Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019048.1 Corchorus olitorius cultivar O-4 contig19081, 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: 64452
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Found at i:15293 original size:2 final size:2
Alignment explanation
Indices: 15247--15273 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15237 TATTACTAGC
15247 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
15274 TCTTTCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19062 original size:2 final size:2
Alignment explanation
Indices: 19046--19080 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
19036 CTGGTACTCC
* *
19046 TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19081 GTATGTATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:19880 original size:49 final size:49
Alignment explanation
Indices: 19790--19988 Score: 254
Period size: 49 Copynumber: 4.0 Consensus size: 49
19780 AGAGTGAATT
** * *
19790 GGATAAGCGGAAGACGGTTATTTTTAGAGTGAATTGGAAGACAGTTCAAA
1 GGATAAGCGGAAGACGG-TCCTTTAAGAGTGAATTGGAAGACAATTCAAA
* * *
19840 GGATAAACGGAAGACGGTCCTTTAAGAGTGAATTGGAAGACAGTTGAAA
1 GGATAAGCGGAAGACGGTCCTTTAAGAGTGAATTGGAAGACAATTCAAA
* * *
19889 AGATAAGCGGAAGATGGTCCTTTAAGATTGAATTGGAAGACAATTCAAA
1 GGATAAGCGGAAGACGGTCCTTTAAGAGTGAATTGGAAGACAATTCAAA
* **
19938 GGATAAGCGGAAGACGGTCCTTTTTATGTTTGAATTGGAAGACAATTCAAA
1 GGATAAGCGGAAGACGGTCC--TTTAAGAGTGAATTGGAAGACAATTCAAA
19989 TAAGTTGATT
Statistics
Matches: 132, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
49 89 0.67
50 16 0.12
51 27 0.20
ACGTcount: A:0.37, C:0.10, G:0.28, T:0.25
Consensus pattern (49 bp):
GGATAAGCGGAAGACGGTCCTTTAAGAGTGAATTGGAAGACAATTCAAA
Found at i:45404 original size:27 final size:25
Alignment explanation
Indices: 45347--45419 Score: 85
Period size: 27 Copynumber: 2.9 Consensus size: 25
45337 GTTTTGTGTC
45347 TTGCGTTTT-TGAAAAAAAAAAGTT
1 TTGCGTTTTCTGAAAAAAAAAAGTT
* * *
45371 TTACGTTTTCTTAAAAAAAAATTGTT
1 TTGCGTTTTCTGAAAAAAAAA-AGTT
*
45397 TCTGCGTTTTCAGAAAAAAAAAA
1 T-TGCGTTTTCTGAAAAAAAAAA
45420 TTATTTTCCT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
24 8 0.21
25 10 0.26
26 4 0.10
27 17 0.44
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.37
Consensus pattern (25 bp):
TTGCGTTTTCTGAAAAAAAAAAGTT
Found at i:46026 original size:27 final size:24
Alignment explanation
Indices: 45966--46032 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 24
45956 GGTTATCCAG
45966 GGGCATTTTGGTCATTTGCACATCTA
1 GGGCA-TTTGGTCATTTGCACATC-A
*
45992 GAGGCATTTGAGTCATTTGCACGTTCA
1 G-GGCATTTG-GTCATTTGCAC-ATCA
46019 GGGACATTTTGGTC
1 GGG-CA-TTTGGTC
46033 TTTTAAGTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
26 7 0.20
27 22 0.63
28 6 0.17
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (24 bp):
GGGCATTTGGTCATTTGCACATCA
Found at i:48812 original size:40 final size:41
Alignment explanation
Indices: 48724--48817 Score: 136
Period size: 41 Copynumber: 2.3 Consensus size: 41
48714 TGTTTCCGTG
* *
48724 TTCAATATGGTCCCTAATTTAGGATTCTATTTACTATTTGA
1 TTCAATTTGGTCCCTAATTTAGGATTCTAGTTACTATTTGA
* * *
48765 TACAATTTAGTCCCTGATTTAGGATTCTAGTT-CTATTTGA
1 TTCAATTTGGTCCCTAATTTAGGATTCTAGTTACTATTTGA
48805 TTCAATTTGGTCC
1 TTCAATTTGGTCC
48818 TTATTTTTCT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 19 0.41
41 27 0.59
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (41 bp):
TTCAATTTGGTCCCTAATTTAGGATTCTAGTTACTATTTGA
Found at i:58911 original size:30 final size:30
Alignment explanation
Indices: 58877--58937 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
58867 TACCCTTTTT
58877 TGTAATTACTCATTTCCTTTCCTTAATTGC
1 TGTAATTACTCATTTCCTTTCCTTAATTGC
*
58907 TGTAATTACTCATTTCTTTTCCTTAATTGC
1 TGTAATTACTCATTTCCTTTCCTTAATTGC
58937 T
1 T
58938 TGTAGTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.21, G:0.07, T:0.52
Consensus pattern (30 bp):
TGTAATTACTCATTTCCTTTCCTTAATTGC
Found at i:60007 original size:10 final size:10
Alignment explanation
Indices: 59994--60018 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
59984 TTAACATTTC
59994 AAATCCTCTG
1 AAATCCTCTG
60004 AAATCCTCTG
1 AAATCCTCTG
60014 AAATC
1 AAATC
60019 TTCAAGCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (10 bp):
AAATCCTCTG
Found at i:63423 original size:36 final size:37
Alignment explanation
Indices: 63299--63425 Score: 132
Period size: 36 Copynumber: 3.4 Consensus size: 37
63289 CTCAACATCT
** *
63299 CAGCCTCTCTCTCCCTCTCCCTCTGAATCTAAGCAGCAG
1 CAGCCTCTCTCTCCCTCTGACTCTG-AGC-AAGCAGCAG
*** *
63338 CAGCCTCTCTCTCAAGCTGACTCTGAGC-AGCAGTAG
1 CAGCCTCTCTCTCCCTCTGACTCTGAGCAAGCAGCAG
* * *
63374 AAGCCTCTGTCTCCCTCTGACTCTGAGCAAG-AACAG
1 CAGCCTCTCTCTCCCTCTGACTCTGAGCAAGCAGCAG
63410 CAGCCTCTCTCTCCCT
1 CAGCCTCTCTCTCCCT
63426 ATAACTCCGA
Statistics
Matches: 71, Mismatches: 16, Indels: 5
0.77 0.17 0.05
Matches are distributed among these distances:
36 47 0.66
37 2 0.03
38 2 0.03
39 20 0.28
ACGTcount: A:0.20, C:0.39, G:0.17, T:0.24
Consensus pattern (37 bp):
CAGCCTCTCTCTCCCTCTGACTCTGAGCAAGCAGCAG
Done.