Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 204 of 206
Found at i:61736785 original size:44 final size:43
Alignment explanation
Indices: 61736696--61736788 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 43
61736686 AGTCATATAT
* *
61736696 ATTAATTAGTATATGCTTATAATAAACATTGATTTATAAAAAA
1 ATTAATTAGTATATGCTTATAATAAACAATAATTTATAAAAAA
* * *
61736739 ATTAATTAAGTATATGCTTA-AACTAAACAATAATTTGTTAATAA
1 ATTAATT-AGTATATGCTTATAA-TAAACAATAATTTATAAAAAA
61736783 ATTAAT
1 ATTAAT
61736789 CCTTAGTCTA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
43 9 0.21
44 34 0.79
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.40
Consensus pattern (43 bp):
ATTAATTAGTATATGCTTATAATAAACAATAATTTATAAAAAA
Found at i:61737399 original size:126 final size:128
Alignment explanation
Indices: 61737203--61737431 Score: 347
Period size: 126 Copynumber: 1.8 Consensus size: 128
61737193 ATTCTTTTTG
* * *
61737203 GTCACCCAACTATAAAAAGTTACAAAATGATCACTTAACTATTCAATTTTGTCTTTTTTAGTCAC
1 GTCACCAAACTATAAAAAGTTACAAAATGATAACTCAACTATTCAATTTTGTCTTTTTTAGTCAC
61737268 CCAACTATATTAAATTTTTGGGTG-TTT-CTATTTTTACTTTAGCCGGTTGGTAACCAAAAAA
66 CCAACTATATTAAATTTTTGGGTGTTTTACTATTTTTACTTTAGCCGGTTGGTAACCAAAAAA
* * *
61737329 GTCACCAAATTATGAAAAGTTACAAAAT-AGTAACTCAACTATTCAATTTTTTCTTTTTTAGTCA
1 GTCACCAAACTATAAAAAGTTACAAAATGA-TAACTCAACTATTCAATTTTGTCTTTTTTAGTCA
* **
61737393 CCCAACTATCTTGGATTTTTGGGTGTTTTACTATTTTTA
65 CCCAACTATATTAAATTTTTGGGTGTTTTACTATTTTTA
61737432 TTTTTACGTT
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
125 1 0.01
126 78 0.86
127 3 0.03
128 9 0.10
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (128 bp):
GTCACCAAACTATAAAAAGTTACAAAATGATAACTCAACTATTCAATTTTGTCTTTTTTAGTCAC
CCAACTATATTAAATTTTTGGGTGTTTTACTATTTTTACTTTAGCCGGTTGGTAACCAAAAAA
Found at i:61744392 original size:2 final size:2
Alignment explanation
Indices: 61744385--61744419 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
61744375 TTTACTTTTA
61744385 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 A
61744420 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:61748676 original size:14 final size:14
Alignment explanation
Indices: 61748657--61748699 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
61748647 AATTATACTT
61748657 ATTATTTTAAATTA
1 ATTATTTTAAATTA
61748671 ATTATTTT--A-TA
1 ATTATTTTAAATTA
61748682 A-TATTTTAAATTA
1 ATTATTTTAAATTA
61748695 ATTAT
1 ATTAT
61748700 GACTTAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
10 6 0.24
11 3 0.12
12 2 0.08
13 3 0.12
14 11 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTATTTTAAATTA
Found at i:61757824 original size:60 final size:59
Alignment explanation
Indices: 61757721--61757840 Score: 134
Period size: 60 Copynumber: 2.0 Consensus size: 59
61757711 TAATCTTTTC
* * *
61757721 AGTGATATAATTTGATGAATTGAAAATTGTGTAATTTACATGAAAGTTGATAATAAGTTT
1 AGTGATATAATTTGATGAATT-AAAATTGTATAACTTACATGAAAATTGATAATAAGTTT
* * * **
61757781 AGTGATTTAATTTGATGAAATT-AACTGTGTATAACTTATATGAAAATTGATGTTAAGTTT
1 AGTGATATAATTTGATG-AATTAAAAT-TGTATAACTTACATGAAAATTGATAATAAGTTT
61757841 GATGACTTAG
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
59 3 0.06
60 43 0.86
61 4 0.08
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.42
Consensus pattern (59 bp):
AGTGATATAATTTGATGAATTAAAATTGTATAACTTACATGAAAATTGATAATAAGTTT
Found at i:61762808 original size:2 final size:2
Alignment explanation
Indices: 61762801--61762839 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
61762791 AATGAGATTA
*
61762801 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
61762840 CATGAGTTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:61766488 original size:17 final size:18
Alignment explanation
Indices: 61766455--61766488 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
61766445 TTTCTTTACA
61766455 TTTAGATCATGAAAGTTC
1 TTTAGATCATGAAAGTTC
*
61766473 TTTAGATTAT-AAAGTT
1 TTTAGATCATGAAAGTT
61766489 GACTTCATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (18 bp):
TTTAGATCATGAAAGTTC
Found at i:61769723 original size:13 final size:13
Alignment explanation
Indices: 61769705--61769733 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
61769695 TTTTTAATTA
61769705 AAAAAATAAATAT
1 AAAAAATAAATAT
61769718 AAAAAATAAATAT
1 AAAAAATAAATAT
61769731 AAA
1 AAA
61769734 TATATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAAAATAAATAT
Found at i:61774643 original size:15 final size:15
Alignment explanation
Indices: 61774623--61774673 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
61774613 ACAACGCGAT
61774623 AACATAAGTGACTAA
1 AACATAAGTGACTAA
* *
61774638 AACATAA-T-ATTTCA
1 AACATAAGTGA-CTAA
61774652 AACATAAGTGACTAA
1 AACATAAGTGACTAA
*
61774667 AATATAA
1 AACATAA
61774674 CCAGAGGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 1 0.04
14 10 0.36
15 16 0.57
16 1 0.04
ACGTcount: A:0.55, C:0.12, G:0.08, T:0.25
Consensus pattern (15 bp):
AACATAAGTGACTAA
Found at i:61777461 original size:40 final size:37
Alignment explanation
Indices: 61777417--61777526 Score: 118
Period size: 37 Copynumber: 2.9 Consensus size: 37
61777407 ATTTTCACTA
61777417 TTTTAATCTTA-AGTTACAGGTACTTGAATCTCTTCTGGAG
1 TTTTAA-CTTATAGTT--AGGT-CTTGAATCTCTTCTGGAG
*
61777457 TTTT-ACTTATTAGTTATGTCTTGAATCTCTTCTGGAG
1 TTTTAACTTA-TAGTTAGGTCTTGAATCTCTTCTGGAG
* *
61777494 TTTT-ACTTATTAGTTATGTCTTGAGTCTCTTCT
1 TTTTAACTTA-TAGTTAGGTCTTGAATCTCTTCT
61777527 AAAGCACCCA
Statistics
Matches: 66, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
37 50 0.76
38 7 0.11
39 1 0.02
40 8 0.12
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.50
Consensus pattern (37 bp):
TTTTAACTTATAGTTAGGTCTTGAATCTCTTCTGGAG
Found at i:61777485 original size:37 final size:37
Alignment explanation
Indices: 61777439--61777526 Score: 167
Period size: 37 Copynumber: 2.4 Consensus size: 37
61777429 GTTACAGGTA
61777439 CTTGAATCTCTTCTGGAGTTTTACTTATTAGTTATGT
1 CTTGAATCTCTTCTGGAGTTTTACTTATTAGTTATGT
61777476 CTTGAATCTCTTCTGGAGTTTTACTTATTAGTTATGT
1 CTTGAATCTCTTCTGGAGTTTTACTTATTAGTTATGT
*
61777513 CTTGAGTCTCTTCT
1 CTTGAATCTCTTCT
61777527 AAAGCACCCA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.17, C:0.16, G:0.16, T:0.51
Consensus pattern (37 bp):
CTTGAATCTCTTCTGGAGTTTTACTTATTAGTTATGT
Found at i:61781400 original size:55 final size:55
Alignment explanation
Indices: 61781316--61781426 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
61781306 CACCATGATA
61781316 TAGCCACCATCGAGTCTGACCCAACAATCAGATTCTTCTTAGACACCCAAGCATT
1 TAGCCACCATCGAGTCTGACCCAACAATCAGATTCTTCTTAGACACCCAAGCATT
*
61781371 TAGCCACCATCGAGTCTGACCCAACAATCAGATTCTTCTTAGACACCCAGGCATT
1 TAGCCACCATCGAGTCTGACCCAACAATCAGATTCTTCTTAGACACCCAAGCATT
61781426 T
1 T
61781427 TTTATAGCTG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.30, C:0.32, G:0.14, T:0.24
Consensus pattern (55 bp):
TAGCCACCATCGAGTCTGACCCAACAATCAGATTCTTCTTAGACACCCAAGCATT
Found at i:61782545 original size:5 final size:5
Alignment explanation
Indices: 61782535--61782569 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
61782525 GCGACAGATT
*
61782535 ATTTA ATTTA ATTTA ATTTA ATTTA TATTGA ATTT
1 ATTTA ATTTA ATTTA ATTTA ATTTA -ATTTA ATTT
61782570 TACTTATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (5 bp):
ATTTA
Found at i:61782555 original size:15 final size:16
Alignment explanation
Indices: 61782535--61782579 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
61782525 GCGACAGATT
*
61782535 ATTTAATTTA-ATTTA
1 ATTTAATTTATATTGA
61782550 ATTTAATTTATATTGA
1 ATTTAATTTATATTGA
* *
61782566 ATTTTACTTATATT
1 ATTTAATTTATATT
61782580 TCATATGGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 10 0.38
16 16 0.62
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTTAATTTATATTGA
Found at i:61787974 original size:5 final size:5
Alignment explanation
Indices: 61787966--61788011 Score: 67
Period size: 5 Copynumber: 9.4 Consensus size: 5
61787956 TTAGTTTATT
* *
61787966 TAATA TAATA TAATA TAATA TAAT- TAATA TAATA TATTA TATTA TA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA
61788012 TAAAACATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
4 4 0.10
5 35 0.90
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (5 bp):
TAATA
Found at i:61787997 original size:24 final size:24
Alignment explanation
Indices: 61787965--61788011 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
61787955 TTTAGTTTAT
61787965 TTAATATAATATAATATAATATAA
1 TTAATATAATATAATATAATATAA
* *
61787989 TTAATATAATATATTATATTATA
1 TTAATATAATATAATATAATATA
61788012 TAAAACATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTAATATAATATAATATAATATAA
Found at i:61788998 original size:14 final size:14
Alignment explanation
Indices: 61788979--61789005 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
61788969 ACATACATAT
61788979 ATATATAGATATAG
1 ATATATAGATATAG
61788993 ATATATAGATATA
1 ATATATAGATATA
61789006 TACACGCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (14 bp):
ATATATAGATATAG
Found at i:61790999 original size:6 final size:6
Alignment explanation
Indices: 61790982--61791011 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
61790972 TTATTATTTT
61790982 TAAATAA TAAATA TAAATA TAAATA TAAAT
1 TAAAT-A TAAATA TAAATA TAAATA TAAAT
61791012 TATTTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
TAAATA
Found at i:61791630 original size:13 final size:15
