Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012827.1 Corchorus capsularis cultivar CVL-1 contig12848, 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: 80621
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4238 original size:2 final size:2
Alignment explanation
Indices: 4226--4257 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4216 GTTACGTACA
4226 AT AT AT A- 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 A
4258 CTCCATACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:7075 original size:12 final size:12
Alignment explanation
Indices: 7058--7082 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7048 GTACAATTAA
7058 TATATATATATT
1 TATATATATATT
7070 TATATATATATT
1 TATATATATATT
7082 T
1 T
7083 CAATGTACCC
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATATATATT
Found at i:8510 original size:2 final size:2
Alignment explanation
Indices: 8503--8537 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
8493 TCAAACTCGA
8503 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 A
8538 CATCATGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13531 original size:59 final size:58
Alignment explanation
Indices: 13439--13555 Score: 198
Period size: 59 Copynumber: 2.0 Consensus size: 58
13429 GGCGTCGCGG
13439 CCCACGACACCAAATTCCAGCCACGACACAACCGTGAACACCTCTTAAACTCAATTATT
1 CCCACGACACCAAATTCCAGCCACGACACAACCGTG-ACACCTCTTAAACTCAATTATT
* * *
13498 CCCACGACACCAAATTCCGGCCGCGACACAACCGTGACACCTCTTAAACTCGATTATT
1 CCCACGACACCAAATTCCAGCCACGACACAACCGTGACACCTCTTAAACTCAATTATT
13556 AATTTGTAAC
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
58 21 0.38
59 34 0.62
ACGTcount: A:0.32, C:0.38, G:0.11, T:0.19
Consensus pattern (58 bp):
CCCACGACACCAAATTCCAGCCACGACACAACCGTGACACCTCTTAAACTCAATTATT
Found at i:15705 original size:2 final size:2
Alignment explanation
Indices: 15700--15732 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
15690 ATATCAATCA
15700 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 A
15733 AACAAGTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16230 original size:32 final size:32
Alignment explanation
Indices: 16189--16272 Score: 159
Period size: 32 Copynumber: 2.6 Consensus size: 32
16179 AGCCACGCGG
*
16189 AGCCTCCCCACTAGGACGGCTCTGCCACGGCT
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
16221 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
16253 AGCCGCCCCACTAGGACGGC
1 AGCCGCCCCACTAGGACGGC
16273 AAGGCTTTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.17, C:0.44, G:0.27, T:0.12
Consensus pattern (32 bp):
AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
Found at i:21577 original size:22 final size:22
Alignment explanation
Indices: 21549--21592 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
21539 ACACGTTCAG
21549 ATGTTGAGGCTTGAATGTCGAA
1 ATGTTGAGGCTTGAATGTCGAA
21571 ATGTTGAGGCTTGAATGTCGAA
1 ATGTTGAGGCTTGAATGTCGAA
21593 GAGAGCCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.09, G:0.32, T:0.32
Consensus pattern (22 bp):
ATGTTGAGGCTTGAATGTCGAA
Found at i:35143 original size:132 final size:133
Alignment explanation
Indices: 34904--35173 Score: 461
Period size: 132 Copynumber: 2.0 Consensus size: 133
34894 CATAAGAGCA
* *
34904 ATTTGGGTATTGTAGTTGGTGGGTAAAGGAAATTCAAAGGCCTTGTAGTTAGTGGGTATGTTGAC
1 ATTTGGGTATTGTAATTGGTGGGTAAAGGAAATTCAAAGGCATTGTAGTTAGTGGGTATGTTGAC
* * *
34969 ACGTAATTTTAACGCATAAAATGCTTAGCGTGTAGTTCAAATGTCATATTCCATCCCATTTAGGT
66 ACGTAATTTTAACGCATAAAATGCTTAGCCTGTAGTTAAAATGTCATATTCCATCCCATTTAGGC
35034 CT-
131 CTG
*
35036 ATTTGGGTATTGTAATTGGTGGGTAAAGGAAATTCAAAGGGATTGTAGTTAGTGGGTATGTTGAC
1 ATTTGGGTATTGTAATTGGTGGGTAAAGGAAATTCAAAGGCATTGTAGTTAGTGGGTATGTTGAC
* *
35101 ATGTAATTTTAACGCATAAAATGCTTAGCCTGTAGTTAAAATGTCATATTTCATCCCATTTAGGC
66 ACGTAATTTTAACGCATAAAATGCTTAGCCTGTAGTTAAAATGTCATATTCCATCCCATTTAGGC
35166 CTG
131 CTG
35169 ATTTG
1 ATTTG
35174 TTCGCTCAAT
Statistics
Matches: 129, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
132 124 0.96
133 5 0.04
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.36
Consensus pattern (133 bp):
ATTTGGGTATTGTAATTGGTGGGTAAAGGAAATTCAAAGGCATTGTAGTTAGTGGGTATGTTGAC
ACGTAATTTTAACGCATAAAATGCTTAGCCTGTAGTTAAAATGTCATATTCCATCCCATTTAGGC
CTG
Found at i:36660 original size:2 final size:2
Alignment explanation
Indices: 36653--36687 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
36643 TTCTAATGTA
36653 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36688 TTTTTTTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:44138 original size:41 final size:41
