Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
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 23 of 135
Found at i:9701201 original size:30 final size:31
Alignment explanation
Indices: 9701149--9701217 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
9701139 TCGTATATTG
* * *
9701149 AAAATTT-ATTTTTTATATTTTT-ATTTTTA
1 AAAATTTAATTTTGTATATTTTTAAATTTAA
9701178 AAAATTTAATTTATGTA-ATTTTTAAATTTAA
1 AAAATTTAATTT-TGTATATTTTTAAATTTAA
9701209 AAAATTTAA
1 AAAATTTAA
9701218 ATTAAATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.21
30 10 0.29
31 17 0.50
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (31 bp):
AAAATTTAATTTTGTATATTTTTAAATTTAA
Found at i:9701370 original size:35 final size:35
Alignment explanation
Indices: 9701324--9701397 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
9701314 AAAGTACCGC
*
9701324 AAAGGACTTGATTTTAATAATGTTTACCACTCTTA
1 AAAGGACTTGATTTTAATAATGTTTACAACTCTTA
9701359 AAAGGACTTGATTTTAATAATGTTTACAACTCTTA
1 AAAGGACTTGATTTTAATAATGTTTACAACTCTTA
9701394 AAAG
1 AAAG
9701398 TATATTAACA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (35 bp):
AAAGGACTTGATTTTAATAATGTTTACAACTCTTA
Found at i:9705288 original size:17 final size:18
Alignment explanation
Indices: 9705262--9705295 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
9705252 AGTTTTAATA
*
9705262 TTTATCTTTTTTTATTCG
1 TTTATCTTTTTTAATTCG
9705280 TTTAT-TTTTTTAATTC
1 TTTATCTTTTTTAATTC
9705296 TTAATTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.15, C:0.09, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTATCTTTTTTAATTCG
Found at i:9706725 original size:4 final size:4
Alignment explanation
Indices: 9706718--9706751 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
9706708 ATGTATGTTT
9706718 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
9706752 GATTCCCGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:9709617 original size:114 final size:114
Alignment explanation
Indices: 9709233--9709672 Score: 415
Period size: 114 Copynumber: 3.8 Consensus size: 114
9709223 GCATGGGAGT
* * **
9709233 CTTCATCTTTTACATGGTC-AAAGTTCATACCTACTGGAATGGTAATGCTCGTCTCTGAGGATG-
1 CTTCATCTTTTACATGGTCTAAA-TTCGTATCTACTGGAATGGTAACACTCGTCTCTGAGGATGC
* * * * *
9709296 TAACTTTAGCCATAGGAGAAGTTACAGGATTCTTGGGGCTATCGGACAAAC
65 T-ACTTTAGCCATGGGATAAGTTACAGGATTCTTGGGGTTGTTGGACAAAC
* * * * * * * *
9709347 CGTT-ATCTGTTATATAGTCTAAATTCGCATCTACTGGAATTGAAACACTCGTCTCTGCGGATTC
1 C-TTCATCTTTTACATGGTCTAAATTCGTATCTACTGGAATGGTAACACTCGTCTCTGAGGATGC
* * * *
9709411 AACTTTAGCCATGGGATAACTTACAGGATTCTCGGGGTTGTTGGATAAAC
65 TACTTTAGCCATGGGATAAGTTACAGGATTCTTGGGGTTGTTGGACAAAC
* * * * *
9709461 CTTTATCTTTTACA-GATTCTAAATTTGTATCTACCGGAATGGTAACACTTGTCTCTGAGGATGC
1 CTTCATCTTTTACATG-GTCTAAATTCGTATCTACTGGAATGGTAACACTCGTCTCTGAGGATGC
* * *
9709525 TACTTCAGCCTTGGGATAAGTTACTA-GATTCTTGGGGTTGTTGGACAAAT
65 TACTTTAGCCATGGGATAAGTTAC-AGGATTCTTGGGGTTGTTGGACAAAC
* * * * *
9709575 CTTCATCTTTTACATGGTCTAAGTTGGTATCTACTGGAATGGTAGTAGCAC-CATGCTCCGGGGA
1 CTTCATCTTTTACATGGTCTAAATTCGTATCTACTGGAATGGTA--A-CACTCGT-CTCTGAGGA
* ** *
9709639 TGCAACTTTAGCCATACGATTAGTTACAGGATTC
62 TGCTACTTTAGCCATGGGATAAGTTACAGGATTC
9709673 ATGGAGTCGG
Statistics
Matches: 259, Mismatches: 55, Indels: 21
0.77 0.16 0.06
Matches are distributed among these distances:
113 2 0.01
114 211 0.81
115 7 0.03
116 3 0.01
117 36 0.14
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.34
Consensus pattern (114 bp):
CTTCATCTTTTACATGGTCTAAATTCGTATCTACTGGAATGGTAACACTCGTCTCTGAGGATGCT
ACTTTAGCCATGGGATAAGTTACAGGATTCTTGGGGTTGTTGGACAAAC
Found at i:9713577 original size:17 final size:18
Alignment explanation
Indices: 9713551--9713589 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
9713541 ATATTATCTG
9713551 AAAAACT-AAATAAAATA
1 AAAAACTAAAATAAAATA
* *
9713568 AAAAATTAAAATAAATTA
1 AAAAACTAAAATAAAATA
9713586 AAAA
1 AAAA
9713590 CAAAAAACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAAACTAAAATAAAATA
Found at i:9718849 original size:32 final size:32
Alignment explanation
Indices: 9718813--9718878 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
9718803 TATGAGCCAC
*
9718813 ATCCAATTTTGAAGCAACAAACAATATTCTTA
1 ATCCAATTTTGAAGCAACAAACAACATTCTTA
9718845 ATCCAATTTTGAAGCAACAAACAACATTCTTA
1 ATCCAATTTTGAAGCAACAAACAACATTCTTA
9718877 AT
1 AT
9718879 TCCTCCTTGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (32 bp):
ATCCAATTTTGAAGCAACAAACAACATTCTTA
Found at i:9720313 original size:2 final size:2
Alignment explanation
Indices: 9720308--9720373 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
9720298 AATCAAATTA
9720308 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9720350 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
9720374 TAACTGCTTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9737602 original size:9 final size:9
Alignment explanation
Indices: 9737590--9737635 Score: 56
Period size: 9 Copynumber: 4.8 Consensus size: 9
9737580 AAATAAACAT
9737590 AAATTATTA
1 AAATTATTA
9737599 AAATTATTA
1 AAATTATTA
9737608 AGAATATATTA
1 A-AAT-TATTA
*
9737619 AAAATATTA
1 AAATTATTA
9737628 ACAATTAT
1 A-AATTAT
9737636 GTTAAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 16 0.50
10 10 0.31
11 6 0.19
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (9 bp):
AAATTATTA
Found at i:9737617 original size:20 final size:21
Alignment explanation
Indices: 9737594--9737644 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
9737584 AAACATAAAT
*
9737594 TATTAAAATTATTAAGAA-TA
1 TATTAAAATTATTAACAATTA
*
9737614 TATTAAAAATATTAACAATTA
1 TATTAAAATTATTAACAATTA
*
9737635 TGTTAAAATT
1 TATTAAAATT
9737645 TTACAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (21 bp):
TATTAAAATTATTAACAATTA
Found at i:9737619 original size:11 final size:10
Alignment explanation
Indices: 9737590--9737643 Score: 51
Period size: 9 Copynumber: 5.4 Consensus size: 10
9737580 AAATAAACAT
9737590 AAAT-TATTA
1 AAATATATTA
9737599 AAAT-TATTA
1 AAATATATTA
9737608 AGAATATATTA
1 A-AATATATTA
9737619 AAA-ATATTA
1 AAATATATTA
*
9737628 ACAATTATGTTA
1 A-AA-TATATTA
9737640 AAAT
1 AAAT
9737644 TTTACAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
9 17 0.44
10 8 0.21
11 8 0.21
12 6 0.15
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.39
Consensus pattern (10 bp):
AAATATATTA
Found at i:9737702 original size:60 final size:59
Alignment explanation
Indices: 9737638--9737768 Score: 145
Period size: 60 Copynumber: 2.2 Consensus size: 59
9737628 ACAATTATGT
* ** * * *
9737638 TAAAATTTTACAAAATTTAGCTCTTGATGTTTATAAAAATTATCATTTTAGTTCTAATTC
1 TAAAATTTTACAAAATTT-GCCCTCAATATTTATAAAAATTATCAATTTAGTCCTAATTC
* * * *
9737698 TAAAAGTTTAATAAAATTTGCCCTCAATATTTATAAAATTTGTCAATTTAGTCCTAATTC
1 TAAAA-TTTTACAAAATTTGCCCTCAATATTTATAAAAATTATCAATTTAGTCCTAATTC
9737758 TAAAAATTTTA
1 T-AAAATTTTA
9737769 AATATATATT
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
60 43 0.74
61 15 0.26
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (59 bp):
TAAAATTTTACAAAATTTGCCCTCAATATTTATAAAAATTATCAATTTAGTCCTAATTC
Found at i:9739298 original size:15 final size:15
Alignment explanation
Indices: 9739241--9739298 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
9739231 TTTGTAAAGT
*
9739241 TTTATATTTTTTTTA
1 TTTATAATTTTTTTA
* *
9739256 TATATATATTTTTTAA
1 TTTATA-ATTTTTTTA
*
9739272 CTTT-TAAATTTTTTA
1 -TTTATAATTTTTTTA
9739287 TTTATAATTTTT
1 TTTATAATTTTT
9739299 ATTTCAAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
14 3 0.09
15 19 0.58
16 9 0.27
17 2 0.06
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTATAATTTTTTTA
Found at i:9742104 original size:52 final size:55
Alignment explanation
Indices: 9742030--9742161 Score: 146
Period size: 55 Copynumber: 2.5 Consensus size: 55
9742020 AAGTTATTTT
** * * * *
9742030 TGGTGACGTTTGAACACGTCACAAAATATAC-A-AAAGGTCAC-AGAAATAGTTA
1 TGGTGACGTTAAAAAACGTCACAAAAAATACAATAAACGTCACGAAAAATAGTTA
