Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold332
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: 507797
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.32
Warning! 15717 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:606 original size:125 final size:125
Alignment explanation
Indices: 465--736 Score: 535
Period size: 125 Copynumber: 2.2 Consensus size: 125
455 TTATTATATT
465 ATTATATTAAATTATGTAAATATCATTTATTGTTATAATAATTTTAAAAATATTCCATATATTAT
1 ATTATATTAAATTATGTAAATATCATTTATTGTTATAATAATTTTAAAAATATTCCATATATTAT
530 TTTTATAAATAATTTATATTAATTACTTAAAAATTATTTAAAATGTATATTTCATGTATA
66 TTTTATAAATAATTTATATTAATTACTTAAAAATTATTTAAAATGTATATTTCATGTATA
590 ATTATATTAAATTATGTAAATATCATTTATTGTTATAATAATTTTAAAAATATTCCATATATTAT
1 ATTATATTAAATTATGTAAATATCATTTATTGTTATAATAATTTTAAAAATATTCCATATATTAT
655 TTTTATAAATAATTTATATTAATTACTTAAAAATTATTTAAAATGTATATTTCATGTATA
66 TTTTATAAATAATTTATATTAATTACTTAAAAATTATTTAAAATGTATATTTCATGTATA
*
715 ATTATATTAAATTATTTAAATA
1 ATTATATTAAATTATGTAAATA
737 ACATCTAAGT
Statistics
Matches: 146, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
125 146 1.00
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.50
Consensus pattern (125 bp):
ATTATATTAAATTATGTAAATATCATTTATTGTTATAATAATTTTAAAAATATTCCATATATTAT
TTTTATAAATAATTTATATTAATTACTTAAAAATTATTTAAAATGTATATTTCATGTATA
Found at i:1351 original size:16 final size:16
Alignment explanation
Indices: 1330--1361 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1320 AAAAAATATT
*
1330 TATTTATTTTTTATAG
1 TATTTAATTTTTATAG
1346 TATTTAATTTTTATAG
1 TATTTAATTTTTATAG
1362 AATATTGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (16 bp):
TATTTAATTTTTATAG
Found at i:4287 original size:34 final size:34
Alignment explanation
Indices: 4221--4287 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
4211 TAATGGCAGC
* *
4221 TATTCCCAGATTTTTCATTCCAGAAGTCAAAAGA
1 TATTCCCAGATTTTTCATTCCACAAGTAAAAAGA
* *
4255 TATTCCCAGA-TTTTCCTTCCACCAGTTAAAAAG
1 TATTCCCAGATTTTTCATTCCACAAG-TAAAAAG
4288 CTCAACTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 12 0.43
34 16 0.57
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (34 bp):
TATTCCCAGATTTTTCATTCCACAAGTAAAAAGA
Found at i:8354 original size:13 final size:13
Alignment explanation
Indices: 8336--8362 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8326 TCATTCATTT
8336 ATTATGGTTCTGA
1 ATTATGGTTCTGA
8349 ATTATGGTTCTGA
1 ATTATGGTTCTGA
8362 A
1 A
8363 GTAATGGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.07, G:0.22, T:0.44
Consensus pattern (13 bp):
ATTATGGTTCTGA
Found at i:10763 original size:21 final size:23
Alignment explanation
Indices: 10728--10779 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
10718 TTCCAGATTA
10728 TTTCTCTCCTATTTCTCCTTTCC
1 TTTCTCTCCTATTTCTCCTTTCC
* *
10751 TTTCTC-CCT-TTTCTTCTTTCT
1 TTTCTCTCCTATTTCTCCTTTCC
*
10772 TTTTTCTC
1 TTTCTCTC
10780 ACAGCAGCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 15 0.60
22 4 0.16
23 6 0.24
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTCTCTCCTATTTCTCCTTTCC
Found at i:20351 original size:44 final size:45
Alignment explanation
Indices: 20286--20376 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
20276 ACCTCTATTC
* * *
20286 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
20330 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
20375 CA
1 CA
20377 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:20378 original size:16 final size:16
Alignment explanation
Indices: 20357--20392 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
20347 GATTAGCTAT
20357 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
20373 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
20389 TACA
1 TACA
20393 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:23452 original size:30 final size:31
Alignment explanation
Indices: 23413--23472 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
23403 GGAGATAGGA
*
23413 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
*
23444 TGGG-AGGGAGTAAAAATTTTAGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
23473 TAAAAGGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:47913 original size:25 final size:25
Alignment explanation
Indices: 47879--47927 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
47869 TTCTTCATTC
47879 AACATAATTTCCTATCAATTAAGCA
1 AACATAATTTCCTATCAATTAAGCA
*
47904 AACATAATTTCCTATCGATTAAGC
1 AACATAATTTCCTATCAATTAAGC
47928 TATCATTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (25 bp):
AACATAATTTCCTATCAATTAAGCA
Found at i:50482 original size:11 final size:13
Alignment explanation
Indices: 50466--50497 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
50456 AATTTTACGG
50466 AAAAATTTTG-T-
1 AAAAATTTTGTTC
50477 AAAAATTTTGTTC
1 AAAAATTTTGTTC
50490 AAAAATTT
1 AAAAATTT
50498 CGACGTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 10 0.53
12 1 0.05
13 8 0.42
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (13 bp):
AAAAATTTTGTTC
Found at i:50531 original size:66 final size:67
Alignment explanation
Indices: 50445--50578 Score: 261
Period size: 66 Copynumber: 2.0 Consensus size: 67
50435 TGTTATATTT
50445 TTATGGTCTACAATTTTACGGAAAAATTTTGTAAAAATTTTGTTCAAAAATTTCGACGTTTGGGC
1 TTATGGTCTACAATTTTACGGAAAAATTTTGTAAAAATTTTGTTCAAAAATTTCGACGTTTGGGC
50510 AC
66 AC
50512 TTATGGTCTA-AATTTTACGGAAAAATTTTGTAAAAATTTTGTTCAAAAATTTCGACGTTTGGGC
1 TTATGGTCTACAATTTTACGGAAAAATTTTGTAAAAATTTTGTTCAAAAATTTCGACGTTTGGGC
50576 AC
66 AC
50578 T
1 T
50579 CAATTTAGTA
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
66 57 0.85
67 10 0.15
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (67 bp):
TTATGGTCTACAATTTTACGGAAAAATTTTGTAAAAATTTTGTTCAAAAATTTCGACGTTTGGGC
AC
Found at i:50548 original size:11 final size:13
Alignment explanation
Indices: 50532--50563 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
50522 AATTTTACGG
50532 AAAAATTTTG-T-
1 AAAAATTTTGTTC
50543 AAAAATTTTGTTC
1 AAAAATTTTGTTC
50556 AAAAATTT
1 AAAAATTT
50564 CGACGTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 10 0.53
12 1 0.05
13 8 0.42
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (13 bp):
AAAAATTTTGTTC
Found at i:56227 original size:8 final size:8
Alignment explanation
Indices: 56214--56279 Score: 50
Period size: 8 Copynumber: 8.4 Consensus size: 8
56204 TAAAAAATAT
56214 ATATTATA
1 ATATTATA
56222 ATATTATA
1 ATATTATA
56230 ATATTAT-
1 ATATTATA
*
56237 ATCTTA-A
1 ATATTATA
*
56244 TTATTA-A
1 ATATTATA
*
56251 GTATATATATT
1 --ATAT-TATA
56262 ATATTAT-
1 ATATTATA
56269 ATATTATA
1 ATATTATA
56277 ATA
1 ATA
56280 AGTAGATATA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
7 17 0.36
8 21 0.45
9 7 0.15
10 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (8 bp):
ATATTATA
Found at i:56264 original size:7 final size:7
Alignment explanation
Indices: 56211--56276 Score: 53
Period size: 7 Copynumber: 8.6 Consensus size: 7
56201 AGTTAAAAAA
56211 TATATAT
1 TATATAT
56218 TATAATAT
1 TAT-ATAT
56226 TATAATAT
1 TAT-ATAT
*
56234 TATATCT
1 TATATAT
56241 TA-ATTAT
1 TATA-TAT
56248 TAAGTATAT
1 T-A-TATAT
56257 ATATTATAT
1 -TA-TATAT
56266 TATATAT
1 TATATAT
56273 TATA
1 TATA
56277 ATAAGTAGAT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
6 1 0.02
7 20 0.40
8 18 0.36
9 9 0.18
10 2 0.04
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (7 bp):
TATATAT
Found at i:56289 original size:30 final size:32
Alignment explanation
Indices: 56230--56289 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 32
56220 TAATATTATA
* * *
56230 ATATTATATCTTAATTATTAAGTATATATATT
1 ATATTATATATTAATTAATAAGTAGATATATT
56262 ATATTATATATT-A-TAATAAGTAGATATA
1 ATATTATATATTAATTAATAAGTAGATATA
56290 ATAAATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 13 0.52
31 1 0.04
32 11 0.44
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (32 bp):
ATATTATATATTAATTAATAAGTAGATATATT
Found at i:57225 original size:41 final size:40
Alignment explanation
Indices: 57180--57315 Score: 111
Period size: 37 Copynumber: 3.5 Consensus size: 40
57170 TGACTTTGAC
* *
57180 TCGATGAGACACTGGGCGTCAATTTATTACTTTGGATTAAT
1 TCGATGAGACACTGGGTGTCAA-TTATTACTTTGGATTAAG
* * * * *
57221 TCGATGAGGCACAGGGTGTGAA-T-TTAC-TTGGGTTTAG
1 TCGATGAGACACTGGGTGTCAATTATTACTTTGGATTAAG
* * *
57258 CCGATGAGACACTGGGTGTCAAATTATTACTTCGAATT-A-
1 TCGATGAGACACTGGGTGTC-AATTATTACTTTGGATTAAG
*
57297 TCTGATGAGGCACTGGGTG
1 TC-GATGAGACACTGGGTG
57316 CTAAATTGGT
Statistics
Matches: 74, Mismatches: 16, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
37 23 0.31
38 6 0.08
39 3 0.04
40 20 0.27
41 22 0.30
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGTCAATTATTACTTTGGATTAAG
Found at i:57304 original size:40 final size:40
Alignment explanation
Indices: 57182--57315 Score: 114
Period size: 40 Copynumber: 3.4 Consensus size: 40
57172 ACTTTGACTC
* * *
57182 GATGAGACACTGGGCGTCAATTTATTACTTTGGATTAAT-T
1 GATGAGACACTGGGTGTCAAATTATTACTTCGGATT-ATCT
* * * * * * *
57222 CGATGAGGCACAGGGTGT-GAA-T-TTACTTGGGTTTAGCC
1 -GATGAGACACTGGGTGTCAAATTATTACTTCGGATTATCT
*
57260 GATGAGACACTGGGTGTCAAATTATTACTTCGAATTATCT
1 GATGAGACACTGGGTGTCAAATTATTACTTCGGATTATCT
*
57300 GATGAGGCACTGGGTG
1 GATGAGACACTGGGTG
57316 CTAAATTGGT
Statistics
Matches: 71, Mismatches: 18, Indels: 9
0.72 0.18 0.09
Matches are distributed among these distances:
37 16 0.23
38 12 0.17
