Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, 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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 9 of 133
Found at i:2357865 original size:17 final size:17
Alignment explanation
Indices: 2357845--2357895 Score: 93
Period size: 17 Copynumber: 3.0 Consensus size: 17
2357835 GTAGCGTGAG
*
2357845 AAAACTTTTTTCATTTT
1 AAAATTTTTTTCATTTT
2357862 AAAATTTTTTTCATTTT
1 AAAATTTTTTTCATTTT
2357879 AAAATTTTTTTCATTTT
1 AAAATTTTTTTCATTTT
2357896 TGTACTAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (17 bp):
AAAATTTTTTTCATTTT
Found at i:2358382 original size:4 final size:4
Alignment explanation
Indices: 2358365--2358398 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
2358355 GTGATGGGTT
* *
2358365 TTTA TTTT TTTA TTTA TTTA TTTA TTTT TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
2358399 GATGGGGTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (4 bp):
TTTA
Found at i:2368625 original size:95 final size:94
Alignment explanation
Indices: 2368462--2368640 Score: 268
Period size: 95 Copynumber: 1.9 Consensus size: 94
2368452 CATATAATGT
* * * *
2368462 CACGAGCCGAGACTCAACCTCCAAGCTTATGCGGCTCCAAGATCCAGACATGCACTCATCCAGCA
1 CACGAGCCAAAACTCAACCTCCAAGCTTATGCGACTCCAAGATCCAGACATGCACTCATCCAACA
2368527 TCCCAAATCAGCCTAACTGTAAGGGTGTGA
66 TCCCAAATCA-CCTAACTGTAAGGGTGTGA
* * * * *
2368557 CACGAGCCAAAACTCAACTTTCAAGCTTATGCGACTCCAAGATCCGGATATGCACTCATCTAACA
1 CACGAGCCAAAACTCAACCTCCAAGCTTATGCGACTCCAAGATCCAGACATGCACTCATCCAACA
2368622 TCCCAAATCACCTAACTGT
66 TCCCAAATCACCTAACTGT
2368641 CACGGTTCAC
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
94 9 0.12
95 66 0.88
ACGTcount: A:0.31, C:0.32, G:0.16, T:0.20
Consensus pattern (94 bp):
CACGAGCCAAAACTCAACCTCCAAGCTTATGCGACTCCAAGATCCAGACATGCACTCATCCAACA
TCCCAAATCACCTAACTGTAAGGGTGTGA
Found at i:2369725 original size:31 final size:31
Alignment explanation
Indices: 2369690--2369750 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
2369680 GAGACCAAAA
* *
2369690 AAAAATTGAAAAGCCTAAAAAGAGAATAGAG
1 AAAAATTAAAAAGACTAAAAAGAGAATAGAG
*
2369721 AAAAATTAAAAAGACTACAAAGAGAATAGA
1 AAAAATTAAAAAGACTAAAAAGAGAATAGA
2369751 AAAGGATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.64, C:0.07, G:0.16, T:0.13
Consensus pattern (31 bp):
AAAAATTAAAAAGACTAAAAAGAGAATAGAG
Found at i:2375012 original size:12 final size:11
Alignment explanation
Indices: 2374997--2375032 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
2374987 TGTGTATATC
2374997 TTTATTTATCTA
1 TTTATTTAT-TA
2375009 TTTATTTATTA
1 TTTATTTATTA
2375020 TTTATTT-TTA
1 TTTATTTATTA
2375030 TTT
1 TTT
2375033 TCCTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 6 0.25
11 9 0.38
12 9 0.38
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTATTTATTA
Found at i:2375177 original size:19 final size:19
Alignment explanation
Indices: 2375155--2375200 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2375145 TGTTAATTTT
2375155 ATTTTTATTC-ATTTATCTG
1 ATTTTTATTCGA-TTATCTG
*
2375174 ATTTTTTTTCGATTATCTG
1 ATTTTTATTCGATTATCTG
*
2375193 ATTATTAT
1 ATTTTTAT
2375201 GATTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.22, C:0.09, G:0.07, T:0.63
Consensus pattern (19 bp):
ATTTTTATTCGATTATCTG
Found at i:2376085 original size:26 final size:25
Alignment explanation
Indices: 2376020--2376087 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 25
2376010 TCCGAGCCGC
*
2376020 TTCAGTTTTTTATTT-TTTTTTATT
1 TTCATTTTTTTATTTATTTTTTATT
* *
2376044 TTCATTTCTTTGTTTATTTGTTTATT
1 TTCATTTTTTTATTTATTT-TTTATT
2376070 TT-ATTTTTTTTATTTATT
1 TTCA-TTTTTTTATTTATT
2376088 AGATTAGGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 12 0.33
25 4 0.11
26 20 0.56
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.78
Consensus pattern (25 bp):
TTCATTTTTTTATTTATTTTTTATT
Found at i:2376131 original size:6 final size:6
Alignment explanation
Indices: 2376110--2376191 Score: 58
Period size: 6 Copynumber: 12.7 Consensus size: 6
2376100 TTTAATATTC
* * *
2376110 TTTTTA TCTTTA -TTTTA TTTTTA TTTTTG TTTTACTT TTCTTTA TTATTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT--TA TT-TTTA TT-TTTA
*
2376161 TTTTTA TTTATTT TTTTTA TTATTCTA TTTT
1 TTTTTA TTT-TTA TTTTTA TT-TT-TA TTTT
2376192 CTTTAAATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
5 4 0.07
6 30 0.49
7 18 0.30
8 7 0.11
9 2 0.03
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:2376132 original size:17 final size:17
Alignment explanation
Indices: 2376110--2376178 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
2376100 TTTAATATTC
2376110 TTTTTATCTTTATTTTA
1 TTTTTATCTTTATTTTA
* *
2376127 TTTTTATTTTTGTTTTA
1 TTTTTATCTTTATTTTA
*
2376144 -CTTT-TCTTTATTATTTA
1 TTTTTATCTTTA-T-TTTA
2376161 TTTTTA--TTTATTTT-
1 TTTTTATCTTTATTTTA
2376175 TTTT
1 TTTT
2376179 ATTATTCTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
14 4 0.10
15 7 0.17
16 5 0.12
17 23 0.55
18 3 0.07
ACGTcount: A:0.14, C:0.04, G:0.01, T:0.80
Consensus pattern (17 bp):
TTTTTATCTTTATTTTA
Found at i:2376142 original size:11 final size:11
Alignment explanation
Indices: 2376026--2376175 Score: 82
Period size: 11 Copynumber: 13.5 Consensus size: 11
2376016 CCGCTTCAGT
2376026 TTTTTATTTT-
1 TTTTTATTTTA
2376036 TTTTTATTTTCA
1 TTTTTATTTT-A
2376048 TTTCTT-TGTTTA
1 TTT-TTAT-TTTA
2376060 TTTGTTTATTTTA
1 -TT-TTTATTTTA
2376073 -TTTT-TTTTA
1 TTTTTATTTTA
**
2376082 TTTATTAGATTA
1 TTT-TTATTTTA
** *
2376094 GGTTTATTTAA
1 TTTTTATTTTA
*
2376105 TATTCT-TTTTA
1 T-TTTTATTTTA
*
2376116 TCTTTATTTTA
1 TTTTTATTTTA
2376127 TTTTTATTTT-
1 TTTTTATTTTA
*
2376137 TGTTTTACTTTTC
1 T-TTTTA-TTTTA
2376150 TTTATTA-TTTA
1 TTT-TTATTTTA
2376161 TTTTTA-TTTA
1 TTTTTATTTTA
2376171 TTTTT
1 TTTTT
2376176 TTTATTATTC
Statistics
Matches: 109, Mismatches: 15, Indels: 32
0.70 0.10 0.21
Matches are distributed among these distances:
9 5 0.05
10 30 0.28
11 38 0.35
12 17 0.16
13 17 0.16
14 2 0.02
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.75
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:2376667 original size:59 final size:58
Alignment explanation
Indices: 2376199--2376665 Score: 555
Period size: 58 Copynumber: 7.9 Consensus size: 58
2376189 TTTCTTTAAA
* * * * *
2376199 TAAAAATCAAAATTTTCAAAAAAAAATATTTTTAGGAAAAAGTTGAAAGCATTAATTTTTCT
1 TAAAAAT--AAATTTTC--AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
* * *
2376261 TAAAAATAAA-TTTCAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTGCT
1 TAAAAATAAATTTTC-AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
*
2376319 TAAAAATAAATTTTCAAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAATAAATTTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
* * * * *
2376377 TGAAAATCAAAATTTTC--GAAAATATTTTTAGGGAAAAGTTAAAAGTATCAGTTTTCCT
1 TAAAAAT--AAATTTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
* *** **
2376435 TAGAAATAAATTTTCAAAAAGGGATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAATAAATTTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
** * * *
2376493 TGGAAATCAAAGTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTCCT
1 TAAAAAT-AAATTTTC-AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
* * *
2376553 TAAAAATAAA-TTTCCAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTTCT
1 TAAAAATAAATTTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
*
2376610 TAAAAATAAATTTTTAAAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 TAAAAATAAATTTTCAAAAAAA-TATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
2376666 TCCTACACAA
Statistics
Matches: 353, Mismatches: 43, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
56 8 0.02
57 48 0.14
58 186 0.53
59 50 0.14
60 54 0.15
62 7 0.02
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.35
Consensus pattern (58 bp):
TAAAAATAAATTTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
Found at i:2383636 original size:12 final size:11
Alignment explanation
Indices: 2383610--2383657 Score: 55
Period size: 10 Copynumber: 4.4 Consensus size: 11
2383600 GAAAAATGAG
*
2383610 AAAAAAGAAAA
1 AAAAAAGATAA
2383621 AAAAAAGATGATA
1 AAAAAAGAT-A-A
2383634 AAAAAA-ATAA
1 AAAAAAGATAA
2383644 AAAAAAGA-AA
1 AAAAAAGATAA
2383654 AAAA
1 AAAA
2383658 TGAGAAAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
10 13 0.39
11 10 0.30
12 3 0.09
13 7 0.21
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.06
Consensus pattern (11 bp):
AAAAAAGATAA
Found at i:2383636 original size:23 final size:23
Alignment explanation
Indices: 2383601--2383651 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
2383591 ACAATGGATG
2383601 AAAA-ATGAGAAAAAAGAA-AAAA
1 AAAAGATGAGAAAAAA-AATAAAA
*
2383623 AAAAGATGATAAAAAAAATAAAA
1 AAAAGATGAGAAAAAAAATAAAA
2383646 AAAAGA
1 AAAAGA
2383652 AAAAAATGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (23 bp):
AAAAGATGAGAAAAAAAATAAAA
Found at i:2383654 original size:17 final size:17
Alignment explanation
Indices: 2383634--2383673 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2383624 AAAGATGATA
2383634 AAAAAAATAAAAAAAAG
1 AAAAAAATAAAAAAAAG
* * *
2383651 AAAAAAATGAGAAAATG
1 AAAAAAATAAAAAAAAG
2383668 AAAAAA
1 AAAAAA
2383674 GAGATTCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.07
Consensus pattern (17 bp):
AAAAAAATAAAAAAAAG
Found at i:2383672 original size:34 final size:35
Alignment explanation
Indices: 2383601--2383673 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 35
2383591 ACAATGGATG
* **
2383601 AAAAATGAGAAAAAAGAAAAAAAAAAGATGATAAA
1 AAAAATGAAAAAAAAGAAAAAAAAAAGAAAATAAA
** *
2383636 AAAAAT-AAAAAAAAGAAAAAAATGAGAAAATGAA
1 AAAAATGAAAAAAAAGAAAAAAAAAAGAAAATAAA
2383670 AAAA
1 AAAA
2383674 GAGATTCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 26 0.81
35 6 0.19
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.08
Consensus pattern (35 bp):
AAAAATGAAAAAAAAGAAAAAAAAAAGAAAATAAA
Found at i:2385037 original size:43 final size:42
Alignment explanation
