Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold385
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: 1395621
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 5 of 10
Found at i:453477 original size:13 final size:13
Alignment explanation
Indices: 453461--453485 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
453451 CTTACTACTC
453461 AAAATATTATTTA
1 AAAATATTATTTA
453474 AAAATATTATTT
1 AAAATATTATTT
453486 TTTTATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAATATTATTTA
Found at i:454310 original size:2 final size:2
Alignment explanation
Indices: 454303--454336 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
454293 ATAAAAAGTT
454303 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
454337 GAGAGAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:454341 original size:2 final size:2
Alignment explanation
Indices: 454336--454368 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
454326 ATATATATAT
454336 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
454369 TATACTAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:455235 original size:2 final size:2
Alignment explanation
Indices: 455228--455254 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
455218 AAACTTCGCA
455228 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
455255 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:455259 original size:2 final size:2
Alignment explanation
Indices: 455254--455292 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
455244 ATATATATAT
455254 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
455293 TTTTAATTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:462554 original size:13 final size:13
Alignment explanation
Indices: 462536--462565 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
462526 TTTTTAATAA
462536 AATATTTATATTC
1 AATATTTATATTC
*
462549 AATATTTATATTT
1 AATATTTATATTC
462562 AATA
1 AATA
462566 GATATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
AATATTTATATTC
Found at i:462714 original size:68 final size:67
Alignment explanation
Indices: 462571--462700 Score: 188
Period size: 68 Copynumber: 1.9 Consensus size: 67
462561 TAATAGATAT
***
462571 TTAAATATAGACGTGAAGTTAAATCTTTTAAATATATATAAAAATTTATAAAAGTTTAAATACAG
1 TTAAATATAGACGTGAAGTTAAATCTTTTAAATATATATAAAAATTTATAAAAAAATAAATACAG
462636 TA
66 TA
* * * *
462638 TTAAATATAGAGGTTGAAGTTGAATCTTTTAAATATATATAAAAGTTTATAAAAAAATGAATA
1 TTAAATATAGACG-TGAAGTTAAATCTTTTAAATATATATAAAAATTTATAAAAAAATAAATA
462701 TATATATATA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
67 12 0.22
68 43 0.78
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.37
Consensus pattern (67 bp):
TTAAATATAGACGTGAAGTTAAATCTTTTAAATATATATAAAAATTTATAAAAAAATAAATACAG
TA
Found at i:462726 original size:11 final size:11
Alignment explanation
Indices: 462700--462736 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
462690 AAAAATGAAT
*
462700 ATATATATA-T
1 ATATATATAGG
462710 ATATATATAGG
1 ATATATATAGG
462721 ATATATATAGG
1 ATATATATAGG
462732 ATATA
1 ATATA
462737 CCTATTTAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.41
Consensus pattern (11 bp):
ATATATATAGG
Found at i:462874 original size:12 final size:12
Alignment explanation
Indices: 462857--462900 Score: 79
Period size: 12 Copynumber: 3.7 Consensus size: 12
462847 CTCTCAATAA
462857 AAGCTGAAGTTG
1 AAGCTGAAGTTG
462869 AAGCTGAAGTTG
1 AAGCTGAAGTTG
*
462881 AAGCTGAAGCTG
1 AAGCTGAAGTTG
462893 AAGCTGAA
1 AAGCTGAA
462901 ATAGTCCAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.36, C:0.11, G:0.32, T:0.20
Consensus pattern (12 bp):
AAGCTGAAGTTG
Found at i:462876 original size:6 final size:6
Alignment explanation
Indices: 462857--462900 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
462847 CTCTCAATAA
* *
462857 AAGCTG AAGTTG AAGCTG AAGTTG AAGCTG AAGCTG AAGCTG AA
1 AAGCTG AAGCTG AAGCTG AAGCTG AAGCTG AAGCTG AAGCTG AA
462901 ATAGTCCAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.36, C:0.11, G:0.32, T:0.20
Consensus pattern (6 bp):
AAGCTG
Found at i:473636 original size:12 final size:12
Alignment explanation
Indices: 473619--473675 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 12
473609 ACCAAAACCC
473619 AGAAAAAAAAAA
1 AGAAAAAAAAAA
*
473631 ACAAAAAAAAAA
1 AGAAAAAAAAAA
** *
473643 AGACCATAAAAA
1 AGAAAAAAAAAA
*
473655 AGAAAAAGAAAA
1 AGAAAAAAAAAA
473667 AGAAAAAAA
1 AGAAAAAAA
473676 GAAGAGATGA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.84, C:0.05, G:0.09, T:0.02
Consensus pattern (12 bp):
AGAAAAAAAAAA
Found at i:474143 original size:18 final size:19
Alignment explanation
Indices: 474112--474174 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 19
474102 ATTTAAATAA
*
474112 AAAATTTAAATTATTTT-T
1 AAAATATAAATTATTTTAT
*
474130 AAAATATAATTTATTTTAT
1 AAAATATAAATTATTTTAT
* *
474149 AAATATTTTAATTAATTTTAT
1 AAA-ATATAAATT-ATTTTAT
*
474170 TAAAT
1 AAAAT
474175 CAATAAACAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 15 0.42
19 4 0.11
20 8 0.22
21 9 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AAAATATAAATTATTTTAT
Found at i:474281 original size:19 final size:19
Alignment explanation
Indices: 474228--474287 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
474218 TTTATTTTTT
474228 ATTTTTTCAAT-TTAAATAA
1 ATTTTTT-AATATTAAATAA
474247 ATTTTTTAACTA-TAAATTAA
1 ATTTTTTAA-TATTAAA-TAA
474267 A-TTTTTAATATTAAA-AA
1 ATTTTTTAATATTAAATAA
474284 ATTT
1 ATTT
474288 AAATTAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
17 3 0.08
18 6 0.17
19 23 0.64
20 4 0.11
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTTTTAATATTAAATAA
Found at i:474311 original size:12 final size:12
Alignment explanation
Indices: 474291--474382 Score: 51
Period size: 15 Copynumber: 6.8 Consensus size: 12
474281 AAAATTTAAA
*
474291 TTAATAATATTT
1 TTAAAAATATTT
474303 TTAAAAATATATTAT
1 TT-AAAA-ATATT-T
474318 TATAAATAATATTT
1 T-TAAA-AATATTT
474332 TTAAAAATATATTAT
1 TT-AAAA-ATATT-T
474347 TATAAATAATATTT
1 T-TAAA-AATATTT
**
474361 TTAATTA-ATTT
1 TTAAAAATATTT
474372 TTAAAAGATAT
1 TTAAAA-ATAT
474383 ATATACATAT
Statistics
Matches: 63, Mismatches: 5, Indels: 23
0.69 0.05 0.25
Matches are distributed among these distances:
11 8 0.13
12 4 0.06
13 10 0.16
14 17 0.27
15 20 0.32
16 4 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (12 bp):
TTAAAAATATTT
Found at i:474311 original size:15 final size:15
Alignment explanation
Indices: 474293--474364 Score: 94
Period size: 14 Copynumber: 4.9 Consensus size: 15
474283 AATTTAAATT
474293 AATAATATTTTTAAA
1 AATAATATTTTTAAA
* *
474308 AAT-ATATTATTATA
1 AATAATATTTTTAAA
474322 AATAATATTTTTAAA
1 AATAATATTTTTAAA
* *
474337 AAT-ATATTATTATA
1 AATAATATTTTTAAA
474351 AATAATATTTTTAA
1 AATAATATTTTTAA
474365 TTAATTTTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
14 24 0.51
15 23 0.49
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AATAATATTTTTAAA
Found at i:474335 original size:29 final size:29
Alignment explanation
Indices: 474293--474364 Score: 144
Period size: 29 Copynumber: 2.5 Consensus size: 29
474283 AATTTAAATT
474293 AATAATATTTTTAAAAATATATTATTATA
1 AATAATATTTTTAAAAATATATTATTATA
474322 AATAATATTTTTAAAAATATATTATTATA
1 AATAATATTTTTAAAAATATATTATTATA
474351 AATAATATTTTTAA
1 AATAATATTTTTAA
474365 TTAATTTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
AATAATATTTTTAAAAATATATTATTATA
Found at i:474386 original size:2 final size:2
Alignment explanation
Indices: 474379--474428 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
474369 TTTTTAAAAG
* * *
474379 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT GT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
474421 AT AT AT AT
1 AT AT AT AT