39 2 0.03
40 27 0.38
41 14 0.20
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.32
Consensus pattern (40 bp):
GATGAGACACTGGGTGTCAAATTATTACTTCGGATTATCT
Found at i:67362 original size:12 final size:12
Alignment explanation
Indices: 67345--67390 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
67335 TTTTAATAAG
67345 ATTTAATATTAA
1 ATTTAATATTAA
67357 ATTTAATATAATAA
1 ATTTAATAT--TAA
67371 ATATT-ATATT-A
1 AT-TTAATATTAA
67382 ATTTAATAT
1 ATTTAATAT
67391 CTTTTCGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
10 2 0.07
11 7 0.23
12 10 0.33
14 9 0.30
15 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:67388 original size:20 final size:21
Alignment explanation
Indices: 67349--67389 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
67339 AATAAGATTT
67349 AATATTAAATTTAATATAATA
1 AATATTAAATTTAATATAATA
* *
67370 AATATTATA-TTAATTTAATA
1 AATATTAAATTTAATATAATA
67390 TCTTTTCGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATATTAAATTTAATATAATA
Found at i:68264 original size:19 final size:19
Alignment explanation
Indices: 68237--68280 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
68227 ACACATATGT
*
68237 ACTTACCGAAATTCCACTC
1 ACTTTCCGAAATTCCACTC
68256 ACTTTCCGAAATTCCACTC
1 ACTTTCCGAAATTCCACTC
68275 ACTTTC
1 ACTTTC
68281 GCTGCATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.27, C:0.36, G:0.05, T:0.32
Consensus pattern (19 bp):
ACTTTCCGAAATTCCACTC
Found at i:69841 original size:39 final size:39
Alignment explanation
Indices: 69742--70090 Score: 330
Period size: 39 Copynumber: 9.0 Consensus size: 39
69732 TAGAAATACA
* *
69742 GTGATTATTC-GGCTTTGTGCCTAGCACGCTTTGTGCCG
1 GTGATTATTCGGGCTTTGTGCCTAGCAGGCTGTGTGCCG
* * ***
69780 GTGATTGTTTGGGAAGTGTGCCTAGCAGGCTGTGTGCCG
1 GTGATTATTCGGGCTTTGTGCCTAGCAGGCTGTGTGCCG
* * * *
69819 GTGATTATTCAGGCTTTATGCCTAGCAGGCTGTG-ACTAG
1 GTGATTATTCGGGCTTTGTGCCTAGCAGGCTGTGTGC-CG
* * * *
69858 GTCATTATTCGGGCTATGTACCTAGCAGGCTTTTTGTGCCG
1 GTGATTATTCGGGCTTTGTGCCTAGCAGGC--TGTGTGCCG
* * *
69899 GTGATTATTCTGGCTTTGTGCCTAGTAGGCTGTATGCCG
1 GTGATTATTCGGGCTTTGTGCCTAGCAGGCTGTGTGCCG
* * * *
69938 GTGATTATTTGGGCTTTGTGCCTTA-CAGGCTATGAGCAG
1 GTGATTATTCGGGCTTTGTGCC-TAGCAGGCTGTGTGCCG
* * * * * * *
69977 GTGATTATTTGAGCTATGTGCCTAGTAGGCTTTTTGCCT
1 GTGATTATTCGGGCTTTGTGCCTAGCAGGCTGTGTGCCG
*
70016 GTGATTATTCGGGCTCTGTGCCTAGCAGGCTGTGTGCCG
1 GTGATTATTCGGGCTTTGTGCCTAGCAGGCTGTGTGCCG
* * *
70055 GTGA-T-TTCGGGCTATGTGCCTAACAGGTTGTGTGCC
1 GTGATTATTCGGGCTTTGTGCCTAGCAGGCTGTGTGCC
70091 AGTGTATTGG
Statistics
Matches: 248, Mismatches: 56, Indels: 15
0.78 0.18 0.05
Matches are distributed among these distances:
37 28 0.11
38 12 0.05
39 176 0.71
40 2 0.01
41 29 0.12
42 1 0.00
ACGTcount: A:0.14, C:0.19, G:0.31, T:0.36
Consensus pattern (39 bp):
GTGATTATTCGGGCTTTGTGCCTAGCAGGCTGTGTGCCG
Found at i:70040 original size:158 final size:154
Alignment explanation
Indices: 69742--70076 Score: 356
Period size: 158 Copynumber: 2.1 Consensus size: 154
69732 TAGAAATACA
* * *
69742 GTGATTATTCGGCTTTGTGCCTAGCACGCTTTGTGCCGGTGATTGTTTGGGAAGTGTGCCTAGCA
1 GTGATTATTCGGCTTTGTGCCTAGCACGCTGTATGCCGGTGATTATTTGGGAAGTGTGCCTAGCA
* * * *
69807 GGCTGTGTGCCGGTGATTATTCAGGCTTTATGCCTAGCAGGCTGTGACTAGGTCATTATTCGGGC
66 GGCTATGAGCAGGTGATTATTCAGGCTATATGCCTAGCAGGCTGTGACTA-GTCATTATTCGGGC
*
69872 TATGTACCTAGCAGGCTTTTTGTGCCG
130 TATGTACCTAGCAGGC--TGTGTGCCG
* * ***
69899 GTGATTATTCTGGCTTTGTGCCTAGTAGGCTGTATGCCGGTGATTATTTGGGCTTTGTGCCTTA-
1 GTGATTATTC-GGCTTTGTGCCTAGCACGCTGTATGCCGGTGATTATTTGGGAAGTGTGCC-TAG
* * * * * *
69963 CAGGCTATGAGCAGGTGATTATT-TGAGCTATGTGCCTAGTAGGCTTTTTGCCT-GTGATTATTC
64 CAGGCTATGAGCAGGTGATTATTCAG-GCTATATGCCTAGCAGGC--TGTGACTAGTCATTATTC
* *
70026 GGGCTCTGTGCCTAGCAGGCTGTGTGCCG
126 GGGCTATGTACCTAGCAGGCTGTGTGCCG
*
70055 GTGA-T-TTCGGGCTATGTGCCTA
1 GTGATTATTC-GGCTTTGTGCCTA
70077 ACAGGTTGTG
Statistics
Matches: 150, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
154 15 0.10
155 1 0.01
156 12 0.08
157 11 0.07
158 104 0.69
159 2 0.01
160 5 0.03
ACGTcount: A:0.14, C:0.19, G:0.31, T:0.36
Consensus pattern (154 bp):
GTGATTATTCGGCTTTGTGCCTAGCACGCTGTATGCCGGTGATTATTTGGGAAGTGTGCCTAGCA
GGCTATGAGCAGGTGATTATTCAGGCTATATGCCTAGCAGGCTGTGACTAGTCATTATTCGGGCT
ATGTACCTAGCAGGCTGTGTGCCG
Found at i:72767 original size:8 final size:8
Alignment explanation
Indices: 72754--72783 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
72744 TTTTAAAGGT
72754 TAATTAGG
1 TAATTAGG
72762 TAATTAGG
1 TAATTAGG
*
72770 TAATTAAG
1 TAATTAGG
72778 TAATTA
1 TAATTA
72784 AAGTTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (8 bp):
TAATTAGG
Found at i:73602 original size:19 final size:19
Alignment explanation
Indices: 73575--73618 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
73565 ACACATATGT
*
73575 ACTTACCGAAATTCCACTC
1 ACTTTCCGAAATTCCACTC
73594 ACTTTCCGAAATTCCACTC
1 ACTTTCCGAAATTCCACTC
73613 ACTTTC
1 ACTTTC
73619 GCTGCATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.27, C:0.36, G:0.05, T:0.32
Consensus pattern (19 bp):
ACTTTCCGAAATTCCACTC
Found at i:75179 original size:39 final size:39
Alignment explanation
Indices: 75080--75428 Score: 330
Period size: 39 Copynumber: 9.0 Consensus size: 39
75070 TAGAAATACA
* *
75080 GTGATTATTC-GGCTTTGTGCCTAGCACGCTTTGTGCCG
1 GTGATTATTCGGGCTTTGTGCCTAGCAGGCTGTGTGCCG
* * ***
75118 GTGATTGTTTGGGAAGTGTGCCTAGCAGGCTGTGTGCCG
1 GTGATTATTCGGGCTTTGTGCCTAGCAGGCTGTGTGCCG
* * * *
75157 GTGATTATTCAGGCTTTATGCCTAGCAGGCTGTG-ACTAG
1 GTGATTATTCGGGCTTTGTGCCTAGCAGGCTGTGTGC-CG
* * * *
75196 GTCATTATTCGGGCTATGTACCTAGCAGGCTTTTTGTGCCG
1 GTGATTATTCGGGCTTTGTGCCTAGCAGGC--TGTGTGCCG
* * *
75237 GTGATTATTCTGGCTTTGTGCCTAGTAGGCTGTATGCCG
1 GTGATTATTCGGGCTTTGTGCCTAGCAGGCTGTGTGCCG
* * * *
75276 GTGATTATTTGGGCTTTGTGCCTTA-CAGGCTATGAGCAG
1 GTGATTATTCGGGCTTTGTGCC-TAGCAGGCTGTGTGCCG
* * * * * * *
75315 GTGATTATTTGAGCTATGTGCCTAGTAGGCTTTTTGCCT
1 GTGATTATTCGGGCTTTGTGCCTAGCAGGCTGTGTGCCG
*
75354 GTGATTATTCGGGCTCTGTGCCTAGCAGGCTGTGTGCCG
1 GTGATTATTCGGGCTTTGTGCCTAGCAGGCTGTGTGCCG
* * *
75393 GTGA-T-TTCGGGCTATGTGCCTAACAGGTTGTGTGCC
1 GTGATTATTCGGGCTTTGTGCCTAGCAGGCTGTGTGCC
75429 AGTGTATTGG
Statistics
Matches: 248, Mismatches: 56, Indels: 15
0.78 0.18 0.05
Matches are distributed among these distances:
37 28 0.11
38 12 0.05
39 176 0.71
40 2 0.01
41 29 0.12
42 1 0.00
ACGTcount: A:0.14, C:0.19, G:0.31, T:0.36
Consensus pattern (39 bp):
GTGATTATTCGGGCTTTGTGCCTAGCAGGCTGTGTGCCG
Found at i:75378 original size:158 final size:154
Alignment explanation
Indices: 75080--75414 Score: 356
Period size: 158 Copynumber: 2.1 Consensus size: 154
75070 TAGAAATACA
* * *
75080 GTGATTATTCGGCTTTGTGCCTAGCACGCTTTGTGCCGGTGATTGTTTGGGAAGTGTGCCTAGCA
1 GTGATTATTCGGCTTTGTGCCTAGCACGCTGTATGCCGGTGATTATTTGGGAAGTGTGCCTAGCA
* * * *
75145 GGCTGTGTGCCGGTGATTATTCAGGCTTTATGCCTAGCAGGCTGTGACTAGGTCATTATTCGGGC
66 GGCTATGAGCAGGTGATTATTCAGGCTATATGCCTAGCAGGCTGTGACTA-GTCATTATTCGGGC
*
75210 TATGTACCTAGCAGGCTTTTTGTGCCG
130 TATGTACCTAGCAGGC--TGTGTGCCG
* * ***
75237 GTGATTATTCTGGCTTTGTGCCTAGTAGGCTGTATGCCGGTGATTATTTGGGCTTTGTGCCTTA-
1 GTGATTATTC-GGCTTTGTGCCTAGCACGCTGTATGCCGGTGATTATTTGGGAAGTGTGCC-TAG
* * * * * *
75301 CAGGCTATGAGCAGGTGATTATT-TGAGCTATGTGCCTAGTAGGCTTTTTGCCT-GTGATTATTC
64 CAGGCTATGAGCAGGTGATTATTCAG-GCTATATGCCTAGCAGGC--TGTGACTAGTCATTATTC
* *
75364 GGGCTCTGTGCCTAGCAGGCTGTGTGCCG
126 GGGCTATGTACCTAGCAGGCTGTGTGCCG
*
75393 GTGA-T-TTCGGGCTATGTGCCTA
1 GTGATTATTC-GGCTTTGTGCCTA
75415 ACAGGTTGTG
Statistics
Matches: 150, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
154 15 0.10
155 1 0.01
156 12 0.08
157 11 0.07
158 104 0.69
159 2 0.01
160 5 0.03
ACGTcount: A:0.14, C:0.19, G:0.31, T:0.36
Consensus pattern (154 bp):
GTGATTATTCGGCTTTGTGCCTAGCACGCTGTATGCCGGTGATTATTTGGGAAGTGTGCCTAGCA
GGCTATGAGCAGGTGATTATTCAGGCTATATGCCTAGCAGGCTGTGACTAGTCATTATTCGGGCT
ATGTACCTAGCAGGCTGTGTGCCG
Found at i:78105 original size:8 final size:8
Alignment explanation
Indices: 78092--78121 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
78082 TTTTAAAGGT
78092 TAATTAGG
1 TAATTAGG
78100 TAATTAGG
1 TAATTAGG
*
78108 TAATTAAG
1 TAATTAGG
78116 TAATTA
1 TAATTA
78122 AAGTTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (8 bp):
TAATTAGG
Found at i:78577 original size:8 final size:8
Alignment explanation
Indices: 78564--78593 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
78554 TTTTAAAGGT
78564 TAATTAGG
1 TAATTAGG
78572 TAATTAGG
1 TAATTAGG
*
78580 TAATTAAG
1 TAATTAGG
78588 TAATTA
1 TAATTA
78594 AAGTTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (8 bp):
TAATTAGG
Found at i:79601 original size:26 final size:23
Alignment explanation
Indices: 79541--79603 Score: 74
Period size: 26 Copynumber: 2.6 Consensus size: 23
79531 ATCAACTCTT
79541 ATAAGCTTACC-ATTTCAGCTCG
1 ATAAGCTTACCGATTTCAGCTCG
*
79563 ATAGAGCTTACCGTTCTTCAGCTCGG
1 ATA-AGCTTACCGAT-TTCAGCTC-G
79589 AATAAGCTTACCGAT
1 -ATAAGCTTACCGAT
79604 CATGGCTCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 3 0.09
23 8 0.24
24 1 0.03
25 8 0.24
26 11 0.32
27 3 0.09
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.30
Consensus pattern (23 bp):
ATAAGCTTACCGATTTCAGCTCG
Found at i:86856 original size:38 final size:38
Alignment explanation
Indices: 86805--86880 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
86795 CACAAGGGTT
86805 ACCGTTTTGGTCGAGCTCCTGCAATTGTTGCAGACTCA
1 ACCGTTTTGGTCGAGCTCCTGCAATTGTTGCAGACTCA
