Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007624.1 Corchorus capsularis cultivar CVL-1 contig07645, whole genome shotgun sequence
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: 17361
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:1470 original size:30 final size:30
Alignment explanation
Indices: 1434--1533 Score: 112
Period size: 30 Copynumber: 3.3 Consensus size: 30
1424 AAGGATCCAT
*
1434 TGGCCGGTTGTGCG-CGGATGCCCCATGCGA
1 TGGCCGGTTGTG-GACGGTTGCCCCATGCGA
1464 TGGCCGGTTGTGGACGGTTGATCCCCATGCGA
1 TGGCCGGTTGTGGACGGTTG--CCCCATGCGA
* * * * *
1496 TGCCCAGTTGTGGCCGGTTGCCCTATTCGA
1 TGGCCGGTTGTGGACGGTTGCCCCATGCGA
1526 TGGCCGGT
1 TGGCCGGT
1534 CAAGTGCCCG
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
29 1 0.02
30 31 0.53
32 27 0.46
ACGTcount: A:0.10, C:0.28, G:0.37, T:0.25
Consensus pattern (30 bp):
TGGCCGGTTGTGGACGGTTGCCCCATGCGA
Found at i:4486 original size:21 final size:21
Alignment explanation
Indices: 4460--4521 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
4450 TCAAAAGGTA
4460 AAAAGGTAATCAGTAAAAAGC
1 AAAAGGTAATCAGTAAAAAGC
* *
4481 AAAAGGGTAATCAGT-AAGAGT
1 AAAA-GGTAATCAGTAAAAAGC
*
4502 AAAAGAGTAATCAATAAAAA
1 AAAAG-GTAATCAGTAAAAA
4522 TTGTAAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.03
21 20 0.59
22 13 0.38
ACGTcount: A:0.58, C:0.06, G:0.19, T:0.16
Consensus pattern (21 bp):
AAAAGGTAATCAGTAAAAAGC
Found at i:4562 original size:34 final size:33
Alignment explanation
Indices: 4517--4617 Score: 143
Period size: 34 Copynumber: 3.0 Consensus size: 33
4507 AGTAATCAAT
*
4517 AAAAATTGTAAAATGTAAAGGGTAATCAGTAAAG
1 AAAAATGGTAAAA-GTAAAGGGTAATCAGTAAAG
4551 AAAAATGGTAAAAAGTAAAGGGTAATCAGTAAAG
1 AAAAATGGT-AAAAGTAAAGGGTAATCAGTAAAG
*
4585 AAAAATGGTAAAGAGTAAAGAGTAA--AGTAAAG
1 AAAAATGGTAAA-AGTAAAGGGTAATCAGTAAAG
4617 A
1 A
4618 GTAATCAGTA
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
32 8 0.13
33 3 0.05
34 48 0.76
35 4 0.06
ACGTcount: A:0.56, C:0.02, G:0.23, T:0.19
Consensus pattern (33 bp):
AAAAATGGTAAAAGTAAAGGGTAATCAGTAAAG
Found at i:4567 original size:20 final size:20
Alignment explanation
Indices: 4544--4605 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
4534 AAGGGTAATC
4544 AGTAAAGAAAAATGGTAAAA
1 AGTAAAGAAAAATGGTAAAA
**
4564 AGTAAAG------GGTAATC
1 AGTAAAGAAAAATGGTAAAA
*
4578 AGTAAAGAAAAATGGTAAAG
1 AGTAAAGAAAAATGGTAAAA
4598 AGTAAAGA
1 AGTAAAGA
4606 GTAAAGTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
14 12 0.38
20 20 0.62
ACGTcount: A:0.58, C:0.02, G:0.24, T:0.16
Consensus pattern (20 bp):
AGTAAAGAAAAATGGTAAAA
Found at i:4615 original size:12 final size:13
Alignment explanation
Indices: 4598--4631 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
4588 AATGGTAAAG
4598 AGTAAAGAGTAA-
1 AGTAAAGAGTAAC
4610 AGTAAAGAGTAATC
1 AGTAAAGAGTAA-C
4624 AGTAAAGA
1 AGTAAAGA
4632 AAGATGGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
14 8 0.40
