Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold79
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: 4189514
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 5041 characters in sequence are not A, C, G, or T
File 18 of 26
Found at i:2477892 original size:25 final size:24
Alignment explanation
Indices: 2477850--2477901 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
2477840 TTTTTAGATT
* *
2477850 TATTAATTTTAAATATAATATAAATA
1 TATTAATTATAAAAATAAT-TAAA-A
2477876 TATT-ATTATAAAAATAATTAAAA
1 TATTAATTATAAAAATAATTAAAA
2477899 TAT
1 TAT
2477902 GATAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.17
24 4 0.17
25 12 0.50
26 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TATTAATTATAAAAATAATTAAAA
Found at i:2477901 original size:36 final size:36
Alignment explanation
Indices: 2477853--2478001 Score: 132
Period size: 36 Copynumber: 4.2 Consensus size: 36
2477843 TTAGATTTAT
* * *
2477853 TAATTTTAAATATAATATAAATATATTATTATAAAAA
1 TAATTATAAATAT-ATAAAAATATAATATTATAAAAA
*
2477890 TAATTA-AAATATGATAAAAATATAAATATAATAAAAA
1 TAATTATAAATAT-ATAAAAATAT-AATATTATAAAAA
* *
2477927 T-A-TATAAATATATTAAAAT-T--TA-TATAAAAT
1 TAATTATAAATATATAAAAATATAATATTATAAAAA
* * * *
2477957 TAATTATTAATATATAAAAATAAAATATTTTAAATA
1 TAATTATAAATATATAAAAATATAATATTATAAAAA
2477993 TAATTATAA
1 TAATTATAA
2478002 TAACATGTAA
Statistics
Matches: 89, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
30 7 0.08
31 3 0.03
32 15 0.17
34 1 0.01
35 11 0.12
36 35 0.39
37 17 0.19
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.40
Consensus pattern (36 bp):
TAATTATAAATATATAAAAATATAATATTATAAAAA
Found at i:2477918 original size:17 final size:17
Alignment explanation
Indices: 2477859--2477944 Score: 75
Period size: 19 Copynumber: 4.8 Consensus size: 17
2477849 TTATTAATTT
*
2477859 TAAATATAATATAAATA
1 TAAATATAATAAAAATA
* *
2477876 T-ATTATTATAAAAATAA
1 TAAATATAATAAAAAT-A
*
2477893 TTAAAATATGATAAAAATA
1 -T-AAATATAATAAAAATA
2477912 TAAATATAATAAAAATATA
1 TAAATATAAT-AAAA-ATA
*
2477931 TAAATATATTAAAA
1 TAAATATAATAAAA
2477945 TTTATATAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
16 11 0.20
17 10 0.18
18 10 0.18
19 13 0.23
20 12 0.21
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (17 bp):
TAAATATAATAAAAATA
Found at i:2477920 original size:28 final size:27
Alignment explanation
Indices: 2477882--2477945 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 27
2477872 AATATATTAT
*
2477882 TATAAAAATAATTAAAATATGATAAAAA
1 TATAAAAATAATAAAAATAT-ATAAAAA
* *
2477910 TATAAATATAATAAAAATATATAAATA
1 TATAAAAATAATAAAAATATATAAAAA
*
2477937 TATTAAAAT
1 TATAAAAAT
2477946 TTATATAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
27 13 0.42
28 18 0.58
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (27 bp):
TATAAAAATAATAAAAATATATAAAAA
Found at i:2478001 original size:22 final size:26
Alignment explanation
Indices: 2477948--2478001 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 26
2477938 ATTAAAATTT
2477948 ATATAAAATTAATTATTAATATATAA
1 ATATAAAATTAATTATTAATATATAA
*
2477974 AAATAAAA-T-ATT-TTAA-ATATAA
1 ATATAAAATTAATTATTAATATATAA
*
2477996 TTATAA
1 ATATAA
2478002 TAACATGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 10 0.40
23 4 0.16
24 3 0.12
25 1 0.04
26 7 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
ATATAAAATTAATTATTAATATATAA
Found at i:2478264 original size:13 final size:13
Alignment explanation
Indices: 2478245--2478283 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
2478235 AATTTTTAAA
2478245 AATATTTATATTT
1 AATATTTATATTT
*
2478258 TATATTTATATTT
1 AATATTTATATTT
2478271 AATA--TATATTT
1 AATATTTATATTT
2478282 AA
1 AA
2478284 ATATAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 9 0.38
13 15 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:2478759 original size:13 final size:14
Alignment explanation
Indices: 2478736--2478765 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2478726 TTATTATTAT
2478736 TATATTAAAAATAA
1 TATATTAAAAATAA
2478750 TATA-TAAAAATAA
1 TATATTAAAAATAA
2478763 TAT
1 TAT
2478766 GTTAGGCCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TATATTAAAAATAA
Found at i:2479270 original size:20 final size:21
Alignment explanation
Indices: 2479245--2479284 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
2479235 ATAAACTTTT
2479245 AAATATATAAA-AAATTAAAA
1 AAATATATAAATAAATTAAAA
2479265 AAATATATAAATAAATTAAA
1 AAATATATAAATAAATTAAA
2479285 TATATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATATATAAATAAATTAAAA
Found at i:2479577 original size:22 final size:22
Alignment explanation
Indices: 2479526--2479580 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
2479516 ATTTTTATTT
* *
2479526 AAATTTAAT-TATAAAATATAT
1 AAATTTAATATATAAAATAAAA
2479547 AAATATTAATATA-AAAATAAAAA
1 AAAT-TTAATATATAAAAT-AAAA
2479570 AAATTTAATAT
1 AAATTTAATAT
2479581 CTTAATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 4 0.14
22 17 0.59
23 8 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATTTAATATATAAAATAAAA
Found at i:2481660 original size:226 final size:226
Alignment explanation
Indices: 2481309--2481758 Score: 821
Period size: 226 Copynumber: 2.0 Consensus size: 226
2481299 CTTTACCATT
*
2481309 TCATTACTGTTACCAAAATATCATCTTAATGCATGAGGGGATAGGAAACTGGGAATAAGTCCTTG
1 TCATTACTGTTACCAAAATATCATCTTAATGCATGAGGGGATAGGAAACTGGGAATAAGTCCTTC
*
2481374 GTGCCACTAAATGATAGTTAAATTACATGCAGAGAGATAAGGAGGCTGTAGAAAGCATCTTTGGT
66 ATGCCACTAAATGATAGTTAAATTACATGCAGAGAGATAAGGAGGCTGTAGAAAGCATCTTTGGT
* * *
2481439 CGGTTATGTTGAAATCAGATAAAACAGTCAACAAACAGCAATGAATACTCTATATTACCGTCTGT
131 CGGTTATGTTGAAATCAGATAAAACAGTCAACAAACAGCAACGAATACTCTATATTACCATCTGC
2481504 TAGGAGAAGGATACTTACCTTGAAATGCATC
196 TAGGAGAAGGATACTTACCTTGAAATGCATC
* *
2481535 TCATTACTGTTACCAAACTATCATCTTAATGCATGAGGGGATAGGAAACTGGGTATAAGTCCTTC
1 TCATTACTGTTACCAAAATATCATCTTAATGCATGAGGGGATAGGAAACTGGGAATAAGTCCTTC
2481600 ATGCCACTAAATGATAGTT-AATATACATGCAGAGAGATAAGGAGGCTGTAGAAAGCATCTTTGG
66 ATGCCACTAAATGATAGTTAAAT-TACATGCAGAGAGATAAGGAGGCTGTAGAAAGCATCTTTGG
2481664 TCGGTTATGTTGAAATCAGATAAAACAGTCAACAAACAGCAACGAATACTCTATATTACCATCTG
130 TCGGTTATGTTGAAATCAGATAAAACAGTCAACAAACAGCAACGAATACTCTATATTACCATCTG
2481729 CTAGGAGAAGGATACTTACCTTGAAATGCA
195 CTAGGAGAAGGATACTTACCTTGAAATGCA
2481759 ATTTACGACT
Statistics
Matches: 216, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
225 3 0.01
226 213 0.99
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (226 bp):
TCATTACTGTTACCAAAATATCATCTTAATGCATGAGGGGATAGGAAACTGGGAATAAGTCCTTC
ATGCCACTAAATGATAGTTAAATTACATGCAGAGAGATAAGGAGGCTGTAGAAAGCATCTTTGGT
CGGTTATGTTGAAATCAGATAAAACAGTCAACAAACAGCAACGAATACTCTATATTACCATCTGC
TAGGAGAAGGATACTTACCTTGAAATGCATC
Found at i:2487064 original size:12 final size:12
Alignment explanation
Indices: 2487025--2487140 Score: 53
Period size: 11 Copynumber: 9.5 Consensus size: 12
2487015 TGTACGATAA
2487025 AAAAATATAATAT
1 AAAAATAT-ATAT
* *
2487038 AAATATATATTT
1 AAAAATATATAT
*
2487050 AAAAATTTATAT
1 AAAAATATATAT
*
2487062 -AAAATAAAT-T
1 AAAAATATATAT
**
2487072 ATTAATAT-T-T
1 AAAAATATATAT
* *
2487082 TAAAATAT-TTT
1 AAAAATATATAT
2487093 AAAAATATGATAT
1 AAAAATAT-ATAT
*
2487106 CATAAAATATATAA
1 -A-AAAATATATAT
2487120 ATAAAATATGAATAT
1 A-AAAATAT--ATAT
2487135 AAAAAT
1 AAAAAT
2487141 TATTAATTTT
Statistics
Matches: 78, Mismatches: 17, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
10 9 0.12
11 19 0.24
12 12 0.15
13 18 0.23
14 9 0.12
15 11 0.14
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (12 bp):
AAAAATATATAT
Found at i:2487136 original size:13 final size:14
Alignment explanation
Indices: 2487094--2487138 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
2487084 AAATATTTTA
2487094 AAAATATGATATCAT
1 AAAATATGATAT-AT
*
2487109 AAAATAT-ATAAAT
1 AAAATATGATATAT
2487122 AAAATATGA-ATAT
1 AAAATATGATATAT
2487135 AAAA
1 AAAA
2487139 ATTATTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 16 0.59
14 4 0.15
15 7 0.26
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (14 bp):
AAAATATGATATAT
Found at i:2488617 original size:20 final size:20
Alignment explanation
Indices: 2488592--2488633 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2488582 ATTTTAAATA
2488592 TAAATATAATATAATATATT
1 TAAATATAATATAATATATT
* *
2488612 TAAATATAATTTATTATATT
1 TAAATATAATATAATATATT
2488632 TA
1 TA
2488634 TATTTATTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAATATAATATAATATATT
Found at i:2488635 original size:26 final size:25
Alignment explanation
Indices: 2488573--2488639 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
2488563 GTTATTAAAA
*