474429 CATGATTTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:474584 original size:2 final size:2
Alignment explanation
Indices: 474577--474612 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
474567 ATAAATTTTC
474577 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
474613 TTAGAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:474765 original size:19 final size:21
Alignment explanation
Indices: 474741--474782 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
474731 ATTAGTAAAC
474741 ATAATAT-ATATTTAAT-TAA
1 ATAATATGATATTTAATATAA
*
474760 ATAATATGATTTTTAATATAA
1 ATAATATGATATTTAATATAA
474781 AT
1 AT
474783 TTAATAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 8 0.40
21 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
ATAATATGATATTTAATATAA
Found at i:474982 original size:26 final size:27
Alignment explanation
Indices: 474935--474987 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
474925 AATTTTTTTA
474935 ATTTATTTTTATCTCAAAATTA-AAAT
1 ATTTATTTTTATCTCAAAATTAGAAAT
* *
474961 ATTTATTTTTCTC-CATATATTAGAAAT
1 ATTTATTTTTATCTCA-AAATTAGAAAT
474988 TACTGCACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 2 0.09
26 17 0.74
27 4 0.17
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (27 bp):
ATTTATTTTTATCTCAAAATTAGAAAT
Found at i:475254 original size:4 final size:4
Alignment explanation
Indices: 475247--475277 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
475237 TACCTAAATC
475247 AATT AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AATT AAT
475278 GTTTATCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:476746 original size:24 final size:26
Alignment explanation
Indices: 476696--476744 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 26
476686 AGTTTCGAAG
*
476696 TTAAATTTATTGACTATAAAATTAAA
1 TTAAATTTATTGAATATAAAATTAAA
476722 TTAAA-TT-TTGAATAT-AAATTAAA
1 TTAAATTTATTGAATATAAAATTAAA
476745 ATATAATGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 8 0.36
24 7 0.32
25 2 0.09
26 5 0.23
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (26 bp):
TTAAATTTATTGAATATAAAATTAAA
Found at i:481038 original size:22 final size:24
Alignment explanation
Indices: 480991--481041 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
480981 ATAATAATAA
480991 TAAATAATTTATATTATATAAACT
1 TAAATAATTTATATTATATAAACT
*
481015 TAAA-AATTATATATT-TAT-ATCT
1 TAAATAATT-TATATTATATAAACT
481037 TAAAT
1 TAAAT
481042 TAAATATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 7 0.29
23 7 0.29
24 10 0.42
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
TAAATAATTTATATTATATAAACT
Found at i:481588 original size:21 final size:21
Alignment explanation
Indices: 481543--481639 Score: 90
Period size: 21 Copynumber: 4.5 Consensus size: 21
481533 TACAACGCTC
*
481543 TTAATTTTAATCTAATTCGAAATT
1 TTAA-TTTAAT-TAATT-TAAATT
** *
481567 TTAAGATAATTCATTTAAATT
1 TTAATTTAATTAATTTAAATT
* *
481588 TAAATTTAATTAATTTAAATA
1 TTAATTTAATTAATTTAAATT
481609 TTATATTTAATTAATTTAAA-T
1 TTA-ATTTAATTAATTTAAATT
481630 TTAA-TTAATT
1 TTAATTTAATT
481640 TAAATATAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
19 6 0.10
20 1 0.02
21 26 0.43
22 20 0.33
23 4 0.07
24 4 0.07
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (21 bp):
TTAATTTAATTAATTTAAATT
Found at i:481604 original size:15 final size:14
Alignment explanation
Indices: 481573--481677 Score: 88
Period size: 15 Copynumber: 7.1 Consensus size: 14
481563 AATTTTAAGA
481573 TAATTCATTTAAATT
1 TAATT-ATTTAAATT
*
481588 TAAATTTAATT-AATT
1 T-AA-TTATTTAAATT
* *
481603 TAAATA-TTATATT
1 TAATTATTTAAATT
481616 TAATTAATTTAAATT
1 TAATT-ATTTAAATT
481631 TAATTAATTTAAATAT
1 TAATT-ATTTAAAT-T
*
481647 AAAATTATTTAAATT
1 -TAATTATTTAAATT
481662 TAAATTATTTAAATT
1 T-AATTATTTAAATT
481677 T
1 T
481678 GATCAAAAAC
Statistics
Matches: 75, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
12 2 0.03
13 9 0.12
14 3 0.04
15 41 0.55
16 14 0.19
17 6 0.08
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (14 bp):
TAATTATTTAAATT
Found at i:481605 original size:5 final size:5
Alignment explanation
Indices: 481579--481642 Score: 53
Period size: 6 Copynumber: 12.2 Consensus size: 5
481569 AAGATAATTC
481579 ATTTAA ATTTAA ATTTA A-TTA ATTTAA ATATTA TATTTA A-TTA ATTTAA
1 ATTT-A ATTT-A ATTTA ATTTA ATTT-A AT-TTA -ATTTA ATTTA ATTT-A
481628 ATTTA A-TTA ATTTA A
1 ATTTA ATTTA ATTTA A
481643 ATATAAAATT
Statistics
Matches: 51, Mismatches: 0, Indels: 15
0.77 0.00 0.23
Matches are distributed among these distances:
4 12 0.24
5 13 0.25
6 22 0.43
7 4 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (5 bp):
ATTTA
Found at i:481619 original size:22 final size:21
Alignment explanation
Indices: 481573--481633 Score: 95
Period size: 22 Copynumber: 2.9 Consensus size: 21
481563 AATTTTAAGA
*
481573 TAATTCATTTAAATTTAAATT
1 TAATTAATTTAAATTTAAATT
*
481594 TAATTAATTTAAATATTATATT
1 TAATTAATTTAAAT-TTAAATT
481616 TAATTAATTTAAATTTAA
1 TAATTAATTTAAATTTAA
481634 TTAATTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 16 0.44
22 20 0.56
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TAATTAATTTAAATTTAAATT
Found at i:481677 original size:37 final size:38
Alignment explanation
Indices: 481574--481667 Score: 138
Period size: 37 Copynumber: 2.5 Consensus size: 38
481564 ATTTTAAGAT
*
481574 AATTCATTTAAATTTAAATTTAATTAATTTAAATATTAT
1 AATT-ATTTAAATTTAAATTTAATTAATTTAAATATTAA
* *
481613 ATTTAATT-AATTTAAATTTAATTAATTTAAATA-TAA
1 AATTATTTAAATTTAAATTTAATTAATTTAAATATTAA
481649 AATTATTTAAATTTAAATT
1 AATTATTTAAATTTAAATT
481668 ATTTAAATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
36 8 0.16
37 35 0.71
38 3 0.06
39 3 0.06
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (38 bp):
AATTATTTAAATTTAAATTTAATTAATTTAAATATTAA
Found at i:481751 original size:3 final size:3
Alignment explanation
Indices: 481743--481777 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
481733 TCGGATTCCT
481743 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
481778 TCATTTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:484692 original size:20 final size:20
Alignment explanation
Indices: 484669--484741 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
484659 ACAACTCAAA
484669 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
484689 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
484710 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
484730 GTATCGATACAT
1 GTATCGATACAT
484742 AAAAAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:484720 original size:41 final size:42
Alignment explanation
Indices: 484669--484763 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
484659 ACAACTCAAA
*
484669 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
484710 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
484752 GTATCGATACAT
1 GTATCGATACAT
484764 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:484820 original size:13 final size:13
Alignment explanation
Indices: 484802--484827 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
484792 TACAGCAAGT
484802 ATGTATCGATACA
1 ATGTATCGATACA
484815 ATGTATCGATACA
1 ATGTATCGATACA
484828 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:487076 original size:21 final size:21
Alignment explanation
Indices: 487043--487087 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
487033 TTGCAAGTTG
*
487043 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
487065 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
487085 AAA
1 AAA
487088 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:488911 original size:15 final size:15
Alignment explanation
Indices: 488891--488921 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
