Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold140
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: 3130556
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82166 characters in sequence are not A, C, G, or T
File 1 of 20
Found at i:4672 original size:16 final size:18
Alignment explanation
Indices: 4634--4672 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
4624 CCCAAGCGCG
4634 CATATATATATATATAAA
1 CATATATATATATATAAA
*
4652 TATATATATATA-AT-AA
1 CATATATATATATATAAA
4668 CATAT
1 CATAT
4673 TTTAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 6 0.32
17 2 0.11
18 11 0.58
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (18 bp):
CATATATATATATATAAA
Found at i:15346 original size:16 final size:17
Alignment explanation
Indices: 15317--15364 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 17
15307 TCAATTATCA
*
15317 TTTAATTATATTATGATT
1 TTTAATT-TATTATAATT
15335 TTTAATTT-TTATAATT
1 TTTAATTTATTATAATT
15351 TATTAATTTGATTA
1 T-TTAATTT-ATTA
15365 ATGTATGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 8 0.31
17 8 0.31
18 7 0.27
19 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (17 bp):
TTTAATTTATTATAATT
Found at i:15808 original size:18 final size:18
Alignment explanation
Indices: 15785--15868 Score: 65
Period size: 18 Copynumber: 4.9 Consensus size: 18
15775 TATGTTATTT
15785 TATATTATATAATTTTTA
1 TATATTATATAATTTTTA
15803 TATATTA-ATAA---TTA
1 TATATTATATAATTTTTA
*
15817 -ATATTATATTAATTTTAA
1 TATATTATA-TAATTTTTA
* *
15835 AATATT-TAAATATTTTTA
1 TATATTATATA-ATTTTTA
15853 TAT-TATATATAATTTT
1 TATAT-TATATAATTTT
15869 AATTTTTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
13 6 0.12
14 4 0.08
15 3 0.06
17 6 0.12
18 25 0.48
19 8 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATTATATAATTTTTA
Found at i:21591 original size:21 final size:21
Alignment explanation
Indices: 21567--21627 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 21
21557 AATCAAATGT
* *
21567 AAATATATATAAATTTTTAAA
1 AAATATATATAAATATTAAAA
21588 AAATATAT-TAAA-ATTAAAA
1 AAATATATATAAATATTAAAA
21607 AAAT-TAATATAAATATATAAA
1 AAATAT-ATATAAATAT-TAAA
21628 TATATCAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 1 0.03
19 11 0.32
20 8 0.24
21 10 0.29
22 4 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATATATATAAATATTAAAA
Found at i:21624 original size:8 final size:8
Alignment explanation
Indices: 21613--21667 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
21603 AAAAAAATTA
21613 ATATAAAT
1 ATATAAAT
21621 ATATAAAT
1 ATATAAAT
21629 ATATCAAA-
1 ATAT-AAAT
* *
21637 ATTTATAT
1 ATATAAAT
21645 AATATAAAT
1 -ATATAAAT
*
21654 -TATTAAT
1 ATATAAAT
21661 ATATAAA
1 ATATAAA
21668 ACAGGAGATC
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
7 8 0.22
8 20 0.54
9 9 0.24
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (8 bp):
ATATAAAT
Found at i:28770 original size:2 final size:2
Alignment explanation
Indices: 28763--28790 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28753 TTTATTTAAT
28763 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
28791 AAGTTTTGCT
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:29183 original size:21 final size:23
Alignment explanation
Indices: 29141--29183 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
29131 CTAGCATACT
* *
29141 AAAATTAATTTAAACCTTAAAAC
1 AAAATTAATTTAAACATCAAAAC
29164 AAAATT-A-TTAAACATCAAAA
1 AAAATTAATTTAAACATCAAAA
29184 GCTCCATCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 1 0.06
23 6 0.33
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAATTAATTTAAACATCAAAAC
Found at i:40167 original size:4 final size:4
Alignment explanation
Indices: 40158--40190 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
40148 AGGGAGGTGG
40158 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A-AA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
40191 CCGAGAGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:42138 original size:22 final size:23
Alignment explanation
Indices: 42111--42153 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
42101 TTATATTAAA
42111 TTAAATTTAAA-TAAAGTAATAT
1 TTAAATTTAAATTAAAGTAATAT
*
42133 TTAAATTTAAATTAAATTAAT
1 TTAAATTTAAATTAAAGTAAT
42154 TATTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TTAAATTTAAATTAAAGTAATAT
Found at i:42193 original size:11 final size:11
Alignment explanation
Indices: 42177--42220 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
42167 ACAAATTATT
42177 TAAAATTAATA
1 TAAAATTAATA
42188 TAAAA-T-ATA
1 TAAAATTAATA
42197 TAAATATTAATA
1 TAAA-ATTAATA
*
42209 TAAAAATAATA
1 TAAAATTAATA
42220 T
1 T
42221 TTTAATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
9 7 0.24
10 2 0.07
11 13 0.45
12 7 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TAAAATTAATA
Found at i:42205 original size:21 final size:21
Alignment explanation
Indices: 42160--42213 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
42150 TAATTATTAT
* * *
42160 ATATTAA-ACAAATTATTTAA
1 ATATTAATATAAAATATATAA
42180 A-ATTAATATAAAATATATAA
1 ATATTAATATAAAATATATAA
42200 ATATTAATATAAAA
1 ATATTAATATAAAA
42214 ATAATATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.17
20 12 0.41
21 12 0.41
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
ATATTAATATAAAATATATAA
Found at i:42448 original size:4 final size:4
Alignment explanation
Indices: 42439--42463 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
42429 TGAAAACGCC
42439 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
42464 GTTGAAACTA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:44382 original size:14 final size:14
Alignment explanation
Indices: 44358--44393 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
44348 TAATCGGATT
44358 AAATTAA-ATTTTA
1 AAATTAATATTTTA
44371 AAATTAATATTTTA
1 AAATTAATATTTTA
*
44385 AATTTAATA
1 AAATTAATA
44394 AATAGTTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATTAATATTTTA
Found at i:46273 original size:2 final size:2
Alignment explanation
Indices: 46266--46292 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
46256 TCAATACATA
46266 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 A
46293 AAATCTTGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59651 original size:64 final size:62
Alignment explanation
Indices: 59553--59675 Score: 153
Period size: 64 Copynumber: 2.0 Consensus size: 62
59543 CACTCTATCG
*
59553 TAATCATAAAAATAAAAATAAAATTTTTTAAATATAATATTAAAAATA-ATTAAAATTTAATT
1 TAATCATAAAAATAAAAATAAAATTTTATAAATATAA-ATTAAAAATATATTAAAATTTAATT
**
59615 TAAT-ATAAAAATAAATATTATAAAA-TTTATATAATATAAATTATTAATATATTAAAATTTA
1 TAATCATAAAAATAAA-A--ATAAAATTTTATA-AATATAAATTAAAAATATATTAAAATTTA
59676 TATAAAATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
61 11 0.21
62 5 0.09
63 13 0.25
64 24 0.45
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.41
Consensus pattern (62 bp):
TAATCATAAAAATAAAAATAAAATTTTATAAATATAAATTAAAAATATATTAAAATTTAATT
Found at i:59654 original size:16 final size:16
Alignment explanation
Indices: 59598--59680 Score: 66
Period size: 16 Copynumber: 5.2 Consensus size: 16
59588 AATATTAAAA
59598 ATAAT-TAAAATTTAAT
1 ATAATATAAAATTT-AT
* * *
59614 TTAATATAAAA-ATAA
1 ATAATATAAAATTTAT
*
59629 ATATTATAAAATTTAT
1 ATAATATAAAATTTAT
*
59645 ATAATATAAATTATTA-
1 ATAATATAAAAT-TTAT
