Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167938.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_20, whole genome shotgun sequence
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: 19866354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 74000 characters in sequence are not A, C, G, or T
File 43 of 100
Found at i:11023262 original size:15 final size:15
Alignment explanation
Indices: 11023111--11023271 Score: 119
Period size: 15 Copynumber: 10.5 Consensus size: 15
11023101 TTTGTGGTTT
*
11023111 GGGGTTTTGA-TTTA
1 GGGGTTTGGATTTTA
*
11023125 AGGGTTTGGATTTTA
1 GGGGTTTGGATTTTA
*
11023140 GGGATTTTGGATTTT-
1 GGG-GTTTGGATTTTA
*
11023155 GGGGTTTGAATTTTA
1 GGGGTTTGGATTTTA
*
11023170 GGGTTTTGGAATTTTA
1 GGGGTTTGG-ATTTTA
* * *
11023186 AGGGTTCGGATTTAA
1 GGGGTTTGGATTTTA
** *
11023201 GAGATTTTAGATTTTTA
1 G-GGGTTTGGA-TTTTA
*
11023218 AGGGTTTGGATTTTA
1 GGGGTTTGGATTTTA
*
11023233 GAAGGTTTTGGATTTTA
1 G--GGGTTTGGATTTTA
*
11023250 GGGGTTTGAATTTTA
1 GGGGTTTGGATTTTA
*
11023265 GGAGTTT
1 GGGGTTT
11023272 TAGAAACCTG
Statistics
Matches: 112, Mismatches: 27, Indels: 15
0.73 0.18 0.10
Matches are distributed among these distances:
14 17 0.15
15 44 0.39
16 33 0.29
17 18 0.16
ACGTcount: A:0.20, C:0.01, G:0.32, T:0.47
Consensus pattern (15 bp):
GGGGTTTGGATTTTA
Found at i:11024669 original size:15 final size:17
Alignment explanation
Indices: 11024638--11024670 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
11024628 TATCTTTTTA
11024638 TATTATTTTTTGATATT
1 TATTATTTTTTGATATT
11024655 TATT-TTTTTTG-TATT
1 TATTATTTTTTGATATT
11024670 T
1 T
11024671 CATATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 7 0.44
17 4 0.25
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (17 bp):
TATTATTTTTTGATATT
Found at i:11025821 original size:36 final size:40
Alignment explanation
Indices: 11025780--11025854 Score: 95
Period size: 36 Copynumber: 2.0 Consensus size: 40
11025770 TATTTAAATT
* *
11025780 AGATTTTATTGAT-AACA-ATATTT-AATTAT-TATTTAC
1 AGATTTTACTGATAAAAATATATTTAAATTATATATTTAC
*
11025816 AGATTTTGCTGATAAAAATATATTTAAATTATATATTTA
1 AGATTTTACTGATAAAAATATATTTAAATTATATATTTA
11025855 TAAAAGAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 11 0.34
37 3 0.09
38 6 0.19
39 6 0.19
40 6 0.19
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (40 bp):
AGATTTTACTGATAAAAATATATTTAAATTATATATTTAC
Found at i:11026444 original size:30 final size:30
Alignment explanation
Indices: 11026376--11026458 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
11026366 GTACAATCAT
*
11026376 AAATTTAATTGAAATAAAAATAGATATTTAA
1 AAATTTAATT-AAATAAAAATAAATATTTAA
** *
11026407 AGGTTTAATTAAATGAAAATAAATATTTAA
1 AAATTTAATTAAATAAAAATAAATATTTAA
* *
11026437 AAATTTAA-TAATTTAAAATAAA
1 AAATTTAATTAAATAAAAATAAA
11026459 AAAATTTAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 12 0.27
30 24 0.55
31 8 0.18
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (30 bp):
AAATTTAATTAAATAAAAATAAATATTTAA
Found at i:11026913 original size:21 final size:21
Alignment explanation
Indices: 11026875--11026915 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11026865 ATACATTATT
*
11026875 TTTAAAAACTAAATAAATAAG
1 TTTAAAAACTAAACAAATAAG
11026896 TTTAAAAA-TATAACAAATAA
1 TTTAAAAACTA-AACAAATAA
11026916 TATTATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.29
Consensus pattern (21 bp):
TTTAAAAACTAAACAAATAAG
Found at i:11026952 original size:22 final size:23
Alignment explanation
Indices: 11026924--11026969 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
11026914 AATATTATTA
*
11026924 ATTTAATATGAT-ATTTTTAAAT
1 ATTTAATATGATGATATTTAAAT
*
11026946 ATTTAATCTGATGATATTTAAAT
1 ATTTAATATGATGATATTTAAAT
11026969 A
1 A
11026970 AATATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (23 bp):
ATTTAATATGATGATATTTAAAT
Found at i:11027465 original size:22 final size:24
Alignment explanation
Indices: 11027426--11027469 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
11027416 TAAAATTAAT
11027426 AATAATAATTTAACAATAATAAAA
1 AATAATAATTTAACAATAATAAAA
*
11027450 AATAA-AA-TTAATAATAATAA
1 AATAATAATTTAACAATAATAA
11027470 TTTAACGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 2 0.11
24 5 0.26
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (24 bp):
AATAATAATTTAACAATAATAAAA
Found at i:11028412 original size:22 final size:21
Alignment explanation
Indices: 11028387--11028428 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
11028377 TAATTTTAAT
11028387 TAATTTAA-AATAATAATTTATA
1 TAATTTAATAA-AA-AATTTATA
11028409 TAATTTAATAAAAAATTTAT
1 TAATTTAATAAAAAATTTAT
11028429 TTACTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 10 0.53
23 2 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAATTTAATAAAAAATTTATA
Found at i:11037420 original size:14 final size:14
Alignment explanation
Indices: 11037385--11037420 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
11037375 AATCTTACAT
11037385 TTATTTTATTAAAA
1 TTATTTTATTAAAA
*
11037399 TTACTTTATTAAAA
1 TTATTTTATTAAAA
*
11037413 TTGTTTTA
1 TTATTTTA
11037421 AGTCAAGTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (14 bp):
TTATTTTATTAAAA
Found at i:11039345 original size:20 final size:19
Alignment explanation
Indices: 11039322--11039387 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
11039312 TTTAATATTT
11039322 TAAAAAGTTTTGAAAAATTC
1 TAAAAAGTTTT-AAAAATTC
*
11039342 TAAAAAGATTTTAAAAATTA
1 TAAAAAG-TTTTAAAAATTC
* **
11039362 TAAAAAAATTCAAAAAATTC
1 T-AAAAAGTTTTAAAAATTC
11039382 TAAAAA
1 TAAAAA
11039388 ATTCGAAAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 5 0.13
20 25 0.64
21 9 0.23
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (19 bp):
TAAAAAGTTTTAAAAATTC
Found at i:11039347 original size:10 final size:10
Alignment explanation
Indices: 11039334--11039396 Score: 67
Period size: 10 Copynumber: 6.3 Consensus size: 10
11039324 AAAAGTTTTG
11039334 AAAAATTCTA
1 AAAAATTCTA
*
11039344 AAAAGATT-TT
1 AAAA-ATTCTA
*
11039354 AAAAATTATAA
1 AAAAATTCT-A
11039365 AAAAATTC-A
1 AAAAATTCTA
11039374 AAAAATTCTA
1 AAAAATTCTA
*
11039384 AAAAATTCGA
1 AAAAATTCTA
11039394 AAA
1 AAA
11039397 GTAATTTGGC
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
9 12 0.27
10 23 0.51
11 10 0.22
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.27
Consensus pattern (10 bp):
AAAAATTCTA
Found at i:11039388 original size:20 final size:20
Alignment explanation
Indices: 11039334--11039388 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
11039324 AAAAGTTTTG
* **
11039334 AAAAATTCTAAAAAGATTTT
1 AAAAATTCTAAAAAAATTCA
*
11039354 AAAAATTATAAAAAAATTCA
1 AAAAATTCTAAAAAAATTCA
11039374 AAAAATTCTAAAAAA
1 AAAAATTCTAAAAAA
11039389 TTCGAAAAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.27
Consensus pattern (20 bp):
AAAAATTCTAAAAAAATTCA
Found at i:11039755 original size:18 final size:19
Alignment explanation
Indices: 11039726--11039766 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
11039716 TTTGAAGTTT
11039726 TTTTTTGAAAATTTTAAAA
1 TTTTTTGAAAATTTTAAAA
*
11039745 TTTTTTG-AAATTTTATAA
1 TTTTTTGAAAATTTTAAAA
11039763 TTTT
1 TTTT
11039767 AAAATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTTTTGAAAATTTTAAAA
Found at i:11039810 original size:24 final size:24
Alignment explanation
Indices: 11039778--11039826 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
11039768 AAATTAAAAA
*
11039778 AATTTTTTTAGAAATTTTCTTTTT
1 AATTTTTTTAGAAAATTTCTTTTT
*
11039802 AATTTTTTTTGAAAATTTCTTTTT
1 AATTTTTTTAGAAAATTTCTTTTT
11039826 A
1 A
11039827 TGTTAACGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (24 bp):
AATTTTTTTAGAAAATTTCTTTTT
Found at i:11045609 original size:33 final size:35
Alignment explanation
Indices: 11045549--11045615 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 35
11045539 CTCTGTGGTA
**
11045549 TATCAGGAATTTTTTGAATCAATAG-TTTGTGATG
1 TATCAGGAATTTTTCAAATCAATAGTTTTGTGATG
* *
11045583 TATCAGGAGTTTTTCAAATTAA-AGTTTTGTGAT
1 TATCAGGAATTTTTCAAATCAATAGTTTTGTGAT
11045616 AAACATCATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 2 0.07
34 26 0.93
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.45
Consensus pattern (35 bp):
TATCAGGAATTTTTCAAATCAATAGTTTTGTGATG
Found at i:11046381 original size:75 final size:75
Alignment explanation
Indices: 11046258--11046408 Score: 275
Period size: 75 Copynumber: 2.0 Consensus size: 75
11046248 TTGCACTGCG
* *
11046258 CAAGTGCAACCATGCAGGTTTAATACTTTTTCTCTCTGGGTTGGTAGATTTGTTATGCTTTCTTC
1 CAAGTGCAACCATGCAGGTTTAATACTTTTTCTCTCTGGGTTGGTAGATTTGTCATGCTTGCTTC
11046323 AGGCATCCAA
66 AGGCATCCAA
*
11046333 CAAGTGCAACCATGCAGGTTTAATCCTTTTTCTCTCTGGGTTGGTAGATTTGTCATGCTTGCTTC
1 CAAGTGCAACCATGCAGGTTTAATACTTTTTCTCTCTGGGTTGGTAGATTTGTCATGCTTGCTTC
