Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015678.1 Corchorus olitorius cultivar O-4 contig15711, 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: 13695
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Found at i:4964 original size:1 final size:1
Alignment explanation
Indices: 4958--4982 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
4948 TCTCCATCAG
4958 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
4983 GCAAAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5472 original size:33 final size:33
Alignment explanation
Indices: 5434--5500 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
5424 ATGAATTATA
5434 TAGAGTTTAGAGTATTTTAAGTGAAAATGTAAT
1 TAGAGTTTAGAGTATTTTAAGTGAAAATGTAAT
5467 TAGAGTTTAGAGTATTTTAAGTGAAAATGTAAT
1 TAGAGTTTAGAGTATTTTAAGTGAAAATGTAAT
5500 T
1 T
5501 TTTAGGGAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.40
Consensus pattern (33 bp):
TAGAGTTTAGAGTATTTTAAGTGAAAATGTAAT
Found at i:7367 original size:2 final size:2
Alignment explanation
Indices: 7360--7385 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7350 TTCTCTTATA
7360 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
7386 ATATAAGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:8976 original size:127 final size:128
Alignment explanation
Indices: 8789--9023 Score: 382
Period size: 129 Copynumber: 1.8 Consensus size: 128
8779 ATATGGAACA
* * * *
8789 AAAAGAAAACATATGAAATTTGGGACAAATTTAAATAAATGGACACCGGCTC-AAAAAAAAAGAA
1 AAAAGAAAACATATGAAATGTAGGACAAATTTAAACAAATGGACACCGGCCCAAAAAAAAAAGAA
*
8853 AAAAAAAACATATGAAATGTGTGCCAAATTTAAACAAATGGAGATACCAGTCCAAGAAAAAAG
66 AAAAAAAACATATGAAATGTGGGCCAAATTTAAACAAATGGAGATACCAGTCCAAGAAAAAAG
* *
8916 AAAAGAAAACATATGAAATGTAGGTCAAATTTAAACAAATGGACATCGGCCCATAAAAAAAAAGA
1 AAAAGAAAACATATGAAATGTAGGACAAATTTAAACAAATGGACACCGGCCCA-AAAAAAAAAGA
*
8981 AAAAGAAAACATATGAAATGTGGGCCAAATTTAAACAAATGGA
65 AAAAAAAAACATATGAAATGTGGGCCAAATTTAAACAAATGGA
9024 AACCGACCCA
Statistics
Matches: 98, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
127 46 0.47
129 52 0.53
ACGTcount: A:0.55, C:0.11, G:0.16, T:0.17
Consensus pattern (128 bp):
AAAAGAAAACATATGAAATGTAGGACAAATTTAAACAAATGGACACCGGCCCAAAAAAAAAAGAA
AAAAAAAACATATGAAATGTGGGCCAAATTTAAACAAATGGAGATACCAGTCCAAGAAAAAAG
Found at i:9010 original size:65 final size:63
Alignment explanation
Indices: 8788--9023 Score: 312
Period size: 65 Copynumber: 3.7 Consensus size: 63
8778 TATATGGAAC
* * * * *
8788 AAAAAGAAAACATATGAAATTTGGGACAAATTTAAATAAATGGACACCGGCTCAAAAAAAAAG
1 AAAAAGAAAACATATGAAATGTGGGCCAAATTTAAACAAATGGACATCGGCCCAAAAAAAAAG
* * * * * *
8851 AAAAAAAAAACATATGAAATGTGTGCCAAATTTAAACAAATGGAGATACCAGTCCAAGAAAAAAG
1 AAAAAGAAAACATATGAAATGTGGGCCAAATTTAAACAAATGGACAT--CGGCCCAAAAAAAAAG
* *
8916 -AAAAGAAAACATATGAAATGTAGGTCAAATTTAAACAAATGGACATCGGCCCATAAAAAAAAAG
1 AAAAAGAAAACATATGAAATGTGGGCCAAATTTAAACAAATGGACATCGGCCC--AAAAAAAAAG
8980 AAAAAGAAAACATATGAAATGTGGGCCAAATTTAAACAAATGGA
1 AAAAAGAAAACATATGAAATGTGGGCCAAATTTAAACAAATGGA
9024 AACCGACCCA
Statistics
Matches: 147, Mismatches: 21, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
62 4 0.03
63 40 0.27
64 50 0.34
65 53 0.36
ACGTcount: A:0.55, C:0.11, G:0.16, T:0.17
Consensus pattern (63 bp):
AAAAAGAAAACATATGAAATGTGGGCCAAATTTAAACAAATGGACATCGGCCCAAAAAAAAAG
Found at i:10057 original size:2 final size:2
Alignment explanation
Indices: 10052--10077 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10042 TCTTTTCAAG
10052 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
10078 GGAGTGCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10377 original size:16 final size:16
Alignment explanation
Indices: 10358--10388 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10348 ACAATCACAA
*
10358 TCACAATCAATATTAT
1 TCACAAGCAATATTAT
10374 TCACAAGCAATATTA
1 TCACAAGCAATATTA
10389 AAGTTTGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.32
Consensus pattern (16 bp):
TCACAAGCAATATTAT
Done.