Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold48
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: 4619657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18863 characters in sequence are not A, C, G, or T
File 5 of 27
Found at i:551210 original size:20 final size:21
Alignment explanation
Indices: 551185--551232 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
551175 AATAATTAAA
*
551185 ATAAAATTAATATTT-TTTAT
1 ATAAAATTAAAATTTATTTAT
551205 ATAAAA-TAAAATTTGATTTAT
1 ATAAAATTAAAATTT-ATTTAT
551226 ATAAAAT
1 ATAAAAT
551233 ACATTTGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.29
20 6 0.25
21 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
ATAAAATTAAAATTTATTTAT
Found at i:554581 original size:40 final size:39
Alignment explanation
Indices: 554477--554581 Score: 176
Period size: 39 Copynumber: 2.7 Consensus size: 39
554467 TTACCTCTTA
*
554477 TTTGT-TTTTTAATTTTTAATATTTTTATTTTAAAAATAT
1 TTTGTATTTTT-ATTTTTAATATTTTTATTTAAAAAATAT
554516 TTTGTATTTTTATTTTTAATATTTTTATTTAAAAAATAT
1 TTTGTATTTTTATTTTTAATATTTTTATTTAAAAAATAT
554555 TTTGTATTTTGTATTTTTAATATTTTT
1 TTTGTATTTT-TATTTTTAATATTTTT
554582 TAATATTTAT
Statistics
Matches: 63, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
39 42 0.67
40 21 0.33
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (39 bp):
TTTGTATTTTTATTTTTAATATTTTTATTTAAAAAATAT
Found at i:554676 original size:24 final size:24
Alignment explanation
Indices: 554634--554689 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
554624 ATTTAATATA
*
554634 ATAAA-TAAAATTATGCAATAATT
1 ATAAATTAAAATTATGCAATAAAT
*
554657 AGTAAATTAAAA-TATTCAATAAAT
1 A-TAAATTAAAATTATGCAATAAAT
554681 ATAAATTAA
1 ATAAATTAA
554690 TATAAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 9 0.31
24 15 0.52
25 5 0.17
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.34
Consensus pattern (24 bp):
ATAAATTAAAATTATGCAATAAAT
Found at i:555754 original size:27 final size:27
Alignment explanation
Indices: 555712--555767 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
555702 TTTAAAACAT
*
555712 ATTTTTTTAAAATTTAATAT-TTAATA
1 ATTTTTTTAAAATTTAATATATAAATA
*
555738 ATTTTTATTAAATTTTAATATATAAATA
1 ATTTTT-TTAAAATTTAATATATAAATA
555766 AT
1 AT
555768 ATATTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 6 0.23
27 13 0.50
28 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
ATTTTTTTAAAATTTAATATATAAATA
Found at i:555920 original size:2 final size:2
Alignment explanation
Indices: 555913--555954 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
555903 TACAGATCTC
555913 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
555955 TATTTATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:557302 original size:17 final size:17
Alignment explanation
Indices: 557265--557303 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
557255 GCTTTAGAAA
*
557265 AAAAAAAAATAAAAAAT
1 AAAAAAAAATAAAAAAC
*
557282 AAAAAAAAATAAAAACC
1 AAAAAAAAATAAAAAAC
557299 AAAAA
1 AAAAA
557304 GGGGAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.87, C:0.05, G:0.00, T:0.08
Consensus pattern (17 bp):
AAAAAAAAATAAAAAAC
Found at i:557558 original size:2 final size:2
Alignment explanation
Indices: 557553--557580 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
557543 ATTAAAACAA
557553 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
557581 CATAATTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:561685 original size:36 final size:37
Alignment explanation
Indices: 561645--561721 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 37
561635 AAGTACATAA
* *
561645 CAAAAACCAAAATTA-TCACTGCCACAATCTGAGTCT
1 CAAAAACCAAAATGAGTCACTACCACAATCTGAGTCT
***
561681 C-AAAACCAGGCTGAGTCACTACCACAATCTGAGTCT
1 CAAAAACCAAAATGAGTCACTACCACAATCTGAGTCT
561717 CAAAA
1 CAAAA
561722 CCAGGCTGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
35 9 0.26
36 22 0.65
37 3 0.09
ACGTcount: A:0.40, C:0.29, G:0.12, T:0.19
Consensus pattern (37 bp):
CAAAAACCAAAATGAGTCACTACCACAATCTGAGTCT
Found at i:561696 original size:18 final size:18
Alignment explanation
Indices: 561673--561729 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
561663 CTGCCACAAT
561673 CTGAGTCTCAAAACCAGG
1 CTGAGTCTCAAAACCAGG
* * * **
561691 CTGAGTCAC-TACCACAAT
1 CTGAGTCTCAAAAC-CAGG
561709 CTGAGTCTCAAAACCAGG
1 CTGAGTCTCAAAACCAGG
561727 CTG
1 CTG
561730 TGTCACTCCC
Statistics
Matches: 27, Mismatches: 10, Indels: 4
0.66 0.24 0.10
Matches are distributed among these distances:
17 2 0.07
18 23 0.85
19 2 0.07
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (18 bp):
CTGAGTCTCAAAACCAGG
Found at i:561722 original size:36 final size:36
Alignment explanation
Indices: 561660--561736 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 36
561650 ACCAAAATTA
*
561660 TCACTGCCACAATCTGAGTCTCAAAACCAGGCTGAG
1 TCACTACCACAATCTGAGTCTCAAAACCAGGCTGAG
*
561696 TCACTACCACAATCTGAGTCTCAAAACCAGGCTGTG
1 TCACTACCACAATCTGAGTCTCAAAACCAGGCTGAG
561732 TCACT
1 TCACT
561737 CCCTTTTTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (36 bp):
TCACTACCACAATCTGAGTCTCAAAACCAGGCTGAG
Found at i:563846 original size:17 final size:17
Alignment explanation
Indices: 563802--563851 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
563792 ATATTTTTAA
*
563802 AATTTAATAATT-TATTT
1 AATTT-ATAATTAAATTT
563819 AA-TTA-AA-TAAATTT
1 AATTTATAATTAAATTT
563833 AATTTATAATTAAATTT
1 AATTTATAATTAAATTT
563850 AA
1 AA
563852 ATATTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
13 1 0.04
14 8 0.29
15 4 0.14
16 4 0.14
17 11 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTTATAATTAAATTT
Found at i:563964 original size:20 final size:23
Alignment explanation
Indices: 563912--563970 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
563902 TATTTTTATT
563912 TAAATTTAATTATATAAATATAA
1 TAAATTTAATTATATAAATATAA
*
563935 TATAATTTTAA-TAT-TTAA-ATAA
1 TA-AA-TTTAATTATATAAATATAA
563957 TAAATTTAAATTAT
1 TAAATTT-AATTAT
563971 CATATTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
20 3 0.10
21 4 0.13
22 9 0.29
23 5 0.16
24 5 0.16
25 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAATTTAATTATATAAATATAA
Found at i:564744 original size:15 final size:15
Alignment explanation
Indices: 564696--564746 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
564686 AATCATTTTG
*
564696 AATATATTATTTAAA
1 AATAAATTATTTAAA
**
564711 AATAAAAAATGTT--A
1 AATAAATTAT-TTAAA
564725 AATAAATTATTTAAA
1 AATAAATTATTTAAA
564740 AATAAAT
1 AATAAAT
564747 AAATAAGCCA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 2 0.07
14 9 0.32
15 15 0.54
16 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (15 bp):
AATAAATTATTTAAA
Found at i:565065 original size:23 final size:24
Alignment explanation
Indices: 565017--565068 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
565007 TATTACTAAA
565017 AATAAAATAAAATTTAATTTAATT
1 AATAAAATAAAATTTAATTTAATT
*
565041 AATAAAAT-AAATTT-TTTTAATTT
1 AATAAAATAAAATTTAATTTAA-TT
565064 AATAA
1 AATAA
565069 CAACAACACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 5 0.19
23 13 0.50
24 8 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
AATAAAATAAAATTTAATTTAATT
Found at i:565189 original size:21 final size:20
Alignment explanation
Indices: 565164--565202 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
565154 TTATAAAAAT
565164 AAATAAATTAAAATATAATAC
1 AAATAAATTAAAA-ATAATAC
*
565185 AAATAACTTAAAAATAAT
1 AAATAAATTAAAAATAAT
565203 TAAACTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
AAATAAATTAAAAATAATAC
Found at i:565696 original size:25 final size:27
Alignment explanation
Indices: 565641--565729 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 27
565631 AGATGATAAT
* *
565641 TTTTTATAAATTAATTAA-ATTTAA-AAA
