Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold412
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: 4645160
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 32
Found at i:271649 original size:2 final size:2
Alignment explanation
Indices: 271642--271669 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
271632 CTATGTTATC
271642 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
271670 TTTAAAATAT
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):
AT
Found at i:275452 original size:2 final size:2
Alignment explanation
Indices: 275445--275479 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
275435 GCTATATGTG
275445 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
275480 TTCTGAACAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:295188 original size:4 final size:4
Alignment explanation
Indices: 295179--295203 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
295169 TTTAAAAATA
295179 AGAT AGAT AGAT AGAT AGAT AGAT A
1 AGAT AGAT AGAT AGAT AGAT AGAT A
295204 AATATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
AGAT
Found at i:296765 original size:6 final size:6
Alignment explanation
Indices: 296757--296789 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
296747 TCCACCCCTG
*
296757 AAACTG AAACTA AAACTA AAACTA AAACTA AAA
1 AAACTA AAACTA AAACTA AAACTA AAACTA AAA
296790 TGAAAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.67, C:0.15, G:0.03, T:0.15
Consensus pattern (6 bp):
AAACTA
Found at i:297201 original size:14 final size:14
Alignment explanation
Indices: 297178--297220 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
297168 TATAATTTTC
*
297178 ATTTAGATAATATA
1 ATTTATATAATATA
*
297192 ATTTATATAATATT
1 ATTTATATAATATA
*
297206 A-TTATATAAAATA
1 ATTTATATAATATA
297219 AT
1 AT
297221 ATATTATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (14 bp):
ATTTATATAATATA
Found at i:297212 original size:22 final size:21
Alignment explanation
Indices: 297187--297240 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
297177 CATTTAGATA
*
297187 ATATAATTTATATAATATTATT
1 ATATAATTAATATAATA-TATT
* *
297209 ATATAAAATAATATATTATATT
1 ATAT-AATTAATATAATATATT
297231 ATATAATTAA
1 ATATAATTAA
297241 AAAGGATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 5 0.19
22 12 0.44
23 10 0.37
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATATAATTAATATAATATATT
Found at i:298484 original size:2 final size:2
Alignment explanation
Indices: 298477--298522 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
298467 CAAAGATTTC
* * * *
298477 TA TA TA TA TA TA TA TA TA TA TA TA TT TC TA TA CA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
298519 TA TA
1 TA TA
298523 ATAGCATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:298593 original size:2 final size:2
Alignment explanation
Indices: 298586--298611 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
298576 TTAGGATGTA
298586 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
298612 GGAAAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:299038 original size:5 final size:5
Alignment explanation
Indices: 299017--299081 Score: 66
Period size: 5 Copynumber: 13.4 Consensus size: 5
299007 AACCCCAGAT
*
299017 AAAAG AAAA- AATA- AAAAG AAAAG AAAAG AAAAG AAAAG CAAAAG CAAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG -AAAAG
*
299067 --AAG AAAGG AAAAG AA
1 AAAAG AAAAG AAAAG AA
299082 TGAAAGCATA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
3 3 0.06
4 6 0.12
5 32 0.62
6 11 0.21
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:301932 original size:9 final size:9
Alignment explanation
Indices: 301909--301937 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
301899 GAATGTCCAA
301909 ATTAAAATT
1 ATTAAAATT
301918 -TTAAAATT
1 ATTAAAATT
301926 ATTAAAATT
1 ATTAAAATT
301935 ATT
1 ATT
301938 TTTTTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
ATTAAAATT
Found at i:307370 original size:2 final size:2
Alignment explanation
Indices: 307354--307393 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
307344 TCAACTTCTT
* *
307354 TA TA TA CA TA CA 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
307394 GGGAGAGATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:307894 original size:2 final size:2
Alignment explanation
Indices: 307887--307912 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
307877 CGAAGGCTGA
307887 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
307913 TTCTGTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:308360 original size:18 final size:18
Alignment explanation
Indices: 308337--308377 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
308327 AATATTTAAT
*
308337 TTTAAATTTTAA-TTCAAA
1 TTTAAA-TTTAATTTAAAA
308355 TTTAAATTTAATTTAAAA
1 TTTAAATTTAATTTAAAA
308373 TTTAA
1 TTTAA
308378 TAAGCTACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAAATTTAATTTAAAA
Found at i:308671 original size:17 final size:17
Alignment explanation
Indices: 308645--308678 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
308635 TACTATTTGA
*
308645 TTATTAAAATTTTATTT
1 TTATTAAAATTTAATTT
*
308662 TTATTTAAATTTAATTT
1 TTATTAAAATTTAATTT
308679 AAAATTATAT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTAAAATTTAATTT
Found at i:308697 original size:22 final size:21
Alignment explanation
Indices: 308662--308720 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
308652 AATTTTATTT
*
308662 TTATTTAAATTTAATTTAAAA
1 TTATATAAATTTAATTTAAAA
308683 TTATATAAATATTAATTTAATATA
1 TTATATAAAT-TTAATTTAA-A-A
*
308707 TTA-AAAAATTTAAT
1 TTATATAAATTTAAT
308721 AAACTACTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 9 0.27
22 14 0.42
23 6 0.18
24 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTATATAAATTTAATTTAAAA
Found at i:309056 original size:17 final size:17
Alignment explanation
Indices: 309034--309072 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
309024 ATTTAATTTA
* *
309034 ATTAAAATTATATAAAT
1 ATTAAAATAAAATAAAT
309051 ATTAAAATAAAATAAAT
1 ATTAAAATAAAATAAAT
*
309068 TTTAA
1 ATTAA
309073 TTTTAATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTAAAATAAAATAAAT
Found at i:310390 original size:58 final size:58
Alignment explanation
Indices: 310320--310438 Score: 211
Period size: 58 Copynumber: 2.1 Consensus size: 58
310310 GTTTAAGTTC
*
310320 CAACATACTCCCACATATTATAACATAACTTGTTTTTTATGCAAATGGAGCTCAAAGA
1 CAACATAATCCCACATATTATAACATAACTTGTTTTTTATGCAAATGGAGCTCAAAGA
* *
310378 CAACATAATCCCACATATTATAGCATAACTTGTTTTTTATGCAAATGGAGTTCAAAGA
1 CAACATAATCCCACATATTATAACATAACTTGTTTTTTATGCAAATGGAGCTCAAAGA
310436 CAA
1 CAA
310439 ATCAGAACAC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (58 bp):
CAACATAATCCCACATATTATAACATAACTTGTTTTTTATGCAAATGGAGCTCAAAGA
Found at i:319015 original size:73 final size:73
Alignment explanation
Indices: 318918--319058 Score: 228
Period size: 73 Copynumber: 1.9 Consensus size: 73
318908 TTGATTTCGA
* * *
318918 CTTGTTAGTACTAAGAAATTTCCTTCCGCCAACCCTTTTATCTTAGTTGTTAAACTCCAAGGTTT
1 CTTGTTAGCACTAAGAAATTTCCTTCCGCCAACCCTTCTATCATAGTTGTTAAACTCCAAGGTTT
318983 AATGCCAT
66 AATGCCAT
* * *
