Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 8 of 316
Found at i:2350650 original size:44 final size:44
Alignment explanation
Indices: 2350583--2351111 Score: 230
Period size: 44 Copynumber: 11.8 Consensus size: 44
2350573 AAAGAATTTC
* * *
2350583 AGATCCTATCTCCCTG-AGATTACAGTGGAGCGGATTAAAATAAA
1 AGATCTTATCTCTCTGAAG-TTACAGTGGAGCAGATTAAAATAAA
** * *** *
2350627 AGATCTTATCTCTCTGAAGTTACAGCAGAGTAGA-TCGCAT--C
1 AGATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTAAAATAAA
* * * * * ** ***
2350668 AGGTCTTATCACCCTGAGGTTACAG-GGAGTAGACCGAAGAATTTC
1 AGATCTTATCTCTCTGAAGTTACAGTGGAGCAGA-TTAA-AATAAA
* * * *** *
2350713 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTAAAATAAA
* * ** **
2350757 AGATCTTATCTCTCTG-AGATTACAGCGGAGTAGATTGAAGCTAGT
1 AGATCTTATCTCTCTGAAG-TTACAGTGGAGCAGATT-AAAATAAA
* * *
2350802 A-ATCCTATATCTCTGAAGTTACAGTGGAGCGGATTAAAATAAA
1 AGATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTAAAATAAA
* * * *
2350845 GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAGATTGAAGCCA
1 AGATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTA-A--A-A-T-AA---A
* * ** ***
2350898 GAGATCTTATCTCCCTG-AGATTACAGTGGAACAGACCGAAAAATTTC
1 -AGATCTTATCTCTCTGAAG-TTACAGTGGAGCAGA--TTAAAATAAA
* * * *** *
2350945 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTAAAATAAA
* * * ** **
2350989 AGATCTTATCTCTCTGAAATTACAGCGGAGTAGATTGAAGCTAGT
1 AGATCTTATCTCTCTGAAGTTACAGTGGAGCAGATT-AAAATAAA
* *
2351034 A-ATCCTATCTCTCTGAAGTTACAGTGGAGCGGATTAAAATAAA
1 AGATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTAAAATAAA
* * *
2351077 GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGAT
1 AGATCTTATCTCTCTGAAGTTACAGTGGAGCAGAT
2351112 CACATCAGAT
Statistics
Matches: 355, Mismatches: 103, Indels: 54
0.69 0.20 0.11
Matches are distributed among these distances:
40 7 0.02
41 21 0.06
43 14 0.04
44 202 0.57
45 34 0.10
46 37 0.10
47 2 0.01
48 1 0.00
49 1 0.00
50 2 0.01
51 1 0.00
52 1 0.00
53 4 0.01
54 26 0.07
55 1 0.00
56 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (44 bp):
AGATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTAAAATAAA
Found at i:2350770 original size:130 final size:131
Alignment explanation
Indices: 2350536--2350791 Score: 354
Period size: 130 Copynumber: 2.0 Consensus size: 131
2350526 GTTTATTATA
* *
2350536 CAGGTCTTATCTCCCTGAGATTATAGTGGAACAGACCAAAGAATTTCAGATCCTATCTCCCTGAG
1 CAGGTCTTATCACCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCCTATCTCCCTGAG
* *
2350601 ATTACAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGA-AGTTACAGCAGAGTAGATCGC
66 ATTACAGTGGAGCAGATTAAAACAAAAGATCTTATCTCTCTGAGA-TTACAGCAGAGTAGATCGC
2350665 AT
130 AT
* ** * *
2350667 CAGGTCTTATCACCCTGAGGTTACAG-GGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATCACCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCCTATCTCCCTGAG
* * * * * *
2350731 GTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCTCTGAGATTACAGCGGAGTAGAT
66 ATTACAGTGGAGCAGATTAAAACAAAAGATCTTATCTCTCTGAGATTACAGCAGAGTAGAT
2350792 TGAAGCTAGT
Statistics
Matches: 109, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
130 85 0.78
131 24 0.22
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (131 bp):
CAGGTCTTATCACCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCCTATCTCCCTGAG
ATTACAGTGGAGCAGATTAAAACAAAAGATCTTATCTCTCTGAGATTACAGCAGAGTAGATCGCA
T
Found at i:2351104 original size:232 final size:231
Alignment explanation
Indices: 2350671--2351171 Score: 896
Period size: 232 Copynumber: 2.2 Consensus size: 231
2350661 TCGCATCAGG
* ** *
2350671 TCTTATCACCCTGAGGTTACAG-GGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGA-GTTACAGTGGAACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGGTTA
*
2350735 CAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCTCTGAGATTACAGCGGAGTAGATTGAAGCTA
65 CAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCTCTGAAATTACAGCGGAGTAGATTGAAGCTA
2350800 GTAATCCTATATCTCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGT
130 GTAATCCTATATCTCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGT
2350865 TACAGTAGAGTAGATCACATCAGATTGAAGCCAGAGA
195 TACAGTAGAGTAGATCACATCAGATTGAAGCCAGAGA
2350902 TCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAG-TTACAGTGGAACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGGTTA
2350967 CAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCTCTGAAATTACAGCGGAGTAGATTGAAGCTA
65 CAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCTCTGAAATTACAGCGGAGTAGATTGAAGCTA
*
2351032 GTAATCCTATCTCTCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGT
130 GTAATCCTATATCTCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGT
2351097 TACAGTAGAGTAGATCACATCAGATTGAAGCCAGAGA
195 TACAGTAGAGTAGATCACATCAGATTGAAGCCAGAGA
* *
2351134 TCTTATCTCCCTGATGTTGCAGTGGAACAGACTGAAAA
1 TCTTATCTCCCTGA-GTTACAGTGGAACAGACCGAAAA
2351172 CATAAATTTC
Statistics
Matches: 259, Mismatches: 8, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
230 1 0.00
231 19 0.07
232 238 0.92
233 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (231 bp):
TCTTATCTCCCTGAGTTACAGTGGAACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGGTTAC
AGTGGAGCAGATTGAAGCCAGAGATCTTATCTCTCTGAAATTACAGCGGAGTAGATTGAAGCTAG
TAATCCTATATCTCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTT
ACAGTAGAGTAGATCACATCAGATTGAAGCCAGAGA
Found at i:2352873 original size:3 final size:3
Alignment explanation
Indices: 2352865--2352893 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2352855 GATTTAGTTC
2352865 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2352894 CCTATTTGTT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2354758 original size:3 final size:3
Alignment explanation
Indices: 2354752--2354781 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2354742 ATAATGTACA
*
2354752 CAT CAT CAT CAT CAT CAT CAT CAT CGT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
2354782 TCAATGAAAG
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:0.30, C:0.33, G:0.03, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:2366828 original size:17 final size:16
Alignment explanation
Indices: 2366796--2366833 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
2366786 CTAGCTTGAA
2366796 TTTTAAATTTTAAATT
1 TTTTAAATTTTAAATT
*
2366812 TTTTAATATTTTTAATT
1 TTTTAA-ATTTTAAATT
2366829 TTTTA
1 TTTTA
2366834 GATACATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTAAATTTTAAATT
Found at i:2367298 original size:31 final size:31
Alignment explanation
Indices: 2367251--2367311 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
2367241 AGAGAATGCC
*
2367251 CAAAATATAAACGATCTAAAACGTGAGTGAA
1 CAAAATAGAAACGATCTAAAACGTGAGTGAA
* *
2367282 CAAAATAGAAATGATCTAAAACGTTAGTGA
1 CAAAATAGAAACGATCTAAAACGTGAGTGA
2367312 CTAAATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.21
Consensus pattern (31 bp):
CAAAATAGAAACGATCTAAAACGTGAGTGAA
Found at i:2367471 original size:8 final size:8
Alignment explanation
Indices: 2367458--2367494 Score: 74
Period size: 8 Copynumber: 4.6 Consensus size: 8
2367448 CTGAATCTTA
2367458 TTTTTTCT
1 TTTTTTCT
2367466 TTTTTTCT
1 TTTTTTCT
2367474 TTTTTTCT
1 TTTTTTCT
2367482 TTTTTTCT
1 TTTTTTCT
2367490 TTTTT
1 TTTTT
2367495 GTGATGGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTCT
Found at i:2372041 original size:10 final size:11
Alignment explanation
Indices: 2372019--2372052 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2372009 TCTATTTCTG
2372019 TTTTATATTTA
1 TTTTATATTTA
2372030 TTTTAT-TTTA
1 TTTTATATTTA
*
2372040 TTTTATAATTA
1 TTTTATATTTA
2372051 TT
1 TT
2372053 CTGACATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTATATTTA
Found at i:2372468 original size:16 final size:16
Alignment explanation
Indices: 2372447--2372499 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
2372437 TAATTTCCTT
2372447 TAAAAATTATA-AAAA
1 TAAAAATTATATAAAA
*
2372462 GTAAAAATTTTATAAAA
1 -TAAAAATTATATAAAA
2372479 TAAAAA-TAT-TAAAA
1 TAAAAATTATATAAAA
2372493 -AAAAATT
1 TAAAAATT
2372500 TAAATTAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 5 0.15
14 6 0.18
15 2 0.06
16 16 0.48
17 4 0.12
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (16 bp):
TAAAAATTATATAAAA
Found at i:2372910 original size:24 final size:25
Alignment explanation
Indices: 2372871--2372925 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
2372861 GGATTAATTT
2372871 TTTTTTAATATTTTTAATTATAA-A