Indices: 2384986--2385067 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 42
2384976 GCCTTTGAAC
* *
2384986 TCAAATGAAAAGCTTT-GAATTTTTGGATGTGAATTTCCAAAAT
1 TCAAATGAAAAGCTTTAG-ACTTTTGGATATGAA-TTCCAAAAT
2385029 TCAAATGAAAAGCTTTAGACTTTTGGATATGAATTCCAA
1 TCAAATGAAAAGCTTTAGACTTTTGGATATGAATTCCAA
2385068 GTTTGCCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 6 0.17
43 29 0.81
44 1 0.03
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (42 bp):
TCAAATGAAAAGCTTTAGACTTTTGGATATGAATTCCAAAAT
Found at i:2385379 original size:41 final size:41
Alignment explanation
Indices: 2385334--2385867 Score: 757
Period size: 41 Copynumber: 13.1 Consensus size: 41
2385324 ATGATTGTCA
*
2385334 AGGAGTAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
2385375 AGGAGCAATTTTCTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
2385416 AGGAGTAATTTA-TTTTCCAAAGTTTCGT--TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAG--TCGTGGTGCCTCTGTTTAG
* *
2385457 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTATTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *
2385498 AGGAGCAATTTACTTTCCAAAAGTCGTGGTACC-CTGTTTAG
1 AGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
2385539 A-G-GCAATTTACTTTTCCAAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-C-AAAGTCGTGGTGCCTCTGTTTAG
*
2385580 AGGAGCAATTTACTTTTCCAAAATCGTGGTG-CTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAG
* *
2385621 AGGAGCAATTTA-TTTTCCAAGTCGTGGTGGCCTCTATTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGT-GCCTCTGTTTAG
2385662 AGGAGCAATTTAC-TTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
2385702 AGGAGCAATTTAC-TTTCAAATTCGTGGTGCCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTG-CCTCTGTTTAG
* *
2385743 AGGAGCAATTTATTTTTCAAAATCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *
2385784 AGGAACAATTTAC-TTTCAAAGTCGTGGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *
2385824 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTATTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
2385865 AGG
1 AGG
2385868 GGTGCCTCTG
Statistics
Matches: 448, Mismatches: 28, Indels: 34
0.88 0.05 0.07
Matches are distributed among these distances:
39 26 0.06
40 101 0.23
41 259 0.58
42 43 0.10
43 19 0.04
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:2385561 original size:123 final size:121
Alignment explanation
Indices: 2385334--2385867 Score: 740
Period size: 122 Copynumber: 4.4 Consensus size: 121
2385324 ATGATTGTCA
* * * *
2385334 AGGAGTAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTTCTTTTCAAAGTC
1 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTC
* *
2385399 GTGGTGCCTCTGTTTAGAGGAGTAATTTATTTTCCAAAGTTTCGT-TGCCTCTGTTTAG
66 GTGGTGCCTCTGTTTAGAGGAGCAATTTACTTT-CAAAG--TCGTGTGCCTCTGTTTAG
*
2385457 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTATTTAGAGGAGCAATTTACTTTCCAAAAGT
1 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCC-AAAGT
*
2385522 CGTGGTACC-CTGTTTAGA-G-GCAATTTACTTTTCCAAAAGTCGTGGTGCCTCTGTTTAG
65 CGTGGTGCCTCTGTTTAGAGGAGCAATTTAC-TTT-C-AAAGTCGT-GTGCCTCTGTTTAG
* *
2385580 AGGAGCAATTTACTTTTCCAAAATCGTGGTG-CTCTGTTTAGAGGAGCAATTTATTTTCC-AAGT
1 AGGAGCAATTTAC-TTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGT
*
2385643 CGTGGTGGCCTCTATTTAGAGGAGCAATTTACTTTCAAAGTCGTGGTGCCTCTGTTTAG
65 CGTGGT-GCCTCTGTTTAGAGGAGCAATTTACTTTCAAAGTCGT-GTGCCTCTGTTTAG
* * * *
2385702 AGGAGCAATTTACTTT-CAAATTCGTGGTGCCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAAT
1 AGGAGCAATTTACTTTCCAAAGTCGTGGTG-CCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGT
* *
2385766 CGTGGTGCCTCTGTTTAGAGGAACAATTTACTTTCAAAGTCGTGGTACCTCTGTTTAG
65 CGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCAAAGTCGT-GTGCCTCTGTTTAG
*
2385824 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTATTTAGAGG
1 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGG
2385868 GGTGCCTCTG
Statistics
Matches: 376, Mismatches: 21, Indels: 29
0.88 0.05 0.07
Matches are distributed among these distances:
120 12 0.03
121 24 0.06
122 149 0.40
123 149 0.40
124 33 0.09
125 9 0.02
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (121 bp):
AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTC
GTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCAAAGTCGTGTGCCTCTGTTTAG
Found at i:2385873 original size:18 final size:18
Alignment explanation
Indices: 2385850--2385885 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2385840 CCAAAGTCGT
2385850 GGTGCCTCTATTTAGAGG
1 GGTGCCTCTATTTAGAGG
*
2385868 GGTGCCTCTGTTTAGAGG
1 GGTGCCTCTATTTAGAGG
2385886 AGCAATTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.17, G:0.36, T:0.33
Consensus pattern (18 bp):
GGTGCCTCTATTTAGAGG
Found at i:2385905 original size:59 final size:59
Alignment explanation
Indices: 2385813--2385926 Score: 219
Period size: 59 Copynumber: 1.9 Consensus size: 59
2385803 AGTCGTGGTA
2385813 CCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTATTTAGAGGGGTG
1 CCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTATTTAGAGGGGTG
*
2385872 CCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGG
1 CCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTATTTAGAGG
2385927 AGCAATTTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.34
Consensus pattern (59 bp):
CCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTATTTAGAGGGGTG
Found at i:2385925 original size:41 final size:41
Alignment explanation
Indices: 2385868--2385970 Score: 197
Period size: 41 Copynumber: 2.5 Consensus size: 41
2385858 TATTTAGAGG
2385868 GGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGT
1 GGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGT
*
2385909 GGTGCCTCTGTTTAGAGGAGCAATTTATTTTCCAAAGTCGT
1 GGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGT
2385950 GGTGCCTCTGTTTAGAGGAGC
1 GGTGCCTCTGTTTAGAGGAGC
2385971 TGTTTAGAGG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.34
Consensus pattern (41 bp):
GGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGT
Found at i:2385941 original size:100 final size:98
Alignment explanation
Indices: 2385769--2386058 Score: 489
Period size: 95 Copynumber: 3.0 Consensus size: 98
2385759 TCAAAATCGT
* *
2385769 GGTGCCTCTGTTTAGAGGAACAATTTACTTT-CAAAGTCGTGGTACCTCTGTTTAGAGGAGCAAT
1 GGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAAT
* *
2385833 TTACTTTCCAAAGTCGTGGTGCCTCTATTTAGA
66 TTATTTTCCAAAGTCGTGGTGCCTCTGTTTAGA
2385866 GGGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 --GGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
2385931 ATTTATTTTCCAAAGTCGTGGTGCCTCTGTTTAGA
64 ATTTATTTTCCAAAGTCGTGGTGCCTCTGTTTAGA
*
2385966 GGAG---CTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAAT
1 GGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAAT
2386028 TTATTTTCCAAAGTCGTGGTGCCTCTGTTTA
66 TTATTTTCCAAAGTCGTGGTGCCTCTGTTTA
2386059 AAGGAGTATT
Statistics
Matches: 185, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
95 89 0.48
98 3 0.02
99 30 0.16
100 63 0.34
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (98 bp):
GGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAAT
TTATTTTCCAAAGTCGTGGTGCCTCTGTTTAGA
Found at i:2385975 original size:13 final size:13
Alignment explanation
Indices: 2385957--2385983 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2385947 CGTGGTGCCT
2385957 CTGTTTAGAGGAG
1 CTGTTTAGAGGAG
2385970 CTGTTTAGAGGAG
1 CTGTTTAGAGGAG
2385983 C
1 C
2385984 AATTTACTTT
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:0.11, G:0.37, T:0.30
Consensus pattern (13 bp):
CTGTTTAGAGGAG
Found at i:2385977 original size:54 final size:54
Alignment explanation
Indices: 2385916--2386024 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
2385906 CGTGGTGCCT
*
2385916 CTGTTTAGAGGAGCAATTTATTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAG
1 CTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAG
2385970 CTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAG
1 CTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAG
2386024 C
1 C
2386025 AATTTATTTT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.34
Consensus pattern (54 bp):
CTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAG
Found at i:2386027 original size:41 final size:41
Alignment explanation
Indices: 2385970--2386148 Score: 227
Period size: 41 Copynumber: 4.3 Consensus size: 41
2385960 TTTAGAGGAG
*
2385970 CTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCT
1 CTGTTTAGAGGAGCAATTTATTTTCCAAAGTCGTGGTGCCT
2386011 CTGTTTAGAGGAGCAATTTATTTTCCAAAGTCGTGGTGCCT
1 CTGTTTAGAGGAGCAATTTATTTTCCAAAGTCGTGGTGCCT
* * * *
2386052 CTGTTTAAAGGAG-TATTTATTTTCAAAAGTCGTAGTGCCT
1 CTGTTTAGAGGAGCAATTTATTTTCCAAAGTCGTGGTGCCT
* * * * *
2386092 TTGTTTAGAGGAGTAATTTATGTTTCTCAAAAGTCATTGAG-CT
1 CTGTTTAGAGGAGCAATTTAT-TTTC-C-AAAGTCGTGGTGCCT
2386135 CTGTTTAGAGGAGC
1 CTGTTTAGAGGAGC
2386149 TTTGGTCAAA
Statistics
Matches: 120, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
40 35 0.29
41 58 0.48
42 4 0.03
43 14 0.12
44 9 0.08
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (41 bp):
CTGTTTAGAGGAGCAATTTATTTTCCAAAGTCGTGGTGCCT
Found at i:2386110 original size:81 final size:84
Alignment explanation
Indices: 2385970--2386148 Score: 222
Period size: 81 Copynumber: 2.2 Consensus size: 84
2385960 TTTAGAGGAG
* * *
2385970 CTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTAT-TT
1 CTGTTTAAAGGAGCAATTTACTTTCAAAAGTCGTAGTGCCTCTGTTTAGAGGAGCAATTTATGTT
2386034 TC-CAAAGTCGTGGTGCCT
66 TCTCAAAGTCGTGGTGCCT
* * * *
2386052 CTGTTTAAAGGAG-TATTTATTTTCAAAAGTCGTAGTGCCTTTGTTTAGAGGAGTAATTTATGTT
1 CTGTTTAAAGGAGCAATTTACTTTCAAAAGTCGTAGTGCCTCTGTTTAGAGGAGCAATTTATGTT
* * *
2386116 TCTCAAAAGTCATTGAG-CT
66 TCTC-AAAGTCGTGGTGCCT
*
2386135 CTGTTTAGAGGAGC
1 CTGTTTAAAGGAGC
2386149 TTTGGTCAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
81 42 0.51
82 16 0.20
83 15 0.18
84 9 0.11
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (84 bp):
