Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1
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: 8764944
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 632878 characters in sequence are not A, C, G, or T
File 31 of 52
Found at i:5344933 original size:21 final size:21
Alignment explanation
Indices: 5344909--5344949 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5344899 AATTATCTAA
5344909 ATTTAAATAAAGTA-TAATTTT
1 ATTTAAA-AAAGTATTAATTTT
*
5344930 ATTTTAAAAAGTATTAATTT
1 ATTTAAAAAAGTATTAATTT
5344950 CATAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
ATTTAAAAAAGTATTAATTTT
Found at i:5345027 original size:9 final size:9
Alignment explanation
Indices: 5345007--5345035 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
5344997 TTAAATTATC
5345007 TTTTAA-AA
1 TTTTAATAA
5345015 TTTTAATAA
1 TTTTAATAA
5345024 TTTTAATAA
1 TTTTAATAA
5345033 TTT
1 TTT
5345036 CTTATATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTAATAA
Found at i:5345210 original size:19 final size:19
Alignment explanation
Indices: 5345183--5345219 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5345173 TGTACCTTAC
*
5345183 ATTACAATAATATCTTATT
1 ATTACAATAATACCTTATT
*
5345202 ATTATAATAATACCTTAT
1 ATTACAATAATACCTTAT
5345220 CATGTGATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTACAATAATACCTTATT
Found at i:5345967 original size:44 final size:47
Alignment explanation
Indices: 5345905--5346008 Score: 126
Period size: 44 Copynumber: 2.3 Consensus size: 47
5345895 CTGACTTATT
* *
5345905 TATATTTAAATTATTATTTATA-A-T-TAATAAAAATTTAAA-AAATA
1 TATATTT-AATTAATATTTATATATTATAATAAAAATTTAAATAAAAA
*
5345949 TATATTTATATTAATATTTATATATTATAATTAAAATTTAAATAAAAA
1 TATATTTA-ATTAATATTTATATATTATAATAAAAATTTAAATAAAAA
*
5345997 TATTTTTAATTA
1 TATATTTAATTA
5346009 TTTAATATCA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
43 1 0.02
44 19 0.37
45 1 0.02
46 1 0.02
47 18 0.35
48 11 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (47 bp):
TATATTTAATTAATATTTATATATTATAATAAAAATTTAAATAAAAA
Found at i:5345970 original size:20 final size:20
Alignment explanation
Indices: 5345943--5345988 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
5345933 AAAAATTTAA
*
5345943 AAAATATATAT-TTAT-ATT
1 AAAATTTATATATTATAATT
*
5345961 AATATTTATATATTATAATT
1 AAAATTTATATATTATAATT
5345981 AAAATTTA
1 AAAATTTA
5345989 AATAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 9 0.39
19 4 0.17
20 10 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAATTTATATATTATAATT
Found at i:5346826 original size:18 final size:19
Alignment explanation
Indices: 5346786--5346829 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
5346776 AAAATTTTTA
5346786 TTTAATA-AAAATATAAAT
1 TTTAATATAAAATATAAAT
* *
5346804 ATTAATATAAAATA-ATAT
1 TTTAATATAAAATATAAAT
5346822 TTTAATAT
1 TTTAATAT
5346830 TATAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTAATATAAAATATAAAT
Found at i:5347608 original size:16 final size:16
Alignment explanation
Indices: 5347587--5347627 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
5347577 AACAAAGTAA
5347587 TAATTCTAATAAAATT
1 TAATTCTAATAAAATT
*
5347603 TAATTC-AATTTAAATT
1 TAATTCTAA-TAAAATT
5347619 TAA-TCTAAT
1 TAATTCTAAT
5347628 TTATTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (16 bp):
TAATTCTAATAAAATT
Found at i:5349005 original size:18 final size:18
Alignment explanation
Indices: 5348971--5349005 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5348961 TTTTTTTCAA
**
5348971 TAAAAATAATAGTAAAAG
1 TAAAAATAATAAAAAAAG
5348989 TAAAAATAATAAAAAAA
1 TAAAAATAATAAAAAAA
5349006 ATTATGAACT
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:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (18 bp):
TAAAAATAATAAAAAAAG
Found at i:5349639 original size:16 final size:16
Alignment explanation
Indices: 5349618--5349682 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 16
5349608 TATTTATATG
*
5349618 TATTTTAGGTTTAAAT
1 TATTTTAGATTTAAAT
* *
5349634 TATTTTAAATTTTAAT
1 TATTTTAGATTTAAAT
* *
5349650 TGTTTTATATTTAAATT
1 TATTTTAGATTTAAA-T
*
5349667 TTTTTTA-ATTTAAAT
1 TATTTTAGATTTAAAT
5349682 T
1 T
5349683 TTTGTAGGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
15 2 0.05
16 32 0.78
17 7 0.17
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (16 bp):
TATTTTAGATTTAAAT
Found at i:5349678 original size:22 final size:22
Alignment explanation
Indices: 5349627--5349683 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 22
5349617 GTATTTTAGG
*
5349627 TTTAAATTAT-TTTAAATTTTA
1 TTTAATTTATATTTAAATTTTA
* ** *
5349648 ATTGTTTTATATTTAAATTTTT
1 TTTAATTTATATTTAAATTTTA
*
5349670 TTTAATTTAAATTT
1 TTTAATTTATATTT
5349684 TTGTAGGTTT
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTAATTTATATTTAAATTTTA
Found at i:5349683 original size:16 final size:16
Alignment explanation
Indices: 5349627--5349685 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
5349617 GTATTTTAGG
* *
5349627 TTTAAATTATTTTAAA
1 TTTAAATTTTTTTTAA
* *
5349643 TTTTAA-TTGTTTTATA
1 TTTAAATTTTTTTTA-A
5349659 TTTAAATTTTTTTTAA
1 TTTAAATTTTTTTTAA
5349675 TTTAAATTTTT
1 TTTAAATTTTT
5349686 GTAGGTTTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 5 0.14
16 23 0.66
17 7 0.20
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTAAATTTTTTTTAA
Found at i:5350477 original size:23 final size:23
Alignment explanation
Indices: 5350451--5350496 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5350441 AGTACTTTTT
* *
5350451 AAAATAAATGGTTAGTTTTTTAA
1 AAAATAAATCGATAGTTTTTTAA
*
5350474 AAAATAAATCGATATTTTTTTAA
1 AAAATAAATCGATAGTTTTTTAA
5350497 GATGTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (23 bp):
AAAATAAATCGATAGTTTTTTAA
Found at i:5352146 original size:2 final size:2
Alignment explanation
Indices: 5352139--5352171 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5352129 TTAGTGATGT
5352139 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 T
5352172 TTTAGTGGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5352587 original size:25 final size:25
Alignment explanation
Indices: 5352559--5352612 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
5352549 TACTAAAATC
5352559 AATTAAATTTTATATAT-T-ATTAATA
1 AATTAAATTTTAT-TATCTAATTAA-A
5352584 AATTAAATTTTATTATCTAATTAAA
1 AATTAAATTTTATTATCTAATTAAA
5352609 AATT
1 AATT
5352613 TTTAATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 3 0.11
25 19 0.70
26 5 0.19
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
AATTAAATTTTATTATCTAATTAAA
Found at i:5353637 original size:7 final size:7
Alignment explanation
Indices: 5353620--5353652 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
5353610 TGTTAATAAA
5353620 CAACA-G
1 CAACAGG
5353626 CAACAGG
1 CAACAGG
5353633 CAACAGG
1 CAACAGG
5353640 CAACAGG
1 CAACAGG
5353647 CAACAG
1 CAACAG
5353653 CCTCCTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.45, C:0.30, G:0.24, T:0.00
Consensus pattern (7 bp):
CAACAGG
Found at i:5356422 original size:18 final size:18
Alignment explanation
Indices: 5356398--5356453 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
5356388 ATGGGGTAAT
5356398 AGGCCTAGCGATTACTCC
1 AGGCCTAGCGATTACTCC
* *
5356416 CGGCCTAGCGATTTCTCC
1 AGGCCTAGCGATTACTCC
*
5356434 AGGCCTAGTGATTACTCC
1 AGGCCTAGCGATTACTCC
5356452 AG
1 AG
5356454 ATGGGGTTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.20, C:0.32, G:0.23, T:0.25
Consensus pattern (18 bp):
AGGCCTAGCGATTACTCC
Found at i:5360195 original size:31 final size:31
Alignment explanation
Indices: 5360160--5360256 Score: 85
Period size: 30 Copynumber: 3.2 Consensus size: 31
5360150 TGCATCAAAT
*
5360160 ATAAATATTTAAAAATTAATAAATTTATATA
1 ATAAATATTTAAAAATTAATAAATTCATATA
* * * *
5360191 ATAAATA-AT-AAAATATATTACA-TCAAAT-
1 ATAAATATTTAAAAAT-TAATAAATTCATATA
* * *
5360219 ATAAATCTTTAAAATTTAACAAATTCATATA
1 ATAAATATTTAAAAATTAATAAATTCATATA
5360250 ATAAATA
1 ATAAATA
5360257 ATAAAATATA
Statistics
Matches: 48, Mismatches: 13, Indels: 10
0.68 0.18 0.14
Matches are distributed among these distances:
28 6 0.12
29 14 0.29
30 15 0.31
31 13 0.27
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (31 bp):
ATAAATATTTAAAAATTAATAAATTCATATA
Found at i:5360215 original size:59 final size:59
Alignment explanation
Indices: 5360152--5360267 Score: 196
Period size: 59 Copynumber: 2.0 Consensus size: 59
5360142 TTGATGATTG
* *
5360152 CATCAAATATAAATATTTAAAAATTAATAAATTTATATAATAAATAATAAAATATATTA
1 CATCAAATATAAATATTTAAAAATTAACAAATTCATATAATAAATAATAAAATATATTA
* *
5360211 CATCAAATATAAATCTTTAAAATTTAACAAATTCATATAATAAATAATAAAATATAT
1 CATCAAATATAAATATTTAAAAATTAACAAATTCATATAATAAATAATAAAATATAT
5360268 AATAATATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (59 bp):
CATCAAATATAAATATTTAAAAATTAACAAATTCATATAATAAATAATAAAATATATTA
Found at i:5361002 original size:17 final size:17
Alignment explanation
Indices: 5360977--5361019 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
5360967 TAAATAAGCT
*
5360977 TTATATTTTATTTAA-A
1 TTATTTTTTATTTAATA
5360993 CTTATTTTTTATTTAATA
1 -TTATTTTTTATTTAATA
5361011 TTATTTTTT
1 TTATTTTTT
5361020 TTCAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 23 0.96
18 1 0.04
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATTTTTTATTTAATA
Found at i:5361834 original size:20 final size:20
Alignment explanation
Indices: 5361805--5361844 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5361795 TATTTTATAG
*
5361805 TTAAATTTAAATAAATTTTT
1 TTAAAATTAAATAAATTTTT
*
5361825 TTAAAATTAAATGAATTTTT
1 TTAAAATTAAATAAATTTTT
5361845 ATCAGAGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TTAAAATTAAATAAATTTTT
Found at i:5364988 original size:19 final size:19
Alignment explanation
Indices: 5364961--5365007 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 19
5364951 GTTTAAATTA
5364961 ATTTAAAA-ATTTTATTAAAT
