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 16 of 402
Found at i:3726889 original size:42 final size:43
Alignment explanation
Indices: 3726804--3726891 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 43
3726794 AGGGAGTAAG
* * *
3726804 TTTCGGAGGATTGACATTAGATTTTTTAGAATTTATTGCGGAT
1 TTTCAGAGGATTGACATTAGATTTTTTAGAATGTATCGCGGAT
* *
3726847 TTTCAGAGGATTTACATTAGA-TTTTTAGAATGTATCGTGGAT
1 TTTCAGAGGATTGACATTAGATTTTTTAGAATGTATCGCGGAT
3726889 TTT
1 TTT
3726892 AAAAGATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 21 0.52
43 19 0.47
ACGTcount: A:0.26, C:0.07, G:0.22, T:0.45
Consensus pattern (43 bp):
TTTCAGAGGATTGACATTAGATTTTTTAGAATGTATCGCGGAT
Found at i:3734039 original size:125 final size:122
Alignment explanation
Indices: 3733789--3734020 Score: 355
Period size: 125 Copynumber: 1.9 Consensus size: 122
3733779 ACAGTAAGTG
* *
3733789 CATGTACATGCAGATGATATACATAAAAAACCATAACCAATTATTTACACACAATACTGGAACCT
1 CATGTACATGCAGATGATATAAATAAAAAACCATAACAAATTATTTA-ACACAATACTGGAACCT
**
3733854 GTCAAATCATCATCACATGCATGCAAACTAGAATGATGGAATATGTCTAAACGGTAAATA
65 GTCAAATCATCAT-ACA-GCATGCAAACTAGAATGATGGAATATGTCTAAACCCTAAATA
*
3733914 CATGTACATGCAGATGCTATAAATAAAAAACCATAACAAATTA-TT-ACACAATACTGGAACCTG
1 CATGTACATGCAGATGATATAAATAAAAAACCATAACAAATTATTTAACACAATACTGGAACCTG
*
3733977 TTAAATCATCAT-CA-CATGCAAACTAGAATGATGGAATATGTCTA
66 TCAAATCATCATACAGCATGCAAACTAGAATGATGGAATATGTCTA
3734021 CGTTGCACCC
Statistics
Matches: 103, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
118 30 0.29
120 2 0.02
122 29 0.28
124 2 0.02
125 40 0.39
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (122 bp):
CATGTACATGCAGATGATATAAATAAAAAACCATAACAAATTATTTAACACAATACTGGAACCTG
TCAAATCATCATACAGCATGCAAACTAGAATGATGGAATATGTCTAAACCCTAAATA
Found at i:3735274 original size:280 final size:280
Alignment explanation
Indices: 3734773--3735323 Score: 1059
Period size: 280 Copynumber: 2.0 Consensus size: 280
3734763 TGGTCAGGTA
3734773 CCTTGCCATTCCATCACCAAATTCAAAACACATTTAAGCAGTGGGAAGATCAATAAAAGTAAACA
1 CCTTGCCATTCCATCACCAAATTCAAAACACATTTAAGCAGTGGGAAGATCAATAAAAGTAAACA
3734838 CTAAAGAACTTGCAATAAAGTAAACAGCTATATGGAGAGCATCCAAAAGAAAAAGGATATTTAAA
66 CTAAAGAACTTGCAATAAAGTAAACAGCTATATGGAGAGCATCCAAAAGAAAAAGGATATTTAAA
3734903 AAAAAACCATGGTAATTAGTATCTTTTCAATGTCATATTTTTTTGGGAAAAGACACAGAGGCCAC
131 AAAAAACCATGGTAATTAGTATCTTTTCAATGTCATATTTTTTTGGGAAAAGACACAGAGGCCAC
3734968 TACGAAGAATGCTTGGCTGATAAATAACTCACTTCTAT-GTCTTCGACACCCTCAGTCACTACAA
196 TACGAAGAATGCTTGGCTGATAAATAACTCACTTCT-TGGTCTTCGACACCCTCAGTCACTACAA
3735032 AACCCCTGATCACTACAAAAC
260 AACCCCTGATCACTACAAAAC
3735053 CCTTGCCATTCCATCACCAAATTCAAAACACATTTAAGCAGTGGGAAGATCAATAAAAGTAAACA
1 CCTTGCCATTCCATCACCAAATTCAAAACACATTTAAGCAGTGGGAAGATCAATAAAAGTAAACA
3735118 CTAAAGAACTTGCAATAAAGTAAACAGCTATATGGAGAGCATCCAAAAGAAAAAGGATATTTAAA
66 CTAAAGAACTTGCAATAAAGTAAACAGCTATATGGAGAGCATCCAAAAGAAAAAGGATATTTAAA
3735183 AAAAAACCATGGTAATTAGTATCTTTTCAATGTCATATTTTTTTGGGAAAAGACACAGAGGCCAC
131 AAAAAACCATGGTAATTAGTATCTTTTCAATGTCATATTTTTTTGGGAAAAGACACAGAGGCCAC
* * *
3735248 TACGAAGAATGCTTGGCTGATAAATAATTCACTTCTTGGTCTTCGACCCCCTCAGTCACTACGAA
196 TACGAAGAATGCTTGGCTGATAAATAACTCACTTCTTGGTCTTCGACACCCTCAGTCACTACAAA
3735313 ACCCCTGATCA
261 ACCCCTGATCA
3735324 GTGCAATGGG
Statistics
Matches: 267, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
279 1 0.00
280 266 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (280 bp):
CCTTGCCATTCCATCACCAAATTCAAAACACATTTAAGCAGTGGGAAGATCAATAAAAGTAAACA
CTAAAGAACTTGCAATAAAGTAAACAGCTATATGGAGAGCATCCAAAAGAAAAAGGATATTTAAA
AAAAAACCATGGTAATTAGTATCTTTTCAATGTCATATTTTTTTGGGAAAAGACACAGAGGCCAC
TACGAAGAATGCTTGGCTGATAAATAACTCACTTCTTGGTCTTCGACACCCTCAGTCACTACAAA
ACCCCTGATCACTACAAAAC
Found at i:3742073 original size:22 final size:23
Alignment explanation
Indices: 3742048--3742102 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
3742038 ATTATTTTTA
* *
3742048 ATTATTTTTTA-TATTAATAAAT
1 ATTATTTTATATTATTAAAAAAT
*
3742070 ATTATTTTATATTTTTAAAAAAT
1 ATTATTTTATATTATTAAAAAAT
*
3742093 AATATTTTAT
1 ATTATTTTAT
3742103 TAATTTCGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTATTTTATATTATTAAAAAAT
Found at i:3742088 original size:20 final size:19
Alignment explanation
Indices: 3742040--3742088 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
3742030 ATAAAAAAAT
*
3742040 TATTTTTAATTATTTTTTA
1 TATTTTTAAATATTTTTTA
**
3742059 TATTAATAAATATTATTTTA
1 TATTTTTAAATATT-TTTTA
3742079 TATTTTTAAA
1 TATTTTTAAA
3742089 AAATAATATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTTTTAAATATTTTTTA
Found at i:3742590 original size:2 final size:2
Alignment explanation
Indices: 3742583--3742615 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3742573 CCTCTATCTT
3742583 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3742616 TTGTGATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3743550 original size:37 final size:37
Alignment explanation
Indices: 3743508--3743578 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
3743498 AAAACAAAAG
3743508 ATATAATATCTACATAATTAGAGT-GATAAAAAAATTC
1 ATATAATATCTACATAATTAGA-TCGATAAAAAAATTC
3743545 ATATAATATCTACATAATTAGATCGATAAAAAAA
1 ATATAATATCTACATAATTAGATCGATAAAAAAA
3743579 ATTCGTACCC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.03
37 32 0.97
ACGTcount: A:0.54, C:0.08, G:0.07, T:0.31
Consensus pattern (37 bp):
ATATAATATCTACATAATTAGATCGATAAAAAAATTC
Found at i:3744514 original size:3 final size:3
Alignment explanation
Indices: 3744506--3744535 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3744496 TTTTAATCAG
3744506 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3744536 CTTCTGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3746438 original size:13 final size:12
Alignment explanation
Indices: 3746414--3746462 Score: 59
Period size: 13 Copynumber: 4.2 Consensus size: 12
3746404 TTTGTTTTGA
3746414 TATTT-TTA-TT
1 TATTTATTATTT
3746424 TATTTTATTATTT
1 TA-TTTATTATTT
3746437 TATTTAGTTATTT
1 TATTTA-TTATTT
3746450 TATTTATT-TTT
1 TATTTATTATTT
3746461 TA
1 TA
3746463 AATATTTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.06
11 8 0.23
12 9 0.26
13 16 0.46
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (12 bp):
TATTTATTATTT
Found at i:3746982 original size:45 final size:45
Alignment explanation
Indices: 3746857--3746998 Score: 194
Period size: 45 Copynumber: 3.1 Consensus size: 45
3746847 AAGAAAAACA
* * * * *
3746857 AAAAAAAAATTATAAATAGACCAAAATGGTGAAAAATTTAGAAAT
1 AAAAAAAAATTTTAAATTGGCCCAAATAGTGAAAAATTTAGAAAT
*
3746902 CAAAAAGAAAATTTCTAAATTGGCTCAAATAGTGAAAAATTTAGAAAT
1 -AAAAA-AAAATTT-TAAATTGGCCCAAATAGTGAAAAATTTAGAAAT
*
3746950 AAAAAAAAATTTTAAATTGGCCCAAATTGTGAAAAATTTAGAAAT
1 AAAAAAAAATTTTAAATTGGCCCAAATAGTGAAAAATTTAGAAAT
3746995 AAAA
1 AAAA
3746999 CTTGTAAAAT
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
45 35 0.41
46 12 0.14
47 11 0.13
48 28 0.33
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.25
Consensus pattern (45 bp):
AAAAAAAAATTTTAAATTGGCCCAAATAGTGAAAAATTTAGAAAT
Found at i:3749187 original size:15 final size:14
Alignment explanation
Indices: 3749156--3749186 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3749146 AAAGTAAAAA
3749156 ATATTTTAAATTAT
1 ATATTTTAAATTAT
3749170 ATATTTTAAATT-T
1 ATATTTTAAATTAT
3749183 ATAT
1 ATAT
3749187 AAATATAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATATTTTAAATTAT
Found at i:3749282 original size:25 final size:23
Alignment explanation
Indices: 3749241--3749300 Score: 57
Period size: 25 Copynumber: 2.5 Consensus size: 23
3749231 CAGACTAAAT
* *
3749241 TTAAAATTTTTAATTTTGAATAGA
1 TTAAAAATTTTAATTTTAAAT-GA
*
3749265 TTAAAAATTTTATTTTTTAAATGA
1 TTAAAAATTTTA-ATTTTAAATGA
*
3749289 TATGAAAATTTT
1 T-TAAAAATTTT
3749301 TACATAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 14 0.47
25 16 0.53
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.52
Consensus pattern (23 bp):
TTAAAAATTTTAATTTTAAATGA
Found at i:3749530 original size:29 final size:29
Alignment explanation
Indices: 3749492--3749548 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
3749482 TAATAAAAAA
* *
3749492 ATAAAAATATTTTAAAT-TATAATATTTT
1 ATAAAAATATTTGAAATATATAAAATTTT
3749520 ATAAAATATATTTGAAATATATAAAATTT
