Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_pilon, 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: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 60 of 78
Found at i:12158915 original size:16 final size:17
Alignment explanation
Indices: 12158885--12158918 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12158875 ATATGATATT
12158885 AAAATAAAATGATTTAAA
1 AAAATAAAA-GATTTAAA
12158903 AAAATAAAA-ATTTAAA
1 AAAATAAAAGATTTAAA
12158919 TATTAAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAATAAAAGATTTAAA
Found at i:12160348 original size:2 final size:2
Alignment explanation
Indices: 12160341--12160366 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12160331 AACAATTACA
12160341 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
12160367 TATGTATGAT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12160425 original size:2 final size:2
Alignment explanation
Indices: 12160418--12160596 Score: 67
Period size: 2 Copynumber: 90.0 Consensus size: 2
12160408 ATGACTCATG
* *
12160418 TA TA TA TA -A AA TA TA -A GTA TA TA TA GT- TA TA TA TG TA -A T-
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA
* * *
12160457 TA TA TA TA AA TA TA -A GTA TA TA TA TA TA TA TA T- TA TA AA GA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
12160498 CA -A AA GGA TA TA -A GTA TA TA -A TA TA AA GTA TA TA AA TA TA
1 TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA
* *
12160538 TA AA CTA T- TA AA GTA TA TA TA TGA GTA TA TA TA TGA -A TA TA TA
1 TA TA -TA TA TA TA -TA TA TA TA T-A -TA TA TA TA T-A TA TA TA TA
12160581 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
12160597 CTGTAAACTA
Statistics
Matches: 136, Mismatches: 18, Indels: 46
0.68 0.09 0.23
Matches are distributed among these distances:
1 12 0.09
2 112 0.82
3 11 0.08
4 1 0.01
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.40
Consensus pattern (2 bp):
TA
Found at i:12160540 original size:17 final size:17
Alignment explanation
Indices: 12160518--12160556 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
12160508 TAAGTATATA
*
12160518 ATATAAAGTATATAAA-T
1 ATATAAACTAT-TAAAGT
12160535 ATATAAACTATTAAAGT
1 ATATAAACTATTAAAGT
12160552 ATATA
1 ATATA
12160557 TATGAGTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (17 bp):
ATATAAACTATTAAAGT
Found at i:12160620 original size:12 final size:12
Alignment explanation
Indices: 12160505--12160621 Score: 75
Period size: 12 Copynumber: 9.5 Consensus size: 12
12160495 AGACAAAAGG
12160505 ATATAAGTATAT
1 ATATAAGTATAT
12160517 AATATAAAGTATAT
1 -ATAT-AAGTATAT
* *
12160531 AAAT-A-TATAA
1 ATATAAGTATAT
12160541 ACTATTAAAGTATAT
1 A-TA-T-AAGTATAT
*
12160556 ATATGAGTATAT
1 ATATAAGTATAT
12160568 ATATGAA-TATAT
1 ATAT-AAGTATAT
12160580 ATATATA-TATAT
1 ATATA-AGTATAT
*
12160592 ATATACTGTA-A-
1 ATATA-AGTATAT
12160603 ACTATAAGTATAT
1 A-TATAAGTATAT
12160616 ATATAA
1 ATATAA
12160622 ACTATAGTCT
Statistics
Matches: 83, Mismatches: 9, Indels: 25
0.71 0.08 0.21
Matches are distributed among these distances:
10 5 0.06
11 7 0.08
12 43 0.52
13 12 0.14
14 11 0.13
15 5 0.06
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (12 bp):
ATATAAGTATAT
Found at i:12165767 original size:8 final size:8
Alignment explanation
Indices: 12165747--12165790 Score: 61
Period size: 8 Copynumber: 5.4 Consensus size: 8
12165737 AGAAATCAAC
12165747 AAAGAGAAA
1 AAAGAG-AA
*
12165756 AAAGGGAA
1 AAAGAGAA
12165764 AAAGAGAA
1 AAAGAGAA
*
12165772 AAAGGGAA
1 AAAGAGAA
12165780 AAAGAGAA
1 AAAGAGAA
12165788 AAA
1 AAA
12165791 AGGGGAAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
8 26 0.84
9 5 0.16
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (8 bp):
AAAGAGAA
Found at i:12165769 original size:17 final size:17
Alignment explanation
Indices: 12165747--12165794 Score: 89
Period size: 16 Copynumber: 2.9 Consensus size: 17
12165737 AGAAATCAAC
12165747 AAAGAGAAAAAAGGGAA
1 AAAGAGAAAAAAGGGAA
12165764 AAAGAG-AAAAAGGGAA
1 AAAGAGAAAAAAGGGAA
12165780 AAAGAGAAAAAAGGG
1 AAAGAGAAAAAAGGG
12165795 GAAGCATGCG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 16 0.53
17 14 0.47
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (17 bp):
AAAGAGAAAAAAGGGAA
Found at i:12166136 original size:22 final size:22
Alignment explanation
Indices: 12166109--12166191 Score: 98
Period size: 22 Copynumber: 3.8 Consensus size: 22
12166099 AATTAAATAA
* *
12166109 AAAGTATAAAAATGTATACTAT
1 AAAGTATAAAAATATATACAAT
*
12166131 AAAGTAT-AAAAT-TATAGAAT
1 AAAGTATAAAAATATATACAAT
* *
12166151 ACAAGTATTAAAGTATATACAAT
1 A-AAGTATAAAAATATATACAAT
12166174 AAAGTATAAAAATATATA
1 AAAGTATAAAAATATATA
12166192 ATATAAGTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
20 7 0.13
21 11 0.21
22 26 0.50
23 8 0.15
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (22 bp):
AAAGTATAAAAATATATACAAT
Found at i:12166139 original size:43 final size:43
Alignment explanation
Indices: 12166084--12166201 Score: 116
Period size: 43 Copynumber: 2.7 Consensus size: 43
12166074 TTCTTGTAGT
*
12166084 CTATATAA-TATAAAGAAT-TA-AATAAAAAGTATAAAAATGTATA
1 CTATA-AAGTATAAA-AATATAGAAT-AAAAGTATAAAAATATATA
* * * *
12166127 CTATAAAGTATAAAATTATAGAATACAAGTATTAAAGTATATA
1 CTATAAAGTATAAAAATATAGAATAAAAGTATAAAAATATATA
* * *
12166170 CAATAAAGTATAAAAATATATAATATAAGTAT
1 CTATAAAGTATAAAAATATAGAATAAAAGTAT
12166202 TAAAGTGTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
42 4 0.06
43 56 0.89
44 3 0.05
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31
Consensus pattern (43 bp):
CTATAAAGTATAAAAATATAGAATAAAAGTATAAAAATATATA
Found at i:12166205 original size:29 final size:29
Alignment explanation
Indices: 12166173--12166712 Score: 246
Period size: 29 Copynumber: 19.1 Consensus size: 29
12166163 GTATATACAA
*
12166173 TAAAGTATAAAAATATATAATATAAGTAT
1 TAAAGTATAAAACTATATAATATAAGTAT
* * *
12166202 TAAAGTGTAAAAGTATAAAAGTATTAAAGTAT
1 TAAAGTATAAAACTATATAA-TA-T-AAGTAT
* * * *
12166234 AAAACTATAGAA-TATA-AGTATTAAAGTAT
1 TAAAGTATAAAACTATATAATA-T-AAGTAT
12166263 TAAAGTATAAAACTATATAATATAAGTAT
1 TAAAGTATAAAACTATATAATATAAGTAT
* * * *
12166292 TAAAGTGTATAAGTAT-TAAAGTATATAATA-
1 TAAAGTATAAAACTATAT-AA-TATA-AGTAT
12166322 TAAAGTATAAAACTATATAATATAAGTAT
1 TAAAGTATAAAACTATATAATATAAGTAT
* * *
12166351 TAAAGTGTATAA--GTAT--TA-AAGTAT
1 TAAAGTATAAAACTATATAATATAAGTAT
* *
12166375 TAAAGTATAAAACTGTAGAATATAAGTAT
1 TAAAGTATAAAACTATATAATATAAGTAT
* * *
12166404 TAAAGTGTATAAGTAT-TAA-AGTATA-TACT
1 TAAAGTATAAAACTATATAATA-TA-AGTA-T
* * * * *
12166433 TAAAGTGTACAAGTAT-TAAAGTATAA-AAC
1 TAAAGTATAAAACTATAT-AA-TATAAGTAT
* * * * *
12166462 TATAGAATATAAGTAT-TAA-AGTATGTACT
1 TAAAGTATAAAACTATATAATA-TAAGTA-T
*
12166491 ATAAAGTATAAAACTATAGAATATAAGTAT
1 -TAAAGTATAAAACTATATAATATAAGTAT
*
12166521 TAAAGTAT-AAA--A-GT-ATAT-AGTA-
1 TAAAGTATAAAACTATATAATATAAGTAT
*
12166543 TAAAGTATAAAACTATAGAATATAAGTAT
1 TAAAGTATAAAACTATATAATATAAGTAT
** * *
12166572 TAAAGTAT-GCACTATA-AAGTATAA-AAC
1 TAAAGTATAAAACTATATAA-TATAAGTAT
** * * * *
12166599 TATGGAATATAAGTAT-TAAAGTATATACTAT
1 TAAAGTATAAAACTATAT-AA-TATA-AGTAT
*
12166630 T-AAGTATAAAACTATAGAATATAAGTAT
1 TAAAGTATAAAACTATATAATATAAGTAT
* *
12166658 TAAAGTATATAA--GTAT--TA-AAGTAT
1 TAAAGTATAAAACTATATAATATAAGTAT
*
12166682 TAAAGTATAAAACTATAGAATATAAGTAT
1 TAAAGTATAAAACTATATAATATAAGTAT
12166711 TA
1 TA
12166713 GTATATAGTA
Statistics
Matches: 388, Mismatches: 76, Indels: 94
0.70 0.14 0.17
Matches are distributed among these distances:
22 8 0.02
23 7 0.02
24 37 0.10
25 5 0.01
26 7 0.02
27 20 0.05
28 44 0.11
29 165 0.43
30 56 0.14
31 23 0.06
32 16 0.04
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.33
Consensus pattern (29 bp):
TAAAGTATAAAACTATATAATATAAGTAT
Found at i:12166207 original size:8 final size:8
Alignment explanation
Indices: 12166196--12166689 Score: 129
Period size: 8 Copynumber: 65.8 Consensus size: 8
12166186 TATATAATAT
12166196 AAGTATTA
1 AAGTATTA
* *
12166204 AAGTGTAA
1 AAGTATTA
*
12166212 AAGTATAA
1 AAGTATTA
12166220 AAGTATTA
1 AAGTATTA
*
12166228 AAGTATAA
1 AAGTATTA
*
12166236 AACTA-TA
1 AAGTATTA
12166243 GAA-TA-T-
1 -AAGTATTA
12166249 AAGTATTA
1 AAGTATTA
12166257 AAGTATTA
1 AAGTATTA
*
12166265 AAGTATAA
1 AAGTATTA
*
12166273 AACTA-TA
1 AAGTATTA
12166280 TAA-TA-T-
1 -AAGTATTA
12166286 AAGTATTA
1 AAGTATTA
*
12166294 AAGT-GTA
1 AAGTATTA
12166301 TAAGTATTA
1 -AAGTATTA
12166310 AAGTA-TA
1 AAGTATTA
12166317 TAA-TA-TA
1 -AAGTATTA
*
12166324 AAGTATAA
1 AAGTATTA
*
12166332 AACTA-TA
1 AAGTATTA
12166339 TAA-TA-T-
1 -AAGTATTA
12166345 AAGTATTA
1 AAGTATTA
*
12166353 AAGT-GTA
1 AAGTATTA
12166360 TAAGTATTA
1 -AAGTATTA
12166369 AAGTATTA
1 AAGTATTA
*
12166377 AAGTATAA
1 AAGTATTA
*
12166385 AACTGTAGAATA
1 AA--GT--ATTA
12166397 TAAGTATTA
1 -AAGTATTA
*
12166406 AAGT-GTA
1 AAGTATTA
12166413 TAAGTATTA
1 -AAGTATTA
12166422 AAGTA-T-
1 AAGTATTA
12166428 -A-TACTTA
1 AAGTA-TTA
*
12166435 AAGT-GTA
1 AAGTATTA
12166442 CAAGTATTA
1 -AAGTATTA
*
12166451 AAGTATAA
1 AAGTATTA
*
12166459 AACTA-TA
1 AAGTATTA
12166466 GAA-TA-T-
1 -AAGTATTA
12166472 AAGTATTA
1 AAGTATTA
12166480 AAGTATGT-
1 AAGTAT-TA
*
12166488 -ACTA-TA
1 AAGTATTA
*
12166494 AAGTATAA
1 AAGTATTA
*
12166502 AACTA-TA
1 AAGTATTA
12166509 GAA-TA-T-
1 -AAGTATTA
12166515 AAGTATTA
1 AAGTATTA
*
12166523 AAGTATAA
1 AAGTATTA
12166531 AAGTA-TA
1 AAGTATTA
*
12166538 TAGTA-TA
1 AAGTATTA
*
12166545 AAGTATAA
1 AAGTATTA
*
12166553 AACTA-TA
1 AAGTATTA
12166560 GAA-TA-T-
1 -AAGTATTA
12166566 AAGTATTA
1 AAGTATTA
*
12166574 AAGTA-TG
1 AAGTATTA
* *
12166581 CACTA-TA
1 AAGTATTA
*
12166588 AAGTATAA
1 AAGTATTA
* **
12166596 AACTATGG
1 AAGTATTA
12166604 AA-TA-T-
1 AAGTATTA
12166609 AAGTATTA
1 AAGTATTA
12166617 AAGTA-TA
1 AAGTATTA
* *
12166624 TACTATT-
1 AAGTATTA
*
12166631 AAGTATAA
1 AAGTATTA
*
12166639 AACTA-TA
1 AAGTATTA
12166646 GAA-TA-T-
1 -AAGTATTA
12166652 AAGTATTA
1 AAGTATTA
12166660 AAGTA-TA
1 AAGTATTA
12166667 TAAGTATTA
1 -AAGTATTA
12166676 AAGTATTA
1 AAGTATTA
12166684 AAGTAT
1 AAGTAT
12166690 AAAACTATAG
Statistics
Matches: 366, Mismatches: 58, Indels: 124
0.67 0.11 0.23
Matches are distributed among these distances:
4 2 0.01
5 18 0.05
6 19 0.05
7 91 0.25
8 213 0.58
9 15 0.04
10 2 0.01
11 2 0.01
12 2 0.01
13 2 0.01
ACGTcount: A:0.51, C:0.03, G:0.12, T:0.33
Consensus pattern (8 bp):
AAGTATTA
Found at i:12166216 original size:37 final size:37
Alignment explanation
Indices: 12166174--12166537 Score: 155
Period size: 37 Copynumber: 9.2 Consensus size: 37
12166164 TATATACAAT
*
12166174 AAAGTATAAAAATATATAATATAAGTATTAAAGTGTA
1 AAAGTATAAAAATATATAATATAAGTATTAAAGTATA
* * *
12166211 AAAGTATAAAAGTATTAAAGTATAAAACTATAG-AATATAAGTATT
1 AAAGTATAAAA--A-T--A-TATAATA-TA-AGTATTA-AAGTATA
* * *
12166256 AAAGTATTAAAGTATAAAACTATATAATATAAGTATTAAAGTGTA
1 AAAGTA-TAAA-AAT-ATA-TA-A---TATAAGTATTAAAGTATA
* * * * *
12166301 TAAGTATTAAAGTATATAATATAAAGTATAAAACTATA
1 AAAGTATAAAAATATATAATAT-AAGTATTAAAGTATA
* ** *
12166339 TAA-TATAAGTAT-TA-AAGTGTATAAGTATTAAAGTATT
1 AAAGTATAAAAATATATAA---TATAAGTATTAAAGTATA
* * * *
12166376 AAAGTATAAAACTGTAGAATATAAGTATTAAAGTGTA
1 AAAGTATAAAAATATATAATATAAGTATTAAAGTATA
* * * * * *
12166413 TAAGTATTAAAGTATATACT-TAAAGT-GTACAAGTATT
1 AAAGTATAAAAATATATAATAT-AAGTATTA-AAGTATA
* *
12166450 AAAGTATAAAACTATAGAATATAAGTATTAAAGTATGTACTA
1 AAAGTATAAAAATATATAATATAAGTATT-AA--A-GTA-TA
* *
12166492 TAAAGTATAAAACTATAGAATATAAGTATTAAAGTATA
1 -AAAGTATAAAAATATATAATATAAGTATTAAAGTATA
12166530 AAAGTATA
1 AAAGTATA
12166538 TAGTATAAAG
Statistics
Matches: 246, Mismatches: 47, Indels: 68
0.68 0.13 0.19
Matches are distributed among these distances:
35 2 0.01
36 5 0.02
37 99 0.40
38 29 0.12
39 7 0.03
40 6 0.02
41 5 0.02
42 7 0.03
43 40 0.16
44 10 0.04
45 26 0.11
46 9 0.04
47 1 0.00
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.33
Consensus pattern (37 bp):
AAAGTATAAAAATATATAATATAAGTATTAAAGTATA
Found at i:12166496 original size:43 final size:43
Alignment explanation
Indices: 12166449--12166746 Score: 339
Period size: 43 Copynumber: 6.6 Consensus size: 43
12166439 GTACAAGTAT
12166449 TAAAGTATAAAACTATAGAATATAAGTATTAAAGTATGTACTA
1 TAAAGTATAAAACTATAGAATATAAGTATTAAAGTATGTACTA
*
12166492 TAAAGTATAAAACTATAGAATATAAGTATTAAAGTATAAAAGTATATAGTA
1 TAAAGTATAAAACTATAGAATATAAGTATTAAAGTAT----G----TACTA
*
12166543 TAAAGTATAAAACTATAGAATATAAGTATTAAAGTATGCACTA
1 TAAAGTATAAAACTATAGAATATAAGTATTAAAGTATGTACTA
* *
12166586 TAAAGTATAAAACTATGGAATATAAGTATTAAAGTATATACTA
1 TAAAGTATAAAACTATAGAATATAAGTATTAAAGTATGTACTA
