Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 94 of 318
Found at i:31253753 original size:27 final size:26
Alignment explanation
Indices: 31253704--31253815 Score: 116
Period size: 27 Copynumber: 4.2 Consensus size: 26
31253694 ATGAAGCGTC
* *
31253704 CTGGTGGCTATGCTACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
31253731 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
* *
31253758 CTGGTGGTTCTACCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
31253786 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
31253812 CTGG
1 CTGG
31253816 CAGCCATGCT
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
26 7 0.10
27 49 0.69
28 15 0.21
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:31262786 original size:218 final size:218
Alignment explanation
Indices: 31262486--31262906 Score: 698
Period size: 218 Copynumber: 1.9 Consensus size: 218
31262476 GGAAAAATAC
* *
31262486 GACATTTTGTAGATTGAAAGAAAGTATAGTGGGAATAAGACTTACAAGGATCCTCCTAGTTTTCT
1 GACATTTCGTAGATTGAAAGAAAGTATAGTGGGAACAAGACTTACAAGGATCCTCCTAGTTTTCT
* * * * * *
31262551 CCTTTATTTGTATTCCTTAGAGGAATGCTTTACCTTTTCATTGCATCTTGTTGCACAATAGGTGT
66 CATTTATTTGCATTCCTTAGAGGAAGGCTTTACCCTTTCATTGCATCTTGTTGCACAAGAGGAGT
*
31262616 TAATTTTTTATCGAATAGCTCCTGGGCAACTATGTAAGACTTCCTGGTGGATATTGACTGGATTT
131 TAATTTTTTATCAAATAGCTCCTGGGCAACTATGTAAGACTTCCTGGTGGATATTGACTGGATTT
31262681 ATTATTTTTTGATAAGAAAGTAG
196 ATTATTTTTTGATAAGAAAGTAG
* * *
31262704 GACATTTCGTAGGTTGAAAGGAAGTATAGTGGGAACAAGACTTACAATGATCCTCCTAGTTTTCT
1 GACATTTCGTAGATTGAAAGAAAGTATAGTGGGAACAAGACTTACAAGGATCCTCCTAGTTTTCT
*
31262769 CATTTCTTTGCATTCCTTAGAGGAAGGCTTTACCCTTTCATTGCATCTTGTTGCACAAGAGGAGT
66 CATTTATTTGCATTCCTTAGAGGAAGGCTTTACCCTTTCATTGCATCTTGTTGCACAAGAGGAGT
* **
31262834 TAATTTTTTATCAAATAGCTCTTGGGCAACTATGTAAGACTTTTTGGTGGATATTGACTGGATTT
131 TAATTTTTTATCAAATAGCTCCTGGGCAACTATGTAAGACTTCCTGGTGGATATTGACTGGATTT
31262899 ATTATTTT
196 ATTATTTT
31262907 CTGACAAAAA
Statistics
Matches: 187, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
218 187 1.00
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (218 bp):
GACATTTCGTAGATTGAAAGAAAGTATAGTGGGAACAAGACTTACAAGGATCCTCCTAGTTTTCT
CATTTATTTGCATTCCTTAGAGGAAGGCTTTACCCTTTCATTGCATCTTGTTGCACAAGAGGAGT
TAATTTTTTATCAAATAGCTCCTGGGCAACTATGTAAGACTTCCTGGTGGATATTGACTGGATTT
ATTATTTTTTGATAAGAAAGTAG
Found at i:31268947 original size:18 final size:18
Alignment explanation
Indices: 31268924--31268960 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
31268914 TTATGGAAAG
31268924 TCTAGGTGGATTTACCCC
1 TCTAGGTGGATTTACCCC
31268942 TCTAGGTGGATTTACCCC
1 TCTAGGTGGATTTACCCC
31268960 T
1 T
31268961 GTAGACTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.27, G:0.22, T:0.35
Consensus pattern (18 bp):
TCTAGGTGGATTTACCCC
Found at i:31270632 original size:21 final size:21
Alignment explanation
Indices: 31270606--31270674 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
31270596 ATTGTTTTGA
31270606 TTACTGAATTGAATTGTGAAG
1 TTACTGAATTGAATTGTGAAG
* *
31270627 TTACTGAA-T--ATTGTTATG
1 TTACTGAATTGAATTGTGAAG
* * *
31270645 TATACTGCATTGAACTGTGAAA
1 T-TACTGAATTGAATTGTGAAG
31270667 TTACTGAA
1 TTACTGAA
31270675 GTAATGAATT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
18 8 0.22
19 6 0.17
20 2 0.06
21 14 0.39
22 6 0.17
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (21 bp):
TTACTGAATTGAATTGTGAAG
Found at i:31270651 original size:40 final size:39
Alignment explanation
Indices: 31270566--31270674 Score: 114
Period size: 40 Copynumber: 2.7 Consensus size: 39
31270556 AATTGAGACT
* * * *
31270566 TATACTGAACTGAATTATGGAA-TATTGAATATTGTTTTG
1 TATACTGAATTGAATTGT-GAATTACTGAATATTGTTATG
31270605 -ATTACTGAATTGAATTGTGAAGTTACTGAATATTGTTATG
1 TA-TACTGAATTGAATTGTGAA-TTACTGAATATTGTTATG
* *
31270645 TATACTGCATTGAACTGTGAAATTACTGAA
1 TATACTGAATTGAATTGTG-AATTACTGAA
31270675 GTAATGAATT
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
38 4 0.07
39 14 0.24
40 38 0.64
41 3 0.05
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.40
Consensus pattern (39 bp):
TATACTGAATTGAATTGTGAATTACTGAATATTGTTATG
Found at i:31270934 original size:51 final size:50
Alignment explanation
Indices: 31270865--31270992 Score: 160
Period size: 45 Copynumber: 2.6 Consensus size: 50
31270855 CAGGCACTTA
31270865 TGTGTCGACA-ACTGTTACTGTTATCGTTACTGTTACTGATTCAACACTTTG
1 TGTGTCGA-ATACTGTTACTGTTA-CGTTACTGTTACTGATTCAACACTTTG
* *
31270916 TGTGTCGAATACTATTACTGTTAC----C-GTTACTGATTCAGCACTTTG
1 TGTGTCGAATACTGTTACTGTTACGTTACTGTTACTGATTCAACACTTTG
*
31270961 TGTGTTGAATACTGTTACTGTTACTGTTACTG
1 TGTGTCGAATACTGTTACTGTTAC-GTTACTG
31270993 CTACCCTTAC
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
45 41 0.62
46 1 0.02
50 3 0.05
51 21 0.32
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (50 bp):
TGTGTCGAATACTGTTACTGTTACGTTACTGTTACTGATTCAACACTTTG
Found at i:31270945 original size:45 final size:45
Alignment explanation
Indices: 31270890--31270992 Score: 170
Period size: 45 Copynumber: 2.3 Consensus size: 45
31270880 TACTGTTATC
31270890 GTTACTGTTACTGATTCAACACTTTGTGTGTCGAATACTATTACT
1 GTTACTGTTACTGATTCAACACTTTGTGTGTCGAATACTATTACT
* * * *
31270935 GTTACCGTTACTGATTCAGCACTTTGTGTGTTGAATACTGTTACT
1 GTTACTGTTACTGATTCAACACTTTGTGTGTCGAATACTATTACT
31270980 GTTACTGTTACTG
1 GTTACTGTTACTG
31270993 CTACCCTTAC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.21, C:0.17, G:0.18, T:0.43
Consensus pattern (45 bp):
GTTACTGTTACTGATTCAACACTTTGTGTGTCGAATACTATTACT
Found at i:31273525 original size:34 final size:34
Alignment explanation
Indices: 31273453--31273526 Score: 112
Period size: 34 Copynumber: 2.2 Consensus size: 34
31273443 GACAGTCTAG
* *
31273453 TATCAGTGTGGGCCTTAGCCCATTACAAAAATAG
1 TATCAGTGTGGGCCTTAGCCCATTACAAAAACAA
**
31273487 TATCAGTGTGGGCCTTAGCCCATTACAGTAACAA
1 TATCAGTGTGGGCCTTAGCCCATTACAAAAACAA
31273521 TATCAG
1 TATCAG
31273527 AAATGCAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (34 bp):
TATCAGTGTGGGCCTTAGCCCATTACAAAAACAA
Found at i:31277067 original size:16 final size:17
Alignment explanation
Indices: 31277046--31277078 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
31277036 CACATTAAAG
31277046 TGTTTT-TTGAAAACCA
1 TGTTTTATTGAAAACCA
31277062 TGTTTTCATTGAAAACC
1 TGTTTT-ATTGAAAACC
31277079 CTTCTTGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (17 bp):
TGTTTTATTGAAAACCA
Found at i:31277773 original size:60 final size:60
Alignment explanation
Indices: 31277701--31277837 Score: 181
Period size: 60 Copynumber: 2.3 Consensus size: 60
31277691 CAAGCTTTAC
*
31277701 TGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCC-ATTAC-AGTATC-AGAGTATAT
1 TGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAG--TCGAGA-TATAT
* *
31277762 TGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACAAGTCGAGATATAT
1 TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGTCGAGATATAT
*
31277822 TGGGCCTTGCCCATAT
1 TGGGCCTAGCCCATAT
31277838 TAACATAGTT
Statistics
Matches: 69, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
60 53 0.77
61 14 0.20
62 2 0.03
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (60 bp):
TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGTCGAGATATAT
Found at i:31277801 original size:28 final size:27
Alignment explanation
Indices: 31277700--31277801 Score: 89
Period size: 28 Copynumber: 3.5 Consensus size: 27
31277690 TCAAGCTTTA
* *
31277700 CTGGGCCTTAGCCCATATCAATATTAAT
1 CTGGGCC-TAGCCCATATCAGTATCAAT
31277728 CTGGGCCATAGCCCAT-TACAGTATCAGAGTAT
1 CTGGGCC-TAGCCCATAT-CAGTATC--A--AT
*
31277760 ATTGGGCCTAGCCCATATCAGTATCAAT
1 -CTGGGCCTAGCCCATATCAGTATCAAT
31277788 CTGGGCCGTAGCCC
1 CTGGGCC-TAGCCC
31277802 TATTACAAGT
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
27 7 0.11
28 28 0.46
30 2 0.03
32 17 0.28
33 7 0.11
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (27 bp):
CTGGGCCTAGCCCATATCAGTATCAAT
Found at i:31279301 original size:14 final size:12
Alignment explanation
Indices: 31279276--31279340 Score: 60
Period size: 14 Copynumber: 5.0 Consensus size: 12
31279266 GCTATAGGGG
31279276 AGAAAAGAAAAACA
1 AGAAAAG-AAAA-A
*
31279290 AGAAGAAGAAAAGT
1 AGAA-AAGAAAA-A
31279304 AGAAGAAGAAAAA
1 AGAA-AAGAAAAA
31279317 ATGAAAA-AAAAA
1 A-GAAAAGAAAAA
31279329 AGAAAAGAAAAA
1 AGAAAAGAAAAA
31279341 TATAAATTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
11 5 0.11
12 11 0.24
13 3 0.07
14 23 0.51
15 3 0.07
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (12 bp):
AGAAAAGAAAAA
Found at i:31280511 original size:3 final size:3
Alignment explanation
Indices: 31280503--31280541 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
31280493 AAACATACTA
*
31280503 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
31280542 TAAAACATCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:31282125 original size:25 final size:25
Alignment explanation
Indices: 31282085--31282134 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
31282075 CTAACATAAT
*
31282085 ATTAACTCCCTCAAACTTATACCTA
1 ATTAACTACCTCAAACTTATACCTA
* *
31282110 ATTAACTACCTTAAACTTATGCCTA
1 ATTAACTACCTCAAACTTATACCTA
31282135 CACCTATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (25 bp):
ATTAACTACCTCAAACTTATACCTA
Found at i:31283841 original size:30 final size:30
Alignment explanation
Indices: 31283805--31283864 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
31283795 TTCCCGAGCC
31283805 TAGGGGCAAAA-GTGTAATTATGCAAAAGTT
1 TAGGGGCAAAATG-GTAATTATGCAAAAGTT
* *
31283835 TAGGGGCAAAATGGTAATTTTGCCAAAGTT
1 TAGGGGCAAAATGGTAATTATGCAAAAGTT
31283865 CTTATTAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATGGTAATTATGCAAAAGTT
Found at i:31284340 original size:47 final size:47
Alignment explanation
Indices: 31284286--31284462 Score: 177
Period size: 47 Copynumber: 3.8 Consensus size: 47
31284276 TGGTTGAACA
* *
31284286 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGTGAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
* * *
31284333 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGT-AACCAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAA--A--CG
* * *
31284380 TTCGAACTCGTTCAGTTGAGTCCGAGTTCACTTATAGAT-TCG-AACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGT-GAAACG
* *
31284426 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
