Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1274
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: 15250
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Found at i:541 original size:15 final size:14
Alignment explanation
Indices: 516--560 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
506 TATATTATAT
*
516 AAATGTTAAAAATA
1 AAATTTTAAAAATA
530 AATATTTTAAAAAATA
1 AA-ATTTT-AAAAATA
546 AAATTTTAAATAATA
1 AAATTTTAAA-AATA
561 TAGTTTCGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.19
15 13 0.48
16 9 0.33
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
AAATTTTAAAAATA
Found at i:544 original size:16 final size:15
Alignment explanation
Indices: 523--560 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
513 TATAAATGTT
523 AAAAATAAATATTTTA
1 AAAAATAAA-ATTTTA
539 AAAAATAAAATTTTA
1 AAAAATAAAATTTTA
*
554 AATAATA
1 AAAAATA
561 TAGTTTCGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAATAAAATTTTA
Found at i:3140 original size:19 final size:20
Alignment explanation
Indices: 3100--3145 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
3090 TATAAATATT
*
3100 TTTTATATTTATTGTAATAA
1 TTTTATATTTATTGTAAAAA
3120 TTTTA-ATTTATT-TAAAAAA
1 TTTTATATTTATTGT-AAAAA
3139 TTTTATA
1 TTTTATA
3146 ATTAAATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 1 0.04
19 16 0.70
20 6 0.26
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTATATTTATTGTAAAAA
Found at i:4535 original size:26 final size:25
Alignment explanation
Indices: 4513--4601 Score: 69
Period size: 25 Copynumber: 3.6 Consensus size: 25
4503 ATCATATTCA
* *
4513 AATTATATTTTAATATTTTATATTAT
1 AATTATA-ATTAAAATTTTATATTAT
*
4539 AATTTTAATTAAAATTTTATATTAT
1 AATTATAATTAAAATTTTATATTAT
* * * *
4564 -A-TAT-ATTCATATTATATATTTT
1 AATTATAATTAAAATTTTATATTAT
4586 AATTAT-ATATAAAATT
1 AATTATAAT-TAAAATT
4602 ATCAAATTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
22 14 0.28
23 3 0.06
24 6 0.12
25 21 0.42
26 6 0.12
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (25 bp):
AATTATAATTAAAATTTTATATTAT
Found at i:4545 original size:13 final size:14
Alignment explanation
Indices: 4515--4595 Score: 89
Period size: 15 Copynumber: 5.9 Consensus size: 14
4505 CATATTCAAA
*
4515 TTATATTTTAATATT
1 TTATATTAT-ATATT
4530 TTATATTATA-ATT
1 TTATATTATATATT
*
4543 TTA-ATTA-AAATT
1 TTATATTATATATT
4555 TTATATTATATATAT
1 TTATATTATATAT-T
*
4570 TCATATTATATATT
1 TTATATTATATATT
4584 TTA-ATTATATAT
1 TTATATTATATAT
4596 AAAATTATCA
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
11 1 0.02
12 10 0.17
13 19 0.33
14 7 0.12
15 21 0.36
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATATTATATATT
Found at i:4554 original size:12 final size:13
Alignment explanation
Indices: 4477--4562 Score: 70
Period size: 13 Copynumber: 6.8 Consensus size: 13
4467 TTAATAATTT
4477 ATTTTATA-T-AA
1 ATTTTATATTAAA
* *
4488 ATTTTAAATAAAA
1 ATTTTATATTAAA
* * *
4501 ATATCATATTCAA
1 ATTTTATATTAAA
* * *
4514 ATTATATTTTAAT
1 ATTTTATATTAAA
*
4527 ATTTTATATTATA
1 ATTTTATATTAAA
4540 ATTTTA-ATTAAA
1 ATTTTATATTAAA
4552 ATTTTATATTA
1 ATTTTATATTA
4563 TATATATTCA
Statistics
Matches: 54, Mismatches: 18, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
11 7 0.13
12 11 0.20
13 36 0.67
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATATTAAA
Found at i:6200 original size:11 final size:9
Alignment explanation
Indices: 6183--6255 Score: 62
Period size: 9 Copynumber: 7.8 Consensus size: 9
6173 TATTTTATAA
6183 ATAAAATTAT
1 ATAAAA-TAT
6193 ATTAAAAT-T
1 A-TAAAATAT
6202 ATAAAAATAT
1 AT-AAAATAT
*
6212 ATAAAATAA
1 ATAAAATAT
6221 ATAAAATAT
1 ATAAAATAT
6230 AATATAAA-ATT
1 -ATA-AAATA-T
6241 ATAAAA-AT
1 ATAAAATAT
6249 ATAAAAT
1 ATAAAAT