* *
9742082 TGGTGACGTTAAAAAACATCACAAAAAATACAATAAACGTCACGAAAAATAGTTT
1 TGGTGACGTTAAAAAACGTCACAAAAAATACAATAAACGTCACGAAAAATAGTTA
*
9742137 TGATGACG-TATAAAAACGTCACAAA
1 TGGTGACGTTA-AAAAACGTCACAAA
9742162 TTAACAATAT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
52 26 0.39
53 1 0.02
54 10 0.15
55 29 0.44
ACGTcount: A:0.47, C:0.15, G:0.16, T:0.22
Consensus pattern (55 bp):
TGGTGACGTTAAAAAACGTCACAAAAAATACAATAAACGTCACGAAAAATAGTTA
Found at i:9746462 original size:15 final size:16
Alignment explanation
Indices: 9746422--9746463 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
9746412 ATGATTGTTT
9746422 TATCATTAATTTTACTAC
1 TATC-TTAATTTTAC-AC
*
9746440 TATTTTAATTTTA-AC
1 TATCTTAATTTTACAC
9746455 TATCTTAAT
1 TATCTTAAT
9746464 ATAAAGGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 10 0.45
17 9 0.41
18 3 0.14
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (16 bp):
TATCTTAATTTTACAC
Found at i:9746576 original size:26 final size:24
Alignment explanation
Indices: 9746547--9746594 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
9746537 TGTTGTTTTA
*
9746547 ATATTTTTAAATGTATTTGATATATC
1 ATATTTTAAAAT-TATTT-ATATATC
9746573 ATATTTTAAAATTATTTATATA
1 ATATTTTAAAATTATTTATATA
9746595 ATAAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 5 0.24
26 11 0.52
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (24 bp):
ATATTTTAAAATTATTTATATATC
Found at i:9747460 original size:6 final size:6
Alignment explanation
Indices: 9747406--9747500 Score: 72
Period size: 6 Copynumber: 16.0 Consensus size: 6
9747396 ACCAAACCAT
* ** * * *
9747406 TTTAAA TTT-AC TTTAAA GATAAA TTT-AT TTTAAA ATTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
9747451 TTTAAA TTTAAA TCTATTAAA TTTAAA TTTAAA TTT-AA TATAAA TTTAAA
1 TTTAAA TTTAAA --T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
9747501 GTTATTATAA
Statistics
Matches: 68, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
5 16 0.24
6 45 0.66
7 1 0.01
8 1 0.01
9 5 0.07
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:9747477 original size:21 final size:23
Alignment explanation
Indices: 9747451--9747500 Score: 77
Period size: 21 Copynumber: 2.3 Consensus size: 23
9747441 TTAAATTTAT
9747451 TTTAAATTTAAATCT-AT-TAAA
1 TTTAAATTTAAATCTAATATAAA
*
9747472 TTTAAATTTAAATTTAATATAAA
1 TTTAAATTTAAATCTAATATAAA
9747495 TTTAAA
1 TTTAAA
9747501 GTTATTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 14 0.54
22 2 0.08
23 10 0.38
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTAAATTTAAATCTAATATAAA
Found at i:9747496 original size:17 final size:17
Alignment explanation
Indices: 9747406--9747516 Score: 105
Period size: 17 Copynumber: 6.3 Consensus size: 17
9747396 ACCAAACCAT
*
9747406 TTTAAATTTACTTTAAA
1 TTTAAATTTATTTTAAA
**
9747423 GATAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
9747440 ATTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
9747457 TTTAAATCTATTAAATTTAAA
1 TTTAAA--T-TT-ATTTTAAA
* *
9747478 TTTAAATTTAATATAAA
1 TTTAAATTTATTTTAAA
* *
9747495 TTTAAAGTTATTATAAA
1 TTTAAATTTATTTTAAA
9747512 TTTAA
1 TTTAA
9747517 TGTCCAAATA
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
17 61 0.76
18 2 0.03
19 2 0.03
20 2 0.03
21 13 0.16
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:9747507 original size:38 final size:40
Alignment explanation
Indices: 9747434--9747516 Score: 109
Period size: 38 Copynumber: 2.1 Consensus size: 40
9747424 ATAAATTTAT
* *
9747434 TTTAAAATTAAATTTATTTTAAATTTAAATCTA-T-TAAA
1 TTTAAAATTAAATTTAATATAAATTTAAATCTATTATAAA
*
9747472 TTTAAATTTAAATTTAATATAAATTTAAAGT-TATTATAAA
1 TTTAAAATTAAATTTAATATAAATTTAAA-TCTATTATAAA
9747512 TTTAA
1 TTTAA
9747517 TGTCCAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
38 28 0.72
39 2 0.05
40 9 0.23
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (40 bp):
TTTAAAATTAAATTTAATATAAATTTAAATCTATTATAAA
Found at i:9748090 original size:18 final size:19
Alignment explanation
Indices: 9748067--9748103 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
9748057 AAAATATATA
*
9748067 CAAAGAA-TCAATACGAAG
1 CAAAGAATTCAAAACGAAG
9748085 CAAAGAATTCAAAACGAAG
1 CAAAGAATTCAAAACGAAG
9748104 AAATCTCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.57, C:0.16, G:0.16, T:0.11
Consensus pattern (19 bp):
CAAAGAATTCAAAACGAAG
Found at i:9759552 original size:18 final size:19
Alignment explanation
Indices: 9759529--9759565 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
9759519 AAAATATATA
*
9759529 CAAAGAA-TCAATACGAAG
1 CAAAGAATTCAAAACGAAG
9759547 CAAAGAATTCAAAACGAAG
1 CAAAGAATTCAAAACGAAG
9759566 AAATCTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.57, C:0.16, G:0.16, T:0.11
Consensus pattern (19 bp):
CAAAGAATTCAAAACGAAG
Found at i:9772475 original size:34 final size:35
Alignment explanation
Indices: 9772436--9772510 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 35
9772426 TTTCCTCTAT
* * * **
9772436 ATTTTTAGTTAAAAAAATATTTAATTCATTTA-AA
1 ATTTTTAATTAAAAAAACATTAAATGAATTTATAA
*
9772470 ATTTTTAATTTAAAAAACATTAAATGAATTTATAA
1 ATTTTTAATTAAAAAAACATTAAATGAATTTATAA
9772505 ATTTTT
1 ATTTTT
9772511 TAAAATTTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 26 0.76
35 8 0.24
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (35 bp):
ATTTTTAATTAAAAAAACATTAAATGAATTTATAA
Found at i:9773316 original size:21 final size:21
Alignment explanation
Indices: 9773292--9773332 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
9773282 TATGAAAAGC
9773292 GTCACAAAAAG-ATCTCAAAAT
1 GTCACAAAAAGTAT-TCAAAAT
9773313 GTCACAAAAAGTATTCAAAA
1 GTCACAAAAAGTATTCAAAA
9773333 AACGTCACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.54, C:0.17, G:0.10, T:0.20
Consensus pattern (21 bp):
GTCACAAAAAGTATTCAAAAT
Found at i:9773339 original size:23 final size:23
Alignment explanation
Indices: 9773286--9773372 Score: 74
Period size: 22 Copynumber: 3.9 Consensus size: 23
9773276 TATAGCTATG
*
9773286 AAAAGCGTCACAAAAAG-ATCTC-
1 AAAAACGTCACAAAAAGTAT-TCA
*
9773308 -AAAATGTCACAAAAAGTATTCA
1 AAAAACGTCACAAAAAGTATTCA
* **
9773330 AAAAACGTCAC-AAAAGGAAACA
1 AAAAACGTCACAAAAAGTATTCA
* *
9773352 AAAAAGGTCACCAAAAGTATT
1 AAAAACGTCACAAAAAGTATT
9773373 TTTATTTGGT
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
21 16 0.31
22 20 0.39
23 15 0.29
ACGTcount: A:0.55, C:0.17, G:0.13, T:0.15
Consensus pattern (23 bp):
AAAAACGTCACAAAAAGTATTCA
Found at i:9773616 original size:23 final size:23
Alignment explanation
Indices: 9773590--9773633 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
9773580 GACGTTTACA
9773590 AAACATCACTGACCATGATACGG
1 AAACATCACTGACCATGATACGG
* *
9773613 AAACGTCATTGACCATGATAC
1 AAACATCACTGACCATGATAC
9773634 TTTATGTGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (23 bp):
AAACATCACTGACCATGATACGG
Found at i:9776682 original size:21 final size:20
Alignment explanation
Indices: 9776623--9776675 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
9776613 AATTTTAATG
9776623 ATTATAAAATTTTAAAAATA
1 ATTATAAAATTTTAAAAATA
* *
9776643 GTTTTATAAATTTTTTAAAAA-A
1 --ATTATAAA-ATTTTAAAAATA
9776665 ATTATAAAATT
1 ATTATAAAATT
9776676 AATTAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 2 0.08
20 7 0.27
22 8 0.31
23 9 0.35
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATTATAAAATTTTAAAAATA
Found at i:9783769 original size:24 final size:24
Alignment explanation
Indices: 9783742--9783787 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
9783732 AAGAAATAAA
*
9783742 CTAATAACCT-AAATTGCAATTAAC
1 CTAA-AACCTAAAATAGCAATTAAC
*
9783766 CTAAAGCCTAAAATAGCAATTA
1 CTAAAACCTAAAATAGCAATTA
9783788 GACCATGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.48, C:0.20, G:0.07, T:0.26
Consensus pattern (24 bp):
CTAAAACCTAAAATAGCAATTAAC
Found at i:9783888 original size:2 final size:2
Alignment explanation
Indices: 9783876--9783927 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
