Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022601.1 Corchorus olitorius cultivar O-4 contig22634, 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: 17781
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7680 original size:30 final size:30
Alignment explanation
Indices: 7644--7753 Score: 202
Period size: 30 Copynumber: 3.7 Consensus size: 30
7634 ACTCTCCAAA
*
7644 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
*
7674 TGACACCGGAAGTTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
7704 TGACACCAGAAGTTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGGTCTTGCAAT
7734 TGACACCAGAAGTTGTCATG
1 TGACACCAGAAGTTGTCATG
7754 CAAATGACAC
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 77 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGGTCTTGCAAT
Found at i:7789 original size:19 final size:19
Alignment explanation
Indices: 7752--7791 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
7742 GAAGTTGTCA
*
7752 TGCAAATGACACTAGAAGT
1 TGCAAATGACACCAGAAGT
* *
7771 TGCAATTGACACCATAAGT
1 TGCAAATGACACCAGAAGT
7790 TG
1 TG
7792 TCATGATCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (19 bp):
TGCAAATGACACCAGAAGT
Found at i:7793 original size:103 final size:105
Alignment explanation
Indices: 7667--7858 Score: 271
Period size: 103 Copynumber: 1.8 Consensus size: 105
7657 TGTCATGATC
* * * *
7667 TTGCAATTGACACCGGAAGTTGTCATGGTCTTGCAATTGACACCAGAAGTTGTCAT-GGTCT-TG
1 TTGCAATTGACACCAGAAGTTGTCATGATCTTGCAATTGACACCAGAAGATGTCATAAGTCTATG
7730 CAATTGACACCAGAAGTTGTCATGCAAATGACACTAGAAG
66 CAATTGACACCAGAAGTTGTCATGCAAATGACACTAGAAG
* ** * * *
7770 TTGCAATTGACACCATAAGTTGTCATGATCTTGCAATTGACACTTGAAGATGTCATAATTTTATT
1 TTGCAATTGACACCAGAAGTTGTCATGATCTTGCAATTGACACCAGAAGATGTCATAAGTCTATG
*
7835 CAATTGAGACCAGAAGTTGTCATG
66 CAATTGACACCAGAAGTTGTCATG
7859 ATAAATTTCC
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
103 50 0.66
104 2 0.03
105 24 0.32
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (105 bp):
TTGCAATTGACACCAGAAGTTGTCATGATCTTGCAATTGACACCAGAAGATGTCATAAGTCTATG
CAATTGACACCAGAAGTTGTCATGCAAATGACACTAGAAG
Found at i:7856 original size:32 final size:32
Alignment explanation
Indices: 7773--7929 Score: 122
Period size: 32 Copynumber: 4.9 Consensus size: 32
7763 CTAGAAGTTG
* * * * *
7773 CAATTGACACCATAAGTTGTCATGA-TCT-TG
1 CAATTGACACCAGAAGATGTCATAATTTTATT
**
7803 CAATTGACACTTGAAGATGTCATAATTTTATT
1 CAATTGACACCAGAAGATGTCATAATTTTATT
* * ** *
7835 CAATTGAGACCAGAAGTTGTCATGATAAATT-TC
1 CAATTGACACCAGAAGATGTCAT-A-ATTTTATT
* **
7868 CAATAGACACTTGAAGATGTCATAATTTTATT
1 CAATTGACACCAGAAGATGTCATAATTTTATT
* *
7900 CAATTGACACCAGAAGTTGTCATGATTTTA
1 CAATTGACACCAGAAGATGTCATAATTTTA
7930 CCTTTCAAAA
Statistics
Matches: 95, Mismatches: 27, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
30 20 0.21
31 5 0.05
32 47 0.49
33 20 0.21
34 3 0.03
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (32 bp):
CAATTGACACCAGAAGATGTCATAATTTTATT
Found at i:7892 original size:65 final size:62
Alignment explanation
Indices: 7773--7925 Score: 234
Period size: 65 Copynumber: 2.4 Consensus size: 62
7763 CTAGAAGTTG
* * *
7773 CAATTGACACCATAAGTTGTCATGATCTTGCAATTGACACTTGAAGATGTCATAATTTTATT
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
* *
7835 CAATTGAGACCAGAAGTTGTCATGATAAATTTCCAATAGACACTTGAAGATGTCATAATTTTATT
1 CAATTGACACCAGAAGTTGTCATGAT---CTTCCAATAGACACTTGAAGATGTCATAATTTTATT
7900 CAATTGACACCAGAAGTTGTCATGAT
1 CAATTGACACCAGAAGTTGTCATGAT
7926 TTTACCTTTC
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
62 24 0.29
65 58 0.71
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Consensus pattern (62 bp):
CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
Found at i:10018 original size:33 final size:33
Alignment explanation
Indices: 9955--10018 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
9945 ATACTGAATA
* **
9955 ATATTGCCCCTGAAGAGGCATTAATTCATGAGC
1 ATATTGCCCCTGAAGAGGCATAAACCCATGAGC
* *
9988 ATATTGCCCCTGTAGTGGCATAAACCCATGA
1 ATATTGCCCCTGAAGAGGCATAAACCCATGA
10019 AAAGATTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (33 bp):
ATATTGCCCCTGAAGAGGCATAAACCCATGAGC
Found at i:12742 original size:19 final size:18
Alignment explanation
Indices: 12714--12750 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
12704 GTTCACTTTT
12714 GAAAAAAGAAAAGAAAAA
1 GAAAAAAGAAAAGAAAAA
12732 GAAAGAAAGAAAAGAAAAA
1 GAAA-AAAGAAAAGAAAAA
12751 TTGGTGTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (18 bp):
GAAAAAAGAAAAGAAAAA
Found at i:13151 original size:15 final size:14
Alignment explanation
Indices: 13133--13162 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13123 CTGTTTCATC
13133 TTGAATTGTTTTTTT
1 TTGAATT-TTTTTTT
13148 TTGAATTTTTTTTT
1 TTGAATTTTTTTTT
13162 T
1 T
13163 GAAAAAAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (14 bp):
TTGAATTTTTTTTT
Found at i:13159 original size:13 final size:13
Alignment explanation
Indices: 13141--13165 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13131 TCTTGAATTG
13141 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
13154 TTTTTTTTTGAA
1 TTTTTTTTTGAA
13166 AAAAACCATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:14734 original size:3 final size:3
Alignment explanation
Indices: 14726--14769 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
14716 TTGGATTATA
*
14726 AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT -AT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
14770 TACTATTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Done.