Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 144 of 190
Found at i:42422233 original size:17 final size:18
Alignment explanation
Indices: 42422200--42422238 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
42422190 TAGGGGGGAA
42422200 AATAAAAAGTTTTTGGGGG
1 AATAAAAAG-TTTTGGGGG
*
42422219 AATAAAAAGTTTGGGGGG
1 AATAAAAAGTTTTGGGGG
42422237 AA
1 AA
42422239 AAGTAAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.33, T:0.26
Consensus pattern (18 bp):
AATAAAAAGTTTTGGGGG
Found at i:42422236 original size:19 final size:20
Alignment explanation
Indices: 42422183--42422245 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
42422173 GGTGAGAAGT
42422183 AAAAGTTTAGGGGGGAAAATA
1 AAAAGTTT-GGGGGGAAAATA
*
42422204 AAAAGTTTTTGGGGG--AATA
1 AAAAG-TTTGGGGGGAAAATA
42422223 AAAAGTTTGGGGGGAAAAGTA
1 AAAAGTTTGGGGGGAAAA-TA
42422244 AA
1 AA
42422246 TACGTGGAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
18 8 0.22
19 9 0.25
20 2 0.06
21 14 0.39
22 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.22
Consensus pattern (20 bp):
AAAAGTTTGGGGGGAAAATA
Found at i:42422624 original size:9 final size:9
Alignment explanation
Indices: 42422610--42422646 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
42422600 TATAGTTTGA
42422610 TATTCGAAT
1 TATTCGAAT
42422619 TATTCGAAT
1 TATTCGAAT
*
42422628 TATTCGAGT
1 TATTCGAAT
42422637 TATTCGAAT
1 TATTCGAAT
42422646 T
1 T
42422647 CGAAAAATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:42422718 original size:9 final size:9
Alignment explanation
Indices: 42422702--42422738 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
42422692 AGTTGATTCA
42422702 AATAACTCG
1 AATAACTCG
*
42422711 ATTAACTCG
1 AATAACTCG
42422720 AATAACTCG
1 AATAACTCG
42422729 AATAACTCG
1 AATAACTCG
42422738 A
1 A
42422739 TTCGTTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.43, C:0.22, G:0.11, T:0.24
Consensus pattern (9 bp):
AATAACTCG
Found at i:42432729 original size:34 final size:37
Alignment explanation
Indices: 42432661--42432729 Score: 99
Period size: 38 Copynumber: 1.9 Consensus size: 37
42432651 TTAGTATCTA
42432661 TATTCTAATATTTATTATTTATCATTTTAAATAAAATT
1 TATTCTAATATTTATTA-TTATCATTTTAAATAAAATT
*
42432699 TATTCTAATATTT-TTA-TAT-ATTTTACATAAA
1 TATTCTAATATTTATTATTATCATTTTAAATAAA
42432730 TTGTTTCACT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 11 0.37
35 3 0.10
37 3 0.10
38 13 0.43
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (37 bp):
TATTCTAATATTTATTATTATCATTTTAAATAAAATT
Found at i:42440242 original size:18 final size:18
Alignment explanation
Indices: 42440219--42440256 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
42440209 TTCAATTAAG
*
42440219 TCTTTCATT-AAGTGTTTT
1 TCTTTC-TTCAAGTATTTT
42440237 TCTTTCTTCAAGTATTTT
1 TCTTTCTTCAAGTATTTT
42440255 TC
1 TC
42440257 ATCTAGTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.61
Consensus pattern (18 bp):
TCTTTCTTCAAGTATTTT
Found at i:42440304 original size:12 final size:12
Alignment explanation
Indices: 42440244--42440344 Score: 69
Period size: 12 Copynumber: 7.9 Consensus size: 12
42440234 TTTTCTTTCT
42440244 TCAAGTATTTTTCA
1 TCAAGT-TTTTT-A
*
42440258 TCTAGTTCTTTTA
1 TCAAGTT-TTTTA
42440271 TCAAGTTTTTAATTA
1 TCAAG-TTTT--TTA
*
42440286 CCAAGTTTTTTA
1 TCAAGTTTTTTA
**
42440298 TCAAGTTTTGCA
1 TCAAGTTTTTTA
*
42440310 GCAAGTTCTTTT-
1 TCAAGTT-TTTTA
* *
42440322 TAAAGTTTTTCA
1 TCAAGTTTTTTA
42440334 TCAAGTTTTTT
1 TCAAGTTTTTT
42440345 CATAAAATTT
Statistics
Matches: 67, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
11 3 0.04
12 32 0.48
13 10 0.15
14 15 0.22
15 7 0.10
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.52
Consensus pattern (12 bp):
TCAAGTTTTTTA
Found at i:42440327 original size:24 final size:24
Alignment explanation
Indices: 42440287--42440355 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 24
42440277 TTTTAATTAC
*
42440287 CAAGTTTTTTATCAAGTTTTGCAG
1 CAAGTTTTTTATAAAGTTTTGCAG
* *
42440311 CAAGTTCTTTT-TAAAGTTTTTCAT
1 CAAGTT-TTTTATAAAGTTTTGCAG
*
42440335 CAAGTTTTTTCATAAAATTTT
1 CAAGTTTTTT-ATAAAGTTTT
42440356 CCATCCAGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
23 4 0.11
24 22 0.58
25 12 0.32
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.51
Consensus pattern (24 bp):
CAAGTTTTTTATAAAGTTTTGCAG
Found at i:42440350 original size:25 final size:24
Alignment explanation
Indices: 42440251--42440368 Score: 94
Period size: 25 Copynumber: 4.7 Consensus size: 24
42440241 TCTTCAAGTA
* *
42440251 TTTTTCATCTAGTTCTTTTATCAAG
1 TTTTTCATCAAGTT-TTTTATAAAG
* *
42440276 TTTTTAATTACCAAGTTTTTTATCAAG
1 TTTTTCA-T--CAAGTTTTTTATAAAG
* *
42440303 TTTTGCAGCAAGTTCTTTT-TAAAG
1 TTTTTCATCAAGTT-TTTTATAAAG
*
42440327 TTTTTCATCAAGTTTTTTCATAAAA
1 TTTTTCATCAAGTTTTTT-ATAAAG
* *
42440352 TTTTCCATCCAGTTTTT
1 TTTTTCATCAAGTTTTT
42440369 AATCATTTCG
Statistics
Matches: 76, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
23 4 0.05
24 22 0.29
25 29 0.38
26 1 0.01
27 15 0.20
28 5 0.07
ACGTcount: A:0.25, C:0.14, G:0.08, T:0.53
Consensus pattern (24 bp):
TTTTTCATCAAGTTTTTTATAAAG
Found at i:42441673 original size:6 final size:6
Alignment explanation
Indices: 42441659--42441693 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
42441649 GGTTTTCTCC
*
42441659 AAAATG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
42441694 TGACTTGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:42442158 original size:246 final size:246
Alignment explanation
Indices: 42441718--42442208 Score: 939
Period size: 246 Copynumber: 2.0 Consensus size: 246
42441708 TGAATTTATG
42441718 TTTTTCGAATTAAATGAAGTTCGAAAATGGAAATAAATCATTTGGTTATAATGAACCGTTGAATG
1 TTTTTCGAATTAAATGAAGTTCGAAAATGGAAATAAATCATTTGGTTATAATGAACCGTTGAATG
42441783 CAAAAATATTAAATATATTTTCTCATAGATTCTTTTACGGTAAAGTCGTCACGATTTTAACGAAA
66 CAAAAATATTAAATATATTTTCTCATAGATTCTTTTACGGTAAAGTCGTCACGATTTTAACGAAA
42441848 TTAGAATTGAGTTGATAAAATTATTTAATTGGAAATATATTGAAGTTTATTTTTGAGAAATAGAA
131 TTAGAATTGAGTTGATAAAATTATTTAATTGGAAATATATTGAAGTTTATTTTTGAGAAATAGAA
*
42441913 AAACAAATATTGGGTTGGATCAAATTATAAAAATACTGGGTTAAAAGTCTA
196 AAAAAAATATTGGGTTGGATCAAATTATAAAAATACTGGGTTAAAAGTCTA
*
42441964 TTTTTTGAATTAAATGAAGTTCGAAAATGGAAATAAATCATTTGGTTATAATGAACCGTTGAATG
1 TTTTTCGAATTAAATGAAGTTCGAAAATGGAAATAAATCATTTGGTTATAATGAACCGTTGAATG
42442029 CAAAAATATTAAATATATTTTC-CAATAGATTCTTTTACGGTAAAGTCGTCACGATTTTAACGAA
66 CAAAAATATTAAATATATTTTCTC-ATAGATTCTTTTACGGTAAAGTCGTCACGATTTTAACGAA
42442093 ATTAGAATTGAGTTGATAAAATTATTTAATTGGAAATATATTGAAGTTTATTTTTGAGAAATAGA
130 ATTAGAATTGAGTTGATAAAATTATTTAATTGGAAATATATTGAAGTTTATTTTTGAGAAATAGA
*
42442158 AAAAAAAATATTGGGTTGGATCAAATTATAAAAATACTGGGTTAATAGTCT
195 AAAAAAAATATTGGGTTGGATCAAATTATAAAAATACTGGGTTAAAAGTCT
42442209 GAGAAGTACT
Statistics
Matches: 241, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
245 1 0.00
246 240 1.00
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (246 bp):
TTTTTCGAATTAAATGAAGTTCGAAAATGGAAATAAATCATTTGGTTATAATGAACCGTTGAATG
CAAAAATATTAAATATATTTTCTCATAGATTCTTTTACGGTAAAGTCGTCACGATTTTAACGAAA
TTAGAATTGAGTTGATAAAATTATTTAATTGGAAATATATTGAAGTTTATTTTTGAGAAATAGAA
AAAAAAATATTGGGTTGGATCAAATTATAAAAATACTGGGTTAAAAGTCTA
Found at i:42449432 original size:103 final size:103
Alignment explanation
Indices: 42449298--42449604 Score: 485
Period size: 103 Copynumber: 3.0 Consensus size: 103
42449288 ATTGCATGTA
** *
42449298 AAGGGGTTGCTGTGTGCTGATTTCCCAATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCAATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
42449363 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
* * *
42449401 GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCAATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
*
42449466 TTAAATGTG-AAGGGGATTGCTAAGTGCTGATTCCCCC
66 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
* *
42449503 AAGGGGTTGCTAAGTGCTGATTCCCCGAA-TGATTGGTGGTTGCTAAGTGCTGATTCCACCATAT
1 AAGGGGTTGCTAAGTGCTGATTCCCC-AATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAT
*
42449567 CTTTGAATGTGAAA-GGGGTTGCTAAGTGCTGATTCCCC
65 -TTTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCC
42449605 GAATCACTGG
Statistics
Matches: 187, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
102 85 0.45
103 100 0.53
104 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (103 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCAATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:42449447 original size:33 final size:33
Alignment explanation
Indices: 42449405--42449631 Score: 142
Period size: 33 Copynumber: 6.5 Consensus size: 33
42449395 TCCCCCGAGG
42449405 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
* *
42449438 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGG
1 GGTTGCTAAGTGCTGATTCC-CC-TA--TT-CAT-TG--GT
*
42449479 GGATTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GG-TTGCTAAGTGCTGATTCCCCTATTCATTGGT
* * *
42449507 GGTTGCTAAGTGCTGATTCCCCGAATGATTGGT
1 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
* *
42449540 GGTTGCTAAGTGCTGATTCCACCATATCTTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CC-TA---TT-CAT-TG---GT
* * *
42449583 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
42449616 GGTTGCTAAGTGCTGA
1 GGTTGCTAAGTGCTGA
42449632 ATCCACCGAT
Statistics
Matches: 154, Mismatches: 15, Indels: 50
0.70 0.07 0.23
Matches are distributed among these distances:
27 20 0.13
28 2 0.01
29 1 0.01
31 2 0.01
32 2 0.01
33 58 0.38
34 4 0.03
35 3 0.02
36 2 0.01
37 3 0.02
38 4 0.03
39 4 0.03
40 2 0.01
41 6 0.04
42 20 0.13
43 21 0.14
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
Found at i:42449514 original size:27 final size:28
Alignment explanation
Indices: 42449475--42449528 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 28
42449465 CTTAAATGTG
42449475 AAGGGGATTGCTAAGTGCTGATTCCCCC
1 AAGGGGATTGCTAAGTGCTGATTCCCCC
42449503 AAGGGG-TTGCTAAGTGCTGATTCCCC
1 AAGGGGATTGCTAAGTGCTGATTCCCC
42449529 GAATGATTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (28 bp):
AAGGGGATTGCTAAGTGCTGATTCCCCC
Found at i:42458850 original size:344 final size:345
Alignment explanation
Indices: 42458216--42458853 Score: 1125
Period size: 344 Copynumber: 1.8 Consensus size: 345
42458206 TATTTCGGAG
42458216 TTTCAGAGCATGGTTTGTAATGCAAATTTGGTTTATGTAATTGAGTGAATTATGGCTACTTGGTT
