Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023797.1 Corchorus olitorius cultivar O-4 contig23830, 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: 16742
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:2888 original size:52 final size:52
Alignment explanation
Indices: 2827--2930 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
2817 CAATAAATCA
*
2827 ATAATCGGGTTTTGACTGATTCAACCGACGGTTGGATCGAAGAATCAGACCG
1 ATAATCGGGTTTTGACTGATTCAACCGACGGTTGGATCAAAGAATCAGACCG
2879 ATAATCGGGTTTTGACTGATTCAACCGACGGTTGGATCAAAGAATCAGACCG
1 ATAATCGGGTTTTGACTGATTCAACCGACGGTTGGATCAAAGAATCAGACCG
2931 GTTTTAAACA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (52 bp):
ATAATCGGGTTTTGACTGATTCAACCGACGGTTGGATCAAAGAATCAGACCG
Found at i:2982 original size:77 final size:77
Alignment explanation
Indices: 2888--3047 Score: 293
Period size: 77 Copynumber: 2.1 Consensus size: 77
2878 GATAATCGGG
2888 TTTTGACTGATTCAACCGACGGTTGGATCAAAGAATCAGACCGGTTTTAAACATGTTGTGTTGAC
1 TTTTGACTGATTCAACCGACGGTTGGATCAAAGAATCAGACCGGTTTTAAACATGTTGTGTTGAC
2953 TCAAATTTTAAA
66 TCAAATTTTAAA
* * *
2965 TTTTGATTGATTCAACCGACGGTTGGATCGAAGAATCAGACCGGTTTTAGACATGTTGTGTTGAC
1 TTTTGACTGATTCAACCGACGGTTGGATCAAAGAATCAGACCGGTTTTAAACATGTTGTGTTGAC
3030 TCAAATTTTAAA
66 TCAAATTTTAAA
3042 TTTTGA
1 TTTTGA
3048 AAAAAGATTT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 80 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (77 bp):
TTTTGACTGATTCAACCGACGGTTGGATCAAAGAATCAGACCGGTTTTAAACATGTTGTGTTGAC
TCAAATTTTAAA
Found at i:6135 original size:40 final size:40
Alignment explanation
Indices: 6056--6184 Score: 154
Period size: 41 Copynumber: 3.2 Consensus size: 40
6046 CCTGTTGACT
* *
6056 GTTGACCAAGTCAACCCGCCACATCATT-TGCCACGTCACC
1 GTTGACC-AGTCAACCTGCCACGTCATTCTGCCACGTCACC
* *
6096 AGTTGACCAGTCCA-CTGCCACGTCATTCTGCCACATCACCC
1 -GTTGACCAGTCAACCTGCCACGTCATTCTGCCACGTCA-CC
* *
6137 GTTGACTAGTCAACCTGCCACGTCATCCTGCCACGTCATCC
1 GTTGACCAGTCAACCTGCCACGTCATTCTGCCACGTCA-CC
6178 GTTGACC
1 GTTGACC
6185 GTTGACAGGG
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
39 11 0.15
40 25 0.33
41 39 0.52
ACGTcount: A:0.22, C:0.40, G:0.16, T:0.22
Consensus pattern (40 bp):
GTTGACCAGTCAACCTGCCACGTCATTCTGCCACGTCACC
Found at i:6166 original size:13 final size:13
Alignment explanation
Indices: 6145--6177 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
6135 CCGTTGACTA
*
6145 GTCAACCTGCCAC
1 GTCATCCTGCCAC
6158 GTCATCCTGCCAC
1 GTCATCCTGCCAC
6171 GTCATCC
1 GTCATCC
6178 GTTGACCGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.45, G:0.15, T:0.21
Consensus pattern (13 bp):
GTCATCCTGCCAC
Found at i:10345 original size:10 final size:10
Alignment explanation
