Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167826.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_1, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 36299135
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Warning! 357000 characters in sequence are not A, C, G, or T
File 18 of 402
Found at i:4238523 original size:34 final size:33
Alignment explanation
Indices: 4238463--4238526 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
4238453 CATTTTCTTT
*
4238463 TTTTCTTTTTTTTACACATTTCTCATTTTTCAC
1 TTTTCATTTTTTTACACATTTCTCATTTTTCAC
*
4238496 TTTTCATTTTTTT-CACTTTTTCATCATTTTT
1 TTTTCATTTTTTTACAC-ATTTC-TCATTTTT
4238527 TTTACTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 3 0.11
33 16 0.59
34 8 0.30
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (33 bp):
TTTTCATTTTTTTACACATTTCTCATTTTTCAC
Found at i:4243403 original size:19 final size:19
Alignment explanation
Indices: 4243379--4243424 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
4243369 ATAAATAAAT
*
4243379 AAAATAATAACATGAAA-CA
1 AAAATAATAA-ATAAAACCA
4243398 AAAATAAATAAATAAAACCA
1 AAAAT-AATAAATAAAACCA
4243418 AAAATAA
1 AAAATAA
4243425 AATAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.74, C:0.09, G:0.02, T:0.15
Consensus pattern (19 bp):
AAAATAATAAATAAAACCA
Found at i:4243419 original size:20 final size:19
Alignment explanation
Indices: 4243379--4243430 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
4243369 ATAAATAAAT
*
4243379 AAAAT-AATAACATGAAACA
1 AAAATAAATAA-ATAAAACA
4243398 AAAATAAATAAATAAAACCA
1 AAAATAAATAAATAAAA-CA
4243418 AAAATAAAATAAA
1 AAAAT-AAATAAA
4243431 ATATCAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 10 0.34
20 12 0.41
21 7 0.24
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.15
Consensus pattern (19 bp):
AAAATAAATAAATAAAACA
Found at i:4256242 original size:55 final size:54
Alignment explanation
Indices: 4256094--4256298 Score: 181
Period size: 53 Copynumber: 3.8 Consensus size: 54
4256084 AAATATATCT
* ** *
4256094 AATTATTTCGTCATTTGGGCCAAACTAGAAATATTTTC-TCTTTTTTAATTTCTA
1 AATT-TTTCATCATTTGGGCCAATTTAGAAATATTTTCTTTTTTTTTAATTTCTA
*
4256148 AATTTTTCATCATTTGGGCCTATTTAG-AAT-TTCTCTCTTTTTTTGTTAGATTTCTA
1 AATTTTTCATCATTTGGGCCAATTTAGAAATATT-T-TCTTTTTTT-TTA-ATTTCTA
* * * *
4256204 AA-TTTTCATTATTTTGGTCAATTTAGAAATATTTTC-TTTTTTTT-ATTTTTA
1 AATTTTTCATCATTTGGGCCAATTTAGAAATATTTTCTTTTTTTTTAATTTCTA
* * * * *
4256255 AATTTTTCACCATTTAGGCCTATTTA-AATTTTTTTTCTTTTTTT
1 AATTTTTCATCATTTGGGCCAATTTAGAA-ATATTTTCTTTTTTT
4256299 ATTGTTTTCG
Statistics
Matches: 124, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
51 12 0.10
52 28 0.23
53 29 0.23
54 15 0.12
55 25 0.20
56 13 0.10
57 2 0.02
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.57
Consensus pattern (54 bp):
AATTTTTCATCATTTGGGCCAATTTAGAAATATTTTCTTTTTTTTTAATTTCTA
Found at i:4256245 original size:56 final size:55
Alignment explanation
Indices: 4256094--4256298 Score: 167
Period size: 55 Copynumber: 3.8 Consensus size: 55
4256084 AAATATATCT
* ** *
4256094 AATTATTTCGTCATTTGGGCCAAACTAGAAATATTTTC--TCTTTTTTAATTTCTA
1 AATT-TTTCATCATTTGGGCCAATTTAGAAATATTTTCTTTTTTTTTTAATTTCTA
* *
4256148 AATTTTTCATCATTTGGGCCTATTTAG-AAT-TTCTCTCTTTTTTTGTTAGATTTCTA
1 AATTTTTCATCATTTGGGCCAATTTAGAAATATT-T-TCTTTTTTTTTTA-ATTTCTA
* * * *
4256204 AA-TTTTCATTATTTTGGTCAATTTAGAAATATTTTC--TTTTTTTT-ATTTTTA
1 AATTTTTCATCATTTGGGCCAATTTAGAAATATTTTCTTTTTTTTTTAATTTCTA
* * * * *
4256255 AATTTTTCACCATTTAGGCCTATTTA-AATTTTTTTTCTTTTTTT
1 AATTTTTCATCATTTGGGCCAATTTAGAA-ATATTTTCTTTTTTT
4256299 ATTGTTTTCG
Statistics
Matches: 121, Mismatches: 19, Indels: 22
0.75 0.12 0.14
Matches are distributed among these distances:
51 12 0.10
52 28 0.23
53 28 0.23
54 9 0.07
55 29 0.24
56 13 0.11
57 2 0.02
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.57
Consensus pattern (55 bp):
AATTTTTCATCATTTGGGCCAATTTAGAAATATTTTCTTTTTTTTTTAATTTCTA
Found at i:4256291 original size:52 final size:53
Alignment explanation
Indices: 4256127--4256299 Score: 174
Period size: 52 Copynumber: 3.2 Consensus size: 53
4256117 ACTAGAAATA
*
4256127 TTTTCTCTTTTTTAATTTCTAAATTTTTCATCATTTGGGCCTATTTAGAATTTCT
1 TTTTCT-TTTTTTAATTTCTAAATTTTTCATCATTTAGGCCTATTTAGAATTT-T
* * * * * * *
4256182 CTCTTT-TTTTGTTAGATTTCTAAA-TTTTCATTATTTTGGTCAATTTAGAA-ATA
1 -T-TTTCTTTTTTTA-ATTTCTAAATTTTTCATCATTTAGGCCTATTTAGAATTTT
* * *
4256235 TTTTCTTTTTTTTATTTTTAAATTTTTCACCATTTAGGCCTATTTA-AATTTT
1 TTTTCTTTTTTTAATTTCTAAATTTTTCATCATTTAGGCCTATTTAGAATTTT
4256287 TTTTCTTTTTTTA
1 TTTTCTTTTTTTA
4256300 TTGTTTTCGA
Statistics
Matches: 94, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
51 13 0.14
52 38 0.40
54 1 0.01
55 28 0.30
56 11 0.12
57 3 0.03
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.61
Consensus pattern (53 bp):
TTTTCTTTTTTTAATTTCTAAATTTTTCATCATTTAGGCCTATTTAGAATTTT
Found at i:4256758 original size:22 final size:21
Alignment explanation
Indices: 4256733--4256778 Score: 69
Period size: 19 Copynumber: 2.2 Consensus size: 21
4256723 AAATTTTATC
4256733 TAAATCATTCCACCATTTGGGA
1 TAAAT-ATTCCACCATTTGGGA
4256755 T-AA-ATTCCACCATTTGGGA
1 TAAATATTCCACCATTTGGGA
4256774 TAAAT
1 TAAAT
4256779 TTTATCTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
19 17 0.77
20 2 0.09
21 2 0.09
22 1 0.05
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (21 bp):
TAAATATTCCACCATTTGGGA
Found at i:4256763 original size:19 final size:19
Alignment explanation
Indices: 4256739--4256779 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
4256729 TATCTAAATC
4256739 ATTCCACCATTTGGGATAA
1 ATTCCACCATTTGGGATAA
4256758 ATTCCACCATTTGGGATAA
1 ATTCCACCATTTGGGATAA
4256777 ATT
1 ATT
4256780 TTATCTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (19 bp):
ATTCCACCATTTGGGATAA
Found at i:4257638 original size:41 final size:41
Alignment explanation
Indices: 4257593--4257713 Score: 129
Period size: 45 Copynumber: 2.9 Consensus size: 41
4257583 TAACAAGTTT
*
4257593 CTCTAAATAGAGGCTGAATGACTTTAAAAAATAAAAGGCTC
1 CTCTAAATAGAGGCTCAATGACTTTAAAAAATAAAAGGCTC
*
4257634 CTCT-AATCAGAGACTCAATGACTTTTTGAAAAAAATAAAAGGCTC
1 CTCTAAAT-AGAGGCTCAATGAC--TTT--AAAAAATAAAAGGCTC
* * *
4257679 CTCTAAACAGAGG-TATAATGACTTTGAAAAATAAA
1 CTCTAAATAGAGGCT-CAATGACTTTAAAAAATAAA
4257714 TGCTCATCTA
Statistics
Matches: 67, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
40 3 0.04
41 25 0.37
43 6 0.09
44 1 0.01
45 30 0.45
46 2 0.03
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.26
Consensus pattern (41 bp):
CTCTAAATAGAGGCTCAATGACTTTAAAAAATAAAAGGCTC
Found at i:4257703 original size:45 final size:45
Alignment explanation
Indices: 4257553--4257690 Score: 146
Period size: 41 Copynumber: 3.2 Consensus size: 45
4257543 AAAACTCCCT
** * *
4257553 TAAACAGAGACTCAACAAC--TTTGAAAAAAATAACAA-GTTTCTC
1 TAAACAGAGACTCAATGACTTTTTGAAAAAAATAA-AAGGCTCCTC
* * *
4257596 TAAATAGAGGCTGAATGAC--TTT--AAAAAATAAAAGGCTCCTC
1 TAAACAGAGACTCAATGACTTTTTGAAAAAAATAAAAGGCTCCTC
*
4257637 TAATCAGAGACTCAATGACTTTTTGAAAAAAATAAAAGGCTCCTC
1 TAAACAGAGACTCAATGACTTTTTGAAAAAAATAAAAGGCTCCTC
4257682 TAAACAGAG
1 TAAACAGAG
4257691 GTATAATGAC
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
40 2 0.03
41 29 0.37
43 20 0.26
45 27 0.35
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.24
Consensus pattern (45 bp):
TAAACAGAGACTCAATGACTTTTTGAAAAAAATAAAAGGCTCCTC
Found at i:4257768 original size:41 final size:41
Alignment explanation
Indices: 4257658--4257910 Score: 289
Period size: 41 Copynumber: 6.1 Consensus size: 41
4257648 TCAATGACTT
* * ** **
4257658 TTTGAAAAAAATAAAAGGCTCCTCTAAACAGAGGTATAATGAC
1 TTTG-AAAAAAT-AAATGCTTCTCTAAACAGAGGTACCACAAC
* * *
4257701 TTTG-AAAAATAAATGC-TCATCTAAACAGAAGCACCACAAA
1 TTTGAAAAAATAAATGCTTC-TCTAAACAGAGGTACCACAAC
* *
4257741 TTTG-AAAAATAAAATGCTTCTCTAAACAGAGGTACCATAAT
1 TTTGAAAAAAT-AAATGCTTCTCTAAACAGAGGTACCACAAC
* *
4257782 TTTGAAAAAACAAATGC-TCTTTTAAACAGAGGTACCACAAC
1 TTTGAAAAAATAAATGCTTC-TCTAAACAGAGGTACCACAAC
*
4257823 TTTGAAAAAATAAATGCTCCTCTAAACAGAGGTACCACAAC
1 TTTGAAAAAATAAATGCTTCTCTAAACAGAGGTACCACAAC
* *
4257864 TTTGAAAAAATAAATGCTTCTCTAAACAGAGGCATCACAAC
1 TTTGAAAAAATAAATGCTTCTCTAAACAGAGGTACCACAAC
4257905 TTTGAA
1 TTTGAA
4257911 GAATAAAAAG
Statistics
Matches: 181, Mismatches: 23, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.01
40 31 0.17
41 137 0.76
42 8 0.04
43 4 0.02
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.25
Consensus pattern (41 bp):
TTTGAAAAAATAAATGCTTCTCTAAACAGAGGTACCACAAC
Found at i:4257819 original size:82 final size:82
Alignment explanation
Indices: 4257664--4257936 Score: 345
Period size: 82 Copynumber: 3.3 Consensus size: 82
4257654 ACTTTTTGAA
* ** * *
4257664 AAAAATAAAAGGCTCCTCTAAACAGAGGTATAATGACTTTG-AAAAATAAATGCTCATCTAAACA
1 AAAAATAAAATGCTCCTCTAAACAGAGGTACCATAACTTTGAAAAAATAAATGCTCTTCTAAACA
* *
4257728 GAAGCACCACAAATTTG
66 GAGGCACCACAACTTTG
* * * *
4257745 AAAAATAAAATGCTTCTCTAAACAGAGGTACCATAATTTTGAAAAAACAAATGCTCTTTTAAACA
1 AAAAATAAAATGCTCCTCTAAACAGAGGTACCATAACTTTGAAAAAATAAATGCTCTTCTAAACA
*
4257810 GAGGTACCACAACTTTG
66 GAGGCACCACAACTTTG
*