Alignment explanation
Indices: 44076--44154 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
44066 CTAATCCCTT
*
44076 TGGGTATTTTTCAAATAAACTAGATTCTCGGAATTCAATTA
1 TGGGCATTTTTCAAATAAACTAGATTCTCGGAATTCAATTA
44117 TGGGCATTTTTCAAATAAACTAGATTCTCGGAATTCAA
1 TGGGCATTTTTCAAATAAACTAGATTCTCGGAATTCAA
44155 CTTAATTGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (41 bp):
TGGGCATTTTTCAAATAAACTAGATTCTCGGAATTCAATTA
Found at i:44801 original size:16 final size:16
Alignment explanation
Indices: 44777--44807 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44767 TTAGGAGGGA
*
44777 AGAGTGAAAGAGAGAT
1 AGAGAGAAAGAGAGAT
44793 AGAGAGAAAGAGAGA
1 AGAGAGAAAGAGAGA
44808 GAACGCGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.39, T:0.06
Consensus pattern (16 bp):
AGAGAGAAAGAGAGAT
Found at i:48407 original size:22 final size:21
Alignment explanation
Indices: 48378--48418 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
48368 AGTTTTGAGA
*
48378 GATTCATTAACATTTAACGCT
1 GATTCATTAACATGTAACGCT
*
48399 GATTACATTTACATGTAACG
1 GATT-CATTAACATGTAACG
48419 GATTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (21 bp):
GATTCATTAACATGTAACGCT
Found at i:52772 original size:16 final size:16
Alignment explanation
Indices: 52751--52782 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
52741 CAATGGGGTT
52751 TCGTCTGCTTTGGAAG
1 TCGTCTGCTTTGGAAG
52767 TCGTCTGCTTTGGAAG
1 TCGTCTGCTTTGGAAG
52783 GTTGGATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.19, G:0.31, T:0.38
Consensus pattern (16 bp):
TCGTCTGCTTTGGAAG
Found at i:53931 original size:181 final size:178
Alignment explanation
Indices: 53590--53943 Score: 591
Period size: 181 Copynumber: 2.0 Consensus size: 178
53580 AAATAAATCA
*
53590 TTTTTTATTGGATTATTTATTAAATAATCCTCATACTTTTATAATTTATGCTATTTAATCCTTAC
1 TTTTTTATTGGATTATTTATTAAATAATCCTCATACTTTTATAATTTATACTATTTAATCCTTAC
*
53655 AATTATATGTTGGACGATTGAATGTTTCGGCTTTAATTGTTTTTTTTTTCTATTTGACCGATCAA
66 AATTATAGGTTGGACGATTGAATGTTTCGGCTTTAATTGTTTTTTTTTTCTATTTGACCGATCAA
* * *
53720 TGTGATTCAGGTGTCTATTTAACGGTAATTCCATGGTCTACAATCATT
131 GGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTACAATCATT
* *
53768 TTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAATCACTTA
1 TTTTTTATTGGATTATTTATTAAATAATCCTCATACTTTTATAATTTATACTATTTAATC-CTTA
* * *
53833 CAATTATGGGTTGGACGATTGAATGTTTCGGTTTTAATTCTTTTATTTTTTTCTATTTGACCGAT
65 CAATTATAGGTTGGACGATTGAATGTTTCGGCTTTAATT-GTTT-TTTTTTTCTATTTGACCGAT
53898 CAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTACAA
128 CAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTACAA
53944 CTTTCATGAA
Statistics
Matches: 163, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
178 57 0.35
179 40 0.25
180 3 0.02
181 63 0.39
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (178 bp):
TTTTTTATTGGATTATTTATTAAATAATCCTCATACTTTTATAATTTATACTATTTAATCCTTAC
AATTATAGGTTGGACGATTGAATGTTTCGGCTTTAATTGTTTTTTTTTTCTATTTGACCGATCAA
GGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTACAATCATT
Found at i:55248 original size:33 final size:33
Alignment explanation
Indices: 55209--55298 Score: 162
Period size: 33 Copynumber: 2.7 Consensus size: 33
55199 TACCATGGGC
55209 AGGCCGCCCCACTTGGGCGGCTTCACTATGAAT
1 AGGCCGCCCCACTTGGGCGGCTTCACTATGAAT
55242 AGGCCGCCCCACTTGGGCGGCTTCACTATGAAT
1 AGGCCGCCCCACTTGGGCGGCTTCACTATGAAT
* *
55275 AGGCCGCCCCACTGGGGCAGCTTC
1 AGGCCGCCCCACTTGGGCGGCTTC
55299 GCCAGGGCAG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.17, C:0.36, G:0.29, T:0.19
Consensus pattern (33 bp):
AGGCCGCCCCACTTGGGCGGCTTCACTATGAAT
Found at i:55471 original size:33 final size:33
Alignment explanation
Indices: 55372--55481 Score: 127
Period size: 32 Copynumber: 3.4 Consensus size: 33
55362 ATTTTGGTCT
** * *
55372 AGCCGCCCCACCG-GGGCGGCCTTCCGTGGCGA
1 AGCCGCCCCAGTGAGGGCGGCCTGCCATGGCGA
*
55404 AGCCGCCCCA-TGAGGGCGGCCTGCCTTGGCGA
1 AGCCGCCCCAGTGAGGGCGGCCTGCCATGGCGA
*
55436 AGCCGCCCCAGTGA-GGCGGCCTGCCCATGGTGA
1 AGCCGCCCCAGTGAGGGCGGCCTG-CCATGGCGA
*
55469 AGCCGTCCCAGTG
1 AGCCGCCCCAGTG
55482 GGGAGGCTCC
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
31 1 0.01
32 46 0.67
33 22 0.32
ACGTcount: A:0.13, C:0.39, G:0.36, T:0.12
Consensus pattern (33 bp):
AGCCGCCCCAGTGAGGGCGGCCTGCCATGGCGA
Found at i:65432 original size:13 final size:13
Alignment explanation
Indices: 65414--65438 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65404 CAAAGGTTTC
65414 TTTCCTTTTCTTA
1 TTTCCTTTTCTTA
65427 TTTCCTTTTCTT
1 TTTCCTTTTCTT
65439 TCATATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCCTTTTCTTA
Done.