Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014294.1 Corchorus capsularis cultivar CVL-1 contig14315, 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: 17397
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:505 original size:5 final size:6
Alignment explanation
Indices: 494--518 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
484 TTCGTTATTC
494 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
519 CGTTTTGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:4591 original size:22 final size:22
Alignment explanation
Indices: 4564--4613 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
4554 TTAATATTTC
4564 ACTCTTTACTGATTA-CCTTCTT
1 ACTCTTTACTGATTACCCTT-TT
4586 ACTC-TTACTGATTACCCTTTT
1 ACTCTTTACTGATTACCCTTTT
4607 -CTCTTTA
1 ACTCTTTA
4614 TCATTCTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 3 0.12
21 15 0.58
22 8 0.31
ACGTcount: A:0.18, C:0.28, G:0.04, T:0.50
Consensus pattern (22 bp):
ACTCTTTACTGATTACCCTTTT
Found at i:4640 original size:14 final size:14
Alignment explanation
Indices: 4623--4662 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
4613 ATCATTCTTC
4623 CTTTACTGATTACT
1 CTTTACTGATTACT
*
4637 CTTTGCTGATTACT
1 CTTTACTGATTACT
4651 -TTTACCTGATTA
1 CTTTA-CTGATTA
4663 TCCTTTTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 3 0.13
14 20 0.87
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.50
Consensus pattern (14 bp):
CTTTACTGATTACT
Found at i:4911 original size:37 final size:40
Alignment explanation
Indices: 4868--4961 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
4858 TTTCCTTTTA
*
4868 CTTAATTACTGGTTTACTGATT-A-CTGT-TACCTTGACT
1 CTTAATTACTGATTTACTGATTAATCTGTCTACCTTGACT
* * * *
4905 CTTAATTATTAATTTACTGATTAATTTTTCTACCTTGACT
1 CTTAATTACTGATTTACTGATTAATCTGTCTACCTTGACT
*
4945 CTTAATTACTGACTTAC
1 CTTAATTACTGATTTAC
4962 CCTTTTACTT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
37 19 0.41
38 1 0.02
39 2 0.04
40 24 0.52
ACGTcount: A:0.26, C:0.18, G:0.09, T:0.48
Consensus pattern (40 bp):
CTTAATTACTGATTTACTGATTAATCTGTCTACCTTGACT
Found at i:5066 original size:38 final size:40
Alignment explanation
Indices: 4996--5078 Score: 98
Period size: 38 Copynumber: 2.1 Consensus size: 40
4986 TGATTGCTAC
* * **
4996 TTTTACTTCTTCTCTTAGTTATCAATTTACTGATTA-ATCT
1 TTTTACTTC-TCTCTTAATTACCAATGGACTGATTACATCT
*
5036 TTTTACTTC-CTCTTAATTACCAATGGACTGATTACTTCT
1 TTTTACTTCTCTCTTAATTACCAATGGACTGATTACATCT
5075 TTTT
1 TTTT
5079 CTTTTCACTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
38 21 0.57
39 7 0.19
40 9 0.24
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.53
Consensus pattern (40 bp):
TTTTACTTCTCTCTTAATTACCAATGGACTGATTACATCT
Found at i:6075 original size:16 final size:17
Alignment explanation
Indices: 6045--6088 Score: 72
Period size: 16 Copynumber: 2.6 Consensus size: 17
6035 TACACACATA
*
6045 TATTTATTATTATTTTT
1 TATTTATTATTATTTGT
6062 TATTTATT-TTATTTGT
1 TATTTATTATTATTTGT
6078 TATTTATTATT
1 TATTTATTATT
6089 TTCTTTACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (17 bp):
TATTTATTATTATTTGT
Found at i:10081 original size:31 final size:31
Alignment explanation
Indices: 10046--10257 Score: 149
Period size: 36 Copynumber: 6.3 Consensus size: 31
10036 AGTAGGTTAG
10046 TAAGTCAA-TTAGTAACTTAATTCAGGGTAAT
1 TAAGT-AAGTTAGTAACTTAATTCAGGGTAAT
*
10077 TAAGTAAGTAATAGGTAACTTAATTCAGGATAAT
1 TAAGTAAGT--TA-GTAACTTAATTCAGGGTAAT
* *
