Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010880.1 Corchorus capsularis cultivar CVL-1 contig10901, 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: 2321
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Found at i:1410 original size:324 final size:322
Alignment explanation
Indices: 6--2319 Score: 3267
Period size: 321 Copynumber: 7.2 Consensus size: 322
1 ATTAC
* *
6 TCAACACCAAAAATATTGACGGGCTTTTTACGCTTCTAATATCGTTTTTCAATTTTTTTCTGAAA
1 TCAACACCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTCTGAAA
* *
71 TAAATTCTAATTAAATCCAAACAAGATTCAGATGCTCTTAAAAACAAATCCTTAAATCCATTGTG
66 TAATTTCTAATTAAATCCAAACAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTGTG
* *
136 TCTAAGATTTGGTTAGAAGAATATAGATATTCGAAGGAGTCTTTCTGCCGAAAATCTTGCATAAC
131 TCTAAGATTTGGTTAGAAGAATATAGATATTCCAAGGAGTCTTTCTGCCAAAAATCTTGCATAAC
* * * * *
201 TGAGCCGGGTCCCCGAAACGAGTTTTTATGCAAAAAATCGTGATGGTTAGTACACGATTTTCGAC
196 TGAGCCGGGGCCCCGAAACGCGTTTTTATGCTAAAAACCGTGATGGTTAGTACACGA-TTTCGGC
* * *
266 T-AAAATTGACCC-AAATTTTTTTTTTTATCAATTTTTTGCCACAATACT-A-AAAAAA-ATATT
260 TAAAAATTGACCCGAAA----GTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATA
326 AT
321 AT
* * * *
328 TCAACCCCAAAAAGATTGACGGGCATTTCACACTTCTAATATCGTTTTTCAATCTTTTTCTGAAA
1 TCAACACCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTCTGAAA
393 TAATTTCTAATTAAATCCAAACAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTGTG
66 TAATTTCTAATTAAATCCAAACAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTGTG
* *
458 TCTAAGATTTGGTTAGAAG-A-AT--ATATTCCAAGGAGTCTTTCTGCTAAAAATCTTACATAAC
131 TCTAAGATTTGGTTAGAAGAATATAGATATTCCAAGGAGTCTTTCTGCCAAAAATCTTGCATAAC
*
519 TGAGCCGGGGCCCCGAAACGCGTTTTTATG-TCAAAAACCTTGATGGTTAGTACACGATTTCGGC
196 TGAGCCGGGGCCCCGAAACGCGTTTTTATGCT-AAAAACCGTGATGGTTAGTACACGATTTCGGC
* * * * *
583 TAGAAATTGACCCGAAAATTTTTTTCACAATTTTTTGCCACGATACTCAGAAAAAATATATCAT
260 TAAAAATTGACCCG-AAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAT
647 TCAACACCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCAA-TTTTTTCTGAAA
1 TCAACACCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTCTGAAA
*
711 TAA-TTCTAATTAAATCCAAACAAGATTCAGATGCTCTTAAAAATAAATCCGTAAATCCATTGTG
66 TAATTTCTAATTAAATCCAAACAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTGTG
* * *
775 TCTAAGATTTGGTTAGAAGAATATATATATTCCAAGGAGTCTTTCTGCTAAAATTCTTGCATAAC
131 TCTAAGATTTGGTTAGAAGAATATAGATATTCCAAGGAGTCTTTCTGCCAAAAATCTTGCATAAC
*
840 TGAACCGGGGTCCCCGAAACGCGTTTTTATG-TCAAAAACCGTGATGGTTAGTACACGATTTCGG
196 TGAGCCGGGG-CCCCGAAACGCGTTTTTATGCT-AAAAACCGTGATGGTTAGTACACGATTTCGG
* * * * *
904 CTAGAAATTGACCCGAAA-ATTTTTCACAATTTTTCGCCACAATACTCAGAAAAATATATATTAT
259 CTAAAAATTGACCCGAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAA-ATATATAAT
968 TCAACACCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTTTCTGA
1 TCAACACCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCAA--TTTTTTTCTGA
*
1033 AATAATTTCTAATTAAATCCAAACAAGATTCAGATGCTCTTAAAAATAAATCCTTAAAGCCATTG
64 AATAATTTCTAATTAAATCCAAACAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTG
* * *
1098 TGTCTAAGATTTGGTAAGAAGAATATAGATATTCCAAGGAGTCTTTCTGCCAAAAATCTAGTATA
129 TGTCTAAGATTTGGTTAGAAGAATATAGATATTCCAAGGAGTCTTTCTGCCAAAAATCTTGCATA
* *
1163 ACTGGGCCGGGGCCCCGAAACGCGTTTTTATGCTAAAAACCGTGATGGTTAGTACACGATTTTGG
194 ACTGAGCCGGGGCCCCGAAACGCGTTTTTATGCTAAAAACCGTGATGGTTAGTACACGATTTCGG
* * * * * *
1228 GTAAAAATTGACCCGATAAGTTTTTTCTTAAATTTTTACCACAATACTTAGGAAAAATATATAAT