11046398 AGGCATCCAA
66 AGGCATCCAA
11046408 C
1 C
11046409 CCATTTAGCT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (75 bp):
CAAGTGCAACCATGCAGGTTTAATACTTTTTCTCTCTGGGTTGGTAGATTTGTCATGCTTGCTTC
AGGCATCCAA
Found at i:11047322 original size:7 final size:7
Alignment explanation
Indices: 11047310--11047339 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
11047300 AAAGTAGACT
11047310 CCTCACC
1 CCTCACC
11047317 CCTCACC
1 CCTCACC
11047324 CCTCACC
1 CCTCACC
11047331 CCTCACC
1 CCTCACC
11047338 CC
1 CC
11047340 ACCCAGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.73, G:0.00, T:0.13
Consensus pattern (7 bp):
CCTCACC
Found at i:11047864 original size:13 final size:14
Alignment explanation
Indices: 11047846--11047874 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11047836 CCTAGCATAC
11047846 AAAAAAG-AAAGAA
1 AAAAAAGAAAAGAA
11047859 AAAAAAGAAAAGAA
1 AAAAAAGAAAAGAA
11047873 AA
1 AA
11047875 GAAGAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAGAA
Found at i:11052515 original size:23 final size:21
Alignment explanation
Indices: 11052475--11052546 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 21
11052465 TAAAATATCT
*
11052475 TAAAATATATTTTATTAATAA
1 TAAAATAAATTTTATTAATAA
**
11052496 TAAAATACAATTTTATTTAATTT
1 TAAAATA-AATTTTA-TTAATAA
* * *
11052519 TAAAATATA-TTTA-AAATAT
1 TAAAATAAATTTTATTAATAA
11052538 TAAAATAAA
1 TAAAATAAA
11052547 ATAGTATAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 12 0.29
21 11 0.26
22 7 0.17
23 12 0.29
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAATAAATTTTATTAATAA
Found at i:11052530 original size:22 final size:21
Alignment explanation
Indices: 11052474--11052544 Score: 74
Period size: 23 Copynumber: 3.4 Consensus size: 21
11052464 ATAAAATATC
11052474 TTAAAATATATTTTATTAATA
1 TTAAAATATATTTTATTAATA
* * *
11052495 ATAAAATACAATTTTATTTAATT
1 TTAAAATA-TATTTTA-TTAATA
*
11052518 TTAAAATATA-TTTA-AAATA
1 TTAAAATATATTTTATTAATA
11052537 TTAAAATA
1 TTAAAATA
11052545 AAATAGTATA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 11 0.27
21 11 0.27
22 7 0.17
23 12 0.29
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (21 bp):
TTAAAATATATTTTATTAATA
Found at i:11054578 original size:3 final size:3
Alignment explanation
Indices: 11054570--11054601 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
11054560 TGAATTTAAA
11054570 ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT A
11054602 AGAAACTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:11062222 original size:2 final size:2
Alignment explanation
Indices: 11062215--11062242 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11062205 TTAATAAACA
11062215 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
11062243 TTGATTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11066521 original size:11 final size:11
Alignment explanation
Indices: 11066507--11066536 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
11066497 TCAAATTAAT
11066507 CTAGAATATTA
1 CTAGAATATTA
11066518 CTAGAATATTA
1 CTAGAATATTA
*
11066529 TTAGAATA
1 CTAGAATA
11066537 ATATCATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.37
Consensus pattern (11 bp):
CTAGAATATTA
Found at i:11067306 original size:23 final size:24
Alignment explanation
Indices: 11067264--11067309 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
11067254 TTTATTTGTT
11067264 TATTATTTATGTTATTTATTTTAC
1 TATTATTTATGTTATTTATTTTAC
*
11067288 TATTGTTTATG-TATTTATTTTA
1 TATTATTTATGTTATTTATTTTA
11067310 TCTGTCTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (24 bp):
TATTATTTATGTTATTTATTTTAC
Found at i:11080324 original size:41 final size:40
Alignment explanation
Indices: 11080267--11080395 Score: 161
Period size: 41 Copynumber: 3.2 Consensus size: 40
11080257 TTGAGGGGCT
* *
11080267 TTTATTTTTTCAAAGTTGTGATGTCTCTGTTTAGAGGAGC
1 TTTATTTTTTCAAAGTTGTGATGCCTCTGTTTAAAGGAGC
* * *
11080307 ATTTATTTTTTCAAAGTTATGATGCCTATGTTTAAAAGAGC
1 -TTTATTTTTTCAAAGTTGTGATGCCTCTGTTTAAAGGAGC
* *
11080348 TTTTTATTTTTT-AAAGTTGTGGTGCCTCTATTTAAAGGAGC
1 --TTTATTTTTTCAAAGTTGTGATGCCTCTGTTTAAAGGAGC
11080389 TTTATTT
1 TTTATTT
11080396 ATTTTTCAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 7 0.09
41 59 0.78
42 10 0.13
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.49
Consensus pattern (40 bp):
TTTATTTTTTCAAAGTTGTGATGCCTCTGTTTAAAGGAGC
Found at i:11080430 original size:84 final size:84
Alignment explanation
Indices: 11080266--11080559 Score: 225
Period size: 84 Copynumber: 3.5 Consensus size: 84
11080256 GTTGAGGGGC
* * *
11080266 TTTTATTTTTTCAAAGTTGTGATGTCTCTGTTTAGAGGAGCATTTATTTTTTCAAAGTTATGATG
1 TTTTATTTTTTCAAAGTTGTGATGCCTCTATTTAAAGGAGCATTTATTTTTTCAAAGTTATGATG
*
11080331 CCTATGTTTAAAAGAGC-T
66 ACTATGTTTAAAAGAGCTT
*
11080349 TTTTATTTTTT-AAAGTTGTGGTGCCTCTATTTAAAGGAGC-TTTATTTATTTTTCAAAGTCGT-
1 TTTTATTTTTTCAAAGTTGTGATGCCTCTATTTAAAGGAGCATTTA--T-TTTTTCAAAGT--TA
* *
11080411 TGA-GACTTTGTTTAGAAGAGCTT
61 TGATGACTATGTTTAAAAGAGCTT
* * * * *
11080434 TCTTTA-TTTTTCAAAAAATCAT-TGA-GCCTCTATTTAGATGAGCATTTTTTATTTTCAAAGTC
1 T-TTTATTTTTTC--AAAGT--TGTGATGCCTCTATTTAAAGGAGCATTTATT-TTTTCAAAGTT
* * *
11080496 ATTGA-GCCTATG-CTAAAATGAGC-C
60 A-TGATGACTATGTTTAAAA-GAGCTT
* *
11080520 TTTTATTTTTTTCAAAATTGTGA-GCCTCTGTTTAAAGGAG
1 TTTTA-TTTTTTCAAAGTTGTGATGCCTCTATTTAAAGGAG
11080560 TTTTGTGACT
Statistics
Matches: 170, Mismatches: 21, Indels: 39
0.74 0.09 0.17
Matches are distributed among these distances:
81 4 0.02
82 25 0.15
83 13 0.08
84 43 0.25
85 19 0.11
86 11 0.06
87 29 0.17
88 20 0.12
89 5 0.03
90 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.46
Consensus pattern (84 bp):
TTTTATTTTTTCAAAGTTGTGATGCCTCTATTTAAAGGAGCATTTATTTTTTCAAAGTTATGATG
ACTATGTTTAAAAGAGCTT
Found at i:11080485 original size:45 final size:43
Alignment explanation
Indices: 11080307--11080504 Score: 156
Period size: 43 Copynumber: 4.6 Consensus size: 43
11080297 TTAGAGGAGC
* * * *
11080307 ATTTATTTTTTCAAAGTTA-TGATGCCTATGTTTAAAAGAGC-TT
1 ATTTA-TTTTTCAAAGTCATTGA-GCCTCTATTTAGAAGAGCTTT
* ** * *
11080350 -TTTATTTTTTAAAGTTGTGGTGCCTCTATTTA-AAGGAGCTTT
1 ATTTATTTTTCAAAGTCATTGAGCCTCTATTTAGAA-GAGCTTT
* * * *
11080392 ATTTATTTTTCAAAGTCGTTGAGACTTTGTTTAGAAGAGCTTT
1 ATTTATTTTTCAAAGTCATTGAGCCTCTATTTAGAAGAGCTTT
* * *
11080435 CTTTATTTTTCAAAAAATCATTGAGCCTCTATTTAGATGAGCATTT
1 ATTTATTTTTC--AAAGTCATTGAGCCTCTATTTAGAAGAGC-TTT
11080481 -TTTA-TTTTCAAAGTCATTGAGCCT
1 ATTTATTTTTCAAAGTCATTGAGCCT
11080505 ATGCTAAAAT
Statistics
Matches: 126, Mismatches: 21, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
40 2 0.02
41 24 0.19
42 21 0.17
43 42 0.33
44 7 0.06
45 27 0.21
46 3 0.02
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (43 bp):
ATTTATTTTTCAAAGTCATTGAGCCTCTATTTAGAAGAGCTTT
Found at i:11080772 original size:4 final size:4
Alignment explanation
Indices: 11080763--11080827 Score: 64
Period size: 4 Copynumber: 16.0 Consensus size: 4
11080753 TCATTAGTTA
11080763 ATTT ATTT A-TT ATTT ATGTT ATTT ATGTT ATTT ATTT -TTCT A-TT ATTT
1 ATTT ATTT ATTT ATTT AT-TT ATTT AT-TT ATTT ATTT ATT-T ATTT ATTT
*
11080811 ATGT ATTT ATTTT ATTT
1 ATTT ATTT A-TTT ATTT
11080828 GTCTAGTTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
3 7 0.13
4 33 0.63
5 12 0.23
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:11080786 original size:9 final size:9
Alignment explanation
Indices: 11080772--11080827 Score: 59
Period size: 9 Copynumber: 6.7 Consensus size: 9
11080762 AATTTATTTA
11080772 TTATTTATG
1 TTATTTATG
11080781 TTATTTATG
1 TTATTTATG
11080790 TTATTTAT-
1 TTATTTATG
11080798 TT-TTCTA--
1 TTATT-TATG
11080805 TTATTTATG
1 TTATTTATG
*
11080814 -TATTTATT
1 TTATTTATG
11080822 TTATTT
1 TTATTT
11080828 GTCTAGTTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
7 6 0.15
8 13 0.32
9 22 0.54
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.71
Consensus pattern (9 bp):
TTATTTATG
Found at i:11087128 original size:37 final size:37
Alignment explanation
Indices: 11087087--11087161 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
11087077 TTTAAAAAAT
* *
11087087 AAAT-AAATAATTTTATTTTAATTTTATATCAAATATA
1 AAATAAAATAATATTA-TTTAATTTAATATCAAATATA
* * *
11087124 AAATAAAATGATATTATTTAATTTAATCTCATATATA
1 AAATAAAATAATATTATTTAATTTAATATCAAATATA
11087161 A
1 A
11087162 TATTATCTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 23 0.72
38 9 0.28
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
AAATAAAATAATATTATTTAATTTAATATCAAATATA
Found at i:11087973 original size:14 final size:14
Alignment explanation
Indices: 11087954--11087986 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
11087944 TGTTTGAGGC
*
11087954 TTTTTATTTTTATT
1 TTTTTATTATTATT
11087968 TTTTTATTATTATT
1 TTTTTATTATTATT
11087982 TTTTT
1 TTTTT