Alignment explanation
Indices: 61791612--61791648 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
61791602 ATTTAAAACA
61791612 ATAATTAA-T-TAAC
1 ATAATTAACTCTAAC
61791625 ATAATTAACTCTAAC
1 ATAATTAACTCTAAC
61791640 ATCAATTAA
1 AT-AATTAA
61791649 GTGATAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.38
14 1 0.05
15 6 0.29
16 6 0.29
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (15 bp):
ATAATTAACTCTAAC
Found at i:61797847 original size:2 final size:2
Alignment explanation
Indices: 61797840--61797870 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
61797830 TTACCATTGC
61797840 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
61797871 ACTATTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61798404 original size:28 final size:30
Alignment explanation
Indices: 61798355--61798413 Score: 77
Period size: 32 Copynumber: 2.0 Consensus size: 30
61798345 GATTTACTTT
*
61798355 TTAAATAAGTCCTTATATTTTTTTATTTTTAA
1 TTAAATAAGTCCTTAT-TTTTGTT-TTTTTAA
61798387 TTAAATAAGTCC-TA-TTTTGTTTTTTTA
1 TTAAATAAGTCCTTATTTTTGTTTTTTTA
61798414 TTCATAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 6 0.23
29 6 0.23
31 2 0.08
32 12 0.46
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (30 bp):
TTAAATAAGTCCTTATTTTTGTTTTTTTAA
Found at i:61799362 original size:30 final size:31
Alignment explanation
Indices: 61799308--61799366 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
61799298 CCAAAAAATA
*
61799308 ATTTTAAAAATAAAAAAATTAAAATAAAAGT
1 ATTTTAAAAATAAAAAAATAAAAATAAAAGT
* *
61799339 ATTTT-AAAATTAATAAATAAAAATAAAA
1 ATTTTAAAAATAAAAAAATAAAAATAAAA
61799367 AATATATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (31 bp):
ATTTTAAAAATAAAAAAATAAAAATAAAAGT
Found at i:61805720 original size:87 final size:86
Alignment explanation
Indices: 61805607--61805769 Score: 272
Period size: 87 Copynumber: 1.9 Consensus size: 86
61805597 TGCTTTAACT
* *
61805607 CACTCGAACCCATATATTCTTCTATTGACAATAATACTCATATAATCTAATTAAGACTCAAACAA
1 CACTCAAACCCATATATTCTTATATTGACAATAATACTCATATAATCTAATTAAGACTCAAACAA
61805672 CTTTTGATCGATAATTTATCG
66 CTTTTGATCGATAATTTATCG
* * *
61805693 CACTCAAACCCATATTTTTCTTATATTGACAATAATACTCATATAATCTAATTAAGACTCAATCG
1 CACTCAAACCCATA-TATTCTTATATTGACAATAATACTCATATAATCTAATTAAGACTCAAACA
61805758 ACTTTTGATCGA
65 ACTTTTGATCGA
61805770 ATTAAAACCA
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
86 13 0.18
87 58 0.82
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.36
Consensus pattern (86 bp):
CACTCAAACCCATATATTCTTATATTGACAATAATACTCATATAATCTAATTAAGACTCAAACAA
CTTTTGATCGATAATTTATCG
Found at i:61807320 original size:18 final size:19
Alignment explanation
Indices: 61807281--61807320 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
61807271 ATTTTATACT
* *
61807281 TTTTTAATATATTATTTTA
1 TTTTTAATATATTATATAA
61807300 TTTTT-ATATATTATATAA
1 TTTTTAATATATTATATAA
61807318 TTT
1 TTT
61807321 ATATTGCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTAATATATTATATAA
Found at i:61813053 original size:29 final size:28
Alignment explanation
Indices: 61812999--61813058 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
61812989 TAATATAGAG
**
61812999 AAATGATCAATTTAGTTTTTCAACTATT
1 AAATGATCAATTTAGTTCCTCAACTATT
**
61813027 AAATGGATCAATTTAGTTCCTGTACTATT
1 AAAT-GATCAATTTAGTTCCTCAACTATT
61813056 AAA
1 AAA
61813059 AAGAATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42
Consensus pattern (28 bp):
AAATGATCAATTTAGTTCCTCAACTATT
Found at i:61820031 original size:4 final size:4
Alignment explanation
Indices: 61820024--61820063 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
61820014 ATTTCATTAT
*
61820024 CATA CATA CATA CATA CATA CATA CATA CTTA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
61820064 TATTGTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (4 bp):
CATA
Found at i:61823142 original size:12 final size:12
Alignment explanation
Indices: 61823125--61823149 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
61823115 ACCAGCTTGC
61823125 GCCTCCGCCTCA
1 GCCTCCGCCTCA
61823137 GCCTCCGCCTCA
1 GCCTCCGCCTCA
61823149 G
1 G
61823150 GCCGGTGAGC
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:0.08, C:0.56, G:0.20, T:0.16
Consensus pattern (12 bp):
GCCTCCGCCTCA
Found at i:61825353 original size:22 final size:22
Alignment explanation
Indices: 61825313--61825354 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
61825303 TTTAATTTAA
*
61825313 TATTTAATAATATTATATATTT
1 TATTTAATAAAATTATATATTT
* *
61825335 TATTTATTAAAATTTTATAT
1 TATTTAATAAAATTATATAT
61825355 AAAATCATCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTAATAAAATTATATATTT
Found at i:61832560 original size:11 final size:11
Alignment explanation
Indices: 61832538--61832571 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
61832528 ATTGAATCGG
61832538 TTTAATAATTTT
1 TTTAA-AATTTT
61832550 TTTAAAATTTT
1 TTTAAAATTTT
*
61832561 TATAAAATTTT
1 TTTAAAATTTT
61832572 AAATATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTAAAATTTT
Found at i:61837713 original size:19 final size:19
Alignment explanation
Indices: 61837689--61837726 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
61837679 AATACAATAA
*
61837689 CATCCATAGTATTTTTACC
1 CATCCATAGTACTTTTACC
61837708 CATCCATAGTACTTTTACC
1 CATCCATAGTACTTTTACC
61837727 TATACATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.05, T:0.39
Consensus pattern (19 bp):
CATCCATAGTACTTTTACC
Found at i:61837734 original size:19 final size:19
Alignment explanation
Indices: 61837693--61837734 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
61837683 CAATAACATC
* *
61837693 CATAGTATTTTTACCCATC
1 CATAGTACTTTTACCCATA
*
61837712 CATAGTACTTTTACCTATA
1 CATAGTACTTTTACCCATA
61837731 CATA
1 CATA
61837735 TATGATGGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.40
Consensus pattern (19 bp):
CATAGTACTTTTACCCATA
Found at i:61844713 original size:14 final size:16
Alignment explanation
Indices: 61844678--61844717 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
61844668 ATTGAAATAT
61844678 TTAAAATCTAAATTAA
1 TTAAAATCTAAATTAA
61844694 TT-AAATCT-AATT-A
1 TTAAAATCTAAATTAA
61844707 TTAAAAT-TAAA
1 TTAAAATCTAAA
61844718 AGTTGATACC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 4 0.18
14 10 0.45
15 6 0.27
16 2 0.09
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAAATCTAAATTAA
Found at i:61847582 original size:26 final size:27
Alignment explanation
Indices: 61847534--61847584 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
61847524 AAGTCTAATT
**
61847534 TAAAAAAAAAAAATGTATCTTGTCTAA
1 TAAAAAAAAAAAACCTATCTTGTCTAA
61847561 TAAAAAAAAAAAACCTAT-TTGTCT
1 TAAAAAAAAAAAACCTATCTTGTCT
61847585 TGTCTCAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.55, C:0.10, G:0.06, T:0.29
Consensus pattern (27 bp):
TAAAAAAAAAAAACCTATCTTGTCTAA
Found at i:61847731 original size:27 final size:27
Alignment explanation
Indices: 61847701--61847753 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
61847691 AATTTTTTAC
* *
61847701 CCTAAATTTGAATCTCGAATTTCAAAT
1 CCTAAATTTGAAACTCGAACTTCAAAT
*
61847728 CCTAAATTTTAAACTCGAACTTCAAA
1 CCTAAATTTGAAACTCGAACTTCAAA
61847754 CCCGAACTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.34
Consensus pattern (27 bp):
CCTAAATTTGAAACTCGAACTTCAAAT
Found at i:61851032 original size:17 final size:17
Alignment explanation
Indices: 61850988--61851033 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
61850978 GTTCGGATCA
61850988 TTTGAGTCA-TTTTAAG
1 TTTGAGTCATTTTTAAG
*
61851004 TTTGAGGTCATTTTTATG
1 TTTGA-GTCATTTTTAAG
*
61851022 TTTGAGACATTT
1 TTTGAGTCATTT
61851034 CAAATTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 5 0.19
17 10 0.38
18 11 0.42
ACGTcount: A:0.22, C:0.07, G:0.20, T:0.52
Consensus pattern (17 bp):
TTTGAGTCATTTTTAAG
Found at i:61853367 original size:31 final size:30
Alignment explanation
Indices: 61853324--61853456 Score: 78
Period size: 31 Copynumber: 4.4 Consensus size: 30
61853314 AAAATTTTAG
61853324 AAATTCTT-ATTAACCCCTTAAAGTTTTTGAA
1 AAATT-TTAATTAACCCCTTAAAGTTTTTG-A
* **
61853355 AAATTTTAATTAAACCAC-TAAAACTTTTGA
1 AAATTTTAATT-AACCCCTTAAAGTTTTTGA
* * * *
61853385 AAATTGTCATTAAGTCCTCTAAAAG-TTTT-A
1 AAATTTTAATTAA--CCCCTTAAAGTTTTTGA
* * **
61853415 AAATTTTTATTTAAACCCTTAATTTTTTTG-
1 AAA-TTTTAATTAACCCCTTAAAGTTTTTGA
61853445 AAATTTTAATTA
1 AAATTTTAATTA
61853457 GTACCCTAAA
Statistics
Matches: 77, Mismatches: 17, Indels: 18
0.69 0.15 0.16
Matches are distributed among these distances:
29 15 0.19
30 23 0.30
31 31 0.40
32 8 0.10
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.44
Consensus pattern (30 bp):
AAATTTTAATTAACCCCTTAAAGTTTTTGA
Found at i:61853397 original size:30 final size:31
Alignment explanation
Indices: 61853348--61853419 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 31
61853338 CCCTTAAAGT
*
61853348 TTTTGAAAAATTTTAATTAA-ACCACTAAAAC
1 TTTTG-AAAATTGTAATTAAGACCACTAAAAC
* * * *
61853379 TTTTGAAAATTGTCATTAAGTCCTCTAAAAG
1 TTTTGAAAATTGTAATTAAGACCACTAAAAC
61853410 TTTT-AAAATT
1 TTTTGAAAATT
61853420 TTTATTTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 18 0.51
31 17 0.49
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (31 bp):
TTTTGAAAATTGTAATTAAGACCACTAAAAC
Found at i:61854905 original size:6 final size:6
Alignment explanation