86843 ACCGTTTTGGTCGAGCTCCTGCAATTGTTGCAGACTCA
1 ACCGTTTTGGTCGAGCTCCTGCAATTGTTGCAGACTCA
86881 CCACAGCTCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (38 bp):
ACCGTTTTGGTCGAGCTCCTGCAATTGTTGCAGACTCA
Found at i:91984 original size:9 final size:9
Alignment explanation
Indices: 91974--92008 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
91964 TTATTTATTC
*
91974 AATTAATTC
1 AATTAATTA
91983 AATTAATTA
1 AATTAATTA
*
91992 AATTAACTA
1 AATTAATTA
92001 AATTAATT
1 AATTAATT
92009 TATCAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (9 bp):
AATTAATTA
Found at i:91997 original size:18 final size:18
Alignment explanation
Indices: 91983--92022 Score: 53
Period size: 21 Copynumber: 2.1 Consensus size: 18
91973 CAATTAATTC
91983 AATTAATTAAATTAACTA
1 AATTAATTAAATTAACTA
92001 AATTAATTTATCAATTAACTA
1 AATTAA-TTA--AATTAACTA
92022 A
1 A
92023 TTTTCTCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 3 0.16
21 10 0.53
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTAATTAAATTAACTA
Found at i:92143 original size:14 final size:14
Alignment explanation
Indices: 92126--92187 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
92116 TCATAATGAC
92126 TAATTAATTTAATT-
1 TAATT-ATTTAATTA
* *
92140 TAATTTTTTAATTT
1 TAATTATTTAATTA
*
92154 TAGTTATTTAATTA
1 TAATTATTTAATTA
*
92168 TAATTAATTAAATTA
1 TAATT-ATTTAATTA
92183 TAATT
1 TAATT
92188 TGAAAATTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
13 7 0.17
14 20 0.50
15 13 0.32
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
TAATTATTTAATTA
Found at i:106924 original size:25 final size:25
Alignment explanation
Indices: 106896--106957 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
106886 ATTGAATCCT
*
106896 TTAAATATTATAAAGATATAAACTA
1 TTAAAAATTATAAAGATATAAACTA
*
106921 TTAAAAATTATAAAGATATAAATTA
1 TTAAAAATTATAAAGATATAAACTA
106946 TTAAAAATTATA
1 TTAAAAATTATA
106958 CTTTGCCACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (25 bp):
TTAAAAATTATAAAGATATAAACTA
Found at i:107508 original size:39 final size:39
Alignment explanation
Indices: 107464--107587 Score: 101
Period size: 39 Copynumber: 3.2 Consensus size: 39
107454 TTTTTTTAAA
107464 TTTCATGAAAAACATATTTTTTTAACGTGAAAAATAATT
1 TTTCATGAAAAACATATTTTTTTAACGTGAAAAATAATT
** * ** *** **
107503 TTTCATTTAAAA-ATA-TATTTTAA-GTTCTATTTTTTTT
1 TTTCATGAAAAACATATTTTTTTAACG-TGAAAAATAATT
107540 AAATTTCATGAAAAACATATTTTTTTAACGTGAAAAATAATT
1 ---TTTCATGAAAAACATATTTTTTTAACGTGAAAAATAATT
107582 TTTCAT
1 TTTCAT
107588 TTCAAAAAGT
Statistics
Matches: 58, Mismatches: 20, Indels: 14
0.63 0.22 0.15
Matches are distributed among these distances:
36 1 0.02
37 12 0.21
38 3 0.05
39 16 0.28
40 10 0.17
41 3 0.05
42 12 0.21
43 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.48
Consensus pattern (39 bp):
TTTCATGAAAAACATATTTTTTTAACGTGAAAAATAATT
Found at i:107529 original size:79 final size:80
Alignment explanation
Indices: 107427--107595 Score: 322
Period size: 79 Copynumber: 2.1 Consensus size: 80
107417 GTTTGTATAT
107427 ATTTAAAAATATATATTTAAGTTCTATTTTTTTTAAATTTCATGAAAAACATATTTTTTTAACGT
1 ATTTAAAAATATATATTTAAGTTCTATTTTTTTTAAATTTCATGAAAAACATATTTTTTTAACGT
107492 GAAAAATAATTTTTC
66 GAAAAATAATTTTTC
107507 ATTTAAAAATATAT-TTTAAGTTCTATTTTTTTTAAATTTCATGAAAAACATATTTTTTTAACGT
1 ATTTAAAAATATATATTTAAGTTCTATTTTTTTTAAATTTCATGAAAAACATATTTTTTTAACGT
107571 GAAAAATAATTTTTC
66 GAAAAATAATTTTTC
107586 ATTTCAAAAA
1 ATTT-AAAAA
107596 GTTGTTTTTT
Statistics
Matches: 88, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
79 69 0.78
80 19 0.22
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.48
Consensus pattern (80 bp):
ATTTAAAAATATATATTTAAGTTCTATTTTTTTTAAATTTCATGAAAAACATATTTTTTTAACGT
GAAAAATAATTTTTC
Found at i:109400 original size:14 final size:14
Alignment explanation
Indices: 109367--109404 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
109357 CATTTAGAAT
*
109367 ATAAATAAGTATTTG
1 ATAAATAA-TATTTA
109382 A-AAATAATATTTA
1 ATAAATAATATTTA
109395 ATAAATAATA
1 ATAAATAATA
109405 AAACACAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 6 0.29
14 14 0.67
15 1 0.05
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (14 bp):
ATAAATAATATTTA
Found at i:109414 original size:24 final size:24
Alignment explanation
Indices: 109387--109433 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
109377 ATTTGAAAAT
109387 AATATTTAATAAATAATAA-AACAC
1 AATATTTAA-AAATAATAATAACAC
*
109411 AATATTTAAAATTAATAATAACA
1 AATATTTAAAAATAATAATAACA
109434 TATGCAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (24 bp):
AATATTTAAAAATAATAATAACAC
Found at i:130155 original size:28 final size:28
Alignment explanation
Indices: 130089--130221 Score: 94
Period size: 28 Copynumber: 4.8 Consensus size: 28
130079 AATATATGAT
* *
130089 AAGGAACACCTTCGTGGTAATCT--AT-A
1 AAGGAA-ACCTTTGTGGTAATCTCCGTAA
* * **
130115 AAGAGACACCTTTGTGGTAATTTTTGTAA
1 AAG-GAAACCTTTGTGGTAATCTCCGTAA
* * *
130144 AAGGAAATCTTTGTGGTGATCTCCGTTA
1 AAGGAAACCTTTGTGGTAATCTCCGTAA
* * *
130172 AAGGAAACCTTTGTGGTGATCTCTGTTA
1 AAGGAAACCTTTGTGGTAATCTCCGTAA
*
130200 AA-GAAAGCCTTTGTGGTGATCT
1 AAGGAAA-CCTTTGTGGTAATCT
130222 TTGGTAAAAA
Statistics
Matches: 89, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
26 17 0.19
27 6 0.07
28 62 0.70
29 4 0.04
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (28 bp):
AAGGAAACCTTTGTGGTAATCTCCGTAA
Found at i:130229 original size:28 final size:28
Alignment explanation
Indices: 130113--130221 Score: 130
Period size: 28 Copynumber: 3.9 Consensus size: 28
130103 TGGTAATCTA
* * * *
130113 TAAAGAGACACCTTTGTGGTAATTTTTGT
1 TAAAG-GAAACCTTTGTGGTGATCTCTGT
* * *
130142 AAAAGGAAATCTTTGTGGTGATCTCCGT
1 TAAAGGAAACCTTTGTGGTGATCTCTGT
130170 TAAAGGAAACCTTTGTGGTGATCTCTGT
1 TAAAGGAAACCTTTGTGGTGATCTCTGT
130198 TAAA-GAAAGCCTTTGTGGTGATCT
1 TAAAGGAAA-CCTTTGTGGTGATCT
130222 TTGGTAAAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
27 4 0.06
28 61 0.88
29 4 0.06
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.36
Consensus pattern (28 bp):
TAAAGGAAACCTTTGTGGTGATCTCTGT
Found at i:130270 original size:29 final size:29
Alignment explanation
Indices: 130124--130319 Score: 131
Period size: 29 Copynumber: 6.9 Consensus size: 29
130114 AAAGAGACAC
* *
130124 CTTTGTGGTAATTTTTG-TAAAAGGAA-A
1 CTTTGTGGTGATCTTTGTTAAAAGGAAGA
**
130151 TCTTTGTGGTGATCTCCGTT-AAAGGAA-A
1 -CTTTGTGGTGATCTTTGTTAAAAGGAAGA
* * *
130179 CCTTTGTGGTGATCTCTGTT-AAAGAAAGC
1 -CTTTGTGGTGATCTTTGTTAAAAGGAAGA
* **
130208 CTTTGTGGTGATCTTTGGTAAAAAAAAGTA
1 CTTTGTGGTGATCTTTGTTAAAAGGAAG-A
130238 -TTTGTGGCT-ATCTTTGTTAAAAGGAAGA
1 CTTTGTGG-TGATCTTTGTTAAAAGGAAGA
* * * * *
130266 CTTTGTGACT-ATCTCTATTAAAAGGATGT
1 CTTTGTG-GTGATCTTTGTTAAAAGGAAGA
*
130295 CTTTGTAGCT-ATCTTTGTTAAAAGG
1 CTTTGT-GGTGATCTTTGTTAAAAGG
130320 GTGCCTTTGT
Statistics
Matches: 138, Mismatches: 22, Indels: 15
0.79 0.13 0.09
Matches are distributed among these distances:
28 63 0.46
29 73 0.53
30 2 0.01
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (29 bp):
CTTTGTGGTGATCTTTGTTAAAAGGAAGA
Found at i:130327 original size:29 final size:29
Alignment explanation
Indices: 130238--130337 Score: 128
Period size: 29 Copynumber: 3.4 Consensus size: 29
130228 AAAAAAAGTA
*
130238 TTTGTGGCTATCTTTGTTAAAAGGAAGAC
1 TTTGTGGCTATCTTTGTTAAAAGGATGAC
* * * *
130267 TTTGTGACTATCTCTATTAAAAGGATGTC
1 TTTGTGGCTATCTTTGTTAAAAGGATGAC
* * *
130296 TTTGTAGCTATCTTTGTTAAAAGGGTGCC
1 TTTGTGGCTATCTTTGTTAAAAGGATGAC
130325 TTTGTGGCTATCT
1 TTTGTGGCTATCT
130338 CAGTTAAATG
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.23, C:0.13, G:0.22, T:0.42
Consensus pattern (29 bp):
TTTGTGGCTATCTTTGTTAAAAGGATGAC
Found at i:130353 original size:29 final size:29
Alignment explanation
Indices: 130152--130355 Score: 98
Period size: 29 Copynumber: 7.1 Consensus size: 29
130142 AAAAGGAAAT
* * *
130152 CTTTGTGG-TGATCTCCGTTAAAGGAA-AC
1 CTTTGTGGCT-ATCTCAGTTAAAAGAATGC
* *
130180 CTTTGTGG-TGATCTCTGTT-AAAGAAAGC
1 CTTTGTGGCT-ATCTCAGTTAAAAGAATGC
** * * * *
130208 CTTTGTGG-TGATCTTTGGTAAAAAAAAGT
1 CTTTGTGGCT-ATCTCAGTTAAAAGAATGC
* ** *
130237 ATTTGTGGCTATCTTTGTTAAAAGGAA-GA
1 CTTTGTGGCTATCTCAGTTAAAA-GAATGC
* * *
130266 CTTTGTGACTATCTCTA-TTAAAAGGATGT
1 CTTTGTGGCTATCTC-AGTTAAAAGAATGC
* ** **
130295 CTTTGTAGCTATCTTTGTTAAAAGGGTGC
1 CTTTGTGGCTATCTCAGTTAAAAGAATGC
*
130324 CTTTGTGGCTATCTCAGTTAAATGAATGC
1 CTTTGTGGCTATCTCAGTTAAAAGAATGC
130353 CTT
1 CTT
130356 GGGGCAAGCT
Statistics
Matches: 140, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
27 5 0.04
28 38 0.27
29 94 0.67
30 3 0.02
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (29 bp):
CTTTGTGGCTATCTCAGTTAAAAGAATGC
Found at i:135267 original size:57 final size:57
Alignment explanation
Indices: 135153--135269 Score: 137
Period size: 57 Copynumber: 2.1 Consensus size: 57
135143 CATTTTCAGG
* * * * *
135153 TCATTTTCATTTTGGAGAAAACCACATTCATTACCAAATGATTCTATTTCTCTATTT
1 TCATTTTCATTTTGGACAAAACCACAATAATTACCAAATGATTCAATTTCTCCATTT
* ** *
135210 TCATTTTCATTTTGGACAAAACCATAATAATTTTCAAATGTTTCCAATTT-TCCATTT
1 TCATTTTCATTTTGGACAAAACCACAATAATTACCAAATGATT-CAATTTCTCCATTT
135267 TCA
1 TCA
135270 CCATTTCTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
57 45 0.90
58 5 0.10
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (57 bp):
TCATTTTCATTTTGGACAAAACCACAATAATTACCAAATGATTCAATTTCTCCATTT
Found at i:138032 original size:16 final size:16