4257827 AAAAA-ATAAATGCTCCTCTAAACAGAGGTACCACAACTTTGAAAAAATAAATGCT-TCTCTAAA
1 AAAAATA-AAATGCTCCTCTAAACAGAGGTACCATAACTTTGAAAAAATAAATGCTCT-TCTAAA
*
4257890 CAGAGGCATCACAACTTTG
64 CAGAGGCACCACAACTTTG
* * * *
4257909 AAGAATAAAAAGCTCATTTAAACAGAGG
1 AAAAATAAAATGCTCCTCTAAACAGAGG
4257937 CATGACTTTT
Statistics
Matches: 165, Mismatches: 23, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
81 37 0.22
82 127 0.77
83 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (82 bp):
AAAAATAAAATGCTCCTCTAAACAGAGGTACCATAACTTTGAAAAAATAAATGCTCTTCTAAACA
GAGGCACCACAACTTTG
Found at i:4257850 original size:123 final size:122
Alignment explanation
Indices: 4257667--4257936 Score: 339
Period size: 123 Copynumber: 2.2 Consensus size: 122
4257657 TTTTGAAAAA
* * * ** **
4257667 AATAAAAGGCTCCTCTAAACAGAGGTATAATGACTTTGAAAAATAAATGCTCATCTAAACAGAAG
1 AATAAAAAGCTCATTTAAACAGAGGTACCACAACTTTGAAAAATAAATGCTCATCTAAACAGAAG
* * *
4257732 CACCACAAATTTG-AAAAATAAAATGCTTCTCTAAACAGAGGTACCATAATTTTGAA-
66 CACCACAAATTTGAAAAAAT-AAATGCTTCTCTAAACAGAGGCACCACAACTTTGAAG
* *
4257788 AA-AACAAATGCTCTTTTAAACAGAGGTACCACAACTTTGAAAAAATAAATGCTCCTCTAAACAG
1 AATAA-AAA-GCTCATTTAAACAGAGGTACCACAACTTTG-AAAAATAAATGCTCATCTAAACAG
* * * *
4257852 AGGTACCACAACTTTGAAAAAATAAATGCTTCTCTAAACAGAGGCATCACAACTTTGAAG
63 AAGCACCACAAATTTGAAAAAATAAATGCTTCTCTAAACAGAGGCACCACAACTTTGAAG
4257912 AATAAAAAGCTCATTTAAACAGAGG
1 AATAAAAAGCTCATTTAAACAGAGG
4257937 CATGACTTTT
Statistics
Matches: 127, Mismatches: 16, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
120 2 0.02
121 4 0.03
122 24 0.19
123 84 0.66
124 11 0.09
125 2 0.02
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (122 bp):
AATAAAAAGCTCATTTAAACAGAGGTACCACAACTTTGAAAAATAAATGCTCATCTAAACAGAAG
CACCACAAATTTGAAAAAATAAATGCTTCTCTAAACAGAGGCACCACAACTTTGAAG
Found at i:4259641 original size:24 final size:23
Alignment explanation
Indices: 4259609--4259712 Score: 75
Period size: 24 Copynumber: 4.3 Consensus size: 23
4259599 GAGTATTTTT
*
4259609 TTCTCTCATTTTCATCTTTTTTCA
1 TTCTTTCATTTTC-TCTTTTTTCA
*
4259633 TTCTTTCATTTTTTTCTTTTTTCA
1 TTCTTTCA-TTTTCTCTTTTTTCA
* * * *
4259657 TCTTTTTTCTTTTTCTTTTTTTTCT
1 --TTCTTTCATTTTCTCTTTTTTCA
*
4259682 TTCTTTTCATTTTTTCTTCTTTTTCA
1 TTC-TTTCATTTTCTC-T-TTTTTCA
4259708 -TCTTT
1 TTCTTT
4259713 TTCCATCCAT
Statistics
Matches: 62, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
23 2 0.03
24 29 0.47
25 19 0.31
26 12 0.19
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (23 bp):
TTCTTTCATTTTCTCTTTTTTCA
Found at i:4259644 original size:16 final size:16
Alignment explanation
Indices: 4259603--4259703 Score: 98
Period size: 17 Copynumber: 5.9 Consensus size: 16
4259593 TAATTTGAGT
4259603 ATTTTTTTCTCTCATTTTC
1 ATTTTTTTCT-TC--TTTC
4259622 ATCTTTTTTCATTCTTTC
1 AT-TTTTTTC-TTCTTTC
*
4259640 ATTTTTTTCTTTTTTC
1 ATTTTTTTCTTCTTTC
4259656 ATCTTTTTTCTT-TTTC
1 AT-TTTTTTCTTCTTTC
*
4259672 TTTTTTTTCTTTCTTTTC
1 ATTTTTTTC-TTC-TTTC
4259690 A-TTTTTTCTTCTTT
1 ATTTTTTTCTTCTTT
4259704 TTCATCTTTT
Statistics
Matches: 73, Mismatches: 3, Indels: 16
0.79 0.03 0.17
Matches are distributed among these distances:
15 10 0.14
16 18 0.25
17 23 0.32
18 10 0.14
19 2 0.03
20 9 0.12
21 1 0.01
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (16 bp):
ATTTTTTTCTTCTTTC
Found at i:4259648 original size:9 final size:9
Alignment explanation
Indices: 4259617--4259715 Score: 72
Period size: 9 Copynumber: 11.6 Consensus size: 9
4259607 TTTTCTCTCA
4259617 TTTTCATCTT
1 TTTTCAT-TT
4259627 TTTTCA-TT
1 TTTTCATTT
*
4259635 CTTTCATTT
1 TTTTCATTT
4259644 TTTTC--TT
1 TTTTCATTT
4259651 TTTTCATCTT
1 TTTTCAT-TT
4259661 TTTTC---T
1 TTTTCATTT
*
4259667 TTTTCTTTT
1 TTTTCATTT
4259676 TTTTC-TTT
1 TTTTCATTT
4259684 CTTTTCA-TT
1 -TTTTCATTT
4259693 TTTTC-TTCT
1 TTTTCATT-T
*
4259702 TTTTCATCT
1 TTTTCATTT
4259711 TTTTC
1 TTTTC
4259716 CATCCATTAG
Statistics
Matches: 74, Mismatches: 3, Indels: 25
0.73 0.03 0.25
Matches are distributed among these distances:
6 6 0.08
7 7 0.09
8 16 0.22
9 31 0.42
10 14 0.19
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTCATTT
Found at i:4259714 original size:26 final size:27
Alignment explanation
Indices: 4259617--4259715 Score: 97
Period size: 25 Copynumber: 3.9 Consensus size: 27
4259607 TTTTCTCTCA
* *
4259617 TTTTCATCTTTTTTCAT-TCTTTCA-T
1 TTTTCTTCTTTTTTCATCTTTTTCATT
4259642 TTTT-TTCTTTTTTCATCTTTTT--TCT
1 TTTTCTTCTTTTTTCATCTTTTTCAT-T
*
4259667 TTTTCTT-TTTTTTC-TTTCTTTTCATT
1 TTTTCTTCTTTTTTCATCT-TTTTCATT
4259693 TTTTCTTC-TTTTTCATCTTTTTC
1 TTTTCTTCTTTTTTCATCTTTTTC
4259716 CATCCATTAG
Statistics
Matches: 61, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
24 13 0.21
25 24 0.39
26 21 0.34
27 3 0.05
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (27 bp):
TTTTCTTCTTTTTTCATCTTTTTCATT
Found at i:4264134 original size:24 final size:24
Alignment explanation
Indices: 4264085--4264139 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
4264075 CAAATTTAGA
* *
4264085 AAAAATTTTCATATAGAGATTCTT
1 AAAAATTTTCAAATAGAAATTCTT
*
4264109 AAAAATTTT-AAATAGTAAATTTTT
1 AAAAATTTTCAAATAG-AAATTCTT
4264133 AAGAAAT
1 AA-AAAT
4264140 CGCATCCTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 5 0.19
24 17 0.65
25 4 0.15
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (24 bp):
AAAAATTTTCAAATAGAAATTCTT
Found at i:4264300 original size:26 final size:26
Alignment explanation
Indices: 4264266--4264325 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
4264256 TTGAGATAAA
*
4264266 TTTA-AAAAAATTCCTTACTTAAAATT
1 TTTATAAAAATTTCC-TACTTAAAATT
* *
4264292 TTTATAAAAATTTGCTATTTAAAATT
1 TTTATAAAAATTTCCTACTTAAAATT
4264318 TTTATAAA
1 TTTATAAA
4264326 TTTCATCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 22 0.73
27 8 0.27
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.47
Consensus pattern (26 bp):
TTTATAAAAATTTCCTACTTAAAATT
Found at i:4265658 original size:2 final size:2
Alignment explanation
Indices: 4265651--4265684 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4265641 TCTCCTTCTA
4265651 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
4265685 TGTCCTCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4265888 original size:2 final size:2
Alignment explanation
Indices: 4265881--4265906 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4265871 AATGTGCTGA
4265881 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
4265907 TATTTATTTA
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:4281555 original size:6 final size:6
Alignment explanation
Indices: 4281544--4281568 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4281534 CTGTCTTTTC
4281544 CTCAGG CTCAGG CTCAGG CTCAGG C
1 CTCAGG CTCAGG CTCAGG CTCAGG C
4281569 ACGTGAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.32, T:0.16
Consensus pattern (6 bp):
CTCAGG
Found at i:4282239 original size:18 final size:18
Alignment explanation
Indices: 4282216--4282250 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4282206 GTATTTGAGC
* *
4282216 AGAAGACAGGTAAGAAGT
1 AGAAGAAAGATAAGAAGT
4282234 AGAAGAAAGATAAGAAG
1 AGAAGAAAGATAAGAAG
4282251 GGGAAGGAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.31, T:0.09
Consensus pattern (18 bp):
AGAAGAAAGATAAGAAGT
Found at i:4284323 original size:3 final size:3
Alignment explanation
Indices: 4284317--4284343 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4284307 AATTAATGAA
4284317 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
4284344 TGAAAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4287870 original size:18 final size:18
Alignment explanation
Indices: 4287850--4287919 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 18
4287840 GTAGGTATTC
*
4287850 TTTTTTTATTTTATTTTC
1 TTTTTTTATTTTATTTTA
4287868 TTTTTTTATTTTGATTTTA
1 TTTTTTTATTTT-ATTTTA
*
4287887 TTTATTTTATGTTGATTTTGA
1 TTT-TTTTAT-TTTATTTT-A
*
4287908 TTTTTTTGTTTT
1 TTTTTTTATTTT
4287920 TTTAAATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
18 12 0.27
19 10 0.23
20 16 0.36
21 6 0.14
ACGTcount: A:0.13, C:0.01, G:0.07, T:0.79
Consensus pattern (18 bp):
TTTTTTTATTTTATTTTA
Found at i:4287871 original size:10 final size:10
Alignment explanation
Indices: 4287853--4287911 Score: 52
Period size: 11 Copynumber: 5.9 Consensus size: 10
4287843 GGTATTCTTT
4287853 TTTTATTTTA
1 TTTTATTTTA
*
4287863 TTTT-CTTT-
1 TTTTATTTTA
4287871 TTTTATTTTGA
1 TTTTATTTT-A
4287882 TTTTA-TTTA
1 TTTTATTTTA
*
4287891 TTTTATGTTGA
1 TTTTAT-TTTA
4287902 TTTTGATTTT
1 TTTT-ATTTT
4287912 TTTGTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
8 4 0.10
9 12 0.31
10 7 0.18
11 14 0.36
12 2 0.05
ACGTcount: A:0.15, C:0.02, G:0.07, T:0.76
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:4287909 original size:6 final size:5
Alignment explanation
Indices: 4287853--4287911 Score: 52
Period size: 5 Copynumber: 11.8 Consensus size: 5
4287843 GGTATTCTTT
* *
4287853 TTTTA TTTTA TTTT- CTTT- TTTTA TTTTGA TTTTA -TTTA TTTTA TGTTGA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA T-TTTA
4287902 TTTTGA TTTT
1 TTTT-A TTTT
