Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold988
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: 84189
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:4558 original size:2 final size:2
Alignment explanation
Indices: 4551--4591 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
4541 TCATACAAGG
4551 TC TC TC TC TC TC 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 TC TC TC TC TC TC T
4592 GTGACACACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:6406 original size:19 final size:18
Alignment explanation
Indices: 6384--6423 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
6374 TATTTAAAAA
*
6384 ATATTAAAATATTGTTTTT
1 ATATTAAAATA-TATTTTT
*
6403 ATATTAATATATATTTTT
1 ATATTAAAATATATTTTT
6421 ATA
1 ATA
6424 ATTATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
ATATTAAAATATATTTTT
Found at i:6977 original size:14 final size:14
Alignment explanation
Indices: 6945--6975 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
6935 ATATTAAATA
6945 TAAATTTATTTTTT
1 TAAATTTATTTTTT
6959 TAAATTT-TTTTTT
1 TAAATTTATTTTTT
6972 TAAA
1 TAAA
6976 ATATATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TAAATTTATTTTTT
Found at i:7594 original size:11 final size:11
Alignment explanation
Indices: 7561--7588 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
7551 AATTATAATT
7561 AATTTTATTTA
1 AATTTTATTTA
7572 AATTTTATTTA
1 AATTTTATTTA
7583 AATTTT
1 AATTTT
7589 TATTAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
AATTTTATTTA
Found at i:8420 original size:21 final size:24
Alignment explanation
Indices: 8394--8451 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 24
8384 TAATTTTTAT
8394 TTAAATTTAATTAT-AAAAT-ATA
1 TTAAATTTAATTATAAAAATAATA
8416 -TAAATATTAA-TATAAAAATAATA
1 TTAAAT-TTAATTATAAAAATAATA
8439 TTTAAATTTAATT
1 -TTAAATTTAATT
8452 CAAATAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
21 8 0.27
22 9 0.30
23 3 0.10
24 4 0.13
25 6 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TTAAATTTAATTATAAAAATAATA
Found at i:8628 original size:21 final size:21
Alignment explanation
Indices: 8604--8646 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
8594 TATTTTTATT
8604 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
8625 TAAATATTAATATAAAATATA
1 TAAATATTAATATAAAATATA
8646 T
1 T
8647 TTTTTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:8630 original size:35 final size:35
Alignment explanation
Indices: 8566--8632 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
8556 AATTGGCTCG
*
8566 ATTTAAATTAATATTTAATAATTAAAAATATTTTT
1 ATTTAAATTAATATATAATAATTAAAAATATTTTT
*
8601 ATTTAAATTTAAT-TATAA-AATATATAAATATT
1 ATTTAAA-TTAATATATAATAAT-TAAAAATATT
8633 AATATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 3 0.11
35 20 0.71
36 5 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
ATTTAAATTAATATATAATAATTAAAAATATTTTT
Found at i:9697 original size:39 final size:39
Alignment explanation
Indices: 9646--9726 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 39
9636 TTTGCCTTGA
* * ** *
9646 TTTCTATCACCTTTGATTCTTTTGCAGTTTACATTTTTT
1 TTTCTATCACCTTTAATTCATGAGCAATTTACATTTTTT
*
9685 TTTCTATTACCTTTAATTCATGAGCAATTTACATTTTTT
1 TTTCTATCACCTTTAATTCATGAGCAATTTACATTTTTT
9724 TTT
1 TTT
9727 GGGTCTTTGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.20, C:0.16, G:0.06, T:0.58
Consensus pattern (39 bp):
TTTCTATCACCTTTAATTCATGAGCAATTTACATTTTTT
Found at i:15236 original size:42 final size:43
Alignment explanation
Indices: 15176--15258 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 43
15166 AAAAACTAGT
*
15176 TATTGATAAAACTTATTGCCAAGCTTCATTCATTTTATATAAG
1 TATTGATAAAACTTATTGCCAAGCTTCATTCATCTTATATAAG
15219 TATTGAT-AAACTTATTGCCAAGCTTCATTCATCTTATATA
1 TATTGATAAAACTTATTGCCAAGCTTCATTCATCTTATATA
15259 CTACTCAAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 32 0.82
43 7 0.18
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (43 bp):
TATTGATAAAACTTATTGCCAAGCTTCATTCATCTTATATAAG
Found at i:18484 original size:2 final size:2
Alignment explanation
Indices: 18479--18504 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18469 ACACATTGGC
18479 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
