Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2032
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: 51657
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Found at i:2297 original size:23 final size:24
Alignment explanation
Indices: 2255--2303 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
2245 TCACATTATA
*
2255 TTTATATTTTTTTTATTATCGTAT
1 TTTATATTTTTTTTATTATCATAT
2279 TTTA-ATTATTTTTTA-TATCATAT
1 TTTATATT-TTTTTTATTATCATAT
2302 TT
1 TT
2304 ATCATTGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTATATTTTTTTTATTATCATAT
Found at i:2576 original size:22 final size:21
Alignment explanation
Indices: 2524--2585 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
2514 TAATATTAAA
2524 AAATATTTTA-TATTAATATTT
1 AAATATTTTATTATTAA-ATTT
* *
2545 ATATGTTTTTATTATTAAATTT
1 AAAT-ATTTTATTATTAAATTT
2567 AAATAATTTT-TTATTAAAT
1 AAAT-ATTTTATTATTAAAT
2586 AATATTTGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
21 12 0.35
22 16 0.47
23 6 0.18
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
AAATATTTTATTATTAAATTT
Found at i:3703 original size:19 final size:19
Alignment explanation
Indices: 3667--3727 Score: 80
Period size: 18 Copynumber: 3.5 Consensus size: 19
3657 TTTTTTTAAT
3667 AATTTAAATAAA-AAATTA
1 AATTTAAATAAATAAATTA
3685 AATTTAAATAAATAAATTA
1 AATTTAAATAAATAAATTA
3704 AA-TTAAAT---TAAATT-
1 AATTTAAATAAATAAATTA
3718 AATTTAAATA
1 AATTTAAATA
3728 GGAGTGGATT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.05
15 12 0.30
18 18 0.45
19 8 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTTAAATAAATAAATTA
Found at i:3705 original size:5 final size:5
Alignment explanation
Indices: 3679--3726 Score: 64
Period size: 5 Copynumber: 9.8 Consensus size: 5
3669 TTTAAATAAA
*
3679 AAATT AAATTT AAA-T AAA-T AAATT AAATT AAATT AAATT AATTT AAAT
1 AAATT AAA-TT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAAT
3727 AGGAGTGGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
4 8 0.21
5 26 0.67
6 5 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:4754 original size:11 final size:11
Alignment explanation
Indices: 4738--4825 Score: 60
Period size: 11 Copynumber: 8.3 Consensus size: 11
4728 TTGATAATTC
4738 TTATATTTATA
1 TTATATTTATA
4749 TTATATTTATA
1 TTATATTTATA
**
4760 CCATA-TTATAA
1 TTATATTTAT-A
* *
4771 TTATGTTTAAA
1 TTATATTTATA
*
4782 GTAT-TTTATA
1 TTATATTTATA
*
4792 TTATATTAAT-
1 TTATATTTATA
4802 TTAATATTT-TA
1 TT-ATATTTATA
*
4813 ATA-ATTTATA
1 TTATATTTATA
4823 TTA
1 TTA
4826 CAAAAATTTA
Statistics
Matches: 58, Mismatches: 13, Indels: 13
0.69 0.15 0.15
Matches are distributed among these distances:
9 4 0.07
10 20 0.34
11 31 0.53
12 3 0.05
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
TTATATTTATA
Found at i:4803 original size:16 final size:16
Alignment explanation
Indices: 4784--4825 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
4774 TGTTTAAAGT
*
4784 ATTTTATATTATATTA
1 ATTTTATATTATAATA
* *
4800 ATTTAATATTTTAATA
1 ATTTTATATTATAATA
4816 A-TTTATATTA
1 ATTTTATATTA
4826 CAAAAATTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTTATATTATAATA
Found at i:6380 original size:22 final size:22
Alignment explanation
Indices: 6355--6396 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
6345 AATTTTTATT
6355 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
6377 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
6397 ATTTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:7614 original size:29 final size:31
Alignment explanation