4287912 TTTGTTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
4 10 0.22
5 21 0.47
6 14 0.31
ACGTcount: A:0.15, C:0.02, G:0.07, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:4300241 original size:40 final size:40
Alignment explanation
Indices: 4300187--4300481 Score: 268
Period size: 40 Copynumber: 7.5 Consensus size: 40
4300177 CCTTTCAGAG
4300187 TTTT-AATTTAAAGTTTCATTGCCTTTGGTCAGAAGAGCC
1 TTTTAAATTTAAAGTTTCATTGCCTTTGGTCAGAAGAGCC
* * *
4300226 TTTTAAATTTAAAGTTTTATAGCCTTTGGTCAGATGAGCC
1 TTTTAAATTTAAAGTTTCATTGCCTTTGGTCAGAAGAGCC
* *
4300266 TTTTAAATTCTAAAGTTTCATTG-CTTCTGGTCGGAAGAGTC
1 TTTTAAATT-TAAAGTTTCATTGCCTT-TGGTCAGAAGAGCC
* * * * *
4300307 TTTTGAATTTAAAGTTTCATAGCCTCTAGTCAGATGAGCC
1 TTTTAAATTTAAAGTTTCATTGCCTTTGGTCAGAAGAGCC
* * *
4300347 TTTTAAATTCTAAAGTTTCATTGCTTTTGGTTAGAGGAGCC
1 TTTTAAATT-TAAAGTTTCATTGCCTTTGGTCAGAAGAGCC
* * * *
4300388 ------ATTTAAAGTTTCATTGCCTATAGTCA-AATAAGCT
1 TTTTAAATTTAAAGTTTCATTGCCTTTGGTCAGAA-GAGCC
* ** ** *
4300422 TTTTGAATTTAAAGTTTCACAG-CTTATATTCAGAAGAGTC
1 TTTTAAATTTAAAGTTTCATTGCCTT-TGGTCAGAAGAGCC
4300462 TTTTAAATTTAAAGTTTCAT
1 TTTTAAATTTAAAGTTTCAT
4300482 AGCCACTGAT
Statistics
Matches: 204, Mismatches: 38, Indels: 27
0.76 0.14 0.10
Matches are distributed among these distances:
33 1 0.00
34 22 0.11
35 3 0.01
39 6 0.03
40 113 0.55
41 59 0.29
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (40 bp):
TTTTAAATTTAAAGTTTCATTGCCTTTGGTCAGAAGAGCC
Found at i:4300319 original size:81 final size:80
Alignment explanation
Indices: 4300187--4300485 Score: 328
Period size: 81 Copynumber: 3.8 Consensus size: 80
4300177 CCTTTCAGAG
*
4300187 TTTT-AATT-TAAAGTTTCATTGCCTTTGGTCAGAAGAGCCTTTTAAATTTAAAGTTTTATAGCC
1 TTTTAAATTCTAAAGTTTCATTG-CTTTGGTCAGAAGAGCCTTTTAAATTTAAAGTTTCATAGCC
* *
4300250 TTTGGTCAGATGAGCC
65 TCTAGTCAGATGAGCC
* * *
4300266 TTTTAAATTCTAAAGTTTCATTGCTTCTGGTCGGAAGAGTCTTTTGAATTTAAAGTTTCATAGCC
1 TTTTAAATTCTAAAGTTTCATTGCTT-TGGTCAGAAGAGCCTTTTAAATTTAAAGTTTCATAGCC
4300331 TCTAGTCAGATGAGCC
65 TCTAGTCAGATGAGCC
* * *
4300347 TTTTAAATTCTAAAGTTTCATTGCTTTTGGTTAGAGGAGCC------ATTTAAAGTTTCATTGCC
1 TTTTAAATTCTAAAGTTTCATTGC-TTTGGTCAGAAGAGCCTTTTAAATTTAAAGTTTCATAGCC
* * * *
4300406 TATAGTCAAATAAGCT
65 TCTAGTCAGATGAGCC
* ** ** *
4300422 TTTTGAATT-TAAAGTTTCACAGCTTATATTCAGAAGAGTCTTTTAAATTTAAAGTTTCATAGCC
1 TTTTAAATTCTAAAGTTTCATTGCTT-TGGTCAGAAGAGCCTTTTAAATTTAAAGTTTCATAGCC
4300486 ACTGATCAAA
Statistics
Matches: 185, Mismatches: 24, Indels: 21
0.80 0.10 0.09
Matches are distributed among these distances:
73 2 0.01
74 21 0.11
75 37 0.20
79 4 0.02
80 24 0.13
81 95 0.51
82 2 0.01
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.41
Consensus pattern (80 bp):
TTTTAAATTCTAAAGTTTCATTGCTTTGGTCAGAAGAGCCTTTTAAATTTAAAGTTTCATAGCCT
CTAGTCAGATGAGCC
Found at i:4301683 original size:27 final size:27
Alignment explanation
Indices: 4301653--4301720 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 27
4301643 TTTCTTTTCT
4301653 TTTTTTTATTTTTTGTTTTGACTTTGA
1 TTTTTTTATTTTTTGTTTTGACTTTGA
* * *
4301680 TTTTTTTATTTTATG--TTGATTTTTA
1 TTTTTTTATTTTTTGTTTTGACTTTGA
*
4301705 TTTTTAT-TTTTTTGTT
1 TTTTTTTATTTTTTGTT
4301721 GTTTTTTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
24 6 0.18
25 14 0.41
27 14 0.41
ACGTcount: A:0.12, C:0.01, G:0.09, T:0.78
Consensus pattern (27 bp):
TTTTTTTATTTTTTGTTTTGACTTTGA
Found at i:4301709 original size:18 final size:19
Alignment explanation
Indices: 4301676--4301711 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4301666 TGTTTTGACT
*
4301676 TTGATTTTTTTATTTTATG
1 TTGATTTTTATATTTTATG
4301695 TTGATTTTTAT-TTTTAT
1 TTGATTTTTATATTTTAT
4301712 TTTTTTGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.17, C:0.00, G:0.08, T:0.75
Consensus pattern (19 bp):
TTGATTTTTATATTTTATG
Found at i:4301771 original size:9 final size:9
Alignment explanation
Indices: 4301759--4301792 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
4301749 GTTGTTGTTG
4301759 TTGTTATTA
1 TTGTTATTA
4301768 TTGTTATTA
1 TTGTTATTA
*
4301777 TTATTATTA
1 TTGTTATTA
4301786 -TGTTATT
1 TTGTTATT
4301793 CATTTTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 6 0.26
9 17 0.74
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (9 bp):
TTGTTATTA
Found at i:4307314 original size:2 final size:2
Alignment explanation
Indices: 4307307--4307355 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
4307297 CTGTGACTTC
* * *
4307307 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
4307349 AC AT AT A
1 AT AT AT A
4307356 AACATAAGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4318861 original size:10 final size:10
Alignment explanation
Indices: 4318837--4318866 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
4318827 TATTTTATCA
4318837 ATTAAAATA-
1 ATTAAAATAT
4318846 ATTAAAATAT
1 ATTAAAATAT
4318856 ATTAAAATAT
1 ATTAAAATAT
4318866 A
1 A
4318867 AAAGTTCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:4320945 original size:13 final size:14
Alignment explanation
Indices: 4320910--4320942 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
4320900 TTATTATTTA
*
4320910 TTTTTTGTTTCTTT
1 TTTTTTCTTTCTTT
4320924 TTTTTTCTTTCTTT
1 TTTTTTCTTTCTTT
4320938 TTTTT
1 TTTTT
4320943 CTTCTTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (14 bp):
TTTTTTCTTTCTTT
Found at i:4320948 original size:12 final size:13
Alignment explanation
Indices: 4320910--4320945 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
4320900 TTATTATTTA
*
4320910 TTTTTTGTTTCTTT
1 TTTTTTCTTTC-TT
4320924 TTTTTTCTTTCTT
1 TTTTTTCTTTCTT
4320937 TTTTTTCTT
1 TTTTTTCTT
4320946 CTTCTTCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (13 bp):
TTTTTTCTTTCTT
Found at i:4320951 original size:15 final size:15
Alignment explanation
Indices: 4320910--4320948 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
4320900 TTATTATTTA
*
4320910 TTTTTTGTTTC-TTT
1 TTTTTTCTTTCTTTT
4320924 TTTTTTCTTTCTTTT
1 TTTTTTCTTTCTTTT
4320939 TTTTCTTCTT
1 TTTT-TTCTT
4320949 CTTCCTTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.45
15 7 0.32
16 5 0.23
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.85
Consensus pattern (15 bp):
TTTTTTCTTTCTTTT
Found at i:4322827 original size:10 final size:10
Alignment explanation
Indices: 4322812--4322837 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
4322802 AAAATTATCC
4322812 TTTTAATAAA
1 TTTTAATAAA
4322822 TTTTAATAAA
1 TTTTAATAAA
4322832 TTTTAA
1 TTTTAA
4322838 GATTTCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTTAATAAA
Found at i:4323795 original size:62 final size:62
Alignment explanation
Indices: 4323646--4323802 Score: 187
Period size: 62 Copynumber: 2.6 Consensus size: 62
4323636 ATGATTACTA
* *
4323646 AAGGTATTTTTGATCAAAAATATCTT-AATAAT-CCTCTTATAAAAATGAAAGGGATTATTC
1 AAGGTATTTTTGATCAAAAATATCTTGAATAATCCCTCTTATAAAAATGAAAAGAATTATTC
* * * * * *
4323706 AAGGCAGTTTTGATTAAAAACATCTTGAATAATCCCT-TTATACAAATGAAAAAGAATTATTG
1 AAGGTATTTTTGATCAAAAATATCTTGAATAATCCCTCTTATAAAAATG-AAAAGAATTATTC
*
4323768 AAGGTATTTTTGGTCAAAAATGA-CTTGAATAATCC
1 AAGGTATTTTTGATCAAAAAT-ATCTTGAATAATCC
4323803 TTTTTAAAAT
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
60 22 0.28
61 16 0.20
62 41 0.51
63 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.34
Consensus pattern (62 bp):
AAGGTATTTTTGATCAAAAATATCTTGAATAATCCCTCTTATAAAAATGAAAAGAATTATTC
Found at i:4324487 original size:29 final size:29
Alignment explanation
Indices: 4324449--4324506 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
4324439 TTAAATAATA
*
4324449 TTATTATCATTAAATATTACAAAAATTTT
1 TTATTATCATTAAATATTAAAAAAATTTT
4324478 TTATTATCATTAAATATTAAAAAAATTTT
1 TTATTATCATTAAATATTAAAAAAATTTT
4324507 AATTAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (29 bp):
TTATTATCATTAAATATTAAAAAAATTTT
Found at i:4325163 original size:64 final size:64
Alignment explanation
Indices: 4325043--4325163 Score: 163
Period size: 65 Copynumber: 1.9 Consensus size: 64
4325033 CAATTTTTTT
* ** *
4325043 TAAGATCATTTAAAGCATTTTTTGTCAAAAAATACCTTAAATAATATTTTACAAAAAAATTTAA
1 TAAGATCATTTAAAGCATTTTTAGAAAAAAAATACCTTAAATAATATCTTACAAAAAAATTTAA
* * *
4325107 TAAGATTATTTAAGGCATTTTCTAGAAAAAAAATACCTTAAATAATCTCTTA-AAAAA
1 TAAGATCATTTAAAGCATTTT-TAGAAAAAAAATACCTTAAATAATATCTTACAAAAA
4325164 TGATCAACAT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
64 24 0.49
65 25 0.51
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.36
Consensus pattern (64 bp):
TAAGATCATTTAAAGCATTTTTAGAAAAAAAATACCTTAAATAATATCTTACAAAAAAATTTAA
Found at i:4328093 original size:21 final size:21
Alignment explanation
Indices: 4328069--4328110 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
4328059 GTGGGATTGA
4328069 GGGCGTTATTAATGCTTGACG
1 GGGCGTTATTAATGCTTGACG
4328090 GGGCGTTATTAATGCTTGACG
1 GGGCGTTATTAATGCTTGACG
4328111 TTTCTGTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.33, T:0.33
Consensus pattern (21 bp):
GGGCGTTATTAATGCTTGACG
Found at i:4329317 original size:18 final size:19
Alignment explanation
Indices: 4329280--4329317 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
4329270 TACAATAATA
