Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1961
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: 173942
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
File 1 of 2
Found at i:1909 original size:2 final size:2
Alignment explanation
Indices: 1902--1929 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1892 TCAAATTCTT
1902 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1930 GTTCAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2710 original size:34 final size:35
Alignment explanation
Indices: 2667--2732 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
2657 TTTCAAGTAC
*
2667 TTATTTATTT-TAAAAAATTATAATTTATGTACTT
1 TTATTTATTTAAAAAAAATTATAATTTATGTACTT
*
2701 TTATTTATTTAAAAAAAATTATAATTTGTGTA
1 TTATTTATTTAAAAAAAATTATAATTTATGTA
2733 TCTATTTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 10 0.34
35 19 0.66
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (35 bp):
TTATTTATTTAAAAAAAATTATAATTTATGTACTT
Found at i:2739 original size:33 final size:33
Alignment explanation
Indices: 2663--2740 Score: 97
Period size: 35 Copynumber: 2.4 Consensus size: 33
2653 TCTTTTTCAA
*
2663 GTACT-TATTTATTTTAAAAAATTATAATTTAT
1 GTACTCTATTTATTTAAAAAAATTATAATTTAT
* *
2695 GTACTTTTATTTATTTAAAAAAAATTATAATTTGT
1 GTAC-TCTATTTATTT-AAAAAAATTATAATTTAT
2730 GTA-TCTATTTA
1 GTACTCTATTTA
2741 GAATCAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
32 4 0.10
33 8 0.20
34 9 0.22
35 19 0.47
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (33 bp):
GTACTCTATTTATTTAAAAAAATTATAATTTAT
Found at i:10262 original size:7 final size:7
Alignment explanation
Indices: 10212--10263 Score: 52
Period size: 8 Copynumber: 7.1 Consensus size: 7
10202 ATTTTTAAAT
10212 TAATTTA
1 TAATTTA
10219 TAAATTTA
1 T-AATTTA
10227 TAAATTTA
1 T-AATTTA
*
10235 -AATTTT
1 TAATTTA
*
10241 TAATTTT
1 TAATTTA
10248 TAATTTTA
1 TAA-TTTA
10256 TAATTTA
1 TAATTTA
10263 T
1 T
10264 TTATTTATCT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
6 5 0.12
7 15 0.38
8 20 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TAATTTA
Found at i:10337 original size:18 final size:17
Alignment explanation
Indices: 10314--10349 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
10304 TAATAAAAAT
*
10314 TTTAAATTATTTATTTTA
1 TTTAAATAATTT-TTTTA
10332 TTTAAATAATTTTTTTA
1 TTTAAATAATTTTTTTA
10349 T
1 T
10350 ATTTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTAAATAATTTTTTTA
Found at i:10624 original size:20 final size:20
Alignment explanation
Indices: 10601--10639 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
10591 AATATTTTGA
*
10601 TATTATAAA-AAATTAAAATT
1 TATTA-AAATAAATAAAAATT
10621 TATTAAAATAAATAAAAAT
1 TATTAAAATAAATAAAAAT
10640 AAAGTTGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TATTAAAATAAATAAAAATT
Found at i:11397 original size:23 final size:23
Alignment explanation
Indices: 11378--11421 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
11368 TAAATTTTGA
11378 TATATTAT-TTTT--TTATATTT
1 TATATTATATTTTAATTATATTT
11398 TATATTATATTTTAATTATATTT
1 TATATTATATTTTAATTATATTT
11421 T
1 T
11422 TCGTTGTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.38
21 4 0.19
23 9 0.43
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TATATTATATTTTAATTATATTT
Found at i:11422 original size:12 final size:12
Alignment explanation
Indices: 11324--11421 Score: 61
Period size: 11 Copynumber: 8.5 Consensus size: 12
11314 GTTATTGATT
11324 TATTTTA-ATTA
1 TATTTTATATTA
*
11335 TA-TTTA-A-AA
1 TATTTTATATTA
*
11344 TATTATATATTA
1 TATTTTATATTA
11356 T-TATTTATTATATA
1 TAT-TTTA-TAT-TA
*
11370 AATTTTGATA-TA
1 TATTTT-ATATTA
11382 TTATTTT-T-TTA
1 -TATTTTATATTA
11393 TATTTTATATTA
1 TATTTTATATTA
11405 TATTTTA-ATTA
1 TATTTTATATTA
11416 TATTTT
1 TATTTT
11422 TCGTTGTAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 24
0.70 0.06 0.24
Matches are distributed among these distances:
9 3 0.04
10 14 0.20
11 18 0.26
12 17 0.25
13 8 0.12
14 7 0.10
15 2 0.03
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (12 bp):
TATTTTATATTA
Found at i:12271 original size:188 final size:189
Alignment explanation
Indices: 11892--12271 Score: 570
Period size: 189 Copynumber: 2.0 Consensus size: 189
11882 ATTTTTTTCT
*
11892 ACTCCTTGAATATTATTTACTTATATAATTTTTTTATTTCCTATAGTCCCTTTATTTATCAAGCA
1 ACTCCTTGAATATTA-TTAC-TATATAATTTTTTTATTTCCTACAGTCCCTTTATTTATCAAGCA
* * *
11957 TATGTTTATATAATGTCGGTAAAATTTTTAAATTTAATACGTGAATTTAAAAAATTAACAAGTAT
64 TATGTTTATATAATGTCGGTAAAATTTTTAAATTTAATAAGTAAATTAAAAAAATTAACAAGTAT
12022 TTTTTTGTAATACTAATTTTAAATATTTTTATTATATAATATAAAAATATAAGTCACTTTG
129 TTTTTTGTAATACTAATTTTAAATATTTTTATTATATAATATAAAAATATAAGTCACTTTG
* * *
12083 ACTCCTTGAATATTA-TA-TATATAATTTTTTTTTATTTCCTACATTCCCTTTATTTATTAAGCC
1 ACTCCTTGAATATTATTACTATATAA--TTTTTTTATTTCCTACAGTCCCTTTATTTATCAAGCA
* *
12146 TATTTTTATATAATGTCGGTTAAATTTTTAAATTTAATAAGTAAAGTTAAAAAAATTAACAAGTA
64 TATGTTTATATAATGTCGGTAAAATTTTTAAATTTAATAAGTAAA-TTAAAAAAATTAACAAGTA
* * * *
12211 -TTTTTT-TAATATTAATTTTAATTATTTTTATTATATAATATAGAAATATATGTCACTTTG
128 TTTTTTTGTAATACTAATTTTAAATATTTTTATTATATAATATAAAAATATAAGTCACTTTG
12271 A
1 A
12272 TAATTTGCTC
Statistics
Matches: 173, Mismatches: 13, Indels: 9
0.89 0.07 0.05
Matches are distributed among these distances:
187 7 0.04
188 51 0.29
189 82 0.47
190 18 0.10
191 15 0.09
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (189 bp):
ACTCCTTGAATATTATTACTATATAATTTTTTTATTTCCTACAGTCCCTTTATTTATCAAGCATA
TGTTTATATAATGTCGGTAAAATTTTTAAATTTAATAAGTAAATTAAAAAAATTAACAAGTATTT
TTTTGTAATACTAATTTTAAATATTTTTATTATATAATATAAAAATATAAGTCACTTTG
Found at i:20424 original size:31 final size:31
Alignment explanation
Indices: 20371--20433 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 31
20361 ATAAAAAATT
20371 TTTATTTAAATAATAATTAAAATT-ATTTAA
1 TTTATTTAAATAATAATTAAAATTAATTTAA
*
20401 TTTA-TTAAATATTATATTTAAAATTAATTTAA
1 TTTATTTAAATA--ATAATTAAAATTAATTTAA
20433 T
1 T
20434 ATAAATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 7 0.24
30 4 0.14
31 11 0.38
32 7 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
TTTATTTAAATAATAATTAAAATTAATTTAA
Found at i:20934 original size:2 final size:2
Alignment explanation
Indices: 20927--20967 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
20917 TACTTTTGAA
*
20927 TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
20968 TCTTTTAAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:23444 original size:41 final size:41
Alignment explanation
Indices: 23397--23519 Score: 246
Period size: 41 Copynumber: 3.0 Consensus size: 41
23387 TCATCAAAGG
23397 AAACACCAATTTCTTTGCTTCTGTGTGAACTGTATGCTAGT
1 AAACACCAATTTCTTTGCTTCTGTGTGAACTGTATGCTAGT
23438 AAACACCAATTTCTTTGCTTCTGTGTGAACTGTATGCTAGT
1 AAACACCAATTTCTTTGCTTCTGTGTGAACTGTATGCTAGT
23479 AAACACCAATTTCTTTGCTTCTGTGTGAACTGTATGCTAGT
1 AAACACCAATTTCTTTGCTTCTGTGTGAACTGTATGCTAGT
23520 TTCTTACTGT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 82 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (41 bp):
AAACACCAATTTCTTTGCTTCTGTGTGAACTGTATGCTAGT
Found at i:23704 original size:62 final size:62
Alignment explanation
Indices: 23607--23731 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
23597 TCGAATCTCG
23607 AAAATTAGTAGTGGAAAAATATGCAAGAAGTAAAAAAGTTTATTCTTCTTAGCAGTAAAGAC
1 AAAATTAGTAGTGGAAAAATATGCAAGAAGTAAAAAAGTTTATTCTTCTTAGCAGTAAAGAC
23669 AAAATTAGTAGTGGAAAAATATGCAAGAAGTAAAAAAGTTTATTCTTCTTAGCAGTAAAGAC
1 AAAATTAGTAGTGGAAAAATATGCAAGAAGTAAAAAAGTTTATTCTTCTTAGCAGTAAAGAC
23731 A
1 A
23732 CTTTTGATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.27
Consensus pattern (62 bp):
AAAATTAGTAGTGGAAAAATATGCAAGAAGTAAAAAAGTTTATTCTTCTTAGCAGTAAAGAC
Found at i:26319 original size:7 final size:7
Alignment explanation
Indices: 26309--26359 Score: 51
Period size: 6 Copynumber: 8.1 Consensus size: 7
26299 TTAATTTTAA
26309 TATAAAT
1 TATAAAT
26316 TAT-AAT
1 TATAAAT
*
26322 TAAAAAT
1 TATAAAT
26329 T-TAAAT
1 TATAAAT
26335 T-T-AA-
1 TATAAAT
26339 TATAAAT
1 TATAAAT
26346 TATAAAT
1 TATAAAT
26353 TA-AAAT
1 TATAAAT
26359 T
1 T
26360 TTATTTACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
4 1 0.03
5 3 0.08
6 18 0.47
7 16 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TATAAAT