59661 AT-ATATTAAAATTTAT
1 ATAATA-TAAAATTTAT
59677 ATAA
1 ATAA
59681 AATATTTTAA
Statistics
Matches: 51, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
15 16 0.31
16 26 0.51
17 9 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAATATAAAATTTAT
Found at i:59664 original size:32 final size:31
Alignment explanation
Indices: 59553--59680 Score: 104
Period size: 32 Copynumber: 4.1 Consensus size: 31
59543 CACTCTATCG
*
59553 TAATCATAAAAATAAA-A-A-TAAAATTT-TT
1 TAAT-ATAAAAATAAATATATTAAAATTTATA
* * * *
59581 TAAATATAATATTAAAAATAATTAAAATTTAATT
1 T-AATATAAAAATAAATAT-ATTAAAATTT-ATA
59615 TAATATAAAAATAAATAT-TATAAAATTTATA
1 TAATATAAAAATAAATATAT-TAAAATTTATA
* *
59646 TAATATAAATTATTAATATATTAAAATTTATA
1 TAATATAAA-AATAAATATATTAAAATTTATA
59678 TAA
1 TAA
59681 AATATTTTAA
Statistics
Matches: 82, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
28 10 0.12
29 4 0.05
31 13 0.16
32 37 0.45
33 15 0.18
34 3 0.04
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.41
Consensus pattern (31 bp):
TAATATAAAAATAAATATATTAAAATTTATA
Found at i:61499 original size:22 final size:21
Alignment explanation
Indices: 61473--61529 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
61463 AAAATTAAAA
61473 ATATATTTTTATATTAATATTT
1 ATATATTTTTATATTAA-ATTT
61495 ATATA-TTTTATAATTAAATTT
1 ATATATTTTTAT-ATTAAATTT
*
61516 AAATATTTTT-TATT
1 ATATATTTTTATATT
61530 TATTAAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.09
21 15 0.47
22 14 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATATTTTTATATTAAATTT
Found at i:61676 original size:11 final size:11
Alignment explanation
Indices: 61662--61700 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
61652 TAAGTTCGAT
61662 TTAATTTTATA
1 TTAATTTTATA
*
61673 TTAATTTTGT-
1 TTAATTTTATA
*
61683 TTAATTATATA
1 TTAATTTTATA
61694 TTAATTT
1 TTAATTT
61701 ATTAATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (11 bp):
TTAATTTTATA
Found at i:61685 original size:21 final size:21
Alignment explanation
Indices: 61661--61700 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
61651 TTAAGTTCGA
*
61661 TTTAATTTTATATTAATTTTG
1 TTTAATTATATATTAATTTTG
61682 TTTAATTATATATTAATTT
1 TTTAATTATATATTAATTT
61701 ATTAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (21 bp):
TTTAATTATATATTAATTTTG
Found at i:63032 original size:2 final size:2
Alignment explanation
Indices: 63025--63049 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
63015 AAAACCATCA
63025 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 A
63050 TATTGTTCTT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:68527 original size:40 final size:40
Alignment explanation
Indices: 68446--68527 Score: 96
Period size: 40 Copynumber: 2.0 Consensus size: 40
68436 ATTGTTTTAA
* ** *
68446 AATTTATTTTTGAAAATATTTATAATTAATATTTATGTTT
1 AATTTATTTTTAAAAATAAATATAATTAATAATTATGTTT
68486 AATTTATTTTTAAAAATAAATATTAA-TATATAATTAT-TTT
1 AATTTATTTTTAAAAATAAATA-TAATTA-ATAATTATGTTT
68526 AA
1 AA
68528 AATTTTTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
40 26 0.72
41 10 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (40 bp):
AATTTATTTTTAAAAATAAATATAATTAATAATTATGTTT
Found at i:68554 original size:19 final size:19
Alignment explanation
Indices: 68526--68571 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
68516 TAATTATTTT
* * *
68526 AAAATTTTTTAAATATATA
1 AAAATATTTTAAAAAAATA
68545 AAAATATTTTAAAAAAATA
1 AAAATATTTTAAAAAAATA
*
68564 AATATATT
1 AAAATATT
68572 CATATTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATATTTTAAAAAAATA
Found at i:70520 original size:20 final size:20
Alignment explanation
Indices: 70495--70532 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
70485 AAATTGACTT
70495 TTAAACTTAGTATCAACACG
1 TTAAACTTAGTATCAACACG
70515 TTAAACTTAGTATCAACA
1 TTAAACTTAGTATCAACA
70533 GAAATTGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (20 bp):
TTAAACTTAGTATCAACACG
Found at i:71406 original size:15 final size:15
Alignment explanation
Indices: 71388--71442 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
71378 TGTTGAAGAA
71388 GAAGATGAACCAGAC
1 GAAGATGAACCAGAC
** *
71403 GAAGATGTTGAAATAGAT
1 GAAGA---TGAACCAGAC
71421 GAAGATGAACCAGAC
1 GAAGATGAACCAGAC
71436 GAAGATG
1 GAAGATG
71443 TTGAAATAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
15 19 0.61
18 12 0.39
ACGTcount: A:0.45, C:0.11, G:0.29, T:0.15
Consensus pattern (15 bp):
GAAGATGAACCAGAC
Found at i:71406 original size:18 final size:18
Alignment explanation
Indices: 71385--71440 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
71375 AGATGTTGAA
71385 GAAGAAGATGAACCAGAC
1 GAAGAAGATGAACCAGAC
* * *
71403 GAAGATGTTGAA--ATA-
1 GAAGAAGATGAACCAGAC
*
71418 GATGAAGATGAACCAGAC
1 GAAGAAGATGAACCAGAC
71436 GAAGA
1 GAAGA
71441 TGTTGAAATA
Statistics
Matches: 27, Mismatches: 8, Indels: 6
0.66 0.20 0.15
Matches are distributed among these distances:
15 9 0.33
16 2 0.07
17 2 0.07
18 14 0.52
ACGTcount: A:0.48, C:0.11, G:0.29, T:0.12
Consensus pattern (18 bp):
GAAGAAGATGAACCAGAC
Found at i:71425 original size:33 final size:33
Alignment explanation
Indices: 71388--71462 Score: 150
Period size: 33 Copynumber: 2.3 Consensus size: 33
71378 TGTTGAAGAA
71388 GAAGATGAACCAGACGAAGATGTTGAAATAGAT
1 GAAGATGAACCAGACGAAGATGTTGAAATAGAT
71421 GAAGATGAACCAGACGAAGATGTTGAAATAGAT
1 GAAGATGAACCAGACGAAGATGTTGAAATAGAT
71454 GAAGATGAA
1 GAAGATGAA
71463 GACTTTGTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.47, C:0.08, G:0.28, T:0.17
Consensus pattern (33 bp):
GAAGATGAACCAGACGAAGATGTTGAAATAGAT
Found at i:71457 original size:18 final size:18
Alignment explanation
Indices: 71403--71460 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
71393 TGAACCAGAC
71403 GAAGATGTTGAAATAGAT
1 GAAGATGTTGAAATAGAT
** *
71421 GAAGA---TGAACCAGAC
1 GAAGATGTTGAAATAGAT
71436 GAAGATGTTGAAATAGAT
1 GAAGATGTTGAAATAGAT
71454 GAAGATG
1 GAAGATG
71461 AAGACTTTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
15 12 0.39
18 19 0.61
ACGTcount: A:0.45, C:0.05, G:0.29, T:0.21
Consensus pattern (18 bp):
GAAGATGTTGAAATAGAT
Found at i:73773 original size:13 final size:13
Alignment explanation
Indices: 73755--73779 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
73745 GTTGTATTTT
73755 TTTAATATTTATA
1 TTTAATATTTATA
73768 TTTAATATTTAT
1 TTTAATATTTAT
73780 TAAAATATAA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTAATATTTATA
Found at i:73833 original size:19 final size:19
Alignment explanation
Indices: 73809--73845 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
73799 ATAATTTTTT
*
73809 AAAATTTTTAAATATATAA
1 AAAATTTTAAAATATATAA
73828 AAAATTTTAAAATATATA
1 AAAATTTTAAAATATATA
73846 TATTTATACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATTTTAAAATATATAA
Found at i:74073 original size:2 final size:2
Alignment explanation
Indices: 74066--74098 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
74056 CACCAATTTC
*
74066 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
74099 CACACACAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:75290 original size:13 final size:13
Alignment explanation
Indices: 75272--75297 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
75262 GGGCAATTAG
75272 CTTTTTTTTTTTT
1 CTTTTTTTTTTTT
75285 CTTTTTTTTTTTT
1 CTTTTTTTTTTTT
75298 TTGAACTCTA