1 TTTTAATAAA-TAA-TAATATTTAATTAA
*
565668 TTTTAATAAATAATAATA-TTAA-TAT
1 TTTTAATAAATAATAATATTTAATTAA
*
565693 TTTTAATAAAAAATAATATTTAATTAA
1 TTTTAATAAATAATAATATTTAATTAA
565720 TTTTAA-AAAT
1 TTTTAATAAAT
565730 TTATACTAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
25 25 0.47
26 11 0.21
27 17 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TTTTAATAAATAATAATATTTAATTAA
Found at i:565769 original size:61 final size:59
Alignment explanation
Indices: 565651--565766 Score: 137
Period size: 61 Copynumber: 1.9 Consensus size: 59
565641 TTTTTATAAA
565651 TTAATTAAATTTAAAAATTTTAATAAATAATAATATTAATATTTTTAATAAAAAATAATAT
1 TTAATTAAATTTAAAAATTTTAATAAATAATAATATTAATATTTTT-AT-AAAAATAATAT
* *
565712 TTAATTAATTTTAAAAATTTATACT-AATAAATTAAATATTAATTATTTTT-TAAAA
1 TTAATTAAATTTAAAAATTT-TAATAAAT-AA-T-AATATTAA-TATTTTTATAAAA
565767 TAAAAATTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
61 22 0.46
62 9 0.19
63 2 0.04
64 8 0.17
65 7 0.15
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.47
Consensus pattern (59 bp):
TTAATTAAATTTAAAAATTTTAATAAATAATAATATTAATATTTTTATAAAAATAATAT
Found at i:565829 original size:22 final size:22
Alignment explanation
Indices: 565804--565864 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 22
565794 ATTATTATTT
565804 TTTAATAAAATTAAAAATAA-TA
1 TTTAATAAAATTAAAAA-AATTA
*
565826 TTTAATTAAATTTAAAAAAATTA
1 TTTAA-TAAAATTAAAAAAATTA
565849 TATTAAT-AAATTAAAA
1 T-TTAATAAAATTAAAA
565865 TATTAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 15 0.44
23 15 0.44
24 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTAATAAAATTAAAAAAATTA
Found at i:566250 original size:25 final size:24
Alignment explanation
Indices: 566104--566252 Score: 77
Period size: 25 Copynumber: 6.3 Consensus size: 24
566094 TTTATAAAAC
*
566104 ATATAATTAATATTTTAATTTGTTA
1 ATATAATTAAT-TTTTAATTTATTA
566129 ATATAATT--TTTTTAAATTTAATTA
1 ATATAATTAATTTTT-AATTT-ATTA
566153 A-AT-ATT-ATTTTTAATTTCATTAA
1 ATATAATTAATTTTTAATTT-ATT-A
* ** *
566176 AAATAA-TAATAATAAATTCT-TT-
1 ATATAATTAATTTTTAATT-TATTA
* *
566198 -T-TAATTTAATTTTTATTTTA-AA
1 ATATAA-TTAATTTTTAATTTATTA
*
566220 AAATAATTAATATTTTAATTTATTA
1 ATATAATTAAT-TTTTAATTTATTA
566245 ATATAATT
1 ATATAATT
566253 TTTTAAAAGT
Statistics
Matches: 93, Mismatches: 15, Indels: 32
0.66 0.11 0.23
Matches are distributed among these distances:
20 3 0.03
21 1 0.01
22 23 0.25
23 20 0.22
24 21 0.23
25 24 0.26
26 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (24 bp):
ATATAATTAATTTTTAATTTATTA
Found at i:566253 original size:116 final size:110
Alignment explanation
Indices: 566006--566278 Score: 347
Period size: 110 Copynumber: 2.4 Consensus size: 110
565996 TTTTAAATGT
* ** * *
566006 TTTTAATTTATTAATGTAAAATTTTTAAATTTAATTAAATATTATTTTTTATTTTATTAAAAAAT
1 TTTTAATTTATTAATATAATTTTTTTAAATTTAATTAAATATTATTTTTAATTTCATTAAAAAAT
566071 AATAATAATAAATACTTTTTATTTTTATAAAACATATAATTAATA
66 AATAATAATAAATACTTTTTATTTTTATAAAACATATAATTAATA
*
566116 TTTTAATTTGTTAATATAATTTTTTTAAATTTAATTAAATATTATTTTTAATTTCATT-AAAAAT
1 TTTTAATTTATTAATATAATTTTTTTAAATTTAATTAAATATTATTTTTAATTTCATTAAAAAAT
*
566180 AATAATAATAAATTCTTTTTAATTTAATTTTTATTTTAAAA-A-ATAATTAATA
66 AATAATAATAAATAC---TT--TTT-ATTTTTA---TAAAACATATAATTAATA
* * *
566232 TTTTAATTTATTAATATAATTTTTTAAAAGTTAATTAATTATT-TTTT
1 TTTTAATTTATTAATATAATTTTTTTAAATTTAATTAAATATTATTTT
566279 ATTAAAAATA
Statistics
Matches: 143, Mismatches: 11, Indels: 13
0.86 0.07 0.08
Matches are distributed among these distances:
109 20 0.14
110 52 0.36
112 2 0.01
114 3 0.02
115 11 0.08
116 49 0.34
117 1 0.01
118 5 0.03
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (110 bp):
TTTTAATTTATTAATATAATTTTTTTAAATTTAATTAAATATTATTTTTAATTTCATTAAAAAAT
AATAATAATAAATACTTTTTATTTTTATAAAACATATAATTAATA
Found at i:566333 original size:67 final size:68
Alignment explanation
Indices: 566198--566336 Score: 166
Period size: 67 Copynumber: 2.1 Consensus size: 68
566188 TAAATTCTTT
* *
566198 TTAATTTAATTTTTATTTTAAAAAATAATTAATATTTTAATTTATTAATATAATTTTTTAAAAGT
1 TTAATTTAATTTTTATTTAAAAAAATAATTAATATATTAATTTATTAATATAATTTTTTAAAAGT
566263 TAA
66 TAA
* *
566266 TTAA-TTATTTTTTA-TTAAAAATAATAATTAATATATT-A-TTATTTAT-TAAATTTTTT--AA
1 TTAATTTAATTTTTATTTAAAAA-AATAATTAATATATTAATTTATTAATAT-AATTTTTTAAAA
*
566324 TTTAA
64 GTTAA
566329 TTAATTTA
1 TTAATTTA
566337 TAAAAAAATT
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
63 10 0.16
64 4 0.06
65 15 0.24
66 7 0.11
67 23 0.37
68 4 0.06
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (68 bp):
TTAATTTAATTTTTATTTAAAAAAATAATTAATATATTAATTTATTAATATAATTTTTTAAAAGT
TAA
Found at i:566406 original size:12 final size:13
Alignment explanation
Indices: 566389--566419 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
566379 ATATTCATAA
566389 AAAAAATATTT-T
1 AAAAAATATTTAT
566401 AAAAAATATTTAT
1 AAAAAATATTTAT
566414 AAAAAA
1 AAAAAA
566420 AATTAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAAATATTTAT
Found at i:566428 original size:13 final size:13
Alignment explanation
Indices: 566385--566428 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
566375 TAACATATTC
566385 ATAAAAAAAATATT
1 ATAAAAAAAAT-TT
* *
566399 TTAAAAAATATTT
1 ATAAAAAAAATTT
*
566412 ATAAAAAAAATTA
1 ATAAAAAAAATTT
566425 ATAA
1 ATAA
566429 TTTAATAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAAAAAAAATTT
Found at i:566737 original size:30 final size:29
Alignment explanation
Indices: 566678--566741 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
566668 AATTTTTATA
*
566678 TAAAATATAAAATTTTAATTTTATCAAAT
1 TAAATTATAAAATTTTAATTTTATCAAAT
* *
566707 TAAATTATTAAATTTTTATTATTAAT-AAAT
1 TAAATTATAAAATTTTAATT-TT-ATCAAAT
566737 TAAAT
1 TAAAT
566742 CACTTACGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 17 0.57
30 11 0.37
31 2 0.07
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (29 bp):
TAAATTATAAAATTTTAATTTTATCAAAT
Found at i:568861 original size:18 final size:17
Alignment explanation
Indices: 568834--568870 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
568824 TTAAAAAATT
568834 AAATAATAATTTCTATAA
1 AAATAATAATTTCTA-AA
*
568852 AAATATTAATTTCTAAA
1 AAATAATAATTTCTAAA
568869 AA
1 AA
568871 TTTATCGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATAATAATTTCTAAA
Found at i:569622 original size:44 final size:41
Alignment explanation
Indices: 569527--569628 Score: 109
Period size: 44 Copynumber: 2.5 Consensus size: 41
569517 TATTTTATAA
* *
569527 TTTTAATTTAATTT-AAT-TTAAATTAAATAATAAAAATAT
1 TTTTAAATTATTTTAAATATTAAATTAAATAATAAAAATAT
* * *
569566 TTTTAAATTATTTATAAATATTAATATTAATATATTAATAATTT
1 TTTTAAATTATTT-TAAATATTAA-ATTAA-ATAATAAAAATAT
*
569610 TTTTATATTATTTTAAATA
1 TTTTAAATTATTTTAAATA
569629 ATATATAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
39 11 0.21
40 1 0.02
41 3 0.06
42 4 0.08
43 11 0.21
44 22 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (41 bp):
TTTTAAATTATTTTAAATATTAAATTAAATAATAAAAATAT
Found at i:569652 original size:43 final size:44
Alignment explanation
Indices: 569565--569652 Score: 101
Period size: 44 Copynumber: 2.0 Consensus size: 44
569555 AATAAAAATA
* * *
569565 TTTTTAAATTATTTATAAATATTAATATTAATATATTAATAATT
1 TTTTTAAATTATTTATAAATAATAATATAAATATATCAATAATT
*
569609 TTTTTATATTATTT-TAAATAAT-ATATAAAT-TATCAGATCAATT
1 TTTTTAAATTATTTATAAATAATAATATAAATATATCA-AT-AATT
569652 T
1 T
569653 AAATTAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
41 4 0.11
42 9 0.24
43 12 0.32
44 13 0.34
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (44 bp):
TTTTTAAATTATTTATAAATAATAATATAAATATATCAATAATT
Found at i:570117 original size:2 final size:2
Alignment explanation
Indices: 570110--570158 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
570100 TTGCTTTGAA
570110 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