1 TTTTTTAATATTTTTAATTATAATA
* *
2372895 TTTTTTAAT-TATTTTACTTTTAATA
1 TTTTTTAATAT-TTTTAATTATAATA
2372920 TTTTTT
1 TTTTTT
2372926 TTAAACATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 1 0.04
24 19 0.70
25 7 0.26
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTTTAATATTTTTAATTATAATA
Found at i:2373851 original size:23 final size:23
Alignment explanation
Indices: 2373805--2373852 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2373795 CTTTTTTTTT
*
2373805 ATTTTATTAAATAAATTATTAAA
1 ATTTTATTAAATAAATTATAAAA
*
2373828 ATTTTATTAAAATATATTA-AAAA
1 ATTTTATT-AAATAAATTATAAAA
2373851 AT
1 AT
2373853 AAAAAAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTTATTAAATAAATTATAAAA
Found at i:2375566 original size:21 final size:22
Alignment explanation
Indices: 2375513--2375559 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
2375503 TCGAGTTTAA
2375513 GCTCAAGCTTGTCAATATTTGG
1 GCTCAAGCTTGTCAATATTTGG
2375535 GCTCAAGCTTGTCAATATTTGG
1 GCTCAAGCTTGTCAATATTTGG
2375557 GCT
1 GCT
2375560 TAGCTTGGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (22 bp):
GCTCAAGCTTGTCAATATTTGG
Found at i:2375672 original size:80 final size:81
Alignment explanation
Indices: 2375527--2375687 Score: 315
Period size: 80 Copynumber: 2.0 Consensus size: 81
2375517 AAGCTTGTCA
2375527 ATATTTGGGCTCAAGCTTGTCAATATTTGGGCTTAGCTTGGCTCAATTACACCCTTAAGAAGGAG
1 ATATTTGGGCTCAAGCTTGTCAATATTTGGGCTTAGCTTGGCTCAATTACACCCTTAAGAAGGAG
2375592 AAATGGGTTACAAACT
66 AAATGGGTTACAAACT
2375608 ATATTTGGGCTCAAGCTTGTCAATATTTGGGC-TAGCTTGGCTCAATTACACCCTTAAGAAGGAG
1 ATATTTGGGCTCAAGCTTGTCAATATTTGGGCTTAGCTTGGCTCAATTACACCCTTAAGAAGGAG
2375672 AAATGGGTTACAAACT
66 AAATGGGTTACAAACT
2375688 CAAGGTTTAA
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 48 0.60
81 32 0.40
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (81 bp):
ATATTTGGGCTCAAGCTTGTCAATATTTGGGCTTAGCTTGGCTCAATTACACCCTTAAGAAGGAG
AAATGGGTTACAAACT
Found at i:2380436 original size:12 final size:12
Alignment explanation
Indices: 2380419--2380443 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2380409 TGTTGACGTG
2380419 GACGTTTTTATT
1 GACGTTTTTATT
2380431 GACGTTTTTATT
1 GACGTTTTTATT
2380443 G
1 G
2380444 GTCTAATAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.20, T:0.56
Consensus pattern (12 bp):
GACGTTTTTATT
Found at i:2383428 original size:37 final size:37
Alignment explanation
Indices: 2383378--2383453 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
2383368 TTTCTTTTAG
*
2383378 CTATATTAGTTTCAATTAGAAATTATCTATAGCTGCT
1 CTATATTAGTTTCAATTAGAAATTATATATAGCTGCT
2383415 CTATATTAGTTTCAATTAGAAATTATATATAGCTGCT
1 CTATATTAGTTTCAATTAGAAATTATATATAGCTGCT
2383452 CT
1 CT
2383454 TAATACAGGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (37 bp):
CTATATTAGTTTCAATTAGAAATTATATATAGCTGCT
Found at i:2388073 original size:2 final size:2
Alignment explanation
Indices: 2388066--2388102 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2388056 TTGTGAAAGG
2388066 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
2388103 GTGATTTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:2389882 original size:40 final size:40
Alignment explanation
Indices: 2389827--2389906 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
2389817 AACTAGACTT
2389827 GACATGAGTTGGATTGGGTTGCGTTAAATCGAGTCGAAGC
1 GACATGAGTTGGATTGGGTTGCGTTAAATCGAGTCGAAGC
2389867 GACATGAGTTGGATTGGGTTGCGTTAAATCGAGTCGAAGC
1 GACATGAGTTGGATTGGGTTGCGTTAAATCGAGTCGAAGC
2389907 AAAATTTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.25, C:0.12, G:0.35, T:0.28
Consensus pattern (40 bp):
GACATGAGTTGGATTGGGTTGCGTTAAATCGAGTCGAAGC
Found at i:2391413 original size:18 final size:18
Alignment explanation
Indices: 2391379--2391413 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2391369 GGCACAGTTT
*
2391379 AAAATGAAAATTTTAAAG
1 AAAATGAAAATTGTAAAG
*
2391397 AAAATGAATATTGTAAA
1 AAAATGAAAATTGTAAA
2391414 AATCACGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (18 bp):
AAAATGAAAATTGTAAAG
Found at i:2393619 original size:23 final size:24
Alignment explanation
Indices: 2393572--2393637 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 24
2393562 TAAATAATTT
*
2393572 AAAAA-TT-ATAAAAATACTTTTAA
1 AAAAAGTTCATAAAAATA-TTTAAA
2393595 AAAAAGTTCATAAAAAT-TTTAAA
1 AAAAAGTTCATAAAAATATTTAAA
**
2393618 AAAAAGAGCATAAAATATAT
1 AAAAAGTTCATAAAA-ATAT
2393638 GTGGATTGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
23 23 0.64
24 4 0.11
25 9 0.25
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (24 bp):
AAAAAGTTCATAAAAATATTTAAA
Found at i:2399495 original size:19 final size:19
Alignment explanation
Indices: 2399471--2399512 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2399461 CTTCAGATAT
2399471 TTTTATTTCTTTTA-TTTTA
1 TTTTATTT-TTTTACTTTTA
*
2399490 TTTTATTTTTTTACTTTTC
1 TTTTATTTTTTTACTTTTA
2399509 TTTT
1 TTTT
2399513 GGTGCTGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTATTTTTTTACTTTTA
Found at i:2421763 original size:29 final size:29
Alignment explanation
Indices: 2421682--2421778 Score: 97
Period size: 31 Copynumber: 3.2 Consensus size: 29
2421672 TTTTTTTTAA
*
2421682 ATGTATAGAATTGAATCAAAATCAAAGTTTC
1 ATGTATATAATTGAATC-AAATCAAA-TTTC
* *
2421713 ATGTATAT-ATATAAACCACAAATCAAATTTC
1 ATGTATATAAT-TGAA--TCAAATCAAATTTC
* *
2421744 ATGTATATAATTGTATCAAATCAAAATTC
1 ATGTATATAATTGAATCAAATCAAATTTC
2421773 ATGTAT
1 ATGTAT
2421779 CAAATTATAC
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
29 18 0.33
30 2 0.04
31 24 0.44
32 10 0.18
33 1 0.02
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.35
Consensus pattern (29 bp):
ATGTATATAATTGAATCAAATCAAATTTC
Found at i:2421931 original size:56 final size:56
Alignment explanation
Indices: 2421853--2421975 Score: 174
Period size: 56 Copynumber: 2.2 Consensus size: 56
2421843 ACTTAAATAT
* *
2421853 TTAACATCCAATTTTTAAGGTTTTAGTTAAATAATTATTGATGCGTAAATTTATAAA
1 TTAACA-CTAATTTTTAAGGTTTTAGTTAAATAATTATCGATGCGTAAATTTATAAA
* * * * *
2421910 TTAACACTAATTTTTAGGGTTTTAGTTTAATGATTATCGATGTGTAAATTTATACA
1 TTAACACTAATTTTTAAGGTTTTAGTTAAATAATTATCGATGCGTAAATTTATAAA
2421966 TTAACACTAA
1 TTAACACTAA
2421976 ATTACATGTG
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
56 53 0.90
57 6 0.10
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (56 bp):
TTAACACTAATTTTTAAGGTTTTAGTTAAATAATTATCGATGCGTAAATTTATAAA
Found at i:2425118 original size:22 final size:24
Alignment explanation
Indices: 2425092--2425153 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 24
2425082 GAAATTAAAT
2425092 TATATATTTTTATAATAGTAA-AA
1 TATATATTTTTATAATAGTAATAA
* * **
2425115 -ATATAATTTTATTATTTTAATAA
1 TATATATTTTTATAATAGTAATAA
*
2425138 TTTATATTTTTATAAT
1 TATATATTTTTATAAT
2425154 TTTTAAAGGA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
22 16 0.53
23 2 0.07
24 12 0.40
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TATATATTTTTATAATAGTAATAA
Found at i:2425147 original size:15 final size:16
Alignment explanation
Indices: 2425117--2425155 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
2425107 TAGTAAAAAT
2425117 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
2425134 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
2425149 ATAATTT
1 ATAATTT
2425156 TTAAAGGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:2426146 original size:18 final size:18
Alignment explanation
Indices: 2426123--2426161 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
2426113 ACTTGCAACC
2426123 AAATGTTTTTAATTAAAT
1 AAATGTTTTTAATTAAAT
2426141 AAATGTTTTTAATTAAAT
1 AAATGTTTTTAATTAAAT
2426159 AAA
1 AAA
2426162 AAAAGGTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (18 bp):
AAATGTTTTTAATTAAAT
Found at i:2428332 original size:84 final size:84
Alignment explanation
Indices: 2428123--2428342 Score: 223
Period size: 84 Copynumber: 2.6 Consensus size: 84
2428113 GAAGAAGAAG
** * **
2428123 AAGAAGAAAAAGGGTTGTTCGAAGTGAAAGAAGTGATAACATCGGAA-GCCGAGTCCGGAGAGGA
1 AAGAAGAAAAAGGGTTGTTCGAAGTGAAAGAAACGATAACATC-GAAGGTCGACCCCGGAGAGGA
* *
2428187 AGAACAAACACGTGAAGTTG
65 AGAACAAACACGTGAAATTA
* * *
2428207 AAGAAGAAGAAGGGTCGTTCGAAGTGAAAGACATC-ATAACATCGAAGGTCGACCCCTTGGA-A-
1 AAGAAGAAAAAGGGTTGTTCGAAGTGAAAGA-AACGATAACATCGAAGGTCGACCCC--GGAGAG
* * *
2428269 GAGGAACGAACATGTGAAATTA
63 GAAGAACAAACACGTGAAATTA
* * * *
2428291 AAGAAGAAAAAGGGTTGATCGAAGTGCAAGAAACGAAAACATGGAAGGTCGA