1 ATTTAAAATATTTTA-T-AAT
5364981 ATTTAAAATATTTTATAAT
1 ATTTAAAATATTTTATAAT
5365000 ATTTAAAA
1 ATTTAAAA
5365008 AATTAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.42
20 9 0.35
21 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTAAAATATTTTATAAT
Found at i:5366127 original size:45 final size:45
Alignment explanation
Indices: 5366063--5366152 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
5366053 TACCTATATG
*
5366063 TATTGATATATTGAAGAATATATCAATATATTTGGGTCAAAAACC
1 TATTGATATATTGAAGAATATATCAATACATTTGGGTCAAAAACC
5366108 TATTGATATATTGAAGAATATATCAATACATTTGGGTCAAAAACC
1 TATTGATATATTGAAGAATATATCAATACATTTGGGTCAAAAACC
5366153 CAGAATGTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (45 bp):
TATTGATATATTGAAGAATATATCAATACATTTGGGTCAAAAACC
Found at i:5366286 original size:20 final size:20
Alignment explanation
Indices: 5366261--5366298 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5366251 TGTATCAAGC
*
5366261 ATCGATACATTCACTTATGT
1 ATCGATACATTAACTTATGT
5366281 ATCGATACATTAACTTAT
1 ATCGATACATTAACTTAT
5366299 TATATTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (20 bp):
ATCGATACATTAACTTATGT
Found at i:5371060 original size:17 final size:17
Alignment explanation
Indices: 5371027--5371059 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5371017 AAAAATGAAA
*
5371027 AAAATTGATTATTTTTT
1 AAAATAGATTATTTTTT
5371044 AAAATAGATT-TTTTTT
1 AAAATAGATTATTTTTT
5371060 TTATTGATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (17 bp):
AAAATAGATTATTTTTT
Found at i:5371314 original size:25 final size:25
Alignment explanation
Indices: 5371283--5371345 Score: 126
Period size: 25 Copynumber: 2.5 Consensus size: 25
5371273 GTAATATTTA
5371283 TTATGAAAATATTAAAATATTTTTG
1 TTATGAAAATATTAAAATATTTTTG
5371308 TTATGAAAATATTAAAATATTTTTG
1 TTATGAAAATATTAAAATATTTTTG
5371333 TTATGAAAATATT
1 TTATGAAAATATT
5371346 GATACTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (25 bp):
TTATGAAAATATTAAAATATTTTTG
Found at i:5371553 original size:18 final size:18
Alignment explanation
Indices: 5371530--5371593 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
5371520 TGAAATAGTG
*
5371530 ATATTT-TTATGTTAAATA
1 ATATTTATTAT-TAAAATA
5371548 ATATTTATTATTAAAATA
1 ATATTTATTATTAAAATA
* * *
5371566 ATAATATATTTATTATATTA
1 AT-ATTTA-TTATTAAAATA
5371586 ATATTTAT
1 ATATTTAT
5371594 AACTGAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 15 0.39
19 12 0.32
20 11 0.29
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
ATATTTATTATTAAAATA
Found at i:5373767 original size:22 final size:22
Alignment explanation
Indices: 5373740--5373847 Score: 78
Period size: 22 Copynumber: 4.8 Consensus size: 22
5373730 ATCTTTCAAC
*
5373740 ATTTATTATCATATTATTAATT
1 ATTTATTATTATATTATTAATT
* * *
5373762 ATTTATTTTTATGTT-GTATATT
1 ATTTATTATTATATTATTA-ATT
*
5373784 ATTTATTATTATTTTAGATATAAATT
1 ATTTATTATTATATT--AT-T-AATT
* *
5373810 -TTTACTTA-TGTATTATAAATT
1 ATTTA-TTATTATATTATTAATT
5373831 ATTTATTATTATATTAT
1 ATTTATTATTATATTAT
5373848 GACGTGCTTA
Statistics
Matches: 66, Mismatches: 11, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
21 9 0.14
22 39 0.59
23 2 0.03
25 8 0.12
26 7 0.11
27 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (22 bp):
ATTTATTATTATATTATTAATT
Found at i:5374253 original size:17 final size:16
Alignment explanation
Indices: 5374231--5374262 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
5374221 CCATCAATCA
5374231 TTTACTATTATATCATC
1 TTTACTATTA-ATCATC
5374248 TTTACTATTAATCAT
1 TTTACTATTAATCAT
5374263 TTATATTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.31, C:0.16, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTACTATTAATCATC
Found at i:5374299 original size:22 final size:22
Alignment explanation
Indices: 5374273--5374322 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
5374263 TTATATTACT
5374273 ATTTATCAATCACTA-ACTATTA
1 ATTTATCAATCA-TATACTATTA
**
5374295 ATTTATTGATCATATACTATTA
1 ATTTATCAATCATATACTATTA
*
5374317 TTTTAT
1 ATTTAT
5374323 AATTATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTTATCAATCATATACTATTA
Found at i:5374374 original size:28 final size:30
Alignment explanation
Indices: 5374343--5374408 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 30
5374333 CTTTTAAATT
5374343 TATTATTATGTTATCAAT-CATT-TACTAA
1 TATTATTATGTTATCAATACATTCTACTAA
* * *
5374371 TATTACTATTTTATCAATAGTATTCTACTAA
1 TATTATTATGTTATCAATA-CATTCTACTAA
5374402 TATTATT
1 TATTATT
5374409 CATCATGAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 16 0.52
30 3 0.10
31 12 0.39
ACGTcount: A:0.35, C:0.11, G:0.03, T:0.52
Consensus pattern (30 bp):
TATTATTATGTTATCAATACATTCTACTAA
Found at i:5374786 original size:21 final size:22
Alignment explanation
Indices: 5374728--5374787 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
5374718 CTATCTTATC
* *
5374728 TTAT-CATAATGTACTATTATT
1 TTATCCATTATGTACTACTATT
*
5374749 TTATCAATTAT-TAACTACTA-T
1 TTATCCATTATGT-ACTACTATT
5374770 TTATCCATTATGTACTAC
1 TTATCCATTATGTACTAC
5374788 AATATTATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.48
Consensus pattern (22 bp):
TTATCCATTATGTACTACTATT
Found at i:5375091 original size:17 final size:18
Alignment explanation
Indices: 5375065--5375103 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
5375055 ACTGAAAATA
* *
5375065 TTTTTGTCAGTAAT-ATT
1 TTTTTATCAGAAATAATT
5375082 TTTTTATCAGAAATAATT
1 TTTTTATCAGAAATAATT
5375100 TTTT
1 TTTT
5375104 CCAACAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.28, C:0.05, G:0.08, T:0.59
Consensus pattern (18 bp):
TTTTTATCAGAAATAATT
Found at i:5375251 original size:22 final size:24
Alignment explanation
Indices: 5375225--5375287 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 24
5375215 GCTTTTTGCT
5375225 TTTTTATTAAATTTATTAAAT-TA
1 TTTTTATTAAATTTATTAAATATA
* *
5375248 TTTTTATTTAATAT-TTAAATAT-
1 TTTTTATTAAATTTATTAAATATA
*
5375270 TTTTTGTTAAA-TTATTAA
1 TTTTTATTAAATTTATTAA
5375288 TTAGAAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
21 1 0.03
22 19 0.58
23 13 0.39
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTTTATTAAATTTATTAAATATA
Found at i:5375368 original size:23 final size:23
Alignment explanation
Indices: 5375318--5375368 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5375308 CATTTATTGT
* *
5375318 AATAAAAATATAAAATGTAAATA
1 AATAAAAAAATAAAATATAAATA
* *
5375341 TATAAAAAAATAAAATATAATTA
1 AATAAAAAAATAAAATATAAATA
5375364 AATAA
1 AATAA
5375369 TTGAGAATGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (23 bp):
AATAAAAAAATAAAATATAAATA
Found at i:5377763 original size:13 final size:13
Alignment explanation
Indices: 5377747--5377771 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5377737 TTCTTAATTG
5377747 TAAGTTAACATAC
1 TAAGTTAACATAC
5377760 TAAGTTAACATA
1 TAAGTTAACATA
5377772 ATTTCAAAAC
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:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (13 bp):
TAAGTTAACATAC
Found at i:5377878 original size:9 final size:9
Alignment explanation
Indices: 5377857--5377896 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
5377847 CTTTATTAAT
5377857 AATTTATATA
1 AATTTATA-A
5377867 AATTTATAA
1 AATTTATAA
5377876 AA--T-TAA
1 AATTTATAA
5377882 AATTTATAA
1 AATTTATAA
5377891 AATTTA
1 AATTTA
5377897 CTACTATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
6 5 0.19
7 1 0.04
8 1 0.04
9 12 0.44
10 8 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
AATTTATAA
Found at i:5377886 original size:15 final size:15
Alignment explanation
Indices: 5377866--5377894 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5377856 TAATTTATAT
5377866 AAATTTATAAAATTA
1 AAATTTATAAAATTA
5377881 AAATTTATAAAATT
1 AAATTTATAAAATT
5377895 TACTACTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATTTATAAAATTA
Found at i:5378572 original size:2 final size:2
Alignment explanation
Indices: 5378565--5378605 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5378555 ATATTAGTAG
5378565 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5378606 AAATTACCGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5380076 original size:113 final size:113
Alignment explanation
Indices: 5379894--5380120 Score: 400
Period size: 113 Copynumber: 2.0 Consensus size: 113
5379884 AATAATTAAG
* *
5379894 TACTATGTCTTGTGTCATACAAGGTTTATGTCACAAGATTTCTCCATTGACTGATTTTTGGAACC
1 TACTATGTCTTGTGTCACACAAGGTTTATGTCACAAGATTTCTCAATTGACTGATTTTTGGAACC
*
5379959 TTTGAGTTTAGTTGTGAATCTAGTTTGGAGCCTTTTTCCATGATGGAT
66 TTTGAGTTTAGTTGTCAATCTAGTTTGGAGCCTTTTTCCATGATGGAT
* *
5380007 TACTATGTCTTGTGTCACACAAGGTTTATGTCTCAAGATTTCTCAATTGACTGATTTTTGGGACC
1 TACTATGTCTTGTGTCACACAAGGTTTATGTCACAAGATTTCTCAATTGACTGATTTTTGGAACC
*
5380072 TTTGAGTTTAGTTGTCAATCTAGTTTGGAGTCTTTTTCCATGATGGAT
66 TTTGAGTTTAGTTGTCAATCTAGTTTGGAGCCTTTTTCCATGATGGAT
5380120 T
1 T
5380121 GATTTATTAG
Statistics
Matches: 108, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 108 1.00
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (113 bp):
TACTATGTCTTGTGTCACACAAGGTTTATGTCACAAGATTTCTCAATTGACTGATTTTTGGAACC
TTTGAGTTTAGTTGTCAATCTAGTTTGGAGCCTTTTTCCATGATGGAT
Found at i:5400491 original size:24 final size:25
Alignment explanation
Indices: 5400459--5400506 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5400449 CCAAATCGTA
5400459 TTTATAAGG-CCAAAT-AGTATTTTT
1 TTTATAAGGCCCAAATCA-TATTTTT
5400483 TTTATAAGGCCCAAATCATATTTT
1 TTTATAAGGCCCAAATCATATTTT
5400507 AAGCTAGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.41
25 12 0.55
26 1 0.05
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.44
Consensus pattern (25 bp):
TTTATAAGGCCCAAATCATATTTTT
Found at i:5400749 original size:24 final size:24
Alignment explanation
Indices: 5400692--5400754 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
5400682 ATATTAAGTA