6256 TAAATTAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
8 8 0.15
9 25 0.46
10 12 0.22
11 9 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
ATAAAATAT
Found at i:6205 original size:19 final size:19
Alignment explanation
Indices: 6183--6251 Score: 79
Period size: 18 Copynumber: 3.6 Consensus size: 19
6173 TATTTTATAA
*
6183 ATAAAATTATATTAAAATT
1 ATAAAAATATATTAAAATT
6202 ATAAAAATATA-TAAAA-T
1 ATAAAAATATATTAAAATT
*
6219 AAATAAAATATAATATAAAATT
1 ATA-AAAATAT-AT-TAAAATT
6241 ATAAAAATATA
1 ATAAAAATATA
6252 AAATTAAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
17 3 0.07
18 12 0.29
19 11 0.26
20 1 0.02
21 12 0.29
22 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAAAATATATTAAAATT
Found at i:6212 original size:8 final size:8
Alignment explanation
Indices: 6195--6254 Score: 54
Period size: 8 Copynumber: 7.6 Consensus size: 8
6185 AAAATTATAT
*
6195 TAAAATTA
1 TAAAAATA
6203 TAAAAATA
1 TAAAAATA
6211 TATAAAATA
1 TA-AAAATA
6220 -AATAAA-A
1 TAA-AAATA
*
6227 T-ATAATA
1 TAAAAATA
*
6234 TAAAATTA
1 TAAAAATA
6242 TAAAAATA
1 TAAAAATA
6250 TAAAA
1 TAAAA
6255 TTAAATTAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
6 2 0.05
7 5 0.12
8 29 0.69
9 6 0.14
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (8 bp):
TAAAAATA
Found at i:6221 original size:38 final size:38
Alignment explanation
Indices: 6179--6271 Score: 129
Period size: 38 Copynumber: 2.5 Consensus size: 38
6169 GGTATATTTT
6179 ATAAATAAAATTATAT-TAAAATTATAAAAATATATAAA
1 ATAAATAAAATTATATATAAAATTATAAAAATATA-AAA
6217 ATAAATAAAA-TATAATATAAAATTATAAAAATATAAAA
1 ATAAATAAAATTAT-ATATAAAATTATAAAAATATAAAA
* *
6255 TTAAAT-TAATTATATAT
1 ATAAATAAAATTATATAT
6272 TTCTATGAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
37 9 0.18
38 23 0.46
39 18 0.36
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (38 bp):
ATAAATAAAATTATATATAAAATTATAAAAATATAAAA
Found at i:6234 original size:21 final size:19
Alignment explanation
Indices: 6182--6251 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
6172 ATATTTTATA
6182 AATAAAAT-TATATTAAAAT
1 AATAAAATATATA-TAAAAT
*
6201 TATAAAA-ATATATAAAAT
1 AATAAAATATATATAAAAT
6219 AAATAAAATATAATATAAAAT
1 -AATAAAATAT-ATATAAAAT
*
6240 TATAAAA-ATATA
1 AATAAAATATATA
6252 AAATTAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
18 9 0.20
19 18 0.41
20 8 0.18
21 9 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AATAAAATATATATAAAAT
Found at i:6249 original size:16 final size:16
Alignment explanation
Indices: 6183--6257 Score: 59
Period size: 16 Copynumber: 4.6 Consensus size: 16
6173 TATTTTATAA
6183 ATAAAATTATATTAAAATT
1 ATAAAATTATA--AAAA-T
*
6202 ATAAAAATATATAAAATAA
1 AT-AAAAT-TATAAAA-AT
6221 ATAAAA-TAT---AAT
1 ATAAAATTATAAAAAT
6233 ATAAAATTATAAAAAT
1 ATAAAATTATAAAAAT
6249 ATAAAATTA
1 ATAAAATTA
6258 AATTAATTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 17
0.71 0.03 0.26
Matches are distributed among these distances:
12 7 0.15
13 4 0.09
16 15 0.32
18 4 0.09
19 7 0.15
20 6 0.13
21 4 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAAAATTATAAAAAT
Found at i:6252 original size:21 final size:20
Alignment explanation
Indices: 6183--6251 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 20
6173 TATTTTATAA
*
6183 ATAAAATTATAT-TAAAATT
1 ATAAAAATATATATAAAATT
6202 AT-AAAA-ATATATAAAA-T
1 ATAAAAATATATATAAAATT
*
6219 AAATAAAATATAATATAAAATT
1 ATA-AAAATAT-ATATAAAATT
6241 ATAAAAATATA
1 ATAAAAATATA
6252 AAATTAAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
17 6 0.15
18 8 0.20
19 6 0.15
20 3 0.07
21 15 0.37
22 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAAAATATATATAAAATT
Found at i:6260 original size:21 final size:21
Alignment explanation
