package org.seqcode.genome.sequence.seqfunctions;
import java.util.HashMap;
import java.util.Map;
/**
* Scores Propeller Twist (degrees) 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 PropTwistStructureFunction implements SeqFunction{
//Variables
final int scoreDimension = 1;
int scoringOffset = 2;
int scoreWindowSize = 5;
boolean isBetweenNucs = false;
final String[] labels = {"PropT"};
final String description = "Propeller Twist (Rohs)";
Map<String, Double> structure = new HashMap<String, Double>();
public PropTwistStructureFunction(){
loadStructureValues();
}
public double[][] score(String seq) throws SeqFunctionException {
if(seq.length()<scoreWindowSize)
throw new SeqFunctionException("Sequence too short for PropTwistStructureFunction");
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 -0.03;}
public double getMinScore(){return -16.51;}
private void loadStructureValues(){
structure.put("AAAAA", -16.51);
structure.put("AAAAT", -14.89);
structure.put("AAAAG", -14.68);
structure.put("AAAAC", -14.47);
structure.put("AAATA", -12.63);
structure.put("AAATT", -14.95);
structure.put("AAATG", -11.76);
structure.put("AAATC", -12.27);
structure.put("AAAGA", -10.71);
structure.put("AAAGT", -11.68);
structure.put("AAAGG", -9.21);
structure.put("AAAGC", -10.58);
structure.put("AAACA", -13.05);
structure.put("AAACT", -12.78);
structure.put("AAACG", -13.15);
structure.put("AAACC", -12.41);
structure.put("AATAA", -9.65);
structure.put("AATAT", -10.43);
structure.put("AATAG", -11.61);
structure.put("AATAC", -10.45);
structure.put("AATTA", -12.20);
structure.put("AATTT", -14.95);
structure.put("AATTG", -11.93);
structure.put("AATTC", -11.18);
structure.put("AATGA", -9.02);
structure.put("AATGT", -10.82);
structure.put("AATGG", -8.98);
structure.put("AATGC", -9.59);
structure.put("AATCA", -9.91);
structure.put("AATCT", -10.31);
structure.put("AATCG", -9.51);
structure.put("AATCC", -9.67);
structure.put("AAGAA", -3.46);
structure.put("AAGAT", -3.55);
structure.put("AAGAG", -3.22);
structure.put("AAGAC", -3.82);
structure.put("AAGTA", -4.26);
structure.put("AAGTT", -6.26);
structure.put("AAGTG", -4.48);
structure.put("AAGTC", -4.07);
structure.put("AAGGA", -1.33);
structure.put("AAGGT", -1.48);
structure.put("AAGGG", -0.14);
structure.put("AAGGC", -1.50);
structure.put("AAGCA", -1.47);
structure.put("AAGCT", -1.56);
structure.put("AAGCG", -1.91);
structure.put("AAGCC", -1.55);
structure.put("AACAA", -10.17);
structure.put("AACAT", -10.22);
structure.put("AACAG", -9.26);
structure.put("AACAC", -9.40);
structure.put("AACTA", -6.07);
structure.put("AACTT", -6.26);
structure.put("AACTG", -5.42);
structure.put("AACTC", -5.23);
structure.put("AACGA", -9.62);
structure.put("AACGT", -10.39);
structure.put("AACGG", -10.04);
structure.put("AACGC", -9.91);
structure.put("AACCA", -8.86);
structure.put("AACCT", -8.15);
structure.put("AACCG", -7.97);
structure.put("AACCC", -7.68);
structure.put("ATAAA", -12.37);
structure.put("ATAAT", -11.27);
structure.put("ATAAG", -10.54);
structure.put("ATAAC", -10.51);
structure.put("ATATA", -8.95);
structure.put("ATATT", -10.43);
structure.put("ATATG", -8.33);
structure.put("ATATC", -8.30);
structure.put("ATAGA", -7.03);
structure.put("ATAGT", -8.26);
structure.put("ATAGG", -6.87);
structure.put("ATAGC", -6.84);
structure.put("ATACA", -8.93);
structure.put("ATACT", -8.21);
structure.put("ATACG", -9.05);
structure.put("ATACC", -8.36);
structure.put("ATTAA", -11.32);
structure.put("ATTAT", -11.27);
structure.put("ATTAG", -11.58);
structure.put("ATTAC", -11.34);
structure.put("ATTTA", -13.87);
structure.put("ATTTT", -14.89);
structure.put("ATTTG", -13.36);
structure.put("ATTTC", -12.09);
structure.put("ATTGA", -10.92);
structure.put("ATTGT", -11.94);
structure.put("ATTGG", -10.72);
structure.put("ATTGC", -10.60);
structure.put("ATTCA", -10.83);
structure.put("ATTCT", -10.15);
structure.put("ATTCG", -10.56);
structure.put("ATTCC", -9.61);
structure.put("ATGAA", -6.07);
structure.put("ATGAT", -6.15);
structure.put("ATGAG", -6.05);
structure.put("ATGAC", -6.37);
structure.put("ATGTA", -7.40);
structure.put("ATGTT", -10.22);
