Please use Java to finish that, thx!

The DNA.txt file is like this:

GGAGGCCGAGACCAGACGCGGAGCCATGGCCGAGGTGTTGCGGACGCTGG CCGGTGAGTGCAGGCCTCGGCCCCGGGTGCCCGCGAGGGAGCCGCTACCG CAGGGAATGCGGGGTGCACCCGACAGCCGGGCCGGGGTGGGGGCGCTCAG GGCTGCGAGGCTTCGGGCCGGCCGCCGCCCCAGCCTCCGAGACCCTGCGT CCTGGGGAGCCGGCGGGCAGGTGGGCTCGGCCGCGCTGTGGGTGCCTGGG ACCCGCAGGGAGGATGGGCGCGGTGGCGCGGCCTGGCGGGGGGCTCGTCT CCGGGGTCCCCGGGTCCTGGTGAGAGCGGGGTCCCTCGACGCCGTGGCGG TCTCCAGCCTCTCCTCGCCCCTCCACGCTCCCCGCCTTCCATGAGCTGCT ATTTTCAGCACCTACCGCCCGACCCTGGACTAGGACAAGGCTCTGGGCTG CCCTGCCCGCCCCCCAGCCCTTCCCTCGGGCACGGCGGCCAGGCGCCCGG GTTGACCGGGAACAGCCTCCATACCCCAAACGCGGAGGCGCCTCGGGAAG GCGAGGTGGGCAAGTTCAATGCCAAGCGTGACGGGGGAACTGTGCCCCGG GCCCTCAGGTGATATAGGAGTTAAGAAGAAATTATTGAGGCAACCAGATG CGGTGACTCAGGCCTGTAACCCCAGCACTTTGGGAGGCCGAGGGTGGATC ACCTGTCCTTAATTTTCTTGGCGCCAGAAGATGAATTGAGTATTTACCCA GACAACAACGTCGCTTCAGAGGGAGGGATGCAGAACGCAGGGCCACGGGG TGCAGGCTGCAGGCCAGTGAACCCCAACGCCAAAGGCCAGGGAGAGCCGG GTGGGGTACCCAGAGCCAGCACACAGCCCTTTAATTTAGAGGAGTGCTGT GTACACATCTGGGGAGAGATGTTTTACTTTGATTTGGAATCAGGTGGCGG ATAAGGCATACTGAGGCCTGACTTGGTGAGGGCTCCTGCCCCGGAGGTGC AGCCCTGGAGGAGCGGGAGGCAGAGGAGTGGAAAATTCATGAAGAAAACC GGGTATGGTGTAGGTCGAGGCCCTGCCCTCAGTAATGCTCACCATTTGTC AGTGTTTACTGTGAGGCAGCACTGTGTTCAGTATCGCTGAGTTCTCAGGA AGGAACGGTAAATACTTCCCGGGTCATTCTTTCACCCACGGGAAAACAGG TTTGGAGAGATCTGGGACAGTGCTCTGGTCCTAGGCAGGAAGGGCTGAGT GGGGCCTGGGACTCAGGTCTGACTGCAAACACCTGCCTCCTCCCTGTGCT GCCAGCGCCTTCCGGGTTCTTCCCTGTCCCTCCTTTGTGGTCTTTGTTTT CCCTTTTTTGTCTTAATATGTTTCAACGGATGTATACAATAAACCGCACA TGAAAGGTACAGCTGGATACATCTTGACCCAGTCAAGATGATGAACACAG CTGCCACCCCAGGAGTCTGTCCTGCCCCACGGGTTATGCTGTCTTAGTTG GTCTCATGTCAGGGAGCCTTGGAGGACCAGGGTCGGGCAGTTGGTCTCTA TACTCCTGGGGTTCTGGCACTGGCTCTGGCCCATGACCGCACCCAAGACA AACGTCTTGAAGACTAAGAGGTTAGGTCTTTGAGAAACCTGGCAAATGAG TGCCCATTCTCAGGTTACCCACATTCTGCATGTTGATTTAGTCATCCAAC CAATGTTGGTTGAACACTGATGAGAACAAGCAGGCCTGTGCTAGAAGGTG CCTGCAGCCAGGAGCTGGTGAGCTGGTGTCCTTAGGGACACCAATGGCGA GGGACCCAGTGTGTGGAAATCTGGGGGACAAGCATGCCAGGGAGAAGAGC TCACATGGGGAAGGCCCGGCTCCACAAATCAGTCAGGCTTGTTGGGGCGG GCAGGAGAGCAGGGTAGTGGAGTCAGAGGGAGTGATCCCCCGAAAGGCAG GAAGAGGACATGAGAGAGCCTTGGAGATGACGGTGAGGATGTGGTTGGTG GGCGGTGAGCTGGGTGTCATGTGCTGGCTCCTTAGAGAATGCTCAGCTCC TTCACACCCATCATAATCCCTGGAGGACTGAGACCACGTGCAGGAGTTTT GGAAGCTGGCAGTGCACCCAGTCCCGGCTCTCCTCCATTCTGGTGGGTCT CACCAGAGATTGGCCAAGAAGAGATCAAACTGTTCCTGGACCAAACTGAG GGTGGGGCTGCTATCTCTCGCGGCCCAATAACGAGATGCAGATGAACTGG GGAGAAAGAGAGTTTTTATTTCTGTAACCAGTTACAAGGAGAAGACCTGG AAATTATCTCCAGACCAACTCAAAATTACAAAGTTTTCCAGAGCTTATAT ACCTTCTAAGCTATATGTCTATGTGTAAGTGTGCATTCATCTCAAGACAT AAGTAATTGACTTATGTTAATCTATAACTAAGGTCTGAGTCCTGAAGACC TTCCTCTGGATCCTCAGTAAATTTACTTAATCTAAAACCCTTATCTTGTC TCCTAAATCATGGGGGTTTGGGAAGTTCCTTCAGACCCCCAGTAAACTTA TTTGTGGAGTCCTGGGGAATTTCTTCAGATCCCCAATAAAACTTGTTTAA