Indices: 10323--10351 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
10313 GGGATGTTAA
10323 TGTAATT-AT
1 TGTAATTGAT
10332 TGTAATTGAT
1 TGTAATTGAT
10342 TGTAATTGAT
1 TGTAATTGAT
10352 ATTGGTATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.37
10 12 0.63
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (10 bp):
TGTAATTGAT
Found at i:13724 original size:480 final size:478
Alignment explanation
Indices: 13132--14089 Score: 1785
Period size: 482 Copynumber: 2.0 Consensus size: 478
13122 CACATCCAAA
13132 CAAAATTTGAATCAAAACACACACACAAAAAAAAACCCTCTGAAACATAAAAAAGTAAAACCATG
1 CAAAATTTGAATCAAAACACACACACAAAAAAAAACCCTCTGAAACATAAAAAAGTAAAACCATG
13197 CTACCTGTCGGCTGTTACAGAGAAAGTAAAGTTTCTTCAGTAATCCTTAATTCCAAACGAATTAA
66 CTACCTGTCGGCTGTTACAGAGAAAGTAAAGTTTCTTCAGTAATCCTTAATTCCAAACGAATTAA
13262 CTTCAGTCTCAGTCAAGTCTCTCTTCCTTCGATCACTGCCATGCTTAATTCCAAACGAAGCTTTT
131 CTTCAGTCTCAGTCAAGTCTCTCTTCCTTCGATCACTGCCATGCTTAATTCCAAACGAAGCTTTT
13327 G-TTTTTTGTCAATTTCTTCGATGATTTTAATTGGATCAATTAATCTCAGGGAAAG-AAAAAAAT
196 GTTTTTTTGTCAATTTCTTCGATGATTTTAATTGGATCAATTAATCTCAGGGAAAGAAAAAAAAT
*
13390 GAGAAGCTCACAGAGAGAAAAGAGGCGGAAGCAAACTGAATAGATTTTTGGGTTTTGGGTTTAAC
261 GAGAAGCTCACAGAGAGAAAAGAGGCGGAAGCAAACCGAATAGATTTTTGGGTTTTGGGTTTAAC
* *
13455 CTTTGGGTGCAGAATCGTGTATTTAAGTAAGAAAAGCCACCGCAATTAAAAGTGGAAAATTGAAT
326 CTTTGGGAGCAGAATCGTGTATTTAAGTAAGAAAAGCCACCACAATTAAAAGTGGAAAATTGAAT
13520 ATATAAATGGGTTAAATTTTTAATGAAGTTGAAATTACTATAAAGGCCAATTCAATATCAAGTGA
391 ATATAAATGGGTTAAATTTTTAATGAAGTTGAAATTACTATAAAGGCCAATTCAATATCAAGTGA
13585 ATCAATGAAATAAACTCTTTAGG
456 ATCAATGAAATAAACTCTTTAGG
*
13608 CAAAATTTGAATCAAAACACACACACACACACACAAAAACCCTTTGAAACATAAAAAAGTAAAAC
1 CAAAATTTGAATCAAAACACACACACA-A-A-A-AAAAACCCTCTGAAACATAAAAAAGTAAAAC
*
13673 CATGCTACCTGTCGGCTGTTACAGAGAAAGTAAAGTTTCTTCAGTAATCCTTAATTCCAAATGAA
62 CATGCTACCTGTCGGCTGTTACAGAGAAAGTAAAGTTTCTTCAGTAATCCTTAATTCCAAACGAA
13738 TTAACTTCAGTCTCAGTCAAGTCTCTCTTCCTTCGATCACTGCCATGCTTAATTCCAAACGAAGC
127 TTAACTTCAGTCTCAGTCAAGTCTCTCTTCCTTCGATCACTGCCATGCTTAATTCCAAACGAAGC
* *
13803 TTTTGTTTTTTTGTCAATTTCTTTGATGATTTTAATTGGATCAATTAATCTTAGGGAAAGAAAAA
192 TTTTGTTTTTTTGTCAATTTCTTCGATGATTTTAATTGGATCAATTAATCTCAGGGAAAGAAAAA
13868 AAATGAGAAGCTCACAGAGAGAAAAGAGGCGGAAGCAAACCGAATAGATTTTTGGGTTTTGGGTT
257 AAATGAGAAGCTCACAGAGAGAAAAGAGGCGGAAGCAAACCGAATAGATTTTTGGGTTTTGGGTT
* *
13933 TAATCTTTGGGAGCAGAATCGTGTATTTAAGTAAGAAAAGCCACCACAATTTAAAGTGGAAAATT
322 TAACCTTTGGGAGCAGAATCGTGTATTTAAGTAAGAAAAGCCACCACAATTAAAAGTGGAAAATT
13998 GAATATATAAATGGGTTAAATTTTTAATGAAGTTGAAATTACTATAAAGGCCAATTCAATATCAA
387 GAATATATAAATGGGTTAAATTTTTAATGAAGTTGAAATTACTATAAAGGCCAATTCAATATCAA
14063 GTGAATCAATGAAATAAACTCTTTAGG
452 GTGAATCAATGAAATAAACTCTTTAGG
14090 AAGATTTTCC
Statistics