CTGTTTAAAGGAGCAATTTACTTTCAAAAGTCGTAGTGCCTCTGTTTAGAGGAGCAATTTATGTT
TCTCAAAGTCGTGGTGCCT
Found at i:2386169 original size:8 final size:8
Alignment explanation
Indices: 2386156--2386191 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
2386146 AGCTTTGGTC
2386156 AAAAATAA
1 AAAAATAA
2386164 AAAAATAA
1 AAAAATAA
2386172 AAAACA-AA
1 AAAA-ATAA
2386180 AAAAATAA
1 AAAAATAA
2386188 AAAA
1 AAAA
2386192 TGACAATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 1 0.04
8 24 0.92
9 1 0.04
ACGTcount: A:0.89, C:0.03, G:0.00, T:0.08
Consensus pattern (8 bp):
AAAAATAA
Found at i:2386323 original size:20 final size:21
Alignment explanation
Indices: 2386285--2386323 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2386275 CTGTAGACAC
2386285 TCAATTGGGTCCAGGCCCAGA
1 TCAATTGGGTCCAGGCCCAGA
*
2386306 TCAATTGGG-CCTGGCCCA
1 TCAATTGGGTCCAGGCCCA
2386324 AATGGGTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.21, C:0.31, G:0.28, T:0.21
Consensus pattern (21 bp):
TCAATTGGGTCCAGGCCCAGA
Found at i:2386401 original size:17 final size:18
Alignment explanation
Indices: 2386381--2386417 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
2386371 TTTTCTTTTG
2386381 TATTTTATGTATT-TTAT
1 TATTTTATGTATTATTAT
*
2386398 TA-TTTATTTATTATTAT
1 TATTTTATGTATTATTAT
2386415 TAT
1 TAT
2386418 GTATTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 3
0.81 0.05 0.14
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (18 bp):
TATTTTATGTATTATTAT
Found at i:2386540 original size:31 final size:31
Alignment explanation
Indices: 2386397--2386540 Score: 76
Period size: 27 Copynumber: 4.8 Consensus size: 31
2386387 ATGTATTTTA
* *
2386397 TTATTTATTTATTATTATTATGTATTAATAT-G
1 TTATATATTTATTATTA-TAT-TATTTATATAG
* *
2386429 TGTATATCTTTATTTATCTAT-TTATTTATTTA-
1 T-TATATATTTA-TTAT-TATATTATTTATATAG
* *
2386461 TT-T-TATTT-TTATTTTCATT-TTT-T-TTG
1 TTATATATTTATTATTAT-ATTATTTATATAG
* *
2386487 TTA-ATATTTA-TAGGTATTTTATTTATATAG
1 TTATATATTTATTA-TTATATTATTTATATAG
2386517 TTATATATTTATTATTATATTATT
1 TTATATATTTATTATTATATTATT
2386541 ATTATTATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 33
0.64 0.10 0.26
Matches are distributed among these distances:
25 1 0.01
26 5 0.06
27 16 0.19
28 7 0.08
29 5 0.06
30 6 0.07
31 16 0.19
32 11 0.13
33 9 0.11
34 5 0.06
35 2 0.02
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (31 bp):
TTATATATTTATTATTATATTATTTATATAG
Found at i:2387069 original size:20 final size:21
Alignment explanation
Indices: 2387044--2387093 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
2387034 TCCGACGAAC
2387044 TTCCGGTGAAC-AAACTCAGA
1 TTCCGGTGAACAAAACTCAGA
*
2387064 TTCCGGCG-ACAAAACTCAGA
1 TTCCGGTGAACAAAACTCAGA
* *
2387084 ATCTGGTGAA
1 TTCCGGTGAA
2387094 TCTTCAACCG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.88
21 1 0.04
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (21 bp):
TTCCGGTGAACAAAACTCAGA
Found at i:2387450 original size:11 final size:10
Alignment explanation
Indices: 2387434--2387510 Score: 61
Period size: 11 Copynumber: 7.7 Consensus size: 10
2387424 TTAATATTCT
2387434 TTTTATCTTTA
1 TTTT-TCTTTA
*
2387445 TTTTATTTTTA
1 TTTT-TCTTTA
*
2387456 TTTTTGTTTTA
1 TTTTT-CTTTA
*
2387467 CTTTTCTTTA
1 TTTTTCTTTA
2387477 -TTTT-TTTA
1 TTTTTCTTTA
*
2387485 TTTTTATTTA
1 TTTTTCTTTA
2387495 TTTTT-TTTA
1 TTTTTCTTTA
*
2387504 TTATTCT
1 TTTTTCT
2387511 ATTTTCTTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
8 4 0.07
9 16 0.28
10 15 0.26
11 23 0.40
ACGTcount: A:0.14, C:0.05, G:0.01, T:0.79
Consensus pattern (10 bp):
TTTTTCTTTA
Found at i:2387455 original size:17 final size:16
Alignment explanation
Indices: 2387434--2387515 Score: 64
Period size: 17 Copynumber: 5.2 Consensus size: 16
2387424 TTAATATTCT
*
2387434 TTTTATCTTTATTTTA
1 TTTTATTTTTATTTTA
*
2387450 TTTTTATTTTTGTTTTA
1 -TTTTATTTTTATTTTA
* *
2387467 CTTT-TCTTTA-TTT-
1 TTTTATTTTTATTTTA
2387480 TTTTATTTTTA-TTTA
1 TTTTATTTTTATTTTA
* *
2387495 TTTTTTTTATTATTCTA
1 TTTTATTT-TTATTTTA
2387512 TTTT
1 TTTT
2387516 CTTTAAATGA
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
13 3 0.06
14 11 0.21
15 11 0.21
16 6 0.12
17 21 0.40
ACGTcount: A:0.15, C:0.05, G:0.01, T:0.79
Consensus pattern (16 bp):
TTTTATTTTTATTTTA
Found at i:2387470 original size:27 final size:25
Alignment explanation
Indices: 2387433--2387515 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 25
2387423 TTTAATATTC
2387433 TTTTTATCTTTATTTTATTTTTATTTT
1 TTTTTA-CTTT-TTTTATTTTTATTTT
2387460 TGTTTTACTTTTCTTTATTTTTTTATTTT
1 T-TTTTACTTTT-TTTA--TTTTTATTTT
* *
2387489 TATTTATTTTTTTTATTATTCTATTTT
1 TTTTTACTTTTTTTATT-TT-TATTTT
2387516 CTTTAAATGA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
25 2 0.04
26 3 0.06
27 19 0.40
28 13 0.27
29 11 0.23
ACGTcount: A:0.14, C:0.05, G:0.01, T:0.80
Consensus pattern (25 bp):
TTTTTACTTTTTTTATTTTTATTTT
Found at i:2387494 original size:18 final size:18
Alignment explanation
Indices: 2387445--2387501 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
2387435 TTTATCTTTA
*
2387445 TTTTATTTTTATTT-TTG
1 TTTTATTTTTATTTATTT
* *
2387462 TTTTACTTTTCTTTATTT
1 TTTTATTTTTATTTATTT
2387480 TTTTATTTTTATTTATTT
1 TTTTATTTTTATTTATTT
2387498 TTTT
1 TTTT
2387502 TATTATTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 12 0.35
18 22 0.65
ACGTcount: A:0.12, C:0.04, G:0.02, T:0.82
Consensus pattern (18 bp):
TTTTATTTTTATTTATTT
Found at i:2387502 original size:22 final size:22
Alignment explanation
Indices: 2387361--2387508 Score: 75
Period size: 22 Copynumber: 6.6 Consensus size: 22
2387351 GCTCCAGGTT
* *
2387361 TTTTTTTTTTTATTTTCATTTC
1 TTTTTTTTTTTATTTTTATTTA
* * * *
2387383 TTTGTTTATTTGTTTTTTTTTA
1 TTTTTTTTTTTATTTTTATTTA
* *** **
2387405 TTTATTAGATTAGGTTTATTTA
1 TTTTTTTTTTTATTTTTATTTA
* * * *
2387427 ATATTCTTTTTATCTTTATTTTA
1 TTTTTTTTTTTATTTTTA-TTTA
* *
2387450 TTTTTATTTTT-GTTTTACTTT-
1 TTTTTTTTTTTATTTTTA-TTTA
2387471 TCTTTATTTTTTTATTTTTATTTA
1 T-TTT-TTTTTTTATTTTTATTTA
*
2387495 TTTTTTTTATTATT
1 TTTTTTTTTTTATT
2387509 CTATTTTCTT
Statistics
Matches: 89, Mismatches: 32, Indels: 10
0.68 0.24 0.08
Matches are distributed among these distances:
21 1 0.01
22 58 0.65
23 24 0.27
24 6 0.07
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (22 bp):
TTTTTTTTTTTATTTTTATTTA
Found at i:2387520 original size:17 final size:16
Alignment explanation
Indices: 2387474--2387520 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 16
2387464 TTACTTTTCT
*
2387474 TTATTT-TTTTATTT-
1 TTATTTATTTTCTTTA
*
2387488 TTATTTATTTTTTTTA
1 TTATTTATTTTCTTTA
2387504 TTATTCTATTTTCTTTA
1 TTATT-TATTTTCTTTA
2387521 AATGAAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 6 0.21
15 7 0.25
16 5 0.18
17 10 0.36
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATTTATTTTCTTTA
Found at i:2387790 original size:59 final size:58
Alignment explanation
Indices: 2387532--2388051 Score: 652
Period size: 58 Copynumber: 8.8 Consensus size: 58
2387522 ATGAAAATCA
* *
2387532 AAATTTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT
1 AAATTTTC--AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
** * * **
2387592 AAA-TTTCAAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGGAAAT
1 AAATTTTCAAAAAAA-TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
** *
2387650 CAAGGTTTCAAAAAAATATATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
1 -AAATTTTC-AAAAAA-ATA-TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
*
2387712 AAATTTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT
1 AAATTTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
* * * *
2387770 CAAAATTTTC-GAAAAATATTTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
1 --AAATTTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
*** * **
2387829 AAATTTTCAAAAAGGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGGAAAT
1 AAATTTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
* * * *
2387887 CAAAGTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTTCTTAAAAAT
1 -AAATTTTC-AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
*
2387947 AAATTTTC-AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT
1 AAATTTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
*
2388004 AAATTTTCAAAAAAAGTATTTTTTGGGAAAAGTTGAAA-TATCAATTTT
1 AAATTTTCAAAAAAA-TATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
2388052 TCCTACACAA
Statistics
Matches: 406, Mismatches: 41, Indels: 28
0.85 0.09 0.06
Matches are distributed among these distances:
57 70 0.17
58 133 0.33
59 88 0.22
60 64 0.16
61 12 0.03
62 39 0.10
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.36
Consensus pattern (58 bp):
AAATTTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
Found at i:2387849 original size:117 final size:117
Alignment explanation
Indices: 2387523--2388051 Score: 692
Period size: 117 Copynumber: 4.5 Consensus size: 117
2387513 TTTCTTTAAA
* *
2387523 TGAAAATCAAAATTTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTAA
1 TGAAAATC-AAATTTTC--AAAAAAATATTTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTTAA
* * *
2387588 AAATAAA-TTTCAAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCT
63 AAATAAATTTTCAAAAAGA-GATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* ** *
2387643 TGGAAATCAAGGTTTCAAAAAAATATATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
1 TGAAAATCAAATTTTC-AAAAAA-ATATTTTTAGA-GAAAAGTTGAAAGTATCAATTTTCCTTAA
* * *
2387708 AAATAAATTTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
63 AAATAAATTTTCAAAAAGAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* *
2387763 TGAAAATCAAAATTTTC-GAAAAATATTTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTTAGAA
1 TGAAAATC-AAATTTTCAAAAAAATATTTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAA
*
2387827 ATAAATTTTCAAAAAGGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
65 ATAAATTTTCAAAAAGAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* * * *
