Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2355
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: 35431
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Found at i:7462 original size:21 final size:22
Alignment explanation
Indices: 7436--7493 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 22
7426 TTTTTTTTGA
7436 ATTAAATAATAATATTTTATTT
1 ATTAAATAATAATATTTTATTT
7458 A-TAAAT-AT--TATTTTATTT
1 ATTAAATAATAATATTTTATTT
*
7476 ATTAGAATAAAAATATTT
1 ATTA-AATAATAATATTT
7494 AAAAATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
18 11 0.37
19 2 0.07
20 5 0.17
21 6 0.20
22 1 0.03
23 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATTAAATAATAATATTTTATTT
Found at i:8349 original size:19 final size:19
Alignment explanation
Indices: 8320--8364 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
8310 GTTAAATTTT
* *
8320 TTAAATTTTTAATTAATA-
1 TTAAATTTTTTATTAAAAC
8338 TTAAATTTTTTATTAAAAC
1 TTAAATTTTTTATTAAAAC
8357 TTAAATTT
1 TTAAATTT
8365 AAATATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TTAAATTTTTTATTAAAAC
Found at i:8408 original size:26 final size:24
Alignment explanation
Indices: 8349--8408 Score: 57
Period size: 26 Copynumber: 2.3 Consensus size: 24
8339 TAAATTTTTT
* *
8349 ATTAAAACTTAAATTTAAATATAA
1 ATTAAAATTTAAAATTAAATATAA
*
8373 ATAATCAAATTTAAAATTAAATATGAGA
1 AT--TAAAATTTAAAATTAAATAT-A-A
8401 ATTAAAAT
1 ATTAAAAT
8409 ATTTTTTATC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
24 2 0.07
26 22 0.79
27 1 0.04
28 3 0.11
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.35
Consensus pattern (24 bp):
ATTAAAATTTAAAATTAAATATAA
Found at i:9383 original size:25 final size:25
Alignment explanation
Indices: 9361--9410 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
9351 CTTTAATTTT
9361 ATTTTATTA-TTATAATTTAAATTTAA
1 ATTTT-TTATTTATAA-TTAAATTTAA
*
9387 ATTTTTTATTTTTAATTAAATTTA
1 ATTTTTTATTTATAATTAAATTTA
9411 TATCATTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
ATTTTTTATTTATAATTAAATTTAA
Found at i:10395 original size:19 final size:18
Alignment explanation
Indices: 10357--10422 Score: 75
Period size: 17 Copynumber: 3.7 Consensus size: 18
10347 TATATTAAAA
*
10357 AAATTAAATAAAAATA-TT
1 AAATTAAA-AAATATATTT
10375 AAATTTAAAAAATATATTT
1 AAA-TTAAAAAATATATTT
*
10394 AAA-TAAAAATTATATTT
1 AAATTAAAAAATATATTT
10411 -AATTAAAAAATA
1 AAATTAAAAAATA
10423 ATTGAGTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
16 2 0.05
17 21 0.50
18 9 0.21
19 10 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATTAAAAAATATATTT
Found at i:10671 original size:15 final size:15
Alignment explanation
Indices: 10606--10671 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 15
10596 ATTTTAAACT
10606 TAAAAATATTAAATTAA
1 TAAAAATA-TAAATT-A
* *
10623 TAAAAA-CTAAATTT
1 TAAAAATATAAATTA
** *
10637 TAAAAATATATTTTC
1 TAAAAATATAAATTA
10652 T-AAAATATAAATTA
1 TAAAAATATAAATTA
10666 TAAAAA
1 TAAAAA
10672 ATATGATATA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
14 17 0.45
15 15 0.39
17 6 0.16
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAAAATATAAATTA
Found at i:11441 original size:18 final size:17
Alignment explanation
Indices: 11391--11478 Score: 81
Period size: 18 Copynumber: 4.9 Consensus size: 17
11381 AATAATTTTA
11391 TTTAAATTTAATTATAAT
1 TTTAAATTTAA-TATAAT
11409 ATATTAATATTTAATATAAT
1 -T-TTAA-ATTTAATATAAT
*
11429 TTTAAATTATAATATATTT
1 TTTAAATT-TAATATA-AT
* *
11448 TTTAAAATTAAT-TTAT
1 TTTAAATTTAATATAAT
11464 TTTAAATTTAA-ATAA
1 TTTAAATTTAATATAA
11479 AAATAAAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
16 13 0.22
17 4 0.07
18 15 0.26
19 10 0.17
20 10 0.17
21 6 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAAATTTAATATAAT
Found at i:12648 original size:15 final size:15
Alignment explanation
Indices: 12630--12721 Score: 54
Period size: 15 Copynumber: 6.3 Consensus size: 15
12620 TAATTGGGAT
12630 AAATTTAAATTTAAA
1 AAATTTAAATTTAAA
*
12645 AAATATT-TATTT-AA
1 AAAT-TTAAATTTAAA
*
12659 AAA-TT-AATTTATAC
