Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020133.1 Corchorus olitorius cultivar O-4 contig20166, 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: 10416
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:6079 original size:76 final size:72
Alignment explanation
Indices: 5946--6093 Score: 199
Period size: 76 Copynumber: 2.0 Consensus size: 72
5936 TTTATCTGGA
* * *
5946 TTGTGAGCAAAGGAATGATGAGTTTTAATCAAAATTTTCAAAATCAGTTTTAATCAAAACTATGA
1 TTGTGAGCAAAGGAATGACGAGTTTAAATCAAAATTTTCAAAATCAGTTTTAATCAAAACAATGA
6011 TTTCGAG
66 TTTCGAG
**
6018 TTGTGAGCAAAGGAATGACG-GTGTCTAAATCAAAAGATGTTTCAAAATCAGTTTTGGTCAAAAC
1 TTGTGAGCAAAGGAATGACGAGT-T-TAAATC-AAA-AT-TTTCAAAATCAGTTTTAATCAAAAC
6082 AATGATTTCGAG
61 AATGATTTCGAG
6094 GTGACTGAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
71 2 0.03
72 20 0.30
73 5 0.08
74 3 0.05
75 2 0.03
76 34 0.52
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (72 bp):
TTGTGAGCAAAGGAATGACGAGTTTAAATCAAAATTTTCAAAATCAGTTTTAATCAAAACAATGA
TTTCGAG
Found at i:6515 original size:20 final size:20
Alignment explanation
Indices: 6493--6529 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6483 AAAAATAAAA
6493 AAAAAG-AAATGAAAAAATG
1 AAAAAGAAAATGAAAAAATG
6512 AAAAAGAAAATGAAAAAA
1 AAAAAGAAAATGAAAAAA
6530 GCACTTGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (20 bp):
AAAAAGAAAATGAAAAAATG
Found at i:6903 original size:11 final size:11
Alignment explanation
Indices: 6887--6947 Score: 74
Period size: 10 Copynumber: 5.7 Consensus size: 11
6877 CTCCATCAAG
6887 AAATTCAAAAA
1 AAATTCAAAAA
6898 AAATTC-AAAA
1 AAATTCAAAAA
6908 AAATTC-AAAA
1 AAATTCAAAAA
6918 AAA-TCAAATAA
1 AAATTCAAA-AA
**
6929 AAAAACAAAAA
1 AAATTCAAAAA
6940 AAATTCAA
1 AAATTCAA
6948 TTAAAAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
9 2 0.05
10 19 0.43
11 19 0.43
12 4 0.09
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:6930 original size:22 final size:23
Alignment explanation
Indices: 6892--6956 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
6882 TCAAGAAATT
**
6892 CAAAAAAAATTC-AA-AAAAATT
1 CAAAAAAAATTCAAATAAAAAAA
6913 C-AAAAAAA-TCAAATAAAAAAA
1 CAAAAAAAATTCAAATAAAAAAA
*
6934 CAAAAAAAATTCAATTAAAAAAA
1 CAAAAAAAATTCAAATAAAAAAA
6957 ATCAAATCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 2 0.05
20 9 0.24
21 7 0.19
22 7 0.19
23 12 0.32
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.15
Consensus pattern (23 bp):
CAAAAAAAATTCAAATAAAAAAA
Found at i:7681 original size:50 final size:50
Alignment explanation
Indices: 7606--7701 Score: 165
Period size: 50 Copynumber: 1.9 Consensus size: 50
7596 TTACAATAAA
* * *
7606 ATTGCTTTTCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAGTAAG
1 ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTTCAAAGTAAG
7656 ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTTCAAAG
1 ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTTCAAAG
7702 GGGATTTAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (50 bp):
ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTTCAAAGTAAG
Found at i:8134 original size:12 final size:12
Alignment explanation
Indices: 8117--8144 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
8107 ATCAGACCAG
8117 AGTTATTTTTCA
1 AGTTATTTTTCA
8129 AGTTATTTTTCA
1 AGTTATTTTTCA
8141 AGTT
1 AGTT
8145 GACCGCACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.57
Consensus pattern (12 bp):
AGTTATTTTTCA
Found at i:8379 original size:69 final size:69
Alignment explanation
Indices: 8301--8636 Score: 510
Period size: 69 Copynumber: 4.9 Consensus size: 69
8291 CGAATGCTTT
*
8301 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCAAAGCCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCCA
8366 CATA
66 CATA
*
8370 GGCTTTTCCACAAGCCAAACTCATTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCCA
8435 CATA
66 CATA
* *
8439 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAATCCTTGGTTCCATCCAAGCCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCCA
*
8504 TATA
66 CATA
* * * *
8508 GGCTATTCCACAAGCCAAATTCGTTTCCACACGAGTCAGTTCAGGCCTTGGTTCCATCCAAGCCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCCA
*
8573 TATA
66 CATA
* * * * * * * *
8577 GACTTTTCCATAAGTCAAACTCGTTTCCATGCGAGTCAGTTTAAACATTGGGTCCATCCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCA
8637 TACAGTAGAG
Statistics
Matches: 243, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 243 1.00
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (69 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCCA
CATA
Done.