318991 CTTGTTAGCACTACGAATTTTCCTTCCGCCAATCCTTCTATCATAGTTGTTAAACTCCAAGGTTT
1 CTTGTTAGCACTAAGAAATTTCCTTCCGCCAACCCTTCTATCATAGTTGTTAAACTCCAAGGTTT
319056 AAT
66 AAT
319059 ACCCCAACAA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 62 1.00
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (73 bp):
CTTGTTAGCACTAAGAAATTTCCTTCCGCCAACCCTTCTATCATAGTTGTTAAACTCCAAGGTTT
AATGCCAT
Found at i:328469 original size:67 final size:67
Alignment explanation
Indices: 328361--328492 Score: 264
Period size: 67 Copynumber: 2.0 Consensus size: 67
328351 CTATGAAGTA
328361 CCAGTAGGAGCTGTTCTTTTTTCCAGAACCAGCTTTGTCTGAAAAATCATAAATAATAGTAGATA
1 CCAGTAGGAGCTGTTCTTTTTTCCAGAACCAGCTTTGTCTGAAAAATCATAAATAATAGTAGATA
328426 GT
66 GT
328428 CCAGTAGGAGCTGTTCTTTTTTCCAGAACCAGCTTTGTCTGAAAAATCATAAATAATAGTAGATA
1 CCAGTAGGAGCTGTTCTTTTTTCCAGAACCAGCTTTGTCTGAAAAATCATAAATAATAGTAGATA
328493 AAACATGACA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (67 bp):
CCAGTAGGAGCTGTTCTTTTTTCCAGAACCAGCTTTGTCTGAAAAATCATAAATAATAGTAGATA
GT
Found at i:335079 original size:2 final size:2
Alignment explanation
Indices: 335072--335110 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
335062 TTATATGCTT
*
335072 TA TA TA TA TA TA TA TA TA TA TA TA TGC TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
335111 AAAGTTAGCG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 33 0.97
3 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:336348 original size:24 final size:24
Alignment explanation
Indices: 336310--336358 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
336300 TAATAAAAAT
336310 AAAATAATATAATTAATTA-ATTA
1 AAAATAATATAATTAATTATATTA
*
336333 AAAATTAATATTATTAATTATATTA
1 AAAA-TAATATAATTAATTATATTA
336358 A
1 A
336359 TACACAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAATAATATAATTAATTATATTA
Found at i:337703 original size:2 final size:2
Alignment explanation
Indices: 337696--337725 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
337686 TAGTCACGAC
337696 AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
337726 AGAGAGAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:337717 original size:13 final size:13
Alignment explanation
Indices: 337699--337724 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
337689 TCACGACATA
337699 TATATATATATAT
1 TATATATATATAT
337712 TATATATATATAT
1 TATATATATATAT
337725 AAGAGAGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:337717 original size:15 final size:15
Alignment explanation
Indices: 337697--337725 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
337687 AGTCACGACA
337697 TATATATATATATAT
1 TATATATATATATAT
337712 TATATATATATATA
1 TATATATATATATA
337726 AGAGAGAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:338357 original size:2 final size:2
Alignment explanation
Indices: 338350--338375 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
338340 GAAAGAGGCA
338350 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
338376 TCCAATTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:338583 original size:23 final size:23
Alignment explanation
Indices: 338556--338618 Score: 94
Period size: 22 Copynumber: 2.8 Consensus size: 23
338546 TGACCAAAAA
338556 AATCCCATAGAAAGCCAAAGCAT
1 AATCCCATAGAAAGCCAAAGCAT
*
338579 AATCCCCTCA-AAA-CCAAAGCAT
1 AATCCCAT-AGAAAGCCAAAGCAT
338601 AATCCCATAGAAAGCCAA
1 AATCCCATAGAAAGCCAA
338619 TACAGAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 1 0.03
22 19 0.54
23 14 0.40
24 1 0.03
ACGTcount: A:0.48, C:0.30, G:0.10, T:0.13
Consensus pattern (23 bp):
AATCCCATAGAAAGCCAAAGCAT
Found at i:342863 original size:14 final size:14
Alignment explanation
Indices: 342822--342886 Score: 63
Period size: 13 Copynumber: 5.1 Consensus size: 14
342812 CTTAGATTAT
342822 TTTATAATTTAATA
1 TTTATAATTTAATA
342836 TTTA-AA---AA-A
1 TTTATAATTTAATA
342845 TTTATAATTTAATA
1 TTTATAATTTAATA
* *
342859 TTTAT-ATTTTATT
1 TTTATAATTTAATA
342872 TTTATAA-TTAATA
1 TTTATAATTTAATA
342885 TT
1 TT
342887 AATTTAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
9 5 0.12
10 4 0.10
13 21 0.51
14 11 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTATAATTTAATA
Found at i:342875 original size:13 final size:13
Alignment explanation
Indices: 342844--342899 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
342834 TATTTAAAAA
342844 ATTTATAATTTAAT
1 ATTTAT-ATTTAAT
*
342858 ATTTATATTTTAT
1 ATTTATATTTAAT
* *
342871 TTTTATAATTAAT
1 ATTTATATTTAAT
*
342884 A-TTA-ATTTAAA
1 ATTTATATTTAAT
342895 ATTTA
1 ATTTA
342900 ATAAAAATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
11 6 0.18
12 6 0.18
13 16 0.47
14 6 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTATATTTAAT
Found at i:343075 original size:24 final size:24
Alignment explanation
Indices: 343021--343122 Score: 70
Period size: 24 Copynumber: 4.3 Consensus size: 24
343011 TTTTTAAAAC
*
343021 ATTAATATAATATTATTA-ATATACTT
1 ATTAATATAATA-TATTATA-AT-TTT
*
343047 A-TAATATCATATATTATAATTTT
1 ATTAATATAATATATTATAATTTT
* *
343070 ATTAATAAAATA-ATAATACA-TTT
1 ATTAATATAATATATTATA-ATTTT
* * *
343093 -TTAATATTATATGTTAAAATTTT
1 ATTAATATAATATATTATAATTTT
343116 ATTAATA
1 ATTAATA
343123 AAAAAAACAC
Statistics
Matches: 60, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
22 10 0.17
23 17 0.28
24 22 0.37
25 10 0.17
26 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (24 bp):
ATTAATATAATATATTATAATTTT
Found at i:357463 original size:2 final size:2
Alignment explanation
Indices: 357452--357480 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
357442 CAAAATGTAA
357452 AT AT -T 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
357481 TGCACATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:361475 original size:24 final size:24
Alignment explanation
Indices: 361448--361501 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
361438 ATTTATTGAT
* *
361448 AAATATAATTTTAAATTAGATATA
1 AAATATAATTTTAAATGAGATAAA
* **
361472 AAATTTAATTTTTTATGAGATAAA
1 AAATATAATTTTAAATGAGATAAA
361496 AAATAT
1 AAATAT
361502 TTTTTATAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.43
Consensus pattern (24 bp):
AAATATAATTTTAAATGAGATAAA
Found at i:366389 original size:2 final size:2
Alignment explanation
Indices: 366377--366406 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
366367 TTTTATATTA
*
366377 AT AT AT CT 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
366407 CAATGCAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:368007 original size:10 final size:9
Alignment explanation
Indices: 367991--368024 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
367981 TACAAGAACA
367991 CCCCCACCC
1 CCCCCACCC
368000 CACCCCACCC
1 C-CCCCACCC
*
368010 CCCCCCCCC
1 CCCCCACCC
368019 CCCCCA
1 CCCCCA
368025 AAAAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.12, C:0.88, G:0.00, T:0.00
Consensus pattern (9 bp):
CCCCCACCC
Found at i:370014 original size:2 final size:2
Alignment explanation
Indices: 370007--370037 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
369997 CTATGTAAGC
*
370007 TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
370038 TATTGTGCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:372383 original size:2 final size:2
