Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 72 of 125
Found at i:22612841 original size:42 final size:42
Alignment explanation
Indices: 22612782--22612861 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
22612772 AGTAAGTTAC
*
22612782 GACACAACAATTCGAATTTTTGAAAATAATAAGCATTTCTAG
1 GACACAACAATTCGAATTTTTGAAAATAACAAGCATTTCTAG
* *
22612824 GACACAATAATTCGAATTTTTGAACATAACAAGCATTT
1 GACACAACAATTCGAATTTTTGAAAATAACAAGCATTT
22612862 TTAATTGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.31
Consensus pattern (42 bp):
GACACAACAATTCGAATTTTTGAAAATAACAAGCATTTCTAG
Found at i:22613326 original size:18 final size:17
Alignment explanation
Indices: 22613271--22613327 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
22613261 CCTAACATAA
22613271 AAACAACTATATATAATT
1 AAACAACTATATA-AATT
* *
22613289 AAATAA-TAACTATAAGTT
1 AAACAACT-A-TATAAATT
22613307 AAACAACTATATACAATT
1 AAACAACTATATA-AATT
22613325 AAA
1 AAA
22613328 TAATAAGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
17 5 0.16
18 21 0.68
19 5 0.16
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.30
Consensus pattern (17 bp):
AAACAACTATATAAATT
Found at i:22613378 original size:8 final size:8
Alignment explanation
Indices: 22613356--22613421 Score: 51
Period size: 8 Copynumber: 7.6 Consensus size: 8
22613346 ATTAATGAAT
22613356 AAAATAAA
1 AAAATAAA
22613364 AATAATAAA
1 AA-AATAAA
22613373 AAAATAAA
1 AAAATAAA
22613381 TAATGAATAAA
1 -AA--AATAAA
* **
22613392 ATAATATG
1 AAAATAAA
*
22613400 AACATAAA
1 AAAATAAA
22613408 AAAAGTAAA
1 AAAA-TAAA
22613417 AAAAT
1 AAAAT
22613422 TAGGGTCAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
8 20 0.44
9 18 0.40
10 1 0.02
11 6 0.13
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.20
Consensus pattern (8 bp):
AAAATAAA
Found at i:22613397 original size:15 final size:16
Alignment explanation
Indices: 22613348--22613395 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
22613338 CAAGCAAAAT
22613348 TAATGAATAAAATAAAAA
1 TAATGAATAAAAT--AAA
*
22613366 TAAT-AAAAAAATAAA
1 TAATGAATAAAATAAA
22613381 TAATGAATAAAATAA
1 TAATGAATAAAATAA
22613396 TATGAACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 7 0.26
16 9 0.33
17 7 0.26
18 4 0.15
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (16 bp):
TAATGAATAAAATAAA
Found at i:22614625 original size:4 final size:4
Alignment explanation
Indices: 22614618--22614645 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
22614608 ATTTTTATTT
22614618 ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA
22614646 TTAGGTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:22638092 original size:17 final size:17
Alignment explanation
Indices: 22638057--22638117 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
22638047 CATTGATTTA
*
22638057 CAATGACAAGTGGAAATG
1 CAATGACAA-TGAAAATG
* *
22638075 CAATGATAATGCAAATG
1 CAATGACAATGAAAATG
* *
22638092 CAGTGACAATTAAAATG
1 CAATGACAATGAAAATG
22638109 CAATGACAA
1 CAATGACAA
22638118 AAGGGCTGTG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
17 28 0.78
18 8 0.22
ACGTcount: A:0.48, C:0.13, G:0.20, T:0.20
Consensus pattern (17 bp):
CAATGACAATGAAAATG
Found at i:22638582 original size:12 final size:12
Alignment explanation
Indices: 22638546--22638592 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
22638536 TTTGCCTCGA
22638546 CTTCTTTTCCTT
1 CTTCTTTTCCTT
*
22638558 CCTCTCTTT-CTT
1 CTTCT-TTTCCTT
22638570 CTTCTTTTCCTT
1 CTTCTTTTCCTT
22638582 CTTCTTCTTCC
1 CTTCTT-TTCC
22638593 ACTTCTTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 3 0.10
12 20 0.67
13 7 0.23
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (12 bp):
CTTCTTTTCCTT
Found at i:22638597 original size:24 final size:24
Alignment explanation
Indices: 22638545--22638599 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
22638535 ATTTGCCTCG
*
22638545 ACTTCTTTTCCTTCCTCTCTTTCT
1 ACTTCTTTTCCTTCCTCTCTTTCC
* *
22638569 TCTTCTTTTCCTTCTTCT-TCTTCC
1 ACTTCTTTTCCTTCCTCTCT-TTCC
22638593 ACTTCTT
1 ACTTCTT
22638600 CCACTTGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.04, C:0.36, G:0.00, T:0.60
Consensus pattern (24 bp):
ACTTCTTTTCCTTCCTCTCTTTCC
Found at i:22640213 original size:20 final size:21
Alignment explanation
Indices: 22640176--22640214 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
22640166 AAATCGAGTA
22640176 TCACTAAGTTAGAAAATGCAG
1 TCACTAAGTTAGAAAATGCAG
22640197 TCACTAAGTTA-AAAATGC
1 TCACTAAGTTAGAAAATGC
22640215 TAAAAATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (21 bp):
TCACTAAGTTAGAAAATGCAG
Found at i:22652934 original size:11 final size:12
Alignment explanation
Indices: 22652913--22652959 Score: 71
Period size: 11 Copynumber: 4.1 Consensus size: 12
22652903 TTAATGAATA
22652913 AAATAAAATAAT
1 AAATAAAATAAT
22652925 AAAT-AAATAAT
1 AAATAAAATAAT
*
22652936 GAAT-AAATAAT
1 AAATAAAATAAT
22652947 AAATAAAATAAT
1 AAATAAAATAAT
22652959 A
1 A
22652960 TGAACATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 20 0.62
12 12 0.38
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (12 bp):
AAATAAAATAAT
Found at i:22654389 original size:40 final size:40
Alignment explanation
Indices: 22654344--22654446 Score: 145
Period size: 40 Copynumber: 2.6 Consensus size: 40
22654334 ACAAAAAATA
22654344 CCGCAAAAAGTAAAGTAATAGCGGCATTTTTCCATAAACG
1 CCGCAAAAAGTAAAGTAATAGCGGCATTTTTCCATAAACG
* ** * *
22654384 CCGCAAAAAGTAAAGCAATAGTAGCGTTTTTTCATAAACG
1 CCGCAAAAAGTAAAGTAATAGCGGCATTTTTCCATAAACG
22654424 CCGC-AAAAGATAAAGTAATAGCG
1 CCGCAAAAAG-TAAAGTAATAGCG
22654447 ACGTTTATGA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
39 5 0.09
40 49 0.91
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.21
Consensus pattern (40 bp):
CCGCAAAAAGTAAAGTAATAGCGGCATTTTTCCATAAACG
Found at i:22654504 original size:41 final size:40
Alignment explanation
Indices: 22654442--22654670 Score: 239
Period size: 41 Copynumber: 5.6 Consensus size: 40
22654432 GATAAAGTAA
* *
22654442 TAGCGACGTTTATGAGAAAAACGCAACAAAAAGTAAGAGCAT
1 TAGCGGCGTTTATGAG-AAAACGC-GCAAAAAGTAAGAGCAT
* *
22654484 TAGCGGCGTTTATGGGAAAACGC-CGAAAAATGTAAGAACAT
1 TAGCGGCGTTTATGAGAAAACGCGC-AAAAA-GTAAGAGCAT
* *
22654525 TAGTGGCGTTTATGGGAAAACGTCGC-AAAAGATAAGAGCAT
1 TAGCGGCGTTTATGAGAAAACG-CGCAAAAAG-TAAGAGCAT
* *
22654566 TAGCTGCGTTTATGAGAAAACGCCGCAAAAAGTAAGAGTAT
1 TAGCGGCGTTTATGAGAAAACG-CGCAAAAAGTAAGAGCAT
* * *
22654607 TAGTGGCGTTTATGAGAAAACACCGCAACAAA-TAAAAGCAT
1 TAGCGGCGTTTATGAGAAAAC-GCGCAA-AAAGTAAGAGCAT
* *
22654648 TAGTGGCTTTTATGAGAAAACGC
1 TAGCGGCGTTTATGAGAAAACGC
22654671 CGCTAAAGGT
Statistics
Matches: 162, Mismatches: 17, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
39 1 0.01
40 7 0.04
41 130 0.80
42 23 0.14
43 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.21
Consensus pattern (40 bp):
TAGCGGCGTTTATGAGAAAACGCGCAAAAAGTAAGAGCAT
Found at i:22654545 original size:82 final size:81
Alignment explanation
Indices: 22654448--22654673 Score: 269
Period size: 82 Copynumber: 2.7 Consensus size: 81
22654438 GTAATAGCGA
* * *
22654448 CGTTTATGAGAAAAACGCAACAAAAAGTAAGAGCATTAGCGGCGTTTATGGGAAAACGCCG-AAA
1 CGTTTATG-GGAAAACGC-GCAAAAAGTAAGAGCATTAGCGGCGTTTATGAGAAAACGCCGCAAA
22654512 AATGTAAGAACATTAGTGG
64 AA-GTAAGAACATTAGTGG
*
22654531 CGTTTATGGGAAAACGTCGC-AAAAGATAAGAGCATTAGCTGCGTTTATGAGAAAACGCCGCAAA
1 CGTTTATGGGAAAACG-CGCAAAAAG-TAAGAGCATTAGCGGCGTTTATGAGAAAACGCCGCAAA
**
22654595 AAGTAAGAGTATTAGTGG
64 AAGTAAGAACATTAGTGG
* * * * *
22654613 CGTTTATGAGAAAACACCGCAACAAA-TAAAAGCATTAGTGGCTTTTATGAGAAAACGCCGC
1 CGTTTATGGGAAAAC-GCGCAA-AAAGTAAGAGCATTAGCGGCGTTTATGAGAAAACGCCGC
22654674 TAAAGGTTAA
Statistics
Matches: 125, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
81 5 0.04
82 102 0.82
83 15 0.12
84 3 0.02
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (81 bp):
CGTTTATGGGAAAACGCGCAAAAAGTAAGAGCATTAGCGGCGTTTATGAGAAAACGCCGCAAAAA
GTAAGAACATTAGTGG
Found at i:22654586 original size:123 final size:123
Alignment explanation
Indices: 22654419--22654698 Score: 354
Period size: 123 Copynumber: 2.3 Consensus size: 123
22654409 GTTTTTTCAT
*
22654419 AAACGCCGCAAAAGATAAAGTAATAGCGACGTTTATGAGAAAAACGCAACAAAAAGTAAGAGCAT
1 AAACGCCGCAAAAGATAAAGCAATAGCGACGTTTATGAGAAAAACGCAACAAAAAGTAAGAGCAT
* * *
22654484 TAGCGGCGTTTATGGGAAAACGCCG-AA-AAATGTAAGAA-CATTAGTGGCGTTTATGGGA
66 TAGCGGCGTTTATGAGAAAACACCGCAACAAA--TAA-AAGCATTAGTGGCGTTTATGAGA
* * ** *
22654542 AAACGTCGCAAAAGATAAGAGCATTAGCTG-CGTTTATGAG-AAAACGCCGCAAAAAGTAAGAGT
1 AAACGCCGCAAAAGATAA-AGCAATAGC-GACGTTTATGAGAAAAACGCAACAAAAAGTAAGAGC
* *
22654605 ATTAGTGGCGTTTATGAGAAAACACCGCAACAAATAAAAGCATTAGTGGCTTTTATGAGA
64 ATTAGCGGCGTTTATGAGAAAACACCGCAACAAATAAAAGCATTAGTGGCGTTTATGAGA
* * *
22654665 AAACGCCGCTAAAGGTTAAGCAATAGCGACGTTT
1 AAACGCCGCAAAAGATAAAGCAATAGCGACGTTT
22654699 TCCCATAAAC
Statistics
Matches: 135, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
121 1 0.01
122 15 0.11
123 96 0.71
124 19 0.14
125 4 0.03
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (123 bp):
AAACGCCGCAAAAGATAAAGCAATAGCGACGTTTATGAGAAAAACGCAACAAAAAGTAAGAGCAT
TAGCGGCGTTTATGAGAAAACACCGCAACAAATAAAAGCATTAGTGGCGTTTATGAGA
Found at i:22665359 original size:21 final size:21
Alignment explanation
Indices: 22665335--22665405 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
22665325 GAATTTCAGC
* *
22665335 AGCAATCTATAGATTTTCAAA
1 AGCAAACTATAAATTTTCAAA
** * *
22665356 AGCAAACTGCATATTTTCAAC
1 AGCAAACTATAAATTTTCAAA
*
22665377 AGTAAACTATAAATTTTCAAA
1 AGCAAACTATAAATTTTCAAA
*
22665398 AGAAAACT
1 AGCAAACT
22665406 GAGGCATCTA
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.30