570152 AT CT AT A
1 AT AT AT A
570159 AGATTAAGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:575819 original size:5 final size:5
Alignment explanation
Indices: 575776--575867 Score: 107
Period size: 5 Copynumber: 17.8 Consensus size: 5
575766 CTAAAGAATG
* *
575776 ATAAT ATTAAT -TAAT A-ATT ATAAT ATAAAA ATAATT ATAAT ATAAT
1 ATAAT A-TAAT ATAAT ATAAT ATAAT AT-AAT ATAA-T ATAAT ATAAT
575822 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAAAT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT--AAT ATAAT ATAA
575868 ATATTTTAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
4 7 0.09
5 52 0.68
6 12 0.16
7 5 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:575895 original size:21 final size:21
Alignment explanation
Indices: 575794--575889 Score: 81
Period size: 22 Copynumber: 4.6 Consensus size: 21
575784 AATTAATAAT
* * *
575794 TATAATATAAAAATAATTATAA
1 TATAATATAAATAT-TTTAAAA
** *
575816 TATAATAT-AATATAATATAA
1 TATAATATAAATATTTTAAAA
* *
575836 TATAATATAATATAATATAAAA
1 TATAATATAA-ATATTTTAAAA
575858 TATAATATAAATATTTTAAAA
1 TATAATATAAATATTTTAAAA
575879 -ATAAT-TAAATA
1 TATAATATAAATA
575890 AATTTTTTTA
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
19 6 0.09
20 19 0.29
21 14 0.22
22 26 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TATAATATAAATATTTTAAAA
Found at i:579509 original size:2 final size:2
Alignment explanation
Indices: 579502--579530 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
579492 TTCTCAGTCA
579502 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
579531 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:579535 original size:2 final size:2
Alignment explanation
Indices: 579530--579557 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
579520 TCTCTCTCTC
579530 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
579558 ATGTATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:582345 original size:2 final size:2
Alignment explanation
Indices: 582338--582380 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
582328 GACCTACCGT
582338 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
582380 T
1 T
582381 TTTTCCTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:582810 original size:6 final size:7
Alignment explanation
Indices: 582788--582845 Score: 55
Period size: 7 Copynumber: 8.0 Consensus size: 7
582778 ATTTTGAAAC
582788 TTTAATT
1 TTTAATT
582795 TTTAATT
1 TTTAATT
582802 TTTAATT
1 TTTAATT
*
582809 TTTAATAA
1 TTTAAT-T
*
582817 TTTAATAA
1 TTTAAT-T
582825 TTT-ATT
1 TTTAATT
*
582831 ATTATATT
1 TTTA-ATT
582839 TTTAATT
1 TTTAATT
582846 ATAAATAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
6 2 0.05
7 25 0.57
8 17 0.39
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (7 bp):
TTTAATT
Found at i:582853 original size:37 final size:37
Alignment explanation
Indices: 582799--582875 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
582789 TTAATTTTTA
* * *
582799 ATTTTTAATTTTTAATAATTTAATA-ATTTATTATTAT
1 ATTTTTAATTATAAATAATTTAATATATTT-TTAATAT
582836 ATTTTTAATTATAAATAATTTAATATATTTTTAATAT
1 ATTTTTAATTATAAATAATTTAATATATTTTTAATAT
582873 ATT
1 ATT
582876 ACAATATAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 32 0.89
38 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (37 bp):
ATTTTTAATTATAAATAATTTAATATATTTTTAATAT
Found at i:582889 original size:26 final size:26
Alignment explanation
Indices: 582834--582894 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
582824 ATTTATTATT
* * *
582834 ATATTTTTAATTATAAATAATTTAAT
1 ATATTTTTAATTATAAACAATATAAC
*
582860 ATATTTTTAA-TATATTACAATATAAC
1 ATATTTTTAATTATA-AACAATATAAC
*
582886 ATATATTTA
1 ATATTTTTA
582895 TTTGTTATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 4 0.14
26 25 0.86
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (26 bp):
ATATTTTTAATTATAAACAATATAAC
Found at i:583036 original size:18 final size:18
Alignment explanation
Indices: 583015--583053 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
583005 TAATCTATTT
*
583015 TTTAAATATATTTTTTTA
1 TTTAAATATATTTTTTAA
*
583033 TTTAAATTTATTTTTTAA
1 TTTAAATATATTTTTTAA
583051 TTT
1 TTT
583054 TATTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTAAATATATTTTTTAA
Found at i:583048 original size:31 final size:31
Alignment explanation
Indices: 583002--583064 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
582992 TGAAATCAAA
583002 ATTTAATCTATTTTTTAAATATATT-TTTTT
1 ATTTAATCTATTTTTTAAATATATTATTTTT
* * *
583032 ATTTAAATTTATTTTTTAATTTTATTATTTTT
1 ATTT-AATCTATTTTTTAAATATATTATTTTT
583064 A
1 A
583065 CTCAACCTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 4 0.14
31 18 0.64
32 6 0.21
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (31 bp):
ATTTAATCTATTTTTTAAATATATTATTTTT
Found at i:586729 original size:24 final size:24
Alignment explanation
Indices: 586701--586780 Score: 117
Period size: 24 Copynumber: 3.3 Consensus size: 24
586691 TGCACGGAAT
*
586701 AGATAATCAGCAAGT-ACCTGCAAA
1 AGATAATCAGCAA-TCGCCTGCAAA
*
586725 AGATAGTCAGCAATCGCCTGCAAA
1 AGATAATCAGCAATCGCCTGCAAA
*
586749 AGATAGTCAGCAATCGCCTGCAAA
1 AGATAATCAGCAATCGCCTGCAAA
586773 AGATAATC
1 AGATAATC
586781 TCAAATTGTC
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
23 1 0.02
24 51 0.98
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (24 bp):
AGATAATCAGCAATCGCCTGCAAA
Found at i:587736 original size:2 final size:2
Alignment explanation
Indices: 587729--587754 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
587719 AAGGTTCCTT
587729 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
587755 ACAGAGTTAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:595480 original size:16 final size:16
Alignment explanation
Indices: 595459--595492 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
595449 TTAAGTTATT
595459 TATAATCTTATTTAAA
1 TATAATCTTATTTAAA
* *
595475 TATAATTTTTTTTAAA
1 TATAATCTTATTTAAA
595491 TA
1 TA
595493 ATTTTAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TATAATCTTATTTAAA
Found at i:595730 original size:3 final size:3
Alignment explanation
Indices: 595722--595750 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
595712 TGGGGATGAC
595722 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
595751 TTACATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:597194 original size:213 final size:213
Alignment explanation
Indices: 596827--597255 Score: 662
Period size: 213 Copynumber: 2.0 Consensus size: 213
596817 AACATAATTA
* * *
596827 CATAAAATCTATACACTATTAAAACGTGTTGTACATGTGTCGTATTTTCATATCGTATCTAAAAT
1 CATAAAATCCATACACTATTAAAACGTGTCGTACATGTGTCGTATTTTCATATCATATCTAAAAT
* * * *
596892 TGTCAGTTCTACTCTCTCTATTACTTTGAATCATAATACAGTAGAGGCCACTAAAGCCATCTACA
66 TGTCAATTCTACTCTCGCTACTACTTCGAATCATAATACAGTAGAGGCCACTAAAGCCATCTACA
596957 GCAGCAGTAGGCAGCACACATGGAAGATTATCGAATGCACTAACGGTTAAAAAAAATTCGAAATA
131 GCAGCAGTAGGCAGCACACATGGAAGATTATCGAATGCACTAACGGTTAAAAAAAATTCGAAATA
597022 AATGTTAAATATAAAATG
196 AATGTTAAATATAAAATG
* * * *
597040 CATAAAATCCATACA-TGATTAAAGCGTGTCGTACATGTGTCGTGTTTTCATGTCATGTCTAAAA
1 CATAAAATCCATACACT-ATTAAAACGTGTCGTACATGTGTCGTATTTTCATATCATATCTAAAA
* *
597104 TTGTCAATTCTACTTTCGCTGCTACTTCGAATCATAATACAGTAGAGGCCACTAAAGCCATCTAC
65 TTGTCAATTCTACTCTCGCTACTACTTCGAATCATAATACAGTAGAGGCCACTAAAGCCATCTAC
* * * * *
597169 AGTAGCAGTAGGCAGCTCACATGGAAGATTATCGGATGCACTAATGGTTAAAAGAAATTCGAAAT
130 AGCAGCAGTAGGCAGCACACATGGAAGATTATCGAATGCACTAACGGTTAAAAAAAATTCGAAAT
* *
597234 AAATGTTAAATATGAGATG
195 AAATGTTAAATATAAAATG
597253 CAT
1 CAT
597256 TTAATATGTT
Statistics
Matches: 195, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
212 1 0.01
213 194 0.99
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (213 bp):
CATAAAATCCATACACTATTAAAACGTGTCGTACATGTGTCGTATTTTCATATCATATCTAAAAT
