Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004992.1 Corchorus capsularis cultivar CVL-1 contig05010, 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: 12936
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Found at i:341 original size:31 final size:31
Alignment explanation
Indices: 306--364 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
296 GGCAATTTAG
*
306 AAATATGTTTTAAAGAA-AAGGGTACAATTGA
1 AAATATATTTTAAA-AATAAGGGTACAATTGA
337 AAATATATTTTAAAAATAAGGGTACAAT
1 AAATATATTTTAAAAATAAGGGTACAAT
365 CGGAAAGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.51, C:0.03, G:0.15, T:0.31
Consensus pattern (31 bp):
AAATATATTTTAAAAATAAGGGTACAATTGA
Found at i:4171 original size:343 final size:342
Alignment explanation
Indices: 3515--4185 Score: 958
Period size: 343 Copynumber: 2.0 Consensus size: 342
3505 AAAAACAAAA
* *** * *
3515 AATGAAGGTTATTGAATTAGTTGATAGTGTTATACCTCTTTTATGATCATTATAGGGTTTTTAGT
1 AATGAAGGTCATTGAATTAGTTGATAGTACCATACCTATTCTATGATCATTATAGGGTTTTTAGT
*
3580 AACTTTTGAGAAAAAAAGATGGTAAATATTCACCATTGATGAAAGTTTACTAATGTTATTAAGAA
66 AACTTTTGAGAAAAAAAGATGATAAATATTCACCATTGATGAAAGTTTACTAATGTTATTAAGAA
* *
3645 TGTAAGGACTGGTTATAAATATAATTTTAACAACTTTTATAGCTTTTTTAGTAAACTTAAGTAAT
131 TGTAAGGACTGG-T-TAAATACAATTTTAACAACTTTTATAGCCTTTTTAGTAAACTTAAGTAAT
* * * *
3710 AAAATTGGTAACTTTTATTAATGATAAAAAGTTACTAAAATTAATAAGGATGTAAGGTTATTTCA
194 AAAATTGGTAACTTTCATTAATGATAAAAAATTACTAAAATTAATAAGGATGTAAGATTATCTCA
* *
3775 ATCTAGATAGTAGCATAATGTTTTCCATAACCTTTAAAACCTTTTAAGTAATCTTAGATGAGAAA
259 ATCTAGATAGTAGCATAATGTTTTCCATAACCTTTAAAACATTTTAAGTAATCTTAGATAAGAAA
3840 ATCAGTATTTTACCTTTAT
324 ATCAGTATTTTACCTTTAT
* **
3859 AATGTAAGGTCATTGAATTAGTTGATAGTACCATTCCTATTCTATGATTGTTATA-GGTTTTTCA
1 AATG-AAGGTCATTGAATTAGTTGATAGTACCATACCTATTCTATGATCATTATAGGGTTTTT-A
* *
3923 GTAACTTTTGAG-AATAAA-ATGATAAATCTTCACCATTGATGAAAGTTTACTAATGTTATTAAG
64 GTAACTTTTGAGAAAAAAAGATGATAAATATTCACCATTGATGAAAGTTTACTAATGTTATTAAG
* * *
3986 AATGTAAGGATTGG-TAAATACAATTTTAATAACTTTTATAGCCTTTTTAGTAGATTACTTGAGT
129 AATGTAAGGACTGGTTAAATACAATTTTAACAACTTTTATAGCCTTTTTAGTA-A--ACTTAAGT
* *
4050 AATAATATTGGTAACTTTCATTATTGATAAAAAATTACTAAAATTAATAAGGATGTAAGATTA-C
191 AATAAAATTGGTAACTTTCATTAATGATAAAAAATTACTAAAATTAATAAGGATGTAAGATTATC
* * *
4114 TCGAATCTAGATAGTA-CTATAATGTTTTCCATAAGCTTTATAACATTTTATGTAATCTTAGATA
256 TC-AATCTAGATAGTAGC-ATAATGTTTTCCATAACCTTTAAAACATTTTAAGTAATCTTAGATA
*
4178 ATAAAATC
319 AGAAAATC
4186 GGTGACCAAT
Statistics
Matches: 291, Mismatches: 29, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
340 35 0.12
341 1 0.00
342 3 0.01
343 182 0.63
344 16 0.05
345 54 0.19
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.40
Consensus pattern (342 bp):
AATGAAGGTCATTGAATTAGTTGATAGTACCATACCTATTCTATGATCATTATAGGGTTTTTAGT
AACTTTTGAGAAAAAAAGATGATAAATATTCACCATTGATGAAAGTTTACTAATGTTATTAAGAA
TGTAAGGACTGGTTAAATACAATTTTAACAACTTTTATAGCCTTTTTAGTAAACTTAAGTAATAA
AATTGGTAACTTTCATTAATGATAAAAAATTACTAAAATTAATAAGGATGTAAGATTATCTCAAT
CTAGATAGTAGCATAATGTTTTCCATAACCTTTAAAACATTTTAAGTAATCTTAGATAAGAAAAT
CAGTATTTTACCTTTAT
Found at i:4944 original size:40 final size:42
Alignment explanation
Indices: 4887--4971 Score: 129
Period size: 40 Copynumber: 2.1 Consensus size: 42
4877 TTATAACTAG
4887 GGGCTAAACCTGAATTTAATTT-TTACCTTAATTA-TCAGGA
1 GGGCTAAACCTGAATTTAATTTGTTACCTTAATTATTCAGGA
* * *
4927 GGGCTAAACCTGGATTTAATTTGTTTCCTTAATTATTTAGGA
1 GGGCTAAACCTGAATTTAATTTGTTACCTTAATTATTCAGGA
4969 GGG
1 GGG
4972 ACAAATTGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 21 0.52
41 11 0.28
42 8 0.20
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (42 bp):
GGGCTAAACCTGAATTTAATTTGTTACCTTAATTATTCAGGA
Found at i:6206 original size:2 final size:2
Alignment explanation
Indices: 6199--6238 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
6189 CATTAACTAG
*
6199 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6239 AGGTTTTGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:9371 original size:12 final size:12
Alignment explanation
Indices: 9356--9381 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9346 GTTTGATGCC
9356 AAAAAAAAAAAG
1 AAAAAAAAAAAG
9368 AAAAAAAAAAAG
1 AAAAAAAAAAAG
9380 AA
1 AA
9382 GAAGCTAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:10366 original size:20 final size:20
Alignment explanation
Indices: 10341--10380 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
10331 AGATTCAACA
*
10341 TTGGCGATTCCCAAGTGAGT
1 TTGGCGATTACCAAGTGAGT
10361 TTGGCGATTACCAAGTGAGT
1 TTGGCGATTACCAAGTGAGT
10381 CTAATTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (20 bp):
TTGGCGATTACCAAGTGAGT
Done.