Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018404.1 Corchorus olitorius cultivar O-4 contig18437, 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: 15087
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Found at i:2624 original size:29 final size:28
Alignment explanation
Indices: 2592--2661 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
2582 GGTTAAATGT
* *
2592 TCAAATAAGGGTCTAATAT-TTAAAAATAC
1 TCAAATTAGGGTCT-AT-TGTTAAAAAAAC
* *
2621 TCAAATTAGGGCCTATTGTTAAAAAAAT
1 TCAAATTAGGGTCTATTGTTAAAAAAAC
2649 TCAAATTAGGGTC
1 TCAAATTAGGGTC
2662 CAATGTTGCA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 1 0.03
28 22 0.63
29 12 0.34
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (28 bp):
TCAAATTAGGGTCTATTGTTAAAAAAAC
Found at i:2674 original size:28 final size:28
Alignment explanation
Indices: 2591--2668 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 28
2581 TGGTTAAATG
* * * *
2591 TTCAAATAAGGGTCTAATATTTAAAAATA
1 TTCAAATTAGGGCCTAAT-GTTAAAAAAA
* *
2620 CTCAAATTAGGGCCTATTGTTAAAAAAA
1 TTCAAATTAGGGCCTAATGTTAAAAAAA
2648 TTCAAATTAGGGTCC-AATGTT
1 TTCAAATTAGGG-CCTAATGTT
2669 GCAAAATCGG
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
28 24 0.60
29 16 0.40
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (28 bp):
TTCAAATTAGGGCCTAATGTTAAAAAAA
Found at i:3454 original size:2 final size:2
Alignment explanation
Indices: 3447--3472 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3437 GGGGACATTT
3447 TA 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 TA
3473 AAAGAAAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3904 original size:11 final size:11
Alignment explanation
Indices: 3888--3912 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3878 AAACCACGAA
3888 GTGGGGAGAGT
1 GTGGGGAGAGT
3899 GTGGGGAGAGT
1 GTGGGGAGAGT
3910 GTG
1 GTG
3913 AGAAAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.64, T:0.20
Consensus pattern (11 bp):
GTGGGGAGAGT
Found at i:11126 original size:12 final size:13
Alignment explanation
Indices: 11109--11139 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
11099 TTACTTTGTG
11109 AAGGTGCAA-ATC
1 AAGGTGCAATATC
11121 AAGGTGCAATATC
1 AAGGTGCAATATC
11134 AAGGTG
1 AAGGTG
11140 GGCTTGCTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.39, C:0.13, G:0.29, T:0.19
Consensus pattern (13 bp):
AAGGTGCAATATC
Found at i:11527 original size:25 final size:25
Alignment explanation
Indices: 11499--11571 Score: 119
Period size: 25 Copynumber: 2.9 Consensus size: 25
11489 TGAACGACGT
*
11499 AAAATATTACTTGAAAAGTATGCGC
1 AAAATATTACTTGAAAAGGATGCGC
* *
11524 AAAATATTGCTTAAAAAGGATGCGC
1 AAAATATTACTTGAAAAGGATGCGC
11549 AAAATATTACTTGAAAAGGATGC
1 AAAATATTACTTGAAAAGGATGC
11572 TTCCAAAACC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (25 bp):
AAAATATTACTTGAAAAGGATGCGC
Found at i:13694 original size:22 final size:21
Alignment explanation
Indices: 13669--13722 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
13659 GAAGTTCGTG
13669 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
13691 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
13710 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
13723 TCAAGAAGCG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:14666 original size:13 final size:13
Alignment explanation
Indices: 14648--14672 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14638 GAAACAGGGT
14648 ATTAAAATTAACA
1 ATTAAAATTAACA
14661 ATTAAAATTAAC
1 ATTAAAATTAAC
14673 TAAGAAAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAAAATTAACA
Found at i:14683 original size:22 final size:22
Alignment explanation
Indices: 14657--14707 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
14647 TATTAAAATT
*
14657 AACAATTAAAATTAACT-AAGAA
1 AACAATTAAAA-AAACTAAAGAA
* *
14679 AACAATCAAAAAAATTAAAGAA
1 AACAATTAAAAAAACTAAAGAA
14701 AACAATT
1 AACAATT
14708 GATAAGATAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.67, C:0.10, G:0.04, T:0.20
Consensus pattern (22 bp):
AACAATTAAAAAAACTAAAGAA
Done.