Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 13 of 135
Found at i:3556563 original size:16 final size:16
Alignment explanation
Indices: 3556513--3556574 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
3556503 AACATTTAAT
*
3556513 TAAATTTTTAAAAATTAA
1 TAAA-TTTT-AAAATTTA
* * *
3556531 AAAATTATAATATTTA
1 TAAATTTTAAAATTTA
**
3556547 TATTTTTTAAAATTTA
1 TAAATTTTAAAATTTA
3556563 TAAATTTTAAAA
1 TAAATTTTAAAA
3556575 AATTAATTAA
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
16 27 0.82
17 3 0.09
18 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAATTTTAAAATTTA
Found at i:3556698 original size:12 final size:11
Alignment explanation
Indices: 3556663--3556694 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
3556653 GAGTGATGTG
3556663 ATAAAAACATAA
1 ATAAAAA-ATAA
3556675 ATAAAAAATAA
1 ATAAAAAATAA
3556686 ATAAAAAAT
1 ATAAAAAAT
3556695 TAAAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (11 bp):
ATAAAAAATAA
Found at i:3558759 original size:10 final size:10
Alignment explanation
Indices: 3558744--3558776 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
3558734 GGATCACCAC
3558744 AAAACGTTTA
1 AAAACGTTTA
*
3558754 AAAACGTTTT
1 AAAACGTTTA
3558764 AAAACGTTTA
1 AAAACGTTTA
3558774 AAA
1 AAA
3558777 CAGTCTCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (10 bp):
AAAACGTTTA
Found at i:3564757 original size:59 final size:59
Alignment explanation
Indices: 3564632--3565041 Score: 474
Period size: 59 Copynumber: 6.9 Consensus size: 59
3564622 TGACTTTCGA
* * *
3564632 GGGTAAAAAT-GTAATTTTTGGTGAAAT-TAGGATCAAAAAATGGAATTTTGGAAAGTTT-G
1 GGGT-AAAATGGTAATTTTGGGTGAAATCGAGG-T-TAAAAATGGAATTTTGGAAAGTTTAG
* * * * * *
3564691 GTGGTAAAACGATAATTTTTGGTGAAACCGAGGTTAAAAATGGGATTTTGGAAAGTTCAG
1 G-GGTAAAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAG
* * * *
3564751 GGGTAAAATGGTAATTTTGGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAAGTTTAA
1 GGGTAAAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAG
* * * * * *
3564810 GGGT-AAACGGTAATTTTTGATAAAAT-TAGGGTTAAAAAT-GAGATTTTAGAAAGTTTAG
1 GGGTAAAATGGTAATTTTGGGTGAAATCGA-GGTTAAAAATGGA-ATTTTGGAAAGTTTAG
* * *
3564868 GGGTAAAATGGTAATTTTAGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTAGG
1 GGGTAAAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTA-G
*
3564928 GGGT-AAATGGTAATTTTGGGTAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAG
1 GGGTAAAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAG
* * *
3564986 GGGTAGATTGGTAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
1 GGGTAAAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTT
3565042 GGGGGCTAGA
Statistics
Matches: 298, Mismatches: 42, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
57 2 0.01
58 50 0.17
59 215 0.72
60 28 0.09
61 3 0.01
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAG
Found at i:3564908 original size:176 final size:177
Alignment explanation
Indices: 3564642--3565041 Score: 529
Period size: 176 Copynumber: 2.3 Consensus size: 177
3564632 GGGTAAAAAT
* *
3564642 GTAATTTTTGGTGAAATTAGGATCAAAAAATGGAATTTTGGAAAGTTTGGTGGTAAAACGATAAT
1 GTAATTTTTGGTGAAATTAGGGT-TAAAAATGGAATTTTGGAAAGTTTGGTGGTAAAACGATAAT
* * *
3564707 TTTTGGTGAAACCGAGGTTAAAAATGGGATTTTGGAAAGTTCA-GGGGTAAAATGGTAATTTTGG
65 TTTAGGTGAAACCGAGGTCAAAAATGGAATTTTGGAAAGTTCAGGGGGT-AAATGGTAATTTTGG
* *
3564771 GTGAAATCGGGGTCAAAAATAGAATTTTGGAAAGTTTAAGGGTA-AACG
129 GTAAAATCGAGGTCAAAAATAGAATTTTGGAAAGTTTAAGGGTAGAACG
* * * * *
3564819 GTAATTTTTGATAAAATTAGGGTTAAAAAT-GAGATTTTAGAAAGTTTAGG-GGTAAAATGGTAA
1 GTAATTTTTGGTGAAATTAGGGTTAAAAATGGA-ATTTTGGAAAGTTT-GGTGGTAAAACGATAA
* * *
3564882 TTTTAGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGGTAAATGGTAATTTTGG
64 TTTTAGGTGAAACCGAGGTCAAAAATGGAATTTTGGAAAGTTCAGGGGGTAAATGGTAATTTTGG
* * * **
3564947 GTAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAGATTG
129 GTAAAATCGAGGTCAAAAATAGAATTTTGGAAAGTTTAAGGGTAGAACG
* **
3564996 GTAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
1 GTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAAGTT
3565042 GGGGGCTAGA
Statistics
Matches: 192, Mismatches: 26, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
175 2 0.01
176 122 0.64
177 66 0.34
178 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.33
Consensus pattern (177 bp):
GTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTGGTGGTAAAACGATAATT
TTAGGTGAAACCGAGGTCAAAAATGGAATTTTGGAAAGTTCAGGGGGTAAATGGTAATTTTGGGT
AAAATCGAGGTCAAAAATAGAATTTTGGAAAGTTTAAGGGTAGAACG
Found at i:3564974 original size:30 final size:31
Alignment explanation
Indices: 3564872--3565035 Score: 92
Period size: 31 Copynumber: 5.5 Consensus size: 31
3564862 GTTTAGGGGT
* * * *
3564872 AAAATGGTAATTTTAGGTGAAATCGGGGTCA
1 AAAATGGTAATTTTGGGTAAAATCGAGGTTA
* ** ***
3564903 AAAATGG-AATTTT-GG-AAAGTTTAGGGGG
1 AAAATGGTAATTTTGGGTAAAATCGAGGTTA
*
3564931 TAAATGGTAATTTTGGGTAAAATCGAGGTTA
1 AAAATGGTAATTTTGGGTAAAATCGAGGTTA
* ** *
3564962 AAAATGG-AATTTT-GG-AAAGTTTAGGGGT-
1 AAAATGGTAATTTTGGGTAAAATCGA-GGTTA
* * * *
3564990 AGATTGGTAATTTTGGGTGAAATCGGGGTTA
1 AAAATGGTAATTTTGGGTAAAATCGAGGTTA
3565021 AAAATGG-AATTTTGG
1 AAAATGGTAATTTTGG
3565036 AAAGTTGGGG
Statistics
Matches: 95, Mismatches: 30, Indels: 17
0.67 0.21 0.12
Matches are distributed among these distances:
28 21 0.22
29 19 0.20
30 27 0.28
31 28 0.29
ACGTcount: A:0.34, C:0.02, G:0.31, T:0.32
Consensus pattern (31 bp):
AAAATGGTAATTTTGGGTAAAATCGAGGTTA
Found at i:3565002 original size:118 final size:118
Alignment explanation
Indices: 3564632--3565041 Score: 551
Period size: 118 Copynumber: 3.5 Consensus size: 118
3564622 TGACTTTCGA
* ** * *
3564632 GGGTAAAAAT-GTAATTTTTGGTGAAATTAGGATCAAAAAATGGAATTTTGGAAAGTTT-GGTGG
1 GGGT-AAAATGGTAATTTTGGGTGAAATCGGGGTC-AAAAATGGAATTTTGGAAAGTTTAGGGGG
* * * * *
3564695 TAAAACGATAATTTTTGGTGAAACCGAGGTTAAAAATGGGATTTTGGAAAGTTCAG
64 T-AAACGGTAATTTTTGGTAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAG
* *
3564751 GGGTAAAATGGTAATTTTGGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAAGTTTA-AGGGTA
1 GGGTAAAATGGTAATTTTGGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGGTA
* * *
3564815 AACGGTAATTTTTGATAAAAT-TAGGGTTAAAAAT-GAGATTTTAGAAAGTTTAG
66 AACGGTAATTTTTGGTAAAATCGA-GGTTAAAAATGGA-ATTTTGGAAAGTTTAG
*
3564868 GGGTAAAATGGTAATTTTAGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGGTA
1 GGGTAAAATGGTAATTTTGGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGGTA
* *
3564933 AATGGTAATTTTGGGTAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAG
66 AACGGTAATTTTTGGTAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAG
* * *
3564986 GGGTAGATTGGTAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
1 GGGTAAAATGGTAATTTTGGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTT
3565042 GGGGGCTAGA
Statistics
Matches: 257, Mismatches: 27, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
116 2 0.01
117 98 0.38
118 130 0.51
119 27 0.11
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (118 bp):
GGGTAAAATGGTAATTTTGGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGGTA
AACGGTAATTTTTGGTAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAG
Found at i:3565046 original size:29 final size:29
Alignment explanation
Indices: 3564722--3565046 Score: 114
Period size: 29 Copynumber: 11.1 Consensus size: 29
3564712 GTGAAACCGA
*
3564722 GGTTAAAAATGGGATTTTGGAAAGTTCAGG
1 GGTTAAAAATGGAATTTTGGAAAGTTC-GG
3564752 GG-T-AAAATGGTAATTTTGGGTGAAA--TCGG
1 GGTTAAAAATGG-AATTTT--G-GAAAGTTCGG
* * **
3564781 GGTCAAAAATAGAATTTTGGAAAGTTTAAG
1 GGTTAAAAATGGAATTTTGGAAAG-TTCGG
* * * *
3564811 GG-T--AAACGGTAATTTTTGATAAAATT-AG
1 GGTTAAAAATGG-AA-TTTTG-GAAAGTTCGG
* *
3564839 GGTTAAAAAT-GAGATTTTAGAAAGTTTAGG
1 GGTTAAAAATGGA-ATTTTGGAAAG-TTCGG
3564869 GG-T-AAAATGGTAATTTTAGGTGAAA--TCGG
1 GGTTAAAAATGG-AATTTT--G-GAAAGTTCGG
* *
3564898 GGTCAAAAATGGAATTTTGGAAAGTTTAGG
1 GGTTAAAAATGGAATTTTGGAAAG-TTCGG
* * *
3564928 GGGT--AAATGGTAATTTTGGGTAAA-ATCGA
1 GGTTAAAAATGG-AATTTT-GG-AAAGTTCGG
*
3564957 GGTTAAAAATGGAATTTTGGAAAGTTTAGG
1 GGTTAAAAATGGAATTTTGGAAAG-TTCGG
* *
3564987 GG-T-AGATTGGTAATTTTGGGTGAAA--TCGG
1 GGTTAAAAATGG-AATTTT--G-GAAAGTTCGG
*
3565016 GGTTAAAAATGGAATTTTGGAAAGTTGGG
1 GGTTAAAAATGGAATTTTGGAAAGTTCGG
3565045 GG
1 GG
3565047 CTAGAGAGTA
Statistics
Matches: 218, Mismatches: 34, Indels: 87
0.64 0.10 0.26
Matches are distributed among these distances:
27 16 0.07
28 38 0.17
29 67 0.31
30 53 0.24
31 32 0.15
32 12 0.06
ACGTcount: A:0.35, C:0.02, G:0.31, T:0.32
Consensus pattern (29 bp):
GGTTAAAAATGGAATTTTGGAAAGTTCGG
Found at i:3566283 original size:6 final size:6
Alignment explanation
Indices: 3566272--3566305 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
3566262 AAGTATTCAA
*
3566272 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTC ATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTT
3566306 CTCTTGTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (6 bp):
ATTTTT
Found at i:3570062 original size:22 final size:24
Alignment explanation
Indices: 3570037--3570086 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
3570027 TATCTTTTAA
3570037 TTATTT-TAA-AATTATAT-TACTT
1 TTATTTATAATAATTATATGTA-TT
3570059 TTATTTAATAATAATTATATGTATT
1 TTATTT-ATAATAATTATATGTATT
3570084 TTA
1 TTA
3570087 ATATAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.25
24 3 0.12
25 13 0.54
26 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
TTATTTATAATAATTATATGTATT
Found at i:3575161 original size:16 final size:15
Alignment explanation
Indices: 3575140--3575191 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
3575130 GAACGACAAT
3575140 TATACGAATGAATAAA
1 TATACGAAT-AATAAA
*
3575156 TATACGAA-AATAAG
1 TATACGAATAATAAA
* *
3575170 CATAAGAATAATAAA
1 TATACGAATAATAAA
3575185 -ATACGAA
1 TATACGAA
3575192 ATACAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 17 0.57
15 5 0.17
16 8 0.27
ACGTcount: A:0.60, C:0.08, G:0.12, T:0.21
Consensus pattern (15 bp):
TATACGAATAATAAA
Found at i:3575375 original size:30 final size:29
Alignment explanation
Indices: 3575314--3575547 Score: 147
Period size: 30 Copynumber: 7.9 Consensus size: 29
3575304 AAAAGGTTGA
* *
3575314 AAAATG-AAGTTTTAGAGAATTTG-GGGTC
1 AAAATGTAA-TTTTGGAAAATTTGAGGGTC
*
3575342 AAAATGTAATTTTGGGAAAATTTGAGGATC
1 AAAATGTAATTTT-GGAAAATTTGAGGGTC
* * *
3575372 AAAATATAATTTTAGGAAAGTTT-AGGGGTT
1 AAAATGTAATTTT-GGAAAATTTGA-GGGTC
* * **
3575402 AAAATGTGATTTTAAGAAGGTTTG-GGGTC
1 AAAATGTAATTTT-GGAAAATTTGAGGGTC
* * * *
3575431 AAATTGTGATTTTGGGAAAGGTTTG-TGGTC
1 AAAATGTAATTTT-GGAAA-ATTTGAGGGTC
* * *
3575461 AAAGTGTAATTTTGGAAAAGTTTAAGGGTT
1 AAAATGTAATTTTGGAAAA-TTTGAGGGTC
* *
3575491 AAAATATAATTTTGAAAAAGTTTGAGGGTC
1 AAAATGTAATTTTGGAAAA-TTTGAGGGTC
* *
3575521 AAAATATGATTTTGGAAAAGTTT-AGGG
1 AAAATGTAATTTTGGAAAA-TTTGAGGG
3575548 ACCTTCTAAG
Statistics
Matches: 167, Mismatches: 31, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
28 10 0.06
29 42 0.25
30 115 0.69
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAATTTGAGGGTC
Found at i:3575414 original size:60 final size:57
Alignment explanation
Indices: 3575333--3575547 Score: 182
Period size: 60 Copynumber: 3.6 Consensus size: 57
3575323 TTTTAGAGAA
*
3575333 TTTGGGGTCAAAATGTAATTTTGGGAAAATTTGAGGATCAAAATATAATTTTAGGAAAG
1 TTTGGGGTCAAAATGTAATTTT-GGAAAATTTGAGGGTCAAAATATAATTTT-GGAAAG
* * * ** * * *
3575392 TTTAGGGGTTAAAATGTGATTTTAAGAAGGTTTG-GGGTCAAATTGTGATTTTGGGAAAGG
1 TTT-GGGGTCAAAATGTAATTTT-GGAAAATTTGAGGGTCAAAATATAATTTT-GGAAA-G
* * * * *
3575452 TTTGTGGTCAAAGTGTAATTTTGGAAAAGTTTAAGGGTTAAAATATAATTTTGAAAAAG
1 TTTGGGGTCAAAATGTAATTTTGGAAAA-TTTGAGGGTCAAAATATAATTTTG-GAAAG
* *
