Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold71
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: 5741892
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 121862 characters in sequence are not A, C, G, or T
File 18 of 33
Found at i:2836387 original size:20 final size:20
Alignment explanation
Indices: 2836340--2836401 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 20
2836330 TTATATATTT
*
2836340 TATATTTATTTAATTTTTTATA
1 TATATTTATATAA-TTTTTA-A
*
2836362 TTTATATTATATAAATTTTTAA
1 TATAT-TTATAT-AATTTTTAA
2836384 TATATTTATATAATTTTT
1 TATATTTATATAATTTTT
2836402 TTTATATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 7 0.20
21 6 0.17
22 9 0.26
23 11 0.31
24 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TATATTTATATAATTTTTAA
Found at i:2836407 original size:20 final size:20
Alignment explanation
Indices: 2836337--2836410 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 20
2836327 ATTTTATATA
*
2836337 TTTTATATTTATTTAATTTT
1 TTTTATATTTATATAATTTT
*
2836357 TTATATTTATATTATATAAATTTT
1 TT-T-TATAT-TTATAT-AATTTT
**
2836381 TAATATATTTATATAATTTT
1 TTTTATATTTATATAATTTT
2836401 TTTTATATTT
1 TTTTATATTT
2836411 TTTACATTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
20 16 0.37
21 7 0.16
22 8 0.19
23 5 0.12
24 7 0.16
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTATATTTATATAATTTT
Found at i:2837842 original size:25 final size:24
Alignment explanation
Indices: 2837814--2837885 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
2837804 TTATGCTAAG
2837814 TTTAATAATTCAGA-ATATAAATTAA
1 TTTAA-AATT-AGAGATATAAATTAA
*
2837839 TTTAAAATTTGAGATATAAATTAA
1 TTTAAAATTAGAGATATAAATTAA
* *
2837863 TTTAAAATTTGAGATAAAAATTA
1 TTTAAAATTAGAGATATAAATTA
2837886 TATCTTATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
23 2 0.05
24 37 0.84
25 5 0.11
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.40
Consensus pattern (24 bp):
TTTAAAATTAGAGATATAAATTAA
Found at i:2837855 original size:24 final size:24
Alignment explanation
Indices: 2837828--2837885 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
2837818 ATAATTCAGA
2837828 ATATAAATTAATTTAAAATTTGAG
1 ATATAAATTAATTTAAAATTTGAG
2837852 ATATAAATTAATTTAAAATTTGAG
1 ATATAAATTAATTTAAAATTTGAG
*
2837876 ATAAAAATTA
1 ATATAAATTA
2837886 TATCTTATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (24 bp):
ATATAAATTAATTTAAAATTTGAG
Found at i:2846606 original size:101 final size:102
Alignment explanation
Indices: 2846412--2846983 Score: 299
Period size: 101 Copynumber: 5.6 Consensus size: 102
2846402 CTATATATAA
* **
2846412 TTTAAAATTAATAAAATTATCCGATTTAAA-ATGTAATTTTATTAATT-TATTAAATTTAAATTA
1 TTTAAAATTAATAATATT-T-TTATTTAAATATGTAATTTTATTAATTAT-TTAAATTTAAATTA
* ** * ****
2846475 ATAAATATTTAAAAATAAAGTTATGGTGATATTAA-TTTT
63 ATAAATATTTAAAAATAAAGTCATCCTGATATCAAGCAAC
* *
2846514 TTTAAAATTAATAATATTTTTATTTAAATATATAATGTTATTAATTATTTAAATTTAAATTAATA
1 TTTAAAATTAATAATATTTTTATTTAAATATGTAATTTTATTAATTATTTAAATTTAAATTAATA
**
2846579 AATATTTAAAAATAGGGTCCA-CCTGATATCAAGCAAC
66 AATATTTAAAAATAAAGT-CATCCTGATATCAAGCAAC
* *
2846616 TTTATAATTAACAAACTATTTTTATTTAAATATGTAATTTTTATTTAATTTATTTAAA-TT---T
1 TTTAAAATTAA-TAA-TATTTTTATTTAAATATGTAA-TTTTA-TTAA-TTATTTAAATTTAAAT
* * * * * *** * *
2846677 GAATAAAT-GTTAAAAATAAA-TGAT-GTAAATACCCTTTTGAAAA
61 TAATAAATATTTAAAAATAAAGTCATCCT-GATA---TCAAGCAAC
* * *
2846720 TTTAAAAATTAACAA-AGTTATCCTT-TTTGAA-AT-TAGTTTTATTAATT-TATTAAATTTAAA
1 TTT-AAAATTAATAATA-TT-T--TTATTTAAATATGTAATTTTATTAATTAT-TTAAATTTAAA
* * * * * * *
2846780 TTAATAAATAGTT-AAAA-AAATTTA-CGTGATATTAATCTAC
60 TTAATAAATATTTAAAAATAAAGTCATCCTGATATCAAGCAAC
*
2846820 TTT-AAATTAATAAAATTTTTATTTAAATATGTAATTTTATTAATTATTTAAATTTAAATTAATA
1 TTTAAAATTAATAATATTTTTATTTAAATATGTAATTTTATTAATTATTTAAATTTAAATTAAT-
* * ** * * * *
2846884 AAATTTTTTAAAA-AATTTCA-CATGATATTAAACGAC
65 AAATATTTAAAAATAAAGTCATCCTGATATCAAGCAAC
* * * * *
2846920 TTTAAGATTAATAA-AGTTTCCCTATTTAAATACGTTATTTTTATTAATTTGTTTAAATTTAAAT
1 TTTAAAATTAATAATA-TTT--TTATTTAAATATG-TAATTTTATTAA-TTATTTAAATTTAAAT
2846984 AAATCAACTA
Statistics
Matches: 371, Mismatches: 59, Indels: 77
0.73 0.12 0.15
Matches are distributed among these distances:
95 2 0.01
96 5 0.01
97 3 0.01
98 40 0.11
99 9 0.02
100 48 0.13
101 79 0.21
102 44 0.12
103 31 0.08
104 59 0.16
105 34 0.09
106 8 0.02
107 9 0.02
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (102 bp):
TTTAAAATTAATAATATTTTTATTTAAATATGTAATTTTATTAATTATTTAAATTTAAATTAATA
AATATTTAAAAATAAAGTCATCCTGATATCAAGCAAC
Found at i:2846888 original size:24 final size:24
Alignment explanation
Indices: 2846820--2846895 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 24
2846810 ATTAATCTAC
2846820 TTTAAATTAATAAAATTTTTATTTAAA
1 TTTAAATTAATAAAA---TTATTTAAA
* * *
2846847 TATGTAATTTTAT-TAATTATTTAAA
1 T-T-TAAATTAATAAAATTATTTAAA
*
2846872 TTTAAATTAATAAAATTTTTTAAA
1 TTTAAATTAATAAAATTATTTAAA
2846896 AAATTTCACA
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
23 7 0.18
24 11 0.28
25 10 0.26
27 1 0.03
28 3 0.08
29 7 0.18
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (24 bp):
TTTAAATTAATAAAATTATTTAAA
Found at i:2846913 original size:52 final size:51
Alignment explanation
Indices: 2846759--2846914 Score: 128
Period size: 52 Copynumber: 3.1 Consensus size: 51
2846749 AAATTAGTTT
** * *
2846759 TATTAATT-TATTAAATTTAAATTAAT-AAATAGTTAAAAAAATTTACGTGA
1 TATTAATTAT-TTAAATTTAAATTAATAAAATTTTTTAAAAAATTTACATGA
* * * * * **
2846809 TATT-A--ATCT-ACTTTAAATTAATAAAATTTTTATTTAAATATGTA-ATTT
1 TATTAATTATTTAAATTTAAATTAATAAAA-TTTT-TTAAAAAATTTACATGA
2846857 TATTAATTATTTAAATTTAAATTAATAAAATTTTTTAAAAAATTTCACATGA
1 TATTAATTATTTAAATTTAAATTAATAAAATTTTTTAAAAAATTT-ACATGA
2846909 TATTAA
1 TATTAA
2846915 ACGACTTTAA
Statistics
Matches: 78, Mismatches: 18, Indels: 18
0.68 0.16 0.16
Matches are distributed among these distances:
46 12 0.15
47 4 0.05
48 8 0.10
49 10 0.13
50 12 0.15
51 8 0.10
52 24 0.31
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (51 bp):
TATTAATTATTTAAATTTAAATTAATAAAATTTTTTAAAAAATTTACATGA
Found at i:2847660 original size:27 final size:26
Alignment explanation
Indices: 2847630--2847691 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
2847620 AATAAAGGTC
2847630 ATATAAAATTAAATTATTTT-AATTAAA
1 ATATAAAA-T-AATTATTTTAAATTAAA
* *
2847657 ATATAAAATATTTATTTTAAATTGAA
1 ATATAAAATAATTATTTTAAATTAAA
2847683 ATGATAAAA
1 AT-ATAAAA
2847692 AGATAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 8 0.26
26 9 0.29
27 14 0.45
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (26 bp):
ATATAAAATAATTATTTTAAATTAAA
Found at i:2850349 original size:26 final size:28
Alignment explanation
Indices: 2850320--2850379 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
2850310 CTTATTAATT
*
2850320 TAAA-AATA-AAAAAGTATATATTTTTG
1 TAAATAATATAAAAAGTATATATTTTTA
* **
2850346 TAAATATTATAAAATTTATATATTTTTA
1 TAAATAATATAAAAAGTATATATTTTTA
2850374 TAAATA
1 TAAATA
2850380 TCATAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 4 0.14
27 3 0.11
28 21 0.75
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (28 bp):
TAAATAATATAAAAAGTATATATTTTTA
Found at i:2850371 original size:27 final size:27
Alignment explanation
Indices: 2850334--2850397 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 27
2850324 AATAAAAAAG
* *
2850334 TATATATTTTTGTAAATATTATAAAATT
1 TATATATTTTTATAAATATCAT-AAATT
2850362 TATATATTTTTATAAATATCATAAATT
1 TATATATTTTTATAAATATCATAAATT
2850389 TATATATTT
1 TATATATTT
2850398 AATTGAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 14 0.41
28 20 0.59
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (27 bp):
TATATATTTTTATAAATATCATAAATT
Found at i:2850406 original size:28 final size:27
Alignment explanation
Indices: 2850334--2850406 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 27
2850324 AATAAAAAAG
*
2850334 TATATATTTTTGTAAATATTATAAAATT
1 TATATATTTTTG-AAATATCATAAAATT
*
2850362 TATATATTTTTATAAATATCAT-AAATT
1 TATATATTTTT-GAAATATCATAAAATT
2850389 TATATATTTAATTGAAAT
1 TATATATTT--TTGAAAT
2850407 TATATATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
27 14 0.36
28 23 0.59
29 2 0.05
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (27 bp):
TATATATTTTTGAAATATCATAAAATT
Found at i:2850514 original size:14 final size:15
Alignment explanation
Indices: 2850489--2850518 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2850479 TTACAACATC
2850489 AAATTAATTAATAAA
1 AAATTAATTAATAAA
2850504 AAATT-ATTAATAAA
1 AAATTAATTAATAAA
2850518 A
1 A
2850519 TTTTATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTAATTAATAAA
Found at i:2850593 original size:2 final size:2
Alignment explanation