* *
5400692 ATAATA-AATACATAACTTTTTCT
1 ATAATATAAGACATAACTTTTTAT
*
5400715 TTAA-ATAAAGACATAACTTTTTAT
1 ATAATAT-AAGACATAACTTTTTAT
*
5400739 ATAATATAAGATATAA
1 ATAATATAAGACATAA
5400755 TACATAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 1 0.03
23 3 0.09
24 26 0.81
25 2 0.06
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.40
Consensus pattern (24 bp):
ATAATATAAGACATAACTTTTTAT
Found at i:5400816 original size:21 final size:20
Alignment explanation
Indices: 5400767--5400857 Score: 76
Period size: 21 Copynumber: 4.3 Consensus size: 20
5400757 CATAATAACT
* *
5400767 TTTAATATGATGTTAGTAAT-
1 TTTAATATGATTTTA-TTATC
5400787 TTTAAATATGATTTTGATTATC
1 TTT-AATATGATTTT-ATTATC
* *
5400809 TTTTATATGATTTTAATATAC
1 TTTAATATGATTTTATTAT-C
* *
5400830 TTTAATACGATTTTTATAATC
1 TTTAATATGA-TTTTATTATC
5400851 TTTAATA
1 TTTAATA
5400858 CTACCATTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
20 7 0.12
21 40 0.69
22 11 0.19
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.54
Consensus pattern (20 bp):
TTTAATATGATTTTATTATC
Found at i:5400917 original size:21 final size:21
Alignment explanation
Indices: 5400869--5401002 Score: 87
Period size: 21 Copynumber: 6.4 Consensus size: 21
5400859 TACCATTTTA
* * *
5400869 ATAATTTTGATAACCTTTAAT
1 ATAATTTTGTTAACTTTTGAT
5400890 ACT-ATTTTAG-TAACTTTTGAT
1 A-TAATTTT-GTTAACTTTTGAT
5400911 ATAATTTTGTTAA-TCTTTGAT
1 ATAATTTTGTTAACT-TTTGAT
* * * *
5400932 ATGAGTTAG-TAACTTTAGAT
1 ATAATTTTGTTAACTTTTGAT
* * *
5400952 ATAATTTTGATAGCATTTTTAT
1 ATAATTTTGTTAAC-TTTTGAT
* *
5400974 TTAATTTTGTTAACCTTTGAT
1 ATAATTTTGTTAACTTTTGAT
*
5400995 AAAATTTT
1 ATAATTTT
5401003 ATGTTCTGAA
Statistics
Matches: 86, Mismatches: 19, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
20 17 0.20
21 51 0.59
22 18 0.21
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (21 bp):
ATAATTTTGTTAACTTTTGAT
Found at i:5401506 original size:24 final size:22
Alignment explanation
Indices: 5401463--5401528 Score: 78
Period size: 24 Copynumber: 2.9 Consensus size: 22
5401453 ATAATAAAAA
*
5401463 ATAATAAATAAATAACTTTTTAT
1 ATAAT-AATAAATAACTTTTGAT
5401486 ATAATATATAATATAACTTTTGAT
1 ATAATA-ATAA-ATAACTTTTGAT
**
5401510 ACGATAATAAATAACTTTT
1 ATAATAATAAATAACTTTT
5401529 AGAATAGATG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
22 10 0.26
23 13 0.34
24 15 0.39
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (22 bp):
ATAATAATAAATAACTTTTGAT
Found at i:5402096 original size:21 final size:20
Alignment explanation
Indices: 5402046--5402096 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
5402036 TGTTGTCATC
5402046 AATAGCTTTTAATACACTTT
1 AATAGCTTTTAATACACTTT
* * *
5402066 CATAGGTTTTAATATGACTTT
1 AATAGCTTTTAATA-CACTTT
*
5402087 AATAACTTTT
1 AATAGCTTTT
5402097 GACATATTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (20 bp):
AATAGCTTTTAATACACTTT
Found at i:5402129 original size:21 final size:18
Alignment explanation
Indices: 5402105--5402158 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 18
5402095 TTGACATATT
5402105 TTTGATAAACTTTTATATAGG
1 TTTGAT-AACTTTTATA-A-G
5402126 TTTGATAACATTTTATAAG
1 TTTGATAAC-TTTTATAAG
*
5402145 TTTAATAACTTTTA
1 TTTGATAACTTTTA
5402159 ATGTAAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 5 0.16
19 9 0.29
20 4 0.13
21 13 0.42
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (18 bp):
TTTGATAACTTTTATAAG
Found at i:5402295 original size:20 final size:20
Alignment explanation
Indices: 5402272--5402310 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5402262 CAATTTTGGT
5402272 TATT-TTTAATATAAGTTTGA
1 TATTCTTTAATA-AAGTTTGA
*
5402292 TATTCTTTTATAAAGTTTG
1 TATTCTTTAATAAAGTTTG
5402311 GTAATTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.56
Consensus pattern (20 bp):
TATTCTTTAATAAAGTTTGA
Found at i:5404938 original size:28 final size:28
Alignment explanation
Indices: 5404906--5404975 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
5404896 TTCATCTATG
*
5404906 GGGATACTTCAACCCCACCATC-TCTGAA
1 GGGATACTTTAACCCCACCATCTTC-GAA
* *
5404934 GGGATACTTTAACCCTACCATCTTCGAG
1 GGGATACTTTAACCCCACCATCTTCGAA
5404962 GGGATACTTTAACC
1 GGGATACTTTAACC
5404976 TCGGTTTTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 36 0.95
29 2 0.05
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (28 bp):
GGGATACTTTAACCCCACCATCTTCGAA
Found at i:5404938 original size:82 final size:80
Alignment explanation
Indices: 5404770--5404948 Score: 193
Period size: 82 Copynumber: 2.2 Consensus size: 80
5404760 AAAATATTAA
*
5404770 GAAGGG-TATTTCAACCCCGTTTTTACTTTTAAAATACTAAATTTTTCATCTCTAAAGATACTCC
1 GAAGGGATATTTCAACCCCGTTTTTACTTTTAAAATACTAAATTTTTCATCTATAAAGATACTCC
*
5404834 AACTCCACCATCTTC
66 AACCCCACCATCTTC
* * ** ** ***
5404849 GAGGGGATATTTCAACCCCTTTTTTTTACTTTTAAAATGTTGCATTTTTCATCTATGGGGATACT
1 GAAGGGATATTTCAACCCC--GTTTTTACTTTTAAAATACTAAATTTTTCATCTATAAAGATACT
*
5404914 TCAACCCCACCATC-TC
64 CCAACCCCACCATCTTC
5404930 TGAAGGGATACTTT-AACCC
1 -GAAGGGATA-TTTCAACCC
5404949 TACCATCTTC
Statistics
Matches: 82, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
79 5 0.06
80 12 0.15
81 2 0.02
82 60 0.73
83 3 0.04
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (80 bp):
GAAGGGATATTTCAACCCCGTTTTTACTTTTAAAATACTAAATTTTTCATCTATAAAGATACTCC
AACCCCACCATCTTC
Found at i:5405586 original size:13 final size:13
Alignment explanation
Indices: 5405568--5405593 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5405558 TTATTCAATA
5405568 TATCGATACATTG
1 TATCGATACATTG
5405581 TATCGATACATTG
1 TATCGATACATTG
5405594 ATCTTTGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:5406558 original size:20 final size:20
Alignment explanation
Indices: 5406513--5406558 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
5406503 GTTAACAGCC
*
5406513 CATGATTCATGCATTTTAAG
1 CATGTTTCATGCATTTTAAG
5406533 CTATGTTTCATGCA-TTTACAG
1 C-ATGTTTCATGCATTTTA-AG
5406554 CATGT
1 CATGT
5406559 CCAGCACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (20 bp):
CATGTTTCATGCATTTTAAG
Found at i:5414188 original size:2 final size:2
Alignment explanation
Indices: 5414181--5414231 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
5414171 GAACTTTACT
5414181 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
5414223 TA TA TA TA T
1 TA TA TA TA T
5414232 GAAATCATAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5418132 original size:33 final size:33
Alignment explanation
Indices: 5418081--5418147 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
5418071 CAGATGTCAG
*
5418081 AATTGATCAACTCTCTAAAGAATTGTACTCTGA
1 AATTGATCAACTCTCTAAAGAATTATACTCTGA
* *
5418114 AATTGATCAGC-CTCCTAAAGAATTATCCTCTGA
1 AATTGATCAACTCT-CTAAAGAATTATACTCTGA
5418147 A
1 A
5418148 GGTAATTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 28 0.93
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (33 bp):
AATTGATCAACTCTCTAAAGAATTATACTCTGA
Found at i:5418410 original size:6 final size:6
Alignment explanation
Indices: 5418395--5418434 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
5418385 GTAATATACA
*
5418395 TTCTTC TTCTTG TTCTTG TTCTTG TTCTTG TTCTTG TTCT
1 TTCTTG TTCTTG TTCTTG TTCTTG TTCTTG TTCTTG TTCT
5418435 GGTAATATCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.20, G:0.12, T:0.68
Consensus pattern (6 bp):
TTCTTG
Found at i:5422656 original size:50 final size:50
Alignment explanation
Indices: 5422591--5422809 Score: 312
Period size: 50 Copynumber: 4.4 Consensus size: 50
5422581 GTTAATTATC
* * * *
5422591 CTTCATCAACCTTTGACAATAGAGAGAAGTGGTCGTAATTGTTGACGATT
1 CTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATT
* * * * * *
5422641 CTTCACTAACTTTTGACAATAAAGAGATGTGACCATTATTGTTGACGATT
1 CTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATT
* * * *
5422691 CTTCACCAACCTTTGATAATAGAGAGAGGTGGTCATTATTGTTAACGATT
1 CTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATT
5422741 CTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATT
1 CTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATT
5422791 CTTCACCAACCTTTGACAA
1 CTTCACCAACCTTTGACAA
5422810 ATGTGGCCAT
Statistics
Matches: 148, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 148 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (50 bp):
CTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATT
Found at i:5425288 original size:21 final size:21
Alignment explanation
Indices: 5425262--5425302 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
5425252 CACTGACCAC
5425262 AAGCTAGTCATCAGCAGAGAA
1 AAGCTAGTCATCAGCAGAGAA
5425283 AAGCTAGTCATCAGCAGAGA
1 AAGCTAGTCATCAGCAGAGA
5425303 TGTTATCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.15
Consensus pattern (21 bp):
AAGCTAGTCATCAGCAGAGAA
Found at i:5427302 original size:77 final size:77
Alignment explanation
Indices: 5427175--5427327 Score: 306
Period size: 77 Copynumber: 2.0 Consensus size: 77
5427165 AGGATGGTGT
5427175 GGAGATTGATTAGTTCTCAATCGAATCTCCAAGTGGGAGAATTGTTAACTAAATGGGTGGAAAGA
1 GGAGATTGATTAGTTCTCAATCGAATCTCCAAGTGGGAGAATTGTTAACTAAATGGGTGGAAAGA
5427240 TGTTGCCATTGC
66 TGTTGCCATTGC
5427252 GGAGATTGATTAGTTCTCAATCGAATCTCCAAGTGGGAGAATTGTTAACTAAATGGGTGGAAAGA
1 GGAGATTGATTAGTTCTCAATCGAATCTCCAAGTGGGAGAATTGTTAACTAAATGGGTGGAAAGA
5427317 TGTTGCCATTG
66 TGTTGCCATTG
5427328 TTGACTATCC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.30
Consensus pattern (77 bp):
GGAGATTGATTAGTTCTCAATCGAATCTCCAAGTGGGAGAATTGTTAACTAAATGGGTGGAAAGA
TGTTGCCATTGC
Found at i:5427399 original size:50 final size:50
Alignment explanation
Indices: 5427324--5427582 Score: 367
Period size: 50 Copynumber: 5.2 Consensus size: 50
5427314 AGATGTTGCC
* * * *
5427324 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* * * *
5427374 ATTGTT-AGCGATTCTTCATCAACCTTTGACAATAGAGAGAGGTGACTATT
1 ATTGTTGA-CGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* *
