Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006827.1 Corchorus capsularis cultivar CVL-1 contig06848, 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: 20565
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:1594 original size:27 final size:28
Alignment explanation
Indices: 1564--1618 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
1554 AAAAATATGC
1564 AAACATAAAC-AAAAATGCAATTTTTTT
1 AAACATAAACAAAAAATGCAATTTTTTT
1591 AAACATAAACAAAAAATGCAATTTTTTT
1 AAACATAAACAAAAAATGCAATTTTTTT
1619 TTACCCTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 10 0.37
28 17 0.63
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.33
Consensus pattern (28 bp):
AAACATAAACAAAAAATGCAATTTTTTT
Found at i:7546 original size:16 final size:16
Alignment explanation
Indices: 7525--7556 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
7515 TTGCATTGGT
7525 TTGCTTTAAATGATTA
1 TTGCTTTAAATGATTA
*
7541 TTGCTTTAATTGATTA
1 TTGCTTTAAATGATTA
7557 CCTATTCCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.06, G:0.12, T:0.53
Consensus pattern (16 bp):
TTGCTTTAAATGATTA
Found at i:10453 original size:21 final size:20
Alignment explanation
Indices: 10429--10476 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
10419 TAGATTTAGA
* *
10429 TTTAATTTACTTTGCTTAGTT
1 TTTAATTTA-ATTGCTTACTT
* *
10450 TTTAGTTTAATTGCTTTCTT
1 TTTAATTTAATTGCTTACTT
10470 TTTAATT
1 TTTAATT
10477 GATAATTTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.65
Consensus pattern (20 bp):
TTTAATTTAATTGCTTACTT
Found at i:12121 original size:22 final size:22
Alignment explanation
Indices: 12090--12156 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
12080 ACTTTTATTA
12090 ATTTCCAAAAGTCTTCTCTTGG
1 ATTTCCAAAAGTCTTCTCTTGG
* ** * *
12112 ATTTCTAAAAAACTTTTACTT-T
1 ATTTCCAAAAGTCTTCT-CTTGG
*
12134 CTTTCCAAAAGTCTTCTCTTGG
1 ATTTCCAAAAGTCTTCTCTTGG
12156 A
1 A
12157 ATTACTAAAA
Statistics
Matches: 31, Mismatches: 12, Indels: 4
0.66 0.26 0.09
Matches are distributed among these distances:
21 3 0.10
22 25 0.81
23 3 0.10
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.43
Consensus pattern (22 bp):
ATTTCCAAAAGTCTTCTCTTGG
Found at i:12142 original size:44 final size:43
Alignment explanation
Indices: 12091--12198 Score: 145
Period size: 39 Copynumber: 2.6 Consensus size: 43
12081 CTTTTATTAA
*
12091 TTTCCAAAAGTCTTCTCTTGG-ATTTCTAAAAAACTTTTACTTTC
1 TTTCCAAAAGTCTTCTCTTGGAATTACT--AAAACTTTTACTTTC
12135 TTTCCAAAAGTCTTCTCTTGGAATTACTAAAACTTTTA----C
1 TTTCCAAAAGTCTTCTCTTGGAATTACTAAAACTTTTACTTTC
*
12174 TTTCCAAAAGTCTTCTTTTGGAATT
1 TTTCCAAAAGTCTTCTCTTGGAATT
12199 GCTTAAATAG
Statistics
Matches: 61, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
39 25 0.41
43 10 0.16
44 21 0.34
45 5 0.08
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.44
Consensus pattern (43 bp):
TTTCCAAAAGTCTTCTCTTGGAATTACTAAAACTTTTACTTTC
Found at i:12357 original size:18 final size:19
Alignment explanation
Indices: 12336--12380 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
12326 CATCTTTTAA
*
12336 TTTTTCTATTTTTTTC-AT
1 TTTTTCTATTTTCTTCAAT
**
12354 TTTTTGGATTTTCTTCAAT
1 TTTTTCTATTTTCTTCAAT
12373 TTTTTCTA
1 TTTTTCTA
12381 ACTTTTACTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.13, C:0.11, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTTTCTATTTTCTTCAAT
Found at i:12823 original size:24 final size:24
Alignment explanation
Indices: 12786--12848 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
12776 GCGAAGTGTA
* *
12786 AAAGACCACATACAAACAAAAGA-T
1 AAAGCCCAAATACAAA-AAAAGACT
* * *
12810 AAAGTCCAATTACATAAAAAGACT
1 AAAGCCCAAATACAAAAAAAGACT
12834 AAAGCCCAAATACAA
1 AAAGCCCAAATACAA
12849 TTGTCAAGCG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
23 6 0.19
24 25 0.81
ACGTcount: A:0.59, C:0.21, G:0.08, T:0.13
Consensus pattern (24 bp):
AAAGCCCAAATACAAAAAAAGACT
Found at i:16682 original size:17 final size:17
Alignment explanation
Indices: 16656--16705 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
16646 TCCCCCTCAT
16656 GGTACCAGGTAGCATGA
1 GGTACCAGGTAGCATGA
*
16673 GGTACTAGGTAGCATGA
1 GGTACCAGGTAGCATGA
16690 GGTACCAGGTAGCATG
1 GGTACCAGGTAGCATG
16706 TTGGATATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.28, C:0.16, G:0.36, T:0.20
Consensus pattern (17 bp):
GGTACCAGGTAGCATGA
Found at i:18991 original size:19 final size:18
Alignment explanation
Indices: 18967--19002 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
18957 TGAAGATTTC
18967 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
18986 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
19003 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.