Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012912.1 Corchorus olitorius cultivar O-4 contig12945, 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: 5594
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:680 original size:28 final size:28
Alignment explanation
Indices: 649--723 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 28
639 TTAAGATGTC
*
649 AAAATTACTGTTTTGCCCTTGGTCAG-CT
1 AAAATTACAGTTTTGCCCTTGGT-AGACT
* * *
677 AAAATTACCA-ATTTGCCCCTGGTTGACT
1 AAAATTA-CAGTTTTGCCCTTGGTAGACT
705 -AAATTACAGTTTTGCCCTT
1 AAAATTACAGTTTTGCCCTT
724 AAATGCCGGA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
26 2 0.05
27 15 0.39
28 20 0.53
29 1 0.03
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (28 bp):
AAAATTACAGTTTTGCCCTTGGTAGACT
Found at i:1161 original size:11 final size:13
Alignment explanation
Indices: 1134--1177 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
1124 ATTTTATTTC
1134 TGTTTTATTAAAT
1 TGTTTTATTAAAT
1147 TGTTTTA-TAAA-
1 TGTTTTATTAAAT
1158 TGTTTTAATTAAAT
1 TGTTTT-ATTAAAT
1172 TGTTTT
1 TGTTTT
1178 GGATGCATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.21
12 5 0.18
13 11 0.39
14 6 0.21
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (13 bp):
TGTTTTATTAAAT
Found at i:4643 original size:15 final size:16
Alignment explanation
Indices: 4623--4665 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
4613 TTTCCTTAAT
4623 TTCCTTTTT-TTTTCC
1 TTCCTTTTTCTTTTCC
4638 TTCCTTTTTCTTTT-C
1 TTCCTTTTTCTTTTCC
* *
4653 TTTCTTTTCCTTT
1 TTCCTTTTTCTTT
4666 CTATTTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TTCCTTTTTCTTTTCC
Found at i:4662 original size:21 final size:21
Alignment explanation
Indices: 4638--4699 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
4628 TTTTTTTTCC
*
4638 TTCCTTTTTCTTTTCTTTCTT
1 TTCCTTTTTCTATTCTTTCTT
4659 TTCC--TTTCTATT-TTTCTT
1 TTCCTTTTTCTATTCTTTCTT
* *
4677 TTCTATTTTTCTCTTC-TTCTT
1 TTC-CTTTTTCTATTCTTTCTT
4698 TT
1 TT
4700 TTTCTCCCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
18 9 0.26
19 7 0.21
21 18 0.53
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (21 bp):
TTCCTTTTTCTATTCTTTCTT
Found at i:4679 original size:13 final size:13
Alignment explanation
Indices: 4642--4693 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
4632 TTTTCCTTCC
*
4642 TTTTTCTTTTCTT
1 TTTTTCTTTTCTA
*
4655 TCTTTTCCTTTCTA
1 T-TTTTCTTTTCTA
4669 TTTTTCTTTTCTA
1 TTTTTCTTTTCTA
*
4682 TTTTTCTCTTCT
1 TTTTTCTTTTCT
4694 TCTTTTTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 23 0.68
14 11 0.32
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTTCTTTTCTA
Found at i:4699 original size:27 final size:27
Alignment explanation
Indices: 4632--4700 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
4622 TTTCCTTTTT
*
4632 TTTTCC-TTC-CTTTTTCTTTTCTTTC
1 TTTTCCTTTCTCTTTTTCTTTTCTATC
*
4657 TTTTCCTTTCTATTTTTCTTTTCTAT-
1 TTTTCCTTTCTCTTTTTCTTTTCTATC
4683 TTTT-CTCTTCTTCTTTTT
1 TTTTCCT-TTC-TCTTTTT
4701 TTCTCCCTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
25 8 0.22
26 10 0.27
27 19 0.51
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (27 bp):
TTTTCCTTTCTCTTTTTCTTTTCTATC
Found at i:4701 original size:16 final size:15
Alignment explanation
Indices: 4642--4705 Score: 57
Period size: 14 Copynumber: 4.5 Consensus size: 15
4632 TTTTCCTTCC
4642 TTTT-TCTTTTCT-T
1 TTTTCTCTTTTCTAT
*
4655 TCTTT-TCCTTTCTA-
1 T-TTTCTCTTTTCTAT
4669 TTTT-TCTTTTCTAT
1 TTTTCTCTTTTCTAT
*
4683 TTTTCTCTTCTTCTTT
1 TTTTCTCTT-TTCTAT
4699 TTTTCTC
1 TTTTCTC
4706 CCTTTTTGGG
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
13 12 0.28
14 15 0.35
15 4 0.09
16 12 0.28
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTCTCTTTTCTAT
Done.