1. Sample C7 >hla nucleotide alignment sequence of C7(No mutations or SNPs were found in this gene) Range 1: 373 to 583 Score Expect Identities Gaps Strand 390 bits(211) 5e-105 211/211(100%) 0/211(0%) Plus/Plus Query 1 TCTGATTACTATCCAAGAAATTCGATTGATACAAAAGAGTATATGAGTACTTTAACTTAT 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 373 TCTGATTACTATCCAAGAAATTCGATTGATACAAAAGAGTATATGAGTACTTTAACTTAT 432 Query 61 GGATTCAACGGTAATGTTACTGGTGATGATACAGGAAAAATTGGCGGCCTTATTGGTGCA 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 433 GGATTCAACGGTAATGTTACTGGTGATGATACAGGAAAAATTGGCGGCCTTATTGGTGCA 492 Query 121 AATGTTTCGATTGGTCATACACTGAAATATGTTCAACCTGATTTCAAAACAATTTTAGAG 180 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 493 AATGTTTCGATTGGTCATACACTGAAATATGTTCAACCTGATTTCAAAACAATTTTAGAG 552 Query 181 AGCCCAACTGATAAAAAAGTAGGCTGGAAAG 211 ||||||||||||||||||||||||||||||| Sbjct 553 AGCCCAACTGATAAAAAAGTAGGCTGGAAAG 583 Notes: >amino acid sequence from your chromatograms SDYYPRNSIDTKEYMSTLTYGFNGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKX Consensus between forward and reverse sequences were between positions 28 to 76 (from VTGDDTGKIGGLIGANVSIGHTLK); thus all sequences before and after this position were found on only one strand viz., either the forward or reverse strand. >hla consensus amino acid alignment sequence Range 1: 28 to 97GenPeptGraphicsNext MatchPrevious Match Alignment statistics for match #1 Score Expect Method Identities Positives Gaps Frame 145 bits(367) 4e-43 Compositional matrix adjust. 70/70(100%) 70/70(100%) 0/70(0%) +1 Query 1 SDYYPRNSIDTKEYMSTLTYGFNGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILE 180 SDYYPRNSIDTKEYMSTLTYGFNGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILE Sbjct 28 SDYYPRNSIDTKEYMSTLTYGFNGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILE 87 Query 181 SPTDKKVGWK 210 SPTDKKVGWK Sbjct 88 SPTDKKVGWK 97 2. Sample C34 >hla nucleotide alignment sequence of C34 (no mutations or sNPs were observed) Staphylococcus aureus strain BESA206 alpha-hemolysin (hla) gene, complete cds Sequence ID: gb|KT279561.1|Length: 960Number of Matches: 1 Range 1: 373 to 583 Score Expect Identities Gaps Strand 390 bits(211) 5e-105 211/211(100%) 0/211(0%) Plus/Plus Query 1 TCTGATTACTATCCAAGAAATTCGATTGATACAAAAGAGTATATGAGTACTTTAACTTAT 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 373 TCTGATTACTATCCAAGAAATTCGATTGATACAAAAGAGTATATGAGTACTTTAACTTAT 432 Query 61 GGATTCAACGGTAATGTTACTGGTGATGATACAGGAAAAATTGGCGGCCTTATTGGTGCA 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 433 GGATTCAACGGTAATGTTACTGGTGATGATACAGGAAAAATTGGCGGCCTTATTGGTGCA 492 Query 121 AATGTTTCGATTGGTCATACACTGAAATATGTTCAACCTGATTTCAAAACAATTTTAGAG 180 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 493 AATGTTTCGATTGGTCATACACTGAAATATGTTCAACCTGATTTCAAAACAATTTTAGAG 552 Query 181 AGCCCAACTGATAAAAAAGTAGGCTGGAAAG 211 ||||||||||||||||||||||||||||||| Sbjct 553 AGCCCAACTGATAAAAAAGTAGGCTGGAAAG 583 >Amino acid sequence of hla of C34 obtained from your chromatograms TCTGATTACTATCCAAGAAATTCGATTGATACAAAAGAGTATATGAGTACTTTAACTTATGGATTCAACGGTAATGTTACTGGTGATGATACAGGAAAAATTGGCGGCCTTATTGGTGCAAATGTTTCGATTGGTCATACACTGAAATATGTTCAACCTGATTTCAAAACAATTTTAGAGAGCCCAACTGATAAAAAAGTAGGCTGGAAAGA >hla amino acid alignment sequence of C34 alpha-hemolysin, partial [Staphylococcus aureus] Sequence ID: gb|AIG51297.1 Identical Proteins-Identical proteins to AIG51297.1 Range 1: 28 to 97 Score Expect Method Identities Positives Gaps Frame 145 bits(366) 6e-43 Compositional matrix adjust. 