488881 TAAAAATGTC
*
488891 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
488906 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
488921 C
1 C
488922 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:490961 original size:20 final size:20
Alignment explanation
Indices: 490935--491012 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 20
490925 AATGTCCAAA
490935 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATGTTTCT
* *
490955 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACA--T-G--TTTCT
*
490980 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATGTTTCT
*
491000 TTGTATCGATACA
1 ATGTATCGATACA
491013 CTGTATCGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 28 0.60
22 1 0.02
23 2 0.04
25 16 0.34
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATGTTTCT
Found at i:491019 original size:13 final size:13
Alignment explanation
Indices: 491001--491025 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
490991 CATTTTTCTT
491001 TGTATCGATACAC
1 TGTATCGATACAC
491014 TGTATCGATACA
1 TGTATCGATACA
491026 GGGTGATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:493494 original size:20 final size:20
Alignment explanation
Indices: 493471--493543 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
493461 ACAACTCAAA
493471 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
493491 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
493512 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
493532 GTATCGATACAT
1 GTATCGATACAT
493544 AAAAAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:493522 original size:41 final size:42
Alignment explanation
Indices: 493471--493565 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
493461 ACAACTCAAA
*
493471 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
493512 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
493554 GTATCGATACAT
1 GTATCGATACAT
493566 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:493622 original size:13 final size:13
Alignment explanation
Indices: 493604--493629 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
493594 TACAGCAAGT
493604 ATGTATCGATACA
1 ATGTATCGATACA
493617 ATGTATCGATACA
1 ATGTATCGATACA
493630 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:498212 original size:19 final size:19
Alignment explanation
Indices: 498182--498225 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
498172 AAATAGTTAA
498182 AATA-TTATTTTTAT-ATT
1 AATATTTATTTTTATAATT
498199 AATATTTATATTTTATAATT
1 AATATTTAT-TTTTATAATT
498219 AA-ATTTA
1 AATATTTA
498226 AATAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.17
18 4 0.17
19 11 0.46
20 5 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATATTTATTTTTATAATT
Found at i:498908 original size:16 final size:17
Alignment explanation
Indices: 498887--498924 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
498877 TATTTATATA
*
498887 ATATAAAT-TACATAAT
1 ATATAAATATAAATAAT
498903 ATATAAATAGTAAATAAT
1 ATATAAATA-TAAATAAT
498921 ATAT
1 ATAT
498925 TAAAAAGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (17 bp):
ATATAAATATAAATAAT
Found at i:500051 original size:2 final size:2
Alignment explanation
Indices: 500044--500088 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
500034 AAAGAGAAAC
* *
500044 AG AG AG AG AC AC AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
500086 AG A
1 AG A
500089 CAAAGAAGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.04, G:0.44, T:0.00
Consensus pattern (2 bp):
AG
Found at i:500057 original size:12 final size:12
Alignment explanation
Indices: 500036--500090 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
500026 TTGCTTTCAA
*
500036 AGAGAAACAGAG
1 AGAGACACAGAG
500048 AGAGACACAGAG
1 AGAGACACAGAG
* *
500060 AGAGAGAGAGAG
1 AGAGACACAGAG
* *
500072 AGAGAGAGAGAG
1 AGAGACACAGAG
500084 AGAGACA
1 AGAGACA
500091 AAGAAGATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.53, C:0.07, G:0.40, T:0.00
Consensus pattern (12 bp):
AGAGACACAGAG
Found at i:500059 original size:10 final size:10
Alignment explanation
Indices: 500036--500088 Score: 61
Period size: 10 Copynumber: 5.3 Consensus size: 10
500026 TTGCTTTCAA
*
500036 AGAGAAACAG
1 AGAGAGACAG
*
500046 AGAGAGACAC
1 AGAGAGACAG
*
500056 AGAGAGAGAG
1 AGAGAGACAG
*
500066 AGAGAGAGAG
1 AGAGAGACAG
*
500076 AGAGAGAGAG
1 AGAGAGACAG
500086 AGA
1 AGA
500089 CAAAGAAGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 39 1.00
ACGTcount: A:0.53, C:0.06, G:0.42, T:0.00
Consensus pattern (10 bp):
AGAGAGACAG
Found at i:504493 original size:31 final size:29
Alignment explanation
Indices: 504446--504524 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
504436 AAATTTAAAC
*
504446 AAATAATAAA-TAAAATA-AAATATTATAA
1 AAATAATAAATTCAAATATAAATA-TATAA
*
504474 AAATTAATCAAATTCAAATATAAATATCTAA
1 AAA-TAAT-AAATTCAAATATAAATATATAA
**
504505 AAATAATAAATAAAAATATA
1 AAATAATAAATTCAAATATA
504525 TGATATATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
28 3 0.07
29 15 0.35
30 7 0.16
31 13 0.30
32 5 0.12
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (29 bp):
AAATAATAAATTCAAATATAAATATATAA
Found at i:505513 original size:8 final size:8
Alignment explanation
Indices: 505500--505606 Score: 62
Period size: 8 Copynumber: 12.8 Consensus size: 8
505490 ATATTCGATA
505500 TTATATAT
1 TTATATAT
505508 TTATATTAT
1 TTATA-TAT
505517 ATTATA-ATT
1 -TTATATA-T
505526 TTATATAT
1 TTATATAT
505534 TATAATTATAT
1 T-T-A-TATAT
*
505545 TTACATTAT
1 TTATA-TAT
*
505554 TTTTATAT
1 TTATATAT
505562 TT-TAATAT
1 TTAT-ATAT
505570 ATTATA-AT
1 -TTATATAT
505578 TTATATTAT
1 TTATA-TAT
505587 TTAT-T-T
1 TTATATAT
*
505593 TAATATAT
1 TTATATAT
505601 TTATAT
1 TTATAT
505607 TATGTAATTA
Statistics
Matches: 79, Mismatches: 5, Indels: 30
0.69 0.04 0.26
Matches are distributed among these distances:
6 4 0.05
7 8 0.10
8 31 0.39
9 22 0.28
10 8 0.10
11 6 0.08
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (8 bp):
TTATATAT
Found at i:505516 original size:5 final size:5
Alignment explanation
Indices: 505487--505626 Score: 80
Period size: 5 Copynumber: 27.8 Consensus size: 5
505477 TTGAGTCGAA
*
505487 ATTAT ATTCGAT ATTAT A-TAT -TTAT ATTAT ATTAT AATTTT A-TAT
1 ATTAT ATT--AT ATTAT ATTAT ATTAT ATTAT ATTAT -ATTAT ATTAT
* * * *
505532 ATTAT AATTAT ATTTAC ATTATT TTTAT ATTTT AATAT ATTAT AATTTAT
1 ATTAT -ATTAT A-TTAT ATTA-T ATTAT ATTAT ATTAT ATTAT -A-TTAT
* *
505582 ATTAT -TTAT -TT-T AATAT ATTTAT ATTAT -GTA- ATTAT ATTAT ATTA
1 ATTAT ATTAT ATTAT ATTAT A-TTAT ATTAT ATTAT ATTAT ATTAT ATTA
505627 AAAAATATAT
Statistics
Matches: 105, Mismatches: 14, Indels: 32
0.70 0.09 0.21
Matches are distributed among these distances:
3 1 0.01
4 20 0.19
5 53 0.50
6 22 0.21
7 9 0.09
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:505547 original size:37 final size:35
Alignment explanation
Indices: 505503--505626 Score: 121
Period size: 37 Copynumber: 3.4 Consensus size: 35
505493 TTCGATATTA
505503 TATATTTATATTATATTATAATTTTATATATTATAAT
1 TATATTTATATTAT-TT-TAATTTTATATATTATAAT
*
505540 TATATTTACATTATTTTTATATTTTAATATATTATAAT
1 TATATTTATATTA-TTTTA-ATTTT-ATATATTATAAT
505578 T-TATATTAT-TTATTTTAATATATT-TATATTATGTAAT
1 TATAT-TTATATTATTTTAAT-T-TTATATATTA--TAAT
505615 TATA-TTATATTA
1 TATATTTATATTA
505627 AAAAATATAT
Statistics
Matches: 75, Mismatches: 2, Indels: 20
0.77 0.02 0.21
Matches are distributed among these distances:
35 9 0.12
36 12 0.16
37 35 0.47
38 19 0.25
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (35 bp):
TATATTTATATTATTTTAATTTTATATATTATAAT
Found at i:505594 original size:14 final size:14
Alignment explanation
Indices: 505559--505604 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
505549 ATTATTTTTA