Alignment explanation
Indices: 372376--372406 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
372366 CTGAGTTAGG
372376 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 A
372407 GGGTAGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:374324 original size:17 final size:16
Alignment explanation
Indices: 374298--374332 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
374288 ACTCTCCAGA
*
374298 CTCTCTTCTTCTTCTTC
1 CTCTCGTCTTCTT-TTC
374315 CTCTCGTCTTCTTTTC
1 CTCTCGTCTTCTTTTC
374331 CT
1 CT
374333 TGAAAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.00, C:0.40, G:0.03, T:0.57
Consensus pattern (16 bp):
CTCTCGTCTTCTTTTC
Found at i:375789 original size:15 final size:15
Alignment explanation
Indices: 375769--375798 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
375759 TTAATATTTA
*
375769 TTTAAATTTTTTATT
1 TTTAAAATTTTTATT
375784 TTTAAAATTTTTATT
1 TTTAAAATTTTTATT
375799 AAAAATTATA
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTAAAATTTTTATT
Found at i:376449 original size:43 final size:43
Alignment explanation
Indices: 376402--376508 Score: 103
Period size: 43 Copynumber: 2.5 Consensus size: 43
376392 ATTATTGTTG
*
376402 TTATTATTTTAAATTTTTATAAA-AATTTATATTTAAAT-ATTTT
1 TTATTATTTT-AATATTTA-AAATAATTTATATTTAAATAATTTT
* * * *
376445 TTATTTATATTCATATTTAAAATATTTTATATTTATATAATTTT
1 TTA-TTATTTTAATATTTAAAATAATTTATATTTAAATAATTTT
*
376489 TTA-TATATTAATAATTTAAA
1 TTATTATTTTAAT-ATTTAAA
376509 TTATATATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
42 11 0.20
43 29 0.54
44 14 0.26
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (43 bp):
TTATTATTTTAATATTTAAAATAATTTATATTTAAATAATTTT
Found at i:376460 original size:27 final size:28
Alignment explanation
Indices: 376430--376482 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
376420 ATAAAAATTT
*
376430 ATATTT-AAATATTTTTTATTTATATTC
1 ATATTTAAAATATTTTATATTTATATTC
376457 ATATTTAAAATATTTTATATTTATAT
1 ATATTTAAAATATTTTATATTTATAT
376483 AATTTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (28 bp):
ATATTTAAAATATTTTATATTTATATTC
Found at i:376492 original size:18 final size:17
Alignment explanation
Indices: 376457--376505 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
376447 ATTTATATTC
*
376457 ATATTTAA-AATATTTT
1 ATATTTAATAATTTTTT
376473 ATATTTATATAATTTTTT
1 ATATTTA-ATAATTTTTT
376491 ATATATTAATAATTT
1 ATAT-TTAATAATTT
376506 AAATTATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 7 0.24
17 1 0.03
18 18 0.62
19 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATTTAATAATTTTTT
Found at i:376530 original size:18 final size:18
Alignment explanation
Indices: 376467--376530 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
376457 ATATTTAAAA
*
376467 TATTTTATATTTATATAAT
1 TATTTTATATATAT-TAAT
*
376486 T-TTTTATATATTAATAATT
1 TATTTTATATA-TATTAA-T
**
376505 TAAATTATATATATTAAT
1 TATTTTATATATATTAAT
376523 TATTTTAT
1 TATTTTAT
376531 TTATGATATA
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
18 18 0.51
19 10 0.29
20 7 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTTTATATATATTAAT
Found at i:376534 original size:42 final size:40
Alignment explanation
Indices: 376457--376539 Score: 85
Period size: 42 Copynumber: 1.9 Consensus size: 40
376447 ATTTATATTC
* * * *
376457 ATATTTAAAATATTTTATATTTATATAATTTTTTATATATTA
1 ATATTTAAATTA-TATATATTAAT-TATTTTTTTATATATTA
376499 ATAATTTAAATTATATATATTAATTATTTTATTTATGATAT
1 AT-ATTTAAATTATATATATTAATTATTTT-TTTAT-ATAT
376540 ATTTATATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
41 5 0.15
42 16 0.47
43 13 0.38
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (40 bp):
ATATTTAAATTATATATATTAATTATTTTTTTATATATTA
Found at i:376544 original size:38 final size:38
Alignment explanation
Indices: 376471--376555 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 38
376461 TTAAAATATT
* *
376471 TTATATTTATATAATTTTTTATATATTAATAATTTAAA
1 TTATATATATATAATTTTTTATATATGAATAATTTAAA
* *
376509 TTATATATAT-TAATTATTTTATTTATGATATATTTATATAA
1 TTATATATATATAATT-TTTTATATATGA-ATAATT-TA-AA
376550 TTATAT
1 TTATAT
376556 TTAATATTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
37 5 0.13
38 19 0.49
39 5 0.13
40 2 0.05
41 8 0.21
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (38 bp):
TTATATATATATAATTTTTTATATATGAATAATTTAAA
Found at i:376556 original size:25 final size:25
Alignment explanation
Indices: 376490--376558 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 25
376480 TATAATTTTT
* *
376490 TATATATTAATAATT-TA--AATTA
1 TATATATTAATAATTATATTTATGA
* *
376512 TATATATTAATTATTTTATTTATGA
1 TATATATTAATAATTATATTTATGA
376537 TATAT-TTATATAATTATATTTA
1 TATATATTA-ATAATTATATTTA
376559 ATATTATTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
22 14 0.37
23 2 0.05
24 3 0.08
25 19 0.50
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (25 bp):
TATATATTAATAATTATATTTATGA
Found at i:376580 original size:34 final size:34
Alignment explanation
Indices: 376477--376582 Score: 84
Period size: 34 Copynumber: 3.2 Consensus size: 34
376467 TATTTTATAT
*
376477 TTATATAATT-T-TTTATATATTAATAAT-TTAA-A
1 TTATATAATTATATTTA-ATATT-ATTATGTTAATA
* *
376509 TTATATATATTA-A-TT-ATTTTATTTATGAT-ATA
1 TTATATA-ATTATATTTAATATTA-TTATGTTAATA
376541 TTTATATAATTATATTTAATATTATTATGTTAATA
1 -TTATATAATTATATTTAATATTATTATGTTAATA
376576 TTATATA
1 TTATATA
376583 TAATATAATT
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
30 1 0.02
31 8 0.14
32 13 0.22
33 13 0.22
34 15 0.26
35 8 0.14
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (34 bp):
TTATATAATTATATTTAATATTATTATGTTAATA
Found at i:376597 original size:38 final size:37
Alignment explanation
Indices: 376486--376597 Score: 91
Period size: 31 Copynumber: 3.2 Consensus size: 37
376476 TTTATATAAT
*
376486 TTTTTATATATTAATAAT-TTAA-ATTATATAT-ATTAA
1 TTTTTA-ATATT-ATTATGTTAATATTATATATAATTAA
*
376522 TTATTT--TA-T-TTATGAT-ATATT-TATATAATT-A
1 TT-TTTAATATTATTATGTTAATATTATATATAATTAA
*
376553 TATTTAATATTATTATGTTAATATTATATATAATATAA
1 TTTTTAATATTATTATGTTAATATTATATATAAT-TAA
376591 TTTTTAA
1 TTTTTAA
376598 AAGATTTTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 22
0.69 0.06 0.26
Matches are distributed among these distances:
30 3 0.05
31 11 0.19
32 9 0.15
33 2 0.03
34 8 0.14
35 5 0.08
36 10 0.17
37 4 0.07
38 7 0.12
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (37 bp):
TTTTTAATATTATTATGTTAATATTATATATAATTAA
Found at i:377113 original size:19 final size:20
Alignment explanation
Indices: 377089--377137 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
377079 TTATTTTATA
377089 ATTTTTAATA-TTAATAAT-T
1 ATTTTTAATATTTAA-AATAT
*
377108 ATTTTTTATATTTAAAATAT
1 ATTTTTAATATTTAAAATAT
377128 ATTTTATAAT
1 ATTTT-TAAT
377138 TAAAATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 12 0.48
20 10 0.40
21 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTTAATATTTAAAATAT
Found at i:377113 original size:20 final size:21
Alignment explanation
Indices: 377085--377137 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
377075 TTTATTATTT
*
377085 TATAATTTTTAATA-TTAATAA
1 TATATTTTTTAATATTTAA-AA
377106 T-TATTTTTT-ATATTTAAAA