structure.put("ATGTG", -8.83);
structure.put("ATGTC", -7.10);
structure.put("ATGGA", -3.37);
structure.put("ATGGT", -4.33);
structure.put("ATGGG", -2.37);
structure.put("ATGGC", -3.12);
structure.put("ATGCA", -3.73);
structure.put("ATGCT", -3.68);
structure.put("ATGCG", -4.03);
structure.put("ATGCC", -3.12);
structure.put("ATCAA", -7.12);
structure.put("ATCAT", -6.15);
structure.put("ATCAG", -6.55);
structure.put("ATCAC", -6.53);
structure.put("ATCTA", -3.20);
structure.put("ATCTT", -3.55);
structure.put("ATCTG", -2.70);
structure.put("ATCTC", -2.78);
structure.put("ATCGA", -7.08);
structure.put("ATCGT", -6.85);
structure.put("ATCGG", -7.15);
structure.put("ATCGC", -6.96);
structure.put("ATCCA", -5.70);
structure.put("ATCCT", -5.29);
structure.put("ATCCG", -4.49);
structure.put("ATCCC", -4.91);
structure.put("AGAAA", -10.55);
structure.put("AGAAT", -10.15);
structure.put("AGAAG", -10.30);
structure.put("AGAAC", -10.59);
structure.put("AGATA", -8.23);
structure.put("AGATT", -10.31);
structure.put("AGATG", -7.85);
structure.put("AGATC", -8.23);
structure.put("AGAGA", -6.62);
structure.put("AGAGT", -7.83);
structure.put("AGAGG", -6.38);
structure.put("AGAGC", -6.50);
structure.put("AGACA", -8.49);
structure.put("AGACT", -7.81);
structure.put("AGACG", -8.81);
structure.put("AGACC", -8.04);
structure.put("AGTAA", -7.55);
structure.put("AGTAT", -8.21);
structure.put("AGTAG", -8.16);
structure.put("AGTAC", -8.16);
structure.put("AGTTA", -10.74);
structure.put("AGTTT", -12.78);
structure.put("AGTTG", -11.29);
structure.put("AGTTC", -10.45);
structure.put("AGTGA", -7.10);
structure.put("AGTGT", -8.48);
structure.put("AGTGG", -7.40);
structure.put("AGTGC", -7.68);
structure.put("AGTCA", -8.11);
structure.put("AGTCT", -7.81);
structure.put("AGTCG", -8.15);
structure.put("AGTCC", -7.34);
structure.put("AGGAA", -4.88);
structure.put("AGGAT", -5.29);
structure.put("AGGAG", -4.81);
structure.put("AGGAC", -5.39);
structure.put("AGGTA", -5.43);
structure.put("AGGTT", -8.15);
structure.put("AGGTG", -6.64);
structure.put("AGGTC", -5.67);
structure.put("AGGGA", -1.76);
structure.put("AGGGT", -2.62);
structure.put("AGGGG", -1.32);
structure.put("AGGGC", -1.88);
structure.put("AGGCA", -2.38);
structure.put("AGGCT", -2.34);
structure.put("AGGCG", -2.82);
structure.put("AGGCC", -2.20);
structure.put("AGCAA", -3.36);
structure.put("AGCAT", -3.68);
structure.put("AGCAG", -3.60);
structure.put("AGCAC", -3.79);
structure.put("AGCTA", -1.30);
structure.put("AGCTT", -1.56);
structure.put("AGCTG", -1.38);
structure.put("AGCTC", -0.83);
structure.put("AGCGA", -3.56);
structure.put("AGCGT", -3.93);
structure.put("AGCGG", -3.78);
structure.put("AGCGC", -3.87);
structure.put("AGCCA", -2.76);
structure.put("AGCCT", -2.34);
structure.put("AGCCG", -3.04);
structure.put("AGCCC", -2.48);
structure.put("ACAAA", -12.03);
structure.put("ACAAT", -11.94);
structure.put("ACAAG", -10.72);
structure.put("ACAAC", -11.70);
structure.put("ACATA", -8.52);
structure.put("ACATT", -10.82);
structure.put("ACATG", -10.15);
structure.put("ACATC", -8.65);
structure.put("ACAGA", -7.00);
structure.put("ACAGT", -8.12);
structure.put("ACAGG", -6.78);
structure.put("ACAGC", -7.34);
structure.put("ACACA", -9.33);
structure.put("ACACT", -8.48);
structure.put("ACACG", -9.43);
structure.put("ACACC", -8.57);
structure.put("ACTAA", -8.10);
structure.put("ACTAT", -8.26);
structure.put("ACTAG", -7.44);
structure.put("ACTAC", -8.16);
structure.put("ACTTA", -9.96);
structure.put("ACTTT", -11.68);
structure.put("ACTTG", -10.21);
structure.put("ACTTC", -8.83);
structure.put("ACTGA", -7.10);
structure.put("ACTGT", -8.12);
structure.put("ACTGG", -7.24);
structure.put("ACTGC", -7.79);
structure.put("ACTCA", -7.50);
structure.put("ACTCT", -7.83);
structure.put("ACTCG", -7.78);
structure.put("ACTCC", -6.75);
structure.put("ACGAA", -6.66);
structure.put("ACGAT", -6.85);
structure.put("ACGAG", -6.50);
structure.put("ACGAC", -6.61);
structure.put("ACGTA", -7.92);
structure.put("ACGTT", -10.39);
structure.put("ACGTG", -8.78);
structure.put("ACGTC", -7.92);
structure.put("ACGGA", -3.36);
structure.put("ACGGT", -4.79);
