Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015296.1 Corchorus capsularis cultivar CVL-1 contig15317, 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: 10417
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Found at i:3906 original size:14 final size:14
Alignment explanation
Indices: 3886--3923 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3876 TTCAAAAATT
3886 GTTTTCAAGAAAAGA
1 GTTTTCAA-AAAAGA
*
3901 -TTTTCAAAAATGA
1 GTTTTCAAAAAAGA
3914 GTTTTCAAAA
1 GTTTTCAAAA
3924 GGTTTCGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (14 bp):
GTTTTCAAAAAAGA
Found at i:5548 original size:60 final size:62
Alignment explanation
Indices: 5467--5587 Score: 183
Period size: 60 Copynumber: 2.0 Consensus size: 62
5457 GGTCCCTTTC
* *
5467 AGGTCATCTTTCATCACTTATCAAGATCGACTGGAAACAAGTCATCTTTCAA-A-TTATCAG
1 AGGTCATCTTTCAACAATTATCAAGATCGACTGGAAACAAGTCATCTTTCAACACTTATCAG
* * *
5527 AGGTTATCTTTCAACAATTATCAAGATTGACTGGAAACAGGTCATCTTTCAACACTTATCA
1 AGGTCATCTTTCAACAATTATCAAGATCGACTGGAAACAAGTCATCTTTCAACACTTATCA
5588 AGATCGACTG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 47 0.87
61 1 0.02
62 6 0.11
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (62 bp):
AGGTCATCTTTCAACAATTATCAAGATCGACTGGAAACAAGTCATCTTTCAACACTTATCAG
Found at i:5571 original size:98 final size:98
Alignment explanation
Indices: 5466--5723 Score: 428
Period size: 98 Copynumber: 2.6 Consensus size: 98
5456 TGGTCCCTTT
5466 CAGGTCATCTTTCATCACTTATCAAGATCGACTGGAAACAAGTCATCTTTCAAATTATCAGAGGT
1 CAGGTCATCTTTCATCACTTATCAAGATCGACTGGAAACAAGTCATCTTTCAAATTATCAGAGGT
5531 TATCTTTCAACAATTATCAAGATTGACTGGAAA
66 TATCTTTCAACAATTATCAAGATTGACTGGAAA
* * *
5564 CAGGTCATCTTTCAACACTTATCAAGATCGACTGGAAACATGTCATCTTTCAAATTATCTGAGGT
1 CAGGTCATCTTTCATCACTTATCAAGATCGACTGGAAACAAGTCATCTTTCAAATTATCAGAGGT
5629 TATCTTTCAACAATTATCAAGATTGACTGGAAA
66 TATCTTTCAACAATTATCAAGATTGACTGGAAA
* * *
5662 CAGGTCATCTTTCAGT-ACTTGTCAAGTTCGACTGGAAACAGGTCATCTTTCAACAATTATCA
1 CAGGTCATCTTTCA-TCACTTATCAAGATCGACTGGAAACAAGTCATCTTTC-A-AATTATCA
5724 AGATCGACTG
Statistics
Matches: 149, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
98 141 0.95
99 1 0.01
100 7 0.05
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (98 bp):
CAGGTCATCTTTCATCACTTATCAAGATCGACTGGAAACAAGTCATCTTTCAAATTATCAGAGGT
TATCTTTCAACAATTATCAAGATTGACTGGAAA
Found at i:5574 original size:38 final size:38
Alignment explanation
Indices: 5527--5616 Score: 144
Period size: 38 Copynumber: 2.4 Consensus size: 38
5517 AAATTATCAG
* *
5527 AGGTTATCTTTCAACAATTATCAAGATTGACTGGAAAC
1 AGGTCATCTTTCAACAATTATCAAGATCGACTGGAAAC
*
5565 AGGTCATCTTTCAACACTTATCAAGATCGACTGGAAAC
1 AGGTCATCTTTCAACAATTATCAAGATCGACTGGAAAC
*
5603 ATGTCATCTTTCAA
1 AGGTCATCTTTCAA
5617 ATTATCTGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (38 bp):
AGGTCATCTTTCAACAATTATCAAGATCGACTGGAAAC
Found at i:5687 original size:38 final size:38
Alignment explanation
Indices: 5625--5754 Score: 181
Period size: 38 Copynumber: 3.4 Consensus size: 38
5615 AAATTATCTG
* *
5625 AGGTTATCTTTCAACAATTATCAAGATTGACTGGAAAC
1 AGGTCATCTTTCAGCAATTATCAAGATTGACTGGAAAC
* * *
5663 AGGTCATCTTTCAGTACTTGTCAAG-TTCGACTGGAAAC
1 AGGTCATCTTTCAGCAATTATCAAGATT-GACTGGAAAC
* *
5701 AGGTCATCTTTCAACAATTATCAAGATCGACTGGAAAC