ACGTcount: A:0.56, C:0.03, G:0.24, T:0.18
Consensus pattern (13 bp):
AGTAAAGAGTAAC
Found at i:4622 original size:46 final size:46
Alignment explanation
Indices: 4562--4665 Score: 163
Period size: 46 Copynumber: 2.2 Consensus size: 46
4552 AAAATGGTAA
*
4562 AAAGTAAAGGGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGT
1 AAAGTAAAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGT
* *
4608 AAAGTAAAGAGTAATCAGTAAAGAAAGATGGTAAAGAGTGAAGAGT
1 AAAGTAAAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGT
4654 AATTAGTAAAGA
1 AA--AGTAAAGA
4666 AAAAGGTAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
46 45 0.85
48 8 0.15
ACGTcount: A:0.54, C:0.02, G:0.26, T:0.18
Consensus pattern (46 bp):
AAAGTAAAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGT
Found at i:4654 original size:34 final size:34
Alignment explanation
Indices: 4610--4715 Score: 162
Period size: 34 Copynumber: 3.1 Consensus size: 34
4600 TAAAGAGTAA
4610 AGTAAAGAGTAATCAGTAAAGAAAGATGGTAAAG
1 AGTAAAGAGTAATCAGTAAAGAAAGATGGTAAAG
* * *
4644 AGTGAAGAGTAATTAGTAAAGAAA-AAGGTAAAG
1 AGTAAAGAGTAATCAGTAAAGAAAGATGGTAAAG
4677 AGTAAAGAGTAATCAGTAAAG-AAGAATGGTAAAG
1 AGTAAAGAGTAATCAGTAAAGAAAG-ATGGTAAAG
4711 AGTAA
1 AGTAA
4716 TCATTCCCTT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
32 2 0.03
33 27 0.42
34 35 0.55
ACGTcount: A:0.54, C:0.02, G:0.26, T:0.18
Consensus pattern (34 bp):
AGTAAAGAGTAATCAGTAAAGAAAGATGGTAAAG
Found at i:4675 original size:46 final size:45
Alignment explanation
Indices: 4562--4677 Score: 128
Period size: 46 Copynumber: 2.5 Consensus size: 45
4552 AAAATGGTAA
* *
4562 AAAGTAAAGGGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGT
1 AAAGTAAAGAG-AATAAGTAAAGAAAAATGGTAAAGAGTAAAGAGT
* * *
4608 AAAGTAAAGAGTAATCAGTAAAGAAAGATGGTAAAGAGTGAAGAGT
1 AAAGTAAAGAG-AATAAGTAAAGAAAAATGGTAAAGAGTAAAGAGT
4654 AATTAGTAAAGA-AA-AAGGTAAAGA
1 AA--AGTAAAGAGAATAA-GTAAAGA
4678 GTAAAGAGTA
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
45 1 0.02
46 54 0.86
48 8 0.13
ACGTcount: A:0.55, C:0.02, G:0.26, T:0.17
Consensus pattern (45 bp):
AAAGTAAAGAGAATAAGTAAAGAAAAATGGTAAAGAGTAAAGAGT
Found at i:4676 original size:6 final size:7
Alignment explanation
Indices: 4592--4715 Score: 77
Period size: 7 Copynumber: 18.6 Consensus size: 7
4582 AAGAAAAATG
4592 GTAAAGA
1 GTAAAGA
4599 GTAAAGA
1 GTAAAGA
4606 GT-AA-A
1 GTAAAGA
4611 GTAAAGA
1 GTAAAGA
**
4618 GTAATCA
1 GTAAAGA
4625 GT-AA-A
1 GTAAAGA
4630 G-AAAGA
1 GTAAAGA
4636 TGGTAAAGA
1 --GTAAAGA
*
4645 GTGAAGA
1 GTAAAGA
**
4652 GTAATTA
1 GTAAAGA
4659 GTAAAGA
1 GTAAAGA
*
4666 -AAAAG-
1 GTAAAGA
4671 GTAAAGA
1 GTAAAGA
4678 GTAAAGA
1 GTAAAGA
**
4685 GTAATCA
1 GTAAAGA
4692 GTAAAGAA
1 GTAAAG-A
*
4700 G-AATG-
1 GTAAAGA
4705 GTAAAGA
1 GTAAAGA
4712 GTAA
1 GTAA
4716 TCATTCCCTT
Statistics
Matches: 88, Mismatches: 17, Indels: 24
0.68 0.13 0.19
Matches are distributed among these distances:
5 8 0.09
6 17 0.19
7 55 0.62
8 3 0.03
9 5 0.06
