Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 181 of 214
Found at i:53195621 original size:31 final size:29
Alignment explanation
Indices: 53195567--53195642 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 29
53195557 GGACACTTAG
*
53195567 AGTTTTTATTTAAGTTACCAAACTATTCAAA
1 AGTTTTTATTTAAGTTAACAAACTATT--AA
* *
53195598 AGTTTTTATTTAAGTTAATAAACTGTTAA
1 AGTTTTTATTTAAGTTAACAAACTATTAA
* *
53195627 GGTTTTTTTTTAAGTT
1 AGTTTTTATTTAAGTT
53195643 CCGTCAGCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 16 0.40
31 24 0.60
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.50
Consensus pattern (29 bp):
AGTTTTTATTTAAGTTAACAAACTATTAA
Found at i:53201990 original size:6 final size:6
Alignment explanation
Indices: 53201979--53202005 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
53201969 GACGAAGGGG
53201979 AAAGAA AAAGAA AAAGAA AAAGAA AAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAA
53202006 AAAGAGAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:53206738 original size:23 final size:24
Alignment explanation
Indices: 53206699--53206744 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
53206689 ATTAATTAAT
*
53206699 TAATTAAAATTAAATTAAGTTTTG
1 TAATTAAAATTAAATTAAATTTTG
*
53206723 TAATTAAAATT-TATTAAATTTT
1 TAATTAAAATTAAATTAAATTTT
53206745 AGGGTTTAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (24 bp):
TAATTAAAATTAAATTAAATTTTG
Found at i:53207088 original size:33 final size:33
Alignment explanation
Indices: 53207046--53207112 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
53207036 TAATTTCGAG
53207046 TTGACGTTTCTAAGCAAATAGTATAAAATCGCT
1 TTGACGTTTCTAAGCAAATAGTATAAAATCGCT
*
53207079 TTGACGTTTCTAGGCAAATAGTATAAAATCGCT
1 TTGACGTTTCTAAGCAAATAGTATAAAATCGCT
53207112 T
1 T
53207113 CTACAAGGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (33 bp):
TTGACGTTTCTAAGCAAATAGTATAAAATCGCT
Found at i:53207237 original size:158 final size:158
Alignment explanation
Indices: 53206921--53207237 Score: 451
Period size: 158 Copynumber: 2.0 Consensus size: 158
53206911 TAATTTCGAG
*
53206921 TTGACGGTTCTGAGCAAATAGTATAAAAACGCTACAAGCAGGATGCTATATGCGAAGAATTTGTG
1 TTGACGGTTCTGAGCAAATAGTATAAAAACGCTACAAGCAGGATGCTATATGAGAAGAATTTGTG
* * * *
53206986 AAATCGCGCCCTCCTGGACGCGCTTTTGCTACAGTTGGTCCTGAAAGAAATAATTTCGAGTTGAC
66 AAATCGCGCCCACCTGGACGCACTTTTGCTACAGTAGGTCCTGAAAAAAATAATTTCGAGTTGAC
*
53207051 GTTTCTAAGCAAATAGTATAAAATCGCT
131 GTTTCTAAGCAAATAGTATAAAAACGCT
* * * * *
53207079 TTGACGTTTCT-AGGCAAATAGTATAAAATCGCTTCTA-CAAGGATGCTTTATGAGAAGAATTTG
1 TTGACGGTTCTGA-GCAAATAGTATAAAAACGCTACAAGC-AGGATGCTATATGAGAAGAATTTG
* * *
53207142 TGAAATCGCGCCCACGTGGACGCACTTTTGCTACAGTAGGTCCT-AAAAAAATTATTTTGAGTTG
64 TGAAATCGCGCCCACCTGGACGCACTTTTGCTACAGTAGGTCCTGAAAAAAATAATTTCGAGTTG
*
53207206 ACGTTTCTGAGCAAATAGTATAAAAAACGCT
129 ACGTTTCTAAGCAAATAGTAT-AAAAACGCT
53207237 T
1 T
53207238 CAAGCAGGAT
Statistics
Matches: 141, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
157 39 0.28
158 102 0.72
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (158 bp):
TTGACGGTTCTGAGCAAATAGTATAAAAACGCTACAAGCAGGATGCTATATGAGAAGAATTTGTG
AAATCGCGCCCACCTGGACGCACTTTTGCTACAGTAGGTCCTGAAAAAAATAATTTCGAGTTGAC
GTTTCTAAGCAAATAGTATAAAAACGCT
Found at i:53207300 original size:125 final size:122
Alignment explanation
Indices: 53207079--53207421 Score: 414
Period size: 125 Copynumber: 2.8 Consensus size: 122
53207069 TAAAATCGCT
53207079 TTGACGTTTCT-AGGCAAATAGTATAAAATCGCTTCTACAAGGATGCTTTATGAGAAGAATTTGT
1 TTGACGTTTCTGA-GCAAATAGTATAAAA-CGCTTCTAC-AGGATGCTTTATGAGAAGAATTTGT
* * *
53207143 GAAATCGCGCCCACGTGGACGCACTTTTGCTACAGTAGGTCCT-AAAAAAATTATTTTGAG
63 GAAAT-GCGCCCTCGTGGACGCACTTTTGCTACAGTAGGTCCTGAAAAAAATAATTTCGAG
* *
53207203 TTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTATT-TGAGAAGAATTTC
1 TTGACGTTTCTGAGCAAATAGTAT--AAAACGCTTCTA-CAGGATGCT-TTATGAGAAGAATTTG
* * *
53207267 TGAAACTGCGCCCTCGTGGACGCACTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAG
62 TGAAA-TGCGCCCTCGTGGACGCACTTTTGCTACAGTAGGTCCTGAAAAAAATAATTTCGAG
* * *
53207329 TTGACGTTTTTGAGTAAATAGTAT----CGCTTCTACCAGGATGATTTATGAGAAGAATTTGTGA
1 TTGACGTTTCTGAGCAAATAGTATAAAACGCTTCTA-CAGGATGCTTTATGAGAAGAATTTGTGA
*
53207390 AATTGCG-CCTACGTGGACGCGCTTTTGCTACA
65 AA-TGCGCCCT-CGTGGACGCACTTTTGCTACA
53207422 ATAGCATGTT
Statistics
Matches: 194, Mismatches: 16, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
119 5 0.03
120 56 0.29
124 22 0.11
125 68 0.35
126 43 0.22
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.31
Consensus pattern (122 bp):
TTGACGTTTCTGAGCAAATAGTATAAAACGCTTCTACAGGATGCTTTATGAGAAGAATTTGTGAA
ATGCGCCCTCGTGGACGCACTTTTGCTACAGTAGGTCCTGAAAAAAATAATTTCGAG
Found at i:53210628 original size:29 final size:30
Alignment explanation
Indices: 53210594--53210653 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
53210584 TATATTTAAC
53210594 TTAAGGGTTAGGGTTTTAAAG-TTAAGGTT
1 TTAAGGGTTAGGGTTTTAAAGTTTAAGGTT
* **
53210623 TTAAGGTTTAGGGTTTTTCAGTTTAAGGTT
1 TTAAGGGTTAGGGTTTTAAAGTTTAAGGTT
53210653 T
1 T
53210654 ATGGTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.23, C:0.02, G:0.28, T:0.47
Consensus pattern (30 bp):
TTAAGGGTTAGGGTTTTAAAGTTTAAGGTT
Found at i:53210639 original size:15 final size:14
Alignment explanation
Indices: 53210594--53210639 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
53210584 TATATTTAAC
53210594 TTAAGGGTTAGGGTT
1 TTAA-GGTTAGGGTT
* *
53210609 TTAAAGTTAAGGTT
1 TTAAGGTTAGGGTT
53210623 TTAAGGTTTAGGGTT
1 TTAAGG-TTAGGGTT
53210638 TT
1 TT
53210640 TCAGTTTAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (14 bp):
TTAAGGTTAGGGTT
Found at i:53210647 original size:22 final size:22
Alignment explanation
Indices: 53210622--53211783 Score: 353
Period size: 22 Copynumber: 53.6 Consensus size: 22
53210612 AAGTTAAGGT
*
53210622 TTTAAGGTTTAGGGTTTTTCAG
1 TTTAAGGTTTAGGGTTTTTAAG
* *
53210644 TTTAAGGTTTATGGTTTTTAGG
1 TTTAAGGTTTAGGGTTTTTAAG
*
53210666 TTT-AGGATTTATGGTTTTTAAG
1 TTTAAGG-TTTAGGGTTTTTAAG
* * *
53210688 ATTAAAGTTTATGGTTTTTAAG
1 TTTAAGGTTTAGGGTTTTTAAG
* *
53210710 -TTAAGGGTTAGGG-TTTTATG
1 TTTAAGGTTTAGGGTTTTTAAG
53210730 TTT-AGAGTTT-GTGGTTTTTAAG
1 TTTAAG-GTTTAG-GGTTTTTAAG
*
53210752 TTTAAGGTTTAGGGTTTTTAGG
1 TTTAAGGTTTAGGGTTTTTAAG
53210774 TTTAAGGTTTAGGGTTTTTAAG
1 TTTAAGGTTTAGGGTTTTTAAG
53210796 TTT-AGGATTTTA-GGTTTTTAAG
1 TTTAAGG--TTTAGGGTTTTTAAG
* *
53210818 TTTAGGGTTTATGGTTTTTAAG
1 TTTAAGGTTTAGGGTTTTTAAG
* *
53210840 TTT-AGGGTTAGTGTTTTTAA-
1 TTTAAGGTTTAGGGTTTTTAAG
* *
53210860 TTTAAGGGTTAGTGTTTTTAA-
1 TTTAAGGTTTAGGGTTTTTAAG
* *
53210881 TTTAAAGG-TTA-GG--ATTAGG
1 TTT-AAGGTTTAGGGTTTTTAAG
* * **
53210900 GTTAGGGTTTTAAAG---TTAATG
1 TTTAAGG-TTTAGGGTTTTTAA-G
* ** *
53210921 TTTTAGGGTTTAATGTTTTTAAA
1 -TTTAAGGTTTAGGGTTTTTAAG
** *
53210944 TTTAAGGTTTAAAGTTTTTAGG
1 TTTAAGGTTTAGGGTTTTTAAG
*
53210966 TTTAGGGTTTTTAGGGGTTTAAGGGTTTTAAG
1 TTTAAGG--TTTA-GGG--T-----TTTTAAG
* *
53210998 -TTAAGGGTTAGGGTTTTT-GG
1 TTTAAGGTTTAGGGTTTTTAAG
* **
53211018 TTTAGGGTTTATGTTTTTCAAGTTTAAAG
1 TTTAAGGTTTA-G-GGTT----TTT-AAG
*
53211047 TTTAAGGTTTAGGG-TTTTAAA
1 TTTAAGGTTTAGGGTTTTTAAG
* * * * *
53211068 GTTTAAGGTTTATGG-TTTTTAA
1 TTTAA-GGTTTAGGGTTTTTAAG
* * *
53211090 GTTTAAGGTTTATGGTTTTTAAA
1 T-TTAAGGTTTAGGGTTTTTAAG
* *
53211113 TTAAAGG-TTAGCGTTTTTAA-
1 TTTAAGGTTTAGGGTTTTTAAG
53211133 TTTAAGAG-TTAGGGTTTTTAAG
1 TTTAAG-GTTTAGGGTTTTTAAG
* **
53211155 -TTAAGGGTTA--G-AATTAAG
1 TTTAAGGTTTAGGGTTTTTAAG
* * **
53211173 GTTATGGTTTTAAAG---TTAATG
1 TTTAAGG-TTTAGGGTTTTTAA-G
* * *
53211194 TTTTAAGGTGTAAGAG-TTTTAAA
1 -TTTAAGGT-TTAGGGTTTTTAAG
* * **
53211217 TTTAGGGCTTAGCATTTTTAAG
1 TTTAAGGTTTAGGGTTTTTAAG
** *
53211239 TTTAAGGTTTATTG-TTTTAGG
1 TTTAAGGTTTAGGGTTTTTAAG
* *
53211260 TTTAAGGTTTAGTGTTTTTAGG
1 TTTAAGGTTTAGGGTTTTTAAG
*
53211282 TTTAAGGTTT-GGGGTTTTAA-
1 TTTAAGGTTTAGGGTTTTTAAG
* * ** *
53211302 ATTAAGGGTTAATGTTTTTATG
1 TTTAAGGTTTAGGGTTTTTAAG
* * * *
53211324 TATAGGGTTTAGTG-TTTTAGG
1 TTTAAGGTTTAGGGTTTTTAAG
* * *
53211345 TTTAGGGTTTAGTG-TTTTAGG
1 TTTAAGGTTTAGGGTTTTTAAG
*
53211366 TTTAAAGTTT-GAGG-TTTTAAG
1 TTTAAGGTTTAG-GGTTTTTAAG
* * *
53211387 TTTAGGGTTT-GTGGGTTTTAGG
1 TTTAAGGTTTAG-GGTTTTTAAG
* ***
53211409 TTTAGGGTTTAATATTTTTAAG
1 TTTAAGGTTTAGGGTTTTTAAG
* * *** *
53211431 -TTAAAGATTAACATTTTCAA-
1 TTTAAGGTTTAGGGTTTTTAAG
* *
53211451 TTTAAGGGTTAAGGTTTTTAAG
1 TTTAAGGTTTAGGGTTTTTAAG
* * *
53211473 -TTAAGGGTTA-GG--ATTAGG
1 TTTAAGGTTTAGGGTTTTTAAG
* * **
53211491 GTTAGGGTTTTAAAG---TTAATG
1 TTTAAGG-TTTAGGGTTTTTAA-G
*
53211512 TTTTAAGGTTTATGGTTTTTAAG
1 -TTTAAGGTTTAGGGTTTTTAAG
* *
53211535 TTTAGGGTTTAAGGG-TTTTAAA
1 TTTAAGGTTT-AGGGTTTTTAAG
*
53211557 TTTAGGGTTTTAGGG-TTTTAAG
1 TTTAAGG-TTTAGGGTTTTTAAG
*
53211579 -TTAA-GTGTTAGGGTTTTTAGG
1 TTTAAGGT-TTAGGGTTTTTAAG
* * *
53211600 TTTAGGGTGTTA-TGTTTTTATG
1 TTTAAGGT-TTAGGGTTTTTAAG
* *
53211622 -TTAAGGGTTT-TGGTTTTTAGGG
1 TTTAA-GGTTTAGGGTTTTTA-AG
* * *
53211644 TTTAGGGTTTATGGTTTTAAAG
1 TTTAAGGTTTAGGGTTTTTAAG
** *
53211666 TTT-AGGGCTAGGGTTTTTAGG
1 TTTAAGGTTTAGGGTTTTTAAG
* * *
53211687 TTTATGGTTTAAGGTTTTTAGG
1 TTTAAGGTTTAGGGTTTTTAAG
53211709 TTTATA-GTTT-GTGGTTTTTAAG
1 TTTA-AGGTTTAG-GGTTTTTAAG
* *
53211731 -TTAAGGGTTAGCGTTTTTAA-
1 TTTAAGGTTTAGGGTTTTTAAG
*
53211751 TTTAAGGGTTAGGG-TTTTAAG
