGG-TTGCCAT
1 TGTTGATTAAATGGGAGATTTGGT-GGCTTACCAT
* *
139696 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTGGCTTACCAT
*
139730 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTGGCTTACCAT
* *
139764 TGTTGACTAAATGGGAGATTTGGTAGG-TTGCCAT
1 TGTTGATTAAATGGGAGATTTGGT-GGCTTACCAT
139798 TGTTGATTAAATGG
1 TGTTGATTAAATGG
139812 TGGTTTTTAC
Statistics
Matches: 253, Mismatches: 27, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
33 41 0.16
34 208 0.82
35 4 0.02
ACGTcount: A:0.25, C:0.08, G:0.28, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTGGCTTACCAT
Found at i:139729 original size:102 final size:102
Alignment explanation
Indices: 139494--139811 Score: 552
Period size: 102 Copynumber: 3.1 Consensus size: 102
139484 TGACCCACAG
* * * *
139494 TGTTGATTAAATGGTG--ATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 TGTTGATTAAATGG-GAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
* *
139557 CCATTGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
65 CCATTGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
139594 TGTTGATTAAATGGGAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTAC
1 TGTTGATTAAATGGGAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTAC
139659 CATTGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
66 CATTGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
139696 TGTTGATTAAATGGGAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTAC
1 TGTTGATTAAATGGGAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTAC
139761 CATTGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
66 CATTGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
139798 TGTTGATTAAATGG
1 TGTTGATTAAATGG
139812 TGGTTTTTAC
Statistics
Matches: 209, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
99 1 0.00
100 14 0.07
101 59 0.28
102 135 0.65
ACGTcount: A:0.25, C:0.08, G:0.28, T:0.40
Consensus pattern (102 bp):
TGTTGATTAAATGGGAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTAC
CATTGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
Found at i:144291 original size:34 final size:34
Alignment explanation
Indices: 144222--144541 Score: 423
Period size: 34 Copynumber: 9.5 Consensus size: 34
144212 AAGTGGGAGA
* * * *
144222 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTGGCTTACC
* * *
144255 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTGGCTTACC
* *
144289 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTGGCTTACC
* *
144322 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTGGCTTACC
*
144356 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTGGCTTACC
* *
144390 ATTGTTGACTAAATGGGAGATTTGGTAGG-TTGCC
1 ATTGTTGATTAAATGGGAGATTTGGT-GGCTTACC
* *
144424 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTGGCTTACC
*
144458 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTGGCTTACC
* *
144492 ATTGTTGACTAAATGGGAGATTTGGTAGG-TTGCC
1 ATTGTTGATTAAATGGGAGATTTGGT-GGCTTACC
144526 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
144542 TGGTTTTTAC
Statistics
Matches: 255, Mismatches: 27, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
33 43 0.17
34 208 0.82
35 4 0.02
ACGTcount: A:0.25, C:0.08, G:0.28, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTGGCTTACC
Found at i:144459 original size:102 final size:102
Alignment explanation
Indices: 144222--144541 Score: 556
Period size: 102 Copynumber: 3.2 Consensus size: 102
144212 AAGTGGGAGA
* * *
144222 ATTGTTGATTAAATGGTG--ATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTT
1 ATTGTTGATTAAATGG-GAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCT
* * *
144285 TGCCATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
65 TACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
144322 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
144387 ACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
66 ACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
144424 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
144489 ACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
66 ACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
144526 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
144542 TGGTTTTTAC
Statistics
Matches: 211, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
99 1 0.00
100 16 0.08
101 59 0.28
102 135 0.64
ACGTcount: A:0.25, C:0.08, G:0.28, T:0.40
Consensus pattern (102 bp):
ATTGTTGATTAAATGGGAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
ACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
Found at i:145201 original size:2 final size:2
Alignment explanation
Indices: 145194--145218 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
145184 AAATAACAAA
145194 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
145219 GAGGATTTAA
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:147677 original size:20 final size:21
Alignment explanation
Indices: 147652--147699 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
147642 CAAACCCTCA
*
147652 AATTTTTAA-TAATTTTATTT
1 AATTTTTAATTAAATTTATTT
147672 AATTTTTAATTAAATTTA-TT
1 AATTTTTAATTAAATTTATTT
*
147692 AATATTTA
1 AATTTTTA
147700 TTTTTAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AATTTTTAATTAAATTTATTT
Found at i:155915 original size:3 final size:3
Alignment explanation
Indices: 155907--155939 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
155897 ATGAAATTGA
155907 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
155940 TCAAACCCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:156608 original size:22 final size:23
Alignment explanation
Indices: 156580--156628 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
156570 ATTTAATCCC
156580 TTAAAATTATAT-TTT-TTTTCAT
1 TTAAAATTATATCTTTGTTTT-AT
*
156602 TTAAAATTATGTCTTTGTTTTAT
1 TTAAAATTATATCTTTGTTTTAT
156625 TTAA
1 TTAA
156629 GATATTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 11 0.46
23 9 0.38
24 4 0.17
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (23 bp):
TTAAAATTATATCTTTGTTTTAT
Found at i:156627 original size:136 final size:137
Alignment explanation
Indices: 156477--156742 Score: 439
Period size: 136 Copynumber: 1.9 Consensus size: 137
156467 TTTTTGTCTA
* ** *
156477 TCTTTGTTTTATTTAAGATAGTTAACATTATTTAAATATTTGATTAATTCAA-AGAAATTCGAGA
1 TCTTTGTTTTATTTAAGATAGTTAAAATTATTTAAATATTAAATTAATTCAAGAG-AATTCAAGA
*
156541 TATTAATTAATTTAATAAAATTTGACTTTATTTAATCCCTTAAAATTA-TATTT-TTTTTCATTT
65 TATTAATTAATTCAATAAAATTTGACTTTATTTAATCCCTTAAAATTACT-TTTCTTTTTCATTT
156604 AAAATTATG
129 AAAATTATG
*
156613 TCTTTGTTTTATTTAAGATATTTAAAATTATTTAAATATTAAATTAATTCAAGAGAATTCAAGAT
1 TCTTTGTTTTATTTAAGATAGTTAAAATTATTTAAATATTAAATTAATTCAAGAGAATTCAAGAT
156678 ATTAATTAATTCAATAAAATTTGACTTTATTTAATCCCTTAAAATTACTTTTCTTTTTCATTTAA
66 ATTAATTAATTCAATAAAATTTGACTTTATTTAATCCCTTAAAATTACTTTTCTTTTTCATTTAA
156743 TATTCTATAT
Statistics
Matches: 121, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
136 106 0.88
137 15 0.12
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.49
Consensus pattern (137 bp):
TCTTTGTTTTATTTAAGATAGTTAAAATTATTTAAATATTAAATTAATTCAAGAGAATTCAAGAT
ATTAATTAATTCAATAAAATTTGACTTTATTTAATCCCTTAAAATTACTTTTCTTTTTCATTTAA
AATTATG
Done.