Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 12 of 171
Found at i:5615425 original size:27 final size:26
Alignment explanation
Indices: 5615370--5615425 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
5615360 AAGTACCATG
**
5615370 TTATTAAATTTTTATATTTTTCTTTT
1 TTATTAAATTTTTATATTTTTCTAGT
5615396 TTATTATAATTTTTATATTTTT-TAAGT
1 TTATTA-AATTTTTATATTTTTCT-AGT
5615423 TTA
1 TTA
5615426 AGGATTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (26 bp):
TTATTAAATTTTTATATTTTTCTAGT
Found at i:5627204 original size:21 final size:21
Alignment explanation
Indices: 5627171--5627211 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5627161 TTGTGAAGAT
*
5627171 ATTTTGTTATTTTAGTTTTTC
1 ATTTTATTATTTTAGTTTTTC
* *
5627192 ATTTTATTTTTTTATTTTTT
1 ATTTTATTATTTTAGTTTTT
5627212 TTAATCTTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.02, G:0.05, T:0.78
Consensus pattern (21 bp):
ATTTTATTATTTTAGTTTTTC
Found at i:5629753 original size:23 final size:23
Alignment explanation
Indices: 5629727--5629844 Score: 108
Period size: 23 Copynumber: 5.4 Consensus size: 23
5629717 AGTGCTGGGC
5629727 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
5629750 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
5629769 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
5629789 ATCAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
5629812 ATCGGAGAGCACACACAA-TGCTA
1 AACAGAGAGCACACA-AAGTGCTA
*
5629835 ATCAGAGAGC
1 AACAGAGAGC
5629845 GCGCTAGTGT
Statistics
Matches: 78, Mismatches: 9, Indels: 16
0.76 0.09 0.16
Matches are distributed among these distances:
16 10 0.13
18 3 0.04
19 1 0.01
20 1 0.01
21 2 0.03
23 59 0.76
24 2 0.03
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:5629787 original size:39 final size:39
Alignment explanation
Indices: 5629733--5629807 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
5629723 GGGCAACAGA
*
5629733 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
5629772 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
5629808 GCTAATCGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:5632559 original size:24 final size:24
Alignment explanation
Indices: 5632527--5632587 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
5632517 TACCTTGCAT
5632527 ATATATATATATATT-GAAATATGA
1 ATATATATATATATTCGAAATAT-A
*
5632551 ATATATATATAT-TTCTAAATATA
1 ATATATATATATATTCGAAATATA
*
5632574 ATAATGTATATATA
1 AT-ATATATATATA
5632588 AAAATTAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 5 0.16
24 27 0.84
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (24 bp):
ATATATATATATATTCGAAATATA
Found at i:5637432 original size:6 final size:6
Alignment explanation
Indices: 5637423--5637449 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5637413 AACTGGCTGG
5637423 CAATTT CAATTT CAATTT CAATTT CAA
1 CAATTT CAATTT CAATTT CAATTT CAA
5637450 GTTCTTCATG
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:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (6 bp):
CAATTT
Found at i:5639979 original size:22 final size:20
Alignment explanation
Indices: 5639936--5639980 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
5639926 CAAGAATAAT
5639936 AAATAAAGAAAATAAACAAA
1 AAATAAAGAAAATAAACAAA
* *
5639956 AAATCAAAGACAAATCAACCAA
1 AAAT-AAAGA-AAATAAACAAA
5639978 AAA
1 AAA
5639981 GGAAGGTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 5 0.24
22 12 0.57
ACGTcount: A:0.73, C:0.13, G:0.04, T:0.09
Consensus pattern (20 bp):
AAATAAAGAAAATAAACAAA
Found at i:5657111 original size:18 final size:20
Alignment explanation
Indices: 5657078--5657116 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
5657068 ACATTCATGG
5657078 TTTTGTTTTGTCCATA-TTT
1 TTTTGTTTTGTCCATAGTTT
*
5657097 TTTTGTTTT-TTCATAGTTT
1 TTTTGTTTTGTCCATAGTTT
5657116 T
1 T
5657117 AAGTAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.10, C:0.08, G:0.10, T:0.72
Consensus pattern (20 bp):
TTTTGTTTTGTCCATAGTTT
Found at i:5659134 original size:17 final size:19
Alignment explanation
Indices: 5659093--5659134 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5659083 TTACTTTTAA
5659093 AATTAATAAAAATTAAATT
1 AATTAATAAAAATTAAATT
* *
5659112 ACTTAATAAAGA-T-AATT
1 AATTAATAAAAATTAAATT
5659129 AATTAA
1 AATTAA
5659135 ATATTGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 9 0.45
18 1 0.05
19 10 0.50
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (19 bp):
AATTAATAAAAATTAAATT
Found at i:5659285 original size:41 final size:41
Alignment explanation
Indices: 5659240--5659324 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
5659230 GGAAGGCAAT
*
5659240 GGCAGAGCCAGGAT-TGGGCTGGCAAGTAGGGATATCAATTG
1 GGCAGAGCCAGG-TGGGGGCTGGCAAGTAGGGATATCAATTG
*
5659281 GGCAGAGTCAGGTGGGGGCTGGCAAGTAGGGATATCAATTG
1 GGCAGAGCCAGGTGGGGGCTGGCAAGTAGGGATATCAATTG
5659322 GGC
1 GGC
5659325 GGCACGGGTG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
40 1 0.02
41 40 0.98
ACGTcount: A:0.25, C:0.14, G:0.42, T:0.19
Consensus pattern (41 bp):
GGCAGAGCCAGGTGGGGGCTGGCAAGTAGGGATATCAATTG
Found at i:5667865 original size:18 final size:18
Alignment explanation
Indices: 5667842--5667878 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5667832 TTTTCTCCTC
5667842 AGCCATTGCCTTAGGTAG
1 AGCCATTGCCTTAGGTAG
5667860 AGCCATTGCCTTAGGTAG
1 AGCCATTGCCTTAGGTAG
5667878 A
1 A
5667879 ACATACGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (18 bp):
AGCCATTGCCTTAGGTAG
Found at i:5674582 original size:15 final size:15
Alignment explanation
Indices: 5674557--5674594 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
5674547 AGACCATGGA
*
5674557 AGAAGAGGTGGA-GT
1 AGAAGAAGTGGAGGT
5674571 ATGAAGAAGTGGAGGT
1 A-GAAGAAGTGGAGGT
5674587 AGAAGAAG
1 AGAAGAAG
5674595 AAGAAGAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 17 0.81
16 3 0.14
ACGTcount: A:0.42, C:0.00, G:0.45, T:0.13
Consensus pattern (15 bp):
AGAAGAAGTGGAGGT
Found at i:5674593 original size:3 final size:3
Alignment explanation
Indices: 5674587--5674643 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
5674577 AAGTGGAGGT
* * * *
5674587 AGA AGA AGA AGA AGA GGA AGA A-A TAGA AGA GGA AGT GGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA AGA AGA
5674632 AGA AGA AGA AGA
1 AGA AGA AGA AGA
5674644 CCTGGATGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 1 0.02
3 42 0.95
4 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.04
Consensus pattern (3 bp):
AGA
Found at i:5674606 original size:15 final size:15
Alignment explanation
Indices: 5674588--5674643 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
5674578 AGTGGAGGTA
5674588 GAAGAAGAAGAAGAG
1 GAAGAAGAAGAAGAG
5674603 GAAGAA-ATAGAAGAG
1 GAAGAAGA-AGAAGAG
** *
5674618 GAAGTGGAAGAAGAA
1 GAAGAAGAAGAAGAG
5674633 GAAGAAGAAGA
1 GAAGAAGAAGA
5674644 CCTGGATGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
14 1 0.03
15 32 0.94
16 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.38, T:0.04
Consensus pattern (15 bp):
GAAGAAGAAGAAGAG
Found at i:5678427 original size:25 final size:25
Alignment explanation
Indices: 5678399--5678446 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
5678389 CAAGCAAGAA
*
5678399 CATTTAGCT-CTTAGGCTTAATATAT
1 CATTT-GCTACTTAAGCTTAATATAT
*
5678424 CATTTGCTACTTAAGTTTAATAT
1 CATTTGCTACTTAAGCTTAATAT
5678447 TTTATTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 17 0.85
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (25 bp):
CATTTGCTACTTAAGCTTAATATAT
Found at i:5678993 original size:24 final size:24
Alignment explanation
Indices: 5678963--5679014 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5678953 TTCCTCCTCC
* *
5678963 TCTTCTTCGTCTTGATCTTGTACT
1 TCTTCTTCGACTTGATCTTCTACT
* *
5678987 TCTTCTTCGACTTGTTCTTCTTCT
1 TCTTCTTCGACTTGATCTTCTACT
5679011 TCTT
1 TCTT
5679015 TATGATTATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.06, C:0.27, G:0.10, T:0.58
Consensus pattern (24 bp):
TCTTCTTCGACTTGATCTTCTACT
Found at i:5681569 original size:39 final size:39
Alignment explanation
Indices: 5681526--5681605 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
5681516 AAAGTGAATT
5681526 AAAAATAAATGAAAAAAAATAACATTATGAGATTAAGTG
1 AAAAATAAATGAAAAAAAATAACATTATGAGATTAAGTG
*
5681565 AAAAATAAATGAAATAAAATAACATTATGAGATTAAGTG
1 AAAAATAAATGAAAAAAAATAACATTATGAGATTAAGTG