2488573 TATATTTAAATTTTAAATATAAATAT
1 TATATTTATA-TTTAAATATAAATAT
* * *
2488599 AATATAATATATTTAAATATAATTTAT
1 TATAT-TTATATTTAAATATAA-ATAT
2488626 TATATTTATATTTA
1 TATATTTATATTTA
2488640 TTGAATAGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
26 23 0.70
27 10 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TATATTTATATTTAAATATAAATAT
Found at i:2488944 original size:19 final size:18
Alignment explanation
Indices: 2488915--2488963 Score: 71
Period size: 19 Copynumber: 2.7 Consensus size: 18
2488905 AAAATAAATT
*
2488915 AAAATATTTTTAAATTTA
1 AAAAAATTTTTAAATTTA
2488933 AACAAAATTTTTAAATTTA
1 AA-AAAATTTTTAAATTTA
*
2488952 AATAAATTTTTA
1 AAAAAATTTTTA
2488964 TAAAATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAAAATTTTTAAATTTA
Found at i:2488944 original size:20 final size:19
Alignment explanation
Indices: 2488915--2488972 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
2488905 AAAATAAATT
2488915 AAAATATTTTTAAATTTAAA
1 AAAAT-TTTTTAAATTTAAA
2488935 CAAAA-TTTTTAAATTTAAA
1 -AAAATTTTTTAAATTTAAA
* *
2488954 TAAATTTTTATAAAATTAA
1 AAAATTTTT-TAAATTTAA
2488973 TTATATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 3 0.09
19 18 0.55
20 8 0.24
21 4 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAATTTTTTAAATTTAAA
Found at i:2488958 original size:18 final size:19
Alignment explanation
Indices: 2488920--2488963 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
2488910 AAATTAAAAT
2488920 ATTTTTAAATTTAAACAAA
1 ATTTTTAAATTTAAACAAA
*
2488939 ATTTTTAAATTTAAA-TAA
1 ATTTTTAAATTTAAACAAA
2488957 ATTTTTA
1 ATTTTTA
2488964 TAAAATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTTTAAATTTAAACAAA
Found at i:2490397 original size:37 final size:39
Alignment explanation
Indices: 2490356--2490436 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 39
2490346 TATTATTTTT
* *
2490356 TATATTAATCATAT-AAATATAAATATAA-AT-TATTAAA
1 TATATTAA-AATATAAAATAAAAATATAATATATATTAAA
*
2490393 TATATTAAAATTTAAAATAAAAATATAATATATATTAAA
1 TATATTAAAATATAAAATAAAAATATAATATATATTAAA
2490432 TATAT
1 TATAT
2490437 CATATTAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 3 0.08
37 21 0.55
38 2 0.05
39 12 0.32
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (39 bp):
TATATTAAAATATAAAATAAAAATATAATATATATTAAA
Found at i:2490821 original size:13 final size:13
Alignment explanation
Indices: 2490800--2490855 Score: 67
Period size: 13 Copynumber: 4.2 Consensus size: 13
2490790 AACATATAAT
*
2490800 TATATTATAAAAA
1 TATAATATAAAAA
2490813 TATAATATAAAAA
1 TATAATATAAAAA
* *
2490826 TAAAAATTTAAAAA
1 T-ATAATATAAAAA
*
2490840 TATAATTTAAAAA
1 TATAATATAAAAA
2490853 TAT
1 TAT
2490856 GAGCATGTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
13 27 0.71
14 11 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TATAATATAAAAA
Found at i:2490837 original size:14 final size:13
Alignment explanation
Indices: 2490807--2490855 Score: 71
Period size: 13 Copynumber: 3.7 Consensus size: 13
2490797 AATTATATTA
*
2490807 TAAAAATATAATA
1 TAAAAATATAATT
*
2490820 TAAAAATAAAAATT
1 TAAAAAT-ATAATT
2490834 TAAAAATATAATT
1 TAAAAATATAATT
2490847 TAAAAATAT
1 TAAAAATAT
2490856 GAGCATGTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
13 21 0.66
14 11 0.34
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAAAATATAATT
Found at i:2490904 original size:32 final size:33
Alignment explanation
Indices: 2490839--2490909 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 33
2490829 AAATTTAAAA
*
2490839 ATATAATTTAAAAATATGAGCATGTTAAAATTT
1 ATATAATTTAAAAATATGAACATGTTAAAATTT
* * *
2490872 ATATAATTT-AAATTATTAACATTTTAAAATTT
1 ATATAATTTAAAAATATGAACATGTTAAAATTT
2490904 ATATAA
1 ATATAA
2490910 ATATATAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 25 0.74
33 9 0.26
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (33 bp):
ATATAATTTAAAAATATGAACATGTTAAAATTT
Found at i:2490936 original size:20 final size:21
Alignment explanation
Indices: 2490908--2490964 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
2490898 AAATTTATAT
*
2490908 AAATATATAATATTTTAAAAA
1 AAATATATAATATATTAAAAA
2490929 AAAT-TATAATATATTAAAAA
1 AAATATATAATATATTAAAAA
*
2490949 ATATATATATATATAT
1 AAATATATA-ATATAT
2490965 ATAATATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 18 0.56
21 8 0.25
22 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATATATAATATATTAAAAA
Found at i:2490956 original size:16 final size:18
Alignment explanation
Indices: 2490926--2490962 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
2490916 AATATTTTAA
2490926 AAAAAATTATAATATATT
1 AAAAAATTATAATATATT
2490944 AAAAAATATATATATATAT
1 AAAAAAT-TATA-ATATAT
2490963 ATATAATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 4 0.24
20 6 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAAATTATAATATATT
Found at i:2493668 original size:14 final size:14
Alignment explanation
Indices: 2493651--2493698 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
2493641 AATATATTTT
2493651 ATTAATTTTAATTA
1 ATTAATTTTAATTA
*
2493665 ATTAATTTAAATTAA
1 ATTAATTTTAATT-A
2493680 ATTAATATTTAA-TA
1 ATTAAT-TTTAATTA
2493694 ATTAA
1 ATTAA
2493699 AAATTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 18 0.60
15 8 0.27
16 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTAATTTTAATTA
Found at i:2493737 original size:22 final size:21
Alignment explanation
Indices: 2493692--2493750 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
2493682 TAATATTTAA
*
2493692 TAATTA-AAAATTATTTAAATT
1 TAATTATAAAA-TATATAAATT
2493713 TAATTATAAAATATATAAATAT
1 TAATTATAAAATATATAAAT-T
2493735 TAA-TATAGAAATATAT
1 TAATTATA-AAATATAT
2493751 TTTAAAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
21 18 0.53
22 16 0.47
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
TAATTATAAAATATATAAATT
Found at i:2494514 original size:15 final size:14
Alignment explanation
Indices: 2494476--2494505 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2494466 ATTAATATTT
*
2494476 ATAATTAAATTTAA
1 ATAATAAAATTTAA
2494490 ATAATAAAATTTAA
1 ATAATAAAATTTAA
2494504 AT
1 AT
2494506 TATTAAAATA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAATAAAATTTAA
Found at i:2494928 original size:11 final size:12
Alignment explanation
Indices: 2494892--2494947 Score: 55
Period size: 11 Copynumber: 4.9 Consensus size: 12
2494882 TTAAATTTAT
*
2494892 TAATTTTAAATA
1 TAATTTAAAATA
* *
2494904 TAATAT-AATTA
1 TAATTTAAAATA
2494915 TAATTTAAAA-A
1 TAATTTAAAATA
2494926 TAA-TTAAAATA
1 TAATTTAAAATA
*
2494937 TAATATAAAAT
1 TAATTTAAAAT
2494948 TAACTTCCGT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
10 6 0.17
11 17 0.47
12 13 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATTTAAAATA
Found at i:2496760 original size:17 final size:18
Alignment explanation
Indices: 2496738--2496795 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 18
2496728 TAAATTTTAA
2496738 TATATTTATATTTAAT-T
1 TATATTTATATTTAATAT
* *
2496755 TATATTAAT-TTTTATAT
1 TATATTTATATTTAATAT
*
2496772 TATA-TTATATTTTATAT
1 TATATTTATATTTAATAT
*
2496789 AATATTT
1 TATATTT
2496796 TTAAAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
16 8 0.24
17 24 0.71
18 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TATATTTATATTTAATAT
Found at i:2496784 original size:49 final size:47
Alignment explanation
Indices: 2496725--2496838 Score: 117
Period size: 49 Copynumber: 2.4 Consensus size: 47
2496715 TATGTTAATA
** *
2496725 ATATAA-ATTTTAATATATTTATATTTAATTTATAT-TAATTTTTATATT
1 ATATAATATTTTAATATATTT-T-TAAAATTT-TATGTAATATTTATATT
*
2496773 ATATTATATTTTATATAATATTTTTAAAATTTTATGTAATATTTATATT
1 ATATAATATTTTA-AT-ATATTTTTAAAATTTTATGTAATATTTATATT
2496822 ATATAAT-TGTTTAATAT
1 ATATAATAT-TTTAATAT
2496839 TTAAAATTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
47 2 0.04
48 11 0.20
49 34 0.61
50 3 0.05
51 6 0.11
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (47 bp):
ATATAATATTTTAATATATTTTTAAAATTTTATGTAATATTTATATT
Found at i:2496786 original size:12 final size:12
Alignment explanation
Indices: 2496771--2496825 Score: 55
Period size: 12 Copynumber: 4.9 Consensus size: 12
2496761 AATTTTTATA
*
2496771 TTATATTATATT
1 TTATATAATATT
2496783 TTATATAATATT
1 TTATATAATATT
2496795 TT-TA-AA-ATT
1 TTATATAATATT
*
2496804 TTATGTAATA-T
1 TTATATAATATT
*
2496815 TTATATTATAT
1 TTATATAATAT
2496826 AATTGTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
9 5 0.14
10 3 0.09
11 13 0.37
12 14 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (12 bp):
TTATATAATATT
Found at i:2497281 original size:8 final size:9
Alignment explanation
Indices: 2497248--2497338 Score: 52