ACGTcount: A:0.54, C:0.02, G:0.27, T:0.18
Consensus pattern (7 bp):
GTAAAGA
Found at i:4773 original size:22 final size:22
Alignment explanation
Indices: 4748--4825 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
4738 TGGGCGCATC
4748 AAAAGGTAAAAAGGTAATCAGT
1 AAAAGGTAAAAAGGTAATCAGT
* * *
4770 AAAAAGCAAAAGGGTAATCAGT
1 AAAAGGTAAAAAGGTAATCAGT
* *
4792 AAGA-GT-AAAAGAGTAATCAAT
1 AAAAGGTAAAAAG-GTAATCAGT
4813 AAAAATGGTAAAA
1 -AAAA-GGTAAAA
4826 TGTAAAGGGT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
20 4 0.09
21 9 0.21
22 25 0.58
24 2 0.05
25 3 0.07
ACGTcount: A:0.58, C:0.05, G:0.21, T:0.17
Consensus pattern (22 bp):
AAAAGGTAAAAAGGTAATCAGT
Found at i:4782 original size:21 final size:21
Alignment explanation
Indices: 4756--4817 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
4746 TCAAAAGGTA
4756 AAAAGGTAATCAGTAAAAAGC
1 AAAAGGTAATCAGTAAAAAGC
* *
4777 AAAAGGGTAATCAGT-AAGAGT
1 AAAA-GGTAATCAGTAAAAAGC
*
4798 AAAAGAGTAATCAATAAAAA
1 AAAAG-GTAATCAGTAAAAA
4818 TGGTAAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.03
21 20 0.59
22 13 0.38
ACGTcount: A:0.58, C:0.06, G:0.19, T:0.16
Consensus pattern (21 bp):
AAAAGGTAATCAGTAAAAAGC
Found at i:4856 original size:34 final size:33
Alignment explanation
Indices: 4813--4913 Score: 152
Period size: 34 Copynumber: 3.0 Consensus size: 33
4803 AGTAATCAAT
4813 AAAAATGGTAAAATGTAAAGGGTAATCAGTAAAG
1 AAAAATGGTAAAA-GTAAAGGGTAATCAGTAAAG
4847 AAAAATGGTAAAAAGTAAAGGGTAATCAGTAAAG
1 AAAAATGGT-AAAAGTAAAGGGTAATCAGTAAAG
*
4881 AAAAATGGTAAAGAGTAAAGAGTAA--AGTAAAG
1 AAAAATGGTAAA-AGTAAAGGGTAATCAGTAAAG
4913 A
1 A
4914 GTAATCAGTA
Statistics
Matches: 64, Mismatches: 1, Indels: 6
0.90 0.01 0.08
Matches are distributed among these distances:
32 8 0.12
33 3 0.05
34 49 0.77
35 4 0.06
ACGTcount: A:0.56, C:0.02, G:0.24, T:0.18
Consensus pattern (33 bp):
AAAAATGGTAAAAGTAAAGGGTAATCAGTAAAG
Found at i:4863 original size:20 final size:20
Alignment explanation
Indices: 4840--4901 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
4830 AAGGGTAATC
4840 AGTAAAGAAAAATGGTAAAA
1 AGTAAAGAAAAATGGTAAAA
**
4860 AGTAAAG------GGTAATC
1 AGTAAAGAAAAATGGTAAAA
*
4874 AGTAAAGAAAAATGGTAAAG
1 AGTAAAGAAAAATGGTAAAA
4894 AGTAAAGA
1 AGTAAAGA
4902 GTAAAGTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
14 12 0.38
20 20 0.62
ACGTcount: A:0.58, C:0.02, G:0.24, T:0.16
Consensus pattern (20 bp):
AGTAAAGAAAAATGGTAAAA
Found at i:4900 original size:7 final size:7
Alignment explanation
Indices: 4888--4995 Score: 68
Period size: 7 Copynumber: 16.0 Consensus size: 7
4878 AAGAAAAATG
4888 GTAAAGA
1 GTAAAGA
4895 GTAAAGA
1 GTAAAGA
4902 GT-AA-A
1 GTAAAGA
4907 GTAAAGA
1 GTAAAGA
**
4914 GTAATCA
1 GTAAAGA
4921 GT-AA-A
1 GTAAAGA
4926 G-AAAGA
1 GTAAAGA
4932 TGGTAAAGA
1 --GTAAAGA
*
4941 GTGAAGA
1 GTAAAGA
**
4948 GTAATCA
1 GTAAAGA
4955 GTAAAGAA
1 GTAAAG-A
*
4963 G-AATG-
1 GTAAAGA
4968 GTAAAGA
1 GTAAAGA
4975 GTAAAGA
1 GTAAAGA
**
4982 GTAATCA