31284463 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 15, Indels: 19
0.76 0.11 0.14
Matches are distributed among these distances:
43 2 0.02
44 5 0.05
45 1 0.01
46 35 0.33
47 55 0.52
48 3 0.03
49 1 0.01
50 4 0.04
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
Found at i:31285412 original size:61 final size:61
Alignment explanation
Indices: 31285317--31285438 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
31285307 TCCCCTGTTC
31285317 CAACTTTAGAAATTTACCATAAATTGTACAAAAATAATTAGGTGGTGTATTTTATATTCTT
1 CAACTTTAGAAATTTACCATAAATTGTACAAAAATAATTAGGTGGTGTATTTTATATTCTT
31285378 CAACTTTAGAAATTTACCATAAATTGTACAAAAATAATTAGGTGGTGTATTTTATATTCTT
1 CAACTTTAGAAATTTACCATAAATTGTACAAAAATAATTAGGTGGTGTATTTTATATTCTT
31285439 GGAATCCTTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (61 bp):
CAACTTTAGAAATTTACCATAAATTGTACAAAAATAATTAGGTGGTGTATTTTATATTCTT
Found at i:31299906 original size:21 final size:20
Alignment explanation
Indices: 31299864--31299936 Score: 51
Period size: 21 Copynumber: 3.5 Consensus size: 20
31299854 TTAATATTTG
*
31299864 AATAATAAT-TTTTAAATAAAA
1 AATAATAATATTTT-TAT-AAA
31299885 AATAATAATATTTTTGATAAA
1 AATAATAATATTTTT-ATAAA
* *
31299906 ATCATAACAATATATTTA-AAA
1 A--ATAATAATATTTTTATAAA
31299927 AATTAATAAT
1 AA-TAATAAT
31299937 TAAACAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
19 1 0.02
20 6 0.14
21 17 0.40
22 7 0.16
23 12 0.28
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (20 bp):
AATAATAATATTTTTATAAA
Found at i:31299912 original size:23 final size:22
Alignment explanation
Indices: 31299864--31299925 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
31299854 TTAATATTTG
31299864 AATAATAAT-TTTTAAATAAAA
1 AATAATAATATTTTAAATAAAA
**
31299885 AATAATAATATTTTTGATAAAA
1 AATAATAATATTTTAAATAAAA
* *
31299907 TCATAACAATATATTTAAA
1 -AATAATAATAT-TTTAAA
31299926 AAATTAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 9 0.28
22 10 0.31
23 9 0.28
24 4 0.12
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (22 bp):
AATAATAATATTTTAAATAAAA
Found at i:31300308 original size:22 final size:21
Alignment explanation
Indices: 31300254--31300311 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 21
31300244 ATATAATTAA
* *
31300254 TTATTTTAATTA-TTAT-ATT
1 TTATTTTATTTATTTATGCTT
31300273 TTATTTTATTTATTTATGCTT
1 TTATTTTATTTATTTATGCTT
*
31300294 TTATTTTTTTCTATTTAT
1 TTATTTTATT-TATTTAT
31300312 TATAATTTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.33
20 4 0.12
21 11 0.33
22 7 0.21
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.72
Consensus pattern (21 bp):
TTATTTTATTTATTTATGCTT
Found at i:31300738 original size:23 final size:24
Alignment explanation
Indices: 31300695--31300740 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
31300685 TATTATTTTA
*
31300695 TGTTAATAATTATTATTTAATTAG
1 TGTTAATAATTATTATCTAATTAG
31300719 TGTT-ATAATTA-TATGCTAATTA
1 TGTTAATAATTATTAT-CTAATTA
31300741 AAAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 13 0.65
24 4 0.20
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.52
Consensus pattern (24 bp):
TGTTAATAATTATTATCTAATTAG
Found at i:31302888 original size:6 final size:6
Alignment explanation
Indices: 31302877--31302919 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
31302867 ATTTAAACAT
*
31302877 TAAATA TAAATA TAAATA TAAATA TAAATA TATATA -AAATA TA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TA
31302920 TTTTAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 4 0.12
6 30 0.88
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATA
Found at i:31310340 original size:17 final size:17
Alignment explanation
Indices: 31310309--31310350 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
31310299 ATTTAAGTTT
*
31310309 TAATTTTTATAAAAAT-
1 TAATTTTAATAAAAATC
*
31310325 TAAATTTTAATTAAAATC
1 T-AATTTTAATAAAAATC
31310343 TAATTTTA
1 TAATTTTA
31310351 TTTATAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 1 0.05
17 20 0.91
18 1 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATTTTAATAAAAATC
Found at i:31312939 original size:29 final size:31
Alignment explanation
Indices: 31312902--31312970 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 31
31312892 AAATTTACTT
* *
31312902 AAAACTACATTTATC-TC-ATATTTAAAATA
1 AAAATTACATATATCATCTATATTTAAAATA
*
31312931 AAAATTACATATATCTATCTATTTTTAAAATA
1 AAAATTACATATATC-ATCTATATTTAAAATA
31312963 AAATATTA
1 AAA-ATTA
31312971 AGTTTTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 13 0.39
31 2 0.06
32 14 0.42
33 4 0.12
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (31 bp):
AAAATTACATATATCATCTATATTTAAAATA
Found at i:31316333 original size:33 final size:33
Alignment explanation
Indices: 31316280--31316348 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
31316270 TTATGAGTCA
*
31316280 GGGATCTCAGACCGGATGTTGGAATCACTTCTT
1 GGGAGCTCAGACCGGATGTTGGAATCACTTCTT
* * *
31316313 GGGAGCTCAGACTGGGTGTTGGAATCACTTGTT
1 GGGAGCTCAGACCGGATGTTGGAATCACTTCTT
31316346 GGG
1 GGG
31316349 TATAGGAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.19, C:0.17, G:0.35, T:0.29
Consensus pattern (33 bp):
GGGAGCTCAGACCGGATGTTGGAATCACTTCTT
Found at i:31317408 original size:22 final size:23
Alignment explanation
Indices: 31317383--31317428 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
31317373 CAACCAAATC
31317383 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
31317405 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
31317428 A
1 A
31317429 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:31317434 original size:23 final size:23
Alignment explanation
Indices: 31317390--31317434 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
31317380 ATCAATTCAA
*
31317390 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
31317413 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
31317435 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:31320801 original size:42 final size:42
Alignment explanation
Indices: 31320743--31320827 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
31320733 TTGTATGATA
31320743 GATAATTAGTGAACAAGTTAAAATTGAACATATATAAATATT
1 GATAATTAGTGAACAAGTTAAAATTGAACATATATAAATATT
31320785 GATAATTAGTGAACAAGTTAAAATTGAACATATATAAATATT
1 GATAATTAGTGAACAAGTTAAAATTGAACATATATAAATATT
31320827 G
1 G
31320828 TTAAATAGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (42 bp):
GATAATTAGTGAACAAGTTAAAATTGAACATATATAAATATT
Found at i:31320878 original size:2 final size:2
Alignment explanation
Indices: 31320873--31320909 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
31320863 ATATATATAT
*
31320873 AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
31320910 TAATGAACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31321245 original size:47 final size:47
Alignment explanation
Indices: 31321191--31321286 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
31321181 GTGACAGCCC
31321191 TAATTTGACCCTATTCGGGAAGTGATTTCGGGACCACAAAACCAAGT
1 TAATTTGACCCTATTCGGGAAGTGATTTCGGGACCACAAAACCAAGT
* * *
31321238 TAATTTGACCCTATTCGGGAAGTGGTTTCGGGACTACAAAACCGAGT
1 TAATTTGACCCTATTCGGGAAGTGATTTCGGGACCACAAAACCAAGT
31321285 TA
1 TA
31321287 TAAAAATAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (47 bp):
TAATTTGACCCTATTCGGGAAGTGATTTCGGGACCACAAAACCAAGT
Found at i:31323859 original size:39 final size:39
Alignment explanation
Indices: 31323802--31323925 Score: 167
Period size: 39 Copynumber: 3.2 Consensus size: 39
31323792 ATTTGATGTG
* *
31323802 TATCCGGACTTAGAGTCCGCAGGCTATGTGTTGGAATTA
1 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
*
31323841 TATCCGGACTTAGGGTCCGCATGCTATGTGCTGGAATTA
1 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
* * * * *
31323880 TATCTGGACTTAAGGTCCACAGGCTACGTGCTGGAAATA
1 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
*
31323919 TGTCCGG
1 TATCCGG
31323926 GCTAAAGTCC
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 74 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (39 bp):
TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
Found at i:31325849 original size:28 final size:28
Alignment explanation
Indices: 31325809--31325869 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
31325799 CTAGTCAGCT
31325809 TAAATAAACGATTGACTACTATTAAAAA
1 TAAATAAACGATTGACTACTATTAAAAA
31325837 TAAATAAACGATTGACTACTATTAAAAA
1 TAAATAAACGATTGACTACTATTAAAAA
31325865 TAAAT
1 TAAAT
31325870 GTAAACTGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.54, C:0.10, G:0.07, T:0.30
Consensus pattern (28 bp):
TAAATAAACGATTGACTACTATTAAAAA
Found at i:31333002 original size:23 final size:22
Alignment explanation
Indices: 31332963--31333007 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
31332953 TATTAAAATA
* * *
31332963 ATAAAATTATATTTTTATTATC
1 ATAAAAATATATATTTAATATC
31332985 ATAAAAATATATAATTTAATATC
1 ATAAAAATATAT-ATTTAATATC
31333008 GTCTTCAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAAAAATATATATTTAATATC
Found at i:31333232 original size:21 final size:21
Alignment explanation
Indices: 31333192--31333232 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
31333182 AAATTTCTTC
*
31333192 AAACTTTTTTTATTAAAATAG
1 AAACTTTGTTTATTAAAATAG
* *
31333213 AAACTTTGTTTCTTACAATA
1 AAACTTTGTTTATTAAAATA
31333233 CTTTAATTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (21 bp):
AAACTTTGTTTATTAAAATAG
Found at i:31333287 original size:15 final size:16
Alignment explanation
Indices: 31333243--31333289 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 16
31333233 CTTTAATTTG
31333243 ATATATTATTTTTTTA
1 ATATATTATTTTTTTA
31333259 ATATATTA-TTTTTTA
1 ATATATTATTTTTTTA
* *
31333274 CT-TGTTATTTTTTTA
1 ATATATTATTTTTTTA
31333289 A
1 A
31333290 AAAAAATTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.15
15 15 0.56
16 8 0.30
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (16 bp):
ATATATTATTTTTTTA
Found at i:31356963 original size:21 final size:21
Alignment explanation
Indices: 31356939--31356978 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31356929 TATGCCTTTA
*
31356939 AAAAT-TTTAATTATATTTAGT
1 AAAATATTTAAATAT-TTTAGT
31356960 AAAATATTTAAATATTTTA
1 AAAATATTTAAATATTTTA
31356979 ATTATATCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (21 bp):