1 TTTAAGGTTTAGGGTTTTTAAG
*
53211772 -TTAAGGGTTAGG
1 TTTAAGGTTTAGG
53211784 ATTAGGGTTA
Statistics
Matches: 885, Mismatches: 163, Indels: 186
0.72 0.13 0.15
Matches are distributed among these distances:
18 15 0.02
19 14 0.02
20 76 0.09
21 318 0.36
22 364 0.41
23 46 0.05
24 16 0.02
25 1 0.00
26 2 0.00
27 4 0.00
28 4 0.00
29 14 0.02
31 5 0.01
32 6 0.01
ACGTcount: A:0.23, C:0.01, G:0.27, T:0.49
Consensus pattern (22 bp):
TTTAAGGTTTAGGGTTTTTAAG
Found at i:53210759 original size:130 final size:130
Alignment explanation
Indices: 53210622--53210856 Score: 375
Period size: 130 Copynumber: 1.8 Consensus size: 130
53210612 AAGTTAAGGT
* *
53210622 TTTAAGGTTTAGGGTTTTTCA-GTTTAAGGTTTATGGTTTTTAGGTTTAGGA-TTTATGGTTTTT
1 TTTAAGGTTTAGGGTTTTT-AGGTTTAAGGTTTAGGGTTTTTAAGTTTAGGATTTTA-GGTTTTT
53210685 AAGATTAAAGTTTATGGTTTTTAAGTTAAGGGTTAGGGTTTTATGTTTAGAGTTTGTGGTTTTTA
64 AAGATTAAAGTTTATGGTTTTTAAGTTAAGGGTTAGGGTTTTATGTTTAGAGTTTGTGGTTTTTA
53210750 AG
129 AG
53210752 TTTAAGGTTTAGGGTTTTTAGGTTTAAGGTTTAGGGTTTTTAAGTTTAGGATTTTAGGTTTTTAA
1 TTTAAGGTTTAGGGTTTTTAGGTTTAAGGTTTAGGGTTTTTAAGTTTAGGATTTTAGGTTTTTAA
* ** * *
53210817 GTTTAGGGTTTATGGTTTTTAAGTTTAGGGTTAGTGTTTT
66 GATTAAAGTTTATGGTTTTTAAGTTAAGGGTTAGGGTTTT
53210857 TAATTTAAGG
Statistics
Matches: 96, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
129 1 0.01
130 91 0.95
131 4 0.04
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.52
Consensus pattern (130 bp):
TTTAAGGTTTAGGGTTTTTAGGTTTAAGGTTTAGGGTTTTTAAGTTTAGGATTTTAGGTTTTTAA
GATTAAAGTTTATGGTTTTTAAGTTAAGGGTTAGGGTTTTATGTTTAGAGTTTGTGGTTTTTAAG
Found at i:53210798 original size:15 final size:16
Alignment explanation
Indices: 53210774--53210806 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
53210764 GGTTTTTAGG
*
53210774 TTTAAGGTTTAGGGTT
1 TTTAAGGTTTAGGATT
53210790 TTTAA-GTTTAGGATT
1 TTTAAGGTTTAGGATT
53210805 TT
1 TT
53210807 AGGTTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.21, C:0.00, G:0.24, T:0.55
Consensus pattern (16 bp):
TTTAAGGTTTAGGATT
Found at i:53210877 original size:130 final size:129
Alignment explanation
Indices: 53210622--53210890 Score: 366
Period size: 130 Copynumber: 2.1 Consensus size: 129
53210612 AAGTTAAGGT
* *
53210622 TTTAAGGTTTAGGGTTTTTCAGTTTAAGGTTTATGGTTTTTAGGTTTAGGATTTATGGTTTTTAA
1 TTTAAGGTTTAGGGTTTTTCAGTTTAAGGTTTAGGGTTTTTAAGTTTAGGATTTATGGTTTTTAA
* *
53210687 GATTAAAGTTTATGGTTTTTAAGTTAAGGGTTAGGGTTTTATGTTTAGAGTTTGTGGTTTTTAA
66 GATTAAAGTTTATGGTTTTTAAGTTAAGGGTTAGGGTTTTATGTTAAGAGTTAGTGGTTTTTAA
53210751 GTTTAAGGTTTAGGGTTTTT-AGGTTTAAGGTTTAGGGTTTTTAAGTTTAGGATTT-TAGGTTTT
1 -TTTAAGGTTTAGGGTTTTTCA-GTTTAAGGTTTAGGGTTTTTAAGTTTAGGATTTAT-GGTTTT
* ** * * *
53210814 TAAGTTTAGGGTTTATGGTTTTTAAGTTTAGGGTTAGTGTTTTTAAT-TTAAGGGTTAGT-GTTT
63 TAAGATTAAAGTTTATGGTTTTTAAGTTAAGGGTTAG-GGTTTT-ATGTTAAGAGTTAGTGGTTT
53210877 TTAA
126 TTAA
53210881 TTTAAAGGTT
1 TTT-AAGGTT
53210891 AGGATTAGGG
Statistics
Matches: 124, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
129 5 0.04
130 103 0.83
131 14 0.11
132 2 0.02
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (129 bp):
TTTAAGGTTTAGGGTTTTTCAGTTTAAGGTTTAGGGTTTTTAAGTTTAGGATTTATGGTTTTTAA
GATTAAAGTTTATGGTTTTTAAGTTAAGGGTTAGGGTTTTATGTTAAGAGTTAGTGGTTTTTAA
Found at i:53210978 original size:53 final size:52
Alignment explanation
Indices: 53210921--53211027 Score: 135
Period size: 53 Copynumber: 2.0 Consensus size: 52
53210911 AAAGTTAATG
* * * *
53210921 TTTTA-GGGTTTAATGTTTTTAAATTTAAGGTTTAAAGTTTTTAGGTTTAGGGT
1 TTTTAGGGGTTTAAGGGTTTT-AAGTTAAGGGTTAAAGTTTTT-GGTTTAGGGT
**
53210974 TTTTAGGGGTTTAAGGGTTTTAAGTTAAGGGTTAGGGTTTTTGGTTTAGGGT
1 TTTTAGGGGTTTAAGGGTTTTAAGTTAAGGGTTAAAGTTTTTGGTTTAGGGT
53211026 TT
1 TT
53211028 ATGTTTTTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
52 12 0.26
53 22 0.47
54 13 0.28
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (52 bp):
TTTTAGGGGTTTAAGGGTTTTAAGTTAAGGGTTAAAGTTTTTGGTTTAGGGT
Found at i:53211055 original size:29 final size:29
Alignment explanation
Indices: 53211017--53211085 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
53211007 AGGGTTTTTG
* * * *
53211017 GTTTAGGGTTTATGTTTTTCAAGTTTAAA
1 GTTTAAGGTTTAGGGTTTTAAAGTTTAAA
*
53211046 GTTTAAGGTTTAGGGTTTTAAAGTTTAAG
1 GTTTAAGGTTTAGGGTTTTAAAGTTTAAA
*
53211075 GTTTATGGTTT
1 GTTTAAGGTTT
53211086 TTAAGTTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.23, C:0.01, G:0.25, T:0.51
Consensus pattern (29 bp):
GTTTAAGGTTTAGGGTTTTAAAGTTTAAA
Found at i:53211071 original size:15 final size:15
Alignment explanation
Indices: 53211032--53211078 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
53211022 GGGTTTATGT
* *
53211032 TTTTCAAGTTTAAAG
1 TTTTAAAGTTTAAGG
* *
53211047 -TTTAAGGTTTAGGG
1 TTTTAAAGTTTAAGG
53211061 TTTTAAAGTTTAAGG
1 TTTTAAAGTTTAAGG
53211076 TTT
1 TTT
53211079 ATGGTTTTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.49
Consensus pattern (15 bp):
TTTTAAAGTTTAAGG
Found at i:53211096 original size:6 final size:7
Alignment explanation
Indices: 53211039--53211107 Score: 59
Period size: 7 Copynumber: 9.6 Consensus size: 7
53211029 TGTTTTTCAA
*
53211039 GTTTAAA
1 GTTTAAG
53211046 GTTTAAG
1 GTTTAAG
*
53211053 GTTTAGG
1 GTTTAAG
*
53211060 GTTTTAAA
1 G-TTTAAG
53211068 GTTTAAG
1 GTTTAAG
*
53211075 GTTTATG
1 GTTTAAG
53211082 GTTTTTAA-
1 G--TTTAAG
53211090 GTTTAAG
1 GTTTAAG
*
53211097 GTTTATG
1 GTTTAAG
53211104 GTTT
1 GTTT
53211108 TTAAATTAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
6 5 0.10
7 35 0.70
8 6 0.12
9 4 0.08
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (7 bp):
GTTTAAG
Found at i:53211116 original size:21 final size:20
Alignment explanation
Indices: 53211048--53211165 Score: 96
Period size: 21 Copynumber: 5.5 Consensus size: 20
53211038 AGTTTAAAGT
*
53211048 TTAAGGTTTAGGGTTTTAAA
1 TTAAGGTTTAGGTTTTTAAA
*
53211068 GTTTAAGGTTTATGGTTTTTAAGT
1 --TTAAGGTTTA-GGTTTTTAA-A
53211092 TTAAGGTTTATGGTTTTTAAA
1 TTAAGGTTTA-GGTTTTTAAA
*
53211113 TTAAAGG-TTAGCGTTTTTAAT
1 TT-AAGGTTTAG-GTTTTTAAA
*
53211134 TTAAGAG-TTAGGGTTTTTAAG
1 TTAAG-GTTTA-GGTTTTTAAA
*
53211155 TTAAGGGTTAG
1 TTAAGGTTTAG
53211166 AATTAAGGTT
Statistics
Matches: 84, Mismatches: 5, Indels: 16
0.80 0.05 0.15
Matches are distributed among these distances:
20 6 0.07
21 35 0.42
22 35 0.42
23 8 0.10
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.47
Consensus pattern (20 bp):
TTAAGGTTTAGGTTTTTAAA
Found at i:53211244 original size:6 final size:7
Alignment explanation
Indices: 53211233--53211291 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
53211223 GCTTAGCATT
53211233 TTTAA-G
1 TTTAAGG
53211239 TTTAAGG
1 TTTAAGG
**
53211246 TTTATTG
1 TTTAAGG
*
53211253 TTTTAGG
1 TTTAAGG
53211260 TTTAAGG
1 TTTAAGG
53211267 TTT-AGTG
1 TTTAAG-G
*
53211274 TTTTTAGG
1 -TTTAAGG
53211282 TTTAAGG
1 TTTAAGG
53211289 TTT
1 TTT
53211292 GGGGTTTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
6 7 0.17
7 29 0.69
8 4 0.10
9 2 0.05
ACGTcount: A:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (7 bp):
TTTAAGG
Found at i:53211262 original size:21 final size:21
Alignment explanation
Indices: 53211232--53211419 Score: 166
Period size: 21 Copynumber: 8.9 Consensus size: 21
53211222 GGCTTAGCAT
* *
53211232 TTTTAAGTTTAAGGTTTATTG
1 TTTTAGGTTTAAGGTTTAGTG
53211253 TTTTAGGTTTAAGGTTTAGTG
1 TTTTAGGTTTAAGGTTTAGTG
* *
53211274 TTTTTAGGTTTAAGGTTTGGGG
1 -TTTTAGGTTTAAGGTTTAGTG
** * *
53211296 TTTTA-AATTAAGGGTTAATG
1 TTTTAGGTTTAAGGTTTAGTG
* * *
53211316 TTTTTATGTATAGGGTTTAGTG
1 -TTTTAGGTTTAAGGTTTAGTG
*
53211338 TTTTAGGTTTAGGGTTTAGTG
1 TTTTAGGTTTAAGGTTTAGTG
*
53211359 TTTTAGGTTTAAAGTTTGAG-G
1 TTTTAGGTTTAAGGTTT-AGTG
* *
53211380 TTTTAAGTTTAGGGTTT-GTGGG
1 TTTTAGGTTTAAGGTTTAGT--G
*
53211402 TTTTAGGTTTAGGGTTTA
1 TTTTAGGTTTAAGGTTTA
53211420 ATATTTTTAA
Statistics
Matches: 135, Mismatches: 24, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
19 1 0.01
20 9 0.07
21 78 0.58
22 47 0.35
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.52
Consensus pattern (21 bp):
TTTTAGGTTTAAGGTTTAGTG
Found at i:53211347 original size:7 final size:7
Alignment explanation
Indices: 53211326--53211411 Score: 59
Period size: 7 Copynumber: 12.0 Consensus size: 7
53211316 TTTTTATGTA
*
53211326 TAGGGTT
1 TAGGTTT
53211333 TAGTGTTT
1 TAG-GTTT
53211341 TAGG-TT
1 TAGGTTT
*
53211347 TAGGGTT
1 TAGGTTT
53211354 TAGTGTTT
1 TAG-GTTT
53211362 TAGGTTT
1 TAGGTTT
* *
53211369 AAAGTTT
1 TAGGTTT
*
53211376 GAGGTTT
1 TAGGTTT
*
53211383 TAAG-TT
1 TAGGTTT
53211389 TAGGGTTT
1 TA-GGTTT
*
53211397 GTGGGTTT
1 -TAGGTTT
53211405 TAGGTTT
1 TAGGTTT
53211412 AGGGTTTAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
6 10 0.16
7 32 0.52
8 19 0.31
9 1 0.02
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (7 bp):
TAGGTTT
Found at i:53211361 original size:14 final size:14
Alignment explanation
Indices: 53211339--53211396 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 14
53211329 GGTTTAGTGT
53211339 TTTAG-GTTTAGGG
1 TTTAGAGTTTAGGG
*
53211352 TTTAGTGTTTTA-GG
1 TTTAGAG-TTTAGGG
* *
53211366 TTTAAAGTTTGAGGT
1 TTTAGAGTTT-AGGG
53211381 TTTA-AGTTTAGGG
1 TTTAGAGTTTAGGG
53211394 TTT
1 TTT
53211397 GTGGGTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 14 0.38
14 14 0.38
15 9 0.24
