AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i320_mixed5_mtub_reg_100.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.66 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 ndkA 42 ndkA #2 valS 87 valS #3 Rv2449c 89 hypothetical protein Rv2449c #4 Rv2450c 81 hypothetical protein Rv2450c #5 aspS 239 aspS #6 Rv2581c 50 hypothetical protein Rv2581c Motif number 1 CAAGATGTATGCCCAAACCGG 1 1 0 GCCCAACCGG 0.99645 -42 CATGAAAGCGCCCGAAACCGCCCGGAT 2 7 0 CCCGAACCGC 0.954305 -81 CTAGAATTGATCGGTGACCGCCAGCCCTCAC 2 55 1 TCGGTACCGC 0.597917 -33 GTGACCGCCAGCCCTCACCCTGCCGCCGAT 2 68 1 GCCCTACCCT 0.874019 -20 ACGCAAAAGCTCCCAAATCCGGTCGGATTTG 3 24 1 TCCCAATCCG 0.91586 -66 ACGCAAAAGCTCCCAAATCCGACCGGATTTG 3 37 0 TCCCAATCCG 0.91586 -53 TTGCGTCTGCTCGCGCACCCCGGAGTAGCGT 3 62 1 TCGCGACCCC 0.9868 -28 CTGGCAGCTAACCCATGCCCGTGGGTTGGCT 4 30 1 ACCCAGCCCG 0.956562 -52 GCTTTGGCGCGCGCGCACCGCGAAAGGAACA 4 58 1 GCGCGACCGC 0.901166 -24 CGGCGAGACGGCGCAGACCCCATC 5 4 0 GCGCAACCCC 0.99447 -236 GCGCCGTCTCGCCGGAGCTCGATCCCGGCGC 5 21 1 GCCGGGCTCG 0.831323 -219 CGGCCACACTCCGCGCGCCGGGATCGAGCTC 5 35 0 CCGCGGCCGG 0.986881 -205 CACAACAGCGGCGAATACCCGGCCTTGTGCA 5 66 1 GCGAAACCCG 0.942898 -174 CGTCGGAACGACGGTCGCCGCGCTGTTGCAC 5 92 0 ACGGTGCCGC 0.669279 -148 CCGTCGTTCCGACGGCACCGGGTCCGACTAG 5 109 1 GACGGACCGG 0.896713 -131 AACAGGCATTGCCCTAGTCGGACCCGGTGCC 5 122 0 GCCCTGTCGG 0.942368 -118 GGTGCCCGCGGCGCACATCGGTCACGCAGGA 5 182 0 GCGCAATCGG 0.982018 -58 GATGTGCGCCGCGGGCACCTCTAGACTGAGC 5 194 1 GCGGGACCTC 0.721241 -46 GTTCGCGGCCCGCCTCGTCCCCG 6 3 1 TCGCGCCCGC 0.9303 -48 CGCCTCGTCCCCGGACGCCGGGGATGGGAAA 6 21 1 CCGGAGCCGG 0.935569 -30 ***** ***** Masking position 9 Map Score: 38.3239 Number of sites scoring better than the average of aligned sites = 32488 Number in coding regions = 30390 Number in noncoding regions = 2098 Number of orfs with sites within 600 bp upstream = 1061 Fraction of orfs with sites within 600 bp upstream = 0.170414 Motif number 2 GGCATACATCTTGCGGCATCTAGTGTTGGG 1 19 1 TTGCGGCATC 0.819625 -24 ATCCGGGCGGTTTCGGGCGC 2 1 1 ATCCGGGCGG 0.735735 -87 ATCCGGGCGGTTTCGGGCGCTTTCATGCCG 2 11 1 TTTCGGGCGC 0.835389 -77 ATTGATCGGTGACCGCCAGCCCTCACCCTG 2 60 1 GACCGCCAGC 0.959115 -28 ATCGGCGGCAGGGTGAGGGCTG 2 76 0 CGGCGGCAGG 0.840325 -12 CTACTCCGGGGTGCGCGAGCAGACGCAAAA 3 60 0 GTGCGCGAGC 0.648207 -30 TCCTTTCGCGGTGCGCGCGCGCCAAAGCCA 4 56 0 GTGCGCGCGC 0.519269 -26 GATGGGGTCTGCGCCGTCTCGCCGGAGC 5 9 1 CTGCGCCGTC 0.932929 -231 CGCCGGGATCGAGCTCCGGCGAGACGGCGC 5 21 0 