18505 GGATTTAATC
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:18707 original size:41 final size:39
Alignment explanation
Indices: 18637--18730 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 39
18627 CAAGTCTTTT
*
18637 TTTTTTACAATTTTATTTTATTAATTTA-TTTTTA-TTTAAA
1 TTTTTTA-AATTTTATCTTATTAATTTATTTTTTAGTTT--A
18677 TTTTTTAAATTTTAATCTT-TTAACTCTTATTTTTTAGTTTA
1 TTTTTTAAATTTT-ATCTTATTAA-T-TTATTTTTTAGTTTA
18718 TTTTTTAAATTTT
1 TTTTTTAAATTTT
18731 TATTTAAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
39 10 0.21
40 12 0.25
41 17 0.35
42 6 0.12
43 3 0.06
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (39 bp):
TTTTTTAAATTTTATCTTATTAATTTATTTTTTAGTTTA
Found at i:18806 original size:19 final size:18
Alignment explanation
Indices: 18760--18821 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
18750 TATTTATATT
*
18760 TTTAATTAATAAATAATTTA
1 TTTAATTAATAAA-AA-ATA
*
18780 TATAATTATATAAAAAATA
1 TTTAATTA-ATAAAAAATA
*
18799 TTTAATTAATTAAAAATA
1 TTTAATTAATAAAAAATA
18817 TTTAA
1 TTTAA
18822 ATAAATTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 14 0.38
19 9 0.24
20 9 0.24
21 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTAATTAATAAAAAATA
Found at i:18808 original size:39 final size:42
Alignment explanation
Indices: 18761--18841 Score: 112
Period size: 41 Copynumber: 1.9 Consensus size: 42
18751 ATTTATATTT
*
18761 TTAATTAATAAATAATTTATAT-AATTATATAAAA-AATATTTAA
1 TTAATTAA-AAAT-ATTTAAATAAATT-TATAAAATAATATTTAA
18804 TTAATTAAAAATATTTAAATAAATTTATAAAATAATAT
1 TTAATTAAAAATATTTAAATAAATTTATAAAATAATAT
18842 ATATTAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
41 14 0.40
42 13 0.37
43 8 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (42 bp):
TTAATTAAAAATATTTAAATAAATTTATAAAATAATATTTAA
Found at i:18828 original size:19 final size:18
Alignment explanation
Indices: 18792--18828 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
18782 TAATTATATA
*
18792 AAAAATATTTAATTAATT
1 AAAAATATTTAATAAATT
18810 AAAAATATTTAAATAAATT
1 AAAAATATTT-AATAAATT
18829 TATAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAAATATTTAATAAATT
Found at i:19176 original size:3 final size:3
Alignment explanation
Indices: 19168--19205 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
19158 TTTGGTTAAA
19168 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
19206 GGTGTTATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:21099 original size:27 final size:29
Alignment explanation
Indices: 21057--21111 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 29
21047 AATATAAACT
* *
21057 TAAAATAAATTATTCGAGCTTAATTCGAA
1 TAAAATAAATTATTCGAGCATAACTCGAA
21086 TAAAA-AAA-TATTCGAGCATAACTCGA
1 TAAAATAAATTATTCGAGCATAACTCGA
21112 TCTATAGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 16 0.67
28 3 0.12
29 5 0.21
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (29 bp):
TAAAATAAATTATTCGAGCATAACTCGAA
Found at i:22210 original size:46 final size:46
Alignment explanation
Indices: 22157--22253 Score: 169
Period size: 46 Copynumber: 2.1 Consensus size: 46
22147 TCTCACTATC
*
22157 TATTCAAATGAAACCTAAATCATCTTTATTAACTTGAAGCCACCAA
1 TATTCAAATGAAACCTAAATCATCTTTACTAACTTGAAGCCACCAA
*
22203 TATTCAAATGAAGCCTAAATCATCTTTACTAACTTGAAGCCACCAA
1 TATTCAAATGAAACCTAAATCATCTTTACTAACTTGAAGCCACCAA
22249 T-TTCA
1 TATTCA
22254 TTTGATTCAT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 4 0.08
46 45 0.92
ACGTcount: A:0.39, C:0.23, G:0.07, T:0.31
Consensus pattern (46 bp):
TATTCAAATGAAACCTAAATCATCTTTACTAACTTGAAGCCACCAA
Found at i:22558 original size:19 final size:19
Alignment explanation
Indices: 22520--22558 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
22510 GATTCAAAAT
*
22520 TTATTTTTCGTTAATCAAA
1 TTATTTTTCGTAAATCAAA
22539 TTATTTTTCGTGAAAT-AAA
1 TTATTTTTCGT-AAATCAAA
22558 T
1 T
22559 ATAAAAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (19 bp):
TTATTTTTCGTAAATCAAA
Found at i:22878 original size:22 final size:20
Alignment explanation
Indices: 22853--22907 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 20
22843 AGTTATTTCA
22853 TAAATATATATTATAAAATTAT
1 TAAATATATATTAT-AAATT-T
22875 TAAA-A-ATATTGATAAATTT
1 TAAATATATATT-ATAAATTT
*