2387880 TGGAAATCAAAGTTTCAAAAAAAATATTTTT-GAGGAAAAGTTGAAAATATCAATTTTTCTTAAA
1 TGAAAATCAAATTTTC-AAAAAAATATTTTTAGA-GAAAAGTTGAAAGTATCAATTTTCCTTAAA
* * *
2387944 AATAAATTTTCAAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCT
64 AATAAATTTTCAAAAAGAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* * *
2387997 TAAAAAT-AAATTTTCAAAAAAAGTATTTTTTGGGAAAAGTTGAAA-TATCAATTTT
1 TGAAAATCAAATTTTCAAAAAAA-TATTTTTAGAGAAAAGTTGAAAGTATCAATTTT
2388052 TCCTACACAA
Statistics
Matches: 366, Mismatches: 34, Indels: 23
0.87 0.08 0.05
Matches are distributed among these distances:
115 17 0.05
116 33 0.09
117 127 0.35
118 72 0.20
119 19 0.05
120 81 0.22
121 17 0.05
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.36
Consensus pattern (117 bp):
TGAAAATCAAATTTTCAAAAAAATATTTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAA
TAAATTTTCAAAAAGAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
Found at i:2387937 original size:28 final size:28
Alignment explanation
Indices: 2387846--2387937 Score: 64
Period size: 28 Copynumber: 3.1 Consensus size: 28
2387836 CAAAAAGGGA
*
2387846 TTTTTGAGGAAAAGTTGAAAGTATCAAT
1 TTTTTGAGGAAAAGTTGAAAATATCAAT
* * *
2387874 TTTCCTTG-GAAATCAAAGTTTCAAAA-A-AAAT
1 TTT--TTGAG-GA--AAAG-TTGAAAATATCAAT
2387905 ATTTTTGAGGAAAAGTTGAAAATATCAAT
1 -TTTTTGAGGAAAAGTTGAAAATATCAAT
2387934 TTTT
1 TTTT
2387938 CTTAAAAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 20
0.64 0.09 0.27
Matches are distributed among these distances:
27 6 0.13
28 12 0.26
29 4 0.09
30 8 0.17
31 4 0.09
32 8 0.17
33 5 0.11
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (28 bp):
TTTTTGAGGAAAAGTTGAAAATATCAAT
Found at i:2388732 original size:25 final size:25
Alignment explanation
Indices: 2388702--2388766 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
2388692 ATAAATTTAG
2388702 ATAAAATTTCTCATCTAAAAATTTT
1 ATAAAATTTCTCATCTAAAAATTTT
* * *
2388727 ATAAAAATTTAC-AATTTAAAATTTTT
1 AT-AAAATTT-CTCATCTAAAAATTTT
2388753 AT-AAATTTCATCAT
1 ATAAAATTTC-TCAT
2388767 TGGATAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
23 1 0.03
24 6 0.19
25 4 0.12
26 20 0.62
27 1 0.03
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.45
Consensus pattern (25 bp):
ATAAAATTTCTCATCTAAAAATTTT
Found at i:2388823 original size:8 final size:7
Alignment explanation
Indices: 2388797--2388821 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2388787 TCAAAAAATA
2388797 TTTTATT
1 TTTTATT
2388804 TTTTATT
1 TTTTATT
2388811 TTTTATT
1 TTTTATT
2388818 TTTT
1 TTTT
2388822 TAATTTAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:2389294 original size:9 final size:8
Alignment explanation
Indices: 2389277--2389301 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2389267 ACTCAACTAC
2389277 TTATTTTT
1 TTATTTTT
2389285 TTATTTTT
1 TTATTTTT
2389293 TTATTTTT
1 TTATTTTT
2389301 T
1 T
2389302 ATTAACAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTATTTTT
Found at i:2394996 original size:44 final size:44
Alignment explanation
Indices: 2394946--2395049 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 44
2394936 CTTACTTTTA
* *
2394946 ACAAAAAGAAAACAAAAAA-AAA-AAAGAAG-AA-AAATGAAATG
1 ACAAAAAAAAAAAAAAAAACAAATAAAGAAGAAACAAAT-AAATG
*
2394987 ACATAAAAAAAAAAAAAAAACAAATGAAGAAGAAACAAATAAATG
1 ACA-AAAAAAAAAAAAAAAACAAATAAAGAAGAAACAAATAAATG
* *
2395032 ACAAAAATAAAATAAAAA
1 ACAAAAAAAAAAAAAAAA
2395050 TGTGAAAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
41 3 0.06
42 14 0.26
43 3 0.06
44 19 0.36
45 10 0.19
46 4 0.08
ACGTcount: A:0.78, C:0.06, G:0.09, T:0.08
Consensus pattern (44 bp):
ACAAAAAAAAAAAAAAAAACAAATAAAGAAGAAACAAATAAATG
Found at i:2394997 original size:45 final size:45
Alignment explanation
Indices: 2394948--2395049 Score: 111
Period size: 45 Copynumber: 2.3 Consensus size: 45
2394938 TACTTTTAAC
* * *
2394948 AAAAAGAAAACAAAAA-AAAAAAAGAAG-AA-AAATGAAATGACAT
1 AAAAAAAAAAAAAAAACAAAAAAAGAAGAAACAAAT-AAATGACAA
**
2394991 AAAAAAAAAAAAAAAACAAATGAAGAAGAAACAAATAAATGACAA
1 AAAAAAAAAAAAAAAACAAAAAAAGAAGAAACAAATAAATGACAA
* *
2395036 AAATAAAATAAAAA
1 AAAAAAAAAAAAAA
2395050 TGTGAAAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
43 14 0.29
44 9 0.18
45 22 0.45
46 4 0.08
ACGTcount: A:0.78, C:0.05, G:0.09, T:0.08
Consensus pattern (45 bp):
AAAAAAAAAAAAAAAACAAAAAAAGAAGAAACAAATAAATGACAA
Found at i:2398378 original size:17 final size:17
Alignment explanation
Indices: 2398358--2398398 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
2398348 GTAAATATAT
* *
2398358 TTAATAGATAAAATTTC
1 TTAATAAATAAAACTTC
2398375 TTAATAAATAAAACTTC
1 TTAATAAATAAAACTTC
2398392 TTAATAA
1 TTAATAA
2398399 TCAAGTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.39
Consensus pattern (17 bp):
TTAATAAATAAAACTTC
Found at i:2400958 original size:15 final size:15
Alignment explanation
Indices: 2400938--2400968 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2400928 AAGAAGAAAG
2400938 AAACAAAACGAAACA
1 AAACAAAACGAAACA
*
2400953 AAACAAAATGAAACA
1 AAACAAAACGAAACA
2400968 A
1 A
2400969 GGCCCTCGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.74, C:0.16, G:0.06, T:0.03
Consensus pattern (15 bp):
AAACAAAACGAAACA
Found at i:2401571 original size:23 final size:23
Alignment explanation
Indices: 2401528--2401578 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
2401518 TGTAGGTTTG
* * *
2401528 ATTATTTAATTATATTTTAATTT
1 ATTAATTAATTATATTATAATAT
2401551 ATTAATTAATTAT-TTAATAATAT
1 ATTAATTAATTATATT-ATAATAT
2401574 ATTAA
1 ATTAA
2401579 GAATGTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATTAATTAATTATATTATAATAT
Found at i:2402494 original size:2 final size:2
Alignment explanation
Indices: 2402487--2402516 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2402477 CCTACTTTTC
2402487 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
2402517 GCTTAATTTT
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:2409672 original size:9 final size:9
Alignment explanation
Indices: 2409658--2409687 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2409648 CTTCACCTTC
*
2409658 ATCATCATT
1 ATCATCATA
2409667 ATCATCATA
1 ATCATCATA
2409676 ATCATCATA
1 ATCATCATA
2409685 ATC
1 ATC
2409688 CAAATCCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (9 bp):
ATCATCATA
Found at i:2412105 original size:72 final size:72
Alignment explanation
Indices: 2411983--2412120 Score: 195
Period size: 72 Copynumber: 1.9 Consensus size: 72
2411973 AAAGATCCAA
* * * * * *
2411983 TGTTCAATCTTGGAGATTTTCGCAACCCAGGCGTCGAATTCACACCATTTGTTGAAAGTTTACTT
1 TGTTCAATCTCGGAGATCTTCGAAACCCAGACGTCGAATTCACACAATTTGTTGAAACTTTACTT
2412048 GATACAC
66 GATACAC
* * *
2412055 TGTTCAATCTCGGAGATCTTCGAAACCGAGACGTTGAATTCACACAATTTGTTGAACCTTTACTT
1 TGTTCAATCTCGGAGATCTTCGAAACCCAGACGTCGAATTCACACAATTTGTTGAAACTTTACTT
2412120 G
66 G
2412121 GTTTTACCGC
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 57 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (72 bp):
TGTTCAATCTCGGAGATCTTCGAAACCCAGACGTCGAATTCACACAATTTGTTGAAACTTTACTT
GATACAC
Found at i:2414961 original size:96 final size:96
Alignment explanation
Indices: 2414797--2414990 Score: 336
Period size: 96 Copynumber: 2.0 Consensus size: 96
2414787 GCTGTCATAC
* *
2414797 CTGATAGCAAGTCGTATATTTCAAATGACCACCGATAAAATTCGAATTCAAAATCTCTTTGTCGA
1 CTGATAGCAAGTCGTATATTCCAAATGACCACCGATAAAATTCGAATTCAAAATCTCTTTATCGA
2414862 AAAGAACGATTTTAACCGATTAAACTAATCA
66 AAAGAACGATTTTAACCGATTAAACTAATCA
*
2414893 CTGATAGCAAGTCGTATATTCCAAATGACCACTGATAAAATTCGAATTCAAAATCT-TTTCATCG
1 CTGATAGCAAGTCGTATATTCCAAATGACCACCGATAAAATTCGAATTCAAAATCTCTTT-ATCG
*
2414957 AAAAGAACGATTTTAATCGATTAAACTAATCA
65 AAAAGAACGATTTTAACCGATTAAACTAATCA
2414989 CT
1 CT
2414991 TGTTGATAAT
Statistics
Matches: 93, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
95 3 0.03
96 90 0.97
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.30
Consensus pattern (96 bp):
CTGATAGCAAGTCGTATATTCCAAATGACCACCGATAAAATTCGAATTCAAAATCTCTTTATCGA
AAAGAACGATTTTAACCGATTAAACTAATCA
Found at i:2416089 original size:21 final size:23
Alignment explanation
Indices: 2416065--2416111 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2416055 AATTATTTAT
* *
2416065 AAATT-TATTTAAAT-ATATTAA
1 AAATTATATTAAAATAATATAAA
2416086 AAATTATATTAAAATAATATAAA
1 AAATTATATTAAAATAATATAAA
2416109 AAA
1 AAA
2416112 CAAAACAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 8 0.36
23 9 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATTATATTAAAATAATATAAA
Found at i:2417025 original size:24 final size:24
Alignment explanation
Indices: 2416984--2417029 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2416974 TTTTTATGAA
**
2416984 TTTTTTAATTGTAATTATAATATT
1 TTTTTTAATTACAATTATAATATT
*
2417008 TTTTTTAATTACAGTTATAATA
1 TTTTTTAATTACAATTATAATA
2417030 ATAATTCTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (24 bp):
TTTTTTAATTACAATTATAATATT
Found at i:2421187 original size:22 final size:21
Alignment explanation
Indices: 2421162--2421202 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2421152 AATAATATGC
2421162 AAAAAATGAAAAAATAAATTTT
1 AAAAAATG-AAAAATAAATTTT
*
2421184 AAAAAATGATAAATAAATT
1 AAAAAATGAAAAATAAATT
2421203 AAATCAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (21 bp):
AAAAAATGAAAAATAAATTTT
Found at i:2422016 original size:26 final size:26
Alignment explanation
Indices: 2421976--2422040 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
2421966 GTATAATTGA
*
2421976 ATTTAAATATTAATTTTATT-TAAATTT
1 ATTT-AATATAAATTTT-TTATAAATTT
*
2422003 ATTTAATATAAATTTTTTATGAATTT
1 ATTTAATATAAATTTTTTATAAATTT
*
2422029 TTTTAACTATAA
1 ATTTAA-TATAA
2422041 TAATTACAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 2 0.06
26 22 0.67
27 9 0.27
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (26 bp):
ATTTAATATAAATTTTTTATAAATTT
Found at i:2422091 original size:12 final size:13
Alignment explanation
Indices: 2422061--2422092 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2422051 TATAATAATA
