Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016326.1 Corchorus capsularis cultivar CVL-1 contig16347, 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: 18224
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Found at i:698 original size:50 final size:49
Alignment explanation
Indices: 475--827 Score: 404
Period size: 49 Copynumber: 7.2 Consensus size: 49
465 TAGCTGTTTA
* * * *
475 TTCCC-AAACACCCTTCCCAGACGGAAGCCATTCACTTTTACTTGCAAT
1 TTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTAT
* * *
523 TTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCAAT
1 TTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTAT
* * * *
572 TTCCCAAAGCGCTCTTCCCAAACAGAAGCCATTTATTTTTACTT-CTTAT
1 TTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGC-TAT
* **
621 TTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTCGCTTGCTAT
1 TTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTAT
* * * * *
670 TTCCCCAAAATGCCCTTCCTAGACGGAAGCCGTTTATTTTTGCTTACTAT
1 TT-CCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTAT
* ** *
720 CTCCCCAAAACGCCCTTCCTGGACGGAAGCCATTTATCTTTACTTGCTAT
1 -TTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTAT
* ** * * *
770 TTCCCAAAACGCCCTTCCCGGACGGAAGGTATTTATTCTTACCTGCCAT
1 TTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTAT
819 TTCCCAAAA
1 TTCCCAAAA
828 TGCCTTTTCC
Statistics
Matches: 266, Mismatches: 34, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
48 6 0.02
49 176 0.66
50 83 0.31
51 1 0.00
ACGTcount: A:0.24, C:0.32, G:0.13, T:0.31
Consensus pattern (49 bp):
TTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTAT
Found at i:6650 original size:32 final size:32
Alignment explanation
Indices: 6614--6687 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
6604 AGCACAATAG
6614 CGGCGTCTAATGATTAAAACGCCACTATTTAA
1 CGGCGTCTAATGATTAAAACGCCACTATTTAA
** * *
6646 CGGCGTCTTTTGATTCAAACGCCACTATTTAG
1 CGGCGTCTAATGATTAAAACGCCACTATTTAA
*
6678 TGGCGTCTAA
1 CGGCGTCTAA
6688 CCACTCAAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (32 bp):
CGGCGTCTAATGATTAAAACGCCACTATTTAA
Found at i:7401 original size:13 final size:13
Alignment explanation
Indices: 7383--7418 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
7373 CAGGTCTCTT
7383 CCTTCCTTTTCTC
1 CCTTCCTTTTCTC
7396 CCTTCCTTTTCTC
1 CCTTCCTTTTCTC
*
7409 CTTTCCTTTT
1 CCTTCCTTTT
7419 ATCTTACTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (13 bp):
CCTTCCTTTTCTC
Found at i:7416 original size:17 final size:15
Alignment explanation
Indices: 7377--7408 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
7367 TTTTCGCAGG
7377 TCTCTTCCTTCCTTT
1 TCTCTTCCTTCCTTT
7392 TCTC--CCTTCCTTT
1 TCTCTTCCTTCCTTT
7405 TCTC
1 TCTC
7409 CTTTCCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.76
15 4 0.24
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (15 bp):
TCTCTTCCTTCCTTT
Found at i:7436 original size:20 final size:20
Alignment explanation
Indices: 7411--7453 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
7401 CTTTTCTCCT
7411 TTCCTTTTATCTTACTTCGA
1 TTCCTTTTATCTTACTTCGA
7431 TTCCTTTTATCTTACTTCGA
1 TTCCTTTTATCTTACTTCGA
7451 TTC
1 TTC
7454 GCAGCTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.26, G:0.05, T:0.56
Consensus pattern (20 bp):
TTCCTTTTATCTTACTTCGA
Found at i:7728 original size:9 final size:9
