Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006262.1 Corchorus capsularis cultivar CVL-1 contig06281, 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, 622
Length: 1038
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Found at i:988 original size:457 final size:456
Alignment explanation
Indices: 1--1036 Score: 1798
Period size: 457 Copynumber: 2.3 Consensus size: 456
*
1 ACTAATGCACCAGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGA
1 ACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGA
* *
66 TAGGTGACCTCCTGGGAAGTCCTCTTGTTGCACCCCTTTTTCA-TTTTTTTTCTTTTAATTTTCT
66 TGGGTGACCTCCT-GGAAGTCCTCGTGTTGCACCCCTTTTTCATTTTTTTTTCTTTTAATTTTCT
130 TCTACTTTCGGAATTTCTTATGGGAAGCAATCGGTTCATGTAAGCATTACGTCTTAGTATGGCTG
130 TCTACTTTCGGAATTTCTTATGGGAAGCAATCGGTTCATGTAAGCATTACGTCTTAGTATGGCTG
*
195 CGAATGAACAACATGTTCGATGAACGGCACGTGATCAAGCTGGATCAAAGGCCGTTTATGTTCGC
195 CGAATGAACAACATGTTCGATGAACGGCACGTGAACAAGCTGGATCAAAGGCCGTTTATGTTCGC
260 TCGGTAAGGTTTCCAAAGAGAAATAAATTTTTCTTCTTCTTTCGAAAACTTTTTGGGTAGTCATC
260 TCGGTAAGGTTTCCAAAGAGAAATAAATTTTTCTTCTTCTTTCGAAAACTTTTTGGGTAGTCATC
325 GGTTGAAGTAAGTATTAAGTCTTAGTACGTATGACGTATACGATCATATGTTGGCAACAATGCAC
325 GGTTGAAGTAAGTATTAAGTCTTAGTACGTATGACGTATACGATCATATGTTGGCAACAATGCAC
390 CGGATCCAATGAGATGTGGCTTGTATAGATTTATCATGCAAAGACCAATGGGTGCGATCATACCA
390 CGGATCCAATGAGATGTGGCTTGTATAGATTTATCATGCAAAGACCAATGGGTGCGATCATACCA
455 GC
455 GC
* * *
457 ACTAATGCACCGGATCCCATCAGAACTCCGTAGTTAAGCGTGTTTGGTCGAGAGTAGTACTAGGA
1 ACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGA
* *
522 TGAGTGACCTCCTGCGAAGTCCTCGAT-TTGCACCCCTTTTTCATTTTTTTTTCTTTTAGTTTTC
66 TGGGTGACCTCCTG-GAAGTCCTCG-TGTTGCACCCCTTTTTCATTTTTTTTTCTTTTAATTTTC
* *
586 TTCTACTTTTGGTATTTCTTATGGGAAGCAATCGGTTCATGTAAGCATTACGTCTTAGTATGGCT
129 TTCTACTTTCGGAATTTCTTATGGGAAGCAATCGGTTCATGTAAGCATTACGTCTTAGTATGGCT
651 GCGAATGAACAACATGTTCGATGAACGGCACGTGAACAAGCTGGATCAAAGGCCGTTTATGTTCG
194 GCGAATGAACAACATGTTCGATGAACGGCACGTGAACAAGCTGGATCAAAGGCCGTTTATGTTCG
716 CTCGGTAAGGTTTCCAAAGAGAAATAAATTTTTC-TCTTCTTTCGAAAAC-TTTTGGG-AGTCAT
259 CTCGGTAAGGTTTCCAAAGAGAAATAAATTTTTCTTCTTCTTTCGAAAACTTTTTGGGTAGTCAT
778 CGGTTGAAGT-AGTATTAAGTCTTAGTACGTATGACGTATACGATCATATGTTGGCAAC-ATGCA
324 CGGTTGAAGTAAGTATTAAGTCTTAGTACGTATGACGTATACGATCATATGTTGGCAACAATGCA
841 CCGGATCCAATGAGATGTGGCTTGTATAGATTTATCATGCAAAAGACCAATGGGTGCGAATCATA
389 CCGGATCCAATGAGATGTGGCTTGTATAGATTTATCATGC-AAAGACCAATGGGTGCG-ATCATA
906 CCAGC
452 CCAGC
*
911 ACTAATGCACCGGATCCCATCAGAACTCCGACAGTTAAACGTGCTTGGGCGAGAGTAGTACGTAG
1 ACTAATGCACCGGATCCCATCAGAACTCCG-CAGTTAAGCGTGCTTGGGCGAGAGTAGTAC-TAG
* *
976 GAGTGGGTGACCTCCTAGGAACGCCCTAGTGTTGCACCCCTTTTTCTATTTTTTTTTCTTT
64 GA-TGGGTGACCTCCT-GGAA-GTCCTCGTGTTGCACCCCTTTTTC-ATTTTTTTTTCTTT
1037 AG
Statistics
Matches: 550, Mismatches: 18, Indels: 21
0.93 0.03 0.04
Matches are distributed among these distances:
452 45 0.08
453 65 0.12
454 57 0.10
455 34 0.06
456 117 0.21
457 197 0.36
458 21 0.04
459 14 0.03
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (456 bp):
ACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGA
TGGGTGACCTCCTGGAAGTCCTCGTGTTGCACCCCTTTTTCATTTTTTTTTCTTTTAATTTTCTT
CTACTTTCGGAATTTCTTATGGGAAGCAATCGGTTCATGTAAGCATTACGTCTTAGTATGGCTGC
GAATGAACAACATGTTCGATGAACGGCACGTGAACAAGCTGGATCAAAGGCCGTTTATGTTCGCT
CGGTAAGGTTTCCAAAGAGAAATAAATTTTTCTTCTTCTTTCGAAAACTTTTTGGGTAGTCATCG
GTTGAAGTAAGTATTAAGTCTTAGTACGTATGACGTATACGATCATATGTTGGCAACAATGCACC
GGATCCAATGAGATGTGGCTTGTATAGATTTATCATGCAAAGACCAATGGGTGCGATCATACCAG
C
Done.