Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006268.1 Corchorus capsularis cultivar CVL-1 contig06287, 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, 718
Length: 1197
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Found at i:948 original size:456 final size:457
Alignment explanation
Indices: 28--1197 Score: 2085
Period size: 456 Copynumber: 2.5 Consensus size: 457
18 AGACGTTGCT
28 TCCCATAAGAAATTACCGAAAGTAAGAAGAAAAATTAAAAGAAAAAAAAAAATAGAAAAAAGGGG
1 TCCCATAAGAAATT-CCGAAAGT-AGAAG-AAAATTAAAAG-AAAAAAAAAAT-G-AAAAAGGGG
* * * *
93 TAGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTATTCTCGCCCAAGCACGGTTAA
60 T-GCAACACGAAGACTTCCAAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAA
*
158 CTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCATTGGTATTTGCAT
124 CTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCATTGGTCTTTGCAT
* *
223 GATAAATCTATACAAGCCACATCTTAGTGGATCCGGTGCATTGTTGCCAACATATGATCGTATAC
189 GATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCATTGTTGCCAACATATGATCGTATAC
288 GTCATACGTACTAAGACTTAATACTCACTTCAACCGATGACTACCCAAAAAGTTTTCGAAAGAAG
254 GTCATACGTACTAAGACTTAATACTCACTTCAACCGATGACTACCCAAAAAGTTTTCGAAAGAAG
353 AAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCGAACATAAACGGCCTTTGATCCAGCTTG
319 AAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCGAACATAAACGGCCTTTGATCCAGCTTG
418 TTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATACTAAGACGTAATGCTTACATGA
384 TTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATACTAAGACGTAATGCTTACATGA
483 ACCGATTGA
449 ACCGATTGA
492 TCCCATAAGAAATTCCGAAAGTAGAAGAAAATTAAAAG-AAAAAAAAATGAAAAAGGGGTGCAAC
1 TCCCATAAGAAATTCCGAAAGTAGAAGAAAATTAAAAGAAAAAAAAAATGAAAAAGGGGTGCAAC
*
556 ACGAAGACTTCCAAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAACACGCTTAACTGCGGA
66 ACGAAGACTTCCAAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGA
621 GTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCATTGGTCTTTGCATGATAAAT
131 GTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCATTGGTCTTTGCATGATAAAT
686 CTATACAAGCCACATCTCATTGGATCCGGTGCATTGTTGCCAACATATGATCGTATACGTCATAC
196 CTATACAAGCCACATCTCATTGGATCCGGTGCATTGTTGCCAACATATGATCGTATACGTCATAC
*
751 GTACTAAGACTTAATACTTACTTCAACCGATGACTACCCAAAAAGTTTTCGAAAGAAGAAGAAAA
261 GTACTAAGACTTAATACTCACTTCAACCGATGACTACCCAAAAAGTTTTCGAAAGAAGAAGAAAA
816 ATTTATTTCTCTTTGGAAACCTTACCGAGCGAACATAAACGGCCTTTGATCCAGCTTGTTCACGT
326 ATTTATTTCTCTTTGGAAACCTTACCGAGCGAACATAAACGGCCTTTGATCCAGCTTGTTCACGT
881 GCCGTTCATCGAACATGTTGTTCATTCGCAGCCATACTAAGACGTAATGCTTACATGAACCGATT
391 GCCGTTCATCGAACATGTTGTTCATTCGCAGCCATACTAAGACGTAATGCTTACATGAACCGATT
946 GA
456 GA
*
948 TCCCATAAGAAATTCTGAAAGTAGAAGAAAATTAAAAGGAAAAAAAAAATGAAAAAGGGGTGCAA
1 TCCCATAAGAAATTCCGAAAGTAGAAGAAAATTAAAA-GAAAAAAAAAATGAAAAAGGGGTGCAA
*
1013 CACGAAGACTTCCCAA-GAGGTCACCCATCCTAGTACTAGTCTCGCCCAAGCACGCTTAACTGCG
65 CACGAAGACTT-CCAAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCG
* * * *
1077 GAGTTCTGATGGAATCCGGTGCATTAGTGTTGGTATGATTGCACCCATTAGTCTTTG-ATTGATA
129 GAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCATTGGTCTTTGCA-TGATA
*
1141 AATCTATACAAGCCACATCTCATTGGATACGGTGCATTGTTGCCAACATATGATCGT
193 AATCTATACAAGCCACATCTCATTGGATCCGGTGCATTGTTGCCAACATATGATCGT
Statistics
Matches: 685, Mismatches: 17, Indels: 14
0.96 0.02 0.02
Matches are distributed among these distances:
456 424 0.62
457 12 0.02
458 197 0.29
459 14 0.02
461 11 0.02
462 5 0.01
463 8 0.01
464 14 0.02
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (457 bp):
TCCCATAAGAAATTCCGAAAGTAGAAGAAAATTAAAAGAAAAAAAAAATGAAAAAGGGGTGCAAC
ACGAAGACTTCCAAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGA
GTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCATTGGTCTTTGCATGATAAAT
CTATACAAGCCACATCTCATTGGATCCGGTGCATTGTTGCCAACATATGATCGTATACGTCATAC
GTACTAAGACTTAATACTCACTTCAACCGATGACTACCCAAAAAGTTTTCGAAAGAAGAAGAAAA
ATTTATTTCTCTTTGGAAACCTTACCGAGCGAACATAAACGGCCTTTGATCCAGCTTGTTCACGT
GCCGTTCATCGAACATGTTGTTCATTCGCAGCCATACTAAGACGTAATGCTTACATGAACCGATT
GA
Done.