70/70(100%) 70/70(100%) 0/70(0%) +1 Query 1 SDYYPRNSIDTKEYMSTLTYGFNGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILE 180 SDYYPRNSIDTKEYMSTLTYGFNGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILE Sbjct 28 SDYYPRNSIDTKEYMSTLTYGFNGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILE 87 Query 181 SPTDKKVGWK 210 SPTDKKVGWK Sbjct 88 SPTDKKVGWK 97 >hla amino acid sequence of C34 (Please note that this is a consensus of both forward and reverse amino acid sequences) SDYYPRNSIDTKEYMSTLTYGFNGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKX Notes: Please note that the region of overlap between the forward and reverse amino acid sequences (from your chromatograms) is between positions 49 to 78 (FNGNVTGDDTGKIGGLIGANVSIGHTLKY) 3. Sample C/S40 >blaZ nucleotide sequence (including both forward and reverse strands/sequences) from chromatograms TACTTCAACACCTGCTGCTTTCGGTAAGACTTTAAATAAACTTATCGCAAATGGAAAATTAAGCAAAGAAAACAAAAAATTCTTACTTGATTTAATGTTAAATAATAAAAGCGGAGATACTTTAATTAAAGACGGTGTTTCAAAAGACTGTAAGGTTGCTGATAAAAGTGGTCA >blaZ nucleotide alignment sequence (no mutations/SNPs were observed) Nocardia veterana strain CNM20081130 beta-lactamase blaZ (blaZ) gene, partial cds Sequence ID: gb|KM194590.1|Length: 772Number of Matches: 1 Range 1: 450 to 623 Score Expect Identities Gaps Strand 322 bits(174) 1e-84 174/174(100%) 0/174(0%) Plus/Plus Query 1 TACTTCAACACCTGCTGCTTTCGGTAAGACTTTAAATAAACTTATCGCAAATGGAAAATT 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 450 TACTTCAACACCTGCTGCTTTCGGTAAGACTTTAAATAAACTTATCGCAAATGGAAAATT 509 Query 61 AAGCAAAGAAAACAAAAAATTCTTACTTGATTTAATGTTAAATAATAAAAGCGGAGATAC 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 510 AAGCAAAGAAAACAAAAAATTCTTACTTGATTTAATGTTAAATAATAAAAGCGGAGATAC 569 Query 121 TTTAATTAAAGACGGTGTTTCAAAAGACTGTAAGGTTGCTGATAAAAGTGGTCA 174 |||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 570 TTTAATTAAAGACGGTGTTTCAAAAGACTGTAAGGTTGCTGATAAAAGTGGTCA 623 >blaZ amino acid sequence (including both forward and reverse strands/sequences) from chromatograms XTSTPAAFGKTLNKLIANGKLSKENKKFLLDLMLNNKSGDTLIKDGVSKDCKVADKSGX BlaZ (plasmid) [Staphylococcus aureus] Sequence ID: gb|AIU96739.1|Length: 196 Range 1: 86 to 142 Alignment statistics for match #1 Score Expect Method Identities Positives Gaps Frame 113 bits(282) 2e-30 Compositional matrix adjust. 57/57(100%) 57/57(100%) 0/57(0%) +2 Query 2 TSTPAAFGKTLNKLIANGKLSKENKKFLLDLMLNNKSGDTLIKDGVSKDCKVADKSG 172 TSTPAAFGKTLNKLIANGKLSKENKKFLLDLMLNNKSGDTLIKDGVSKDCKVADKSG Sbjct 86 TSTPAAFGKTLNKLIANGKLSKENKKFLLDLMLNNKSGDTLIKDGVSKDCKVADKSG 142 Notes: Forward and reverse sequences only overlapped at SKENKKFLLDLML 4. Sample C41 >Consensus TCGATAGGAACAGCAGTATATGGACCAAGATWRCTCWRACTWATAYMAATAATWAAMAAWTTKTTWATTATTGGTATATARTTTSAGMTGWMTTKGTYCATWKAYTGCTGTTCCTATCGA Notes: The chromatograms obtained from this sequence were not in complete agreement in terms of the forward and reverse sequence. The disparity in the forward and reverse strand makes further analysis impossible. As can be seen in the consensus sequence above, there were several "Ws", "Ys", "Ms", "Ks" etc., symbolysing a discrepancy between the forward and reverse strand. Therefore, all further analysis for this sample has been stopped. 