package org.seqcode.genome.sequence.seqfunctions;
import java.util.HashMap;
import java.util.Map;
/**
* Scores Minor Groove Width (Angstroms) of a sequence using score defined by Remo Rohs' lab.
* Source:
* http://rohslab.cmb.usc.edu/DNAshape/
* Zhou,,T., Yang,L., Lu,Y., Dror,I., Dantas Machado,A.C., Ghane,T., Di Felice,R. and Rohs,R.
* DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale.
* Nucleic Acids Res. (2013) 41, W56-W62.
*
* @author mahony
*
*/
public class MGWStructureFunction implements SeqFunction{
//Variables
final int scoreDimension = 1;
int scoringOffset = 2;
int scoreWindowSize = 5;
boolean isBetweenNucs = false;
final String[] labels = {"MGW"};
final String description = "Minor Groove Width (Rohs)";
Map<String, Double> structure = new HashMap<String, Double>();
public MGWStructureFunction(){
loadStructureValues();
}
public double[][] score(String seq) throws SeqFunctionException {
if(seq.length()<scoreWindowSize)
throw new SeqFunctionException("Sequence too short for MGWStructureFunction");
double [][] scores = new double[scoreDimension][seq.length()];
String seqU = seq.toUpperCase();
for(int i=0; i<seqU.length(); i++)
scores[0][i]=0;
for(int i=0; i<seqU.length()-scoreWindowSize+1; i++){
String kmer = seqU.substring(i, i+scoreWindowSize);
scores[0][i+scoringOffset]=structure.get(kmer);
}
return scores;
}
public int scoreDimension() {
return scoreDimension;
}
public int scoringOffset() {
return scoringOffset;
}
public int scoreWindowSize() {
return scoreWindowSize;
}
public boolean isBetweenNucleotides() {
return isBetweenNucs;
}
public String[] dimensionLabels() {
return labels;
}
public String scoreDescription() {
return description;
}
public double getMaxScore(){return 6.2;}
public double getMinScore(){return 2.85;}
private void loadStructureValues(){
structure.put("AAAAA", 3.38);
structure.put("AAAAT", 3.63);
structure.put("AAAAG", 3.68);
structure.put("AAAAC", 4.05);
structure.put("AAATA", 3.79);
structure.put("AAATT", 2.85);
structure.put("AAATG", 3.84);
structure.put("AAATC", 4.12);
structure.put("AAAGA", 4.02);
structure.put("AAAGT", 3.35);
structure.put("AAAGG", 4.05);
structure.put("AAAGC", 4.03);
structure.put("AAACA", 4.65);
structure.put("AAACT", 3.85);
structure.put("AAACG", 4.43);
structure.put("AAACC", 4.06);
structure.put("AATAA", 5.53);
structure.put("AATAT", 4.8);
structure.put("AATAG", 4.65);
structure.put("AATAC", 5.3);
structure.put("AATTA", 4.36);
structure.put("AATTT", 2.85);
structure.put("AATTG", 4.24);
structure.put("AATTC", 3.75);
structure.put("AATGA", 4.46);
structure.put("AATGT", 4.27);
structure.put("AATGG", 5.08);
structure.put("AATGC", 4.89);
structure.put("AATCA", 4.46);
structure.put("AATCT", 3.75);
structure.put("AATCG", 4.56);
structure.put("AATCC", 4.19);
structure.put("AAGAA", 4.8);
structure.put("AAGAT", 3.9);
structure.put("AAGAG", 4.68);
structure.put("AAGAC", 4.65);
structure.put("AAGTA", 4.03);
structure.put("AAGTT", 3.34);
structure.put("AAGTG", 4.14);
structure.put("AAGTC", 3.74);
structure.put("AAGGA", 4.31);
structure.put("AAGGT", 3.75);
structure.put("AAGGG", 4.42);
structure.put("AAGGC", 4.51);
structure.put("AAGCA", 4.61);
structure.put("AAGCT", 4.14);
structure.put("AAGCG", 4.63);
structure.put("AAGCC", 4.17);
structure.put("AACAA", 4.97);
structure.put("AACAT", 4.3);
structure.put("AACAG", 4.95);
structure.put("AACAC", 5.05);
structure.put("AACTA", 4.24);
structure.put("AACTT", 3.34);
structure.put("AACTG", 4.49);
structure.put("AACTC", 3.95);
structure.put("AACGA", 4.8);
structure.put("AACGT", 4.21);
structure.put("AACGG", 4.62);
structure.put("AACGC", 4.64);
structure.put("AACCA", 4.33);
structure.put("AACCT", 3.64);
structure.put("AACCG", 4.36);
structure.put("AACCC", 4.03);
structure.put("ATAAA", 5.66);
structure.put("ATAAT", 5.28);
structure.put("ATAAG", 5.48);
structure.put("ATAAC", 5.62);
structure.put("ATATA", 5.76);
structure.put("ATATT", 4.8);
structure.put("ATATG", 5.32);
structure.put("ATATC", 5.4);
structure.put("ATAGA", 5.69);
structure.put("ATAGT", 4.86);
structure.put("ATAGG", 5.6);
