Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009574.1 Corchorus capsularis cultivar CVL-1 contig09595, 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: 8205
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Found at i:4118 original size:22 final size:22
Alignment explanation
Indices: 4093--4136 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4083 ACATCAAAGT
4093 CTATTTCTCATTCACATAATTA
1 CTATTTCTCATTCACATAATTA
*
4115 CTATTTCTTATTCACATAATTA
1 CTATTTCTCATTCACATAATTA
4137 GAACCCGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTATTTCTCATTCACATAATTA
Found at i:4167 original size:78 final size:78
Alignment explanation
Indices: 4038--4192 Score: 283
Period size: 78 Copynumber: 2.0 Consensus size: 78
4028 TTTCAAAGTT
* *
4038 TATTTCTCATTCACATAATTAGAACTCGAGATGTTGCTTAACGAGACATCAAAGTCTATTTCTCA
1 TATTTCTCATTCACATAATTAGAACCCGAGATATTGCTTAACGAGACATCAAAGTCTATTTCTCA
4103 TTCACATAATTAC
66 TTCACATAATTAC
*
4116 TATTTCTTATTCACATAATTAGAACCCGAGATATTGCTTAACGAGACATCAAAGTCTATTTCTCA
1 TATTTCTCATTCACATAATTAGAACCCGAGATATTGCTTAACGAGACATCAAAGTCTATTTCTCA
4181 TTCACATAATTA
66 TTCACATAATTA
4193 GAACCCGAGA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (78 bp):
TATTTCTCATTCACATAATTAGAACCCGAGATATTGCTTAACGAGACATCAAAGTCTATTTCTCA
TTCACATAATTAC
Found at i:6987 original size:28 final size:30
Alignment explanation
Indices: 6955--7034 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 30
6945 GGCTGTTTTA
6955 ACTATTTTTATTT-TTTTTAAG-TTTAATC
1 ACTATTTTTATTTGTTTTTAAGATTTAATC
* *
6983 ACTATTTTTATTTGTTTTTTAGATTTAATTTA
1 ACTATTTTTATTTGTTTTTAAGATTTAA--TC
*
7015 ACTATTTTTGTATTGTTTTT
1 ACTATTTTTAT-TTGTTTTT
7035 CTTTTTTTGG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
28 13 0.30
29 7 0.16
30 5 0.11
32 11 0.25
33 8 0.18
ACGTcount: A:0.23, C:0.05, G:0.06, T:0.66
Consensus pattern (30 bp):
ACTATTTTTATTTGTTTTTAAGATTTAATC
Found at i:7948 original size:11 final size:11
Alignment explanation
Indices: 7932--7957 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
7922 TACTTAAAAT
7932 AAAATAAATAA
1 AAAATAAATAA
7943 AAAATAAATAA
1 AAAATAAATAA
7954 AAAA
1 AAAA
7958 ACTCTACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAATAAATAA
Found at i:8025 original size:2 final size:2
Alignment explanation
Indices: 8020--8055 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
8010 TTTTTAAGTA
8020 AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8056 TTCTTCCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8143 original size:2 final size:2
Alignment explanation
Indices: 8138--8205 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
8128 ATATATAGAT
8138 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
8180 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.