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (14 bp):
TTTAGAGTTTAGGG
Found at i:53211477 original size:21 final size:21
Alignment explanation
Indices: 53211296--53211781 Score: 139
Period size: 21 Copynumber: 22.8 Consensus size: 21
53211286 AGGTTTGGGG
* *
53211296 TTTTAAATTAAGGGTTAATGT
1 TTTTAAGTTAAGGGTTAAGGT
* *
53211317 TTTTATG-TATAGGGTTTA-GT
1 TTTTAAGTTA-AGGGTTAAGGT
* * *
53211337 GTTTTAGGTTTAGGGTTTA-GT
1 -TTTTAAGTTAAGGGTTAAGGT
* * * *
53211358 GTTTTAGGTTTAAAGTTTGAGG-
1 -TTTTAAG-TTAAGGGTTAAGGT
* ** *
53211380 TTTTAAGTTTAGGGTTTGTGGG
1 TTTTAAGTTAAGGG-TTAAGGT
* * **
53211402 TTTTAGGTTTAGGGTTTAATAT
1 TTTTAAGTTAAGGG-TTAAGGT
* * **
53211424 TTTTAAGTTAAAGATTAACAT
1 TTTTAAGTTAAGGGTTAAGGT
* *
53211445 TTTCAATTTAAGGGTTAAGGT
1 TTTTAAGTTAAGGGTTAAGGT
53211466 TTTTAAGTTAAGGGTT-AGG-
1 TTTTAAGTTAAGGGTTAAGGT
* * *
53211485 -ATTAGGGTT-AGGGTTTTAAAGT
1 TTTTA-AGTTAAGGG--TTAAGGT
** *** * *
53211507 TAATGTTTTAAGGTTTATGGT
1 TTTTAAGTTAAGGGTTAAGGT
* *
53211528 TTTTAAGTTTAGGGTTTAAGGG
1 TTTTAAGTTAAGGG-TTAAGGT
* * * *
53211550 TTTTAAATTTAGGGTTTTAGGG
1 TTTTAAGTTAAGGG-TTAAGGT
* *
53211572 TTTTAAGTTAAGTGTTAGGGT
1 TTTTAAGTTAAGGGTTAAGGT
* * * *
53211593 TTTTAGGTTTAGGGTGTTATGT
1 TTTTAAGTTAAGGGT-TAAGGT
* **
53211615 TTTTATGTTAAGGGTTTTGGT
1 TTTTAAGTTAAGGGTTAAGGT
* * *
53211636 TTTTAGGGTTTAGGGTTTATGGT
1 TTTTA-AGTTAAGGG-TTAAGGT
* * * *
53211659 TTTAAAGTTTAGGGCTAGGGT
1 TTTTAAGTTAAGGGTTAAGGT
* * *
53211680 TTTTAGGTTTATGGTTTAAGGT
1 TTTTAAG-TTAAGGGTTAAGGT
* * **
53211702 TTTTAGGTTTATA-GTTTGTGGT
1 TTTTAAG-TTA-AGGGTTAAGGT
53211724 TTTTAAGTTAAGGGTT-AGCGT
1 TTTTAAGTTAAGGGTTAAG-GT
* *
53211745 TTTTAATTTAAGGGTT-AGGG
1 TTTTAAGTTAAGGGTTAAGGT
53211765 TTTTAAGTTAAGGGTTA
1 TTTTAAGTTAAGGGTTA
53211782 GGATTAGGGT
Statistics
Matches: 349, Mismatches: 93, Indels: 46
0.72 0.19 0.09
Matches are distributed among these distances:
18 7 0.02
19 3 0.01
20 31 0.09
21 156 0.45
22 136 0.39
23 16 0.05
ACGTcount: A:0.22, C:0.01, G:0.28, T:0.49
Consensus pattern (21 bp):
TTTTAAGTTAAGGGTTAAGGT
Found at i:53211537 original size:15 final size:16
Alignment explanation
Indices: 53211512--53211544 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
53211502 AAAGTTAATG
*
53211512 TTTTAAGGTTTATGGT
1 TTTTAAGGTTTAGGGT
53211528 TTTTAA-GTTTAGGGT
1 TTTTAAGGTTTAGGGT
53211543 TT
1 TT
53211545 AAGGGTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.18, C:0.00, G:0.24, T:0.58
Consensus pattern (16 bp):
TTTTAAGGTTTAGGGT
Found at i:53211606 original size:43 final size:43
Alignment explanation
Indices: 53211520--53211957 Score: 235
Period size: 43 Copynumber: 10.2 Consensus size: 43
53211510 TGTTTTAAGG
* **
53211520 TTTATGGTTTTTAAGTTTAGGGTTTAAGGG-TTTTAAATTTAGGGT
1 TTTA-GGTTTTTAAGTTAAGGG-TT-AGGGTTTTTAGGTTTAGGGT
* *
53211565 TTTAGGGTTTTAAGTTAAGTGTTAGGGTTTTTAGGTTTAGGGT
1 TTTAGGTTTTTAAGTTAAGGGTTAGGGTTTTTAGGTTTAGGGT
* * * **
53211608 GTTATGTTTTTATGTTAAGGGTTTTGGTTTTTAGGGTTTAGGG-
1 TTTAGGTTTTTAAGTTAAGGGTTAGGGTTTTTA-GGTTTAGGGT
* * * *
53211651 TTTATGGTTTTAAAGTTTAGGGCTAGGGTTTTTAGGTTTATGGT
1 TTTA-GGTTTTTAAGTTAAGGGTTAGGGTTTTTAGGTTTAGGGT
* * * ** * * *
53211695 TTAAGGTTTTTAGGTTTATAGTTTGTGGTTTTTAAGTTAAGGG-
1 TTTAGGTTTTTAAGTTAAGGGTTAG-GGTTTTTAGGTTTAGGGT
* * *
53211738 -TTAGCGTTTTTAATTTAAGGGTTAGGG-TTTTAAGTTAAGGG-
1 TTTAG-GTTTTTAAGTTAAGGGTTAGGGTTTTTAGGTTTAGGGT
* * ** *
53211779 -TTAGG--ATTAGGGTT-AGGGTTTTAAAG--TTAAGGTTATAGGG-
1 TTTAGGTTTTTA-AGTTAAGGG--TTAGGGTTTTTAGGTT-TAGGGT
* ** * * **
53211819 TTTATGG-TTTTGAGTTTTGAGTCTAGTG-TTTTAGGTTTA-TTT
1 TTTA-GGTTTTTAAGTTAAGGGT-TAGGGTTTTTAGGTTTAGGGT
* *
53211861 TTTAGGGTTTTTAAGTTAAGGGTTAAGGTTTTTAAGTTTAGGGT
1 TTTA-GGTTTTTAAGTTAAGGGTTAGGGTTTTTAGGTTTAGGGT
* *
53211905 TTGAGGTTTTTAAGTTAAGGGTTATGGG-TTTTAGGGTTTGGGGT
1 TTTAGGTTTTTAAGTTAAGGGTTA-GGGTTTTTA-GGTTTAGGGT
*
53211949 TTAAGGTTT
1 TTTAGGTTT
53211958 GGGGTTTGTG
Statistics
Matches: 300, Mismatches: 71, Indels: 45
0.72 0.17 0.11
Matches are distributed among these distances:
38 7 0.02
39 8 0.03
40 9 0.03
41 22 0.07
42 28 0.09
43 138 0.46
44 84 0.28
45 4 0.01
ACGTcount: A:0.20, C:0.01, G:0.30, T:0.49
Consensus pattern (43 bp):
TTTAGGTTTTTAAGTTAAGGGTTAGGGTTTTTAGGTTTAGGGT
Found at i:53211682 original size:65 final size:65
Alignment explanation
Indices: 53211613--53211768 Score: 165
Period size: 65 Copynumber: 2.4 Consensus size: 65
53211603 AGGGTGTTAT
* * *
53211613 GTTTTTATGTTAAGGGTTT-TGGTTTTTAGGGTTTAGGGTTTATGGTTTTAAAGTTTAGGGCTAG
1 GTTTTTATGTTAAGGGTTTAAGGTTTTTA-GGTTTAGAGTTTATGGTTTTAAAGTTAAGGGCTAG
*
53211677 G
65 C
* * * * * * *
53211678 GTTTTTAGGTTTATGGTTTAAGGTTTTTAGGTTTATAGTTTGTGGTTTTTAAGTTAAGGGTTAGC
1 GTTTTTATGTTAAGGGTTTAAGGTTTTTAGGTTTAGAGTTTATGGTTTTAAAGTTAAGGGCTAGC
*
53211743 GTTTTTAAT-TTAAGGG-TTAGGGTTTT
1 GTTTTT-ATGTTAAGGGTTTAAGGTTTT
53211769 AAGTTAAGGG
Statistics
Matches: 74, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
64 9 0.12
65 56 0.76
66 9 0.12
ACGTcount: A:0.18, C:0.01, G:0.29, T:0.51
Consensus pattern (65 bp):
GTTTTTATGTTAAGGGTTTAAGGTTTTTAGGTTTAGAGTTTATGGTTTTAAAGTTAAGGGCTAGC
Found at i:53211893 original size:22 final size:21
Alignment explanation
Indices: 53211866--53211937 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
53211856 TATTTTTTAG
53211866 GGTTTTTAAGTTAAGGGTTAA
1 GGTTTTTAAGTTAAGGGTTAA
* *
53211887 GGTTTTTAAGTTTAGGGTTTGA
1 GGTTTTTAAGTTAAGGG-TTAA
*
53211909 GGTTTTTAAGTTAAGGGTTAT
1 GGTTTTTAAGTTAAGGGTTAA
*
53211930 GGGTTTTA
1 GGTTTTTA
53211938 GGGTTTGGGG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
21 25 0.57
22 19 0.43
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (21 bp):
GGTTTTTAAGTTAAGGGTTAA
Found at i:53211948 original size:7 final size:7
Alignment explanation
Indices: 53211923--53211983 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
53211913 TTTAAGTTAA
53211923 GGGTTATG
1 GGGTT-TG
* *
53211931 GGTTTTA
1 GGGTTTG
53211938 GGGTTTG
1 GGGTTTG
*
53211945 GGGTTTA
1 GGGTTTG
*
53211952 AGGTTTG
1 GGGTTTG
53211959 GGGTTTG
1 GGGTTTG
*
53211966 TGG-TTG
1 GGGTTTG
*
53211972 GGGTTTA
1 GGGTTTG
53211979 GGGTT
1 GGGTT
53211984 ATCGTTTTTA
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
6 5 0.12
7 32 0.78
8 4 0.10
ACGTcount: A:0.08, C:0.00, G:0.48, T:0.44
Consensus pattern (7 bp):
GGGTTTG
Found at i:53211951 original size:14 final size:14
Alignment explanation
Indices: 53211922--53211983 Score: 74
Period size: 14 Copynumber: 4.4 Consensus size: 14
53211912 TTTTAAGTTA
*
53211922 AGGGTTATGGGTTTT
1 AGGGTT-TGGGGTTT
53211937 AGGGTTTGGGGTTT
1 AGGGTTTGGGGTTT
*
53211951 AAGGTTTGGGGTTT
1 AGGGTTTGGGGTTT
53211965 -GTGG-TTGGGGTTT
1 AG-GGTTTGGGGTTT
53211978 AGGGTT
1 AGGGTT
53211984 ATCGTTTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
13 11 0.27
14 24 0.59
15 6 0.15
ACGTcount: A:0.10, C:0.00, G:0.47, T:0.44
Consensus pattern (14 bp):
AGGGTTTGGGGTTT
Found at i:53212012 original size:21 final size:21
Alignment explanation
Indices: 53211988--53212027 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53211978 AGGGTTATCG
* *
53211988 TTTTTAATTTTAGGGTTAGAA
1 TTTTTAAGTTAAGGGTTAGAA
53212009 TTTTTAAGTTAAGGGTTAG
1 TTTTTAAGTTAAGGGTTAG
53212028 GATTAGGGTT
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:0.28, C:0.00, G:0.23, T:0.50
Consensus pattern (21 bp):
TTTTTAAGTTAAGGGTTAGAA
Found at i:53216002 original size:18 final size:19
Alignment explanation
Indices: 53215978--53216028 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 19
53215968 TAGGCAACTT
53215978 TTTTTTTGCGCTTTTGCGC
1 TTTTTTTGCGCTTTTGCGC
* *
53215997 -TTTTTTGC-TTTTTGCTC
1 TTTTTTTGCGCTTTTGCGC
53216014 TTTTTTTGCGCTTTT
1 TTTTTTTGCGCTTTT
53216029 TACTCTCTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 7 0.26
18 16 0.59
19 4 0.15
ACGTcount: A:0.00, C:0.18, G:0.16, T:0.67
Consensus pattern (19 bp):
TTTTTTTGCGCTTTTGCGC
Found at i:53216075 original size:9 final size:10
Alignment explanation
Indices: 53216050--53216074 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
53216040 TTTTTTGCAC
53216050 TTTTTTGTTT
1 TTTTTTGTTT
53216060 TTTTTTGTTT
1 TTTTTTGTTT
53216070 TTTTT
1 TTTTT
53216075 GCGCTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:53216099 original size:29 final size:29
Alignment explanation
Indices: 53216040--53216100 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
53216030 ACTCTCTCTC
** *
53216040 TTTTTTGCACTTTTTTGTTTTTTTTTGTT
1 TTTTTTGCACTTTTTACTTTTTCTTTGTT
*
53216069 TTTTTTGCGCTTTTTACTTTTTACTTT-TT
1 TTTTTTGCACTTTTTACTTTTT-CTTTGTT
53216098 TTT
1 TTT
53216101 GCTTTTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 24 0.89
30 3 0.11
ACGTcount: A:0.05, C:0.10, G:0.08, T:0.77
Consensus pattern (29 bp):
TTTTTTGCACTTTTTACTTTTTCTTTGTT
Found at i:53216687 original size:31 final size:32
Alignment explanation
Indices: 53216649--53216711 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
53216639 AGGCAAATTA
53216649 CAAGAGTAATTGAATCCTAAT-AAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
53216680 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
53216712 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 21 0.68
32 10 0.32
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.32
Consensus pattern (32 bp):
CAAGAGTAATTGAATCCTAATAAAAACTCTTT
Found at i:53218252 original size:11 final size:12