505559 TATTTTAATATATT
1 TATTTTAATATATT
*
505573 ATAATTT-ATATTATT
1 -TATTTTAATA-TATT
505588 TATTTTAATATATT
1 TATTTTAATATATT
505602 TAT
1 TAT
505605 ATTATGTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTTTAATATATT
Found at i:505596 original size:19 final size:20
Alignment explanation
Indices: 505498--505626 Score: 81
Period size: 18 Copynumber: 7.1 Consensus size: 20
505488 TTATATTCGA
505498 TATTATATATTTATATTATAT
1 TATTATA-ATTTATATTATAT
*
505519 TA-TA-ATTTTATA-TATTAT
1 TATTATAATTTATATTA-TAT
* *
505537 AATTAT-ATTTACATTAT-T
1 TATTATAATTTATATTATAT
505555 T-TTAT-ATTT-TA--ATA-
1 TATTATAATTTATATTATAT
505569 TATTATAATTTATATTAT-T
1 TATTATAATTTATATTATAT
* *
505588 TATTTTAATATAT-TTATAT
1 TATTATAATTTATATTATAT
*
505607 TA-TGTAA-TTATATTATAT
1 TATTATAATTTATATTATAT
505625 TA
1 TA
505627 AAAAATATAT
Statistics
Matches: 85, Mismatches: 10, Indels: 29
0.69 0.08 0.23
Matches are distributed among these distances:
14 3 0.04
15 4 0.05
16 5 0.06
17 15 0.18
18 27 0.32
19 25 0.29
20 4 0.05
21 2 0.02
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (20 bp):
TATTATAATTTATATTATAT
Found at i:505624 original size:53 final size:50
Alignment explanation
Indices: 505486--505626 Score: 131
Period size: 53 Copynumber: 2.7 Consensus size: 50
505476 ATTGAGTCGA
* *
505486 AATTATATTCGATATTATATATTTATATTATATTATAATTTTATATATTAT
1 AATTATATT-TATATTATATAATTATATTATATTATAATTTTATATATTAT
* * * * *
505537 AATTATATTTACATTATTTTTATATTTTAATATATTATAATTTATATTATTTATTTT
1 AATTATATTTATATTA--TATA-ATTATATTATATTATAATTT-TA-TA--TATTAT
*
505594 AA-TATATTTATATTATGTAATTATATTATATTA
1 AATTATATTTATATTATATAATTATATTATATTA
505627 AAAAATATAT
Statistics
Matches: 72, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
50 5 0.07
51 9 0.12
52 3 0.04
53 29 0.40
54 5 0.07
55 2 0.03
56 12 0.17
57 7 0.10
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (50 bp):
AATTATATTTATATTATATAATTATATTATATTATAATTTTATATATTAT
Found at i:506207 original size:36 final size:36
Alignment explanation
Indices: 506106--506208 Score: 95
Period size: 36 Copynumber: 2.9 Consensus size: 36
506096 TTATAATTTA
* *
506106 AATTGTTTAAAATAATTA-TTTAAATAATTAATAAAT
1 AATTTTTTAAAATTATTATTTTAAATAA-TAATAAAT
* * * * *
506142 -ATTTTATTTAAATT-TAATTATATATTAATATTAAAT
1 AATTTT-TTAAAATTATTATTTTA-AATAATAATAAAT
506178 AATTTTTTAAAATTATTATTTTAAATAATAA
1 AATTTTTTAAAATTATTATTTTAAATAATAA
506209 AATTAGTTTT
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
35 6 0.12
36 29 0.58
37 15 0.30
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (36 bp):
AATTTTTTAAAATTATTATTTTAAATAATAATAAAT
Found at i:507131 original size:32 final size:32
Alignment explanation
Indices: 507095--507155 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
507085 GCGTATTCTT
*
507095 GCATTGTTACTCTGGCTCTTTATTTTCTCAAA
1 GCATTGTTACTCTGACTCTTTATTTTCTCAAA
*
507127 GCATTGTTACTTTGACTCTTTATTTTCTC
1 GCATTGTTACTCTGACTCTTTATTTTCTC
507156 GAAATACTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.16, C:0.21, G:0.11, T:0.51
Consensus pattern (32 bp):
GCATTGTTACTCTGACTCTTTATTTTCTCAAA
Found at i:509715 original size:2 final size:2
Alignment explanation
Indices: 509710--509743 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
509700 AAAGGAAAAT
509710 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC -C AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
509744 TTTGATATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:513919 original size:18 final size:19
Alignment explanation
Indices: 513893--513928 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
513883 ATAACAGTGA
*
513893 TAAACCGACG-TGTTTTTG
1 TAAAACGACGCTGTTTTTG
513911 TAAAACGACGCTGTTTTT
1 TAAAACGACGCTGTTTTT
513929 AATTAGTCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (19 bp):
TAAAACGACGCTGTTTTTG
Found at i:514107 original size:13 final size:13
Alignment explanation
Indices: 514052--514118 Score: 50
Period size: 13 Copynumber: 5.3 Consensus size: 13
514042 TTATTAATTT
*
514052 AATATTTAATA-A
1 AATATTAAATATA
*
514064 AATA-TAAAAATA
1 AATATTAAATATA
*
514076 AATTTTAAA-ATA
1 AATATTAAATATA
** *
514088 TTTTATTAATTATA
1 -AATATTAAATATA
514102 AATATTAAATATA
1 AATATTAAATATA
514115 AATA
1 AATA
514119 ATTTAAATGA
Statistics
Matches: 41, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
11 4 0.10
12 11 0.27
13 23 0.56
14 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AATATTAAATATA
Found at i:514339 original size:18 final size:20
Alignment explanation
Indices: 514312--514363 Score: 72
Period size: 18 Copynumber: 2.7 Consensus size: 20
514302 TTACTATAAA
514312 TTATATTAATTTTATAT-AT
1 TTATATTAATTTTATATGAT
514331 TTATA-TAATTTTATATGAT
1 TTATATTAATTTTATATGAT
* *
514350 TTAAATTTATTTTA
1 TTATATTAATTTTA
514364 CACGAACATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 11 0.38
19 11 0.38
20 7 0.24
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTATATTAATTTTATATGAT
Found at i:521068 original size:16 final size:16
Alignment explanation
Indices: 521047--521090 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
521037 TTTTTATATC
521047 AATTTAAATAATAAAT
1 AATTTAAATAATAAAT
* *
521063 AATTTAAATTATTAATT
1 AATTTAAA-TAATAAAT
*
521080 AAATTAAATAA
1 AATTTAAATAA
521091 ATTATTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTTAAATAATAAAT
Found at i:521606 original size:12 final size:13
Alignment explanation
Indices: 521584--521616 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
521574 TACAAATCAA
521584 TAATATTTAATTT
1 TAATATTTAATTT
521597 TAAT-TTTAATTT
1 TAATATTTAATTT
521609 TAATATTT
1 TAATATTT
521617 TCAATCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TAATATTTAATTT
Found at i:521932 original size:15 final size:15
Alignment explanation
Indices: 521905--521950 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
521895 ATATTTTATC
521905 ATAATTAATTATAATA
1 ATAATT-ATTATAATA
* * *
521921 ATATTTATTATATTT
1 ATAATTATTATAATA
521936 ATAATTATTATAATA
1 ATAATTATTATAATA
521951 TTCGATCATC
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATAATTATTATAATA
Found at i:522329 original size:18 final size:18
Alignment explanation
Indices: 522308--522369 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 18
522298 TTATTTAATA
522308 ATAAAAATAATATTTTAT
1 ATAAAAATAATATTTTAT
* *
522326 ATAAAATTATAAAAATATTAAT
1 ATAAAA--AT-AATAT-TTTAT
522348 ATAAAAAATAATATTTTA-
1 AT-AAAAATAATATTTTAT
522366 ATAA
1 ATAA
522370 TATAATAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
17 2 0.06
18 8 0.23
19 3 0.09
20 6 0.17
21 6 0.17
22 6 0.17
23 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAAAAATAATATTTTAT
Found at i:522355 original size:41 final size:40
Alignment explanation
Indices: 522302--522378 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 40
522292 AAATTATTAT
*
522302 TTAATAATAAAAATAATATTTTATATAAAATTATAAAAATA
1 TTAATAATAAAAATAATATTTTA-ATAAAATAATAAAAATA
*
522343 TTAAT-ATAAAAAATAATATTTTAATAATATAATAAA
1 TTAATAAT-AAAAATAATATTTTAATAAAATAATAAA
522379 TAGTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
40 13 0.39
41 20 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (40 bp):
TTAATAATAAAAATAATATTTTAATAAAATAATAAAAATA
Found at i:522466 original size:39 final size:39
Alignment explanation
Indices: 522392--522470 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
522382 TAAAATTAAT
* *
522392 TTTTAAATTAATTTGAACTTAAAAATAAAAATTAAAAAA
1 TTTTAAATTAAATTCAACTTAAAAATAAAAATTAAAAAA
* * *
522431 TTTTAAATTACAATTCAATTTATAAAT-AAATTTAAAAAA
1 TTTTAAATTA-AATTCAACTTAAAAATAAAAATTAAAAAA
522470 T
1 T
522471 AATATTTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 22 0.65
40 12 0.35
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (39 bp):
TTTTAAATTAAATTCAACTTAAAAATAAAAATTAAAAAA