5. Sample C45 TetK Staphylococcus aureus pT181 tet(K) gene for tetracycline efflux MFS transporter Tet(K), complete CDS Sequence ID: ref|NG_048200.1|Length: 1380 Number of Matches: 1 Range 1: 187 to 355 Score Expect Identities Gaps Strand 313 bits(169) 9e-82 169/169(100%) 0/169(0%) Plus/Plus Query 1 TCGATAGGAACAGCAGTATATGGAAAATTATCTGATTATATAAATATaaaaaaaTTGTTA 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 187 TCGATAGGAACAGCAGTATATGGAAAATTATCTGATTATATAAATATAAAAAAATTGTTA 246 Query 61 ATTATTGGTATTAGTTTGAGCTGTCTTGGTTCATTGATTGCTTTTATTGGTCACAATCAC 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 247 ATTATTGGTATTAGTTTGAGCTGTCTTGGTTCATTGATTGCTTTTATTGGTCACAATCAC 306 Query 121 ttttttattttgatttttGGTAGGTTAGTACAAGGAGTAGGATCTGCTG 169 ||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 307 TTTTTTATTTTGATTTTTGGTAGGTTAGTACAAGGAGTAGGATCTGCTG 355 >nucleotide sequence of TetK (This was obtained from the chromatogram file) TCGATAGGAACAGCAGTATATGGAAAATTATCTGATTATATAAATATAAAAAAATTGTTAATTATTGGTATTAGTTTGAGCTGTCTTGGTTCATTGATTGCTTTTATTGGTCACAATCACTTTTTTATTTTGATTTTTGGTAGGTTAGTACAAGGAGTAGGATCTGCTGA Notes: The region of overlap between the forward and reverse sequence of the chromatogram files is TAGTTTGAGCTGTCTTGGTTCATTGATTGCTTTTATTG >TetK, partial [Staphylococcus aureus]amino acid alignment sequence Sequence ID: gb|AKZ18228.1|Length: 56 Identical Proteins-Identical proteins to AKZ18228.1 Score Expect Method Identities Positives Gaps 107 bits(266) 1e-29 Compositional matrix adjust. 56/56(100%) 56/56(100%) 0/56(0%) Query 1 SIGTAVYGKLSDYINIKKLLIIGISLSCLGSLIAFIGHNHFFILIFGRLVQGVGSA 56 SIGTAVYGKLSDYINIKKLLIIGISLSCLGSLIAFIGHNHFFILIFGRLVQGVGSA Sbjct 1 SIGTAVYGKLSDYINIKKLLIIGISLSCLGSLIAFIGHNHFFILIFGRLVQGVGSA 56 >Amino acid sequence of TetK from both the forward and reverse consensus. (Actual overlap occurs at SLSCLGSLIAFI) SIGTAVYGKLSDYINIKKLLIIGISLSCLGSLIAFIGHNHFFILIFGRLVQGVGSA 6. Sample C69 aac-aph >nucleotide consensus sequence OF AAC-APH forward and reverse sequences. CGTTAATCCAAGAGAAATAAGSKCATAYYAAAWATYTSRTTGCCTTAGAMWTATTGWRGMWTTRYCAKMAYATSWATTAYWCSAGGKYAAAWAASAAKMTTCKTTWTTGCCCTMRTGKAATWYATGWTMTGATGMWAATSYTCAMWAATKYTAAGGCAAYSARATWTTTRRTATGASCMTTATTGCTCTTGGATTAACG Notes: The consensus sequence has many mismatches shown as K, Y, R, W, M etc. This must be changed by doing base calling by comparing the chromatograms to get the best base to use to replace the mismatch in either the forward or reverse sequence to get a consensus/agreement. Therefore, I advise you only mention that you found this enzyme in this strain without detailing if there was mutation or not. 7. Sample C69 erm (No mutations, SNPs or IN-DELS observed) >erm nucleotide alignment sequence Staphylococcus hominis 736153 pSES5 erm(C) gene for 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(C), complete CDS Sequence ID: ref|NG_047812.1|Length: 877 Range 1: 314 to 503 Score Expect Identities Gaps Strand 351 bits(190) 2e-93 190/190(100%) 0/190(0%) Plus/Plus Query 4 CTTGTTGATCACGATAATTTCCAAGTTTTAAACAAGGATATATTGCAGTTTAAATTTCCT 63 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 314 CTTGTTGATCACGATAATTTCCAAGTTTTAAACAAGGATATATTGCAGTTTAAATTTCCT 373 Query 64 AAAAACCAATCCTATAAAATATTTGGTAATATACCTTATAACATAAGTACGGATATAATA 