9783866 AAAACAATTT
*
9783876 TA TA CA 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 TA TA TA
9783918 TA TA TA TA TA
1 TA TA TA TA TA
9783928 ATGAGATAGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:9784870 original size:15 final size:16
Alignment explanation
Indices: 9784836--9784903 Score: 84
Period size: 16 Copynumber: 4.2 Consensus size: 16
9784826 TTAGTTTGGG
* *
9784836 AAAATATTTTCTCTTAA
1 AAAATATTTT-TATTTA
*
9784853 AAAATA-GTTTATTTA
1 AAAATATTTTTATTTA
9784868 AAAATATTTTTATTTA
1 AAAATATTTTTATTTA
*
9784884 AAAATATTTTTATTTC
1 AAAATATTTTTATTTA
9784900 AAAA
1 AAAA
9784904 GTGCTTATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
15 10 0.22
16 29 0.64
17 6 0.13
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (16 bp):
AAAATATTTTTATTTA
Found at i:9785414 original size:21 final size:21
Alignment explanation
Indices: 9785388--9785429 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
9785378 ATTAATATAA
9785388 TAATA-TCTAATTATATTATTT
1 TAATATTCTAATTA-ATTATTT
*
9785409 TAATATTTTAATTAATTATTT
1 TAATATTCTAATTAATTATTT
9785430 ATAGTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TAATATTCTAATTAATTATTT
Found at i:9788010 original size:5 final size:5
Alignment explanation
Indices: 9788000--9788027 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
9787990 CATTCTTAAA
9788000 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
9788028 TGTTCTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:9793576 original size:21 final size:20
Alignment explanation
Indices: 9793547--9793601 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
9793537 TAACGTGATT
*
9793547 TAATAAAAAATATAAATTAAA
1 TAATTAAAAATATAAA-TAAA
* *
9793568 TAATTAAAAAAATTAAATAGA
1 TAATTAAAAATA-TAAATAAA
*
9793589 TAATTGAAAATAT
1 TAATTAAAAATAT
9793602 TTTTTTTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.04
21 23 0.82
22 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (20 bp):
TAATTAAAAATATAAATAAA
Found at i:9793584 original size:22 final size:22
Alignment explanation
Indices: 9793551--9793598 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
9793541 GTGATTTAAT
9793551 AAAAAATATAAATTAAATAATTA
1 AAAAAATATAAA-TAAATAATTA
* *
9793574 AAAAAAT-TAAATAGATAATTG
1 AAAAAATATAAATAAATAATTA
9793595 AAAA
1 AAAA
9793599 TATTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 12 0.52
22 4 0.17
23 7 0.30
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAAATATAAATAAATAATTA
Found at i:9802453 original size:21 final size:20
Alignment explanation
Indices: 9802416--9802468 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
9802406 AAACAGTGAC
*
9802416 ATTA-TTATTTTTTATTTTT
1 ATTATTTATTTTTCATTTTT
9802435 ATTATTTACTTTTTCATTTTT
1 ATTATTTA-TTTTTCATTTTT
*
9802456 CTTACTTTATTTT
1 ATTA-TTTATTTT
9802469 CTATTTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 3 0.10
21 18 0.62
22 4 0.14
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.74
Consensus pattern (20 bp):
ATTATTTATTTTTCATTTTT
Found at i:9802474 original size:21 final size:19
Alignment explanation
Indices: 9802424--9802476 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
9802414 ACATTATTAT
9802424 TTTTTATTTTTATTATTTA
1 TTTTTATTTTTATTATTTA
*
9802443 CTTTTTCATTTTTCTTACTTTA
1 -TTTTT-ATTTTTATTA-TTTA
9802465 TTTTCTATTTTT
1 TTTT-TATTTTT
9802477 TGTTTTCCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 5 0.17
21 19 0.66
22 5 0.17
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTTATTTTTATTATTTA
Found at i:9803481 original size:20 final size:20
Alignment explanation
Indices: 9803428--9803493 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
9803418 TTAAATTTTA
9803428 ATAAAAAATTAG-AAAA-AAT
1 ATAAAAAATT-GTAAAATAAT
* *
9803447 AGAAAAATAAT-TAAAATAAT
1 ATAAAAA-ATTGTAAAATAAT
**
9803467 ATAAAAAATTGTAAAATTTT
1 ATAAAAAATTGTAAAATAAT
9803487 ATAAAAA
1 ATAAAAA
9803494 TCGTAAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
19 12 0.32
20 25 0.68
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (20 bp):
ATAAAAAATTGTAAAATAAT
Found at i:9803538 original size:56 final size:59
Alignment explanation
Indices: 9803464--9803587 Score: 175
Period size: 56 Copynumber: 2.2 Consensus size: 59
9803454 TAATTAAAAT
* * *
9803464 AATATAAAAAATTGTAAAATTTTATAAAAATCGT-AA-AAAATTGT-CA-AATATATAGA
1 AATATAAAAAATTATAAAATTTTAT-AAAATCGTAAAGAAAATTATACATAATATAAAGA
*
9803520 AATATAAAAAATTATAAAATTTTATAAAGTCGTAAAGAAAATTATACATAATATAAAGA
1 AATATAAAAAATTATAAAATTTTATAAAATCGTAAAGAAAATTATACATAATATAAAGA
9803579 AATATAAAA
1 AATATAAAA
9803588 TTCGTAAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
55 7 0.12
56 26 0.43
57 7 0.12
58 2 0.03
59 18 0.30
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (59 bp):
AATATAAAAAATTATAAAATTTTATAAAATCGTAAAGAAAATTATACATAATATAAAGA
Found at i:9803857 original size:35 final size:36
Alignment explanation
Indices: 9803803--9803872 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
9803793 GCATTTTATA
* *
9803803 ATTTTTTATGATTTCTAT-AAAATTTTACAATTTTTT
1 ATTTTTTACGATTTCTATAAAAAATTTA-AATTTTTT
9803839 ATTTTTTACGATTT-TATAAAAAATTTAAATTTTT
1 ATTTTTTACGATTTCTATAAAAAATTTAAATTTTT
9803873 AATAAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
35 10 0.32
36 21 0.68
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (36 bp):
ATTTTTTACGATTTCTATAAAAAATTTAAATTTTTT
Found at i:9803872 original size:19 final size:20
Alignment explanation
Indices: 9803850--9803894 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
9803840 TTTTTTACGA
9803850 TTTTATAAAAAATTTAAA-T
1 TTTTATAAAAAATTTAAAGT
* *
9803869 TTTTA-ATAAATTTTAAAGT
1 TTTTATAAAAAATTTAAAGT
9803888 TTTTATA
1 TTTTATA
9803895 TTTTTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 10 0.45
19 11 0.50
20 1 0.05
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTTATAAAAAATTTAAAGT
Found at i:9803883 original size:18 final size:17
Alignment explanation
Indices: 9803849--9803892 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
9803839 ATTTTTTACG
9803849 ATTTTATAAAAAATTTAA
1 ATTTT-TAAAAAATTTAA
*
9803867 ATTTTTAATAAATTTTAA
1 ATTTTTAA-AAAATTTAA
9803885 AGTTTTTA
1 A-TTTTTA
9803893 TATTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 14 0.61
19 6 0.26
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
ATTTTTAAAAAATTTAA
Found at i:9804131 original size:90 final size:93
Alignment explanation
Indices: 9803979--9804175 Score: 274
Period size: 90 Copynumber: 2.1 Consensus size: 93
9803969 GCTTCATTGC
* * *
9803979 TTTTTTGAAAAATTTTGAGGGTCTTTTTTGATGCATTTTGAAAGTTCAAGTACCTGATTGAGTG-
1 TTTTTTGAAAAAGTTTGAGGGCCTTTTTTGATGCATTTTGAAAGTTCAAGTACCTAATTGAGTGA
* ** *
9804043 GAAAAAAAAA-GTTGGGGCTTAATTACT
66 AAAAAAAAAAGGAAGGGACTTAATTACT
* *
9804070 TTTTTTGAAAAAGTTTGAGGGCCTTTTTT-ATGCATTTTGAAAGTTCAAGTGCTTAATTGAGTGC
1 TTTTTTGAAAAAGTTTGAGGGCCTTTTTTGATGCATTTTGAAAGTTCAAGTACCTAATTGAGTG-
*
9804134 AAAAAAAAAAAGGAAGGGACTTAATTATT
65 AAAAAAAAAAAGGAAGGGACTTAATTACT
9804163 TTTTTTGAAAAAG
1 TTTTTTGAAAAAG
9804176 GTTAAGGACT
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
90 31 0.33
91 27 0.29
92 9 0.10
93 26 0.28
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.39
Consensus pattern (93 bp):
TTTTTTGAAAAAGTTTGAGGGCCTTTTTTGATGCATTTTGAAAGTTCAAGTACCTAATTGAGTGA
AAAAAAAAAAGGAAGGGACTTAATTACT
Found at i:9813582 original size:23 final size:23
Alignment explanation
Indices: 9813556--9813601 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
9813546 GATATGATAA
9813556 TAAATATTTTATATTTAAAATAG
1 TAAATATTTTATATTTAAAATAG
9813579 TAAATATTTTATATTTAAAATAG
1 TAAATATTTTATATTTAAAATAG
9813602 AAAAATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (23 bp):
TAAATATTTTATATTTAAAATAG
Found at i:9814313 original size:27 final size:27
Alignment explanation
Indices: 9814279--9814340 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 27
9814269 GTACTCAAAT
9814279 AAATTAATTTTATTT-GTCAAAATAAA
