<div dir="ltr"><div>Thanks for answers!<br><div class="gmail_quote"><div dir="ltr"><div><span><div><br></div><div>I use 3.1. Today I checked results in SNAPSHOT version, but the problem remained.<br></div><div>Also I aligned sequences with themselves and recieved bad numbers  again.<br></div><div>As
 I understand it, score of alignment must be between minScore and 
maxScore , so similarity of sequences, which calculates according to<span lang="en"><span> formula<br><br></span></span></div><div><span lang="en"><span>(score - minScore)/(maxScore - minScore)<br></span></span></div><span lang="en"><span><br></span></span><span lang="en"><span>must be </span></span></span><span lang="en"><span>between 0.0 and 1.0. <br><br>Here is my code</span> <span>and</span> <span>two sequences. Notice, that the output of &quot;getMaxScore&quot; method is negative.<br>Sorry for terrible appearance of letter, but all examples is too large.<br></span></span></div><div><span lang="en"><span><br><br><br>public class NWSimilarity {<br><br></span></span></div><div><span lang="en"><span>   public static void main (String[] args) {<br></span></span></div><div><span><span lang="en"><span><br></span></span><span lang="en"><span><span lang="en"><span>      </span></span>SubstitutionMatrix&lt;NucleotideCompound&gt; matrix = SubstitutionMatrixHelper.getNuc4_4();<br></span></span><span lang="en"><span><span lang="en"><span>      </span></span>SimpleGapPenalty gap = new SimpleGapPenalty();<br><br></span></span></span><span lang="en"><span><span lang="en"><span>      </span></span>String str1 =<br>      &quot;AGATATATCTGAAGCTTAAAGGGCAGTGACAATGGCTGGCTCGGTTAACGGGAATCATAGTGCTGTAGGACCTGGTATAAATTATGAGACGGTGTCTCAAGTGGATGAGTTCTGTAAAGCACTTAGAGGGAAAAGGCCGATCCATAGTATTTTGATAGCTAACAATGGAATGGCGGCTGTGAAGTTTATACGTAGTGTCAGAACATGGGCTTATGAAACATTTGGTACGGAAAAAGCCATATTGTTGGTGGGGATGGCAACCCCTGAAGACATGCGGATCAATGCGGAGCATATCAGAATCGCTGATCAGTTTGTTGAGGTTCCCGGAGGAACCAACAATAACAATTATGCTAACGTTCAGCTGATTGTGGAGATGGCTGAAGTAACACGCGTGGATGCAGTTTGGCCTGGTTGGGGTCATGCATCTGAAAACCCCGAATTACCTGATGCCCTAGATGCAAAAGGAATCATATTTCTTGGTCCTCCAGCATCTTCAATGGCAGCACTGGGAGATAAGATTGGTTCTTCGTTGATTGCACAAGCTGCTGATGTACCCACTCTGCCATGGAGTGGTTCCCATGTTAAAATACCTCCTAATAGCAACTTGGTAACCATCCCAGAGGAGATCTACCGGCAAGCATGTGTCTACACAACTGAAGAAGCGATTGCTAGCTGTCAAGTTGTCGGTTACCCAGCAATGATCAAAGCATCGTGGGGTGGTGGTGGTAAAGGAATCAGGAAGGTTCATAATGATGATGAGGTTAGGGCTCTATTCAAGCAAGTTCAGGGTGAGGTCCCAGGCTCACCAATATTCATAATGAAGGTTGCGTCACAGAGTCGGCATCTAGAGGTCCAGCTGCTCTGTGACAAGCATGGAAATGTTTCAGCTCTGCATAGCCGTGATTGTAGCGTCCAGAGAAGACATCAAAAGATCATAGAGGAGGGTCCAATTACTGTGGCTCCGCCAGAAACTGTCAAGAAACTTGAACAAGCAGCTAGAAGGTTGGCTAAGAGTGTTAACTATGTTGGAGCTGCTACTGTTGAGTATCTCTACAGTATGGACACTGGGGAGTACTACTTCTTAGAGCTTAACCCTCGCTTACAGGTTGAGCATCCTGTCACTGAGTGGATTGCCGAGATAAATCTTCCTGCTGCCCAAGTTGCTGTGGGGATGGGAATTCCTCTCTGGCAAATCCCTGAGATAAGACGGTTCTATGGAATAGAACATGGTGGAGGTTATGATTCTTGGCGAAAAACATCTGTTGTAGCCTTCCCTTTTGATTTTGATAAAGCTCAATCTATAAGGCCAAAAGGTCATTGTGTGGCTGTACGTGTGACAAGTGAGGATCCTGATGACGGGTTCAAACCAACCAGCGGTAGAGTTCAGGAGTTGAGTTTTAAGAGCAAGCCAAATGTGTGGGCGTACTTCTCTGTCAAGTCTGGTGGAGGCATCCACGAGTTCTCGGATTCCCAGTTTGGACATGTTTTTGCATTTGGGGAATCCAGAGCCCTGGCGATAGCGAATATGGTTCTTGGGCTAAAAGAAATTCAGATCCGTGGAGAAATTAGGACTAACGTTGACTACACGATCGACCTTTTACATGCTTCTGATTACCGTGATAACAAAATTCACACTGGTTGGTTGGATAGTAGGATTGCTATGCGGGTCAGAGCTGAGAGGCCTCCATGGTATCTCTCTGTTGTCGGCGGAGCTCTCTATAAAGCATCAGCGACCAGTGCTGCTGTGGTTTCAGATTACGTTGGTTATCTGGAGAAGGGGCAAATCCCTCCAAAGCATATATCTCTTGTACATTCTCAAGTGTCTCTGAATATTGAAGGAAGTAAATATACGATTGATGTAGTCCGGGGTGGATCAGGAACCTACAGGCTAAGAATGAACAAGTCAGAAGTGGTAGCAGAAATACACACTCTACGTGATGGAGGTCTGTTGATGCAGTTGGATGGCAAAAGCCATGTGATATATGCAGAGGAAGAAGCTGCAGGAACTCGTCTTCTCATTGATGGAAGAACTTGTTTGCTACAGAATGACCACGATCCATCAAAGTTAATGGCTGAGACACCGTGCAAGTTGATGAGGTATTTGATTTCCGACAACAGCAATATTGACGCTGATACGCCTTATGCCGAAGTTGAGGTCATGAAGATGTGCATGCCACTTCTTTCACCTGCTTCAGGAGTTATCCATTTTAAAATGTCTGAAGGACAAGCCATGCAGGCTGGTGAACTTATAGCCAATCTTGATCTTGATGATCCTTCTGCTGTAAGAAAGGCCGAACCCTTCCATGGAAGTTTCCCAAGATTAGGGCTTCCAACTGCAATATCCGGTAGAGTTCATCAGAGATGTGCCGCAACATTAAATGCTGCACGCATGATTCTTGCTGGCTATGAGCATAAAGTAGATGAGGTTGTTCAAGACTTACTTAATTGCCTTGATAGCCCTGAACTCCCATTTCTTCAGTGGCAAGAGTGCTTTGCAGTTCTGGCGACACGACTACCTAAAAATCTCAGGAACATGCTAGAATCAAAGTATAGGGAATTTGAGAGTATTTCCAGAAACTCTTTGACCACCGATTTCCCTGCCAAACTTTTAAAAGGCATTCTTGAGGCACATTTATCTTCTTGTGATGAGAAAGAGAGAGGTGCCCTTGAAAGGCTCATTGAACCATTGATGAGCCTTGCAAAATCTTATGAAGGTGGTAGAGAAAGTCATGCCCGTGTTATTGTTCATTCTCTCTTTGAAGAATATCTATCAGTAGAAGAATTATTCAATGATAACATGCTGGCTGATGTTATAGAACGCATGCGTCAGCTATACAAGAAAGATCTGTTGAAAATTGTGGATATAGTGCTCTCACACCAGGGCATAAAAAACAAAAACAAACTCGTTCTCCGGCTCATGGAGCAGCTTGTTTACCCTAATCCTGCTGCTTACAGAGATAAACTTATTCGATTCTCAACACTTAACCATACTAACTACTCTGAGTTGGCGCTCAAGGCGAGTCAATTACTTGAACAGACCAAACTAAGTGAGCTTCGTTCAAACATTGCTAGAAGCCTTTCAGAGTTAGAAATGTTTACAGAGGACGGAGAAAATATGGATACTCCCAAGAGGAAAAGTGCCATTAATGAAAGAATAGAAGATCTTGTAAGCGCATCTTTAGCTGTTGAAGACGCTCTCGTGGGACTATTTGACCATAGCGATCACACACTTCAAAGACGGGTTGTTGAGACTTATATTCGCAGATTATACCAGCCCTACGTCGTTAAAGATAGCGTGAGGATGCAGTGGCACCGTTCTGGTCTTCTTGCTTCCTGGGAGTTCCTAGAGGAGCATATGGAAAGAAAAAACATTGGCTTAGACGATCCCGACACATCTGAAAAAGGATTGGTTGAGAAGCGTAGTAAGAGAAAATGGGGGGCTATGGTTATAATCAAATCTTTGCAGTTTCTTCCAAGTATAATAAGTGCAGCATTGAGAGAAACAAAGCACAACGACTATGAAACTGCCGGAGCTCCTTTATCTGGCAATATGATGCACATTGCTATTGTGGGCATCAACAACCAGATGAGTCTGCTTCAGGACAGTGGGGATGAAGACCAAGCTCAGGAAAGAGTAAACAAGTTGGCCAAAATTCTTAAAGAGGAAGAAGTGAGTTCAAGCCTCTGTTCTGCCGGTGTTGGTGTAATCAGCTGTATAATTCAGCGAGATGAAGGACGAACACCCATGAGACATTCTTTCCATTGGTCGTTGGAGAAACAGTATTATGTAGAAGAGCCGTTGCTGCGTCATCTTGAACCTCCTCTGTCCATTTACCTTGAGTTGGATAAGCTGAAAGGATACTCAAATATACAATATACGCCTTCTCGAGATCGTCAATGGCATCTGTATACTGTTACAGACAAGCCAGTGCCAATCAAGAGGATGTTCCTGAGATCTCTTGTTCGACAGGCTACAATGAACGATGGATTTATATTGCAGCAAGGGCAGGATAAGCAGCTTAGCCAAACACTGATCTCCATGGCGTTTACGTCGAAATGTGTTCTGAGGTCTTTGATGGATGCCATGGAGGAACTGGAACTGAATGCCCATAATGCTGCAATGAAACCAGATCACGCACATATGTTTCTTTGCATATTGCGTGAGCAGCAGATAGATGATCTTGTGCCTTTCCCCAGGAGAGTTGAAGTGAATGCGGAGGATGAAGAAACTACAGTTGAAATGATCTTAGAAGAAGCAGCACGAGAGATACATAGATCTGTTGGAGTGAGAATGCATAGGTTGGGCGTGTGCGAGTGGGAAGTGCGGCTGTGGTTGGTGTCCTCTGGACTGGCATGTGGTGCTTGGAGGGTTGTGGTTGCAAACGTGACAGGCCGTACATGCACTGTCCACATATACCGAGAAGTTGAAACTCCTGGAAGAAACAGTTTAATCTACCACTCAATAACCAAGAAGGGACCTTTGCATGAAACACCAATCAGTGATCAATATAAGCCCCTGGGATATCTCGACAGGCAACGTTTAGCAGCAAGGAGGAGTAACACTACTTATTGCTATGACTTCCCGTTGGCATTTGGGACAGCCTTGGAACTGTTGTGGGCATCACAACACCCAGGAGTTAAGAAACCATATAAGGATACTCTGATCAATGTTAAAGAGCTTGTATTCTCAAAACCAGAAGGTTCTTCGGGTACATCTCTAGATCTGGTTGAAAGACCACCCGGTCTCAACGACTTTGGAATGGTTGCCTGGTGCCTAGATATGTCGACCCCAGAGTTTCCTATGGGGCGGAAACTTCTCGTGATTGCGAATGATGTCACCTTCAAAGCTGGTTCTTTTGGTCCTAGAGAGGACGCGTTTTTCCTTGCTGTTACTGAACTCGCTTGTGCCAAGAAGCTTCCCTTGATTTACTTGGCAGCAAATTCTGGTGCCCGACTTGGGGTTGCTGAAGAAGTCAAAGCCTGCTTCAAAGTTGGATGGTCGGATGAAATTTCCCCTGAGAATGGTTTTCAGTATATATACCTAAGCCCTGAAGACCACGAAAGGATTGGATCATCTGTCATTGCCCATGAAGTAAAGCTCTCTAGTGGGGAAACTAGGTGGGTGATTGATACGATCGTTGGCAAAGAAGATGGTATTGGTGTAGAGAACTTAACAGGAAGTGGGGCCATAGCGGGTGCTTACTCAAAGGCATACAATGAAACTTTTACTTTAACCTTTGTTAGTGGAAGAACGGTTGGAATTGGTGCTTATCTTGCCCGCCTAGGTATGCGGTGCATACAGAGACTTGATCAGCCGATCATCTTGACTGGCTTCTCTACACTCAACAAGTTACTTGGGCGTGAGGTCTATAGCTCTCACATGCAACTGGGTGGCCCGAAAATCATGGGCACAAATGGTGTTGTTCATCTTACAGTCTCAGATGATCTTGAAGGCGTATCAGCAATTCTCAACTGGCTCAGCTACATTCCTGCTTACGTGGGTGGTCCTCTTCCTGTTCTTGCCCCTTTAGATCCACCGGAGAGAATTGTGGAGTATGTCCCAGAGAACTCTTGCGACCCACGAGCGGCTATAGCTGGGGTCAAAGACAATACCGGTAAATGGCTTGGAGGTATCTTTGATAAAAATAGTTTCATTGAGACTCTTGAAGGCTGGGCAAGGACGGTAGTGACTGGTAGAGCCAAGCTCGGGGGAATACCCGTTGGAGTTGTTGCAGTTGAGACACAGACTGTCATGCAGATCATCCCAGCCGATCCTGGACAGCTTGACTCTCATGAAAGAGTGGTTCCGCAAGCAGGGCAAGTCTGGTTTCCTGATTCAGCGGCCAAGACTGCTCAAGCGCTTATGGATTTCAACCGGGAAGAGCTTCCATTGTTTATCCTAGCGAACTGGAGAGGGTTTTCAGGTGGGCAGAGAGATCTTTTCGAAGGAATACTTCAGGCAGGTTCAACTATAGTAGAAAATCTGAGAACCTATCGTCAGCCAGTGTTTGTGTACATCCCAATGATGGGAGAGCTGCGCGGTGGAGCGTGGGTTGTTGTTGACAGCCAGATAAATTCGGATTATGTTGAAATGTATGCTGATGAAACAGCTCGTGGAAATGTGCTTGAGCCAGAAGGGACAATAGAGATAAAATTTAGAACAAAAGAGCTATTAGAGTGCATGGGAAGGTTGGACCAGAAGCTAATCAGTCTGAAAGCAAAACTGCAAGATGCCAAGCAAAGCGAGGCCTATGCAAACATCGAGCTTCTCCAGCAACAGATTAAAGCCCGAGAGAAACAGCTTTTACCAGTTTATATCCAAATCGCCACCAAATTTGCAGAACTTCATGACACTTCCATGAGAATGGCTGCAAAGGGAGTGATCAAAAGTGTTGTGGAATGGAGCGGCTCGCGGTCCTTCTTCTACAAAAAGCTCAATAGGAGAATCGCTGAGAGCTCTCTTGTGAAAAACGTAAGAGAAGCATCTGGAGACAACTTAGCATATAAATCTTCAATGCGTCTGATTCAGGATTGGTTCTGCAACTCTGATATTGCAAAGGGGAAAGAAGAAGCTTGGACAGACGACCAAGTGTTCTTTACATGGAAGGACAATGTTAGTAACTACGAGTTGAAGCTGAGCGAGTTGAGAGCGCAGAAACTACTGAACCAACTTGCAGAGATTGGGAATTCCTCAGATTTGCAAGCTCTGCCACAAGGACTTGCTAATCTTCTAAACAAGGTGGAGCCGTCGAAAAGAGAAGAGCTGGTGGCTGCTATTCGAAAGGTCTTGGGTTGACTGATATCGAAGACTTTAGCTTCTAATCCAAGAAAGATGGACATTTAAAGTTTGCTTGTGTCCGTTTGGATTGATAATTATATATTTGTTGGTCACAGTTGTAAATGTTGTTGTAGCTTTGTCATTTCCGTATAAACAAATACGCAATAATTCATTCAAC&quot;;<br><br></span></span></div><span