Found at i:26340 original size:30 final size:31
Alignment explanation
Indices: 26299--26362 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
26289 ACGTTAACAA
*
26299 TTAATTTTAATATAAATTAT-AATTAAAAAT
1 TTAAATTTAATATAAATTATAAATTAAAAAT
*
26329 TTAAATTTAATATAAATTATAAATTAAAATT
1 TTAAATTTAATATAAATTATAAATTAAAAAT
26360 TTA
1 TTA
26363 TTTACATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 19 0.61
31 12 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
TTAAATTTAATATAAATTATAAATTAAAAAT
Found at i:27239 original size:3 final size:3
Alignment explanation
Indices: 27231--27266 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
27221 CTTGCTTCAA
27231 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
27267 CTCTTGATTT
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:28418 original size:247 final size:244
Alignment explanation
Indices: 27977--28450 Score: 548
Period size: 247 Copynumber: 1.9 Consensus size: 244
27967 AACTAATCAT
* * *
27977 TAAACAAACACCCCAAAGCTAAAAGGTCAGCAAAATGGGTATATCGAGCATAAGCCATTCATGCT
1 TAAACAAACACCCCAAAGCAAAAAAGTCAGCAAAAT--GTATATCGAGCATAACCCATTCATGCT
* * * **
28042 TTAAGTTCATCTTGGACTCATTACAGTGACTTAAAAACTATCATTCAGGATGATTTTCATATTGC
64 TTAAGTTCATCTTGGACTCATAACAGTGACTTAAAAACTATCAGTCAGGATGATTTTCACATCAC
* * * * * * * *
28107 CATCCAAATTAATCAGGAGGATGAAAAAGCAATACTAAAGGAAAATGAATCTTACTCGCTCATCA
129 AATCCAAAATAATCAGCAGGATCAAAAAACAAGACTAAAGGAAAA-GAATCTGACTCACTCATCA
* *
28172 -TGAGAAAATTTACATCCA-GCACCACGACTGCATCCATGATTTTATTTTCACA
193 TTCA-AAAATTTACA-ACATGCACCACGACTGCATCCATGATTTTATTTTCACA
* * *
28224 TAAACAAACACCCCAAGGCAAAAAAAAGTCAGCAAAAT-TAGTATCTAGCATACCCCATTCATGC
1 TAAACAAACACCCCAAAGC--AAAAAAGTCAGCAAAATGTA-TATCGAGCATAACCCATTCATGC
* * * *
28288 TTTAAGTTCATCTTGGACTCCTAAGAGTGACTTAGAAAC-ACTCAGTC-GGAGTGATTTTCGCAT
63 TTTAAGTTCATCTTGGACTCATAACAGTGACTTAAAAACTA-TCAGTCAGGA-TGATTTTCACAT
28351 CACAATCCAAAATAATC-GCATGGATCAAAAAACAAGACTAAATGGAAACA-AATCTGACTCACT
126 CACAATCCAAAATAATCAGCA-GGATCAAAAAACAAGACTAAA-GGAAA-AGAATCTGACTCACT
*
28414 CATCATTCAAAAATTTACAACATGCACCATGACTGCA
188 CATCATTCAAAAATTTACAACATGCACCACGACTGCA
28451 CTCACCTCTG
Statistics
Matches: 191, Mismatches: 26, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
246 10 0.05
247 158 0.83
248 7 0.04
249 16 0.08
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (244 bp):
TAAACAAACACCCCAAAGCAAAAAAGTCAGCAAAATGTATATCGAGCATAACCCATTCATGCTTT
AAGTTCATCTTGGACTCATAACAGTGACTTAAAAACTATCAGTCAGGATGATTTTCACATCACAA
TCCAAAATAATCAGCAGGATCAAAAAACAAGACTAAAGGAAAAGAATCTGACTCACTCATCATTC
AAAAATTTACAACATGCACCACGACTGCATCCATGATTTTATTTTCACA
Found at i:29824 original size:20 final size:20
Alignment explanation
Indices: 29795--29865 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 20
29785 GTATCATAAT
*
29795 TTTATTTAAAATATTATATA
1 TTTATATAAAATATTATATA
29815 TTTATAT-AAAT-TTA-ACGTAA
1 TTTATATAAAATATTATA--T-A
* *
29835 TTATATTTAAAACATTATATA
1 TT-TATATAAAATATTATATA
29856 TTTATATAAA
1 TTTATATAAA
29866 TTTCAATATG
Statistics
Matches: 40, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
17 1 0.03
18 3 0.08
19 5 0.12
20 16 0.40
21 7 0.17
22 4 0.10
23 3 0.08
24 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (20 bp):
TTTATATAAAATATTATATA
Found at i:29842 original size:41 final size:41
Alignment explanation
Indices: 29791--29868 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
29781 ATACGTATCA
* *
29791 TAATTTTATTTAAAATATTATATATTTATATAAATTTAACG
1 TAATTATATTTAAAACATTATATATTTATATAAATTTAACG
29832 TAATTATATTTAAAACATTATATATTTATATAAATTT
1 TAATTATATTTAAAACATTATATATTTATATAAATTT
29869 CAATATGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (41 bp):
TAATTATATTTAAAACATTATATATTTATATAAATTTAACG
Found at i:31420 original size:2 final size:2
Alignment explanation
Indices: 31413--31449 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
31403 AAATAGTTAA
31413 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
31450 CCCCAAAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:32307 original size:2 final size:2
Alignment explanation
Indices: 32300--32331 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
32290 ACATACATAC
32300 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32332 CATCCAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35386 original size:18 final size:18
Alignment explanation
Indices: 35345--35401 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
35335 AAATTAAATA
* *
35345 AATATTTAATTATATAATT
1 AATATATAA-TATATATTT
35364 AATATATAATATATATTT
1 AATATATAATATATATTT
* * *
35382 TATATTTTATATTATATTT
1 AATATATAATA-TATATTT
35401 A
1 A
35402 TACTTACATA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
18 16 0.52
19 15 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATATATAATATATATTT
Found at i:36606 original size:9 final size:9
Alignment explanation
Indices: 36593--36659 Score: 52
Period size: 9 Copynumber: 7.7 Consensus size: 9
36583 ATGATAAATA
36593 AAAAATAAT
1 AAAAATAAT
*
36602 TAAAAT-AT
1 AAAAATAAT
36610 AAAAATAA-
1 AAAAATAAT
*
36618 AAATAA-GAT
1 AAA-AATAAT
*
36627 AAAAATAAA
1 AAAAATAAT
36636 AAATAAT-AT
1 AAA-AATAAT
36645 AAAAATAAT
1 AAAAATAAT
*
36654 ATAAAT
1 AAAAAT
36660 TTATAAATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
8 16 0.36
9 26 0.58
10 3 0.07
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.24
Consensus pattern (9 bp):
AAAAATAAT
Found at i:36615 original size:17 final size:16
Alignment explanation
Indices: 36574--36695 Score: 70
Period size: 17 Copynumber: 7.3 Consensus size: 16
36564 TTTTATATAT
* *
36574 AATATAAATATGAT-A
1 AATATAAAAATAATAA
36589 AATA-AAAAATAATTAA
1 AATATAAAAATAA-TAA
*
36605 AATATAAAAATAAAAA
1 AATATAAAAATAATAA
* *
36621 TAAGATAAAAATAAAAAA
1 -AATATAAAAAT-AATAA
36639 TAATATAAAAATAATATA
1 -AATATAAAAATAATA-A
* *
36657 AATTTATAAATATATTAA
1 AA--TATAAAAATAATAA
* *
36675 AATTTATATAAT-ATAA
1 AATATA-AAAATAATAA
36691 AATAT
1 AATAT
36696 TAACACGTTA
Statistics
Matches: 85, Mismatches: 13, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
14 6 0.07
15 5 0.06
16 17 0.20
17 26 0.31
18 20 0.24
19 11 0.13
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (16 bp):
AATATAAAAATAATAA
Found at i:36623 original size:23 final size:25
Alignment explanation
Indices: 36579--36637 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 25
36569 TATATAATAT
* *
36579 AAATATGATAAATAAAAAATAA-TTA
1 AAATAT-AAAAATAAAAAATAAGATA
36604 AAATATAAAAAT-AAAAATAAGATA
1 AAATATAAAAATAAAAAATAAGATA
36628 AAA-ATAAAAA
1 AAATATAAAAA
36638 ATAATATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 15 0.48
24 10 0.32
25 6 0.19
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (25 bp):
AAATATAAAAATAAAAAATAAGATA
Found at i:36648 original size:11 final size:11
Alignment explanation
Indices: 36589--36658 Score: 62
Period size: 11 Copynumber: 6.7 Consensus size: 11
36579 AAATATGATA
36589 AATA-AAAAAT
1 AATATAAAAAT
36599 AAT-TAAAATAT
1 AATATAAAA-AT
*
36610 AAAAATAAAAAT
1 -AATATAAAAAT
*
36622 AAGAT--AAA-
1 AATATAAAAAT
36630 AATA-AAAAAT
1 AATATAAAAAT
36640 AATATAAAAAT
1 AATATAAAAAT
36651 AATATAAA
1 AATATAAA
36659 TTTATAAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 15
0.73 0.04 0.22
Matches are distributed among these distances:
8 3 0.06
9 6 0.12
10 11 0.22
11 20 0.41
12 4 0.08
13 5 0.10
ACGTcount: A:0.76, C:0.00, G:0.01, T:0.23
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:36650 original size:18 final size:18
Alignment explanation
Indices: 36605--36652 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
36595 AAATAATTAA
36605 AATATAAAAAT-AAAAAT
1 AATATAAAAATAAAAAAT
*
36622 AAGATAAAAATAAAAAAT
1 AATATAAAAATAAAAAAT
36640 AATATAAAAATAA
1 AATATAAAAATAA
36653 TATAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 10 0.36
18 18 0.64
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (18 bp):
AATATAAAAATAAAAAAT
Found at i:36657 original size:23 final size:23
Alignment explanation
Indices: 36589--36658 Score: 55
Period size: 21 Copynumber: 3.3 Consensus size: 23
36579 AAATATGATA
36589 AATAAAAAATAAT-TAAA-ATATA
1 AATAAAAAATAATATAAATA-ATA
* *
36611 AA-AATAAA-AATA-AGATAA-A
1 AATAAAAAATAATATAAATAATA
36630 AATAAAAAATAATATAAA-AATA
1 AATAAAAAATAATATAAATAATA
