Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold452
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: 589716
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
File 3 of 5
Found at i:170486 original size:13 final size:13
Alignment explanation
Indices: 170468--170507 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
170458 TCACGTGATA
170468 TAAACATCACATG
1 TAAACATCACATG
170481 TAAACATCACATG
1 TAAACATCACATG
*
170494 TAAACATCATATG
1 TAAACATCACATG
170507 T
1 T
170508 TTGTCATATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.45, C:0.20, G:0.07, T:0.28
Consensus pattern (13 bp):
TAAACATCACATG
Found at i:171300 original size:11 final size:11
Alignment explanation
Indices: 171284--171357 Score: 73
Period size: 11 Copynumber: 6.8 Consensus size: 11
171274 TATATTCATC
171284 TATTTATATTT
1 TATTTATATTT
171295 TATTTATATTT
1 TATTTATATTT
*
171306 T-TTTCATATTA
1 TATTT-ATATTT
171317 T-TTTAT-TTT
1 TATTTATATTT
171326 TATATTATATTT
1 TAT-TTATATTT
* *
171338 TAATTATTTTT
1 TATTTATATTT
*
171349 TAATTATAT
1 TATTTATAT
171358 CCATATTATG
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
9 3 0.06
10 6 0.11
11 40 0.74
12 5 0.09
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTTATATTT
Found at i:171317 original size:27 final size:26
Alignment explanation
Indices: 171287--171357 Score: 65
Period size: 27 Copynumber: 2.6 Consensus size: 26
171277 ATTCATCTAT
171287 TTATATTTTATTTATATT-T-TTTTCATA
1 TTAT-TTTTATTTATATTATATTTT-A-A
*
171314 TTATTTTATTTTTATATTATATTTTAA
1 TTATTTT-TATTTATATTATATTTTAA
*
171341 TTATTTTTTAATTATAT
1 TTA-TTTTTATTTATAT
171358 CCATATTATG
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
26 3 0.08
27 24 0.65
28 6 0.16
29 4 0.11
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.70
Consensus pattern (26 bp):
TTATTTTTATTTATATTATATTTTAA
Found at i:171325 original size:16 final size:15
Alignment explanation
Indices: 171284--171347 Score: 57
Period size: 13 Copynumber: 4.4 Consensus size: 15
171274 TATATTCATC
171284 TATTTATATTTTAT-T
1 TATTT-TATTTTATAT
171299 TATATTT-TTTTCATAT
1 TAT-TTTATTTT-ATAT
171315 TATTTTATTTT-TA-
1 TATTTTATTTTATAT
*
171328 TATTATATTTTA-AT
1 TATTTTATTTTATAT
171342 TATTTT
1 TATTTT
171348 TTAATTATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
13 11 0.27
14 11 0.27
15 9 0.22
16 10 0.24
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (15 bp):
TATTTTATTTTATAT
Found at i:171674 original size:17 final size:19
Alignment explanation
Indices: 171652--171693 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
171642 TTAAGTCAAA
171652 AAAATATTTT-ATTATT-T
1 AAAATATTTTAATTATTAT
171669 AAAATATTTTAAATTATTAT
1 AAAATATTTT-AATTATTAT
171689 AAAAT
1 AAAAT
171694 TAATTTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.45
19 6 0.27
20 6 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAATATTTTAATTATTAT
Found at i:171684 original size:19 final size:18
Alignment explanation
Indices: 171652--171706 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 18
171642 TTAAGTCAAA
171652 AAAATATTTTATTATT-T
1 AAAATATTTTATTATTAT
171669 AAAATATTTTAAATTATTAT
1 AAAATATTTT--ATTATTAT
171689 AAAATTAATTTTA-TATTA
1 AAAA-T-ATTTTATTATTA
171707 ATATTTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 10 0.30
19 11 0.33
20 6 0.18
21 1 0.03
22 5 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AAAATATTTTATTATTAT
Found at i:171688 original size:22 final size:24
Alignment explanation
Indices: 171660--171713 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
171650 AAAAAATATT
171660 TTATTATTTAAAA-T-ATTTTAAA
1 TTATTATTTAAAATTAATTTTAAA
*
171682 TTATTA--TAAAATTAATTTTATA
1 TTATTATTTAAAATTAATTTTAAA
*
171704 TTAATATTTA
1 TTATTATTTA
171714 TATATGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 5 0.19
21 1 0.04
22 18 0.69
24 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTATTATTTAAAATTAATTTTAAA
Found at i:172005 original size:65 final size:65
Alignment explanation
Indices: 171922--172057 Score: 227
Period size: 65 Copynumber: 2.1 Consensus size: 65
171912 AAATTATGTT
* * *
171922 ACTTAGATTTAAGAGTGTGTCAAATATTAGTACATGATCAATATAGGATATATTCAATTTTTTAA
1 ACTTATATTTAAAAGTGTGTCAAATATTAGTACACGATCAATATAGGATATATTCAATTTTTTAA
*
171987 ACTTATATTTAAAAGTGTGTCAAATATTAGTATACGATCAATATAGGATATATTCAATTTTTTAA
1 ACTTATATTTAAAAGTGTGTCAAATATTAGTACACGATCAATATAGGATATATTCAATTTTTTAA
*
172052 AATTAT
1 ACTTAT
172058 TTATGTATTT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (65 bp):
ACTTATATTTAAAAGTGTGTCAAATATTAGTACACGATCAATATAGGATATATTCAATTTTTTAA
Found at i:172463 original size:2 final size:2
Alignment explanation
Indices: 172456--172484 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
172446 GACTTTTAGC
172456 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 A
172485 GATTGACCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:177856 original size:3 final size:3
Alignment explanation
Indices: 177848--177887 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
177838 AGCTAAATTC
*
177848 TCT TCT TCT TCT TCT TCT TCT TCT TCT ATC- TAT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT -TCT TCT TCT TCT T
177888 AGTTTTCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 30 0.91
4 2 0.06
ACGTcount: A:0.05, C:0.30, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:180569 original size:51 final size:47
Alignment explanation
Indices: 180481--180574 Score: 118
Period size: 47 Copynumber: 1.9 Consensus size: 47
180471 TATTTTTAAA
*
180481 ATTAAATTTATTTCATGAAAAAAAATAAAGTAGTTTATACTTATTCG
1 ATTAAATTTATTTCATGAAAAAAAATAAACTAGTTTATACTTATTCG
*
180528 ATTAAATTTATTT-ATTTAATAAAAAATAAATCTAAGTTTTATACTTA
1 ATTAAATTTATTTCA-TGAA-AAAAAATAAA-CT-AG-TTTATACTTA
180575 ATTTCAAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
46 1 0.03
47 16 0.40
48 10 0.25
49 1 0.03
50 2 0.05
51 10 0.25
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (47 bp):
ATTAAATTTATTTCATGAAAAAAAATAAACTAGTTTATACTTATTCG
Found at i:181281 original size:22 final size:22
Alignment explanation
Indices: 181242--181294 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
181232 ACATTTTTAT
*
181242 TTAAAATTAATTATAAAAATATA
1 TTAATATTAATTATAAAAATA-A
181265 TTAATATTAA-TATAAAAATAA
1 TTAATATTAATTATAAAAATAA
181286 TTAAATATT
1 TT-AATATT
181295 TTAATATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 3 0.11
22 16 0.57
23 9 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAATATTAATTATAAAAATAA
Found at i:182601 original size:19 final size:19
Alignment explanation
Indices: 182551--182601 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
182541 ATCCCTCTTT
*
182551 AAAAATAAATTTATTTTTTA
1 AAAAATAAA-TTATTTATTA
* *
182571 AAAATTATATTA-TTATTA
1 AAAAATAAATTATTTATTA
182589 ATAAAATAAATTA
1 A-AAAATAAATTA
182602 ATTAAATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 6 0.24
19 12 0.48
20 7 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAAATAAATTATTTATTA
Found at i:182857 original size:14 final size:13
Alignment explanation
Indices: 182832--182856 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
182822 TCCCAATCTA
182832 AAATTAAAAAAAT
1 AAATTAAAAAAAT
182845 AAATTAAAAAAA
1 AAATTAAAAAAA
182857 AACCTGAATT
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATTAAAAAAAT
Found at i:185719 original size:17 final size:16
Alignment explanation
Indices: 185645--185730 Score: 71
Period size: 14 Copynumber: 5.7 Consensus size: 16
185635 ATTTAGATAT
185645 TTATAAATTTTATTA-A
1 TTAT-AATTTTATTATA
185661 TTATAATTTTATT-TA
1 TTATAATTTTATTATA
**
185676 AAAT-ATTTTA-TAT-
1 TTATAATTTTATTATA
185689 TTAT-ATTTTAATTATA
1 TTATAATTTT-ATTATA
185705 TTAGTAATTTTATTATA
1 TTA-TAATTTTATTATA