TCCTAAATGGGTCCTGTTAAGAATTCCTTCGTTATTTTGTCATGCTTGAA GGCCCAGGAAAGGTCTAGGCAAAACTCTTGGTGGGATTTTGTTATATTCC AGCCTTTTTATAAGGGCACTGGCTTTTAATATTTAATTTAACCACTCAGT CAGTACTGAAACAGTTGTTAGGGAGGCCTGCGTTAGTGAGACCTGACCTG CCACAACACATCTTACTCGGAATGCTGCCCATAACTTCAAAAAATCAGCT TTGACGGAGCCCTACTGAACACACCTAGCATCTCTCTTCCTTCAGCTTAG GGTCAAGGGGCTGGGGTTGATGGCACCATTGAAAGAAACAGCTTTATTGC CGTGTCATTGATATGCCATAAAATTCACCTGTTTCAAATGAATTATTTTC AGTTAGTTTACAGAGTTGTGAAATAAATTTTATAACTTTTCCATCCCCAG CCCACCAAAACTCCCTGGAACTCCTCCGCAGTCATTCCCCATTCCCACCT GGCCTCAGACAATCACTTTCTGTCTCTCCAGTCTTGCCTTTTCTGGACAG TTCCTATGAATGGAGTCCTGTGTTACATGGTCTTTTGCATCTGACTTCCT TCACTTAGAATAATGATTCCGAGATTCATGTATGTTGTAGTATGTATCAG TATTTAATTCCTTTTTATTACTGAATAATCCATTGTACAGATAGACCACA TTTTGTTTATCCATTCATCAGCTGAAGGACATTTCGGCTGTTTCTGCTTT TTTAGCTATTTTAAACTGCACGCAGCACTGCTATGAACATTTGTGTACAA GACTTTGTGTGAACATGTTTTCATTTCTCTTGGGTTGATACCCAGCAGAG GAATTGCTGGGTCATACAGAAAGTCTGATTTAACATTTTAAGAAACTAGC AAACTGTTTTCCAAAGTGACTGCCCCATTTTACATTCCCATCAGCAGTGT ATAACGGTTCTAATTTTCTTTTCCTTTTTCTTTTCTTGAGACAAGGTTTT GCTCTGTCACCCAGGCTGGAGTGCAGTGGCATGATCTTGGCTCACTGCAG CCTCAATCTCTTGGGCTCAATTGGTCCTCCCACCTCAGCCTCCTGAGTAG CTGGGACTACAGGTGAGTACCACCACATCCAGCTAATTTTTGTATTTTTG GTAGAGATGGGGTTTTGCCATGTTGCCCAGGCTGTTCTCAAACTCCTGGG CTCAAGTGATCTGCCCACCTCGGCCTCCCCAAGTCCTGGGATTATAGGTG TGAGCCGCTGCGCCTGGCTGAGGGTTCCACTGTCTGTACGTCTGCAGCAA TACATACCATTCTTGTGGGTAAAAGGTGGTATCTCATTATAGTTTTGATT TGCATTTCCCCAAGGTCAAATGATGGCAAGTGGCTTTTCTTGTGCTTTTT AGCCATTTGTATATGTTTTTGGTGAAATGCCTATTGAAATGTTTTGCCTT TTTAAAAATTGAGTTGTCTCCTTTGTTCAGTTTTGAGAGTTCTTTACATA CACAGTATCATATATATATATATATATATATATATATATATATATATATA CACACCAGATATATGATTTGCAAATATTTTCAACCATCAATAGTTTAACA CTTTTTTATTGGTATTTTGAAGTAGAAAAGTTTTACATTTTGATCCATTC CAATTTATTAACTTTTTCTTTTATTGTGTATCTGGTATCATATCTAAGAA ATCTTAATCCAGTGTCACAAAGATTTAATCTTATATTTTCTTCTAACCGC TTTCTAGTTTATGTGTAAGAATCTGTCCATTTTACCTAAGTTGCATAATT TGTTGGCAAACAGTTGTACATAGTATTTCCTTGAAATCCTTTTAATCTCT GTAAGATTGGAATTGCTGTCTCCTCTTTTAGTCCTGATTTTAGTTATTTG TGTTCTCTCTCTCTCTGGTCAATGTAGCTAAAGCTTTGTCAATTCTCTTG ATCTTTTCAGAGAACTGCCATTTGATATTTTTTTACTTTATCTTTTTCTT TCTGTTCTCTAGTTCATTGGTTTCCACTCTTCTCACTTTGGGTTTAATTC GTTCTGTCTTTTCTTATTGTAGTTACTTACAATGGAAGCTTACACACTTG ATTTAAGATTTTTTTTTCTAATGTAGACATTTACAGCTATAAATTTCCCT TGAAACACAGCTTTAGTTATATCTCATAAATTTTGGTATGTTGTGTTTAC ATTTTCATTCAGCTCAGTGTATCTTTTGATTTTCTTCTTTGACCCATTGC TTATTTAGAATTATGTTGTTTAATTTCTATGTATTTATAGGTTTCCCAAA TTTCTTTTGTTAATTTCTGATTTCATTCCCCTGTGGCTAGAGAAGAAACT CTGTGGATATCAGTCCTTTCGAATTTCTCAGAATTGTTTTATGGTCCAGC ATATGATTGACCTTGGACACTGTTCCATGTGCACTTGAGGAGAACGTGAC TTCGGCTCTTGCCAGGTGGAGTGTTCTAGAGATGTCAGTTGGTGTCCAGT GATGTCAAGTCATTTGTATCTACTGATTTTCTTTCTAATTATTCTATCCA TTACTGAGAGTGGGGTAGGATTTTGGTGTCCAATTATTGTTTTTTTGTTT TTTTTTTTTTGTTTGTTTTTTTTTTTTTTTGAGGTGGAGTCTCACTTTGT CACCCAGGCTGGAGTGCAGTGGTATGATCACAGCTCACTGCAGCCCCCAC