AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i099_bsub_mtub_100.orf -o099_bsub_mtub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -x5 -e 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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yqgH 68 alternate gene name: yzmC; similar to phosphate ABC transporter (permease) #2 yqgG 153 alternate gene name: yzmB; similar to phosphate ABC transporter (binding protein) #3 phoY2 57 phoY2 #4 Rv0822c 165 hypothetical protein Rv0822c #5 phoS2 271 phoS2 #6 pstB 215 pstB #7 pstC 59 pstC #8 phoY1 107 phoY1 Motif number 1 CGCCACGAGTCGGCGCCGCACAATGCAGCA 4 66 0 CGGCGCCGCA 0.978176 -100 CGACTCGTGGCGGTGCTGCGCGAAGGTGCG 4 84 1 CGGTGCTGCG 0.716455 -82 CGGTGCTGCGCGAAGGTGCGCGTAGGACAC 4 94 1 CGAAGGTGCG 0.81601 -72 GTCTAGGTGGCGGACGCCCGCGGTGTTGGC 4 127 0 CGGACGCCCG 0.840798 -39 CCTAGACTCTCGGAGGCCGGTAGGAC 4 150 1 CGGAGGCCGG 0.946796 -16 CCGTTTCGGCCGACAGCCGGAAAAGAGGGC 5 14 0 CGACAGCCGG 0.974558 -258 TGACTGCTCCCGAAACCTGGGGGTGTGCCT 5 68 1 CGAAACCTGG 0.628589 -204 GTGGCTGGTTCGACCGCGGGTCTCAGGGGA 5 127 0 CGACCGCGGG 0.993357 -145 GGGTCAACCCCGGCCAAGGGCGACGGCACG 5 171 1 CGGCCAAGGG 0.837121 -101 CGGCCAAGGGCGACGGCACGCCAAGTTCGC 5 181 1 CGACGGCACG 0.983303 -91 CAGTTCCTAACGGCCGACCAGCTGTTTTGC 5 250 0 CGGCCGACCA 0.736756 -22 GGATCCGCCACCACGACCCCCTCGAGAGGA 6 16 0 CCACGACCCC 0.727152 -200 GGTGGCTCGGCGACCACCGGTGGCGAGTGG 6 44 0 CGACCACCGG 0.962597 -172 GACCCCGGGTCGGTGGCTCGGCGACCACCG 6 55 0 CGGTGGCTCG 0.845975 -161 GCTCGAATACCGACCCCGGGTCGGTGGCTC 6 66 0 CGACCCCGGG 0.990145 -150 TGCACAACGGTGACGGCTCGAATACCGACC 6 81 0 TGACGGCTCG 0.81858 -135 TCAGTATCAGCGGCCCCTCCTGAACGCTAG 6 137 0 CGGCCCCTCC 0.947427 -79 TACTGAGGGTCGACGGCGCGCTTTGTCCAA 6 161 1 CGACGGCGCG 0.997742 -55 CGGCGCAGGGTACTACATGC 6 206 0 CGGCGCAGGG 0.949994 -10 CCTCGTTGACCACCACGCGACAGCAACCT 7 10 1 CCACCACGCG 0.923649 -50 CAAAGCAGCCCGATGGCCCGACGGAGGTTG 7 34 0 CGATGGCCCG 0.902506 -26 TCGACCATGGCGGCACCGCGCGACATACCC 8 25 0 CGGCACCGCG 0.990762 -83 TGCCGCGGATCCACACCGCCATCATCGACC 8 49 0 CCACACCGCC 0.735917 -59 TGTGGATCCGCGGCAGCACCACACGACGAC 8 64 1 CGGCAGCACC 0.823241 -44 CAGCACCACACGACGACTCAGGGTCAGAGA 8 77 1 CGACGACTCA 0.802481 -31 ********** Masking position 1 Map Score: 41.2386 Number of sites scoring better than the average of aligned sites = 3161 Number in coding regions = 2930 Number in noncoding