*
4329280 ATAAATATAATAATATTTT
1 ATAAATATAATAATACTTT
*
4329299 ATAAA-ATAATAATCCTTT
1 ATAAATATAATAATACTTT
4329317 A
1 A
4329318 AAAGGCTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAAATATAATAATACTTT
Found at i:4330523 original size:38 final size:36
Alignment explanation
Indices: 4330451--4330525 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 36
4330441 TCTAAAATTA
* **
4330451 ATAAAATATTTTTAAATATAAAATATTATTTTAAAT
1 ATAAAATATTTTTAAATATAAAATATAAAATTAAAT
4330487 ATAAAATATTATTTTAAATATAAAATATAAAATTAAAT
1 ATAAAATA-T-TTTTAAATATAAAATATAAAATTAAAT
4330525 A
1 A
4330526 CATATAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 8 0.24
37 1 0.03
38 25 0.74
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (36 bp):
ATAAAATATTTTTAAATATAAAATATAAAATTAAAT
Found at i:4330525 original size:19 final size:19
Alignment explanation
Indices: 4330451--4330514 Score: 114
Period size: 19 Copynumber: 3.5 Consensus size: 19
4330441 TCTAAAATTA
4330451 ATAAAATA-T-TTTTAAAT
1 ATAAAATATTATTTTAAAT
4330468 ATAAAATATTATTTTAAAT
1 ATAAAATATTATTTTAAAT
4330487 ATAAAATATTATTTTAAAT
1 ATAAAATATTATTTTAAAT
4330506 ATAAAATAT
1 ATAAAATAT
4330515 AAAATTAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
17 8 0.18
18 1 0.02
19 36 0.80
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAAAATATTATTTTAAAT
Found at i:4331552 original size:21 final size:22
Alignment explanation
Indices: 4331528--4331575 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
4331518 ATATATTATT
* *
4331528 TTTAAAATTTTATTTTTTC-AA
1 TTTAAAATTTTATATTATCAAA
*
4331549 TTT-AATTTTTATATTATCAAA
1 TTTAAAATTTTATATTATCAAA
4331570 TTTAAA
1 TTTAAA
4331576 TATGTATGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 12 0.55
21 8 0.36
22 2 0.09
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTAAAATTTTATATTATCAAA
Found at i:4333457 original size:3 final size:3
Alignment explanation
Indices: 4333445--4333486 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
4333435 TTATAAAATT
*
4333445 ATA A-A ATA ATA ATA ATTA AGTG ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA A-TA A-TA ATA ATA ATA ATA ATA ATA AT
4333487 GAAAATGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.06
3 27 0.79
4 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4333536 original size:12 final size:12
Alignment explanation
Indices: 4333521--4333545 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4333511 TTTTCTTTTT
4333521 AAATAATAATAA
1 AAATAATAATAA
4333533 AAATAATAATAA
1 AAATAATAATAA
4333545 A
1 A
4333546 GTAGAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAATAATAA
Found at i:4333719 original size:18 final size:17
Alignment explanation
Indices: 4333698--4333735 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
4333688 ATAAAAAAGT
*
4333698 ATAAAAAGATAATAAATA
1 ATAAAAAAATAATAAA-A
4333716 ATAAAAAAATAATAAAA
1 ATAAAAAAATAATAAAA
4333733 ATA
1 ATA
4333736 GATAGACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
ATAAAAAAATAATAAAA
Found at i:4333850 original size:15 final size:16
Alignment explanation
Indices: 4333832--4333891 Score: 52
Period size: 17 Copynumber: 3.7 Consensus size: 16
4333822 ATTTCTAACC
4333832 CCTAAA-CCTTCAAAT
1 CCTAAACCCTTCAAAT
*
4333847 CCTAAACCCTCCAAA-
1 CCTAAACCCTTCAAAT
* *
4333862 CCTCAAAATCTTTCAAAT
1 CCT--AAACCCTTCAAAT
4333880 CCTAAAACCCTT
1 CCT-AAACCCTT
4333892 TTTACCTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
15 9 0.26
16 7 0.20
17 16 0.46
18 3 0.09
ACGTcount: A:0.38, C:0.37, G:0.00, T:0.25
Consensus pattern (16 bp):
CCTAAACCCTTCAAAT
Found at i:4335395 original size:2 final size:2
Alignment explanation
Indices: 4335388--4335412 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4335378 TTGCCTTTGC
4335388 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4335413 ATTTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4337656 original size:20 final size:20
Alignment explanation
Indices: 4337620--4337678 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
4337610 CATAAAAAAA
* * *
4337620 AAAAAATAGTAAAACATGAG
1 AAAAAATAGCAACACATAAG
*
4337640 AAAAAATGGCAACACATAAG
1 AAAAAATAGCAACACATAAG
* *
4337660 ACAAAGTAGCAACACATAA
1 AAAAAATAGCAACACATAA
4337679 AGAATTGGTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.61, C:0.14, G:0.14, T:0.12
Consensus pattern (20 bp):
AAAAAATAGCAACACATAAG
Found at i:4337738 original size:17 final size:17
Alignment explanation
Indices: 4337718--4337760 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
4337708 AATTTATAAA
4337718 AAAAAAAAGTAATACAT
1 AAAAAAAAGTAATACAT
** *
4337735 AAAAAATTGTAATTCAT
1 AAAAAAAAGTAATACAT
4337752 AAGAAAAAA
1 AA-AAAAAA
4337761 TTATAATTCA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (17 bp):
AAAAAAAAGTAATACAT
Found at i:4338027 original size:19 final size:19
Alignment explanation
Indices: 4338005--4338059 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
4337995 AGCGATATTT
4338005 CATAAGAAAAATAATAACA
1 CATAAGAAAAATAATAACA
* * * **
4338024 CATAA-AGAAGTAAAAATT
1 CATAAGAAAAATAATAACA
4338042 CATAAGAAAAATAATAAC
1 CATAAGAAAAATAATAAC
4338060 CTATAAAAAT
Statistics
Matches: 26, Mismatches: 9, Indels: 2
0.70 0.24 0.05
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.65, C:0.09, G:0.07, T:0.18
Consensus pattern (19 bp):
CATAAGAAAAATAATAACA
Found at i:4338044 original size:37 final size:35
Alignment explanation
Indices: 4338003--4338111 Score: 114
Period size: 37 Copynumber: 3.1 Consensus size: 35
4337993 AAAGCGATAT
4338003 TTCATAAGAAAAATAATAACACATAAAGAAGTAAAAA
1 TTCATAAGAAAAATAATAACACATAAA-AA-TAAAAA
* *
4338040 TTCATAAGAAAAATAATAAC-CTATAAAAATGACAA
1 TTCATAAGAAAAATAATAACAC-ATAAAAATAAAAA
* * * *
4338075 TTTATAAGAAAAAGTAGTAATACATAAGAA-AAAAA
1 TTCATAAGAAAAA-TAATAACACATAAAAATAAAAA
4338110 TT
1 TT
4338112 GTAATTAATA
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
35 21 0.34
36 14 0.23
37 26 0.43
ACGTcount: A:0.61, C:0.07, G:0.08, T:0.23
Consensus pattern (35 bp):
TTCATAAGAAAAATAATAACACATAAAAATAAAAA
Found at i:4338126 original size:16 final size:16
Alignment explanation
Indices: 4338113--4338143 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4338103 AAAAAAATTG
4338113 TAATTAATAAAAATAA
1 TAATTAATAAAAATAA
*
4338129 TAATTAGTAAAAATA
1 TAATTAATAAAAATA
4338144 TTTATAAAAA
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:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
TAATTAATAAAAATAA
Found at i:4345719 original size:40 final size:40
Alignment explanation
Indices: 4345656--4345748 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 40
4345646 GCCTCTCAGA
* * *
4345656 TTTTAACATTTAAAGTTCATTGCCTTTGGTTA-AATAAGCC
1 TTTTAACATTTAAAATTCATTGCCTTTGATCAGAA-AAGCC
**
4345696 TTTTAACATTTAAAATTTGTTGCCTTTGATCAGAAAAGCC
1 TTTTAACATTTAAAATTCATTGCCTTTGATCAGAAAAGCC
4345736 TTTTAA-ATTTAAA
1 TTTTAACATTTAAA
4345749 GTTTATCGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
39 7 0.15
40 38 0.81
41 2 0.04
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (40 bp):
TTTTAACATTTAAAATTCATTGCCTTTGATCAGAAAAGCC
Found at i:4345788 original size:40 final size:39
Alignment explanation
Indices: 4345736--4345827 Score: 112
Period size: 40 Copynumber: 2.3 Consensus size: 39
4345726 CAGAAAAGCC
* * *
4345736 TTTTAAATTTAAAGTTTATCGCCTCTAGTGAGAGGAGCT
1 TTTTAAATTTAAAGTTCATCACCTCTAATGAGAGGAGCT
* * *
4345775 TTTTAACATTTAAAGTTCATTACCTCTAATTAGATGAGCT
1 TTTTAA-ATTTAAAGTTCATCACCTCTAATGAGAGGAGCT
*
4345815 TTTTAATTTTAAA
1 TTTTAAATTTAAA
4345828 AGTCTCCGGT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 12 0.27
40 33 0.73
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (39 bp):
TTTTAAATTTAAAGTTCATCACCTCTAATGAGAGGAGCT
Found at i:4346042 original size:39 final size:38
Alignment explanation
Indices: 4345906--4346149 Score: 210
Period size: 39 Copynumber: 6.4 Consensus size: 38
4345896 TCCTCTTAGA
* *
4345906 TTTTTAATTTAAAGTTTGTTGCCTTTGGTTAAATGAGC
1 TTTTGAATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGC
* * * * * * * *
4345944 -----CATTTAAAGTTCGTTACCTCTGATCAGATGAGCC
1 TTTTGAATTTAAAGTTTGTTGCCTTTGGTTAAAGGAG-C
* * *
4345978 TTTTTAATTTAAAGTTTGTTACCTTTGGTTAAAGAAGC
1 TTTTGAATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGC
* *
4346016 TTTTGAAATTTAAAGTATGCTGCCTTTGGTTAAAGGAGC
1 TTTTG-AATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGC
*
4346055 TTTTTGAATTTAAAGTTTGTTGCATTTGGTTAAAGGAGC
1 -TTTTGAATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGC
* * * * * *
4346094 TTTTTGGATTTAAAGTTTGTTGCTTTTGATGATATGAGC
1 -TTTTGAATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGC
4346133 TTTTTGAATTTAAAGTT
1 -TTTTGAATTTAAAGTT
4346150 CATTACATCT
Statistics
Matches: 168, Mismatches: 30, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
33 25 0.15
34 1 0.01
38 5 0.03
39 132 0.79
40 5 0.03
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.45
Consensus pattern (38 bp):
TTTTGAATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGC
Found at i:4346069 original size:78 final size:78
Alignment explanation
Indices: 4345977--4346187 Score: 237
