Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010408.1 Corchorus capsularis cultivar CVL-1 contig10429, 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: 21197
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1429 original size:198 final size:200
Alignment explanation
Indices: 969--1451 Score: 723
Period size: 199 Copynumber: 2.4 Consensus size: 200
959 AAATCAAATC
* *
969 ACGGT-TA-TAGTATAATTTTTCTTATAGGATTACTATACAATACACAT-TCAGTGTAAATTTTG
1 ACGGTGTATTAGTATAATTTTTCTTATAGGATTATTATATAATACAC-TGTCAGTGTAAATTTTG
*
1031 GACT-TCATAAGCGGGTTAAGAAGTTGACACATACCTTATTTCATAATTAATAAAATATTTAATA
65 GACTCT-ATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATAAAATATTTAATA
*
1095 TTAATACATATTCCCTAAGGGCACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAAC
129 TTAATACATATTCCCTAAGAGCACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAAC
*
1160 TCCAGTG
194 TCCACTG
* * * *
1167 ACGGTGTATT-GTATAATTGTTCTTATAGAATTATTATATAATACCCTGTCAGTGTGAATTTTGG
1 ACGGTGTATTAGTATAATTTTTCTTATAGGATTATTATATAATACACTGTCAGTGTAAATTTTGG
1231 ACTCTATAAGCGGGTTAAGAAGTTGACACATACAC-CATTTCATAATTAATAAAATATTTAATAT
66 ACTCTATAAGCGGGTTAAGAAGTTGACACATAC-CTCATTTCATAATTAATAAAATATTTAATAT
*
1295 TAATACATATTCCCTAAGAG-ACACATGTCAACCCTTAAAACCC-GCACGTGCAGTCTGCTAAAT
130 TAATACATATTCCCTAAGAGCACACATGTCAACCCTT-AAACCCTGCACGTGCAGTCTGCTAAAC
*
1358 TCCACTT
194 TCCACTG
* *
1365 ACGGTGT-TTAGTATAATTTTTCTTATAGGATTATTATATAATAAACTGTGAGTGTAAATTTTGG
1 ACGGTGTATTAGTATAATTTTTCTTATAGGATTATTATATAATACACTGTCAGTGTAAATTTTGG
* *
1429 ACTCCATAAACGGGTTAAAGAAG
66 ACTCTATAAGCGGGTT-AAGAAG
1452 GTAAAAAAAA
Statistics
Matches: 258, Mismatches: 19, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
197 2 0.01
198 115 0.45
199 138 0.53
200 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (200 bp):
ACGGTGTATTAGTATAATTTTTCTTATAGGATTATTATATAATACACTGTCAGTGTAAATTTTGG
ACTCTATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATAAAATATTTAATATT
AATACATATTCCCTAAGAGCACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTC
CACTG
Found at i:5185 original size:215 final size:215
Alignment explanation
Indices: 4811--5201 Score: 683
Period size: 215 Copynumber: 1.8 Consensus size: 215
4801 GTGAACCAAT
*
4811 TATTAAGCTAAAACAGTAAAATGCTCATATTAACGTTGAGGTTTGATCAAATGGTAAATGACTTG
1 TATTAAGCTAAAACAGTAAAATGCTCATATTAACGTTGAGGTTTGATCAAATGATAAATGACTTG
* * *