Consensus pattern (21 bp):
AGCAAACTATAAATTTTCAAA
Found at i:22669185 original size:20 final size:22
Alignment explanation
Indices: 22669160--22669199 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
22669150 CCAATATTTT
22669160 TTTTATTT-TTT-TATTTTTAG
1 TTTTATTTATTTATATTTTTAG
22669180 TTTTATTTATTTATATTTTT
1 TTTTATTTATTTATATTTTT
22669200 TCTATTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 3 0.17
22 7 0.39
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (22 bp):
TTTTATTTATTTATATTTTTAG
Found at i:22669188 original size:16 final size:15
Alignment explanation
Indices: 22669154--22669198 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 15
22669144 GGCAACCCAA
22669154 TATTT-TTTTTATTT
1 TATTTATTTTTATTT
22669168 T-TTTATTTTTAGTTT
1 TATTTATTTTTA-TTT
*
22669183 TATTTATTTATATTT
1 TATTTATTTTTATTT
22669198 T
1 T
22669199 TTCTATTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 3 0.11
14 7 0.26
15 8 0.30
16 9 0.33
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (15 bp):
TATTTATTTTTATTT
Found at i:22670133 original size:92 final size:93
Alignment explanation
Indices: 22669994--22670169 Score: 246
Period size: 92 Copynumber: 1.9 Consensus size: 93
22669984 TCGGAGTGTG
* * * *
22669994 TTAGACTGAGTAACCGGGCTGGAGTACTTGGTTGTCATTTCACTTCGCGTCAAAAGGGCTAACGC
1 TTAGACTGAGTAACCGGGATGAAGTACTTGGGTGTCATTTCACTTCGCATCAAAAGGGCTAACGC
*
22670059 ATTC-TAAATAAAAAAAATGAGTGCATA
66 ATTCTTAAAGAAAAAAAATGAGTGCATA
* * * * * *
22670086 TTAGGCTGAGTAACCGGGATGAAGTGCTTGGGTGTCATTTCATTTCGCATCAAAAGGTCTAATGT
1 TTAGACTGAGTAACCGGGATGAAGTACTTGGGTGTCATTTCACTTCGCATCAAAAGGGCTAACGC
22670151 ATTCTTAAAGAAAAAAAAT
66 ATTCTTAAAGAAAAAAAAT
22670170 AAAATTGAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
92 59 0.82
93 13 0.18
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (93 bp):
TTAGACTGAGTAACCGGGATGAAGTACTTGGGTGTCATTTCACTTCGCATCAAAAGGGCTAACGC
ATTCTTAAAGAAAAAAAATGAGTGCATA
Found at i:22672055 original size:19 final size:18
Alignment explanation
Indices: 22672025--22672064 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
22672015 AACTAAATTA
22672025 ACAAAAAGAAATGCAATG
1 ACAAAAAGAAATGCAATG
22672043 ACAAAATAGAAATGCAATG
1 ACAAAA-AGAAATGCAATG
22672062 ACA
1 ACA
22672065 GTAAAATGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.60, C:0.12, G:0.15, T:0.12
Consensus pattern (18 bp):
ACAAAAAGAAATGCAATG
Found at i:22673703 original size:52 final size:52
Alignment explanation
Indices: 22673625--22673970 Score: 575
Period size: 52 Copynumber: 6.7 Consensus size: 52
22673615 ATTCCATTTA
* * * * * *
22673625 ATACTCACGATGACACATAATCATCGGACCTCTTAAACCGTGAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
*
22673677 ATACTCACGATGACATATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
22673729 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
22673781 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
*
22673833 ATACTCACGATGACACATAATCATCGGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* * *
22673885 ATACTCATGATGACACATAGTCATAGGACCTTTTAACCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* *
22673937 ATACTCACGATGACACATAGTTATTGGACCTTTT
1 ATACTCACGATGACACATAGTCATCGGACCTTTT
22673971 CTTTATTTAC
Statistics
Matches: 278, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 278 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.29
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
Found at i:22678286 original size:15 final size:14
Alignment explanation
Indices: 22678261--22678298 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
22678251 GCAAAGAAAT
*
22678261 TAAAATGAAACAAG
1 TAAAATGAAACAAA
22678275 TAAAATTGAAACAAA
1 TAAAA-TGAAACAAA
22678290 TAAAA-GAAA
1 TAAAATGAAA
22678299 ATGTGAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 4 0.18
14 5 0.23
15 13 0.59
ACGTcount: A:0.68, C:0.05, G:0.11, T:0.16
Consensus pattern (14 bp):
TAAAATGAAACAAA
Found at i:22684830 original size:12 final size:13
Alignment explanation
Indices: 22684807--22684847 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
22684797 TGAAAATAAG
22684807 AAAAAGAAAGAAAA
1 AAAAAG-AAGAAAA
22684821 AAAAAG-AGAAAA
1 AAAAAGAAGAAAA
*
22684833 GAAAAGAAGAAAA
1 AAAAAGAAGAAAA
22684846 AA
1 AA
22684848 TGTTTTCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 11 0.46
13 7 0.29
14 6 0.25
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAGAAGAAAA
Found at i:22684830 original size:22 final size:22
Alignment explanation
Indices: 22684799--22684847 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
22684789 TTAAAAAATG
*
22684799 AAAATAAGA-AAAAG-AAAGAA
1 AAAAAAAGAGAAAAGAAAAGAA
22684819 AAAAAAAGAGAAAAGAAAAGAA
1 AAAAAAAGAGAAAAGAAAAGAA
*
22684841 GAAAAAA
1 AAAAAAA
22684848 TGTTTTCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.32
21 5 0.20
22 12 0.48
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (22 bp):
AAAAAAAGAGAAAAGAAAAGAA
Found at i:22684847 original size:10 final size:10
Alignment explanation
Indices: 22684799--22684847 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
22684789 TTAAAAAATG
*
22684799 AAAATAAGAA
1 AAAAAAAGAA
*
22684809 AAAGAAAGAA
1 AAAAAAAGAA
22684819 AAAAAAAGAGA
1 AAAAAAAGA-A
22684830 AAAGAAAAGAA
1 AAA-AAAAGAA
22684841 GAAAAAA
1 -AAAAAA
22684848 TGTTTTCTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
10 16 0.48
11 8 0.24
12 9 0.27
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:22690114 original size:16 final size:18
Alignment explanation
Indices: 22690093--22690131 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
22690083 TGTTTGATGG
*
22690093 AAATAGAT-CCAAGAA-T
1 AAATAGATGACAAGAATT
22690109 AAATAGATGACAAGAATT
1 AAATAGATGACAAGAATT
22690127 AAATA
1 AAATA
22690132 AGAATCAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 6 0.30
18 6 0.30
ACGTcount: A:0.59, C:0.08, G:0.13, T:0.21
Consensus pattern (18 bp):
AAATAGATGACAAGAATT
Found at i:22690687 original size:3 final size:3
Alignment explanation
Indices: 22690679--22690729 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
22690669 CCCAAACCAA
* *
22690679 AAT AAT AAT GAC AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
22690726 AAT A
1 AAT A
22690730 TGATGTAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:22691841 original size:20 final size:20
Alignment explanation
Indices: 22691802--22691863 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
22691792 AACGGTCAAA
* * *
22691802 GTCAACGATCAAGGTTAACG
1 GTCAACGATTAAAGTCAACG
22691822 GTCAACGATTAAAGTCAACG
1 GTCAACGATTAAAGTCAACG
* *
22691842 ATCAACGGTTAACAGTCAACG
1 GTCAACGATTAA-AGTCAACG
22691863 G
1 G
22691864 CCGGTCAACG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
20 27 0.77
21 8 0.23
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (20 bp):
GTCAACGATTAAAGTCAACG
Found at i:22695770 original size:24 final size:24
Alignment explanation
Indices: 22695737--22695806 Score: 113
Period size: 24 Copynumber: 2.9 Consensus size: 24
22695727 TCGTTAACAT
*
22695737 TGTTCGTGAACATGTTCAATTATA
1 TGTTCATGAACATGTTCAATTATA
22695761 TGTTCATGAACATGTTCAATTATA
1 TGTTCATGAACATGTTCAATTATA
* *
22695785 CGTTCATGAACATGTTCGATTA
1 TGTTCATGAACATGTTCAATTA
22695807 AGTTAAATGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (24 bp):
TGTTCATGAACATGTTCAATTATA
Found at i:22697265 original size:18 final size:20
Alignment explanation
Indices: 22697247--22697300 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
22697237 TTAAAAATAT
22697247 AATA-TTTGAATTTTTTATA
1 AATATTTTGAATTTTTTATA
*
22697266 AATATTTTGAA--TTTTAAA
1 AATATTTTGAATTTTTTATA
22697284 AATTATTTTG-ATTTTTT
1 AA-TATTTTGAATTTTTT
22697301 TTAATTTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 9 0.30
19 11 0.37
20 10 0.33
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (20 bp):
AATATTTTGAATTTTTTATA
Found at i:22697290 original size:19 final size:17
Alignment explanation
Indices: 22697259--22697298 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
22697249 TATTTGAATT
*
22697259 TTTTATAAATATTTTGAA
1 TTTTAAAAATATTTTG-A
22697277 TTTTAAAAATTATTTTGA
1 TTTTAAAAA-TATTTTGA
22697295 TTTT
1 TTTT
22697299 TTTTAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (17 bp):
TTTTAAAAATATTTTGA
Found at i:22697306 original size:19 final size:19
Alignment explanation
Indices: 22697251--22697306 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
22697241 AAATATAATA
*
22697251 TTTGAATTTTTTATAAATAT
1 TTTG-ATTTTTTATAATTAT
* * *
22697271 TTTGAATTTTAAAAATTAT
1 TTTGATTTTTTATAATTAT
*
22697290 TTTGATTTTTTTTAATT
1 TTTGATTTTTTATAATT
22697307 TTTGTTGAGA
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
19 24 0.86
20 4 0.14
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTGATTTTTTATAATTAT
Found at i:22700932 original size:61 final size:63
Alignment explanation
Indices: 22700860--22700987 Score: 152
Period size: 63 Copynumber: 2.1 Consensus size: 63
22700850 GTTCAATATG
* * *
22700860 GTACTTGTAC-TT-TGAAAATGTCTACTTTGATACCTGAACTATCAATATGTGCTTTATTATA
1 GTACTTGTACTTTCTGAAAATGTCCACTGTAATACCTGAACTATCAATATGTGCTTTATTATA
* * * * * * *
22700921 GTACTTGTACTTTCTTAAAATGTCCAGTGTAATGCTTGAATTATCAATATGTGTTTTATTATG
1 GTACTTGTACTTTCTGAAAATGTCCACTGTAATACCTGAACTATCAATATGTGCTTTATTATA
22700984 GTAC
1 GTAC
22700988 ATGATGTTAA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
61 10 0.18
62 2 0.04
63 43 0.78
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (63 bp):
GTACTTGTACTTTCTGAAAATGTCCACTGTAATACCTGAACTATCAATATGTGCTTTATTATA
Found at i:22701522 original size:59 final size:59