5681604 AA
1 AA
5681606 GACAATAATG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.61, C:0.03, G:0.12, T:0.24
Consensus pattern (39 bp):
AAAAATAAATGAAAAAAAATAACATTATGAGATTAAGTG
Found at i:5686296 original size:18 final size:19
Alignment explanation
Indices: 5686252--5686297 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
5686242 TATTTTAGAA
5686252 AATAAAATATTAAAATATAT
1 AATAAAA-ATTAAAATATAT
**
5686272 CCT-AAAATTAAAATAT-T
1 AATAAAAATTAAAATATAT
5686289 AATAAAAAT
1 AATAAAAAT
5686298 AAATTTTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 4
0.72 0.14 0.14
Matches are distributed among these distances:
17 2 0.10
18 15 0.71
19 3 0.14
20 1 0.05
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
AATAAAAATTAAAATATAT
Found at i:5689757 original size:12 final size:13
Alignment explanation
Indices: 5689728--5689759 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5689718 CTTAAATAAC
5689728 TATTTAAAAATAG
1 TATTTAAAAATAG
5689741 T-TTTAAAAATA-
1 TATTTAAAAATAG
5689752 TATTTAAA
1 TATTTAAA
5689760 TATAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.06
12 16 0.89
13 1 0.06
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (13 bp):
TATTTAAAAATAG
Found at i:5690593 original size:17 final size:17
Alignment explanation
Indices: 5690567--5690605 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
5690557 GGCAAACAGC
*
5690567 AAAAAGAGAGAAATAAA-
1 AAAAAAAGAGAAA-AAAG
5690584 AAAAAAAGAGAAAAAAG
1 AAAAAAAGAGAAAAAAG
5690601 AAAAA
1 AAAAA
5690606 GGAAAAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (17 bp):
AAAAAAAGAGAAAAAAG
Found at i:5690604 original size:19 final size:19
Alignment explanation
Indices: 5690567--5690605 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5690557 GGCAAACAGC
*
5690567 AAAAAGAGAGAAATAAAAA
1 AAAAAGAGAGAAAAAAAAA
5690586 AAAAAGAGA-AAAAAGAAAA
1 AAAAAGAGAGAAAAA-AAAA
5690605 A
1 A
5690606 GGAAAAGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (19 bp):
AAAAAGAGAGAAAAAAAAA
Found at i:5699562 original size:43 final size:43
Alignment explanation
Indices: 5699494--5699591 Score: 133
Period size: 43 Copynumber: 2.3 Consensus size: 43
5699484 TTATGAGGAA
* * * *
5699494 AAATGCCGCTAATGATCATGGTCTTTAGCGGCGCTTATCTCAC
1 AAATGCCGCTAAAGACCATGATCTTTAGCGGCGCTTATCCCAC
* *
5699537 AAATGCCGCTAAAGACCATGATCTTTAGCGGCGCTTTTCCCGC
1 AAATGCCGCTAAAGACCATGATCTTTAGCGGCGCTTATCCCAC
*
5699580 AAACGCCGCTAA
1 AAATGCCGCTAA
5699592 CATTAACAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.26
Consensus pattern (43 bp):
AAATGCCGCTAAAGACCATGATCTTTAGCGGCGCTTATCCCAC
Found at i:5701741 original size:2 final size:2
Alignment explanation
Indices: 5701734--5701769 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5701724 TCAAACACCC
5701734 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5701770 CACGATGTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5703359 original size:30 final size:30
Alignment explanation
Indices: 5703301--5703364 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
5703291 TTAATTTCGT
* *
5703301 AAATATAAAATTTCACTTTAATTTCTTTAA
1 AAATATAAAATTTCAATTTAATTACTTTAA
*
5703331 AAATAATAAAATTTTAATTTAA-TACTTTAA
1 AAAT-ATAAAATTTCAATTTAATTACTTTAA
5703361 AAAT
1 AAAT
5703365 TATATTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (30 bp):
AAATATAAAATTTCAATTTAATTACTTTAA
Found at i:5705629 original size:81 final size:81
Alignment explanation
Indices: 5705529--5705686 Score: 246
Period size: 81 Copynumber: 2.0 Consensus size: 81
5705519 TAGCAATGCA
* *
5705529 CATTGTGTTATTGTGAGAATAAAATATTTGGAAATAAATCTGCCAGACTTGGCACAAAAGGACAT
1 CATTGTGTTACTGTGAGAATAAAATATTTGGAAATAAATCTGCCAGACTTGGCACAAAAAGACAT
5705594 ACAGCAAAAGTTGTCT
66 ACAGCAAAAGTTGTCT
* * *
5705610 CATTGTGTT-CTGCTGAGAATAAAATATTTGGAAATAAATCTGGCATACTTGGCACAAAAAGTCA
1 CATTGTGTTACTG-TGAGAATAAAATATTTGGAAATAAATCTGCCAGACTTGGCACAAAAAGACA
*
5705674 TGCAGCAAAAGTT
65 TACAGCAAAAGTT
5705687 ACCTAATAGA
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
80 2 0.03
81 68 0.97
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (81 bp):
CATTGTGTTACTGTGAGAATAAAATATTTGGAAATAAATCTGCCAGACTTGGCACAAAAAGACAT
ACAGCAAAAGTTGTCT
Found at i:5714763 original size:2 final size:2
Alignment explanation
Indices: 5714756--5714794 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5714746 AGTATTTTTG
5714756 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5714795 CTGATTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5716707 original size:14 final size:14
Alignment explanation
Indices: 5716690--5716721 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5716680 ATTTGTTTTT
*
5716690 AAATTAAAAAAATC
1 AAATTAAAAAAATA
5716704 AAATTAAAAAAATA
1 AAATTAAAAAAATA
5716718 AAAT
1 AAAT
5716722 AGCTTGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATTAAAAAAATA
Found at i:5729730 original size:3 final size:3
Alignment explanation
Indices: 5729724--5729759 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
5729714 TTTAAAGGAC
* *
5729724 GAA GAA GAA GAA GAA AAA AAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
5729760 AAAAAAAGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5729748 original size:18 final size:19
Alignment explanation
Indices: 5729725--5729763 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
5729715 TTAAAGGACG
5729725 AAGAAGAAGAAGAA-AAAA
1 AAGAAGAAGAAGAAGAAAA
5729743 AAGAAGAAGAAGAAGAAAA
1 AAGAAGAAGAAGAAGAAAA
5729762 AA
1 AA
5729764 AAAGTCATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (19 bp):
AAGAAGAAGAAGAAGAAAA
Found at i:5729750 original size:21 final size:21
Alignment explanation
Indices: 5729724--5729765 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
5729714 TTTAAAGGAC
5729724 GAAGAAGAAGAAGAAAAAAAA
1 GAAGAAGAAGAAGAAAAAAAA
5729745 GAAGAAGAAGAAGAAAAAAAA
1 GAAGAAGAAGAAGAAAAAAAA
5729766 AGTCATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (21 bp):
GAAGAAGAAGAAGAAAAAAAA
Found at i:5731391 original size:2 final size:2
Alignment explanation
Indices: 5731384--5731414 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5731374 ACTGTTTTAA
5731384 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5731415 GAGCATTTCT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5745133 original size:24 final size:24
Alignment explanation
Indices: 5745101--5745148 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
5745091 CAAAGGTTAG
5745101 GTGAGGGGGAAATCTTCTGCTTCT
1 GTGAGGGGGAAATCTTCTGCTTCT
5745125 GTGAGGGGGAAATCTTCTGCTTCT
1 GTGAGGGGGAAATCTTCTGCTTCT
5745149 CTTCTCAGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (24 bp):
GTGAGGGGGAAATCTTCTGCTTCT
Found at i:5748077 original size:20 final size:18
Alignment explanation
Indices: 5748054--5748093 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
5748044 TTGGTATTTT
*
5748054 ATATATTTATATATTTTTAA
1 ATATATTT-TA-ATATTTAA
5748074 ATATATTTTAATATTTAA
1 ATATATTTTAATATTTAA
5748092 AT
1 AT
5748094 TGAATTCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 2 0.11
20 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATATTTTAATATTTAA
Found at i:5749291 original size:36 final size:33
Alignment explanation
Indices: 5749218--5749307 Score: 92
Period size: 33 Copynumber: 2.6 Consensus size: 33
5749208 AGATTATAGC
* *
5749218 TAATTCTAAATTTTGTATAAAAAAATTAATCAA
1 TAATTTTAAATTTTGTATAAAAAAAATAATCAA
*
5749251 TAATTTTAAATTTTGTATACAAAGAAAAT-ATTAA
1 TAATTTTAAATTTTGTATA-AAA-AAAATAATCAA
5749285 TTTAATTTTAAAATTTTAGTATA
1 --TAATTTT-AAATTTT-GTATA
5749308 GAGATTATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
33 18 0.38
34 7 0.15
35 4 0.08
36 7 0.15
37 7 0.15
38 5 0.10
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.44
Consensus pattern (33 bp):
TAATTTTAAATTTTGTATAAAAAAAATAATCAA
Found at i:5749675 original size:22 final size:22
Alignment explanation
Indices: 5749634--5749675 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5749624 ATATTTTAAT
* *
5749634 ATTACTTATGATATAAAAATAC
1 ATTACTTATCAAATAAAAATAC
*
5749656 ATTACTTATCAAATACAAAT
1 ATTACTTATCAAATAAAAAT
5749676 CCTTATTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (22 bp):
ATTACTTATCAAATAAAAATAC
Found at i:5749705 original size:11 final size:11
Alignment explanation
Indices: 5749679--5749729 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
