Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167938.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_20, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19866354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 74000 characters in sequence are not A, C, G, or T
File 35 of 100
Found at i:9438414 original size:37 final size:36
Alignment explanation
Indices: 9438351--9438434 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 36
9438341 AATGTTTATT
* *
9438351 AATATAATATTATTTATTTATTAATATATTATTTTA
1 AATATAATATAATTTATTTATTAATATAATATTTTA
*
9438387 AATATATTATAATATTATTTATTAATATAATATTTATTA
1 AATATAATATAAT-TTATTTATTAATATAATA-TT-TTA
9438426 AA-ATAATAT
1 AATATAATAT
9438435 TTATATAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 11 0.27
37 17 0.41
38 8 0.20
39 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (36 bp):
AATATAATATAATTTATTTATTAATATAATATTTTA
Found at i:9438435 original size:41 final size:41
Alignment explanation
Indices: 9438353--9438435 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 41
9438343 TGTTTATTAA
* *
9438353 TATAATATTATTTATTTATTAATATATTATTTTAAATATAT
1 TATAATATTATTTATTAATTAATATATTATTTAAAATATAT
9438394 TATAATATTATTTATTAATATAATAT-TTA-TTAAAATAATAT
1 TATAATATTATTTATTAAT-TAATATATTATTTAAAAT-ATAT
9438435 T
1 T
9438436 TATATAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 6 0.16
41 26 0.68
42 6 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (41 bp):
TATAATATTATTTATTAATTAATATATTATTTAAAATATAT
Found at i:9438448 original size:20 final size:20
Alignment explanation
Indices: 9438425--9438464 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
9438415 AATATTTATT
9438425 AAAATAAT-ATTTATATAATA
1 AAAATAATAATTTAT-TAATA
*
9438445 AAAATATTAATTTATTAATA
1 AAAATAATAATTTATTAATA
9438465 TAATAATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATAATAATTTATTAATA
Found at i:9438701 original size:21 final size:21
Alignment explanation
Indices: 9438675--9438718 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
9438665 TTTAATTTTT
* * *
9438675 AAAAAAATTGAAAACGAAAAC
1 AAAAAAACTAAAAACAAAAAC
9438696 AAAAAAACTAAAAACAAAAAC
1 AAAAAAACTAAAAACAAAAAC
9438717 AA
1 AA
9438719 GCATCCCCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.77, C:0.11, G:0.05, T:0.07
Consensus pattern (21 bp):
AAAAAAACTAAAAACAAAAAC
Found at i:9442631 original size:12 final size:13
Alignment explanation
Indices: 9442610--9442638 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
9442600 ATTTCTTCTT
9442610 TTTAG-TTTTTTA
1 TTTAGATTTTTTA
9442622 TTTAGATTTTTTA
1 TTTAGATTTTTTA
9442635 TTTA
1 TTTA
9442639 AAATTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (13 bp):
TTTAGATTTTTTA
Found at i:9442696 original size:19 final size:19
Alignment explanation
Indices: 9442665--9442706 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
9442655 TTATTATTAT
9442665 TTAA-TTTAATATAATAAA
1 TTAATTTTAATATAATAAA
*
9442683 TTAATTTTACTATAATAAA
1 TTAATTTTAATATAATAAA
9442702 TTAAT
1 TTAAT
9442707 AAATAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAATTTTAATATAATAAA
Found at i:9442706 original size:8 final size:8
Alignment explanation
Indices: 9442695--9442767 Score: 60
Period size: 8 Copynumber: 9.1 Consensus size: 8
9442685 AATTTTACTA
9442695 TAATAAAT
1 TAATAAAT
9442703 TAATAAAT
1 TAATAAAT
* *
9442711 AAACAAAT
1 TAATAAAT
9442719 TAATAAA-
1 TAATAAAT
9442726 TAATAAAT
1 TAATAAAT
* *
9442734 T-TTATTAT
1 TAATA-AAT
*
9442742 GTAATAAAC
1 -TAATAAAT
9442751 TAATAAAT
1 TAATAAAT
*
9442759 AAATAAAT
1 TAATAAAT
9442767 T
1 T
9442768 TTAATATTAT
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
7 9 0.18
8 36 0.73
9 2 0.04
10 2 0.04
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (8 bp):
TAATAAAT
Found at i:9442723 original size:48 final size:47
Alignment explanation
Indices: 9442670--9442767 Score: 126
Period size: 48 Copynumber: 2.0 Consensus size: 47
9442660 ATTATTTAAT
* *
9442670 TTAATATAATAAATTAATTTTACTA-TAATAAATTAATAAATAAACAAA
1 TTAATA-AAT-AATAAATTTTACTAGTAATAAACTAATAAATAAACAAA
* *
9442718 TTAATAAATAATAAATTTTATTATGTAATAAACTAATAAATAAATAAA
1 TTAATAAATAATAAATTTTACTA-GTAATAAACTAATAAATAAACAAA
9442766 TT
1 TT
9442768 TTAATATTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
46 12 0.27
47 3 0.07
48 29 0.66
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (47 bp):
TTAATAAATAATAAATTTTACTAGTAATAAACTAATAAATAAACAAA
Found at i:9442765 original size:16 final size:16
Alignment explanation
Indices: 9442696--9442767 Score: 67
Period size: 16 Copynumber: 4.5 Consensus size: 16
9442686 ATTTTACTAT
9442696 AATAAATTAATAAATA
1 AATAAATTAATAAATA
*
9442712 AACAAATTAATAAAT-
1 AATAAATTAATAAATA
* * *
9442727 AATAAATT-TTATTATGT
1 AATAAATTAATA-AAT-A
*
9442744 AATAAACTAATAAATA
1 AATAAATTAATAAATA
9442760 AATAAATT
1 AATAAATT
9442768 TTAATATTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
14 2 0.05
15 9 0.21
16 21 0.49
17 9 0.21
18 2 0.05
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (16 bp):
AATAAATTAATAAATA
Found at i:9442782 original size:33 final size:32
Alignment explanation
Indices: 9442719--9442782 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
9442709 ATAAACAAAT
*
9442719 TAATAAATAATAAATTTTATTATGTAATAAAC
1 TAATAAATAATAAATTTTAATATGTAATAAAC
9442751 TAATAAATAAATAAATTTTAATAT-TATATAAA
1 TAATAAAT-AATAAATTTTAATATGTA-ATAAA
9442783 AATTTTTGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 10 0.34
33 19 0.66
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (32 bp):
TAATAAATAATAAATTTTAATATGTAATAAAC
Found at i:9442981 original size:19 final size:19
Alignment explanation
Indices: 9442938--9442981 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
9442928 ATAATAATTT
9442938 ATTAATTTTATAAATATTAA
1 ATTAA-TTTATAAATATTAA
* *
9442958 A-TAATTTATACATTTTAA
1 ATTAATTTATAAATATTAA
9442976 ATTAAT
1 ATTAAT
9442982 GTTTTTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 13 0.62
19 7 0.33
20 1 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTAATTTATAAATATTAA
Found at i:9445831 original size:34 final size:35
Alignment explanation
Indices: 9445749--9445830 Score: 114
Period size: 34 Copynumber: 2.4 Consensus size: 35
9445739 ATCCTAAAAA
* **
9445749 TTTTTAAAATTTTTGAATATATAAATTTGAAAA-C
1 TTTTTAAAATTTTTAAATATATAAATTCAAAAATC
9445783 -TTTTAAAAGTTTTTAAATATATAAATTCAAAAATC
1 TTTTTAAAA-TTTTTAAATATATAAATTCAAAAATC
9445818 TTTTTAAAATTTT
1 TTTTTAAAATTTT
9445831 AGATTTGCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 8 0.19
34 21 0.50
35 5 0.12
36 8 0.19
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (35 bp):
TTTTTAAAATTTTTAAATATATAAATTCAAAAATC
Found at i:9448442 original size:15 final size:15
Alignment explanation
Indices: 9448404--9448478 Score: 72
Period size: 15 Copynumber: 5.3 Consensus size: 15
9448394 TTTTGTTTTG
*
9448404 TTTTGT-TTTTATTTT
1 TTTTGTATTTTA-TAT
9448419 TTATTGTATTTTATAT
1 TT-TTGTATTTTATAT
9448435 TTTTGTA---T-T-T
1 TTTTGTATTTTATAT
9448445 TTTTGTATTTTATAT
1 TTTTGTATTTTATAT
*
9448460 TTTTGTATTTTGTAT
1 TTTTGTATTTTATAT
9448475 TTTT
1 TTTT
9448479 ATTTAATTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
10 8 0.16
11 1 0.02
12 1 0.02
13 1 0.02
14 1 0.02
15 26 0.51
16 8 0.16
17 5 0.10
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (15 bp):
TTTTGTATTTTATAT
Found at i:9448445 original size:25 final size:25
Alignment explanation
Indices: 9448417--9448470 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
9448407 TGTTTTTATT
9448417 TTTTATTGTATTTTATATTTTTGTA
1 TTTTATTGTATTTTATATTTTTGTA
*
9448442 TTTTTTTGTATTTTATATTTTTGTA
1 TTTTATTGTATTTTATATTTTTGTA
9448467 TTTT
1 TTTT
9448471 GTATTTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (25 bp):
TTTTATTGTATTTTATATTTTTGTA
Found at i:9448500 original size:19 final size:18
Alignment explanation
Indices: 9448466--9448504 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
9448456 ATATTTTTGT
9448466 ATTTTGTATTTTTATTTA
1 ATTTTGTATTTTTATTTA
9448484 ATTTT-TATTATTGTATTTA
1 ATTTTGTATT-TT-TATTTA
9448503 AT
1 AT
9448505 AATATTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 7 0.37
19 8 0.42
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (18 bp):
ATTTTGTATTTTTATTTA
Found at i:9448532 original size:12 final size:12