regions = 231 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 2 ACGCAGCCAACACCGCGGGCGTCCGCCACC 4 122 1 CACCGCGGGC 0.990112 -44 CGTTTCGGCCGACAGCCGGAAAAGAGGGCG 5 13 0 GACAGCCGGA 0.961256 -259 GCCGTGCATACACAGCAGGCACACCCCCAG 5 84 0 CACAGCAGGC 0.915788 -188 TGGCTGGTTCGACCGCGGGTCTCAGGGGAA 5 126 0 GACCGCGGGT 0.990248 -146 GGCCAAGGGCGACGGCACGCCAAGTTCGCC 5 182 1 GACGGCACGC 0.983315 -90 GTGGCTCGGCGACCACCGGTGGCGAGTGGA 6 43 0 GACCACCGGT 0.936083 -173 CTCGAATACCGACCCCGGGTCGGTGGCTCG 6 65 0 GACCCCGGGT 0.943392 -151 GCACAACGGTGACGGCTCGAATACCGACCC 6 80 0 GACGGCTCGA 0.955657 -136 ACTGAGGGTCGACGGCGCGCTTTGTCCAAG 6 162 1 GACGGCGCGC 0.993764 -54 CCTCGTTGACCACCACGCGACAGCAACCTC 7 11 1 CACCACGCGA 0.975543 -49 AAAGCAGCCCGATGGCCCGACGGAGGTTGC 7 33 0 GATGGCCCGA 0.849402 -27 ACCATGGCGGCACCGCGCGACATACCCGCT 8 22 0 CACCGCGCGA 0.994495 -86 TCCGCGGCAGCACCACACGACGACTCAGGG 8 70 1 CACCACACGA 0.928941 -38 ********** Masking position 2 Map Score: 23.2491 Number of sites scoring better than the average of aligned sites = 529 Number in coding regions = 494 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 ACGGTTGTCCCCGCACTCCTCTTTTTATTA 1 14 0 CCGCACTCCT 0.930972 -55 GCAGCCAACACCGCGGGCGTCCGCCACCTA 4 124 1 CCGCGGGCGT 0.951652 -42 GCTGGTTCGACCGCGGGTCTCAGGGGAAGG 5 124 0 CCGCGGGTCT 0.962017 -148 CCAAGGGCGACGGCACGCCAAGTTCGCCGA 5 184 1 CGGCACGCCA 0.946309 -88 GGTGGCGGATCCACTCGCCACCGGTGGTCG 6 34 1 CCACTCGCCA 0.96027 -182 TGAGGGTCGACGGCGCGCTTTGTCCAAGGA 6 164 1 CGGCGCGCTT 0.871313 -52 TCGTTGACCACCACGCGACAGCAACCTCCG 7 13 1 CCACGCGACA 0.980044 -47 CAGCAACCTCCGTCGGGCCATCGGGCTGCT 7 31 1 CGTCGGGCCA 0.920894 -29 CATGGCGGCACCGCGCGACATACCCGCTTG 8 20 0 CCGCGCGACA 0.963864 -88 CGCGGCAGCACCACACGACGACTCAGGGTC 8 72 1 CCACACGACG 0.876815 -36 ********** Masking position 4 Map Score: 10.7481 Number of sites scoring better than the average of aligned sites = 657 Number in coding regions = 625 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 TTTACTCTATACGTGTAGGACAAATTACACA 2 109 1 ACTGTAGGAC 0.825165 -45 GCCGCACAATGCAGCAAGGCCCACATCGTAC 4 51 0 GCGCAAGGCC 0.96795 -115 GCACCTTCGCGCAGCACCGCCACGAGTCGGC 4 82 0 GCGCACCGCC 0.870263 -84 GCGCGAAGGTGCGCGTAGGACACGCAGCCAA 4 101 1 GCCGTAGGAC 0.991909 -65 ACTCTCGGAGGCCGGTAGGAC 4 155 1 GCGGTAGGAC 0.994111 -11 CCTCTTTTCCGGCTGTCGGCCGAAACGGTAA 5 16 1 GGTGTCGGCC 0.836114 -256 