1 TTTCAGAGCATGGTTTGTAATGCAAATTTGGTTTATGTAATTGAGTGAATTATGGCTACTTGGTT
*
42458281 CATGAATGATTCATGATTTATTTAATGGGATATGTGATATATATATATATGTAATGACTTGATAT
66 CATGAATGATTCATGATTTATTTAATGGGATATGTGA-ATATATATATATGTAATGACTTGACAT
42458346 TTATGTATAATTAGTGAGATGTTATTTGAGCTTGAGAACTTTGATAAAGAAGTTGATAAAATTTT
130 TTATGTATAATTAGTGAGATGTTATTTGAGCTTGAGAACTTTGATAAAGAAGTTGATAAAATTTT
* * *
42458411 ATACATGAATTGTAATAAGTGATTGTTCTGATCTGTACTTATGTTCAGTAATGTCTCATGACCCT
195 ATACAGGAATTGTAATAAGTGATTATTCTGATCTGTACTTATGTTCAGTAATGCCTCATGACCCT
* * *
42458476 AGTCTGGCGACAGATACGGGTTTGGGGTGTTACATTTGGTTGGTATCACAATATTTGAATAAGTA
260 AATCTGGCGACAGATACGAGTTTAGGGTGTTACATTTGGTTGGTATCACAATATTTGAATAAGTA
42458541 AATGGTAATGACTTGGTTGAA
325 AATGGTAATGACTTGGTTGAA
* *
42458562 TTTCAGAGCATGGTTTGTAATGCGAATTTGGTTTATTTAATTGAGTGAATTATGGCTACTTGGTT
1 TTTCAGAGCATGGTTTGTAATGCAAATTTGGTTTATGTAATTGAGTGAATTATGGCTACTTGGTT
* *
42458627 CGTGAATGATTCATGATTTATTTAATGGGATATGTG-ATATATATATATGTAATTACTTGACATT
66 CATGAATGATTCATGATTTATTTAATGGGATATGTGAATATATATATATGTAATGACTTGACATT
*
42458691 TATGTATGATTAGTGAGATGTTATTTGAGCTTGAGAACTTTGATAAAGAAGTTGATAAAATTTTA
131 TATGTATAATTAGTGAGATGTTATTTGAGCTTGAGAACTTTGATAAAGAAGTTGATAAAATTTTA
*
42458756 TACAGGAATTGTAATAAGTGATTATTCTGATCTGTACTTATGTTCAGTAATGCCTCGTGACCCTA
196 TACAGGAATTGTAATAAGTGATTATTCTGATCTGTACTTATGTTCAGTAATGCCTCATGACCCTA
* *
42458821 ATCTTGCGACGGATACGAGTTTAGGGTGTTACA
261 ATCTGGCGACAGATACGAGTTTAGGGTGTTACA
42458854 ATAAATGTCG
Statistics
Matches: 277, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
344 179 0.65
346 98 0.35
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.40
Consensus pattern (345 bp):
TTTCAGAGCATGGTTTGTAATGCAAATTTGGTTTATGTAATTGAGTGAATTATGGCTACTTGGTT
CATGAATGATTCATGATTTATTTAATGGGATATGTGAATATATATATATGTAATGACTTGACATT
TATGTATAATTAGTGAGATGTTATTTGAGCTTGAGAACTTTGATAAAGAAGTTGATAAAATTTTA
TACAGGAATTGTAATAAGTGATTATTCTGATCTGTACTTATGTTCAGTAATGCCTCATGACCCTA
ATCTGGCGACAGATACGAGTTTAGGGTGTTACATTTGGTTGGTATCACAATATTTGAATAAGTAA
ATGGTAATGACTTGGTTGAA
Found at i:42460635 original size:23 final size:23
Alignment explanation
Indices: 42460609--42460652 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
42460599 AGCAAATTGA
42460609 AAAT-ACATTAAACAAAGTTACTT
1 AAATAACATT-AACAAAGTTACTT
*
42460632 AAATAACATTAACATAGTTAC
1 AAATAACATTAACAAAGTTAC
42460653 AAATTAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.30
Consensus pattern (23 bp):
AAATAACATTAACAAAGTTACTT
Found at i:42460744 original size:14 final size:14
Alignment explanation
Indices: 42460721--42460754 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
42460711 TACAATATCC
*
42460721 AAATAATAACAATA
1 AAATAGTAACAATA
42460735 AAATAGTAACAATA
1 AAATAGTAACAATA
*
42460749 TAATAG
1 AAATAG
42460755 CAAATAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (14 bp):
AAATAGTAACAATA
Found at i:42461722 original size:33 final size:33
Alignment explanation
Indices: 42461685--42461815 Score: 181
Period size: 33 Copynumber: 4.0 Consensus size: 33
42461675 TGGGACCCCG
* * *
42461685 ATTTCCAGGTATTCTAATTCTTGTTGGATCTCT
1 ATTTCCAGGCATTCTAATTCCTGTTGGATCTCC
* * *
42461718 ATTTCCAGGGATTCTAATTCCTGTAGGAGCTCC
1 ATTTCCAGGCATTCTAATTCCTGTTGGATCTCC
*
42461751 ATTTCCAGGCATTCCAATTCCTGTTGGATCTCC
1 ATTTCCAGGCATTCTAATTCCTGTTGGATCTCC
* *
42461784 ATTTCCAGCCATTCTAATTTCTGTTGGATCTC
1 ATTTCCAGGCATTCTAATTCCTGTTGGATCTC
42461816 TATGATCTCC
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 86 1.00
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.40
Consensus pattern (33 bp):
ATTTCCAGGCATTCTAATTCCTGTTGGATCTCC
Found at i:42468854 original size:25 final size:26
Alignment explanation
Indices: 42468825--42468873 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
42468815 TATAAAGCTA
42468825 CAAATA-ATAAAAA-AGTTTTAAAATT
1 CAAATATATAAAAATA-TTTTAAAATT
42468850 CAAATATATAAAAATATTTTAAAA
1 CAAATATATAAAAATATTTTAAAA
42468874 AATAAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 6 0.27
26 15 0.68
27 1 0.05
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (26 bp):
CAAATATATAAAAATATTTTAAAATT
Found at i:42477423 original size:21 final size:20
Alignment explanation
Indices: 42477371--42477429 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
42477361 GACTTTATAG
42477371 TAATGTTAA-TTTATTGTATT
1 TAATGTTAATTTTATT-TATT
* *
42477391 TAATTTTGATTTTATTTATT
1 TAATGTTAATTTTATTTATT
42477411 TACATGTTAATTTTCATTT
1 TA-ATGTTAATTTT-ATTT
42477430 TCATTTTCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 13 0.41
21 15 0.47
22 4 0.12
ACGTcount: A:0.27, C:0.03, G:0.07, T:0.63
Consensus pattern (20 bp):
TAATGTTAATTTTATTTATT
Found at i:42481116 original size:14 final size:14
Alignment explanation
Indices: 42481097--42481123 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42481087 TTCTATTTCA
42481097 TTTTATTATACTTT
1 TTTTATTATACTTT
42481111 TTTTATTATACTT
1 TTTTATTATACTT
42481124 AATATTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTATTATACTTT
Found at i:42507518 original size:53 final size:50
Alignment explanation
Indices: 42507445--42507616 Score: 179
Period size: 53 Copynumber: 3.3 Consensus size: 50
42507435 TTTCAATTTA
*
42507445 ATTT-CTTATTTATTTAATTTCAGCTCTTCATTAATTTTTTTATTTCATTATT
1 ATTTACTTATTTATTTAATTTCAGCTTTTCATT-A-TTTTTTATTTC-TTATT
* **
42507497 ATTTACTTATTTATTTAATTTCAACTTTTCATTATTTTTCCTTT-TT-TT
1 ATTTACTTATTTATTTAATTTCAGCTTTTCATTATTTTTTATTTCTTATT
*
42507545 ATTTACTTATTTATTATGGCAATTTCAGCCTTTTCATGATTTTTTATTTGCTTATTT
1 ATTTACTTATTTATT-T---AATTTCAG-CTTTTCATTATTTTTTATTT-CTTA-TT
*
42507602 ATTTATTTATTTATT
1 ATTTACTTATTTATT
42507617 ATTGCCTTGC
Statistics
Matches: 101, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
48 17 0.17
49 3 0.03
51 8 0.08
52 12 0.12
53 43 0.43
55 2 0.02
57 16 0.16
ACGTcount: A:0.22, C:0.11, G:0.03, T:0.63
Consensus pattern (50 bp):
ATTTACTTATTTATTTAATTTCAGCTTTTCATTATTTTTTATTTCTTATT
Found at i:42511117 original size:10 final size:10
Alignment explanation
Indices: 42511104--42511144 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
42511094 CATATTTTTA
42511104 ATCTCAATTT
1 ATCTCAATTT
42511114 ATCTCATATTT
1 ATCTCA-ATTT
42511125 -TACT-AATTT
1 AT-CTCAATTT
42511134 ATCTCAATTT
1 ATCTCAATTT
42511144 A
1 A
42511145 ATTCTACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
9 6 0.22
10 15 0.56
11 6 0.22
ACGTcount: A:0.32, C:0.17, G:0.00, T:0.51
Consensus pattern (10 bp):
ATCTCAATTT
Found at i:42513260 original size:19 final size:19
Alignment explanation
Indices: 42513215--42513261 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
42513205 AATAAAATAG
*
42513215 TAACAACATAATAGTGAAA
1 TAACAACAAAATAGTGAAA
* *
42513234 TGATAACAAAATAGTGAGAA
1 TAACAACAAAATAGTGA-AA
42513254 -AACAACAA
1 TAACAACAA
42513262 GAAAATAACA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 20 0.91
20 2 0.09
ACGTcount: A:0.60, C:0.11, G:0.13, T:0.17
Consensus pattern (19 bp):
TAACAACAAAATAGTGAAA
Found at i:42514239 original size:6 final size:6
Alignment explanation
Indices: 42514228--42514258 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
42514218 TTCCAAATTC
42514228 CCCTTT CCCTTT CCCTTT CCCTTT CCCTTT C
1 CCCTTT CCCTTT CCCTTT CCCTTT CCCTTT C
42514259 TCTGTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
CCCTTT
Found at i:42519612 original size:3 final size:3
Alignment explanation
Indices: 42519604--42519630 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
42519594 TAACTAATTA
42519604 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
42519631 TGTATTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:42521392 original size:3 final size:3
Alignment explanation
Indices: 42521378--42521407 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
42521368 TTAATGATAC
*
42521378 TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42521408 AGCCAACTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:42525157 original size:17 final size:18
Alignment explanation
Indices: 42525117--42525160 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
42525107 ATTTATATTT
42525117 TAAAAATATTAGTTACTA
1 TAAAAATATTAGTTACTA
42525135 TAAAAAATATTAG-TA-TGA
1 T-AAAAATATTAGTTACT-A
42525153 TAAAAATA
1 TAAAAATA
42525161 ATTTCTAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.33
18 5 0.21
19 11 0.46
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (18 bp):
TAAAAATATTAGTTACTA
Found at i:42531552 original size:105 final size:105
Alignment explanation
Indices: 42531370--42531579 Score: 420
Period size: 105 Copynumber: 2.0 Consensus size: 105
42531360 ACAAAATACA
42531370 ATATGCTAATAAAGACAAATGTAAAGTTAATTATTGGAGATTTATTCTTCGATGGCATCTCGATC
1 ATATGCTAATAAAGACAAATGTAAAGTTAATTATTGGAGATTTATTCTTCGATGGCATCTCGATC
42531435 CGTTCTTCACAATCCAAAGGATTTGATTACTTGATCTGAT
66 CGTTCTTCACAATCCAAAGGATTTGATTACTTGATCTGAT
42531475 ATATGCTAATAAAGACAAATGTAAAGTTAATTATTGGAGATTTATTCTTCGATGGCATCTCGATC
1 ATATGCTAATAAAGACAAATGTAAAGTTAATTATTGGAGATTTATTCTTCGATGGCATCTCGATC
42531540 CGTTCTTCACAATCCAAAGGATTTGATTACTTGATCTGAT
66 CGTTCTTCACAATCCAAAGGATTTGATTACTTGATCTGAT
42531580 CTGATGCAAT
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 105 1.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (105 bp):
ATATGCTAATAAAGACAAATGTAAAGTTAATTATTGGAGATTTATTCTTCGATGGCATCTCGATC
CGTTCTTCACAATCCAAAGGATTTGATTACTTGATCTGAT
Found at i:42543745 original size:13 final size:11
Alignment explanation
Indices: 42543713--42543755 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
42543703 CCTTTTTTAA
*
42543713 AATAAAATAAT
1 AATAAAATATT
42543724 AAT-AAATATCT
1 AATAAAATAT-T
42543735 AAGTAAAATATT
1 AA-TAAAATATT
42543747 AATAAAATA
1 AATAAAATA
42543756 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:42544616 original size:10 final size:10
Alignment explanation
Indices: 42544583--42544660 Score: 57
Period size: 10 Copynumber: 7.5 Consensus size: 10
42544573 AATGATTTCT
*
42544583 TAAATAATTA
1 TAAAAAATTA
* *
42544593 TGAAAATATCA
1 T-AAAAAATTA
42544604 TAAAAAATTA
1 TAAAAAATTA
*
42544614 TAAAAAAGTA
1 TAAAAAATTA
*
42544624 TTTAAAAATTA
1 -TAAAAAATTA
* * *
42544635 TTAAGAACTA
1 TAAAAAATTA
42544645 TAAAAAATTA
1 TAAAAAATTA
42544655 CTAAAA
1 -TAAAA
42544661 TTTTAAATTA
Statistics
Matches: 52, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
10 32 0.62
11 20 0.38
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:42545056 original size:31 final size:30