1 AAATTAATTTTATTTAGTCAAAATAAA
*
9814305 AAATATAATTTTATTTACTTCAAAATAAA
1 AAAT-TAATTTTATTTA-GTCAAAATAAA
9814334 AAATTAA
1 AAATTAA
9814341 ATTAAATTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 4 0.12
27 11 0.34
28 3 0.09
29 14 0.44
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (27 bp):
AAATTAATTTTATTTAGTCAAAATAAA
Found at i:9814778 original size:15 final size:16
Alignment explanation
Indices: 9814745--9814778 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9814735 CTCTTTTTCT
9814745 CTTTTTCTTTTTTGTG
1 CTTTTTCTTTTTTGTG
*
9814761 CTTTTTTTTTTTTG-G
1 CTTTTTCTTTTTTGTG
9814776 CTT
1 CTT
9814779 ATGGAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.76
Consensus pattern (16 bp):
CTTTTTCTTTTTTGTG
Found at i:9821541 original size:20 final size:21
Alignment explanation
Indices: 9821512--9821556 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
9821502 ATGATTATGG
9821512 TAAAAAAATT-AT-TATATTA
1 TAAAAAAATTGATGTATATTA
*
9821531 TAAAAATAATTGATGTATTTTA
1 TAAAAA-AATTGATGTATATTA
9821553 TAAA
1 TAAA
9821557 GTTATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
20 4 0.18
21 2 0.09
22 10 0.45
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (21 bp):
TAAAAAAATTGATGTATATTA
Found at i:9821896 original size:16 final size:16
Alignment explanation
Indices: 9821875--9821908 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
9821865 AAAATATTTT
9821875 TTATAAAGATTATATA
1 TTATAAAGATTATATA
**
9821891 TTATAAATTTTATATA
1 TTATAAAGATTATATA
9821907 TT
1 TT
9821909 TTTTATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTATAAAGATTATATA
Found at i:9823215 original size:19 final size:22
Alignment explanation
Indices: 9823175--9823215 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
9823165 TGTTAATTTT
9823175 AAATATAATATTATAAAGTAAA
1 AAATATAATATTATAAAGTAAA
9823197 AAATAT-ATATT-TAAA-TAAA
1 AAATATAATATTATAAAGTAAA
9823216 GTTCAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 4 0.21
21 5 0.26
22 6 0.32
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
AAATATAATATTATAAAGTAAA
Found at i:9836236 original size:17 final size:17
Alignment explanation
Indices: 9836198--9836236 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
9836188 AGGTGGAGAA
* *
9836198 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
9836215 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
*
9836232 TTTGT
1 CTTGT
9836237 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.15, C:0.10, G:0.26, T:0.49
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:9836651 original size:6 final size:6
Alignment explanation
Indices: 9836640--9836668 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
9836630 CACTACTCTT
9836640 CTCTCA CTCTCA CTCTCA CTCTCA CTCTC
1 CTCTCA CTCTCA CTCTCA CTCTCA CTCTC
9836669 TTTTACATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.52, G:0.00, T:0.34
Consensus pattern (6 bp):
CTCTCA
Found at i:9837213 original size:19 final size:19
Alignment explanation
Indices: 9837175--9837214 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
9837165 GAGTTTAGTT
* *
9837175 TAATTTTTGTCTCTCATTA
1 TAATTTTTATCTCGCATTA
*
9837194 TAATTTTTATCTCGCGTTA
1 TAATTTTTATCTCGCATTA
9837213 TA
1 TA
9837215 GTATCTAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.07, T:0.55
Consensus pattern (19 bp):
TAATTTTTATCTCGCATTA
Found at i:9838969 original size:21 final size:20
Alignment explanation
Indices: 9838932--9838970 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
9838922 AAAAAATACA
**
9838932 TTTTCTTTTTTTTTTCTTTC
1 TTTTCTTTTTTAATTCTTTC
9838952 TTTTCATTTTTTAATTCTT
1 TTTTC-TTTTTTAATTCTT
9838971 CCAAGCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTCTTTTTTAATTCTTTC
Found at i:9842012 original size:18 final size:17
Alignment explanation
Indices: 9841976--9842015 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
9841966 TACTAAAAAT
9841976 ATAATTTTATCATTTTA
1 ATAATTTTATCATTTTA
9841993 ATAA-TTTAT-ATCTTT-
1 ATAATTTTATCAT-TTTA
9842008 ATAATTTT
1 ATAATTTT
9842016 TAAAAAGTTA
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:9850492 original size:5 final size:5
Alignment explanation
Indices: 9850469--9850506 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
9850459 AGTGAATTGC
*
9850469 TAAAT T-AAC TAAA- TAAAT TAAAT TAAAT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT
9850507 AAAAAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
4 7 0.23
5 23 0.77
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (5 bp):
TAAAT
Found at i:9857750 original size:158 final size:158
Alignment explanation
Indices: 9857460--9857774 Score: 488
Period size: 158 Copynumber: 2.0 Consensus size: 158
9857450 TATGCCTATC
*
9857460 GCCTTACAAAAAATCACGCAGTTAAGAGCACCAGAACTGTGCCTCATCAAATGCGCCTCGCCTGA
1 GCCTTACAAAAAATCACGCAGTTAAGAGCACCAGAACTGTGCCTCATCAAATGCGCCTCACCTGA
* *
9857525 AAGGGTCGAGGTGCTTTTGTTGCCTAGCGCTAAGGCGCAAGGCATAGGCATGCCTAGGTGCAAAA
66 AAGGGTCGAGGTGCTTTTGTTGCCTAGCGCTAAGGCGCAAAGCATAGACATGCCTAGGTGCAAAA
*
9857590 CTTCAGAACACCGATAAATCCAACCATA
131 CTTCAGAACACCAATAAATCCAACCATA
* * * * *
9857618 GCCTTACAAAACA-CAATGCAGTTAAGAGCACCAGAAGTGTGCCTGATCAAATGTGCCTCACCTG
1 GCCTTACAAAAAATC-ACGCAGTTAAGAGCACCAGAACTGTGCCTCATCAAATGCGCCTCACCTG
* * * *
9857682 AAAGGGTTGAGGTGCTTTTGTTGCCTAGTGCTAAGGCGCAAAGCATAGACGTGCCTAGGTGCAGA
65 AAAGGGTCGAGGTGCTTTTGTTGCCTAGCGCTAAGGCGCAAAGCATAGACATGCCTAGGTGCAAA
*
9857747 ACTTGAGAACACCAATAAATCCAACCAT
130 ACTTCAGAACACCAATAAATCCAACCAT
9857775 GGACAAGGCT
Statistics
Matches: 142, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
157 1 0.01
158 141 0.99
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (158 bp):
GCCTTACAAAAAATCACGCAGTTAAGAGCACCAGAACTGTGCCTCATCAAATGCGCCTCACCTGA
AAGGGTCGAGGTGCTTTTGTTGCCTAGCGCTAAGGCGCAAAGCATAGACATGCCTAGGTGCAAAA
CTTCAGAACACCAATAAATCCAACCATA
Found at i:9869566 original size:16 final size:16
Alignment explanation
Indices: 9869545--9869601 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 16
9869535 ATATTTAGTC
9869545 ATATAATAAATTATTA
1 ATATAATAAATTATTA
9869561 ATATAATTTATATATTATTA
1 ATATAA--TA-A-ATTATTA
* *
9869581 TTTTAATAAATTATTTA
1 ATATAATAAATTA-TTA
9869598 ATAT
1 ATAT
9869602 TTCAAATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
16 10 0.31
17 6 0.19
18 4 0.12
19 1 0.03
20 11 0.34
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:9869643 original size:15 final size:17
Alignment explanation
Indices: 9869617--9869651 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
9869607 ATTTATTTTG
9869617 ATAATAAATTTTAAA-A
1 ATAATAAATTTTAAACA
9869633 ATAAT-AATTTTAAACA
1 ATAATAAATTTTAAACA
9869649 ATA
1 ATA
9869652 TTTTTCACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAATAAATTTTAAACA
Found at i:9869704 original size:15 final size:15
Alignment explanation
Indices: 9869684--9869739 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
9869674 ATTCAATATT
9869684 AATATTTTAATAATA
1 AATATTTTAATAATA
*
9869699 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
9869718 AATATATTAATAATA
1 AATATTTTAATAATA
9869733 AATATTT
1 AATATTT
9869740 CGTAGCATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:9872194 original size:10 final size:10
Alignment explanation
Indices: 9872179--9872206 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
9872169 CTTACAACAC
9872179 TCCTCCTTCA
1 TCCTCCTTCA
9872189 TCCTCCTTCA
1 TCCTCCTTCA
9872199 TCCTCCTT
1 TCCTCCTT
9872207 GTTACTTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.07, C:0.50, G:0.00, T:0.43
Consensus pattern (10 bp):
TCCTCCTTCA
Found at i:9887493 original size:24 final size:24
Alignment explanation
Indices: 9887461--9887522 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
9887451 ACATGGAGGA
*
9887461 ATCCATTAAACTTTTTGGTTGGTT
1 ATCCATTAAACTTTTTGGTTGATT
*
9887485 ATCCATTAAACTTCTTGGTTGATT
1 ATCCATTAAACTTTTTGGTTGATT
9887509 ATCCATTAAACTTT
1 ATCCATTAAACTTT