3575511 TTTGAGGGTCAAAATATGATTTTGGAAAAGTTT-AGGG
1 TTTG-GGGTCAAAATGTAATTTTGGAAAA-TTTGAGGG
3575548 ACCTTCTAAG
Statistics
Matches: 122, Mismatches: 28, Indels: 12
0.75 0.17 0.07
Matches are distributed among these distances:
58 3 0.02
59 50 0.41
60 69 0.57
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (57 bp):
TTTGGGGTCAAAATGTAATTTTGGAAAATTTGAGGGTCAAAATATAATTTTGGAAAG
Found at i:3575427 original size:89 final size:88
Alignment explanation
Indices: 3575333--3575539 Score: 249
Period size: 89 Copynumber: 2.3 Consensus size: 88
3575323 TTTTAGAGAA
* *
3575333 TTTGGGGTCAAAATGTAATTTTGGGAAAATTTGAGGATCAAAATATAATTTTAGG-AAAGTTTAG
1 TTTGGGGTCAAAATGTGATTTTGGGAAAATTTGAGG-TCAAAATATAATTTT-GGAAAAGTTTAA
* * *
3575397 GGGTTAAAATGTGATTTT-AAGAAGG
64 GGGTTAAAATATAATTTTGAA-AAAG
* * * * *
3575422 TTTGGGGTCAAATTGTGATTTTGGGAAAGGTTTGTGGTCAAAGTGTAATTTTGGAAAAGTTTAAG
1 TTTGGGGTCAAAATGTGATTTTGGGAAA-ATTTGAGGTCAAAATATAATTTTGGAAAAGTTTAAG
3575487 GGTTAAAATATAATTTTGAAAAAG
65 GGTTAAAATATAATTTTGAAAAAG
*
3575511 TTTGAGGGTCAAAATATGATTTT-GGAAAA
1 TTTG-GGGTCAAAATGTGATTTTGGGAAAA
3575540 GTTTAGGGAC
Statistics
Matches: 101, Mismatches: 13, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
88 2 0.02
89 75 0.74
90 24 0.24
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (88 bp):
TTTGGGGTCAAAATGTGATTTTGGGAAAATTTGAGGTCAAAATATAATTTTGGAAAAGTTTAAGG
GTTAAAATATAATTTTGAAAAAG
Found at i:3576506 original size:18 final size:18
Alignment explanation
Indices: 3576479--3576513 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3576469 CGAAAAAATG
3576479 TTTTTCTTTGATTTTTCT
1 TTTTTCTTTGATTTTTCT
* *
3576497 TTTTTTTTTGCTTTTTC
1 TTTTTCTTTGATTTTTC
3576514 CCCTTTTTTT
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:0.03, C:0.11, G:0.06, T:0.80
Consensus pattern (18 bp):
TTTTTCTTTGATTTTTCT
Found at i:3576714 original size:21 final size:21
Alignment explanation
Indices: 3576688--3576727 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3576678 TCTTCCTTTT
* *
3576688 TATTTATTACTTATTTATTAA
1 TATTTATTAATTATGTATTAA
3576709 TATTTATTAATTATGTATT
1 TATTTATTAATTATGTATT
3576728 TGTTATACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (21 bp):
TATTTATTAATTATGTATTAA
Found at i:3577581 original size:37 final size:37
Alignment explanation
Indices: 3577539--3577611 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
3577529 GGCTTCATCT
* *
3577539 TTTGATCCACTTCTCTGTATCTTATCAAGAAGATGAA
1 TTTGATCCACTTCTCTGCATCTCATCAAGAAGATGAA
* *
3577576 TTTGATTCACTTCTCTGCATCTCGTCAAGAAGATGA
1 TTTGATCCACTTCTCTGCATCTCATCAAGAAGATGA
3577612 CCACTTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (37 bp):
TTTGATCCACTTCTCTGCATCTCATCAAGAAGATGAA
Found at i:3578068 original size:209 final size:201
Alignment explanation
Indices: 3577543--3578073 Score: 656
Period size: 209 Copynumber: 2.6 Consensus size: 201
3577533 TCATCTTTTG
* * * * *
3577543 ATCCACTTCTCTGTATCTTATCAAGAAGATGAATTTGATTCACTTCTCTGCATCTCGTCAAGAAG
1 ATCCACTTCTCTGTATCTCATCAAGAAGATGAATTTGGTTCACTTCTCTGTATCTCATCAGGAAG
* * *
3577608 ATGACCACTTTATTGCTTCGACCCACTTTTCTGTATCTCATCAGGAAGGTGGGTTTAGAATTTCA
66 ATGACCGCTTTATTGCTTCGACCCACTTTTCTGTATCTCATCAGGAAGATGGGGTTAGAATTTCA
* * * *
3577673 CTCACATTGAACTTTGCTTCATTTGATTTGGTCTTCTTCTCATCAGGAAGATGATTGCTTCATTA
131 CTCACATTGAACTTCGCTTCATTTGAATTGGTCTTCTTCTCATCAGGAAGATGACTGATTCATTA
*
3577738 TTTGTG
196 TTTGTA
* ** *
3577744 ATCCACTTCTCTGTACCTCATCGGGAAGATGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAG
1 ATCCACTTCTCTGTATCTCATCAAGAAGATGAATTTGGTTCACTTCTCTGTATCTCATCAGGAAG
* ** * * *
3577809 ATGACCGCTTTATTGTTTTAACCCACTTCTCAGTATCTCATCCA-GAAGATGGGAGTTCGAAGTT
66 ATGACCGCTTTATTGCTTCGACCCACTTTTCTGTATCTCAT-CAGGAAGATGGG-GTTAGAA-TT
*
3577873 TCACTCACATTGAGCTTCGCTTCA-TTGAATTGGTCTTCTTCTTTGTATCTCATCAGGAAGATGA
128 TCACTCACATTGAACTTCGCTTCATTTGAATTGG---TCTTC----T-TCTCATCAGGAAGATGA
3577937 CTGATTCATTGA-TT-TA
185 CTGATTCATT-ATTTGTA
* * * *
3577953 ATCCACTTCTTTATATCTCATCAAGAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAGGAAG
1 ATCCACTTCTCTGTATCTCATCAAGAAGATGAATTTGGTTCACTTCTCTGTATCTCATCAGGAAG
* *
3578018 GTGACCGCTTTATTGCTTCGACCCACTTTTCTGTATCTCATTAGGAAGATGGGGTT
66 ATGACCGCTTTATTGCTTCGACCCACTTTTCTGTATCTCATCAGGAAGATGGGGTT
3578074 TGGAAATTTT
Statistics
Matches: 278, Mismatches: 39, Indels: 19
0.83 0.12 0.06
Matches are distributed among these distances:
201 99 0.36
202 15 0.05
203 24 0.09
205 5 0.02
208 4 0.01
209 103 0.37
210 27 0.10
211 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (201 bp):
ATCCACTTCTCTGTATCTCATCAAGAAGATGAATTTGGTTCACTTCTCTGTATCTCATCAGGAAG
ATGACCGCTTTATTGCTTCGACCCACTTTTCTGTATCTCATCAGGAAGATGGGGTTAGAATTTCA
CTCACATTGAACTTCGCTTCATTTGAATTGGTCTTCTTCTCATCAGGAAGATGACTGATTCATTA
TTTGTA
Found at i:3579736 original size:23 final size:22
Alignment explanation
Indices: 3579683--3579726 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
3579673 AGTGCTGGGG
3579683 AAACAGTAAGCACACACAGTGA
1 AAACAGTAAGCACACACAGTGA
*
3579705 AAATCAGTAGGCACACACAGTG
1 AAA-CAGTAAGCACACACAGTG
3579727 CTGAACAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.11
Consensus pattern (22 bp):
AAACAGTAAGCACACACAGTGA
Found at i:3585869 original size:29 final size:28
Alignment explanation
Indices: 3585820--3586050 Score: 216
Period size: 29 Copynumber: 7.9 Consensus size: 28
3585810 GAAGGGTCGA
* * *
3585820 AAAATG-AATTTT-GATGAATTTGGGGTT
1 AAAATGTAATTTTGGA-AAATTTAGGGTC
*
3585847 AAAATGTAATTTTGGGAAAATTTAAGGATC
1 AAAATGTAATTTT-GGAAAATTT-AGGGTC
*
3585877 AAAATGTAATTTTAGGAAAGTTTAGGGTC
1 AAAATGTAATTTT-GGAAAATTTAGGGTC
* ** *
3585906 AAAATATAATTTTGGGAAGGTTTAGGGTT
1 AAAATGTAATTTT-GGAAAATTTAGGGTC
*
3585935 AAAATGTAATTTTAGGAAAGGTTTAGGGTC
1 AAAATGTAATTTT-GGAAA-ATTTAGGGTC
*
3585965 AAAATGTAATTTTGGAAAAGTTTAAGGGTT
1 AAAATGTAATTTTGGAAAA-TTT-AGGGTC
*
3585995 AAAATTTAA-TTTGGAAAAGTTTATGGGTC
1 AAAATGTAATTTTGGAAAA-TTTA-GGGTC
*
3586024 AAAATATAATTTTGGAAAAGTTTAGGG
1 AAAATGTAATTTTGGAAAA-TTTAGGG
3586051 ACCTCTTGAG
Statistics
Matches: 175, Mismatches: 20, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
27 6 0.03
28 7 0.04
29 87 0.50
30 75 0.43
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTGGAAAATTTAGGGTC
Found at i:3585918 original size:59 final size:59
Alignment explanation
Indices: 3585842--3586047 Score: 276
Period size: 59 Copynumber: 3.5 Consensus size: 59
3585832 GATGAATTTG
* * * *
3585842 GGGTTAAAATGTAATTTTGGGAAAA-TTTAAGGATCAAAATGTAATTTTAGGAAAGTTTA
1 GGGTCAAAATATAATTTT-GGAAAAGTTTAAGGGTTAAAATGTAATTTTAGGAAAGTTTA
* *
3585901 GGGTCAAAATATAATTTTGGGAAGGTTT-AGGGTTAAAATGTAATTTTAGGAAAGGTTTA
1 GGGTCAAAATATAATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTAGGAAA-GTTTA
* *
3585960 GGGTCAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATTTAA-TTT-GGAAAAGTTTA
1 GGGTCAAAATATAATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTAGG-AAAGTTTA
3586018 TGGGTCAAAATATAATTTTGGAAAAGTTTA
1 -GGGTCAAAATATAATTTTGGAAAAGTTTA
3586048 GGGACCTCTT
Statistics
Matches: 131, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
58 34 0.26
59 83 0.63
60 14 0.11
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (59 bp):
GGGTCAAAATATAATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTAGGAAAGTTTA
Found at i:3587203 original size:21 final size:21
Alignment explanation
Indices: 3587177--3587216 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3587167 CTTCCCTTTT
* *
3587177 TATTTATTACTTATTTATTAA
1 TATTTATTAATTATGTATTAA
3587198 TATTTATTAATTATGTATT
1 TATTTATTAATTATGTATT
3587217 TATTATACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (21 bp):
TATTTATTAATTATGTATTAA
Found at i:3591139 original size:27 final size:27
Alignment explanation
Indices: 3591101--3591165 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
3591091 CAATTAGGTC
*
3591101 CACTTTGGTATCTCTATATTTTTGGTT
1 CACTTTGGTATCTCTACATTTTTGGTT
*
3591128 CACTTTGGTATCTCTACATTTTTTGTT
1 CACTTTGGTATCTCTACATTTTTGGTT
*
3591155 CATTTTGGTAT
1 CACTTTGGTAT
3591166 TTGAACTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.15, C:0.15, G:0.14, T:0.55
Consensus pattern (27 bp):
CACTTTGGTATCTCTACATTTTTGGTT
Found at i:3593816 original size:29 final size:29
Alignment explanation
Indices: 3593758--3593816 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
3593748 TTTTCAAAGT
*
3593758 AGGTATTTCTATAAATAATCAAAATTATA
1 AGGTATTTCTATAAATAATCAAAATAATA
*
3593787 AGGTCATTTTTAT-AATAAT-AATAATAATA
1 AGGT-ATTTCTATAAATAATCAA-AATAATA
3593816 A
1 A
3593817 AACCTCAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 2 0.08
29 17 0.65
30 7 0.27
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (29 bp):
AGGTATTTCTATAAATAATCAAAATAATA
Found at i:3605875 original size:16 final size:17
Alignment explanation
Indices: 3605853--3605896 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
3605843 TAAAAAAAAT
3605853 TATATTTTTTAATTTTA
1 TATATTTTTTAATTTTA
**
3605870 -ATATTTAATAATTTTA
1 TATATTTTTTAATTTTA
3605886 TATATTTTTTA
1 TATATTTTTTA
3605897 TTTATTGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATATTTTTTAATTTTA
Found at i:3615384 original size:2 final size:2
Alignment explanation
Indices: 3615377--3615416 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3615367 TTGAAATTCA
3615377 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
3615417 GTTGGTGTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3615640 original size:22 final size:22
Alignment explanation
Indices: 3615612--3615659 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
3615602 TTTAAGTTTG
3615612 AGCTCAGCTCAAGTTCGGTTAA
1 AGCTCAGCTCAAGTTCGGTTAA
3615634 AGCTCAGCTCAAGTTCGGTTAA
1 AGCTCAGCTCAAGTTCGGTTAA
3615656 AGCT
1 AGCT
3615660 TGTTTATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (22 bp):
AGCTCAGCTCAAGTTCGGTTAA
Found at i:3619925 original size:51 final size:53
Alignment explanation
Indices: 3619865--3619970 Score: 162
Period size: 55 Copynumber: 2.0 Consensus size: 53
3619855 ATTTCACCTG
3619865 CATATCAAACCGAATTAACTAATC-TTA-TCTTTCATTATTTATATTATTGTA
1 CATATCAAACCGAATTAACTAATCTTTATTCTTTCATTATTTATATTATTGTA
* *
3619916 CATATCAAACTGAATTAATTAATCTTTATCTTCTTTCATTATTTATATTATTGTA
1 CATATCAAACCGAATTAACTAATCTTTA--TTCTTTCATTATTTATATTATTGTA
3619971 ATAGCAATGA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
51 22 0.45
52 3 0.06
55 24 0.49
ACGTcount: A:0.34, C:0.14, G:0.04, T:0.48
Consensus pattern (53 bp):
CATATCAAACCGAATTAACTAATCTTTATTCTTTCATTATTTATATTATTGTA
Found at i:3629530 original size:2 final size:2
Alignment explanation
Indices: 3629525--3629561 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3629515 TTTTTAAAAG
3629525 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
3629562 GTATTATACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3631778 original size:23 final size:23
Alignment explanation
Indices: 3631742--3631803 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 23
3631732 ATTATATTGT
*
3631742 TATTTTTG-TGCTGTTTTTTTAC
1 TATTTTGGTTGCTGTTTTTTTAC
3631764 TATTTTGGTTGCTG-TTTTTTAC
1 TATTTTGGTTGCTGTTTTTTTAC
* * *
3631786 TGTTTTGATTGTTGTTTT
1 TATTTTGGTTGCTGTTTT
3631804 GGTGCTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 26 0.76
23 8 0.24
ACGTcount: A:0.08, C:0.06, G:0.18, T:0.68
Consensus pattern (23 bp):
TATTTTGGTTGCTGTTTTTTTAC
Found at i:3631822 original size:21 final size:23
Alignment explanation
Indices: 3631798--3631839 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
3631788 TTTTGATTGT
*
3631798 TGTTTTGGTGCT-TT-TTTTTAC
1 TGTTTTGATGCTATTATTTTTAC
3631819 TGTTTTGATGCTATTATTTTT
1 TGTTTTGATGCTATTATTTTT
3631840 GTTGCTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 2 0.11
23 5 0.28
ACGTcount: A:0.10, C:0.07, G:0.17, T:0.67