Indices: 7552--7611 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 31
7542 TAACGTAAAT
*
7552 ATATGTATAAAATATTTTAAATATAATTATA
1 ATATGTATAAAATATTATAAATATAATTATA
7583 ATAT-TATAAAATA-TATAAATATAA-TATA
1 ATATGTATAAAATATTATAAATATAATTATA
7611 A
1 A
7612 ATAAATGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 5 0.18
29 10 0.36
30 9 0.32
31 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (31 bp):
ATATGTATAAAATATTATAAATATAATTATA
Found at i:7617 original size:23 final size:23
Alignment explanation
Indices: 7572--7616 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
7562 AATATTTTAA
* *
7572 ATATAATTATAATATTATAAAAT
1 ATATAAATATAATATAATAAAAT
7595 ATATAAATATAATATAAATAAA
1 ATATAAATATAATAT-AATAAA
7617 TGAATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
ATATAAATATAATATAATAAAAT
Found at i:7629 original size:20 final size:19
Alignment explanation
Indices: 7561--7629 Score: 54
Period size: 20 Copynumber: 3.6 Consensus size: 19
7551 TATATGTATA
7561 AAATATT-T-TAAATATAATT
1 AAATATTATATAAATA-AA-T
*
7580 ATAATATTATA-AAATATAT
1 A-AATATTATATAAATAAAT
*
7599 AAATATAATATAAATAAAT
1 AAATATTATATAAATAAAT
*
7618 GAATTATTATAT
1 -AAATATTATAT
7630 TTAATTTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
18 8 0.20
19 10 0.25
20 16 0.40
21 6 0.15
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (19 bp):
AAATATTATATAAATAAAT
Found at i:12037 original size:12 final size:12
Alignment explanation
Indices: 12020--12044 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12010 GCTTTGGAGC
12020 TGTTGGAAGCTT
1 TGTTGGAAGCTT
12032 TGTTGGAAGCTT
1 TGTTGGAAGCTT
12044 T
1 T
12045 ATTAGTGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.32, T:0.44
Consensus pattern (12 bp):
TGTTGGAAGCTT
Found at i:12201 original size:21 final size:20
Alignment explanation
Indices: 12150--12202 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
12140 AAGTATCAAT
12150 TGTATCAATACATTCCTTAA
1 TGTATCAATACATTCCTTAA
** *
12170 TGTATTGATACATTCCTTATG
1 TGTATCAATACATTCCTTA-A
12191 TGTATCAATACA
1 TGTATCAATACA
12203 AGTACTTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.42
Consensus pattern (20 bp):
TGTATCAATACATTCCTTAA
Found at i:12990 original size:2 final size:2
Alignment explanation
Indices: 12983--13008 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12973 TCTCATGAAA
12983 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
13009 TTCCTATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18980 original size:2 final size:2
Alignment explanation
Indices: 18973--18997 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18963 CAAAGATTAC
18973 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
18998 CACACACACA
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:20672 original size:2 final size:2
Alignment explanation
Indices: 20661--20698 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
20651 TATTTTTATG
*
20661 TA TA -A TA TA TA TA TA TA TA TA CA 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
20699 TCTTAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:21259 original size:25 final size:25
Alignment explanation
Indices: 21221--21274 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
21211 GGGAATAGTA
*
21221 ATTTAAAAAAATTTT-ATTTATTTTT
1 ATTTAAAAAAATTTTAATTTA-ATTT
* *
21246 ATTTAAATATATTTTAATTTAATTT
1 ATTTAAAAAAATTTTAATTTAATTT
21271 ATTT
1 ATTT
21275 TATATTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
ATTTAAAAAAATTTTAATTTAATTT
Found at i:21260 original size:16 final size:15
Alignment explanation