22894 AAAATGATATATTA
1 TAAAT-ATATATTA
22908 CAATAGCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
19 4 0.14
20 10 0.36
21 5 0.18
22 9 0.32
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (20 bp):
TAAATATATATTATAAATTT
Found at i:23180 original size:21 final size:19
Alignment explanation
Indices: 23132--23180 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
23122 AATTTAATTT
23132 AAATTATTATTTATTAAATA
1 AAATTA-TATTTATTAAATA
*
23152 AAAATATATTTATTTTAAATA
1 AAATTATATTTA--TTAAATA
*
23173 TAATTATA
1 AAATTATA
23181 AAAATATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 6 0.25
20 5 0.21
21 13 0.54
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATTATATTTATTAAATA
Found at i:23979 original size:2 final size:2
Alignment explanation
Indices: 23972--24016 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
23962 GAGTGAAAGA
23972 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
24014 AT A
1 AT A
24017 GTAAGCTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30596 original size:9 final size:9
Alignment explanation
Indices: 30570--30604 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
30560 ATTAATGGAA
30570 TTCTTTTCTT
1 TTCTTTT-TT
30580 TTCTTTTTT
1 TTCTTTTTT
*
30589 TCCTTTTTT
1 TTCTTTTTT
30598 TTCTTTT
1 TTCTTTT
30605 ATGGAGGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.70
10 7 0.30
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:32911 original size:19 final size:18
Alignment explanation
Indices: 32884--32928 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
32874 AATAAATAAT
*
32884 TTATATAATTATATAGAAA
1 TTATTTAATTATATA-AAA
*
32903 TTATTTAATTATTTAAAA
1 TTATTTAATTATATAAAA
*
32921 ATATTTAA
1 TTATTTAA
32929 ATAAATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TTATTTAATTATATAAAA
Found at i:35365 original size:15 final size:15
Alignment explanation
Indices: 35338--35377 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
35328 TTAATAGATA
35338 AATAAAA-ATATAAT
1 AATAAAATATATAAT
*
35352 ATTAAAATATATAAT
1 AATAAAATATATAAT
35367 AATAATAATAT
1 AATAA-AATAT
35378 CATATTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 6 0.27
15 11 0.50
16 5 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAAAATATATAAT
Found at i:35507 original size:18 final size:18
Alignment explanation
Indices: 35472--35507 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
35462 AATAAAATTT
*
35472 TTAAAATATTAAATAAAA
1 TTAAAATATTAAACAAAA
*
35490 TTAAAATATTATACAAAA
1 TTAAAATATTAAACAAAA
35508 AGATAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TTAAAATATTAAACAAAA
Found at i:37770 original size:2 final size:2
Alignment explanation
Indices: 37765--37793 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
37755 TTTTAGTGTG
37765 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 T
37794 TGATCTAATC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40441 original size:13 final size:15
Alignment explanation
Indices: 40412--40450 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
40402 ATTGCAATAG
40412 AATTATAAATATCAA
1 AATTATAAATATCAA
40427 AATT-TAAAT-TCAA
1 AATTATAAATATCAA
40440 AATTATCAAAT
1 AATTAT-AAAT
40451 GCCATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.36
14 6 0.27
15 8 0.36
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (15 bp):
AATTATAAATATCAA
Found at i:40779 original size:50 final size:50
Alignment explanation
Indices: 40674--40785 Score: 126
Period size: 49 Copynumber: 2.3 Consensus size: 50
40664 TTGACTCGAT
*
40674 TTTTTTATATTATCTATTTATACTATTCATAATTAAAAAAATAAAAAATTA
1 TTTTTTATATTATATATTTATACTATTCATAATTAAAAAAAT-AAAAATTA
* *
40725 -TTTTTATATTA-ATATTTATA-TATTTTATAATTAAATTTAAAT-AAAATTA
1 TTTTTTATATTATATATTTATACTA-TTCATAATTAAA--AAAATAAAAATTA
40774 TTTTTTA-ATTAT
1 TTTTTTATATTAT
40786 CAAATATCAA
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
48 2 0.04
49 30 0.57
50 17 0.32
51 4 0.08
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (50 bp):
TTTTTTATATTATATATTTATACTATTCATAATTAAAAAAATAAAAATTA
Found at i:41528 original size:11 final size:11
Alignment explanation
Indices: 41514--41564 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
41504 ACAATAAACG
41514 AATTTTAAATA