Indices: 2850588--2850613 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2850578 AAAAAAACTA
2850588 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
2850614 CACCAAAAGA
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):
AT
Found at i:2850837 original size:2 final size:2
Alignment explanation
Indices: 2850830--2850860 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2850820 TTTGTACGTG
2850830 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 T
2850861 GTTATTAACT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2851111 original size:16 final size:16
Alignment explanation
Indices: 2851092--2851122 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2851082 TTATAAAATT
*
2851092 ATATTTTATATTTATC
1 ATATTTTAAATTTATC
2851108 ATATTTTAAATTTAT
1 ATATTTTAAATTTAT
2851123 ATTAAATATA
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:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTTTAAATTTATC
Found at i:2853031 original size:38 final size:39
Alignment explanation
Indices: 2852976--2853065 Score: 110
Period size: 39 Copynumber: 2.3 Consensus size: 39
2852966 CTCGAGATTT
* *
2852976 GATTTGATTTTTTTTTTTTTGGGGTT-GTTCATACTCAA
1 GATTTGATTTTTCTTTTTTTGGGGTTCGTCCATACTCAA
**** *
2853014 GATTTGATTTTTCTTTTTTTTTTTTTCGTCCATACTCCA
1 GATTTGATTTTTCTTTTTTTGGGGTTCGTCCATACTCAA
2853053 GATTTGATTTTTC
1 GATTTGATTTTTC
2853066 ACGCTTGTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
38 21 0.48
39 23 0.52
ACGTcount: A:0.14, C:0.12, G:0.13, T:0.60
Consensus pattern (39 bp):
GATTTGATTTTTCTTTTTTTGGGGTTCGTCCATACTCAA
Found at i:2855125 original size:16 final size:16
Alignment explanation
Indices: 2855106--2855161 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
2855096 TAATACTTAA
2855106 TTAATATAATTATTTT
1 TTAATATAATTATTTT
* *
2855122 TTAAT-TAAATTTAATTA
1 TTAATAT-AA-TTATTTT
* *
2855139 TAAAAATAATTATTTT
1 TTAATATAATTATTTT
2855155 TTAATAT
1 TTAATAT
2855162 TATTTTAAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
15 1 0.03
16 17 0.59
17 10 0.34
18 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAATATAATTATTTT
Found at i:2855808 original size:21 final size:23
Alignment explanation
Indices: 2855757--2855811 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 23
2855747 AAATACAATA
2855757 ATTTT-AAATATAAAATTTATTT
1 ATTTTAAAATATAAAATTTATTT
* *
2855779 TTTTTAAAATTTAAAA-TT-TTT
1 ATTTTAAAATATAAAATTTATTT
2855800 ATTTTAAAATAT
1 ATTTTAAAATAT
2855812 TTATATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 13 0.46
22 6 0.21
23 9 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTTAAAATATAAAATTTATTT
Found at i:2855813 original size:23 final size:23
Alignment explanation
Indices: 2855762--2855814 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
2855752 CAATAATTTT
* * *
2855762 AAATATAAAATTTATTTTTTTTA
1 AAATTTAAAATTTATTATTTTAA
2855785 AAATTTAAAATTT-TTATTTTAA
1 AAATTTAAAATTTATTATTTTAA
2855807 AATATTTA
1 AA-ATTTA
2855815 TATAATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AAATTTAAAATTTATTATTTTAA
Found at i:2855847 original size:22 final size:22
Alignment explanation
Indices: 2855798--2855851 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
2855788 TTTAAAATTT
*
2855798 TTATTTTAAAATATTTATATAA
1 TTATTTTAAAATATTTATAAAA
*
2855820 TAATTTT-AAATATTTAATAAAA
1 TTATTTTAAAATATTT-ATAAAA
2855842 TTA-TTTAAAA
1 TTATTTTAAAA
2855852 GTAAATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTATTTTAAAATATTTATAAAA
Found at i:2855850 original size:21 final size:21
Alignment explanation
Indices: 2855800--2855843 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
2855790 TAAAATTTTT
2855800 ATTTTAAAATATTTATATAATA
1 ATTTT-AAATATTTATATAATA
2855822 ATTTTAAATATTTA-ATAA-A
1 ATTTTAAATATTTATATAATA
2855841 ATT
1 ATT
2855844 ATTTAAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.18
20 4 0.18
21 9 0.41
22 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTTAAATATTTATATAATA
Found at i:2856034 original size:29 final size:30
Alignment explanation
Indices: 2856002--2856069 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
2855992 AAAACAACAA
*
2856002 TATTTTAATAAATAATTTTAAAA-TAATAT
1 TATTTTAATAAATAATTTTAAAATTAAAAT
* *
2856031 TATTTTAATAATTTATTTTAAAATTAAAAT
1 TATTTTAATAAATAATTTTAAAATTAAAAT
*
2856061 TACTTTAAT
1 TATTTTAAT
2856070 TAATTTACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 21 0.62
30 13 0.38
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (30 bp):
TATTTTAATAAATAATTTTAAAATTAAAAT
Found at i:2856037 original size:16 final size:16
Alignment explanation
Indices: 2856016--2856068 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
2856006 TTAATAAATA
2856016 ATTTTAAAATAATATT
1 ATTTTAAAATAATATT
2856032 ATTTT--AATAAT-TT
1 ATTTTAAAATAATATT
*
2856045 ATTTTAAAATTAAAATT
1 ATTTTAAAA-TAATATT
*
2856062 ACTTTAA
1 ATTTTAA
2856069 TTAATTTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
13 7 0.23
14 6 0.19
15 2 0.06
16 8 0.26
17 8 0.26
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTTAAAATAATATT
Found at i:2856040 original size:14 final size:14
Alignment explanation
Indices: 2856002--2856051 Score: 59
Period size: 13 Copynumber: 3.6 Consensus size: 14
2855992 AAAACAACAA
2856002 TATTTTAATAA-AT
1 TATTTTAATAATAT
*
2856015 AATTTTAAAATAATAT
1 TATTTT--AATAATAT
2856031 TATTTTAATAAT-T
1 TATTTTAATAATAT
2856044 TATTTTAA
1 TATTTTAA
2856052 AATTAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 14 0.44
14 6 0.19
15 5 0.16
16 7 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATTTTAATAATAT
Found at i:2861780 original size:42 final size:43
Alignment explanation
Indices: 2861710--2861798 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
2861700 TATTATAAAA
2861710 ATTATTTGATATATAATAAATAATTAAA-TGTAAAATATAATTAT
1 ATTATTTGATATATAATAAATAATTAAATTGTAAAA-ATAATT-T
* * *
2861754 ATTATTTGATA-ATAGTAAAT-TTTAAATTTTAAAAATAATTT
1 ATTATTTGATATATAATAAATAATTAAATTGTAAAAATAATTT
2861795 ATTA
1 ATTA
2861799 AATAATTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
41 5 0.12
42 11 0.27
43 14 0.34
44 11 0.27
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (43 bp):
ATTATTTGATATATAATAAATAATTAAATTGTAAAAATAATTT
Found at i:2862305 original size:23 final size:22
Alignment explanation
Indices: 2862278--2862326 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
2862268 TAAATATTTT
2862278 TTAAATATAAATATATAAATT-AA
1 TTAAAT-TAAAT-TATAAATTCAA
*
2862301 TTAAATTAAATTATATATTCAA
1 TTAAATTAAATTATAAATTCAA
2862323 TTAA
1 TTAA
2862327 CTTTAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 11 0.46
23 6 0.25
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAAATTAAATTATAAATTCAA
Found at i:2864405 original size:2 final size:2
Alignment explanation
Indices: 2864398--2864430 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2864388 TAAGTTGGAC
2864398 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 A
2864431 ACTCTGTGAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2867342 original size:18 final size:18
Alignment explanation
Indices: 2867288--2867343 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
2867278 ACACAAACAG
*
2867288 TACATATATATATTTATTTA
1 TACA-ATAT-TATTTAATTA
* *
2867308 TACAATATTAATGAATTA
1 TACAATATTATTTAATTA
*
2867326 TATAATATTATTTAATTA
1 TACAATATTATTTAATTA
2867344 AAGATGCATC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 22 0.73
19 4 0.13
20 4 0.13
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (18 bp):
TACAATATTATTTAATTA
Found at i:2868480 original size:17 final size:18
Alignment explanation
Indices: 2868458--2868495 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2868448 TAATAAAATT
2868458 ATTTAAAAATT-TAAAAA
1 ATTTAAAAATTATAAAAA
* *
2868475 ATTTAACAATTATATAAA
1 ATTTAAAAATTATAAAAA
2868493 ATT
1 ATT
2868496 AAGGTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTTAAAAATTATAAAAA
Found at i:2869911 original size:21 final size:21
Alignment explanation
Indices: 2869874--2869936 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
2869864 TTTTTTTATT
**
2869874 TTTTATTTAAATTTTAATTAAA
1 TTTTATTTAAAAATTAA-TAAA
2869896 -TTTATTTAAAAATTAA-AAA
1 TTTTATTTAAAAATTAATAAA
*
2869915 TTATTATTTATAAATTAATAAA
1 TT-TTATTTAAAAATTAATAAA
2869937 AAATTAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 3 0.09
20 1 0.03
21 28 0.80
22 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTATTTAAAAATTAATAAA
Found at i:2871031 original size:29 final size:29
Alignment explanation
Indices: 2870976--2871031 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
2870966 TGATTAGTTC
*
2870976 ATAATATAAATATAAATATTTTTTAATTT
1 ATAATATAAATATAAATATTTTATAATTT
2871005 ATAAT-TAAATTATAAAT-TATTTATAAT
