Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024561.1 Corchorus olitorius cultivar O-4 contig24594, 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: 18028
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1453 original size:76 final size:76
Alignment explanation
Indices: 1316--1467 Score: 175
Period size: 76 Copynumber: 2.0 Consensus size: 76
1306 ACAAGGACCC
* * *
1316 CGACTCTACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
1381 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * **
1392 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
1454 GATGGGCTGTGTCA
63 GATGGGCAGTGTCA
1468 TAGCTCATCA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
75 4 0.06
76 54 0.84
77 6 0.09
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:2525 original size:4 final size:4
Alignment explanation
Indices: 2516--2542 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2506 TTTTCTTAAT
2516 ATTA ATTA ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATT
2543 TTTTTTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:4879 original size:21 final size:21
Alignment explanation
Indices: 4855--4899 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4845 GTAAGTGATG
*
4855 AAGT-AGTGAAATTGATGATTA
1 AAGTGAGTGAAATTG-TGAATA
*
4876 AAGTGAGTGAATTTGTGAATA
1 AAGTGAGTGAAATTGTGAATA
4897 AAG
1 AAG
4900 GTATTAGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (21 bp):
AAGTGAGTGAAATTGTGAATA
Found at i:11018 original size:22 final size:22
Alignment explanation
Indices: 10960--11020 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
10950 CATAGCCCAG
* *
10960 GCCGCTTGGCCCTGAGCTGCTA
1 GCCGCTTGGGCCTGCGCTGCTA
*
10982 GCCGCCTGGGCCTGCGCTGCTA
1 GCCGCTTGGGCCTGCGCTGCTA
*
11004 GCCTCTTGGGCCTGCGC
1 GCCGCTTGGGCCTGCGC
11021 GCGGCCCAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.05, C:0.39, G:0.34, T:0.21
Consensus pattern (22 bp):
GCCGCTTGGGCCTGCGCTGCTA
Found at i:11161 original size:14 final size:13
Alignment explanation
Indices: 11144--11199 Score: 64
Period size: 14 Copynumber: 4.4 Consensus size: 13
11134 GGAAGGGAAA
11144 AAAAGAAGAAAAAG
1 AAAAG-AGAAAAAG
*
11158 AAAAGAGAAATGAG
1 AAAAGAGAAA-AAG
11172 AAAAGAGAAAAAG
1 AAAAGAGAAAAAG
11185 -AAA-A-AAAAAG
1 AAAAGAGAAAAAG
11195 AAAAG
1 AAAAG
11200 TAAAGGGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
10 6 0.16
11 4 0.11
12 3 0.08
13 7 0.19
14 17 0.46
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (13 bp):
AAAAGAGAAAAAG
Found at i:11172 original size:7 final size:7
Alignment explanation
Indices: 11144--11188 Score: 58
Period size: 7 Copynumber: 6.6 Consensus size: 7
11134 GGAAGGGAAA
11144 AAAAGAAG
1 AAAAG-AG
11152 AAAA-AG
1 AAAAGAG
11158 AAAAGAG
1 AAAAGAG
*
11165 AAATGAG
1 AAAAGAG
11172 AAAAGAG
1 AAAAGAG
11179 AAAA-AG
1 AAAAGAG
11185 AAAA
1 AAAA
11189 AAAAAGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 12 0.35
7 18 0.53
8 4 0.12
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (7 bp):
AAAAGAG
Found at i:15864 original size:19 final size:19
Alignment explanation
Indices: 15840--15876 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
15830 GATCGTCGTA
15840 TTTGTATATTTATGGTCCT
1 TTTGTATATTTATGGTCCT
15859 TTTGTATATTTATGGTCC
1 TTTGTATATTTATGGTCC
15877 CTAAGTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.57
Consensus pattern (19 bp):
TTTGTATATTTATGGTCCT
Done.