1 ATAAAA-ATATTTGAAATATATAAAATTT
3749549 AATTTTTTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.24
29 10 0.40
30 9 0.36
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (29 bp):
ATAAAAATATTTGAAATATATAAAATTTT
Found at i:3758418 original size:23 final size:22
Alignment explanation
Indices: 3758378--3758422 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
3758368 GAAAATTTTT
* *
3758378 CTTATCATATTGTCAAATGAATC
1 CTTATCATATTATAAAAT-AATC
*
3758401 CTTATTATATTATAAAATAATC
1 CTTATCATATTATAAAATAATC
3758423 AATTTACCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (22 bp):
CTTATCATATTATAAAATAATC
Found at i:3762629 original size:18 final size:19
Alignment explanation
Indices: 3762608--3762657 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
3762598 TTTATTTTTT
*
3762608 AAAAT-ATTTATTTAATAA
1 AAAATAATTTATTCAATAA
3762626 AAAATTAATTT-TTCAATAA
1 AAAA-TAATTTATTCAATAA
3762645 AAAATAATTTATT
1 AAAATAATTTATT
3762658 AATTAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 10 0.36
19 14 0.50
20 4 0.14
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAATAATTTATTCAATAA
Found at i:3762747 original size:16 final size:16
Alignment explanation
Indices: 3762728--3762758 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3762718 TTCGAAAAAT
3762728 AATTATTTATCAATAA
1 AATTATTTATCAATAA
*
3762744 AATTATTTATTAATA
1 AATTATTTATCAATA
3762759 TTTTTAAGTA
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTATTTATCAATAA
Found at i:3762823 original size:19 final size:21
Alignment explanation
Indices: 3762780--3762823 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
3762770 AATTTCACTT
*
3762780 ATAAATAATTATATTAATATTA
1 ATAAATAATTATATT-ATATAA
3762802 ATAAATAA-TATATT-TATAA
1 ATAAATAATTATATTATATAA
3762821 ATA
1 ATA
3762824 TTATTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
21 6 0.29
22 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAAATAATTATATTATATAA
Found at i:3762825 original size:31 final size:28
Alignment explanation
Indices: 3762790--3762896 Score: 98
Period size: 27 Copynumber: 3.8 Consensus size: 28
3762780 ATAAATAATT
3762790 ATATTAATATTAATAAATAATATATTTATA
1 ATATT-ATATTAATAAATAATATA-TTATA
3762820 A-A-TATTATT-ATAAATAA-ATATTATA
1 ATATTA-TATTAATAAATAATATATTATA
* *
3762845 ATAATATATTAA-ATAATAATATACTAATA
1 ATATTATATTAATA-AATAATATA-TTATA
3762874 ATATAATATATTAATAAATAATA
1 ATAT--TATATTAATAAATAATA
3762897 AATAAATAAT
Statistics
Matches: 65, Mismatches: 2, Indels: 19
0.76 0.02 0.22
Matches are distributed among these distances:
25 6 0.09
26 9 0.14
27 17 0.26
28 8 0.12
29 8 0.12
30 1 0.02
31 15 0.23
32 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (28 bp):
ATATTATATTAATAAATAATATATTATA
Found at i:3762881 original size:16 final size:15
Alignment explanation
Indices: 3762800--3762896 Score: 73
Period size: 15 Copynumber: 6.8 Consensus size: 15
3762790 ATATTAATAT
*
3762800 TAATAAATAATATAT
1 TAATAAATAATATAC
*
3762815 TTATAAAT-AT-TA-
1 TAATAAATAATATAC
*
3762827 TTATAAATAA-ATA-
1 TAATAAATAATATAC
* *
3762840 TTAT-AATAATATAT
1 TAATAAATAATATAC
3762854 TAA-ATAATAATATAC
1 TAATA-AATAATATAC
*
3762869 TAATAATATAATATAT
1 TAATAA-ATAATATAC
3762885 TAATAAATAATA
1 TAATAAATAATA
3762897 AATAAATAAT
Statistics
Matches: 70, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
12 13 0.19
13 12 0.17
14 4 0.06
15 26 0.37
16 15 0.21
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAAATAATATAC
Found at i:3762900 original size:11 final size:10
Alignment explanation
Indices: 3762829--3762906 Score: 57
Period size: 11 Copynumber: 6.9 Consensus size: 10
3762819 AAATATTATT
3762829 ATAAATAAATA
1 ATAAAT-AATA
*
3762840 TTATAATAATA
1 ATA-AATAATA
3762851 TATTAAATAATA
1 -A-TAAATAATA
*
3762863 ATATACTAATA
1 ATA-AATAATA
3762874 ATATAATATATTA
1 ATA-AATA-A-TA
3762887 ATAAATAATAA
1 ATAAATAAT-A
3762898 ATAAATAAT
1 ATAAATAAT
3762907 TTTATTTTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
10 3 0.05
11 31 0.55
12 15 0.27
13 7 0.12
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (10 bp):
ATAAATAATA
Found at i:3762905 original size:31 final size:31
Alignment explanation
Indices: 3762801--3762906 Score: 99
Period size: 31 Copynumber: 3.3 Consensus size: 31
3762791 TATTAATATT
* * * *
3762801 AATAAATAATAT-ATTTATAAATATTATTATA
1 AATAAATAATATAATATATTAATA-AATAATA
* *
3762832 AATAAATATTATAATA-ATATATTAAATAATA
1 AATAAATAATATAATATAT-TAATAAATAATA
3762863 ATATACTAATAATATAATATATTAATAAATAATA
1 A-ATA--AATAATATAATATATTAATAAATAATA
3762897 AATAAATAAT
1 AATAAATAAT
3762907 TTTATTTTAA
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
31 25 0.41
32 8 0.13
33 3 0.05
34 23 0.38
35 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (31 bp):
AATAAATAATATAATATATTAATAAATAATA
Found at i:3762972 original size:34 final size:34
Alignment explanation
Indices: 3762892--3763017 Score: 111
Period size: 34 Copynumber: 3.7 Consensus size: 34
3762882 TATTAATAAA
* *
3762892 TAATAA-ATAAATAATTTT-ATTTTAAGTAT-TTT
1 TAATAATAT-AATAATTTTAATATTAAATATATTT
*
3762924 TATATTAACATAAT-ATTTTAATATTAAATATTATTAT
1 TA-A-TAATATAATAATTTTAATATTAAATA-TATT-T
*
3762961 TAA-AATATAATAATTTTAATAATAAATATATTT
1 TAATAATATAATAATTTTAATATTAAATATATTT
*
3762994 TAATAATA-AATCATTTTTAATATT
1 TAATAATATAAT-AATTTTAATATT
3763018 TTAATAATTA
Statistics
Matches: 78, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
32 2 0.03
33 13 0.17
34 39 0.50
35 18 0.23
36 3 0.04
37 3 0.04
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.50
Consensus pattern (34 bp):
TAATAATATAATAATTTTAATATTAAATATATTT
Found at i:3762993 original size:17 final size:17
Alignment explanation
Indices: 3762936--3763015 Score: 94
Period size: 17 Copynumber: 4.6 Consensus size: 17
3762926 TATTAACATA
*
3762936 ATATTTTAATATTAAAT
1 ATATTTTAATAATAAAT
3762953 ATTATTATTAA-AATATAAT
1 A-TATT-TTAATAATA-AAT
3762972 A-ATTTTAATAATAAAT
1 ATATTTTAATAATAAAT
3762988 ATATTTTAATAATAAAT
1 ATATTTTAATAATAAAT
3763005 CAT-TTTTAATA
1 -ATATTTTAATA
3763016 TTTTAATAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
16 8 0.14
17 31 0.55
18 9 0.16
19 8 0.14
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATTTTAATAATAAAT
Found at i:3765507 original size:101 final size:102
Alignment explanation
Indices: 3765304--3765510 Score: 249
Period size: 101 Copynumber: 2.0 Consensus size: 102
3765294 CATTTTTTAA
* * * *
3765304 TTTCCATTTCTCTATTTGTGGATAGAGCATTCTATATGAGGTGCATATCACCGCTTGTCTGGGAA
1 TTTCCATTTCTCTATTTGTGGACAGAGCATTCTATATCAGGTGCAAATCACCGCTTGTCTAGGAA
* * *
3765369 ACTTACTAATCTTCCCTTTCCAAACTTCGTAGGGAAG
66 ACTTACTAATCTTCCCTTTCCAAACCTCATAGCGAAG
*
3765406 TTTCGATTTCTCTATTTGTGGACA-AGCATTCTATATCAGGTGCAAATCACCGCTTGT-TCAGGA
1 TTTCCATTTCTCTATTTGTGGACAGAGCATTCTATATCAGGTGCAAATCACCGCTTGTCT-AGGA
** * * * *
3765469 AACTTTTTAGTC-TCCATTTTCCTAGCCTCATAGCGAAG
65 AACTTACTAATCTTCC-CTTTCCAAACCTCATAGCGAAG
3765507 TTTC
1 TTTC
3765511 AGGGGAAACT
Statistics
Matches: 89, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
100 4 0.04
101 63 0.71
102 22 0.25
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.37
Consensus pattern (102 bp):
TTTCCATTTCTCTATTTGTGGACAGAGCATTCTATATCAGGTGCAAATCACCGCTTGTCTAGGAA
ACTTACTAATCTTCCCTTTCCAAACCTCATAGCGAAG
Found at i:3769556 original size:3 final size:3
Alignment explanation
Indices: 3769550--3769609 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
3769540 CTTCTAATTG
* * * **
3769550 TTC TTC TTC TTC TTC TT- TGTC ATC TTA TTA TTC TTC AGC TTC TTC
1 TTC TTC TTC TTC TTC TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC
3769595 TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC
3769610 CTCTCCCATG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
2 1 0.02
3 46 0.98
ACGTcount: A:0.07, C:0.28, G:0.03, T:0.62
Consensus pattern (3 bp):
TTC
Found at i:3770671 original size:18 final size:19
Alignment explanation
Indices: 3770650--3770685 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3770640 TATTATAAAC
*
3770650 ATAGAA-ATTATAAATAAT
1 ATAGAACATCATAAATAAT
3770668 ATAGAACATCATAAATAA
1 ATAGAACATCATAAATAA
3770686 GTACTAATCT
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:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (19 bp):
ATAGAACATCATAAATAAT
Found at i:3773675 original size:17 final size:16