GGGGAAGGATGTCCGTATGCCGTGCATACAC 5 101 0 GTCGTATGCC 0.709893 -171 TGGACACGTGGCTGGTTCGACCGCGGGTCTC 5 133 0 GCGGTTCGAC 0.951458 -139 GAGCAAAACAGCTGGTCGGCCGTTAGGAACT 5 248 1 GCGGTCGGCC 0.995282 -24 TCCTTGGGATGCTCCTTGGACAAAGCGCGCC 6 175 0 GCCCTTGGAC 0.958154 -41 ATCCCAAGGAGCATGTAGTACCCTGCGCCG 6 196 1 GCTGTAGTAC 0.825163 -20 CCGCAAAGCAGCCCGATGGCCCGACGGAGGT 7 36 0 GCCGATGGCC 0.949127 -24 GCTACGCCAAGCGGGTATGTCGCGCGGTGCC 8 13 1 GCGGTATGTC 0.877862 -95 GGTGTCACGCCTCTCTGACCCTGAGTCGT 8 89 0 GCTCTCTGAC 0.868102 -19 ** ******** Masking position 11 Map Score: 17.4838 Number of sites scoring better than the average of aligned sites = 865 Number in coding regions = 810 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 CCTTGGAAAATGCCGTAAGCGTCGTGTCAA 3 16 0 TGCCGTAAGC 0.957258 -42 CGCCGCACAATGCAGCAAGGCCCACATCGT 4 53 0 TGCAGCAAGG 0.974071 -113 CACAGGAAGCTGCAGCAAGCTTGTTACCGT 5 40 0 TGCAGCAAGC 0.968079 -232 GTTAACCTAGTGCTGTTAGCTTCATTTGCT 5 216 1 TGCTGTTAGC 0.960237 -56 TAGCTTCATTTGCTGCGAGCAAAACAGCTG 5 232 1 TGCTGCGAGC 0.983892 -40 ACAGCTGGTCGGCCGTTAGGAACTGAA 5 255 1 GGCCGTTAGG 0.894064 -17 CTCCTTGGGATGCTCCTTGGACAAAGCGCG 6 177 0 TGCTCCTTGG 0.935826 -39 GGGTACTACATGCTCCTTGGGATGCTCCTT 6 189 0 TGCTCCTTGG 0.935826 -27 CGGAGGTTGCTGTCGCGTGGTGGTCAACGA 7 13 0 TGTCGCGTGG 0.824526 -47 ********** Masking position 2 Map Score: 6.53409 Number of sites scoring better than the average of aligned sites = 1057 Number in coding regions = 996 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 6 TAACACATTCATAGGAGTGTAAAACA 1 53 1 ATAGGAGTGT 0.820508 -16 CGCCCACATCATGTGAGCGTTTTTT 2 6 0 ATGTGAGCGT 0.97301 -148 CGCTCACATGATGTGGGCGTTTTTTTTATA 2 17 1 ATGTGGGCGT 0.993686 -137 AATCAGTACGATGTGGGCCTTGCTGCATTG 4 46 1 ATGTGGGCCT 0.95801 -120 TGCTGCGCGAAGGTGCGCGTAGGACACGCA 4 97 1 AGGTGCGCGT 0.961184 -69 CTCCCGAAACCTGGGGGTGTGCCTGCTGTG 5 74 1 CTGGGGGTGT 0.959537 -198 ACTCCTCTCGAGGGGGTCGTGGTGGCGGAT 6 14 1 AGGGGGTCGT 0.961543 -202 ATGGTCGATGATGGCGGTGTGGATCCGCGG 8 47 1 ATGGCGGTGT 0.943806 -61 ACTCAGGGTCAGAGAGGCGTGACACC 8 92 1 AGAGAGGCGT 0.84887 -16 ********** Masking position 10 Map Score: 7.58212 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 330 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 TCCCCGCACTCCTCTTTTTATTAAGA 1 7 0 CCTCTTTTTA 0.768512 -62 TTCGGTTCAAACCCTTTTTACATAGAACCT 2 80 1 ACCCTTTTTA 0.846756 -74 