Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006381.1 Corchorus olitorius cultivar O-4 contig06406, 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, 786
Length: 1311
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:835 original size:338 final size:323
Alignment explanation
Indices: 290--1135 Score: 896
Period size: 324 Copynumber: 2.6 Consensus size: 323
280 GTGAAAGCGC
* * * * * * *
290 AAAGACTCCTTCAAATATCTATATTCATCGAACCAAATTTCAGCCACATTGGATATAAGGATTTG
1 AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCATCCACATTGAATTTAAGGATTTT
*** * * * * *
355 TAAAACAAACATCTGAATCTTATTTCGATTTAATTAGAAATTAATTGGGAAAAAATGGAATAACG
66 TTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATT-CGAAAAAATAGAAAAACG
* * * * *
420 ATATTAGTAGCGTGAAAAACCCGTCAATCTTTTTGGTGTTGAATTATAAAT-TTTTTATGAATAT
130 ATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGTGTTGAATTATATATATATATATGAATAT
* * * * * *
484 TTTGTAACAAAAA-TTGTGTAAAAACTTTTCGGGTCAGTTTTTAGCCGAATTCGTACTAAAAAGA
195 ATTGTAACAAAAATTTGAGGAAAAACTTTTCGGATCAATTTTTAGCCGAAATCG---T-----GA
** * *
548 ATCTGTGATGATTACATCACGGTTTTTGGTTAAAAACGTGTGTCGGGGTCCAAG-CTCAATTATG
252 A-C--T-A--A--ACATCACGGTTTTTGCCTAAAAACGCGTGTCGGGGT-CAAGTCTCAATTATC
*
612 CAT-GATTTTTGGTAG
308 CATGGATTTTTGGCAG
*
627 AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCATCCACAATGAATTTAAGGATTTC
1 AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCATCCACATTGAATTTAAGGATTT-
* *
692 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAATAGAAAAAT
65 TTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCG-AAAAAATAGAAAAAC
* **
757 GATATTAGAAGCGTGAAAAACCCTTCAAT-TTTTTGGCGTTGAATTATATATATATATAT-TTTA
129 GATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGTGTTGAATTATATATATATATATGAATA
** * *
820 GTATTGTGGCAAAAATTTGAGGAAAAACTTTTCGGATCAATTTTTAGCCGAAATCGTGTACTAAC
194 -TATTGTAACAAAAATTTGAGGAAAAACTTTTCGGATCAATTTTTAGCCGAAATCGTGAACTAAA
* * * * * *
885 CATCACGGTTTTTGCCTAAAAATGCGTTTCGGGGTCACGTCTCAGTTTTCCATGGTTTTTTGGCA
258 CATCACGGTTTTTGCCTAAAAACGCGTGTCGGGGTCAAGTCTCAATTATCCATGGATTTTTGGCA
*
950 T
323 G
* ** *
951 AAAGACTCCTTGAAATATCTTTATTCATCTAATTAAATCTCAGT-CATATTGAATTTAAGGATTT
1 AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCA-TCCACATTGAATTTAAGGATTT
*
1015 GTTTTTACGTGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCTGAAAAAATATGAAAA
65 -TTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTC-GAAAAAATA-GAAAA
* *** *
1080 ACGATATTAAAAGCGTGAAATGTCCTACAATCTTTTTGGTGTTGAATTATATATAT
127 ACGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGTGTTGAATTATATATAT
1136 CAAAAATGAA
Statistics
Matches: 435, Mismatches: 63, Indels: 33
0.82 0.12 0.06
Matches are distributed among these distances:
322 3 0.01
323 40 0.09
324 120 0.28
325 33 0.08
326 23 0.05
327 1 0.00
328 1 0.00
330 1 0.00
331 2 0.00
336 1 0.00
337 80 0.18
338 95 0.22
339 35 0.08
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.37
Consensus pattern (323 bp):
AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCATCCACATTGAATTTAAGGATTTT
TTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCGAAAAAATAGAAAAACGA
TATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGTGTTGAATTATATATATATATATGAATATA
TTGTAACAAAAATTTGAGGAAAAACTTTTCGGATCAATTTTTAGCCGAAATCGTGAACTAAACAT
CACGGTTTTTGCCTAAAAACGCGTGTCGGGGTCAAGTCTCAATTATCCATGGATTTTTGGCAG
Done.