36652 ATATAAA
1 A-ATAAA
36659 TTTATAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
19 3 0.08
20 11 0.30
21 12 0.32
22 6 0.16
23 5 0.14
ACGTcount: A:0.76, C:0.00, G:0.01, T:0.23
Consensus pattern (23 bp):
AATAAAAAATAATATAAATAATA
Found at i:36671 original size:16 final size:16
Alignment explanation
Indices: 36647--36693 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
36637 AATAATATAA
36647 AAATAATATAAATTTAT
1 AAAT-ATATAAATTTAT
36664 AAATATATTAAAATTTAT
1 AAATATA-T-AAATTTAT
36682 ATAATATA-AAAT
1 A-AATATATAAAT
36694 ATTAACACGT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 7 0.26
17 5 0.19
18 9 0.33
19 6 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATATATAAATTTAT
Found at i:36687 original size:33 final size:32
Alignment explanation
Indices: 36649--36722 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
36639 TAATATAAAA
* * *
36649 ATAATATAAATTTATAAATATATTAAAATTTAT
1 ATAATATAAA-ATATAAACACATTAAAATTTAT
* *
36682 ATAATATAAAATATTAACACGTTAAAATTTAT
1 ATAATATAAAATATAAACACATTAAAATTTAT
36714 ATATATATA
1 ATA-ATATA
36723 CACAACATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 20 0.57
33 15 0.43
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (32 bp):
ATAATATAAAATATAAACACATTAAAATTTAT
Found at i:36958 original size:18 final size:17
Alignment explanation
Indices: 36937--37013 Score: 60
Period size: 17 Copynumber: 4.7 Consensus size: 17
36927 TTTAAAATCT
36937 ATATAATACAAATTATTA
1 ATATAATA-AAATTATTA
*
36955 ATATATTAAAATTGATATA
1 ATATAATAAAATT-AT-TA
36974 AT-T-ATAAAA-TATT-
1 ATATAATAAAATTATTA
36987 ATA-AATATAAATTA-TA
1 ATATAATA-AAATTATTA
37003 ATATAA-AAAAT
1 ATATAATAAAAT
37014 ATACGAATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 19
0.70 0.03 0.27
Matches are distributed among these distances:
13 2 0.04
14 4 0.08
15 10 0.20
16 7 0.14
17 12 0.24
18 10 0.20
19 4 0.08
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (17 bp):
ATATAATAAAATTATTA
Found at i:37011 original size:29 final size:28
Alignment explanation
Indices: 36970--37032 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
36960 TTAAAATTGA
*
36970 TATAATTATAAAATATTATA-AATATAAAT
1 TATAATTATAAAA-A-TATACAATATAAAC
36999 TATAA-TATAAAAAATATACGAATATAAAC
1 TATAATTAT-AAAAATATAC-AATATAAAC
37028 TATAA
1 TATAA
37033 GTAGAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
27 4 0.13
28 4 0.13
29 22 0.73
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (28 bp):
TATAATTATAAAAATATACAATATAAAC
Found at i:37135 original size:3 final size:3
Alignment explanation
Indices: 37129--37164 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
37119 ATTTTCATCA
*
37129 TCT TCT TCT TTT TCT TCT TCT TCT TCT TCT T-T TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
37165 ATTATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TCT
Found at i:37322 original size:24 final size:26
Alignment explanation
Indices: 37295--37343 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
37285 TATAATTTTA
37295 AAAAATTAATA-ATT-TATATTATAT
1 AAAAATTAATATATTATATATTATAT
*
37319 AAAATTTAATATATTAATATATTAT
1 AAAAATTAATATATT-ATATATTAT
37344 TTTATATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 10 0.48
25 3 0.14
27 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
AAAAATTAATATATTATATATTATAT
Found at i:37959 original size:3 final size:3
Alignment explanation
Indices: 37906--37940 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
37896 CTCTTCAGAG
37906 GAA GAA GAA GAA GAA GAA GAA G-A GCAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA GAA GA
37941 TCCACCATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 26 0.87
4 2 0.07
ACGTcount: A:0.63, C:0.03, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:39678 original size:240 final size:240
Alignment explanation
Indices: 39255--39709 Score: 829
Period size: 240 Copynumber: 1.9 Consensus size: 240
39245 TCAGCTTATG
*
39255 ATGTTAAAAGCTTAGCTTTCTATGCATTTGAACTTCATATTTATTCAGTTTGTGCTGTCAGATTT
1 ATGTTAAAAGCTTAGCTTTCTATGCATTTGAACTTCATATTTATTCAGTTTGTGCTGTCAGATTG
* *
39320 ACGAGATTTACAATTTGGTGTTCGTTGATTTTGCTGAATAGTTTCGTTTGGAACCTGTCAAATTG
66 AAGAGATTTACAATTTAGTGTTCGTTGATTTTGCTGAATAGTTTCGTTTGGAACCTGTCAAATTG
39385 TCTGTTCGATGGTTAAATTCGAGAGAGATCCTGTGATTCTTTGCATAAAATGAATTTATTTTACT
131 TCTGTTCGATGGTTAAATTCGAGAGAGATCCTGTGATTCTTTGCATAAAATGAATTTATTTTACT
39450 CTTCTTTTATTTACTCAATAAAATGAATTTATTCGAGAGAGATTT
196 CTTCTTTTATTTACTCAATAAAATGAATTTATTCGAGAGAGATTT
* **
39495 ATGTTAAAAGCTTAGCTTTCTATGCATTTGAACTTCATATTTATTCAGTTTGTGCTTTTGGATTG
1 ATGTTAAAAGCTTAGCTTTCTATGCATTTGAACTTCATATTTATTCAGTTTGTGCTGTCAGATTG
* *
39560 AAGAGATTTACAATTTAGTGTTTGTTGATTTTGCTGAATAGTTTCGTTTGGAACCTTTCAAATTG
66 AAGAGATTTACAATTTAGTGTTCGTTGATTTTGCTGAATAGTTTCGTTTGGAACCTGTCAAATTG
39625 TCTGTTCGATGGTTAAATTCGAGAGAGATCCTGTGATTCTTTGCATAAAATGAATTTATTTTACT
131 TCTGTTCGATGGTTAAATTCGAGAGAGATCCTGTGATTCTTTGCATAAAATGAATTTATTTTACT
*
39690 CTTCTTTTATTTGCTCAATA
196 CTTCTTTTATTTACTCAATA
39710 GATCAAGCCA
Statistics
Matches: 206, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
240 206 1.00
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.44
Consensus pattern (240 bp):
ATGTTAAAAGCTTAGCTTTCTATGCATTTGAACTTCATATTTATTCAGTTTGTGCTGTCAGATTG
AAGAGATTTACAATTTAGTGTTCGTTGATTTTGCTGAATAGTTTCGTTTGGAACCTGTCAAATTG
TCTGTTCGATGGTTAAATTCGAGAGAGATCCTGTGATTCTTTGCATAAAATGAATTTATTTTACT
CTTCTTTTATTTACTCAATAAAATGAATTTATTCGAGAGAGATTT
Found at i:45865 original size:32 final size:33
Alignment explanation
Indices: 45823--45892 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 33
45813 TATAATATTT
* * *
45823 TTTATTTTATATAATTTTTAATATATTAATA-A
1 TTTATATTATATAAATTTTAAAATATTAATATA
*
45855 TTTATATTATATAAATTTTAAAATATTTATATA
1 TTTATATTATATAAATTTTAAAATATTAATATA
45888 TTTAT
1 TTTAT
45893 TACTATTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 27 0.82
33 6 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (33 bp):
TTTATATTATATAAATTTTAAAATATTAATATA
Found at i:45874 original size:16 final size:17
Alignment explanation
Indices: 45794--45874 Score: 66
Period size: 16 Copynumber: 4.9 Consensus size: 17
45784 ATCATAGGTA
*
45794 ATTATATAATA-ATTAT
1 ATTATATAATATTTTAT
45810 ATT-TATAATATTTTTTAT
1 ATTATATAATA--TTTTAT
*
45828 TTTATATAAT-TTTTA-
1 ATTATATAATATTTTAT
*
45843 A-TATATTAATAATTTAT
1 ATTATA-TAATATTTTAT
45860 ATTATATAA-ATTTTA
1 ATTATATAATATTTTA
45875 AAATATTTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
14 4 0.08
15 11 0.21
16 17 0.33
17 4 0.08
18 10 0.19
19 6 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTATATAATATTTTAT
Found at i:46379 original size:18 final size:18
Alignment explanation
Indices: 46298--46387 Score: 55
Period size: 18 Copynumber: 5.0 Consensus size: 18
46288 AAATTTGATA
*
46298 ATATTTTTTAATAT-TTT
1 ATATATTTTAATATATTT
*
46315 A-ATTATATTTAATTTA-TT
1 ATA-TAT-TTTAATATATTT
*
46333 ATATA-TTTATATAAAATTT
1 ATATATTTTA-AT-ATATTT
*
46352 A-AGATATTTAATATATTT
1 ATATAT-TTTAATATATTT
*
46370 ATATATTTTATTATATTT
1 ATATATTTTAATATATTT
46388 TTTATTTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 19
0.67 0.10 0.23
Matches are distributed among these distances:
16 5 0.09
17 5 0.09
18 32 0.58
19 9 0.16
20 4 0.07
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (18 bp):
ATATATTTTAATATATTT
Found at i:46385 original size:27 final size:27
Alignment explanation
Indices: 46308--46395 Score: 51
Period size: 27 Copynumber: 3.3 Consensus size: 27
46298 ATATTTTTTA
* *
46308 ATAT-TTTAATTATATTTAATTTA-TT
1 ATATATTTTATTATATTTAATATATTT
* * *
46333 ATATATTTATATAAAATTTAAGATATTT
1 ATATATTT-TATTATATTTAATATATTT
*
46361 A-ATATATTTA-TATATTTTATTATATTT
1 ATATAT-TTTATTATA-TTTAATATATTT
*
46388 -TTTATTTT
1 ATATATTTT
46396 TTTAATGCCG
Statistics
Matches: 47, Mismatches: 10, Indels: 11
0.69 0.15 0.16
Matches are distributed among these distances:
25 4 0.09
26 8 0.17
27 30 0.64
28 5 0.11
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (27 bp):
ATATATTTTATTATATTTAATATATTT
Found at i:51957 original size:2 final size:2
Alignment explanation
Indices: 51950--51974 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
51940 TAATTTAATG
51950 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