Alignment explanation
Indices: 22701443--22701577 Score: 198
Period size: 59 Copynumber: 2.3 Consensus size: 59
22701433 ACATTTTATG
* * * * * *
22701443 AAAGTGCAAGCACCATAATAAAGCATATTAATAGTTTAGGTATTACATTGGGTATTTTC
1 AAAGTACAAGTACCACAATAAAGCATATTAATAGTTCAGGTATCACATTGGATATTTTC
22701502 AAAGTACAAGTACCACAATAAAGCATATTAATAGTTCAGGTATCACATTGGATATTTTC
1 AAAGTACAAGTACCACAATAAAGCATATTAATAGTTCAGGTATCACATTGGATATTTTC
* *
22701561 AAAATATAAGTACCACA
1 AAAGTACAAGTACCACA
22701578 TTAGATATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 68 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (59 bp):
AAAGTACAAGTACCACAATAAAGCATATTAATAGTTCAGGTATCACATTGGATATTTTC
Found at i:22703216 original size:33 final size:34
Alignment explanation
Indices: 22703155--22703222 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 34
22703145 TGTTATGTTA
* *
22703155 TGCTTGAAAGTTTTGTTAAGGGATTACTTATATT
1 TGCTTGAAAGTTTTGTTAAGGAACTACTTATATT
*
22703189 TGCTTGAAAG-TTTGTTAATGAACTACTTATATT
1 TGCTTGAAAGTTTTGTTAAGGAACTACTTATATT
22703222 T
1 T
22703223 ATATTAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
33 21 0.68
34 10 0.32
ACGTcount: A:0.28, C:0.07, G:0.18, T:0.47
Consensus pattern (34 bp):
TGCTTGAAAGTTTTGTTAAGGAACTACTTATATT
Found at i:22708058 original size:24 final size:24
Alignment explanation
Indices: 22707991--22708059 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
22707981 GTGGATATTC
*
22707991 AACCTTTCACCTTTCATCTCCATT
1 AACCTTTCACCTTTCATCTTCATT
* * **
22708015 AACCTTCCACCTTTTATCTTTTTT
1 AACCTTTCACCTTTCATCTTCATT
*
22708039 AACCTTTAACCTTTCATCTTC
1 AACCTTTCACCTTTCATCTTC
22708060 TTGTAATCCT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.20, C:0.33, G:0.00, T:0.46
Consensus pattern (24 bp):
AACCTTTCACCTTTCATCTTCATT
Found at i:22716440 original size:52 final size:52
Alignment explanation
Indices: 22716357--22716716 Score: 335
Period size: 52 Copynumber: 6.7 Consensus size: 52
22716347 GTAAATAAAG
*
22716357 AAAAGGTCCGATGACTTTGTGTCATCGTGAGTATATGAATCCTTTATGGATT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
* * * *
22716409 AAAAGATTCGATGACTATGTGTTATCATGAGTATATGAATCCTTTATGGATT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
* *
22716461 AAAAGGTCCAATGACTATGTGTCATCGTCATCGTGAGTATATGAATTCTTTATGGATT
1 AAAAGGTCCGATGACTA--TG---T-GTCATCGTGAGTATATGAATCCTTTATGGATT
* * *
22716519 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGATTCCTTCACGGATT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
* * * * ** * *
22716571 AAGAGGTTCGTTGGCTATGTGTCATCGTGAGTATTAAATGTAATGAATTTCATTACAGAAT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTA-T--ATG-AAT-CCTTT-A-T--GGATT
* * * * * *
22716632 -AAAGGTTCGATGACTATGTGCCATCGTGAGTATATGATTCCTTCACGGATC
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
* * *
22716683 AAGAGGTCTGTTGACTATGTGTCATCGTGAGTAT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTAT
22716717 TAAATGGAAT
Statistics
Matches: 248, Mismatches: 44, Indels: 32
0.77 0.14 0.10
Matches are distributed among these distances:
51 2 0.01
52 146 0.59
53 2 0.01
54 3 0.01
55 5 0.02
56 6 0.02
57 6 0.02
58 46 0.19
59 1 0.00
60 28 0.11
61 3 0.01
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (52 bp):
AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
Found at i:22716526 original size:58 final size:58
Alignment explanation
Indices: 22716377--22716546 Score: 253
Period size: 58 Copynumber: 3.0 Consensus size: 58
22716367 ATGACTTTGT
* *
22716377 GTCATCGTGAGTATATGAATCCTTTATGGATTAAAAGATTCGATGACTATGTG---T-
1 GTCATCGTGAGTATATGAATCCTTTATGGATTAAAAGGTCCGATGACTATGTGTCATC
* *
22716431 -T-ATCATGAGTATATGAATCCTTTATGGATTAAAAGGTCCAATGACTATGTGTCATC
1 GTCATCGTGAGTATATGAATCCTTTATGGATTAAAAGGTCCGATGACTATGTGTCATC
*
22716487 GTCATCGTGAGTATATGAATTCTTTATGGATTAAAAGGTCCGATGACTATGTGTCATC
1 GTCATCGTGAGTATATGAATCCTTTATGGATTAAAAGGTCCGATGACTATGTGTCATC
22716545 GT
1 GT
22716547 GAGTATATGA
Statistics
Matches: 103, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
52 46 0.45
53 1 0.01
55 1 0.01
57 1 0.01
58 54 0.52
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.36
Consensus pattern (58 bp):
GTCATCGTGAGTATATGAATCCTTTATGGATTAAAAGGTCCGATGACTATGTGTCATC
Found at i:22716550 original size:110 final size:110
Alignment explanation
Indices: 22716377--22716710 Score: 402
Period size: 110 Copynumber: 3.0 Consensus size: 110
22716367 ATGACTTTGT
* * * *
22716377 GTCATCGTGAGTATATGAATCCTTTATGGATTAAAAGATTCGATGACTATGTGTTATCATGAGTA
1 GTCATCGTGAGTATATGAATTCTTTATGGATTAAAAGGTTCGATGACTATGTGTCATCGTGAGTA
* * * * **
22716442 TATGAATCCTTTATGGATTAAAAGGTCCAATGACTATGTGTCATC
66 TATGATTCCTTCACGGATTAAGAGGTCCGTTGACTATGTGTCATC
*
22716487 GTCATCGTGAGTATATGAATTCTTTATGGATTAAAAGGTCCGATGACTATGTGTCATCGTGAGTA
1 GTCATCGTGAGTATATGAATTCTTTATGGATTAAAAGGTTCGATGACTATGTGTCATCGTGAGTA
* *
22716552 TATGATTCCTTCACGGATTAAGAGGTTCGTTGGCTATGTGTCATC
66 TATGATTCCTTCACGGATTAAGAGGTCCGTTGACTATGTGTCATC
* ** * * ** * *
22716597 GTGAGTATTAAATGTA-ATGAATTTCATTACAGAAT-AAAGGTTCGATGACTATGTGCCATCGTG
1 GTCA-TCGT-GA-GTATATGAA-TTCTTTATGGATTAAAAGGTTCGATGACTATGTGTCATCGTG
* *
22716660 AGTATATGATTCCTTCACGGATCAAGAGGTCTGTTGACTATGTGTCATC
62 AGTATATGATTCCTTCACGGATTAAGAGGTCCGTTGACTATGTGTCATC
22716709 GT
1 GT
22716711 GAGTATTAAA
Statistics
Matches: 193, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
110 100 0.52
111 2 0.01
112 79 0.41
113 12 0.06
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (110 bp):
GTCATCGTGAGTATATGAATTCTTTATGGATTAAAAGGTTCGATGACTATGTGTCATCGTGAGTA
TATGATTCCTTCACGGATTAAGAGGTCCGTTGACTATGTGTCATC
Found at i:22716774 original size:112 final size:112
Alignment explanation
Indices: 22716520--22716776 Score: 399
Period size: 112 Copynumber: 2.3 Consensus size: 112
22716510 TTATGGATTA
* * *
22716520 AAAGGTCCGATGACTATGTGTCATCGTGAGTATATGATTCCTTCACGGATTAAGAGGTTCGTTGG
1 AAAGGTTCGATGACTATGTGTCATCGTGAGTATATGATTCCTTCACGGATCAAGAGGTTCGTTGA
* *
22716585 CTATGTGTCATCGTGAGTATTAAATGTAATGAATTTCATTACAGAAT
66 CTATGTGTCATCGTGAGTATTAAATGGAATGAATTCCATTACAGAAT
*
22716632 AAAGGTTCGATGACTATGTGCCATCGTGAGTATATGATTCCTTCACGGATCAAGAGG-TCTGTTG
1 AAAGGTTCGATGACTATGTGTCATCGTGAGTATATGATTCCTTCACGGATCAAGAGGTTC-GTTG
*
22716696 ACTATGTGTCATCGTGAGTATTAAATGGAATGAATTCCATTACGGAAT
65 ACTATGTGTCATCGTGAGTATTAAATGGAATGAATTCCATTACAGAAT
* * * *
22716744 AAAGGTTCGATGGCTCTGTATCATCATGAGTAT
1 AAAGGTTCGATGACTATGTGTCATCGTGAGTAT
22716777 CAAATGCAAA
Statistics
Matches: 132, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
111 2 0.02
112 130 0.98
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.33
Consensus pattern (112 bp):
AAAGGTTCGATGACTATGTGTCATCGTGAGTATATGATTCCTTCACGGATCAAGAGGTTCGTTGA
CTATGTGTCATCGTGAGTATTAAATGGAATGAATTCCATTACAGAAT
Found at i:22720457 original size:3 final size:3
Alignment explanation
Indices: 22720449--22720505 Score: 62
Period size: 3 Copynumber: 17.7 Consensus size: 3
22720439 CATTTCCTTT
22720449 TTA TTA TTA TTTA TTA TTA TTA TTA TCTGA TTTA GTTA TT- TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA T-T-A -TTA -TTA TTA TTA TTA
22720495 TTA TTA TTA TT
1 TTA TTA TTA TT
22720506 GTTGTTGTTG
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
2 2 0.04
3 35 0.73
4 8 0.17
5 2 0.04
6 1 0.02
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:22720521 original size:15 final size:15
Alignment explanation
Indices: 22720501--22720529 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
22720491 ATTATTATTA
22720501 TTATTGTTGTTGTTG
1 TTATTGTTGTTGTTG
22720516 TTATTGTTGTTGTT
1 TTATTGTTGTTGTT
22720530 ATTCCTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.24, T:0.69
Consensus pattern (15 bp):
TTATTGTTGTTGTTG
Found at i:22720522 original size:12 final size:12
Alignment explanation
Indices: 22720507--22720532 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
22720497 ATTATTATTG
22720507 TTGTTGTTGTTA
1 TTGTTGTTGTTA
22720519 TTGTTGTTGTTA
1 TTGTTGTTGTTA
22720531 TT
1 TT
22720533 CCTATTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.23, T:0.69
Consensus pattern (12 bp):
TTGTTGTTGTTA
Found at i:22722051 original size:25 final size:23
Alignment explanation
Indices: 22722020--22722074 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
22722010 ATTGATCTCA
22722020 TTTATTTCTAGTTGCT-TTATTTATT
1 TTTATTTCTAGTTG-TATT-TTTA-T
*
22722045 TTTATTTTTAGTTGTATTTTTAT
1 TTTATTTCTAGTTGTATTTTTAT
22722068 TTTATTT
1 TTTATTT
22722075 TTGATTGTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 8 0.29
24 5 0.18
25 15 0.54
ACGTcount: A:0.16, C:0.04, G:0.07, T:0.73
Consensus pattern (23 bp):
TTTATTTCTAGTTGTATTTTTAT
Found at i:22722070 original size:5 final size:6
Alignment explanation
Indices: 22722039--22722094 Score: 60
Period size: 6 Copynumber: 9.2 Consensus size: 6
22722029 AGTTGCTTTA
* * *
22722039 TTTATT TTTATT TTTAGT TGTATT TTTA-T TTTATT TTTGATT GTTCATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTT-ATT -TTTATT
22722088 TTTATT T
1 TTTATT T
22722095 GTGAGACCTC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
5 5 0.12
6 28 0.68
7 6 0.15
8 2 0.05
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.75
Consensus pattern (6 bp):
TTTATT
Found at i:22727720 original size:19 final size:20
Alignment explanation
Indices: 22727698--22727744 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
22727688 GAATAAAACG
22727698 AAAACCAAAACACAA-CCCA
1 AAAACCAAAACACAATCCCA
**
22727717 AAAA-CAAAATGCAATCCCA
1 AAAACCAAAACACAATCCCA
22727736 AAAATCCAA
1 AAAA-CCAA
22727745 GAATAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 8 0.35
19 12 0.52
21 3 0.13
ACGTcount: A:0.62, C:0.30, G:0.02, T:0.06
