Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012035.1 Corchorus olitorius cultivar O-4 contig12068, 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: 23914
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:708 original size:124 final size:126
Alignment explanation
Indices: 487--734 Score: 412
Period size: 124 Copynumber: 1.9 Consensus size: 126
477 ATTTAAGAAA
487 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGT---AATAAAA
552 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
63 T--GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
617 G
126 G
618 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGT-A-AAAAT-
1 TATATTTAAAAAATTCTAATATATATAAG-TTTTTTAATTAAAATAGTAAAATGGTAATAAAATG
*
680 TATAATGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACT
65 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACT
735 ATACAAGTTT
Statistics
Matches: 115, Mismatches: 1, Indels: 9
0.92 0.01 0.07
Matches are distributed among these distances:
124 54 0.47
127 5 0.04
128 1 0.01
131 29 0.25
132 26 0.23
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.39
Consensus pattern (126 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAATAAAATGT
ATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAG
Found at i:10009 original size:42 final size:42
Alignment explanation
Indices: 9947--10033 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
9937 GATGATGTAG
9947 AAGTTTATATGGTTTCTGTTCCATATAAATCATGAACCACCT
1 AAGTTTATATGGTTTCTGTTCCATATAAATCATGAACCACCT
*
9989 AAGTTTATATGGTTTTTGTTCCATATAAATCATGAACCACCT
1 AAGTTTATATGGTTTCTGTTCCATATAAATCATGAACCACCT
10031 AAG
1 AAG
10034 CAGCGTATTG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (42 bp):
AAGTTTATATGGTTTCTGTTCCATATAAATCATGAACCACCT
Found at i:16250 original size:39 final size:39
Alignment explanation
Indices: 16168--16250 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 39
16158 AAAGGCCAAT
*
16168 GGGCCAGTCAGCATGGCCCAACGCGCAAGCCAGGCGCGC
1 GGGCCAGTCAGCATGGCCCAACGCGCAAGCCAGGCGAGC
* * *
16207 GGGCCAG-C-GCATGGCCCAAGCGCGCCAGGCTAGGCGAGG
1 GGGCCAGTCAGCATGGCCCAA-CGCG-CAAGCCAGGCGAGC
16246 GGGCC
1 GGGCC
16251 TGCTGCGCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
37 11 0.29
38 5 0.13
39 22 0.58
ACGTcount: A:0.18, C:0.36, G:0.41, T:0.05
Consensus pattern (39 bp):
GGGCCAGTCAGCATGGCCCAACGCGCAAGCCAGGCGAGC
Found at i:16328 original size:13 final size:13
Alignment explanation
Indices: 16312--16336 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16302 CCAAAAGTTT
16312 AAAAAAAAAGAGA
1 AAAAAAAAAGAGA
16325 AAAAAAAAAGAG
1 AAAAAAAAAGAG
16337 TGAGAGAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAGA
Done.