AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i334_bsub_mtub_300.orf -o334_bsub_mtub_300.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 ywlC 156 alternate gene name: ipc-29d; similar to hypothetical proteins #2 ywlB 66 alternate gene name: ipc-28d #3 spoIIR 140 alternate gene name: ipc-27d, csfX #4 prfA 125 peptide chain release factor 1 #5 argS 300 argS #6 thrB 217 thrB #7 rho 256 rho #8 rpmE 150 rpmE #9 prfA 89 prfA Motif number 1 TCGGCGCCACCCGCGAGGGCGGCCGCATAGTTGGC 5 49 0 CCGCGAGGCG 0.880122 -252 CCCTGAGCTACGGGGGCGCACGACGACACGTTGCG 5 181 1 CGGGGGCCCG 0.920626 -120 TGCGCTACTCTGGCGGGGCCCCATGGCGCAACGTG 5 207 0 TGGCGGCCTG 0.980328 -94 CAGTGGGTAGCCGCGATGCGCTACTCTGGCGGGGC 5 223 0 CCGCGACCCT 0.853986 -78 TGGCGATCGCAAGCGCGGCGGAGCC 6 1 1 TGGCGAGACG 0.96707 -217 ATCGCAAGCGCGGCGGAGCCGGGTGCGGCGGGTCG 6 16 1 CGGCGGCGTG 0.998471 -202 GAGCCGGGTGCGGCGGGTCGGCACGGTTTGGATTG 6 31 1 CGGCGGCGCG 0.999043 -187 TTGGATTGGGTGGCGATCGCAAGCGCGGCGGAGCC 6 58 1 TGGCGAGACG 0.96707 -160 ATCGCAAGCGCGGCGGAGCCGGGTGCGGCGGGTCG 6 73 1 CGGCGGCGTG 0.998471 -145 GAGCCGGGTGCGGCGGGTCGGCACGGTTTGGATTG 6 88 1 CGGCGGCGCG 0.999043 -130 TTGGATTGGGTGGCGATCGCAAGCGCGGCGGAGCC 6 115 1 TGGCGAGACG 0.96707 -103 ATCGCAAGCGCGGCGGAGCCGGGTGCGGCGGGTCG 6 130 1 CGGCGGCGTG 0.998471 -88 GAGCCGGGTGCGGCGGGTCGGCACGGTTTGGATTG 6 145 1 CGGCGGCGCG 0.999043 -73 TTGGATTGGGTGGCGATCGCAAGCGCGGCGGAGCC 6 172 1 TGGCGAGACG 0.96707 -46 ATCGCAAGCGCGGCGGAGCCGGGTGCGGCGGGTCG 6 187 1 CGGCGGCGTG 0.998471 -31 GAGCCGGGTGCGGCGGGTCGGCACGC 6 202 1 CGGCGGCGCG 0.999043 -16 GCTGTCCTAGCGGCAAGGCAGTACGTATGCAGATG 7 85 0 CGGCAACGCG 0.993009 -172 GCGGCGAATACGGCGAACCTCGTCCACAAGAAGAA 7 126 0 CGGCGACCCC 0.988252 -131 TCCGGCGAGACGGCTCGCCGGGAATGT 8 3 1 CGGCGACGCG 0.998829 -148 ACCAGGTTCTCGGCACGCCACGACGGGCGGCCACC 8 110 1 CGGCACCCCG 0.906487 -41 AACTGTGCACCAGCGGTACAGGACGGGCGTCGGTT 9 29 1 CAGCGGCGCG 0.99372 -61 AACCTTCTTCCCGCGAGCGCGGACCCTAACGCGAA 9 62 0 CCGCGAGGCC 0.939384 -28 ****** * * ** Masking position 3 Map Score: 77.9898 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 359 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 