Alignment explanation
Indices: 9448487--9448533 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
9448477 TTATTTAATT
*
9448487 TTTATTATTGTA
1 TTTATTATTTTA
* *
9448499 TTTAATAATATTA
1 TTT-ATTATTTTA
9448512 -TTATTATTTTA
1 TTTATTATTTTA
9448523 TTTATTATTTT
1 TTTATTATTTT
9448534 TCTGTGATCG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
11 7 0.25
12 15 0.54
13 6 0.21
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:9450999 original size:24 final size:24
Alignment explanation
Indices: 9450967--9451014 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
9450957 AGGCAATTTT
9450967 TATCAAACAAATTGATACAAAATG
1 TATCAAACAAATTGATACAAAATG
* *
9450991 TATCAAACAAATTTATACAGAATG
1 TATCAAACAAATTGATACAAAATG
9451015 AAGTCTGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.27
Consensus pattern (24 bp):
TATCAAACAAATTGATACAAAATG
Found at i:9452614 original size:2 final size:2
Alignment explanation
Indices: 9452607--9452631 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9452597 AGGTGGATTC
9452607 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 A
9452632 ATAAACAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9459946 original size:12 final size:12
Alignment explanation
Indices: 9459929--9459964 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
9459919 ATTAAAAGTG
9459929 TTCTTTTTTTTT
1 TTCTTTTTTTTT
9459941 TTCTTTTTTTTT
1 TTCTTTTTTTTT
9459953 TT-TTTTGTTTTT
1 TTCTTTT-TTTTT
9459965 ACAAATAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 4 0.17
12 19 0.83
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.92
Consensus pattern (12 bp):
TTCTTTTTTTTT
Found at i:9459953 original size:16 final size:16
Alignment explanation
Indices: 9459932--9459964 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
9459922 AAAAGTGTTC
9459932 TTTTTTTTTTTCTTTT
1 TTTTTTTTTTTCTTTT
*
9459948 TTTTTTTTTTTGTTTT
1 TTTTTTTTTTTCTTTT
9459964 T
1 T
9459965 ACAAATAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.03, G:0.03, T:0.94
Consensus pattern (16 bp):
TTTTTTTTTTTCTTTT
Found at i:9464013 original size:20 final size:20
Alignment explanation
Indices: 9463988--9464031 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
9463978 AAATTTTTAC
*
9463988 TTTTTTAT-ATTTTAAAATT
1 TTTTTTATGATTTCAAAATT
9464007 ATTTTTTATGATTTCAAAATT
1 -TTTTTTATGATTTCAAAATT
9464028 TTTT
1 TTTT
9464032 AACATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTTTATGATTTCAAAATT
Found at i:9473295 original size:37 final size:37
Alignment explanation
Indices: 9473245--9473318 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
9473235 GGAGGAAGAT
9473245 AGTTTCTTCTTTTTAATAACTGTTTGGAAGACGGAGC
1 AGTTTCTTCTTTTTAATAACTGTTTGGAAGACGGAGC
* *
9473282 AGTTTGTTCTTTTTAATAACTGTTTGGAAGATGGAGC
1 AGTTTCTTCTTTTTAATAACTGTTTGGAAGACGGAGC
9473319 CAACCTTGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.24, C:0.11, G:0.23, T:0.42
Consensus pattern (37 bp):
AGTTTCTTCTTTTTAATAACTGTTTGGAAGACGGAGC
Found at i:9474352 original size:10 final size:10
Alignment explanation
Indices: 9474333--9474382 Score: 82
Period size: 10 Copynumber: 4.9 Consensus size: 10
9474323 GTATGTTAAG
9474333 ATTTATTTAT
1 ATTTATTTAT
*
9474343 ATTAATTTAT
1 ATTTATTTAT
9474353 ATTTATTTAT
1 ATTTATTTAT
9474363 GATTTATTTAT
1 -ATTTATTTAT
9474374 ATTTATTTA
1 ATTTATTTA
9474383 ATTATGATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
10 27 0.73
11 10 0.27
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (10 bp):
ATTTATTTAT
Found at i:9474372 original size:15 final size:14
Alignment explanation
Indices: 9474333--9474399 Score: 64
Period size: 14 Copynumber: 4.5 Consensus size: 14
9474323 GTATGTTAAG
*
9474333 ATTTATTTATATTA
1 ATTTATTTATATTT
9474347 ATTTATATT-TATTTAT
1 ATTTAT-TTATA-TT-T
9474363 GATTTATTTATATTT
1 -ATTTATTTATATTT
*
9474378 ATTTAATTATGATTT
1 ATTTATTTAT-ATTT
9474393 ATTTATT
1 ATTTATT
9474400 ATTCATAAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
14 17 0.39
15 15 0.34
16 4 0.09
17 8 0.18
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (14 bp):
ATTTATTTATATTT
Found at i:9474392 original size:21 final size:21
Alignment explanation
Indices: 9474333--9474394 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
9474323 GTATGTTAAG
9474333 ATTTATTTATATTA-ATTTAT
1 ATTTATTTATATTATATTTAT
9474353 ATTTATTTATGATT-TATTTAT
1 ATTTATTTAT-ATTATATTTAT
9474374 ATTTATTTA-ATTATGATTTAT
1 ATTTATTTATATTAT-ATTTAT
9474395 TTATTATTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
19 3 0.08
20 11 0.29
21 24 0.63
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (21 bp):
ATTTATTTATATTATATTTAT
Found at i:9474414 original size:36 final size:36
Alignment explanation
Indices: 9474337--9474416 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
9474327 GTTAAGATTT
* ** *
9474337 ATTTATATTAATTTATATTTATTTATGATTTATTTAT
1 ATTTAT-TTAATTTATATTTATTTATGATTCATAAAC
*
9474374 ATTTATTTAA-TTATGATTTATTTATTATTCATAAAC
1 ATTTATTTAATTTAT-ATTTATTTATGATTCATAAAC
9474410 ATTTATT
1 ATTTATT
9474417 CGTTCATATA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
35 4 0.11
36 27 0.73
37 6 0.16
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (36 bp):
ATTTATTTAATTTATATTTATTTATGATTCATAAAC
Found at i:9476747 original size:2 final size:2
Alignment explanation
Indices: 9476742--9476770 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9476732 TCTCTCTCTC
9476742 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9476771 CCACTTTGAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9478164 original size:16 final size:14
Alignment explanation
Indices: 9478145--9478178 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
9478135 TTCTCATTAA
9478145 ATTTGAATTTAATTTT
1 ATTTGAATTT--TTTT
9478161 ATTTGAATTTTTTT
1 ATTTGAATTTTTTT
9478175 ATTT
1 ATTT
9478179 TTTGAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
16 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (14 bp):
ATTTGAATTTTTTT
Found at i:9478293 original size:44 final size:43
Alignment explanation
Indices: 9478234--9478331 Score: 105
Period size: 43 Copynumber: 2.2 Consensus size: 43
9478224 TCGAAATTAA
9478234 TAAAATATTATTTTTTAAATATAAATATTTAAAT-AAA-AAA-TTATTT
1 TAAAAT-TTATTTTTT--ATAT-AATA-TTAAATCAAATAAATTTA-TT
9478280 TAAAATTTA-TTTTTATATAATATTAAATCAAATTAAATTTATT
1 TAAAATTTATTTTTTATATAATATTAAATCAAA-TAAATTTATT
9478323 TAAAATTTA
1 TAAAATTTA
9478332 AATCTCCGAA
Statistics
Matches: 48, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
40 6 0.12
41 7 0.15
42 4 0.08
43 14 0.29
44 8 0.17
45 3 0.06
46 6 0.12
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (43 bp):
TAAAATTTATTTTTTATATAATATTAAATCAAATAAATTTATT
Found at i:9483920 original size:2 final size:2
Alignment explanation
Indices: 9483915--9483948 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9483905 GTATACATAC
9483915 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9483949 TTAGAACACG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9488164 original size:18 final size:18
Alignment explanation
Indices: 9488136--9488176 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
9488126 TTCATCGATT
*
9488136 TTTAATTTTTAAT-TTTA
1 TTTAATTTTTTATATTTA
9488153 TTTAATTTTTTATATTTA
1 TTTAATTTTTTATATTTA
9488171 TTTAAT
1 TTTAAT
9488177 ATATTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTAATTTTTTATATTTA
Found at i:9488247 original size:16 final size:16
Alignment explanation
Indices: 9488226--9488256 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
9488216 TTATAAATAT
9488226 TTAAAATATATATAAA
1 TTAAAATATATATAAA
9488242 TTAAAATATATATAA
1 TTAAAATATATATAA
9488257 TTTAGTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAAATATATATAAA
Found at i:9490787 original size:12 final size:13
Alignment explanation
Indices: 9490770--9490808 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
9490760 AGTTTAATTA
9490770 ATATTAAAAAAAG
1 ATATTAAAAAAAG
*
9490783 A-ATTAAAAAGAAA
1 ATATTAAAAA-AAG
9490796 ATATTAAAAAAAG
1 ATATTAAAAAAAG
9490809 GGTTGGGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 8 0.36
13 6 0.27
14 8 0.36
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.21
Consensus pattern (13 bp):
ATATTAAAAAAAG
Found at i:9495629 original size:17 final size:17