1 AATTTTAAATA
*
41525 AATTAATAAATA
1 AATT-TTAAATA
*
41537 AGTTTTAAATA
1 AATTTTAAATA
*
41548 AATTATAAATA
1 AATTTTAAATA
41559 AATTTT
1 AATTTT
41565 TTTAACATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
11 24 0.73
12 9 0.27
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (11 bp):
AATTTTAAATA
Found at i:41532 original size:23 final size:23
Alignment explanation
Indices: 41506--41556 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
41496 ACACTCAAAC
41506 AATAAACGAA-TTTTAAATAAATT
1 AATAAA-GAAGTTTTAAATAAATT
*
41529 AATAAATAAGTTTTAAATAAATT
1 AATAAAGAAGTTTTAAATAAATT
41552 -ATAAA
1 AATAAA
41557 TAAATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (23 bp):
AATAAAGAAGTTTTAAATAAATT
Found at i:41565 original size:23 final size:23
Alignment explanation
Indices: 41516--41564 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
41506 AATAAACGAA
41516 TTTTAAATAAATTAATAAATAAG
1 TTTTAAATAAATTAATAAATAAG
*
41539 TTTTAAATAAATT-ATAAATAAA
1 TTTTAAATAAATTAATAAATAAG
41561 TTTT
1 TTTT
41565 TTTAACATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TTTTAAATAAATTAATAAATAAG
Found at i:41719 original size:19 final size:19
Alignment explanation
Indices: 41695--41732 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
41685 TTGCTTTTGG
*
41695 GCTTTTGAAGGAATTTCAT
1 GCTTTTAAAGGAATTTCAT
41714 GCTTTTAAAGGAATTTCAT
1 GCTTTTAAAGGAATTTCAT
41733 TATATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (19 bp):
GCTTTTAAAGGAATTTCAT
Found at i:41740 original size:2 final size:2
Alignment explanation
Indices: 41733--41765 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
41723 GGAATTTCAT
41733 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 T
41766 TGTTTGTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42037 original size:16 final size:17
Alignment explanation
Indices: 42005--42046 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
41995 TTAAAGGTTG
42005 ATTTATTATTATAATTAT
1 ATTT-TTATTATAATTAT
*
42023 TTTTTTATTAT-ATTAT
1 ATTTTTATTATAATTAT
42039 ATTTTTAT
1 ATTTTTAT
42047 GTTTATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 12 0.55
17 7 0.32
18 3 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTATTATAATTAT
Found at i:42601 original size:29 final size:30
Alignment explanation
Indices: 42564--42620 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
42554 AAATATTATT
*
42564 TTAATATTAATTTATATT-TTTTAATTAAAG
1 TTAATATTAA-TAATATTATTTTAATTAAAG
42594 TTAA-ATTAATAATATTATTTTAATTAA
1 TTAATATTAATAATATTATTTTAATTAA
42621 TGAGTAGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 6 0.24
29 15 0.60
30 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (30 bp):
TTAATATTAATAATATTATTTTAATTAAAG
Found at i:43419 original size:118 final size:119
Alignment explanation
Indices: 43211--43443 Score: 288
Period size: 118 Copynumber: 2.0 Consensus size: 119
43201 ATATCATCGT
* * * *
43211 TTGTTATTTCGTTTACTAATTTCAATCCAAATATAAATTTAAAATTTTTTTATTCAATTTCATCC
1 TTGTTATTTCGATTACTAATTTCAATCCAAACATAAACTTAAAATTTTTTTATTCAATCTCATCC
* * *
43276 AATCGAATATCATCCATTAATAATTTTATTTCTCACATTAAATTATCAAACCTA
66 AATCAAATATCATCCAGTAAAAATTTTATTTCTCACATTAAATTATCAAACCTA
** * * * * *
43330 TTGTTATTTCGATTACTAATTT-AATTTAGACGTAAACTTAAATTTTTTTTATTCAATCTCGTCT
1 TTGTTATTTCGATTACTAATTTCAATCCAAACATAAACTTAAAATTTTTTTATTCAATCTCATCC
* * * * *
43394 GATCAAATATGATCTAGTAAAAATTTTATTTTTCATATTAAATTATCAAA
66 AATCAAATATCATCCAGTAAAAATTTTATTTCTCACATTAAATTATCAAA
43444 TAATCAAGAT
Statistics
Matches: 95, Mismatches: 19, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
118 74 0.78
119 21 0.22
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.46
Consensus pattern (119 bp):
TTGTTATTTCGATTACTAATTTCAATCCAAACATAAACTTAAAATTTTTTTATTCAATCTCATCC
AATCAAATATCATCCAGTAAAAATTTTATTTCTCACATTAAATTATCAAACCTA
Found at i:43725 original size:13 final size:13
Alignment explanation
Indices: 43709--43744 Score: 63
Period size: 13 Copynumber: 2.7 Consensus size: 13
43699 TTAAATTTAG
43709 TTTAAATTATTAT
1 TTTAAATTATTAT
43722 TTTAAATTATTAT
1 TTTAAATTATTAT
43735 TTTATAATTA
1 TTTA-AATTA
43745 AATTTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTAAATTATTAT
Found at i:43749 original size:13 final size:13