GAGCTCCGGC 0.767264 -219 TGCGGCCACACTCCGCGCGCCGGGATCGAG 5 38 0 CTCCGCGCGC 0.590198 -202 CGCCGCTGTTGTGCGGCCACACTCCGCGCG 5 49 0 GTGCGGCCAC 0.973208 -191 TTGTGCAACAGCGCGGCGACCGTCGTTCCG 5 90 1 GCGCGGCGAC 0.897734 -150 GCGACCGTCGTTCCGACGGCACCGGGTCCG 5 105 1 TTCCGACGGC 0.859031 -135 GACCGATGTGCGCCGCGGGCACCTCTAGAC 5 190 1 CGCCGCGGGC 0.87964 -50 GGACGAGGCGGGCCGCGAAC 6 1 0 GGCCGCGAAC 0.707206 -50 CATCCCCGGCGTCCGGGGACGAGGCGGGCC 6 17 0 GTCCGGGGAC 0.67999 -34 ********** Masking position 4 Map Score: 23.1846 Number of sites scoring better than the average of aligned sites = 37801 Number in coding regions = 35570 Number in noncoding regions = 2231 Number of orfs with sites within 600 bp upstream = 1052 Fraction of orfs with sites within 600 bp upstream = 0.168969 Motif number 3 ATCCGGGCGGTTTCGGGCGCTTTCA 2 6 1 GGCGGTTTCG 0.955941 -82 CGGATTTGGGAGCTTTTGCGTCTTTTCGCG 3 15 0 AGCTTTTGCG 0.99145 -75 CGGATTTGGGAGCTTTTGCGTCTGCTCGCG 3 47 1 AGCTTTTGCG 0.99145 -43 CCCGTGGGTTGGCTTTGGCGCGCGCGCACC 4 47 1 GGCTTTGGCG 0.987741 -35 GGGTATTCGCCGCTGTTGTGCGGCCACACT 5 56 0 CGCTGTTGTG 0.979709 -184 ACGGTCGCCGCGCTGTTGCACAAGGCCGGG 5 83 0 CGCTGTTGCA 0.990125 -157 CTAGGGCAATGCCTGTTGCAATGTTTGTTG 5 136 1 GCCTGTTGCA 0.966114 -104 ********** Masking position 6 Map Score: 10.0692 Number of sites scoring better than the average of aligned sites = 1740 Number in coding regions = 1585 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 4 CGGCATCTAGTGTTGGGCACC 1 32 1 TTTGGGCACC 0.974746 -11 ATCCGGGCGGTTTCGGGCGCTTTCATGCCGG 2 11 1 TTCGGGCGCT 0.963989 -77 CACCGATCAATTCTAGGAACCGCTTCACACC 2 40 0 TCTAGGAACC 0.833574 -48 ATCCGACCGGATTTGGGAGCTTTTGCGTCTT 3 21 0 ATTGGGAGCT 0.988944 -69 ATCCGGTCGGATTTGGGAGCTTTTGCGTCTG 3 40 1 ATTGGGAGCT 0.988944 -50 CCTCGAATGCACCTGGCAGCTAACCCATGCC 4 18 1 ACTGGCAGCT 0.954753 -64 CAAGGCCGGGTATTCGCCGCTGTTGTGCGGC 5 62 0 TTTCGCCGCT 0.872647 -178 GGGGATGGGAAACTGGGAACC 6 40 1 ACTGGGAACC 0.974493 -11 * ********* Masking position 6 Map Score: 6.87846 Number of sites scoring better than the average of aligned sites = 1933 Number in coding regions = 1772 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 5 CAAGATGTATGCCCAAACCGG 1 1 0 GCCCAACCGG 0.971011 -42 CTAGGAACCGCTTCACACCGGCATGAAAGCG 2 28 0 CTTCACCCGG 0.984466 -60 CGCAAAAGCTCCCAAATCCGGTCGGATTTGG 3 25 1 CCCAAACCGG 0.974072 -65 GGGTTTGACGCTACTCCGGGGTGCGCGAG 3 71 0 CGCTACCCGG 0.994238 -19 GGGTCTGCGCCGTCTCGCCGGAGCTCGATCC 5 15 1 CGTCTCCCGG 0.994743 -225 CGGCCACACTCCGCGCGCCGGGATCGAGCTC 