Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006182.1 Corchorus capsularis cultivar CVL-1 contig06200, 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, 849
Length: 1415
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Found at i:1314 original size:458 final size:459
Alignment explanation
Indices: 1--1415 Score: 2246
Period size: 467 Copynumber: 3.0 Consensus size: 459
1 GCCACATCTCATTGGATCCGGTGCATTGTTGCCAACATATGATCGTATACGTCATACGTACTAAG
1 GCCACATCTCATTGGATCCGGTGCATTGTTGCCAACATATGATCGTATACGTCATACGTACTAAG
* * * * *
66 ACTTAATACTTACTTCAACCGATGACTACCCGAAAAAGTTTTCCAAAGAAGAAGAAAGATTTATT
66 ACTTAATACTTACTTCAACCGATGACTACCCAAAAAAATTTTCGAAAGAAGAAGAAAAAATTATT
131 TCTCTTTGGAAACCTTACCGAGCGAACATAAACGGCCTTTGATCCAGCTTGTTCACGTGCCGTTC
131 TCTCTTTGGAAACCTTACCGAGCGAACATAAACGGCCTTTGATCCAGCTTGTTCACGTGCCGTTC
* *
196 ATCGAACATGTTGTTCATTCGCAGACACACTAAGACGTAATGCTTACATGAAAAAGGGGTGCAAA
196 ATCGAACATGTTGTTCATTCGCAGCCATACTAAGACGTAATGCTTAC-------A----TG--AA
261 TTCCGATTGCTTCCCATAAGAAATTCCGAAAGTAGAAAGAAAAATTAAAAAGAAAAAAAAAATGA
248 --CCGATTGCTTCCCATAAGAAATTCCGAAAGTAG-AAG-AAAATT-AAAAG-AAAAAAAAATG-
*
326 AAAAAGGGGTGACAACACGAGGACTTCCCGAGGAGGTCATCCATCCTAGTACTACTCTCGCCCAA
306 AAAAAGGGGTGACAACACGAGGACTTCCC-AGGAGGTCACCCATCCTAGTACTACTCTCGCCCAA
* *
391 GCACACTTAACTGCGGAGTTCTGATGGGGATCCGGTGCATTAGTGCTGGGTATGATCACACCCAT
370 GCACGCTTAACTGCGGAGTTCTGAT-GGGATCCGGTGCATTAGTGCT-GGTATGATCGCACCCAT
*
456 TGG-CTTTGCATGATGAATCTATACAA
433 TGGTCTTTGCATGATAAATCTATACAA
*
482 GCCACATCTCATTGGATCCGGTGCATTGTTGCCAACATATGATCGTATACGCCATACGTACTAAG
1 GCCACATCTCATTGGATCCGGTGCATTGTTGCCAACATATGATCGTATACGTCATACGTACTAAG
547 ACTTAATACTTACTTCAAACCGATGACTACCCAAAAAAATTTTCGAAAAGAAGAAGAAAAAAATT
66 ACTTAATACTTACTTC-AACCGATGACTACCCAAAAAAATTTTCG-AAAGAAGAAG-AAAAAATT
612 ATTTCTCTTTGGAAAACCTTACCCGAGCGAACATAAACGGACCTTTGATCCAGCGTTGTTCACGT
128 ATTTCTCTTTGG-AAACCTTA-CCGAGCGAACATAAACGG-CCTTTGATCCAGC-TTGTTCACGT
*
677 GCCGTTCATCGAACATGTTGGTCATTCGCAGGCCATACTAAGACGTAATGCTTACATGAACCGAT
189 GCCGTTCATCGAACATGTTGTTCATTCGCA-GCCATACTAAGACGTAATGCTTACATGAACCGAT
742 TGCTTCCCATAAGAAATTCCGAAAGTAGAAGAAAATTAAAAGAAAAAAAAATGAAAAAGGGGTG-
253 TGCTTCCCATAAGAAATTCCGAAAGTAGAAGAAAATTAAAAGAAAAAAAAATGAAAAAGGGGTGA
* *
806 CAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTTCTACTCTCGCCCAAGCACGCTTAAGGT
318 CAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAA-CT
