From sankar.achuth at gmail.com Thu Jul 11 01:43:43 2013 From: sankar.achuth at gmail.com (Dr. Achuthsankar S. Nair) Date: Thu, 11 Jul 2013 11:13:43 +0530 Subject: [BiO BB] extracting mutation data from MSA Message-ID: >From file such as the one attached having an alignment in standard format (MSA), is there any tool that can fish out the nucleotide changes and their positions in some format like this: 1.G-A( 760), 2.A-G (1000) 3.C-T (9385) -- *Dr Achuthsankar S Nair* *??. ??????? ??????? ??? ?????? *Head, Dept of Computational Biology and Bioinformatics University of Kerala, Trivandrum 695581, Kerala, INDIA Tel (O) 0471-2308759 (R) 0471-3192346/ 0471-2542220 Personal Web Page www.achu.keralauniversity.edu Dept Web page dcb.keralauniversity.ac.in *GREEN TIP #2:* *Adopt a green charter for academic seminars and class room practices* -------------- next part -------------- CLUSTAL 2.1 multiple sequence alignment R1 ACGTAGCCTACCAGTTTCTTACTGCTCTACTCTGCTTAGCAAGAGACTTGAGAACCCATC 60 R2 ACGTAGCCTACCAGTTTCTTACTGCTCTACTCTGCTTAGCAAGAGACTTGAGAACCCATC 60 ************************************************************ R1 ATGGATCCCGTGTACGTGGACATAGACGCCGACAGCGCCTTTTTGAAGGCCCTGCAGCGT 120 R2 ATGGATCCCGTGTACGTGGACATAGACGCCGACAGCGCCTTTTTGAAGGCCCTGCAGCGT 120 ************************************************************ R1 GCGTACCCCATGTTTGAGGTGGAACCAAGGCAGGTCACACCGAATGACCATGCCAATGCT 180 R2 GCGTACCCCATGTTTGAGGTGGAACCAAGGCAGGTCACACCGAATGACCATGCCAATGCT 180 ************************************************************ R1 AGAGCATTCTCGCATCTAGCTATAAAACTAATAGAGCAGGAAATTGATCCCGACTCAACC 240 R2 AGAGCATTCTCGCATCTAGCTATAAAACTAATAGAGCAGGAAATTGATCCCGACTCAACC 240 ************************************************************ R1 ATCCTGGACATAGGCAGCGCGCCAGCAAGGAGGATGATGTCGGATAGGAAGTATCACTGC 300 R2 ATCCTGGACATAGGCAGCGCGCCAGCAAGGAGGATGATGTCGGATAGGAAGTATCACTGC 300 ************************************************************ R1 GTTTGCCCAATGCGCAGCGCAGAAGACCCTGAGAGACTCGCCAACTACGCGAGAAAACTA 360 R2 GTTTGCCCAATGCGCAGCGCAGAAGACCCTGAGAGACTCGCCAACTACGCGAGAAAACTA 360 ************************************************************ R1 GCATCTGCCGCAGGAAAAGTCTTGGACAGAAACATCTCCGGAAAAATCGGAGATCTACAA 420 R2 GCATCTGCCGCAGGAAAAGTCTTGGACAGAAACATCTCCGGAAAAATCGGAGATCTACAA 420 ************************************************************ R1 GCAGTAATGGCTGTACCAGACGCAGAAACGCCCACATTCTGCTTGCACACTGACGTCTCA 480 R2 GCAGTAATGGCTGTACCAGACGCAGAAACGCCCACATTCTGCTTGCACACTGACGTCTCA 480 ************************************************************ R1 TGTAGACAAAGGGCGGACGTCGCTATATACCAGGACGTCTACGCCGTGCATGCACCAACA 540 R2 TGTAGACAAAGGGCGGACGTCGCTATATACCAGGACGTCTACGCCGTGCATGCACCAACA 540 ************************************************************ R1 TCGCTATACCACCAGGCGATTAAAGGAGTCCGTGTAGCATACTGGATAGGGTTTGATACA 600 R2 TCGCTATACCACCAGGCGATTAAAGGAGTCCGTGTAGCATACTGGATAGGGTTTGATACA 600 ************************************************************ R1 ACCCCGTTCATGTATAATGCCATGGCAGGTGCATACCCCTCGTACTCGACAAACTGGGCA 660 R2 ACCCCGTTCATGTATAATGCCATGGCAGGTGCATACCCCTCGTACTCGACAAACTGGGCA 660 ************************************************************ R1 GATGAGCAGGTGCTGAAGGCAAAGAACATAGGATTATGTTCAACAGACCTGACGGAAGGT 720 R2 GATGAGCAGGTGCTGAAGGCAAAGAACATAGGATTATGTTCAACAGACCTGACGGAAGGT 720 ************************************************************ R1 AGACGAGGTAAATTGTCTATCATGAGAGGAAAAAAGATGGAGCCATGTGACCGCGTACTG 780 R2 AGACGAGGTAAATTGTCTATCATGAGAGGAAAAAAGATGAAGCCATGTGACCGCGTACTG 780 ***************************************.******************** R1 TTCTCAGTCGGGTCAACGCTTTACCCGGAGAGCCGTAAGCTTCTTAAGAGTTGGCACTTA 840 R2 TTCTCAGTCGGGTCAACGCTTTACCCGGAGAGCCGTAAGCTTCTTGAGAGTTGGCACTTA 840 *********************************************.************** R1 CCTTCAGTGTTCCATCTAAAAGGGAAGCTCAGCTTCACGTGCCGCTGTGATACAGTGGTT 900 R2 CCTTCAGTGTTCCATCTAAAAGGGAAGCTCAGCTTCACGTGCCGCTGTGATACAGTGGTT 900 ************************************************************ R1 TCGTGTGAAGGCTATGTCGTTAAGAGAATAACGATTAGCCCGGGCCTCTACGGTAAAACC 960 R2 TCGTGTGAAGGCTATGTCGTTAAGAGAATAACGATTAGCCCGGGCCTCTACGGTAAAACC 960 ************************************************************ R1 ACAGGGTACGCAGTAACCCACCATGCAGACGGATTCCTAATGTGCAAAACAACCGATACG 1020 R2 ACAGGGTACGCAGTAACCCACCATGCAGACGGATTCCTAGTGTGCAAAACAACCGATACG 1020 ***************************************.******************** R1 GTAGATGGCGAGAGAGTGTCATTTTCGGTATGCACGTACGTACCCGCAACCATTTGTGAT 1080 R2 GTAGATGGCGAGAGAGTGTCATTTTCGGTATGCACGTACGTACCCGCAACCATTTGTGAT 1080 ************************************************************ R1 CAAATGACAGGTATTCTTGCCACGGAGGTTACACCGGAGGATGCACAGAAGCTGCTGGTG 1140 R2 CAAATGACAGGTATTCTTGCCACGGAGGTTACACCGGAGGATGCACAGAAGCTGCTGGTG 1140 ************************************************************ R1 GGACTGAACCAGAGGATAGTGGTCAATGGCAGAACGCAGAGGAACACGAACACAATGAAG 1200 R2 GGACTGAACCAGAGGATAGTGGTCAATGGCAGAACGCAGAGGAACACGAACACAATGAAG 1200 ************************************************************ R1 AATTACTTGCTTCCTGTGGTTGCCCAAGCCTTCAGTAAGTGGGCAAAGGAATGCCGGAAA 1260 R2 AATTACTTGCTTCCTGTGGTTGCCCAAGCCTTCAGTAAGTGGGCAAAGGAATGCCGGAAA 1260 ************************************************************ R1 GATATGGAAGATGAAAAACTTTTGGGCATCAGAGAAAGGACACTGACATGCTGCTGCCTT 1320 R2 GATATGGAAGATGAAAAACTTTTGGGCATCAGAGAAAGGACACTGACATGCTGCTGCCTT 1320 ************************************************************ R1 TGGGCGTTCAAGAAGCAGAAGACACACACGGTCTACAAGAGGCCTGACACTCAGTCAATT 1380 R2 TGGGCGTTCAAGAAGCAGAAGACACACACGGTCTACAAGAGGCCTGACACTCAGTCAATT 1380 ************************************************************ R1 CAGAAAGTCCCAGCCGAATTTGACAGCTTTGTGGTACCAAGTCTGTGGTCATCTGGACTG 1440 R2 CAGAAAGTCCCAGCCGAATTTGACAGCTTTGTGGTACCAAGTCTGTGGTCATCTGGACTG 1440 ************************************************************ R1 TCGATCCCGCTACGGACCAGAATCAAGTGGCTGCTAAGCAAAGTGCCAAAGACTGATTTG 1500 R2 TCGATCCCGCTACGGACCAGAATCAAGTGGCTGCTAAGCAAAGTGCCAAAGACTGATTTG 1500 ************************************************************ R1 ATCCCTTACAGCGGTGACGCCAAAGAAGCCCGCGATGCTGAAAAAGAAGCAGAAGAAGAA 1560 R2 ATCCCTTACAGCGGTGACGCCAAAGAAGCCCGCGATGCTGAAAAAGAAGCAGAAGAAGAA 1560 ************************************************************ R1 CGAGAAGCGGAGCTAACTCGCGAGGCACTACCACCACTACAGGCGGCACAGGATGACGTC 1620 R2 CGAGAAGCGGAGCTAACTCGCGAGGCACTACCACCACTACAGGCGGCACAGGATGACGTC 