structure.put("ACGGG", -2.81);
structure.put("ACGGC", -3.97);
structure.put("ACGCA", -4.25);
structure.put("ACGCT", -3.93);
structure.put("ACGCG", -4.73);
structure.put("ACGCC", -3.63);
structure.put("ACCAA", -4.69);
structure.put("ACCAT", -4.33);
structure.put("ACCAG", -4.44);
structure.put("ACCAC", -5.00);
structure.put("ACCTA", -1.54);
structure.put("ACCTT", -1.48);
structure.put("ACCTG", -1.68);
structure.put("ACCTC", -0.88);
structure.put("ACCGA", -4.29);
structure.put("ACCGT", -4.79);
structure.put("ACCGG", -5.03);
structure.put("ACCGC", -4.55);
structure.put("ACCCA", -3.38);
structure.put("ACCCT", -2.62);
structure.put("ACCCG", -3.53);
structure.put("ACCCC", -2.37);
structure.put("TAAAA", -13.29);
structure.put("TAAAT", -13.87);
structure.put("TAAAG", -12.85);
structure.put("TAAAC", -13.54);
structure.put("TAATA", -9.98);
structure.put("TAATT", -12.20);
structure.put("TAATG", -10.52);
structure.put("TAATC", -10.25);
structure.put("TAAGA", -8.51);
structure.put("TAAGT", -9.96);
structure.put("TAAGG", -8.13);
structure.put("TAAGC", -8.92);
structure.put("TAACA", -11.35);
structure.put("TAACT", -10.74);
structure.put("TAACG", -11.31);
structure.put("TAACC", -10.83);
structure.put("TATAA", -7.14);
structure.put("TATAT", -8.95);
structure.put("TATAG", -7.69);
structure.put("TATAC", -7.88);
structure.put("TATTA", -9.98);
structure.put("TATTT", -12.63);
structure.put("TATTG", -9.70);
structure.put("TATTC", -10.01);
structure.put("TATGA", -7.00);
structure.put("TATGT", -8.52);
structure.put("TATGG", -6.69);
structure.put("TATGC", -8.11);
structure.put("TATCA", -7.32);
structure.put("TATCT", -8.23);
structure.put("TATCG", -7.63);
structure.put("TATCC", -7.47);
structure.put("TAGAA", -3.73);
structure.put("TAGAT", -3.20);
structure.put("TAGAG", -3.22);
structure.put("TAGAC", -3.62);
structure.put("TAGTA", -3.97);
structure.put("TAGTT", -6.07);
structure.put("TAGTG", -4.24);
structure.put("TAGTC", -3.90);
structure.put("TAGGA", -1.39);
structure.put("TAGGT", -1.54);
structure.put("TAGGG", -0.56);
structure.put("TAGGC", -1.23);
structure.put("TAGCA", -1.60);
structure.put("TAGCT", -1.30);
structure.put("TAGCG", -1.63);
structure.put("TAGCC", -1.22);
structure.put("TACAA", -7.17);
structure.put("TACAT", -7.40);
structure.put("TACAG", -6.49);
structure.put("TACAC", -6.58);
structure.put("TACTA", -3.97);
structure.put("TACTT", -4.26);
structure.put("TACTG", -4.20);
structure.put("TACTC", -3.05);
structure.put("TACGA", -6.48);
structure.put("TACGT", -7.92);
structure.put("TACGG", -6.70);
structure.put("TACGC", -7.22);
structure.put("TACCA", -5.96);
structure.put("TACCT", -5.43);
structure.put("TACCG", -5.99);
structure.put("TACCC", -5.01);
structure.put("TTAAA", -10.70);
structure.put("TTAAT", -11.32);
structure.put("TTAAG", -9.57);
structure.put("TTAAC", -10.44);
structure.put("TTATA", -7.14);
structure.put("TTATT", -9.65);
structure.put("TTATG", -8.06);
structure.put("TTATC", -7.66);
structure.put("TTAGA", -6.61);
structure.put("TTAGT", -8.10);
structure.put("TTAGG", -5.77);
structure.put("TTAGC", -6.12);
structure.put("TTACA", -7.55);
structure.put("TTACT", -7.55);
structure.put("TTACG", -7.71);
structure.put("TTACC", -7.21);
structure.put("TTTAA", -10.70);
structure.put("TTTAT", -12.37);
structure.put("TTTAG", -11.18);
structure.put("TTTAC", -11.89);
structure.put("TTTTA", -13.29);
structure.put("TTTTT", -16.51);
structure.put("TTTTG", -13.79);
structure.put("TTTTC", -13.16);
structure.put("TTTGA", -10.28);
structure.put("TTTGT", -12.03);
structure.put("TTTGG", -9.32);
structure.put("TTTGC", -10.88);
structure.put("TTTCA", -10.81);
structure.put("TTTCT", -10.55);
structure.put("TTTCG", -10.58);
structure.put("TTTCC", -10.09);
structure.put("TTGAA", -5.98);
structure.put("TTGAT", -7.12);
structure.put("TTGAG", -6.36);
structure.put("TTGAC", -7.07);
structure.put("TTGTA", -7.17);
structure.put("TTGTT", -10.17);
structure.put("TTGTG", -8.23);
structure.put("TTGTC", -7.48);
structure.put("TTGGA", -2.74);
structure.put("TTGGT", -4.69);
structure.put("TTGGG", -3.45);
structure.put("TTGGC", -3.85);
structure.put("TTGCA", -3.80);