Matches: 467, Mismatches: 9, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
476 27 0.06
477 1 0.00
478 1 0.00
479 1 0.00
480 164 0.35
481 52 0.11
482 221 0.47
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (478 bp):
CAAAATTTGAATCAAAACACACACACAAAAAAAAACCCTCTGAAACATAAAAAAGTAAAACCATG
CTACCTGTCGGCTGTTACAGAGAAAGTAAAGTTTCTTCAGTAATCCTTAATTCCAAACGAATTAA
CTTCAGTCTCAGTCAAGTCTCTCTTCCTTCGATCACTGCCATGCTTAATTCCAAACGAAGCTTTT
GTTTTTTTGTCAATTTCTTCGATGATTTTAATTGGATCAATTAATCTCAGGGAAAGAAAAAAAAT
GAGAAGCTCACAGAGAGAAAAGAGGCGGAAGCAAACCGAATAGATTTTTGGGTTTTGGGTTTAAC
CTTTGGGAGCAGAATCGTGTATTTAAGTAAGAAAAGCCACCACAATTAAAAGTGGAAAATTGAAT
ATATAAATGGGTTAAATTTTTAATGAAGTTGAAATTACTATAAAGGCCAATTCAATATCAAGTGA
ATCAATGAAATAAACTCTTTAGG
Found at i:14953 original size:30 final size:31
Alignment explanation
Indices: 14884--14953 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
14874 GTCTATCAGC
*
14884 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
**
14915 AATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 TTTTAATTTGTTTAATTTAA-GACTTTAATTT
14944 TTTTAATTTG
1 TTTTAATTTG
14954 CAATAATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
29 8 0.25
30 21 0.66
31 3 0.09
ACGTcount: A:0.27, C:0.04, G:0.07, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:15435 original size:16 final size:16
Alignment explanation
Indices: 15410--15452 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
15400 CTACCCGAGA
15410 CCGAACCCGAAAATA-C
1 CCGAACCCGAAAA-AGC
*
15426 CCGAATCCGAAAAAGC
1 CCGAACCCGAAAAAGC
15442 CCGAACCCGAA
1 CCGAACCCGAA
15453 CCTGCCCGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 1 0.04
16 23 0.96
ACGTcount: A:0.42, C:0.37, G:0.16, T:0.05
Consensus pattern (16 bp):
CCGAACCCGAAAAAGC
Found at i:15885 original size:3 final size:3
Alignment explanation
Indices: 15871--15917 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
15861 CGATGCATCG
*
15871 TCT TCG TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
15918 GACAATTATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.00, C:0.34, G:0.02, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:16295 original size:29 final size:28
Alignment explanation
Indices: 16214--16296 Score: 105
Period size: 27 Copynumber: 3.0 Consensus size: 28
16204 GCATTAAGGT
*
16214 CATTCAGGGGCATTTTGATCATTTTT-A
1 CATTCAGGGGCATTTTGGTCATTTTTGA
*
16241 CATTCAGGGGCATTTTGGTCACTTTTGCA
1 CATTCAGGGGCATTTTGGTCATTTTTG-A
** *
16270 CATTCAGGGGTGTTTTGGCCATTTTTG
1 CATTCAGGGGCATTTTGGTCATTTTTG
16297 GCTCATCTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
27 24 0.50
29 24 0.50
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.42
Consensus pattern (28 bp):
CATTCAGGGGCATTTTGGTCATTTTTGA
Done.