1620 ************************************************************ R1 CAGGTCGAAATTGACGTGGAACAGCTCGAAGACAGAGCTGGGGCAGGAATAATTGAAACT 1680 R2 CAGGTCGAAATTGACGTGGAACAGCTCGAAGACAGAGCTGGGGCAGGAATAATTGAAACT 1680 ************************************************************ R1 CCAAGAGGAGCTATCAAAGTCACTGCCCAACCAACAGACCACGTCGTGGGAGAGTACTTG 1740 R2 CCAAGAGGAGCTATCAAAGTCACTGCCCAACCAACAGACCACGTCGTGGGAGAGTACTTG 1740 ************************************************************ R1 GTACTTTCCCCGCAGACCGTGTTACGAAGCCAGAAGCTCAGCCTGATCCACGCATTGGCG 1800 R2 GTACTTTCCCCGCAGACCGTGTTACGAAGCCAGAAGCTCAGCCTGATCCACGCATTGGCG 1800 ************************************************************ R1 GAACAAGTGAAGACATGCACACACAGCGGACGAGCAGGAAGGTACGCGGTCGAAGCATAT 1860 R2 GAACAAGTGAAGACATGCACACACAGCGGACGAGCAGGAAGGTACGCGGTCGAAGCATAT 1860 ************************************************************ R1 GACGGCAGAATCCTTGTGCCCTCAGGCTATGCAATATCACCTGAAGACTTCCAGAGCCTG 1920 R2 GACGGCAGAATCCTTGTGCCCTCAGGCTATGCAATATCACCTGAAGACTTCCAGAGCCTG 1920 ************************************************************ R1 AGCGAAAGTGCGACGATGGTGTACAACGAAAGGGAGTTCGTAAATAGGAAATTACACCAT 1980 R2 AGCGAAAGTGCGACGATGGTGTACAACGAAAGGGAGTTCGTAAATAGGAAATTACACCAT 1980 ************************************************************ R1 ATCGCGTTGCACGGACCAGCCCTGAACACTGACGAGGAGTCGTACGAGCTGGTAAGGGCA 2040 R2 ATCGCGTTGCACGGACCAGCCCTGAACACTGACGAGGAGTCGTACGAGCTGGTAAGGGCA 2040 ************************************************************ R1 GAAAGGACAGAGCATGAGTACGTCTATGATGTGGACCAAAGAAGGTGCTGCAAGAAAGAG 2100 R2 GAAAGGACAGAGCATGAGTACGTCTATGATGTGGACCAAAGAAGGTGCTGCAAGAAAGAG 2100 ************************************************************ R1 GAGGCAGCCGGGCTGGTACTGGTCGGCGACTTGACCAACCCGCCCTACCATGAGTTCGCA 2160 R2 GAGGCAGCCGGGCTGGTACTGGTCGGCGACTTGACCAACCCGCCCTACCATGAGTTCGCA 2160 ************************************************************ R1 TATGAAGGGCTGAGAATCCGCCCCGCCTGCCCATACAAGACCGCAGTAATAGGGGTCTTT 2220 R2 TATGAAGGGCTGAGAATCCGCCCCGCCTGCCCATACAAGACCGCAGTAATAGGGGTCTTT 2220 ************************************************************ R1 GGAGTGCCAGGATCCGGCAAATCAGCAATCATTAAGAACCTAGTTACCAGGCAAGACCTA 2280 R2 GGAGTGCCAGGATCCGGCAAATCAGCAATCATTAAGAACCTAGTTACCAGGCAAGACCTA 2280 ************************************************************ R1 GTGACCAGTGGAAAGAAAGAAAACTGCCAAGAAATCTCCACCGACGTGATGCGACAGAGG 2340 R2 GTGACCAGTGGAAAGAAAGAAAACTGCCAAGAAATCTCCACCGACGTGATGCGACAGAGG 2340 ************************************************************ R1 AATCTGGAGATATCTGCACGCACGGTCGACTCACTGCTCTTGAACGGATGCAACAGACCA 2400 R2 AATCTGGAGATATCTGCACGCACGGTCGACTCACTGCTCTTGAACGGATGCAACAGACCA 2400 ************************************************************ R1 GTCGACGTGTTGTACGTCGACGAAGCGTTTGCGTGCCATTCTGGCACGCTACTTGCTCTG 2460 R2 GTCGACGTGTTGTACGTCGACGAAGCGTTTGCGTGCCATTCTGGCACGCTACTTGCTCTG 2460 ************************************************************ R1 ATAGCCTTGGTGAGACCGAGGCAGAAAGTCGTGCTATGCGGTGATCCGAAACAGTGCGGC 2520 R2 ATAGCCTTGGTGAGACCGAGGCAGAAAGTCGTGCTATGCGGTGATCCGAAACAGTGCGGC 2520 ************************************************************ R1 TTCTTCAATATGATGCAGATGAAAGTTAACTACAACCATAACATCTGCACCCAAGTGTAC 2580 R2 TTCTTCAATATGATGCAGATGAAAGTTAACTACAACCATAACATCTGCACCCAAGTGTAC 2580 ************************************************************ R1 CATAAAAGTATTTCCAGGCGGTGTACACTGCCTGTGACTGCCATTGTGTCCTCGTTGCAT 2640 R2 CATAAAAGTATTTCCAGGCGGTGTACACTGCCTGTGACTGCCATTGTGTCCTCGTTGCAT 2640 ************************************************************ R1 TACGAAGGCAAAATGCGCACAACAAATGAGTACAACAAGCCAATTGTAGTGGATACTACA 2700 R2 TACGAAGGCAAAATGCGCACAACAAATGAGTACAACAAGCCAATTGTAGTGGATACTACA 2700 ************************************************************ R1 GGCTCGACAAAACCCGACCCCGGAGACCTTGTGCTAACATGTTTCAGAGGGTGGGTTAAG 2760 R2 GGCTCGACAAAACCCGACCCCGGAGACCTTGTGCTAACATGTTTCAGAGGGTGGGTTAAG 2760 ************************************************************ R1 CAACTGCAAATTGACTACCGTGGACACGAGGTCATGACAGCAGCTGCATCTCAGGGGCTA 2820 R2 CAACTGCAAATTGACTACCGTGGACACGAGGTCATGACAGCAGCTGCATCTCAGGGGCTA 2820 ************************************************************ R1 ACCAGAAAAGGGGTCTATGCCGTCAGGCAAAAAGTCAATGAAAACCCCCTTTACGCATCA 2880 R2 ACCAGAAAAGGGGTCTATGCCGTCAGGCAAAAAGTCAATGAAAACCCCCTTTACGCATCA 2880 ************************************************************ R1 ACATCAGAGCACGTGAACGTGCTACTGACGCGTACGGAAGGCAAACTAGTATGGAAGACA 2940 R2 ACATCAGAGCACGTGAACGTGCTACTGACGCGTACGGAAGGCAAACTAGTATGGAAGACA 2940 ************************************************************ R1 CTTTCTGGAGACCCATGGATAAAGACACTGCAGAACCCGCCGAAAGGAAATTTTAAAGCA 3000 R2 CTTTCTGGAGACCCATGGATAAAGACACTGCAGAACCCGCCGAAAGGAAATTTTAAAGCA 3000 ************************************************************ R1 ACAATTAAGGAATGGGAAGTGGAACATGCTTCAATAATGGCGGGTATCTGTAACCACCAA 3060 R2 ACAATTAAGGAATGGGAAGTGGAACATGCTTCAATAATGGCGGGTATCTGTAACCACCAA 3060 ************************************************************ R1 GTGACCTTTGACACGTTCCAGAATAAAGCCAATGTCTGCTGGGCGAAGAGCTTAGTCCCC 3120 R2 GTGACCTTTGACACGTTCCAGAATAAAGCCAATGTCTGCTGGGCGAAGAGCTTAGTCCCC 3120 ************************************************************ R1 ATCCTAGAAACAGCAGGAATAAAATTAAACGACAGGCAGTGGTCCCAGATAATCCAGGCT 3180 R2 ATCCTAGAAACAGCAGGAATAAAATTAAACGACAGGCAGTGGTCCCAGATAATCCAGGCT 3180 ************************************************************ R1 TTTAAAGAAGACAGAGCATACTCACCCGAGGTGGCCCTGAATGAGATATGCACGCGCATG 3240 R2 TTTAAAGAAGACAGAGCATACTCACCCGAGGTGGCCCTGAATGAGATATGCACGCGCATG 3240 ************************************************************ R1 TACGGGGTAGACCTGGACAGCGGGCTGTTCTCTAAACCACTGGTGTCCGTGCATTATGCG 3300 R2 TACGGGGTAGACCTGGACAGCGGGCTGTTCTCTAAACCACTGGTGTCCGTGCATTATGCG 3300 ************************************************************ R1 GATAATCACTGGGACAACAGGCCGGGAGGGAAGATGTTCGGATTCAACCCCGAAGCGGCG 3360 R2 GATAATCACTGGGACAACAGGCCGGGAGGGAAGATGTTCGGATTCAACCCCGAAGCGGCG 3360 ************************************************************ R1 TCCATACTGGAGAGGAAATACCCGTTTACAAAAGGGAAGTGGAATACCAACAAGCAAATC 3420 R2 TCCATACTGGAGAGGAAATACCCGTTTACAAAAGGGAAGTGGAATACCAACAAGCAAATC 3420 ************************************************************ R1 TGTGTGACTACTAGGAGGATTGAAGATTTTAACCCGAACACCAACATTATACCTGCCAAC 3480 R2 TGTGTGACTACTAGGAGGATTGAAGATTTTAACCCGAACACCAACATTATACCTGCCAAC 