# This program is based on research paper [SA-SSR](www.ncbi.nlm.nih.gov/pubmed/27170037)

# Right now it is finding only Exact tandem repeats of any length

#Test data
Dna Sequence: 
>gi|568815580|ref|NC_000018.10| Homo sapiens chromosome 18, GRCh38.p7 Primary Assembly


# Src files TandemRepeatFinder.java TandemRepeatFinderSeq.java
Compile:
javac TandemRepeatFinder.java
javac TandemRepeatFinderSeq.java

Run:
javac TandemRepeatFinder
javac TandemRepeatFinderSeq

# Compare Output and running time

$ time java TandemRepeatFinder > output_par.txt
$ time java TandemRepeatFinderSeq > output_seq.txt

System.out.println("Usage: java TandemRepeatFinderSeq <fasta_file> <output_type>" + 
            "\n1.PrintUnit, 2.PrintSequence, 3.PrintFrequency, 4.PrintUnitSequence, 5.PrintRange\n\t f

time java TandemRepeatFinderSeq data.fasta <options>