AAAATATTTAAATATTTTAGT
Found at i:31357624 original size:25 final size:25
Alignment explanation
Indices: 31357569--31357624 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
31357559 AGTATACATA
31357569 TTTTTA-AAAAAAATTATTTTCAAT
1 TTTTTAGAAAAAAATTATTTTCAAT
* * *
31357593 TTGTTAGAAAACATTTATTTT-AAT
1 TTTTTAGAAAAAAATTATTTTCAAT
31357617 GTTTTTAG
1 -TTTTTAG
31357625 TATTTTTGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.52
Consensus pattern (25 bp):
TTTTTAGAAAAAAATTATTTTCAAT
Found at i:31359021 original size:11 final size:11
Alignment explanation
Indices: 31359005--31359038 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
31358995 CGCATCTAGT
31359005 TTTGTTCTTGA
1 TTTGTTCTTGA
*
31359016 TTTGTTCTTAA
1 TTTGTTCTTGA
*
31359027 TTTATTCTTGA
1 TTTGTTCTTGA
31359038 T
1 T
31359039 GATTTGACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.15, C:0.09, G:0.12, T:0.65
Consensus pattern (11 bp):
TTTGTTCTTGA
Found at i:31365438 original size:2 final size:2
Alignment explanation
Indices: 31365431--31365459 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31365421 CATAGTTGCA
31365431 AT AT 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 AT AT A
31365460 ACGCAGAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31367288 original size:24 final size:24
Alignment explanation
Indices: 31367256--31367302 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
31367246 CTGTCAGGAG
**
31367256 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGCAGATAAGGGAT
31367280 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGCAGATAAGGGA
31367303 GGAAATCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.38, T:0.23
Consensus pattern (24 bp):
AGGATTTAGGAGCAGATAAGGGAT
Found at i:31368764 original size:28 final size:26
Alignment explanation
Indices: 31368723--31368835 Score: 109
Period size: 27 Copynumber: 4.2 Consensus size: 26
31368713 AGGAAGCGTC
*
31368723 CTGGTGGCTATGCCACAAATTATCTGAT
1 CTGGTGGCTCTGCCAC--ATTATCTGAT
* *
31368751 CTGGTGGCTCTGCCACATATACCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
* *
31368778 CTGGTGGTTCTGCCACGATTATCTCTAT
1 CTGGTGGCTCTGCCAC-ATTATCT-GAT
* * *
31368806 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
31368832 CTGG
1 CTGG
31368836 CAGCCATGCT
Statistics
Matches: 70, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
26 7 0.10
27 32 0.46
28 31 0.44
ACGTcount: A:0.17, C:0.25, G:0.22, T:0.36
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:31368808 original size:55 final size:54
Alignment explanation
Indices: 31368723--31368835 Score: 138
Period size: 55 Copynumber: 2.1 Consensus size: 54
31368713 AGGAAGCGTC
*
31368723 CTGGTGGCTATGCCACAAATTATCTGATCTGGTGGCTCTGCCACATATACCTGTT
1 CTGGTGGCTATGCCACAAATTATCTGATCTGGTGACTCTGCCACAT-TACCTGTT
* * * * * *
31368778 CTGGTGGTTCTGCCAC-GATTATCTCTATCTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTATGCCACAAATTATCT-GATCTGGTGACTCTGCCACATTACCTGTT
31368832 CTGG
1 CTGG
31368836 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
54 18 0.36
55 32 0.64
ACGTcount: A:0.17, C:0.25, G:0.22, T:0.36
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAAATTATCTGATCTGGTGACTCTGCCACATTACCTGTT
Found at i:31372267 original size:40 final size:40
Alignment explanation
Indices: 31372140--31372289 Score: 169
Period size: 40 Copynumber: 3.7 Consensus size: 40
31372130 ATTATGTTTG
* * * *
31372140 GCACTTAGTGTGCGTATTGAGATAACTTCGGCTATATAAA
1 GCACTTAGTGTGCGAATCGAGATAGCTTCAGCTATATAAA
* * * *
31372180 GCACTTAATGTACGTATCGAGATAGCTGCAGCTATATAAA
1 GCACTTAGTGTGCGAATCGAGATAGCTTCAGCTATATAAA
**
31372220 GCACTTAGTGTGCGAATCG-GAATAGCTTCAGCTATATATG
1 GCACTTAGTGTGCGAATCGAG-ATAGCTTCAGCTATATAAA
31372260 GCACTTAGTGTGCGAGA-CTGAGATAGCTTC
1 GCACTTAGTGTGCGA-ATC-GAGATAGCTTC
31372290 GACTGTGAAA
Statistics
Matches: 94, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.01
40 82 0.87
41 10 0.11
42 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (40 bp):
GCACTTAGTGTGCGAATCGAGATAGCTTCAGCTATATAAA
Found at i:31374074 original size:19 final size:20
Alignment explanation
Indices: 31374021--31374075 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
31374011 TTTGTAACCA
31374021 ATTAGTTTAGGAAAAACCTTC
1 ATTA-TTTAGGAAAAACCTTC
*
31374042 ATTATTTATG-AAAACCTT-
1 ATTATTTAGGAAAAACCTTC
31374060 AGTT-TTTAGGAAAAAC
1 A-TTATTTAGGAAAAAC
31374076 TTGATTTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 6 0.20
19 15 0.50
20 5 0.17
21 4 0.13
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (20 bp):
ATTATTTAGGAAAAACCTTC
Found at i:31389595 original size:26 final size:26
Alignment explanation
Indices: 31389559--31389611 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
31389549 CAAACATGGT
31389559 TCGTTTATAACACATTTGTTCTTTGC
1 TCGTTTATAACACATTTGTTCTTTGC
31389585 TCGTTTATAACACATTTGTTCTTTGC
1 TCGTTTATAACACATTTGTTCTTTGC
31389611 T
1 T
31389612 GACAAGCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.51
Consensus pattern (26 bp):
TCGTTTATAACACATTTGTTCTTTGC
Found at i:31392676 original size:46 final size:46
Alignment explanation
Indices: 31392589--31392760 Score: 172
Period size: 46 Copynumber: 3.7 Consensus size: 46
31392579 GAGGTAGGAT
* * *
31392589 GCCGATGCCATGTCCTAGACATGGTCTTAAACTGGC-TCATCTCGTA-
1 GCCGATGCCATGTCCCAGACAT-GTCTTACACTAGCTTCATCTCG-AG
* *
31392635 GCCGATG-CATGTCCAAGACACGTCTTACACTAGCTTACATCTCGAG
1 GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTT-CATCTCGAG
* * * * * *
31392681 GCCAATG-CATGTCCCAGATATGCCTTACACTAGCTCTCGTCTCAAT
1 GCCGATGCCATGTCCCAGACATGTCTTACACTAGCT-TCATCTCGAG
*
31392727 GCTGATGCCATGTCCCAGACATGTCTTACACTAG
1 GCCGATGCCATGTCCCAGACATGTCTTACACTAG
31392761 GTCACAATAA
Statistics
Matches: 105, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
44 11 0.10
45 14 0.13
46 55 0.52
47 25 0.24
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (46 bp):
GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTTCATCTCGAG
Found at i:31396888 original size:19 final size:19
Alignment explanation
Indices: 31396864--31396901 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
31396854 CATTTCTTTA
31396864 TTATCAGCCTAAGAAAATG
1 TTATCAGCCTAAGAAAATG
*
31396883 TTATCAGCCTTAGAAAATG
1 TTATCAGCCTAAGAAAATG
31396902 ATTTCTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (19 bp):
TTATCAGCCTAAGAAAATG
Found at i:31405720 original size:24 final size:24
Alignment explanation
Indices: 31405643--31405708 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 24
31405633 ATTTTTTTAA
* *
31405643 TTCTTTATTTTCTTTTACATTATTTTC
1 TTCTTTATTTT-TCTTAC-TT-TTTCC
31405670 TCTCTTTATTTTTCTTACTTTTTCC
1 T-TCTTTATTTTTCTTACTTTTTCC
31405695 TTCTTT-TTTTTCTT
1 TTCTTTATTTTTCTT
31405709 GTTTTCTTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
23 8 0.22
24 5 0.14
25 5 0.14
26 2 0.06
27 6 0.17
28 10 0.28
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (24 bp):
TTCTTTATTTTTCTTACTTTTTCC
Found at i:31410728 original size:60 final size:62
Alignment explanation
Indices: 31410658--31410777 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 62
31410648 TATCTCGACT
*
31410658 TGTAATGGGGCTACGGCCCAGATTGATACTGACATGGGCT-AGGCCCAG-TATACTCTGATAC
1 TGTAATGGGGCTACGGCCCAGATTAATACTGACATGGGCTAAGGCCCAGTTA-ACTCTGATAC
* * * *
31410719 TGTAA-GGGGCTATGGCCCAGATTAATATTTATATGGGCTAAGGCCCAGTTAACTCTGAT
1 TGTAATGGGGCTACGGCCCAGATTAATACTGACATGGGCTAAGGCCCAGTTAACTCTGAT
31410778 TTCTGAATAG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
60 29 0.56
61 21 0.40
62 2 0.04
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.28
Consensus pattern (62 bp):
TGTAATGGGGCTACGGCCCAGATTAATACTGACATGGGCTAAGGCCCAGTTAACTCTGATAC
Found at i:31411049 original size:9 final size:10
Alignment explanation
Indices: 31411027--31411051 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
31411017 AATAAGGCCG
31411027 TTTTAATTAT
1 TTTTAATTAT
31411037 TTTTAATTAT
1 TTTTAATTAT
31411047 TTTTA
1 TTTTA
31411052 GTATGTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTAATTAT
Found at i:31412824 original size:8 final size:8
Alignment explanation
Indices: 31412811--31412883 Score: 53
Period size: 8 Copynumber: 8.6 Consensus size: 8
31412801 TTATGTTTAA
31412811 TATATTAT
1 TATATTAT
31412819 TATATTAT
1 TATATTAT
31412827 TATATAATAT
1 TATAT--TAT
*
31412837 AGATATT-T
1 -TATATTAT
31412845 TATATT-T
1 TATATTAT
31412852 TA-ATTAT
1 TATATTAT
31412859 AATATATTACAT
1 --TATATT--AT
31412871 TATATTAT
1 TATATTAT
31412879 TATAT
1 TATAT
31412884 ATATAAACTA
Statistics
Matches: 54, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
6 3 0.06
7 9 0.17
8 21 0.39
9 3 0.06
10 12 0.22
11 4 0.07
12 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (8 bp):
TATATTAT
Found at i:31420787 original size:25 final size:24
Alignment explanation
Indices: 31420753--31420818 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 24
31420743 AGAATAAACT
* * *
31420753 ATATACATAATAGATTTGAAAGGAA
1 ATATATATAATAAATTT-AAAAGAA
31420778 ATATATATAAATAAATTTAAAAGAA
1 ATATATAT-AATAAATTTAAAAGAA
* *
31420803 ATTTTATATAAAAAAT
1 A-TATATATAATAAAT
31420819 AACAACGGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
25 20 0.59
26 14 0.41
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.33
Consensus pattern (24 bp):
ATATATATAATAAATTTAAAAGAA
Found at i:31420800 original size:26 final size:26
Alignment explanation
Indices: 31420752--31420818 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
31420742 AAGAATAAAC
* * *
31420752 TATATACATAATAGATTTGAAAGGAAA-
1 TATATATA-AATAAATTT-AAAAGAAAT
31420779 TATATATAAATAAATTTAAAAGAAAT
1 TATATATAAATAAATTTAAAAGAAAT
*
31420805 TTTATATAAA-AAAT
1 TATATATAAATAAAT
31420819 AACAACGGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 11 0.31
26 17 0.49
27 7 0.20
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.34
Consensus pattern (26 bp):
TATATATAAATAAATTTAAAAGAAAT
Found at i:31426138 original size:19 final size:20
Alignment explanation
Indices: 31426114--31426153 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
31426104 AATCTTCGAG
31426114 GATATGCAATCTTAG-ATAT
1 GATATGCAATCTTAGAATAT
*
31426133 GATATGTAATCTTAGAATAT
1 GATATGCAATCTTAGAATAT
31426153 G
1 G
31426154 GGATTTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (20 bp):
GATATGCAATCTTAGAATAT
