Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015982.1 Corchorus olitorius cultivar O-4 contig16015, 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: 43604
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:759 original size:334 final size:333
Alignment explanation
Indices: 1--1052 Score: 1472
Period size: 333 Copynumber: 3.1 Consensus size: 333
* * * *
1 GATACTTGTAAAAATAAATCCGTAAATGCGTTGTGGTTGAGAGATTTGATTAGATGAATTTAGAT
1 GATACTTGTAAAAATAAATCCGTAAATCCATTGTGGCT-AGAGATTTGATTAGATGAATATAGAT
** *
66 ATTTCGAGAAGTCTTTCTATCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCATTTTTA
65 ATTTCGAGAAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTA
*
131 GCTAAAAA-TCGTGAT-G-ACGTACACGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAA
130 GC-AAAAACT-GTGATGGTAC-TACACGATTTAGGCTAAAATTTTGCAAAAAACTGACCCGAAAA
* * *
193 GTTTTTCCCCCATTTTTTGCCACAATACACAGAAAAATCATATAATTCAACGCCATAACTATTTT
192 GTTTTTCCCCAATTTTTTGCCACAATACTCAGAAAAATCATATAATTCAACGCCAAAACTATTTT
* *
258 AGGGTTTTTCACGCTTCTAATATCGTTTTTCC-ATTTTTTTCTAAATTTATTTCAAATTAAATCG
257 AGGGTATTTCACGCTTCTAATATCGTTTTTCCAATTTTTTTCTAAATTTATTTCTAATTAAATCG
322 AAACAAGATTCA
322 AAACAAGATTCA
334 GATACTTGTAAAAATAAATCCGTAAATCCATTGTGGCTGAGAGATTTGATTAGATGAATATAGAT
1 GATACTTGTAAAAATAAATCCGTAAATCCATTGTGGCT-AGAGATTTGATTAGATGAATATAGAT
* * * *
399 ATTTAGAGAAGTCTTTCTGCCAAAAATCAAGCAGAACTGA-TGAGGGCCCCGAAACGCATTTTTA
65 ATTTCGAGAAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTA
* * *
463 GCAAAAAACTGTGATGGTTACTACACGATTTTGGCTAAAATTTTGCAAAAAACTGAACCGAAATG
130 GC-AAAAACTGTGATGG-TACTACACGATTTAGGCTAAAATTTTGCAAAAAACTGACCCGAAAAG
* * *
528 CTTTTGT-CCCAATTTTTTGCCACAATACTCAAAAAAATCATATAATTAAACGCCAAAAATATTT
193 -TTTT-TCCCCAATTTTTTGCCACAATACTCAGAAAAATCATATAATTCAACGCCAAAACTATTT
* *
592 TAGGATGTTTCACGCTTCTAATATCG-TTTTCCAATTTGTTTTCTAAATTTATTTCTAATTAAAT
256 TAGGGTATTTCACGCTTCTAATATCGTTTTTCCAATTT-TTTTCTAAATTTATTTCTAATTAAAT
**
656 CTTAACAAGATTCA
320 CGAAACAAGATTCA
* * * * * *
670 AATGCTCGTAAAAACAAATCCGTAAATCCAATGTGGCT-GAGATTTGGTTAGATGAATATAGATA
1 GATACTTGTAAAAATAAATCCGTAAATCCATTGTGGCTAGAGATTTGATTAGATGAATATAGATA
* * *
734 TTTCGAGAAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCATGGTCCCGAAACGCGTTTTTAG
66 TTTCGAGAAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAG
* * *
799 CCAAATCTGTGATGGTAGTACACGATTTAGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGTTT
131 CAAAAACTGTGATGGTACTACACGATTTAGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGTTT
* *
864 TTCCCCAATTTCTTGGCACAATACTCAGAAAAATCATATAATTCAACGCCAAAACTATTTTAGGG
196 TTCCCCAATTTTTTGCCACAATACTCAGAAAAATCATATAATTCAACGCCAAAACTATTTTAGGG
* *
929 TATTTCACGTTTCTAATATCGTTTTTCCAATGTTTTTTTTTTCTGAATTTATTTCTAATTAAATC
261 TATTTCACGCTTCTAATATCGTTTTTCCAA-----TTTTTTTCTAAATTTATTTCTAATTAAATC
*
994 GAAATAAGATTCA
321 GAAACAAGATTCA
* * * *
1007 GATACTTGTAAAAATAAATCAGTAAATGCGTTGTGGTTGAGAGATT
