Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015893.1 Corchorus olitorius cultivar O-4 contig15926, 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: 35185
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Found at i:2236 original size:27 final size:27
Alignment explanation
Indices: 2198--2334 Score: 105
Period size: 27 Copynumber: 4.9 Consensus size: 27
2188 CGACCGATCA
2198 CATGCTGAAGCTCCTGCAGTTGGGACT
1 CATGCTGAAGCTCCTGCAGTTGGGACT
* **
2225 CATGCTGAAGCTCCCGTGGTTGGGACT
1 CATGCTGAAGCTCCTGCAGTTGGGACT
** * *
2252 CACACCGAAGCTCCCGCCTCGCAATTGGGACT
1 CATGCTGAAGCT----CCT-GCAGTTGGGACT
**
2284 CATGCCAAAGCCTCC-GCAGTTGGGACT
1 CATGCTGAAG-CTCCTGCAGTTGGGACT
* * *
2311 TATGTTGAAGCTCCTGCAATTGGG
1 CATGCTGAAGCTCCTGCAGTTGGG
2335 TTTTGTGTTG
Statistics
Matches: 84, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
26 4 0.05
27 58 0.69
29 2 0.02
31 2 0.02
32 16 0.19
33 2 0.02
ACGTcount: A:0.20, C:0.29, G:0.28, T:0.23
Consensus pattern (27 bp):
CATGCTGAAGCTCCTGCAGTTGGGACT
Found at i:2849 original size:37 final size:37
Alignment explanation
Indices: 2808--3030 Score: 270
Period size: 37 Copynumber: 6.0 Consensus size: 37
2798 GTAGTGATTT
*
2808 GTAAGGAGAGCTCTACGGTAAAGAGAGTGCTACCGCA
1 GTAAGGAGAGCTCTACGGTAAAGAGGGTGCTACCGCA
* * *
2845 GTAAGGAGTGCTCTACGGTGAAGAGGGTG-TCGCCGCA
1 GTAAGGAGAGCTCTACGGTAAAGAGGGTGCT-ACCGCA
* * * *
2882 GTAAGCAGAGCTC-AGCGGTAAAGAAGGTGTTATCGCA
1 GTAAGGAGAGCTCTA-CGGTAAAGAGGGTGCTACCGCA
** * *
2919 GTAATAAGAGCTCTGCGGTAAAGAGGGTGCTACCGCG
1 GTAAGGAGAGCTCTACGGTAAAGAGGGTGCTACCGCA
* *
2956 GTAAGGGGAGCTCTGCGGTAAAGAGGGTGCTACCGCA
1 GTAAGGAGAGCTCTACGGTAAAGAGGGTGCTACCGCA
* *
2993 GTAAGGGGAGCTCTATGGTAAAGAGGGTGCTACCGCA
1 GTAAGGAGAGCTCTACGGTAAAGAGGGTGCTACCGCA
3030 G
1 G
3031 GATTGGCTTT
Statistics
Matches: 159, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
36 2 0.01
37 156 0.98
38 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.37, T:0.18
Consensus pattern (37 bp):
GTAAGGAGAGCTCTACGGTAAAGAGGGTGCTACCGCA
Found at i:2958 original size:20 final size:20
Alignment explanation
Indices: 2933--3028 Score: 87
Period size: 18 Copynumber: 5.1 Consensus size: 20
2923 TAAGAGCTCT
2933 GCGGTAAAGAGGGTGCTACC
1 GCGGTAAAGAGGGTGCTACC
* *
2953 GCGGT-AAG-GGGAGCT-CT
1 GCGGTAAAGAGGGTGCTACC
2970 GCGGTAAAGAGGGTGCTACC
1 GCGGTAAAGAGGGTGCTACC
* * *
2990 GCAGT-AAG-GGGAGCT-CT
1 GCGGTAAAGAGGGTGCTACC
**
3007 ATGGTAAAGAGGGTGCTACC
1 GCGGTAAAGAGGGTGCTACC
3027 GC
1 GC
3029 AGGATTGGCT
Statistics
Matches: 56, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
17 9 0.16
18 18 0.32
19 18 0.32
20 11 0.20
ACGTcount: A:0.24, C:0.19, G:0.41, T:0.17
Consensus pattern (20 bp):
GCGGTAAAGAGGGTGCTACC
Found at i:2973 original size:17 final size:19
Alignment explanation
Indices: 2926--3019 Score: 79
Period size: 19 Copynumber: 5.1 Consensus size: 19