structure.put("ATAGC", 5.37);
structure.put("ATACA", 5.82);
structure.put("ATACT", 5.37);
structure.put("ATACG", 5.53);
structure.put("ATACC", 5.46);
structure.put("ATTAA", 5.58);
structure.put("ATTAT", 5.28);
structure.put("ATTAG", 5.57);
structure.put("ATTAC", 5.44);
structure.put("ATTTA", 4.75);
structure.put("ATTTT", 3.63);
structure.put("ATTTG", 4.12);
structure.put("ATTTC", 4.27);
structure.put("ATTGA", 5.46);
structure.put("ATTGT", 5.03);
structure.put("ATTGG", 5.3);
structure.put("ATTGC", 5.15);
structure.put("ATTCA", 5.22);
structure.put("ATTCT", 4.43);
structure.put("ATTCG", 4.88);
structure.put("ATTCC", 4.69);
structure.put("ATGAA", 5.5);
structure.put("ATGAT", 4.79);
structure.put("ATGAG", 5.23);
structure.put("ATGAC", 5.45);
structure.put("ATGTA", 5.27);
structure.put("ATGTT", 4.3);
structure.put("ATGTG", 5.15);
structure.put("ATGTC", 5.02);
structure.put("ATGGA", 5.34);
structure.put("ATGGT", 4.97);
structure.put("ATGGG", 5.19);
structure.put("ATGGC", 5.23);
structure.put("ATGCA", 5.55);
structure.put("ATGCT", 5.23);
structure.put("ATGCG", 5.6);
structure.put("ATGCC", 5.33);
structure.put("ATCAA", 5.52);
structure.put("ATCAT", 4.79);
structure.put("ATCAG", 5.34);
structure.put("ATCAC", 5.35);
structure.put("ATCTA", 4.74);
structure.put("ATCTT", 3.9);
structure.put("ATCTG", 4.98);
structure.put("ATCTC", 4.74);
structure.put("ATCGA", 5.23);
structure.put("ATCGT", 4.8);
structure.put("ATCGG", 5.25);
structure.put("ATCGC", 5.28);
structure.put("ATCCA", 4.94);
structure.put("ATCCT", 4.51);
structure.put("ATCCG", 4.47);
structure.put("ATCCC", 4.81);
structure.put("AGAAA", 4.74);
structure.put("AGAAT", 4.43);
structure.put("AGAAG", 4.5);
structure.put("AGAAC", 4.85);
structure.put("AGATA", 4.72);
structure.put("AGATT", 3.75);
structure.put("AGATG", 4.66);
structure.put("AGATC", 4.36);
structure.put("AGAGA", 5.0);
structure.put("AGAGT", 4.86);
structure.put("AGAGG", 4.97);
structure.put("AGAGC", 5.04);
structure.put("AGACA", 4.99);
structure.put("AGACT", 4.57);
structure.put("AGACG", 4.83);
structure.put("AGACC", 4.73);
structure.put("AGTAA", 5.37);
structure.put("AGTAT", 5.37);
structure.put("AGTAG", 5.2);
structure.put("AGTAC", 5.54);
structure.put("AGTTA", 4.67);
structure.put("AGTTT", 3.85);
structure.put("AGTTG", 4.38);
structure.put("AGTTC", 4.25);
structure.put("AGTGA", 5.22);
structure.put("AGTGT", 5.1);
structure.put("AGTGG", 5.31);
structure.put("AGTGC", 5.3);
structure.put("AGTCA", 4.89);
structure.put("AGTCT", 4.57);
structure.put("AGTCG", 4.59);
structure.put("AGTCC", 4.51);
structure.put("AGGAA", 4.76);
structure.put("AGGAT", 4.51);
structure.put("AGGAG", 4.63);
structure.put("AGGAC", 4.81);
structure.put("AGGTA", 4.33);
structure.put("AGGTT", 3.64);
structure.put("AGGTG", 4.42);
structure.put("AGGTC", 4.18);
structure.put("AGGGA", 4.68);
structure.put("AGGGT", 4.29);
structure.put("AGGGG", 4.62);
structure.put("AGGGC", 4.73);
structure.put("AGGCA", 4.82);
structure.put("AGGCT", 4.33);
structure.put("AGGCG", 4.77);
structure.put("AGGCC", 4.72);
structure.put("AGCAA", 5.08);
structure.put("AGCAT", 5.23);
structure.put("AGCAG", 5.16);
structure.put("AGCAC", 5.43);
structure.put("AGCTA", 4.88);
structure.put("AGCTT", 4.14);
structure.put("AGCTG", 4.8);
structure.put("AGCTC", 4.63);
structure.put("AGCGA", 5.19);
structure.put("AGCGT", 4.86);
structure.put("AGCGG", 5.15);
structure.put("AGCGC", 5.18);
structure.put("AGCCA", 4.53);
structure.put("AGCCT", 4.33);
structure.put("AGCCG", 4.83);
structure.put("AGCCC", 4.61);
structure.put("ACAAA", 5.21);
structure.put("ACAAT", 5.03);
structure.put("ACAAG", 5.19);
structure.put("ACAAC", 5.58);
structure.put("ACATA", 5.14);
structure.put("ACATT", 4.27);
structure.put("ACATG", 4.99);
structure.put("ACATC", 4.82);
structure.put("ACAGA", 5.33);
structure.put("ACAGT", 5.2);
structure.put("ACAGG", 5.29);
structure.put("ACAGC", 5.31);
structure.put("ACACA", 5.5);
structure.put("ACACT", 5.1);
structure.put("ACACG", 5.47);
structure.put("ACACC", 5.31);
structure.put("ACTAA", 5.73);
structure.put("ACTAT", 4.86);
structure.put("ACTAG", 5.13);