Found at i:524019 original size:19 final size:20
Alignment explanation
Indices: 523995--524033 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
523985 ATTTAATATT
523995 TTATTATTTTA-TTTAAAAA
1 TTATTATTTTATTTTAAAAA
524014 TTATTATTTTATTTTAAAAA
1 TTATTATTTTATTTTAAAAA
524034 ATCACTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATTATTTTATTTTAAAAA
Found at i:524572 original size:2 final size:2
Alignment explanation
Indices: 524565--524595 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
524555 ATGTAGATTG
524565 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
524596 AGGGGCATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:525655 original size:2 final size:2
Alignment explanation
Indices: 525648--525672 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
525638 ATTCAAAGTG
525648 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
525673 TAATTACCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:530010 original size:141 final size:141
Alignment explanation
Indices: 529756--530035 Score: 542
Period size: 141 Copynumber: 2.0 Consensus size: 141
529746 TCTCTGGGTG
529756 CCAGAACTGCCAAACTGTTGGTGGGAGAAACTCTGAAAAGCAAAACTATCCTCAGCAGGACTAGA
1 CCAGAACTGCCAAACTGTTGGTGGGAGAAACTCTGAAAAGCAAAACTATCCTCAGCAGGACTAGA
*
529821 ACCTCTAACAGTCTTGAATGCAAGCTCAAAGCATGGATCAGACCAAGAGTTCCCAAATGGAATTG
66 ACCTCTAACAGTCTTGAATGCAAGCTCAAAACATGGATCAGACCAAGAGTTCCCAAATGGAATTG
529886 CAGACTGCAGC
131 CAGACTGCAGC
*
529897 CCAGAACTGCCAAACTGTTGGTGGGAGTAACTCTGAAAAGCAAAACTATCCTCAGCAGGACTAGA
1 CCAGAACTGCCAAACTGTTGGTGGGAGAAACTCTGAAAAGCAAAACTATCCTCAGCAGGACTAGA
529962 ACCTCTAACAGTCTTGAATGCAAGCTCAAAACATGGATCAGACCAAGAGTTCCCAAATGGAATTG
66 ACCTCTAACAGTCTTGAATGCAAGCTCAAAACATGGATCAGACCAAGAGTTCCCAAATGGAATTG
530027 CAGACTGCA
131 CAGACTGCA
530036 ACCCGGGACT
Statistics
Matches: 137, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 137 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (141 bp):
CCAGAACTGCCAAACTGTTGGTGGGAGAAACTCTGAAAAGCAAAACTATCCTCAGCAGGACTAGA
ACCTCTAACAGTCTTGAATGCAAGCTCAAAACATGGATCAGACCAAGAGTTCCCAAATGGAATTG
CAGACTGCAGC
Found at i:537976 original size:15 final size:16
Alignment explanation
Indices: 537946--537977 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
537936 ATTAAAATAT
537946 TTTTAAAATAATTTTA
1 TTTTAAAATAATTTTA
537962 TTTTAAAAT-ATTTTA
1 TTTTAAAATAATTTTA
537977 T
1 T
537978 ATGTATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTAAAATAATTTTA
Found at i:538013 original size:12 final size:13
Alignment explanation
Indices: 537988--538036 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
537978 ATGTATATAA
537988 ATTTTAATATATT
1 ATTTTAATATATT
538001 ATTTTAATA-ATT
1 ATTTTAATATATT
538013 A---T-AT-TATT
1 ATTTTAATATATT
538021 ATTTTAATATATT
1 ATTTTAATATATT
538034 ATT
1 ATT
538037 ATTTTTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
8 6 0.20
9 1 0.03
11 1 0.03
12 6 0.20
13 16 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTTTAATATATT
Found at i:538017 original size:17 final size:17
Alignment explanation
Indices: 537995--538142 Score: 74
Period size: 17 Copynumber: 9.2 Consensus size: 17
537985 TAAATTTTAA
537995 TATATTATTTTAATAAT
1 TATATTATTTTAATAAT
*
538012 TATATTATTATT-TTAA-
1 TATATTATT-TTAATAAT
538028 TATATTATTATT--T--T
1 TATATTATT-TTAATAAT
*
538042 TATATTATATTT--TTAT
1 TATATTAT-TTTAATAAT
538058 TA-ATT-TTTTAAT-AT
1 TATATTATTTTAATAAT
*
538072 TAT-TTA-TTTAATAAA
1 TATATTATTTTAATAAT
538087 TATATTATATTTAA-AAT
1 TATATTAT-TTTAATAAT
* *
538104 TTTAATATATTTAATATATT
1 TATATTAT-TTTAATA-A-T
*
538124 TATATTATATTAAT-AT
1 TATATTATTTTAATAAT
538140 TAT
1 TAT
538143 CATAATTTAT
Statistics
Matches: 107, Mismatches: 8, Indels: 33
0.72 0.05 0.22
Matches are distributed among these distances:
13 3 0.03
14 24 0.22
15 10 0.09
16 22 0.21
17 27 0.25
18 8 0.07
19 6 0.06
20 7 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATATTATTTTAATAAT
Found at i:538027 original size:33 final size:31
Alignment explanation
Indices: 537970--538142 Score: 116
Period size: 30 Copynumber: 5.6 Consensus size: 31
537960 TATTTTAAAA
*
537970 TATTTT-ATATGTATA-TAAATTTTAATATAT
1 TATTTTAATAT-TATATTATATTTTAATATAT
538000 TATTTTAATAATTATATTATTATTTTAATATAT
1 TATTTTAAT-ATTATATTA-TATTTTAATATAT
*
538033 TATTATT--T-TTATATTATATTTTTAT-TAAT
1 TATT-TTAATATTATATTATATTTTAATAT-AT
*
538062 T-TTTTAATATTAT-TTAT-TTAATAAATATAT
1 TATTTTAATATTATATTATATT--TTAATATAT
* * *
538092 TATATTTAAAATTTTAATATA-TTTAATATATT
1 TAT-TTTAATATTATATTATATTTTAATATA-T
*
538124 TATATT-ATATTAATATTAT
1 TATTTTAATATT-ATATTAT
538143 CATAATTTAT
Statistics
Matches: 113, Mismatches: 12, Indels: 35
0.71 0.08 0.22
Matches are distributed among these distances:
27 2 0.02
28 5 0.04
29 16 0.14
30 28 0.25
31 22 0.19
32 18 0.16
33 20 0.18
34 2 0.02
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (31 bp):
TATTTTAATATTATATTATATTTTAATATAT
Found at i:538118 original size:9 final size:9
Alignment explanation
Indices: 538076--538139 Score: 60
Period size: 9 Copynumber: 7.1 Consensus size: 9
538066 TAATATTATT
538076 TATTTAATA
1 TATTTAATA
* * *
538085 AATATATTA
1 TATTTAATA
*
538094 TATTTAAAA
1 TATTTAATA
538103 T-TTTAATA
1 TATTTAATA
538111 TATTTAATA
1 TATTTAATA
538120 TATTT-ATA
1 TATTTAATA
538128 TTATATTAATA
1 -TAT-TTAATA
538139 T
1 T
538140 TATCATAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
8 10 0.23
9 27 0.63
10 3 0.07
11 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TATTTAATA
Found at i:538132 original size:11 final size:11
Alignment explanation
Indices: 538033--538142 Score: 58
Period size: 11 Copynumber: 10.5 Consensus size: 11
538023 TTTAATATAT
*
538033 TATTATTTTTA
1 TATTATATTTA
*
538044 TATTATATTTT
1 TATTATATTTA
*
538055 TATTA-ATTTTT
1 TATTATA-TTTA
*
538066 TAATATTATTTA
1 TATTA-TATTTA
**
538078 T-TTAATAAATA
1 TATT-ATATTTA
538089 TATTATATTTA
1 TATTATATTTA
538100 -A--A-ATTT-
1 TATTATATTTA
*
538106 TAATATATTTA
1 TATTATATTTA
538117 -A-TATATTTA
1 TATTATATTTA
*
538126 TATTATATTAA
1 TATTATATTTA
538137 TATTAT
1 TATTAT
538143 CATAATTTAT
Statistics
Matches: 77, Mismatches: 10, Indels: 24
0.69 0.09 0.22
Matches are distributed among these distances:
7 5 0.06
8 1 0.01
9 9 0.12
10 8 0.10
11 46 0.60
12 7 0.09
13 1 0.01
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATTATATTTA
Found at i:542434 original size:30 final size:30
Alignment explanation
Indices: 542397--542460 Score: 65
Period size: 30 Copynumber: 2.0 Consensus size: 30
542387 TTGAAATAAA
* *
542397 TTATTATTATGATTATTTTATTTTATTTCAATT
1 TTATTA-TATTATTA-TT-ATTTTATTTAAATT
* *
542430 TTATTATATTTTTATTATTTTTTTTAAATT
1 TTATTATATTATTATTATTTTATTTAAATT
542460 T
1 T
542461 AAATATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
30 13 0.48
31 2 0.07
32 6 0.22
33 6 0.22
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (30 bp):
TTATTATATTATTATTATTTTATTTAAATT
Found at i:542510 original size:9 final size:9
Alignment explanation
Indices: 542498--542532 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
542488 ATTTAATATA
542498 AATATTTTT
1 AATATTTTT
542507 AATATTTTT
1 AATATTTTT
*
542516 AAATTTTTTT
1 -AATATTTTT
542526 AATATTT
1 AATATTT
542533 AAATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
AATATTTTT
Found at i:542541 original size:17 final size:18
Alignment explanation
Indices: 542496--542544 Score: 73
Period size: 17 Copynumber: 2.7 Consensus size: 18
542486 ATATTTAATA
*
542496 TAAATATTTTTAATATTTT
1 TAAATTTTTTTAATA-TTT
542515 TAAATTTTTTTAATA-TT
1 TAAATTTTTTTAATATTT
542532 TAAATTTTTTTAA
1 TAAATTTTTTTAA
542545 AAATTATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 15 0.52
19 14 0.48
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TAAATTTTTTTAATATTT
Found at i:545457 original size:12 final size:13