CTCCCAAGGCTTAGGTCACCTCAGCCTCCTGAGTAGCTGCAACTACAGGC AAGTACCATCATGCCTAGCTGATTTTTGCATTTTTTATAGACAGGGTTTT GCCATGTTACTTAGGCTGGTCACGAACTCCTGGGCTCAAGTGACCCACCC ACCTCGGCCTCCCAAAGTGCTGGGATTACAAGCGTGAGTCACCATGCCTG GCCCAACCATTACTGGTGAATTGACTGTTTCACCCTTCAATTCTGTGAGT TTTTGCTTCATGTATTGCTGCGGGATAATTAAGGAATCAGAGAGACCGAT GGGGTTGAGGAGGAATTATTTAATTATTTAGGTGCACCGACCCAATCAGA TTAACATCCAAAGGACTGGGCCCCAAACAAAGAGTCAAGCTACCTTTTAA GCATTTTGTGGGGTGGGGGGAGATTTGTGCAGGGGGAAGAGTATTACAGA AGCAAGAAACAAAGACAGTTATTCAGTTAAGACATGCATTACATTATTTC TTACTTTTCAAGGAACAACACGTTTTATGACTCAAGATTATCTGTTTAGT GACCTTGCAGCTGCACAGCTAGAGAAACAGAGTCTTCGCAATGCCTGGGA AAGGGAGAGATAAGGCTCACTAGCCACAGAAAAACAGCCAGTTAATTTTT AAAGGACTCCAGCCCTTTCTCTTCCTCAAGGGGAATTGGTTTTTTACATA CAACTGAGTTTTTGCTTACACAGTTTTTAATTTCTTTTAATTCCTGTTCT AGTATTTTGGGGCTAGGTTGTCAGGTATGTATATATTTCTGTTTGTTATA TTTTCGTGATGTATTCACTTTATATCATGGCAGAATGTTTCTCTTTAGTA AGATTTTTGATCTTAAAAAAGTTGGCCAGATGGGGTGGCTCATGCCTGTG ATCCCAGCACTTTGGGAGGCCAAGGCAGGTGGATCACCTGAGGTCAGGAG TTCAAGACTAGCCTGGCGAACATGGTGAAACCCCGTCTCTACTGAAAATA CAAAAAAATTAGCCAGCTGTGATGGTGTGCGCCTGTAATCCCTGCTACTT GGGAGGCTGAGGCACGAGAATTGCTTGAACCCGGGAGGCTGAGGTTACAG TCAGCCAAGATCGTGCCACTGCACTCCAACCTGGGTGATAGAGTGAGACT CTGTCTCAAAAAAACAAAAAAATTATTTAGTCTGACGTTAGCATTTCTCC TCAAGCTCCCTTACGGTTGTTTGCATAGCAAATCTACTATCCTTTTGCTT TGACCTATTTGTATCTTTGTTTCTAAAGTATGTATGTCTCTCACAGGCAG CATATAGTCAAAGCTTAAAAAAAAAATCCAGTCTAACGATCTCTGCCTTT TGATTGGCATGTTCATTCTATTCCCATTCAATGTTATTATTGCTGTGGTT GGATTTCCATCTATCAGTTCACAATTTGTTTTCTATGTTTTATGCCTTTT TGTTCTTCTGTTCATCTTTTACTACCTTCTTTTGTATTAAGTATTTTCTA GTGTAGCATTTAAATTCCCTTTTTCTTTTTAAGTGTATATTTTAAAGTTA TTTTGTTAGTGTTTGCTCCAGGGATTACAATATGCATTTTAATTTATCAG GATCTACTTCAGATTAATACTAATTTTAGTAAAATACAGGAACTTGACTC CAGTATAACTCCATTTCCTCCCTCCTTGCTTGTGGTTTGTAGTATTATTG TCGTATATGTTCATCTATATATGTTATAAACTCAACAACATGGTGTTATA ATTATTGTTTCACACAATCTTATTTCTTTTCAATTCAGTAAGACAAGTAA GGAGAAAAACACTTTTCAAGTCTTTTATATTACACTGTATATTTATCACT GACTTTACTCTTGATTTCTTCCTGTATATTCAAGCTATTGTCTGGTGACC TTTCCTTGCTCCAGTATATATAATAACTTCATTGCCTCCTTGCTCCTTTA TGCTATTATTGTCATATATATTATATATGTTTATGCTGTGAGCCCATCAG CTAAGTCAGCTTAGCAAGGTCTCAAGATACAAAGTCAATGAATAAATCAG GCTGGGTGTGGTGGCTCACACCTGCAATCCCAGCACTTTGGGAGGCCAAG ATAGGTAGATCACTTGAGGCCAGGAGTTTGAGAGCAGCCTGGCCCACATG GCAAGACTCCATCTTTACAAAAATACAAAAAAAAAAAAAAAGTTGAGTGT GGTGGTGCGCCTGTAATCCCACCTACTTGGGAGGCTGAGGCATGAGAATT GCTTGAACCCAGGAGGGAGAGGTTGCAGTGACTGGAGATCACACCACTGC ACTCCAGACTGGGCAACAGGGCAAGACACAGTCTAAAAAAAAAAAAAAAA GAAAAAAGAAAAACAAGAATAAATCAATTATTTTTCTATAATACTTGCCA CAATCAATTGAACCATGAAAAATTTTAAATACCATTTACAGTAGCATCAT AAAACATGAAATATTTAGAGAATAATTTACCAAATTAGGAGAAATGTCTA TACAATTAAAACTGCAATATAAACCAGGCACCATGGCTCATGCCTGTAAT CCCAGCACTTTGGGAGGTCAAGGTGGCCAGATCACTTGAGCCCAGAAGTT TGAGACCAGCCTGGGTGACATAGTGAGACCCTGTCTCTACAAAAAAAAAA