3480 ************************************************************ R1 AGGAGACTACCGCATTCATTGGTGGCCGAACATCGCCCGGTAAAAGGGGAGAGGATGGAA 3540 R2 AGGAGACTACCGCATTCATTGGTGGCCGAACATCGCCCGGTAAAAGGGGAGAGGATGGAA 3540 ************************************************************ R1 TGGTTGGTCAACAAAATAAATGGCCACCATGTGCTCCTGGTCAGCGGCTACAACCTCGTT 3600 R2 TGGTTGGTCAACAAAATAAATGGCCACCATGTGCTCCTGGTCAGCGGCTACAACCTCGTT 3600 ************************************************************ R1 CTGCCCACTAAGAGAGTCACCTGGGTGGCGCCGCTGGGCATCCGGGGAGCTGACTACACA 3660 R2 CTGCCCACTAAGAGAGTCACCTGGGTGGCGCCGCTGGGCATCCGGGGAGCTGACTACACA 3660 ************************************************************ R1 TACAACCTAGAGTTAGGCCTACCAGCAACGCTCGGTAGATATGACCTAGTGATTATAAAC 3720 R2 TACAACCTAGAGTTAGGCCTACCAGCAACGCTCGGTAGATATGACCTAGTGATTATAAAC 3720 ************************************************************ R1 ATCCACACACCCTTTCGCATACATCATTACCAACAGTGCGTGGATCATGCAATGAAGCTG 3780 R2 ATCCACACACCCTTTCGCATACATCATTACCAACAGTGCGTGGATCATGCAATGAAGCTG 3780 ************************************************************ R1 CAGATGCTCGGAGGAGACTCCCTGAGACTGCTCAAGCCGGGTGGTTCATTACTGATCAGG 3840 R2 CAGATGCTCGGAGGAGACTCCCTGAGACTGCTCAAGCCGGGTGGTTCATTACTGATCAGG 3840 ************************************************************ R1 GCATACGGCTACGCAGACAGAACAAGCGAACGAGTAGTCTGCGTACTGGGACGCAAGTTT 3900 R2 GCATACGGCTACGCAGACAGAACAAGCGAACGAGTAGTCTGCGTACTGGGACGCAAGTTT 3900 ************************************************************ R1 CGATCATCCAGAGCGTTGAAACCGCCGTGCGTCACTAGCAACACCGAGATGTTTTTCTTG 3960 R2 CGATCATCCAGAGCGTTGAAACCGCCGTGCGTCACTAGCAACACCGAGATGTTTTTCTTG 3960 ************************************************************ R1 TTCAGCAACTTTGATAACGGCAGAAGGAACTTTACAACGCACGTAATGAACAACCAGCTG 4020 R2 TTCAGCAACTTTGATAACGGCAGAAGGAACTTTACAACGCACGTAATGAACAACCAGCTG 4020 ************************************************************ R1 AATGCTGCTTTTGTTGGTCAGGCCACCCGAGCAGGGTGTGCACCGTCGTACCGGGTTAAA 4080 R2 AATGCTGCTTTTGTTGGTCAGGCCACCCGAGCAGGGTGTGCACCGTCGTACCGGGTTAAA 4080 ************************************************************ R1 CGCATGGACATCGCAAAGAACGATGAAGAGTGCGTAGTCAACGCCGCCAACCCTCGTGGG 4140 R2 CGCATGGACATCGCAAG-AACGATGAAGAGTGCGTAGTCAACGCCGCCAACCCTCGTGGG 4139 ****************. ****************************************** R1 CTACCAGGCGATGGCGTCTGTAAAGCAGTATACAAAAAATGGCCGGAGTCCTTCAAGAAC 4200 R2 CTACCAGGCGATGGCGTCTGTAAAGCAGTATACAAAAAATGGCCGGAGTCCTTCAAGAAC 4199 ************************************************************ R1 AGTGCAACACCAGTGGGAACCGCAAAGACAGTCATGTGCGGTACATACCCGGTAATCCAT 4260 R2 AGTGCAACACCAGTGGGAACCGCAAAGACAGTCATGTGCGGTACATACCCGGTAATCCAT 4259 ************************************************************ R1 GCAGTAGGACCTAATTTCTCAAATTACTCTGAGTCCGAAGGAGACCGGGAATTGGCAGCT 4320 R2 GCAGTAGGACCTAATTTCTCAAATTACTCTGAGTCCGAAGGAGACCGGGAATTGGCAGCT 4319 ************************************************************ R1 GCTTACCGAGAAGTCGCTAAAGAGGTGACTAGACTAGGAGTAAACAGCGTAGCTATACCG 4380 R2 GCTTACCGAGAAGTCGCTAAAGAGGTGACTAGACTAGGAGTAAACAGCGTAGCTATACCG 4379 ************************************************************ R1 CTCCTTTCCACCGGCGTGTACTCTGGAGGGAAAGACAGGCTGACTCAGTCATTAAACCAC 4440 R2 CTCCTTTCCACCGGCGTGTACTCTGGAGGGAAAGACAGGCTGACTCAGTCATTAAACCAC 4439 ************************************************************ R1 CTTTTTACAGCATTAGACTCAACTGATGCAGATGTGGTTATCTACTGCCGCGACAAGGAG 4500 R2 CTTTTTACAGCATTAGACTCAACTGATGCAGATGTGGTTATCTACTGCCGCGACAAGGAG 4499 ************************************************************ R1 TGGGAGAAGAAAATAGCCGAGGCCATACAAATGAGGACCCAAGTGGAACTACTAGATGAA 4560 R2 TGGGAGAAGAAAATAGCCGAGGCCATACAAATGAGGACCCAAGTGGAACTACTAGATGAA 4559 ************************************************************ R1 CACATCTCTGTAGACTGCGATATCATCCGAGTGCACCCTGACAGCAGTTTGGCAGGTAGA 4620 R2 CACATCTCTGTAGACTGCGATATCATCCGAGTGCACCCTGACAGCAGTTTGGCAGGTAGA 4619 ************************************************************ R1 AAAGGGTACAGCACTACAGAAGGTTCACTGTACTCCTACTTGGAAGGGACACGGTTCCAT 4680 R2 AAAGGGTACAGCACTACAGAAGGTTCACTGTACTCCTACTTGGAAGGGACACGGTTCCAT 4679 ************************************************************ R1 CAGACGGCAGTGGACATGGCAGAAGTATACACCATGTGGCCAAAGCAGACGGAGGCTAAT 4740 R2 CAGACGGCAGTGGACATGGCAGAAGTATACACCATGTGGCCAAAGCAGACGGAGGCTAAT 4739 ************************************************************ R1 GAACAAGTTTGCTTGTACGCATTGGGGGAAAGTATAGAATCAATCAGGCAAAAGTGCCCA 4800 R2 GAACAAGTTTGCTTGTACGCATTGGGGGAAAGTATAGAATCAATCAGGCAAAAGTGCCCA 4799 ************************************************************ R1 GTGGATGACGCAGATGCATCGTCGCCCCCAAAAACCGTCCCGTGCCTCTGCCGTTATGCC 4860 R2 GTGGATGACGCAGATGCATCGTCGCCCCCAAAAACCGTCCCGTGCCTCTGCCGTTATGCC 4859 ************************************************************ R1 ATGACACCCGAACGAGTCACCAGGCTTCGTATGAACCATGTCACAAACATAATAGTATGC 4920 R2 ATGACACCCGAACGAGTCACCAGGCTTCGTATGAACCATGTCACAAACATAATAGTATGC 4919 ************************************************************ R1 TCATCATTCCCCCTTCCAAAGTATAAAATAGAAGGAGTGCAGAAAGTCAAGTGTTCTAAA 4980 R2 TCATCATTCCCCCTTCCAAAGTATAAAATAGAAGGAGTGCAGAAAGTCAAGTGTTCTAAA 4979 ************************************************************ R1 GTGATGCTGTTCGACCATAACGTGCCATCACGCGTTAGTCCAAGGGAATATAAATCGCCT 5040 R2 GTGATGCTGTTCGACCATAACGTGCCATCACGCGTTAGTCCAAGGGAATATAAATCGCCT 5039 ************************************************************ R1 CAGGAGACCGCACAAGAAGTAAGTTCGACCACGTCACTGACGCACAGCCAATTCGACCTT 5100 R2 CAGGAGACCGCACAAGAAGTAAGTTCGACCACGTCACTGACGCACAGCCAATTCGACCTT 5099 ************************************************************ R1 AGCGTTGACGGTGAGGTACTGCCCGCTCCGTCTGACCTGGAAGCTGATGCTCCGATTTCG 5160 R2 AGCGTTGACGGTGAGGTACTGCCCGCTCCGTCTGACCTGGAAGCTGATGCTCCGATTTCG 5159 ************************************************************ R1 GAGCCAACACCAGACGACAGAGCGGTACTTACTTTGCCTCCCACGATTGAAAATTTTTCG 5220 R2 GAGCCAACACCAGACGACAGAGCGGTACTTACTTTGCCTCCCACGATTGAAAATTTTTCG 5219 ************************************************************ R1 GCTGTGTCAGACTGGGTAATGAATACCGCGCCAGTCGCACCACCCAGAAGAAGACGTGGG 5280 R2 GCTGTGTCAGACTGGGTAATGAATACCGCGCCAGTCGCACCACCCAGAAGAAGACGTGGG 5279 ************************************************************ R1 AAAAACTTGAATGTCACCTGCGACGAGAGAGAAGGGAACGTACTTCCCATGGCTAGCGTT 5340 R2 AAAAACTTGAATGTCACCTGCGACGAGAGAGAAGGGAACGTACTTCCCATGGCTAGCGTT 