5749669 TACAAATCCT
*
5749679 TATTTTATTATA
1 TATTTTAAT-TA
*
5749691 TATTTTCATTA
1 TATTTTAATTA
5749702 TATTTTAATTA
1 TATTTTAATTA
5749713 T-TTTCTATATTA
1 TATTT-TA-ATTA
5749725 TATTT
1 TATTT
5749730 ATATCTATAG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
10 3 0.09
11 15 0.45
12 12 0.36
13 3 0.09
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTTTAATTA
Found at i:5755278 original size:64 final size:63
Alignment explanation
Indices: 5755207--5755373 Score: 214
Period size: 60 Copynumber: 2.7 Consensus size: 63
5755197 CAATAATTGT
*
5755207 TTGTTTATATGTTTAAATCGATTGTTATGGTAAAATATTACTTCTTCTTCTTCTTTTGAATCGA
1 TTGTTTATATGTTTAAATCGATTGTTATGGTAAAATATTACTT-TTCTTCTTCTTTTAAATCGA
* * * *
5755271 TTGTTTATATTTTTAAATAGATTGTTAT-GTTAGA-A-TACTTTTCTTCTTCTTTTAAATCGA
1 TTGTTTATATGTTTAAATCGATTGTTATGGTAAAATATTACTTTTCTTCTTCTTTTAAATCGA
* * * * *
5755331 TTATTTATATGTTTAAATCAATTATTATGTTGAAATATTACTT
1 TTGTTTATATGTTTAAATCGATTGTTATGGTAAAATATTACTT
5755374 ATTTTGAATC
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
60 42 0.48
61 8 0.09
62 2 0.02
63 9 0.10
64 26 0.30
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (63 bp):
TTGTTTATATGTTTAAATCGATTGTTATGGTAAAATATTACTTTTCTTCTTCTTTTAAATCGA
Found at i:5755339 original size:60 final size:59
Alignment explanation
Indices: 5755210--5755422 Score: 211
Period size: 60 Copynumber: 3.6 Consensus size: 59
5755200 TAATTGTTTG
* * *
5755210 TTTATATGTTTAAATCGATTGTTATGGTAAAATATTACTTCTTCTTCTTCTTTTGAATCGATTG
1 TTTATATGTTTAAAT-AATTGTTAT-GTTAAA-A-TACTT-TTCTTCTTCTTTTGAATCGATTA
* * *
5755274 TTTATATTTTTAAATAGATTGTTATGTTAGAATACTTTTCTTCTTCTTTTAAATCGATTA
1 TTTATATGTTTAAATA-ATTGTTATGTTAAAATACTTTTCTTCTTCTTTTGAATCGATTA
* * * * *
5755334 TTTATATGTTTAAATCAATTATTATGTTGAAATA----T-TACTTATTTTGAATCAATTA
1 TTTATATGTTTAAAT-AATTGTTATGTTAAAATACTTTTCTTCTTCTTTTGAATCGATTA
*
5755389 TTTATATCTTTAAATTAATTGTTATGTTAAAATA
1 TTTATATGTTTAAA-TAATTGTTATGTTAAAATA
5755423 TTATTTTTAA
Statistics
Matches: 129, Mismatches: 17, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
55 45 0.35
56 2 0.02
60 49 0.38
61 6 0.05
62 1 0.01
63 4 0.03
64 22 0.17
ACGTcount: A:0.31, C:0.08, G:0.09, T:0.53
Consensus pattern (59 bp):
TTTATATGTTTAAATAATTGTTATGTTAAAATACTTTTCTTCTTCTTTTGAATCGATTA
Found at i:5755361 original size:18 final size:18
Alignment explanation
Indices: 5755338--5755390 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
5755328 CGATTATTTA
5755338 TATGTTTAAATCAATTAT
1 TATGTTTAAATCAATTAT
*
5755356 TATGTTGAAAT--ATTACT
1 TATGTTTAAATCAATTA-T
*
5755373 TAT-TTTGAATCAATTAT
1 TATGTTTAAATCAATTAT
5755390 T
1 T
5755391 TATATCTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 9 0.31
17 6 0.21
18 14 0.48
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.51
Consensus pattern (18 bp):
TATGTTTAAATCAATTAT
Found at i:5755440 original size:51 final size:55
Alignment explanation
Indices: 5755320--5755465 Score: 176
Period size: 55 Copynumber: 2.7 Consensus size: 55
5755310 TTTCTTCTTC
*
5755320 TTTTAAATCGATTATTTATATGTTTAAATCAATTATTATGTTGAAATATTACTTA
1 TTTTAAATCGATTATTTATATATTTAAATCAATTATTATGTTGAAATATTACTTA
* * * * *
5755375 TTTTGAATCAATTATTTATATCTTTAAATTAATTGTTATGTT-AAA-A-TA-TTA
1 TTTTAAATCGATTATTTATATATTTAAATCAATTATTATGTTGAAATATTACTTA
* * *
5755426 TTTTTAATCGATTATTTTTATATTTAAAT-AGTTATTATGT
1 TTTTAAATCGATTATTTATATATTTAAATCAATTATTATGT
5755466 AGCACGTTTA
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
50 9 0.11
51 28 0.35
52 2 0.03
53 1 0.01
54 3 0.04
55 37 0.46
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (55 bp):
TTTTAAATCGATTATTTATATATTTAAATCAATTATTATGTTGAAATATTACTTA
Found at i:5768356 original size:2 final size:2
Alignment explanation
Indices: 5768349--5768373 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5768339 TTAGTTTGAA
5768349 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5768374 ATTATTTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5775145 original size:31 final size:31
Alignment explanation
Indices: 5775110--5775172 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
5775100 TTAGTACTTG
* *
5775110 AACTTGACATTTTTTCTTAATTTGGTACCTA
1 AACTTGACATCTTTTCCTAATTTGGTACCTA
* *
5775141 AACTTGGCATCTTTTCCTAATTTGGTATCTA
1 AACTTGACATCTTTTCCTAATTTGGTACCTA
5775172 A
1 A
5775173 GCTTTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.46
Consensus pattern (31 bp):
AACTTGACATCTTTTCCTAATTTGGTACCTA
Found at i:5775457 original size:31 final size:31
Alignment explanation
Indices: 5775422--5775480 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
5775412 ACCAACTTAA
5775422 AAAAAGTGA-CAAGTTT-AGGTATCAAATTAGG
1 AAAAAGT-ATCAAGTTTGA-GTATCAAATTAGG
5775453 AAAAAGTATCAAGTTTGAGTATCAAATT
1 AAAAAGTATCAAGTTTGAGTATCAAATT
5775481 GGACCAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 1 0.04
31 24 0.92
32 1 0.04
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.29
Consensus pattern (31 bp):
AAAAAGTATCAAGTTTGAGTATCAAATTAGG
Found at i:5781408 original size:22 final size:21
Alignment explanation
Indices: 5781372--5781428 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
5781362 GATTAATTCT
5781372 TATTTTACTCAATTTTAAATA
1 TATTTTACTCAATTTTAAATA
* *
5781393 TATTTTACTTATATTTTTAATA
1 TATTTTACTCA-ATTTTAAATA
*
5781415 TTTTATTA-TCAATT
1 TATT-TTACTCAATT
5781429 AATTTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 13 0.43
22 14 0.47
23 3 0.10
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTACTCAATTTTAAATA
Found at i:5783133 original size:22 final size:22
Alignment explanation
Indices: 5783092--5783133 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5783082 TTTAGAATTA
* *
5783092 ATTTAATTTTAAAATGAATTTT
1 ATTTAATATTAAAATAAATTTT
*
5783114 ATTTAATATTAGAATAAATT
1 ATTTAATATTAAAATAAATT
5783134 ATTGTAGATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
ATTTAATATTAAAATAAATTTT
Found at i:5784409 original size:31 final size:30
Alignment explanation
Indices: 5784374--5784439 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
5784364 GATAAAAATA
5784374 TTTAACAATTCAATGATTTAAA-TGAAAATTT
1 TTTAACAATTCAATGA-TTAAATTG-AAATTT
* * * *
5784405 TTTAATAGTTTAATGATTAAATTGTAATTT
1 TTTAACAATTCAATGATTAAATTGAAATTT
5784435 TTTAA
1 TTTAA
5784440 TTAAGTGATC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (30 bp):
TTTAACAATTCAATGATTAAATTGAAATTT
Found at i:5784619 original size:60 final size:57
Alignment explanation
Indices: 5784553--5784681 Score: 132
Period size: 57 Copynumber: 2.2 Consensus size: 57
5784543 ATTTGGGGCA
* * *** * *
5784553 TAAACTTGACAACTATTCTCATATTAAAATTTTAAATTTTTTTTTGTTCGAGTTAAGTCT
1 TAAACTTGACAACTATCCCCATATT-AAAGCATAAA--TTTTTTTATTCAAGTTAAGTCT
* * *
5784613 TAAACTTGATAATTATCCCCATATTAAGGCATAAATTTTTTTATTCAAGTTAAGTCT
1 TAAACTTGACAACTATCCCCATATTAAAGCATAAATTTTTTTATTCAAGTTAAGTCT
*
5784670 TGAACTTGACAA
1 TAAACTTGACAA
5784682 TTACTTTCAA
Statistics
Matches: 57, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
57 30 0.53
59 6 0.11
60 21 0.37
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.43
Consensus pattern (57 bp):
TAAACTTGACAACTATCCCCATATTAAAGCATAAATTTTTTTATTCAAGTTAAGTCT
Found at i:5786533 original size:16 final size:16
Alignment explanation
Indices: 5786509--5786576 Score: 100
Period size: 16 Copynumber: 4.2 Consensus size: 16
5786499 TGGTTCGCTA
* *
5786509 TAATAGAATAGAGGTG
1 TAATGGAATAGAGCTG
*
5786525 TAATGGAATAGAACTG
1 TAATGGAATAGAGCTG
*
5786541 TAATGGAATATAGCTG
1 TAATGGAATAGAGCTG
5786557 TAATGGAATAGAGCTG
1 TAATGGAATAGAGCTG
5786573 TAAT
1 TAAT
5786577 CAGTAATTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.41, C:0.04, G:0.26, T:0.28
Consensus pattern (16 bp):
TAATGGAATAGAGCTG
Found at i:5786617 original size:46 final size:44
Alignment explanation
Indices: 5786558--5786651 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
5786548 ATATAGCTGT
* *
5786558 AATGGAATAGAGCTGTAATCAGTAATTCAAT-TGTTTGGTTGATTGG
1 AATGGAATAGAGCTGTAAT-AAT-ATTC-ATGTGTTTGGTTGAATGG
*
5786604 AATGGAATAGAGCTGTAATAATATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
5786648 AATG
1 AATG
5786652 ATGCTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 2 0.05
46 19 0.43
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
Found at i:5786813 original size:58 final size:55
Alignment explanation