Consensus pattern (23 bp):
TGTTTTGATGCTATTATTTTTAC
Found at i:3631850 original size:12 final size:12
Alignment explanation
Indices: 3631833--3631928 Score: 72
Period size: 12 Copynumber: 7.9 Consensus size: 12
3631823 TTGATGCTAT
3631833 TATTTTTGTTGC
1 TATTTTTGTTGC
* *
3631845 TATTTTTGCTGT
1 TATTTTTGTTGC
3631857 TATTTTTGTTGC
1 TATTTTTGTTGC
*
3631869 TATTTTTATT--
1 TATTTTTGTTGC
3631879 T-TTTTTGTTTTGC
1 TATTTTTG--TTGC
*
3631892 TATTATTTTGCTGC
1 TA-T-TTTTGTTGC
* *
3631906 TATTTTGGTTGT
1 TATTTTTGTTGC
*
3631918 TATTTTGGTTG
1 TATTTTTGTTG
3631929 TTTGGATGTT
Statistics
Matches: 67, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
9 5 0.07
10 1 0.01
11 2 0.03
12 46 0.69
13 2 0.03
14 5 0.07
15 1 0.01
16 5 0.07
ACGTcount: A:0.09, C:0.06, G:0.17, T:0.68
Consensus pattern (12 bp):
TATTTTTGTTGC
Found at i:3631854 original size:24 final size:24
Alignment explanation
Indices: 3631827--3631875 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
3631817 ACTGTTTTGA
3631827 TGCTATTATTTTTGTTGCTATTTT
1 TGCTATTATTTTTGTTGCTATTTT
*
3631851 TGCTGTTATTTTTGTTGCTATTTT
1 TGCTATTATTTTTGTTGCTATTTT
3631875 T
1 T
3631876 ATTTTTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.10, C:0.08, G:0.14, T:0.67
Consensus pattern (24 bp):
TGCTATTATTTTTGTTGCTATTTT
Found at i:3632103 original size:26 final size:26
Alignment explanation
Indices: 3632056--3632106 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
3632046 ATATAAAGAA
3632056 TTTTTAATGTATTTTAAATTTATTTAT
1 TTTTTAA-GTATTTTAAATTTATTTAT
*
3632083 TTTTTAA-TATTTGTAAGTTTATTT
1 TTTTTAAGTATTT-TAAATTTATTT
3632107 GATATATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 10 0.45
27 7 0.32
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (26 bp):
TTTTTAAGTATTTTAAATTTATTTAT
Found at i:3635270 original size:4 final size:4
Alignment explanation
Indices: 3635261--3635285 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3635251 CAAGTATTTA
3635261 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
3635286 GAACTATACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:3639024 original size:14 final size:14
Alignment explanation
Indices: 3639005--3639031 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3638995 TCTTTCAGCG
3639005 AATTAAATTTATTA
1 AATTAAATTTATTA
3639019 AATTAAATTTATT
1 AATTAAATTTATT
3639032 TATTTTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AATTAAATTTATTA
Found at i:3639672 original size:34 final size:34
Alignment explanation
Indices: 3639625--3639706 Score: 80
Period size: 34 Copynumber: 2.4 Consensus size: 34
3639615 AAGTTATAAC
*
3639625 TTAACAA-ATAAATACTTCTAAAATA-ATAATAAAA
1 TTAACAATA-AAATACTTATAAAATATATAA-AAAA
* * *
3639659 TTAACAATAAAATAACTTATACAATATTTAAATAA
1 TTAACAATAAAAT-ACTTATAAAATATATAAAAAA
3639694 TT-ACAATAAAATA
1 TTAACAATAAAATA
3639707 GTAGGAATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
33 1 0.02
34 21 0.51
35 16 0.39
36 3 0.07
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.32
Consensus pattern (34 bp):
TTAACAATAAAATACTTATAAAATATATAAAAAA
Found at i:3649178 original size:28 final size:28
Alignment explanation
Indices: 3649146--3649212 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
3649136 GTAAACATTA
* *
3649146 AAATAATATAAAAATATATAAAAATTTT
1 AAATAATATAAAAATACATAAAAATATT
*
3649174 CAATAA-ATAAAAAATACATAAAAATATT
1 AAATAATAT-AAAAATACATAAAAATATT
*
3649202 AAATATTATAA
1 AAATAATATAA
3649213 TATAATTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
27 2 0.06
28 28 0.88
29 2 0.06
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (28 bp):
AAATAATATAAAAATACATAAAAATATT
Found at i:3652199 original size:32 final size:32
Alignment explanation
Indices: 3652163--3652223 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
3652153 GAGTTAAAAG
3652163 TTAGAATAGAGAATCAACATTACTTTCTTGAT
1 TTAGAATAGAGAATCAACATTACTTTCTTGAT
3652195 TTAGAATAGAGAATCAACATTACTTTCTT
1 TTAGAATAGAGAATCAACATTACTTTCTT
3652224 TCTAATGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (32 bp):
TTAGAATAGAGAATCAACATTACTTTCTTGAT
Found at i:3655295 original size:3 final size:3
Alignment explanation
Indices: 3655287--3655337 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
3655277 ATTGTGCAGT
3655287 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
3655335 GAA
1 GAA
3655338 TTGTAATTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3656770 original size:26 final size:27
Alignment explanation
Indices: 3656705--3656806 Score: 102
Period size: 28 Copynumber: 3.7 Consensus size: 27
3656695 AACAACTCTG
* *
3656705 GATTTT-AGCTCGGATAGAGCATAATTTT
1 GATTTTGA-CTCGGGTAGAGC-TAATTCT
* * *
3656733 GATTCTGGCTCGAGTAGAGC-AATTCT
1 GATTTTGACTCGGGTAGAGCTAATTCT
3656759 GATTTTGACTCGGGTAGAGCTTAATTCT
1 GATTTTGACTCGGGTAGAGC-TAATTCT
3656787 -ATTTTTGACTCGGGTAGAGC
1 GA-TTTTGACTCGGGTAGAGC
3656807 GTTATTCTAT
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
26 22 0.35
27 1 0.02
28 39 0.63
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (27 bp):
GATTTTGACTCGGGTAGAGCTAATTCT
Found at i:3656813 original size:28 final size:28
Alignment explanation
Indices: 3656761--3656846 Score: 104
Period size: 28 Copynumber: 3.1 Consensus size: 28
3656751 GCAATTCTGA
3656761 TTTTGACTCGGGTAGAGC-TTAATTCTAT
1 TTTTGACTCGGGTAGAGCGTT-ATTCTAT
3656789 TTTTGACTCGGGTAGAGCGTTATTCTA-
1 TTTTGACTCGGGTAGAGCGTTATTCTAT
** * *
3656816 TTTCCAGCTCGGTTAGAGCGTTAATCTAT
1 TTTTGA-CTCGGGTAGAGCGTTATTCTAT
3656845 TT
1 TT
3656847 CTGGTTCGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
27 4 0.08
28 43 0.84
29 4 0.08
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (28 bp):
TTTTGACTCGGGTAGAGCGTTATTCTAT
Found at i:3658898 original size:18 final size:16
Alignment explanation
Indices: 3658866--3658909 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
3658856 ATCGAATGAG
3658866 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
3658882 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
3658896 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
3658910 ACCCTAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:3661703 original size:33 final size:33
Alignment explanation
Indices: 3661661--3661729 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
3661651 TCATCTTAGT
3661661 ATAACATAAAAAATAAGGTTGGATCGTACTAAC
1 ATAACATAAAAAATAAGGTTGGATCGTACTAAC
3661694 ATAACATAAAAAATAAGGTTGGATCGTACTAAC
1 ATAACATAAAAAATAAGGTTGGATCGTACTAAC
3661727 ATA
1 ATA
3661730 TTGCATATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (33 bp):
ATAACATAAAAAATAAGGTTGGATCGTACTAAC
Found at i:3664301 original size:23 final size:23
Alignment explanation
Indices: 3664254--3664303 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
3664244 TAATAAATAA
*
3664254 AAAATATAAAATTAATATATATT
1 AAAATAAAAAATTAATATATATT
3664277 AAAATAAAACAATATAA-ATAT-TT
1 AAAATAAAA-AAT-TAATATATATT
3664300 AAAA
1 AAAA
3664304 AATTAGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 14 0.58
24 7 0.29
25 3 0.12
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
AAAATAAAAAATTAATATATATT
Found at i:3667532 original size:15 final size:14
Alignment explanation
Indices: 3667512--3667563 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
3667502 ATTTTATTTT
3667512 CTTAAAAACAATAAA
1 CTTAAAAA-AATAAA
*
3667527 CTTAAAAAACT-AA
1 CTTAAAAAAATAAA
* *
3667540 CTTGCAAATAATAAA
1 CTT-AAAAAAATAAA
3667555 CTTAAAAAA
1 CTTAAAAAA
3667564 CTTAGATGCA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
13 5 0.17
14 11 0.38
15 13 0.45
ACGTcount: A:0.62, C:0.13, G:0.02, T:0.23
Consensus pattern (14 bp):
CTTAAAAAAATAAA
Found at i:3667573 original size:28 final size:28
Alignment explanation
Indices: 3667521--3667577 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
3667511 TCTTAAAAAC
*
3667521 AATAAACTTAAAAAACTAACTTGCAAAT
1 AATAAACTTAAAAAACTAACATGCAAAT
* *
3667549 AATAAACTTAAAAAACTTAGATGCAAAT
1 AATAAACTTAAAAAACTAACATGCAAAT
3667577 A
1 A
3667578 GATCAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.58, C:0.12, G:0.05, T:0.25
Consensus pattern (28 bp):
AATAAACTTAAAAAACTAACATGCAAAT
Found at i:3667772 original size:2 final size:2
Alignment explanation
Indices: 3667765--3667795 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3667755 AATTTTAAAC
3667765 TA TA TA 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 TA TA TA T
3667796 TTTTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3669351 original size:4 final size:4
Alignment explanation
Indices: 3669342--3669367 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3669332 AATAGATGGT
3669342 TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TG
3669368 CTTTGTAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:3669627 original size:76 final size:76
Alignment explanation
Indices: 3669526--3669718 Score: 278
Period size: 76 Copynumber: 2.5 Consensus size: 76
3669516 GATAGTGATA
* *
3669526 ATGATGTATCTGACCGCAATCTAAATATGAGGATTAGAAATATGATATATTTATTACATATGCAA
1 ATGATGTATCTGACCGCAATCTAAATATGAGGCTTAGAAATATGATATATCTATTACATATGCAA
* **
3669591 TGGTGATAAAT
66 TCGCCATAAAT
* * * **
3669602 ATGATGTATCTGACCCCAATTTAAATATGAGGCTTAGAAATATGATGTATCTATTGTATATGCAA
1 ATGATGTATCTGACCGCAATCTAAATATGAGGCTTAGAAATATGATATATCTATTACATATGCAA
3669667 TCGCCATAAAT
66 TCGCCATAAAT
* *
3669678 ATGATGTATTTGACCGCAATCTACATATGAGGCTTAGAAAT
1 ATGATGTATCTGACCGCAATCTAAATATGAGGCTTAGAAAT
3669719 GTAAACGTGA
Statistics
Matches: 103, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
76 103 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (76 bp):
ATGATGTATCTGACCGCAATCTAAATATGAGGCTTAGAAATATGATATATCTATTACATATGCAA
TCGCCATAAAT
Found at i:3683965 original size:16 final size:16
Alignment explanation
Indices: 3683944--3683974 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3683934 CGTAATTAAA
3683944 ACGTAAGAACAGAGTC
1 ACGTAAGAACAGAGTC
*
3683960 ACGTAATAACAGAGT
1 ACGTAAGAACAGAGT
3683975 TCAGGCGGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.16
Consensus pattern (16 bp):
ACGTAAGAACAGAGTC
Found at i:3686711 original size:22 final size:22
Alignment explanation
Indices: 3686686--3686729 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3686676 CAGTTCAGTT
3686686 CAGTTGATTCATGCAATCACTA
1 CAGTTGATTCATGCAATCACTA
3686708 CAGTTGATTCATGCAATCACTA
1 CAGTTGATTCATGCAATCACTA
3686730 ATATAGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (22 bp):
CAGTTGATTCATGCAATCACTA
Found at i:3687384 original size:22 final size:21
Alignment explanation
Indices: 3687326--3687380 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
3687316 TCATGCATTA
*
3687326 TTATTATTTTTTAATA-AAAT
1 TTATAATTTTTTAATATAAAT
* * *
3687346 TTGTAATTTTTTTATATAATT
1 TTATAATTTTTTAATATAAAT
3687367 TTATAATTTTTTAA
1 TTATAATTTTTTAA
3687381 ATATCTTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTATAATTTTTTAATATAAAT
Found at i:3687389 original size:20 final size:19
Alignment explanation
Indices: 3687331--3687398 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 19
3687321 CATTATTATT
*
3687331 ATTTTTTAATAAAATTTGTAA
1 ATTTTTTAA-ATAATTT-TAA
* *
3687352 TTTTTTTATATAATTTTATA
1 ATTTTTTAAATAATTTTA-A
3687372 ATTTTTTAAAT-ATCTTTAA
1 ATTTTTTAAATAAT-TTTAA
3687391 ATTATTTT
1 ATT-TTTT
3687399 TGATGTGTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 8 0.21
20 24 0.62
21 7 0.18
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (19 bp):
ATTTTTTAAATAATTTTAA
Found at i:3694813 original size:16 final size:18
Alignment explanation
Indices: 3694792--3694827 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3694782 TTTAAAGTGT
3694792 TATAAAT-T-ACATAATA
1 TATAAATATAACATAATA
3694808 TATAAATATAACATAATA