1 ATAATATAAA-TATAAATAT-TTTATAAT
2871032 AAAATTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
ATAATATAAATATAAATATTTTATAATTT
Found at i:2873039 original size:3 final size:3
Alignment explanation
Indices: 2873031--2873065 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
2873021 TATGGTATTG
*
2873031 AAT AAT AAT AAT AAT AAT CAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2873066 ATCATTGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2873467 original size:16 final size:15
Alignment explanation
Indices: 2873442--2873475 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2873432 ATGCATACGT
*
2873442 GATATATCTTGATTA
1 GATATATCTTGATAA
2873457 GATATTATCTTGATAA
1 GATA-TATCTTGATAA
2873473 GAT
1 GAT
2873476 GTATAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (15 bp):
GATATATCTTGATAA
Found at i:2885196 original size:19 final size:19
Alignment explanation
Indices: 2885160--2885197 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2885150 AATTTTTTTA
*
2885160 TATATTTATAAATTTATAT
1 TATATTTATAAATATATAT
2885179 TATATTTA-AATATATATAT
1 TATATTTATAA-ATATATAT
2885198 CAAACATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATATTTATAAATATATAT
Found at i:2885612 original size:14 final size:14
Alignment explanation
Indices: 2885589--2885618 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2885579 TAAACAGAAT
2885589 TAATAAATTTAATA
1 TAATAAATTTAATA
*
2885603 TAATATATTTAATA
1 TAATAAATTTAATA
2885617 TA
1 TA
2885619 TATCGTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATAAATTTAATA
Found at i:2886134 original size:17 final size:18
Alignment explanation
Indices: 2886114--2886150 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
2886104 ATTATTAATA
2886114 TTTTCAAAAAA-TTATTT
1 TTTTCAAAAAATTTATTT
*
2886131 TTTTTAAAAAATTTATTT
1 TTTTCAAAAAATTTATTT
2886149 TT
1 TT
2886151 CATGAATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTCAAAAAATTTATTT
Found at i:2886140 original size:18 final size:18
Alignment explanation
Indices: 2886114--2886150 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2886104 ATTATTAATA
*
2886114 TTTTCAAAAAATTATTTT
1 TTTTAAAAAAATTATTTT
*
2886132 TTTTAAAAAATTTATTTT
1 TTTTAAAAAAATTATTTT
2886150 T
1 T
2886151 CATGAATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTAAAAAAATTATTTT
Found at i:2888466 original size:28 final size:28
Alignment explanation
Indices: 2888426--2888497 Score: 126
Period size: 28 Copynumber: 2.5 Consensus size: 28
2888416 GAGACACGAA
2888426 ACATGACACAATACAAAAAATAATGTAT
1 ACATGACACAATACAAAAAATAATGTAT
2888454 ACATGACACAATACAAAAAATAATGTAT
1 ACATGACACAATACAAAAAATAATGTAT
*
2888482 ACACGACACAAATACA
1 ACATGACAC-AATACA
2888498 CAAATTTATC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 36 0.86
29 6 0.14
ACGTcount: A:0.57, C:0.18, G:0.07, T:0.18
Consensus pattern (28 bp):
ACATGACACAATACAAAAAATAATGTAT
Found at i:2892433 original size:16 final size:16
Alignment explanation
Indices: 2892412--2892442 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2892402 TTATTCGAAT
*
2892412 TCAATTCATTTTAAAC
1 TCAATTAATTTTAAAC
2892428 TCAATTAATTTTAAA
1 TCAATTAATTTTAAA
2892443 TTTATCAAAT
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:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (16 bp):
TCAATTAATTTTAAAC
Found at i:2892479 original size:23 final size:26
Alignment explanation
Indices: 2892430--2892481 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 26
2892420 TTTTAAACTC
*
2892430 AATTAATTTTAAATTTATCAAATTTTT
1 AATTAATTTTAAATTTA-CAAAATTTT
2892457 AATT-ATTTTAAA-TTA-AAAATTTT
1 AATTAATTTTAAATTTACAAAATTTT
2892480 AA
1 AA
2892482 AATTAAGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 9 0.38
25 3 0.12
26 8 0.33
27 4 0.17
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
AATTAATTTTAAATTTACAAAATTTT
Found at i:2892578 original size:21 final size:21
Alignment explanation
Indices: 2892548--2892588 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2892538 TTTTACTTAT
2892548 TTCAAATGAA-AATTATTCATA
1 TTCAAATGAATAATT-TTCATA
*
2892569 TTCAATTGAATAATTTTCAT
1 TTCAAATGAATAATTTTCAT
2892589 CTTTATTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (21 bp):
TTCAAATGAATAATTTTCATA
Found at i:2893214 original size:19 final size:19
Alignment explanation
Indices: 2893182--2893219 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2893172 GAAATTAAAT
*
2893182 TAATTTTATAATTTTTTTA
1 TAATTTTATAATTTATTTA
2893201 TAATATTTAT-ATTTATTTA
1 TAAT-TTTATAATTTATTTA
2893220 ATTCGATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TAATTTTATAATTTATTTA
Found at i:2894776 original size:14 final size:14
Alignment explanation
Indices: 2894736--2894785 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
2894726 TTAATTTATT
* *
2894736 TTTAATACATCAAA
1 TTTAATAAAACAAA
*
2894750 -TTAA-AAAAGAAA
1 TTTAATAAAACAAA
*
2894762 TTTTATAAAACAAA
1 TTTAATAAAACAAA
2894776 TTTAATAAAA
1 TTTAATAAAA
2894786 TATATTCCGA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
12 5 0.18
13 7 0.25
14 16 0.57
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (14 bp):
TTTAATAAAACAAA
Found at i:2895229 original size:24 final size:22
Alignment explanation
Indices: 2895194--2895269 Score: 64
Period size: 24 Copynumber: 3.3 Consensus size: 22
2895184 AATCATAACA
*
2895194 TATTATATTTTATTTATTATAT
1 TATTTTATTTTATTTATTATAT
** *
2895216 TATTTTCATATTTATCAAATATAT
1 TATTTT-AT-TTTATTTATTATAT
2895240 TATATTTATTTCGTATTT-TTATAT
1 TAT-TTTATTT--TATTTATTATAT
2895264 TATTTT
1 TATTTT
2895270 TAAAATTATA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
22 5 0.12
23 7 0.17
24 24 0.57
25 6 0.14
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (22 bp):
TATTTTATTTTATTTATTATAT
Found at i:2896346 original size:14 final size:14
Alignment explanation
Indices: 2896327--2896356 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2896317 TCTAAACTAT
*
2896327 TTAAATTTGAATCA
1 TTAAATTTAAATCA
2896341 TTAAATTTAAATCA
1 TTAAATTTAAATCA
2896355 TT
1 TT
2896357 TCGAGTACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (14 bp):
TTAAATTTAAATCA
Found at i:2908315 original size:7 final size:7
Alignment explanation
Indices: 2908305--2908346 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
2908295 TTTTAAAACA
2908305 TAAAAAT
1 TAAAAAT
2908312 T-AAAAT
1 TAAAAAT
*
2908318 TAAAATT
1 TAAAAAT
*
2908325 TAATAAT
1 TAAAAAT
2908332 ATAAAAAT
1 -TAAAAAT
2908340 TAAAAAT
1 TAAAAAT
2908347 ATTTCTTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 17 0.59
8 6 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
TAAAAAT
Found at i:2913884 original size:2 final size:2
Alignment explanation
Indices: 2913877--2913929 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
2913867 TTAGGGCCTA
*
2913877 AT AT AT AT AT AT AT AT AT GT 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
2913919 AT AT AT AT AT A
1 AT AT AT AT AT A
2913930 GAGAGAGAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2915610 original size:22 final size:23
Alignment explanation
Indices: 2915577--2915623 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
2915567 AAAGTTATCA
2915577 AATATGTTTAA-TTTTTAATTTT
1 AATATGTTTAATTTTTTAATTTT
2915599 AATAT-TTATAATTTTTTAATTTT
1 AATATGTT-TAATTTTTTAATTTT
2915622 AA
1 AA
2915624 ATTACGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 2 0.09
22 8 0.35
23 13 0.57
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
AATATGTTTAATTTTTTAATTTT
Found at i:2915825 original size:58 final size:59
Alignment explanation
Indices: 2915745--2915861 Score: 200
Period size: 58 Copynumber: 2.0 Consensus size: 59
2915735 TCTCAAGTTT
2915745 AAGAGTTCTAGTCAGAACCAAATACCTCATACATTGAA-AACTTGCTGGAGGGAAGTAA
1 AAGAGTTCTAGTCAGAACCAAATACCTCATACATTGAACAACTTGCTGGAGGGAAGTAA
* * *
2915803 AAGAGTTCTAGTTAGAATCAAATACCTCATACATTGAACACCTTGCTGGAGGGAAGTAA
1 AAGAGTTCTAGTCAGAACCAAATACCTCATACATTGAACAACTTGCTGGAGGGAAGTAA
2915862 CTATGGCAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
58 36 0.65
59 19 0.35
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (59 bp):
AAGAGTTCTAGTCAGAACCAAATACCTCATACATTGAACAACTTGCTGGAGGGAAGTAA
Found at i:2917452 original size:44 final size:44
Alignment explanation
Indices: 2917389--2917478 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
2917379 ATCAGAAACC
*
2917389 TGTTATTTACCAATCTTTCTTGAAGATATCATTTACTATTTTCT
1 TGTTATTTACCAATCTTTCTTGAAGAGATCATTTACTATTTTCT
* *
2917433 TGTTATTTCCCAATCTTTCTTGAAGGGATCATTTACTATTTTCT
1 TGTTATTTACCAATCTTTCTTGAAGAGATCATTTACTATTTTCT
2917477 TG
1 TG
2917479 CTTGAAGGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.22, C:0.17, G:0.10, T:0.51
Consensus pattern (44 bp):