123 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 374 AAAAACCAATCCTATAAAATATTTGGTAATATACCTTATAACATAAGTACGGATATAATA 433 Query 124 CGCAAAATTGTTTTTGATAGTATAGCTGATGAGATTTATTTAATCGTGGAATACGGGTTT 183 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 434 CGCAAAATTGTTTTTGATAGTATAGCTGATGAGATTTATTTAATCGTGGAATACGGGTTT 493 Query 184 GCTAAAAGAT 193 |||||||||| Sbjct 494 GCTAAAAGAT 503 >nucleotide sequence of erm gene obtained from the forward and reverse sequence of the chromatograms. TATCTTGTTGATCACGATAATTTCCAAGTTTTAAACAAGGATATATTGCAGTTTAAATTTCCTAAAAACCAATCCTATAAAATATTTGGTAATATACCTTATAACATAAGTACGGATATAATACGCAAAATTGTTTTTGATAGTATAGCTGATGAGATTTATTTAATCGTGGAATACGGGTTTGCTAAAAGATAGTT Notes: The forward and reverse sequence overlaps at TTAAATTTCCTAAAAACCAATCCTATAAAATATTTGGTAATATACCTTATAACATAAGTACGGATATAATACGCAAAATTGTTT >amino acid alignment sequence of erm gene ErmC, partial [Staphylococcus aureus] Sequence ID: gb|AAL75490.1|Length: 127 Range 1: 43 to 105 Score Expect Method Identities Positives Gaps 129 bits(324) 2e-37 Compositional matrix adjust. 63/63(100%) 63/63(100%) 0/63(0%) Query 2 LVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPYNISTDIIRKIVFDSIADEIYLIVEYGF 61 LVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPYNISTDIIRKIVFDSIADEIYLIVEYGF Sbjct 43 LVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPYNISTDIIRKIVFDSIADEIYLIVEYGF 102 Query 62 AKR 64 AKR Sbjct 103 AKR 105 >Consensus amino acid sequence of erm from chromatograms (Note: forward and reverse overlaps occur at KFPKNQSYKIFGNIPYNISTDIIRKIV) YLVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPYNISTDIIRKIVFDSIADEIYLIVEYGFAKR 8. Sample S2 aac6-aph >Nucleotide alignment sequence of aac6'-aph Staphylococcus aureus SK18 pSK1 gene for bifunctional aminoglycoside N-acetyltransferase AAC(6')-Ie/aminoglycoside O-phosphotransferase APH(2'')-Ia, complete CDS Sequence ID: ref|NG_047055.1|Length: 1640 Range 1: 520 to 747GenBankGraphics Score Expect Identities Gaps Strand 422 bits(228) 2e-114 228/228(100%) 0/228(0%) Plus/Plus Query 2 TAATCCAAGAGCAATAAGGGCATACCAAAAATCTGGTTTTAGAATTATTGAAGATTTGCC 61 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 520 TAATCCAAGAGCAATAAGGGCATACCAAAAATCTGGTTTTAGAATTATTGAAGATTTGCC 579 Query 62 AGAACATGAATTACACGAGGGCAAAAAAGAAGATTGTTATTTAATGGAATATAGATATGA 121 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 580 AGAACATGAATTACACGAGGGCAAAAAAGAAGATTGTTATTTAATGGAATATAGATATGA 639 Query 122 TGATAATGCCACAAATGTTAAGGCAATGAAATATTTAATTGAGCATTACTTTGATAATTT 181 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 640 TGATAATGCCACAAATGTTAAGGCAATGAAATATTTAATTGAGCATTACTTTGATAATTT 699 Query 182 CAAAGTAGATAGTATTGAAATAATCGGTAGTGGTTATGATAGTGTGGC 229 |||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 700 CAAAGTAGATAGTATTGAAATAATCGGTAGTGGTTATGATAGTGTGGC 747 >nucleotide sequence of aac6-aph gene TTAATCCAAGAGCAATAAGGGCATACCAAAAATCTGGTTTTAGAATTATTGAAGATTTGCCAGAACATGAATTACACGAGGGCAAAAAAGAAGATTGTTATTTAATGGAATATAGATATGATGATAATGCCACAAATGTTAAGGCAATGAAATATTTAATTGAGCATTACTTTGATAATTTCAAAGTAGATAGTATTGAAATAATCGGTAGTGGTTATGATAGTGTGGC Note: Forward and reverse sequence agreed or overlapped at ATTTGCCAGAACATGAATTACACGAGGGCAAAAAAGAAGATTGTTATTTAATGGAATATAGATATGATGATAATGCCACAAATGTTAAGGCAATGAAATATTTAATTGAGC >amino acid alignment sequence of aac6-aph (no mutations were observed) acetyltransferase family protein [Staphylococcus aureus subsp. aureus CIG1770] Sequence ID: gb|EHT69980.1|Length: 169 Range 1: 64 to 138 Score Expect Method Identities Positives Gaps 157 bits(397) 8e-48 Compositional matrix adjust. 