1 AAGAAGAAAAAGGGTTGTTCGAAGTGAAAGAAACGATAACATCGAAGGTCGA
2428343 ACATGGAAGG
Statistics
Matches: 112, Mismatches: 19, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
83 5 0.04
84 102 0.91
85 2 0.02
86 3 0.03
ACGTcount: A:0.43, C:0.13, G:0.30, T:0.15
Consensus pattern (84 bp):
AAGAAGAAAAAGGGTTGTTCGAAGTGAAAGAAACGATAACATCGAAGGTCGACCCCGGAGAGGAA
GAACAAACACGTGAAATTA
Found at i:2428345 original size:14 final size:14
Alignment explanation
Indices: 2428328--2428356 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2428318 AAGAAACGAA
2428328 AACATGGAAGGTCG
1 AACATGGAAGGTCG
2428342 AACATGGAAGGTCG
1 AACATGGAAGGTCG
2428356 A
1 A
2428357 TTGTTAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.14, G:0.34, T:0.14
Consensus pattern (14 bp):
AACATGGAAGGTCG
Found at i:2429288 original size:34 final size:34
Alignment explanation
Indices: 2429245--2429316 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
2429235 ATAAAATTTT
*
2429245 AAATTCATATTTCGATTGAACATAAGTAATTATA
1 AAATTCATATTTCGATTGAACATAAGTAAATATA
** *
2429279 AAATTCATATTTCGATTGGGCTTAAGTAAATATA
1 AAATTCATATTTCGATTGAACATAAGTAAATATA
2429313 AAAT
1 AAAT
2429317 GTATTAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (34 bp):
AAATTCATATTTCGATTGAACATAAGTAAATATA
Found at i:2430105 original size:66 final size:66
Alignment explanation
Indices: 2429999--2430131 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
2429989 GGATTAAATG
2429999 GTTCCTAGGTAACTCATGCCAGAGGGATAAACTGGAGATATGCAGGTAATCCAACAAAAGAGACT
1 GTTCCTAGGTAACTCATGCCAGAGGGATAAACTGGAGATATGCAGGTAATCCAACAAAAGAGACT
2430064 T
66 T
* * *
2430065 GTTCCTAGGTAAGTCATGGCAGAGGGATAAACTGGAGATATGCAGGTAATCCAACAAAAGCGACT
1 GTTCCTAGGTAACTCATGCCAGAGGGATAAACTGGAGATATGCAGGTAATCCAACAAAAGAGACT
2430130 T
66 T
2430131 G
1 G
2430132 AACTATAAAC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.21
Consensus pattern (66 bp):
GTTCCTAGGTAACTCATGCCAGAGGGATAAACTGGAGATATGCAGGTAATCCAACAAAAGAGACT
T
Found at i:2434258 original size:17 final size:18
Alignment explanation
Indices: 2434227--2434260 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2434217 CATATTAAGG
2434227 TTTTGATATATTTAATTA
1 TTTTGATATATTTAATTA
*
2434245 TTTTTATATA-TTAATT
1 TTTTGATATATTTAATT
2434261 TTTATATTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTTGATATATTTAATTA
Found at i:2444403 original size:19 final size:20
Alignment explanation
Indices: 2444379--2444422 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2444369 ATTGTTAGAA
*
2444379 TTTTACCTCCTT-TTATATT
1 TTTTACCTCATTATTATATT
* *
2444398 TTTTACTTGATTATTATATT
1 TTTTACCTCATTATTATATT
2444418 TTTTA
1 TTTTA
2444423 TTTATTAACG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.20, C:0.11, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTACCTCATTATTATATT
Found at i:2447237 original size:17 final size:17
Alignment explanation
Indices: 2447204--2447237 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2447194 CTGATTTTAT
*
2447204 AATTTTTAAATATCTAA
1 AATTTTTAAATAACTAA
*
2447221 AATTTTTAATTAACTAA
1 AATTTTTAAATAACTAA
2447238 TTAATTAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTTTAAATAACTAA
Found at i:2455438 original size:18 final size:18
Alignment explanation
Indices: 2455390--2455443 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
2455380 TTATAATATA
2455390 TATTTTTATT-TTTATAAT
1 TATTTTTATTATTTA-AAT
** *
2455408 TAAATTTA-AATTTAAAT
1 TATTTTTATTATTTAAAT
2455425 TATTTTTATTATTTAAAT
1 TATTTTTATTATTTAAAT
2455443 T
1 T
2455444 GAATTTGAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
17 9 0.32
18 19 0.68
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTTTTATTATTTAAAT
Found at i:2461334 original size:20 final size:18
Alignment explanation
Indices: 2461309--2461367 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 18
2461299 CGTGTGAATG
2461309 TTGACCAGTCAAAAACTGGA
1 TTGACCAGT-AAAAAC-GGA
*
2461329 TTGACCGGTATGAAAACGGA
1 TTGACCAGTA--AAAACGGA
2461349 TTGAACCAGTTAAAAACGG
1 TTG-ACCAG-TAAAAACGG
2461368 TTTTTTATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
19 1 0.03
20 21 0.64
21 9 0.27
22 2 0.06
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (18 bp):
TTGACCAGTAAAAACGGA
Found at i:2470695 original size:19 final size:19
Alignment explanation
Indices: 2470649--2470696 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
2470639 GTATATATTT
*
2470649 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTACGTAGA
*
2470667 TAAATCTTATTTACGTAGA
1 TAAATTTTATTTACGTAGA
*
2470686 TAAGTTTTATT
1 TAAATTTTATT
2470697 CATATTTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTACGTAGA
Found at i:2472522 original size:30 final size:30
Alignment explanation
Indices: 2472486--2472545 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
2472476 TTCCCGAGCC
2472486 TAGGGGTAAAA-GTGTAATTATGCAAAAGTT
1 TAGGGGTAAAATG-GTAATTATGCAAAAGTT
* *
2472516 TAGGGGTAAAATGGTAATTTTGCCAAAGTT
1 TAGGGGTAAAATGGTAATTATGCAAAAGTT
2472546 CGTATTAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.32
Consensus pattern (30 bp):
TAGGGGTAAAATGGTAATTATGCAAAAGTT
Found at i:2473018 original size:47 final size:46
Alignment explanation
Indices: 2472967--2473143 Score: 216
Period size: 47 Copynumber: 3.8 Consensus size: 46
2472957 TGGTTGAACA
*
2472967 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGT-AAACG
* * *
2473014 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAA--A--CG
* *
2473061 TCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACG
* *
2473107 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
2473144 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
43 2 0.02
44 5 0.05
45 1 0.01
46 37 0.33
47 57 0.51
48 3 0.03
50 6 0.05
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACG
Found at i:2478599 original size:47 final size:47
Alignment explanation
Indices: 2478447--2478623 Score: 213
Period size: 47 Copynumber: 3.8 Consensus size: 47
2478437 TGTAACCCGC
* *
2478447 CCATAAGTGAACTCGGACTCAACTCAACGAGCTT-GGGC-GTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCGGACAGTTCACAT
*
2478493 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-AGTTCACAT
* * *
2478543 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACAGTTCACAT
2478587 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
2478624 TGTTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
43 3 0.03
44 5 0.04
45 3 0.03
46 34 0.30
47 57 0.51
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (47 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACAGTTCACAT
Found at i:2478619 original size:94 final size:93
Alignment explanation
Indices: 2478455--2478625 Score: 281
Period size: 94 Copynumber: 1.8 Consensus size: 93
2478445 GCCCATAAGT
* *
2478455 GAACTCGGACTCAACTCAACGAGCTTGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTTGGACGTTCACATCCATAAGTGAACTCGGACTCAACTCAA
*
2478520 TGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
2478548 GAACTCGGACTCAACTCAACGAG-TTCGGACATTTCACATCCATAAGTGAACTCGGACTCAACTC
1 GAACTCGGACTCAACTCAACGAGCTT-GGAC-GTTCACATCCATAAGTGAACTCGGACTCAACTC
2478612 AACGAGTTCGGATG
64 AACGAGTTCGGATG
2478626 TTCAACCATC
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
92 2 0.03
93 26 0.36
94 44 0.61
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTTGGACGTTCACATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:2479079 original size:30 final size:30
Alignment explanation
Indices: 2479045--2479104 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
2479035 CCTTAATACG
2479045 AACTTTGGCAAAATTAC-CATTTTGCCCCTA
1 AACTTTGGCAAAATTACAC-TTTTGCCCCTA
* *
2479075 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
2479105 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.28, C:0.27, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:2480172 original size:42 final size:42
Alignment explanation
Indices: 2480113--2480201 Score: 160
Period size: 42 Copynumber: 2.1 Consensus size: 42
2480103 TTAGGAATAT
* *
2480113 TTTTATTTTATGTTTTAGTAGTTTATTAGAATAAGGGAACTA
1 TTTTCTTTTATATTTTAGTAGTTTATTAGAATAAGGGAACTA
2480155 TTTTCTTTTATATTTTAGTAGTTTATTAGAATAAGGGAACTA
1 TTTTCTTTTATATTTTAGTAGTTTATTAGAATAAGGGAACTA
2480197 TTTTC
1 TTTTC
2480202 CCAATTAGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.29, C:0.04, G:0.15, T:0.52
Consensus pattern (42 bp):
TTTTCTTTTATATTTTAGTAGTTTATTAGAATAAGGGAACTA
Found at i:2487144 original size:56 final size:56
Alignment explanation