Alignment explanation
Indices: 545429--545460 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
545419 TACGAATACA
545429 AATT-TAAATAAT
1 AATTATAAATAAT
545441 AATTATAAATAAT
1 AATTATAAATAAT
545454 -ATTATAA
1 AATTATAA
545461 TTATTAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AATTATAAATAAT
Found at i:545462 original size:18 final size:19
Alignment explanation
Indices: 545439--545476 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
545429 AATTTAAATA
545439 ATAATTA-TAAATAATATT
1 ATAATTATTAAATAATATT
*
545457 ATAATTATTAAATCATATT
1 ATAATTATTAAATAATATT
545476 A
1 A
545477 AATATATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAATTATTAAATAATATT
Found at i:548448 original size:2 final size:2
Alignment explanation
Indices: 548441--548502 Score: 62
Period size: 2 Copynumber: 33.5 Consensus size: 2
548431 ACGCATCTTT
*
548441 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TG T- 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
* *
548479 TA TG TA TA TA TA AA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
548503 TAAATATGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
1 5 0.10
2 45 0.90
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:548486 original size:28 final size:28
Alignment explanation
Indices: 548441--548511 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
548431 ACGCATCTTT
* * * *
548441 TATATATATATATATATATATATATATAT
1 TATAT-TAAATATGTATATATAAATATAA
* *
548470 TATGTTAATTATGTATATATAAATATAA
1 TATATTAAATATGTATATATAAATATAA
548498 TATATTAAATATGT
1 TATATTAAATATGT
548512 TAATCGGTGT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
28 30 0.88
29 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (28 bp):
TATATTAAATATGTATATATAAATATAA
Found at i:558087 original size:42 final size:42
Alignment explanation
Indices: 558028--558111 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
558018 TCCGTCCTAG
* * * * *
558028 AACCAACATTCTTATGCGAATGCTTGTTGGTTCTTCAAACAC
1 AACCAAAATTCTCATGCGAATGCCTATCGGTTCTTCAAACAC
* *
558070 AACCAAAATTCTCATGCGGATGCCTATCGTTTCTTCAAACAC
1 AACCAAAATTCTCATGCGAATGCCTATCGGTTCTTCAAACAC
558112 TTTGCATTTG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (42 bp):
AACCAAAATTCTCATGCGAATGCCTATCGGTTCTTCAAACAC
Found at i:559164 original size:17 final size:18
Alignment explanation
Indices: 559132--559176 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
559122 TAAATTAATC
559132 ATTAAATTTAATAATATA
1 ATTAAATTTAATAATATA
*
559150 ATTATATTT-ATAATATA
1 ATTAAATTTAATAATATA
*
559167 CATAAAATTT
1 -ATTAAATTT
559177 TGAATTGGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTAAATTTAATAATATA
Found at i:560087 original size:2 final size:2
Alignment explanation
Indices: 560080--560110 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
560070 ATTTACTTGA
560080 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
560111 GAAGGGAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:561257 original size:21 final size:23
Alignment explanation
Indices: 561216--561258 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
561206 TAATTTAACT
*
561216 CAATTTTTTTTGCATTAGGAATG
1 CAATTTTTATTGCATTAGGAATG
561239 CAATTTTTATTG-ATT-GGAAT
1 CAATTTTTATTGCATTAGGAAT
561259 TTGAATACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.49
Consensus pattern (23 bp):
CAATTTTTATTGCATTAGGAATG
Found at i:562424 original size:26 final size:28
Alignment explanation
Indices: 562370--562440 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 28
562360 TAAATATAAA
* *
562370 TATATATTTAATATAAATATTTATAAATTT
1 TATATATAT-ATA-AAATAATTATAAATTT
*
562400 TTTATATAT-TAAAATAATTAT-AATTT
1 TATATATATATAAAATAATTATAAATTT
*
562426 TATATTTATATAAAA
1 TATATATATATAAAA
562441 AAATATGTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
26 12 0.34
27 14 0.40
28 2 0.06
30 7 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
TATATATATATAAAATAATTATAAATTT
Found at i:563965 original size:2 final size:2
Alignment explanation
Indices: 563958--564000 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
563948 CAAAATTACC
*
563958 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
564000 A
1 A
564001 GGATGCATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:565244 original size:16 final size:15
Alignment explanation
Indices: 565208--565236 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
565198 AATTTTTAGT
565208 AAAATTATAGCAATA
1 AAAATTATAGCAATA
565223 AAAATTATAG-AATA
1 AAAATTATAGCAATA
565237 GGAAAATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (15 bp):
AAAATTATAGCAATA
Found at i:565573 original size:11 final size:11
Alignment explanation
Indices: 565557--565614 Score: 61
Period size: 11 Copynumber: 5.5 Consensus size: 11
565547 TATTACGATT
565557 ATATAATATAA
1 ATATAATATAA
565568 ATATAATAT-A
1 ATATAATATAA
565578 A-A-AATATAA
1 ATATAATATAA
565587 A-ATAATATTAA
1 ATATAATA-TAA
*
565598 AAATTAATATAA
1 ATA-TAATATAA
565610 ATATA
1 ATATA
565615 TAAATTTATC
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
8 5 0.12
9 4 0.10
10 6 0.15
11 15 0.37
12 6 0.15
13 5 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
ATATAATATAA
Found at i:565591 original size:18 final size:18
Alignment explanation
Indices: 565561--565619 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
565551 ACGATTATAT
565561 AATATAAATATAATATAAA
1 AATATAAA-ATAATATAAA
565580 AATATAAAATAATATTAAA
1 AATATAAAATAATA-TAAA
* *
565599 AAT-TAATATAAATATATA
1 AATATAAAAT-AATATAAA
565617 AAT
1 AAT
565620 TTATCAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
18 17 0.47
19 19 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AATATAAAATAATATAAA
Found at i:565620 original size:18 final size:18
Alignment explanation
Indices: 565562--565620 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
565552 CGATTATATA
*
565562 ATATAAATATAATATAAAA
1 ATATAAAT-TAATATAAAT
*
565581 ATATAAAATAATAT---T
1 ATATAAATTAATATAAAT
565596 A-A-AAATTAATATAAAT
1 ATATAAATTAATATAAAT
565612 ATATAAATT
1 ATATAAATT
565621 TATCAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 11
0.70 0.07 0.24
Matches are distributed among these distances:
13 9 0.28
14 1 0.03
15 1 0.03
16 2 0.06
17 1 0.03
18 11 0.34
19 7 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATATAAATTAATATAAAT
Found at i:565658 original size:32 final size:33
Alignment explanation
Indices: 565604--565666 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
565594 TTAAAAATTA
565604 ATATAAATATATAAATTTATCAAAATTTATATG
1 ATATAAATATATAAATTTATCAAAATTTATATG
* *
565637 ATATAAA-ATATTAATTTATCAATATTTATA
1 ATATAAATATATAAATTTATCAAAATTTATA
565667 AAAAGTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 21 0.75
33 7 0.25
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (33 bp):
ATATAAATATATAAATTTATCAAAATTTATATG
Found at i:565909 original size:11 final size:11
Alignment explanation
Indices: 565893--565937 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
565883 TAATATTTTA
*
565893 AATATAATTAT
1 AATATAAATAT
*
565904 AATATAAAAAT
1 AATATAAATAT
**
565915 AATACGAATAT
1 AATATAAATAT
565926 AATATAAATAT
1 AATATAAATAT
565937 A
1 A
565938 TAAAATGTCA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (11 bp):
AATATAAATAT
Found at i:565911 original size:17 final size:17
Alignment explanation
Indices: 565872--565918 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
565862 ATTAAAATTT
*
565872 TATAAAAATAATAATAT
1 TATAAAAATAATAATAA
* * *
565889 TTTAAATATAATTATAA
1 TATAAAAATAATAATAA
565906 TATAAAAATAATA
1 TATAAAAATAATA
565919 CGAATATAAT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TATAAAAATAATAATAA
Found at i:567986 original size:18 final size:18
Alignment explanation