Alignment explanation
Indices: 43709--43752 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
43699 TTAAATTTAG
*
43709 TTTAAATTATTAT
1 TTTAAATTATAAT
*
43722 TTTAAATTATTAT
1 TTTAAATTATAAT
43735 TTTATAATTA-AAT
1 TTTA-AATTATAAT
43748 TTTAA
1 TTTAA
43753 TAAAATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 1 0.03
13 23 0.79
14 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTAAATTATAAT
Found at i:47708 original size:17 final size:17
Alignment explanation
Indices: 47686--47759 Score: 53
Period size: 17 Copynumber: 4.4 Consensus size: 17
47676 TTGATATTTA
47686 TAAAATTAATAAATAAT
1 TAAAATTAATAAATAAT
**
47703 TAAAATTTTTAAA-ATAT
1 TAAAATTAATAAATA-AT
* * *
47720 TTACATTAATTAATAAT
1 TAAAATTAATAAATAAT
** *
47737 T-TTATTAATAAATAGT
1 TAAAATTAATAAATAAT
47753 TAAAATT
1 TAAAATT
47760 TCATAAATAT
Statistics
Matches: 41, Mismatches: 13, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
16 13 0.32
17 27 0.66
18 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (17 bp):
TAAAATTAATAAATAAT
Found at i:47876 original size:27 final size:27
Alignment explanation
Indices: 47830--47894 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
47820 TAATTAATTC
* *
47830 ATATTAATTTTATAATAATAAAT-TATAT
1 ATATT-ATTGTATAAAAATAAATGT-TAT
47858 ATATTATTGTATAAAAATAAATGTTAT
1 ATATTATTGTATAAAAATAAATGTTAT
*
47885 ATATTTTTGT
1 ATATTATTGT
47895 TACCTGTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 27 0.82
28 6 0.18
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.51
Consensus pattern (27 bp):
ATATTATTGTATAAAAATAAATGTTAT
Found at i:48158 original size:16 final size:15
Alignment explanation
Indices: 48101--48156 Score: 76
Period size: 16 Copynumber: 3.6 Consensus size: 15
48091 AATTTGAATT
*
48101 TGATTTAAATTAAAA
1 TGATTTAAATTTAAA
48116 TTGATTTAAATTTTAAA
1 -TGATTTAAA-TTTAAA
*
48133 TAATTTAAATTTAAA
1 TGATTTAAATTTAAA
48148 TGATTTAAA
1 TGATTTAAA
48157 ATAATTAGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
15 14 0.39
16 17 0.47
17 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.46
Consensus pattern (15 bp):
TGATTTAAATTTAAA
Found at i:50363 original size:21 final size:21
Alignment explanation
Indices: 50339--50406 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
50329 TCATAATCTC
*
50339 TTATCATTATAATATTTAATT
1 TTATTATTATAATATTTAATT
*
50360 TTATTATTATAATAATTAATT
1 TTATTATTATAATATTTAATT
* * *
50381 TTTTTATTAT-TTTTTTAATT
1 TTATTATTATAATATTTAATT
50401 TTATTA
1 TTATTA
50407 CAATCAATCT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 12 0.30
21 28 0.70
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATTATTATAATATTTAATT
Found at i:51983 original size:11 final size:11
Alignment explanation
Indices: 51967--52033 Score: 59
Period size: 11 Copynumber: 6.0 Consensus size: 11
51957 AATTTTTTCG
51967 ATTTTAAATAT
1 ATTTTAAATAT
51978 ATTTTATTAAATAT
1 A--TT-TTAAATAT
*
51992 TTTTTAAATAT
1 ATTTTAAATAT
52003 A-TTT--ATAT
1 ATTTTAAATAT
*
52011 TTTATTAAATAT
1 ATT-TTAAATAT
52023 ATTTTAAATAT
1 ATTTTAAATAT
52034 TTTAACTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
8 4 0.09
9 1 0.02
10 5 0.11
11 17 0.38
12 8 0.18
13 2 0.04
14 8 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTTTAAATAT
Found at i:51989 original size:14 final size:14
Alignment explanation
Indices: 51970--52028 Score: 64
Period size: 14 Copynumber: 4.0 Consensus size: 14
51960 TTTTTCGATT
51970 TTAAATATATTTTA
1 TTAAATATATTTTA
*
51984 TTAAATATTTTTTAAA
1 TTAAATATATTTT--A
**
52000 TATATTTATATTTTA
1 T-TAAATATATTTTA
52015 TTAAATATATTTTA
1 TTAAATATATTTTA
52029 AATATTTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
14 23 0.64
15 2 0.06
16 2 0.06
17 9 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAAATATATTTTA
Found at i:51995 original size:31 final size:31
Alignment explanation
Indices: 51971--52033 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
51961 TTTTCGATTT
*
51971 TAAATATATTTTATTAAATATTTTTTAAATA
1 TAAATATATTTTATTAAATATTTTTCAAATA
**
52002 TATTTATATTTTATTAAATATATTTT-AAATA
1 TAAATATATTTTATTAAATAT-TTTTCAAATA
52033 T
1 T
52034 TTTAACTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
TAAATATATTTTATTAAATATTTTTCAAATA
Found at i:52018 original size:20 final size:19