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
CTTTTTTTTTTTT
Found at i:88328 original size:23 final size:21
Alignment explanation
Indices: 88302--88379 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 21
88292 AGATAATAAG
88302 TATTTCATCATTTAATATAAAAA
1 TATTT-AT-ATTTAATATAAAAA
**
88325 TATTATATTATTTAA-ATTTAAA
1 TATT-TA-TATTTAATATAAAAA
* *
88347 TAATTATATTTAATATAAATA
1 TATTTATATTTAATATAAAAA
*
88368 TATATAT-TTTAA
1 TATTTATATTTAA
88380 ATTTTTTAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
20 12 0.27
21 11 0.25
22 8 0.18
23 11 0.25
24 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTTATATTTAATATAAAAA
Found at i:88367 original size:19 final size:20
Alignment explanation
Indices: 88274--88381 Score: 67
Period size: 23 Copynumber: 5.0 Consensus size: 20
88264 CGTGTATATT
* *
88274 TATATATATATATATATTAGA
1 TATAAATATATATAT-TTAAA
* *
88295 TAATAAGTATTTCATCATTTAATA
1 T-ATAAATATAT-AT-ATTTAA-A
*
88319 TAAAAATATTATATTATTTAAA
1 TATAAATA-TATA-TATTTAAA
*
88341 TTTAAATA-ATTATATTT-AA
1 TATAAATATA-TATATTTAAA
88360 TATAAATATATATATTTTAAA
1 TATAAATATATATA-TTTAAA
88381 T
1 T
88382 TTTTTAATAT
Statistics
Matches: 67, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
19 13 0.19
20 10 0.15
21 6 0.09
22 14 0.21
23 17 0.25
24 7 0.10
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
TATAAATATATATATTTAAA
Found at i:88388 original size:43 final size:40
Alignment explanation
Indices: 88311--88399 Score: 94
Period size: 43 Copynumber: 2.1 Consensus size: 40
88301 GTATTTCATC
88311 ATTTAATATAAAAATATTATATTATTTAAATTTAAATAATTA
1 ATTTAATATAAAAATATTATATTATTTAAATTT-AAT-ATTA
*
88353 TATTTAATATAAATATA-TATA-T-TTTAAATTTTTTAATATTA
1 -ATTTAATATAAAAATATTATATTATTTAAA---TTTAATATTA
88394 ATTTAA
1 ATTTAA
88400 AAAATTAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
40 12 0.29
41 5 0.12
42 7 0.17
43 18 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (40 bp):
ATTTAATATAAAAATATTATATTATTTAAATTTAATATTA
Found at i:94343 original size:22 final size:23
Alignment explanation
Indices: 94296--94346 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
94286 TAAAATATTT
* *
94296 TTTAAATAATTATACTTTAAATAA
1 TTTAAAAAATTATA-TTTAAAAAA
94320 TTTAAAAAATTAT-TTTAAAAAA
1 TTTAAAAAATTATATTTAAAAAA
94342 TTTAA
1 TTTAA
94347 TAATTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 13 0.52
24 12 0.48
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAAAAAATTATATTTAAAAAA
Found at i:95054 original size:2 final size:2
Alignment explanation
Indices: 95047--95097 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
95037 AAAATTAACA
95047 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
95089 AG AG AG AG A
1 AG AG AG AG A
95098 TTTGAACTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:103020 original size:2 final size:2
Alignment explanation
Indices: 103013--103055 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
103003 GTCTTTGCAC
103013 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
103055 A
1 A
103056 AATAGAGAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:103269 original size:17 final size:16
Alignment explanation
Indices: 103213--103269 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 16
103203 ATTGATCTTC
103213 AATATTATTAAA-TTA
1 AATATTATTAAATTTA
*
103228 AATATAACATTAATATTT-
1 AATAT--TATTAA-ATTTA
103246 AATATTATTAAATTTA
1 AATATTATTAAATTTA
103262 AGATATTA
1 A-ATATTA
103270 AAAATATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
15 9 0.26
16 6 0.18
17 11 0.32
18 6 0.18
19 2 0.06
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (16 bp):
AATATTATTAAATTTA
Found at i:103696 original size:15 final size:15
Alignment explanation
Indices: 103676--103715 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
103666 TAGTTATCTC
103676 AGGAATCATGTTCTA
1 AGGAATCATGTTCTA
*
103691 AGGAATCATGTTCTC
1 AGGAATCATGTTCTA
103706 AGGAATCATG
1 AGGAATCATG
103716 CAGAGCCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (15 bp):
AGGAATCATGTTCTA
Found at i:108545 original size:21 final size:20
Alignment explanation
Indices: 108516--108554 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
108506 GATAAATTTA
108516 ATTAAATTAAAATTTAAATAT
1 ATTAAATT-AAATTTAAATAT
* *
108537 ATTATATTATATTTAAAT
1 ATTAAATTAAATTTAAAT
108555 TTAATTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTAAATTAAATTTAAATAT
Found at i:116533 original size:16 final size:16
Alignment explanation
Indices: 116502--116534 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
116492 ATTGATTTAT
116502 ATAATTATTTTAAAAA
1 ATAATTATTTTAAAAA
*
116518 ATAA-TATTTTATAAA
1 ATAATTATTTTAAAAA
116533 AT
1 AT
116535 TTAAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAATTATTTTAAAAA
Found at i:118627 original size:20 final size:20
Alignment explanation
Indices: 118602--118650 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
118592 AGTATTTTTA
118602 TAAAAATATTTAATTTAT-TT
1 TAAAAATATTT-ATTTATATT
*
118622 TAAAAAT-TTTGTTTATATT
1 TAAAAATATTTATTTATATT
118641 TAAAAA-ATTT
1 TAAAAATATTT
118651 TAAAAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 5 0.19
19 14 0.54
20 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TAAAAATATTTATTTATATT
Found at i:121098 original size:22 final size:23
Alignment explanation
Indices: 121073--121119 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
121063 AGTTTTTGTT
121073 AATTAATTT-A-TTTAATTTTATA
1 AATTAATTTAATTTTAATTTT-TA
121095 AATTAATTTAATTTTAATTTTTA
1 AATTAATTTAATTTTAATTTTTA
121118 AA
1 AA
121120 ATTTCAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.39
23 5 0.22
24 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
AATTAATTTAATTTTAATTTTTA
Found at i:121889 original size:14 final size:14
Alignment explanation
Indices: 121844--121890 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
121834 AAGATCGTAA
*
121844 ATAAAATAAAATAT
1 ATAAAATATAATAT
* *
121858 GAAAAAATAT-ATAA
1 -ATAAAATATAATAT
121872 ATAAAATATAATAT
1 ATAAAATATAATAT
121886 ATAAA
1 ATAAA
121891 TATGTTAAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
13 8 0.31
14 11 0.42
15 7 0.27
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (14 bp):
ATAAAATATAATAT
Found at i:121891 original size:13 final size:11
Alignment explanation
Indices: 121842--121893 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 11
121832 ATAAGATCGT
121842 AAATA-AAATA
1 AAATATAAATA
121852 AAATATGAAA-A
1 AAATAT-AAATA
121863 AATATATAAATA
1 AA-ATATAAATA
121875 AAATATAATATA
1 AAATATAA-ATA
121887 TAAATAT
1 -AAATAT
121894 GTTAAAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
10 5 0.14
11 12 0.33
12 13 0.36
13 6 0.17
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (11 bp):
AAATATAAATA
Found at i:121913 original size:37 final size:38
Alignment explanation
Indices: 121871--121968 Score: 96
Period size: 37 Copynumber: 2.6 Consensus size: 38
121861 AAAATATATA
*
121871 AATAAAATATAATATATAAATATGTTAAAGTTTAT-ATGAT
1 AATAAAATATAATATATAAATATGTTAAA---TATGATTAT
* *
121911 AA-AAATTATTAATATAT-AATATTTTAAATATGATTAT
1 AATAAAATA-TAATATATAAATATGTTAAATATGATTAT
*
121948 AATAAAAAATAATATA-AAATA
1 AATAAAATATAATATATAAATA
121969 AAATATGAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
36 3 0.06
37 17 0.35
38 4 0.08
39 15 0.31
40 10 0.20
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (38 bp):
