Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023155.1 Corchorus olitorius cultivar O-4 contig23188, 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: 10023
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:199 original size:2 final size:2
Alignment explanation
Indices: 192--223 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
182 TGATTGATGC
192 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
224 CACATCCAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5153 original size:21 final size:21
Alignment explanation
Indices: 5124--5168 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5114 ATGACACTAC
* *
5124 CCACCTGGGTGATCAGGCAAA
1 CCACATGGGTGATCAGACAAA
**
5145 CCACATGGGTTTTCAGACAAA
1 CCACATGGGTGATCAGACAAA
5166 CCA
1 CCA
5169 TGTGGGCGCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (21 bp):
CCACATGGGTGATCAGACAAA
Found at i:6447 original size:13 final size:13
Alignment explanation
Indices: 6431--6457 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6421 GTTTTTGATT
6431 AATTGTTTTCTTA
1 AATTGTTTTCTTA
6444 AATTGTTTTCTTA
1 AATTGTTTTCTTA
6457 A
1 A
6458 CCCTTAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (13 bp):
AATTGTTTTCTTA
Found at i:6499 original size:31 final size:33
Alignment explanation
Indices: 6435--6502 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
6425 TTGATTAATT
6435 GTTTTCTTAAATTGTTTTCTTAACCCTTAGTTTA
1 GTTTTCTTAAATTGTTTTCTTAA-CCTTAGTTTA
*
6469 GTTTTACTT-AATTGTTTTC-TAA-TTTAGTTTA
1 GTTTT-CTTAAATTGTTTTCTTAACCTTAGTTTA
6500 GTT
1 GTT
6503 ATTTTGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
31 11 0.34
33 3 0.09
34 15 0.47
35 3 0.09
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.59
Consensus pattern (33 bp):
GTTTTCTTAAATTGTTTTCTTAACCTTAGTTTA
Found at i:8001 original size:11 final size:11
Alignment explanation
Indices: 7985--8015 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
7975 CATTTTGCCC
*
7985 TCAAGAAGTCA
1 TCAAGAAGCCA
7996 TCAAGAAGCCA
1 TCAAGAAGCCA
8007 TCAAGAAGC
1 TCAAGAAGC
8016 TCCATTTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.13
Consensus pattern (11 bp):
TCAAGAAGCCA
Found at i:8172 original size:18 final size:18
Alignment explanation
Indices: 8149--8192 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
8139 TAAACCTCTC
*
8149 TTACTATTTCCTTTATCA
1 TTACTATTTCCCTTATCA
*
8167 TTACTATTTCCCTTATTA
1 TTACTATTTCCCTTATCA
*
8185 TTATTATT
1 TTACTATT
8193 ATTATTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.23, C:0.18, G:0.00, T:0.59
Consensus pattern (18 bp):
TTACTATTTCCCTTATCA
Found at i:8187 original size:3 final size:3
Alignment explanation
Indices: 8179--8206 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
8169 ACTATTTCCC
8179 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
8207 CTTTACTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.