Alignment explanation
Indices: 3773634--3773680 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
3773624 TTTGATTATA
3773634 ATTAATTTTATAAATCG
1 ATTAATTTT-TAAATCG
*
3773651 ATTAAATTTATTAAATTG
1 ATT-AATTT-TTAAATCG
3773669 ATTAATTTTTAA
1 ATTAATTTTTAA
3773681 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 4 0.15
17 8 0.30
18 14 0.52
19 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (16 bp):
ATTAATTTTTAAATCG
Found at i:3774658 original size:19 final size:19
Alignment explanation
Indices: 3774621--3774658 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
3774611 TCTATAGGAT
3774621 ATAAAAAAATTTTAATTATA
1 ATAAAAAAATTTT-ATTATA
3774641 ATAAAAAATATTTT-TTAT
1 ATAAAAAA-ATTTTATTAT
3774659 TACAATCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 8 0.47
21 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAAAAAAATTTTATTATA
Found at i:3775291 original size:3 final size:3
Alignment explanation
Indices: 3775283--3775308 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3775273 CTCTGCCCAA
3775283 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
3775309 CTCTTGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3776044 original size:21 final size:20
Alignment explanation
Indices: 3775986--3776058 Score: 87
Period size: 20 Copynumber: 3.5 Consensus size: 20
3775976 AAAAAATAAA
3775986 AAATCATAAAAAATAATTTTG
1 AAAT-ATAAAAAATAATTTTG
3776007 AAATATAAAATAA-AATTTT-
1 AAATATAAAA-AATAATTTTG
3776026 AAATATTTAAAAAATAATTTTG
1 AAATA--TAAAAAATAATTTTG
*
3776048 GAATATAAAAA
1 AAATATAAAAA
3776059 CAAGTGAATA
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
19 5 0.11
20 20 0.43
21 17 0.37
22 4 0.09
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (20 bp):
AAATATAAAAAATAATTTTG
Found at i:3776138 original size:317 final size:319
Alignment explanation
Indices: 3775568--3776207 Score: 1239
Period size: 317 Copynumber: 2.0 Consensus size: 319
3775558 TCCATTTTTA
3775568 TTTATTTGTTTGTATTAAGTTTTACAAAGTTTAAGAAAAAAATTTTGATTTTAACCTATTTAATA
1 TTTATTTGTTTGTATTAAGTTTTACAAAGTTTAAGAAAAAAATTTTGATTTTAACCTATTTAATA
* *
3775633 TTAAAATTAAAAATTTTTATGTTAAAAAAATAAAAAATCATAAACAAATAATTTTTAAATATAAA
66 TTAAAATTAAAAATTTCTATGTTAAAAAAATAAAAAATCATAAACAAATAATTTTGAAATATAAA
3775698 ATAAAATTTTAAATATTTTAAAAAATAATTTTGGAATATAAAAACAAGTGAATAAAGAAAATGTG
131 ATAAAATTTTAAATATTTTAAAAAATAATTTTGGAATATAAAAACAAGTGAATAAAGAAAATGTG
3775763 ATAGAGGAAATAACGTTTTGGGCTTACAACTTACAATTGAAATATATAATTTTAGGTTTTAAAAT
196 ATAGAGGAAATAACGTTTTGGGCTTACAACTTACAATTGAAATATATAATTTTAGGTTTTAAAAT
3775828 TGAAAATTGACCACTTATAAAAAGAATAGAGAAAAATTTTATAGTTGCATACTTGCATT
261 TGAAAATTGACCACTTATAAAAAGAATAGAGAAAAATTTTATAGTTGCATACTTGCATT
3775887 TTTATTTGTTTGTATTAAGTTTTACAAAGTTTAAGAAAAAAATTTTGATTTTAACCTATTTAATA
1 TTTATTTGTTTGTATTAAGTTTTACAAAGTTTAAGAAAAAAATTTTGATTTTAACCTATTTAATA
3775952 TTAAAATTAAAAATTTCTATGTTAAAAAAATAAAAAATCATAAA-AAATAATTTTGAAATATAAA
66 TTAAAATTAAAAATTTCTATGTTAAAAAAATAAAAAATCATAAACAAATAATTTTGAAATATAAA
3776016 ATAAAATTTTAAATA-TTTAAAAAATAATTTTGGAATATAAAAACAAGTGAATAAAGAAAATGTG
131 ATAAAATTTTAAATATTTTAAAAAATAATTTTGGAATATAAAAACAAGTGAATAAAGAAAATGTG
3776080 ATAGAGGAAATAACGTTTTGGGCTTACAACTTACAATTGAAATATATAATTTTAGGTTTTAAAAT
196 ATAGAGGAAATAACGTTTTGGGCTTACAACTTACAATTGAAATATATAATTTTAGGTTTTAAAAT
*
3776145 TGAAAATTGACCACTTATAAAAAGAATAGAGAAAAATTTTGTAGTTGCATACTTGCATT
261 TGAAAATTGACCACTTATAAAAAGAATAGAGAAAAATTTTATAGTTGCATACTTGCATT
3776204 TTTA
1 TTTA
3776208 GAAAAGGGTA
Statistics
Matches: 318, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
317 176 0.55
318 34 0.11
319 108 0.34
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.37
Consensus pattern (319 bp):
TTTATTTGTTTGTATTAAGTTTTACAAAGTTTAAGAAAAAAATTTTGATTTTAACCTATTTAATA
TTAAAATTAAAAATTTCTATGTTAAAAAAATAAAAAATCATAAACAAATAATTTTGAAATATAAA
ATAAAATTTTAAATATTTTAAAAAATAATTTTGGAATATAAAAACAAGTGAATAAAGAAAATGTG
ATAGAGGAAATAACGTTTTGGGCTTACAACTTACAATTGAAATATATAATTTTAGGTTTTAAAAT
TGAAAATTGACCACTTATAAAAAGAATAGAGAAAAATTTTATAGTTGCATACTTGCATT
Found at i:3777107 original size:21 final size:21
Alignment explanation
Indices: 3777071--3777123 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
3777061 AATGCAAACT
*
3777071 ATTTGT-ATTTTAAAATTCAA
1 ATTTGTAATTTTAAAATTAAA
*
3777091 ATTTGTAATTTTCAAATTAAA
1 ATTTGTAATTTTAAAATTAAA
* *
3777112 ATATCTAATTTT
1 ATTTGTAATTTT
3777124 TACTGTTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.51
Consensus pattern (21 bp):
ATTTGTAATTTTAAAATTAAA
Found at i:3777806 original size:27 final size:26
Alignment explanation
Indices: 3777758--3777820 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 26
3777748 TTTTATTTTT
* *
3777758 TAATATTTAAATGATATTTAATATAA
1 TAATATTAAAATGATATATAATATAA
* *
3777784 TAATATATAAAATTATATATAATTTAA
1 TAATAT-TAAAATGATATATAATATAA
*
3777811 TAAAATTAAA
1 TAATATTAAA
3777821 TTAATAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 10 0.32
27 21 0.68
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
TAATATTAAAATGATATATAATATAA
Found at i:3777873 original size:8 final size:8
Alignment explanation
Indices: 3777842--3777893 Score: 56
Period size: 8 Copynumber: 6.8 Consensus size: 8
3777832 TTATTTTTAA
3777842 ATATAAAT
1 ATATAAAT
3777850 ATA-AAATT
1 ATATAAA-T
*
3777858 AAATAAAT
1 ATATAAAT
3777866 ATATAAAT
1 ATATAAAT
3777874 ATATAAA-
1 ATATAAAT
3777881 AT-TAAAT
1 ATATAAAT
*
3777888 AAATAA
1 ATATAA
3777894 TTAAAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
6 4 0.11
7 6 0.16
8 24 0.65
9 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
ATATAAAT
Found at i:3782863 original size:2 final size:2
Alignment explanation
Indices: 3782856--3782895 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3782846 TTTGCACTGT
3782856 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3782896 ATGTGTGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3787208 original size:33 final size:33
Alignment explanation
Indices: 3787139--3787238 Score: 128
Period size: 33 Copynumber: 2.9 Consensus size: 33
3787129 AGTATTGGCT
* * *
3787139 TCAGTGCTTTCCTCAGCAGCAGCAGGGGGAGGAGCC
1 TCAGTGCTTTCCTCAACTGAAGCA---GGAGGAGCC
*
3787175 TCAGTGCTTTCCTCAACTGGAGCAGGAGGAGCC
1 TCAGTGCTTTCCTCAACTGAAGCAGGAGGAGCC
*
3787208 TCAGTGCTTTCCTCAACTGAAGCAGCAGGAG
1 TCAGTGCTTTCCTCAACTGAAGCAGGAGGAG
3787239 TCTCCACTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
33 38 0.64
36 21 0.36
ACGTcount: A:0.22, C:0.27, G:0.31, T:0.20
Consensus pattern (33 bp):
TCAGTGCTTTCCTCAACTGAAGCAGGAGGAGCC
Found at i:3791492 original size:18 final size:18
Alignment explanation
Indices: 3791471--3791523 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
3791461 TTATAATATT
3791471 TTATATAATTATATTTTA
1 TTATATAATTATATTTTA
* * * *
3791489 TTATTTAAATAAATTTGA
1 TTATATAATTATATTTTA
*
3791507 TTAAATAATTATATTTT
1 TTATATAATTATATTTT
3791524 TGTTTAAATA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TTATATAATTATATTTTA
Found at i:3791530 original size:20 final size:20
Alignment explanation
Indices: 3791502--3791542 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3791492 TTTAAATAAA
3791502 TTTGATTAAATA-ATTATATT
1 TTTGATTAAATATATT-TATT
*
3791522 TTTGTTTAAATATATTTATT
1 TTTGATTAAATATATTTATT
3791542 T
1 T
3791543 AAATCATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTGATTAAATATATTTATT
Found at i:3791545 original size:34 final size:35
Alignment explanation
Indices: 3791470--3791585 Score: 128
Period size: 34 Copynumber: 3.2 Consensus size: 35
3791460 ATTATAATAT
* * *
3791470 TTTATATAATTATATTTTATTATTTAAATAAATTTGA
1 TTTAAATAATTATATTTT-TTGTTTAAATATATTT-A
3791507 -TTAAATAATTATA-TTTTTGTTTAAATATATTTA
1 TTTAAATAATTATATTTTTTGTTTAAATATATTTA
*
3791540 TTTAAATCATTATATTTTTTACTGTTTAAATATATTTA
1 TTTAAATAATTATA-TTTTT--TGTTTAAATATATTTA
3791578 TTCTAAAT
1 TT-TAAAT
3791586 TAAAAACATT
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
33 1 0.01
34 26 0.38
35 3 0.04
36 16 0.23
38 18 0.26
39 5 0.07
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (35 bp):
TTTAAATAATTATATTTTTTGTTTAAATATATTTA
Found at i:3791588 original size:20 final size:20
Alignment explanation
Indices: 3791527--3791589 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
3791517 ATATTTTTGT
3791527 TTAAATATATTTATT-TAAA
1 TTAAATATATTTATTCTAAA