AATAAAATATAATATATAAATATGTTAAATATGATTAT
Found at i:121981 original size:18 final size:18
Alignment explanation
Indices: 121936--121983 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
121926 ATAATATTTT
*
121936 AAATATG-AT-TATAATA
1 AAATATGAATATAAAATA
*
121952 AAAAAT-AATATAAAATA
1 AAATATGAATATAAAATA
121969 AAATATGAATATAAA
1 AAATATGAATATAAA
121984 TTATTTGATC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 7 0.27
17 11 0.42
18 8 0.31
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (18 bp):
AAATATGAATATAAAATA
Found at i:123627 original size:3 final size:3
Alignment explanation
Indices: 123619--123659 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
123609 TGAGTCTTGG
123619 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
123660 TTATCCGAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:126314 original size:15 final size:14
Alignment explanation
Indices: 126294--126327 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
126284 TGATATAAAT
126294 TATATAATATATATA
1 TATATAATAT-TATA
126309 TATATAATATTATA
1 TATATAATATTATA
126323 T-TATA
1 TATATA
126328 CAATTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.21
14 5 0.26
15 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATAATATTATA
Found at i:130153 original size:21 final size:21
Alignment explanation
Indices: 130129--130195 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
130119 TTTATGTTTT
**
130129 ATATATATTTTATTATAATAA
1 ATATATATAATATTATAATAA
130150 ATATATATAATATTATAATATA
1 ATATATATAATATTATAATA-A
* *
130172 A-ATATTAAAAAATATATAATAA
1 ATATA-TATAATAT-TATAATAA
130194 AT
1 AT
130196 TATTTATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
21 21 0.55
22 10 0.26
23 7 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATATATAATATTATAATAA
Found at i:130158 original size:23 final size:23
Alignment explanation
Indices: 130128--130176 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
130118 TTTTATGTTT
* *
130128 TATATAT-ATTTTATTATAATAAA
1 TATATATAATATTATAAT-ATAAA
130151 TATATATAATATTATAATATAAA
1 TATATATAATATTATAATATAAA
130174 TAT
1 TAT
130177 TAAAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TATATATAATATTATAATATAAA
Found at i:130226 original size:37 final size:36
Alignment explanation
Indices: 130148--130253 Score: 109
Period size: 37 Copynumber: 3.0 Consensus size: 36
130138 TTATTATAAT
*
130148 AAATATAT-ATAATATTA-TAA-TA-TAAATATTAAA
1 AAATATATAATAA-ATTATTAATTATTAAATTTTAAA
130181 AAATATATAATAAATTATTTATATT-TTAAATTTTAATA
1 AAATATATAATAAATTA-TTA-ATTATTAAATTTTAA-A
*
130219 AAA-ATATAATTAATTATTAATTATTAAA-TTTAAA
1 AAATATATAATAAATTATTAATTATTAAATTTTAAA
130253 A
1 A
130254 TATTTTTTAA
Statistics
Matches: 63, Mismatches: 2, Indels: 15
0.79 0.03 0.19
Matches are distributed among these distances:
33 12 0.19
34 6 0.10
35 10 0.16
36 9 0.14
37 22 0.35
38 4 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (36 bp):
AAATATATAATAAATTATTAATTATTAAATTTTAAA
Found at i:130355 original size:24 final size:25
Alignment explanation
Indices: 130308--130355 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
130298 ATATAAAAAA
* **
130308 TTAAAATATAATTTATATTTATATT
1 TTAAAATATAATTTAAATAAATATT
130333 TTAAAAT-TAATTTAAATAAATAT
1 TTAAAATATAATTTAAATAAATAT
130356 AAATAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TTAAAATATAATTTAAATAAATATT
Found at i:130583 original size:21 final size:20
Alignment explanation
Indices: 130537--130585 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
130527 ATTAAATTAA
130537 AATTAAATAATATAAAGTTT
1 AATTAAATAATATAAAGTTT
*
130557 ATTTAAATAATTTATAAA-TTT
1 AATTAAATAA--TATAAAGTTT
130578 AATTAAAT
1 AATTAAAT
130586 TTTTAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.36
21 10 0.40
22 6 0.24
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
AATTAAATAATATAAAGTTT
Found at i:130627 original size:33 final size:32
Alignment explanation
Indices: 130575--130636 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
130565 AATTTATAAA
**
130575 TTTAATTAAATTTTTAATT-AATATTAAAAAAT
1 TTTAATTAAATTTAAAATTAAATA-TAAAAAAT
130607 TTTAATTTAAATTTAAAATTAAATATAAAA
1 TTTAA-TTAAATTTAAAATTAAATATAAAA
130637 TTGATTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 5 0.19
33 17 0.65
34 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
TTTAATTAAATTTAAAATTAAATATAAAAAAT
Found at i:131802 original size:25 final size:26
Alignment explanation
Indices: 131774--131828 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
131764 GGTATGGATC
131774 CTTC-CATAGTTTTTTCATCCAATCA
1 CTTCGCATAGTTTTTTCATCCAATCA
* *
131799 CTTCGCCTAGTTTTTTCATCTAATCA
1 CTTCGCATAGTTTTTTCATCCAATCA
131825 CTTC
1 CTTC
131829 ACCATCTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 4 0.15
26 23 0.85
ACGTcount: A:0.20, C:0.29, G:0.05, T:0.45
Consensus pattern (26 bp):
CTTCGCATAGTTTTTTCATCCAATCA
Found at i:133167 original size:2 final size:2
Alignment explanation
Indices: 133160--133195 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
133150 TTCTAGTTTG
133160 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
133196 TGCTGTGTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:135145 original size:2 final size:2
Alignment explanation
Indices: 135138--135162 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
135128 AGTTATGGGG
135138 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
135163 TTAATTGTGA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:135975 original size:39 final size:39
Alignment explanation
Indices: 135932--136065 Score: 144
Period size: 39 Copynumber: 3.4 Consensus size: 39
135922 GGCTCAATAC
* * ** * *
135932 AAAGTGAAACAGAAAAGCCTGATTCTGTTGGTTTGGCAG
1 AAAGTGAAACAGAAAAGCCCGATTCTGCTCATTCGACAG
* *
135971 AAAGTGAAAAAGAAAAGCCCGTTTCTGCTCATTCGACAG
1 AAAGTGAAACAGAAAAGCCCGATTCTGCTCATTCGACAG
* * *
136010 AAAGTGAAACAGAAAAGCCCGTTTCTTG-TCCTTCAACAG
1 AAAGTGAAACAGAAAAGCCCGATTC-TGCTCATTCGACAG
*
136049 AAAGTGAAAGAGAAAAG
1 AAAGTGAAACAGAAAAG
136066 GAGGTGCAGC
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
39 80 0.98
40 2 0.02
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (39 bp):
AAAGTGAAACAGAAAAGCCCGATTCTGCTCATTCGACAG
Found at i:145798 original size:19 final size:18
Alignment explanation
Indices: 145774--145812 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
145764 CGTGATTGGC
145774 TTTTAGCATTTTTACTTTT
1 TTTTAGCATTTTTA-TTTT
145793 TTTTAGCATTTTTATTTT
1 TTTTAGCATTTTTATTTT
145811 TT
1 TT
145813 GGACCACTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.72
Consensus pattern (18 bp):
TTTTAGCATTTTTATTTT
Found at i:146360 original size:11 final size:11
Alignment explanation
Indices: 146346--146381 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
146336 TGTTTTTTGG
146346 TTAATTAATAT
1 TTAATTAATAT
146357 TTAATATAAT-T
1 TTAAT-TAATAT
146368 TTAATTAATAT
1 TTAATTAATAT
146379 TTA
1 TTA
146382 TATTTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.17
11 15 0.65
12 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTAATTAATAT
Found at i:146424 original size:28 final size:28
Alignment explanation
Indices: 146377--146460 Score: 77
Period size: 28 Copynumber: 3.0 Consensus size: 28
146367 TTTAATTAAT
**
146377 ATTTATAT-T-TTAAATTTTATAAATAA
1 ATTTATATATATTAAAAATTATAAATAA
*
146403 ATTTATATATATTAAAAATTAT-TA-AA