Alignment explanation
Indices: 42544978--42545057 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 30
42544968 TTTTTAATAA
42544978 ATTTTCAATAATTTTT-AATAATATCTTATC
1 ATTTT-AATAATTTTTAAATAATATCTTATC
* * *
42545008 ATTCTTATTAATTTTTAAATAACTTTTTTAT-
1 ATT-TTAATAATTTTTAAATAA-TATCTTATC
42545039 ATTTTAATAATTATTTAAA
1 ATTTTAATAATT-TTTAAA
42545058 AATTTATATG
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
30 20 0.48
31 16 0.38
32 6 0.14
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (30 bp):
ATTTTAATAATTTTTAAATAATATCTTATC
Found at i:42548255 original size:31 final size:29
Alignment explanation
Indices: 42548220--42548280 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
42548210 ACCATTTTCC
* * *
42548220 CAAGTTGGTGCTGAAACTTTTTTTTCGGTTA
1 CAAG-TGGTACTGAAAC-TATTCTTCGGTTA
*
42548251 CAAGTGGTACTTAAACTATTCTTCGGTTA
1 CAAGTGGTACTGAAACTATTCTTCGGTTA
42548280 C
1 C
42548281 TCATTTTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 12 0.46
30 10 0.38
31 4 0.15
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (29 bp):
CAAGTGGTACTGAAACTATTCTTCGGTTA
Found at i:42553428 original size:19 final size:19
Alignment explanation
Indices: 42553404--42553442 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
42553394 GGGTGTTTTA
42553404 TTTTTTTCTTATTTTTTCCT
1 TTTTTTTC-TATTTTTTCCT
*
42553424 TTTTTTTCTCTTTTTTCCT
1 TTTTTTTCTATTTTTTCCT
42553443 CGTGCCCACG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTTTCTATTTTTTCCT
Found at i:42568506 original size:66 final size:68
Alignment explanation
Indices: 42568428--42568561 Score: 211
Period size: 66 Copynumber: 2.0 Consensus size: 68
42568418 TAAGTTTTGA
* *
42568428 GGTGTTTTTTGAACTAATTTTTGGGTTCTTTGCATCTTGGAATATGTCGGTA-CTCAATC-TTTT
1 GGTGTTTTTTGAACTAATTTTTAGGTTCTTTGCATCTTGGAATATGTCAGTACCT-AATCTTTTT
42568491 AAGT
65 AAGT
*
42568495 GGTG-TTTTTGAACTAATTTTTAGGTTTTTTGCATCTTGGAATATGTCAGTACCTAATCTTTTTA
1 GGTGTTTTTTGAACTAATTTTTAGGTTCTTTGCATCTTGGAATATGTCAGTACCTAATCTTTTTA
42568559 AGT
66 AGT
42568562 ATCGATATAT
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
66 48 0.77
67 14 0.23
ACGTcount: A:0.21, C:0.11, G:0.19, T:0.49
Consensus pattern (68 bp):
GGTGTTTTTTGAACTAATTTTTAGGTTCTTTGCATCTTGGAATATGTCAGTACCTAATCTTTTTA
AGT
Found at i:42573401 original size:3 final size:3
Alignment explanation
Indices: 42573393--42573422 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
42573383 CAAACAAAAG
42573393 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
42573423 AATAAGCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:42574511 original size:11 final size:11
Alignment explanation
Indices: 42574485--42574526 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
42574475 TATTTTTTAT
**
42574485 AAAAATATTTA
1 AAAAATATAAA
42574496 AAAAAT-TAAA
1 AAAAATATAAA
42574506 AGAAAATATAAA
1 A-AAAATATAAA
42574518 AAAAATATA
1 AAAAATATA
42574527 TAATTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 3 0.11
11 19 0.70
12 5 0.19
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (11 bp):
AAAAATATAAA
Found at i:42574542 original size:27 final size:27
Alignment explanation
Indices: 42574508--42574569 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
42574498 AAATTAAAAG
* *
42574508 AAAATATAAAAAAAA-TATATAATTTTT
1 AAAATATAAAAAAAATTATA-AATTATA
*
42574535 AAAATATAAAAGAAATTATAAATTATA
1 AAAATATAAAAAAAATTATAAATTATA
42574562 AAAATATA
1 AAAATATA
42574570 TGTGTCTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (27 bp):
AAAATATAAAAAAAATTATAAATTATA
Found at i:42577893 original size:36 final size:38
Alignment explanation
Indices: 42577818--42577902 Score: 106
Period size: 36 Copynumber: 2.3 Consensus size: 38
42577808 TATATTTTTT
* *
42577818 ATAAT-ATTATATATTATGATTTTTTAATTCATATCTTA
1 ATAATAATTATATATTAT-ATTTATTAAATCATATCTTA
42577856 ATAATAATTATATATTAT-TTTATTAAAT-AGTAT-TTA
1 ATAATAATTATATATTATATTTATTAAATCA-TATCTTA
42577892 ATAATAATTAT
1 ATAATAATTAT
42577903 GTTAAAATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
36 15 0.35
37 11 0.26
38 5 0.12
39 12 0.28
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (38 bp):
ATAATAATTATATATTATATTTATTAAATCATATCTTA
Found at i:42577987 original size:25 final size:26
Alignment explanation
Indices: 42577936--42577987 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
42577926 ATTTTTATTT
*
42577936 TTATTAAAATATATTTAATAATAATC
1 TTATTAAAATATATATAATAATAATC
* *
42577962 TTATTAAAATTTA-ATAATAATCATC
1 TTATTAAAATATATATAATAATAATC
42577987 T
1 T
42577988 ACTTAACCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (26 bp):
TTATTAAAATATATATAATAATAATC
Found at i:42579754 original size:16 final size:16
Alignment explanation
Indices: 42579733--42579779 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
42579723 CCCCTAACAA
42579733 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
** *
42579749 CTCTATTTAATTATAG
1 CTCTATTCCATTACAG
*
42579765 CCCTATTCCATTACA
1 CTCTATTCCATTACA
42579780 ATCAACCAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:42580322 original size:10 final size:10
Alignment explanation
Indices: 42580307--42580332 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
42580297 GTTAGGGAGG
42580307 TAACGGAGCT
1 TAACGGAGCT
42580317 TAACGGAGCT
1 TAACGGAGCT
42580327 TAACGG
1 TAACGG
42580333 TAGAGTGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.31, T:0.19
Consensus pattern (10 bp):
TAACGGAGCT
Found at i:42580635 original size:18 final size:18
Alignment explanation
Indices: 42580612--42580661 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 18
42580602 TCTCTGCTAC
42580612 GCTGGTTCTTTGCCCTCT
1 GCTGGTTCTTTGCCCTCT
*
42580630 GCTGGTTTGTTCTGCCCTCT
1 GCTGG-TTCTT-TGCCCTCT
42580650 GCTGGTTCTTTG
1 GCTGGTTCTTTG
42580662 TTCCTCTGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 7 0.25
19 8 0.29
20 13 0.46
ACGTcount: A:0.00, C:0.28, G:0.26, T:0.46
Consensus pattern (18 bp):
GCTGGTTCTTTGCCCTCT
Found at i:42580669 original size:19 final size:19
Alignment explanation
Indices: 42580612--42580670 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
42580602 TCTCTGCTAC
42580612 GCTGGTTCTTTG-CCCTCT
1 GCTGGTTCTTTGTCCCTCT
*
42580630 GCTGGTT-TGTTCTGCCCTCT
1 GCTGGTTCT-TTGT-CCCTCT
*
42580650 GCTGGTTCTTTGTTCCTCT
1 GCTGGTTCTTTGTCCCTCT
42580669 GC
1 GC
42580671 CCTCTACCGG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 1 0.03
18 9 0.26
19 7 0.21
20 16 0.47
21 1 0.03
ACGTcount: A:0.00, C:0.31, G:0.24, T:0.46
Consensus pattern (19 bp):
GCTGGTTCTTTGTCCCTCT
Found at i:42580672 original size:26 final size:25
Alignment explanation
Indices: 42580569--42580675 Score: 86
Period size: 26 Copynumber: 4.5 Consensus size: 25
42580559 CCTTCTTCGC
*
42580569 TCTCTGCTCTCTGCTGGTTCTTTGTT
1 TCTCTGCCCTCTGCTGGTTCTTTG-T
* * *
42580595 TCTCTGCTCTCTGCTACG--C-TGGT
1 TCTCTGCCCTCTGCT-GGTTCTTTGT
*
42580618 TCTTTGCCCTCTGCTGGTT---TG-
1 TCTCTGCCCTCTGCTGGTTCTTTGT
42580639 T-TCTGCCCTCTGCTGGTTCTTTGT
1 TCTCTGCCCTCTGCTGGTTCTTTGT
42580663 TCCTCTGCCCTCT
1 T-CTCTGCCCTCT
42580676 ACCGGTGAGT
Statistics
Matches: 65, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
20 16 0.25
21 1 0.02
22 2 0.03
23 16 0.25
24 3 0.05
25 1 0.02
26 25 0.38
27 1 0.02
ACGTcount: A:0.01, C:0.33, G:0.20, T:0.47
Consensus pattern (25 bp):
TCTCTGCCCTCTGCTGGTTCTTTGT
Found at i:42580753 original size:17 final size:17
Alignment explanation
Indices: 42580731--42580764 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
42580721 ATTTTTGTTT
42580731 GTCTGGGATTGATTTTC
1 GTCTGGGATTGATTTTC
42580748 GTCTGGGATTGATTTTC
1 GTCTGGGATTGATTTTC
42580765 CTGAGGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.29, T:0.47
Consensus pattern (17 bp):
GTCTGGGATTGATTTTC
Found at i:42583592 original size:3 final size:3
Alignment explanation
Indices: 42583584--42583612 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
42583574 CTTAAAATGA
42583584 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
42583613 AGTTTAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:42584899 original size:25 final size:27
Alignment explanation
Indices: 42584849--42584908 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 27
42584839 TTTTAGTTCT
42584849 TTTATATATTTATATATATTTCATAAA
1 TTTATATATTTATATATATTTCATAAA
* *
42584876 TTTATA-ATTTATA-ATTTTTGATAAA
1 TTTATATATTTATATATATTTCATAAA
*
42584901 TGTATATA
1 TTTATATA
42584909 ATATATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 15 0.52
26 8 0.28
27 6 0.21
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (27 bp):
TTTATATATTTATATATATTTCATAAA
Found at i:42592110 original size:20 final size:21
Alignment explanation
Indices: 42592070--42592110 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
42592060 AAGTGTTGAA
*
42592070 TGGATTAAAAATTATTTTAAT
1 TGGATTAAAAATTAATTTAAT
*
42592091 TGGATT-AAAGTTAATTTAAT
1 TGGATTAAAAATTAATTTAAT
42592111 CATCTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (21 bp):
TGGATTAAAAATTAATTTAAT
Found at i:42604911 original size:25 final size:25
Alignment explanation
Indices: 42604877--42604929 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
42604867 TAGAGCACTT
*
42604877 AGTGCCTTTAGGTCAGTACATC-CA
1 AGTGCCTTTAAGTCAGTACATCTCA
42604901 AGTGCTCTTTAAGTCAGTACATCTCA
1 AGTGC-CTTTAAGTCAGTACATCTCA
42604927 AGT
1 AGT
42604930 TGCAAAGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 5 0.19
25 16 0.62
26 5 0.19
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (25 bp):
AGTGCCTTTAAGTCAGTACATCTCA
Found at i:42611585 original size:199 final size:199
Alignment explanation
Indices: 42611243--42611605 Score: 501
Period size: 199 Copynumber: 1.8 Consensus size: 199
42611233 CCGTTGGCAC
*
42611243 TGCTAAGTCTAAAGAAAAATTAGAAGCAGAAAGTCAAGATGTTCAAGTTATTGATCTAGTCAATA
1 TGCTAAGTCTAAAGAAAAATTAGAAGCAGAAAGTCAAGATGTTCAAGTTACTGATCTAGTCAATA
* * * *
42611308 ATCAGTATAATGATGATGGGCCACTTCAAACTTTAGTAAGAGTTCGAAAGAATAACTCACCTACT
66 ATCAGTATAATAATGATGGGACACTTCAAACTTTAGCAAGAGTTAGAAAGAATAACTCACCTACT
* *
42611373 AATATACTTGGTGATAATCATGATAAGATCAAAACAAGAGGCAGAGGGAGTGCCCTCTCTCCTTA
131 AACATAATTGGTGATAATCATGATAAGATCAAAACAAGAGGCAGAGGGAGTGCCCTCTCTCCTTA
42611438 ACAT
196 ACAT
* * * *
42611442 TGCTAAGTCTAAAGAAAAGTTAGAAGTAGAAAGTCAAGATGTTCAAGTTACTGATCTAGTCAGTG
1 TGCTAAGTCTAAAGAAAAATTAGAAGCAGAAAGTCAAGATGTTCAAGTTACTGATCTAGTCAATA
