Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016087.1 Corchorus olitorius cultivar O-4 contig16120, 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: 48859
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2159 original size:27 final size:28
Alignment explanation
Indices: 2101--2166 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
2091 AAAAGTACAC
* **
2101 AAAATTATATTTTAATAATGGTATAGTT
1 AAAAATATATTTTAATAATGACATAGTT
*
2129 -AAAATATATTTTAATAATGACA-ATTT
1 AAAAATATATTTTAATAATGACATAGTT
*
2155 AAAAATACATTT
1 AAAAATATATTT
2167 GAAAAAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
26 3 0.09
27 29 0.91
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (28 bp):
AAAAATATATTTTAATAATGACATAGTT
Found at i:2249 original size:95 final size:98
Alignment explanation
Indices: 2089--2269 Score: 278
Period size: 95 Copynumber: 1.9 Consensus size: 98
2079 ATATATTTGA
** **
2089 AAAAAAGTACACAAAATTATATTTTAATAATGGTATAGTTAAAATATATTTTAATAATGACAATT
1 AAAAAAGTACACAAAATTATATTTTAATAATGACATAAATAAAATATATTTTAATAATGACAATT
2154 TAAAAATACATTTGAAAAAAATAGTACAATCGG
66 TAAAAATACATTTGAAAAAAATAGTACAATCGG
*
2187 AAAAAA-TACATAAAATTATATTTTAATAATGACATAAAT-AAA-ATATTTTAATAATGACAATT
1 AAAAAAGTACACAAAATTATATTTTAATAATGACATAAATAAAATATATTTTAATAATGACAATT
* *
2249 TAGAAATATATTTGAAAAAAA
66 TAAAAATACATTTGAAAAAAA
2270 GGGTATAATC
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
95 39 0.51
96 3 0.04
97 28 0.37
98 6 0.08
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (98 bp):
AAAAAAGTACACAAAATTATATTTTAATAATGACATAAATAAAATATATTTTAATAATGACAATT
TAAAAATACATTTGAAAAAAATAGTACAATCGG
Found at i:3835 original size:19 final size:19
Alignment explanation
Indices: 3811--3850 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
3801 TATTACCAGC
*
3811 TCAACCAAGTATCAATTGA
1 TCAACCAACTATCAATTGA
3830 TCAACCAACTATCAATTGA
1 TCAACCAACTATCAATTGA
3849 TC
1 TC
3851 GGCAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.28
Consensus pattern (19 bp):
TCAACCAACTATCAATTGA
Found at i:4283 original size:2 final size:2
Alignment explanation
Indices: 4276--4309 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4266 TTGCCTTTAA
4276 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4310 GAATGGCTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4430 original size:6 final size:6
Alignment explanation
Indices: 4419--4448 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
4409 CTAGGCCGGG
4419 CAATGC CAATGC CAATGC CAATGC CAATGC
1 CAATGC CAATGC CAATGC CAATGC CAATGC
4449 ATGAGTCGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17
Consensus pattern (6 bp):
CAATGC
Found at i:6617 original size:23 final size:23
Alignment explanation
Indices: 6587--6636 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
6577 TATACATATA
*
6587 TATATATATATATAACCCAATTAAT
1 TATATA-ATAT-TAAACCAATTAAT
*
6612 TATATAATATTAAAGCAATTAAT
1 TATATAATATTAAACCAATTAAT
6635 TA
1 TA
6637 GATCCATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 13 0.57
24 4 0.17
25 6 0.26
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (23 bp):
TATATAATATTAAACCAATTAAT
Found at i:13296 original size:6 final size:6
Alignment explanation
Indices: 13285--13343 Score: 118
Period size: 6 Copynumber: 9.8 Consensus size: 6
13275 ATGTTTCAGC
13285 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT
13333 ATATTT ATATT
1 ATATTT ATATT
13344 AATTAATATG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATATTT
Found at i:23420 original size:19 final size:19
Alignment explanation
Indices: 23370--23420 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
23360 TGTGGAATTT
23370 TTAATAA-TAATTATTCAA
1 TTAATAATTAATTATTCAA
* *
23388 TAAAATAATT-ATTATTTAA
1 T-TAATAATTAATTATTCAA
23407 TTAATAATTAATTA
1 TTAATAATTAATTA
23421 ATTTCAGCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.30
19 18 0.67
20 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATAATTAATTATTCAA
Found at i:23791 original size:13 final size:13
Alignment explanation
Indices: 23773--23798 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23763 AAAGTAACAA
23773 CAAAAATCATCAC
1 CAAAAATCATCAC
23786 CAAAAATCATCAC
1 CAAAAATCATCAC
23799 TCATGCCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:28950 original size:22 final size:23
Alignment explanation
Indices: 28891--28945 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
28881 GCAAATAATA
28891 AAAAAAATGAAAAATATGCAAAC
1 AAAAAAATGAAAAATATGCAAAC
* *
28914 AAAAAAAAGAAAAATATGTAAAC
1 AAAAAAATGAAAAATATGCAAAC
28937 AAAAAAATG
1 AAAAAAATG
28946 CAAATTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.73, C:0.05, G:0.09, T:0.13
Consensus pattern (23 bp):
AAAAAAATGAAAAATATGCAAAC
Found at i:36170 original size:9 final size:9
Alignment explanation
Indices: 36156--36189 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
36146 TATTTGAACT
36156 TTTTTTGTC
1 TTTTTTGTC
36165 TTTTTTGTC
1 TTTTTTGTC
*
36174 ATTTTCTGTC
1 -TTTTTTGTC
36184 TTTTTT
1 TTTTTT
36190 CACTTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.03, C:0.12, G:0.09, T:0.76
Consensus pattern (9 bp):
TTTTTTGTC
Found at i:40649 original size:10 final size:10
Alignment explanation
Indices: 40622--40660 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
40612 ATCTACCTCA
*
40622 TAAGCTCCAC
1 TAAGCTCTAC
40632 TAAGCTCTAC
1 TAAGCTCTAC
*
40642 TAAGCTCTAT
1 TAAGCTCTAC
*
40652 TATGCTCTA
1 TAAGCTCTA
40661 TCACACCCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.33
Consensus pattern (10 bp):
TAAGCTCTAC
Found at i:47152 original size:23 final size:23
Alignment explanation
Indices: 47122--47168 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
47112 GATAAGCAGC
47122 TAGGATGAATTCATGCTGTCTCG
1 TAGGATGAATTCATGCTGTCTCG
47145 TAGGATGAATTCATGCTGTCTCG
1 TAGGATGAATTCATGCTGTCTCG
47168 T
1 T
47169 CTGCCAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (23 bp):
TAGGATGAATTCATGCTGTCTCG
Done.