1 TATAAATATAACATAATA
3694826 TA
1 TA
3694828 ATATATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 1 0.06
18 10 0.56
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (18 bp):
TATAAATATAACATAATA
Found at i:3705841 original size:24 final size:24
Alignment explanation
Indices: 3705806--3705852 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3705796 ATATTACAAG
*
3705806 GTATTAGAAATAATCATAAGTGGC
1 GTATTAGAAATAATCACAAGTGGC
*
3705830 GTATCTAG-AATAATGACAAGTGG
1 GTAT-TAGAAATAATCACAAGTGG
3705853 ATGGTCTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (24 bp):
GTATTAGAAATAATCACAAGTGGC
Found at i:3713072 original size:6 final size:6
Alignment explanation
Indices: 3713061--3713085 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3713051 ACCTTAGTGA
3713061 CCTCTT CCTCTT CCTCTT CCTCTT C
1 CCTCTT CCTCTT CCTCTT CCTCTT C
3713086 AAGGATCAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
CCTCTT
Found at i:3714784 original size:30 final size:30
Alignment explanation
Indices: 3714748--3714931 Score: 180
Period size: 30 Copynumber: 6.2 Consensus size: 30
3714738 CCTTTTTTAA
* *
3714748 AAAAATTGTGTTTTGACCCCCAAACTATCC
1 AAAAATTATGTTTTGACCCCCAAACTTTCC
* * *
3714778 AAAAATTATGTTTTGACCTCCAAACTAT-A
1 AAAAATTATGTTTTGACCCCCAAACTTTCC
*
3714807 AAAAATT-TGGATTTGA-CCCCAAACTTTCC
1 AAAAATTAT-GTTTTGACCCCCAAACTTTCC
* *
3714836 AAAAATTATGTTTTGACCCTCAAACTTTCT
1 AAAAATTATGTTTTGACCCCCAAACTTTCC
* * *
3714866 AAAAATTAAGTTTT-AACCCTAAACTTTCC
1 AAAAATTATGTTTTGACCCCCAAACTTTCC
* ** *
3714895 AAAAATT-TGGATTTGAATCCTAAACTTTCC
1 AAAAATTAT-GTTTTGACCCCCAAACTTTCC
3714925 AAAAATT
1 AAAAATT
3714932 CAAATTTGAT
Statistics
Matches: 130, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
28 10 0.08
29 48 0.37
30 72 0.55
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (30 bp):
AAAAATTATGTTTTGACCCCCAAACTTTCC
Found at i:3714837 original size:58 final size:58
Alignment explanation
Indices: 3714745--3714901 Score: 190
Period size: 59 Copynumber: 2.7 Consensus size: 58
3714735 GCCCCTTTTT
* *
3714745 TAAAAAAATTGTGTTTTGACCCCCAAACTATCCAAAAATTATGTTTTGA-CCTCCAAACTA
1 TAAAAAATTTG-GTTTTGA-CCCCAAACTTTCCAAAAATTATGTTTTGACCCT-CAAACTA
* *
3714805 TAAAAAATTTGGATTTGACCCCAAACTTTCCAAAAATTATGTTTTGACCCTCAAACTT
1 TAAAAAATTTGGTTTTGACCCCAAACTTTCCAAAAATTATGTTTTGACCCTCAAACTA
* ** * *
3714863 TCTAAAAATTAAGTTTTAACCCTAAACTTTCCAAAAATT
1 T-AAAAAATTTGGTTTTGACCCCAAACTTTCCAAAAATT
3714902 TGGATTTGAA
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
58 35 0.41
59 40 0.47
60 10 0.12
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (58 bp):
TAAAAAATTTGGTTTTGACCCCAAACTTTCCAAAAATTATGTTTTGACCCTCAAACTA
Found at i:3714899 original size:88 final size:89
Alignment explanation
Indices: 3714748--3714931 Score: 246
Period size: 88 Copynumber: 2.1 Consensus size: 89
3714738 CCTTTTTTAA
* * *
3714748 AAAAATTGTGTTTTGACCCCCAAACTATCCAAAAATTATGTTTTGACCTCCAAACTATAAAAAAT
1 AAAAATTATGTTTTGACCCCCAAACTATCCAAAAATTAAGTTTTAACCTCCAAACTATAAAAAAT
3714813 TTGGATTTG-ACCCCAAACTTTCC
66 TTGGATTTGAACCCCAAACTTTCC
* * * * * *
3714836 AAAAATTATGTTTTGACCCTCAAACTTTCTAAAAATTAAGTTTTAACC-CTAAACTTTCCAAAAA
1 AAAAATTATGTTTTGACCCCCAAACTATCCAAAAATTAAGTTTTAACCTCCAAACTAT-AAAAAA
* *
3714900 TTTGGATTTGAATCCTAAACTTTCC
65 TTTGGATTTGAACCCCAAACTTTCC
3714925 AAAAATT
1 AAAAATT
3714932 CAAATTTGAT
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
87 7 0.08
88 57 0.69
89 19 0.23
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (89 bp):
AAAAATTATGTTTTGACCCCCAAACTATCCAAAAATTAAGTTTTAACCTCCAAACTATAAAAAAT
TTGGATTTGAACCCCAAACTTTCC
Found at i:3714939 original size:30 final size:28
Alignment explanation
Indices: 3714817--3714988 Score: 130
Period size: 30 Copynumber: 5.8 Consensus size: 28
3714807 AAAAATTTGG
* *
3714817 ATTTGACCCCAAACTTTCCAAAAATTATG
1 ATTTGACCCTAAACTTTCCAAAAATTA-A
* *
3714846 TTTTGACCCTCAAACTTTCTAAAAATTAA
1 ATTTGACCCT-AAACTTTCCAAAAATTAA
* * **
3714875 GTTTTAACCCTAAACTTTCCAAAAATTTGG
1 -ATTTGACCCTAAACTTTCCAAAAA-TTAA
*
3714905 ATTTGAATCCTAAACTTTCCAAAAATTCAA
1 ATTTG-ACCCTAAACTTTCCAAAAATT-AA
**
3714935 ATTTGATGCCC-AAACTTTTGAAAAATTCAA
1 ATTTGA--CCCTAAACTTTCCAAAAATT-AA
* *
3714965 ATTTGGCCCCAAAACTTTCCAAAA
1 ATTT-GACCCTAAACTTTCCAAAA
3714989 TTTTATTTTT
Statistics
Matches: 115, Mismatches: 19, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
29 30 0.26
30 82 0.71
31 3 0.03
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.33
Consensus pattern (28 bp):
ATTTGACCCTAAACTTTCCAAAAATTAA
Found at i:3715018 original size:26 final size:27
Alignment explanation
Indices: 3714980--3715031 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
3714970 GCCCCAAAAC
3714980 TTTCCAAAATTTTAT-TTTTACCCCTT
1 TTTCCAAAATTTTATATTTTACCCCTT
* *
3715006 TTTCCTAATTTTTATAATTTTACCCC
1 TTTCCAAAATTTTAT-ATTTTACCCC
3715032 AAAATTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 13 0.59
28 9 0.41
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTCCAAAATTTTATATTTTACCCCTT
Found at i:3715064 original size:26 final size:29
Alignment explanation
Indices: 3715035--3715087 Score: 76
Period size: 26 Copynumber: 1.9 Consensus size: 29
3715025 TTACCCCAAA
3715035 ATTTTCATTT-TT-TAAT-TTAATCCTTT
1 ATTTTCATTTCTTCTAATATTAATCCTTT
*
3715061 ATTTTTATTTCTTCTAATATTAATCCT
1 ATTTTCATTTCTTCTAATATTAATCCT
3715088 GTCTTTTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 9 0.39
27 2 0.09
28 4 0.17
29 8 0.35
ACGTcount: A:0.25, C:0.13, G:0.00, T:0.62
Consensus pattern (29 bp):
ATTTTCATTTCTTCTAATATTAATCCTTT
Found at i:3716413 original size:59 final size:59
Alignment explanation
Indices: 3716337--3716752 Score: 495
Period size: 59 Copynumber: 7.1 Consensus size: 59
3716327 AAAATGCATA
* *
3716337 TTTGG-GAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATT
1 TTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTAATT
* * * *
3716395 TTTGATGAAATCGAGGTTAAAAATGGGATTTTGAAAAG-TTCAGGGGTAAAATGGTAA-T
1 TTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGA-GGGTAAAATGGTAATT
* * * **
3716453 TTTGGTAAAATCGAGGTTAAAAATAGAATTTTGGGAAGTTCAAGGGTAAAATGGTAATT
1 TTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTAATT
*
3716512 TTTGGTGAAATCGAGGTTAAAAAT-GAGGTTTTGGAAAGTTTGAGGGTAAAATGGTAATT
1 TTTGGTGAAATCGAGGTTAAAAATGGA-ATTTTGGAAAGTTTGAGGGTAAAATGGTAATT
* * ** * *
3716571 TTTGGTGAAATTGGGGTTAAAAATGGGCTTTTCGAAAAGTTTG-GGAGTAAAATGG-AAAT
1 TTTGGTGAAATCGAGGTTAAAAATGGAATTTT-GGAAAGTTTGAGG-GTAAAATGGTAATT
* * * *
3716630 TTTGGTAAAATTGAGGTTAAAAAT-GAGATTTTAGAAAGTTTGGGGGTAAAATGGTAATT
1 TTTGGTGAAATCGAGGTTAAAAATGGA-ATTTTGGAAAGTTTGAGGGTAAAATGGTAATT
* * * * *
3716689 TTTGGTGAAATCGGGGTTAAAAATGGGATTTTAGAATGTTTGAGGGTAAAATGATAATT
1 TTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTAATT
3716748 TTTGG
1 TTTGG
3716753 ACAGTCCAGG
Statistics
Matches: 307, Mismatches: 39, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
58 73 0.24
59 214 0.70
60 20 0.07
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.33
Consensus pattern (59 bp):
TTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTAATT
Found at i:3717695 original size:28 final size:28
Alignment explanation
Indices: 3717663--3717717 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
3717653 AAGGGTTGTA
*
3717663 TTGATTTTCAGAA-CAGGGTTTGTAACCG
1 TTGATTTTCA-AAGCAGGGTTCGTAACCG
*
3717691 TTGATTTTCAAAGCTGGGTTCGTAACC
1 TTGATTTTCAAAGCAGGGTTCGTAACC
3717718 CTTTTACAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (28 bp):
TTGATTTTCAAAGCAGGGTTCGTAACCG
Found at i:3719001 original size:29 final size:29
Alignment explanation
Indices: 3718935--3719061 Score: 82
Period size: 28 Copynumber: 4.4 Consensus size: 29
3718925 GAAGAAACGA
* * *
3718935 TAAAATCGGGGGTGAAAATGGGACTTTTGG
1 TAAAATCGGGGG-AAAAATGGTAATTTTGG
* * *
3718965 -ATACTCGGGGGCAAAATGGTAATTTTGG
1 TAAAATCGGGGGAAAAATGGTAATTTTGG
** *
3718993 TAAAATCGGGTTAAAAATAG-AATTTT--
1 TAAAATCGGGGGAAAAATGGTAATTTTGG
* * *
3719019 TAAGAGTTCGAGGGTAAAATGGTAATTTTTGG
1 TAA-A-ATCGGGGGAAAAATGGTAA-TTTTGG
3719051 TAAAATCGGGG
1 TAAAATCGGGG
3719062 TTAAAAATTG
Statistics
Matches: 71, Mismatches: 19, Indels: 14
0.68 0.18 0.13
Matches are distributed among these distances:
26 3 0.04
27 1 0.01
28 30 0.42
29 24 0.34
30 9 0.13
31 1 0.01
32 3 0.04
ACGTcount: A:0.34, C:0.06, G:0.30, T:0.30
Consensus pattern (29 bp):
TAAAATCGGGGGAAAAATGGTAATTTTGG
Found at i:3719075 original size:59 final size:59
Alignment explanation
Indices: 3718935--3719460 Score: 552
Period size: 59 Copynumber: 9.0 Consensus size: 59
3718925 GAAGAAACGA
* * * * * *
3718935 TAAAATCGGGGGTGAAAATGGGACTTTTGGATA-CTCGGGGGCAAAATGGTAA-TTTTGG
1 TAAAATCGGGGTTAAAAAT-GGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
* * *
3718993 TAAAATC-GGGTTAAAAATAGAATTTT-TAAGAGTTCGAGGGTAAAATGGTAATTTTTGG
1 TAAAATCGGGGTTAAAAATGGAATTTTGGAA-AGTTCGGGGGTAAAATGGTAATTTTTGG
* *
3719051 TAAAATCGGGGTTAAAAATTGAATTTT--AAGAGTTCAGGGGGTAAAATGGTAATTTTTGA
1 TAAAATCGGGGTTAAAAATGGAATTTTGGAA-AGTTC-GGGGGTAAAATGGTAATTTTTGG
* * * * * ** *
3719110 TGAAACCGAGGTTAAAAATGGAATTTTAGAAGGTTTAGGGGTAAAATGGCAATTTTTGG
1 TAAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
* * * * *
3719169 TAAAATTGAGGTTAAAAATGGAATTTTAGAAGGTTTGGGGGTAAAATGGTAATTTTTGG
1 TAAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
* * * * *
3719228 TGAAACCGGGTTTATAAAA-AGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGG
1 TAAAATCGGGGTTA-AAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
* * *** *
3719287 TGAAATCGGGG-TCAAAAT-TTTTTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGG
1 TAAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
** *
3719344 TAAAATCAAGGTTAAAAATGGAATTTTGGAAAGTT-TGGGGTAAAATGGTAATTTTTGG
1 TAAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
** *
3719402 -AAGTTTCAGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
1 TAA-AATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
3719461 AAGTTTCGGG
Statistics
Matches: 399, Mismatches: 56, Indels: 25
0.83 0.12 0.05
Matches are distributed among these distances:
55 1 0.00
56 7 0.02
57 73 0.18
58 86 0.22
59 223 0.56
60 7 0.02
61 2 0.01
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.33
Consensus pattern (59 bp):
TAAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
Found at i:3719739 original size:162 final size:163
Alignment explanation
Indices: 3719560--3720067 Score: 704
Period size: 162 Copynumber: 3.1 Consensus size: 163
3719550 GGCATCCTGA
* * *
3719560 AGTCAAAGGATTAATTTAAAAATCTTGAAAAAAAT-TTAGGCCAATTTTGTAATTAAACAGAACT
1 AGTCAAAGGACTAATTTAAAAATCTTGAAAAAATTCTTAGGTCAATTTTGTAATTAAACAGAACT
*
3719624 TGATTTTGGGACTAAATTAAAACAAATTAAAAGTGACTGGGACTAGATACTGAAATAAACCAAAA
66 TGATTTTGGGACTAAATTAAAACAAATTAAAAGTGACAGGGACTAGATACTGAAATAAACCAAAA
3719689 AGTGACACGTGGAGGCCTCTGGTGCAGTCAAAC
131 AGTGACACGTGGAGGCCTCTGGTGCAGTCAAAC
* * * *
3719722 AATCAAAGGACTAATTTATAAATATT-AAAAAATTCTTGGGTCAATTTTGTAATTAAACAGAACT
1 AGTCAAAGGACTAATTTAAAAATCTTGAAAAAATTCTTAGGTCAATTTTGTAATTAAACAGAACT
* *
3719786 TGATTTTGTGATTAAATTAAAACAAATTAAAAGTGACAGGGACTAGATACTGAAATAAACCAAAA
66 TGATTTTGGGACTAAATTAAAACAAATTAAAAGTGACAGGGACTAGATACTGAAATAAACCAAAA
*
3719851 AGTGACATGTGGAGGCCTCTGGTGCAGTCAAAC
131 AGTGACACGTGGAGGCCTCTGGTGCAGTCAAAC
* * * *
3719884 AGTCAAAGGACTAATTTATAAATCTTG-AAAAATTCTTAGGTCAATTTTGTAATTAAATAAAAGT
1 AGTCAAAGGACTAATTTAAAAATCTTGAAAAAATTCTTAGGTCAATTTTGTAATTAAACAGAACT
** * * * * * *
3719948 TGATTTAT-GGACCGAATTAAAACAAATTAAAAATAAAAGGGACTAAATGCAT-AAATAAGCCAA
66 TGATTT-TGGGACTAAATTAAAACAAATTAAAAGTGACAGGGACTAGATAC-TGAAATAAACCAA
* *
3720011 AAAGTGACACGTGGCA-ACCTCTGGTGTAGTCAAAC
129 AAAGTGACACGTGG-AGGCCTCTGGTGCAGTCAAAC
* *
3720046 AGTCAAAGGATTAAATTAAAAA
1 AGTCAAAGGACTAATTTAAAAA