1 TATATTTTTTAATATTTAAAA
*
377125 TATATTTTATAAT
1 TATATTTTTTAAT
377138 TAAAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 6 0.22
20 18 0.67
21 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TATATTTTTTAATATTTAAAA
Found at i:377388 original size:3 final size:3
Alignment explanation
Indices: 377376--377425 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
377366 TCTCTTTGAG
377376 CTT C-T CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
377423 CTT
1 CTT
377426 TCTCGAGTAC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:378954 original size:4 final size:4
Alignment explanation
Indices: 378945--378985 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
378935 CACGTTTTAT
*
378945 ATAC ATAC ATAC ATAC CTAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
378986 ATATATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:380157 original size:49 final size:48
Alignment explanation
Indices: 380085--380181 Score: 128
Period size: 49 Copynumber: 2.0 Consensus size: 48
380075 TTTAATAATA
*
380085 ATTTTTTAAAATTTAATTATAAATATATAA-AAATATTAA-TATAAAAT
1 ATTTTTTAAAATTTAATTATAAATAAATAATAAA-ATTAATTATAAAAT
380132 ATTTTTTAAATATTTTAA-TATTAAATAAATAATAAAATTAATTATAAAAT
1 ATTTTTTAAA-A-TTTAATTA-TAAATAAATAATAAAATTAATTATAAAAT
380182 TAATTTATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
47 10 0.23
48 3 0.07
49 20 0.45
50 11 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (48 bp):
ATTTTTTAAAATTTAATTATAAATAAATAATAAAATTAATTATAAAAT
Found at i:380279 original size:24 final size:24
Alignment explanation
Indices: 380226--380277 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
380216 AATTTAATTC
*
380226 ATAAATTTATATTATAAAAAATAC
1 ATAAATTTATATTATAAAAAATAA
**
380250 ATAAATTTATA-TATAATCAATAA
1 ATAAATTTATATTATAAAAAATAA
380273 ATAAA
1 ATAAA
380278 ATATTTTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (24 bp):
ATAAATTTATATTATAAAAAATAA
Found at i:383001 original size:21 final size:21
Alignment explanation
Indices: 382961--383001 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
382951 AAAAAAATAT
** *
382961 ATTTTAAATTCATTCGAAAAA
1 ATTTTAAATTCAAACAAAAAA
382982 ATTTTAAATTCAAACAAAAA
1 ATTTTAAATTCAAACAAAAA
383002 TTGAAAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (21 bp):
ATTTTAAATTCAAACAAAAAA
Found at i:384167 original size:22 final size:21
Alignment explanation
Indices: 384128--384168 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
384118 TTTAAAAAAT
384128 TATTTTATATTAATATTTATA
1 TATTTTATATTAATATTTATA
384149 TATTCTTATAATTAA-ATTTA
1 TATT-TTAT-ATTAATATTTA
384169 AATAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 9 0.50
23 5 0.28
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTTATATTAATATTTATA
Found at i:387560 original size:176 final size:177
Alignment explanation
Indices: 387264--387615 Score: 589
Period size: 176 Copynumber: 2.0 Consensus size: 177
387254 AGAATTCCGG
* * *
387264 CCAAAGTTTACTTTCAGTGCGGTCATTGTTGAAAAAAAAAAAAATGAATGGGATAATTGTTGTTT
1 CCAAAGTTTACTTTCAGTACAGTCATTGTTG-AAAAAAAAAAAATGAATGGGATAATTATTGTTT
* *
387329 AGTCCCTAAACATTAAGCTATTTACAAGATTGATCCTTGAAGCTTCAACTATAAATAGGTCTTCC
65 AGTCCCTAAACATTAAGCTATTTACAAGATTGATCCTTGAAGCTTCAACTATAAATAAGCCTTCC
387394 CATTTCACTTCTGTATCATCCCAAAATTCTCAAAAACACAAGTTTCTT
130 CATTTCACTTCTGTATCATCCCAAAATTCTCAAAAACACAAGTTTCTT
* *
387442 CCAAAGTTTGCTTTCAGTACAGTCATTGTTG-AAAAAAAAAATTGAATGGGATAATTATTGTTTA
1 CCAAAGTTTACTTTCAGTACAGTCATTGTTGAAAAAAAAAAAATGAATGGGATAATTATTGTTTA
* * * *
387506 GTCCCTAAACTTTAGGCTATTTACAAGATTGATCCTTGGAGCTTCAACTATAAATAAGCCTTTCC
66 GTCCCTAAACATTAAGCTATTTACAAGATTGATCCTTGAAGCTTCAACTATAAATAAGCCTTCCC
387571 ATTTCACTTCTGTATCATCCCAAAATTCTCAAAAACACAAGTTTC
131 ATTTCACTTCTGTATCATCCCAAAATTCTCAAAAACACAAGTTTC
387616 CTCTTGTAGA
Statistics
Matches: 163, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
176 135 0.83
178 28 0.17
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (177 bp):
CCAAAGTTTACTTTCAGTACAGTCATTGTTGAAAAAAAAAAAATGAATGGGATAATTATTGTTTA
GTCCCTAAACATTAAGCTATTTACAAGATTGATCCTTGAAGCTTCAACTATAAATAAGCCTTCCC
ATTTCACTTCTGTATCATCCCAAAATTCTCAAAAACACAAGTTTCTT
Found at i:394005 original size:2 final size:2
Alignment explanation
Indices: 393998--394035 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
393988 AATATCTATC
393998 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
394036 AAAGAAAGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:400879 original size:20 final size:20
Alignment explanation
Indices: 400854--400927 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
400844 CAAGCACTTA
* * *
400854 GCCTTTTCAGGTTCTCTATT
1 GCCTTTTCAGGCTCGCAATT
* * *
400874 GCCTTTTCAAGCTAGCCATAT
1 GCCTTTTCAGGCTCGCAAT-T
400895 GCCTTTTCAGGCTCGCAATT
1 GCCTTTTCAGGCTCGCAATT
400915 GCCTTTTCAGGCT
1 GCCTTTTCAGGCT
400928 TGCCAAAGGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 28 0.62
21 17 0.38
ACGTcount: A:0.15, C:0.28, G:0.18, T:0.39
Consensus pattern (20 bp):
GCCTTTTCAGGCTCGCAATT
Found at i:400916 original size:41 final size:41
Alignment explanation
Indices: 400854--400932 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
400844 CAAGCACTTA
* * *
400854 GCCTTTTCAGGTTCTCTATTGCCTTTTCAAGCTAGCCATAT
1 GCCTTTTCAGGCTCGCAATTGCCTTTTCAAGCTAGCCATAT
* *
400895 GCCTTTTCAGGCTCGCAATTGCCTTTTCAGGCTTGCCA
1 GCCTTTTCAGGCTCGCAATTGCCTTTTCAAGCTAGCCA
400933 AAGGTCTTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.15, C:0.29, G:0.18, T:0.38
Consensus pattern (41 bp):
GCCTTTTCAGGCTCGCAATTGCCTTTTCAAGCTAGCCATAT
Found at i:405418 original size:21 final size:21
Alignment explanation
Indices: 405394--405436 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
405384 CAACCACTAT
405394 ACCCCTTTTATACTGTCATAC
1 ACCCCTTTTATACTGTCATAC
405415 ACCCCTTTTATACTGTCATAC
1 ACCCCTTTTATACTGTCATAC
405436 A
1 A
405437 AATATTTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.33, G:0.05, T:0.37
Consensus pattern (21 bp):
ACCCCTTTTATACTGTCATAC
Found at i:411855 original size:71 final size:71
Alignment explanation
Indices: 411739--411883 Score: 254
Period size: 71 Copynumber: 2.0 Consensus size: 71
411729 CTAAAATTGG
411739 CCTTTGTGACATAACAAAAGTGAGAATTTAATTAGGAATGTAAGTTAATAATGTATATGTAATAG
1 CCTTTGTGACATAACAAAAGTGAGAATTTAATTAGGAATGTAAGTTAATAATGTATATGTAATAG
411804 TAAGGA
66 TAAGGA
* * *
411810 CCTTTGTGACATCACAAATGTGAGAATTTAATTATGAATGTAAGTTAATAATGTATATGTAATAG
1 CCTTTGTGACATAACAAAAGTGAGAATTTAATTAGGAATGTAAGTTAATAATGTATATGTAATAG
*
411875 TAGGGA
66 TAAGGA
411881 CCT
1 CCT
411884 GTATTCAGGT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (71 bp):
CCTTTGTGACATAACAAAAGTGAGAATTTAATTAGGAATGTAAGTTAATAATGTATATGTAATAG
TAAGGA
Found at i:414143 original size:21 final size:21
Alignment explanation
Indices: 414118--414221 Score: 61
Period size: 21 Copynumber: 4.9 Consensus size: 21
414108 ATTCATAAAA
414118 AATAATTAAAAATATAAATAT
1 AATAATTAAAAATATAAATAT
* *
414139 AATAACTAAAATTTATATAATA-
1 AATAATTAAAA-ATATA-AATAT
* ** **
414161 AATTATTTTAAATATACTTAT
1 AATAATTAAAAATATAAATAT
*
414182 AATATAATAAAATATATAAATAT
1 AATA-ATTAAAA-ATATAAATAT
* *
414205 ATTAA--AAATATATAAAT
1 AATAATTAAAAATATAAAT
414222 GATTAAATCT
Statistics