9887523 GGTAAGAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (24 bp):
ATCCATTAAACTTTTTGGTTGATT
Found at i:9888687 original size:8 final size:8
Alignment explanation
Indices: 9888670--9888699 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
9888660 AAATTTATAA
*
9888670 TTTAATTT
1 TTTAAATT
9888678 TTTAAATT
1 TTTAAATT
9888686 TTTAAATT
1 TTTAAATT
9888694 TTTAAA
1 TTTAAA
9888700 ATTAATAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TTTAAATT
Found at i:9897307 original size:24 final size:24
Alignment explanation
Indices: 9897280--9897331 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
9897270 TTAAAAATTT
9897280 AAAATTAATTACAACTGAAAAAGA
1 AAAATTAATTACAACTGAAAAAGA
* * *
9897304 AAAATTTATTACGATTGAAAAAGA
1 AAAATTAATTACAACTGAAAAAGA
9897328 AAAA
1 AAAA
9897332 CTCAGTTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.62, C:0.06, G:0.10, T:0.23
Consensus pattern (24 bp):
AAAATTAATTACAACTGAAAAAGA
Found at i:9901352 original size:22 final size:23
Alignment explanation
Indices: 9901322--9901375 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
9901312 TATATTATGT
* *
9901322 ATATGATATAAAGTTAAA-TATA
1 ATATAATATAAACTTAAATTATA
9901344 ATATAATATAAACTTAAATTATA
1 ATATAATATAAACTTAAATTATA
9901367 A-ATTAATAT
1 ATA-TAATAT
9901376 TTAAATCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 17 0.61
23 11 0.39
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.39
Consensus pattern (23 bp):
ATATAATATAAACTTAAATTATA
Found at i:9903513 original size:32 final size:34
Alignment explanation
Indices: 9903458--9903520 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
9903448 GCTATCAGTG
*
9903458 TAAAAATATCGATAATAATAAAA-TTAAATATTA
1 TAAAAATATCGATAATAAAAAAATTTAAATATTA
*
9903491 TAAAAATATTG-TAATAAAAAAATTTAAATA
1 TAAAAATATCGATAATAAAAAAATTTAAATA
9903521 CACCACAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 10 0.37
33 17 0.63
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (34 bp):
TAAAAATATCGATAATAAAAAAATTTAAATATTA
Found at i:9904104 original size:31 final size:35
Alignment explanation
Indices: 9904069--9904141 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 35
9904059 GCTCAACTAT
9904069 TATGTTATAA-AATAA-TAT-TATA-TTA-ATTATA
1 TATGTTATAATAATAATTATATATATTTATATT-TA
9904100 TATGTTA-AATAATAATTATATATATTTATATTTA
1 TATGTTATAATAATAATTATATATATTTATATTTA
9904134 TAT-TTATA
1 TATGTTATA
9904142 TTAAATCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
30 2 0.06
31 12 0.33
32 3 0.08
33 7 0.19
34 9 0.25
35 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (35 bp):
TATGTTATAATAATAATTATATATATTTATATTTA
Found at i:9904664 original size:26 final size:29
Alignment explanation
Indices: 9904630--9904685 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
9904620 TAACATTAAT
*
9904630 TCATAGC-TTTAA-GTTTTTTT-ATTTAG
1 TCATAGCTTTTAATATTTTTTTAATTTAG
*
9904656 TCATTGCTTTTAATATTTTTTTAATTTAG
1 TCATAGCTTTTAATATTTTTTTAATTTAG
9904685 T
1 T
9904686 TTACATCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.24
27 5 0.20
28 7 0.28
29 7 0.28
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.61
Consensus pattern (29 bp):
TCATAGCTTTTAATATTTTTTTAATTTAG
Found at i:9905324 original size:15 final size:15
Alignment explanation
Indices: 9905267--9905325 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 15
9905257 TTCAATTTTT
*
9905267 TTTG-TTAATGTTCA
1 TTTGTTTAATATTCA
* *
9905281 TTTATTTAAAATT-A
1 TTTGTTTAATATTCA
* *
9905295 TATGTGTTCATATTCA
1 TTTGT-TTAATATTCA
9905311 TTTGTTTAATATTCA
1 TTTGTTTAATATTCA
9905326 CGAACATGTT
Statistics
Matches: 33, Mismatches: 9, Indels: 5
0.70 0.19 0.11
Matches are distributed among these distances:
14 7 0.21
15 21 0.64
16 5 0.15
ACGTcount: A:0.29, C:0.07, G:0.08, T:0.56
Consensus pattern (15 bp):
TTTGTTTAATATTCA
Found at i:9905341 original size:23 final size:23
Alignment explanation
Indices: 9905326--9905407 Score: 69
Period size: 23 Copynumber: 3.5 Consensus size: 23
9905316 TTAATATTCA
*
9905326 CGAACATGTTCATTTAACTTAAT
1 CGAACATGTTCATTTAAATTAAT
** *
9905349 CGAACATGTTCA-CGAACATTAAA
1 CGAACATGTTCATTTAA-ATTAAT
*
9905372 CTAACATGTTCA-TTAACATATAAT
1 CGAACATGTTCATTTAA-AT-TAAT
*
9905396 TGAACATGTTCA
1 CGAACATGTTCA
9905408 CGAACAATGT
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
22 2 0.04
23 32 0.68
24 13 0.28
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (23 bp):
CGAACATGTTCATTTAAATTAAT
Found at i:9906109 original size:14 final size:14
Alignment explanation
Indices: 9906090--9906137 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
9906080 TTAAGTAAAA
9906090 ATAATATAAAATTT
1 ATAATATAAAATTT
9906104 ATAATATATAACATTT
1 ATAATATA-AA-ATTT
*
9906120 AT-ATAAAAAAATTT
1 ATAAT-ATAAAATTT
9906134 ATAA
1 ATAA
9906138 ATTGTTCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 14 0.48
15 7 0.24
16 8 0.28
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAATATAAAATTT
Found at i:9906114 original size:16 final size:16
Alignment explanation
Indices: 9906093--9906137 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
9906083 AGTAAAAATA
9906093 ATATAAAATTTATAAT
1 ATATAAAATTTATAAT
*
9906109 ATATAACATTTAT-AT
1 ATATAAAATTTATAAT
*
9906124 A-AAAAAATTTATAA
1 ATATAAAATTTATAA
9906138 ATTGTTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 9 0.36
15 4 0.16
16 12 0.48
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAAAATTTATAAT
Found at i:9906525 original size:22 final size:21
Alignment explanation
Indices: 9906481--9906543 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 21
9906471 AAATCTAAGG
* *
9906481 AAAAATAAA-AGAAACAGATTT
1 AAAAATAAAGA-AAATAGAATT
9906502 AAAAATTAAAGAAAATAGAATT
1 AAAAA-TAAAGAAAATAGAATT
9906524 AAAAGA-AATAGAAAATAGAA
1 AAAA-ATAA-AGAAAATAGAA
9906544 AAGTCAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
21 7 0.19
22 27 0.75
23 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.11, T:0.17
Consensus pattern (21 bp):
AAAAATAAAGAAAATAGAATT
Found at i:9907362 original size:19 final size:19
Alignment explanation
Indices: 9907340--9907381 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
9907330 AACATAAATC
9907340 AAATACAAAT-TTAAATAAT
1 AAATA-AAATCTTAAATAAT
* *
9907359 AAATAATATCTTAAATATT
1 AAATAAAATCTTAAATAAT
9907378 AAAT
1 AAAT
9907382 CCTAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATAAAATCTTAAATAAT
Found at i:9907630 original size:24 final size:22
Alignment explanation
Indices: 9907588--9907634 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 22
9907578 AGTATCATAC
9907588 TCTAAAATATATATATTTAATA
1 TCTAAAATATATATATTTAATA
*
9907610 TCTAAAAGTATGTCATATTTAATA
1 TCTAAAA-TATAT-ATATTTAATA
9907634 T
1 T
9907635 ATAACCTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.32
23 4 0.18
24 11 0.50
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (22 bp):
TCTAAAATATATATATTTAATA
Found at i:9915114 original size:22 final size:22
Alignment explanation
Indices: 9915074--9915115 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
9915064 CAGTGTGCTA
* * *
9915074 TTAAAAATTATATTTTTAAATT
1 TTAAAAATAATAATATTAAATT
9915096 TTAAAAATAATAATATTAAA
1 TTAAAAATAATAATATTAAA
9915116 AAAAATAAAT
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAAAAATAATAATATTAAATT
Found at i:9918583 original size:30 final size:31
Alignment explanation
Indices: 9918549--9918836 Score: 255
Period size: 30 Copynumber: 9.7 Consensus size: 31
9918539 TTTGGCGAAA
**
9918549 TTGGGGTTAAAAATGGGATTTAGG-AAAGTT
1 TTGGGGTTAAAAATGTAATTTAGGAAAAGTT
* *
9918579 TTGGGG-T-AAAATGGTCATTT--TAAAAGTT
1 TTGGGGTTAAAAAT-GTAATTTAGGAAAAGTT
* *
9918607 TTGGGG-TCAAAATGTAATTTTGGAAAAGTT
1 TTGGGGTTAAAAATGTAATTTAGGAAAAGTT
* *
9918637 TCGGGG-TCAAAATGTAATTTAGGAAAAGTT
1 TTGGGGTTAAAAATGTAATTTAGGAAAAGTT
*
9918667 TTGGGGTT-AAAATGTAATTTTGGAAAAGTT
1 TTGGGGTTAAAAATGTAATTTAGGAAAAGTT
* * *
9918697 TTGGGGTT-AAAATATAATTTTGGAAAGGTT
1 TTGGGGTTAAAAATGTAATTTAGGAAAAGTT
* *