Alignment explanation
Indices: 9495592--9495629 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
9495582 GATGTTTCTA
9495592 GAAAACAAAAAAAAAAT
1 GAAAACAAAAAAAAAAT
9495609 -AAAACAAAAAAAAAAT
1 GAAAACAAAAAAAAAAT
9495625 GAAAA
1 GAAAA
9495630 AAGAAAGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.84, C:0.05, G:0.05, T:0.05
Consensus pattern (17 bp):
GAAAACAAAAAAAAAAT
Found at i:9497528 original size:75 final size:74
Alignment explanation
Indices: 9497401--9497569 Score: 239
Period size: 75 Copynumber: 2.3 Consensus size: 74
9497391 AAATTTTTAC
* * * *
9497401 ATTTTGAAGTTTCATTACCTCTGATTAAGAAAACATTCAAAGATTTTGAAATTTTTAAGACCTTT
1 ATTTTAAAGTTTCATTGCCTCTAATTAAGAAAACATTCAAAGATTTTGAAATTTTTAAGACCTAT
9497466 AGGCAAAAT
66 AGGCAAAAT
* * *
9497475 ATTTTAAAGTTTCATTGCCTCTAATTAGGATGAGCATTCAAAGATTTTGAAATTTTTAAGACCTA
1 ATTTTAAAGTTTCATTGCCTCTAATTAAGA-AAACATTCAAAGATTTTGAAATTTTTAAGACCTA
*
9497540 TGGGCAAAAT
65 TAGGCAAAAT
* *
9497550 ATTTTCAAGTTTTATTGCCT
1 ATTTTAAAGTTTCATTGCCT
9497570 ATTTTCAAGT
Statistics
Matches: 84, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
74 26 0.31
75 58 0.69
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (74 bp):
ATTTTAAAGTTTCATTGCCTCTAATTAAGAAAACATTCAAAGATTTTGAAATTTTTAAGACCTAT
AGGCAAAAT
Found at i:9497574 original size:20 final size:20
Alignment explanation
Indices: 9497549--9497589 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
9497539 ATGGGCAAAA
9497549 TATTTTCAAGTTTTATTGCC
1 TATTTTCAAGTTTTATTGCC
9497569 TATTTTCAAGTTTTATTGCC
1 TATTTTCAAGTTTTATTGCC
9497589 T
1 T
9497590 TTGATCAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (20 bp):
TATTTTCAAGTTTTATTGCC
Found at i:9497597 original size:20 final size:20
Alignment explanation
Indices: 9497549--9497598 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
9497539 ATGGGCAAAA
*
9497549 TATTTTCAAGTTTTATTGCC
1 TATTATCAAGTTTTATTGCC
*
9497569 TATTTTCAAGTTTTATTGCC
1 TATTATCAAGTTTTATTGCC
9497589 T-TTGATCAAG
1 TATT-ATCAAG
9497599 AGGAGCATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.22, C:0.14, G:0.12, T:0.52
Consensus pattern (20 bp):
TATTATCAAGTTTTATTGCC
Found at i:9497701 original size:97 final size:98
Alignment explanation
Indices: 9497449--9497720 Score: 265
Period size: 95 Copynumber: 2.8 Consensus size: 98
9497439 AAAGATTTTG
* * * * *
9497449 AAATTTTTAAGACCTTTAGGCAAAATATTTTAAAGTTTCATTGCCTCTAATTAGGATGAGCATTC
1 AAATTTTCAATACCTTTAGGCAAAACATTTTAAAGTTTCATTGCCTCTTATTAGGAGGAGCATTC
* * *
9497514 AAAGATTTTGAAATTTTTAAGACCTATGGGCAA
66 AAAGATTTTAAAATTTCTAAAACCTATGGGCAA
* * * * *
9497547 AATATTTTCAAGT---TTTATTGC----CTATTTTCAAGTTTTATTGCCT-TTGATCAAGAGGAG
1 AA-ATTTTCAA-TACCTTTA-GGCAAAAC-ATTTTAAAGTTTCATTGCCTCTT-ATTAGGAGGAG
* *
9497604 CATTCAAAGACTTTAAAATTTCTAAAACCTCTGGGC-A
61 CATTCAAAGATTTTAAAATTTCTAAAACCTATGGGCAA
* * *
9497641 CAATTTTCAATACCTCTAGGCAAAACATTTTAAAGTTTCATTGCCTCTTATTGGGAGGAGCATTC
1 AAATTTTCAATACCTTTAGGCAAAACATTTTAAAGTTTCATTGCCTCTTATTAGGAGGAGCATTC
*
9497706 AAAGATTTTACAATT
66 AAAGATTTTAAAATT
9497721 ACCAAGACCT
Statistics
Matches: 136, Mismatches: 25, Indels: 27
0.72 0.13 0.14
Matches are distributed among these distances:
92 1 0.01
93 8 0.06
94 5 0.04
95 60 0.44
97 48 0.35
98 7 0.05
99 7 0.05
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (98 bp):
AAATTTTCAATACCTTTAGGCAAAACATTTTAAAGTTTCATTGCCTCTTATTAGGAGGAGCATTC
AAAGATTTTAAAATTTCTAAAACCTATGGGCAA
Found at i:9497813 original size:76 final size:75
Alignment explanation
Indices: 9497660--9497813 Score: 211
Period size: 76 Copynumber: 2.0 Consensus size: 75
9497650 ATACCTCTAG
* *
9497660 GCAAAACATTTTAAAGTTTCATTGCCTCTTATTGGGAGGAGCATTCAAAGATTTTACAATTACCA
1 GCAAAACATTTTAAAGTTTCATTGCCTCTGATTGAGAGGAGCATTCAAAGATTTTACAATTACCA
**
9497725 AGACCTTTAA
66 AGACCTCCAA
* ** *
9497735 GCAAAAGATTTTAAAGTTTCATTTGCCTCTGATTGAGAGGAGCATTCAAAGATTTTGGAATTTCT
1 GCAAAACATTTTAAAGTTTCA-TTGCCTCTGATTGAGAGGAGCATTCAAAGATTTTACAATTAC-
9497800 C-AGACCTCCAA
64 CAAGACCTCCAA
9497811 GCA
1 GCA
9497814 TAATCTTTAA
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
75 20 0.29
76 48 0.70
77 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (75 bp):
GCAAAACATTTTAAAGTTTCATTGCCTCTGATTGAGAGGAGCATTCAAAGATTTTACAATTACCA
AGACCTCCAA
Found at i:9498015 original size:116 final size:117
Alignment explanation
Indices: 9497723--9498157 Score: 428
Period size: 116 Copynumber: 3.7 Consensus size: 117
9497713 TTACAATTAC
* * * *
9497723 CAAGACCTTTAAGCAAAAGATTTTAAAGTTTCATTTGCCTCTGATTGAGAGGAGCATTCAAAGAT
1 CAAGACCTTTAGGTAAAACATTTTAAAGTTTCA-TTACCTCTGATTGAGAGGAGCATTCAAAGAT
* * * * *
9497788 TTTGGAATTTCTC-AGACCTCCAAGCATAATCTTTAAAGACCTTTGGATACAATTTT
65 TTTGTAATTTC-CAAGACCTTCAGGCATAATCTCT-AAGACTTTTGGAT--AATTTT
* * * **
9497844 CAAGACCTCTAAGTAAAACATTTTAAAGTTTCATTACCTCTGATTAAGAAAAGCATTCAAAGATT
1 CAAGACCTTTAGGTAAAACATTTTAAAGTTTCATTACCTCTGATTGAGAGGAGCATTCAAAGATT
* * *
9497909 TTATAATTTCCAAGACCTTCAGGTATAATCTCTAAGACTTTTAG-TAATTTT
66 TTGTAATTTCCAAGACCTTCAGGCATAATCTCTAAGACTTTTGGATAATTTT
* * * * * * * * *
9497960 TAAGATCTTTGGGTAAAATATTTTAAAATTTCATTGCCTCTGATTGGGAGGAGCATTTAAAAATT
1 CAAGACCTTTAGGTAAAACATTTTAAAGTTTCATTACCTCTGATTGAGAGGAGCATTCAAAGATT
* * **
9498025 TTGTAATTTTCAAGACCTTC-GAGCATAATCTCTAA-AATCTCGGGCATAATTTT
66 TTGTAATTTCCAAGACCTTCAG-GCATAATCTCTAAGACT-TTTGG-ATAATTTT
* * * * * *
9498078 CAAGACCTTCAGGCAAAACATTTTAAAGTTTCATTATCTCTGATCGGGATGAGCATTCAAAGATT
1 CAAGACCTTTAGGTAAAACATTTTAAAGTTTCATTACCTCTGATTGAGAGGAGCATTCAAAGATT
* *
9498143 TTGCAATTTCTAAGA
66 TTGTAATTTCCAAGA
9498158 TCTCCGAGCA
Statistics
Matches: 257, Mismatches: 52, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
115 3 0.01
116 89 0.35
118 72 0.28
119 10 0.04
120 53 0.21
121 30 0.12
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (117 bp):
CAAGACCTTTAGGTAAAACATTTTAAAGTTTCATTACCTCTGATTGAGAGGAGCATTCAAAGATT
TTGTAATTTCCAAGACCTTCAGGCATAATCTCTAAGACTTTTGGATAATTTT
Found at i:9498213 original size:22 final size:23
Alignment explanation
Indices: 9498188--9498231 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
9498178 AACCTCCGGG
*
9498188 CACAA-TCTCTAATACCTTTGGA
1 CACAATTCTCTAATACATTTGGA
*
9498210 CACAATTTTCTAATACATTTGG
1 CACAATTCTCTAATACATTTGG
9498232 GCATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (23 bp):
CACAATTCTCTAATACATTTGGA
Found at i:9498225 original size:23 final size:23
Alignment explanation
Indices: 9498195--9498250 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
9498185 GGGCACAATC
9498195 TCTAATACCTTTGGACACAATTT
1 TCTAATACCTTTGGACACAATTT
* * *
9498218 TCTAATACATTTGGGCATAATTT
1 TCTAATACCTTTGGACACAATTT
*
9498241 T-TAAGACCTT
1 TCTAATACCTT
9498251 CAGCATAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 7 0.25
23 21 0.75
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (23 bp):
TCTAATACCTTTGGACACAATTT
Found at i:9498701 original size:3 final size:3
Alignment explanation
Indices: 9498695--9498733 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
9498685 TTAAAATTAT
* *
9498695 TAA TAA TTA TAA TAG TAAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TA
9498734 TTGGTTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.94
4 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:9498774 original size:14 final size:13
Alignment explanation
Indices: 9498745--9498789 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
9498735 TGGTTTAATT
*
9498745 AAAATTTAAAAAA
1 AAAAGTTAAAAAA
9498758 AAAAGTTAAAAAGA
1 AAAAGTTAAAAA-A
*
9498772 AAAGGTTAAAAAA
1 AAAAGTTAAAAAA
9498785 AAAAG
1 AAAAG
9498790 GTTGGGACAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (13 bp):
AAAAGTTAAAAAA
Found at i:9498790 original size:14 final size:14
Alignment explanation
Indices: 9498750--9498792 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
9498740 TAATTAAAAT
9498750 TTAAAAAAAAAA-G
1 TTAAAAAAAAAAGG
*
9498763 TTAAAAAGAAAAGG
1 TTAAAAAAAAAAGG
9498777 TTAAAAAAAAAAGG
1 TTAAAAAAAAAAGG
9498791 TT
1 TT
9498793 GGGACAGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.67, C:0.00, G:0.14, T:0.19
Consensus pattern (14 bp):
TTAAAAAAAAAAGG
Found at i:9499093 original size:24 final size:24
Alignment explanation
Indices: 9499066--9499115 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
9499056 AAAACCTTAA
* *
9499066 CTCCTATACTTAGAAACGCCAGCT