Alignment explanation
Indices: 51988--52026 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
51978 ATTTTATTAA
51988 ATATTTTTTAAATATATTT
1 ATATTTTTTAAATATATTT
52007 ATATTTTATTAAATATATTT
1 ATATTTT-TTAAATATATTT
52027 TAAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATTTTTTAAATATATTT
Found at i:52160 original size:9 final size:9
Alignment explanation
Indices: 52146--52181 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
52136 ATTTAAATCG
*
52146 AATTAACTA
1 AATTAATTA
52155 AATTAATTA
1 AATTAATTA
52164 AATTAAATTA
1 AATT-AATTA
52174 AATTAATT
1 AATTAATT
52182 TTTTTAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTAATTA
Found at i:52211 original size:28 final size:28
Alignment explanation
Indices: 52157--52212 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
52147 ATTAACTAAA
* *
52157 TTAATTAAATTAAATTAAATTAATTTTT
1 TTAATTAAATCAAATTAAATCAATTTTT
* * *
52185 TTAATTAAATCAATTTTAATCACTTTTT
1 TTAATTAAATCAAATTAAATCAATTTTT
52213 ATTCTCTTAC
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:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (28 bp):
TTAATTAAATCAAATTAAATCAATTTTT
Found at i:53337 original size:14 final size:15
Alignment explanation
Indices: 53286--53343 Score: 59
Period size: 14 Copynumber: 3.9 Consensus size: 15
53276 ACTATTTATA
53286 TAATTATAAAAATAAT
1 TAATTATAAAAAT-AT
* *
53302 T-TTTTTAATAAAT-T
1 TAATTATAA-AAATAT
53316 TAATTATAAAAATAT
1 TAATTATAAAAATAT
53331 TAA-TATAAAAATA
1 TAATTATAAAAATA
53344 ATTTTAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 16 0.46
15 14 0.40
16 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATTATAAAAATAT
Found at i:54056 original size:26 final size:25
Alignment explanation
Indices: 54037--54096 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
54027 TATAAAAAAT
54037 AATATA-AATATAAAAATATATTAAA
1 AATATATAATATAAAAATATA-TAAA
*
54062 AATATATAATAT-AAATTAT-TAAA
1 AATATATAATATAAAAATATATAAA
*
54085 TATAT-TAATATA
1 AATATATAATATA
54097 TTTATAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 6 0.19
23 8 0.26
25 12 0.39
26 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
AATATATAATATAAAAATATATAAA
Found at i:54123 original size:29 final size:29
Alignment explanation
Indices: 54054--54132 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 29
54044 ATATAAAAAT
* *
54054 ATATTAAAAATATATAATATAAATTATTAA
1 ATATTATAAATATAT-TTATAAATTATTAA
*
54084 ATA-TATTAATATATTTATAAATT-TTAAA
1 ATATTATAAATATATTTATAAATTATT-AA
*
54112 ATATTATAAATATAATTATAA
1 ATATTATAAATATATTTATAA
54133 TATAATAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
27 2 0.05
28 13 0.31
29 24 0.57
30 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
ATATTATAAATATATTTATAAATTATTAA
Found at i:54149 original size:29 final size:28
Alignment explanation
Indices: 54065--54152 Score: 88
Period size: 29 Copynumber: 3.1 Consensus size: 28
54055 TATTAAAAAT
* * *
54065 ATATAA-TATAAATTATTAAATATATTA
1 ATATAATTATAAATAATAAAATATATAA
* **
54092 ATATATTTATAAATTTTAAAATATTATAA
1 ATATAATTATAAATAATAAAATA-TATAA
*
54121 ATATAATTATAATATAATAAAATAAATAA
1 ATATAATTATAA-ATAATAAAATATATAA
54150 ATA
1 ATA
54153 CGTGTAATTA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
27 5 0.10
28 14 0.28
29 22 0.44
30 9 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
ATATAATTATAAATAATAAAATATATAA
Found at i:54151 original size:8 final size:9
Alignment explanation
Indices: 54027--54152 Score: 52
Period size: 9 Copynumber: 14.2 Consensus size: 9
54017 TTTATATTTT
*
54027 TATAAAAAA
1 TATAATAAA
54036 TA-ATATAAA
1 TATA-ATAAA
54045 TATAA-AAA
1 TATAATAAA
*
54053 TATATTAAA
1 TATAATAAA
* *
54062 AAT-ATATA
1 TATAATAAA
54070 -AT-ATAAA
1 TATAATAAA
*
54077 T-TATTAAA
1 TATAATAAA
*
54085 TATATTAATA
1 TATAATAA-A
*
54095 TATTTATAAA
1 TA-TAATAAA
* *
54105 TTTTA-AAA
1 TATAATAAA
*
54113 TATTATAAA
1 TATAATAAA
54122 TATAATTATAA
1 TATAA-TA-AA
54133 TATAATAAA
1 TATAATAAA
54142 -ATAAATAAA
1 TAT-AATAAA
54151 TA
1 TA
54153 CGTGTAATTA
Statistics
Matches: 92, Mismatches: 12, Indels: 25
0.71 0.09 0.19
Matches are distributed among these distances:
7 7 0.08
8 25 0.27
9 38 0.41
10 11 0.12
11 11 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
TATAATAAA