185722 -TA-AATTTTA
1 TTATAATTTTA
185731 AAATTTATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
13 8 0.14
14 15 0.25
15 15 0.25
16 9 0.15
17 7 0.12
18 5 0.08
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (16 bp):
TTATAATTTTATTATA
Found at i:186111 original size:25 final size:24
Alignment explanation
Indices: 186083--186129 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
186073 ATAATTATAG
*
186083 ATATAAAATAAATATTTTAAAATTT
1 ATATAAAATAAAT-TATTAAAATTT
*
186108 ATATAATATAAATTATTAAAAT
1 ATATAAAATAAATTATTAAAAT
186130 ATTTAATGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATAAAATAAATTATTAAAATTT
Found at i:186477 original size:29 final size:32
Alignment explanation
Indices: 186426--186494 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 32
186416 AAAGTAATTG
* * *
186426 AATTAATATTTAAAATATTTTTAATATAAT-T
1 AATTAAAATTTAAAATATATTTAATAAAATAT
186457 AA-TAAAATTT-AAATATATTTAATAAAATAT
1 AATTAAAATTTAAAATATATTTAATAAAATAT
186487 AATTAAAA
1 AATTAAAA
186495 CCAAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 16 0.48
30 10 0.30
31 7 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
AATTAAAATTTAAAATATATTTAATAAAATAT
Found at i:186579 original size:32 final size:33
Alignment explanation
Indices: 186522--186587 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
186512 CCGATCGATC
* * *
186522 TTGATATCAGTTTGATTTTTTTAATTTGAAAAT
1 TTGATATCAATTTGAATTTTTTAATTTAAAAAT
186555 TTGATATCAATTT-AATTTTTTAATTTAAAAAT
1 TTGATATCAATTTGAATTTTTTAATTTAAAAAT
186587 T
1 T
186588 AACATAATCG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.55
Consensus pattern (33 bp):
TTGATATCAATTTGAATTTTTTAATTTAAAAAT
Found at i:186979 original size:2 final size:2
Alignment explanation
Indices: 186972--187000 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
186962 AGCAAAAATC
186972 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 A
187001 AATAGTAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:189512 original size:50 final size:48
Alignment explanation
Indices: 189452--189556 Score: 124
Period size: 48 Copynumber: 2.2 Consensus size: 48
189442 TTAATAATTA
*
189452 AAAAAT-ATTTTT-ATTTAAATTTAATTATAAAATATATAAATATTAAAAT
1 AAAAATAATTTTTAATTTAAA-TTAATT-TAAAATA-ATAAATATAAAAAT
** *
189501 AAAAATAATTTTTAATTTTTATTAATTTTAAATAATAAATATAAAAAT
1 AAAAATAATTTTTAATTTAAATTAATTTAAAATAATAAATATAAAAAT
*
189549 ATAAATAA
1 AAAAATAA
189557 ATTAAATAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
48 20 0.41
49 12 0.24
50 12 0.24
51 5 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (48 bp):
AAAAATAATTTTTAATTTAAATTAATTTAAAATAATAAATATAAAAAT
Found at i:189553 original size:21 final size:21
Alignment explanation
Indices: 189529--189569 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
189519 TTATTAATTT
189529 TAAAT-AATAAATATAAAAATA
1 TAAATAAATAAA-ATAAAAATA
*
189550 TAAATAAATTAAATAAAAAT
1 TAAATAAATAAAATAAAAAT
189570 TTTAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAATAAATAAAATAAAAATA
Found at i:189911 original size:10 final size:10
Alignment explanation
Indices: 189896--189921 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
189886 CTAGAAATAA
189896 AAATAAAAAT
1 AAATAAAAAT
189906 AAATAAAAAT
1 AAATAAAAAT
189916 AAATAA
1 AAATAA
189922 GGATGTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:194057 original size:36 final size:36
Alignment explanation
Indices: 193986--194057 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
193976 TTCCTCCTGA
*
193986 ACCTCCTGCCCCAATTAGGGCCAGTCCTCCTCCACC
1 ACCTCCTGCCCCAATTAGGGCCAGTCCTCCACCACC
194022 ACCTCCTGCCCCAATTAGGGCCAGTCCTCCACCACC
1 ACCTCCTGCCCCAATTAGGGCCAGTCCTCCACCACC
194058 TCCTGCACCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.18, C:0.50, G:0.14, T:0.18
Consensus pattern (36 bp):
ACCTCCTGCCCCAATTAGGGCCAGTCCTCCACCACC
Found at i:195686 original size:22 final size:21
Alignment explanation
Indices: 195661--195709 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
195651 TATAATGATT
*
195661 TATGAACTAATCTTGGTATTGA
1 TATGAACAAATC-TGGTATTGA
* * *
195683 TATGCAGAAATCTGGTTTTGA
1 TATGAACAAATCTGGTATTGA
195704 TATGAA
1 TATGAA
195710 AATATTTCTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (21 bp):
TATGAACAAATCTGGTATTGA
Found at i:197407 original size:12 final size:12
Alignment explanation
Indices: 197390--197416 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
197380 CAGCCGAAAG
197390 GGCTAAGGGAGT
1 GGCTAAGGGAGT
197402 GGCTAAGGGAGT
1 GGCTAAGGGAGT
197414 GGC
1 GGC
197417 ATTAGTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.11, G:0.52, T:0.15
Consensus pattern (12 bp):
GGCTAAGGGAGT
Found at i:198046 original size:2 final size:2
Alignment explanation
Indices: 198041--198075 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
198031 ATATATATAT
198041 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 A
198076 ATTTATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:198452 original size:16 final size:16
Alignment explanation
Indices: 198407--198454 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
198397 TTAAATGTTT
198407 TAAAATTTATATA-ATA
1 TAAAATTTATATATA-A
*
198423 TAAATTATTA-ATATAA
1 TAAAAT-TTATATATAA
198439 TAAAATTTATATATAA
1 TAAAATTTATATATAA
198455 AAATAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 3 0.11
16 20 0.74
17 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAATTTATATATAA
Found at i:198464 original size:29 final size:32
Alignment explanation
Indices: 198407--198465 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
198397 TTAAATGTTT
* *
198407 TAAAATTTATATAATATAAATTATTAATATAA
1 TAAAATTTATATAATATAAAATATAAATATAA
198439 TAAAATTTATAT-ATA-AAAATA-AAATAT
1 TAAAATTTATATAATATAAAATATAAATAT
198466 TTTAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.20
30 5 0.20
31 3 0.12
32 12 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (32 bp):
TAAAATTTATATAATATAAAATATAAATATAA
Found at i:204990 original size:2 final size:2
Alignment explanation
Indices: 204983--205022 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
204973 CATGAGCAAC
204983 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
205023 CTTGGTGATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:208125 original size:17 final size:17
Alignment explanation
Indices: 208103--208147 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 17
208093 AGAACAACTA
*
208103 AATTTATTTAAAATTTT
1 AATTTATTTAAAATATT
208120 AATTTA-TT-AAATATT
1 AATTTATTTAAAATATT
208135 -A-TTATTTAAAATA
1 AATTTATTTAAAATA
208148 ATACATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
13 3 0.12
14 3 0.12
15 11 0.44
16 2 0.08
17 6 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTATTTAAAATATT
Found at i:208544 original size:61 final size:60
Alignment explanation
Indices: 208464--208616 Score: 164
Period size: 61 Copynumber: 2.5 Consensus size: 60
208454 AACTGGAGCA
* * * * * * *
208464 AAGACAATGACATAGTGCCATCTCTAGCTCCCTGTGGCGGGTCTCCACCACCCG-GAACAG
1 AAGAGAATGACATAATGCCATCTCCAGC-CCCTCTGGCGAGTCTCCACCAACCGAAAACAG
* * * *
208524 AAGATATATGACATAATGCCATCTCCGGCCTCCTCTGGCTAGTCTCCACCAACCGAAAACAT
1 AAGAGA-ATGACATAATGCCATCTCCAGCC-CCTCTGGCGAGTCTCCACCAACCGAAAACAG
*
208586 TAGAGAATGACATAATGCCATCTCCAGCCCC
1 AAGAGAATGACATAATGCCATCTCCAGCCCC
208617 CTCCTGGAAG
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
60 8 0.10
61 61 0.79
62 8 0.10
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (60 bp):
AAGAGAATGACATAATGCCATCTCCAGCCCCTCTGGCGAGTCTCCACCAACCGAAAACAG
Found at i:213021 original size:27 final size:27
Alignment explanation
Indices: 212983--213035 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
212973 CCTTTGAAAA