structure.put("ACTAC", 5.62);
structure.put("ACTTA", 4.48);
structure.put("ACTTT", 3.35);
structure.put("ACTTG", 4.52);
structure.put("ACTTC", 4.31);
structure.put("ACTGA", 5.48);
structure.put("ACTGT", 5.2);
structure.put("ACTGG", 5.32);
structure.put("ACTGC", 5.4);
structure.put("ACTCA", 4.89);
structure.put("ACTCT", 4.86);
structure.put("ACTCG", 4.93);
structure.put("ACTCC", 4.73);
structure.put("ACGAA", 5.21);
structure.put("ACGAT", 4.8);
structure.put("ACGAG", 5.13);
structure.put("ACGAC", 5.34);
structure.put("ACGTA", 4.84);
structure.put("ACGTT", 4.21);
structure.put("ACGTG", 4.85);
structure.put("ACGTC", 4.7);
structure.put("ACGGA", 5.06);
structure.put("ACGGT", 4.73);
structure.put("ACGGG", 4.92);
structure.put("ACGGC", 5.08);
structure.put("ACGCA", 5.27);
structure.put("ACGCT", 4.86);
structure.put("ACGCG", 5.2);
structure.put("ACGCC", 5.08);
structure.put("ACCAA", 5.08);
structure.put("ACCAT", 4.97);
structure.put("ACCAG", 5.19);
structure.put("ACCAC", 5.38);
structure.put("ACCTA", 4.68);
structure.put("ACCTT", 3.75);
structure.put("ACCTG", 4.54);
structure.put("ACCTC", 4.37);
structure.put("ACCGA", 5.02);
structure.put("ACCGT", 4.73);
structure.put("ACCGG", 5.16);
structure.put("ACCGC", 5.08);
structure.put("ACCCA", 4.66);
structure.put("ACCCT", 4.29);
structure.put("ACCCG", 4.7);
structure.put("ACCCC", 4.58);
structure.put("TAAAA", 4.89);
structure.put("TAAAT", 4.75);
structure.put("TAAAG", 4.7);
structure.put("TAAAC", 5.1);
structure.put("TAATA", 5.11);
structure.put("TAATT", 4.36);
structure.put("TAATG", 4.9);
structure.put("TAATC", 4.81);
structure.put("TAAGA", 4.93);
structure.put("TAAGT", 4.48);
structure.put("TAAGG", 4.81);
structure.put("TAAGC", 5.01);
structure.put("TAACA", 5.17);
structure.put("TAACT", 4.67);
structure.put("TAACG", 5.15);
structure.put("TAACC", 4.87);
structure.put("TATAA", 6.07);
structure.put("TATAT", 5.76);
structure.put("TATAG", 5.79);
structure.put("TATAC", 6.01);
structure.put("TATTA", 5.11);
structure.put("TATTT", 3.79);
structure.put("TATTG", 5.02);
structure.put("TATTC", 4.51);
structure.put("TATGA", 5.84);
structure.put("TATGT", 5.14);
structure.put("TATGG", 5.88);
structure.put("TATGC", 5.76);
structure.put("TATCA", 5.38);
structure.put("TATCT", 4.72);
structure.put("TATCG", 5.32);
structure.put("TATCC", 4.98);
structure.put("TAGAA", 5.33);
structure.put("TAGAT", 4.74);
structure.put("TAGAG", 5.41);
structure.put("TAGAC", 5.32);
structure.put("TAGTA", 5.33);
structure.put("TAGTT", 4.24);
structure.put("TAGTG", 5.11);
structure.put("TAGTC", 5.08);
structure.put("TAGGA", 4.98);
structure.put("TAGGT", 4.68);
structure.put("TAGGG", 4.99);
structure.put("TAGGC", 4.97);
structure.put("TAGCA", 5.36);
structure.put("TAGCT", 4.88);
structure.put("TAGCG", 5.22);
structure.put("TAGCC", 5.0);
structure.put("TACAA", 5.89);
structure.put("TACAT", 5.27);
structure.put("TACAG", 5.41);
structure.put("TACAC", 5.74);
structure.put("TACTA", 5.33);
structure.put("TACTT", 4.03);
structure.put("TACTG", 5.13);
structure.put("TACTC", 4.69);
structure.put("TACGA", 5.61);
structure.put("TACGT", 4.84);
structure.put("TACGG", 5.33);
structure.put("TACGC", 5.32);
structure.put("TACCA", 5.13);
structure.put("TACCT", 4.33);
structure.put("TACCG", 4.96);
structure.put("TACCC", 4.71);
structure.put("TTAAA", 5.73);
structure.put("TTAAT", 5.58);
structure.put("TTAAG", 5.58);
structure.put("TTAAC", 5.85);
structure.put("TTATA", 6.07);
structure.put("TTATT", 5.53);
structure.put("TTATG", 6.02);
structure.put("TTATC", 5.89);
structure.put("TTAGA", 6.0);
structure.put("TTAGT", 5.73);
structure.put("TTAGG", 5.96);
structure.put("TTAGC", 5.82);
structure.put("TTACA", 5.99);
structure.put("TTACT", 5.37);
structure.put("TTACG", 6.11);
structure.put("TTACC", 5.43);
structure.put("TTTAA", 5.73);
structure.put("TTTAT", 5.66);
structure.put("TTTAG", 5.82);
structure.put("TTTAC", 5.91);
structure.put("TTTTA", 4.89);
structure.put("TTTTT", 3.38);
structure.put("TTTTG", 4.76);
structure.put("TTTTC", 4.35);
structure.put("TTTGA", 5.6);
structure.put("TTTGT", 5.21);