structure.put("TTGCT", -3.36);
structure.put("TTGCG", -4.14);
structure.put("TTGCC", -3.14);
structure.put("TTCAA", -5.98);
structure.put("TTCAT", -6.07);
structure.put("TTCAG", -5.95);
structure.put("TTCAC", -6.21);
structure.put("TTCTA", -3.73);
structure.put("TTCTT", -3.46);
structure.put("TTCTG", -3.52);
structure.put("TTCTC", -2.40);
structure.put("TTCGA", -5.99);
structure.put("TTCGT", -6.66);
structure.put("TTCGG", -6.08);
structure.put("TTCGC", -6.08);
structure.put("TTCCA", -5.20);
structure.put("TTCCT", -4.88);
structure.put("TTCCG", -5.36);
structure.put("TTCCC", -4.39);
structure.put("TGAAA", -10.81);
structure.put("TGAAT", -10.83);
structure.put("TGAAG", -10.24);
structure.put("TGAAC", -10.38);
structure.put("TGATA", -7.32);
structure.put("TGATT", -9.91);
structure.put("TGATG", -8.13);
structure.put("TGATC", -7.81);
structure.put("TGAGA", -6.62);
structure.put("TGAGT", -7.50);
structure.put("TGAGG", -6.36);
structure.put("TGAGC", -6.75);
structure.put("TGACA", -8.28);
structure.put("TGACT", -8.11);
structure.put("TGACG", -8.47);
structure.put("TGACC", -7.96);
structure.put("TGTAA", -7.55);
structure.put("TGTAT", -8.93);
structure.put("TGTAG", -8.60);
structure.put("TGTAC", -8.00);
structure.put("TGTTA", -11.35);
structure.put("TGTTT", -13.05);
structure.put("TGTTG", -11.69);
structure.put("TGTTC", -10.91);
structure.put("TGTGA", -7.82);
structure.put("TGTGT", -9.33);
structure.put("TGTGG", -7.33);
structure.put("TGTGC", -8.30);
structure.put("TGTCA", -8.28);
structure.put("TGTCT", -8.49);
structure.put("TGTCG", -8.25);
structure.put("TGTCC", -7.71);
structure.put("TGGAA", -5.20);
structure.put("TGGAT", -5.70);
structure.put("TGGAG", -5.45);
structure.put("TGGAC", -5.78);
structure.put("TGGTA", -5.96);
structure.put("TGGTT", -8.86);
structure.put("TGGTG", -7.00);
structure.put("TGGTC", -6.17);
structure.put("TGGGA", -2.42);
structure.put("TGGGT", -3.38);
structure.put("TGGGG", -2.02);
structure.put("TGGGC", -2.77);
structure.put("TGGCA", -2.98);
structure.put("TGGCT", -2.76);
structure.put("TGGCG", -2.98);
structure.put("TGGCC", -2.54);
structure.put("TGCAA", -3.80);
structure.put("TGCAT", -3.73);
structure.put("TGCAG", -3.68);
structure.put("TGCAC", -3.74);
structure.put("TGCTA", -1.60);
structure.put("TGCTT", -1.47);
structure.put("TGCTG", -1.72);
structure.put("TGCTC", -0.94);
structure.put("TGCGA", -3.81);
structure.put("TGCGT", -4.25);
structure.put("TGCGG", -4.13);
structure.put("TGCGC", -3.94);
structure.put("TGCCA", -2.98);
structure.put("TGCCT", -2.38);
structure.put("TGCCG", -3.11);
structure.put("TGCCC", -2.52);
structure.put("TCAAA", -10.28);
structure.put("TCAAT", -10.92);
structure.put("TCAAG", -9.98);
structure.put("TCAAC", -10.22);
structure.put("TCATA", -7.00);
structure.put("TCATT", -9.02);
structure.put("TCATG", -9.26);
structure.put("TCATC", -7.37);
structure.put("TCAGA", -6.32);
structure.put("TCAGT", -7.10);
structure.put("TCAGG", -5.31);
structure.put("TCAGC", -6.36);
structure.put("TCACA", -7.82);
structure.put("TCACT", -7.10);
structure.put("TCACG", -8.08);
structure.put("TCACC", -7.04);
structure.put("TCTAA", -6.61);
structure.put("TCTAT", -7.03);
structure.put("TCTAG", -6.98);
structure.put("TCTAC", -6.38);
structure.put("TCTTA", -8.51);
structure.put("TCTTT", -10.71);
structure.put("TCTTG", -9.12);
structure.put("TCTTC", -8.18);
structure.put("TCTGA", -6.32);
structure.put("TCTGT", -7.00);
structure.put("TCTGG", -6.09);
structure.put("TCTGC", -6.69);
structure.put("TCTCA", -6.62);
structure.put("TCTCT", -6.62);
structure.put("TCTCG", -6.80);
structure.put("TCTCC", -6.10);
structure.put("TCGAA", -5.99);
structure.put("TCGAT", -7.08);
structure.put("TCGAG", -6.72);
structure.put("TCGAC", -6.68);
structure.put("TCGTA", -6.48);
structure.put("TCGTT", -9.62);
structure.put("TCGTG", -7.95);
structure.put("TCGTC", -7.11);
structure.put("TCGGA", -3.04);
structure.put("TCGGT", -4.29);
structure.put("TCGGG", -2.92);
structure.put("TCGGC", -3.40);
structure.put("TCGCA", -3.81);
structure.put("TCGCT", -3.56);
structure.put("TCGCG", -4.27);
structure.put("TCGCC", -2.99);
structure.put("TCCAA", -2.74);