2422061 ATTA-TTATTATT
1 ATTATTTATTATT
2422073 ATTATTTATT-TT
1 ATTATTTATTATT
2422085 ATTATTTA
1 ATTATTTA
2422093 ACCAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTATTTATTATT
Found at i:2426648 original size:120 final size:123
Alignment explanation
Indices: 2426491--2426734 Score: 386
Period size: 124 Copynumber: 2.0 Consensus size: 123
2426481 TGCAGTGAAA
* *
2426491 ACATCAAATCGTATAAATTGCCTTTCCTATAAGCTAGCTAGCTA-C-GC-TCATACTTATCTCTA
1 ACATCAAATCGTATAAACTGCCTTTCCTATAAGCTAGCTAGCTAGCTACTTCATACTTATCTCTA
*
2426553 ACTGCTACTTGAATTGCTGCTACTGATCCTTGGGTGTCTGTCACATCAACATATATAC
66 ACTGCTACTTGAATTGCTGCTAATGATCCTTGGGTGTCTGTCACATCAACATATATAC
2426611 ACATCAAATCGTATAAACTGCCTTTCCTATAAGCTAGCTAGCTAGCTACTTTCATACTTATCTCT
1 ACATCAAATCGTATAAACTGCCTTTCCTATAAGCTAGCTAGCTAGCTAC-TTCATACTTATCTCT
* * * * *
2426676 ACCTGTTACTTGAATTTCTGCTAATGGTCCTTGTGTGTCTGTCACATCAACATATATAC
65 AACTGCTACTTGAATTGCTGCTAATGATCCTTGGGTGTCTGTCACATCAACATATATAC
2426735 CCATTCCTCC
Statistics
Matches: 112, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
120 43 0.38
121 1 0.01
122 1 0.01
124 67 0.60
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.36
Consensus pattern (123 bp):
ACATCAAATCGTATAAACTGCCTTTCCTATAAGCTAGCTAGCTAGCTACTTCATACTTATCTCTA
ACTGCTACTTGAATTGCTGCTAATGATCCTTGGGTGTCTGTCACATCAACATATATAC
Found at i:2426845 original size:14 final size:14
Alignment explanation
Indices: 2426821--2426862 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
2426811 ATTAGGTACT
2426821 TAAAAAGAAAATTTA
1 TAAAAA-AAAATTTA
2426836 TAAAAAAAAATTTA
1 TAAAAAAAAATTTA
2426850 -AAATAAATAAATT
1 TAAA-AAA-AAATT
2426863 ATTTAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.12
14 11 0.44
15 11 0.44
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (14 bp):
TAAAAAAAAATTTA
Found at i:2427065 original size:19 final size:20
Alignment explanation
Indices: 2427043--2427082 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2427033 CATTTGATAC
2427043 TTAAATT-ATAATTAAAATT
1 TTAAATTAATAATTAAAATT
* *
2427062 TTAATTTAATATTTAAAATT
1 TTAAATTAATAATTAAAATT
2427082 T
1 T
2427083 ATAATTAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAAATTAATAATTAAAATT
Found at i:2427090 original size:20 final size:21
Alignment explanation
Indices: 2427054--2427096 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
2427044 TAAATTATAA
2427054 TTAAAATTTTAATTTAA-TAT
1 TTAAAATTTTAATTTAAGTAT
2427074 TTAAAATTTATAA-TTAAGTAT
1 TTAAAATTT-TAATTTAAGTAT
2427095 TT
1 TT
2427097 CAACTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTAAAATTTTAATTTAAGTAT
Found at i:2427095 original size:21 final size:21
Alignment explanation
Indices: 2427054--2427105 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2427044 TAAATTATAA
2427054 TTAAAATTT-TAATTTAATAT
1 TTAAAATTTATAATTTAATAT
2427074 TTAAAATTTATAA-TTAAGTAT
1 TTAAAATTTATAATTTAA-TAT
* *
2427095 TTCAACTTTAT
1 TTAAAATTTAT
2427106 TTATGTCTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (21 bp):
TTAAAATTTATAATTTAATAT
Found at i:2427508 original size:26 final size:26
Alignment explanation
Indices: 2427426--2427508 Score: 66
Period size: 26 Copynumber: 3.3 Consensus size: 26
2427416 TATTTATTTT
2427426 AATTAAT-TAAAT-TTTATAATTTT--
1 AATTAATATAAATATTTAT-ATTTTAA
* * * **
2427449 ATTTTATAAAAATATTTTATAAATTAA
1 AATTAATATAAATA-TTTATATTTTAA
*
2427476 AAATAATATAAATATTTATATTTTAA
1 AATTAATATAAATATTTATATTTTAA
2427502 AATTAAT
1 AATTAAT
2427509 TTTAATACAT
Statistics
Matches: 43, Mismatches: 12, Indels: 7
0.69 0.19 0.11
Matches are distributed among these distances:
23 5 0.12
24 4 0.09
25 3 0.07
26 21 0.49
27 10 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
AATTAATATAAATATTTATATTTTAA
Found at i:2427826 original size:17 final size:19
Alignment explanation
Indices: 2427792--2427827 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
2427782 TTACTCTTTT
2427792 TGTATTAAAATATTTATCA
1 TGTATTAAAATATTTATCA
2427811 TGTATT-AAAT-TTTATCA
1 TGTATTAAAATATTTATCA
2427828 AAATTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 4 0.24
19 6 0.35
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (19 bp):
TGTATTAAAATATTTATCA
Found at i:2431984 original size:32 final size:32
Alignment explanation
Indices: 2431943--2432008 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
2431933 TATAGACGTT
* *
2431943 AAATTTTATATAAAATATGATATAAATATATA
1 AAATTTTATATAAAATATAAAATAAATATATA
***
2431975 AAATTTTATATTTTATATAAAATAAATATATA
1 AAATTTTATATAAAATATAAAATAAATATATA
2432007 AA
1 AA
2432009 TTATCATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (32 bp):
AAATTTTATATAAAATATAAAATAAATATATA
Found at i:2442154 original size:58 final size:58
Alignment explanation
Indices: 2442064--2442179 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
2442054 TTTCATATTC
2442064 AAATCTGTATATGATGACATTCAATACATGGATAACACACTCTTTATGGCAGAAAATT
1 AAATCTGTATATGATGACATTCAATACATGGATAACACACTCTTTATGGCAGAAAATT
2442122 AAATCTGTATATGATGACATTCAATACATGGATAACACACTCTTTATGGCAGAAAATT
1 AAATCTGTATATGATGACATTCAATACATGGATAACACACTCTTTATGGCAGAAAATT
2442180 TTGGCAAATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.31
Consensus pattern (58 bp):
AAATCTGTATATGATGACATTCAATACATGGATAACACACTCTTTATGGCAGAAAATT
Found at i:2447311 original size:30 final size:31
Alignment explanation
Indices: 2447276--2447343 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 31
2447266 TATTTCGAAT
*
2447276 AATTAAA-CTTTTAAATATTTATTTTTAT-TA
1 AATTAAATC-TTTAAACATTTATTTTTATCTA
2447306 AATTAAATCTTTAAACATTTATTTTTATCTA
1 AATTAAATCTTTAAACATTTATTTTTATCTA
2447337 AA-TAAAT
1 AATTAAAT
2447344 TATTGATGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
30 30 0.86
31 5 0.14
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (31 bp):
AATTAAATCTTTAAACATTTATTTTTATCTA
Found at i:2450350 original size:27 final size:26
Alignment explanation
Indices: 2450312--2450364 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
2450302 TTATAATGAC
2450312 ATTATTTAATCTAATTCTATTCATAAT
1 ATTATTTAATCTAATTCTA-TCATAAT
*
2450339 ATTATCTT-ATCTTATTCTATCATAAT
1 ATTAT-TTAATCTAATTCTATCATAAT
2450365 CTTGTATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 7 0.29
27 15 0.62
28 2 0.08
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.53
Consensus pattern (26 bp):
ATTATTTAATCTAATTCTATCATAAT
Found at i:2453469 original size:2 final size:2
Alignment explanation
Indices: 2453462--2453495 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2453452 CCTTGTCTTT
2453462 GA GA GA GA GA GA GA GA GA GA GA GA GA GA -A GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2453496 GGGAAGGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2458625 original size:25 final size:25
Alignment explanation
Indices: 2458597--2458672 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 25
2458587 AAAAACATAA
2458597 AAAATAATTTTAAAATATAAAAAAT
1 AAAATAATTTTAAAATATAAAAAAT
*
2458622 -AAA-AATTTT-AGATGATAAAAAA-
1 AAAATAATTTTAAAAT-ATAAAAAAT
* *
2458644 AAACATAATATTAAGACATCTAAAAAAT
1 AAA-ATAATTTTAA-A-ATATAAAAAAT
2458672 A
1 A
2458673 TATGAACAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
22 3 0.08
23 16 0.41
24 4 0.10
25 5 0.13
26 1 0.03
27 7 0.18
28 3 0.08
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (25 bp):
AAAATAATTTTAAAATATAAAAAAT
Found at i:2458800 original size:28 final size:26
Alignment explanation
Indices: 2458755--2458808 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
2458745 GTTGAATATA
*
2458755 AATATAAATTTTAATAAAATTTATTT
1 AATATAAATTTTAATAAAATTAATTT
*
2458781 AATATAAAATTTTTATTAAAATTAATTT
1 AATAT-AAA-TTTTAATAAAATTAATTT
2458809 TTTTAATCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.21
27 3 0.12
28 16 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
AATATAAATTTTAATAAAATTAATTT
Found at i:2459230 original size:30 final size:29
Alignment explanation
Indices: 2459189--2459249 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
2459179 TGAATTTGGA
2459189 AAAGTATTTTTTTTTTTTGAAG-TAATGTT
1 AAAGTA-TTTTTTTTTTTGAAGTTAATGTT
2459218 AAAGTGATTTTTTTTTTTGAAGTTAATGTT
1 AAAGT-ATTTTTTTTTTTGAAGTTAATGTT
2459248 AA
1 AA
2459250 GTTTGAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (29 bp):
AAAGTATTTTTTTTTTTGAAGTTAATGTT
Found at i:2470615 original size:24 final size:24
Alignment explanation
Indices: 2470569--2470615 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2470559 ACATGATTCT
* *
2470569 TTTTTTTGTTTTCTTTTTTTTTAA
1 TTTTTTTGTTTTCTTTATATTTAA
2470593 TTTTTTTGTCTTT-TTTATATTTA
1 TTTTTTTGT-TTTCTTTATATTTA
2470616 GTAAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.11, C:0.04, G:0.04, T:0.81
Consensus pattern (24 bp):
TTTTTTTGTTTTCTTTATATTTAA
Found at i:2474980 original size:23 final size:24
Alignment explanation
Indices: 2474940--2474985 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
2474930 TGAGTTTGAT
*
2474940 TTAAATATAAAATTATA-TATTTA
1 TTAAATATAAAATAATATTATTTA
*
2474963 TTAAATATAAGATAATATTATTT
1 TTAAATATAAAATAATATTATTT
2474986 TAACATATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
TTAAATATAAAATAATATTATTTA
Found at i:2489042 original size:36 final size:36
Alignment explanation
Indices: 2488982--2489115 Score: 151
Period size: 36 Copynumber: 3.7 Consensus size: 36
2488972 AAAAAGCAGC
* * * *
2488982 TTGGCGTTAACAATGGTATTGGGCCTGGCCGGCCTG
1 TTGGTGTTAGCAATGGTATCGGGCCTGGCCGACCTG
* *
2489018 TTGGTGTTAGCAATGGTATGGGGCCTGGCCGTCCTG
1 TTGGTGTTAGCAATGGTATCGGGCCTGGCCGACCTG
* * * *
2489054 TTAGTATTAGCAATGGAATCAGGCCTGGCCGACCTG
1 TTGGTGTTAGCAATGGTATCGGGCCTGGCCGACCTG
* **
2489090 TTGGTGTTAGCAGTGGTGCCGGGCCT
1 TTGGTGTTAGCAATGGTATCGGGCCT
2489116 AAAGCTGTTC
Statistics
Matches: 81, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 81 1.00
ACGTcount: A:0.15, C:0.21, G:0.36, T:0.28
Consensus pattern (36 bp):
TTGGTGTTAGCAATGGTATCGGGCCTGGCCGACCTG
Found at i:2490518 original size:7 final size:7