structure.put("TTTGG", 5.42);
structure.put("TTTGC", 5.41);
structure.put("TTTCA", 5.4);
structure.put("TTTCT", 4.74);
structure.put("TTTCG", 4.98);
structure.put("TTTCC", 4.63);
structure.put("TTGAA", 6.0);
structure.put("TTGAT", 5.52);
structure.put("TTGAG", 5.9);
structure.put("TTGAC", 5.91);
structure.put("TTGTA", 5.89);
structure.put("TTGTT", 4.97);
structure.put("TTGTG", 5.2);
structure.put("TTGTC", 5.57);
structure.put("TTGGA", 5.42);
structure.put("TTGGT", 5.08);
structure.put("TTGGG", 5.44);
structure.put("TTGGC", 5.56);
structure.put("TTGCA", 5.78);
structure.put("TTGCT", 5.08);
structure.put("TTGCG", 5.81);
structure.put("TTGCC", 5.3);
structure.put("TTCAA", 6.0);
structure.put("TTCAT", 5.5);
structure.put("TTCAG", 5.93);
structure.put("TTCAC", 5.94);
structure.put("TTCTA", 5.33);
structure.put("TTCTT", 4.8);
structure.put("TTCTG", 5.14);
structure.put("TTCTC", 4.67);
structure.put("TTCGA", 5.75);
structure.put("TTCGT", 5.21);
structure.put("TTCGG", 5.38);
structure.put("TTCGC", 5.53);
structure.put("TTCCA", 4.97);
structure.put("TTCCT", 4.76);
structure.put("TTCCG", 5.09);
structure.put("TTCCC", 4.73);
structure.put("TGAAA", 5.4);
structure.put("TGAAT", 5.22);
structure.put("TGAAG", 5.15);
structure.put("TGAAC", 5.35);
structure.put("TGATA", 5.38);
structure.put("TGATT", 4.46);
structure.put("TGATG", 5.22);
structure.put("TGATC", 4.77);
structure.put("TGAGA", 5.29);
structure.put("TGAGT", 4.89);
structure.put("TGAGG", 5.3);
structure.put("TGAGC", 5.4);
structure.put("TGACA", 5.43);
structure.put("TGACT", 4.89);
structure.put("TGACG", 5.39);
structure.put("TGACC", 4.94);
structure.put("TGTAA", 5.99);
structure.put("TGTAT", 5.82);
structure.put("TGTAG", 5.74);
structure.put("TGTAC", 6.2);
structure.put("TGTTA", 5.17);
structure.put("TGTTT", 4.65);
structure.put("TGTTG", 5.24);
structure.put("TGTTC", 4.85);
structure.put("TGTGA", 5.84);
structure.put("TGTGT", 5.5);
structure.put("TGTGG", 5.8);
structure.put("TGTGC", 5.94);
structure.put("TGTCA", 5.43);
structure.put("TGTCT", 4.99);
structure.put("TGTCG", 5.28);
structure.put("TGTCC", 5.02);
structure.put("TGGAA", 4.97);
structure.put("TGGAT", 4.94);
structure.put("TGGAG", 5.02);
structure.put("TGGAC", 5.19);
structure.put("TGGTA", 5.13);
structure.put("TGGTT", 4.33);
structure.put("TGGTG", 4.84);
structure.put("TGGTC", 4.84);
structure.put("TGGGA", 4.93);
structure.put("TGGGT", 4.66);
structure.put("TGGGG", 4.89);
structure.put("TGGGC", 4.96);
structure.put("TGGCA", 5.24);
structure.put("TGGCT", 4.53);
structure.put("TGGCG", 5.06);
structure.put("TGGCC", 4.93);
structure.put("TGCAA", 5.78);
structure.put("TGCAT", 5.55);
structure.put("TGCAG", 5.79);
structure.put("TGCAC", 5.94);
structure.put("TGCTA", 5.36);
structure.put("TGCTT", 4.61);
structure.put("TGCTG", 5.27);
structure.put("TGCTC", 5.1);
structure.put("TGCGA", 5.68);
structure.put("TGCGT", 5.27);
structure.put("TGCGG", 5.59);
structure.put("TGCGC", 5.71);
structure.put("TGCCA", 5.24);
structure.put("TGCCT", 4.82);
structure.put("TGCCG", 5.17);
structure.put("TGCCC", 5.02);
structure.put("TCAAA", 5.6);
structure.put("TCAAT", 5.46);
structure.put("TCAAG", 5.4);
structure.put("TCAAC", 5.65);
structure.put("TCATA", 5.84);
structure.put("TCATT", 4.46);
structure.put("TCATG", 5.27);
structure.put("TCATC", 5.08);
structure.put("TCAGA", 5.47);
structure.put("TCAGT", 5.48);
structure.put("TCAGG", 5.47);
structure.put("TCAGC", 5.74);
structure.put("TCACA", 5.84);
structure.put("TCACT", 5.22);
structure.put("TCACG", 5.71);
structure.put("TCACC", 5.4);
structure.put("TCTAA", 6.0);
structure.put("TCTAT", 5.69);
structure.put("TCTAG", 5.84);
structure.put("TCTAC", 5.76);
structure.put("TCTTA", 4.93);
structure.put("TCTTT", 4.02);
structure.put("TCTTG", 4.92);
structure.put("TCTTC", 4.52);
structure.put("TCTGA", 5.47);
structure.put("TCTGT", 5.33);
structure.put("TCTGG", 5.56);
structure.put("TCTGC", 5.75);
structure.put("TCTCA", 5.29);
structure.put("TCTCT", 5.0);
structure.put("TCTCG", 5.17);
structure.put("TCTCC", 4.92);
structure.put("TCGAA", 5.75);
structure.put("TCGAT", 5.23);
