Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017533.1 Corchorus olitorius cultivar O-4 contig17566, 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: 12263
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Found at i:8 original size:3 final size:3
Alignment explanation
Indices: 1--64 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
1 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
1 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
49 CTA CTA CTA CT- CTA CT
1 CTA CTA CTA CTA CTA CT
65 CTCTCTCTCT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 58 0.97
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
CTA
Found at i:70 original size:2 final size:2
Alignment explanation
Indices: 58--160 Score: 163
Period size: 2 Copynumber: 51.5 Consensus size: 2
48 ACTACTACTA
58 CT CT ACT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT -CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
101 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C- CG CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* *
142 CT CT CC CT CT CT CG CT CT C
1 CT CT CT CT CT CT CT CT CT C
161 GTCTTCTTAG
Statistics
Matches: 94, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
1 1 0.01
2 91 0.97
3 2 0.02
ACGTcount: A:0.01, C:0.51, G:0.02, T:0.46
Consensus pattern (2 bp):
CT
Found at i:2648 original size:34 final size:35
Alignment explanation
Indices: 2601--2667 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
2591 ATTCTACTTC
* *
2601 ATCTCTAGGTAATTCATCAAAA-TACAACTAATTT
1 ATCTCTAGATAATTCATCAAAAGTAAAACTAATTT
2635 ATCTCTAGATAATTCATCAAAAGTAAAACTAAT
1 ATCTCTAGATAATTCATCAAAAGTAAAACTAAT
2668 ATTAATTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 21 0.70
35 9 0.30
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.33
Consensus pattern (35 bp):
ATCTCTAGATAATTCATCAAAAGTAAAACTAATTT
Found at i:6382 original size:33 final size:34
Alignment explanation
Indices: 6318--6386 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
6308 ACAGATGTAA
6318 TTGTTTTTATTAGTAAAACTCTTTTGTAGACTCT
1 TTGTTTTTATTAGTAAAACTCTTTTGTAGACTCT
*
6352 TTGTTTTTATTAGTAAACCTC-TTTGTAGACTCT
1 TTGTTTTTATTAGTAAAACTCTTTTGTAGACTCT
6385 TT
1 TT
6387 ATTTGTTTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 14 0.41
34 20 0.59
ACGTcount: A:0.22, C:0.13, G:0.12, T:0.54
Consensus pattern (34 bp):
TTGTTTTTATTAGTAAAACTCTTTTGTAGACTCT
Found at i:8148 original size:4 final size:4
Alignment explanation
Indices: 8139--8167 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
8129 CTCATTTTGA
8139 TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
8168 GTGTTACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:9869 original size:31 final size:31
Alignment explanation
Indices: 9831--9892 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
9821 AAAGTCATTA
*
9831 ATGAATATTGTGATTATTCATAAATCAAGAG
1 ATGAATATTGTAATTATTCATAAATCAAGAG
*
9862 ATGAATATTGTAATTATTCATGAATCAAGAG
1 ATGAATATTGTAATTATTCATAAATCAAGAG
9893 TTCTCCTCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.35
Consensus pattern (31 bp):
ATGAATATTGTAATTATTCATAAATCAAGAG
Done.