75/75(100%) 75/75(100%) 0/75(0%) Query 1 NPRAIRAYQKSGFRIIEDLPEHELHEGKKEDCYLMEYRYDDNATNVKAMKYLIEHYFDNF 60 NPRAIRAYQKSGFRIIEDLPEHELHEGKKEDCYLMEYRYDDNATNVKAMKYLIEHYFDNF Sbjct 64 NPRAIRAYQKSGFRIIEDLPEHELHEGKKEDCYLMEYRYDDNATNVKAMKYLIEHYFDNF 123 Query 61 KVDSIEIIGSGYDSV 75 KVDSIEIIGSGYDSV Sbjct 124 KVDSIEIIGSGYDSV 138 >amino acid sequence NPRAIRAYQKSGFRIIEDLPEHELHEGKKEDCYLMEYRYDDNATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSV Note: The forward and reverse strand agreed at LPEHELHEGKKEDCYLMEYRYDDNATNVKAMKYLIE 9. Sample S2 mec >nucleotide alignment sequence of mecA gene (no mutations were observed) Staphylococcus aureus TN/CN/1/12 mecA gene for PBP2a family beta-lactam-resistant peptidoglycan transpeptidase MecA, complete CDS Sequence ID: ref|NG_047945.1|Length: 2107 Range 1: 1059 to 1230 Score Expect Identities Gaps Strand 318 bits(172) 2e-83 172/172(100%) 0/172(0%) Plus/Plus Query 2 AACAGGTGAATTATTAGCACTTGTAAGCACACCTTCATATGACGTCTATCCATTTATGTA 61 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1059 AACAGGTGAATTATTAGCACTTGTAAGCACACCTTCATATGACGTCTATCCATTTATGTA 1118 Query 62 TGGCATGAGTAACGAAGAATATAATAAATTAACCGAAGATAAAAAAGAACCTCTGCTCAA 121 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1119 TGGCATGAGTAACGAAGAATATAATAAATTAACCGAAGATAAAAAAGAACCTCTGCTCAA 1178 Query 122 CAAGTTCCAGATTACAACTTCACCAGGTTCAACTCAAAAAATATTAACAGCA 173 |||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1179 CAAGTTCCAGATTACAACTTCACCAGGTTCAACTCAAAAAATATTAACAGCA 1230 >consensus Nucleotide sequence of mec gene as obtained from the chromatograms TAACAGGTGAATTATTAGCACTTGTAAGCACACCTTCATATGACGTCTATCCATTTATGTATGGCATGAGTAACGAAGAATATAATAAATTAACCGAAGATAAAAAAGAACCTCTGCTCAACAAGTTCCAGATTACAACTTCACCAGGTTCAACTCAAAAAATATTAACAGCA Note: The forward and reverse sequences agreed at ATGAGTAACGAAGAATATAATAA >mecA amino acid alignment sequence penicillin-binding protein 2, partial [Staphylococcus aureus] Sequence ID: gb|ADG26745.1|Length: 95 Identical Proteins-Identical proteins to ADG26745.1 Range 1: 6 to 62 Score Expect Method Identities Positives Gaps 117 bits(292) 4e-33 Compositional matrix adjust. 57/57(100%) 57/57(100%) 0/57(0%) Query 1 TGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTA 57 TGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTA Sbjct 6 TGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTA 62 >Consensus amino acid sequence of mec gene as obtained from the chromatograms TGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTA Note that the amino acid sequences (both forward and reverse sequences) agree at MSNEEYN 10. Sample S4 mec >mec A nucleotide alignment sequence (No mutations were observed) Staphylococcus aureus JCSC6945 mecA gene for PBP2a family beta-lactam-resistant peptidoglycan transpeptidase MecA, complete CDS Sequence ID: ref|NG_047944.1|Length: 2210 Range 1: 1162 to 1332 Score Expect Identities Gaps Strand 316 bits(171) 7e-83 171/171(100%) 0/171(0%) Plus/Plus Query 2 AACAGGTGAATTATTAGCACTTGTAAGCACACCTTCATATGACGTCTATCCATTTATGTA 61 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1162 