structure.put("TCGAG", 5.42);
structure.put("TCGAC", 5.64);
structure.put("TCGTA", 5.61);
structure.put("TCGTT", 4.8);
structure.put("TCGTG", 5.29);
structure.put("TCGTC", 5.16);
structure.put("TCGGA", 5.36);
structure.put("TCGGT", 5.02);
structure.put("TCGGG", 5.22);
structure.put("TCGGC", 5.43);
structure.put("TCGCA", 5.68);
structure.put("TCGCT", 5.19);
structure.put("TCGCG", 5.42);
structure.put("TCGCC", 5.4);
structure.put("TCCAA", 5.42);
structure.put("TCCAT", 5.34);
structure.put("TCCAG", 5.31);
structure.put("TCCAC", 5.58);
structure.put("TCCTA", 4.98);
structure.put("TCCTT", 4.31);
structure.put("TCCTG", 4.92);
structure.put("TCCTC", 4.8);
structure.put("TCCGA", 5.36);
structure.put("TCCGT", 5.06);
structure.put("TCCGG", 5.39);
structure.put("TCCGC", 5.27);
structure.put("TCCCA", 4.93);
structure.put("TCCCT", 4.68);
structure.put("TCCCG", 4.95);
structure.put("TCCCC", 4.76);
structure.put("GAAAA", 4.35);
structure.put("GAAAT", 4.27);
structure.put("GAAAG", 4.36);
structure.put("GAAAC", 4.74);
structure.put("GAATA", 4.51);
structure.put("GAATT", 3.75);
structure.put("GAATG", 4.39);
structure.put("GAATC", 4.36);
structure.put("GAAGA", 4.52);
structure.put("GAAGT", 4.31);
structure.put("GAAGG", 4.63);
structure.put("GAAGC", 4.82);
structure.put("GAACA", 4.85);
structure.put("GAACT", 4.25);
structure.put("GAACG", 4.74);
structure.put("GAACC", 4.46);
structure.put("GATAA", 5.89);
structure.put("GATAT", 5.4);
structure.put("GATAG", 5.54);
structure.put("GATAC", 5.65);
structure.put("GATTA", 4.81);
structure.put("GATTT", 4.12);
structure.put("GATTG", 4.81);
structure.put("GATTC", 4.36);
structure.put("GATGA", 5.08);
structure.put("GATGT", 4.82);
structure.put("GATGG", 5.53);
structure.put("GATGC", 5.38);
structure.put("GATCA", 4.77);
structure.put("GATCT", 4.36);
structure.put("GATCG", 4.96);
structure.put("GATCC", 4.63);
structure.put("GAGAA", 4.67);
structure.put("GAGAT", 4.74);
structure.put("GAGAG", 4.93);
structure.put("GAGAC", 5.04);
structure.put("GAGTA", 4.69);
structure.put("GAGTT", 3.95);
structure.put("GAGTG", 4.78);
structure.put("GAGTC", 4.53);
structure.put("GAGGA", 4.8);
structure.put("GAGGT", 4.37);
structure.put("GAGGG", 4.78);
structure.put("GAGGC", 4.85);
structure.put("GAGCA", 5.1);
structure.put("GAGCT", 4.63);
structure.put("GAGCG", 5.02);
structure.put("GAGCC", 4.67);
structure.put("GACAA", 5.57);
structure.put("GACAT", 5.02);
structure.put("GACAG", 5.26);
structure.put("GACAC", 5.49);
structure.put("GACTA", 5.08);
structure.put("GACTT", 3.74);
structure.put("GACTG", 5.0);
structure.put("GACTC", 4.53);
structure.put("GACGA", 5.16);
structure.put("GACGT", 4.7);
structure.put("GACGG", 5.1);
structure.put("GACGC", 5.09);
structure.put("GACCA", 4.84);
structure.put("GACCT", 4.18);
structure.put("GACCG", 4.69);
structure.put("GACCC", 4.45);
structure.put("GTAAA", 5.91);
structure.put("GTAAT", 5.44);
structure.put("GTAAG", 5.62);
structure.put("GTAAC", 5.86);
structure.put("GTATA", 6.01);
structure.put("GTATT", 5.3);
structure.put("GTATG", 5.93);
structure.put("GTATC", 5.65);
structure.put("GTAGA", 5.76);
structure.put("GTAGT", 5.62);
structure.put("GTAGG", 5.76);
structure.put("GTAGC", 5.88);
structure.put("GTACA", 6.2);
structure.put("GTACT", 5.54);
structure.put("GTACG", 5.93);
structure.put("GTACC", 5.84);
structure.put("GTTAA", 5.85);
structure.put("GTTAT", 5.62);
structure.put("GTTAG", 5.8);
structure.put("GTTAC", 5.86);
structure.put("GTTTA", 5.1);
structure.put("GTTTT", 4.05);
structure.put("GTTTG", 4.95);
structure.put("GTTTC", 4.74);
structure.put("GTTGA", 5.65);
structure.put("GTTGT", 5.58);
structure.put("GTTGG", 5.42);
structure.put("GTTGC", 5.7);
structure.put("GTTCA", 5.35);
structure.put("GTTCT", 4.85);
structure.put("GTTCG", 5.1);
structure.put("GTTCC", 4.84);
structure.put("GTGAA", 5.94);
structure.put("GTGAT", 5.35);
structure.put("GTGAG", 5.8);
structure.put("GTGAC", 6.01);
structure.put("GTGTA", 5.74);
structure.put("GTGTT", 5.05);
structure.put("GTGTG", 5.73);
structure.put("GTGTC", 5.49);
structure.put("GTGGA", 5.58);
structure.put("GTGGT", 5.38);