Found at i:31432887 original size:16 final size:16
Alignment explanation
Indices: 31432858--31432900 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
31432848 TGAAAGTTGT
*
31432858 AAGAA-AGGGAGAA-G
1 AAGAAGAGGGGGAAGG
31432872 AATGAAGAGGGGGAAGG
1 AA-GAAGAGGGGGAAGG
31432889 AAGAAGAGGGGG
1 AAGAAGAGGGGG
31432901 CTTAAAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 2 0.08
15 3 0.12
16 17 0.68
17 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.51, T:0.02
Consensus pattern (16 bp):
AAGAAGAGGGGGAAGG
Found at i:31434372 original size:20 final size:21
Alignment explanation
Indices: 31434329--31434372 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
31434319 ATTACAATTG
* **
31434329 TATTTTATTATTATAAAACTT
1 TATTTTATAATTATAAAAAAT
31434350 TATTTTATAATT-TAAAAAAT
1 TATTTTATAATTATAAAAAAT
31434370 TAT
1 TAT
31434373 ATAGATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTTTATAATTATAAAAAAT
Found at i:31438609 original size:31 final size:32
Alignment explanation
Indices: 31438574--31438641 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 32
31438564 CCAACTTAAG
* *
31438574 AAAAAGTGTCAAGTTTAGGTATCAAATTAGA-
1 AAAAAGTGTCAAGTTTAGGTACCAAATAAGAC
*
31438605 AAAAATTGTCAAGTTTAGGTACCAAATAAGAC
1 AAAAAGTGTCAAGTTTAGGTACCAAATAAGAC
31438637 AAAAA
1 AAAAA
31438642 AAAATTTAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 28 0.85
32 5 0.15
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.25
Consensus pattern (32 bp):
AAAAAGTGTCAAGTTTAGGTACCAAATAAGAC
Found at i:31445405 original size:3 final size:3
Alignment explanation
Indices: 31445399--31445445 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
31445389 TATTATTATT
31445399 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
31445446 TATTATTGAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:31445597 original size:8 final size:8
Alignment explanation
Indices: 31445580--31445612 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
31445570 TTGTTTTTTA
*
31445580 TTTTATTT
1 TTTTAATT
31445588 TTTTAATT
1 TTTTAATT
31445596 TTTTAATT
1 TTTTAATT
31445604 TTTT-ATT
1 TTTTAATT
31445611 TT
1 TT
31445613 CAACTTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
7 5 0.21
8 19 0.79
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTAATT
Found at i:31445599 original size:16 final size:16
Alignment explanation
Indices: 31445566--31445612 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
31445556 TTGCGATTTA
31445566 TAATTTGTTT-TTTATTT
1 TAATTT-TTTATTT-TTT
* *
31445583 TATTTTTTTAATTTTT
1 TAATTTTTTATTTTTT
31445599 TAATTTTTTATTTT
1 TAATTTTTTATTTT
31445613 CAACTTTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (16 bp):
TAATTTTTTATTTTTT
Found at i:31454419 original size:47 final size:47
Alignment explanation
Indices: 31454341--31454594 Score: 366
Period size: 47 Copynumber: 5.3 Consensus size: 47
31454331 CCCTTCGGGA
* * *
31454341 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTT-GGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCA-TTAGGC
* * *
31454388 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
31454435 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
31454482 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
31454531 CTTATCACATATATATACACTTTCACATTCATCATATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTAGGC
31454580 CTTATCACATATATA
1 CTTATCACATATATA
31454595 TAATGGCCTT
Statistics
Matches: 193, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
46 2 0.01
47 98 0.51
49 93 0.48
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:31454515 original size:49 final size:49
Alignment explanation
Indices: 31454341--31455197 Score: 1041
Period size: 49 Copynumber: 17.2 Consensus size: 49
31454331 CCCTTCGGGA
* * *
31454341 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTT-GGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCA-TTCGGC
* * *
31454388 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
*
31454435 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
*
31454482 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
* *
31454531 CTTATCACATATATATACACTTTCACATTCATCATATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
**
31454580 CTTATCACATATATATA-ATGGCCTTATCACATATATATACACTTTCACATTCATCACATT-GGC
1 CTTATCACATATATATACA----CTT-TCAC----AT-T-CA---TCACA-TCGGC-CATTCGGC
* * * * * * *
31454643 CAT-TCGGCCTTATCACATATA-TATACACTTTCA-CATTCATC-G-CATT-GGC
1 CTTATC--ACATAT-ATATACACT-TTCACATTCATCA--CATCGGCCATTCGGC
*
31454692 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
*
31454739 CTTATCACATATATATACACTTTCACATTCATCACATGGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
*
31454788 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGG--------C
*
31454845 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
* *
31454894 CTTATCTCATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
31454943 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
31454992 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
*
31455041 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
* *
31455090 CTTATCAC--ATATGTACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
*
31455137 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
31455186 CTTATCACATAT
1 CTTATCACATAT
31455198 CACATTGGCC
Statistics
Matches: 722, Mismatches: 42, Indels: 90
0.85 0.05 0.11
Matches are distributed among these distances:
44 4 0.01
45 14 0.02
46 12 0.02
47 144 0.20
48 2 0.00
49 442 0.61
50 2 0.00
51 2 0.00
52 5 0.01
53 6 0.01
55 2 0.00
56 1 0.00
57 52 0.07
58 1 0.00
59 2 0.00
61 4 0.01
62 7 0.01
63 7 0.01
64 8 0.01
65 4 0.01
66 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.34
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
Found at i:31454602 original size:22 final size:22
Alignment explanation
Indices: 31454577--31454618 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
31454567 TTGGCCATTC
31454577 GGCCTTATCACATATATATAAT
1 GGCCTTATCACATATATATAAT
31454599 GGCCTTATCACATATATATA
1 GGCCTTATCACATATATATA
31454619 CACTTTCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (22 bp):
GGCCTTATCACATATATATAAT
Found at i:31454664 original size:71 final size:71
Alignment explanation
Indices: 31454528--31454667 Score: 271
Period size: 71 Copynumber: 2.0 Consensus size: 71
31454518 TTGGCCATTC
*
31454528 GGCCTTATCACATATATATACACTTTCACATTCATCATATTGGCCATTCGGCCTTATCACATATA
1 GGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATA
31454593 TATAAT
66 TATAAT
31454599 GGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATA
1 GGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATA
31454664 TATA
66 TATA
31454668 CACTTTCACA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.36
Consensus pattern (71 bp):
GGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATA
TATAAT
Found at i:31454881 original size:27 final size:27
Alignment explanation
Indices: 31454791--31454881 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 27
31454781 ATTCGGCCTT
31454791 ATCACATATATATACACTTTCACATTC
1 ATCACATATATATACACTTTCACATTC
** * * *
31454818 ATCACAT-TGGCCATTCGGCCTTATCACCTT-
1 ATCACATAT--ATATAC--ACTT-TCACATTC
31454848 ATCACATATATATACACTTTCACATTC
1 ATCACATATATATACACTTTCACATTC
31454875 ATCACAT
1 ATCACAT
31454882 TGGCCATTCG
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
26 7 0.15
27 17 0.36
28 3 0.06
29 3 0.06
30 10 0.21
31 7 0.15
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (27 bp):
ATCACATATATATACACTTTCACATTC
Found at i:31455200 original size:78 final size:78
Alignment explanation
Indices: 31455118--31455275 Score: 298
Period size: 78 Copynumber: 2.0 Consensus size: 78
31455108 TTTCACATTC
31455118 ATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTC
1 ATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTC
31455183 GGCCTTATCACAT
66 GGCCTTATCACAT
* *
31455196 ATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTC
1 ATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTC
31455261 GGCCTTATCACAT
66 GGCCTTATCACAT
31455274 AT
1 AT
31455276 ATACACTTTC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.33
Consensus pattern (78 bp):
ATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTC
GGCCTTATCACAT
Found at i:31455203 original size:29 final size:29
Alignment explanation
Indices: 31455167--31455226 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
31455157 TTTCACATTC
31455167 ATCACATTGGCCATTCGGCCTTATCACAT
1 ATCACATTGGCCATTCGGCCTTATCACAT
31455196 ATCACATTGGCCATTCGGCCTTATCACAT
1 ATCACATTGGCCATTCGGCCTTATCACAT
31455225 AT
1 AT
31455227 ATATACACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.25, C:0.30, G:0.13, T:0.32
Consensus pattern (29 bp):
ATCACATTGGCCATTCGGCCTTATCACAT
Found at i:31455211 original size:125 final size:124
Alignment explanation
Indices: 31455071--31455322 Score: 425
Period size: 125 Copynumber: 2.0 Consensus size: 124
31455061 TTTCACATTC
*
31455071 ATCACATTGGCCATTCGGCCTTATCAC-ATATGTACACTTTCACATTCATCACATCGGCCATTAG
1 ATCACATTGGCCATTCGGCCTTATCACAATATATACACTTTCACATTCATCACATCGGCCATTAG
* *
31455135 GCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACAT
66 GCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
* *
31455196 ATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTC
1 ATCACATTGGCCATTCGGCCTTATCACA-ATATATACACTTTCACATTCATCACATCGGCCATTA
31455261 GGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
65 GGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
31455321 AT
1 AT
31455323 ATATACACTT
Statistics
Matches: 120, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
125 76 0.63
127 44 0.37
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.33
Consensus pattern (124 bp):
ATCACATTGGCCATTCGGCCTTATCACAATATATACACTTTCACATTCATCACATCGGCCATTAG
GCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
Found at i:31455234 original size:174 final size:174
Alignment explanation
Indices: 31454844--31455371 Score: 727
Period size: 174 Copynumber: 2.9 Consensus size: 174
31454834 GGCCTTATCA
*
31454844 CCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATA
1 CCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTA--TCACATATA
31454909 TACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