* * * **
3791546 -TCATTATATTTTTTACT-GT
1 TTAAATATATTTATT-CTAAA
3791565 TTAAATATATTTATTCTAAA
1 TTAAATATATTTATTCTAAA
3791585 TTAAA
1 TTAAA
3791590 AACATTTTGA
Statistics
Matches: 30, Mismatches: 10, Indels: 7
0.64 0.21 0.15
Matches are distributed among these distances:
18 11 0.37
19 2 0.07
20 17 0.57
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.54
Consensus pattern (20 bp):
TTAAATATATTTATTCTAAA
Found at i:3793352 original size:19 final size:19
Alignment explanation
Indices: 3793328--3793372 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3793318 TATTCGTGAA
*
3793328 TTTAATTTAATTTTTA-TAT
1 TTTAATTT-ATTTTAATTAT
*
3793347 TTTAATATATTTTAATTAT
1 TTTAATTTATTTTAATTAT
3793366 TTTAATT
1 TTTAATT
3793373 AATAAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTAATTTATTTTAATTAT
Found at i:3793355 original size:10 final size:10
Alignment explanation
Indices: 3793342--3793371 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3793332 ATTTAATTTT
3793342 TATATTTTAA
1 TATATTTTAA
3793352 TATATTTTAA
1 TATATTTTAA
3793362 T-TATTTTAA
1 TATATTTTAA
3793371 T
1 T
3793372 TAATAAATAT
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:3793368 original size:9 final size:9
Alignment explanation
Indices: 3793344--3793373 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
3793334 TTAATTTTTA
3793344 TATTTTAAT
1 TATTTTAAT
3793353 ATATTTTAAT
1 -TATTTTAAT
3793363 TATTTTAAT
1 TATTTTAAT
3793372 TA
1 TA
3793374 ATAAATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTTAAT
Found at i:3797852 original size:16 final size:17
Alignment explanation
Indices: 3797831--3797863 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3797821 TTCAAAACTA
*
3797831 TTTAAT-TTTAATTTTT
1 TTTAATATTAAATTTTT
3797847 TTTAATATTAAATTTTT
1 TTTAATATTAAATTTTT
3797864 AAAATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTAATATTAAATTTTT
Found at i:3815171 original size:15 final size:15
Alignment explanation
Indices: 3815138--3815184 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
3815128 CCTATAAGAG
**
3815138 AAAAAATAA-AAAAT
1 AAAAAATAATAATTT
3815152 AAAAAACTAATAATTT
1 AAAAAA-TAATAATTT
*
3815168 AAAAAATTATAATTT
1 AAAAAATAATAATTT
3815183 AA
1 AA
3815185 TCAAGAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 6 0.21
15 13 0.46
16 9 0.32
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAAAATAATAATTT
Found at i:3817715 original size:9 final size:10
Alignment explanation
Indices: 3817697--3817731 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
3817687 TCAATATGCA
3817697 AATAAATAAT
1 AATAAATAAT
*
3817707 ACT-AATAAT
1 AATAAATAAT
3817716 AATAAATAAT
1 AATAAATAAT
3817726 AATAAA
1 AATAAA
3817732 GAAATTACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (10 bp):
AATAAATAAT
Found at i:3819286 original size:14 final size:15
Alignment explanation
Indices: 3819267--3819295 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3819257 AATCATTTGA
3819267 ATTGCT-AAATAAAT
1 ATTGCTAAAATAAAT
3819281 ATTGCTAAAATAAAT
1 ATTGCTAAAATAAAT
3819296 TAATGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (15 bp):
ATTGCTAAAATAAAT
Found at i:3819665 original size:14 final size:14
Alignment explanation
Indices: 3819646--3819691 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
3819636 CTCTCATACT
3819646 ATTTTAATTTAATA
1 ATTTTAATTTAATA
* *
3819660 ATTTTAATCTAATC
1 ATTTTAATTTAATA
3819674 A--TTAATTTAATCA
1 ATTTTAATTTAAT-A
3819687 ATTTT
1 ATTTT
3819692 TTGTTATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
12 9 0.36
13 1 0.04
14 13 0.52
15 2 0.08
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTTTAATTTAATA
Found at i:3820077 original size:29 final size:30
Alignment explanation
Indices: 3820014--3820079 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
3820004 TTTTTTGGAA
* *
3820014 TTTTTATGTTTTTCAAAAAAATTTCATAAT
1 TTTTTATGTTTTTAAAAAAAATTACATAAT
* *
3820044 ATTTTATG-TTTTAAAAAAGAATTACAT-TT
1 TTTTTATGTTTTTAAAAAA-AATTACATAAT
3820073 TTTTTAT
1 TTTTTAT
3820080 CTTATTCAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (30 bp):
TTTTTATGTTTTTAAAAAAAATTACATAAT
Found at i:3820551 original size:19 final size:20
Alignment explanation
Indices: 3820519--3820566 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
3820509 AAGTAAATTT
3820519 AATATTTTTAAAAAATT-AA
1 AATATTTTTAAAAAATTCAA
3820538 AA-ATTTTATAAAAAATTCAA
1 AATATTTT-TAAAAAATTCAA
3820558 AATATTTTT
1 AATATTTTT
3820567 TTTATATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 5 0.19
19 11 0.42
20 5 0.19
21 5 0.19
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATTTTTAAAAAATTCAA
Found at i:3827147 original size:26 final size:25
Alignment explanation
Indices: 3827101--3827153 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
3827091 AAAAATATTA
*
3827101 AAATAATTTTGGTAATTTAATATAAT
1 AAATAATTTTGGTAATATAATA-AAT
*
3827127 AAATAAATTTT-GTTATATAATAAAT
1 AAAT-AATTTTGGTAATATAATAAAT
3827152 AA
1 AA
3827154 TATATATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.21
26 13 0.54
27 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (25 bp):
AAATAATTTTGGTAATATAATAAAT
Found at i:3828282 original size:23 final size:25
Alignment explanation
Indices: 3828248--3828306 Score: 77
Period size: 23 Copynumber: 2.4 Consensus size: 25
3828238 AAACAGTAAC
*
3828248 AAAAAATATTATAATTATAATT-A-A
1 AAAAAAT-TTATAATTACAATTGACA
3828272 AAAAAATTTATAATTACAATTGACA
1 AAAAAATTTATAATTACAATTGACA
*
3828297 AATAAATTTA
1 AAAAAATTTA
3828307 ACAAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 13 0.42
24 8 0.26
25 10 0.32
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (25 bp):
AAAAAATTTATAATTACAATTGACA
Found at i:3828339 original size:14 final size:15
Alignment explanation
Indices: 3828296--3828340 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 15
3828286 TACAATTGAC
*
3828296 AAATAAATTTA-A-C
1 AAATAAATTTATATT
*
3828309 AAAAAAATTTATATT
1 AAATAAATTTATATT
3828324 AAATAAATTT-TATT
1 AAATAAATTTATATT
3828338 AAA
1 AAA
3828341 ATTAATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 10 0.37
14 8 0.30
15 9 0.33
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATAAATTTATATT
Found at i:3829184 original size:34 final size:34
Alignment explanation
Indices: 3829116--3829182 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
3829106 TTCATATAAA
*
3829116 ATATGATATAAATACAAAAAATTATTAATTTTTT
1 ATATGATATAAATACAAAAAATGATTAATTTTTT
* * *
3829150 ATATGATATAAATACATAAACTGA-TAGTTTTTT
1 ATATGATATAAATACAAAAAATGATTAATTTTTT
3829183 TAGGAGAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 8 0.28
34 21 0.72
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.43
Consensus pattern (34 bp):
ATATGATATAAATACAAAAAATGATTAATTTTTT
Found at i:3829521 original size:67 final size:68
Alignment explanation
Indices: 3829439--3829570 Score: 212
Period size: 67 Copynumber: 2.0 Consensus size: 68
3829429 TTAAAAAAAT
*
3829439 AAAAAATACAAAATTACTTACTACATTAATATCATTCTATAATTAAATACAATTATTTTATAAAT
1 AAAAAATACAAAATTACTTACTACATCAATATCATTCTATAATTAAATACAATTATTTTATAAAT
3829504 CGA
66 CGA
* * * *
3829507 AAAAAATA-AAAATTACTTATTGCATCAATATCATTTTATAATTAAATACCATTATTTTATAAAT
1 AAAAAATACAAAATTACTTACTACATCAATATCATTCTATAATTAAATACAATTATTTTATAAAT
3829571 TGACTGTATA
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
67 51 0.86
68 8 0.14
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.39
Consensus pattern (68 bp):
AAAAAATACAAAATTACTTACTACATCAATATCATTCTATAATTAAATACAATTATTTTATAAAT
CGA
Found at i:3830071 original size:3 final size:3
Alignment explanation
Indices: 3830057--3830108 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
3830047 TATTTTCAAG
* * * * * *
3830057 ATA ATA ACA ATA ATA ATA GTA ACA ACA ACA ATA ACA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3830105 ATA A
1 ATA A
3830109 CTTACACAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.65, C:0.10, G:0.02, T:0.23
Consensus pattern (3 bp):
ATA
Found at i:3830071 original size:9 final size:9
Alignment explanation
Indices: 3830057--3830109 Score: 61
Period size: 9 Copynumber: 5.9 Consensus size: 9
3830047 TATTTTCAAG
3830057 ATAATAACA
1 ATAATAACA
*
3830066 ATAATAATA
1 ATAATAACA
* *
3830075 GTAACAACA
1 ATAATAACA
*
3830084 ACAATAACA