1 AAATTTAAATTTA-AA
12673 AAA-TTAAA--TAAA
1 AAATTTAAATTTAAA
* *
12685 TAATTTAATATTTAGAT
1 AAATTTAA-ATTTA-AA
*
12702 AAATTTAATTTTAAA
1 AAATTTAAATTTAAA
12717 AAATT
1 AAATT
12722 AGGATATTAT
Statistics
Matches: 59, Mismatches: 9, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
12 9 0.15
13 6 0.10
14 12 0.20
15 16 0.27
16 8 0.14
17 8 0.14
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (15 bp):
AAATTTAAATTTAAA
Found at i:13076 original size:29 final size:29
Alignment explanation
Indices: 13041--13142 Score: 91
Period size: 29 Copynumber: 3.3 Consensus size: 29
13031 TAAAATAAAA
13041 TAAATAAAAAATTAAATTTTTATTATTTT
1 TAAATAAAAAATTAAATTTTTATTATTTT
*
13070 TAAATAATAAAATTTAAA-TTTT-TTAATTT
1 TAAATAA-AAAA-TTAAATTTTTATTATTTT
* * *
13099 TATATTAAAAATTAAAAATATTTATTATTTAAT
1 TAAATAAAAAATT--AAATTTTTATTATTT--T
13132 TAATATAAAAA
1 TAA-ATAAAAA
13143 TTCTTTATTA
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
27 2 0.04
28 4 0.07
29 21 0.37
30 11 0.19
31 10 0.18
33 3 0.05
34 6 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TAAATAAAAAATTAAATTTTTATTATTTT
Found at i:14280 original size:19 final size:19
Alignment explanation
Indices: 14233--14280 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
14223 ATTTAATAAA
* * *
14233 AATTTAATTTTATTAACAT
1 AATTTAATATTATGAAAAT
14252 AATATT-ATATTATGAAAAT
1 AAT-TTAATATTATGAAAAT
14271 AATTTAATAT
1 AATTTAATAT
14281 GTGTGTGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.08
19 20 0.83
20 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
AATTTAATATTATGAAAAT
Found at i:14592 original size:3 final size:3
Alignment explanation
Indices: 14584--14609 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
14574 TAATTGTGTT
14584 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
14610 TTGTCTCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:18655 original size:2 final size:2
Alignment explanation
Indices: 18648--18687 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
18638 CGCTCTCCAC
*
18648 AT AT AT AT AT AT AT AT AT AA 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
18688 TAACCTTGGA
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19894 original size:20 final size:21
Alignment explanation
Indices: 19864--19902 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
19854 AGTATAAAAA
19864 TAAATAAATATATAAATATTT
1 TAAATAAATATATAAATATTT
19885 TAAA-AAATATATAAATAT
1 TAAATAAATATATAAATAT
19903 AAAATAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATAAATATATAAATATTT
Found at i:20297 original size:2 final size:2
Alignment explanation
Indices: 20290--20343 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
20280 GATCAGAAGA
20290 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
20332 AT AT AT AT AT AT
1 AT AT AT AT AT AT
20344 GAAAACCAGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21096 original size:2 final size:2
Alignment explanation
Indices: 21089--21173 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
21079 GAAAATGAAA
21089 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
21131 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
21173 A
1 A
21174 AAAGGAGATG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21331 original size:2 final size:2
Alignment explanation
Indices: 21326--21350 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21316 AAAAATTAAG
21326 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
21351 AAATTCTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21810 original size:17 final size:16
Alignment explanation
Indices: 21769--21811 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
21759 AAAAACTAAC
*
21769 TAATATATTTTTATAA
1 TAATATAATTTTATAA
*
21785 TAATAATAATTTTATAT
1 TAAT-ATAATTTTATAA
21802 TAAATATAAT
1 T-AATATAAT
21812 AATTAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 4 0.17
17 16 0.70
18 3 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATATAATTTTATAA
Found at i:23902 original size:13 final size:13