AAAAATTAGCTGGGCATGGTGGCATGCACCTGTAGCCCCTGCTACTCAGG AGGCTGAGGTGAGAGGATGACTTGAGCCCAGTAGGCAGAGATTGCAGTGC ATTCCAGCCTGGGCTACACAGCAAGACCCTGACAAAAAAAAAAAAAAAAA GAAAAAGAAGGTCACAAAAAAACAGAAAACTGCAAAATATTGATGACAAA AATTAAAGAAGACATAAATAAATGGAGAAATATACCATGCTCATGGATTG GAAGACTTACATTGCTAAACTGTCACTTCTCCCCAGATGGATCTACAGAG TCCACATAATCTCACTTAAAACTCCAGAAGAAATTTTTGTAAAGTTGACA GCTGATTCTAAAATTTTACATAGTAATCAGAATAGGTTGATATTAGGATA GACAGATAGTTCAATGGAATAGAATGCAGAGTTTAGAAATAGACCTACAC AGAAATAGTCCATTGATTTTTTAAGAGTTGCTTTTTGATAAGGGTGCTAA GGTAATGTGATAGAGAAAGGAAAGTATTTTCAATTCAAATGGCTGAAATG ACTGGATATCCATTGAGGGAAGAAAGGGACTTTAGCCTTTCACACAATAC ACAAAAATTATGGAATTCTGAAGAAAATAAGAGAAAATGTTCATGAACTT GGGGTAGGCAAAAATTTAATAGATGAGGCAAAAAAAAAAAAAGGCCCAAA CCATAAAAATGGTTTCATTTTTATAAGGATAAATTAGAGTTTATAAAAAT TAACACTTCCCTTCAAAAGAAAAATTAAGGAAAAATGAATAAATAAGCCA CCGACTGAAAGAAAATATTTGTTTTCTAAGAAGTATTTTGTTTTTCATTT TATGGGTTCATAGTAGGTGTATATATTTATGGGGTCCCTGAGATATTGTG GTTCAGTCATACAATGGAAAATTCACATCATGGAGAACTGGTATCCATCC TCTTGAGCAATTATCCTTTGTGTTACAAACAATCCAACTATACTCTTTTA GTTATTTTTATTCTTTTTTTTTTTTTTTTTGAGATGGAGTCTCGCTCTGT CACCCAGGCTGGAGTGTGGTGGCGCCATCTCAACTCACTGCAACCTCCGC CTCCCAGGTTTAAGTGATTCTCCTGCCTCAGTTTCCTGAGTAGCTGGGAC TACAGGCACCCACCACCACGCCCGGCTAGTTTTTGTATTTTTAAACTTTT TTTTTCTTTTTTCTTTTTCTTCTTTTTTTTTTTTTGAGATGGAGTCTCGC TCTGTCGCCCGGGCTGGAGTGCAGTGGTGCAATCTCGGCTCACTGCAACC TCCGTCTCCCAGGTTCAGGAGATTCTCCTGCCTCAGCCTCCCAAGTAGCT GGGATTACAGGCATGCGCCACCACACCCAGCTAATTTTTTGTATTTTTAG TAGAGGCAGGATTTCACCGTGTTGGTCAGGCTAGACTCGAATGCCTGACC TCGTGATCCACCCACCTCGGCCTCCCAAAGTGCTGGGGTTACGGGCGTGA GCCACCACGCCTGGCCTTAGTTTTTGTATTTTTAGTAGAGATGAGGTTTC ACCATGTTGGCCAGGCTGGTCTTGAACTCCTGATCTCAGGTGATCCACCT GCCTCGGCCTCCCAAAGTGCTGAGATTACAGGCATGAGCCACTGTGCCCG ACCTCTCTTTTAGTTATTTTTAAATGTGCAATTAAATTATTATTGACTAT AGTCTCCCTGTTATGCTATCAAATACTGGGTCTTATTCATTCTTTCTATT TATTTGTACACATTAACCATCCCTACATACCCTCTCACCCCTGCCACTAC CCTTCCAAGTCTCTGCGAACCATCCTTCTATTCTCTATCTCCATGAGTTT AATTGTTTCGATGTTTTGATACTACAGATAAGTGAGAACATGCAGTGTCT GTCTCTCTGTGCCTGGCGAGAAAATATTTGTAATATTTGTATTTGGCAAA GGACTTGTATCCAAAATATAGAAATAAATTCTGCTCAATAATAAAAAGAG AAACAACTTAATGAGACCCAGTGTCTACAAAAAGTAGAATAATTAGCCGG GCATGTTGGTGCATGTCTGTAGTCCCACCTAATCAGGAGGCTGAGGGGGA AAGATCACTTAAGCTCAGGAGTTCGAGGTTGCAGCGAGCTGTGATCGTGC CACTGCACTCCAGCCTGGGTGACAGAGTAAGATCCTGTCTAAAAAAAATA AAAATAGAGGGCCAGGTGAGGTGGCTTATGCCTGTAATCCCAGCACATTG GGAGGCTGAGGCAGGTGGATTGCTTAAGCCCAGGAGTTCAAGACCAGCCT GGGCAACATGGTGAAACCCCATCTCTACCAAAACCACAAAAAATCAGCTA GATGTGGTGCATGCCTATAGTCTCAGCTACTCAAAAGGCTGAGGTGGGAG GATCACCTGAGCCCAGGAAGTCGAGGCTGTAGTGAGCCATGATCATGCCA CCACACTCCAGCCTGGGCAACTGGAGTGGGACTGTGCCCCCCAAAAATAT ATATAAGTAAATAAATAAATAAATAAATAATAAAATGAGCTAAAGATCTG GACAGGCTTCATAAGAAGCAAGCAAATGGCCAATAAATACATGAAAAGAT GATTTACCTCCTTAGTCATTGGACACACTTAGATACCACTCCTCATCCAC TAGCATGGCTAAAGGATAAAAGAGTGACCATCAAGTGTTGGCAAGGACTG