Indices: 2487052--2487158 Score: 126
Period size: 56 Copynumber: 1.9 Consensus size: 56
2487042 TTTATTAAGT
* * * *
2487052 TTTCATTTGGGTTATCCATCACTAATTCAATATTATTGTACAATTATTTTAATAAA
1 TTTCATTTGAGTTATCCATCACTAATTCAAGATTATTATACAATCATTTTAATAAA
* * * *
2487108 TTTCATTTTAGTTA-CCAGTCATTAATTCAAGGTTATTATACACTCATTTTA
1 TTTCATTTGAGTTATCCA-TCACTAATTCAAGATTATTATACAATCATTTTA
2487159 GTGATAACTT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
55 3 0.07
56 39 0.93
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.47
Consensus pattern (56 bp):
TTTCATTTGAGTTATCCATCACTAATTCAAGATTATTATACAATCATTTTAATAAA
Found at i:2487735 original size:21 final size:20
Alignment explanation
Indices: 2487711--2487749 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2487701 AAATTAGGTT
2487711 TTTTAAAAAAAAATAAAATTA
1 TTTT-AAAAAAAATAAAATTA
**
2487732 TTTTTGAAAAAATAAAAT
1 TTTTAAAAAAAATAAAAT
2487750 GAATAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
TTTTAAAAAAAATAAAATTA
Found at i:2499381 original size:5 final size:5
Alignment explanation
Indices: 2499365--2499423 Score: 54
Period size: 5 Copynumber: 12.6 Consensus size: 5
2499355 CTCATTATAC
* * *
2499365 TTTCT TTCCT TTTC- TTTCT TTTCT TTAC- TTTCT TTTCT TTTC- CTT-T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
*
2499411 TTTCT TATCT TTT
1 TTTCT TTTCT TTT
2499424 TTACCCCTCT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
4 11 0.26
5 31 0.74
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTCT
Found at i:2499383 original size:14 final size:14
Alignment explanation
Indices: 2499364--2499422 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
2499354 TCTCATTATA
*
2499364 CTTTCTTTCCTTTT
1 CTTTCTTTTCTTTT
*
2499378 CTTTCTTTTCTTTA
1 CTTTCTTTTCTTTT
2499392 CTTTCTTTTCTTTT
1 CTTTCTTTTCTTTT
* *
2499406 CCTT-TTTTCTTAT
1 CTTTCTTTTCTTTT
2499419 CTTT
1 CTTT
2499423 TTTACCCCTC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
13 11 0.28
14 28 0.72
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (14 bp):
CTTTCTTTTCTTTT
Found at i:2500410 original size:19 final size:19
Alignment explanation
Indices: 2500386--2500428 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
2500376 CCTCATTATA
2500386 GTTTTTTATCATATATGCT
1 GTTTTTTATCATATATGCT
2500405 GTTTTTTATCATATATGCT
1 GTTTTTTATCATATATGCT
2500424 -TTTTT
1 GTTTTT
2500429 AACTTAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.19, C:0.09, G:0.09, T:0.63
Consensus pattern (19 bp):
GTTTTTTATCATATATGCT
Found at i:2501547 original size:20 final size:21
Alignment explanation
Indices: 2501524--2501564 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2501514 CTAAATTTCA
2501524 TAAATT-AAAAATAAAAAGAT
1 TAAATTCAAAAATAAAAAGAT
*
2501544 TAAATTCCAAAAATAAGAAGA
1 TAAATT-CAAAAATAAAAAGA
2501565 ATAACGAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
22 12 0.67
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.22
Consensus pattern (21 bp):
TAAATTCAAAAATAAAAAGAT
Found at i:2501978 original size:23 final size:23
Alignment explanation
Indices: 2501951--2501994 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2501941 AGTCTTTGTA
2501951 CTTTTACTTTTAAGAATTTAATT
1 CTTTTACTTTTAAGAATTTAATT
* * *
2501974 CTTTTGCTTTTCAGATTTTAA
1 CTTTTACTTTTAAGAATTTAA
2501995 AATGTAGGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.11, G:0.07, T:0.57
Consensus pattern (23 bp):
CTTTTACTTTTAAGAATTTAATT
Found at i:2520364 original size:32 final size:32
Alignment explanation
Indices: 2520321--2520384 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
2520311 ATCCACAACT
2520321 AATAACATATCTTGAATCCATTAGATTACTTG
1 AATAACATATCTTGAATCCATTAGATTACTTG
* *
2520353 AATAACCTATCTTGAATCCATTAGATTGCTTG
1 AATAACATATCTTGAATCCATTAGATTACTTG
2520385 CTAATGATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (32 bp):
AATAACATATCTTGAATCCATTAGATTACTTG
Found at i:2520749 original size:103 final size:103
Alignment explanation
Indices: 2520619--2520824 Score: 412
Period size: 103 Copynumber: 2.0 Consensus size: 103
2520609 GCCTCCAGTA
2520619 GATCTTAATAATTAAATTCCCTACTTACTCTATTGGTATCATATTGAAGTGATGAATATACCAAA
1 GATCTTAATAATTAAATTCCCTACTTACTCTATTGGTATCATATTGAAGTGATGAATATACCAAA
2520684 CTAGAACATTGTCAAAATCGACCTGAAAGGATTGGATG
66 CTAGAACATTGTCAAAATCGACCTGAAAGGATTGGATG
2520722 GATCTTAATAATTAAATTCCCTACTTACTCTATTGGTATCATATTGAAGTGATGAATATACCAAA
1 GATCTTAATAATTAAATTCCCTACTTACTCTATTGGTATCATATTGAAGTGATGAATATACCAAA
2520787 CTAGAACATTGTCAAAATCGACCTGAAAGGATTGGATG
66 CTAGAACATTGTCAAAATCGACCTGAAAGGATTGGATG
2520825 AGTCATCAAC
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (103 bp):
GATCTTAATAATTAAATTCCCTACTTACTCTATTGGTATCATATTGAAGTGATGAATATACCAAA
CTAGAACATTGTCAAAATCGACCTGAAAGGATTGGATG
Found at i:2523877 original size:30 final size:30
Alignment explanation
Indices: 2523841--2523901 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
2523831 ATTTTATTGT
*
2523841 TAATTTTTTTATTATTTTAAAGACATTTGC
1 TAATTTTGTTATTATTTTAAAGACATTTGC
* *
2523871 TAATTTTGTTATTATTTTAGAGGCATTTGC
1 TAATTTTGTTATTATTTTAAAGACATTTGC
2523901 T
1 T
2523902 TATTAAGTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (30 bp):
TAATTTTGTTATTATTTTAAAGACATTTGC
Found at i:2524046 original size:12 final size:12
Alignment explanation
Indices: 2524025--2524058 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2524015 TATATATTTT
*
2524025 AAAATCATATAA
1 AAAATAATATAA
2524037 AAAATAATATAA
1 AAAATAATATAA
*
2524049 AAATTAATAT
1 AAAATAATAT
2524059 GGGCGGACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:2525065 original size:11 final size:11
Alignment explanation
Indices: 2525051--2525091 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
2525041 TATTTTCTCC
2525051 CTATTTTGCTA
1 CTATTTTGCTA
*
2525062 CTATTTTACTA
1 CTATTTTGCTA
* *
2525073 TTATGTTGCTA
1 CTATTTTGCTA
2525084 CTATTTTG
1 CTATTTTG
2525092 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:2528096 original size:31 final size:31
Alignment explanation
Indices: 2528060--2528122 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
2528050 AATTACAAAA
* **
2528060 TGATCACCTAATTATTTGACTTTTTCTTTTT
1 TGATCACCTAACTATTTGAAATTTTCTTTTT
*
2528091 TGATCACTTAACTATTTGAAATTTTCTTTTT
1 TGATCACCTAACTATTTGAAATTTTCTTTTT
2528122 T
1 T
2528123 AGATTGTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.06, T:0.57
Consensus pattern (31 bp):
TGATCACCTAACTATTTGAAATTTTCTTTTT
Found at i:2537160 original size:45 final size:45
Alignment explanation
Indices: 2537105--2537193 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
2537095 TTGTACTAAA
*
2537105 TTTTATTCATATTATTTATTTAACATGTTAGATTTAAGTTGTTCG
1 TTTTATTCATATTATTTATTTAACATGTTAAATTTAAGTTGTTCG
*
2537150 TTTTATTCATATTATTTATTTAATATGTTAAATTTAAGTTGTTC
1 TTTTATTCATATTATTTATTTAACATGTTAAATTTAAGTTGTTC
2537194 ATACGATTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.57
Consensus pattern (45 bp):
TTTTATTCATATTATTTATTTAACATGTTAAATTTAAGTTGTTCG
Found at i:2544542 original size:19 final size:19
Alignment explanation
Indices: 2544520--2544556 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2544510 CAACTTTTTC
2544520 ATATATTATAATATTTTAA
1 ATATATTATAATATTTTAA
*
2544539 ATATATTATTATATTTTA
1 ATATATTATAATATTTTA
2544557 GCATACCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATATTATAATATTTTAA
Found at i:2554345 original size:200 final size:202
Alignment explanation
Indices: 2553932--2554448 Score: 618
Period size: 202 Copynumber: 2.6 Consensus size: 202
2553922 AATGTTCTAT
* * * * *
2553932 GATAGTCTTTACCTATGTGAGTCAAATTCTTCAT-TTTTTCCCCAAAA-TATTGATGCTAGGCAC
1 GATAGTCTTTACCTATGTTACTCGAACTCTTCATATTTTT----AAAAGTATCGATGCTAGGCAC
* * * * * **
2553995 TAGTTTCGAACATTTACGAT-CTGGCAAATATATGAAAAAAAAAACCCAAAAAAAAGTTAAAAAT
62 TAGTTTAGAACATGTATGATCCT-CCAATTATATGAAAAAAAAAAAACAAAAAAAAGTTAAAAAT
* * * *
2554059 TGAGCACACCGGTGTCAAATACATGCACCTAACATATCCAACACCAACATTCGATTCCAATAGCA
126 TGAGCACACCAGTGTC-AAGACATGCACCTAACATATCCAACACCAACATTCAAGTCCAATAGCA
2554124 GACAGCATACTAC
190 GACAGCATACTAC
* * *
2554137 GATAGTCTTTACCTATGTTACTTGAACTGTTCAT-TTTTCT-GAAGTATCGATGCTAGGCACTAG
1 GATAGTCTTTACCTATGTTACTCGAACTCTTCATATTTT-TAAAAGTATCGATGCTAGGCACTAG
**
2554200 TTTAGAACATGTATGATCCTCCAATTATATGAAAAAAAAAAAACTCAAAAAAGTTAAAAATTGAG
65 TTTAGAACATGTATGATCCTCCAATTATATGAAAAAAAAAAAACAAAAAAAAGTTAAAAATTGAG
* * *
2554265 CACACTAGTGTC-AGACATGCACCTAACATATCCAACACCCACATTCAAGTCCAATAGCAGACGG