11087987 TAAAATTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTATTATTATT
Found at i:11088387 original size:29 final size:30
Alignment explanation
Indices: 11088326--11088389 Score: 94
Period size: 29 Copynumber: 2.1 Consensus size: 30
11088316 ACAATTGATT
11088326 TTTAAATTATAATAAAATATTTAATATAATA
1 TTTAAATTATAAT-AAATATTTAATATAATA
* *
11088357 TTTAAATTTTAAT-AATCTTTAATATAATA
1 TTTAAATTATAATAAATATTTAATATAATA
11088386 TTTA
1 TTTA
11088390 TTTTGAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 19 0.61
31 12 0.39
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (30 bp):
TTTAAATTATAATAAATATTTAATATAATA
Found at i:11091104 original size:99 final size:98
Alignment explanation
Indices: 11090933--11091130 Score: 342
Period size: 99 Copynumber: 2.0 Consensus size: 98
11090923 TATCCAACTT
* *
11090933 ATATTTATACAGATATAAAAGTATGAGGTTCTGATAGTTCATATGCTATAGTAAAGTGTAACGAT
1 ATATTTATACAGATATAAAAGTATGAGGTTCCGATAGTTCATATGCTATAGTAAAGTGTAAAGAT
11090998 GAGCAAAAGAGTGCTGCTAAAATCTATATGACAC
66 GAGCAAAAGAGTGCTGCT-AAATCTATATGACAC
* *
11091032 ATATTTCTACAGGTATAAAAGTATGAGGTTCCGATAGTTCATATGCTATAGTAAAGTGTAAAGAT
1 ATATTTATACAGATATAAAAGTATGAGGTTCCGATAGTTCATATGCTATAGTAAAGTGTAAAGAT
*
11091097 GAGCAAAAGAGTGGTGCTAAATCTATATGACAC
66 GAGCAAAAGAGTGCTGCTAAATCTATATGACAC
11091130 A
1 A
11091131 CATACAGTAA
Statistics
Matches: 94, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
98 16 0.17
99 78 0.83
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (98 bp):
ATATTTATACAGATATAAAAGTATGAGGTTCCGATAGTTCATATGCTATAGTAAAGTGTAAAGAT
GAGCAAAAGAGTGCTGCTAAATCTATATGACAC
Found at i:11093255 original size:27 final size:27
Alignment explanation
Indices: 11093198--11093262 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 27
11093188 ATATATTTAG
* *
11093198 TAAATAATT-TTTT-TATTAAATAATA
1 TAAATAATTATTTTAAATTAAATAAAA
*
11093223 TAAATAATTATTTTAAATTAATTAAAA
1 TAAATAATTATTTTAAATTAAATAAAA
*
11093250 TTAAT-A-TATTTTA
1 TAAATAATTATTTTA
11093263 TTGAAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 16 0.47
26 5 0.15
27 13 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TAAATAATTATTTTAAATTAAATAAAA
Found at i:11094289 original size:15 final size:16
Alignment explanation
Indices: 11094215--11094290 Score: 55
Period size: 18 Copynumber: 4.4 Consensus size: 16
11094205 ATAGTGACGT
11094215 TATAATTATTATATTAA
1 TATAA-TATTATATTAA
* * *
11094232 TAAAATAGTATTTTTATTA
1 TATAATATTA-TATTA--A
*
11094251 TAAAATATTATATTAA
1 TATAATATTATATTAA
11094267 TAAATAATATTATATTAA
1 T--ATAATATTATATTAA
11094285 T-TAATA
1 TATAATA
11094291 AATAATAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
15 5 0.10
16 6 0.12
17 8 0.17
18 19 0.40
19 10 0.21
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (16 bp):
TATAATATTATATTAA
Found at i:11094289 original size:22 final size:23
Alignment explanation
Indices: 11094255--11094297 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
11094245 TTATTATAAA
11094255 ATATTATATTAATAAATAATATT
1 ATATTATATTAATAAATAATATT
11094278 ATATTA-ATTAATAAATAATA
1 ATATTATATTAATAAATAATA
11094298 AAATCTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATTATATTAATAAATAATATT
Found at i:11094334 original size:26 final size:25
Alignment explanation
Indices: 11094305--11094373 Score: 63
Period size: 24 Copynumber: 2.8 Consensus size: 25
11094295 ATAAAATCTA
11094305 TTAACAATATATTATAATATTATT-T
1 TTAA-AATATATTATAATATTATTAT
* *
11094330 TTTAAATATTTTATAATA-TATTAT
1 TTAAAATATATTATAATATTATTAT
* *
11094354 TTATTAATATA-AATAATATT
1 TTA-AAATATATTATAATATT
11094374 GTATTAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
23 4 0.11
24 22 0.63
25 9 0.26
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (25 bp):
TTAAAATATATTATAATATTATTAT
Found at i:11094343 original size:24 final size:23
Alignment explanation
Indices: 11094310--11094356 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
11094300 ATCTATTAAC
*
11094310 AATATATTATAATATTATTTTTTA
1 AATATATTATAATA-TATTATTTA
*
11094334 AATATTTTATAATATATTATTTA
1 AATATATTATAATATATTATTTA
11094357 TTAATATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
AATATATTATAATATATTATTTA
Found at i:11094361 original size:15 final size:15
Alignment explanation
Indices: 11094321--11094364 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
11094311 ATATATTATA
*
11094321 ATATTATTTTTTAA-
1 ATATTATTTATTAAT
11094335 ATA-T-TTTA-TAAT
1 ATATTATTTATTAAT
11094347 ATATTATTTATTAAT
1 ATATTATTTATTAAT
11094362 ATA
1 ATA
11094365 AATAATATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
11 3 0.12
12 6 0.24
13 2 0.08
14 7 0.28
15 7 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATTATTTATTAAT
Found at i:11094378 original size:20 final size:19
Alignment explanation
Indices: 11094341--11094386 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
11094331 TTAAATATTT
*
11094341 TATAATATATTATTTATTAA
1 TATAA-ATAATATTTATTAA
11094361 TATAAATAATATTGTATTAA
1 TATAAATAATATT-TATTAA
*
11094381 AATAAA
1 TATAAA
11094387 ATATTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
TATAAATAATATTTATTAA
Found at i:11094418 original size:19 final size:19
Alignment explanation
Indices: 11094391--11094448 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
11094381 AATAAAATAT
*
11094391 TAAAAAAATATTATATTAA
1 TAAATAAATATTATATTAA
**
11094410 TAAATAAATAACATATTAA
1 TAAATAAATATTATATTAA
*
11094429 TAAAT-ATTATTATATTAA
1 TAAATAAATATTATATTAA
11094447 TA
1 TA
11094449 TTATTGTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 12 0.36
19 21 0.64
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATAAATATTATATTAA
Found at i:11094426 original size:35 final size:37
Alignment explanation
Indices: 11094380--11094448 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
11094370 TATTGTATTA
11094380 AAATAAAATATTAA-AAA-AATATTATATTAATAAAT
1 AAATAAAATATTAATAAATAATATTATATTAATAAAT
* *
11094415 AAATAACATATTAATAAATATTATTATATTAATA
1 AAATAAAATATTAATAAATAATATTATATTAATA
11094449 TTATTGTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 13 0.43
36 3 0.10
37 14 0.47
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (37 bp):
AAATAAAATATTAATAAATAATATTATATTAATAAAT
Found at i:11097615 original size:18 final size:18
Alignment explanation
Indices: 11097592--11097628 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
11097582 CAAAGAATGC
11097592 AGTTAAATGTTACTCTAG
1 AGTTAAATGTTACTCTAG
11097610 AGTTAAATGTTACTCTAG
1 AGTTAAATGTTACTCTAG
11097628 A
1 A
11097629 TATTTGTTGA
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:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (18 bp):
AGTTAAATGTTACTCTAG
Found at i:11098853 original size:28 final size:27
Alignment explanation
Indices: 11098822--11098890 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 27
11098812 AGGGTTTCGA
*
11098822 GATTTAGGGTCTT-GGATTTTAGGATTTT
1 GATTTAGGGT-TTGGGA-TTTAAGATTTT
11098850 GATTTCAGGGTTTGGGATTTAAGATTTT
1 GATTT-AGGGTTTGGGATTTAAGATTTT
11098878 -AGTTTAGGGTTTG
1 GA-TTTAGGGTTTG
11098891 TTAGGGTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
27 9 0.24
28 20 0.54
29 8 0.22
ACGTcount: A:0.19, C:0.03, G:0.30, T:0.48
Consensus pattern (27 bp):
GATTTAGGGTTTGGGATTTAAGATTTT
Found at i:11099007 original size:28 final size:29
Alignment explanation
Indices: 11098970--11099079 Score: 86
Period size: 28 Copynumber: 3.9 Consensus size: 29
11098960 TTTTAAAGGA
*
11098970 TTTAAAGTTTTAG-TTTAAGGGTTTGGGG
1 TTTAAGGTTTTAGATTTAAGGGTTTGGGG
*
11098998 TTTAAGGTTTT-GATTTAA-GGTTTAAAGGG
1 TTTAAGGTTTTAGATTTAAGGGTTT--GGGG
* * * *
11099027 TAT-AGAGTTTTAGTTTTGAGGATTTGGGG
1 TTTAAG-GTTTTAGATTTAAGGGTTTGGGG
* *
11099056 TTTAAGGTTTT-GGTTTTAGGGTTT
1 TTTAAGGTTTTAGATTTAAGGGTTT
11099080 AAAAGGTTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
27 6 0.09
28 27 0.42
29 20 0.31
30 7 0.11
31 4 0.06
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (29 bp):
TTTAAGGTTTTAGATTTAAGGGTTTGGGG
Found at i:11099011 original size:58 final size:58
Alignment explanation
Indices: 11098946--11099082 Score: 177
Period size: 58 Copynumber: 2.3 Consensus size: 58
11098936 CAAAATTAGA
* * *
11098946 GTTTTGATTTTAGATTTTAAAGGATTTAAAGTTTTAG-TTTAAGGGTTTGGGGTTTAAG
1 GTTTTGATTTTAG-GTTTAAAGGATATAAAGTTTTAGTTTTAAGGATTTGGGGTTTAAG
* * * *
11099004 GTTTTGATTTAAGGTTTAAAGGGTATAGAGTTTTAGTTTTGAGGATTTGGGGTTTAAG
1 GTTTTGATTTTAGGTTTAAAGGATATAAAGTTTTAGTTTTAAGGATTTGGGGTTTAAG
*
11099062 GTTTTGGTTTTAGGGTTTAAA
1 GTTTTGATTTTA-GGTTTAAA
11099083 AGGTTTATGG
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 19 0.28
58 41 0.60
59 8 0.12
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.47
Consensus pattern (58 bp):
GTTTTGATTTTAGGTTTAAAGGATATAAAGTTTTAGTTTTAAGGATTTGGGGTTTAAG
Found at i:11102166 original size:30 final size:30
Alignment explanation