TGTCAATTCTACTCTCGCTACTACTTCGAATCATAATACAGTAGAGGCCACTAAAGCCATCTACA
GCAGCAGTAGGCAGCACACATGGAAGATTATCGAATGCACTAACGGTTAAAAAAAATTCGAAATA
AATGTTAAATATAAAATG
Found at i:600333 original size:2 final size:2
Alignment explanation
Indices: 600326--600369 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
600316 TGCTGTTTGG
*
600326 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
600368 AT
1 AT
600370 TGCTCATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:605393 original size:16 final size:17
Alignment explanation
Indices: 605376--605475 Score: 62
Period size: 16 Copynumber: 5.6 Consensus size: 17
605366 AAATTTTAAA
605376 AAATATTTTAATATAAAAT
1 AAATATTTTAATAT--AAT
*
605395 AAATA-TTAAATATAAT
1 AAATATTTTAATATAAT
* *
605411 AAATA-ATTAATAAAAT
1 AAATATTTTAATATAAT
* *
605427 AAATA-TTTGATTTAAT
1 AAATATTTTAATATAAT
605443 AATATAATGTTTAATATAAAAT
1 AA-AT-AT-TTTAATAT--AAT
*
605465 AAAAATTTTAA
1 AAATATTTTAA
605476 ATATTTAAAT
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
16 30 0.47
17 2 0.03
18 8 0.12
19 10 0.16
20 8 0.12
21 1 0.02
22 5 0.08
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
AAATATTTTAATATAAT
Found at i:605443 original size:32 final size:33
Alignment explanation
Indices: 605388--605450 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
605378 ATATTTTAAT
605388 ATAAAATAAATATTAAATATAATAA-ATAATTA
1 ATAAAATAAATATTAAATATAATAATATAATTA
** *
605420 ATAAAATAAATATTTGATTTAATAATATAAT
1 ATAAAATAAATATTAAATATAATAATATAAT
605451 GTTTAATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 22 0.81
33 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (33 bp):
ATAAAATAAATATTAAATATAATAATATAATTA
Found at i:605829 original size:74 final size:73
Alignment explanation
Indices: 605743--605906 Score: 195
Period size: 74 Copynumber: 2.2 Consensus size: 73
605733 TTAAATATTC
* * * **
605743 TTTA-TTATTAATAAATTCATCACTATTTATAAATAAAAAATTTAAATCTATTGAACGATTTTAA
1 TTTATTTAATAATAAATTCATCA-TATTTAAAAATAAAAAATTTAAATCTATTAAAAAATTTTAA
*
605807 TTAAATAAA
65 TTAAAAAAA
* * * *
605816 TTTATTTAATAATAAAATTTATTATATTTAAAAATAAAAATTTTAATTCTATTAAAAAATTTTAA
1 TTTATTTAATAAT-AAATTCATCATATTTAAAAATAAAAAATTTAAATCTATTAAAAAATTTTAA
605881 TTAAAAAAA
65 TTAAAAAAA
* *
605890 GTTATTTGATAATAAAT
1 TTTATTTAATAATAAAT
605907 AAAAAGAGTT
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
73 8 0.10
74 61 0.79
75 8 0.10
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (73 bp):
TTTATTTAATAATAAATTCATCATATTTAAAAATAAAAAATTTAAATCTATTAAAAAATTTTAAT
TAAAAAAA
Found at i:605868 original size:25 final size:22
Alignment explanation
Indices: 605814--605875 Score: 63
Period size: 25 Copynumber: 2.7 Consensus size: 22
605804 TAATTAAATA
*
605814 AATTTATTTAATAATAAAATTT
1 AATTTATTTAAAAATAAAATTT
605836 -ATTATATTTAAAAATAAAAATTTT
1 AATT-TATTTAAAAAT-AAAA-TTT
*
605860 AATTCTATTAAAAAAT
1 AATT-TATTTAAAAAT
605876 TTTAATTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 3 0.09
22 10 0.30
23 4 0.12
24 3 0.09
25 13 0.39
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTTATTTAAAAATAAAATTT
Found at i:607858 original size:17 final size:17
Alignment explanation
Indices: 607836--607868 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
607826 ATTAAACTTT
*
607836 TATAAAATATCAAAATA
1 TATAAAATATAAAAATA
607853 TATAAAATATAAAAAT
1 TATAAAATATAAAAAT
607869 TCAAAGAAAA
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:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
TATAAAATATAAAAATA
Found at i:608425 original size:14 final size:14
Alignment explanation
Indices: 608387--608425 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
608377 AATTTTTATG
*
608387 TATTTAAAAATTTA
1 TATTTAAATATTTA
*
608401 TATTTATATATTTA
1 TATTTAAATATTTA
608415 TATTTAAATAT
1 TATTTAAATAT
608426 GAGTAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TATTTAAATATTTA
Found at i:613864 original size:6 final size:7
Alignment explanation
Indices: 613845--613870 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
613835 ATACATTATG
613845 AATTTTT
1 AATTTTT
613852 AATTTTT
1 AATTTTT
613859 AATTTTT
1 AATTTTT
613866 AATTT
1 AATTT
613871 GATACTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
AATTTTT
Found at i:630587 original size:2 final size:2
Alignment explanation
Indices: 630582--630633 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
630572 ATATTATCCC
* * *
630582 AT AT AT AG AT AT AT AT AG AT AT AT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
630624 AT AT AT AT AT
1 AT AT AT AT AT
630634 TTCATTACTT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:631945 original size:17 final size:18
Alignment explanation
Indices: 631913--631946 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
631903 TAATTAATCA
631913 TTTTTAAGAAAGGATTAT
1 TTTTTAAGAAAGGATTAT
*
631931 TTTTTTAGAAA-GATTA
1 TTTTTAAGAAAGGATTA
631947 ATCCTCTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (18 bp):
TTTTTAAGAAAGGATTAT
Found at i:632413 original size:21 final size:20
Alignment explanation
Indices: 632389--632456 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 20
632379 TCATTCCCTC
*
632389 TTAAAAGAAAATTAATTTTT
1 TTAAAAGAAAATCAATTTTT
**
632409 CTTAAAA-AAAATCAATACTT
1 -TTAAAAGAAAATCAATTTTT
632429 TTAAAACGAAAATCAATATTTT
1 TTAAAA-GAAAATCAAT-TTTT
632451 TTAAAA
1 TTAAAA
632457 ATGATTCATC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 6 0.15
20 10 0.26
21 15 0.38
22 8 0.21
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (20 bp):
TTAAAAGAAAATCAATTTTT
Found at i:632875 original size:90 final size:85
Alignment explanation
Indices: 632727--632888 Score: 243
Period size: 90 Copynumber: 1.8 Consensus size: 85
632717 TAATATATAA
* * *
632727 AATTTAATAAAAAAAACTCGATCTATGAAAATGTATTCCATCCTTTGTTTAAAATTGTTTTATGT
1 AATTTAATAAAAAAAACTCCATCTATGAAAATGTATTCCATCCTTTGCTTAAAATTGTTTTATGC
632792 GCACTGAGTTTTTATCTTTT
66 GCACTGAGTTTTTATCTTTT
*
632812 AATTTAATAAAAAAAAATATCTCCATCTATGAACTATGTATTCCATCCTTTGCTTAAAATTGTTT
1 AATTTAAT--AAAAAAA-A-CTCCATCTATGAA-AATGTATTCCATCCTTTGCTTAAAATTGTTT
632877 TATGCGCACTGA
61 TATGCGCACTGA
632889 ATTTAATGAA
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
85 8 0.12
87 7 0.10
88 1 0.01
89 12 0.18
90 40 0.59
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (85 bp):
AATTTAATAAAAAAAACTCCATCTATGAAAATGTATTCCATCCTTTGCTTAAAATTGTTTTATGC
GCACTGAGTTTTTATCTTTT
Found at i:638227 original size:32 final size:31
Alignment explanation
Indices: 638112--638233 Score: 83
Period size: 32 Copynumber: 3.8 Consensus size: 31
638102 ATTTATACCG
638112 TATTTATATATTTTTATATCATAATTATATTTAAAA
1 TATTTATATATTTTT-TAT-ATAA--A-ATTTAAAA
* *
638148 TATTT-TATA--TTTCATATAAATTTTAAAA
1 TATTTATATATTTTTTATATAAAATTTAAAA
* *
638176 TGA-TAAT-TATTCATATTATATAAAATTTAAAA
1 T-ATTTATATATT--TTTTATATAAAATTTAAAA
*
638208 TATTTATATTATTTTTTATATTAAAT
1 TATTTATA-TATTTTTTATATAAAAT
638234 AATATTTTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
28 11 0.16
29 3 0.04
31 5 0.07
32 33 0.49
33 3 0.04
34 4 0.06
35 4 0.06
36 5 0.07
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (31 bp):
TATTTATATATTTTTTATATAAAATTTAAAA
Found at i:638238 original size:28 final size:28
Alignment explanation
Indices: 638206--638333 Score: 77
Period size: 28 Copynumber: 4.5 Consensus size: 28
638196 TAAAATTTAA
638206 AATATTTATATTATTTTTTATATTAAAT
1 AATATTTATATTATTTTTTATATTAAAT
*
638234 AATATTT-TAATTATTTAATTTATATTATAAA
1 AATATTTAT-ATTATTT--TTTATATTA-AAT
* * * * * *
638265 AAT-TTTAAAATA-CTTATAAATT-TAT
1 AATATTTATATTATTTTTTATATTAAAT
* *
638290 ACCATATTTATATTATTTTTAATATTATAT
1 A--ATATTTATATTATTTTTTATATTAAAT
638320 AAT-TTTATCATTAT
1 AATATTTAT-ATTAT
638334 CTAAATGTTG
Statistics
Matches: 75, Mismatches: 14, Indels: 22
0.68 0.13 0.20