structure.put("GTGGG", 5.41);
structure.put("GTGGC", 5.46);
structure.put("GTGCA", 5.94);
structure.put("GTGCT", 5.43);
structure.put("GTGCG", 5.88);
structure.put("GTGCC", 5.66);
structure.put("GTCAA", 5.91);
structure.put("GTCAT", 5.45);
structure.put("GTCAG", 5.67);
structure.put("GTCAC", 6.01);
structure.put("GTCTA", 5.32);
structure.put("GTCTT", 4.65);
structure.put("GTCTG", 5.22);
structure.put("GTCTC", 5.04);
structure.put("GTCGA", 5.64);
structure.put("GTCGT", 5.34);
structure.put("GTCGG", 5.54);
structure.put("GTCGC", 5.56);
structure.put("GTCCA", 5.19);
structure.put("GTCCT", 4.81);
structure.put("GTCCG", 5.08);
structure.put("GTCCC", 4.9);
structure.put("GGAAA", 4.63);
structure.put("GGAAT", 4.69);
structure.put("GGAAG", 4.63);
structure.put("GGAAC", 4.84);
structure.put("GGATA", 4.98);
structure.put("GGATT", 4.19);
structure.put("GGATG", 4.84);
structure.put("GGATC", 4.63);
structure.put("GGAGA", 4.92);
structure.put("GGAGT", 4.73);
structure.put("GGAGG", 4.93);
structure.put("GGAGC", 5.05);
structure.put("GGACA", 5.02);
structure.put("GGACT", 4.51);
structure.put("GGACG", 5.02);
structure.put("GGACC", 4.8);
structure.put("GGTAA", 5.43);
structure.put("GGTAT", 5.46);
structure.put("GGTAG", 5.55);
structure.put("GGTAC", 5.84);
structure.put("GGTTA", 4.87);
structure.put("GGTTT", 4.06);
structure.put("GGTTG", 4.82);
structure.put("GGTTC", 4.46);
structure.put("GGTGA", 5.4);
structure.put("GGTGT", 5.31);
structure.put("GGTGG", 5.56);
structure.put("GGTGC", 5.56);
structure.put("GGTCA", 4.94);
structure.put("GGTCT", 4.73);
structure.put("GGTCG", 4.82);
structure.put("GGTCC", 4.8);
structure.put("GGGAA", 4.73);
structure.put("GGGAT", 4.81);
structure.put("GGGAG", 4.85);
structure.put("GGGAC", 4.9);
structure.put("GGGTA", 4.71);
structure.put("GGGTT", 4.03);
structure.put("GGGTG", 4.77);
structure.put("GGGTC", 4.45);
structure.put("GGGGA", 4.76);
structure.put("GGGGT", 4.58);
structure.put("GGGGG", 4.75);
structure.put("GGGGC", 4.82);
structure.put("GGGCA", 5.02);
structure.put("GGGCT", 4.61);
structure.put("GGGCG", 4.96);
structure.put("GGGCC", 4.77);
structure.put("GGCAA", 5.3);
structure.put("GGCAT", 5.33);
structure.put("GGCAG", 5.41);
structure.put("GGCAC", 5.66);
structure.put("GGCTA", 5.0);
structure.put("GGCTT", 4.17);
structure.put("GGCTG", 4.95);
structure.put("GGCTC", 4.67);
structure.put("GGCGA", 5.4);
structure.put("GGCGT", 5.08);
structure.put("GGCGG", 5.29);
structure.put("GGCGC", 5.41);
structure.put("GGCCA", 4.93);
structure.put("GGCCT", 4.72);
structure.put("GGCCG", 4.96);
structure.put("GGCCC", 4.77);
structure.put("GCAAA", 5.41);
structure.put("GCAAT", 5.15);
structure.put("GCAAG", 5.45);
structure.put("GCAAC", 5.7);
structure.put("GCATA", 5.76);
structure.put("GCATT", 4.89);
structure.put("GCATG", 5.5);
structure.put("GCATC", 5.38);
structure.put("GCAGA", 5.75);
structure.put("GCAGT", 5.4);
structure.put("GCAGG", 5.52);
structure.put("GCAGC", 5.67);
structure.put("GCACA", 5.94);
structure.put("GCACT", 5.3);
structure.put("GCACG", 5.74);
structure.put("GCACC", 5.56);
structure.put("GCTAA", 5.82);
structure.put("GCTAT", 5.37);
structure.put("GCTAG", 5.67);
structure.put("GCTAC", 5.88);
structure.put("GCTTA", 5.01);
structure.put("GCTTT", 4.03);
structure.put("GCTTG", 4.94);
structure.put("GCTTC", 4.82);
structure.put("GCTGA", 5.74);
structure.put("GCTGT", 5.31);
structure.put("GCTGG", 5.53);
structure.put("GCTGC", 5.67);
structure.put("GCTCA", 5.4);
structure.put("GCTCT", 5.04);
structure.put("GCTCG", 5.2);
structure.put("GCTCC", 5.05);
structure.put("GCGAA", 5.53);
structure.put("GCGAT", 5.28);
structure.put("GCGAG", 5.46);
structure.put("GCGAC", 5.56);
structure.put("GCGTA", 5.32);
structure.put("GCGTT", 4.64);
structure.put("GCGTG", 5.25);
structure.put("GCGTC", 5.09);
structure.put("GCGGA", 5.27);
structure.put("GCGGT", 5.08);
structure.put("GCGGG", 5.3);
structure.put("GCGGC", 5.37);
structure.put("GCGCA", 5.71);
structure.put("GCGCT", 5.18);
structure.put("GCGCG", 5.54);
structure.put("GCGCC", 5.41);
structure.put("GCCAA", 5.56);