* * * * * * * * *
42611507 ATCAGTCTAATAATGATGTGACACTTTAACCTTTAGCAAGAGTTAGGAAGAATCACTTATCTATT
66 ATCAGTATAATAATGATGGGACACTTCAAACTTTAGCAAGAGTTAGAAAGAATAACTCACCTACT
* ** **
42611572 GACATAATTGGTGATGTTCATGATGGGATCAAAA
131 AACATAATTGGTGATAATCATGATAAGATCAAAA
42611606 TAAGGGGTAG
Statistics
Matches: 139, Mismatches: 25, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
199 139 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (199 bp):
TGCTAAGTCTAAAGAAAAATTAGAAGCAGAAAGTCAAGATGTTCAAGTTACTGATCTAGTCAATA
ATCAGTATAATAATGATGGGACACTTCAAACTTTAGCAAGAGTTAGAAAGAATAACTCACCTACT
AACATAATTGGTGATAATCATGATAAGATCAAAACAAGAGGCAGAGGGAGTGCCCTCTCTCCTTA
ACAT
Found at i:42612894 original size:14 final size:13
Alignment explanation
Indices: 42612854--42612904 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
42612844 TGAAGTATAT
*
42612854 TATTATTTTATTA
1 TATTATTATATTA
* *
42612867 TATT-GTAAATTA
1 TATTATTATATTA
42612879 TATTAATTATATTA
1 TATT-ATTATATTA
42612893 TATTATTATATT
1 TATTATTATATT
42612905 TCAAATAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 9 0.29
13 12 0.39
14 10 0.32
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TATTATTATATTA
Found at i:42613036 original size:11 final size:11
Alignment explanation
Indices: 42613017--42613047 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
42613007 AAGTAAGAAA
42613017 TATTATATTGT
1 TATTATATTGT
*
42613028 TATTTTATTGT
1 TATTATATTGT
42613039 TATTATATT
1 TATTATATT
42613048 AAACTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (11 bp):
TATTATATTGT
Found at i:42613763 original size:37 final size:38
Alignment explanation
Indices: 42613704--42613799 Score: 106
Period size: 39 Copynumber: 2.5 Consensus size: 38
42613694 CGGATAGATT
* * * *
42613704 CGATGAGGTACTGGGTACCAAC-TTGCTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACATTGCTTCGAACTAT-C
* *
42613741 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAAC-ATTGCTTCGAACTATC
42613780 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
42613800 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 18 0.38
39 27 0.56
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (38 bp):
CGATGAGGCACTGGGTGCCAACATTGCTTCGAACTATC
Found at i:42613783 original size:39 final size:38
Alignment explanation
Indices: 42613663--42613796 Score: 103
Period size: 39 Copynumber: 3.4 Consensus size: 38
42613653 AACCTTGAGT
* * *
42613663 CGATGAGACACTGGGTGTCATACTGTTACTTCGGATA-GATT
1 CGATGAGACACTGGGTGTCA-ACT-TTGCTTC-GA-ACTATC
** ** * *
42613704 CGATGAGGTACTGGGTACCAAC-TTGCTTCG-GCTTTGC
1 CGATGAGACACTGGGTGTCAACTTTGCTTCGAACTAT-C
42613741 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGACACTGGGTGTCAACT-TTGCTTCGAACTATC
*
42613780 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
42613797 CCATTCTGGT
Statistics
Matches: 72, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
36 1 0.01
37 19 0.26
38 6 0.08
39 25 0.35
40 5 0.07
41 16 0.22
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCAACTTTGCTTCGAACTATC
Found at i:42619786 original size:16 final size:16
Alignment explanation
Indices: 42619752--42619804 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
42619742 ATAGCATTAG
42619752 TCATGCAATACTCAAT
1 TCATGCAATACTCAAT
*
42619768 TCATG-AATACATCATT
1 TCATGCAATAC-TCAAT
* *
42619784 TCATACCATACTCAAT
1 TCATGCAATACTCAAT
42619800 TCATG
1 TCATG
42619805 AGTATATAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 5 0.17
16 21 0.70
17 4 0.13
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
TCATGCAATACTCAAT
Found at i:42620070 original size:37 final size:39
Alignment explanation
Indices: 42620023--42620125 Score: 129
Period size: 37 Copynumber: 2.6 Consensus size: 39
42620013 AATTCAAAGT
* *
42620023 AGTAAATTGACACCCAGTGTCTCATC-AGTTAAACCG-A
1 AGTAAATTGACACCCAGTGTCTCATCGAATAAAACCGAA
* *
42620060 AGTAAATTGACACCCAATGCCTCATCGAATAAAACCGAA
1 AGTAAATTGACACCCAGTGTCTCATCGAATAAAACCGAA
*
42620099 ATGATGAATTGACACCCAGTGTCTCAT
1 A-G-TAAATTGACACCCAGTGTCTCAT
42620126 TGACTTTAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
37 24 0.44
38 8 0.15
39 2 0.04
40 1 0.02
41 20 0.36
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (39 bp):
AGTAAATTGACACCCAGTGTCTCATCGAATAAAACCGAA
Found at i:42620265 original size:2 final size:2
Alignment explanation
Indices: 42620258--42620323 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
42620248 ATCATATTTG
42620258 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
42620300 CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA
42620324 TATATATATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:42622550 original size:3 final size:3
Alignment explanation
Indices: 42622544--42622581 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
42622534 GACGACCACG
42622544 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
42622582 TCAATTAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:42630625 original size:13 final size:13
Alignment explanation
Indices: 42630607--42630634 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42630597 TATAGGTAAA
42630607 CCTAGTTGTTTCT
1 CCTAGTTGTTTCT
42630620 CCTAGTTGTTTCT
1 CCTAGTTGTTTCT
42630633 CC
1 CC
42630635 ACTCTCGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.29, G:0.14, T:0.50
Consensus pattern (13 bp):
CCTAGTTGTTTCT
Found at i:42633674 original size:55 final size:55
Alignment explanation
Indices: 42633595--42633727 Score: 151
Period size: 55 Copynumber: 2.4 Consensus size: 55
42633585 AGACTTATAG
* * * * *
42633595 GGCCATGTGACCTTATTTCAAATACACACAC-GGTCTAGCACACGATTTGAGACAC
1 GGCCGTGTGACCTTATTTCGAATACACACACATG-CGAGCACACGAGTTGAGACAC
* * * *
42633650 GGTCGTGTGACCTTATTTCGAATACTCACACATGCGGGCACACGGGTTGAGACAC
1 GGCCGTGTGACCTTATTTCGAATACACACACATGCGAGCACACGAGTTGAGACAC
*
42633705 GGCCGTGTGACCCATATTTCGAA
1 GGCCGTGTGA-CCTTATTTCGAA
42633728 CTGTACACGA
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
55 53 0.82
56 12 0.18
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.24
Consensus pattern (55 bp):
GGCCGTGTGACCTTATTTCGAATACACACACATGCGAGCACACGAGTTGAGACAC
Found at i:42640337 original size:50 final size:50
Alignment explanation
Indices: 42640222--42640470 Score: 291
Period size: 50 Copynumber: 4.8 Consensus size: 50
42640212 GATAATAACA
* * ** * *
42640222 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
42640273 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
42640323 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
42640373 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTC---TCATC-T-CGG
* *
42640428 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
42640471 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
50 92 0.54
51 33 0.19
53 4 0.02
54 1 0.01
55 2 0.01
56 38 0.22
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:42640408 original size:100 final size:104
Alignment explanation
Indices: 42640221--42640470 Score: 346
Period size: 100 Copynumber: 2.4 Consensus size: 104
42640211 TGATAATAAC
** * *
42640221 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCCATGCCATG
* *
42640286 TCCCAGACATGGTCTTATAGGGGACCTC-TCATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
* *
42640323 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
*
42640387 CCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTC-T-TCATCTTAAGG
* *
42640428 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
42640471 TTACCCAAAT
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
100 48 0.37
101 36 0.27
103 4 0.03
104 1 0.01
105 2 0.02
106 40 0.31
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.27
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
Found at i:42656541 original size:16 final size:17
Alignment explanation
Indices: 42656506--42656544 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
42656496 AATAAATGAA
42656506 AAATATAAAAATATATT
1 AAATATAAAAATATATT
42656523 AAAT-TAAAAATA-ATAT
1 AAATATAAAAATATAT-T
42656539 AAATAT
1 AAATAT
42656545 TTTTTCAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.10
16 13 0.65
17 5 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATATAAAAATATATT
Found at i:42656542 original size:25 final size:24
Alignment explanation
Indices: 42656484--42656544 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
42656474 AATTATCTAT
* * *
42656484 ATATAAAATTGTAATAAATGAAAA
1 ATATAAAAATATATTAAATGAAAA
*
42656508 ATATAAAAATATATTAAATTAAAA
1 ATATAAAAATATATTAAATGAAAA
*
42656532 ATAATATAAATAT
1 AT-ATAAAAATAT
42656545 TTTTTCAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
24 22 0.71
25 9 0.29
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (24 bp):
ATATAAAAATATATTAAATGAAAA
Found at i:42660289 original size:72 final size:68
Alignment explanation
Indices: 42660213--42660350 Score: 195
Period size: 72 Copynumber: 2.0 Consensus size: 68
42660203 TGATTAAACT
* *
42660213 TAATCACTTTAATATTAAATTAATAGAATATTTATCTACAAAATAATTATTAAAATTAATTTAAT
1 TAATCACTTTAATATTAAATTAATAAAATA-TTAT-T--AAAATAAGTATTAAAATTAATTTAAT
42660278 ATTAAGC
62 ATTAAGC
* * *
42660285 TAATCACTTTAATATTAAATTAATAAAATATTATTAAGATGAGTATTAAATTTAATTTAATATTA
1 TAATCACTTTAATATTAAATTAATAAAATATTATTAAAATAAGTATTAAAATTAATTTAATATTA
42660350 A
66 A
42660351 ATCTATTAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
68 27 0.44
70 1 0.02
71 4 0.07
72 29 0.48
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.43
Consensus pattern (68 bp):
TAATCACTTTAATATTAAATTAATAAAATATTATTAAAATAAGTATTAAAATTAATTTAATATTA
AGC
Found at i:42660305 original size:36 final size:36
Alignment explanation
Indices: 42660213--42660317 Score: 106
Period size: 36 Copynumber: 2.9 Consensus size: 36
42660203 TGATTAAACT
* * *
42660213 TAATCACTTTAATATTAAATTAATAGAATATTTATC
1 TAATCACTTTAATATTAAATTAATAAAATATTAAGC
*** **
42660249 T-A-CAAAATAATTATTAAAATTAATTTAATATTAAGC
1 TAATCACTTTAA-TATT-AAATTAATAAAATATTAAGC
42660285 TAATCACTTTAATATTAAATTAATAAAATATTA
1 TAATCACTTTAATATTAAATTAATAAAATATTA
42660318 TTAAGATGAG
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
34 5 0.09
35 5 0.09
36 33 0.62
37 5 0.09
38 5 0.09
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.42
Consensus pattern (36 bp):
TAATCACTTTAATATTAAATTAATAAAATATTAAGC
Found at i:42660369 original size:68 final size:71
Alignment explanation