1 GTAAAGA
4989 GTAAAGA
1 GTAAAGA
4996 AAAAATGGTG
Statistics
Matches: 76, Mismatches: 15, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
5 8 0.11
6 9 0.12
7 51 0.67
8 3 0.04
9 5 0.07
ACGTcount: A:0.53, C:0.03, G:0.27, T:0.18
Consensus pattern (7 bp):
GTAAAGA
Found at i:4911 original size:12 final size:13
Alignment explanation
Indices: 4894--4927 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
4884 AATGGTAAAG
4894 AGTAAAGAGTAA-
1 AGTAAAGAGTAAC
4906 AGTAAAGAGTAATC
1 AGTAAAGAGTAA-C
4920 AGTAAAGA
1 AGTAAAGA
4928 AAGATGGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
14 8 0.40
ACGTcount: A:0.56, C:0.03, G:0.24, T:0.18
Consensus pattern (13 bp):
AGTAAAGAGTAAC
Found at i:4912 original size:80 final size:81
Alignment explanation
Indices: 4827--4995 Score: 268
Period size: 80 Copynumber: 2.1 Consensus size: 81
4817 ATGGTAAAAT
* *
4827 GTAAAGGGTAATCAGTAAAGAAAAATGGTAAAAAGTAAAGGGTAATCAGTAAAGAAAAATGGTAA
1 GTAAAGAGTAATCAGTAAAGAAAAATGGTAAAAAGTAAAGAGTAATCAGTAAAGAAAAATGGTAA
4892 AGAGTAAAGAGTAA-A
66 AGAGTAAAGAGTAACA
* * * *
4907 GTAAAGAGTAATCAGTAAAGAAAGATGGTAAAGAGTGAAGAGTAATCAGTAAAGAAGAATGGTAA
1 GTAAAGAGTAATCAGTAAAGAAAAATGGTAAAAAGTAAAGAGTAATCAGTAAAGAAAAATGGTAA
4972 AGAGTAAAGAGTAATCA
66 AGAGTAAAGAGTAA-CA
4989 GTAAAGA
1 GTAAAGA
4996 AAAAATGGTG
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
80 73 0.90
82 8 0.10
ACGTcount: A:0.53, C:0.03, G:0.26, T:0.18
Consensus pattern (81 bp):
GTAAAGAGTAATCAGTAAAGAAAAATGGTAAAAAGTAAAGAGTAATCAGTAAAGAAAAATGGTAA
AGAGTAAAGAGTAACA
Found at i:4919 original size:46 final size:46
Alignment explanation
Indices: 4858--4961 Score: 163
Period size: 46 Copynumber: 2.2 Consensus size: 46
4848 AAAATGGTAA
*
4858 AAAGTAAAGGGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGT
1 AAAGTAAAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGT
* *
4904 AAAGTAAAGAGTAATCAGTAAAGAAAGATGGTAAAGAGTGAAGAGT
1 AAAGTAAAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGT
4950 AATCAGTAAAGA
1 AA--AGTAAAGA
4962 AGAATGGTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
46 45 0.85
48 8 0.15
ACGTcount: A:0.54, C:0.03, G:0.26, T:0.17
Consensus pattern (46 bp):
AAAGTAAAGAGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGT
Found at i:4950 original size:34 final size:35
Alignment explanation
Indices: 4906--5029 Score: 171
Period size: 34 Copynumber: 3.6 Consensus size: 35
4896 TAAAGAGTAA
4906 AGTAAAGAGTAATCAGTAAAGAAAG-ATGGTAAAG
1 AGTAAAGAGTAATCAGTAAAGAAAGAATGGTAAAG
*
4940 AGTGAAGAGTAATCAGTAAAG-AAGAATGGTAAAG
1 AGTAAAGAGTAATCAGTAAAGAAAGAATGGTAAAG
* * *
4974 AGTAAAGAGTAATCAGTAAAGAAAAAATGGTGAGG
1 AGTAAAGAGTAATCAGTAAAGAAAGAATGGTAAAG
* *
5009 AGTAAAATATTAATCAGTAAA
1 AGT-AAAGAGTAATCAGTAAA
5030 AAGTAATGGC
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
33 3 0.04
34 49 0.61
35 13 0.16
36 15 0.19
ACGTcount: A:0.52, C:0.03, G:0.25, T:0.19
Consensus pattern (35 bp):
AGTAAAGAGTAATCAGTAAAGAAAGAATGGTAAAG