* *
12166629 TTAAGTATAAAACTATAGAATATAAGTATTAAAGTATATAAGTATTAAAGTA
1 TAAAGTATAAAACTATAGAATATAAGTATTAAAG--TAT--G---T--ACTA
* *
12166681 TTAAAGTATAAAACTATAGAATATAAGTATT--AGTATATAGTA
1 -TAAAGTATAAAACTATAGAATATAAGTATTAAAGTATGTACTA
*
12166723 TAAAGTATAAAACTATATAATATA
1 TAAAGTATAAAACTATAGAATATA
12166747 TGTAACACCC
Statistics
Matches: 224, Mismatches: 13, Indels: 38
0.81 0.05 0.14
Matches are distributed among these distances:
41 23 0.10
42 4 0.02
43 112 0.50
44 1 0.00
45 3 0.01
47 2 0.01
49 3 0.01
50 1 0.00
51 43 0.19
52 3 0.01
53 29 0.13
ACGTcount: A:0.52, C:0.04, G:0.11, T:0.33
Consensus pattern (43 bp):
TAAAGTATAAAACTATAGAATATAAGTATTAAAGTATGTACTA
Found at i:12166561 original size:94 final size:91
Alignment explanation
Indices: 12166444--12166746 Score: 386
Period size: 94 Copynumber: 3.3 Consensus size: 91
12166434 AAAGTGTACA
12166444 AGTATTAAAGTATAAAACTATAGAATATAAGTATTAAAGTATGTACTATAAAGTATAAAACTATA
1 AGTA-TAAAGTATAAAACTATAGAATATAAGTATTAAAGTATGTACTATAAAGTATAAAACTATA
12166509 GAATATAAGTATTAAAGTATAAAAGTATAT
65 GAATATAAGTATTAAAGTAT---AGTATAT
* *
12166539 AGTATAAAGTATAAAACTATAGAATATAAGTATTAAAGTATGCACTATAAAGTATAAAACTATGG
1 AGTATAAAGTATAAAACTATAGAATATAAGTATTAAAGTATGTACTATAAAGTATAAAACTATAG
*
12166604 AATATAAGTATTAAAGTATA-TA-CT
66 AATATAAGTATTAAAGTATAGTATAT
* * * *
12166628 A-T-T-AAGTATAAAACTATAGAATATAAGTATTAAAGTATATAAGTATTAAAGTATTAAAGTAT
1 AGTATAAAGTATAAAACTATAGAATATAAGTATTAAAGTATGT-ACTA-TAAAGTATAAAACTAT
* *
12166690 AAAACTAT-AG-AATATAAGTATTAGTATAT
64 AGAA-TATAAGTATTA-AAGTA-TAGTATAT
*
12166719 AGTATAAAGTATAAAACTATATAATATA
1 AGTATAAAGTATAAAACTATAGAATATA
12166747 TGTAACACCC
Statistics
Matches: 185, Mismatches: 13, Indels: 21
0.84 0.06 0.10
Matches are distributed among these distances:
86 35 0.19
87 7 0.04
88 24 0.13
89 7 0.04
90 4 0.02
91 3 0.02
92 1 0.01
93 1 0.01
94 99 0.54
95 4 0.02
ACGTcount: A:0.52, C:0.04, G:0.11, T:0.33
Consensus pattern (91 bp):
AGTATAAAGTATAAAACTATAGAATATAAGTATTAAAGTATGTACTATAAAGTATAAAACTATAG
AATATAAGTATTAAAGTATAGTATAT
Found at i:12166658 original size:86 final size:90
Alignment explanation
Indices: 12166126--12166316 Score: 157
Period size: 90 Copynumber: 2.2 Consensus size: 90
12166116 AAAAATGTAT
* * ** *
12166126 ACTA-TAAAGTATAAAATTATAGAATACAAGTATTAAAGTATATACAATAAAGTATAAAAATATA
1 ACTATTAAAGTATAAAACTATAGAATATAAGTATTAAAGTATATAGTATAAAGTATAAAACTATA
* * *
12166190 TAATATAAGTATTAAAGTGTAAAAGTATAAA
66 GAATATAAGTATTAAAG-AT-ATAG--T--A
*
12166221 AGTATTAAAGTATAAAACTATAGAATATAAGTATTAAAG----TA-T-TAAAGTATAAAACTATA
1 ACTATTAAAGTATAAAACTATAGAATATAAGTATTAAAGTATATAGTATAAAGTATAAAACTATA
* *
12166280 TAATATAAGTATTAAAG-TGTA-TA
66 GAATATAAGTATTAAAGATATAGTA
*
12166303 AGTATTAAAGTATA
1 ACTATTAAAGTATA
12166317 TAATATAAAG
Statistics
Matches: 88, Mismatches: 7, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
82 15 0.17
84 1 0.01
87 1 0.01
88 1 0.01
90 33 0.38
92 2 0.02
95 3 0.03
96 32 0.36
ACGTcount: A:0.54, C:0.03, G:0.10, T:0.32
Consensus pattern (90 bp):
ACTATTAAAGTATAAAACTATAGAATATAAGTATTAAAGTATATAGTATAAAGTATAAAACTATA
GAATATAAGTATTAAAGATATAGTA
Found at i:12166746 original size:7 final size:8
Alignment explanation
Indices: 12166605--12166747 Score: 54
Period size: 8 Copynumber: 19.5 Consensus size: 8
12166595 AAACTATGGA
12166605 ATATAAGT
1 ATATAAGT
12166613 AT-TAAAGT
1 ATAT-AAGT
*
12166621 ATAT-ACT
1 ATATAAGT
12166628 AT-TAAGT
1 ATATAAGT
12166635 ATA-AA--
1 ATATAAGT
*
12166640 ACTAT-AGA
1 A-TATAAGT
12166648 ATATAAGT
1 ATATAAGT
12166656 AT-TAAAGT
1 ATAT-AAGT
12166664 ATATAAGT
1 ATATAAGT
12166672 AT-TAAAGT
1 ATAT-AAGT
12166680 AT-TAAAGT
1 ATAT-AAGT
12166688 ATA-AA--
1 ATATAAGT
*
12166693 ACTAT-AGA
1 A-TATAAGT
12166701 ATATAAGT
1 ATATAAGT
12166709 AT-T-AGT
1 ATATAAGT
12166715 ATAT-AGT
1 ATATAAGT
12166722 ATA-AAGT
1 ATATAAGT
* *
12166729 ATAAAACT
1 ATATAAGT
12166737 ATATAA-T
1 ATATAAGT
12166744 ATAT
1 ATAT
12166748 GTAACACCCA
Statistics
Matches: 108, Mismatches: 6, Indels: 43
0.69 0.04 0.27
Matches are distributed among these distances:
5 2 0.02
6 12 0.11
7 40 0.37
8 52 0.48
9 2 0.02
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.36
Consensus pattern (8 bp):
ATATAAGT
Found at i:12167454 original size:2 final size:2
Alignment explanation
Indices: 12167447--12167517 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
12167437 TATGCGTGGT
12167447 TA TA TA 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
12167489 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12167518 TATCCCTTCA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12168253 original size:57 final size:57
Alignment explanation
Indices: 12168077--12168545 Score: 652
Period size: 57 Copynumber: 8.2 Consensus size: 57
12168067 TCCAATACAA
* * * * ** ** *
12168077 AAATTCATCCACTTAGTATAAATTTCTTATCATGTTAGCACACGAAGTGCCTTATCTAG
1 AAATTCATACACTTAGTAT-GATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT-G
* * *
12168136 AAATTCATACACTTAGTATGATTTCGTTATCATTTTAGCGTACGAAATGCCCTATATG
1 AAATTCATACACTTAGTATGATTTC-TTAACATTTTAGCGTACGAAACGCCCTATCTG
*
12168194 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAGCGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * *
12168251 AAATTCATACACTTGGTATGATTTTTTAACATTTTAGCGTACGAAACACCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* *
12168308 AAATTCATACACTTAGTATGATTTCGTTATCATTTTAGCGTACGAAACGCCCTATATG
1 AAATTCATACACTTAGTATGATTTC-TTAACATTTTAGCGTACGAAACGCCCTATCTG
*
12168366 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAGCGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * *
12168423 AAATTCATACACTTGGTATGATTTTTTAACATTTTAGCGTACGAAACACCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * ** *
12168480 AAATTCATACACTTAGTATGATTTCTTATCATTTTAGTGTACGAAA-TTCCTATCTA
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
12168536 AAATTCATAC
1 AAATTCATAC
12168546 TGTTGAGTTA
Statistics
Matches: 373, Mismatches: 35, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
56 17 0.05
57 228 0.61
58 85 0.23
59 43 0.12
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (57 bp):
AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
Found at i:12168325 original size:172 final size:172
Alignment explanation
Indices: 12168129--12168545 Score: 766
Period size: 172 Copynumber: 2.4 Consensus size: 172
12168119 CGAAGTGCCT
12168129 TATCTAGAAATTCATACACTTAGTATGATTTCGTTATCATTTTAGCGTACGAAATGCCCTATATG
1 TATCT-GAAATTCATACACTTAGTATGATTTCGTTATCATTTTAGCGTACGAAATGCCCTATATG
12168194 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAGCGCCCTATCTGAAATTCAT
65 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAGCGCCCTATCTGAAATTCAT
12168259 ACACTTGGTATGATTTTTTAACATTTTAGCGTACGAAACACCC
130 ACACTTGGTATGATTTTTTAACATTTTAGCGTACGAAACACCC
*
12168302 TATCTGAAATTCATACACTTAGTATGATTTCGTTATCATTTTAGCGTACGAAACGCCCTATATGA
1 TATCTGAAATTCATACACTTAGTATGATTTCGTTATCATTTTAGCGTACGAAATGCCCTATATGA
12168367 AATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAGCGCCCTATCTGAAATTCATA
66 AATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAGCGCCCTATCTGAAATTCATA
12168432 CACTTGGTATGATTTTTTAACATTTTAGCGTACGAAACACCC
131 CACTTGGTATGATTTTTTAACATTTTAGCGTACGAAACACCC
* * * *
12168474 TATCTGAAATTCATACACTTAGTATGATTTC-TTATCATTTTAGTGTACGAAAT-TCCTATCTAA
1 TATCTGAAATTCATACACTTAGTATGATTTCGTTATCATTTTAGCGTACGAAATGCCCTATATGA
12168537 AATTCATAC
66 AATTCATAC
12168546 TGTTGAGTTA
Statistics
Matches: 238, Mismatches: 6, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
170 16 0.07
171 20 0.08
172 197 0.83
173 5 0.02
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (172 bp):
TATCTGAAATTCATACACTTAGTATGATTTCGTTATCATTTTAGCGTACGAAATGCCCTATATGA
AATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAGCGCCCTATCTGAAATTCATA
CACTTGGTATGATTTTTTAACATTTTAGCGTACGAAACACCC
Found at i:12168360 original size:115 final size:114
Alignment explanation
Indices: 12168077--12168545 Score: 652
Period size: 115 Copynumber: 4.1 Consensus size: 114
12168067 TCCAATACAA
* * * * ** ** *
12168077 AAATTCATCCACTTAGTATAAATTTCTTATCATGTTAGCACACGAAGTGCCTTATCTAGAAATTC
1 AAATTCATACACTTAGTAT-GATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT-GAAATTC
* * *
12168142 ATACACTTAGTATGATTTCGTTATCATTTTAGCGTACGAAATGCCCTATATG
64 ATACACTTAGTATGATTTC-TTAACATTTTAGCGTACGAAACGCCCTATCTG
*
12168194 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAGCGCCCTATCTGAAATTCAT
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCAT
* * *
12168259 ACACTTGGTATGATTTTTTAACATTTTAGCGTACGAAACACCCTATCTG
66 ACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* *
12168308 AAATTCATACACTTAGTATGATTTCGTTATCATTTTAGCGTACGAAACGCCCTATATGAAATTCA
1 AAATTCATACACTTAGTATGATTTC-TTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCA
*
12168373 TACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAGCGCCCTATCTG
65 TACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * *
12168423 AAATTCATACACTTGGTATGATTTTTTAACATTTTAGCGTACGAAACACCCTATCTGAAATTCAT
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCAT
* * ** *
12168488 ACACTTAGTATGATTTCTTATCATTTTAGTGTACGAAA-TTCCTATCTA
66 ACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
12168536 AAATTCATAC
1 AAATTCATAC
12168546 TGTTGAGTTA
Statistics
Matches: 319, Mismatches: 32, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
113 17 0.05
114 125 0.39
115 129 0.40
116 30 0.09
117 18 0.06
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (114 bp):
AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCAT
ACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
Found at i:12171979 original size:23 final size:23
Alignment explanation
Indices: 12171953--12172002 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
12171943 GGGGTATTGG
12171953 TACCCATTCAAAGAGGGTATCAA
1 TACCCATTCAAAGAGGGTATCAA
* *
12171976 TACCCATTCAAAGGGGGTATCGA
1 TACCCATTCAAAGAGGGTATCAA
12171999 TACC
1 TACC
12172003 TAGTGCATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (23 bp):
TACCCATTCAAAGAGGGTATCAA
Found at i:12175860 original size:22 final size:21
Alignment explanation
Indices: 12175818--12175857 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12175808 AACACTATTT
12175818 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
12175839 TCATTTTTTTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
12175858 ATAAAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.57
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:12178245 original size:2 final size:2
Alignment explanation
Indices: 12178238--12178267 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12178228 ATTAACCATA
12178238 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
12178268 CTTTCTGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12180194 original size:81 final size:82
Alignment explanation
Indices: 12180069--12180220 Score: 200
Period size: 81 Copynumber: 1.9 Consensus size: 82
12180059 TCAACAGTGT
* * * *
12180069 TTAACCCTTTATCTAACTGGCATAATTAACACCTTTTTGCCAATTGCACAGTTAGACCATTA-TT
1 TTAACCCTTCATCTAACTGGCATAATTAACACCTTTTTACCAATTGCACAGCTAGACCATCACTT
12180133 CTTTTACGCAATGGTAC
66 CTTTTACGCAATGGTAC
* * * * *
12180150 TTAACCGTTCATCTAACTGGCATAATTGATA-CTTTTCTATCAATTGCACAGCTAGGCCATCACT
1 TTAACCCTTCATCTAACTGGCATAATTAACACCTTTT-TACCAATTGCACAGCTAGACCATCACT
12180214 TCTTTTA
65 TCTTTTA
12180221 ATTTGGAATT
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
80 5 0.08
81 47 0.78
82 8 0.13
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.38
Consensus pattern (82 bp):
TTAACCCTTCATCTAACTGGCATAATTAACACCTTTTTACCAATTGCACAGCTAGACCATCACTT
CTTTTACGCAATGGTAC
Found at i:12180730 original size:57 final size:57
Alignment explanation
Indices: 12180553--12181096 Score: 730
Period size: 57 Copynumber: 9.5 Consensus size: 57
12180543 TCCAATACAT
* * * ** * **
12180553 AAATTCTTACACTTAGTATGAATTTCTTATCATGTTAGCACAAGAAGTGCCCTATCTGG
1 AAATTCATACACTTAGTATG-ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT-G
* * * * *
12180612 AAATTCATACACTTATTATGATTTCTTTATCATTTTAACGTACAAAATGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTC-TTAACATTTTAGCGTACGAAACGCCCTATCTG
* *
12180670 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACACCCTATTTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * * *
12180727 AAATTCATAGACTTGGTGTGATTTTTTAACATTTTAGCGTACGAAACGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * *
12180784 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGAGTATGAAACGCCCTATATG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