5427424 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* *
5427474 ATTGTTGACGATTTTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* * *
5427524 ATTGTTGACGATTCTTCACCAACCTTTAACAATAGAGAGAGATGACCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
5427574 ATTGTTGAC
1 ATTGTTGAC
5427583 TCTAAGTATA
Statistics
Matches: 190, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
49 1 0.01
50 188 0.99
51 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:5430867 original size:24 final size:23
Alignment explanation
Indices: 5430822--5430868 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
5430812 TTGTAATTAT
*
5430822 TAAATTTTATATTTATTTCTTTC
1 TAAATTTTATATTTATTCCTTTC
5430845 TAAATTTTTAATATTT-TTCCTTTC
1 TAAA-TTTT-ATATTTATTCCTTTC
5430869 CATATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 11 0.52
25 6 0.29
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.64
Consensus pattern (23 bp):
TAAATTTTATATTTATTCCTTTC
Found at i:5432172 original size:20 final size:18
Alignment explanation
Indices: 5432134--5432172 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
5432124 TCAATAATAT
*
5432134 TATAATTAAATTTATCTA
1 TATAATTAAATTCATCTA
5432152 TATAATTATATATTCATCTA
1 TATAATTA-A-ATTCATCTA
5432172 T
1 T
5432173 CATACGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 1 0.06
20 9 0.50
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (18 bp):
TATAATTAAATTCATCTA
Found at i:5433015 original size:24 final size:23
Alignment explanation
Indices: 5432988--5433033 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
5432978 CCCCAGATAT
*
5432988 ATGTTTTTTAAACTTTTTTTTTAA
1 ATGTTTTTTAAA-TATTTTTTTAA
*
5433012 ATGTTTTTTCAATATTTTTTTA
1 ATGTTTTTTAAATATTTTTTTA
5433034 GTTTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (23 bp):
ATGTTTTTTAAATATTTTTTTAA
Found at i:5433041 original size:12 final size:12
Alignment explanation
Indices: 5433026--5433052 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5433016 TTTTTCAATA
5433026 TTTTTTTAGTTT
1 TTTTTTTAGTTT
5433038 TTTTTTTAGTTT
1 TTTTTTTAGTTT
5433050 TTT
1 TTT
5433053 ATAGGTTTAT
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:0.07, C:0.00, G:0.07, T:0.85
Consensus pattern (12 bp):
TTTTTTTAGTTT
Found at i:5440635 original size:91 final size:89
Alignment explanation
Indices: 5440400--5440802 Score: 540
Period size: 91 Copynumber: 4.5 Consensus size: 89
5440390 CTATCATGTT
* * * *
5440400 ATTAGTCAAATATTTTATGTCGTGTTTGAAGAAATCTGATACCCCATGCATCTGTCACATTTTTC
1 ATTAGTCAAATATTTTA--TCATGTTAGAAGGAATCTGATACCCCATGCATCTGTCACATCTTTC
* *
5440465 GGGTTTCAAAATTAAATTTATTAGGC
64 GGGTTCCAAGATTAAATTTATTAGGC
*
5440491 ATT-GTCAAATATTTTATCATGTTAGAAGGAATCTGATACCCCATGCACCTGTCACATCTTTCGG
1 ATTAGTCAAATATTTTATCATGTTAGAAGGAATCTGATACCCCATGCATCTGTCACATCTTTCGG
5440555 GTTCCAAGATTAAATTTATTAGGC
66 GTTCCAAGATTAAATTTATTAGGC
* * *
5440579 ATTAGTTAAATATTTTCT-ATCGTATCAAAAGGAATCTGATACCCCATGCATCTGTCACATCTTT
1 ATTAGTCAAATATTTTATCAT-GT-T-AGAAGGAATCTGATACCCCATGCATCTGTCACATCTTT
*
5440643 CGGGTTCCAAGATTAAATTTTTTAGGC
63 CGGGTTCCAAGATTAAATTTATTAGGC
* * ** * * *
5440670 ATTGGTCAAATATATTTTTTTTGTGTTAGAAGGAATCTGATACCCTATGCATTTGTCACATATTT
1 ATTAGTC-AA-ATA-TTTTATCATGTTAGAAGGAATCTGATACCCCATGCATCTGTCACATCTTT
*
5440735 CGAGTTCCAAGATTAAATTTATTAGGC
63 CGGGTTCCAAGATTAAATTTATTAGGC
*
5440762 ATTAGTCAAATATTTTGTCATGTTAGAAGGAATCTGATACC
1 ATTAGTCAAATATTTTATCATGTTAGAAGGAATCTGATACC
5440803 AATTGAATTT
Statistics
Matches: 278, Mismatches: 26, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
88 70 0.25
89 40 0.14
90 17 0.06
91 72 0.26
92 67 0.24
93 4 0.01
94 7 0.03
95 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (89 bp):
ATTAGTCAAATATTTTATCATGTTAGAAGGAATCTGATACCCCATGCATCTGTCACATCTTTCGG
GTTCCAAGATTAAATTTATTAGGC
Found at i:5440775 original size:183 final size:177
Alignment explanation
Indices: 5440400--5440802 Score: 547
Period size: 183 Copynumber: 2.2 Consensus size: 177
5440390 CTATCATGTT
* * * *
5440400 ATTAGTCAAATATTTTATGTCGTGTTTGAAGAAATCTGATACCCCATGCATCTGTCACATTTTTC
1 ATTAGTCAAATATTTTATATC--GTTAGAAGGAATCTGATACCCCATGCATCTGTCACATCTTTC
*
5440465 GGGTTTCAAAATTAAATTTATTAGGCATTGTCAAATATTTTATCATGTTAGAAGGAATCTGATAC
64 GGGTTCCAAAATTAAATTTATTAGGCATTGTCAAATATTTTATCATGTTAGAAGGAATCTGATAC
* *
5440530 CCCATGCACCTGTCACATCTTTCGGGTTCCAAGATTAAATTTATTAGGC
129 CCCATGCACCTGTCACATATTTCGAGTTCCAAGATTAAATTTATTAGGC
* * *
5440579 ATTAGTTAAATATTTTCTATCGTATCAAAAGGAATCTGATACCCCATGCATCTGTCACATCTTTC
1 ATTAGTCAAATATTTTATATCGT-T-AGAAGGAATCTGATACCCCATGCATCTGTCACATCTTTC
* * * **
5440644 GGGTTCCAAGATTAAATTTTTTAGGCATTGGTCAAATATATTTTTTTTGTGTTAGAAGGAATCTG
64 GGGTTCCAAAATTAAATTTATTAGGCATT-GTC-AA-ATA-TTTTATCATGTTAGAAGGAATCTG
* **
5440709 ATACCCTATGCATTTGTCACATATTTCGAGTTCCAAGATTAAATTTATTAGGC
125 ATACCCCATGCACCTGTCACATATTTCGAGTTCCAAGATTAAATTTATTAGGC
*
5440762 ATTAGTCAAATATTTTGTCAT-GTTAGAAGGAATCTGATACC
1 ATTAGTCAAATATTTTAT-ATCGTTAGAAGGAATCTGATACC
5440803 AATTGAATTT
Statistics
Matches: 196, Mismatches: 21, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
177 2 0.01
178 1 0.01
179 79 0.40
180 3 0.02
181 18 0.09
182 4 0.02
183 87 0.44
184 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (177 bp):
ATTAGTCAAATATTTTATATCGTTAGAAGGAATCTGATACCCCATGCATCTGTCACATCTTTCGG
GTTCCAAAATTAAATTTATTAGGCATTGTCAAATATTTTATCATGTTAGAAGGAATCTGATACCC
CATGCACCTGTCACATATTTCGAGTTCCAAGATTAAATTTATTAGGC
Found at i:5440970 original size:88 final size:88
Alignment explanation
Indices: 5440808--5441335 Score: 485
Period size: 88 Copynumber: 5.9 Consensus size: 88
5440798 ATACCAATTG
* * * *
5440808 AATTTATTAGGCATTAGTTAAATATTTTCTATCGTATCAGAAGGAATCTGAT-GTCCTATGCATC
1 AATTTATTAGGCATTAGTCAAATATTTTCTATCATATCAGAAAGAATCTGATACTCC-ATGCATC
* *
5440872 TCTCATATCTTTCGAGTTTCAAGA
65 TGTCACATCTTTCGAGTTTCAAGA
* * * * *
5440896 AATTTATTAGGCATTTGTCAAATATTTTCTATCATGTTAGAAAGAATCTGATACTCCATTCATTT
1 AATTTATTAGGCATTAGTCAAATATTTTCTATCATATCAGAAAGAATCTGATACTCCATGCATCT
*
5440961 GTCACATCTTT-TAGGTTTCAAGA
66 GTCACATCTTTCGA-GTTTCAAGA
* *
5440984 TTAATTTTATTAAGTATTAGTCAAATATTTTCTATCATATCAG-AAGAAATCTGATA-TCTCATG
1 --AA-TTTATTAGGCATTAGTCAAATATTTTCTATCATATCAGAAAG-AATCTGATACTC-CATG
* * * * *
5441047 CATCTATTACATCTTTTGGGTTTTAAGA
61 CATCTGTCACATCTTTCGAGTTTCAAGA
* * * * * * *
5441075 AATTTATTAGGCATTAGTCAAATATTTTTTGTCGTGTCAAAAAGAATCTAATAC-CTTATGCATC
1 AATTTATTAGGCATTAGTCAAATATTTTCTATCATATCAGAAAGAATCTGATACTC-CATGCATC
* ** *
5441139 TATTGCATCTTTCGGGTTTCAAGCA
65 TGTCACATCTTTCGAGTTTCAAG-A
* * * *
5441164 TAATTTTATTAGGCATTAGTCAAATATTTTCTGTTATATCAGAAGGAATCTGATAC-CCAATGTA
1 -AA-TTTATTAGGCATTAGTCAAATATTTTCTATCATATCAGAAAGAATCTGATACTCC-ATGCA
5441228 TCTGTCACATCTTTC-AGGTTTCAAGA
63 TCTGTCACATCTTTCGA-GTTTCAAGA
* * * ** * * * * *
5441254 AATTTATTAGGCATCAGTAAAATATTTTCTGTTGTATTAGTAGGAATCTGATACCCCATGCATTT
1 AATTTATTAGGCATTAGTCAAATATTTTCTATCATATCAGAAAGAATCTGATACTCCATGCATCT
*
5441319 GCCACATCTTTCGAGTT
66 GTCACATCTTTCGAGTT
5441336 CGGAGATTAA
Statistics
Matches: 366, Mismatches: 57, Indels: 34
0.80 0.12 0.07
Matches are distributed among these distances:
87 1 0.00
88 205 0.56
89 14 0.04
90 10 0.03
91 136 0.37
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (88 bp):
AATTTATTAGGCATTAGTCAAATATTTTCTATCATATCAGAAAGAATCTGATACTCCATGCATCT
GTCACATCTTTCGAGTTTCAAGA
Found at i:5441331 original size:179 final size:177
Alignment explanation
Indices: 5440810--5441353 Score: 615
Period size: 179 Copynumber: 3.0 Consensus size: 177
5440800 ACCAATTGAA
* * * * *
5440810 TTTATTAGGCATTAGTTAAATATTTTCTATCGTATCAGAAGGAATCTGATGTCCTATGCATCTCT
1 TTTATTAGGCATTAGTCAAATATTTTCTATCATATCAGAAGGAATCTGAT-ACCCATGCATCTAT
* * * *
5440875 CATATCTTTCGAGTTTCAAGAAATTTATTAGGCATTTGTCAAATATTTTCTATCATGTTAGAAAG
65 CACATCTTTCG-GTTTCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTGTCGTGTTAGAAAG
* * **
5440940 AATCTGATACTCCATTCATTTGTCACATCTTTTAGGTTTCAAGATTAAT
129 AATCTGATACCCCATGCATTTGTCACATCTTTCGGGTTTCAAGATTAAT
* * * *
5440989 TTTATTAAGTATTAGTCAAATATTTTCTATCATATCAGAAGAAATCTGATATCTCATGCATCTAT
1 TTTATTAGGCATTAGTCAAATATTTTCTATCATATCAGAAGGAATCTGATA-CCCATGCATCTAT
* * * * * *
5441054 TACATCTTTTGGGTTTTAAGAAATTTATTAGGCATTAGTCAAATATTTTTTGTCGTGTCAAAAAG
65 CACATC-TTTCGGTTTCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTGTCGTGTTAGAAAG
* ** * * **
5441119 AATCTAATACCTTATGCATCTATTGCATCTTTCGGGTTTCAAGCA-TAAT
129 AATCTGATACCCCATGCATTTGTCACATCTTTCGGGTTTCAAG-ATTAAT
* * * *
5441168 TTTATTAGGCATTAGTCAAATATTTTCTGTTATATCAGAAGGAATCTGATACCCAATGTATCTGT
1 TTTATTAGGCATTAGTCAAATATTTTCTATCATATCAGAAGGAATCTGATACCC-ATGCATCTAT
* * * * * *
5441233 CACATCTTTCAGGTTTCAAGAAATTTATTAGGCATCAGTAAAATATTTTCTGTTGTATTAGTAGG
65 CACATCTTTC-GGTTTCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTGTCGTGTTAGAAAG
* * *
5441298 AATCTGATACCCCATGCATTTGCCACATCTTTCGAG-TTCGGAGATTAAT
129 AATCTGATACCCCATGCATTTGTCACATCTTTCGGGTTTC-AAGATTAAT
5441347 TTTATTA
1 TTTATTA
5441354 CATATTATAA
Statistics
Matches: 298, Mismatches: 60, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
178 9 0.03
179 284 0.95
180 5 0.02
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (177 bp):
TTTATTAGGCATTAGTCAAATATTTTCTATCATATCAGAAGGAATCTGATACCCATGCATCTATC
ACATCTTTCGGTTTCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTGTCGTGTTAGAAAGAA
TCTGATACCCCATGCATTTGTCACATCTTTCGGGTTTCAAGATTAAT
Found at i:5441674 original size:15 final size:15
Alignment explanation
Indices: 5441654--5441703 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
5441644 CATCATTAGT
5441654 GCTTTTTCCTGAATG
1 GCTTTTTCCTGAATG
* * *
5441669 GCTTTTTCTTGACTA
1 GCTTTTTCCTGAATG
5441684 GCTTTTTCCTGAATG
1 GCTTTTTCCTGAATG
5441699 GCTTT
1 GCTTT
5441704 ATTTGTAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.12, C:0.20, G:0.18, T:0.50
Consensus pattern (15 bp):
GCTTTTTCCTGAATG
Found at i:5442802 original size:31 final size:32
Alignment explanation