TGTTATTTACCAATCTTTCTTGAAGAGATCATTTACTATTTTCT
Found at i:2917482 original size:28 final size:28
Alignment explanation
Indices: 2917446--2917502 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
2917436 TATTTCCCAA
*
2917446 TCTTTCTTGAAGGGATCATTTACTATTT
1 TCTTGCTTGAAGGGATCATTTACTATTT
2917474 TCTTGCTTGAAGGGATCATTTACTATTT
1 TCTTGCTTGAAGGGATCATTTACTATTT
2917502 T
1 T
2917503 TTTGTTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.49
Consensus pattern (28 bp):
TCTTGCTTGAAGGGATCATTTACTATTT
Found at i:2917524 original size:72 final size:72
Alignment explanation
Indices: 2917402--2917549 Score: 260
Period size: 72 Copynumber: 2.1 Consensus size: 72
2917392 TATTTACCAA
* *
2917402 TCTTTCTTGAAGATATCATTTACTATTTTCTTGTTATTTCCCAATCTTTCTTGAAGGGATCATTT
1 TCTTGCTTGAAGAGATCATTTACTATTTTCTTGTTATTTCCCAATCTTTCTTGAAGGGATCATTT
2917467 ACTATTT
66 ACTATTT
* *
2917474 TCTTGCTTGAAGGGATCATTTACTATTTTTTTGTTATTTCCCAATCTTTCTTGAAGGGATCATTT
1 TCTTGCTTGAAGAGATCATTTACTATTTTCTTGTTATTTCCCAATCTTTCTTGAAGGGATCATTT
2917539 ACTATTT
66 ACTATTT
2917546 TCTT
1 TCTT
2917550 AGTACTAGCA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.21, C:0.16, G:0.11, T:0.51
Consensus pattern (72 bp):
TCTTGCTTGAAGAGATCATTTACTATTTTCTTGTTATTTCCCAATCTTTCTTGAAGGGATCATTT
ACTATTT
Found at i:2918506 original size:9 final size:9
Alignment explanation
Indices: 2918466--2918564 Score: 58
Period size: 9 Copynumber: 10.7 Consensus size: 9
2918456 TTTTTTATTT
*
2918466 TTAAATAAA
1 TTAATTAAA
2918475 TTAAATTAAA
1 TT-AATTAAA
** *
2918485 AAAATGTATA
1 TTAAT-TAAA
2918495 TTAATTAAA
1 TTAATTAAA
*
2918504 TTAAAATT-AT
1 TT--AATTAAA
*
2918514 TTTATTAAA
1 TTAATTAAA
* *
2918523 TTTAA-TCAG
1 -TTAATTAAA
*
2918532 TTAATTAAG
1 TTAATTAAA
2918541 TTAATTAAA
1 TTAATTAAA
2918550 TTAATTAAA
1 TTAATTAAA
2918559 TTAATT
1 TTAATT
2918565 TTTTATATTA
Statistics
Matches: 68, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
8 7 0.10
9 39 0.57
10 18 0.26
11 4 0.06
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (9 bp):
TTAATTAAA
Found at i:2918551 original size:14 final size:14
Alignment explanation
Indices: 2918466--2918562 Score: 58
Period size: 14 Copynumber: 6.9 Consensus size: 14
2918456 TTTTTTATTT
*
2918466 TTAAATAAATTAAA
1 TTAATTAAATTAAA
** *
2918480 TTAAAAAAATGTATA
1 TTAATTAAAT-TAAA
2918495 TTAATTAAATTAAAA
1 TTAATTAAATT-AAA
**
2918510 TT-ATTTTATTAAA
1 TTAATTAAATTAAA
* *
2918523 TTTAA-TCAGTT-AA
1 -TTAATTAAATTAAA
2918536 TTAAGTT-AATTAAA
1 TTAA-TTAAATTAAA
2918550 TTAATTAAATTAA
1 TTAATTAAATTAA
2918563 TTTTTTATAT
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
12 4 0.06
13 10 0.16
14 34 0.53
15 16 0.25
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (14 bp):
TTAATTAAATTAAA
Found at i:2918731 original size:16 final size:15
Alignment explanation
Indices: 2918697--2918725 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2918687 CATAAGTTAA
2918697 AAAATTTAACAATAT
1 AAAATTTAACAATAT
2918712 AAAATTTAA-AATAT
1 AAAATTTAACAATAT
2918726 TTAAAAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAATTTAACAATAT
Found at i:2919185 original size:21 final size:22
Alignment explanation
Indices: 2919146--2919194 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
2919136 AAAAATATTT
*
2919146 TTATTTAAATTTAATTATAAAA
1 TTATATAAATTTAATTATAAAA
2919168 -TATATAAATATTAA-TATAAAA
1 TTATATAAAT-TTAATTATAAAA
2919189 TTATAT
1 TTATAT
2919195 TTTAATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TTATATAAATTTAATTATAAAA
Found at i:2920897 original size:59 final size:58
Alignment explanation
Indices: 2920778--2920903 Score: 189
Period size: 59 Copynumber: 2.2 Consensus size: 58
2920768 TTGTATGACA
* **
2920778 TATTTAAAATTTAAATTAAATCAAATCTAAAATAATTAAATGTATAATTCATTCTAAT
1 TATTTAAAATTTAAATAAAATCAAATCTAAAATAATTAAATGTATAATTCATAATAAT
* * *
2920836 TATTTTAAAATTTAAATAAAATTAAATCTAAAATAATTAAATGTATGATTCATAATCAT
1 TA-TTTAAAATTTAAATAAAATCAAATCTAAAATAATTAAATGTATAATTCATAATAAT
2920895 TATTTAAAA
1 TATTTAAAA
2920904 CAATCTACAC
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 9 0.15
59 52 0.85
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (58 bp):
TATTTAAAATTTAAATAAAATCAAATCTAAAATAATTAAATGTATAATTCATAATAAT
Found at i:2928692 original size:96 final size:96
Alignment explanation
Indices: 2928528--2928704 Score: 327
Period size: 96 Copynumber: 1.8 Consensus size: 96
2928518 AAGAAGTTTG
* *
2928528 AATTTTGGGATGTTACCTAAAGGCGTGCCTATTCCTCCCTCCGGGCCTAGTAGGCGTACATCGGA
1 AATTTTGGGATGTTACCTAAAGGCGTGCCCATTCCTCCCTCCGGACCTAGTAGGCGTACATCGGA
2928593 TCCCCCACCTCCTCCATCAACAACAAATTTA
66 TCCCCCACCTCCTCCATCAACAACAAATTTA
*
2928624 AATTTTGGGATGTTGCCTAAAGGCGTGCCCATTCCTCCCTCCGGACCTAGTAGGCGTACATCGGA
1 AATTTTGGGATGTTACCTAAAGGCGTGCCCATTCCTCCCTCCGGACCTAGTAGGCGTACATCGGA
2928689 TCCCCCACCTCCTCCA
66 TCCCCCACCTCCTCCA
2928705 GCATTGTAAT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 78 1.00
ACGTcount: A:0.21, C:0.34, G:0.19, T:0.25
Consensus pattern (96 bp):
AATTTTGGGATGTTACCTAAAGGCGTGCCCATTCCTCCCTCCGGACCTAGTAGGCGTACATCGGA
TCCCCCACCTCCTCCATCAACAACAAATTTA
Found at i:2930004 original size:38 final size:38
Alignment explanation
Indices: 2929932--2930006 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
2929922 ACATTCAAAT
*
2929932 TAAAAATAATATATCTTATATTAATTTAATATAATTTG
1 TAAAAATAATATATCTTAAATTAATTTAATATAATTTG
* *
2929970 TAAAAATAA-AT-TTTTAAATTTATTTAATGAATAATTT
1 TAAAAATAATATATCTTAAATTAATTTAAT--ATAATTT
2930007 AATTTTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 14 0.44
37 2 0.06
38 16 0.50
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (38 bp):
TAAAAATAATATATCTTAAATTAATTTAATATAATTTG
Found at i:2935605 original size:34 final size:34
Alignment explanation
Indices: 2935559--2935743 Score: 239
Period size: 34 Copynumber: 5.5 Consensus size: 34
2935549 GTAAAAACCA
*
2935559 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2935593 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* * *
2935627 CCATTTAATCAATAATGGTAAGCTATCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2935661 TCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2935695 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
2935728 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
2935744 TCTCCCACTT
Statistics
Matches: 131, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
33 18 0.14
34 109 0.83
35 4 0.03
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.27
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2939836 original size:19 final size:19
Alignment explanation
Indices: 2939809--2939871 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
2939799 TCACGTGTAC
* *
2939809 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
2939828 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
2939847 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
2939866 AGTACC
1 AGTACC
2939872 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:2940219 original size:34 final size:34
Alignment explanation
Indices: 2940173--2940356 Score: 237
Period size: 34 Copynumber: 5.4 Consensus size: 34
2940163 GTAAAAACCA
*
2940173 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2940207 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* * *
2940241 CCATTTAATCAATAATGGTAAGCTATCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2940275 TCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2940309 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
2940342 CCATTTAATCAACAA
1 CCATTTAATCAACAA
2940357 AAATCACTTT
Statistics
Matches: 130, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
33 17 0.13
34 109 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.27
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2941601 original size:126 final size:126
Alignment explanation
Indices: 2941376--2941613 Score: 379
Period size: 126 Copynumber: 1.9 Consensus size: 126
2941366 AAGGCGTACC
* *
2941376 TATTCTTTCATCCGGGCCTAGCAGAGGCCATTGGGATTCTCCACCTCCTCCATCAGCAATAAATT
1 TATTCTTTCATCCGGGCCTAGCAGAGGCCATTCGGATTCTCCACCTCCTCCATCAACAATAAATT
* *
2941441 TGAATCTCGGGATGTTACCTAAAGACGGGCCTATTCCTCCATCCGGGTCTAATGGTGTGCG
66 TGAATCTCGGAATGTTACCTAAAGACGGGCCTATTCATCCATCCGGGTCTAATGGTGTGCG
* *
2941502 TATTCTTTCATCCGGGCCTAGCCCG-GGCCTTTCGGATTCTCCACCTCCTCCATCAACAATAAAT
1 TATTCTTTCATCCGGGCCTAG-CAGAGGCCATTCGGATTCTCCACCTCCTCCATCAACAATAAAT
* * *
2941566 TTGAATTTTGGAATGTTACCTAAAGACGTGCCTATTCATCCATCCGGG
65 TTGAATCTCGGAATGTTACCTAAAGACGGGCCTATTCATCCATCCGGG
2941614 CCTAGTAGTC
Statistics
Matches: 102, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
126 100 0.98
127 2 0.02
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.30
Consensus pattern (126 bp):