Matches are distributed among these distances:
25 2 0.03
27 14 0.19
28 28 0.37
29 7 0.09
30 19 0.25
31 5 0.07
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (28 bp):
AATATTTATATTATTTTTTATATTAAAT
Found at i:638315 original size:9 final size:9
Alignment explanation
Indices: 638188--638327 Score: 54
Period size: 9 Copynumber: 14.9 Consensus size: 9
638178 ATAATTATTC
638188 ATATTATATA
1 ATATT-TATA
* *
638198 AAATTTAAA
1 ATATTTATA
638207 ATATTTATA
1 ATATTTATA
* * *
638216 TTATTTTTT
1 ATATTTATA
*
638225 ATATTAAATA
1 ATATT-TATA
638235 ATATTT-TA
1 ATATTTATA
638243 ATTATTTA-A
1 A-TATTTATA
*
638252 TTTATATTATAA
1 -ATAT-TTAT-A
* *
638264 AAATTTTAAA
1 ATA-TTTATA
*
638274 ATACTTATA
1 ATATTTATA
638283 A-ATTTATA
1 ATATTTATA
638291 CCATATTTATA
1 --ATATTTATA
* *
638302 TTATTTTTA
1 ATATTTATA
638311 ATATTATATA
1 ATATT-TATA
638321 AT-TTTAT
1 ATATTTAT
638328 CATTATCTAA
Statistics
Matches: 94, Mismatches: 24, Indels: 26
0.65 0.17 0.18
Matches are distributed among these distances:
8 12 0.13
9 47 0.50
10 22 0.23
11 11 0.12
12 2 0.02
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (9 bp):
ATATTTATA
Found at i:640875 original size:16 final size:16
Alignment explanation
Indices: 640856--640917 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 16
640846 TTTAAAACCA
*
640856 AAAAGAATTTAAATCT
1 AAAATAATTTAAATCT
** *
640872 AAAATAATAAAAATTT
1 AAAATAATTTAAATCT
*
640888 AAAATAATTTAAATTT
1 AAAATAATTTAAATCT
* *
640904 AACATAATCTAAAT
1 AAAATAATTTAAAT
640918 TTACCTATAC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.34
Consensus pattern (16 bp):
AAAATAATTTAAATCT
Found at i:640897 original size:32 final size:32
Alignment explanation
Indices: 640856--640920 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
640846 TTTAAAACCA
640856 AAAAGAATTTAAATCTAAAATAATAAAAATTT
1 AAAAGAATTTAAATCTAAAATAATAAAAATTT
* * * **
640888 AAAATAATTTAAATTTAACATAATCTAAATTT
1 AAAAGAATTTAAATCTAAAATAATAAAAATTT
640920 A
1 A
640921 CCTATACGCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (32 bp):
AAAAGAATTTAAATCTAAAATAATAAAAATTT
Found at i:640918 original size:16 final size:16
Alignment explanation
Indices: 640865--640920 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
640855 AAAAAGAATT
* *
640865 TAAATCTAAAATAATA
1 TAAATTTAAAATAATC
* *
640881 AAAATTTAAAATAATT
1 TAAATTTAAAATAATC
*
640897 TAAATTTAACATAATC
1 TAAATTTAAAATAATC
640913 TAAATTTA
1 TAAATTTA
640921 CCTATACGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATTTAAAATAATC
Found at i:642558 original size:2 final size:2
Alignment explanation
Indices: 642551--642580 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
642541 AGTCAAGTAG
642551 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
642581 GTGTATATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:650182 original size:97 final size:97
Alignment explanation
Indices: 649996--650182 Score: 275
Period size: 97 Copynumber: 1.9 Consensus size: 97
649986 ATTTAAATTG
* *
649996 AATACAAATTTAAATTATTAATTAATAATAAAAAAATTTAGATATTTTATAAATTAAACAGATTT
1 AATACAAATTTAAATAATAAATTAATAATAAAAAAATTTAGATATTTTATAAATTAAACAGATTT
* *
650061 AAATAGTTAAAAATTTTTACATAAATTATTTT
66 AAATAGTTAAAAAGTTATACATAAATTATTTT
* * * *
650093 AATACAAATTTAAATAATAAATTAATAATAAATAAATTTAGATATTTTATTAATTTAACAGGTTT
1 AATACAAATTTAAATAATAAATTAATAATAAAAAAATTTAGATATTTTATAAATTAAACAGATTT
** *
650158 AAATAGTTCCAAAGTTATATATAAA
66 AAATAGTTAAAAAGTTATACATAAA
650183 ATATCTAATT
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
97 79 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (97 bp):
AATACAAATTTAAATAATAAATTAATAATAAAAAAATTTAGATATTTTATAAATTAAACAGATTT
AAATAGTTAAAAAGTTATACATAAATTATTTT
Found at i:650329 original size:20 final size:20
Alignment explanation
Indices: 650293--650338 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
650283 AATAAATTAA
* *
650293 ATAAA-TATTTTACATTTTT
1 ATAAATTATTTAACATTTAT
*
650312 ATAAATTATTTAATATTTAT
1 ATAAATTATTTAACATTTAT
650332 A-AAATTA
1 ATAAATTA
650339 ATTTTAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
ATAAATTATTTAACATTTAT
Found at i:652232 original size:12 final size:13
Alignment explanation
Indices: 652176--652229 Score: 62
Period size: 12 Copynumber: 4.4 Consensus size: 13
652166 ATAAAATTTA
652176 AATATTAAATTAT
1 AATATTAAATTAT
*
652189 AATTATT--TTTA-
1 AA-TATTAAATTAT
652200 AATATTAAATTAT
1 AATATTAAATTAT
652213 AA-ATTAAATTAT
1 AATATTAAATTAT
652225 AATAT
1 AATAT
652230 AAAAATTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
10 4 0.12
11 2 0.06
12 18 0.53
13 6 0.18
14 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AATATTAAATTAT
Found at i:652238 original size:31 final size:30
Alignment explanation
Indices: 652164--652250 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 30
652154 TACGTGACTG
*
652164 ATATAAAATTTAAA-TATTAAATTATAATTAT
1 ATATAAAAATTAAATTA-TAAATTA-AATTAT
* * *
652195 TTTTAAATATTAAATTATAAATTAAATTAT
1 ATATAAAAATTAAATTATAAATTAAATTAT
* *
652225 AATATAAAAATTAAATGATATATTAA
1 -ATATAAAAATTAAATTATAAATTAA
652251 TCTTTTTAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
30 6 0.13
31 37 0.82
32 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (30 bp):
ATATAAAAATTAAATTATAAATTAAATTAT
Found at i:652396 original size:17 final size:17
Alignment explanation
Indices: 652376--652422 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
652366 AAAATAATGT
652376 AAAA-ATTTAAATATAAA
1 AAAATATTTAAA-ATAAA
*
652393 AAAATATTTAAAATAAT
1 AAAATATTTAAAATAAA
*
652410 ATAAT-TTTAAAAT
1 AAAATATTTAAAAT
652423 TTTAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 8 0.30
17 12 0.44
18 7 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATATTTAAAATAAA
Found at i:652421 original size:25 final size:25
Alignment explanation
Indices: 652393--652440 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
652383 TAAATATAAA
*
652393 AAAATATTTAAAA-TAATATAATTTT
1 AAAAT-TTTAAAATTAATAAAATTTT
652418 AAAATTTTAAAATTAATAAAATT
1 AAAATTTTAAAATTAATAAAATT
652441 ATTTTATCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
AAAATTTTAAAATTAATAAAATTTT
Found at i:655439 original size:18 final size:19
Alignment explanation
Indices: 655416--655462 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
655406 GTGATGGAAA
655416 ATGCTGGGCTGAA-AGGAT
1 ATGCTGGGCTGAAGAGGAT
655434 ATGCTGGGCT-AAGAGGAT
1 ATGCTGGGCTGAAGAGGAT
*
655452 ATGCGGGGCTG
1 ATGCTGGGCTG
655463 CTGTGATAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 2 0.08
18 24 0.92
ACGTcount: A:0.23, C:0.13, G:0.43, T:0.21
Consensus pattern (19 bp):
ATGCTGGGCTGAAGAGGAT
Found at i:659440 original size:1 final size:1
Alignment explanation
Indices: 659434--659460 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
659424 CTCCTATCTT
659434 CCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCC
659461 AAGATTCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:663715 original size:22 final size:22
Alignment explanation
Indices: 663658--663724 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
663648 TATATATCAT
*
663658 AATATAATATTTTAAATTTAAA-A
1 AATAT-ATA-TTTAAAATTAAATA
*
663681 AAT-TA-AATTAAAATTAAATA
1 AATATATATTTAAAATTAAATA
* *
663701 AATATATATTTAAAAATATATA
1 AATATATATTTAAAATTAAATA
663723 AA
1 AA
663725 ATTAAAATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
19 10 0.28
20 5 0.14
21 3 0.08
22 15 0.42
23 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AATATATATTTAAAATTAAATA
Found at i:663729 original size:16 final size:15
Alignment explanation
Indices: 663685--663731 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
663675 TTAAAAAATT
663685 AAAT-TAAAATTAAA
1 AAATATAAAATTAAA
* *
663699 TAAATATATATTTAAA
1 -AAATATAAAATTAAA
663715 AATATATAAAATTAAA
1 AA-ATATAAAATTAAA
663731 A
1 A