* *
212983 TGAATTGAAATCAGGAAAGCAGGAGAT
1 TGAATTGAAATCAAGAAAGAAGGAGAT
213010 TGAATTGAAATCAAGAAAGAAGGAGA
1 TGAATTGAAATCAAGAAAGAAGGAGA
213036 ATGCCAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.49, C:0.06, G:0.28, T:0.17
Consensus pattern (27 bp):
TGAATTGAAATCAAGAAAGAAGGAGAT
Found at i:216655 original size:12 final size:12
Alignment explanation
Indices: 216635--216668 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
216625 ATTTGAAAAC
*
216635 ATATATATATGT
1 ATATATATATCT
*
216647 ATGTATATATCT
1 ATATATATATCT
216659 ATATATATAT
1 ATATATATAT
216669 AGAAAAGAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (12 bp):
ATATATATATCT
Found at i:216829 original size:18 final size:18
Alignment explanation
Indices: 216793--216844 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
216783 CCTTACGTGG
* *
216793 TTTTTCATATGTATATATT
1 TTTTTCA-ATTTATTTATT
216812 TTTTTCAATTTATTTATT
1 TTTTTCAATTTATTTATT
* * *
216830 TATTTAAATTAATTT
1 TTTTTCAATTTATTT
216845 CTATGTGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 21 0.75
19 7 0.25
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTTCAATTTATTTATT
Found at i:217413 original size:28 final size:28
Alignment explanation
Indices: 217382--217440 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
217372 TATTACACAT
* * *
217382 AAATATAATATAATATAAAAAA-TAACTA
1 AAATATAAAACAACATAAAAAATTAA-TA
217410 AAATATAAAACAACATAAAAAATTAATA
1 AAATATAAAACAACATAAAAAATTAATA
217438 AAA
1 AAA
217441 CTACGTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (28 bp):
AAATATAAAACAACATAAAAAATTAATA
Found at i:218007 original size:15 final size:15
Alignment explanation
Indices: 217989--218122 Score: 53
Period size: 15 Copynumber: 8.6 Consensus size: 15
217979 ATTATTTTTA
217989 TATATTTTATTATAT
1 TATATTTTATTATAT
* * *
218004 TATAATTGATT-TAA
1 TATATTTTATTATAT
*
218018 TATATTTTATATAAAT
1 TATATTTTAT-TATAT
* * *
218034 TTTAATATATTAATAAT
1 TATATTTTATT-AT-AT
*
218051 TCATATTATA-TATAT
1 T-ATATTTTATTATAT
*
218066 TAAAAATATTTA-TATAT
1 T--ATAT-TTTATTATAT
218083 TATATATTTA-TAT-T
1 TATAT-TTTATTATAT
*
218097 ATATGTTTATATTATAT
1 -TATATTT-TATTATAT
218114 TATATTTTA
1 TATATTTTA
218123 ATTTTTTATA
Statistics
Matches: 89, Mismatches: 19, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
14 13 0.15
15 33 0.37
16 23 0.26
17 14 0.16
18 6 0.07
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (15 bp):
TATATTTTATTATAT
Found at i:218021 original size:19 final size:18
Alignment explanation
Indices: 217994--218086 Score: 62
Period size: 21 Copynumber: 4.8 Consensus size: 18
217984 TTTTATATAT
*
217994 TTTATTATATTATAATTGA
1 TTTAATATATTATAATT-A
* *
218013 TTTAATATATTTTATATAAA
1 TTTAATATATTATA-AT-TA
218033 TTTTAATATATTAATAATTCA
1 -TTTAATATATT-ATAATT-A
* *
218054 TATTATATATATTAAAAATA
1 T-TTA-ATATATTATAATTA
218074 TTT-ATATATTATA
1 TTTAATATATTATA
218087 TATTTATATT
Statistics
Matches: 59, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
17 9 0.15
19 14 0.24
20 6 0.10
21 21 0.36
22 9 0.15
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (18 bp):
TTTAATATATTATAATTA
Found at i:218081 original size:39 final size:39
Alignment explanation
Indices: 217967--218108 Score: 122
Period size: 39 Copynumber: 3.7 Consensus size: 39
217957 ATCTTACTAT
217967 TTATAAATTCATATTAT-T-T-TTATAT--ATTTTATTATA
1 TTAT-AATTCATATTATATATATTATATAAATTTTA-TATA
* *
218003 TTATAATTGAT-TTAATATATTTTATATAAATTTTAATATA
1 TTATAATTCATATT-ATATATATTATATAAATTTT-ATATA
218043 TTAATAATTCATATTATATATATTA-A-AAATATTTATATA
1 TT-ATAATTCATATTATATATATTATATAAAT-TTTATATA
* *
218082 TTATATATTTATATTATATGT-TTATAT
1 TTATA-ATTCATATTATATATATTATAT
218109 TATATTATAT
Statistics
Matches: 88, Mismatches: 5, Indels: 22
0.77 0.04 0.19
Matches are distributed among these distances:
34 2 0.02
35 8 0.09
36 5 0.06
37 1 0.01
38 12 0.14
39 25 0.28
40 15 0.17
41 18 0.20
42 2 0.02
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (39 bp):
TTATAATTCATATTATATATATTATATAAATTTTATATA
Found at i:218087 original size:13 final size:13
Alignment explanation
Indices: 217977--218136 Score: 60
Period size: 13 Copynumber: 12.5 Consensus size: 13
217967 TTATAAATTC
217977 ATATTAT-TTT-T
1 ATATTATATTTAT
217988 ATA-TAT-TTTATT
1 ATATTATATTTA-T
*
218000 ATATTATAATTGAT
1 ATATTAT-ATTTAT
* *
218014 TTAATATATTT-T
1 ATATTATATTTAT
*
218026 ATA-TAAATTT-T
1 ATATTATATTTAT
*
218037 A-A-TATATTAAT
1 ATATTATATTTAT
218048 A-ATTCATATTATAT
1 ATATT-ATATT-TAT
218062 ATATTAAAAATATTTAT
1 ATATT----ATATTTAT
218079 ATATTATATATT-T
1 ATATTATAT-TTAT
218092 ATATTATATGTT-T
1 ATATTATAT-TTAT
218105 ATATTATA-TTAT
1 ATATTATATTTAT
* *
218117 ATTTTA-ATTTTTT
1 ATATTATA-TTTAT
218130 ATATTAT
1 ATATTAT
218137 TTAATCATGT
Statistics
Matches: 117, Mismatches: 14, Indels: 33
0.71 0.09 0.20
Matches are distributed among these distances:
10 12 0.10
11 17 0.15
12 14 0.12
13 44 0.38
14 11 0.09
15 6 0.05
17 8 0.07
18 5 0.04
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (13 bp):
ATATTATATTTAT
Found at i:218089 original size:26 final size:27
Alignment explanation
Indices: 218053--218119 Score: 77
Period size: 26 Copynumber: 2.5 Consensus size: 27
218043 TTAATAATTC
218053 ATATTATATATATTA-AAAATAT-TTAT
1 ATATTATATATATTATAAAATATGTT-T
**
218079 ATATTATATAT-TTATATTATATGTTT
1 ATATTATATATATTATAAAATATGTTT
218105 ATATTATATTATATT
1 ATATTATA-TATATT
218120 TTAATTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 3 0.09
26 25 0.71
27 5 0.14
28 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (27 bp):
ATATTATATATATTATAAAATATGTTT
Found at i:218111 original size:18 final size:18
Alignment explanation
Indices: 218078--218134 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
218068 AAAATATTTA
*
218078 TATATTATATATTTATAT
1 TATATTTTATATTTATAT
218096 TATATGTTTATA-TTATAT
1 TATAT-TTTATATTTATAT
218114 TATATTTTA-ATTT-T-T
1 TATATTTTATATTTATAT
218129 TATATT
1 TATATT
218135 ATTTAATCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
15 7 0.19
16 2 0.06
17 6 0.17
18 16 0.44
19 5 0.14
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TATATTTTATATTTATAT
Found at i:219679 original size:49 final size:49
Alignment explanation
Indices: 219567--219680 Score: 112
Period size: 46 Copynumber: 2.3 Consensus size: 49
219557 TATTACGATT
*
219567 TATTAAATTATTATTTTTATATTAATATTTATATAATTAAATTTAAATA
1 TATTAAATTTTTATTTTTATATTAATATTTATATAATTAAATTTAAATA
* * *
219616 -A--AAAATTTTATTATTAT-TTAATTTATTTTAAATTTAATT-AATTTAAATA
1 TATTAAATTTTTATTTTTATATTAA--TA-TTT--ATATAATTAAATTTAAATA
219665 TATTAAATTTTTATTT
1 TATTAAATTTTTATTT
219681 AAAATTTAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
45 4 0.08
46 13 0.25
47 2 0.04
48 4 0.08
49 10 0.20
50 8 0.16
52 10 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (49 bp):
TATTAAATTTTTATTTTTATATTAATATTTATATAATTAAATTTAAATA
Found at i:223626 original size:40 final size:40
Alignment explanation
Indices: 223572--223662 Score: 109
Period size: 40 Copynumber: 2.3 Consensus size: 40
223562 TATTTGAATA
* *
223572 TTTATATTATTATTTAAAATT-ATTTTAATTAAAAA-ATATT
1 TTTATATTAATATTTAAAATTAAATTTAA-TAAAAATA-ATT
*
223612 TTTATATTAATATTTATAATTAAATTTAATAAAAATAATT
1 TTTATATTAATATTTAAAATTAAATTTAATAAAAATAATT
223652 TTTA-A-TAATAT
1 TTTATATTAATAT
223663 AAATAATAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
38 6 0.13
39 1 0.02
40 32 0.70
41 7 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (40 bp):
TTTATATTAATATTTAAAATTAAATTTAATAAAAATAATT
Found at i:224276 original size:19 final size:20
Alignment explanation
Indices: 224244--224281 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
224234 TTATAATTAA
*
224244 ATTTTAAATATATATATATT
1 ATTTTAAATATATAAATATT
*