Indices: 21239--21285 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
21229 AAATTTTATT
21239 TATTTTTATTTAAATA
1 TATTTTTATTT-AATA
* *
21255 TATTTTAATTTAATT
1 TATTTTTATTTAATA
21270 TA-TTTTATATTAATA
1 TATTTTTAT-TTAATA
21285 T
1 T
21286 TTATATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 5 0.19
15 11 0.42
16 10 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTTTTATTTAATA
Found at i:21278 original size:22 final size:20
Alignment explanation
Indices: 21259--21309 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
21249 TAAATATATT
21259 TTAATTTAATTTATTTTATA
1 TTAATTTAATTTATTTTATA
* *
21279 TTAATATTTATATATTTTATAA
1 TTAAT-TTAATTTATTTTAT-A
21301 TTAATTTAA
1 TTAATTTAA
21310 ATTAATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 15 0.58
22 6 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTAATTTAATTTATTTTATA
Found at i:21283 original size:15 final size:16
Alignment explanation
Indices: 21231--21280 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
21221 ATTTAAAAAA
*
21231 ATTTTATTTATTTT-T
1 ATTTAATTTATTTTAT
*
21246 ATTTAAATATATTTTA-
1 ATTT-AATTTATTTTAT
21262 ATTTAATTTATTTTAT
1 ATTTAATTTATTTTAT
21278 ATT
1 ATT
21281 AATATTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 14 0.48
16 15 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTAATTTATTTTAT
Found at i:21317 original size:22 final size:22
Alignment explanation
Indices: 21259--21352 Score: 58
Period size: 21 Copynumber: 4.4 Consensus size: 22
21249 TAAATATATT
*
21259 TTAATTT-AATTTATTTTAT-A
1 TTAATTTAAATTAATTTTATAA
*
21279 TTAATATT-TA-TATATTTTATAA
1 TTAAT-TTAAATTA-ATTTTATAA
*
21301 TTAATTTAAATTAATTTTTTTAA
1 TTAATTTAAATTAA-TTTTATAA
*
21324 TT-A-TTAAATATAAATTTA-AA
1 TTAATTTAAAT-TAATTTTATAA
*
21344 TTAAATTAA
1 TTAATTTAA
21353 TATGAATTCA
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
20 10 0.17
21 22 0.37
22 16 0.27
23 11 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTTAAATTAATTTTATAA
Found at i:21550 original size:20 final size:22
Alignment explanation
Indices: 21496--21556 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
21486 TATAAAAATT
*
21496 TTAATATGTT-TA-TATTTTT-
1 TTAATATTTTATATTATTTTTA
*
21515 TTAATTTTTTATATTATTTTTA
1 TTAATATTTTATATTATTTTTA
21537 TT-ATATTTTA-ATTATTTTTA
1 TTAATATTTTATATTATTTTTA
21557 ATTTATTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 8 0.22
20 12 0.33
21 14 0.39
22 2 0.06
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
TTAATATTTTATATTATTTTTA
Found at i:21563 original size:11 final size:10
Alignment explanation
Indices: 21494--21559 Score: 61
Period size: 10 Copynumber: 6.8 Consensus size: 10
21484 GTTATAAAAA
21494 TTTTAA-TAT
1 TTTTAATTAT
*
21503 GTTTATATT-T
1 TTTTA-ATTAT
21513 TTTTAA-T-T
1 TTTTAATTAT
21521 TTTTATATTAT
1 TTTTA-ATTAT
21532 TTTT-ATTAT
1 TTTTAATTAT
21541 ATTTTAATTAT
1 -TTTTAATTAT
21552 TTTTAATT
1 TTTTAATT
21560 TATTATATTA
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
8 7 0.15
9 11 0.23
10 19 0.40
11 11 0.23
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (10 bp):
TTTTAATTAT
Found at i:21563 original size:20 final size:21
Alignment explanation
Indices: 21504--21563 Score: 76
Period size: 20 Copynumber: 3.0 Consensus size: 21
21494 TTTTAATATG
21504 TTTATATT-TTTTTAA-TT-T
1 TTTATATTATTTTTAATTTAT
21522 TTTATATTATTTTT-ATTATAT
1 TTTATATTATTTTTAATT-TAT
21543 TTTA-ATTATTTTTAATTTAT
1 TTTATATTATTTTTAATTTAT
21563 T
1 T
21564 ATATTAATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
18 9 0.24
19 6 0.16
20 14 0.38
21 8 0.22