Indices: 5786743--5786891 Score: 183
Period size: 58 Copynumber: 2.6 Consensus size: 55
5786733 TTAAATTTTA
*
5786743 ATAATTATTATTAAATATAATTGAATAAAAATAT-TAATTTATTTAATTATATTTTAAC
1 ATAATTATTATTAAATATAATT-AATAAAAATATGTAATTTA-ATAA-TAT-TTTTAAC
*
5786801 ATAATTATTATTAAATATAATTTAATAAAATAATATGTAATTTAATAATATTTTTAAT
1 ATAATTATTATTAAATATAA-TTAAT-AAA-AATATGTAATTTAATAATATTTTTAAC
*
5786859 ATAATTATTATTAAAATATGAATTAGTAAAAAT
1 ATAATTATTATT-AAATAT-AATTAATAAAAAT
5786892 TATAATATAT
Statistics
Matches: 82, Mismatches: 3, Indels: 13
0.84 0.03 0.13
Matches are distributed among these distances:
57 3 0.04
58 44 0.54
59 18 0.22
60 10 0.12
61 7 0.09
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (55 bp):
ATAATTATTATTAAATATAATTAATAAAAATATGTAATTTAATAATATTTTTAAC
Found at i:5841602 original size:17 final size:18
Alignment explanation
Indices: 5841574--5841615 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
5841564 TTATTACTTG
5841574 AATTATATTTAAA-GAATA
1 AATTA-ATTTAAAGGAATA
5841592 AATTAATTTAAAGGAATA
1 AATTAATTTAAAGGAATA
5841610 AATTAA
1 AATTAA
5841616 AAGAGGCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (18 bp):
AATTAATTTAAAGGAATA
Found at i:5841693 original size:18 final size:19
Alignment explanation
Indices: 5841672--5841711 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
5841662 TTATTACTTT
*
5841672 AATTTCATTTAAAGG-ATA
1 AATTTAATTTAAAGGAATA
5841690 AA-TTAATTTAAAGGAATA
1 AATTTAATTTAAAGGAATA
5841708 AATT
1 AATT
5841712 AAAAGTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 11 0.58
18 7 0.37
19 1 0.05
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.38
Consensus pattern (19 bp):
AATTTAATTTAAAGGAATA
Found at i:5841700 original size:17 final size:18
Alignment explanation
Indices: 5841678--5841713 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
5841668 CTTTAATTTC
5841678 ATTTAAAGG-ATAAATTA
1 ATTTAAAGGAATAAATTA
5841695 ATTTAAAGGAATAAATTA
1 ATTTAAAGGAATAAATTA
5841713 A
1 A
5841714 AAGTAATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (18 bp):
ATTTAAAGGAATAAATTA
Found at i:5844951 original size:20 final size:21
Alignment explanation
Indices: 5844926--5844964 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
5844916 TACTTTTCTG
5844926 ATTTTTTTGTA-TTTATTTCC
1 ATTTTTTTGTATTTTATTTCC
5844946 ATTTTTTTGTATTTTATTT
1 ATTTTTTTGTATTTTATTT
5844965 TTATAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.74
Consensus pattern (21 bp):
ATTTTTTTGTATTTTATTTCC
Found at i:5845736 original size:17 final size:18
Alignment explanation
Indices: 5845716--5845754 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
5845706 TAATTAATTT
*
5845716 AATTAAAAT-AATAATAA
1 AATTAAAATAAAAAATAA
5845733 AATTAAAATAAAAAATAA
1 AATTAAAATAAAAAATAA
5845751 AATT
1 AATT
5845755 TTTAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AATTAAAATAAAAAATAA
Found at i:5845794 original size:21 final size:21
Alignment explanation
Indices: 5845751--5845794 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5845741 TAAAAAATAA
* *
5845751 AATTTTTAATTAATTCATATT
1 AATTTTTAATTAACTAATATT
5845772 AATTTTTAATCTAACTAAT-TT
1 AATTTTTAAT-TAACTAATATT
5845793 AA
1 AA
5845795 AATTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTTTTAATTAACTAATATT
Found at i:5865940 original size:34 final size:34
Alignment explanation
Indices: 5865875--5865941 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
5865865 CAGAAGAGAA
**
5865875 TATACTTTTTAAATGTTTTTAGATTTATATTTTT
1 TATACTTTTTAAAACTTTTTAGATTTATATTTTT
* *
5865909 TATATTTTTTAAAACTTTTATATATTT-TATTTT
1 TATACTTTTTAAAACTTTT-TAGATTTATATTTT
5865942 CAAACATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 22 0.79
35 6 0.21
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (34 bp):
TATACTTTTTAAAACTTTTTAGATTTATATTTTT
Found at i:5865989 original size:19 final size:20
Alignment explanation
Indices: 5865964--5866015 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
5865954 ATTTATATAG
5865964 ATTTTAAATTTTATC-TAAC
1 ATTTTAAATTTTATCTTAAC
* * *
5865983 TTTTTAAAATTTA-CTTAAG
1 ATTTTAAATTTTATCTTAAC
5866002 ATTTTAAATTTTAT
1 ATTTTAAATTTTAT
5866016 TTATTTAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 1 0.04
19 25 0.96
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTTTAAATTTTATCTTAAC
Found at i:5867967 original size:23 final size:23
Alignment explanation
Indices: 5867894--5868046 Score: 132
Period size: 23 Copynumber: 6.6 Consensus size: 23
5867884 TATATGGAAC
* *
5867894 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
5867916 -AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
5867937 GGGCAACAGAGAGCACACACAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
5867963 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
5867986 AATCAGAGAGCACATAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
5868009 AATCAGAGACCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
5868032 AATAACAGAGAGCAC
1 -A-AACAGAGAGCAC
5868047 GAGACGTGCT
Statistics
Matches: 105, Mismatches: 18, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
21 17 0.16
23 58 0.55
24 1 0.01
25 23 0.22
26 6 0.06
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:5867993 original size:46 final size:47
Alignment explanation
Indices: 5867942--5868059 Score: 132
Period size: 46 Copynumber: 2.5 Consensus size: 47
5867932 GTGCTGGGCA
**
5867942 ACAGAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTAAT
1 ACAGAGAGCACACACAGTGCTAAACAGAGACCACACAAAGTACTAAT
* * * * *
5867989 -CAGAGAGCACATAAAGTGCTAATCAGAGACCACACACAGTGCTAAT
1 ACAGAGAGCACACACAGTGCTAAACAGAGACCACACAAAGTACTAAT
*
5868035 AACAGAGAGCACGAGAC-GTGCTAAA
1 -ACAGAGAGCAC-ACACAGTGCTAAA
5868060 TAAAGAGCGT
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
46 39 0.67
48 17 0.29
49 2 0.03
ACGTcount: A:0.44, C:0.22, G:0.21, T:0.13
Consensus pattern (47 bp):
ACAGAGAGCACACACAGTGCTAAACAGAGACCACACAAAGTACTAAT
Found at i:5868016 original size:69 final size:67
Alignment explanation
Indices: 5867894--5868043 Score: 205
Period size: 69 Copynumber: 2.1 Consensus size: 67
5867884 TATATGGAAC
*
5867894 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAG
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCT--G-AACAGAGACCACACACAG
5867959 TGCT-
63 TGCTA
5867963 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACATAAAGTGCT-AATCAGAGACCACACACA
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACAT-AAGTGCTGAA-CAGAGACCACACACA
5868027 GTGCTA
62 GTGCTA
5868033 ATAACAGAGAG
1 A-AACAGAGAG
5868044 CACGAGACGT
Statistics
Matches: 74, Mismatches: 1, Indels: 10
0.87 0.01 0.12
Matches are distributed among these distances:
68 2 0.03
69 32 0.43
70 12 0.16
71 21 0.28
72 7 0.09
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.13
Consensus pattern (67 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGAACAGAGACCACACACAGTGC
TA
Found at i:5871074 original size:30 final size:30
Alignment explanation
Indices: 5871032--5871167 Score: 93
Period size: 30 Copynumber: 4.6 Consensus size: 30
5871022 TTTTATGGCC
* *
5871032 AAAACTTT-AAAATTTTAATTAAACT-TGT
1 AAAATTTTCAAAATTTTAATTAAACTCTCT
* *
5871060 AAAAGTTTTGAAAATTTTAATTTAACTCTCT
1 AAAA-TTTTCAAAATTTTAATTAAACTCTCT
* * *
5871091 AAAATTTTCAAAAAGTCTAATTAATC-CTCT
1 AAAATTTTC-AAAATTTTAATTAAACTCTCT
* * * *
5871121 GAAATTTTTTAAAACTTTAATTAGAA--CACT
1 -AAAATTTTCAAAATTTTAATTA-AACTCTCT
*
5871151 AAAATTTTTAAAATTTT
1 AAAATTTTCAAAATTTT
5871168 GTGCGAATTT
Statistics
Matches: 86, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
28 4 0.05
29 18 0.21
30 38 0.44
31 26 0.30
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (30 bp):
AAAATTTTCAAAATTTTAATTAAACTCTCT
Found at i:5878838 original size:16 final size:16
Alignment explanation
Indices: 5878817--5878847 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5878807 GATCTATCAA
*
5878817 CCCCCCTCCCCCCCAG
1 CCCCCCCCCCCCCCAG
5878833 CCCCCCCCCCCCCCA
1 CCCCCCCCCCCCCCA
5878848 AAAAAAGAGA
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:0.06, C:0.87, G:0.03, T:0.03
Consensus pattern (16 bp):
CCCCCCCCCCCCCCAG
Found at i:5883500 original size:15 final size:17
Alignment explanation
Indices: 5883468--5883505 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
5883458 ATTAAAATAC
*
5883468 AATTTTATTATTTTAAT
1 AATTTTATTATCTTAAT
5883485 -ATTTTA-TATCTTAAT
