Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022555.1 Corchorus olitorius cultivar O-4 contig22588, 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: 10761
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Found at i:281 original size:39 final size:40
Alignment explanation
Indices: 227--307 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
217 AATACTAAGA
* *
227 ATTTAATTAATGTAAGTATTTAAGTTATTATA-GTATTAC
1 ATTTAACTAATGTAAGTATTTAAGTTATTATATATATTAC
*
266 ATTTAACTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAACTAATGTAAGTATTTAAGTTATTATATATATTAC
306 AT
1 AT
308 AGGAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (40 bp):
ATTTAACTAATGTAAGTATTTAAGTTATTATATATATTAC
Found at i:1181 original size:4 final size:4
Alignment explanation
Indices: 1172--1214 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
1162 ATTCCTTTAA
*
1172 ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1215 TGCACTTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:1710 original size:2 final size:2
Alignment explanation
Indices: 1703--1767 Score: 78
Period size: 2 Copynumber: 33.0 Consensus size: 2
1693 GTTCCGCCCC
* * ** *
1703 TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA T- TC GG TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1744 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
1768 AATACACGTA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3703 original size:2 final size:2
Alignment explanation
Indices: 3696--3729 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3686 ACAGAAAGAG
*
3696 TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3730 GAGAGAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4701 original size:25 final size:25
Alignment explanation
Indices: 4658--4708 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 25
4648 TGATAAATTT
4658 TTATATATAGTTATGATTTCTTAAAAA
1 TTATATATAGTTATGA-TT-TTAAAAA
*
4685 TTATATGTA-TTAT-ATTTTAAAAA
1 TTATATATAGTTATGATTTTAAAAA
4708 T
1 T
4709 AATGTGGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 8 0.35
24 2 0.09
25 1 0.04
26 4 0.17
27 8 0.35
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (25 bp):
TTATATATAGTTATGATTTTAAAAA
Found at i:10670 original size:30 final size:30
Alignment explanation
Indices: 10634--10755 Score: 165
Period size: 30 Copynumber: 4.0 Consensus size: 30
10624 CAAATTTTTT
10634 TCTTACAAATGACACCAGAAGTTGTCATGG
1 TCTTACAAATGACACCAGAAGTTGTCATGG
*
10664 TCTTACAATTTGACACCAGTAAGATTTGTCATGG
1 TCTTACAA-ATGACACCAG-AAG--TTGTCATGG
*
10698 TCTTAC-AATGACACCAGAAGTTGTCATGC
1 TCTTACAAATGACACCAGAAGTTGTCATGG
* *
10727 TCTTGCAATTGACACCAGAAGTTGTCATG
1 TCTTACAAATGACACCAGAAGTTGTCATG
10756 ATTTGC
Statistics
Matches: 82, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
29 13 0.16
30 29 0.35
31 12 0.15
32 12 0.15
33 1 0.01
34 15 0.18
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (30 bp):
TCTTACAAATGACACCAGAAGTTGTCATGG
Found at i:10713 original size:63 final size:60
Alignment explanation
Indices: 10634--10755 Score: 183
Period size: 63 Copynumber: 2.0 Consensus size: 60
10624 CAAATTTTTT
*
10634 TCTTACAAATGACACCAGAAGTTGTCATGGTCTTACAATTTGACACCAGTAAGATTTGTCATGG
1 TCTTACAAATGACACCAGAAGTTGTCATGCTCTTACAA-TTGACACCAG-AAG--TTGTCATGG
*
10698 TCTTAC-AATGACACCAGAAGTTGTCATGCTCTTGCAATTGACACCAGAAGTTGTCATG
1 TCTTACAAATGACACCAGAAGTTGTCATGCTCTTACAATTGACACCAGAAGTTGTCATG
10756 ATTTGC
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
59 8 0.14
61 3 0.05
62 10 0.18
63 29 0.52
64 6 0.11
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (60 bp):
TCTTACAAATGACACCAGAAGTTGTCATGCTCTTACAATTGACACCAGAAGTTGTCATGG
Done.