TGGTTCTCGTACATTCCTGGCGGGAATGGAAAATTCAGTCACCACTTTGG AACACAGTTTCTTACAAAGTTAAACATACACTTACCATATGACCCATCTT TTCCATTCCTTGGTATTTACTCAAGGGAAATGAAAACACAGGTCCACAAA TACCTGCACATGAGTGTTTACAGAAGCTTTGTTGCTAGTGGCCCCGAACA GTGAAAAAACCACAGTGTCTGTCAATAGGAGACAGAATAAATGAATTGTG GCGGATTAACAATGGCGTGCTTCTCAGAAATGAAAAAGAACGAACGATTG ATACACGTGACAATATAGGTGAATCTTCAAAACAGCATGCGGTGTGATGC GGCCAGACATAAAAGAGCATGTATCAGAGGATTCCGTGTATGGGAAACGC CAGGGAATCAGATCCATGGTTGTCAGGGTCAGGAGGGACCTTACTGGGGT GATTACATGTGTACATACATTGTGTGAAACTCATCAAAACCGTATACCTA AAGTGGGCACATTTTATTGGATGTAAGTTATCCCTCAAATTAAATTAATT TTCAAAGTTTTAAAAAATGGAACCATTTTTGCCACATTGAAGGAAAATTA TTTCCACCAAGATTTCCCTACAGCCAAACGATCTACCAACTACAAAAATG GAAAAAATAATTTAGGACATGTAAAGTTCAAATGTTTTGCCTCCCACGTT TCTGTTTCAAGAAGCTATTCGAGATAAATCGCTCCGTGGTCACAGGACTT AGAAAGGTGGAGGTAAACACACACAAGCATTATAAGATAAGAAGTAACAG ATGAATTAGTTGAAAGGGACTGATTTCGGGGGAAGGAATAGGAACTGGGC CAGGAGATAGACGCCTTTCAGGCTTGCCCTTGTGAAAACGATAGTCCCCT CTTACCTGCGGGGGATAGGTTCCGAGATCCCCAGTGGATGTCTGAAACCA CAGATAGTACCAAACCCTACAGAGAGTATGTTTTCTCCTGTACACACATA CCTATGATAGGGTTTAATTTATAAATTAGGCACCGGGTGGGATTAACAAC CATAATTAATAGTAAAATAGAACAATTATAACAATATACTGTCCGAGGCG GGTGGATCACTTGAAGTCAGGAGATCGAGACCAGCCTGGCCAACATGGTG AAACCTGTCTCTACTAAAAATACAAAAAATTAGCCAGGCGTAGTGGTGGG CGCCTGTAAACCCAGCTACTCGGGAGGCTGAGGCAGGAGAATTGCTTGAA CCCGGGAGGCGGAGGCTGTAGTGAGCCGAAGGTGCCCCTTTGCACTCCAG CCTGGGCAACGAGCAAAACTCCATCTCAAAAACAACAACAAAACAACAAC AACAACAAAAACAATATACTGTAATAAAGGTTACGTGAATGTGGTCTCTC TAAAAAAAAATGTGTATATATCTTAGTTTGTGGGTTTTTTGTTGTTGTAG TTTTGTTTATTATTAAGAGACAGGGTCTTGCTCTGTTACCCAGGCTGGAG TGCAGTGGTGTGATCATGGCTTACTGCAGCCTTCACCTCCTAGGCTCAAG TGATCCTTCCACCTCAGCCTCCTGGGACCAGAGGCATGCACCACTATGCC CAGCTAATTGTTTTTTTTTTTTTTTTCTTGATAGAAATGAGTTCTCACTA TGTTGCCCAGGCTGGTCTAGAACTCCTGGCTTCCAGCAATTCTGCTGGCT CAGCCTCCCAAAGTCCTGGGATTATAGGCACGAGCCACGATGCCTGTCCT CAAAATATTTTACTGTACTGTACTCACCTATTATTGGCCTTTGGTTGACC ATGGGTAACTGAAACTCCAGCAAGCGAAGGTGTGGATAAGGGAACTACTG TACGTGACTTTAATATACATAAAATCACCTTAAAGACAATGATTGTTTCC AGAACATGAGCCTCTGAGACAGCAGGGAGATACTAGGGGAAGTTGGTGGC TCCTCTCCCTGGCAGGAACTGGTCTGGGCTCCTGGCTCAGCCTGGCCATG AGGCTGTCCTGGCCTCCCTCGGTGGGTTCGACAGTGACCTCGACGTGCTC ATTTCAGTGTGGTTCATTCCGGTCTCCCAGGGGAAGGGGGTGCTGAGTGG AAGGAGGTCAATGGGAAGCCGGGGTGGCTCTCAGAGTCTGCAGGAGCAGT CGGGCTGATGAGCTGGGAGGAGCAGACCGCCTCCCTCTTCTCTGAGTGGG AGGAGGGCCAGATCTGGACTGGGTTTGGAGATGCTCAGGTGGGGCTCAGA GCATCACCTGTGGGGCAGAGGGACCATCTTGGCAGATGAAGGCCCGTCGC AGGGTGTGATGCCTGAATTACAAGGCGGGACAGGTAAAGTGGGGCAGGTG AGAGAAGGAGGGTGAGTGATGTGATTTTTCTACTCCTGTTTTCCAGGAAA ACCAAAATGCCACGCACTTCGACCTATGATCCTTTTCCTAATAATGCTTG TCTTGGTCTTGTTTGGGTAAGACACATTTGACCATCGAGGCTGGCCTGGT TTGGGGAGAAGTGACCACAGCAGCCAATCAGACCCATGGGGCCTCCCTGA GCTCCCCAAGTATCACAGTTATCAGGGTCCTAAGGACAGTTATTGCCTGC GTCCAGCTCTGGCGGAGGGTGTGCTTACTTGCTCCCTTATTTTAGCCTCA