Indices: 61854894--61854919 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
61854884 TTTACCCATA
61854894 TATATG TATATG TATATG TATATG TA
1 TATATG TATATG TATATG TATATG TA
61854920 CATATCACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:61863043 original size:3 final size:3
Alignment explanation
Indices: 61863031--61863066 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
61863021 CGTCATCGTT
*
61863031 ATC ATT ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
61863067 CTGTTCTCCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:61867011 original size:21 final size:20
Alignment explanation
Indices: 61866971--61867031 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
61866961 TAATAATGAG
* * *
61866971 AATACCAATTTTGTAGTAAT
1 AATATCAATTTTATAATAAT
61866991 AATATCAATTTTTATAATAAT
1 AATATCAA-TTTTATAATAAT
*
61867012 AATATCGATTTTATAATAAT
1 AATATCAATTTTATAATAAT
61867032 TATGCTACTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
20 19 0.53
21 17 0.47
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (20 bp):
AATATCAATTTTATAATAAT
Found at i:61869203 original size:16 final size:16
Alignment explanation
Indices: 61869182--61869223 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
61869172 AATAATTTGA
*
61869182 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
61869198 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
61869214 TAGTTTTAAT
1 TAATTTTAAT
61869224 TTTATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:61869207 original size:22 final size:23
Alignment explanation
Indices: 61869197--61869258 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
61869187 TTACTAACAA
* * *
61869197 TTAATTTTA-ATAACAATTAGTT
1 TTAATTTTATATAAAAAATAATT
*
61869219 TTAATTTTATTTAAAAAATAATT
1 TTAATTTTATATAAAAAATAATT
*
61869242 TTAATTTTA-ATTAAAAA
1 TTAATTTTATATAAAAAA
61869259 CGGGCCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 15 0.45
23 18 0.55
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TTAATTTTATATAAAAAATAATT
Found at i:61870902 original size:26 final size:26
Alignment explanation
Indices: 61870873--61870936 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
61870863 ATAGAAATTA
61870873 AATTATAATTTTATAATAAAAAATAT
1 AATTATAATTTTATAATAAAAAATAT
* * **
61870899 AATT-TTATTATTTTAATAAATTATAT
1 AATTATAATT-TTATAATAAAAAATAT
*
61870925 ATTTATAATTTT
1 AATTATAATTTT
61870937 TAAAAGATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
25 4 0.13
26 22 0.73
27 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
AATTATAATTTTATAATAAAAAATAT
Found at i:61873918 original size:2 final size:2
Alignment explanation
Indices: 61873911--61873936 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
61873901 AGACTACTTT
61873911 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
61873937 ACAAAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:61875271 original size:21 final size:20
Alignment explanation
Indices: 61875231--61875291 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
61875221 TAATAATGAG
* * *
61875231 AATACCAATTTTGTAGTAAT
1 AATATCAATTTTATAATAAT
61875251 AATATCAATTTTTATAATAAT
1 AATATCAA-TTTTATAATAAT
*
61875272 AATATCGATTTTATAATAAT
1 AATATCAATTTTATAATAAT
61875292 TATGGTACTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
20 19 0.53
21 17 0.47
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (20 bp):
AATATCAATTTTATAATAAT
Found at i:61875386 original size:3 final size:3
Alignment explanation
Indices: 61875380--61875410 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
61875370 AGGAAAAATA
*
61875380 AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
61875411 CAATAAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:61876558 original size:38 final size:38
Alignment explanation
Indices: 61876516--61876590 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
61876506 CAAAAAGCGC
*
61876516 AAAAAAAAAGAGTTGAGAAAAGTCGTAAAAAAAAAAGA
1 AAAAAAAAAGAGTTGAGAAAAATCGTAAAAAAAAAAGA
61876554 AAAAAAAAAGAGTTGAGAAAAATCGTAAAAAAAAAAG
1 AAAAAAAAAGAGTTGAGAAAAATCGTAAAAAAAAAAG
61876591 TTGCCTACCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.69, C:0.03, G:0.17, T:0.11
Consensus pattern (38 bp):
AAAAAAAAAGAGTTGAGAAAAATCGTAAAAAAAAAAGA
Found at i:61880908 original size:17 final size:18
Alignment explanation
Indices: 61880864--61880919 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 18
61880854 TACATTTATC
61880864 TTAATATTATTTAAGTATAT
1 TTAATATT-TTTAA-TATAT
* *
61880884 TTATTATTTTTAATTTA-
1 TTAATATTTTTAATATAT
61880901 TTAATATTTTTAATA-AT
1 TTAATATTTTTAATATAT
61880918 TT
1 TT
61880920 TTTATGTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
16 1 0.03
17 15 0.48
18 3 0.10
19 5 0.16
20 7 0.23
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TTAATATTTTTAATATAT
Found at i:61880919 original size:27 final size:26
Alignment explanation
Indices: 61880889--61880939 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
61880879 TATATTTATT
* *
61880889 ATTTTTAATTTATTAATATTTTTAATA
1 ATTTTTAATGTATT-ATAATTTTAATA
*
61880916 ATTTTTTATGTATTATAATTTTAA
1 ATTTTTAATGTATTATAATTTTAA
61880940 AAAAATTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 9 0.43
27 12 0.57
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (26 bp):
ATTTTTAATGTATTATAATTTTAATA
Found at i:61884730 original size:22 final size:21
Alignment explanation
Indices: 61884690--61884731 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
61884680 ATTTTTTGAA
*
61884690 AATATTAAAATATTGATATTG
1 AATATTAAAATATTAATATTG
*
61884711 AATATTATAAATTTTAATATT
1 AATATTA-AAATATTAATATT
61884732 ATTAAATAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (21 bp):
AATATTAAAATATTAATATTG
Found at i:61889720 original size:16 final size:16
Alignment explanation
Indices: 61889701--61889731 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61889691 ATTTAAACCT
61889701 AAAATAATTAGAACTC
1 AAAATAATTAGAACTC
*
61889717 AAAATTATTAGAACT
1 AAAATAATTAGAACT
61889732 TGCAATATTT
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:0.55, C:0.10, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAATAATTAGAACTC
Found at i:61892109 original size:2 final size:2
Alignment explanation
Indices: 61892102--61892135 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
61892092 AAATTCATAC
*
61892102 AT AT AT AT AC 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
61892136 TAGTTTTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:61892113 original size:10 final size:10
Alignment explanation
Indices: 61892098--61892135 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
61892088 CCCCAAATTC
61892098 ATACATATAT
1 ATACATATAT
61892108 ATACATATAT
1 ATACATATAT
*
61892118 ATATATATAT
1 ATACATATAT
*
61892128 ATATATAT
1 ATACATAT
61892136 TAGTTTTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (10 bp):
ATACATATAT
Found at i:61893042 original size:4 final size:4
Alignment explanation
Indices: 61893033--61893062 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
61893023 AAAAATAATT
*
61893033 ATAC ATAC ATAC ATAT ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
61893063 TGAATGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (4 bp):
ATAC
Found at i:61893053 original size:16 final size:16
Alignment explanation
Indices: 61893032--61893062 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
61893022 CAAAAATAAT
61893032 TATACATACATACATA
1 TATACATACATACATA
61893048 TATACATACATACAT
1 TATACATACATACAT
61893063 TGAATGTATA
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:0.48, C:0.19, G:0.00, T:0.32
Consensus pattern (16 bp):
TATACATACATACATA
Found at i:61898471 original size:27 final size:27
Alignment explanation
Indices: 61898410--61898490 Score: 67
Period size: 27 Copynumber: 2.9 Consensus size: 27
61898400 TCCACACTCA
*
61898410 AATATTATTATAATTTATTAATATATTT
1 AATA-TATTATAATTTATTAATATATTC
*
61898438 AAAATATTATATATTTATATAA-AT-TTC
1 AATATATTATA-ATTTAT-TAATATATTC
* * *
61898465 AATATATTCGTAATTTAATATTATAT
1 AATATATT-ATAATTTATTAATATAT
61898491 AATTTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
26 2 0.05
27 23 0.55
28 14 0.33
29 3 0.07
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52
Consensus pattern (27 bp):
AATATATTATAATTTATTAATATATTC
Found at i:61906302 original size:34 final size:35
Alignment explanation
Indices: 61906247--61906313 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
61906237 CAAACACCAA
*
61906247 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
61906282 AAAACATTTTCCTG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
61906314 TACTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:61911380 original size:3 final size:3
Alignment explanation
Indices: 61911374--61911401 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
61911364 TTCTCTTCTT
61911374 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
61911402 GTGGTTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:61921549 original size:20 final size:21
Alignment explanation
Indices: 61921510--61921549 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
61921500 GACGCATTTC
*
61921510 TTGAATGAAGTAATGAATAGT
1 TTGAATGAAGAAATGAATAGT
*
61921531 TTGAATGAA-AAATGTATAG
1 TTGAATGAAGAAATGAATAG
61921550 CTTAGGTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.33