Indices: 5442742--5442819 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 32
5442732 TACATGTATG
** *
5442742 GATGTATCGATATGTTCTATCTTTTTTACCCA
1 GATGTATCGATACATTCTATCTTTTTTACCAA
*
5442774 TATGTATCGATACATTCTATC-TTTTTACCAA
1 GATGTATCGATACATTCTATCTTTTTTACCAA
5442805 GATGTATCGATACAT
1 GATGTATCGATACAT
5442820 GTATGAATGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 23 0.56
32 18 0.44
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.44
Consensus pattern (32 bp):
GATGTATCGATACATTCTATCTTTTTTACCAA
Found at i:5442854 original size:71 final size:71
Alignment explanation
Indices: 5442775--5442907 Score: 232
Period size: 71 Copynumber: 1.9 Consensus size: 71
5442765 TTTTACCCAT
*
5442775 ATGTATCGATACATTCTATCTTTTTACCAAGATGTATCGATACA-TGTATGAATGTATCAATACA
1 ATGTATCGATACATTCTATCTTTTTACCAAGATGTATCGATACATTGAAT-AATGTATCAATACA
5442839 TTCTTTA
65 TTCTTTA
*
5442846 ATGTATCGATACATTCTGTCTTTTTACCAAGATGTATCGATACATTGAATAATGTATCAATA
1 ATGTATCGATACATTCTATCTTTTTACCAAGATGTATCGATACATTGAATAATGTATCAATA
5442908 GATCTAGTTA
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
71 55 0.93
72 4 0.07
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (71 bp):
ATGTATCGATACATTCTATCTTTTTACCAAGATGTATCGATACATTGAATAATGTATCAATACAT
TCTTTA
Found at i:5442862 original size:20 final size:20
Alignment explanation
Indices: 5442806--5442862 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
5442796 TTTTACCAAG
*
5442806 ATGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTGA
* *
5442826 ATGTATCAATACATTCTTTA
1 ATGTATCGATACATTCTTGA
5442846 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
5442863 GTCTTTTTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTCTTGA
Found at i:5446359 original size:23 final size:23
Alignment explanation
Indices: 5446329--5446375 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
5446319 TACAACTTGG
5446329 AAGCATATCAGTGCCGTATTTGC
1 AAGCATATCAGTGCCGTATTTGC
*
5446352 AAGCATATCAGTGCTGTATTTGC
1 AAGCATATCAGTGCCGTATTTGC
5446375 A
1 A
5446376 TGCCATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (23 bp):
AAGCATATCAGTGCCGTATTTGC
Found at i:5450735 original size:20 final size:20
Alignment explanation
Indices: 5450710--5450762 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
5450700 AACTCTTATT
5450710 TGTATCGATACACA-TGCAGA
1 TGTATCGATACACAGTGCA-A
5450730 TGTATCGATACA-AGTTGCAA
1 TGTATCGATACACAG-TGCAA
5450750 TGTATCGATACAC
1 TGTATCGATACAC
5450763 TATGGAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.03
20 25 0.83
21 4 0.13
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (20 bp):
TGTATCGATACACAGTGCAA
Found at i:5451318 original size:34 final size:33
Alignment explanation
Indices: 5451277--5451373 Score: 131
Period size: 34 Copynumber: 2.9 Consensus size: 33
5451267 AAGTGATTGA
**
5451277 AAAGTTCTATCTTAGCCTTCGAAAAGATACTAT
1 AAAGTTCTATCTTAGCCTTCGAAAAGATAAGAT
* *
5451310 AGAGGTTCTATCTTAGCCTTTGAAAAGATAAAGAT
1 A-AAGTTCTATCTTAGCCTTCGAAAAGAT-AAGAT
*
5451345 AAAGTTCTATCTTAGCTTTCGAAAAGATA
1 AAAGTTCTATCTTAGCCTTCGAAAAGATA
5451374 GTGTTGTAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
33 2 0.04
34 49 0.89
35 4 0.07
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.33
Consensus pattern (33 bp):
AAAGTTCTATCTTAGCCTTCGAAAAGATAAGAT
Found at i:5455200 original size:21 final size:21
Alignment explanation
Indices: 5455175--5455217 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5455165 ATTGGTTTTC
5455175 TTCATTGCATCCATGTTGCTT
1 TTCATTGCATCCATGTTGCTT
5455196 TTCATTGCATCCATGTTGCTT
1 TTCATTGCATCCATGTTGCTT
5455217 T
1 T
5455218 GCTATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.23, G:0.14, T:0.49
Consensus pattern (21 bp):
TTCATTGCATCCATGTTGCTT
Found at i:5456686 original size:62 final size:62
Alignment explanation
Indices: 5456494--5457010 Score: 418
Period size: 62 Copynumber: 8.4 Consensus size: 62
5456484 TGAGAACGGT
* * * ** * * *
5456494 TGCCACCAAATTATGTGGGCGTT-GAAA-GAAAA-ACATCTTGCTCTTTGGGGACTAGAAGG
1 TGCCACCAACTTATGTGGGCTTTAAAAAGGAAAAGGTATCCTGCTCTTTGAGGACTAAAAGG
* * * * ** * * *
5456553 TGCCACCAACTCATCTAGGCTTTGAAAAGG-AAAGGCGTCCTGCACTTTGAGGACTGAAAGA
1 TGCCACCAACTTATGTGGGCTTTAAAAAGGAAAAGGTATCCTGCTCTTTGAGGACTAAAAGG
* * * * * * * *
5456614 TGCCAACAACTTGTGTGGGCTTTAGAAAGGAAAAAGTATCTTGCTCTTTGAGAATTGAAAGG
1 TGCCACCAACTTATGTGGGCTTTAAAAAGGAAAAGGTATCCTGCTCTTTGAGGACTAAAAGG
* * * * *
5456676 TGTCACCAACTCATGTGAGCTTTAAAAAGGAAAAGGCATCCTACTCTTTGAGGACTGAAAA-G
1 TGCCACCAACTTATGTGGGCTTTAAAAAGGAAAAGGTATCCTGCTCTTTGAGGACT-AAAAGG
* * * * * * *
5456738 TGCCATCACCTTATATGGGCTTTAAAAAGGAAAAGGTGTCTTGCTCTTTAAGGACTAAAAGA
1 TGCCACCAACTTATGTGGGCTTTAAAAAGGAAAAGGTATCCTGCTCTTTGAGGACTAAAAGG
* * * * *
5456800 TGCCATCAACTTATGTGGGC-TTAAAAATGAAAAGGCATCATGTTCTTTGAGGACTAAAAGG
1 TGCCACCAACTTATGTGGGCTTTAAAAAGGAAAAGGTATCCTGCTCTTTGAGGACTAAAAGG
* * * * * * * * *
5456861 TGCCACCAACTTGTGTAGGTTTTAAAAAGAAAAAGGTGTCCTACTATTTGACGACTAAAAAG
1 TGCCACCAACTTATGTGGGCTTTAAAAAGGAAAAGGTATCCTGCTCTTTGAGGACTAAAAGG
* * ** * * *
5456923 TGCCACCAACTTGTGTGGCCTTTAAAAAGGAAAAGGTGGCATGCTCTTTAAGGACTAATAGG
1 TGCCACCAACTTATGTGGGCTTTAAAAAGGAAAAGGTATCCTGCTCTTTGAGGACTAAAAGG
* * * *
5456985 TACCACTAACTTGTGT-GGCCTTAAAA
1 TGCCACCAACTTATGTGGGCTTTAAAA
5457011 GGCGTCCTCC
Statistics
Matches: 358, Mismatches: 93, Indels: 12
0.77 0.20 0.03
Matches are distributed among these distances:
59 18 0.05
60 6 0.02
61 105 0.29
62 226 0.63
63 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.26
Consensus pattern (62 bp):
TGCCACCAACTTATGTGGGCTTTAAAAAGGAAAAGGTATCCTGCTCTTTGAGGACTAAAAGG
Found at i:5456771 original size:124 final size:124
Alignment explanation
Indices: 5456528--5456958 Score: 383
Period size: 123 Copynumber: 3.5 Consensus size: 124
5456518 AAAGAAAAAC
** * * * * *
5456528 ATCTTGCTCTTTGGGGACTAGAAGGTGCCACCAACTCATCT-AGGCTTTGAAAAGG-AAAGGCGT
1 ATCTTGCTCTTTAAGAACTAAAAGGTGCCACCAACTCATGTGA-GCTTTAAAAAGGAAAAGGCAT
* * * *
5456591 CCTGCACTTTGAGGACTG-AAAGATGCCAACAACTTGTGTGGGCTTTAGAAAGGAAAAAGT
65 CCTGCTCTTTGAGGACTGAAAAG-TGCCAACAACTTATATGGGCTTTAAAAAGGAAAAAGT
* * * *
5456651 ATCTTGCTCTTTGAGAATTGAAAGGTGTCACCAACTCATGTGAGCTTTAAAAAGGAAAAGGCATC
1 ATCTTGCTCTTTAAGAACTAAAAGGTGCCACCAACTCATGTGAGCTTTAAAAAGGAAAAGGCATC
* * * *
5456716 CTACTCTTTGAGGACTGAAAAGTGCCATCACCTTATATGGGCTTTAAAAAGGAAAAGGT
66 CTGCTCTTTGAGGACTGAAAAGTGCCAACAACTTATATGGGCTTTAAAAAGGAAAAAGT
* * * * * * *
5456775 GTCTTGCTCTTTAAGGACTAAAAGATGCCATCAACTTATGTGGGC-TTAAAAATGAAAAGGCATC
1 ATCTTGCTCTTTAAGAACTAAAAGGTGCCACCAACTCATGTGAGCTTTAAAAAGGAAAAGGCATC
* * * * * * *
5456839 ATGTTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTAGGTTTTAAAAA-GAAAAAGGT
66 CTGCTCTTTGAGGACTGAAAA-GTGCCAACAACTTATATGGGCTTTAAAAAGGAAAAA-GT
* * * * * * **
5456898 GTCCTACTATTTGACG-ACTAAAAAGTGCCACCAACTTGTGTG-GCCTTTAAAAAGGAAAAGG
1 ATCTTGCTCTTT-AAGAACTAAAAGGTGCCACCAACTCATGTGAG-CTTTAAAAAGGAAAAGG
5456959 TGGCATGCTC
Statistics
Matches: 253, Mismatches: 47, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
122 10 0.04
123 133 0.53
124 106 0.42
125 4 0.02
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.26
Consensus pattern (124 bp):
ATCTTGCTCTTTAAGAACTAAAAGGTGCCACCAACTCATGTGAGCTTTAAAAAGGAAAAGGCATC
CTGCTCTTTGAGGACTGAAAAGTGCCAACAACTTATATGGGCTTTAAAAAGGAAAAAGT
Found at i:5456862 original size:185 final size:186
Alignment explanation
Indices: 5456543--5456980 Score: 497
Period size: 185 Copynumber: 2.4 Consensus size: 186
5456533 GCTCTTTGGG
* * * * * * * * * *
5456543 GACTAGAAGGTGCCACCAACTCATCTAGGCTTTGAAAAGG-AAAGGCGTCCTGCACTTTGAGGAC
1 GACTAAAAAGTGCCACCAACTTATATGGGCTTTAAAAAGGAAAAGGTGTCATGCTCTTTAAGGAC
* * * * * * *
5456607 TGAAAGATGCCAACAACTTGTGTGGGCTTTAGAAAGGAAAAAGTATCTTGCTCTTTGAGAATTGA
66 TAAAAGATGCCAACAACTTATGTGGGCTTTAAAAAGGAAAAAGCATCATGCTCTTTGAGAACTAA
* * * *
5456672 AAGGTGTCACCAACTCATGTG-A-GCTTTAAAAAGGAAAAGGCATCCTACTCTTTGAG
131 AAGGTGCCACCAACT--TGTGTAGGCTTTAAAAAGAAAAAGGCATCCTACTATTTGAC
* * * *
5456728 GACTGAAAAGTGCCATCACCTTATATGGGCTTTAAAAAGGAAAAGGTGTCTTGCTCTTTAAGGAC
1 GACTAAAAAGTGCCACCAACTTATATGGGCTTTAAAAAGGAAAAGGTGTCATGCTCTTTAAGGAC
* * * * *
5456793 TAAAAGATGCCATCAACTTATGTGGGC-TTAAAAATGAAAAGGCATCATGTTCTTTGAGGACTAA
66 TAAAAGATGCCAACAACTTATGTGGGCTTTAAAAAGGAAAAAGCATCATGCTCTTTGAGAACTAA
* **
5456857 AAGGTGCCACCAACTTGTGTAGGTTTTAAAAAGAAAAAGGTGTCCTACTATTTGAC
131 AAGGTGCCACCAACTTGTGTAGGCTTTAAAAAGAAAAAGGCATCCTACTATTTGAC
* * * *
5456913 GACTAAAAAGTGCCACCAACTTGTGTGGCCTTTAAAAAGGAAAAGGTGGCATGCTCTTTAAGGAC
1 GACTAAAAAGTGCCACCAACTTATATGGGCTTTAAAAAGGAAAAGGTGTCATGCTCTTTAAGGAC
5456978 TAA
66 TAA
5456981 TAGGTACCAC
Statistics
Matches: 210, Mismatches: 40, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
183 4 0.02
184 1 0.00
185 161 0.77
186 44 0.21
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (186 bp):
GACTAAAAAGTGCCACCAACTTATATGGGCTTTAAAAAGGAAAAGGTGTCATGCTCTTTAAGGAC
TAAAAGATGCCAACAACTTATGTGGGCTTTAAAAAGGAAAAAGCATCATGCTCTTTGAGAACTAA
AAGGTGCCACCAACTTGTGTAGGCTTTAAAAAGAAAAAGGCATCCTACTATTTGAC
Found at i:5457154 original size:154 final size:153
Alignment explanation
Indices: 5456888--5457165 Score: 389
Period size: 154 Copynumber: 1.8 Consensus size: 153
5456878 GGTTTTAAAA
**
5456888 AGAAAAAGGTGTCCTACTATTTGACGACTAAAAAGTGCCACCAACTTGTGTGGCCTTTAAAAAGG
1 AGAAAAAGGCATCCTACTATTTGACGACTAAAAAGTGCCACCAACTTGTGTGGCCTTTAAAAAGG
* * *
5456953 AAAAGGTGGCATGCTCTTTAAGGACTAATAGGTACCACTAACTTGTGT-GGCCTTAAAAGGCGTC
66 AAAAGGCGGCATGCTCTTTAAGGACTAAAAGGTACCACCAACTTGTGTAGGCCTTAAAAGGCGTC
5457017 CTCCTTTTTTAGGACTAAAGTAT
131 CTCCTTTTTTAGGACTAAAGTAT
* * *
5457040 AGAAAAAGGCATCCTACTCTTTGATGACTAAAAAAAAGTGCCACCAACTTGTGTGGGCTTT-AAA
1 AGAAAAAGGCATCCTACTATTTGACGACT---AAAAAGTGCCACCAACTTGTGTGGCCTTTAAAA
* * * * * *
5457104 AGGAGAAGGCGTCCTGCTCTTTTAGGACTAAAAGGTGCCACCAACTTGTGTAGGCTTTAAAA
63 AGGAAAAGGCGGCATGCTCTTTAAGGACTAAAAGGTACCACCAACTTGTGTAGGCCTTAAAA
5457166 AGAGAAGGCG
Statistics