Matches: 61, Mismatches: 17, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
19 8 0.13
20 5 0.08
21 17 0.28
22 16 0.26
23 15 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AATAATTAAAAATATAAATAT
Found at i:414175 original size:43 final size:43
Alignment explanation
Indices: 414127--414208 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
414117 AAATAATTAA
* *
414127 AAATATAAATATAATA-ACTAAAATTTATATAATAAATTATTTT
1 AAATATAAATATAATATAATAAAATATATA-AATAAATTATTTT
** *
414170 AAATATACTTATAATATAATAAAATATATAAATATATTA
1 AAATATAAATATAATATAATAAAATATATAAATAAATTA
414209 AAAATATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
43 22 0.67
44 11 0.33
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (43 bp):
AAATATAAATATAATATAATAAAATATATAAATAAATTATTTT
Found at i:415738 original size:16 final size:17
Alignment explanation
Indices: 415719--415757 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
415709 AATATCGATA
415719 TAAAAATATAA-TCTTT
1 TAAAAATATAATTCTTT
* *
415735 TAAATATATAATTTTTT
1 TAAAAATATAATTCTTT
415752 TAAAAA
1 TAAAAA
415758 GATTAATCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAAATATAATTCTTT
Found at i:418127 original size:22 final size:22
Alignment explanation
Indices: 418086--418127 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
418076 ATTTAAATTT
*
418086 AAATTATTATTTATTTTATTAA
1 AAATTATTATTTATTATATTAA
418108 AAATTATT-TTTATTAATATT
1 AAATTATTATTTATT-ATATT
418128 TTTATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
AAATTATTATTTATTATATTAA
Found at i:418513 original size:50 final size:50
Alignment explanation
Indices: 418389--418597 Score: 176
Period size: 50 Copynumber: 4.2 Consensus size: 50
418379 AGGTGTTGTC
* * * * * * *
418389 ATTGTTAATTATTTTTTATTAACTTTTGACAATCGAAAAAAATGATCGTA
1 ATTGTTGACTATTTTTTATCAACGTTTGACAATCGAGAGAAATGATCATA
* * * *
418439 ATTGTTGACGATTCTTCATCAATC-TTTGACAATTGAGAGAAATGATCATA
1 ATTGTTGACTATTTTTTATCAA-CGTTTGACAATCGAGAGAAATGATCATA
* * ***
418489 ATTGTTGACTATTTTTTAGT-AATC-TTTGATAATAGAGAGAGGCGA-CAATA
1 ATTGTTGACTATTTTTTA-TCAA-CGTTTGACAATCGAGAGAAATGATC-ATA
* *
418539 ATTATTGA-TGATTTTTTATCAACGTTTGACAATCGAGAGAAATGACCATA
1 ATTGTTGACT-ATTTTTTATCAACGTTTGACAATCGAGAGAAATGATCATA
418589 ATTGTTGAC
1 ATTGTTGAC
418598 AATTGTTGAC
Statistics
Matches: 126, Mismatches: 25, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
49 4 0.03
50 119 0.94
51 3 0.02
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.39
Consensus pattern (50 bp):
ATTGTTGACTATTTTTTATCAACGTTTGACAATCGAGAGAAATGATCATA
Found at i:418517 original size:100 final size:100
Alignment explanation
Indices: 418389--418597 Score: 217
Period size: 100 Copynumber: 2.1 Consensus size: 100
418379 AGGTGTTGTC
* * * * * * *
418389 ATTGTTAATTATTTTTTATTAACTTTTGACAATCGAAAAAAATGATC-GTAATTGTTGACGATTC
1 ATTGTTGACTATTTTTTAGTAACTTTTGACAATAGAAAAAAACGA-CAATAATTATTGACGATTC
* *
418453 TTCATCAATC-TTTGACAATTGAGAGAAATGATCATA
65 TTCATCAA-CGTTTGACAATCGAGAGAAATGACCATA
* * * ** * *
418489 ATTGTTGACTATTTTTTAGTAA-TCTTTGATAATAGAGAGAGGCGACAATAATTATTGATGATTT
1 ATTGTTGACTATTTTTTAGTAACT-TTTGACAATAGAAAAAAACGACAATAATTATTGACGATTC
*
418553 TTTATCAACGTTTGACAATCGAGAGAAATGACCATA
65 TTCATCAACGTTTGACAATCGAGAGAAATGACCATA
418589 ATTGTTGAC
1 ATTGTTGAC
418598 AATTGTTGAC
Statistics
Matches: 89, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
99 3 0.03
100 86 0.97
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.39
Consensus pattern (100 bp):
ATTGTTGACTATTTTTTAGTAACTTTTGACAATAGAAAAAAACGACAATAATTATTGACGATTCT
TCATCAACGTTTGACAATCGAGAGAAATGACCATA
Found at i:418712 original size:50 final size:49
Alignment explanation
Indices: 418658--418775 Score: 112
Period size: 50 Copynumber: 2.4 Consensus size: 49
418648 ATCAACCTTA
*
418658 GACAATCGAGAA-AGGTGACCGTAATTATTGACGATTATTTACCAATCTTT
1 GACAATCGA-AAGAGGTGACCATAATTATTGACGATTATTTACCAA-CTTT
* * * ** *
418708 GACAATTGAAAGAGGTGATCATAATTGTTGATTATTTTTTACCAACTTTT
1 GACAATCGAAAGAGGTGACCATAATTATTGACGATTATTTACCAAC-TTT
* **
418758 GATAATAAAAAGAGGTGA
1 GACAATCGAAAGAGGTGA
418776 TTGTAATTGT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
49 3 0.05
50 53 0.95
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (49 bp):
GACAATCGAAAGAGGTGACCATAATTATTGACGATTATTTACCAACTTT
Found at i:419759 original size:32 final size:32
Alignment explanation
Indices: 419714--419779 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
419704 TAAATAAAAA
*
419714 ATAAATTACATAAAATAATTAAATTAAACTCG
1 ATAAATTAAATAAAATAATTAAATTAAACTCG
* *
419746 ATAAATTAAATAAATTAATTAAATTAAATTCG
1 ATAAATTAAATAAAATAATTAAATTAAACTCG
419778 AT
1 AT
419780 TTGATGAGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (32 bp):
ATAAATTAAATAAAATAATTAAATTAAACTCG
Found at i:420341 original size:28 final size:27
Alignment explanation
Indices: 420279--420343 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 27
420269 TATTTTTAAA
420279 ATTTTTATATATTTAAAAAATATAAATT
1 ATTTTT-TATATTTAAAAAATATAAATT
420307 ATATTTTTATATTTATATTAAAATAT-AA-T
1 AT-TTTTTATATTTA-A--AAAATATAAATT
420336 ATTTTTTA
1 ATTTTTTA
420344 AAAAAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
28 16 0.48
29 8 0.24
30 2 0.06
31 7 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
ATTTTTTATATTTAAAAAATATAAATT
Found at i:422658 original size:5 final size:5
Alignment explanation
Indices: 422648--422694 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
422638 ACATAGTACA
* * *
422648 AATAT AATAT AATAA AAAAT -ATAA AATAT AATAT AAATAT AATAT AA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AA
422695 ATGTTATAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
4 2 0.06
5 27 0.79
6 5 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (5 bp):
AATAT
Found at i:422677 original size:19 final size:18
Alignment explanation
Indices: 422653--422689 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
422643 GTACAAATAT
422653 AATATAATAAAAAATATAA
1 AATATAAT-AAAAATATAA
*
422672 AATATAATATAAATATAA
1 AATATAATAAAAATATAA
422690 TATAAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AATATAATAAAAATATAA
Found at i:423795 original size:2 final size:2
Alignment explanation
Indices: 423788--423815 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
423778 TTGCTGCAGC
423788 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
423816 GTGCTAATTG
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):
AT
Found at i:424917 original size:13 final size:14
Alignment explanation
Indices: 424899--424930 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
424889 TAATCAAAAA
424899 TAAATTAATATAT-
1 TAAATTAATATATG
424912 TAAATTAATATATG
1 TAAATTAATATATG
424926 TAAAT
1 TAAAT
424931 CTTTCTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (14 bp):
TAAATTAATATATG
Found at i:425470 original size:26 final size:24
Alignment explanation
Indices: 425413--425488 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 24
425403 AATTTTTTTA
*
425413 TTAATATTAAA-A-AAAAATTAAT
1 TTAAAATTAAATATAAAAATTAAT
*
425435 TTAAATTTAAATATAAATAATTAATT
1 TTAAAATTAAATATAAA-AATTAA-T
425461 TTAAAATT-AATAATAAAAATTAAAT
1 TTAAAATTAAAT-ATAAAAATT-AAT
425486 TTA
1 TTA