Found at i:4960 original size:296 final size:297
Alignment explanation
Indices: 4419--4996 Score: 1122
Period size: 296 Copynumber: 1.9 Consensus size: 297
4409 TCCTTGGCGC
4419 ATCATTCCCTTCATGATAAGTCTTGGGCGCATCAAAAGGTAAAAAGGTAATCAGTAAAAAGCAAA
1 ATCATTCCCTTCATGATAAGTCTTGGGCGCATCAAAAGGTAAAAAGGTAATCAGTAAAAAGCAAA
*
4484 AGGGTAATCAGTAAGAGTAAAAGAGTAATCAATAAAAATTGTAAAATGTAAAGGGTAATCAGTAA
66 AGGGTAATCAGTAAGAGTAAAAGAGTAATCAATAAAAATGGTAAAATGTAAAGGGTAATCAGTAA
4549 AGAAAAATGGTAAAAAGTAAAGGGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGTA
131 AGAAAAATGGTAAAAAGTAAAGGGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGTA
*
4614 AAGAGTAATCAGTAAAGAAAGATGGTAAAGAGTGAAGAGTAATTAGTAAAGAA-AAAGGTAAAGA
196 AAGAGTAATCAGTAAAGAAAGATGGTAAAGAGTGAAGAGTAATCAGTAAAGAAGAAAGGTAAAGA
4678 GTAAAGAGTAATCAGTAAAGAAGAATGGTAAAGAGTA
261 GTAAAGAGTAATCAGTAAAGAAGAATGGTAAAGAGTA
4715 ATCATTCCCTTCATGATAAGTCTTGGGCGCATCAAAAGGTAAAAAGGTAATCAGTAAAAAGCAAA
1 ATCATTCCCTTCATGATAAGTCTTGGGCGCATCAAAAGGTAAAAAGGTAATCAGTAAAAAGCAAA
4780 AGGGTAATCAGTAAGAGTAAAAGAGTAATCAATAAAAATGGTAAAATGTAAAGGGTAATCAGTAA
66 AGGGTAATCAGTAAGAGTAAAAGAGTAATCAATAAAAATGGTAAAATGTAAAGGGTAATCAGTAA
4845 AGAAAAATGGTAAAAAGTAAAGGGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGTA
131 AGAAAAATGGTAAAAAGTAAAGGGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGTA
*
4910 AAGAGTAATCAGTAAAGAAAGATGGTAAAGAGTGAAGAGTAATCAGTAAAGAAGAATGGTAAAGA
196 AAGAGTAATCAGTAAAGAAAGATGGTAAAGAGTGAAGAGTAATCAGTAAAGAAGAAAGGTAAAGA
4975 GTAAAGAGTAATCAGTAAAGAA
261 GTAAAGAGTAATCAGTAAAGAA
4997 AAAATGGTGA
Statistics
Matches: 278, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
296 246 0.88
297 32 0.12
ACGTcount: A:0.51, C:0.06, G:0.23, T:0.20
Consensus pattern (297 bp):
ATCATTCCCTTCATGATAAGTCTTGGGCGCATCAAAAGGTAAAAAGGTAATCAGTAAAAAGCAAA
AGGGTAATCAGTAAGAGTAAAAGAGTAATCAATAAAAATGGTAAAATGTAAAGGGTAATCAGTAA
AGAAAAATGGTAAAAAGTAAAGGGTAATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGTA
AAGAGTAATCAGTAAAGAAAGATGGTAAAGAGTGAAGAGTAATCAGTAAAGAAGAAAGGTAAAGA
GTAAAGAGTAATCAGTAAAGAAGAATGGTAAAGAGTA
Found at i:5084 original size:56 final size:56
Alignment explanation
Indices: 4984--5091 Score: 128
Period size: 56 Copynumber: 1.9 Consensus size: 56
4974 AGTAAAGAGT
* * *
4984 AATCAGTAAAGAAAAAATGGTGAGGAGTAAAATATTAATCAGTAAAAAGTAATGGC
1 AATCAGTAAAGAAAAAATGGTGAGGACTAAAATAGTAAACAGTAAAAAGTAATGGC
** * * *
5040 AATCAGTAAAGAATAAAATGGTGATTACT-AATTAGTAAAGAGTAAAGAGTAA
1 AATCAGTAAAGAA-AAAATGGTGAGGACTAAAATAGTAAACAGTAAAAAGTAA
5092 CCAGTAAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
56 31 0.72
57 12 0.28
ACGTcount: A:0.52, C:0.05, G:0.20, T:0.23
Consensus pattern (56 bp):
AATCAGTAAAGAAAAAATGGTGAGGACTAAAATAGTAAACAGTAAAAAGTAATGGC
Found at i:7315 original size:33 final size:33
Alignment explanation
Indices: 7197--7303 Score: 169
Period size: 33 Copynumber: 3.2 Consensus size: 33
7187 CTAATTGTGA
* *
7197 TGAAAACAAATCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