130 CACACCAGTGTCAAGACATGCACCTAACATATCCAACACCAACATTCAAGTCCAATAGCAGACAG
*
2554329 CATACTAT
195 CATACTAC
* * **
2554337 GGTAGTCTTTACCTATGTTACTCGAACTCTTCATATTTTTACAAAGTATCGACGCTAAACACTAG
1 GATAGTCTTTACCTATGTTACTCGAACTCTTCATATTTTTA-AAAGTATCGATGCTAGGCACTAG
* * *
2554402 TTCAGAA-ATGTATGATCCTCCAATTTTATGAAAAAATAAAAA-AAAAA
65 TTTAGAACATGTATGATCCTCCAATTATATGAAAAAAAAAAAACAAAAA
2554449 CCAAAATCAA
Statistics
Matches: 269, Mismatches: 37, Indels: 17
0.83 0.11 0.05
Matches are distributed among these distances:
200 89 0.33
201 39 0.14
202 106 0.39
203 2 0.01
205 32 0.12
206 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.28
Consensus pattern (202 bp):
GATAGTCTTTACCTATGTTACTCGAACTCTTCATATTTTTAAAAGTATCGATGCTAGGCACTAGT
TTAGAACATGTATGATCCTCCAATTATATGAAAAAAAAAAAACAAAAAAAAGTTAAAAATTGAGC
ACACCAGTGTCAAGACATGCACCTAACATATCCAACACCAACATTCAAGTCCAATAGCAGACAGC
ATACTAC
Found at i:2556905 original size:25 final size:25
Alignment explanation
Indices: 2556871--2556921 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
2556861 TTCCTTATAA
**
2556871 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
2556896 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
2556921 A
1 A
2556922 TTTTCCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:2556920 original size:12 final size:12
Alignment explanation
Indices: 2556874--2556921 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
2556864 CTTATAAACT
2556874 TTAAATTAGGAA
1 TTAAATTAGGAA
** *
2556886 TTCTATTAGGACT
1 TTAAATTAGGA-A
2556899 TTAAATTAGGAA
1 TTAAATTAGGAA
*
2556911 TTAGATTAGGA
1 TTAAATTAGGA
2556922 TTTTCCTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (12 bp):
TTAAATTAGGAA
Found at i:2561475 original size:25 final size:25
Alignment explanation
Indices: 2561441--2561491 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
2561431 TTCCTTATAA
**
2561441 ACTTTAAATTAAGAATTCTATTAGG
1 ACTTTAAATTAAGAATTAGATTAGG
*
2561466 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAAGAATTAGATTAGG
2561491 A
1 A
2561492 TTTTCCTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAAGAATTAGATTAGG
Found at i:2566059 original size:17 final size:17
Alignment explanation
Indices: 2566037--2566083 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 17
2566027 ATTTTGTCAT
2566037 ATTATTTTTATAAATAA
1 ATTATTTTTATAAATAA
*
2566054 ATTA-TTAT-TAAA-AA
1 ATTATTTTTATAAATAA
2566068 ATTATTTTTATAAATA
1 ATTATTTTTATAAATA
2566084 TATGTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 6 0.24
15 7 0.28
16 7 0.28
17 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTATTTTTATAAATAA
Found at i:2566092 original size:21 final size:21
Alignment explanation
Indices: 2566068--2566111 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2566058 TTATTAAAAA
2566068 ATTATTTTTATAA-ATATATGT
1 ATTATTTTTATAATATATA-GT
2566089 ATTATTTTTATAATATATAGT
1 ATTATTTTTATAATATATAGT
2566110 AT
1 AT
2566112 GGACACTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
ATTATTTTTATAATATATAGT
Found at i:2568334 original size:197 final size:197
Alignment explanation
Indices: 2567999--2568389 Score: 622
Period size: 197 Copynumber: 2.0 Consensus size: 197
2567989 GATTATGATA
* * *
2567999 GTGGTATGCTATTGGATCACTATCTTCTTTGGTTGAATGCTCTTTATTCTTTTGAGCATATATCT
1 GTGGTATGCTATTAGATCACTATCATCTTTGGTTGAATGCTCTTTATGCTTTTGAGCATATATCT
* * *
2568064 GTATGTCTGTGTATTCTCAATGGTTATAATGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
66 CTATGTCAGTGTATTCTCAATGGTTATAAAGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
* * * *
2568129 TAAATCCAACATTGTCTCCAAAAACAATGAGTGATTAAATTGAATGG-CATGGTAAGAAGGTTGG
131 TAAATCCAACATTATCTCCAAAAACAATGAGTGATTAAATGGAATGGTC-TGATAAGAAGATTGG
2568193 GTT
195 GTT
* * * *
2568196 GTGGTATGCTTTTAGATCACTTTCATCTTTGGTTGAATGCTCTTTATGCTTTTGAGCATATGTTT
1 GTGGTATGCTATTAGATCACTATCATCTTTGGTTGAATGCTCTTTATGCTTTTGAGCATATATCT
* *
2568261 CTATGTCAGTGTATTCTCAATTGTTATAAAGTCTATCGAGGCTTTAGGTTGAATCCTTTATATGT
66 CTATGTCAGTGTATTCTCAATGGTTATAAAGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
2568326 TAAATCCAACATTATCTCCAAAAACAATGAGTGATTAAATGGAATGGTCTGATAAGAAGATTGG
131 TAAATCCAACATTATCTCCAAAAACAATGAGTGATTAAATGGAATGGTCTGATAAGAAGATTGG
2568390 ATTGCATTCA
Statistics
Matches: 177, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
197 176 0.99
198 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (197 bp):
GTGGTATGCTATTAGATCACTATCATCTTTGGTTGAATGCTCTTTATGCTTTTGAGCATATATCT
CTATGTCAGTGTATTCTCAATGGTTATAAAGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
TAAATCCAACATTATCTCCAAAAACAATGAGTGATTAAATGGAATGGTCTGATAAGAAGATTGGG
TT
Found at i:2576658 original size:17 final size:17
Alignment explanation
Indices: 2576636--2576668 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2576626 ACATCTTGGG
2576636 TTGTTTTTTAAATTTGT
1 TTGTTTTTTAAATTTGT
*
2576653 TTGTTTTTTAGATTTG
1 TTGTTTTTTAAATTTG
2576669 GGTTTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (17 bp):
TTGTTTTTTAAATTTGT
Found at i:2579095 original size:7 final size:7
Alignment explanation
Indices: 2579054--2579078 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2579044 AATAAATAAA
2579054 AAATATT
1 AAATATT
2579061 AAATATT
1 AAATATT
2579068 AAATATT
1 AAATATT
2579075 AAAT
1 AAAT
2579079 TAAAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATATT
Found at i:2579669 original size:21 final size:21
Alignment explanation
Indices: 2579645--2579691 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2579635 GAAGAGATTT
*
2579645 TTTTTTAAATTCAAGAAGAGA
1 TTTTTGAAATTCAAGAAGAGA
* * *
2579666 TTTTTGAGATTCAAGAGGGGA
1 TTTTTGAAATTCAAGAAGAGA
2579687 TTTTT
1 TTTTT
2579692 CTTTTTTCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.04, G:0.21, T:0.43
Consensus pattern (21 bp):
TTTTTGAAATTCAAGAAGAGA
Found at i:2580179 original size:3 final size:3
Alignment explanation
Indices: 2580173--2580205 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
2580163 ATAATAATAA
2580173 TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
2580206 GTGTATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2580308 original size:3 final size:3
Alignment explanation
Indices: 2580300--2580335 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2580290 TGTATTTCTA
2580300 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2580336 AATATGGTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2580462 original size:16 final size:15
Alignment explanation
Indices: 2580431--2580473 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
2580421 CCTTCATTCC
*
2580431 ATTATTATTATTACT
1 ATTATTATTTTTACT
2580446 ATTATTATATTTTACT
1 ATTATTAT-TTTTACT
*
2580462 ATCATTATTTTT
1 ATTATTATTTTT
2580474 CATACGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTATTTTTACT
Found at i:2580597 original size:16 final size:16
Alignment explanation
Indices: 2580576--2580608 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2580566 ACTATTGTTA
2580576 TTGTTATTATCATCAC
1 TTGTTATTATCATCAC
*
2580592 TTGTTATTCTCATCAC
1 TTGTTATTATCATCAC
2580608 T
1 T
2580609 ATTATTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.52
Consensus pattern (16 bp):
TTGTTATTATCATCAC
Found at i:2580705 original size:3 final size:3
Alignment explanation
Indices: 2580697--2580746 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
2580687 AACTTAATAG
* * *
2580697 ATT ATT ATT ATT ATT ATT ATT ATT ATT -TA ATAT ATT ATT TTT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT
2580742 ATT AT
1 ATT AT
2580747 CGTCATATTG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 1 0.03
3 36 0.92
4 2 0.05
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2580710 original size:33 final size:33
Alignment explanation
Indices: 2580673--2580746 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
2580663 CATCATTACC
2580673 ATTATT-TTCATTATAACTTAATAGATTATTATT
1 ATTATTATT-ATTATAACTTAATAGATTATTATT
* * * *
2580706 ATTATTATTATTATTATTTAATATATTATTTTT
1 ATTATTATTATTATAACTTAATAGATTATTATT
*
2580739 ACTATTAT
1 ATTATTAT
2580747 CGTCATATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 33 0.94
34 2 0.06
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (33 bp):
ATTATTATTATTATAACTTAATAGATTATTATT
Found at i:2583728 original size:29 final size:31
Alignment explanation
Indices: 2583696--2583765 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
2583686 TAATAATAAT
2583696 AAAATTATATTTTAA-TCCTT-AAAAATATA
1 AAAATTATATTTTAACTCCTTAAAAAATATA
* *