*
12180841 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTAC-AGAACGCCCTATCTA
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGA-AACGCCCTATCTG
* * * * * *
12180898 AAATTCATACACTTAATATGATTTCTTAATAATTTAGCATATGAAACGCCCTATTTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * *
12180955 AAATTCATACACTTAGTATGATTTTTTAACATTTTAGCGTACAAAACCCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* *
12181012 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAATGCCCTTTCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
*
12181069 AAATTCATACACTTATTATGATTTCTTA
1 AAATTCATACACTTAGTATGATTTCTTA
12181097 TATTTCACAC
Statistics
Matches: 427, Mismatches: 55, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
56 1 0.00
57 353 0.83
58 31 0.07
59 42 0.10
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (57 bp):
AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
Found at i:12182516 original size:16 final size:16
Alignment explanation
Indices: 12182495--12182525 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12182485 GGTATTACAA
12182495 TATAAGTATTAAAGTG
1 TATAAGTATTAAAGTG
12182511 TATAAGTATTAAAGT
1 TATAAGTATTAAAGT
12182526 ATAAAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (16 bp):
TATAAGTATTAAAGTG
Found at i:12182529 original size:14 final size:14
Alignment explanation
Indices: 12182486--12182529 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 14
12182476 AAAATTTGGG
12182486 GTATTACAA-TATAA
1 GTATTA-AAGTATAA
12182500 GTATTAAAGTGTATAA
1 GTATTAAA--GTATAA
12182516 GTATTAAAGTATAA
1 GTATTAAAGTATAA
12182530 AATTATTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 2 0.07
14 12 0.44
16 13 0.48
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (14 bp):
GTATTAAAGTATAA
Found at i:12182536 original size:16 final size:16
Alignment explanation
Indices: 12182498--12182559 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 16
12182488 ATTACAATAT
* *
12182498 AAGTATTAAAGTGTAT
1 AAGTATTAAAGTATAA
12182514 AAGTATTAAAGTATAA
1 AAGTATTAAAGTATAA
* *
12182530 AATTATT---GAATAA
1 AAGTATTAAAGTATAA
*
12182543 AAGTATGAAAGTATAA
1 AAGTATTAAAGTATAA
12182559 A
1 A
12182560 CATATACATA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
13 10 0.28
16 26 0.72
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (16 bp):
AAGTATTAAAGTATAA
Found at i:12182597 original size:8 final size:8
Alignment explanation
Indices: 12182586--12182832 Score: 121
Period size: 8 Copynumber: 31.2 Consensus size: 8
12182576 AACTATAATG
*
12182586 TATAAGTG
1 TATAAGTA
*
12182594 TATAAG-C
1 TATAAGTA
12182601 TATAAGTA
1 TATAAGTA
12182609 TATAAGTA
1 TATAAGTA
12182617 TATAA-TA
1 TATAAGTA
12182624 TA-AAGTA
1 TATAAGTA
12182631 TAATAAAAGTTTA
1 T-AT--AAG--TA
12182644 TATATA-TA
1 TATA-AGTA
*
12182652 TATATGTA
1 TATAAGTA
* *
12182660 TGTATGTA
1 TATAAGTA
* *
12182668 TGTATGTA
1 TATAAGTA
*
12182676 TGTATATGTA
1 --TATAAGTA
* *
12182686 TGTATGTA
1 TATAAGTA
* *
12182694 TGTATGTA
1 TATAAGTA
12182702 T-TAAGTA
1 TATAAGTA
12182709 -ATAAAGTA
1 TAT-AAGTA
12182717 TA-AAGTATA
1 TATAAG--TA
12182726 TATAAGTA
1 TATAAGTA
*
12182734 T-TAAATA
1 TATAAGTA
*
12182741 TA-AAATA
1 TATAAGTA
12182748 TATAAGTA
1 TATAAGTA
12182756 TATAA-TA
1 TATAAGTA
12182763 TATAA-TA
1 TATAAGTA
12182770 TATAA-TA
1 TATAAGTA
12182777 TA-AAGTA
1 TATAAGTA
12182784 TATAAGTA
1 TATAAGTA
*
12182792 T-TAAATA
1 TATAAGTA
12182799 TA-AAGTA
1 TATAAGTA
12182806 TA-AAGTA
1 TATAAGTA
*
12182813 TGTATAAATA
1 --TATAAGTA
12182823 TATAAGTA
1 TATAAGTA
12182831 TA
1 TA
12182833 ATTATATTAA
Statistics
Matches: 200, Mismatches: 13, Indels: 52
0.75 0.05 0.20
Matches are distributed among these distances:
6 4 0.02
7 74 0.37
8 91 0.46
9 7 0.04
10 15 0.08
11 4 0.02
12 2 0.01
13 3 0.01
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (8 bp):
TATAAGTA
Found at i:12182604 original size:15 final size:14
Alignment explanation
Indices: 12182579--12182839 Score: 71
Period size: 14 Copynumber: 19.2 Consensus size: 14
12182569 ATATATAAAC
*
12182579 TATAATGTATAAGTG
1 TATAA-GTATAAGTA
12182594 TATAAGCTATAAGTA
1 TATAAG-TATAAGTA
*
12182609 TATAAGTATATAATA
1 TATAAGTATA-AGTA
12182624 TA-AAGTATAA-TA
1 TATAAGTATAAGTA
*
12182636 -A-AAGT-TTA-TA
1 TATAAGTATAAGTA
*
12182646 TATATA-TATATGTA
1 TATA-AGTATAAGTA
* *
12182660 TGTATGTAT--GTA
1 TATAAGTATAAGTA
* * *
12182672 TGTATGTATATGTA
1 TATAAGTATAAGTA
* *
12182686 TGTATGTAT--GTA
1 TATAAGTATAAGTA
*
12182698 TGT-A-T-TAAGTA
1 TATAAGTATAAGTA
12182709 -ATAAAGTATAAAGTATA
1 TAT-AAGTAT-AAG--TA
*
12182726 TATAAGTATTAAATA
1 TATAAGTA-TAAGTA
* *
12182741 TAAAATATATAAGTA
1 TATAA-GTATAAGTA
*
12182756 TATAA-TATATAATA
1 TATAAGTATA-AGTA
12182770 TATAA-TATAAAGTA
1 TATAAGTAT-AAGTA
*
12182784 TATAAGTATTAAATA
1 TATAAGTA-TAAGTA
12182799 TA-AAGTATAA--A
1 TATAAGTATAAGTA
*
12182810 GTAT--GTATAAATA
1 -TATAAGTATAAGTA
*
12182823 TATAAGTATAATTA
1 TATAAGTATAAGTA
12182837 TAT
1 TAT
12182840 TAATATGAAT
Statistics
Matches: 196, Mismatches: 18, Indels: 65
0.70 0.06 0.23
Matches are distributed among these distances:
9 1 0.01
10 6 0.03
11 16 0.08
12 28 0.14
13 12 0.06
14 68 0.35
15 50 0.26
16 3 0.02
17 9 0.05
18 3 0.02
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.40
Consensus pattern (14 bp):
TATAAGTATAAGTA
Found at i:12182629 original size:14 final size:16
Alignment explanation
Indices: 12182586--12182832 Score: 121
Period size: 15 Copynumber: 15.6 Consensus size: 16
12182576 AACTATAATG
* *
12182586 TATAAGTGTATAAG-C
1 TATAAGTATATAAGTA
12182601 TATAAGTATATAAGTA
1 TATAAGTATATAAGTA
12182617 TATAA-TATA-AAGTA
1 TATAAGTATATAAGTA
12182631 TAATAAAAGTTTATATATA-TA
1 T-AT--AAG--TATATA-AGTA
* * *
12182652 TATATGTATGTATGTA
1 TATAAGTATATAAGTA
* * *
12182668 TGTATGTATGTATATGTA
1 TATAAGTA--TATAAGTA
* * * *
12182686 TGTATGTATGTATGTA
1 TATAAGTATATAAGTA
12182702 T-TAAGTA-ATAAAGTA
1 TATAAGTATAT-AAGTA
12182717 TA-AAGTATATATAAGTA
1 TATAAG--TATATAAGTA
* *
12182734 T-TAAATATA-AAATA
1 TATAAGTATATAAGTA
12182748 TATAAGTATATAA-TA
1 TATAAGTATATAAGTA
12182763 TATAA-TATATAA-TA
1 TATAAGTATATAAGTA
12182777 TA-AAGTATATAAGTA
1 TATAAGTATATAAGTA
*
12182792 T-TAAATATA-AAGTA
1 TATAAGTATATAAGTA
*
12182806 TA-AAGTATGTATAAATA
1 TATAAGTA--TATAAGTA
12182823 TATAAGTATA
1 TATAAGTATA
12182833 ATTATATTAA
Statistics
Matches: 187, Mismatches: 17, Indels: 55
0.72 0.07 0.21
Matches are distributed among these distances:
13 2 0.01
14 40 0.21
15 59 0.32
16 33 0.18
17 18 0.10
18 24 0.13
20 6 0.03
21 4 0.02
22 1 0.01
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (16 bp):
TATAAGTATATAAGTA
Found at i:12182636 original size:23 final size:22
Alignment explanation
Indices: 12182570--12182632 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 22
12182560 CATATACATA
*
12182570 TATATAAACTATAA-TGTATAAG
1 TATAT-AACTATAAGTATATAAG
*
12182592 TGTATAAGCTATAAGTATATAAG
1 TATATAA-CTATAAGTATATAAG
12182615 TATATAA-TATAAAGTATA
1 TATATAACTAT-AAGTATA
12182633 ATAAAAGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
21 5 0.14
22 17 0.49
23 13 0.37
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.37
Consensus pattern (22 bp):
TATATAACTATAAGTATATAAG
Found at i:12182661 original size:4 final size:4
Alignment explanation
Indices: 12182654--12182702 Score: 84
Period size: 4 Copynumber: 12.8 Consensus size: 4
12182644 TATATATATA
12182654 TATG TATG TATG TATG TATG TATG TA-- TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
12182700 TAT
1 TAT
12182703 TAAGTAATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
4 41 0.95
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:12182681 original size:26 final size:26
Alignment explanation
Indices: 12182652--12182702 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
12182642 TATATATATA
12182652 TATATGTATGTATGTATGTATGTATG
1 TATATGTATGTATGTATGTATGTATG
12182678 TATATGTATGTATGTATGTATGTAT
1 TATATGTATGTATGTATGTATGTAT
12182703 TAAGTAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (26 bp):
TATATGTATGTATGTATGTATGTATG
Found at i:12182686 original size:22 final size:22
Alignment explanation
Indices: 12182658--12182702 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
12182648 TATATATATG
12182658 TATGTATGTATGTATGTATGTA
1 TATGTATGTATGTATGTATGTA
12182680 TATGTATGTATGTATGTATGTA
1 TATGTATGTATGTATGTATGTA
12182702 T
1 T
12182703 TAAGTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (22 bp):
TATGTATGTATGTATGTATGTA
Found at i:12182721 original size:7 final size:7
Alignment explanation
Indices: 12182699--12182833 Score: 81
Period size: 7 Copynumber: 18.9 Consensus size: 7
12182689 ATGTATGTAT
*
12182699 GTATTAA
1 GTATAAA
12182706 GTAATAAA
1 GT-ATAAA
12182714 GTATAAA
1 GTATAAA
12182721 GTATATATAA
1 G--TATA-AA
12182731 GTATTAAA
1 GTA-TAAA
12182739 -TATAAA
1 GTATAAA
*
12182745 ATATATAA
1 GTATA-AA
12182753 GTATATAA
1 GTATA-AA
12182761 -TATATAA
1 GTATA-AA
12182768 -TATATAA
1 GTATA-AA
12182775 -TATAAA
1 GTATAAA
12182781 GTATATAA
1 GTATA-AA
12182789 GTATTAAA
1 GTA-TAAA
12182797 -TATAAA
1 GTATAAA
12182803 GTATAAA
1 GTATAAA
12182810 GTAT---
1 GTATAAA
12182814 GTATAAA
1 GTATAAA
12182821 -TATATAA
1 GTATA-AA
12182828 GTATAA
1 GTATAA
12182834 TTATATTAAT
Statistics
Matches: 110, Mismatches: 2, Indels: 32
0.76 0.01 0.22
Matches are distributed among these distances:
4 4 0.04
6 14 0.13
7 51 0.46
8 30 0.27
9 8 0.07
10 3 0.03
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (7 bp):
GTATAAA
Found at i:12182724 original size:22 final size:22
Alignment explanation
Indices: 12182699--12182833 Score: 111
Period size: 22 Copynumber: 6.0 Consensus size: 22
12182689 ATGTATGTAT
12182699 GTAT-TAAGTAATAAAGTATAAA
1 GTATATAAGT-ATAAAGTATAAA
12182721 GTATATATAAGTATTAAA-TATAAA
1 G--TATATAAGTA-TAAAGTATAAA
*
12182745 ATATATAAGTATATAA-TATATAA
1 GTATATAAGTATA-AAGTATA-AA
12182768 -TATATAA-TATAAAGTATATAA
1 GTATATAAGTATAAAGTATA-AA
*
12182789 GTAT-TAAATATAAAGTATAAA
1 GTATATAAGTATAAAGTATAAA
*
12182810 GTATGTATAAATATATAAGTATAA
1 GTA--TATAAGTATA-AAGTATAA
12182834 TTATATTAAT
Statistics
Matches: 99, Mismatches: 1, Indels: 23
0.80 0.01 0.19
Matches are distributed among these distances:
20 2 0.02
21 21 0.21
22 38 0.38
23 3 0.03
24 18 0.18
25 17 0.17
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (22 bp):
GTATATAAGTATAAAGTATAAA
Found at i:12182797 original size:58 final size:61
Alignment explanation
Indices: 12182715--12182832 Score: 172
Period size: 58 Copynumber: 2.0 Consensus size: 61
12182705 AGTAATAAAG
12182715 TATAAAGTATATATAAGTATTAAATATAAAATATATAAGTA-TAT-AATATATAA-TATATAA
1 TATAAAG-ATATATAAGTATTAAATATAAAATATA-AAGTAGTATAAATATATAAGTATATAA
*
12182775 TATAAAG-TATATAAGTATTAAATATAAAGTATAAAGTATGTATAAATATATAAGTATA
1 TATAAAGATATATAAGTATTAAATATAAAATATAAAGTA-GTATAAATATATAAGTATA
12182833 ATTATATTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
57 5 0.09
58 25 0.47
59 3 0.06
60 16 0.30
61 4 0.08
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (61 bp):
TATAAAGATATATAAGTATTAAATATAAAATATAAAGTAGTATAAATATATAAGTATATAA
Found at i:12197590 original size:85 final size:85
Alignment explanation
Indices: 12197447--12197754 Score: 474
Period size: 85 Copynumber: 3.6 Consensus size: 85
12197437 TATGACGTGC
* *
12197447 ATTTATGACGCGCATGTATGACTTACATTGCGCGTCATTGAAGCCTCCGTCATAAATTAATATGA
1 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATTAATATGA
*
12197512 CAGACATTTGTGTGTCATAA
66 CACACATTTGTGTGTCATAA
* * *
12197532 ATTTATGACACGCATGTATGACTTACATTGTGCGTCATTAAAGCCCCCGTCATAAATTAAGATGA
1 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATTAATATGA
*
12197597 CACACATTTGTGCGTCATAA
66 CACACATTTGTGTGTCATAA
* *
12197617 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATCT-GTTTG
1 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAAT-TAATATG
*
12197681 ACATACATTTGTGTGTCATAA
65 ACACACATTTGTGTGTCATAA
* * * *
12197702 ATTTATGACACGCATATATGACTTACATTGCGTGTCATTGAAGCGCACGTCAT
1 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCAT
12197755 TTAAAAAGAC
Statistics
Matches: 204, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
85 203 1.00
86 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATTAATATGA
CACACATTTGTGTGTCATAA
Found at i:12203844 original size:15 final size:15
Alignment explanation
Indices: 12203819--12203859 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
12203809 GATGCTTTCT
12203819 TTTTCCTTCTTTAACG
1 TTTT-CTTCTTTAACG
*
12203835 TTTTCTTCTTTGACG
1 TTTTCTTCTTTAACG