Alignment explanation
Indices: 23886--23910 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23876 AATAAAACTC
23886 AAATATAAATATT
1 AAATATAAATATT
23899 AAATATAAATAT
1 AAATATAAATAT
23911 ATATCTAATA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATATAAATATT
Found at i:23903 original size:7 final size:6
Alignment explanation
Indices: 23886--23927 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
23876 AATAAAACTC
* *
23886 AAATAT AAATATT AAATAT AAATAT ATATCT -AATAT AAATAT
1 AAATAT AAATA-T AAATAT AAATAT AAATAT AAATAT AAATAT
23928 TTTTTATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
5 3 0.10
6 21 0.70
7 6 0.20
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (6 bp):
AAATAT
Found at i:27329 original size:23 final size:23
Alignment explanation
Indices: 27306--27349 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
27296 CAAAAACATA
27306 AAATA-AATATAATACATTTAAT
1 AAATATAATATAATACATTTAAT
* *
27328 AAATATAATATTATATATTTAA
1 AAATATAATATAATACATTTAA
27350 ATATAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATATAATATAATACATTTAAT
Found at i:27420 original size:22 final size:22
Alignment explanation
Indices: 27374--27414 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
27364 AAATTTGTTA
27374 ATTTAATATATATAATATTTAT
1 ATTTAATATATATAATATTTAT
*
27396 ATTTAATAT-TTTAATATTT
1 ATTTAATATATATAATATTT
27415 TTTATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTTAATATATATAATATTTAT
Found at i:28687 original size:111 final size:111
Alignment explanation
Indices: 28470--28698 Score: 291
Period size: 111 Copynumber: 2.1 Consensus size: 111
28460 AAATTCCACC
* * * * *
28470 TATTTTA-TTATTCTTTTTCATTGCATATCTTCATTTCTCTTCATCCATTCTTCGAATTCTCCTT
1 TATTTTATTTATTATTTTTCATTACATATCTTCATTTCTATTCATACATTCTTCGAACTCTCCTT
* * *
28534 TTACGATTTAAAAATCCATCAATAATATTATAACTATAATTGATAT
66 TTACGATTTAAAAATCCATCAACAATACTACAACTATAATTGATAT
* ** *
28580 TATTTTATTTATTATTTTTCATTACATATCTTCATTTTTATTCATATTTTTTTCGAACTCT-CTA
1 TATTTTATTTATTATTTTTCATTACATATCTTCATTTCTATTCATACATTCTTCGAACTCTCCT-
* * * *
28644 TTTATGATTTAAAAATCCATTAACAATACTACAATTATTATTGATAT
65 TTTACGATTTAAAAATCCATCAACAATACTACAACTATAATTGATAT
28691 TATTTTAT
1 TATTTTAT
28699 AAACTTTTAC
Statistics
Matches: 101, Mismatches: 16, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
110 9 0.09
111 92 0.91
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.52
Consensus pattern (111 bp):
TATTTTATTTATTATTTTTCATTACATATCTTCATTTCTATTCATACATTCTTCGAACTCTCCTT
TTACGATTTAAAAATCCATCAACAATACTACAACTATAATTGATAT
Found at i:30884 original size:13 final size:13
Alignment explanation
Indices: 30866--30890 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30856 GAAGGACCCG
30866 GGGGGGGGGGGGT
1 GGGGGGGGGGGGT
30879 GGGGGGGGGGGG
1 GGGGGGGGGGGG
30891 GGGAGAGGGT
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:0.00, C:0.00, G:0.96, T:0.04
Consensus pattern (13 bp):
GGGGGGGGGGGGT
Found at i:30884 original size:14 final size:14
Alignment explanation
Indices: 30865--30891 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30855 GGAAGGACCC
30865 GGGGGGGGGGGGGT
1 GGGGGGGGGGGGGT
30879 GGGGGGGGGGGGG
1 GGGGGGGGGGGGG
30892 GGAGAGGGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.96, T:0.04
Consensus pattern (14 bp):
GGGGGGGGGGGGGT
Found at i:32688 original size:23 final size:23
Alignment explanation
Indices: 32646--32689 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
32636 TATAAGTTAT
32646 TAATTTTTAAATTTATATTTAAA
1 TAATTTTTAAATTTATATTTAAA
32669 TAATTTTTAATATTTA-ATTTA
1 TAATTTTTAA-ATTTATATTTA
32690 TATTTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TAATTTTTAAATTTATATTTAAA
Found at i:32731 original size:30 final size:30
Alignment explanation
Indices: 32646--32731 Score: 120
Period size: 30 Copynumber: 2.9 Consensus size: 30
32636 TATAAGTTAT
**
32646 TAATTTTTAAATTTATATTTAAAT-AATTTT
1 TAATTTTT-AATTTATATTTAAATAAATTCA
*
32676 TAATATTTAATTTATATTTAAATAAATTCA
1 TAATTTTTAATTTATATTTAAATAAATTCA
*
