Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024398.1 Corchorus olitorius cultivar O-4 contig24431, 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: 3582
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.30
Found at i:1664 original size:23 final size:23
Alignment explanation
Indices: 1636--1679 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1626 TAAAATGCAC
1636 CAAAACAGTCACCACTAACCCAT
1 CAAAACAGTCACCACTAACCCAT
1659 CAAAACAGTCACCACTAACCC
1 CAAAACAGTCACCACTAACCC
1680 TCTTCCTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.41, G:0.05, T:0.11
Consensus pattern (23 bp):
CAAAACAGTCACCACTAACCCAT
Found at i:2364 original size:75 final size:75
Alignment explanation
Indices: 2280--2454 Score: 165
Period size: 75 Copynumber: 2.3 Consensus size: 75
2270 GATGCTCAAA
* * *
2280 ATTTAAATTCGAATCAGAAACCTGATAAAGTGAATCAGCTTCAAG-TTGTTG-CAAATCATCATC
1 ATTTGAATTCGAATCAGAAACCTGATAAAGTGAATCAACTTCAAGATT-TTGCCAAA-CACCATC
*
2343 AGAAAACTTAGT
64 AGAAAACTCAGT
* ** * * * * * *
2355 ATTTGAATTCAAAAGAGGAATCTGGTCAGGTGAATCAACTTCAAGATTTTGCCTAACACCATCAG
1 ATTTGAATTCGAATCAGAAACCTGATAAAGTGAATCAACTTCAAGATTTTGCCAAACACCATCAG
* *
2420 CAAACTCATT
66 AAAACTCAGT
* *
2430 ATTTGAATTCGAATTAGCAACCTGA
1 ATTTGAATTCGAATCAGAAACCTGA
2455 GAAGGAGAAT
Statistics
Matches: 77, Mismatches: 21, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
75 72 0.94
76 5 0.06
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (75 bp):
ATTTGAATTCGAATCAGAAACCTGATAAAGTGAATCAACTTCAAGATTTTGCCAAACACCATCAG
AAAACTCAGT
Done.