Consensus pattern (21 bp):
TTGAATGAAGAAATGAATAGT
Found at i:61922864 original size:21 final size:20
Alignment explanation
Indices: 61922840--61922885 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 20
61922830 TTAGATGAAC
61922840 ATATTTTCTCTATTTTTTAATAT
1 ATATTTT-TCTA-TTTTTAA-AT
61922863 ATATTTTT-TATTTTTAAAT
1 ATATTTTTCTATTTTTAAAT
61922882 -TATT
1 ATATT
61922886 ATAAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 4 0.17
19 2 0.09
20 7 0.30
21 2 0.09
22 1 0.04
23 7 0.30
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
ATATTTTTCTATTTTTAAAT
Found at i:61922888 original size:23 final size:23
Alignment explanation
Indices: 61922840--61922881 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
61922830 TTAGATGAAC
*
61922840 ATATTTTCTCTATTTTTTAATAT
1 ATATTTTCTCTATTTTTAAATAT
61922863 ATATTTT-T-TATTTTTAAAT
1 ATATTTTCTCTATTTTTAAAT
61922882 TATTATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 1 0.06
23 7 0.39
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (23 bp):
ATATTTTCTCTATTTTTAAATAT
Found at i:61933101 original size:60 final size:59
Alignment explanation
Indices: 61933030--61933200 Score: 186
Period size: 59 Copynumber: 2.9 Consensus size: 59
61933020 ATTTGATACT
* *
61933030 TTTTTCC-AATTTGATATCTAAACTTTTTTTTGTCCCAATTTGGTATCTAAACTTGACA
1 TTTTTCCTAATTTGATATCTAAACTTTTTTTTGACCCAATTTGGTACCTAAACTTGACA
* * * *
61933088 GTTTTTCCTAATTTGGTA-CTTAAAC-TTTTTTGGACCCAATTTGGTACCTGAACTTGGCA
1 -TTTTTCCTAATTTGATATC-TAAACTTTTTTTTGACCCAATTTGGTACCTAAACTTGACA
* * ***
61933147 TTTTATCCTAATTTGAAATCTAAGCTTTTTTTTAGGTTCAATTTGGTACCTAAA
1 TTTT-TCCTAATTTGATATCTAAACTTTTTTTT-GACCCAATTTGGTACCTAAA
61933201 TTTATTAAAT
Statistics
Matches: 92, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
58 4 0.04
59 52 0.57
60 20 0.22
61 16 0.17
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.46
Consensus pattern (59 bp):
TTTTTCCTAATTTGATATCTAAACTTTTTTTTGACCCAATTTGGTACCTAAACTTGACA
Found at i:61933682 original size:31 final size:31
Alignment explanation
Indices: 61933637--61933703 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
61933627 GACCCCCAAA
*
61933637 AAGTTTAAGCACCAACTTAAGAAAAAGTATC
1 AAGTTTAAGCACCAAATTAAGAAAAAGTATC
* * * *
61933668 AAGTTTAGGTACCAAATTAGGAAAAAGTGTC
1 AAGTTTAAGCACCAAATTAAGAAAAAGTATC
61933699 AAGTT
1 AAGTT
61933704 GATGTGCCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (31 bp):
AAGTTTAAGCACCAAATTAAGAAAAAGTATC
Found at i:61933714 original size:31 final size:31
Alignment explanation
Indices: 61933647--61933715 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
61933637 AAGTTTAAGC
* *
61933647 ACCAACTTAAGAAAAAGTATCAAGTTTAGGT
1 ACCAAATTAAGAAAAAGTATCAAGTTGAGGT
* * *
61933678 ACCAAATTAGGAAAAAGTGTCAAGTTGATGT
1 ACCAAATTAAGAAAAAGTATCAAGTTGAGGT
*
61933709 GCCAAAT
1 ACCAAAT
61933716 GTTATATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (31 bp):
ACCAAATTAAGAAAAAGTATCAAGTTGAGGT
Found at i:61937254 original size:54 final size:54
Alignment explanation
Indices: 61937190--61937301 Score: 224
Period size: 54 Copynumber: 2.1 Consensus size: 54
61937180 AAAATAATCC
61937190 ACTTGTTGATCCAAAGAAAAATGTGCTTTATTAGTAAATTGACCCCTAAACTAT
1 ACTTGTTGATCCAAAGAAAAATGTGCTTTATTAGTAAATTGACCCCTAAACTAT
61937244 ACTTGTTGATCCAAAGAAAAATGTGCTTTATTAGTAAATTGACCCCTAAACTAT
1 ACTTGTTGATCCAAAGAAAAATGTGCTTTATTAGTAAATTGACCCCTAAACTAT
61937298 ACTT
1 ACTT
61937302 CAATTTCTAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (54 bp):
ACTTGTTGATCCAAAGAAAAATGTGCTTTATTAGTAAATTGACCCCTAAACTAT
Found at i:61937837 original size:20 final size:19
Alignment explanation
Indices: 61937793--61937842 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
61937783 AGTTAAACTG
*
61937793 ATTTTTT-TTATTTTTAAA
1 ATTTTTTATGATTTTTAAA
61937811 ATATTTTTATGATTTTTAATA
1 AT-TTTTTATGATTTTTAA-A
61937832 ATTTTTATATG
1 ATTTTT-TATG
61937843 GTTAAAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 2 0.07
19 5 0.19
20 13 0.48
21 7 0.26
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (19 bp):
ATTTTTTATGATTTTTAAA
Found at i:61938033 original size:22 final size:22
Alignment explanation
Indices: 61938008--61938049 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
61937998 CCTATCAATA
61938008 TTATTTT-TTTGAAATATTTATT
1 TTATTTTATTT-AAATATTTATT
*
61938030 TTATTTTATTTTAATATTTA
1 TTATTTTATTTAAATATTTA
61938050 ATAATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
TTATTTTATTTAAATATTTATT
Found at i:61944809 original size:33 final size:33
Alignment explanation
Indices: 61944772--61944915 Score: 105
Period size: 33 Copynumber: 4.3 Consensus size: 33
61944762 ATAACACAGT
61944772 TATGGTCTTATCATCAGAATGCCATAACCCAAC
1 TATGGTCTTATCATCAGAATGCCATAACCCAAC
* ***
61944805 TATGGTCTTAGAT-AT-AAACACTGCCATGGTCCAAC
1 TATGGTCTT--ATCATCAGA-A-TGCCATAACCCAAC
* * * * * *
61944840 CATGGTCTTA-CGCTCATAGTGTCATAACCCAAT
1 TATGGTCTTATC-ATCAGAATGCCATAACCCAAC
* *
61944873 TATGGTCTTATCATCAGAATGTCATAGCCCAAC
1 TATGGTCTTATCATCAGAATGCCATAACCCAAC
*
61944906 TATGGCCTTA
1 TATGGTCTTA
61944916 CATATAAACA
Statistics
Matches: 83, Mismatches: 20, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
33 55 0.66
34 5 0.06
35 23 0.28
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (33 bp):
TATGGTCTTATCATCAGAATGCCATAACCCAAC
Found at i:61944930 original size:101 final size:101
Alignment explanation
Indices: 61944755--61944983 Score: 386
Period size: 101 Copynumber: 2.3 Consensus size: 101
61944745 TTTACATTCG
* * * *
61944755 TAGTGTCATAACACAGTTATGGTCTTATCATCAGAATGCCATAACCCAACTATGGTCTTAGATAT
1 TAGTGTCATAACCCAATTATGGTCTTATCATCAGAATGCCATAACCCAACTATGGCCTTACATAT
61944820 AAACACTGCCATGGTCCAACCATGGTCTTACGCTCA
66 AAACACTGCCATGGTCCAACCATGGTCTTACGCTCA
* *
61944856 TAGTGTCATAACCCAATTATGGTCTTATCATCAGAATGTCATAGCCCAACTATGGCCTTACATAT
1 TAGTGTCATAACCCAATTATGGTCTTATCATCAGAATGCCATAACCCAACTATGGCCTTACATAT
*
61944921 AAACACTGCCATGGTCCAACCATGGTCTTACGTTCA
66 AAACACTGCCATGGTCCAACCATGGTCTTACGCTCA
*
61944957 TAGTGCCATAACCCAATTATGGTCTTA
1 TAGTGTCATAACCCAATTATGGTCTTA
61944984 ACCGTCAATT
Statistics
Matches: 120, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 120 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (101 bp):
TAGTGTCATAACCCAATTATGGTCTTATCATCAGAATGCCATAACCCAACTATGGCCTTACATAT
AAACACTGCCATGGTCCAACCATGGTCTTACGCTCA
Found at i:61944979 original size:33 final size:33
Alignment explanation
Indices: 61944791--61944983 Score: 93
Period size: 33 Copynumber: 5.7 Consensus size: 33
61944781 ATCATCAGAA
* * *
61944791 TGCCATAACCCAACTATGGTCTTA-GATATAAACAC
1 TGCCATAACCCAACTATGGTCTTACG-T-T-CATAG
*** * *
61944826 TGCCATGGTCCAACCATGGTCTTACGCTCATAG
1 TGCCATAACCCAACTATGGTCTTACGTTCATAG
* * * * *
61944859 TGTCATAACCCAATTATGGTCTTATC-ATCAGAA
1 TGCCATAACCCAACTATGGTCTTA-CGTTCATAG
* * * * * * *
61944892 TGTCATAGCCCAACTATGGCCTTACATATAAACAC
1 TGCCATAACCCAACTATGGTCTTACGT-T-CATAG
*** *
61944927 TGCCATGGTCCAACCATGGTCTTACGTTCATAG
1 TGCCATAACCCAACTATGGTCTTACGTTCATAG
*
61944960 TGCCATAACCCAATTATGGTCTTA
1 TGCCATAACCCAACTATGGTCTTA
61944984 ACCGTCAATT
Statistics
Matches: 115, Mismatches: 38, Indels: 12
0.70 0.23 0.07
Matches are distributed among these distances:
32 1 0.01
33 66 0.57
34 4 0.03
35 43 0.37
36 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (33 bp):
TGCCATAACCCAACTATGGTCTTACGTTCATAG
Found at i:61957518 original size:27 final size:27
Alignment explanation
Indices: 61957480--61957533 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
61957470 ATAAATTGGT
61957480 AAAATTTTCCACTCACGCTAATAGACC
1 AAAATTTTCCACTCACGCTAATAGACC
61957507 AAAATTTTCCACTCACGCTAATAGACC
1 AAAATTTTCCACTCACGCTAATAGACC
61957534 GACTTTTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.30, G:0.07, T:0.26
Consensus pattern (27 bp):
AAAATTTTCCACTCACGCTAATAGACC
Found at i:61958905 original size:26 final size:26
Alignment explanation
Indices: 61958869--61958919 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
61958859 ACAAGTTGAT
61958869 ATCGGTCCACTTTCAAGAATACTTTA
1 ATCGGTCCACTTTCAAGAATACTTTA
61958895 ATCGGTCCACTTTCAAGAATACTTT
1 ATCGGTCCACTTTCAAGAATACTTT
61958920 CATTCATGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (26 bp):
ATCGGTCCACTTTCAAGAATACTTTA
Found at i:61964817 original size:19 final size:20
Alignment explanation
Indices: 61964781--61964833 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
61964771 AATTACAAAA
*
61964781 AAAAAATCAAAATAATTT-T
1 AAAAATTCAAAATAATTTAT
61964800 CAAAAATTCAAAAT-ATTTAT
1 -AAAAATTCAAAATAATTTAT
61964820 AAAAATTCTAAAAT
1 AAAAATTC-AAAAT
61964834 TTATATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTAT
Found at i:61964824 original size:20 final size:20
Alignment explanation
Indices: 61964780--61964838 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
61964770 AAATTACAAA
*
61964780 AAAAAAATCAAAATAATTT-T
1 AAAAAATTCAAAAT-ATTTAT
*
61964800 CAAAAATTCAAAATATTTAT
1 AAAAAATTCAAAATATTTAT
*
61964820 -AAAAATTCTAAA-ATTTAT
1 AAAAAATTCAAAATATTTAT
61964838 A
1 A
61964839 TTTTTTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 6 0.18
19 15 0.44
20 13 0.38
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAAAATTCAAAATATTTAT
Found at i:61964873 original size:20 final size:19
Alignment explanation
Indices: 61964840--61964878 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
61964830 AAATTTATAT
*
61964840 TTTTTTAAAAAATTATAAA