Period size: 10 Copynumber: 10.4 Consensus size: 9
2497238 TGTATTTTTA
2497248 ATATGTATAT
1 ATAT-TATAT
2497258 ATATATATAT
1 ATAT-TATAT
2497268 ATATTATAT
1 ATATTATAT
2497277 A-A-T-TAT
1 ATATTATAT
*
2497283 AT-TTA-AA
1 ATATTATAT
*
2497290 ATATTTTAT
1 ATATTATAT
2497299 AT-TTATAT
1 ATATTATAT
* *
2497307 AAATTTTAAT
1 ATATTAT-AT
2497317 ATATTA-AT
1 ATATTATAT
*
2497325 AAATTATATT
1 ATATTATA-T
2497335 ATAT
1 ATAT
2497339 AAAGTAAAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 18
0.68 0.12 0.20
Matches are distributed among these distances:
6 4 0.07
7 5 0.08
8 16 0.26
9 13 0.21
10 23 0.38
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (9 bp):
ATATTATAT
Found at i:2497326 original size:18 final size:17
Alignment explanation
Indices: 2497279--2497341 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 17
2497269 TATTATATAA
2497279 TTATATTTA-A-AATATT
1 TTATATTTATATAA-ATT
2497295 TTATATTTATATAAATT
1 TTATATTTATATAAATT
2497312 TTAATATATTA-ATAAA--
1 TT-ATAT-TTATATAAATT
2497328 TTATA-TTATATAAA
1 TTATATTTATATAAA
2497342 GTAAAAAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 3 0.07
14 5 0.12
15 3 0.07
16 11 0.26
17 6 0.14
18 11 0.26
19 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:2497527 original size:21 final size:21
Alignment explanation
Indices: 2497503--2497543 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2497493 TACGAAAATA
2497503 TAATTAT-TTATAAATATATTT
1 TAATTATATT-TAAATATATTT
2497524 TAATTATATTTAAATATATT
1 TAATTATATTTAAATATATT
2497544 AAATAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TAATTATATTTAAATATATTT
Found at i:2497545 original size:19 final size:19
Alignment explanation
Indices: 2497503--2497567 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 19
2497493 TACGAAAATA
2497503 TAATTAT-TTATAAATATATTT
1 TAATTATATT-TAAATATA--T
2497524 TAATTATATTTAAATATAT
1 TAATTATATTTAAATATAT
* *
2497543 TAAATAATATTT-ATTATAT
1 T-AATTATATTTAAATATAT
2497562 TAATTA
1 TAATTA
2497568 AATATATCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 4 0.10
19 9 0.23
20 9 0.23
21 15 0.38
22 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATTATATTTAAATATAT
Found at i:2497580 original size:23 final size:22
Alignment explanation
Indices: 2497524--2497584 Score: 54
Period size: 23 Copynumber: 2.7 Consensus size: 22
2497514 AAATATATTT
*
2497524 TAAT-TATATTTAAATATATTAAA
1 TAATATATATTT-ATTA-ATTAAA
*
2497547 TAATATTTATTATATTAATTAAA
1 TAATATATATT-TATTAATTAAA
2497570 T-ATATCATATTTATT
1 TAATAT-ATATTTATT
2497585 TCATAATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
22 8 0.25
23 15 0.47
24 8 0.25
25 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATATATATTTATTAATTAAA
Found at i:2498487 original size:2 final size:2
Alignment explanation
Indices: 2498425--2498471 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2498415 ATATATATAT
2498425 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2498467 AG AG A
1 AG AG A
2498472 AGATGGAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2498786 original size:15 final size:15
Alignment explanation
Indices: 2498766--2498807 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
2498756 GGTGTGAAAG
2498766 AGATTATAAATATTA
1 AGATTATAAATATTA
*
2498781 AGATTATAAATGTTA
1 AGATTATAAATATTA
2498796 AGATTGATAAAT
1 AGATT-ATAAAT
2498808 TGAATGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (15 bp):
AGATTATAAATATTA
Found at i:2499355 original size:93 final size:93
Alignment explanation
Indices: 2499196--2499380 Score: 361
Period size: 93 Copynumber: 2.0 Consensus size: 93
2499186 TCCGAATAAC
2499196 ACTGTAAAAACATCCAACAAAGCATAGACTTTTGTACTAATTAAAATGGCTACTTCATCTCCTTC
1 ACTGTAAAAACATCCAACAAAGCATAGACTTTTGTACTAATTAAAATGGCTACTTCATCTCCTTC
2499261 AAATCTGTAATGAAGAAGACGAGAGCCG
66 AAATCTGTAATGAAGAAGACGAGAGCCG
*
2499289 ACTGTAAAATCATCCAACAAAGCATAGACTTTTGTACTAATTAAAATGGCTACTTCATCTCCTTC
1 ACTGTAAAAACATCCAACAAAGCATAGACTTTTGTACTAATTAAAATGGCTACTTCATCTCCTTC
2499354 AAATCTGTAATGAAGAAGACGAGAGCC
66 AAATCTGTAATGAAGAAGACGAGAGCC
2499381 TAACAAGAAT
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 91 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (93 bp):
ACTGTAAAAACATCCAACAAAGCATAGACTTTTGTACTAATTAAAATGGCTACTTCATCTCCTTC
AAATCTGTAATGAAGAAGACGAGAGCCG
Found at i:2512625 original size:11 final size:11
Alignment explanation
Indices: 2512597--2512638 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
2512587 TATATTAATA
2512597 ATTATAAACAAT
1 ATTATAAA-AAT
*
2512609 A-AATAAAAAT
1 ATTATAAAAAT
2512619 ATTATAAAAA-
1 ATTATAAAAAT
2512629 ATTATAAAAA
1 ATTATAAAAA
2512639 GTAAAGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 14 0.52
11 12 0.44
12 1 0.04
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (11 bp):
ATTATAAAAAT
Found at i:2516923 original size:3 final size:3
Alignment explanation
Indices: 2516915--2516958 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
2516905 CATTACAACG
*
2516915 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT- TT- TTA TTA ATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2516959 TATAATAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 6 0.16
3 31 0.84
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:2517339 original size:17 final size:17
Alignment explanation
Indices: 2517317--2517351 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2517307 TTAAATTTAA
2517317 ATTTAAATAAAAATATT
1 ATTTAAATAAAAATATT
* *
2517334 ATTTAATTATAAATATT
1 ATTTAAATAAAAATATT
2517351 A
1 A
2517352 ACTCAAACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTAAATAAAAATATT
Found at i:2521884 original size:190 final size:188
Alignment explanation
Indices: 2521538--2521916 Score: 677
Period size: 190 Copynumber: 2.0 Consensus size: 188
2521528 TTAAAATATG
*
2521538 TTCTGTCAAAAGGAAAGAGATATTGTCTGTTTTAAATTGTAGATAGCTGTAAATATTTTGCAATT
1 TTCTGTCAAAAAGAAAGAGATATTGTCTGTTTTAAATTGTAGATAGCTGTAAATATTTTGCAATT
2521603 ACTAAGGATTCCTTAAATCAAGGAATTAGTTATCCTAGAGATAAGATAGTTGACTTAGGCATTTA
66 ACTAAGGATTCCTTAAATCAAGGAATTAGTTATCCTAGAGATAAGATAGTTGACTTAGGCATTTA
*
2521668 AAATAAAATTTTCTAGTTTCCTTTTCTATCTAGGATACTACTTTTGAAGGTTCAAACC
131 AAATAAAATTTTCTAGTTTCCTTTTCTAACTAGGATACTACTTTTGAAGGTTCAAACC
* *
2521726 TTCTGTTAAAAAGAAAGAGATATTGTCTGTTTTAAATTGTAGATAGTTGTAAATATTTTGCAATT
1 TTCTGTCAAAAAGAAAGAGATATTGTCTGTTTTAAATTGTAGATAGCTGTAAATATTTTGCAATT
*
2521791 ACTAAGGATTCCTTAAATATTAAGGAATTAGTTATCCTAGAGATAAGATAGTTGACTTAGGCATT
66 ACTAAGGATTCCTT-AA-ATCAAGGAATTAGTTATCCTAGAGATAAGATAGTTGACTTAGGCATT
* *
2521856 TAAAATAAAATTTTCTAGTTTTCTTTTCTAACTAGGATACTATTTTTGAAGGTTCAAACC
129 TAAAATAAAATTTTCTAGTTTCCTTTTCTAACTAGGATACTACTTTTGAAGGTTCAAACC
2521916 T
1 T
2521917 ATTGTATAAA
Statistics
Matches: 182, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
188 76 0.42
189 2 0.01
190 104 0.57
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.39
Consensus pattern (188 bp):
TTCTGTCAAAAAGAAAGAGATATTGTCTGTTTTAAATTGTAGATAGCTGTAAATATTTTGCAATT
ACTAAGGATTCCTTAAATCAAGGAATTAGTTATCCTAGAGATAAGATAGTTGACTTAGGCATTTA
AAATAAAATTTTCTAGTTTCCTTTTCTAACTAGGATACTACTTTTGAAGGTTCAAACC
Found at i:2524662 original size:21 final size:18
Alignment explanation
Indices: 2524633--2524692 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
2524623 TACCTAAACT
2524633 CAAACACAACATCAATCC
1 CAAACACAACATCAATCC
* *
2524651 CAAGCTACACAATC-TCAAACT
1 CAA---ACACAA-CATCAATCC
2524672 CAAACACAACATCAATCC
1 CAAACACAACATCAATCC
2524690 CAA
1 CAA
2524693 CCTATAGAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
17 1 0.03
18 17 0.52
21 14 0.42
22 1 0.03
ACGTcount: A:0.48, C:0.37, G:0.02, T:0.13
Consensus pattern (18 bp):
CAAACACAACATCAATCC
Found at i:2527855 original size:16 final size:16
Alignment explanation
Indices: 2527834--2527867 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2527824 GATTAAGACA
2527834 CATAGAAAGAGAAAAG
1 CATAGAAAGAGAAAAG
2527850 CATAGAAAGAGAAAAG
1 CATAGAAAGAGAAAAG
2527866 CA
1 CA
2527868 CGGAGAAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.62, C:0.09, G:0.24, T:0.06
Consensus pattern (16 bp):
CATAGAAAGAGAAAAG
Found at i:2535347 original size:178 final size:177
Alignment explanation
Indices: 2535048--2535401 Score: 654
Period size: 178 Copynumber: 2.0 Consensus size: 177
2535038 AAAGGCTACT
2535048 TAAGTTTTACGAAAATTATTGAGGAACTCAAGTTAAATACCATGATTCTAATTTGACACAATTCA
1 TAAGTTTTACGAAAATTATTGAGGAACTCAAGTTAAATACCATGATTCTAATTTGACACAATTCA
2535113 GAGCAGCAAAATACTTATACTAAATCAGAATACACCAAACAATCATTTGATGAGATTTCCAAAAG
66 GAGCAGCAAAATACTTATACTAAATCAGAATACACCAAACAATCATTTGATGAGATTTCCAAAAG
* *
2535178 ATTCCGGCAGTATGAATTCACAACTGGATTCAAAAATGCAGCAAAACA
131 ATTCAGGCAGTATGAATTCACAACTGGATTC-AAAATGAAGCAAAACA