structure.put("TCCAT", -3.37);
structure.put("TCCAG", -2.98);
structure.put("TCCAC", -3.48);
structure.put("TCCTA", -1.39);
structure.put("TCCTT", -1.33);
structure.put("TCCTG", -0.90);
structure.put("TCCTC", -0.44);
structure.put("TCCGA", -3.04);
structure.put("TCCGT", -3.36);
structure.put("TCCGG", -3.19);
structure.put("TCCGC", -3.15);
structure.put("TCCCA", -2.42);
structure.put("TCCCT", -1.76);
structure.put("TCCCG", -2.56);
structure.put("TCCCC", -1.44);
structure.put("GAAAA", -13.16);
structure.put("GAAAT", -12.09);
structure.put("GAAAG", -11.93);
structure.put("GAAAC", -12.76);
structure.put("GAATA", -10.01);
structure.put("GAATT", -11.18);
structure.put("GAATG", -9.43);
structure.put("GAATC", -9.46);
structure.put("GAAGA", -8.18);
structure.put("GAAGT", -8.83);
structure.put("GAAGG", -7.38);
structure.put("GAAGC", -8.01);
structure.put("GAACA", -10.91);
structure.put("GAACT", -10.45);
structure.put("GAACG", -11.06);
structure.put("GAACC", -10.08);
structure.put("GATAA", -7.66);
structure.put("GATAT", -8.30);
structure.put("GATAG", -8.88);
structure.put("GATAC", -8.06);
structure.put("GATTA", -10.25);
structure.put("GATTT", -12.27);
structure.put("GATTG", -10.33);
structure.put("GATTC", -9.46);
structure.put("GATGA", -7.37);
structure.put("GATGT", -8.65);
structure.put("GATGG", -7.48);
structure.put("GATGC", -7.60);
structure.put("GATCA", -7.81);
structure.put("GATCT", -8.23);
structure.put("GATCG", -7.79);
structure.put("GATCC", -7.56);
structure.put("GAGAA", -2.40);
structure.put("GAGAT", -2.78);
structure.put("GAGAG", -2.54);
structure.put("GAGAC", -3.46);
structure.put("GAGTA", -3.05);
structure.put("GAGTT", -5.23);
structure.put("GAGTG", -3.31);
structure.put("GAGTC", -3.11);
structure.put("GAGGA", -0.44);
structure.put("GAGGT", -0.88);
structure.put("GAGGG", -0.03);
structure.put("GAGGC", -0.70);
structure.put("GAGCA", -0.94);
structure.put("GAGCT", -0.83);
structure.put("GAGCG", -1.32);
structure.put("GAGCC", -0.53);
structure.put("GACAA", -7.48);
structure.put("GACAT", -7.10);
structure.put("GACAG", -6.88);
structure.put("GACAC", -7.25);
structure.put("GACTA", -3.90);
structure.put("GACTT", -4.07);
structure.put("GACTG", -3.96);
structure.put("GACTC", -3.11);
structure.put("GACGA", -7.11);
structure.put("GACGT", -7.92);
structure.put("GACGG", -7.15);
structure.put("GACGC", -7.38);
structure.put("GACCA", -6.17);
structure.put("GACCT", -5.67);
structure.put("GACCG", -5.99);
structure.put("GACCC", -5.33);
structure.put("GTAAA", -11.89);
structure.put("GTAAT", -11.34);
structure.put("GTAAG", -10.31);
structure.put("GTAAC", -10.83);
structure.put("GTATA", -7.88);
structure.put("GTATT", -10.45);
structure.put("GTATG", -8.42);
structure.put("GTATC", -8.06);
structure.put("GTAGA", -6.38);
structure.put("GTAGT", -8.16);
structure.put("GTAGG", -6.19);
structure.put("GTAGC", -6.96);
structure.put("GTACA", -8.00);
structure.put("GTACT", -8.16);
structure.put("GTACG", -8.84);
structure.put("GTACC", -8.12);
structure.put("GTTAA", -10.44);
structure.put("GTTAT", -10.51);
structure.put("GTTAG", -10.65);
structure.put("GTTAC", -10.83);
structure.put("GTTTA", -13.54);
structure.put("GTTTT", -14.47);
structure.put("GTTTG", -13.10);
structure.put("GTTTC", -12.76);
structure.put("GTTGA", -10.22);
structure.put("GTTGT", -11.70);
structure.put("GTTGG", -9.80);
structure.put("GTTGC", -10.75);
structure.put("GTTCA", -10.38);
structure.put("GTTCT", -10.59);
structure.put("GTTCG", -10.48);
structure.put("GTTCC", -9.91);
structure.put("GTGAA", -6.21);
structure.put("GTGAT", -6.53);
structure.put("GTGAG", -6.50);
structure.put("GTGAC", -6.82);
structure.put("GTGTA", -6.58);
structure.put("GTGTT", -9.40);
structure.put("GTGTG", -8.16);
structure.put("GTGTC", -7.25);
structure.put("GTGGA", -3.48);
structure.put("GTGGT", -5.00);
structure.put("GTGGG", -2.94);
structure.put("GTGGC", -4.03);
structure.put("GTGCA", -3.74);
structure.put("GTGCT", -3.79);
structure.put("GTGCG", -4.13);
structure.put("GTGCC", -3.41);
structure.put("GTCAA", -7.07);
structure.put("GTCAT", -6.37);
structure.put("GTCAG", -6.43);
structure.put("GTCAC", -6.82);