1 TTTTTAAAAAAATTATAAA
*
61964859 TTTTTAAAAACAATTCTAAA
1 TTTTTAAAAA-AATTATAAA
61964879 GAATATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTTTAAAAAAATTATAAA
Found at i:61965697 original size:4 final size:4
Alignment explanation
Indices: 61965680--61965802 Score: 84
Period size: 4 Copynumber: 31.0 Consensus size: 4
61965670 GAAGGAGAGG
61965680 GAAA G-AA G-AA GAAA GAAA GAAA GAAA G-AA -AAA GAAA GAAAA GGAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA
* *
61965726 GGAGAG GAAA GAAA G-AA -AAA GAAG GAAA GAAAA GGAAA GGAGAA -AAA
1 -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA -GA-AA GAAA
*
61965773 GAAA GAAA GAAA G-AA -AAA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
61965803 AGGAAAGGAG
Statistics
Matches: 99, Mismatches: 6, Indels: 28
0.74 0.05 0.21
Matches are distributed among these distances:
3 20 0.20
4 54 0.55
5 20 0.20
6 5 0.05
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:61965703 original size:18 final size:18
Alignment explanation
Indices: 61965680--61965868 Score: 117
Period size: 18 Copynumber: 10.5 Consensus size: 18
61965670 GAAGGAGAGG
61965680 GAAAG-AAGAAGAAAGAAA
1 GAAAGAAAGAAG-AAGAAA
*
61965698 GAAAGAAAGAAAAAGAAA
1 GAAAGAAAGAAGAAGAAA
* *
61965716 GAAAAGGAAAGGAGAGGAAA
1 G-AAA-GAAAGAAGAAGAAA
61965736 GAAAGAAA-AAGAAGGAAA
1 GAAAGAAAGAAGAA-GAAA
*
61965754 GAAAAGGAAAGGAGAA-AAA
1 G-AAA-GAAAGAAGAAGAAA
61965773 GAAAGAAAGAAAGAA-AAA
1 GAAAGAAAG-AAGAAGAAA
*
61965791 GAAGGAAAGAA-AAGGAAA
1 GAAAGAAAGAAGAA-GAAA
*
61965809 G-GAGAAGAGAA-AA-AAA
1 GAAAGAA-AGAAGAAGAAA
* **
61965825 AAAAG-AAGAAGAAGAGG
1 GAAAGAAAGAAGAAGAAA
* * * *
61965842 GGAGGAAGGAAAAAGAAA
1 GAAAGAAAGAAGAAGAAA
61965860 GAAAGAAAG
1 GAAAGAAAG
61965869 GTAATTTTTT
Statistics
Matches: 131, Mismatches: 25, Indels: 30
0.70 0.13 0.16
Matches are distributed among these distances:
15 4 0.03
16 8 0.06
17 18 0.14
18 63 0.48
19 18 0.14
20 16 0.12
21 4 0.03
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (18 bp):
GAAAGAAAGAAGAAGAAA
Found at i:61965754 original size:38 final size:40
Alignment explanation
Indices: 61965679--61965832 Score: 183
Period size: 38 Copynumber: 3.8 Consensus size: 40
61965669 GGAAGGAGAG
* *
61965679 GGAAAGAAGAAGAAAGAAAGAAAGAAAGAA-AAAGAAAGAAAA
1 GGAAAGGAGAAG--AGAAAGAAAGAAA-AAGAAGGAAAGAAAA
61965721 GGAAAGGAG-AG-GAAAGAAAGAAAAAGAAGGAAAGAAAA
1 GGAAAGGAGAAGAGAAAGAAAGAAAAAGAAGGAAAGAAAA
61965759 GGAAAGGAGAAAAAGAAAGAAAGAAAGAAAAAGAAGGAAAGAAAA
1 GGAAAGGAG---AAG--AGAAAGAAAGAAAAAGAAGGAAAGAAAA
61965804 GGAAAGGAGAAGAGAAA-AAA-AAAAAGAAG
1 GGAAAGGAGAAGAGAAAGAAAGAAAAAGAAG
61965833 AAGAAGAGGG
Statistics
Matches: 102, Mismatches: 2, Indels: 20
0.82 0.02 0.16
Matches are distributed among these distances:
37 2 0.02
38 41 0.40
39 3 0.03
40 5 0.05
41 2 0.02
42 13 0.13
45 36 0.35
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (40 bp):
GGAAAGGAGAAGAGAAAGAAAGAAAAAGAAGGAAAGAAAA
Found at i:61965796 original size:45 final size:44
Alignment explanation
Indices: 61965732--61965868 Score: 169
Period size: 45 Copynumber: 3.2 Consensus size: 44
61965722 GAAAGGAGAG
61965732 GAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAAAAGAAA
1 GAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAG-AAAAGAAA
*
61965777 GAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAA
1 GAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAAAGAAA
* ***
61965821 -AAA-AAA-AAGAAGAA-GAAGAGGGGAGG-AAGGA-AAAAGAAA
1 GAAAGAAAGAAAAAGAAGGAA-AGAAAAGGAAAGGAGAAAAGAAA
61965860 GAAAGAAAG
1 GAAAGAAAG
61965869 GTAATTTTTT
Statistics
Matches: 82, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
39 7 0.09
40 11 0.13
41 15 0.18
42 3 0.04
43 3 0.04
44 7 0.09
45 36 0.44
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (44 bp):
GAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAAAGAAA
Found at i:61965803 original size:83 final size:82
Alignment explanation
Indices: 61965682--61965868 Score: 247
Period size: 83 Copynumber: 2.3 Consensus size: 82
61965672 AGGAGAGGGA
*
61965682 AAGAAGAAGAAAGAAAGAAAGAAAGAAAAAGAAAGAAAAGGAAAGGAG-AG-GAAAGAAAGAAAA
1 AAGAAAAAGAAAGAAAGAAAGAAAGAAAAAGAAAGAAAAGGAAAGGAGAAGAGAAA-AAA-AAAA
61965745 AGAAGGAAAGAAAAGGAAAGG
64 AGAA-G-AAGAAAAGGAAAGG
*
61965766 -AGAAAAAGAAAGAAAGAAAGAAA-AAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAA
1 AAGAAAAAGAAAGAAAGAAAGAAAGAA-AAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAA
* **
61965829 GAAGAAGAAGAGGGGAGG
65 GAAGAAGAAAAGGAAAGG
61965847 AAGGAAAAAGAAAGAAAGAAAG
1 AA-GAAAAAGAAAGAAAGAAAG
61965869 GTAATTTTTT
Statistics
Matches: 93, Mismatches: 5, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
81 11 0.12
82 4 0.04
83 69 0.74
84 5 0.05
85 4 0.04
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (82 bp):
AAGAAAAAGAAAGAAAGAAAGAAAGAAAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAAG
AAGAAGAAAAGGAAAGG
Found at i:61965867 original size:14 final size:14
Alignment explanation
Indices: 61965680--61965837 Score: 108
Period size: 14 Copynumber: 10.9 Consensus size: 14
61965670 GAAGGAGAGG
*
61965680 GAAAGAAGAAGAAA
1 GAAAGAAAAAGAAA
61965694 GAAAG--AAAGAAA
1 GAAAGAAAAAGAAA
61965706 GAAA-AAGAAAGAAAA
1 GAAAGAA-AAAG-AAA
* * *
61965721 GGAAAGGAGAGGAAA
1 -GAAAGAAAAAGAAA
*
61965736 GAAAGAAAAAGAAG
1 GAAAGAAAAAGAAA
*
61965750 GAAAGAAAAGGAAA
1 GAAAGAAAAAGAAA
*
61965764 GGAGAAAAAGAAAGAAA
1 -GA-AAGAA-AAAGAAA
*
61965781 GAAAGAAAAAGAAG
1 GAAAGAAAAAGAAA
*
61965795 GAAAGAAAAGGAAA
1 GAAAGAAAAAGAAA
61965809 GGAGAAGAGAAAA-AAA
1 -GA-AAGA-AAAAGAAA
* *
61965825 AAAAGAAGAAGAA
1 GAAAGAAAAAGAA
61965838 GAGGGGAGGA
Statistics
Matches: 112, Mismatches: 19, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
12 10 0.09
13 3 0.03
14 55 0.49
15 15 0.13
16 19 0.17
17 10 0.09
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (14 bp):
GAAAGAAAAAGAAA
Found at i:61966748 original size:285 final size:286
Alignment explanation
Indices: 61966233--61967094 Score: 1514
Period size: 285 Copynumber: 3.0 Consensus size: 286
61966223 TGAAATAAAG
* **
61966233 TAAAATTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCAAAGAAAAAAATACGA
1 TAAATTTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGA
* * *
61966298 AGAAATGGCCGAAGTAAGAGCGTTTTACAAAATTTTATAAAAATTCAGAAATAATTAATACAAAT
66 AGAAATGGCCGAAGTAAGAGTGTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAATACAAAT
* * *
61966363 ATTTCAAACAAAATATACTGAAATAATATAAAATAATAAAATACAAAAATAATA-TTTTTATTCA
131 ATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATTTTTTATTGA
* * *
61966427 AAGTAATAAAATTCGAGAAAATAATACGAGCAAAGGGCAGGAATAAAAGTTTTTTTTACACTAAA
196 AAGTAATAAAATTCGGGAAAATAATACGAGCAAAGGGCAGGAATAAAGGTTTTTTTGACACTAAA
61966492 TTAATTTAAAAAACACACTAAATTAA
261 TTAATTTAAAAAACACACTAAATTAA
*
61966518 TAAATTTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATACGGAG-AAAAAATACGA
1 TAAATTTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGA
*
61966582 AGAAATGGCCGAAGTAAGAGTGTTTTGCTAAATTTTTTAAAAATTCAGAAATAATTAATACAAAT
66 AGAAATGGCCGAAGTAAGAGTGTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAATACAAAT
61966647 ATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATTTTTTATTGA
131 ATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATTTTTTATTGA
* * * *
61966712 AAGTAACAAAATTCGGGAAAATAATATGAGCAAAGGGCATGAATAATGGTTTTTTTGACACTAAA
196 AAGTAATAAAATTCGGGAAAATAATACGAGCAAAGGGCAGGAATAAAGGTTTTTTTGACACTAAA
*
61966777 TTAATCTAAAAAACACACTAAATTAA
261 TTAATTTAAAAAACACACTAAATTAA
61966803 TAAATTTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGA
1 TAAATTTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGA
61966868 AGAAATGGCCGAAGTAAGAGTGTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAATACAAAT
66 AGAAATGGCCGAAGTAAGAGTGTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAATACAAAT
61966933 ATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATTTTTTATTGA
131 ATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATTTTTTATTGA
*
61966998 AAGTAATAAAATTCGGGAAAATAATACGAGCAAAGGGCAGGAATAAGGGTTTTTTTGACACTAAA
196 AAGTAATAAAATTCGGGAAAATAATACGAGCAAAGGGCAGGAATAAAGGTTTTTTTGACACTAAA
*
61967063 TTAATTT-AAAAACACATTAAATTAA
261 TTAATTTAAAAAACACACTAAATTAA
61967088 TAAATTT
1 TAAATTT
61967095 CAAACATAAT
Statistics
Matches: 548, Mismatches: 27, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
284 124 0.23
285 217 0.40
286 207 0.38
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (286 bp):
TAAATTTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGA
AGAAATGGCCGAAGTAAGAGTGTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAATACAAAT
ATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATTTTTTATTGA
AAGTAATAAAATTCGGGAAAATAATACGAGCAAAGGGCAGGAATAAAGGTTTTTTTGACACTAAA
TTAATTTAAAAAACACACTAAATTAA
Found at i:61968500 original size:315 final size:315
Alignment explanation
Indices: 61967928--61968877 Score: 1810
Period size: 315 Copynumber: 3.0 Consensus size: 315
61967918 TTAGCTGATT
* *
61967928 TGTCCAGTGTTAGCTCGTATAGCTGGGGCTCCGCCGTTCTAGCAGTGTTGTATCAGGAGCTTTGT
1 TGTCCAGTGTTAGCTCGTATAGCTGGGGCTCCGTCGTTCTAGCAGTGTTGTATCGGGAGCTTTGT
*
61967993 CGGGTGACAAACCCAGATGTTGTAGACATGAGCGAATGCCTCACATTGCTGCAATCCTGGGCGCT
66 CGGGTGACAAACCCAGATGTTGTAGACATGGGCGAATGCCTCACATTGCTGCAATCCTGGGCGCT
* * *
61968058 CTATCGGATGTCATTTTTAGCATCGGTTAGTCACCAACCGTATGTTTATCCACTGGTGAACAGGT
131 CTATCGGATGACATTTTTGGCATCAGTTAGTCACCAACCGTATGTTTATCCACTGGTGAACAGGT