lang="en"><span><span lang="en"><span>      </span></span>String str2 = <br></span></span><span lang="en"><span><span lang="en"><span>      </span></span>&quot;TAAAGTCTTCGATATCAGTCAACCCAAGACCTTTCGAATAGCAGCCACCAGCTCTTCTCTTTTCGACGGCTCCACCTTGTTTAGAAGATTAGCAAGTCCTTGTGGCAGAGCTTGCAAATCTGAGGAATTCCCAATCTCTGCAAGTTGGTTCAGTAGTTTCTGCGCTCTCAACTCGCTCAGCTTCAACTCGTAGTTACTAACATTGTCCTTCCATGTAAAGAACACTTGGTCGTCTGTCCAAGCTTCTTCTTTCCCCTTTGCAATATCAGAGTTGCAGAACCAATCCTGAATCAGACGCATTGAAGATTTATATGCTAAGTTGTCTCCAGATGCTTCTCTTACGTTTTTTACAAGAGAGCTCTCAGCGATTCTCCTATTGAGCTTTTTGTAGAAGAAGGACCGCGAGCCGCTCCATTCCACAACACTTTTGATCACTCCCTTTGCAGCCATTCTCATGGAAGTGTCATGAAGTTCTGCAAATTTGGTGGCGATTTGGATATAAACTGGTAAAAGCTGTTTCTCTCGGGCTTTAATCTGTTGCTGGAGAAGCTCGATGTTTGCATAGGCCTCGCTTTGCTTGGCATCTTGCAGTTTTGCTTTCAGACTGATTAGCTTCTGGTCCAACCTTCCCATGCACTCTAATAGCTCTTTTGTTCTAAATTTTATCTCTATTGTCCCTTCTGGCTCGAGCACATTTCCACGAGCTGTTTCATCAGCATACATTTCAACATAATCCGAATTTATCTGGCTGTCAACAACAACCCACGCTCCACCGCGCAGCTCTCCCATCATTGGGATGTACACAAACACTGGCTGACGATAGGTTCTCAGATTTTCTACTATAGTTGAACCTGCCTGAAGTATTCCTTCGAAAAGATCTCTCTGCCCACCTGAAAACCCTCTCCAGTTCGCTAGGATAAACAATGGAAGCTCTTCCCGGTTGAAATCCATAAGTGCTTGAGCAGTCTTGGCCGCTGAATCAGGAAACCAGACTTGCCCTGCTTGCGGAACCACTCTTTCATGAGAGTCAAGCTGTCCAGGATCGGCTGGGATGATCTGCATGACAGTCTGTGTCTCAACTGCAACAACTCCAACGGGTATTCCCCCGAGCTTGGCTCTACCAGTCACTACCGTCCTTGCCCAGCCTTCAAGAGTCTCAATGAAACTATTTTTATCAAAGATACCTCCAAGCCATTTACCGGTATTGTCTTTGACCCCAGCTATAGCCGCTCGTGGGTCGCAAGAGTTCTCTGGGACATACTCCACAATTCTCTCCGGTGGATCTAAAGGGGCAAGAACAGGAAGAGGACCACCCACGTAAGCAGGAATGTAGCTGAGCCAGTTGAGAATTGCTGATACGCCTTCAAGATCATCTGAGACTGTAAGATGAACAACACCATTTGTGCCCATGATTTTCGGGCCACCCAGTTGCATGTGAGAGCTATAGACCTCACGCCCAAGTAACTTGTTGAGTGTAGAGAAGCCAGTCAAGATGATCGGCTGATCAAGTCTCTGTATGCACCGCATACCTAGGCGGGCAAGATAAGCACCAATTCCAACCGTTCTTCCACTAACAAAGGTTAAAGTAAAAGTTTCATTGTATGCCTTTGAGTAAGCACCCGCTATGGCCCCACTTCCTGTTAAGTTCTCTACACCAATACCATCTTCTTTGCCAACGATCGTATCAATCACCCACCTAGTTTCCCCACTAGGGAGCTTTACTTCATGGGCAATGACAGATGATCCAATCCTTTCGTGGTCTTCAGGGCTTAGGTATATATACTGAAAACCATTCTCAGGGGAAATTTCATCCGACCATCCAACTTTGAAGCAGGCTTTGACTTCTTCAGCAACCCCAAGTCGGGCACCAGAATTTGCTGCCAAGTAAATCAAGGGAAGCTTCTTGGCACAAGCGAGTTCAGTAACAGCAAGGAAAAACGCGTCCTCTCTAGGACCAAAAGAACCAGCTTTGAAGGTGACATCATTCGCAATCACGAGAAGTTTCCGCCCCATAGGAAACTCTGGGGTCGACATATCTAGGCACCAGGCAACCATTCCAAAGTCGTTGAGACCGGGTGGTCTTTCAACCAGATCTAGAGATGTACCCGAAGAACCTTCTGGTTTTGAGAATACAAGCTCTTTAACATTGATCAGAGTATCCTTATATGGTTTCTTAACTCCTGGGTGTTGTGATGCCCACAACAGTTCCAAGGCTGTCCCAAATGCCAACGGGAAGTCATAGCAATAAGTAGTGTTACTCCTCCTTGCTGCTAAACGTTGCCTGTCGAGATATCCCAGGGGCTTATATTGATCACTGATTGGGGTTTCATGCAAAGGTCCCTTCTTGGTTATTGAGTGGTAGATTAAACTGTTTCTTCCAGGAGTTTCAACTTCTCGGTATATGTGGACAGTGCATGTACGGCCTGTCACGTTTGCAACCACAACCCTCCAAGCACCACATGCCAGTCCAGAGGACACCAACCACAGCCGCACTTCCCACTCGCACACGCCCAACCTATGCATTCTCACTCCAACAGATCTATGTATCTCTCGTGCTGCTTCTTCTAAGATCATTTCAACTGTAGTTTCTTCATCCTCCGCATTCACTTCAACTCTCCTGGGGAAAGGCACAAGATCATCTATCTGCTGCTCACGCAATATGCAAAGAAACATATGTGCGTGATCTGGTTTCATTGCAGCATTATGGGCATTCAGTTCCAGTTCCTCCATGGCATCCATCAAAGACCTCAGAACACATTTCGACGTAAACGCCATGGAGATCAGTGTTTGGCTAAGCTGCTTATCCTGCCCTTGCTGCAATATAAATCCATCGTTCATTGTAGCCTGTCGAACAAGAGATCTCAGGAACATCCTCTTGATTGGCACTGGCTTGTCTGTAACAGTATACAGATGCCATTGACGATCTCGAGAAGGCGTATATTGTATATTTGAGTATCCTTTCAGCTTATCCAACTCAAGGTAAATGGACAGAGGAGGTTCAAGATGACGCAGCAACGGCTCTTCTACATAATACTGTTTCTCCAACGACCAATGGAAAGAATGTCTCATGGGTGTTCGTCCTTCATCTCGCTGAATTATACAGCTGATTACACCAACACCGGCAGAACAGAGGCTTGAACTCACTTCTTCCTCTTTAAGAATTTTGGCCAACTTGTTTACTCTTTCCTGAGCTTGGTCTTCATCCCCACTGTCCTGAAGCAGACTCATCTGGTTGTTGATGCCCACAATAGCAATGTGCATCATATTGCCAGATAAAGGAGCTCCGGCAGTTTCATAGTCGTTGTGCTTTGTTTCTCTCAATGCTGCACTTATTATACTTGGAAGAAACTGCAAAGATTTGATTATAACCATAGCCCCCCATTTTCTCTTACTACGCTTCTCAACCAATCCTTTTTCAGATGTGTCGTGATCGTCTAAGCCAATGTTTTTTCTTTCCATATGCTCCTCTAGGAAATCCCAGGAAGCAAGAAGACCAGAACGGTGCCACTGCATCCTCACGCTATCTTTAACGACGTAGGGCTGGTATAATCTGCGAATATAAGTCTCAACAACCCGTCTTTGAAGTGTGTGATCGCTATGGTCAAATAGTCCCACGAGAGCGTCTTCAACAGCTAAAGATGCGCTTACAAGATCTTCTATTCTTTCATTAATGGCACTTTTCCTCTTGGGAGTATCCATATTTTCTCCGTCCTCTGTAAACATTTCTAACTCTGAAAGGCTTCTAGCAATGTTTGAACGAAGCTCACTTAGTTTGGTCTGTTCAAGTAATTGACTCGCCTTGAGCGCCAACTCAGAGTAGTTAGTATGGTTAAGTGTTGAGAATCGAATAAGTTTATCTCTGTAAGCAGCAGGATTAGGGTAAACAAGCTGCTCCATGAGCCGGAGAACGAGTTTGTTTTTGTTTTTTATGCCCTGGTGTGAGAGCACTATATCCACAATTTTCAACAGATCTTTCTTGTATAGCTGACGCATGCGTTCTATAACATCAGCCAGCATGTTATCATTGAATAATTCTTCTACTGATAGATATTCTTCAAAGAGAGAATGAACAATAACACGGGCATGACTTTCTCTACCACCTTCATAAGATTTTGCAAGGCTCATCAATGGTTCAATGAGCCTTTCAAGGGCACCTCTCTCTTTCTCATCACAAGAAGATAAATGTGCCTCAAGAATGCCTTTTAAAAGTTTGGCAGGGAAATCGGTGGTCAAAGAGTTTCTGGAAATACTCTCAAATTCCCTATACTTTGATTCTAGCATGTTCCTGAGATTTTTAGGTAGTCGTGTCGCCAGAACTGCAAAGCACTCTTGCCACTGAAGAAATGGGAGTTCAGGGCTATCAAGGCAATTAAGTAAGTCTTGAACAACCTCATCTACTTTATGCTCATAGCCAGCAAGAATCATGCGTGCAGCATTTAATGTTGCGGCACATCTCTGATGAACTCTACCGGATATTGCAGTTGGAAGCCCTAATCTTGGGAAACTTCCATGGAAGGGTTCGGCCTTTCTTACAGCAGAAGGATCATCAAGATCAAGATTGGCGATAAGTTCACCAGCCTGCATGGCTTGTCCTTCAGACATTTTAAAATGGATAACTCCTGAAGCAGGTGAAAGAAGTGGCATGCACATCTTCATGACCTCAACTTCGGCATAAGGCGTATCAGCGTCAATATTGCTGTTGTCAGAAACCAAATACCTCATCAACTTGCACGGTGTCTCAGCCATTAACTTTGATGGATCATGGTCATTCTGTAGCAAACAAGTTCTTCCATCAATGAGAAGACGAGTTCCTGCAGCTTCTTCCTCTGCATATATCACATGGCTTTTGCCATCCAACTGCATCAACAGACCTCCATCACGTAGAGTGTGTATTTCTGCTACCACTTCTGACTTGTTCATTCTTAGCCTGTAGGTTCCTGATCCACCCCGGACTACATCAATCGTATATTTACTTCCTTCAATATTCAGAGACACTTGAGAATGCACAAGAGATATATGCTTTGGGGGAATTTGCCCCTTTTCTAGATAGCCAACGTAATCCGAAACTACAGCAGAACTGGTCGTAGATGCTTTATAAAGAGCCCCACCGACTACAGAGAGATACCATGGAGGTCTCTCTGCTCTGACCCGCATAGCAATCCTACTGTCCAACCAACCAGTGTGTATTTTGTTTTCCCGGTAATCAGAAGCATGTAGAAGGTCGATCGTGTAGTCAACGTTAGTCCTAATTTCTCCACGGATCTGAATTTCTTTTAGCCCAAGAACCATATTCGCTATCGCCAGGGCTCTGGATTCCCCAAATGCAAAAACATGTCCAAACTGGGAATCCGAGAACTCGTGGATGCCTCCACCAGACTTGACAGAGAAGTACGCCCACACATTTGGCTTGCTCTTAAAACTCAACTCCTGAACTCTACCGCTGGTTGGTTTGAACCCGTCATCAGGATCCTCACTTGTCACACGTACAGCCACACAATGACCTTTTGGCCTTATAGATTGAGCTTTATCAAAATCAAAAGGGAAGGCTACAACAGATGTTTTTCGCCAAGAATCATAACCTCCACCATGTTCTATTCCATAGAACCGTCTTATCTCAGGGATTTGCCAGAGAGGAATTCCCATCCCCACAGCAACTTGGGCAGCAGGAAGATTTATCTCGGCAATCCACTCAGTGACAGGATGCTCAACCTGTAAGCGAGGGTTAAGCTCTAAGAAGTAGTACTCCCCAGTGTCCATACTGTAGAGATACTCAACAGTAGCAGCTCCAACATAGTTAACACTCTTAGCCAACCTTCTAGCTGCTTGTTCAAGTTTCTTGACAGTTTCTGGCGGAGCCACAGTAATTGGACCCTCCTCTATGATCTTTTGATGTCTTCTCTGGACGCTACAATCACGGCTATGCAGAGCTGAAACATTTCCATGCTTGTCACAGAGCAGCTGGACCTCTAGATGCCGACTCTGTGACGCAACCTTCATTATGAATATTGGTGAGCCTGGGACCTCACCCTGAACTTGCTTGAATAGAGCCCTAACCTCATCATCATTATGAACCTTCCTGATTCCTTTACCACCACCACCCCACGATGCTTTGATCATTGCTGGGTAACCGACAACTTGACAGCTAGCAATCGCTTCTTCAGTTGTGTAGACACATGCTTGCCGGTAGATCTCCTCTGGGATGGTTACCAAGTTGCTATTAGGAGGTATTTTAACATGGGAACCACTCCATGGCAGAGTGGGTACATCAGCAGCTTGTGCAATCAACGAAGAACCAATCTTATCTCCCAGTGCTGCCATTGAAGATGCTGGAGGACCAAGAAATATGATTCCTTTTGCATCTAGGGCATCAGGTAATTCGGGGTTTTCAGATGCATGACCCCAACCAGGCCAAACTGCATCCACGCGTGTTACTTCAGCCATCTCCACAATCAGCTGAACGTTAGCATAATTGTTATTGTTAGTTCCTCCGGGAACCTCAACAAACTGATCAGCGATTCTGATATGCTCCGCATTGATCCGCATGTCTTCAGGGGTTGCCATCCCCACCAACAATATGGCTTTTTCCGTACCAAATGTTTCATAAGCCCATGTTCTGACACTACGTATAAACTTCACAGCCGCCATTCCATTGTTAGCTATCAAAATACTATGGATCGGCCTTTTCCCTCTAAGTGCTTTACAGAACTCATCCACTTGAGACACCGTCTCATAATTTATACCAGGTCCTACAGCACTATGATTCCCGTTAACCGAGCCAGCCATTGTCACTGCCCTTTAATCTTCAGATATATCTTGTAAGGAAGCAGA&quot;;<br><br></span></span><span lang="en"><span><span lang="en"><span>      </span></span>DNASequence target = new DNASequence(str1,<br>                    AmbiguityDNACompoundSet.getDNACompoundSet());<br><br></span></span><span lang="en"><span><span lang="en"><span>      </span></span>DNASequence query = new DNASequence(str2,<br>                        AmbiguityDNACompoundSet.getDNACompoundSet());<br><br></span></span><span lang="en"><span><span lang="en"><span>      </span></span>NeedlemanWunsch aligner = new NeedlemanWunsch(query, target, gap, matrix);<br><br></span></span><span lang="en"><span><span lang="en"><span>      </span></span>System.out.println(&quot;getScore: &quot; + aligner.getScore());<br></span></span><span lang="en"><span><span lang="en"><span>      </span></span>System.out.println(&quot;getMaxScore: &quot; + aligner.getMaxScore());<br></span></span><span lang="en"><span><span lang="en"><span>      </span></span>System.out.println(&quot;getMinScore: &quot; + aligner.getMinScore());<br></span></span><span lang="en"><span><span lang="en"><span>      </span></span>System.out.println(&quot;getSimilarity: &quot; + aligner.getSimilarity());<br>   }             <br>}<br></span></span></div><div><div><div class="gmail_extra"><br></div>
</div></div></div><br><br>Regards,<br></div>Alexander Beskrovnyy<br></div>