Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007702.1 Corchorus capsularis cultivar CVL-1 contig07723, 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: 18645
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.31
Found at i:1765 original size:42 final size:42
Alignment explanation
Indices: 1701--1792 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
1691 AACTTGAAAT
*
1701 TACAAAACATACATAAAACTAAAACTACT-AAACATATCAAA
1 TACAAAACAAACATAAAACTAAAACTACTAAAACATATCAAA
*
1742 CTACAAAACAAACATAAAGCTAAAACTACTAAAACATATCAAA
1 -TACAAAACAAACATAAAACTAAAACTACTAAAACATATCAAA
1785 TAACAAAA
1 T-ACAAAA
1793 AACTCTTCTC
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
42 28 0.61
43 18 0.39
ACGTcount: A:0.62, C:0.20, G:0.01, T:0.17
Consensus pattern (42 bp):
TACAAAACAAACATAAAACTAAAACTACTAAAACATATCAAA
Found at i:5714 original size:30 final size:30
Alignment explanation
Indices: 5678--5779 Score: 113
Period size: 30 Copynumber: 3.4 Consensus size: 30
5668 CTGTGTTACA
* *
5678 TGTGTTTGGGGAGTTTAGTATAGATGCCTC
1 TGTGTTTAGGGACTTTAGTATAGATGCCTC
*
5708 TGTGTTTAGGGACTTTAATATAGATGCC-C
1 TGTGTTTAGGGACTTTAGTATAGATGCCTC
5737 TTGTGTTT-GAGGACTTTGATGTA-A-ATGCCTC
1 -TGTGTTTAG-GGACTTT-A-GTATAGATGCCTC
5768 TGTGTTTAGGGA
1 TGTGTTTAGGGA
5780 TGAATACCCT
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
29 2 0.03
30 54 0.87
31 4 0.06
32 2 0.03
ACGTcount: A:0.20, C:0.11, G:0.29, T:0.40
Consensus pattern (30 bp):
TGTGTTTAGGGACTTTAGTATAGATGCCTC
Found at i:5829 original size:53 final size:51
Alignment explanation
Indices: 5734--5916 Score: 224
Period size: 53 Copynumber: 3.4 Consensus size: 51
5724 AATATAGATG
5734 CCCTTGTGTTTGAGGACTTTGATGTA-AATGCCTCTGTGTTTAGGGATGAATA
1 CCCTTGTGTTTGAGGACTTTGA-G-AGAATGCCTCTGTGTTTAGGGATGAATA
*
5786 CCCTTGTGTTTGAGGACTTTTGAGAGAGGTGCCTCTGTGTTTAGGGATGAATA
1 CCCTTGTGTTTGAGGAC-TTTGAGAGA-ATGCCTCTGTGTTTAGGGATGAATA
* * *
5839 CCCTTGTGTTTGAGGACTTTGATATAGAATTGCCTCTGTGTTTAGGGACTTATAAATG
1 CCCTTGTGTTTGAGGACTTTG--AGAGAA-TGCCTCTGTGTTTAGGG----ATGAATA
5897 CCCTTGTGTTTGAGGACTTT
1 CCCTTGTGTTTGAGGACTTT
5917 AATTATTGGG
Statistics
Matches: 116, Mismatches: 5, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
51 1 0.01
52 23 0.20
53 46 0.40
54 21 0.18
58 25 0.22
ACGTcount: A:0.20, C:0.14, G:0.27, T:0.39
Consensus pattern (51 bp):
CCCTTGTGTTTGAGGACTTTGAGAGAATGCCTCTGTGTTTAGGGATGAATA
Found at i:10681 original size:8 final size:8
Alignment explanation
Indices: 10664--10715 Score: 63
Period size: 8 Copynumber: 6.8 Consensus size: 8
10654 TATGATGAGC
*
10664 ATTTGAAT
1 ATTTGGAT
10672 ATTTGGAT
1 ATTTGGAT
10680 ATTTGG-T
1 ATTTGGAT
10687 ATTTGG-T
1 ATTTGGAT
*
10694 ATTTGAAT
1 ATTTGGAT
*
10702 ATTTGAAT
1 ATTTGGAT
10710 ATTTGG
1 ATTTGG
10716 GTATGCATGG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
7 13 0.32
8 27 0.68
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (8 bp):
ATTTGGAT
Found at i:18384 original size:30 final size:30
Alignment explanation
Indices: 18348--18449 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 30
18338 CTGTGTTACA
*
18348 TGTGTTTGGGGACTTTAGTATAGATGCCTC
1 TGTGTTTAGGGACTTTAGTATAGATGCCTC
*
18378 TGTGTTTAGGGACTTTAATATAGATGCC-C
1 TGTGTTTAGGGACTTTAGTATAGATGCCTC
18407 TTGTGTTT-GAGGACTTTGATGTA-A-ATGCCTC
1 -TGTGTTTAG-GGACTTT-A-GTATAGATGCCTC
18438 TGTGTTTAGGGA
1 TGTGTTTAGGGA
18450 TGAATACCCT
Statistics
Matches: 63, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
29 2 0.03
30 55 0.87
31 4 0.06
32 2 0.03
ACGTcount: A:0.20, C:0.12, G:0.28, T:0.40
Consensus pattern (30 bp):
TGTGTTTAGGGACTTTAGTATAGATGCCTC
Found at i:18528 original size:58 final size:57
Alignment explanation
Indices: 18346--18533 Score: 219
Period size: 60 Copynumber: 3.3 Consensus size: 57
18336 CCCTGTGTTA
* *
18346 CATGTGTTTGGGGACTTT-AGTATAG-ATGCCTCTGTGTTTAGGGACTTTAATATAGATGCC
1 CATGTGTTTGAGGACTTTGA-TATAGAATGCCTCTGTGTTTAGGGAC-TT-ATA-A-ATACC
* * *
18406 CTTGTGTTTGAGGACTTTGATGTA-AATGCCTCTGTGTTTAGGG----ATGAATACC
1 CATGTGTTTGAGGACTTTGATATAGAATGCCTCTGTGTTTAGGGACTTATAAATACC
*
18458 CTTGTGTTTGAGGACTTTGATATAGAATTGCCTCTGTGTTTAGGGACTTATAAATACC
1 CATGTGTTTGAGGACTTTGATATAGAA-TGCCTCTGTGTTTAGGGACTTATAAATACC
18516 CATGTGTTTGAGGACTTT
1 CATGTGTTTGAGGACTTT
18534 AATTATTGGG
Statistics
Matches: 112, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
52 27 0.24
53 3 0.03
54 19 0.17
58 25 0.22
60 37 0.33
61 1 0.01
ACGTcount: A:0.22, C:0.13, G:0.26, T:0.39
Consensus pattern (57 bp):
CATGTGTTTGAGGACTTTGATATAGAATGCCTCTGTGTTTAGGGACTTATAAATACC
Done.