1 ATTTATATATATTAAAAATTATAAATAA
*
146429 ATTGATGAATATATTAAAAATTATTAAATAA
1 ATTTAT--ATATATTAAAAATTA-TAAATAA
146460 A
1 A
146461 AAGTATTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
26 15 0.33
27 2 0.04
28 24 0.52
29 1 0.02
30 1 0.02
31 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (28 bp):
ATTTATATATATTAAAAATTATAAATAA
Found at i:146430 original size:26 final size:27
Alignment explanation
Indices: 146401--146456 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 27
146391 TTTTATAAAT
*
146401 AAATTTAT-ATATATTAAAAATTATTA
1 AAATTGATAATATATTAAAAATTATTA
146427 AAATTGATGAATATATTAAAAATTATTA
1 AAATTGAT-AATATATTAAAAATTATTA
146455 AA
1 AA
146457 TAAAAAGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 7 0.26
28 20 0.74
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (27 bp):
AAATTGATAATATATTAAAAATTATTA
Found at i:146568 original size:20 final size:22
Alignment explanation
Indices: 146529--146577 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
146519 TGAAATATAA
*
146529 ATTTTTTAAATTTAATTAAAATT
1 ATTTTTTAAA-TTAATTAAAAAT
146552 ATTTTTTAAA-TAA-TAAAAAT
1 ATTTTTTAAATTAATTAAAAAT
146572 ATTTTT
1 ATTTTT
146578 ATTTAGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 12 0.48
21 3 0.12
23 10 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTTTTAAATTAATTAAAAAT
Found at i:147241 original size:2 final size:2
Alignment explanation
Indices: 147229--147267 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
147219 TTGCAAATGT
*
147229 TA TA CA 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 TA TA T
147268 CTTAACAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:150575 original size:2 final size:2
Alignment explanation
Indices: 150568--150596 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
150558 AGCTACAGCA
150568 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
150597 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:150601 original size:2 final size:2
Alignment explanation
Indices: 150596--150621 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
150586 TCTCTCTCTC
150596 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
150622 CCAGTAGCAA
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
Found at i:151703 original size:131 final size:131
Alignment explanation
Indices: 151469--151734 Score: 514
Period size: 131 Copynumber: 2.0 Consensus size: 131
151459 TTGCGACAAA
*
151469 AAAACACAGTTGCTTCACCCTTACCATGATGGTGTTTAGAAGATAACTCTTTTGCTATTTGATAG
1 AAAACACAGTTGCTTCACCCTTACCATGATGGTATTTAGAAGATAACTCTTTTGCTATTTGATAG
151534 TCTTCTTCAATGGCCGTGAAGAGACTATTTTAGGATTTTCTGGATAAAGTATAGGCTAGAACCCA
66 TCTTCTTCAATGGCCGTGAAGAGACTATTTTAGGATTTTCTGGATAAAGTATAGGCTAGAACCCA
151599 G
131 G
*
151600 AAAACACAGTTGCTTCACCCTTACCTTGATGGTATTTAGAAGATAACTCTTTTGCTATTTGATAG
1 AAAACACAGTTGCTTCACCCTTACCATGATGGTATTTAGAAGATAACTCTTTTGCTATTTGATAG
151665 TCTTCTTCAATGGCCGTGAAGAGACTATTTTAGGATTTTCTGGATAAAGTATAGGCTAGAACCCA
66 TCTTCTTCAATGGCCGTGAAGAGACTATTTTAGGATTTTCTGGATAAAGTATAGGCTAGAACCCA
151730 G
131 G
151731 AAAA
1 AAAA
151735 TTACTGGCCA
Statistics
Matches: 133, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
131 133 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (131 bp):
AAAACACAGTTGCTTCACCCTTACCATGATGGTATTTAGAAGATAACTCTTTTGCTATTTGATAG
TCTTCTTCAATGGCCGTGAAGAGACTATTTTAGGATTTTCTGGATAAAGTATAGGCTAGAACCCA
G
Found at i:153034 original size:23 final size:21
Alignment explanation
Indices: 152986--153034 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
152976 AAAATATATT
* *
152986 AATAAAAAATTAAATTAATTT
1 AATAAAAAATTAAATTAAATA
*
153007 TATAAAAAATTTCAAATTAAATA
1 AATAAAAAA-TT-AAATTAAATA
153030 AATAA
1 AATAA
153035 TTATCTCTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 8 0.36
22 2 0.09
23 12 0.55
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAAAAAATTAAATTAAATA
Found at i:154001 original size:2 final size:2
Alignment explanation
Indices: 153994--154046 Score: 72
Period size: 2 Copynumber: 26.5 Consensus size: 2
153984 CGATGCTTCA
* *
153994 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
154036 -T CAT AT AT AT A
1 AT -AT AT AT AT A
154047 CATACACTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 43 0.96
3 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:154488 original size:22 final size:22
Alignment explanation
Indices: 154444--154495 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
154434 TTATAAATAT
*
154444 TAATATAAATATATAATTAAAA
1 TAATATAAATATATAAATAAAA
*
154466 TAATATAAATATTTAAGAT-AAA
1 TAATATAAATATATAA-ATAAAA
154488 TAA-ATAAA
1 TAATATAAA
154496 ATAAATACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 5 0.19
22 21 0.78
23 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
TAATATAAATATATAAATAAAA
Found at i:155503 original size:10 final size:9
Alignment explanation
Indices: 155468--155519 Score: 52
Period size: 10 Copynumber: 5.4 Consensus size: 9
155458 AATAATTAAA
155468 ATAAAATAT
1 ATAAAATAT
155477 GATATAAATAT
1 -ATA-AAATAT
155488 AT-AAATAT
1 ATAAAATAT
*
155496 ATTAAAATTT
1 A-TAAAATAT
155506 ATATAAATAT
1 ATA-AAATAT
155516 ATAA
1 ATAA
155520 TAATTTGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
8 7 0.19
9 4 0.11
10 19 0.53
11 6 0.17
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (9 bp):
ATAAAATAT
Found at i:155549 original size:17 final size:17
Alignment explanation
Indices: 155506--155559 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 17
155496 ATTAAAATTT
*
155506 ATATAAATAT-ATAATA
1 ATATAAATATAATTATA
* *
155522 ATTTGAA-ATAATTATA
1 ATATAAATATAATTATA
*
155538 ATATAAATATAATTAAA
1 ATATAAATATAATTATA
155555 ATATA
1 ATATA
155560 CGTATCATCA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
15 2 0.07
16 15 0.50
17 13 0.43
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
ATATAAATATAATTATA
Found at i:155959 original size:13 final size:13
Alignment explanation
Indices: 155943--155967 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
155933 TTACTTAAAT
155943 TATTTATAATTAC
1 TATTTATAATTAC
155956 TATTTATAATTA
1 TATTTATAATTA
155968 ATAAAAATTA
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:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTTATAATTAC
Found at i:156012 original size:13 final size:14
Alignment explanation
Indices: 155994--156022 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
155984 TTATAATTTA
155994 TTTTAAATA-TAAT
1 TTTTAAATATTAAT
156007 TTTTAAATATTAAT
1 TTTTAAATATTAAT
156021 TT
1 TT
156023 AAATCAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTAAATATTAAT
Found at i:156380 original size:11 final size:11
Alignment explanation
Indices: 156353--156392 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
156343 AATACAAAAT
156353 ATATATTATTAA
1 ATATATTA-TAA
*
156365 ATATATTATCA
1 ATATATTATAA
*
156376 ATATAATATAA
1 ATATATTATAA
156387 ATATAT
1 ATATAT
156393 AAATATATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (11 bp):
ATATATTATAA
Found at i:157044 original size:119 final size:118
Alignment explanation
Indices: 156677--157015 Score: 624
Period size: 118 Copynumber: 2.9 Consensus size: 118
156667 ATATATATTA
156677 ATTATAATATCAATTTTTATTAATTATTAATTATAATATCAGTATTTGATTAATAATATTAATTT
1 ATTA-AATATCAATTTTTATTAATTATTAATTATAATATCAGTATTTGATTAATAATATTAATTT