Alignment explanation
Indices: 53218236--53218290 Score: 71
Period size: 11 Copynumber: 4.8 Consensus size: 12
53218226 ATTAAATATG
53218236 AATTTGAGA-GA
1 AATTTGAGAGGA
*
53218247 AATTTGAAAGGA
1 AATTTGAGAGGA
53218259 AA-TTGAGAGGA
1 AATTTGAGAGGA
53218270 AA-TTGAGAGGA
1 AATTTGAGAGGA
*
53218281 AATTCGAGAG
1 AATTTGAGAG
53218291 AGAATTTGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
11 29 0.74
12 10 0.26
ACGTcount: A:0.45, C:0.02, G:0.31, T:0.22
Consensus pattern (12 bp):
AATTTGAGAGGA
Found at i:53218264 original size:22 final size:22
Alignment explanation
Indices: 53218239--53218298 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 22
53218229 AAATATGAAT
53218239 TTGAGAGAAATTTGAAAGGAAA
1 TTGAGAGAAATTTGAAAGGAAA
*
53218261 TTGAGAGGAAA-TTGAGAGGAAA
1 TTGAGA-GAAATTTGAAAGGAAA
53218283 TTCGAGAGAGAATTTG
1 TT-GAGAGA-AATTTG
53218299 TTTGTGAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 20 0.61
23 10 0.30
24 3 0.09
ACGTcount: A:0.43, C:0.02, G:0.32, T:0.23
Consensus pattern (22 bp):
TTGAGAGAAATTTGAAAGGAAA
Found at i:53221257 original size:11 final size:10
Alignment explanation
Indices: 53221224--53221256 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
53221214 CCCATGTTGC
53221224 TTTCTCTTACT
1 TTTCTCTTA-T
53221235 TTTCT-TTAT
1 TTTCTCTTAT
53221244 TTTCTCTTAT
1 TTTCTCTTAT
53221254 TTT
1 TTT
53221257 TTTCACGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.29
10 10 0.48
11 5 0.24
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTCTCTTAT
Found at i:53223153 original size:14 final size:13
Alignment explanation
Indices: 53223125--53223167 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
53223115 TTAGCGTTGC
*
53223125 ATTTGAAAAAA-T
1 ATTTAAAAAAATT
53223137 ATTGTAAAAAAATT
1 ATT-TAAAAAAATT
*
53223151 ATTTAAAAAAATA
1 ATTTAAAAAAATT
53223164 ATTT
1 ATTT
53223168 TGAAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 3 0.11
13 20 0.74
14 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (13 bp):
ATTTAAAAAAATT
Found at i:53236935 original size:38 final size:38
Alignment explanation
Indices: 53236884--53236960 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
53236874 CTGGAAGTAT
*
53236884 ATTCTTTCAATCTCCGAAGATTCATTATTATTCATTTA
1 ATTCTTTCAATCTCCAAAGATTCATTATTATTCATTTA
*
53236922 ATTCTTTCAATCTCTAAAGATTCATTATTATTCATTTA
1 ATTCTTTCAATCTCCAAAGATTCATTATTATTCATTTA
53236960 A
1 A
53236961 ACTGACCATC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.31, C:0.17, G:0.04, T:0.48
Consensus pattern (38 bp):
ATTCTTTCAATCTCCAAAGATTCATTATTATTCATTTA
Found at i:53242305 original size:31 final size:29
Alignment explanation
Indices: 53242267--53242344 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
53242257 CTAACGGCTC
* *
53242267 AGTGACTAAAATGTTACAACGTGATAACATA
1 AGTGACTAAAATGTAAC-ACGTCA-AACATA
* **
53242298 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACACGTCAAACATA
53242327 AGTGACTAAAATGTAACA
1 AGTGACTAAAATGTAACA
53242345 TGAGCCAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 23 0.56
30 3 0.07
31 15 0.37
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACGTCAAACATA
Found at i:53242361 original size:31 final size:29
Alignment explanation
Indices: 53242292--53242365 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
53242282 ACAACGTGAT
**
53242292 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAACGTAACATGCCA
*
53242321 AACATAAGTGACTAAAATGTAACATGAGCCA
1 AACATAAGTGACTAAAACGTAACAT--GCCA
*
53242352 AACAAAAGTGACTA
1 AACATAAGTGACTA
53242366 TTTTGGTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACATGCCA
Found at i:53242919 original size:15 final size:15
Alignment explanation
Indices: 53242899--53242928 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
53242889 TGCCATCGTC
53242899 AAATCAACTTGACGA
1 AAATCAACTTGACGA
53242914 AAATCAACTTGACGA
1 AAATCAACTTGACGA
53242929 TGAATTACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (15 bp):
AAATCAACTTGACGA
Found at i:53243780 original size:20 final size:20
Alignment explanation
Indices: 53243744--53243783 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
53243734 TGGACAAAAT
*
53243744 AAAACTACAAAGCTGTGGGC
1 AAAACTACAAAGATGTGGGC
53243764 AAAACTACAATA-ATGTGGGC
1 AAAACTACAA-AGATGTGGGC
53243784 TGAAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.17
Consensus pattern (20 bp):
AAAACTACAAAGATGTGGGC
Found at i:53246547 original size:22 final size:22
Alignment explanation
Indices: 53246515--53246559 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
53246505 TATATTAATT
53246515 TTTGAAGTATAAATTCATTTAA
1 TTTGAAGTATAAATTCATTTAA
*
53246537 TTTGAATTATAAATTCATTTAA
1 TTTGAAGTATAAATTCATTTAA
53246559 T
1 T
53246560 ATGATTTGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (22 bp):
TTTGAAGTATAAATTCATTTAA
Found at i:53247528 original size:16 final size:16
Alignment explanation
Indices: 53247507--53247546 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
53247497 CTCAAAACCA
53247507 TACCTATCGATATTTC
1 TACCTATCGATATTTC
53247523 TACCTATCGATATTTC
1 TACCTATCGATATTTC
53247539 TACCTATC
1 TACCTATC
53247547 CCACACACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.25, C:0.28, G:0.05, T:0.42
Consensus pattern (16 bp):
TACCTATCGATATTTC
Found at i:53247866 original size:21 final size:21
Alignment explanation
Indices: 53247842--53247882 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
53247832 GATAATTTTA
*
53247842 AATACAATATAATTA-AAAAAC
1 AATACAA-AAAATTATAAAAAC
53247863 AATACAAAAAATTATAAAAA
1 AATACAAAAAATTATAAAAA
53247883 TATAAATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (21 bp):
AATACAAAAAATTATAAAAAC
Found at i:53247904 original size:26 final size:24
Alignment explanation
Indices: 53247863--53247910 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
53247853 ATTAAAAAAC
*
53247863 AATACAAAAAATTATAAAAATATA
1 AATACAAAAAAATATAAAAATATA
*
53247887 AATACAGAACAAAATATACAAATA
1 AATACA-AA-AAAATATAAAAATA
53247911 ATTATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 2 0.10
26 12 0.60
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.21
Consensus pattern (24 bp):
AATACAAAAAAATATAAAAATATA
Found at i:53252694 original size:28 final size:29
Alignment explanation
Indices: 53252632--53252705 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 29
53252622 TTTGAGTCAT
*
53252632 TATATATATACATACATGCGTTTTCATAA
1 TATATATACACATACATGCGTTTTCATAA
** *
53252661 TATATATACACATACAT-TTTTTTTATAA
1 TATATATACACATACATGCGTTTTCATAA
* *
53252689 TTTATATACATATACAT
1 TATATATACACATACAT
53252706 ACTTATATAC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 23 0.59
29 16 0.41
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.46
Consensus pattern (29 bp):
TATATATACACATACATGCGTTTTCATAA
Found at i:53257580 original size:17 final size:17
Alignment explanation
Indices: 53257558--53257591 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
53257548 GATATGATAC
53257558 ATAGTATAAATTATAAA
1 ATAGTATAAATTATAAA
53257575 ATAGTATAAATTATAAA
1 ATAGTATAAATTATAAA
53257592 TAAATCGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (17 bp):
ATAGTATAAATTATAAA
Found at i:53261924 original size:16 final size:17
Alignment explanation
Indices: 53261891--53261925 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
53261881 AACAATTCTA
*
53261891 ATAATTTTAAATACAAT
1 ATAATTATAAATACAAT
53261908 ATAATTATAAA-ACAAT
1 ATAATTATAAATACAAT
53261924 AT
1 AT
53261926 GAAAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAATTATAAATACAAT
Found at i:53265184 original size:14 final size:14
Alignment explanation
Indices: 53265165--53265195 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
53265155 TTAAATGATT
53265165 TTTAATTAATTAAA
1 TTTAATTAATTAAA
53265179 TTTAATTAATTAAA
1 TTTAATTAATTAAA
53265193 TTT
1 TTT
53265196 TCTAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTAATTAATTAAA
Found at i:53267666 original size:16 final size:18
Alignment explanation
Indices: 53267631--53267676 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
53267621 ACCTTCAAAG
53267631 TAAAAAAAAATCACTAAA
1 TAAAAAAAAATCACTAAA
*
53267649 TAAACAAAAA-CA-TAAA
1 TAAAAAAAAATCACTAAA
53267665 TACATAAAAAAA
1 TA-A-AAAAAAA
53267677 ATGCTCATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 6 0.25
17 3 0.12
18 15 0.62
ACGTcount: A:0.74, C:0.11, G:0.00, T:0.15
Consensus pattern (18 bp):
TAAAAAAAAATCACTAAA
Found at i:53269475 original size:32 final size:31
Alignment explanation
Indices: 53269436--53269528 Score: 159
Period size: 32 Copynumber: 2.9 Consensus size: 31
53269426 ACAGATATTG
53269436 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTTAAGCTTGTT-GATATTGAATTT
53269468 ATTATGTTTTAAGCTTGTTGAATATTGAATTT
1 ATTATGTTTTAAGCTTGTTG-ATATTGAATTT
53269500 ATTATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTTAAGCTTGTT-GATATTGAA
53269529 ATGATTGACA
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
31 1 0.02
32 57 0.97
33 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.52
Consensus pattern (31 bp):
ATTATGTTTTAAGCTTGTTGATATTGAATTT
Found at i:53270935 original size:14 final size:15
Alignment explanation
Indices: 53270912--53270949 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