1 AATTTTATTATCTTAAT
5883500 AATTTT
1 AATTTT
5883506 CTAAAATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
AATTTTATTATCTTAAT
Found at i:5889765 original size:12 final size:12
Alignment explanation
Indices: 5889750--5889797 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
5889740 ATACACTTAA
5889750 AAATATTAAAAC
1 AAATATTAAAAC
5889762 AAATATTAAAAC
1 AAATATTAAAAC
*
5889774 AAAT-TAAAAAC
1 AAATATTAAAAC
*
5889785 -GATATTAAAAC
1 AAATATTAAAAC
5889796 AA
1 AA
5889798 TTCTAAAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
10 2 0.07
11 12 0.40
12 16 0.53
ACGTcount: A:0.67, C:0.08, G:0.02, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:5889782 original size:22 final size:22
Alignment explanation
Indices: 5889746--5889808 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
5889736 TCAAATACAC
*
5889746 TTAAAA-ATATTAAAACAAATA
1 TTAAAACAAATTAAAACAAATA
*
5889767 TTAAAACAAATTAAAA-ACGATA
1 TTAAAACAAATTAAAACA-AATA
*
5889789 TTAAAACAATTCTAAAACAA
1 TTAAAACAAAT-TAAAACAA
5889809 CAAACAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 21 0.62
23 5 0.15
24 1 0.03
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.25
Consensus pattern (22 bp):
TTAAAACAAATTAAAACAAATA
Found at i:5890312 original size:34 final size:35
Alignment explanation
Indices: 5890250--5890331 Score: 121
Period size: 34 Copynumber: 2.3 Consensus size: 35
5890240 GTTTACTTGG
* **
5890250 TTTGTCTTTTCATTAGTTGTAAATATTTTATTTGCT
1 TTTGTCTTTTCATTAG-TCTAAATATTTTACCTGCT
5890286 TTTGTCTTTTCATTAG-CTAAATATTTTACCTGCT
1 TTTGTCTTTTCATTAGTCTAAATATTTTACCTGCT
5890320 TTTGTCTTTTCA
1 TTTGTCTTTTCA
5890332 ACAGCCTGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
34 27 0.63
36 16 0.37
ACGTcount: A:0.18, C:0.13, G:0.10, T:0.59
Consensus pattern (35 bp):
TTTGTCTTTTCATTAGTCTAAATATTTTACCTGCT
Found at i:5890783 original size:37 final size:37
Alignment explanation
Indices: 5890733--5890942 Score: 176
Period size: 37 Copynumber: 5.7 Consensus size: 37
5890723 TTGCACAATA
5890733 TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGTT
1 TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGTT
* *
5890770 TTCAGGCTATGTGCCTAGCAGGCTTCGTGCTGGTGTT
1 TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGTT
5890807 TTCAGGCT-TCGTGCCGGT-GTTTTTAGGCTAT-GTGCC--TAG--
1 TTCAGGCTAT-GTGCC--TAG----TAGGCT-TCGTGCCGGT-GTT
* **
5890846 -T-AGGCT-TCGTGCC--GGAGGCTTCGTATCGGTAG-T
1 TTCAGGCTAT-GTGCCTAGTAGGCTTCGTGCCGGT-GTT
*
5890879 TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGATGTT
1 TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGTT
5890916 TTCAGGCTATGTGCCTAGTAGGCTTCG
1 TTCAGGCTATGTGCCTAGTAGGCTTCG
5890943 AGACGGTGAT
Statistics
Matches: 143, Mismatches: 11, Indels: 38
0.74 0.06 0.20
Matches are distributed among these distances:
29 1 0.01
30 8 0.06
32 3 0.02
34 2 0.01
35 10 0.07
36 3 0.02
37 101 0.71
38 2 0.01
39 1 0.01
40 1 0.01
41 1 0.01
42 9 0.06
43 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.32, T:0.35
Consensus pattern (37 bp):
TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGTT
Found at i:5890821 original size:58 final size:57
Alignment explanation
Indices: 5890752--5890923 Score: 214
Period size: 58 Copynumber: 3.1 Consensus size: 57
5890742 TGTGCCTAGT
*
5890752 AGGCTTCGTGCCGGTGTTTTCAGGCTATGTGCCTAGCAGGCTTCGTGCTGGTGTTTTC
1 AGGCTTCGTGCCGGTGTTTTCAGGCTATGTGCCTAGTAGGCTTCGTGC-GGTGTTTTC
* *
5890810 AGGCTTCGTGCCGGTGTTTTTAGGCTATGTGCCTAGTAGGCTTCGTGCCG-G-----
1 AGGCTTCGTGCCGGTGTTTTCAGGCTATGTGCCTAGTAGGCTTCGTGCGGTGTTTTC
** *
5890861 AGGCTTCGTATCGGTAG-TTTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGATGTTTTC
1 AGGCTTCGTGCCGGT-GTTTTCAGGCTATGTGCCTAGTAGGCTTCGTG-CGGTGTTTTC
5890919 AGGCT
1 AGGCT
5890924 ATGTGCCTAG
Statistics
Matches: 98, Mismatches: 8, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
51 42 0.43
52 2 0.02
53 1 0.01
56 1 0.01
57 1 0.01
58 51 0.52
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.35
Consensus pattern (57 bp):
AGGCTTCGTGCCGGTGTTTTCAGGCTATGTGCCTAGTAGGCTTCGTGCGGTGTTTTC
Found at i:5890842 original size:21 final size:21
Alignment explanation
Indices: 5890752--5890835 Score: 83
Period size: 21 Copynumber: 4.2 Consensus size: 21
5890742 TGTGCCTAGT
5890752 AGGCTTCGTGCCGGTGTTTTC
1 AGGCTTCGTGCCGGTGTTTTC
5890773 AGGCTAT-GTGCC--TAG----C
1 AGGCT-TCGTGCCGGT-GTTTTC
*
5890789 AGGCTTCGTGCTGGTGTTTTC
1 AGGCTTCGTGCCGGTGTTTTC
*
5890810 AGGCTTCGTGCCGGTGTTTTT
1 AGGCTTCGTGCCGGTGTTTTC
5890831 AGGCT
1 AGGCT
5890836 ATGTGCCTAG
Statistics
Matches: 51, Mismatches: 3, Indels: 18
0.71 0.04 0.25
Matches are distributed among these distances:
15 1 0.02
16 10 0.20
17 1 0.02
18 1 0.02
19 1 0.02
20 1 0.02
21 35 0.69
22 1 0.02
ACGTcount: A:0.08, C:0.21, G:0.33, T:0.37
Consensus pattern (21 bp):
AGGCTTCGTGCCGGTGTTTTC
Found at i:5893124 original size:21 final size:23
Alignment explanation
Indices: 5893088--5893133 Score: 78
Period size: 21 Copynumber: 2.1 Consensus size: 23
5893078 AAATTAAAGC
5893088 TAGTTAAAACACTGAAAAAATAA
1 TAGTTAAAACACTGAAAAAATAA
5893111 TAGTT-AAA-ACTGAAAAAATAA
1 TAGTTAAAACACTGAAAAAATAA
5893132 TA
1 TA
5893134 AACTGTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 15 0.65
22 3 0.13
23 5 0.22
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.24
Consensus pattern (23 bp):
TAGTTAAAACACTGAAAAAATAA
Found at i:5893665 original size:19 final size:19
Alignment explanation
Indices: 5893641--5893679 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5893631 TTCAAGAAAA
5893641 TAAAAACAAAATAAAT-TTT
1 TAAAAACAAAA-AAATATTT
*
5893660 TAAAAATAAAAAAATATTT
1 TAAAAACAAAAAAATATTT
5893679 T
1 T
5893680 TTTTACGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAAACAAAAAAATATTT
Found at i:5895203 original size:72 final size:71
Alignment explanation
Indices: 5895083--5895216 Score: 169
Period size: 72 Copynumber: 1.9 Consensus size: 71
5895073 GGGTGATTCG
* * * * * *
5895083 AAAGGTTCCTCAATGATAGCCTGATAAATTTTACTTTGGCTTTCACTATTCAAAAGGTGATATGG
1 AAAGGTTCCTCAATAATAGACTCATAAATATTACTTTGACTTTCACTATCCAAAAGGT-ATATGG
5895148 TGGATCA
65 TGGATCA
* ** *
5895155 AAAGGTTCTTCAATAATAGACTCATAAATATTGGTTTGACTTTTACTATCCAAAAGGTATAT
1 AAAGGTTCCTCAATAATAGACTCATAAATATTACTTTGACTTTCACTATCCAAAAGGTATAT
5895217 AGCCTCTTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
71 4 0.08
72 48 0.92
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (71 bp):
AAAGGTTCCTCAATAATAGACTCATAAATATTACTTTGACTTTCACTATCCAAAAGGTATATGGT
GGATCA
Found at i:5895335 original size:21 final size:21
Alignment explanation
Indices: 5895311--5895354 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5895301 TCAACAATTT
* *
5895311 AATATTGATATTAAAATTACA
1 AATATTAATATTAAAATCACA
*
5895332 AATATTAATATTATAATCACA
1 AATATTAATATTAAAATCACA
5895353 AA
1 AA
5895355 GAATACTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (21 bp):
AATATTAATATTAAAATCACA
Found at i:5897925 original size:87 final size:87
Alignment explanation
Indices: 5897779--5898159 Score: 358
Period size: 87 Copynumber: 4.4 Consensus size: 87
5897769 CTTTCTCTTT
* *
5897779 CCAGTAATCAGGA-TATCAGTTTTCAATACTTTGATCTCCCTCATTGCTGATAAATCCATCTT-T
1 CCAGTAATC-GGAGTATCAGTTTCCAATACTTTGATCTCCCTCATTGCTGATATATCCATCTTAT
5897842 CCAGTGACACAAAGGTTATCAGTG
65 -CAGTGACACAAAGGTTATCAGTG
**
5897866 CCAGTAATCGGAGTATCAGTTTCCAATACTTCAATCTCCCTCATTGCTGATATATCCATCTTATC
1 CCAGTAATCGGAGTATCAGTTTCCAATACTTTGATCTCCCTCATTGCTGATATATCCATCTTATC
*
5897931 AGTGACACAAAGGTTATCTGTG
66 AGTGACACAAAGGTTATCAGTG
* * * * * * *
5897953 CCAATAATCAGAGCATCAGCTTCCCATTCTTTGATCTCCCCCA---CTG-------C-T-TTATC
1 CCAGTAATCGGAGTATCAGTTTCCAATACTTTGATCTCCCTCATTGCTGATATATCCATCTTATC
* *
5898006 AGTGACAAAAAGATTATCAGTG
66 AGTGACACAAAGGTTATCAGTG
* * * * *
5898028 CCAGTAATTGGGGTATAAGTTTCTAATCCTTTGATCTCCCTCATTGCTGATAGATCCAGATCCAT
1 CCAGTAATCGGAGTATCAGTTTCCAATACTTTGATCTCCCTCATTGCTGAT--AT----ATCCAT
* * *
5898093 CTTATCAGTGACATAAAGGTCACCAGTG
60 CTTATCAGTGACACAAAGGTTATCAGTG
* * * *
5898121 CCAGCAATCGGAGTATCACTTTCCAAAACTTCGATCTCC
1 CCAGTAATCGGAGTATCAGTTTCCAATACTTTGATCTCC
5898160 ATTACTGCTG
Statistics
Matches: 233, Mismatches: 41, Indels: 34
0.76 0.13 0.11
Matches are distributed among these distances:
75 56 0.24
76 1 0.00
77 1 0.00
78 3 0.01
84 3 0.01
86 3 0.01
87 110 0.47
88 1 0.00
91 1 0.00
92 1 0.00
93 53 0.23