12203850 TTTTCTTCTT
1 TTTTCTTCTT
12203860 AGACATTGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.07, C:0.22, G:0.07, T:0.63
Consensus pattern (15 bp):
TTTTCTTCTTTAACG
Found at i:12204128 original size:18 final size:18
Alignment explanation
Indices: 12204105--12204142 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
12204095 TAACCTTTGG
12204105 TAACACACCCCGAAAGAT
1 TAACACACCCCGAAAGAT
12204123 TAACACACCCCGAAAGAT
1 TAACACACCCCGAAAGAT
12204141 TA
1 TA
12204143 CCATATGCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.32, G:0.11, T:0.13
Consensus pattern (18 bp):
TAACACACCCCGAAAGAT
Found at i:12207680 original size:228 final size:226
Alignment explanation
Indices: 12207283--12207725 Score: 787
Period size: 228 Copynumber: 2.0 Consensus size: 226
12207273 CTACAACAAC
*
12207283 AGTCTGACAAACCAAGGGTTATAGATAACGTTGAGTAGTATTGTCATAGCAACCGTCTAAGAATA
1 AGTCTGACAAACCAAGGGTTATAGATAACGCTGAGTAGTATTGTCATAGCAACCGTCTAAGAATA
*
12207348 CTTAGTAATCCTGTCGGGCAGCTTAAGCATGTCATAATAATTCATTCTAGACTTAGAATCATTGT
66 CTTAGCAATCCTGTCGGGCAGCTTAAGCATGTCATAATAATTCATTCTAGACTTAGAATCATTGT
* *
12207413 TTGTCAATACAAAAGATTAGTATAAGTGCTTTGTGATAAGTTTGAATATGTGAGGTTGTTTGAAT
131 TTGTCAATACAAAAGATTAGCATAAGTGCTCTGTGATAAGTTTGAATATGTGAGGTTGTTTGAA-
12207478 TATATTTAAATCAACGTTTGTCTTTATTTTGTT
195 T-TATTTAAATCAACGTTTGTCTTTATTTTGTT
* *
12207511 AGTCTGACAAACCAAGGGTTGTAGATAACGCTGAGTAGTATTGTCATAGCAACCGTCTAATAATA
1 AGTCTGACAAACCAAGGGTTATAGATAACGCTGAGTAGTATTGTCATAGCAACCGTCTAAGAATA
* *
12207576 CTTAGCAATCCTTTCGGGCAGCTTAAGCATGTCATAATAATTCATTCTGGACTTAGAATCATTGT
66 CTTAGCAATCCTGTCGGGCAGCTTAAGCATGTCATAATAATTCATTCTAGACTTAGAATCATTGT
12207641 TTGTCAATACAAAAGATTAGCATAAGTGCTCTGTGATAAGTTTGAATATGTGAGGTTGTTTGAAT
131 TTGTCAATACAAAAGATTAGCATAAGTGCTCTGTGATAAGTTTGAATATGTGAGGTTGTTTGAAT
*
12207706 TATTTAAATCAATGTTTGTC
196 TATTTAAATCAACGTTTGTC
12207726 CTTGGTTTGT
Statistics
Matches: 206, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
226 19 0.09
227 1 0.00
228 186 0.90
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (226 bp):
AGTCTGACAAACCAAGGGTTATAGATAACGCTGAGTAGTATTGTCATAGCAACCGTCTAAGAATA
CTTAGCAATCCTGTCGGGCAGCTTAAGCATGTCATAATAATTCATTCTAGACTTAGAATCATTGT
TTGTCAATACAAAAGATTAGCATAAGTGCTCTGTGATAAGTTTGAATATGTGAGGTTGTTTGAAT
TATTTAAATCAACGTTTGTCTTTATTTTGTT
Found at i:12209584 original size:21 final size:20
Alignment explanation
Indices: 12209556--12209595 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
12209546 CATTGCTGGA
12209556 ATTTATGGCCTCAACAAAAG
1 ATTTATGGCCTCAACAAAAG
* *
12209576 ATTTCATGGCTTTAACAAAA
1 ATTT-ATGGCCTCAACAAAA
12209596 ACCTTGATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.30
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:12223245 original size:14 final size:13
Alignment explanation
Indices: 12223222--12223273 Score: 54
Period size: 14 Copynumber: 4.0 Consensus size: 13
12223212 TACAAGCACT
12223222 CAAAAGAAGAAAA
1 CAAAAGAAGAAAA
12223235 CAAAGAGAAGAAAA
1 CAAA-AGAAGAAAA
*
12223249 -AGAA-AAGAAAA
1 CAAAAGAAGAAAA
*
12223260 GAAAAGAAAGAAAA
1 CAAAAG-AAGAAAA
12223274 GTTGAAAGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
11 7 0.21
12 4 0.12
13 6 0.18
14 16 0.48
ACGTcount: A:0.77, C:0.04, G:0.19, T:0.00
Consensus pattern (13 bp):
CAAAAGAAGAAAA
Found at i:12223250 original size:11 final size:11
Alignment explanation
Indices: 12223223--12223268 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
12223213 ACAAGCACTC
12223223 AAAAGAAGAA-A
1 AAAAGAA-AAGA
*
12223234 ACAAAGAGAAGA
1 A-AAAGAAAAGA
12223246 AAAAGAAAAG-
1 AAAAGAAAAGA
12223256 AAAAGAAAAGA
1 AAAAGAAAAGA
12223267 AA
1 AA
12223269 GAAAAGTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 10 0.33
11 13 0.43
12 7 0.23
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:12223271 original size:4 final size:5
Alignment explanation
Indices: 12223236--12223274 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
12223226 AGAAGAAAAC
*
12223236 AAAGA GAAGAA AAAGA AAAGA AAAGA AAAG- AAAGA AAAG
1 AAAGA AAAG-A AAAGA AAAGA AAAGA AAAGA AAAGA AAAG
12223275 TTGAAAGCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 4 0.13
5 22 0.73
6 4 0.13
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:12223274 original size:9 final size:9
Alignment explanation
Indices: 12223223--12223274 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
12223213 ACAAGCACTC
12223223 AAAAG-AAG
1 AAAAGAAAG
*
12223231 AAAACAAAG
1 AAAAGAAAG
*
12223240 AGAAGAAAAAG
1 A-AA-AGAAAG
12223251 AAAAGAAAAG
1 AAAAG-AAAG
12223261 AAAAGAAAG
1 AAAAGAAAG
12223270 AAAAG
1 AAAAG
12223275 TTGAAAGCAC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
8 4 0.11
9 14 0.38
10 13 0.35
11 6 0.16
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:12223274 original size:14 final size:14
Alignment explanation
Indices: 12223228--12223274 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
12223218 CACTCAAAAG
* *
12223228 AAGAAAACAAAGAG
1 AAGAAAAGAAAGAA
12223242 AAGAAAAAGAAAAGAA
1 AAG-AAAAG-AAAGAA
12223258 AAGAAAAGAAAGAA
1 AAGAAAAGAAAGAA
12223272 AAG
1 AAG
12223275 TTGAAAGCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 12 0.41
15 9 0.31
16 8 0.28
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (14 bp):
AAGAAAAGAAAGAA
Found at i:12233420 original size:25 final size:24
Alignment explanation
Indices: 12233376--12233453 Score: 99
Period size: 23 Copynumber: 3.3 Consensus size: 24
12233366 TCTAATATGC
*
12233376 TTTC-AAAAATTATATA-ATATAT
1 TTTCAAAAAAATATATATATATAT
12233398 TTTCAAAAAAATATAT-TATATAT
1 TTTCAAAAAAATATATATATATAT
**
12233421 TTTCAAAATTATATATTATATATAT
1 TTTCAAAAAAATATA-TATATATAT
12233446 TTTCAAAA
1 TTTCAAAA
12233454 CCACATATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.08
23 29 0.59
24 1 0.02
25 15 0.31
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (24 bp):
TTTCAAAAAAATATATATATATAT
Found at i:12239251 original size:21 final size:21
Alignment explanation
Indices: 12239211--12239251 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12239201 ATTTTTTCCC
*
12239211 AATGGTGACATGTCACTATCT
1 AATGGTGACATATCACTATCT
* *
12239232 AATGGTGATATATCATTATC
1 AATGGTGACATATCACTATC
12239252 ATTGTAATTT
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:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (21 bp):
AATGGTGACATATCACTATCT
Found at i:12241096 original size:287 final size:283
Alignment explanation
Indices: 12240465--12241253 Score: 940
Period size: 287 Copynumber: 2.8 Consensus size: 283
12240455 CAAGGTATGA
* * * * * * *
12240465 AGTAAATTAGAAAAATATAAATAATTATGGGATAG-TTTAGGATAAAAATATACTTTTAAGGATT
1 AGTAAATTAAAAAAATAAAAATAATTATGGG-TCGATTTTGAAT-AAAATAAACTTTTAAGGACT
** * *
12240529 AAATTGAACAAACATTAAATTATTAA-TTAACATTTAAATAAATTAAGCAACATGAAAGGATCAA
64 AAATTGAACAAACATTAAATTACAAACTGAA-ATTTAAATAAATTAAGCAACA-CAAAGGATCAA
* * * * ** * *
12240593 ATTGAAACAATAGTAGAGTGTGAAGCTGAAATTAGTATAAAAATATACTAAATTGCATTCA-TTA
127 ATTGAAACAATTGTAAAATGT-AAGCTGAAATTAGTATAAAATTGGACTAAATTACATTCATTTT
** * *
12240657 AAAAGTTGGTGAATGAAAGTTTATATGATTTGGAGATTATGATATAATATATAGGTTTGAAATAA
191 AAAAGTTGGTGAACAAAAGTTTATAAGATTTGGAGATTATAATATAATATATAGGTTTGAAATAA
*
12240722 AGTTTATGATGTGATTTATTGGGTTTGG
256 AGTTTATGATGTGATTTATAGGGTTTGG
* ** * * * *
12240750 CGTAAATTACAAAAAATGGAAATAATAATGGG-CTAATTTAAGATAAAATAAACTTTTAAGGACT
1 AGTAAATTA-AAAAAATAAAAATAATTATGGGTCGATTTTGA-ATAAAATAAACTTTTAAGGACT
* * * * *
12240814 AAATTGAGCAAACATAAAATTGCAAACTGAAATTTAAATAAATTAAACAATACACAAGGATCAAA
64 AAATTGAACAAACATTAAATTACAAACTGAAATTTAAATAAATTAAGCAACACA-AAGGATCAAA
* * *
12240879 TTGAAACATTTGTAAAATGTAAGGCTGAAATTAGTATAAAATTGGACAAAATTACATTTATTTTA
128 TTGAAACAATTGTAAAATGTAA-GCTGAAATTAGTATAAAATTGGACTAAATTACATTCATTTTA
* * *
12240944 AAAGGTGGTGAACAAAAGTTTATAAGGTTTGGAGATTATAATATAATTTATAAGGTTTGAAATGA
192 AAAGTTGGTGAACAAAAGTTTATAAGATTTGGAGATTATAATATAATATAT-AGGTTTGAAAT-A
12241009 AA-TTTATGATGTGATTTATAGGGTTTGG
255 AAGTTTATGATGTGATTTATAGGGTTTGG
12241037 AGTAAATTATAAAAAATAAAAATAATTATGGGTCGATTTTGAATAAAATAAACTTTTAAGGACTA
1 AGTAAATTA-AAAAAATAAAAATAATTATGGGTCGATTTTGAATAAAATAAACTTTTAAGGACTA
* * * *
12241102 CATTGAATAAACATTAAATTACAAACTGAAATTTAAATAAATTAAGCAACACATAGGGATCGAAT
65 AATTGAACAAACATTAAATTACAAACTGAAATTTAAATAAATTAAGCAACACA-AAGGATCAAAT
* * * * * *
12241167 TGAAACAATTGTCAAATGTAAAGATGAAACTAATATCAAATTGGGACTAAATTATATTCATTTTA
129 TGAAACAATTGTAAAATGT-AAGCTGAAATTAGTATAAAATT-GGACTAAATTACATTCATTTTA
12241232 AAAGTTGGTGAACAAAAGTTTA
192 AAAGTTGGTGAACAAAAGTTTA
12241254 ACGTCTTAAT
Statistics
Matches: 423, Mismatches: 69, Indels: 21
0.82 0.13 0.04
Matches are distributed among these distances:
284 3 0.01
285 125 0.30
286 70 0.17
287 174 0.41
288 51 0.12
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (283 bp):
AGTAAATTAAAAAAATAAAAATAATTATGGGTCGATTTTGAATAAAATAAACTTTTAAGGACTAA
ATTGAACAAACATTAAATTACAAACTGAAATTTAAATAAATTAAGCAACACAAAGGATCAAATTG
AAACAATTGTAAAATGTAAGCTGAAATTAGTATAAAATTGGACTAAATTACATTCATTTTAAAAG
TTGGTGAACAAAAGTTTATAAGATTTGGAGATTATAATATAATATATAGGTTTGAAATAAAGTTT
ATGATGTGATTTATAGGGTTTGG
Found at i:12242656 original size:14 final size:14
Alignment explanation
Indices: 12242633--12242663 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12242623 TTTCGTTTTA
12242633 TATTAGATTATTAT
1 TATTAGATTATTAT
*
12242647 TATTATATTATTAT
1 TATTAGATTATTAT
12242661 TAT
1 TAT
12242664 AATTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (14 bp):
TATTAGATTATTAT
Found at i:12256176 original size:20 final size:20
Alignment explanation
Indices: 12256132--12256169 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
12256122 AAACAAGATA
12256132 AGATAGATTAGGTACAAGTG
1 AGATAGATTAGGTACAAGTG
12256152 AGATAGATTAGGTACAAG
1 AGATAGATTAGGTACAAG
12256170 CTAGATATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.05, G:0.29, T:0.24
Consensus pattern (20 bp):
AGATAGATTAGGTACAAGTG
Found at i:12264851 original size:55 final size:55
Alignment explanation
Indices: 12264759--12264930 Score: 292
Period size: 55 Copynumber: 3.1 Consensus size: 55
12264749 AATACATGTA
* * *
12264759 ATGAATTTCCGTATGGGCGCTGT-TGTGCAAAATTAAGAAATTCATAATAAGTTT
1 ATGAATTTTCGTATGGGCACTGTCTGTGCAAAACTAAGAAATTCATAATAAGTTT
* *
12264813 ATGAATTTTTGTATGGGCACTATCTGTGCAAAACTAAGAAATTCATAATAAGTTT
1 ATGAATTTTCGTATGGGCACTGTCTGTGCAAAACTAAGAAATTCATAATAAGTTT
12264868 ATGAATTTTCGTATGGGCACTGTCTGTGCAAAACTAAGAAATTCATAATAAGTTT
1 ATGAATTTTCGTATGGGCACTGTCTGTGCAAAACTAAGAAATTCATAATAAGTTT
12264923 ATGAATTT
1 ATGAATTT
12264931 CCGTTATGAA
Statistics
Matches: 110, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
54 19 0.17
55 91 0.83
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (55 bp):
ATGAATTTTCGTATGGGCACTGTCTGTGCAAAACTAAGAAATTCATAATAAGTTT
Found at i:12264939 original size:13 final size:13
Alignment explanation
Indices: 12264921--12264960 Score: 80
Period size: 13 Copynumber: 3.1 Consensus size: 13
12264911 CATAATAAGT
12264921 TTATGAATTTCCG
1 TTATGAATTTCCG
12264934 TTATGAATTTCCG
1 TTATGAATTTCCG
12264947 TTATGAATTTCCG
1 TTATGAATTTCCG
12264960 T
1 T
12264961 ATGGGCACTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.47
Consensus pattern (13 bp):
TTATGAATTTCCG
Found at i:12266152 original size:250 final size:250
Alignment explanation
Indices: 12265711--12266195 Score: 889
Period size: 250 Copynumber: 1.9 Consensus size: 250
12265701 AAGCCCAAAT
*
12265711 CGACAACCGAAACGGTTTGCAAAGAGGGGTTGGAACGGTTTTGTGTTTAGGGAGTAAGGAGATTG
1 CGACAACCGAAACGGTTTGCAAAGAGGGGTCGGAACGGTTTTGTGTTTAGGGAGTAAGGAGATTG
*
12265776 AATGATAGAGAATTGCACAGCGATTTATAGTGGTTCGACTTTCTCAACCAAAGTCTACGTCCACT
66 AAAGATAGAGAATTGCACAGCGATTTATAGTGGTTCGACTTTCTCAACCAAAGTCTACGTCCACT
*
12265841 ACCTTAGCTCCTCACCAAGGATTTTCCAATAAATTCACTAATTTGTTCTTTCTTTTGAGGATAAA
131 ACCTTAGCTCCTCACCAAGGATTTTCCAACAAATTCACTAATTTGTTCTTTCTTTTGAGGATAAA
12265906 GAGTAACCTTACAAACTCACTAGTTTTTCCGGGCTAAACTTTTGGAAGCTCGAAA
196 GAGTAACCTTACAAACTCACTAGTTTTTCCGGGCTAAACTTTTGGAAGCTCGAAA
* *
12265961 CGACAACCGGAACGGTTTGCAAAGAGGGGTCGGAATGGTTTTGTGTTTAGGGAGTAAGGAGATTG
1 CGACAACCGAAACGGTTTGCAAAGAGGGGTCGGAACGGTTTTGTGTTTAGGGAGTAAGGAGATTG
*
12266026 AAAGATAGAGAATTGCACAGTGATTTATAGTGGTTCGACTTTCTCAACCAAAGTCTACGTCCACT
66 AAAGATAGAGAATTGCACAGCGATTTATAGTGGTTCGACTTTCTCAACCAAAGTCTACGTCCACT
*
12266091 ACCTTAGCTCCTCACCAAGGATTTTCCAGCAAATTCACTAATTTGTTCTTTCTTTTGAGGATAAA
131 ACCTTAGCTCCTCACCAAGGATTTTCCAACAAATTCACTAATTTGTTCTTTCTTTTGAGGATAAA
* *
12266156 GAGTAACCTTACAAACTCCCTAGTTTTTCTGGGCTAAACT
196 GAGTAACCTTACAAACTCACTAGTTTTTCCGGGCTAAACT
