Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017082.1 Corchorus olitorius cultivar O-4 contig17115, 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: 24476
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:1776 original size:266 final size:266
Alignment explanation
Indices: 1301--1979 Score: 1178
Period size: 266 Copynumber: 2.5 Consensus size: 266
1291 CATAGGGTTG
* *
1301 GCCTTTGCTGAATGCAAGTTAAATGGCCAACATCTCCTATAAATAGAGGAGGTTATTGCGCTTTC
1 GCCTTTGGTGAATGCAAGTTAAATGGCCAACATCTCCTATAAATAGAGGAGGTTATTGCACTTTC
1366 AATAAGATCCCAAGCCAGAGCAATCTAAAGCTCTTTCTTACAAACTTTCCTTCCAGCCTAATTTC
66 AATAAGATCCCAAGCCAGAGCAATCTAAAGCTCTTTCTTACAAACTTTCCTTCCAGCCTAATTTC
* * *
1431 ATTTGTAGCTTGATCTTATAAGAAATTCCCAACTTATTAAAAATACAATACACAAAGCAGCGATT
131 ATTTGTAGCTTGATCTTACAAGAAATTCCCAACTTATTAAAAATACAATACACAAAGCAGCAAAT
*
1496 AGATATGGTGAAACAAATATATCACTTAGCCAAATAGCTCACATATATAGCAATTTATATAAGGA
196 AGATATGATGAAACAAATATATCACTTAGCCAAATAGCTCACATATATAGCAATTTATATAAGGA
1561 CAACTA
261 CAACTA
*
1567 GCCTTTGGTGAATGCAAGTTAAATGGCCAACATCTCCTATAAATAAAGGAGGTTATTGCACTTTC
1 GCCTTTGGTGAATGCAAGTTAAATGGCCAACATCTCCTATAAATAGAGGAGGTTATTGCACTTTC
* *
1632 AATAAGATCCCAAGCCAGAGCAATCTAAAGCTCTTTCTTACAAGCTTTACTTCCAGCCTAATTTC
66 AATAAGATCCCAAGCCAGAGCAATCTAAAGCTCTTTCTTACAAACTTTCCTTCCAGCCTAATTTC
* * *
1697 ATTTGTAGCTTGATCTTACAAGATATTCCCACCTTATTAAAAATACAATACACAAAGGAGCAAAT
131 ATTTGTAGCTTGATCTTACAAGAAATTCCCAACTTATTAAAAATACAATACACAAAGCAGCAAAT
* *
1762 AGATATGATGAAACAAATATATTACTTAGCCAAATAGCTCACATATATAGCAATTTATATAAGGG
196 AGATATGATGAAACAAATATATCACTTAGCCAAATAGCTCACATATATAGCAATTTATATAAGGA
1827 CAACTA
261 CAACTA
* * *
1833 GCCTTTGGTGAATGCAAGTTCAATGGCCAACATCTCCTATAAATAGAGAAGGATATTGCACTTTC
1 GCCTTTGGTGAATGCAAGTTAAATGGCCAACATCTCCTATAAATAGAGGAGGTTATTGCACTTTC
* *
1898 AGTAAGATCCCAAGCCAGAGCAATCTAAAGCTCTTTCTCACAAACTTTCCCTTCCAGCCTAATTT
66 AATAAGATCCCAAGCCAGAGCAATCTAAAGCTCTTTCTTACAAACTTT-CCTTCCAGCCTAATTT
1963 CATTTGTAGCTTGATCT
130 CATTTGTAGCTTGATCT
1980 CTGATTCCAC
Statistics
Matches: 390, Mismatches: 22, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
266 358 0.92
267 32 0.08
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (266 bp):
GCCTTTGGTGAATGCAAGTTAAATGGCCAACATCTCCTATAAATAGAGGAGGTTATTGCACTTTC
AATAAGATCCCAAGCCAGAGCAATCTAAAGCTCTTTCTTACAAACTTTCCTTCCAGCCTAATTTC
ATTTGTAGCTTGATCTTACAAGAAATTCCCAACTTATTAAAAATACAATACACAAAGCAGCAAAT
AGATATGATGAAACAAATATATCACTTAGCCAAATAGCTCACATATATAGCAATTTATATAAGGA
CAACTA
Found at i:6351 original size:29 final size:29
Alignment explanation
Indices: 6318--6387 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
6308 TCGTTGTCTG
*
6318 ATCTTTTAGGGCCTTTCGACCTAAAAAGA
1 ATCTTTTAGGGCCTTTCGACCTAAAAAAA
*
6347 ATCTTTTACGGCCTTTCGACCTAAAAAAA
1 ATCTTTTAGGGCCTTTCGACCTAAAAAAA
6376 ATCTTTTAGGGC
1 ATCTTTTAGGGC