64 TACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCA
* * * *
31454974 TCACATCGGCCATTCGGCCTTATCACATATATATACACTTTC-ACATTCATCACATCGG
129 TCACATTGGCCATTAGGCCTTATCAC----ATAT-CAC-ATCGGC---CAT----TCGG
* * *
31455032 CCAT-TCGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATC
1 CCTTATC--AC--AT-AT----ATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATC
*
31455096 ACATATGTACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTC
57 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTC
* *
31455161 ACATTCATCACATTGGCCATTCGGCCTTATCACATATCACATTGGCCATTCGG
122 ACATTCATCACATTGGCCATTAGGCCTTATCACATATCACATCGGCCATTCGG
31455214 CCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATA
1 CCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATA
31455279 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATC
66 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATC
31455344 ACATTGGCCATTAGGCCTTATCACATAT
131 ACATTGGCCATTAGGCCTTATCACATAT
31455372 ATATACACTT
Statistics
Matches: 315, Mismatches: 14, Indels: 36
0.86 0.04 0.10
Matches are distributed among these distances:
174 143 0.45
178 1 0.00
179 2 0.01
181 1 0.00
182 7 0.02
183 2 0.01
186 3 0.01
187 2 0.01
188 4 0.01
189 5 0.02
190 4 0.01
191 2 0.01
192 1 0.00
194 97 0.31
196 41 0.13
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.34
Consensus pattern (174 bp):
CCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATA
CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATC
ACATTGGCCATTAGGCCTTATCACATATCACATCGGCCATTCGG
Found at i:31455251 original size:49 final size:49
Alignment explanation
Indices: 31455196--31455388 Score: 345
Period size: 49 Copynumber: 4.0 Consensus size: 49
31455186 CTTATCACAT
*
31455196 ATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTC
1 ATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTC
*
31455245 ATCACATTGGCCATTCGGCCTTATCAC--ATATATACACTTTCACATTC
1 ATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTC
*
31455292 ATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTC
1 ATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTC
31455341 ATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATT
1 ATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATT
31455389 TATTCAAATA
Statistics
Matches: 139, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
47 45 0.32
49 94 0.68
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (49 bp):
ATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTC
Found at i:31455304 original size:96 final size:97
Alignment explanation
Indices: 31455196--31455388 Score: 343
Period size: 96 Copynumber: 2.0 Consensus size: 97
31455186 CTTATCACAT
* * *
31455196 ATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTC
1 ATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTA
31455261 GGCCTTATCAC-ATATATACACTTTCACATTC
66 GGCCTTATCACAATATATACACTTTCACATTC
31455292 ATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTA
1 ATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTA
31455357 GGCCTTATCACATATATATACACTTTCACATT
66 GGCCTTATCACA-ATATATACACTTTCACATT
31455389 TATTCAAATA
Statistics
Matches: 92, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
96 73 0.79
98 19 0.21
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (97 bp):
ATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTA
GGCCTTATCACAATATATACACTTTCACATTC
Found at i:31460606 original size:50 final size:50
Alignment explanation
Indices: 31460552--31460654 Score: 152
Period size: 50 Copynumber: 2.1 Consensus size: 50
31460542 AGTGGGACGG
*
31460552 ATTGAAGTTATAATGGCAAATCTTATCTCCCTAAAGTTGTAGTAGAGCAT
1 ATTGAAGTTATAATGGCAAATCTTATCTCCCTAAAGTTGCAGTAGAGCAT
* * * * *
31460602 ATTGAAGTTATCATGGCGAATCTTATCTCCCTGAAGTTGCATTGGAGCAT
1 ATTGAAGTTATAATGGCAAATCTTATCTCCCTAAAGTTGCAGTAGAGCAT
31460652 ATT
1 ATT
31460655 AAAGCCACTA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (50 bp):
ATTGAAGTTATAATGGCAAATCTTATCTCCCTAAAGTTGCAGTAGAGCAT
Found at i:31460683 original size:44 final size:44
Alignment explanation
Indices: 31460620--31461217 Score: 278
Period size: 44 Copynumber: 13.1 Consensus size: 44
31460610 TATCATGGCG
* * *
31460620 AATCTTATCTCCCTGAAGTTGCATTGGAGCATATTAAAGCCACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA
* * * **
31460664 AATCTCATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTATCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-CA
** * *
31460709 TGGTGAATCTTATCTCTTTGAAGTTGCAGTGGAGTAGGTTAAAGCCACA
1 -----AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA
* * *
31460758 AATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTGAAGCCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA
* ** * * * *
31460802 AATCTTATCTCCCTAAAGTTATAATAGAGCTGATTGAAGTTATCACAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AA---AGC-CA-CA
* *
31460852 AATCTTATCTCCTTGGAGTTGCAGTGGAGCAGATTGAAA-CCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCCACA
* * * * * *
31460896 AAACTTATCTCCC-AAAGTTGTAGTGGGATGGATTGAAATTATTAAG--GCG
1 AATCTTATCTCCCTGAAGTTGCAGT-GGA-GCA--G--ATTA--AAGCCACA
* * *
31460945 AATCTTATCTCCTTGAAGTTGCAGTGGAACAGATTGAAA-CCATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCCACA
* * *
31460989 AATCTTATCTCCCTGAAGTTGCAGTGG-G-ATGGATTAAAATCATTAAAGCG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCA--GATT-AAAGC----CA-CA
* * *** * ** * *
31461039 AATCTTATATCCCTGAAATAATAGTAGAATAGATTAAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA
* * * ** *
31461083 AA-CTTTATCTTCTTGAAGATGCAGTGGAGCAGGA-TAAAGTTACT
1 AATC-TTATCTCCCTGAAGTTGCAGTGGAGCA-GATTAAAGCCACA
* * * * * *
31461127 AATCTTATCTCCTTGAAGATACAGTGGAGCAAATTAAGGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA
* * * * *
31461171 AATCTTATCTACTTGAAGTTGCAGTAGAGCAGGTTAAAGCGACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA
31461215 AAT
1 AAT
31461218 TATATACCTT
Statistics
Matches: 415, Mismatches: 100, Indels: 78
0.70 0.17 0.13
Matches are distributed among these distances:
42 1 0.00
43 12 0.03
44 251 0.60
45 12 0.03
46 2 0.00
47 2 0.00
48 4 0.01
49 27 0.07
50 103 0.25
52 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA
Found at i:31460700 original size:94 final size:94
Alignment explanation
Indices: 31460568--31460796 Score: 314
Period size: 94 Copynumber: 2.4 Consensus size: 94
31460558 GTTATAATGG
* * * *
31460568 CAAATCTTATCTCCCTAAAGTTGTAGTAGAGCATATTGAAGTTATCATGGCGAATCTTATCTCCC
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGTTATCATGGCGAATCTTATCTCCC
* *
31460633 TGAAGTTGCATTGGAGCATATTAAAGCCA
66 TGAAGTTGCAGTGGAGCAGATTAAAGCCA
* * * * * **
31460662 CTAATCTCATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTATCATGGTGAATCTTATCTCTT
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGTTATCATGGCGAATCTTATCTCCC
* *
31460727 TGAAGTTGCAGTGGAGTAGGTTAAAGCCA
66 TGAAGTTGCAGTGGAGCAGATTAAAGCCA
*
31460756 CAAATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTGAAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAG
31460797 CCACAAATCT
Statistics
Matches: 116, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
94 116 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (94 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGTTATCATGGCGAATCTTATCTCCC
TGAAGTTGCAGTGGAGCAGATTAAAGCCA
Found at i:31460739 original size:50 final size:50
Alignment explanation
Indices: 31460551--31461015 Score: 249
Period size: 44 Copynumber: 9.9 Consensus size: 50
31460541 TAGTGGGACG
* * * * *
31460551 GATTGAAGTTATAATGGCAAATCTTATCTCCCTAAAGTTGTAGTAGAGCA
1 GATTGAAGTTATCATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* *
31460601 TATTGAAGTTATCATGGCGAATCTTATCTCCCTGAAGTTGCATTGGAGCA
1 GATTGAAGTTATCATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* * * * * *
31460651 TATTAAAG---CCA---CTAATCTCATCTCCCTGAAGTTGCAGTGGAGTA
1 GATTGAAGTTATCATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* ** *
31460695 GATTGAAGTTATCATGGTGAATCTTATCTCTTTGAAGTTGCAGTGGAGTA
1 GATTGAAGTTATCATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* * * * *
31460745 GGTTAAAG---CCA---CAAATCTTATCTCCCTGAAGTTGCAATGGAGCA
1 GATTGAAGTTATCATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* * * * ** * * *
31460789 AATTGAAG---CCA---CAAATCTTATCTCCCTAAAGTTATAATAGAGCT
1 GATTGAAGTTATCATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
** * * *
31460833 GATTGAAGTTATCACAGCAAATCTTATCTCCTTGGAGTTGCAGTGGAGCA
1 GATTGAAGTTATCATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* * * * *
31460883 GATTGAA---ACCA---CAAAACTTATCTCCC-AAAGTTGTAGTGG-G-A
1 GATTGAAGTTATCATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* * * * *
31460924 TGGATTGAAATTATTAAGGCGAATCTTATCTCCTTGAAGTTGCAGTGGAACA
1 --GATTGAAGTTATCATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* *
31460976 GATTGAA---ACCAT---AAATCTTATCTCCCTGAAGTTGCAGTGG
1 GATTGAAGTTATCATGGCGAATCTTATCTCCCTGAAGTTGCAGTGG
31461016 GATGGATTAA
Statistics
Matches: 325, Mismatches: 67, Indels: 52
0.73 0.15 0.12
Matches are distributed among these distances:
41 1 0.00
42 1 0.00
43 17 0.05
44 144 0.44
46 2 0.01
47 13 0.04
49 12 0.04
50 134 0.41
52 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (50 bp):
GATTGAAGTTATCATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
Found at i:31460812 original size:138 final size:138
Alignment explanation
Indices: 31460620--31460908 Score: 375
Period size: 138 Copynumber: 2.1 Consensus size: 138
31460610 TATCATGGCG
* * * * *
31460620 AATCTTATCTCCCTGAAGTTGCATTGGAGCATATTAAAGCCACTAATCTCATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTAAAGCCACAAATCTCATCTCCCTAAAGTTA
* * ** ** * * *
31460685 CAGTGGAG-TAGATTGAAGTTATCATGGTGAATCTTATCTCTTTGAAGTTGCAGTGGAGTAGGTT
66 CAATAGAGCT-GATTGAAGTTATCACAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATT
31460749 -AAAGCCACA
130 GAAA-CCACA
* *
31460758 AATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTGAAGCCACAAATCTTATCTCCCTAAAGTTA
1 AATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTAAAGCCACAAATCTCATCTCCCTAAAGTTA
* *
31460823 TAATAGAGCTGATTGAAGTTATCACAGCAAATCTTATCTCCTTGGAGTTGCAGTGGAGCAGATTG
66 CAATAGAGCTGATTGAAGTTATCACAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTG
31460888 AAACCACA
131 AAACCACA
*
31460896 AAACTTATCTCCC
1 AATCTTATCTCCC
31460909 AAAGTTGTAG