* *
7230 TGAAAATAATTTTATTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
*
7263 TGGAAATAATTCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
7296 TGAAAATA
1 TGAAAATA
7304 GGACTGTTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40
Consensus pattern (33 bp):
TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
Found at i:9308 original size:21 final size:18
Alignment explanation
Indices: 9282--9322 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
9272 GCTTGAAGAC
9282 CATTGAAGATCAATTGGAGAG
1 CATTGAAG-TC-ATTGGA-AG
9303 CATTGAAGTCATTGGAAG
1 CATTGAAGTCATTGGAAG
9321 CA
1 CA
9323 AGAATATTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 6 0.30
20 2 0.10
21 8 0.40
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (18 bp):
CATTGAAGTCATTGGAAG
Found at i:11154 original size:30 final size:30
Alignment explanation
Indices: 11118--11178 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
11108 CAAAGGATCA
11118 AATGGCATCTTTGGTGCGATTCCTCCATCC
1 AATGGCATCTTTGGTGCGATTCCTCCATCC
*
11148 AATGGCATCTTTGGTGTGATTCCTCCATCC
1 AATGGCATCTTTGGTGCGATTCCTCCATCC
11178 A
1 A
11179 TTGATGTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.34
Consensus pattern (30 bp):
AATGGCATCTTTGGTGCGATTCCTCCATCC
Found at i:11189 original size:30 final size:30
Alignment explanation
Indices: 11118--11197 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 30
11108 CAAAGGATCA
* *
11118 AATGGCATCTTTGGTGCGATTCCTCCATCC
1 AATGACATCTTTGGTGTGATTCCTCCATCC
*
11148 AATGGCATCTTTGGTGTGATTCCTCCATCC
1 AATGACATCTTTGGTGTGATTCCTCCATCC
* **
11178 ATTGATGTCTTTGGTGTGAT
1 AATGACATCTTTGGTGTGAT
11198 CCCATCTCCT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.39
Consensus pattern (30 bp):
AATGACATCTTTGGTGTGATTCCTCCATCC
Found at i:12371 original size:23 final size:23
Alignment explanation
Indices: 12341--12399 Score: 118
Period size: 23 Copynumber: 2.6 Consensus size: 23
12331 ATGGCCCAAT
12341 CGATGGCCGGTTGGTGCGTCAAG
1 CGATGGCCGGTTGGTGCGTCAAG
12364 CGATGGCCGGTTGGTGCGTCAAG
1 CGATGGCCGGTTGGTGCGTCAAG
12387 CGATGGCCGGTTG
1 CGATGGCCGGTTG
12400 TGGCCGGACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.12, C:0.22, G:0.44, T:0.22
Consensus pattern (23 bp):
CGATGGCCGGTTGGTGCGTCAAG
Found at i:12464 original size:33 final size:31
Alignment explanation
Indices: 12390--12496 Score: 106
Period size: 33 Copynumber: 3.3 Consensus size: 31
12380 CGTCAAGCGA
* *
12390 TGGCCGGTTGTGGCCGGACATGTCCATGTCGCG
1 TGGCCGG-TGTGGCCGGGCATCTCCA-GTCGCG
12423 TGGCCGGTGATGGCCGGGCATCTCCGAGTCGCG
1 TGGCCGGTG-TGGCCGGGCATCTCC-AGTCGCG
* * * *
12456 TGGCCGGTGTTGGCCAGGCTTTTCCAAGTCGCA
1 TGGCCGGTG-TGGCCGGGCATCTCC-AGTCGCG
12489 TGGCCGGT
1 TGGCCGGT
12497 CACTCGCGCC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
32 2 0.03
33 61 0.95
34 1 0.02
ACGTcount: A:0.09, C:0.28, G:0.39, T:0.23
Consensus pattern (31 bp):
TGGCCGGTGTGGCCGGGCATCTCCAGTCGCG
Done.