Found at i:56752 original size:22 final size:22
Alignment explanation
Indices: 56709--56752 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
56699 AATTTATTCT
* * *
56709 TTAAAATTATTATTATATTAAA
1 TTAAAATTATTAATAAAATAAA
*
56731 TTAAAATTCTTAATAAAATAAA
1 TTAAAATTATTAATAAAATAAA
56753 AATCATAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAAAATTATTAATAAAATAAA
Found at i:57100 original size:20 final size:20
Alignment explanation
Indices: 57077--57118 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
57067 TAATCATATT
57077 TAAAATATT-TTATATTT-A
1 TAAAATATTATTATATTTAA
*
57095 TATAAATTTTATTATATTTAA
1 TA-AAATATTATTATATTTAA
57116 TAA
1 TAA
57119 TTTATATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
18 2 0.10
19 6 0.30
20 9 0.45
21 3 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAAAATATTATTATATTTAA
Found at i:57105 original size:17 final size:17
Alignment explanation
Indices: 57083--57138 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
57073 TATTTAAAAT
57083 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
* *
57100 ATTTTAT-TATATTTAA
1 ATTTTATATTTATATAA
*
57116 TAATTTATA-TTATATAA
1 -ATTTTATATTTATATAA
57133 ATTTTA
1 ATTTTA
57139 AAATATTTTC
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:57118 original size:19 final size:20
Alignment explanation
Indices: 57086--57130 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
57076 TTAAAATATT
57086 TTATATTTATATAAATTT-TA
1 TTATATTTATAT-AATTTATA
57106 TTATATTTA-ATAATTTATA
1 TTATATTTATATAATTTATA
57125 TTATAT
1 TTATAT
57131 AAATTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.21
19 10 0.42
20 9 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATATTTATATAATTTATA
Found at i:57145 original size:33 final size:34
Alignment explanation
Indices: 57080--57146 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 34
57070 TCATATTTAA
* **
57080 AATATTTTATATTTATATAAATTTTATTATATTT
1 AATAATTTATATTTATATAAATTTTAAAATATTT
57114 AATAATTTATA-TTATATAAATTTTAAAATATTT
1 AATAATTTATATTTATATAAATTTTAAAATATTT
57147 TCATTTTCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 20 0.67
34 10 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (34 bp):
AATAATTTATATTTATATAAATTTTAAAATATTT
Found at i:57721 original size:13 final size:13
Alignment explanation
Indices: 57703--57727 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57693 TCATGAGTAT
57703 TTTAAAATTATTC
1 TTTAAAATTATTC
57716 TTTAAAATTATT
1 TTTAAAATTATT
57728 ATAATAAAAT
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):
TTTAAAATTATTC
Found at i:57742 original size:20 final size:17
Alignment explanation
Indices: 57717--57758 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 17
57707 AAATTATTCT
57717 TTAAAATTATTATAATAAAA
1 TTAAAATT-TT-TAAT-AAA
57737 TTAAAATTTTTAATAAA
1 TTAAAATTTTTAATAAA
57754 TTAAA
1 TTAAA
57759 CTTAATCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 2 0.09
20 8 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAAATTTTTAATAAA
Found at i:58003 original size:16 final size:16
Alignment explanation
Indices: 57978--58097 Score: 84
Period size: 16 Copynumber: 7.7 Consensus size: 16
57968 TTTGATATAT
*
57978 TTTTAGATTTAAATTA
1 TTTTAAATTTAAATTA
57994 TTTTAAATTT-AATT-
1 TTTTAAATTTAAATTA
* *
58008 TTTT-TATTTAAATAA
1 TTTTAAATTTAAATTA
*
58023 TTTTAAATTTAGATTA
1 TTTTAAATTTAAATTA
** * * *
58039 TTTTAGTTTTGAGTCA
1 TTTTAAATTTAAATTA
* ** *
58055 TTTTAGATACAAATTT
1 TTTTAAATTTAAATTA
*
58071 TTTTAAGTTTAAATTA
1 TTTTAAATTTAAATTA
*
58087 TTTTGAATTTA
1 TTTTAAATTTA
58098 GATCGATTCG
Statistics
Matches: 75, Mismatches: 26, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
13 4 0.05
14 7 0.09
15 8 0.11
16 56 0.75
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (16 bp):
TTTTAAATTTAAATTA
Found at i:58008 original size:29 final size:29
Alignment explanation
Indices: 57976--58033 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
57966 GATTTGATAT
*
57976 ATTTTTAGATTTAAATTATTTTAAATTTA
1 ATTTTTAGATTTAAATAATTTTAAATTTA
**
58005 ATTTTTTTATTTAAATAATTTTAAATTTA
1 ATTTTTAGATTTAAATAATTTTAAATTTA
58034 GATTATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (29 bp):
ATTTTTAGATTTAAATAATTTTAAATTTA