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31
Consensus pattern (87 bp):
CCAGTAATCGGAGTATCAGTTTCCAATACTTTGATCTCCCTCATTGCTGATATATCCATCTTATC
AGTGACACAAAGGTTATCAGTG
Found at i:5898909 original size:39 final size:39
Alignment explanation
Indices: 5898866--5898950 Score: 127
Period size: 39 Copynumber: 2.2 Consensus size: 39
5898856 TTCACAGCTA
*
5898866 CAAGCTTTGGTTTCTTTT-CCTTGACTTGCATTGGAGTTG
1 CAAGCTTTGGTTTCTTTTCCCTT-ACCTGCATTGGAGTTG
* *
5898905 CAAGCCTTGGTTTCTTTTCCCTTACCTGCTTTGGAGTTG
1 CAAGCTTTGGTTTCTTTTCCCTTACCTGCATTGGAGTTG
5898944 CAAGCTT
1 CAAGCTT
5898951 CAGTGTGGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 37 0.90
40 4 0.10
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (39 bp):
CAAGCTTTGGTTTCTTTTCCCTTACCTGCATTGGAGTTG
Found at i:5900411 original size:89 final size:89
Alignment explanation
Indices: 5900232--5900414 Score: 321
Period size: 90 Copynumber: 2.0 Consensus size: 89
5900222 TAGGGTTGGG
* *
5900232 TTTTGTGTTTTCGCCTTTGGTTTGGGTATTCTATTAGTCATCTTGTTTTTTCAATTGGGGGATCA
1 TTTTTTGTTTTCGCCTTTGGTTTGGGTATTCTATTAGTCATCTTGTTTTTTCAATTGGGGAATCA
5900297 ACATAATATCAACTAAATACTTTT
66 ACATAATATCAACTAAATACTTTT
*
5900321 TTTTTTGTTTTCGCCTTTGGTTTGGGTATTCTATTAGTCATCTTCTTTTTTTCAATTGGGGAATC
1 TTTTTTGTTTTCGCCTTTGGTTTGGGTATTCTATTAGTCATCTT-GTTTTTTCAATTGGGGAATC
*
5900386 AACATAATATCTACTAAATACTTTT
65 AACATAATATCAACTAAATACTTTT
5900411 TTTT
1 TTTT
5900415 ATAGTCCCTA
Statistics
Matches: 89, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 43 0.48
90 46 0.52
ACGTcount: A:0.21, C:0.14, G:0.15, T:0.51
Consensus pattern (89 bp):
TTTTTTGTTTTCGCCTTTGGTTTGGGTATTCTATTAGTCATCTTGTTTTTTCAATTGGGGAATCA
ACATAATATCAACTAAATACTTTT
Found at i:5904004 original size:5 final size:5
Alignment explanation
Indices: 5903994--5904020 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5903984 TCCACCTCTT
5903994 CCTCA CCTCA CCTCA CCTCA CCTCA CC
1 CCTCA CCTCA CCTCA CCTCA CCTCA CC
5904021 CTCTCCCCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.63, G:0.00, T:0.19
Consensus pattern (5 bp):
CCTCA
Found at i:5912338 original size:25 final size:27
Alignment explanation
Indices: 5912280--5912338 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
5912270 TTTTATTAAT
*
5912280 TTATTTTTAATTATATTTTTTATGTAAC
1 TTATTTTT-ATTATATTTTTCATGTAAC
*
5912308 TT-TTTTT-TTATATTTTTCATGT-TC
1 TTATTTTTATTATATTTTTCATGTAAC
5912332 TTATTTT
1 TTATTTT
5912339 GAATTTGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 3 0.11
25 18 0.64
27 5 0.18
28 2 0.07
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.71
Consensus pattern (27 bp):
TTATTTTTATTATATTTTTCATGTAAC
Found at i:5913265 original size:13 final size:13
Alignment explanation
Indices: 5913247--5913288 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
5913237 TGAGGGAGCC
*
5913247 CTTGTATTTATGT
1 CTTGTATTTATCT
*
5913260 CTTGTATTTATTT
1 CTTGTATTTATCT
*
5913273 CTTGTCTTTATCT
1 CTTGTATTTATCT
5913286 CTT
1 CTT
5913289 AGTTATAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.12, C:0.14, G:0.10, T:0.64
Consensus pattern (13 bp):
CTTGTATTTATCT
Found at i:5921022 original size:25 final size:25
Alignment explanation
Indices: 5920975--5921021 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
5920965 TTATAAAAAA
* *
5920975 TAAAATAATTAAATGTGATTTTTAT
1 TAAAATAATTAAATCTAATTTTTAT
5921000 TAAAATAA-TAAATCTAATTTTT
1 TAAAATAATTAAATCTAATTTTT
5921022 TTGGAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (25 bp):
TAAAATAATTAAATCTAATTTTTAT
Found at i:5922120 original size:2 final size:2
Alignment explanation
Indices: 5922113--5922145 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5922103 AAAGCTTAAT
5922113 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 T
5922146 CTGCTCGTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5925807 original size:15 final size:16
Alignment explanation
Indices: 5925783--5925822 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
5925773 TGTTTTTTAC
*
5925783 ATAAAAAAATAT-AAA
1 ATAAATAAATATCAAA
5925798 ATAAATAAATATCAAA
1 ATAAATAAATATCAAA
5925814 ATAAGATAA
1 ATAA-ATAA
5925823 TAGGAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.50
16 7 0.32
17 4 0.18
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (16 bp):
ATAAATAAATATCAAA
Found at i:5926836 original size:13 final size:13
Alignment explanation
Indices: 5926818--5926842 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5926808 GTTTTTTTAA
5926818 TTAATATTGTTAT
1 TTAATATTGTTAT
5926831 TTAATATTGTTA
1 TTAATATTGTTA
5926843 AAGTATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
TTAATATTGTTAT
Found at i:5927110 original size:13 final size:13
Alignment explanation
Indices: 5927092--5927116 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5927082 TTTTTTTTAA
5927092 TTAATATTGTTAT
1 TTAATATTGTTAT
5927105 TTAATATTGTTA
1 TTAATATTGTTA
5927117 AAGTAGATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
TTAATATTGTTAT
Found at i:5927214 original size:272 final size:274
Alignment explanation
Indices: 5926577--5927295 Score: 1098
Period size: 272 Copynumber: 2.6 Consensus size: 274
5926567 TATTAATAGG
*
5926577 TTATATTTTTTATTAATTAAGAAGTTAGTATTTAATTAATTTATTATTTCC-AGAAATTAAATAA
1 TTATATTTTTTGTTAATTAAGAAGTTAGTATTTAATTAATTTATTATTTCCGA-AAATTAAATAA
* *
5926641 AAAATATGGTTAA--TTTTTAATATAATTAGTTATATTAATAGATTTTTGTACTAATTAATTTGT
65 AAAATATGGTTAATTTTTTTAATATAATTAGTTATATTAATAGGTTTTTGTACTAATTAATTTAT
* *
5926704 ATATTTAATTTTTTTATATCACAGACATTTAGAATTTTGTTAAAACACTTTTCAACTCTTTTACT
130 ATATTTAATTTTTTTATATTACA-ACATTTAGAATTGTGTTAAAACACTTTTCAACTCTTTTACT
*
5926769 CTCTCATACAGGTAAGTTCTTTTCTTCTCTTCTTACTTTGTTTTTTTAATTAATATTGTTATTTA
194 CCCTCATACAGGTAAGTTCTTTTCTTCTCTTCTTACTTTGTTTTTTTAATTAATATTGTTATTTA
*
5926834 ATATTGTTAAAGTATA
259 ATATTGTTAAAGTAGA
*
5926850 TTATATTTTTTGTTAATTAAGAAGTTAGTATTTAATTAATTTATTATTTCTGAAAATTAAATAAA
1 TTATATTTTTTGTTAATTAAGAAGTTAGTATTTAATTAATTTATTATTTCCGAAAATTAAATAAA
* * * *
5926915 AAATATGATTAATTTTTTTAATATAATTAGTTATATTAGTAGGTTTCTGTATTAATTAAATTT-T
66 AAATATGGTTAATTTTTTTAATATAATTAGTTATATTAATAGGTTTTTGTACTAATT-AATTTAT
*
5926979 ATATTCAATTTTTTTATATTACAACCATTTAGAATTGTGTTAAAACAAC-TTTCGAACTCTTTT-
130 ATATTTAATTTTTTTATATTACAA-CATTTAGAATTGTGTTAAAAC-ACTTTTC-AACTCTTTTA
* * * *
5927042 TTCCCTCGTCCATGTAAGTTCTTTTCTTCTCCTT-TTACTTT-TTTTTTTAATTAATATTGTTAT
192 CTCCCTCATACAGGTAAGTTCTTTTCTTCT-CTTCTTACTTTGTTTTTTTAATTAATATTGTTAT
5927105 TTAATATTGTTAAAGTAGA
256 TTAATATTGTTAAAGTAGA
* *
5927124 TT-T-TTTTTTGTTAATTAAGAAGTTACTATTTAATTAAATTATTATTTCCGAAAATTAAATAAA
1 TTATATTTTTTGTTAATTAAGAAGTTAGTATTTAATTAATTTATTATTTCCGAAAATTAAATAAA
* *
5927187 AAATATGGTTAATTTTTTTAGTATAATTAGTTATATTAATGGGTTTTTGTACTAATTAATTTATA
66 AAATATGGTTAATTTTTTTAATATAATTAGTTATATTAATAGGTTTTTGTACTAATTAATTTATA
*
5927252 TATTTAATTTTTTTATATTACAAACATTTAAAATTGTGTTAAAA
131 TATTTAATTTTTTTATATTAC-AACATTTAGAATTGTGTTAAAA
5927296 GTTTAATTTT
Statistics
Matches: 409, Mismatches: 27, Indels: 21
0.89 0.06 0.05
Matches are distributed among these distances:
271 5 0.01
272 149 0.36
273 75 0.18
274 44 0.11
275 117 0.29
276 19 0.05
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51
Consensus pattern (274 bp):
TTATATTTTTTGTTAATTAAGAAGTTAGTATTTAATTAATTTATTATTTCCGAAAATTAAATAAA
AAATATGGTTAATTTTTTTAATATAATTAGTTATATTAATAGGTTTTTGTACTAATTAATTTATA
TATTTAATTTTTTTATATTACAACATTTAGAATTGTGTTAAAACACTTTTCAACTCTTTTACTCC
CTCATACAGGTAAGTTCTTTTCTTCTCTTCTTACTTTGTTTTTTTAATTAATATTGTTATTTAAT
ATTGTTAAAGTAGA
Found at i:5928952 original size:2 final size:2
Alignment explanation
Indices: 5928945--5928982 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5928935 CCATGGATAA
5928945 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
5928983 CTTAAACTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5930133 original size:18 final size:17
Alignment explanation
Indices: 5930071--5930133 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 17
5930061 AATTTAGACA
*
5930071 AAATAATATAAAAATTAT
1 AAAT-ATATAACAATTAT
* *
5930089 -AATATTTAACATTTAT
1 AAATATATAACAATTAT
*
5930105 AAATTTCATAACAATTAT
1 AAATAT-ATAACAATTAT
5930123 AAATAATATAA
1 AAAT-ATATAA
5930134 TTTTTTGTCA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
16 10 0.29
17 7 0.20
18 17 0.49
19 1 0.03
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATATATAACAATTAT
Found at i:5930411 original size:43 final size:42
Alignment explanation
Indices: 5930331--5930416 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 42
5930321 AAAATTAGGA
5930331 TTTAAAATATATTTTTGAAACTTTATAAAATACAAAAATTATT
1 TTTAAAATATATTTTTGAAACTTTATAAAATACAAAAA-TATT
* * *
5930374 TTTATAATATAATTTTTTAGAA-TTTATAATATA-AAAAATATT
1 TTTAAAATAT-ATTTTTGA-AACTTTATAAAATACAAAAATATT
5930416 T
1 T
5930417 GATCATAGTC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
42 5 0.13
43 14 0.37
44 17 0.45
45 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (42 bp):
TTTAAAATATATTTTTGAAACTTTATAAAATACAAAAATATT
Found at i:5944494 original size:2 final size:2
Alignment explanation
Indices: 5944487--5944518 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5944477 AGAATATTAA
5944487 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
5944519 GTGGATAGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5945465 original size:3 final size:3
Alignment explanation
Indices: 5945457--5945494 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
5945447 CATGTTGTAT
*
5945457 TTC TTC TTC TTC GTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
5945495 TCCTTTTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.32, G:0.03, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:5946380 original size:2 final size:2
Alignment explanation
Indices: 5946373--5946397 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5946363 ATCTGAGTAG
5946373 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
5946398 TATATAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5946957 original size:12 final size:12
Alignment explanation
Indices: 5946940--5946965 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5946930 TAATTAGCAT
5946940 TAAATCTAGGTA
1 TAAATCTAGGTA
5946952 TAAATCTAGGTA
1 TAAATCTAGGTA
5946964 TA
1 TA
5946966 TATATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (12 bp):
TAAATCTAGGTA
Found at i:5951393 original size:47 final size:47
Alignment explanation
Indices: 5951339--5951430 Score: 157
Period size: 47 Copynumber: 2.0 Consensus size: 47
5951329 AAATCAGTTA
*
5951339 TAACCAACTTTTATAGAATTATAATAAACTTTTATGTGATTTTAATT
1 TAACCAACTTTTATAGAATTATAATAAACTCTTATGTGATTTTAATT
* *
5951386 TAACCAACTTTTATAGAATTATAATACACTCTTATTTGATTTTAA
1 TAACCAACTTTTATAGAATTATAATAAACTCTTATGTGATTTTAA
5951431 CCTTTTTTAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (47 bp):
TAACCAACTTTTATAGAATTATAATAAACTCTTATGTGATTTTAATT
Found at i:5951410 original size:26 final size:25
Alignment explanation
Indices: 5951339--5951410 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 25
5951329 AAATCAGTTA
5951339 TAACCAACTTTTATAGAATTATAA-
1 TAACCAACTTTTATAGAATTATAAT
* *
5951363 T-A--AACTTTTAT-GTGATTTTAATT
1 TAACCAACTTTTATAG-AATTATAA-T
5951386 TAACCAACTTTTATAGAATTATAAT
1 TAACCAACTTTTATAGAATTATAAT
5951411 ACACTCTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
20 1 0.03
21 15 0.41
23 2 0.05
24 2 0.05
25 1 0.03
26 15 0.41
27 1 0.03
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (25 bp):
TAACCAACTTTTATAGAATTATAAT
Found at i:5951758 original size:21 final size:21
Alignment explanation
Indices: 5951734--5951775 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
5951724 ATATGATAAG
5951734 TTAACTTTGATTTGGATATAT
1 TTAACTTTGATTTGGATATAT
5951755 TTAACTTTGATTTGGATATAT
1 TTAACTTTGATTTGGATATAT
5951776 GCTTCCTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.52
Consensus pattern (21 bp):
TTAACTTTGATTTGGATATAT
Found at i:5962672 original size:29 final size:28
Alignment explanation
Indices: 5962640--5962706 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
5962630 ATTATGATTT
5962640 TATT-TTAATTGTATATATTTAAATAAATA
1 TATTATTAATT-TATATA-TTAAATAAATA
* *
5962669 TATTAATTTATTTATATATTAGATAAATA
1 TATT-ATTAATTTATATATTAAATAAATA
5962698 TAATTATTA
1 T-ATTATTA
5962707 TTTTGACTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
29 18 0.56
30 9 0.28
31 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (28 bp):
TATTATTAATTTATATATTAAATAAATA
Found at i:5965091 original size:15 final size:14
Alignment explanation
Indices: 5965047--5965100 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
5965037 ATATGATCAG
5965047 TAAAAAAA-ATTTA
1 TAAAAAAATATTTA
5965060 TATAACAAATATATTTA
1 TA-AA-AAA-ATATTTA
5965077 TAAAAAAATACTTTA
1 TAAAAAAATA-TTTA
5965092 -AAAAAAATA
1 TAAAAAAATA
5965101 AATTTTTTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 2 0.06
14 14 0.39
15 10 0.28
16 3 0.08
17 7 0.19
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAAAAAATATTTA
Found at i:5966721 original size:81 final size:81
Alignment explanation
Indices: 5966586--5966750 Score: 330
Period size: 81 Copynumber: 2.0 Consensus size: 81
5966576 AGGGCACATG
5966586 CCCTTAATATCACATCTATCAAGTTTTATAATGGTAGGACACCATTTTGCCTGTACATGATCAGG
1 CCCTTAATATCACATCTATCAAGTTTTATAATGGTAGGACACCATTTTGCCTGTACATGATCAGG
5966651 AAAAATAACCAAAACC
66 AAAAATAACCAAAACC
5966667 CCCTTAATATCACATCTATCAAGTTTTATAATGGTAGGACACCATTTTGCCTGTACATGATCAGG
1 CCCTTAATATCACATCTATCAAGTTTTATAATGGTAGGACACCATTTTGCCTGTACATGATCAGG
5966732 AAAAATAACCAAAACC
66 AAAAATAACCAAAACC
5966748 CCC
1 CCC
5966751 ATGTTTTTTG
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 84 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (81 bp):
CCCTTAATATCACATCTATCAAGTTTTATAATGGTAGGACACCATTTTGCCTGTACATGATCAGG
AAAAATAACCAAAACC
Found at i:5970611 original size:17 final size:16
Alignment explanation
Indices: 5970578--5970611 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5970568 ACAATTTTTT
*
5970578 TAAAAAATATAATACA
1 TAAAAAATATAAAACA
5970594 TAAAAAATACTAAAACA
1 TAAAAAATA-TAAAACA
5970611 T
1 T
5970612 TAACATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.24
Consensus pattern (16 bp):
TAAAAAATATAAAACA
Found at i:5975191 original size:18 final size:19
Alignment explanation
Indices: 5975147--5975192 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
5975137 TAATATTTAT
5975147 ATATTTAATTTTTATAATAA
1 ATATTTAA-TTTTATAATAA
*
5975167 A-A-ATAATTTT-TAATAA
1 ATATTTAATTTTATAATAA
5975183 ATATTTAATT
1 ATATTTAATT
5975193 GATAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
16 7 0.32
17 5 0.23
18 8 0.36
19 1 0.05
20 1 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATATTTAATTTTATAATAA
Found at i:5982588 original size:12 final size:12
Alignment explanation
Indices: 5982571--5982595 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5982561 CAAGAGTAAT
5982571 TTTTTAATATTA
1 TTTTTAATATTA
5982583 TTTTTAATATTA
1 TTTTTAATATTA
5982595 T
1 T
5982596 AAAAATATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTAATATTA
Found at i:5990522 original size:37 final size:37
Alignment explanation
Indices: 5990453--5990526 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
5990443 GAAGGCGGTA
* * *
5990453 ACTAGGGCAAATGGAGAAGGAAAAAGGAAGTAAAGAG
1 ACTAAGGCAAATGGAGAAGAAAAAAAGAAGTAAAGAG
5990490 ACTAAGGCAAATGGAGACAGAAAAAAAG-AGTAAAGAG
1 ACTAAGGCAAATGGAGA-AGAAAAAAAGAAGTAAAGAG
5990527 TGAAAAACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 25 0.76
38 8 0.24
ACGTcount: A:0.54, C:0.07, G:0.31, T:0.08
Consensus pattern (37 bp):
ACTAAGGCAAATGGAGAAGAAAAAAAGAAGTAAAGAG
Found at i:5995156 original size:3 final size:3
Alignment explanation
Indices: 5995144--5995177 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
5995134 GTTGTCCCAT
5995144 GAA G-A GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
5995178 TGGGAAACCG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:6015746 original size:79 final size:79
Alignment explanation
Indices: 6015614--6015966 Score: 373
Period size: 79 Copynumber: 4.5 Consensus size: 79
6015604 AGTTTAATTG
* * ** ** *
6015614 ACTAGTGCTGGGCACACATTTGCGGTTTATCCGCTAGGTGCTGAGTGTTAGGATTTGACGGATAT
1 ACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTGAGTGCCAAGATTTGACGGATAT
* * *
6015679 TATTAGTTAATCAA
66 TGTTGGTTAATCTA
* * * * * * *
6015693 ACTAGAGCTGGGCTCACATTTGCGGTTTATCCGTTAGGCATTGGGTGCCAGGATTTAATGTATAT
1 ACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTGAGTGCCAAGATTTGACGGATAT
*
6015758 TGTTGGTTAATTTA
66 TGTTGGTTAATCTA
* * * * *
6015772 ACTAGAGCTGAGCTCACATTTACGGTTTATCCGCTAGACACTGAGTGCCAATATTTGATGGATAT
1 ACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTGAGTGCCAAGATTTGACGGATAT