156742 AAAATTTTAATATATTTTAACAAAATAAAAATTTAAAATTTTTACTATTATTTT
65 AAAATTTTAATATATTTTAACAAAATAAAAATTTAAAATTTTTACTATTATTTT
*
156796 CTTAAATATCAATTTTTATTAATTATTAATTATAATATCAGTATTTGATTAATAATATTAATTTA
1 ATTAAATATCAATTTTTATTAATTATTAATTATAATATCAGTATTTGATTAATAATATTAATTTA
156861 AAATTTTAATATATTTTAACAAAATAAAAATTTAAAATTTTTACTATTATTTT
66 AAATTTTAATATATTTTAACAAAATAAAAATTTAAAATTTTTACTATTATTTT
*
156914 ATTAAATATCAATTTTTTATTAATTATTAATTATAATATTAGTATTTGATTAATAATATTAATTT
1 ATTAAATATCAA-TTTTTATTAATTATTAATTATAATATCAGTATTTGATTAATAATATTAATTT
* *
156979 AGAATTTTAATATATTTTAACGAAATAAAAATTTAAA
65 AAAATTTTAATATATTTTAACAAAATAAAAATTTAAA
157016 TGTTAAATTA
Statistics
Matches: 214, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
118 125 0.58
119 89 0.42
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (118 bp):
ATTAAATATCAATTTTTATTAATTATTAATTATAATATCAGTATTTGATTAATAATATTAATTTA
AAATTTTAATATATTTTAACAAAATAAAAATTTAAAATTTTTACTATTATTTT
Found at i:158267 original size:22 final size:22
Alignment explanation
Indices: 158241--158283 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
158231 CACTTAAAGG
* *
158241 TTCATTTATTATTTTGATTTTT
1 TTCATTTAATATTTTAATTTTT
158263 TTCATTTAATATTTTAATTTT
1 TTCATTTAATATTTTAATTTT
158284 ATTGGATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (22 bp):
TTCATTTAATATTTTAATTTTT
Found at i:166970 original size:33 final size:33
Alignment explanation
Indices: 166932--167008 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
166922 TATATATACT
*
166932 ATATAAATATATAA-ATATCTCAAAATTTATAT-A
1 ATATAAATATATAACATA-AT-AAAATTTATATAA
* *
166965 ATATAAATTTTTAACATAATAAAATTTATATAA
1 ATATAAATATATAACATAATAAAATTTATATAA
166998 ATATAAA-ATAT
1 ATATAAATATAT
167009 TATAATTATA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
32 13 0.35
33 21 0.57
34 3 0.08
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (33 bp):
ATATAAATATATAACATAATAAAATTTATATAA
Found at i:166974 original size:15 final size:15
Alignment explanation
Indices: 166954--167004 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
166944 AAATATCTCA
166954 AAATTTATATAATAT
1 AAATTTATATAATAT
*
166969 AAATTTTTA-ACATAAT
1 AAATTTATATA-AT-AT
166985 AAAATTTATATAAATAT
1 -AAATTTATAT-AATAT
167002 AAA
1 AAA
167005 ATATTATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 1 0.03
15 10 0.34
16 5 0.17
17 10 0.34
18 2 0.07
19 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATTTATATAATAT
Found at i:167018 original size:16 final size:17
Alignment explanation
Indices: 166910--167046 Score: 55
Period size: 17 Copynumber: 8.4 Consensus size: 17
166900 ATAACATCAC
* *
166910 ATAAAAATATAATATAT
1 ATAAATATAAAATATAT
*
166927 AT-ACTATATAAATATAT
1 ATAAATATA-AAATATAT
* *
166944 A-AATATCTCAAAATTTAT
1 ATAA-ATAT-AAAATATAT
166962 AT-AATAT-AAAT-T-T
1 ATAAATATAAAATATAT
* *
166975 TTAACATAATAAAATTTAT
1 ATAA-AT-ATAAAATATAT
166994 ATAAATATAAAATAT-T
1 ATAAATATAAAATATAT
*
167010 AT-AAT-TATAAT-TAT
1 ATAAATATAAAATATAT
*
167024 A-AAATA-AAAAAATTAT
1 ATAAATATAAAATA-TAT
167040 ATAAATA
1 ATAAATA
167047 CAATACAAAT
Statistics
Matches: 90, Mismatches: 13, Indels: 34
0.66 0.09 0.25
Matches are distributed among these distances:
13 3 0.03
14 15 0.17
15 9 0.10
16 13 0.14
17 31 0.34
18 14 0.16
19 5 0.06
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAAATATAAAATATAT
Found at i:167037 original size:22 final size:22
Alignment explanation
Indices: 166993--167040 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
166983 ATAAAATTTA
** *
166993 TATAAATATAAAATATTATAAT
1 TATAAATATAAAATAAAAAAAT
*
167015 TATAATTATAAAATAAAAAAAT
1 TATAAATATAAAATAAAAAAAT
167037 TATA
1 TATA
167041 TAAATACAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TATAAATATAAAATAAAAAAAT
Found at i:167637 original size:13 final size:13
Alignment explanation
Indices: 167614--167647 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
167604 ATTTTTTTAA
167614 AAAATTATAAATATT
1 AAAATTA-AAAT-TT
167629 AAAATTAAAATTT
1 AAAATTAAAATTT
167642 AAAATT
1 AAAATT
167648 TATTAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 4 0.21
15 7 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:170252 original size:8 final size:8
Alignment explanation
Indices: 170235--170359 Score: 54
Period size: 8 Copynumber: 15.8 Consensus size: 8
170225 TCCTTCGTTC
170235 ATTT-TAT
1 ATTTATAT
170242 ATTTATAT
1 ATTTATAT
170250 ATTTTATTAT
1 A-TTTA-TAT
170260 ATTATGAATAT
1 ATT-T--ATAT
170271 ATTTAATAT
1 ATTT-ATAT
170280 ATTTATAT
1 ATTTATAT
*
170288 -TTATATAAA
1 ATT-TAT-AT
*
170297 ATTT-TAA
1 ATTTATAT
**
170304 AAATA-AT
1 ATTTATAT
*
170311 AATT-TAT
1 ATTTATAT
170318 ATTTATAT
1 ATTTATAT
170326 ATTTATGA-
1 ATTTAT-AT
170334 A-TTATA-
1 ATTTATAT
170340 A-TT-TAT
1 ATTTATAT
170346 ATTTATAT
1 ATTTATAT
170354 ATTTAT
1 ATTTAT
170360 GAATTATCTT
Statistics
Matches: 96, Mismatches: 6, Indels: 31
0.72 0.05 0.23
Matches are distributed among these distances:
5 2 0.02
6 5 0.05
7 25 0.26
8 31 0.32
9 18 0.19
10 8 0.08
11 6 0.06
12 1 0.01
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (8 bp):
ATTTATAT
Found at i:170285 original size:21 final size:18
Alignment explanation
Indices: 170239--170287 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
170229 TCGTTCATTT
*
170239 TATATTTATATATTTTAT
1 TATATTTATATATTTTAA
170257 TATA-TTATGAATATATTTAA
1 TATATTTAT--ATAT-TTTAA
170277 TATATTTATAT
1 TATATTTATAT
170288 TTATATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
17 4 0.15
18 4 0.15
19 6 0.23
20 8 0.31
21 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TATATTTATATATTTTAA
Found at i:170340 original size:28 final size:28
Alignment explanation
Indices: 170309--170366 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
170299 TTTAAAAATA
170309 ATAATTTATATTTATATATTTATGAATT
1 ATAATTTATATTTATATATTTATGAATT
170337 ATAATTTATATTTATATATTTATGAATT
1 ATAATTTATATTTATATATTTATGAATT
170365 AT
1 AT
170367 CTTATTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (28 bp):
ATAATTTATATTTATATATTTATGAATT
Found at i:180659 original size:2 final size:2
Alignment explanation
Indices: 180641--180687 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
180631 TGATTAAGAA
* * *
180641 AG AG AG AA AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG AT
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
180683 AG AG A
1 AG AG A
180688 AGCTTCTTCT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.47, T:0.02
Consensus pattern (2 bp):
AG
Found at i:194972 original size:12 final size:12
Alignment explanation
Indices: 194957--194986 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
194947 TTGATGCAGA
194957 TGATGATAGTAG
1 TGATGATAGTAG
*
194969 TGATTATAGTAG
1 TGATGATAGTAG
194981 TGATGA
1 TGATGA
194987 GGGAAGCTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (12 bp):
TGATGATAGTAG
Found at i:195825 original size:30 final size:30
Alignment explanation
Indices: 195791--195848 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
195781 TCTCTGACTT
*
195791 GTAATTTGTATCT-AAATAAATTTTTAATCG
1 GTAATTTATATCTCAAA-AAATTTTTAATCG
195821 GTAATTTATATCTCAAAAAATTTTTAAT
1 GTAATTTATATCTCAAAAAATTTTTAAT
195849 GTAAATCAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 23 0.88
31 3 0.12
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (30 bp):
GTAATTTATATCTCAAAAAATTTTTAATCG
Found at i:201122 original size:16 final size:17
