Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold538
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: 40247
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:120 original size:17 final size:17
Alignment explanation
Indices: 98--174 Score: 54
Period size: 17 Copynumber: 4.6 Consensus size: 17
88 TCTTAGATTT
98 TATATATTATTATATAA
1 TATATATTATTATATAA
115 TATATAATTAATTATA-AA
1 TATAT-ATT-ATTATATAA
* *
133 -GTATATTATTAAATTAA
1 TATATATTATTATA-TAA
* * *
150 T-TACATTATAATATTA
1 TATATATTATTATATAA
166 TAT-TATTAT
1 TATATATTAT
175 AAAAGAAACA
Statistics
Matches: 47, Mismatches: 7, Indels: 13
0.70 0.10 0.19
Matches are distributed among these distances:
15 5 0.11
16 11 0.23
17 20 0.43
18 5 0.11
19 6 0.13
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (17 bp):
TATATATTATTATATAA
Found at i:128 original size:19 final size:18
Alignment explanation
Indices: 98--144 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
88 TCTTAGATTT
98 TATATATT-ATTATATAA-
1 TATATATTAATTATA-AAG
115 TATATAATTAATTATAAAG
1 TATAT-ATTAATTATAAAG
134 TATATTATTAA
1 TATA-TATTAA
145 ATTAATTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.19
18 5 0.19
19 15 0.58
20 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TATATATTAATTATAAAG
Found at i:1481 original size:18 final size:18
Alignment explanation
Indices: 1458--1500 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1448 ATGTGAGGTA
1458 AGTATTAATATTAGTATT
1 AGTATTAATATTAGTATT
*
1476 AGTATTATTATTAGTATT
1 AGTATTAATATTAGTATT
*
1494 ATTATTA
1 AGTATTA
1501 TGAGTGGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
AGTATTAATATTAGTATT
Found at i:1501 original size:6 final size:6
Alignment explanation
Indices: 1458--1500 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
1448 ATGTGAGGTA
* * *
1458 AGTATT AATATT AGTATT AGTATT ATTATT AGTATT ATTATT A
1 AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT A
1501 TGAGTGGGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (6 bp):
AGTATT
Found at i:1679 original size:23 final size:26
Alignment explanation
Indices: 1642--1710 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 26
1632 TGTTAATTGC
*
1642 GGAAATAATTATTG-ATTGAAAG-GT
1 GGAAATAATGATTGAATTGAAAGTGT
1666 GGAAA-AATGATTGAATTGAAAGTGT
1 GGAAATAATGATTGAATTGAAAGTGT
*
1691 GAGAAAGT-GTGATTGAATTG
1 G-GAAA-TAATGATTGAATTG
1711 GGATTATATG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
23 7 0.18
24 13 0.34
25 3 0.08
26 4 0.11
27 11 0.29
ACGTcount: A:0.41, C:0.00, G:0.29, T:0.30
Consensus pattern (26 bp):
GGAAATAATGATTGAATTGAAAGTGT
Found at i:1914 original size:37 final size:39
Alignment explanation
Indices: 1855--1950 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
1845 CGGATAGATT
* * * *
1855 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
1892 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
1931 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
1951 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:7944 original size:28 final size:29
Alignment explanation
Indices: 7913--7968 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
7903 TATTATTATT
*
7913 TATATAAATATATAAATTA-ATTATAAAG
1 TATATAAATAAATAAATTACATTATAAAG
* * *
7941 TATATTATTAAATTAATTACATTATAAA
1 TATATAAATAAATAAATTACATTATAAA
7969 TATTATATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (29 bp):
TATATAAATAAATAAATTACATTATAAAG
Found at i:9325 original size:18 final size:18
Alignment explanation
Indices: 9302--9344 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
9292 ATGTGAGGTA
9302 AGTATTAATATTAGTATT
1 AGTATTAATATTAGTATT
*
9320 AGTATTATTATTAGTATT
1 AGTATTAATATTAGTATT
*
9338 ATTATTA
1 AGTATTA
9345 TGAGTGGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
AGTATTAATATTAGTATT
Found at i:9345 original size:6 final size:6
Alignment explanation
Indices: 9302--9344 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
9292 ATGTGAGGTA
* * *
9302 AGTATT AATATT AGTATT AGTATT ATTATT AGTATT ATTATT A
1 AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT A
9345 TGAGTGGGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (6 bp):
AGTATT
Found at i:9529 original size:24 final size:27
Alignment explanation
Indices: 9497--9555 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
9487 CGGATTAATT
9497 ATTG-ATTGAAAG-GTG-GAAA-AATG
1 ATTGAATTGAAAGTGTGAGAAAGAATG
**
9520 ATTGAATTGAAAGTGTGAGAAAGTGTG
1 ATTGAATTGAAAGTGTGAGAAAGAATG
9547 ATTGAATTG
1 ATTGAATTG
9556 GATTATATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 4 0.13
24 8 0.27
25 3 0.10
26 4 0.13
27 11 0.37
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31
Consensus pattern (27 bp):
ATTGAATTGAAAGTGTGAGAAAGAATG
Found at i:9758 original size:37 final size:39
Alignment explanation
Indices: 9699--9794 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
9689 CGGATAGATT
* * * *