Statistics
Matches: 130, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
138 126 0.97
139 4 0.03
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (138 bp):
AATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTAAAGCCACAAATCTCATCTCCCTAAAGTTA
CAATAGAGCTGATTGAAGTTATCACAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTG
AAACCACA
Found at i:31460854 original size:94 final size:94
Alignment explanation
Indices: 31460756--31461008 Score: 323
Period size: 93 Copynumber: 2.7 Consensus size: 94
31460746 GTTAAAGCCA
* * * *
31460756 CAAATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTGAAGCCACAAATCTTATCTCCCTAAAGT
1 CAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACCACAAATCTTATCTCCCTAAAGT
* *
31460821 TATAATAGAGCT-GATTGAAGTTATCACA-G
66 TATAAT-GAGATGGATTGAAATTATCA-AGG
* *
31460850 CAAATCTTATCTCCTTGGAGTTGCAGTGGAGCAGATTGAAACCACAAAACTTATCTCCC-AAAGT
1 CAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACCACAAATCTTATCTCCCTAAAGT
* * * *
31460914 TGTAGTGGGATGGATTGAAATTATTAAGG
66 TATAATGAGATGGATTGAAATTATCAAGG
* * * *
31460943 CGAATCTTATCTCCTTGAAGTTGCAGTGGAACAGATTGAAACCATAAATCTTATCTCCCTGAAGT
1 CAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACCACAAATCTTATCTCCCTAAAGT
31461008 T
66 T
31461009 GCAGTGGGAT
Statistics
Matches: 138, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
92 4 0.03
93 76 0.55
94 58 0.42
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (94 bp):
CAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACCACAAATCTTATCTCCCTAAAGT
TATAATGAGATGGATTGAAATTATCAAGG
Found at i:31461073 original size:94 final size:93
Alignment explanation
Indices: 31460881--31461109 Score: 246
Period size: 94 Copynumber: 2.4 Consensus size: 93
31460871 TGCAGTGGAG
* * * * * *
31460881 CAGATTGAAACCACAAAACTTATCTCCC-AAAGTTGTAGTGGGATGGATTGAAATTATTAAGGCG
1 CAGATTGAAACCA-TAAACTTATCTCCCTGAAGTTGCAGTGGGATGGATTAAAATCATTAAAGCG
* * * ** *
31460945 AATCTTATCTCCTTGAAGTTGCAGTGGAA
65 AATCTTATATCCCTGAAATAACAGTAGAA
31460974 CAGATTGAAACCATAAATCTTATCTCCCTGAAGTTGCAGTGGGATGGATTAAAATCATTAAAGCG
1 CAGATTGAAACCATAAA-CTTATCTCCCTGAAGTTGCAGTGGGATGGATTAAAATCATTAAAGCG
*
31461039 AATCTTATATCCCTGAAATAATAGTAGAA
65 AATCTTATATCCCTGAAATAACAGTAGAA
* * * * *
31461068 TAGATT-AAAGCTATAAACTTTATCTTCTTGAAGATGCAGTGG
1 CAGATTGAAA-CCATAAAC-TTATCTCCCTGAAGTTGCAGTGG
31461110 AGCAGGATAA
Statistics
Matches: 114, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
92 3 0.03
93 27 0.24
94 84 0.74
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.30
Consensus pattern (93 bp):
CAGATTGAAACCATAAACTTATCTCCCTGAAGTTGCAGTGGGATGGATTAAAATCATTAAAGCGA
ATCTTATATCCCTGAAATAACAGTAGAA
Found at i:31471674 original size:43 final size:43
Alignment explanation
Indices: 31471599--31471830 Score: 378
Period size: 43 Copynumber: 5.4 Consensus size: 43
31471589 AATAAATCCC
* * *
31471599 GCAGGCCTAGTGCTGGT-AT-TATATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
31471640 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
31471683 GCAGGCTTAGTGCCGATGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
31471726 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
31471769 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
31471812 GCAGGCGTAATGCCGGTGA
1 GCAGGCTTAGTGCCGGTGA
31471831 AATGATATGT
Statistics
Matches: 180, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
41 15 0.08
42 2 0.01
43 163 0.91
ACGTcount: A:0.12, C:0.24, G:0.34, T:0.29
Consensus pattern (43 bp):
GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
Found at i:31475600 original size:39 final size:39
Alignment explanation
Indices: 31475541--31475629 Score: 151
Period size: 39 Copynumber: 2.3 Consensus size: 39
31475531 AAAATTAGTA
*
31475541 ATTTTTCTCAACTGATACAAAGAAATCCAACATTTTGCTC
1 ATTTTTC-AAACTGATACAAAGAAATCCAACATTTTGCTC
*
31475581 ATTTTTCAAACTTATACAAAGAAATCCAACATTTTGCTC
1 ATTTTTCAAACTGATACAAAGAAATCCAACATTTTGCTC
31475620 ATTTTTCAAA
1 ATTTTTCAAA
31475630 TTTACATTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 40 0.85
40 7 0.15
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (39 bp):
ATTTTTCAAACTGATACAAAGAAATCCAACATTTTGCTC
Found at i:31476977 original size:31 final size:31
Alignment explanation
Indices: 31476941--31477000 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
31476931 GTAACTTTTC
31476941 ATAATTTAG-TGACTAAAAATAAAATTTATTA
1 ATAA-TTAGATGACTAAAAATAAAATTTATTA
** *
31476972 ATAATTAGATGACTACTAATATAATTTAT
1 ATAATTAGATGACTAAAAATAAAATTTAT
31477001 CCATTATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (31 bp):
ATAATTAGATGACTAAAAATAAAATTTATTA
Found at i:31479437 original size:11 final size:11
Alignment explanation
Indices: 31479415--31479443 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
31479405 AGTTTTAACT
31479415 ATTTTA-ATAA
1 ATTTTATATAA
31479425 ATTTTATATAA
1 ATTTTATATAA
31479436 ATTTTATA
1 ATTTTATA
31479444 AATTTCTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTTTATATAA
Found at i:31485722 original size:13 final size:14
Alignment explanation
Indices: 31485704--31485732 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31485694 CGTCTCCTTC
31485704 TTTTC-TTCTTTCT
1 TTTTCTTTCTTTCT
31485717 TTTTCTTTCTTTCT
1 TTTTCTTTCTTTCT
31485731 TT
1 TT
31485733 CTAAATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTCTTTCTTTCT
Found at i:31485810 original size:25 final size:25
Alignment explanation
Indices: 31485776--31485851 Score: 68
Period size: 25 Copynumber: 3.0 Consensus size: 25
31485766 TACCTATTTG
31485776 TTTTA-TTAATATTATATAATATAT
1 TTTTACTTAATATTATATAATATAT
* *
31485800 TTTTACTTAATAATTAAGATAACATA-
1 TTTTACTTAAT-ATT-ATATAATATAT
*
31485826 TTTTATCTTTA-ATTATTATAATATAT
1 TTTTA-CTTAATATTA-TATAATATAT
31485852 AAAATAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
24 6 0.15
25 15 0.37
26 8 0.20
27 12 0.29
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (25 bp):
TTTTACTTAATATTATATAATATAT
Found at i:31486911 original size:3 final size:3
Alignment explanation
Indices: 31486896--31486927 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
31486886 CCATTTTTTC
*
31486896 TCT TCT ACT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
31486928 CCTTCTCTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:31488687 original size:3 final size:3
Alignment explanation
Indices: 31488671--31488742 Score: 53
Period size: 3 Copynumber: 25.0 Consensus size: 3
31488661 TTTACCATTT
** *
31488671 TTA TTA TT- TT- TTA TTA TTA -TA TTTA CCA TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
* * *
31488714 TTA TTA TTA GTA -TA TTT TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31488743 GAATTATTTT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
2 8 0.15
3 44 0.81
4 2 0.04
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:31488897 original size:24 final size:24
Alignment explanation
Indices: 31488841--31488901 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 24
31488831 AATAAATGTA
* *
31488841 TGTATACATATTTAAATATTATAT
1 TGTATACATATTTAAATATCACAT
* * * *
31488865 TATACACATATTTTAATATCACGT
1 TGTATACATATTTAAATATCACAT
31488889 TGTATACAT-TTTA
1 TGTATACATATTTA
31488902 TTATTATTAT
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.48
Consensus pattern (24 bp):
TGTATACATATTTAAATATCACAT
Found at i:31489330 original size:23 final size:24
Alignment explanation
Indices: 31489302--31489353 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
31489292 TCTTTAATAT
*
31489302 TATATTATGCATACATAT-TTTTA
1 TATATTACGCATACATATCTTTTA
* *
31489325 TATATTACGTATATATATCTTTTA
1 TATATTACGCATACATATCTTTTA
31489349 -ATATT
1 TATATT
31489354 GTATTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.54
Consensus pattern (24 bp):
TATATTACGCATACATATCTTTTA
Found at i:31489381 original size:36 final size:36
Alignment explanation
Indices: 31489312--31489404 Score: 100
Period size: 36 Copynumber: 2.6 Consensus size: 36
31489302 TATATTATGC
*
31489312 ATAC-ATATTTTTATATATTACGTATATATATCTTTTA
1 ATACTATATTTTTATATATTAC-TATATACATC-TTTA
* * * *
31489349 ATATTGTATTTTTATATGTTA-TGTATACATCTTTA
1 ATACTATATTTTTATATATTACTATATACATCTTTA
31489384 ATACTATATTATTTATATATT
1 ATACTATATT-TTTATATATT
31489405 TTTTTATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
35 12 0.26
36 17 0.37
37 3 0.07
38 14 0.30
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.56
Consensus pattern (36 bp):
ATACTATATTTTTATATATTACTATATACATCTTTA
Found at i:31489853 original size:21 final size:20
Alignment explanation
Indices: 31489813--31489868 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 20
31489803 ATTATAATAA
31489813 TTATTAT-TA-GTATAT-GT
1 TTATTATATATGTATATAGT
31489830 TTATTATATATGTATATAGCT
1 TTATTATATATGTATATAG-T
* * *
31489851 TTAATACATATATATATA
1 TTATTATATATGTATATA
31489869 TATTTATGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 7 0.22
18 2 0.06
19 6 0.19
20 1 0.03
21 16 0.50
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.52
Consensus pattern (20 bp):
TTATTATATATGTATATAGT
Found at i:31489914 original size:28 final size:28
Alignment explanation
Indices: 31489860--31489914 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
31489850 TTTAATACAT
*
31489860 ATATATATATATTTATGTAGTATTATTA
1 ATATATATATATTTATGTAGTAGTATTA
* *
31489888 ATATATAT-TTTTTATGTTATTAGTATT
1 ATATATATATATTTATG-TAGTAGTATT
31489915 TCTAATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (28 bp):
ATATATATATATTTATGTAGTAGTATTA
Found at i:31489943 original size:13 final size:13
Alignment explanation
Indices: 31489863--31489979 Score: 70
Period size: 13 Copynumber: 9.2 Consensus size: 13
31489853 AATACATATA
31489863 TATATATATTTATG
1 TATATATA-TTATG
*
31489877 TAGTAT-TATTAATA
1 TA-TATATATT-ATG
* *
31489891 TATATTTTTTATG
1 TATATATATTATG
*
31489904 T-TATTAGTATT-TC
1 TATA-TA-TATTATG
31489917 TA-ATATATT-T-
1 TATATATATTATG
31489927 TATATATATTATG
1 TATATATATTATG
*
31489940 TATATATATCATG
1 TATATATATTATG
*
31489953 TATATATA-TATT
1 TATATATATTATG
31489965 TAGTAT-TATTATG
1 TA-TATATATTATG
31489978 TA
1 TA
31489980 GACACTTCTC
Statistics
Matches: 82, Mismatches: 10, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
10 2 0.02
11 12 0.15
12 11 0.13
13 40 0.49
14 14 0.17
15 3 0.04
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (13 bp):