1 CTCCCATACTTAGAAACGCAAGCT
*
9499090 CTCCCATACTTAGAAACTCAAGCT
1 CTCCCATACTTAGAAACGCAAGCT
9499114 CT
1 CT
9499116 TCAATGCCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.34, G:0.10, T:0.26
Consensus pattern (24 bp):
CTCCCATACTTAGAAACGCAAGCT
Found at i:9499898 original size:12 final size:12
Alignment explanation
Indices: 9499867--9499909 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
9499857 GATTGCTTTT
9499867 AATAATAATAAA
1 AATAATAATAAA
9499879 AAT--T-ATAAA
1 AATAATAATAAA
9499888 AATAATAATAAA
1 AATAATAATAAA
9499900 AATAAGTAAT
1 AATAA-TAAT
9499910 GAAATATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
9 8 0.30
10 1 0.04
11 1 0.04
12 13 0.48
13 4 0.15
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:9499973 original size:3 final size:3
Alignment explanation
Indices: 9499951--9500021 Score: 108
Period size: 3 Copynumber: 23.7 Consensus size: 3
9499941 AACTTTACAG
* *
9499951 AAT AA- AAT AAA AAC 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
9499998 AAT AAT AAT AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT AAT AAT A-AT AA
9500022 AATGCTTATA
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
2 2 0.03
3 58 0.92
4 3 0.05
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:9500307 original size:14 final size:14
Alignment explanation
Indices: 9500288--9500559 Score: 58
Period size: 14 Copynumber: 18.9 Consensus size: 14
9500278 GTGTTTTCTT
9500288 TAAACCCTAAAATC
1 TAAACCCTAAAATC
**
9500302 TAAACCCTAAACCC
1 TAAACCCTAAAATC
*
9500316 TAAATCCTAAAATC
1 TAAACCCTAAAATC
** * *
9500330 -AAAATCTTAAACC
1 TAAACCCTAAAATC
*
9500343 TTCAAACCTTAAAA-C
1 -T-AAACCCTAAAATC
* *
9500358 TAAAACCCTAAACCCTT
1 T-AAACCCTAAA--ATC
**
9500375 TAAATTCTAAAATC
1 TAAACCCTAAAATC
* **
9500389 AAAACCCTAATCTC
1 TAAACCCTAAAATC
*
9500403 TTAAACCTTAAAA-C
1 -TAAACCCTAAAATC
* *
9500417 TAAAATCCTAAACTC
1 T-AAACCCTAAAATC
9500432 TTTAAA-CCTCAAAA-C
1 --TAAACCCT-AAAATC
* **
9500447 TAAAACTCTAAACCC
1 T-AAACCCTAAAATC
* *
9500462 CAAACCATAAAAT-
1 TAAACCCTAAAATC
*
9500475 TGAAACCTTAAACCATC
1 T-AAACCCTAAA--ATC
9500492 TAAACCCTAAAA-C
1 TAAACCCTAAAATC
* **
9500505 CAAACCCTTAAACCC
1 TAAACCC-TAAAATC
9500520 TTAAAACCC--AAATC
1 -T-AAACCCTAAAATC
*
9500534 AAAACCCTAAAATC
1 TAAACCCTAAAATC
* *
9500548 CAAAACCTAAAA
1 TAAACCCTAAAA
9500560 CCCTAAATTT
Statistics
Matches: 181, Mismatches: 52, Indels: 50
0.64 0.18 0.18
Matches are distributed among these distances:
12 6 0.03
13 18 0.10
14 98 0.54
15 18 0.10
16 32 0.18
17 9 0.05
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAAATC
Found at i:9500409 original size:59 final size:58
Alignment explanation
Indices: 9500287--9500524 Score: 209
Period size: 59 Copynumber: 4.1 Consensus size: 58
9500277 TGTGTTTTCT
* * *
9500287 TTAAACCCTAAAATCT-AAACCCTAAACCC--TAAATCCTAAAATCAAAATCTTAAACC
1 TTAAACCTTAAAA-CTAAAACCCTAAACCCTTTAAATCCTAAAATCAAAACCCTAAACC
* *
9500343 TTCAAACCTTAAAACTAAAACCCTAAACCCTTTAAATTCTAAAATCAAAACCCTAATCTC
1 TT-AAACCTTAAAACTAAAACCCTAAACCCTTTAAATCCTAAAATCAAAACCCTAAAC-C
* * *
9500403 TTAAACCTTAAAACTAAAATCCTAAACTCTTTAAA-CCTCAAAA-CTAAAACTCTAAACC
1 TTAAACCTTAAAACTAAAACCCTAAACCCTTTAAATCCT-AAAATC-AAAACCCTAAACC
** * * * * * * * *
9500461 CCAAACCATAAAATTGAAACCTTAAACCATCTAAACCCTAAAA-CCAAACCCTTAAACCC
1 TTAAACCTTAAAACTAAAACCCTAAACCCTTTAAATCCTAAAATCAAAACCC-TAAA-CC
9500520 TTAAA
1 TTAAA
9500525 ACCCAAATCA
Statistics
Matches: 148, Mismatches: 24, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
56 4 0.03
57 28 0.19
58 38 0.26
59 75 0.51
60 3 0.02
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (58 bp):
TTAAACCTTAAAACTAAAACCCTAAACCCTTTAAATCCTAAAATCAAAACCCTAAACC
Found at i:9500439 original size:30 final size:30
Alignment explanation
Indices: 9500284--9500459 Score: 145
Period size: 30 Copynumber: 6.0 Consensus size: 30
9500274 GTTTGTGTTT
*
9500284 TCTTTAAACCCTAAAATCT-AAACCCTAAAC
1 TCTTTAAACCTTAAAA-CTAAAACCCTAAAC
* * *
9500314 -C-CTAAATCC-TAAAA-TCAAAATCTTAAAC
1 TCTTTAAA-CCTTAAAACT-AAAACCCTAAAC
*
9500342 -CTTCAAACCTTAAAACTAAAACCCTAAAC
1 TCTTTAAACCTTAAAACTAAAACCCTAAAC
* * *
9500371 CCTTTAAA-TTCTAAAA-TCAAAACCCTAATC
1 TCTTTAAACCT-TAAAACT-AAAACCCTAAAC
*
9500401 TC-TTAAACCTTAAAACTAAAATCCTAAAC
1 TCTTTAAACCTTAAAACTAAAACCCTAAAC
* *
9500430 TCTTTAAACCTCAAAACTAAAACTCTAAAC
1 TCTTTAAACCTTAAAACTAAAACCCTAAAC
9500460 CCCAAACCAT
Statistics
Matches: 117, Mismatches: 17, Indels: 24
0.74 0.11 0.15
Matches are distributed among these distances:
26 1 0.01
28 21 0.18
29 45 0.38
30 50 0.43
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.26
Consensus pattern (30 bp):
TCTTTAAACCTTAAAACTAAAACCCTAAAC
Found at i:9500517 original size:21 final size:21
Alignment explanation
Indices: 9500493--9500566 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 21
9500483 TAAACCATCT
*
9500493 AAACCCTAAAA-CCAAACCCTT
1 AAACCCTAAAACCCAAA-CCTA
*
9500514 AAACCCTTAAAACCCAAATC-A
1 AAACCC-TAAAACCCAAACCTA
*
9500535 AAACCCTAAAATCCAAAACCTA
1 AAACCCTAAAA-CCCAAACCTA
9500557 AAACCCTAAA
1 AAACCCTAAA
9500567 TTTAAAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
20 5 0.11
21 18 0.40
22 17 0.38
23 5 0.11
ACGTcount: A:0.53, C:0.34, G:0.00, T:0.14
Consensus pattern (21 bp):
AAACCCTAAAACCCAAACCTA
Found at i:9500527 original size:30 final size:29
Alignment explanation
Indices: 9500287--9500541 Score: 138
Period size: 30 Copynumber: 8.8 Consensus size: 29
9500277 TGTGTTTTCT
*
9500287 TTAAACCCTAAAATCTAAACCC-TAAACCC
1 TTAAACCCTAAAA-CAAAACCCTTAAACCC
* *
9500316 -TAAATCCTAAAATCAAAA-TCTTAAA-CC
1 TTAAACCCTAAAA-CAAAACCCTTAAACCC
*
9500343 TTCAAACCTTAAAACTAAAACCC-TAAACCC
1 TT-AAACCCTAAAAC-AAAACCCTTAAACCC
** * *
9500373 TTTAAATTCTAAAATCAAAACCC-TAATCTC
1 -TTAAACCCTAAAA-CAAAACCCTTAAACCC
* * *
9500403 TTAAACCTTAAAACTAAAATCC-TAAACTCT
1 TTAAACCCTAAAAC-AAAACCCTTAAAC-CC
*
9500433 TTAAA-CCTCAAAACTAAAACTC-TAAACCC
1 TTAAACCCT-AAAAC-AAAACCCTTAAACCC
* * ** *
9500462 -CAAACCATAAAATTGAAA-CCTTAAACCA
1 TTAAACCCTAAAA-CAAAACCCTTAAACCC
*
9500490 TCTAAACCCTAAAACCAAACCCTTAAACCC
1 T-TAAACCCTAAAACAAAACCCTTAAACCC
*
9500520 TTAAAACCC-AAATCAAAACCCT
1 TT-AAACCCTAAAACAAAACCCT
9500542 AAAATCCAAA
Statistics
Matches: 173, Mismatches: 35, Indels: 36
0.71 0.14 0.15
Matches are distributed among these distances:
27 4 0.02
28 39 0.23
29 57 0.33
30 70 0.40
31 3 0.02
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.23
Consensus pattern (29 bp):
TTAAACCCTAAAACAAAACCCTTAAACCC
Found at i:9500562 original size:22 final size:21
Alignment explanation
Indices: 9500493--9500566 Score: 87
Period size: 22 Copynumber: 3.5 Consensus size: 21
9500483 TAAACCATCT
* *
9500493 AAACCCTAAAACCAAACCCTT
1 AAACCCTAAAACCAAAACCTA
* *
9500514 AAACCCTTAAAACCCAAATC-A
1 AAACCC-TAAAACCAAAACCTA
9500535 AAACCCTAAAATCCAAAACCTA
1 AAACCCTAAAA-CCAAAACCTA
9500557 AAACCCTAAA
1 AAACCCTAAA
9500567 TTTAAAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 5 0.11
21 18 0.41
22 21 0.48
ACGTcount: A:0.53, C:0.34, G:0.00, T:0.14
Consensus pattern (21 bp):
AAACCCTAAAACCAAAACCTA
Found at i:9500564 original size:8 final size:8
Alignment explanation
Indices: 9500493--9500566 Score: 50
Period size: 8 Copynumber: 9.2 Consensus size: 8
9500483 TAAACCATCT
9500493 AAACCCTA
1 AAACCCTA
9500501 AAA-CC--
1 AAACCCTA
*
9500506 AAACCCTT
1 AAACCCTA
9500514 AAACCCTTA
1 AAACCC-TA
9500523 AAACCCAAATCA
1 AAACCC---T-A
9500535 AAACCCTA
1 AAACCCTA
*
9500543 AAATCC-A
1 AAACCCTA
9500550 AAA-CCTA
1 AAACCCTA
9500557 AAACCCTA
1 AAACCCTA
9500565 AA
1 AA
9500567 TTTAAAAATT
Statistics
Matches: 54, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
5 3 0.06
6 4 0.07
7 10 0.19
8 21 0.39
9 8 0.15
11 1 0.02
12 7 0.13
ACGTcount: A:0.53, C:0.34, G:0.00, T:0.14
Consensus pattern (8 bp):
AAACCCTA
Found at i:9500580 original size:29 final size:29
Alignment explanation
Indices: 9500542--9500598 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
9500532 TCAAAACCCT
*
9500542 AAAATCCAAAACCTAAAACCCTAAATTTA
1 AAAATCCAAAACCTAAAACCCCAAATTTA
* *
9500571 AAAATTCAAAACCTTAAACCCCAAATTT
1 AAAATCCAAAACCTAAAACCCCAAATTT
9500599 GGTACATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.23
Consensus pattern (29 bp):
AAAATCCAAAACCTAAAACCCCAAATTTA
Found at i:9506662 original size:19 final size:19
Alignment explanation