Period size: 78 Copynumber: 2.7 Consensus size: 78
4345967 TCAGATGAGC
*
4345977 CTTTTT-AATTTAAAGTTTGTTACCTTTGGTTAAAGAAGC-TTTTGAAATTTAAAGTATGCTGCC
1 CTTTTTGAATTTAAAGTTTGTTACATTTGGTTAAAGAAGCTTTTTG-AATTTAAAGTATGCTGCC
* *
4346040 TTTGGTTAAAGGAG
65 TTTGATGAAAGGAG
* * * * * *
4346054 CTTTTTGAATTTAAAGTTTGTTGCATTTGGTTAAAGGAGCTTTTTGGATTTAAAGTTTGTTGCTT
1 CTTTTTGAATTTAAAGTTTGTTACATTTGGTTAAAGAAGCTTTTTGAATTTAAAGTATGCTGCCT
* *
4346119 TTGATGATATGAG
66 TTGATGAAAGGAG
** * * * * *
4346132 CTTTTTGAATTTAAAGTTCATTACATCTAGTGAGATAAGCTTTTTGAATTTAAAGT
1 CTTTTTGAATTTAAAGTTTGTTACATTTGGTTAAAGAAGCTTTTTGAATTTAAAGT
4346188 TTTATAGCCT
Statistics
Matches: 111, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
77 6 0.05
78 100 0.90
79 5 0.05
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.45
Consensus pattern (78 bp):
CTTTTTGAATTTAAAGTTTGTTACATTTGGTTAAAGAAGCTTTTTGAATTTAAAGTATGCTGCCT
TTGATGAAAGGAG
Found at i:4346118 original size:23 final size:23
Alignment explanation
Indices: 4346053--4346120 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
4346043 GGTTAAAGGA
*
4346053 GCTTTTTGAATTTAAAGTTTGTT
1 GCTTTTTGGATTTAAAGTTTGTT
* *
4346076 GC-ATTTGG--TTAAAG---G-A
1 GCTTTTTGGATTTAAAGTTTGTT
4346092 GCTTTTTGGATTTAAAGTTTGTT
1 GCTTTTTGGATTTAAAGTTTGTT
4346115 GCTTTT
1 GCTTTT
4346121 GATGATATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 14
0.63 0.10 0.27
Matches are distributed among these distances:
16 2 0.06
17 6 0.18
19 6 0.18
20 6 0.18
22 5 0.15
23 8 0.24
ACGTcount: A:0.21, C:0.06, G:0.22, T:0.51
Consensus pattern (23 bp):
GCTTTTTGGATTTAAAGTTTGTT
Found at i:4346940 original size:20 final size:20
Alignment explanation
Indices: 4346884--4346940 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
4346874 TTTATGAAAT
** *
4346884 TTTGAATTTTTCGACAACCA
1 TTTGAATTTTTCGATGACAA
* *
4346904 TTTAAATTTTTCAATGACAA
1 TTTGAATTTTTCGATGACAA
*
4346924 TTTGAATTTTTTGATGA
1 TTTGAATTTTTCGATGA
4346941 TCGAAATCTA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (20 bp):
TTTGAATTTTTCGATGACAA
Found at i:4347238 original size:11 final size:11
Alignment explanation
Indices: 4347222--4347256 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
4347212 GTTTCGTAGG
4347222 TTTTTTCTTTT
1 TTTTTTCTTTT
4347233 TTTTTTCTTTT
1 TTTTTTCTTTT
4347244 TATTTTTCGTTTT
1 T-TTTTTC-TTTT
4347257 CGTTTTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 12 0.55
12 6 0.27
13 4 0.18
ACGTcount: A:0.03, C:0.09, G:0.03, T:0.86
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:4347268 original size:6 final size:6
Alignment explanation
Indices: 4347259--4347299 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
4347249 TTCGTTTTCG
* *
4347259 TTTTGA TTTTGA TTTTGA TTTTTTA TGTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA -TTTTGA TTTTGA TTTTGA TTTT
4347300 TTTTATGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.71
Consensus pattern (6 bp):
TTTTGA
Found at i:4347281 original size:19 final size:19
Alignment explanation
Indices: 4347259--4347300 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
4347249 TTCGTTTTCG
*
4347259 TTTTGATTTTGATTTTGAT
1 TTTTGATGTTGATTTTGAT
*
4347278 TTTTTATGTTGATTTTGAT
1 TTTTGATGTTGATTTTGAT
4347297 TTTT
1 TTTT
4347301 TTTATGTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (19 bp):
TTTTGATGTTGATTTTGAT
Found at i:4347313 original size:3 final size:3
Alignment explanation
Indices: 4347307--4347333 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4347297 TTTTTTTATG
4347307 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
4347334 CTGGTAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4348473 original size:20 final size:20
Alignment explanation
Indices: 4348440--4348479 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4348430 CCATCAATTT
*
4348440 TTTTAGTAAGTTTTAATTAA
1 TTTTAATAAGTTTTAATTAA
* *
4348460 TTTTAATAATTTTTTATTAA
1 TTTTAATAAGTTTTAATTAA
4348480 AAATAATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTTAATAAGTTTTAATTAA
Found at i:4361685 original size:22 final size:22
Alignment explanation
Indices: 4361660--4361714 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
4361650 AATTATTTGG
4361660 ATTCGATTCGAAGAAAATTCGA
1 ATTCGATTCGAAGAAAATTCGA
4361682 ATTCGATTCGAAGAAAATTCGA
1 ATTCGATTCGAAGAAAATTCGA
4361704 ATTCGATTCGA
1 ATTCGATTCGA
4361715 TTATTATCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (22 bp):
ATTCGATTCGAAGAAAATTCGA
Found at i:4363308 original size:15 final size:16
Alignment explanation
Indices: 4363280--4363319 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
4363270 AAAATAAAGG
4363280 AAAATATTATAATTATT
1 AAAATATTATAATT-TT
4363297 AAAAT-TTA-AATTTT
1 AAAATATTATAATTTT
4363311 AAAA-ATTAT
1 AAAATATTAT
4363320 TATATAGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
14 9 0.43
15 4 0.19
16 3 0.14
17 5 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAAATATTATAATTTT
Found at i:4364291 original size:3 final size:3
Alignment explanation
Indices: 4364283--4364319 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
4364273 TACAGGCTAA
* *
4364283 TGG TGG TGG TGG TGG TGG TGG TGG TGT TGG GGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG T
4364320 AACCGCCTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:4369681 original size:10 final size:10
Alignment explanation
Indices: 4369666--4369692 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
4369656 TAAAATTATC
4369666 ATTTTAATAA
1 ATTTTAATAA
4369676 ATTTTAATAA
1 ATTTTAATAA
4369686 ATTTTAA
1 ATTTTAA
4369693 AATTTCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
ATTTTAATAA
Found at i:4381195 original size:48 final size:45
Alignment explanation
Indices: 4381093--4381436 Score: 323
Period size: 45 Copynumber: 7.5 Consensus size: 45
4381083 AAAGAAAAAA
* * * * * *
4381093 TTTTAAAGTTGTTGAGCATTTGCTAAAATGAACATTTTCAAGACT
1 TTTTAAAGTTGTTGAGCCTCTGCTAAGAGGAGCATTTTCAAGAAT
** * *
4381138 TTTTAAAGTTGCGGAGCCTCTGCCT-ATAGGAGCTTTTTCAAGATAAAT
1 TTTTAAAGTTGTTGAGCCTCTG-CTAAGAGGAGCATTTTCAAG---AAT
* * * *
4381186 TTTTAAAGTTATTGAACCTCTGTTAAAAGGAGCATTTTCAAGAAT
1 TTTTAAAGTTGTTGAGCCTCTGCTAAGAGGAGCATTTTCAAGAAT
* * * * * *
4381231 TTTTAAAGTTATAGAGCTTCTGCTTATAGGAGCTTTTTCAAGATGAGT
1 TTTTAAAGTTGTTGAGCCTCTGCTAAGAGGAGCATTTTCAAGA--A-T
* * **
4381279 TTTTAAAGTTGTTAAGCCTCTGCTGAGATAAGCATTTTCAAGAA-
1 TTTTAAAGTTGTTGAGCCTCTGCTAAGAGGAGCATTTTCAAGAAT
*
4381323 TTTTAAAGTTGTTGAGCCTCTGCTAAGAGGATCATTTTCAAGAAT
1 TTTTAAAGTTGTTGAGCCTCTGCTAAGAGGAGCATTTTCAAGAAT
* * * *
4381368 TTTTAAAGTTATAGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATGAAT
1 TTTTAAAGTTGTTGAGCCTCTGCTAAGAGGAGCATTTTC-A-A-GAAT
4381416 TTTTAAAGTTGTTGAGCCTCT
1 TTTTAAAGTTGTTGAGCCTCT
4381437 ACTGAGAGAA
Statistics
Matches: 243, Mismatches: 44, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
44 39 0.16
45 104 0.43
46 4 0.02
47 3 0.01
48 93 0.38
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.39
Consensus pattern (45 bp):
TTTTAAAGTTGTTGAGCCTCTGCTAAGAGGAGCATTTTCAAGAAT
Found at i:4381253 original size:93 final size:93
Alignment explanation
Indices: 4381084--4381436 Score: 331
Period size: 93 Copynumber: 3.8 Consensus size: 93
4381074 GTTTCAAGAA
* * * * * * * * *
4381084 AAGAAAAAATTTTAAAGTTGTTGAGCATTTGCTAAAATGAACATTTTCAAGACTTTTTAAAGTTG
1 AAGATAAATTTTTAAAGTTATTGAACCTCTGCTAAAAGGAGCATTTTCAAGAATTTTTAAAGTTG
**
4381149 CGGAGCCTCTGCCTATAGGAGCTTTTTC
66 TAGAGCCTCTGCCTATAGGAGCTTTTTC
* *
4381177 AAGATAAATTTTTAAAGTTATTGAACCTCTGTTAAAAGGAGCATTTTCAAGAATTTTTAAAGTTA
1 AAGATAAATTTTTAAAGTTATTGAACCTCTGCTAAAAGGAGCATTTTCAAGAATTTTTAAAGTTG
* *
4381242 TAGAGCTTCTGCTTATAGGAGCTTTTTC
66 TAGAGCCTCTGCCTATAGGAGCTTTTTC
* * * * * **
4381270 AAGATGAGTTTTTAAAGTTGTT-AAGCCTCTGCTGAGATAAGCATTTTCAAGAA-TTTTAAAGTT
1 AAGATAAATTTTTAAAGTTATTGAA-CCTCTGCTAAAAGGAGCATTTTCAAGAATTTTTAAAGTT
* * * *
4381333 GTTGAGCCTCTG-CTAAGAGGATCATTTTC
65 GTAGAGCCTCTGCCT-ATAGGAGCTTTTTC
* * * * *
4381362 AAG---AATTTTTAAAGTTATAGAGCCTCTGCTTAGAGGAGCTTTTTCAAGATGAATTTTTAAAG
1 AAGATAAATTTTTAAAGTTATTGAACCTCTGCTAAAAGGAGCATTTTC-A-A-GAATTTTTAAAG
*
4381424 TTGTTGAGCCTCT
63 TTGTAGAGCCTCT
4381437 ACTGAGAGAA
Statistics
Matches: 215, Mismatches: 38, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
89 32 0.15
90 2 0.01
91 2 0.01
92 38 0.18
93 141 0.66
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (93 bp):
AAGATAAATTTTTAAAGTTATTGAACCTCTGCTAAAAGGAGCATTTTCAAGAATTTTTAAAGTTG
TAGAGCCTCTGCCTATAGGAGCTTTTTC
Found at i:4381367 original size:137 final size:137
Alignment explanation
Indices: 4381186--4381453 Score: 428
Period size: 137 Copynumber: 2.0 Consensus size: 137
4381176 CAAGATAAAT
* *
4381186 TTTTAAAGTTATTGAACCTCTGTTAAAAGGAGCATTTTCAAGAATTTTTAAAGTTATAGAGCTTC
1 TTTTAAAGTTATTGAACCTCTGCTAAAAGGAGCATTTTCAAGAATTTTTAAAGTTATAGAGCCTC
* * * *
4381251 TGCTTATAGGAGCTTTTTCAAGATGAGTTTTTAAAGTTGTTAAGCCTCTGCTGAGATAAGCATTT
66 TGCTTAGAGGAGCTTTTTCAAGATGAATTTTTAAAGTTGTTAAGCCTCTACTGAGAGAAGCATTT
4381316 TCAAGAA
131 TCAAGAA
* * * *
4381323 TTTTAAAGTTGTTGAGCCTCTGCTAAGAGGATCATTTTCAAGAATTTTTAAAGTTATAGAGCCTC
1 TTTTAAAGTTATTGAACCTCTGCTAAAAGGAGCATTTTCAAGAATTTTTAAAGTTATAGAGCCTC