*
2535226 TAAGTTTTACGAAAATTATTGAGGAATTCAAGTTAAATACCATGATTCTAATTTGACACAATTCA
1 TAAGTTTTACGAAAATTATTGAGGAACTCAAGTTAAATACCATGATTCTAATTTGACACAATTCA
*
2535291 GAGCAGCAAAATACTTATACTAAATCAGAATACACCAAACTATCATTTGATGAGATTTCCAAAAG
66 GAGCAGCAAAATACTTATACTAAATCAGAATACACCAAACAATCATTTGATGAGATTTCCAAAAG
*
2535356 ATTCATGCAGTATGAATTCACAACTGGATTCAAAATGAAGCAAAAC
131 ATTCAGGCAGTATGAATTCACAACTGGATTCAAAATGAAGCAAAAC
2535402 TTATTTTGCA
Statistics
Matches: 171, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
177 14 0.08
178 157 0.92
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (177 bp):
TAAGTTTTACGAAAATTATTGAGGAACTCAAGTTAAATACCATGATTCTAATTTGACACAATTCA
GAGCAGCAAAATACTTATACTAAATCAGAATACACCAAACAATCATTTGATGAGATTTCCAAAAG
ATTCAGGCAGTATGAATTCACAACTGGATTCAAAATGAAGCAAAACA
Found at i:2542080 original size:228 final size:228
Alignment explanation
Indices: 2541526--2542081 Score: 659
Period size: 228 Copynumber: 2.4 Consensus size: 228
2541516 TTAAACCAGT
* * * * *
2541526 AGGAGTCGACCCTTCACTCGGTTCTTCGTCTTCGTGGTGGCATGCAAATCTTCGTCAAGACTCTC
1 AGGAGTCAACCCTCCACCCGGTGCTTCGTCTTCGTGGTGGCATGCAAATCTTCGTCAAGACACTC
* * * * * * * *
2541591 AAC-GGAAAGACAATTGCCTTGGAGGTTGAAAGCTCCGATACCATTGATAATGTCAAGACTAAGA
66 -ACTGGAAAGACAATTACCTTGCAGGTTGAGAGTTCCGACACCATTAACAATGTCAAGACAAAGA
* * * *
2541655 TCCAAGACAGGGAAGGAATCCCCCCAGACCAACAGAGGCTTATCTTTGCTAGAAAGCAGCTAGAA
130 TCCAAGACAAGGAAGGAATCCCACCAGACCAACAAACGCTTATCTTTGCTAGAAAGCAGCTAGAA
* * * *
2541720 GATGGCCGTACACTGGCAGACTATAACATCCAGA
195 GATGGCCGCACACTAGCAGACTACAACATCCAAA
* * * * * *
2541754 AGGAATCTACCCTCCACCTGGTGCTTCGTCTTCGTGGTGGCGTGCAAATCTTCGTCAAAACCCTC
1 AGGAGTCAACCCTCCACCCGGTGCTTCGTCTTCGTGGTGGCATGCAAATCTTCGTCAAGACACTC
* * * * * *
2541819 ACTGGCAAGACCATTACCCT-CGAAGTTGAGAGTTCCGACACCATTAACAATGTCAGGGCAAAGA
66 ACTGGAAAGACAATTACCTTGC-AGGTTGAGAGTTCCGACACCATTAACAATGTCAAGACAAAGA
* * * *
2541883 TCCAAGACAAGGAATGG-ATTCCACCAGACCAGCAAACGCTTATTTTTGCTAGAAAGCAGCTTGA
130 TCCAAGACAAGGAA-GGAATCCCACCAGACCAACAAACGCTTATCTTTGCTAGAAAGCAGCTAGA
* * *
2541947 AGATGGCCGCGCCCTAGCTGACTACAACATCCAAA
194 AGATGGCCGCACACTAGCAGACTACAACATCCAAA
* * * *
2541982 AGGAGTCAACCCTCCACCCGGTGCTTCGTCTTGGAGGTGGCATGCAAATCTTTGTGAAGACACTC
1 AGGAGTCAACCCTCCACCCGGTGCTTCGTCTTCGTGGTGGCATGCAAATCTTCGTCAAGACACTC
*
2542047 ACTGGAAAGACAATTACCTTGCAGGTCGAGAGTTC
66 ACTGGAAAGACAATTACCTTGCAGGTTGAGAGTTC
2542082 AGATGCCATT
Statistics
Matches: 271, Mismatches: 53, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
227 2 0.01
228 266 0.98
229 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (228 bp):
AGGAGTCAACCCTCCACCCGGTGCTTCGTCTTCGTGGTGGCATGCAAATCTTCGTCAAGACACTC
ACTGGAAAGACAATTACCTTGCAGGTTGAGAGTTCCGACACCATTAACAATGTCAAGACAAAGAT
CCAAGACAAGGAAGGAATCCCACCAGACCAACAAACGCTTATCTTTGCTAGAAAGCAGCTAGAAG
ATGGCCGCACACTAGCAGACTACAACATCCAAA
Found at i:2542137 original size:228 final size:226
Alignment explanation
Indices: 2541526--2542144 Score: 641
Period size: 228 Copynumber: 2.7 Consensus size: 226
2541516 TTAAACCAGT
* * * * *
2541526 AGGAGTCGACCCTTCACTCGGTTCTTCGTCTTCGTGGTGGCATGCAAATCTTCGTCAAGACTCTC
1 AGGAGTCAACCCTCCACCCGGTGCTTCGTCTTCGTGGTGGCATGCAAATCTTCGTCAAGACACTC
* * * * * * *
2541591 AAC-GGAAAGACAATTGCCTTGGAGGTTGAAAGCTCCGATACCATTGATAATGTCAAGACTAAGA
66 -ACTGGAAAGACAATTACCTTGCAGGTTGAGAGTTCCGATACCATTAATAATGTAAAG-CTAAAA
* * * * *
2541655 TCCAAGACAGGGAAGGAATCCCCCCAGACCAACAGAGGCTTATCTTTGCTAGAAAGCAGCTAGAA
129 TCCAAGACAAGGAAGG-ATCCCACCAGACCAGCAAACGCTTATCTTTGCTAGAAAGCAGCTAGAA
* * * *
2541720 GATGGCCGTACACTGGCAGACTATAACATCCAGA
193 GATGGCCGCACACTAGCAGACTACAACATCCAAA
* * * * * *
2541754 AGGAATCTACCCTCCACCTGGTGCTTCGTCTTCGTGGTGGCGTGCAAATCTTCGTCAAAACCCTC
1 AGGAGTCAACCCTCCACCCGGTGCTTCGTCTTCGTGGTGGCATGCAAATCTTCGTCAAGACACTC
* * * * * * **
2541819 ACTGGCAAGACCATTACCCT-CGAAGTTGAGAGTTCCGACACCATTAACAATGTCAGGGC-AAAG
66 ACTGGAAAGACAATTACCTTGC-AGGTTGAGAGTTCCGATACCATTAATAATGT-AAAGCTAAA-
* * *
2541882 ATCCAAGACAAGGAATGGATTCCACCAGACCAGCAAACGCTTATTTTTGCTAGAAAGCAGCTTGA
128 ATCCAAGACAAGGAA-GGATCCCACCAGACCAGCAAACGCTTATCTTTGCTAGAAAGCAGCTAGA
* * *
2541947 AGATGGCCGCGCCCTAGCTGACTACAACATCCAAA
192 AGATGGCCGCACACTAGCAGACTACAACATCCAAA
* * * *
2541982 AGGAGTCAACCCTCCACCCGGTGCTTCGTCTTGGAGGTGGCATGCAAATCTTTGTGAAGACACTC
1 AGGAGTCAACCCTCCACCCGGTGCTTCGTCTTCGTGGTGGCATGCAAATCTTCGTCAAGACACTC
* * * * *
2542047 ACTGGAAAGACAATTACCTTGCAGGTCGAGAGTTCAGATGCCATTCATAACGTGAAAGCTAAAAT
66 ACTGGAAAGACAATTACCTTGCAGGTTGAGAGTTCCGATACCATTAATAATGT-AAAGCTAAAAT
* * * * *
2542112 TCAGGAAAAAGAGGGTATCCCACCAGACCAGCA
130 CCAAGACAAGGAAGG-ATCCCACCAGACCAGCA
2542145 GAGATTGATT
Statistics
Matches: 314, Mismatches: 69, Indels: 16
0.79 0.17 0.04
Matches are distributed among these distances:
227 6 0.02
228 301 0.96
229 7 0.02
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (226 bp):
AGGAGTCAACCCTCCACCCGGTGCTTCGTCTTCGTGGTGGCATGCAAATCTTCGTCAAGACACTC
ACTGGAAAGACAATTACCTTGCAGGTTGAGAGTTCCGATACCATTAATAATGTAAAGCTAAAATC
CAAGACAAGGAAGGATCCCACCAGACCAGCAAACGCTTATCTTTGCTAGAAAGCAGCTAGAAGAT
GGCCGCACACTAGCAGACTACAACATCCAAA
Found at i:2542918 original size:4 final size:4
Alignment explanation
Indices: 2542911--2542941 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2542901 TATATATATA
2542911 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
2542942 CTCCAAGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:2543145 original size:22 final size:21
Alignment explanation
Indices: 2543103--2543150 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
2543093 AAAAATTTAA
*
2543103 TAATTTAAATTATTATTTATT
1 TAATTAAAATTATTATTTATT
2543124 TAATTAAATATTATT-TTATATT
1 TAATTAAA-ATTATTATT-TATT
2543146 TAATT
1 TAATT
2543151 TTGTATGCGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TAATTAAAATTATTATTTATT
Found at i:2543447 original size:23 final size:25
Alignment explanation
Indices: 2543421--2543486 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 25
2543411 TTTGATTTGA
2543421 TAAAAAAATTAATAAT-TTAA-ATT
1 TAAAAAAATTAATAATATTAATATT
* *
2543444 TAAAATAATAAATTAGATATTAATATT
1 TAAAAAAATTAA-TA-ATATTAATATT
*
2543471 TTAAAAAA-TAATAATA
1 TAAAAAAATTAATAATA
2543487 AAAAATTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
23 10 0.29
24 5 0.15
25 4 0.12
26 6 0.18
27 9 0.26
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
TAAAAAAATTAATAATATTAATATT
Found at i:2544545 original size:15 final size:16
Alignment explanation
Indices: 2544512--2544552 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
2544502 GTTTGTATAA
*
2544512 ATATTAAATATAAGTAT
1 ATATTTAATATAAG-AT
2544529 ATATTTAATATAA-AT
1 ATATTTAATATAAGAT
2544544 ATATTTAAT
1 ATATTTAAT
2544553 TTTTATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.48
17 12 0.52
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
ATATTTAATATAAGAT
Found at i:2544619 original size:27 final size:27
Alignment explanation
Indices: 2544568--2544646 Score: 67
Period size: 26 Copynumber: 3.0 Consensus size: 27
2544558 TAAATTTTTT
*
2544568 TTATATATTTAAATTT-T-TTTAAAAAAA
1 TTATAT-TTTATATTTATATTT-AAAAAA
2544595 TTATATTTTATATTTATATTT-AAAAA
1 TTATATTTTATATTTATATTTAAAAAA
** **
2544621 -TATATTAAATATAAATATTTAAAAAA
1 TTATATTTTATATTTATATTTAAAAAA
2544647 ATAAGAATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
25 16 0.36
26 18 0.41
27 7 0.16
28 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TTATATTTTATATTTATATTTAAAAAA
Found at i:2544647 original size:27 final size:27
Alignment explanation
Indices: 2544585--2544649 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 27
2544575 TTTAAATTTT
** **
2544585 TTTAAAAAAATTATATTTTATATTTATA
1 TTTAAAAAAA-TATATTAAATATAAATA
2544613 TTT--AAAAATATATTAAATATAAATA
1 TTTAAAAAAATATATTAAATATAAATA
2544638 TTTAAAAAAATA
1 TTTAAAAAAATA
2544650 AGAATTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
25 16 0.52
26 5 0.16
27 7 0.23
28 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TTTAAAAAAATATATTAAATATAAATA
Found at i:2545105 original size:13 final size:13
Alignment explanation
Indices: 2545089--2545119 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2545079 ATTTTTTTAA
*
2545089 AATATTTATATTT
1 AATATTTATAATT
2545102 AATATTTATAATT
1 AATATTTATAATT
2545115 AATAT
1 AATAT
2545120 ATTTTTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AATATTTATAATT
Found at i:2550608 original size:2 final size:2
Alignment explanation
Indices: 2550603--2550650 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
2550593 GTGTGTGTGT
* *
2550603 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GC GA GC GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2550645 GA GA GA
1 GA GA GA