Indices: 42660222--42660369 Score: 160
Period size: 68 Copynumber: 2.1 Consensus size: 71
42660212 TTAATCACTT
* *
42660222 TAATATTAAATTAATAGAATATTTATCTACAAAATAATTATTAAAATTAATTTAATATTAAGCTA
1 TAATATTAAATTAATAAAATATTTATCTA-AAAATAAGTATTAAAATTAATTTAATATTAAGCTA
***
42660287 ATCACTT
65 ATCAAAA
* * * *
42660294 TAATATTAAATTAATAAAATA-TTAT-T-AAGATGAGTATTAAATTTAATTTAATATTAAATCT-
1 TAATATTAAATTAATAAAATATTTATCTAAAAATAAGTATTAAAATTAATTTAATATT-AAGCTA
*
42660355 ATTAAAA
65 ATCAAAA
42660362 TAATATTA
1 TAATATTA
42660370 TTTTTGGAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
68 36 0.55
69 4 0.06
70 1 0.02
71 4 0.06
72 20 0.31
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (71 bp):
TAATATTAAATTAATAAAATATTTATCTAAAAATAAGTATTAAAATTAATTTAATATTAAGCTAA
TCAAAA
Found at i:42665095 original size:21 final size:21
Alignment explanation
Indices: 42665071--42665182 Score: 100
Period size: 21 Copynumber: 5.3 Consensus size: 21
42665061 GTGTTTTACT
* *
42665071 TTCTGTTTAGCTCTTTTGAGC
1 TTCTGTTCAGCTCTTTCGAGC
42665092 TTCTGTTCAGCTCTTTCGAGC
1 TTCTGTTCAGCTCTTTCGAGC
* * *
42665113 TTTTGTCCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTTCGAGC
* ** *
42665134 TTCTATTCAATTCTTAT-GAGT
1 TTCTGTTCAGCTCTT-TCGAGC
** *
42665155 TTCTGTTCAGCTCTCACGTGC
1 TTCTGTTCAGCTCTTTCGAGC
42665176 TTCTGTT
1 TTCTGTT
42665183 GGCGTGTTCA
Statistics
Matches: 70, Mismatches: 19, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
21 70 1.00
ACGTcount: A:0.12, C:0.24, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTTCGAGC
Found at i:42665166 original size:42 final size:43
Alignment explanation
Indices: 42665069--42665179 Score: 111
Period size: 42 Copynumber: 2.6 Consensus size: 43
42665059 TCGTGTTTTA
* ** * *
42665069 CTTTCTGTTTAGCTCTTTTGAGCTTCTGTTCAGCTCTTTCGAG
1 CTTTCTGTTCAGCTCTTACGAGCTTCTATTCAACTCTTTCGAG
* *
42665112 CTTT-TGTCCAGCTCTTACGAGCTTCTATTCAATTCTTAT-GAG
1 CTTTCTGTTCAGCTCTTACGAGCTTCTATTCAACTCTT-TCGAG
* *
42665154 -TTTCTGTTCAGCTCTCACGTGCTTCT
1 CTTTCTGTTCAGCTCTTACGAGCTTCT
42665180 GTTGGCGTGT
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
41 3 0.05
42 48 0.86
43 5 0.09
ACGTcount: A:0.13, C:0.25, G:0.16, T:0.46
Consensus pattern (43 bp):
CTTTCTGTTCAGCTCTTACGAGCTTCTATTCAACTCTTTCGAG
Found at i:42668147 original size:51 final size:52
Alignment explanation
Indices: 42668057--42668175 Score: 165
Period size: 52 Copynumber: 2.3 Consensus size: 52
42668047 ATAGAAATTG
* *
42668057 TGAAAATGGAGAAATGAGAAACATTTGGAAATGATTGTGG-TTTTCTCCAAAA
1 TGAAAATGGAGAAATGAG-AACATTTGGAAATGAATGTGGTTTTTCTCAAAAA
*
42668109 TGAAAATGGAGAAATGTAG-TCATTTGGAAATGAATGTGGTTTTTCTCAAAAA
1 TGAAAATGGAGAAATG-AGAACATTTGGAAATGAATGTGGTTTTTCTCAAAAA
42668161 TGAAAAT-GA-AAATGA
1 TGAAAATGGAGAAATGA
42668176 CTTGGAAATG
Statistics
Matches: 62, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
49 1 0.02
50 5 0.08
51 20 0.32
52 34 0.55
53 2 0.03
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.29
Consensus pattern (52 bp):
TGAAAATGGAGAAATGAGAACATTTGGAAATGAATGTGGTTTTTCTCAAAAA
Found at i:42669112 original size:22 final size:22
Alignment explanation
Indices: 42669084--42669129 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
42669074 ACTACGATTT
*
42669084 AAAAAAA-AAGTTACTCTCTTGA
1 AAAAAAATAAATTAC-CTCTTGA
*
42669106 AAAAAAATAAATTTCCTCTTGA
1 AAAAAAATAAATTACCTCTTGA
42669128 AA
1 AA
42669130 GTTATTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.28
Consensus pattern (22 bp):
AAAAAAATAAATTACCTCTTGA
Found at i:42669396 original size:10 final size:10
Alignment explanation
Indices: 42669362--42669388 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
42669352 CGAGCATAAA
42669362 TTAAAAAAAT
1 TTAAAAAAAT
42669372 TTAAAAAAAT
1 TTAAAAAAAT
42669382 TTAAAAA
1 TTAAAAA
42669389 TATATAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
TTAAAAAAAT
Found at i:42670998 original size:18 final size:18
Alignment explanation
Indices: 42670975--42671025 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
42670965 TTTAGAGTTA
42670975 TGGGCCCACATGCCCGTG
1 TGGGCCCACATGCCCGTG
* *
42670993 TGGGCCTATATGCCCGTG
1 TGGGCCCACATGCCCGTG
*
42671011 TAGGCCCACATGCCC
1 TGGGCCCACATGCCC
42671026 ATATTGGCCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.14, C:0.37, G:0.29, T:0.20
Consensus pattern (18 bp):
TGGGCCCACATGCCCGTG
Found at i:42675221 original size:20 final size:20
Alignment explanation
Indices: 42675196--42675234 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
42675186 TACTCGCTTC
42675196 TTTACTTACTCGCTTACTTG
1 TTTACTTACTCGCTTACTTG
*
42675216 TTTACTTACTTGCTTACTT
1 TTTACTTACTCGCTTACTT
42675235 AAATAACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.23, G:0.08, T:0.54
Consensus pattern (20 bp):
TTTACTTACTCGCTTACTTG
Found at i:42685240 original size:22 final size:22
Alignment explanation
Indices: 42685202--42685253 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
42685192 ATTTTGAATA
42685202 AGGGATT-AAAATAAAATTGGT
1 AGGGATTAAAAATAAAATTGGT
*
42685223 AGGGATTAAAAATCAAATTGGT
1 AGGGATTAAAAATAAAATTGGT
42685245 AGGGATTAA
1 AGGGATTAA
42685254 CATGTCTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 7 0.24
22 22 0.76
ACGTcount: A:0.46, C:0.02, G:0.25, T:0.27
Consensus pattern (22 bp):
AGGGATTAAAAATAAAATTGGT
Found at i:42685655 original size:12 final size:11
Alignment explanation
Indices: 42685630--42685667 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
42685620 GAAAATGATG
42685630 AATTTTA-ATT
1 AATTTTATATT
42685640 AATTTTATAGTT
1 AATTTTATA-TT
42685652 AATTTT-TATT
1 AATTTTATATT
42685662 AATTTT
1 AATTTT
42685668 GACTATTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.58
11 3 0.12
12 8 0.31
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (11 bp):
AATTTTATATT
Found at i:42688835 original size:33 final size:33
Alignment explanation
Indices: 42688789--42688863 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
42688779 GATAAAATAA
* *
42688789 TAAATAAAATAGTTTAAATTTTTGTAGAACAAT
1 TAAATGAAGTAGTTTAAATTTTTGTAGAACAAT
42688822 TAAATGAAGTAGTTTAAATTTTTGTAGAACAAT
1 TAAATGAAGTAGTTTAAATTTTTGTAGAACAAT
42688855 TAAATGAAG
1 TAAATGAAG
42688864 CAGTCAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37
Consensus pattern (33 bp):
TAAATGAAGTAGTTTAAATTTTTGTAGAACAAT
Found at i:42689462 original size:23 final size:23
Alignment explanation
Indices: 42689430--42689483 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
42689420 GTTACTAAGC
* * *
42689430 ATATATTAATAATTAATATAATA
1 ATATAATAATAATTAAAATAAAA
*
42689453 ATATAATAATATTTAAAATAAAA
1 ATATAATAATAATTAAAATAAAA
*
42689476 ATAAAATA
1 ATATAATA
42689484 TAAATGATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
ATATAATAATAATTAAAATAAAA
Found at i:42689744 original size:24 final size:22
Alignment explanation
Indices: 42689667--42689744 Score: 59
Period size: 24 Copynumber: 3.3 Consensus size: 22
42689657 ATGTATAATA
*
42689667 AATATAAAAATTAATAATTATTT
1 AATATAAAAATTAA-AATTATAT
*
42689690 AATATTACAAAATTTAAATT-TAAT
1 AATA-TA-AAAATTAAAATTAT-AT
*
42689714 GATTATATAAAATATAAAATTATAT
1 -AATATA-AAAAT-TAAAATTATAT
42689739 AATATA
1 AATATA
42689745 CTAATTTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
23 5 0.12
24 19 0.44
25 18 0.42
26 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (22 bp):
AATATAAAAATTAAAATTATAT
Found at i:42696671 original size:16 final size:16
Alignment explanation
Indices: 42696650--42696680 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
42696640 TGAATGTCTA
42696650 GTTGGATTCATGATCG
1 GTTGGATTCATGATCG
42696666 GTTGGATTCATGATC
1 GTTGGATTCATGATC
42696681 CATAAGTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.13, G:0.29, T:0.39
Consensus pattern (16 bp):
GTTGGATTCATGATCG
Found at i:42702718 original size:14 final size:15
Alignment explanation
Indices: 42702699--42702731 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
42702689 GGTATAAAAT
*
42702699 AAAT-AAAGTAATAA
1 AAATAAAAGAAATAA
42702713 AAATAAAAGAAATAA
1 AAATAAAAGAAATAA
42702728 AAAT
1 AAAT
42702732 GCTAGATGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (15 bp):
AAATAAAAGAAATAA
Found at i:42704624 original size:45 final size:45
Alignment explanation
Indices: 42704530--42704918 Score: 373
Period size: 44 Copynumber: 8.6 Consensus size: 45
42704520 CTCATCCAAC
* * *
42704530 CCACTGCAACTTCAGGG-GTATAGGAATTG-TAAT-TTCAATCTACT
1 CCACTGCAACTTCAGGGAG-ATAAGATTTGCT-ATCTTCAATCTGCT
* * *
42704574 CCACTGCAACTTTAGAGAAATAAGATTTGCTATCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGCT
* * * * *
42704619 GCACTGTAACTTCAGGGAGATAAGATTCGTAGCTTGTAGCTTTAATCTGTT
1 CCACTGCAACTTCAGGGAGATAAGATT--T-GC---TATCTTCAATCTGCT
* * * *
42704670 TCACTGCAACTTTAGGGAAATAAGATTTGCTATCTTCAATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGCT
* * *
42704715 TCATTGCAACTTCAGGTAGATAAGATTTG-TATCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGCT
* *
42704759 CCACTGCAACTTCAAGGAGATAAGATTTACTATCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGCT
* *
42704804 CCACTTCAACCTT-AGGGAGA-AGAGATTTG-TAGT-TTTAATCTGCT
1 CCACTGCAA-CTTCAGGGAGATA-AGATTTGCTA-TCTTCAATCTGCT
* * ** *
42704848 CCAATGCAACTTCAGGGGGATAAGATTTG-TGGCTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGCT
42704892 CCACTGCAACTTCAGGGAGATAAGATT
1 CCACTGCAACTTCAGGGAGATAAGATT
42704919 CTCCACGATG
Statistics
Matches: 286, Mismatches: 43, Indels: 32
0.79 0.12 0.09
Matches are distributed among these distances:
43 3 0.01
44 133 0.47
45 106 0.37
46 3 0.01
47 1 0.00
48 4 0.01
49 1 0.00
51 35 0.12
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (45 bp):
CCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGCT
Found at i:42704830 original size:89 final size:88
Alignment explanation
Indices: 42704530--42704918 Score: 342
Period size: 89 Copynumber: 4.3 Consensus size: 88
42704520 CTCATCCAAC
* * * * * * * *
42704530 CCACTGCAACTTCAGGG-GTATAGGAATTGTAAT-TTCAATCTACTCCACTGCAACTTTAGAGAA
1 CCACTTCAACTTCAGGGAG-ATAAGATTTGT-ATCTTTAATCTGCTCCACTGCAACTTCAGGGAG
42704593 ATAAGATTTGCTATCTTCAATCTGCT
64 ATAAGATTT-CTATCTTCAATCTGCT
* * * * *
42704619 GCACTGT-AACTTCAGGGAGATAAGATTCGTAGCTTGTAGCTTTAATCTGTTTCACTGCAACTTT
1 CCACT-TCAACTTCAGGGAGATAAGA----T---TTGTATCTTTAATCTGCTCCACTGCAACTTC
* *
42704683 AGGGAAATAAGATTTGCTATCTTCAATCTACT
58 AGGGAGATAAGATTT-CTATCTTCAATCTGCT
* * * *