TATATATATTATG
Found at i:31493778 original size:4 final size:4
Alignment explanation
Indices: 31493771--31493827 Score: 66
Period size: 4 Copynumber: 15.0 Consensus size: 4
31493761 TTCATGACTA
* * *
31493771 CATT CATT CA-T CATT TATT CA-A CATT CATT TA-T CATT CATT CATT
1 CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT
31493816 CATT CATT CATT
1 CATT CATT CATT
31493828 GCATGTACAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
3 7 0.16
4 37 0.84
ACGTcount: A:0.28, C:0.23, G:0.00, T:0.49
Consensus pattern (4 bp):
CATT
Found at i:31493790 original size:11 final size:11
Alignment explanation
Indices: 31493771--31493826 Score: 76
Period size: 11 Copynumber: 5.0 Consensus size: 11
31493761 TTCATGACTA
31493771 CATTCATTCAT
1 CATTCATTCAT
* *
31493782 CATTTATTCAA
1 CATTCATTCAT
*
31493793 CATTCATTTAT
1 CATTCATTCAT
31493804 CATTCATTCATT
1 CATTCATTCA-T
31493816 CATTCATTCAT
1 CATTCATTCAT
31493827 TGCATGTACA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
11 27 0.71
12 11 0.29
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.48
Consensus pattern (11 bp):
CATTCATTCAT
Found at i:31493799 original size:15 final size:16
Alignment explanation
Indices: 31493772--31493827 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 16
31493762 TCATGACTAC
*
31493772 ATTCATTCA-TCATTT
1 ATTCATACATTCATTT
31493787 ATTCA-ACATTCATTT
1 ATTCATACATTCATTT
* *
31493802 A-TCATTCATTCATTC
1 ATTCATACATTCATTT
*
31493817 ATTCATTCATT
1 ATTCATACATT
31493828 GCATGTACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 5 0.14
15 21 0.60
16 9 0.26
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTCATACATTCATTT
Found at i:31502343 original size:75 final size:75
Alignment explanation
Indices: 31502129--31502430 Score: 360
Period size: 75 Copynumber: 4.0 Consensus size: 75
31502119 TTTCTGTTAC
* * * * *
31502129 AAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAACCTCAGGACACGCTGAGGTATTTTCAATTTC
* *
31502194 TATCTTTCAAAAA
66 TGTTTTTC---AA
* *
31502207 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAACCTCAGGACACGCTGAGGTATTTTCAATTTC
*
31502270 TGTTTTGCAA
66 TGTTTTTCAA
* * * *
31502280 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAACCTCGGGATATGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAACCTCAGGACACGCTGAGGTATTTTCAATTTC
31502345 TGTTTTTC-A
66 TGTTTTTCAA
* * * * *
31502354 AAAAATCAAGCTCATATTGCGAA-AGGTGAGTTGAACTTCGGGACATGCTGAGGCATTTTCAGTT
1 AAAAATCAA-CTCATATTGC-AAGAGGTGAGTTGAACCTCAGGACACGCTGAGGTATTTTCAATT
31502418 TCTGTTTTTCAA
64 TCTGTTTTTCAA
31502430 A
1 A
31502431 TTTTGTTTTT
Statistics
Matches: 202, Mismatches: 17, Indels: 12
0.87 0.07 0.05
Matches are distributed among these distances:
73 40 0.20
74 10 0.05
75 83 0.41
76 30 0.15
78 39 0.19
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (75 bp):
AAAAATCAACTCATATTGCAAGAGGTGAGTTGAACCTCAGGACACGCTGAGGTATTTTCAATTTC
TGTTTTTCAA
Found at i:31504353 original size:3 final size:3
Alignment explanation
Indices: 31504340--31504414 Score: 53
Period size: 3 Copynumber: 24.0 Consensus size: 3
31504330 TTTACCATTT
** **
31504340 TTA TTA TTTA TTA TTA TTA -TA TTTA CCA TTA TCG TTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
* *
31504386 TTA TTA TTA GTA TATA TTTA CTA TTA TTA
1 TTA TTA TTA TTA T-TA -TTA TTA TTA TTA
31504415 GAATTATTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
2 2 0.04
3 43 0.78
4 9 0.16
5 1 0.02
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:31504980 original size:25 final size:27
Alignment explanation
Indices: 31504959--31505028 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 27
31504949 TACTATGTAA
31504959 ATATCTTTAATATTATATTATGTATAC
1 ATATCTTTAATATTATATTATGTATAC
* *
31504986 ATAT-TTT--TA-TATATTACGTATAT
1 ATATCTTTAATATTATATTATGTATAC
31505009 ATATCTTTTAATATTATATT
1 ATATC-TTTAATATTATATT
31505029 TTTATATGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
23 16 0.44
24 2 0.06
25 3 0.08
26 3 0.08
27 6 0.17
28 6 0.17
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (27 bp):
ATATCTTTAATATTATATTATGTATAC
Found at i:31505000 original size:23 final size:24
Alignment explanation
Indices: 31504945--31505025 Score: 80
Period size: 23 Copynumber: 3.4 Consensus size: 24
31504935 TTCTAATATG
*
31504945 TATATACTATGTA-A-ATATCTTT
1 TATATATTATGTATACATATCTTT
31504967 AATATTATATTATGTATACATAT-TTT
1 --TA-TATATTATGTATACATATCTTT
* *
31504993 TATATATTACGTATATATATCTTT
1 TATATATTATGTATACATATCTTT
31505017 TA-ATATTAT
1 TATATATTAT
31505026 ATTTTTATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
23 22 0.45
24 9 0.18
25 10 0.20
26 4 0.08
27 4 0.08
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (24 bp):
TATATATTATGTATACATATCTTT
Found at i:31505051 original size:36 final size:36
Alignment explanation
Indices: 31504982--31505074 Score: 109
Period size: 36 Copynumber: 2.6 Consensus size: 36
31504972 TATATTATGT
*
31504982 ATAC-ATATTTTTATATATTACGTATATATATCTTTTA
1 ATACTATATTTTTATATATTAC-TATATACATC-TTTA
* * *
31505019 ATATTATATTTTTATATGTTA-TGTATACATCTTTA
1 ATACTATATTTTTATATATTACTATATACATCTTTA
31505054 ATACTATATTATTTATATATT
1 ATACTATATT-TTTATATATT
31505075 TTTTTTTCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
35 13 0.27
36 17 0.35
37 3 0.06
38 15 0.31
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.56
Consensus pattern (36 bp):
ATACTATATTTTTATATATTACTATATACATCTTTA
Found at i:31505525 original size:21 final size:20
Alignment explanation
Indices: 31505485--31505547 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 20
31505475 ATAATAATAA
31505485 TTATTAT-TA-GTATAT-GT
1 TTATTATATATGTATATAGT
31505502 TTATTATATATGTATATAGCT
1 TTATTATATATGTATATAG-T
*
31505523 TTAATACATATATGTATATA-T
1 TT-AT-TATATATGTATATAGT
31505544 TTAT
1 TTAT
31505548 GTAGTATTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
17 7 0.18
18 2 0.05
19 6 0.15
20 3 0.08
21 6 0.15
22 2 0.05
23 13 0.33
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.54
Consensus pattern (20 bp):
TTATTATATATGTATATAGT
Found at i:31507609 original size:21 final size:19
Alignment explanation
Indices: 31507568--31507609 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
31507558 TTATCTATAT
*
31507568 TTATTATTTAATACTAAAA
1 TTATTATTTAATACCAAAA
31507587 TTATCTATTTAATATCCAAAA
1 TTAT-TATTTAATA-CCAAAA
31507608 TT
1 TT
31507610 TCAATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 9 0.45
21 7 0.35
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (19 bp):
TTATTATTTAATACCAAAA
Found at i:31510656 original size:3 final size:3
Alignment explanation
Indices: 31510648--31510681 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
31510638 CTAGGAGTTG
31510648 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
31510682 TGCTTAGAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:31513785 original size:15 final size:15
Alignment explanation
Indices: 31513757--31513797 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
31513747 ATTAAATTTG
31513757 TAATATTAATTCTATT
1 TAATATT-ATTCTATT
31513773 TAATATTATTCTATT
1 TAATATTATTCTATT
*
31513788 TACTATTATT
1 TAATATTATT
31513798 ATTTATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (15 bp):
TAATATTATTCTATT
Found at i:31513844 original size:17 final size:16
Alignment explanation
Indices: 31513821--31513869 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
31513811 ACTGTACTTT
31513821 GTATGTATATATTATTA
1 GTATGTATATATT-TTA
*
31513838 TTATGTATAT-TTTTA
1 GTATGTATATATTTTA
31513853 GTATGTATATATATTTA
1 GTATGTATATAT-TTTA
31513870 TGAAGTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 12 0.43
16 3 0.11
17 13 0.46
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (16 bp):
GTATGTATATATTTTA
Found at i:31513848 original size:15 final size:15
Alignment explanation
Indices: 31513828--31513867 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
31513818 TTTGTATGTA
*
31513828 TATATTATTATTATG
1 TATATTATTAGTATG
*
31513843 TATATTTTTAGTATG
1 TATATTATTAGTATG
31513858 TATATATATT
1 TATAT-TATT
31513868 TATGAAGTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 18 0.86
16 3 0.14
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
TATATTATTAGTATG
Found at i:31513950 original size:24 final size:24
Alignment explanation
Indices: 31513913--31513989 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
31513903 TATTCTTTAA
*
31513913 TATATTATGCATATATTTTAATAC
1 TATATTATACATATATTTTAATAC
*
31513937 TATATTATATATATACATTTT-ATAC
1 TATATTATACATAT--ATTTTAATAC
* * *
31513962 TAT-GTATACATA-CTTTTAATAT
1 TATATTATACATATATTTTAATAC
31513984 TATATT
1 TATATT
31513990 TCATATGTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
21 4 0.10
22 6 0.14
23 1 0.02
24 19 0.45
25 7 0.17
26 5 0.12
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.52
Consensus pattern (24 bp):
TATATTATACATATATTTTAATAC
Found at i:31521486 original size:31 final size:30
Alignment explanation
Indices: 31521451--31521511 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
31521441 GAAACAGAAT
*
31521451 GAAAGCAAACGAAAC-AGAGAAGAACAGGGGA
1 GAAAG-AAACGAAACAAGA-AAGAAAAGGGGA
* *
31521482 GAAAGAAAGGAAAGAAGAAAGAAAAGGGGA
1 GAAAGAAACGAAACAAGAAAGAAAAGGGGA
31521512 AATAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.34, T:0.00
Consensus pattern (30 bp):
GAAAGAAACGAAACAAGAAAGAAAAGGGGA
Found at i:31527447 original size:46 final size:44
Alignment explanation
Indices: 31527396--31527572 Score: 185
Period size: 46 Copynumber: 3.9 Consensus size: 44
31527386 ATGTTTGGGC
31527396 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
* *** * *
31527440 ATGTCCGAACTCGTTGAGTTGAGTTCGAGTTCGAGAGATGTAACTAG-GC
1 A--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGA
* *
31527489 ATCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-A
* *
31527534 CACCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
31527573 GCGGGTTATA
Statistics
Matches: 108, Mismatches: 16, Indels: 16
0.77 0.11 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 68 0.63
47 30 0.28
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (44 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
Found at i:31527552 original size:93 final size:93
Alignment explanation
Indices: 31527393--31527564 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