Indices: 567958--568028 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
567948 ATCGTGTTTA
567958 AAATATTTAATATTTATAT
1 AAAT-TTTAATATTTATAT
*
567977 AAATTTTAATAAATTA-AT
1 AAATTTTAAT-ATTTATAT
567995 -AA-TTT-ATA-TTATAT
1 AAATTTTAATATTTATAT
568009 AAATTTTATAATATTTATAT
1 AAA-TTT-TAATATTTATAT
568029 TATATAATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 3 0.07
14 3 0.07
15 4 0.09
16 3 0.07
17 4 0.09
18 9 0.21
19 11 0.26
20 6 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AAATTTTAATATTTATAT
Found at i:568011 original size:32 final size:32
Alignment explanation
Indices: 567959--568049 Score: 107
Period size: 32 Copynumber: 2.8 Consensus size: 32
567949 TCGTGTTTAA
567959 AATATTTAATATTTATATAAATTTTAATAA-ATT
1 AATATTT-ATA-TTATATAAATTTTAATAATATT
567992 AATAATTTATATTATATAAATTTT-ATAATATT
1 AAT-ATTTATATTATATAAATTTTAATAATATT
* *
568024 TATA-TTATATAATATAATATTTTAAT
1 AATATTTATATTATATAA-ATTTTAAT
568050 TATTTTTTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
30 12 0.23
31 10 0.19
32 20 0.38
33 6 0.12
34 4 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
AATATTTATATTATATAAATTTTAATAATATT
Found at i:568016 original size:16 final size:16
Alignment explanation
Indices: 567971--568052 Score: 50
Period size: 16 Copynumber: 5.2 Consensus size: 16
567961 TATTTAATAT
567971 TTATATAAATTTTAATAAA
1 TTATATAAATTTT-AT--A
567990 TTA-AT-AA-TTTATA
1 TTATATAAATTTTATA
568003 TTATATAAATTTTATA
1 TTATATAAATTTTATA
** *
568019 --ATATTTATATTATA
1 TTATATAAATTTTATA
*
568033 TAATATAATATTTTA-A
1 TTATATAA-ATTTTATA
568049 TTAT
1 TTAT
568053 TTTTTATATT
Statistics
Matches: 50, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
13 4 0.08
14 13 0.26
15 4 0.08
16 17 0.34
17 7 0.14
18 2 0.04
19 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATATAAATTTTATA
Found at i:568054 original size:30 final size:28
Alignment explanation
Indices: 567997--568061 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 28
567987 AAATTAATAA
*
567997 TTTATATTATATAAATTTTATAATATTT
1 TTTATATAATATAAATTTTATAATATTT
*
568025 ATATTATATAATATAATATTTTA-ATTATTT
1 -T-TTATATAATATAA-ATTTTATAATATTT
568055 TTTATAT
1 TTTATAT
568062 TCCGTACTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 6 0.19
29 2 0.06
30 18 0.56
31 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTATATAATATAAATTTTATAATATTT
Found at i:568060 original size:21 final size:21
Alignment explanation
Indices: 568003--568060 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
567993 ATAATTTATA
*
568003 TTATA-TAAATTTTATAATAT
1 TTATATTATATTTTATAATAT
**
568023 TTATATTATATAATATAATAT
1 TTATATTATATTTTATAATAT
*
568044 TT-TAATTATTTTTTATA
1 TTAT-ATTATATTTTATA
568061 TTCCGTACTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 6 0.20
21 24 0.80
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATATTATATTTTATAATAT
Found at i:570183 original size:22 final size:22
Alignment explanation
Indices: 570158--570199 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
570148 AATTATTTTA
570158 TAAAAA-TATAAAAATTTAAAAT
1 TAAAAATTAT-AAAATTTAAAAT
*
570180 TAAATATTATAAAATTTAAA
1 TAAAAATTATAAAATTTAAA
570200 TTTTTGGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAAAATTATAAAATTTAAAAT
Found at i:570420 original size:26 final size:25
Alignment explanation
Indices: 570366--570429 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 25
570356 TATTTATTAT
*
570366 TAATATATA-TCATAATTAATTAAA
1 TAATATATATTTATAATTAATTAAA
*
570390 AAATATATATTTATAATTAATCGT-AA
1 TAATATATATTTATAATTAAT--TAAA
570416 TAATATATATTTAT
1 TAATATATATTTAT
570430 TATATGCGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.24
25 10 0.29
26 15 0.44
27 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (25 bp):
TAATATATATTTATAATTAATTAAA
Found at i:570929 original size:9 final size:8
Alignment explanation
Indices: 570894--570939 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 8
570884 TCATTTATAT
570894 AAATTTTA
1 AAATTTTA
570902 AAATTTTA
1 AAATTTTA
570910 ATAA--TTA
1 A-AATTTTA
570917 AAATTTTA
1 AAATTTTA
570925 TAAATTTTA
1 -AAATTTTA
570934 ATAATT
1 A-AATT
570940 ATATTTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
6 2 0.06
7 4 0.12
8 13 0.39
9 14 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
AAATTTTA
Found at i:570929 original size:24 final size:23
Alignment explanation
Indices: 570894--570940 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 23
570884 TCATTTATAT
570894 AAATTTTAAAATTTTAATAATTA
1 AAATTTTAAAATTTTAATAATTA
570917 AAATTTTATAAATTTTAATAATTA
1 AAATTTTA-AAATTTTAATAATTA
570941 TATTTATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAATTTTAAAATTTTAATAATTA
Found at i:570955 original size:32 final size:32
Alignment explanation
Indices: 570919--570994 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 32
570909 AATAATTAAA
570919 ATTTTATAAATTTTAA-TA-ATTATATTTATATT
1 ATTTTATAAATTTTAATTATATTAT-TTT-TATT
570951 ATTTTAT--ATTTTAATTATATTATTTTTATT
1 ATTTTATAAATTTTAATTATATTATTTTTATT
570981 ATATTTATATAATT
1 AT-TTTATA-AATT
570995 ATATCTAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
30 13 0.34
31 10 0.26
32 12 0.32
34 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (32 bp):
ATTTTATAAATTTTAATTATATTATTTTTATT
Found at i:570957 original size:16 final size:15
Alignment explanation
Indices: 570938--570990 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 15
570928 ATTTTAATAA
570938 TTATATTTATATTATT
1 TTATATTT-TATTATT
*
570954 TTATATTTTAATTATA
1 TTATATTTT-ATTATT
570970 TTAT-TTTTATTATAT
1 TTATATTTTATTAT-T
570985 TTATAT
1 TTATAT
570991 AATTATATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 5 0.16
15 9 0.28
16 18 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATATTTTATTATT
Found at i:571076 original size:23 final size:22
Alignment explanation
Indices: 571019--571077 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
571009 TAAAATTAAA
*
571019 TAATAAATTAATATTTAATATAT
1 TAATAAATT-ATATTTAATACAT
571042 TAAT-AATATATATTT-ATACAT
1 TAATAAAT-TATATTTAATACAT
571063 TCATATAAATTATAT
1 T-A-ATAAATTATAT
571078 AATATTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
21 6 0.19
22 10 0.32
23 12 0.39
24 3 0.10
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATAAATTATATTTAATACAT
Found at i:572559 original size:37 final size:36
Alignment explanation
Indices: 572472--572575 Score: 88
Period size: 37 Copynumber: 2.8 Consensus size: 36
572462 TTTAAATTAT
*
572472 TATTTAAA-AATTAATAAAAAATTTAAAAATTATTTTTTA
1 TATTTAAATAA-TAAT-ATAAA-TTAAAAA-TATTTTTTA
**
572511 TATTTTTATAATTAAATATAAA-TAAAAATATTTTTTA
1 TATTTAAATAA-T-AATATAAATTAAAAATATTTTTTA
*
572548 T-TATTAAATAATAATTTAAATTAAAAAT
1 TAT-TTAAATAATAATATAAATTAAAAAT
572576 TTTATTAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
35 7 0.13
36 9 0.16
37 16 0.29
38 6 0.11
39 6 0.11
40 8 0.15
41 3 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (36 bp):
TATTTAAATAATAATATAAATTAAAAATATTTTTTA
Found at i:572680 original size:23 final size:23
Alignment explanation
Indices: 572641--572699 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 23
572631 AATAATATTT
572641 AAATAGAAACATA-ATTAAAATAA-A
1 AAATA-AAA-ATATATT-AAATAATA
* *
572665 AATTAATAATATATTAAATAATA
1 AAATAAAAATATATTAAATAATA
572688 AAATAAAAATAT
1 AAATAAAAATAT
572700 TTATATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
22 9 0.31
23 16 0.55
24 4 0.14
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (23 bp):
AAATAAAAATATATTAAATAATA
Found at i:573248 original size:21 final size:20
Alignment explanation
Indices: 573193--573248 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
573183 TTAAATTTGG
*
573193 TAAAATAAATATTAATTTAAA
1 TAAAATAAATA-TAATTCAAA
573214 -AAATATAAA-A-AATTCAATA
