Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011730.1 Corchorus capsularis cultivar CVL-1 contig11751, 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: 45768
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Found at i:13682 original size:18 final size:18
Alignment explanation
Indices: 13661--13695 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
13651 TTGGGGTTAA
*
13661 TGAGGTTGTTGATGTTTC
1 TGAGGTTGTTAATGTTTC
13679 TGAGGTTGTTAATGTTT
1 TGAGGTTGTTAATGTTT
13696 GAACCAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.03, G:0.31, T:0.51
Consensus pattern (18 bp):
TGAGGTTGTTAATGTTTC
Found at i:21559 original size:105 final size:105
Alignment explanation
Indices: 21423--21752 Score: 380
Period size: 105 Copynumber: 3.1 Consensus size: 105
21413 ATAAGGCATG
21423 AATTAGAGAATTATAAGTGACAACATTAGGCTTTATGCCTCTTTGAGTCATTAAATTGAAGAGAG
1 AATTAGAGAATTATAAGTGACAACATTAGGCTTTATGCCTCTTTGAGTCATTAAATTGAAGAGAG
21488 AAGTGGCTTCTTGGATCTTCCCATCCTTGCAGAGAGAGTC
66 AAGTGGCTTCTTGGATCTTCCCATCCTTGCAGAGAGAGTC
* * * ****
21528 AATTAGGGAATTATAAGTGACAACATCAGGCTTTATGCCTCTTTGAGTCATTGAATTTTCTATGT
1 AATTAGAGAATTATAAGTGACAACATTAGGCTTTATGCCTCTTTGAGTCATTAAATTGAAGA-G-
*** * * *** ** * *
21593 ACTTTGTTGCCCGTCTCCAATC--CCCAGACTTGCATA-AG-GCATG
64 A-GAAG-TG-GCTTCTTGGATCTTCCCATCCTTGCAGAGAGAG--TC
*
21636 AATTAGAGAAGTATAAGTGACAACATTAGGCTTTATGCCTCTTTGAGTCATTAAATTGAAGAGAG
1 AATTAGAGAATTATAAGTGACAACATTAGGCTTTATGCCTCTTTGAGTCATTAAATTGAAGAGAG
21701 AAGTGGCTTCTTGGATCTTCCCATCCTTGCAGAGAGAGTC
66 AAGTGGCTTCTTGGATCTTCCCATCCTTGCAGAGAGAGTC
*
21741 AATTAAAGAATT
1 AATTAGAGAATT
21753 GAAAGTGTAT
Statistics
Matches: 173, Mismatches: 41, Indels: 22
0.73 0.17 0.09
Matches are distributed among these distances:
103 7 0.04
104 2 0.01
105 78 0.45
106 5 0.03
107 5 0.03
108 67 0.39
109 2 0.01
110 7 0.04
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (105 bp):
AATTAGAGAATTATAAGTGACAACATTAGGCTTTATGCCTCTTTGAGTCATTAAATTGAAGAGAG
AAGTGGCTTCTTGGATCTTCCCATCCTTGCAGAGAGAGTC
Found at i:21659 original size:108 final size:105
Alignment explanation
Indices: 21382--21699 Score: 365
Period size: 105 Copynumber: 3.0 Consensus size: 105
21372 TTCCAGGTAG
21382 TTTGTTGCCCGTCTCCAATCCCCAGACTTGCATAAGGCATGAATTAGAGAATTATAAGTGACAAC
1 TTTGTTGCCCGTCTCCAATCCCCAGACTTGCATAAGGCATGAATTAGAGAATTATAAGTGACAAC
21447 ATTAGGCTTTATGCCTCTTTGAGTCATTAAATTGAAGAGA
66 ATTAGGCTTTATGCCTCTTTGAGTCATTAAATTGAAGAGA
*** * * *** ** * * *
21487 GAAG-TG-GCTTCTTGGATCTTCCCATCCTTGCA-GAGAG-AGTCAATTAGGGAATTATAAGTGA
1 TTTGTTGCCCGTCTCCAATC--CCCAGACTTGCATAAG-GCA-TGAATTAGAGAATTATAAGTGA
* * ****
21548 CAACATCAGGCTTTATGCCTCTTTGAGTCATTGAATTTTCTATGTA
62 CAACATTAGGCTTTATGCCTCTTTGAGTCATTAAATTGAAGA-G-A
*
21594 CTTTGTTGCCCGTCTCCAATCCCCAGACTTGCATAAGGCATGAATTAGAGAAGTATAAGTGACAA
1 -TTTGTTGCCCGTCTCCAATCCCCAGACTTGCATAAGGCATGAATTAGAGAATTATAAGTGACAA
21659 CATTAGGCTTTATGCCTCTTTGAGTCATTAAATTGAAGAGA
65 CATTAGGCTTTATGCCTCTTTGAGTCATTAAATTGAAGAGA
21700 GAAGTGGCTT
Statistics
Matches: 163, Mismatches: 39, Indels: 21
0.73 0.17 0.09
Matches are distributed among these distances:
103 7 0.04
104 5 0.03
105 68 0.42
106 2 0.01
107 2 0.01
108 67 0.41
109 5 0.03
110 7 0.04
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (105 bp):
TTTGTTGCCCGTCTCCAATCCCCAGACTTGCATAAGGCATGAATTAGAGAATTATAAGTGACAAC
ATTAGGCTTTATGCCTCTTTGAGTCATTAAATTGAAGAGA
Found at i:25213 original size:2 final size:2
Alignment explanation
Indices: 25201--25236 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
25191 ATATTATTTA
*
25201 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25237 TGAAATTGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38060 original size:24 final size:24
Alignment explanation
Indices: 37977--38062 Score: 138
Period size: 24 Copynumber: 3.6 Consensus size: 24
37967 ACCAGCTTGA
* *
37977 GTTTATTCCTCCTGTTACTCCTGG
1 GTTTGTTCCCCCTGTTACTCCTGG
38001 GTTTGCTT-CCCCTGTTACTCCTGG
1 GTTTG-TTCCCCCTGTTACTCCTGG
38025 GTTTGTTCCCCCTGTTACTCCTGG
1 GTTTGTTCCCCCTGTTACTCCTGG
38049 GTTTGTTCCCCCTG
1 GTTTGTTCCCCCTG
38063 AATATTGTCC
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.05, C:0.33, G:0.20, T:0.43
Consensus pattern (24 bp):
GTTTGTTCCCCCTGTTACTCCTGG
Found at i:40094 original size:51 final size:51
Alignment explanation
Indices: 40018--40117 Score: 191
Period size: 51 Copynumber: 2.0 Consensus size: 51
40008 TTATTTGCGA
*
40018 GGGAATGCCATAGCTGGTTTTGTTGAAATTCATCATCATTATCAAGGTTTT
1 GGGAATGCCATAGCTGGTTTTGTTGAAATTCATCATCATCATCAAGGTTTT
40069 GGGAATGCCATAGCTGGTTTTGTTGAAATTCATCATCATCATCAAGGTT
1 GGGAATGCCATAGCTGGTTTTGTTGAAATTCATCATCATCATCAAGGTT
40118 GCTTGCTTCT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (51 bp):
GGGAATGCCATAGCTGGTTTTGTTGAAATTCATCATCATCATCAAGGTTTT
Found at i:40483 original size:5 final size:5
Alignment explanation
Indices: 40468--40505 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
40458 TCATCAATTA
*
40468 TATAC TCTAC TATAC TATAC TATAC TATAC TATAC TAT
1 TATAC TATAC TATAC TATAC TATAC TATAC TATAC TAT
40506 TCAGAGATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAC
Done.