TATTCTTTCATCCGGGCCTAGCAGAGGCCATTCGGATTCTCCACCTCCTCCATCAACAATAAATT
TGAATCTCGGAATGTTACCTAAAGACGGGCCTATTCATCCATCCGGGTCTAATGGTGTGCG
Found at i:2941650 original size:24 final size:21
Alignment explanation
Indices: 2941606--2941647 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2941596 CCTATTCATC
*
2941606 CATCCGGGCCTAGTAGTCGTA
1 CATCCGGGCCTAATAGTCGTA
2941627 CATCCGGGCCTAATAGT-GTA
1 CATCCGGGCCTAATAGTCGTA
2941647 C
1 C
2941648 GTATTCTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.21, C:0.29, G:0.26, T:0.24
Consensus pattern (21 bp):
CATCCGGGCCTAATAGTCGTA
Found at i:2941748 original size:147 final size:146
Alignment explanation
Indices: 2941480--2941994 Score: 805
Period size: 147 Copynumber: 3.5 Consensus size: 146
2941470 CCTATTCCTC
* *
2941480 CATCCGGGTCTAATGGTGTGCGTATTCTTTCATCCGGGCCTAGCCCGGGCCTTTCGGATTCTCCA
1 CATCCGGGCCTAATGGTGTACGTATTCTTTCATCCGGGCCTAGCCCGGGCCTTTCGGATTCTCCA
*
2941545 CCTCCTCCATCAACAATAAATTTGAATTTTGGAATGTTACCTAAAGACGTGCCTATTCATCCATC
66 CCTCCTCCATCAACAATAAATTTGAATTTTGGGATGTTACCTAAAGACGTG-CTATTCATCCATC
*
2941610 CGGGCCTAGTAGTCGTA
130 CGGACCTAGTAGTCGTA
*
2941627 CATCCGGGCCTAATAGTGTACGTATTCTTTCATCCGGGCCTAGCCCGGGCCTTTCGGATTCTCCA
1 CATCCGGGCCTAATGGTGTACGTATTCTTTCATCCGGGCCTAGCCCGGGCCTTTCGGATTCTCCA
2941692 CCTCCTCCATCAACAATAAATTTGAATTTTGGGATGTTACCTAAAGACGTGTCTATTCATCCATC
66 CCTCCTCCATCAACAATAAATTTGAATTTTGGGATGTTACCTAAAGACGTG-CTATTCATCCATC
*
2941757 CGGACCTAGTAGTCATA
130 CGGACCTAGTAGTCGTA
* *
2941774 CATCCGGGTCTAATGGTGTGCGTATTCTTTCATCCGGGCCTAGCCCGGGCCTTTCGGATTCTCCA
1 CATCCGGGCCTAATGGTGTACGTATTCTTTCATCCGGGCCTAGCCCGGGCCTTTCGGATTCTCCA
* *
2941839 CCTCCTCCATCAACAATAAATTTGAATTTTGGGATGTTACCTAAAGATGTGCTTATTCCTCCATC
66 CCTCCTCCATCAACAATAAATTTGAATTTTGGGATGTTACCTAAAGACGTGC-TATTCATCCATC
2941904 CGGACCTAGTAGTCGTA
130 CGGACCTAGTAGTCGTA
** ** * * * ** * * *
2941921 CATCCGACCCTAATGGCATACCTATTCTTTCATCCGGACCCAGCAGGGGCCATTGGGATTCCCCA
1 CATCCGGGCCTAATGGTGTACGTATTCTTTCATCCGGGCCTAGCCCGGGCCTTTCGGATTCTCCA
2941986 CCTCCTCCA
66 CCTCCTCCA
2941995 GCACTGTGAT
Statistics
Matches: 340, Mismatches: 27, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
146 1 0.00
147 339 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.30
Consensus pattern (146 bp):
CATCCGGGCCTAATGGTGTACGTATTCTTTCATCCGGGCCTAGCCCGGGCCTTTCGGATTCTCCA
CCTCCTCCATCAACAATAAATTTGAATTTTGGGATGTTACCTAAAGACGTGCTATTCATCCATCC
GGACCTAGTAGTCGTA
Found at i:2943680 original size:18 final size:18
Alignment explanation
Indices: 2943659--2943706 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 18
2943649 TTTTAATAAA
2943659 ATATTAAA-AATTATTTTT
1 ATATTAAATAA-TATTTTT
2943677 ATATTAATATTAATATTTTT
1 ATATTAA-A-TAATATTTTT
2943697 ATAATTAAAT
1 AT-ATTAAAT
2943707 TTAAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 7 0.27
19 2 0.08
20 10 0.38
21 7 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTAAATAATATTTTT
Found at i:2945134 original size:17 final size:18
Alignment explanation
Indices: 2945109--2945142 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2945099 TAATATCATC
*
2945109 ATACTAAAATATTAAAAA
1 ATACTAAAAAATTAAAAA
2945127 ATAC-AAAAAATTAAAA
1 ATACTAAAAAATTAAAA
2945143 TACAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (18 bp):
ATACTAAAAAATTAAAAA
Found at i:2946508 original size:111 final size:111
Alignment explanation
Indices: 2946310--2947300 Score: 1552
Period size: 111 Copynumber: 8.9 Consensus size: 111
2946300 TCCATCATTG
* * *
2946310 TCATCCTTACCAGCAAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
1 TCATCCTCACCAACGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
* *
2946375 AGGGCCTGAACCTGGTACAAATTCACCGCCGCCGCCATCACTATCT
66 AGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCATCACAATCT
*
2946421 TTATCCTCACCAACGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
1 TCATCCTCACCAACGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
* * * *
2946486 AGGGCCTGACCCTGGTATAAATTCACCACCACCACCATCACAATCT
66 AGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCATCACAATCT
* * *
2946532 TCATCTTCACCAAGGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCCAGCCTACTCCGCCGTC
1 TCATCCTCACCAACGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
* * *
2946597 AGGGCCTGAACCTGGTACAAATTCACCACCACCGCCATCACAATCT
66 AGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCATCACAATCT
* *
2946643 TCATCTTCACCAAGGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
1 TCATCCTCACCAACGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
* *
2946708 AGGGCCTGACCCTGGTACAAATTCACCACCACCGCCATCACAATCT
66 AGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCATCACAATCT
* *
2946754 TCATCTTCACCAAGGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
1 TCATCCTCACCAACGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
* *
2946819 AGGGCCTGACCCTGGTACAAATTCACCACCACCGCCATCACAATCT
66 AGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCATCACAATCT
* *
2946865 TCATCTTCACCAAGGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
1 TCATCCTCACCAACGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
* * *
2946930 AGGGCCTGAACCTGGTACAAATTCACCGCCGCCACCATCACCATCT
66 AGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCATCACAATCT
* * * * *
2946976 TCATCCTCACCGACGAAGAGTTTGAATTTTAGGATGTTGCCTAAAGGGGAGCCTACTCCACCATC
1 TCATCCTCACCAACGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
*
2947041 AGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCATCACCATCT
66 AGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCATCACAATCT
* ** * *
2947087 TCATCCTCACCAACGAAGAGTTTGAATTTTAGGATGTTGCCTAAAGGTAAGCCTACTCCACCATC
1 TCATCCTCACCAACGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
* *
2947152 AGGGCCTGAACCTGGTACAAATTCACCGCCGCCGCCATCACCATCT
66 AGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCATCACAATCT
* * *
2947198 TCATCCTCACCAACGAAGAGTTTGAATTTTAGGACT-TTGCCTAAAGACGAGCCTACTCCACCGT
1 TCATCCTCACCAACGAAGAGTTTGAATTTTGGGA-TGTTGCCTAAAGGCGAGCCTACTCCGCCGT
*
2947262 CAGGGCCTGACCCTGGTACAAATTCACCGCCGCCACCAT
65 CAGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCAT
2947301 TTCGTCTTCA
Statistics
Matches: 836, Mismatches: 43, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
111 835 1.00
112 1 0.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.23
Consensus pattern (111 bp):
TCATCCTCACCAACGAAGAGTTTGAATTTTGGGATGTTGCCTAAAGGCGAGCCTACTCCGCCGTC
AGGGCCTGACCCTGGTACAAATTCACCGCCGCCGCCATCACAATCT
Found at i:2948089 original size:26 final size:25
Alignment explanation
Indices: 2948062--2948121 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
2948052 TTATTTATTA
2948062 TTTAAAATAAAATAAAATAATTAATAT
1 TTTAAAA-AAAATAAAATAA-TAATAT
* * *
2948089 TTTTAAAAAAATTAAATAATAATAC
1 TTTAAAAAAAATAAAATAATAATAT
*
2948114 TATAAAAA
1 TTTAAAAA
2948122 CATTAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 11 0.39
26 11 0.39
27 6 0.21
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
TTTAAAAAAAATAAAATAATAATAT
Found at i:2948389 original size:16 final size:16
Alignment explanation
Indices: 2948368--2948413 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
2948358 AAATTATTTT
2948368 ATAATATTATATATTA
1 ATAATATTATATATTA
*
2948384 ATAATATTAT-TTTTA
1 ATAATATTATATATTA
2948399 ATTAATATT-TATATT
1 A-TAATATTATATATT
2948414 TTTATGATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 6 0.23
16 20 0.77
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATAATATTATATATTA
Found at i:2950395 original size:16 final size:16
Alignment explanation
Indices: 2950374--2950434 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 16
2950364 ATATTTATAT
2950374 TATATTTAAAAAATTA
1 TATATTTAAAAAATTA
*
2950390 TATATTTATATAAATTAAAA
1 TATATTTA-AAAAATT---A
* *
2950410 TTATTTTTAAATAATTA
1 -TATATTTAAAAAATTA
2950427 TATATTTA
1 TATATTTA
2950435 TGTAATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
16 15 0.43
17 7 0.20
20 6 0.17
21 7 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATATTTAAAAAATTA
Found at i:2950395 original size:21 final size:21
Alignment explanation
Indices: 2950369--2950432 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
2950359 TTAATATATT
2950369 TATATTATATTTAAAAAATTA
1 TATATTATATTTAAAAAATTA
*
2950390 TATATT-TA--T-ATAAATTA
1 TATATTATATTTAAAAAATTA
* * *
2950407 -AAATTATTTTTAAATAATTA
1 TATATTATATTTAAAAAATTA
2950427 TATATT
1 TATATT
2950433 TATGTAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
16 4 0.12
17 8 0.25
18 1 0.03
19 1 0.03
20 8 0.25
21 10 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATATTATATTTAAAAAATTA
Found at i:2950407 original size:25 final size:28
Alignment explanation