Indices: 6197--6262 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
6187 AATTATATTA
*
6197 AAATTATAAAAATATATAAAAT
1 AAATTATAAAAATATA-AAATT
* *
6219 -AA--AT-AAAATATAATATA
1 AAATTATAAAAATATAAAATT
6236 AAATTATAAAAATATAAAATT
1 AAATTATAAAAATATAAAATT
6257 AAATTA
1 AAATTA
6263 ATTATATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
17 2 0.06
18 10 0.29
19 2 0.06
20 2 0.06
21 19 0.54
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATTATAAAAATATAAAATT
Found at i:6482 original size:27 final size:28
Alignment explanation
Indices: 6452--6505 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
6442 AATTTAAAAG
*
6452 TTATTATATATTTACT-TAT-TTTTATTT
1 TTATTATAT-TTTAATATATATTTTATTT
6479 TTATTATATTTTAATATATATTTTATT
1 TTATTATATTTTAATATATATTTTATT
6506 AATTTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 5 0.21
27 12 0.50
28 7 0.29
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (28 bp):
TTATTATATTTTAATATATATTTTATTT
Found at i:6490 original size:10 final size:10
Alignment explanation
Indices: 6452--6519 Score: 56
Period size: 10 Copynumber: 6.9 Consensus size: 10
6442 AATTTAAAAG
6452 TTATTATATAT
1 TTATTATAT-T
*
6463 TTACT-TA-T
1 TTATTATATT
6471 TT-TTAT-TT
1 TTATTATATT
6479 TTATTATATT
1 TTATTATATT
6489 TTAATATATATT
1 TT-AT-TATATT
6501 TTATTA-ATT
1 TTATTATATT
6510 TTATTTATAT
1 TTA-TTATAT
6520 AATTTAATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
7 1 0.02
8 7 0.15
9 10 0.21
10 11 0.23
11 10 0.21
12 8 0.17
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATTATATT
Found at i:6505 original size:22 final size:22
Alignment explanation
Indices: 6477--6534 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
6467 TTATTTTTAT
6477 TTTTATTATATTTTA-ATATATA
1 TTTTATTA-ATTTTATATATATA
*
6499 TTTTATTAATTTTATTTATATA
1 TTTTATTAATTTTATATATATA
* *
6521 ATTTAATAATTTTA
1 TTTTATTAATTTTA
6535 GTAGAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 6 0.19
22 26 0.81
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTATTAATTTTATATATATA
Found at i:8012 original size:33 final size:33
Alignment explanation
Indices: 7935--8039 Score: 110
Period size: 33 Copynumber: 3.2 Consensus size: 33
7925 ATCAAACAAT
*
7935 TAAAAGTAAATATTAAATAT-A-AAAT-TTTAA
1 TAAAAATAAATATTAAATATAATAAATATTTAA
**
7965 TTTTAAATAAATATTAAATATAATAAATATTTAA
1 -TAAAAATAAATATTAAATATAATAAATATTTAA
* *
7999 TAAAAATATATATTTAACT-TAATAAATATTTAA
1 TAAAAATAAATA-TTAAATATAATAAATATTTAA
8032 TAGAAAAT
1 TA-AAAAT
8040 TCACAATTGA
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
31 17 0.27
32 1 0.02
33 29 0.47
34 15 0.24
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (33 bp):
TAAAAATAAATATTAAATATAATAAATATTTAA
Found at i:8465 original size:22 final size:22
Alignment explanation
Indices: 8424--8466 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
8414 TATAAAATTT
* *
8424 TTTTCTATTTGTCTCGTTTTTA
1 TTTTATATTTGTCTCATTTTTA
*
8446 TTTTATATTTGTCTTATTTTT
1 TTTTATATTTGTCTCATTTTT
8467 CTATTTGTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.09, G:0.07, T:0.72
Consensus pattern (22 bp):
TTTTATATTTGTCTCATTTTTA
Found at i:8471 original size:17 final size:17
Alignment explanation
Indices: 8446--8482 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
8436 CTCGTTTTTA
*
8446 TTTTATATTTGTCTTAT
1 TTTTATATTTGTCTCAT
*
8463 TTTTCTATTTGTCTCAT
1 TTTTATATTTGTCTCAT
8480 TTT
1 TTT
8483 GCTACTTCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (17 bp):
TTTTATATTTGTCTCAT
Found at i:8728 original size:2 final size:2
Alignment explanation
Indices: 8721--8761 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
8711 GTTGTAAAAG
8721 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8762 GGGATTTTGG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10851 original size:25 final size:24
