Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005850.1 Corchorus capsularis cultivar CVL-1 contig05868, 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, 655
Length: 1092
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:1072 original size:332 final size:332
Alignment explanation
Indices: 1--1092 Score: 1891
Period size: 332 Copynumber: 3.3 Consensus size: 332
*
1 TTTTTTGGCATTGAATTAGTAT-TTTTTTATGTGTTTCTAGGCCAAAAATAAAGGAAAAATATTT
1 TTTTTT-GCATTGAATTA-TATATTTTTTATGTGTGTCTAGGCCAAAAATAAAGGAAAAATATTT
65 CGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGACTAAAAC
64 CGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGACTAAAAC
* *
130 CGCGTTCCGGGGCACCAGCTCATTTTTGTTTGATTTTTGGTGATGAGAGCCGTTAAAATATCTAT
129 CGCGTTCCGGGGCACCAGCTCATTTTTGTATGATTTTTGGTGACGAGAGCCGTTAAAATATCTAT
* * * *
195 ATTCAACTAACCAAATCTCAGCCACACTAGCTTTCAGAATTTATTTTTACGAGCATCTAAATCTT
194 ATTCATCTAACCAAATCTCAGCCACACTAGATTTCAGGATTTATTTTTACGAGTATCTAAATCTT
*
260 GTTTTGATTTAATCAGAAATTAATTTATAAAAAAATTGGAAAACGATATTAGAAACGTTAAAAGC
259 GTTTTGATTTAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATATTAGAAACGTTAAAAGC
325 CCTTCAAAC
324 CCTTCAAAC
* * * * * **
334 TTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAATATTTCG
1 TTTTTTGCATTGAATTATATATTTTTTATGTGTGTCTAGGCCAAAAATAAAGGAAAAATATTTCG
*
399 GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGACTAAAATCG
66 GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGACTAAAACCG
*
464 CGTTCCGGGCCACCAGCTCATTTTTGTATGATTTTTGGTGACGAGAGCCGTTAAAATATCTATAT
131 CGTTCCGGGGCACCAGCTCATTTTTGTATGATTTTTGGTGACGAGAGCCGTTAAAATATCTATAT
529 TCATCTAACCAAATCTCAGCCACACTAGATTTCAGGATTTA-TTTTACGAGTATCTAAATCTTGT
196 TCATCTAACCAAATCTCAGCCACACTAGATTTCAGGATTTATTTTTACGAGTATCTAAATCTTGT
*
593 TTTGATTTAATCAAAAATTAATTTAGAAAAAAATTGGAAAACGATATTAGAAACGTTAAAAGCCC
261 TTTGATTTAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATATTAGAAACGTTAAAAGCCC
658 TTCAAAC
326 TTCAAAC
665 TTTTTTGCATTGAATTATATATTTTTTATGTGTGTCTAGGCCAAAAATAAAGGAAAAATATTTCG
1 TTTTTTGCATTGAATTATATATTTTTTATGTGTGTCTAGGCCAAAAATAAAGGAAAAATATTTCG
730 GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGACTAAAACCG
66 GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGACTAAAACCG
* *
795 TGTTCCGGGGCACCAGCTCATTTTTGTATGATTTTTGGTGACGAGAACCGTTAAAATATCTATAT
131 CGTTCCGGGGCACCAGCTCATTTTTGTATGATTTTTGGTGACGAGAGCCGTTAAAATATCTATAT
* * * * * *
860 TCATCTAACCAAATCTTAACCAAATTGGATTTTAGGATTTATTTTTACGAGTATCTAAATCTTGT
196 TCATCTAACCAAATCTCAGCCACACTAGATTTCAGGATTTATTTTTACGAGTATCTAAATCTTGT
* * *
925 TTTGATTTAATCAGAAATTAAATTAGAAAAAAATTGGAAAACGATATTAGAAATGTTAAAAGTCC
261 TTTGATTTAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATATTAGAAACGTTAAAAGCCC
990 TTCAAAC
326 TTCAAAC
997 TTTTTTGCATTGAATTATATATTTTTTATGTGTGTCTAGGCCAAAAATAAAGGAAAAATATTTCG
1 TTTTTTGCATTGAATTATATATTTTTTATGTGTGTCTAGGCCAAAAATAAAGGAAAAATATTTCG
1062 GGTCAATTTTTGCAAAATTTTAGCCGAAATC
66 GGTCAATTTTTGCAAAATTTTAGCCGAAATC
Statistics
Matches: 719, Mismatches: 38, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
331 314 0.44
332 400 0.56
333 5 0.01
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (332 bp):
TTTTTTGCATTGAATTATATATTTTTTATGTGTGTCTAGGCCAAAAATAAAGGAAAAATATTTCG
GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGACTAAAACCG
CGTTCCGGGGCACCAGCTCATTTTTGTATGATTTTTGGTGACGAGAGCCGTTAAAATATCTATAT
TCATCTAACCAAATCTCAGCCACACTAGATTTCAGGATTTATTTTTACGAGTATCTAAATCTTGT
TTTGATTTAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATATTAGAAACGTTAAAAGCCC
TTCAAAC
Done.