Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022816.1 Corchorus olitorius cultivar O-4 contig22849, 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: 20292
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:8057 original size:16 final size:15
Alignment explanation
Indices: 8021--8062 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
8011 GCAGAGGGTT
8021 AAGAAGAACAATTAAA
1 AAGAA-AACAATTAAA
8037 AAGAAAACAATTAAA
1 AAGAAAACAATTAAA
8052 ATAGAAAACAA
1 A-AGAAAACAA
8063 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.71, C:0.07, G:0.10, T:0.12
Consensus pattern (15 bp):
AAGAAAACAATTAAA
Found at i:11589 original size:26 final size:27
Alignment explanation
Indices: 11524--11594 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 27
11514 AAAAATCCAG
* *
11524 GGGCATTTTGGTCATTTTTCACATTTA
1 GGGCATTTTGGTCATTTTTCACACTAA
*
11551 GTGGCATTATGGTCATTTTT-ACACTAA
1 G-GGCATTTTGGTCATTTTTCACACTAA
11578 GGGCATTTTGGTCATTT
1 GGGCATTTTGGTCATTT
11595 GCATATTCAG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
26 15 0.38
27 7 0.18
28 17 0.44
ACGTcount: A:0.20, C:0.14, G:0.21, T:0.45
Consensus pattern (27 bp):
GGGCATTTTGGTCATTTTTCACACTAA
Found at i:11790 original size:25 final size:25
Alignment explanation
Indices: 11761--11808 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
11751 GTATTTTGCG
*
11761 TTCATGTAGCTCAAAACTAATTTCA
1 TTCATGTACCTCAAAACTAATTTCA
*
11786 TTCATGTACCTCAAATCTAATTT
1 TTCATGTACCTCAAAACTAATTT
11809 GACATTGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (25 bp):
TTCATGTACCTCAAAACTAATTTCA
Found at i:13418 original size:16 final size:16
Alignment explanation
Indices: 13397--13430 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
13387 AACACTTAAA
13397 TTTCTAT-TTTTAATTT
1 TTTCTATCTTTT-ATTT
13413 TTTCTATCTTTTATTT
1 TTTCTATCTTTTATTT
13429 TT
1 TT
13431 ATTTCGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTCTATCTTTTATTT
Found at i:15493 original size:5 final size:5
Alignment explanation
Indices: 15483--15523 Score: 66
Period size: 5 Copynumber: 8.4 Consensus size: 5
15473 AATAAAATGG
*
15483 TTGTT TTGTT TTGTT TTGGT TTGTT TTGTT TTG-T TTGTT TT
1 TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TT
15524 AATGTTTTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (5 bp):
TTGTT
Found at i:19688 original size:8 final size:7
Alignment explanation
Indices: 19668--19720 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
19658 TCCCAATAAT
*
19668 AAAAAAT
1 AAAAAAG
19675 AAAAAAG
1 AAAAAAG
19682 AAGAAAAG
1 AA-AAAAG
19690 AAAAAATG
1 AAAAAA-G
19698 -AAAAAG
1 AAAAAAG
*
19704 AAAAATG
1 AAAAAAG
19711 AAAAAA-
1 AAAAAAG
19717 AAAA
1 AAAA
19721 CACTTGGAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
6 5 0.12
7 27 0.68
8 8 0.20
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (7 bp):
AAAAAAG
Found at i:19696 original size:22 final size:21
Alignment explanation
Indices: 19668--19720 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
19658 TCCCAATAAT
19668 AAAAAATAAAAAAGAAGAAAAG
1 AAAAAATAAAAAAGAA-AAAAG
* *
19690 AAAAAATGAAAAAGAAAAATG
1 AAAAAATAAAAAAGAAAAAAG
19711 AAAAAA-AAAA
1 AAAAAATAAAA
19721 CACTTGGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 3 0.11
21 10 0.36
22 15 0.54
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (21 bp):
AAAAAATAAAAAAGAAAAAAG
Found at i:19700 original size:13 final size:12
Alignment explanation
Indices: 19675--19720 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
19665 AATAAAAAAT
*
19675 AAAAAAGAA-GA
1 AAAAAAAAATGA
19686 AAAGAAAAAATGA
1 AAA-AAAAAATGA
19699 AAAAGAAAAATGA
1 AAAA-AAAAATGA
19712 AAAAAAAAA
1 AAAAAAAAA
19721 CACTTGGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
11 3 0.10
12 11 0.35
13 17 0.55
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (12 bp):
AAAAAAAAATGA
Found at i:20108 original size:16 final size:16
Alignment explanation
Indices: 20084--20132 Score: 80
Period size: 16 Copynumber: 3.0 Consensus size: 16
20074 CCACTCCATC
20084 AAGAAATTCAAAAAAA
1 AAGAAATTCAAAAAAA
*
20100 AAGATATTCAAAAAAA
1 AAGAAATTCAAAAAAA
20116 AGAGAAATTCAAAAAAA
1 A-AGAAATTCAAAAAAA
20133 TCAAATCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 16 0.53
17 14 0.47
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.14
Consensus pattern (16 bp):
AAGAAATTCAAAAAAA
Found at i:20115 original size:17 final size:17
Alignment explanation
Indices: 20084--20132 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
20074 CCACTCCATC
20084 AAGAAATTC-AAAAAAA
1 AAGAAATTCAAAAAAAA
*
20100 AAGATATTCAAAAAAAA
1 AAGAAATTCAAAAAAAA
*
20117 GAGAAATTCAAAAAAA
1 AAGAAATTCAAAAAAA
20133 TCAAATCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 8 0.28
17 21 0.72
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.14
Consensus pattern (17 bp):
AAGAAATTCAAAAAAAA
Done.