12266196 AGAACCTTTC
Statistics
Matches: 226, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
250 226 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (250 bp):
CGACAACCGAAACGGTTTGCAAAGAGGGGTCGGAACGGTTTTGTGTTTAGGGAGTAAGGAGATTG
AAAGATAGAGAATTGCACAGCGATTTATAGTGGTTCGACTTTCTCAACCAAAGTCTACGTCCACT
ACCTTAGCTCCTCACCAAGGATTTTCCAACAAATTCACTAATTTGTTCTTTCTTTTGAGGATAAA
GAGTAACCTTACAAACTCACTAGTTTTTCCGGGCTAAACTTTTGGAAGCTCGAAA
Found at i:12266614 original size:22 final size:22
Alignment explanation
Indices: 12266588--12266630 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
12266578 CCGTTAGACA
12266588 GGGGGAATCGGTACCCCCTGGG
1 GGGGGAATCGGTACCCCCTGGG
*
12266610 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
12266631 ACAATCTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.28, G:0.42, T:0.16
Consensus pattern (22 bp):
GGGGGAATCGGTACCCCCTGGG
Found at i:12268122 original size:19 final size:20
Alignment explanation
Indices: 12268079--12268126 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
12268069 TCTAAATCCT
*
12268079 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
12268099 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
12268118 TTTTCAAAA
1 TTTTCAAAA
12268127 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:12269364 original size:21 final size:21
Alignment explanation
Indices: 12269338--12269379 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12269328 CCAGAATGGG
* *
12269338 GGGAATCGGTATCCCTTCATA
1 GGGAATCGATACCCCTTCATA
12269359 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
12269380 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:12269517 original size:21 final size:20
Alignment explanation
Indices: 12269492--12269554 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
12269482 AAACCATGCA
*
12269492 GGGGGAATATGTTCCCCCTGG
1 GGGGGAAT-TGTACCCCCTGG
* *
12269513 GGGGGAATCGATACCCCCTGA
1 GGGGGAATTG-TACCCCCTGG
12269534 GGGGGAATCTGTACCCCCTGG
1 GGGGGAAT-TGTACCCCCTGG
12269555 ACAATCTGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.17, C:0.27, G:0.37, T:0.19
Consensus pattern (20 bp):
GGGGGAATTGTACCCCCTGG
Found at i:12276010 original size:55 final size:55
Alignment explanation
Indices: 12275789--12275993 Score: 331
Period size: 55 Copynumber: 3.7 Consensus size: 55
12275779 ACTATACGTG
*
12275789 AAAACTAA-AATATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGC
1 AAAACTAAGAA-ATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGTGTGTGC
* * *
12275844 AAAATTAGGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGTGTGTAC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGTGTGTGC
* *
12275899 AAAACTATGAAATTCATAATAAGATTATGAATTTTCGTATGGGCACTGTGTGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGTGTGTGC
*
12275954 AAAACTAAGAAATTAATAATAAGTTTATGAATTTTCGTAT
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTAT
12275994 TGGTAGTGGG
Statistics
Matches: 138, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
55 136 0.99
56 2 0.01
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.36
Consensus pattern (55 bp):
AAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGTGTGTGC
Found at i:12294704 original size:55 final size:55
Alignment explanation
Indices: 12294373--12294681 Score: 519
Period size: 55 Copynumber: 5.6 Consensus size: 55
12294363 ACTATACGTG
* ** *
12294373 AAAATTAAGAAATTCATAATAAGTTTATGAATTTTTGTATGGGCACTGTGTGTGT
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGC
* *
12294428 AAAATTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGT
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGC
* *
12294483 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTATATGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGC
12294538 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGC
* * *
12294593 AAAAGTAAAAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTGTGTGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGC
12294648 AAAACTAAGAAATTCATAATAAGTTTATGAATTT
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTT
12294682 TCGTGTTGGT
Statistics
Matches: 241, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 241 1.00
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.35
Consensus pattern (55 bp):
AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGC
Found at i:12294716 original size:110 final size:109
Alignment explanation
Indices: 12294378--12294716 Score: 461
Period size: 110 Copynumber: 3.1 Consensus size: 109
12294368 ACGTGAAAAT
* * *
12294378 TAAG-AAATTCATAATAAGTTTATGAATTTTTGTATGGGCACTGTGTGTGTAAAATTAAGAAATT
1 TAAGTAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTGTGTGTGCAAAACTAAGAAATT
**
12294442 CATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGTAAAAC
66 CATAATAAGTTTATGAATTTCCGTATGGGCA--GTGTGTGTGCAAC
* * *
12294488 TAAG-AAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTATATGTGCAAAACTAAGAAATT
1 TAAGTAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTGTGTGTGCAAAACTAAGAAATT
*
12294552 CATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGCAA-
66 CATAATAAGTTTATGAATTTCCGTATGGGCAGTGTGTGTGCAAC
12294595 -AAGTAAAAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTGTGTGTGCAAAACTAAGAA
1 TAAGT---AAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTGTGTGTGCAAAACTAAGAA
* * * * *
12294659 ATTCATAATAAGTTTATGAATTTTCGTGTTGGTAGTGGGTGTGCAAC
63 ATTCATAATAAGTTTATGAATTTCCGTATGGGCAGTGTGTGTGCAAC
*
12294706 TCACGTAAATT
1 T-AAGTAAATT
12294717 ATAGTGAGTG
Statistics
Matches: 203, Mismatches: 19, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
106 3 0.01
108 9 0.04
110 188 0.93
113 3 0.01
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (109 bp):
TAAGTAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTGTGTGTGCAAAACTAAGAAATT
CATAATAAGTTTATGAATTTCCGTATGGGCAGTGTGTGTGCAAC
Found at i:12295518 original size:66 final size:69
Alignment explanation
Indices: 12295342--12295531 Score: 199
Period size: 66 Copynumber: 2.7 Consensus size: 69
12295332 TTTTCTGTCA
* * * *
12295342 CCTTAGAGATTGTTTCTCTCGAAACAAAGTTTCATCTCGTTTGAGACAATTTTTCTTTAAACAAA
1 CCTT-GAGATTGTTCCTCTCGAAACAAA-TTTCATCTCGCTTGAGACAATTTCTCTTGAAACAAA
12295407 ATTAATTT
64 A-TAA-TT
* ** ** *
12295415 CACTTGAGAGTGTTTCCTCTAAAAAC-AATTTTTTCTCGCTTGAGACAATTTCTCTTGAAAC-AC
1 C-CTTGAGATTG-TTCCTCTCGAAACAAATTTCATCTCGCTTGAGACAATTTCTCTTGAAACAAA
12295478 A-AA-T
64 ATAATT
*
12295482 CCTTGAGATTGTTCCTCTCGAAACAAATTTCATCTCGCTTGAGATAATTT
1 CCTTGAGATTGTTCCTCTCGAAACAAATTTCATCTCGCTTGAGACAATTT
12295532 TCCCAAAATT
Statistics
Matches: 98, Mismatches: 16, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
65 11 0.11
66 31 0.32
67 2 0.02
69 2 0.02
71 2 0.02
72 28 0.29
73 9 0.09
74 13 0.13
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.38
Consensus pattern (69 bp):
CCTTGAGATTGTTCCTCTCGAAACAAATTTCATCTCGCTTGAGACAATTTCTCTTGAAACAAAAT
AATT
Found at i:12295668 original size:103 final size:103
Alignment explanation
Indices: 12295542--12295792 Score: 299
Period size: 103 Copynumber: 2.4 Consensus size: 103
12295532 TCCCAAAATT
* * *
12295542 TTGAAATTGTTTCACTTGGAACAAAATTGATCTCGCTTGAGATAG-TTTTCCTAAAAACTAATTT
1 TTGAAATTGTTTCACTTGAAACAAAATTGATCTCACTTGAGATAGTTTTTCCTAAAAACAAATTT
* *
12295606 CGTCTCGCTTGAGATATTTTTCCCTCAAAACGCAAAAA
66 CATCTCGCTTGAGATAGTTTTCCCTCAAAACGCAAAAA
** * * *
12295644 TTGGAAATTGTTTCACTTGAAACAAAATTGATAACATTTGAGATTGTTTTTCTTAAAAACAAATT
1 TT-GAAATTGTTTCACTTGAAACAAAATTGATCTCACTTGAGATAGTTTTTCCTAAAAACAAATT
** * **
12295709 TCATCTCGCTTGAGATAGTTTTCCCTTGAAACGTAAATC
65 TCATCTCGCTTGAGATAGTTTTCCCTCAAAACGCAAAAA
* * * *
12295748 TT-AAAATGTTTCACTCGAAACAAAATTTTATCTCACCTGAGATAG
1 TTGAAATTGTTTCACTTGAAACAAAA-TTGATCTCACTTGAGATAG
12295793 CTCTTCTTGA
Statistics
Matches: 123, Mismatches: 23, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
102 23 0.19
103 50 0.41
104 50 0.41
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (103 bp):
TTGAAATTGTTTCACTTGAAACAAAATTGATCTCACTTGAGATAGTTTTTCCTAAAAACAAATTT
CATCTCGCTTGAGATAGTTTTCCCTCAAAACGCAAAAA
Found at i:12295731 original size:104 final size:102
Alignment explanation
Indices: 12295542--12295774 Score: 288
Period size: 104 Copynumber: 2.3 Consensus size: 102
12295532 TCCCAAAATT
* ** * *
12295542 TTGAAATTGTTTCACTTGGAACAAAATTGATCTCGCTTGAGATAGTTTTCCTAAAAACTAATTTC
1 TTGAAATTGTTTCACTTGAAACAAAATTGATAACACTTGAGATAGTTTTCCTAAAAACAAATTTC
* *
12295607 GTCTCGCTTGAGATATTTTTCCCTCAAAACGCAAAAA
66 ATCTCGCTTGAGATAGTTTTCCCTCAAAACGCAAAAA
* * *
12295644 TTGGAAATTGTTTCACTTGAAACAAAATTGATAACATTTGAGATTGTTTTTCTTAAAAACAAATT
1 TT-GAAATTGTTTCACTTGAAACAAAATTGATAACACTTGAGATAG-TTTTCCTAAAAACAAATT
** * **
12295709 TCATCTCGCTTGAGATAGTTTTCCCTTGAAACGTAAATC
64 TCATCTCGCTTGAGATAGTTTTCCCTCAAAACGCAAAAA
* *
12295748 TT-AAAATGTTTCACTCGAAACAAAATT
1 TTGAAATTGTTTCACTTGAAACAAAATT
12295775 TTATCTCACC
Statistics
Matches: 112, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
102 25 0.22
103 37 0.33
104 50 0.45
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.36
Consensus pattern (102 bp):
TTGAAATTGTTTCACTTGAAACAAAATTGATAACACTTGAGATAGTTTTCCTAAAAACAAATTTC
ATCTCGCTTGAGATAGTTTTCCCTCAAAACGCAAAAA
Found at i:12296311 original size:219 final size:218
Alignment explanation
Indices: 12295930--12297016 Score: 1350
Period size: 219 Copynumber: 5.0 Consensus size: 218
12295920 ATTGGCAACT
* * * * *
12295930 ATGACCAGATCTCTTCAACATGGATGAGCAGTGTCGTATTCAACATCAAATTAGTTCTAGATTGA
1 ATGACCAGATCTCTTCAACACGGATGAGCAGTGTCGTCTTCAACA-CCAATT-TTTCCAGATTGA
* * *
12295995 CTCGATCTCCTCAACGGGAAGGAGCAGTG-CATCCTTAGACAATCAGACTTCCTCAACACGAAGG
64 CCCGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACACGAAGG
** * * ** * * *
12296059 AACTGTATTGTCTCCAAATTCTCTCCGGATTGACCGGATTTCCACAACAAGAAGGAACATCATCA
129 AACCATGTTGTCTCCAAATTATCTCATGATTGACCCGATTTCCTCAACAAGAAGGAACATCGTCA
* *
12296124 TCTCCAGCAAACAATTTACCTGAAA
194 TCTTCAGCAAACAATTTATCTGAAA
* * *
12296149 ATGACCAAATCTCTTCAACACGGATGAGCAGTGTCGTCTTTAACACCAAGTTTTTCCAGTTTGAC
1 ATGACCAGATCTCTTCAACACGGATGAGCAGTGTCGTCTTCAACACCAA-TTTTTCCAGATTGAC
* * *
12296214 CCGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGAAAATCATACTTCCTCAACACGAAAGA
65 CCGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACACGAAGGA
* *
12296279 ACCATGTTGTCTCCAAATTATCTCATGATTGACCCGATTTCCTCAATACGAAGGAACATCGTCAT
130 ACCATGTTGTCTCCAAATTATCTCATGATTGACCCGATTTCCTCAACAAGAAGGAACATCGTCAT
** * *
12296344 CTTCAATAAAAAAATTATCTGAAA
195 CTTCAGCAAACAATTTATCTGAAA
** * *
12296368 GCGACCAGATCTCTTCAACACGGATGAGCAGTGTCATCTTCAACACCAAGTTTTTCCAGTTTGAC
1 ATGACCAGATCTCTTCAACACGGATGAGCAGTGTCGTCTTCAACACCAA-TTTTTCCAGATTGAC
* *
12296433 CCGATCTCCTCAACGCGAAGGAGCAGTGTTATCCTCAGACAATCAGACTTCCTCAACGCGAAGGA
65 CCGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACACGAAGGA
* * * *
12296498 ACCGTGTTGTCTCCAAATTATCTCATGATTGACTCGATTTCCTTAACGCA-AAGGAACATCGTCA
130 ACCATGTTGTCTCCAAATTATCTCATGATTGACCCGATTTCCTCAAC-AAGAAGGAACATCGTCA
*
12296562 TCTTCATCAAACAATTTATCTGAAA
194 TCTTCAGCAAACAATTTATCTGAAA
* *
12296587 GTGACTAGATCTCTTCAACACGGATGAGCAGTGTCGTCTTCAACACC-ATATTTTCCAGATTGAC
1 ATGACCAGATCTCTTCAACACGGATGAGCAGTGTCGTCTTCAACACCAAT-TTTTCCAGATTGAC
* * * *
12296651 CCGATCTCCTCAACGCGAAGGAGCATTTTCATCCAT-AGACAATCAGACTTCCTTAATGA-GAAG
65 CCGATCTCCTCAACGCGAAGGAGCAGTGTCATCC-TCAGACAATCAGACTTCCTCAA-CACGAAG
* ** *
12296714 GAA-CAGTGTTGTCTACAAATTATCTCATGATTGACCCGATTTCCTCAACGCGAAGGAACAACGT
128 GAACCA-TGTTGTCTCCAAATTATCTCATGATTGACCCGATTTCCTCAACAAGAAGGAACATCGT
*
12296778 CATCTTCAGTAAACAATTTATCT-AAA
192 CATCTTCAGCAAACAATTTATCTGAAA
* * *
12296804 A-GCAACCAGATCTCTTCAACACGGATGAGCGGTGTCGTCATCAACACCAAATTTTCCAGATTGA
1 ATG--ACCAGATCTCTTCAACACGGATGAGCAGTGTCGTCTTCAACACCAATTTTTCCAGATTGA
* * ** **
12296868 CCAGATCTCCTCAACGCAAAGGAGCAGTGTCATCCTCAGACAATCAGACTTATTCAACGTGAAGG
64 CCCGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACACGAAGG
* * * *
12296933 AGCCATGTTGTCTCCAAATTATCTCCA-GATTGACACAATTTCCTCAA-AGAGAAGGAGCAGT-G
129 AACCATGTTGTCTCCAAATTATCT-CATGATTGACCCGATTTCCTCAACA-AGAAGGAACA-TCG
* * *
12296995 TCACCTTCAACAAACGATTTAT
191 TCATCTTCAGCAAACAATTTAT
12297017 TTCAAAATAC
Statistics
Matches: 755, Mismatches: 96, Indels: 35
0.85 0.11 0.04
Matches are distributed among these distances:
216 1 0.00
217 6 0.01
218 353 0.47
219 395 0.52
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.26
Consensus pattern (218 bp):
ATGACCAGATCTCTTCAACACGGATGAGCAGTGTCGTCTTCAACACCAATTTTTCCAGATTGACC
CGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACACGAAGGAA
CCATGTTGTCTCCAAATTATCTCATGATTGACCCGATTTCCTCAACAAGAAGGAACATCGTCATC
TTCAGCAAACAATTTATCTGAAA
Found at i:12296825 original size:437 final size:434
Alignment explanation
Indices: 12295933--12296988 Score: 1424
Period size: 437 Copynumber: 2.4 Consensus size: 434
12295923 GGCAACTATG
* * * * * *
12295933 ACCAGATCTCTTCAACATGGATGAGCAGTGTCGTATTCAACATCAAATTAGTTCTAGATTGACTC
1 ACCAGATCTCTTCAACACGGATGAGCAGTGTCGTCTTCAACA-CCAATT-TTTCCAGATTGACCC
* * *
12295998 GATCTCCTCAACGGGAAGGAGCAGTG-CATCCTTAGACAATCAGACTTCCTCAACACGAAGGAAC
64 GATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACGCGAAGGAAC
* * * * *
12296062 TGTATTGTCTCCAAATTCTCTCCGGATTGACCGGATTTCCACAACAAGAAGGAACATCATCATCT
129 CGTGTTGTCTCCAAATTATCT-CAGATTGACC-GATTTCCTCAACAAGAAGGAACATCATCATCT
*
12296127 CCAGCAAACAATTTACCTGAAAATGACCAAATCTCTTCAACACGGATGAGCAGTGTCGTCTTTAA
192 CCAGCAAACAATTTACCTGAAAATGACCAAATCTCTTCAACACGGATGAGCAGTGTCGTCTTCAA
*
12296192 CACCAAGTTTTTCCAGTTTGACCCGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGAAAAT
257 CACCAAG-TTTTCCAGATTGACCCGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGAAAAT
* *
12296257 CATACTTCCTCAACACGAAAGAACCATGTTGTCTCCAAATTATCTCATGATTGACCCGATTTCCT
321 CAGACTTCCTCAACACGAAAGAACCATGTTGTCTACAAATTATCTCATGATTGACCCGATTTCCT
* * * *
12296322 CAATACGAAGGAACATCGTCATCTTCAATAAAAAAATTATCTGAAAGCG
386 CAACACGAAGGAACAACGTCATCTTCAATAAAAAAATTATCTAAAAGCA
* *
12296371 ACCAGATCTCTTCAACACGGATGAGCAGTGTCATCTTCAACACCAAGTTTTTCCAGTTTGACCCG
1 ACCAGATCTCTTCAACACGGATGAGCAGTGTCGTCTTCAACACCAA-TTTTTCCAGATTGACCCG
*
12296436 ATCTCCTCAACGCGAAGGAGCAGTGTTATCCTCAGACAATCAGACTTCCTCAACGCGAAGGAACC
65 ATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACGCGAAGGAACC
* * *
12296501 GTGTTGTCTCCAAATTATCTCATGATTGACTCGATTTCCTTAACGCA-AAGGAACATCGTCATCT
130 GTGTTGTCTCCAAATTATCTCA-GATTGAC-CGATTTCCTCAAC-AAGAAGGAACATCATCATCT
* * * * * *
12296565 TCATCAAACAATTTATCTGAAAGTGACTAGATCTCTTCAACACGGATGAGCAGTGTCGTCTTCAA
192 CCAGCAAACAATTTACCTGAAAATGACCAAATCTCTTCAACACGGATGAGCAGTGTCGTCTTCAA
* * *
12296630 CACCATA-TTTTCCAGATTGACCCGATCTCCTCAACGCGAAGGAGCATTTTCATCCAT-AGACAA
257 CACCA-AGTTTTCCAGATTGACCCGATCTCCTCAACGCGAAGGAGCAGTGTCATCC-TCAGAAAA
* * *
12296693 TCAGACTTCCTTAATGA-GAAGGAA-CAGTGTTGTCTACAAATTATCTCATGATTGACCCGATTT
320 TCAGACTTCCTCAA-CACGAAAGAACCA-TGTTGTCTACAAATTATCTCATGATTGACCCGATTT
* * * *
12296756 CCTCAACGCGAAGGAACAACGTCATCTTCAGTAAACAATTTATCTAAAAGCA
383 CCTCAACACGAAGGAACAACGTCATCTTCAATAAAAAAATTATCTAAAAGCA
* * * *
12296808 ACCAGATCTCTTCAACACGGATGAGCGGTGTCGTCATCAACACCAAATTTTCCAGATTGACCAGA
1 ACCAGATCTCTTCAACACGGATGAGCAGTGTCGTCTTCAACACCAATTTTTCCAGATTGACCCGA
* ** * * *
12296873 TCTCCTCAACGCAAAGGAGCAGTGTCATCCTCAGACAATCAGACTTATTCAACGTGAAGGAGCCA
66 TCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACGCGAAGGAACCG
*
12296938 TGTTGTCTCCAAATTATCTCCAGATTGACACAATTTCCTCAA-AGAGAAGGA
131 TGTTGTCTCCAAATTATCT-CAGATTGAC-CGATTTCCTCAACA-AGAAGGA
12296989 GCAGTGTCAC
Statistics
Matches: 545, Mismatches: 61, Indels: 26
0.86 0.10 0.04
Matches are distributed among these distances:
435 1 0.00
436 117 0.21
437 232 0.43
438 192 0.35
439 3 0.01
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.26
Consensus pattern (434 bp):
ACCAGATCTCTTCAACACGGATGAGCAGTGTCGTCTTCAACACCAATTTTTCCAGATTGACCCGA
TCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCAACGCGAAGGAACCG
TGTTGTCTCCAAATTATCTCAGATTGACCGATTTCCTCAACAAGAAGGAACATCATCATCTCCAG
CAAACAATTTACCTGAAAATGACCAAATCTCTTCAACACGGATGAGCAGTGTCGTCTTCAACACC
AAGTTTTCCAGATTGACCCGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGAAAATCAGAC
TTCCTCAACACGAAAGAACCATGTTGTCTACAAATTATCTCATGATTGACCCGATTTCCTCAACA
CGAAGGAACAACGTCATCTTCAATAAAAAAATTATCTAAAAGCA
Found at i:12298628 original size:33 final size:33
Alignment explanation
Indices: 12298556--12298667 Score: 86
Period size: 33 Copynumber: 3.4 Consensus size: 33
12298546 TCTAACATTT
* *
12298556 ATTTTATTTTATCATTCGAACTAATATTCTAAC
1 ATTTTATTTTATCATTCGAACTAACATGCTAAC
*
12298589 ACTTTATTTTATTCATTC-ATACTAACATGCTAA-
1 ATTTTATTTTA-TCATTCGA-ACTAACATGCTAAC
* * * * *
12298622 TTTTTATTTTTATC-GTCGTTACTAACTTACTAAC
1 ATTTTA-TTTTATCATTCG-AACTAACATGCTAAC
*
12298656 CTTTTATTTTAT
1 ATTTTATTTTAT
12298668 TGCACAAACT
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
32 2 0.03
33 34 0.54
34 27 0.43
ACGTcount: A:0.29, C:0.16, G:0.04, T:0.52
Consensus pattern (33 bp):
ATTTTATTTTATCATTCGAACTAACATGCTAAC
Found at i:12301085 original size:16 final size:16
Alignment explanation
Indices: 12301064--12301095 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12301054 TTACAACTTA
12301064 CAAGTTAAGTAAATAT
1 CAAGTTAAGTAAATAT
*
12301080 CAAGTTGAGTAAATAT
1 CAAGTTAAGTAAATAT
12301096 ATATATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (16 bp):
CAAGTTAAGTAAATAT
Found at i:12301329 original size:39 final size:39
Alignment explanation
Indices: 12301269--12301368 Score: 110
Period size: 39 Copynumber: 2.6 Consensus size: 39
12301259 ATTAATTTTT
* *
12301269 TTAATCTAATGATCATCATTAATATAGAAAATAAATTTA
1 TTAACCTAATGATCATAATTAATATAGAAAATAAATTTA
* * * *
12301308 TTAACCTAATGTTCATAATTAATATATAAAGTAATTTTA
1 TTAACCTAATGATCATAATTAATATAGAAAATAAATTTA
* * **
12301347 TTAATCAAACCATCATAATTAA
1 TTAACCTAATGATCATAATTAA
12301369 GTTTATTAAT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (39 bp):
TTAACCTAATGATCATAATTAATATAGAAAATAAATTTA
Found at i:12304907 original size:12 final size:11
Alignment explanation
Indices: 12304887--12304935 Score: 62
Period size: 12 Copynumber: 4.2 Consensus size: 11
12304877 AGGAAAGAAA
12304887 AAAATATAAAT
1 AAAATATAAAT
12304898 AAAATAATAAAT
1 AAAAT-ATAAAT
12304910 ATAAATATAAAT
1 A-AAATATAAAT
*
12304922 AAATAAATAAAT
1 AAA-ATATAAAT
12304934 AA
1 AA
12304936 TAAAGAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
11 7 0.21
12 23 0.68
13 4 0.12
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAATATAAAT
Found at i:12304913 original size:6 final size:6
Alignment explanation
Indices: 12304888--12304922 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
12304878 GGAAAGAAAA
12304888 AAATAT AAATA- AAATAAT AAATAT AAATAT AAATA
1 AAATAT AAATAT AAAT-AT AAATAT AAATAT AAATA
12304923 AATAAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 4 0.15
6 19 0.70
7 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAATAT
Found at i:12304920 original size:24 final size:25
Alignment explanation
Indices: 12304888--12304939 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 25
12304878 GGAAAGAAAA
12304888 AAATATAAATAAA-ATAATAAAT-AT
1 AAATATAAATAAATA-AATAAATAAT
12304912 AAATATAAATAAATAAATAAATAAT
1 AAATATAAATAAATAAATAAATAAT
12304937 AAA
1 AAA
12304940 GAAAATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (25 bp):
AAATATAAATAAATAAATAAATAAT
Found at i:12304945 original size:24 final size:24
Alignment explanation
Indices: 12304892--12304950 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 24
12304882 AGAAAAAAAT
*
12304892 ATAAATAAAATAATAAATATAAAT
1 ATAAATAAAATAATAAATATAAAG
12304916 ATAAAT-AAATAAATAAATAATAAAG
1 ATAAATAAAAT-AATAAAT-ATAAAG
12304941 A-AAATGAAAA
1 ATAAAT-AAAA
12304951 ACAAACAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 4 0.13
24 17 0.57
25 6 0.20
26 3 0.10
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (24 bp):
ATAAATAAAATAATAAATATAAAG
Found at i:12306123 original size:11 final size:11
Alignment explanation
Indices: 12306100--12306139 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
12306090 TCAGAACTTG
12306100 AAAA-AATACAA
1 AAAATAATA-AA
12306111 AAAATAATAAA
1 AAAATAATAAA
12306122 AAAATAATAAA
1 AAAATAATAAA
12306133 AAAATAA
1 AAAATAA
12306140 AATATTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 24 0.86
12 4 0.14
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAATAATAAA
Found at i:12306124 original size:19 final size:19
Alignment explanation
Indices: 12306100--12306141 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
12306090 TCAGAACTTG
12306100 AAAAAATACAAAAAATAATA
1 AAAAAATA-AAAAAATAATA
12306120 AAAAAATAATAAAAA-AATA
1 AAAAAATAA-AAAAATAATA
12306139 AAA
1 AAA
12306142 TATTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.14
Consensus pattern (19 bp):
AAAAAATAAAAAAATAATA
Found at i:12306240 original size:34 final size:34
Alignment explanation
Indices: 12306171--12306276 Score: 99
Period size: 35 Copynumber: 3.0 Consensus size: 34
12306161 TTATATGTTT
* *
12306171 TTTTTAAAAATGTTTTCAAAACCCTATAATATATA
1 TTTTCAAAAATATTTTCAAAA-CCTATAATATATA
*
12306206 TTTTCAAAAATATTTTCCAAAACTATATATTATATATA
1 TTTTCAAAAATATTTT-CAAAAC-CTATA--ATATATA
* * *
12306244 TTTTC-AAAATGTTTT-AAAAACTATATTATATA
1 TTTTCAAAAATATTTTCAAAACCTATAATATATA
12306276 T
1 T
12306277 ATATATATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
32 7 0.12
34 4 0.07
35 19 0.32
36 9 0.15
37 9 0.15
38 12 0.20
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (34 bp):
TTTTCAAAAATATTTTCAAAACCTATAATATATA
Found at i:12306311 original size:42 final size:40
Alignment explanation
Indices: 12306195--12306357 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
12306185 TTCAAAACCC
* * *
12306195 TATA-ATATATATTTTCAAAAATATTTTCCAAAACTATA-TA
1 TATATATATATATATTC-AAAATGTTTT-AAAAACTATATTA
12306235 T-TATATATAT-T-TTCAAAATGTTTTAAAAACTATATTA
1 TATATATATATATATTCAAAATGTTTTAAAAACTATATTA
*
12306272 TATATATATATATATTCAATATGTTTTAAAAACTATA-TA
1 TATATATATATATATTCAAAATGTTTTAAAAACTATATTA
* * * * *
12306311 T-TATATATATGTTTTCAAATATGTTTTCAAAAGTATATAA
1 TATATATATATATATTCAAA-ATGTTTTAAAAACTATATTA
*
12306351 TACATAT
1 TATATAT
12306358 GTTTTCAAAA
Statistics
Matches: 105, Mismatches: 10, Indels: 15
0.81 0.08 0.12
Matches are distributed among these distances:
36 9 0.09
37 12 0.11
38 27 0.26
39 22 0.21
40 31 0.30
41 4 0.04
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (40 bp):
TATATATATATATATTCAAAATGTTTTAAAAACTATATTA
Found at i:12306334 original size:12 final size:12
Alignment explanation
Indices: 12306317--12306341 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12306307 TATATTATAT
12306317 ATATGTTTTCAA
1 ATATGTTTTCAA
12306329 ATATGTTTTCAA
1 ATATGTTTTCAA
12306341 A
1 A
12306342 AGTATATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (12 bp):
ATATGTTTTCAA
Found at i:12306348 original size:39 final size:37
Alignment explanation
Indices: 12306145--12306545 Score: 279
Period size: 38 Copynumber: 10.9 Consensus size: 37
12306135 AATAAAATAT
* * * *
12306145 TTTTTAAAACTATATATTATATGTTTTTTTTAAAAATG
1 TTTTCAAAACTATATATTATAT-ATATTTTTCAAAATG
** *
12306183 TTTTCAAAACCCTATA--ATATATA-TTTTCAAAAATA
1 TTTTCAAAACTATATATTATATATATTTTTC-AAAATG
12306218 TTTTCCAAAACTATATATTATATATA-TTTTCAAAATG
1 TTTT-CAAAACTATATATTATATATATTTTTCAAAATG
* * *
12306255 TTTTAAAAACTATATTATATATATATATATATTCAATATG
1 TTTTCAAAACTATA-TAT-TATATATAT-TTTTCAAAATG
*
12306295 TTTTAAAAACTATATATTATATATATGTTTTCAAATATG
1 TTTTCAAAACTATATATTATATATAT-TTTTCAAA-ATG
* *
12306334 TTTTC-AAA--A-GTA-TATA-ATA-----C-ATATG
1 TTTTCAAAACTATATATTATATATATTTTTCAAAATG
* *
12306359 TTTTCAAAAACTATATATTATATATATATTTTAAAAATA
1 TTTTC-AAAACTATATATTATATATAT-TTTTCAAAATG
* * *
12306398 TTTTCAAAAATGATATATTATATATA-TATTCAAGAACG
1 TTTTCAAAACT-ATATATTATATATATTTTTCAA-AATG
*
12306436 TTTTCAAAAACTATATATTAT-TATATGTTTTCGAAATG
1 TTTTC-AAAACTATATATTATATATAT-TTTTCAAAATG
**
12306474 TTTTCAAAACTATATA--ATATATA-TTTTCGAAAACCA
1 TTTTCAAAACTATATATTATATATATTTTTC-AAAA-TG
* *
12306510 TTTTCTAAAAATTATATATTATAT-TTTTTTTCAAAA
1 TTTTC--AAAACTATATATTATATATATTTTTCAAAA
12306546 AAACATTTTC
Statistics
Matches: 290, Mismatches: 37, Indels: 71
0.73 0.09 0.18
Matches are distributed among these distances:
25 8 0.03
26 1 0.00
27 4 0.01
29 1 0.00
30 2 0.01
31 4 0.01
32 3 0.01
33 3 0.01
34 13 0.04
35 17 0.06
36 33 0.11
37 32 0.11
38 90 0.31
39 47 0.16
40 32 0.11
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (37 bp):
TTTTCAAAACTATATATTATATATATTTTTCAAAATG
Found at i:12306385 original size:37 final size:38
Alignment explanation
Indices: 12306344--12306497 Score: 131
Period size: 39 Copynumber: 4.1 Consensus size: 38
12306334 TTTTCAAAAG
*
12306344 TATATAATAC-ATATGTTTTCAAAAACTATATATTATA
1 TATATAATACAAAATGTTTTCAAAAACTATATATTATA
* *
12306381 TATATATTTTA-AAAATATTTTCAAAAA-TGATATATTATA
1 TATATA--ATACAAAATGTTTTCAAAAACT-ATATATTATA
* *
12306420 TATAT-ATTCAAGAACGTTTTCAAAAACTATATATTAT-
1 TATATAATACAA-AATGTTTTCAAAAACTATATATTATA
** * * *
12306457 TATATGTTTTCGAAATGTTTTC-AAAACTATATAATATA
1 TATAT-AATACAAAATGTTTTCAAAAACTATATATTATA