CCTGGGCAACAGGCTCATCTCACTCCCATTTAAAATTTTCCTAAGTGTGG AGTCTGGGGCTGGGAGAGCAAGCCCCTTGCCCACAATTGCGTGGCTGGGG GTGGGGAAGGCAATTCTGGGTCCCAAGCTGTTAGTCGCTTCCAGACACAG AAGGTCCCAGAACCAAGAGTGAAGTCACCTGTCACCTCTACTGGGGCATC TCTGGACACGGTCTGGAAACACTCCCTGACGTGGCCTCAGGGACTGCACT GACCAAGGCACTGGTGGCGGGGGGTGAGGGAGCTGGGGCTCTGGAGCTCC AGCAGGTGCCCATACGTGAGCAATATCCCAGGGACCACCCTCCTGCCCAC CTCCCGGTGTGGGACGTGGCGAGGCGCCTGAGCTTTGCTGAGAACTTGCC CTACCTGCCTCGAGGCCTTGCAGCTTCACCGGGAACTCTTGTGCTCACGC TGCTGGCCGCACCATGCACTTTTTGGAGGAAGGGACCAACAGGCAGTCTT CGTTCTGTGTCCTGAGTCTTGGCACACTTCCTTTCTGCAGTTACGGGGTC CTAAGCCCCAGAAGTCTAATGCCAGGAAGCCTGGAACGGGGGTTCTGGTG AGTGCAGGGAAGAGCAGGTGGAGCATCCATGCTGGCCGGGGTGCTGGCTG TGGGCGGGGGTCCCACTCTGGGAACTCCCCCTCCCCTTCCTGGGCCCGCT CTCTATGCTCTGCCCAGTGTAGACATGCTCAACTCTGTGGCCTTGAAGGG TCACCTGGATACCTCTGGAGTCAGCCTTGACCTCCCTTCTGACCTCCAGT CCCCAACTCCAGGCTTACCCAGAGTTCCCATGCATGGTCTCTGCTCCCCC ATCCCCACCCCTCCTCCACCAGCCATCCTCAACTCTCCCTTTGCTCTCAC CCCTACACTGGGTTCCCAAATCCTGCCAGCCCTGCTCTTCAGCAGCTCGC GTGCCCACTGGCCTCCCTGCCTTCGACGTCCTGCTCCAGGGCTCCGGTGG GGCTGCCCTCATCTCTGTGACAGCCTCAGACTTGTCTCCCCATCCCCATC AGCCCTGTCCCCCTTCTTCTCACAGCAGCTGGAGTGATCTTTCCAGAACA TAAGGTAGGAGGCTCTCCATGATCTGATCCTGCCTTCCTGACCTCCCCAG CCTCATCTCTCCCTCCTCTGCCCTCGCCCTCTGTGCTCCAGCCAACGTGG CCTGTCACTCGTCCACCTGCCATACTGTCCTGACTCCAGGCCTTTGCCTG TGCTATGGCCTCTGTTGGGACCACTCTTGTCTCTCCCCTGCTGTGTCTGC TAATTCCCACTCGTGTCAGTGATCCATGGCTGCAGAACACACCACTCCAT CCATGGAAAACAATCACAATCATTGATTACTATCTCTCCCTGGGCTTCCT GGGGTGGACTGGGCTCAGCTGGGTGGTTCACTTTGGGGCCTCAGCAGTCA TGGGCAGACAGTGGCTGGGGTCACTGCAAAGACTTCCCTGCATCTCTGGC AGTTGATGCTGGCTGTCATCTGAGACACCTACCCAGGGCCTCTCCCTGGG GCCTGGGCTCCTGCTTAGCTTGGTTGGGAGGCTCCAAGACCAACATCCCA AGAAAGATGAGACAGAAGCCAGATCACCTTTTTGGGCCTGGCTTCAGAAG TCACCCAGCATCACTTCTGCTGCATTTATTTCTTAGAAACACAGAATATC AGACCCCATCTCTTGATGGGAGGGGGCCTCATGGTTTGTAGACATGTTCT GAAACTCCACTCTGCCCGGCCTTGGCTTCGACGTGTCTGGTGAATGTGTG GGCTGTGAGGCTCCCCGAACGTAGACCTCAGACTGCAACGCTGGCCGTTA CAGGGTCTGGCACACGGGCCCACGTCAGGCCCATCGCCACAGTGATGGTT GTTCTGTGACTGTTTCTGGTGGCCTCTGCTCCACACTCCAGGCTGACGCT GTGCCCCTTCCACTGGGACCCTCGGGTGGCTTCCATGCACTTGTGCCCTA AATCCTGCTCCTAGACTAAACTTCATCTCCTGTGTTCTCATTCTGCAGCA TGGCTGTTAGGGAACCTGACCATCTGCAGCGCGTCTCGTTGCCAAGGTAT AATGTCAGTGCCTCCCTTCAGTGGCTCCCATGTCACAGAATTGTCCTGCA GCCCTGGCACATGTGTGCCATGTGGGAGCTGGGGCAGGTCCTCTTTCCTC CTGTGGCTCCGAGGGAGGGGGCCGCTCCTTCCCCAGTCTCTACCCTGACT TGGCCCTCGTCCTGCAGCCACTCAGAGAGCACGATGGAGCTGGAGCTTCA GTTTTGACCAAATGCGTGTCGCCGGCTTTTGTGTGTGTGTGTGTGTGATG GAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCATTGGCACCATCTCTGCCC ACTGCAACCTCTGCCTCCTGGGCTCAAGTGATTCTCCTGCCTCAGCCTCC TGAGTAGCTGGGATTACAGGCGCCCACCACCACACCTGGCTAATTTTTGT ATTTTTAGCAGAGACAGCGTTTCACCATGTTGGCCAGGCTAGTCTTGAAC TCCTGACTTCAAATGATCCGCCCGCCTCAGCCTCCCAAAGTGCTGGGATT ACAGGCATGAGCCCCGGCACCTGGCCTTCAAATTGGCTTTTAAAGAAGAT GACCAGCTGGTCTGTTCTGTCTGGGGCCTTGGAGGGCTGTTTCCCAGGAT