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTATATTATTTTTAATTTAT
Found at i:22850 original size:109 final size:109
Alignment explanation
Indices: 22708--22926 Score: 402
Period size: 109 Copynumber: 2.0 Consensus size: 109
22698 CCGCAAACTA
* *
22708 TGGAGCTAAGGTATCTCTAATTTTCTGGTATCTCTTAATTTAAGCAAATCGAATTTGTTCGAAAA
1 TGGAGCTAAGGTATCTCAAATTTTCTGGCATCTCTTAATTTAAGCAAATCGAATTTGTTCGAAAA
*
22773 ATAGATTAGCAATTTGTTAATTTGCTAGCTTGATAAATACTTAT
66 AAAGATTAGCAATTTGTTAATTTGCTAGCTTGATAAATACTTAT
22817 TGGAGCTAAGGTATCTCAAATTTTCTGGCATCTCTTAATTTAAGCAAATCGAATTTGTTCGAAAA
1 TGGAGCTAAGGTATCTCAAATTTTCTGGCATCTCTTAATTTAAGCAAATCGAATTTGTTCGAAAA
*
22882 AAAGATTAGTAATTTGTTAATTTGCTAGCTTGATAAATACTTAT
66 AAAGATTAGCAATTTGTTAATTTGCTAGCTTGATAAATACTTAT
22926 T
1 T
22927 TTCATATATG
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 106 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (109 bp):
TGGAGCTAAGGTATCTCAAATTTTCTGGCATCTCTTAATTTAAGCAAATCGAATTTGTTCGAAAA
AAAGATTAGCAATTTGTTAATTTGCTAGCTTGATAAATACTTAT
Found at i:32978 original size:20 final size:20
Alignment explanation
Indices: 32955--33005 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
32945 ATTATTATTA
*
32955 TTAT-ATTAATATTTATATAT
1 TTATAATTAA-ATTTAAATAT
32975 TTATAATTAAATTTAAATA-
1 TTATAATTAAATTTAAATAT
*
32994 TTATTATTAAAT
1 TTATAATTAAAT
33006 AGTAATTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 11 0.39
20 12 0.43
21 5 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATAATTAAATTTAAATAT
Found at i:34037 original size:12 final size:14
Alignment explanation
Indices: 34003--34041 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
33993 TTTTAACTTA
*
34003 ATATTGTAAATATT
1 ATATTATAAATATT
34017 ATATTATAAAT-TT
1 ATATTATAAATATT
34030 AT-TTATAAATAT
1 ATATTATAAATAT
34042 AATTTTAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 8 0.35
13 5 0.22
14 10 0.43
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (14 bp):
ATATTATAAATATT
Found at i:34797 original size:2 final size:2
Alignment explanation
Indices: 34790--34835 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
34780 TACCTTTTAC
34790 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
34832 AT AT
1 AT AT
34836 GAAGTGAGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35100 original size:2 final size:2
Alignment explanation
Indices: 35093--35117 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35083 TAGGCAATAA
35093 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
35118 ATTATAAACC
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:37963 original size:14 final size:14
Alignment explanation
Indices: 37946--37982 Score: 51
Period size: 12 Copynumber: 2.7 Consensus size: 14
37936 TATATTTAAG
37946 TATAAATATAAAAA
1 TATAAATATAAAAA
37960 TAT-AAT-TAAAAA
1 TATAAATATAAAAA
37972 TATTAAATATA
1 TA-TAAATATA
37983 TTTATATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 8 0.40
13 4 0.20
14 6 0.30
15 2 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TATAAATATAAAAA
Found at i:37991 original size:15 final size:16
Alignment explanation
Indices: 37971--38006 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
37961 ATAATTAAAA
37971 ATATTAAATATAT-TT
1 ATATTAAATATATATT
37986 ATATTAAATATATATT
1 ATATTAAATATATATT
38002 ATATT
1 ATATT
38007 CGATGCGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTAAATATATATT
Found at i:38524 original size:28 final size:28
Alignment explanation
Indices: 38493--38570 Score: 72
Period size: 28 Copynumber: 2.9 Consensus size: 28
38483 AATGGATTTA
38493 ATTTAAATTATTATTTAATAATAAAAAT