3720068 CCAATCAAAA
Statistics
Matches: 308, Mismatches: 33, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
161 7 0.02
162 298 0.97
163 3 0.01
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (163 bp):
AGTCAAAGGACTAATTTAAAAATCTTGAAAAAATTCTTAGGTCAATTTTGTAATTAAACAGAACT
TGATTTTGGGACTAAATTAAAACAAATTAAAAGTGACAGGGACTAGATACTGAAATAAACCAAAA
AGTGACACGTGGAGGCCTCTGGTGCAGTCAAAC
Found at i:3720736 original size:6 final size:6
Alignment explanation
Indices: 3720725--3720794 Score: 58
Period size: 6 Copynumber: 11.8 Consensus size: 6
3720715 TTAAATTTGA
*
3720725 TTAAAT TTAAAT AAGTAAAT TTAAAT TT--AT CTTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT TTAAAT
* *
3720773 ATAAAT TTAAAA TT-AAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAA
3720795 CTTTGAAAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
4 2 0.04
5 10 0.20
6 32 0.63
7 2 0.04
8 5 0.10
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (6 bp):
TTAAAT
Found at i:3720777 original size:11 final size:11
Alignment explanation
Indices: 3720763--3720794 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3720753 ATCTTAAATT
3720763 TAAATTTAAAA
1 TAAATTTAAAA
3720774 TAAATTTAAAA
1 TAAATTTAAAA
*
3720785 TTAATTTAAA
1 TAAATTTAAA
3720795 CTTTGAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:3720777 original size:17 final size:17
Alignment explanation
Indices: 3720725--3720788 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
3720715 TTAAATTTGA
3720725 TTAAATTTAAATAAGTAAAT
1 TTAAATTT-AA-AA-TAAAT
***
3720745 TTAAATTTATCTTAAAT
1 TTAAATTTAAAATAAAT
3720762 TTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAT
*
3720779 TTAAAATTAA
1 TTAAATTTAA
3720789 TTTAAACTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
17 28 0.76
19 1 0.03
20 8 0.22
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:3720794 original size:17 final size:17
Alignment explanation
Indices: 3720740--3720794 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
3720730 TTTAAATAAG
*
3720740 TAAATTT-AAATTTATCT
1 TAAATTTAAAATTAAT-T
* **
3720757 TAAATTTAAATTTAAAA
1 TAAATTTAAAATTAATT
3720774 TAAATTTAAAATTAATT
1 TAAATTTAAAATTAATT
3720791 TAAA
1 TAAA
3720795 CTTTGAAAAC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 25 0.83
18 5 0.17
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATTTAAAATTAATT
Found at i:3721141 original size:45 final size:44
Alignment explanation
Indices: 3721064--3721297 Score: 145
Period size: 40 Copynumber: 5.6 Consensus size: 44
3721054 TATCTTGCTC
3721064 TTACTTCAATTTC-AGAGAGAT---AAAGA-CTTGATGTCCAGCT
1 TTACTTCAATTTCAAGAG-GATAGGAAAGATCTTGATGTCCAGCT
* *
3721104 TTACTTAAATTTCAAGAGGATAGGAAATGATCTTGATGCTCTGTCTTGCT
1 TTACTTCAATTTCAAGAGGATAGGAAA-GATCTTGATG-TC---C-AGCT
*
3721154 CTTACTTCAATTTC-AGAGAGAT---AAAGA-CTTGATATCCAGCT
1 -TTACTTCAATTTCAAGAG-GATAGGAAAGATCTTGATGTCCAGCT
*
3721195 TTACTTCAATTTCAAGAGGATAGGAAAAGATC-T--TG-CTA---
1 TTACTTCAATTTCAAGAGGATAGG-AAAGATCTTGATGTCCAGCT
* * * *
3721233 TTACTTCAATTTC-AGA-GAT---AAAGA-CGTGTTATCCAACT
1 TTACTTCAATTTCAAGAGGATAGGAAAGATCTTGATGTCCAGCT
3721271 TTACTTCAATTTCAAGAGGATAGGAAA
1 TTACTTCAATTTCAAGAGGATAGGAAA
3721298 TGGTCTTGCT
Statistics
Matches: 154, Mismatches: 9, Indels: 59
0.69 0.04 0.27
Matches are distributed among these distances:
31 1 0.01
32 6 0.04
34 1 0.01
35 2 0.01
36 3 0.02
37 3 0.02
38 26 0.17
39 3 0.02
40 34 0.22
41 13 0.08
42 2 0.01
43 6 0.04
44 8 0.05
45 10 0.06
46 8 0.05
47 2 0.01
48 3 0.02
49 1 0.01
50 7 0.05
51 15 0.10
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (44 bp):
TTACTTCAATTTCAAGAGGATAGGAAAGATCTTGATGTCCAGCT
Found at i:3721158 original size:91 final size:91
Alignment explanation
Indices: 3721056--3721229 Score: 321
Period size: 91 Copynumber: 1.9 Consensus size: 91
3721046 GGGGGTCTTA
*
3721056 TCTTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGATGTCCAGCTTTACTTAAATTTCAAGA
1 TCTTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGATATCCAGCTTTACTTAAATTTCAAGA
*
3721121 GGATAGGAAATGATCTTGATGCTCTG
66 GGATAGGAAAAGATCTTGATGCTCTG
*
3721147 TCTTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGA
1 TCTTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGATATCCAGCTTTACTTAAATTTCAAGA
3721212 GGATAGGAAAAGATCTTG
66 GGATAGGAAAAGATCTTG
3721230 CTATTACTTC
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 80 1.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (91 bp):
TCTTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGATATCCAGCTTTACTTAAATTTCAAGA
GGATAGGAAAAGATCTTGATGCTCTG
Found at i:3721246 original size:38 final size:38
Alignment explanation
Indices: 3721195--3721398 Score: 152
Period size: 38 Copynumber: 5.4 Consensus size: 38
3721185 ATATCCAGCT
*
3721195 TTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTA
1 TTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTA
* ** ***
3721233 TTACTTCAATTTC-AGA-GATAAAGACGTGTTATCCAACT-
1 TTACTTCAATTTCAAGAGGAT-AGGAAATG--ATCTTGCTA
* *
3721271 TTACTTCAATTTCAAGAGGATAGGAAATGGTCTTGCTC
1 TTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTA
* * ** * *
3721309 TTAGTTCAATTTC-AGA-GATAAAGACTTG-T-TATCCAA
1 TTACTTCAATTTCAAGAGGAT-AGGAAATGATCT-TGCTA
*
3721345 CTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTC
1 -T-TACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTA
3721385 TTACTTCAATTTCA
1 TTACTTCAATTTCA
3721399 GAGATAAAGA
Statistics
Matches: 124, Mismatches: 28, Indels: 28
0.69 0.16 0.16
Matches are distributed among these distances:
35 1 0.01
36 9 0.07
37 20 0.16
38 62 0.50
39 22 0.18
40 9 0.07
41 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Consensus pattern (38 bp):
TTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTA
Found at i:3721275 original size:76 final size:76
Alignment explanation
Indices: 3721147--3721501 Score: 542
Period size: 76 Copynumber: 4.7 Consensus size: 76
3721137 TGATGCTCTG
* * *
3721147 TCTTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGA
1 TCTTGCTCTTACTTCAATTTC--AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGA
*
3721212 GGATAGGAAAAGA
64 GGATAGGAAATGA
* * *
3721225 TCTTGCTATTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTTTACTTCAATTTCAAGAGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
*
3721290 ATAGGAAATGG
66 ATAGGAAATGA
*
3721301 TCTTGCTCTTAGTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
3721366 ATAGGAAATGA
66 ATAGGAAATGA
* *
3721377 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTACCCAACTCTA---C---TTCAAGCGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
3721436 ATAGGAAATGA
66 ATAGGAAATGA
*
3721447 TCTTTCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAA
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAA
3721502 GCGGATAGGA
Statistics
Matches: 256, Mismatches: 16, Indels: 13
0.90 0.06 0.05
Matches are distributed among these distances:
70 66 0.26
73 2 0.01
76 168 0.66
78 20 0.08
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (76 bp):
TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
ATAGGAAATGA
Found at i:3726376 original size:14 final size:15
Alignment explanation
Indices: 3726349--3726382 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3726339 GGTCGTGCTC
*
3726349 TTCTTGTCTCTTTCT
1 TTCTTGTCTATTTCT
3726364 TTCTT-TCTATTTCT
1 TTCTTGTCTATTTCT
3726378 TTCTT
1 TTCTT
3726383 CCTTTCTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.03, C:0.24, G:0.03, T:0.71
Consensus pattern (15 bp):
TTCTTGTCTATTTCT
Found at i:3727786 original size:22 final size:22
Alignment explanation
Indices: 3727758--3727801 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3727748 CAATGCTGAA
3727758 TCTCATGACCTCCAGCGTTGTG
1 TCTCATGACCTCCAGCGTTGTG
*
3727780 TCTCATGACCTTCAGCGTTGTG
1 TCTCATGACCTCCAGCGTTGTG
3727802 GAAATCACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.14, C:0.30, G:0.23, T:0.34
Consensus pattern (22 bp):
TCTCATGACCTCCAGCGTTGTG
Found at i:3733770 original size:59 final size:59
Alignment explanation
Indices: 3733665--3734036 Score: 456
Period size: 59 Copynumber: 6.4 Consensus size: 59
3733655 TTGGATACTC
* * *
3733665 AGGGGCAAAATGATAA-TTTTGGTGAAATCGGGCG-TAAAAATGGAATTTT-AAGAGTTT
1 AGGGGTAAAATGGTAATTTTTGGTGAAATCGGG-GTTAAAAATGGAATTTTGAAAAGTTT
** * *
3733722 AGAGGGTAAAATGGTAATTTTTTATGAAACCGGGGTTAAAAATTGAATTTT-AAAAGGTTT
1 AG-GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAA-GTTT
*
3733782 AGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGAAAAGTTT
1 AGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAAGTTT
* * * *
3733841 AGGGGTAAAATGGTAATTTTTGGTAAAATCGGGTTTAAAAA-AGAATTTTGGAAAGTTT
1 AGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAAGTTT
3733899 AGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-AGAAAG-TT
1 AGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGA-AAAGTTT
* * * * * * *
3733957 CGGGGTAAAATGGTAACTTTT-G-GAAGTTTTGGGGTTAAAAATAGAATTTTGGAAAGTTC
1 AGGGGTAAAATGGTAATTTTTGGTGAA--ATCGGGGTTAAAAATGGAATTTTGAAAAGTTT
3734016 AGGGGTAAAATGGTAATTTTT
1 AGGGGTAAAATGGTAATTTTT
3734037 AGAAGTTTCG
Statistics
Matches: 274, Mismatches: 30, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
56 3 0.01
57 3 0.01
58 112 0.41
59 146 0.53
60 10 0.04
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (59 bp):
AGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAAGTTT
Found at i:3733917 original size:117 final size:116
Alignment explanation
Indices: 3733665--3734036 Score: 484
Period size: 117 Copynumber: 3.2 Consensus size: 116
3733655 TTGGATACTC
* * * *
3733665 AGGGGCAAAATGATAA-TTTTGGTGAAATCGGGCGTAAAAATGGAATTTTAAGAGTTTAGAGGGT
1 AGGGGTAAAATGGTAATTTTTGGTGAAATCGGG-TTAAAAATGGAATTTTAAAAGTTTAG-GGGT
** * * * *
3733729 AAAATGGTAATTTTTTATGAAACCGGGGTTAAAAATTGAATTTT-AAAAGGTTT
64 AAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATAGAATTTTGGAAA-GTTT
3733782 AGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGAAAAGTTTAGGGGT
1 AGGGGTAAAATGGTAATTTTTGGTGAAATCG-GGTTAAAAATGGAATTTT-AAAAGTTTAGGGGT
*
3733847 AAAATGGTAATTTTTGGTAAAATCGGGTTTAAAAA-AGAATTTTGGAAAGTTT
64 AAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTT
*
3733899 AGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAG-TTCGGGGT
1 AGGGGTAAAATGGTAATTTTTGGTGAAATC-GGGTTAAAAATGGAATTTTA-AAAGTTTAGGGGT
* ** * *
3733963 AAAATGGTAACTTTTGG-AAGTTTTGGGGTTAAAAATAGAATTTTGGAAAGTTC
64 AAAATGGTAATTTTTGGTAA-AATCGGGGTTAAAAATAGAATTTTGGAAAGTTT
3734016 AGGGGTAAAATGGTAATTTTT
1 AGGGGTAAAATGGTAATTTTT
3734037 AGAAGTTTCG
Statistics
Matches: 229, Mismatches: 18, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
115 2 0.01
116 35 0.15
117 114 0.50
118 67 0.29
119 11 0.05
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (116 bp):
AGGGGTAAAATGGTAATTTTTGGTGAAATCGGGTTAAAAATGGAATTTTAAAAGTTTAGGGGTAA
AATGGTAATTTTTGGTAAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTT
Found at i:3734315 original size:162 final size:161
Alignment explanation
Indices: 3734138--3734629 Score: 688
Period size: 162 Copynumber: 3.0 Consensus size: 161
3734128 AGCATCCTGA
* *
3734138 AGTCAAAGAACTAATTTAAAAATCTTGAAAAATT-TCTGGGTCAATTTTGTAATTAAACAGAACT
1 AGTCAAAGGACTAATTTATAAATCTTGAAAAATTCT-TGGGTCAATTTTGTAATTAAACAGAACT
* *
3734202 TTATTTTGGAACTAAATTAAAACAAATTAAAAGTGACAGGGACTAGATACTGAAATAACCCAAAA
65 TGATTTTGGAACTAAATTAAAACAAATTAAAAGTGACAGGGACTAGATACT-AAATAAACCAAAA
* * *
3734267 AGTGACACGTGGAGGCCTCTAGCGCAATCAAAC
129 AGTGACACGTGGAGGCCTCTGGTGCAGTCAAAC
3734300 AGTCAAAGGACTAATTTATAAATCTTGAAAAATTCTTGGGTCAATTTTGTAATTAAACAGAACTT
1 AGTCAAAGGACTAATTTATAAATCTTGAAAAATTCTTGGGTCAATTTTGTAATTAAACAGAACTT
*
3734365 GATTTT-GAGACTAAATTAAAACAAATTAAAAGTGACAAGGACTAGATACTAAAATAAACCAAAA