Alignment explanation
Indices: 10817--10866 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
10807 ATAAAATATG
*
10817 ATAATTAAATTAAATAAATATTAA
1 ATAATTAAATTAAATAAATAGTAA
*
10841 ATAATTAAAATTATATAAATAGTAA
1 ATAATT-AAATTAAATAAATAGTAA
10866 A
1 A
10867 ATAAATTCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
ATAATTAAATTAAATAAATAGTAA
Found at i:11093 original size:13 final size:13
Alignment explanation
Indices: 11077--11143 Score: 66
Period size: 13 Copynumber: 5.2 Consensus size: 13
11067 TTATTTCGTA
11077 TTTATATTATATT
1 TTTATATTATATT
*
11090 TTTATA-TA-ATA
1 TTTATATTATATT
*
11101 TTTATATTATCTT
1 TTTATATTATATT
* *
11114 TTTATAATATAATAA
1 TTTATATTAT-AT-T
11129 TTTATATTATATT
1 TTTATATTATATT
11142 TT
1 TT
11144 AATTTTTTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
11 8 0.19
12 4 0.10
13 18 0.43
14 3 0.07
15 9 0.21
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTATATTATATT
Found at i:11102 original size:24 final size:26
Alignment explanation
Indices: 11075--11144 Score: 99
Period size: 24 Copynumber: 2.7 Consensus size: 26
11065 ATTTATTTCG
11075 TATTTATATTATATTTT-T-ATATAA
1 TATTTATATTATATTTTATAATATAA
*
11099 TATTTATATTATCTTTTTATAATATAA
1 TATTTATATTAT-ATTTTATAATATAA
11126 TAATTTATATTATATTTTA
1 T-ATTTATATTATATTTTA
11145 ATTTTTTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
24 12 0.30
25 4 0.10
26 1 0.03
27 12 0.30
28 11 0.28
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (26 bp):
TATTTATATTATATTTTATAATATAA
Found at i:11644 original size:18 final size:16
Alignment explanation
Indices: 11623--11697 Score: 55
Period size: 18 Copynumber: 4.3 Consensus size: 16
11613 TTTAAAAATT
11623 TTTAAAATTTACTATTTA
1 TTTAAAATTTA-T-TTTA
*
11641 TTT-AATTTTAATTTTA
1 TTTAAAATTT-ATTTTA
11657 TTTATAAATTTAATTAATT-
1 TTTA-AAATTT-ATT--TTA
11676 TTTAAAAATTTATTTTA
1 TTT-AAAATTTATTTTA
11693 TTTAA
1 TTTAA
11698 TATTATATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
16 11 0.23
17 9 0.19
18 16 0.33
19 9 0.19
20 3 0.06
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTAAAATTTATTTTA
Found at i:11696 original size:52 final size:53
Alignment explanation
Indices: 11610--11723 Score: 141
Period size: 52 Copynumber: 2.2 Consensus size: 53
11600 TCGAGTAGAA
* * *
11610 AAATTTAA-AAATTTTTAAAATTTACTATTTATTTAATTTTA-ATTTTATTTAT
1 AAATTTAATTAATTTTTAAAATTTACTATTTATTTAATATTATATATT-TTTAT
11662 AAATTTAATTAATTTTTAAAAATTTA-T-TTTATTTAATATTATATATTTTTAT
1 AAATTTAATTAATTTTT-AAAATTTACTATTTATTTAATATTATATATTTTTAT
11714 -AA-TTAATTAA
1 AAATTTAATTAA
11724 ATAAAAATTT
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
50 8 0.14
51 2 0.04
52 26 0.46
53 12 0.21
54 8 0.14
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (53 bp):
AAATTTAATTAATTTTTAAAATTTACTATTTATTTAATATTATATATTTTTAT
Found at i:11738 original size:20 final size:20
Alignment explanation
Indices: 11715--11769 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
11705 TATTTTTATA
11715 ATTAATTAAATAAAAATTTT
1 ATTAATTAAATAAAAATTTT
*
11735 ATTAATTAAATAATAA-TTT
1 ATTAATTAAATAAAAATTTT
*
11754 A--AATTAAATTAAAATT
1 ATTAATTAAATAAAAATT
11770 GTTGGACCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 11 0.35
18 1 0.03
19 4 0.13
20 15 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTAATTAAATAAAAATTTT
Found at i:12755 original size:3 final size:3
Alignment explanation
Indices: 12747--12794 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
12737 CCTCTTGTTT
* * * * *
12747 ATC ATC ATC ATC ATC TTC ATC ATT ATC ACC ATC ACC ATC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
12795 CTCGACCTCA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Done.