Alignment explanation
Indices: 138007--138040 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
137997 ATCACTATAG
*
138007 TTTCAAAATCTACAGT
1 TTTCAAAATCTAAAGT
*
138023 TTTCAGAATCTAAAGT
1 TTTCAAAATCTAAAGT
138039 TT
1 TT
138041 CATGGTCTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (16 bp):
TTTCAAAATCTAAAGT
Found at i:138099 original size:14 final size:15
Alignment explanation
Indices: 138067--138102 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
138057 CACATTGTAT
*
138067 AGTTTCACAATCTAA
1 AGTTTCACAATCAAA
138082 AGTTTCACAAT-AAA
1 AGTTTCACAATCAAA
138096 AGTTTCA
1 AGTTTCA
138103 GTAAATTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (15 bp):
AGTTTCACAATCAAA
Found at i:147161 original size:17 final size:17
Alignment explanation
Indices: 147135--147182 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
147125 ACAAGAAAAT
*
147135 GGAAGGTGAAAGGTTAA
1 GGAAGATGAAAGGTTAA
*
147152 GGAAGATGAAAGATTAA
1 GGAAGATGAAAGGTTAA
*
147169 GGGAGATGAAAGGT
1 GGAAGATGAAAGGT
147183 GAAAGGTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.40, T:0.17
Consensus pattern (17 bp):
GGAAGATGAAAGGTTAA
Found at i:151371 original size:9 final size:9
Alignment explanation
Indices: 151357--151387 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
151347 GTTAAACGAA
151357 TCGAGTTAT
1 TCGAGTTAT
*
151366 TCGAGTTAA
1 TCGAGTTAT
151375 TCGAGTTAT
1 TCGAGTTAT
151384 TCGA
1 TCGA
151388 ATCAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:151458 original size:9 final size:9
Alignment explanation
Indices: 151441--151477 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
151431 TGAGTTTTCG
151441 AATTCGAAT
1 AATTCGAAT
*
151450 AACTCGAAT
1 AATTCGAAT
151459 AATTCGAAT
1 AATTCGAAT
151468 AATTCGAAT
1 AATTCGAAT
151477 A
1 A
151478 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:153464 original size:17 final size:17
Alignment explanation
Indices: 153438--153482 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
153428 AAAACATGGG
153438 TCACATGGCTGTGTGCC
1 TCACATGGCTGTGTGCC
*
153455 TCACACGGCTGTGTGCC
1 TCACATGGCTGTGTGCC
153472 TCACATGGCTG
1 TCACATGGCTG
153483 AGACACACGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.13, C:0.31, G:0.29, T:0.27
Consensus pattern (17 bp):
TCACATGGCTGTGTGCC
Found at i:154678 original size:31 final size:33
Alignment explanation
Indices: 154613--154680 Score: 86
Period size: 31 Copynumber: 2.1 Consensus size: 33
154603 AACCACATTT
* * *
154613 ATTCATACAATGACATTAGTCATTCAATATTCA
1 ATTCATACAATGACATCAGTCATCCAATACTCA
*
154646 ATTCATA-AAT-ACATCATTCATCCAATACTCA
1 ATTCATACAATGACATCAGTCATCCAATACTCA
154677 ATTC
1 ATTC
154681 TCATCAGTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 21 0.68
32 3 0.10
33 7 0.23
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.35
Consensus pattern (33 bp):
ATTCATACAATGACATCAGTCATCCAATACTCA
Found at i:155002 original size:40 final size:39
Alignment explanation
Indices: 154935--155070 Score: 123
Period size: 40 Copynumber: 3.4 Consensus size: 39
154925 ACCAGTTTGG
* *
154935 CACCCAGTGCCTCATTGGATAATTCGAAGTAATATATTGA
1 CACCCAGTGCCTCATCGGATAAATCGAAGTAATA-ATTGA
* * * *
154975 CACCTAGTGTCTCATCGGCTAAATCGAAGT-A-AATTGG
1 CACCCAGTGCCTCATCGGATAAATCGAAGTAATAATTGA
* * *
155012 CAACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
1 C-ACCCAGTGCCTCATCGGATAAAT-CGAAGTAAT-AATTGA
* *
155054 CACCTAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
155071 ACTCGAAGTT
Statistics
Matches: 76, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
37 5 0.07
38 19 0.25
39 7 0.09
40 25 0.33
41 14 0.18
42 6 0.08
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAAATCGAAGTAATAATTGA
Found at i:155906 original size:4 final size:4
Alignment explanation
Indices: 155893--155934 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
155883 AGCCCTTGTG
*
155893 TTTC -TTC TTTC TTTC TTTC TTTC TTTC TTTT TTTC TTT- TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
155935 CTTTTCCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 6 0.18
4 28 0.82
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:155999 original size:22 final size:21
Alignment explanation
Indices: 155974--156029 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 21
155964 TCTTTCCCTT
155974 TTTATTTCATTTACTTATTATA
1 TTTA-TTCATTTACTTATTATA
155996 TTTA--C-TTTA-TTATTATA
1 TTTATTCATTTACTTATTATA
156013 TTATATAT-ATTTACTTA
1 TT-TAT-TCATTTACTTA
156030 ATTCTTAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
17 10 0.36
18 6 0.21
19 1 0.04
21 4 0.14
22 7 0.25
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATTCATTTACTTATTATA
Found at i:161374 original size:22 final size:23
Alignment explanation
Indices: 161343--161387 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
161333 ATTATTAATG
161343 TAAACATTATGAA-TCTCTACTC
1 TAAACATTATGAATTCTCTACTC
* *
161365 TAAACTTTATGAATTTTCTACTC
1 TAAACATTATGAATTCTCTACTC
161388 ATCATTAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.42
Consensus pattern (23 bp):
TAAACATTATGAATTCTCTACTC
Found at i:171710 original size:87 final size:85
Alignment explanation
Indices: 171539--171759 Score: 275
Period size: 87 Copynumber: 2.5 Consensus size: 85
171529 TTAAGGATGT
* *
171539 AAAAAGTCCTCAAACTTTTTCAAAAAAAGTAATTAAGCCCCT-CTTTTTTTTTTTCACTCAATTG
1 AAAAAGACCTCAAACTTTTTC-AAAAAAGCAATTAAGCCCCTGC----TTTTTTTCACTCAATTG
*
171603 AACACTTGAACTTTCAAAATGCATC
61 AACACTTGAACTGTCAAAATGCATC
* ***
171628 AAAAAGACTCTCAAACTTCTTCAGAAAAAGCAATTAAGCCCCTGCTTTTTTTCACTCAATTGGGT
1 AAAAAGAC-CTCAAACTTTTTCA-AAAAAGCAATTAAGCCCCTGCTTTTTTTCACTCAATTGAAC
171693 ACTTGAACTGTCAAAATGCATC
64 ACTTGAACTGTCAAAATGCATC
*
171715 AAAAAGACCCTC-AACATTTTTCAAAAATGCAATTAAGCCCCTGCT
1 AAAAAGA-CCTCAAAC-TTTTTCAAAAAAGCAATTAAGCCCCTGCT
171760 CTTATTAAAA
Statistics
Matches: 118, Mismatches: 9, Indels: 13
0.84 0.06 0.09
Matches are distributed among these distances:
86 24 0.20
87 54 0.46
88 1 0.01
89 8 0.07
90 30 0.25
91 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (85 bp):
AAAAAGACCTCAAACTTTTTCAAAAAAGCAATTAAGCCCCTGCTTTTTTTCACTCAATTGAACAC
TTGAACTGTCAAAATGCATC
Found at i:171880 original size:21 final size:22
Alignment explanation
Indices: 171837--171880 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
171827 AAATTAAAAA
*
171837 TTTATTAAAAATTAGAAATTTT
1 TTTATTAAAAATTAGAAAATTT
171859 TTTA-TAAAAATT-GTAAAATTT
1 TTTATTAAAAATTAG-AAAATTT
171880 T
1 T
171881 GTAAAAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 15 0.75
22 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
TTTATTAAAAATTAGAAAATTT
Found at i:172154 original size:11 final size:11
Alignment explanation
Indices: 172138--172165 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
172128 TATATTTTAT
172138 ATTTTTTTCTA
1 ATTTTTTTCTA
172149 ATTTTTTTCTA
1 ATTTTTTTCTA
172160 ATTTTT
1 ATTTTT
172166 AATATTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (11 bp):
ATTTTTTTCTA
Found at i:172370 original size:87 final size:88
Alignment explanation
Indices: 172245--172413 Score: 225
Period size: 87 Copynumber: 1.9 Consensus size: 88
172235 AAAAGCATGA
* *
172245 GCTTAATTGCTTTTTTTTTAAAAGTTTGAGGATATTTTTTATACATTTCGAAAGTTAAAGTATC-
1 GCTTAATTGCTTTTTTTTTAAAAGTTTGAGGACATTTTTGATACATTTCGAAAGTTAAAGTA-CA
* *
172309 CAATTGAGTGTAAAAAAAGTAGGG
65 CAAATGAGTGAAAAAAAAGTAGGG
* * * * * *
172333 GCTTAATTGC-TTTTTTTTAAAGGTTTGAGGGCCTTTTTGGTACATTTTGAAAGTTCAAGTACAC
1 GCTTAATTGCTTTTTTTTTAAAAGTTTGAGGACATTTTTGATACATTTCGAAAGTTAAAGTACAC
172397 AAATGAGTGAAAAAAAA
66 AAATGAGTGAAAAAAAA
172414 AAAACAAGAG
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
86 1 0.01
87 59 0.84
88 10 0.14
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (88 bp):
GCTTAATTGCTTTTTTTTTAAAAGTTTGAGGACATTTTTGATACATTTCGAAAGTTAAAGTACAC
AAATGAGTGAAAAAAAAGTAGGG
Found at i:175252 original size:15 final size:15
Alignment explanation
Indices: 175232--175273 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
175222 GATAAACTAA
*
175232 AAAAATTAAGTGTTG
1 AAAAATTAAGTATTG
*
175247 AAAAATTAAATATTG
1 AAAAATTAAGTATTG
*
175262 AAAATTTAAGTA
1 AAAAATTAAGTA
175274 CTAAATTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (15 bp):
AAAAATTAAGTATTG
Found at i:180935 original size:35 final size:35
Alignment explanation
Indices: 180889--180989 Score: 121
Period size: 35 Copynumber: 2.9 Consensus size: 35
180879 CTGTTTGGTG
*
180889 TGTTTTGGTTGGACTAGCTCTTATGAGCATTGGCC
1 TGTTTCGGTTGGACTAGCTCTTATGAGCATTGGCC
* * * *
180924 TGTTTCGGTTGGACTAGCTCTTATAAGTATAGGCG
1 TGTTTCGGTTGGACTAGCTCTTATGAGCATTGGCC
* * * *
180959 TGCTACGGTTGGACTAACTCTTGTGAGCATT
1 TGTTTCGGTTGGACTAGCTCTTATGAGCATT
180990 TGATGTTTTT
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.18, C:0.17, G:0.28, T:0.38
Consensus pattern (35 bp):
TGTTTCGGTTGGACTAGCTCTTATGAGCATTGGCC
Found at i:188412 original size:19 final size:21
Alignment explanation
Indices: 188388--188427 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
188378 AAGAAACGGC
188388 TCTCATGCT-AA-TCTCTCAA
1 TCTCATGCTCAATTCTCTCAA
*
188407 TCTCATGTTCAATTCTCTCAA
1 TCTCATGCTCAATTCTCTCAA
188428 ACCAAAACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 2 0.11
21 8 0.44
ACGTcount: A:0.25, C:0.30, G:0.05, T:0.40
Consensus pattern (21 bp):
TCTCATGCTCAATTCTCTCAA
Found at i:199142 original size:230 final size:230
Alignment explanation
Indices: 198739--199188 Score: 882