53270902 CCAGAAAAGT
53270912 AAAA-CATTTTCCA-
1 AAAATCATTTTCCAG
53270925 AAAATCATTTTCCAG
1 AAAATCATTTTCCAG
53270940 AAAAT-ATTTT
1 AAAATCATTTT
53270950 ACTGGAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.17
14 14 0.61
15 5 0.22
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.37
Consensus pattern (15 bp):
AAAATCATTTTCCAG
Found at i:53278106 original size:40 final size:40
Alignment explanation
Indices: 53278054--53278137 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
53278044 GTCTCAGAGA
53278054 ACATGCACAATGTCCTTAGTATCATGACCACATAATGAGC
1 ACATGCACAATGTCCTTAGTATCATGACCACATAATGAGC
*
53278094 ACATGCATAATGTCCTTAGTATCATGACCACATAATGAGC
1 ACATGCACAATGTCCTTAGTATCATGACCACATAATGAGC
53278134 ACAT
1 ACAT
53278138 ATTGTTTTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (40 bp):
ACATGCACAATGTCCTTAGTATCATGACCACATAATGAGC
Found at i:53285563 original size:14 final size:14
Alignment explanation
Indices: 53285544--53285574 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
53285534 TAAATGATTT
53285544 TTTAATTAATTAAA
1 TTTAATTAATTAAA
53285558 TTTAATTAATTAAA
1 TTTAATTAATTAAA
53285572 TTT
1 TTT
53285575 TCTAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTAATTAATTAAA
Found at i:53287832 original size:15 final size:16
Alignment explanation
Indices: 53287807--53287841 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
53287797 TTTTAAATAT
53287807 TTATCATTATTTATTA
1 TTATCATTATTTATTA
53287823 TTAT-ATTATTTATTA
1 TTATCATTATTTATTA
53287838 TTAT
1 TTAT
53287842 TGTTACTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATCATTATTTATTA
Found at i:53288999 original size:17 final size:16
Alignment explanation
Indices: 53288975--53289020 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 16
53288965 ACCTTCAAAG
53288975 TAAAAAAAAATCACTAAA
1 TAAAAAAAAA-CA-TAAA
53288993 TAAAAAAAAACATAAA
1 TAAAAAAAAACATAAA
53289009 TACATAAAAAAA
1 TA-A-AAAAAAA
53289021 AATGCTCATC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.23
17 3 0.12
18 17 0.65
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (16 bp):
TAAAAAAAAACATAAA
Found at i:53288999 original size:20 final size:20
Alignment explanation
Indices: 53288976--53289022 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
53288966 CCTTCAAAGT
* *
53288976 AAAAAAAAATCACTAAATAA
1 AAAAAAAAATAAATAAATAA
* *
53288996 AAAAAAACATAAATACATAA
1 AAAAAAAAATAAATAAATAA
53289016 AAAAAAA
1 AAAAAAA
53289023 TGCTCATCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.13
Consensus pattern (20 bp):
AAAAAAAAATAAATAAATAA
Found at i:53291280 original size:32 final size:31
Alignment explanation
Indices: 53291238--53291330 Score: 150
Period size: 32 Copynumber: 2.9 Consensus size: 31
53291228 ATAGATATTG
*
53291238 ATTATATTTTAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTTAAGCTTGTT-GATATTGAATTT
53291270 ATTATGTTTTAAGCTTGTTGAATATTGAATTT
1 ATTATGTTTTAAGCTTGTTG-ATATTGAATTT
53291302 ATTATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTTAAGCTTGTT-GATATTGAA
53291331 ATGATTGACA
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
31 1 0.02
32 56 0.97
33 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.52
Consensus pattern (31 bp):
ATTATGTTTTAAGCTTGTTGATATTGAATTT
Found at i:53292735 original size:14 final size:15
Alignment explanation
Indices: 53292712--53292749 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
53292702 CCAGAAAAGT
53292712 AAAA-CATTTTCCA-
1 AAAATCATTTTCCAG
53292725 AAAATCATTTTCCAG
1 AAAATCATTTTCCAG
53292740 AAAAT-ATTTT
1 AAAATCATTTT
53292750 ACTGGAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.17
14 14 0.61
15 5 0.22
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.37
Consensus pattern (15 bp):
AAAATCATTTTCCAG
Found at i:53299700 original size:40 final size:40
Alignment explanation
Indices: 53299650--53299733 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
53299640 GTCTCAGAGA
53299650 ACATGCATAATGTCCTTAGTATCATGACCACATAATGAGC
1 ACATGCATAATGTCCTTAGTATCATGACCACATAATGAGC
53299690 ACATGCATAATGTCCTTAGTATCATGACCACATAATGAGC
1 ACATGCATAATGTCCTTAGTATCATGACCACATAATGAGC
53299730 ACAT
1 ACAT
53299734 ATTGTTTTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (40 bp):
ACATGCATAATGTCCTTAGTATCATGACCACATAATGAGC
Found at i:53306942 original size:12 final size:14
Alignment explanation
Indices: 53306915--53306943 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
53306905 ATTCATTTAA
53306915 TTTTAATATAATTT
1 TTTTAATATAATTT
53306929 TTTTAAT-TAATTT
1 TTTTAATATAATTT
53306942 TT
1 TT
53306944 AAAATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTAATATAATTT
Found at i:53307162 original size:14 final size:14
Alignment explanation
Indices: 53307143--53307173 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
53307133 TAAATGATTT
53307143 TTTAATTAATTAAA
1 TTTAATTAATTAAA
53307157 TTTAATTAATTAAA
1 TTTAATTAATTAAA
53307171 TTT
1 TTT
53307174 TCTAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTAATTAATTAAA
Found at i:53307662 original size:3 final size:3
Alignment explanation
Indices: 53307654--53307678 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
53307644 GTGCGTCCAT
53307654 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
53307679 CTATAGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:53309431 original size:15 final size:16
Alignment explanation
Indices: 53309406--53309440 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
53309396 TTTTAAATAT
53309406 TTATCATTATTTATTA
1 TTATCATTATTTATTA
53309422 TTAT-ATTATTTATTA
1 TTATCATTATTTATTA
53309437 TTAT
1 TTAT
53309441 TGTTACTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATCATTATTTATTA
Found at i:53315285 original size:32 final size:32
Alignment explanation
Indices: 53315239--53315331 Score: 159
Period size: 32 Copynumber: 2.9 Consensus size: 32
53315229 TGTCAATCAT
*
53315239 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCTAACAAGCTTAAAACATAATAAA
*
53315271 TTCAATATTTAACAAGCTTAAAACATAATAAA
1 TTCAATATCTAACAAGCTTAAAACATAATAAA
*
53315303 TTCAATATCTAATAAGCTTAAAACATAAT
1 TTCAATATCTAACAAGCTTAAAACATAAT
53315332 CAATATCTAT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.52, C:0.15, G:0.03, T:0.30
Consensus pattern (32 bp):
TTCAATATCTAACAAGCTTAAAACATAATAAA
Found at i:53316026 original size:59 final size:63
Alignment explanation
Indices: 53315963--53316091 Score: 153
Period size: 59 Copynumber: 2.1 Consensus size: 63
53315953 TTGTTGGCTT
*
53315963 TTGAAATTATTATGTCTTGAA-TTTGATAG-ATATTG-A-TTA-TA-TTTTAAGCTTGTTAGATA
1 TTGAAATTATTATGT-TTGAAGCTTG-TAGAATATTGAATTTATTATTTTTAAGCTTGTTAGATA
* * * *
53316022 TTGAATTTATTATGTTTTAAGCTTGTTGAATATTGAATTTATTATTTTTAAGCTTGTTGGATA
1 TTGAAATTATTATGTTTGAAGCTTGTAGAATATTGAATTTATTATTTTTAAGCTTGTTAGATA
53316085 TTGAAAT
1 TTGAAAT
53316092 GATTGACAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
58 6 0.10
59 23 0.40
60 1 0.02
61 3 0.05
62 2 0.03
63 23 0.40
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.51
Consensus pattern (63 bp):
TTGAAATTATTATGTTTGAAGCTTGTAGAATATTGAATTTATTATTTTTAAGCTTGTTAGATA
Found at i:53316074 original size:31 final size:32
Alignment explanation
Indices: 53315998--53316089 Score: 143
Period size: 32 Copynumber: 2.9 Consensus size: 32
53315988 ATAGATATTG
53315998 ATTATATTTTAAGCTTGTT-AGATATTGAATTT
1 ATTATATTTTAAGCTTGTTGA-ATATTGAATTT
*
53316030 ATTATGTTTTAAGCTTGTTGAATATTGAATTT
1 ATTATATTTTAAGCTTGTTGAATATTGAATTT
*
53316062 ATTAT-TTTTAAGCTTGTTGGATATTGAA
1 ATTATATTTTAAGCTTGTTGAATATTGAA
53316090 ATGATTGACA
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
31 22 0.39
32 34 0.60
33 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.15, T:0.52
Consensus pattern (32 bp):
ATTATATTTTAAGCTTGTTGAATATTGAATTT
Found at i:53324482 original size:40 final size:40
Alignment explanation
Indices: 53324430--53324513 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
53324420 GTCTCAGAGA
53324430 ACATGCACAATGTCCTTAGTATCATGACCACATAATGAGC
1 ACATGCACAATGTCCTTAGTATCATGACCACATAATGAGC
*
53324470 ACATGCATAATGTCCTTAGTATCATGACCACATAATGAGC
1 ACATGCACAATGTCCTTAGTATCATGACCACATAATGAGC
53324510 ACAT
1 ACAT
53324514 ATTGTTTTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (40 bp):
ACATGCACAATGTCCTTAGTATCATGACCACATAATGAGC
Found at i:53329152 original size:1 final size:1
Alignment explanation
Indices: 53329148--53329191 Score: 61
Period size: 1 Copynumber: 44.0 Consensus size: 1
53329138 GTTAAGCTTA
* * *
53329148 TTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTATTATTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
53329192 CTACATCTAC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.05, C:0.02, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:53339994 original size:3 final size:3
Alignment explanation
Indices: 53339986--53340010 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
53339976 GTGCGTCCAT
53339986 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
53340011 CTATAGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:53341760 original size:15 final size:16
Alignment explanation
Indices: 53341735--53341767 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
53341725 TTTTAAATAT
53341735 TTATCATTATTTATTA