6015837 TGTTGGTTAATCTA
66 TGTTGGTTAATCTA
* * ** ** *
6015851 ACTAGAGTTGGGCTCACTTTTGCAATTTATCCATTAGGCACTGAATGCCAAGATTTGACGGATAT
1 ACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTGAGTGCCAAGATTTGACGGATAT
*
6015916 TGTTGGTTAATCCA
66 TGTTGGTTAATCTA
* * * * * *
6015930 ATTAGAGTTGGACTCACAATTGCAGTTTATCTGCTAG
1 ACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAG
6015967 ATATCGGGTG
Statistics
Matches: 226, Mismatches: 48, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
79 226 1.00
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (79 bp):
ACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTGAGTGCCAAGATTTGACGGATAT
TGTTGGTTAATCTA
Found at i:6038835 original size:18 final size:17
Alignment explanation
Indices: 6038799--6038838 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
6038789 TAGTAAAAAC
6038799 ATAATTTTATCATTTTA
1 ATAATTTTATCATTTTA
6038816 ATAA-TTTAT-ATCTTT-
1 ATAATTTTATCAT-TTTA
6038831 ATAATTTT
1 ATAATTTT
6038839 TAAACTACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.29
16 11 0.52
17 4 0.19
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (17 bp):
ATAATTTTATCATTTTA
Found at i:6040747 original size:27 final size:27
Alignment explanation
Indices: 6040683--6040750 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
6040673 ATAATTTTAA
6040683 AAAATTAAATCAAATCTTTATCATTTTT
1 AAAATTAAAT-AAATCTTTATCATTTTT
* **
6040711 AAAGA-AAAATATAAT-TTTATTTTTTTT
1 AAA-ATTAAATA-AATCTTTATCATTTTT
6040738 AAAATTAAATAAA
1 AAAATTAAATAAA
6040751 AAAATTTCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
26 3 0.09
27 19 0.58
28 10 0.30
29 1 0.03
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.44
Consensus pattern (27 bp):
AAAATTAAATAAATCTTTATCATTTTT
Found at i:6042273 original size:2 final size:2
Alignment explanation
Indices: 6042266--6042290 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6042256 GTTCTTATTT
6042266 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
6042291 TTTGGTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6042346 original size:23 final size:23
Alignment explanation
Indices: 6042320--6042378 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
6042310 TTATTTGCTT
* * * *
6042320 TTGTAGCACGTTTTTTCTCTGTC
1 TTGTGGCACGCTTTCTCTCTGAC
*
6042343 TTGTGGCACGCTTTCTCTTTGAC
1 TTGTGGCACGCTTTCTCTCTGAC
6042366 TTGTGGCACGCTT
1 TTGTGGCACGCTT
6042379 CTGCCTTATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.08, C:0.24, G:0.22, T:0.46
Consensus pattern (23 bp):
TTGTGGCACGCTTTCTCTCTGAC
Found at i:6050475 original size:21 final size:21
Alignment explanation
Indices: 6050449--6050513 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
6050439 CTCTGGATCC
*
6050449 TAAATCTTGGACCCTGAATCT
1 TAAATCTTAGACCCTGAATCT
* *** *
6050470 TAAATCATAGATTTTGAACCT
1 TAAATCTTAGACCCTGAATCT
6050491 TAAATCTTAGACCCTGAACTCT
1 TAAATCTTAGACCCTGAA-TCT
6050513 T
1 T
6050514 TTTTAACCTA
Statistics
Matches: 32, Mismatches: 11, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
21 29 0.91
22 3 0.09
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (21 bp):
TAAATCTTAGACCCTGAATCT
Found at i:6050600 original size:35 final size:36
Alignment explanation
Indices: 6050553--6050630 Score: 83
Period size: 35 Copynumber: 2.2 Consensus size: 36
6050543 AAACCGTAGA
6050553 CCTAAA-CTTTGAACCTTT-GACT-TCATACTCTAAAT
1 CCTAAATCTTTGAA-CTTTGGACTCTCA-ACTCTAAAT
* *
6050588 CCTAAATC-TTGAATTTTGGACTCTGAACTCTAAAT
1 CCTAAATCTTTGAACTTTGGACTCTCAACTCTAAAT
*
6050623 TCTAAATC
1 CCTAAATC
6050631 ATAAACCCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
34 3 0.08
35 31 0.84
36 3 0.08
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (36 bp):
CCTAAATCTTTGAACTTTGGACTCTCAACTCTAAAT
Found at i:6061217 original size:21 final size:19
Alignment explanation
Indices: 6061171--6061227 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
6061161 ATACATTAAA
*
6061171 TTAAAAAAATAAGTCTTAATT
1 TTAAAAAAATAA-AC-TAATT
6061192 TTAAAAAAATAAACTAATT
1 TTAAAAAAATAAACTAATT
*
6061211 ATCTAAAAAAATTAACT
1 -T-TAAAAAAATAAACT
6061228 CAGTAGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.16
20 2 0.06
21 25 0.78
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (19 bp):
TTAAAAAAATAAACTAATT
Found at i:6071184 original size:20 final size:20
Alignment explanation
Indices: 6071161--6071215 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
6071151 TAAACACTTT
6071161 TAAAATTTAAAAATTATAAA
1 TAAAATTTAAAAATTATAAA
*
6071181 TAAAATCATAAAAATTATAAA
1 TAAAAT-TTAAAAATTATAAA
*
6071202 CAAAATTTATAAAA
1 TAAAATTTA-AAAA
6071216 AAATGTATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.27
21 22 0.73
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAATTTAAAAATTATAAA
Found at i:6071206 original size:12 final size:11
Alignment explanation
Indices: 6071169--6071226 Score: 57
Period size: 12 Copynumber: 5.1 Consensus size: 11
6071159 TTTAAAATTT
6071169 AAAAATTATAA
1 AAAAATTATAA
*
6071180 ATAAAATCAT--
1 A-AAAATTATAA
6071190 AAAAATTATAA
1 AAAAATTATAA
6071201 ACAAAATTTATAA
1 A-AAAA-TTATAA
6071214 AAAAATGTATAA
1 AAAAAT-TATAA
6071226 A
1 A
6071227 GTTTTTCTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
9 7 0.18
10 1 0.03
11 3 0.08
12 21 0.54
13 7 0.18
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:6095875 original size:6 final size:6
Alignment explanation
Indices: 6095864--6095896 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
6095854 CGTGGAACTT
*
6095864 GGAGGG GGAGGG GGAGGG GGAGGG GGGGGG GGA
1 GGAGGG GGAGGG GGAGGG GGAGGG GGAGGG GGA
6095897 AACAGAGCGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.15, C:0.00, G:0.85, T:0.00
Consensus pattern (6 bp):
GGAGGG
Found at i:6098154 original size:17 final size:19
Alignment explanation
Indices: 6098134--6098175 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
6098124 ATTAATATAA
*
6098134 TTAATATATT-TAT-TATT
1 TTAATAAATTATATATATT
6098151 TTAATAAATTATATAATATT
1 TTAATAAATTATAT-ATATT
6098171 TTAAT
1 TTAAT
6098176 TTTATTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 9 0.43
18 3 0.14
20 9 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTAATAAATTATATATATT
Found at i:6098154 original size:26 final size:26
Alignment explanation
Indices: 6098120--6098179 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
6098110 GTCATATAAA
6098120 AATTATTAATATAATTA-AT-ATATTTAT
1 AATT-TTAATA-AATTATATAATATTT-T
*
6098147 TATTTTAATAAATTATATAATATTTT
1 AATTTTAATAAATTATATAATATTTT
6098173 AATTTTA
1 AATTTTA
6098180 TTTTAAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 5 0.17
26 15 0.52
27 9 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
AATTTTAATAAATTATATAATATTTT
Found at i:6098172 original size:20 final size:20
Alignment explanation
Indices: 6098119--6098175 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
6098109 AGTCATATAA
*
6098119 AAATTAT-TAATATAATTAAT
1 AAATTATATAATAT-TTTAAT
*
6098139 ATATT-TAT--TATTTTAAT
1 AAATTATATAATATTTTAAT
6098156 AAATTATATAATATTTTAAT
1 AAATTATATAATATTTTAAT
6098176 TTTATTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
17 9 0.30
18 6 0.20
19 1 0.03
20 14 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATTATATAATATTTTAAT
Found at i:6098269 original size:15 final size:17
Alignment explanation
Indices: 6098256--6098316 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 17
6098246 ATTAATATTA
6098256 TAATAATAAATATTTAT
1 TAATAATAAATATTTAT
*
6098273 TACAATTATAAATA--TAT
1 T--AATAATAAATATTTAT
6098290 TAATAATAAATATTT-T
1 TAATAATAAATATTTAT
6098306 ATAAT-ATAAAT
1 -TAATAATAAAT
6098317 GTTAAAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
15 10 0.27
16 7 0.19
17 10 0.27
19 10 0.27
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATAATAAATATTTAT
Found at i:6098283 original size:19 final size:19
Alignment explanation
Indices: 6098251--6098304 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
6098241 ACAATATTAA
*
6098251 TATTATAATAATAAATATT
1 TATTACAATAATAAATATT
*
6098270 TATTACAATTATAAATA--
1 TATTACAATAATAAATATT
6098287 TATT--AATAATAAATATT
1 TATTACAATAATAAATATT
6098304 T
1 T
6098305 TATAATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 10 0.33
17 5 0.17
19 15 0.50
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTACAATAATAAATATT
Done.