Indices: 9506638--9506676 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
9506628 GATCGTTTGT
9506638 AGTGATGAAAAGATAATTA
1 AGTGATGAAAAGATAATTA
*
9506657 AGTGATGAAAATATAATTA
1 AGTGATGAAAAGATAATTA
9506676 A
1 A
9506677 CATCTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.18, T:0.28
Consensus pattern (19 bp):
AGTGATGAAAAGATAATTA
Found at i:9511656 original size:23 final size:25
Alignment explanation
Indices: 9511630--9511683 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
9511620 AAAAAATCAT
*
9511630 AAAAAATGA-TTTTAAA-A-TATAA
1 AAAAAAAGAGTTTTAAATATTATAA
*
9511652 AAAAATAAGAGTTTTAAATATTCTAA
1 AAAAA-AAGAGTTTTAAATATTATAA
9511678 AAAAAA
1 AAAAAA
9511684 GACATAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.19
23 3 0.12
24 7 0.27
25 2 0.08
26 9 0.35
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.30
Consensus pattern (25 bp):
AAAAAAAGAGTTTTAAATATTATAA
Found at i:9512298 original size:15 final size:16
Alignment explanation
Indices: 9512273--9512314 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
9512263 TTCTTGGCTT
*
9512273 TTTTCTAATTTTTG-TA
1 TTTT-TAATTTTAGTTA
*
9512289 TTTTTAATTTTAGTTC
1 TTTTTAATTTTAGTTA
9512305 TTTTTAATTT
1 TTTTTAATTT
9512315 ATAGATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (16 bp):
TTTTTAATTTTAGTTA
Found at i:9513309 original size:24 final size:22
Alignment explanation
Indices: 9513277--9513334 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
9513267 GTATCTTAAT
9513277 TTAATAAAATAATATATTTATA
1 TTAATAAAATAATATATTTATA
*
9513299 TATAATTAAAAT-ATA-ATTTTTA
1 T-TAA-TAAAATAATATATTTATA
9513321 TTAA-AAAATAATAT
1 TTAATAAAATAATAT
9513335 TTTCATGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
19 5 0.16
20 3 0.10
21 3 0.10
22 8 0.26
23 6 0.19
24 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAATAAAATAATATATTTATA
Found at i:9513325 original size:17 final size:18
Alignment explanation
Indices: 9513303--9513337 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
9513293 TTTATATATA
*
9513303 ATTAAAATATAAT-TTTT
1 ATTAAAAAATAATATTTT
9513320 ATTAAAAAATAATATTTT
1 ATTAAAAAATAATATTTT
9513338 CATGAATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTAAAAAATAATATTTT
Found at i:9513336 original size:19 final size:21
Alignment explanation
Indices: 9513277--9513337 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 21
9513267 GTATCTTAAT
9513277 TTAATAAAATAATATATTTATA
1 TTAATAAAATAATAT-TTTATA
9513299 TATAATTAAAAT-ATAATTTT-TA
1 T-TAA-TAAAATAAT-ATTTTATA
9513321 TTAA-AAAATAATATTTT
1 TTAATAAAATAATATTTT
9513338 CATGAATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
19 10 0.29
20 2 0.06
21 3 0.09
22 4 0.11
23 8 0.23
24 8 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAATAAAATAATATTTTATA
Found at i:9515351 original size:17 final size:18
Alignment explanation
Indices: 9515310--9515351 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
9515300 AAAGAATGTA
9515310 TTATATATTTTATTAATT
1 TTATATATTTTATTAATT
9515328 TTATATATTTT-TTAAATT
1 TTATATATTTTATT-AATT
9515346 TT-TATA
1 TTATATA
9515352 AAATAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATATATTTTATTAATT
Found at i:9515378 original size:16 final size:16
Alignment explanation
Indices: 9515359--9515438 Score: 53
Period size: 15 Copynumber: 5.1 Consensus size: 16
9515349 ATAAAATAAA
9515359 AAAATTATTTTATATT
1 AAAATTATTTTATATT
9515375 AAAATTTATTTTAATATAT
1 AAAA-TTATTTT-ATAT-T
*
9515394 TAAA--ATTTTATATT
1 AAAATTATTTTATATT
* * *
9515408 -AACTTAATTTATA-A
1 AAAATTATTTTATATT
*
9515422 AAAAAT-TTTTATATT
1 AAAATTATTTTATATT
9515437 AA
1 AA
9515439 CTTAATATAT
Statistics
Matches: 49, Mismatches: 8, Indels: 15
0.68 0.11 0.21
Matches are distributed among these distances:
13 2 0.04
14 7 0.14
15 16 0.33
16 9 0.18
17 7 0.14
18 4 0.08
19 4 0.08
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (16 bp):
AAAATTATTTTATATT
Found at i:9515409 original size:21 final size:20
Alignment explanation
Indices: 9515369--9515409 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
9515359 AAAATTATTT
*
9515369 TATATTAAAATTTATTTTAA
1 TATATTAAAATTTATATTAA
9515389 TATATTAAAATTTTATATTAA
1 TATATTAAAA-TTTATATTAA
9515410 CTTAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATATTAAAATTTATATTAA
Found at i:9515439 original size:29 final size:28
Alignment explanation
Indices: 9515395--9515452 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 28
9515385 TTAATATATT
*
9515395 AAAATTTTATATTAACTTAATTTATAAA
1 AAAATTTTATATTAACTTAATATATAAA
9515423 AAAATTTTTATATTAACTTAATATATAAA
1 AAAA-TTTTATATTAACTTAATATATAAA
9515452 A
1 A
9515453 CGAGATCCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (28 bp):
AAAATTTTATATTAACTTAATATATAAA
Found at i:9515730 original size:22 final size:21
Alignment explanation
Indices: 9515700--9515740 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
9515690 ATTGTTTTTA
*
9515700 ATAATAATAAAAATGAAAAAAT
1 ATAAAAATAAAAAT-AAAAAAT
*
9515722 ATAAAAATAATAATAAAAA
1 ATAAAAATAAAAATAAAAA
9515741 TAAGTAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (21 bp):
ATAAAAATAAAAATAAAAAAT
Found at i:9515804 original size:9 final size:9
Alignment explanation
Indices: 9515790--9515822 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
9515780 AACCTTACAG
9515790 AATAAAAAT
1 AATAAAAAT
9515799 AATAAAAAT
1 AATAAAAAT
*
9515808 AATAAATAT
1 AATAAAAAT
9515817 -ATAAAA
1 AATAAAA
9515823 TGCTTATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AATAAAAAT
Found at i:9516131 original size:14 final size:14
Alignment explanation
Indices: 9516086--9516124 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
9516076 GTGTTTTCTT
9516086 TAAACCCTAAAATC
1 TAAACCCTAAAATC
**
9516100 TAAACTTTAAAATC
1 TAAACCCTAAAATC
9516114 TAAACCCTAAA
1 TAAACCCTAAA
9516125 TCCTAAAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAACCCTAAAATC
Found at i:9516177 original size:30 final size:30
Alignment explanation
Indices: 9516143--9516266 Score: 146
Period size: 30 Copynumber: 4.2 Consensus size: 30
9516133 TCGAGATCTT
9516143 AACCCTTCAAACCTTAAAACTAAAACCCTA
1 AACCCTTCAAACCTTAAAACTAAAACCCTA
* *
9516173 AACCCTTTAAA-TTCTAAAA-TCAAAACCCTA
1 AACCCTTCAAACCT-TAAAACT-AAAACCCTA
* *
9516203 ATCCC-TCAAACCTTAAAACTAAAATCCTA
1 AACCCTTCAAACCTTAAAACTAAAACCCTA
* * *
9516232 AACTCTTTAAACCTCAAAACTAAAACCCTA
1 AACCCTTCAAACCTTAAAACTAAAACCCTA
9516262 AACCC
1 AACCC
9516267 CAAACTATAA
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
29 22 0.29
30 55 0.71
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (30 bp):
AACCCTTCAAACCTTAAAACTAAAACCCTA
Found at i:9516190 original size:59 final size:59
Alignment explanation
Indices: 9516113--9516293 Score: 178
Period size: 59 Copynumber: 3.1 Consensus size: 59
9516103 ACTTTAAAAT
* * * *
9516113 CTAAACCC--TAAATCCTAAAATCGAGATCTTAA-CCCTTCAAACCTTAAAACTAAAACC
1 CTAAACCCTTTAAATCCTAAAATCAAAACCCTAATCCC-TCAAACCTTAAAACTAAAACC
* *
9516170 CTAAACCCTTTAAATTCTAAAATCAAAACCCTAATCCCTCAAACCTTAAAACTAAAATC
1 CTAAACCCTTTAAATCCTAAAATCAAAACCCTAATCCCTCAAACCTTAAAACTAAAACC
* * * *
9516229 CTAAACTCTTTAAA-CCTCAAAA-CTAAAACCCTAAACCC-CAAA-CTATAAAATTGAAACC
1 CTAAACCCTTTAAATCCT-AAAATC-AAAACCCTAATCCCTCAAACCT-TAAAACTAAAACC
*
9516287 TTAAACC
1 CTAAACC
9516294 ATCTATACCC
Statistics
Matches: 104, Mismatches: 14, Indels: 11
0.81 0.11 0.09
Matches are distributed among these distances:
57 10 0.10
58 22 0.21
59 69 0.66
60 3 0.03
ACGTcount: A:0.46, C:0.29, G:0.02, T:0.23
Consensus pattern (59 bp):
CTAAACCCTTTAAATCCTAAAATCAAAACCCTAATCCCTCAAACCTTAAAACTAAAACC
Found at i:9516356 original size:8 final size:8
Alignment explanation
Indices: 9516300--9516380 Score: 71
Period size: 8 Copynumber: 10.0 Consensus size: 8
9516290 AACCATCTAT
9516300 ACCCTAAA
1 ACCCTAAA
9516308 ACCCTTAAA
1 ACCC-TAAA
9516317 ACCCAAATCAAA
1 ACCC---T-AAA
9516329 ACCCTAAA
1 ACCCTAAA
*
9516337 ATCC-AAA
1 ACCCTAAA
9516344 A-CCTAAA
1 ACCCTAAA
9516351 ACCCTAAA
1 ACCCTAAA
*
9516359 ATCC-AAA
1 ACCCTAAA
9516366 A-CCTAAA
1 ACCCTAAA
9516373 ACCCTAAA
1 ACCCTAAA
9516381 TTTAAAAATT
Statistics
Matches: 62, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
6 4 0.06
7 16 0.26
8 25 0.40
9 9 0.15
11 1 0.02
12 7 0.11
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.14
