Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010009.1 Corchorus olitorius cultivar O-4 contig10041, 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: 6221
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Found at i:3379 original size:130 final size:130
Alignment explanation
Indices: 3176--3707 Score: 782
Period size: 131 Copynumber: 4.1 Consensus size: 130
3166 ATTGATTGCG
* * **
3176 CAACGAC-TTATAAAATTGTTACGAATAGATTATGATTTTC-CAACAACTTAAGAATTTGTTGTT
1 CAACGACTTTATAAAATTGTTACGAATAGATTATGA-TTTCGCAACGACTT-TGTTTTTGTTGTT
* ** *
3239 ACGAATATTGTAAATATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAATTCACTTA
64 ACGAAAATTGTAAGCATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTA
*
3304 GG
129 GA
* *
3306 CAACG-CTTTTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACGACTTTGTTTTTGTTGTTA
1 CAACGAC-TTTATAAAATTGTTACGAATAGATTATGATTTCGCAACGACTTTGTTTTTGTTGTTA
* *
3370 CGAAAATTGTAAGCATTGGCAACGACTAAAAAAAGTGTTGTGTAAAATACCATCAAAATCATTTA
65 CGAAAATTGTAAGCATTGGCAACAACT-AAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTA
3435 GA
129 GA
* *
3437 CAACGACTTCATAAAATTGTTACGAATAGATTGTGATTTCGCAACGACTTTGTTTTTGTTGTTAC
1 CAACGACTTTATAAAATTGTTACGAATAGATTATGATTTCGCAACGACTTTGTTTTTGTTGTTAC
* * *
3502 GAAAATTGTAAGCATTGGCAACGACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCATTTAGG
66 GAAAATTGTAAGCATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGA
*
3567 CAACGACTTTATAAAATTGTTACGAATAGATTGTGATTTCGCAACGACTTTGTTTTTGTTGTTAC
1 CAACGACTTTATAAAATTGTTACGAATAGATTATGATTTCGCAACGACTTTGTTTTTGTTGTTAC
* * * * *
3632 GAAAACTGTAAGCATTGGCAACAATTAAAAAATTCGTTGGGTAAAATACCATCAAAATCACTAAG
66 GAAAATTGTAAGCATTGGCAACAACTAAAAAAGT-GTTGTGTAAAATACCATCAAAATCACTTAG
3697 A
130 A
3698 CAACGACTTT
1 CAACGACTTT
3708 CAATTATTGT
Statistics
Matches: 369, Mismatches: 27, Indels: 11
0.91 0.07 0.03
Matches are distributed among these distances:
129 1 0.00
130 175 0.47
131 192 0.52
132 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (130 bp):
CAACGACTTTATAAAATTGTTACGAATAGATTATGATTTCGCAACGACTTTGTTTTTGTTGTTAC
GAAAATTGTAAGCATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGA
Found at i:3593 original size:261 final size:261
Alignment explanation
Indices: 3176--3706 Score: 809
Period size: 261 Copynumber: 2.0 Consensus size: 261
3166 ATTGATTGCG
3176 CAACGACTTATAAAATTGTTACGAATAGATTATGATTTTCCAACAACTTAAGAATTTGTTGTTAC
1 CAACGACTTATAAAATTGTTACGAATAGATTATGATTTTCCAACAACTTAAGAATTTGTTGTTAC
* * *
3241 GAATATTGTAAATATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAATTCACTTAGG
66 GAAAATTGTAAACATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGG
* *
3306 CAACGCTTTTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACGACTTTGTTTTTGTTGTTAC
131 CAACGCTTTTATAAAATTGTTACGAATAGATTATGATTTCGCAACGACTTTGTTTTTGTTGTTAC
* * * * *
3371 GAAAATTGTAAGCATTGGCAACGACTAAAAAAAGT-GTTGTGTAAAATACCATCAAAATCATTTA
196 GAAAACTGTAAGCATTGGCAAC-AATAAAAAAAGTCGTTGGGTAAAATACCATCAAAATCACTAA
3435 GA
260 GA
* * * **
3437 CAACGACTTCATAAAATTGTTACGAATAGATTGTGA-TTTCGCAACGACTT-TGTTTTTGTTGTT
1 CAACGACTT-ATAAAATTGTTACGAATAGATTATGATTTTC-CAACAACTTAAGAATTTGTTGTT
* * *
3500 ACGAAAATTGTAAGCATTGGCAACGACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCATTTA
64 ACGAAAATTGTAAACATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTA
*
3565 GGCAACGAC-TTTATAAAATTGTTACGAATAGATTGTGATTTCGCAACGACTTTGTTTTTGTTGT
129 GGCAACG-CTTTTATAAAATTGTTACGAATAGATTATGATTTCGCAACGACTTTGTTTTTGTTGT
* *
3629 TACGAAAACTGTAAGCATTGGCAACAATTAAAAAATTCGTTGGGTAAAATACCATCAAAATCACT
193 TACGAAAACTGTAAGCATTGGCAACAATAAAAAAAGTCGTTGGGTAAAATACCATCAAAATCACT
3694 AAGA
258 AAGA
3698 CAACGACTT
1 CAACGACTT
3707 TCAATTATTG
Statistics
Matches: 245, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
260 9 0.04
261 202 0.82
262 34 0.14
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (261 bp):
CAACGACTTATAAAATTGTTACGAATAGATTATGATTTTCCAACAACTTAAGAATTTGTTGTTAC
GAAAATTGTAAACATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGG
CAACGCTTTTATAAAATTGTTACGAATAGATTATGATTTCGCAACGACTTTGTTTTTGTTGTTAC
GAAAACTGTAAGCATTGGCAACAATAAAAAAAGTCGTTGGGTAAAATACCATCAAAATCACTAAG
A
Done.