Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007220.1 Corchorus capsularis cultivar CVL-1 contig07241, 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: 16753
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Found at i:2069 original size:15 final size:15
Alignment explanation
Indices: 2049--2080 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2039 TTGAACTTCT
2049 TCATTTCTGAATCTG
1 TCATTTCTGAATCTG
*
2064 TCATTTCTGTATCTG
1 TCATTTCTGAATCTG
2079 TC
1 TC
2081 TCGTCCATGG
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:0.16, C:0.22, G:0.12, T:0.50
Consensus pattern (15 bp):
TCATTTCTGAATCTG
Found at i:6785 original size:70 final size:70
Alignment explanation
Indices: 6704--6898 Score: 329
Period size: 70 Copynumber: 2.8 Consensus size: 70
6694 ACGTTTTTTA
*
6704 ACAAGCCAAACTCGTTTCCACACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATTCAGGGGCT
1 ACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATTCAGGGGCT
6769 TTTCC
66 TTTCC
6774 ACAAGCCAAACTCGTTTCCATACGAGAT-AGTTCAAGCTTTGGTTCCATCCAAGCATTCAGGGGC
1 ACAAGCCAAACTCGTTTCCATACGAG-TCAGTTCAAGCTTTGGTTCCATCCAAGCATTCAGGGGC
6838 TTTTCC
65 TTTTCC
* * * *
6844 ACAAGCCAAACTCGTTTCCATACGAGACAATTCAAGCATTGGTTCTATCCAAGCA
1 ACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCA
6899 ATATGAGCTT
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
70 117 0.99
71 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (70 bp):
ACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATTCAGGGGCT
TTTCC
Found at i:7100 original size:47 final size:47
Alignment explanation
Indices: 7031--7316 Score: 374
Period size: 47 Copynumber: 6.0 Consensus size: 47
7021 ATCCAGGCAA
*
7031 TCTTCTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGTTGG
1 TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG
* *
7078 TCTTCTCTCGCTTCCACGCGAGTTTGCAACTCAGTGACCAAAGTTGG
1 TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG
* * * * *
7125 TCTTCTCTCGCTTCCATGCGAATTTTCAACTCAGTGACCAAAGTTGG
1 TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG
* * *
7172 TGTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGGCCAAAGGTGG
1 TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG
* * * * * *
7219 CCTTTTCTCGCTTCCATGCGAGTTGGCAATTTAGTGGCCAAATTTGG
1 TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG
* * *
7266 CATTTTCTCTCGCTTCCACGCGAGTCTGCGATTTAGTGACCAAAGTTGG
1 --TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG
7315 TC
1 TC
7317 AACGGGTTTT
Statistics
Matches: 206, Mismatches: 31, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
47 168 0.82
49 38 0.18
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.34
Consensus pattern (47 bp):
TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG
Found at i:7397 original size:22 final size:20
Alignment explanation
Indices: 7365--7406 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 20
7355 GAGTAGGTCT
7365 AAAAAAAAAAGACAAAAAAAA
1 AAAAAAAAAAG-CAAAAAAAA
7386 AAAAAAAGAAAGCTAAAAAAA
1 AAAAAAA-AAAGC-AAAAAAA
7407 GGGAAGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.86, C:0.05, G:0.07, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAAGCAAAAAAAA
Found at i:7431 original size:5 final size:6
Alignment explanation
Indices: 7365--7436 Score: 51
Period size: 6 Copynumber: 11.5 Consensus size: 6
7355 GAGTAGGTCT
*
7365 AAAAA- AAAAAG ACAAAA- AAAAAA AAAAAG AAAGCTAA- AAAAAGGG
1 AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG AAA---AAG AAAAA--G
*
7410 AAGAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA
7437 CATGCAAACA
Statistics
Matches: 55, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
5 11 0.20
6 31 0.56
7 4 0.07
8 7 0.13
9 2 0.04
ACGTcount: A:0.81, C:0.03, G:0.15, T:0.01
Consensus pattern (6 bp):
AAAAAG
Found at i:7436 original size:18 final size:17
Alignment explanation
Indices: 7365--7436 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
7355 GAGTAGGTCT
7365 AAAAAAAAAAGACAAAA-
1 AAAAAAAAAAGA-AAAAG
*
7382 AAAAAAAAAA-AGAAAG
1 AAAAAAAAAAGAAAAAG
* ** *
7398 CTAAAAAAAGGGAAGAAG
1 -AAAAAAAAAAGAAAAAG
7416 AAAAAGAAAAAGAAAAAG
1 AAAAA-AAAAAGAAAAAG
7434 AAA
1 AAA
7437 CATGCAAACA
Statistics
Matches: 41, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
15 3 0.07
16 1 0.02
17 21 0.51
18 16 0.39
ACGTcount: A:0.81, C:0.03, G:0.15, T:0.01
Consensus pattern (17 bp):
AAAAAAAAAAGAAAAAG
Found at i:7662 original size:26 final size:28
Alignment explanation
Indices: 7614--7672 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 28
7604 TGTTAATTGA
* * *
7614 CATTTGGGTCACCTAGGGGCATTTTTGT
1 CATTTCGGTCACCTAGGGGCATTCTGGT
*
7642 CATTTCGG-CACC-AGGTGCATTCTGGT
1 CATTTCGGTCACCTAGGGGCATTCTGGT
7668 CATTT
1 CATTT
7673 GCACATTCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 16 0.59
27 4 0.15
28 7 0.26
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.37
Consensus pattern (28 bp):
CATTTCGGTCACCTAGGGGCATTCTGGT
Done.