Alignment explanation
Indices: 2490508--2490534 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2490498 ATAAAAAAAC
2490508 GAAAATT
1 GAAAATT
2490515 GAAAATT
1 GAAAATT
2490522 GAAAATT
1 GAAAATT
2490529 GAAAAT
1 GAAAAT
2490535 CTTCAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (7 bp):
GAAAATT
Found at i:2493455 original size:2 final size:2
Alignment explanation
Indices: 2493448--2493491 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2493438 GGATGATTTT
2493448 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2493490 AC
1 AC
2493492 TATTTTACTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2497940 original size:2 final size:2
Alignment explanation
Indices: 2497933--2497969 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2497923 ACAGGAAGAA
2497933 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 A
2497970 AGGTTATGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2498270 original size:8 final size:8
Alignment explanation
Indices: 2498257--2498281 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2498247 GTAAGTTGAA
2498257 ATTATGCT
1 ATTATGCT
2498265 ATTATGCT
1 ATTATGCT
2498273 ATTATGCT
1 ATTATGCT
2498281 A
1 A
2498282 AGGGTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (8 bp):
ATTATGCT
Found at i:2508020 original size:2 final size:2
Alignment explanation
Indices: 2508013--2508041 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2508003 CATTTCAACT
2508013 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 T
2508042 GAAGAGTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2510337 original size:38 final size:40
Alignment explanation
Indices: 2510220--2510337 Score: 106
Period size: 38 Copynumber: 3.0 Consensus size: 40
2510210 TTATGTTGAA
* *
2510220 ATAAATTTAACATAATTTATAT-ATAAAATATAATTCAAATAT
1 ATAAATTTTA-ATATTTTATATAATAAAAT-TAATT-AAATAT
2510262 ATAAATTTTAATATTTTATATAATACAAA-TACA-TAAATCAT
1 ATAAATTTTAATATTTTATATAATA-AAATTA-ATTAAAT-AT
2510303 -TAAA-TTTAAT-TTTTAT-TAAATAAAATTAATTAAAT
1 ATAAATTTTAATATTTTATAT-AATAAAATTAATTAAAT
2510338 TGATAAAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 18
0.77 0.02 0.21
Matches are distributed among these distances:
37 5 0.07
38 17 0.25
39 6 0.09
40 8 0.12
41 15 0.22
42 13 0.19
43 3 0.04
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (40 bp):
ATAAATTTTAATATTTTATATAATAAAATTAATTAAATAT
Found at i:2516734 original size:22 final size:22
Alignment explanation
Indices: 2516709--2516752 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2516699 AGTGGGCAGT
2516709 AACAGCCTTTGAAATTTTTTAC
1 AACAGCCTTTGAAATTTTTTAC
2516731 AACAGCCTTTGAAATTTTTTAC
1 AACAGCCTTTGAAATTTTTTAC
2516753 TTTTGGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (22 bp):
AACAGCCTTTGAAATTTTTTAC
Found at i:2524650 original size:73 final size:73
Alignment explanation
Indices: 2524564--2524711 Score: 296
Period size: 73 Copynumber: 2.0 Consensus size: 73
2524554 CGGGCTGCTT
2524564 AGCAAACAAACATGTTCTTAACTGAGCTATCAGGGTTTTGATGCAATCATAGATTAATATCAATC
1 AGCAAACAAACATGTTCTTAACTGAGCTATCAGGGTTTTGATGCAATCATAGATTAATATCAATC
2524629 ATATGCAC
66 ATATGCAC
2524637 AGCAAACAAACATGTTCTTAACTGAGCTATCAGGGTTTTGATGCAATCATAGATTAATATCAATC
1 AGCAAACAAACATGTTCTTAACTGAGCTATCAGGGTTTTGATGCAATCATAGATTAATATCAATC
2524702 ATATGCAC
66 ATATGCAC
2524710 AG
1 AG
2524712 TAATTAAAAC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30
Consensus pattern (73 bp):
AGCAAACAAACATGTTCTTAACTGAGCTATCAGGGTTTTGATGCAATCATAGATTAATATCAATC
ATATGCAC
Found at i:2531115 original size:30 final size:30
Alignment explanation
Indices: 2531042--2531115 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 30
2531032 CAATAAATAT
*
2531042 TTAAGGGATTT-TTTAGGTATAAATTAAAGG
1 TTAAGGG-TTTATTTAGGTATAAATTAAAAG
* ***
2531072 TTATGGACCTATTT-GGATATAAATTAAAAG
1 TTAAGGGTTTATTTAGG-TATAAATTAAAAG
2531102 TTAAGGGTTTATTT
1 TTAAGGGTTTATTT
2531116 TGGTGTAATA
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
29 3 0.09
30 30 0.91
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.42
Consensus pattern (30 bp):
TTAAGGGTTTATTTAGGTATAAATTAAAAG
Found at i:2532680 original size:30 final size:30
Alignment explanation
Indices: 2532579--2532680 Score: 93
Period size: 30 Copynumber: 3.4 Consensus size: 30
2532569 TTATTACAAG
*
2532579 TAAGTTCTTAA-CTTTTAATGTGAATCAAAA
1 TAAGTTCTTAATC-TTTAATCTGAATCAAAA
* * * *
2532609 TAAGCTCTTAAACTTTAATTTGTATCAAAA
1 TAAGTTCTTAATCTTTAATCTGAATCAAAA
* *
2532639 TAAGATT-TTAATCTTTAATCTGCA-CATAAG
1 TAAG-TTCTTAATCTTTAATCTGAATCA-AAA
2532669 TAAGTTCTTAAT
1 TAAGTTCTTAAT
2532681 ATAAATCAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
29 4 0.07
30 54 0.90
31 2 0.03
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (30 bp):
TAAGTTCTTAATCTTTAATCTGAATCAAAA
Found at i:2533715 original size:2 final size:2
Alignment explanation
Indices: 2533708--2533746 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2533698 TGTCATTGTT
2533708 TA TA TA 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 TA TA TA T
2533747 TATTCTTACC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2534210 original size:19 final size:20
Alignment explanation
Indices: 2534174--2534211 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2534164 ATTAATCTAA
2534174 AATAAAAATTTATATTATTT
1 AATAAAAATTTATATTATTT
2534194 AATAAAAATTTAT-TTATT
1 AATAAAAATTTATATTATT
2534212 AAACATATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATAAAAATTTATATTATTT
Found at i:2534466 original size:20 final size:20
Alignment explanation
Indices: 2534434--2534480 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
2534424 AATAATTAAT
* *
2534434 AAAAACAAAAAAAAGA-TA-
1 AAAAAAAAAAAAAAAATTAC
2534452 AAAAAAAAAACAAAAAATTAC
1 AAAAAAAAAA-AAAAAATTAC
2534473 AAAAAAAA
1 AAAAAAAA
2534481 GGAGAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 9 0.38
19 5 0.21
20 2 0.08
21 8 0.33
ACGTcount: A:0.85, C:0.06, G:0.02, T:0.06
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAATTAC
Found at i:2534807 original size:11 final size:11
Alignment explanation
Indices: 2534789--2534892 Score: 50
Period size: 12 Copynumber: 8.9 Consensus size: 11
2534779 TATCTTTGTC
2534789 ATTTTTATTTTT
1 ATTTTTA-TTTT
2534801 ATTTTATATTTT
1 ATTTT-TATTTT
* * *
2534813 ATGTATATCTT
1 ATTTTTATTTT
2534824 ATGTATTTATTATT
1 AT-T-TTTATT-TT
* ** *
2534838 ACTAATATATAT
1 ATTTTTAT-TTT
*
2534850 ATTTTTATTAT
1 ATTTTTATTTT
2534861 -TTTTTATTTT
1 ATTTTTATTTT
2534871 ATTTATT-TTTGT
1 ATTT-TTATTT-T
2534883 ATTTTTATTT
1 ATTTTTATTT
2534893 ATCTAATTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
10 9 0.13
11 18 0.26
12 31 0.45
13 8 0.12
14 3 0.04
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:2534814 original size:18 final size:17
Alignment explanation
Indices: 2534791--2534894 Score: 68
Period size: 18 Copynumber: 5.9 Consensus size: 17
2534781 TCTTTGTCAT
2534791 TTTTATTTTTATTTTATA
1 TTTTATTTTTA-TTTATA
* * *
2534809 TTTTATGTATATCTTATG
1 TTTTATTTTTAT-TTATA
* * *
2534827 TATTTATTATTACTAATA
1 T-TTTATTTTTATTTATA
* *
2534845 TATATATTTTTA-TTATT
1 T-TTTATTTTTATTTATA
*
2534862 TTTTA-TTTTATTTATT
1 TTTTATTTTTATTTATA
2534878 TTTGTATTTTTATTTAT
1 TTT-TATTTTTATTTAT
2534895 CTAATTATAT
Statistics
Matches: 67, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
15 5 0.07
16 11 0.16
17 7 0.10
18 37 0.55
19 7 0.10
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTTATTTTTATTTATA
Found at i:2534870 original size:16 final size:17
Alignment explanation
Indices: 2534849--2534891 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
2534839 CTAATATATA
2534849 TATTTTTATTATTTTT-
1 TATTTTTATTATTTTTG
2534865 TA-TTTTATTTATTTTTG
1 TATTTTTA-TTATTTTTG
2534882 TATTTTTATT
1 TATTTTTATT
2534892 TATCTAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.21
16 10 0.42
17 4 0.17
18 5 0.21
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (17 bp):
TATTTTTATTATTTTTG
Found at i:2534885 original size:27 final size:28
Alignment explanation
Indices: 2534839--2534921 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 28
2534829 TTTATTATTA
2534839 CTAATATATATATTTT-TATTATTTTTTAT
1 CTAAT-TATAT-TTTTGTATTATTTTTTAT
* *
2534868 TTTATT-TATTTTTGTATT-TTTATTTAT
1 CTAATTATATTTTTGTATTATTT-TTTAT
* *
2534895 CTAATTATATATCTGATATTATTTTTT
1 CTAATTATATTTTTG-TATTATTTTTT
2534922 TTATTTATCC
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
26 7 0.16
27 16 0.37
28 7 0.16
29 10 0.23
30 3 0.07
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (28 bp):
CTAATTATATTTTTGTATTATTTTTTAT
Found at i:2534925 original size:23 final size:22
Alignment explanation
Indices: 2534899--2534954 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
2534889 ATTTATCTAA
* *
2534899 TTATATATCTGATATTATTTTTT
1 TTATTTATCT-ATAATATTTTTT
2534922 TTATTTATCCTATAATATTTTTT
1 TTATTTAT-CTATAATATTTTTT
2534945 TTATTTATCT
1 TTATTTATCT
2534955 TTTCTAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 2 0.07
23 26 0.87
24 2 0.07
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.66
Consensus pattern (22 bp):
TTATTTATCTATAATATTTTTT
Found at i:2536006 original size:60 final size:60
Alignment explanation
Indices: 2535942--2536280 Score: 401
Period size: 59 Copynumber: 5.7 Consensus size: 60
2535932 AATAAAAAAA
*
2535942 TCAAAAAAATATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTTAAAAATAAATTT
1 TCAAAAAAATATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCCTTAAAAATAAATTT
* * ** *
2536002 TCAAAAAAA-AGATTTTTGAGAAAAAGTTGAAAGTATCAATTTTT-CTTCGAAATCAAA-GT
1 TCAAAAAAATA-TTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCCTTAAAAAT-AAATTT
* * * *
2536061 TCCAAAAAATATTTTTGGA-AAAAAGTTGAAAGTATCAA-TTTTCCTTGAAAATCAAAATTT
1 TCAAAAAAATATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCCTTAAAAAT--AAATTT
** *
2536121 T-TGAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAA-TTTTCCTTAAAAAATAAATTT
1 TCAAAAAAATATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCCTT-AAAAATAAATTT