2550651 TCTTACTGTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.46, C:0.04, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2555137 original size:18 final size:20
Alignment explanation
Indices: 2555114--2555151 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
2555104 ATAATTGTAA
2555114 AATTTAAAA-A-TTAAAATT
1 AATTTAAAATATTTAAAATT
2555132 AATTTAAAATATTTAAAATT
1 AATTTAAAATATTTAAAATT
2555152 TTATATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 1 0.06
20 8 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTTAAAATATTTAAAATT
Found at i:2555266 original size:31 final size:32
Alignment explanation
Indices: 2555203--2555277 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 32
2555193 AAAAAATTAT
* * * *
2555203 AAATAAAATTAATAAATAATATATATTTAATA
1 AAATAAAATTAATAAAAAATAAATAATAAATA
*
2555235 AAATAAAATT-CTAAAAAATAAATAATAAATA
1 AAATAAAATTAATAAAAAATAAATAATAAATA
*
2555266 AGATAAATATTA
1 AAATAAA-ATTA
2555278 TTTATATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
31 22 0.63
32 13 0.37
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (32 bp):
AAATAAAATTAATAAAAAATAAATAATAAATA
Found at i:2556673 original size:16 final size:16
Alignment explanation
Indices: 2556654--2556692 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2556644 ATTAAATAAT
2556654 AATTTAAA-AAAATTTA
1 AATTTAAATAAAA-TTA
*
2556670 AATTTAAATTAAATTA
1 AATTTAAATAAAATTA
2556686 AATTTAA
1 AATTTAA
2556693 TTCGATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTTAAATAAAATTA
Found at i:2556783 original size:21 final size:20
Alignment explanation
Indices: 2556738--2556784 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
2556728 TTTTATTAAG
* *
2556738 AATTT-TATTTTTTATTTTA
1 AATTTATATATTTTATATTA
2556757 ATATTTATATATTTTATAATTA
1 A-ATTTATATATTTTAT-ATTA
2556779 AATTTA
1 AATTTA
2556785 AATAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 14 0.61
22 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
AATTTATATATTTTATATTA
Found at i:2557627 original size:20 final size:18
Alignment explanation
Indices: 2557601--2557663 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 18
2557591 ATTTGATGCG
*
2557601 TATAATTTATATAAATATA
1 TATAA-TTATATAAATAAA
*
2557620 TAATAATTAAATTAAATAAA
1 T-ATAATTATA-TAAATAAA
2557640 TATAAATTATATAAA-AAA
1 TAT-AATTATATAAATAAA
2557658 TTATAA
1 -TATAA
2557664 AATTAATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 5 0.14
19 14 0.38
20 18 0.49
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TATAATTATATAAATAAA
Found at i:2557630 original size:15 final size:17
Alignment explanation
Indices: 2557609--2557664 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 17
2557599 CGTATAATTT
2557609 ATATAAATATATAAT-A
1 ATATAAATATATAATAA
2557625 AT-TAAAT-TA-AATAA
1 ATATAAATATATAATAA
*
2557639 ATATAAATTATATAAAAA
1 ATATAAA-TATATAATAA
2557657 ATTATAAA
1 A-TATAAA
2557665 ATTAATTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
13 3 0.09
14 5 0.15
15 9 0.27
16 3 0.09
17 2 0.06
18 5 0.15
19 6 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATATAAATATATAATAA
Found at i:2557654 original size:24 final size:25
Alignment explanation
Indices: 2557601--2557654 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
2557591 ATTTGATGCG
* *
2557601 TATAATTTATATAAATATATAATAA
1 TATAAATTAAATAAATATATAATAA
*
2557626 T-TAAATTAAATAAATATA-AATTA
1 TATAAATTAAATAAATATATAATAA
2557649 TATAAA
1 TATAAA
2557655 AAATTATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 5 0.20
24 19 0.76
25 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
TATAAATTAAATAAATATATAATAA
Found at i:2557666 original size:20 final size:22
Alignment explanation
Indices: 2557611--2557674 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 22
2557601 TATAATTTAT
2557611 ATAAATATATAATAATTAAATTAA
1 ATAAAT-TATAA-AATTAAATTAA
*
2557635 ATAAA-TAT-AAATTATA-TAA
1 ATAAATTATAAAATTAAATTAA
*
2557654 A-AAATTATAAAATTAATTTAA
1 ATAAATTATAAAATTAAATTAA
2557675 TTTTAAACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
18 3 0.09
19 7 0.21
20 12 0.35
21 4 0.12
22 3 0.09
24 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAAATTATAAAATTAAATTAA
Found at i:2557706 original size:2 final size:2
Alignment explanation
Indices: 2557701--2557725 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2557691 TTTTTCTTAT
2557701 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 T
2557726 TAGAAATATC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2559285 original size:47 final size:44
Alignment explanation
Indices: 2559196--2559297 Score: 109
Period size: 47 Copynumber: 2.2 Consensus size: 44
2559186 AAATTTTTAA
* *
2559196 TTTAAATTAATATTTATTATTATTAAAAAATATTTAAAAAATAT
1 TTTATATTAATATTTATTATTATTAAAAAATATTAAAAAAATAT
2559240 TTTATATTAATATTTATATATT-TTATAATTAAATA-TAAATAAAATAT
1 TTTATATTAATATTTAT-TATTATTA-AA--AAATATTAAA-AAAATAT
* *
2559287 ATTATTTTAAT
1 TTTATATTAAT
2559298 TTAAAATCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
44 19 0.39
45 6 0.12
46 3 0.06
47 21 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (44 bp):
TTTATATTAATATTTATTATTATTAAAAAATATTAAAAAAATAT
Found at i:2562988 original size:16 final size:14
Alignment explanation
Indices: 2562967--2563002 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
2562957 TTCTATGTAA
2562967 AAAGAAGAAAAGTTAG
1 AAAGAAGAAAAG--AG
2562983 AAAGAAGAAAAGAG
1 AAAGAAGAAAAGAG
2562997 AAAGAA
1 AAAGAA
2563003 TAACGATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
16 12 0.60
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (14 bp):
AAAGAAGAAAAGAG
Found at i:2564403 original size:23 final size:24
Alignment explanation
Indices: 2564377--2564424 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2564367 TATGATTTTT
2564377 TAAA-AATTTTTAAATTAAACACA
1 TAAATAATTTTTAAATTAAACACA
**
2564400 TAAATTTTTTTTAAATTAAACACA
1 TAAATAATTTTTAAATTAAACACA
2564424 T
1 T
2564425 CAATGTCGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (24 bp):
TAAATAATTTTTAAATTAAACACA
Found at i:2565775 original size:2 final size:2
Alignment explanation
Indices: 2565764--2565792 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2565754 TGAAAGAAGA
2565764 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2565793 GCAATTTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2566174 original size:11 final size:11
Alignment explanation
Indices: 2566158--2566202 Score: 63
Period size: 11 Copynumber: 3.9 Consensus size: 11
2566148 TGTCACTATT
*
2566158 TTATTTTTTTA
1 TTATTTATTTA
2566169 TTATTTATTTA
1 TTATTTATTTA
2566180 TTATTTATTTA
1 TTATTTATTTA
2566191 TTTATTATATTT
1 -TTATT-TATTT
2566203 TAAAAGCTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 21 0.68
12 5 0.16
13 5 0.16
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:2566175 original size:15 final size:16
Alignment explanation
Indices: 2566157--2566201 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
2566147 TTGTCACTAT
2566157 TTTATTT-TTTTATTA
1 TTTATTTATTTTATTA
*
2566172 TTTATTTATTAT-TTA
1 TTTATTTATTTTATTA
*
2566187 TTTATTTATTATATT
1 TTTATTTATTTTATT
2566202 TTAAAAGCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 22 0.81
16 5 0.19
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTTATTTTATTA
Found at i:2566178 original size:4 final size:4
Alignment explanation
Indices: 2566157--2566202 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
2566147 TTGTCACTAT
*
2566157 TTTA TTTT TTTA -TTA TTTA TTTA -TTA TTTA TTTA TTTA TTATA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTT
2566203 TAAAAGCTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
3 6 0.16
4 27 0.73
5 4 0.11
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:2566914 original size:16 final size:16
Alignment explanation
Indices: 2566893--2566925 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2566883 ATATCATTTC
2566893 ATATTCAAGTCAATTA
1 ATATTCAAGTCAATTA
*
2566909 ATATTCAAGTTAATTA
1 ATATTCAAGTCAATTA
2566925 A
1 A
2566926 ATTTGAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.39
Consensus pattern (16 bp):
ATATTCAAGTCAATTA
Found at i:2566957 original size:21 final size:21
Alignment explanation
Indices: 2566933--2566975 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2566923 TAAATTTGAG
2566933 TTAT-TTTGAGTTCGAATTATT
1 TTATGTTTGAGTT-GAATTATT
* *
2566954 TTATGTTTGTGTTTAATTATT
1 TTATGTTTGAGTTGAATTATT
2566975 T
1 T
2566976 AAATTTAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.21, C:0.02, G:0.14, T:0.63
Consensus pattern (21 bp):
TTATGTTTGAGTTGAATTATT
Found at i:2570863 original size:22 final size:22
Alignment explanation