Indices: 11102112--11102197 Score: 118
Period size: 30 Copynumber: 2.8 Consensus size: 30
11102102 TTGTCTAATC
11102112 AAAAGTTTAATTGAAATAAAAATAAATGTTT
1 AAAAGTTTAATT-AAATAAAAATAAATGTTT
* *
11102143 AAAGGTTTAATTAAATGAAAATAAATGTTT
1 AAAAGTTTAATTAAATAAAAATAAATGTTT
* * *
11102173 AAAAATTTAATTAATTTAAAATAAA
1 AAAAGTTTAATTAAATAAAAATAAA
11102198 AAATTTAAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
30 38 0.78
31 11 0.22
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (30 bp):
AAAAGTTTAATTAAATAAAAATAAATGTTT
Found at i:11106272 original size:16 final size:16
Alignment explanation
Indices: 11106251--11106281 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11106241 AAGCTCATAC
*
11106251 CAATTGTTAAGGATAT
1 CAATTGTTAAAGATAT
11106267 CAATTGTTAAAGATA
1 CAATTGTTAAAGATA
11106282 AGTTATCACA
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:0.06, G:0.16, T:0.35
Consensus pattern (16 bp):
CAATTGTTAAAGATAT
Found at i:11106496 original size:10 final size:10
Alignment explanation
Indices: 11106481--11106505 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
11106471 ATTTTGATAT
11106481 CAATTGTTAG
1 CAATTGTTAG
11106491 CAATTGTTAG
1 CAATTGTTAG
11106501 CAATT
1 CAATT
11106506 TTATTCAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (10 bp):
CAATTGTTAG
Found at i:11112689 original size:12 final size:12
Alignment explanation
Indices: 11112672--11112730 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
11112662 TTTTTATATT
11112672 ATATTTATTCTC
1 ATATTTATTCTC
11112684 ATATTTATATC-C
1 ATATTTAT-TCTC
*
11112696 AATATATATT-TC
1 -ATATTTATTCTC
* *
11112708 AAATTTATTCTT
1 ATATTTATTCTC
*
11112720 ATCTTTATTCT
1 ATATTTATTCT
11112731 TGTGGGTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
11 7 0.19
12 21 0.57
13 9 0.24
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATTTATTCTC
Found at i:11112852 original size:18 final size:16
Alignment explanation
Indices: 11112829--11112867 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
11112819 TATTTAATTA
*
11112829 ATTTTTTTATAAATATAT
1 ATTTTTTT-TAAA-AAAT
11112847 ATTTTTTTTAAAAAAT
1 ATTTTTTTTAAAAAAT
11112863 ATTTT
1 ATTTT
11112868 AATTTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 4 0.20
18 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTTTTTAAAAAAT
Found at i:11112906 original size:27 final size:27
Alignment explanation
Indices: 11112853--11112907 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
11112843 ATATATTTTT
* *
11112853 TTTAAAAAATATTTTAATTTTAATTAA
1 TTTAAAAAATAATTTAATATTAATTAA
*
11112880 TTTAAAATAATAATTT-ATATTATTTAA
1 TTTAAAA-AATAATTTAATATTAATTAA
11112907 T
1 T
11112908 AAAAATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTTAAAAAATAATTTAATATTAATTAA
Found at i:11112908 original size:20 final size:19
Alignment explanation
Indices: 11112884--11112927 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
11112874 AATTAATTTA
*
11112884 AAATAATAATTTATATTATT
1 AAATAAAAATTTAT-TTATT
*
11112904 TAATAAAAATTTATTTATT
1 AAATAAAAATTTATTTATT
11112923 AAATA
1 AAATA
11112928 TATATATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AAATAAAAATTTATTTATT
Found at i:11118452 original size:37 final size:37
Alignment explanation
Indices: 11118402--11118473 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
11118392 TACGTGAGAT
11118402 AGAAAATAGAAAAAGAGAGTAAAGAAGAAGAAAGAAC
1 AGAAAATAGAAAAAGAGAGTAAAGAAGAAGAAAGAAC
*
11118439 AGAAAATAGAAAAAGAGAGTAAAGGAGAAGAAAGA
1 AGAAAATAGAAAAAGAGAGTAAAGAAGAAGAAAGA
11118474 GCACAAGAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.67, C:0.01, G:0.26, T:0.06
Consensus pattern (37 bp):
AGAAAATAGAAAAAGAGAGTAAAGAAGAAGAAAGAAC
Found at i:11122084 original size:9 final size:9
Alignment explanation
Indices: 11122083--11122205 Score: 57
Period size: 9 Copynumber: 12.4 Consensus size: 9
11122073 AAAATTTAAA
11122083 AAAAAATTTTT
1 AAAAAA-TT-T
*
11122094 AAAAATTTT
1 AAAAAATTT
**
11122103 AAAATGTTTT
1 AAAAAAT-TT
11122113 AAAAAATTTT
1 AAAAAA-TTT
*
11122123 GAAAAATTCTT
1 -AAAAAAT-TT
**
11122134 AAAATTTTT
1 AAAAAATTT
*
11122143 TAAAAATTAT
1 AAAAAATT-T
*
11122153 AAAAAAAATTG
1 -A-AAAAATTT
**
11122164 AAAAAAAAT
1 AAAAAATTT
11122173 AAAAAATTT
1 AAAAAATTT
11122182 AAAAAATTCT
1 AAAAAATT-T
11122192 AAAAAATTT
1 AAAAAATTT
11122201 GAAAA
1 -AAAA
11122206 GTAATTTGGC
Statistics
Matches: 86, Mismatches: 17, Indels: 19
0.70 0.14 0.16
Matches are distributed among these distances:
9 34 0.40
10 32 0.37
11 13 0.15
12 7 0.08
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (9 bp):
AAAAAATTT
Found at i:11122086 original size:10 final size:10
Alignment explanation
Indices: 11122083--11122205 Score: 90
Period size: 10 Copynumber: 12.4 Consensus size: 10
11122073 AAAATTTAAA
11122083 AAAAAATTTT
1 AAAAAATTTT
*
11122093 TAAAAATTTT
1 AAAAAATTTT
**
11122103 AAAATGTTTT
1 AAAAAATTTT
11122113 AAAAAATTTT
1 AAAAAATTTT
*
11122123 GAAAAATTCTT
1 AAAAAATT-TT
*
11122134 -AAAATTTTT
1 AAAAAATTTT
* *
11122143 TAAAAATTATA
1 AAAAAATT-TT
* *
11122154 AAAAAAATTG
1 AAAAAATTTT
**
11122164 AAAAAA-AAT
1 AAAAAATTTT
11122173 AAAAAA-TTT
1 AAAAAATTTT
*
11122182 AAAAAATTCT
1 AAAAAATTTT
*
11122192 AAAAAATTTG
1 AAAAAATTTT
11122202 AAAA
1 AAAA
11122206 GTAATTTGGC
Statistics
Matches: 88, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
9 15 0.17
10 64 0.73
11 9 0.10
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (10 bp):
AAAAAATTTT
Found at i:11122551 original size:11 final size:11
Alignment explanation
Indices: 11122537--11122593 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
11122527 TGAAGTTTTT
11122537 TTTTTTGAAAA
1 TTTTTTGAAAA
11122548 --TTTT-AAAA
1 TTTTTTGAAAA
*
11122556 TTTTTTGAAATTT
1 TTTTTTGAAA--A
*
11122569 TTTTTTGAAAG
1 TTTTTTGAAAA
11122580 TTTTTTGAAAA
1 TTTTTTGAAAA
11122591 TTT
1 TTT
11122594 CTTTTTATGT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
8 4 0.11
9 4 0.11
10 4 0.11
11 16 0.42
13 10 0.26
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (11 bp):
TTTTTTGAAAA
Found at i:11126737 original size:10 final size:10
Alignment explanation
Indices: 11126734--11126856 Score: 90
Period size: 10 Copynumber: 12.4 Consensus size: 10
11126724 AAAATTTAAA
11126734 AAAAAATTTT
1 AAAAAATTTT
*
11126744 TAAAAATTTT
1 AAAAAATTTT
**
11126754 AAAATGTTTT
1 AAAAAATTTT
11126764 AAAAAA-TTT
1 AAAAAATTTT
*
11126773 GAAAAATTCTT
1 AAAAAATT-TT
**
11126784 AAAATTTTTT
1 AAAAAATTTT
*
11126794 AAAAAATTATA
1 AAAAAATT-TT
* *
11126805 AAAAAAATTG
1 AAAAAATTTT
**
11126815 AAAAAA-AAT
1 AAAAAATTTT
11126824 AAAAAA-TTT
1 AAAAAATTTT
*
11126833 AAAAAATTCT
1 AAAAAATTTT
*
11126843 AAAAAATTTG
1 AAAAAATTTT
11126853 AAAA
1 AAAA
11126857 GTAATTTGGC
Statistics
Matches: 86, Mismatches: 23, Indels: 8
0.74 0.20 0.07
Matches are distributed among these distances:
9 21 0.24
10 50 0.58
11 15 0.17
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (10 bp):
AAAAAATTTT
Found at i:11126768 original size:30 final size:31
Alignment explanation
Indices: 11126734--11126801 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 31
11126724 AAAATTTAAA
*
11126734 AAAAAATTTTTAAAAATT-TTAAAATGTTTT
1 AAAAAATTTTGAAAAATTCTTAAAATGTTTT
*
11126764 AAAAAA-TTTGAAAAATTCTTAAAATTTTTT
1 AAAAAATTTTGAAAAATTCTTAAAATGTTTT
11126794 AAAAAATT
1 AAAAAATT
11126802 ATAAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 10 0.29
30 23 0.68
31 1 0.03
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (31 bp):
AAAAAATTTTGAAAAATTCTTAAAATGTTTT
Found at i:11127201 original size:11 final size:11
Alignment explanation
Indices: 11127187--11127243 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
11127177 TGAAGTTTTT
11127187 TTTTTTGAAAA
1 TTTTTTGAAAA
11127198 --TTTT-AAAA
1 TTTTTTGAAAA
*
11127206 TTTTTTGAAATTT
1 TTTTTTGAAA--A
*
11127219 TTTTTTGAAAG
1 TTTTTTGAAAA
11127230 TTTTTTGAAAA
1 TTTTTTGAAAA
11127241 TTT
1 TTT
11127244 CTTTTTATGT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
8 4 0.11
9 4 0.11
10 4 0.11
11 16 0.42
13 10 0.26
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (11 bp):
TTTTTTGAAAA
Found at i:11129530 original size:14 final size:14
Alignment explanation
Indices: 11129495--11129521 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11129485 AATCTTACAT
11129495 TTACTTTATTAAAA
1 TTACTTTATTAAAA
11129509 TTACTTTATTAAA
1 TTACTTTATTAAA
11129522 GTTGTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (14 bp):
TTACTTTATTAAAA
Found at i:11131384 original size:10 final size:10
Alignment explanation
Indices: 11131381--11131503 Score: 97
Period size: 10 Copynumber: 12.4 Consensus size: 10
11131371 AAAATTTAAA
11131381 AAAAAATTTT
1 AAAAAATTTT
*
11131391 TAAAAATTTT
1 AAAAAATTTT
**
11131401 AAAATGTTTT
1 AAAAAATTTT
11131411 AAAAAATTTT
1 AAAAAATTTT
*
11131421 GAAAAATTCTT