31527383 AGGATGTTTG
***
31527393 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAG
*
31527458 TTGAGTTCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * *
31527486 GGCATCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAG
31527551 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
31527565 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:31534692 original size:251 final size:249
Alignment explanation
Indices: 31534242--31534812 Score: 853
Period size: 251 Copynumber: 2.3 Consensus size: 249
31534232 GCTTTTCAAA
* * *
31534242 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCT-TGGCTCACATGTCGAGGTATTTTCAGT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGT-GAGGTATTTTCA--
* *
31534306 TTTTATTTATTTCAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
60 ---AATTTATTTCAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC
* *
31534371 GGGTTGCATGACGAGGTATTTTCAAAAGCTACTTTTTAAATTAAGTTTCAAAAAAGACCAACTCA
122 GGGTTACATGACGAGGTATTTTCAAAAGCTACTTTTCAAATTAAGTTTCAAAAAAGACCAACTCA
* * *
31534436 TATTGCTAGAAGTGAGTTGAGCCTTGGCTCACGTGTTGAGCTATTTTCGATTTCTGTCTGTTT
187 TATTGCAAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATTTCTGTCTGTTT
31534499 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAATT
1 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG-TGAGGTATTTTCAAATT
* *
31534564 CTATTT-AATTTATACTTTTCAAAAATCAATTTATATTGCGAGAAGTGAGTTGAGCCTCGGGTTA
64 -TATTTCAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTTA
31534628 CATGACGAGGTATTTTCAAAAGCTACTTTTCAAATTAAGTTTCAAAAAAGACCAACTCATATTGC
128 CATGACGAGGTATTTTCAAAAGCTACTTTTCAAATTAAGTTTCAAAAAAGACCAACTCATATTGC
*
31534693 AAGAAGTGAGTTGAGCCTTGGCTTACGTGCTGAGCTATTTTCAATTTCTGTCTGTTT
193 AAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATTTCTGTCTGTTT
* * *
31534750 -TAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTCAGGATACGTTGAGGTATTTT-AAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG-TGAGGTATTTTCAAATTT
31534813 CTGTTTGTCA
Statistics
Matches: 293, Mismatches: 17, Indels: 17
0.90 0.05 0.05
Matches are distributed among these distances:
247 1 0.00
248 5 0.02
249 53 0.18
251 174 0.59
252 5 0.02
256 16 0.05
257 1 0.00
258 36 0.12
259 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (249 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTGAGGTATTTTCAAATTTA
TTTCAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTTACAT
GACGAGGTATTTTCAAAAGCTACTTTTCAAATTAAGTTTCAAAAAAGACCAACTCATATTGCAAG
AAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATTTCTGTCTGTTT
Found at i:31534839 original size:73 final size:73
Alignment explanation
Indices: 31534680--31534879 Score: 240
Period size: 73 Copynumber: 2.7 Consensus size: 73
31534670 CAAAAAAGAC
* * * * *
31534680 CAACTCATATTGCAAGAAGTGAGTTGAGCCT-TGGCTTACGTGCTGAGCTATTTTCAATTTCTGT
1 CAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGG-ATACGT--TGAGGTATTTTAAATTTCTGT
***
31534744 CTGTTTTAAAT
63 CTGTCAAAAAT
* *
31534755 CAACTCATATTGCGAGATGTGAGTTGAGCCTCAGGATACGTTGAGGTATTTTAAATTTCTGTTTG
1 CAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGATACGTTGAGGTATTTTAAATTTCTGTCTG
31534820 TCAAAAAT
66 TCAAAAAT
* * **
31534828 CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTT
1 CAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGATACGTTGAGGTATTTT
31534880 CATATTCTGT
Statistics
Matches: 110, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
73 74 0.67
75 34 0.31
76 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (73 bp):
CAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGATACGTTGAGGTATTTTAAATTTCTGTCTG
TCAAAAAT
Found at i:31534864 original size:322 final size:324
Alignment explanation
Indices: 31534429--31535064 Score: 1028
Period size: 322 Copynumber: 2.0 Consensus size: 324
31534419 CAAAAAAGAC
* * * **
31534429 CAACTCATATTGCTAGAAGTGAGTTGAGCCTTGGCTCACGTGTTGAGCTATTTTCGATTTCTGTC
1 CAACTCATATTGCGAGAAGTGAGTTGAGCCTAGGATCACG-GTTGAGCTATTTTAAATTTCTGTC
* *
31534494 TGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
65 TGTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTC
* *
31534559 AAATTCTATTTAATTTATACTTTTCAAAAATCAATTTATATTGCGAGAAGTGAGTTGAGCCTCGG
130 AAATTCTATTTAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGG
* *
31534624 GTTACATGACGAGGTATTTTCAAAAGCTACTTTTCAAATTAAGTTTCAAAAAAGACCAACTCATA
195 GTCACATGACGAGGTATTTTCAAAACCTACTTTTCAAATTAAGTTTCAAAAAA-ACCAACTCATA
* **
31534689 TTGCAAGAAGTGAGTTGAGCCTTGGCTTACGTGCTGAGCTATTTTCAATTTCTGTCTGTTTTAAA
259 TTGCAAGAAGTGAGTTGAGCCTTGGCTCACGCACTGAGCTATTTTCAATTTCTGTCTGTTTTAAA
31534754 T
324 T
* *
31534755 CAACTCATATTGCGAGATGTGAGTTGAGCCTCAGGAT-AC-GTTGAGGTATTTTAAATTTCTGT-
1 CAACTCATATTGCGAGAAGTGAGTTGAGCCT-AGGATCACGGTTGAGCTATTTTAAATTTCTGTC
31534817 T-TGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTC
65 TGTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTC
* *
31534881 ATATTCTGTTTAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGG
130 AAATTCTATTTAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGG
*
31534946 GTCACATGACGAGGTATTTTCAAAACCTACTTTTCAAATTAAGTTTCAAAAAAATCAACTCATAT
195 GTCACATGACGAGGTATTTTCAAAACCTACTTTTCAAATTAAGTTTCAAAAAAACCAACTCATAT
* *
31535011 TGCGAGAGGTGAGTTGAGCCTTGGCTCACGCACTGAGCTATTTTCAATTTCTGT
260 TGCAAGAAGTGAGTTGAGCCTTGGCTCACGCACTGAGCTATTTTCAATTTCTGT
31535065 TTTTTAGTTT
Statistics
Matches: 288, Mismatches: 21, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
321 60 0.21
322 173 0.60
323 1 0.00
324 20 0.07
326 31 0.11
327 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (324 bp):
CAACTCATATTGCGAGAAGTGAGTTGAGCCTAGGATCACGGTTGAGCTATTTTAAATTTCTGTCT
GTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCA
AATTCTATTTAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGG
TCACATGACGAGGTATTTTCAAAACCTACTTTTCAAATTAAGTTTCAAAAAAACCAACTCATATT
GCAAGAAGTGAGTTGAGCCTTGGCTCACGCACTGAGCTATTTTCAATTTCTGTCTGTTTTAAAT
Found at i:31535012 original size:89 final size:84
Alignment explanation
Indices: 31534820--31535031 Score: 252
Period size: 84 Copynumber: 2.5 Consensus size: 84
31534810 TTTCTGTTTG
*
31534820 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCATAT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAAAT
* * *
31534885 TCTGTTTAATTTATACTTT
66 ACTGTTTAAATTATACGTT
* * *
31534904 TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACA-TGACGAGGTATTTTCA
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACT---GAGGTATTTTC-
31534968 AAACCTACT-TTTCAAATTA-A-GTT
62 AAA--TACTGTTT-AAATTATACGTT
31534991 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
31535032 TGGCTCACGC
Statistics
Matches: 111, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
83 1 0.01
84 45 0.41
86 11 0.10
87 6 0.05
88 4 0.04
89 44 0.40
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (84 bp):
TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAAAT
ACTGTTTAAATTATACGTT
Found at i:31535057 original size:89 final size:86
Alignment explanation
Indices: 31534820--31535057 Score: 249
Period size: 89 Copynumber: 2.7 Consensus size: 86
31534810 TTTCTGTTTG
*
31534820 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACACTGAGGTATTTTC-A
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGTCACGCACTGAGGTATTTTCAA
* * * *
31534882 TATTCTGTTTAATTTATACTTT
65 AATACTGTTTAAATTATACGTT
* *
31534904 TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACATG-AC-GAGGTATTTTC
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGTCAC--GCACTGAGGTATTTTC
31534967 AAAACCTACT-TTTCAAATTA-A-GTT
63 AAAA--TACTGTTT-AAATTATACGTT
* *
31534991 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCACTGAGCTATTTTC
1 TC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGG-TCACGCACTGAGGTATTTTC
31535056 AA
63 AA
31535058 TTTCTGTTTT
Statistics
Matches: 131, Mismatches: 10, Indels: 21
0.81 0.06 0.13
Matches are distributed among these distances:
84 41 0.31
86 13 0.10
87 9 0.07
88 8 0.06
89 60 0.46
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (86 bp):
TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGTCACGCACTGAGGTATTTTCAAA
ATACTGTTTAAATTATACGTT
Found at i:31536921 original size:15 final size:15
Alignment explanation
Indices: 31536901--31536931 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31536891 CTATTAATTC
31536901 TATTTAATATTATTA
1 TATTTAATATTATTA
*
31536916 TATTTACTATTATTA
1 TATTTAATATTATTA
31536931 T
1 T
31536932 TTATAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTAATATTATTA
Found at i:31536988 original size:15 final size:15
Alignment explanation
Indices: 31536954--31536996 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
31536944 GTGTACTTTT
*
31536954 TATGTATA-TATTAT
1 TATGTATATTATTAG
*
31536968 TATGTATATTTTTAG
1 TATGTATATTATTAG
31536983 TATGTATATATATT
1 TATGTATAT-TATT
31536997 TATGAAGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 8 0.33
15 13 0.54
16 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (15 bp):
TATGTATATTATTAG
Found at i:31537377 original size:2 final size:2
Alignment explanation
Indices: 31537370--31537404 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
31537360 ATTATACATG
* *
31537370 TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31537405 TTTTTAGTAC
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:0.00, G:0.06, T:0.46
Consensus pattern (2 bp):
TA
Found at i:31553633 original size:29 final size:28
Alignment explanation
Indices: 31553569--31553630 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
31553559 TCTATTTTAT
* * *
31553569 TAAATACATAATTTAATTTAACTTTAGTT
1 TAAATATAT-ATTTAATTTAACTTTAATA
31553598 TAAATATATATTTAAATTTAACTATTAATA
1 TAAATATATATTT-AATTTAACT-TTAATA
31553628 TAA
1 TAA
31553631 TATGATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 4 0.14
29 17 0.61
30 7 0.25
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (28 bp):
TAAATATATATTTAATTTAACTTTAATA
Found at i:31555867 original size:4 final size:4
Alignment explanation
Indices: 31555854--31555889 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
31555844 TGTTCATATA
* *
31555854 TATG TGTG TATG TATG CATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG
31555890 CAACTATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.22, C:0.03, G:0.28, T:0.47
Consensus pattern (4 bp):
TATG
Done.