structure.put("GTCTA", -3.62);
structure.put("GTCTT", -3.82);
structure.put("GTCTG", -3.97);
structure.put("GTCTC", -3.46);
structure.put("GTCGA", -6.68);
structure.put("GTCGT", -6.61);
structure.put("GTCGG", -6.74);
structure.put("GTCGC", -6.90);
structure.put("GTCCA", -5.78);
structure.put("GTCCT", -5.39);
structure.put("GTCCG", -6.07);
structure.put("GTCCC", -5.28);
structure.put("GGAAA", -10.09);
structure.put("GGAAT", -9.61);
structure.put("GGAAG", -9.44);
structure.put("GGAAC", -9.91);
structure.put("GGATA", -7.47);
structure.put("GGATT", -9.67);
structure.put("GGATG", -7.65);
structure.put("GGATC", -7.56);
structure.put("GGAGA", -6.10);
structure.put("GGAGT", -6.75);
structure.put("GGAGG", -5.75);
structure.put("GGAGC", -6.07);
structure.put("GGACA", -7.71);
structure.put("GGACT", -7.34);
structure.put("GGACG", -8.11);
structure.put("GGACC", -7.55);
structure.put("GGTAA", -7.21);
structure.put("GGTAT", -8.36);
structure.put("GGTAG", -8.07);
structure.put("GGTAC", -8.12);
structure.put("GGTTA", -10.83);
structure.put("GGTTT", -12.41);
structure.put("GGTTG", -4.14);
structure.put("GGTTC", -10.08);
structure.put("GGTGA", -7.04);
structure.put("GGTGT", -8.57);
structure.put("GGTGG", -7.11);
structure.put("GGTGC", -7.89);
structure.put("GGTCA", -7.96);
structure.put("GGTCT", -8.04);
structure.put("GGTCG", -8.09);
structure.put("GGTCC", -7.55);
structure.put("GGGAA", -4.39);
structure.put("GGGAT", -4.91);
structure.put("GGGAG", -4.60);
structure.put("GGGAC", -5.28);
structure.put("GGGTA", -5.01);
structure.put("GGGTT", -7.68);
structure.put("GGGTG", -5.89);
structure.put("GGGTC", -5.33);
structure.put("GGGGA", -1.44);
structure.put("GGGGT", -2.37);
structure.put("GGGGG", -1.03);
structure.put("GGGGC", -2.13);
structure.put("GGGCA", -2.52);
structure.put("GGGCT", -2.48);
structure.put("GGGCG", -2.89);
structure.put("GGGCC", -1.93);
structure.put("GGCAA", -3.14);
structure.put("GGCAT", -3.12);
structure.put("GGCAG", -3.20);
structure.put("GGCAC", -3.41);
structure.put("GGCTA", -1.22);
structure.put("GGCTT", -1.55);
structure.put("GGCTG", -1.20);
structure.put("GGCTC", -0.53);
structure.put("GGCGA", -2.99);
structure.put("GGCGT", -3.63);
structure.put("GGCGG", -3.13);
structure.put("GGCGC", -3.39);
structure.put("GGCCA", -2.54);
structure.put("GGCCT", -2.20);
structure.put("GGCCG", -2.72);
structure.put("GGCCC", -1.93);
structure.put("GCAAA", -10.88);
structure.put("GCAAT", -10.60);
structure.put("GCAAG", -9.90);
structure.put("GCAAC", -10.75);
structure.put("GCATA", -8.11);
structure.put("GCATT", -9.59);
structure.put("GCATG", -9.43);
structure.put("GCATC", -7.60);
structure.put("GCAGA", -6.69);
structure.put("GCAGT", -7.79);
structure.put("GCAGG", -5.92);
structure.put("GCAGC", -6.76);
structure.put("GCACA", -8.30);
structure.put("GCACT", -7.68);
structure.put("GCACG", -8.40);
structure.put("GCACC", -7.89);
structure.put("GCTAA", -6.12);
structure.put("GCTAT", -6.84);
structure.put("GCTAG", -6.54);
structure.put("GCTAC", -6.96);
structure.put("GCTTA", -8.92);
structure.put("GCTTT", -10.58);
structure.put("GCTTG", -8.63);
structure.put("GCTTC", -8.01);
structure.put("GCTGA", -6.36);
structure.put("GCTGT", -7.34);
structure.put("GCTGG", -5.87);
structure.put("GCTGC", -6.76);
structure.put("GCTCA", -6.75);
structure.put("GCTCT", -6.50);
structure.put("GCTCG", -6.78);
structure.put("GCTCC", -6.07);
structure.put("GCGAA", -6.08);
structure.put("GCGAT", -6.96);
structure.put("GCGAG", -6.31);
structure.put("GCGAC", -6.90);
structure.put("GCGTA", -7.22);
structure.put("GCGTT", -9.91);
structure.put("GCGTG", -7.98);
structure.put("GCGTC", -7.38);
structure.put("GCGGA", -3.15);
structure.put("GCGGT", -4.55);
structure.put("GCGGG", -2.75);
structure.put("GCGGC", -3.73);
structure.put("GCGCA", -3.94);
structure.put("GCGCT", -3.87);
structure.put("GCGCG", -4.22);
structure.put("GCGCC", -3.39);
structure.put("GCCAA", -3.85);
structure.put("GCCAT", -3.12);
structure.put("GCCAG", -3.34);
structure.put("GCCAC", -4.03);
structure.put("GCCTA", -1.23);
structure.put("GCCTT", -1.50);
structure.put("GCCTG", -1.28);
structure.put("GCCTC", -0.70);
structure.put("GCCGA", -3.40);
