Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016177.1 Corchorus olitorius cultivar O-4 contig16210, 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: 8395
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.31
Found at i:315 original size:154 final size:154
Alignment explanation
Indices: 35--345 Score: 586
Period size: 154 Copynumber: 2.0 Consensus size: 154
25 TTTTATTTAT
*
35 TAAATGTTAGGTGATCCCTCGTGTTCCTTACTTTTTATATTTTAAACAATCCAAACAAGGATTGA
1 TAAATGTTAGGTGATCCCTCATGTTCCTTACTTTTTATATTTTAAACAATCCAAACAAGGATTGA
*
100 TCCTTCCCTTCCTTTCCTTTAAAAAACCCTCCTTTCCCATCCTATCATGTCCTATACTGATCCCT
66 TCATTCCCTTCCTTTCCTTTAAAAAACCCTCCTTTCCCATCCTATCATGTCCTATACTGATCCCT
165 CAAAAAGTTTATCCAAACACACTG
131 CAAAAAGTTTATCCAAACACACTG
*
189 TAAATGTTAGGTGATCCCTCATGTTCCTTACTTTTTATATTTTAAACAATCCAAACAAGGATTGG
1 TAAATGTTAGGTGATCCCTCATGTTCCTTACTTTTTATATTTTAAACAATCCAAACAAGGATTGA
*
254 TCATTCCCTTCCTTTCCTTTAAAAAACCCTCCTTTCCCATCCTATCTTGTCCTATACTGATCCCT
66 TCATTCCCTTCCTTTCCTTTAAAAAACCCTCCTTTCCCATCCTATCATGTCCTATACTGATCCCT
319 CAAAAAGTTTATCCAAACACACTG
131 CAAAAAGTTTATCCAAACACACTG
343 TAA
1 TAA
346 GAATAATATT
Statistics
Matches: 153, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
154 153 1.00
ACGTcount: A:0.28, C:0.27, G:0.08, T:0.36
Consensus pattern (154 bp):
TAAATGTTAGGTGATCCCTCATGTTCCTTACTTTTTATATTTTAAACAATCCAAACAAGGATTGA
TCATTCCCTTCCTTTCCTTTAAAAAACCCTCCTTTCCCATCCTATCATGTCCTATACTGATCCCT
CAAAAAGTTTATCCAAACACACTG
Found at i:478 original size:32 final size:32
Alignment explanation
Indices: 437--500 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
427 ACACAAGGTC
*
437 TCAAATCTAAAACCTGTTTAAGTTGGAACATA
1 TCAAATCTAAAACCTGCTTAAGTTGGAACATA
469 TCAAATCTAAAACCTGCTTAAGTTGGAACATA
1 TCAAATCTAAAACCTGCTTAAGTTGGAACATA
501 CCACTTAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (32 bp):
TCAAATCTAAAACCTGCTTAAGTTGGAACATA
Found at i:2774 original size:38 final size:40
Alignment explanation
Indices: 2732--2807 Score: 111
Period size: 38 Copynumber: 1.9 Consensus size: 40
2722 GACACATACC
* *
2732 CATTTTCAAATTAATTATTT-T-TTAATTAATATTTAAAT
1 CATTTCCAAATTAATTATTTATAGTAATTAATATTTAAAT
2770 CATTTCCAAATTAATTATTTAATAGTAATTAATATTTA
1 CATTTCCAAATTAATTATTT-ATAGTAATTAATATTTA
2808 GATCTATTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 19 0.58
40 1 0.03
41 13 0.39
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (40 bp):
CATTTCCAAATTAATTATTTATAGTAATTAATATTTAAAT
Found at i:3028 original size:43 final size:43
Alignment explanation
Indices: 2980--3107 Score: 233
Period size: 43 Copynumber: 3.0 Consensus size: 43
2970 ACTCATGAAC
2980 ATGATTAGAATTTAGGCACTTCCAATACTAAATATTTTTTTCT
1 ATGATTAGAATTTAGGCACTTCCAATACTAAATATTTTTTTCT
3023 ATGATTAGAATTTAGGCACTTCCAATACTAAATA--TTTTTCT
1 ATGATTAGAATTTAGGCACTTCCAATACTAAATATTTTTTTCT
*
3064 ATGATTAGAATTTAGGTACTTCCAATACTAAATATTTTTTTCT
1 ATGATTAGAATTTAGGCACTTCCAATACTAAATATTTTTTTCT
3107 A
1 A
3108 CTCATGAACA
Statistics
Matches: 82, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
41 40 0.49
43 42 0.51
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (43 bp):
ATGATTAGAATTTAGGCACTTCCAATACTAAATATTTTTTTCT
Found at i:3073 original size:41 final size:41
Alignment explanation
Indices: 2980--3102 Score: 219
Period size: 41 Copynumber: 3.0 Consensus size: 41
2970 ACTCATGAAC
2980 ATGATTAGAATTTAGGCACTTCCAATACTAAATATTTTTTTCT
1 ATGATTAGAATTTAGGCACTTCCAATACTAAATA--TTTTTCT
3023 ATGATTAGAATTTAGGCACTTCCAATACTAAATATTTTTCT
1 ATGATTAGAATTTAGGCACTTCCAATACTAAATATTTTTCT
*
3064 ATGATTAGAATTTAGGTACTTCCAATACTAAATATTTTT
1 ATGATTAGAATTTAGGCACTTCCAATACTAAATATTTTT
3103 TTCTACTCAT
Statistics
Matches: 79, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
41 45 0.57
43 34 0.43
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (41 bp):
ATGATTAGAATTTAGGCACTTCCAATACTAAATATTTTTCT
Found at i:4429 original size:15 final size:15
Alignment explanation
Indices: 4409--4439 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4399 CTGGACAGAA
4409 TGTTACAAATTCGGT
1 TGTTACAAATTCGGT
4424 TGTTACAAATTCGGT
1 TGTTACAAATTCGGT
4439 T
1 T
4440 CAATTTAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (15 bp):
TGTTACAAATTCGGT
Found at i:6567 original size:16 final size:16
Alignment explanation
Indices: 6546--6587 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
6536 AAAGTTAATG
6546 GAATAAAATCTCCTAA
1 GAATAAAATCTCCTAA
6562 GAATAAAATCTCCTAA
1 GAATAAAATCTCCTAA
6578 GAATAAAATC
1 GAATAAAATC
6588 AAGCACATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.52, C:0.17, G:0.07, T:0.24
Consensus pattern (16 bp):
GAATAAAATCTCCTAA
Done.