** *
2536179 TCAAAAAAGGATTTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCCTTAGAAATAAATTT
1 TCAAAAAAATATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCCTTAAAAATAAATTT
* *
2536238 CCAAAAAAAGA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTT
1 TCAAAAAAATATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTT
2536281 TCTACACAGG
Statistics
Matches: 242, Mismatches: 26, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
57 4 0.02
58 60 0.25
59 99 0.41
60 79 0.33
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.36
Consensus pattern (60 bp):
TCAAAAAAATATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCCTTAAAAATAAATTT
Found at i:2536219 original size:177 final size:178
Alignment explanation
Indices: 2535946--2536279 Score: 523
Period size: 177 Copynumber: 1.9 Consensus size: 178
2535936 AAAAAATCAA
* * *
2535946 AAAAATATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTTAAAAATAAATTTTCAAAAAAA
1 AAAAATATTTTTAGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAATAAATTTTCAAAAAAA
* * *
2536011 AGATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTCGAAATCAAAGTTCC-AAAAAATATTT
66 AGATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT-AAAGTTCCAAAAAAAGATTT
2536075 TTG-GAAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTTTG
130 TTGAG-AAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTTTG
2536124 AAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAATAAATTTTC-AAAAAA
1 AAAAATATTTTTAGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAATAAATTTTCAAAAAAA
* * *
2536187 GGATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAAAGATTT
66 AGA-TTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAGTTCCAAAAAAAGATTT
*
2536252 TTGAGGAAAAGTTGAAAGTATCAATTTT
130 TTGAGAAAAAGTTGAAAGTATCAATTTT
2536280 TTCTACACAG
Statistics
Matches: 143, Mismatches: 10, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
176 15 0.10
177 114 0.80
178 14 0.10
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.36
Consensus pattern (178 bp):
AAAAATATTTTTAGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAATAAATTTTCAAAAAAA
AGATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAGTTCCAAAAAAAGATTTT
TGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTTTG
Found at i:2540158 original size:19 final size:17
Alignment explanation
Indices: 2540112--2540158 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 17
2540102 AACAATAGAT
2540112 GAAAAATGAGAAAAAAA
1 GAAAAATGAGAAAAAAA
2540129 GAAAAA--A-AAAAGAAA
1 GAAAAATGAGAAAA-AAA
2540144 GAAAGAATGAGAAAA
1 GAAA-AATGAGAAAA
2540159 TGGAAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 4 0.16
15 8 0.32
16 2 0.08
17 6 0.24
18 1 0.04
19 4 0.16
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (17 bp):
GAAAAATGAGAAAAAAA
Found at i:2541375 original size:43 final size:42
Alignment explanation
Indices: 2541325--2541405 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 42
2541315 AATTGTTGAA
* *
2541325 CAAATGAAAAG-TTTTGAACTTTTGGATGTGAATCTCCAAAATT
1 CAAATGAAAAGCTTTAG-ACTTTTGGATATGAAT-TCCAAAATT
*
2541368 CAAATGAAAAGCTTTAGATTTTTGGATATGAATTCCAA
1 CAAATGAAAAGCTTTAGACTTTTGGATATGAATTCCAA
2541406 GTTTGCCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
42 5 0.15
43 25 0.74
44 4 0.12
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (42 bp):
CAAATGAAAAGCTTTAGACTTTTGGATATGAATTCCAAAATT
Found at i:2541718 original size:41 final size:42
Alignment explanation
Indices: 2541673--2542174 Score: 750
Period size: 41 Copynumber: 12.1 Consensus size: 42
2541663 GATTGTCAAT
*
2541673 GAGCAATTTACTTTT-CAAAGTCGTGGTGCCTTTGTTTAGAG
1 GAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
*
2541714 GAGCAATTTACATTT-CAAAGTCGTGGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
* *
2541755 GAGCAATTTAC-ATTCCAAAAGTCATGGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCC-AAAGTCGTGGTGCCTCTGTTTAGAG
2541797 GAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
*
2541838 GAACAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
2541880 GAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
* *
2541921 TAACAATTTACTTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCC-AAAGTCGTGGTGCCTCTGTTTAGAG
* ** *
2541964 AAGCAATTTA-TTTTCCAAAGTTTTGTTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
* *
2542005 GAGCAATTTACTTTT-CAAAGTCATGGTGCCTCTATTTAGAG
1 GAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
*
2542046 GAGTAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
* *
2542088 GAGCAATTTATTTTTCCAAAGTCGTGGAGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
* * * *
2542130 GAGCAATTTA-TTTTCCAAAATCGTTGAGCCTCTGCTTAGAG
1 GAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
2542171 GAGC
1 GAGC
2542175 TTTGGTAAAA
Statistics
Matches: 424, Mismatches: 29, Indels: 16
0.90 0.06 0.03
Matches are distributed among these distances:
40 2 0.00
41 227 0.54
42 160 0.38
43 35 0.08
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.36
Consensus pattern (42 bp):
GAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
Found at i:2541792 original size:83 final size:83
Alignment explanation
Indices: 2541673--2542174 Score: 726
Period size: 83 Copynumber: 6.0 Consensus size: 83
2541663 GATTGTCAAT
* * *
2541673 GAGCAATTTACTTTTCAAAGTCGTGGTGCCTTTGTTTAGAGGAGCAATTTACATTT-CAAAGTCG
1 GAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCG
2541737 TGGTGCCTCTGTTTAGAG
66 TGGTGCCTCTGTTTAGAG
* *
2541755 GAGCAATTTACATTCCAAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGTC
1 GAGCAATTTACTTTCC-AAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTC
2541819 GTGGTGCCTCTGTTTAGAG
65 GTGGTGCCTCTGTTTAGAG
*
2541838 GAACAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGTC
1 GAGCAATTTAC-TTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTC
2541902 GTGGTGCCTCTGTTTAGAG
65 GTGGTGCCTCTGTTTAGAG
* * *
2541921 TAACAATTTACTTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGAAGCAATTTA-TTTTCCAAAGT
1 GAGCAATTTAC-TTTCC-AAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGT
** *
2541985 TTTGTTGCCTCTGTTTAGAG
64 CGTGGTGCCTCTGTTTAGAG
* * * *
2542005 GAGCAATTTACTTTTCAAAGTCATGGTGCCTCTATTTAGAGGAGTAATTTACTTTTCCAAAGTCG
1 GAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCG
2542070 TGGTGCCTCTGTTTAGAG
66 TGGTGCCTCTGTTTAGAG
* * *
2542088 GAGCAATTTATTTTTCCAAAGTCGTGGAGCCTCTGTTTAGAGGAGCAATTTA-TTTTCCAAAATC
1 GAGCAATTTA-CTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTC
* * *
2542152 GTTGAGCCTCTGCTTAGAG
65 GTGGTGCCTCTGTTTAGAG
2542171 GAGC
1 GAGC
2542175 TTTGGTAAAA
Statistics
Matches: 381, Mismatches: 33, Indels: 11
0.90 0.08 0.03
Matches are distributed among these distances:
82 45 0.12
83 231 0.61
84 105 0.28
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.36
Consensus pattern (83 bp):
GAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCG
TGGTGCCTCTGTTTAGAG
Found at i:2541978 original size:125 final size:124
Alignment explanation
Indices: 2541673--2542174 Score: 733
Period size: 125 Copynumber: 4.0 Consensus size: 124
2541663 GATTGTCAAT
* * *
2541673 GAGCAATTTACTTTTCAAAGTCGTGGTGCCTTTGTTTAGAGGAGCAATTTACATTT-CAAAGTCG
1 GAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGAAGCAATTTACTTTTCCAAAGTCG
* *
2541737 TGGTGCCTCTGTTTAGAGGAGCAATTTACATTCCAAAAGTCATGGTGCCTCTGTTTAGAG
66 TGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTC-AAAGTCATGGTGCCTCTGTTTAGAG
2541797 GAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAA-CAATTTACTTTTCCAAAGTC
1 GAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGA-GAAGCAATTTACTTTTCCAAAGTC
*
2541861 GTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAG
65 GTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCATGGTGCCTCTGTTTAGAG
* *
2541921 TAACAATTTACTTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGAAGCAATTTA-TTTTCCAAAGT
1 GAGCAATTTACTTTT-C-AAAGTCGTGGTGCCTCTGTTTAGAGAAGCAATTTACTTTTCCAAAGT
** * *
2541985 TTTGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCATGGTGCCTCTATTTAGAG
64 CGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCATGGTGCCTCTGTTTAGAG
* * *
2542046 GAGTAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTC
1 GAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGAAGCAATTTACTTTTCCAAAGTC
* * * * * *
2542111 GTGGAGCCTCTGTTTAGAGGAGCAATTTA-TTTTCCAAAATCGTTGAGCCTCTGCTTAGAG
65 GTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGTCATGGTGCCTCTGTTTAGAG
2542171 GAGC
1 GAGC
2542175 TTTGGTAAAA
Statistics
Matches: 343, Mismatches: 28, Indels: 13
0.89 0.07 0.03
Matches are distributed among these distances:
124 125 0.36
125 187 0.55
126 31 0.09
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.36
Consensus pattern (124 bp):
GAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGAAGCAATTTACTTTTCCAAAGTCG
TGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCATGGTGCCTCTGTTTAGAG
Found at i:2542224 original size:8 final size:8
Alignment explanation
Indices: 2542188--2542231 Score: 63
Period size: 8 Copynumber: 5.5 Consensus size: 8
2542178 GGTAAAAATT
*
2542188 AAAAAATA
1 AAAAAACA
2542196 AAAAAACA
1 AAAAAACA
2542204 AAAAAAC-
1 AAAAAACA
2542211 AAAAAACA
1 AAAAAACA
2542219 AAAAAACA
1 AAAAAACA
2542227 TAAAA
1 -AAAA
2542232 TGAAAATGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
7 7 0.21
8 22 0.67
9 4 0.12
ACGTcount: A:0.86, C:0.09, G:0.00, T:0.05
Consensus pattern (8 bp):
AAAAAACA
Found at i:2542237 original size:15 final size:15
Alignment explanation
Indices: 2542196--2542231 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
2542186 TTAAAAAATA
2542196 AAAAAACAAAAAAAC
1 AAAAAACAAAAAAAC
2542211 AAAAAACAAAAAAAC
1 AAAAAACAAAAAAAC
2542226 ATAAAA
1 A-AAAA
2542232 TGAAAATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.86, C:0.11, G:0.00, T:0.03
Consensus pattern (15 bp):
AAAAAACAAAAAAAC
Found at i:2543510 original size:3 final size:3
Alignment explanation