2 AAACAAAGCACGGAGAGGAACGGTGGGGACCG 3 119 1 CGGAGGACGG 0.950373 -22 ACAATGTGATCGGCGCCACCCGCGAGGGCGGCC 5 60 0 CGGCCACCGC 0.9943 -241 GCCGCAGGTTCGAATCCTGCCGGGGGCACAAGG 5 120 0 CGACCTCCGG 0.946744 -181 CCTTCTGCTCCGGAGGCAGACGCTCTATCCCCT 5 152 1 CGGGCAACGC 0.989114 -149 CCCTGAGCTACGGGGGCGCACGACGACACGTTG 5 181 1 CGGGCGACGA 0.946298 -120 GGGCGCACGACGACACGTTGCGCCATGGGGCCC 5 194 1 CGACGTGCGC 0.974335 -107 TGGCGATCGCAAGCGCGGCGGAGCCG 6 4 1 CGAGCAGCGC 0.978215 -214 GCAAGCGCGGCGGAGCCGGGTGCGGCGGGTCGG 6 19 1 CGGCCGGTGC 0.995111 -199 CCGGGTGCGGCGGGTCGGCACGGTTTGGATTGG 6 34 1 CGGCGGACGG 0.974353 -184 GATTGGGTGGCGATCGCAAGCGCGGCGGAGCCG 6 61 1 CGAGCAGCGC 0.978215 -157 GCAAGCGCGGCGGAGCCGGGTGCGGCGGGTCGG 6 76 1 CGGCCGGTGC 0.995111 -142 CCGGGTGCGGCGGGTCGGCACGGTTTGGATTGG 6 91 1 CGGCGGACGG 0.974353 -127 GATTGGGTGGCGATCGCAAGCGCGGCGGAGCCG 6 118 1 CGAGCAGCGC 0.978215 -100 GCAAGCGCGGCGGAGCCGGGTGCGGCGGGTCGG 6 133 1 CGGCCGGTGC 0.995111 -85 CCGGGTGCGGCGGGTCGGCACGGTTTGGATTGG 6 148 1 CGGCGGACGG 0.974353 -70 GATTGGGTGGCGATCGCAAGCGCGGCGGAGCCG 6 175 1 CGAGCAGCGC 0.978215 -43 GCAAGCGCGGCGGAGCCGGGTGCGGCGGGTCGG 6 190 1 CGGCCGGTGC 0.995111 -28 CCGGGTGCGGCGGGTCGGCACGC 6 205 1 CGGCGGACGC 0.997409 -13 AGCAAACCCCCGCAACCTTGCGGA 7 2 0 CGCCCTGCGG 0.919922 -255 GGGCTATCCTCGGAGCCGTCCAGCAATCGCAGC 7 53 1 CGGCCGCCAG 0.920944 -204 TCCGGCGAGACGGCTCGCCGGGAATGTC 8 6 1 CGACGGTCGC 0.941401 -145 GACGGCTCGCCGGGAATGTCCGCACGCATCTCG 8 19 1 CGGATGCCGC 0.747449 -132 TGTGCACCAGCGGTACAGGACGGGCGTCGGTTC 9 32 1 CGGCAGACGG 0.959783 -58 CCCGCGAGCGCGGACCCTAACGCGAACCGACGC 9 55 0 CGGCCTACGC 0.993876 -35 *** *** **** Masking position 2 Map Score: 62.974 Number of sites scoring better than the average of aligned sites = 644 Number in coding regions = 617 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 3 AATTTGAGAGCGAGACCACGAAGCCAACTA 5 27 1 CGAGACCACG 0.727735 -274 ACTATGCGGCCGCCCTCGCGGGTGGCGCCG 5 53 1 CGCCCTCGCG 0.735184 -248 AGGTTCGAATCCTGCCGGGGGCACAAGGGT 5 118 0 CCTGCCGGGG 0.778059 -183 CGGCAGGATTCGAACCTGCGGCCTTCTGCT 5 131 1 CGAACCTGCG 0.789098 -170 CGACACGTTGCGCCATGGGGCCCCGCCAGA 