Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006238.1 Corchorus capsularis cultivar CVL-1 contig06257, 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, 846
Length: 1410
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Found at i:967 original size:461 final size:458
Alignment explanation
Indices: 1--1327 Score: 2272
Period size: 457 Copynumber: 2.9 Consensus size: 458
* * *
1 CTCGCCCAAGCACGCTTTACTGCGGAATTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCG
1 CTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGTTGGTATGATCG
66 CACCCATTGGTCTTTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCATTGTTG
66 CACCCATTGGTCTTTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCATTGTTG
*
131 CCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTACTTGAACCGATGACTACCC
131 CCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTACTTCAACCGATGACTACCC
196 -AAAAA--GTTCTCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCGAACAT
196 AAAAAATTGTT-TCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCGAACAT
*
258 AAACGGCCTTTGATCCAGCTTATTCACGTGCCTGTTCATCGAACATGTTGTTCATTCGCAGCCAT
260 AAACGGCCTTTGATCCAGCTTGTTCACGTGCC-GTTCATCGAACATGTTGTTCATTCGCAGCCAT
* *
323 ACTAAGACGTAATGATTACATGAACCGATTGCTTCCCATAAGAAATTCCGAAAGTAGAAGGAAAT
324 ACTAAGACGTAATGCTTACATGAACCGATTGCTTCCCATAAGAAATTCCGAAAGTAGAAGAAAAT
* * *
388 TAAAAGAAAAAAAATGAAAAAGGGGTGCAACAAGAGGAATTCCCAGGAGGTCAACCATCCTAGTA
389 TAAAAGAAAAAAAATGAAAAAGAGGTGCAACAAGAGGAAGTACCAGGAGGTCAACCATCCTAGTA
453 CTACT
454 CTACT
* *
458 CTTGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTTGTGTTGGTATGATCG
1 CTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGTTGGTATGATCG
**
523 CACCCATTGGTCTTTGCATGATAAATCTATTGAAGCCACATCTCATTGGATCCGGTGCATTGTTG
66 CACCCATTGGTCTTTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCATTGTTG
588 CCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTACTTCAACCGATGACTACCC
131 CCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTACTTCAACCGATGACTACCC
*
653 AAAAAATTGATTTCGAAAGAAGAAAGTAAAATTTATTTCTCTTTGGAAACCTTACCGAGCGAACA
196 AAAAAATTG-TTTCGAAAGAAG-AAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCGAACA
718 TAAACGGCCTTTGATCCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCAT
259 TAAACGGCCTTTGATCCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCAT
* * *
783 ACTAAGACTTAATGCTTACATGAACCGATTGCTTCCCATAAGAAATTCCAAAAGTAGAAGAAAAC
324 ACTAAGACGTAATGCTTACATGAACCGATTGCTTCCCATAAGAAATTCCGAAAGTAGAAGAAAAT
* * *
848 TAAAAGAAAAAAAAATGAAAAAGAGGTGCAA-ATCGAGGACGTACCAGGAGGTCACCCATCCTAG
389 TAAAAG-AAAAAAAATGAAAAAGAGGTGCAACA-AGAGGAAGTACCAGGAGGTCAACCATCCTAG
912 TACTACT
452 TACTACT
* * * * *
919 CTCGACCAAGCACGCTTAATTGCGGAGTTCTAATGGGATCCTGTGCATTAGTGTTGGTATGATCA
1 CTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGTTGGTATGATCG
984 CACCCATTGGTCTTTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCATTGTTG
66 CACCCATTGGTCTTTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCATTGTTG
1049 CCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTACTTCAACCGATGACTACCC
131 CCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTACTTCAACCGATGACTACCC
* *
1114 AAAAAGTT-TTT-GAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTACCGGGCGAACATA
196 AAAAAATTGTTTCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCGAACATA
*
1177 AACGGCCTTTGATCCAGCTTGTTCATGAT-CCGTTCATCGAACATGTTGTTCATTCGCAGCCATA
261 AACGGCCTTTGATCCAGCTTGTTCACG-TGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATA
1241 CTAAGACGTAATGCTTACATGAACCGATTGCTTCCCATAAGAAATTCCGAAAGTAGAAGAAAATT
325 CTAAGACGTAATGCTTACATGAACCGATTGCTTCCCATAAGAAATTCCGAAAGTAGAAGAAAATT
1306 AAAAGGAAAAAAAATGAAAAAG
390 AAAA-GAAAAAAAATGAAAAAG
1328 GGGACTCTCG
Statistics
Matches: 824, Mismatches: 37, Indels: 18
0.94 0.04 0.02
Matches are distributed among these distances:
457 372 0.45
458 15 0.02
459 3 0.00
460 110 0.13
461 324 0.39
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (458 bp):
CTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGTTGGTATGATCG
CACCCATTGGTCTTTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCATTGTTG
CCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTACTTCAACCGATGACTACCC
AAAAAATTGTTTCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCGAACATA
AACGGCCTTTGATCCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATAC
TAAGACGTAATGCTTACATGAACCGATTGCTTCCCATAAGAAATTCCGAAAGTAGAAGAAAATTA
AAAGAAAAAAAATGAAAAAGAGGTGCAACAAGAGGAAGTACCAGGAGGTCAACCATCCTAGTACT
ACT
Done.