66 GATTTTGGA-ACTAAATTAAAACAAATTAAAAGTGACAGGGACTAGATACT-AAATAAACCAAAA
3734429 AGTGACACGTGGAGGCCTCTGGTGCAGTCAAAC
129 AGTGACACGTGGAGGCCTCTGGTGCAGTCAAAC
* * * *
3734462 AGTAAAAGGACTAATTTATAAATCTTGAAAAATTCTTGGGTCAATTTTGTAATTAAATAAAAGTT
1 AGTCAAAGGACTAATTTATAAATCTTGAAAAATTCTTGGGTCAATTTTGTAATTAAACAGAACTT
* * * * * * * * *
3734527 GATTTAAGGATC-GAATTAAAACAAATTAAAAATAAAAGGGACTAAATGCATAAATAAGCC-AAA
66 GATTT-TGGAACTAAATTAAAACAAATTAAAAGTGACAGGGACTAGATAC-TAAATAAACCAAAA
*
3734590 AGTGACACGTGGCA-GCCTCTGGTGTAGTCAAAC
129 AGTGACACGTGG-AGGCCTCTGGTGCAGTCAAAC
3734623 AGTCAAA
1 AGTCAAA
3734630 TGATTAAATT
Statistics
Matches: 299, Mismatches: 25, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
161 41 0.14
162 253 0.85
163 3 0.01
164 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (161 bp):
AGTCAAAGGACTAATTTATAAATCTTGAAAAATTCTTGGGTCAATTTTGTAATTAAACAGAACTT
GATTTTGGAACTAAATTAAAACAAATTAAAAGTGACAGGGACTAGATACTAAATAAACCAAAAAG
TGACACGTGGAGGCCTCTGGTGCAGTCAAAC
Found at i:3735382 original size:13 final size:13
Alignment explanation
Indices: 3735361--3735398 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
3735351 TTGTTATTAA
*
3735361 ATTATTAATATTT
1 ATTAATAATATTT
3735374 ATTAATAATATTT
1 ATTAATAATATTT
*
3735387 ATTAGTAATATT
1 ATTAATAATATT
3735399 AATGTCATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (13 bp):
ATTAATAATATTT
Found at i:3736218 original size:17 final size:17
Alignment explanation
Indices: 3736198--3736241 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
3736188 TAAATTTGAT
3736198 TAAATTTAAATCTAAAA
1 TAAATTTAAATCTAAAA
*
3736215 TAAATTTAAATTTAAAA
1 TAAATTTAAATCTAAAA
*
3736232 TTAATTTAAA
1 TAAATTTAAA
3736242 CTTTGAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATCTAAAA
Found at i:3736614 original size:6 final size:6
Alignment explanation
Indices: 3736603--3736684 Score: 76
Period size: 6 Copynumber: 12.8 Consensus size: 6
3736593 TGAAATTTGA
* *
3736603 TTAAAT TTAAAT TTAAAT AGGTAAAT TTAAAT TTAAAT AGGTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT
*
3736655 TTAAA- ATAAAT TTAAATT TATAAAT TTAAA
1 TTAAAT TTAAAT TTAAA-T T-TAAAT TTAAA
3736685 ATCAATTAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
5 4 0.06
6 41 0.65
7 4 0.06
8 14 0.22
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (6 bp):
TTAAAT
Found at i:3736629 original size:20 final size:20
Alignment explanation
Indices: 3736604--3736674 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
3736594 GAAATTTGAT
3736604 TAAATTTAAATTTAAATAGG
1 TAAATTTAAATTTAAATAGG
3736624 TAAATTTAAATTTAAATAGG
1 TAAATTTAAATTTAAATAGG
3736644 TAAATTTAAATTTAAA-A--
1 TAAATTTAAATTTAAATAGG
3736661 TAAATTTAAATTTA
1 TAAATTTAAATTTA
3736675 TAAATTTAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
17 14 0.27
19 1 0.02
20 36 0.71
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (20 bp):
TAAATTTAAATTTAAATAGG
Found at i:3743936 original size:46 final size:45
Alignment explanation
Indices: 3743837--3743936 Score: 105
Period size: 46 Copynumber: 2.2 Consensus size: 45
3743827 AAATATATCT
* * * * *
3743837 AAATTTAAATTAAAATAAACAGTTATATATGATAATATTTAAAATC
1 AAATTAAAATTAAAATAAAAACTTATATAT-ATAATATATAAAATA
*
3743883 AAA-TAAAATTTAAACTAAAAACTTATATAT-TAATTATATAAAATA
1 AAATTAAAA-TTAAAATAAAAACTTATATATATAA-TATATAAAATA
3743928 AAATTAAAA
1 AAATTAAAA
3743937 ACTCAAAGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
44 3 0.07
45 16 0.36
46 26 0.58
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (45 bp):
AAATTAAAATTAAAATAAAAACTTATATATATAATATATAAAATA
Found at i:3744525 original size:15 final size:16
Alignment explanation
Indices: 3744505--3744537 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3744495 TCATATCTCC
*
3744505 CAAGAACAT-CCATCT
1 CAAGAAAATACCATCT
3744520 CAAGAAAATACCATCT
1 CAAGAAAATACCATCT
3744536 CA
1 CA
3744538 TAAATGGCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.45, C:0.30, G:0.06, T:0.18
Consensus pattern (16 bp):
CAAGAAAATACCATCT
Found at i:3746060 original size:15 final size:15
Alignment explanation
Indices: 3746042--3746072 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3746032 TAGAAATTTT
*
3746042 AAAAATTTAAATTAA
1 AAAAAATTAAATTAA
3746057 AAAAAATTAAATTAA
1 AAAAAATTAAATTAA
3746072 A
1 A
3746073 TTTTGATTCC
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAAATTAAATTAA
Found at i:3750315 original size:6 final size:6
Alignment explanation
Indices: 3750269--3750332 Score: 67
Period size: 6 Copynumber: 10.0 Consensus size: 6
3750259 GTAAAAAATT
*
3750269 TAAAAA TAAAACT TAAAAA TTCAAAAA -AAAAA TATATAAA TAAAAA TAAAAA
1 TAAAAA TAAAA-A TAAAAA -T-AAAAA TAAAAA TA-A-AAA TAAAAA TAAAAA
3750321 TAAAAA TAAAAA
1 TAAAAA TAAAAA
3750333 AGGTTAAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
5 5 0.10
6 27 0.54
7 8 0.16
8 10 0.20
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:3750332 original size:34 final size:34
Alignment explanation
Indices: 3750261--3750333 Score: 85
Period size: 34 Copynumber: 2.2 Consensus size: 34
3750251 AATATGATGT
* * **
3750261 AAAAAATTTAAAAATAAAACTTAAAAATTCAAAA
1 AAAAAATATAAAAATAAAACATAAAAATAAAAAA
* *
3750295 AAAAAATATATAAATAAAA-ATAAAAATAAAAAT
1 AAAAAATATAAAAATAAAACATAAAAATAAAAAA
3750328 AAAAAA
1 AAAAAA
3750334 GGTTAAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 16 0.48
34 17 0.52
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (34 bp):
AAAAAATATAAAAATAAAACATAAAAATAAAAAA
Found at i:3760373 original size:20 final size:21
Alignment explanation
Indices: 3760350--3760396 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
3760340 AAAATTGGTT
*
3760350 TTTTTTATAGAATTT-ATAA-A
1 TTTTTGATA-AATTTAATAATA
3760370 TTTTATGATAAATTTAATAATA
1 TTTT-TGATAAATTTAATAATA
3760392 TTTTT
1 TTTTT
3760397 AGTTCAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 9 0.39
21 9 0.39
22 5 0.22
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
TTTTTGATAAATTTAATAATA
Found at i:3761256 original size:45 final size:44
Alignment explanation
Indices: 3761206--3761706 Score: 327
Period size: 45 Copynumber: 10.9 Consensus size: 44
3761196 CCGGAGGTTT
** *
3761206 TTTTGGAGGCTCATAAACTGGTGGTTTGGGTTTTGGCTTGTCTTC
1 TTTTGGAGG-TCATAAACTGGTGGTTTGGGTTCAGGCTTCTCTTC
*
3761251 TTTTGGTGGTGCATAAACTGGTGGCTTTGGTGGCTT-AGGCTCATACACCGGTGGCTTC
1 TTTTGGAGGT-CATAAACTGGTGG-TTT-G-GG-TTCAGGCT--T----C--T--CTTC
* * * *
3761309 -TTTGGAGGCTCATAAACCGGTGGTTTGGGTTCTGGTTTTTCTT-
1 TTTTGGAGG-TCATAAACTGGTGGTTTGGGTTCAGGCTTCTCTTC
* * *
3761352 TCTTTGGAGGTGCATAAACTGGTGGCTTAGGTTCAGGTTTCTCCTTC
1 T-TTTGGAGGT-CATAAACTGGTGGTTTGGGTTCAGGCTTCT-CTTC
* *
3761399 -TTTGGTGGTTCATACACTGGTGGTTTGGGTTCAGGCTTCTCTT-
1 TTTTGGAGG-TCATAAACTGGTGGTTTGGGTTCAGGCTTCTCTTC
* * * * *
3761442 TCTTTGGAGGTGTATAAACTGGTGGCTTAGGCTCAGGTTTCTCCTTC
1 T-TTTGGAGGT-CATAAACTGGTGGTTTGGGTTCAGGCTTCT-CTTC
* * * *
3761489 -TTTGGAGGTTCATACACTGGTGGTTTAGGTTTAGGCTTCTCTTT
1 TTTTGGAGG-TCATAAACTGGTGGTTTGGGTTCAGGCTTCTCTTC
* * *
3761533 TTTTGGTGGTTCATACACTGGTGGTTTGGGTTCAGGTTTCTCTT-
1 TTTTGGAGG-TCATAAACTGGTGGTTTGGGTTCAGGCTTCTCTTC
* * * *
3761577 TCTTTGGAGGTGTATAAACTGGTGGCTTAGGCTCAGGCTTCTCCTTC
1 T-TTTGGAGGT-CATAAACTGGTGGTTTGGGTTCAGGCTTCT-CTTC
* * *
3761624 -TTCGGAGGTTCATACACTGGTGGTTTGGGTTCAGGTTTCTCTT-
1 TTTTGGAGG-TCATAAACTGGTGGTTTGGGTTCAGGCTTCTCTTC
* * * *
3761667 TCTTTGGAGGTGTATAAACGGGTGGCTTAGGTTCAGGCTT
1 T-TTTGGAGGT-CATAAACTGGTGGTTTGGGTTCAGGCTT
3761707 AGGTTCAGGC
Statistics
Matches: 361, Mismatches: 57, Indels: 76
0.73 0.12 0.15
Matches are distributed among these distances:
44 18 0.05
45 280 0.78
46 16 0.04
47 1 0.00
48 6 0.02
49 2 0.01
50 1 0.00
52 1 0.00
53 2 0.01
54 5 0.01
55 1 0.00
56 4 0.01
57 19 0.05
58 5 0.01
ACGTcount: A:0.13, C:0.16, G:0.30, T:0.41
Consensus pattern (44 bp):
TTTTGGAGGTCATAAACTGGTGGTTTGGGTTCAGGCTTCTCTTC
Found at i:3761412 original size:90 final size:90
Alignment explanation
Indices: 3761305--3761706 Score: 493
Period size: 90 Copynumber: 4.5 Consensus size: 90
3761295 ACACCGGTGG
* * * * * *
3761305 CTTCTTTGGAGGCTCATAAACCGGTGGTTTGGGTTCTGGTTTTTCTTTCTTTGGAGGTGCATAAA
1 CTTCTTTGGAGGTTCATAAACTGGTGGTTTAGGTTCAGGCTTCTCTTTCTTTGGAGGTGCATAAA
3761370 CTGGTGGCTTAGGTTCAGGTTTCTC
66 CTGGTGGCTTAGGTTCAGGTTTCTC
* * * *
3761395 CTTCTTTGGTGGTTCATACACTGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAA
1 CTTCTTTGGAGGTTCATAAACTGGTGGTTTAGGTTCAGGCTTCTCTTTCTTTGGAGGTGCATAAA
*
3761460 CTGGTGGCTTAGGCTCAGGTTTCTC
66 CTGGTGGCTTAGGTTCAGGTTTCTC
* * * * * *
3761485 CTTCTTTGGAGGTTCATACACTGGTGGTTTAGGTTTAGGCTTCTCTTTTTTTGGTGGTTCATACA
1 CTTCTTTGGAGGTTCATAAACTGGTGGTTTAGGTTCAGGCTTCTCTTTCTTTGGAGGTGCATAAA
* *
3761550 CTGGTGGTTTGGGTTCAGGTTTCTC
66 CTGGTGGCTTAGGTTCAGGTTTCTC
* * * * * * *
3761575 TTTCTTTGGAGGTGT-ATAAACTGGTGGCTTAGGCTCAGGCTTCTCCTTCTTCGGAGGTTCATAC
1 CTTCTTTGGAGGT-TCATAAACTGGTGGTTTAGGTTCAGGCTTCTCTTTCTTTGGAGGTGCATAA
* *
3761639 ACTGGTGGTTTGGGTTCAGGTTTCTC
65 ACTGGTGGCTTAGGTTCAGGTTTCTC
* * *
3761665 TTTCTTTGGAGGTGT-ATAAACGGGTGGCTTAGGTTCAGGCTT
1 CTTCTTTGGAGGT-TCATAAACTGGTGGTTTAGGTTCAGGCTT
3761707 AGGTTCAGGC
Statistics
Matches: 280, Mismatches: 31, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
90 279 1.00
91 1 0.00
ACGTcount: A:0.13, C:0.17, G:0.29, T:0.41
Consensus pattern (90 bp):
CTTCTTTGGAGGTTCATAAACTGGTGGTTTAGGTTCAGGCTTCTCTTTCTTTGGAGGTGCATAAA
CTGGTGGCTTAGGTTCAGGTTTCTC
Found at i:3761481 original size:135 final size:135
Alignment explanation
Indices: 3761306--3761706 Score: 554
Period size: 135 Copynumber: 3.0 Consensus size: 135
3761296 CACCGGTGGC
* * * * * * * * * *
3761306 TTCTTTGGAGGCT-CATAAACCGGTGGTTTGGGTTCTGGTTTTTCTTTCTTTGGAGGTGCATAAA
1 TTCTTTGGAGG-TGTATAAACTGGTGGCTTAGGCTCAGGTTTCTCCTTCTTTGGAGGTTCATACA
* *
3761370 CTGGTGGCTTAGGTTCAGGTTTCTCCTTCTTTGGTGGTTCATACACTGGTGGTTTGGGTTCAGGC
65 CTGGTGGTTTAGGTTCAGGTTTCTCTTTCTTTGGTGGTTCATACACTGGTGGTTTGGGTTCAGGC
3761435 TTCTCT
130 TTCTCT
3761441 TTCTTTGGAGGTGTATAAACTGGTGGCTTAGGCTCAGGTTTCTCCTTCTTTGGAGGTTCATACAC
1 TTCTTTGGAGGTGTATAAACTGGTGGCTTAGGCTCAGGTTTCTCCTTCTTTGGAGGTTCATACAC
* * * *
3761506 TGGTGGTTTAGGTTTAGGCTTCTCTTTTTTTGGTGGTTCATACACTGGTGGTTTGGGTTCAGGTT
66 TGGTGGTTTAGGTTCAGGTTTCTCTTTCTTTGGTGGTTCATACACTGGTGGTTTGGGTTCAGGCT
3761571 TCTCT
131 TCTCT
* *
3761576 TTCTTTGGAGGTGTATAAACTGGTGGCTTAGGCTCAGGCTTCTCCTTCTTCGGAGGTTCATACAC
1 TTCTTTGGAGGTGTATAAACTGGTGGCTTAGGCTCAGGTTTCTCCTTCTTTGGAGGTTCATACAC
* * * * * *
3761641 TGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGT-ATAAACGGGTGGCTTAGGTTCAGGC
66 TGGTGGTTTAGGTTCAGGTTTCTCTTTCTTTGGTGGT-TCATACACTGGTGGTTTGGGTTCAGGC
3761705 TT
130 TT
3761707 AGGTTCAGGC
Statistics
Matches: 236, Mismatches: 28, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
134 1 0.00
135 234 0.99
136 1 0.00
ACGTcount: A:0.13, C:0.16, G:0.29, T:0.41
Consensus pattern (135 bp):
TTCTTTGGAGGTGTATAAACTGGTGGCTTAGGCTCAGGTTTCTCCTTCTTTGGAGGTTCATACAC
TGGTGGTTTAGGTTCAGGTTTCTCTTTCTTTGGTGGTTCATACACTGGTGGTTTGGGTTCAGGCT
TCTCT
Found at i:3761705 original size:12 final size:12
Alignment explanation
Indices: 3761690--3761718 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3761680 ATAAACGGGT
3761690 GGCTTAGGTTCA
1 GGCTTAGGTTCA
3761702 GGCTTAGGTTCA
1 GGCTTAGGTTCA
3761714 GGCTT
1 GGCTT
3761719 CTCCTTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.17, G:0.34, T:0.34
Consensus pattern (12 bp):
GGCTTAGGTTCA
Found at i:3762512 original size:24 final size:22
Alignment explanation
Indices: 3762461--3762512 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
3762451 TTATTTAAAT
*
3762461 TTAATTATAAAACTATATAATA
1 TTAATTATAAAAATATATAATA
*
3762483 TCAATTAATAAAAATA-ATAATTTA
1 TTAATT-ATAAAAATATATAA--TA
3762507 TTAATT
1 TTAATT
3762513 TTTTAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