Consensus pattern (20 bp):
AAAACCAAAACACAATCCCA
Found at i:22727724 original size:18 final size:19
Alignment explanation
Indices: 22727698--22727739 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
22727688 GAATAAAACG
*
22727698 AAAACCAAAACACAA-CCC
1 AAAAACAAAACACAATCCC
**
22727716 AAAAACAAAATGCAATCCC
1 AAAAACAAAACACAATCCC
22727735 AAAAA
1 AAAAA
22727740 TCCAAGAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.64, C:0.29, G:0.02, T:0.05
Consensus pattern (19 bp):
AAAAACAAAACACAATCCC
Found at i:22728075 original size:20 final size:20
Alignment explanation
Indices: 22728050--22728089 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
22728040 TAAATCATAC
22728050 CATATCG-GATCATATAATAT
1 CATATCGAG-TCATATAATAT
*
22728070 CATATCGAGTCATATCATAT
1 CATATCGAGTCATATAATAT
22728090 AATGCCTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (20 bp):
CATATCGAGTCATATAATAT
Found at i:22728766 original size:36 final size:36
Alignment explanation
Indices: 22728726--22728819 Score: 134
Period size: 36 Copynumber: 2.6 Consensus size: 36
22728716 TACACAATCA
22728726 GCATGATTTCACAAGACCGTGTGCCCTACACGACCT
1 GCATGATTTCACAAGACCGTGTGCCCTACACGACCT
* * * * *
22728762 GCATGATTTCACATGATCGTGTGGCCTACATGGCCT
1 GCATGATTTCACAAGACCGTGTGCCCTACACGACCT
*
22728798 GCATGATTTCACACGACCGTGT
1 GCATGATTTCACAAGACCGTGT
22728820 TCCTCACAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (36 bp):
GCATGATTTCACAAGACCGTGTGCCCTACACGACCT
Found at i:22732081 original size:35 final size:35
Alignment explanation
Indices: 22732035--22732113 Score: 131
Period size: 35 Copynumber: 2.3 Consensus size: 35
22732025 CCCTTTTCAA
* *
22732035 GGTGTCACCCCGAAGGATCTATATACCGTTTACAT
1 GGTGTCACCCCGAAGGACCTATATACCATTTACAT
*
22732070 GGTGTCGCCCCGAAGGACCTATATACCATTTACAT
1 GGTGTCACCCCGAAGGACCTATATACCATTTACAT
22732105 GGTGTCACC
1 GGTGTCACC
22732114 TTGAAAGACC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.27
Consensus pattern (35 bp):
GGTGTCACCCCGAAGGACCTATATACCATTTACAT
Found at i:22734287 original size:29 final size:29
Alignment explanation
Indices: 22734230--22734298 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
22734220 TATTATTTTT
* * **
22734230 AGTTAAATTTGACCCTCAACCTTTTAAAA
1 AGTTAAATTTAACCATCAACCTTCCAAAA
*
22734259 AGTTGAATTTAACCATCAACCTTCCAAAA
1 AGTTAAATTTAACCATCAACCTTCCAAAA
22734288 TGAGTTAAATT
1 --AGTTAAATT
22734299 GTTGTTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 24 0.75
31 8 0.25
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (29 bp):
AGTTAAATTTAACCATCAACCTTCCAAAA
Found at i:22735593 original size:26 final size:28
Alignment explanation
Indices: 22735546--22735627 Score: 66
Period size: 27 Copynumber: 3.0 Consensus size: 28
22735536 TTCAGATGAC
* *
22735546 TATATAAAATTTTTTAATAAATAAAAAA
1 TATATAAAATTTATGAATAAATAAAAAA
22735574 TATATAAAA-TTATGAA-AAATTAAAATAA
1 TATATAAAATTTATGAATAAA-TAAAA-AA
* *
22735602 -AT-TAAATATTT-TAAAAAAATAAAAAA
1 TATATAAA-ATTTATGAATAAATAAAAAA
22735628 AATAATATGG
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
26 9 0.20
27 21 0.46
28 16 0.35
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (28 bp):
TATATAAAATTTATGAATAAATAAAAAA
Found at i:22735634 original size:25 final size:25
Alignment explanation
Indices: 22735564--22735635 Score: 63
Period size: 27 Copynumber: 2.7 Consensus size: 25
22735554 ATTTTTTAAT
* *
22735564 AAATAAAAAATATATAAAATTATGAAA
1 AAATAAAAAA-A-ATAATATTATAAAA
* * *
22735591 AATTAAAATAAATTAAATATTTTAAAA
1 AAATAAAA-AAAAT-AATATTATAAAA
22735618 AAATAAAAAAAATAATAT
1 AAATAAAAAAAATAATAT
22735636 GGGAGGACTT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
25 5 0.14
26 5 0.14
27 24 0.67
28 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.29
Consensus pattern (25 bp):
AAATAAAAAAAATAATATTATAAAA
Found at i:22736783 original size:3 final size:3
Alignment explanation
Indices: 22736775--22736799 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
22736765 TTTTGTTTGG
22736775 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
22736800 GTACCAGATG
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:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:22738035 original size:56 final size:56
Alignment explanation
Indices: 22737949--22738059 Score: 186
Period size: 56 Copynumber: 2.0 Consensus size: 56
22737939 AAAAATATTG
*
22737949 TAATACCCTAAAACCCGTTACCGTTATCGGTTAGGGTCCCGAGGTCATCCAACCTA
1 TAATACCCTAAAACCCGTTACCGTCATCGGTTAGGGTCCCGAGGTCATCCAACCTA
* * *
22738005 TAATACCCTAAAACTCGTTACCGTCGTCGGTTAGGGTCTCGAGGTCATCCAACCT
1 TAATACCCTAAAACCCGTTACCGTCATCGGTTAGGGTCCCGAGGTCATCCAACCT
22738060 TATACCGCAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (56 bp):
TAATACCCTAAAACCCGTTACCGTCATCGGTTAGGGTCCCGAGGTCATCCAACCTA
Found at i:22738308 original size:21 final size:21
Alignment explanation
Indices: 22738256--22738308 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
22738246 ATTCAAAAAT
* *
22738256 AGTGTAGACTTCTACCGATACT
1 AGTGT-GACTTATACCGATACA
*
22738278 TGTGAT-ACTTATACCGATACA
1 AGTG-TGACTTATACCGATACA
22738299 AGTGTGACTT
1 AGTGTGACTT
22738309 CTACTAAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
20 1 0.04
21 20 0.80
22 3 0.12
23 1 0.04
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (21 bp):
AGTGTGACTTATACCGATACA
Found at i:22740327 original size:41 final size:43
Alignment explanation
Indices: 22740250--22740348 Score: 116
Period size: 43 Copynumber: 2.3 Consensus size: 43
22740240 AAATATCTAT
* * *
22740250 AAAAATT-TCAAATATTATATTTAAAAAGATTATAAAATTTTTA
1 AAAAATTCTAAAATATTATATATAAAAAGAGTATAAAA-TTTTA
22740293 AAAAATTCTAAAATA-TATATATAAAAA-AGT-TAAAATTTTA
1 AAAAATTCTAAAATATTATATATAAAAAGAGTATAAAATTTTA
*
22740333 AAAATGTTCTAAAATA
1 AAAA-ATTCTAAAATA
22740349 ATAATTTTGA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
40 9 0.18
41 15 0.30
42 2 0.04
43 18 0.36
44 6 0.12
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (43 bp):
AAAAATTCTAAAATATTATATATAAAAAGAGTATAAAATTTTA
Found at i:22740595 original size:35 final size:35
Alignment explanation
Indices: 22740532--22740605 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
22740522 AACTCGAACA
* ***
22740532 ATTTCACTCGATTCGATTCGATTCAACTCAAATTC
1 ATTTCACTCGACTCGATTCGAAAAAACTCAAATTC
* *
22740567 ATTTCACTCGACTCGATTTGAAAAAACTCAAATTG
1 ATTTCACTCGACTCGATTCGAAAAAACTCAAATTC
22740602 ATTT
1 ATTT
22740606 AGAATGATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.36
Consensus pattern (35 bp):
ATTTCACTCGACTCGATTCGAAAAAACTCAAATTC
Found at i:22741339 original size:31 final size:33
Alignment explanation
Indices: 22741304--22741365 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
22741294 ATATTAAAAT
* *
22741304 AAAATAAAATAAATAT-TTTAAAA-AAATTTAA
1 AAAATAAAATAAACATACTTAAAATAAATTTAA
*
22741335 AAAATAATATAAACATACTTAAAATAAATTT
1 AAAATAAAATAAACATACTTAAAATAAATTT
22741366 GAATTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 14 0.54
32 6 0.23
33 6 0.23
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (33 bp):
AAAATAAAATAAACATACTTAAAATAAATTTAA
Found at i:22746179 original size:28 final size:28
Alignment explanation
Indices: 22746090--22746247 Score: 99
Period size: 29 Copynumber: 5.5 Consensus size: 28
22746080 ACCCGAGGGC
*
22746090 AAAATGGTAATTTTGATGAAATTC-AGGTCA
1 AAAATGG-AATTTTGGTGAAA-TCGAGG-CA
* * **
22746120 AAAATAGAATTTTGG-AAAGATCGAGGGT
1 AAAATGGAATTTTGGTGAA-ATCGAGGCA
22746148 AAAATGGCAATTTTGGTGAAATCGAGGCA
1 AAAATGG-AATTTTGGTGAAATCGAGGCA
* * * **
22746177 AAAATGGAATTTT--AGAAAGTTTGGGGGT
1 AAAATGGAATTTTGGTGAAA--TCGAGGCA
*
22746205 AAAATGGTAATTTTGGTGAAATTAGAGGCA
1 AAAATGG-AATTTTGGTGAAA-TCGAGGCA
*
22746235 AAAATGTAATTTT
1 AAAATGGAATTTT
22746248 AGAAAGTTTA
Statistics
Matches: 99, Mismatches: 20, Indels: 19
0.72 0.14 0.14
Matches are distributed among these distances:
26 4 0.04
28 27 0.27
29 45 0.45
30 19 0.19
31 4 0.04
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.30
Consensus pattern (28 bp):
AAAATGGAATTTTGGTGAAATCGAGGCA
Found at i:22746254 original size:58 final size:57
Alignment explanation
Indices: 22746090--22746276 Score: 234
Period size: 58 Copynumber: 3.2 Consensus size: 57
22746080 ACCCGAGGGC
* * * * * *
22746090 AAAATGGTAATTTTGATGAAATTCAG-GTCAAAAATAGAATTTTGGAAAGATCGAGGGT
1 AAAATGGTAATTTTGGTGAAATT-AGAGGCAAAAAT-GAATTTTAGAAAGTTTGGGGGT
* *
22746148 AAAATGGCAATTTTGGTGAAA-TCGAGGCAAAAATGGAATTTTAGAAAGTTTGGGGGT
1 AAAATGGTAATTTTGGTGAAATTAGAGGCAAAAAT-GAATTTTAGAAAGTTTGGGGGT
*
22746205 AAAATGGTAATTTTGGTGAAATTAGAGGCAAAAATGTAATTTTAGAAAGTTTAGGGGT
1 AAAATGGTAATTTTGGTGAAATTAGAGGCAAAAATG-AATTTTAGAAAGTTTGGGGGT
*
22746263 AAAATGATAATTTT
1 AAAATGGTAATTTT
22746277 AATAAAATCG
Statistics
Matches: 113, Mismatches: 13, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
56 1 0.01
57 48 0.42
58 64 0.57
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (57 bp):
AAAATGGTAATTTTGGTGAAATTAGAGGCAAAAATGAATTTTAGAAAGTTTGGGGGT
Found at i:22746267 original size:86 final size:88
Alignment explanation
Indices: 22746177--22746391 Score: 219
Period size: 86 Copynumber: 2.5 Consensus size: 88
22746167 AATCGAGGCA
* * *
22746177 AAAATGGAATTTTAGAAAGTTTGGGGGT-AAAATGGTAATTTTGGTGAAA-TTAGAGGCAAAAAT
1 AAAATGTAATTTTAGAAAGTTTAGGGGTCAAAATGGTAATTTTGG-AAAACTTAGAGGCAAAAAT
*
22746240 GTAATTTTAGAAAG-TTTAGGGGT
65 GTAATTTTAGAAAGTTTTAAGGGT
** * * * * *
22746263 AAAATGATAATTTTA-ATAA-AATCGAGGTCAAAATGG-AATTATGGAAAACTTAGGGGTAAAAA
1 AAAATG-TAATTTTAGA-AAGTTTAGGGGTCAAAATGGTAATTTTGGAAAACTTAGAGGCAAAAA
*
22746325 TGTAATTTTAGAAAGTTTTAAGGTT
64 TGTAATTTTAGAAAGTTTTAAGGGT
* *
22746350 AAAATATAATTTTAGAAAAGTTCAGGGGTCAAAAT-GTAATTT