2583725 AAAATT-TAATTTAACCTCTTTAAAAAATATA
1 AAAATTATATTTTAA-CTCCTTAAAAAATATA
*
2583756 AAAATAATAT
1 AAAATTATAT
2583766 ATTATTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
28 7 0.21
29 6 0.18
30 4 0.12
31 14 0.42
32 2 0.06
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (31 bp):
AAAATTATATTTTAACTCCTTAAAAAATATA
Found at i:2584167 original size:17 final size:17
Alignment explanation
Indices: 2584145--2584182 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
2584135 ATTTAGTTAA
2584145 TTTATATTATTATT-TTT
1 TTTATATTA-TATTATTT
2584162 TTTATATTATATTATTT
1 TTTATATTATATTATTT
2584179 TTTA
1 TTTA
2584183 CATAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATATTATATTATTT
Found at i:2584240 original size:9 final size:9
Alignment explanation
Indices: 2584207--2584234 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2584197 ATATATAGTA
2584207 TATTAAAAT
1 TATTAAAAT
2584216 TATTAAAAT
1 TATTAAAAT
2584225 TATTAAAAT
1 TATTAAAAT
2584234 T
1 T
2584235 TCTAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TATTAAAAT
Found at i:2590605 original size:25 final size:26
Alignment explanation
Indices: 2590580--2590629 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
2590570 TATAAAAAAT
2590580 ATTAAATGAATTATATATAT-TTAATA
1 ATTAAAT-AATTATATATATATTAATA
* *
2590606 ATTATATATTTATATATATATTAA
1 ATTAAATAATTATATATATATTAA
2590630 ATCACCAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
ATTAAATAATTATATATATATTAATA
Found at i:2590610 original size:17 final size:18
Alignment explanation
Indices: 2590578--2590614 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
2590568 ATTATAAAAA
2590578 ATATTAAATGAATTATAT
1 ATATTAAATGAATTATAT
*
2590596 ATATTTAAT-AATTATAT
1 ATATTAAATGAATTATAT
2590613 AT
1 AT
2590615 TTATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
ATATTAAATGAATTATAT
Found at i:2590779 original size:39 final size:41
Alignment explanation
Indices: 2590725--2590815 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 41
2590715 TAAAATTATA
* * *
2590725 TTTAATACAATAAAATATTTATTATATTTAT-TTA-TATTT
1 TTTAATATAAAAAAATATTTATTATATTTATGGTAGTATTT
*
2590764 TTTAATATAAAAAAATATTTATTATATTTATGGTAGTGTTT
1 TTTAATATAAAAAAATATTTATTATATTTATGGTAGTATTT
2590805 TTTAATATAAA
1 TTTAATATAAA
2590816 TATTTTTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 29 0.63
40 2 0.04
41 15 0.33
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (41 bp):
TTTAATATAAAAAAATATTTATTATATTTATGGTAGTATTT
Found at i:2594148 original size:25 final size:23
Alignment explanation
Indices: 2594101--2594153 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 23
2594091 AAATAATGAA
2594101 AATTTTTATTTTAATTAATTTTT
1 AATTTTTATTTTAATTAATTTTT
2594124 AATTTTTATAATTTAATTTAA-TTTT
1 AATTTTTAT--TTTAA-TTAATTTTT
2594149 AATTT
1 AATTT
2594154 AAAAATATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 9 0.33
25 14 0.52
26 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
AATTTTTATTTTAATTAATTTTT
Found at i:2594323 original size:30 final size:30
Alignment explanation
Indices: 2594224--2594325 Score: 93
Period size: 30 Copynumber: 3.4 Consensus size: 30
2594214 TGGGTAACAG
* *
2594224 AATATAGTTTAGATATCACTTAGTGTAACAA
1 AATATAGTTTAGGTATCACTTAGTG-AAAAA
* * * *
2594255 AGTATAATTTAAGTACCACTT-GTGATAAAA
1 AATATAGTTTAGGTATCACTTAGTGA-AAAA
*
2594285 AA-AAAGTTTAGGTATCAACTTAG-GAAAAA
1 AATATAGTTTAGGTATC-ACTTAGTGAAAAA
2594314 AATATAGTTTAG
1 AATATAGTTTAG
2594326 ATACCATTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
29 17 0.31
30 21 0.38
31 17 0.31
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.32
Consensus pattern (30 bp):
AATATAGTTTAGGTATCACTTAGTGAAAAA
Found at i:2595566 original size:37 final size:38
Alignment explanation
Indices: 2595511--2595586 Score: 120
Period size: 37 Copynumber: 2.0 Consensus size: 38
2595501 AATTAAATTA
2595511 AAATATTACTATTTTTAAGA-GGAGAAAAGTGTAATTTT
1 AAATATTACTATTTTTAAGAGGGA-AAAAGTGTAATTTT
*
2595549 AAAT-TTATTATTTTTAAGAGGGAAAAAGTGTAATTTT
1 AAATATTACTATTTTTAAGAGGGAAAAAGTGTAATTTT
2595586 A
1 A
2595587 CCATTGTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
37 29 0.81
38 7 0.19
ACGTcount: A:0.42, C:0.01, G:0.16, T:0.41
Consensus pattern (38 bp):
AAATATTACTATTTTTAAGAGGGAAAAAGTGTAATTTT
Found at i:2606139 original size:19 final size:17
Alignment explanation
Indices: 2606093--2606137 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
2606083 AAATTAACTT
*
2606093 TTAATATTAGAAAAAAAG
1 TTAA-ATTATAAAAAAAG
2606111 TTAAATTATAAAAAAAG
1 TTAAATTATAAAAAAAG
2606128 TTAAATTATA
1 TTAAATTATA
2606138 TATATGTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 22 0.85
18 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (17 bp):
TTAAATTATAAAAAAAG
Found at i:2625333 original size:24 final size:24
Alignment explanation
Indices: 2625303--2625349 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
2625293 TGTTTCCATG
2625303 AAAGAGGGTGACATATTCTTTGGT
1 AAAGAGGGTGACATATTCTTTGGT
2625327 AAAGAGGGTGACATATTCTTTGG
1 AAAGAGGGTGACATATTCTTTGG
2625350 ACTGGGCGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.32
Consensus pattern (24 bp):
AAAGAGGGTGACATATTCTTTGGT
Found at i:2627976 original size:29 final size:29
Alignment explanation
Indices: 2627944--2628003 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
2627934 AATGTTGAAT
*
2627944 TTTTTAT-AAATTTTAAATATATTCTTTAA
1 TTTTTATGAAATTTTAAATAT-TTATTTAA
*
2627973 TTTTTATGAAATTTTAATTATTTATTTAA
1 TTTTTATGAAATTTTAAATATTTATTTAA
2628002 TT
1 TT
2628004 ACTAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (29 bp):
TTTTTATGAAATTTTAAATATTTATTTAA
Found at i:2627977 original size:30 final size:30
Alignment explanation
Indices: 2627941--2628003 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
2627931 AAAAATGTTG
*
2627941 AATTTTTTAT-AAATTTTAAATATATTCTTT
1 AATTTTTTATGAAATTTTAAATAT-TTATTT
*
2627971 AA-TTTTTATGAAATTTTAATTATTTATTT
1 AATTTTTTATGAAATTTTAAATATTTATTT
2628000 AATT
1 AATT
2628004 ACTAAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (30 bp):
AATTTTTTATGAAATTTTAAATATTTATTT
Found at i:2637422 original size:14 final size:14
Alignment explanation
Indices: 2637396--2637452 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2637386 TTTTTTGTGT
2637396 TTTTATATTTATTTA
1 TTTTAT-TTTATTTA
2637411 TTTTATTTTATTTA
1 TTTTATTTTATTTA
*
2637425 TTTTACTTATTTTTTA
1 TTTTA-TT-TTATTTA
2637441 TTATTAATTTTA
1 TT-TT-ATTTTA
2637453 AAAATTTTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
14 13 0.36
15 8 0.22
16 10 0.28
17 4 0.11
18 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTATTTTATTTA
Found at i:2637429 original size:23 final size:23
Alignment explanation
Indices: 2637397--2637452 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
2637387 TTTTTGTGTT
*
2637397 TTTATATTTATTTATTTTATT-TTA
1 TTTAT-TTTACTTATTTT-TTATTA
2637421 TTTATTTTACTTATTTTTTATTA
1 TTTATTTTACTTATTTTTTATTA
*
2637444 TTAATTTTA
1 TTTATTTTA
2637453 AAAATTTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 2 0.07
23 22 0.76
24 5 0.17
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTATTTTACTTATTTTTTATTA
Found at i:2637514 original size:22 final size:22
Alignment explanation
Indices: 2637447--2637613 Score: 90
Period size: 23 Copynumber: 7.4 Consensus size: 22
2637437 TTTATTATTA
* *
2637447 ATTTTAAAAATTTTGAAATGTAT
1 ATTTTTAAAATTTT-AAATATAT
*
2637470 A-TTTGAAATATTTTATAATATAT
1 ATTTTTAAA-ATTTTA-AATATAT
2637493 ATTTTTAAAATTTTAAATATAT
1 ATTTTTAAAATTTTAAATATAT
* * *
2637515 ATATTTGAAATTATTTTTAAAAATTTT
1 AT-TTTTAAA--A-TTTTAAATA-TAT
** * * *
2637542 AAATATATATTTTTGAAAT-TAT
1 ATTTTTAAAATTTT-AAATATAT
* *
2637564 -TTTTTGAAATTTTGAATAT-T
1 ATTTTTAAAATTTTAAATATAT
* *
2637584 ATTTTTTAAATATTAAATATAT
1 ATTTTTAAAATTTTAAATATAT
2637606 ATTTTTAA
1 ATTTTTAA
2637614 TAATATAAAA
Statistics
Matches: 107, Mismatches: 25, Indels: 25
0.68 0.16 0.16
Matches are distributed among these distances:
20 4 0.04
21 24 0.22
22 26 0.24
23 29 0.27
24 9 0.08
25 1 0.01
26 11 0.10
27 3 0.03
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (22 bp):
ATTTTTAAAATTTTAAATATAT
Found at i:2637552 original size:57 final size:56
Alignment explanation
Indices: 2637454--2637613 Score: 164
Period size: 57 Copynumber: 2.8 Consensus size: 56
2637444 TTAATTTTAA
* *
2637454 AAATTTTGAAATGTATATTTGAAATATTTTATAATATATATTTTTAAAATT-TTAAATAT-
1 AAATTTTGAAAT-TAT-TTTTAAAAATTTTA-AATATATATTTTTAAAATTATT--ATATG
* * * *