GTGGGCCTTTATCAGTGCTGACCTAGGCAATCAAGGCCAAGCTGGCCACA CTGCTTTTGATTTTTTTTAAATTGTGATGAAATACGCTTAACATAAAATT TGCCATCTTAGTCATTTTGGAGTGTTCAGTAGCTTTAAGTCCATTCACAT TGCTGTGCAGCCATCACCACCATCCATCTCCAGAACTCTTTTCATCTTGC CAACCTGAAGCTCTGTCCCCATAAAATAGCAACTCCATTTTCCCTCCCCC AGCTCACCATTCCATGGTCTGTTGTTATGAGTCTGCTACTCCAACTACCT TTTATAAGTGGAGTCAATGGTACCTGTGTTTTTATGTCGGGCTCAAATCA CTGAGCGTGATGTCCTCACGGTCCATCCAGGTTGTACCAAGTGTCAGAAT TTCCTTCCTGTTTTCTGCTGACTCCCTGCTTTTAAAGGCCATCTTGGACA TTCAAATTGTGGCCATTACTGACAGTTAAAATGGCCCCGGCTCATGTCTC CTGAGCCTCTACAATCCTTTAGGTGGGGACAGTACTGCGGCCCACACGTC CCCACAGGCTGCGTGTGACACCTGACAGTGCTTTGTGCCACTGTGGAGCA GGTGTCACTCTCCCACTTCTCAGAGAGGAAGCCGGGCTCTGGAAGCCAGC AGCCCACAAGGAGGCCCAGCAGGCTTCGGGCCCAGGTGGGGAGGTCTGCA CATCTCAGGGCCTTTCCCTGGGAACAACCAGGGACAGAGGCCACACACCC AGCCTCCTCTCTGCCCACAGTGAATTGAGACACAACCCCTTACGTCCCTC CCAGCCTTAAGTCAAGTGGAAAGCAATGGCCCCTGAGGTCACTTAGTCCC TCTTGCCAGTTTGTAAGTGCTGAATCAGAGACTCTGAGCTTTGGCCCTTT CCCGAGTTCCCGGGATTATGAGCTGACACAGCCCCCAAGCAACCACAGTG ATTCCAGCCTGGGAGTGTGGCCTTGGCGGGAGGGTCAATGCCCAGTCATG GTTCAGCGGCTGTGCACACCCCTGCTTACCTGCATCCCACGCTTTCCATG CAAACTCACGTGGCGGCGCTTTGCGCTTGCAGGATGGTCTACCCCCAGCC AAAGGTGCTGACACCGTGGTGAGTAAAGTTACTGACACTGAAACTGAACG CAGCTCAAGGGGCTGTTCTGAAGGTATTAGAGGGCGGTTTCCTTGATGTA AATCTCAGTTGGGGCTGCTTCGTTCTCTCCTCTCAGATTCTCCTGACATC TGAATTCAGAGGCCCACATGGCTGTCCTCTTTCCCTTTGCTTTCTCTGAC TTGCGTCTCTTGTTTCCTGTCCCTTTGTTCTCCAAAGCCCCTGCAAAGGC CTGATAGGTACCTCCTACCTGGGGAGGGGCAGCGGGGGTTGGGTGCTGGG GAGGGTTTGTTCCTATCTCTTTGCCAGCAAAGCTCAGCTTGCTGTGTGTT CCCACAGGTCCAATGTTGAGGGAGGGCTGGGAATGATTTGCCCGGTTGGA GTCGCATTTGCCTCTGGTTGGTTTCCCGGGGAAGGGCGGCTGCCTCTGGA AGGGTGGTCAGAGGAGGCAGAAGCTGAGTGGAGTTTCCAGGTGGGGGCGG CCGTGTGCCAGAGGCGCATGTGGGTGGCACCCTGCCAGCTCCATGTGACC GCACGCCTCTCTCCATGTGCAGTAGGAAGGATGTCCTCGTGGTACCCCTT GGCTGGCTCCCATTGTCTGGGAGGGCACATTCAACATCGACATCCTCAAC GAGCAGTTCAGGCTCCAGAACACCACCATTGGGTTAACTGTGTTTGCCAT CAAGAAGTAAGTCAGTGAGGTGGCCGAGGGTAGAGACCCAGGCAGTGGCG AGTGACTGTGGACATTGAGGTCTCTCCTTGTGTTCAAGACAGAGTGGGGT GGCGGCCAGCCTTGTCCTCCCAGAGGGTAGATGGGAAAGGTCATTCATGC AGCATCTTACTGAGCTCATGTGGGCTCGTGGGCTCGTGGGCTCGCCAGGT CGGTAAAACCCAGCTCCTTCTCCAGAGGCTGCGTCTCACCCAGGGATGGT GGCTTCTGCTGCCCCCTCCTCTCTGTAACTGTGGCCGGCCGTCATGCTGA GCCACCCCCTCAATACAAGGCTCCAGATGTTTCCTGCTCACTGACCAGAG ATAGCAGGAGGGGGACACCTGTTTGCTGTCCTTGGACCCTAGAAAGAGGA TGCTGGCAGAGCCGTGGTCACTTCTCTGTCAGATGTAGGTGGGGCAGGCA AAGCAGTTGGCCCCAGACACCAAAGGAAGTGGCTGACCCACAAGGCCCTG GGACTCTGGGCCAGGCCAGAGAGGGAGCTAGCCAGGCAACCGCAGACACA TACTTGACTTCTCGGCAGCTGTGGGCAGCTGGGCCAGCGACAGTGGCGGA GGCCAGGAATGACTTACTCTTAGGAATAGGTGCAGTTCAAGCCTGGAGGG AGGAAGCTCTAGGGTGCAGAGGCGGGTGTGTGGAGGCCTCGCGTGCAGCT TATAATGAGGGAGCACGTGGCCGGCCTGGCCATAAGAGGGGCAGCTGCGT GGGGAGGCGTGGCTCAGGCCAGGCTGAGGGGGAGTGAGCAGACGCCAGCC TGCGGCCTGCTACCAGCCTCCAGCCACCTGCCCTCAGCCCTCCTTAGTAA