1 AAAATGTAATTTTAG-AAAGTTTAGGGGTCAAAATGGTAATTT
22746392 ACACAAAGTT
Statistics
Matches: 102, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
85 3 0.03
86 53 0.52
87 31 0.30
88 15 0.15
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (88 bp):
AAAATGTAATTTTAGAAAGTTTAGGGGTCAAAATGGTAATTTTGGAAAACTTAGAGGCAAAAATG
TAATTTTAGAAAGTTTTAAGGGT
Found at i:22746295 original size:58 final size:58
Alignment explanation
Indices: 22746090--22746333 Score: 248
Period size: 57 Copynumber: 4.2 Consensus size: 58
22746080 ACCCGAGGGC
* * * * *
22746090 AAAATGGTAATTTTGATGAAATTC-AGGTCAAAAATAGAATTTTGGAAAG-ATCGAGGGT
1 AAAATGGTAATTTTGATGAAAATCGAGG-CAAAAATGGAATTTTAGAAAGTTTAG-GGGT
* * *
22746148 AAAATGGCAATTTTGGTG-AAATCGAGGCAAAAATGGAATTTTAGAAAGTTTGGGGGT
1 AAAATGGTAATTTTGATGAAAATCGAGGCAAAAATGGAATTTTAGAAAGTTTAGGGGT
* * * *
22746205 AAAATGGTAATTTTGGTGAAATTAGAGGCAAAAATGTAATTTTAGAAAGTTTAGGGGT
1 AAAATGGTAATTTTGATGAAAATCGAGGCAAAAATGGAATTTTAGAAAGTTTAGGGGT
* * * * **
22746263 AAAATGATAATTTTAAT-AAAATCGAGGTC-AAAATGGAATTATGGAAAACTTAGGGGT
1 AAAATGGTAATTTTGATGAAAATCGAGG-CAAAAATGGAATTTTAGAAAGTTTAGGGGT
22746320 AAAAAT-GTAATTTT
1 -AAAATGGTAATTTT
22746334 AGAAAGTTTT
Statistics
Matches: 158, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
57 82 0.52
58 76 0.48
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.30
Consensus pattern (58 bp):
AAAATGGTAATTTTGATGAAAATCGAGGCAAAAATGGAATTTTAGAAAGTTTAGGGGT
Found at i:22746296 original size:115 final size:116
Alignment explanation
Indices: 22746090--22746333 Score: 275
Period size: 115 Copynumber: 2.1 Consensus size: 116
22746080 ACCCGAGGGC
* * * *
22746090 AAAATGGTAATTTTGATGAAATTCAGGTCAAAAATAGAATTTTGGAAAGATCGAGGGTAAAATGG
1 AAAATGGTAATTTTGATGAAATTCAGGGCAAAAATAGAATTTTAGAAAGATAGAGGGTAAAATGA
** * * ** *
22746155 CAATTTTGGTGAAATCGAGGCAAAAATGGAATTTTAGAAAGTTTGGGGGT-
66 CAATTTTAATAAAATCGAGGCAAAAATGGAATTATAGAAAACTTAGGGGTA
* *
22746205 AAAATGGTAATTTTGGTGAAATT-AGAGGCAAAAAT-GTAATTTTAGAAAGTTTAG-GGGTAAAA
1 AAAATGGTAATTTTGATGAAATTCAG-GGCAAAAATAG-AATTTTAGAAAG-ATAGAGGGTAAAA
* *
22746267 TGATAATTTTAATAAAATCGAGGTC-AAAATGGAATTATGGAAAACTTAGGGGTA
63 TGACAATTTTAATAAAATCGAGG-CAAAAATGGAATTATAGAAAACTTAGGGGTA
22746321 AAAAT-GTAATTTT
1 AAAATGGTAATTTT
22746334 AGAAAGTTTT
Statistics
Matches: 109, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
114 3 0.03
115 98 0.90
116 8 0.07
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.30
Consensus pattern (116 bp):
AAAATGGTAATTTTGATGAAATTCAGGGCAAAAATAGAATTTTAGAAAGATAGAGGGTAAAATGA
CAATTTTAATAAAATCGAGGCAAAAATGGAATTATAGAAAACTTAGGGGTA
Found at i:22746370 original size:30 final size:30
Alignment explanation
Indices: 22746321--22746464 Score: 127
Period size: 30 Copynumber: 4.8 Consensus size: 30
22746311 CTTAGGGGTA
*
22746321 AAAATGTAATTTTAG-AAAGTTTTAAGGTT
1 AAAATGTAATTTTAGAAAAGTTTTAAGGTC
* * *
22746350 AAAATATAATTTTAGAAAAG-TTCAGGGGTC
1 AAAATGTAATTTTAGAAAAGTTTTA-AGGTC
* *
22746380 AAAATGTAA-TTTACACAAAGTTTTAGGGTC
1 AAAATGTAATTTTAGA-AAAGTTTTAAGGTC
* * * *
22746410 AAAATATAATTTTGGAAAAG-TTCAAGGGTT
1 AAAATGTAATTTTAGAAAAGTTTTAA-GGTC
22746440 AAAATGTAATTTTCA-AAAAGTTTTA
1 AAAATGTAATTTT-AGAAAAGTTTTA
22746465 GGATCTAAAA
Statistics
Matches: 91, Mismatches: 16, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
29 25 0.27
30 56 0.62
31 10 0.11
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTAGAAAAGTTTTAAGGTC
Found at i:22746392 original size:29 final size:30
Alignment explanation
Indices: 22746177--22746461 Score: 161
Period size: 29 Copynumber: 9.7 Consensus size: 30
22746167 AATCGAGGCA
* **
22746177 AAAATGGAATTTTAG-AAAGTTTGGGGGT-
1 AAAATGTAATTTTAGAAAAGTTCAGGGGTC
* * *
22746205 AAAATGGTAATTTTGGTGAAA-TT-AGAGG-C
1 AAAAT-GTAATTTTAG-AAAAGTTCAGGGGTC
*
22746234 AAAAATGTAATTTTAG-AAAGTTTAGGGGT-
1 -AAAATGTAATTTTAGAAAAGTTCAGGGGTC
* *
22746263 AAAATGATAATTTTA-ATAAA-ATC-GAGGTC
1 AAAATG-TAATTTTAGA-AAAGTTCAGGGGTC
* * * * *
22746292 AAAATGGAATTATGGAAAACTT-AGGGGTA
1 AAAATGTAATTTTAGAAAAGTTCAGGGGTC
* * *
22746321 AAAATGTAATTTTAG-AAAGTTTTA-AGGTT
1 AAAATGTAATTTTAGAAAAG-TTCAGGGGTC
*
22746350 AAAATATAATTTTAGAAAAGTTCAGGGGTC
1 AAAATGTAATTTTAGAAAAGTTCAGGGGTC
* *
22746380 AAAATGTAA-TTTACACAAAGTTTTA-GGGTC
1 AAAATGTAATTTTAGA-AAAG-TTCAGGGGTC
* * * *
22746410 AAAATATAATTTTGGAAAAGTTCAAGGGTT
1 AAAATGTAATTTTAGAAAAGTTCAGGGGTC
22746440 AAAATGTAATTTTCA-AAAAGTT
1 AAAATGTAATTTT-AGAAAAGTT
22746462 TTAGGATCTA
Statistics
Matches: 198, Mismatches: 35, Indels: 46
0.71 0.13 0.16
Matches are distributed among these distances:
27 3 0.02
28 28 0.14
29 87 0.44
30 70 0.35
31 10 0.05
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.33
Consensus pattern (30 bp):
AAAATGTAATTTTAGAAAAGTTCAGGGGTC
Found at i:22746418 original size:60 final size:59
Alignment explanation
Indices: 22746288--22746466 Score: 216
Period size: 60 Copynumber: 3.0 Consensus size: 59
22746278 ATAAAATCGA
** * * * * *
22746288 GGTCAAAATGGAATTATGGAAAACTT-AGGGGTAAAAATGTAATTTTAGAAAGTTTTAA
1 GGTCAAAATATAATTTTGGAAAAGTTCAGGGGTAAAAATGTAATTTCAAAAAGTTTTAG
* * * *
22746346 GGTTAAAATATAATTTTAGAAAAGTTCAGGGGTCAAAATGTAATTTACACAAAGTTTTAG
1 GGTCAAAATATAATTTTGGAAAAGTTCAGGGGTAAAAATGTAATTT-CAAAAAGTTTTAG
* *
22746406 GGTCAAAATATAATTTTGGAAAAGTTCAAGGGTTAAAATGTAATTTTCAAAAAGTTTTAG
1 GGTCAAAATATAATTTTGGAAAAGTTCAGGGGTAAAAATGTAA-TTTCAAAAAGTTTTAG
22746466 G
1 G
22746467 ATCTAAAAAC
Statistics
Matches: 103, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
58 20 0.19
59 18 0.17
60 62 0.60
61 3 0.03
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (59 bp):
GGTCAAAATATAATTTTGGAAAAGTTCAGGGGTAAAAATGTAATTTCAAAAAGTTTTAG
Found at i:22746807 original size:32 final size:31
Alignment explanation
Indices: 22746758--22746826 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
22746748 AATTATTGGG
22746758 CTAAATTAAAATAATTAAAATTAT-AAGAAGGA
1 CTAAATTAAAATAATTAAAA--ATGAAGAAGGA
* * *
22746790 CTAAATTGAAATGATTAAAAATGCAGAAGGA
1 CTAAATTAAAATAATTAAAAATGAAGAAGGA
22746821 CTAAAT
1 CTAAAT
22746827 GCATAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 2 0.06
31 13 0.39
32 18 0.55
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.26
Consensus pattern (31 bp):
CTAAATTAAAATAATTAAAAATGAAGAAGGA
Found at i:22748375 original size:17 final size:17
Alignment explanation
Indices: 22748355--22748424 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
22748345 AAACAATTTT
*
22748355 AATTCAACATAAATTCA
1 AATTCAAAATAAATTCA
* *
22748372 AATTTAAAATAAATT-T
1 AATTCAAAATAAATTCA
* *
22748388 AATCCCAAAATAAATTTA
1 AAT-TCAAAATAAATTCA
*
22748406 AATTTAAAATAAATTCA
1 AATTCAAAATAAATTCA
22748423 AA
1 AA
22748425 AATAAATTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
16 3 0.07
17 36 0.86
18 3 0.07
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTCAAAATAAATTCA
Found at i:22748387 original size:34 final size:35
Alignment explanation
Indices: 22748349--22748420 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 35
22748339 AATATTAAAC
* *
22748349 AATTTTAAT-TCAACATAAATTCAAATTTAAAATA
1 AATTTTAATCCCAAAATAAATTCAAATTTAAAATA
*
22748383 AA-TTTAATCCCAAAATAAATTTAAATTTAAAATA
1 AATTTTAATCCCAAAATAAATTCAAATTTAAAATA
22748417 AATT
1 AATT
22748421 CAAAAATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 6 0.18
34 26 0.79
35 1 0.03
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (35 bp):
AATTTTAATCCCAAAATAAATTCAAATTTAAAATA
Found at i:22748792 original size:61 final size:61
Alignment explanation
Indices: 22748697--22748817 Score: 224
Period size: 61 Copynumber: 2.0 Consensus size: 61
22748687 TCAACACAAA
22748697 AAATCTCTCATTCAATACCATCAGCCTACAGCCTTACAAGTTTTCTCAGGAATGTGGATGT
1 AAATCTCTCATTCAATACCATCAGCCTACAGCCTTACAAGTTTTCTCAGGAATGTGGATGT
* *
22748758 AAATCTCTCATTCAATACCATCAGCCTACAGCCTTGCAAGTTTTCTCAGGAATGTTGATG
1 AAATCTCTCATTCAATACCATCAGCCTACAGCCTTACAAGTTTTCTCAGGAATGTGGATG
22748818 CAGCTGTGAG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (61 bp):
AAATCTCTCATTCAATACCATCAGCCTACAGCCTTACAAGTTTTCTCAGGAATGTGGATGT
Found at i:22764781 original size:15 final size:15
Alignment explanation
Indices: 22764761--22764789 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
22764751 ATGCCTCACA
22764761 CACCGTGTTATCAAT
1 CACCGTGTTATCAAT
22764776 CACCGTGTTATCAA
1 CACCGTGTTATCAA
22764790 GAAATAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (15 bp):
CACCGTGTTATCAAT
Found at i:22771556 original size:15 final size:15
Alignment explanation
Indices: 22771536--22771566 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
22771526 TAACCAGTAC
*
22771536 TTGGCACGTGTTGGA
1 TTGGCACATGTTGGA
22771551 TTGGCACATGTTGGA
1 TTGGCACATGTTGGA
22771566 T
1 T
22771567 CACCTCCCCT
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:0.16, C:0.13, G:0.35, T:0.35
Consensus pattern (15 bp):
TTGGCACATGTTGGA
Found at i:22777933 original size:21 final size:21
Alignment explanation
Indices: 22777909--22777948 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
22777899 TAACACAATA
*
22777909 TAAAAAAAATTAATGTGTTAT
1 TAAAAAAAATCAATGTGTTAT
*
22777930 TAAAAAAAATCAATTTGTT
1 TAAAAAAAATCAATGTGTT
22777949 GGTGATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.38
Consensus pattern (21 bp):
TAAAAAAAATCAATGTGTTAT
Found at i:22778082 original size:28 final size:28
Alignment explanation
Indices: 22778013--22778070 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
22778003 TTGGGTCACT
*
22778013 AAAACATAGTATTTCTTTCAAGAACTTA
1 AAAACAAAGTATTTCTTTCAAGAACTTA
22778041 AAAACAAAGTATTTCTTTCAAGAACTTA
1 AAAACAAAGTATTTCTTTCAAGAACTTA
22778069 AA
1 AA