663732 TTAATTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 6 0.23
16 20 0.77
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATATAAAATTAAA
Found at i:663943 original size:28 final size:28
Alignment explanation
Indices: 663889--663943 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
663879 TAAAAATAAA
* * *
663889 TTTAATTTAATTTAAATAATTATAATTT
1 TTTAATTTAATATAAAAAATCATAATTT
663917 TTTAATTTATATATAAAAAATCA-AATT
1 TTTAATTTA-ATATAAAAAATCATAATT
663944 GAATCCTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 13 0.57
29 10 0.43
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTAATTTAATATAAAAAATCATAATTT
Found at i:663955 original size:2 final size:2
Alignment explanation
Indices: 663950--663982 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
663940 AATTGAATCC
663950 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
663983 CCTTAATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:668624 original size:39 final size:39
Alignment explanation
Indices: 668570--668649 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
668560 GTGATATATG
668570 ATGATTTAGTATTAATCAATTAAATCACATTAGTATTTT
1 ATGATTTAGTATTAATCAATTAAATCACATTAGTATTTT
*
668609 ATGATTTAGTGTTAATCAATTAAATCACATTAGTATTTT
1 ATGATTTAGTATTAATCAATTAAATCACATTAGTATTTT
668648 AT
1 AT
668650 TACAATGATG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (39 bp):
ATGATTTAGTATTAATCAATTAAATCACATTAGTATTTT
Found at i:669450 original size:12 final size:12
Alignment explanation
Indices: 669435--669481 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
669425 AAATTTAAAA
*
669435 ATTTATTTTATT
1 ATTTATTATATT
669447 ATTTATTATATT
1 ATTTATTATATT
**
669459 A-TTAAAATATT
1 ATTTATTATATT
669470 ATTT-TTATATT
1 ATTTATTATATT
669481 A
1 A
669482 ATATTTGTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 15 0.52
12 14 0.48
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTATTATATT
Found at i:669610 original size:27 final size:28
Alignment explanation
Indices: 669539--669611 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 28
669529 ATAATAATTT
* *
669539 AAATTAAATAAAATTAACTTAAATTTATAA
1 AAATTAATTAAAA--AATTTAAATTTATAA
669569 AAATT--TTATATAAAATTTAAA-TTATAA
1 AAATTAATTA-A-AAAATTTAAATTTATAA
669596 AAATTAATTAAAAAAT
1 AAATTAATTAAAAAAT
669612 AATTCAACTA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
27 16 0.43
28 10 0.27
29 4 0.11
30 7 0.19
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (28 bp):
AAATTAATTAAAAAATTTAAATTTATAA
Found at i:669726 original size:19 final size:18
Alignment explanation
Indices: 669689--669724 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
669679 CACTTAACAA
669689 TAAAATTTAAAATAATAT
1 TAAAATTTAAAATAATAT
669707 TAAAATTT--AATAATAT
1 TAAAATTTAAAATAATAT
669723 TA
1 TA
669725 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
18 8 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATTTAAAATAATAT
Found at i:670389 original size:5 final size:5
Alignment explanation
Indices: 670329--670366 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
670319 ATTTTTACTT
* *
670329 ATTTA AGTTA ATTTA ATTTA ATTTA AATTA ATTTA ATT
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATT
670367 AATAAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (5 bp):
ATTTA
Found at i:670411 original size:26 final size:26
Alignment explanation
Indices: 670355--670417 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
670345 TTTAATTTAA
* **
670355 ATTAATTTAATTAATAAAAAATTTAT
1 ATTAATTTAAATAATAAAAAATAGAT
*
670381 TTTAATTTAAAT-ATAAAAATATAGAT
1 ATTAATTTAAATAATAAAAA-ATAGAT
*
670407 ATTAATATAAA
1 ATTAATTTAAA
670418 ATGATGTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
25 7 0.23
26 23 0.77
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTAATTTAAATAATAAAAAATAGAT
Found at i:670624 original size:17 final size:16
Alignment explanation
Indices: 670590--670666 Score: 109
Period size: 16 Copynumber: 4.8 Consensus size: 16
670580 AAAAATGATT
*
670590 TAATTTAAAATTAAAA
1 TAATTTAAATTTAAAA
*
670606 TAATATAAATTTAAAAA
1 TAATTTAAATTT-AAAA
670623 TAATTTAAATTTAAAA
1 TAATTTAAATTTAAAA
*
670639 TAATTTAAATATAAAA
1 TAATTTAAATTTAAAA
*
670655 TAATTAAAATTT
1 TAATTTAAATTT
670667 TTAAATTAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
16 39 0.72
17 15 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATTTAAATTTAAAA
Found at i:670637 original size:33 final size:32
Alignment explanation
Indices: 670590--670666 Score: 109
Period size: 33 Copynumber: 2.4 Consensus size: 32
670580 AAAAATGATT
* *
670590 TAATTTAAAATTAAAATAATATAAATTTAAAAA
1 TAATTTAAATTTAAAATAATATAAATAT-AAAA
*
670623 TAATTTAAATTTAAAATAATTTAAATATAAAA
1 TAATTTAAATTTAAAATAATATAAATATAAAA
*
670655 TAATTAAAATTT
1 TAATTTAAATTT
670667 TTAAATTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 15 0.38
33 25 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (32 bp):
TAATTTAAATTTAAAATAATATAAATATAAAA
Found at i:673675 original size:14 final size:13
Alignment explanation
Indices: 673657--673703 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 13
673647 TAAATTTTAA
673657 AAAAAATAATTAT
1 AAAAAATAATTAT
673670 AAAAAAT-ATTAT
1 AAAAAATAATTAT
* *
673682 -TAAAATAATTGT
1 AAAAAATAATTAT
673694 GAAAAAATAA
1 -AAAAAATAA
673704 AATAAAATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.18
12 9 0.32
13 7 0.25
14 7 0.25
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (13 bp):
AAAAAATAATTAT
Found at i:673709 original size:24 final size:23
Alignment explanation
Indices: 673654--673711 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
673644 GAATAAATTT
673654 TAAAA-AAAATAATTATAAAAAA
1 TAAAATAAAATAATTATAAAAAA
* * *
673676 TATTATTAAAATAATTGTGAAAAAA
1 TA-AAATAAAATAATTAT-AAAAAA
673701 TAAAATAAAAT
1 TAAAATAAAAT
673712 CTGGGTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
22 2 0.07
23 1 0.04
24 17 0.61
25 8 0.29
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.29
Consensus pattern (23 bp):
TAAAATAAAATAATTATAAAAAA
Found at i:678918 original size:18 final size:19
Alignment explanation
Indices: 678895--678950 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 19
678885 TAATTATATT
678895 TTTTAATTTTATAA-ATAA
1 TTTTAATTTTATAATATAA
*** *
678913 TTTTAATAAAATAATATAT
1 TTTTAATTTTATAATATAA
678932 TTTTAATTTTA-AATATAA
1 TTTTAATTTTATAATATAA
678950 T
1 T
678951 AAAATAATTA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
18 18 0.62
19 11 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTAATTTTATAATATAA
Found at i:678961 original size:18 final size:19
Alignment explanation
Indices: 678940--678977 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
678930 ATTTTTAATT
*
678940 TTAAATATAA-TAAAATAA
1 TTAAATAAAATTAAAATAA
678958 TTAAATAAAATTAAAATAA
1 TTAAATAAAATTAAAATAA
678977 T
1 T
678978 CACATAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TTAAATAAAATTAAAATAA
Found at i:679287 original size:20 final size:19
Alignment explanation
Indices: 679258--679305 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
679248 ATGAGAGAAA
679258 TTTT-TTTATG-TATTTATAT
1 TTTTATTTATGTTATTT-T-T
679277 TTTTATTTATGTTATTTTT
1 TTTTATTTATGTTATTTTT
679296 TTATTATTTA
1 TT-TTATTTA
679306 AAGTATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 7 0.27
20 14 0.54
21 5 0.19
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (19 bp):
TTTTATTTATGTTATTTTT
Found at i:679291 original size:17 final size:16
Alignment explanation
Indices: 679260--679305 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
679250 GAGAGAAATT
*
679260 TTTTTATGTATTTATA
1 TTTTTATTTATTTATA
*
679276 TTTTTATTTATGTTATT
1 TTTTTATTTAT-TTATA
679293 TTTTTA-TTATTTA
1 TTTTTATTTATTTA
679306 AAGTATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 3 0.11
16 14 0.52
17 10 0.37