9918727 TTGGGG-TCAAAATATAACTTTA-GAAAAGTT
1 TTGGGGTTAAAAATGTAA-TTTAGGAAAAGTT
* * * *
9918757 TT-AGGATCAAAATATAATTTTA-GAAAAGTT
1 TTGGGGTTAAAAATGTAA-TTTAGGAAAAGTT
* *
9918787 TTGGGG-TCAAAATGTAATTTTGGAAAAGTT
1 TTGGGGTTAAAAATGTAATTTAGGAAAAGTT
*
9918817 TTGGGG-TCAAAATGTAATTT
1 TTGGGGTTAAAAATGTAATTT
9918837 CTAGACAATT
Statistics
Matches: 229, Mismatches: 18, Indels: 22
0.85 0.07 0.08
Matches are distributed among these distances:
28 24 0.10
29 17 0.07
30 182 0.79
31 6 0.03
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.36
Consensus pattern (31 bp):
TTGGGGTTAAAAATGTAATTTAGGAAAAGTT
Found at i:9918671 original size:60 final size:60
Alignment explanation
Indices: 9918600--9918836 Score: 350
Period size: 60 Copynumber: 4.0 Consensus size: 60
9918590 TGGTCATTTT
* *
9918600 AAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTCGGGGTCAAAATGTAATTTAGG
1 AAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTAGG
* * *
9918660 AAAAGTTTTGGGGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAATATAATTTTGG
1 AAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTAGG
* * * * * *
9918720 AAAGGTTTTGGGGTCAAAATATAACTTTAGAAAAGTTTTAGGATCAAAATATAATTTTA-G
1 AAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAA-TTTAGG
*
9918780 AAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTT
1 AAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTT
9918837 CTAGACAATT
Statistics
Matches: 155, Mismatches: 21, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
59 3 0.02
60 149 0.96
61 3 0.02
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (60 bp):
AAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTAGG
Found at i:9918715 original size:90 final size:89
Alignment explanation
Indices: 9918566--9918836 Score: 388
Period size: 90 Copynumber: 3.0 Consensus size: 89
9918556 TAAAAATGGG
*
9918566 ATTTAGG-AAAGTTTTGGGG-TAAAATGGTCATTTT-AAAAGTTTTGGGGTCAAAATGTAATTTT
1 ATTTAGGAAAAGTTTTGGGGTTAAAAT-GTAATTTTGAAAAGTTTTGGGGTCAAAATGTAATTTT
*
9918628 GGAAAAGTTTCGGGGTCAAAATGTA
65 GGAAAAGTTTTGGGGTCAAAATGTA
* *
9918653 ATTTAGGAAAAGTTTTGGGGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAATATAATTTT
1 ATTTAGGAAAAGTTTTGGGGTTAAAATGTAATTTT-GAAAAGTTTTGGGGTCAAAATGTAATTTT
* *
9918718 GGAAAGGTTTTGGGGTCAAAATATA
65 GGAAAAGTTTTGGGGTCAAAATGTA
* * * *
9918743 ACTTTA-GAAAAGTTTTAGGATCAAAATATAATTTTAGAAAAGTTTTGGGGTCAAAATGTAATTT
1 A-TTTAGGAAAAGTTTTGGGGTTAAAATGTAATTTT-GAAAAGTTTTGGGGTCAAAATGTAATTT
9918807 TGGAAAAGTTTTGGGGTCAAAATGTA
64 TGGAAAAGTTTTGGGGTCAAAATGTA
9918833 ATTT
1 ATTT
9918837 CTAGACAATT
Statistics
Matches: 164, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
87 7 0.04
88 19 0.12
89 9 0.05
90 125 0.76
91 4 0.02
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (89 bp):
ATTTAGGAAAAGTTTTGGGGTTAAAATGTAATTTTGAAAAGTTTTGGGGTCAAAATGTAATTTTG
GAAAAGTTTTGGGGTCAAAATGTA
Found at i:9920573 original size:16 final size:16
Alignment explanation
Indices: 9920552--9920582 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9920542 CAGGGCATGG
9920552 TGGAGCAGGTGGTGGA
1 TGGAGCAGGTGGTGGA
*
9920568 TGGAGCTGGTGGTGG
1 TGGAGCAGGTGGTGG
9920583 TAGCAGCACG
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:0.13, C:0.06, G:0.58, T:0.23
Consensus pattern (16 bp):
TGGAGCAGGTGGTGGA
Found at i:9920767 original size:6 final size:6
Alignment explanation
Indices: 9920758--9920857 Score: 91
Period size: 6 Copynumber: 16.8 Consensus size: 6
9920748 TTTTTTAATG
* ** * *
9920758 TTAAAT TTAATAT TTTAAT TTTTAT TTAAAT TTAAAT TCAAA- GTAAAT
1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
9920806 TTAAAT AATTAAAT TTAAAT TTAAA- ATAAAT TTAAAT TTAAA- -TAAAT
1 TTAAAT --TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
9920853 TTAAA
1 TTAAA
9920858 ATCAATTTAA
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
4 4 0.05
5 7 0.09
6 55 0.71
7 5 0.06
8 6 0.08
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (6 bp):
TTAAAT
Found at i:9920804 original size:17 final size:16
Alignment explanation
Indices: 9920784--9920885 Score: 95
Period size: 16 Copynumber: 6.4 Consensus size: 16
9920774 AATTTTTATT
9920784 TAAATTTAAATTCAAA
1 TAAATTTAAATTCAAA
*
9920800 GTAAATTTAAA-T-AAT
1 -TAAATTTAAATTCAAA
*
9920815 TAAATTTAAATTTAAAA
1 TAAATTTAAA-TTCAAA
*
9920832 TAAATTTAAATTTAAA
1 TAAATTTAAATTCAAA
* *
9920848 TAAATTTAAAATCAAT
1 TAAATTTAAATTCAAA
*
9920864 TTAATTCTAAATT-AAA
1 TAAATT-TAAATTCAAA
9920880 -AAATTT
1 TAAATTT
9920886 CAAGCCTGGT
Statistics
Matches: 71, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
14 11 0.15
15 6 0.08
16 27 0.38
17 27 0.38
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (16 bp):
TAAATTTAAATTCAAA
Found at i:9920818 original size:31 final size:32
Alignment explanation
Indices: 9920783--9920862 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 32
9920773 TAATTTTTAT
*
9920783 TTAAATTTAAATTCAAAGTAAATTTAAA-TAA
1 TTAAATTTAAATTCAAAATAAATTTAAATTAA
*
9920814 TTAAATTTAAATTTAAAATAAATTTAAATTTAA
1 TTAAATTTAAATTCAAAATAAATTTAAA-TTAA
* *
9920847 ATAAATTTAAAATCAA
1 TTAAATTTAAATTCAA
9920863 TTTAATTCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 26 0.62
33 16 0.38
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (32 bp):
TTAAATTTAAATTCAAAATAAATTTAAATTAA
Found at i:9920832 original size:27 final size:27
Alignment explanation
Indices: 9920802--9920881 Score: 66
Period size: 23 Copynumber: 3.1 Consensus size: 27
9920792 AATTCAAAGT
9920802 AAATTTAAATAATTAAATTTAAATTTA
1 AAATTTAAATAATTAAATTTAAATTTA
9920829 AAA--TAAAT--TTAAATTTAAA--T-
1 AAATTTAAATAATTAAATTTAAATTTA
* *
9920849 AAATTTAAAATCAATTTAATTCTAAATTAA
1 AAATTT-AAAT-AATTAAATT-TAAATTTA
9920879 AAA
1 AAA
9920882 ATTTCAAGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 17
0.68 0.03 0.28
Matches are distributed among these distances:
20 3 0.07
21 1 0.02
22 1 0.02
23 15 0.37
25 5 0.12
26 6 0.15
27 7 0.17
30 3 0.07
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (27 bp):
AAATTTAAATAATTAAATTTAAATTTA
Found at i:9928692 original size:16 final size:15
Alignment explanation
Indices: 9928655--9928701 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
9928645 TTTTTTTGAA
9928655 AATTTTTAAAAATAT
1 AATTTTTAAAAATAT
*
9928670 -ATATTTTAAAAGATTT
1 AAT-TTTTAAAA-ATAT
9928686 AATTTTTTAAAAATAT
1 AA-TTTTTAAAAATAT
9928702 TTTATAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
14 2 0.08
15 8 0.31
16 6 0.23
17 9 0.35
18 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
AATTTTTAAAAATAT
Found at i:9941709 original size:2 final size:2
Alignment explanation
Indices: 9941702--9941727 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9941692 AAAGGTCCAC
9941702 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
9941728 TCTGTGATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:9943232 original size:28 final size:26
Alignment explanation
Indices: 9943172--9943237 Score: 62
Period size: 28 Copynumber: 2.4 Consensus size: 26
9943162 AATTGAAAGT
* *
9943172 TAAATAAT-AAATTTATTTTTATTTT
1 TAAAAAATAAAATTTATTTTTATTTA
9943197 TAAGAAAAATAAAATTTATATTTTATTATA
1 T-A-AAAAATAAAATTTAT-TTTTATT-TA
*
9943227 TAAAAACTAAA
1 TAAAAAATAAA
9943238 CCGAGACTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 1 0.03
26 1 0.03
27 5 0.15
28 16 0.48
29 8 0.24
30 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (26 bp):
TAAAAAATAAAATTTATTTTTATTTA
Found at i:9943689 original size:28 final size:29
Alignment explanation
Indices: 9943636--9943692 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
9943626 TAAATCATCG
***
9943636 ATTTTAATAATTAATTAAATTTTTAGGTC
1 ATTTTAATAATTAATTAAAAAATTAGGTC
9943665 ATTTTAA-AATTAATTAAAAAATTAGGTC
1 ATTTTAATAATTAATTAAAAAATTAGGTC
9943693 TGTTTTGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (29 bp):
ATTTTAATAATTAATTAAAAAATTAGGTC
Found at i:9943850 original size:24 final size:24
Alignment explanation
Indices: 9943820--9943868 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