51975 TATTATCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:52244 original size:129 final size:129
Alignment explanation
Indices: 51993--52244 Score: 287
Period size: 129 Copynumber: 2.0 Consensus size: 129
51983 TTCATGATTA
*
51993 TATTAATCAAATATGACTTATAAAAAAAATATTTATATAGTGTAATATGATTGGAAGGGACCATA
1 TATTAATCAAATATGACTTATAAAAAAAATATTTATATAGTGTAATATGATTGGAAGAGACCATA
** * * * **
52058 ATTGATGTCATAAAAAAACTTATCTAATAGCTTATTGATAAAATATATTATTTTTTATTGTTTG
66 ACCGATGTAATAAAAAAACTTATCTAATAACTTATCGATAAAATATATTATAATTTATTGTTTG
* * *
52122 TATTAATCAAATATGA-TATATAAAAAAAATATTTATATTGATGTGATATTATTGGAAGAGACCA
1 TATTAATCAAATATGACT-TATAAAAAAAATATTTATATAG-TGTAATATGATTGGAAGAGACCA
* * * * * *
52186 TAACCGAATGTAATAAACAAATTTA-CTTAATAATTTCTCGAT-TAA-ATGTTATAATTTAT
64 TAACCG-ATGTAATAAAAAAACTTATC-TAATAACTTATCGATAAAATATATTATAATTTAT
52245 ATTTTTTGTG
Statistics
Matches: 102, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
128 1 0.01
129 48 0.47
130 27 0.26
131 26 0.25
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (129 bp):
TATTAATCAAATATGACTTATAAAAAAAATATTTATATAGTGTAATATGATTGGAAGAGACCATA
ACCGATGTAATAAAAAAACTTATCTAATAACTTATCGATAAAATATATTATAATTTATTGTTTG
Found at i:52424 original size:15 final size:16
Alignment explanation
Indices: 52396--52432 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
52386 ATTTTAATCA
52396 TTATT-TTATAAATAT
1 TTATTATTATAAATAT
*
52411 TT-TTATTATTAATAT
1 TTATTATTATAAATAT
52426 TTATTAT
1 TTATTAT
52433 CATGCGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 2 0.11
15 13 0.68
16 4 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTATTATAAATAT
Found at i:54768 original size:17 final size:17
Alignment explanation
Indices: 54746--54778 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
54736 AATATCATAT
54746 AATTTTGATTT-TTTATC
1 AATTTT-ATTTATTTATC
54763 AATTTTATTTATTTAT
1 AATTTTATTTATTTAT
54779 ATATTTGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (17 bp):
AATTTTATTTATTTATC
Found at i:55121 original size:3 final size:3
Alignment explanation
Indices: 55113--55151 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
55103 AACATGGAAT
55113 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55152 ATATTATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:55159 original size:3 final size:3
Alignment explanation
Indices: 55153--55179 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
55143 TAATAATAAA
55153 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
55180 AGTTATTCAT
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):
TAT
Found at i:55454 original size:18 final size:18
Alignment explanation
Indices: 55431--55484 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 18
55421 TTTATATTCA
55431 TATTATATTTAAATATTT
1 TATTATATTTAAATATTT
55449 TATTATATTATAATTATATTT
1 TATTATATT-TAA--ATATTT
*
55470 TA-AATATTTTAAATA
1 TATTATA-TTTAAATA
55485 AATTTTGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 12 0.39
19 3 0.10
20 6 0.19
21 10 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTATATTTAAATATTT
Found at i:55456 original size:29 final size:30
Alignment explanation
Indices: 55412--55480 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
55402 AATTCAAAAA
*
55412 TAAATAATTT-TTATATTCAT-ATTATA-TT
1 TAAATATTTTATTATATT-ATAATTATATTT
55440 TAAATATTTTATTATATTATAATTATATTT
1 TAAATATTTTATTATATTATAATTATATTT
55470 TAAATATTTTA
1 TAAATATTTTA
55481 AATAAATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
28 11 0.30
29 13 0.35
30 13 0.35
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (30 bp):
TAAATATTTTATTATATTATAATTATATTT
Found at i:55469 original size:21 final size:20
Alignment explanation
Indices: 55431--55471 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
55421 TTTATATTCA
55431 TATTATATTTAA--ATATTT
1 TATTATATTTAATTATATTT
55449 TATTATATTATAATTATATTT
1 TATTATATT-TAATTATATTT
55470 TA
1 TA
55472 AATATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
19 3 0.15
21 8 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTATATTTAATTATATTT
Found at i:55487 original size:43 final size:42
Alignment explanation
Indices: 55440--55551 Score: 104
Period size: 42 Copynumber: 2.6 Consensus size: 42
55430 ATATTATATT
*
55440 TAAATATTTTATTATATTATAATTATATTTTAAATATTTTAAA
1 TAAATATTTTATTATATTATAATTATAATTTAAA-ATTTTAAA
* * *
55483 TAAAT-TTTGA-TACATAAATAATTCATAATTTAAAATTTTAAA
1 TAAATATTTTATTATAT-TATAATT-ATAATTTAAAATTTTAAA
* *
55525 -AATATATTTTTATCATATTTTAATTAT
1 TAA-ATA-TTTTATTATATTATAATTAT
55552 TTTATGTGTG
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
41 6 0.11
42 20 0.37
43 16 0.30
44 9 0.17
45 3 0.06
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.52
Consensus pattern (42 bp):
TAAATATTTTATTATATTATAATTATAATTTAAAATTTTAAA
Found at i:55549 original size:44 final size:42
Alignment explanation
Indices: 55440--55551 Score: 111
Period size: 43 Copynumber: 2.6 Consensus size: 42
55430 ATATTATATT
* *
55440 TAAATATTTTATTATATTATAATTATATTTTAAATATTTTAAA
1 TAAAT-TTTTATCATATTATAATTATAATTTAAATATTTTAAA
* *
55483 TAAATTTTGATACATA-AATAATTCATAATTTAAA-ATTTTAAAAA
1 TAAATTTTTAT-CATATTATAATT-ATAATTTAAATATTTT--AAA
* *
55527 TATATTTTTATCATATTTTAATTAT
1 TAAATTTTTATCATATTATAATTAT
55552 TTTATGTGTG
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
42 16 0.29
43 23 0.41
44 17 0.30
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.52
Consensus pattern (42 bp):
TAAATTTTTATCATATTATAATTATAATTTAAATATTTTAAA
Found at i:60222 original size:2 final size:2
Alignment explanation
Indices: 60215--60244 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
60205 TGTAAGGGTA
60215 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60245 CAATAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60434 original size:2 final size:2
Alignment explanation
Indices: 60427--60472 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
60417 TCATAAAATC
60427 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60469 AT AT
1 AT AT
60473 GAATAATTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60656 original size:16 final size:17
Alignment explanation
Indices: 60627--60660 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
60617 ATATATAATT
*
60627 TTTTAAATATATAAAAA
1 TTTTAAATAAATAAAAA
60644 TTTTAAA-AAATAAAAA
1 TTTTAAATAAATAAAAA
60660 T
1 T
60661 ATTTTCGCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTTTAAATAAATAAAAA
Found at i:61185 original size:21 final size:22
Alignment explanation
Indices: 61142--61186 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
61132 ATATATGATT
*
61142 ATATAAATATGATATGTACAAA
1 ATATAAATATGATATGCACAAA
61164 ATATAAA-AT-ATATGACACAAA
1 ATATAAATATGATATG-CACAAA
61185 AT
1 AT
61187 GAATATATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.29
Consensus pattern (22 bp):
ATATAAATATGATATGCACAAA
Found at i:61251 original size:17 final size:17
Alignment explanation
Indices: 61199--61253 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
61189 ATATATGTTT
61199 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
*
61215 T-AAA-TTAT-TAACGTA
1 TAAAATTTATATAA-ATA
61230 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
61248 TAAAAT
1 TAAAAT
61254 ACTTCAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 5 0.16
16 2 0.06
17 9 0.29
18 6 0.19
19 3 0.10
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:61264 original size:22 final size:23
Alignment explanation
Indices: 61238--61295 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 23
61228 TATTAAAATT
* **
61238 TATATAAATATAAAATACTTCAA
1 TATATAAATATAAAATAATAAAA
* *
61261 -ATATGATTATAAAATAATAAAA
1 TATATAAATATAAAATAATAAAA
61283 TATATAAATATAA
1 TATATAAATATAA
61296 TATGAATATA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (23 bp):
TATATAAATATAAAATAATAAAA
Found at i:61524 original size:25 final size:26
Alignment explanation
Indices: 61496--61556 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 26
61486 CTATATCATT
*
61496 ATTTAAATAATATTATAAATTA-TAA
1 ATTTAAATAATAATATAAATTATTAA
** * **
61521 ATTTTTATACTAATATTTATTATTAA
1 ATTTAAATAATAATATAAATTATTAA
61547 ATTTAAATAA
1 ATTTAAATAA
61557 AAAATATTTT
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTTAAATAATAATATAAATTATTAA
Found at i:62297 original size:2 final size:2
Alignment explanation
Indices: 62292--62326 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
62282 ACACACACAC
62292 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
62327 GCAATGAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:62794 original size:12 final size:13
Alignment explanation
Indices: 62766--62807 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
62756 ATATGATATG
*
62766 AATATAATATACTA
1 AATA-AATATAATA
62780 AATAAATATAA-A
1 AATAAATATAATA
62792 AAT-AATATAATA
1 AATAAATATAATA
62804 AATA
1 AATA
62808 TAACATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 7 0.28
12 8 0.32
13 6 0.24
14 4 0.16
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (13 bp):
AATAAATATAATA
Found at i:62848 original size:14 final size:14
Alignment explanation
Indices: 62824--62863 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
62814 TATATTTTTA
*
62824 AATATAATTAATAT
1 AATATATTTAATAT
62838 AATATATTTAATAT
1 AATATATTTAATAT
62852 ATATCATATTTA
1 A-AT-ATATTTA
62864 TATTTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.61
15 2 0.09
16 7 0.30
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (14 bp):
AATATATTTAATAT
Found at i:62891 original size:30 final size:30
Alignment explanation
Indices: 62857--62914 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
62847 AATATATATC
*
62857 ATATTTATATTTAAAATTTTA-AAATAATTA
1 ATATTT-TATTTAAAATTTAATAAATAATTA
*
62887 ATATTTTATTTATAATTTAATAAATAAT
1 ATATTTTATTTAAAATTTAATAAATAAT
62915 ATAAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
ATATTTTATTTAAAATTTAATAAATAATTA
Found at i:64569 original size:2 final size:2
Alignment explanation
Indices: 64562--64590 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
64552 AAGTTTTTAT
64562 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
64591 GACAGTCACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:66310 original size:13 final size:13
Alignment explanation
Indices: 66292--66318 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
66282 CATCATCAAA
66292 GAAGATTTGAGCT
1 GAAGATTTGAGCT
66305 GAAGATTTGAGCT
1 GAAGATTTGAGCT
66318 G
1 G
66319 TGCTACTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.33, T:0.30
Consensus pattern (13 bp):
GAAGATTTGAGCT
Found at i:72329 original size:36 final size:36
Alignment explanation
Indices: 72255--72321 Score: 88
Period size: 35 Copynumber: 1.9 Consensus size: 36
72245 TTATATTATA
72255 AAAATAAATATTTTGTGTTTAAATTAATAAAAAAAT
1 AAAATAAATATTTTGTGTTTAAATTAATAAAAAAAT
*
72291 AAAAT-AATATGTTT-TTTTTAAATT--TAAAAAA
1 AAAATAAATAT-TTTGTGTTTAAATTAATAAAAAA
72322 TCAATAAAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 7 0.24
35 14 0.48
36 8 0.28
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (36 bp):
AAAATAAATATTTTGTGTTTAAATTAATAAAAAAAT
Found at i:81067 original size:17 final size:17
Alignment explanation
Indices: 81038--81071 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
81028 TATTTAGTCA
81038 TAAATTTATTTAATAAG
1 TAAATTTATTTAATAAG
81055 TAAATATTA-TTAATAAG
1 TAAAT-TTATTTAATAAG
81072 AAAAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
TAAATTTATTTAATAAG
Found at i:81264 original size:46 final size:45
Alignment explanation
Indices: 81199--81317 Score: 118
Period size: 46 Copynumber: 2.6 Consensus size: 45
81189 GTTTGTTAAA
* *
81199 AAGTTCATAATTTTCTTCATATAAAAATTACTAA-TTATATGTTAGATG
1 AAGTTTATAA-TTTATTCATATAAAAATTAC-AAGTTATATG-T-GATG
* *
81247 -A-TTTATAACTTTATTCATGTAAAAATTACAAGTTATTTGTGATG
1 AAGTTTATAA-TTTATTCATATAAAAATTACAAGTTATATGTGATG
81291 ACAGTTTATAGATTTATTCATATAAAA
1 A-AGTTTATA-ATTTATTCATATAAAA
81318 GCGACAAATT
Statistics
Matches: 60, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
44 4 0.07
45 3 0.05
46 31 0.52
47 21 0.35
48 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.44
Consensus pattern (45 bp):
AAGTTTATAATTTATTCATATAAAAATTACAAGTTATATGTGATG
Found at i:81590 original size:24 final size:24
Alignment explanation
Indices: 81555--81618 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 24
81545 TATTTATATA
* *
81555 TTTATG-TAATATTTAT-GTTATT
1 TTTATGATTATATTTATAATTATT
*
81577 TTTTTGTATTATATTT-TAATTATT
1 TTTATG-ATTATATTTATAATTATT
*
81601 TTTATGCTTATATTTATA
1 TTTATGATTATATTTATA
81619 CCCATATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
22 5 0.15
23 9 0.27
24 19 0.58
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.66
Consensus pattern (24 bp):
TTTATGATTATATTTATAATTATT
Found at i:82243 original size:14 final size:13
Alignment explanation
Indices: 82218--82263 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
82208 TTATTTACTA
82218 ATAATTTTAAAAT
1 ATAATTTTAAAAT
82231 ATAATTATTAAAAT
1 ATAATT-TTAAAAT
*
82245 ATTAAATTTAATAAT
1 A-TAATTTTAA-AAT
82260 ATAA
1 ATAA
82264 AAAATTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 6 0.21
14 15 0.52
15 8 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATAATTTTAAAAT
Found at i:84668 original size:35 final size:35
Alignment explanation
Indices: 84622--84695 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
84612 GCTTACGTGT
84622 ATTATTTTTTTCTATTACTTTATCATAAATCTTTA
1 ATTATTTTTTTCTATTACTTTATCATAAATCTTTA
84657 ATTATTTTTTTCTATTACTTTATCATAAATCTTTA
1 ATTATTTTTTTCTATTACTTTATCATAAATCTTTA
84692 ATTA
1 ATTA
84696 ATATTCATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (35 bp):
ATTATTTTTTTCTATTACTTTATCATAAATCTTTA
Found at i:84751 original size:2 final size:2
Alignment explanation
Indices: 84744--84768 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
84734 CATAATTCTC
84744 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
84769 AGGTAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:85590 original size:29 final size:29
Alignment explanation
Indices: 85547--85604 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
85537 TATTTGCTAC
* *
85547 AAATTTAAAATTATAGAGATTAAAATATT
1 AAATTTAAAATTATAAAAATTAAAATATT
85576 AAATTTAATAA-TATAAAAATTAAAATATT
1 AAATTTAA-AATTATAAAAATTAAAATATT
85605 TTTTTACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (29 bp):
AAATTTAAAATTATAAAAATTAAAATATT
Found at i:85592 original size:14 final size:14
Alignment explanation
Indices: 85566--85604 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
85556 ATTATAGAGA
85566 TTAAAATATTAAAT
1 TTAAAATATTAAAT
* *
85580 TTAATAATATAAAAA
1 TTAA-AATATTAAAT
85595 TTAAAATATT
1 TTAAAATATT
85605 TTTTTACTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAAAATATTAAAT
Found at i:87304 original size:20 final size:20
Alignment explanation
Indices: 87281--87351 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
87271 TTTTTATATT
*
87281 AATATTTATATTTTAATTTA
1 AATATTAATATTTTAATTTA
** *
87301 AATAAAAATATTTTTATTATA
1 AATATTAATATTTTAATT-TA
* *
87322 ATTATTAAAATTTTAATTTA
1 AATATTAATATTTTAATTTA
87342 AAT-TTAATAT
1 AATATTAATAT
87352 GAACCAAATT
Statistics
Matches: 39, Mismatches: 11, Indels: 3
0.74 0.21 0.06
Matches are distributed among these distances:
19 6 0.15
20 18 0.46
21 15 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AATATTAATATTTTAATTTA
Found at i:87345 original size:21 final size:21
Alignment explanation
Indices: 87288--87345 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
87278 ATTAATATTT
87288 ATATTTTAATTTAAA-TAAAA
1 ATATTTTAATTTAAATTAAAA
* *
87308 ATATTTTTA-TTATAATTATTAA
1 ATATTTTAATTTA-AATTA-AAA
87330 A-ATTTTAATTTAAATT
1 ATATTTTAATTTAAATT
87346 TAATATGAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 3 0.10
20 10 0.32
21 12 0.39
22 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATTTTAATTTAAATTAAAA
Found at i:89003 original size:102 final size:104
Alignment explanation
Indices: 88810--89004 Score: 236
Period size: 107 Copynumber: 1.9 Consensus size: 104
88800 TTGATCCTAT
* *
88810 ATTTTATTGGTCGACAAGAAAGGATCTTCAGTGAATCTTTGAATTGTTTTTTCAACCGATTTCCC
1 ATTTAATTGGTCGACAAGAAAGGATCTTCAATGAATCTTTGAATTG---TTTCAACCGATTTCCC
88875 TTTTTCCACAGTAAACGCAAAATTGTCTACTTTGGCTTATCG
63 TTTTTCCACAGTAAACGCAAAATTGTCTACTTTGGCTTATCG
* * * * *
88917 ATTTAATTGGTCTAC-AGCAAGGATCTTTCAATGAGTCTTTGAATTG-TTCAACTG-TTTTCCTT
1 ATTTAATTGGTCGACAAGAAAGGATC-TTCAATGAATCTTTGAATTGTTTCAACCGATTTCCCTT
* *
88979 TTTTCACAGTGAAA-GCAAATTTGTCT