1 ATAATAACA
*
3830093 ATAATAATA
1 ATAATAACA
3830102 ATAATAAC
1 ATAATAAC
3830110 TTACACAATA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.64, C:0.11, G:0.02, T:0.23
Consensus pattern (9 bp):
ATAATAACA
Found at i:3835681 original size:27 final size:27
Alignment explanation
Indices: 3835643--3835703 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
3835633 TTTCATTGAA
*
3835643 AATTTTTTTTTCAATCGCAGTTATAAT
1 AATTTTTTTTTCAATCGCAGTTACAAT
* *
3835670 AATTTTTTTTTCAATTGTAGTTACAAT
1 AATTTTTTTTTCAATCGCAGTTACAAT
3835697 AATTTTT
1 AATTTTT
3835704 ATTACTGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.30, C:0.08, G:0.07, T:0.56
Consensus pattern (27 bp):
AATTTTTTTTTCAATCGCAGTTACAAT
Found at i:3849332 original size:23 final size:23
Alignment explanation
Indices: 3849306--3849350 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3849296 AATTATAATA
3849306 TTTATTTCAATTT-AATTAATTTT
1 TTTATTT-AATTTGAATTAATTTT
*
3849329 TTTATTTAATTTGATTTAATTT
1 TTTATTTAATTTGAATTAATTT
3849351 AGATATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTATTTAATTTGAATTAATTTT
Found at i:3849517 original size:13 final size:13
Alignment explanation
Indices: 3849474--3849536 Score: 57
Period size: 13 Copynumber: 5.3 Consensus size: 13
3849464 TAAAAATAAC
3849474 AATTTTATATTAA
1 AATTTTATATTAA
3849487 AA-TTTAT-TT-A
1 AATTTTATATTAA
3849497 AA---TATATTAA
1 AATTTTATATTAA
3849507 AATTTTATATTAA
1 AATTTTATATTAA
** *
3849520 AATAATATATAAA
1 AATTTTATATTAA
3849533 AATT
1 AATT
3849537 CAAAATTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 3 0.07
9 2 0.05
10 6 0.15
11 2 0.05
12 5 0.12
13 23 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTTTATATTAA
Found at i:3849542 original size:33 final size:33
Alignment explanation
Indices: 3849474--3849544 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
3849464 TAAAAATAAC
* *
3849474 AATTTTATATTAAAATTTATTTAAATATATTAA
1 AATTTTATATTAAAATATATATAAATATATTAA
3849507 AATTTTATATTAAAATAATATATAAA-A-ATTCAA
1 AATTTTATATTAAAAT-ATATATAAATATATT-AA
3849540 AATTT
1 AATTT
3849545 ATAAATTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 3 0.09
33 24 0.71
34 7 0.21
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (33 bp):
AATTTTATATTAAAATATATATAAATATATTAA
Found at i:3853581 original size:30 final size:30
Alignment explanation
Indices: 3853545--3853605 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
3853535 ATTATATCTT
3853545 AATGCAATATGAAAATTATATTATCTTATA
1 AATGCAATATGAAAATTATATTATCTTATA
3853575 AATGCAATATGAAAATTATATTATCTTATA
1 AATGCAATATGAAAATTATATTATCTTATA
3853605 A
1 A
3853606 TAATAATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (30 bp):
AATGCAATATGAAAATTATATTATCTTATA
Found at i:3854834 original size:19 final size:19
Alignment explanation
Indices: 3854812--3854883 Score: 55
Period size: 19 Copynumber: 4.1 Consensus size: 19
3854802 TAATTTTTAT
3854812 ATATTATTTTTAATATAAA
1 ATATTATTTTTAATATAAA
* * *
3854831 ATATTA-ATAT-AT-TTAA
1 ATATTATTTTTAATATAAA
* *
3854847 ATA--AATTTTAATAAAAA
1 ATATTATTTTTAATATAAA
*
3854864 ATATTATTTTTAATTTAAA
1 ATATTATTTTTAATATAAA
3854883 A
1 A
3854884 ATATAAAATA
Statistics
Matches: 38, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
14 1 0.03
15 2 0.05
16 8 0.21
17 7 0.18
18 2 0.05
19 18 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTATTTTTAATATAAA
Found at i:3854908 original size:16 final size:17
Alignment explanation
Indices: 3854882--3854916 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
3854872 TTTAATTTAA
3854882 AAATATAAAATATATAT
1 AAATATAAAATATATAT
3854899 AAAT-TAAAATATATAT
1 AAATATAAAATATATAT
3854915 AA
1 AA
3854917 TTCAATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATATAAAATATATAT
Found at i:3854992 original size:13 final size:13
Alignment explanation
Indices: 3854959--3854992 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3854949 ATCTCTTAAA
3854959 TTAAATTTAATAT
1 TTAAATTTAATAT
* *
3854972 GTACATTTAATAT
1 TTAAATTTAATAT
3854985 TTAAATTT
1 TTAAATTT
3854993 GATTTAAATC
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (13 bp):
TTAAATTTAATAT
Found at i:3855012 original size:22 final size:22
Alignment explanation
Indices: 3854987--3855049 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 22
3854977 TTTAATATTT
*
3854987 AAATTTGATTTAAATCAAATAA
1 AAATTTAATTTAAATCAAATAA
*
3855009 AAATTTAATTTAAATTAAATTAA
1 AAATTTAATTTAAATCAAA-TAA
*
3855032 ATATTATAATTTTAAATC
1 AAATT-TAA-TTTAAATC
3855050 TATTTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 17 0.50
23 7 0.21
24 3 0.09
25 7 0.21
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (22 bp):
AAATTTAATTTAAATCAAATAA
Found at i:3857822 original size:2 final size:2
Alignment explanation
Indices: 3857810--3857845 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3857800 TGGCCAGATG
*
3857810 TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3857846 ATCGTATCGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:3869160 original size:14 final size:14
Alignment explanation
Indices: 3869141--3869170 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3869131 TATTAAGCGG
3869141 CTGATATGTACTTT
1 CTGATATGTACTTT
3869155 CTGATATGTACTTT
1 CTGATATGTACTTT
3869169 CT
1 CT
3869171 AGGTGAGTGT
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:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (14 bp):
CTGATATGTACTTT
Found at i:3870248 original size:16 final size:15
Alignment explanation
Indices: 3870229--3870262 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3870219 TTTCTCTTAA
*
3870229 ATTATAATTATTATAT
1 ATTATAACTATT-TAT
3870245 ATTATAACTATTTAT
1 ATTATAACTATTTAT
3870260 ATT
1 ATT
3870263 TTCAATCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTATAACTATTTAT
Found at i:3870451 original size:20 final size:20
Alignment explanation
Indices: 3870410--3870453 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3870400 TTTTATATAA
** *
3870410 TTTATATTATAAAATTTTAG
1 TTTATATTATAAAAAGTCAG
3870430 TTTATATTATAAAAAGTCAG
1 TTTATATTATAAAAAGTCAG
3870450 TTTA
1 TTTA
3870454 CTATCAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (20 bp):
TTTATATTATAAAAAGTCAG
Found at i:3872030 original size:18 final size:18
Alignment explanation
Indices: 3872004--3872039 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3871994 TTTAATTAAA
* *
3872004 ATATTATAAAAATTATAT
1 ATATAATAAAAAATATAT
3872022 ATATAATAAAAAATATAT
1 ATATAATAAAAAATATAT
3872040 GAAATAGTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATAATAAAAAATATAT
Found at i:3872089 original size:14 final size:13
Alignment explanation
Indices: 3872070--3872124 Score: 65
Period size: 13 Copynumber: 3.9 Consensus size: 13
3872060 ATGTTATTAG
3872070 TATTTTTAATTTAA
1 TATTTTT-ATTTAA
3872084 TATTTTATTATTTGAA
1 TA-TTT-TTATTT-AA
*
3872100 TATTTTTATTAAA
1 TATTTTTATTTAA
3872113 TATTTTTATTTA
1 TATTTTTATTTA
3872125 TTTTATTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
13 13 0.36
14 7 0.19
15 10 0.28
16 6 0.17
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (13 bp):
TATTTTTATTTAA
Found at i:3872104 original size:30 final size:31
Alignment explanation
Indices: 3872070--3872127 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
3872060 ATGTTATTAG
*
3872070 TATTTTTAATTTAATA-TTTTA-TTATTTGAA
1 TATTTTT-ATTAAATATTTTTATTTATTTGAA
3872100 TATTTTTATTAAATATTTTTATTTATTT
1 TATTTTTATTAAATATTTTTATTTATTT
3872128 TATTTTACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 7 0.28
30 12 0.48
31 6 0.24
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (31 bp):
TATTTTTATTAAATATTTTTATTTATTTGAA
Found at i:3872233 original size:15 final size:15
Alignment explanation
Indices: 3872201--3872230 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3872191 TCACTCGAAC
3872201 TAATCAAATTAATTT
1 TAATCAAATTAATTT
3872216 TAATC-AATTAATTT
1 TAATCAAATTAATTT
3872230 T
1 T
3872231 TAAAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATCAAATTAATTT
Found at i:3872729 original size:24 final size:24
Alignment explanation
Indices: 3872688--3872747 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
3872678 AATGTCAAAA
*
3872688 ATTAAAAAAATTA-A-TTTTAAA-
1 ATTAAAAAAATAAGAGTTTTAAAT
* *
3872709 ATATAAAAAAGTAAGAGTTTTAGAT
