1. Calculating inverse non-complementary repeats of length at least 20 from nucleotide (DNA) sequences in Halobacterium salinarum R1 (NC_010364) genome  

Input file  : Halobacterium_salinarum_R1.fasta
Syntax:     : ./StatRepeats Halobacterium_salinarum_R1.fasta 20 -in -out Halobacterium_salinarum_R1.in_20.out
Output file : Halobacterium_salinarum_R1.in_20.out


2. Calculating inverse non-complementary repeats of length at least 14 from nucleotide (DNA) sequences in Halobacterium salinarum R1 (NC_010364) genome  
andd its plasmids: Halobacterium salinarum R1 plasmid PHS1 (NC_010366), Halobacterium salinarum R1 plasmid PHS2 (NC_010369), Halobacterium salinarum R1 plasmid PHS3 (NC_010368), Halobacterium salinarum R1 plasmid PHS4 (NC_010367). All four fasta sequences are stored in file Halobacterium_salinarum_R1_with_plasmids.fasta. 


Input file  : Halobacterium_salinarum_R1_with_plasmids.fasta
Syntax:     : ./StatRepeats Halobacterium_salinarum_R1_with_plasmids.fasta 14 -in -out Halobacterium_salinarum_R1_with_plasmids.in_14.out
Output file : Halobacterium_salinarum_R1_with_plasmids.in_14.out


3.Calculating inverse complementary repeats from nucleotide (RNA) sequences, minimal length 10 from sequence Homo sapiens long intergenic non-protein coding RNA 261 (LINC00261), long non-coding RNA. 
Source: http://rnacentral.org/rna/URS000075C45D

Input file  : URS000075C45D.rna
Syntax:     : ./StatRepeats URS000075C45D.rna 10 -rna -ic -out URS000075C45D.rna.ic_10.out
Output file : URS000075C45D.rna.ic_10.out


4. Change input alphabet and/or complementary letters.
File "rules.txt" contain ATTACGGC (this content of file specifies A->T, T->A, C->G, G->C). IMPORTANT: put additional blank character og new line after last letter in file. 

Calculating inverse complementary repeats of length at least 20 from nucleotide (DNA) sequences in Halobacterium salinarum R1 (NC_010364) genome  

Input file  : Halobacterium_salinarum_R1.fasta
Syntax:     : ./StatRepeats Halobacterium_salinarum_R1.fasta 20 -compl rules.txt -ic -out Halobacterium_salinarum_R1.ic_20.atcg.out
Output file : Halobacterium_salinarum_R1.ic_20.atcg.out


5. Change input alphabet and/or complementary letters.
File "rules1.txt" contain ACCATGGTC (this content of file specifies 'unusual' complement pairs A->C, C->A, T->G, G->T). 

Calculating inverse complementary repeats of length at least 15 from nucleotide (DNA) sequences in Halobacterium salinarum R1 (NC_010364) genome  

Input file  : Halobacterium_salinarum_R1.fasta
Syntax:     : ./StatRepeats Halobacterium_salinarum_R1.fasta 15 -compl rules1.txt -ic -out Halobacterium_salinarum_R1.ic_15.actg.out
Output file : Halobacterium_salinarum_R1.ic_15.actg.out

6. Using different alphabet and complementary letters. 
File "rules2.txt" contain abbacddceffeghhgijjikllkmnnmoppoqrrqsttsuvvuwxxwyzzyABBACDDCEFFEGHHGIJJIKLLKMNNMOPPOQRRQSTTSUVVUWXXWYZZY.,,.  
(lowercase and uppercase leter from alphabet, where two consecutive letters are defined as complementary: A/B, C/D, etc. 

Calculating inverse non-complementary repeats of length at least 5 from text from file "input_text.txt"

Input file  : input_text.txt
Syntax:     : ./StatRepeats input_text.txt 5 -compl rules2.txt -in -out input_text.in_5.out
Output file : input_text.in_5.out