425489 TTTTTTAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
22 9 0.20
23 1 0.02
24 3 0.07
25 17 0.38
26 15 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TTAAAATTAAATATAAAAATTAAT
Found at i:426592 original size:2 final size:2
Alignment explanation
Indices: 426585--426614 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
426575 ACCCCCAATA
426585 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
426615 GTATGTATGT
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:431507 original size:32 final size:32
Alignment explanation
Indices: 431471--431563 Score: 105
Period size: 32 Copynumber: 2.9 Consensus size: 32
431461 AGTTAAACAT
* * *
431471 AATTATTCACAAATTTGATAAATTTTAAATAA
1 AATTATTCATAAATTTAATAAATATTAAATAA
* * * *
431503 AATTATTTATAAATTTAATTAATATTAGATAC
1 AATTATTCATAAATTTAATAAATATTAAATAA
* *
431535 AATTACTCATAAATTTAATAGATATTAAA
1 AATTATTCATAAATTTAATAAATATTAAA
431564 AAAGTTTCAA
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42
Consensus pattern (32 bp):
AATTATTCATAAATTTAATAAATATTAAATAA
Found at i:437727 original size:2 final size:2
Alignment explanation
Indices: 437722--437790 Score: 50
Period size: 2 Copynumber: 34.0 Consensus size: 2
437712 TTTATTGATA
* * * * *
437722 AT AT AT AT AT AT AT AT AT AT AT AA AT -T AT CT GT AC AT CAA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
* *
437764 AT AA ACT TT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT
437791 CGTTAAAATC
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
1 1 0.02
2 49 0.96
3 1 0.02
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (2 bp):
AT
Found at i:439193 original size:28 final size:27
Alignment explanation
Indices: 439162--439229 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 27
439152 ATTATCATTG
439162 ATAAAATTTTATAAATAAAATTAATAAA
1 ATAAAATTTTATAAAT-AAATTAATAAA
* **
439190 ATAAATATATTT-TAAATATATTTTTAAA
1 ATAAA-AT-TTTATAAATAAATTAATAAA
439218 ATAAAAATTTTA
1 AT-AAAATTTTA
439230 ATTTAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
27 3 0.09
28 17 0.52
29 10 0.30
30 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
ATAAAATTTTATAAATAAATTAATAAA
Found at i:439230 original size:14 final size:13
Alignment explanation
Indices: 439162--439230 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 13
439152 ATTATCATTG
439162 ATAAAATTTTATAA
1 ATAAAATTTTA-AA
*
439176 ATAAAATTAATAAA
1 ATAAAATT-TTAAA
*
439190 ATAAATATATTTTAA
1 ATAAA-AT-TTTAAA
* *
439205 ATATATTTTTAAA
1 ATAAAATTTTAAA
439218 ATAAAAATTTTAA
1 AT-AAAATTTTAA
439231 TTTAAAATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
13 7 0.16
14 24 0.56
15 11 0.26
16 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATAAAATTTTAAA
Found at i:439401 original size:14 final size:14
Alignment explanation
Indices: 439382--439414 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
439372 TTTAAAAAGT
439382 ATATATAAATATAG
1 ATATATAAATATAG
439396 ATATATAAATATAG
1 ATATATAAATATAG
*
439410 GTATA
1 ATATA
439415 GATAGTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (14 bp):
ATATATAAATATAG
Found at i:449676 original size:2 final size:2
Alignment explanation
Indices: 449669--449708 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
449659 CATGACTTGC
*
449669 AT AT AT AT AT GT 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
449709 GCATGTATCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:453125 original size:67 final size:67
Alignment explanation
Indices: 453017--453150 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
453007 CATCATATTA
453017 TCATTTCTTCCCGTGTTCATCACCTCTTGAATAACAATGACTGCTCCAGTTGCGGGCTACTGACT
1 TCATTTCTTCCCGTGTTCATCACCTCTTGAATAACAATGACTGCTCCAGTTGCGGGCTACTGACT
453082 AC
66 AC
453084 TCATTTCTTCCCGTGTTCATCACCTCTTGAATAACAATGACTGCTCCAGTTGCGGGCTACTGACT
1 TCATTTCTTCCCGTGTTCATCACCTCTTGAATAACAATGACTGCTCCAGTTGCGGGCTACTGACT
453149 AC
66 AC
453151 ACATGATGTT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (67 bp):
TCATTTCTTCCCGTGTTCATCACCTCTTGAATAACAATGACTGCTCCAGTTGCGGGCTACTGACT
AC
Found at i:457071 original size:21 final size:20
Alignment explanation
Indices: 457032--457071 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
457022 GGTTATGTTA
**
457032 TTTTATTTTTTAAGTAATTT
1 TTTTATTTTTTAACAAATTT
457052 TTTTATTATTTTAACAAATT
1 TTTTATT-TTTTAACAAATT
457072 AATAATTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (20 bp):
TTTTATTTTTTAACAAATTT
Found at i:468205 original size:20 final size:18
Alignment explanation
Indices: 468167--468207 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
468157 TATAATCGAG
*
468167 TTAAAAATATTATATAAT
1 TTAAAAATATAATATAAT
468185 TTAAAAATAATAATAATAAT
1 TTAAAAAT-ATAAT-ATAAT
468205 TTA
1 TTA
468208 TATTATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 4 0.20
20 8 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TTAAAAATATAATATAAT
Found at i:472442 original size:2 final size:2
Alignment explanation
Indices: 472435--472474 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
472425 TCCATAATTA
472435 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
472475 TCACATTATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:479923 original size:13 final size:13
Alignment explanation
Indices: 479901--479931 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
479891 TATATTACTC
479901 AAAT-TTAAATAT
1 AAATATTAAATAT
479913 AAATATTAAATAT
1 AAATATTAAATAT
479926 AAATAT
1 AAATAT
479932 ATTTAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AAATATTAAATAT
Found at i:490048 original size:17 final size:17
Alignment explanation
Indices: 490014--490058 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
490004 TTTTATTTTG
*
490014 ATATATAAGA-TATTAAA
1 ATATATAA-ATTATAAAA
490031 ATATATAAATTATAAAA
1 ATATATAAATTATAAAA
490048 A-AT-TAAATTAT
1 ATATATAAATTAT
490059 TTTAATAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 8 0.31
16 3 0.12
17 15 0.58
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
ATATATAAATTATAAAA
Found at i:490384 original size:15 final size:14
Alignment explanation
Indices: 490361--490394 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
490351 TCATATTTTT
*
490361 ATATTAATTATATAA
1 ATATAAATTATA-AA
490376 ATATAAATTATAAA
1 ATATAAATTATAAA
490390 ATATA
1 ATATA
490395 TAAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATAAATTATAAA
Found at i:491197 original size:3 final size:3
Alignment explanation
Indices: 491189--491222 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
491179 TCCGTCACTA
491189 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
491223 ATAGAGCAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:491345 original size:16 final size:16
Alignment explanation
Indices: 491308--491337 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
491298 TTTCACGATT
491308 AAAA-AATTAAAATAA
1 AAAATAATTAAAATAA
491323 AAAATAATTAAAATA
1 AAAATAATTAAAATA
491338 TAATATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATAATTAAAATAA
Found at i:491391 original size:28 final size:26
Alignment explanation
Indices: 491317--491392 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 26
491307 TAAAAAATTA
* *
491317 AAATAAAAAATAATTAAAATATAATAT
