Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006590.1 Corchorus capsularis cultivar CVL-1 contig06611, 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, 678
Length: 1130
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Found at i:1080 original size:457 final size:452
Alignment explanation
Indices: 1--1130 Score: 2010
Period size: 452 Copynumber: 2.5 Consensus size: 452
*
1 TACTTTCGGAATTTCTTATGGGAAGCAATCGGTTCATGTAAGCATTACGTCTTAGTATGGCTGGG
1 TACTTTCGGAATTTCTTATGGGAAGCAATCGGTTCATGTAAGCATTACGTCTTAGTATGGCTGCG
*
66 AATGAACAACATGTTCGATGACCGGCACGTGAACAAGCTGGATCAAAGGCCGTTTATGTTCGCTC
66 AATGAACAACATGTTCGATGACAGGCACGTGAACAAGCTGGATCAAAGGCCGTTTATGTTCGCTC
131 GGTAAGGTTTCCAAAGAGAAATAATTTTTTCTTCTTCTTTCGAAAATTTTTTGGGTAGTCATCGG
131 GGTAAGGTTTCCAAAGAGAAATAATTTTTTCTTCTTCTTTCGAAAATTTTTTGGGTAGTCATCGG
196 TTGAAGTAAGTATTAAGTCTTAGTACGTATGACGTATACGATCATATGTTGGCAACAATGCACCG
196 TTGAAGTAAGTATTAAGTCTTAGTACGTATGACGTATACGATCATATGTTGGCAACAATGCACCG
261 GATCCAATGAGATGTGGCTTGTATAGATTTATCATGCAAAGACCAATGGGTGCGATCATACCAGC
261 GATCCAATGAGATGTGGCTTGTATAGATTTATCATGCAAAGACCAATGGGTGCGATCATACCAGC
* * * * *
326 ATTACTGCACCGGATCCCATCAGAACTCCGTAGTTAAGCGTGCTTGGGCGAGAACTATAATGGGT
326 ACTAATGCACCGGATCCCATCAGAAATCCGCAATTAAGCGTGCTTGGGCGAGAACTATAATGGGT
* *
391 GACCTCCTGGGAAGTACTCGTGTTGTAACCCTTTTTCATTATTTTTTCTTTTAATTTTCTTC
391 GACCTCCTGGGAAGTACTCGTGTTGCAACCCTTATTCATTATTTTTTCTTTTAATTTTCTTC
453 TACTTTCGGAATTTCTTATGGGAAGCAATCGGTTCATGTAAGCATTACGTCTTAGTATGGCTGCG
1 TACTTTCGGAATTTCTTATGGGAAGCAATCGGTTCATGTAAGCATTACGTCTTAGTATGGCTGCG
* *
518 AATGAACAACATGTTCGATGA-ACGGCACGTGAACAAGCTAGATCAAAGGCCGTTTATGTTTGCT
66 AATGAACAACATGTTCGATGACA-GGCACGTGAACAAGCTGGATCAAAGGCCGTTTATGTTCGCT
* *
582 CGGTAAGGTTTCCAAAGAGTAATAATTTTTTCTTCTTCTTTCGAAAATTTTTTGGGTAGTGATCG
130 CGGTAAGGTTTCCAAAGAGAAATAATTTTTTCTTCTTCTTTCGAAAATTTTTTGGGTAGTCATCG
647 GTTGAAGTAAGTATTAAGTCTTAGTACGTATGACGTATACGATCATATGTTGGCAACAATGCACC
195 GTTGAAGTAAGTATTAAGTCTTAGTACGTATGACGTATACGATCATATGTTGGCAACAATGCACC
*
712 GGATCCAATGAGATGTGGCTTGTATAGATTTATCATGCAAAGACCAATGGGTGCTATCATACCAG
260 GGATCCAATGAGATGTGGCTTGTATAGATTTATCATGCAAAGACCAATGGGTGCGATCATACCAG
*
777 CACTAATGCACCGGATCCCATCAGAAATCCGCAATTAAGCGTGCTTGGGCGAGAGTAGTACTAGG
325 CACTAATGCACCGGATCCCATCAGAAATCCGCAATTAAGCGTGCTTGGGCGAGA--ACTA-TA--
* * *
842 ATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTATTCATTTTTTTTTCTTTTAATTTTC
385 ATGGGTGACCTCCTGGGAAGTACTCGTGTTGCAACCCTTATTCATTATTTTTTCTTTTAATTTTC
907 TTC
450 TTC
*
910 TACTTTCGGAATTTCTTATGGGAAGCAATCGGTTCATGTGAGCATTACGTCTTAGTATGGCTGCG
1 TACTTTCGGAATTTCTTATGGGAAGCAATCGGTTCATGTAAGCATTACGTCTTAGTATGGCTGCG
975 AATGAACAACATGTTCGATGACAGGCACGTGAACAAGCTGGATCAAAGGCCGTTTATGTTCGCTC
66 AATGAACAACATGTTCGATGACAGGCACGTGAACAAGCTGGATCAAAGGCCGTTTATGTTCGCTC
*
1040 GGTAAGGTTTCCAAAGAGAAATAATTTTTTCTCCTTCTTTCGAAAATTTTTTGGGTAGTCATCGG
131 GGTAAGGTTTCCAAAGAGAAATAATTTTTTCTTCTTCTTTCGAAAATTTTTTGGGTAGTCATCGG
*
1105 TTGAAGTAAGTATTAAGTCTTTGTAC
196 TTGAAGTAAGTATTAAGTCTTAGTAC
Statistics
Matches: 646, Mismatches: 25, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
452 365 0.57
454 3 0.00
455 2 0.00
457 275 0.43
458 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Consensus pattern (452 bp):
TACTTTCGGAATTTCTTATGGGAAGCAATCGGTTCATGTAAGCATTACGTCTTAGTATGGCTGCG
AATGAACAACATGTTCGATGACAGGCACGTGAACAAGCTGGATCAAAGGCCGTTTATGTTCGCTC
GGTAAGGTTTCCAAAGAGAAATAATTTTTTCTTCTTCTTTCGAAAATTTTTTGGGTAGTCATCGG
TTGAAGTAAGTATTAAGTCTTAGTACGTATGACGTATACGATCATATGTTGGCAACAATGCACCG
GATCCAATGAGATGTGGCTTGTATAGATTTATCATGCAAAGACCAATGGGTGCGATCATACCAGC
ACTAATGCACCGGATCCCATCAGAAATCCGCAATTAAGCGTGCTTGGGCGAGAACTATAATGGGT
GACCTCCTGGGAAGTACTCGTGTTGCAACCCTTATTCATTATTTTTTCTTTTAATTTTCTTC
Done.