1 AT-TAAAAAAATAAGAGTTTTAAAT
3872734 ATTAAAAAAATAAG
1 ATTAAAAAAATAAG
3872748 GCATAATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 2 0.06
22 9 0.29
23 1 0.03
24 17 0.55
25 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (24 bp):
ATTAAAAAAATAAGAGTTTTAAAT
Found at i:3873608 original size:13 final size:14
Alignment explanation
Indices: 3873578--3873608 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3873568 GCAAAATAAC
3873578 ATATAAAATTTAAT
1 ATATAAAATTTAAT
3873592 ATATAAAATTT-AT
1 ATATAAAATTTAAT
3873605 ATAT
1 ATAT
3873609 CGATAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATAAAATTTAAT
Found at i:3881639 original size:2 final size:2
Alignment explanation
Indices: 3881632--3881661 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3881622 AACCTCATTA
3881632 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
3881662 CTTAATTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3882859 original size:34 final size:34
Alignment explanation
Indices: 3882782--3882867 Score: 102
Period size: 34 Copynumber: 2.5 Consensus size: 34
3882772 ATGTATGTAT
** *
3882782 TTTCAAAAATAAATTTTTGAAAATAAAATATAAC
1 TTTCAAAAATTCATTTTTAAAAATAAAATATAAC
*
3882816 TTTCAAAAATTCATTTTTAAAAATACAATATAA-
1 TTTCAAAAATTCATTTTTAAAAATAAAATATAAC
**
3882849 TTCTTGAAAATTCATTTTT
1 TT-TCAAAAATTCATTTTT
3882868 GAGATTTGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 2 0.04
34 43 0.96
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (34 bp):
TTTCAAAAATTCATTTTTAAAAATAAAATATAAC
Found at i:3889700 original size:2 final size:2
Alignment explanation
Indices: 3889693--3889718 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3889683 TCTTCTACTG
3889693 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
3889719 GTTCTCCAGT
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:3898221 original size:81 final size:81
Alignment explanation
Indices: 3898086--3898244 Score: 282
Period size: 81 Copynumber: 2.0 Consensus size: 81
3898076 AAACTTTGAG
*
3898086 AGAAACTTTGAGTGAAAATTTTTCACTTTGGCAGGAGTCTCTTTTGCCCCATAGTTTATTTTGGG
1 AGAAACTTTGAGTGAAAATTTTTCACTTTGGCAGGAATCTCTTTTGCCCCATAGTTTATTTTGGG
*
3898151 CAGGAGTATATTTATC
66 CAGGAATATATTTATC
* *
3898167 AGAAACTTTGAGTTAAAATTTTTCACTTTGGCAGGAATCTCTTTTGCCTCATAGTTTATTTTGGG
1 AGAAACTTTGAGTGAAAATTTTTCACTTTGGCAGGAATCTCTTTTGCCCCATAGTTTATTTTGGG
3898232 CAGGAATATATTT
66 CAGGAATATATTT
3898245 TAGTACTTGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 74 1.00
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (81 bp):
AGAAACTTTGAGTGAAAATTTTTCACTTTGGCAGGAATCTCTTTTGCCCCATAGTTTATTTTGGG
CAGGAATATATTTATC
Found at i:3901822 original size:14 final size:15
Alignment explanation
Indices: 3901796--3901829 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3901786 ATTAAAAATT
3901796 TTCTTTCTTTTATAA
1 TTCTTTCTTTTATAA
3901811 TTCTTT-TTTTATAA
1 TTCTTTCTTTTATAA
*
3901825 GTCTT
1 TTCTT
3901830 ATTGTCCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.18, C:0.12, G:0.03, T:0.68
Consensus pattern (15 bp):
TTCTTTCTTTTATAA
Found at i:3902412 original size:12 final size:13
Alignment explanation
Indices: 3902395--3902423 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3902385 ATTGAAGTGC
3902395 TTTATTTTTTG-G
1 TTTATTTTTTGAG
3902407 TTTATTTTTTGAG
1 TTTATTTTTTGAG
3902420 TTTA
1 TTTA
3902424 CTCGAATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.72
Consensus pattern (13 bp):
TTTATTTTTTGAG
Found at i:3903529 original size:20 final size:21
Alignment explanation
Indices: 3903506--3903546 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3903496 AAATTAAATT
3903506 TATT-AATTAAAAATTTTATA
1 TATTCAATTAAAAATTTTATA
*
3903526 TATTCAATTAAAACTTTTATA
1 TATTCAATTAAAAATTTTATA
3903547 ACAATTATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
TATTCAATTAAAAATTTTATA
Found at i:3906329 original size:18 final size:17
Alignment explanation
Indices: 3906289--3906338 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
3906279 TTATTTATTA
3906289 ATATTTATTAATATAATTT
1 ATATTTA-TAA-ATAATTT
3906308 -TATTTATAAATAATGTT
1 ATATTTATAAATAAT-TT
*
3906325 ATATTAATAAATAA
1 ATATTTATAAATAA
3906339 ATAATATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 5 0.18
17 5 0.18
18 18 0.64
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
ATATTTATAAATAATTT
Found at i:3906358 original size:22 final size:22
Alignment explanation
Indices: 3906313--3906548 Score: 85
Period size: 22 Copynumber: 10.4 Consensus size: 22
3906303 AATTTTATTT
*
3906313 ATAAATAATGTTATATTAATAA
1 ATAAATAATATTATATTAATAA
3906335 ATAAATAATATTATATTACA-AA
1 ATAAATAATATTATATTA-ATAA
3906357 ATATTAATAA-ATTAT-TT--T-A
1 ATA--AATAATATTATATTAATAA
* * * *
3906376 AGAAATGATATTATAATATATTA
1 ATAAATAATATTATATTA-ATAA
* *
3906399 ATGAAATATTATTATATAAAT-A
1 AT-AAATAATATTATATTAATAA
* *
3906421 ATATAATAATAAATATTATTAATTTA
1 ATA-AATAAT-ATTA-TATTAA-TAA
* * * * *
3906447 ATTAATAAATATTGTAATAACAT
1 ATAAAT-AATATTATATTAATAA
* * *
3906470 ATCAATAAATAATATATT-ATCA
1 ATAAAT-AATATTATATTAATAA
3906492 ATAAATAATA-TACTATTAATATA
1 ATAAATAATATTA-TATTAATA-A
* *
3906515 ATATAGTAATAAATATTATTAATAA
1 ATA-AATAAT-ATTA-TATTAATAA
3906540 ATAATATAA
1 ATAA-ATAA
3906549 AGAATAATAA
Statistics
Matches: 159, Mismatches: 31, Indels: 45
0.68 0.13 0.19
Matches are distributed among these distances:
17 4 0.03
18 5 0.03
19 4 0.03
20 2 0.01
21 9 0.06
22 41 0.26
23 31 0.19
24 33 0.21
25 14 0.09
26 16 0.10
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (22 bp):
ATAAATAATATTATATTAATAA
Found at i:3906397 original size:36 final size:38
Alignment explanation
Indices: 3906347--3906431 Score: 95
Period size: 36 Copynumber: 2.3 Consensus size: 38
3906337 AAATAATATT
* * *
3906347 ATATTACAAAATATTAAT-AAATTATT-TTA-AGAAATG
1 ATATTATAATATATTAATGAAA-TATTATTATAGAAATA
*
3906383 ATATTATAATATATTAATGAAATATTATTATATAAATA
1 ATATTATAATATATTAATGAAATATTATTATAGAAATA
*
3906421 ATATAATAATA
1 ATATTATAATA
3906432 AATATTATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
36 20 0.49
37 6 0.15
38 15 0.37
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (38 bp):
ATATTATAATATATTAATGAAATATTATTATAGAAATA
Found at i:3906419 original size:14 final size:14
Alignment explanation
Indices: 3906390--3906441 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
3906380 ATGATATTAT
3906390 AATA-TATTA-ATGA
1 AATATTATTATAT-A
3906403 AATATTATTATATA
1 AATATTATTATATA
* *
3906417 AATAATATAATAATA
1 AATATTATTAT-ATA
3906432 AATATTATTA
1 AATATTATTA
3906442 ATTTAATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 4 0.12
14 15 0.47
15 13 0.41
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
AATATTATTATATA
Found at i:3906490 original size:18 final size:18
Alignment explanation
Indices: 3906469--3906517 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
3906459 TGTAATAACA
*
3906469 TATCAATAAATAATATAT
1 TATCAATAAATAATATAC
3906487 TATCAATAAATAATATAC
1 TATCAATAAATAATATAC
*
3906505 TATTAATATAATA
1 TATCAATA-AATA
3906518 TAGTAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (18 bp):
TATCAATAAATAATATAC
Found at i:3906555 original size:60 final size:61
Alignment explanation
Indices: 3906385--3906555 Score: 163
Period size: 60 Copynumber: 2.8 Consensus size: 61
3906375 AAGAAATGAT
* * *
3906385 ATTATAATATATTAATGAAATATTATTATATAAATAATAT-AATAATAAATATTATTAATTTA
1 ATTATAATATAGTAAT-AAATATTATTA-ATAAATAATATAAACAATAAATAATATTAATTTA
* * * * *
3906447 ATTAATAAATATTGTAAT-AACA-TATCAATAAATAATATATTATCAATAAATAATA-TACTATT
1 ATT-AT-AATATAGTAATAAATATTATTAATAAATAATATA--AACAATAAATAATATTAAT-TT
3906509 A
61 A
*
3906510 A-TATAATATAGTAATAAATATTATTAATAAATAATATAAAGAATAA
1 ATTATAATATAGTAATAAATATTATTAATAAATAATATAAACAATAA
3906556 TAAATAGTTT
Statistics
Matches: 88, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
60 27 0.31
61 9 0.10
62 26 0.30
63 17 0.19
64 9 0.10
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (61 bp):
ATTATAATATAGTAATAAATATTATTAATAAATAATATAAACAATAAATAATATTAATTTA
Found at i:3906618 original size:13 final size:13
Alignment explanation
Indices: 3906602--3906631 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3906592 AATATTTTAA
*
3906602 TATTAAATATTAT
1 TATTAAATATAAT
3906615 TATTAAATATAAT
1 TATTAAATATAAT
3906628 TATT