10111 TAAGTCAGTCAGTTAGTAACTTGATTCAAGGTAAT
1 TAAGT-A---AGTTAGTAACTTAATTCAGGGTAAT
10146 TAAGTAAAGTCAGTTAGTAACTTAATTCAGGG-AAGT
1 TAAGT--A---AGTTAGTAACTTAATTCAGGGTAA-T
** * *
10182 TAAGTAAGGCAGTAACTTAATTCAAGATAAT
1 TAAGTAAGTTAGTAACTTAATTCAGGGTAAT
* * *
10213 TAAGTAATTGGGTAATCAACTTAAATCCAGGGTAAT
1 TAAGTAA---GTTAGT-AACTT-AATTCAGGGTAAT
10249 TAAGTAAGT
1 TAAGTAAGT
10258 CAATAAGTAA
Statistics
Matches: 148, Mismatches: 17, Indels: 30
0.76 0.09 0.15
Matches are distributed among these distances:
30 2 0.01
31 31 0.21
32 2 0.01
33 3 0.02
34 29 0.20
35 30 0.20
36 48 0.32
38 3 0.02
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (31 bp):
TAAGTAAGTTAGTAACTTAATTCAGGGTAAT
Found at i:10258 original size:102 final size:103
Alignment explanation
Indices: 10044--10269 Score: 262
Period size: 102 Copynumber: 2.2 Consensus size: 103
10034 TAAGTAGGTT
* *
10044 AGTAAGTCAATTAGTAACTTAATTCAGGGTAATTAAGTAAGTAATAGGTAACTTAATTCAGGATA
1 AGTAAGTCAATTAGTAACTTAATTCAGGGTAATTAAGTAAG-AACAGGTAACTTAATTCAAGATA
* * * * *
10109 ATTAAGTCAGTCAGTTAGTAACTTGATTCAAGGTAATTA
65 ATTAAGTCAATCAGGTAATAACTTAATCCAAGGTAATTA
* *
10148 AGTAAAGTCAGTTAGTAACTTAATTCAGGG-AAGTTAAGTAAG-GCA-GTAACTTAATTCAAGAT
1 AGT-AAGTCAATTAGTAACTTAATTCAGGGTAA-TTAAGTAAGAACAGGTAACTTAATTCAAGAT
** *
10210 AATTAAGT-AATTGGGTAATCAACTTAAATCCAGGGTAATTA
64 AATTAAGTCAATCAGGTAAT-AACTT-AATCCAAGGTAATTA
*
10251 AGTAAGTCAATAAGTAACT
1 AGTAAGTCAATTAGTAACT
10270 GATCGTGTCG
Statistics
Matches: 104, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
101 6 0.06
102 43 0.41
103 16 0.15
104 5 0.05
105 34 0.33
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (103 bp):
AGTAAGTCAATTAGTAACTTAATTCAGGGTAATTAAGTAAGAACAGGTAACTTAATTCAAGATAA
TTAAGTCAATCAGGTAATAACTTAATCCAAGGTAATTA
Found at i:13109 original size:21 final size:22
Alignment explanation
Indices: 13061--13106 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
13051 AATTTTGTCA
13061 AAATTTTCGAAAAAATTATACC
1 AAATTTTCGAAAAAATTATACC
13083 AAATTTTCGAAAAAATTATACC
1 AAATTTTCGAAAAAATTATACC
13105 AA
1 AA
13107 TTTAACCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.52, C:0.13, G:0.04, T:0.30
Consensus pattern (22 bp):
AAATTTTCGAAAAAATTATACC
Found at i:13736 original size:10 final size:10
Alignment explanation
Indices: 13716--13767 Score: 50
Period size: 10 Copynumber: 4.8 Consensus size: 10
13706 CGGATGGCAT
13716 GGCATTGGCCG
1 GGCA-TGGCCG
13727 GGCATGGCCG
1 GGCATGGCCG
13737 GGCATGGTGCGCG
1 GGCAT-G-GC-CG
* *
13750 GACATGGCCA
1 GGCATGGCCG
13760 GGCATGGC
1 GGCATGGC
13768 TTGGTGTCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
10 19 0.54
11 7 0.20
12 3 0.09
13 6 0.17
ACGTcount: A:0.13, C:0.27, G:0.46, T:0.13
Consensus pattern (10 bp):
GGCATGGCCG
Found at i:17307 original size:27 final size:27
Alignment explanation
Indices: 17217--17307 Score: 75
Period size: 28 Copynumber: 3.4 Consensus size: 27
17207 CCTAAATTTT
* *
17217 AAAAATGGAAAAATAATTTTTTTTTAAG
1 AAAAACGGAAAAACAATTTTTTTTT-AG
* *
17245 AAAAATCGGAAAAAC-CTTTTTTTTATCG
1 AAAAA-CGGAAAAACAATTTTTTTT-TAG
*
17273 ----ACGCAAAAACAATTTTTTTTTAG
1 AAAAACGGAAAAACAATTTTTTTTTAG
17296 AAAAACGGAAAA
1 AAAAACGGAAAA
17308 CAAAACAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 15
0.68 0.11 0.21
Matches are distributed among these distances:
23 10 0.21
24 9 0.19
27 7 0.15
28 14 0.29
29 8 0.17
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (27 bp):
AAAAACGGAAAAACAATTTTTTTTTAG
Done.