* *
4381388 TGCTTAGAGGAGCTTTTTCAAGATGAATTTTTAAAGTTGTTGAGCCTCTACTGAGAGAAGTATTT
66 TGCTTAGAGGAGCTTTTTCAAGATGAATTTTTAAAGTTGTTAAGCCTCTACTGAGAGAAGCATTT
4381453 T
131 T
4381454 TTTAAGATAG
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
137 119 1.00
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (137 bp):
TTTTAAAGTTATTGAACCTCTGCTAAAAGGAGCATTTTCAAGAATTTTTAAAGTTATAGAGCCTC
TGCTTAGAGGAGCTTTTTCAAGATGAATTTTTAAAGTTGTTAAGCCTCTACTGAGAGAAGCATTT
TCAAGAA
Found at i:4381504 original size:51 final size:50
Alignment explanation
Indices: 4381171--4381504 Score: 179
Period size: 45 Copynumber: 7.1 Consensus size: 50
4381161 CTATAGGAGC
* * * ** * * *
4381171 TTTTTCAAGATAAATTTTTAAAGTTATTGAACCTCTGTTAAAAGGAGCA-
1 TTTTTCAAGATGAATTTTTAAAGTTATCGAGCCTCTACTGAGAGAAGCAT
* * * * * *
4381220 -TTTTC-A-A-GAATTTTTAAAGTTATAGAGCTTCTGCTTATAGGAGC--
1 TTTTTCAAGATGAATTTTTAAAGTTATCGAGCCTCTACTGAGAGAAGCAT
* * ** * *
4381264 TTTTTCAAGATGAGTTTTTAAAGTTGTTAAGCCTCTGCTGAGATAAGCA-
1 TTTTTCAAGATGAATTTTTAAAGTTATCGAGCCTCTACTGAGAGAAGCAT
* * * * * *
4381313 -TTTTC-A-A-GAA-TTTTAAAGTTGTTGAGCCTCTGCTAAGAGGATCA-
1 TTTTTCAAGATGAATTTTTAAAGTTATCGAGCCTCTACTGAGAGAAGCAT
* * * *
4381357 -TTTTC-A-A-GAATTTTTAAAGTTATAGAGCCTCTGCTTAGAGGAGC--
1 TTTTTCAAGATGAATTTTTAAAGTTATCGAGCCTCTACTGAGAGAAGCAT
* * *
4381401 TTTTTCAAGATGAATTTTTAAAGTTGTTGAGCCTCTACTGAGAGAAGTAT
1 TTTTTCAAGATGAATTTTTAAAGTTATCGAGCCTCTACTGAGAGAAGCAT
* * *
4381451 TTTTTTAAGATAGAA-TTTTAAAGTTATCGAGCCTCTATTGAGATAAGCCAT
1 TTTTTCAAGAT-GAATTTTTAAAGTTATCGAGCCTCTACTGAGAGAAG-CAT
4381502 TTT
1 TTT
4381505 AAATTTTCAA
Statistics
Matches: 233, Mismatches: 38, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
44 39 0.17
45 71 0.30
46 4 0.02
47 4 0.02
48 69 0.30
50 38 0.16
51 8 0.03
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (50 bp):
TTTTTCAAGATGAATTTTTAAAGTTATCGAGCCTCTACTGAGAGAAGCAT
Found at i:4384622 original size:12 final size:13
Alignment explanation
Indices: 4384607--4384646 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
4384597 ATTCAATTTT
4384607 TTATTTTAA-ATA
1 TTATTTTAATATA
4384619 TTATTTTAATATA
1 TTATTTTAATATA
**
4384632 AAATTTTAATATA
1 TTATTTTAATATA
4384645 TT
1 TT
4384647 TAAATTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATTTTAATATA
Found at i:4387147 original size:3 final size:3
Alignment explanation
Indices: 4387141--4387171 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4387131 GATCATCATC
4387141 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
4387172 GATGACAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:4410347 original size:15 final size:15
Alignment explanation
Indices: 4410327--4410451 Score: 52
Period size: 15 Copynumber: 8.6 Consensus size: 15
4410317 TGACTAGGTT
4410327 TTTCTTTCTTCTTTC
1 TTTCTTTCTTCTTTC
*
4410342 TTTCTTTCCTC-TTC
1 TTTCTTTCTTCTTTC
*
4410356 AATTCTTGT-TTC-TTC
1 -TTTCTT-TCTTCTTTC
4410371 TTCTCTTT-TTC-TTC
1 TT-TCTTTCTTCTTTC
*
4410385 TTTC-GTCTTCGTTTC
1 TTTCTTTCTTC-TTTC
* * *
4410400 CTCCTTTCCTTCTCTC
1 TTTCTTT-CTTCTTTC
*
4410416 TTTC-TTCCT-TTTC
1 TTTCTTTCTTCTTTC
* *
4410429 TTT-TCTCTTCCTTC
1 TTTCTTTCTTCTTTC
*
4410443 TTTCCTTCT
1 TTTCTTTCT
4410452 CATTGGTCCT
Statistics
Matches: 81, Mismatches: 18, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
12 1 0.01
13 14 0.17
14 21 0.26
15 34 0.42
16 7 0.09
17 4 0.05
ACGTcount: A:0.02, C:0.32, G:0.02, T:0.64
Consensus pattern (15 bp):
TTTCTTTCTTCTTTC
Found at i:4410424 original size:20 final size:19
Alignment explanation
Indices: 4410327--4410452 Score: 73
Period size: 19 Copynumber: 6.5 Consensus size: 19
4410317 TGACTAGGTT
*
4410327 TTTCTTTCT-TCTTTCTTTC
1 TTTCCTTCTCTCTTTC-TTC
* *
4410346 TTTCC-TCT-TCAATTCTTG
1 TTTCCTTCTCTC-TTTCTTC
*
4410364 TTTCTTCTTCTCTTTTTCTTC
1 TTTC--CTTCTCTCTTTCTTC
* *
4410385 TTT-CGTCT-TCGTTTCCTCC
1 TTTCCTTCTCTC-TTT-CTTC
4410404 TTTCCTTCTCTCTTTCTTCC
1 TTTCCTTCTCTCTTTCTT-C
* * *
4410424 TTTTCTTTTCTCTTCCTTC
1 TTTCCTTCTCTCTTTCTTC
4410443 TTTCCTTCTC
1 TTTCCTTCTC
4410453 ATTGGTCCTC
Statistics
Matches: 81, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
17 1 0.01
18 18 0.22
19 24 0.30
20 24 0.30
21 13 0.16
22 1 0.01
ACGTcount: A:0.02, C:0.33, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTCCTTCTCTCTTTCTTC
Found at i:4410497 original size:12 final size:12
Alignment explanation
Indices: 4410462--4410513 Score: 68
Period size: 12 Copynumber: 4.2 Consensus size: 12
4410452 CATTGGTCCT
*
4410462 CTTCTCCTCCTC
1 CTTCTCCTTCTC
* *
4410474 TTTTCTCTTTCTC
1 -CTTCTCCTTCTC
4410487 CTTCTCCTTCTC
1 CTTCTCCTTCTC
4410499 CTTCTCCTTCTC
1 CTTCTCCTTCTC
4410511 CTT
1 CTT
4410514 TGCGTTCTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 25 0.74
13 9 0.26
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (12 bp):
CTTCTCCTTCTC
Found at i:4410521 original size:18 final size:18
Alignment explanation
Indices: 4410462--4410513 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
4410452 CATTGGTCCT
* *
4410462 CTTCTCCTCCTCTTTTCTC
1 CTTCTCCTTCTC-CTTCTC
*
4410481 TTTCTCCTTCTCCTTCTC
1 CTTCTCCTTCTCCTTCTC
4410499 CTTCTCCTTCTCCTT
1 CTTCTCCTTCTCCTT
4410514 TGCGTTCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 19 0.66
19 10 0.34
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (18 bp):
CTTCTCCTTCTCCTTCTC
Found at i:4414701 original size:21 final size:21
Alignment explanation
Indices: 4414660--4414701 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4414650 TTTTAATCTC
*
4414660 AAAAAGTAAAAAAATATATAT
1 AAAAAGTAAAAAAATAGATAT
*
4414681 AAAAA-TAAAAATTATAGATAT
1 AAAAAGTAAAAA-AATAGATAT
4414702 TTTAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (21 bp):
AAAAAGTAAAAAAATAGATAT
Found at i:4414718 original size:13 final size:13
Alignment explanation
Indices: 4414700--4414724 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4414690 AATTATAGAT
4414700 ATTTTAAAAAATA
1 ATTTTAAAAAATA
4414713 ATTTTAAAAAAT
1 ATTTTAAAAAAT
4414725 CTATAAAATA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTTTAAAAAATA
Found at i:4414760 original size:3 final size:3
Alignment explanation
Indices: 4414752--4414786 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4414742 AAACAGAAAA
4414752 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4414787 GAAAAAGACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4424312 original size:23 final size:22
Alignment explanation
Indices: 4424286--4424333 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
4424276 TGCTAAGAGC
4424286 AGTAATGGATCCCTAAAAATAAA
1 AGTAA-GGATCCCTAAAAATAAA
* *
4424309 AGT-AGGATCCCTAAAAGTATA
1 AGTAAGGATCCCTAAAAATAAA
4424330 AGTA
1 AGTA
4424334 GCACAATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 18 0.82
22 1 0.05
23 3 0.14
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.23
Consensus pattern (22 bp):
AGTAAGGATCCCTAAAAATAAA
Found at i:4424316 original size:21 final size:21
Alignment explanation
Indices: 4424292--4424334 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
4424282 GAGCAGTAAT
4424292 GGATCCCTAAAAATAAAAGTA
1 GGATCCCTAAAAATAAAAGTA
* *
4424313 GGATCCCTAAAAGTATAAGTA
1 GGATCCCTAAAAATAAAAGTA
4424334 G
1 G
4424335 CACAATGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.21
Consensus pattern (21 bp):
GGATCCCTAAAAATAAAAGTA
Found at i:4434437 original size:14 final size:14
Alignment explanation
Indices: 4434418--4434444 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4434408 AAAAAAAAGG
4434418 TTTAATTATTTTTA
1 TTTAATTATTTTTA
4434432 TTTAATTATTTTT
1 TTTAATTATTTTT
4434445 TGTTGAAAAT
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTAATTATTTTTA
Found at i:4437701 original size:23 final size:23
Alignment explanation
Indices: 4437675--4437750 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 23
4437665 CACCTAAGGC
4437675 ATTCTTAAAAATCACTATTAGGA
1 ATTCTTAAAAATCACTATTAGGA
*
4437698 ATTCTTAAAAAT--C--TT--GC
1 ATTCTTAAAAATCACTATTAGGA
*
4437715 ATTCTTGAAAATCACTATTAGGA
1 ATTCTTAAAAATCACTATTAGGA
*
4437738 ATTCTAAAAAATC
1 ATTCTTAAAAATC
4437751 TTATATTCGG
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
17 12 0.29
19 3 0.07
21 3 0.07
23 24 0.57
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (23 bp):
ATTCTTAAAAATCACTATTAGGA
Found at i:4437717 original size:40 final size:40
Alignment explanation
Indices: 4437673--4437752 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
4437663 CTCACCTAAG
*
4437673 GCATTCTTAAAAATCACTATTAGGAATTCTTAAAAATCTT
1 GCATTCTTAAAAATCACTATTAGGAATTCTAAAAAATCTT
*
4437713 GCATTCTTGAAAATCACTATTAGGAATTCTAAAAAATCTT
1 GCATTCTTAAAAATCACTATTAGGAATTCTAAAAAATCTT
4437753 ATATTCGGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (40 bp):
GCATTCTTAAAAATCACTATTAGGAATTCTAAAAAATCTT
Found at i:4438934 original size:3 final size:3
Alignment explanation
Indices: 4438926--4438975 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
4438916 ATCTTTGAAG
*
4438926 ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4438974 AT
1 AT
4438976 GTACACGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4439930 original size:12 final size:12