Alignment explanation
Indices: 7714--7772 Score: 100
Period size: 9 Copynumber: 6.3 Consensus size: 9
7704 ACTGATGCTT
7714 TTTGGAATG
1 TTTGGAATG
7723 TTTGGAATG
1 TTTGGAATG
7732 TTTGGAATG
1 TTTGGAATG
7741 TTTCTGGAATG
1 -TT-TGGAATG
7752 TTTGGAATG
1 TTTGGAATG
7761 TTTGGAATG
1 TTTGGAATG
7770 TTT
1 TTT
7773 CTGGAACAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
9 37 0.77
10 4 0.08
11 7 0.15
ACGTcount: A:0.20, C:0.02, G:0.31, T:0.47
Consensus pattern (9 bp):
TTTGGAATG
Found at i:7758 original size:29 final size:29
Alignment explanation
Indices: 7716--7778 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
7706 TGATGCTTTT
7716 TGGAATGTTTGGAATGTTTGGAATGTTTC
1 TGGAATGTTTGGAATGTTTGGAATGTTTC
7745 TGGAATGTTTGGAATGTTTGGAATGTTTC
1 TGGAATGTTTGGAATGTTTGGAATGTTTC
7774 TGGAA
1 TGGAA
7779 CAATTATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.22, C:0.03, G:0.32, T:0.43
Consensus pattern (29 bp):
TGGAATGTTTGGAATGTTTGGAATGTTTC
Found at i:8751 original size:13 final size:13
Alignment explanation
Indices: 8735--8779 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
8725 AATAACCTTT
*
8735 GTTTATAAAAGGA
1 GTTTATAAAATGA
8748 GTTTATATAAAATGA
1 G-TT-TATAAAATGA
8763 GTTTATAAAATGA
1 GTTTATAAAATGA
8776 GTTT
1 GTTT
8780 TTGTATCATG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 15 0.52
14 4 0.14
15 10 0.34
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.40
Consensus pattern (13 bp):
GTTTATAAAATGA
Found at i:8758 original size:15 final size:15
Alignment explanation
Indices: 8738--8769 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
8728 AACCTTTGTT
8738 TATAAAAGGAGTTTA
1 TATAAAAGGAGTTTA
*
8753 TATAAAATGAGTTTA
1 TATAAAAGGAGTTTA
8768 TA
1 TA
8770 AAATGAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.38
Consensus pattern (15 bp):
TATAAAAGGAGTTTA
Found at i:9880 original size:9 final size:10
Alignment explanation
Indices: 9867--9894 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
9857 CGAAAAATAT
9867 AAAAAAAATC
1 AAAAAAAATC
9877 AAAAAAAATC
1 AAAAAAAATC
9887 AAAAAAAA
1 AAAAAAAA
9895 ATTTCGACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:15620 original size:27 final size:27
Alignment explanation
Indices: 15584--15698 Score: 196
Period size: 27 Copynumber: 4.3 Consensus size: 27
15574 CACTTCTCTC
15584 CCCACTTCGACCCCAGAAGTGGATCCT
1 CCCACTTCGACCCCAGAAGTGGATCCT
*
15611 CCCACTTCGACCCCAGCAGTGGATCCT
1 CCCACTTCGACCCCAGAAGTGGATCCT
15638 CCCACTTCGACCCCA-ATAGTGGATCCT
1 CCCACTTCGACCCCAGA-AGTGGATCCT
*
15665 CCCACTTCGACCCCAGCAGTGGATCCT
1 CCCACTTCGACCCCAGAAGTGGATCCT
15692 CCCACTT
1 CCCACTT
15699 TGCCTATGGT
Statistics
Matches: 83, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
27 83 1.00
ACGTcount: A:0.20, C:0.43, G:0.17, T:0.20
Consensus pattern (27 bp):
CCCACTTCGACCCCAGAAGTGGATCCT
Found at i:18122 original size:32 final size:32
Alignment explanation
Indices: 18076--18155 Score: 151
Period size: 32 Copynumber: 2.5 Consensus size: 32
18066 GGATATACCT
*
18076 TTATATAGCAGCGTCTGAAGAACAAAACGCCC
1 TTATATAGCGGCGTCTGAAGAACAAAACGCCC
18108 TTATATAGCGGCGTCTGAAGAACAAAACGCCC
1 TTATATAGCGGCGTCTGAAGAACAAAACGCCC
18140 TTATATAGCGGCGTCT
1 TTATATAGCGGCGTCT
18156 AAATATCCAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (32 bp):
TTATATAGCGGCGTCTGAAGAACAAAACGCCC
Done.