1 AAAAAATT-TT
**
11131432 AAAATTTTTT
1 AAAAAATTTT
* *
11131442 TAAAAATTAT
1 AAAAAATTTT
* *
11131452 AAAAAAATTG
1 AAAAAATTTT
**
11131462 AAAAAA-AAT
1 AAAAAATTTT
11131471 AAAAAA-TTT
1 AAAAAATTTT
*
11131480 AAAAAATTCT
1 AAAAAATTTT
*
11131490 AAAAAATTTG
1 AAAAAATTTT
11131500 AAAA
1 AAAA
11131504 GTAATTTGGC
Statistics
Matches: 85, Mismatches: 26, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
9 13 0.15
10 65 0.76
11 7 0.08
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (10 bp):
AAAAAATTTT
Found at i:11131395 original size:9 final size:9
Alignment explanation
Indices: 11131383--11131440 Score: 53
Period size: 9 Copynumber: 6.0 Consensus size: 9
11131373 AATTTAAAAA
11131383 AAAATTTTT
1 AAAATTTTT
*
11131392 AAAAATTTT
1 AAAATTTTT
11131401 AAAATGTTTT
1 AAAAT-TTTT
*
11131411 AAAAAATTTTGA
1 --AAAATTTT-T
*
11131423 AAAATTCTT
1 AAAATTTTT
11131432 AAAATTTTT
1 AAAATTTTT
11131441 TTAAAAATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
9 20 0.51
10 11 0.28
11 3 0.08
12 5 0.13
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (9 bp):
AAAATTTTT
Found at i:11131434 original size:31 final size:30
Alignment explanation
Indices: 11131381--11131449 Score: 102
Period size: 31 Copynumber: 2.3 Consensus size: 30
11131371 AAAATTTAAA
*
11131381 AAAAAATTTTTAAAAATTTTAAAATGTTTT
1 AAAAAATTTTGAAAAATTTTAAAATGTTTT
*
11131411 AAAAAATTTTGAAAAATTCTTAAAATTTTTT
1 AAAAAATTTTGAAAAATT-TTAAAATGTTTT
*
11131442 TAAAAATT
1 AAAAAATT
11131450 ATAAAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 17 0.49
31 18 0.51
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (30 bp):
AAAAAATTTTGAAAAATTTTAAAATGTTTT
Found at i:11131849 original size:11 final size:11
Alignment explanation
Indices: 11131835--11131891 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
11131825 TGAAGTTTTT
11131835 TTTTTTGAAAA
1 TTTTTTGAAAA
11131846 --TTTT-AAAA
1 TTTTTTGAAAA
*
11131854 TTTTTTGAAATTT
1 TTTTTTGAAA--A
*
11131867 TTTTTTGAAAG
1 TTTTTTGAAAA
11131878 TTTTTTGAAAA
1 TTTTTTGAAAA
11131889 TTT
1 TTT
11131892 CTTTTTATGT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
8 4 0.11
9 4 0.11
10 4 0.11
11 16 0.42
13 10 0.26
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (11 bp):
TTTTTTGAAAA
Found at i:11134180 original size:14 final size:14
Alignment explanation
Indices: 11134145--11134171 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11134135 AATCTTACAT
11134145 TTACTTTATTAAAA
1 TTACTTTATTAAAA
11134159 TTACTTTATTAAA
1 TTACTTTATTAAA
11134172 GTTGTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (14 bp):
TTACTTTATTAAAA
Found at i:11136047 original size:10 final size:10
Alignment explanation
Indices: 11136034--11136078 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
11136024 AAAATTAAAA
11136034 AAAAATTTTG
1 AAAAATTTTG
11136044 -AAAATTTT-
1 AAAAATTTTG
*
11136052 -AAAATGTTTT
1 AAAAAT-TTTG
11136062 AAAAATTTTG
1 AAAAATTTTG
11136072 AAAAATT
1 AAAAATT
11136079 CTAAAATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
8 5 0.16
9 11 0.35
10 10 0.32
11 5 0.16
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (10 bp):
AAAAATTTTG
Found at i:11136066 original size:29 final size:29
Alignment explanation
Indices: 11136034--11136098 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 29
11136024 AAAATTAAAA
*
11136034 AAAAATTTTG-AAAATTTTAAAATGTTTT
1 AAAAATTTTGAAAAATTCTAAAATGTTTT
*
11136062 AAAAATTTTGAAAAATTCTAAAATTTTTTT
1 AAAAATTTTGAAAAATTCTAAAA-TGTTTT
11136092 AAAAATT
1 AAAAATT
11136099 ATAAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 10 0.30
29 11 0.33
30 12 0.36
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.45
Consensus pattern (29 bp):
AAAAATTTTGAAAAATTCTAAAATGTTTT
Found at i:11136090 original size:20 final size:20
Alignment explanation
Indices: 11136067--11136104 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11136057 GTTTTAAAAA
*
11136067 TTTTGAAAAATTCTAAAATT
1 TTTTGAAAAATTATAAAATT
*
11136087 TTTTTAAAAATTATAAAA
1 TTTTGAAAAATTATAAAA
11136105 AAAATTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
TTTTGAAAAATTATAAAATT
Found at i:11136104 original size:29 final size:28
Alignment explanation
Indices: 11136034--11136105 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
11136024 AAAATTAAAA
* *
11136034 AAAAATTTTGAAAATTTTAAAATGTTTT
1 AAAAATTTTAAAAATTCTAAAATGTTTT
*
11136062 AAAAATTTTGAAAAATTCTAAAATTTTTTT
1 AAAAATTTT-AAAAATTCTAAAA-TGTTTT
*
11136092 AAAAATTATAAAAA
1 AAAAATTTTAAAAA
11136106 AAATTGAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 9 0.24
29 16 0.42
30 13 0.34
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (28 bp):
AAAAATTTTAAAAATTCTAAAATGTTTT
Found at i:11136146 original size:10 final size:9
Alignment explanation
Indices: 11136103--11136153 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
11136093 AAAATTATAA
*
11136103 AAAAAATTG
1 AAAAAATTT
**
11136112 AAAAAAAAT
1 AAAAAATTT
11136121 AAAAAATTT
1 AAAAAATTT
11136130 AAAAAATTCT
1 AAAAAATT-T
11136140 AAAAAATTT
1 AAAAAATTT
11136149 GAAAA
1 -AAAA
11136154 GTAATTTGGC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 22 0.63
10 13 0.37
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.24
Consensus pattern (9 bp):
AAAAAATTT
Found at i:11136153 original size:20 final size:20
Alignment explanation
Indices: 11136061--11136153 Score: 75
Period size: 19 Copynumber: 4.8 Consensus size: 20
11136051 TAAAATGTTT
* *
11136061 TAAAAATTTTG-AAAAATTC
1 TAAAAAATTTGAAAAAATTA
** **
11136080 TAAAATTTTTTTAAAAATTA
1 TAAAAAATTTGAAAAAATTA
* *
11136100 TAAAAAAAATTGAAAAAA-AA
1 T-AAAAAATTTGAAAAAATTA
*
11136120 TAAAAAATTT-AAAAAATTC
1 TAAAAAATTTGAAAAAATTA
11136139 TAAAAAATTTGAAAA
1 TAAAAAATTTGAAAA
11136154 GTAATTTGGC
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
18 6 0.10
19 27 0.47
20 14 0.24
21 11 0.19
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.32
Consensus pattern (20 bp):
TAAAAAATTTGAAAAAATTA
Found at i:11136485 original size:10 final size:10
Alignment explanation
Indices: 11136459--11136533 Score: 61
Period size: 10 Copynumber: 7.8 Consensus size: 10
11136449 CAATTCTAAC
*
11136459 ATTTTTAGAA
1 ATTTTTTGAA
11136469 ATTTTTTGAA
1 ATTTTTTGAA
*
11136479 GTTTTTT---
1 ATTTTTTGAA
11136486 -TTTTTTGAA
1 ATTTTTTGAA
* *
11136495 A-ATTTTAAA
1 ATTTTTTGAA
11136504 ATTTTTTGAA
1 ATTTTTTGAA
11136514 ATTTTTTTTGAA
1 A--TTTTTTGAA
11136526 ATTTTTTG
1 ATTTTTTG
11136534 GAAAATTTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
6 6 0.12
9 7 0.13
10 29 0.56
12 10 0.19
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (10 bp):
ATTTTTTGAA
Found at i:11136500 original size:12 final size:12
Alignment explanation
Indices: 11136485--11136546 Score: 55
Period size: 12 Copynumber: 5.6 Consensus size: 12
11136475 TGAAGTTTTT
11136485 TTTTTTTGAAAA
1 TTTTTTTGAAAA
11136497 ---TTTT-AAAA
1 TTTTTTTGAAAA
*
11136505 -TTTTTTGAAAT
1 TTTTTTTGAAAA
11136516 TTTTTTTG-AAA
1 TTTTTTTGAAAA
*
11136527 TTTTTTGGAAAA
1 TTTTTTTGAAAA
11136539 TTTCTTTT
1 TTT-TTTT
11136547 TATGTTAACT
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
8 4 0.10
9 4 0.10
10 4 0.10
11 12 0.30
12 13 0.32
13 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.08, T:0.61
Consensus pattern (12 bp):
TTTTTTTGAAAA
Found at i:11138833 original size:14 final size:14
Alignment explanation
Indices: 11138798--11138824 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11138788 AATCTTACAT
11138798 TTACTTTATTAAAA
1 TTACTTTATTAAAA
11138812 TTACTTTATTAAA
1 TTACTTTATTAAA
11138825 GTTGTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (14 bp):
TTACTTTATTAAAA
Found at i:11140697 original size:15 final size:15
Alignment explanation
Indices: 11140677--11140706 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11140667 ATGTCAATAT
*
11140677 AAAAAATTTTTAAAA
1 AAAAAATTTTGAAAA
11140692 AAAAAATTTTGAAAA
1 AAAAAATTTTGAAAA
11140707 TTTTAAAATG
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:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (15 bp):
AAAAAATTTTGAAAA
Found at i:11140706 original size:10 final size:10
Alignment explanation
Indices: 11140693--11140738 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
11140683 TTTTTAAAAA
11140693 AAAAATTTTG
1 AAAAATTTTG
11140703 -AAAATTTT-
1 AAAAATTTTG
* *
11140711 AAAATGTTTTA
1 AAAA-ATTTTG
11140722 AAAAATTTTG
1 AAAAATTTTG
11140732 AAAAATT
1 AAAAATT
11140739 CTAAAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
9 11 0.37
10 15 0.50
11 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (10 bp):
AAAAATTTTG
Found at i:11140737 original size:30 final size:29
Alignment explanation
Indices: 11140692--11140758 Score: 98
Period size: 30 Copynumber: 2.3 Consensus size: 29
11140682 ATTTTTAAAA
*
11140692 AAAAAATTTTGAAAATTTTAAAATGTTTT