224264 ATTTT-AATTTATAAATAT
1 ATTTTAAATATATAAATAT
224282 GTTTTGAGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTTAAATATATAAATATT
Found at i:224384 original size:23 final size:23
Alignment explanation
Indices: 224357--224404 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
224347 AAAAGTCTAT
*
224357 TTAAAATATAAAAAATAAATTAA
1 TTAAAAAATAAAAAATAAATTAA
* *
224380 TTAAAAAATAAAATATAAGTTAA
1 TTAAAAAATAAAAAATAAATTAA
224403 TT
1 TT
224405 TCTTAAACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
TTAAAAAATAAAAAATAAATTAA
Found at i:224870 original size:5 final size:5
Alignment explanation
Indices: 224860--224928 Score: 63
Period size: 5 Copynumber: 13.8 Consensus size: 5
224850 AAAATTGGGC
* *
224860 ATAAT ATAAT A-AAA ATAATT AAAAT ATAAT AT-AT A-AAT ATAAT ATAAAT
1 ATAAT ATAAT ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT AT-AAT
*
224909 ATAAT ATAAAT ATGAT ATAA
1 ATAAT AT-AAT ATAAT ATAA
224929 ATTTTTAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
4 9 0.17
5 30 0.58
6 13 0.25
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (5 bp):
ATAAT
Found at i:224895 original size:24 final size:24
Alignment explanation
Indices: 224860--224916 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 24
224850 AAAATTGGGC
224860 ATAATATAATAAAAATAAT-TAAAAT
1 ATAATAT-ATAAAAATAATAT-AAAT
*
224885 ATAATATATAAATATAATATAAAT
1 ATAATATATAAAAATAATATAAAT
224909 ATAATATA
1 ATAATATA
224917 AATATGATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 22 0.73
25 8 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
ATAATATATAAAAATAATATAAAT
Found at i:224919 original size:11 final size:11
Alignment explanation
Indices: 224862--224930 Score: 81
Period size: 11 Copynumber: 6.3 Consensus size: 11
224852 AATTGGGCAT
224862 AATATAATA-A
1 AATATAATATA
224872 AA-ATAAT-TAA
1 AATATAATAT-A
224882 AATATAATATATA
1 AATAT-A-ATATA
224895 AATATAATATA
1 AATATAATATA
224906 AATATAATATA
1 AATATAATATA
*
224917 AATATGATATA
1 AATATAATATA
224928 AAT
1 AAT
224931 TTTTAAATAT
Statistics
Matches: 52, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
9 5 0.10
10 5 0.10
11 31 0.60
12 2 0.04
13 8 0.15
14 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (11 bp):
AATATAATATA
Found at i:224920 original size:35 final size:33
Alignment explanation
Indices: 224862--224927 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 33
224852 AATTGGGCAT
224862 AATATAATAAAAATAATTAAAATATAATATATA
1 AATATAATAAAAATAATTAAAATATAATATATA
*
224895 AATATAATATAAATATAA-TATAAATATGATATA
1 AATATAATA-AAA-ATAATTA-AAATATAATATA
224928 AATTTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 9 0.31
34 5 0.17
35 15 0.52
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (33 bp):
AATATAATAAAAATAATTAAAATATAATATATA
Found at i:224950 original size:18 final size:18
Alignment explanation
Indices: 224927--224983 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
224917 AATATGATAT
***
224927 AAATTTTTAAATATTTTA
1 AAATTTTTAAATAAAATA
*
224945 AAATTTATAAATAAAATA
1 AAATTTTTAAATAAAATA
224963 AAATATTTTAAAT-AAATA
1 AAAT-TTTTAAATAAAATA
224981 AAA
1 AAA
224984 AATATAACAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
18 26 0.79
19 7 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATTTTTAAATAAAATA
Found at i:224981 original size:27 final size:28
Alignment explanation
Indices: 224935--224990 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
224925 ATAAATTTTT
**
224935 AAATATTTTAAAATTTATAAATAAA-ATA
1 AAATATTTTAAAATAAATAAA-AAATATA
224963 AAATATTTT-AAATAAATAAAAAATATA
1 AAATATTTTAAAATAAATAAAAAATATA
224990 A
1 A
224991 CATGAGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 3 0.12
27 13 0.52
28 9 0.36
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
AAATATTTTAAAATAAATAAAAAATATA
Found at i:224985 original size:20 final size:20
Alignment explanation
Indices: 224947--224988 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
224937 ATATTTTAAA
*
224947 ATTTATAAATAAAATAAAAT
1 ATTTATAAATAAAAAAAAAT
224967 ATTT-TAAATAAATAAAAAAT
1 ATTTATAAATAAA-AAAAAAT
224987 AT
1 AT
224989 AACATGAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTTATAAATAAAAAAAAAT
Found at i:231376 original size:16 final size:15
Alignment explanation
Indices: 231355--231409 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
231345 TTATTTTATT
231355 ATTATTTAACATTAAA
1 ATTATTTAA-ATTAAA
*
231371 ATTATTTAATTTAAA
1 ATTATTTAAATTAAA
* *
231386 A-T-TTAAAATTAAT
1 ATTATTTAAATTAAA
*
231399 TTTATTTAAAT
1 ATTATTTAAAT
231410 CATCAATTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
13 8 0.26
14 2 0.06
15 12 0.39
16 9 0.29
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTATTTAAATTAAA
Found at i:231391 original size:22 final size:22
Alignment explanation
Indices: 231358--231408 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
231348 TTTTATTATT
*
231358 ATTTAACATTAAAATT-ATTTA
1 ATTTAAAATTAAAATTAATTTA
*
231379 ATTTAAAATTTAAAATTAATTTT
1 ATTTAAAA-TTAAAATTAATTTA
231402 ATTTAAA
1 ATTTAAA
231409 TCATCAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 7 0.27
22 8 0.31
23 11 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTAAAATTAAAATTAATTTA
Found at i:231409 original size:22 final size:21
Alignment explanation
Indices: 231350--231409 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 21
231340 AATATTTATT
231350 TTATTATTATTTAACA-TTAAAA
1 TTATT-TTATTTAA-ATTTAAAA
*
231372 TTATTTAATTTAAAATTTAAAA
1 TTATTTTATTT-AAATTTAAAA
231394 TTAATTTTATTTAAAT
1 TT-ATTTTATTTAAAT
231410 CATCAATTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 6 0.18
22 19 0.58
23 8 0.24
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TTATTTTATTTAAATTTAAAA
Found at i:237908 original size:8 final size:8
Alignment explanation
Indices: 237895--237957 Score: 51
Period size: 8 Copynumber: 7.6 Consensus size: 8
237885 TTTAAATATG
237895 ATATATAA
1 ATATATAA
237903 ATATATTAA
1 ATATA-TAA
237912 A-ATAT-A
1 ATATATAA
237918 ATAATATAA
1 AT-ATATAA
237927 AT-TATTAA
1 ATATA-TAA
237935 ATATATTTAA
1 ATATA--TAA
*
237945 ATTTATAA
1 ATATATAA
237953 ATATA
1 ATATA
237958 ATATTTTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
6 2 0.04
7 3 0.07
8 24 0.52
9 9 0.20
10 8 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATATAA
Found at i:237916 original size:18 final size:18
Alignment explanation
Indices: 237895--237957 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
237885 TTTAAATATG
237895 ATATATAAATATATTAAA
1 ATATATAAATATATTAAA
*
237913 ATATA-ATA-ATA-TAAA
1 ATATATAAATATATTAAA
* *
237928 TTAT-TAAATATATTTAA
1 ATATATAAATATATTAAA
*
237945 ATTTATAAATATA
1 ATATATAAATATA
237958 ATATTTTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
15 9 0.26
16 6 0.17
17 7 0.20
18 13 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATATAAATATATTAAA
Found at i:237924 original size:56 final size:54
Alignment explanation
Indices: 237841--237976 Score: 136
Period size: 56 Copynumber: 2.5 Consensus size: 54
237831 TAATTATACG
*
237841 ATATAAATATA-AAATAATTATAA-AATAT-AATTGAGTAAAAATAATTTAAATATGAT
1 ATATAAATATATTAA-AA-TATAATAATATAAATT-AGTAAAAAT-ATTTAAAT-TGAT
* * *
237897 ATATAAATATATTAAAATATAATAATATAAATTATTAAATATATTTAAATTTAT
1 ATATAAATATATTAAAATATAATAATATAAATTAGTAAAAATATTTAAATTGAT
* *
237951 AAATATAATAT-TTTAAATATAATAAT
1 ATATA-AATATATTAAAATATAATAAT
237977 TAACATGTGT
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
54 21 0.30
55 18 0.26
56 25 0.36
57 6 0.09
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (54 bp):
ATATAAATATATTAAAATATAATAATATAAATTAGTAAAAATATTTAAATTGAT
Found at i:237932 original size:23 final size:23
Alignment explanation
Indices: 237856--237940 Score: 75