Matches: 108, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
152 25 0.23
154 46 0.43
155 37 0.34
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (153 bp):
AGAAAAAGGCATCCTACTATTTGACGACTAAAAAGTGCCACCAACTTGTGTGGCCTTTAAAAAGG
AAAAGGCGGCATGCTCTTTAAGGACTAAAAGGTACCACCAACTTGTGTAGGCCTTAAAAGGCGTC
CTCCTTTTTTAGGACTAAAGTAT
Found at i:5457160 original size:61 final size:61
Alignment explanation
Indices: 5457043--5457766 Score: 589
Period size: 62 Copynumber: 11.5 Consensus size: 61
5457033 AAAGTATAGA
* * * *
5457043 AAAAGGCATCCTACTCTTTGATGACTAAAAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
1 AAAAGGCGTCCTGCTCTTTGAGGACT---AAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG
* * * *
5457107 AGAAGGCGTCCTGCTCTTTTAGGACTAAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAAG
1 AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG
* * * *
5457168 AGAAGGCGTTCTGCTTTTTGAGGACTAAAAGGTGCCAGCAACTTGTGT-GGCTTTAAAAAGG
1 AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGG
* * * * * *
5457229 AAAAGACGTCCTGCTTTTTGAGGACTGAAAA-GTGCTATCAACTTATGTGGGCTTTGAAAAGA
1 AAAAGGCGTCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGG
* * *
5457291 AAAAGACGTCTTGCT-TTCTGAGGACTAACACA-ATGCCACCAACTTGTGTGGGCTTTGAAAAGA
1 AAAAGGCGTCCTGCTCTT-TGAGGACTAA-A-AGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-
*
5457354 A
61 G
* * * * ** * *
5457355 AAAAGGTGTCCTTCTCTTGGAGGACT-AAAGGATAG-AAAAAGACGTCTTTCTCTTTAAGGGC-T
1 AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGG-T-GCCACCA-A---C--T-TGTGT--GGGCTT
* *
5457417 AAATGATAGA
55 TAA--A-AGG
* * * *
5457427 AAAAGGCATCCCGCTCTTTGAGGACTAAAAAGGGTGCCACCAACTTGTGTGAGCTTTAAAAGA
1 AAAAGGCGTCCTGCTCTTTGAGGACT-AAAA-GGTGCCACCAACTTGTGTGGGCTTTAAAAGG
* * *
5457490 AAAAGGCATCTTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGG
1 AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGG
* * *
5457552 AAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGCGCCACCAACTTGTGTGGGTTTTAAAAAGG
1 AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGG
* * * * * * * *
5457614 AAAAAGTGTCCTACTCTTTGAGGAGTAAAAGTTGTCACCAACTTGTGTGAGCCTTAAAAAGG
1 AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTG-GGCTTTAAAAGG
** * * * *
5457676 AAAAGATGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTATGGGCTCTAAAAAGG
1 AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCT-TTAAAAGG
* * *
5457738 AAAAGTCATCCTGCTCTTTGAGAACTAAA
1 AAAAGGCGTCCTGCTCTTTGAGGACTAAA
5457767 GAATAGAAAA
Statistics
Matches: 545, Mismatches: 84, Indels: 64
0.79 0.12 0.09
Matches are distributed among these distances:
60 6 0.01
61 150 0.28
62 225 0.41
63 61 0.11
64 43 0.08
65 5 0.01
66 3 0.01
67 4 0.01
68 1 0.00
69 1 0.00
70 6 0.01
71 1 0.00
72 27 0.05
73 4 0.01
74 6 0.01
75 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (61 bp):
AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG
Found at i:5457845 original size:64 final size:65
Alignment explanation
Indices: 5457771--5458055 Score: 282
Period size: 62 Copynumber: 4.5 Consensus size: 65
5457761 ACTAAAGAAT
* *
5457771 AGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAG-AGGAGTGCCACCAACTTGTGTGGGCTTT-AA
1 AGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGCA-GAGTACCACCAACTCGTGTGGGCTTTGAA
5457834 A
65 A
** *
5457835 AGAAAAAGGCGTCCTTTTCTTTGAGGACT--AGCAGAATACCACCAACTCGTGTGGGCTTTGAAA
1 AGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGCAGAGTACCACCAACTCGTGTGGGCTTTGAAA
* ** * *
5457898 AGAAAAAAGAAT-TTGCTCTTTGAGGACT--AGCAGAGTGCCACCAACTCGTGTGGGCTTTGAAA
1 AGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGCAGAGTACCACCAACTCGTGTGGGCTTTGAAA
* * * * * * * **
5457960 AGAAAAATGCATCCTACTTTTTGAGGACTAAA-AATAGGTACCACCAATTTATGTGGGCTTT-AA
1 AGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGCAGA-GTACCACCAACTCGTGTGGGCTTTGAA
5458023 A
65 A
* * * *
5458024 AGAGAAAGGTGTCATGTTCTTTGAGGACTAAA
1 AGAAAAAGGCGTCCTGCTCTTTGAGGACTAAA
5458056 AGATAAAAAA
Statistics
Matches: 183, Mismatches: 32, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
62 80 0.44
63 26 0.14
64 56 0.31
65 21 0.11
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (65 bp):
AGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGCAGAGTACCACCAACTCGTGTGGGCTTTGAAA
Found at i:5457872 original size:101 final size:98
Alignment explanation
Indices: 5457683--5457864 Score: 240
Period size: 100 Copynumber: 1.8 Consensus size: 98
5457673 AGGAAAAGAT
* * *
5457683 GTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTATGGGCTCTAAAAAGGAAAAGTCATC
1 GTCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTATGGGCTCTAAAAAGAAAAAGGCATC
5457748 CTGCTCTTTGAGAACTAAAGAATAGAAAAAGGC
66 CTGCTCTTTGAGAACTAAAGAATAGAAAAAGGC
* * *
5457781 GTCCTGCTCTTTGAGGACTAAAGAGGAGTGCCACCAACTTGTGTGGGCT-TTAAAAGAAAAAGGC
1 GTCCTACTCTTTGAGGACTAAA-A-G-GTGCCACCAACTTGTATGGGCTCTAAAAAGAAAAAGGC
* ** *
5457845 GTCCTTTTCTTTGAGGACTA
63 ATCCTGCTCTTTGAGAACTA
5457865 GCAGAATACC
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
98 20 0.28
99 1 0.01
100 29 0.41
101 21 0.30
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (98 bp):
GTCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTATGGGCTCTAAAAAGAAAAAGGCATC
CTGCTCTTTGAGAACTAAAGAATAGAAAAAGGC
Found at i:5457940 original size:225 final size:220
Alignment explanation
Indices: 5457552--5457996 Score: 497
Period size: 225 Copynumber: 2.0 Consensus size: 220
5457542 TTTAAAAAGG
* *
5457552 AAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGCGCCACCAACTTGTGTGGGTTTTAAAAAGGAAA
1 AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGCGCCACCAACTTGTGTGGGCTTTAAAAAGGAAA
* * * ** * *
5457617 AAGTGTCCTACTCTTTGAGGAGTAAAAGTTGTCACCAACTTGTGTGAGCCTTAAAAAGGAAAAGA
66 AAGCGTCCTACTCTTTGAGGACTAAAAGATACCACCAACTCGTGTGAGCCTTAAAAAGAAAAAGA
* *
5457682 TGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTATGGGCTCTAAAAAGGAAAA-GTCA
131 TGT-CTACTCTTTGAGGACTGAAAGGTGCCACCAACTCGTATGGGCTCTAAAAAGAAAAATG-CA
*
5457746 TCCTGCTCTTTGAGAACTAAAGAATAGA
194 TCCTACTCTTTGAGAACTAAA-AATAGA
*
5457774 AAAAGGCGTCCTGCTCTTTGAGGACTAAAGAGGAGTGCCACCAACTTGTGTGGGCTTT-AAAA-G
1 AAAAGGCGTCCTGCTCTTTGAGGACTAAA-A-G-GCGCCACCAACTTGTGTGGGCTTTAAAAAGG
** ** * * *
5457837 AAAAAGGCGTCCTTTTCTTTGAGGACTAGCAGAATACCACCAACTCGTGTGGGCTTTGAAAAGAA
63 AAAAA-GCGTCCTACTCTTTGAGGACTAAAAG-ATACCACCAACTCGTGTGAGCCTTAAAAAG-A
* * * * *
5457902 AAAAGAAT-T-TGCTCTTTGAGGACT-AGCAGAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAA
125 AAAAG-ATGTCTACTCTTTGAGGACTGA-AAG-GTGCCACCAACTCGTATGGGCTCTAAAAAGAA
* *
5457964 AAATGCATCCTACTTTTTGAGGACTAAAAATAG
187 AAATGCATCCTACTCTTTGAGAACTAAAAATAG
5457997 GTACCACCAA
Statistics
Matches: 186, Mismatches: 27, Indels: 18
0.81 0.12 0.08
Matches are distributed among these distances:
222 28 0.15
223 8 0.04
224 46 0.25
225 95 0.51
226 7 0.04
227 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (220 bp):
AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGCGCCACCAACTTGTGTGGGCTTTAAAAAGGAAA
AAGCGTCCTACTCTTTGAGGACTAAAAGATACCACCAACTCGTGTGAGCCTTAAAAAGAAAAAGA
TGTCTACTCTTTGAGGACTGAAAGGTGCCACCAACTCGTATGGGCTCTAAAAAGAAAAATGCATC
CTACTCTTTGAGAACTAAAAATAGA
Found at i:5458179 original size:61 final size:62
Alignment explanation
Indices: 5458100--5458280 Score: 238
Period size: 62 Copynumber: 2.9 Consensus size: 62
5458090 CTAAAAAGGG
*
5458100 GTGCCACCAACTTGTGTGGGCTTT-AAAAAAAAAGGTATCCTGCTCTTTGAGGACTAGCAGA
1 GTGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAGATATCCTGCTCTTTGAGGACTAGCAGA
* * * *
5458161 GTGCCACTAACTCGTGTGGGCTTTGAAAAGAAAAGATATCCTACTCTTTGAGGACTAGCAGA
1 GTGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAGATATCCTGCTCTTTGAGGACTAGCAGA
* * * * * * *
5458223 ATGCCACCAACTTGTGCGAGCTTTGAAAAGAAAAATATGTCATGTTCTTTGAGGACTA
1 GTGCCACCAACTTGTGTGGGCTTTGAAAA-AAAAAGATATCCTGCTCTTTGAGGACTA
5458281 AAGGATAAAA
Statistics
Matches: 102, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
61 22 0.22
62 58 0.57
63 22 0.22
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (62 bp):
GTGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAGATATCCTGCTCTTTGAGGACTAGCAGA
Found at i:5458192 original size:291 final size:285
Alignment explanation
Indices: 5457483--5458282 Score: 895
Period size: 291 Copynumber: 2.8 Consensus size: 285
5457473 GTGTGAGCTT
* *
5457483 TAAAAGAAAAAGGCATCTTGCTCTTTGAGGACT-GAAA--GGTGCCACCAACTTGTGTGGGCTTT
1 TAAAAGAAAAAGGCGTCTTGCTCTTTGAGGACTAAAAAGGGGTGCCACCAACTTGTGTGGGCTTT
* * * * *
5457545 AAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-G-AAAGGCGCCACCAACTTGTGTGGGTTTTA
66 AAAAA--AAAAGGCGTCCTGCTCTTTGAGGACTAGCAGA-GTGCCACCAACTCGTGTGGGCTTTG
** * * * * *
5457608 AAAAGGAAAAAGTGTCCTACTCTTTGAGGAGTA--AAAGTTGTCACCAACTTGTGTGAGCCTTAA
128 AAAA-GAAAAAGAATCCTACTCTTTGAGGACTAGCAGAG-TGCCACCAACTTGTGTGAGCTTTGA
* * *
5457671 AAAGGAAAAGATGTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTATGGGCTCTAAAAA
191 AAA-GAAAA-ATGTCCTACTCTTTGAGGACTAAAAGGTACCACCAACTTATATGGGCTCTAAAAA
*
5457736 GGAAAAGTCATCCTGCTCTTTGAGAACTAAAG
254 GGAAAAGTCATCATGCTCTTTGAGAACTAAAG
* * * *
5457768 -AATAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGAGGAGTGCCACCAACTTGTGTGGGCTTT
1 TAAAAGAAAAAGGCGTCTTGCTCTTTGAGGACTAAAAAGGGGTGCCACCAACTTGTGTGGGCTTT
** * *
5457832 AAAAGAAAAAGGCGTCCTTTTCTTTGAGGACTAGCAGAATACCACCAACTCGTGTGGGCTTTGAA
66 AAAA-AAAAAGGCGTCCTGCTCTTTGAGGACTAGCAGAGTGCCACCAACTCGTGTGGGCTTTGAA
* * * *
5457897 AAGAAAAAAGAAT-TTGCTCTTTGAGGACTAGCAGAGTGCCACCAACTCGTGTGGGCTTTGAAAA
130 AAG-AAAAAGAATCCTACTCTTTGAGGACTAGCAGAGTGCCACCAACTTGTGTGAGCTTTGAAAA
* * * *
5457961 GAAAAATGCATCCTACTTTTTGAGGACTAAAAATAGGTACCACCAATTTATGTGGGCT-TTAAAA
194 GAAAAATG--TCCTACTCTTTGAGGACT--AAA-AGGTACCACCAACTTATATGGGCTCTAAAAA
* * * *
5458025 GAGAAAGGT-GTCATGTTCTTTGAGGACTAAAAG
254 G-GAAAAGTCATCATGCTCTTTGAGAACT-AAAG
* **
5458058 ATAAAAAAAAAAGGCGTCTTGCTCTTTGAAAACTAAAAAGGGGTGCCACCAACTTGTGTGGGCTT