1 TTATCATTATTTATTA
53341751 TTAT-ATTATTTATTA
1 TTATCATTATTTATTA
53341766 TT
1 TT
53341768 GTTACTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATCATTATTTATTA
Found at i:53345793 original size:3 final size:3
Alignment explanation
Indices: 53345785--53345818 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
53345775 ATTTATTTTC
53345785 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
53345819 TTGTTTTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:53352899 original size:21 final size:21
Alignment explanation
Indices: 53352873--53352923 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
53352863 TTTCCCTAAG
* *
53352873 ATGTAACTTGGATTGAATTGA
1 ATGTAAATTGGATTAAATTGA
*
53352894 ATGTAAATTGTATTAAATTG-
1 ATGTAAATTGGATTAAATTGA
53352914 ATGTTAAATT
1 ATG-TAAATT
53352924 TACTCGTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.43
Consensus pattern (21 bp):
ATGTAAATTGGATTAAATTGA
Found at i:53353416 original size:24 final size:24
Alignment explanation
Indices: 53353371--53353438 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
53353361 CTTCCTGTTA
* * *
53353371 TAAG-GCTATTCGGTGCTTCCCGT
1 TAAGTGCTCTTCGGAGCTACCCGT
53353394 TAAGTGCTCTTCGGAGCTACCCGT
1 TAAGTGCTCTTCGGAGCTACCCGT
* *
53353418 TAATTGCTCTTCGGAGATACC
1 TAAGTGCTCTTCGGAGCTACC
53353439 AATTATAGGC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 4 0.10
24 35 0.90
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (24 bp):
TAAGTGCTCTTCGGAGCTACCCGT
Found at i:53356026 original size:46 final size:46
Alignment explanation
Indices: 53355889--53356027 Score: 224
Period size: 46 Copynumber: 3.0 Consensus size: 46
53355879 TGGCAAAGTG
* * *
53355889 TGAAACGTAGGTATCGTATTTCAGTGAAGAAAACCATACTGAGTTG
1 TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
* *
53355935 TGAAAAATAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTA
1 TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
*
53355981 TGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGTTA
1 TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
53356027 T
1 T
53356028 AGCAGTGTGA
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 85 1.00
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.29
Consensus pattern (46 bp):
TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
Found at i:53365250 original size:49 final size:48
Alignment explanation
Indices: 53365160--53365256 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 48
53365150 TTTCTTTGCT
* *
53365160 TAAAAACGCCTAAGTCAGCCTAACTCACAATGATAACGGATTCAACAG
1 TAAAAACACCTAAGTCAGCCTAACTCACAATGATAAAGGATTCAACAG
* * *
53365208 TAAAAACACCTAAGTTAGCTTAATCTCGCAATGATAAAGGATTCAACAG
1 TAAAAACACCTAAGTCAGCCTAA-CTCACAATGATAAAGGATTCAACAG
53365257 AATTCCCTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
48 20 0.47
49 23 0.53
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (48 bp):
TAAAAACACCTAAGTCAGCCTAACTCACAATGATAAAGGATTCAACAG
Found at i:53366573 original size:23 final size:24
Alignment explanation
Indices: 53366530--53366581 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 24
53366520 AAATTGAAAG
53366530 TTAAATACCAAAATGATAAAAAAA
1 TTAAATACCAAAATGATAAAAAAA
*
53366554 TTAAAT-CTAAAAT-ATAAAAAAA
1 TTAAATACCAAAATGATAAAAAAA
53366576 -TAAATA
1 TTAAATA
53366582 TTTAAAGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 5 0.19
22 9 0.35
23 6 0.23
24 6 0.23
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (24 bp):
TTAAATACCAAAATGATAAAAAAA
Found at i:53366964 original size:32 final size:29
Alignment explanation
Indices: 53366928--53366995 Score: 57
Period size: 32 Copynumber: 2.2 Consensus size: 29
53366918 AATTAGTAAA
* *
53366928 GATAAAATTAT-ACTTTAATTCACTTTAAAAAT
1 GATAAAATT-TGA-TTTAATTC-TTTAAAAA-T
53366960 GATAAAAATTTGATTTAATTCTTTAAAAAT
1 GATA-AAATTTGATTTAATTCTTTAAAAAT
*
53366990 TATAAA
1 GATAAA
53366996 GATAGATGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
29 2 0.06
30 4 0.13
31 6 0.19
32 13 0.42
33 6 0.19
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (29 bp):
GATAAAATTTGATTTAATTCTTTAAAAAT
Found at i:53368792 original size:25 final size:24
Alignment explanation
Indices: 53368743--53368792 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
53368733 TAATTAACAC
*
53368743 AAAAAAATATAAAATAATTAAGATT
1 AAAAAAATATAAAAAAATT-AGATT
53368768 AAAAAAATATTAATAAAAATT-GATT
1 AAAAAAATA-TAA-AAAAATTAGATT
53368793 TTGTGAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 13 0.59
26 3 0.14
27 6 0.27
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (24 bp):
AAAAAAATATAAAAAAATTAGATT
Found at i:53371294 original size:16 final size:16
Alignment explanation
Indices: 53371262--53371296 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
53371252 GGTTGGAGTG
* *
53371262 AATGGAATAGGGCTGT
1 AATGGAATAGAGATGT
53371278 AATGGAATAGAGATGT
1 AATGGAATAGAGATGT
53371294 AAT
1 AAT
53371297 CAGCAATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.31, T:0.26
Consensus pattern (16 bp):
AATGGAATAGAGATGT
Found at i:53371687 original size:26 final size:29
Alignment explanation
Indices: 53371651--53371716 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 29
53371641 ATTAAAGTAT
53371651 TTTTATATATTTG-GAATTTAATT-TTTATA
1 TTTT-TAT-TTTGAGAATTTAATTCTTTATA
*
53371680 TTTTTATTTTGAAGAATTTAATTCCTTTATT
1 TTTTTATTTTG-AGAATTTAATT-CTTTATA
53371711 TTTTTA
1 TTTTTA
53371717 ATTTAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 4 0.12
28 3 0.09
29 14 0.44
31 11 0.34
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (29 bp):
TTTTTATTTTGAGAATTTAATTCTTTATA
Found at i:53371726 original size:29 final size:29
Alignment explanation
Indices: 53371664--53371727 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
53371654 TATATATTTG
*
53371664 GAATTTAATTTTTATATTTTTATTTTGAA
1 GAATTTAATTTTTATATTTTTAATTTGAA
*
53371693 GAATTTAATTCCTTTATTTTTTTAATTT-AA
1 GAATTTAATT--TTTATATTTTTAATTTGAA
53371723 -AATTT
1 GAATTT
53371728 TAAGCTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 15 0.48
30 2 0.06
31 14 0.45
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (29 bp):
GAATTTAATTTTTATATTTTTAATTTGAA
Found at i:53385548 original size:19 final size:19
Alignment explanation
Indices: 53385524--53385634 Score: 163
Period size: 19 Copynumber: 5.8 Consensus size: 19
53385514 AAAATTTTGA
53385524 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
53385543 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
53385562 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
53385583 GATAT--AATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
53385600 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
53385619 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
53385635 ATATATGATT
Statistics
Matches: 84, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
17 17 0.20
19 49 0.58
21 18 0.21
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:53386398 original size:24 final size:24
Alignment explanation
Indices: 53386371--53386424 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
53386361 TACATGTATA
53386371 TATATTTTTTAAACGAATATTTTC
1 TATATTTTTTAAACGAATATTTTC
* *
53386395 TATATTTTTTTAATGAATATTTTC
1 TATATTTTTTAAACGAATATTTTC
53386419 -ATATTT
1 TATATTT
53386425 ATATGTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 6 0.21
24 22 0.79
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (24 bp):
TATATTTTTTAAACGAATATTTTC
Found at i:53387229 original size:96 final size:98
Alignment explanation
Indices: 53387080--53387272 Score: 345
Period size: 96 Copynumber: 2.0 Consensus size: 98
53387070 AAAAATCATG
53387080 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTT
53387145 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
* *
53387178 AAGGAAATATT-CGAGTTTGGGATTCTAAAGGGA-TGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTT
*
53387241 AAATCTTGGATGAGTGGATGTTCTTTTAAAGT
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGT
53387273 TTTATTGTAT
Statistics
Matches: 92, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
96 61 0.66
97 20 0.22
98 11 0.12
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.37
Consensus pattern (98 bp):
AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTT
AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
Found at i:53393018 original size:19 final size:20
Alignment explanation
Indices: 53392994--53393032 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
53392984 AGTTCAGATT
53392994 AAAAAAAACAAAAAA-AAAA
1 AAAAAAAACAAAAAATAAAA
53393013 AAAAAAAACAAAAAATAAAA
1 AAAAAAAACAAAAAATAAAA
53393033 GTGAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.92, C:0.05, G:0.00, T:0.03
Consensus pattern (20 bp):
AAAAAAAACAAAAAATAAAA
Found at i:53393044 original size:1 final size:1
Alignment explanation
Indices: 53392994--53393032 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
53392984 AGTTCAGATT
* * *
53392994 AAAAAAAACAAAAAAAAAAAAAAAAAACAAAAAATAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
53393033 GTGAAAGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.92, C:0.05, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:53393052 original size:11 final size:10
Alignment explanation