5 35 0 CCGCGCCCGG 0.952954 -205 ACAACAGCGGCGAATACCCGGCCTTGTGCAA 5 67 1 CGAATACCGG 0.854829 -173 CGGCGACCGTCGTTCCGACGGCACCGGGTCC 5 103 1 CGTTCCACGG 0.705172 -137 GGCGCACATCGGTCACGCAGGATAATTTCGG 5 173 0 GGTCACCAGG 0.873468 -67 CTGAGCAGTCGGTTAATCCGGTTGAAGGGGA 5 219 1 GGTTAACCGG 0.923836 -21 CGCGGCCCGCCTCGTCCCCGGACGCCGGGGA 6 14 1 CTCGTCCCGG 0.940564 -37 TTCCCAGTTTCCCATCCCCGGCGTCCGGGGA 6 28 0 CCCATCCCGG 0.987604 -23 ****** **** Masking position 10 Map Score: 16.4853 Number of sites scoring better than the average of aligned sites = 11530 Number in coding regions = 10776 Number in noncoding regions = 754 Number of orfs with sites within 600 bp upstream = 578 Fraction of orfs with sites within 600 bp upstream = 0.0928365 Motif number 6 ATCCGGGCGGTTTCGGGCGCTTTCAT 2 7 1 GCGGTTTCGG 0.887031 -81 GCGGCAGGGTGAGGGCTGGCGGTCACCGAT 2 64 0 GAGGGCTGGC 0.945839 -24 GAGCTTTTGCGTCTTTTCGCGGTGG 3 6 0 GTCTTTTCGC 0.906199 -84 GAGCTTTTGCGTCTGCTCGCGCACCCCGGA 3 56 1 GTCTGCTCGC 0.982988 -34 ACCCATGCCCGTGGGTTGGCTTTGGCGCGC 4 40 1 GTGGGTTGGC 0.963158 -42 GTTGGCTTTGGCGCGCGCGCACCGCGAAAG 4 54 1 GCGCGCGCGC 0.499892 -28 TGGGGTCTGCGCCGTCTCGCCGGAGCTCGA 5 13 1 GCCGTCTCGC 0.989278 -227 GGAGCTCGATCCCGGCGCGCGGAGTGTGGC 5 34 1 CCCGGCGCGC 0.85617 -206 CGGAACGACGGTCGCCGCGCTGTTGCACAA 5 90 0 GTCGCCGCGC 0.983459 -150 ********** Masking position 9 Map Score: 10.9228 Number of sites scoring better than the average of aligned sites = 12946 Number in coding regions = 11801 Number in noncoding regions = 1145 Number of orfs with sites within 600 bp upstream = 737 Fraction of orfs with sites within 600 bp upstream = 0.118375 Motif number 7 GGGAGCTTTTGCGTCTTTTCGCGGTGG 3 8 0 GCGTCTTTTC 0.935766 -82 GGGAGCTTTTGCGTCTGCTCGCGCACCCCG 3 54 1 GCGTCTGCTC 0.996755 -36 GATGGGGTCTGCGCCGTCTCGCCG 5 5 1 GGGTCTGCGC 0.982583 -235 GACCGTCGTTCCGACGGCACCGGGTCCGAC 5 107 1 CCGACGGCAC 0.968401 -133 ACCGGATTAACCGACTGCTCAGTCTAGAGG 5 211 0 CCGACTGCTC 0.994669 -29 ********** Masking position 5 Map Score: 3.59558 Number of sites scoring better than the average of aligned sites = 2106 Number in coding regions = 1855 Number in noncoding regions = 251 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 8 ********** No masking Map Score: 1.60826e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 9 ********** No masking Map Score: 1.60826e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 10 ********** No masking Map Score: 1.60826e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0