6388 GACAAGCCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (29 bp):
ATCTTTTAGGGCCTTTCGACCTAAAAAAA
Found at i:11836 original size:117 final size:117
Alignment explanation
Indices: 11683--11908 Score: 434
Period size: 117 Copynumber: 1.9 Consensus size: 117
11673 ATGCGAAGGA
*
11683 GGGTGAGGGTGATGCTGTGGAATTTTCTCAAGGGCAAGAGGGTCAACGAGGCAGAGGCGGAGGCG
1 GGGTGAGGGTGATGCTGTGGAATTTTCTCAAGGGCAAGAGGGTCAACGAGGCAGAGGCAGAGGCG
11748 GTGGCGGTGGAGGCAGGGGAAGAGGCAAATACTACAACAACAATATCGATGC
66 GTGGCGGTGGAGGCAGGGGAAGAGGCAAATACTACAACAACAATATCGATGC
*
11800 GGGTGAGGGTGTTGCTGTGGAATTTTCTCAAGGGCAAGAGGGTCAACGAGGCAGAGGCAGAGGCG
1 GGGTGAGGGTGATGCTGTGGAATTTTCTCAAGGGCAAGAGGGTCAACGAGGCAGAGGCAGAGGCG
11865 GTGGCGGTGGAGGCAGGGGAAGAGGCAAATACTACAACAACAAT
66 GTGGCGGTGGAGGCAGGGGAAGAGGCAAATACTACAACAACAAT
11909 GGTGCTGTTG
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 107 1.00
ACGTcount: A:0.28, C:0.15, G:0.41, T:0.15
Consensus pattern (117 bp):
GGGTGAGGGTGATGCTGTGGAATTTTCTCAAGGGCAAGAGGGTCAACGAGGCAGAGGCAGAGGCG
GTGGCGGTGGAGGCAGGGGAAGAGGCAAATACTACAACAACAATATCGATGC
Found at i:13129 original size:21 final size:21
Alignment explanation
Indices: 13105--13163 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
13095 AGAAATCCGG
*
13105 TGGCTACGCGAAGAGCAACGC
1 TGGCTACGAGAAGAGCAACGC
* *
13126 TGGCTGCGGGAAGAGCAACGC
1 TGGCTACGAGAAGAGCAACGC
13147 TGGCTACGAGAAGAGCA
1 TGGCTACGAGAAGAGCA
13164 GCGGTGGTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.37, T:0.10
Consensus pattern (21 bp):
TGGCTACGAGAAGAGCAACGC
Found at i:17487 original size:10 final size:10
Alignment explanation
Indices: 17469--17498 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
17459 CAATAATGTT
17469 TTTTTTTTTC
1 TTTTTTTTTC
*
17479 TTTTATTTTC
1 TTTTTTTTTC
17489 TTTTTTTTTC
1 TTTTTTTTTC
17499 GGGGTCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:18012 original size:16 final size:17
Alignment explanation
Indices: 17986--18019 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17976 TAGTCATAGA
*
17986 GGGCACTTGGGGCTCTT
1 GGGCACTTGGGCCTCTT
18003 GGGC-CTTGGGCCTCTT
1 GGGCACTTGGGCCTCTT
18019 G
1 G
18020 ACTAATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.03, C:0.26, G:0.41, T:0.29
Consensus pattern (17 bp):
GGGCACTTGGGCCTCTT
Found at i:23830 original size:26 final size:27
Alignment explanation
Indices: 23794--23863 Score: 124
Period size: 26 Copynumber: 2.6 Consensus size: 27
23784 AAAAATTTAC
23794 CAGGGGCATTTTGGTCATTTTCA-CCT
1 CAGGGGCATTTTGGTCATTTTCAGCCT
23820 CAGGGGCATTTTGGTCATTTTCAGCCT
1 CAGGGGCATTTTGGTCATTTTCAGCCT
*
23847 CAGGGGCATTTAGGTCA
1 CAGGGGCATTTTGGTCA
23864 AAACTACTAG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 23 0.55
27 19 0.45
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.34
Consensus pattern (27 bp):
CAGGGGCATTTTGGTCATTTTCAGCCT
Done.