1 ATTTAAATTATTATTTAATAATAAAAAT
** **
38521 ATTTTTATTAAAATTTAAT-A-AAAAAT
1 ATTTAAATTATTATTTAATAATAAAAAT
* *
38547 ATATAAA-TATTATTATAAAAATAA
1 ATTTAAATTATTATT-TAATAATAA
38571 TTTTTTATTA
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
25 5 0.14
26 13 0.35
27 2 0.05
28 17 0.46
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
ATTTAAATTATTATTTAATAATAAAAAT
Found at i:38821 original size:25 final size:25
Alignment explanation
Indices: 38771--38836 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
38761 TACTATTTAA
*
38771 TAATAATAAATATTTTGTTTAAATT
1 TAATAATAAATATTATGTTTAAATT
38796 TAATAA-AAATATATAT-TTTAATATT
1 TAATAATAAATAT-TATGTTTAA-ATT
* *
38821 TTATGAATAATTATTA
1 TAAT-AATAAATATTA
38837 AAGTTTTAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
24 11 0.32
25 14 0.41
26 4 0.12
27 5 0.15
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (25 bp):
TAATAATAAATATTATGTTTAAATT
Found at i:40259 original size:22 final size:21
Alignment explanation
Indices: 40234--40293 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
40224 ATATTAACTG
40234 ATAAAAAAATATAAAATAAAAA
1 ATAAAAAAATATAAAAT-AAAA
* *
40256 ATAAAATATAATATGATATAAAA
1 ATAAAA-A-AATATAAAATAAAA
*
40279 ATAATATAAATATAA
1 ATAA-AAAAATATAA
40294 TAAAATATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
22 12 0.39
23 10 0.32
24 9 0.29
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.27
Consensus pattern (21 bp):
ATAAAAAAATATAAAATAAAA
Found at i:40279 original size:37 final size:38
Alignment explanation
Indices: 40232--40312 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 38
40222 TTATATTAAC
40232 TGATAAAAAAAT-ATA-AAATAAAAAATAAAATAT-AATA
1 TGATAAAAAAATAATATAAAT--AAAATAAAATATAAATA
* *
40269 TGATATAAAAATAATATAAATATAATAAAATATAAATA
1 TGATAAAAAAATAATATAAATAAAATAAAATATAAATA
40307 TGATAA
1 TGATAA
40313 TCTATTTAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
37 22 0.58
38 12 0.32
39 4 0.11
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (38 bp):
TGATAAAAAAATAATATAAATAAAATAAAATATAAATA
Found at i:40295 original size:27 final size:25
Alignment explanation
Indices: 40251--40304 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 25
40241 AATATAAAAT
**
40251 AAAAAATAAAATATAATATGATATA
1 AAAAAATAAAATATAATAAAATATA
40276 AAAATAATATAAATATAATAAAATATA
1 AAAA-AATA-AAATATAATAAAATATA
40303 AA
1 AA
40305 TATGATAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.16
26 4 0.16
27 17 0.68
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (25 bp):
AAAAAATAAAATATAATAAAATATA
Found at i:40300 original size:16 final size:16
Alignment explanation
Indices: 40234--40312 Score: 66
Period size: 16 Copynumber: 5.4 Consensus size: 16
40224 ATATTAACTG
*
40234 ATAAAAAAATATAAA-
1 ATAATAAAATATAAAT
40249 ATAA-AAAATA-AAAT
1 ATAATAAAATATAAAT
**
40263 ATAATATGATAT-AA-
1 ATAATAAAATATAAAT
40277 A-AAT--AATATAAAT
1 ATAATAAAATATAAAT
40290 ATAATAAAATATAAAT
1 ATAATAAAATATAAAT
*
40306 ATGATAA
1 ATAATAA
40313 TCTATTTAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
11 4 0.08
12 2 0.04
13 7 0.13
14 14 0.27
15 10 0.19
16 15 0.29
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (16 bp):
ATAATAAAATATAAAT
Found at i:41952 original size:25 final size:25
Alignment explanation
Indices: 41915--41963 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
41905 AATATTAAAA
*
41915 TATTATATCAATGTTAAATACTATTT
1 TATTATATAAATGTTAAATA-TATTT
*
41941 TATTATA-AAATGTTATATATATT
1 TATTATATAAATGTTAAATATATT
41964 AAGATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 10 0.48