structure.put("GCCAT", 5.23);
structure.put("GCCAG", 5.43);
structure.put("GCCAC", 5.46);
structure.put("GCCTA", 4.97);
structure.put("GCCTT", 4.51);
structure.put("GCCTG", 4.94);
structure.put("GCCTC", 4.85);
structure.put("GCCGA", 5.43);
structure.put("GCCGT", 5.08);
structure.put("GCCGG", 5.36);
structure.put("GCCGC", 5.37);
structure.put("GCCCA", 4.96);
structure.put("GCCCT", 4.73);
structure.put("GCCCG", 4.95);
structure.put("GCCCC", 4.82);
structure.put("CAAAA", 4.76);
structure.put("CAAAT", 4.12);
structure.put("CAAAG", 4.52);
structure.put("CAAAC", 4.95);
structure.put("CAATA", 5.02);
structure.put("CAATT", 4.24);
structure.put("CAATG", 4.69);
structure.put("CAATC", 4.81);
structure.put("CAAGA", 4.92);
structure.put("CAAGT", 4.52);
structure.put("CAAGG", 4.65);
structure.put("CAAGC", 4.94);
structure.put("CAACA", 5.24);
structure.put("CAACT", 4.38);
structure.put("CAACG", 4.98);
structure.put("CAACC", 4.82);
structure.put("CATAA", 6.02);
structure.put("CATAT", 5.32);
structure.put("CATAG", 5.53);
structure.put("CATAC", 5.93);
structure.put("CATTA", 4.9);
structure.put("CATTT", 3.84);
structure.put("CATTG", 4.69);
structure.put("CATTC", 4.39);
structure.put("CATGA", 5.27);
structure.put("CATGT", 4.99);
structure.put("CATGG", 5.34);
structure.put("CATGC", 5.5);
structure.put("CATCA", 5.22);
structure.put("CATCT", 4.66);
structure.put("CATCG", 4.94);
structure.put("CATCC", 4.84);
structure.put("CAGAA", 5.14);
structure.put("CAGAT", 4.98);
structure.put("CAGAG", 5.14);
structure.put("CAGAC", 5.22);
structure.put("CAGTA", 5.13);
structure.put("CAGTT", 4.49);
structure.put("CAGTG", 4.98);
structure.put("CAGTC", 5.0);
structure.put("CAGGA", 4.92);
structure.put("CAGGT", 4.54);
structure.put("CAGGG", 4.85);
structure.put("CAGGC", 4.94);
structure.put("CAGCA", 5.27);
structure.put("CAGCT", 4.8);
structure.put("CAGCG", 5.13);
structure.put("CAGCC", 4.95);
structure.put("CACAA", 5.2);
structure.put("CACAT", 5.15);
structure.put("CACAG", 5.32);
structure.put("CACAC", 5.73);
structure.put("CACTA", 5.11);
structure.put("CACTT", 4.14);
structure.put("CACTG", 4.98);
structure.put("CACTC", 4.78);
structure.put("CACGA", 5.29);
structure.put("CACGT", 4.85);
structure.put("CACGG", 5.1);
structure.put("CACGC", 5.25);
structure.put("CACCA", 4.84);
structure.put("CACCT", 4.42);
structure.put("CACCG", 4.92);
structure.put("CACCC", 4.77);
structure.put("CTAAA", 5.82);
structure.put("CTAAT", 5.57);
structure.put("CTAAG", 5.49);
structure.put("CTAAC", 5.8);
structure.put("CTATA", 5.79);
structure.put("CTATT", 4.65);
structure.put("CTATG", 5.53);
structure.put("CTATC", 5.54);
structure.put("CTAGA", 5.84);
structure.put("CTAGT", 5.13);
structure.put("CTAGG", 5.69);
structure.put("CTAGC", 5.67);
structure.put("CTACA", 5.74);
structure.put("CTACT", 5.2);
structure.put("CTACG", 5.77);
structure.put("CTACC", 5.55);
structure.put("CTTAA", 5.58);
structure.put("CTTAT", 5.48);
structure.put("CTTAG", 5.49);
structure.put("CTTAC", 5.62);
structure.put("CTTTA", 4.7);
structure.put("CTTTT", 3.68);
structure.put("CTTTG", 4.52);
structure.put("CTTTC", 4.36);
structure.put("CTTGA", 5.4);
structure.put("CTTGT", 5.19);
structure.put("CTTGG", 5.31);
structure.put("CTTGC", 5.45);
structure.put("CTTCA", 5.15);
structure.put("CTTCT", 4.5);
structure.put("CTTCG", 4.92);
structure.put("CTTCC", 4.63);
structure.put("CTGAA", 5.93);
structure.put("CTGAT", 5.34);
structure.put("CTGAG", 5.56);
structure.put("CTGAC", 5.67);
structure.put("CTGTA", 5.41);
structure.put("CTGTT", 4.95);
structure.put("CTGTG", 5.32);
structure.put("CTGTC", 5.26);
structure.put("CTGGA", 5.31);
structure.put("CTGGT", 5.19);
structure.put("CTGGG", 5.39);
structure.put("CTGGC", 5.43);
structure.put("CTGCA", 5.79);
structure.put("CTGCT", 5.16);
structure.put("CTGCG", 5.67);
structure.put("CTGCC", 5.41);
structure.put("CTCAA", 5.9);
structure.put("CTCAT", 5.23);
structure.put("CTCAG", 5.56);
structure.put("CTCAC", 5.8);
structure.put("CTCTA", 5.41);
structure.put("CTCTT", 4.68);
structure.put("CTCTG", 5.14);
structure.put("CTCTC", 4.93);
structure.put("CTCGA", 5.42);