42704715 TCA-TTGCAACTTCAGGTAGATAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTCAAGGAGA
1 CCACTT-CAACTTCAGGGAGATAAGATTTGTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGA
42704779 TAAGATTTACTATCTTCAATCTGCT
65 TAAGATTT-CTATCTTCAATCTGCT
* *
42704804 CCACTTCAACCTT-AGGGAGA-AGAGATTTGTAGT-TTTAATCTGCTCCAATGCAACTTCAGGGG
1 CCACTTCAA-CTTCAGGGAGATA-AGATTTGTA-TCTTTAATCTGCTCCACTGCAACTTCAGGGA
* ** *
42704866 GATAAGATTTGTGGCTTTAATCTGCT
63 GATAAGATTTCTATCTTCAATCTGCT
*
42704892 CCACTGCAACTTCAGGGAGATAAGATT
1 CCACTTCAACTTCAGGGAGATAAGATT
42704919 CTCCACGATG
Statistics
Matches: 249, Mismatches: 33, Indels: 37
0.78 0.10 0.12
Matches are distributed among these distances:
87 3 0.01
88 33 0.13
89 129 0.52
90 7 0.03
92 1 0.00
94 1 0.00
95 2 0.01
96 73 0.29
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (88 bp):
CCACTTCAACTTCAGGGAGATAAGATTTGTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGAT
AAGATTTCTATCTTCAATCTGCT
Found at i:42709317 original size:24 final size:25
Alignment explanation
Indices: 42709276--42709351 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 25
42709266 AGCCCGGGCC
42709276 CCCAAACTAAACCTAACCCATCAGA
1 CCCAAACTAAACCTAACCCATCAGA
* *
42709301 CCCAAA-TAAATCAAACCCA-C---
1 CCCAAACTAAACCTAACCCATCAGA
*
42709321 CCCAAACTAAACCTAACCTATCAGA
1 CCCAAACTAAACCTAACCCATCAGA
42709346 CCCAAA
1 CCCAAA
42709352 TACAACCCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
20 6 0.15
21 10 0.24
22 1 0.02
23 1 0.02
24 11 0.27
25 12 0.29
ACGTcount: A:0.46, C:0.39, G:0.03, T:0.12
Consensus pattern (25 bp):
CCCAAACTAAACCTAACCCATCAGA
Found at i:42711771 original size:16 final size:15
Alignment explanation
Indices: 42711752--42711785 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
42711742 AATAAGCAAG
42711752 TAAATAAATAAATGGA
1 TAAATAAATAAAT-GA
42711768 TAAATAAATAAATGA
1 TAAATAAATAAATGA
42711783 TAA
1 TAA
42711786 TAAGAATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (15 bp):
TAAATAAATAAATGA
Found at i:42712685 original size:61 final size:61
Alignment explanation
Indices: 42712610--42712731 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
42712600 GAGAATGGTT
42712610 CTCTAAGTTTCAAAAACCCGTATGCCCGAAAGATGTGATCTTTCATCGGAGATGGCTGTCC
1 CTCTAAGTTTCAAAAACCCGTATGCCCGAAAGATGTGATCTTTCATCGGAGATGGCTGTCC
42712671 CTCTAAGTTTCAAAAACCCGTATGCCCGAAAGATGTGATCTTTCATCGGAGATGGCTGTCC
1 CTCTAAGTTTCAAAAACCCGTATGCCCGAAAGATGTGATCTTTCATCGGAGATGGCTGTCC
42712732 TCAGCCACTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (61 bp):
CTCTAAGTTTCAAAAACCCGTATGCCCGAAAGATGTGATCTTTCATCGGAGATGGCTGTCC
Found at i:42719680 original size:20 final size:20
Alignment explanation
Indices: 42719647--42719686 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
42719637 CTAACCCTCA
*
42719647 AAACTTTTTATTTTCCCCCT
1 AAACTTTTTATTTTCACCCT
42719667 AAAC-TTTTACTTTTCACCCT
1 AAACTTTTTA-TTTTCACCCT
42719687 TTACCCCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (20 bp):
AAACTTTTTATTTTCACCCT
Found at i:42723023 original size:18 final size:18
Alignment explanation
Indices: 42722989--42723022 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
42722979 AGAATGGGCT
42722989 TAAAAATATTATGAAAAC
1 TAAAAATATTATGAAAAC
42723007 TAAAAATATT-TGAAAA
1 TAAAAATATTATGAAAA
42723023 AAACTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (18 bp):
TAAAAATATTATGAAAAC
Found at i:42723078 original size:24 final size:24
Alignment explanation
Indices: 42723043--42723088 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
42723033 TAAATTAAAA
42723043 AATCAACAAAAATAAAAAAATTTT
1 AATCAACAAAAATAAAAAAATTTT
*
42723067 AATCAA-AGAAAATTAAAAAATT
1 AATCAACA-AAAATAAAAAAATT
42723089 AATGTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (24 bp):
AATCAACAAAAATAAAAAAATTTT
Found at i:42724049 original size:27 final size:27
Alignment explanation
Indices: 42724008--42724066 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
42723998 TGTTCAATAT
*
42724008 TATTAAATATATTAATTGAATTATTT-A
1 TATTAAATATATTAA-TAAATTATTTAA
* *
42724035 TATTTAATATTTTAATAAATTATTTAA
1 TATTAAATATATTAATAAATTATTTAA
42724062 TATTA
1 TATTA
42724067 CAATTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (27 bp):
TATTAAATATATTAATAAATTATTTAA
Found at i:42724317 original size:30 final size:28
Alignment explanation
Indices: 42724278--42724344 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
42724268 ACCAAAAAAA
42724278 GCCATTTTTTTAAAAAATTTACCGAAATGG
1 GCCA-TTTTTT-AAAAATTTACCGAAATGG
** *
42724308 GCCACTTTTTTAATTATTTACCGGAATGG
1 GCCA-TTTTTTAAAAATTTACCGAAATGG
42724337 GCCATTTT
1 GCCATTTT
42724345 CCGCGAAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 4 0.12
29 19 0.58
30 10 0.30
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.40
Consensus pattern (28 bp):
GCCATTTTTTAAAAATTTACCGAAATGG
Found at i:42724791 original size:125 final size:124
Alignment explanation
Indices: 42724566--42724843 Score: 425
Period size: 125 Copynumber: 2.2 Consensus size: 124
42724556 TTTCGAGTTC
**
42724566 ACGTTTCTG-GTCAAATAGTATAAAATCGCTTTTACCAGGATGCTATCAGAGAAGAAATTGTGAA
1 ACGTTTCTGAG-CAAATAGTATAAAATCGCTGATACCAGGATGCTATCAGAGAAGAAATTGTGAA
* * * *
42724630 ATCGTGCCCTCGTGGACGCGATTTTGGTACAATTGGTCATGTAAGAAATAATTTTTTTTG
65 ATCGAGCCCTCGTGGACGCGATTTCGCTACAATTGGTCATGTAAGAAATAATTATTTTTG
42724690 ACGTTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTAT-ATGAGAAGAAATTGTGA
1 ACG-TTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATCA-GAGAAGAAATTGTGA
* *
42724754 AATCGAGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTATTTTTG
64 AATCGAGCCCTCGTGGACGCGATTTCGCTACAATTGGTCATGTAAGAAATAATTATTTTTG
* *
42724815 ACGTTTCTGAGCAAATAGTGTCAAATCGC
1 ACGTTTCTGAGCAAATAGTATAAAATCGC
42724844 GCCCTCGTGG
Statistics
Matches: 141, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
124 28 0.20
125 112 0.79
126 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (124 bp):
ACGTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATCAGAGAAGAAATTGTGAAA
TCGAGCCCTCGTGGACGCGATTTCGCTACAATTGGTCATGTAAGAAATAATTATTTTTG
Found at i:42725813 original size:30 final size:30
Alignment explanation
Indices: 42725725--42725842 Score: 152
Period size: 29 Copynumber: 4.0 Consensus size: 30
42725715 TTTATTTTTG
42725725 CATTTTGACCCCTAAACTTTCTC-AAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
** * *
42725754 CATTTCAACACCTAAACTTT-TCTAAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
42725783 CATTTTGACCCCTAAACTTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
* * *
42725813 CATTTGGA-CCTTAAAATTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
42725842 C
1 C
42725843 GTTTCGGCCC
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
28 2 0.03
29 60 0.78
30 15 0.19
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (30 bp):
CATTTTGACCCCTAAACTTTCTCAAAATTA
Found at i:42725857 original size:29 final size:28
Alignment explanation
Indices: 42725777--42725857 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
42725767 AAACTTTTCT
* *
42725777 AAATTACATTTTGACCCCTAAACTTTCTCA
1 AAATTACA-TTTGGCCCC-AAAATTTCTCA
**
42725807 AAATTACATTTGGACCTTAAAATTTCTCA
1 AAATTACATTTGG-CCCCAAAATTTCTCA
*
42725836 AAATTACGTTTCGGCCCCAAAA
1 AAATTACATTT-GGCCCCAAAA
42725858 GATTTACTGC
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
29 30 0.71
30 12 0.29
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (28 bp):
AAATTACATTTGGCCCCAAAATTTCTCA
Found at i:42726218 original size:10 final size:10
Alignment explanation
Indices: 42726179--42726245 Score: 55
Period size: 10 Copynumber: 6.4 Consensus size: 10
42726169 CCAAGAGGCA
42726179 AAAAAAGAA-
1 AAAAAAGAAG
*
42726188 AAAAAACAAG
1 AAAAAAGAAG
*
42726198 CAAGCAAAAGAGG
1 -AA--AAAAGAAG
42726211 AAAAAAGAAAG
1 AAAAAAG-AAG
**
42726222 AGTAAAGAAG
1 AAAAAAGAAG
42726232 AAAAAAGAAG
1 AAAAAAGAAG
42726242 AAAA
1 AAAA
42726246 GAGAGGAGAG
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
9 8 0.18
10 20 0.44
11 9 0.20
12 2 0.04
13 6 0.13
ACGTcount: A:0.75, C:0.04, G:0.19, T:0.01
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:42726362 original size:4 final size:4
Alignment explanation
Indices: 42726355--42726438 Score: 93
Period size: 4 Copynumber: 20.8 Consensus size: 4
42726345 AAAATGGAAG
*
42726355 AAGA AAGA AAGA AAGA AAGA AAGA AAG- AAGA AAGA AAGA AAAA GAAGAA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA -AAG-A
*
42726404 AAGGA AAGA AA-A AAGA AA-A AAGAA AAAA AAGA AAG
1 AA-GA AAGA AAGA AAGA AAGA AAG-A AAGA AAGA AAG
42726439 GAAAAAAATA
Statistics
Matches: 69, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
3 9 0.13
4 48 0.70
5 10 0.14
6 2 0.03
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:42726384 original size:27 final size:26
Alignment explanation
Indices: 42726352--42726444 Score: 89
Period size: 27 Copynumber: 3.3 Consensus size: 26
42726342 AGAAAAATGG
42726352 AAGAAGAAAGAAAGAAAGAAAGAAAGA
1 AAGAA-AAAGAAAGAAAGAAAGAAAGA
*
42726379 AAGAAGAAAGAAAGAAAAAGAAGAAAAGGA
1 AAGAA-AAAGAAAGAAAGA-AAG-AAA-GA
*
42726409 AAGAAAAAAGAAA-AAAGAAAAAAAAGA
1 AAG-AAAAAGAAAGAAAG-AAAGAAAGA
42726436 AAGGAAAAA
1 AA-GAAAAA
42726445 AATATTCTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
27 27 0.47
28 7 0.12
29 8 0.14
30 13 0.23
31 2 0.04
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (26 bp):
AAGAAAAAGAAAGAAAGAAAGAAAGA
Found at i:42726385 original size:23 final size:23
Alignment explanation
Indices: 42726359--42726438 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
42726349 TGGAAGAAGA
42726359 AAGAAAGAAAGAAAGAAAGAAAG
1 AAGAAAGAAAGAAAGAAAGAAAG
*
42726382 AAGAAAGAAAGAAAAAGAAGAAA-
1 AAGAAAGAAAGAAAGA-AAGAAAG
*
42726405 AGGAAAGAAA-AAAGAAA-AAAG
1 AAGAAAGAAAGAAAGAAAGAAAG
42726426 AA-AAA-AAAGAAAG
1 AAGAAAGAAAGAAAG
42726439 GAAAAAAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
19 3 0.06
20 10 0.20
21 3 0.06
22 4 0.08
23 24 0.48
24 6 0.12
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (23 bp):
AAGAAAGAAAGAAAGAAAGAAAG
Found at i:42726385 original size:41 final size:40
Alignment explanation
Indices: 42726335--42726431 Score: 108
Period size: 41 Copynumber: 2.4 Consensus size: 40
42726325 TGCTGAAAGG
* * *
42726335 AGAAGGAAGAAAAATGGAAGAAGAA-AGAAA-GAAAGAAAGAA
1 AGAAAGAAGAAAAA-AGAAAAAGAAGA-AAAGGAAAGAAA-AA
42726376 AGAAAGAAGAAAGAAAGAAAAAGAAGAAAAGGAAAGAAAAA
1 AGAAAGAAGAAA-AAAGAAAAAGAAGAAAAGGAAAGAAAAA