65 TTTCCACAGT-AAACGCAAAATTGTCT
89005 GATTTTGCCT
Statistics
Matches: 77, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
102 27 0.35
103 10 0.13
106 9 0.12
107 31 0.40
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (104 bp):
ATTTAATTGGTCGACAAGAAAGGATCTTCAATGAATCTTTGAATTGTTTCAACCGATTTCCCTTT
TTCCACAGTAAACGCAAAATTGTCTACTTTGGCTTATCG
Found at i:89018 original size:102 final size:104
Alignment explanation
Indices: 88810--89018 Score: 230
Period size: 102 Copynumber: 2.0 Consensus size: 104
88800 TTGATCCTAT
* *
88810 ATTTTATTGGTCGACAAGAAAGGATCTTCAGTGAATCTTTGAATTGTTTTTTCAACCGATTTCCC
1 ATTTAATTGGTCGACAAGAAAGGATCTTCAATGAATCTTTGAATTG---TTTCAACCGATTTCCC
*
88875 TTTTTCCACAGTAAACGCAAAATTGTCTACTTTGGCTTATCG
63 TTTTTCCACAGTAAACGCAAAATTGTCTACTTTGGCCTATCG
* * * * *
88917 ATTTAATTGGTCTAC-AGCAAGGATCTTTCAATGAGTCTTTGAATTG-TTCAACTG-TTTTCCTT
1 ATTTAATTGGTCGACAAGAAAGGATC-TTCAATGAATCTTTGAATTGTTTCAACCGATTTCCCTT
* * *
88979 TTTTCACAGTGAAA-GCAAATTTGTCTGA-TTTTGCCTATCG
65 TTTCCACAGT-AAACGCAAAATTGTCT-ACTTTGGCCTATCG
89019 TTTCACCTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
102 37 0.42
103 11 0.12
106 9 0.10
107 31 0.35
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (104 bp):
ATTTAATTGGTCGACAAGAAAGGATCTTCAATGAATCTTTGAATTGTTTCAACCGATTTCCCTTT
TTCCACAGTAAACGCAAAATTGTCTACTTTGGCCTATCG
Found at i:92514 original size:20 final size:21
Alignment explanation
Indices: 92481--92531 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
92471 GGATTATCTC
*
92481 ATTTAAT-ATTTTTATTAAAT
1 ATTTAATAATATTTATTAAAT
**
92501 ATTT-ATAATATTTATTATTT
1 ATTTAATAATATTTATTAAAT
92521 ATTTAATAATA
1 ATTTAATAATA
92532 AAATTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 2 0.08
20 18 0.69
21 6 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTAATAATATTTATTAAAT
Found at i:92537 original size:20 final size:21
Alignment explanation
Indices: 92514--92562 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
92504 TATAATATTT
92514 ATTATTTATTTAATA-ATAAA
1 ATTATTTATTTAATATATAAA
*
92534 ATTATTTATTTAATATTTAAA
1 ATTATTTATTTAATATATAAA
*
92555 TTTATTTA
1 ATTATTTA
92563 AAAAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTATTTATTTAATATATAAA
Found at i:93029 original size:16 final size:16
Alignment explanation
Indices: 93010--93050 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
93000 TAATATTAAA
*
93010 ATTATATTTAATTATT
1 ATTATATTAAATTATT
*
93026 ATTAAATTAAATTATT
1 ATTATATTAAATTATT
93042 ATTATATTA
1 ATTATATTA
93051 TTTTAATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTATATTAAATTATT
Found at i:95514 original size:13 final size:13
Alignment explanation
Indices: 95473--95506 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
95463 GATCGTTATT
95473 TTATT-ATAATAA
1 TTATTAATAATAA
*
95485 ATATTAATAATAA
1 TTATTAATAATAA
95498 TTATTAATA
1 TTATTAATA
95507 TTTATTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TTATTAATAATAA
Found at i:96125 original size:2 final size:2
Alignment explanation
Indices: 96118--96173 Score: 51
Period size: 2 Copynumber: 26.5 Consensus size: 2
96108 TATTGAATTT
*
96118 TA TA TA TA TCA AA TA TCA TA TA TA TA TA TA TA T- TA TA TA TA TCA
1 TA TA TA TA T-A TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA T-A
*
96162 AA TA TCA TA TA T
1 TA TA T-A TA TA T
96174 CAATGAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
1 1 0.02
2 38 0.84
3 6 0.13
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:96159 original size:33 final size:32
Alignment explanation
Indices: 96075--96173 Score: 121
Period size: 33 Copynumber: 3.0 Consensus size: 32
96065 AAAATATCCC
*
96075 TATATATATTATATATATCAAATAT-AGGGATAT
1 TATATATATTATATATATCAAATATCA--TATAT
*
96108 TAT-TGAATTTTATATATATCAAATATCATATAT
1 TATAT--ATATTATATATATCAAATATCATATAT
96141 ATATATATATTATATATATCAAATATCATATAT
1 -TATATATATTATATATATCAAATATCATATAT
96174 CAATGAAATT
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
32 1 0.02
33 33 0.57
34 22 0.38
35 2 0.03
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (32 bp):
TATATATATTATATATATCAAATATCATATAT
Found at i:96166 original size:9 final size:9
Alignment explanation
Indices: 96119--96173 Score: 66
Period size: 9 Copynumber: 6.7 Consensus size: 9
96109 ATTGAATTTT
96119 ATATATATC
1 ATATATATC
96128 A-A-ATATC
1 ATATATATC
96135 ATATATAT-
1 ATATATATC
*
96143 ATATATATT
1 ATATATATC
96152 ATATATATC
1 ATATATATC
96161 A-A-ATATC
1 ATATATATC
96168 ATATAT
1 ATATAT
96174 CAATGAAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
7 12 0.30
8 12 0.30
9 16 0.40
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (9 bp):
ATATATATC
Found at i:96664 original size:32 final size:33
Alignment explanation
Indices: 96623--96701 Score: 108
Period size: 32 Copynumber: 2.4 Consensus size: 33
96613 TTAAATATGA
*
96623 ATATGATATAAAATTATAAATAT-TTTAAAATT
1 ATATAATATAAAATTATAAATATATTTAAAATT
* *
96655 ATATAATAT-AAATTATTAATATATTTAAATTT
1 ATATAATATAAAATTATAAATATATTTAAAATT
96687 ATATAAATATAAAAT
1 ATAT-AATATAAAAT
96702 ATGATACGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 12 0.29
32 20 0.49
33 5 0.12
34 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (33 bp):
ATATAATATAAAATTATAAATATATTTAAAATT
Found at i:96701 original size:17 final size:16
Alignment explanation
Indices: 96628--96727 Score: 61
Period size: 15 Copynumber: 6.3 Consensus size: 16
96618 TATGAATATG
96628 ATATAAAATTATA-AA
1 ATATAAAATTATATAA
*
96643 TATTTTAAAATTATAT-A
1 -A-TATAAAATTATATAA
96660 ATAT-AAATTAT-TAA
1 ATATAAAATTATATAA
*
96674 TATATTTAAATTTATATAA
1 -ATA--TAAAATTATATAA
96693 ATATAAAA-TATGAT-A
1 ATATAAAATTAT-ATAA
**
96708 CGATAAAA-TATATAA
1 ATATAAAATTATATAA
96723 ATATA
1 ATATA
96728 TGATGATTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 21
0.69 0.08 0.22
Matches are distributed among these distances:
13 1 0.02
14 10 0.15
15 22 0.33
16 8 0.12
17 13 0.20
18 9 0.14
19 3 0.05
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (16 bp):
ATATAAAATTATATAA
Found at i:96739 original size:23 final size:23
Alignment explanation
Indices: 96693--96741 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
96683 ATTTATATAA
96693 ATATAAAATATGATACGATAAAAT
1 ATATAAAATATGATA-GATAAAAT
*
96717 ATATAAATATATGAT-GATTAAAT
1 ATATAAA-ATATGATAGATAAAAT
96740 AT
1 AT
96742 GAATTATTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 9 0.39
24 7 0.30
25 7 0.30
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (23 bp):
ATATAAAATATGATAGATAAAAT
Found at i:99042 original size:21 final size:21
Alignment explanation
Indices: 99018--99058 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
99008 TATTAAAATA
99018 ATATTTTAT-ATTAATATTTAT
1 ATATTTTATAATTAA-ATTTAT
99039 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
99059 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:100026 original size:11 final size:11
Alignment explanation
Indices: 100012--100047 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
100002 TTTATAATTT
*
100012 TATTCTTTTTA
1 TATTATTTTTA
*
100023 TATTATATTTA
1 TATTATTTTTA
100034 TATTATTTTTA
1 TATTATTTTTA
100045 TAT
1 TAT
100048 AAAATAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (11 bp):
TATTATTTTTA
Found at i:100028 original size:22 final size:22
Alignment explanation
Indices: 100003--100047 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
99993 AAACATTTTT
*
100003 TTATAATTT-TATTCTTTTTATA
1 TTAT-ATTTATATTATTTTTATA
100025 TTATATTTATATTATTTTTATA
1 TTATATTTATATTATTTTTATA
100047 T
1 T
100048 AAAATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (22 bp):
TTATATTTATATTATTTTTATA
Found at i:100138 original size:33 final size:31
Alignment explanation
Indices: 100040--100142 Score: 93
Period size: 33 Copynumber: 3.1 Consensus size: 31
100030 TTTATATTAT
*
100040 TTTTATATAAAA--TAAAAATTTAAAATATTATA
1 TTTTATATAAAATTTAATAATTT--AATATT-TA
* *
100072 TATTTATATAAAATTTTGATAAATTAATGATTTA
1 T-TTTATATAAAA-TTTAATAATTTAAT-ATTTA
100106 TTTTATATAAAATTTAATATATTTAGATATTTA
1 TTTTATATAAAATTTAATA-ATTTA-ATATTTA
100139 TTTT
1 TTTT
100143 GTATTTATAT
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
32 7 0.12
33 35 0.59
34 8 0.14
35 3 0.05
36 6 0.10
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (31 bp):
