Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024471.1 Corchorus olitorius cultivar O-4 contig24504, 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: 21167
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:3548 original size:32 final size:33
Alignment explanation
Indices: 3506--3568 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
3496 AGCTCAAATC
* **
3506 AAATTAAAAAACACAGATGGTTCTTCTCATAAA
1 AAATTAAAAAACACAGAAGAATCTTCTCATAAA
3539 AAATT-AAAAACACAGAAGAATCTTCTCATA
1 AAATTAAAAAACACAGAAGAATCTTCTCATA
3569 GTTAAATGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 22 0.81
33 5 0.19
ACGTcount: A:0.51, C:0.16, G:0.08, T:0.25
Consensus pattern (33 bp):
AAATTAAAAAACACAGAAGAATCTTCTCATAAA
Found at i:4894 original size:22 final size:23
Alignment explanation
Indices: 4880--4926 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
4870 AATTAAAATT
4880 AACTAAAAAAGCAA-TAAAAGAA
1 AACTAAAAAAGCAATTAAAAGAA
* *
4902 AATTAAAAAAGCAATTGATAAGAA
1 AACTAAAAAAGCAATT-AAAAGAA
4926 A
1 A
4927 GTAGTGAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.62
23 1 0.05
24 7 0.33
ACGTcount: A:0.68, C:0.06, G:0.11, T:0.15
Consensus pattern (23 bp):
AACTAAAAAAGCAATTAAAAGAA
Found at i:14486 original size:22 final size:20
Alignment explanation
Indices: 14461--14509 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
14451 GAAGTTCGTG
14461 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGAC-T-TTGAAGATAA
*
14483 TTTGAAGA-TTTGAAGATCA
1 TTTGAAGACTTTGAAGATAA
14502 -TTGAAGAC
1 TTTGAAGAC
14510 ACGAGAAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.28
19 9 0.36
20 1 0.04
22 8 0.32
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (20 bp):
TTTGAAGACTTTGAAGATAA
Found at i:16023 original size:6 final size:6
Alignment explanation
Indices: 16012--16037 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
16002 TTGTGTATTA
16012 TTTTCT TTTTCT TTTTCT TTTTCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TT
16038 GCTATATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:18290 original size:32 final size:31
Alignment explanation
Indices: 18217--18291 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
18207 CGGCGTCTAC
* * *
18217 AGACGCCGCCATTTAGTGGCGTCTGACATAG
1 AGACGCCGCCATTTAGTGGCGTCTGAAAGAA
* *
18248 TGACGCCGCCATTTAGTGGCGTTTCGAAAGAA
1 AGACGCCGCCATTTAGTGGCGTCT-GAAAGAA
18280 AGACGCCGCCAT
1 AGACGCCGCCAT
18292 ATTAATATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 22 0.59
32 15 0.41
ACGTcount: A:0.24, C:0.27, G:0.28, T:0.21
Consensus pattern (31 bp):
AGACGCCGCCATTTAGTGGCGTCTGAAAGAA
Found at i:18428 original size:31 final size:30
Alignment explanation
Indices: 18392--18480 Score: 130
Period size: 27 Copynumber: 3.0 Consensus size: 30
18382 CCTATAATAT
* *
18392 ATAGCGGCGTTTAGACATCAGACGCCGCTA
1 ATAGCGGCGTTTAAACATAAGACGCCGCTA
18422 AGTAGCGGCGTTTAAACATAAGACGCCGC--
1 A-TAGCGGCGTTTAAACATAAGACGCCGCTA
18451 -TAGCGGCGTTTAAACATAAGACGCCGCTA
1 ATAGCGGCGTTTAAACATAAGACGCCGCTA
18480 A
1 A
18481 ATGAAACGCC
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
27 27 0.51
30 1 0.02
31 25 0.47
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (30 bp):
ATAGCGGCGTTTAAACATAAGACGCCGCTA
Done.