Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006106.1 Corchorus capsularis cultivar CVL-1 contig06124, 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: 11315
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Found at i:1200 original size:167 final size:167
Alignment explanation
Indices: 550--1150 Score: 891
Period size: 167 Copynumber: 3.6 Consensus size: 167
540 TGAGTCATTT
* * * *
550 GTCAATTGAGAAATGGCCAAAATGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGAACAT
1 GTCAATTGAGAAATGACCAAAAAGTTTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
** ** * * ** * *
615 TTAAGTAATCTGCCAAGTAGGTGAAGACGAAAAAAATTAGTTTTCTAGCT-CATCATCAATCCTT
66 TTAAGTAATCTATCAAGTAGGAAAAGACGAAAAAAATAAGTTTTCTAACTCCAAAAGCAAGCCTT
* * * *
679 GAT-GGAGATCTTTTATTAATTCCACTACTCTAATCAA
131 GGTAGG-GATCTTTTAGTAATTCCACTACTCTATTAAA
* ** *
716 GTCCATTGAGAAATGACCAAAAAAATTATTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGTTTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* *
781 TTAAGTAATCTATCAAATAGGAAAATACGAAAAAAATAAGTTTTCTAACTCCAAAAGCAAGCCTT
66 TTAAGTAATCTATCAAGTAGGAAAAGACGAAAAAAATAAGTTTTCTAACTCCAAAAGCAAGCCTT
846 GGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
131 GGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
*
883 GTCAATTGAGAAATGACCAAAAAGTTTAATTATTTAATCGCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGTTTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* *
948 TTAAGTAATCTATCAAGTAGAAAAATACGAAAAAAATAAGTTTTCTAACTCCAAAAGCAAGCCTT
66 TTAAGTAATCTATCAAGTAGGAAAAGACGAAAAAAATAAGTTTTCTAACTCCAAAAGCAAGCCTT
*
1013 GGTAGGGATCTTTTAGTAATTACACTACTCTATTAAA
131 GGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
*
1050 GTCAATTGAGAAATGACCAAAAAGTTTAATTATTTAATCCCCTCAAGAATTAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGTTTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * *
1115 TTAAGTAATCTGTCAAGTGGGAAAAGACAAAAAAAA
66 TTAAGTAATCTATCAAGTAGGAAAAGACGAAAAAAA
1151 ATTAGTTCTC
Statistics
Matches: 395, Mismatches: 38, Indels: 3
0.91 0.09 0.01
Matches are distributed among these distances:
166 100 0.25
167 293 0.74
168 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.29
Consensus pattern (167 bp):
GTCAATTGAGAAATGACCAAAAAGTTTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
TTAAGTAATCTATCAAGTAGGAAAAGACGAAAAAAATAAGTTTTCTAACTCCAAAAGCAAGCCTT
GGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:3991 original size:40 final size:40
Alignment explanation
Indices: 3938--4016 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
3928 ACGCATACAA
* *
3938 CTAAGCCCAAATAACAGGTGTAATCCCCATATGTTAACAG
1 CTAAACCCAAATAACAGGTGTAATCCCCATATATTAACAG
* * *
3978 CTAAACCCAAATAACATGTGTAATCTCCATCTATTAACA
1 CTAAACCCAAATAACAGGTGTAATCCCCATATATTAACA
4017 TCTATTAATC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.39, C:0.25, G:0.10, T:0.25
Consensus pattern (40 bp):
CTAAACCCAAATAACAGGTGTAATCCCCATATATTAACAG
Found at i:8258 original size:13 final size:12
Alignment explanation
Indices: 8229--8261 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
8219 ATTGAATATG
8229 TTTTTTT-ATAA
1 TTTTTTTAATAA
8240 TTTTTTTAATAA
1 TTTTTTTAATAA
8252 TTATTTTTAA
1 TT-TTTTTAA
8262 GACTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.35
12 6 0.30
13 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTTTTAATAA
Found at i:9366 original size:13 final size:13
Alignment explanation
Indices: 9348--9372 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9338 AAAGGAGTCG
9348 TAAGTCCTAACCC
1 TAAGTCCTAACCC
9361 TAAGTCCTAACC
1 TAAGTCCTAACC
9373 ACGATTAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.36, G:0.08, T:0.24
Consensus pattern (13 bp):
TAAGTCCTAACCC
Found at i:11145 original size:33 final size:33
Alignment explanation
Indices: 11095--11218 Score: 144
Period size: 33 Copynumber: 3.7 Consensus size: 33
11085 CCGCGCAACA
11095 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGT
11130 CCGGCCATC-ACCGGCCACGCGACATGGACATGT
1 CCGGCCA-CAACCGGCCACGCGACATGGACATGT
* ** * *
11163 CCGGCTACAACCGGCCAAACGAC-TCGGCCATGC
1 CCGGCCACAACCGGCCACGCGACAT-GGACATGT
*
11196 CCGACCACAACCGGCCACGCGAC
1 CCGGCCACAACCGGCCACGCGAC
11219 CCTTTGTCTA
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
32 2 0.03
33 67 0.87
35 7 0.09
36 1 0.01
ACGTcount: A:0.24, C:0.42, G:0.26, T:0.08
Consensus pattern (33 bp):
CCGGCCACAACCGGCCACGCGACATGGACATGT
Done.