*
42726417 AGAAAAAAGAAAAAA
1 AGAAAGAAGAAAAAA
42726432 AAGAAAGGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
40 3 0.06
41 35 0.71
42 11 0.22
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.01
Consensus pattern (40 bp):
AGAAAGAAGAAAAAAGAAAAAGAAGAAAAGGAAAGAAAAA
Found at i:42726443 original size:19 final size:17
Alignment explanation
Indices: 42726352--42726438 Score: 90
Period size: 19 Copynumber: 4.9 Consensus size: 17
42726342 AGAAAAATGG
42726352 AAGAAGAAAGAAAGAAAGA
1 AAGAA-AAA-AAAGAAAGA
42726371 AAGAAAGAAAGAAGAAAGA
1 AAGAAA-AAA-AAGAAAGA
*
42726390 AAGAAAAAGAAGAAAAGGA
1 AAGAAAAAAAAG-AAA-GA
42726409 AAG--AAAAAAGAAA-A
1 AAGAAAAAAAAGAAAGA
42726423 AAGAAAAAAAAGAAAG
1 AAGAAAAAAAAGAAAG
42726439 GAAAAAAATA
Statistics
Matches: 59, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
14 4 0.07
16 13 0.22
17 9 0.15
18 7 0.12
19 26 0.44
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAGAAAGA
Found at i:42726486 original size:10 final size:11
Alignment explanation
Indices: 42726471--42726499 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
42726461 TCGGGTTAAA
42726471 CCGACCCGAC-
1 CCGACCCGACT
42726481 CCGACCCGACT
1 CCGACCCGACT
42726492 CCGACCCG
1 CCGACCCG
42726500 TGACCGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.17, C:0.59, G:0.21, T:0.03
Consensus pattern (11 bp):
CCGACCCGACT
Found at i:42726750 original size:7 final size:7
Alignment explanation
Indices: 42726739--42726815 Score: 79
Period size: 7 Copynumber: 11.0 Consensus size: 7
42726729 ATAAAGAGAG
42726739 AAGAAAA
1 AAGAAAA
*
42726746 CAGAAAA
1 AAGAAAA
42726753 AAGAAAA
1 AAGAAAA
42726760 AGAGAAAAA
1 A-AG-AAAA
*
42726769 AAGGAAA
1 AAGAAAA
42726776 AAGAAAA
1 AAGAAAA
42726783 AAG--AA
1 AAGAAAA
42726788 AAG-AAA
1 AAGAAAA
*
42726794 AGGAAAA
1 AAGAAAA
42726801 AAGAGAAA
1 AAGA-AAA
42726809 AAGAAAA
1 AAGAAAA
42726816 GAAAAGGTCA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
5 5 0.08
6 4 0.07
7 34 0.58
8 11 0.19
9 5 0.08
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:42726760 original size:8 final size:8
Alignment explanation
Indices: 42726749--42726815 Score: 66
Period size: 8 Copynumber: 8.4 Consensus size: 8
42726739 AAGAAAACAG
42726749 AAAAAAGA
1 AAAAAAGA
*
42726757 AAAAGAGA
1 AAAAAAGA
42726765 AAAAAAG-
1 AAAAAAGA
*
42726772 GAAAAAG-
1 AAAAAAGA
42726779 AAAAAAGAA
1 AAAAAAG-A
*
42726788 AAGAAAAGG
1 AA-AAAAGA
42726797 AAAAAAGA
1 AAAAAAGA
*
42726805 GAAAAAGA
1 AAAAAAGA
42726813 AAA
1 AAA
42726816 GAAAAGGTCA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
7 12 0.25
8 27 0.56
9 4 0.08
10 5 0.10
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:42726765 original size:15 final size:15
Alignment explanation
Indices: 42726742--42726815 Score: 68
Period size: 13 Copynumber: 5.2 Consensus size: 15
42726732 AAGAGAGAAG
*
42726742 AAAACAGAAAAAAGA
1 AAAAGAGAAAAAAGA
*
42726757 AAAAGAGAAAAAAAGG
1 AAAAGAG-AAAAAAGA
42726773 AAAA-AGAAAAAAG-
1 AAAAGAGAAAAAAGA
**
42726786 AAAAGA-AAAGGA-A
1 AAAAGAGAAAAAAGA
42726799 AAAAGAG-AAAAAGA
1 AAAAGAGAAAAAAGA
42726813 AAA
1 AAA
42726816 GAAAAGGTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
13 17 0.35
14 12 0.25
15 8 0.17
16 11 0.23
ACGTcount: A:0.80, C:0.01, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAGAGAAAAAAGA
Found at i:42726777 original size:18 final size:18
Alignment explanation
Indices: 42726756--42726810 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
42726746 CAGAAAAAAG
*
42726756 AAAAAGAGAAAAAA-AG-G
1 AAAAAG-GAAAAAAGAGAA
42726773 AAAAA-GAAAAAAGA-AA
1 AAAAAGGAAAAAAGAGAA
42726789 AGAAAAGGAAAAAAGAGAA
1 A-AAAAGGAAAAAAGAGAA
42726808 AAA
1 AAA
42726811 GAAAAGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
15 7 0.22
16 2 0.06
17 9 0.28
18 11 0.34
19 3 0.09
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGGAAAAAAGAGAA
Found at i:42726802 original size:20 final size:20
Alignment explanation
Indices: 42726751--42726820 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
42726741 GAAAACAGAA
42726751 AAAAGAAAAAGAGAA-AAAAAGG
1 AAAAGAAAAA-A-AAGAAAAA-G
*
42726773 AAAA-AGAAAAAAG-AAAAG
1 AAAAGAAAAAAAAGAAAAAG
*
42726791 AAAAGGAAAAAAGAGAAAAAG
1 AAAA-GAAAAAAAAGAAAAAG
42726812 AAAAGAAAA
1 AAAAGAAAA
42726821 GGTCAATTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
18 5 0.12
19 6 0.15
20 13 0.32
21 13 0.32
22 4 0.10
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAAAAAGAAAAAG
Found at i:42726802 original size:26 final size:25
Alignment explanation
Indices: 42726739--42726822 Score: 111
Period size: 26 Copynumber: 3.4 Consensus size: 25
42726729 ATAAAGAGAG
*
42726739 AAGAAAACAGAAAAAAG-AAAAAGAGA
1 AAGAAAA-GGAAAAAAGAAAAAAGA-A
42726765 AA-AAAAGG-AAAAAGAAAAAAGAA
1 AAGAAAAGGAAAAAAGAAAAAAGAA
42726788 AAGAAAAGGAAAAAAGAGAAAAAGAA
1 AAGAAAAGGAAAAAAGA-AAAAAGAA
42726814 AAGAAAAGG
1 AAGAAAAGG
42726823 TCAATTTGTG
Statistics
Matches: 53, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
23 9 0.17
24 14 0.26
25 11 0.21
26 19 0.36
ACGTcount: A:0.77, C:0.01, G:0.21, T:0.00
Consensus pattern (25 bp):
AAGAAAAGGAAAAAAGAAAAAAGAA
Found at i:42727003 original size:22 final size:23
Alignment explanation
Indices: 42726959--42727005 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
42726949 GCATTTTTAT
*
42726959 ATTTTTATTTTTAATTTAATTCA
1 ATTTTTATTTTTAATATAATTCA
42726982 ATTTTTA-TTTTAA-ATAATTTCA
1 ATTTTTATTTTTAATATAA-TTCA
42727004 AT
1 AT
42727006 AAATAAGGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 12 0.55
23 7 0.32
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTTTTATTTTTAATATAATTCA
Found at i:42727157 original size:15 final size:16
Alignment explanation
Indices: 42727124--42727159 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
42727114 AAATATTCTA
42727124 AAATTCTCGTGATTTTT
1 AAATTCTCGTGA-TTTT
42727141 AAATTCTCGTG-TTTT
1 AAATTCTCGTGATTTT
42727156 AAAT
1 AAAT
42727160 AGAATCACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.42
17 11 0.58
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (16 bp):
AAATTCTCGTGATTTT
Found at i:42727294 original size:17 final size:18
Alignment explanation
Indices: 42727274--42727315 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
42727264 TTAAAAAAAA
*
42727274 TCGTG-TGTCAAAAATTT
1 TCGTGTTGTAAAAAATTT
*
42727291 TCGTGTTTTAAAAAATTT
1 TCGTGTTGTAAAAAATTT
*
42727309 TCATGTT
1 TCGTGTT
42727316 TTCAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.48
Consensus pattern (18 bp):
TCGTGTTGTAAAAAATTT
Found at i:42727304 original size:18 final size:18
Alignment explanation
Indices: 42727283--42727458 Score: 90
Period size: 18 Copynumber: 9.3 Consensus size: 18
42727273 ATCGTGTGTC
42727283 AAAAATTTTCGTGTTTTA
1 AAAAATTTTCGTGTTTTA
*
42727301 AAAAATTTTCATGTTTTCAA
1 AAAAATTTTCGTGTTTT--A
** *
42727321 AAAAATTCCCCGTGTTTTC
1 AAAAATT-TTCGTGTTTTA
* * *
42727340 AAAAATTCTCGT-ATTTC
1 AAAAATTTTCGTGTTTTA
* *
42727357 GAAAATTTTCTTGTTTTCAAA
1 AAAAATTTTCGTGTTTT---A
*
42727378 AAAAATTTTCCGTG-TTTC
1 AAAAATTTT-CGTGTTTTA
*
42727396 ATAAA-TTTCTGTGTTTTCAAA
1 AAAAATTTTC-GTGTTTT---A
* *
42727417 AAAAATTTCTCGT-CTTTC
1 AAAAATTT-TCGTGTTTTA
42727435 AAAAATTTTCGTGTTTTCA
1 AAAAATTTTCGTGTTTT-A
42727454 AAAAA
1 AAAAA
42727459 ATTGACCGTG
Statistics
Matches: 119, Mismatches: 22, Indels: 33
0.68 0.13 0.19
Matches are distributed among these distances:
16 1 0.01
17 23 0.19
18 41 0.34
19 12 0.10
20 8 0.07
21 25 0.21
22 7 0.06
23 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.44
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTA
Found at i:42727384 original size:21 final size:21
Alignment explanation
Indices: 42727358--42727459 Score: 78
Period size: 21 Copynumber: 5.1 Consensus size: 21
42727348 TCGTATTTCG
42727358 AAAATTTTCTTGTTTTCAAAA
1 AAAATTTTCTTGTTTTCAAAA
*
42727379 AAAATTTTC-CGTGTTTC---A
1 AAAATTTTCTTGT-TTTCAAAA
*
42727397 TAAA-TTTCTGTGTTTTCAAAA
1 AAAATTTTCT-TGTTTTCAAAA
*
42727418 AAAA-TTTCTCGTCTTTC---A
1 AAAATTTTCTTGT-TTTCAAAA
*
42727436 AAAATTTTCGTGTTTTCAAAA
1 AAAATTTTCTTGTTTTCAAAA
42727457 AAA
1 AAA
42727460 TTGACCGTGT
Statistics
Matches: 63, Mismatches: 7, Indels: 22
0.68 0.08 0.24
Matches are distributed among these distances:
17 4 0.06
18 17 0.27
19 8 0.13
20 4 0.06
21 30 0.48
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (21 bp):
AAAATTTTCTTGTTTTCAAAA
Found at i:42727396 original size:56 final size:56
Alignment explanation
Indices: 42727275--42727419 Score: 150
Period size: 56 Copynumber: 2.6 Consensus size: 56
42727265 TAAAAAAAAT
* * *
42727275 CGTGTGTCAAAAATTTTCGTGTTTTAAAAAATTTTCATGTTTTCAAAAAAATTCCC
1 CGTGTTTCAAAAATTCTCGTGATTTAAAAAATTTTCATGTTTTCAAAAAAATTCCC
** * **
42727331 CGTGTTTTCAAAAATTCTCGT-ATTTCGAAAATTTTCTTGTTTTCAAAAAAAATTTTC
1 CGTG-TTTCAAAAATTCTCGTGATTTAAAAAATTTTCATGTTTTC-AAAAAAATTCCC
* *
42727388 CGTGTTTCATAAATT-TCTGTGTTTTCAAAAAA
1 CGTGTTTCAAAAATTCTC-GTGATTT-AAAAAA
42727420 AATTTCTCGT
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
55 2 0.03
56 35 0.49
57 31 0.43
58 4 0.06
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.43
Consensus pattern (56 bp):
CGTGTTTCAAAAATTCTCGTGATTTAAAAAATTTTCATGTTTTCAAAAAAATTCCC
Found at i:42727412 original size:39 final size:39
Alignment explanation
Indices: 42727359--42727499 Score: 182
Period size: 39 Copynumber: 3.6 Consensus size: 39
42727349 CGTATTTCGA
*
42727359 AAATTTTCTTGTTTTCAAAAAAAATTTTCCGTGTTTCAT
1 AAATTTTCGTGTTTTCAAAAAAAATTTTCCGTGTTTCAT
* *
42727398 AAA-TTTCTGTGTTTTCAAAAAAAA-TTTCTCGTCTTTCAA
1 AAATTTTC-GTGTTTTCAAAAAAAATTTTC-CGTGTTTCAT
**
42727437 AAATTTTCGTGTTTTC-AAAAAAATTGACCGTGTTTCAT
1 AAATTTTCGTGTTTTCAAAAAAAATTTTCCGTGTTTCAT
42727475 AAATTTTCGTG-TTTCAAAAGAAAAT
1 AAATTTTCGTGTTTTCAAAA-AAAAT
42727500 CCTCGTGTTT
Statistics
Matches: 89, Mismatches: 7, Indels: 12
0.82 0.06 0.11
Matches are distributed among these distances:
37 4 0.04
38 37 0.42
39 44 0.49
40 4 0.04
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (39 bp):
AAATTTTCGTGTTTTCAAAAAAAATTTTCCGTGTTTCAT
Found at i:42727457 original size:77 final size:77
Alignment explanation
Indices: 42727281--42727499 Score: 231
Period size: 77 Copynumber: 2.9 Consensus size: 77
42727271 AAATCGTGTG
* * * *
42727281 TCAAAAATTTTCGTGTTTT--AAAAAATTTT-CATGTTTTCAAAAAAATTCCCCGTGTTTTC---
1 TCAAAAATTTTCGTGTTTTCAAAAAAATTTTCCGTG-TTTC--ATAAATT-TCTGTGTTTTCAAA