26 7 0.33
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (25 bp):
TATTATATAAATGTTAAATATATTT
Found at i:42229 original size:15 final size:15
Alignment explanation
Indices: 42209--42242 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
42199 CATGCAATCT
42209 AATAATTTATGTGAA
1 AATAATTTATGTGAA
* *
42224 AATAATTTGTGTTAA
1 AATAATTTATGTGAA
42239 AATA
1 AATA
42243 TTCTAAACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (15 bp):
AATAATTTATGTGAA
Found at i:42705 original size:23 final size:20
Alignment explanation
Indices: 42652--42709 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 20
42642 ATAACAAATA
*
42652 TTAATATTAAAAATAATATT
1 TTAATATAAAAAATAATATT
*
42672 TTAGTATTAAAATAATAAATAATT
1 TTAATA-TAAAA-AAT-AAT-ATT
42696 TTAATATAAAAAAT
1 TTAATATAAAAAAT
42710 TCATGTCATA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 5 0.16
21 4 0.13
22 6 0.19
23 8 0.26
24 8 0.26
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
TTAATATAAAAAATAATATT
Found at i:43062 original size:2 final size:2
Alignment explanation
Indices: 43055--43082 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43045 AATTACTCGA
43055 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
43083 GTGAATTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43281 original size:2 final size:2
Alignment explanation
Indices: 43274--43324 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
43264 ACCCATTGGA
43274 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
43316 AT AT AT AT A
1 AT AT AT AT A
43325 GATAGAGAGA
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43333 original size:2 final size:2
Alignment explanation
Indices: 43328--43356 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43318 ATATATAGAT
43328 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 A
43357 AATGGAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:43729 original size:3 final size:3
Alignment explanation
Indices: 43721--43770 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
43711 AAACCTGGTA
43721 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT ATAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
43766 TAT TA
1 TAT TA
43771 GACTACTACC
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:44116 original size:2 final size:2
Alignment explanation
Indices: 44109--44142 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
44099 TTTTCCTTTA
*
44109 AT AT AT AT TT 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
44143 TAAAAGAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:44449 original size:20 final size:20
Alignment explanation
Indices: 44424--44463 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
44414 AGTAACTCGG
44424 ACTTATAAATAAGTAAGACA
1 ACTTATAAATAAGTAAGACA
*
44444 ACTTATGAATAAGTAAGACA
1 ACTTATAAATAAGTAAGACA
44464 TATGTGACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (20 bp):
ACTTATAAATAAGTAAGACA
Found at i:44919 original size:29 final size:28
Alignment explanation
Indices: 44869--44940 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 28
44859 AATTTAAATA
*
44869 AAAATTAATTTTATTAATAAATAA-TAATCT
1 AAAATTAA-TTTA--AATAAAAAATTAATCT
*
44899 -AAATTAATTTAAATAAAAAATTAATTT
1 AAAATTAATTTAAATAAAAAATTAATCT
44926 AAAATTAATTTAAAT
1 AAAATTAATTTAAAT
44941 TAAATCAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 8 0.21
27 5 0.13
28 18 0.47
29 7 0.18
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (28 bp):
AAAATTAATTTAAATAAAAAATTAATCT
Found at i:44931 original size:11 final size:11