Alignment explanation
Indices: 201081--201133 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
201071 GTAGTTGAAA
*
201081 AAGAAATCTCTCCAATAT
1 AAGAAATCTCTCTAAT-T
* *
201099 AATAAGAATCTCTTTAATT
1 AA-GA-AATCTCTCTAATT
201118 AAGAAATCTCTCTAAT
1 AAGAAATCTCTCTAAT
201134 ATAATATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
17 11 0.39
18 3 0.11
19 4 0.14
20 10 0.36
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (17 bp):
AAGAAATCTCTCTAATT
Found at i:201804 original size:13 final size:13
Alignment explanation
Indices: 201786--201859 Score: 53
Period size: 13 Copynumber: 5.7 Consensus size: 13
201776 TGGAAAATAT
*
201786 ATAATTTTTTTAA
1 ATAATTTATTTAA
*
201799 ATAATTATAATATAA
1 ATAATT-T-ATTTAA
*
201814 AT-ATTTATTTAT
1 ATAATTTATTTAA
*
201826 ATAATTTTTTTAA
1 ATAATTTATTTAA
* *
201839 AT-ACTTAATTAA
1 ATAATTTATTTAA
*
201851 AAAATTTAT
1 ATAATTTAT
201860 ATAATACAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
12 14 0.31
13 21 0.47
14 4 0.09
15 6 0.13
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (13 bp):
ATAATTTATTTAA
Found at i:201824 original size:27 final size:26
Alignment explanation
Indices: 201781--201831 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
201771 GTCAATGGAA
201781 AATATATAATTTTTTTAAATAATTAT
1 AATATATAATTTTTTTAAATAATTAT
*
201807 AATATA-AATATTTATTTATATAATT
1 AATATATAAT-TTT-TTTAAATAATT
201832 TTTTTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 3 0.14
26 9 0.41
27 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
AATATATAATTTTTTTAAATAATTAT
Found at i:201858 original size:38 final size:40
Alignment explanation
Indices: 201783--201859 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
201773 CAATGGAAAA
*
201783 TATATAATTTTTTTAAATAATTATAATATAAATATTTATT
1 TATATAATTTTTTTAAATAATTATAATATAAAAATTTATT
* *
201823 TATATAATTTTTTTAAATACTTA-ATTA-AAAAATTTAT
1 TATATAATTTTTTTAAATAATTATAATATAAAAATTTAT
201860 ATAATACAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 9 0.26
39 3 0.09
40 22 0.65
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (40 bp):
TATATAATTTTTTTAAATAATTATAATATAAAAATTTATT
Found at i:202182 original size:24 final size:22
Alignment explanation
Indices: 202141--202191 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
202131 ATAAGCAAAT
* *
202141 TTATATATTTTTTAAAATTTTA
1 TTATATATTTTTTAAAATATAA
*
202163 TTATATTTATTTTTATAAATATAA
1 TTATATAT-TTTTTA-AAATATAA
202187 TTATA
1 TTATA
202192 CTGTATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 7 0.29
23 6 0.25
24 11 0.46
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTATATATTTTTTAAAATATAA
Found at i:202227 original size:23 final size:23
Alignment explanation
Indices: 202174--202219 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
202164 TATATTTATT
*
202174 TTTATAAATATAATTATACTGTA
1 TTTATAAATATAATAATACTGTA
*
202197 TTTATAAATATACTAATA-TGTA
1 TTTATAAATATAATAATACTGTA
202219 T
1 T
202220 CTTTTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (23 bp):
TTTATAAATATAATAATACTGTA
Found at i:202549 original size:18 final size:16
Alignment explanation
Indices: 202526--202576 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 16
202516 TTATTTATTT
202526 TTAATTTCGTAAAAATAA
1 TTAATTT-GTAAAAAT-A
*
202544 TTAATTTAATAAAAAT-
1 TTAATTT-GTAAAAATA
202560 TTAATTTGTTAAAAATA
1 TTAATTTG-TAAAAATA
202577 GTTGAAGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 14 0.50
18 14 0.50
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (16 bp):
TTAATTTGTAAAAATA
Found at i:203545 original size:18 final size:19
Alignment explanation
Indices: 203524--203579 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
203514 TTTTTAATCA
*
203524 AATATTAATTTT-TATATT
1 AATATAAATTTTATATATT
203542 AATATAAATTTTAATATATT
1 AATATAAATTTT-ATATATT
* *
203562 AATAATGAATATTATATA
1 AAT-ATAAATTTTATATA
203580 AATTTAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 11 0.34
20 14 0.44
21 7 0.22
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
AATATAAATTTTATATATT
Found at i:203561 original size:20 final size:18
Alignment explanation
Indices: 203511--203565 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
203501 ATTAAATTTA
*
203511 AAATTTTTA-ATCAAATAT
1 AAATTTTTATAT-TAATAT
*
203529 TAATTTTTATATTAATAT
1 AAATTTTTATATTAATAT
203547 AAATTTTAATATATTAATA
1 AAATTTT--TATATTAATA
203566 ATGAATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 19 0.61
19 2 0.06
20 10 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATTTTTATATTAATAT
Found at i:203563 original size:32 final size:32
Alignment explanation
Indices: 203525--203623 Score: 82
Period size: 32 Copynumber: 3.2 Consensus size: 32
203515 TTTTAATCAA
*
203525 ATATTAATTTTTATATTAATATAAATTTTAAT
1 ATATTAATTTATATATTAATATAAATTTTAAT
* *
203557 ATATTAA-TAATGAATATT-ATATAAATTTAAAT
1 ATATTAATTTAT--ATATTAATATAAATTTTAAT
* * *
203589 ATTTTTATTTATATTTTTAATAT--ATTTTAAT
1 ATATTAATTTATA-TATTAATATAAATTTTAAT
203620 -TATT
1 ATATT
203624 TTTTACTATC
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
30 3 0.06
31 10 0.19
32 28 0.53
33 12 0.23
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (32 bp):
ATATTAATTTATATATTAATATAAATTTTAAT
Found at i:203578 original size:20 final size:20
Alignment explanation
Indices: 203536--203591 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
203526 TATTAATTTT
*
203536 TATATTAATATAAATTTTAA
1 TATATTAATATAAATATTAA
*
203556 TATATTAATAATGAATATT-A
1 TATATTAAT-ATAAATATTAA
*
203576 TATA--AATTTAAATATT
1 TATATTAATATAAATATT
203592 TTTATTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 7 0.23
18 3 0.10
20 14 0.45
21 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TATATTAATATAAATATTAA
Found at i:203597 original size:23 final size:24
Alignment explanation
Indices: 203571--203622 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
203561 TAATAATGAA
203571 TATTATATAAATTTAA-ATATTTT
1 TATTATATAAATTTAATATATTTT
**
203594 TATT-TATATTTTTAATATATTTT
1 TATTATATAAATTTAATATATTTT
*
203617 AATTAT
1 TATTAT
203623 TTTTTACTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 9 0.38
23 14 0.58
24 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TATTATATAAATTTAATATATTTT
Found at i:203607 original size:22 final size:22
Alignment explanation
Indices: 203582--203628 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
203572 ATTATATAAA
*
203582 TTTAAATAT-TTTTATTTATATT
1 TTTAAATATATTTTAATTAT-TT
203604 TTT-AATATATTTTAATTATTT
1 TTTAAATATATTTTAATTATTT
203625 TTTA
1 TTTA
203629 CTATCTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTAAATATATTTTAATTATTT
Found at i:203626 original size:21 final size:21
Alignment explanation
Indices: 203586--203628 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
203576 TATAAATTTA
*
203586 AATATTTTTATTTATATTTTT
1 AATATTTTTAATTATATTTTT
203607 AATATATTTTAATTAT-TTTTT
1 AATAT-TTTTAATTATATTTTT
203628 A
1 A
203629 CTATCTAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
AATATTTTTAATTATATTTTT
Found at i:203924 original size:2 final size:2
Alignment explanation
Indices: 203917--203952 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
203907 TTCTGAATAG
203917 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
203953 TTTAACCTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:204759 original size:2 final size:2