Indices: 2950357--2950409 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
2950347 TTTATGTTAT
*
2950357 AATTAATATATTTATATTATATTTAAAA
1 AATTAATATATTTATATTATAATTAAAA
2950385 AATT-ATATATTTATA-TA-AATTAAAA
1 AATTAATATATTTATATTATAATTAAAA
2950410 TTATTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 7 0.29
26 2 0.08
27 11 0.46
28 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
AATTAATATATTTATATTATAATTAAAA
Found at i:2950413 original size:37 final size:37
Alignment explanation
Indices: 2950372--2950445 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
2950362 ATATATTTAT
2950372 ATTATATTTAAAAAATTATATATTTATATAAATTAAA
1 ATTATATTTAAAAAATTATATATTTATATAAATTAAA
* * * *
2950409 ATTATTTTTAAATAATTATATATTTATGTAATTTAAA
1 ATTATATTTAAAAAATTATATATTTATATAAATTAAA
2950446 TTTTGTATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (37 bp):
ATTATATTTAAAAAATTATATATTTATATAAATTAAA
Found at i:2950491 original size:12 final size:13
Alignment explanation
Indices: 2950441--2950496 Score: 55
Period size: 12 Copynumber: 4.5 Consensus size: 13
2950431 TTTATGTAAT
*
2950441 TTAA-ATTTTGTA
1 TTAATATTTTATA
*
2950453 TTAATATTATTAAA
1 TTAATATT-TTATA
*
2950467 TTAATAATTTATA
1 TTAATATTTTATA
2950480 TT-ATATTTTATA
1 TTAATATTTTATA
2950492 -TAATA
1 TTAATA
2950497 AATATTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
11 1 0.03
12 16 0.44
13 9 0.25
14 10 0.28
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (13 bp):
TTAATATTTTATA
Found at i:2950564 original size:27 final size:27
Alignment explanation
Indices: 2950466--2950564 Score: 92
Period size: 27 Copynumber: 3.6 Consensus size: 27
2950456 ATATTATTAA
*
2950466 ATTA-ATAATTTATATTATATTTTATAT
1 ATTATATAATTTA-ATTATATTTTAAAT
* * * *
2950493 AATAAATATTTTAATTATTTTTGTAAAAT
1 ATTATATAATTTAATTATATTT-T-AAAT
**
2950522 ATTATATAATCAAATTATATTTTAAAT
1 ATTATATAATTTAATTATATTTTAAAT
*
2950549 ATTATTTAATTTAATT
1 ATTATATAATTTAATT
2950565 TTTTAAGCTA
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
27 28 0.50
28 9 0.16
29 19 0.34
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (27 bp):
ATTATATAATTTAATTATATTTTAAAT
Found at i:2950988 original size:33 final size:34
Alignment explanation
Indices: 2950946--2951014 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
2950936 TTTCGGTGTG
2950946 TAAGTTTATTTTTAA-TAAGTAATGAATGAAATT
1 TAAGTTTATTTTTAAGTAAGTAATGAATGAAATT
*
2950979 TAAGTTTATTTTTAAGTAAGTATTGAATGAAATT
1 TAAGTTTATTTTTAAGTAAGTAATGAATGAAATT
2951013 TA
1 TA
2951015 TTTATATTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 15 0.44
34 19 0.56
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (34 bp):
TAAGTTTATTTTTAAGTAAGTAATGAATGAAATT
Found at i:2952225 original size:11 final size:11
Alignment explanation
Indices: 2952209--2952304 Score: 51
Period size: 10 Copynumber: 9.1 Consensus size: 11
2952199 AATGAAATGG
2952209 ATATAAATATA
1 ATATAAATATA
*
2952220 ATATAAAAATA
1 ATATAAATATA
*
2952231 ATAAAAATA-A
1 ATATAAATATA
* *
2952241 AAATAAATTTA
1 ATATAAATATA
* * *
2952252 TTA-AAATTTT
1 ATATAAATATA
2952262 ATAT-AATATA
1 ATATAAATATA
*
2952272 A-AT-TAT-TA
1 ATATAAATATA
*
2952280 ATATAAATTTA
1 ATATAAATATA
2952291 ATTATAACATATA
1 A-TATAA-ATATA
2952304 A
1 A
2952305 AATGTAAAAT
Statistics
Matches: 63, Mismatches: 15, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
8 3 0.05
9 6 0.10
10 22 0.35
11 22 0.35
12 5 0.08
13 5 0.08
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (11 bp):
ATATAAATATA
Found at i:2952283 original size:13 final size:14
Alignment explanation
Indices: 2952260--2952288 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2952250 TATTAAAATT
2952260 TTATATAATATAAA
1 TTATATAATATAAA
2952274 TTAT-TAATATAAA
1 TTATATAATATAAA
2952287 TT
1 TT
2952289 TAATTATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTATATAATATAAA
Found at i:2953207 original size:5 final size:5
Alignment explanation
Indices: 2953197--2953229 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
2953187 TTTCGAATCT
2953197 TTGGA TTGGA TTGGA TTGGA TTGGA TTGGA TTG
1 TTGGA TTGGA TTGGA TTGGA TTGGA TTGGA TTG
2953230 CAAAGCTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.39, T:0.42
Consensus pattern (5 bp):
TTGGA
Found at i:2953510 original size:28 final size:28
Alignment explanation
Indices: 2953473--2953549 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 28
2953463 AAAATAAAAA
*
2953473 TAATATTTATATAAATATTTAATTAAAT
1 TAATAATTATATAAATATTTAATTAAAT
* * *
2953501 TAATAATTATATATATATCTAAATTCAAT
1 TAATAATTATATAAATAT-TTAATTAAAT
2953530 TACATTAATT-TA-AAATATTT
1 TA-A-TAATTATATAAATATTT
2953550 TTTATTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
28 17 0.43
29 15 0.38
30 3 0.08
31 5 0.12
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (28 bp):
TAATAATTATATAAATATTTAATTAAAT
Found at i:2953625 original size:12 final size:12
Alignment explanation
Indices: 2953610--2953710 Score: 58
Period size: 11 Copynumber: 8.8 Consensus size: 12
2953600 ATAATAAATT
2953610 ATATAAAATATA
1 ATATAAAATATA
*
2953622 ATAT-AAATTTAA
1 ATATAAAATAT-A
*
2953634 ATATAAAAAATA
1 ATATAAAATATA
*
2953646 AT-TAAAAAATA
1 ATATAAAATATA
2953657 ATTTGATAAAA-ATA
1 A--T-ATAAAATATA
2953671 ATAT--AATA-A
1 ATATAAAATATA
2953680 ATATAAAATAT-
1 ATATAAAATATA
* *
2953691 GT-TAAAAT-TT
1 ATATAAAATATA
2953701 ATATAAAATA
1 ATATAAAATA
2953711 AATTATTAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 26
0.70 0.05 0.25
Matches are distributed among these distances:
9 8 0.11
10 8 0.11
11 28 0.39
12 13 0.18
13 5 0.07
14 4 0.06
15 5 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (12 bp):
ATATAAAATATA
Found at i:2953902 original size:73 final size:69
Alignment explanation
Indices: 2953824--2954033 Score: 180
Period size: 69 Copynumber: 3.0 Consensus size: 69
2953814 ATAAATCAGG
*
2953824 TAAAATATATTATTAATTTAAATATGACATAAATATATCACAAATATATAAAAAAAT-TTAATAA
1 TAAAATATATTATAAATTTAAATAT-ACATAAATATAT-A-AAATATATAAAAAAATATTAA-AA
2953888 T-TAATTAT
62 TATAA-TAT
* * * * *
2953896 ATAAAATATATGATGAATTAAAACATA-ATATAA-ATATAATATATATAAAAAAATAATTAAAAT
1 -TAAAATATATTATAAATTTAAATATACATA-AATATATAAAATATATAAAAAAAT-ATTAAAAT
2953959 ATAATAT
63 ATAATAT
* * * **
2953966 TAAAA-ATAATAAAAATATAAATATCACATAAATATAT-AAATATATAAAAATTTATATAAAATA
1 TAAAATATATTATAAATTTAAATAT-ACATAAATATATAAAATATATAAAAAAATAT-TAAAATA
*
2954029 AAATA
64 TAATA
2954034 AATTATTTAC
Statistics
Matches: 113, Mismatches: 16, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
68 14 0.12
69 47 0.42
70 14 0.12
71 14 0.12
72 3 0.03
73 21 0.19
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.34
Consensus pattern (69 bp):
TAAAATATATTATAAATTTAAATATACATAAATATATAAAATATATAAAAAAATATTAAAATATA
ATAT
Found at i:2953951 original size:23 final size:23
Alignment explanation
Indices: 2953925--2954015 Score: 64
Period size: 23 Copynumber: 4.0 Consensus size: 23
2953915 AAAACATAAT
2953925 ATAAATATAATATATATAAAAAA
1 ATAAATATAATATATATAAAAAA
* *
2953948 ATAATTAAAATATAATATTAAAAATA
1 ATAAATATAATAT-ATA-TAAAAA-A
* * * *
2953974 ATAAAAAT-ATAAATATCACATAA
1 ATAAATATAATATATAT-AAAAAA
2953997 AT--ATATAA-ATATATAAAAA
1 ATAAATATAATATATATAAAAA
2954016 TTTATATAAA
Statistics
Matches: 51, Mismatches: 12, Indels: 13
0.67 0.16 0.17
Matches are distributed among these distances:
20 3 0.06
21 8 0.16
22 1 0.02
23 15 0.29
24 9 0.18
25 9 0.18
26 6 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (23 bp):
ATAAATATAATATATATAAAAAA
Found at i:2954023 original size:20 final size:19
Alignment explanation
Indices: 2953998--2954068 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
2953988 ATCACATAAA
2953998 TATATAAATATATAAAAATT
1 TATATAAATATA-AAAAATT
*
2954018 TATATAAA-ATAAAATAAAT
1 TATATAAATATAAAA-AATT
* *
2954037 TATTTACATATAAAAAA-T
1 TATATAAATATAAAAAATT
*
2954055 TATA-ATATATAAAA
1 TATATAAATATAAAA
2954069 TATGTAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
17 9 0.20
18 7 0.16
19 14 0.32
20 14 0.32
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (19 bp):
TATATAAATATAAAAAATT
Found at i:2954076 original size:9 final size:9
Alignment explanation
Indices: 2953929--2954094 Score: 59
Period size: 8 Copynumber: 18.8 Consensus size: 9
2953919 CATAATATAA
*
2953929 ATATAATAT
1 ATATAAAAT
2953938 ATATAAAA-
1 ATATAAAAT
* *
2953946 AAATAATTAAA
1 ATATAA--AAT
*
2953957 ATATAATAT
1 ATATAAAAT
2953966 -TA-AAAAT
1 ATATAAAAT
2953973 A-ATAAAA-
1 ATATAAAAT
2953980 ATAT-AAAT
1 ATATAAAAT
*
2953988 ATCACATAAAT
1 AT-ATA-AAAT
2953999 ATAT-AAAT
1 ATATAAAAT
2954007 ATATAAAAATTT
1 ATAT-AAAA--T
2954019 ATATAAAAT
1 ATATAAAAT
* *
2954028 AAAATAAATT
1 -ATATAAAAT
* *
2954038 AT-TTACAT
1 ATATAAAAT
2954046 ATA-AAAA-
1 ATATAAAAT
*
2954053 AT-TATAAT
1 ATATAAAAT
2954061 ATATAAAAT
