Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006002.1 Corchorus capsularis cultivar CVL-1 contig06020, 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: 14408
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Found at i:4656 original size:23 final size:22
Alignment explanation
Indices: 4630--4679 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
4620 GGGCCTAATA
4630 TTTGCAAAACCATACA-ATGAAAT
1 TTTG-AAAACC-TACATATGAAAT
* *
4653 TTTGATAACCTCCATATGAAAT
1 TTTGAAAACCTACATATGAAAT
4675 TTTGA
1 TTTGA
4680 TGACATCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 3 0.12
22 17 0.71
23 4 0.17
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (22 bp):
TTTGAAAACCTACATATGAAAT
Found at i:4662 original size:22 final size:22
Alignment explanation
Indices: 4637--4704 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
4627 ATATTTGCAA
*
4637 AACCATACAATGAAATTTTGAT
1 AACCATCCAATGAAATTTTGAT
4659 AACC-TCCATATGAAATTTTGAT
1 AACCATCCA-ATGAAATTTTGAT
* *
4681 GA-CATCCTTATGAAATTTTGAT
1 AACCATCC-AATGAAATTTTGAT
4703 AA
1 AA
4705 TCTTATTATG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 4 0.10
22 35 0.90
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (22 bp):
AACCATCCAATGAAATTTTGAT
Found at i:4713 original size:22 final size:21
Alignment explanation
Indices: 4646--4726 Score: 76
Period size: 22 Copynumber: 3.7 Consensus size: 21
4636 AAACCATACA
*
4646 ATGAAATTTTGATAACCTCCA-T
1 ATGAAATTTTGATAA--TCTATT
*
4668 ATGAAATTTTGATGACATC-CTT
1 ATGAAATTTTGAT-A-ATCTATT
4690 ATGAAATTTTGATAATCTTATT
1 ATGAAATTTTGATAATC-TATT
*
4712 ATGGAATTTTGATAA
1 ATGAAATTTTGATAA
4727 ACCGAACAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
20 3 0.06
21 1 0.02
22 45 0.88
23 1 0.02
24 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGAAATTTTGATAATCTATT
Found at i:6554 original size:5 final size:5
Alignment explanation
Indices: 6544--6570 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
6534 TATATAGTAG
6544 TAAGA TAAGA TAAGA TAAGA TAAGA TA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TA
6571 TACTAACCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.19, T:0.22
Consensus pattern (5 bp):
TAAGA
Found at i:11452 original size:12 final size:12
Alignment explanation
Indices: 11435--11465 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
11425 CCTGGCAATC
*
11435 CGTGTTTTGTGT
1 CGTGTTTCGTGT
11447 CGTGTTTCGTGT
1 CGTGTTTCGTGT
11459 CGTGTTT
1 CGTGTTT
11466 ACATAGGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.13, G:0.32, T:0.55
Consensus pattern (12 bp):
CGTGTTTCGTGT
Found at i:11696 original size:12 final size:12
Alignment explanation
Indices: 11679--11704 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11669 CTAAACTATA
11679 TATATATATAAT
1 TATATATATAAT
11691 TATATATATAAT
1 TATATATATAAT
11703 TA
1 TA
11705 AAGATAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TATATATATAAT
Found at i:11941 original size:42 final size:43
Alignment explanation
Indices: 11871--11953 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 43
11861 CTTAAACGTG
11871 TTAATCGTGTCTTGACACGATTACGACACGAAACACGATAATC
1 TTAATCGTGTCTTGACACGATTACGACACGAAACACGATAATC
*
11914 TTAATCGTGTC-TGACACGATT-CAGACACGAGACACGATAA
1 TTAATCGTGTCTTGACACGATTAC-GACACGAAACACGATAA
11954 GCCAAACACG
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
41 1 0.03
42 26 0.68
43 11 0.29
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (43 bp):
TTAATCGTGTCTTGACACGATTACGACACGAAACACGATAATC
Found at i:13360 original size:23 final size:23
Alignment explanation
Indices: 13330--13377 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
13320 TTACTTCCAC
13330 GTGCGTTGCACATGACCTAATCT
1 GTGCGTTGCACATGACCTAATCT
13353 GTGCGTTGCACATGACCTAATCT
1 GTGCGTTGCACATGACCTAATCT
13376 GT
1 GT
13378 TTTAAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (23 bp):
GTGCGTTGCACATGACCTAATCT
Done.