Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009680.1 Corchorus olitorius cultivar O-4 contig09712, 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: 2647
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:455 original size:7 final size:7
Alignment explanation
Indices: 436--503 Score: 88
Period size: 7 Copynumber: 9.9 Consensus size: 7
426 ATTTAAGGTC
436 AGGGTTT
1 AGGGTTT
443 AGGGGTTT
1 A-GGGTTT
451 AGGG-TT
1 AGGGTTT
457 AGGGTTT
1 AGGGTTT
464 AGGGTTTT
1 AGGG-TTT
*
472 AGTG-TT
1 AGGGTTT
478 AGGGTTT
1 AGGGTTT
485 AGGG-TT
1 AGGGTTT
491 AGGGTTT
1 AGGGTTT
498 AGGGTT
1 AGGGTT
504 ATGGTTTATT
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
6 17 0.31
7 24 0.44
8 13 0.24
ACGTcount: A:0.15, C:0.00, G:0.44, T:0.41
Consensus pattern (7 bp):
AGGGTTT
Found at i:460 original size:6 final size:6
Alignment explanation
Indices: 449--509 Score: 59
Period size: 6 Copynumber: 9.3 Consensus size: 6
439 GTTTAGGGGT
*
449 TTAGGG TTAGGG TTTAGGG TTTTAGTG TTAGGG TTTAGGG TTAGGG TTTAGGG
1 TTAGGG TTAGGG -TTAGGG --TTAGGG TTAGGG -TTAGGG TTAGGG -TTAGGG
*
502 TTATGG TT
1 TTAGGG TT
510 TATTTCAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
6 24 0.50
7 18 0.38
8 6 0.12
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.44
Consensus pattern (6 bp):
TTAGGG
Found at i:460 original size:21 final size:21
Alignment explanation
Indices: 427--503 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
417 GTGGCTGGGA
* *
427 TTTAAGGTCAGGGTTTAGGGG
1 TTTAGGGTTAGGGTTTAGGGG
*
448 TTTAGGGTTAGGGTTTAGGGT
1 TTTAGGGTTAGGGTTTAGGGG
*
469 TTTAGTGTTAGGGTTTA-GGG
1 TTTAGGGTTAGGGTTTAGGGG
489 -TTAGGGTTTAGGGTT
1 TTTAGGG-TTAGGGTT
504 ATGGTTTATT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
19 5 0.10
20 10 0.20
21 34 0.69
ACGTcount: A:0.16, C:0.01, G:0.42, T:0.42
Consensus pattern (21 bp):
TTTAGGGTTAGGGTTTAGGGG
Found at i:461 original size:13 final size:13
Alignment explanation
Indices: 436--511 Score: 91
Period size: 13 Copynumber: 5.6 Consensus size: 13
426 ATTTAAGGTC
436 AGGGTTTAGGGGTTT
1 AGGGTTTA-GGG-TT
451 AGGG-TTAGGGTTT
1 AGGGTTTAGGG-TT
*
464 AGGGTTTTAGTGTT
1 AGGG-TTTAGGGTT
478 AGGGTTTAGGGTT
1 AGGGTTTAGGGTT
491 AGGGTTTAGGGTT
1 AGGGTTTAGGGTT
*
504 ATGGTTTA
1 AGGGTTTA
512 TTTCAAATTA
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
13 38 0.68
14 9 0.16
15 9 0.16
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (13 bp):
AGGGTTTAGGGTT
Found at i:1671 original size:13 final size:13
Alignment explanation
Indices: 1625--1736 Score: 99
Period size: 13 Copynumber: 8.7 Consensus size: 13
1615 GGGTTGGGAT
1625 TTAGGGTTTTAGGG
1 TTAGGG-TTTAGGG
**
1639 TTTATAGTTTAGGG
1 -TTAGGGTTTAGGG
*
1653 TTAGGGTTTAAGG
1 TTAGGGTTTAGGG
*
1666 TCAGGGTTTAGGG
1 TTAGGGTTTAGGG
1679 TTAGGGTTTA---
1 TTAGGGTTTAGGG
* *
1689 -T-GGTTTTAGTG
1 TTAGGGTTTAGGG
1700 TTAGGGTTTAGGG
1 TTAGGGTTTAGGG
1713 TTTTAGGGTTTAGGG
1 --TTAGGGTTTAGGG
1728 TTAGGGTTT
1 TTAGGGTTT
1737 TGGGATATGG
Statistics
Matches: 79, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
8 6 0.08
9 1 0.01
12 1 0.01
13 47 0.59
14 7 0.09
15 17 0.22
ACGTcount: A:0.16, C:0.01, G:0.38, T:0.45
Consensus pattern (13 bp):
TTAGGGTTTAGGG
Found at i:1680 original size:7 final size:7
Alignment explanation
Indices: 1624--1736 Score: 110
Period size: 7 Copynumber: 16.4 Consensus size: 7
1614 AGGGTTGGGA
1624 TTTAGGG
1 TTTAGGG
1631 TTTTAGGG
1 -TTTAGGG
**
1639 TTTATAG
1 TTTAGGG
1646 TTTAGGG
1 TTTAGGG
1653 -TTAGGG
1 TTTAGGG
*
1659 TTTAAGG
1 TTTAGGG
*
1666 -TCAGGG
1 TTTAGGG
1672 TTTAGGG
1 TTTAGGG
1679 -TTAGGG
1 TTTAGGG
*
1685 TTTATGGT
1 TTTA-GGG
*
1693 TTTAGTG
1 TTTAGGG
1700 -TTAGGG
1 TTTAGGG
1706 TTTAGGG
1 TTTAGGG
1713 TTTTAGGG
1 -TTTAGGG
1721 TTTAGGG
1 TTTAGGG
1728 -TTAGGG
1 TTTAGGG
1734 TTT
1 TTT
1737 TGGGATATGG
Statistics
Matches: 86, Mismatches: 12, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
6 27 0.31
7 39 0.45
8 20 0.23
ACGTcount: A:0.16, C:0.01, G:0.38, T:0.45
Consensus pattern (7 bp):
TTTAGGG
Done.