5339 ************************************************************ R1 CGGTTTTTCAGAGCGGATCTGCACTCCATCGTACAGGAAACGGCAGAGATACGCGATACG 5400 R2 CGGTTTTTCAGAGCGGATCTGCACTCCATCGTACAGGAAACGGCAGAGATACGCGATACG 5399 ************************************************************ R1 GCCGCGTCCCTCCAGGCGCCCCTGAGTGTCGCTACAGAACCAAATCAACTGCCGATCTCA 5460 R2 GCCGCGTCCCTCCAGGCGCCCCTGAGTGTCGCTACAGAACCAAATCAACTGCCGATCTCA 5459 ************************************************************ R1 TTTGGAGCACCAAACGAGACTTTCCCCATAACGTTCGGGGATTTTGATGAAGGGGAGATT 5520 R2 TTTGGAGCACCAAACGAGACTTTCCCCATAACGTTCGGGGATTTTGATGAAGGGGAGATT 5519 ************************************************************ R1 GAAAGCTTGTCCTCTGAGTTACTGACCTTTGGGGACTTCTCGCCGGGCGAAGTGGATGAC 5580 R2 GAAAGCTTGTCCTCTGAGTTACTGACCTTTGGGGACTTCTCGCCGGGCGAAGTGGATGAC 5579 ************************************************************ R1 CTGACAGACAGCGACTGGTCCACGTGTTCAGACACGGACGACGAATTATGACTAGATAGG 5640 R2 CTGACAGACAGCGACTGGTCCACGTGTTCAGACACGGACGACGAATTANGACTAGATAGG 5639 ************************************************.*********** R1 GCAGGTGGGTACATATTCTCATCCGACACCGGCCCCGGCCACCTGCAACAGAGGTCTGTC 5700 R2 GCAGGTGGGTACATATTCTCATCCGACACCGGCCCCGGCCACCTGCAACAGAGGTCTGTC 5699 ************************************************************ R1 CGTCAGACAGTACTGCCGGTAAATACCTTGGAGGAAGTTCAGGAGGAGAAATGTTACCCA 5760 R2 CGTCAGACAGTACTGCCGGTAAATACCTTGGAGGAAGTTCAGGAGGAGAAATGTTACCCA 5759 ************************************************************ R1 CCTAAGTTGGATGAAGTGAAAGAGCAGTTGTTACTTAAGAAACTCCAGGAAAGTGCGTCC 5820 R2 CCTAAGTTGGATGAAGTGAAAGAGCAGTTGTTACTTAAGAAACTCCAGGAAAGTGCGTCC 5819 ************************************************************ R1 ATGGCTAACAGAAGCAGGTACCAATCCCGCAAAGTAGAGAACATGAAAGCAACAATAGTC 5880 R2 ATGGCTAACAGAAGCAGGTACCAATCCCGCAAAGTAGAGAACATGAAAGCAACAATAGTC 5879 ************************************************************ R1 CAAAGGCTGAAGGGTGGTTGCAAACTTTATTTAATGTCGGAGACTCCGAAAGTTCCTACC 5940 R2 CAAAGGCTGAAGGGTGGTTGCAAACTTTATTTAATGTCGGAGACTCCGAAAGTTCCTACC 5939 ************************************************************ R1 TACCGAACTACATATCCGGCACCAGTGTACTCACCCCCAATCAATATCCGACTGTCCAAC 6000 R2 TACCGAACTACATATCCGGCACCAGTGTACTCACCCCCAATCAATATCCGACTGTCCAAC 5999 ************************************************************ R1 CCCGAGTCTGCTGTGGCAGCGTGCAATGAGTTCCTAGCAAGGAACTATCCGACAGTTGCG 6060 R2 CCCGAGTCTGCTGTGGCAGCGTGCAATGAGTTCCTAGCAAGGAACTATCCGACAGTTGCG 6059 ************************************************************ R1 TCGTACCAAATCACTGATGAGTACGATGCATACCTGGACATGGTGGACGGGTCGGAAAGT 6120 R2 TCGTACCAAATCACTGATGAGTACGATGCATACCTGGACATGGTGGACGGGTCGGAAAGT 6119 ************************************************************ R1 TGCCTTGACCGGGCGACGTTCAATCCATCAAAGCTTAGAAGTTATCCAAAACAGCACTCC 6180 R2 TGCCTTGACCGGGCGACGTTCAATCCATCAAAGCTTAGAAGTTATCCAAAACAGCACTCC 6179 ************************************************************ R1 TACCATGCACCCACAATCAGAAGTGCCGTACCTTCCCCGTTCCAGAATACGTTGCAGAAC 6240 R2 TACCATGCACCCACAATCAGAAGTGCCGTACCTTCCCCGTTCCAGAATACGTTGCAGAAC 6239 ************************************************************ R1 GTACTGGCTGCTGCCACGAAAAGAAATTGCAACGTCACACAGATGAGAGAACTGCCTACT 6300 R2 GTACTGGCTGCTGCCACGAAAAGAAATTGCAACGTCACACAGATGAGAGAACTGCCTACT 6299 ************************************************************ R1 TTGGATTCAGCGGTATTTAATGTTGAGTGCTTTAAAAAATTTGCGTGCAATCAAGAATAC 6360 R2 TTGGATTCAGCGGTATTTAATGTTGAGTGCTTTAAAAAATTTGCGTGCAATCAAGAATAC 6359 ************************************************************ R1 TGGAAGGAATTTGCCGCCAGTCCTATTAGGATAACGACTGAGAACTTGACAACTTATGTC 6420 R2 TGGAAGGAATTTGCCGCCAGTCCTATTAGGATAACGACTGAGAACTTGACAACTTATGTC 6419 ************************************************************ R1 ACAAAACTAAAAGGACCAAAAGCAGCAGCATTGTTTGCCAAGACACATAACCTGCTACCA 6480 R2 ACAAAACTAAAAGGACCAAAAGCAGCAGCATTGTTTGCCAAGACACATAACCTGCTACCA 6479 ************************************************************ R1 CTGCAGGAGGTACCGATGGACAGGTTTACTGTAGACATGAAAAGGGACGTGAAGGTGACT 6540 R2 CTGCAGGAGGTACCGATGGACAGGTTTACTGTAGACATGAAAAGGGACGTGAAGGTGACT 6539 ************************************************************ R1 CCGGGGACGAAGCACACTGAGGAAAGACCTAAAGTGCAGGTCATACAGGCAGCCGAACCT 6600 R2 CCGGGGACGAAGCACACTGAGGAAAGACCTAAAGTGCAGGTCATACAGGCAGCCGAACCT 6599 ************************************************************ R1 TTGGCAACAGCGTATCTGTGTGGGATCCACAGAGAGTTGGTCAGAAGGCTGAATGCAGTC 6660 R2 TTGGCAACAGCGTATCTGTGTGGGATCCACAGAGAGTTGGTCAGAAGGCTGAATGCAGTC 6659 ************************************************************ R1 CTTCTACCTAATGTACACACGCTGTTTGACATGTCTGCCGAGGACTTTGACGCCATTATT 6720 R2 CTTCTACCTAATGTACACACGCTGTTTGACATGTCTGCCGAGGACTTTGACGCCATTATT 6719 ************************************************************ R1 GCCGCGCACTTCAAGCCAGGGGACGCCGTATTGGAAACCGATATAGCCTCCTTTGACAAG 6780 R2 GCCGCGCACTTCAAGCCAGGGGACGCCGTATTGGAAACCGATATAGCCTCCTTTGACAAG 6779 ************************************************************ R1 AGCCAAGACGACTCGTTGGCGCTCACTGCTCTAATGTTGCTAGAGGATTTGGGGGTGGAT 6840 R2 AGCCAAGACGACTCGTTGGCGCTCACTGCTCTAATGTTGCTAGAGGATTTGGGGGTGGAT 6839 ************************************************************ R1 CATCCCCTGTTGGACTTGATAGAGGCTGCCTTCGGGGAGATCTCCAGCTGCCACCTACCG 6900 R2 CATCCCCTGTTGGACTTGATAGAGGCTGCCTTCGGGGAGATCTCCAGCTGCCACCTACCG 6899 ************************************************************ R1 ACGGGCACCCGTTTTAAGTTCGGCGCCATGATGAAGTCTGGTATGTTCCTAACCCTGTTC 6960 R2 ACGGGCACCCGTTTTAAGTTCGGCGCCATGATGAAGTCTGGTATGTTCCTAACCCTGTTC 6959 ************************************************************ R1 GTCAATACACTGCTAAACATCACCATAGCCAGCCGAGTGCTGGAGGACCGCTTGACAAAG 7020 R2 GTCAATACACTGCTAAACATCACCATAGCCAGCCGAGTGCTGGAGGACCGCTTGACAAAG 7019 ************************************************************ R1 TCTGCGTGCGCGGCCTTCATCGGCGACGACAATATAATACATGGGGTTGTCTCTGACGAA 7080 R2 TCTGCGTGCGCGGCCTTCATCGGCGACGACAATATAATACATGGGGTTGTCTCTGACGAA 7079 ************************************************************ R1 CTGATGGCAGCAAGATGCGCTACATGGATGAACATGGAAGTGAAGATCATAGATGCGGTC 7140 R2 CTGATGGCAGCAAGATGCGCTACATGGATGAACATGGAAGTGAAGATCATAGATGCGGTC 7139 ************************************************************ R1 GTGTCTCAGAAAGCCCCGTACTTCTGCGGAGGGTTTATACTGTATGATACAGTAGCAGGC 7200 R2 GTGTCTCAGAAAGCCCCGTACTTCTGCGGAGGGTTTATACTGTATGATACAGTAGCAGGC 