Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011812.1 Corchorus capsularis cultivar CVL-1 contig11833, 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: 20108
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Found at i:1217 original size:21 final size:23
Alignment explanation
Indices: 1184--1227 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
1174 AAATCAATCA
*
1184 TTTATCTTATTTATTTCTGTTTT
1 TTTATCTTATTTATTCCTGTTTT
1207 TTTA-CTT-TTTATTCCTGTTTT
1 TTTATCTTATTTATTCCTGTTTT
1228 AAAAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
22 3 0.15
23 4 0.20
ACGTcount: A:0.11, C:0.11, G:0.05, T:0.73
Consensus pattern (23 bp):
TTTATCTTATTTATTCCTGTTTT
Found at i:3268 original size:20 final size:20
Alignment explanation
Indices: 3243--3282 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3233 GAGGAATGGA
*
3243 TGTAAAAAATTAGATCTAGG
1 TGTAAAAAAATAGATCTAGG
3263 TGTAAAAAAATAGATCTAGG
1 TGTAAAAAAATAGATCTAGG
3283 GGCTGAGCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.28
Consensus pattern (20 bp):
TGTAAAAAAATAGATCTAGG
Found at i:3619 original size:13 final size:13
Alignment explanation
Indices: 3587--3620 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3577 GTTTTTTCTT
3587 AAATTATTTTTTA
1 AAATTATTTTTTA
**
3600 AGGTTATTTTTTA
1 AAATTATTTTTTA
3613 AAATTATT
1 AAATTATT
3621 AGTTTTAATA
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (13 bp):
AAATTATTTTTTA
Found at i:4022 original size:54 final size:54
Alignment explanation
Indices: 3985--4107 Score: 219
Period size: 54 Copynumber: 2.3 Consensus size: 54
3975 GCTAGGTTCG
* *
3985 GTTATTATGATGGGGCAGCTTAGGCGGGTTACCATGATAATAATGCTGACCCCC
1 GTTATTATGATGGGGCAGCTCAGGCGGGTTACCATGATAAGAATGCTGACCCCC
*
4039 GTTATTATGATGGGGCAGCTCAGGCGGGTTACCATGATAATAATGCTGACCCCC
1 GTTATTATGATGGGGCAGCTCAGGCGGGTTACCATGATAAGAATGCTGACCCCC
4093 GTTATTATGATGGGG
1 GTTATTATGATGGGG
4108 GTGACTTTGA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 68 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (54 bp):
GTTATTATGATGGGGCAGCTCAGGCGGGTTACCATGATAAGAATGCTGACCCCC
Found at i:6126 original size:20 final size:21
Alignment explanation
Indices: 6100--6149 Score: 70
Period size: 18 Copynumber: 2.5 Consensus size: 21
6090 TCGAATCGGA
6100 AATATTTTGATTTACAACTTG
1 AATATTTTGATTTACAACTTG
6121 -ATA-TTT-ATTTACAACTTG
1 AATATTTTGATTTACAACTTG
6139 AAATATTTTGA
1 -AATATTTTGA
6150 AATATTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
18 12 0.48
19 3 0.12
20 6 0.24
21 3 0.12
22 1 0.04
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (21 bp):
AATATTTTGATTTACAACTTG
Found at i:10082 original size:10 final size:10
Alignment explanation
Indices: 10067--10097 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
10057 AGTTTGAAGT
*
10067 TTTCAGAGGA
1 TTTCAGAGAA
10077 TTTCAGAGAA
1 TTTCAGAGAA
10087 TTTCAGAGAA
1 TTTCAGAGAA
10097 T
1 T
10098 GTAAAAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.32
Consensus pattern (10 bp):
TTTCAGAGAA
Done.