61968123 GATAAAATATAAATTGTCATTATTTGTAGTCATAATATATTGACTAATGTTACCAACCCTAAACC
196 GATAAAATATAAATTGTCATTATTTGTAGTCATAATATATTGACTAATGTTACCAACCCTAAACC
61968188 CTATATTTGTTTTTTGTAGGTGGAGTGTTCGTCCGGGTATCGGGAGGTCACACAC
261 CTATATTTGTTTTTTGTAGGTGGAGTGTTCGTCCGGGTATCGGGAGGTCACACAC
61968243 TGTCCAGTGTTAGCTCGTATAGCTGGGGCTCCGTCGTTCTAGCAGTGTTGTATCGGGAGCTTTGT
1 TGTCCAGTGTTAGCTCGTATAGCTGGGGCTCCGTCGTTCTAGCAGTGTTGTATCGGGAGCTTTGT
61968308 CGGGTGACAAACCCAGATGTTGTAGACATGGGCGAATGCCTCACATTGCTGCAATCCTGGGCGCT
66 CGGGTGACAAACCCAGATGTTGTAGACATGGGCGAATGCCTCACATTGCTGCAATCCTGGGCGCT
*
61968373 CTATCGGATGACATTTTTGGCATCCGTTAGTCACCAACCGTATGTTTATCCACTGGTGAACAGGT
131 CTATCGGATGACATTTTTGGCATCAGTTAGTCACCAACCGTATGTTTATCCACTGGTGAACAGGT
61968438 GATAAAATATAAATTGTCATTATTTGTAGTCATAATATATTGACTAATGTTACCAACCCTAAACC
196 GATAAAATATAAATTGTCATTATTTGTAGTCATAATATATTGACTAATGTTACCAACCCTAAACC
61968503 CTATATTTGTTTTTTGTAGGTGGAGTGTTCGTCCGGGTATCGGGAGGTCACACAC
261 CTATATTTGTTTTTTGTAGGTGGAGTGTTCGTCCGGGTATCGGGAGGTCACACAC
61968558 TGTCCAGTGTTAGCTCGTATAGCTGGGGCTCCGTCGTTCTAGCAGTGTTGTATCGGGAGCTTTGT
1 TGTCCAGTGTTAGCTCGTATAGCTGGGGCTCCGTCGTTCTAGCAGTGTTGTATCGGGAGCTTTGT
61968623 CGGGTGACAAACCCAGATGTTGTAGACATGGGCGAATGCCTCACATTGCTGCAATCCTGGGCGCT
66 CGGGTGACAAACCCAGATGTTGTAGACATGGGCGAATGCCTCACATTGCTGCAATCCTGGGCGCT
* *
61968688 CTATCGGATGCCATTTTTGACATCAGTTAGTCACCAACCGTATGTTTATCCACTGGTGAACAGGT
131 CTATCGGATGACATTTTTGGCATCAGTTAGTCACCAACCGTATGTTTATCCACTGGTGAACAGGT
61968753 GATAAAATATAAATTGTCATTATTTGTAGTCATAATATATTGACTAATGTTACCAACCCTAAACC
196 GATAAAATATAAATTGTCATTATTTGTAGTCATAATATATTGACTAATGTTACCAACCCTAAACC
*
61968818 CTATATTTGTTTTTTGTAGGTGGAGTGTTCGTCCGGGTATCGAGAGGTCACACAC
261 CTATATTTGTTTTTTGTAGGTGGAGTGTTCGTCCGGGTATCGGGAGGTCACACAC
61968873 TGTCC
1 TGTCC
61968878 TGATATACAG
Statistics
Matches: 625, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
315 625 1.00
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.32
Consensus pattern (315 bp):
TGTCCAGTGTTAGCTCGTATAGCTGGGGCTCCGTCGTTCTAGCAGTGTTGTATCGGGAGCTTTGT
CGGGTGACAAACCCAGATGTTGTAGACATGGGCGAATGCCTCACATTGCTGCAATCCTGGGCGCT
CTATCGGATGACATTTTTGGCATCAGTTAGTCACCAACCGTATGTTTATCCACTGGTGAACAGGT
GATAAAATATAAATTGTCATTATTTGTAGTCATAATATATTGACTAATGTTACCAACCCTAAACC
CTATATTTGTTTTTTGTAGGTGGAGTGTTCGTCCGGGTATCGGGAGGTCACACAC
Found at i:61978162 original size:22 final size:22
Alignment explanation
Indices: 61978126--61978171 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
61978116 TTTTAAAACA
*
61978126 ACAATTAATCCAATCCAAATAG
1 ACAATTAATCAAATCCAAATAG
* *
61978148 ACAATTGATCAAATCTAAATAG
1 ACAATTAATCAAATCCAAATAG
61978170 AC
1 AC
61978172 TCGATTCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.50, C:0.20, G:0.07, T:0.24
Consensus pattern (22 bp):
ACAATTAATCAAATCCAAATAG
Found at i:61981751 original size:30 final size:30
Alignment explanation
Indices: 61981710--61981767 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
61981700 TGCCACAAGT
61981710 TCTTATACTTTT-TATTTTCAGAAATTTAATC
1 TCTTATACTTTTATATTTT-A-AAATTTAATC
61981741 TCTT-TACTTTTCATATTTTAAAATTTA
1 TCTTATACTTTT-ATATTTTAAAATTTA
61981768 TGTCTGCCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
30 14 0.56
31 5 0.20
32 6 0.24
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.57
Consensus pattern (30 bp):
TCTTATACTTTTATATTTTAAAATTTAATC
Found at i:61985916 original size:210 final size:206
Alignment explanation
Indices: 61985550--61985962 Score: 546
Period size: 210 Copynumber: 2.0 Consensus size: 206
61985540 ATGAAAACCA
* *
61985550 GATCCACAATAATAAACAGAATTCAGATAATCGAATCTGAACTGGTAATCTGCAAAAGTAGAGCG
1 GATCCACAATAATAAACAGAATTCAGATAATCGAATCTGAACTGGAAATCTGCAAAAGTAGAGAG
*
61985615 AATTTGAACAATAAATATCTACACTCGTTCCAAATGCATTATGGATAATAATTAAAATATCGAAT
66 AATTTGAACAATAAATATCTACACTCGTTCCAAATGCATTACGGATAATAATTAAAATATCGAAT
** ** **
61985680 CTATATAATATACGAATCTGCATTATCCATTGCCGTGCATAAACTCAACAAACATTTCTTGAAGA
131 CTATATAATATACGAATCCACATTATCCATTGCAATGCATAAACTCAACAAACATTTCCAGAAGA
61985745 AACTAAAATTG
196 AACTAAAATTG
61985756 GATCCACAATAATAAACAGAATTCAGATAATCAATATATGAATCTGAAC-GGAAATCTGCAAAAG
1 GATCCACAATAATAAACAGAATTCAGATAATC-------GAATCTGAACTGGAAATCTGCAAAAG
* * * * * *
61985820 TGGAGAGGATTTGAGCAAT-AA-AT-TAGCATTCTTTCCAAATGCGTTACGGATAATAATTAAAA
59 TAGAGAGAATTTGAACAATAAATATCTA-CACTCGTTCCAAATGCATTACGGATAATAATTAAAA
** * *
61985882 TATCGAATCTATATTTTATACGAATCCACATTATCCATTGCAATGCTTAAACTCAACCAACATTT
123 TATCGAATCTATATAATATACGAATCCACATTATCCATTGCAATGCATAAACTCAACAAACATTT
*
61985947 CCAGAATAAACTAAAA
188 CCAGAAGAAACTAAAA
61985963 GAAACAGGTT
Statistics
Matches: 179, Mismatches: 20, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
206 32 0.18
209 2 0.01
210 104 0.58
211 2 0.01
212 29 0.16
213 10 0.06
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (206 bp):
GATCCACAATAATAAACAGAATTCAGATAATCGAATCTGAACTGGAAATCTGCAAAAGTAGAGAG
AATTTGAACAATAAATATCTACACTCGTTCCAAATGCATTACGGATAATAATTAAAATATCGAAT
CTATATAATATACGAATCCACATTATCCATTGCAATGCATAAACTCAACAAACATTTCCAGAAGA
AACTAAAATTG
Found at i:61987167 original size:56 final size:57
Alignment explanation
Indices: 61987038--61987213 Score: 203
Period size: 56 Copynumber: 3.1 Consensus size: 57
61987028 GTTCATACCT
** * * *
61987038 CAATATGAGAACAATTGTTAAGTTTAGGGATTAACTTGAAAAAAAAAGTTCATGCCC
1 CAATATGAGAACAATTGCCAAGTTCAGGGACTAACTTGAAAAAAAAAGTTCAAGCCC
* * *
61987095 AAATATGAGAACAATTGCCAAGTTCAGGGGCTAACTTG-AAACAAAAGTTCAAGCCC
1 CAATATGAGAACAATTGCCAAGTTCAGGGACTAACTTGAAAAAAAAAGTTCAAGCCC
* ** *
61987151 CAATGTGAGAACAATTGCCAAG-TCTAAAGACTAACTTAGACAAAGAAAAGTTCAAGCCC
1 CAATATGAGAACAATTGCCAAGTTC-AGGGACTAACTT-GA-AAAAAAAAGTTCAAGCCC
61987210 CAAT
1 CAAT
61987214 GTGAAAAAAA
Statistics
Matches: 101, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
55 2 0.02
56 45 0.45
57 33 0.33
59 21 0.21
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.22
Consensus pattern (57 bp):
CAATATGAGAACAATTGCCAAGTTCAGGGACTAACTTGAAAAAAAAAGTTCAAGCCC
Found at i:61988064 original size:17 final size:17
Alignment explanation
Indices: 61988011--61988058 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
61988001 GAACTGAGTT
*
61988011 TTTTTTATTATTTTAAA
1 TTTTTAATTATTTTAAA
*
61988028 TTTTTAATT-TGTTTGAA
1 TTTTTAATTAT-TTTAAA
61988045 TTTTTAATTATTTT
1 TTTTTAATTATTTT
61988059 TTATTTAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 1 0.04
17 25 0.93
18 1 0.04
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (17 bp):
TTTTTAATTATTTTAAA
Found at i:61994905 original size:12 final size:12
Alignment explanation
Indices: 61994888--61994912 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
61994878 TTTAGGGGTC
61994888 TAAAACAAAAAT
1 TAAAACAAAAAT
61994900 TAAAACAAAAAT
1 TAAAACAAAAAT
61994912 T
1 T
61994913 CCTTATTTTA
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:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (12 bp):
TAAAACAAAAAT
Found at i:61998109 original size:3 final size:3
Alignment explanation
Indices: 61998101--61998128 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
61998091 TCAAGACGAC
61998101 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
61998129 TGATGATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:61998978 original size:31 final size:31
Alignment explanation
Indices: 61998943--61999008 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
61998933 AGGTCCGTTA
**
61998943 ATATTATTTTTTAGATTTT-TAATTTTTTATT
1 ATATTATTTAATA-ATTTTATAATTTTTTATT
*
61998974 ATATTATTTAATAATTTTATATTTTTTTATT
1 ATATTATTTAATAATTTTATAATTTTTTATT
61999005 -TATT
1 ATATT
61999009 GAAATTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 9 0.29
31 22 0.71
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (31 bp):
ATATTATTTAATAATTTTATAATTTTTTATT
Found at i:61998988 original size:23 final size:23
Alignment explanation
Indices: 61998962--61999020 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
61998952 TTTAGATTTT
61998962 TAATTTTTTATTATATTATTTAA
1 TAATTTTTTATTATATTATTTAA
* * * *
61998985 TAATTTTATATTTTTTTATTTAT
1 TAATTTTTTATTATATTATTTAA
61999008 TGAAATTTTTTAT
1 T--AATTTTTTAT
61999021 ATAGTCATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
23 20 0.69
25 9 0.31
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (23 bp):
TAATTTTTTATTATATTATTTAA
Found at i:62002423 original size:3 final size:3
Alignment explanation
Indices: 62002415--62002441 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
62002405 GGACGACACT
62002415 ACC ACC ACC ACC ACC ACC ACC ACC ACC
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC
62002442 CAAAGTTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:62007401 original size:6 final size:6
Alignment explanation
Indices: 62007390--62007434 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
62007380 CAAATTTGCT
* *
62007390 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTG TTTTT- TTTTTC TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
62007435 AATCTAACAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
5 5 0.14
6 32 0.86
ACGTcount: A:0.09, C:0.02, G:0.02, T:0.87
Consensus pattern (6 bp):
TTTTTA
Found at i:62012797 original size:29 final size:29
Alignment explanation
Indices: 62012759--62012834 Score: 134
Period size: 29 Copynumber: 2.6 Consensus size: 29
62012749 AACGATAACG
62012759 TAAGTGACTAAAATGTAACATTTTAAACA