7199 ************************************************************ R1 ACGGCCTGCAGAGTGGCAGACCCGCTAAAGCGGCTGTTCAAGCTGGGCAAACCGCTGGCG 7260 R2 ACGGCCTGCAGAGTGGCAGACCCGCTAAAGCGGCTGTTCAAGCTGGGCAAACCGCTGGCG 7259 ************************************************************ R1 GCGGGAGATGAACAAGACGACGACAGAAGACGTGCACTGGCTGACGAAGTGGTTAGATGG 7320 R2 GCGGGAGATGAACAAGACGACGACAGAAGACGTGCACTGGCTGACGAAGTGGTTAGATGG 7319 ************************************************************ R1 CAACGAACAGGGCTAACTGATGAGCTAGAAAAAGCGGTACACTCCAGGTATGAAGTGCAG 7380 R2 CAACGAACAGGGCTAACTGATGAGCTAGAAAAAGCGGTACACTCCAGGTATGAAGTGCAG 7379 ************************************************************ R1 GGCATATCTGTCGTGGTAATGTCTATGGCCACCTTTGCAAGCTCTAGATCTAACTTTGAG 7440 R2 GGCATATCTGTCGTGGTAATGTCTATGGCCACCTTTGCAAGCTCTAGATCTAACTTTGAG 7439 ************************************************************ R1 AAGCTCAGAGGACCCATCGTAACCCTGTACGGTGGTCCTAAATAGGTACGCACTACAGCT 7500 R2 AAGCTCAGAGGACCCATCGTAACCCTGTACGGTGGTCCTAAATAGGTACGCACTACAGCT 7499 ************************************************************ R1 ACCTATTTCGTCAGAAACCAATCGCAGCTACTTGCATACCTACCAGCTACAATGGAGTTC 7560 R2 ACCTATTTCGTCAGAAACCAATCGCAGCTACTTGCATACCTACCAGCTACAATGGAGTTC 7559 ************************************************************ R1 ATCCCGACGCAAACTTTCTATAACAGAAGGTACCAACCCCGACCCTGGGCCCCACGCCCT 7620 R2 ATCCCGACGCAAACTTTCTATAACAGAAGGTACCAACCCCGACCCTGGGCCCCACGCCCT 7619 ************************************************************ R1 ACAATTCAAGTAATTAGACCTAGACCACGTCCACAGAGGCAGGCTGGGCAACTCGCCCAG 7680 R2 ACAATTCAAGTAATTAGACCTAGACCACGTCCACAGAGGCAGGCTGGGCAACTCGCCCAG 7679 ************************************************************ R1 CTGATCTCTGCAGTCAACAAATTGACCATGCGCGCGGTACCTCAACAGAAGCCTCGCAGA 7740 R2 CTGATCTCTGCAGTCAACAAATTGACCATGCGCGCGGTACCTCAACAGAAGCCTCGCAGA 7739 ************************************************************ R1 AATCGGAAAAACAAGAAGCAAAGGCAGAAGAAGCAGGCGCCGCAAAACGACCCAAAGCAA 7800 R2 AATCGGAAAAACAAGAAGCAAAGGCAGAAGAAGCAGGCGCCGCAAAACGACCCAAAGCAA 7799 ************************************************************ R1 AAGAAGCAACCACCACAAAAGAAGCCGGCTCAAAAGAAGAAGAAACCAGGCCGTAGGGAG 7860 R2 AAGAAGCAACCACCACAAAAGAAGCCGGCTCAAAAGAAGAAGAAACCAGGCCGTAGGGAG 7859 ************************************************************ R1 AGAATGTGCATGAAAATTGAAAATGATTGCATCTTCGAAGTCAAGCATGAAGGCAAAGTG 7920 R2 AGAATGTGCATGAAAATTGAAAATGATTGCATCTTCGAAGTCAAGCATGAAGGCAAAGTG 7919 ************************************************************ R1 ATGGGCTACGCATGCCTGGTGGGGGATAAAGTAATGAAACCAGCACATGTGAAGGGAACT 7980 R2 ATGGGCTACGCATGCCTGGTGGGGGATAAAGTAATGAAACCAGCACATGTGAAGGGAACT 7979 ************************************************************ R1 ATCGACAATGCCGATTTGGCTAAACTGGCCTTCAAGCGGTCGTCTAAATACGATCTTGAA 8040 R2 ATCGACAATGCCGATTTGGCTAAACTGGCCTTCAAGCGGTCGTCTAAATACGATCTTGAA 8039 ************************************************************ R1 TGTGCACAGATACCAGTGCACATGAAGTCTGATGCCTCGAAGTTTACCCACGAGAAACCC 8100 R2 TGTGCACAGATACCAGTGCACATGAAGTCTGATGCCTCGAAGTTTACCCACGAGAAACCC 8099 ************************************************************ R1 GAGGGGTACTATAACTGGCATCACGGAGCAGTGCAGTATTCAGGAGGCCGGTTCACTATC 8160 R2 GAGGGGTACTATAACTGGCATCACGGAGCAGTGCAGTATTCAGGAGGCCGGTTCACTATC 8159 ************************************************************ R1 CCGACGGGTGCAGGCAAGCCGGGAGACAGCGGCAGACCGATCTTCGACAACAAAGGACGG 8220 R2 CCGACGGGTGCAGGCAAGCCGGGAGACAGCGGCAGACCGATCTTCGACAACAAAGGACGG 8219 ************************************************************ R1 GTGGTGGCCATCGTCCTAGGAGGGGCCAACGAAGGTGCCCGCACGGCCCTCTCCGTGGTG 8280 R2 GTGGTGGCCATCGTCCTAGGAGGGGCCAACGAAGGTGCCCGCACGGCCCTCTCCGTGGTG 8279 ************************************************************ R1 ACGTGGAACAAAGACATCGTCACAAAAATTACCCCTGAGGGAGCCGAAGAGTGGAGCCTC 8340 R2 ACGTGGAACAAAGACATCGTCACAAAAATTACCCCTGAGGGAGCCGAAGAGTGGAGCCTC 8339 ************************************************************ R1 GCCCTCCCGGTCTTGTGCCTGTTGGCAAACACCACATTCCCCTGCTCTCAGCCGCCTTGC 8400 R2 GCCCTCCCGGTCTTGTGCCTGTTGGCAAACACCACATTCCCCTGCTCTCAGCCGCCTTGC 8399 ************************************************************ R1 ACACCCTGCTGCTACGAAAAGGAACCGGAAAGCACCTTGCGCATGCTTGAGGACAACGTG 8460 R2 ACACCCTGCTGCTACGAAAAGGAACCGGAAAGCACCTTGCGCATGCTTGAGGACAACGTG 8459 ************************************************************ R1 ATGAGACCCGGATACTACCAGCTGCTAAAAGCATCGCTGACTTGTTCTCCCCACCGCCAA 8520 R2 ATGAGACCCGGATACTACCAGCTGCTAAAAGCATCGCTGACTTGTTCTCCCCACCGCCAA 8519 ************************************************************ R1 AGACGCAGTACTAAGGACAATTTTAATGTCTATAAAGCTACAAGACCATATCTAGCTCAT 8580 R2 AGACGCAGTACTAAGGACAATTTTAATGTCTATAAAGCTACAAGACCATATCTAGCTCAT 8579 ************************************************************ R1 TGTCCTGACTGCGGAGAAGGGCATTCGTGCCACAGCCCTATCGCATTGGAGCGCATCAGA 8640 R2 TGTCCTGACTGCGGAGAAGGGCATTCGTGCCACAGCCCTATCGCATTGGAGCGCATCAGA 8639 ************************************************************ R1 AATGAAGCAACGGACGGAACGCTGAAAATCCAGGTCTCTTTGCAGATCGGGATAAAGACA 8700 R2 AATGAAGCAACGGACGGAACGCTGAAAATCCAGGTCTCTTTGCAGATCGGGATAAAGACA 8699 ************************************************************ R1 GATGACAGCCACGATTGGACCAAGCTGCGCTATATGGATAGCCATACGCCAGCGGACGCG 8760 R2 GATGGCAGCCACGATTGGACCAAGCTGCGCTATATGGATAGCCATACGCCAGCGGACGCG 8759 ****.******************************************************* R1 GAGCGAGCCGGATTGCTTGTAAGGACTTCAGCACCGTGCACGATCACCGGGACCATGGGA 8820 R2 GAGCGAGCCGGATTGCTTGTAAGGACTTCAGCACCGTGCACGATCACCGGGACCATGGGA 8819 ************************************************************ R1 CACTTTATTCTCGCCCGATGCCCGAAAGGAGAGACGCTGACAGTGGGATTTACGGACAGC 8880 R2 CACTTTATTCTCGCCCGATGCCCGAAAGGAGAGACGCTGACAGTGGGATTTACGGACAGC 8879 ************************************************************ R1 AGAAAGATCAGCCACACATGCACACACCCGTTCCATCATGAACCACCTGTGATAGGTAGG 8940 R2 AGAAAGATCAGCCACACATGCACACACCCGTTCCATCATGAACCACCTGTGATAGGTAGG 8939 ************************************************************ R1 GAGAGGTTCCACTCTCGACCACAACATGGTAAAGAGTTACCTTGCAGCACGTACGTGCAG 9000 R2 GAGAGGTTCCACTCTCGACCACAACATGGTAAAGAGTTACCTTGCAGCACGTACGTGCAG 8999 ************************************************************ R1 AGCACCGCTGCCACTGCCGAGGAGATAGAGGTGCATATGCCCCCAGATACTCCTGACCGC 9060 R2 AGCACCGCTGCCACTGCCGAGGAGATAGAGGTGCATATGCCCCCAGATACTCCTGACCGC 9059 ************************************************************ R1 ACGCTGATGACGCAGCAGTCTGGCAACGTGAAGATCACAGTTAATGGGCAGACGGTGCGG 9120 R2 ACGCTGATGACGCAGCAGTCTGGCAACGTGAAGATCACAGTTAATGGGCAGACGGTGCGG 9119 ************************************************************ R1 TACAAGTGCAACTGCGGCGGCTCAAACGAGGGACTGACAACCACAGACAAAGTGATCAAT 9180 R2 TACAAGTGCAACTGCGGCGGCTCAAACGAGGGACTGACAACCACAGACAAAGTGATCAAT 9179 ************************************************************ R1 AACTGCAAAATTGATCAGTGCCATGCTGCAGTCACTAATCACAAGAAGTGGCAATACAAC 9240 R2 AACTGCAAAATTGATCAGTGCCATGCTGCAGTCACTAATCACAAGAAGTGGCAATACAAC 9239 ************************************************************ R1 TCCCCTTTAGTCCCGCGTAACGCTGAACTCGGGGACCGTAAAGGAAAGATTCACATCCCA 9300 R2 TCCCCTTTAGTCCCGCGTAACGCTGAACTCGGGGACCGTAAAGGAAAGATTCACATCCCA 9299 ************************************************************ R1 TTCCCATTGGCAAACGTGACTTGCAGAGTGCCAAAAGCAAGAAACCCCACAGTAACGTAC 9360 R2 TTCCCATTGGCAAACGTGACTTGCAGAGTGCCAAAAGCAAGAAACCCCACAGTAACGTAC 9359 ************************************************************ R1 GGAAAAAACCAAGTCACCATGCTGCTGTATCCTGACCATCCGACACTCTTGTCTTATCGT 9420 R2 GGAAAAAACCAAGTCACCATGCTGTTGTATCCTGACCATCCGACACTCTTGTCTTATCGT 9419 ************************ *********************************** R1 AACATGGGACAGGAACCAAATTACCACGAGGAGTGGGTGACACACAAGAAGGAGGTTACC 9480 R2 AACATGGGACAGGAACCAAATTACCACGAGGAGTGGGTGACACACAAGAAGGAGGTTACC 9479 ************************************************************ R1 TTGACCGTGCCTACTGAGGGTCTGGAGGTCACTTGGGGCAACAACGAACCATACAAGTAC 9540 R2 TTGACCGTGCCTACTGAGGGTCTGGAGGTCACTTGGGGCAACAACGAACCATACAAGTAC 9539 ************************************************************ R1 TGGCCGCAGATGTCTACGAACGGTACTGCTCATGGTCACCCACATGAGATAATCTTGTAC 9600 R2 TGGCCGCAGATGTCTACGAACGGTACTGCTCATGGTCACCCACATGAGATAATCTTGTAC 9599 ************************************************************ R1 TATTATGAGCTGTACCCCACTATGACTGTAATCATTGTGTCGGTGGCCTCGTTCGTGCTT 9660 R2 TATTATGAGCTGTACCCCACTATGACTGTAATCATTGTGTCGGTGGCCTCGTTCGTGCTT 9659 ************************************************************ R1 CTGTCGATGGTGGGCACAGCAGTGGGGATGTGTGTGTGCGCACGGCGCAGATGCATTACA 9720 R2 CTGTCGATGGTGGGCACAGCAGTGGGGATGTGTGTGTGCGCACGGCGCAGATGCATTACA 9719 ************************************************************ R1 CCATATGAATTAACACCAGGAGCCACCGTTCCCTTTCTGCTCAGCCTGCTATGTTGCGTC 9780 R2 CCATATGAATTAACACCAGGAGCCACCGTTCCCTTTCTGCTCAGCCTGCTATGTTGCGTC 9779 ************************************************************ R1 AGAACGACCAAGGCGGCCACATATTACGAGGCTGTGGCATATCTATGGAACGAACAGCAG 9840 R2 AGAACGACCAAGGCGGCCACATATTACGAGGCTGTGGCATATCTATGGAACGAACAGCAG 9839 ************************************************************ R1 CCCCTGTTCTGGTTGCAGGCTCTTATCCCGCTGGCCGCCTTGATCGTCCTGTGCAACTGT 9900 R2 CCCCTGTTCTGGTTGCAGGCTCTTATCCCGCTGGCCGCCTTGATCGTCCTGTGCAACTGT 9899 ************************************************************ R1 CTGAAACTCTTGCCATGCTGCTGTAAGACCCTGGCTTTTTTAGCCGTAATGAGCATCGGT 9960 R2 CTGAAACTCTTGCCATGCTGCTGTAAGACCCTGGCTTTTTTAGCCGTAATGAGCATCGGT 9959 ************************************************************ R1 GCCCACACTGTGAGCGCGTACGAACACGTAACAGTGATCCCGAACACGGTGGGAGTACCG 10020 R2 GCCCACACTGTGAGCGCGTACGAACACGTAACAGTGATCCCGAACACGGTGGGAGTACCG 10019 ************************************************************ R1 TATAAGACTCTTGTCAACAGACCGGGTTACAGCCCCATGGTATTGGAGATGGAGCTACAA 10080 R2 TATAAGACTCTTGTCAACAGACCGGGTTACAGCCCCATGGTATTGGAGATGGAGCTACAA 10079 ************************************************************ R1 TCGGTCACCTTGGAACCAACACTGTCACTTGACTACATCACGTGCGAGTACAAAACTGTC 10140 R2 TCGGTCACCTTGGAACCAACACTGTCACTTGACTACATCACGTGCGAGTACAAAACTGTC 10139 ************************************************************ R1 ATCCCCTCCCCGTACGTGAAGTGCTGTGGTACAGCAGAGTGCAAGGACAAGAGCCTACCA 10200 R2 ATCCCCTCCCCGTACGTGAAGTGCTGTGGTACAGCAGAGTGCAAGGACAAGAGCCTACCA 10199 ************************************************************ R1 GACTACAGCTGCAAGGTCTTTACTGGAGTCTACCCATTTATGTGGGGCGGCGCCTACTGC 10260 R2 GACTACAGCTGCAAGGTCTTTACTGGAGTCTACCCATTTATGTGGGGCGGCGCCTACTGC 10259 ************************************************************ R1 TTTTGCGACGCCGAAAATACGCAATTGAGCGAGGCACATGTAGAGAAATCTGAATCTTGC 10320 R2 TTTTGCGACGCCGAAAATACGCAATTGAGCGAGGCACATGTAGAGAAATCTGAATCTTGC 10319 ************************************************************ R1 AAAACAGAGTTTGCATCGGCCTACAGAGCCCACACCGCATCGGCGTCGGCGAAGCTCCGC 10380 R2 AAAACAGAGTTTGCATCGGCCTACAGAGCCCACACCGCATCGGCGTCGGCGAAGCTCCGC 10379 ************************************************************ R1 GTCCTTTACCAAGGAAACAACATTACTGTAGCTGCCTACGCTAACGGCGACCATGCCGTC 10440 R2 GTCCTTTACCAAGGAAACAACATTACTGTAGCTGCCTACGCTAACGGCGACCATGCCGTC 10439 ************************************************************ R1 ACAGTAAAGGACGCCAAGTTTGTCGTGGGACCAATGTCCTCCGCCTGGACACCTTTTGAC 10500 R2 ACAGTAAAGGACGCCAAGTTTGTCGTGGGACCAATGTCCTCCGCCTGGACACCTTTTGAC 10499 ************************************************************ R1 AACAAAATCGTGGTGTACAAAGGCGACGTCTACAACATGGACTACCCACCTTTTGGCGCA 10560 R2 AACAAAATCGTGGTGTACAAAGGCGACGTCTACAACATGGACTACCCACCTTTTGGCGCA 10559 ************************************************************ R1 GGAAGACCAGGACAATTTGGTGACATTCAAAGTCGTACACCGGAAAGTAAAGACGTTTAT 10620 R2 GGAAGACCAGGACAATTTGGTGACATTCAAAGTCGTACACCGGAAAGTAAAGACGTTTAT 10619 ************************************************************ R1 GCCAACACTCAGTTGGTACTACAGAGGCCAGCAGCAGGCACGGTACATGTACCATACTCT 10680 R2 GCCAACACTCAGTTGGTACTACAGAGGCCAGCAGCAGGCACGGTACATGTACCATACTCT 10679 ************************************************************ R1 CAGGCACCATCTGGCTTCAAGTATTGGCTGAAGGAACGAGGAGCATCGCTACAGCACACG 10740 R2 CAGGCACCATCTGGCTTCAAGTATTGGCTGAAGGAACGAGGAGCATCGCTACAGCACACG 10739 ************************************************************ R1 GCACCGTTCGGTTGCCAGATTGCGACAAACCCGGTAAGAGCTGTAAATTGCGCTGTGGGG 10800 R2 GCACCGTTCGGTTGCCAGATTGCGACAAACCCGGTAAGAGCTGTAAATTGCGCTGTGGGG 10799 ************************************************************ R1 AACATACCAATTTCCATCGACATACCGGATGCGGCCTTTACTAGGGTTGTCGATGCACCC 10860 R2 AACATACCAATTTCCATCGACATACCGGATGCGGCCTTTACTAGGGTTGTCGATGCACCC 10859 ************************************************************ R1 TCTGTAACGGACATGTCATGCGAAGTACCAGCCTGCACTCACTCCTCCGACTTTGGGGGC 10920 R2 TCTGTAACGGACATGTCATGCGAAGTACCAGCCTGCACTCACTCCTCCGACTTTGGGGGC 