Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005455.1 Corchorus capsularis cultivar CVL-1 contig05473, 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, 1000
Length: 9619
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Found at i:743 original size:16 final size:17
Alignment explanation
Indices: 722--753 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
712 CGGTCCGGTT
722 CATGT-ATTGACCCAAA
1 CATGTAATTGACCCAAA
738 CATGTAATTGACCCAA
1 CATGTAATTGACCCAA
754 TAAAAACCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (17 bp):
CATGTAATTGACCCAAA
Found at i:3253 original size:32 final size:32
Alignment explanation
Indices: 3181--3283 Score: 118
Period size: 32 Copynumber: 3.2 Consensus size: 32
3171 AATGGCTCAA
* * *
3181 GCCGCCC-CACTGGGGCGGCTTCACCATGGGCAG
1 GCCGCCCTC-CTGGTGCGGCTTCGCCA-CGGCAG
*
3214 GCTGCCCTCCTGGTGCGGCTTCGCCACGGCAG
1 GCCGCCCTCCTGGTGCGGCTTCGCCACGGCAG
* *
3246 GCCGCCCTCATGGTGTGGCTTCGCCACGGCAG
1 GCCGCCCTCCTGGTGCGGCTTCGCCACGGCAG
*
3278 ACCGCC
1 GCCGCC
3284 TCGGTGGGGC
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
32 39 0.64
33 21 0.34
34 1 0.02
ACGTcount: A:0.10, C:0.41, G:0.34, T:0.16
Consensus pattern (32 bp):
GCCGCCCTCCTGGTGCGGCTTCGCCACGGCAG
Found at i:3547 original size:2 final size:2
Alignment explanation
Indices: 3540--3568 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3530 CTATACCTCT
3540 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3569 TTACTTACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6712 original size:24 final size:24
Alignment explanation
Indices: 6680--6732 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
6670 AAGTTTTAAA
6680 AGTAAGATTTGATAATGAAAGATT
1 AGTAAGATTTGATAATGAAAGATT
6704 AGTAAGATTTGATAATGAAAGATT
1 AGTAAGATTTGATAATGAAAGATT
6728 AGTAA
1 AGTAA
6733 ATGTTAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (24 bp):
AGTAAGATTTGATAATGAAAGATT
Found at i:8653 original size:201 final size:201
Alignment explanation
Indices: 8009--8989 Score: 1657
Period size: 201 Copynumber: 4.9 Consensus size: 201
7999 ACTATAAATT
*
8009 GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGAGATATG
1 GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGAGGTATG
** * *
8074 TGTCGACTTCTTAACCCGTTTATGGAGTCCAAAATTCACACTGACAGTGTATTGTATAATAATCC
66 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCC
* * *
8139 TATAAGAAAATTTATACAATACACCGTTAGTGGAGTTTAGCAGACTGCACGTGCGGGGCTTAACT
131 TATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACT
8204 TTAAGG
196 TTAAGG
* * *
8210 GTTGACATGTGTACCCTTAGGGAGTATGTATTAATATTAAATATATAATTATGAAATGGGGTATG
1 GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGAGGTATG
*
8275 TGTTAACTTCTTAACCTGCTTATGGAGTCCAAAATTTTACACTGACAGTGTATTGTAT-ATAATC
66 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAA-TTTACACTGACAGTGTATTGTATAATAATC
* * * *
8339 CTATAAG-AAATTTATACAATACAACGTTAGTGGAGTTTAGCAGACTGCACGTGCGAGGTTTAAC
130 CTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAC
8403 TTTAAGG
195 TTTAAGG
*
8410 GTTGACATGTGTACCCTTAGGGAGA-ATGTATTAATATTAAATATTTAATTATGAAATGGGGTAT
1 GTTGACATGTGTACCCTTAGGGA-ATATGTATTAATATTAAATATTTAATTATGAAATGAGGTAT
* * *
8474 GTGTTAACTTCTTAACCCGTTTATGGAGTCGAAAATTTACACTAACAGTGTATTGTATAATAATC
65 GTGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATC
* *
8539 CTATAAGAAAAATTATACAATACACCGTCAGTGCAGTTTAGCAGACTGCACGTGTGGGGTTTAAC
130 CTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAC
8604 TTTAAGG
195 TTTAAGG
*
8611 GTTGACATGTGTACCCTTTGGGAATATGTATTAATATTAAATATTTAATTATGAAAT--GGTATG
1 GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGAGGTATG
8674 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCC
66 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCC
*
8739 TATAAGAAAACTTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACT
131 TATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACT
8804 TTAAGG
196 TTAAGG
* *
8810 GTTGACATGTGTACCCTTTGGGAATATGTATTAATATTAAATATTTAATTATGAAATAAGGTATG
1 GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGAGGTATG
*
8875 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTCCACTGACAGTGTATTGTATAATAATCC
66 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCC
*
8940 TATAAGAAAAATTATACAATACACCGTAAGTGGAGTTTAGCAGACTGCAC
131 TATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCAC
8990 TAATACCGAT
Statistics
Matches: 739, Mismatches: 34, Indels: 14
0.94 0.04 0.02
Matches are distributed among these distances:
199 215 0.29
200 168 0.23
201 334 0.45
202 22 0.03
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (201 bp):
GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGAGGTATG
TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCC
TATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACT
TTAAGG
Done.