22 9 0.38
23 8 0.33
24 7 0.29
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAATTATAAAAATATATAATA
Found at i:3764316 original size:16 final size:15
Alignment explanation
Indices: 3764292--3764338 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
3764282 AAAATTTAAT
3764292 AAAT-ATAAAATATA
1 AAATAATAAAATATA
* *
3764306 AAATTATTAAATATTA
1 AAATAATAAAATA-TA
*
3764322 AAATAATATAATATA
1 AAATAATAAAATATA
3764337 AA
1 AA
3764339 TATTTTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.15
15 11 0.41
16 12 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATAATAAAATATA
Found at i:3765216 original size:145 final size:144
Alignment explanation
Indices: 3765050--3765313 Score: 386
Period size: 144 Copynumber: 1.8 Consensus size: 144
3765040 AAATTTCGTC
* * * *
3765050 GGCATCCTATTGTGATGAACTTTAAATAATATTTACTTGATTTCGAGTATAACTTTTTTTGTTTA
1 GGCATCCTATTGTGATAAACTTTAAATAATATTTACTTGATTTCGAGTATAA-ATTATTTATTTA
* *
3765115 TCTT-TTATAAAACAAATAGTAAATTAAAGATAATATAAAAAATTAAAAATATTATTTTGTAATT
65 T-TTATTACAAAACAAATAGTAAATTAAAGATAACATAAAAAATTAAAAATATTATTTTGTAATT
3765179 CCACCAAAACTTCATT
129 CCACCAAAACTTCATT
* * * * *
3765195 GGCATCTTATTGTGGTAAACTTTAATTAATATTTATTTGATTTCGATTATAAATTATTTATTTAT
1 GGCATCCTATTGTGATAAACTTTAAATAATATTTACTTGATTTCGAGTATAAATTATTTATTTAT
* *
3765260 TTATTACAAAACAAATCGTAAATTAAAGATAACATAAAAAATTACAAATATTAT
66 TTATTACAAAACAAATAGTAAATTAAAGATAACATAAAAAATTAAAAATATTAT
3765314 ATTCCAATAT
Statistics
Matches: 105, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
143 2 0.02
144 57 0.54
145 46 0.44
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (144 bp):
GGCATCCTATTGTGATAAACTTTAAATAATATTTACTTGATTTCGAGTATAAATTATTTATTTAT
TTATTACAAAACAAATAGTAAATTAAAGATAACATAAAAAATTAAAAATATTATTTTGTAATTCC
ACCAAAACTTCATT
Found at i:3767167 original size:102 final size:101
Alignment explanation
Indices: 3766960--3767258 Score: 265
Period size: 90 Copynumber: 3.0 Consensus size: 101
3766950 GTGACCATAC
* * * *
3766960 GGTGGTTTCTTTGGAGGTTCATAAACTGGTGGTTTGGGTT-TTG-ATTTCTCTTTCTTTGGTGGT
1 GGTGGTTTCTTTGGAGGTT-ATAAACCGGTGGTTTGGGTTCTAGCTTTTCTC-TTCTTTGGAGGT
* *** *
3767023 GCATAAACTGGTGGTTTGGGT--GGCTTAGGC-TCATAAACT
64 GCATAAACTGGTGGTTTGGCTCAGGCTTTTCCTTC-T---TT
* *
3767062 GGTGGTTTCTTTGGAGGTTGATAAACGGGTGGTTTGGGTTCTGGCTTTTCTCTT-TTTGGAGGTG
1 GGTGGTTTCTTTGGAGGTT-ATAAACCGGTGGTTTGGGTTCTAGCTTTTCTCTTCTTTGGAGGTG
3767126 CATAAACTGGTGGTTTAGGCTCAGGCTTTTCCTTCTTT
65 CATAAACTGGTGGTTT-GGCTCAGGCTTTTCCTTCTTT
* * *
3767164 GGTGG-TTC-----A---TAT--ACCGGTGGTTTGGGTTCAAGCTTCTCT-TTCTTTGGAGGTGT
1 GGTGGTTTCTTTGGAGGTTATAAACCGGTGGTTTGGGTTCTAGCTTTTCTCTTCTTTGGAGGTGC
3767217 ATAAACTGGTGGCTTTGGCTCAGGCTTTTCCTTCTTT
66 ATAAACTGGTGG-TTTGGCTCAGGCTTTTCCTTCTTT
3767254 GGTGG
1 GGTGG
3767259 CTCATACACT
Statistics
Matches: 174, Mismatches: 15, Indels: 28
0.80 0.07 0.13
Matches are distributed among these distances:
89 2 0.01
90 71 0.41
91 3 0.02
92 2 0.01
93 1 0.01
96 1 0.01
101 3 0.02
102 69 0.40
103 7 0.04
104 6 0.03
105 7 0.04
106 2 0.01
ACGTcount: A:0.13, C:0.14, G:0.31, T:0.42
Consensus pattern (101 bp):
GGTGGTTTCTTTGGAGGTTATAAACCGGTGGTTTGGGTTCTAGCTTTTCTCTTCTTTGGAGGTGC
ATAAACTGGTGGTTTGGCTCAGGCTTTTCCTTCTTT
Found at i:3767318 original size:135 final size:136
Alignment explanation
Indices: 3767067--3767366 Score: 315
Period size: 135 Copynumber: 2.2 Consensus size: 136
3767057 AAACTGGTGG
* * * *
3767067 TTTCTTTGGAGGTTGATAAACGGGTGG-TTTGGGTTCTGGCTTTTCTCTTTTTGGAGGTGCATAA
1 TTTCTTTGGAGGTTCATAAACAGGTGGCTTTGGGCTCAGGCTTTTCTCTTTTTGGAGGTGCATAA
* * * * * * *
3767131 ACTGGTGGTTTAGGCTCAGGCTTTTCCTTCTTTGGTGGTTCATATACCGGTGGTTTGGGTTCAAG
66 ACTGGTGGCTTAGGCTCAGGCTTCTCCTTCTTTGGTGATTCATAAACCGGTGGCTTAGGCTCAAG
3767196 CTTCTC
131 CTTCTC
* *
3767202 TTTCTTTGGAGGTGT-ATAAACTGGTGGCTTT-GGCTCAGGCTTTTC-CTTCTTTGGTGGCT-CA
1 TTTCTTTGGAGGT-TCATAAACAGGTGGCTTTGGGCTCAGGCTTTTCTCTT-TTTGGAGG-TGCA
* * * * * *
3767263 TACACTGGTGGCTTGGGTTCAGGCTTCTCTTTTTTTGGTGATGT-ATAAACTGGTGGCTTAGGCT
63 TAAACTGGTGGCTTAGGCTCAGGCTTCTCCTTCTTTGGTGAT-TCATAAACCGGTGGCTTAGGCT
* * *
3767327 CAGGTTTTTC
127 CAAGCTTCTC
*
3767337 TTTCTTTGGAGGTTCATAGACAGGTGGCTT
1 TTTCTTTGGAGGTTCATAAACAGGTGGCTT
3767367 ATGTTCATAT
Statistics
Matches: 137, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
134 4 0.03
135 127 0.93
136 6 0.04
ACGTcount: A:0.13, C:0.16, G:0.29, T:0.42
Consensus pattern (136 bp):
TTTCTTTGGAGGTTCATAAACAGGTGGCTTTGGGCTCAGGCTTTTCTCTTTTTGGAGGTGCATAA
ACTGGTGGCTTAGGCTCAGGCTTCTCCTTCTTTGGTGATTCATAAACCGGTGGCTTAGGCTCAAG
CTTCTC
Found at i:3767363 original size:45 final size:45
Alignment explanation
Indices: 3767067--3767367 Score: 275
Period size: 45 Copynumber: 6.7 Consensus size: 45
3767057 AAACTGGTGG
* * * * * *
3767067 TTTCTTTGGAGGTTGATAAACGGGTGGTTTGGGTTCTGGCTTTTC
1 TTTCTTTGGAGGTTCATAAACTGGTGGCTTAGGCTCAGGCTTTTC
* *
3767112 TCTT-TTTGGAGGTGCATAAACTGGTGGTTTAGGCTCAGGCTTTTC
1 T-TTCTTTGGAGGTTCATAAACTGGTGGCTTAGGCTCAGGCTTTTC
* * * * * * * * *
3767157 CTTCTTTGGTGGTTCATATACCGGTGGTTTGGGTTCAAGCTTCTC
1 TTTCTTTGGAGGTTCATAAACTGGTGGCTTAGGCTCAGGCTTTTC
*
3767202 TTTCTTTGGAGGTGT-ATAAACTGGTGGCTTTGGCTCAGGCTTTTC
1 TTTCTTTGGAGGT-TCATAAACTGGTGGCTTAGGCTCAGGCTTTTC
* * * * * * *
3767247 CTTCTTTGGTGGCTCATACACTGGTGGCTTGGGTTCAGGCTTCTC
1 TTTCTTTGGAGGTTCATAAACTGGTGGCTTAGGCTCAGGCTTTTC
* * * *
3767292 TTTTTTTGGTGATGT-ATAAACTGGTGGCTTAGGCTCAGGTTTTTC
1 TTTCTTTGGAGGT-TCATAAACTGGTGGCTTAGGCTCAGGCTTTTC
* *
3767337 TTTCTTTGGAGGTTCATAGACAGGTGGCTTA
1 TTTCTTTGGAGGTTCATAAACTGGTGGCTTA
3767368 TGTTCATATG
Statistics
Matches: 205, Mismatches: 45, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
44 4 0.02
45 197 0.96
46 4 0.02
ACGTcount: A:0.13, C:0.16, G:0.29, T:0.42
Consensus pattern (45 bp):
TTTCTTTGGAGGTTCATAAACTGGTGGCTTAGGCTCAGGCTTTTC
Found at i:3767373 original size:90 final size:90
Alignment explanation
Indices: 3767068--3767366 Score: 382
Period size: 90 Copynumber: 3.3 Consensus size: 90
3767058 AACTGGTGGT
* * * * * * *
3767068 TTCTTTGGAGGTTGATAAACGGGTGGTTTGGGTTCTGGCTTTTCTCTTTTTGGAGGTGCATAAAC
1 TTCTTTGGAGGTTCATAAACAGGTGGCTTGGGTTCAGGCTTCTCTTTTTTTGGAGGTGTATAAAC
*
3767133 TGGTGGTTTAGGCTCAGGCTTTTCC
66 TGGTGGCTTAGGCTCAGGCTTTTCC
* * * * * *
3767158 TTCTTTGGTGGTTCATATACCGGTGGTTTGGGTTCAAGCTTCTCTTTCTTTGGAGGTGTATAAAC
1 TTCTTTGGAGGTTCATAAACAGGTGGCTTGGGTTCAGGCTTCTCTTTTTTTGGAGGTGTATAAAC
*
3767223 TGGTGGCTTTGGCTCAGGCTTTTCC
66 TGGTGGCTTAGGCTCAGGCTTTTCC
* * * * * *
3767248 TTCTTTGGTGGCTCATACACTGGTGGCTTGGGTTCAGGCTTCTCTTTTTTTGGTGATGTATAAAC
1 TTCTTTGGAGGTTCATAAACAGGTGGCTTGGGTTCAGGCTTCTCTTTTTTTGGAGGTGTATAAAC
* *
3767313 TGGTGGCTTAGGCTCAGGTTTTTCT
66 TGGTGGCTTAGGCTCAGGCTTTTCC
*
3767338 TTCTTTGGAGGTTCATAGACAGGTGGCTT
1 TTCTTTGGAGGTTCATAAACAGGTGGCTT
3767367 ATGTTCATAT
Statistics
Matches: 182, Mismatches: 27, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
90 182 1.00
ACGTcount: A:0.13, C:0.16, G:0.29, T:0.42
Consensus pattern (90 bp):
TTCTTTGGAGGTTCATAAACAGGTGGCTTGGGTTCAGGCTTCTCTTTTTTTGGAGGTGTATAAAC
TGGTGGCTTAGGCTCAGGCTTTTCC
Found at i:3767811 original size:32 final size:31
Alignment explanation
Indices: 3767758--3767824 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 31
3767748 ATAATTTATT
*
3767758 TTTTTATAATTTTTAAAAGATTAAATTA-AA
1 TTTTTATAATTTTTAAAAGATTAAAATATAA
* *
3767788 TTTTTATTATTTTTAGGAGAGATTAAAATATAA
1 TTTTTATAATTTTTA--AAAGATTAAAATATAA
3767821 TTTT
1 TTTT
3767825 ATTTTTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 14 0.45
32 11 0.35
33 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (31 bp):
TTTTTATAATTTTTAAAAGATTAAAATATAA
Found at i:3770151 original size:13 final size:13
Alignment explanation
Indices: 3770135--3770192 Score: 61
Period size: 13 Copynumber: 4.7 Consensus size: 13
3770125 AGAGAAGAGA
*
3770135 AGAGCAGAACGAC
1 AGAGAAGAACGAC
3770148 AGAGAAGAA-GA-
1 AGAGAAGAACGAC
*
3770159 AGAGCAGAACGAC
1 AGAGAAGAACGAC
3770172 AGAGAAGAA-GA-
1 AGAGAAGAACGAC
3770183 AGAAGAAGAA
1 AG-AGAAGAA
3770193 GAATGATGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 16 0.41
ACGTcount: A:0.57, C:0.10, G:0.33, T:0.00
Consensus pattern (13 bp):
AGAGAAGAACGAC
Found at i:3770158 original size:3 final size:3
Alignment explanation
Indices: 3770121--3770195 Score: 54
Period size: 3 Copynumber: 25.7 Consensus size: 3
3770111 GTTACCATCA
*
3770121 AAG AAG -AG AAG -AG AAG -AG CAG AACG ACAG -AG AAG AAG AAG -AG
1 AAG AAG AAG AAG AAG AAG AAG AAG AA-G A-AG AAG AAG AAG AAG AAG
*
3770163 CAG AACG ACAG -AG AAG AAG AAG AAG AAG AAG AA
1 AAG AA-G A-AG AAG AAG AAG AAG AAG AAG AAG AA
3770196 TGATGGGTGT
Statistics
Matches: 60, Mismatches: 2, Indels: 20
0.73 0.02 0.24
Matches are distributed among these distances:
2 12 0.20
3 40 0.67
4 6 0.10
5 2 0.03
ACGTcount: A:0.59, C:0.08, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3770163 original size:24 final size:24
Alignment explanation
Indices: 3770125--3770185 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
3770115 CCATCAAAGA
3770125 AGAGAAG-AGAAGAGCAGAACGAC
1 AGAGAAGAAGAAGAGCAGAACGAC
3770148 AGAGAAGAAGAAGAGCAGAACGAC
1 AGAGAAGAAGAAGAGCAGAACGAC
3770172 AGAGAAGAAGAAGA
1 AGAGAAGAAGAAGA
3770186 AGAAGAAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 7 0.19
24 30 0.81
ACGTcount: A:0.56, C:0.10, G:0.34, T:0.00
Consensus pattern (24 bp):
AGAGAAGAAGAAGAGCAGAACGAC
Found at i:3770633 original size:3 final size:3
Alignment explanation
Indices: 3770596--3770670 Score: 95
Period size: 3 Copynumber: 25.7 Consensus size: 3
3770586 GTTACCATCA
*
3770596 AAG AAG -AG AAG -AG AAG -AG CAG AACG ACAG -AG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AA-G A-AG AAG AAG AAG AAG AAG
3770639 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
3770671 TGATGGGTGT
Statistics
Matches: 65, Mismatches: 1, Indels: 12
0.83 0.01 0.15
Matches are distributed among these distances:
2 8 0.12
3 53 0.82
4 3 0.05
5 1 0.02
ACGTcount: A:0.63, C:0.04, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3770934 original size:475 final size:475
Alignment explanation
Indices: 3770044--3770969 Score: 1721
Period size: 475 Copynumber: 1.9 Consensus size: 475
3770034 ATGAAAATAG
3770044 AATACAAAATTTTACCTTAAAACCTAATTTTCTCCGGTTTAAAAAGAAGCAACAGTTGAGGTTTT
1 AATACAAAATTTTACCTTAAAACCTAATTTTCTCCGGTTTAAAAAGAAGCAACAGTTGAGGTTTT
*
3770109 TTGTTACCATCAAAGAAGAGAAGAGAAGAGCAGAACGACAGAGAAGAAGAAGAGCAGAACGACAG
66 TTGTTACCATCAAAGAAGAGAAGAGAAGAGCAGAACGACAGAGAAGAAGAAGAGAAGAACGACAG
3770174 AGAAGAAGAAGAAGAAGAAGAATGATGGGTGTCGAATCCACCAAATATAATTATTCCTACGATAA
131 AGAAGAAGAAGAAGAAGAAGAATGATGGGTGTCGAATCCACCAAATATAATTATTCCTACGATAA
3770239 ATAATACAAAATAGTAGTATAAAGCAGTAGGGTCGATTCCACAGGGACTGATTGCTGTAATCTAC
196 ATAATACAAAATAGTAGTATAAAGCAGTAGGGTCGATTCCACAGGGACTGATTGCTGTAATCTAC
* *
3770304 TCTCGTGTCTTCCTCTTGAACGTCGTGTCGAAAGGCGTGCTCACGACTCATGAATGTCTCCTAAC
261 TCTCGTATCTTCCTCTTGAACGTCGTGTCGAAAGGCGTGCCCACGACTCATGAATGTCTCCTAAC
3770369 AAAAATAAAAATAAATAAGTGAGGGTTCAAAGATAAAATGTTAAAACTAAAATAAAACCAAAATA
326 AAAAATAAAAATAAATAAGTGAGGGTTCAAAGATAAAATGTTAAAACTAAAATAAAACCAAAATA
*
3770434 AAATAAATAAAGTGAAATAAATCTTGATGCAAATAGTTAATCAAGATAAAAAAGAGAAAAAAACT
391 AAATAAATAAAGTGAAATAAATCTTGATGCAAATAATTAATCAAGATAAAAAAGAGAAAAAAACT
3770499 CAAACAAAAGTTGAGGTTTA
456 CAAACAAAAGTTGAGGTTTA
*
3770519 AATACAAAATTTTGCCTTAAAACCTAATTTTCTCCGGTTTAAAAAGAAGCAACAGTTGAGGTTTT
1 AATACAAAATTTTACCTTAAAACCTAATTTTCTCCGGTTTAAAAAGAAGCAACAGTTGAGGTTTT
3770584 TTGTTACCATCAAAGAAGAGAAGAGAAGAGCAGAACGACAGAGAAGAAGAAGAAGAAGAA-GA-A
66 TTGTTACCATCAAAGAAGAGAAGAGAAGAGCAGAACGACAGAGAAGAAGAAG-AGAAGAACGACA
*
3770647 GAAGAAGAAGAAGAAGAAGAAGAATGATGGGTGTCGAATCCACCAAATATAATTATTCTTACGAT
130 G-AGAAGAAGAAGAAGAAGAAGAATGATGGGTGTCGAATCCACCAAATATAATTATTCCTACGAT
* *