Indices: 53392994--53393027 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
53392984 AGTTCAGATT
53392994 AAAAAAAACA
1 AAAAAAAACA
53393004 AAAAAAAA-A
1 AAAAAAAACA
53393013 AAAAAAAACA
1 AAAAAAAACA
53393023 AAAAA
1 AAAAA
53393028 TAAAAGTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:53394534 original size:128 final size:128
Alignment explanation
Indices: 53394273--53394558 Score: 434
Period size: 131 Copynumber: 2.2 Consensus size: 128
53394263 CGACGAATCT
*
53394273 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAGCCTTGTCTTCCTGAGCAGCAGCGGA
1 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAGCCTTGTCTCCCTGAGCAGCAGCGGA
* * **
53394338 GAAGGTGAAGATGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATGAAGATGGCGGAT-CT
66 GAAGGTGAAGATGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATAAAGA-GCCGGATAAA
53394401 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGG
1 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA-CAAGCCTTGTCTCCCTGAGCAGCAGCGG
53394466 AGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGA-CCGG-TA
65 AGAAGG-TGAAGA-TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT-AAAGAGCCGGATA
53394529 AA
127 AA
53394531 TCTTATCTTTCCAAGATAGTGGGAAGCA
1 ---TATCTTTCCAAGATAGTGGGAAGCA
53394559 TAGATTAAGC
Statistics
Matches: 145, Mismatches: 5, Indels: 11
0.90 0.03 0.07
Matches are distributed among these distances:
128 36 0.25
129 34 0.23
130 9 0.06
131 37 0.26
132 4 0.03
133 25 0.17
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (128 bp):
TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAGCCTTGTCTCCCTGAGCAGCAGCGGA
GAAGGTGAAGATGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATAAAGAGCCGGATAAA
Found at i:53409234 original size:40 final size:40
Alignment explanation
Indices: 53409190--53409274 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
53409180 GCTTTTTAAC
53409190 AAACGCCG-TAATAGATCAAGAATTAGCAACG-CTTTCTAGA
1 AAACGCCGCT-ATAGATCAAGAATTAGCAACGCCTTT-TAGA
* * **
53409230 AAACGCGGCTATAGATCAAGTATTAGCGGCGCCTTTTAGA
1 AAACGCCGCTATAGATCAAGAATTAGCAACGCCTTTTAGA
53409270 AAACG
1 AAACG
53409275 TCGCAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
40 34 0.87
41 5 0.13
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.22
Consensus pattern (40 bp):
AAACGCCGCTATAGATCAAGAATTAGCAACGCCTTTTAGA
Found at i:53409614 original size:21 final size:21
Alignment explanation
Indices: 53409590--53409650 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
53409580 TGGTTTGTGA
*
53409590 TTTAAGGTTTATGGTTTAGGG
1 TTTAAGGTTTAGGGTTTAGGG
*
53409611 TTT-AGAGTTTAGGGGTTAGGGG
1 TTTAAG-GTTTAGGGTTTA-GGG
* *
53409633 TTTAGGGATTAGGGTTTA
1 TTTAAGGTTTAGGGTTTA
53409651 AAGTTTTATG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 2 0.06
21 13 0.41
22 16 0.50
23 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.43
Consensus pattern (21 bp):
TTTAAGGTTTAGGGTTTAGGG
Found at i:53409615 original size:7 final size:7
Alignment explanation
Indices: 53409590--53409724 Score: 72
Period size: 7 Copynumber: 17.9 Consensus size: 7
53409580 TGGTTTGTGA
*
53409590 TTTAAGG
1 TTTAGGG
*
53409597 TTTATGG
1 TTTAGGG
53409604 TTTAGGG
1 TTTAGGG
*
53409611 TTTAGAG
1 TTTAGGG
53409618 TTTAGGG
1 TTTAGGG
*
53409625 GTTAGGGG
1 TTTA-GGG
53409633 TTTAGGG
1 TTTAGGG
*
53409640 ATTAGGG
1 TTTAGGG
* *
53409647 TTTAAAGT
1 TTT-AGGG
53409655 TTTATGGGG
1 TTTA--GGG
* *
53409664 TTTTGGA
1 TTTAGGG
53409671 TTTAGGGG
1 TTTA-GGG
*
53409679 TTTTTGGGTG
1 --TTTAGG-G
53409689 TTTAGGG
1 TTTAGGG
*
53409696 TTTATGG
1 TTTAGGG
*
53409703 TTTTGGG
1 TTTAGGG
53409710 TTTTAGGGG
1 -TTTA-GGG
53409719 TTTAGG
1 TTTAGG
53409725 ATTTTTTTGT
Statistics
Matches: 96, Mismatches: 22, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
7 58 0.60
8 25 0.26
9 9 0.09
10 4 0.04
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:53409620 original size:14 final size:15
Alignment explanation
Indices: 53409602--53409724 Score: 72
Period size: 15 Copynumber: 8.0 Consensus size: 15
53409592 TAAGGTTTAT
53409602 GGTTTAGGGTTTA-G
1 GGTTTAGGGTTTAGG
* *
53409616 AGTTTAGGGGTTAGG
1 GGTTTAGGGTTTAGG
*
53409631 GGTTTAGGGATTA-G
1 GGTTTAGGGTTTAGG
* *
53409645 GGTTTAAAGTTTTATGG
1 GGTTT-AGGGTTTA-GG
* *
53409662 GGTTTTGGATTTAGG
1 GGTTTAGGGTTTAGG
*
53409677 GGTTTTTGGGTGTTTA-G
1 GG--TTTAGG-GTTTAGG
* *
53409694 GGTTTATGGTTTTGG
1 GGTTTAGGGTTTAGG
*
53409709 GTTTTAGGGGTTTAGG
1 GGTTTA-GGGTTTAGG
53409725 ATTTTTTTGT
Statistics
Matches: 82, Mismatches: 18, Indels: 16
0.71 0.16 0.14
Matches are distributed among these distances:
14 21 0.26
15 31 0.38
16 12 0.15
17 14 0.17
18 4 0.05
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.45
Consensus pattern (15 bp):
GGTTTAGGGTTTAGG
Found at i:53409635 original size:36 final size:38
Alignment explanation
Indices: 53409595--53409665 Score: 101
Period size: 36 Copynumber: 1.9 Consensus size: 38
53409585 TGTGATTTAA
* * *
53409595 GGTTTATGGTTTAGGGTTTAGAG-TTTA-GGGGTTAGG
1 GGTTTAGGGATTAGGGTTTAAAGTTTTATGGGGTTAGG
53409631 GGTTTAGGGATTAGGGTTTAAAGTTTTATGGGGTT
1 GGTTTAGGGATTAGGGTTTAAAGTTTTATGGGGTT
53409666 TTGGATTTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 20 0.67
37 4 0.13
38 6 0.20
ACGTcount: A:0.18, C:0.00, G:0.39, T:0.42
Consensus pattern (38 bp):
GGTTTAGGGATTAGGGTTTAAAGTTTTATGGGGTTAGG
Found at i:53410325 original size:43 final size:43
Alignment explanation
Indices: 53410236--53410325 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 43
53410226 CCTCGGAGAG
* *
53410236 AAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGTCGCT
1 AAAGGTCATGTTCTTTAGCGGCATTTGTGATAAAAGCGCCGCT
* *
53410279 AAAGGTCATGCTT-TTTAGCGGCATTTGTGATAAAAGTGCCGGT
1 AAAGGTCATG-TTCTTTAGCGGCATTTGTGATAAAAGCGCCGCT
53410322 AAAG
1 AAAG
53410326 AACATGGCCT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 40 0.95
44 2 0.05
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (43 bp):
AAAGGTCATGTTCTTTAGCGGCATTTGTGATAAAAGCGCCGCT
Found at i:53410339 original size:43 final size:43
Alignment explanation
Indices: 53410242--53410340 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 43
53410232 AGAGAAAGGT
* * * **
53410242 CATGTTCTTTAGCGGCGTTTGTGATAAAAGCGTCGCTAAAGGT
1 CATGCTCTTTAGCGGCATTTGTGATAAAAGCGCCGCTAAAGAA
* * *
53410285 CATGCTTTTTAGCGGCATTTGTGATAAAAGTGCCGGTAAAGAA
1 CATGCTCTTTAGCGGCATTTGTGATAAAAGCGCCGCTAAAGAA
53410328 CATGGC-CTTTAGC
1 CAT-GCTCTTTAGC
53410341 AGTGCTTCTT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
43 44 0.96
44 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (43 bp):
CATGCTCTTTAGCGGCATTTGTGATAAAAGCGCCGCTAAAGAA
Found at i:53410827 original size:5 final size:5
Alignment explanation
Indices: 53410817--53410845 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
53410807 TTATAATTCT
53410817 TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
53410846 TTAATTCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:53417750 original size:15 final size:16
Alignment explanation
Indices: 53417730--53417784 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
53417720 TTTTTATTTA
53417730 AATTTA-AATTTATAT
1 AATTTAGAATTTATAT
53417745 AATTTAGGAATTTATAT
1 AATTTA-GAATTTATAT
* *
53417762 ATTTTATGGATTTATAT
1 AATTTA-GAATTTATAT
53417779 ACATTT
1 A-ATTT
53417785 TTTTAAGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 6 0.18
17 24 0.73
18 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (16 bp):
AATTTAGAATTTATAT
Found at i:53417758 original size:17 final size:18
Alignment explanation
Indices: 53417736--53417784 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
53417726 TTTAAATTTA
53417736 AATTTATATAATTTA-GG
1 AATTTATATAATTTATGG
*
53417753 AATTTATATATTTTATGG
1 AATTTATATAATTTATGG
53417771 -ATTTATATACATTT
1 AATTTATATA-ATTT
53417785 TTTTAAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 23 0.82
18 5 0.18
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (18 bp):
AATTTATATAATTTATGG
Found at i:53420635 original size:10 final size:11
Alignment explanation
Indices: 53420611--53420639 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
53420601 TTTCAATATC
53420611 CTCTCAAATTT
1 CTCTCAAATTT
53420622 CTCTCAAA-TT
1 CTCTCAAATTT
53420632 CTCTCAAA
1 CTCTCAAA
53420640 GCTCTCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (11 bp):
CTCTCAAATTT
Found at i:53421757 original size:11 final size:11
Alignment explanation
Indices: 53421720--53421751 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
53421710 TAAAGAGAGC
*
53421720 TTTGAGAGGAA
1 TTTGAGAGAAA
53421731 TTTGAGAGAAA
1 TTTGAGAGAAA
53421742 TTTGAGAGAA
1 TTTGAGAGAA
53421752 CATTGAAAGA
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:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (11 bp):
TTTGAGAGAAA
Found at i:53422327 original size:30 final size:30
Alignment explanation
Indices: 53422256--53422333 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
53422246 ACTCAATTAT
53422256 ATAAAAAATTTA-T--TTTAAGTACTCAAA
1 ATAAAAAATTTATTAATTTAAGTACTCAAA
53422283 ATAAAAAATTTATTAATTTAAGTACTCAAA
1 ATAAAAAATTTATTAATTTAAGTACTCAAA
*
53422313 ATAAAAAGTTTATTAATTTAA
1 ATAAAAAATTTATTAATTTAA
53422334 TCACCCACAT
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
27 12 0.26
28 1 0.02
30 34 0.72