1 -TAAAAGAAAAAGGCGTCTTGCTCTTTGAGGACTAAAAAGGGGTGCCACCAACTTGTGTGGGCTT
** *
5458123 TAAAAAAAAAGGTATCCTGCTCTTTGAGGACTAGCAGAGTGCCACTAACTCGTGTGGGCTTTGAA
65 TAAAAAAAAAGGCGTCCTGCTCTTTGAGGACTAGCAGAGTGCCACCAACTCGTGTGGGCTTTGAA
* *
5458188 AAG-AAAAGATATCCTACTCTTTGAGGACTAGCAGAATGCCACCAACTTGTGCGAGCTTTGAAAA
130 AAGAAAAAGA-ATCCTACTCTTTGAGGACTAGCAGAGTGCCACCAACTTGTGTGAGCTTTGAAAA
* **
5458252 GAAAAATATGTCATGTTCTTTGAGGACTAAA
194 G-AAAA-ATGTCCTACTCTTTGAGGACTAAA
5458283 GGATAAAAAA
Statistics
Matches: 431, Mismatches: 62, Indels: 40
0.81 0.12 0.08
Matches are distributed among these distances:
284 29 0.07
285 5 0.01
286 44 0.10
287 99 0.23
288 6 0.01
289 32 0.07
290 32 0.07
291 116 0.27
292 65 0.15
293 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (285 bp):
TAAAAGAAAAAGGCGTCTTGCTCTTTGAGGACTAAAAAGGGGTGCCACCAACTTGTGTGGGCTTT
AAAAAAAAAGGCGTCCTGCTCTTTGAGGACTAGCAGAGTGCCACCAACTCGTGTGGGCTTTGAAA
AGAAAAAGAATCCTACTCTTTGAGGACTAGCAGAGTGCCACCAACTTGTGTGAGCTTTGAAAAGA
AAAATGTCCTACTCTTTGAGGACTAAAAGGTACCACCAACTTATATGGGCTCTAAAAAGGAAAAG
TCATCATGCTCTTTGAGAACTAAAG
Found at i:5458355 original size:63 final size:63
Alignment explanation
Indices: 5458287--5458482 Score: 200
Period size: 63 Copynumber: 3.1 Consensus size: 63
5458277 ACTAAAGGAT
* * *
5458287 AAAAAAA-GCCGTGCTCTTTGAGAACTA-AAAAGGGGTGCCACCAACTTGTGTGAGCTTT-AAAA
1 AAAAAAAGGCCATGCTCTTTGAGGACTAGAAAA---GTGCCACCAACTCGTGTGAGCTTTGAAAA
5458349 G
63 G
* * *
5458350 AAAAAAAGGCGCCATACTCTTTGAGGACTAGCAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAG
1 AAAAAAA-G-GCCATGCTCTTTGAGGACTAGAAAAGTGCCACCAACTCGTGTGAGCTTTGAAAAG
* * * * * * **
5458415 AAAAAAATGTCATGCTCTTTGAGGACTAGCAGAGTGCCATCAACTCGTGTGGGGGTTGAAAAG
1 AAAAAAAGGCCATGCTCTTTGAGGACTAGAAAAGTGCCACCAACTCGTGTGAGCTTTGAAAAG
5458478 AAAAA
1 AAAAA
5458483 TACATCTTGC
Statistics
Matches: 115, Mismatches: 13, Indels: 10
0.83 0.09 0.07
Matches are distributed among these distances:
63 61 0.53
64 22 0.19
65 12 0.10
66 17 0.15
67 3 0.03
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (63 bp):
AAAAAAAGGCCATGCTCTTTGAGGACTAGAAAAGTGCCACCAACTCGTGTGAGCTTTGAAAAG
Found at i:5458610 original size:62 final size:63
Alignment explanation
Indices: 5458321--5458631 Score: 270
Period size: 63 Copynumber: 4.9 Consensus size: 63
5458311 CTAAAAAGGG
* * ** * * *
5458321 GTGCCACCAACTTGTGTGAGCTTT-AAAAGAAAAAAAGGCGCCATACTCTTTGAGGACTAGCAAA
1 GTGCCACCAACTCGTGTGGGCTTTGAAAAG--AAAAAGATGTCTTGCTCTTTGAGGACTAGCAAA
* * *
5458385 GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAAATGTCATGCTCTTTGAGGACTAGCAGA
1 GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGATGTCTTGCTCTTTGAGGACTAGCAAA
* ** * ** * * * * *
5458448 GTGCCATCAACTCGTGTGGGGGTTGAAAAGAAAAATACATCTTGCTTTTTCAAGATTA-AAAA
1 GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGATGTCTTGCTCTTTGAGGACTAGCAAA
* ** * * *
5458510 GGGGTGTCACCAACTTATGTGGG-TTTTAAAAGAAAAAGGTGTCTTGCTTTTTGAGGACTAGCAA
1 ---GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGATGTCTTGCTCTTTGAGGACTAGCAA
5458574 A
63 A
* * **
5458575 GTGCCACCAACTCGTGCGGGCTTTGAAAA-TAAAAGGCGTCTTGCTCTTTGAGGACTA
1 GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGATGTCTTGCTCTTTGAGGACTA
5458632 AAGGATTAAG
Statistics
Matches: 198, Mismatches: 43, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
62 43 0.22
63 81 0.41
64 50 0.25
65 24 0.12
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (63 bp):
GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGATGTCTTGCTCTTTGAGGACTAGCAAA
Found at i:5459193 original size:17 final size:18
Alignment explanation
Indices: 5459161--5459194 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5459151 TATCCTGATG
*
5459161 CAAATTTTACTCAATTAT
1 CAAATATTACTCAATTAT
5459179 CAAATATTA-TCAATTA
1 CAAATATTACTCAATTA
5459195 AATGACAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (18 bp):
CAAATATTACTCAATTAT
Found at i:5459811 original size:22 final size:21
Alignment explanation
Indices: 5459766--5459868 Score: 75
Period size: 23 Copynumber: 4.6 Consensus size: 21
5459756 CATGTCATTG
5459766 TTTTTTTATTTTTG-TTGTTC-C
1 TTTTTTTA-TTTTGCTT-TTCAC
5459787 TTTTTTTATTTTGCTTTTGCAC
1 TTTTTTTATTTTGCTTTT-CAC
* * *
5459809 TTTTTTTTGTTTTTCTTTTCAT
1 -TTTTTTTATTTTGCTTTTCAC
* *
5459831 TTTTTTGTGCTTTTGCTTTTGAC
1 TTTTTT-T-ATTTTGCTTTTCAC
5459854 TTTTTTATCATTTTG
1 TTTTTT-T-ATTTTG
5459869 AAGGGAACTT
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
20 7 0.11
21 17 0.26
22 4 0.06
23 38 0.58
ACGTcount: A:0.07, C:0.11, G:0.10, T:0.73
Consensus pattern (21 bp):
TTTTTTTATTTTGCTTTTCAC
Found at i:5459813 original size:23 final size:23
Alignment explanation
Indices: 5459787--5459868 Score: 80
Period size: 23 Copynumber: 3.6 Consensus size: 23
5459777 TTGTTGTTCC
5459787 TTTTTTTATTTTGCTTTTGCACT
1 TTTTTTTATTTTGCTTTTGCACT
* *
5459810 TTTTTTTGTTTTTCTTTT-CA-T
1 TTTTTTTATTTTGCTTTTGCACT
*
5459831 TTTTTTGTGCTTTTGCTTTTG-ACT
1 TTTTTT-T-ATTTTGCTTTTGCACT
*
5459855 TTTTTATCATTTTG
1 TTTTT-TTATTTTG
5459869 AAGGGAACTT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
21 7 0.15
22 3 0.06
23 31 0.65
24 6 0.12
25 1 0.02
ACGTcount: A:0.07, C:0.11, G:0.10, T:0.72
Consensus pattern (23 bp):
TTTTTTTATTTTGCTTTTGCACT
Found at i:5466848 original size:21 final size:21
Alignment explanation
Indices: 5466823--5466865 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5466813 ATTGGTTTTC
*
5466823 TTCATTGCATCCATGTTGCTT
1 TTCATTGCATCCATCTTGCTT
*
5466844 TTCATTGCATCCGTCTTGCTT
1 TTCATTGCATCCATCTTGCTT
5466865 T
1 T
5466866 GCCATCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.12, C:0.26, G:0.14, T:0.49
Consensus pattern (21 bp):
TTCATTGCATCCATCTTGCTT
Found at i:5467123 original size:23 final size:21
Alignment explanation
Indices: 5467084--5467125 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
5467074 ATGGTGTGAA
*
5467084 AAATGAAGGAAAGTATGCATG
1 AAATGAAGGAAAATATGCATG
5467105 AAATGCAAGGAAATATATGCA
1 AAATG-AAGGAAA-ATATGCA
5467126 AATGAATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 7 0.39
23 6 0.33
ACGTcount: A:0.50, C:0.07, G:0.24, T:0.19
Consensus pattern (21 bp):
AAATGAAGGAAAATATGCATG
Found at i:5467338 original size:12 final size:12
Alignment explanation
Indices: 5467321--5467345 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5467311 TATTTGATTT
5467321 TTTTATTTTTTA
1 TTTTATTTTTTA
5467333 TTTTATTTTTTA
1 TTTTATTTTTTA
5467345 T
1 T
5467346 GAAAGATGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:5469132 original size:21 final size:20
Alignment explanation
Indices: 5469086--5469126 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
5469076 TAATCTTCTT
5469086 GAAAAGAAATTAAATGAGTTA
1 GAAAAGAAA-TAAATGAGTTA
*
5469107 GAAAAGAAGATAAGTGAGTT
1 GAAAAGAA-ATAAATGAGTT
5469127 GTAAAATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.54, C:0.00, G:0.24, T:0.22
Consensus pattern (20 bp):
GAAAAGAAATAAATGAGTTA
Found at i:5472888 original size:13 final size:13
Alignment explanation
Indices: 5472870--5472896 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5472860 TACAAGTTAT
5472870 AATGTATGGATAC
1 AATGTATGGATAC
5472883 AATGTATGGATAC
1 AATGTATGGATAC
5472896 A
1 A
5472897 CATTGTAATG
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:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (13 bp):
AATGTATGGATAC
Found at i:5481380 original size:26 final size:26
Alignment explanation
Indices: 5481349--5481436 Score: 149
Period size: 26 Copynumber: 3.3 Consensus size: 26
5481339 ATCAAATCCC
*
5481349 AATTCCTAAATCCAACTTAAATCCTA
1 AATTCCCAAATCCAACTTAAATCCTA
5481375 AATTCCCAAATCCAACTTAAATCCTA
1 AATTCCCAAATCCAACTTAAATCCTA
*
5481401 AATTCCCAAATCCAACTCAAATCCTA
1 AATTCCCAAATCCAACTTAAATCCTA
5481427 AATTCGCCAA
1 AATTC-CCAA
5481437 GGGAGCCCAT
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
26 55 0.93
27 4 0.07
ACGTcount: A:0.42, C:0.31, G:0.01, T:0.26
Consensus pattern (26 bp):
AATTCCCAAATCCAACTTAAATCCTA
Found at i:5482891 original size:16 final size:16
Alignment explanation
Indices: 5482872--5482902 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5482862 CTTTTGTTAA
5482872 TTATTAATTTTATTTT
1 TTATTAATTTTATTTT
*
5482888 TTATTATTTTTATTT
1 TTATTAATTTTATTT
5482903 AAAATATTTT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTATTAATTTTATTTT
Found at i:5482913 original size:16 final size:17
Alignment explanation
Indices: 5482892--5482925 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
5482882 TATTTTTTAT
5482892 TATTTTT-ATT-TAAAA
1 TATTTTTAATTATAAAA
5482907 TATTTTTAATTATAAAA
1 TATTTTTAATTATAAAA
5482924 TA
1 TA
5482926 ATAAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTTTAATTATAAAA
Found at i:5483242 original size:19 final size:18
Alignment explanation
Indices: 5483208--5483243 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5483198 TACTAAAATA
*
5483208 TAATTTTTTTGTTTTAAT
1 TAATTTTTTTATTTTAAT
5483226 TAATTTTTTTATCTTTAA
1 TAATTTTTTTAT-TTTAA
5483244 AAATTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (18 bp):
TAATTTTTTTATTTTAAT
Found at i:5483248 original size:18 final size:18
Alignment explanation
Indices: 5483204--5483251 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
5483194 TAAATACTAA
*
5483204 AATATAATTTTTTTGTTTT
1 AATA-AATTTTTTTATTTT
*
5483223 AATTAATTTTTTTATCTTT
1 AATAAATTTTTTTAT-TTT
5483242 AA-AAATTTTT
1 AATAAATTTTT
5483252 AAATAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
AATAAATTTTTTTATTTT
Found at i:5483267 original size:24 final size:24
Alignment explanation
Indices: 5483240--5483286 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
5483230 TTTTTTATCT
5483240 TTAA-AAATTTTTAAATAATAATAA
1 TTAATAAATTTTTAAATAA-AATAA
**
5483264 TTAATTTATTTTTAAATAAAATA
1 TTAATAAATTTTTAAATAAAATA
5483287 TCAAAGTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTAATAAATTTTTAAATAAAATAA
Found at i:5483296 original size:24 final size:25
Alignment explanation