32706 TAATTTTTAATTTTTATTTAAATAAA
1 TAATTTTTAATTTATATTTAAATAAA
32732 GATTTATCGT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
29 15 0.30
30 35 0.70
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (30 bp):
TAATTTTTAATTTATATTTAAATAAATTCA
Found at i:32807 original size:24 final size:24
Alignment explanation
Indices: 32759--32814 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
32749 TATTTCATTT
32759 AAAATAAATTTAATTAGAATCAAAA
1 AAAAT-AATTTAATTAGAATCAAAA
* *
32784 AATAATAATTT-ATTTGAATTAAAA
1 AA-AATAATTTAATTAGAATCAAAA
32808 AAAATAA
1 AAAATAA
32815 AGATTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 5 0.18
24 13 0.46
25 7 0.25
26 3 0.11
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (24 bp):
AAAATAATTTAATTAGAATCAAAA
Found at i:33682 original size:28 final size:28
Alignment explanation
Indices: 33651--33706 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
33641 CCATCCATAC
33651 TAAAAAAAATTAAAATGAATAAAATAAT
1 TAAAAAAAATTAAAATGAATAAAATAAT
** * * *
33679 TAAAGGAGATTAAAATGATTAAGATAAT
1 TAAAAAAAATTAAAATGAATAAAATAAT
33707 CTCTATCCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (28 bp):
TAAAAAAAATTAAAATGAATAAAATAAT
Found at i:34167 original size:2 final size:2
Alignment explanation
Indices: 34160--34190 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
34150 ACCAAAAGCC
34160 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 A
34191 AATATGAAAA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:34711 original size:19 final size:19
Alignment explanation
Indices: 34675--34712 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
34665 TAAAATTAGT
*
34675 TTTAAATTATATTTTATTA
1 TTTAAAATATATTTTATTA
34694 TTTAAAATAT-TTTATATTA
1 TTTAAAATATATTT-TATTA
34713 ATATTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTAAAATATATTTTATTA
Found at i:34722 original size:19 final size:19
Alignment explanation
Indices: 34700--34738 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
34690 ATTATTTAAA
*
34700 ATATTTTAT-ATTAATATTT
1 ATATATTATAATTAA-ATTT
34719 ATATATTATAATTAAATTT
1 ATATATTATAATTAAATTT
34738 A
1 A
34739 AATAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATATTATAATTAAATTT
Found at i:34743 original size:14 final size:14
Alignment explanation
Indices: 34726--34765 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
34716 TTTATATATT
34726 ATAATTAAATTTAA
1 ATAATTAAATTTAA
*
34740 ATAATTAATATTTTA
1 ATAATTAA-ATTTAA
*
34755 TTAATTAAATT
1 ATAATTAAATT
34766 ATGACTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAATTAAATTTAA
Found at i:34899 original size:12 final size:12
Alignment explanation
Indices: 34882--34930 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
34872 AAAAAAGCAC
34882 TATCCATACATA
1 TATCCATACATA
34894 TATCCATACATA
1 TATCCATACATA
*
34906 TAT--ATATATA
1 TATCCATACATA
* *
34916 TATCTATATATA
1 TATCCATACATA
34928 TAT
1 TAT
34931 ATACACACAC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
10 9 0.26
12 25 0.74
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (12 bp):
TATCCATACATA
Found at i:34908 original size:2 final size:2
Alignment explanation
Indices: 34903--34933 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
34893 ATATCCATAC
*
34903 AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34934 CACACACAGC
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):
AT
Found at i:35164 original size:40 final size:37
Alignment explanation
Indices: 35079--35168 Score: 101
Period size: 38 Copynumber: 2.3 Consensus size: 37
35069 ATCAATTCGT
* *
35079 TAAAATAAAATAAAATTATGAAAAAATAATTAATTTA
1 TAAAATAAAATAAAATAATGAAAAAATAATTAATTGA
35116 TAAGAATAAAATAAAATAAT-AATAATAATAATTTAATTGA
1 TAA-AATAAAATAAAATAATGAA-AA-AATAA-TTAATTGA
*
35156 GTGAAATAAAATA
1 -TAAAATAAAATA
35169 TTAATAATTC
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
37 5 0.11
38 17 0.38
39 5 0.11
40 16 0.36
41 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (37 bp):
TAAAATAAAATAAAATAATGAAAAAATAATTAATTGA
Done.