GAGGGGGTGCTGGTGGTCCCCCATCGCTGGGAAGAGGATGAAGTGAATCG CAGCCCGAGGACTCGCTCAGGACAGGGCAGGAGAACGTGGTGCATCTGCT GCTCTAAGCCTTCCAATGGCCGCTGGCGGGCGGGTGCAGGACGGGCCTCC TGCAGCCCAGGGGTGCACGGCCGGCGGCTCCCCCAGCCCCCGTCCGCCTG CCTTGCAGATACGTGGCTTTCCTGAAGCTGTTCCTGGAGACGGCGGAGAA GCACTTCATGGTGGGCCACCGTGTCCACTACTATGTCTTCACCGACCAGC CGGCCGCGGTGCCCCGCGTGACGCTGGGGACCGGTCGGCAGCTGTCAGTG CTGGAGGTGCGCGCCTACAAGCGCTGGCAGGACGTGTCCATGCGCCGCAT GGAGATGATCAGTGACTTCTGCGAGCGGCGCTTCCTCAGCGAGGTGGATT ACCTGGTGTGCGTGGACGTGGACATGGAGTTCCGCGACCACGTGGGCGTG GAGATCCTGACTCCGCTGTTCGGCACCCTGCACCCCGGCTTCTACGGAAG CAGCCGGGAGGCCTTCACCTACGAGCGCCGGCCCCAGTCCCAGGCCTACA TCCCCAAGGACGAGGGCGATTTCTACTACCTGGGGGGGTTCTTCGGGGGG TCGGTGCAAGAGGTGCAGCGGCTCACCAGGGCCTGCCACCAGGCCATGAT GGTCGACCAGGCCAACGGCATCGAGGCCGTGTGGCACGACGAGAGCCACC TGAACAAGTACCTGCTGCGCCACAAACCCACCAAGGTGCTCTCCCCCGAG TACTTGTGGGACCAGCAGCTGCTGGGCTGGCCCGCCGTCCTGAGGAAGCT GAGGTTCACTGCGGTGCCCAAGAACCACCAGGCGGTCCGGAACCCGTGAG CGGCTGCCAGGGGCTCTGGGAGGGCTGCCGGCAGCCCCGTCCCCCTCCCG CCCTTGGTTTTAGCAGAACGGGTAAACTCTGTTTCCTTTGTCCGTCCTGT TGTGAGTAACTGAAGCCTAGGCCCCGTCCCCACCTCAAATCACACACACC CCCTCCCCACCACAGAGACACCATTACATACACAGACACACACAGAAAGA CACACACAGACACAAAATCACACACACACCCTCCCCGCCACAGAGACACC ATTACATACACAGACACACACAGAAAGACACAGACACAAAATCACACACA CACCCTCCCCGCCACAGAGACACACCATTACATACACAGACACGCAATCG CAGATACGCCCTTCCGGCCACAGAAACACACCATTACACACACATACACA GAAAGACACACACAGACACACAATCACACGCAGCCCCTCCCCGCCACAGA

Programming Question 2 Pattern Matching: String matching or pattern matching, simple as it may seem, is an important problem in computer science with numerous applications, especially in the fields of bio-informatics, DNA sequencing and analysis. Exercise 2(A). Start off with this simple exercise. Write a program (name it StringMatch.java) that prompts the user to enter two strings and tests whether the second string is a substring of the first string. The number of times the substring appears should be displayed. Do not use the indexOf method in the String class (you are actually implementing a version of the indexof method from scratch). Instead, you would run through the string character by character using charAt and check if the substring exists. If the second string is not a substring of the first string, then you should display something like "No matches -substring (aaa) was not found in (bbb)'" display was not found in The following sample runs give you an idea what the program is supposed to do. You can use these as your test cases. Enter a string: mississippi Enter a substring: ssi Substring ssi was found in mississippi 2 times Enter a string: mississippi Enter a substring: p Substring p was found in mississippi 2 times The following example shows that if the substring is longer than the first string, it should report no match