Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015484.1 Corchorus olitorius cultivar O-4 contig15517, 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: 16713
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:2103 original size:93 final size:93
Alignment explanation
Indices: 1944--2129 Score: 372
Period size: 93 Copynumber: 2.0 Consensus size: 93
1934 ACAAACCCCT
1944 TCCCCAAATCCTTCCCCAGATCCACGTTTGTACTCCTATGATTTTTTTTTTTTCATTTCTTAAAG
1 TCCCCAAATCCTTCCCCAGATCCACGTTTGTACTCCTATGATTTTTTTTTTTTCATTTCTTAAAG
2009 AGTTTGAGATTACAAACGCACAGGACCC
66 AGTTTGAGATTACAAACGCACAGGACCC
2037 TCCCCAAATCCTTCCCCAGATCCACGTTTGTACTCCTATGATTTTTTTTTTTTCATTTCTTAAAG
1 TCCCCAAATCCTTCCCCAGATCCACGTTTGTACTCCTATGATTTTTTTTTTTTCATTTCTTAAAG
2102 AGTTTGAGATTACAAACGCACAGGACCC
66 AGTTTGAGATTACAAACGCACAGGACCC
2130 GTACACCGCT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.37
Consensus pattern (93 bp):
TCCCCAAATCCTTCCCCAGATCCACGTTTGTACTCCTATGATTTTTTTTTTTTCATTTCTTAAAG
AGTTTGAGATTACAAACGCACAGGACCC
Found at i:2224 original size:14 final size:14
Alignment explanation
Indices: 2205--2232 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2195 CAACAAACAA
2205 ACCCAGTGAAATCT
1 ACCCAGTGAAATCT
2219 ACCCAGTGAAATCT
1 ACCCAGTGAAATCT
2233 CATTACAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (14 bp):
ACCCAGTGAAATCT
Found at i:12781 original size:22 final size:22
Alignment explanation
Indices: 12755--12914 Score: 121
Period size: 22 Copynumber: 7.2 Consensus size: 22
12745 GGGAGAAAAA
12755 TCATATGGTGGTTATCAAAATT
1 TCATATGGTGGTTATCAAAATT
** *
12777 TCATA-GAAAGGTTTATTAAAATT
1 TCATATG-GTGG-TTATCAAAATT
* **
12800 TCATA-GTTAGGTTATCAGTATT
1 TCATATGGT-GGTTATCAAAATT
*** *
12822 TCAT-TAGGAATTTATCACAATT
1 TCATAT-GGTGGTTATCAAAATT
* **
12844 TCATAGGGTAATTATCAAAATT
1 TCATATGGTGGTTATCAAAATT
12866 TCATAAT-GTGGTTATCAAAATT
1 TCAT-ATGGTGGTTATCAAAATT
*
12888 TCATAGGGTGGTTATCAAAATT
1 TCATATGGTGGTTATCAAAATT
12910 TCATA
1 TCATA
12915 AAAATATTTT
Statistics
Matches: 108, Mismatches: 22, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
21 2 0.02
22 86 0.80
23 20 0.19
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (22 bp):
TCATATGGTGGTTATCAAAATT
Found at i:12903 original size:66 final size:65
Alignment explanation
Indices: 12755--12914 Score: 166
Period size: 66 Copynumber: 2.4 Consensus size: 65
12745 GGGAGAAAAA
* * * **
12755 TCATATGGTGGTTATCAAAATTTCATAGAAAGGTTTATTAAAATTTCATAGTTAGGTTATCAGTA
1 TCATAGGGTGGTTATCAAAATTTCATAG--AGGTTTATCAAAATTTCATAATTAGGTTATCAAAA
12820 TT
64 TT
* *
12822 TCATTAGGAAT--TTATCACAATTTCATAG-GGTAATTATCAAAATTTCATAATGT-GGTTATCA
1 TCA-TAGG-GTGGTTATCAAAATTTCATAGAGGT--TTATCAAAATTTCATAAT-TAGGTTATCA
12883 AAATT
61 AAATT
12888 TCATAGGGTGGTTATCAAAATTTCATA
1 TCATAGGGTGGTTATCAAAATTTCATA
12915 AAAATATTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
64 4 0.05
65 4 0.05
66 45 0.58
67 20 0.26
68 3 0.04
69 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (65 bp):
TCATAGGGTGGTTATCAAAATTTCATAGAGGTTTATCAAAATTTCATAATTAGGTTATCAAAATT
Done.