1 AAATATAAAATAATT-AAATATAATAC
* *
491344 AAATATAAATTTAACATAAATATAATAC
1 AAATATAAA-ATAA-TTAAATATAATAC
491372 AAATATATAAATAAGTTAAAT
1 AAATATA-AAATAA-TTAAAT
491393 TTTATATAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
27 8 0.21
28 28 0.72
29 3 0.08
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (26 bp):
AAATATAAAATAATTAAATATAATAC
Found at i:491417 original size:19 final size:20
Alignment explanation
Indices: 491375--491424 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
491365 ATAATACAAA
* *
491375 TATATAAATAAGTTAAATTT
1 TATATAAATAAGTTAAAATG
*
491395 TATAT-AATATGTTAAAATG
1 TATATAAATAAGTTAAAATG
491414 TATATTAAATA
1 TATA-TAAATA
491425 TAAAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 15 0.60
20 6 0.24
21 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (20 bp):
TATATAAATAAGTTAAAATG
Found at i:491445 original size:26 final size:28
Alignment explanation
Indices: 491395--491446 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
491385 AGTTAAATTT
* *
491395 TATATAATATGTTAAAATGTATATTAAA
1 TATAAAATATGTTAAAATATATATTAAA
491423 TATAAAATAT-TTAAAATAT-TATTA
1 TATAAAATATGTTAAAATATATATTA
491447 CGATACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 8 0.36
28 9 0.41
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (28 bp):
TATAAAATATGTTAAAATATATATTAAA
Found at i:491485 original size:26 final size:28
Alignment explanation
Indices: 491435--491487 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
491425 TAAAATATTT
*
491435 AAAATATTATTACGATACAAAAATTATA
1 AAAATATTATCACGATACAAAAATTATA
*
491463 AAAATATTA-CAC-ATACACAAATTAT
1 AAAATATTATCACGATACAAAAATTAT
491488 CTTTAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.52
27 2 0.09
28 9 0.39
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (28 bp):
AAAATATTATCACGATACAAAAATTATA
Found at i:491620 original size:19 final size:19
Alignment explanation
Indices: 491594--491648 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
491584 TAAACTATTT
491594 TAATATATTAAATTAA-TA
1 TAATATATTAAATTAATTA
* *
491612 TATATATATTAAAATAATTT
1 TA-ATATATTAAATTAATTA
*
491632 TAATATATAAAATTAAT
1 TAATATATTAAATTAAT
491649 GTATTTTCGC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 2 0.06
19 26 0.84
20 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAATATATTAAATTAATTA
Found at i:491980 original size:4 final size:4
Alignment explanation
Indices: 491971--492009 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
491961 TCTCTTCCTC
*
491971 TTTA TTTA TTTA TTTA TATATA TATA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA T-T-TA TTTA TTTA TTTA TTTA T
492010 AGTTAAAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 27 0.87
5 1 0.03
6 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:492320 original size:29 final size:30
Alignment explanation
Indices: 492249--492333 Score: 104
Period size: 29 Copynumber: 2.9 Consensus size: 30
492239 TTGATTAATT
492249 TATATAATTATTTTTAAAATATAATATTTA
1 TATATAATTATTTTTAAAATATAATATTTA
*
492279 -ATA-AATTTAATTTTTAAAAT-TTATATTTA
1 TATATAA-TT-ATTTTTAAAATATAATATTTA
* *
492308 TATATAATTATTTTCAAATTATAATA
1 TATATAATTATTTTTAAAATATAATA
492334 GCTTTTGTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
28 2 0.04
29 22 0.48
30 20 0.43
31 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (30 bp):
TATATAATTATTTTTAAAATATAATATTTA
Found at i:492464 original size:26 final size:26
Alignment explanation
Indices: 492435--492487 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
492425 ATATATGTTC
*
492435 AAAATAAATATATTT-ATTTTTTTAAA
1 AAAAT-AATATATTTAAATTTTTTAAA
**
492461 AAAATTCTATATTTAAATTTTTTAAA
1 AAAATAATATATTTAAATTTTTTAAA
492487 A
1 A
492488 TTATATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
AAAATAATATATTTAAATTTTTTAAA
Found at i:500306 original size:13 final size:13
Alignment explanation
Indices: 500288--500313 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
500278 AATTTATAAC
500288 TAAATATCAAATA
1 TAAATATCAAATA
500301 TAAATATCAAATA
1 TAAATATCAAATA
500314 AATATAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAATATCAAATA
Found at i:502043 original size:18 final size:17
Alignment explanation
Indices: 502020--502054 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
502010 GGCTTGGTTG
502020 CCTCAGGATCATCTATCT
1 CCTCAGGATCATC-ATCT
*
502038 CCTCAGGCTCATCATCT
1 CCTCAGGATCATCATCT
502055 AACCATCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.20, C:0.37, G:0.11, T:0.31
Consensus pattern (17 bp):
CCTCAGGATCATCATCT
Found at i:504156 original size:20 final size:20
Alignment explanation
Indices: 504130--504180 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
504120 CTTTTTTAAC
*
504130 ATTTTTAATTTAAAAA-ATA
1 ATTTTTTATTTAAAAATATA
*
504149 ATTTTTTATTAAAAAATATA
1 ATTTTTTATTTAAAAATATA
504169 ATTTTTTTATTT
1 A-TTTTTTATTT
504181 GTTATTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 14 0.52
20 4 0.15
21 9 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTTTATTTAAAAATATA
Found at i:510053 original size:2 final size:2
Alignment explanation
Indices: 510046--510115 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
510036 CTGAAGCCTC
510046 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
510088 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
510116 CTTGTCCTAG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:510212 original size:22 final size:23
Alignment explanation
Indices: 510150--510229 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 23
510140 ATCGGATTTA
*
510150 AATTATTATTTAATTATAAAAAT
1 AATTTTTATTTAATTATAAAAAT
510173 AATTTTATTTAAATTTAATTATAAAAAT
1 AA--TT-TTT--ATTTAATTATAAAAAT
*
510201 AATTTTTA-TTAATTTTTAAATAAT
1 AATTTTTATTTAA-TTATAAA-AAT
510225 AATTT
1 AATTT
510230 AAACTTTTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
22 4 0.08
23 9 0.19
24 8 0.17
25 5 0.10
26 4 0.08
28 18 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
AATTTTTATTTAATTATAAAAAT
Found at i:510437 original size:24 final size:26
Alignment explanation
Indices: 510398--510451 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
510388 ATTTTTTATT
510398 TATATATAAATAAAAT-ATA-ATACA
1 TATATATAAATAAAATCATATATACA
*
510422 TATATATTAAAT-AAATCATATTTACA
1 TATATA-TAAATAAAATCATATATACA
510448 TATA
1 TATA
510452 CCATATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 10 0.38
25 8 0.31
26 8 0.31
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (26 bp):
TATATATAAATAAAATCATATATACA
Found at i:510883 original size:3 final size:3
Alignment explanation
Indices: 510871--510912 Score: 57
Period size: 3 Copynumber: 13.0 Consensus size: 3
510861 AAAAATGTGG
510871 AGA AGAA AGA AGA AGA AGA AGA AGAA AGA AGAA AGA AGA AGA
1 AGA AG-A AGA AGA AGA AGA AGA AG-A AGA AG-A AGA AGA AGA
510913 CAGCTTTTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 27 0.75
4 9 0.25
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:510883 original size:7 final size:7
Alignment explanation
Indices: 510871--510910 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
510861 AAAAATGTGG
510871 AGAAGAA
1 AGAAGAA
510878 AGAAG-A
1 AGAAGAA
510884 AGAAG-A
1 AGAAGAA
510890 AGAAGAA
