Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006216.1 Corchorus capsularis cultivar CVL-1 contig06235, 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, 894
Length: 1490
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Found at i:1217 original size:456 final size:454
Alignment explanation
Indices: 1--1490 Score: 2457
Period size: 456 Copynumber: 3.3 Consensus size: 454
* *
1 CATTGTTGCCAACATATGATCGTATACATCGTACGTACTAAGACTTAATACTTACTTCAACCGAT
1 CATTGTTGCCAACATATGATCGTATACATCATACGTACTAAGACTTAATACTTACTTCAAACGAT
66 GACTACCCAAAAAGTTTTCG-AAGAAGAAG-AAAATTTATTTCTCTTTGGAAACCTTACCGAGCG
66 GACTACCCAAAAAGTTTTCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCG
**
129 AACATAAACGGCCCCTGATCCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTTCGCA
131 AACATAAACGGCCTTTGATCCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCA-TTCGCA
* *
194 GTCCATACTAAGACGTAATGCGTACATGAACAGATTGCTTCCCATAAGAAATTCCGAAAGTAGAA
195 G-CCATACTAAGACGTAATGCTTACATGAACCGATTGCTTCCCATAAGAAATTCCGAAAGTAGAA
*
259 AAAATT-AAAGAAAAAAAAATGAAAAAAGGGTCCAACATGAGGACTTCCCAGGAGGTACACCCAT
259 AAAATTAAAAGAAAAAAAAATG-AAAAAGGGTGCAACATGAGGACTTCCCAGGAGGT-CACCCAT
* * *
323 CTTAGTACTACTCTCGCCCAAGCACGCTAAACTGCAGAGTTCTGATGGGATCCGGTGCATTAGTG
322 CCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTG
388 CTGGTATGATCGC-ACTCATTGGTCTTGCATGATAAATCTATACAAGCCACATCTCATTGGATCC
387 CTGGTATGATCGCAAC-CATTGGTCTTGCATGATAAATCTATACAAGCCACATCTCATTGGATCC
452 GGTG
451 GGTG
456 CATTGTTGCCAACATATGATCGTATACATCATACGTACTAAGACTTAATACATTACTTC-AACGA
1 CATTGTTGCCAACATATGATCGTATACATCATACGTACTAAGACTTAATAC-TTACTTCAAACGA
*
520 TGAATCTATCC-AAAAGTTTTCGAAACGAAG-AGAAAAA-TTATTTCTCTTTAGGAAACCTTACC
65 TG-A-CTACCCAAAAAGTTTTCGAAA-GAAGAAGAAAAATTTATTTCTCTTT-GGAAACCTTACC
582 GAGCGAACATAAACGGCCTTTGATCCAGCTTGTTCACGTGCCGTTCATCGAACA---TGTTCATT
126 GAGCGAACATAAACGGCCTTTGATCCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATT
* *
644 CGCAGCCATACTAAGACATAATGCTTACATGAACCAATTGCTTCCCATAAGAAATTCCGAAAGTA
191 CGCAGCCATACTAAGACGTAATGCTTACATGAACCGATTGCTTCCCATAAGAAATTCCGAAAGTA
* *
709 GAAAAAAATTAAAAGAAAAAAAAATGAAAAAGGGGTGCAAGATGACGACTTCCCAGGTA-GTCAC
256 G-AAAAAATTAAAAGAAAAAAAAATGAAAAA-GGGTGCAACATGAGGACTTCCCAGG-AGGTCAC
773 CCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATT
318 CCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATT
* ** *
838 AGTGCTGGTATGATCGCAACAATTAATTCTTGCATGATAAATCTATACAAGCAACATCTCATTGG
383 AGTGCTGGTATGATCGCAACCATT-GGTCTTGCATGATAAATCTATACAAGCCACATCTCATTGG
903 ATCCGGTG
447 ATCCGGTG
*
911 CATTGTTGCCAACATATGATCGTATACATCATACGTACTAAGAATT-ATACTTACTTCAAACGAT
1 CATTGTTGCCAACATATGATCGTATACATCATACGTACTAAGACTTAATACTTACTTCAAACGAT
975 GACTACCCAAAAAGTTTTCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCG
66 GACTACCCAAAAAGTTTTCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCG
*
1040 AACATAAACGGCCTTTGATCCAGCTTGTTCACATGCCGTTCATCGAACATGTTGTTCATTCGCAG
131 AACATAAACGGCCTTTGATCCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAG
1105 CCATACTAAGACGTAATGCTTACATGAACCGATTGCTTCCCATAAGAAATTCCGAAAGTAGAAGA
196 CCATACTAAGACGTAATGCTTACATGAACCGATTGCTTCCCATAAGAAATTCCGAAAGTAGAA-A
* * *
1170 AAATTAAAAGAAAGAAAAATGGAAAAGGAGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCC
260 AAATTAAAAGAAAAAAAAATGAAAAAGG-GTGCAACATGAGGACTTCCCAGGAGGTCACCCATCC
* * *
1235 TAGTATTGCTCTCGCCCAAGCAAGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCT
324 TAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCT
*
1300 GGTATGATCGCACCCATTGGTCTTTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGG
389 GGTATGATCGCAACCATTGGTC-TTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGG
1365 TG
453 TG
* * *
1367 CATTGTTGCCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTGCTTCAACCGAT
1 CATTGTTGCCAACATATGATCGTATACATCATACGTACTAAGACTTAATACTTACTTCAAACGAT
1432 GACTACCCAAAAAGTTTTCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTAC
66 GACTACCCAAAAAGTTTTCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTAC
Statistics
Matches: 969, Mismatches: 41, Indels: 48
0.92 0.04 0.05
Matches are distributed among these distances:
452 9 0.01
453 151 0.16
454 128 0.13
455 200 0.21
456 313 0.32
457 96 0.10
458 72 0.07
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (454 bp):
CATTGTTGCCAACATATGATCGTATACATCATACGTACTAAGACTTAATACTTACTTCAAACGAT
GACTACCCAAAAAGTTTTCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCG
AACATAAACGGCCTTTGATCCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAG
CCATACTAAGACGTAATGCTTACATGAACCGATTGCTTCCCATAAGAAATTCCGAAAGTAGAAAA
AATTAAAAGAAAAAAAAATGAAAAAGGGTGCAACATGAGGACTTCCCAGGAGGTCACCCATCCTA
GTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGG
TATGATCGCAACCATTGGTCTTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTG
Done.