9699 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
9736 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
9775 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
9795 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:12549 original size:48 final size:52
Alignment explanation
Indices: 12479--12577 Score: 118
Period size: 52 Copynumber: 2.0 Consensus size: 52
12469 AATAATTATT
12479 ATTTTAAATTATACAAATTCATA-AACT-A-T-AATCATATTAGTTATAATA
1 ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
* * **
12527 ATTTTAAATTTTATTAAA-TCATATATTTAATTAAATCATATTAGTTATAAT
1 ATTTTAAATTATA-CAAATTCATATAACTAATTAAATCATATTAGTTATAAT
12578 CATATATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
48 17 0.40
49 5 0.12
50 1 0.02
51 1 0.02
52 18 0.43
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (52 bp):
ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
Found at i:12559 original size:17 final size:17
Alignment explanation
Indices: 12534--12567 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12524 ATAATTTTAA
*
12534 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
12551 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
12568 TAGTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:12584 original size:17 final size:16
Alignment explanation
Indices: 12539--12586 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
12529 TTTAAATTTT
12539 ATTAAATCATATATTTA
1 ATTAAATCATATA-TTA
12556 ATTAAATC--ATATTA
1 ATTAAATCATATATTA
*
12570 GTTATAATCATATATTA
1 ATTA-AATCATATATTA
12587 TGATTTGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
17 14 0.52
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (16 bp):
ATTAAATCATATATTA
Found at i:12641 original size:54 final size:54
Alignment explanation
Indices: 12583--12761 Score: 137
Period size: 54 Copynumber: 3.1 Consensus size: 54
12573 ATAATCATAT
12583 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
* * * * * * * *
12637 ATTATATATTTTAATTATATT-ATATTTAATAATAATTATGTTATTTTA-TATTTTACAGTATCA
1 ATTAT-GA-TTTGAGTAAATTCATA--TAAGAAT-ATTA-ATTA-TTAAGAATTTT--A-T-T-A
12700 TA
54 -A
*
12702 TATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 -ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
12757 ATTAT
1 ATTAT
12762 ATATTTTAAT
Statistics
Matches: 92, Mismatches: 17, Indels: 32
0.65 0.12 0.23
Matches are distributed among these distances:
54 10 0.11
55 5 0.05
56 10 0.11
57 7 0.08
58 5 0.05
59 9 0.10
60 6 0.07
61 9 0.10
62 5 0.05
63 7 0.08
64 10 0.11
65 4 0.04
66 5 0.05
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (54 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
Found at i:12644 original size:61 final size:61
Alignment explanation
Indices: 12579--12766 Score: 190
Period size: 61 Copynumber: 3.1 Consensus size: 61
12569 AGTTATAATC
12579 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * * * * *
12640 ATATATTTTAATTAT-ATTATATTTA-ATAATAATTATGTTATT-TT-A-TATTTTA-CAGTATC
1 ATATATTATGATT-TGAGTAAATTCATATAAGAA-TAT-TAATTATTAAGAATTTTATTA-AATT
*
12699 ATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
12760 ATATATT
1 ATATATT
12767 TTAATTAAAA
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
58 6 0.06
59 30 0.32
60 14 0.15
61 38 0.40
62 6 0.06
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:12658 original size:18 final size:17
Alignment explanation
Indices: 12627--12661 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12617 ATTATTAAGA
12627 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
12644 ATTTTAATTATATTATAT
1 ATTTT-ATTAAATTATAT
12662 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:12700 original size:120 final size:120
Alignment explanation
Indices: 12576--12798 Score: 419
Period size: 120 Copynumber: 1.9 Consensus size: 120
12566 ATTAGTTATA
12576 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
* *
12641 TATATTTTAATTATATTATATTTAATAATAATTATGTTATTTTATATTTTACAGT
66 TATATTTTAATTAAAATATATTTAATAATAATTATGTTATTTTATATTTTACAGT
*
12696 ATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
12761 TATATTTTAATTAAAATATATTTAATAATAATTATGTT
66 TATATTTTAATTAAAATATATTTAATAATAATTATGTT
12799 TAAATATGAT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 100 1.00
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
TATATTTTAATTAAAATATATTTAATAATAATTATGTTATTTTATATTTTACAGT
Found at i:12775 original size:18 final size:17
Alignment explanation
Indices: 12747--12781 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12737 ATTATTAAGA
*
12747 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
12764 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
12782 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:12793 original size:54 final size:54
Alignment explanation
Indices: 12610--12795 Score: 142
Period size: 54 Copynumber: 3.2 Consensus size: 54
12600 TTCATATAAG
* *
12610 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATATTATATTT
1 AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAATTATATTT
* * * *
12664 AATAATAATTATGT--TATTTTATATTTTACAGTATCATATATTATGGTTTGAGTAAATTCATAT
1 AATAATAATTAT-TAAGAATTT-TA--TTA-A--AT--TATA-TAT--TTTAATTAAATT-ATAT
**
12727 AAG
53 -TT
* *
12730 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTT
1 AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAATTATATTT
12784 AATAATAATTAT
1 AATAATAATTAT
12796 GTTTAAATAT
Statistics
Matches: 99, Mismatches: 17, Indels: 32
0.67 0.11 0.22
Matches are distributed among these distances:
53 4 0.04
54 24 0.24
55 5 0.05
56 12 0.12
57 1 0.01
58 3 0.03
59 6 0.06
61 6 0.06
62 3 0.03
63 1 0.01
64 12 0.12
65 5 0.05
66 13 0.13
67 4 0.04
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (54 bp):
AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAATTATATTT
Found at i:12902 original size:144 final size:147
Alignment explanation
Indices: 12735--13006 Score: 487
Period size: 144 Copynumber: 1.9 Consensus size: 147
12725 ATAAGAATAT
*
12735 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
12800 AAATATGATTAAATTATTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAA-AATAATTTA
66 AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
12862 CCAAAACAAATTTCTGC
131 CCAAAACAAATTTCTGC
12879 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
12944 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAAT--ATAATCTTATTAAAATTTAAATAACAATAA
13007 CAATAATCAT
Statistics
Matches: 121, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
144 91 0.75
145 2 0.02
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
CCAAAACAAATTTCTGC
Found at i:12919 original size:18 final size:17
Alignment explanation
Indices: 12891--12925 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12881 ATTATTAAGA
*
12891 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
12908 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
12926 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:13136 original size:44 final size:45
Alignment explanation
Indices: 13087--13181 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
13077 TTACACCTCT
* *
13087 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
13131 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
13176 ATTACA
1 ATTACA
13182 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:13181 original size:16 final size:16
Alignment explanation
Indices: 13160--13192 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
13150 TTGATTTGCT
*
13160 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
13176 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
13192 A
1 A
13193 ATCCAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:13202 original size:21 final size:21
Alignment explanation
Indices: 13173--13215 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
13163 ACACCTCTAT
*
13173 TCCATTACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
13194 TCCAATACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
13215 T
1 T
13216 ACAGCGAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (21 bp):
TCCAATACACCTCTAATCCAA
Found at i:17081 original size:46 final size:46
Alignment explanation
Indices: 17007--17123 Score: 211
Period size: 46 Copynumber: 2.6 Consensus size: 46
16997 TACGTATGAA
*
17007 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAAGGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAT
17051 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAT
17097 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
17124 AGTACTCAAA
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
44 10 0.14
45 5 0.07
46 55 0.79
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAT
Found at i:26233 original size:21 final size:23
Alignment explanation
Indices: 26191--26233 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
26181 TTTTTATTAA
* *
26191 AAAAATTATTTATTTTTACTGTT
1 AAAAATTAATTATTTGTACTGTT
26214 AAAAATTAATT-TTTGT-CTGT
1 AAAAATTAATTATTTGTACTGT
26234 CAATATAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 4 0.22
23 10 0.56
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (23 bp):
AAAAATTAATTATTTGTACTGTT
Found at i:39746 original size:12 final size:13
Alignment explanation
Indices: 39729--39759 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
39719 ATGATAGTAC
39729 AATTATTA-TAAG
1 AATTATTATTAAG
39741 AATTATTATTAAG
1 AATTATTATTAAG
39754 AATTAT
1 AATTAT
39760 AATATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (13 bp):
AATTATTATTAAG
Found at i:40039 original size:17 final size:17
Alignment explanation
Indices: 40014--40047 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40004 ATTATTAAGA
* *
40014 ATTTTATTAAAGTATAT
1 ATTTAATTAAAATATAT
40031 ATTTAATTAAAATATAT
1 ATTTAATTAAAATATAT
40048 TAAATAATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAAATATAT
Done.