TCCTGAATTCCCCCTGCGTATAATGTGTAA 2 133 0 CCCCTGCGTA 0.936666 -21 ATCGAGACCCTGTCGAAATCGCGTCT 4 7 1 ACCCTGTCGA 0.953734 -159 CCGGGGTTGACCCCTGATGATGGACACGTG 5 154 0 CCCCTGATGA 0.957732 -118 GCAACTCCTCTCGAGGGGGTCGTG 6 5 1 CTCCTCTCGA 0.860456 -211 AATGATCAGACCTCTTTCGATGCACAACGG 6 101 0 CCTCTTTCGA 0.887345 -115 GTATCAGCGGCCCCTCCTGAACGCTAGGAT 6 134 0 CCCCTCCTGA 0.97226 -82 CGCGCCGTCGACCCTCAGTATCAGCGGCCC 6 151 0 ACCCTCAGTA 0.758078 -65 ********** Masking position 5 Map Score: 2.80345 Number of sites scoring better than the average of aligned sites = 566 Number in coding regions = 407 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 8 CTTAATAAAAAGAGGAGTGCGGGGACAACCG 1 12 1 AGAGAGTGCG 0.42007 -57 AACGCTCACATGATGTGGGCGTTTTTTTTAT 2 15 1 TGAGTGGGCG 0.90813 -139 ATCGAGACCCTGTCGAAATCGCGTC 4 5 1 AGACCTGTCG 0.623023 -161 TAAATCAGTACGATGTGGGCCTTGCTGCATT 4 44 1 CGAGTGGGCC 0.890899 -122 GTGCGGCGCCGACTCGTGGCGGTGCTGCGCG 4 75 1 GACCGTGGCG 0.676427 -91 ACGCAGCCAACACCGCGGGCGTCCGCCACCT 4 122 1 CACGCGGGCG 0.913254 -44 CCTCCGAGAGTCTAGGTGGCGGACGCCCGCG 4 135 0 TCTGGTGGCG 0.497077 -31 CGACAGCCGGAAAAGAGGGCGCC 5 3 0 AAAGAGGGCG 0.867041 -269 TGCTCCCGAAACCTGGGGGTGTGCCTGCTGT 5 72 1 ACCGGGGGTG 0.715492 -200 TTCCCCTGAGACCCGCGGTCGAACCAGCCAC 5 126 1 ACCGCGGTCG 0.86172 -146 GGCGTGCCGTCGCCCTTGGCCGGGGTTGACC 5 172 0 CGCCTTGGCC 0.685535 -100 TAACGGTCGGCGAACTTGGCGTGCCGTCGCC 5 189 0 CGACTTGGCG 0.937649 -83 TGCGAGCAAAACAGCTGGTCGGCCGTTAGGA 5 245 1 ACACTGGTCG 0.732471 -27 CAACTCCTCTCGAGGGGGTCGTGGTGGCGGA 6 12 1 CGAGGGGTCG 0.965993 -204 GCTCGGCGACCACCGGTGGCGAGTGGATCCG 6 39 0 CACGGTGGCG 0.970968 -177 CGAGCCACCGACCCGGGGTCGGTATTCGAGC 6 65 1 ACCGGGGTCG 0.93354 -151 TTTCGATGCACAACGGTGACGGCTCGAATAC 6 86 0 CAAGGTGACG 0.617722 -130 GCGCGACATACCCGCTTGGCGTAGCCT 8 7 0 CCCCTTGGCG 0.942856 -101 CCGCCATGGTCGATGATGGCGGTGTGGATCC 8 42 1 CGAGATGGCG 0.949567 -66 *** ******* Masking position 8 Map Score: 16.1285 Number of sites scoring better than the average of aligned sites = 3109 Number in coding regions = 2901 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 9 ********** No masking Map Score: 1.66429e-14 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: 1.66429e-14 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 11 ********** No masking Map Score: 1.66429e-14 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