2916 GCAGTAATAA
2926 GAGCTCTGCGGTAAAGAGG
1 GAGCTCTGCGGTAAAGAGG
* *
2945 GTGCTACCGCGGT-AAG-GG
1 GAGCT-CTGCGGTAAAGAGG
2963 GAGCTCTGCGGTAAAGAGG
1 GAGCTCTGCGGTAAAGAGG
* * *
2982 GTGCTACCGCAGT-AAG-GG
1 GAGCT-CTGCGGTAAAGAGG
**
3000 GAGCTCTATGGTAAAGAGG
1 GAGCTCTGCGGTAAAGAGG
3019 G
1 G
3020 TGCTACCGCA
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
17 9 0.16
18 18 0.32
19 19 0.33
20 11 0.19
ACGTcount: A:0.24, C:0.17, G:0.41, T:0.17
Consensus pattern (19 bp):
GAGCTCTGCGGTAAAGAGG
Found at i:5592 original size:6 final size:6
Alignment explanation
Indices: 5570--5617 Score: 64
Period size: 6 Copynumber: 8.2 Consensus size: 6
5560 CTTCAAAAAT
*
5570 GAGCTC GAAGCT- GAGCTT GAGCTC GA-CTC GAGCTC GAGCTC GAGCTC
1 GAGCTC G-AGCTC GAGCTC GAGCTC GAGCTC GAGCTC GAGCTC GAGCTC
5617 G
1 G
5618 GAATTTTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
5 9 0.24
6 25 0.66
7 4 0.11
ACGTcount: A:0.19, C:0.29, G:0.33, T:0.19
Consensus pattern (6 bp):
GAGCTC
Found at i:5608 original size:17 final size:18
Alignment explanation
Indices: 5570--5617 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
5560 CTTCAAAAAT
*
5570 GAGCTCGAAGCT-GAGCTT
1 GAGCTCG-AGCTCGAGCTC
5588 GAGCTCGA-CTCGAGCTC
1 GAGCTCGAGCTCGAGCTC
5605 GAGCTCGAGCTCG
1 GAGCTCGAGCTCG
5618 GAATTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 2 0.07
17 14 0.52
18 11 0.41
ACGTcount: A:0.19, C:0.29, G:0.33, T:0.19
Consensus pattern (18 bp):
GAGCTCGAGCTCGAGCTC
Found at i:5608 original size:23 final size:23
Alignment explanation
Indices: 5573--5617 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5563 CAAAAATGAG
*
5573 CTCGAAGCTGAGCTTGAGCTCGA
1 CTCGAAGCTGAGCTCGAGCTCGA
5596 CTCG-AGCTCGAGCTCGAGCTCG
1 CTCGAAGCT-GAGCTCGAGCTCG
5618 GAATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.18, C:0.31, G:0.31, T:0.20
Consensus pattern (23 bp):
CTCGAAGCTGAGCTCGAGCTCGA
Found at i:6282 original size:178 final size:178
Alignment explanation
Indices: 6013--6336 Score: 494
Period size: 178 Copynumber: 1.8 Consensus size: 178
6003 CCGATTAAGG
* * *
6013 TGATTTAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTTATGAAGGGCTCGAAAACTA
1 TGATTTAAGTGTCTATTAAAAGATTATTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
* *
6078 AATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAA-AATT-TGTTGTTTCAG-TTAATGGAAAT
66 AATTTAATGTTTCAAGTATAAAAAATGCTTCC-AAAGAATTAT-TTGTTTC-GTTTAACGGAAAT
*
6140 AGACGGTCCACTTAATATTATATAACTTTTGCTCCAGATGTCTAATTGAGA
128 AGACAGTCCACTTAATATTATATAACTTTTGCTCCAGATGTCTAATTGAGA
* *
6191 TGATTTAAGTGTCTCTTAAAAGGTTATTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTTAAGTGTCTATTAAAAGATTATTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
6256 AATTTAATG-TTCAAGGTATAAAAAATGCTTCCAAAGAATTATTTGTTTCGTTTAACGGAAATAG
66 AATTTAATGTTTCAA-GTATAAAAAATGCTTCCAAAGAATTATTTGTTTCGTTTAACGGAAATAG