4876 TTCCAGTTTAAGTCGGTCTCAGGTTCGAGATCTTATGTACGCAGCTGCCCTGTTGATAGACTTAC
66 TTCCAGTTTAAGTCGGTCTCAGATTCGAGATCTTATGTACGCAACTGCCCTATTGATAGACTTAC
* *
4941 CCACCAATACCATATGCACGATGTGAGTCGGAGGATTCAGATTAGTCAAAGCAACAAGGTTAAAT
131 CCACCAATACCAGATGCACGATATGAGTCGGAGGATTCAGATTAGTCAAAGCAACAAGGTTAAAT
5006 TGTAAATATACCAAACGGTG
196 TGTAAATATACCAAACGGTG
*
5026 TATTAAGCTAAAACAGTAAAATGCTCATATTAACGTTGAGGTTTGATCAAATGATAAATGGCTTG
1 TATTAAGCTAAAACAGTAAAATGCTCATATTAACGTTGAGGTTTGATCAAATGATAAATGACTTG
* *
5091 TTCCAGTTTAAGTCGGTCTCAGATTCGAGATCTTATGTATGCAACTGCCCTATTGATAGATTTAC
66 TTCCAGTTTAAGTCGGTCTCAGATTCGAGATCTTATGTACGCAACTGCCCTATTGATAGACTTAC
* *
5156 CCACCAATACCAGATGCATGATATGAGTCGGAGGATTCGGATTAGT
131 CCACCAATACCAGATGCACGATATGAGTCGGAGGATTCAGATTAGT
5202 TAAACCAAAG
Statistics
Matches: 165, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
215 165 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (215 bp):
TATTAAGCTAAAACAGTAAAATGCTCATATTAACGTTGAGGTTTGATCAAATGATAAATGACTTG
TTCCAGTTTAAGTCGGTCTCAGATTCGAGATCTTATGTACGCAACTGCCCTATTGATAGACTTAC
CCACCAATACCAGATGCACGATATGAGTCGGAGGATTCAGATTAGTCAAAGCAACAAGGTTAAAT
TGTAAATATACCAAACGGTG
Found at i:5986 original size:17 final size:17
Alignment explanation
Indices: 5960--5995 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5950 GTTTTTCTGT
5960 TTTTTATTTTAATTTTG
1 TTTTTATTTTAATTTTG
* *
5977 TTTTTGTTTTATTTTTG
1 TTTTTATTTTAATTTTG
5994 TT
1 TT
5996 GCGCCGTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.08, T:0.81
Consensus pattern (17 bp):
TTTTTATTTTAATTTTG
Found at i:9077 original size:20 final size:20
Alignment explanation
Indices: 9042--9079 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
9032 GGGCCAGGTT
* *
9042 TTTTTTTTCTTTTTTTAAAA
1 TTTTTTTTCCTATTTTAAAA
9062 TTTTTTTTCCTATTTTAA
1 TTTTTTTTCCTATTTTAA
9080 GAGTTTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTTTTCCTATTTTAAAA
Found at i:9975 original size:344 final size:344
Alignment explanation
Indices: 9345--10033 Score: 1263
Period size: 344 Copynumber: 2.0 Consensus size: 344
9335 ATACTTAATG
* *
9345 AGAGGCCAGCTTTCGCACTATTCATAGACTGTTCAAAATCTAACAGTGCAATTCAACCCAACTTG
1 AGAGGCCAACTTTCACACTATTCATAGACTGTTCAAAATCTAACAGTGCAATTCAACCCAACTTG
* *
9410 GCCCAATTTTGTGCCACGTGTCCAATTGCTTAACCCAATTTTGATAACTAATCCCGACCTGTCTC
66 GCCCAATTTTGTGCCACGTGTCCAATTGCTTAACCCAATTTCGATAACTAATCCCGACCCGTCTC
* *