Period size: 23 Copynumber: 3.6 Consensus size: 23
237846 AATATAAAAT
* *
237856 AATTA-TAAAATATAATTGAGTAAA
1 AATTATTAAAATATAA-T-AATATA
* * *
237880 AATAATTTAAATATGAT-ATATA
1 AATTATTAAAATATAATAATATA
237902 AATATATTAAAATATAATAATATA
1 AAT-TATTAAAATATAATAATATA
237926 AATTATTAAATATAT
1 AATTATTAAA-ATAT
237941 TTAAATTTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
22 6 0.12
23 18 0.37
24 17 0.35
25 8 0.16
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.39
Consensus pattern (23 bp):
AATTATTAAAATATAATAATATA
Found at i:237936 original size:32 final size:32
Alignment explanation
Indices: 237887--237971 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 32
237877 AAAAATAATT
* *
237887 TAAATATGATA-TATAAATATATTAAAATATAA
1 TAAATATAATATTTTAAATATATTAAAAT-TAA
* *
237919 T-AATATAA-ATTATTAAATATATTTAAATTTA
1 TAAATATAATATT-TTAAATATATTAAAATTAA
237950 TAAATATAATATTTTAAATATA
1 TAAATATAATATTTTAAATATA
237972 ATAATTAACA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
30 1 0.02
31 10 0.22
32 31 0.69
33 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (32 bp):
TAAATATAATATTTTAAATATATTAAAATTAA
Found at i:237969 original size:14 final size:15
Alignment explanation
Indices: 237945--237974 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
237935 ATATATTTAA
237945 ATTTATAAATATAAT
1 ATTTATAAATATAAT
237960 ATTT-TAAATATAAT
1 ATTTATAAATATAAT
237974 A
1 A
237975 ATTAACATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTATAAATATAAT
Found at i:238243 original size:2 final size:2
Alignment explanation
Indices: 238238--238263 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
238228 TATATATAGC
238238 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
238264 ACTCCCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:244638 original size:2 final size:2
Alignment explanation
Indices: 244631--244671 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
244621 CCAATTATTG
*
244631 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
244672 TTTAACTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:246222 original size:31 final size:32
Alignment explanation
Indices: 246165--246224 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
246155 ATATTTGAGT
*
246165 TAATTTAATTTATTATTTAATAATAAAAATAA
1 TAATTTAATTTATAATTTAATAATAAAAATAA
* *
246197 TAATTTTATTTA-AATTTAATTATAAAAA
1 TAATTTAATTTATAATTTAATAATAAAAA
246225 ATATATAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 14 0.56
32 11 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
TAATTTAATTTATAATTTAATAATAAAAATAA
Found at i:246225 original size:32 final size:33
Alignment explanation
Indices: 246165--246232 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
246155 ATATTTGAGT
*
246165 TAATTTAATTTATTATTTAATAATAAAAATA-A
1 TAATTTAATTTATAATTTAATAATAAAAATATA
* *
246197 TAATTTTATTTA-AATTTAATTATAAAAAATATA
1 TAATTTAATTTATAATTTAATAAT-AAAAATATA
246230 TAA
1 TAA
246233 ATATTAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 9 0.29
32 18 0.58
33 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
TAATTTAATTTATAATTTAATAATAAAAATATA
Found at i:246270 original size:20 final size:18
Alignment explanation
Indices: 246224--246270 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
246214 AATTATAAAA
246224 AATAT-ATAAATATTAAT
1 AATATAATAAATATTAAT
*
246241 AA-A-AATAATATTTTAAT
1 AATATAATAA-ATATTAAT
246258 AATATAATAAATA
1 AATATAATAAATA
246271 AAATAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
16 5 0.21
17 11 0.46
18 3 0.12
19 5 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATATAATAAATATTAAT
Found at i:246276 original size:34 final size:33
Alignment explanation
Indices: 246224--246288 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
246214 AATTATAAAA
* *
246224 AATATATAAATATTAATAAAAATAATATTTTAAT
1 AATATATAAATATAAAT-AAAATAAAATTTTAAT
246258 AATATAATAAATA-AAATAAAATAAAATTTTA
1 AATAT-ATAAATATAAATAAAATAAAATTTTA
246289 CATTAATTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 13 0.46
34 8 0.29
35 7 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (33 bp):
AATATATAAATATAAATAAAATAAAATTTTAAT
Found at i:246770 original size:17 final size:16
Alignment explanation
Indices: 246748--246795 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
246738 AATTAATTTA
*
246748 ATTTAATTTTAATTAAT
1 ATTTAATTTTAA-AAAT
*
246765 ATTTAATAATTAAAAAT
1 ATTTAAT-TTTAAAAAT
*
246782 ATTTAATTATAAAA
1 ATTTAATTTTAAAA
246796 TAAATAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 5 0.19
17 17 0.65
18 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTAATTTTAAAAAT
Found at i:246774 original size:10 final size:10
Alignment explanation
Indices: 246724--246775 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
246714 TGAATATATT
*
246724 TTTTTATTAA
1 TTTTAATTAA
*
246734 TTTAAATTAA
1 TTTTAATTAA
246744 -TTTAATTTAA
1 TTTTAA-TTAA
246754 TTTTAATTAA
1 TTTTAATTAA
246764 TATTTAA-TAA
1 T-TTTAATTAA
246774 TT
1 TT
246776 AAAAATATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
9 5 0.14
10 21 0.58
11 10 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTAATTAA
Found at i:246826 original size:19 final size:19
Alignment explanation
Indices: 246778--246834 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
246768 TAATAATTAA
*
246778 AAATATTTAATTATAAAAT
1 AAATATTTAAATATAAAAT
**
246797 AAATAAATAAATATAAATAT
1 AAATATTTAAATATAAA-AT
*
246817 AAA-ATTTAAATTTAAAAT
1 AAATATTTAAATATAAAAT
246835 TTTATTAATC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 2 0.06
19 24 0.77
20 5 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATATTTAAATATAAAAT
Found at i:246835 original size:13 final size:13
Alignment explanation
Indices: 246782--246836 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
246772 AATTAAAAAT
*
246782 ATTTAATTATAAA
1 ATTTAAATATAAA
*
246795 A--TAAATAAATAA
1 ATTTAAATATA-AA
*
246807 ATATAAATATAAA
1 ATTTAAATATAAA
*
246820 ATTTAAATTTAAA
1 ATTTAAATATAAA
246833 ATTT
1 ATTT
246837 TATTAATCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
11 6 0.18
12 3 0.09
13 18 0.53
14 7 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTTAAATATAAA
Found at i:252021 original size:2 final size:2
Alignment explanation
Indices: 252014--252048 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
252004 GCTTTTTGTT
252014 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
252049 GTATGTGTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:257761 original size:17 final size:17
Alignment explanation
Indices: 257721--257762 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
257711 TAAAAAATAA
* *
257721 ATATATTTATATTCGAT
1 ATATATTTATATTCAAC
257738 ATATATTTATATTCAAC
1 ATATATTTATATTCAAC
*
257755 ATTTATTT
1 ATATATTT
257763 TTGAATTCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (17 bp):
ATATATTTATATTCAAC
Found at i:260062 original size:17 final size:17
Alignment explanation
Indices: 260042--260096 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 17
260032 ATTAACATAT
260042 TAAAATTTATATAAATA
1 TAAAATTTATATAAATA
260059 TAAAAATATT-T-TAAATA
1 T-AAAAT-TTATATAAATA
*
260076 CAAAA--TATATAAATA
1 TAAAATTTATATAAATA
260091 TAAAAT
1 TAAAAT
260097 AAATATACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
13 1 0.03
14 1 0.03
15 10 0.32
16 4 0.13
17 7 0.23
18 6 0.19
19 2 0.06
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:262438 original size:22 final size:22
Alignment explanation
Indices: 262393--262439 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
262383 GTTAAAATTT
* *
262393 ATATAAATAAATAATATCTTAA
1 ATATAAATAAATAATATATAAA
* *
262415 ATATAATTATATAATATATAAA
1 ATATAAATAAATAATATATAAA
262437 ATA
1 ATA