1 AGGTCATCTTTCAGCAATTATCAAGATTGACTGGAAAC
5739 AGGTCATCTTTCAGCA
1 AGGTCATCTTTCAGCA
5755 GTTTTCGGTT
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
37 2 0.03
38 76 0.96
39 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (38 bp):
AGGTCATCTTTCAGCAATTATCAAGATTGACTGGAAAC
Found at i:5837 original size:16 final size:15
Alignment explanation
Indices: 5787--5842 Score: 76
Period size: 15 Copynumber: 3.5 Consensus size: 15
5777 GGGCACTCCA
5787 ACAACTTTTCAATTT
1 ACAACTTTTCAATTT
*
5802 ACAACTTTTCAGCTTTT
1 ACAACTTTTCA--ATTT
5819 ACAACTTTTTCAATTT
1 ACAAC-TTTTCAATTT
5835 ACAACTTT
1 ACAACTTT
5843 CAGCATTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
15 14 0.39
16 8 0.22
17 8 0.22
18 6 0.17
ACGTcount: A:0.30, C:0.21, G:0.02, T:0.46
Consensus pattern (15 bp):
ACAACTTTTCAATTT
Found at i:5850 original size:16 final size:17
Alignment explanation
Indices: 5787--5850 Score: 75
Period size: 16 Copynumber: 4.0 Consensus size: 17
5777 GGGCACTCCA
5787 ACAACTTTTCA--ATTT
1 ACAACTTTTCAGCATTT
*
5802 ACAACTTTTCAGCTTTT
1 ACAACTTTTCAGCATTT
5819 ACAACTTTTTCA--ATTT
1 ACAAC-TTTTCAGCATTT
5835 ACAAC-TTTCAGCATTT
1 ACAACTTTTCAGCATTT
5851 CAATTCACAA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
14 5 0.12
15 11 0.26
16 12 0.29
17 8 0.19
18 6 0.14
ACGTcount: A:0.30, C:0.22, G:0.03, T:0.45
Consensus pattern (17 bp):
ACAACTTTTCAGCATTT
Found at i:5967 original size:48 final size:47
Alignment explanation
Indices: 5875--6021 Score: 206
Period size: 47 Copynumber: 3.1 Consensus size: 47
5865 TCAATTGACA
* *
5875 ACTTCCATGTGAGTCA-ACAATCCTTTGACCCAAGTTGGTTTTTCCTC
1 ACTTCCATGTGAGTCAGA-AATCCTTCGACCCAAGTTGGTCTTTCCTC
*
5922 ACTTCCATGTGAGTCAGAAATCGTTCCGACCCAAGTTGGTCTTTCCTC
1 ACTTCCATGTGAGTCAGAAATCCTT-CGACCCAAGTTGGTCTTTCCTC
* * * *
5970 ACTTCCATTTGGGTCAGAAATCCTTCGACCAAAGTTGGTCTTTTCTC
1 ACTTCCATGTGAGTCAGAAATCCTTCGACCCAAGTTGGTCTTTCCTC
6017 ACTTC
1 ACTTC
6022 TATGCAAAGT
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
47 47 0.52
48 43 0.48
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35
Consensus pattern (47 bp):
ACTTCCATGTGAGTCAGAAATCCTTCGACCCAAGTTGGTCTTTCCTC
Found at i:6094 original size:47 final size:48
Alignment explanation
Indices: 5994--6096 Score: 131
Period size: 47 Copynumber: 2.2 Consensus size: 48
5984 CAGAAATCCT
* * * *
5994 TCGACCAAAGTTGGTCTTTTCTCACTTCTATGCAAAGTTACAATTTGG
1 TCGACCACAGTTGGTCTTTGCTCACTTCCATGCAAAGTTACAATTTGA
*
6042 T-GACCACAGTTGGTCTTTGCTCGCTTCCATGC-AAGTCTACAATTT-A
1 TCGACCACAGTTGGTCTTTGCTCACTTCCATGCAAAGT-TACAATTTGA
6088 TCGACCACA
1 TCGACCACA
6097 AACTGTTCTT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
46 5 0.10
47 42 0.88
48 1 0.02
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (48 bp):
TCGACCACAGTTGGTCTTTGCTCACTTCCATGCAAAGTTACAATTTGA
Found at i:6172 original size:60 final size:61
Alignment explanation
Indices: 6086--6205 Score: 188
Period size: 60 Copynumber: 2.0 Consensus size: 61
6076 GTCTACAATT
* * * *
6086 TATCGACCACAAACTGTTCTTCTTCAATTTCAGA-CTTAGACAGGTCTTTCTCAATTTCAA
1 TATCGACCACAAACTGGTCCTATTCAATTTCAGACCTCAGACAGGTCTTTCTCAATTTCAA
*
6146 TATCGACCACAGACTGGTCCTATTCAATTTCAGACCTCAGACAGGTCTTTCTCAATTTCA
1 TATCGACCACAAACTGGTCCTATTCAATTTCAGACCTCAGACAGGTCTTTCTCAATTTCA
6206 TTTATCAAAG
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