259 CTAAAAATTGACCCGA-AAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAT
* * * *
1293 TCAACACCAAAAACATTTACTGGCTTTTCACGTTTCTAATATCGTTTTTCAATTTTTATTCTGAA
1 TCAACACCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCAATTTTT-TTCTGAA
* * *
1358 ATAATTTCTAATTAAATCGAAACAAGATTTAGATACTCTTAAAAATAAATCCTTAAATCCATTGT
65 ATAATTTCTAATTAAATCCAAACAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTGT
* * *
1423 GTCTAAGATTTGGTTAGAAGAATATAGATATTCCAAGAAATCTTTCTGACAAAAATCTTGCATAA
130 GTCTAAGATTTGGTTAGAAGAATATAGATATTCCAAGGAGTCTTTCTGCCAAAAATCTTGCATAA
* * * ** *
1488 CTAAGCCGGGGCCCCGAAACTCGTTTTTATGCCAAAAAGTCAAAAACTGTGATAATTATTACACG
195 CTGAGCCGGGGCCCCGAAACGCGTTTTTATG-C------T-AAAAACCGTGATGGTTAGTACACG
* * *** * *
1553 ATTTCGGCTAAAAACTGACACGGGTCGTTTTTTTCTCAATTTTTTGCTAGAATACTCAGAAAAAA
252 ATTTCGGCTAAAAATTGAC-CCGAAAG-TTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAA
1618 TATATAAT
315 TATATAAT
* * * *
1626 TCAAAACCAAAAAGATTGACGGGCATTTCCCGCTTCTAATATCGTTTTTCAATTTTTTTCCGAAA
1 TCAACACCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTCTGAAA
* * * *
1691 TAATTTCTAATTAAATCGAAACAAGATTCAGAAGCTCTTAAAAACAAATCCTTAAATCCATTGTA
66 TAATTTCTAATTAAATCCAAACAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTGTG
* * ** *
1756 CCTAAGATTTGGTAAGGTGAATAGAGATATTCCAAGGAGTCTTTCTGCCAAAAATCTTGCATAAC
131 TCTAAGATTTGGTTAGAAGAATATAGATATTCCAAGGAGTCTTTCTGCCAAAAATCTTGCATAAC
* * * *
1821 TGAGCCGGAGCTCCGAAAAGCGTTTTTATGC-AAAAACAGTGATGGTTAGTACACGATTTCGGCT
196 TGAGCCGGGGCCCCGAAACGCGTTTTTATGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCT
* *
1885 AAAAATTGACCCGAGAGATTTTTTCTCAATTTTTTGCCACAATACTCAG-AAAAATATATTAT
261 AAAAATTGACCCGAAAG-TTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAT
* *
1947 TCAACACCAAAAAGATTGACGGGATTTTCACACTTCTAATATCGTTTTTCAATTTTTTTCTGAAA
1 TCAACACCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTCTGAAA
* * *
2012 TAATTTCTGATTAAATCTAAACAAGATTCAGATGCTCTTAAAATTAAATCCTTAAATCCATTGTG
66 TAATTTCTAATTAAATCCAAACAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTGTG
* * * *
2077 TCTAAGATTTGGTTAGAAGAATATATATATTCCAAGGAGTCTTTCTACTAAAATTCTTGCATAAC
131 TCTAAGATTTGGTTAGAAGAATATAGATATTCCAAGGAGTCTTTCTGCCAAAAATCTTGCATAAC
**
2142 TGAGCCGGGGCCCCCGAAACGCGTTTTTATGCCGAAAACC------G-T-G--CACGATTTCGGC
196 TGAGCCGGGG-CCCCGAAACGCGTTTTTATGCTAAAAACCGTGATGGTTAGTACACGATTTCGGC
* * *
2197 TAAAAATTGACCTGAAATTTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAC
260 TAAAAATTGACCCGAAA-GTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAT
2261 TCAACACCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTT
1 TCAACACCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTT
2320 TG
Statistics
Matches: 1792, Mismatches: 165, Indels: 78
0.88 0.08 0.04
Matches are distributed among these distances:
313 58 0.03
314 68 0.04
315 1 0.00
316 27 0.02
317 88 0.05
318 117 0.07
319 57 0.03
320 38 0.02
321 305 0.17
322 259 0.14
323 48 0.03
324 234 0.13
325 186 0.10
326 28 0.02
331 2 0.00
332 186 0.10
333 90 0.05
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (322 bp):
TCAACACCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTCTGAAA
TAATTTCTAATTAAATCCAAACAAGATTCAGATGCTCTTAAAAATAAATCCTTAAATCCATTGTG
TCTAAGATTTGGTTAGAAGAATATAGATATTCCAAGGAGTCTTTCTGCCAAAAATCTTGCATAAC
TGAGCCGGGGCCCCGAAACGCGTTTTTATGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCT
AAAAATTGACCCGAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAT
Done.