1 TATT
3906632 TTTTAAAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATTAAATATAAT
Found at i:3906624 original size:20 final size:19
Alignment explanation
Indices: 3906575--3906620 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3906565 TTATTTTAAG
*
3906575 TATTTTTATATTAATATAA
1 TATTTTAATATTAATATAA
*
3906594 TATTTTAATATTAA-ATAT
1 TATTTTAATATTAATATAA
3906612 TATTATTAA
1 TATT-TTAA
3906621 ATATAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTTAATATTAATATAA
Found at i:3906678 original size:34 final size:33
Alignment explanation
Indices: 3906551--3906678 Score: 88
Period size: 34 Copynumber: 3.8 Consensus size: 33
3906541 TAATATAAAG
*
3906551 AATAATAAAT-AGTTTT-AT-TTTAAGTATTTTT
1 AATAATAAATAATTTTTAATATTTAA-TATTTTT
* * *
3906582 -ATATTAATATAATATTTTAATATTAAATATTATT
1 AATAATAA-ATAAT-TTTTAATATTTAATATTTTT
* * *
3906616 ATTAAATATAATTATTTTTTAA-A-GTAATATTTTT
1 AAT-AATA-AA-TAATTTTTAATATTTAATATTTTT
3906650 AATAATAAATAATTTTTAATATTTTAATA
1 AATAATAAATAATTTTTAATA-TTTAATA
3906679 ATTATATTAA
Statistics
Matches: 72, Mismatches: 13, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
30 6 0.08
31 11 0.15
32 4 0.06
33 8 0.11
34 23 0.32
35 6 0.08
36 10 0.14
37 4 0.06
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (33 bp):
AATAATAAATAATTTTTAATATTTAATATTTTT
Found at i:3908486 original size:3 final size:3
Alignment explanation
Indices: 3908480--3908504 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3908470 CTTCTTCTTT
3908480 TCC TCC TCC TCC TCC TCC TCC TCC T
1 TCC TCC TCC TCC TCC TCC TCC TCC T
3908505 TCTTCTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (3 bp):
TCC
Found at i:3925620 original size:2 final size:2
Alignment explanation
Indices: 3925608--3925655 Score: 71
Period size: 2 Copynumber: 24.0 Consensus size: 2
3925598 TTTGCGTGAA
*
3925608 AT AT GAT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3925651 A- AT AT
1 AT AT AT
3925656 TCTGCATGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3931335 original size:17 final size:17
Alignment explanation
Indices: 3931313--3931348 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
3931303 CTTTTGAATC
3931313 ATAATAAGATATTTAAT
1 ATAATAAGATATTTAAT
3931330 ATAATAAGATATTTAAT
1 ATAATAAGATATTTAAT
3931347 AT
1 AT
3931349 GATATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
ATAATAAGATATTTAAT
Found at i:3931365 original size:17 final size:17
Alignment explanation
Indices: 3931340--3931381 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
3931330 ATAATAAGAT
*
3931340 ATTTAATATGATATTTAA
1 ATTT-ATATAATATTTAA
3931358 ATTTATATAATATTTAA
1 ATTTATATAATATTTAA
*
3931375 AATTATA
1 ATTTATA
3931382 AATTTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
ATTTATATAATATTTAA
Found at i:3931494 original size:14 final size:14
Alignment explanation
Indices: 3931477--3931518 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
3931467 ATTAATATAT
3931477 TTATAATTTAAATA
1 TTATAATTTAAATA
3931491 TTATAATTTAAATA
1 TTATAATTTAAATA
*
3931505 TTGT-A-TTAAATA
1 TTATAATTTAAATA
3931517 TT
1 TT
3931519 TTATTATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 9 0.33
13 1 0.04
14 17 0.63
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (14 bp):
TTATAATTTAAATA
Found at i:3931515 original size:12 final size:12
Alignment explanation
Indices: 3931455--3931524 Score: 52
Period size: 12 Copynumber: 5.4 Consensus size: 12
3931445 AAATATTTTT
*
3931455 TATTATATATTA
1 TATTAAATATTA
3931467 -ATTAATATATTTA
1 TATTAA-ATA-TTA
3931480 TAATTTAAATATTA
1 T-A-TTAAATATTA
*
3931494 TAATTTAAATATTG
1 T-A-TTAAATATTA
*
3931508 TATTAAATATTT
1 TATTAAATATTA
3931520 TATTA
1 TATTA
3931525 TAATTTAAGT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
11 4 0.08
12 17 0.34
13 4 0.08
14 17 0.34
15 4 0.08
16 4 0.08
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (12 bp):
TATTAAATATTA
Found at i:3931586 original size:18 final size:18
Alignment explanation
Indices: 3931563--3931597 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3931553 ACTTAAAAAC
*
3931563 AGAAACTAATTAAAATTA
1 AGAAACCAATTAAAATTA
3931581 AGAAACCAATTAAAATT
1 AGAAACCAATTAAAATT
3931598 TAAAAATCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.09, G:0.06, T:0.26
Consensus pattern (18 bp):
AGAAACCAATTAAAATTA
Found at i:3954441 original size:13 final size:13
Alignment explanation
Indices: 3954423--3954449 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3954413 TGGTTCATGT
3954423 TTTTTTTAATTTA
1 TTTTTTTAATTTA
3954436 TTTTTTTAATTTA
1 TTTTTTTAATTTA
3954449 T
1 T
3954450 ATATATATAT
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:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTTTAATTTA
Found at i:3955379 original size:23 final size:23
Alignment explanation
Indices: 3955336--3955391 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
3955326 ATTTAATTAT
3955336 ATATATTTATATATTTAAAAAATA
1 ATAT-TTTATATATTTAAAAAATA
* *
3955360 ATATTTTATATTTTTTAAAAATA
1 ATATTTTATATATTTAAAAAATA
3955383 ATATTTTAT
1 ATATTTTAT
3955392 TAATTTCAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 26 0.87
24 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
ATATTTTATATATTTAAAAAATA
Found at i:3955770 original size:17 final size:17
Alignment explanation
Indices: 3955729--3955770 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3955719 TTTTAATTTA
3955729 TATTTAAATAATCTCTT
1 TATTTAAATAATCTCTT
* *
3955746 AATATAAATCAATCT-TT
1 TATTTAAAT-AATCTCTT
3955763 TATTTAAA
1 TATTTAAA
3955771 ATAAAAACTT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTTAAATAATCTCTT
Found at i:3955847 original size:17 final size:17
Alignment explanation
Indices: 3955827--3955885 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
3955817 ATATAGCAAA
3955827 AATATAAAATTTTATTT
1 AATATAAAATTTTATTT
3955844 AATATAAATCAATCTTTTATTT
1 AATAT-AA--AA--TTTTATTT
* *
3955866 AAAATAAAAATTTATTT
1 AATATAAAATTTTATTT
3955883 AAT
1 AAT
3955886 CTTAACAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
17 14 0.41
18 2 0.06
19 2 0.06
20 2 0.06
21 2 0.06
22 12 0.35
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AATATAAAATTTTATTT
Found at i:3956758 original size:136 final size:136
Alignment explanation
Indices: 3956593--3956863 Score: 461
Period size: 136 Copynumber: 2.0 Consensus size: 136
3956583 ATAGAAAATT
*
3956593 AAAAGGTTTGAATAAAGTTTAAGCTATTAAAAATTGGATTGAGATTTGTTTTTAAGATAAATTAA
1 AAAAGGTTTGAATAAAGTTTAAGCTATTAAAAATTGGATTGAGATTTATTTTTAAGATAAATTAA
* * *
3956658 AGTTTTGGTAATAATTCAATTTTTAAATTTGAAATCCTAGATGAGTTGAAATCCCTATTGATTTG
66 AGTTTTGGTAATAATTCAATTTTTAAATTTGAAATACTACATGAATTGAAATCCCTATTGATTTG
3956723 CCTCTC
131 CCTCTC
* * * *
3956729 AAAAGGTTTGAATAGAGTTTAAGCTATTAAAAATTTGATTGGGATTTATTTTTAAGATAAATTTA
1 AAAAGGTTTGAATAAAGTTTAAGCTATTAAAAATTGGATTGAGATTTATTTTTAAGATAAATTAA
*
3956794 AGTTTTGGTAATAATTCAATTTTTAAGTTTGAAATACTACATGAATTGAAATCCCTATTGATTTG
66 AGTTTTGGTAATAATTCAATTTTTAAATTTGAAATACTACATGAATTGAAATCCCTATTGATTTG
3956859 CCTCT
131 CCTCT
3956864 ATAAATAGCT
Statistics
Matches: 126, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
136 126 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (136 bp):
AAAAGGTTTGAATAAAGTTTAAGCTATTAAAAATTGGATTGAGATTTATTTTTAAGATAAATTAA
AGTTTTGGTAATAATTCAATTTTTAAATTTGAAATACTACATGAATTGAAATCCCTATTGATTTG
CCTCTC
Found at i:3957537 original size:12 final size:12
Alignment explanation
Indices: 3957522--3957557 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
3957512 AAAAAGTAAT
3957522 ATAAAATTTTAA
1 ATAAAATTTTAA
*
3957534 ATAAAACTTT-A
1 ATAAAATTTTAA
3957545 ATAAAATTTTAA
1 ATAAAATTTTAA
3957557 A
1 A
3957558 AATTAATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (12 bp):
ATAAAATTTTAA
Found at i:3957549 original size:11 final size:11
Alignment explanation
Indices: 3957522--3957556 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
3957512 AAAAAGTAAT
3957522 ATAAAATTTTAA
1 ATAAAATTTT-A
*
3957534 ATAAAACTTTA
1 ATAAAATTTTA
3957545 ATAAAATTTTA
1 ATAAAATTTTA
3957556 A
1 A
3957557 AAATTAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (11 bp):
ATAAAATTTTA
Found at i:3958118 original size:13 final size:13
Alignment explanation
Indices: 3958100--3958127 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3958090 TAAGATTATC
