- sequence1. fasta > sequence 1 GTGGATTCCCCGCGGTGGCGGCGCTCTAGAACTAGTGGGATCCCCCGGGCTGCAGGAATT CGGCACGAGGGCGGACCCCACTTCGACGTGGCTCTGGGCCGACGTGACGGGCTGGCCCCA GCGTTGGAGGATCTCGTCTCCACCCTACCGGCGCCCTCCTTCACCGTGCCGGAACTCCTC AAGTCTTTCGGCGACCGAAACCTCGACAAGGCGGACCTGGTGTCCCTCTCTGGCGCGCAC TCCTTCGGCATCGCCCACTGCTCCTCCTTCTCCGACCGCTTCACGCCGGTCGACGACACC GACCTAGTCATCGACCCCAATTTCGCGGCCAAGTTGAGGGCCAAGTGTGCTAAGGACATG CCTGCGGGCACCGTCAACCAGACCCTCGATTTGCGTACGCCGGACGTGTTCGACAACAAG TACTACTTTGATCTCATTGCCAAGCAGGGTCTGTTCAAGTCGGACCAGGGCCTCATCGTC CACCCCAACACCACGCGCATGGCGACGCGGTTCTCGCTCAACCAGGGGGCATTCTTCGAG CAGTTCGCCAAATCCATGGTGAAGATGAGCAACATGGACTTGCTCACCGGCAGCCAGGGC GAGATCCGGTTCAACTGCGCCGTCCCCAACAGCCGTGTCAAGGGCATCGAGACCGCCAGC GACGAGGGCCATGCCGCCGCCATGTAAGAGATTGGTTAGTCGCCGTGCTTGCTTGAAGCG TGTGAGTCGTGTGTGCGCTACGATCGTGTCATGGTGCTAGTGGTTITGCGTAATCGTGAT GTTGNAATAAAGTGAGTGAACAGACATTCATGCCCCAAGTATATGAAAAANAAANCAANA AAACTTCGAGGGGGGGGCCCGGTACCCAATTTCGCCCTATAAGGAGTCGTATTAACAATT CCCC sequence2. fasta > sequence 2 CTCCACGCGGTGGCGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCGGCA CGAGGCGTCGACGTTCTACGACACGTCGTGCCCCAGGGCTCTGGCCACCATCAAGAGCGG CGTGGCGGCAGCCGTGAGCAGCGATCCCCGCATGGGCGCCTCCCTGCTCAGGCTGCACTT CCACGACTGCTTTGTCCAAGGCTGTGACGCGTCTGTTCTTCTGTCCGGCATGGAACAAAA CGCGGGTCCGAACGTGGGGTCGCTGAGGGGCTTCGGCGTCATCGACAACATCAAGACCCA GCTGGAGAGTATATGCAAGCAGACCGTCTCCTGCGCCGACATCCTCACCGTCGCCGCCCG CGACTCCGTTGTCGCCCTTGGAGGGCCATCGTGGACTGTCCCGCTGGGGAGACGGGACTC CACCACCGCAAGTGCCTCGCTGGCGAACAGTGACCTCCCTGGCCCGAGCTCTAGCCGGTC ACAGCTCGAGGCCGCGTTCCTCAAGAAGAACCTTAACACGGTCGACATGGTCGCGCTCTC AGGCGCGCACCACATCGGGAAGNCCAGTGCTCCAACTTTCGGACTCGGATCTACGGGGGT GACAACAACATCAAACACTGGCTTCCGACGTCTCTCAAGGNCAAACTGCCCCCCAGTCCC GGGGGGCAAACAACCAAACCTTGGNCGNAACCNTGGGAACACNNANCGAACGCCCCCAAA NGGCGTTTTCNGAACAAAACGGCCCTTNACTTNCAACCCAAAACCCTTCCCTTGGTCAAC AAAAAAAAAANGGGGGNTTCCCCTTGGGNAACTTCGNGGAAANCCAAANGGNGGGGTTTC TTTTAAAAACAAAC sequence3. fasta > sequence3 GAGTTCCACGCGGNGGCGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCG GCACGAGGTCCACCAGTAAAGAAGTGCAGGCAACTAGCTAGCTAACCATGGCCGCCTCTG CCTCTTGCATTTCACTGGTGGTGCTCGTGGCTCTGGCCACGGTGGCGTCGGCGCAGCTGT CGCCGACGTTCTACGACACGTCGTGCCCCAGGGCCCTGGCCACCATCAAGAGCGGCGTCA TGGCCGCCGNGAGCAGCGACCCTCGGATGGGCGCGTCGCTGCTCCGGNTGCACTTCCACG ACTGCTTCGTCCAAGGCTGTGANNCGTCTGTTCTGNTGTCTGGCATGGAACAAAACGCTC TCCCGAACAACGGGTCACTGCGGGGNTTCNGCGTCCATCGACAGCATNCAANACACAGAT CGAGGCCATCTGCGNCCAGACCGTCTCCTGCGCCGACATCCTCACCGNCNNTGCCCGNGA CTCCGTCCNTCNTCCCTCGNAAGGATCTATACATGNACAGTCCCCTCTGGGNAAAAAACG CANNTTTNCNCAANNATCCCAACCNATAGNCGCAAGANNANACAACNACACGACCNNCAC CTNANNANCCCATNNNCANNCTAAGNCCGCTANACANCANNNANCTCANNCTCTNNCCAA CTTACNTCTANNANNNATAAGCTACCCTTCATNTNTAACTNAGACACTGAACNNNNGGAG NTAGNGACCAACNTCTCTCTCAGCACNNTACACANNNATNACTATCCANTATCGCCTCNA TCTNCCATCNTCACCTACAATNGAAGCCNCTNAANCACNCCCTNCTTCTTAANAGNGNTA CTCTACTGCGCTNTCTCTACNTNANNCTCACAGCNTGCACACCTNCCTTNCCCACCTCAC TNNGAGTANAATNCNATACGTNAANNTCTNTCCTNTCTCCGCGACTCNACCAAAACANNN CNATNCTCTTTTCTTNTACNCAGCTTATNCTCCCATCTTANCTTTNTCNACCCTCAACCT CCCTCNATCCANACNCCAACNNAANNGGNACNCTCANCTAANACNTAAAGTCCAANAAAA CACACATCTNNTNACNCTACCCATTCCCCCCCCCTCCCCACNCCCCCNNANTTCNCTCAC NCNTTACACCACNCNNTTNCNCCNACTCAANTCCANCNCNTCATCCTCTATCCTANACTC ANAAGCCTGCCACACCTTNTAACCCNTCCCTACTTTATNCACTAAACTCATNCNNCTACA ATATGCNGNTNCACTCNCCNCCNATATACTNTACCTAAGCATTCTCCTCACACACA Using the dotmatcher program, create dot plots of the three possible pairings of sequence1, sequence2, and sequence3 (above). Which pair of sequences shows an obvious area of similarity? Try adjusting the parameters to the program (e.g. window size and threshold) so that "noise" is reduced and the areas of similarity are more distinct. To choose an appropriate threshold parameter, you will need to determine the scoring matrix used by dotmatcher. This is given in the on-line documentation