Period size: 230 Copynumber: 2.0 Consensus size: 230
198729 TGCCACCATC
*
198739 TCAAGTGCATACAAGTCCCATTTCATGCTATTTTGGGATCTTAATTTAAATAAAGCTTTTTCTTC
1 TCAAGTGCATACAAGTCCCATTTCATGCTATTTTGGGATCTTAATTTAAATAAAACTTTTTCTTC
198804 ATGCAATTAACATAATCCAGAAAACAAGAGGGTAGAAGTAATAACAAGACAATCAGACAACTAAG
66 ATGCAATTAACATAATCCAGAAAACAAGAGGGTAGAAGTAATAACAAGACAATCAGACAACTAAG
*
198869 ATTACTATTCATATCTGACCAAAGAATTTGAGGATTGGAAAAAAAGATCACAGAATCAGTCTTAA
131 ATTACCATTCATATCTGACCAAAGAATTTGAGGATTGGAAAAAAAGATCACAGAATCAGTCTTAA
198934 TTGCTTCAAAAGAAAGGGTAACTGGGATTTTAATT
196 TTGCTTCAAAAGAAAGGGTAACTGGGATTTTAATT
198969 TCAAGTGCATACAAGTCCCATTTCATGCTATTTTGGGATCTTAATTTAAATAAAACTTTTTCTTC
1 TCAAGTGCATACAAGTCCCATTTCATGCTATTTTGGGATCTTAATTTAAATAAAACTTTTTCTTC
199034 ATGCAATTAACATAATCCAGAAAACAAGAGGGTAGAAGTAATAACAAGACAATCAGACAACTAAG
66 ATGCAATTAACATAATCCAGAAAACAAGAGGGTAGAAGTAATAACAAGACAATCAGACAACTAAG
199099 ATTACCATTCATATCTGACCAAAGAATTTGAGGATTGGAAAAAAAGATCACAGAATCAGTCTTAA
131 ATTACCATTCATATCTGACCAAAGAATTTGAGGATTGGAAAAAAAGATCACAGAATCAGTCTTAA
199164 TTGCTTCAAAAGAAAGGGTAACTGG
196 TTGCTTCAAAAGAAAGGGTAACTGG
199189 AGGTAGTTGT
Statistics
Matches: 218, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
230 218 1.00
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.28
Consensus pattern (230 bp):
TCAAGTGCATACAAGTCCCATTTCATGCTATTTTGGGATCTTAATTTAAATAAAACTTTTTCTTC
ATGCAATTAACATAATCCAGAAAACAAGAGGGTAGAAGTAATAACAAGACAATCAGACAACTAAG
ATTACCATTCATATCTGACCAAAGAATTTGAGGATTGGAAAAAAAGATCACAGAATCAGTCTTAA
TTGCTTCAAAAGAAAGGGTAACTGGGATTTTAATT
Found at i:199888 original size:94 final size:94
Alignment explanation
Indices: 199775--199962 Score: 367
Period size: 94 Copynumber: 2.0 Consensus size: 94
199765 AAAAGTAAGA
199775 ACCAAAAAGAATATGAATATGAAAGAAAAAGGAATTTCTCAATTGAAATTCTACCTGATATGAAG
1 ACCAAAAAGAATATGAATATGAAAGAAAAAGGAATTTCTCAATTGAAATTCTACCTGATATGAAG
*
199840 TTCTCAATTGAAAGTTTTAGAGCAATAAC
66 TTCTCAATTGAAAGTCTTAGAGCAATAAC
199869 ACCAAAAAGAATATGAATATGAAAGAAAAAGGAATTTCTCAATTGAAATTCTACCTGATATGAAG
1 ACCAAAAAGAATATGAATATGAAAGAAAAAGGAATTTCTCAATTGAAATTCTACCTGATATGAAG
199934 TTCTCAATTGAAAGTCTTAGAGCAATAAC
66 TTCTCAATTGAAAGTCTTAGAGCAATAAC
199963 TCGTCAAAGG
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 93 1.00
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (94 bp):
ACCAAAAAGAATATGAATATGAAAGAAAAAGGAATTTCTCAATTGAAATTCTACCTGATATGAAG
TTCTCAATTGAAAGTCTTAGAGCAATAAC
Found at i:207916 original size:18 final size:19
Alignment explanation
Indices: 207890--207926 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
207880 AATTTTGGGA
207890 TGGAAAGAAGAGA-GAAAG
1 TGGAAAGAAGAGAGGAAAG
*
207908 TGGAGAGAAGAGAGGAAAG
1 TGGAAAGAAGAGAGGAAAG
207927 ATGTGAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.43, T:0.05
Consensus pattern (19 bp):
TGGAAAGAAGAGAGGAAAG
Found at i:208833 original size:90 final size:90
Alignment explanation
Indices: 208680--208943 Score: 501
Period size: 90 Copynumber: 2.9 Consensus size: 90
208670 AATAAAAACC
208680 CATAAAAATACCCAAATTCAATTTTCTTATAAATTAAAGGCTAAAAATGAAAGCTGATGCGGTTG
1 CATAAAAATACCCAAATTCAATTTTCTTATAAATTAAAGGCTAAAAATGAAAGCTGATGCGGTTG
208745 TGTGGCCATCATCGAGTCCTTTTTA
66 TGTGGCCATCATCGAGTCCTTTTTA
208770 CATAAAAATACCCAAATTCAATTTTCTTATAAATTAAAGGCTAAAAATGAAAGCTGATGCGGTTG
1 CATAAAAATACCCAAATTCAATTTTCTTATAAATTAAAGGCTAAAAATGAAAGCTGATGCGGTTG
208835 TGTGGCCATCATCGAGTCCTTTTTA
66 TGTGGCCATCATCGAGTCCTTTTTA
*
208860 CATAAAAATACCCAAATTCAATTTTCTTATAAATTAAAGGCTAAAAATGAAAGCTGATGTGGTTG
1 CATAAAAATACCCAAATTCAATTTTCTTATAAATTAAAGGCTAAAAATGAAAGCTGATGCGGTTG
* *
208925 TGTAGCCATCATCAAGTCC
66 TGTGGCCATCATCGAGTCC
208944 CTCATAGCAC
Statistics
Matches: 171, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 171 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (90 bp):
CATAAAAATACCCAAATTCAATTTTCTTATAAATTAAAGGCTAAAAATGAAAGCTGATGCGGTTG
TGTGGCCATCATCGAGTCCTTTTTA
Found at i:209728 original size:27 final size:26
Alignment explanation
Indices: 209673--209755 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 26
209663 ACATAAGGCC
*
209673 ATAACAGTCATTTCATCTCCTA-GGGGT
1 ATAACAGTCATTTTA-C-CCTATGGGGT
209700 ATAACAGTCATTTTACCCTATGGGAGT
1 ATAACAGTCATTTTACCCTATGGG-GT
** *
209727 ATTTCGGTCATTTTACCCTATTGGGGT
1 ATAACAGTCATTTTACCCTA-TGGGGT
209754 AT
1 AT
209756 TTTGGTTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.08
26 4 0.08
27 37 0.76
28 4 0.08
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.37
Consensus pattern (26 bp):
ATAACAGTCATTTTACCCTATGGGGT
Found at i:209756 original size:27 final size:27
Alignment explanation
Indices: 209706--209768 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 27
209696 GGGTATAACA
209706 GTCATTTTACCCTATGGGAGTATTTCG
1 GTCATTTTACCCTATGGGAGTATTTCG
*
209733 GTCATTTTACCCTATTGGG-GTATTTTG
1 GTCATTTTACCCTA-TGGGAGTATTTCG
*
209760 GTTATTTTA
1 GTCATTTTA
209769 TCTATTTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 29 0.88
28 4 0.12
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGAGTATTTCG
Found at i:215174 original size:30 final size:30
Alignment explanation
Indices: 215118--215176 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
215108 CTTTTTGAAA
* * *
215118 ATATTTACAAAAAGAGGAATCTAATTTTTT
1 ATATTTACAAAAAGAGCAACCAAATTTTTT
215148 ATATTTACAAAAAGAGCAACCAAATTTTT
1 ATATTTACAAAAAGAGCAACCAAATTTTT
215177 AAAAATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (30 bp):
ATATTTACAAAAAGAGCAACCAAATTTTTT
Found at i:226105 original size:9 final size:9
Alignment explanation
Indices: 226091--226121 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
226081 GTTAAACGAA
226091 TCGAGTTAT
1 TCGAGTTAT
*
226100 TCGAGTTAA
1 TCGAGTTAT
226109 TCGAGTTAT
1 TCGAGTTAT
226118 TCGA
1 TCGA
226122 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:226192 original size:9 final size:9
Alignment explanation
Indices: 226175--226211 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
226165 TGAGTTTTCG
226175 AATTCGAAT
1 AATTCGAAT
*
226184 AACTCGAAT
1 AATTCGAAT
226193 AATTCGAAT
1 AATTCGAAT
226202 AATTCGAAT
1 AATTCGAAT
226211 A
1 A
226212 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:227059 original size:3 final size:3
Alignment explanation
Indices: 227051--227076 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
227041 CTCCTTAGCA
227051 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
227077 CTCCAGTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:231976 original size:37 final size:37
Alignment explanation
Indices: 231913--232097 Score: 106
Period size: 38 Copynumber: 4.7 Consensus size: 37
231903 ATAGTATTAT
* *
231913 ATATTATG-ATTTTAGTAAATTCATATAAGAATATTTA
1 ATATTAAGAATTTTATTAAATT-ATATAAGAATATTTA
**** *
231950 ATATTAAGAATTTTATTAAATTATATATTTTTATTAAATT
1 ATATTAAGAATTTTATTAAATTATATAAGAATATT---TA
* * ***
231990 ATATTTAATAATAATTATGTTAAAATTATAT-TTTATAGTATTA
1 ATA-TTAAGAAT--TT-TATT-AAATTATATAAGAATA-T-TTA
* *
232033 TATATTATG-ATTTTAGTAAATTCATATAAGAATATTTA
1 -ATATTAAGAATTTTATTAAATT-ATATAAGAATATTTA
232071 ATATTAAGAATTTTATTAAATTATATA
1 ATATTAAGAATTTTATTAAATTATATA
232098 TTTTTATTAA
Statistics
Matches: 113, Mismatches: 20, Indels: 30
0.69 0.12 0.18
Matches are distributed among these distances:
37 28 0.25
38 32 0.28
39 7 0.06
40 9 0.08
41 7 0.06
42 2 0.02
43 6 0.05
44 11 0.10
45 10 0.09
46 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (37 bp):
ATATTAAGAATTTTATTAAATTATATAAGAATATTTA
Found at i:232153 original size:121 final size:121
Alignment explanation
Indices: 231723--232136 Score: 812
Period size: 121 Copynumber: 3.4 Consensus size: 121
231713 CAAACTTTAG
*
231723 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAT-TTTAAATTATATTTTATAGT
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAATTATATTTTATAGT
231787 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
66 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
231843 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAATTATATTTTATAGT
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAATTATATTTTATAGT
231908 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
66 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
231964 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAATTATATTTTATAGT
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAATTATATTTTATAGT
232029 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
66 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
232085 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAAT
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAAT
232137 ATTTATTACT
Statistics
Matches: 292, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
120 44 0.15
121 248 0.85
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (121 bp):
ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAATTATATTTTATAGT
ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
Found at i:232316 original size:44 final size:45
Alignment explanation
Indices: 232267--232356 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
232257 ACCTCTATTC
*
232267 CATTCAACCAAAC-ATTAGA-ATACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAATT-GATATACTATTACGCATCTATTCCATTA
* *
232311 CATTCAACCAAACAATTGATTTGCTATTACGCATCTATTCCATTA
1 CATTCAACCAAACAATTGATATACTATTACGCATCTATTCCATTA
232356 C
1 C
232357 GCCTCTATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
44 15 0.37
45 26 0.63