1 TAAGTGACTAAAATGTAACATTTTAAACA
*
62012788 TAAGTAACTAAAATGTAACATTTTAAACA
1 TAAGTGACTAAAATGTAACATTTTAAACA
*
62012817 TAAATGACTAAAATGTAA
1 TAAGTGACTAAAATGTAA
62012835 TATGAGGCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.30
Consensus pattern (29 bp):
TAAGTGACTAAAATGTAACATTTTAAACA
Found at i:62014998 original size:29 final size:30
Alignment explanation
Indices: 62014939--62015005 Score: 100
Period size: 29 Copynumber: 2.2 Consensus size: 30
62014929 TTACAAAATG
*
62014939 GTCATTGAATTATTCAAAAGTTTTCATTTAA
1 GTCATTGAACTATTC-AAAGTTTTCATTTAA
*
62014970 GTCATTGAACTATTC-AAGTTTTTATTTAA
1 GTCATTGAACTATTCAAAGTTTTCATTTAA
62014999 GTCATTG
1 GTCATTG
62015006 GATTGTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 20 0.59
31 14 0.41
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.46
Consensus pattern (30 bp):
GTCATTGAACTATTCAAAGTTTTCATTTAA
Found at i:62015312 original size:17 final size:17
Alignment explanation
Indices: 62015290--62015324 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
62015280 CTTTCCCCTG
* *
62015290 ATTTTGTTGTTTTAGAT
1 ATTTTGTTATTTCAGAT
62015307 ATTTTGTTATTTCAGAT
1 ATTTTGTTATTTCAGAT
62015324 A
1 A
62015325 ATGTTTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.14, T:0.60
Consensus pattern (17 bp):
ATTTTGTTATTTCAGAT
Found at i:62018518 original size:21 final size:22
Alignment explanation
Indices: 62018490--62018532 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
62018480 TAATTTTGAT
62018490 TAAAAAAATTTAAGTATCAAAC
1 TAAAAAAATTTAAGTATCAAAC
*
62018512 TAAAAAAATTTAGGTATCAAA
1 TAAAAAAATTTAAGTATCAAA
62018533 AAATATCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.28
Consensus pattern (22 bp):
TAAAAAAATTTAAGTATCAAAC
Found at i:62032057 original size:147 final size:149
Alignment explanation
Indices: 62031793--62032227 Score: 493
Period size: 148 Copynumber: 2.9 Consensus size: 149
62031783 TTTAATTCAA
** * * * * * *
62031793 CAAATAGCTAACAATTCACCTAAATATTCAAGAAACAGTACGATTCAGCTTTGAACTAGGATCTA
1 CAAATAGCTAACAGCTCACATAAAGATACAAAAAACAGTACGATTCAGCTTCGAACTAGAATCTA
* * * * *
62031858 AAAACAAGCTAAGGTTGTTCTCCCTACGTAAATCTTGGAAAACTTAGCTCGTAAACTTCAGATCT
66 AAAACAAGCTAAAGCTGTTCTTCCTACGTAAATCTTAGCAAACTTAGCTCGTAAACTTCAGATCT
* *
62031923 GTATTTTTTTGTAATTCAT
131 GTATTTTTTTGCAACTCAT
* *
62031942 CAAATAGCT-ACAGCTCACATAAGGATACAAAAAACAGTACGATTCAGCTTCGAACTATAATCT-
1 CAAATAGCTAACAGCTCACATAAAGATACAAAAAACAGTACGATTCAGCTTCGAACTAGAATCTA
* * * *
62032005 AAAACAAGCTAAAGCTGTTCTTCCTACGCT-AGTCATAGCAAACATAGCTCGTAAACTTCAGTTT
66 AAAACAAGCTAAAGCTGTTCTTCCTACG-TAAATCTTAGCAAACTTAGCTCGTAAACTTCAG--A
* * *
62032069 TTTTTTTTTTTTTGCAACTCAT
128 TCTGTATTTTTTTGCAACTCAT
* * * * *
62032091 CAAATAGCTAACAGTTCACATAAAGATTCAAAAAGCGGTACCATTCAAGCTTCGAACTAGAATCT
1 CAAATAGCTAACAGCTCACATAAAGATACAAAAAACAGTACGATTC-AGCTTCGAACTAGAATCT
* * ** *
62032156 AAAAACAAGTTAAATCTGTTCTTCCTACGTAAATCTTAGCAGTCTTAGCTCGTAAGCTTC--ATC
65 AAAAACAAGCTAAAGCTGTTCTTCCTACGTAAATCTTAGCAAACTTAGCTCGTAAACTTCAGATC
62032219 TGTATTTTT
130 TGTATTTTT
62032228 AAGCAAAACA
Statistics
Matches: 236, Mismatches: 43, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
147 51 0.22
148 53 0.22
149 35 0.15
150 30 0.13
151 18 0.08
152 49 0.21
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (149 bp):
CAAATAGCTAACAGCTCACATAAAGATACAAAAAACAGTACGATTCAGCTTCGAACTAGAATCTA
AAAACAAGCTAAAGCTGTTCTTCCTACGTAAATCTTAGCAAACTTAGCTCGTAAACTTCAGATCT
GTATTTTTTTGCAACTCAT
Found at i:62044228 original size:16 final size:15
Alignment explanation
Indices: 62044188--62044229 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
62044178 GCTTGAGTGT
62044188 CAAATCTG-AATGAC
1 CAAATCTGAAATGAC
* *
62044202 AAAACCTGAAATGACC
1 CAAATCTGAAATGA-C
62044218 CAAATCTGAAAT
1 CAAATCTGAAAT
62044230 TATCCGACCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 6 0.27
15 5 0.23
16 11 0.50
ACGTcount: A:0.48, C:0.21, G:0.12, T:0.19
Consensus pattern (15 bp):
CAAATCTGAAATGAC
Found at i:62049388 original size:139 final size:139
Alignment explanation
Indices: 62049222--62049541 Score: 425
Period size: 139 Copynumber: 2.3 Consensus size: 139
62049212 TTCAGTGTGG
* * * * ** *
62049222 CGGCCACAACTTGGAATGCTTACCACTAAACTACAGCCACAATTTGTTAAAATTTGA-AAAGTAA
1 CGGCCACAACGTGGAATTCTTACCACTAAACTACAGCCACAACTTGTTAAAAGTCAAGAAACTAA
*
62049286 AAGGACTAATAGTAA-AAATTAACCAAATT-AA-AAAAAA-GTTTAATGTGGCTGCTGGGATTCG
66 AA--ACTAAAAGTAACAAA--AA-CAAATTAAAGAAAAAAGGTTTAATGTGGCTGCTGGGATTCG
62049347 AGCCCAGGTCTCCA
126 AGCCCAGGTCTCCA
*
62049361 CGGCCACAACGTGGAATTCTTACCACTAAACTACAGCCACAACTTGTTAAAGGTCAAGAAACTAA
1 CGGCCACAACGTGGAATTCTTACCACTAAACTACAGCCACAACTTGTTAAAAGTCAAGAAACTAA
* * * * * *
62049426 TATCTAAAATTAACCAAAACATATTAAAGAAAAAAGGTTTAGTGTGGCTGCTGGGATTCGAGCCC
66 AAACTAAAAGTAACAAAAACAAATTAAAGAAAAAAGGTTTAATGTGGCTGCTGGGATTCGAGCCC
62049491 AGGTCTCCA
131 AGGTCTCCA
62049500 CGGCCACAACGTGGAATTCTTACCACTAAACTACAGCCACAA
1 CGGCCACAACGTGGAATTCTTACCACTAAACTACAGCCACAA
62049542 GTTGACATAG
Statistics
Matches: 161, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
136 5 0.03
137 4 0.02
138 14 0.09
139 131 0.81
140 7 0.04
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (139 bp):
CGGCCACAACGTGGAATTCTTACCACTAAACTACAGCCACAACTTGTTAAAAGTCAAGAAACTAA
AAACTAAAAGTAACAAAAACAAATTAAAGAAAAAAGGTTTAATGTGGCTGCTGGGATTCGAGCCC
AGGTCTCCA
Found at i:62054271 original size:4 final size:4
Alignment explanation
Indices: 62054264--62054310 Score: 85
Period size: 4 Copynumber: 11.8 Consensus size: 4
62054254 ACACACACAC
*
62054264 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AAAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
62054311 CTCTTTACCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:62059612 original size:19 final size:19
Alignment explanation
Indices: 62059584--62059627 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
62059574 TTTAGGAATA
*
62059584 TTTTTATCAAAAAAATGTT
1 TTTTTATCAAAAAAAGGTT
*
62059603 TTTTTGTCAAAAAAAGGTT
1 TTTTTATCAAAAAAAGGTT
62059622 TTTTTA
1 TTTTTA
62059628 AAAACAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (19 bp):
TTTTTATCAAAAAAAGGTT
Found at i:62063481 original size:115 final size:114
Alignment explanation
Indices: 62063280--62063509 Score: 363
Period size: 115 Copynumber: 2.0 Consensus size: 114
62063270 TCATTTTCTG
*
62063280 GCCTTTTGTTTTGGTATGAAATCTAGCATTTGAATTAGGGTTTAAGGTGTTACTTTTATCTTGTT
1 GCCTTTTGTTTTGGTATGAAATCTAGCATTTGAATTAGGGTTTAAGGTGTTACTTTTATCTTGAT
* * *
62063345 TCTCGAAAGAATATCGGGTCATTTGAGATTGTTTAGTGTGTGTTTATGT
66 TCTCGAAAGAATATCAGGTCATTCGAGATTGTTTAGGGTGTGTTTATGT
*
62063394 GCCTTTTGTTTTGGTATTGAAATGTAGCATTTGAATTAGGGTTTAAGGTGTTACTTTTATGC-TG
1 GCCTTTTGTTTTGGTA-TGAAATCTAGCATTTGAATTAGGGTTTAAGGTGTTACTTTTAT-CTTG
* * *
62063458 ATTCTCGAAAGAATTTCAGGTCATTCGTGTTTGTTTAGGGTGTGTTTATGT
64 ATTCTCGAAAGAATATCAGGTCATTCGAGATTGTTTAGGGTGTGTTTATGT
62063509 G
1 G
62063510 TTACAAAGTT
Statistics
Matches: 106, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
114 16 0.15
115 89 0.84
116 1 0.01
ACGTcount: A:0.20, C:0.09, G:0.25, T:0.46
Consensus pattern (114 bp):
GCCTTTTGTTTTGGTATGAAATCTAGCATTTGAATTAGGGTTTAAGGTGTTACTTTTATCTTGAT
TCTCGAAAGAATATCAGGTCATTCGAGATTGTTTAGGGTGTGTTTATGT
Found at i:62063637 original size:270 final size:270
Alignment explanation
Indices: 62063148--62063664 Score: 797
Period size: 270 Copynumber: 1.9 Consensus size: 270
62063138 GGCATTGTTT
* **
62063148 TAGCATTTGAATTAGGGTTGAAGGTGATACTTTTATGCTGTTTCTCGAAAGAATTTTGGGTCATT
1 TAGCATTTGAATTAGGGTTGAAGGTGATACTTTTATGCTGATTCTCGAAAGAATTTCAGGTCATT
* * * *
62063213 TGAGATTGTTTAATGTGTGTTTGTGTGTTGCAAAGTTCAAGTAATACTTAATTATAGTCATTTTC
66 CGAGATTGTTTAAGGTGTGTTTATGTGTTACAAAGTTCAAGTAATACTTAATTATAGTCATTTTC
*
62063278 TGGCCTTTTGTTTTGGTATGAAATCTAGCATTTGAATTAGGGTTTAAGGTGTTACTTTTATCTTG
131 TGGCCTTCTGTTTTGGTATGAAATCTAGCATTTGAATTAGGGTTTAAGGTGTTACTTTTATCTTG
* * * *
62063343 TTTCTCGAAAGAATATCGGGTCATTTGAGATTGTTTAGTGTGTGTTTATGTGCCTTTTGTTTTGG
196 ATTCTCGAAAGAATATCAGGTCATTCGAGATTGTTTAGGGTGTGTTTATGTGCCTTTTGTTTTGG
62063408 TATTGAAATG
261 TATTGAAATG
* *
62063418 TAGCATTTGAATTAGGGTTTAAGGTGTTACTTTTATGCTGATTCTCGAAAGAATTTCAGGTCATT
1 TAGCATTTGAATTAGGGTTGAAGGTGATACTTTTATGCTGATTCTCGAAAGAATTTCAGGTCATT
* * *
62063483 CGTGTTTGTTTAGGGTGTGTTTATGTGTTACAAAGTTCAAGT-ATACTTAATTAT-GTTCATTTT
66 CGAGATTGTTTAAGGTGTGTTTATGTGTTACAAAGTTCAAGTAATACTTAATTATAG-TCATTTT
*
62063546 CTGGCCTTCTGTTTTGGTACTGAAATGTAGCATTTGAATTAGGGTTTAAGGTGTTACTTTTATGC
130 CTGGCCTTCTGTTTTGGTA-TGAAATCTAGCATTTGAATTAGGGTTTAAGGTGTTACTTTTAT-C
* * *
62063611 -TGATTCTCGAAAGAATTTCAGGTCATTCGTGTTTGTTTAGGGTGTGTTTATGTG
193 TTGATTCTCGAAAGAATATCAGGTCATTCGAGATTGTTTAGGGTGTGTTTATGTG
62063665 TTACAAAGTT
Statistics
Matches: 223, Mismatches: 21, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
268 1 0.00
269 37 0.17
270 184 0.83
271 1 0.00
ACGTcount: A:0.22, C:0.09, G:0.23, T:0.45
Consensus pattern (270 bp):
TAGCATTTGAATTAGGGTTGAAGGTGATACTTTTATGCTGATTCTCGAAAGAATTTCAGGTCATT
CGAGATTGTTTAAGGTGTGTTTATGTGTTACAAAGTTCAAGTAATACTTAATTATAGTCATTTTC
TGGCCTTCTGTTTTGGTATGAAATCTAGCATTTGAATTAGGGTTTAAGGTGTTACTTTTATCTTG
ATTCTCGAAAGAATATCAGGTCATTCGAGATTGTTTAGGGTGTGTTTATGTGCCTTTTGTTTTGG
TATTGAAATG
Found at i:62063676 original size:155 final size:155
Alignment explanation
Indices: 62063394--62063890 Score: 804
Period size: 155 Copynumber: 3.2 Consensus size: 155
62063384 GTGTTTATGT
* *