12306495 TAT
1 TAT
12306498 TTTCGAAAAC
Statistics
Matches: 96, Mismatches: 11, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
36 1 0.01
37 27 0.28
38 33 0.34
39 35 0.36
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (38 bp):
TATATAATACAAAATGTTTTCAAAAACTATATATTATA
Found at i:12306452 original size:38 final size:37
Alignment explanation
Indices: 12306359--12306578 Score: 171
Period size: 38 Copynumber: 5.8 Consensus size: 37
12306349 AATACATATG
* *
12306359 TTTTCAAAAACTATATATTATATATATATTTTAAAAATA
1 TTTTCAAAAACTATATATTATATATATA--TTCAAAACA
*
12306398 TTTTCAAAAA-TGATATATTATATATATATTCAAGAACG
1 TTTTCAAAAACT-ATATATTATATATATATTCAA-AACA
* * * **
12306436 TTTTCAAAAACTATATATTATTATATGTTTTCGAAATG
1 TTTTCAAAAACTATATATTA-TATATATATTCAAAACA
*
12306474 TTTTC-AAAACTATATA--ATATATATTTTCGAAAACCA
1 TTTTCAAAAACTATATATTATATATATATTC-AAAA-CA
* * * *
12306510 TTTTCTAAAAATTATATATTATATTTTTTTTCAAAAAAACA
1 TTTTC-AAAAACTATATATTATATATATATTC---AAAACA
*
12306551 TTTTCAAAAATTATACTA-TATATATATA
1 TTTTCAAAAACTATA-TATTATATATATA
12306579 ATAATATAAT
Statistics
Matches: 150, Mismatches: 18, Indels: 25
0.78 0.09 0.13
Matches are distributed among these distances:
34 10 0.07
35 4 0.03
36 5 0.03
37 15 0.10
38 39 0.26
39 37 0.25
40 27 0.18
41 9 0.06
42 4 0.03
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (37 bp):
TTTTCAAAAACTATATATTATATATATATTCAAAACA
Found at i:12306456 original size:77 final size:76
Alignment explanation
Indices: 12306358--12306578 Score: 229
Period size: 77 Copynumber: 2.9 Consensus size: 76
12306348 TAATACATAT
12306358 GTTTTCAAAAACTATATATTATATATATATTTTAAAAATATTTTCAAAAATGATATATTATATAT
1 GTTTTCAAAAACTATATATTATATATATATTTTAAAAATATTTTCAAAAAT-ATATA-TATATAT
12306423 ATATTC-AAGAA-C
64 ATATTCGAA-AACC
* ** * *
12306435 GTTTTCAAAAACTATATATTAT-TATATGTTTTCGAAATGTTTTCAAAACTATATA-ATATATAT
1 GTTTTCAAAAACTATATATTATATATATATTTTAAAAATATTTTCAAAAATATATATATATATAT
*
12306498 TTTCGAAAACC
66 ATTCGAAAACC
* * * *
12306509 ATTTTCTAAAAATTATATATTATAT-T-TTTTTTCAAAAAAACATTTTCAAAAATTATACTATAT
1 GTTTTC-AAAAACTATATATTATATATATATTTT---AAAAATATTTTCAAAAA-TATA-TATAT
12306572 ATATATA
60 ATATATA
12306579 ATAATATAAT
Statistics
Matches: 119, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
73 13 0.11
74 13 0.11
75 21 0.18
76 24 0.20
77 34 0.29
78 4 0.03
79 2 0.02
80 8 0.07
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (76 bp):
GTTTTCAAAAACTATATATTATATATATATTTTAAAAATATTTTCAAAAATATATATATATATAT
ATTCGAAAACC
Found at i:12307410 original size:85 final size:85
Alignment explanation
Indices: 12307218--12307612 Score: 445
Period size: 85 Copynumber: 4.7 Consensus size: 85
12307208 TACCATGCAA
* * * * * * *
12307218 TTGATATGTCGTCGAGCTGAAGGGAATCAAACTCGACA-GTTTTTGTTGACAGATAGCTTTTC-C
1 TTGATATGTCCTTGAGCTGAATGTAATCGAACTCGA-AGGTTTTTGTTGACAGATAACTCTTCTC
* * *
12307281 GACTTAAGCTATGTTGTAAAG
65 GCCTTGAGCTATGCTGTAAAG
* * * *
12307302 TTGACATGCCCTTGAGCTGAATGTAATTGAACTCGAAGGTTTTTATTGACAGATAACTCTTCTCG
1 TTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAACTCTTCTCG
* * *
12307367 CCTTGAGTTATGTTGTAAAT
66 CCTTGAGCTATGCTGTAAAG
* * * * * *
12307387 TTGATATGTCCTTGAGCTAAATGTAATCAAACTCGAAGGTTTTGGTTGACCGATAGCCCTTCTCG
1 TTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAACTCTTCTCG
* **
12307452 CCTTGAGCTATACTACAAAG
66 CCTTGAGCTATGCTGTAAAG
* * * *
12307472 TTGATATGTCCTTGAGATGAATGTAATCGAACTCGAACGTTTTGGTTGACAGATAGAC-CTTCTT
1 TTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATA-ACTCTTCTC
12307536 GCCTTGAGCTATGCTGTAAAG
65 GCCTTGAGCTATGCTGTAAAG
* * * *
12307557 TTGATATGTCATTGAGCTGAGTGTAATCGAACTCGAAGGTTTTTGCTGGCAGATAA
1 TTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAA
12307613 GCTTTGAGCT
Statistics
Matches: 260, Mismatches: 48, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
83 1 0.00
84 50 0.19
85 208 0.80
86 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (85 bp):
TTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAACTCTTCTCG
CCTTGAGCTATGCTGTAAAG
Found at i:12308911 original size:95 final size:96
Alignment explanation
Indices: 12308747--12308943 Score: 288
Period size: 95 Copynumber: 2.1 Consensus size: 96
12308737 AACTCAATAC
* * *
12308747 TATAATCACCTTTATCAGGCTAGCCAAATCTCATCCATAAAGTCGGGGCGTTTAACCAATTGCTC
1 TATAATCACATTTATCAGGATAGCCAAATCTCATCCATAAAGTCGGGGCATTTAACCAATTGCTC
*
12308812 TAGAGGGATAACTCAAGCTTTATTGTATAT-
66 TAGAGGGACAACTCAAGCTTTATTGTATATA
*** * * * *
12308842 TATAATCACATTTATCAGGATAGTTGAATCTTATCGATAAAGTTGGGGCATTTAACCAATTGCTT
1 TATAATCACATTTATCAGGATAGCCAAATCTCATCCATAAAGTCGGGGCATTTAACCAATTGCTC
12308907 TAGAGGGACAACTCAAGCTTTATTGTATATA
66 TAGAGGGACAACTCAAGCTTTATTGTATATA
12308938 TATAAT
1 TATAAT
12308944 ATTATAATCT
Statistics
Matches: 90, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
95 84 0.93
96 6 0.07
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (96 bp):
TATAATCACATTTATCAGGATAGCCAAATCTCATCCATAAAGTCGGGGCATTTAACCAATTGCTC
TAGAGGGACAACTCAAGCTTTATTGTATATA
Found at i:12311247 original size:17 final size:18
Alignment explanation
Indices: 12311225--12311267 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
12311215 TCCGGATTTG
12311225 TTTTATTTTATTTTGT-T
1 TTTTATTTTATTTTGTAT
* *
12311242 TTTTATATTATTTTTTAT
1 TTTTATTTTATTTTGTAT
12311260 TTTTATTT
1 TTTTATTT
12311268 ATATATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.81
Consensus pattern (18 bp):
TTTTATTTTATTTTGTAT
Found at i:12311253 original size:22 final size:22
Alignment explanation
Indices: 12311227--12311271 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
12311217 CGGATTTGTT
12311227 TTATTTTATT-TTGTTT-TTTATA
1 TTATTTT-TTATT-TTTATTTATA
12311249 TTATTTTTTATTTTTATTTATA
1 TTATTTTTTATTTTTATTTATA
12311271 T
1 T
12311272 ATATATAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (22 bp):
TTATTTTTTATTTTTATTTATA
Found at i:12311269 original size:17 final size:16
Alignment explanation
Indices: 12311221--12311269 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
12311211 TTCATCCGGA
*
12311221 TTTGTTTTAT-TTTAT
1 TTTGTTTTTTATTTAT
12311236 TTTGTTTTTTATATTAT
1 TTTGTTTTTTAT-TTAT
*
12311253 TTTTTATTTTTATTTAT
1 TTTGT-TTTTTATTTAT
12311270 ATATATATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 9 0.31
16 1 0.03
17 12 0.41
18 7 0.24
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (16 bp):
TTTGTTTTTTATTTAT
Found at i:12311359 original size:2 final size:2
Alignment explanation
Indices: 12311352--12311381 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12311342 CAGTTTTCAA
12311352 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12311382 GTTTTGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12311408 original size:38 final size:37
Alignment explanation
Indices: 12311364--12311641 Score: 164
Period size: 37 Copynumber: 7.7 Consensus size: 37
12311354 ATATATATAT
*
12311364 ATATATATATATATTATAGTTTTGAAAACATTTCGAAA
1 ATATATATA-ATATTATAGTTTTGAAAACATTTTGAAA
* *
12311402 ACATATATAATA-TATAGTTTTTGAAAACGTTTTTGAAA
1 ATATATATAATATTATAG-TTTTGAAAAC-ATTTTGAAA
* * * * *
12311440 ATATATATAATATAAAATTTTTGAAAATATTTTTAAA
1 ATATATATAATATTATAGTTTTGAAAACATTTTGAAA
* *
12311477 ATATATATATATATATATA-ATAT-AATATA-ATTTTTGAAA
1 ATATATATA-ATAT-TATAGTTTTGAA-A-ACA-TTTTGAAA
* * * * *
12311516 ACATTTTTGAA-A--ACATTTTTGAAAAC---------
1 ATATATAT-AATATTATAGTTTTGAAAACATTTTGAAA
12311542 ATATATATAATA-TATAGTTTT-AAAACATTTTGAAAAA
1 ATATATATAATATTATAGTTTTGAAAACATTTTG--AAA
*
12311579 ATATATATAATA-TATAGTTTTTAAAACATTTTGAAA
1 ATATATATAATATTATAGTTTTGAAAACATTTTGAAA
12311615 ATATATATAATA-TATAGTTTTGGAAAA
1 ATATATATAATATTATAGTTTT-GAAAA
12311642 TATATATTAT
Statistics
Matches: 186, Mismatches: 27, Indels: 55
0.69 0.10 0.21
Matches are distributed among these distances:
25 2 0.01
26 11 0.06
27 6 0.03
35 3 0.02
36 32 0.17
37 58 0.31
38 55 0.30
39 18 0.10
40 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.43
Consensus pattern (37 bp):
ATATATATAATATTATAGTTTTGAAAACATTTTGAAA
Found at i:12311514 original size:50 final size:50
Alignment explanation
Indices: 12311440--12311594 Score: 153
Period size: 50 Copynumber: 3.2 Consensus size: 50
12311430 GTTTTTGAAA
* *
12311440 ATATATATAATAT-A-A-AATTTTTGAAAATATTTTTAAAATATATATAT
1 ATATATATAATATAATATAATTTTTGAAAACATTTTTAAAAAATATATAT
* * *
12311487 ATATATATAATATAATATAATTTTTGAAAACATTTTTGAAAACATTTTTGA-
1 ATATATATAATATAATATAATTTTTGAAAACATTTTT-AAAAAATATAT-AT
* * * *
12311538 AAACATAT-ATATAATATATAGTTTT-AAAACATTTTGAAAAAATATATAT
1 ATATATATAATATAATATA-ATTTTTGAAAACATTTTTAAAAAATATATAT
12311587 A-ATATATA
1 ATATATATA
12311595 GTTTTTAAAA
Statistics
Matches: 88, Mismatches: 12, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
47 13 0.15
48 7 0.08
49 10 0.11
50 38 0.43
51 19 0.22
52 1 0.01
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (50 bp):
ATATATATAATATAATATAATTTTTGAAAACATTTTTAAAAAATATATAT
Found at i:12311521 original size:12 final size:12
Alignment explanation
Indices: 12311506--12311543 Score: 76
Period size: 12 Copynumber: 3.2 Consensus size: 12
12311496 ATATAATATA
12311506 ATTTTTGAAAAC
1 ATTTTTGAAAAC
12311518 ATTTTTGAAAAC
1 ATTTTTGAAAAC
12311530 ATTTTTGAAAAC
1 ATTTTTGAAAAC
12311542 AT
1 AT
12311544 ATATATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (12 bp):
ATTTTTGAAAAC
Found at i:12311583 original size:37 final size:37
Alignment explanation
Indices: 12311520--12311635 Score: 182
Period size: 37 Copynumber: 3.1 Consensus size: 37
12311510 TTGAAAACAT
*
12311520 TTTTGAAAACATTTTTGAAAACATATATATAATATATAG
1 TTTT-AAAACA-TTTTGAAAAAATATATATAATATATAG
12311559 TTTTAAAACATTTTGAAAAAATATATATAATATATAG
1 TTTTAAAACATTTTGAAAAAATATATATAATATATAG
12311596 TTTTTAAAACATTTTG--AAAATATATATAATATATAG
1 -TTTTAAAACATTTTGAAAAAATATATATAATATATAG
12311632 TTTT
1 TTTT
12311636 GGAAAATATA
Statistics
Matches: 75, Mismatches: 1, Indels: 6
0.91 0.01 0.07
Matches are distributed among these distances:
35 4 0.05
36 20 0.27
37 26 0.35
38 21 0.28
39 4 0.05
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (37 bp):
TTTTAAAACATTTTGAAAAAATATATATAATATATAG
Found at i:12311658 original size:24 final size:24
Alignment explanation
Indices: 12311607--12311664 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 24
12311597 TTTTAAAACA
*
12311607 TTTTGAAAATATATATAATATATAG
1 TTTTGAAAATATATAT-ATATAGAG
*
12311632 TTTTGGAAAATATATAT-TATAGGG
1 TTTT-GAAAATATATATATATAGAG
12311656 TTTTGAAAA
1 TTTTGAAAA
12311665 CATTTTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 5 0.17
24 9 0.30
25 4 0.13
26 12 0.40
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (24 bp):
TTTTGAAAATATATATATATAGAG
Found at i:12311716 original size:3 final size:3
Alignment explanation
Indices: 12311704--12311741 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
12311694 TTTTAAAAAA
*
12311704 ATT ATT -TT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12311742 TGTATTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:12312942 original size:4 final size:4
Alignment explanation
Indices: 12312933--12312962 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
12312923 TTTATTATTA
12312933 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
12312963 CAAACCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:12314629 original size:3 final size:3
Alignment explanation
Indices: 12314621--12314653 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
12314611 TTTAATGTTA
12314621 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12314654 GTTTTGTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:12315055 original size:34 final size:34
Alignment explanation
Indices: 12314999--12315110 Score: 188
Period size: 34 Copynumber: 3.3 Consensus size: 34
12314989 AGAATCAAAC
* * *
12314999 ACGCTGAATGTTGAACGATTCCATTCAGCATTCA
1 ACGCTGAATGCTAAACGGTTCCATTCAGCATTCA
*
12315033 GCGCTGAATGCTAAACGGTTCCATTCAGCATTCA
1 ACGCTGAATGCTAAACGGTTCCATTCAGCATTCA
12315067 ACGCTGAATGCTAAACGGTTCCATTCAGCATTCA
1 ACGCTGAATGCTAAACGGTTCCATTCAGCATTCA
12315101 ACGCTGAATG
1 ACGCTGAATG
12315111 GTTCCATTCA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 73 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.27
Consensus pattern (34 bp):
ACGCTGAATGCTAAACGGTTCCATTCAGCATTCA
Found at i:12315057 original size:27 final size:27
Alignment explanation
Indices: 12315027--12315122 Score: 75
Period size: 27 Copynumber: 3.3 Consensus size: 27
12315017 TTCCATTCAG
12315027 CATTCAGCGCTGAATGCTAAACGGTTC
1 CATTCAGCGCTGAATGCTAAACGGTTC