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (16 bp):
TTTTTATTTATTTATA
Found at i:679551 original size:26 final size:25
Alignment explanation
Indices: 679506--679556 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
679496 TTTATGCGTG
*
679506 TTAATATTATTTTTTGTGTTATGTT
1 TTAATATTATTTTTTATGTTATGTT
*
679531 TTAATTATT-TTTATTTATGTTGTGTT
1 TTAA-TATTATTT-TTTATGTTATGTT
679557 CTTATCATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.69
Consensus pattern (25 bp):
TTAATATTATTTTTTATGTTATGTT
Found at i:685235 original size:7 final size:7
Alignment explanation
Indices: 685208--685280 Score: 51
Period size: 7 Copynumber: 9.9 Consensus size: 7
685198 GGATCTATCA
*
685208 TTCTTTC
1 TTCTTTT
*
685215 TTATTTT
1 TTCTTTT
685222 TTC-TTT
1 TTCTTTT
685228 TTCTTTTT
1 TTC-TTTT
685236 TTCTTTT
1 TTCTTTT
685243 TTCTTTT
1 TTCTTTT
685250 CCTT-TTTCT
1 --TTCTTT-T
685259 TCTCTTTT
1 T-TCTTTT
*
685267 TTTTTTT
1 TTCTTTT
685274 GTTCTTT
1 -TTCTTT
685281 GATTTTCTCA
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
6 6 0.11
7 24 0.45
8 17 0.32
9 6 0.11
ACGTcount: A:0.01, C:0.16, G:0.01, T:0.81
Consensus pattern (7 bp):
TTCTTTT
Found at i:685243 original size:15 final size:14
Alignment explanation
Indices: 685211--685280 Score: 68
Period size: 15 Copynumber: 4.5 Consensus size: 14
685201 TCTATCATTC
685211 TTTCTTATTTTTTCTT
1 TTTCTT-TTTTTT-TT
685227 TTTCTTTTTTTCTTT
1 TTTCTTTTTTT-TTT
685242 TTTCTTTTCCTTTTTCT
1 TTTCTTTT--TTTTT-T
*
685259 TCTCTTTTTTTTTT
1 TTTCTTTTTTTTTT
685273 TGTTCTTT
1 T-TTCTTT
685281 GATTTTCTCA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
14 2 0.04
15 25 0.53
16 9 0.19
17 11 0.23
ACGTcount: A:0.01, C:0.16, G:0.01, T:0.81
Consensus pattern (14 bp):
TTTCTTTTTTTTTT
Found at i:685279 original size:32 final size:33
Alignment explanation
Indices: 685219--685280 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
685209 TCTTTCTTAT
*
685219 TTTTTCTTTTTCTTTTTTTCTTTTTTCTTTTCC
1 TTTTTCTTTCTCTTTTTTTCTTTTTTCTTTTCC
685252 TTTTTC-TTCTCTTTTTTT-TTTTGTTCTTT
1 TTTTTCTTTCTCTTTTTTTCTTTT-TTCTTT
685281 GATTTTCTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 4 0.15
32 17 0.63
33 6 0.22
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (33 bp):
TTTTTCTTTCTCTTTTTTTCTTTTTTCTTTTCC
Found at i:686508 original size:20 final size:20
Alignment explanation
Indices: 686485--686528 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
686475 ATAAATACAA
*
686485 TTAAGTCTTTGTTAATATTT
1 TTAAGTATTTGTTAATATTT
* *
686505 TTAATTATTTTTTAATATTT
1 TTAAGTATTTGTTAATATTT
686525 TTAA
1 TTAA
686529 AATTTGAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (20 bp):
TTAAGTATTTGTTAATATTT
Found at i:689571 original size:17 final size:17
Alignment explanation
Indices: 689535--689580 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
689525 AAATATAATT
*
689535 AATTTTTTATTTTAAAA
1 AATTTTATATTTTAAAA
689552 AATTTTATATATTT-AAA
1 AATTTTATAT-TTTAAAA
689569 AA-TTTATATTTT
1 AATTTTATATTTT
689581 TTATAATCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 3 0.11
16 7 0.26
17 14 0.52
18 3 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTTTATATTTTAAAA
Found at i:689611 original size:17 final size:16
Alignment explanation
Indices: 689582--689615 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
689572 TTATATTTTT
*
689582 TATAATCATATTTAAA
1 TATAATCAAATTTAAA
689598 TATATATCAAATTTAAA
1 TATA-ATCAAATTTAAA
689615 T
1 T
689616 TTTAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
TATAATCAAATTTAAA
Found at i:689628 original size:30 final size:29
Alignment explanation
Indices: 689594--689656 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
689584 TAATCATATT
* *
689594 TAAATA-TATATCAAATTTAAATTTTAAATA
1 TAAATATTATA-CAAATTAAAAATTT-AATA
*
689624 TAAATATTTTACAAATTAAAAATTTAATA
1 TAAATATTATACAAATTAAAAATTTAATA
689653 TAAA
1 TAAA
689657 ATGTAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 8 0.28
30 18 0.62
31 3 0.10
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (29 bp):
TAAATATTATACAAATTAAAAATTTAATA
Found at i:692180 original size:2 final size:2
Alignment explanation
Indices: 692173--692216 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
692163 CAATTTGTTT
*
692173 TA TA TA TA CA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
692213 TA TA
1 TA TA
692217 GTTTACATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:693815 original size:20 final size:20
Alignment explanation
Indices: 693771--693809 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
693761 CTGGCTTGAC
693771 TCCTCGTAGAAGCAAGAGTA
1 TCCTCGTAGAAGCAAGAGTA
693791 TCCTCGTAGAAGCAAGAGT
1 TCCTCGTAGAAGCAAGAGT
693810 GACCTCAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.21
Consensus pattern (20 bp):
TCCTCGTAGAAGCAAGAGTA
Found at i:694589 original size:113 final size:113
Alignment explanation
Indices: 694391--694595 Score: 383
Period size: 113 Copynumber: 1.8 Consensus size: 113
694381 ACATGTGAGA
*
694391 ACAGATAGATAGTGCATATTCATATAACAGACGGGTAAATCTAAATCCACTTGCCATCTTACATG
1 ACAGATAGATAGTGCATATTCATATAACAGACAGGTAAATCTAAATCCACTTGCCATCTTACATG
*
694456 TGAAAGGAACACAATCTTACCATATCCGTCACACTGTGATCTTGAATG
66 TGAAAGGAACACAATCTTACCACATCCGTCACACTGTGATCTTGAATG
*
694504 ACAGATGGATAGTGCATATTCATATAACAGACAGGTAAATCTAAATCCACTTGCCATCTTACATG
1 ACAGATAGATAGTGCATATTCATATAACAGACAGGTAAATCTAAATCCACTTGCCATCTTACATG
694569 TGAAAGGAACACAATCTTACCACATCC
66 TGAAAGGAACACAATCTTACCACATCC
694596 ATCTAGTTTT
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 89 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (113 bp):
ACAGATAGATAGTGCATATTCATATAACAGACAGGTAAATCTAAATCCACTTGCCATCTTACATG
TGAAAGGAACACAATCTTACCACATCCGTCACACTGTGATCTTGAATG
Found at i:701292 original size:15 final size:14
Alignment explanation
Indices: 701265--701291 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
701255 TCTTTATATA
701265 TTTATTTAAAAAAT
1 TTTATTTAAAAAAT
701279 TTTATTTAAAAAA
1 TTTATTTAAAAAA
701292 AATAAAAGTT
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:0.00, T:0.48
Consensus pattern (14 bp):
TTTATTTAAAAAAT
Found at i:701327 original size:17 final size:17
Alignment explanation
Indices: 701315--701346 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
701305 TTAATTTTAA
701315 AATTATT-TTAATTATT
1 AATTATTGTTAATTATT
701331 AATTATTGTTAATTAT
1 AATTATTGTTAATTAT
701347 ATTTTAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
AATTATTGTTAATTATT
Found at i:701365 original size:28 final size:27
Alignment explanation
Indices: 701308--701383 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 27
701298 AGTTTACTTA
* *
701308 ATTTTAAAATTATTTTAATTATTAATT
1 ATTTTAAATTTATTTTAATTATTAAGT
* *
701335 ATTGTT-AATTATATTTTAATTGTTCAGT
1 ATT-TTAAATT-TATTTTAATTATTAAGT
701363 ATTTTAAATTTATTCTTAATT
1 ATTTTAAATTTATT-TTAATT
701384 TTATATGATT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
27 12 0.29
28 29 0.71
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (27 bp):
ATTTTAAATTTATTTTAATTATTAAGT
Found at i:702684 original size:24 final size:25
Alignment explanation
Indices: 702646--702693 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
702636 TATGTATATA
* *
702646 TATTTTTATATAAA-TATATTTAAT
1 TATTTTTAAAAAAATTATATTTAAT
702670 TATTTTTAAAAAAATTTATATTTA
1 TATTTTTAAAAAAA-TTATATTTA
702694 TAAAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
26 8 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTTTTAAAAAAATTATATTTAAT
Found at i:702864 original size:21 final size:21
Alignment explanation
Indices: 702840--702897 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
702830 AAGATACTAA
702840 TATATATATATTTAAAAAAAT
1 TATATATATATTTAAAAAAAT
**
702861 TATATATATATTT-TTAAAAT
1 TATATATATATTTAAAAAAAT
*
702881 AAT-TATATATTTAAAAA
1 TATATATATATTTAAAAA