22778071 TACATTTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.33
Consensus pattern (28 bp):
AAAACAAAGTATTTCTTTCAAGAACTTA
Found at i:22780991 original size:16 final size:16
Alignment explanation
Indices: 22780970--22781001 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
22780960 AGTTTGTATT
22780970 TTTTTTCTGTAAAAAA
1 TTTTTTCTGTAAAAAA
22780986 TTTTTTCTGTAAAAAA
1 TTTTTTCTGTAAAAAA
22781002 GAATAGCCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (16 bp):
TTTTTTCTGTAAAAAA
Found at i:22782177 original size:20 final size:21
Alignment explanation
Indices: 22782138--22782179 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
22782128 ATTGACTTAT
*
22782138 AAATAGGATTAATTAGAGTTA
1 AAATAGGATTAAGTAGAGTTA
*
22782159 AAATATGATTAAGTA-AGTTA
1 AAATAGGATTAAGTAGAGTTA
22782179 A
1 A
22782180 TCATGAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (21 bp):
AAATAGGATTAAGTAGAGTTA
Found at i:22783293 original size:36 final size:36
Alignment explanation
Indices: 22783245--22783348 Score: 136
Period size: 36 Copynumber: 2.9 Consensus size: 36
22783235 TGGTAACAGG
*
22783245 CATGACCTTTGGGTCAACAGGGAATAAATTGAGCAT
1 CATGACCTTTGGGTCAACAGGGAATAAAATGAGCAT
* * *
22783281 TATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAATAAAATGAGCAT
* * * *
22783317 CACGACCTTTGAGTCAACAGGGAGTTAAATGA
1 CATGACCTTTGGGTCAACAGGGAATAAAATGA
22783349 ATAACAATAA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAGGGAATAAAATGAGCAT
Found at i:22784061 original size:21 final size:21
Alignment explanation
Indices: 22784037--22784086 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
22784027 ACTTGTTTCG
22784037 GTAGAAGTTACACT-AGTATCA
1 GTAGAAGTTAC-CTAAGTATCA
* *
22784058 GTAGAACTTTCCTAAGTATCA
1 GTAGAAGTTACCTAAGTATCA
22784079 GTAGAAGT
1 GTAGAAGT
22784087 CTGCACTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (21 bp):
GTAGAAGTTACCTAAGTATCA
Found at i:22789751 original size:36 final size:36
Alignment explanation
Indices: 22789709--22789796 Score: 95
Period size: 36 Copynumber: 2.4 Consensus size: 36
22789699 TGGTAACAGG
* * *
22789709 CATGACCTTTGGGTCAACATGGAGTAAATTGGGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
* * **
22789745 TATGACCCTTGGGTCAGTAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
* *
22789781 CACGACCTTTGAGTCA
1 CATGACCTTTGGGTCA
22789797 GTAGGAAGTA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.26
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
Found at i:22789797 original size:36 final size:36
Alignment explanation
Indices: 22789729--22789809 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 36
22789719 GGGTCAACAT
* * * * *
22789729 GGAGTAAATTGGGCATTATGACCCTTGGGTCAGTAG
1 GGAGTAAAATGAGCATCACGACCCTTGAGTCAGTAG
*
22789765 GGAGTAAAATGAGCATCACGACCTTTGAGTCAGTAG
1 GGAGTAAAATGAGCATCACGACCCTTGAGTCAGTAG
*
22789801 GAAGTAAAA
1 GGAGTAAAA
22789810 CGAATAACGA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (36 bp):
GGAGTAAAATGAGCATCACGACCCTTGAGTCAGTAG
Found at i:22791300 original size:28 final size:29
Alignment explanation
Indices: 22791261--22791320 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
22791251 GGGCCATTCT
*
22791261 TTTAACAGAGATC-TCTACAAAGGC-TTCC
1 TTTAACAGAGATCGTC-ACAAAGACTTTCC
*
22791289 TTTAATAGAGATCGTCACAAAGACTTTCC
1 TTTAACAGAGATCGTCACAAAGACTTTCC
22791318 TTT
1 TTT
22791321 TAGAATTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (29 bp):
TTTAACAGAGATCGTCACAAAGACTTTCC
Found at i:22796744 original size:21 final size:21
Alignment explanation
Indices: 22796697--22796745 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
22796687 GACACCTAAA
22796697 AGAAAATTGAAAAAGAGTCAG
1 AGAAAATTGAAAAAGAGTCAG
*
22796718 AAAAAATTGAAACAA-A-TCAG
1 AGAAAATTGAAA-AAGAGTCAG
22796738 TAGAAAAT
1 -AGAAAAT
22796746 AAAAGTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 4 0.17
21 18 0.75
22 2 0.08
ACGTcount: A:0.61, C:0.06, G:0.16, T:0.16
Consensus pattern (21 bp):
AGAAAATTGAAAAAGAGTCAG
Found at i:22805112 original size:16 final size:17
Alignment explanation
Indices: 22805076--22805119 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
22805066 CTAAAAAAAT
*
22805076 ATTTTTCTTTTTACA-A
1 ATTTTTCTTTTAACATA
*
22805092 ATTTTTCTTTTAACATT
1 ATTTTTCTTTTAACATA
*
22805109 TTTTTTCTTTT
1 ATTTTTCTTTT
22805120 TCTTTTCTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTTCTTTTAACATA
Found at i:22810221 original size:6 final size:6
Alignment explanation
Indices: 22810210--22810259 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
22810200 AAAACTTTCC
* *
22810210 TTCTTT TTCTTT TTCTTT TTC--T TCCTTT TTCTCTT TTTTTT TTCTTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCT-TT TTCTTT TTCTTT
22810257 TTC
1 TTC
22810260 AAGTGACTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
4 3 0.08
6 29 0.78
7 5 0.14
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTCTTT
Found at i:22810246 original size:23 final size:22
Alignment explanation
Indices: 22810212--22810255 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
22810202 AACTTTCCTT
22810212 CTTTTTCTTTTTCTTTTTCTTC
1 CTTTTTCTTTTTCTTTTTCTTC
*
22810234 CTTTTTCTCTTTTTTTTTTCTT
1 CTTTTTCT-TTTTCTTTTTCTT
22810256 TTTCAAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (22 bp):
CTTTTTCTTTTTCTTTTTCTTC
Found at i:22812993 original size:3 final size:3
Alignment explanation
Indices: 22812933--22812981 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
22812923 CATCTCATTC
* *
22812933 TCT TCT TCT TCT TCT TTT TCT TTT TCT TCT TCT TCAT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT
22812979 TCT
1 TCT
22812982 GGCCATCTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:22821862 original size:51 final size:51
Alignment explanation
Indices: 22821802--22821915 Score: 192
Period size: 51 Copynumber: 2.2 Consensus size: 51
22821792 ACGCTTCATT
* * *
22821802 GTATCGATAGAAATTTGAGGGTTTCATTTGGTATCGGTAGAACCCATTAGA
1 GTATCGATAGAAATCTGAAGGTTTCATTTGGTATCGGTAAAACCCATTAGA
22821853 GTATCGATAGAAATCTGAAGGTTTCATTTGGTATCGGTAAAACCCATTAGA
1 GTATCGATAGAAATCTGAAGGTTTCATTTGGTATCGGTAAAACCCATTAGA
*
22821904 GCATCGATAGAA
1 GTATCGATAGAA
22821916 GTGCAGGGGA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (51 bp):
GTATCGATAGAAATCTGAAGGTTTCATTTGGTATCGGTAAAACCCATTAGA
Found at i:22823377 original size:16 final size:16
Alignment explanation
Indices: 22823356--22823386 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22823346 TACAAACTTC
22823356 TTTTTTTTAAAATTTA
1 TTTTTTTTAAAATTTA
*
22823372 TTTTTTTTATAATTT
1 TTTTTTTTAAAATTT
22823387 TTTAATAAAA
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTTTAAAATTTA
Found at i:22831165 original size:26 final size:26
Alignment explanation
Indices: 22831136--22831185 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
22831126 AAGAAAAGTT
*
22831136 AAAATG-TAACAATTAAATTAAAAACA
1 AAAATGTTAA-AATTAAAATAAAAACA
22831162 AAAATGTTAAAATTAAAATAAAAA
1 AAAATGTTAAAATTAAAATAAAAA
22831186 ATGGCTAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.24
Consensus pattern (26 bp):
AAAATGTTAAAATTAAAATAAAAACA
Found at i:22834087 original size:26 final size:25
Alignment explanation
Indices: 22834028--22834091 Score: 85
Period size: 24 Copynumber: 2.6 Consensus size: 25
22834018 CCCCAACATG
**
22834028 ATTTTGATAATTTTACCCTGATAAA
1 ATTTTGACGATTTTACCCTGATAAA
*
22834053 A-TTTGACGATTTTACCTCTGGTAAA
1 ATTTTGACGATTTTACC-CTGATAAA
22834078 ATTTTGACGATTTT
1 ATTTTGACGATTTT
22834092 GCCCAAGGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.38
25 9 0.26
26 12 0.35
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (25 bp):
ATTTTGACGATTTTACCCTGATAAA
Found at i:22834101 original size:26 final size:26
Alignment explanation
Indices: 22834049--22834107 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
22834039 TTTACCCTGA
*
22834049 TAAAA-TTTGACGATTTTACCTCTGG
1 TAAAATTTTGACGATTTTACCTCAGG
*
22834074 TAAAATTTTGACGATTTTGCC-CAAGG
1 TAAAATTTTGACGATTTTACCTC-AGG
22834100 TAAAATTT
1 TAAAATTT
22834108 CAAGAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 6 0.20
26 24 0.80
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (26 bp):
TAAAATTTTGACGATTTTACCTCAGG
Found at i:22856936 original size:24 final size:24
Alignment explanation
Indices: 22856915--22856963 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
22856905 ATTCCATTGA
22856915 TATCCTTTTCGACCTTTTCATTAT
1 TATCCTTTTCGACCTTTTCATTAT
*
22856939 TATCCTTTTTGACCTTTTCATTAT
1 TATCCTTTTCGACCTTTTCATTAT
22856963 T
1 T
22856964 TCGAGGATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.16, C:0.22, G:0.04, T:0.57
Consensus pattern (24 bp):
TATCCTTTTCGACCTTTTCATTAT
Found at i:22857043 original size:45 final size:44
Alignment explanation
Indices: 22856969--22857089 Score: 102
Period size: 45 Copynumber: 2.7 Consensus size: 44
22856959 TTATTTCGAG
* * *
22856969 GATGTCATGGTATCTTTCAACCA-AT-GTCTTACACAATCTCGAAAT
1 GATGCCATAGTATCTTTCAA--ATATGGTCTTA-ACAATCCCGAAAT
* **** *
22857014 GGTGCCATAGTATCTTTCAAATATGGTCTTGATTGTTCCCGATAT
1 GATGCCATAGTATCTTTCAAATATGGTCTT-AACAATCCCGAAAT
*
22857059 GATGCCATAGTATCTTTCAACTATGGTCTTA
1 GATGCCATAGTATCTTTCAAATATGGTCTTA
22857090 TACGTATCAG
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
43 1 0.02
44 3 0.05
45 57 0.92
46 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (44 bp):
GATGCCATAGTATCTTTCAAATATGGTCTTAACAATCCCGAAAT
Found at i:22857109 original size:45 final size:45
Alignment explanation
Indices: 22857016--22857179 Score: 192
Period size: 45 Copynumber: 3.6 Consensus size: 45
22857006 CTCGAAATGG
* * * *
22857016 TGCCATAGTATCTTTCAAATATGGTCTTGAT-TGTTCCCGATATGA