Indices: 2543502--2543532 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2543492 ATAAAAAATA
2543502 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2543533 TGTAAAATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2549720 original size:30 final size:30
Alignment explanation
Indices: 2549686--2549778 Score: 72
Period size: 30 Copynumber: 3.2 Consensus size: 30
2549676 TTTTTAGGAG
2549686 AAGTTGAAAGTATCAATTTTCTTTGAAAAT
1 AAGTTGAAAGTATCAATTTTCTTTGAAAAT
* * *
2549716 AAGTTTTCTAAA-T-T---TTTTTTTTTAGAAA-
1 AAG--TT-GAAAGTATCAATTTTCTTTGA-AAAT
*
2549744 AAGTTGAAAGTATCAATTTTCCTTGAAAAT
1 AAGTTGAAAGTATCAATTTTCTTTGAAAAT
2549774 AAGTT
1 AAGTT
2549779 TTCTAAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 20
0.63 0.10 0.27
Matches are distributed among these distances:
25 3 0.07
26 3 0.07
27 1 0.02
28 11 0.24
29 6 0.13
30 15 0.33
31 1 0.02
32 3 0.07
33 3 0.07
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (30 bp):
AAGTTGAAAGTATCAATTTTCTTTGAAAAT
Found at i:2549748 original size:58 final size:59
Alignment explanation
Indices: 2549661--2549940 Score: 297
Period size: 58 Copynumber: 4.8 Consensus size: 59
2549651 TAAATTTTTT
* * *
2549661 TTTTTTAAAAAATA-TTTTTTAGGAGAAGTTGAAAGTATCAATTTTCTTTGAAAATAAG
1 TTTTCTAAAAAATATTTTTTTAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAG
** * *
2549719 TTTTCT-AAATTTTTTTTTTTAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAG
1 TTTTCTAAAAAATATTTTTTTAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAG
***
2549777 TTTTCTAAAAAATATTTTCAAAGAAAAA-TTGAAAGTATCAATTTTCTTTGAAAATAA-
1 TTTTCTAAAAAATATTTTTTTAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAG
* * * * *
2549834 TTTTCTGAAAAAA-GTTTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAG
1 TTTTCT-AAAAAATATTTTTTTAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAAT-AAG
* * ** *
2549894 -TTTCAAAAAAACA-TTTTGGAGAAAAA-TTAAAAGTATCAAATTTTCTT
1 TTTTCTAAAAAATATTTTTTTAGAAAAAGTTGAAAGTATC-AATTTTCTT
2549941 GTACAAAAAC
Statistics
Matches: 188, Mismatches: 26, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
57 31 0.16
58 136 0.72
59 21 0.11
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (59 bp):
TTTTCTAAAAAATATTTTTTTAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAG
Found at i:2549819 original size:116 final size:116
Alignment explanation
Indices: 2549612--2549940 Score: 376
Period size: 116 Copynumber: 2.8 Consensus size: 116
2549602 AATAAAAAAA
* * * *
2549612 TTTTGAGAAAAAGTTGAAAGCATCAATTTTTCTTGAAAATAAATTTTTTTTTTTTAAAAAATATT
1 TTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAA-----GTTTTCTAAAAAATA-T
* * * * ****
2549677 TTTTAGGAGAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGTTTTCT-AAATTTTTT
60 TTTAAAGAAAAATTGAAAGTATCAATTTTCTTTGAAAATAA-TTTTCTGAAAAAAGTT
*
2549734 TTTTTAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAGTTTTCTAAAAAATATTTTCAA
1 TTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAGTTTTCTAAAAAATATTTT-AA
2549798 AGAAAAATTGAAAGTATCAATTTTCTTTGAAAATAATTTTCTGAAAAAAGTT
65 AGAAAAATTGAAAGTATCAATTTTCTTTGAAAATAATTTTCTGAAAAAAGTT
* * * * **
2549850 TTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAG-TTTCAAAAAAACATTTTGGA
1 TTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAGTTTTCTAAAAAATATTTTAAA
*
2549914 GAAAAATTAAAAGTATCAAATTTTCTT
66 GAAAAATTGAAAGTATC-AATTTTCTT
2549941 GTACAAAAAC
Statistics
Matches: 182, Mismatches: 21, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
115 27 0.15
116 113 0.62
117 3 0.02
121 2 0.01
122 37 0.20
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (116 bp):
TTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAGTTTTCTAAAAAATATTTTAAA
GAAAAATTGAAAGTATCAATTTTCTTTGAAAATAATTTTCTGAAAAAAGTT
Found at i:2551145 original size:20 final size:21
Alignment explanation
Indices: 2551108--2551147 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2551098 ATTTTCAAAA
2551108 AAAAAAAATACCCGAAAATTCC
1 AAAAAAAATA-CCGAAAATTCC
*
2551130 AAAAAAAAT-CCTAAAATT
1 AAAAAAAATACCGAAAATT
2551148 TCTCAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.62, C:0.17, G:0.03, T:0.17
Consensus pattern (21 bp):
AAAAAAAATACCGAAAATTCC
Found at i:2577009 original size:70 final size:71
Alignment explanation
Indices: 2576802--2577015 Score: 394
Period size: 71 Copynumber: 3.0 Consensus size: 71
2576792 GGAAAAGATA
*
2576802 ATGACACGAGACATGCACTAATTAAAATGTTATTTATAGAAATATTTTTCACATTTAATGTGAAA
1 ATGACACGACACATGCACTAATTAAAATGTTATTTATAGAAATATTTTTCACATTTAATGTGAAA
2576867 TAATTG
66 TAATTG
*
2576873 ATGACACGACACATGCACTAATTAAAATGTTATTTATAGAAATATTTTTCACATTTAATGTAAAA
1 ATGACACGACACATGCACTAATTAAAATGTTATTTATAGAAATATTTTTCACATTTAATGTGAAA
2576938 TAATTG
66 TAATTG
*
2576944 ATGACACGACACATGGAC-AATTAAAATGTTATTTATAGAAATATTTTTCACATTTAATGTGAAA
1 ATGACACGACACATGCACTAATTAAAATGTTATTTATAGAAATATTTTTCACATTTAATGTGAAA
2577008 TAATTG
66 TAATTG
2577014 AT
1 AT
2577016 AATTAATTTA
Statistics
Matches: 139, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
70 53 0.38
71 86 0.62
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (71 bp):
ATGACACGACACATGCACTAATTAAAATGTTATTTATAGAAATATTTTTCACATTTAATGTGAAA
TAATTG
Found at i:2577358 original size:16 final size:16
Alignment explanation
Indices: 2577337--2577367 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2577327 AGTTTAATGT
*
2577337 AAAAATTAATAATATA
1 AAAAATTAAAAATATA
2577353 AAAAATTAAAAATAT
1 AAAAATTAAAAATAT
2577368 TATTTATAAT
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATTAAAAATATA
Found at i:2583441 original size:2 final size:2
Alignment explanation
Indices: 2583436--2583471 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2583426 GTGTGTGTGT
2583436 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2583472 AGACTGAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2589275 original size:23 final size:23
Alignment explanation
Indices: 2589246--2589289 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2589236 ATAATTATTA
* *
2589246 TTATTATAATTATAATTAAAATT
1 TTATTATAATTAAAATAAAAATT
2589269 TTATTATAATTAAAATAAAAA
1 TTATTATAATTAAAATAAAAA
2589290 AATTTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTATTATAATTAAAATAAAAATT
Found at i:2590485 original size:2 final size:2
Alignment explanation
Indices: 2590478--2590509 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2590468 GTCAAAGACA
*
2590478 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2590510 CCATCTGACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2595654 original size:13 final size:14
Alignment explanation
Indices: 2595636--2595669 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
2595626 ACTTGAATTT
2595636 AATTTAATTA-ATA
1 AATTTAATTATATA
*
2595649 AATTTAATTATTTA
1 AATTTAATTATATA
2595663 AATTTAA
1 AATTTAA
2595670 ATTCGATTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTTAATTATATA
Found at i:2617484 original size:32 final size:32
Alignment explanation
Indices: 2617438--2617498 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
2617428 GCCAGACACA
* * *
2617438 GCAACACTGGTTTGGTAGGGTAATGTTTTTGT
1 GCAAAACTGGTTTGGCAGGGTAATATTTTTGT
2617470 GCAAAACTGGTTTGGCAGGGTAATATTTT
1 GCAAAACTGGTTTGGCAGGGTAATATTTT
2617499 CAAGGAATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.23, C:0.10, G:0.30, T:0.38
Consensus pattern (32 bp):
GCAAAACTGGTTTGGCAGGGTAATATTTTTGT
Found at i:2623928 original size:15 final size:15
Alignment explanation
Indices: 2623910--2623960 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
2623900 TTTTCTTTGC
2623910 TCTCTTCTA-TCTCCT
1 TCTCTTC-ACTCTCCT
2623925 TCTCTTCACTCTCCT
1 TCTCTTCACTCTCCT
* ** *
2623940 TTTCCCCACTTTCCT
1 TCTCTTCACTCTCCT
2623955 TCTCTT
1 TCTCTT
2623961 TAGTCTCTTC
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
14 1 0.04
15 27 0.96
ACGTcount: A:0.06, C:0.43, G:0.00, T:0.51
Consensus pattern (15 bp):
TCTCTTCACTCTCCT
Found at i:2629451 original size:14 final size:15
Alignment explanation
Indices: 2629432--2629465 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2629422 AACAAAATAA
2629432 TTTATTATAA-TATT
1 TTTATTATAACTATT
*
2629446 TTTATTATAACTTTT
1 TTTATTATAACTATT
2629461 TTTAT
1 TTTAT
2629466 AAAATAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTATTATAACTATT
Found at i:2631225 original size:23 final size:23
Alignment explanation
Indices: 2631181--2631225 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2631171 ATAAAATGGG
*
2631181 AAAACTTATTTCGATTCAAATTC
1 AAAACTTATTTCGATACAAATTC
*
2631204 AAAACTTGTTT-GATACAGAATT
1 AAAACTTATTTCGATACA-AATT
2631226 GTTCAGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
AAAACTTATTTCGATACAAATTC
Found at i:2631992 original size:31 final size:31
Alignment explanation
Indices: 2631957--2632017 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
2631947 ATGATCAAAA
* * *
2631957 TTGTTTTAAAATTAAAAATACAATAATAAAT
1 TTGTTTCAAAATAAAAAATAAAATAATAAAT
*
2631988 TTGTTTCAAAATAAAAAATAAAATGATAAA
1 TTGTTTCAAAATAAAAAATAAAATAATAAA
2632018 AATATATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.34
Consensus pattern (31 bp):
TTGTTTCAAAATAAAAAATAAAATAATAAAT
Found at i:2641760 original size:17 final size:18
Alignment explanation
Indices: 2641720--2641763 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2641710 AACGGAACTT
*
2641720 AATTATATATTTTTATTA
1 AATTTTATATTTTTATTA
*
2641738 ATTTTTATATTTTT-TTA
1 AATTTTATATTTTTATTA
2641755 AATTTTATA
1 AATTTTATA
2641764 AAATAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
AATTTTATATTTTTATTA
Found at i:2641800 original size:10 final size:10
Alignment explanation
Indices: 2641780--2641821 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
2641770 AAAATTATTT
*
2641780 TATATAAAAA
1 TATATTAAAA
*
2641790 TATATTTAAA
1 TATATTAAAA
2641800 TATATTAAAA
1 TATATTAAAA
*
2641810 TTTATTAAAA
1 TATATTAAAA
2641820 TA
1 TA
2641822 ACATATACAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TATATTAAAA
Done.