Found at i:69022 original size:3 final size:3
Alignment explanation
Indices: 69014--69054 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
69004 CCTCCCTTGT
*
69014 CTC CTC CTC TTC CTC CTC CTC CTC CTC CTC CGT- CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C-TC CTC CTC CT
69055 TCACACTCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 32 0.94
4 1 0.03
ACGTcount: A:0.00, C:0.61, G:0.02, T:0.37
Consensus pattern (3 bp):
CTC
Found at i:69943 original size:23 final size:23
Alignment explanation
Indices: 69904--69964 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
69894 GTAATATGTT
* *
69904 TATAAATATGATA-AAAATATAA
1 TATAAATATAATATAAAAAATAA
69926 T-TAAAATATAATATAAAAAATAA
1 TAT-AAATATAATATAAAAAATAA
*
69949 TATAAATATAACATAA
1 TATAAATATAATATAA
69965 GTATATAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 1 0.03
22 10 0.30
23 21 0.64
24 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (23 bp):
TATAAATATAATATAAAAAATAA
Found at i:69964 original size:11 final size:11
Alignment explanation
Indices: 69904--69969 Score: 62
Period size: 11 Copynumber: 5.9 Consensus size: 11
69894 GTAATATGTT
*
69904 TATAAATATGA
1 TATAAATATAA
*
69915 TAAAAATATAA
1 TATAAATATAA
69926 T-TAAAATATAA
1 TAT-AAATATAA
*
69937 TATAAAAAATAA
1 TAT-AAATATAA
69949 TATAAATATAA
1 TATAAATATAA
* *
69960 CATAAGTATA
1 TATAAATATA
69970 TAAATATTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
11 34 0.74
12 12 0.26
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.32
Consensus pattern (11 bp):
TATAAATATAA
Found at i:70228 original size:19 final size:19
Alignment explanation
Indices: 70204--70240 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
70194 ATTTAAGATA
70204 TTTTATAT-TTATATAATTT
1 TTTTATATATTA-ATAATTT
70223 TTTTATATATTAATAATT
1 TTTTATATATTAATAATT
70241 AATATTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTATATATTAATAATTT
Found at i:70286 original size:18 final size:18
Alignment explanation
Indices: 70225--70297 Score: 53
Period size: 20 Copynumber: 3.9 Consensus size: 18
70215 TATAATTTTT
*
70225 TTATATATTAATAATTAATA
1 TTATATATTTAT-ATT-ATA
**
70245 TTATATAAATTT-TAAAATA
1 TTATAT--ATTTATATTATA
70264 TTTATATATTTATATTATA
1 -TTATATATTTATATTATA
70283 TTATAT-TTTA-ATTAT
1 TTATATATTTATATTAT
70298 TTTTCATATA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
16 5 0.11
17 4 0.09
18 10 0.23
19 8 0.18
20 13 0.30
21 1 0.02
22 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATATATTTATATTATA
Found at i:70299 original size:33 final size:33
Alignment explanation
Indices: 70168--70299 Score: 109
Period size: 33 Copynumber: 4.1 Consensus size: 33
70158 TTATATTTTG
*
70168 TTTATATATTTTCGTATTATAATTATA-TTTAAGATA
1 TTTATATA-TTT-ATATTAT-ATTATATTTTAA-ATA
*
70204 TTT-TATATTTATA-TA-ATT-T-TTTTATATA
1 TTTATATATTTATATTATATTATATTTTAAATA
* * *
70232 TTAATA-ATTAATATTATA-TAAATTTTAAAATA
1 TTTATATATTTATATTATATTATATTTT-AAATA
*
70264 TTTATATATTTATATTATATTATATTTTAATTA
1 TTTATATATTTATATTATATTATATTTTAAATA
70297 TTT
1 TTT
70300 TTCATATATA
Statistics
Matches: 77, Mismatches: 10, Indels: 21
0.71 0.09 0.19
Matches are distributed among these distances:
28 11 0.14
29 10 0.13
30 4 0.05
31 4 0.05
32 11 0.14
33 20 0.26
34 10 0.13
35 4 0.05
36 3 0.04
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.59
Consensus pattern (33 bp):
TTTATATATTTATATTATATTATATTTTAAATA
Found at i:72424 original size:22 final size:20
Alignment explanation
Indices: 72383--72426 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
72373 CACAATATCT
72383 TAAAAATAAATAAAATATAA
1 TAAAAATAAATAAAATATAA
*
72403 TAAAAATAACATGAGAATATAA
1 TAAAAATAA-AT-AAAATATAA
72425 TA
1 TA
72427 TTAGTATACG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
21 2 0.10
22 10 0.48
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (20 bp):
TAAAAATAAATAAAATATAA
Found at i:73082 original size:14 final size:14
Alignment explanation
Indices: 73063--73105 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
73053 TTTTTTTATA
73063 AAAAAATTAAAAAT
1 AAAAAATTAAAAAT
*
73077 AAAAAATTATAAAT
1 AAAAAATTAAAAAT
* *
73091 ATTAAAATTTAAAAT
1 A-AAAAATTAAAAAT
73106 TTAAATTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAAAATTAAAAAT
Done.