9943810 TCGATTCTTT
*
9943820 TTTCATTCATA-TTTATATTTTTTA
1 TTTCATT-ATATTTTAAATTTTTTA
*
9943844 TTTCATTTTATTTTAAATTTTTTA
1 TTTCATTATATTTTAAATTTTTTA
9943868 T
1 T
9943869 ATTTCTCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTCATTATATTTTAAATTTTTTA
Found at i:9946629 original size:49 final size:48
Alignment explanation
Indices: 9946562--9946705 Score: 173
Period size: 49 Copynumber: 3.0 Consensus size: 48
9946552 TTCATATAAA
*
9946562 ACTACACTT-TTTTATTTTATTTTGATTAGAATATGATTTTTCAATCTT
1 ACTACACTTCTTTTATTTTATTTTGATTAGAATA-GATTTTTCAACCTT
* * *
9946610 ATTACACTTCTTTTATTTTATTTTGATTAGCATAAAGTTTTTCAACCTT
1 ACTACACTTCTTTTATTTTATTTTGATTAGAATAGA-TTTTTCAACCTT
* * * * * *
9946659 ACTACACTTCATCTATTTAACTTTGATTAGTATAGTTTTTTCAACCT
1 ACTACACTTCTTTTATTTTATTTTGATTAGAATAGATTTTTCAACCT
9946706 ATAAATAGAT
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
48 20 0.24
49 62 0.76
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (48 bp):
ACTACACTTCTTTTATTTTATTTTGATTAGAATAGATTTTTCAACCTT
Found at i:9950203 original size:16 final size:16
Alignment explanation
Indices: 9950182--9950214 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
9950172 TACAATACAA
9950182 AAGTGATAATTGAGGG
1 AAGTGATAATTGAGGG
9950198 AAGTGATAATTGAGGG
1 AAGTGATAATTGAGGG
9950214 A
1 A
9950215 GGTTAAGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.36, T:0.24
Consensus pattern (16 bp):
AAGTGATAATTGAGGG
Found at i:9953501 original size:15 final size:16
Alignment explanation
Indices: 9953483--9953519 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
9953473 AAAAACTAGG
*
9953483 AAAATAAAA-GGATTT
1 AAAATAAAAGGGATCT
9953498 AAAA-AAAAGGGATCT
1 AAAATAAAAGGGATCT
9953513 AAAATAA
1 AAAATAA
9953520 TGATAAAGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 4 0.21
15 13 0.68
16 2 0.11
ACGTcount: A:0.65, C:0.03, G:0.14, T:0.19
Consensus pattern (16 bp):
AAAATAAAAGGGATCT
Found at i:9955206 original size:15 final size:15
Alignment explanation
Indices: 9955186--9955236 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
9955176 TAGTGCTGAT
9955186 GTGGCAAGGGATGAC
1 GTGGCAAGGGATGAC
* * *
9955201 GTGGC-AGTGCTGAA
1 GTGGCAAGGGATGAC
*
9955215 GTGTCAAGGGATGAC
1 GTGGCAAGGGATGAC
9955230 GTGGCAA
1 GTGGCAA
9955237 AGTGGCAAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 10 0.37
15 17 0.63
ACGTcount: A:0.25, C:0.14, G:0.43, T:0.18
Consensus pattern (15 bp):
GTGGCAAGGGATGAC
Found at i:9955209 original size:29 final size:29
Alignment explanation
Indices: 9955151--9955235 Score: 100
Period size: 29 Copynumber: 3.0 Consensus size: 29
9955141 CTGACGTGTC
* ** * *
9955151 TGCTGACGTGGCAA-GGATGATATTGTAG
1 TGCTGAAGTGGCAAGGGATGACGTGGCAG
*
9955179 TGCTGATGTGGCAAGGGATGACGTGGCAG
1 TGCTGAAGTGGCAAGGGATGACGTGGCAG
*
9955208 TGCTGAAGTGTCAAGGGATGACGTGGCA
1 TGCTGAAGTGGCAAGGGATGACGTGGCA
9955236 AAGTGGCAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 13 0.27
29 36 0.73
ACGTcount: A:0.24, C:0.13, G:0.40, T:0.24
Consensus pattern (29 bp):
TGCTGAAGTGGCAAGGGATGACGTGGCAG
Found at i:9955457 original size:13 final size:12
Alignment explanation
Indices: 9955416--9955454 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
9955406 TTTTATTATT
*
9955416 TAAATTTAGA-A
1 TAAATTTAAATA
*
9955427 TAATTTTAAATA
1 TAAATTTAAATA
9955439 TAAATTTAAATA
1 TAAATTTAAATA
9955451 TAAA
1 TAAA
9955455 ATTGGACTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (12 bp):
TAAATTTAAATA
Found at i:9957300 original size:21 final size:21
Alignment explanation
Indices: 9957271--9957314 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
9957261 TATTTTATAA
9957271 TATTAATTAATAA-AATATTAT
1 TATTAATT-ATAATAATATTAT
* *
9957292 TATTTATTATAATACTATTAT
1 TATTAATTATAATAATATTAT
9957313 TA
1 TA
9957315 ATGAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTAATTATAATAATATTAT
Found at i:9957614 original size:2 final size:2
Alignment explanation
Indices: 9957607--9957631 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9957597 ACTTATACAT
9957607 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
9957632 TTAAAGTGGG
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:9960721 original size:3 final size:3
Alignment explanation
Indices: 9960713--9960737 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
9960703 GTTATTCTTT
9960713 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
9960738 GTTTTAAATA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9961992 original size:30 final size:30
Alignment explanation
Indices: 9961958--9962019 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
9961948 CAACTTAACA
* *
9961958 AACAAATATCTCTAAAATAGTAACAAAATT
1 AACAAATACCTCTAAAATAATAACAAAATT
*
9961988 AACAAATACCTCTAAAATAATAATAAAATT
1 AACAAATACCTCTAAAATAATAACAAAATT
9962018 AA
1 AA
9962020 TAATAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.26
Consensus pattern (30 bp):
AACAAATACCTCTAAAATAATAACAAAATT
Found at i:9962022 original size:12 final size:12
Alignment explanation
Indices: 9962000--9962028 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
9961990 CAAATACCTC
9962000 TAAAA-TAATAA
1 TAAAATTAATAA
9962011 TAAAATTAATAA
1 TAAAATTAATAA
9962023 TAAAAT
1 TAAAAT
9962029 AAGTTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATTAATAA
Found at i:9972912 original size:5 final size:5
Alignment explanation
Indices: 9972904--9972974 Score: 58
Period size: 5 Copynumber: 14.2 Consensus size: 5
9972894 CTTACAACCC
* * *
9972904 AAATA AAATA AAAT- AAACA AAGTA TAATAA AAATTCA AAATA AAAT-
1 AAATA AAATA AAATA AAATA AAATA AAAT-A AAA-T-A AAATA AAATA
*
9972950 -AATA AGATA AAATA AAATA AAATA A
1 AAATA AAATA AAATA AAATA AAATA A
9972975 TAAGTTTATA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
3 3 0.06
4 3 0.06
5 37 0.71
6 4 0.08
7 5 0.10
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:9972969 original size:23 final size:23
Alignment explanation
Indices: 9972906--9972978 Score: 78
Period size: 23 Copynumber: 3.0 Consensus size: 23
9972896 TACAACCCAA
9972906 ATAAAATAAAATAAACA-AAGTATA-
1 ATAAAATAAAATAAA-ATAA-TA-AG
9972930 ATAAAAATTCAAAATAAAATAATAAG
1 AT-AAAA-T-AAAATAAAATAATAAG
9972956 ATAAAATAAAATAAAATAATAAG
1 ATAAAATAAAATAAAATAATAAG
9972979 TTTATAAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
23 16 0.36
24 3 0.07
25 9 0.20
26 6 0.14
27 10 0.23
ACGTcount: A:0.71, C:0.03, G:0.04, T:0.22
Consensus pattern (23 bp):
ATAAAATAAAATAAAATAATAAG
Found at i:9972977 original size:18 final size:17
Alignment explanation
Indices: 9972904--9972974 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 17
9972894 CTTACAACCC
9972904 AAATAAAATAAAATAAA
1 AAATAAAATAAAATAAA
* **
9972921 CAAAGTATAATAAAAATTCA
1 -AAA-TAAAAT-AAAATAAA
* *
9972941 AAATAAAATAATAAGATA
1 AAATAAAATAA-AATAAA
9972959 AAATAAAATAAAATAA
1 AAATAAAATAAAATAA
9972975 TAAGTTTATA
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
17 5 0.12
18 22 0.54
19 8 0.20
20 6 0.15
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (17 bp):
AAATAAAATAAAATAAA
Found at i:9974436 original size:20 final size:20
Alignment explanation
Indices: 9974407--9974445 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
9974397 AACATTGATA
*
9974407 TTTATTTATTTTTATAAAAT
1 TTTATGTATTTTTATAAAAT
9974427 TTTATGTATTTTTATAAAA
1 TTTATGTATTTTTATAAAA
9974446 AAATAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTATGTATTTTTATAAAAT
Found at i:9977872 original size:2 final size:2
Alignment explanation
Indices: 9977865--9977889 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9977855 TATTAAAATA
9977865 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
9977890 AATAATCAAA
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:9990751 original size:14 final size:14
Alignment explanation
Indices: 9990732--9990759 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9990722 TATTTTATAC
9990732 TATTAAACATTTAT
1 TATTAAACATTTAT
