Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012601.1 Corchorus olitorius cultivar O-4 contig12634, 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: 10487
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:6257 original size:42 final size:43
Alignment explanation
Indices: 6206--6299 Score: 120
Period size: 45 Copynumber: 2.2 Consensus size: 43
6196 AGTGCATTAC
* * *
6206 CTAA-ATTCTA-CTCCGTCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
*
6247 TTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
6292 CTAATATT
1 CTAATATT
6300 AATTGTTGCT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 3 0.07
42 6 0.14
45 35 0.80
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:7478 original size:60 final size:59
Alignment explanation
Indices: 7379--7541 Score: 211
Period size: 60 Copynumber: 2.7 Consensus size: 59
7369 TGAACACCGT
* *
7379 GGCCTTATTTGAGCATTTTCGCAAACGTTAGGGCCCTATTTGACCAAATTAAAAGTATG-
1 GGCCTTATTTGAGCATTTTCGCATACGTTAGGG-CCTATTTGACCAAATTAAAAGCATGA
* **
7438 GGCCCTTATTTGAGCATTTTCGCATACATTAGGGCTCTATTCAACCAAATTAAAAGCATGA
1 GG-CCTTATTTGAGCATTTTCGCATACGTTAGGGC-CTATTTGACCAAATTAAAAGCATGA
* * *
7499 TGCCTAAATTGAGCATTTTCGCATACGTTAAGGGCCTATTTGA
1 GGCCTTATTTGAGCATTTTCGCATACGTT-AGGGCCTATTTGA
7542 GCAATTAGCC
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
59 3 0.03
60 80 0.90
61 6 0.07
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (59 bp):
GGCCTTATTTGAGCATTTTCGCATACGTTAGGGCCTATTTGACCAAATTAAAAGCATGA
Found at i:7737 original size:34 final size:34
Alignment explanation
Indices: 7699--7765 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
7689 CTACTTTGTT
7699 TCCTTTCACTTCATACCTTCGCACCCCGACTTTC
1 TCCTTTCACTTCATACCTTCGCACCCCGACTTTC
7733 TCCTTTCACTTCATACCTTCGCACCCCGACTTT
1 TCCTTTCACTTCATACCTTCGCACCCCGACTTT
7766 TTCATTGATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.15, C:0.43, G:0.06, T:0.36
Consensus pattern (34 bp):
TCCTTTCACTTCATACCTTCGCACCCCGACTTTC
Found at i:8321 original size:25 final size:25
Alignment explanation
Indices: 8291--8365 Score: 96
Period size: 25 Copynumber: 3.0 Consensus size: 25
8281 TGTGTTTTCC
*
8291 AAACGCAAGCACATGCTCGTTTGCT
1 AAACGCAAGCACAGGCTCGTTTGCT
* * * *
8316 ATACGCAAGCATAGGTTCGTTTTCT
1 AAACGCAAGCACAGGCTCGTTTGCT
*
8341 AAACGCAAGCACAGGCGCGTTTGCT
1 AAACGCAAGCACAGGCTCGTTTGCT
8366 CAGCGCACGC
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (25 bp):
AAACGCAAGCACAGGCTCGTTTGCT
Found at i:9120 original size:20 final size:20
Alignment explanation
Indices: 9091--9132 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
9081 ATCAAGTAAG
* *
9091 GAAGAGTCTCCAAGGCCCAT
1 GAAGACTCTCCAAGACCCAT
9111 GAAGACTCTCCAAGACCCAT
1 GAAGACTCTCCAAGACCCAT
9131 GA
1 GA
9133 CCAACCCCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.31, G:0.21, T:0.14
Consensus pattern (20 bp):
GAAGACTCTCCAAGACCCAT
Found at i:9798 original size:11 final size:11
Alignment explanation
Indices: 9782--9826 Score: 90
Period size: 11 Copynumber: 4.1 Consensus size: 11
9772 GTTAAGGAAA
9782 AGCTAGGAAGG
1 AGCTAGGAAGG
9793 AGCTAGGAAGG
1 AGCTAGGAAGG
9804 AGCTAGGAAGG
1 AGCTAGGAAGG
9815 AGCTAGGAAGG
1 AGCTAGGAAGG
9826 A
1 A
9827 CCCTACTCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.38, C:0.09, G:0.44, T:0.09
Consensus pattern (11 bp):
AGCTAGGAAGG
Done.