TTTTATATAAAATTTAATAATTTAATATTTA
Found at i:100139 original size:28 final size:28
Alignment explanation
Indices: 100054--100139 Score: 75
Period size: 32 Copynumber: 2.9 Consensus size: 28
100044 ATATAAAATA
* *
100054 AAAATTTAAAATA-TTATATATTTATAT
1 AAAATTTAATATATTTAGATATTTATAT
* * *
100081 AAAATTTTGATAAATTAATGATTTATTTTATAT
1 AAAA-TTTAATATATTTA-GA--TA-TTTATAT
100114 AAAATTTAATATATTTAGATATTTAT
1 AAAATTTAATATATTTAGATATTTAT
100140 TTTGTATTTA
Statistics
Matches: 45, Mismatches: 8, Indels: 11
0.70 0.12 0.17
Matches are distributed among these distances:
27 4 0.09
28 11 0.24
29 4 0.09
30 1 0.02
31 2 0.04
32 12 0.27
33 11 0.24
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (28 bp):
AAAATTTAATATATTTAGATATTTATAT
Found at i:100917 original size:23 final size:22
Alignment explanation
Indices: 100891--100935 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
100881 ATAATAGTTA
100891 CTTAACAATTTTGATAATTATAT
1 CTTAACAATTTTGAT-ATTATAT
** *
100914 CTTAATTATTTTTATATTATAT
1 CTTAACAATTTTGATATTATAT
100936 TCAAAAGCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (22 bp):
CTTAACAATTTTGATATTATAT
Found at i:101186 original size:2 final size:2
Alignment explanation
Indices: 101181--101234 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
101171 TGTGTTTCTG
101181 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
101223 TA TA TA T- TA TA T
1 TA TA TA TA TA TA T
101235 TTGTATGGAT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:101545 original size:12 final size:12
Alignment explanation
Indices: 101513--101547 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
101503 TTATTTTTAT
101513 TAAATATTTAAA
1 TAAATATTTAAA
*
101525 AAAATTATTTAAA
1 TAAA-TATTTAAA
101538 TAAATATTTA
1 TAAATATTTA
101548 TATTATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TAAATATTTAAA
Found at i:102116 original size:30 final size:30
Alignment explanation
Indices: 102080--102143 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
102070 AGATTGCAAA
102080 ATCTGAATTCAATCACCAACATCAACTGAT
1 ATCTGAATTCAATCACCAACATCAACTGAT
102110 ATCTGAATTCAATCACCAACATCAACTGAT
1 ATCTGAATTCAATCACCAACATCAACTGAT
102140 ATCT
1 ATCT
102144 ATCTCAATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.39, C:0.27, G:0.06, T:0.28
Consensus pattern (30 bp):
ATCTGAATTCAATCACCAACATCAACTGAT
Found at i:102861 original size:29 final size:29
Alignment explanation
Indices: 102829--102903 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
102819 ACTAGTAATT
*
102829 TTATTTTATTATTTAAAAATAT-TAAAATA
1 TTATTTTATTAATTAAAAATATATAAAA-A
**
102858 TTATTTTA-TAATTAAATTTATATAAAAA
1 TTATTTTATTAATTAAAAATATATAAAAA
*
102886 TTATTTTTATTAAATAAA
1 TTA-TTTTATTAATTAAA
102904 TAATTATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
28 14 0.36
29 18 0.46
30 7 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TTATTTTATTAATTAAAAATATATAAAAA
Found at i:102889 original size:28 final size:28
Alignment explanation
Indices: 102829--102901 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
102819 ACTAGTAATT
* *
102829 TTATTTTATTATTTAAAAATATTAAAATA
1 TTATTTTA-TAATTAAATATATTAAAATA
*
102858 TTATTTTATAATTAAATTTATATAAAA-A
1 TTATTTTATAATTAAATATAT-TAAAATA
102886 TTATTTT-T-ATTAAATA
1 TTATTTTATAATTAAATA
102902 AATAATTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
26 7 0.18
27 1 0.03
28 18 0.46
29 13 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TTATTTTATAATTAAATATATTAAAATA
Found at i:102918 original size:21 final size:20
Alignment explanation
Indices: 102869--102931 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
102859 TATTTTATAA
*
102869 TTAAATTTATATAAAAATTAT
1 TTAAA-TTAAATAAAAATTAT
**
102890 TTTTATTAAATAAATAATTAT
1 TTAAATTAAATAAA-AATTAT
102911 TTAAATT--ATAAAAATTTAT
1 TTAAATTAAATAAAAA-TTAT
102930 TT
1 TT
102932 TCAAACTCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 2 0.06
19 11 0.31
20 8 0.23
21 14 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAAATTAAATAAAAATTAT
Found at i:103933 original size:13 final size:12
Alignment explanation
Indices: 103884--103929 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
103874 ACCTTCACTG
103884 TTTCAAATTGAA
1 TTTCAAATTGAA
*
103896 TTTCAACATTTACTA
1 TTTCAA-ATTGA--A
103911 TTTCAAATTGAA
1 TTTCAAATTGAA
103923 TTTCAAA
1 TTTCAAA
103930 ATTGGCGGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 14 0.48
13 4 0.14
14 4 0.14
15 7 0.24
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.43
Consensus pattern (12 bp):
TTTCAAATTGAA
Found at i:108691 original size:12 final size:12
Alignment explanation
Indices: 108674--108698 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
108664 AAATTGACGA
108674 CACAGTTGGCAG
1 CACAGTTGGCAG
108686 CACAGTTGGCAG
1 CACAGTTGGCAG
108698 C
1 C
108699 CTTGTTTTCA
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:0.24, C:0.28, G:0.32, T:0.16
Consensus pattern (12 bp):
CACAGTTGGCAG
Found at i:110090 original size:13 final size:13
Alignment explanation
Indices: 110072--110126 Score: 60
Period size: 13 Copynumber: 4.3 Consensus size: 13
110062 TTTAAATTTT
110072 TTATTAATAATAA
1 TTATTAATAATAA
* *
110085 TTATTATTAATAT
1 TTATTAATAATAA
110098 TTATT-ATAATAAA
1 TTATTAATAAT-AA
*
110111 TTA-TAATAATAT
1 TTATTAATAATAA
110123 TTAT
1 TTAT
110127 GATCATAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 9 0.26
13 25 0.74
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTATTAATAATAA
Found at i:110120 original size:25 final size:26
Alignment explanation
Indices: 110071--110135 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 26
110061 TTTTAAATTT
*
110071 TTTATTAATAAT-AATTATTATTAATA
1 TTTATT-ATAATAAATTATTAATAATA
110097 TTTATTATAATAAATTA-TAATAATA
1 TTTATTATAATAAATTATTAATAATA
* *
110122 TTTATGATCATAAA
1 TTTATTATAATAAA
110136 AATCATTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
25 24 0.69
26 11 0.31
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (26 bp):
TTTATTATAATAAATTATTAATAATA
Found at i:110842 original size:40 final size:40
Alignment explanation
Indices: 110781--110856 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
110771 ATTTTAAGTT
* * * *
110781 TATATAATATGAATTATTAAAATATCTAAATTTGTATACA
1 TATAAAATATGAATGATTAAAATATATAAATATGTATACA
110821 TATAAAATATGATATGA-TAAAATATATAAATATGTA
1 TATAAAATATGA-ATGATTAAAATATATAAATATGTA
110857 ACGATACAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 28 0.90
41 3 0.10
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (40 bp):
TATAAAATATGAATGATTAAAATATATAAATATGTATACA
Found at i:111259 original size:15 final size:16
Alignment explanation
Indices: 111233--111262 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
111223 TTAAATTTGT
111233 ATATATATAAAATATG
1 ATATATATAAAATATG
111249 ATATA-ATAAAATAT
1 ATATATATAAAATAT
111263 ATAAATACGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
ATATATATAAAATATG
Found at i:111326 original size:417 final size:417
Alignment explanation
Indices: 110552--111382 Score: 1482
Period size: 417 Copynumber: 2.0 Consensus size: 417
110542 GTTATATAGA
*
110552 CAAATAATTAATAAAATTTAATTTTAATTTAAAATTATTCAAAATATGAAAGGATTTTAATATTG
1 CAAATAATTAATAAAATTTAATTTTAATTTAAAATTATTCAAAATATAAAAGGATTTTAATATTG
*
110617 TAATAATGAAAGTTTAAGATTATGGGTGAATTGAATTACTTCCTCAAGCTTGAACCACCTTGAAC
66 TAATAATAAAAGTTTAAGATTATGGGTGAATTGAATTACTTCCTCAAGCTTGAACCACCTTGAAC
* *
110682 TTATCTATGAAATCTCTAACTTAAATAGGTCTTATACATGAAAAATAAACTTACAATATTAAACA
131 TTATCTACGAAATCTCTAACTTAAATAAGTCTTATACATGAAAAATAAACTTACAATATTAAACA
*
110747 CGAATATGATAAAAATACATAAATATTTTAAGTTTATATAATATGAATTATTAAAATATCTAAAT
196 CGAATATGATAAAAATACATAAATATTTTAAATTTATATAATATGAATTATTAAAATATCTAAAT
* * *
110812 TTGTATACATATAAAATATGATATGATAAAATATATAAATATGTAACGATACAAATACATAAATT
261 TTGTATACATATAAAATATGATATAATAAAATATATAAATACGTAACGACACAAATACATAAATT
* *
110877 ATCAAGTCTAATCATAAACTACAAACTTGAGTTGGGTGTTGTTTTGCTTTCAAGATATGATCGTT
326 ATCAAATCTAATCATAAACTACAAACTTGAGTTAGGTGTTGTTTTGCTTTCAAGATATGATCGTT
*
110942 GGAAAGCAAAGGTCATTCAACGTTGGT
391 GGAAAGCAAAGGCCATTCAACGTTGGT
110969 CAAATAATTAATAAAATTTAATTTTAATTTAAAATTATTCAAAATATAAAAGGATTTTAATATTG
1 CAAATAATTAATAAAATTTAATTTTAATTTAAAATTATTCAAAATATAAAAGGATTTTAATATTG
*
111034 TAATAATAAAAGTTTAAGATTATGGGTGAATTGTATTACTTCCTCAAGCTTGAACCACCTTGAAC