**
6320 ACAGTTTACTTAATATT
130 ACAGTCCACTTAATATT
6337 TCGCCTACTT
Statistics
Matches: 132, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
177 9 0.07
178 122 0.92
179 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (178 bp):
TGATTTAAGTGTCTATTAAAAGATTATTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
AATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAGAATTATTTGTTTCGTTTAACGGAAATAGA
CAGTCCACTTAATATTATATAACTTTTGCTCCAGATGTCTAATTGAGA
Found at i:12858 original size:54 final size:54
Alignment explanation
Indices: 12785--12889 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
12775 ACATAAACTT
* * ** *
12785 CAGTGCTAGATATTGGGTATGTTGGTAGAATGTTGGACTCTTAATTCCAATATC
1 CAGTACTAGATATTGGGTATGGTGACAAAATGTTGGACTCTTAATTCCAATATC
* * *
12839 CAGTACTAGATATTTGGTATGGTGACAAAATGTTGGAGTCTTAGTTCCAAT
1 CAGTACTAGATATTGGGTATGGTGACAAAATGTTGGACTCTTAATTCCAAT
12890 GGCTAAATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (54 bp):
CAGTACTAGATATTGGGTATGGTGACAAAATGTTGGACTCTTAATTCCAATATC
Found at i:13777 original size:15 final size:15
Alignment explanation
Indices: 13759--13798 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
13749 TTAATATAAT
*
13759 TTTTTAATTATTTTA
1 TTTTTAATTATTTAA
13774 TTTTTACATT-TTTAA
1 TTTTTA-ATTATTTAA
13789 TTTTTAATTA
1 TTTTTAATTA
13799 AAAAAGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 3 0.14
15 16 0.73
16 3 0.14
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTAATTATTTAA
Found at i:13791 original size:7 final size:7
Alignment explanation
Indices: 13759--13797 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
13749 TTAATATAAT
13759 TTTTTAA
1 TTTTTAA
*
13766 TTATTTTA
1 TT-TTTAA
13774 TTTTTACA
1 TTTTTA-A
13782 TTTTTAA
1 TTTTTAA
13789 TTTTTAA
1 TTTTTAA
13796 TT
1 TT
13798 AAAAAAGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 15 0.54
8 13 0.46
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTTAA
Found at i:14255 original size:23 final size:23
Alignment explanation
Indices: 14212--14255 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
14202 TAATGAAGAA
* *
14212 TTTAAATCAAAATAAAGATATTT
1 TTTAAAACAAAATAAACATATTT
14235 TTTAAAACAAAA-ATAACATAT
1 TTTAAAACAAAATA-AACATAT
14256 GTTATTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.06
23 17 0.94
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (23 bp):
TTTAAAACAAAATAAACATATTT
Found at i:16022 original size:23 final size:25
Alignment explanation
Indices: 15996--16053 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
15986 GACACAATCT
*
15996 ACTTCCGCCCCTT-AAGAATC-AAA
1 ACTTCTGCCCCTTCAAGAATCGAAA
* *
16019 ACTTGTGCCCTTTCAAGAATCGAAA
1 ACTTCTGCCCCTTCAAGAATCGAAA
16044 A-TTCTGCCCC
1 ACTTCTGCCCC
16054 CTCCTAAAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 10 0.36
24 14 0.50
25 4 0.14
ACGTcount: A:0.29, C:0.33, G:0.12, T:0.26