10919 ************************************************************ R1 GTCGCCATCATCAAATATACAGCTAGCAAGAAAGGTAAATGTGCAGTACATTCGATGACC 10980 R2 GTCGCCATCATCAAATATACAGCTAGCAAGAAAGGTAAATGTGCAGTACATTCGATGACC 10979 ************************************************************ R1 AACGCCGTTACCATTCGAGAAGCCGACGTAGAAGTAGAGGGGAATTCCCAGCTGCAAATA 11040 R2 AACGCCGTTACCATTCGAGAAGCCGACGTAGAAGTAGAGGGGAATTCCCAGCTGCAAATA 11039 ************************************************************ R1 TCCTTCTCAACAGCCTTGGCAAGCGCCGAGTTTCGCGTGCAAGTGTGCTCCACACAAGTA 11100 R2 TCCTTCTCAACAGCCTTGGCAAGCGCCGAGTTTCGCGTGCAAGTGTGCTCCACACAAGTA 11099 ************************************************************ R1 CACTGCGCAGCCGCATGCCACCCTCCAAAGGACCACATAGTCAATTACCCAGCATCACAC 11160 R2 CACTGCGCAGCCGCATGCCACCCTCCAAAGGACCACATAGTCAATTACCCAGCATCACAC 11159 ************************************************************ R1 ACCACCCTTGGGGTCCAGGATATATCCACAACGGCAATGTCTTGGGTGCAGAAGATTACG 11220 R2 ACCACCCTTGGGGTCCAGGATATATCCACAACGGCAATGTCTTGGGTGCAGAAGATTACG 11219 ************************************************************ R1 GGAGGAGTAGGATTAATTGTTGCTGTTGCTGCCTTAATTTTAATTGTGGTGCTATGCGTG 11280 R2 GGAGGAGTAGGATTAATTGTTGCTGTTGCTGCCTTAATTTTAATTGTGGTGCTATGCGTG 11279 ************************************************************ R1 TCGTTTAGCAGGCACTAAACTGATGATAAGGCACGAAATAACTAAACAGCAAAAGTAGAA 11340 R2 TCGTTTAGCAGGCACTAAACTGATGATAAGGCACGAAATAACTAAACAGCAAAAGTAGAA 11339 ************************************************************ R1 AGTACATAACCAGGTATATGTGCCCCCTAAGAGGCACAATATATATAGCTAAGCACTATT 11400 R2 AGTACATAACCAGGTATATGTGCCCCCTAAGAGGCACAATATATATAGCTAAGCACTATT 11399 ************************************************************ R1 AGATCAAAGGGCTATACAACCCCTGAATAGTAACAAAACACAAAAATCAATAAAAATCAT 11460 R2 AGATCAAAGGGCTATACAACCCCTGAATAGTAACAAAACACAAAAATCAATAAAAATCAT 11459 ************************************************************ R1 AAAAAGAAAAATCTCATAAACAGGTATACGTGTCCCCTAAGAGACACATTGTATGTAGGT 11520 R2 AAAAAGAAAAATCTCATAAACAGGTATACGTGTCCCCTAAGAGACACATTGTATGTAGGT 11519 ************************************************************ R1 AGTAAGTATAGATCAAAGGGCTATATTAACCCCTGAATAGTAACAAAACACAAAAACAAT 11580 R2 AGTAAGTATAGATCAAAGGGCTATATTAACCCCTGAATAGTAACAAAACACAAAAACAAT 11579 ************************************************************ R1 AAAAACTACAAAATAGAAAATCTATAAATAAAAGTAGTTCAAAGGGCTACAAAACCCCTG 11640 R2 AAAAACTACAAAATAGAAAATCTATAAATAAAAGTAGTTCAAAGGGCTACAAAACCCCTG 11639 ************************************************************ R1 AATAGTAACAAAACATAAAATGTAATAAAAATTAAGTGTGTACCCAAAAGAGGTACAGTA 11700 R2 AATAGTAACAAAACATAAAATGTAATAAAAATTAAGTGTGTACCCAAAAGAGGTACAGTA 11699 ************************************************************ R1 AGAATCAGTGAATATCACAATTGGCAACGAGAAGAGACGTAGGTATTTAAGCTTCCTAAA 11760 R2 AGAATCAGTGAATATCACAATTGGCAACGAGAAGAGACGTAGGTATTTAAGCTTCCTAAA 11759 ************************************************************ R1 AGCAGCCGAACTCACTTTGAGACGTAGGCATAGCATACCGAACTCTTCCACTATTCTCCG 11820 R2 AGCAGCCGAACTCACTTTGAGACGTAGGCATAGCATACCGAACTCTTCCACTATTCTCCG 11819 ************************************************************ R1 AACCCACAGGGACGTAGGAGATGT 11844 R2 AACCCACAGGGACGTAGGAGATGT 11843 ************************ From mireji at gmail.com Fri Jul 12 10:11:00 2013 From: mireji at gmail.com (Paul Mireji) Date: Fri, 12 Jul 2013 17:11:00 +0300 Subject: [BiO BB] Biochemical Society of Kenya - Bioinformatics Workshop and Annual Scientific Symposium Message-ID: Dear All, Kindly circulate within your networks and accept my apologies for cross-posting. *Biochemical Society of Kenya* * **Bioinformatics Workshop and Annual Scientific Symposium* *Call for Applications and Papers* The Biochemical Society of Kenya (BSK) was formed in 1980, as a society for scientist involved in research and teaching of biochemistry and related subjects in Kenya. The society has since grown to include members in academic and research institutions across Africa and beyond, and encompass all aspects of cellular and molecular life Sciences, bioinformatics/computational biology and related functional genomics studies. The primary goal of the society is to advance knowledge of the members through annual 1) short inductive trainings in contemporary research methodologies and tools to enhance their ability to design, interrogate and understand scientific research/outputs and 2) symposia to share research experiences and communicate the scientific outputs of their investigations. Trypanosomiasis Research Centre (TRC) is one of the 23 main centres of the Kenya Agricultural Reseach Institute (KARI) with a mandate to carry out research and develop technologies for effective control of tsetse and trypanosomiasis in the country. In 2004, the Centre was competitively selected by the World Health Organization Special Programme on Tropical Diseases Research (WHO/TDR) as the lead organization in Africa to coordinate the capacity strengthening activities for human African trypanosomiasis (HAT). The Centre is also the Biosciences eastern and central Africa Network (BecANet) Centre of Excellence for Tsetse & Trypanosomiasis Research and Training. In these initatives, TRC works with government agencies, regional research and academic institutions to strengthen the biomedical capacity in the areas of Vector Biology and Ecology, Biology of parasites, drug resistance, diagnostics, parasite/vector genetics, applied genomics/bioinformatics, vector control, data analysis/ management/ presentation and development of animal disease models. KARI-TRC is a founder member of Eastern African Network of Trypanosomiasis (EANETT).The institution is also an active participant in the International *Glossina* Genome Initiative (IGGI), a WHO/TDR initiative that is advancing tsetse genomics activities and works with Fogarty International Center at National Institutes of Health (USA) to build capacity in tsetse/trypanosomiasis research. Yale School of Public Health (YSPH) has been working with the TRC and their collaborators to strengthen the biomedical capacity and to acquire and implement the recent advances in applied vector genomics, genetics and bioinformatics in their research activities to enhance the existing