62063394 GCCTTTTGTTTTGGTATTGAAATGTAGCATTTGAATTAGGGTTTAAGGTGTTACTTTTATGCTGA
1 GCCTTCTGTTTTGGTACTGAAATGTAGCATTTGAATTAGGGTTTAAGGTGTTACTTTTATGCTGA
62063459 TTCTCGAAAGAATTTCAGGTCATTCGTGTTTGTTTAGGGTGTGTTTATGTGTTACAAAGTTCAAG
66 TTCTCGAAAGAATTTCAGGTCATTCGTGTTTGTTTAGGGTGTGTTTATGTGTTACAAAGTTCAAG
62063524 TATACTTAATTATGTTCATTTTCTG
131 TATACTTAATTATGTTCATTTTCTG
62063549 GCCTTCTGTTTTGGTACTGAAATGTAGCATTTGAATTAGGGTTTAAGGTGTTACTTTTATGCTGA
1 GCCTTCTGTTTTGGTACTGAAATGTAGCATTTGAATTAGGGTTTAAGGTGTTACTTTTATGCTGA
62063614 TTCTCGAAAGAATTTCAGGTCATTCGTGTTTGTTTAGGGTGTGTTTATGTGTTACAAAGTTCAAG
66 TTCTCGAAAGAATTTCAGGTCATTCGTGTTTGTTTAGGGTGTGTTTATGTGTTACAAAGTTCAAG
62063679 TATACTTAATTATGTTCATTTTCTG
131 TATACTTAATTATGTTCATTTTCTG
* *
62063704 GCCTTCTGTTTTGGTACTGAAATGTAGCATTTGAATTAGGGTTTAAGTTGTTACTTTTACT-CTC
1 GCCTTCTGTTTTGGTACTGAAATGTAGCATTTGAATTAGGGTTTAAGGTGTTACTTTTA-TGCTG
* * * * * **
62063768 TTTCTCGAAAGAATTTCAGGGTCATTTGAGATTGTTTAGTGTGTGTTTATGCATTACAAAGTTCA
65 ATTCTCGAAAGAATTTCA-GGTCATTCGTGTTTGTTTAGGGTGTGTTTATGTGTTACAAAGTTCA
*
62063833 AGTATACTTAATTATAG-TCA-TATCTG
129 AGTATACTTAATTAT-GTTCATTTTCTG
* *
62063859 GCCTTTTTATTTTGGTACTGAAATGT-GCATTT
1 GCC-TTCTGTTTTGGTACTGAAATGTAGCATTT
62063891 TGCTCTCTGA
Statistics
Matches: 324, Mismatches: 14, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
155 244 0.75
156 79 0.24
157 1 0.00
ACGTcount: A:0.23, C:0.11, G:0.21, T:0.45
Consensus pattern (155 bp):
GCCTTCTGTTTTGGTACTGAAATGTAGCATTTGAATTAGGGTTTAAGGTGTTACTTTTATGCTGA
TTCTCGAAAGAATTTCAGGTCATTCGTGTTTGTTTAGGGTGTGTTTATGTGTTACAAAGTTCAAG
TATACTTAATTATGTTCATTTTCTG
Found at i:62069203 original size:2 final size:2
Alignment explanation
Indices: 62069196--62069240 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
62069186 GATTCATACA
* * *
62069196 AT AT AT AT AT AT AT AT AT AT AT TT AT AT TT AT GAT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
62069239 AT
1 AT
62069241 TTAGAAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (2 bp):
AT
Found at i:62077636 original size:4 final size:4
Alignment explanation
Indices: 62077627--62077658 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
62077617 TGAATTGAGA
62077627 AATT AATT AATT AATT AAATT AATT AATT AAT
1 AATT AATT AATT AATT -AATT AATT AATT AAT
62077659 ATTTATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (4 bp):
AATT
Found at i:62077648 original size:17 final size:17
Alignment explanation
Indices: 62077626--62077658 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
62077616 TTGAATTGAG
62077626 AAATTAATTAATTAATT
1 AAATTAATTAATTAATT
62077643 AAATTAATTAATTAAT
1 AAATTAATTAATTAAT
62077659 ATTTATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATTAATTAATTAATT
Found at i:62080096 original size:17 final size:17
Alignment explanation
Indices: 62080076--62080108 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
62080066 ATAATAGCAA
62080076 TATCTAAATATAAATTG
1 TATCTAAATATAAATTG
*
62080093 TATCTAAATATTAATT
1 TATCTAAATATAAATT
62080109 AGGTAAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (17 bp):
TATCTAAATATAAATTG
Found at i:62080152 original size:61 final size:60
Alignment explanation
Indices: 62080017--62080153 Score: 152
Period size: 61 Copynumber: 2.2 Consensus size: 60
62080007 ATTTAGTAAA
* *
62080017 CTAATACAAATTTAGCATCTAAATATTAATTTGATAAAAATAATATTTAATAATAGCAATAT
1 CTAATACAAA-TT-GCATCTAAATATTAATTAGATAAAAATAATATTAAATAATAGCAATAT
* * * *
62080079 CTAAATATAAATTGTATCTAAATATTAATTAGGTAAAAACTAA-AGTTAAATAATTA-TAATAT
1 CT-AATACAAATTGCATCTAAATATTAATTAGATAAAAA-TAATA-TTAAATAA-TAGCAATAT
62080141 CTAATACAAATTG
1 CTAATACAAATTG
62080154 AACATTTAAC
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
61 34 0.53
62 21 0.33
63 9 0.14
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.36
Consensus pattern (60 bp):
CTAATACAAATTGCATCTAAATATTAATTAGATAAAAATAATATTAAATAATAGCAATAT
Found at i:62083312 original size:24 final size:24
Alignment explanation
Indices: 62083276--62083324 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
62083266 TGATCCCTAT
62083276 ATTTTTTTCCTTTTAAGTAATTTA
1 ATTTTTTTCCTTTTAAGTAATTTA
* * *
62083300 ATTTTTTTTCTTTTATGTTATTTA
1 ATTTTTTTCCTTTTAAGTAATTTA
62083324 A
1 A
62083325 ACTTTCCTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.67
Consensus pattern (24 bp):
ATTTTTTTCCTTTTAAGTAATTTA
Found at i:62101476 original size:18 final size:19
Alignment explanation
Indices: 62101437--62101477 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
62101427 GTTATTTGGA
*
62101437 TATTGTATAATTCTTGTTT
1 TATTGTATAATTCTTGTAT
62101456 TATTGT-TAATT-TTGCTAT
1 TATTGTATAATTCTTG-TAT
62101474 TATT
1 TATT
62101478 TTAGATAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 3 0.15
18 11 0.55
19 6 0.30
ACGTcount: A:0.22, C:0.05, G:0.10, T:0.63
Consensus pattern (19 bp):
TATTGTATAATTCTTGTAT
Found at i:62104247 original size:29 final size:29
Alignment explanation
Indices: 62104215--62104300 Score: 73
Period size: 30 Copynumber: 2.9 Consensus size: 29
62104205 CTTTTTTTAA
62104215 TCACTCAACTATGAATTTTTTAAATTTGG
1 TCACTCAACTATGAATTTTTTAAATTTGG
* * * ***
62104244 TCACTTAATTATGGATTTGTTTCTTTTTGG
1 TCACTCAACTATGAATTT-TTTAAATTTGG
* **
62104274 TCACCCAACTATGTGTTATTTTAAATT
1 TCACTCAACTATGAATT-TTTTAAATT
62104301 GGTTACCCTA
Statistics
Matches: 41, Mismatches: 14, Indels: 3
0.71 0.24 0.05
Matches are distributed among these distances:
29 15 0.37
30 25 0.61
31 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.49
Consensus pattern (29 bp):
TCACTCAACTATGAATTTTTTAAATTTGG
Found at i:62106115 original size:13 final size:13
Alignment explanation
Indices: 62106097--62106121 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62106087 GATTGAAATA
62106097 AAAAAAAAATTTT
1 AAAAAAAAATTTT
62106110 AAAAAAAAATTT
1 AAAAAAAAATTT
62106122 AATAAGTATA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAAAAAATTTT
Found at i:62110972 original size:116 final size:118
Alignment explanation
Indices: 62110780--62110991 Score: 322
Period size: 116 Copynumber: 1.8 Consensus size: 118
62110770 TTTGAAAAAC
* * *
62110780 GAAAACGCGGGAGAGTTTTGAATTTTTTTTGTTTTGTTTGATGGGTTTAAATCTTCTTCTAATCC
1 GAAAACGCGGGAGAGCTTTGAA-TTTTTTTGTTTTGTTTGATAGGTTCAAATCTTCTTCTAATCC
* *
62110845 CTTTGGTTTTTTAATATTTAAAATTTAGTCCCTCTATTTTTAATATGGAGGAAA
65 CTGTGATTTTTTAATATTTAAAATTTAGTCCCTCTATTTTTAATATGGAGGAAA
*
62110899 GAAAACGCGGGAGAGCTTTGAA-TTTTTT-TTTTGTTTTATAGG-TCAAACTCTTCTTCTAATCC
1 GAAAACGCGGGAGAGCTTTGAATTTTTTTGTTTTGTTTGATAGGTTCAAA-TCTTCTTCTAATCC
*
62110961 CTGTGATTTTTTAGTATTTAAAATTTAGTCC
65 CTGTGATTTTTTAATATTTAAAATTTAGTCC
62110992 TTTTTTTTAA
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
115 4 0.05
116 54 0.64
117 6 0.07
119 21 0.25
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (118 bp):
GAAAACGCGGGAGAGCTTTGAATTTTTTTGTTTTGTTTGATAGGTTCAAATCTTCTTCTAATCCC
TGTGATTTTTTAATATTTAAAATTTAGTCCCTCTATTTTTAATATGGAGGAAA
Found at i:62112790 original size:20 final size:20
Alignment explanation
Indices: 62112765--62112831 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
62112755 CCTTTTCTAT
62112765 TTAAAATATAATTTTAAAAA
1 TTAAAATATAATTTTAAAAA
**
62112785 TTAAAATATCAA-AATAATAAA
1 TTAAAATAT-AATTTTAA-AAA
*
62112806 TAAAAAT-TAATTTTAAAAA
1 TTAAAATATAATTTTAAAAA
*
62112825 TCAAAAT
1 TTAAAAT
62112832 CATATAGCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
19 11 0.29
20 16 0.42
21 11 0.29
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAAAATATAATTTTAAAAA
Found at i:62114030 original size:112 final size:114
Alignment explanation
Indices: 62113851--62114078 Score: 352
Period size: 112 Copynumber: 2.0 Consensus size: 114
62113841 TCAATCGATA
* * * *
62113851 ACCTTATCCCACTTACCATAATCAAAATCATAGATCAAAACAGCAGATATAACACATCTTAATCA
1 ACCTTATCCCACTCACCACAATCAAAACCATAGATC-AAACAGCAGATATAACACATCTTAACCA
*
62113916 TATGCAAAGATGAAAAATGT-CTTCAGGGGCCAGCTGATGCTTAGATTTT
65 TATGCAAAGATGAAAAATATGCTTCAGGGGCCAGCTGATGCTTAGATTTT
* *
62113965 ACCTTTTCCCACTCACCACAATCAAAACCATAGATC-AACAGCTGATATAACACATCTTAACCAT
1 ACCTTATCCCACTCACCACAATCAAAACCATAGATCAAACAGCAGATATAACACATCTTAACCAT
* *
62114029 ATGCAAAGATGAAAAATATGCTTGAGGGGTCAGCTGATGCTTAGATTTT
66 ATGCAAAGATGAAAAATATGCTTCAGGGGCCAGCTGATGCTTAGATTTT
62114078 A
1 A
62114079 GCTTCGGGTA
Statistics
Matches: 104, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
112 44 0.42
113 28 0.27
114 32 0.31
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.27
Consensus pattern (114 bp):
ACCTTATCCCACTCACCACAATCAAAACCATAGATCAAACAGCAGATATAACACATCTTAACCAT
ATGCAAAGATGAAAAATATGCTTCAGGGGCCAGCTGATGCTTAGATTTT
Found at i:62119473 original size:13 final size:13
Alignment explanation
Indices: 62119451--62119480 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
62119441 AGCAAGGTTG
*
62119451 TTGTTTAGTTACT
1 TTGTTGAGTTACT
62119464 TTGTTGAGTTACT
1 TTGTTGAGTTACT
62119477 TTGT
1 TTGT
62119481 AATGTTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.07, G:0.20, T:0.60
Consensus pattern (13 bp):
TTGTTGAGTTACT
Found at i:62123875 original size:20 final size:19
Alignment explanation
Indices: 62123839--62123881 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
62123829 AATGATTAAA
* *
62123839 AAAAATTAAAGTCATTTTC
1 AAAAATTAAAATAATTTTC
*
62123858 AAAAATTCAAAATAATTTTT
1 AAAAATT-AAAATAATTTTC
62123878 AAAA
1 AAAA
62123882 TTTTATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAAATTAAAATAATTTTC
Done.