Indices: 2570832--2570873 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2570822 GTCGATTTCT
*
2570832 CTCTCGACATAGTTAGAATCCC
1 CTCTCAACATAGTTAGAATCCC
2570854 CTCTCAACATAGTTAGAATC
1 CTCTCAACATAGTTAGAATC
2570874 ATGTGATCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (22 bp):
CTCTCAACATAGTTAGAATCCC
Found at i:2572362 original size:84 final size:85
Alignment explanation
Indices: 2572224--2572386 Score: 265
Period size: 84 Copynumber: 1.9 Consensus size: 85
2572214 CAAGTAACAA
* *
2572224 ACTAATTGTACTTTATCCATTCCAAACTATTATAATTAAAAGTCCAATGCTTTCATCGTTCCTTA
1 ACTAATGGTACTTTATCCATTCCAAACTATTATAATTAAAAGTCCAATACTTTCATCGTTCCTTA
2572289 AGTAC-ACGCTGAGTAACGG
66 AGTACTACGCTGAGTAACGG
* * *
2572308 ACTAATGGTACTTTATCCATTTCAAACTATTATTATTAAAAGTCCAATATTTTCATCGTTCCTTA
1 ACTAATGGTACTTTATCCATTCCAAACTATTATAATTAAAAGTCCAATACTTTCATCGTTCCTTA
*
2572373 AGTACTATGCTGAG
66 AGTACTACGCTGAG
2572387 AGATTTCAGT
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
84 65 0.90
85 7 0.10
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (85 bp):
ACTAATGGTACTTTATCCATTCCAAACTATTATAATTAAAAGTCCAATACTTTCATCGTTCCTTA
AGTACTACGCTGAGTAACGG
Found at i:2573579 original size:14 final size:14
Alignment explanation
Indices: 2573560--2573589 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2573550 CACCCAAATC
2573560 TGGGTAACATAAGG
1 TGGGTAACATAAGG
2573574 TGGGTAACATAAGG
1 TGGGTAACATAAGG
2573588 TG
1 TG
2573590 ATATTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.37, T:0.23
Consensus pattern (14 bp):
TGGGTAACATAAGG
Found at i:2575459 original size:25 final size:26
Alignment explanation
Indices: 2575407--2575459 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
2575397 AAGTTCAACA
* *
2575407 GTATCAAAGAAAAGGCATCAATTAATT
1 GTATCAAAG-AAAGACAGCAATTAATT
*
2575434 GTATCAAAG-AAGACAGCAATTGATT
1 GTATCAAAGAAAGACAGCAATTAATT
2575459 G
1 G
2575460 CCGAGACAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 14 0.61
27 9 0.39
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.25
Consensus pattern (26 bp):
GTATCAAAGAAAGACAGCAATTAATT
Found at i:2579447 original size:13 final size:13
Alignment explanation
Indices: 2579429--2579453 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2579419 GTGTACGATG
2579429 ATTTTTTTTCTTA
1 ATTTTTTTTCTTA
2579442 ATTTTTTTTCTT
1 ATTTTTTTTCTT
2579454 TTTCTTACCT
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:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
ATTTTTTTTCTTA
Found at i:2579669 original size:19 final size:20
Alignment explanation
Indices: 2579610--2579675 Score: 82
Period size: 19 Copynumber: 3.3 Consensus size: 20
2579600 TTAATATTTT
*
2579610 ATAATTTTTAATTTAATTAA
1 ATAATTATTAATTTAATTAA
2579630 A-AATTATATAATTTAAATTAA
1 ATAATTAT-TAATTT-AATTAA
*
2579651 ATAATTATT-ATTTATTTAA
1 ATAATTATTAATTTAATTAA
2579670 ATAATT
1 ATAATT
2579676 TTTTATATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
19 16 0.39
20 11 0.27
21 8 0.20
22 6 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATAATTATTAATTTAATTAA
Found at i:2579681 original size:20 final size:20
Alignment explanation
Indices: 2579610--2579676 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
2579600 TTAATATTTT
*
2579610 ATAATTTTTAATTTAATTAA
1 ATAATTTATAATTTAATTAA
2579630 A-AATTATATAATTTAAATTAA
1 ATAATT-TATAATTT-AATTAA
* *
2579651 ATAA-TTATTATTTATTTAA
1 ATAATTTATAATTTAATTAA
2579670 ATAATTT
1 ATAATTT
2579677 TTTATATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 13 0.32
20 17 0.43
21 8 0.20
22 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATAATTTATAATTTAATTAA
Found at i:2580752 original size:8 final size:8
Alignment explanation
Indices: 2580739--2580764 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2580729 TTACTTACAT
2580739 TTTTTTTA
1 TTTTTTTA
2580747 TTTTTTTA
1 TTTTTTTA
2580755 TTTTTTTA
1 TTTTTTTA
2580763 TT
1 TT
2580765 CAAAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTA
Found at i:2581216 original size:25 final size:23
Alignment explanation
Indices: 2581164--2581227 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 23
2581154 AGCCTAAGGG
2581164 AAGAGAAAAAAAAAAAAAAAAAA
1 AAGAGAAAAAAAAAAAAAAAAAA
**
2581187 AAGAGAAAAAGGAAAAAAAAAAGGA
1 AAGAGAAAAA--AAAAAAAAAAAAA
* *
2581212 CAGAGAAAATAAAAAA
1 AAGAGAAAAAAAAAAA
2581228 GACGACAAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
23 16 0.46
25 19 0.54
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.02
Consensus pattern (23 bp):
AAGAGAAAAAAAAAAAAAAAAAA
Found at i:2581234 original size:21 final size:18
Alignment explanation
Indices: 2581179--2581228 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
2581169 AAAAAAAAAA
* *
2581179 AAAAAAAAAAGAGAAAAAGG
1 AAAAAAAAAAG-GACAGA-G
2581199 AAAAAAAAAAGGACAGAG
1 AAAAAAAAAAGGACAGAG
2581217 AAAATAAAAAAG
1 AAAA-AAAAAAG
2581229 ACGACAAGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 5 0.19
19 11 0.41
20 11 0.41
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (18 bp):
AAAAAAAAAAGGACAGAG
Found at i:2581637 original size:11 final size:11
Alignment explanation
Indices: 2581623--2581657 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2581613 ATTTATTTTT
2581623 ATTTTAATTAA
1 ATTTTAATTAA
*
2581634 ATTTTATTTAA
1 ATTTTAATTAA
*
2581645 ATTATAATTAA
1 ATTTTAATTAA
2581656 AT
1 AT
2581658 ATATTTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATTTTAATTAA
Found at i:2581640 original size:16 final size:17
Alignment explanation
Indices: 2581619--2581653 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2581609 TAGTATTTAT
*
2581619 TTTTATTTTAATTA-AA
1 TTTTATTTAAATTATAA
2581635 TTTTATTTAAATTATAA
1 TTTTATTTAAATTATAA
2581652 TT
1 TT
2581654 AAATATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTATTTAAATTATAA
Found at i:2582390 original size:14 final size:13
Alignment explanation
Indices: 2582371--2582527 Score: 75
Period size: 12 Copynumber: 12.2 Consensus size: 13
2582361 ATAATAAATG
2582371 TATTTAATATTATA
1 TATTT-ATATTATA
*
2582385 TATTTATA-TAAA
1 TATTTATATTATA
2582397 TATTAATATATTA-A
1 TATT--TATATTATA
*
2582411 TAATTTATGTTATA
1 T-ATTTATATTATA
*
2582425 TATATT-T-TAATA
1 TAT-TTATATTATA
2582437 TATTAATATATTA-A
1 TATT--TATATTATA
*
2582451 TTTTTTATATTAT-
1 -TATTTATATTATA
*
2582464 T-TTAATATTATA
1 TATTTATATTATA
*
2582476 TTATATT-TATAATA
1 -TAT-TTATATTATA
*
2582490 TATTT-TAAT-TA
1 TATTTATATTATA
2582501 TATTTATATTATA
1 TATTTATATTATA
*
2582514 T-TTTATAATATA
1 TATTTATATTATA
2582526 TA
1 TA
2582528 ATTGTGTAAT
Statistics
Matches: 112, Mismatches: 12, Indels: 39
0.69 0.07 0.24
Matches are distributed among these distances:
11 17 0.15
12 33 0.29
13 27 0.24
14 24 0.21
15 11 0.10
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (13 bp):
TATTTATATTATA
Found at i:2582393 original size:8 final size:8
Alignment explanation
Indices: 2582335--2582486 Score: 54
Period size: 7 Copynumber: 19.0 Consensus size: 8
2582325 ACATGTCTCT
2582335 TATTTATA
1 TATTTATA
2582343 -ATTTATA
1 TATTTATA
2582350 TATTT-T-
1 TATTTATA
*
2582356 TATATATA
1 TATTTATA
** *
2582364 -ATAAATG
1 TATTTATA
2582371 TATTTA-A
1 TATTTATA
2582378 TA-TTATA
1 TATTTATA
2582385 TATTTATA
1 TATTTATA
2582393 TAAATATTAATA
1 T--AT-TT-ATA
*
2582405 TATTAATA
1 TATTTATA
*
2582413 -ATTTATG
1 TATTTATA
*
2582420 T-TATATA
1 TATTTATA
2582427 TATTTTAATA
1 TA-TTT-ATA
*
2582437 TATTAATA
1 TATTTATA
*
2582445 TATTAAT-
1 TATTTATA
*
2582452 TTTTTATA
1 TATTTATA
2582460 TTATTT-TAA
1 -TATTTAT-A
2582469 TATTATATTA
1 TATT-TA-TA
2582479 TATTTATA
1 TATTTATA
2582487 ATATATTTTA
Statistics
Matches: 108, Mismatches: 16, Indels: 40
0.66 0.10 0.24
Matches are distributed among these distances:
6 7 0.06
7 34 0.31
8 33 0.31
9 13 0.12
10 14 0.13
11 3 0.03
12 4 0.04
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (8 bp):
TATTTATA
Found at i:2582440 original size:40 final size:39
Alignment explanation
Indices: 2582381--2582515 Score: 115
Period size: 34 Copynumber: 3.5 Consensus size: 39
2582371 TATTTAATAT
*
2582381 TATATATTTATATAAATATTAATATATTAATAATTTATGTTA
1 TATATATTTATA-ATATATTAATATATT-ATAATTTAT-TTA
2582423 TATATATTT-TAATATATTAATATA-T-TAATTT-TTTA
1 TATATATTTATAATATATTAATATATTATAATTTATTTA
* *
2582458 TAT-TATTT-TAATAT-TATATTATATTTATAATATATTT-
1 TATATATTTATAATATAT-TAATATA-TTATAATTTATTTA
*
2582495 TAATTATATTTATATTATATT
1 T-A-TATATTTATAATATATT
2582516 TTATAATATA
Statistics
Matches: 79, Mismatches: 4, Indels: 21
0.76 0.04 0.20
Matches are distributed among these distances:
33 1 0.01
34 17 0.22
35 6 0.08
36 2 0.03
37 12 0.15
38 4 0.05
39 2 0.03
40 17 0.22
41 8 0.10
42 10 0.13
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.59
Consensus pattern (39 bp):