1 AAAAAATTTTGAAAATTCTAAAATGTTTT
*
11140721 AAAAAATTTTGAAAAATTCTAAAATTTTTT
1 AAAAAATTTTG-AAAATTCTAAAATGTTTT
*
11140751 TAAAAATT
1 AAAAAATT
11140759 ATAAAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 11 0.32
30 23 0.68
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (29 bp):
AAAAAATTTTGAAAATTCTAAAATGTTTT
Found at i:11140766 original size:30 final size:30
Alignment explanation
Indices: 11140703--11140795 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 30
11140693 AAAAATTTTG
* * *
11140703 AAAATTTTAAAATGTTTTAAAAAATTTTGA
1 AAAATTCTAAAATGTTTTAAAAAATTATAA
* *
11140733 AAAATTCTAAAATTTTTTTAAAAATTATAA
1 AAAATTCTAAAATGTTTTAAAAAATTATAA
* ** *
11140763 AAAA--ATAAAA-AATTTAAAAAATTCTAA
1 AAAATTCTAAAATGTTTTAAAAAATTATAA
11140790 AAAATT
1 AAAATT
11140796 TGAAAAGTAA
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
27 17 0.33
28 5 0.10
30 29 0.57
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (30 bp):
AAAATTCTAAAATGTTTTAAAAAATTATAA
Found at i:11140801 original size:10 final size:9
Alignment explanation
Indices: 11140718--11140801 Score: 62
Period size: 10 Copynumber: 8.9 Consensus size: 9
11140708 TTTAAAATGT
11140718 TTTAAAAAA
1 TTTAAAAAA
*
11140727 TTTTGAAAAA
1 -TTTAAAAAA
**
11140737 TTCTAAAATTT
1 TT-TAAAA-AA
*
11140748 TTTTAAAAA
1 TTTAAAAAA
11140757 TTATAAAAAA
1 TT-TAAAAAA
*
11140767 -ATAAAAAA
1 TTTAAAAAA
11140775 TTTAAAAAA
1 TTTAAAAAA
11140784 TTCTAAAAAA
1 TT-TAAAAAA
*
11140794 TTTGAAAA
1 TTTAAAAA
11140802 GTAATTTGGC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
8 7 0.12
9 18 0.31
10 31 0.53
11 2 0.03
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:11141147 original size:11 final size:11
Alignment explanation
Indices: 11141133--11141188 Score: 64
Period size: 11 Copynumber: 5.3 Consensus size: 11
11141123 TGAAGTGTTT
11141133 TTTTTTGAAAA
1 TTTTTTGAAAA
11141144 --TTTT-AAAA
1 TTTTTTGAAAA
*
11141152 TTTTTTGAAATT
1 TTTTTTGAAA-A
*
11141164 TTTTTTGAAAT
1 TTTTTTGAAAA
11141175 TTTTTTGAAAA
1 TTTTTTGAAAA
11141186 TTT
1 TTT
11141189 CTTTTTATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 4 0.10
9 4 0.10
10 4 0.10
11 17 0.44
12 10 0.26
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (11 bp):
TTTTTTGAAAA
Found at i:11150780 original size:21 final size:20
Alignment explanation
Indices: 11150756--11150818 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 20
11150746 AAAAAAAAAA
11150756 TTAAAACTTTTTTTATATATT
1 TTAAAA-TTTTTTTATATATT
*
11150777 TTAAAATTATTTTTCATGATTTT
1 TTAAAATT-TTTTT-AT-ATATT
*
11150800 TTAAAAATTTTTTGATATA
1 TT-AAAATTTTTTTATATA
11150819 AAAACCATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
20 2 0.06
21 13 0.37
22 4 0.11
23 10 0.29
24 6 0.17
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (20 bp):
TTAAAATTTTTTTATATATT
Found at i:11152606 original size:22 final size:21
Alignment explanation
Indices: 11152557--11152606 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
11152547 ATTGGGCAAG
11152557 ATATTTTATTAATAATAAAAT
1 ATATTTTATTAATAATAAAAT
* **
11152578 ACAATTTTATTTAATTTTAAAAT
1 A-TATTTTA-TTAATAATAAAAT
11152601 ATATTT
1 ATATTT
11152607 AAAATATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 1 0.04
22 10 0.43
23 12 0.52
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
ATATTTTATTAATAATAAAAT
Found at i:11153217 original size:22 final size:22
Alignment explanation
Indices: 11153186--11153239 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
11153176 ATTATGTGTT
* *
11153186 ATTTTTATTTTGGATAAAAATG
1 ATTTTAATTTTGGATAAAAATA
11153208 ATTTTAATTTTGGATAAAAATA
1 ATTTTAATTTTGGATAAAAATA
11153230 ATTTTAATTT
1 ATTTTAATTT
11153240 AAAATTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
ATTTTAATTTTGGATAAAAATA
Found at i:11155198 original size:10 final size:10
Alignment explanation
Indices: 11155183--11155224 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
11155173 TAGCTTACCC
11155183 TTTTTTCTCT
1 TTTTTTCTCT
*
11155193 TTTTTTCTTT
1 TTTTTTCTCT
11155203 TTTTTTC-CT
1 TTTTTTCTCT
11155212 AATTTTTTCTCT
1 --TTTTTTCTCT
11155224 T
1 T
11155225 AGTTACGCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
9 1 0.04
10 17 0.63
11 7 0.26
12 2 0.07
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTCTCT
Found at i:11163295 original size:2 final size:2
Alignment explanation
Indices: 11163288--11163315 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11163278 TTAATAAACA
11163288 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
11163316 TTGATTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11168646 original size:33 final size:33
Alignment explanation
Indices: 11168587--11168654 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
11168577 AGTAAAGATT
* * *
11168587 AAGTTCAATGGACTTTCTTCTTCAAAAATAAAA
1 AAGTTCAATGGACTTTCTACTACAAAAAAAAAA
*
11168620 AAGTTCAATGGGCTTTC-ACATACAAAAAAAAAA
1 AAGTTCAATGGACTTTCTAC-TACAAAAAAAAAA
11168653 AA
1 AA
11168655 AAACAGAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 1 0.03
33 29 0.97
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.26
Consensus pattern (33 bp):
AAGTTCAATGGACTTTCTACTACAAAAAAAAAA
Found at i:11170044 original size:44 final size:44
Alignment explanation
Indices: 11169993--11170345 Score: 302
Period size: 44 Copynumber: 8.0 Consensus size: 44
11169983 TGTTTAGAAT
* ***
11169993 AGCTTTATTTATTTTCCAGAAGTCATTGAATATCTATTTAAAGG
1 AGCTTTATTTATTTTCCAAAAGTCATTGAGCCTCTATTTAAAGG
* * * * *
11170037 AGTTTTATTTATTTTCTAAAAGTCGTTGAGCCTCTGTTTAAAGA
1 AGCTTTATTTATTTTCCAAAAGTCATTGAGCCTCTATTTAAAGG
* * *
11170081 AGCCTTATTTATTTTTCAAAAGTCATTGAGCCTCTATTTAGAGG
1 AGCTTTATTTATTTTCCAAAAGTCATTGAGCCTCTATTTAAAGG
** *
11170125 AGCTTTATTTATTTTCCAAAAGTTGTTGAGCCTCTATTTAGAA-A
1 AGCTTTATTTATTTTCCAAAAGTCATTGAGCCTCTATTTA-AAGG
* * * *
11170169 AACCTTATTTATTTTTCAAAAGTTATTGAGCCAT-TATTTAAAGG
1 AGCTTTATTTATTTTCCAAAAGTCATTGAGCC-TCTATTTAAAGG
** * * * * *
11170213 AGCTTTATTTATTTTTTAGAAGTCATTGAACCTTTATTTAGAGA
1 AGCTTTATTTATTTTCCAAAAGTCATTGAGCCTCTATTTAAAGG
* * * * *
11170257 AACTTTATTTATTTAT-CAAAAGTCTTTGAGCTTCTATGTAGAGG
1 AGCTTTATTTATTT-TCCAAAAGTCATTGAGCCTCTATTTAAAGG
** ** * *
11170301 AGCCCTATAAATTTTTCAAAAGT--TGTGAGCCTTTATTTAAAGG
1 AGCTTTATTTATTTTCCAAAAGTCAT-TGAGCCTCTATTTAAAGG
11170344 AG
1 AG
11170346 TTTTTATGTT
Statistics
Matches: 248, Mismatches: 54, Indels: 15
0.78 0.17 0.05
Matches are distributed among these distances:
42 1 0.00
43 20 0.08
44 224 0.90
45 3 0.01
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (44 bp):
AGCTTTATTTATTTTCCAAAAGTCATTGAGCCTCTATTTAAAGG
Found at i:11170109 original size:88 final size:88
Alignment explanation
Indices: 11169978--11170303 Score: 350
Period size: 88 Copynumber: 3.7 Consensus size: 88
11169968 GATCCATAAG
* * * * * * * *
11169978 GCCTCTGTTTAGAATAGCTTTATTTATTTTCCAGAAGTCATTGAATATCTATTTAAAGGAGTTTT
1 GCCTCTATTTAGAAAAACCTTATTTATTTTTCAAAAGTCATTGAACATCTATTTAAAGGAGCTTT
11170043 ATTTATTTTCTAAAAGTCGTTGA
66 ATTTATTTTCTAAAAGTCGTTGA
* * * * *
11170066 GCCTCTGTTTA-AAGAAGCCTTATTTATTTTTCAAAAGTCATTGAGCCTCTATTTAGAGGAGCTT
1 GCCTCTATTTAGAA-AAACCTTATTTATTTTTCAAAAGTCATTGAACATCTATTTAAAGGAGCTT
* *
11170130 TATTTATTTTCCAAAAGTTGTTGA
65 TATTTATTTTCTAAAAGTCGTTGA
* *
11170154 GCCTCTATTTAGAAAAACCTTATTTATTTTTCAAAAGTTATTGAGCCAT-TATTTAAAGGAGCTT
1 GCCTCTATTTAGAAAAACCTTATTTATTTTTCAAAAGTCATTGA-ACATCTATTTAAAGGAGCTT
* * *
11170218 TATTTATTTTTTAGAAGTCATTGA
65 TATTTATTTTCTAAAAGTCGTTGA
* * * * * * * * * *
11170242 ACCTTTATTTAGAGAAACTTTATTTATTTATCAAAAGTCTTTGAGCTTCTATGTAGAGGAGC
1 GCCTCTATTTAGAAAAACCTTATTTATTTTTCAAAAGTCATTGAACATCTATTTAAAGGAGC
11170304 CCTATAAATT
Statistics
Matches: 201, Mismatches: 33, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
87 4 0.02
88 193 0.96
89 4 0.02
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (88 bp):
GCCTCTATTTAGAAAAACCTTATTTATTTTTCAAAAGTCATTGAACATCTATTTAAAGGAGCTTT
ATTTATTTTCTAAAAGTCGTTGA
Found at i:11170221 original size:132 final size:130
Alignment explanation
Indices: 11170041--11170345 Score: 346
Period size: 132 Copynumber: 2.3 Consensus size: 130
11170031 TAAAGGAGTT
* * *
11170041 TTATTTA-TTTTCTAAAAGTCGTTGAGCCTCTGTTTAAAGAAGCCTTATTTATTTTTCAAAAGTC
1 TTATTTATTTTTC-AAAAGT-TTTGAGCCT-TATTTAAAGGAGCCTTATTTATTTTTCAAAAGTC
* * * *
11170105 ATTGAGCCTCTATTTAGAGGAGCTTTATTTATTT-TCCAAAAGT-TGTTGAGCCTCTATTTAGAA
63 ATTGAACCTCTATTTAGAGAAACTTTATTTATTTAT-CAAAAGTCT-TTGAGCCTCTATGTAGAA
11170168 AAACC
126 AAACC
* * *
11170173 TTATTTATTTTTCAAAAGTTATTGAGCCATTATTTAAAGGAGCTTTATTTATTTTTTAGAAGTCA
1 TTATTTATTTTTCAAAAGTT-TTGAGCC-TTATTTAAAGGAGCCTTATTTATTTTTCAAAAGTCA
* * ** *
11170238 TTGAACCTTTATTTAGAGAAACTTTATTTATTTATCAAAAGTCTTTGAGCTTCTATGTAGAGGAG
64 TTGAACCTCTATTTAGAGAAACTTTATTTATTTATCAAAAGTCTTTGAGCCTCTATGTAGAAAAA
11170303 CC
129 CC
* ** *