Consensus pattern (8 bp):
ACCCTAAA
Found at i:9516388 original size:22 final size:22
Alignment explanation
Indices: 9516302--9516380 Score: 117
Period size: 22 Copynumber: 3.6 Consensus size: 22
9516292 CCATCTATAC
*
9516302 CCTAAAACCCTTAAAA-CCCAAA
1 CCTAAAACCC-TAAAATCCAAAA
*
9516324 TC-AAAACCCTAAAATCCAAAA
1 CCTAAAACCCTAAAATCCAAAA
9516345 CCTAAAACCCTAAAATCCAAAA
1 CCTAAAACCCTAAAATCCAAAA
9516367 CCTAAAACCCTAAA
1 CCTAAAACCCTAAA
9516381 TTTAAAAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
20 5 0.10
21 13 0.25
22 34 0.65
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.14
Consensus pattern (22 bp):
CCTAAAACCCTAAAATCCAAAA
Found at i:9516388 original size:29 final size:29
Alignment explanation
Indices: 9516356--9516412 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
9516346 CTAAAACCCT
*
9516356 AAAATCCAAAACCTAAAACCCTAAATTTA
1 AAAATCCAAAACCTAAAACCCCAAATTTA
* *
9516385 AAAATTCAAAACCTTAAACCCCAAATTT
1 AAAATCCAAAACCTAAAACCCCAAATTT
9516413 GGTACACAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.23
Consensus pattern (29 bp):
AAAATCCAAAACCTAAAACCCCAAATTTA
Found at i:9522462 original size:19 final size:19
Alignment explanation
Indices: 9522438--9522476 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
9522428 GATCGTTTGT
9522438 AGTGATGAAAAGATAATTA
1 AGTGATGAAAAGATAATTA
*
9522457 AGTGATGAAAATATAATTA
1 AGTGATGAAAAGATAATTA
9522476 A
1 A
9522477 CATCTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.18, T:0.28
Consensus pattern (19 bp):
AGTGATGAAAAGATAATTA
Found at i:9527459 original size:23 final size:25
Alignment explanation
Indices: 9527433--9527486 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
9527423 AAAAAATCAT
*
9527433 AAAAAATGA-TTTTAAA-A-TATAA
1 AAAAAAAGAGTTTTAAATATTATAA
*
9527455 AAAAATAAGAGTTTTAAATATTCTAA
1 AAAAA-AAGAGTTTTAAATATTATAA
9527481 AAAAAA
1 AAAAAA
9527487 GACATAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.19
23 3 0.12
24 7 0.27
25 2 0.08
26 9 0.35
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.30
Consensus pattern (25 bp):
AAAAAAAGAGTTTTAAATATTATAA
Found at i:9528833 original size:17 final size:18
Alignment explanation
Indices: 9528811--9528845 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
9528801 TTTATATATA
*
9528811 ATTAAAATATAAT-TTTT
1 ATTAAAAAATAATATTTT
9528828 ATTAAAAAATAATATTTT
1 ATTAAAAAATAATATTTT
9528846 CATGAATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTAAAAAATAATATTTT
Found at i:9528841 original size:22 final size:22
Alignment explanation
Indices: 9528784--9528842 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
9528774 GTATCTTAAT
*
9528784 TTAATAAAATAATATTATTTATA
1 TTAA-AAAATAATATAATTTATA
** *
9528807 TATAATTAA-AATATAATTTTTA
1 T-TAAAAAATAATATAATTTATA
9528829 TTAAAAAATAATAT
1 TTAAAAAATAATAT
9528843 TTTCATGAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
21 5 0.18
22 17 0.61
23 3 0.11
24 3 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAAAAAATAATATAATTTATA
Found at i:9530419 original size:23 final size:23
Alignment explanation
Indices: 9530389--9530435 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
9530379 TTATGAGAGT
9530389 GATTGTGGTTTGTGAATTAGATG
1 GATTGTGGTTTGTGAATTAGATG
9530412 GATTGTGGTTTGTGAATTAGATG
1 GATTGTGGTTTGTGAATTAGATG
9530435 G
1 G
9530436 TCCAAACCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.43
Consensus pattern (23 bp):
GATTGTGGTTTGTGAATTAGATG
Found at i:9530877 original size:17 final size:18
Alignment explanation
Indices: 9530836--9530877 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
9530826 AAAGAATGTA
9530836 TTATATATTTTATTAATT
1 TTATATATTTTATTAATT
9530854 TTATATATTTT-TTAAATT
1 TTATATATTTTATT-AATT
9530872 TT-TATA
1 TTATATA
9530878 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATATATTTTATTAATT
Found at i:9530936 original size:21 final size:20
Alignment explanation
Indices: 9530896--9530936 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
9530886 ATAATTATTT
*
9530896 TATATTAAAATTTATTTTAA
1 TATATTAAAATTTATATTAA
9530916 TATATTAAAATTTTATATTAA
1 TATATTAAAA-TTTATATTAA
9530937 CTTAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATATTAAAATTTATATTAA
Found at i:9530941 original size:26 final size:25
Alignment explanation
Indices: 9530912--9530978 Score: 89
Period size: 28 Copynumber: 2.5 Consensus size: 25
9530902 AAAATTTATT
9530912 TTAATATATTAAAATTTTATATTAAC
1 TTAATATA-TAAAATTTTATATTAAC
*
9530938 TTAATTTATAAAAAAATTTTATATTAAC
1 TTAA--TAT-ATAAAATTTTATATTAAC
9530966 TTAATATATAAAA
1 TTAATATATAAAA
9530979 CGAGATCCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
25 5 0.14
26 7 0.19
28 23 0.64
29 1 0.03
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAATATATAAAATTTTATATTAAC
Found at i:9530954 original size:28 final size:28
Alignment explanation
Indices: 9530922--9530978 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
9530912 TTAATATATT
*
9530922 AAAATTTTATATTAACTTAATTTATAAA
1 AAAATTTTATATTAACTTAATATATAAA
9530950 AAAATTTTATATTAACTTAATATATAAA
1 AAAATTTTATATTAACTTAATATATAAA
9530978 A
1 A
9530979 CGAGATCCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (28 bp):
AAAATTTTATATTAACTTAATATATAAA
Found at i:9531257 original size:22 final size:21
Alignment explanation
Indices: 9531227--9531267 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
9531217 ATTGTTTTTA
*
9531227 ATAATAATAAAAATGAAAAAAT
1 ATAAAAATAAAAAT-AAAAAAT
*
9531249 ATAAAAATAATAATAAAAA
1 ATAAAAATAAAAATAAAAA
9531268 TAAGTAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (21 bp):
ATAAAAATAAAAATAAAAAAT
Found at i:9531331 original size:9 final size:9
Alignment explanation
Indices: 9531317--9531346 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
9531307 AACCTTACAG
9531317 AATAAAAAT
1 AATAAAAAT
9531326 AATAAAAAT
1 AATAAAAAT
9531335 AATAAAATAT
1 AATAAAA-AT
9531345 AA
1 AA
9531347 AATGCTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.80
10 4 0.20
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AATAAAAAT
Found at i:9531657 original size:14 final size:14
Alignment explanation
Indices: 9531612--9531650 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
9531602 GTGTTTTCTT
9531612 TAAACCCTAAAATC
1 TAAACCCTAAAATC
**
9531626 TAAACTTTAAAATC
1 TAAACCCTAAAATC
9531640 TAAACCCTAAA
1 TAAACCCTAAA
9531651 TCCTAAAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAACCCTAAAATC
Found at i:9531817 original size:74 final size:74
Alignment explanation
Indices: 9531669--9531847 Score: 179
Period size: 74 Copynumber: 2.4 Consensus size: 74
9531659 TCGAGATCTT
* * * * *
9531669 AACCCTTCAAACCTTAAAACTAAAACCCTAAACCCTTTAAATTCTAAAATCAAAACCTTAAAACT
1 AACCCTTAAAACCTCAAAACTAAAACCCTAAACCC-TCAAACTATAAAATCAAAACCTTAAAACT
*
9531734 AAAATCCT-A
65 AAAACCCTAA
* * **
9531743 AACTCTTTAAACCTCAAAACTAAAACCCTAAACCC-CAAACTATAAAATTGAAACCTTAAACCAT
1 AACCCTTAAAACCTCAAAACTAAAACCCTAAACCCTCAAACTATAAAATCAAAACCTTAAA--A-
*
9531807 CT-ATACCCTAA
63 CTAAAACCCTAA
*
9531818 AACCCTTAAAACC-CAAATC-AAAACCCTAAA
1 AACCCTTAAAACCTCAAAACTAAAACCCTAAA
9531848 ATCCAAAACC
Statistics
Matches: 88, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
72 20 0.23
73 11 0.12
74 43 0.49
75 14 0.16
ACGTcount: A:0.49, C:0.29, G:0.01, T:0.22
Consensus pattern (74 bp):
AACCCTTAAAACCTCAAAACTAAAACCCTAAACCCTCAAACTATAAAATCAAAACCTTAAAACTA
AAACCCTAA
Found at i:9531867 original size:8 final size:8
Alignment explanation
Indices: 9531811--9531891 Score: 71
Period size: 8 Copynumber: 10.0 Consensus size: 8
9531801 AACCATCTAT
9531811 ACCCTAAA
1 ACCCTAAA
9531819 ACCCTTAAA
1 ACCC-TAAA
9531828 ACCCAAATCAAA
1 ACCC---T-AAA
9531840 ACCCTAAA
1 ACCCTAAA
*
9531848 ATCC-AAA
1 ACCCTAAA
9531855 A-CCTAAA
1 ACCCTAAA
9531862 ACCCTAAA
1 ACCCTAAA
*
9531870 ATCC-AAA
1 ACCCTAAA
9531877 A-CCTAAA
1 ACCCTAAA
9531884 ACCCTAAA
1 ACCCTAAA
9531892 TTTAAAAATT
Statistics
Matches: 62, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
6 4 0.06
7 16 0.26
8 25 0.40
9 9 0.15
11 1 0.02
12 7 0.11
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.14
Consensus pattern (8 bp):
ACCCTAAA
Found at i:9531899 original size:22 final size:22
Alignment explanation
Indices: 9531813--9531891 Score: 117
Period size: 22 Copynumber: 3.6 Consensus size: 22
9531803 CCATCTATAC
*