2637513 ATATATTTGAAATTATTTTTAAAAATTTTAAATATATATTTTTGAAATTATTTTTTG
1 AAAT-TTTGAAATTATTTTTAAAAATTTTAAATATATATTTTTAAAATTATTATATG
* *
2637570 AAATTTTGAATATTATTTTT-TAAATATTAAATATATATTTTTAA
1 AAATTTTGAA-ATTATTTTTAAAAATTTTAAATATATATTTTTAA
2637614 TAATATAAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
56 29 0.33
57 30 0.34
58 14 0.16
59 6 0.07
60 8 0.09
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (56 bp):
AAATTTTGAAATTATTTTTAAAAATTTTAAATATATATTTTTAAAATTATTATATG
Found at i:2637567 original size:13 final size:14
Alignment explanation
Indices: 2637538--2637574 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
2637528 TTTTTAAAAA
2637538 TTTT-AAATATATAT
1 TTTTGAAAT-TATAT
2637552 TTTTGAAATTAT-T
1 TTTTGAAATTATAT
2637565 TTTTGAAATT
1 TTTTGAAATT
2637575 TTGAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.50
14 7 0.32
15 4 0.18
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (14 bp):
TTTTGAAATTATAT
Found at i:2637578 original size:21 final size:20
Alignment explanation
Indices: 2637552--2637613 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
2637542 AAATATATAT
2637552 TTTTGAAATTATTTTTTGAAA
1 TTTTGAAATTATTTTTT-AAA
2637573 TTTTGAATATTATTTTTTAAA
1 TTTTGAA-ATTATTTTTTAAA
*
2637594 TATT-AAATATATATTTTTAA
1 TTTTGAAAT-TAT-TTTTTAA
2637614 TAATATAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 2 0.05
20 5 0.14
21 20 0.54
22 10 0.27
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTTGAAATTATTTTTTAAA
Found at i:2637590 original size:35 final size:35
Alignment explanation
Indices: 2637494--2637594 Score: 150
Period size: 35 Copynumber: 2.9 Consensus size: 35
2637484 ATAATATATA
*
2637494 TTTTTAAAATTTTAAATATATATATTTGAAATTAT
1 TTTTTAAAATTTTAAATATATATTTTTGAAATTAT
*
2637529 TTTTAAAAATTTTAAATATATATTTTTGAAATTAT
1 TTTTTAAAATTTTAAATATATATTTTTGAAATTAT
* * *
2637564 TTTTTGAAATTTTGAATAT-TATTTTTTAAAT
1 TTTTTAAAATTTTAAATATATATTTTTGAAAT
2637595 ATTAAATATA
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
34 11 0.18
35 49 0.82
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (35 bp):
TTTTTAAAATTTTAAATATATATTTTTGAAATTAT
Found at i:2637605 original size:23 final size:23
Alignment explanation
Indices: 2637578--2637626 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2637568 TGAAATTTTG
* *
2637578 AATAT-TATTTTTTA-AATATTA
1 AATATATATTTTTAATAATATAA
2637599 AATATATATTTTTAATAATATAA
1 AATATATATTTTTAATAATATAA
2637622 AATAT
1 AATAT
2637627 TTAAATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.21
22 8 0.33
23 11 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AATATATATTTTTAATAATATAA
Found at i:2637626 original size:21 final size:21
Alignment explanation
Indices: 2637578--2637626 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
2637568 TGAAATTTTG
*
2637578 AATATTATTTTTTAAATATTAA
1 AATA-TATTTTTAAAATATTAA
2637600 ATATATATTTTTAATAATA-TAA
1 A-ATATATTTTTAA-AATATTAA
2637622 AATAT
1 AATAT
2637627 TTAAATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 4 0.17
22 13 0.54
23 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATATTTTTAAAATATTAA
Found at i:2637708 original size:22 final size:23
Alignment explanation
Indices: 2637676--2637734 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
2637666 GTTTTTTAAT
2637676 ATTTTTAATATTATTTAATT-TG
1 ATTTTTAATATTATTTAATTATG
*
2637698 -TTTTATAATATT-TTAAATTATG
1 ATTTT-TAATATTATTTAATTATG
2637720 ATTTTTAA-ATTATTT
1 ATTTTTAATATTATTT
2637735 TTAAAGATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
21 13 0.42
22 14 0.45
23 4 0.13
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (23 bp):
ATTTTTAATATTATTTAATTATG
Found at i:2638111 original size:9 final size:9
Alignment explanation
Indices: 2638069--2638116 Score: 51
Period size: 9 Copynumber: 4.9 Consensus size: 9
2638059 AAAAATCATA
2638069 ATTTAAAAT
1 ATTTAAAAT
2638078 ATTATAAAAT
1 ATT-TAAAAT
*
2638088 AAATTAAACAAT
1 --ATTTAA-AAT
2638100 ATTTAAAAT
1 ATTTAAAAT
2638109 ATTTAAAA
1 ATTTAAAA
2638117 ACTAATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
9 14 0.42
10 11 0.33
11 2 0.06
12 6 0.18
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (9 bp):
ATTTAAAAT
Found at i:2638198 original size:20 final size:20
Alignment explanation
Indices: 2638150--2638209 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
2638140 GTATCTTTAA
2638150 AATATTT-AAATAT-T-TTAT
1 AATATTTAAAATATATATT-T
* *
2638168 ATTATTAAAAATATATATTT
1 AATATTTAAAATATATATTT
2638188 AATATTTAAAA-ATAATATTT
1 AATATTTAAAATAT-ATATTT
2638208 AA
1 AA
2638210 AAAATAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 5 0.15
19 8 0.24
20 19 0.56
21 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATATTTAAAATATATATTT
Found at i:2638203 original size:13 final size:13
Alignment explanation
Indices: 2638187--2638225 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
2638177 AATATATATT
2638187 TAATATTTAAAAA
1 TAATATTTAAAAA
2638200 TAATATTTAAAAAA
1 TAATATTT-AAAAA
*
2638214 TAATATTCAAAA
1 TAATATTTAAAA
2638226 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATATTTAAAAA
Found at i:2638226 original size:12 final size:14
Alignment explanation
Indices: 2638187--2638225 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
2638177 AATATATATT
2638187 TAATATTT-AAAAA
1 TAATATTTAAAAAA
2638200 TAATATTTAAAAAA
1 TAATATTTAAAAAA
*
2638214 TAATATTCAAAA
1 TAATATTTAAAA
2638226 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (14 bp):
TAATATTTAAAAAA
Found at i:2638257 original size:20 final size:20
Alignment explanation
Indices: 2638232--2638311 Score: 57
Period size: 20 Copynumber: 4.2 Consensus size: 20
2638222 AAAATTTTAA
2638232 AAAATTCAAAATATATATTT
1 AAAATTCAAAATATATATTT
** *
2638252 AAAATTTTAAA-A-ATAGTT
1 AAAATTCAAAATATATATTT
2638270 ----T-CAAATATATATATTT
1 AAAATTCAAA-ATATATATTT
*
2638286 AAAATTTAAAATATATATTAT
1 AAAATTCAAAATATATATT-T
2638307 AAAAT
1 AAAAT
2638312 ATTTCAAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 17
0.65 0.10 0.25
Matches are distributed among these distances:
13 2 0.05
14 2 0.05
15 1 0.02
16 5 0.11
18 5 0.11
19 1 0.02
20 19 0.43
21 9 0.20
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (20 bp):
AAAATTCAAAATATATATTT
Found at i:2638264 original size:22 final size:20
Alignment explanation
Indices: 2638171--2638266 Score: 66
Period size: 21 Copynumber: 4.5 Consensus size: 20
2638161 ATTTTATATT
*
2638171 ATTAAAAATATATATTTAATA
1 ATTAAAAATA-ATATTTAAAA
*
2638192 TTTAAAAATAATATTTAAAA
1 ATTAAAAATAATATTTAAAA
* * * *
2638212 AATAATATTCAAAATTTTAAAAA
1 ATTAAAAAT-AATA-TTT-AAAA
*
2638235 ATTCAAAATATATATTTAAAA
1 ATTAAAAATA-ATATTTAAAA
*
2638256 TTTTAAAAATA
1 -ATTAAAAATA
2638267 GTTTCAAATA
Statistics
Matches: 56, Mismatches: 14, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
20 14 0.25
21 16 0.29
22 15 0.27
23 11 0.20
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTAAAAATAATATTTAAAA
Found at i:2638284 original size:64 final size:63
Alignment explanation
Indices: 2638175--2638296 Score: 158
Period size: 64 Copynumber: 1.9 Consensus size: 63
2638165 TATATTATTA
* *
2638175 AAAATATATATTTAATATTTAAAAATAATATTTAAAAAATAATATTCAAAATTTTAAAAAATTC
1 AAAATATATATTTAAAATTTAAAAATAATATTCAAAAAATAATATTCAAAA-TTTAAAAAATTC
* * *
2638239 AAAATATATATTTAAAATTTTAAAAATAGT-TTC-AAATATATATATTTAAAATTTAAAA
1 AAAATATATATTTAAAA-TTTAAAAATAATATTCAAAAAATA-ATATTCAAAATTTAAAA
2638297 TATATATTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
63 13 0.25
64 27 0.53
65 11 0.22
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (63 bp):
AAAATATATATTTAAAATTTAAAAATAATATTCAAAAAATAATATTCAAAATTTAAAAAATTC
Found at i:2638320 original size:23 final size:23
Alignment explanation
Indices: 2638261--2638343 Score: 82
Period size: 23 Copynumber: 3.6 Consensus size: 23
2638251 TAAAATTTTA
2638261 AAAATAGTTTCAAATATATATATT-T
1 AAAATA-TTT-AAA-ATATATATTAT
2638286 -AAA-ATTTAAAATATATATTAT
1 AAAATATTTAAAATATATATTAT
* * *
2638307 AAAATATTTCAAATATACATTTT
1 AAAATATTTAAAATATATATTAT
*
2638330 AAAATTTTTAAAAT
1 AAAATATTTAAAAT
2638344 TAATAATAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
20 9 0.18
21 4 0.08
22 6 0.12
23 28 0.56
24 3 0.06
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (23 bp):
AAAATATTTAAAATATATATTAT
Found at i:2638353 original size:44 final size:46
Alignment explanation
Indices: 2638261--2638354 Score: 124
Period size: 44 Copynumber: 2.1 Consensus size: 46
2638251 TAAAATTTTA