11170305 CTATAAATTTTTCAAAAGTTGTGAGCCTTTATTTAAAGGAG
1 TTATTTATTTTTCAAAAGTTTTGAGCC-TTATTTAAAGGAG
11170346 TTTTTATGTT
Statistics
Matches: 148, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
131 19 0.13
132 121 0.82
133 8 0.05
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (130 bp):
TTATTTATTTTTCAAAAGTTTTGAGCCTTATTTAAAGGAGCCTTATTTATTTTTCAAAAGTCATT
GAACCTCTATTTAGAGAAACTTTATTTATTTATCAAAAGTCTTTGAGCCTCTATGTAGAAAAACC
Found at i:11170579 original size:5 final size:6
Alignment explanation
Indices: 11170563--11170608 Score: 78
Period size: 6 Copynumber: 8.0 Consensus size: 6
11170553 CCAATTATCA
11170563 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A-TTTT A-TTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
11170609 TGGTTTTATC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 10 0.26
6 29 0.74
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:11170617 original size:18 final size:16
Alignment explanation
Indices: 11170565--11170609 Score: 63
Period size: 16 Copynumber: 2.7 Consensus size: 16
11170555 AATTATCAAT
11170565 TTTTATTTTTATTTTTA
1 TTTTATTTTT-TTTTTA
*
11170582 TTTTTATTTTTATTTTA
1 -TTTTATTTTTTTTTTA
11170599 TTTTATTTTTT
1 TTTTATTTTTT
11170610 GGTTTTATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.40
17 5 0.20
18 10 0.40
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTATTTTTTTTTTA
Found at i:11171522 original size:20 final size:20
Alignment explanation
Indices: 11171497--11171548 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
11171487 GAGCCGTTTC
**
11171497 TTTATTTTGGTTTTTTTTAA
1 TTTATTTTGGTTTTTGCTAA
*
11171517 TTTATTTTGG-TTTTGCTGA
1 TTTATTTTGGTTTTTGCTAA
11171536 TTTATTTTGGTTT
1 TTTATTTTGGTTT
11171549 CATATTATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.12, C:0.02, G:0.15, T:0.71
Consensus pattern (20 bp):
TTTATTTTGGTTTTTGCTAA
Found at i:11173235 original size:16 final size:16
Alignment explanation
Indices: 11173216--11173276 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
11173206 CACTTCATCA
11173216 TTTT-TTTTCTTCTTT
1 TTTTCTTTTCTTCTTT
*
11173231 CTTTTCCTTTCCTTCTTT
1 -TTTT-CTTTTCTTCTTT
*
11173249 TTTTCTATTCTTCCTTT
1 TTTTCTTTTCTT-CTTT
*
11173266 TTAT-TTTTCTT
1 TTTTCTTTTCTT
11173277 TTCTAATTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
16 16 0.43
17 11 0.30
18 10 0.27
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTCTTTTCTTCTTT
Found at i:11173264 original size:20 final size:21
Alignment explanation
Indices: 11173239--11173280 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11173229 TTCTTTTCCT
11173239 TTCCTTCTT-TTTTTCTATTC
1 TTCCTTCTTATTTTTCTATTC
* *
11173259 TTCCTTTTTATTTTTCTTTTC
1 TTCCTTCTTATTTTTCTATTC
11173280 T
1 T
11173281 AATTTCACCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (21 bp):
TTCCTTCTTATTTTTCTATTC
Found at i:11176187 original size:16 final size:18
Alignment explanation
Indices: 11176168--11176204 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
11176158 AGGTGGCTTC
11176168 TTCCC-TTACT-ATTTCT
1 TTCCCTTTACTCATTTCT
*
11176184 TTCCCTTTACTCATTTTT
1 TTCCCTTTACTCATTTCT
11176202 TTC
1 TTC
11176205 ACCATTTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 5 0.28
18 8 0.44
ACGTcount: A:0.11, C:0.30, G:0.00, T:0.59
Consensus pattern (18 bp):
TTCCCTTTACTCATTTCT
Found at i:11180530 original size:14 final size:13
Alignment explanation
Indices: 11180494--11180531 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
11180484 CTCAATTCTC
11180494 ATAATATATATAT
1 ATAATATATATAT
*
11180507 ATGAAAATATATAT
1 AT-AATATATATAT
11180521 ATAAT-TATATA
1 ATAATATATATA
11180532 ATTATTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 4 0.18
14 12 0.55
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (13 bp):
ATAATATATATAT
Found at i:11185543 original size:121 final size:121
Alignment explanation
Indices: 11185329--11185554 Score: 317
Period size: 121 Copynumber: 1.9 Consensus size: 121
11185319 AAGATAATTA
* * * ** *
11185329 CATTTTGATTAGCACTGGTAACAGGAACAAGTTGAAGAGTTTGAGCAAGCAAATGGTGACAAATG
1 CATTTTGATCAGCACTAGTAACAGAAACAAGTCAAAGAGTTTAAGCAAGCAAATGGTGACAAATG
* *
11185394 AATTTACAATTAATTTCAATATGTTTAGTACGCTCATGAAAAACATCGTACATCTG
66 AATTGACAATCAATTTCAATATGTTTAGTACGCTCATGAAAAACATCGTACATCTG
* * * **
11185450 CATTTTGATCAGCACTAGTAACAGAAATAAGTCAAAGAGTTTAAGCAAGTAGATGGTGATGAATG
1 CATTTTGATCAGCACTAGTAACAGAAACAAGTCAAAGAGTTTAAGCAAGCAAATGGTGACAAATG
* *
11185515 AATTGACAGTCAATTTCAATATGTTTAGTACGCTTATGAA
66 AATTGACAATCAATTTCAATATGTTTAGTACGCTCATGAA
11185555 GACAATCATT
Statistics
Matches: 90, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
121 90 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (121 bp):
CATTTTGATCAGCACTAGTAACAGAAACAAGTCAAAGAGTTTAAGCAAGCAAATGGTGACAAATG
AATTGACAATCAATTTCAATATGTTTAGTACGCTCATGAAAAACATCGTACATCTG
Found at i:11189819 original size:23 final size:23
Alignment explanation
Indices: 11189786--11189830 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
11189776 ATATCACCAA
11189786 AATATTACTAAAATATCATTGAG
1 AATATTACTAAAATATCATTGAG
*
11189809 AATATTGCTAAAATATCATTGA
1 AATATTACTAAAATATCATTGA
11189831 CAAATAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (23 bp):
AATATTACTAAAATATCATTGAG
Found at i:11190511 original size:10 final size:10
Alignment explanation
Indices: 11190484--11190516 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
11190474 ATTTAAAAAT
11190484 TTTATTAATT-
1 TTTATT-ATTA
11190494 TTTATTATTA
1 TTTATTATTA
11190504 TTTATTATTA
1 TTTATTATTA
11190514 TTT
1 TTT
11190517 TCATTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 3 0.14
10 19 0.86
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTATTATTA
Found at i:11190954 original size:19 final size:20
Alignment explanation
Indices: 11190926--11190964 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
11190916 TAATTTTGTA
11190926 TTATTATT-AAGTTTATTTT
1 TTATTATTAAAGTTTATTTT
*
11190945 TTATTTTTAAAGTTTATTTT
1 TTATTATTAAAGTTTATTTT
11190965 AAAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (20 bp):
TTATTATTAAAGTTTATTTT
Found at i:11192119 original size:17 final size:17
Alignment explanation
Indices: 11192099--11192153 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
11192089 TCCCCTTTCA
11192099 TTTGTTTTTTTCTTTTT
1 TTTGTTTTTTTCTTTTT
* *
11192116 TTTGTATTCTTCTGTTTT
1 TTTGTTTTTTTCT-TTTT
11192134 TTT-TTTATTTTCATTTTT
1 TTTGTTT-TTTTC-TTTTT
11192152 TT
1 TT
11192154 CCTTTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 13 0.42
18 17 0.55
19 1 0.03
ACGTcount: A:0.05, C:0.07, G:0.05, T:0.82
Consensus pattern (17 bp):
TTTGTTTTTTTCTTTTT
Found at i:11193545 original size:20 final size:20
Alignment explanation
Indices: 11193503--11193548 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
11193493 TTGTTAATGT
*
11193503 ATAAATATTATATATTATCA
1 ATAAATATTATATACTATCA
* * *
11193523 ATAAATATTATGTACTGTTA
1 ATAAATATTATATACTATCA
11193543 ATAAAT
1 ATAAAT
11193549 CACGCTTCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (20 bp):
ATAAATATTATATACTATCA
Found at i:11197576 original size:6 final size:6
Alignment explanation
Indices: 11197565--11197591 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
11197555 TTGGCACTTA
11197565 GTGCTG GTGCTG GTGCTG GTGCTG GTG
1 GTGCTG GTGCTG GTGCTG GTGCTG GTG
11197592 TGCTTTGGTT
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:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GTGCTG
Found at i:11199510 original size:3 final size:3
Alignment explanation
Indices: 11199502--11199544 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
11199492 TTGAAAAATG
11199502 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
11199545 GTTATTGAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:11200249 original size:18 final size:18
Alignment explanation
Indices: 11200214--11200249 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11200204 TTTAAAAAGT
**
11200214 AAATATATTTAATCTTAA
1 AAATATATTTAAAATTAA
11200232 AAATATATTTAAAATTAA
1 AAATATATTTAAAATTAA
11200250 TTTTTATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATATTTAAAATTAA
Found at i:11209378 original size:12 final size:12
Alignment explanation
Indices: 11209361--11209389 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
11209351 TAATGGCTAG
11209361 TTTCTAAATGCA
1 TTTCTAAATGCA
11209373 TTTCTAAATGCA
1 TTTCTAAATGCA
11209385 TTTCT
1 TTTCT
11209390 GTAGAGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (12 bp):
TTTCTAAATGCA
Found at i:11212896 original size:15 final size:15
Alignment explanation
Indices: 11212876--11212911 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
11212866 TTCTCTTTTT
*
11212876 TTTTTTTGTAATTTA
1 TTTTTTTATAATTTA
*
11212891 TTTTTTTATACTTTA
1 TTTTTTTATAATTTA
11212906 TTTTTT
1 TTTTTT
