Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017985.1 Corchorus olitorius cultivar O-4 contig18018, 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: 13664
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.34
Found at i:351 original size:6 final size:6
Alignment explanation
Indices: 331--702 Score: 487
Period size: 6 Copynumber: 62.3 Consensus size: 6
321 CAGCATGCCT
* * *
331 TTCTTC CTC-TC TTCTTC TTCTTC TTCCTC TTCTTC TTCTTC TTCCTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
* * *
378 TTCCTC TTCTTC TTCTTC TTCCTC TTCTTC TTCTTC TTCGTC TTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
* * *
426 TGCTTC TTCCTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCCTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
* * * * * *
474 TTCTTC TTCCTC TTCTTC TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
* * * * *
522 -TCCTC TTCTTC CTGTTC TTCTTC TTCTTC TTCTTC TTCGTC TTCCTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
* * *
569 TTCTTC CTCTTC TTCTTC CTCTTC TTCTTC TTCTTC CTCTTC TTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
* * *
617 CTCTTC TTCTTC TTCTTC CTCTTC TTCTTC CTCTTC TTCTTC TTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
*
665 TTCTTC TTCCTC TTCTTC TTCTTC TTCTTC TTCTTC TT
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TT
703 AAGGCTAGGC
Statistics
Matches: 323, Mismatches: 41, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
5 9 0.03
6 314 0.97
ACGTcount: A:0.00, C:0.39, G:0.01, T:0.60
Consensus pattern (6 bp):
TTCTTC
Found at i:5199 original size:13 final size:11
Alignment explanation
Indices: 5171--5225 Score: 56
Period size: 13 Copynumber: 4.5 Consensus size: 11
5161 GTTCAGGAAC
*
5171 TGTTTTATCAA
1 TGTTTTATAAA
5182 TGTTTTATTAATA
1 TGTTTTA-TAA-A
5195 TGTTTTATAAA
1 TGTTTTATAAA
5206 TGATTTTAATAAAA
1 TG-TTTT-AT-AAA
5220 TGTTTT
1 TGTTTT
5226 GGGTGCATGA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 9 0.24
13 14 0.37
14 5 0.13
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (11 bp):
TGTTTTATAAA
Found at i:5222 original size:25 final size:24
Alignment explanation
Indices: 5171--5225 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
5161 GTTCAGGAAC
* * *
5171 TGTTTTATCAATGTTTTATTAATA
1 TGTTTTATAAATGTTTTAATAAAA
5195 TGTTTTATAAATGATTTTAATAAAA
1 TGTTTTATAAATG-TTTTAATAAAA
5220 TGTTTT
1 TGTTTT
5226 GGGTGCATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (24 bp):
TGTTTTATAAATGTTTTAATAAAA
Found at i:9240 original size:5 final size:5
Alignment explanation
Indices: 9230--9278 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
9220 TTATTTATTT
*
9230 TTTTC TTTTC -TTT- TTTCC TTTTCC TTTTC TTTTCC TTTT- TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTT-C TTTTC TTTT-C TTTTC TTTTC TTTTC
9279 CAGGCCTGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 9 0.24
5 18 0.49
6 10 0.27
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:9256 original size:19 final size:18
Alignment explanation
Indices: 9230--9277 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
9220 TTATTTATTT
9230 TTTTCTTTTCTTTTTTCC
1 TTTTCTTTTCTTTTTTCC
9248 TTTTCCTTTTC--TTTTCC
1 TTTT-CTTTTCTTTTTTCC
9265 TTTT-TTTTCTTTT
1 TTTTCTTTTCTTTT
9278 CCAGGCCTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 5 0.19
17 12 0.44
18 4 0.15
19 6 0.22
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTCTTTTCTTTTTTCC
Done.