HAT control/management tools. The BSK in collaboration with TRC, Institute of Primate Research (IPR), Yale School of Public Health (YSPH), and Technical University of Kenya (TUK) invites applications for bioinformatics workshop and scientific symposium. The workshop will be held on September 2-10, 2013 at TRC Campus in Muguga Kenya, and the 19th international conference/symposium on September 11-13, 2013 at Kenya School of Government, Nairobi, Kenya. * * *Workshop (*September 2-10, 2013)** *Theme: From Genomes to Functions, a Practical Approach to Interrogating Genomic Data * *Scope* The workshop will update the participants on recent developments in genome sequencing and analyses and equip participants with theoretical knowledge and practical skills for designing genomics based research experiments to understand biological phenomena. *Learning outcomes:* At the end of the course, the participants will be gain: 1) Working knowledge of genome/transcriptome sequencing and understanding of current status genome sequencing projects and opportunities, especially in trypansomiasis. 2) Skills for designing experiments involving/exploiting high throughput Next Generation Sequencing (NGS) technology. 3) Skill for generation and processing of the NGS data to identify genes associated phenotypes of interest 4) Downstream functional genomics process for validation of the NGS based findings. The consortium has arrays of NGS data and tools from real world experiments in trypanosomiasis research that will be used for training. Participants will be encouraged to interrogate their own data where possible in the context of the training. *Requirements* Basic computational knowledge Basic understanding of molecular biology *Target Audience * Postgraduate students, postdoctoral scientist, scientist and academicians interested in applying NGS technology to understand biological phenomena. * * * * *Conference and Symposia (11th-13th Sept 2013)* The BSK symposium will be held jointly with the 19th International Scientific Conference 2013 on Basic and Clinical Research for Improved Healthand the Kenya Society for Immunology (KSI) Symposium * * *Theme: * *Closing the Gap in Bioscience; Challenges and Opportunities*** *Scope:* The consortium is seeking for original research contributions presenting innovative advances in genomics research, concepts and solutions in the areas outline below. 1. *Immunology and pathology of diseases.*** 2. *Fertility and contraceptive research.* 3. *Drug discovery and product testing.* 4. *Diagnostic research.* 5. *Basic pathogen and disease studies.* 6. *Ecology and conservation.* 7. *Non-communicable diseases.* 8. *Socio-economic aspects of biomedical research.* 9. *Neglected Tropical Diseases (NTDs).* 10. *Agriculture and Food Security.* *Registration for Participation* * * * * * * *19th Int. Conference/Symposia** *Status* *Workshop* *Early* *Late* Local Student Ksh 15,000 Ksh 2000 Ksh 3,000 Local Participants Ksh 25,000 Ksh 7,000 Ksh 10,000 International Participants/Students US $400 $150 $200 Industry Ksh 50,000 Ksh 20000 Ksh 20000 * Those who have already applied through the 19th International Scientific Conference 2013 on Basic and Clinical Research for Improved Healthsecretariat do not need to submit their application for the Conference/symposium again. *Those that will pay for the Workshop and participate will be given free access to the 19th International conference /symposia (i.e they will not pay registration charges for 19th International conference) *The payments should be made to account below or on arrival* National Museums of Kenya-IPR, Standard Chartered Bank Karen Branch Account No: 0102044700000 please send a scanned copy of payment slip to: isc2013 at primateresearch.org *Submission of Application* 1) *Workshop and Symposium* All applications for the workshop and symposium should be submitted online using the link below. https://docs.google.com/forms/d/1zxs8jO2KYbBQcI5_2LeLTwSuMrxlzNQ_355URiUeEko/viewform 2) *Workshop Only* *An institutional letter of support *(ie, letter from your supervisor, department chair, division, or organizational director) which specifically comments on potential impact of the training in enhancing research output and capacity building in your institution. Please note: We anticipate some letters may be available for submission after the application deadline.*Please submit to peterpaul.mireji at yale.edu *at your earliest convenience. *Sponsorship* The consortium has limited funds to facilitate participation by needy applicants. The sponsorship will competitively be awarded and will not cover travel-related costs for the workshop and symposium. These costs will have to be covered by the participants. * * *Important Dates* * * *Deadline for submission of application** Jul 31, 2013* *Early registration Jul 31, 2013* *Late registration Sept 6, 2013* *Publication of abstract book Sept 8, 2013* *Workshop: Sept 2 - 10, 2013*** *Conference/symposia Sept 11-13, 2013* *Release of published Conference proceedings Oct 31, 2013* Questions can be directed to Paul Mireji at *peterpaul.mireji at yale.edu *and secretariat at* *isc2013 at primateresearch.org From sgadagkar at gmail.com Fri Jul 12 05:06:52 2013 From: sgadagkar at gmail.com (Sudhindra Gadagkar) Date: Fri, 12 Jul 2013 02:06:52 -0700 Subject: [BiO BB] extracting mutation data from MSA In-Reply-To: References: Message-ID: MEGA5 gives you this information. On Thursday, July 11, 2013, Dr. Achuthsankar S. Nair wrote: > From file such as the one attached having an alignment in standard format > (MSA), is there any tool that can fish out the nucleotide changes and their > positions in some format like this: > 1.G-A( 760), > 2.A-G (1000) > 3.C-T (9385) > > > > -- > *Dr Achuthsankar S Nair* *??. ??????? ??????? ??? ?????? > *Head, Dept of Computational Biology and Bioinformatics > University of Kerala, Trivandrum 695581, Kerala, INDIA > Tel (O) 0471-2308759 (R) 0471-3192346/ 0471-2542220 > > Personal Web Page www.achu.keralauniversity.edu > Dept Web page dcb.keralauniversity.ac.in > > *GREEN TIP #2:* *Adopt a green charter for academic seminars and class room > practices* >