11212912 CAAATCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.78
Consensus pattern (15 bp):
TTTTTTTATAATTTA
Found at i:11213651 original size:18 final size:19
Alignment explanation
Indices: 11213612--11213652 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
11213602 TATTTTATTT
*
11213612 TATAAAAATTTAAAATACA
1 TATAAAAATTTAAAATAAA
11213631 TATAAAAA-TTAATAA-AAA
1 TATAAAAATTTAA-AATAAA
11213649 TATA
1 TATA
11213653 TAATTCAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
TATAAAAATTTAAAATAAA
Found at i:11217557 original size:2 final size:2
Alignment explanation
Indices: 11217550--11217586 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11217540 TCACAAGGGA
11217550 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 A
11217587 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11223981 original size:16 final size:15
Alignment explanation
Indices: 11223953--11223987 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
11223943 AAGAAAATAG
11223953 AGAAAAGAAAGAAAA
1 AGAAAAGAAAGAAAA
11223968 AGAAAAGAAAAGAAAA
1 AGAAAAG-AAAGAAAA
11223984 AGAA
1 AGAA
11223988 TAAAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAAGAAAA
Found at i:11224078 original size:30 final size:30
Alignment explanation
Indices: 11224042--11224133 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
11224032 TGTGATAAAT
11224042 TTTTATCTATTTTATTAATATAACATGAAA
1 TTTTATCTATTTTATTAATATAACATGAAA
* * * *
11224072 TTTTATCT-TAGTTA-GAA-A-AAAAT--AC
1 TTTTATCTAT-TTTATTAATATAACATGAAA
*
11224097 TTTTATCTATTTTATTAATATAACATGAGA
1 TTTTATCTATTTTATTAATATAACATGAAA
11224127 TTTTATC
1 TTTTATC
11224134 GTAGTTAGAA
Statistics
Matches: 46, Mismatches: 9, Indels: 14
0.67 0.13 0.20
Matches are distributed among these distances:
25 12 0.26
26 3 0.07
27 5 0.11
28 5 0.11
29 3 0.07
30 18 0.39
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (30 bp):
TTTTATCTATTTTATTAATATAACATGAAA
Found at i:11224104 original size:55 final size:55
Alignment explanation
Indices: 11224042--11224149 Score: 198
Period size: 55 Copynumber: 2.0 Consensus size: 55
11224032 TGTGATAAAT
*
11224042 TTTTATCTATTTTATTAATATAACATGAAATTTTATCTTAGTTAGAAAAAAATAC
1 TTTTATCTATTTTATTAATATAACATGAAATTTTATCGTAGTTAGAAAAAAATAC
*
11224097 TTTTATCTATTTTATTAATATAACATGAGATTTTATCGTAGTTAGAAAAAAAT
1 TTTTATCTATTTTATTAATATAACATGAAATTTTATCGTAGTTAGAAAAAAAT
11224150 TAACTGTGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.45
Consensus pattern (55 bp):
TTTTATCTATTTTATTAATATAACATGAAATTTTATCGTAGTTAGAAAAAAATAC
Found at i:11224670 original size:15 final size:15
Alignment explanation
Indices: 11224645--11224699 Score: 60
Period size: 15 Copynumber: 3.6 Consensus size: 15
11224635 TTTAATTAGA
11224645 TAATT-AATTAATAT
1 TAATTAAATTAATAT
11224659 TAATTAAATTAA-AT
1 TAATTAAATTAATAT
*
11224673 ATAATTATAATAAATAAT
1 -TAATTA-AATTAAT-AT
11224691 TAATTAAAT
1 TAATTAAAT
11224700 ATTTAAACAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
14 7 0.20
15 12 0.34
16 8 0.23
17 6 0.17
18 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATTAAATTAATAT
Found at i:11224712 original size:42 final size:42
Alignment explanation
Indices: 11224644--11224754 Score: 111
Period size: 42 Copynumber: 2.6 Consensus size: 42
11224634 ATTTAATTAG
11224644 ATAATTAATT-AATA-TTAATTAAATT-AAATATAATTATAATAA
1 ATAATTAATTAAATATTTAA--AAATTAAAATATAATTA-AATAA
* * *
11224686 ATAATTAATTAAATATTTAAACATTAAAATATTATTAAATTA
1 ATAATTAATTAAATATTTAAAAATTAAAATATAATTAAATAA
*
11224728 ATATTTCATATTAAATATTATAAAAAT
1 ATAATT-A-ATTAAATATT-TAAAAAT
11224755 AATATTATAA
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
42 23 0.40
43 15 0.26
44 14 0.24
45 6 0.10
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (42 bp):
ATAATTAATTAAATATTTAAAAATTAAAATATAATTAAATAA
Found at i:11224727 original size:16 final size:15
Alignment explanation
Indices: 11224650--11224762 Score: 73
Period size: 14 Copynumber: 7.9 Consensus size: 15
11224640 TTAGATAATT
11224650 AATT-AATATTAATTA
1 AATTAAATATT-ATTA
*
11224665 AATTAAATATAATTA
1 AATTAAATATTATTA
11224680 TAA-TAAATA--ATT-
1 -AATTAAATATTATTA
*
11224692 AATTAAATATT-TAA
1 AATTAAATATTATTA
11224706 ACATTAAAATATTATTA
1 A-ATT-AAATATTATTA
*
11224723 AATT-AATATT-TCA
1 AATTAAATATTATTA
* *
11224736 TATTAAATATTATAA
1 AATTAAATATTATTA
*
11224751 AAAT-AATATTAT
1 AATTAAATATTAT
11224763 AATATTATAA
Statistics
Matches: 79, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
11 2 0.03
12 6 0.08
13 9 0.11
14 21 0.27
15 21 0.27
16 17 0.22
17 3 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTAAATATTATTA
Found at i:11224759 original size:58 final size:57
Alignment explanation
Indices: 11224654--11225201 Score: 193
Period size: 59 Copynumber: 9.6 Consensus size: 57
11224644 ATAATTAATT
* *
11224654 AATATTAATTAAATTAAATATAATT-ATAATAAATAATTAATT-AAAT-AT-TTAAACATTAA
1 AATATT-ATTAAATT-AATAT--TTAATATTAAAT-ATT-ATTAAAATAATATTAAAAATTAA
* * *
11224713 AATATTATTAAATTAATATTTCATATTAAATATTATAAAAATAATATTATAATATTATA
1 AATATTATTAAATTAATATTTAATATTAAATATTATTAAAATAATATTA-AAAATTA-A
* * * ** *
11224772 AAT-TTATTAAAAATAATATTTAATAATCAATATTATTAATGTAATATTAAAAATTTTA
1 AATATTATT-AAATTAATATTTAATATTAAATATTATTAAAATAATATTAAAAA-TTAA
* *
11224830 AA-ATTATTAAATTAAT-TTTAAATATTGAAATAATATTAAAATAATAATAAAATATT--
1 AATATTATTAAATTAATATTT-AATATT-AAATATTATTAAAATAATATTAAAA-ATTAA
** * * *
11224886 -ATAGCATT-AGTTAA-A--TAATGTTAAATATTATTAAATTAATATTAAATAA-TAA
1 AATATTATTAAATTAATATTTAATATTAAATATTATTAAAATAATATTAAA-AATTAA
* * * ** * * *
11224938 AACACTATTAAAAT-ATATGCAATATTAAAAAATATT---A-AATATTAAATATT-A
1 AATATTATTAAATTAATATTTAATATTAAATATTATTAAAATAATATTAAAAATTAA
** ** * * ** * *
11224989 AATATTGCTAAATTAATCGTTAGTATAAAATAACATTAAAATATTATT-ACAA-TAA
1 AATATTATTAAATTAATATTTAATATTAAATATTATTAAAATAATATTAAAAATTAA
* * * * * *
11225044 TAATAATTATTAAA--AAAATTATGAACATCATATTTTATATTAAAATAATTTTCAAATAA-TAC
1 -AAT-ATTATTAAATTAATATT-T-AATATTA-AATAT-TATTAAAATAATATT-AAA-AATTA-
11225106 A
57 A
* * *
11225107 AAAATTA-AAAAGTTAATATTT-TTATTAAAATATTATTAAAATAA-ATTAAATACTATTAA
1 AATATTATTAAA-TTAATATTTAATATT-AAATATTATTAAAATAATATTAAA-A--ATTAA
* *
11225166 AATATTTATTAATTTAATGTTTAATAATT-AATATTA
1 AATA-TTATTAAATTAATATTTAAT-ATTAAATATTA
11225202 AAGTATTAGT
Statistics
Matches: 357, Mismatches: 82, Indels: 99
0.66 0.15 0.18
Matches are distributed among these distances:
50 1 0.00
51 33 0.09
52 30 0.08
53 7 0.02
54 6 0.02
55 22 0.06
56 39 0.11
57 36 0.10
58 56 0.16
59 74 0.21
60 28 0.08
61 9 0.03
62 10 0.03
63 6 0.02
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (57 bp):
AATATTATTAAATTAATATTTAATATTAAATATTATTAAAATAATATTAAAAATTAA
Found at i:11224845 original size:29 final size:29
Alignment explanation
Indices: 11224716--11224851 Score: 75
Period size: 29 Copynumber: 4.7 Consensus size: 29
11224706 ACATTAAAAT
** *
11224716 ATTATTAAATTAATATT--TCATATTAAA
1 ATTATTAAATTAATATTAAAAATTTTAAA
* * * *
11224743 TATTATAAAAATAATATTATAATATTATAAA
1 -ATTATTAAATTAATATTA-AAAATTTTAAA
* * * * *
11224774 TTTATTAAAAATAATATTTAATAA--TCAAT
1 ATTATT-AAATTAATA-TTAAAAATTTTAAA
11224803 ATTATT-AATGTAATATTAAAAATTTTAAA
1 ATTATTAAAT-TAATATTAAAAATTTTAAA
*
11224832 ATTATTAAATTAATTTTAAA
1 ATTATTAAATTAATATTAAA
11224852 TATTGAAATA
Statistics
Matches: 80, Mismatches: 19, Indels: 17
0.69 0.16 0.15
Matches are distributed among these distances:
27 8 0.10
28 20 0.25
29 25 0.31
30 7 0.09
31 17 0.21
32 3 0.04
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (29 bp):
ATTATTAAATTAATATTAAAAATTTTAAA
Found at i:11224855 original size:18 final size:17
Alignment explanation
Indices: 11224814--11224869 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 17
11224804 TTATTAATGT
11224814 AATATTAAA-AATTTTAA
1 AATATTAAATAATTTT-A
11224831 AATTATTAAATTAATTTTA
1 AA-TATTAAA-TAATTTTA
*
11224850 AATATTGAAATAATATTA
1 AATATT-AAATAATTTTA
11224868 AA
1 AA
11224870 ATAATAATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
17 2 0.06
18 20 0.59
19 6 0.18
20 6 0.18
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
AATATTAAATAATTTTA
Found at i:11224864 original size:11 final size:11
Alignment explanation
Indices: 11224850--11224936 Score: 51
Period size: 11 Copynumber: 8.4 Consensus size: 11
11224840 ATTAATTTTA
*
11224850 AATATTGAAAT
1 AATATTAAAAT
11224861 AATATTAAAAT
1 AATATTAAAAT
*
11224872 AATAATAAAAT
1 AATATTAAAAT
* **
11224883 ATTA-TAGCAT
1 AATATTAAAAT
11224893 --TAGTT-AAAT
1 AATA-TTAAAAT
*
11224902 AATGTT-AAAT
1 AATATTAAAAT
* *
11224912 ATTATTAAATT
1 AATATTAAAAT
11224923 AATATT-AAAT
1 AATATTAAAAT
11224933 AATA
1 AATA
11224937 AAACACTATT
Statistics
Matches: 58, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
8 2 0.03
9 2 0.03
10 22 0.38
11 32 0.55
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (11 bp):
AATATTAAAAT
Done.