60 30 0.56
61 24 0.44
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.34
Consensus pattern (61 bp):
TATCGACCACAAACTGGTCCTATTCAATTTCAGACCTCAGACAGGTCTTTCTCAATTTCAA
Found at i:6186 original size:28 final size:27
Alignment explanation
Indices: 6141--6205 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 27
6131 CTTTCTCAAT
* *
6141 TTCAATATC-GACCACAGACTGGTCCTA
1 TTCAATTTCAGACCACAGACAGGT-CTA
* *
6168 TTCAATTTCAGACCTCAGACAGGTCTT
1 TTCAATTTCAGACCACAGACAGGTCTA
6195 TCTCAATTTCA
1 T-TCAATTTCA
6206 TTTATCAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 11 0.34
28 21 0.66
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (27 bp):
TTCAATTTCAGACCACAGACAGGTCTA
Found at i:7984 original size:22 final size:22
Alignment explanation
Indices: 7959--8005 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
7949 AGACCACTCT
* *
7959 TGCCATGTTACCAAGGCCTTCC
1 TGCCATGTCACCAAAGCCTTCC
7981 TGCCATGTCACCAAAGCCTTCC
1 TGCCATGTCACCAAAGCCTTCC
8003 TGC
1 TGC
8006 AGGGGATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.38, G:0.17, T:0.26
Consensus pattern (22 bp):
TGCCATGTCACCAAAGCCTTCC
Found at i:10036 original size:49 final size:49
Alignment explanation
Indices: 9974--10067 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
9964 CAAAATGCCC
* *
9974 TTCCCGGACGGAAGGCACTAATTTTTACTTGC-TTTTCCCTAAAACACCT
1 TTCCCAGACGGAAGGCACTAATTTTTACCTGCTTTTTCCC-AAAACACCT
* **
10023 TTCCCAGATGGAAGGCACTTGTTTTTACCTGCTTTTTCCCAAAAC
1 TTCCCAGACGGAAGGCACTAATTTTTACCTGCTTTTTCCCAAAAC
10068 GCCCTTTCAG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 32 0.82
50 7 0.18
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.34
Consensus pattern (49 bp):
TTCCCAGACGGAAGGCACTAATTTTTACCTGCTTTTTCCCAAAACACCT
Found at i:10293 original size:63 final size:62
Alignment explanation
Indices: 10224--10381 Score: 176
Period size: 63 Copynumber: 2.5 Consensus size: 62
10214 AAGTTTAGTA
* * * ** ** *
10224 TTCCAAAAATACTCTTTCAGACAAAGGG-CTAGTTTTGTTACATCCT-AGTGTATAGTTTCTAT
1 TTCCCAAAATACCCTTTCGGACAAAGGGTC-AGTTTTGCCACATCCTCA-CATATAGTTTCAAT
*
10286 TTCCCAAAATACACCTTTTGGACAAAGGGTCAGTTTTGCCACATCCTCACATATAGTTTCAAT
1 TTCCCAAAATAC-CCTTTCGGACAAAGGGTCAGTTTTGCCACATCCTCACATATAGTTTCAAT
* *
10349 TTCCCAGAATACCCTTTCGGATAAAGGGTCAGT
1 TTCCCAAAATACCCTTTCGGACAAAGGGTCAGT
10382 CCAGTCACAC
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
62 30 0.37
63 49 0.60
64 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (62 bp):
TTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGCCACATCCTCACATATAGTTTCAAT
Found at i:10399 original size:62 final size:63
Alignment explanation
Indices: 10274--10399 Score: 157
Period size: 62 Copynumber: 2.0 Consensus size: 63
10264 CATCCTAGTG
* * ***
10274 TATAGTTTCTATTTCCCAAAATACACCTTTTGGACAAAGGGTCAGTTTTGCCACATCCTCACA
1 TATAGTTTCAATTTCCCAAAATACACCTTTCGGACAAAGGGTCAGTCCAGCCACATCCTCACA
* * *
10337 TATAGTTTCAATTTCCCAGAATAC-CCTTTCGGATAAAGGGTCAGTCCAGTCACACTCC-CACA
1 TATAGTTTCAATTTCCCAAAATACACCTTTCGGACAAAGGGTCAGTCCAGCCACA-TCCTCACA
10399 T
1 T
10400 TTAATTTCTG
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
62 29 0.54
63 25 0.46
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (63 bp):
TATAGTTTCAATTTCCCAAAATACACCTTTCGGACAAAGGGTCAGTCCAGCCACATCCTCACA
Done.