Alignment explanation
Indices: 4439886--4439957 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 12
4439876 CGACTTGGTA
*
4439886 TATATATATAAAT
1 TATATAT-TTAAT
4439899 TAT-T-TTTAAT
1 TATATATTTAAT
4439909 TA-ATTATTTAAT
1 TATA-TATTTAAT
*
4439921 TATATGTTT-A-
1 TATATATTTAAT
4439931 TATATATTTAAT
1 TATATATTTAAT
*
4439943 TTTATATTTACAT
1 TATATATTTA-AT
4439956 TA
1 TA
4439958 AAAATGATAG
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
10 14 0.30
11 4 0.09
12 22 0.47
13 7 0.15
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (12 bp):
TATATATTTAAT
Found at i:4442034 original size:22 final size:23
Alignment explanation
Indices: 4441984--4442034 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
4441974 CATAATTAAT
* *
4441984 TGATAAACTTAGTAGTAAATGAA
1 TGATAAACTTAGTAATAAATCAA
**
4442007 AAATAAAC-TAGTAATAAATCAA
1 TGATAAACTTAGTAATAAATCAA
4442029 TGATAA
1 TGATAA
4442035 TTTAATAGTT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.55, C:0.06, G:0.12, T:0.27
Consensus pattern (23 bp):
TGATAAACTTAGTAATAAATCAA
Found at i:4442124 original size:22 final size:21
Alignment explanation
Indices: 4442027--4442129 Score: 64
Period size: 22 Copynumber: 4.6 Consensus size: 21
4442017 GTAATAAATC
*
4442027 AATGATAATTTAATAGTTAAT
1 AATGATAACTTAATAGTTAAT
* * * *
4442048 AGTTGAAAACTTAAAAGTAAAT
1 A-ATGATAACTTAATAGTTAAT
*
4442070 AAAT-ATAACTTAGCAATAGATAAT
1 -AATGATAACTT---AATAGTTAAT
*
4442094 TATGAATAACTTAATAGTTAAT
1 AATG-ATAACTTAATAGTTAAT
*
4442116 CAATGATAATTTAA
1 -AATGATAACTTAA
4442130 CAATAAATTA
Statistics
Matches: 60, Mismatches: 14, Indels: 15
0.67 0.16 0.17
Matches are distributed among these distances:
21 7 0.12
22 33 0.55
23 6 0.10
24 7 0.12
25 7 0.12
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (21 bp):
AATGATAACTTAATAGTTAAT
Found at i:4442234 original size:10 final size:10
Alignment explanation
Indices: 4442216--4442289 Score: 69
Period size: 11 Copynumber: 6.9 Consensus size: 10
4442206 TGATAATTTT
4442216 ATAGTAAATA
1 ATAGTAAATA
*
4442226 ATAGAAAATTA
1 ATAGTAAA-TA
4442237 AGTAGTAAATCA
1 A-TAGTAAAT-A
4442249 ATA-TAACATA
1 ATAGTAA-ATA
4442259 ATAGTAAATA
1 ATAGTAAATA
*
4442269 CATAATAACATA
1 -ATAGTAA-ATA
4442281 ATAGTAAAT
1 ATAGTAAAT
4442290 CATTGATAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
10 19 0.36
11 23 0.43
12 11 0.21
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.28
Consensus pattern (10 bp):
ATAGTAAATA
Found at i:4442326 original size:43 final size:44
Alignment explanation
Indices: 4442273--4442363 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 44
4442263 TAAATACATA
* * *
4442273 ATAACATAATAGTAAATCATTGATAATTTAAATGTAAATTATTG
1 ATAACATAATAGTAAATCATTAATAATTTAAATGTAAATAAGTG
**
4442317 ATAAC-TAATAGTAAATCATTAATAATTTAGTTGTAAATAAGTG
1 ATAACATAATAGTAAATCATTAATAATTTAAATGTAAATAAGTG
4442360 ATAA
1 ATAA
4442364 TTTAGTAGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 37 0.88
44 5 0.12
ACGTcount: A:0.48, C:0.04, G:0.10, T:0.37
Consensus pattern (44 bp):
ATAACATAATAGTAAATCATTAATAATTTAAATGTAAATAAGTG
Found at i:4442353 original size:22 final size:22
Alignment explanation
Indices: 4442099--4442375 Score: 145
Period size: 22 Copynumber: 12.7 Consensus size: 22
4442089 ATAATTATGA
* * *
4442099 ATAACTTAATAGTTAATCAATG
1 ATAATTTAATAGTAAATCATTG
* * * *
4442121 ATAATTTAACAATAAATTATGG
1 ATAATTTAATAGTAAATCATTG
* *
4442143 ATACTTTAATA-TAAATCAGTG
1 ATAATTTAATAGTAAATCATTG
* * * * *
4442164 ACAACTTGATAATAAATCATGG
1 ATAATTTAATAGTAAATCATTG
* * * *
4442186 TTAATTTAATAATAAGT-TTGTG
1 ATAATTTAATAGTAAATCAT-TG
* * *
4442208 ATAATTTTATAGTAAATAATAG
1 ATAATTTAATAGTAAATCATTG
* *
4442230 A-AAATTAAGTAGTAAATCAAT-
1 ATAATTTAA-TAGTAAATCATTG
** *
4442251 ATAACATAATAGTAAATACA-TA
1 ATAATTTAATAGTAAAT-CATTG
**
4442273 ATAACATAATAGTAAATCATTG
1 ATAATTTAATAGTAAATCATTG
*
4442295 ATAATTTAA-ATGTAAATTATTG
1 ATAATTTAATA-GTAAATCATTG
* *
4442317 ATAA-CTAATAGTAAATCATTA
1 ATAATTTAATAGTAAATCATTG
* * * *
4442338 ATAATTTAGTTGTAAATAAGTG
1 ATAATTTAATAGTAAATCATTG
*
4442360 ATAATTTAGTAGTAAA
1 ATAATTTAATAGTAAA
4442376 ATTAATTAAT
Statistics
Matches: 192, Mismatches: 52, Indels: 22
0.72 0.20 0.08
Matches are distributed among these distances:
21 49 0.26
22 142 0.74
23 1 0.01
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.36
Consensus pattern (22 bp):
ATAATTTAATAGTAAATCATTG
Found at i:4442375 original size:65 final size:64
Alignment explanation
Indices: 4442216--4442375 Score: 155
Period size: 65 Copynumber: 2.5 Consensus size: 64
4442206 TGATAATTTT
* *
4442216 ATAGTAAATAATAGAAAATTAAGTAGTAAATCAATATAACATAATAGTAAATACATAATAACATA
1 ATAGTAAATAAT-GATAATTTAGTAGTAAATCAATATAACATAATAGTAAATACATAATAACATA
* * * * *
4442281 ATAGTAAATCATTGATAATTTA-AATGTAAATTATTGATAAC-TAATAGTAAAT-CATTAATAAT
1 ATAGTAAAT-AATGATAATTTAGTA-GTAAATCAAT-ATAACATAATAGTAAATACA-TAATAAC
*
4442343 TTA
62 ATA
* *
4442346 GTTGTAAATAAGTGATAATTTAGTAGTAAA
1 ATAGTAAATAA-TGATAATTTAGTAGTAAA
4442376 ATTAATTAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
64 4 0.05
65 65 0.84
66 8 0.10
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.34
Consensus pattern (64 bp):
ATAGTAAATAATGATAATTTAGTAGTAAATCAATATAACATAATAGTAAATACATAATAACATA
Found at i:4442450 original size:21 final size:21
Alignment explanation
Indices: 4442426--4442467 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
4442416 AATTAATAAT
4442426 AAATCAATATTAATTTAGTAG
1 AAATCAATATTAATTTAGTAG
*
4442447 AAATCATTATTAATTTAGTAG
1 AAATCAATATTAATTTAGTAG
4442468 TATATCGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (21 bp):
AAATCAATATTAATTTAGTAG
Found at i:4442899 original size:21 final size:20
Alignment explanation
Indices: 4442842--4442909 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
4442832 TAATAAAAAA
* *
4442842 TTACCAAAATTGTATCAATAG
1 TTACTAAAATTGTATTAA-AG
*
4442863 TTA-TCAAAATTATATTATAAG
1 TTACT-AAAATTGTATTA-AAG
4442884 TTACTAAAATTGTATTAAAGG
1 TTACTAAAATTGTATTAAA-G
4442905 TTACT
1 TTACT
4442910 TAAGTTTCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 2 0.05
21 35 0.90
22 2 0.05
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (20 bp):
TTACTAAAATTGTATTAAAG
Found at i:4443878 original size:3 final size:3
Alignment explanation
Indices: 4443872--4443915 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
4443862 TTTTTTAAAG
4443872 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4443916 CCATATTCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4444276 original size:24 final size:22
Alignment explanation
Indices: 4444244--4444288 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
4444234 TCTTATTGCG
4444244 ATTATTTTAAATTATTTATTATTT
1 ATTATTTT-AATTATTT-TTATTT
4444268 ATTATTTTAATTATTTTTATT
1 ATTATTTTAATTATTTTTATT
4444289 ATATAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.24
23 8 0.38
24 8 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
ATTATTTTAATTATTTTTATTT
Found at i:4445314 original size:19 final size:19
Alignment explanation
Indices: 4445290--4445346 Score: 114
Period size: 19 Copynumber: 3.0 Consensus size: 19
4445280 TTCTAGTTTT
4445290 CTGTTATTGAAAAATTCAA
1 CTGTTATTGAAAAATTCAA
4445309 CTGTTATTGAAAAATTCAA
1 CTGTTATTGAAAAATTCAA
4445328 CTGTTATTGAAAAATTCAA
1 CTGTTATTGAAAAATTCAA
4445347 AGTTTTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (19 bp):
CTGTTATTGAAAAATTCAA
Found at i:4445941 original size:3 final size:3
Alignment explanation
Indices: 4445935--4445961 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4445925 TTTTTTGTTA
4445935 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
4445962 TTTTTATAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4446535 original size:34 final size:33
Alignment explanation
Indices: 4446497--4446629 Score: 124
Period size: 34 Copynumber: 3.8 Consensus size: 33
4446487 TGCTCCTCTA
*
4446497 ACCAAAGGCTATGAAACTTTAAATAGCTCATTTG
1 ACCAAAGGCAATGAAACTTTAAATAGCTC-TTTG
* *
4446531 ACCAAAGTCAATGAAATTTTAAATTTAAGAGGCTTCTTTG
1 ACCAAAGGCAATGAAACTTTAAA--T---A-GC-TCTTTG
*
4446571 ACCAAAGGTAATGAAACTTTAAAT-GACTCTTTTG
1 ACCAAAGGCAATGAAACTTTAAATAG-CTC-TTTG
*
4446605 ACCAAAGCCAATGAAACTTTAAATA
1 ACCAAAGGCAATGAAACTTTAAATA
4446630 AAAAAGGCTC
Statistics
Matches: 81, Mismatches: 8, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
33 3 0.04
34 47 0.58
36 1 0.01
38 1 0.01
39 1 0.01
40 26 0.32
41 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (33 bp):
ACCAAAGGCAATGAAACTTTAAATAGCTCTTTG
Found at i:4446638 original size:74 final size:74
Alignment explanation
Indices: 4446483--4446646 Score: 199
Period size: 74 Copynumber: 2.2 Consensus size: 74
4446473 CTCTTGAAAT
* * * * *
4446483 AAAATGCTCCTCTAACCAAAGGCTATGAAACTTTAAATAGCTCATTTGACCAAAGTCAATGAAAT
1 AAAAGGCTCTTCTGACCAAAGGCTATGAAACTTTAAATAGCTCATTTGACCAAAGCCAATGAAAC
**
4446548 TTTAAATTT
66 TTTAAATAA
* *
4446557 AAGAGGCTTCTT-TGACCAAAGG-TAATGAAACTTTAAAT-GACTCTTTTGACCAAAGCCAATGA
1 AAAAGGC-TCTTCTGACCAAAGGCT-ATGAAACTTTAAATAG-CTCATTTGACCAAAGCCAATGA
4446619 AACTTTAAATAA
63 AACTTTAAATAA
4446631 AAAAGGCTCTTCTGAC
1 AAAAGGCTCTTCTGAC
4446647 TAGAGGCAAC