structure.put("GCCGT", -3.97);
structure.put("GCCGG", -3.58);
structure.put("GCCGC", -3.73);
structure.put("GCCCA", -2.77);
structure.put("GCCCT", -1.88);
structure.put("GCCCG", -2.73);
structure.put("GCCCC", -2.13);
structure.put("CAAAA", -13.79);
structure.put("CAAAT", -13.36);
structure.put("CAAAG", -12.85);
structure.put("CAAAC", -13.10);
structure.put("CAATA", -9.70);
structure.put("CAATT", -11.93);
structure.put("CAATG", -10.42);
structure.put("CAATC", -10.33);
structure.put("CAAGA", -9.12);
structure.put("CAAGT", -10.21);
structure.put("CAAGG", -9.16);
structure.put("CAAGC", -8.63);
structure.put("CAACA", -11.69);
structure.put("CAACT", -11.29);
structure.put("CAACG", -11.71);
structure.put("CAACC", -4.14);
structure.put("CATAA", -8.06);
structure.put("CATAT", -8.33);
structure.put("CATAG", -8.20);
structure.put("CATAC", -8.42);
structure.put("CATTA", -10.52);
structure.put("CATTT", -11.76);
structure.put("CATTG", -10.42);
structure.put("CATTC", -9.43);
structure.put("CATGA", -9.26);
structure.put("CATGT", -10.15);
structure.put("CATGG", -9.01);
structure.put("CATGC", -9.43);
structure.put("CATCA", -8.13);
structure.put("CATCT", -7.85);
structure.put("CATCG", -8.32);
structure.put("CATCC", -7.65);
structure.put("CAGAA", -3.52);
structure.put("CAGAT", -2.70);
structure.put("CAGAG", -3.06);
structure.put("CAGAC", -3.97);
structure.put("CAGTA", -4.20);
structure.put("CAGTT", -5.42);
structure.put("CAGTG", -4.52);
structure.put("CAGTC", -3.96);
structure.put("CAGGA", -0.90);
structure.put("CAGGT", -1.68);
structure.put("CAGGG", -0.14);
structure.put("CAGGC", -1.28);
structure.put("CAGCA", -1.72);
structure.put("CAGCT", -1.38);
structure.put("CAGCG", -1.72);
structure.put("CAGCC", -1.20);
structure.put("CACAA", -8.23);
structure.put("CACAT", -8.83);
structure.put("CACAG", -8.12);
structure.put("CACAC", -8.16);
structure.put("CACTA", -4.24);
structure.put("CACTT", -4.48);
structure.put("CACTG", -4.52);
structure.put("CACTC", -3.31);
structure.put("CACGA", -7.95);
structure.put("CACGT", -8.78);
structure.put("CACGG", -8.46);
structure.put("CACGC", -7.98);
structure.put("CACCA", -7.00);
structure.put("CACCT", -6.64);
structure.put("CACCG", -6.56);
structure.put("CACCC", -5.89);
structure.put("CTAAA", -11.18);
structure.put("CTAAT", -11.58);
structure.put("CTAAG", -10.31);
structure.put("CTAAC", -10.65);
structure.put("CTATA", -7.69);
structure.put("CTATT", -11.61);
structure.put("CTATG", -8.20);
structure.put("CTATC", -8.88);
structure.put("CTAGA", -6.98);
structure.put("CTAGT", -7.44);
structure.put("CTAGG", -6.51);
structure.put("CTAGC", -6.54);
structure.put("CTACA", -8.60);
structure.put("CTACT", -8.16);
structure.put("CTACG", -8.43);
structure.put("CTACC", -8.07);
structure.put("CTTAA", -9.57);
structure.put("CTTAT", -10.54);
structure.put("CTTAG", -10.31);
structure.put("CTTAC", -10.31);
structure.put("CTTTA", -12.85);
structure.put("CTTTT", -14.68);
structure.put("CTTTG", -12.85);
structure.put("CTTTC", -11.93);
structure.put("CTTGA", -9.98);
structure.put("CTTGT", -10.72);
structure.put("CTTGG", -9.71);
structure.put("CTTGC", -9.90);
structure.put("CTTCA", -10.24);
structure.put("CTTCT", -10.30);
structure.put("CTTCG", -9.80);
structure.put("CTTCC", -9.44);
structure.put("CTGAA", -5.95);
structure.put("CTGAT", -6.55);
structure.put("CTGAG", -6.08);
structure.put("CTGAC", -6.43);
structure.put("CTGTA", -6.49);
structure.put("CTGTT", -9.26);
structure.put("CTGTG", -8.12);
structure.put("CTGTC", -6.88);
structure.put("CTGGA", -2.98);
structure.put("CTGGT", -4.44);
structure.put("CTGGG", -2.47);
structure.put("CTGGC", -3.34);
structure.put("CTGCA", -3.68);
structure.put("CTGCT", -3.60);
structure.put("CTGCG", -3.85);
structure.put("CTGCC", -3.20);
structure.put("CTCAA", -6.36);
structure.put("CTCAT", -6.05);
structure.put("CTCAG", -6.08);
structure.put("CTCAC", -6.50);
structure.put("CTCTA", -3.22);
structure.put("CTCTT", -3.22);
structure.put("CTCTG", -3.06);
structure.put("CTCTC", -2.54);
structure.put("CTCGA", -6.72);
structure.put("CTCGT", -6.50);
structure.put("CTCGG", -6.12);
structure.put("CTCGC", -6.31);