1 GATACTTGTAAAAATAAATCCGTAAATCCATTGTGGCT-AGAGATT
1053 ATATCTAGTA
Statistics
Matches: 635, Mismatches: 66, Indels: 30
0.87 0.09 0.04
Matches are distributed among these distances:
331 1 0.00
332 113 0.18
333 149 0.23
334 120 0.19
335 107 0.17
336 71 0.11
337 65 0.10
338 3 0.00
339 6 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (333 bp):
GATACTTGTAAAAATAAATCCGTAAATCCATTGTGGCTAGAGATTTGATTAGATGAATATAGATA
TTTCGAGAAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAG
CAAAAACTGTGATGGTACTACACGATTTAGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGTTT
TTCCCCAATTTTTTGCCACAATACTCAGAAAAATCATATAATTCAACGCCAAAACTATTTTAGGG
TATTTCACGCTTCTAATATCGTTTTTCCAATTTTTTTCTAAATTTATTTCTAATTAAATCGAAAC
AAGATTCA
Found at i:41756 original size:29 final size:31
Alignment explanation
Indices: 41724--41790 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
41714 ATGCAATTTG
41724 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
*
41753 GGATATAACGTTACGAAAAGCGAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
41784 GGATATA
1 GGATATA
41791 GTCCGTTAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (31 bp):
GGATATAACGTTACGAAAAGCAAGCAATTAA
Found at i:41957 original size:31 final size:31
Alignment explanation
Indices: 41922--41995 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
41912 CTAACTGATT
** *
41922 ATATCCTTAATTGCTTAAAATCGAAAATGTC
1 ATATCCTTAATTGCTTAAAATAAAAAACGTC
* * *
41953 ATATCCCTAATTGCTTGAAATAAAAAACGTT
1 ATATCCTTAATTGCTTAAAATAAAAAACGTC
41984 ATATCCTTAATT
1 ATATCCTTAATT
41996 ACTTGTTTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.36
Consensus pattern (31 bp):
ATATCCTTAATTGCTTAAAATAAAAAACGTC
Found at i:43078 original size:31 final size:30
Alignment explanation
Indices: 43063--43170 Score: 101
Period size: 31 Copynumber: 3.6 Consensus size: 30
43053 GTTTGCTGCC
43063 ACAAGCAATTAAGGATATAACG-TTACAAA
1 ACAAGCAATTAAGGATATAACGTTTACAAA
** **
43092 ACAAGCAATTAAGGATATAACGTTTTTTATT
1 ACAAGCAATTAAGGATATAACG-TTTACAAA
* * * **
43123 TCAAGCAATTAAGGATATGACGTTTTCGATT
1 ACAAGCAATTAAGGATATAACGTTTAC-AAA
*
43154 TCAAGCAATTAAGGATA
1 ACAAGCAATTAAGGATA
43171 AATCAGTTAG
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
29 22 0.32
30 4 0.06
31 43 0.62
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.31
Consensus pattern (30 bp):
ACAAGCAATTAAGGATATAACGTTTACAAA
Found at i:43376 original size:29 final size:31
Alignment explanation
Indices: 43302--43368 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
43292 CCTAACGGAC
43302 TATATCCTTAATTGCTCGTTTTTCGTAACGT
1 TATATCCTTAATTGCTCGTTTTTCGTAACGT
*
43333 TATATCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCTTAATTGCTCGTTTTTCGTAACGT
43362 TATATCC
1 TATATCC
43369 CAAATTGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.49
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGTTTTTCGTAACGT
Done.