Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022643.1 Corchorus olitorius cultivar O-4 contig22676, 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: 10989
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Found at i:1072 original size:21 final size:21
Alignment explanation
Indices: 1048--1097 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1038 TTGTCGCTGG
1048 GCGCCCAGGC-AAAATGCCTCA
1 GCGCCCAGGCGAAAA-GCCTCA
* *
1069 GCGCCCAGGCGACAAGGCTCA
1 GCGCCCAGGCGAAAAGCCTCA
1090 GCGCCCAG
1 GCGCCCAG
1098 CTGGATCCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.24, C:0.40, G:0.30, T:0.06
Consensus pattern (21 bp):
GCGCCCAGGCGAAAAGCCTCA
Found at i:3304 original size:20 final size:21
Alignment explanation
Indices: 3279--3322 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3269 TATATTTGTG
* *
3279 TTTTGCGTCA-AAAAAAAAGT
1 TTTTGCATCATAAAAAAAAAT
3299 TTTTGCATCATAAAAAAAAAT
1 TTTTGCATCATAAAAAAAAAT
3320 TTT
1 TTT
3323 GTTTCTGCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (21 bp):
TTTTGCATCATAAAAAAAAAT
Found at i:3323 original size:20 final size:20
Alignment explanation
Indices: 3279--3323 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3269 TATATTTGTG
* *
3279 TTTTGCGTCAAAAAAAAAGT
1 TTTTGCATCAAAAAAAAAGA
3299 TTTTGCATCATAAAAAAAA-A
1 TTTTGCATCA-AAAAAAAAGA
3319 TTTTG
1 TTTTG
3324 TTTCTGCGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (20 bp):
TTTTGCATCAAAAAAAAAGA
Found at i:6134 original size:21 final size:21
Alignment explanation
Indices: 6110--6160 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
6100 CCGGCCACGG
6110 CCCGGCCACCCGAGCCATCTA
1 CCCGGCCACCCGAGCCATCTA
6131 CCCGGCCACCCGAGCCATCTA
1 CCCGGCCACCCGAGCCATCTA
6152 CCCGGCCAC
1 CCCGGCCAC
6161 AAGCGCTACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.18, C:0.55, G:0.20, T:0.08
Consensus pattern (21 bp):
CCCGGCCACCCGAGCCATCTA
Found at i:10110 original size:7 final size:7
Alignment explanation
Indices: 10098--10122 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
10088 ACAATTGAGT
10098 TTTTCCC
1 TTTTCCC
10105 TTTTCCC
1 TTTTCCC
10112 TTTTCCC
1 TTTTCCC
10119 TTTT
1 TTTT
10123 AATTTCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTCCC
Found at i:10922 original size:4 final size:4
Alignment explanation
Indices: 10913--10939 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
10903 TCTTTGAAAA
10913 AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AAT
10940 AAGTTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Done.