1 TGCCATAGTATCTTTCAACTATGGTCTT-ATATGTTCCAGATTTAA
*
22857061 TGCCATAGTATCTTTCAACTATGGTCTTATACGTAT-CAGATTTAA
1 TGCCATAGTATCTTTCAACTATGGTCTTATATGT-TCCAGATTTAA
* * *
22857106 TGCCATAATATCTTTCAA-TAATGGTCTTATATATTTCCAG-GTTAA
1 TGCCATAGTATCTTTCAACT-ATGGTCTTATAT-GTTCCAGATTTAA
22857151 TGCCATAGTATCTTTCAACTATGGTCTTA
1 TGCCATAGTATCTTTCAACTATGGTCTTA
22857180 CTCAAGGCGG
Statistics
Matches: 103, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
44 3 0.03
45 94 0.91
46 6 0.06
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (45 bp):
TGCCATAGTATCTTTCAACTATGGTCTTATATGTTCCAGATTTAA
Found at i:22857131 original size:90 final size:90
Alignment explanation
Indices: 22857016--22857179 Score: 235
Period size: 90 Copynumber: 1.8 Consensus size: 90
22857006 CTCGAAATGG
* * *
22857016 TGCCATAGTATCTTTCAAATATGGTCTTGAT-T-GTTCCCGATATGATGCCATAGTATCTTTCAA
1 TGCCATAATATCTTTCAAATATGGTCTT-ATATAGTTCCAGAT-TAATGCCATAGTATCTTTCAA
22857079 CTATGGTCTTATACGTATCAGATTTAA
64 CTATGGTCTTATACGTATCAGATTTAA
* *
22857106 TGCCATAATATCTTTC-AATAATGGTCTTATATATTTCCAGGTTAATGCCATAGTATCTTTCAAC
1 TGCCATAATATCTTTCAAAT-ATGGTCTTATATAGTTCCAGATTAATGCCATAGTATCTTTCAAC
22857170 TATGGTCTTA
65 TATGGTCTTA
22857180 CTCAAGGCGG
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
89 5 0.08
90 55 0.83
91 6 0.09
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (90 bp):
TGCCATAATATCTTTCAAATATGGTCTTATATAGTTCCAGATTAATGCCATAGTATCTTTCAACT
ATGGTCTTATACGTATCAGATTTAA
Found at i:22857232 original size:90 final size:88
Alignment explanation
Indices: 22857016--22857232 Score: 217
Period size: 90 Copynumber: 2.4 Consensus size: 88
22857006 CTCGAAATGG
* * *
22857016 TGCCATAGTATCTTTCAAATATGGTCTTGATT-GTTCCCGATATGATGCCATAGTATCTTTCAAC
1 TGCCATAGTATCTTTC-AATATGGTCTTG-TTATTTCCAGATATAATGCCATAGTATCTTTCAAC
* * *
22857080 TATGGTCTTATACGTATCAGATTTAA
64 TATGGTCTTATAAG-AGCAGATTAAA
* * *
22857106 TGCCATAATATCTTTCAATAATGGTCTTATATATTTCCAGGT-TAATGCCATAGTATCTTTCAAC
1 TGCCATAGTATCTTTCAAT-ATGGTCTTGT-TATTTCCAGATATAATGCCATAGTATCTTTCAAC
*
22857170 TATGGTCTTACTCAAG-GC-GGTTAAAA
64 TATGGTCTTA-T-AAGAGCAGATT-AAA
*
22857196 TGTCATAGTATCTTTCAACTATGGTCTTGTTCATTTC
1 TGCCATAGTATCTTTCAA-TATGGTCTTGTT-ATTTC
22857233 AGTAAAGATG
Statistics
Matches: 106, Mismatches: 13, Indels: 16
0.79 0.10 0.12
Matches are distributed among these distances:
89 8 0.08
90 88 0.83
91 8 0.08
92 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.41
Consensus pattern (88 bp):
TGCCATAGTATCTTTCAATATGGTCTTGTTATTTCCAGATATAATGCCATAGTATCTTTCAACTA
TGGTCTTATAAGAGCAGATTAAA
Found at i:22857245 original size:45 final size:44
Alignment explanation
Indices: 22857016--22857238 Score: 166
Period size: 45 Copynumber: 5.0 Consensus size: 44
22857006 CTCGAAATGG
* * * * **
22857016 TGCCATAGTATCTTTCAAATATGGTCTTGATT-GTTCCCGATATGA
1 TGCCATAGTATCTTTCAACTATGGTCTT-ATTCATTTCAG-TAAAA
* * * **
22857061 TGCCATAGTATCTTTCAACTATGGTCTTATACGTATCAGATTTAA
1 TGCCATAGTATCTTTCAACTATGGTCTTATTCATTTCAG-TAAAA
* *
22857106 TGCCATAATATCTTTCAA-TAATGGTCTTATAT-ATTTCCAGGT-TAA
1 TGCCATAGTATCTTTCAACT-ATGGTCTTAT-TCATTT-CA-GTAAAA
* *** *
22857151 TGCCATAGTATCTTTCAACTATGGTCTTACTCAAGGCGGTTAAAA
1 TGCCATAGTATCTTTCAACTATGGTCTTATTCATTTCAG-TAAAA
* *
22857196 TGTCATAGTATCTTTCAACTATGGTCTTGTTCATTTCAGTAAA
1 TGCCATAGTATCTTTCAACTATGGTCTTATTCATTTCAGTAAA
22857239 GATGTCACAG
Statistics
Matches: 144, Mismatches: 25, Indels: 19
0.77 0.13 0.10
Matches are distributed among these distances:
43 1 0.01
44 10 0.07
45 128 0.89
46 4 0.03
47 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (44 bp):
TGCCATAGTATCTTTCAACTATGGTCTTATTCATTTCAGTAAAA
Found at i:22857342 original size:16 final size:17
Alignment explanation
Indices: 22857321--22857361 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
22857311 TACAAATAAT
22857321 AAATTAAGTAA-TTACC
1 AAATTAAGTAACTTACC
*
22857337 AAATTAA-CAACTTACC
1 AAATTAAGTAACTTACC
22857353 AAATTAAGT
1 AAATTAAGT
22857362 TGAAAACATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (17 bp):
AAATTAAGTAACTTACC
Found at i:22857704 original size:20 final size:20
Alignment explanation
Indices: 22857681--22857745 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
22857671 CCGCTGACCA
22857681 TTGACCGTTGACATTGA-CTG
1 TTGACCGTTGACATTGATC-G
*
22857701 TTGA-CTTTGACTATTGATCG
1 TTGACCGTTGAC-ATTGATCG
* * *
22857721 TTGACAGTTGACTTTGATCA
1 TTGACCGTTGACATTGATCG
22857741 TTGAC
1 TTGAC
22857746 TTTTTTTGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
19 6 0.16
20 25 0.68
21 6 0.16
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGACCGTTGACATTGATCG
Found at i:22857712 original size:13 final size:13
Alignment explanation
Indices: 22857681--22857737 Score: 60
Period size: 13 Copynumber: 4.3 Consensus size: 13
22857671 CCGCTGACCA
* *
22857681 TTGACCGTTGACA
1 TTGACTGTTGACT
22857694 TTGACTGTTGACT
1 TTGACTGTTGACT
* *
22857707 TTGACTATTGATCG
1 TTGACTGTTGA-CT
*
22857721 TTGACAGTTGACT
1 TTGACTGTTGACT
22857734 TTGA
1 TTGA
22857738 TCATTGACTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
13 26 0.72
14 10 0.28
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (13 bp):
TTGACTGTTGACT
Found at i:22861925 original size:40 final size:40
Alignment explanation
Indices: 22861869--22861948 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
22861859 AAGCAACCTA
*
22861869 AGAATATTTTTGAGATTCGTAGTTTCTTGGGTTTAGCTGG
1 AGAATATTTTTGAGATTCGTAGTTTCTTAGGTTTAGCTGG
*
22861909 AGAATATTTTTTAGATTCGTAGTTTCTTAGGTTTAGCTGG
1 AGAATATTTTTGAGATTCGTAGTTTCTTAGGTTTAGCTGG
22861949 CTATTATAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.21, C:0.07, G:0.25, T:0.46
Consensus pattern (40 bp):
AGAATATTTTTGAGATTCGTAGTTTCTTAGGTTTAGCTGG
Found at i:22864890 original size:27 final size:26
Alignment explanation
Indices: 22864858--22864961 Score: 106
Period size: 27 Copynumber: 3.9 Consensus size: 26
22864848 TTGACCAACT
22864858 CGTTGACTA-TTGACTGTTGACTATTGA
1 CGTTGA-TAGTTGACTGTTGACT-TTGA
*
22864885 CGTTGATAGTTGACT-TTGACTGTTGGC
1 CGTTGATAGTTGACTGTTGACT-TT-GA
*
22864912 CGTTGATAGTTGACCGTTGACTTTGA
1 CGTTGATAGTTGACTGTTGACTTTGA
**
22864938 TCGTTGATA-TTGACCATTGACTTT
1 -CGTTGATAGTTGACTGTTGACTTT
22864962 TTTCGAGAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
26 25 0.37
27 37 0.54
28 6 0.09
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.41
Consensus pattern (26 bp):
CGTTGATAGTTGACTGTTGACTTTGA
Found at i:22864957 original size:13 final size:13
Alignment explanation
Indices: 22864858--22864957 Score: 71
Period size: 13 Copynumber: 7.5 Consensus size: 13
22864848 TTGACCAACT
22864858 CGTTGACTATTGAC
1 CGTTGA-TATTGAC
*
22864872 TGTTGACTATTGA-
1 CGTTGA-TATTGAC
22864885 CGTTGATAGTTGA-
1 CGTTGATA-TTGAC
* * *
22864898 CTTTGACTGTTGGC
1 CGTTGA-TATTGAC
22864912 CGTTGATAGTTGAC
1 CGTTGATA-TTGAC
*
22864926 CGTTGACT-TTGAT
1 CGTTGA-TATTGAC
22864939 CGTTGATATTGAC
1 CGTTGATATTGAC
*
22864952 CATTGA
1 CGTTGA
22864958 CTTTTTTCGA
Statistics
Matches: 69, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
12 3 0.04
13 37 0.54
14 28 0.41
15 1 0.01
ACGTcount: A:0.20, C:0.15, G:0.25, T:0.40
Consensus pattern (13 bp):
CGTTGATATTGAC
Found at i:22866145 original size:12 final size:12
Alignment explanation
Indices: 22866124--22866154 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
22866114 AATTAGAGAC
22866124 TATATATATATT
1 TATATATATATT
*
22866136 TATATTTATATT
1 TATATATATATT
22866148 TATATAT
1 TATATAT
22866155 GTGAATGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATATATATATT
Found at i:22874836 original size:137 final size:137
Alignment explanation
Indices: 22874590--22874864 Score: 487
Period size: 137 Copynumber: 2.0 Consensus size: 137
22874580 TTTGAATTCT
* * * * *
22874590 AATAACCTTAAAACTTTAGATACCTATAAAAACCAAGAGAAACACTAGAAAACTTTCATCACGTT
1 AATAACCTTAAAACTTTAGATACATATAAAAACAAAGAGAAACACCAAAAAACCTTCATCACGTT
22874655 CATCTTCTTCATCATCTTCTCCAAATGTGGATTTTTCCGGATTCATGTCAAAGCTCGTTTTTCTT
66 CATCTTCTTCATCATCTTCTCCAAATGTGGATTTTTCCGGATTCATGTCAAAGCTCGTTTTTCTT
22874720 CAAGAAA
131 CAAGAAA
22874727 AATAACCTTAAAACTTTAGATACATATAAAAACAAAGAGAAACACCAAAAAACCTTCATCACGTT
1 AATAACCTTAAAACTTTAGATACATATAAAAACAAAGAGAAACACCAAAAAACCTTCATCACGTT
* *
22874792 CATCTTCTTCATCATCTTCTCCAAATGTGGGTTTTTTCGGATTCATGTCAAAGCTCGTTTTTCTT
66 CATCTTCTTCATCATCTTCTCCAAATGTGGATTTTTCCGGATTCATGTCAAAGCTCGTTTTTCTT
22874857 CAAGAAA
131 CAAGAAA
22874864 A
1 A
22874865 GGTAATCAAT
Statistics
Matches: 131, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
137 131 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.32
Consensus pattern (137 bp):
AATAACCTTAAAACTTTAGATACATATAAAAACAAAGAGAAACACCAAAAAACCTTCATCACGTT
CATCTTCTTCATCATCTTCTCCAAATGTGGATTTTTCCGGATTCATGTCAAAGCTCGTTTTTCTT
CAAGAAA
Found at i:22875527 original size:23 final size:23
Alignment explanation
Indices: 22875499--22875853 Score: 521
Period size: 23 Copynumber: 15.4 Consensus size: 23
22875489 TTCTTATTTC
22875499 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
22875522 TGTGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
*
22875545 TATGATTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
22875568 TGTGCTTAAGTATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
22875591 TATGCTTAAATATTAATATGGTT
1 TATGCTTAAATATTAATGTGATT
* *
22875614 TGTGCTCAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
22875637 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
22875660 TATGCTTAAATATTATTGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
22875683 TATGCTTAAATGTTAATATGATT
1 TATGCTTAAATATTAATGTGATT
*