66 TAATAATAAAAGTTTAAGATTATGGGTGAATTGAATTACTTCCTCAAGCTTGAACCACCTTGAAC
*
111099 TTATCTACGAAATCTCTAGCTTAAATAAGTCTTATACATGAAAAATAAACTTACAATATTAAACA
131 TTATCTACGAAATCTCTAACTTAAATAAGTCTTATACATGAAAAATAAACTTACAATATTAAACA
*
111164 CGAATATGATAAAAATACATAAATATTTTAAATTTATATAATATGAATTATTAAAATATTTAAAT
196 CGAATATGATAAAAATACATAAATATTTTAAATTTATATAATATGAATTATTAAAATATCTAAAT
* * * *
111229 TTGTATATATATAAAATATGATATAATAAAATATATAAATACGTGACGACATAAATATATAAATT
261 TTGTATACATATAAAATATGATATAATAAAATATATAAATACGTAACGACACAAATACATAAATT
* *
111294 ATCAAATCTAATCATGAACTACAAACTTGAGTTAGGTGTTGTTTTGCTTTCAAGATATGTTCGTT
326 ATCAAATCTAATCATAAACTACAAACTTGAGTTAGGTGTTGTTTTGCTTTCAAGATATGATCGTT
111359 GGAAAGCAAAGGCCATTCAACGTT
391 GGAAAGCAAAGGCCATTCAACGTT
111383 AGCCCTCCAT
Statistics
Matches: 394, Mismatches: 20, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
417 394 1.00
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.36
Consensus pattern (417 bp):
CAAATAATTAATAAAATTTAATTTTAATTTAAAATTATTCAAAATATAAAAGGATTTTAATATTG
TAATAATAAAAGTTTAAGATTATGGGTGAATTGAATTACTTCCTCAAGCTTGAACCACCTTGAAC
TTATCTACGAAATCTCTAACTTAAATAAGTCTTATACATGAAAAATAAACTTACAATATTAAACA
CGAATATGATAAAAATACATAAATATTTTAAATTTATATAATATGAATTATTAAAATATCTAAAT
TTGTATACATATAAAATATGATATAATAAAATATATAAATACGTAACGACACAAATACATAAATT
ATCAAATCTAATCATAAACTACAAACTTGAGTTAGGTGTTGTTTTGCTTTCAAGATATGATCGTT
GGAAAGCAAAGGCCATTCAACGTTGGT
Found at i:112893 original size:18 final size:18
Alignment explanation
Indices: 112870--112907 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
112860 TAATCGATTC
112870 TTAATTGAATC-GATTTGA
1 TTAATT-AATCTGATTTGA
112888 TTAATTAATCTGATTTGA
1 TTAATTAATCTGATTTGA
112906 TT
1 TT
112908 TTTTATTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (18 bp):
TTAATTAATCTGATTTGA
Found at i:113594 original size:13 final size:13
Alignment explanation
Indices: 113576--113618 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
113566 GCAAAAATAT
113576 TAAATTTAAAAAA
1 TAAATTTAAAAAA
113589 TAAATTTGAAAAAA
1 TAAATTT-AAAAAA
*
113603 AAACCATTTAAAAAA
1 TAA--ATTTAAAAAA
113618 T
1 T
113619 GAGTTTAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 7 0.28
14 8 0.32
15 6 0.24
16 4 0.16
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (13 bp):
TAAATTTAAAAAA
Found at i:113706 original size:22 final size:21
Alignment explanation
Indices: 113657--113711 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
113647 GCGATATTTT
113657 TTTAA-TTATA-TAATATATA
1 TTTAATTTATATTAATATATA
*
113676 -TTATTTTTATATTAATATATTA
1 TTTA-ATTTATATTAATATA-TA
113698 TTTAATTTATATTA
1 TTTAATTTATATTA
113712 TGTTAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 3 0.10
20 5 0.17
21 7 0.24
22 11 0.38
23 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTAATTTATATTAATATATA
Found at i:114575 original size:22 final size:22
Alignment explanation
Indices: 114550--114609 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 22
114540 TATTTTATAT
114550 ATTTTATAATTAAATTTAAATA
1 ATTTTATAATTAAATTTAAATA
*
114572 ATTTT-TTATTAAA--TAAATA
1 ATTTTATAATTAAATTTAAATA
114591 ATAATTTA-AATT-AATTTAA
1 AT--TTTATAATTAAATTTAA
114610 TTTAATTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
19 8 0.26
20 2 0.06
21 13 0.42
22 8 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTTATAATTAAATTTAAATA
Found at i:114607 original size:10 final size:10
Alignment explanation
Indices: 114592--114622 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
114582 AAATAAATAA
114592 TAATTTAAAT
1 TAATTTAAAT
*
114602 TAATTTAATT
1 TAATTTAAAT
114612 TAATTTAAAT
1 TAATTTAAAT
114622 T
1 T
114623 CAAAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
TAATTTAAAT
Found at i:114986 original size:45 final size:47
Alignment explanation
Indices: 114937--115046 Score: 120
Period size: 47 Copynumber: 2.4 Consensus size: 47
114927 TTAAATTAAA
* *
114937 TTAATTTT-ATT-TAAATTATTATTTAATAATTAA-A-AAAATTATTTT
1 TTAATTTTAATTATAAA--ATTATATAAAAATTAATATAAAATTATTTT
114982 TTAATTTTAATTATAAAATTATATAAAAATTAATATAAAATTATTTT
1 TTAATTTTAATTATAAAATTATATAAAAATTAATATAAAATTATTTT
** *
115029 AAAATTTTTATTAATAAA
1 TTAATTTTAATT-ATAAA
115047 TAAATAATAA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
45 22 0.40
46 4 0.07
47 24 0.44
48 5 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (47 bp):
TTAATTTTAATTATAAAATTATATAAAAATTAATATAAAATTATTTT
Found at i:115012 original size:11 final size:12
Alignment explanation
Indices: 114993--115034 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
114983 TAATTTTAAT
114993 TATAAAATTATA
1 TATAAAATTATA
115005 TA-AAAATTA-A
1 TATAAAATTATA
115015 TATAAAATTAT-
1 TATAAAATTATA
*
115026 TTTAAAATT
1 TATAAAATT
115035 TTTATTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 3 0.11
11 22 0.81
12 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TATAAAATTATA
Found at i:115021 original size:22 final size:23
Alignment explanation
Indices: 114988--115034 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
114978 TTTTTTAATT
114988 TTAATTATAAAATTATATAAAAA
1 TTAATTATAAAATTATATAAAAA
* *
115011 TTAA-TATAAAATTATTTTAAAA
1 TTAATTATAAAATTATATAAAAA
115033 TT
1 TT
115035 TTTATTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTAATTATAAAATTATATAAAAA
Found at i:115059 original size:47 final size:46
Alignment explanation
Indices: 114960--115059 Score: 109
Period size: 47 Copynumber: 2.2 Consensus size: 46
114950 AATTATTATT
** *
114960 TAAT-AATTAAAAAAATTATTTTTTAATTTTAATTATAAAATTATA
1 TAATAAATTAAAAAAATTATTTTAAAATTTTAATTATAAAATTAAA
*
115005 TAA-AAATTAATATAAAATTATTTTAAAATTTTTATTA-ATAAA-TAAA
1 TAATAAATTAA-A-AAAATTATTTTAAAATTTTAATTATA-AAATTAAA
115051 TAATAAATT
1 TAATAAATT
115060 TAAATTTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
45 9 0.20
46 8 0.17
47 29 0.63
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (46 bp):
TAATAAATTAAAAAAATTATTTTAAAATTTTAATTATAAAATTAAA
Found at i:115930 original size:22 final size:21
Alignment explanation
Indices: 115881--115944 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
115871 TTAAGTTCGA
* **
115881 ATTATTTTTTATATTATTAAAT
1 ATTATTTTTTA-ATTAATATTT
115903 ATTATTTTTTAATTAATATTT
1 ATTATTTTTTAATTAATATTT
*
115924 ATATATTTTATAATTAA-ATTT
1 AT-TATTTTTTAATTAATATTT
115945 TAAATTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 13 0.35
22 24 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTATTTTTTAATTAATATTT
Found at i:116086 original size:17 final size:19
Alignment explanation
Indices: 116064--116105 Score: 70
Period size: 17 Copynumber: 2.3 Consensus size: 19
116054 TATGATGGAT
116064 ATATATTCTT-AAA-AAAA
1 ATATATTCTTAAAATAAAA
116081 ATATATTCTTAAAATAAAA
1 ATATATTCTTAAAATAAAA
116100 ATATAT
1 ATATAT
116106 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 10 0.43
18 3 0.13
19 10 0.43
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
ATATATTCTTAAAATAAAA
Found at i:116352 original size:16 final size:17
Alignment explanation
Indices: 116317--116358 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
116307 CTATAATTTT
*
116317 TTATAATTATATTTAAA
1 TTATATTTATATTTAAA
* *
116334 TTATTTTTAT-TTTATA
1 TTATATTTATATTTAAA
116350 TTATATTTA
1 TTATATTTA
116359 AAATTATGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATATTTATATTTAAA
Found at i:118254 original size:29 final size:26
Alignment explanation
Indices: 118200--118271 Score: 67
Period size: 28 Copynumber: 2.7 Consensus size: 26
118190 ATCTGTAAGT
* **
118200 TTATTTTATTATTTAAAAATATTAAAATA
1 TTATTTTA-TAATTAAATTTATT-AAA-A
118229 TTATTTTATAATTAAATTTATATAAAA
1 TTATTTTATAATTAAATTTAT-TAAAA
118256 TTA-TTT-TAATTAAATT
1 TTATTTTATAATTAAATT
118272 AATAATAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
25 10 0.26
26 3 0.08
27 4 0.10
28 13 0.33
29 9 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTATTTTATAATTAAATTTATTAAAA
Found at i:120616 original size:15 final size:16
Alignment explanation
Indices: 120589--120622 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
120579 AATTTTAAAA
*
120589 ATTTTATATATTTTTT
1 ATTTTATATATTTATT
120605 ATTTTA-ATATTTATT
1 ATTTTATATATTTATT
120620 ATT
1 ATT
120623 AAATTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTATATATTTATT
Done.