AACAGGTGAATTATTAGCACTTGTAAGCACACCTTCATATGACGTCTATCCATTTATGTA 1221 Query 62 TGGCATGAGTAACGAAGAATATAATAAATTAACCGAAGATAAAAAAGAACCTCTGCTCAA 121 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1222 TGGCATGAGTAACGAAGAATATAATAAATTAACCGAAGATAAAAAAGAACCTCTGCTCAA 1281 Query 122 CAAGTTCCAGATTACAACTTCACCAGGTTCAACTCAAAAAATATTAACAGC 172 ||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1282 CAAGTTCCAGATTACAACTTCACCAGGTTCAACTCAAAAAATATTAACAGC 1332 >nucleotide sequence of mec gene as obtained from the chromatograms TAACAGGTGAATTATTAGCACTTGTAAGCACACCTTCATATGACGTCTATCCATTTATGTATGGCATGAGTAACGAAGAATATAATAAATTAACCGAAGATAAAAAAGAACCTCTGCTCAACAAGTTCCAGATTACAACTTCACCAGGTTCAACTCAAAAAATATTAACAGC Notes: The forward and reverse strands overlapped at GAGTAACGAAGAATATAATAAA >mecA amino acid alignment sequence penicillin-binding protein 2, partial [Staphylococcus aureus] Sequence ID: gb|ADG26745.1|Length: 95 Identical Proteins-Identical proteins to ADG26745.1 Range 1: 6 to 61 Score Expect Method Identities Positives Gaps Frame 114 bits(286) 3e-32 Compositional matrix adjust. 56/56(100%) 56/56(100%) 0/56(0%) +3 Query 3 TGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILT 170 TGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILT Sbjct 6 TGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILT 61 >amino acid sequence of mecA (NB: The forward and reverse strands only overlapped/agreed at SNEEYNK) TGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILT 11. Sample S15 hla > nucleotide alignment sequence of hla gene (3 SNPs were observed as shown on alignment outside the overlap regions) Staphylococcus aureus strain BB155 genome assembly, chromosome: 1 Sequence ID: emb|LN854556.1|Length: 2778079 Range 1: 1095131 to 1095341 Score Expect Identities Gaps Strand 374 bits(202) 5e-100 208/211(99%) 0/211(0%) Plus/Minus Query 1 TCTGATTACTATCCAAGAAATTCGATTGATACAAAAGAATATATGAGTACACTAACTTAT 60 ||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1095341 TCTGATTACTACCCTAGAAATTCGATTGATACAAAAGAATATATGAGTACACTAACTTAT 1095282 Query 61 GGATTCAACGGTAATGTAACTGGTGATGATTCAGGGAAAATTGGCGGTCTAATTGGTGCT 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1095281 GGATTCAACGGTAATGTAACTGGTGATGATTCAGGGAAAATTGGCGGTCTAATTGGTGCT 1095222 Query 121 TCTGTATCAATTGGTCATACACTGAAATATGTTCAACCGGATTTCAAAACTATTTTAGAG 180 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1095221 TCTGTATCAATTGGTCATACACTGAAATATGTTCAACCGGATTTCAAAACTATTTTAGAG 1095162 Query 181 AGTCCTACTGATAAAAAAGTAGGCTGGAAAG 211 ||||||||||||||||||||||| ||||||| Sbjct 1095161 AGTCCTACTGATAAAAAAGTAGGTTGGAAAG 1095131 > nucleotide sequence obtained from chromatogram of hla gene TCTGATTACTATCCAAGAAATTCGATTGATACAAAAGAATATATGAGTACACTAACTTATGGATTCAACGGTAATGTAACTGGTGATGATTCAGGGAAAATTGGCGGTCTAATTGGTGCTTCTGTATCAATTGGTCATACACTGAAATATGTTCAACCGGATTTCAAAACTATTTTAGAGAGTCCTACTGATAAAAAAGTAGGCTGGAAAGA NOTES: The forward and reverse strands overlapped in this region GGATTCAACGGTAATGTAACTGGTGATGATTCAGGGAAAATTGGCGGTCTAATTGGTGCTTCTGTATCAATTGGTC >amino acid alignment sequence for hla gene (N68S mutation observed) alpha-hemolysin, partial [Staphylococcus aureus] Sequence ID: gb|AIG51324.1|Length: 188 Range 1: 28 to 97 Score Expect Method Identities Positives Gaps Frame 144 bits(363) 2e-42 Compositional matrix adjust. 