262440 CGATATTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
ATATAAATAAATAATATATAAA
Found at i:264183 original size:20 final size:20
Alignment explanation
Indices: 264158--264215 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
264148 GTTATAATTA
264158 TATATAAAGTATTTTATAT-T
1 TATATAAA-TATTTTATATAT
*
264178 TATATAAAT-TTTAATATAT
1 TATATAAATATTTTATATAT
*
264197 TA-ATAAATTATATTATATA
1 TATATAAA-TATTTTATATA
264216 AATTTTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 12 0.38
19 5 0.16
20 15 0.47
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TATATAAATATTTTATATAT
Found at i:264194 original size:18 final size:18
Alignment explanation
Indices: 264158--264223 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 18
264148 GTTATAATTA
*
264158 TATATAAAGTATTTTATATT
1 TATATAAA-T-TTTAATATT
264178 TATATAAATTTTAATATAT
1 TATATAAATTTTAATAT-T
264197 TA-ATAAA--TT-ATA-T
1 TATATAAATTTTAATATT
264210 TATATAAATTTTAA
1 TATATAAATTTTAA
264224 AAATTTATAC
Statistics
Matches: 40, Mismatches: 1, Indels: 13
0.74 0.02 0.24
Matches are distributed among these distances:
13 3 0.08
14 5 0.12
15 3 0.08
16 4 0.10
17 1 0.03
18 12 0.30
19 4 0.10
20 8 0.20
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TATATAAATTTTAATATT
Found at i:264529 original size:2 final size:2
Alignment explanation
Indices: 264522--264551 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
264512 AAGTAGCAGA
264522 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
264552 GAGAAAACTT
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:273735 original size:25 final size:25
Alignment explanation
Indices: 273708--273754 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
273698 ACTATCATAA
*
273708 AAAATTAAATAT-TTTAATTTATTC
1 AAAATTAAATATATATAATTTATTC
*
273732 AAAATTTAATATATATAATTTAT
1 AAAATTAAATATATATAATTTAT
273755 ATGAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
AAAATTAAATATATATAATTTATTC
Found at i:273801 original size:15 final size:15
Alignment explanation
Indices: 273781--273810 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
273771 ATTTGATAAT
273781 TAAATTAAATAAATA
1 TAAATTAAATAAATA
*
273796 TAAATTATATAAATA
1 TAAATTAAATAAATA
273811 ATTCAAACTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATTAAATAAATA
Found at i:273853 original size:2 final size:2
Alignment explanation
Indices: 273846--273870 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
273836 ATGCAATTGA
273846 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
273871 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:273875 original size:2 final size:2
Alignment explanation
Indices: 273870--273926 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
273860 TCTCTCTCTC
273870 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
273912 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
273927 GATTCAAACA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:274427 original size:35 final size:33
Alignment explanation
Indices: 274369--274433 Score: 85
Period size: 35 Copynumber: 1.9 Consensus size: 33
274359 TTACGTAAAA
*
274369 AATAAAAAATATTTAAATTTAATTATAAATATT
1 AATAAAAAATATTTAAATATAATTATAAATATT
* *
274402 AATATAAAAATATTTTTAATATAATTTTAAAT
1 AATA-AAAAATA-TTTAAATATAATTATAAAT
274434 TACGATACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 4 0.15
34 7 0.26
35 16 0.59
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
AATAAAAAATATTTAAATATAATTATAAATATT
Found at i:280118 original size:21 final size:21
Alignment explanation
Indices: 280094--280139 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
280084 TATCAAAACC
* * *
280094 AAAAGCAAAAATTACTAA-AA
1 AAAAACAAAAATCACAAATAA
280114 AAAAACAAAAATCACAAATAA
1 AAAAACAAAAATCACAAATAA
280135 AAAAA
1 AAAAA
280140 AGAGTAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.76, C:0.11, G:0.02, T:0.11
Consensus pattern (21 bp):
AAAAACAAAAATCACAAATAA
Found at i:282994 original size:25 final size:24
Alignment explanation
Indices: 282966--283020 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
282956 ATTTAATTAT
*
282966 ATATATAAATATTA-AGATAAAAATA
1 ATATATAAATAATATA-ATAAAAA-A
* *
282991 ATATTTTAATAATATAATAAAAAA
1 ATATATAAATAATATAATAAAAAA
283015 ATATAT
1 ATATAT
283021 TTTTGTATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 6 0.24
25 18 0.72
26 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
ATATATAAATAATATAATAAAAAA
Found at i:283193 original size:27 final size:27
Alignment explanation
Indices: 283145--283198 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
283135 TATTAATTTT
283145 ATTTTTGATTAATGAATTAAATCAAAAA
1 ATTTTTGATTAATGAATTAAAT-AAAAA
*
283173 ATTTTTTATT-AT-AATTCAAATAAAAA
1 ATTTTTGATTAATGAATT-AAATAAAAA
283199 TATAATACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 9 0.38
27 6 0.25
28 9 0.38
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (27 bp):
ATTTTTGATTAATGAATTAAATAAAAA
Found at i:283276 original size:99 final size:98
Alignment explanation
Indices: 283171--283369 Score: 253
Period size: 98 Copynumber: 2.0 Consensus size: 98
283161 TTAAATCAAA
* * * *
283171 AAATTTTTTA-TTATAATTCAAA-TAAAAATATAATACCAAATATTTTTTGAAAGTGAAATTTGT
1 AAATATTTTATTTACAATTCAAATTAAAAAAATAATACCAAATA-ATTTTGAAAGTGAAATTTGT
* *
283234 GC-TATGTATTCACAATTCAAATATTTTT-AATAGT
65 GCATACGT-TT-ACAATTCAAATATTTTTGAAAAGT
* **
283268 AAATATTTTATTTACAATTCAAATTAAAAAAATAATGCTGAATAATTTTGAAAGTGAAATTTGTG
1 AAATATTTTATTTACAATTCAAATTAAAAAAATAATACCAAATAATTTTGAAAGTGAAATTTGTG
283333 CGATACGTTTACAATTCAAATATTTTTGAAAAGT
66 C-ATACGTTTACAATTCAAATATTTTTGAAAAGT
283367 AAA
1 AAA
283370 ATATATATAT
Statistics
Matches: 88, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
97 9 0.10
98 49 0.56
99 26 0.30
100 4 0.05
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (98 bp):
AAATATTTTATTTACAATTCAAATTAAAAAAATAATACCAAATAATTTTGAAAGTGAAATTTGTG
CATACGTTTACAATTCAAATATTTTTGAAAAGT
Found at i:284341 original size:17 final size:19
Alignment explanation
Indices: 284308--284343 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
284298 TAAAATTTTG
284308 TATATTTTTATTATATTAT
1 TATATTTTTATTATATTAT
284327 TATA-TTTTA-TATATTAT
1 TATATTTTTATTATATTAT
284344 AATCGTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 5 0.29
19 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATATTTTTATTATATTAT
Found at i:286277 original size:27 final size:27
Alignment explanation
Indices: 286205--286278 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
286195 ATAAGTTACT
* *
286205 ATTTTTGACAAACAAAAAAGAACTACC
1 ATTTTTGACAAACAAAAAGGAACCACC
* *
286232 ATTTTTTACAAACACAAAGGAACCACC
1 ATTTTTGACAAACAAAAAGGAACCACC
*
286259 ATTTTTGACAAACATAAAGG
1 ATTTTTGACAAACAAAAAGG
286279 GTGACTTTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.24
Consensus pattern (27 bp):
ATTTTTGACAAACAAAAAGGAACCACC
Found at i:290756 original size:24 final size:24
Alignment explanation
Indices: 290728--290773 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
290718 AATAAAAATT
290728 AGCCACCAATTTTAACAAACAATA
1 AGCCACCAATTTTAACAAACAATA
* *
290752 AGCCACCATTTTTGACAAACAA
1 AGCCACCAATTTTAACAAACAA
290774 AAAGGAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.07, T:0.22
Consensus pattern (24 bp):
AGCCACCAATTTTAACAAACAATA
Found at i:290792 original size:27 final size:27
Alignment explanation
Indices: 290730--290833 Score: 124
Period size: 27 Copynumber: 3.9 Consensus size: 27
290720 TAAAAATTAG
* * *
290730 CCACCAATTTTAACAAACAATAA-G--
1 CCACCATTTTTGACAAACAAAAAGGAA
290754 CCACCATTTTTGACAAACAAAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
* * *
290781 CCACAATTTTTGAAAAACACAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