42727340 AAAAA-TTCTCGTATT
62 AAAAATTTCTCGTATT
* *
42727355 TCGAAAATTTTCTTGTTTTCAAAAAAAATTTTCCGTGTTTCATAAATTTCTGTGTTTTCAAAAAA
1 TCAAAAATTTTCGTGTTTTC-AAAAAAATTTTCCGTGTTTCATAAATTTCTGTGTTTTCAAAAAA
*
42727420 AATTTCTCGTCTT
65 AATTTCTCGTATT
**
42727433 TCAAAAATTTTCGTGTTTTCAAAAAAATTGACCGTGTTTCATAAATTT-TCGTG-TTTCAAAAGA
1 TCAAAAATTTTCGTGTTTTCAAAAAAATTTTCCGTGTTTCATAAATTTCT-GTGTTTTCAAAA-A
42727496 AAAT
64 AAAT
42727500 CCTCGTGTTT
Statistics
Matches: 124, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
74 26 0.21
75 6 0.05
76 9 0.07
77 53 0.43
78 30 0.24
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.43
Consensus pattern (77 bp):
TCAAAAATTTTCGTGTTTTCAAAAAAATTTTCCGTGTTTCATAAATTTCTGTGTTTTCAAAAAAA
ATTTCTCGTATT
Found at i:42727507 original size:38 final size:38
Alignment explanation
Indices: 42727340--42727510 Score: 190
Period size: 38 Copynumber: 4.4 Consensus size: 38
42727330 CCGTGTTTTC
* *
42727340 AAAAATTCTCGTATTTCGA-AAATTTTCTTGTTTTCAAA
1 AAAAATTCTCGTGTTTC-ATAAATTTTCGTGTTTTCAAA
*
42727378 AAAAATTTTCCGTGTTTCATAAA-TTTCTGTGTTTTCAAA
1 AAAAATTCT-CGTGTTTCATAAATTTTC-GTGTTTTCAAA
* *
42727417 AAAAATTTCTCGTCTTTCAAAAATTTTCGTGTTTTC-AA
1 AAAAA-TTCTCGTGTTTCATAAATTTTCGTGTTTTCAAA
42727455 AAAAATTGAC-CGTGTTTCATAAATTTTCGTG-TTTCAAA
1 AAAAATT--CTCGTGTTTCATAAATTTTCGTGTTTTCAAA
*
42727493 AGAAAATCCTCGTGTTTC
1 A-AAAATTCTCGTGTTTC
42727511 GTATTTTATC
Statistics
Matches: 114, Mismatches: 9, Indels: 20
0.80 0.06 0.14
Matches are distributed among these distances:
37 7 0.06
38 50 0.44
39 50 0.44
40 7 0.06
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.43
Consensus pattern (38 bp):
AAAAATTCTCGTGTTTCATAAATTTTCGTGTTTTCAAA
Found at i:42734667 original size:14 final size:14
Alignment explanation
Indices: 42734650--42734676 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42734640 CTTTTAAGAA
42734650 TTATATTTTTCAAT
1 TTATATTTTTCAAT
42734664 TTATATTTTTCAA
1 TTATATTTTTCAA
42734677 AAAAATCAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (14 bp):
TTATATTTTTCAAT
Found at i:42734779 original size:76 final size:74
Alignment explanation
Indices: 42734678--42736069 Score: 1641
Period size: 76 Copynumber: 18.2 Consensus size: 74
42734668 ATTTTTCAAA
* * *
42734678 AAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGT-CATGCCGAGGTATTTCTTTTAAA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTA--T-TTTTAAA
42734742 TTTCTGTTTTTT
63 TTTCTGTTTTTT
* * * *
42734754 TAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT-CACGCTGAGGTATTTTTTTAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTA-TTTTTAAATT
*
42734818 TCTATTTTTTT
65 TCT-GTTTTTT
* ** *
42734829 CAAAAATCAACTCATAATATGAGAGGTGAGTTGAGCCTCGGGT-CACGCTGAGGTATTTTTCTAA
1 --AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTTT-AAA
42734893 TTTCTGTTTTTT
63 TTTCTGTTTTTT
* *
42734905 CAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT-CACGCTGAGGTATTTTTTTTA
1 --AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTA---TTTTT-
*
42734969 AAATTTCTATTTTTT
60 AAATTTCTGTTTTTT
* *
42734984 AAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA-TTTTAAAT
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTTTAAAT
42735048 TTCTGTTTTTT
64 TTCTGTTTTTT
*
42735059 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCGCACGCTGAGGTA-TTTTAAA
1 --AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTTTAAA
42735123 TTTCTGTTTTTT
63 TTTCTGTTTTTT
42735135 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA-TTTTAAA
1 --AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTTTAAA
*
42735199 TTTCTATTTTTT
63 TTTCTGTTTTTT
*
42735211 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGTTGAGGTA-TTTTAAA
1 --AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTTTAAA
* *
42735275 TTTTTATTTTTT
63 TTTCTGTTTTTT
42735287 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTAAA
1 --AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTTTAAA
* *
42735352 TTTCTATTTTTCAA
63 TTTCTGTTTTT--T
42735366 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTA--T-TTTTAA
**
42735431 ATTTCTGTTTTCA
62 ATTTCTGTTTTTT
*
42735444 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGGGTCGCACGCTGAGGTA-TTTTAAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTTTAAATT
*
42735508 TCTGTTTTTCAA
65 TCTGTTTTT--T
*
42735520 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCCGGT-CACGCTGAGGTA-TTTTAAA-TT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTTTAAATTT
*
42735582 AT-TTTTTT
66 CTGTTTTTT
* * * *
42735590 -AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-CGACACATGCTGAGGTATTTCTTTTAA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTA--T-TTTTAA
*
42735653 ATTTCTGTTTTTCA
62 ATTTCTGTTTTT-T
* * *
42735667 AAAATCAACTCATAATGTGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA-TTTTAAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTTTAAATT
*
42735731 TCTATTTTTT
65 TCTGTTTTTT
42735741 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTTTT
1 --AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTA---TTTTT
* *
42735806 GAATTTCTG-TTTTC
60 AAATTTCTGTTTTTT
*
42735820 AAATATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA-TTTTAAAT
1 AAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTTTAAAT
*
42735884 TTCTGTTTTTCAA
64 TTCTGTTTTT--T
* * *
42735897 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGGCTCGGGTCGTACGCTGAGGTATTTTTTTTAA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTA---TTTTTAA
42735962 ATTTCTGCTTTTTTT
62 ATTTCTG--TTTTTT
42735977 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTT
1 --AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTA--T-TTTT
**
42736042 AAATTTCTGTTTTCA
60 AAATTTCTGTTTTTT
42736057 AAAATCAACTCAT
1 AAAATCAACTCAT
42736070 NNNNNNNNNN
Statistics
Matches: 1201, Mismatches: 67, Indels: 94
0.88 0.05 0.07
Matches are distributed among these distances:
68 1 0.00
69 35 0.03
70 11 0.01
72 5 0.00
73 3 0.00
74 66 0.05
75 46 0.04
76 539 0.45
77 137 0.11
78 193 0.16
79 36 0.03
80 56 0.05
81 3 0.00
82 70 0.06
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (74 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTTTAAATTT
CTGTTTTTT
Found at i:42735053 original size:154 final size:151
Alignment explanation
Indices: 42734677--42736069 Score: 1826
Period size: 154 Copynumber: 9.1 Consensus size: 151
42734667 TATTTTTCAA
* * *
42734677 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGT--CATGCCGAGGTATTTCTTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA--T-TTTTA
* * *
42734740 AATTTCTGTTTTTT--TAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT-CACGCTG
63 AATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTG
*
42734802 AGGTATTTTTTTAATTTCTATTTTTTT
128 AGGTA--TTTTAAATTTCTA-TTTTTT
* ** *
42734829 CAAAAATCAACTCATAATATGAGAGGTGAGTTGAGCCTCGGGT--CACGCTGAGGTATTTTTCTA
1 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTT-AA
* *
42734892 ATTTCTGTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT-CACGCTGA
64 ATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGA
42734956 GGTATTTTTTTTAAAATTTCTATTTTTT
129 GGTA----TTTT-AAATTTCTATTTTTT
* *
42734984 AAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA-TTTTAAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTAAAT
*
42735048 TTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCGCACGCTGAG
66 TTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAG
*
42735113 GTATTTTAAATTTCTGTTTTTT
130 GTATTTTAAATTTCTATTTTTT
42735135 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA-TTTTAAA
1 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTAAA
* *
42735199 TTTCTATTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGTTGA
65 TTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGA
*
42735264 GGTATTTTAAATTTTTATTTTTT
129 GGTATTTTAAATTTCTATTTTTT
42735287 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTAAA
1 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTAAA
*
42735352 TTTCT-ATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTG
65 TTTCTGTTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTG
* *
42735416 AGGTATTTCTTTTAAATTTCT-GTTTTC
128 AGGTA----TTTTAAATTTCTATTTTTT
*
42735443 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGGGTCGCACGCTGAGGTA-TTTTAAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTAAAT
*
42735507 TTCTG-TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCCGGT-CACGCTGAG
66 TTCTGTTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAG
42735570 GTATTTTAAA--T-TATTTTTT
130 GTATTTTAAATTTCTATTTTTT
* * * * * *
42735589 -TAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-CGACACATGCTGAGGTATTTCTTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA--T-TTTTA
* * *
42735652 AATTTCTG-TTTTTCAAAAATCAACTCATAATGTGAGAAGTGAGTTGAGCCTCGGGTCGCACGCT
63 AATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCT
42735716 GAGGTATTTTAAATTTCTATTTTTT
127 GAGGTATTTTAAATTTCTATTTTTT
42735741 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTTTT
1 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA---TTTTT
* * *
42735806 GAATTTCTG--TTTTCAAATATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCGCACGC
62 AAATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGC
* *
42735869 TGAGGTATTTTAAATTTCTGTTTTTCA
126 TGAGGTATTTTAAATTTCTATTTTT-T
* * *
42735896 AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGGCTCGGGTCGTACGCTGAGGTATTTTTTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA---TTTTTA
42735961 AATTTCTGCTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACG
63 AATTTCTG--TTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACG
* *
42736026 CTGAGGTATTTCTTTTAAATTTCT-GTTTTC
125 CTGAGGTA----TTTTAAATTTCTATTTTTT
42736056 AAAAATCAACTCAT
1 AAAAATCAACTCAT
42736070 NNNNNNNNNN
Statistics
Matches: 1136, Mismatches: 63, Indels: 75
0.89 0.05 0.06
Matches are distributed among these distances:
144 13 0.01
145 35 0.03
146 5 0.00
147 38 0.03
148 26 0.02
149 19 0.02
150 4 0.00
151 30 0.03
152 231 0.20
153 169 0.15
154 332 0.29
155 96 0.08
156 39 0.03
157 11 0.01
158 59 0.05
160 13 0.01
161 4 0.00
162 12 0.01
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (151 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTAAAT
TTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGG
TATTTTAAATTTCTATTTTTT
Done.