9531813 CCTAAAACCCTTAAAA-CCCAAA
1 CCTAAAACCC-TAAAATCCAAAA
*
9531835 TC-AAAACCCTAAAATCCAAAA
1 CCTAAAACCCTAAAATCCAAAA
9531856 CCTAAAACCCTAAAATCCAAAA
1 CCTAAAACCCTAAAATCCAAAA
9531878 CCTAAAACCCTAAA
1 CCTAAAACCCTAAA
9531892 TTTAAAAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
20 5 0.10
21 13 0.25
22 34 0.65
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.14
Consensus pattern (22 bp):
CCTAAAACCCTAAAATCCAAAA
Found at i:9531899 original size:29 final size:29
Alignment explanation
Indices: 9531867--9531923 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
9531857 CTAAAACCCT
*
9531867 AAAATCCAAAACCTAAAACCCTAAATTTA
1 AAAATCCAAAACCTAAAACCCCAAATTTA
* *
9531896 AAAATTCAAAACCTTAAACCCCAAATTT
1 AAAATCCAAAACCTAAAACCCCAAATTT
9531924 GGTACACAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.23
Consensus pattern (29 bp):
AAAATCCAAAACCTAAAACCCCAAATTTA
Found at i:9537982 original size:18 final size:19
Alignment explanation
Indices: 9537947--9537984 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
9537937 GATCGTTTGT
9537947 AGTGATGAAAAGATAATTA
1 AGTGATGAAAAGATAATTA
*
9537966 AGTGATG-AAATATAATTA
1 AGTGATGAAAAGATAATTA
9537984 A
1 A
9537985 CATCTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (19 bp):
AGTGATGAAAAGATAATTA
Found at i:9546985 original size:15 final size:15
Alignment explanation
Indices: 9546967--9546995 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9546957 AAAATTGAAT
9546967 ATTTTTAATTTTTTA
1 ATTTTTAATTTTTTA
9546982 ATTTTTAATTTTTT
1 ATTTTTAATTTTTT
9546996 TAAAAAAATA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTTTAATTTTTTA
Found at i:9557672 original size:20 final size:20
Alignment explanation
Indices: 9557647--9557705 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
9557637 CAGGTCCGGG
9557647 CCCGGATCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
9557667 CCCGGATCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
* *
9557687 CCCAGATCATTTGGGCCTG
1 CCCGGATCAATTGGGCCTG
9557706 CCCCAAATGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.19, C:0.31, G:0.29, T:0.22
Consensus pattern (20 bp):
CCCGGATCAATTGGGCCTGA
Found at i:9557774 original size:16 final size:15
Alignment explanation
Indices: 9557753--9557782 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
9557743 ATTCTTTATT
9557753 TTTTATTTTTATTTTA
1 TTTTATTTTT-TTTTA
9557769 TTTTATTTTTTTTT
1 TTTTATTTTTTTTT
9557783 CTCTCTTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTATTTTTTTTTA
Found at i:9558031 original size:11 final size:12
Alignment explanation
Indices: 9558011--9558043 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
9558001 TTATCTAGAT
*
9558011 TTTTTTTTTTAA
1 TTTTTATTTTAA
9558023 -TTTTATTTTAA
1 TTTTTATTTTAA
9558034 TTTTTATTTT
1 TTTTTATTTT
9558044 GGAGGGCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTATTTTAA
Found at i:9558481 original size:20 final size:20
Alignment explanation
Indices: 9558458--9558501 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
9558448 TGCCCAGTTT
*
9558458 CCGGCGAAGAATCCCAGAAA
1 CCGGCAAAGAATCCCAGAAA
9558478 CCGGCAAAGAATCCCAGAAA
1 CCGGCAAAGAATCCCAGAAA
9558498 CCGG
1 CCGG
9558502 TGAATTTCCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.32, G:0.25, T:0.05
Consensus pattern (20 bp):
CCGGCAAAGAATCCCAGAAA
Found at i:9558557 original size:62 final size:63
Alignment explanation
Indices: 9558456--9558573 Score: 150
Period size: 62 Copynumber: 1.9 Consensus size: 63
9558446 ACTGCCCAGT
* *
9558456 TTCCGGCGAAGAATCCCAGAAACCGGCAAAGAATCCCAGAAACCGGTGAAT-TTCCGGCCAAC
1 TTCCGGCGAAAAAACCCAGAAACCGGCAAAGAATCCCAGAAACCGGTGAATCTTCCGGCCAAC
** * * *
9558518 TTCCGGCGAAAAAACCCAGATTCCGGCGAAA-ATTTCCAGAATCCGGTGAATCTTCC
1 TTCCGGCGAAAAAACCCAGAAACCGGC-AAAGAATCCCAGAAACCGGTGAATCTTCC
9558574 ACCGGAGTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
62 40 0.85
63 7 0.15
ACGTcount: A:0.32, C:0.30, G:0.21, T:0.17
Consensus pattern (63 bp):
TTCCGGCGAAAAAACCCAGAAACCGGCAAAGAATCCCAGAAACCGGTGAATCTTCCGGCCAAC
Found at i:9558562 original size:20 final size:20
Alignment explanation
Indices: 9558519--9558563 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
9558509 CCGGCCAACT
*
9558519 TCCGGCGAAAAAACCCAGAT
1 TCCGGCGAAAAAACCCAGAA
***
9558539 TCCGGCGAAAATTTCCAGAA
1 TCCGGCGAAAAAACCCAGAA
9558559 TCCGG
1 TCCGG
9558564 TGAATCTTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (20 bp):
TCCGGCGAAAAAACCCAGAA
Found at i:9558829 original size:14 final size:15
Alignment explanation
Indices: 9558810--9558851 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
9558800 CCGAGCCGAG
9558810 CCGAGCCGTTCTTC-
1 CCGAGCCGTTCTTCT
9558824 CCGAGCCG--CTTCT
1 CCGAGCCGTTCTTCT
9558837 CCGAGCCGTT-TTCT
1 CCGAGCCGTTCTTCT
9558851 C
1 C
9558852 TTCCTTGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.16
13 8 0.32
14 13 0.52
ACGTcount: A:0.07, C:0.43, G:0.21, T:0.29
Consensus pattern (15 bp):
CCGAGCCGTTCTTCT
Found at i:9558842 original size:13 final size:14
Alignment explanation
Indices: 9558810--9558846 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
9558800 CCGAGCCGAG
9558810 CCGAGCCGTTCTTC
1 CCGAGCCGTTCTTC
9558824 CCGAGCCG--CTTC
1 CCGAGCCGTTCTTC
9558836 TCCGAGCCGTT
1 -CCGAGCCGTT
9558847 TTCTCTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 4 0.20
13 8 0.40
14 8 0.40
ACGTcount: A:0.08, C:0.43, G:0.24, T:0.24
Consensus pattern (14 bp):
CCGAGCCGTTCTTC
Found at i:9558941 original size:13 final size:14
Alignment explanation
Indices: 9558898--9558946 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
9558888 CCGCTCCAGG
*
9558898 TTTTTTTTTTT--T
1 TTTTTTTTTTTGAA
9558910 TTTTTTTTTTTGAA
1 TTTTTTTTTTTGAA
9558924 TTTTTTTTTTTGAA
1 TTTTTTTTTTTGAA
9558938 TTTTTTTTT
1 TTTTTTTTT
9558947 ATTTGACTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
12 11 0.32
14 23 0.68
ACGTcount: A:0.08, C:0.00, G:0.04, T:0.88
Consensus pattern (14 bp):
TTTTTTTTTTTGAA
Found at i:9558943 original size:16 final size:16
Alignment explanation
Indices: 9558908--9558952 Score: 67
Period size: 14 Copynumber: 2.9 Consensus size: 16
9558898 TTTTTTTTTT
9558908 TTTTTTTTTTTTTGAA
1 TTTTTTTTTTTTTGAA
9558924 --TTTTTTTTTTTGAA
1 TTTTTTTTTTTTTGAA
*
9558938 TTTTTTTTTATTTGA
1 TTTTTTTTTTTTTGA
9558953 CTTTGATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 14 0.54
16 12 0.46
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (16 bp):
TTTTTTTTTTTTTGAA
Found at i:9559258 original size:154 final size:157
Alignment explanation
Indices: 9558981--9559262 Score: 507
Period size: 154 Copynumber: 1.8 Consensus size: 157
9558971 TTTTTTTTCT
*
9558981 TTTTTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACT
1 TTTTTCTTTAAATAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACT
9559046 CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTT
66 CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTT
9559111 GATAATTAATTAATTGGTTGATCTTGA
131 GATAATTAATTAATTGGTTGATCTTGA
**
9559138 TTTTTCTTTAAATAATCCGACGACGGAGCCTCTGTAAGT-AAAACAGTAG-TTTTCTTGCATACT
1 TTTTTCTTTAAATAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACT
*
9559201 CCTGAGGTGAGGGAATTTTTTCAA-TTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTT
66 CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTT
9559263 CCAATAACTA
Statistics
Matches: 121, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
154 38 0.31
155 37 0.31
156 10 0.08
157 36 0.30
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (157 bp):
TTTTTCTTTAAATAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACT
CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTT
GATAATTAATTAATTGGTTGATCTTGA
Found at i:9562223 original size:35 final size:35
Alignment explanation
Indices: 9562172--9562251 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
9562162 TTTTTAATTG
*
9562172 AATATAATAAATAAATTTATCATTATATAATAAACT
1 AATA-AATAAATAAATTTATCATTATATAATAAAAT
*
9562208 AATAAATAAATAAATTTATTATTATATAATAAAAT
1 AATAAATAAATAAATTTATCATTATATAATAAAAT
9562243 AATAAATAA
1 AATAAATAA
9562252 TATGTATTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
35 38 0.90
36 4 0.10
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (35 bp):
AATAAATAAATAAATTTATCATTATATAATAAAAT
Found at i:9564450 original size:21 final size:19