TATATATTTATAATATATTAATATATTATAATTTATTTA
Found at i:2582445 original size:16 final size:16
Alignment explanation
Indices: 2582399--2582493 Score: 59
Period size: 16 Copynumber: 5.6 Consensus size: 16
2582389 TATATAAATA
*
2582399 TTAATATATTAATAAT
1 TTAATATATTAATATT
*
2582415 TT-ATGT-TATATATATT
1 TTAATATAT-TA-ATATT
*
2582431 TTAATATATTAATATA
1 TTAATATATTAATATT
* *
2582447 TTAATTTTTTATATTATT
1 TTAATATATTA-A-TATT
*
2582465 TTAATATTATATTATATT
1 TTAATA-TAT-TAATATT
2582483 TATAATATATT
1 T-TAATATATT
2582494 TTAATTATAT
Statistics
Matches: 60, Mismatches: 10, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
14 1 0.02
15 5 0.08
16 21 0.35
17 7 0.12
18 17 0.28
19 8 0.13
20 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (16 bp):
TTAATATATTAATATT
Found at i:2582446 original size:22 final size:22
Alignment explanation
Indices: 2582421--2582518 Score: 80
Period size: 22 Copynumber: 4.6 Consensus size: 22
2582411 TAATTTATGT
2582421 TATATATATTTTAATATATTAA
1 TATATATATTTTAATATATTAA
* *
2582443 TATAT-TAATTTT-TTATATTAT
1 TATATAT-ATTTTAATATATTAA
* * * *
2582464 TTTA-ATATTATATTATATTTA
1 TATATATATTTTAATATATTAA
*
2582485 TA-ATATATTTTAATTATATTTA
1 TATATATATTTTAA-TATATTAA
2582507 TAT-TATATTTTA
1 TATATATATTTTA
2582519 TAATATATAA
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
20 5 0.08
21 27 0.44
22 29 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TATATATATTTTAATATATTAA
Found at i:2582478 original size:29 final size:29
Alignment explanation
Indices: 2582420--2582526 Score: 95
Period size: 34 Copynumber: 3.8 Consensus size: 29
2582410 ATAATTTATG
*
2582420 TTATA-TATATTT-TAATATA-TTAATATA
1 TTATATTATATTTATAATATATTTTA-ATA
2582447 TTA-ATT-T-TTTAT-AT-TATTTTAATA
1 TTATATTATATTTATAATATATTTTAATA
2582471 TTATATTATATTTATAATATATTTTAATTATA
1 TTATATTATATTTATAATATATTTT-A--ATA
2582503 TTTATATTATATTTTATAATATAT
1 -TTATATTATA-TTTATAATATAT
2582527 AATTGTGTAA
Statistics
Matches: 66, Mismatches: 1, Indels: 19
0.77 0.01 0.22
Matches are distributed among these distances:
24 8 0.12
25 11 0.17
26 4 0.06
27 9 0.14
28 2 0.03
29 6 0.09
30 1 0.02
32 3 0.05
33 10 0.15
34 12 0.18
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
TTATATTATATTTATAATATATTTTAATA
Found at i:2582501 original size:16 final size:16
Alignment explanation
Indices: 2582420--2582526 Score: 55
Period size: 16 Copynumber: 6.7 Consensus size: 16
2582410 ATAATTTATG
2582420 TTAT-ATATATTTTAA
1 TTATAATATATTTTAA
2582435 TATATTAATATA--TTAA
1 T-TA-TAATATATTTTAA
* *
2582451 TTTTTTATATTATTTTAA
1 -TTATAATA-TATTTTAA
* *
2582469 -TAT--TATATTATAT
1 TTATAATATATTTTAA
2582482 TTATAATATATTTTAA
1 TTATAATATATTTTAA
* * *
2582498 TTATATTTATATTATATT
1 TTATA-ATATATTTTA-A
2582516 TTATAATATAT
1 TTATAATATAT
2582527 AATTGTGTAA
Statistics
Matches: 69, Mismatches: 11, Indels: 22
0.68 0.11 0.22
Matches are distributed among these distances:
13 6 0.09
14 5 0.07
15 5 0.07
16 24 0.35
17 15 0.22
18 14 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATAATATATTTTAA
Found at i:2582502 original size:11 final size:11
Alignment explanation
Indices: 2582475--2582518 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
2582465 TTAATATTAT
2582475 ATTATATTTATA
1 ATTATATTT-TA
2582487 A-TATATTTTA
1 ATTATATTTTA
2582497 ATTATA-TTTA
1 ATTATATTTTA
2582507 TATTATATTTTA
1 -ATTATATTTTA
2582519 TAATATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 7 0.24
11 17 0.59
12 5 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTATATTTTA
Found at i:2582520 original size:40 final size:42
Alignment explanation
Indices: 2582371--2582529 Score: 111
Period size: 46 Copynumber: 3.7 Consensus size: 42
2582361 ATAATAAATG
*
2582371 TATTTAATATTATATATTTATATAAATATTAATATATTAATAATT-
1 TATTTAATATTATAT-TTTATAT-AATA-TAATATATT-TTAATTA
* *
2582416 TATGTT-ATA-TATATTTTAATATATTAATATATTAATTTTTTATATTA
1 TAT-TTAATATTATA-TTT--TATA-TAATATAAT-ATATTTTA-ATTA
*
2582463 T-TTTAATATTATA--TTATAT-TTATAATATATTTTAATTA
1 TATTTAATATTATATTTTATATAATATAATATATTTTAATTA
2582501 TATTT-ATATTATATTTTATA-ATATATAAT
1 TATTTAATATTATATTTTATATA-ATATAAT
2582530 TGTGTAATAT
Statistics
Matches: 92, Mismatches: 7, Indels: 34
0.69 0.05 0.26
Matches are distributed among these distances:
38 13 0.14
39 10 0.11
40 10 0.11
41 7 0.08
42 4 0.04
44 7 0.08
45 14 0.15
46 21 0.23
47 6 0.07
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.58
Consensus pattern (42 bp):
TATTTAATATTATATTTTATATAATATAATATATTTTAATTA
Found at i:2582524 original size:34 final size:32
Alignment explanation
Indices: 2582343--2582526 Score: 152
Period size: 33 Copynumber: 5.8 Consensus size: 32
2582333 CTTATTTATA
* * *
2582343 ATTTATA-TAT-TTTTATATATA-ATAAATGT
1 ATTTATATTATATTTTATATATATTTTAATAT
* *
2582372 ATTTAATATTATATATTTATATAAATATTAATAT
1 ATTT-ATATTATAT-TTTATATATATTTTAATAT
* *
2582406 ATTAATAATT-TATGTTATATATATTTTAATAT
1 ATTTAT-ATTATATTTTATATATATTTTAATAT
*
2582438 ATTAATATATTA-ATTTTTTATATTATTTT-A-AT
1 ATT--TATATTATATTTTATATA-TATTTTAATAT
2582470 A-TTATATTATA-TTTATAATATATTTTAATTAT
1 ATTTATATTATATTTTAT-ATATATTTTAA-TAT
2582502 ATTTATATTATATTTTATAATATAT
1 ATTTATATTATATTTTAT-ATATAT
2582527 AATTGTGTAA
Statistics
Matches: 127, Mismatches: 11, Indels: 29
0.76 0.07 0.17
Matches are distributed among these distances:
29 21 0.17
30 8 0.06
31 4 0.03
32 26 0.20
33 36 0.28
34 32 0.25
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (32 bp):
ATTTATATTATATTTTATATATATTTTAATAT
Found at i:2583120 original size:24 final size:24
Alignment explanation
Indices: 2583092--2583137 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
2583082 TGCCCGTAAT
2583092 TTTAAAAT-TATTTAAATTTAAAAA
1 TTTAAAATAT-TTTAAATTTAAAAA
2583116 TTTAAAATATTTTAAATTTAAA
1 TTTAAAATATTTTAAATTTAAA
2583138 TTTAAACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTAAAATATTTTAAATTTAAAAA
Found at i:2583187 original size:16 final size:15
Alignment explanation
Indices: 2583135--2583193 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 15
2583125 TTTTAAATTT
2583135 AAATTTAAACTTAA-A
1 AAATTTAAA-TTAATA
2583150 AAATATATAAAATTAATA
1 AAAT-T-T-AAATTAATA
*
2583168 AAATTTAAATTGAATT
1 AAATTTAAATT-AATA
2583184 AAATTTAAAT
1 AAATTTAAAT
2583194 ATAAAAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
15 9 0.24
16 15 0.39
17 6 0.16
18 8 0.21
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (15 bp):
AAATTTAAATTAATA
Found at i:2583288 original size:11 final size:13
Alignment explanation
Indices: 2583272--2583309 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
2583262 AACTTATTAT
2583272 AATATT-AATA-A
1 AATATTAAATATA
2583283 AATATTAAATATA
1 AATATTAAATATA
2583296 AATATATAAATATA
1 AATAT-TAAATATA
2583310 TAAAAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 6 0.25
12 4 0.17
13 6 0.25
14 8 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATTAAATATA
Found at i:2583305 original size:14 final size:14
Alignment explanation
Indices: 2583273--2583309 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
2583263 ACTTATTATA
*
2583273 ATATTAATA-AAAT
1 ATATAAATATAAAT
2583286 AT-TAAATATAAAT
1 ATATAAATATAAAT
2583299 ATATAAATATA
1 ATATAAATATA
2583310 TAAAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 5 0.24
13 8 0.38
14 8 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATATAAATATAAAT
Found at i:2585192 original size:14 final size:14
Alignment explanation
Indices: 2585170--2585220 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
2585160 TTTTGAATTT
2585170 TTTTTATATATAAA
1 TTTTTATATATAAA
* *
2585184 TTTTGATATATTAA
1 TTTTTATATATAAA
2585198 TTTTATATTATATAAA
1 TTTT-TA-TATATAAA
2585214 TTTTTAT
1 TTTTTAT
2585221 TTTTATGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 17 0.55
15 3 0.10
16 11 0.35
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (14 bp):
TTTTTATATATAAA
Found at i:2585193 original size:16 final size:15
Alignment explanation
Indices: 2585169--2585217 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
2585159 TTTTTGAATT
*
2585169 TTTTTTATATATAAA
1 TTTTATATATATAAA
2585184 TTTTGATATAT-T-AA
1 TTTT-ATATATATAAA
2585198 TTTTATATTATATAAA
1 TTTTATA-TATATAAA
2585214 TTTT
1 TTTT
2585218 TATTTTTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 3 0.10
14 9 0.31
15 6 0.21
16 11 0.38
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (15 bp):
TTTTATATATATAAA
Found at i:2586324 original size:2 final size:2
Alignment explanation
Indices: 2586317--2586343 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2586307 ACATACATAC
2586317 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 A
2586344 ATGATTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2586971 original size:14 final size:14