69/70(99%) 70/70(100%) 0/70(0%) +1 Query 1 SDYYPRNSIDTKEYMSTLTYGFNGNVTGDDSGKIGGLIGASVSIGHTLKYVQPDFKTILE 180 SDYYPRNSIDTKEYMSTLTYGFNGNVTGDDSGKIGGLIGA+VSIGHTLKYVQPDFKTILE Sbjct 28 SDYYPRNSIDTKEYMSTLTYGFNGNVTGDDSGKIGGLIGANVSIGHTLKYVQPDFKTILE 87 Query 181 SPTDKKVGWK 210 SPTDKKVGWK Sbjct 88 SPTDKKVGWK 97 >amino acid sequence of hla gene SDYYPRNSIDTKEYMSTLTYGFNGNVTGDDSGKIGGLIGASVSIGHTLKYVQPDFKTILESPTDKKVGWK Note: The forward and reverse strands overlapped at GFNGNVTGDDSGKIGGLIGASVSIG. Fortunately, the mutation (N68S) was within the overlapping region. 12. Sample S15 luks >nucleotide alignment of luks gene (showing one insertion of G and an SNP of G to C) Staphylococcus aureus strain UTSW MRSA 55, complete sequence Sequence ID: gb|CP013231.1|Length: 2898306 Range 1: 590230 to 590663 Score Expect Identities Gaps Strand 791 bits(428) 0.0 433/435(99%) 1/435(0%) Plus/Minus Query 2 ATCATTAGGGTAAAATGTCTGGACATGATCCAAATTTATTTGTTGGATATAAACCATATA 61 ||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 590663 ATCATTA-GGTAAAATGTCTGGACATGATCCAAATTTATTTGTTGGATATAAACCATATA 590605 Query 62 GTCAAAATCCGAGAGACTATTTTGTTCCAGACAATGAATTACCCCCATTAGTACACAGTG 121 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 590604 GTCAAAATCCGAGAGACTATTTTGTTCCAGACAATGAATTACCCCCATTAGTACACAGTG 590545 Query 122 GTTTCAATCCTTCATTTATTGCAACTGTTTCTCATGAAAAAGGCTCAGGAGATACAAGTG 181 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 590544 GTTTCAATCCTTCATTTATTGCAACTGTTTCTCATGAAAAAGGCTCAGGAGATACAAGTG 590485 Query 182 AATTTGAAATAACGTATGGCAGAAATATGGATGTTACTCATGCTACTAGAAGAACAACAC 241 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 590484 AATTTGAAATAACGTATGGCAGAAATATGGATGTTACTCATGCTACTAGAAGAACAACAC 590425 Query 242 ACTATGGCAATAGTTATTTAGAAGGATCTAGAATACACAACGCATTTGTAAACAGAAATT 301 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 590424 ACTATGGCAATAGTTATTTAGAAGGATCTAGAATACACAACGCATTTGTAAACAGAAATT 590365 Query 302 ACACAGTTAAATATGAAGTGAACTGGAAAACTCATGAAATTAAAGTGAAAGGACATAATT 361 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 590364 ACACAGTTAAATATGAAGTGAACTGGAAAACTCATGAAATTAAAGTGAAAGGACATAATT 590305 Query 362 GATATGaaaaaaaTAGTCAAATCATCAGTTGTTACATCAATTGCATTGCTTTTGCTATCC 421 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 590304 GATATGAAAAAAATAGTCAAATCATCAGTTGTTACATCAATTGCATTGCTTTTGCTATCC 590245 Query 422 AATACACTTGATGCA 436 |||||| |||||||| Sbjct 590244 AATACAGTTGATGCA 590230 >Nucleotide sequence of luks gene TATCATTAGGGTAAAATGTCTGGACATGATCCAAATTTATTTGTTGGATATAAACCATATAGTCAAAATCCGAGAGACTATTTTGTTCCAGACAATGAATTACCCCCATTAGTACACAGTGGTTTCAATCCTTCATTTATTGCAACTGTTTCTCATGAAAAAGGCTCAGGAGATACAAGTGAATTTGAAATAACGTATGGCAGAAATATGGATGTTACTCATGCTACTAGAAGAACAACACACTATGGCAATAGTTATTTAGAAGGATCTAGAATACACAACGCATTTGTAAACAGAAATTACACAGTTAAATATGAAGTGAACTGGAAAACTCATGAAATTAAAGTGAAAGGACATAATTGATATGAAAAAAATAGTCAAATCATCAGTTGTTACATCAATTGCATTGCTTTTGCTATCCAATACACTTGATGCAC Note: The forward and reverse sequence sequence agreed or overlapped at ATTTATTTGTTGGATATAAACCATATAGTCAAAATCCGAGAGACTATTTTGTTCCAGACAATGAATTACCCCCATTAGTACACAGTGGTTTCAATCCTTCATTTATTGCAACTGTTTCTCATGAAAAAGGCTCAGGAGATACAAGTGAATTTGAAATAACGTATGGCAGAAATATGGATGTTACTCATGCTACTAGAAGAACAACACACTATGGCAATAGTTATTTAGAAGGATCTAGAATACACAACGCATTTGTAAACAGAAATTACACAGTTAAATATGAAGTGAACTGGAAAACTCATGAAATTAAAGTGAAAGGA >Amino acid alignment sequence of luks gene (no mutation was observed) LukPVS, partial [Staphylococcus aureus] Sequence ID: gb|AEO79837.1|Length: 119 Score Expect Method Identities Positives Gaps Frame 244 bits(622) 1e-81 Compositional matrix adjust. 