1 ATATAAAAT
* *
2954070 ATGTAAAAA
1 ATATAAAAT
2954079 ATAATAAAA-
1 AT-ATAAAAT
2954088 ATATAAA
1 ATATAAA
2954095 TGTTTTTCCT
Statistics
Matches: 116, Mismatches: 21, Indels: 41
0.65 0.12 0.23
Matches are distributed among these distances:
7 14 0.12
8 37 0.32
9 27 0.23
10 18 0.16
11 15 0.13
12 5 0.04
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.33
Consensus pattern (9 bp):
ATATAAAAT
Found at i:2954147 original size:13 final size:13
Alignment explanation
Indices: 2954129--2954154 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2954119 GTTTTTTTCT
2954129 TTTCCTTTCCTTC
1 TTTCCTTTCCTTC
2954142 TTTCCTTTCCTTC
1 TTTCCTTTCCTTC
2954155 CTTATCACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTCCTTTCCTTC
Found at i:2954421 original size:16 final size:17
Alignment explanation
Indices: 2954402--2954436 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2954392 TGTGAAATAA
*
2954402 ATTAAATATAA-AAAAT
1 ATTAAAAATAACAAAAT
2954418 ATTAAAAATAACAAAAT
1 ATTAAAAATAACAAAAT
2954435 AT
1 AT
2954437 ATTAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
ATTAAAAATAACAAAAT
Found at i:2954760 original size:22 final size:20
Alignment explanation
Indices: 2954735--2954788 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
2954725 ATTTTTTCTC
2954735 ATTAAAATATAAAATTAAATAA
1 ATTAAAATATAAAATT-AAT-A
*
2954757 ATTAAAATAATCAAATTAATA
1 ATTAAAAT-ATAAAATTAATA
*
2954778 TTTAAAATATA
1 ATTAAAATATA
2954789 TTTAATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 2 0.07
21 8 0.29
22 11 0.39
23 7 0.25
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
ATTAAAATATAAAATTAATA
Found at i:2954806 original size:19 final size:20
Alignment explanation
Indices: 2954782--2954821 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
2954772 TTAATATTTA
2954782 AAATATATTTAAT-AAATAT
1 AAATATATTTAATAAAATAT
2954801 AAATATATTTAATAAAATAT
1 AAATATATTTAATAAAATAT
2954821 A
1 A
2954822 TTTAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATATATTTAATAAAATAT
Found at i:2954820 original size:14 final size:15
Alignment explanation
Indices: 2954796--2954832 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
2954786 ATATTTAATA
2954796 AATATAAATATATTT
1 AATATAAATATATTT
2954811 AATA-AAATATATTT
1 AATATAAATATATTT
*
2954825 AAAATAAA
1 AATATAAA
2954833 AAAATAACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATATAAATATATTT
Found at i:2954935 original size:21 final size:21
Alignment explanation
Indices: 2954918--2954963 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2954908 TTCAATTATT
2954918 TTAATATTAAATTTAATTAAA
1 TTAATATTAAATTTAATTAAA
* * *
2954939 TTAATTTTTAATTTAAATAAA
1 TTAATATTAAATTTAATTAAA
2954960 TTAA
1 TTAA
2954964 ACTCTCATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAATATTAAATTTAATTAAA
Found at i:2954948 original size:16 final size:17
Alignment explanation
Indices: 2954929--2954961 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2954919 TAATATTAAA
*
2954929 TTTAA-TTAAATTAATT
1 TTTAATTTAAATAAATT
2954945 TTTAATTTAAATAAATT
1 TTTAATTTAAATAAATT
2954962 AAACTCTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATTTAAATAAATT
Found at i:2963343 original size:24 final size:24
Alignment explanation
Indices: 2963307--2963352 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2963297 TTAAGAAAAC
*
2963307 TAATTTAAATAAATATTTAAATTA
1 TAATTTAAATAAATATATAAATTA
* *
2963331 TAATTTTATTAAATATATAAAT
1 TAATTTAAATAAATATATAAAT
2963353 ATTTATATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TAATTTAAATAAATATATAAATTA
Found at i:2963449 original size:16 final size:17
Alignment explanation
Indices: 2963424--2963468 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
2963414 TTATATTATT
2963424 AAAT-TTTAAAA-TTTA
1 AAATATTTAAAAGTTTA
2963439 AAATATTTAAAAGTTTA
1 AAATATTTAAAAGTTTA
2963456 AATATATTTAAAA
1 AA-ATATTTAAAA
2963469 ATATATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.15
16 7 0.26
17 6 0.22
18 10 0.37
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
AAATATTTAAAAGTTTA
Found at i:2963467 original size:10 final size:9
Alignment explanation
Indices: 2963434--2963484 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
2963424 AAATTTTAAA
2963434 ATTTAAAAT
1 ATTTAAAAT
2963443 ATTTAAAA-
1 ATTTAAAAT
*
2963451 GTTTAAATAT
1 ATTTAAA-AT
2963461 ATTTAAAAAT
1 ATTT-AAAAT
* *
2963471 ATATAAAAA
1 ATTTAAAAT
2963480 ATTTA
1 ATTTA
2963485 TTAAAAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
8 6 0.18
9 17 0.50
10 8 0.24
11 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (9 bp):
ATTTAAAAT
Found at i:2963472 original size:12 final size:11
Alignment explanation
Indices: 2963455--2963524 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
2963445 TTAAAAGTTT
2963455 AAATATATTTAA
1 AAATATA-TTAA
*
2963467 AAATATATAAA
1 AAATATATTAA
*
2963478 AAATTTATTAA
1 AAATATATTAA
*
2963489 AAA-A-ATAAA
1 AAATATATTAA
2963498 AAATTATATATAA
1 AAA-TATAT-TAA
2963511 AAA-AT-TTAA
1 AAATATATTAA
2963520 AAATA
1 AAATA
2963525 AAATAAATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
9 13 0.28
10 2 0.04
11 18 0.38
12 9 0.19
13 5 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATATATTAA
Found at i:2963491 original size:22 final size:22
Alignment explanation
Indices: 2963458--2963522 Score: 80
Period size: 22 Copynumber: 2.9 Consensus size: 22
2963448 AAAGTTTAAA
2963458 TATATTTAAAAATATATAAAAAAT
1 TATA-TTAAAAA-ATATAAAAAAT
2963482 T-TATTAAAAAA-ATAAAAAAT
1 TATATTAAAAAATATAAAAAAT
*
2963502 TATATATAAAAAATTTAAAAA
1 TATAT-TAAAAAATATAAAAA
2963523 TAAAATAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
20 10 0.27
21 4 0.11
22 14 0.38
23 8 0.22
24 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
TATATTAAAAAATATAAAAAAT
Found at i:2963941 original size:28 final size:31
Alignment explanation
Indices: 2963883--2963943 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 31
2963873 TGATATATAT
2963883 TTTATGAGTATTTAAATTATATATGTAATTA
1 TTTATGAGTATTTAAATTATATATGTAATTA
* *
2963914 TTTATGA-TA-TTATATTAT-TATGTCATTA
1 TTTATGAGTATTTAAATTATATATGTAATTA
2963942 TT
1 TT
2963944 AAAAATCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 11 0.39
29 8 0.29
30 2 0.07
31 7 0.25
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (31 bp):
TTTATGAGTATTTAAATTATATATGTAATTA
Found at i:2968474 original size:19 final size:19
Alignment explanation
Indices: 2968438--2968474 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2968428 TATAAATCTC
*
2968438 TAGTCTAATTTATATAAAT
1 TAGTCTAATCTATATAAAT
*
2968457 TAGTCTAATCTATTTAAA
1 TAGTCTAATCTATATAAA
2968475 AATAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (19 bp):
TAGTCTAATCTATATAAAT
Found at i:2975002 original size:13 final size:13
Alignment explanation
Indices: 2974984--2975008 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2974974 ATGGGTCGAG
2974984 CAATATACTTGAT
1 CAATATACTTGAT
2974997 CAATATACTTGA
1 CAATATACTTGA
2975009 GTTGAGCTTC
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
CAATATACTTGAT
Found at i:2975707 original size:2 final size:2
Alignment explanation
Indices: 2975700--2975731 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2975690 ACCTAATTAC
2975700 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
2975732 TAAATAAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2976924 original size:24 final size:24
Alignment explanation
Indices: 2976887--2976943 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
2976877 TTTATAAAAA
*
2976887 TATTT-TAAATAAATTAAA-ATTTT
1 TATTTATAAATAAA-TAAATATTAT
*
2976910 TATTTATAATTAAATAAATATTAT
1 TATTTATAAATAAATAAATATTAT
*
2976934 TATTAATAAA
1 TATTTATAAA
2976944 AATATTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TATTTATAAATAAATAAATATTAT
Found at i:2976938 original size:17 final size:18
Alignment explanation
Indices: 2976913--2976960 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
2976903 AAATTTTTAT
*
2976913 TTATAATTAA-ATAAATA
1 TTATAATTAATAAAAATA
*
2976930 TTATTATTAATAAAAATA
1 TTATAATTAATAAAAATA
2976948 TTTATAA-TAATAA
1 -TTATAATTAATAA
2976961 TTTTAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 9 0.35
18 12 0.46
19 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTATAATTAATAAAAATA
Found at i:2982167 original size:28 final size:29
Alignment explanation
Indices: 2982115--2982173 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
2982105 AAACTTATAC
*
2982115 TTTTATTCTAAAAAATATTAAATTTTTAT
1 TTTTATTCTAAAAAATAATAAATTTTTAT
*
2982144 TTTTATT-TAACAAAATAATAATTTTTTAT
1 TTTTATTCTAA-AAAATAATAAATTTTTAT
2982173 T
1 T
2982174 AAATTAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 3 0.11
29 24 0.89