Alignment explanation
Indices: 2586952--2586978 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2586942 AGGAAGCATC
2586952 AAAAATAAATAAAT
1 AAAAATAAATAAAT
2586966 AAAAATAAATAAA
1 AAAAATAAATAAA
2586979 AGGTGGAGGA
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAAATAAATAAAT
Found at i:2590758 original size:8 final size:8
Alignment explanation
Indices: 2590745--2590798 Score: 63
Period size: 8 Copynumber: 6.8 Consensus size: 8
2590735 ATCACTACTC
2590745 ACATATAT
1 ACATATAT
2590753 ACATATAT
1 ACATATAT
*
2590761 ACATACAT
1 ACATATAT
*
2590769 ACATACAT
1 ACATATAT
*
2590777 ACATACAT
1 ACATATAT
*
2590785 ATATATAT
1 ACATATAT
*
2590793 ATATAT
1 ACATAT
2590799 GTATGTGTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 43 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (8 bp):
ACATATAT
Found at i:2590798 original size:4 final size:4
Alignment explanation
Indices: 2590745--2590785 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
2590735 ATCACTACTC
* *
2590745 ACAT ATAT ACAT ATAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
2590786 TATATATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (4 bp):
ACAT
Found at i:2591967 original size:23 final size:25
Alignment explanation
Indices: 2591941--2591992 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
2591931 ATAAAAAATT
2591941 TTAAAAATATTA-TT-ATATTTATA
1 TTAAAAATATTATTTGATATTTATA
* *
2591964 TTAAATATATTATTTGATATTTATT
1 TTAAAAATATTATTTGATATTTATA
2591989 TTAA
1 TTAA
2591993 TATAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 11 0.44
24 2 0.08
25 12 0.48
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TTAAAAATATTATTTGATATTTATA
Found at i:2591992 original size:25 final size:23
Alignment explanation
Indices: 2591938--2591996 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 23
2591928 AATATAAAAA
*
2591938 ATTTTAAAAATATTATTATATTT
1 ATTTTAAATATATTATTATATTT
*
2591961 ATATTAAATATATTATTTGATATTT
1 ATTTTAAATATATTA-TT-ATATTT
2591986 ATTTT-AATATA
1 ATTTTAAATATA
2591997 AAAATTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 13 0.42
24 8 0.26
25 10 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTTTAAATATATTATTATATTT
Found at i:2592696 original size:24 final size:23
Alignment explanation
Indices: 2592648--2592693 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2592638 AAGATTTTAG
*
2592648 TTTTTATATATTTATTATATGAA
1 TTTTTATATATTTATTATATAAA
*
2592671 TTTTTATATTTTTAATTAT-TAAA
1 TTTTTATATATTT-ATTATATAAA
2592694 ATTATTACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTTTATATATTTATTATATAAA
Found at i:2593992 original size:22 final size:20
Alignment explanation
Indices: 2593966--2594014 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
2593956 AAATAAAAAA
* *
2593966 TTAAATAAATTTTATAAATTAT
1 TTAAATAAATATTA-AAA-TAC
2593988 TTAAATTAAATATTAAAATAC
1 TTAAA-TAAATATTAAAATAC
2594009 TTAAAT
1 TTAAAT
2594015 TTAACTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.04
21 7 0.29
22 8 0.33
23 8 0.33
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAAATAAATATTAAAATAC
Found at i:2594012 original size:21 final size:21
Alignment explanation
Indices: 2593950--2594015 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
2593940 ATTTTTTATT
*
2593950 AATTAAA-AATAAAA-AATTA
1 AATTAAATATTAAAATAATTA
* *
2593969 AA-TAAATTTTATAAATTATTTA
1 AATTAAATATTA-AAA-TAATTA
*
2593991 AATTAAATATTAAAATACTTA
1 AATTAAATATTAAAATAATTA
2594012 AATT
1 AATT
2594016 TAACTAAATC
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
18 4 0.11
19 4 0.11
20 3 0.08
21 9 0.24
22 9 0.24
23 8 0.22
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
AATTAAATATTAAAATAATTA
Found at i:2594385 original size:19 final size:20
Alignment explanation
Indices: 2594361--2594407 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
2594351 AAAATGGAAG
2594361 ATATATTTC-AATAATATTT
1 ATATATTTCGAATAATATTT
*
2594380 ATATA-TTCGTATAATATTT
1 ATATATTTCGAATAATATTT
2594399 ATATTATTT
1 ATA-TATTT
2594408 TTTATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 3 0.12
19 17 0.71
20 2 0.08
21 2 0.08
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (20 bp):
ATATATTTCGAATAATATTT
Found at i:2601418 original size:19 final size:20
Alignment explanation
Indices: 2601384--2601421 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2601374 CAACCGATAA
*
2601384 TAAATATATAATTTTAATAG
1 TAAATAAATAATTTTAATAG
2601404 TAAATAAAT-ATTTTAATA
1 TAAATAAATAATTTTAATA
2601422 AAAATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
TAAATAAATAATTTTAATAG
Found at i:2602250 original size:16 final size:17
Alignment explanation
Indices: 2602225--2602270 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
2602215 ATTATATCTT
2602225 TTAAATATATTTTAA-A
1 TTAAATATATTTTAATA
* *
2602241 TTACATATATTTTAATT
1 TTAAATATATTTTAATA
2602258 TTAAATATATTTT
1 TTAAATATATTTT
2602271 TTTGGTTAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATATATTTTAATA
Found at i:2609055 original size:36 final size:37
Alignment explanation
Indices: 2609014--2609089 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
2609004 ATAATAATAT
2609014 TAAAAATA-TTTTATATTATTTATAAT-TAAATTTAAA
1 TAAAAATATTTTTATATTATTTA-AATATAAATTTAAA
* *
2609050 TAAAAATATTTTTTTATTATTTAAATATTAATTTAAA
1 TAAAAATATTTTTATATTATTTAAATATAAATTTAAA
2609087 TAA
1 TAA
2609090 TATCAACTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 11 0.31
37 25 0.69
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (37 bp):
TAAAAATATTTTTATATTATTTAAATATAAATTTAAA
Found at i:2609844 original size:70 final size:70
Alignment explanation
Indices: 2609731--2609870 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
2609721 TCCATCCTTC
2609731 TAAACCACTTTCTTCAATCCAACTTCATATAGCTACTTAGTAATCATCATCCATGACCCAACCAG
1 TAAACCACTTTCTTCAATCCAACTTCATATAGCTACTTAGTAATCATCATCCATGACCCAACCAG
2609796 TCATT
66 TCATT
2609801 TAAACCACTTTCTTCAATCCAACTTCATATAGCTACTTAGTAATCATCATCCATGACCCAACCAG
1 TAAACCACTTTCTTCAATCCAACTTCATATAGCTACTTAGTAATCATCATCCATGACCCAACCAG
2609866 TCATT
66 TCATT
2609871 GCAATGCTTA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.31
Consensus pattern (70 bp):
TAAACCACTTTCTTCAATCCAACTTCATATAGCTACTTAGTAATCATCATCCATGACCCAACCAG
TCATT
Found at i:2613810 original size:17 final size:15
Alignment explanation
Indices: 2613788--2613829 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
2613778 CCTAACCAAA
2613788 AAAATATATTTAAAATT
1 AAAATATATTT--AATT
*
2613805 AAAATATATGTAATT
1 AAAATATATTTAATT
2613820 AAAATATATT
1 AAAATATATT
2613830 AAAGATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 13 0.57
17 10 0.43
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
AAAATATATTTAATT
Found at i:2614636 original size:19 final size:20
Alignment explanation
Indices: 2614612--2614649 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2614602 TAAATATTTT
*
2614612 TATTAAAA-TATTTATTTAC
1 TATTAAAATTATATATTTAC
2614631 TATTAAAATTATATATTTA
1 TATTAAAATTATATATTTA
2614650 TTATCGGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTAAAATTATATATTTAC
Found at i:2614649 original size:20 final size:19
Alignment explanation
Indices: 2614599--2614649 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
2614589 TTATTTAATT
* *
2614599 AAATAAATATTT-TTATTA
1 AAATATATATTTACTATTA
*
2614617 AAATATTTATTTACTATTA
1 AAATATATATTTACTATTA
2614636 AAATTATATATTTA
1 AAA-TATATATTTA
2614650 TTATCGGTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 10 0.37
19 8 0.30
20 9 0.33
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATATATATTTACTATTA
Found at i:2622560 original size:27 final size:28
Alignment explanation
Indices: 2622509--2622561 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
2622499 GCAATAAAAC
* *
2622509 AAATAAAAGTTTAAATTTTTCTCATAAA
1 AAATAAAAGTTTAAATTATTATCATAAA
*
2622537 AAATATAAG-TTAAATTATTATCATA
1 AAATAAAAGTTTAAATTATTATCATA
2622562 TTACCATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 14 0.64
28 8 0.36
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.40
Consensus pattern (28 bp):
AAATAAAAGTTTAAATTATTATCATAAA
Found at i:2624083 original size:27 final size:27
Alignment explanation
Indices: 2624034--2624087 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
2624024 CTTTGCTCCC
*
2624034 CCCCCCGATCCCTCGCTCACCCCGCCCT
1 CCCCCCGATCCCTCCCTCACCCC-CCCT
**
2624062 CCCCCCG-TCCCTCCCTTGCCCCCCCT
1 CCCCCCGATCCCTCCCTCACCCCCCCT
2624088 GGCCTTGTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 4 0.17
27 12 0.52
28 7 0.30
ACGTcount: A:0.04, C:0.70, G:0.09, T:0.17
Consensus pattern (27 bp):
CCCCCCGATCCCTCCCTCACCCCCCCT
Done.