3958100 AAACCAAAACCAA
1 AAACCAAAACCAA
3958113 AAACCAAAACCAA
1 AAACCAAAACCAA
3958126 AA
1 AA
3958128 CATCTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.29, G:0.00, T:0.00
Consensus pattern (13 bp):
AAACCAAAACCAA
Found at i:3959636 original size:23 final size:22
Alignment explanation
Indices: 3959609--3959658 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
3959599 TCTTCAGATA
* *
3959609 TCTTGAATCATTGTTTTATGATC
1 TCTTGAA-CACTGCTTTATGATC
*
3959632 TCTTGGACACTGCTTTATGATC
1 TCTTGAACACTGCTTTATGATC
3959654 TCTTG
1 TCTTG
3959659 GGCCCACGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (22 bp):
TCTTGAACACTGCTTTATGATC
Found at i:3962259 original size:300 final size:301
Alignment explanation
Indices: 3961693--3962294 Score: 897
Period size: 299 Copynumber: 2.0 Consensus size: 301
3961683 TTTTTTCAAC
* *
3961693 TTTCATTTCTTTAGCTTTTCCTCCAAATTGAGATATTAAAAAAATGAGGATTACAAGAAAAACCA
1 TTTCATTTCCTTAGCTTTTCCTCCAAATTGAGATATTAAAAAAATAAGGATTACAAGAAAAACCA
* * * *
3961758 AAAGTTATTGAATTTTCACGTATTTCCTTTTCTTTAAGTTAAAAATTTATTCAAACAAAGGAAAA
66 AAAGTTATTGAATTTTCACCTATTTCCTTTCCTTTAAGTTAAAAATTTATCCAAACAAAGAAAAA
*** *
3961823 TTTTTTCTATTTCCTTTACTTTCCTTTATTTTTCTTTCATTTCCTTCCCTTCCTCTTAATACAAA
131 AAATTTCTATTTCCTTTACTTTCCTTTATTTTTCTTTCATTTCCTTCCCTTCCTCTCAATACAAA
* *
3961888 CATAGTGTTAGTCAAATTTAGAATGTTCTCTAAAGATAAATTAAATCAAATGACTAATCATATCC
196 CATAGTGTTAGTCAAATTTAAAATGTTCTCAAAAGATAAATTAAATCAAATGACTAATCATATCC
*
3961953 AAAT-AAAAAAA-AATGGTAATTTTTAAAAATTATATTTAA
261 AAATAAAAAAAATAATGATAATTTTTAAAAATTATATTTAA
* * * * *
3961992 TTTCTTTTCCTTAGCTTTTCTTTCAAATTGAGGTGTTAAAAGAAATAAGGATTACACAG-AAAAC
1 TTTCATTTCCTTAGCTTTTCCTCCAAATTGAGATATTAAAA-AAATAAGGATTACA-AGAAAAAC
*
3962056 TAAAAGTTATTGAATTTTCACCTATTTCCTTTCCTTTAAGTTAAAAATTTATCCAAACAAA-AAA
64 CAAAAGTTATTGAATTTTCACCTATTTCCTTTCCTTTAAGTTAAAAATTTATCCAAACAAAGAAA
* * * *
3962120 AAAAATTTCTATTTCCTTTACTTTCCTTTATTTTTCTTTCCTTTCCTTCTCTTTCTCTCAATCCA
129 AAAAATTTCTATTTCCTTTACTTTCCTTTATTTTTCTTTCATTTCCTTCCCTTCCTCTCAATACA
* * *
3962185 AACATAGTGTTAGTCAAATTTAAAATGTTCTCAAAATGATAAATTAACTTAAATGACTAATCATG
194 AACATAGTGTTAGTCAAATTTAAAATGTTCTCAAAA-GATAAATTAAATCAAATGACTAATCATA
*
3962250 TCTAAATAAAAAAAATTAATGATAATTTTTAAAAATTATATTTAA
258 TCCAAATAAAAAAAA-TAATGATAATTTTTAAAAATTATATTTAA
3962295 CGATATGTTT
Statistics
Matches: 270, Mismatches: 27, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
299 128 0.47
300 106 0.39
301 9 0.03
303 27 0.10
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (301 bp):
TTTCATTTCCTTAGCTTTTCCTCCAAATTGAGATATTAAAAAAATAAGGATTACAAGAAAAACCA
AAAGTTATTGAATTTTCACCTATTTCCTTTCCTTTAAGTTAAAAATTTATCCAAACAAAGAAAAA
AAATTTCTATTTCCTTTACTTTCCTTTATTTTTCTTTCATTTCCTTCCCTTCCTCTCAATACAAA
CATAGTGTTAGTCAAATTTAAAATGTTCTCAAAAGATAAATTAAATCAAATGACTAATCATATCC
AAATAAAAAAAATAATGATAATTTTTAAAAATTATATTTAA
Found at i:3964573 original size:2 final size:2
Alignment explanation
Indices: 3964566--3964599 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3964556 GCTATCTATC
3964566 TA 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 TA
3964600 GAGAGAGAGA
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):
TA
Found at i:3964604 original size:2 final size:2
Alignment explanation
Indices: 3964599--3964639 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3964589 ATATATATAT
3964599 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3964640 ATAGGTGGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3965460 original size:30 final size:30
Alignment explanation
Indices: 3965386--3965467 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 30
3965376 CAATTATTTA
* *
3965386 ATTT-TATTTAAATAAATTTTTATATTTTT
1 ATTTGTATTTAAATAAATTTTTATACTTTC
* *
3965415 A-GTGTATTCAAATAAATTTTTATACTTTC
1 ATTTGTATTTAAATAAATTTTTATACTTTC
* *
3965444 ATTTGTATTTATATAAAATTTTAT
1 ATTTGTATTTAAATAAATTTTTAT
3965468 TTCAAATAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
28 1 0.02
29 24 0.56
30 18 0.42
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (30 bp):
ATTTGTATTTAAATAAATTTTTATACTTTC
Found at i:3965487 original size:18 final size:17
Alignment explanation
Indices: 3965466--3965509 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
3965456 ATAAAATTTT
3965466 ATTTCAAATAAAAAATTA
1 ATTT-AAATAAAAAATTA
* * *
3965484 ATTTATATTAAAAATTT
1 ATTTAAATAAAAAATTA
3965501 ATTTAAATA
1 ATTTAAATA
3965510 CAAATAAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTAAATAAAAAATTA
Found at i:3966023 original size:29 final size:28
Alignment explanation
Indices: 3965982--3966038 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 28
3965972 GTATATTTAA
3965982 AAATAATATTTTATATTAAAAATAATATT
1 AAATAATATTTTATATTAAAAA-AATATT
3966011 AAATAATATTTTATATTAAAAAAATATT
1 AAATAATATTTTATATTAAAAAAATATT
3966039 TTATATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AAATAATATTTTATATTAAAAAAATATT
Found at i:3966066 original size:18 final size:19
Alignment explanation
Indices: 3965973--3966063 Score: 85
Period size: 19 Copynumber: 5.2 Consensus size: 19
3965963 ATTTTATATG
3965973 TATATTTAAAAATAATATTT
1 TATA-TTAAAAATAATATTT
3965993 TATATT--AAA-AATA---
1 TATATTAAAAATAATATTT
3966006 -ATATT--AAATAATATTT
1 TATATTAAAAATAATATTT
3966022 TATATTAAAAA-AATATTT
1 TATATTAAAAATAATATTT
3966040 TATATTTAAAAATTAATATTT
1 TATA-TTAAAAA-TAATATTT
3966061 TAT
1 TAT
3966064 TAATTTTGAA
Statistics
Matches: 61, Mismatches: 0, Indels: 19
0.76 0.00 0.24
Matches are distributed among these distances:
12 8 0.13
13 4 0.07
16 4 0.07
17 8 0.13
18 11 0.18
19 12 0.20
20 4 0.07
21 10 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TATATTAAAAATAATATTT
Found at i:3977887 original size:31 final size:31
Alignment explanation
Indices: 3977828--3977897 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
3977818 TAAAAGAGAT
3977828 TTTTTTATTATTTGAATTAATTAATAAAAATA
1 TTTTTTATTATTTGAATTAATTAATAAAAA-A
* **
3977860 TTTTTTATTATTT-AATTATTTTTTAAAAAA
1 TTTTTTATTATTTGAATTAATTAATAAAAAA
3977890 TCTTTTTA
1 T-TTTTTA
3977898 AAAATAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 2 0.06
31 19 0.56
32 13 0.38
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (31 bp):
TTTTTTATTATTTGAATTAATTAATAAAAAA
Found at i:3977931 original size:32 final size:35
Alignment explanation
Indices: 3977895--3977963 Score: 92
Period size: 32 Copynumber: 2.1 Consensus size: 35
3977885 AAAAATCTTT
3977895 TTAAAAATAATATTAATA-T-AAT-TATT-AAAATA
1 TTAAAAATAAT-TTAATATTAAATATATTGAAAATA
*
3977927 TTAAAAATAATTTATTATTAAATATATTGAAAATA
1 TTAAAAATAATTTAATATTAAATATATTGAAAATA
3977962 TT
1 TT
3977964 TATTATTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
31 5 0.16
32 12 0.38
33 3 0.09
34 4 0.12
35 8 0.25
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (35 bp):
TTAAAAATAATTTAATATTAAATATATTGAAAATA
Found at i:3977970 original size:28 final size:25
Alignment explanation
Indices: 3977915--3977981 Score: 100
Period size: 25 Copynumber: 2.6 Consensus size: 25
3977905 TATTAATATA
3977915 ATTATTAAAATATTAAAAATAATTT
1 ATTATTAAAATATTAAAAATAATTT
*
3977940 ATTATTAAATATATTGAAAAT-ATTT
1 ATTATTAAA-ATATTAAAAATAATTT
3977965 ATTATTAAAATTATTAA
1 ATTATTAAAA-TATTAA
3977982 TATTAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
24 1 0.03
25 27 0.71
26 10 0.26
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (25 bp):
ATTATTAAAATATTAAAAATAATTT
Found at i:3978131 original size:16 final size:17
Alignment explanation
Indices: 3978087--3978133 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
3978077 AAGTATTGAT
*
3978087 AAATAATTTTATTT-AA
1 AAATAATTTTTTTTAAA
*
3978103 AAATAATTATTTTTAAA
1 AAATAATTTTTTTTAAA
3978120 AAAT-ATTTTTTTTA
1 AAATAATTTTTTTTA
3978134 TTTTGTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 21 0.78
17 6 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAATAATTTTTTTTAAA
Found at i:3978135 original size:22 final size:22
Alignment explanation
Indices: 3978109--3978151 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3978099 TTAAAAATAA
3978109 TTATTTT-TAAAAAATATTTTTT
1 TTATTTTGTAAAAAA-ATTTTTT
*
3978131 TTATTTTGTAAAATAATTTTT
1 TTATTTTGTAAAAAAATTTTT
3978152 AAAATAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TTATTTTGTAAAAAAATTTTTT
Done.