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
73 6 0.08
74 67 0.88
75 3 0.04
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (74 bp):
AAAAGGCTCTTCTGACCAAAGGCTATGAAACTTTAAATAGCTCATTTGACCAAAGCCAATGAAAC
TTTAAATAA
Found at i:4446666 original size:40 final size:40
Alignment explanation
Indices: 4446617--4446708 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
4446607 CAAAGCCAAT
4446617 GAAACTTTAAATAAAAAAGGCTCT-TCTGACTAGAGGCAAC
1 GAAACTTTAAATAAAAAAGGCT-TATCTGACTAGAGGCAAC
* ** * *
4446657 GAAATTTTAAATTCAAAAGGCTTATCTTACTAGAGTCAAC
1 GAAACTTTAAATAAAAAAGGCTTATCTGACTAGAGGCAAC
*
4446697 AAAACTTTAAAT
1 GAAACTTTAAAT
4446709 GGTTCTTTTG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 1 0.02
40 43 0.98
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (40 bp):
GAAACTTTAAATAAAAAAGGCTTATCTGACTAGAGGCAAC
Found at i:4446666 original size:74 final size:74
Alignment explanation
Indices: 4446497--4446668 Score: 195
Period size: 74 Copynumber: 2.3 Consensus size: 74
4446487 TGCTCCTCTA
* * * * ** *
4446497 ACCAAAGGCTATGAAACTTTAAATAGCTCATTTGACCAAAGTCAATGAAATTTTAAATTTAAGAG
1 ACCAAAGGCAACGAAACTTTAAATAGCTCATTTGACCAAAGCCAATGAAACTTTAAATAAAAAAG
4446562 GCTTCTTTG
66 GCTTCTTTG
* * *
4446571 ACCAAAGGTAATGAAACTTTAAAT-GACTCTTTTGACCAAAGCCAATGAAACTTTAAATAAAAAA
1 ACCAAAGGCAACGAAACTTTAAATAG-CTCATTTGACCAAAGCCAATGAAACTTTAAATAAAAAA
4446635 GGC-TCTTCTG
65 GGCTTCTT-TG
* * *
4446645 ACTAGAGGCAACGAAATTTTAAAT
1 ACCAAAGGCAACGAAACTTTAAAT
4446669 TCAAAAGGCT
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
73 5 0.06
74 78 0.94
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.29
Consensus pattern (74 bp):
ACCAAAGGCAACGAAACTTTAAATAGCTCATTTGACCAAAGCCAATGAAACTTTAAATAAAAAAG
GCTTCTTTG
Found at i:4454149 original size:13 final size:13
Alignment explanation
Indices: 4454133--4454174 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
4454123 CCGACAACCA
4454133 TCAGTGAACCGAT
1 TCAGTGAACCGAT
*
4454146 TCAGATTAACC-A-
1 TCAG-TGAACCGAT
4454158 TCAGTGAACCGAT
1 TCAGTGAACCGAT
4454171 TCAG
1 TCAG
4454175 ATTAACCGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
11 5 0.21
12 5 0.21
13 9 0.38
14 5 0.21
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (13 bp):
TCAGTGAACCGAT
Found at i:4454183 original size:14 final size:14
Alignment explanation
Indices: 4454139--4454183 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
4454129 ACCATCAGTG
4454139 AACCGATTCAGATT
1 AACCGATTCAGATT
*
4454153 AACC-A-TCAG-TG
1 AACCGATTCAGATT
4454164 AACCGATTCAGATT
1 AACCGATTCAGATT
4454178 AACCGA
1 AACCGA
4454184 CCTTGAACCG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 5 0.19
12 5 0.19
13 5 0.19
14 11 0.42
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (14 bp):
AACCGATTCAGATT
Found at i:4454220 original size:25 final size:25
Alignment explanation
Indices: 4454128--4454218 Score: 130
Period size: 25 Copynumber: 3.6 Consensus size: 25
4454118 CCGACCCGAC
4454128 AACCATCAGTGAACCGATTCAGATT
1 AACCATCAGTGAACCGATTCAGATT
4454153 AACCATCAGTGAACCGATTCAGATT
1 AACCATCAGTGAACCGATTCAGATT
** *
4454178 AACCGA-CCTTGAACCGGTTCAGATT
1 AACC-ATCAGTGAACCGATTCAGATT
*
4454203 AACCGTCAGTGAACCG
1 AACCATCAGTGAACCG
4454219 GTCTAAATCG
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
25 57 0.98
26 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (25 bp):
AACCATCAGTGAACCGATTCAGATT
Found at i:4454839 original size:16 final size:15
Alignment explanation
Indices: 4454808--4455026 Score: 102
Period size: 16 Copynumber: 13.7 Consensus size: 15
4454798 CTAAGTTTTT
4454808 AAAACCCCTAAAAATCC
1 AAAA-CCCT-AAAATCC
4454825 AAAATCCCTAAAATCC
1 AAAA-CCCTAAAATCC
**
4454841 AAAATCTGTAAAATCC
1 AAAA-CCCTAAAATCC
*
4454857 AAACCCCCTAAAAATCC
1 AAA-ACCCT-AAAATCC
* *
4454874 AAAATACCTTAAATCC
1 AAAA-CCCTAAAATCC
*
4454890 AAACCCCCTCTAAAATCC
1 AAA--ACC-CTAAAATCC
* *
4454908 GAAACGACTAAAATCC
1 AAAAC-CCTAAAATCC
*
4454924 AAAACCTTCCAAAATCC
1 AAAACC--CTAAAATCC
* **
4454941 AAAATCCC-AAACTTT
1 AAAA-CCCTAAAATCC
* ** *
4454956 TAAACTATTAAA-CC
1 AAAACCCTAAAATCC
* *
4454970 TAAACCCTCTAAATCC
1 AAAACCCT-AAAATCC
4454986 AAAATCCCTAAAATCC
1 AAAA-CCCTAAAATCC
*
4455002 AAAACCCTTAAAT-C
1 AAAACCCTAAAATCC
4455016 AAAACCCTAAA
1 AAAACCCTAAA
4455027 CCTCAAAATC
Statistics
Matches: 154, Mismatches: 34, Indels: 31
0.70 0.16 0.14
Matches are distributed among these distances:
14 18 0.12
15 21 0.14
16 65 0.42
17 38 0.25
18 12 0.08
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.19
Consensus pattern (15 bp):
AAAACCCTAAAATCC
Found at i:4454853 original size:33 final size:33
Alignment explanation
Indices: 4454818--4454946 Score: 101
Period size: 33 Copynumber: 3.9 Consensus size: 33
4454808 AAAACCCCTA
*
4454818 AAAATCCAAAATCCCT-AAAATCCAAAATCTGT
1 AAAATCCAAAACCCCTAAAAATCCAAAATCTGT
*
4454850 AAAATCCAAACCCCCTAAAAATCCAAAATACCT-T
1 AAAATCCAAAACCCCTAAAAATCCAAAAT--CTGT
* * *
4454884 -AAATCCAAACCCCCTCTAAAATCCGAAA-C-GACT
1 AAAATCCAAAACCCCT-AAAAATCCAAAATCTG--T
4454917 AAAATCCAAAACCTTCC--AAAATCCAAAATC
1 AAAATCCAAAACC--CCTAAAAATCCAAAATC
4454947 CCAAACTTTT
Statistics
Matches: 80, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
31 1 0.01
32 14 0.17
33 38 0.47
34 23 0.29
35 2 0.03
36 2 0.03
ACGTcount: A:0.49, C:0.31, G:0.02, T:0.18
Consensus pattern (33 bp):
AAAATCCAAAACCCCTAAAAATCCAAAATCTGT
Found at i:4460987 original size:2 final size:2
Alignment explanation
Indices: 4460980--4461011 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4460970 GCCACCAATT
4460980 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
4461012 GGGTGTGATT
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:4461648 original size:26 final size:25
Alignment explanation
Indices: 4461610--4461676 Score: 64
Period size: 27 Copynumber: 2.6 Consensus size: 25
4461600 TTAATTAATT
*
4461610 AATTAATTCTTATT-GTGCTTATTTTA
1 AATT-ATTTTTATTAGTGCTT-TTTTA
* *
4461636 AATTATTTATTATTTATTTCTTTTTTA
1 AATTATTT-TTA-TTAGTGCTTTTTTA
4461663 AATTATTTTTATTA
1 AATTATTTTTATTA
4461677 TATAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
25 6 0.17
26 10 0.29
27 15 0.43
28 4 0.11
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.64
Consensus pattern (25 bp):
AATTATTTTTATTAGTGCTTTTTTA
Found at i:4462129 original size:3 final size:3
Alignment explanation
Indices: 4462121--4462167 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
4462111 TCTTAAATAG
4462121 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4462168 TAAGGTTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4462316 original size:5 final size:5
Alignment explanation
Indices: 4462306--4462370 Score: 50
Period size: 5 Copynumber: 13.4 Consensus size: 5
4462296 CAATAATATC
*
4462306 AATAA AAT-A AAT-A AATAA AA-ATA AATAA AA-AA AACAA AAT-A AATAA
1 AATAA AATAA AATAA AATAA AATA-A AATAA AATAA AATAA AATAA AATAA
*
4462352 AATCAA AATCAA AACAA AA
1 AAT-AA AAT-AA AATAA AA
4462371 AAGAACAAGA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
4 17 0.33
5 24 0.46
6 11 0.21
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.15
Consensus pattern (5 bp):
AATAA
Found at i:4462318 original size:18 final size:17
Alignment explanation
Indices: 4462297--4462359 Score: 60
Period size: 18 Copynumber: 3.8 Consensus size: 17
4462287 TAGCAATAAC
*
4462297 AATAATATCAATAAAATA
1 AATAAAATCAA-AAAATA
4462315 AAT-AAAT--AAAAATA
1 AATAAAATCAAAAAATA
**
4462329 AATAAAAAAAACAAAATA
1 AATAAAATCAA-AAAATA
4462347 AATAAAATCAAAA
1 AATAAAATCAAAA
4462360 TCAAAACAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
14 9 0.24
15 4 0.11
17 6 0.16
18 18 0.49
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (17 bp):
AATAAAATCAAAAAATA
Found at i:4462740 original size:19 final size:20
Alignment explanation
Indices: 4462716--4462765 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
4462706 TCTGGTGGCC
4462716 AAAAAATTCAACTATCATAA
1 AAAAAATTCAACTATCATAA
4462736 AAAAAATTCAACTATCAT-A
1 AAAAAATTCAACTATCATAA
4462755 AAAAAATTCAA
1 AAAAAATTCAA
4462766 AGTTTTTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAAATTCAACTATCATAA
Found at i:4463944 original size:13 final size:13
Alignment explanation
Indices: 4463926--4463952 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4463916 AAAAATAATG
4463926 TTTGAATTGCATA
1 TTTGAATTGCATA
4463939 TTTGAATTGCATA
1 TTTGAATTGCATA
4463952 T
1 T
4463953 AGTGGAGCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (13 bp):
TTTGAATTGCATA
Found at i:4464911 original size:49 final size:49
Alignment explanation
Indices: 4464806--4464903 Score: 153
Period size: 49 Copynumber: 2.0 Consensus size: 49
4464796 TTTAAATTAA
*
4464806 TAAATATTA-TTTTTTAAAATAATTATATAAATTAATTAAATTAATTTT
1 TAAATAATATTTTTTTAAAATAATTATATAAATTAATTAAATTAATTTT
* * *
4464854 TAAATAATATTTTTTTGAAATAATTATATAAATTAATTGAGTTAATTTT
1 TAAATAATATTTTTTTAAAATAATTATATAAATTAATTAAATTAATTTT
4464903 T
1 T
4464904 TTTTAATAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 8 0.18
49 37 0.82
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (49 bp):
TAAATAATATTTTTTTAAAATAATTATATAAATTAATTAAATTAATTTT
Done.