* *
2638261 AAAATAGTTTCAAATATATATATTTAAAATTTAAAATATATATTAT
1 AAAATAGTTTCAAATATACATATTTAAAATTTAAAATATATATAAT
2638307 AAAATA-TTTCAAATATACAT-TTTAAAATTTTTAAAAT-TA-ATAAT
1 AAAATAGTTTCAAATATACATATTTAAAA--TTTAAAATATATATAAT
2638351 AAAA
1 AAAA
2638355 AATAAGTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
44 15 0.34
45 15 0.34
46 14 0.32
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (46 bp):
AAAATAGTTTCAAATATACATATTTAAAATTTAAAATATATATAAT
Found at i:2638357 original size:46 final size:46
Alignment explanation
Indices: 2638260--2638358 Score: 123
Period size: 46 Copynumber: 2.2 Consensus size: 46
2638250 TTAAAATTTT
* *
2638260 AAAAATAGTTTCAAATATATATATTTAAAATTTAAAATATATATTA
1 AAAAATAGTTTCAAATATACATATTTAAAATTTAAAATATATAATA
*
2638306 TAAAATA-TTTCAAATATACAT-TTTAAAATTTTTAAAAT-TAATAATA
1 AAAAATAGTTTCAAATATACATATTTAAAA--TTTAAAATAT-ATAATA
2638352 AAAAATA
1 AAAAATA
2638359 AGTAAAATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
44 7 0.15
45 14 0.30
46 25 0.54
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (46 bp):
AAAAATAGTTTCAAATATACATATTTAAAATTTAAAATATATAATA
Found at i:2638379 original size:10 final size:11
Alignment explanation
Indices: 2638338--2638378 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 11
2638328 TTAAAATTTT
2638338 TAAAATTAATAA
1 TAAAA-TAATAA
2638350 TAAAA-AATAA
1 TAAAATAATAA
2638360 GTAAAATAA-AA
1 -TAAAATAATAA
2638371 TAAAATAA
1 TAAAATAA
2638379 AGATAAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 13 0.48
11 7 0.26
12 7 0.26
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:2642248 original size:82 final size:82
Alignment explanation
Indices: 2642141--2642300 Score: 182
Period size: 83 Copynumber: 1.9 Consensus size: 82
2642131 CTTCCTAAAG
* * * * *
2642141 TTTTAAAATGGTAAATTTTCAATTTAGACCC-TTTATAATTTATAAAATTTTAAATTAGT-AATA
1 TTTTAAAATGATAAATTTTCAATTTA-ACCCTTTTA-AAATTATAAAAATATAAACTAGTAAATA
2642204 ATAAAATTATATTTTAACT
64 ATAAAATTATATTTTAACT
* ** *
2642223 TTTTAAAATGATAAAATTTT-GATTTAACTGTTTTAAAATTATAAAAATATAAACTATTAAAATA
1 TTTTAAAATGAT-AAATTTTCAATTTAACCCTTTTAAAATTATAAAAATATAAACTAGT-AAATA
2642287 ATAAAATTATATTT
64 ATAAAATTATATTT
2642301 ATTACTCATC
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
81 20 0.31
82 20 0.31
83 25 0.38
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (82 bp):
TTTTAAAATGATAAATTTTCAATTTAACCCTTTTAAAATTATAAAAATATAAACTAGTAAATAAT
AAAATTATATTTTAACT
Found at i:2653404 original size:15 final size:15
Alignment explanation
Indices: 2653380--2653409 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2653370 TGTTATCCTC
2653380 CTCTCCTCTCTCTCT
1 CTCTCCTCTCTCTCT
*
2653395 CTCTCTTCTCTCTCT
1 CTCTCCTCTCTCTCT
2653410 TTTGGTTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (15 bp):
CTCTCCTCTCTCTCT
Found at i:2654903 original size:5 final size:5
Alignment explanation
Indices: 2654887--2654927 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
2654877 CCTATAGTAG
*
2654887 TATTA T-TTA TATTA TATTA TATAA TATTTA TATTA TATTA T
1 TATTA TATTA TATTA TATTA TATTA TA-TTA TATTA TATTA T
2654928 TTTAATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 4 0.12
5 24 0.75
6 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATTA
Found at i:2654906 original size:14 final size:14
Alignment explanation
Indices: 2654887--2654929 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
2654877 CCTATAGTAG
2654887 TATTAT-TTATATTA
1 TATTATATTAT-TTA
2654901 TATTATATAATATTTA
1 TATTATAT--TATTTA
2654917 TATTATATTATTT
1 TATTATATTATTT
2654930 TAATATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.42
15 1 0.04
16 11 0.42
17 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTATATTATTTA
Found at i:2654914 original size:21 final size:22
Alignment explanation
Indices: 2654890--2654938 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 22
2654880 ATAGTAGTAT
2654890 TATTTATATTATATTA-TATAA
1 TATTTATATTATATTATTATAA
*
2654911 TATTTATATTATATTATTTTAA
1 TATTTATATTATATTATTATAA
2654933 TATTTA
1 TATTTA
2654939 ATAATTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTTATATTATATTATTATAA
Found at i:2654919 original size:16 final size:15
Alignment explanation
Indices: 2654898--2654949 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
2654888 ATTATTTATA
2654898 TTATATTATATAATAT
1 TTATATTATATAAT-T
*
2654914 TTATATTATATTATT
1 TTATATTATATAATT
2654929 TTAATATT-TAATAATT
1 TT-ATATTAT-ATAATT
2654945 TTATA
1 TTATA
2654950 CATTTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 7 0.22
16 25 0.78
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATATTATATAATT
Found at i:2656699 original size:16 final size:16
Alignment explanation
Indices: 2656680--2656712 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2656670 CTCAAGGGGG
2656680 ATAAAAAAAAATTAAA
1 ATAAAAAAAAATTAAA
*
2656696 ATAAGAAAAAATTAAA
1 ATAAAAAAAAATTAAA
2656712 A
1 A
2656713 ACTCTCCTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (16 bp):
ATAAAAAAAAATTAAA
Found at i:2657074 original size:14 final size:14
Alignment explanation
Indices: 2657055--2657094 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
2657045 GCCTTTATCT
*
2657055 ATCTATTTATCTAA
1 ATCTATATATCTAA
2657069 ATCTATATATCTACA
1 ATCTATATATCTA-A
2657084 TATCTATATAT
1 -ATCTATATAT
2657095 ATAGAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.52
15 1 0.04
16 10 0.43
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (14 bp):
ATCTATATATCTAA
Found at i:2657080 original size:8 final size:8
Alignment explanation
Indices: 2657054--2657094 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
2657044 TGCCTTTATC
*
2657054 TATCTATT
1 TATCTATA
2657062 TATCTA-A
1 TATCTATA
2657069 -ATCTATA
1 TATCTATA
*
2657076 TATCTACA
1 TATCTATA
2657084 TATCTATA
1 TATCTATA
2657092 TAT
1 TAT
2657095 ATAGAGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
6 5 0.18
7 1 0.04
8 22 0.79
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.49
Consensus pattern (8 bp):
TATCTATA
Found at i:2658999 original size:3 final size:3
Alignment explanation
Indices: 2658991--2659098 Score: 80
Period size: 3 Copynumber: 35.3 Consensus size: 3
2658981 AATTTTGCTA
*
2658991 TAT TAT TAT TAT T-T TAT TGT TACT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
* * * *
2659036 TGT TAT ATACA TAT TAT T-T ATAC TA- TACT TAA TAT TAT TAT TAT TA-
1 TAT TAT -TA-T TAT TAT TAT -TAT TAT TA-T TAT TAT TAT TAT TAT TAT
*
2659082 TATT TAG TAT TAT TAT T
1 TA-T TAT TAT TAT TAT T
2659099 TATAAATATT
Statistics
Matches: 84, Mismatches: 11, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
2 7 0.08
3 66 0.79
4 11 0.13
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:2659043 original size:50 final size:47
Alignment explanation
Indices: 2658990--2659098 Score: 114
Period size: 50 Copynumber: 2.2 Consensus size: 47
2658980 TAATTTTGCT
* * *
2658990 ATATTATTATTATTT-TATTGTTACTTATTATTATTATTATTATTATTGT
1 ATATTATTATTATTTATACT-ATACTTAATATTATTATTATTA-TATT-T
*
2659039 -TATATACATATTATTTATACTATACTTAATATTATTATTATTATATTT
1 ATAT-TA-TTATTATTTATACTATACTTAATATTATTATTATTATATTT
2659087 AGTATTATTATT
1 A-TATTATTATT
2659099 TATAAATATT
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
48 8 0.16
49 8 0.16
50 31 0.62
51 3 0.06
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.61
Consensus pattern (47 bp):
ATATTATTATTATTTATACTATACTTAATATTATTATTATTATATTT
Found at i:2661142 original size:25 final size:26
Alignment explanation
Indices: 2661114--2661166 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
2661104 AATACTAATG
* *
2661114 ATTTTTAAATTACT-TTATATTATTT
1 ATTTTTAAATTACTCTTATAGTATCT
*
2661139 A-TTTTAAATTGCTCTTATAGTATCT
1 ATTTTTAAATTACTCTTATAGTATCT
2661164 ATT
1 ATT
2661167 CTAAACCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
24 11 0.48
25 11 0.48
26 1 0.04
ACGTcount: A:0.30, C:0.08, G:0.04, T:0.58
Consensus pattern (26 bp):
ATTTTTAAATTACTCTTATAGTATCT
Found at i:2661145 original size:24 final size:25
Alignment explanation
Indices: 2661116--2661171 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
2661106 TACTAATGAT
* *
2661116 TTTTAAATTACT-TTATATTATTTA
1 TTTTAAATTACTCTTATAGTATCTA
*
2661140 TTTTAAATTGCTCTTATAGTATCTA
1 TTTTAAATTACTCTTATAGTATCTA
*
2661165 TTCTAAA
1 TTTTAAA
2661172 CCTTTATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.32, C:0.09, G:0.04, T:0.55
Consensus pattern (25 bp):
TTTTAAATTACTCTTATAGTATCTA
Done.