9475 TGACTCGACTTAACTCGCAAAATTCAGCTCCAATTGGCCAATAATCTGGCGCCACGTTGTCTCCT
131 TGACTCGACTTAACTCGCAAAATTCAGCTCCAATTGGCCAATAATCTGGCACCACGTCGTCTCCT
9540 CTTCAATCCAATTCAAACCCAACCCAATTCTCCGTTCCCCTGATTTTCTGCGATTCCCCTCTGCA
196 CTTCAATCCAATTCAAACCCAACCCAATTCTCCGTTCCCCTGATTTTCTGCGATTCCCCTCTGCA
* * *
9605 TCGGATTCATTTTGGTTACCTGCTCCTTTCTCTTTCGTTTATCTATTCTCCTCTTCGGATTCTTC
261 GCGGATTCATTTTGGTTACATGCTCCTTTCTCTTTCGTTTATCTATTCTCCTCTTCAGATTCTTC
9670 TTAGTTCTTTCTTTCATCA
326 TTAGTTCTTTCTTTCATCA
9689 AGAGGCCAACTTTCACACTATTCATAGACTGTTCAAAATCTAACAGTGCAATTCAACCCAACTTG
1 AGAGGCCAACTTTCACACTATTCATAGACTGTTCAAAATCTAACAGTGCAATTCAACCCAACTTG
*
9754 GCCCAATTTTGTGCCACGTGTCCAATTGCTTAACCTAATTTCGATATAC-AATCCCGACCCGTCT
66 GCCCAATTTTGTGCCACGTGTCCAATTGCTTAACCCAATTTCGATA-ACTAATCCCGACCCGTCT
9818 CTGACTCGACTTAACTCGCAAAATTCAGCTCCAATTGGCCAATAATCTGGCACCACGTCGTCTCC
130 CTGACTCGACTTAACTCGCAAAATTCAGCTCCAATTGGCCAATAATCTGGCACCACGTCGTCTCC
9883 TCTTCAATCCAATTCAAACCCAACCCAATTCTCCGTTCCCCTGATTTTCTGCGATTCCCCTCTGC
195 TCTTCAATCCAATTCAAACCCAACCCAATTCTCCGTTCCCCTGATTTTCTGCGATTCCCCTCTGC
*
9948 AGCGGATTCATTTTGGTTGCATGCTCCTTTCTCTTTCGTTTATCTATTCTCCTCTTCAGATTCTT
260 AGCGGATTCATTTTGGTTACATGCTCCTTTCTCTTTCGTTTATCTATTCTCCTCTTCAGATTCTT
10013 CTTAGTTCTTTCTTTCATCA
325 CTTAGTTCTTTCTTTCATCA
10033 A
1 A
10034 AAACTTCATC
Statistics
Matches: 333, Mismatches: 11, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
344 331 0.99
345 2 0.01
ACGTcount: A:0.22, C:0.31, G:0.12, T:0.34
Consensus pattern (344 bp):
AGAGGCCAACTTTCACACTATTCATAGACTGTTCAAAATCTAACAGTGCAATTCAACCCAACTTG
GCCCAATTTTGTGCCACGTGTCCAATTGCTTAACCCAATTTCGATAACTAATCCCGACCCGTCTC
TGACTCGACTTAACTCGCAAAATTCAGCTCCAATTGGCCAATAATCTGGCACCACGTCGTCTCCT
CTTCAATCCAATTCAAACCCAACCCAATTCTCCGTTCCCCTGATTTTCTGCGATTCCCCTCTGCA
GCGGATTCATTTTGGTTACATGCTCCTTTCTCTTTCGTTTATCTATTCTCCTCTTCAGATTCTTC
TTAGTTCTTTCTTTCATCA
Found at i:20218 original size:31 final size:31
Alignment explanation
Indices: 20183--20268 Score: 118
Period size: 31 Copynumber: 2.8 Consensus size: 31
20173 CACGTGTACC
*
20183 AAAAAGTTACACGTGTCACGCCACATCTACA
1 AAAAAGTGACACGTGTCACGCCACATCTACA
* * * *
20214 AAAAAGTGACACATGTCACGTCACGTGTACA
1 AAAAAGTGACACGTGTCACGCCACATCTACA
*
20245 AAAAAGTGACACGTGTCATGCCAC
1 AAAAAGTGACACGTGTCACGCCAC
20269 CAGGGGCGTA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (31 bp):
AAAAAGTGACACGTGTCACGCCACATCTACA
Done.