structure.put("CTCCA", -5.45);
structure.put("CTCCT", -4.81);
structure.put("CTCCG", -5.07);
structure.put("CTCCC", -4.60);
structure.put("CGAAA", -10.58);
structure.put("CGAAT", -10.56);
structure.put("CGAAG", -9.80);
structure.put("CGAAC", -10.48);
structure.put("CGATA", -7.63);
structure.put("CGATT", -9.51);
structure.put("CGATG", -8.32);
structure.put("CGATC", -7.79);
structure.put("CGAGA", -6.80);
structure.put("CGAGT", -7.78);
structure.put("CGAGG", -6.32);
structure.put("CGAGC", -6.78);
structure.put("CGACA", -8.25);
structure.put("CGACT", -8.15);
structure.put("CGACG", -8.49);
structure.put("CGACC", -8.09);
structure.put("CGTAA", -7.71);
structure.put("CGTAT", -9.05);
structure.put("CGTAG", -8.43);
structure.put("CGTAC", -8.84);
structure.put("CGTTA", -11.31);
structure.put("CGTTT", -13.15);
structure.put("CGTTG", -11.71);
structure.put("CGTTC", -11.06);
structure.put("CGTGA", -8.08);
structure.put("CGTGT", -9.43);
structure.put("CGTGG", -7.87);
structure.put("CGTGC", -8.40);
structure.put("CGTCA", -8.47);
structure.put("CGTCT", -8.81);
structure.put("CGTCG", -8.49);
structure.put("CGTCC", -8.11);
structure.put("CGGAA", -5.36);
structure.put("CGGAT", -4.49);
structure.put("CGGAG", -5.07);
structure.put("CGGAC", -6.07);
structure.put("CGGTA", -5.99);
structure.put("CGGTT", -7.97);
structure.put("CGGTG", -6.56);
structure.put("CGGTC", -5.99);
structure.put("CGGGA", -2.56);
structure.put("CGGGT", -3.53);
structure.put("CGGGG", -1.95);
structure.put("CGGGC", -2.73);
structure.put("CGGCA", -3.11);
structure.put("CGGCT", -3.04);
structure.put("CGGCG", -3.17);
structure.put("CGGCC", -2.72);
structure.put("CGCAA", -4.14);
structure.put("CGCAT", -4.03);
structure.put("CGCAG", -3.85);
structure.put("CGCAC", -4.13);
structure.put("CGCTA", -1.63);
structure.put("CGCTT", -1.91);
structure.put("CGCTG", -1.72);
structure.put("CGCTC", -1.32);
structure.put("CGCGA", -4.27);
structure.put("CGCGT", -4.73);
structure.put("CGCGG", -4.25);
structure.put("CGCGC", -4.22);
structure.put("CGCCA", -2.98);
structure.put("CGCCT", -2.82);
structure.put("CGCCG", -3.17);
structure.put("CGCCC", -2.89);
structure.put("CCAAA", -9.32);
structure.put("CCAAT", -10.72);
structure.put("CCAAG", -9.71);
structure.put("CCAAC", -9.80);
structure.put("CCATA", -6.69);
structure.put("CCATT", -8.98);
structure.put("CCATG", -9.01);
structure.put("CCATC", -7.48);
structure.put("CCAGA", -6.09);
structure.put("CCAGT", -7.24);
structure.put("CCAGG", -5.54);
structure.put("CCAGC", -5.87);
structure.put("CCACA", -7.33);
structure.put("CCACT", -7.40);
structure.put("CCACG", -7.87);
structure.put("CCACC", -7.11);
structure.put("CCTAA", -5.77);
structure.put("CCTAT", -6.87);
structure.put("CCTAG", -6.51);
structure.put("CCTAC", -6.19);
structure.put("CCTTA", -8.13);
structure.put("CCTTT", -9.21);
structure.put("CCTTG", -9.16);
structure.put("CCTTC", -7.38);
structure.put("CCTGA", -5.31);
structure.put("CCTGT", -6.78);
structure.put("CCTGG", -5.54);
structure.put("CCTGC", -5.92);
structure.put("CCTCA", -6.36);
structure.put("CCTCT", -6.38);
structure.put("CCTCG", -6.32);
structure.put("CCTCC", -5.75);
structure.put("CCGAA", -6.08);
structure.put("CCGAT", -7.15);
structure.put("CCGAG", -6.12);
structure.put("CCGAC", -6.74);
structure.put("CCGTA", -6.70);
structure.put("CCGTT", -10.04);
structure.put("CCGTG", -8.46);
structure.put("CCGTC", -7.15);
structure.put("CCGGA", -3.19);
structure.put("CCGGT", -5.03);
structure.put("CCGGG", -3.26);
structure.put("CCGGC", -3.58);
structure.put("CCGCA", -4.13);
structure.put("CCGCT", -3.78);
structure.put("CCGCG", -4.25);
structure.put("CCGCC", -3.13);
structure.put("CCCAA", -3.45);
structure.put("CCCAT", -2.37);
structure.put("CCCAG", -2.47);
structure.put("CCCAC", -2.94);
structure.put("CCCTA", -0.56);
structure.put("CCCTT", -0.14);
structure.put("CCCTG", -0.14);
structure.put("CCCTC", -0.03);
structure.put("CCCGA", -2.92);
structure.put("CCCGT", -2.81);
structure.put("CCCGG", -3.26);
structure.put("CCCGC", -2.75);
structure.put("CCCCA", -2.02);
structure.put("CCCCT", -1.32);
structure.put("CCCCG", -1.95);
structure.put("CCCCC", -1.03);
}
}