22875706 TATACTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
22875729 TATGCTTAAATATTAATGTGGTT
1 TATGCTTAAATATTAATGTGATT
** * *
22875752 GGTGCTCAAATATTAATGTGGTT
1 TATGCTTAAATATTAATGTGATT
22875775 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
22875798 TATGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
*
22875821 TATGATTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
22875844 TGTGCTTAAA
1 TATGCTTAAA
22875854 GAATTAAGAT
Statistics
Matches: 293, Mismatches: 39, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 293 1.00
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.47
Consensus pattern (23 bp):
TATGCTTAAATATTAATGTGATT
Found at i:22877466 original size:6 final size:6
Alignment explanation
Indices: 22877441--22877483 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
22877431 ACAGTTCATA
* * *
22877441 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACTT T
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT T
22877484 TGATTTTGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.21, C:0.30, G:0.00, T:0.49
Consensus pattern (6 bp):
TCACTT
Found at i:22887133 original size:82 final size:81
Alignment explanation
Indices: 22886996--22887231 Score: 301
Period size: 82 Copynumber: 2.9 Consensus size: 81
22886986 GTATAGTTCC
* * * *
22886996 GTCAATTCATGGCACCCAGTGCCTAGCGGATAAACCGCAATAAGTGTGTCCAGCTCTAATTGGAT
1 GTCAATTCCTGG-AACCAGTGCCTAGCGGATAAACCGCAATAAGTGAGGCCAGCTCTAATTGGAT
**
22887061 TAAGTAACAATAAATTT
65 TAACCAACAATAAATTT
* * *
22887078 GTCAATTCCTGGTACCTAGTGCCTAGCGGATAAATCGCAATAAGTGAGGCCAGCTCTAGTTGGAT
1 GTCAATTCCTGGAACC-AGTGCCTAGCGGATAAACCGCAATAAGTGAGGCCAGCTCTAATTGGAT
22887143 TAACCAACAATAAATTT
65 TAACCAACAATAAATTT
* * * * * * *
22887160 GTTAATTCCTGGCAACCAGTGCCTATCGGATAAACCGCAATAAGTGAGTCTAACTCTAGTTAGAT
1 GTCAATTCCTGG-AACCAGTGCCTAGCGGATAAACCGCAATAAGTGAGGCCAGCTCTAATTGGAT
22887225 TAACCAA
65 TAACCAA
22887232 TGGTTTTGCG
Statistics
Matches: 135, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
81 2 0.01
82 130 0.96
83 3 0.02
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (81 bp):
GTCAATTCCTGGAACCAGTGCCTAGCGGATAAACCGCAATAAGTGAGGCCAGCTCTAATTGGATT
AACCAACAATAAATTT
Found at i:22889107 original size:74 final size:75
Alignment explanation
Indices: 22888982--22889120 Score: 201
Period size: 74 Copynumber: 1.9 Consensus size: 75
22888972 CCTTCTTCAA
* * * *
22888982 TTTATCTGACTAGTGCTGGGCACACTTCTTATATTCGTTGGTTACCTGACTAG-GCTGGGTGCAA
1 TTTATCTGACTAGTGCTGGGCACACTACTTATATTCGTCGGATACCTGACTAGCGCTGGGCGCAA
22889046 CCTTTGCTAG
66 CCTTTGCTAG
* *
22889056 TTTATCTGACTAGTGCTGGGCACACTACTTATATTTGTCGGATA-TTCGACTAGCGCTGGGCGCA
1 TTTATCTGACTAGTGCTGGGCACACTACTTATATTCGTCGGATACCT-GACTAGCGCTGGGCGCA
22889120 A
65 A
22889121 AAGCATAATG
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
73 1 0.02
74 46 0.81
75 10 0.18
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.35
Consensus pattern (75 bp):
TTTATCTGACTAGTGCTGGGCACACTACTTATATTCGTCGGATACCTGACTAGCGCTGGGCGCAA
CCTTTGCTAG
Found at i:22893784 original size:13 final size:12
Alignment explanation
Indices: 22893764--22893803 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
22893754 TATAGTAATA
22893764 TTTCTTTTTCTTT
1 TTTC-TTTTCTTT
*
22893777 TCTCTTTTCTTTT
1 TTTCTTTTC-TTT
22893790 TTTCTTTTCTTT
1 TTTCTTTTCTTT
22893802 TT
1 TT
22893804 CTCATTCAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTCTTTTCTTT
Found at i:22893793 original size:20 final size:19
Alignment explanation
Indices: 22893768--22893805 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
22893758 GTAATATTTC
22893768 TTTTTCTTTTCTCTTTTCTT
1 TTTTTCTTTTCT-TTTTCTT
22893788 TTTTTCTTTTCTTTTTCT
1 TTTTTCTTTTCTTTTTCT
22893806 CATTCAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTCTTTTCTTTTTCTT
Found at i:22893969 original size:13 final size:13
Alignment explanation
Indices: 22893953--22893978 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22893943 TTGGCTAAAT
22893953 GATATTTCTAACA
1 GATATTTCTAACA
22893966 GATATTTCTAACA
1 GATATTTCTAACA
22893979 CATGCAGCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
GATATTTCTAACA
Found at i:22894542 original size:167 final size:167
Alignment explanation
Indices: 22894266--22894601 Score: 672
Period size: 167 Copynumber: 2.0 Consensus size: 167
22894256 TCATTAACTA
22894266 AAGAAACAAGTAAAATTCAAATATGTGGGTGCAATCGCATTTCCATTTCACACAATATCCCCCCA
1 AAGAAACAAGTAAAATTCAAATATGTGGGTGCAATCGCATTTCCATTTCACACAATATCCCCCCA
22894331 AACTTAACGTTTGTATTGTCCCCAAGGCATTGACAATATTATACAAATAAGAATGGAAATGCAAC
66 AACTTAACGTTTGTATTGTCCCCAAGGCATTGACAATATTATACAAATAAGAATGGAAATGCAAC
22894396 TAAAATGCAGTTAAACTAATATGAAAAATGCAGTGAC
131 TAAAATGCAGTTAAACTAATATGAAAAATGCAGTGAC
22894433 AAGAAACAAGTAAAATTCAAATATGTGGGTGCAATCGCATTTCCATTTCACACAATATCCCCCCA
1 AAGAAACAAGTAAAATTCAAATATGTGGGTGCAATCGCATTTCCATTTCACACAATATCCCCCCA
22894498 AACTTAACGTTTGTATTGTCCCCAAGGCATTGACAATATTATACAAATAAGAATGGAAATGCAAC
66 AACTTAACGTTTGTATTGTCCCCAAGGCATTGACAATATTATACAAATAAGAATGGAAATGCAAC
22894563 TAAAATGCAGTTAAACTAATATGAAAAATGCAGTGAC
131 TAAAATGCAGTTAAACTAATATGAAAAATGCAGTGAC
22894600 AA
1 AA
22894602 ATAACAATGC
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 169 1.00
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (167 bp):
AAGAAACAAGTAAAATTCAAATATGTGGGTGCAATCGCATTTCCATTTCACACAATATCCCCCCA
AACTTAACGTTTGTATTGTCCCCAAGGCATTGACAATATTATACAAATAAGAATGGAAATGCAAC
TAAAATGCAGTTAAACTAATATGAAAAATGCAGTGAC
Found at i:22895112 original size:18 final size:18
Alignment explanation
Indices: 22895064--22895112 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
22895054 CCTTCTCAAG
**
22895064 TTCTTCTTCCTCTCGTTC
1 TTCTTCTTCCTCTCGGCC
*
22895082 TTTTTCCTT-CTCTCGGCC
1 TTCTT-CTTCCTCTCGGCC
22895100 TTCTTCTTCCTCT
1 TTCTTCTTCCTCT
22895113 GCTTCCTCTG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 3 0.12
18 19 0.76
19 3 0.12
ACGTcount: A:0.00, C:0.39, G:0.06, T:0.55
Consensus pattern (18 bp):
TTCTTCTTCCTCTCGGCC
Found at i:22904469 original size:36 final size:35
Alignment explanation
Indices: 22904402--22904469 Score: 82
Period size: 36 Copynumber: 1.9 Consensus size: 35
22904392 ACAGAAATGA
* **
22904402 AAATAACAAAGGAAATGAAAAATAATTAAAATCCT
1 AAATAACAAAGGAAACGAAAAATAAGGAAAATCCT
* *
22904437 AAATTACAAAGAGAAACGAAAACTAAGGAAAAT
1 AAATAACAAAG-GAAACGAAAAATAAGGAAAAT
22904470 GTGTGTAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 10 0.37
36 17 0.63
ACGTcount: A:0.63, C:0.09, G:0.12, T:0.16
Consensus pattern (35 bp):
AAATAACAAAGGAAACGAAAAATAAGGAAAATCCT
Found at i:22905559 original size:20 final size:21
Alignment explanation
Indices: 22905534--22905576 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
22905524 TACCTCATTC
*
22905534 CCTCTCACC-GCCTTATTTCT
1 CCTCTCACCTGCCTTATCTCT
*
22905554 CCTCTCACCTTCCTTATCTCT
1 CCTCTCACCTGCCTTATCTCT
22905575 CC
1 CC
22905577 ATTTTAGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.09, C:0.49, G:0.02, T:0.40
Consensus pattern (21 bp):
CCTCTCACCTGCCTTATCTCT
Found at i:22908238 original size:16 final size:16
Alignment explanation
Indices: 22908217--22908247 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22908207 ATAATCTGAA
22908217 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
22908233 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
22908248 GGATCCACAA
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:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:22910886 original size:21 final size:22
Alignment explanation
Indices: 22910847--22910922 Score: 72
Period size: 21 Copynumber: 3.6 Consensus size: 22
22910837 ATAGTGCAGA
*
22910847 CTTCTACCGATA-ACTGTGATAG
1 CTTCTACCGATACA-AGTGATAG
22910869 -TTCTACCGATACAAGTGA-AG
1 CTTCTACCGATACAAGTGATAG
* *
22910889 CTTCTATCGGA-ACAAGTAAT-G
1 CTTCTA-CCGATACAAGTGATAG
22910910 CTTCTACCGATAC
1 CTTCTACCGATAC
22910923 TAAAAACTCT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
20 5 0.11
21 36 0.80
22 4 0.09
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (22 bp):
CTTCTACCGATACAAGTGATAG
Found at i:22923654 original size:25 final size:25
Alignment explanation
Indices: 22923621--22923758 Score: 143
Period size: 25 Copynumber: 5.5 Consensus size: 25
22923611 CTAAAGACTG
22923621 GCTCGTAAGAGCGATATTCTGTCTA
1 GCTCGTAAGAGCGATATTCTGTCTA
* * * *
22923646 GCTCATAAGAGCAATATTCTGACTG
1 GCTCGTAAGAGCGATATTCTGTCTA
* *
22923671 GCTCGTAAGAGTGATATTTTGTCTA
1 GCTCGTAAGAGCGATATTCTGTCTA
** * ** *
22923696 GCTCGTAAGAATGATGTTCTAACTG
1 GCTCGTAAGAGCGATATTCTGTCTA
22923721 GCTCGTAAGAGCGATACTT-TGTCTA
1 GCTCGTAAGAGCGATA-TTCTGTCTA
22923746 GGCTCGTAAGAGC
1 -GCTCGTAAGAGC
22923759 TAAACTCTAT
Statistics
Matches: 89, Mismatches: 22, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
25 75 0.84
26 14 0.16
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (25 bp):
GCTCGTAAGAGCGATATTCTGTCTA
Found at i:22923679 original size:50 final size:49
Alignment explanation
Indices: 22923616--22923758 Score: 187
Period size: 50 Copynumber: 2.8 Consensus size: 49
22923606 ATTTACTAAA
*
22923616 GACTGGCTCGTAAGAGCGATATTCTGTCTAGCTCATAAGAGCAATATTCT
1 GACTGGCTCGTAAGAGCGATATT-TGTCTAGCTCGTAAGAGCAATATTCT
* *** *
22923666 GACTGGCTCGTAAGAGTGATATTTTGTCTAGCTCGTAAGAATGATGTTCT
1 GACTGGCTCGTAAGAGCGATA-TTTGTCTAGCTCGTAAGAGCAATATTCT
*
22923716 AACTGGCTCGTAAGAGCGATACTTTGTCTAGGCTCGTAAGAGC
1 GACTGGCTCGTAAGAGCGATA-TTTGTCTA-GCTCGTAAGAGC
22923759 TAAACTCTAT
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
50 68 0.85
51 12 0.15
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (49 bp):
GACTGGCTCGTAAGAGCGATATTTGTCTAGCTCGTAAGAGCAATATTCT
Done.