Indices: 5483246--5483297 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
5483236 ATCTTTAAAA
* *
5483246 ATTTTTAAATAATAATAATTAATTT
1 ATTTTTAAATAATAATAATAAAGTT
5483271 ATTTTTAAATAA-AAT-ATCAAAGTT
1 ATTTTTAAATAATAATAAT-AAAGTT
5483295 ATT
1 ATT
5483298 ATATATAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 2 0.08
24 10 0.42
25 12 0.50
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
ATTTTTAAATAATAATAATAAAGTT
Found at i:5483345 original size:15 final size:15
Alignment explanation
Indices: 5483324--5483359 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
5483314 AAGATAAATT
5483324 TAAAAAAATTTATA-
1 TAAAAAAATTTATAG
5483338 TAAAAAAATTTA-AG
1 TAAAAAAATTTATAG
5483352 TAAAAAAA
1 TAAAAAAA
5483360 AGTTATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 1 0.05
14 20 0.95
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
TAAAAAAATTTATAG
Found at i:5483517 original size:18 final size:18
Alignment explanation
Indices: 5483483--5483516 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5483473 AACGTAATAG
*
5483483 TAATTAAATATAATTTTA
1 TAATTAAAAATAATTTTA
5483501 TAATTAAAAAT-ATTTT
1 TAATTAAAAATAATTTT
5483517 TTAAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAAAATAATTTTA
Found at i:5483872 original size:2 final size:2
Alignment explanation
Indices: 5483865--5483901 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5483855 TTCTCGCAGT
5483865 TC TC TC TC TC TC 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 TC TC TC TC TC TC T
5483902 TAGCCTTGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5488429 original size:25 final size:26
Alignment explanation
Indices: 5488392--5488460 Score: 95
Period size: 25 Copynumber: 2.7 Consensus size: 26
5488382 TATTAAATAA
*
5488392 TTAAAATATAAAAAAATTAAGAGAATT
1 TTAAAAGA-AAAAAAATTAAGAGAATT
*
5488419 TTAAAA-AAAAATAATTAAGAGAATT
1 TTAAAAGAAAAAAAATTAAGAGAATT
*
5488444 TTAAAAGATAAAAAATT
1 TTAAAAGAAAAAAAATT
5488461 CAGAAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 23 0.61
26 9 0.24
27 6 0.16
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (26 bp):
TTAAAAGAAAAAAAATTAAGAGAATT
Found at i:5488477 original size:19 final size:19
Alignment explanation
Indices: 5488454--5488496 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5488444 TTAAAAGATA
*
5488454 AAAAATTCAGAAAAAATTCT
1 AAAACTTCA-AAAAAATTCT
* *
5488474 AAAACTTTAAAAAAATTTT
1 AAAACTTCAAAAAAATTCT
5488493 AAAA
1 AAAA
5488497 AATAGAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAACTTCAAAAAAATTCT
Found at i:5489200 original size:2 final size:2
Alignment explanation
Indices: 5489188--5489222 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5489178 GAATGTGTAA
5489188 AT AT A- 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
5489223 CTACACACGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5494982 original size:11 final size:11
Alignment explanation
Indices: 5494955--5494988 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
5494945 AATTTTTTTA
5494955 ATTTTAAATAT
1 ATTTTAAATAT
5494966 ATTTTTAAATAT
1 A-TTTTAAATAT
5494978 ATTTTAAATAT
1 ATTTTAAATAT
5494989 TTAATATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTTTAAATAT
Found at i:5495039 original size:13 final size:13
Alignment explanation
Indices: 5495009--5495112 Score: 65
Period size: 13 Copynumber: 7.8 Consensus size: 13
5494999 TATTTATATT
5495009 TTAA-TAATTAAA
1 TTAATTAATTAAA
*
5495021 --AATTAATTTAA
1 TTAATTAATTAAA
5495032 TTAATTAATTAAA
1 TTAATTAATTAAA
5495045 TTGACATT--TTAAA
1 TT-A-ATTAATTAAA
*
5495058 TCAATTAAAATTTAAA
1 TTAATT--AA-TTAAA
*
5495074 TTAAATTAACTAAA
1 TT-AATTAATTAAA
*
5495088 TCAATTAAATTAAA
1 TTAATT-AATTAAA
5495102 TTTAATTAATT
1 -TTAATTAATT
5495113 TTTTAATTAA
Statistics
Matches: 71, Mismatches: 8, Indels: 24
0.69 0.08 0.23
Matches are distributed among these distances:
10 2 0.03
11 10 0.14
12 1 0.01
13 22 0.31
14 16 0.23
15 10 0.14
16 6 0.08
17 4 0.06
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (13 bp):
TTAATTAATTAAA
Found at i:5495046 original size:9 final size:9
Alignment explanation
Indices: 5495013--5495112 Score: 62
Period size: 9 Copynumber: 10.6 Consensus size: 9
5495003 TATATTTTAA
5495013 TAATTAAA-
1 TAATTAAAT
*
5495021 -AATTAATT
1 TAATTAAAT
5495029 TAATT-AAT
1 TAATTAAAT
5495037 TAATTAAAT
1 TAATTAAAT
5495046 TGACATTTTAAAT
1 T-A-A--TTAAAT
*
5495059 CAATTAAAATT
1 TAATT-AAA-T
5495070 TAAATTAAAT
1 T-AATTAAAT
*
5495080 TAACTAAAT
1 TAATTAAAT
*
5495089 CAATTAAAT
1 TAATTAAAT
*
5495098 TAAATTTAAT
1 T-AATTAAAT
5495108 TAATT
1 TAATT
5495113 TTTTAATTAA
Statistics
Matches: 72, Mismatches: 9, Indels: 21
0.71 0.09 0.21
Matches are distributed among these distances:
7 6 0.08
8 7 0.10
9 28 0.39
10 14 0.19
11 6 0.08
12 5 0.07
13 6 0.08
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (9 bp):
TAATTAAAT
Found at i:5495088 original size:30 final size:28
Alignment explanation
Indices: 5495054--5495110 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
5495044 ATTGACATTT
5495054 TAAATCAATTAAAATTTAAATTAAATTAAC
1 TAAATCAATT-AAA-TTAAATTAAATTAAC
*
5495084 TAAATCAATTAAATTAAATTTAATTAA
1 TAAATCAATTAAATTAAATTAAATTAA
5495111 TTTTTTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 13 0.50
29 3 0.12
30 10 0.38
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (28 bp):
TAAATCAATTAAATTAAATTAAATTAAC
Found at i:5496017 original size:20 final size:21
Alignment explanation
Indices: 5495973--5496026 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 21
5495963 AGTTTGATTA
*
5495973 ATATAATATATTTATTAACATT
1 ATATAATATATTTAGTAACA-T
5495995 ATAATAATATATTT-GTAAC-T
1 AT-ATAATATATTTAGTAACAT
5496015 ATATAATTATAT
1 ATATAA-TATAT
5496027 ACTAATTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 4 0.14
20 8 0.28
22 6 0.21
23 11 0.38
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (21 bp):
ATATAATATATTTAGTAACAT
Found at i:5496019 original size:22 final size:23
Alignment explanation
Indices: 5495975--5496027 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
5495965 TTTGATTAAT
*
5495975 ATAATATATTTATTAACATTATA
1 ATAATATATTTAGTAACATTATA
5495998 ATAATATATTT-GTAAC-TATATA
1 ATAATATATTTAGTAACAT-TATA
*
5496020 ATTATATA
1 ATAATATA
5496028 CTAATTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 1 0.04
22 15 0.56
23 11 0.41
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (23 bp):
ATAATATATTTAGTAACATTATA
Found at i:5497824 original size:21 final size:20
Alignment explanation
Indices: 5497787--5497825 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5497777 ACTAAATAAA
*
5497787 TTTATTTAAATGTTAAATAG
1 TTTATTTAAATGATAAATAG
*
5497807 TTTATTTAATTTGATAAAT
1 TTTATTTAA-ATGATAAAT
5497826 TTAATATGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (20 bp):
TTTATTTAAATGATAAATAG
Found at i:5497899 original size:22 final size:22
Alignment explanation
Indices: 5497874--5497915 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
5497864 TATTTTTATT
5497874 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
5497896 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
5497916 AATTTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:5498356 original size:20 final size:20
Alignment explanation
Indices: 5498331--5498370 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5498321 TCAGTTTCCC
*
5498331 ATATAAATATTATTAATACT
1 ATATAAATATCATTAATACT
5498351 ATATAAATATCATTAATACT
1 ATATAAATATCATTAATACT
5498371 CCCCTGTCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (20 bp):
ATATAAATATCATTAATACT
Found at i:5501423 original size:29 final size:29
Alignment explanation
Indices: 5501387--5501484 Score: 74
Period size: 29 Copynumber: 3.3 Consensus size: 29
5501377 ATTAATAAAA
5501387 TAAAAATATTAATTACCTATTATCATTAT
1 TAAAAATATTAATTACCTATTATCATTAT
** * * *
5501416 TAAAAATA--AATTTACAAAATTAATTAATAAAA
1 TAAAAATATTAA-TTAC-CTATT-A-TCAT-TAT
*
5501448 TAAAAATATTAATTACCTATTATCTTTAT
1 TAAAAATATTAATTACCTATTATCATTAT
*
5501477 AAAAAATA
1 TAAAAATA
5501485 ATTTTTTTGG
Statistics
Matches: 50, Mismatches: 12, Indels: 14
0.66 0.16 0.18
Matches are distributed among these distances:
27 2 0.04
28 4 0.08
29 19 0.38
30 3 0.06
31 4 0.08
32 12 0.24
33 4 0.08
34 2 0.04
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (29 bp):
TAAAAATATTAATTACCTATTATCATTAT
Found at i:5501459 original size:61 final size:61
Alignment explanation
Indices: 5501364--5501485 Score: 226
Period size: 61 Copynumber: 2.0 Consensus size: 61
5501354 ATGTTTGAAG
*
5501364 ATTTACAAAATTAATTAATAAAATAAAAATATTAATTACCTATTATCATTATTAAAAATAA
1 ATTTACAAAATTAATTAATAAAATAAAAATATTAATTACCTATTATCATTATAAAAAATAA
*
5501425 ATTTACAAAATTAATTAATAAAATAAAAATATTAATTACCTATTATCTTTATAAAAAATAA
1 ATTTACAAAATTAATTAATAAAATAAAAATATTAATTACCTATTATCATTATAAAAAATAA
5501486 TTTTTTTGGA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38
Consensus pattern (61 bp):
ATTTACAAAATTAATTAATAAAATAAAAATATTAATTACCTATTATCATTATAAAAAATAA
Found at i:5504384 original size:23 final size:23
Alignment explanation
Indices: 5504358--5504405 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
5504348 GTATATAATT
*
5504358 AATTTTAAT-TTTTTTAAATTTCA
1 AATTTT-ATGTTTATTAAATTTCA
*
5504381 AATTTTATGTTTATTGAATTTCA
1 AATTTTATGTTTATTAAATTTCA
5504404 AA
1 AA
5504406 AGACATATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.56
Consensus pattern (23 bp):
AATTTTATGTTTATTAAATTTCA
Found at i:5508502 original size:21 final size:20
Alignment explanation
Indices: 5508476--5508527 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
5508466 TCTATAATTT
5508476 GTATCGATACAAACAGTAAAG
1 GTATCGATACAAA-AGTAAAG
* * *
5508497 GTATCGATACATAAGTGAAT
1 GTATCGATACAAAAGTAAAG
5508517 GTATCGATACA
1 GTATCGATACA
5508528 TGCCTAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.25
Consensus pattern (20 bp):
GTATCGATACAAAAGTAAAG
Done.