9990746 TATTAAACATTTAT
1 TATTAAACATTTAT
9990760 AAATTATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
TATTAAACATTTAT
Found at i:9990875 original size:17 final size:17
Alignment explanation
Indices: 9990855--9990893 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
9990845 AAATAAAATT
9990855 TTAATTTATATAATT-TA
1 TTAATTTATA-AATTATA
9990872 TTAATTTATAAATTATA
1 TTAATTTATAAATTATA
9990889 TTAAT
1 TTAAT
9990894 AAATTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAATTTATAAATTATA
Found at i:9990878 original size:8 final size:8
Alignment explanation
Indices: 9990855--9990893 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
9990845 AAATAAAATT
9990855 TTAATTTA
1 TTAATTTA
9990863 TATAATTTA
1 T-TAATTTA
9990872 TTAATTTA
1 TTAATTTA
*
9990880 TAAATTATA
1 TTAATT-TA
9990889 TTAAT
1 TTAAT
9990894 AAATTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 13 0.48
9 14 0.52
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTAATTTA
Found at i:9990903 original size:16 final size:16
Alignment explanation
Indices: 9990884--9990914 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9990874 AATTTATAAA
9990884 TTATATTAATAAATTT
1 TTATATTAATAAATTT
*
9990900 TTATATTATTAAATT
1 TTATATTAATAAATT
9990915 ATAAACAATT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATATTAATAAATTT
Found at i:9990983 original size:21 final size:21
Alignment explanation
Indices: 9990943--9990983 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9990933 ATATTTAATA
*
9990943 ATATTAACATTATAATATTTT
1 ATATTAACATTATAACATTTT
* *
9990964 ATATTAATATTTTAACATTT
1 ATATTAACATTATAACATTT
9990984 AAAAAAATTA
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:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATTAACATTATAACATTTT
Found at i:9991092 original size:19 final size:21
Alignment explanation
Indices: 9991070--9991111 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 21
9991060 AAATTTTGAT
*
9991070 AAAAGAGTT-CTTTTTT-AAA
1 AAAAGAATTACTTTTTTCAAA
*
9991089 AAAATAATTACTTTTTTCAAA
1 AAAAGAATTACTTTTTTCAAA
9991110 AA
1 AA
9991112 GAATAGGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 7 0.37
20 7 0.37
21 5 0.26
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (21 bp):
AAAAGAATTACTTTTTTCAAA
Found at i:9991965 original size:3 final size:3
Alignment explanation
Indices: 9991957--9992013 Score: 91
Period size: 3 Copynumber: 19.3 Consensus size: 3
9991947 TACATCCCAA
9991957 AAT AAT AAT AAT AAT AAT AAT -AT ATAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
9992002 AAT AA- AAT AAT A
1 AAT AAT AAT AAT A
9992014 GAATATTCTA
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.08
3 44 0.86
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:9993110 original size:20 final size:19
Alignment explanation
Indices: 9993051--9993110 Score: 77
Period size: 20 Copynumber: 3.1 Consensus size: 19
9993041 GTTTTTCGAA
9993051 AAAGTCAAC-GTCACGGTC
1 AAAGTCAACGGTCACGGTC
* *
9993069 AAAGTCAACGATCAACGATC
1 AAAGTCAACGGTC-ACGGTC
9993089 AAAGTCAACGGTCAGCGGTC
1 AAAGTCAACGGTCA-CGGTC
9993109 AA
1 AA
9993111 CGATCAATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
18 9 0.26
19 3 0.09
20 23 0.66
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (19 bp):
AAAGTCAACGGTCACGGTC
Found at i:9993127 original size:27 final size:27
Alignment explanation
Indices: 9993072--9993135 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
9993062 CACGGTCAAA
*
9993072 GTCAACGATCAACGATCAAAGTCAACG
1 GTCAACGGTCAACGATCAAAGTCAACG
*
9993099 GTCAGCGGTCAACGATC-AA-TCACATCG
1 GTCAACGGTCAACGATCAAAGTCA-A-CG
9993126 GTCAACGGTC
1 GTCAACGGTC
9993136 GGTTAACATC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 3 0.09
26 3 0.09
27 26 0.81
ACGTcount: A:0.33, C:0.28, G:0.22, T:0.17
Consensus pattern (27 bp):
GTCAACGGTCAACGATCAAAGTCAACG
Found at i:9993170 original size:10 final size:10
Alignment explanation
Indices: 9993123--9993171 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
9993113 ATCAATCACA
9993123 TCGGTCAACGG
1 TCGGTCAAC-G
* *
9993134 TCGGTTAACA
1 TCGGTCAACG
9993144 TCGGTCAACG
1 TCGGTCAACG
* *
9993154 CCAGTCAACG
1 TCGGTCAACG
9993164 TCGGTCAA
1 TCGGTCAA
9993172 TGGTTTGACT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (10 bp):
TCGGTCAACG
Found at i:9993228 original size:15 final size:15
Alignment explanation
Indices: 9993208--9993237 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9993198 TGGTTCTTTT
9993208 GGTTTGGTTCAAATG
1 GGTTTGGTTCAAATG
*
9993223 GGTTTGGTTTAAATG
1 GGTTTGGTTCAAATG
9993238 AATTTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTTGGTTCAAATG
Found at i:9993247 original size:21 final size:21
Alignment explanation
Indices: 9993221--9993288 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
9993211 TTGGTTCAAA
9993221 TGGGTTTGGTTTAAATGAATT
1 TGGGTTTGGTTTAAATGAATT
*
9993242 TGGGTTTGGTTTAAATGAATG
1 TGGGTTTGGTTTAAATGAATT
*
9993263 TGGGTTTGGTTTAAATAGGATT
1 TGGGTTTGGTTTAAAT-GAATT
9993285 TGGG
1 TGGG
9993289 CTTAATGCGT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
21 36 0.84
22 7 0.16
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (21 bp):
TGGGTTTGGTTTAAATGAATT
Found at i:9993686 original size:20 final size:21
Alignment explanation
Indices: 9993657--9993704 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
9993647 ATTAAAAGAG
9993657 GAAG-AAAAT-AGAAAAGAAA
1 GAAGAAAAATAAGAAAAGAAA
* *
9993676 GAAGAAAAATAAGAAATGAAT
1 GAAGAAAAATAAGAAAAGAAA
9993697 G-AGAAAAA
1 GAAGAAAAA
9993705 GAAAAGAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 12 0.48
21 9 0.36
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (21 bp):
GAAGAAAAATAAGAAAAGAAA
Found at i:9999082 original size:3 final size:3
Alignment explanation
Indices: 9999074--9999106 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
9999064 CATCCCAAAA
*
9999074 AAT AAT AAT AAT AAT GAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
9999107 GAATAGAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:10000173 original size:13 final size:13
Alignment explanation
Indices: 10000151--10000220 Score: 70
Period size: 13 Copynumber: 5.3 Consensus size: 13
10000141 TTTCGAAAAA
*
10000151 GTCAACGTCAACG
1 GTCAAAGTCAACG
10000164 GTCAAAGTCAACG
1 GTCAAAGTCAACG
* *
10000177 GTCAACGGTCAA-A
1 GTCAA-AGTCAACG
*
10000190 GTCAACGATCAACG
1 GTCAAAG-TCAACG
*
10000204 ATCAAAGTCAACG
1 GTCAAAGTCAACG
10000217 GTCA
1 GTCA
10000221 GCGGTCACGA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
12 1 0.02
13 35 0.76
14 10 0.22
ACGTcount: A:0.37, C:0.26, G:0.21, T:0.16
Consensus pattern (13 bp):
GTCAAAGTCAACG
Found at i:10000180 original size:7 final size:7
Alignment explanation
Indices: 10000151--10000227 Score: 72
Period size: 7 Copynumber: 11.6 Consensus size: 7
10000141 TTTCGAAAAA
10000151 GTCAAC-
1 GTCAACG
10000157 GTCAACG
1 GTCAACG
*
10000164 GTCAA-A
1 GTCAACG
10000170 GTCAACG
1 GTCAACG
10000177 GTCAACG
1 GTCAACG
*
10000184 GTCAA-A
1 GTCAACG
10000190 GTCAACG
1 GTCAACG
*
10000197 ATCAACG
1 GTCAACG
* *
10000204 ATCAA-A
1 GTCAACG
10000210 GTCAACG
1 GTCAACG
*
10000217 GTCAGCG
1 GTCAACG
10000224 GTCA
1 GTCA
10000228 CGATCAATCA
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
6 20 0.34
7 38 0.66
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:10000182 original size:20 final size:20
Alignment explanation
Indices: 10000148--10000227 Score: 126
Period size: 20 Copynumber: 4.0 Consensus size: 20
10000138 GTTTTTCGAA
10000148 AAAGTCAAC-GTCAACGGTC
1 AAAGTCAACGGTCAACGGTC
10000167 AAAGTCAACGGTCAACGGTC
1 AAAGTCAACGGTCAACGGTC
* *
10000187 AAAGTCAACGATCAACGATC
1 AAAGTCAACGGTCAACGGTC
*
10000207 AAAGTCAACGGTCAGCGGTC
1 AAAGTCAACGGTCAACGGTC
10000227 A
1 A
10000228 CGATCAATCA
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 9 0.16
20 46 0.84
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.15
Consensus pattern (20 bp):
AAAGTCAACGGTCAACGGTC
Done.