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (30 bp):
ATAAAAAATTTATTAATTTAAGTACTCAAA
Found at i:53422383 original size:32 final size:32
Alignment explanation
Indices: 53422347--53422408 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
53422337 CCCACATAAG
53422347 TTAGCCCTTAAATTTTATATATTATATCAAAC
1 TTAGCCCTTAAATTTTATATATTATATCAAAC
53422379 TTAGCCCTTAAATTTTATATATTATATCAA
1 TTAGCCCTTAAATTTTATATATTATATCAA
53422409 TTTAGTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.15, G:0.03, T:0.45
Consensus pattern (32 bp):
TTAGCCCTTAAATTTTATATATTATATCAAAC
Found at i:53423052 original size:28 final size:28
Alignment explanation
Indices: 53422994--53423053 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
53422984 GATTTTTTGT
* * *
53422994 TTTATTTAACATTATTATTATAGTTATA
1 TTTATTTAACATTAATATTATAGTAAAA
*
53423022 TTTATTTAATATTAATATTAATA-TAAAA
1 TTTATTTAACATTAATATT-ATAGTAAAA
53423050 TTTA
1 TTTA
53423054 AATTTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (28 bp):
TTTATTTAACATTAATATTATAGTAAAA
Found at i:53423656 original size:18 final size:19
Alignment explanation
Indices: 53423635--53423682 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
53423625 TTACATATTA
53423635 TTAAAATA-ATAGAAAAGT-
1 TTAAAATATATA-AAAAGTG
53423653 TTAAATATATATAAAAAGTG
1 TTAAA-ATATATAAAAAGTG
53423673 TATAAAATAT
1 T-TAAAATAT
53423683 TATTTAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 5 0.19
19 9 0.35
20 8 0.31
21 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (19 bp):
TTAAAATATATAAAAAGTG
Found at i:53426974 original size:22 final size:23
Alignment explanation
Indices: 53426922--53426978 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
53426912 TTTTAATTAA
* * *
53426922 AATTAAAATTAAAATTATTTTTT
1 AATTAAAATTAAAACTAATTGTT
53426945 AATTAAAATTAAAACTAATTGTT
1 AATTAAAATTAAAACTAATTGTT
53426968 -ATTAAAATTAA
1 AATTAAAATTAA
53426979 TTGCTAGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 11 0.35
23 20 0.65
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
AATTAAAATTAAAACTAATTGTT
Found at i:53426989 original size:16 final size:16
Alignment explanation
Indices: 53426954--53426993 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
53426944 TAATTAAAAT
* * *
53426954 TAAAACTAATTGTTAT
1 TAAAATTAATTGCTAG
53426970 TAAAATTAATTGCTAG
1 TAAAATTAATTGCTAG
53426986 TAAAATTA
1 TAAAATTA
53426994 TCAAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (16 bp):
TAAAATTAATTGCTAG
Found at i:53427099 original size:9 final size:9
Alignment explanation
Indices: 53427066--53427093 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
53427056 TTTATCAAAT
53427066 TATTAATTG
1 TATTAATTG
53427075 TATTAATTG
1 TATTAATTG
53427084 TATTAATTG
1 TATTAATTG
53427093 T
1 T
53427094 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:53427102 original size:68 final size:68
Alignment explanation
Indices: 53426983--53427191 Score: 359
Period size: 68 Copynumber: 3.1 Consensus size: 68
53426973 AATTAATTGC
* *
53426983 TAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACAGTT
1 TAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
53427046 GAT
66 GAT
53427049 TAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
1 TAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
53427114 GAT
66 GAT
* * *
53427117 TAGTAAATTTATCAAATTATTAATTATATTAATTGTATTAATTGTTGTAACAAAATCTAATATTT
1 TAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
53427182 GAT
66 GAT
53427185 TAGTAAA
1 TAGTAAA
53427192 ACAAACTTGA
Statistics
Matches: 136, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
66 25 0.18
68 111 0.82
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.45
Consensus pattern (68 bp):
TAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
GAT
Found at i:53427298 original size:22 final size:24
Alignment explanation
Indices: 53427258--53427301 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
53427248 AAATAAACTT
53427258 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
53427282 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
53427302 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:53428555 original size:18 final size:19
Alignment explanation
Indices: 53428532--53428585 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 19
53428522 ATGGGTCAAG
53428532 TGTGAATTTAGAAGAATTT
1 TGTGAATTTAGAAGAATTT
*
53428551 T-TGAA-TTAG-TGAATTT
1 TGTGAATTTAGAAGAATTT
* *
53428567 TGTGATTTTAAAAGAATTT
1 TGTGAATTTAGAAGAATTT
53428586 AATAGGTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
16 7 0.25
17 7 0.25
18 7 0.25
19 7 0.25
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (19 bp):
TGTGAATTTAGAAGAATTT
Found at i:53429861 original size:46 final size:46
Alignment explanation
Indices: 53429792--53429976 Score: 255
Period size: 46 Copynumber: 4.0 Consensus size: 46
53429782 CATGGCAAAG
* * * *
53429792 TGTGAAACGTAGGTATGGCATTTCAGTGAATAAAACCATACTGATT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* * *
53429838 TGTGAAAAGTAGGTATGGTATTTC-GATAAAAAAAACCATATTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAG-TGAAGAAAACCATACTGAGT
*
53429884 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* * *
53429930 TATGAAAAGTAGGTATGGTATTTCCGTGAAGAAAATCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
53429976 T
1 T
53429977 ATAGCAATGT
Statistics
Matches: 123, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
45 1 0.01
46 121 0.98
47 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:53431837 original size:39 final size:38
Alignment explanation
Indices: 53431779--53431909 Score: 120
Period size: 39 Copynumber: 3.4 Consensus size: 38
53431769 AATAAATATA
* * * *
53431779 TTTATTTTTTTTAATTTTAAACTATTTTTTACATAATTT
1 TTTAATTTTTTTAATTTTAAAATATTTTTAAAAT-ATTT
53431818 TTTAATTTTTTTAATTTTAAAATATTTTTAAAATATTT
1 TTTAATTTTTTTAATTTTAAAATATTTTTAAAATATTT
* ** * *
53431856 TTAAATTTTAAAATATTTTTAAAATATATTTTTAAA-ATTT
1 TTTAATTTT--TTTAATTTTAAAATAT-TTTTAAAATATTT
**
53431896 TTTAAAATTTTTAA
1 TTTAATTTTTTTAA
53431910 AATAAAAATG
Statistics
Matches: 74, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
38 14 0.19
39 30 0.41
40 23 0.31
41 7 0.09
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (38 bp):
TTTAATTTTTTTAATTTTAAAATATTTTTAAAATATTT
Found at i:53431846 original size:11 final size:11
Alignment explanation
Indices: 53431832--53431913 Score: 97
Period size: 11 Copynumber: 7.9 Consensus size: 11
53431822 ATTTTTTTAA
53431832 TTTTAAAATAT
1 TTTTAAAATAT
53431843 TTTTAAAATAT
1 TTTTAAAATAT
53431854 TTTT--AA-A-
1 TTTTAAAATAT
53431861 TTTTAAAATAT
1 TTTTAAAATAT
53431872 TTTTAAAATATAT
1 TTTT-AAA-ATAT
53431885 TTTTAAAAT-T
1 TTTTAAAATAT
53431895 TTTT-AAA-AT
1 TTTTAAAATAT
53431904 TTTTAAAATA
1 TTTTAAAATA
53431914 AAAATGGGCC
Statistics
Matches: 62, Mismatches: 0, Indels: 18
0.77 0.00 0.22
Matches are distributed among these distances:
7 4 0.06
8 1 0.02
9 12 0.19
10 9 0.15
11 22 0.35
12 6 0.10
13 8 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:53431856 original size:29 final size:29
Alignment explanation
Indices: 53431824--53431913 Score: 119
Period size: 29 Copynumber: 3.0 Consensus size: 29
53431814 ATTTTTTAAT
53431824 TTTTTTAATTTTAAAATATTTTTAAAATA
1 TTTTTTAATTTTAAAATATTTTTAAAATA
*
53431853 TTTTTAAATTTTAAAATATTTTTAAAATA
1 TTTTTTAATTTTAAAATATTTTTAAAATA
*
53431882 TATTTTTAAAATTTTTTAAA-ATTTTTAAAATA
1 T-TTTTT--AA-TTTTAAAATATTTTTAAAATA
53431914 AAAATGGGCC
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
29 29 0.54
30 4 0.07
32 14 0.26
33 7 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TTTTTTAATTTTAAAATATTTTTAAAATA
Found at i:53431876 original size:18 final size:18
Alignment explanation
Indices: 53431843--53431878 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
53431833 TTTAAAATAT
53431843 TTTTAAAATATTTTTAAA
1 TTTTAAAATATTTTTAAA
53431861 TTTTAAAATATTTTTAAA
1 TTTTAAAATATTTTTAAA
53431879 ATATATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAAAATATTTTTAAA
Found at i:53431886 original size:13 final size:13
Alignment explanation
Indices: 53431868--53431893 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53431858 AAATTTTAAA
53431868 ATATTTTTAAAAT
1 ATATTTTTAAAAT
53431881 ATATTTTTAAAAT
1 ATATTTTTAAAAT
53431894 TTTTTAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATTTTTAAAAT
Found at i:53435837 original size:30 final size:31
Alignment explanation
Indices: 53435782--53435849 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
53435772 ACCCTTAAAA
** * **
53435782 TATTTACACTATTGGTCCTTCAAATTTTTTG
1 TATTTACACTATTAATCCCTCAAATTTTGAG
53435813 TATTTACACT-TTAATCCCTCAAATTTTGAG
1 TATTTACACTATTAATCCCTCAAATTTTGAG
53435843 TATTTAC
1 TATTTAC
53435850 TCTTGGGCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (31 bp):
TATTTACACTATTAATCCCTCAAATTTTGAG
Found at i:53436030 original size:23 final size:23
Alignment explanation
Indices: 53436004--53436048 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
53435994 TTTCTTACTA
*
53436004 TAGTAATTTTCGGGGTATTACAG
1 TAGTAATTTTCGGGATATTACAG
53436027 TAGTAATTTTCGGGATATTACA
1 TAGTAATTTTCGGGATATTACA
53436049 TTGGTCGTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (23 bp):
TAGTAATTTTCGGGATATTACAG
Done.