Alignment explanation
Indices: 44915--44943 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
44905 ATTTAAATAA
44915 AAAATTAATTT
1 AAAATTAATTT
44926 AAAATTAATTT
1 AAAATTAATTT
44937 -AAATTAA
1 AAAATTAA
44944 ATCAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AAAATTAATTT
Found at i:44943 original size:16 final size:16
Alignment explanation
Indices: 44854--44944 Score: 56
Period size: 16 Copynumber: 6.1 Consensus size: 16
44844 ATATTTTTAT
*
44854 AATTAAATTTAAATAAA
1 AATT-AATTTAAATTAA
*
44871 AATTAATTT-TATTAA
1 AATTAATTTAAATTAA
*
44886 TAAATAA--T-AATCT-A
1 -AATTAATTTAAAT-TAA
44900 AATTAATTTAAA-TAA
1 AATTAATTTAAATTAA
*
44915 AA--AA-TTAATTTAA
1 AATTAATTTAAATTAA
44928 AATTAATTTAAATTAA
1 AATTAATTTAAATTAA
44944 A
1 A
44945 TCAATAAATT
Statistics
Matches: 57, Mismatches: 7, Indels: 21
0.67 0.08 0.25
Matches are distributed among these distances:
12 4 0.07
13 12 0.21
14 5 0.09
15 11 0.19
16 21 0.37
17 4 0.07
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTAATTTAAATTAA
Found at i:45313 original size:19 final size:19
Alignment explanation
Indices: 45291--45332 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
45281 ATTTAAATAA
* *
45291 AAATATTTGTTGAATATTT
1 AAATATTTATTAAATATTT
45310 AAATATTTATTAAATATTT
1 AAATATTTATTAAATATTT
45329 AAAT
1 AAAT
45333 CTATTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
AAATATTTATTAAATATTT
Found at i:46656 original size:35 final size:36
Alignment explanation
Indices: 46565--46656 Score: 98
Period size: 35 Copynumber: 2.5 Consensus size: 36
46555 TAAACACTTA
46565 TTTTATTATTTAAAATAATATTAAAATATTAAAAATAAT
1 TTTTATTATTT-AAAT-A-ATTAAAATATTAAAAATAAT
* * * *
46604 TTATA-TATAATATATAATT-AAATTTTAAAAATAAT
1 TTTTATTAT-TTAAATAATTAAAATATTAAAAATAAT
46639 TTTTATTATTTAAATAAT
1 TTTTATTATTTAAATAAT
46657 AATTTAAACC
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
35 26 0.59
36 6 0.14
37 1 0.02
38 6 0.14
39 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (36 bp):
TTTTATTATTTAAATAATTAAAATATTAAAAATAAT
Found at i:48069 original size:2 final size:2
Alignment explanation
Indices: 48062--48109 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
48052 ATCTGATCTT
* * *
48062 TA TA TA TA TA TA TA TA TA TA TG CA TA TA TA TA TA -A TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48103 TA TA TA T
1 TA TA TA T
48110 TTCATATACA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:50000 original size:17 final size:18
Alignment explanation
Indices: 49974--50013 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
49964 TAAATACGAT
49974 CATAACATAACA-AAATA
1 CATAACATAACATAAATA
* *
49991 TATAATATAACATAAATA
1 CATAACATAACATAAATA
50009 CATAA
1 CATAA
50014 ATTATTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (18 bp):
CATAACATAACATAAATA
Found at i:50424 original size:25 final size:25
Alignment explanation
Indices: 50391--50441 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
50381 ATTTAAATCG
*
50391 ATTTGATTTATTATTATTAATAAAAT
1 ATTTGATTTAATATTATTAA-AAAAT
*
50417 ATTT-ATTTAATATTTTTAAAAAAT
1 ATTTGATTTAATATTATTAAAAAAT
50441 A
1 A
50442 AAATAAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 6 0.26
25 13 0.57
26 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
ATTTGATTTAATATTATTAAAAAAT
Found at i:50902 original size:2 final size:2
Alignment explanation
Indices: 50895--50932 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
50885 TACCTAAAGC
50895 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
50933 TTTTTTGGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.