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (45 bp):
CATTCAACCAAACAATTGATATACTATTACGCATCTATTCCATTA
Found at i:232357 original size:16 final size:16
Alignment explanation
Indices: 232336--232400 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
232326 TTGATTTGCT
*
232336 ATTACGCATCTATTCC
1 ATTACGCCTCTATTCC
*
232352 ATTACGCCTCTATTAC
1 ATTACGCCTCTATTCC
232368 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
232384 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
232400 A
1 A
232401 ATACAGCGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.23, C:0.34, G:0.06, T:0.37
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:251917 original size:28 final size:28
Alignment explanation
Indices: 251863--251954 Score: 91
Period size: 27 Copynumber: 3.4 Consensus size: 28
251853 TAAGCATGTG
** *
251863 TTTAAATTTT-CAAGTG-TATCCTTTAT
1 TTTAAATTTTGCTGGTGTTATCATTTAT
251889 TTTAAATTTTGCTGGTGTTATCATTTAT
1 TTTAAATTTTGCTGGTGTTATCATTTAT
* * * * *
251917 TTTGAA-TTTGCTGTTGTTGTCGTTTTT
1 TTTAAATTTTGCTGGTGTTATCATTTAT
251944 TTTAAATTTTG
1 TTTAAATTTTG
251955 TCGTTTGTTA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
26 10 0.19
27 26 0.48
28 18 0.33
ACGTcount: A:0.20, C:0.08, G:0.14, T:0.59
Consensus pattern (28 bp):
TTTAAATTTTGCTGGTGTTATCATTTAT
Found at i:269620 original size:21 final size:21
Alignment explanation
Indices: 269581--269620 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
269571 ATTACATGTT
**
269581 TATATTTTTATTATTTAATAA
1 TATATTTTTATTACGTAATAA
*
269602 TATATTTTTATTCCGTAAT
1 TATATTTTTATTACGTAAT
269621 TATTATAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.60
Consensus pattern (21 bp):
TATATTTTTATTACGTAATAA
Found at i:272824 original size:19 final size:19
Alignment explanation
Indices: 272802--272841 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
272792 TTATATATTA
*
272802 TTTTAATTTGTCTTATATG
1 TTTTAAATTGTCTTATATG
* *
272821 TTTTAAATTGTTTTGTATG
1 TTTTAAATTGTCTTATATG
272840 TT
1 TT
272842 GTTTATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.20, C:0.03, G:0.12, T:0.65
Consensus pattern (19 bp):
TTTTAAATTGTCTTATATG
Found at i:272851 original size:26 final size:26
Alignment explanation
Indices: 272821--272921 Score: 89
Period size: 26 Copynumber: 4.0 Consensus size: 26
272811 GTCTTATATG
** * *
272821 TTTTAAATTGTTTTGTATGTTGTTTA
1 TTTTAAATTGTTTTACATATTATTTA
*
272847 TTTTAATTTGTTTTACATATTATTTA
1 TTTTAAATTGTTTTACATATTATTTA
* *
272873 CTTTAAATTGTTTT--ATACTATTTA
1 TTTTAAATTGTTTTACATATTATTTA
* * * *
272897 CTTCAAATTGTTCTATATATTATTT
1 TTTTAAATTGTTTTACATATTATTT
272922 TGGTTCACTT
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
24 21 0.34
26 41 0.66
ACGTcount: A:0.26, C:0.06, G:0.07, T:0.61
Consensus pattern (26 bp):
TTTTAAATTGTTTTACATATTATTTA
Found at i:272899 original size:24 final size:23
Alignment explanation
Indices: 272843--272917 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 23
272833 TTGTATGTTG
* *
272843 TTTATTTTAATTTGTTTTACATATTA
1 TTTACTTTAAATTGTTTT--ATA-TA
272869 TTTACTTTAAATTGTTTTATACTA
1 TTTACTTTAAATTGTTTTATA-TA
* *
272893 TTTACTTCAAATTGTTCTATATA
1 TTTACTTTAAATTGTTTTATATA
272916 TT
1 TT
272918 ATTTTGGTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
23 4 0.09
24 24 0.55
26 16 0.36
ACGTcount: A:0.28, C:0.08, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTACTTTAAATTGTTTTATATA
Found at i:275006 original size:20 final size:20
Alignment explanation
Indices: 274983--275031 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
274973 CGACTCAAAT
*
274983 AAAATAAAACTAAAA-AGAAC
1 AAAATAAAA-TAAAATAAAAC
275003 AAAAT-AAATAAAATAAAAC
1 AAAATAAAATAAAATAAAAC
275022 ACAAATAAAA
1 A-AAATAAAA
275032 AGTCCATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 5 0.20
19 8 0.32
20 9 0.36
21 3 0.12
ACGTcount: A:0.78, C:0.08, G:0.02, T:0.12
Consensus pattern (20 bp):
AAAATAAAATAAAATAAAAC
Found at i:275848 original size:23 final size:25
Alignment explanation
Indices: 275800--275856 Score: 75
Period size: 23 Copynumber: 2.4 Consensus size: 25
275790 CTATTATTTG
*
275800 ATTTGTTTTTCTTTATTTGTGTATT
1 ATTTGTTTTTCTTAATTTGTGTATT
275825 ATTTGTTTTT-TTAATTT-T-TAATT
1 ATTTGTTTTTCTTAATTTGTGT-ATT
275848 ATTTGTTTT
1 ATTTGTTTT
275857 ATAATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 1 0.03
23 13 0.43
24 6 0.20
25 10 0.33
ACGTcount: A:0.16, C:0.02, G:0.09, T:0.74
Consensus pattern (25 bp):
ATTTGTTTTTCTTAATTTGTGTATT
Found at i:275866 original size:23 final size:23
Alignment explanation
Indices: 275822--275884 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 23
275812 TTATTTGTGT
*
275822 ATTATTTGTTTTTTTAAT-TTTTA
1 ATTATTTG-TTTTATAATATTTTA
275845 ATTATTTGTTTTATAATATTTTA
1 ATTATTTGTTTTATAATATTTTA
275868 A--A--TGTTTTATAATATTT
1 ATTATTTGTTTTATAATATTT
275885 GTTTATTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
19 15 0.39
21 1 0.03
22 8 0.21
23 14 0.37
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (23 bp):
ATTATTTGTTTTATAATATTTTA
Found at i:287249 original size:14 final size:15
Alignment explanation
Indices: 287232--287261 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
287222 CATTATTCAA
287232 AAAATAT-ATTTTAC
1 AAAATATAATTTTAC
287246 AAAATATAATTTTAC
1 AAAATATAATTTTAC
287261 A
1 A
287262 TTTCAAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATATAATTTTAC
Found at i:289329 original size:19 final size:21
Alignment explanation
Indices: 289278--289330 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
289268 AAGGATTGAC
*
289278 AATTTGAGCTACAATATTATT
1 AATTTGAGCTACAATATCATT
*
289299 AATATT-AACTACAATA-CA-T
1 AAT-TTGAGCTACAATATCATT
289318 AATTTGAGCTACA
1 AATTTGAGCTACA
289331 TATTACAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 2 0.07
19 10 0.37
20 1 0.04
21 12 0.44
22 2 0.07
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (21 bp):
AATTTGAGCTACAATATCATT
Found at i:290196 original size:32 final size:32
Alignment explanation
Indices: 290134--290200 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
290124 GAATTTTAAA
290134 TTAGAGTTTAGGTTTTTTTAATTTGTAAGTGT
1 TTAGAGTTTAGGTTTTTTTAATTTGTAAGTGT
290166 TTAG-GTTTAGGGTTTTATTT-ATTT-TCAAGTGT
1 TTAGAGTTTA-GGTTTT-TTTAATTTGT-AAGTGT
290198 TTA
1 TTA
290201 TTAATTATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
31 6 0.19
32 23 0.72
33 3 0.09
ACGTcount: A:0.21, C:0.01, G:0.21, T:0.57
Consensus pattern (32 bp):
TTAGAGTTTAGGTTTTTTTAATTTGTAAGTGT
Found at i:292761 original size:32 final size:32
Alignment explanation
Indices: 292699--292765 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
292689 GAATTTTAAA
292699 TTAGAGTTTAGGTTTTTTTAATTTGTAAGTGT
1 TTAGAGTTTAGGTTTTTTTAATTTGTAAGTGT
292731 TTAG-GTTTAGGGTTTTATTT-ATTT-TCAAGTGT
1 TTAGAGTTTA-GGTTTT-TTTAATTTGT-AAGTGT
292763 TTA
1 TTA
292766 TTAATTATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
31 6 0.19
32 23 0.72
33 3 0.09
ACGTcount: A:0.21, C:0.01, G:0.21, T:0.57
Consensus pattern (32 bp):
TTAGAGTTTAGGTTTTTTTAATTTGTAAGTGT
Found at i:296320 original size:136 final size:136
Alignment explanation
Indices: 296076--296345 Score: 495
Period size: 136 Copynumber: 2.0 Consensus size: 136
296066 ATTTACAATG
* * * *
296076 TGTGAAGACACGTATTCCTACTAGTCCTAGATAAACGTAAGTGGTCGTCTATATTTATTGCTTCG
1 TGTGAAGACACGTATTCCCACTAGTCCCAGATAAACGTAAGTGGTCGTCTATATTGATTGCTCCG
296141 TTTAAGTTCTTACCCGATAGAGAATTGTGTCACAAACCAAAAGGTCAACCGTTCTTGCATAGGCA
66 TTTAAGTTCTTACCCGATAGAGAATTGTGTCACAAACCAAAAGGTCAACCGTTCTTGCATAGGCA
296206 CTGACA
131 CTGACA
296212 TGTGAAGACACGTATTCCCACTAGTCCCAGATAAACGTAAGTGGTCGTCTATATTGATTGCTCCG
1 TGTGAAGACACGTATTCCCACTAGTCCCAGATAAACGTAAGTGGTCGTCTATATTGATTGCTCCG
*
296277 TTTAAGTTCTTACCCGATAGAGAATTGTGTCACAAACCAAAAGGTCAACCGTTCTTGCGTAGGCA
66 TTTAAGTTCTTACCCGATAGAGAATTGTGTCACAAACCAAAAGGTCAACCGTTCTTGCATAGGCA
296342 CTGA
131 CTGA
296346 TGATGGGCCC
Statistics
Matches: 129, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
136 129 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (136 bp):
TGTGAAGACACGTATTCCCACTAGTCCCAGATAAACGTAAGTGGTCGTCTATATTGATTGCTCCG
TTTAAGTTCTTACCCGATAGAGAATTGTGTCACAAACCAAAAGGTCAACCGTTCTTGCATAGGCA
CTGACA
Found at i:298285 original size:150 final size:151
Alignment explanation
Indices: 298103--298403 Score: 577
Period size: 150 Copynumber: 2.0 Consensus size: 151
298093 GTAATTTTAA
298103 GAGCCAATATAATTTATTTGTTTTTGTTTGTAGTTTAAAGGAGAAATAAAGGAATAGAAAGAAAA
1 GAGCCAATATAATTTATTTGTTTTTGTTTGTAGTTTAAAGGAGAAATAAAGGAATAGAAAGAAAA
*
298168 ATTATTAAATTTTAAAATATATTAAGTTCAATATTTTTATAAATGATCTTTTAAAATATTAATTT
66 ATTATTAAATTTTAAAATATATTAAGGTCAATATTTTTATAAATGATCTTTTAAAATATTAATTT
298233 AAATTTAATATAAATATCTTT
131 AAATTTAATATAAATATCTTT
298254 GAGCCAATAT-ATTTATTTGTTTTTGTTTGTAGTTTAAAGGAGAAATAAAGGAATAGAAAGAAAA
1 GAGCCAATATAATTTATTTGTTTTTGTTTGTAGTTTAAAGGAGAAATAAAGGAATAGAAAGAAAA
*
298318 ATTATTAAATTTTAAAATATATTAAGGTCCATATTTTTATAAATGATCTTTTAAAATATTAATTT
66 ATTATTAAATTTTAAAATATATTAAGGTCAATATTTTTATAAATGATCTTTTAAAATATTAATTT
298383 AAATTTAATATAAATATCTTT
131 AAATTTAATATAAATATCTTT
298404 TCTAGAAAAA
Statistics
Matches: 148, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
150 138 0.93
151 10 0.07
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (151 bp):
GAGCCAATATAATTTATTTGTTTTTGTTTGTAGTTTAAAGGAGAAATAAAGGAATAGAAAGAAAA
ATTATTAAATTTTAAAATATATTAAGGTCAATATTTTTATAAATGATCTTTTAAAATATTAATTT
AAATTTAATATAAATATCTTT
