Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006591.1 Corchorus capsularis cultivar CVL-1 contig06612, 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, 723
Length: 1205
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Found at i:902 original size:460 final size:455
Alignment explanation
Indices: 1--1205 Score: 2188
Period size: 460 Copynumber: 2.6 Consensus size: 455
1 TCGGTTGAAGTAAGTATTAAGTCTTAGTACGTATGACGTATACGATCATATGTTGGCAACAATGC
1 TCGGTTGAAGTAAGTATTAAGTCTTAGTACGTATGACGTATACGATCATATGTTGGCAACAATGC
66 ACCGGATCCAATGAGATGTGGCTTGTATAGATTTATCATGCAAAGACCAATGGGTGCGATCATAC
66 ACCGGATCCAATGAGATGTGGCTTGTATAGATTTATCATGCAAAGACCAATGGGTGCGATCATAC
131 CAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAACGTGCTTGGGCGAGAGTAGTACT
131 CAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTT-AACGTGCTTGGGCGAGAGTAGTACT
196 AGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTCATTTTTTTTC-TTT-AGTT
195 AGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTCATTTTTTTTCTTTTAAGTT
259 TCTTCTACTTTCGGAATTTCTTATGGGAAGCAATCGGTTCATGTAAGCATTACGTCTTAGTATGG
260 TCTTCTACTTTCGGAATTTCTTATGGGAAGCAATCGGTTCATGTAAGCATTACGTCTTAGTATGG
*
324 CTGCGAATGAACAACATGTTCGATGAACGGATCATGAACAAGCTGGATCAAAGGCCGTTTATGTT
325 CTGCGAATGAACAACATGTTCGATGAACGGATCACGAACAAGCTGGATCAAAGGCCGTTTATGTT
389 CGCTCGGTAAGGTTTCCAAAGAGAAATAAATTTTTCTTCTTCTTTCGAAAAC-TTTTGGGTAGTC
390 CGCTCGGTAAGGTTTCCAAAGAGAAATAAATTTTTCTTCTTCTTTCGAAAACTTTTTGGGTAGTC
453 A
455 A
454 TCGGTTGAAGTAAGTATTAAGTCGTTAGTACGTATGACGTATACGATCCATATGTTGGCAACAAT
1 TCGGTTGAAGTAAGTATTAAGTC-TTAGTACGTATGACGTATACGAT-CATATGTTGGCAACAAT
519 GCACCGGATCCAATGAGATGTGGCTTGTATAGATTTATCATGCAAAG-CCGAATGGGTGCGATCA
64 GCACCGGATCCAATGAGATGTGGCTTGTATAGATTTATCATGCAAAGACC-AATGGGTGCGATCA
* *
583 TACCGAGCACTAATGCACCGGATCCCATCAGAACTACGCAGTGAAGCGTGCTTGGGCGAGAGTAG
128 TACC-AGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAA-CGTGCTTGGGCGAGAGTAG
* *
648 TACTAAGATGGGTGACCTCTTGGGAAGTCCTCGTGTTGCACCCCTTTTTCATTTTTTTATTCTTT
191 TACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTCA-TTTTTT-TTCTTT
*
713 TAATTTTCTTCTACTTTCGGAATTTCTTATGGGAAGCAATCGGTTCATGTAAGCATTACGTCTTA
254 TAAGTTTCTTCTACTTTCGGAATTTCTTATGGGAAGCAATCGGTTCATGTAAGCATTACGTCTTA
*
778 GTATGGCTGCGAATGAACAACATGTTCGATGATA-GGCA-CGCGAACAAGCTGGATCAAAGGCCG
319 GTATGGCTGCGAATGAACAACATGTTCGATGA-ACGG-ATCACGAACAAGCTGGATCAAAGGCCG
*
841 TTTATGTTCGCTCGGTAAGGTTTCCAAAGGGAAATAAATTTTTCTTCTTCTTTCGAAAACTTTTT
382 TTTATGTTCGCTCGGTAAGGTTTCCAAAGAGAAATAAATTTTTCTTCTTCTTTCGAAAACTTTTT
906 GGGTAGTCA
447 GGGTAGTCA
915 TCGGTTGAAGTAAGTATTAAGTCTTAGTACGTATGACGTATACGATCATATGTTGGCAACAATGC
1 TCGGTTGAAGTAAGTATTAAGTCTTAGTACGTATGACGTATACGATCATATGTTGGCAACAATGC
980 ACCGGATCCAATGAGATGTGGCTTGTATAGATTTATCATGCAAAGACCAATGGGTGCGATCATAC
66 ACCGGATCCAATGAGATGTGGCTTGTATAGATTTATCATGCAAAGACCAATGGGTGCGATCATAC
1045 CAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTTAACGTGCTTGGGCGAGAGTAGTACT
131 CAGCACTAATGCACCGGATCCCATCAGAACTCCGCAG-TTAACGTGCTTGGGCGAGAGTAGTACT
*
1110 AGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTCATTTTTTTTCTTTTAGGTT
195 AGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTCATTTTTTTTCTTTTAAGTT
1175 TCTTCTACTTTCGGAATTTCTTATGGGAAGC
260 TCTTCTACTTTCGGAATTTCTTATGGGAAGC
Statistics
Matches: 724, Mismatches: 14, Indels: 25
0.95 0.02 0.03
Matches are distributed among these distances:
453 23 0.03
454 25 0.03
455 84 0.12
456 145 0.20
457 12 0.02
458 106 0.15
459 88 0.12
460 203 0.28
461 38 0.05
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (455 bp):
TCGGTTGAAGTAAGTATTAAGTCTTAGTACGTATGACGTATACGATCATATGTTGGCAACAATGC
ACCGGATCCAATGAGATGTGGCTTGTATAGATTTATCATGCAAAGACCAATGGGTGCGATCATAC
CAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAACGTGCTTGGGCGAGAGTAGTACTA
GGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTTTTTCATTTTTTTTCTTTTAAGTTT
CTTCTACTTTCGGAATTTCTTATGGGAAGCAATCGGTTCATGTAAGCATTACGTCTTAGTATGGC
TGCGAATGAACAACATGTTCGATGAACGGATCACGAACAAGCTGGATCAAAGGCCGTTTATGTTC
GCTCGGTAAGGTTTCCAAAGAGAAATAAATTTTTCTTCTTCTTTCGAAAACTTTTTGGGTAGTCA
Done.