117/117(100%) 117/117(100%) 0/117(0%) +1 Query 10 GKMSGHDPNLFVGYKPYSQNPRDYFVPDNELPPLVHSGFNPSFIATVSHEKGSGDTSEFE 189 GKMSGHDPNLFVGYKPYSQNPRDYFVPDNELPPLVHSGFNPSFIATVSHEKGSGDTSEFE Sbjct 3 GKMSGHDPNLFVGYKPYSQNPRDYFVPDNELPPLVHSGFNPSFIATVSHEKGSGDTSEFE 62 Query 190 ITYGRNMDVTHATRRTTHYGNSYLEGSRIHNAFVNRNYTVKYEVNWKTHEIKVKGHN 360 ITYGRNMDVTHATRRTTHYGNSYLEGSRIHNAFVNRNYTVKYEVNWKTHEIKVKGHN Sbjct 63 ITYGRNMDVTHATRRTTHYGNSYLEGSRIHNAFVNRNYTVKYEVNWKTHEIKVKGHN 119 >amino acid sequence of luks gene YH*GKMSGHDPNLFVGYKPYSQNPRDYFVPDNELPPLVHSGFNPSFIATVSHEKGSGDTSEFEITYGRNMDVTHATRRTTHYGNSYLEGSRIHNAFVNRNYTVKYEVNWKTHEIKVKGHN*YEKNSQIISCYINCIAFAIQYT*CX Note: the forward and reverse sequence agreed at positions PRDYFVPDNELPPLVHSGFNPSFIATVSHEKGSGDTSEFEITYGRNMDVTHATRRTTHYGNSYLEGSRIHNAFVNRNYTVKYEVNWKTHEIKVKG 13. Sample S15 mec >Consensus nucleotide sequence of forward and reverse mec sequences TGTATGGCATGAGTAACGAAGAATATAATAAATTAACMGRWGAWWWAWWAGMACYTSTRMKCAACAMSTTCCAKATKACRWCTTMWCCAGGTTYAWSTCAWRRMATGAKTAACAGCA Notes:The forward and revers sequences had several mismatches, accounting for the several "Ws", "Rs" and other non-nucleotide alphabets present in the sequence. Mutations can therefore not be confirmed. I suggest you only report on their presence. 14. Sample 31 >nucleotide alignment sequence of blaZ (2 SNPs were observed) Staphylococcus aureus subsp. aureus N315 pN315 blaPC1 gene for penicillin-hydrolyzing class A beta-lactamase, complete CDS Sequence ID: ref|NG_047533.1|Length: 1046 Range 1: 610 to 783 Score Expect Identities Gaps Strand 311 bits(168) 3e-81 172/174(99%) 0/174(0%) Plus/Plus Query 1 TACTTCAACACCTGCTGCTTTCGGCAAGACTTTAAATAAACTTATCGCAAATGGAAAATT 60 ||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 610 TACTTCAACGCCTGCTGCTTTCGGCAAGACTTTAAATAAACTTATCGCAAATGGAAAATT 669 Query 61 AAGCaaaaaaaataaaaaTTTCTTACTTGATTTAATGTTTAATAATAAAACCGGAGACAC 120 |||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||| Sbjct 670 AAGCAAAAAAAATAAAAATTTCTTACTTGATTTAATGTTTAATAATAAAAACGGAGACAC 729 Query 121 TTTAATTAAAGATGGTGTTCCAAAAGACTATAAGGTTGCTGATAAAAGTGGTCA 174 |||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 730 TTTAATTAAAGATGGTGTTCCAAAAGACTATAAGGTTGCTGATAAAAGTGGTCA 783 >nucleotide sequence of consensus (forward and reverse) sequence of blaZ TACTTCAACACCTGCTGCTTTCGGCAAGACTTTAAATAAACTTATCGCAAATGGAAAATTAAGCAAAAAAAATAAAAATTTCTTACTTGATTTAATGTTTAATAATAAAACCGGAGACACTTTAATTAAAGATGGTGTTCCAAAAGACTATAAGGTTGCTGATAAAAGTGGTCA Notes: forward and reverse sequence only overalapped at TAAAAATTTCTTACTTGATTTAATGTTTAATA >Amino acid sequence of blaZ beta-lactamase, partial [Staphylococcus aureus] Sequence ID: gb|ACP40660.1|Length: 125 Range 1: 62 to 118 Alignment statistics for match #1 Score Expect Method Identities Positives Gaps Frame 111 bits(277) 2e-30 Compositional matrix adjust. 56/57(98%) 56/57(98%) 0/57(0%) +2 Query 2 TSTPAAFGKTLNKLIANGKLSKKNKNFLLDLMFNNKTGDTLIKDGVPKDYKVADKSG 172 TSTPAAFGKTLNKLIANGKLSKKNKNFLLDLMFNNK GDTLIKDGVPKDYKVADKSG Sbjct 62 TSTPAAFGKTLNKLIANGKLSKKNKNFLLDLMFNNKNGDTLIKDGVPKDYKVADKSG 118 >amino acid sequence of blaZ (the forward and reverse sequence overlapped at KNFLLDLMFN) TSTPAAFGKTLNKLIANGKLSKKNKNFLLDLMFNNKTGDTLIKDGVPKDYKVADKSG