290808 CCACCATTTTTGACAAACATAAAAGG
1 CCACCATTTTTGACAAACA-AAAAGG
290834 TGGCTTTTGT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
24 20 0.30
25 1 0.01
27 41 0.61
28 5 0.07
ACGTcount: A:0.48, C:0.22, G:0.10, T:0.20
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGGAA
Found at i:295168 original size:2 final size:2
Alignment explanation
Indices: 295163--295188 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
295153 GAATATATTT
295163 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
295189 ATGTAATATA
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):
TA
Found at i:295847 original size:16 final size:16
Alignment explanation
Indices: 295826--295856 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
295816 TCTCTTTTAA
295826 TTATATATCAATATAC
1 TTATATATCAATATAC
*
295842 TTATATATCGATATA
1 TTATATATCAATATA
295857 TACGTCACTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (16 bp):
TTATATATCAATATAC
Found at i:296293 original size:16 final size:16
Alignment explanation
Indices: 296256--296298 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
296246 TTCTTAAATT
*
296256 TAATAAAAAA-TAATA
1 TAATAAAAAATTAAAA
*
296271 TATTAAAAAATTAAAA
1 TAATAAAAAATTAAAA
296287 TAATAAATAAAT
1 TAATAAA-AAAT
296299 AATTTTTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 9 0.39
16 10 0.43
17 4 0.17
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATAAAAAATTAAAA
Found at i:297771 original size:18 final size:18
Alignment explanation
Indices: 297750--297784 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
297740 ATTATAAAAT
297750 ATATTAATAATATATTTA
1 ATATTAATAATATATTTA
**
297768 ATATTCTTAATATATTT
1 ATATTAATAATATATTT
297785 TTAATAATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTAATAATATATTTA
Found at i:302266 original size:4 final size:4
Alignment explanation
Indices: 302247--302293 Score: 67
Period size: 4 Copynumber: 11.0 Consensus size: 4
302237 ATTGAACAAT
302247 ATAA ATAAA ATAAA ATAA ATAAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA AT-AA AT-AA ATAA AT-AA ATAA ATAA ATAA ATAA ATAA ATAA
302294 TCAAATGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 28 0.68
5 13 0.32
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:303469 original size:21 final size:23
Alignment explanation
Indices: 303429--303474 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
303419 TAATATATGG
* *
303429 AAAATTATTTCATATTAAAATTA
1 AAAATTAATTCATATTAAAAATA
303452 AAAATTAATT-AT-TTAAAAATA
1 AAAATTAATTCATATTAAAAATA
303473 AA
1 AA
303475 TATAAAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 2 0.10
23 9 0.43
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
AAAATTAATTCATATTAAAAATA
Found at i:306870 original size:206 final size:206
Alignment explanation
Indices: 306488--307085 Score: 829
Period size: 206 Copynumber: 2.9 Consensus size: 206
306478 CCAATAGTAT
* ** * * ** * *
306488 CAACATCTTAATGCCATAGACTTTCAATCTATCCAGCTCGACATCCAGTGAGCTCTAAATTCCTG
1 CAACATCTT-ATGCAATAGACTAAC-ACCTATCCAGCTTGACATCCAGAAAGCTCTAAGTTCATG
* * * *
306553 ACAATGTAGAGGCTGGTATCAAGTTTGA-GAGGGTTATAGACACTACTTGAAGGTTATAGACTTC
64 ACAATGGAAAGGCTGGTATCGAGTTT-ACGAGGCTTATAGACACTACTTGAAGGTTATAGACTTC
* ** *
306617 AGAACCTGAAAGGTGACCTACATGCCCTTCGTGGTACTGTTCCAATGATATAAAACCCCATCACA
128 AGAACCTGAAAGGTGACCTACATGCCCTTTGCAGTACTGTTCCAATGATATAAAACCCCACCACA
** *
306682 GTGTAAATATTTAC
193 GCATAAACATTTAC
* *
306696 CAACTTCTTATGCAATAGACTAACACCTATCCAGCTTGACATCCAGCAAGCTCTAAGTTCATGAC
1 CAACATCTTATGCAATAGACTAACACCTATCCAGCTTGACATCCAGAAAGCTCTAAGTTCATGAC
* *
306761 AATGGAAAGGCTGGTATCGAGTTTACGAGGTTTATAGACACTACTTTAAGGTTATAGACTTCAGA
66 AATGGAAAGGCTGGTATCGAGTTTACGAGGCTTATAGACACTACTTGAAGGTTATAGACTTCAGA
* * **
306826 ACCTGAAAGGTGAGCAACATGCCCTTTGCAGTACTGTTCCAATGATATAAAACCCCACCATGGCA
131 ACCTGAAAGGTGACCTACATGCCCTTTGCAGTACTGTTCCAATGATATAAAACCCCACCACAGCA
306891 TAAACATTTAC
196 TAAACATTTAC
* * * *
306902 CAACATCTTATGCCATAGACTTACACCTATCCAGCTTGACATCCGGAAAGCTCTACGTTCATGAC
1 CAACATCTTATGCAATAGACTAACACCTATCCAGCTTGACATCCAGAAAGCTCTAAGTTCATGAC
* *
306967 AATGGAAAGGCTGGTATTGAGTTGACGAGGCTTATAGACACTACTTGAAGGTTATAGACTTCAGA
66 AATGGAAAGGCTGGTATCGAGTTTACGAGGCTTATAGACACTACTTGAAGGTTATAGACTTCAGA
* * *
307032 ACCTGAAAGGTGACCTACTTGCCCTTTGCAGTACTGTTCCATTGCTATAAAACC
131 ACCTGAAAGGTGACCTACATGCCCTTTGCAGTACTGTTCCAATGATATAAAACC
307086 TGATCACGGC
Statistics
Matches: 348, Mismatches: 41, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
205 1 0.00
206 327 0.94
207 12 0.03
208 8 0.02
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (206 bp):
CAACATCTTATGCAATAGACTAACACCTATCCAGCTTGACATCCAGAAAGCTCTAAGTTCATGAC
AATGGAAAGGCTGGTATCGAGTTTACGAGGCTTATAGACACTACTTGAAGGTTATAGACTTCAGA
ACCTGAAAGGTGACCTACATGCCCTTTGCAGTACTGTTCCAATGATATAAAACCCCACCACAGCA
TAAACATTTAC
Found at i:308417 original size:44 final size:48
Alignment explanation
Indices: 308368--308459 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 48
308358 TATATTATTT
*
308368 ATAATTAAATTTAAA-TAAA-AAATAAAATTT-TAAT-TATTTAAATA
1 ATAATTAAAGTTAAATTAAATAAATAAAATTTATAATCTATTTAAATA
* *
308412 ATAATTCAAGTTAAATTAAATAAATAAAATTTATTATCTATTTAAATA
1 ATAATTAAAGTTAAATTAAATAAATAAAATTTATAATCTATTTAAATA
308460 GTAAAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
44 13 0.32
45 4 0.10
46 11 0.27
47 3 0.07
48 10 0.24
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (48 bp):
ATAATTAAAGTTAAATTAAATAAATAAAATTTATAATCTATTTAAATA
Found at i:310069 original size:87 final size:87
Alignment explanation
Indices: 309903--310073 Score: 263
Period size: 87 Copynumber: 2.0 Consensus size: 87
309893 TTCATTAGGC
** *
309903 TCTTTAGCTACAATTCACCATGTGGGACACCTTGTTAAAGACTGAGCTCTTTAAGTGCTTTGATA
1 TCTTTAGCTACAATTCACCAAATGGGACACCTTGCTAAAGACTGAGCTCTTTAAGTGCTTTGATA
309968 TGTTATGTTATGCTGCCCAGGT
66 TGTTATGTTATGCTGCCCAGGT
* * * *
309990 TCTTTAGCTATGAATTCACCAAATGGGACACCTTGCTAACGATTGAGCTCTTT-AGTGGTTTGAT
1 TCTTTAGCTA-CAATTCACCAAATGGGACACCTTGCTAAAGACTGAGCTCTTTAAGTGCTTTGAT
310054 ATGTTATGTTATGCTGCCCA
65 ATGTTATGTTATGCTGCCCA
310074 TTTGTGAGAG
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
87 40 0.53
88 36 0.47
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.37
Consensus pattern (87 bp):
TCTTTAGCTACAATTCACCAAATGGGACACCTTGCTAAAGACTGAGCTCTTTAAGTGCTTTGATA
TGTTATGTTATGCTGCCCAGGT
Found at i:311886 original size:2 final size:2
Alignment explanation
Indices: 311879--311907 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
311869 TGAAATGAGA
311879 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 A
311908 CTCGAGTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:315213 original size:26 final size:23
Alignment explanation
Indices: 315145--315213 Score: 57
Period size: 28 Copynumber: 2.7 Consensus size: 23
315135 TAAGATTTTA
315145 ATATATTTAATAATTAAAAAATT
1 ATATATTTAATAATTAAAAAATT
*
315168 ATTTATATTAGTATAAAATTAAATTAAATT
1 A--TATATT--TA-ATAATTAAA--AAATT
315198 ATATATTTACATAATT
1 ATATATTTA-ATAATT
315214 TTATATATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
23 1 0.03
25 6 0.17
26 7 0.19
27 2 0.06
28 14 0.39
30 6 0.17
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (23 bp):
ATATATTTAATAATTAAAAAATT
Found at i:319213 original size:30 final size:30
Alignment explanation
Indices: 319177--319240 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
319167 CTTTCTTAAA
*
319177 ATTTTTTAATATAATTA-TTTTTAA-CTATTT
1 ATTTTTT-ATATAA-AAGTTTTTAAGCTATTT
*
319207 ATTTTTTATTTAAAAGTTTTTAAGCTATTT
1 ATTTTTTATATAAAAGTTTTTAAGCTATTT
319237 ATTT
1 ATTT
319241 GGTTACTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 12 0.40
30 17 0.57
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (30 bp):