Found at i:313553 original size:2 final size:2
Alignment explanation
Indices: 313546--313574 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
313536 ATGATATAAA
313546 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
313575 AGCATCCCAT
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:315102 original size:3 final size:3
Alignment explanation
Indices: 315094--315145 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
315084 ATTTGTCTTA
315094 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
315142 AAT A
1 AAT A
315146 CATCAAATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:315201 original size:43 final size:39
Alignment explanation
Indices: 315139--315219 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 39
315129 TAATAATAAT
315139 AATAATACATCAAATAAAAAATTATATACCTGCTTGTTC
1 AATAATACATCAAATAAAAAATTATATACCTGCTTGTTC
*
315178 NNNNAATAATCCA-CAAATAAAAAATTATATACCTGCTTGTTC
1 ----AATAATACATCAAATAAAAAATTATATACCTGCTTGTTC
315220 TCCATGATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
42 29 0.78
43 8 0.22
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.31
Consensus pattern (39 bp):
AATAATACATCAAATAAAAAATTATATACCTGCTTGTTC
Found at i:317693 original size:19 final size:20
Alignment explanation
Indices: 317655--317693 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
317645 TTATTGGTTA
* *
317655 TTAATCTTTTTAACATATTT
1 TTAATCTTTTTAAAAAATTT
317675 TTAAT-TTTTTAAAAAATTT
1 TTAATCTTTTTAAAAAATTT
317694 AATTTGACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TTAATCTTTTTAAAAAATTT
Found at i:324187 original size:22 final size:22
Alignment explanation
Indices: 324141--324188 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
324131 TATAATAGCA
*
324141 GAAATAATTAAAATATTAATGC
1 GAAATAATTAAAATATTAATCC
324163 GAAACTAATT-AAATATATAA-CC
1 GAAA-TAATTAAAATAT-TAATCC
324185 GAAA
1 GAAA
324189 AAACAGCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.27
Consensus pattern (22 bp):
GAAATAATTAAAATATTAATCC
Found at i:325074 original size:56 final size:56
Alignment explanation
Indices: 324922--325078 Score: 192
Period size: 54 Copynumber: 2.8 Consensus size: 56
324912 GTCACTTGAG
*** * * *
324922 TGTAGCGTCGTTTGGACGCTTTATCACTTGAGATTATAATATAAGATGTGTTAATT
1 TGTAGCGTCGTTTGGACGCTTTATCACTTGAGATTGCCATATAAGCTATGATAATT
* * * * *
324978 TATAACATCGTTTGGACGC-TT-TCACTTAAGATTGCCATATAAGCTATGATAGTT
1 TGTAGCGTCGTTTGGACGCTTTATCACTTGAGATTGCCATATAAGCTATGATAATT
*
325032 TGTAGCGTCATTTGGACGCTTTATCACTTGAGATTGCCATATAAGCT
1 TGTAGCGTCGTTTGGACGCTTTATCACTTGAGATTGCCATATAAGCT
325079 GTTTAAGAAT
Statistics
Matches: 83, Mismatches: 16, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
54 40 0.48
55 4 0.05
56 39 0.47
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (56 bp):
TGTAGCGTCGTTTGGACGCTTTATCACTTGAGATTGCCATATAAGCTATGATAATT
Found at i:328122 original size:24 final size:25
Alignment explanation
Indices: 328064--328126 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 25
328054 TAAGAATTAT
* *
328064 ATAATGGGAAGCTCATGAGAGCCAA
1 ATAACGGGATGCTCATGAGAGCCAA
* * *
328089 ATATCAGGATGCTCATGAGAG-CTA
1 ATAACGGGATGCTCATGAGAGCCAA
328113 ATAACGGGATGCTC
1 ATAACGGGATGCTC
328127 TTTCGAGCTA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 14 0.45
25 17 0.55
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (25 bp):
ATAACGGGATGCTCATGAGAGCCAA
Found at i:329784 original size:23 final size:23
Alignment explanation
Indices: 329746--330249 Score: 238
Period size: 23 Copynumber: 21.5 Consensus size: 23
329736 ATCTACTCTG
* *
329746 TTTGGACAGC-TCTTATACATCAA
1 TTTGGACAGCAT-ATATACAACAA
* * *
329769 TTTGGACAGCATTTATATACCAA
1 TTTGGACAGCATATATACAACAA
* * * *
329792 ATTAGACAGCAT-TTTCACACCAAAA
1 TTTGGACAGCATATAT-ACA--ACAA
*
329817 TTTGGACAGCATAAATACAACAA
1 TTTGGACAGCATATATACAACAA
*
329840 TTTGGGCAGCATATATACAACAA
1 TTTGGACAGCATATATACAACAA
* * * *
329863 TTT-GAGCAGTATTTTTACACCAAA
1 TTTGGA-CAGCATATATACAAC-AA
* * * * *
329887 ATTGGACAGAATAAATTCAAGAA
1 TTTGGACAGCATATATACAACAA
*
329910 TTTGGGCAGCATATATACAACAA
1 TTTGGACAGCATATATACAACAA
* * *
329933 TTT-GAGCAGCATTTTTACACCAAA
1 TTTGGA-CAGCATATATACAAC-AA
* * * *
329957 ATTGGACATCATAAATTCAACAA
1 TTTGGACAGCATATATACAACAA
*
329980 TTTGGGCAGCATATATACAACAA
1 TTTGGACAGCATATATACAACAA
* * * *
330003 TTT-GAGCAACATTTTTACACCAAA
1 TTTGGA-CAGCATATATACAAC-AA
* * *
330027 ATTGGACAGCATAAATAAAACAA
1 TTTGGACAGCATATATACAACAA
* *
330050 TTTTGAGCAGCATATATACAGCAA
1 TTTGGA-CAGCATATATACAACAA
* * * *
330074 TTT-GAGTAGCATTTTTACACCAAA
1 TTTGGA-CAGCATATATACAAC-AA
* *
330098 ATTGGACAGCATATATAAAACAAA
1 TTTGGACAGCATATATACAAC-AA
* * *
330122 TTAGG-CAGCATTTA-AGCATCAAA
1 TTTGGACAGCATATATA-CAAC-AA
* *
330145 ATTGGACAGCATATATGCAACAA
1 TTTGGACAGCATATATACAACAA
* *
330168 ATTGGGCAGCATATATACAACAGA
1 TTTGGACAGCATATATACAACA-A
* *
330192 -TTGGACAACACT-TA-AGCATCAAA
1 TTTGGACAGCA-TATATA-CAAC-AA
* *
330215 ATTGGACAGCATATATGCAACAA
1 TTTGGACAGCATATATACAACAA
* *
330238 ATTGGGCAGCAT
1 TTTGGACAGCAT
330250 TTAAGCATCA
Statistics
Matches: 358, Mismatches: 96, Indels: 54
0.70 0.19 0.11
Matches are distributed among these distances:
22 7 0.02
23 223 0.62
24 104 0.29
25 23 0.06
26 1 0.00
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (23 bp):
TTTGGACAGCATATATACAACAA
Found at i:329915 original size:70 final size:70
Alignment explanation
Indices: 329760--330132 Score: 516
Period size: 70 Copynumber: 5.3 Consensus size: 70
329750 GACAGCTCTT
* * * * *
329760 ATACATCAATTTGGACAGCATTTATATACCA-AATTAGA-CAGCATTTTCACACCAAAATTTGGA
1 ATACAACAATTTGGGCAGCA--TATATACAACAATTTGAGCAGCATTTTTACACCAAAA-TTGGA
329823 CAGCATAA
63 CAGCATAA
*
329831 ATACAACAATTTGGGCAGCATATATACAACAATTTGAGCAGTATTTTTACACCAAAATTGGACAG
1 ATACAACAATTTGGGCAGCATATATACAACAATTTGAGCAGCATTTTTACACCAAAATTGGACAG
*
329896 AATAA
66 CATAA
* * *
329901 ATTCAAGAATTTGGGCAGCATATATACAACAATTTGAGCAGCATTTTTACACCAAAATTGGACAT
1 ATACAACAATTTGGGCAGCATATATACAACAATTTGAGCAGCATTTTTACACCAAAATTGGACAG
329966 CATAA
66 CATAA
* *
329971 ATTCAACAATTTGGGCAGCATATATACAACAATTTGAGCAACATTTTTACACCAAAATTGGACAG
1 ATACAACAATTTGGGCAGCATATATACAACAATTTGAGCAGCATTTTTACACCAAAATTGGACAG
330036 CATAA
66 CATAA
* * * *
330041 ATAAAACAATTTTGAGCAGCATATATACAGCAATTTGAGTAGCATTTTTACACCAAAATTGGACA
1 ATACAACAA-TTTGGGCAGCATATATACAACAATTTGAGCAGCATTTTTACACCAAAATTGGACA
*
330106 GCATAT
65 GCATAA
* * *
330112 ATAAAACAAATTAGGCAGCAT
1 ATACAACAATTTGGGCAGCAT
330133 TTAAGCATCA
Statistics
Matches: 274, Mismatches: 25, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
69 8 0.03
70 166 0.61
71 100 0.36
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (70 bp):
ATACAACAATTTGGGCAGCATATATACAACAATTTGAGCAGCATTTTTACACCAAAATTGGACAG
CATAA
Found at i:330181 original size:70 final size:70
Alignment explanation
Indices: 330096--330249 Score: 247
Period size: 70 Copynumber: 2.2 Consensus size: 70
330086 TTTTACACCA
* * *
330096 AAATTGGACAGCATATATAAAACAAATTAGG-CAGCATTTAAGCATCAAAATTGGACAGCATATA
1 AAATTGGGCAGCATATATAAAACAAATT-GGACAACACTTAAGCATCAAAATTGGACAGCATATA
330160 TGCAAC
65 TGCAAC
* *
330166 AAATTGGGCAGCATATATACAACAGATTGGACAACACTTAAGCATCAAAATTGGACAGCATATAT
1 AAATTGGGCAGCATATATAAAACAAATTGGACAACACTTAAGCATCAAAATTGGACAGCATATAT
330231 GCAAC
66 GCAAC
330236 AAATTGGGCAGCAT
1 AAATTGGGCAGCAT
330250 TTAAGCATCA
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
69 2 0.03
70 76 0.97
ACGTcount: A:0.44, C:0.17, G:0.18, T:0.22
Consensus pattern (70 bp):
AAATTGGGCAGCATATATAAAACAAATTGGACAACACTTAAGCATCAAAATTGGACAGCATATAT
GCAAC
Found at i:330217 original size:47 final size:47
Alignment explanation
Indices: 330166--330259 Score: 134
Period size: 47 Copynumber: 2.0 Consensus size: 47
330156 TATATGCAAC
* *
330166 AAATTGGGCAGCATATATACAACAGATTGGACAACACTTAAGCATCA
1 AAATTGGACAGCATATATACAACAAATTGGACAACACTTAAGCATCA
* * * *
330213 AAATTGGACAGCATATATGCAACAAATTGGGCAGCATTTAAGCATCA
1 AAATTGGACAGCATATATACAACAAATTGGACAACACTTAAGCATCA
330260 CCTATTCGGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.22
Consensus pattern (47 bp):
AAATTGGACAGCATATATACAACAAATTGGACAACACTTAAGCATCA
Found at i:340579 original size:23 final size:22
Alignment explanation
Indices: 340548--340691 Score: 119
Period size: 23 Copynumber: 6.2 Consensus size: 22
340538 TAAAGCTATC
*
340548 ACCCACCAAACACAACCAATCAT
1 ACCCTCCAAACACAACCAAT-AT
* * *
340571 AGCCTCCAAATACAACCATATGT
1 ACCCTCCAAACACAACCA-ATAT
* * *
340594 ACCCTTCAGACACAACCAAATTT
1 ACCCTCCAAACACAACC-AATAT
*
340617 ACCCTTCAAACACAACCATATATAT
1 ACCCTCCAAACACAACC--A-ATAT
*
340642 AACCTCCAAACACAA-CAAGGTAT
1 ACCCTCCAAACACAACCAA--TAT
*
340665 AGCCTCCAAACACAACCAATAT
1 ACCCTCCAAACACAACCAATAT
340687 ACCCT
1 ACCCT
340692 TCAACATATC
Statistics
Matches: 98, Mismatches: 16, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.01
22 8 0.08
23 65 0.66
24 8 0.08
25 16 0.16
ACGTcount: A:0.43, C:0.35, G:0.04, T:0.17
Consensus pattern (22 bp):
ACCCTCCAAACACAACCAATAT
Found at i:341007 original size:30 final size:30
Alignment explanation
Indices: 340971--341032 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
340961 ATTAGCTTAC
* *
340971 CAAAGCTCCCCTTTAACACATTTATTTGTG
1 CAAAGCTACCATTTAACACATTTATTTGTG
*
341001 CAAAGCTACCATTTAACACTTTTATTTGTG
1 CAAAGCTACCATTTAACACATTTATTTGTG
341031 CA
1 CA
341033 TAATTGTAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (30 bp):
CAAAGCTACCATTTAACACATTTATTTGTG
Found at i:343312 original size:23 final size:23