structure.put("CTCGT", 5.13);
structure.put("CTCGG", 5.65);
structure.put("CTCGC", 5.46);
structure.put("CTCCA", 5.02);
structure.put("CTCCT", 4.63);
structure.put("CTCCG", 5.01);
structure.put("CTCCC", 4.85);
structure.put("CGAAA", 4.98);
structure.put("CGAAT", 4.88);
structure.put("CGAAG", 4.92);
structure.put("CGAAC", 5.1);
structure.put("CGATA", 5.32);
structure.put("CGATT", 4.56);
structure.put("CGATG", 4.94);
structure.put("CGATC", 4.96);
structure.put("CGAGA", 5.17);
structure.put("CGAGT", 4.93);
structure.put("CGAGG", 5.18);
structure.put("CGAGC", 5.2);
structure.put("CGACA", 5.28);
structure.put("CGACT", 4.59);
structure.put("CGACG", 5.19);
structure.put("CGACC", 4.82);
structure.put("CGTAA", 6.11);
structure.put("CGTAT", 5.53);
structure.put("CGTAG", 5.77);
structure.put("CGTAC", 5.93);
structure.put("CGTTA", 5.15);
structure.put("CGTTT", 4.43);
structure.put("CGTTG", 4.98);
structure.put("CGTTC", 4.74);
structure.put("CGTGA", 5.71);
structure.put("CGTGT", 5.47);
structure.put("CGTGG", 5.64);
structure.put("CGTGC", 5.74);
structure.put("CGTCA", 5.39);
structure.put("CGTCT", 4.83);
structure.put("CGTCG", 5.19);
structure.put("CGTCC", 5.02);
structure.put("CGGAA", 5.09);
structure.put("CGGAT", 4.47);
structure.put("CGGAG", 5.01);
structure.put("CGGAC", 5.08);
structure.put("CGGTA", 4.96);
structure.put("CGGTT", 4.36);
structure.put("CGGTG", 4.92);
structure.put("CGGTC", 4.69);
structure.put("CGGGA", 4.95);
structure.put("CGGGT", 4.7);
structure.put("CGGGG", 4.94);
structure.put("CGGGC", 4.95);
structure.put("CGGCA", 5.17);
structure.put("CGGCT", 4.83);
structure.put("CGGCG", 5.09);
structure.put("CGGCC", 4.96);
structure.put("CGCAA", 5.81);
structure.put("CGCAT", 5.6);
structure.put("CGCAG", 5.67);
structure.put("CGCAC", 5.88);
structure.put("CGCTA", 5.22);
structure.put("CGCTT", 4.63);
structure.put("CGCTG", 5.13);
structure.put("CGCTC", 5.02);
structure.put("CGCGA", 5.42);
structure.put("CGCGT", 5.2);
structure.put("CGCGG", 5.51);
structure.put("CGCGC", 5.54);
structure.put("CGCCA", 5.06);
structure.put("CGCCT", 4.77);
structure.put("CGCCG", 5.09);
structure.put("CGCCC", 4.96);
structure.put("CCAAA", 5.42);
structure.put("CCAAT", 5.3);
structure.put("CCAAG", 5.31);
structure.put("CCAAC", 5.42);
structure.put("CCATA", 5.88);
structure.put("CCATT", 5.08);
structure.put("CCATG", 5.34);
structure.put("CCATC", 5.53);
structure.put("CCAGA", 5.56);
structure.put("CCAGT", 5.32);
structure.put("CCAGG", 5.4);
structure.put("CCAGC", 5.53);
structure.put("CCACA", 5.8);
structure.put("CCACT", 5.31);
structure.put("CCACG", 5.64);
structure.put("CCACC", 5.56);
structure.put("CCTAA", 5.96);
structure.put("CCTAT", 5.6);
structure.put("CCTAG", 5.69);
structure.put("CCTAC", 5.76);
structure.put("CCTTA", 4.81);
structure.put("CCTTT", 4.05);
structure.put("CCTTG", 4.65);
structure.put("CCTTC", 4.63);
structure.put("CCTGA", 5.47);
structure.put("CCTGT", 5.29);
structure.put("CCTGG", 5.4);
structure.put("CCTGC", 5.52);
structure.put("CCTCA", 5.3);
structure.put("CCTCT", 4.97);
structure.put("CCTCG", 5.18);
structure.put("CCTCC", 4.93);
structure.put("CCGAA", 5.38);
structure.put("CCGAT", 5.25);
structure.put("CCGAG", 5.65);
structure.put("CCGAC", 5.54);
structure.put("CCGTA", 5.33);
structure.put("CCGTT", 4.62);
structure.put("CCGTG", 5.1);
structure.put("CCGTC", 5.1);
structure.put("CCGGA", 5.39);
structure.put("CCGGT", 5.16);
structure.put("CCGGG", 5.19);
structure.put("CCGGC", 5.36);
structure.put("CCGCA", 5.59);
structure.put("CCGCT", 5.15);
structure.put("CCGCG", 5.51);
structure.put("CCGCC", 5.29);
structure.put("CCCAA", 5.44);
structure.put("CCCAT", 5.19);
structure.put("CCCAG", 5.39);
structure.put("CCCAC", 5.41);
structure.put("CCCTA", 4.99);
structure.put("CCCTT", 4.42);
structure.put("CCCTG", 4.85);
structure.put("CCCTC", 4.78);
structure.put("CCCGA", 5.22);
structure.put("CCCGT", 4.92);
structure.put("CCCGG", 5.19);
structure.put("CCCGC", 5.3);
structure.put("CCCCA", 4.89);
structure.put("CCCCT", 4.62);
structure.put("CCCCG", 4.94);
structure.put("CCCCC", 4.75);
}
}