Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005008.1 Corchorus capsularis cultivar CVL-1 contig05026, 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: 6424
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Found at i:102 original size:32 final size:32
Alignment explanation
Indices: 28--102 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 32
18 AAAATAGCCG
* * *
28 AGCCGCCCCACCGGGGCGGCCTGCCGTGGCGA
1 AGCCGCCCCATCGGGACGGCCTGCCCTGGCGA
*
60 AGCCGCCCCATCGGGACGGCCTGCCCTGGCTA
1 AGCCGCCCCATCGGGACGGCCTGCCCTGGCGA
92 AGCCGCCCCAT
1 AGCCGCCCCAT
103 GAGGGCGACT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.12, C:0.45, G:0.33, T:0.09
Consensus pattern (32 bp):
AGCCGCCCCATCGGGACGGCCTGCCCTGGCGA
Found at i:939 original size:16 final size:17
Alignment explanation
Indices: 918--949 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
908 AATAGAGTAA
918 TATTGA-AGTTTCTAAC
1 TATTGAGAGTTTCTAAC
934 TATTGAGAGTTTCTAA
1 TATTGAGAGTTTCTAA
950 TAAGTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (17 bp):
TATTGAGAGTTTCTAAC
Found at i:1600 original size:29 final size:31
Alignment explanation
Indices: 1549--1607 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
1539 TTAAGGTATT
1549 AATATAAATTATTCAACTTTATCAT-TTATA
1 AATATAAATTATTCAACTTTATCATATTATA
*
1579 AATAT-AATTATTTAA-TTATATCATATTAT
1 AATATAAATTATTCAACTT-TATCATATTAT
1608 TTATATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 2 0.08
29 15 0.58
30 9 0.35
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (31 bp):
AATATAAATTATTCAACTTTATCATATTATA
Found at i:1614 original size:30 final size:29
Alignment explanation
Indices: 1545--1614 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 29
1535 TTAATTAAGG
1545 TATTAATATAAATTATTCAACTTTATCATT
1 TATTAATAT-AATTATTCAACTTTATCATT
* *
1575 TATAAATATAATTATTTAA-TTATATCATAT
1 TATTAATATAATTATTCAACTT-TATCAT-T
*
1605 TATTTATATA
1 TATTAATATA
1615 TAAATACGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 2 0.06
29 15 0.44
30 17 0.50
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (29 bp):
TATTAATATAATTATTCAACTTTATCATT
Found at i:3104 original size:108 final size:109
Alignment explanation
Indices: 2868--3162 Score: 448
Period size: 109 Copynumber: 2.7 Consensus size: 109
2858 TAAATTAAAA
** * *
2868 TGGTAAAAATAAAAAAAATTATATAAAATATTGGATTTAATTAAATGAAAATAGAGTTTTTAGTA
1 TGGTAAAAAT-AAAGTAATTATA-AAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTA
2933 GAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTC
64 GAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTC
2979 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
* *
3044 ATAAAATTGTATATTAGAAAAAA-TTTAGTATATCCAAATTTTT
66 ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTC
* *
3087 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTA
3152 GTAGAATAAAA
61 GTAGAATAAAA
3163 CTAAGCAAGG
Statistics
Matches: 171, Mismatches: 8, Indels: 8
0.91 0.04 0.04
Matches are distributed among these distances:
108 56 0.33
109 66 0.39
110 11 0.06
111 10 0.06
113 28 0.16
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.37
Consensus pattern (109 bp):
TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTC
Found at i:4069 original size:50 final size:50
Alignment explanation
Indices: 4008--4106 Score: 198
Period size: 50 Copynumber: 2.0 Consensus size: 50
3998 TATATCTATA
4008 TATATAGATAGAAAATAAAAAATATATTCTATATATAATAGAATTATAGT
1 TATATAGATAGAAAATAAAAAATATATTCTATATATAATAGAATTATAGT
4058 TATATAGATAGAAAATAAAAAATATATTCTATATATAATAGAATTATAG
1 TATATAGATAGAAAATAAAAAATATATTCTATATATAATAGAATTATAG
4107 AATACATAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (50 bp):
TATATAGATAGAAAATAAAAAATATATTCTATATATAATAGAATTATAGT
Found at i:5569 original size:16 final size:15
Alignment explanation
Indices: 5545--5574 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5535 ATGTTATCTC
5545 AAAAAAAAAAAGAAA
1 AAAAAAAAAAAGAAA
5560 AAAAAGAAAAAAGAA
1 AAAAA-AAAAAAGAA
5575 TTGAATGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAGAAA
Done.