Alignment explanation
Indices: 343238--343374 Score: 109
Period size: 23 Copynumber: 5.9 Consensus size: 23
343228 ATCACCCACG
*
343238 AAACACAACC-AATCATAGCCTCC
1 AAACACAACCAAAT-ATACCCTCC
* * *
343261 AAACACAACCATATGTACCCT-T
1 AAACACAACCAAATATACCCTCC
* *
343283 AGGACACAACCAAATTTACCCTCC
1 A-AACACAACCAAATATACCCTCC
* * *
343307 AAACACAACTATATATATAACCTAC
1 AAACACAACCA-A-ATATACCCTCC
* * *
343332 GAACACTACCAAGTATACCCTCC
1 AAACACAACCAAATATACCCTCC
343355 AAACACAACC-AATATACCCT
1 AAACACAACCAAATATACCCT
343375 TCAACATATC
Statistics
Matches: 87, Mismatches: 22, Indels: 11
0.73 0.18 0.09
Matches are distributed among these distances:
22 10 0.11
23 56 0.64
24 5 0.06
25 16 0.18
ACGTcount: A:0.43, C:0.34, G:0.04, T:0.18
Consensus pattern (23 bp):
AAACACAACCAAATATACCCTCC
Found at i:344685 original size:23 final size:22
Alignment explanation
Indices: 344658--344711 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
344648 AAATAAATAA
*
344658 TAAATAATAATAAAATATCTCAT
1 TAAATAATAATAAAATAT-TAAT
* *
344681 TAAATATTAGTAAAATATTAAT
1 TAAATAATAATAAAATATTAAT
*
344703 AAAATAATA
1 TAAATAATA
344712 TTTATCTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (22 bp):
TAAATAATAATAAAATATTAAT
Found at i:347031 original size:19 final size:20
Alignment explanation
Indices: 346989--347031 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
346979 TCATGCTTTC
*
346989 TATTCACATTTTCATATTCA
1 TATTCACATTTTCATAATCA
347009 -ATTCACATTTTCA-AATCA
1 TATTCACATTTTCATAATCA
347027 TATTC
1 TATTC
347032 CACAATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTCACATTTTCATAATCA
Found at i:347752 original size:22 final size:22
Alignment explanation
Indices: 347721--347789 Score: 97
Period size: 22 Copynumber: 3.1 Consensus size: 22
347711 TATGCACTAT
347721 TAAACAGAGAGCACTAAA-GTG-
1 TAAACAGAGAGCAC-AAATGTGC
347742 TAATACAGAGAGCACAAATGTGC
1 TAA-ACAGAGAGCACAAATGTGC
*
347765 TAAACAGAGAGCACCAATGTGC
1 TAAACAGAGAGCACAAATGTGC
347787 TAA
1 TAA
347790 TAATCAGAGA
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
21 6 0.14
22 35 0.80
23 3 0.07
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (22 bp):
TAAACAGAGAGCACAAATGTGC
Found at i:347806 original size:19 final size:19
Alignment explanation
Indices: 347782--347819 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
347772 AGAGCACCAA
347782 TGTGCTAATAATCAGAGAG
1 TGTGCTAATAATCAGAGAG
*
347801 TGTGCTAGTAATCAGAGAG
1 TGTGCTAATAATCAGAGAG
347820 CACTGACGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (19 bp):
TGTGCTAATAATCAGAGAG
Found at i:347830 original size:25 final size:25
Alignment explanation
Indices: 347802--347897 Score: 174
Period size: 25 Copynumber: 3.8 Consensus size: 25
347792 ATCAGAGAGT
*
347802 GTGCTAGTAATCAGAGAGCACTGAC
1 GTGCTAATAATCAGAGAGCACTGAC
347827 GTGCTAATAATCAGAGAGCACTGAC
1 GTGCTAATAATCAGAGAGCACTGAC
*
347852 GTGCTAATAATCAGAGAGCACTGAT
1 GTGCTAATAATCAGAGAGCACTGAC
347877 GTGCTAATAATCAGAGAGCAC
1 GTGCTAATAATCAGAGAGCAC
347898 AATAAACTCT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 69 1.00
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (25 bp):
GTGCTAATAATCAGAGAGCACTGAC
Found at i:347881 original size:50 final size:48
Alignment explanation
Indices: 347725--347897 Score: 177
Period size: 44 Copynumber: 3.7 Consensus size: 48
347715 CACTATTAAA
* *
347725 CAGAGAGCACTAAAGTG-TAAT-A-CAGAGAGCACAAATGTGCT-A-AA-
1 CAGAGAGCACTAATGTGCTAATAATCAGAGAGCAC-TA-GTGCTAATAAT
* *
347769 CAGAGAGCACCAATGTGCTAATAATCAGAGAG---T-GTGCTAGTAAT
1 CAGAGAGCACTAATGTGCTAATAATCAGAGAGCACTAGTGCTAATAAT
* *
347813 CAGAGAGCACTGACGTGCTAATAATCAGAGAGCACTGACGTGCTAATAAT
1 CAGAGAGCACTAATGTGCTAATAATCAGAGAGCACT-A-GTGCTAATAAT
*
347863 CAGAGAGCACTGATGTGCTAATAATCAGAGAGCAC
1 CAGAGAGCACTAATGTGCTAATAATCAGAGAGCAC
347898 AATAAACTCT
Statistics
Matches: 108, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
41 5 0.05
43 2 0.02
44 44 0.41
45 4 0.04
46 1 0.01
47 8 0.07
50 44 0.41
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (48 bp):
CAGAGAGCACTAATGTGCTAATAATCAGAGAGCACTAGTGCTAATAAT
Found at i:366554 original size:5 final size:5
Alignment explanation
Indices: 366544--366574 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
366534 ACTCAAAGGG
*
366544 ATAAA ATAAA ATAAA ATAAA ATAAA GTAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
366575 GGCATCTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:370629 original size:31 final size:32
Alignment explanation
Indices: 370588--370648 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
370578 TAAACTTAAA
* * *
370588 TAAATATTAAAAATTATATTACTTTTTATAGT
1 TAAATATTAAAAATAATATTAATTATTATAGT
*
370620 TAAAT-TTAAATATAATATTAATTATTATA
1 TAAATATTAAAAATAATATTAATTATTATA
370649 AAAATTGTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (32 bp):
TAAATATTAAAAATAATATTAATTATTATAGT
Found at i:370963 original size:21 final size:21
Alignment explanation
Indices: 370937--370976 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
370927 AACGGGACCA
370937 CTGATGTGGCAAGTTAACTAG
1 CTGATGTGGCAAGTTAACTAG
*
370958 CTGATGTGGCCAGTTAACT
1 CTGATGTGGCAAGTTAACT
370977 TACCATGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (21 bp):
CTGATGTGGCAAGTTAACTAG
Found at i:372702 original size:21 final size:21
Alignment explanation
Indices: 372676--372715 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
372666 TTTTTAAAAA
*
372676 TTAAAAGTCAAAACAATTAAG
1 TTAAAAGACAAAACAATTAAG
*
372697 TTAAAAGACAAAACTATTA
1 TTAAAAGACAAAACAATTA
372716 TATTGTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.25
Consensus pattern (21 bp):
TTAAAAGACAAAACAATTAAG
Found at i:377126 original size:21 final size:21
Alignment explanation
Indices: 377100--377194 Score: 57
Period size: 21 Copynumber: 4.5 Consensus size: 21
377090 AAGCCCGAAG
* *
377100 GCTAAATAGAAGCACATAAGT
1 GCTAAACAGAAACACATAAGT
* *
377121 GCTAAACAGAAACCCATAAGG
1 GCTAAACAGAAACACATAAGT
* * * *
377142 GTTGAAC-GAAAGCTCATAAGA
1 GCTAAACAGAAA-CACATAAGT
* * * *
377163 GCTGAACGGAAACCCATAAGG
1 GCTAAACAGAAACACATAAGT
*
377184 GTTAAACAGAA
1 GCTAAACAGAA
377195 GCTCAAAAGA
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
20 4 0.07
21 50 0.86
22 4 0.07
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (21 bp):
GCTAAACAGAAACACATAAGT
Found at i:377161 original size:42 final size:42
Alignment explanation
Indices: 377102--377228 Score: 157
Period size: 42 Copynumber: 3.0 Consensus size: 42
377092 GCCCGAAGGC
* * * *
377102 TAAATAGAAGCACATAAGTGCTAAACAGAAACCCATAAGGGT
1 TAAACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGT
* *
377144 TGAAC-GAAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGT
1 TAAACAG-AAGCTCATAAGAGCTGAACAGAAACCCATAAGGGT
* * *
377186 TAAACAGAAGCTCAAAAGAGCTGAATAGAAACCCATTAGGGT
1 TAAACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGT
377228 T
1 T
377229 CAATGGAAAC
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
41 1 0.01
42 70 0.97
43 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (42 bp):
TAAACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGT
Found at i:383369 original size:91 final size:91
Alignment explanation
Indices: 383214--383394 Score: 344
Period size: 91 Copynumber: 2.0 Consensus size: 91
383204 TTCTAGTAAG
*
383214 CTCATAATTTATTAGTATTAATTATGTTTTGTAAAATTGTGGGTAAATATTATCTTGCTGATGCT
1 CTCATAATTTATTAGTATTAATTATGTTTTGTAAAATTGTAGGTAAATATTATCTTGCTGATGCT
*
383279 GGATATGGCATCCGAAATGGATATAA
66 AGATATGGCATCCGAAATGGATATAA
383305 CTCATAATTTATTAGTATTAATTATGTTTTGTAAAATTGTAGGTAAATATTATCTTGCTGATGCT
1 CTCATAATTTATTAGTATTAATTATGTTTTGTAAAATTGTAGGTAAATATTATCTTGCTGATGCT
383370 AGATATGGCATCCGAAATGGATATA
66 AGATATGGCATCCGAAATGGATATA
383395 TTACCCCATA
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 88 1.00
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.41
Consensus pattern (91 bp):
CTCATAATTTATTAGTATTAATTATGTTTTGTAAAATTGTAGGTAAATATTATCTTGCTGATGCT
AGATATGGCATCCGAAATGGATATAA
Found at i:383960 original size:27 final size:27
Alignment explanation
Indices: 383930--384002 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 27
383920 TGTCTTGAAT
383930 TTGTTAGATATTGATTATGTTTTAAGC
1 TTGTTAGATATTGATTATGTTTTAAGC
383957 TTGTTAGATATTGAATTTATTATGTTTTAAGC
1 TTGTTAGATATTG-----ATTATGTTTTAAGC
* *
383989 TTGTTGGTTATTGA
1 TTGTTAGATATTGA
384003 AATGATTGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
27 14 0.36
32 25 0.64
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (27 bp):
TTGTTAGATATTGATTATGTTTTAAGC
Found at i:383982 original size:32 final size:32
Alignment explanation
Indices: 383943--384003 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
383933 TTAGATATTG
383943 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
* *
383975 ATTATGTTTTAAGCTTGTTGGTTATTGAA
1 ATTATGTTTTAAGCTTGTTAGATATTGAA
384004 ATGATTGACA
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:0.26, C:0.03, G:0.18, T:0.52
Consensus pattern (32 bp):
ATTATGTTTTAAGCTTGTTAGATATTGAATTT
Found at i:385389 original size:18 final size:19
Alignment explanation
Indices: 385363--385402 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
385353 AAACACCAGA
385363 AAAGGAAATCA-TTTCTAG
1 AAAGGAAATCATTTTCTAG
*
385381 AAAGTAAATCATTTTCTAG
1 AAAGGAAATCATTTTCTAG
385400 AAA
1 AAA
385403 TCATTTTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30
Consensus pattern (19 bp):
AAAGGAAATCATTTTCTAG
Done.