702898 TTTTAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 9 0.29
20 9 0.29
21 13 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATATATATATTTAAAAAAAT
Found at i:702865 original size:23 final size:23
Alignment explanation
Indices: 702839--702890 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
702829 TAAGATACTA
702839 ATATATATATATTTAAAAAAATT
1 ATATATATATATTTAAAAAAATT
* *
702862 ATATATATATTTTTAAAATAATT
1 ATATATATATATTTAAAAAAATT
702885 ATATAT
1 ATATAT
702891 TTAAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATATATATATTTAAAAAAATT
Found at i:702866 original size:19 final size:19
Alignment explanation
Indices: 702842--702897 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
702832 GATACTAATA
702842 TATATATATTTAAAAAAAT
1 TATATATATTTAAAAAAAT
***
702861 TATATATATATTTTTAAAAT
1 TATATATAT-TTAAAAAAAT
*
702881 AATTATATATTTAAAAA
1 TA-TATATATTTAAAAA
702898 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
19 9 0.32
20 12 0.43
21 7 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATATATATTTAAAAAAAT
Found at i:704051 original size:43 final size:43
Alignment explanation
Indices: 704003--704137 Score: 261
Period size: 43 Copynumber: 3.1 Consensus size: 43
703993 TTAATTATTT
704003 TTAAAAATATTTTATCAAAGATTTGAACAATAATTTTATATAA
1 TTAAAAATATTTTATCAAAGATTTGAACAATAATTTTATATAA
704046 TTAAAAATATTTTATCAAAGATTTGAACAATAATTTTATATAA
1 TTAAAAATATTTTATCAAAGATTTGAACAATAATTTTATATAA
704089 TTAAAAATATTTTATCAAAGATTTGAACAATAATTTTATATAA
1 TTAAAAATATTTTATCAAAGATTTGAACAATAATTTTATATAA
*
704132 TCAAAA
1 TTAAAA
704138 TTACAACAGA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 91 1.00
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (43 bp):
TTAAAAATATTTTATCAAAGATTTGAACAATAATTTTATATAA
Found at i:710555 original size:33 final size:33
Alignment explanation
Indices: 710502--710590 Score: 88
Period size: 33 Copynumber: 2.6 Consensus size: 33
710492 TACAAAAAAT
* *
710502 ATAATATAAATATATAAATATATTAAAATTTAC
1 ATAAAATAAATATATAAATATATAAAAATTTAC
* * * *
710535 ATAAAATAAATTTATTAATATGTAAAAATTTAT
1 ATAAAATAAATATATAAATATATAAAAATTTAC
*
710568 ATAAATATATAATAATTTAAATA
1 ATAAA-ATA-AAT-ATATAAATA
710591 CGAATATAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
33 32 0.73
34 3 0.07
35 3 0.07
36 6 0.14
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (33 bp):
ATAAAATAAATATATAAATATATAAAAATTTAC
Found at i:710565 original size:18 final size:20
Alignment explanation
Indices: 710542--710586 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
710532 TACATAAAAT
*
710542 AAATTTAT-T-AATATGTAA
1 AAATTTATATAAATATATAA
710560 AAATTTATATAAATATATAA
1 AAATTTATATAAATATATAA
*
710580 TAATTTA
1 AAATTTA
710587 AATACGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
19 1 0.04
20 14 0.61
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
AAATTTATATAAATATATAA
Found at i:710584 original size:20 final size:18
Alignment explanation
Indices: 710499--710586 Score: 60
Period size: 18 Copynumber: 4.8 Consensus size: 18
710489 TGATACAAAA
*
710499 AATATAATATAAATATATA-
1 AATAT-ATA-AAATTTATAT
*
710518 AATATATTAAAATTTACAT
1 AATATA-TAAAATTTATAT
710537 AA-A-AT-AAATTTAT-T
1 AATATATAAAATTTATAT
*
710551 AATATGTAAAAATTTATAT
1 AATATAT-AAAATTTATAT
710570 AAATATATAATAATTTA
1 -AATATATAA-AATTTA
710587 AATACGAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 17
0.71 0.06 0.22
Matches are distributed among these distances:
14 3 0.05
15 8 0.15
16 2 0.04
17 1 0.02
18 17 0.31
19 12 0.22
20 12 0.22
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (18 bp):
AATATATAAAATTTATAT
Found at i:711086 original size:22 final size:22
Alignment explanation
Indices: 711047--711088 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
711037 AAATTGTAGT
*
711047 ATTAAATTTTTATAATTAATAA
1 ATTAAATTTATATAATTAATAA
711069 ATTAAA-TTATATATATTAAT
1 ATTAAATTTATATA-ATTAAT
711089 TTTAGGGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTAAATTTATATAATTAATAA
Found at i:717772 original size:4 final size:4
Alignment explanation
Indices: 717759--717788 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
717749 TGCCATTATT
717759 TTTA -TTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
717789 TTATATAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:718187 original size:16 final size:17
Alignment explanation
Indices: 718166--718197 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
718156 AAAAATATAT
718166 ATATATAT-ATATTAAA
1 ATATATATGATATTAAA
718182 ATATATATGATATTAA
1 ATATATATGATATTAA
718198 TTATTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATATATATGATATTAAA
Found at i:718241 original size:16 final size:18
Alignment explanation
Indices: 718210--718242 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
718200 ATTAATTTAT
718210 TAATTTTATATAAATATA
1 TAATTTTATATAAATATA
718228 TAATTTT-T-TAAATAT
1 TAATTTTATATAAATAT
718243 TATCATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATTTTATATAAATATA
Found at i:720282 original size:15 final size:15
Alignment explanation
Indices: 720235--720282 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
720225 ACAACTTAAA
*
720235 TTTTTTTCTCCTTTC
1 TTTTCTTCTCCTTTC
*
720250 TTCTCTTCTCCTTTC
1 TTTTCTTCTCCTTTC
720265 TTTTCTT-TCCTTCTC
1 TTTTCTTCTCCTT-TC
720280 TTT
1 TTT
720283 GCCTGCTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 5 0.17
15 24 0.83
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTCTTCTCCTTTC
Found at i:720400 original size:12 final size:11
Alignment explanation
Indices: 720364--720410 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
720354 AAGTTAGATA
720364 AATAT-AAAA-
1 AATATAAAAAT
* *
720373 AATTTAAACAT
1 AATATAAAAAT
720384 AATATAAAAATT
1 AATATAAAAA-T
720396 AATATAAAAAT
1 AATATAAAAAT
720407 AATA
1 AATA
720411 CGAATACACG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 4 0.13
10 3 0.10
11 13 0.42
12 11 0.35
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:720595 original size:21 final size:21
Alignment explanation
Indices: 720569--720619 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
720559 TACATAAAAT
720569 AAAATA-AAT-TATTAATATATA
1 AAAATATAATATATTAA-ATA-A
*
720590 AAAATATAATATTTTAAATAA
1 AAAATATAATATATTAAATAA
720611 AAAATATAA
1 AAAATATAA
720620 ATACAAACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 16 0.59
22 6 0.22
23 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATATAATATATTAAATAA
Found at i:720656 original size:4 final size:4
Alignment explanation
Indices: 720649--720694 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
720639 AAAATTTTCC
* * *
720649 CTTT CTTT C-TT CTTT CTTT CTTT -TTT TTTT TTTT TTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
720695 TTCAGCTGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
3 6 0.15
4 33 0.85
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (4 bp):
CTTT
Found at i:720665 original size:11 final size:10
Alignment explanation
Indices: 720649--720697 Score: 52
Period size: 11 Copynumber: 5.1 Consensus size: 10
720639 AAAATTTTCC
720649 CTTTCTTTCTT
1 CTTTCTTT-TT
720660 CTTTCTTTCTT
1 CTTTCTTT-TT
720671 -TTT-TTTTT
1 CTTTCTTTTT
720679 -TTT-TTTTT
1 CTTTCTTTTT
720687 CTTTCTTTTT
1 CTTTCTTTTT
720697 C
1 C
720698 AGCTGAAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
8 10 0.28
9 6 0.17
10 9 0.25
11 11 0.31
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:725953 original size:20 final size:20
Alignment explanation
Indices: 725928--725968 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
725918 TTTTATACCA
725928 TATATATAG-ATGTATGTATG
1 TATATAT-GCATGTATGTATG
725948 TATATATGCATGTATGTATG
1 TATATATGCATGTATGTATG
725968 T
1 T
725969 TTCTTTCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (20 bp):
TATATATGCATGTATGTATG
Done.