ATTTTTTATATAAAAGTTTTTAAGCTATTT
Found at i:321269 original size:15 final size:16
Alignment explanation
Indices: 321221--321274 Score: 67
Period size: 15 Copynumber: 3.4 Consensus size: 16
321211 AAGATAAGAT
321221 TTTTATAATTTAAATAA
1 TTTT-TAATTTAAATAA
*
321238 -ATTTAATTTAAATTAA
1 TTTTTAATTTAAA-TAA
321254 TTTTTAA-TTAAATAA
1 TTTTTAATTTAAATAA
321269 TTTTTA
1 TTTTTA
321275 TTATAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 18 0.55
16 10 0.30
17 5 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTTAATTTAAATAA
Found at i:321281 original size:16 final size:15
Alignment explanation
Indices: 321228--321281 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
321218 GATTTTTATA
* *
321228 ATTTAAATAAATTTA
1 ATTTAAATAATTTTT
321243 ATTTAAATTAATTTTT
1 ATTTAAA-TAATTTTT
*
321259 AATTAAATAATTTTT
1 ATTTAAATAATTTTT
321274 ATTATAAA
1 ATT-TAAA
321282 ATTATATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 17 0.52
16 16 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTAAATAATTTTT
Found at i:321290 original size:22 final size:22
Alignment explanation
Indices: 321259--321305 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
321249 ATTAATTTTT
* * *
321259 AATTAAATAATTTTTATTATAA
1 AATTAAATAAATATTAATATAA
*
321281 AATTATATAAATATTAATATAA
1 AATTAAATAAATATTAATATAA
321303 AAT
1 AAT
321306 AATTTTTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTAAATAAATATTAATATAA
Found at i:321466 original size:7 final size:7
Alignment explanation
Indices: 321451--321485 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
321441 TGAGAAATAG
321451 TTATCTAT
1 TTAT-TAT
321459 TTATTAT
1 TTATTAT
321466 TTATTAT
1 TTATTAT
321473 TTATTTAT
1 TTA-TTAT
321481 TTATT
1 TTATT
321486 TATATTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 15 0.58
8 11 0.42
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (7 bp):
TTATTAT
Found at i:321469 original size:4 final size:4
Alignment explanation
Indices: 321451--321488 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
321441 TGAGAAATAG
*
321451 TTAT CTAT TTA- TTAT TTA- TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
321489 ATTAAAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 6 0.20
4 24 0.80
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:321491 original size:18 final size:18
Alignment explanation
Indices: 321451--321488 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
321441 TGAGAAATAG
*
321451 TTATCTATTTATTATTTA
1 TTATTTATTTATTATTTA
321469 TTATTTATTTATTTATTTA
1 TTATTTATTTA-TTATTTA
321488 T
1 T
321489 ATTAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTTATTTATTATTTA
Found at i:321793 original size:22 final size:25
Alignment explanation
Indices: 321765--321816 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
321755 AGTGTCTTTA
321765 AATTTTTT-TA-AAAA-AATTAA-TT
1 AATTTTTTATATAAAACAA-TAACTT
321787 AATTTTTTATATAAAACAATAACTT
1 AATTTTTTATATAAAACAATAACTT
321812 AATTT
1 AATTT
321817 AAAGAGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 8 0.31
23 2 0.08
24 7 0.27
25 9 0.35
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (25 bp):
AATTTTTTATATAAAACAATAACTT
Found at i:322051 original size:21 final size:21
Alignment explanation
Indices: 322022--322073 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
322012 GGGATTTTTT
* *
322022 ATTTGATTTTTATTAAATTTG
1 ATTTAATTTTTATAAAATTTG
322043 ATTTAATTTTTATAAAATTTG
1 ATTTAATTTTTATAAAATTTG
322064 ATTTAATTTT
1 ATTTAATTTT
322074 AAGTTGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.62
Consensus pattern (21 bp):
ATTTAATTTTTATAAAATTTG
Found at i:322349 original size:5 final size:5
Alignment explanation
Indices: 322339--322407 Score: 56
Period size: 5 Copynumber: 14.2 Consensus size: 5
322329 TTATTTATTT
** *
322339 TTTAA TTTAA TTTAA TTTAA TTTAA AATAA TTTTTCA TTT-A TTT-- TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA --TTTAA TTTAA TTTAA TTTAA
*
322388 -TTAA TTAAA TTTAA TTTAA T
1 TTTAA TTTAA TTTAA TTTAA T
322408 ATAAAATTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
3 3 0.06
4 8 0.15
5 39 0.75
7 2 0.04
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (5 bp):
TTTAA
Found at i:323325 original size:23 final size:24
Alignment explanation
Indices: 323277--323331 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
323267 CTTTTATTTC
323277 AAATTAAAATTAAATTATAAAAAAA
1 AAATTAAAA-TAAATTATAAAAAAA
*
323302 AAATTAAAA-AAATT-TAAATTAAA
1 AAATTAAAATAAATTATAAA-AAAA
323325 AAATTAA
1 AAATTAA
323332 TCACAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 4 0.14
23 15 0.54
25 9 0.32
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (24 bp):
AAATTAAAATAAATTATAAAAAAA
Found at i:323329 original size:14 final size:15
Alignment explanation
Indices: 323282--323327 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
323272 ATTTCAAATT
323282 AAAA-TTAAATTATAA
1 AAAATTTAAATTA-AA
*
323297 AAAA--AAAATTAAA
1 AAAATTTAAATTAAA
323310 AAAATTTAAATTAAA
1 AAAATTTAAATTAAA
323325 AAA
1 AAA
323328 TTAATCACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 6 0.22
14 6 0.22
15 15 0.56
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATTTAAATTAAA
Found at i:324227 original size:18 final size:17
Alignment explanation
Indices: 324195--324228 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
324185 TTACTTTCCT
*
324195 TTTTAATTTTGTAAATA
1 TTTTAATTTTATAAATA
324212 TTTTAATTATTATAAAT
1 TTTTAATT-TTATAAAT
324229 TGACATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTTAATTTTATAAATA
Found at i:324578 original size:24 final size:22
Alignment explanation
Indices: 324551--324603 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 22
324541 TAAAATATTA
*
324551 AAATATAATAAATTATTATTAATT
1 AAATATAATAAATTAAT-TTAA-T
324575 AAAT-TCAATAAATTAATTTAAT
1 AAATAT-AATAAATTAATTTAAT
324597 AAATATA
1 AAATATA
324604 TTTTATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 6 0.23
23 6 0.23
24 14 0.54
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATATAATAAATTAATTTAAT
Found at i:324715 original size:10 final size:10
Alignment explanation
Indices: 324697--324760 Score: 65
Period size: 10 Copynumber: 6.4 Consensus size: 10
324687 AAATGTAAAA
*
324697 AATAAAAATT
1 AATATAAATT
* *
324707 TATATAAATC
1 AATATAAATT
*
324717 AATATATATT
1 AATATAAATT
*
324727 AGTATAAATT
1 AATATAAATT
* *
324737 GATATAAAAT
1 AATATAAATT
324747 AATATAAATT
1 AATATAAATT
324757 AATA
1 AATA
324761 AAAAAATAAA
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
10 41 1.00
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (10 bp):
AATATAAATT
Found at i:324741 original size:20 final size:20
Alignment explanation
Indices: 324729--324768 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
324719 TATATATTAG
324729 TATAAATTGATATAAAATAA
1 TATAAATTGATATAAAATAA
*
324749 TATAAATT-A-ATAAAAAAA
1 TATAAATTGATATAAAATAA
324767 TA
1 TA
324769 AAAAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 1 0.05
20 8 0.42
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
TATAAATTGATATAAAATAA
Found at i:325661 original size:3 final size:3
Alignment explanation
Indices: 325653--325683 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
325643 AGAGGTTTGA
*
325653 TTC TTC TTC TTC TTC CTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
325684 ACTTGTGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:330457 original size:2 final size:2
Alignment explanation
Indices: 330450--330491 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
330440 GAAACTGCTT
*
330450 GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
330492 ACACTATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Done.