1 AGAAGAA
510897 AGAAGAA
1 AGAAGAA
510904 AGAAGAA
1 AGAAGAA
510911 GACAGCTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 12 0.38
7 20 0.62
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (7 bp):
AGAAGAA
Found at i:511633 original size:28 final size:27
Alignment explanation
Indices: 511598--511655 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
511588 TATAATCTTA
511598 TTTAAAATATTTAATATTTATATAAAT
1 TTTAAAATATTTAATATTTATATAAAT
* * *
511625 TTTATAAATTTTTTATATTTATATCAAT
1 TTTA-AAATATTTAATATTTATATAAAT
511653 TTT
1 TTT
511656 TTCCGTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTAAAATATTTAATATTTATATAAAT
Found at i:511916 original size:13 final size:13
Alignment explanation
Indices: 511898--511922 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
511888 CATGCATGCT
511898 AAATAAATTAAAC
1 AAATAAATTAAAC
511911 AAATAAATTAAA
1 AAATAAATTAAA
511923 GTTACGAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAATTAAAC
Found at i:517482 original size:13 final size:13
Alignment explanation
Indices: 517464--517568 Score: 59
Period size: 13 Copynumber: 8.4 Consensus size: 13
517454 AGAATTTTAT
517464 TTAATATAAATTA
1 TTAATATAAATTA
517477 TTAATAATATAATTA
1 TTAAT-ATA-AATTA
*
517492 TATAA-ATAAAATAA
1 T-TAATAT-AAATTA
517506 TTAA-ATATAA-TA
1 TTAATATA-AATTA
517518 -TAATA-AAA-TA
1 TTAATATAAATTA
*
517528 TAAATATAAATT-
1 TTAATATAAATTA
*
517540 TTAA-AT--TTTA
1 TTAATATAAATTA
517550 TTTAATATAAATTA
1 -TTAATATAAATTA
517564 TTAAT
1 TTAAT
517569 TAATAAAATT
Statistics
Matches: 72, Mismatches: 6, Indels: 28
0.68 0.06 0.26
Matches are distributed among these distances:
9 2 0.03
10 4 0.06
11 14 0.19
12 11 0.15
13 18 0.25
14 13 0.18
15 7 0.10
16 3 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAATATAAATTA
Found at i:517508 original size:29 final size:29
Alignment explanation
Indices: 517466--517533 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
517456 AATTTTATTT
*
517466 AATATAAATTATTAATAATATAAT-T-ATATA
1 AATATAAATAATT-A-AATATAATATAATA-A
517496 AATA-AAATAATTAAATATAATATAATAA
1 AATATAAATAATTAAATATAATATAATAA
517524 AATATAAATA
1 AATATAAATA
517534 TAAATTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
27 8 0.24
28 7 0.21
29 15 0.44
30 4 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
AATATAAATAATTAAATATAATATAATAA
Found at i:517550 original size:87 final size:91
Alignment explanation
Indices: 517456--517626 Score: 244
Period size: 87 Copynumber: 1.9 Consensus size: 91
517446 TTATATAAAG
* *
517456 AATTTTATTTAATATAAATTATTAA-TAATATAA-TTATATAA-ATAAAATA-ATTAAATATAAT
1 AATTTTATTTAATATAAATTATTAATTAATAAAATTTATAAAATATAAAATATATTAAATATAAT
517517 -ATAATAAAATATAAATATAAATTTTA
66 CATAATAAAATA-AAATATAAATTTTA
*
517543 AATTTTATTTAATATAAATTATTAATTAATAAAATTTTTATAAAATATAAAATATTTTAAATATA
1 AATTTTATTTAATATAAATTATTAATTAATAAAA--TTTATAAAATATAAAATATATTAAATATA
*
517608 ATCATAATATAATAAAATA
64 ATCATAATAAAATAAAATA
517627 CATCGATCGT
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
87 25 0.34
88 7 0.10
91 7 0.10
92 8 0.11
93 16 0.22
94 10 0.14
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (91 bp):
AATTTTATTTAATATAAATTATTAATTAATAAAATTTATAAAATATAAAATATATTAAATATAAT
CATAATAAAATAAAATATAAATTTTA
Found at i:517556 original size:34 final size:35
Alignment explanation
Indices: 517480--517561 Score: 87
Period size: 34 Copynumber: 2.3 Consensus size: 35
517470 TAAATTATTA
517480 ATAATATAATTATATAAATAAAATAATTAAATATAAT
1 ATAATATAA--ATATAAATAAAATAATTAAATATAAT
* * *
517517 ATAATA-AAATATAAATATAAAT-TTTAAATTTTAT
1 ATAATATAAATATAAATA-AAATAATTAAATATAAT
*
517551 TTAATATAAAT
1 ATAATATAAAT
517562 TATTAATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
34 23 0.59
35 8 0.21
36 2 0.05
37 6 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (35 bp):
ATAATATAAATATAAATAAAATAATTAAATATAAT
Found at i:517590 original size:33 final size:29
Alignment explanation
Indices: 517520--517598 Score: 77
Period size: 33 Copynumber: 2.6 Consensus size: 29
517510 ATATAATATA
* *
517520 ATAAAATATAAATATAAATTTTAAATTTT
1 ATAAAATATAAATATTAATTTAAAATTTT
**
517549 ATTTAATATAAATTATTAATTAATAAAATTTTT
1 ATAAAATATAAA-TATTAATT--TAAAA-TTTT
517582 ATAAAATATAAAATATT
1 ATAAAATAT-AAATATT
517599 TTAAATATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
29 10 0.26
30 7 0.18
32 4 0.10
33 15 0.38
34 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
ATAAAATATAAATATTAATTTAAAATTTT
Found at i:517604 original size:16 final size:18
Alignment explanation
Indices: 517571--517608 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
517561 TTATTAATTA
*
517571 ATAAAATTTTTATAAAAT
1 ATAAAATATTTATAAAAT
517589 ATAAAATATTT-T-AAAT
1 ATAAAATATTTATAAAAT
517605 ATAA
1 ATAA
517609 TCATAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 1 0.05
18 10 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAAAATATTTATAAAAT
Found at i:518093 original size:36 final size:36
Alignment explanation
Indices: 518052--518128 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
518042 TTATACGTAA
518052 TATTTATAATCAAATCTAAATAATAAAAAAACAAAT
1 TATTTATAATCAAATCTAAATAATAAAAAAACAAAT
*
518088 TATTTATAATCAAATCTAAATAATAAAAAAATAAAT
1 TATTTATAATCAAATCTAAATAATAAAAAAACAAAT
518124 TATTT
1 TATTT
518129 TTGTTATTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (36 bp):
TATTTATAATCAAATCTAAATAATAAAAAAACAAAT
Found at i:521708 original size:40 final size:40
Alignment explanation
Indices: 521619--521708 Score: 96
Period size: 40 Copynumber: 2.2 Consensus size: 40
521609 TCTATCAGTT
*
521619 TTTAATTATATAAAAAATATTATATTTATATATTATTAAA
1 TTTAATTATATAAAAAATAATATATTTATATATTATTAAA
* *
521659 TTTATATTAT-TTAAAAATAA-ATATATTATATTATATGTTAAA
1 TTTA-ATTATATAAAAAATAATATAT-TTATA-TAT-TATTAAA
521701 -TTAATTAT
1 TTTAATTAT
521709 GTTTTAGAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
39 4 0.09
40 22 0.51
41 11 0.26
42 6 0.14
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (40 bp):
TTTAATTATATAAAAAATAATATATTTATATATTATTAAA
Found at i:522929 original size:3 final size:3
Alignment explanation
Indices: 522921--522950 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
522911 GTCTAAAGTT
522921 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
522951 TTACAAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:524505 original size:2 final size:2
Alignment explanation
Indices: 524498--524536 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
524488 AGTCCGAGTA
524498 AT AT 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 AT AT A
524537 GAGAGAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:524541 original size:2 final size:2
Alignment explanation
Indices: 524536--524574 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
524526 ATATATATAT
524536 AG 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 AG A
524575 TATTATATAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:537185 original size:2 final size:2
Alignment explanation
Indices: 537178--537203 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
537168 ATCTTAAATT
537178 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
537204 ATGAAAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.