12315054 CATTCAGCATTCAACGCTGAATGCTAAACGGTTC
1 CATTCAG-------CGCTGAATGCTAAACGGTTC
** * * * *
12315088 CATTCAGCATTCAACGCTGAATGGTTC
1 CATTCAGCGCTGAATGCTAAACGGTTC
12315115 CATTCAGC
1 CATTCAGC
12315123 ATTCAACGTT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
27 29 0.52
34 27 0.48
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (27 bp):
CATTCAGCGCTGAATGCTAAACGGTTC
Found at i:12315123 original size:27 final size:27
Alignment explanation
Indices: 12315083--12315150 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
12315073 AATGCTAAAC
12315083 GGTTCCATTCAGCATTCAACGCTGAAT
1 GGTTCCATTCAGCATTCAACGCTGAAT
*
12315110 GGTTCCATTCAGCATTCAACGTTGAAT
1 GGTTCCATTCAGCATTCAACGCTGAAT
12315137 GGTTCCATTCAGCA
1 GGTTCCATTCAGCA
12315151 ATAAACAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (27 bp):
GGTTCCATTCAGCATTCAACGCTGAAT
Found at i:12315260 original size:30 final size:32
Alignment explanation
Indices: 12315226--12315295 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 32
12315216 TTTCATTTAA
*
12315226 TATATATTATATATTATATAGT-A-TAATATT
1 TATATATTATATAGTATATAGTAATTAATATT
* *
12315256 TATAT-TT-TATAGTATATATTAATTAGTATT
1 TATATATTATATAGTATATAGTAATTAATATT
12315286 TATATATTAT
1 TATATATTAT
12315296 TAATGTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 11 0.33
29 3 0.09
30 16 0.48
31 2 0.06
32 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (32 bp):
TATATATTATATAGTATATAGTAATTAATATT
Found at i:12315306 original size:18 final size:16
Alignment explanation
Indices: 12315272--12315364 Score: 63
Period size: 15 Copynumber: 5.7 Consensus size: 16
12315262 TTATAGTATA
12315272 TATTAATTA-GTATTTAT
1 TATT-ATTATGTA-TTAT
12315289 ATATTATTAATGTATTA-
1 -TATTATT-ATGTATTAT
12315306 TATT-TGTAT-TA-TAT
1 TATTAT-TATGTATTAT
*
12315320 TATTAGTAATGTTATTAT
1 TATTA-TTATG-TATTAT
12315338 TATTATTAT-TATTAT
1 TATTATTATGTATTAT
12315353 TATTATTCATGT
1 TATTATT-ATGT
12315365 TCAGAAGAGA
Statistics
Matches: 62, Mismatches: 2, Indels: 23
0.71 0.02 0.26
Matches are distributed among these distances:
13 2 0.03
14 6 0.10
15 18 0.29
16 8 0.13
17 9 0.15
18 16 0.26
19 3 0.05
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.59
Consensus pattern (16 bp):
TATTATTATGTATTAT
Found at i:12315337 original size:3 final size:3
Alignment explanation
Indices: 12315285--12315359 Score: 66
Period size: 3 Copynumber: 24.7 Consensus size: 3
12315275 TAATTAGTAT
* * *
12315285 TTA TATA TTA TTAA TGTA TTA -TA TT- TGTA TTA -TA TTA TTA GTA ATG
1 TTA T-TA TTA TT-A T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
12315331 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12315360 CATGTTCAGA
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
2 5 0.08
3 46 0.77
4 8 0.13
5 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:12317191 original size:61 final size:59
Alignment explanation
Indices: 12317084--12317214 Score: 158
Period size: 61 Copynumber: 2.2 Consensus size: 59
12317074 TATTTTATAT
*
12317084 TCTTAACTTTTAAAAATATATTTTTATTTTTATTTTAATATAAAAATATATGTTTTAATCTTA
1 TCTTAAC--TTAAAAATATATTTTTATTCTTATTTTAATATAAAAATATA--TTTTAATCTTA
* * *
12317147 TCTTCACTTAAAAGTATA-TTTTATTCTTATTTTAACT-TAAAAAATATATTTTATTCTTA
1 TCTTAACTTAAAAATATATTTTTATTCTTATTTTAA-TAT-AAAAATATATTTTAATCTTA
12317206 TCTTAACTT
1 TCTTAACTT
12317215 TTTTTTAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
59 18 0.30
60 17 0.28
61 20 0.33
63 6 0.10
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (59 bp):
TCTTAACTTAAAAATATATTTTTATTCTTATTTTAATATAAAAATATATTTTAATCTTA
Found at i:12317212 original size:30 final size:30
Alignment explanation
Indices: 12317084--12317214 Score: 140
Period size: 30 Copynumber: 4.3 Consensus size: 30
12317074 TATTTTATAT
* *
12317084 TCTTAACTTTTAAAAATATATTTTTATTTTTA
1 TCTTAAC-TTAAAAAATATA-TTTTATTCTTA
* * *
12317116 TTTTAA-TATAAAAATATATGTTTTAATCTTA
1 TCTTAACT-TAAAAA-ATATATTTTATTCTTA
* *
12317147 TCTTCACTT-AAAAGTATATTTTATTCTTA
1 TCTTAACTTAAAAAATATATTTTATTCTTA
*
12317176 TTTTAACTTAAAAAATATATTTTATTCTTA
1 TCTTAACTTAAAAAATATATTTTATTCTTA
12317206 TCTTAACTT
1 TCTTAACTT
12317215 TTTTTTAAAA
Statistics
Matches: 81, Mismatches: 14, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
29 20 0.25
30 32 0.40
31 19 0.23
32 10 0.12
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (30 bp):
TCTTAACTTAAAAAATATATTTTATTCTTA
Found at i:12317256 original size:29 final size:27
Alignment explanation
Indices: 12317223--12317307 Score: 89
Period size: 28 Copynumber: 3.0 Consensus size: 27
12317213 TTTTTTTTAA
12317223 AAAATATTTTTAAAAGTTAAGATAATAAT
1 AAAATATTTTT--AAGTTAAGATAATAAT
* * *
12317252 AAAATATATTTTTAATTTAAAATAAGAAT
1 -AAA-ATATTTTTAAGTTAAGATAATAAT
*
12317281 AAAATAATTTTTAAGTGAAGATAATAA
1 AAAAT-ATTTTTAAGTTAAGATAATAA
12317308 CATATATATA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
27 2 0.04
28 20 0.43
29 13 0.28
30 3 0.07
31 8 0.17
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (27 bp):
AAAATATTTTTAAGTTAAGATAATAAT
Found at i:12317261 original size:31 final size:29
Alignment explanation
Indices: 12317220--12317307 Score: 106
Period size: 29 Copynumber: 3.0 Consensus size: 29
12317210 AACTTTTTTT
*
12317220 TAAAAAATATTTTTAAAAGTTAAGATAATAA
1 TAAAATATATTTTT--AAGTTAAGATAATAA
* * *
12317251 TAAAATATATTTTTAATTTAAAATAAGAA
1 TAAAATATATTTTTAAGTTAAGATAATAA
*
12317280 TAAAATA-ATTTTTAAGTGAAGATAATAA
1 TAAAATATATTTTTAAGTTAAGATAATAA
12317308 CATATATATA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
28 17 0.35
29 19 0.39
31 13 0.27
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (29 bp):
TAAAATATATTTTTAAGTTAAGATAATAA
Found at i:12317420 original size:31 final size:30
Alignment explanation
Indices: 12317385--12317454 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
12317375 ATATTTTTAA
*
12317385 AAAATATATCTTTAAAAATTAAGAT-AAGAAT
1 AAAATATAT-TTTAAAAATGAAGATAAAG-AT
** *
12317416 AAAATATATTTTTTAAGTGAAGATAAAGAT
1 AAAATATATTTTAAAAATGAAGATAAAGAT
12317446 AAAATATAT
1 AAAATATAT
12317455 ATATTTATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.65
31 12 0.35
ACGTcount: A:0.56, C:0.01, G:0.09, T:0.34
Consensus pattern (30 bp):
AAAATATATTTTAAAAATGAAGATAAAGAT
Found at i:12317516 original size:31 final size:32
Alignment explanation
Indices: 12317467--12317536 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 32
12317457 ATTTATACAT
12317467 TAAAATAAAAAATATTTAACAAATTAAGAA-A
1 TAAAATAAAAAATATTTAACAAATTAAGAATA
* *
12317498 -AAAATAAAAATATATTTAATAAGTTAAGAATA
1 TAAAATAAAAA-ATATTTAACAAATTAAGAATA
12317530 TAAAATA
1 TAAAATA
12317537 TTATGAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 10 0.29
31 17 0.50
32 1 0.03
33 6 0.18
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (32 bp):
TAAAATAAAAAATATTTAACAAATTAAGAATA
Found at i:12320905 original size:17 final size:16
Alignment explanation
Indices: 12320885--12320942 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
12320875 AATAAGCTAC
12320885 TTCATTAAGTAAGTTGG
1 TTCATTAA-TAAGTTGG
12320902 TTCATTCAATAAAGTTGG
1 TTCATT-AAT-AAGTTGG
* * *
12320920 ATCATTAATTAAGCTAG
1 TTCATTAA-TAAGTTGG
12320937 TTCATT
1 TTCATT
12320943 CATTAAACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 19 0.56
18 15 0.44
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (16 bp):
TTCATTAATAAGTTGG
Found at i:12320918 original size:18 final size:18
Alignment explanation
Indices: 12320895--12320949 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
12320885 TTCATTAAGT
12320895 AAGTTGGTTCATTCAATA
1 AAGTTGGTTCATTCAATA
* *
12320913 AAGTTGGATCATT-AATT
1 AAGTTGGTTCATTCAATA
* * *
12320930 AAGCTAGTTCATTCATTA
1 AAGTTGGTTCATTCAATA
12320948 AA
1 AA
12320950 CTAGTTCATT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
17 13 0.45
18 16 0.55
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (18 bp):
AAGTTGGTTCATTCAATA
Found at i:12320947 original size:17 final size:17
Alignment explanation
Indices: 12320921--12320973 Score: 88
Period size: 17 Copynumber: 3.1 Consensus size: 17
12320911 TAAAGTTGGA
*
12320921 TCATTAATTAAGCTAGT
1 TCATTAATTAAACTAGT
*
12320938 TCATTCATTAAACTAGT
1 TCATTAATTAAACTAGT
12320955 TCATTAATTAAACTAGT
1 TCATTAATTAAACTAGT
12320972 TC
1 TC
12320974 TTTTAATGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.42
Consensus pattern (17 bp):
TCATTAATTAAACTAGT
Found at i:12321311 original size:17 final size:17
Alignment explanation
Indices: 12321289--12321322 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12321279 TTGGACGACA
*
12321289 ATGTGTTTACATACATC
1 ATGTGTCTACATACATC
*
12321306 ATGTGTCTACATTCATC
1 ATGTGTCTACATACATC
12321323 CCCTTTTCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (17 bp):
ATGTGTCTACATACATC
Found at i:12322435 original size:45 final size:46
Alignment explanation
Indices: 12322336--12322446 Score: 138
Period size: 45 Copynumber: 2.4 Consensus size: 46
12322326 TCATTGATAA
* * *
12322336 CATCCCTTCAT-CCTTATAATACACCATTATACCATTTCCATTATGG
1 CATCCTTTCATGCCTT-TTATACACCATTATACCATTTCCATTATGC
*
12322382 CATCCTTTCATGCCTTTTATACACTATTATA-CATTT-CATTTATGC
1 CATCCTTTCATGCCTTTTATACACCATTATACCATTTCCA-TTATGC
*
12322427 CATTCTTTCATGCCTTTTAT
1 CATCCTTTCATGCCTTTTAT
12322447 GTTCTGTTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
44 2 0.03
45 29 0.50
46 23 0.40
47 4 0.07
ACGTcount: A:0.24, C:0.27, G:0.05, T:0.44
Consensus pattern (46 bp):
CATCCTTTCATGCCTTTTATACACCATTATACCATTTCCATTATGC
Found at i:12322929 original size:59 final size:59
Alignment explanation
Indices: 12322837--12322963 Score: 218
Period size: 59 Copynumber: 2.2 Consensus size: 59
12322827 TCCCATACGA
*
12322837 AAATTCATACACTTTGTATGATTTCCTTATCATTTTACCACACAAAGTGCCCTATCTGG
1 AAATTCATACACTTAGTATGATTTCCTTATCATTTTACCACACAAAGTGCCCTATCTGG
* * *
12322896 AAATTCATACCCTTAGTATGATTTCCTTATCATTTTAGCACACAAATTGCCCTATCTGG
1 AAATTCATACACTTAGTATGATTTCCTTATCATTTTACCACACAAAGTGCCCTATCTGG
12322955 AAATTCATA
1 AAATTCATA
12322964 ATTAATTTAT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 64 1.00
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.37
Consensus pattern (59 bp):
AAATTCATACACTTAGTATGATTTCCTTATCATTTTACCACACAAAGTGCCCTATCTGG
Found at i:12323045 original size:54 final size:54
Alignment explanation
Indices: 12322987--12323269 Score: 431
Period size: 54 Copynumber: 5.2 Consensus size: 54
12322977 TTTCATGCTT
* * *
12322987 TGCACACATAGTGCCGAAACGGTTATTCATCCTCATAGAATGAATTCCATGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGAATGAATTCCGTGAAA
** *
12323041 TGCACACTTAGTGCCGAAACAATTATTCATCCTCATAGAATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGAATGAATTCCGTGAAA
* * *
12323095 TGCACACTTAGTGCCGAAACGGTTATTCATCAACATAGGATGAATTCCTTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGAATGAATTCCGTGAAA
* * *
12323149 TGCACACTTAGTGCCAAAACGGTTATTCATCCACATGGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGAATGAATTCCGTGAAA
**
12323203 TGCACACTTAGTGCCGAAATAGTTATTCATCCACATAGAATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGAATGAATTCCGTGAAA
*
12323257 TACACACTTAGTG
1 TGCACACTTAGTG
12323270 TCGTTTGGAA
Statistics
Matches: 209, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 209 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGAATGAATTCCGTGAAA
Found at i:12324930 original size:18 final size:17
Alignment explanation
Indices: 12324909--12324947 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
12324899 AGGCATGCAT
12324909 TTCATTTAAAGCATATAG
1 TTCA-TTAAAGCATATAG
* *
12324927 TTCATTATAGCATGTAG
1 TTCATTAAAGCATATAG
12324944 TTCA
1 TTCA
12324948 GTTAGTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (17 bp):
TTCATTAAAGCATATAG
Found at i:12328902 original size:24 final size:23
Alignment explanation
Indices: 12328858--12328902 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
12328848 TGAAAGATTT
* *
12328858 TAAAGTAAATAAAGAATATAATC
1 TAAAGAAAATAAAGAAAATAATC
12328881 TAAAGAAAATTAAAGAAAATAA
1 TAAAGAAAA-TAAAGAAAATAA
12328903 ATTAAGATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.22
Consensus pattern (23 bp):
TAAAGAAAATAAAGAAAATAATC
Found at i:12332554 original size:15 final size:15
Alignment explanation
Indices: 12332530--12332561 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12332520 TGGCTTGTAC
12332530 CTTTTAATCACATAG
1 CTTTTAATCACATAG
*
12332545 CTTTTTATCACATAG
1 CTTTTAATCACATAG
12332560 CT
1 CT
12332562 CATATAACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (15 bp):
CTTTTAATCACATAG
Done.