Consensus pattern (25 bp):
ACTTCTGCCCCTTCAAGAATCGAAA
Found at i:17342 original size:31 final size:31
Alignment explanation
Indices: 17285--17343 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
17275 TTCAGCTCAT
* *
17285 CTGGATTCAGGTCATTCGGGTCTCGGGTCTG
1 CTGGATTCAGGTCATGCAGGTCTCGGGTCTG
*
17316 CTGGATTTAGGGTCATGCAGGT-TCGGGT
1 CTGGATTCA-GGTCATGCAGGTCTCGGGT
17344 TTTGGCCTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 14 0.58
32 10 0.42
ACGTcount: A:0.12, C:0.19, G:0.37, T:0.32
Consensus pattern (31 bp):
CTGGATTCAGGTCATGCAGGTCTCGGGTCTG
Found at i:23863 original size:16 final size:16
Alignment explanation
Indices: 23842--23873 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
23832 TGAGATTATG
*
23842 CTGTCCCTAGCTTACT
1 CTGTCCATAGCTTACT
23858 CTGTCCATAGCTTACT
1 CTGTCCATAGCTTACT
23874 GAAAAAAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.34, G:0.12, T:0.38
Consensus pattern (16 bp):
CTGTCCATAGCTTACT
Found at i:32428 original size:12 final size:13
Alignment explanation
Indices: 32402--32441 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
32392 CGGAATGTGG
*
32402 GTTTAGTTAATTT
1 GTTTATTTAATTT
32415 GTTTATTT-ATTT
1 GTTTATTTAATTT
*
32427 GTTTGTTTAATTT
1 GTTTATTTAATTT
32440 GT
1 GT
32442 AGTTGGTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.68
Consensus pattern (13 bp):
GTTTATTTAATTT
Found at i:32662 original size:107 final size:103
Alignment explanation
Indices: 32502--32711 Score: 341
Period size: 102 Copynumber: 2.0 Consensus size: 103
32492 TAAGATATTT
*
32502 AGGCATAAGGAAATATTCTGATTGTAATGAGATTTCATTGTACCACTTCAAAAAAAAAAAAAACC
1 AGGCATAAGGAAATATTCTGATTGTAATGAGATTTCATTATACCACTTC----AAAAAAAAAACC
*
32567 ATCATGTTTCTTAAAAATAAAAAATAATAATAAACTAAAAAA
62 ATCATGTTTCTTAAAAATAAAAAATAATAATAAACCAAAAAA
*
32609 AGGCATAAGGAAATATTTTGATTGTAATGAGATTTCATTATACCAC-TCAAAAAAAAAACCATCA
1 AGGCATAAGGAAATATTCTGATTGTAATGAGATTTCATTATACCACTTCAAAAAAAAAACCATCA
*
32673 TGTTTCTTAAAAATGAAAAATAATAATAAACCAAAAAA
66 TGTTTCTTAAAAATAAAAAATAATAATAAACCAAAAAA
32711 A
1 A
32712 CACAAAGTGA
Statistics
Matches: 99, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
102 53 0.54
106 2 0.02
107 44 0.44
ACGTcount: A:0.52, C:0.11, G:0.10, T:0.27
Consensus pattern (103 bp):
AGGCATAAGGAAATATTCTGATTGTAATGAGATTTCATTATACCACTTCAAAAAAAAAACCATCA
TGTTTCTTAAAAATAAAAAATAATAATAAACCAAAAAA
Found at i:32820 original size:31 final size:31
Alignment explanation
Indices: 32764--32822 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
32754 TTTGTAAAAC
*
32764 TTTTGAAACGCCTATTGTACCCTTATTTAAT
1 TTTTGAAACGCCTATTATACCCTTATTTAAT
* **
32795 TTTTGAAACGTCTATTATATTCTTATTT
1 TTTTGAAACGCCTATTATACCCTTATTT
32823 GTCTAACATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.25, C:0.15, G:0.08, T:0.51
Consensus pattern (31 bp):
TTTTGAAACGCCTATTATACCCTTATTTAAT
Done.