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTTATTCTAAAAAATAATAAATTTTTAT
Found at i:2987759 original size:12 final size:12
Alignment explanation
Indices: 2987739--2987768 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2987729 TCATCACTAC
*
2987739 ATATATATATAT
1 ATATGTATATAT
2987751 ATATGTATATAT
1 ATATGTATATAT
2987763 ATATGT
1 ATATGT
2987769 GCATTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (12 bp):
ATATGTATATAT
Found at i:2988371 original size:18 final size:18
Alignment explanation
Indices: 2988344--2988385 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2988334 GTGTATTTAT
*
2988344 ATAAATTTAAATAAATTA
1 ATAAAATTAAATAAATTA
**
2988362 ATAAAATTAAATATTTTA
1 ATAAAATTAAATAAATTA
2988380 ATAAAA
1 ATAAAA
2988386 AACTAATACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAAATTAAATAAATTA
Found at i:2988578 original size:27 final size:26
Alignment explanation
Indices: 2988488--2988580 Score: 89
Period size: 28 Copynumber: 3.5 Consensus size: 26
2988478 AATTTAAAAA
*
2988488 TTAAAAAAAATATTTATATCGTTTACCT
1 TTAAAAAAAATATTTATA-C-TTTACTT
** *
2988516 TTAAAAAAAATACCTATATTATTCACTT
1 TTAAAAAAAATATTTATACT-TT-ACTT
*
2988544 TT-AAAAAAATATTTATACTTTATTT
1 TTAAAAAAAATATTTATACTTTACTT
*
2988569 TTAAATAAAATA
1 TTAAAAAAAATA
2988581 ATTTTATATA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
25 5 0.09
26 11 0.21
27 16 0.30
28 21 0.40
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.43
Consensus pattern (26 bp):
TTAAAAAAAATATTTATACTTTACTT
Found at i:2991583 original size:2 final size:2
Alignment explanation
Indices: 2991576--2991607 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2991566 TTTCAACAAT
2991576 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2991608 AATAGAACCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2993499 original size:148 final size:147
Alignment explanation
Indices: 2993220--2993630 Score: 431
Period size: 148 Copynumber: 2.8 Consensus size: 147
2993210 ATATAAGTAT
* * *
2993220 ACACACTATATTTGGATATAGCTTGTAAGTATTAATTGGTTGGGATACTTA-TTCAAATCCTAAT
1 ACACACTATATTTGAATATAGCTT-AAAGTATTAATTGGTT-GG-TACTTACTT-AAATCCCAAT
* * ** * * *
2993284 ATTTAAATATATAGT--GATTTATTATTATATATTATATTAAGCTATTAGATTTTAAATAGAAAT
62 ATTTAAATATATAGTAAGATTTATTGTTACATATTATGCTAAGGTATTAAATTTTAAATAGAAAC
* * *
2993347 TAATTTACTAT-TTTACATAT
127 TAATTCACTATAATTACATAC
* * * *
2993367 ACATATTATTTTTGAATATAGCTTAAAATATTAATTGGTTAGGTTACTTACTTAAATCCCAATAT
1 ACACACTATATTTGAATATAGCTTAAAGTATTAATTGGTT-GG-TACTTACTTAAATCCCAATAT
* *
2993432 TTGAATATATGGTAAGATTTATTGTTACATATTATGCTAAGGTATTAAATTTTAAATAGAAACTA
64 TTAAATATATAGTAAGATTTATTGTTACATATTATGCTAAGGTATTAAATTTTAAATAGAAACTA
* *
2993497 ATTCATTATAAATTACATGC
129 ATTCACTAT-AATTACATAC
* * * *
2993517 ACACACTATATTT-AGATATAGCTTATAAGTATTAATGGGTT-GAAGC-TGCTTAAATCTCAATA
1 ACACACTATATTTGA-ATATAGCTTA-AAGTATTAATTGGTTGGTA-CTTACTTAAATCCCAATA
* * *
2993579 TTTCAAGATATAGTAAGATTTATTGTTACATATTATGCTAGGGTATTAAATT
63 TTTAAATATATAGTAAGATTTATTGTTACATATTATGCTAAGGTATTAAATT
2993631 AATTTATTAT
Statistics
Matches: 221, Mismatches: 35, Indels: 15
0.82 0.13 0.06
Matches are distributed among these distances:
146 44 0.20
147 22 0.10
148 113 0.51
149 3 0.01
150 26 0.12
151 13 0.06
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (147 bp):
ACACACTATATTTGAATATAGCTTAAAGTATTAATTGGTTGGTACTTACTTAAATCCCAATATTT
AAATATATAGTAAGATTTATTGTTACATATTATGCTAAGGTATTAAATTTTAAATAGAAACTAAT
TCACTATAATTACATAC
Found at i:2995515 original size:27 final size:27
Alignment explanation
Indices: 2995485--2995539 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
2995475 CATTTATATT
2995485 TAAATAAAATTAATA-TCATTAGTCAAA
1 TAAATAAAATTAATACT-ATTAGTCAAA
** *
2995512 TAAATAGCATTAATACTATTAGTTAAA
1 TAAATAAAATTAATACTATTAGTCAAA
2995539 T
1 T
2995540 TGAATCTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.36
Consensus pattern (27 bp):
TAAATAAAATTAATACTATTAGTCAAA
Found at i:2995925 original size:16 final size:17
Alignment explanation
Indices: 2995897--2995929 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2995887 TTTTTATATT
2995897 TTAAAAATAAAAATTAA
1 TTAAAAATAAAAATTAA
2995914 TTAAAAAT-AAAATTAA
1 TTAAAAATAAAAATTAA
2995930 ACTTTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TTAAAAATAAAAATTAA
Found at i:2996250 original size:20 final size:20
Alignment explanation
Indices: 2996227--2996270 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2996217 GTAATTCTAG
*
2996227 ATTTCATATATAAATTATTT
1 ATTTCAAATATAAATTATTT
* *
2996247 ATTTTAAATTTAAATTATTT
1 ATTTCAAATATAAATTATTT
2996267 ATTT
1 ATTT
2996271 TTAAAATTAT
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:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTCAAATATAAATTATTT
Found at i:2996264 original size:16 final size:16
Alignment explanation
Indices: 2996245--2996306 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
2996235 TATAAATTAT
2996245 TTATTTTAAATTTAAA
1 TTATTTTAAATTTAAA
**
2996261 TTA-TTTATTTTTAAAA
1 TTATTTTAAATTT-AAA
2996277 TTATTTT-AATTTAAA
1 TTATTTTAAATTTAAA
* *
2996292 TTAATTCAAATTTAA
1 TTATTTTAAATTTAA
2996307 TTTAAGTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
15 15 0.41
16 19 0.51
17 3 0.08
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATTTTAAATTTAAA
Found at i:2996306 original size:32 final size:32
Alignment explanation
Indices: 2996245--2996306 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
2996235 TATAAATTAT
* **
2996245 TTATTTTAAATTTAAATTATTTATTTTTAAAA
1 TTATTTTAAATTTAAATTATTCAAATTTAAAA
2996277 TTATTTT-AATTTAAATTAATTCAAATTTAA
1 TTATTTTAAATTTAAATT-ATTCAAATTTAA
2996307 TTTAAGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (32 bp):
TTATTTTAAATTTAAATTATTCAAATTTAAAA
Found at i:3000702 original size:13 final size:13
Alignment explanation
Indices: 3000684--3000709 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3000674 TACACCAAGT
3000684 ATGTATCGATACA
1 ATGTATCGATACA
3000697 ATGTATCGATACA
1 ATGTATCGATACA
3000710 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3000707 original size:32 final size:33
Alignment explanation
Indices: 3000666--3000729 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
3000656 TAGCCAAACT
* **
3000666 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
3000698 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
3000730 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:3005956 original size:32 final size:33
Alignment explanation
Indices: 3005898--3005982 Score: 127
Period size: 32 Copynumber: 2.5 Consensus size: 33
3005888 TATCATAAAA
* *
3005898 ATAATATAAATATATAAATAATTTAAAATTTAT
1 ATAATATAAATATATTAATAAATTAAAATTTAT
3005931 ATAATATAAAT-TATTAATAAATTAAAATTTAT
1 ATAATATAAATATATTAATAAATTAAAATTTAT
3005963 ATAAATATAAAATATATTAA
1 AT-AATAT-AAATATATTAA
3005983 ATATAATAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
32 21 0.45
33 16 0.34
34 4 0.09
35 6 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
ATAATATAAATATATTAATAAATTAAAATTTAT
Found at i:3006003 original size:20 final size:18
Alignment explanation
Indices: 3005884--3006040 Score: 75
Period size: 16 Copynumber: 8.7 Consensus size: 18
3005874 ACTTAATTAA
*
3005884 AATATATCATAAAAATAAT
1 AATATAT-ATAAATATAAT
*
3005903 ATAAATATATAAATAATTTAA-
1 A-ATATATATAAAT-A--TAAT
*
3005924 AATTTATAT-AATATAA-
1 AATATATATAAATATAAT
*
3005940 ATTAT-TAATAAAT-TAA-
1 AATATAT-ATAAATATAAT
*
3005956 AATTTATATAAATATAA-
1 AATATATATAAATATAAT
3005973 AATATAT-TAAATATAAT
1 AATATATATAAATATAAT
3005990 AATAATATGATAAA-ATATAT
1 AAT-ATAT-ATAAATATA-AT
* *
3006010 AATCACAATATAAATATAAA
1 AAT-A-TATATAAATATAAT
3006030 AAT-TAT-TAAAT
1 AATATATATAAAT
3006041 TTATTTAACC
Statistics
Matches: 110, Mismatches: 13, Indels: 33
0.71 0.08 0.21
Matches are distributed among these distances:
15 1 0.01
16 34 0.31
17 18 0.16
18 5 0.05
19 12 0.11
20 31 0.28
21 6 0.05
22 3 0.03
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.38
Consensus pattern (18 bp):
AATATATATAAATATAAT
Found at i:3007255 original size:11 final size:10
Alignment explanation
Indices: 3007226--3007306 Score: 64
Period size: 11 Copynumber: 8.2 Consensus size: 10
3007216 TAGACTTCTC
3007226 AAATATAATA
1 AAATATAATA
*
3007236 CAAAAATAATTA
1 -AAATATAA-TA
3007248 AAATATAATA
1 AAATATAATA
*
3007258 TAATAT-A-A
1 AAATATAATA
3007266 AAA-ATAATA
1 AAATATAATA
3007275 TAAATATAATA
1 -AAATATAATA
3007286 TAAATAT-AT-
1 -AAATATAATA
*
3007295 AAATATCATA
1 AAATATAATA
3007305 AA
1 AA
3007307 TTTTTATAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
7 2 0.03
8 10 0.17
9 4 0.07
10 14 0.24
11 27 0.46
12 2 0.03
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (10 bp):
AAATATAATA
Done.