Alignment explanation
Indices: 9564418--9564469 Score: 50
Period size: 21 Copynumber: 2.6 Consensus size: 19
9564408 GAAACACCAA
* *
9564418 AAATTTTAAAAATATTTAT
1 AAATTTTAAAAAAATATAT
9564437 AAATATTTATAAAAAATATAT
1 AAAT-TTTA-AAAAAATATAT
*
9564458 AATTTTTTAAAA
1 AA-ATTTTAAAA
9564470 TTTTCAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 4 0.15
20 7 0.26
21 15 0.56
22 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATTTTAAAAAAATATAT
Found at i:9564546 original size:19 final size:18
Alignment explanation
Indices: 9564522--9564558 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
9564512 ATAAAATGTT
*
9564522 AAAATTTGAAAAATATAAA
1 AAAATTTAAAAAAT-TAAA
9564541 AAAATTTAAAAAATTAAA
1 AAAATTTAAAAAATTAAA
9564559 TATTGCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (18 bp):
AAAATTTAAAAAATTAAA
Found at i:9564623 original size:20 final size:21
Alignment explanation
Indices: 9564600--9564654 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
9564590 AAATAAGAAA
*
9564600 ATTTTTAAAAATTAAATT-TG
1 ATTTTTAAAAATTAAATTCCG
9564620 ATTTTTAAGAAA--AAATTCCG
1 ATTTTTAA-AAATTAAATTCCG
9564640 ATTTTT-AAAATTAAA
1 ATTTTTAAAAATTAAA
9564655 AAAAATATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
18 3 0.10
19 6 0.20
20 18 0.60
21 3 0.10
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (21 bp):
ATTTTTAAAAATTAAATTCCG
Found at i:9567284 original size:24 final size:23
Alignment explanation
Indices: 9567244--9567288 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
9567234 ATATTTATTT
9567244 AAAATCAATTAATAATAATAAATG
1 AAAATCAATTAATAAT-ATAAATG
*
9567268 AAAATTCAATTTA-AATATAAA
1 AAAA-TCAATTAATAATATAAA
9567289 ATTATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 7 0.37
25 7 0.37
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (23 bp):
AAAATCAATTAATAATATAAATG
Found at i:9570332 original size:2 final size:2
Alignment explanation
Indices: 9570327--9570359 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
9570317 GTAGTTTCTT
*
9570327 TA TA TA TA TA TA TA TA TG 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
9570360 TTTTAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9571447 original size:19 final size:20
Alignment explanation
Indices: 9571423--9571465 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
9571413 ATTTTTATTT
*
9571423 TATAAAAATTTA-AAAAATA
1 TATAAAAATTAATAAAAATA
9571442 TAT-AAAATTAATAAAAATA
1 TATAAAAATTAATAAAAATA
9571461 TATAA
1 TATAA
9571466 TTCATTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 7 0.33
19 13 0.62
20 1 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TATAAAAATTAATAAAAATA
Found at i:9573462 original size:17 final size:17
Alignment explanation
Indices: 9573442--9573475 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
9573432 AACATTCATG
9573442 AAAATATTAT-TTTTAAT
1 AAAA-ATTATATTTTAAT
9573459 AAAAATTATATTTTAAT
1 AAAAATTATATTTTAAT
9573476 TATATATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAAAATTATATTTTAAT
Found at i:9576949 original size:19 final size:19
Alignment explanation
Indices: 9576925--9576963 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
9576915 AATTAAGATG
9576925 TTAATTATATTTTCATCAC
1 TTAATTATATTTTCATCAC
*
9576944 TTAATTATCTTTTCATCAC
1 TTAATTATATTTTCATCAC
9576963 T
1 T
9576964 ACAAACGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.18, G:0.00, T:0.54
Consensus pattern (19 bp):
TTAATTATATTTTCATCAC
Found at i:9580946 original size:23 final size:23
Alignment explanation
Indices: 9580905--9580949 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
9580895 ATACTAATAA
* **
9580905 AATTATATTTTTATTTTTATTTT
1 AATTATATTTTAAGATTTATTTT
9580928 AATTATATTTTAAGATTTATTT
1 AATTATATTTTAAGATTTATTT
9580950 ATATTCTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
AATTATATTTTAAGATTTATTTT
Found at i:9581073 original size:18 final size:18
Alignment explanation
Indices: 9581039--9581107 Score: 50
Period size: 19 Copynumber: 3.6 Consensus size: 18
9581029 AATGTTTACG
9581039 AATAAAATAATTAAATTA
1 AATAAAATAATTAAATTA
*
9581057 AATATAAATATTTAATTATTTA
1 AATA-AAATAATTAA--A-TTA
* *
9581079 AATAAATTGAGTTCAAA-TA
1 AATAAAAT-AATT-AAATTA
9581098 AATAAAATAA
1 AATAAAATAA
9581108 ATTTTTTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 5 0.12
19 18 0.45
21 5 0.12
22 10 0.25
23 2 0.05
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36
Consensus pattern (18 bp):
AATAAAATAATTAAATTA
Found at i:9581627 original size:21 final size:20
Alignment explanation
Indices: 9581601--9581640 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
9581591 GGGAAAATCT
9581601 AAAATAAGAAAAAAATATTTA
1 AAAATAAGAAAAAAA-ATTTA
*
9581622 AAAATAATAAAAAAAATTT
1 AAAATAAGAAAAAAAATTT
9581641 TCCTTTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (20 bp):
AAAATAAGAAAAAAAATTTA
Found at i:9583056 original size:29 final size:29
Alignment explanation
Indices: 9583010--9583066 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
9583000 ATTGTGTACC
*
9583010 AAATTTGGGGTTTAAGGTTTTGAATTTTT
1 AAATTTAGGGTTTAAGGTTTTGAATTTTT
* *
9583039 AAATTTAGGGTTTTAGGTTTTGGATTTT
1 AAATTTAGGGTTTAAGGTTTTGAATTTT
9583067 AGGGGTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.53
Consensus pattern (29 bp):
AAATTTAGGGTTTAAGGTTTTGAATTTTT
Found at i:9583067 original size:22 final size:21
Alignment explanation
Indices: 9583042--9583096 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 21
9583032 AATTTTTAAA
* *
9583042 TTTAGGGTTTTAGGTTTTGGAT
1 TTTAGGGTTTAAGGGTTTGG-T
9583064 TTTAGGGGTTTAAGGGTTTGGT
1 TTTA-GGGTTTAAGGGTTTGGT
9583086 TTTAGGGTTTA
1 TTTAGGGTTTA
9583097 GATGGTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 7 0.23
22 9 0.30
23 14 0.47
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.51
Consensus pattern (21 bp):
TTTAGGGTTTAAGGGTTTGGT
Found at i:9583171 original size:30 final size:30
Alignment explanation
Indices: 9583042--9583250 Score: 139
Period size: 30 Copynumber: 7.1 Consensus size: 30
9583032 AATTTTTAAA
* *
9583042 TTTAGGGTTTTAGGTTTT--GGATTTTAGGGG
1 TTTAGGGTTTTA-GTTTTAAGG-TTTAAAGGG
* * * *
9583072 TTTAAGGG-TTTGGTTTTAGGGTTTAGATGG
1 TTT-AGGGTTTTAGTTTTAAGGTTTAAAGGG
* * * *
9583102 TTTAAGGTTTCAATTTTATA-GTTT--GGGG
1 TTTAGGGTTTTAGTTTTA-AGGTTTAAAGGG
* * *
9583130 TTTATGGTTTTAGTTTTGAGGTTTAAAGAG
1 TTTAGGGTTTTAGTTTTAAGGTTTAAAGGG
* *
9583160 TTTAGGATTTTAGTTTTAAGGTTT-GAGGG
1 TTTAGGGTTTTAGTTTTAAGGTTTAAAGGG
* *
9583189 ATTAGGGTTTT-GATTTT-AGAATTTAAAGGG
1 TTTAGGGTTTTAG-TTTTAAG-GTTTAAAGGG
*
9583219 TTTAGGGTTTTAGTTTTAAGGTTTGAAGGG
1 TTTAGGGTTTTAGTTTTAAGGTTTAAAGGG
9583249 TT
1 TT
9583251 AAGATCTCGA
Statistics
Matches: 136, Mismatches: 30, Indels: 26
0.71 0.16 0.14
Matches are distributed among these distances:
27 1 0.01
28 23 0.17
29 27 0.20
30 76 0.56
31 9 0.07
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (30 bp):
TTTAGGGTTTTAGTTTTAAGGTTTAAAGGG
Found at i:9583263 original size:59 final size:59
Alignment explanation
Indices: 9583151--9583299 Score: 164
Period size: 59 Copynumber: 2.6 Consensus size: 59
9583141 AGTTTTGAGG
* * * *
9583151 TTTAAAGAGTTTAGGATTTTAGTTTTAAGGTTTGAGGGATTAGGGTTTTGATTTTAGAA
1 TTTAAAGAGTTTAGGATTTTAGTTTTAAGGTTTGAGGGATTAAGATCTCGATTTTAGAA
* * *
9583210 TTTAAAGGGTTTAGGGTTTTAGTTTTAAGGTTTGAAGGG-TTAAGATCTCGA-TTTAAAGA
1 TTTAAAGAGTTTAGGATTTTAGTTTTAAGGTTTG-AGGGATTAAGATCTCGATTTTAGA-A
*
9583269 TTT-AAG-GTTTAGGA-TTTAGATTTTAAAGTTT
1 TTTAAAGAGTTTAGGATTTTAG-TTTTAAGGTTT
9583300 AGATTTTAGG
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
56 5 0.06
57 17 0.22
58 8 0.10
59 44 0.56
60 4 0.05
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (59 bp):
TTTAAAGAGTTTAGGATTTTAGTTTTAAGGTTTGAGGGATTAAGATCTCGATTTTAGAA
Found at i:9583307 original size:21 final size:21
Alignment explanation
Indices: 9583259--9583317 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
9583249 TTAAGATCTC
* *
9583259 GATTTAAAGATTTAAGGTTTAG
1 GATTTAGAG-TTTAAAGTTTAG
*
9583281 GATTTAGATTTTAAAGTTTA-
1 GATTTAGAGTTTAAAGTTTAG
*
9583301 GATTTTAGGGTTTAAAG
1 GA-TTTAGAGTTTAAAG
9583318 AAAACACAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 2 0.06
21 22 0.71
22 7 0.23
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (21 bp):
GATTTAGAGTTTAAAGTTTAG
Done.