Alignment explanation
Indices: 204752--204780 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
204742 AGCCTAAAAA
204752 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
204781 ATATAAACTT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:207241 original size:33 final size:31
Alignment explanation
Indices: 207204--207288 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 31
207194 ATTGTTTATG
207204 TATAT-TTTATATAATTTATTTTAAAAAATAT
1 TATATATTTATATAATTTATTTTAAAAAAT-T
* *
207235 TATATATTTATATAA---ATTTTAATATATT
1 TATATATTTATATAATTTATTTTAAAAAATT
207263 TATATATTTATATTATATTTATTTTA
1 TATATATTTATA-TA-ATTTATTTTA
207289 TATATTTTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
28 13 0.28
29 12 0.26
30 1 0.02
31 5 0.11
32 9 0.20
33 6 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (31 bp):
TATATATTTATATAATTTATTTTAAAAAATT
Found at i:207281 original size:11 final size:10
Alignment explanation
Indices: 207235--207323 Score: 55
Period size: 10 Copynumber: 9.0 Consensus size: 10
207225 TAAAAAATAT
207235 TATATATTTA
1 TATATATTTA
*
207245 TATAAATTT-
1 TATATATTTA
207254 TAATATATTTA
1 T-ATATATTTA
207265 TATATTTATATTA
1 TATA--TAT-TTA
*
207278 TATTTATTT-
1 TATATATTTA
207287 TATATATTT-
1 TATATATTTA
*
207296 TATCGTA-TTA
1 TAT-ATATTTA
*
207306 TA-ATTTTTA
1 TATATATTTA
207315 TATAT-TTTA
1 TATATATTTA
207324 ATTACTCACG
Statistics
Matches: 63, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
8 1 0.02
9 23 0.37
10 26 0.41
11 4 0.06
12 3 0.05
13 6 0.10
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (10 bp):
TATATATTTA
Found at i:207293 original size:24 final size:25
Alignment explanation
Indices: 207234--207321 Score: 81
Period size: 28 Copynumber: 3.4 Consensus size: 25
207224 TTAAAAAATA
*
207234 TTATATATTTATATAAATTTTAATATAT
1 TTATATATTTATAT-AATATT-ATAT-T
*
207262 TTATATATTTATATTATATT-TATT
1 TTATATATTTATATAATATTATATT
**
207286 TTATATATTT-TATCGTATTATAATTT
1 TTATATATTTATATAATATTAT-A-TT
207312 TTATATATTT
1 TTATATATTT
207322 TAATTACTCA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
23 7 0.13
24 12 0.23
25 4 0.08
26 12 0.23
27 4 0.08
28 14 0.26
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (25 bp):
TTATATATTTATATAATATTATATT
Found at i:207935 original size:3 final size:3
Alignment explanation
Indices: 207927--207962 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
207917 TATATATTTA
207927 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
207963 ATCCATATAA
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:208134 original size:19 final size:20
Alignment explanation
Indices: 208110--208167 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 20
208100 TTTTTCATCA
208110 TTTAAAATTATTATTATTT-
1 TTTAAAATTATTATTATTTC
*
208129 TTTAAAATATTTTATATATTTC
1 TTTAAAAT-TATTAT-TATTTC
* *
208151 TTTTATATTA-TATTATT
1 TTTAAAATTATTATTATT
208168 AAAATCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
19 12 0.38
20 8 0.25
21 6 0.19
22 6 0.19
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTAAAATTATTATTATTTC
Found at i:208472 original size:9 final size:9
Alignment explanation
Indices: 208427--208478 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
208417 TTTACAATAA
208427 AAAATATAT
1 AAAATATAT
208436 AAAA-ATATT
1 AAAATATA-T
* *
208445 AAATTTTAT
1 AAAATATAT
*
208454 GAAA-ATAT
1 AAAATATAT
208462 AAAATATAT
1 AAAATATAT
208471 AAAATATA
1 AAAATATA
208479 ATTATAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
8 9 0.26
9 23 0.68
10 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (9 bp):
AAAATATAT
Found at i:209596 original size:2 final size:2
Alignment explanation
Indices: 209589--209632 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
209579 AGTTGAAACG
* *
209589 TA 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 TA
209631 TA
1 TA
209633 CACACACACA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:216422 original size:16 final size:16
Alignment explanation
Indices: 216365--216424 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
216355 AAATAAATAA
* *
216365 TAATTTAATTTTAATA
1 TAATTTAAATTTAATT
216381 T-A-TTATAATTATAATAT
1 TAATTTA-AATT-TAAT-T
216398 TATATTTAAATTTAATT
1 TA-ATTTAAATTTAATT
216415 TAATTTAAAT
1 TAATTTAAAT
216425 AAAATATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
14 3 0.08
15 4 0.11
16 13 0.36
17 4 0.11
18 4 0.11
19 5 0.14
20 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATTTAAATTTAATT
Found at i:216431 original size:34 final size:32
Alignment explanation
Indices: 216353--216431 Score: 79
Period size: 34 Copynumber: 2.4 Consensus size: 32
216343 ATAAATTTTA
* *
216353 TTAAAT-AAATAATAATTTAATTTTAATATAT
1 TTAAATAAAATATTAATTTAAATTTAATATAT
* * *
216384 TATAATTATAATATTATATTTAAATTTAATTTAAT
1 T-TAAATAAAATATTA-ATTTAAATTTAATAT-AT
216419 TTAAATAAAATAT
1 TTAAATAAAATAT
216432 ATTTTTTAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
31 1 0.03
32 4 0.11
33 6 0.16
34 23 0.62
35 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
TTAAATAAAATATTAATTTAAATTTAATATAT
Found at i:217599 original size:60 final size:60
Alignment explanation
Indices: 217506--217626 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
217496 GAGACCGGTA
217506 TGTGATGAATCTTCCATTCGTTTAAACTTTCTTCCCTGATCAAACCTTACTTTTATGATC
1 TGTGATGAATCTTCCATTCGTTTAAACTTTCTTCCCTGATCAAACCTTACTTTTATGATC
*
217566 TGTGATGAATCTTCCATTCGTTTAAACTTTCTTCCTTGATCAAACCTTACTTTTATGATC
1 TGTGATGAATCTTCCATTCGTTTAAACTTTCTTCCCTGATCAAACCTTACTTTTATGATC
217626 T
1 T
217627 TTAAAATTTG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.45
Consensus pattern (60 bp):
TGTGATGAATCTTCCATTCGTTTAAACTTTCTTCCCTGATCAAACCTTACTTTTATGATC
Found at i:219017 original size:10 final size:10
Alignment explanation
Indices: 219002--219035 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
218992 ATCTCCTTAA
*
219002 ATATATATAT
1 ATATATGTAT
219012 ATATATGTAT
1 ATATATGTAT
*
219022 ATGTATGTAT
1 ATATATGTAT
219032 ATAT
1 ATAT
219036 TCAAAAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (10 bp):
ATATATGTAT
Found at i:219648 original size:22 final size:24
Alignment explanation
Indices: 219623--219673 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
219613 AAAAAATTAA
*
219623 ATAAA-GATTAT-TTTTATTTTTG
1 ATAAAGGATTATATTTTATTATTG
*
219645 ATAAAGTGATTTTATTTTATTATTG
1 ATAAAG-GATTATATTTTATTATTG
219670 ATAA
1 ATAA
219674 TATATAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.21
24 5 0.21
25 14 0.58
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (24 bp):
ATAAAGGATTATATTTTATTATTG
Found at i:225402 original size:11 final size:11
Alignment explanation
Indices: 225370--225401 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
225360 TTTATTTTAG
225370 TAATTTGA-TT
1 TAATTTGATTT
225380 TAATTTGATTT
1 TAATTTGATTT
225391 TAATTT-ATTT
1 TAATTTGATTT
225401 T
1 T
225402 TTAAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 13 0.62
11 8 0.38
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (11 bp):
TAATTTGATTT
Found at i:226508 original size:2 final size:2
Alignment explanation
Indices: 226503--226531 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
226493 CTATCATGAT
226503 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
226532 ATAGTGTTTA
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):
TA
Done.