3770712 AAATAATACAAAATAGTAGTATAAAGCAGTAGGGTCGATTTCACAGGGACTGGTTGCTGTAATCT
194 AAATAATACAAAATAGTAGTATAAAGCAGTAGGGTCGATTCCACAGGGACTGATTGCTGTAATCT
*
3770777 ACTCTCGTATCTTCCTCTTGAATGTCGTGTCGAAAGGCGTGCCCACGACTCATGAATGTCTCCTA
259 ACTCTCGTATCTTCCTCTTGAACGTCGTGTCGAAAGGCGTGCCCACGACTCATGAATGTCTCCTA
3770842 ACAAAAATAAAAATAAATAAGTGAGGGTTCAAAGATAAAATGTTAAAACTAAAATAAAACCAAAA
324 ACAAAAATAAAAATAAATAAGTGAGGGTTCAAAGATAAAATGTTAAAACTAAAATAAAACCAAAA
* *
3770907 TAAAATAAATAAAGTGAAATGAATCTTGATGCAAATAATTAATCAAGATAAAAAAGATAAAAA
389 TAAAATAAATAAAGTGAAATAAATCTTGATGCAAATAATTAATCAAGATAAAAAAGAGAAAAA
3770970 TTATATTTAA
Statistics
Matches: 438, Mismatches: 11, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
474 2 0.00
475 430 0.98
476 6 0.01
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (475 bp):
AATACAAAATTTTACCTTAAAACCTAATTTTCTCCGGTTTAAAAAGAAGCAACAGTTGAGGTTTT
TTGTTACCATCAAAGAAGAGAAGAGAAGAGCAGAACGACAGAGAAGAAGAAGAGAAGAACGACAG
AGAAGAAGAAGAAGAAGAAGAATGATGGGTGTCGAATCCACCAAATATAATTATTCCTACGATAA
ATAATACAAAATAGTAGTATAAAGCAGTAGGGTCGATTCCACAGGGACTGATTGCTGTAATCTAC
TCTCGTATCTTCCTCTTGAACGTCGTGTCGAAAGGCGTGCCCACGACTCATGAATGTCTCCTAAC
AAAAATAAAAATAAATAAGTGAGGGTTCAAAGATAAAATGTTAAAACTAAAATAAAACCAAAATA
AAATAAATAAAGTGAAATAAATCTTGATGCAAATAATTAATCAAGATAAAAAAGAGAAAAAAACT
CAAACAAAAGTTGAGGTTTA
Found at i:3771036 original size:24 final size:23
Alignment explanation
Indices: 3771004--3771049 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
3770994 TTAGTCTCGG
*
3771004 TTTTCTTGTTTTGCTCTTCCTTTC
1 TTTTCTTGTTTTGATC-TCCTTTC
*
3771028 TTTTTTTGTTTTGATCTCCTTT
1 TTTTCTTGTTTTGATCTCCTTT
3771050 TTCTTTCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.02, C:0.20, G:0.09, T:0.70
Consensus pattern (23 bp):
TTTTCTTGTTTTGATCTCCTTTC
Found at i:3771853 original size:6 final size:6
Alignment explanation
Indices: 3771818--3771923 Score: 101
Period size: 6 Copynumber: 17.2 Consensus size: 6
3771808 TTCTTGGACT
* *
3771818 TTTAATA TTTAATG TTTAAA TTTATTA TTTAAA TTTAAA TTTAAA TTTAAA
1 TTTAA-A TTTAA-A TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA
**
3771869 TTT-AA GGTAAA TTTAAA TAATTAAA TTTAAA TTTAAGA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA T--TTAAA TTTAAA TTTAA-A TTTAAA TTTAAA
3771917 TTTAAA T
1 TTTAAA T
3771924 AAACTTAAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
4 1 0.01
5 6 0.07
6 54 0.64
7 17 0.20
8 6 0.07
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:3771868 original size:31 final size:29
Alignment explanation
Indices: 3771847--3771923 Score: 127
Period size: 31 Copynumber: 2.6 Consensus size: 29
3771837 ATTTATTATT
*
3771847 TAAATTTAAATTTAAATTTAAATTTAAGG
1 TAAATTTAAATTTAAATTTAAATTTAAGA
3771876 TAAATTTAAATAATTAAATTTAAATTTAAGA
1 TAAATTTAAAT--TTAAATTTAAATTTAAGA
3771907 TAAATTTAAATTTAAAT
1 TAAATTTAAATTTAAAT
3771924 AAACTTAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
29 17 0.38
31 28 0.62
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (29 bp):
TAAATTTAAATTTAAATTTAAATTTAAGA
Found at i:3771881 original size:11 final size:11
Alignment explanation
Indices: 3771865--3771915 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
3771855 AATTTAAATT
*
3771865 TAAATTTAAGG
1 TAAATTTAAGA
3771876 TAAATTTAA-A
1 TAAATTTAAGA
* **
3771886 T-AATTAAATT
1 TAAATTTAAGA
3771896 TAAATTTAAGA
1 TAAATTTAAGA
3771907 TAAATTTAA
1 TAAATTTAA
3771916 ATTTAAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
9 6 0.19
10 2 0.06
11 24 0.75
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (11 bp):
TAAATTTAAGA
Found at i:3771881 original size:17 final size:17
Alignment explanation
Indices: 3771844--3771921 Score: 99
Period size: 17 Copynumber: 4.7 Consensus size: 17
3771834 TAAATTTATT
*
3771844 ATTTAAATTTAAATTTAA
1 ATTTAAATTT-AAGTTAA
*
3771862 ATTTAAATTTAAGGTAA
1 ATTTAAATTTAAGTTAA
3771879 ATTTAAA--TAA-TTAA
1 ATTTAAATTTAAGTTAA
*
3771893 ATTTAAATTTAAGATAA
1 ATTTAAATTTAAGTTAA
3771910 ATTTAAATTTAA
1 ATTTAAATTTAA
3771922 ATAAACTTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
14 10 0.19
15 3 0.06
16 3 0.06
17 27 0.51
18 10 0.19
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (17 bp):
ATTTAAATTTAAGTTAA
Found at i:3771934 original size:17 final size:17
Alignment explanation
Indices: 3771859--3771934 Score: 61
Period size: 17 Copynumber: 4.6 Consensus size: 17
3771849 AATTTAAATT
* *
3771859 TAAATTTAAATTTAAGG
1 TAAATTAAAATTTAAGA
* *
3771876 TAAATTTAAA--TAA-T
1 TAAATTAAAATTTAAGA
*
3771890 TAAATTTAAATTTAAGA
1 TAAATTAAAATTTAAGA
*
3771907 TAAATTTAAATTTAA-A
1 TAAATTAAAATTTAAGA
3771923 TAAACTTAAAAT
1 TAAA-TTAAAAT
3771935 CAATTTAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
14 10 0.19
15 3 0.06
16 8 0.15
17 31 0.60
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (17 bp):
TAAATTAAAATTTAAGA
Found at i:3774917 original size:45 final size:45
Alignment explanation
Indices: 3774612--3774898 Score: 326
Period size: 45 Copynumber: 6.4 Consensus size: 45
3774602 CACCGGTGGC
* * * *
3774612 TTCTTTGGAGGCTT-ATAAATTGGTGG-TCTGGGTTCTGGTTTTTCT
1 TTCTTTGGAGG-TTCATAAACTGGTGGCT-TGGGTTCAGGCTTCTCT
* * * * *
3774657 TTTTTTGGAGGTGCATAAACTGGTGGCTTAGGTTTAGGCTTCTCC
1 TTCTTTGGAGGTTCATAAACTGGTGGCTTGGGTTCAGGCTTCTCT
* *
3774702 TTCTTTGGAGGTTCATAAACTGGTGGCTTGGGTTCAGGTTTCTCC
1 TTCTTTGGAGGTTCATAAACTGGTGGCTTGGGTTCAGGCTTCTCT
* * * *
3774747 TTCTTTGGTGGTTCATACACTGGTGGTTTGGGCTCAGGCTTCTCT
1 TTCTTTGGAGGTTCATAAACTGGTGGCTTGGGTTCAGGCTTCTCT
* ** *
3774792 TTCTTTGGAGGTTCATATACTGGTGATTTGGGCTCAGGCTTCTCT
1 TTCTTTGGAGGTTCATAAACTGGTGGCTTGGGTTCAGGCTTCTCT
* ** *
3774837 TTCTTTGGTGGTGAATAAACTGGTGGTTTGGGTTCAGGCTTCTCT
1 TTCTTTGGAGGTTCATAAACTGGTGGCTTGGGTTCAGGCTTCTCT
*
3774882 TTCTTTGGTGGTTCATA
1 TTCTTTGGAGGTTCATA
3774899 GACAGGAGGC
Statistics
Matches: 209, Mismatches: 31, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
44 1 0.00
45 207 0.99
46 1 0.00
ACGTcount: A:0.13, C:0.16, G:0.29, T:0.43
Consensus pattern (45 bp):
TTCTTTGGAGGTTCATAAACTGGTGGCTTGGGTTCAGGCTTCTCT
Found at i:3779649 original size:59 final size:58
Alignment explanation
Indices: 3779578--3779814 Score: 248
Period size: 57 Copynumber: 4.1 Consensus size: 58
3779568 GGTCAAAACA
* * *
3779578 GAATTTTGGAAAGGTCGAGGGTAAAATGGTAATATTTGGTAAAATCGGGGTTAAAAATG
1 GAATTTTAGAAAGGTCGAGGGTAAAATGATAAT-TTTGGTAAAATCGGGGGTAAAAATG
* ** * * *
3779637 GAATTTTAGAAAGTTCGA-GAAAAAATGACAATTTTGGTGAAATCGGGGGCAAAAATG
1 GAATTTTAGAAAGGTCGAGGGTAAAATGATAATTTTGGTAAAATCGGGGGTAAAAATG
* * *
3779694 GAA-TTTAG-AAGGTTAGGGGGTAAAAT-AGTAATTTTGGTGAAATCGGGGGTAAAAATG
1 GAATTTTAGAAAGG-TCGAGGGTAAAATGA-TAATTTTGGTAAAATCGGGGGTAAAAATG
* * * * *
3779751 GAATTTTAGAAAGTTTGGGGGGTAAAATGATAATTTTGGTAAAATCAGGGTTAAAAATG
1 GAATTTTAGAAAG-GTCGAGGGTAAAATGATAATTTTGGTAAAATCGGGGGTAAAAATG
*
3779810 AAATT
1 GAATT
3779815 ATTGAAAACT
Statistics
Matches: 149, Mismatches: 22, Indels: 14
0.81 0.12 0.08
Matches are distributed among these distances:
55 3 0.02
56 8 0.05
57 61 0.41
58 15 0.10
59 61 0.41
60 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.29, T:0.29
Consensus pattern (58 bp):
GAATTTTAGAAAGGTCGAGGGTAAAATGATAATTTTGGTAAAATCGGGGGTAAAAATG
Found at i:3779698 original size:29 final size:28
Alignment explanation
Indices: 3779600--3779757 Score: 81
Period size: 29 Copynumber: 5.5 Consensus size: 28
3779590 GGTCGAGGGT
* *
3779600 AAAATGGTAATATTTGGTAAAATCGGGGTTA
1 AAAATGG-AAT-TTTGGTGAAATCGGGG-GA
* * *
3779631 AAAATGGAATTTT--AGAAAGTTC-GAGAA
1 AAAATGGAATTTTGGTGAAA--TCGGGGGA
*
3779658 AAAATGACAATTTTGGTGAAATCGGGGGCA
1 AAAATG-GAATTTTGGTGAAATCGGGGG-A
* ** ** * *
3779688 AAAATGGAATTTAGAAG-GTTAGGGGGT
1 AAAATGGAATTTTGGTGAAATCGGGGGA
*
3779715 AAAATAGTAATTTTGGTGAAATCGGGGGTA
1 AAAAT-GGAATTTTGGTGAAATCGGGGG-A
3779745 AAAATGGAATTTT
1 AAAATGGAATTTT
3779758 AGAAAGTTTG
Statistics
Matches: 92, Mismatches: 25, Indels: 22
0.66 0.18 0.16
Matches are distributed among these distances:
27 15 0.16
28 24 0.26
29 27 0.29
30 19 0.21
31 7 0.08
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (28 bp):
AAAATGGAATTTTGGTGAAATCGGGGGA
Found at i:3779786 original size:30 final size:30
Alignment explanation
Indices: 3779739--3780172 Score: 286
Period size: 30 Copynumber: 14.6 Consensus size: 30
3779729 GGTGAAATCG
* * *
3779739 GGGGTAAAAATG-GAATTTTAGAAAGTTTGG
1 GGGGTCAAAATGATAATTTTAGAAAGTTT-A
* * *
3779769 GGGGT-AAAATGATAATTTTGGTAAA-ATCA
1 GGGGTCAAAATGATAATTTTAG-AAAGTTTA
* * **
3779798 GGGTTAAAAATGA-AATTATT-GAAAACTTA
1 GGGGTCAAAATGATAATT-TTAGAAAGTTTA
* *
3779827 GGGGTAAAAAT-ATATTTTTAGAAAGTTTTA
1 GGGGTCAAAATGATAATTTTAGAAAG-TTTA
* * *
3779857 -AGGTTAAAAT-ATAATTTTAGAAAAGCTTA
1 GGGGTCAAAATGATAATTTTAG-AAAGTTTA
*
3779886 GGGGTCACAATG-TAATTTATAGAAAGTTTTA
1 GGGGTCAAAATGATAATTT-TAGAAAG-TTTA
3779917 -GGGTCAAAAT-ATAATTTT-GAAAAGGTTTA
1 GGGGTCAAAATGATAATTTTAG-AAA-GTTTA
* * *
3779946 GAGGTTAAAATG-TAATTTATAGAAAGTTTT
1 GGGGTCAAAATGATAATTT-TAGAAAGTTTA
*
3779976 GGGGTCAAAAT-ATAATTTTGGAAAAGTTTA
1 GGGGTCAAAATGATAATTTTAG-AAAGTTTA
*
3780006 GGGGTTAAAATG-TAATTTTTAGAAAGTTTTA
1 GGGGTCAAAATGATAA-TTTTAGAAAG-TTTA
* *
3780037 -GGGTTAAAAT-ATAATTTTGGAAAGGTTTA
1 GGGGTCAAAATGATAATTTTAGAAA-GTTTA
* *
3780066 GGGGTTAAAATG-TAATTTATGGAAAGTTTTA
1 GGGGTCAAAATGATAATTT-TAGAAAG-TTTA
*
3780097 -GGGTCAAAAT-ATAATTTTGGAAAAGTTTA
1 GGGGTCAAAATGATAATTTTAG-AAAGTTTA
*
3780126 GGGGT-TAAATG-TAATTTTTAGAAAGTTTTA
1 GGGGTCAAAATGATAA-TTTTAGAAAG-TTTA
3780156 -GGGTCAAAAT-ATAATTT
1 GGGGTCAAAATGATAATTT
3780173 CTTAGGGATT
Statistics
Matches: 330, Mismatches: 35, Indels: 79
0.74 0.08 0.18
Matches are distributed among these distances:
28 7 0.02
29 101 0.31
30 189 0.57
31 32 0.10
32 1 0.00
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.36
Consensus pattern (30 bp):
GGGGTCAAAATGATAATTTTAGAAAGTTTA
Found at i:3779926 original size:60 final size:60
Alignment explanation
Indices: 3779824--3780172 Score: 524
Period size: 60 Copynumber: 5.8 Consensus size: 60
3779814 TATTGAAAAC
* * * * * * *
3779824 TTAGGGGTAAAAATAT-ATTTTTAGAAAGTTTTAAGGTTAAAATATAATTTTAGAAAAGC
1 TTAGGGGTTAAAATGTAATTTATAGAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGT
* *
3779883 TTAGGGGTCACAATGTAATTTATAGAAAGTTTTAGGGTCAAAATATAATTTT-GAAAAGGT
1 TTAGGGGTTAAAATGTAATTTATAGAAAGTTTTAGGGTCAAAATATAATTTTGGAAAA-GT
* *
3779943 TTAGAGGTTAAAATGTAATTTATAGAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGT
1 TTAGGGGTTAAAATGTAATTTATAGAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGT
* * *
3780003 TTAGGGGTTAAAATGTAATTTTTAGAAAGTTTTAGGGTTAAAATATAATTTTGGAAAGGT
1 TTAGGGGTTAAAATGTAATTTATAGAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGT
*
3780063 TTAGGGGTTAAAATGTAATTTATGGAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGT
1 TTAGGGGTTAAAATGTAATTTATAGAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGT
*
3780123 TTAGGGGTT-AAATGTAATTTTTAGAAAGTTTTAGGGTCAAAATATAATTT
1 TTAGGGGTTAAAATGTAATTTATAGAAAGTTTTAGGGTCAAAATATAATTT
3780173 CTTAGGGATT
Statistics
Matches: 265, Mismatches: 22, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
59 57 0.22
60 203 0.77
61 5 0.02
ACGTcount: A:0.39, C:0.02, G:0.21, T:0.38
Consensus pattern (60 bp):
TTAGGGGTTAAAATGTAATTTATAGAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGT
Found at i:3781302 original size:15 final size:15
Alignment explanation
Indices: 3781282--3781333 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
3781272 TGACCAATAT
3781282 TTATCATTAATGTTA
1 TTATCATTAATGTTA
*
3781297 TTATCAGTAA--TTA
1 TTATCATTAATGTTA
* *
3781310 TTATTATTACTGTTA
1 TTATCATTAATGTTA
*
3781325 TTATTATTA
1 TTATCATTA
3781334 GCATGTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 10 0.32
15 21 0.68
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (15 bp):
TTATCATTAATGTTA
Done.