*
871 GCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCATTGGTCTTTGCATGG
382 GCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCATTGGTCTTTGCATGA
*
936 TAAATCGATACAA
447 TAAATCTATACAA
* *
949 GCCACATCTCATTGGATCCGGTGCATTGTTGCCAACATATGATTGTATACGTCATACGTACTTAG
1 GCCACATCTCATTGGATCCGGTGCATTGTTGCCAACATATGATCGTATACGTCATACGTACTAAG
* *
1014 AATTAATACTTACTTCAACCGATGACTACCC-AAAAAATTTTCGAATGAAGAAGAAAAAATTATT
66 ACTTAATACTTACTTCAACCGATGACTACCCAAAAAAATTTTCGAAAGAAGAAGAAAAAATTATT
*
1078 TCTCTTTGGAAACCTTACCGAGCGAACATAAACGGCCTTTGATTCAGCTTGTTCACGTGCCGTTC
131 TCTCTTTGGAAACCTTACCGAGCGAACATAAACGGCCTTTGATCCAGCTTGTTCACGTGCCGTTC
1143 ATCGAACATGTTGTTCATTCGCAGCCATACTAAGACGTAATGCTTACATGAACCGATTGCTTCCC
196 ATCGAACATGTTGTTCATTCGCAGCCATACTAAGACGTAATGCTTACATGAACCGATTGCTTCCC
* *
1208 ATAAGAAATTCCGAAAGTAGAAGAAAATTAAAAGAAAAAAAAATGAAAAAGGGGAGACAA-AAGA
261 ATAAGAAATTCCGAAAGTAGAAGAAAATTAAAAGAAAAAAAAATGAAAAAGGGGTGACAACACGA
1272 GGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTC
326 GGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTC
* * * *
1337 TGATGGGATCTGGTGCA-TAGTGCTGGTATGATCGCACCAATAGGTTTTTGCATGATAAATCTAT
391 TGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCATTGGTCTTTGCATGATAAATCTAT
*
1401 AAAA
456 ACAA
1405 GCCACATCTCA
1 GCCACATCTCA
Statistics
Matches: 888, Mismatches: 35, Indels: 47
0.92 0.04 0.05
Matches are distributed among these distances:
456 56 0.06
457 26 0.03
458 153 0.17
459 42 0.05
460 12 0.01
461 18 0.02
462 8 0.01
463 20 0.02
464 9 0.01
465 12 0.01
466 34 0.04
467 160 0.18
468 31 0.03
469 11 0.01
470 11 0.01
471 5 0.01
472 6 0.01
473 3 0.00
474 33 0.04
476 2 0.00
478 2 0.00
481 80 0.09
482 26 0.03
483 10 0.01
484 18 0.02
485 8 0.01
486 18 0.02
487 13 0.01
488 39 0.04
489 22 0.02
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (459 bp):
GCCACATCTCATTGGATCCGGTGCATTGTTGCCAACATATGATCGTATACGTCATACGTACTAAG
ACTTAATACTTACTTCAACCGATGACTACCCAAAAAAATTTTCGAAAGAAGAAGAAAAAATTATT
TCTCTTTGGAAACCTTACCGAGCGAACATAAACGGCCTTTGATCCAGCTTGTTCACGTGCCGTTC
ATCGAACATGTTGTTCATTCGCAGCCATACTAAGACGTAATGCTTACATGAACCGATTGCTTCCC
ATAAGAAATTCCGAAAGTAGAAGAAAATTAAAAGAAAAAAAAATGAAAAAGGGGTGACAACACGA
GGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTC
TGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCATTGGTCTTTGCATGATAAATCTAT
ACAA
Done.