1 TAAA-ATAAATATAATTCAA-A
573233 TAAAATAAATATAATT
1 TAAAATAAATATAATT
573249 TTGAGAGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
18 6 0.21
19 6 0.21
20 8 0.28
21 9 0.31
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAATAAATATAATTCAAA
Found at i:573664 original size:21 final size:21
Alignment explanation
Indices: 573622--573666 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
573612 AAGGCTGTTA
* **
573622 AAACTTTAAATTTTAATTCTT
1 AAACTCTAAATTTTAAACCTT
573643 AAACTCTAAATTTTAAACCTT
1 AAACTCTAAATTTTAAACCTT
573664 AAA
1 AAA
573667 TCGTATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.42
Consensus pattern (21 bp):
AAACTCTAAATTTTAAACCTT
Found at i:579124 original size:16 final size:16
Alignment explanation
Indices: 579103--579142 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
579093 AAAATAATGA
579103 AAAATAA-AGTAAATTC
1 AAAATAATA-TAAATTC
*
579119 AAAATAATATAAATTT
1 AAAATAATATAAATTC
579135 AAAATAAT
1 AAAATAAT
579143 GTACGTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (16 bp):
AAAATAATATAAATTC
Found at i:579413 original size:31 final size:30
Alignment explanation
Indices: 579356--579413 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
579346 TATTTTTATT
**
579356 TTTATTTATATAAATTTTAATATATTAATA
1 TTTATTTATATAAATTAAAATATATTAATA
*
579386 TTTATATTATATAAATTAAAATTTATTA
1 TTTAT-TTATATAAATTAAAATATATTA
579414 CACTTACCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
TTTATTTATATAAATTAAAATATATTAATA
Found at i:579594 original size:19 final size:19
Alignment explanation
Indices: 579570--579614 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
579560 TAAAAAATAA
* *
579570 ATATTTTTAATTTTATTTT
1 ATATTTTTAATTTAAATTT
*
579589 ATATTTATAATTTAAATTT
1 ATATTTTTAATTTAAATTT
579608 A-ATTTTT
1 ATATTTTT
579615 TATTATTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATATTTTTAATTTAAATTT
Found at i:579609 original size:30 final size:27
Alignment explanation
Indices: 579575--579645 Score: 83
Period size: 26 Copynumber: 2.6 Consensus size: 27
579565 AATAAATATT
579575 TTTAATTTTATTTTATATTTATAATTTAAA
1 TTTAATTTTATTTT-TATTT-TAA-TTAAA
*
579605 TTTAATTTT-TTATTATTTTAATTAAA
1 TTTAATTTTATTTTTATTTTAATTAAA
*
579631 -TTAATATTATTTTTA
1 TTTAATTTTATTTTTA
579646 AAAATTTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
25 7 0.19
26 10 0.27
27 3 0.08
28 5 0.14
29 3 0.08
30 9 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTAATTTTATTTTTATTTTAATTAAA
Found at i:579622 original size:21 final size:21
Alignment explanation
Indices: 579592--579632 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
579582 TTATTTTATA
*
579592 TTTATAATTTAAATTTAATTT
1 TTTATAATTTAAATTAAATTT
* *
579613 TTTATTATTTTAATTAAATT
1 TTTATAATTTAAATTAAATT
579633 AATATTATTT
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTATAATTTAAATTAAATTT
Found at i:579812 original size:15 final size:15
Alignment explanation
Indices: 579792--579822 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
579782 TTTATTTTGT
*
579792 TTAAAAAATAATAAA
1 TTAAAAAATAAGAAA
579807 TTAAAAAATAAGAAA
1 TTAAAAAATAAGAAA
579822 T
1 T
579823 AATTTATGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
TTAAAAAATAAGAAA
Found at i:579963 original size:21 final size:21
Alignment explanation
Indices: 579933--579973 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
579923 TATATTTATA
*
579933 TTTATAATTTAAATTTAATTT
1 TTTATAATTTAAATTAAATTT
* *
579954 TTTATTATTTTAATTAAATT
1 TTTATAATTTAAATTAAATT
579974 AATATTATTT
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTATAATTTAAATTAAATTT
Found at i:580027 original size:341 final size:338
Alignment explanation
Indices: 579441--580109 Score: 1184
Period size: 341 Copynumber: 2.0 Consensus size: 338
579431 AAAAAAATTA
*
579441 AAAATTTATTTTGTATAAAAGATAATAAATTAAAAAAATAAGAAATAATTTATGTCAAGTAAGTT
1 AAAATTTATTTTGTATAAAAAATAATAAATTAAAAAAATAAGAAATAATTTATGTCAAGTAAGTT
579506 GATATTTTTTAAAAAATAAAATATATACTAAAAATTAATAATTATTTTTAAGATTAAAAAATAAA
66 GATATTTTTTAAAAAATAAAATATATACTAAAAATTAATAATTATTTTTAAGATTAAAAAATAAA
579571 TATTTTTAATTTTATTTTATATTTATAATTTAAATTTAATTTTTTATTATTTTAATTAAATTAAT
131 TATTTTTAATTTTATTTTATATTTATAATTTAAATTTAATTTTTTATTATTTTAATTAAATTAAT
* *
579636 ATTATTTTTAAAAATTTATATATGACATAAAAATATAAATAATATAAATTTTAAAATTTATGTTT
196 ATTATTTTTAAAAATTTATATATAACATAAAAATATAAAAAATATAAATTTTAAAATTTATGTTT
*
579701 ATGGATATAATTTTTAATTATTTTATTTATA-TATATTTGAATAAATTATATTTAATGTTGTCTG
261 ATGGATATAATTTTTAATTATTTTATTTATATTATATTTGAATAAATTATATTTAATATTGTCTG
579765 AAAAAAATTTATT
326 AAAAAAATTTATT
*
579778 AAAATTTATTTTGTTTAAAAAATAATAAATT-AAAAAATAAGAAATAATTTATGTCAAGTGAA-T
1 AAAATTTATTTTGTATAAAAAATAATAAATTAAAAAAATAAGAAATAATTTATGTCAAGT-AAGT
*
579841 TGATATTTTTTAAAAAATAAAATATATACTAATAATTAATAATTATTTTTAAGATTAAAAAAGTT
65 TGATATTTTTTAAAAAATAAAATATATACTAAAAATTAATAATTATTTTTAAGATTAAAAAA--T
579906 AAAT-TTTTTAATTTTTTTATATTTATATTTATAATTTAAATTTAATTTTTTATTATTTTAATTA
128 AAATATTTTTAA---TTTTAT-TTTATATTTATAATTTAAATTTAATTTTTTATTATTTTAATTA
579970 AATTAATATTATTTTTAAAAATTTATATATAACATAAAAATATAAAAAATATAAATTTTAAAATT
189 AATTAATATTATTTTTAAAAATTTATATATAACATAAAAATATAAAAAATATAAATTTTAAAATT
*
580035 TATGTTTATGGGTATAATTTTTAATTATTTTATTTATATTATATTTGAATAAATTATATTTAATA
254 TATGTTTATGGATATAATTTTTAATTATTTTATTTATATTATATTTGAATAAATTATATTTAATA
580100 TTGTCTGAAA
319 TTGTCTGAAA
580110 TCCGCTTCTT
Statistics
Matches: 317, Mismatches: 7, Indels: 11
0.95 0.02 0.03
Matches are distributed among these distances:
336 90 0.28
337 38 0.12
338 5 0.02
340 6 0.02
341 143 0.45
342 35 0.11
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (338 bp):
AAAATTTATTTTGTATAAAAAATAATAAATTAAAAAAATAAGAAATAATTTATGTCAAGTAAGTT
GATATTTTTTAAAAAATAAAATATATACTAAAAATTAATAATTATTTTTAAGATTAAAAAATAAA
TATTTTTAATTTTATTTTATATTTATAATTTAAATTTAATTTTTTATTATTTTAATTAAATTAAT
ATTATTTTTAAAAATTTATATATAACATAAAAATATAAAAAATATAAATTTTAAAATTTATGTTT
ATGGATATAATTTTTAATTATTTTATTTATATTATATTTGAATAAATTATATTTAATATTGTCTG
AAAAAAATTTATT
Found at i:581435 original size:66 final size:66
Alignment explanation
Indices: 581360--581495 Score: 220
Period size: 66 Copynumber: 2.1 Consensus size: 66
581350 CTGTTTTTAC
581360 TTTTATGCTTTTAAGTTACCCTCTTAAATAAGTATAATTGTCATGGATTATGTTTATCTTGTTG-
1 TTTTATGCTTTTAAGTTACCCTCTTAAATAAGTATAATT-TCATGGATTATGTTTATCTTGTTGC
581424 TT
65 TT
* * * *
581426 TTTTATGCTTTTCAGTTGCCCTCTTAAATAAGTATAATTTTATGGATTATGTTTATTTTGTTGCT
1 TTTTATGCTTTTAAGTTACCCTCTTAAATAAGTATAATTTCATGGATTATGTTTATCTTGTTGCT
581491 T
66 T
581492 TTTT
1 TTTT
581496 TGGGTGCACT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
65 22 0.34
66 43 0.66
ACGTcount: A:0.22, C:0.10, G:0.13, T:0.54
Consensus pattern (66 bp):
TTTTATGCTTTTAAGTTACCCTCTTAAATAAGTATAATTTCATGGATTATGTTTATCTTGTTGCT
T
Found at i:587485 original size:25 final size:25
Alignment explanation
Indices: 587445--587509 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
587435 GATATTTAAA
* * * **
587445 ATAAATATTATCTTAACAAATTTTT
1 ATAAATATAATTTTAAAAAATAATT
587470 ATAAATATAATTTTAAAAAATAATT
1 ATAAATATAATTTTAAAAAATAATT
*
587495 ATTAAAAATAATTTT
1 A-TAAATATAATTTT
587510 TTAATAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 21 0.64
26 12 0.36
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (25 bp):
ATAAATATAATTTTAAAAAATAATT
Found at i:587513 original size:14 final size:13
Alignment explanation
Indices: 587463--587510 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
587453 TATCTTAACA
587463 AATTTTTATAAATAT
1 AATTTTTA-AAA-AT
*
587478 AATTTTAAAAAAT
1 AATTTTTAAAAAT
*
587491 AATTATTAAAAAT
1 AATTTTTAAAAAT
587504 AATTTTT
1 AATTTTT
587511 TAATAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 19 0.66
14 3 0.10
15 7 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTTTTAAAAAT
Done.