5 204 1 CGCCATGGGG 0.549629 -97 ATCGCGGCTACCCACTGACCACCGCAACGG 5 241 1 CCCACTGACC 0.757862 -60 GGATTCGAAGCCCAACCACCTCAGCCCATA 5 269 1 CCCAACCACC 0.611098 -32 CCGGCTCCGCCGCGCTTGCGATCGCCA 6 8 0 CGCGCTTGCG 0.797145 -210 GCCGACCCGCCGCACCCGGCTCCGCCGCGC 6 23 0 CGCACCCGGC 0.984384 -195 CAATCCAAACCGTGCCGACCCGCCGCACCC 6 36 0 CGTGCCGACC 0.957885 -182 CCGGCTCCGCCGCGCTTGCGATCGCCACCC 6 65 0 CGCGCTTGCG 0.797145 -153 GCCGACCCGCCGCACCCGGCTCCGCCGCGC 6 80 0 CGCACCCGGC 0.984384 -138 CAATCCAAACCGTGCCGACCCGCCGCACCC 6 93 0 CGTGCCGACC 0.957885 -125 CCGGCTCCGCCGCGCTTGCGATCGCCACCC 6 122 0 CGCGCTTGCG 0.797145 -96 GCCGACCCGCCGCACCCGGCTCCGCCGCGC 6 137 0 CGCACCCGGC 0.984384 -81 CAATCCAAACCGTGCCGACCCGCCGCACCC 6 150 0 CGTGCCGACC 0.957885 -68 CCGGCTCCGCCGCGCTTGCGATCGCCACCC 6 179 0 CGCGCTTGCG 0.797145 -39 GCCGACCCGCCGCACCCGGCTCCGCCGCGC 6 194 0 CGCACCCGGC 0.984384 -24 GCGTGCCGACCCGCCGCACCC 6 207 0 CGTGCCGACC 0.957885 -11 CAACGGTGATCGCCATCAGCGGCGAATACG 7 149 0 CGCCATCAGC 0.68702 -108 CGATGATTGGCGCACTCGGCGATTTGGCTG 7 185 1 CGCACTCGGC 0.968384 -72 CCCCGTATGACGTGATCAGCGGGGGAAGGA 7 227 1 CGTGATCAGC 0.605885 -30 GTTCTCGGCACGCCACGACGGGCGGCCACC 8 115 1 CGCCACGACG 0.805866 -36 GACCCTAACGCGAACCGACGCCCGTCCTGT 9 46 0 CGAACCGACG 0.837721 -44 CGTTAGGGTCCGCGCTCGCGGGAAGAAGGT 9 66 1 CGCGCTCGCG 0.72288 -24 ********** Masking position 1 Map Score: 52.5327 Number of sites scoring better than the average of aligned sites = 1788 Number in coding regions = 1678 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 4 TGGGATAAACGTGCAGGGTGAAAAAAATCTA 3 61 0 GGCAGGGTGA 0.975201 -80 AATTCCAGTATAGCAGAGGGAGCTTTTCCAG 4 23 1 TGCAGAGGGA 0.876463 -103 GGTTCGAATCCTGCCGGGGGCACAAGGGTTG 5 116 0 CGCCGGGGGC 0.993678 -185 TCTGCCTCCGGAGCAGAAGGCCGCAGGTTCG 5 141 0 GGCAGAAGGC 0.950765 -160 AAGCGCGGCGGAGCCGGGTGCGGCGGGTCGG 6 21 1 GGCCGGGTGC 0.998046 -197 AAGCGCGGCGGAGCCGGGTGCGGCGGGTCGG 6 78 1 GGCCGGGTGC 0.998046 -140 AAGCGCGGCGGAGCCGGGTGCGGCGGGTCGG 6 135 1 GGCCGGGTGC 0.998046 -83 AAGCGCGGCGGAGCCGGGTGCGGCGGGTCGG 6 192 1 GGCCGGGTGC 0.998046 -26 GCCCGCTTCCTGGCCGGAAGCAAGCAAACCC 7 26 0 TGCCGGAAGC 0.942596 -231 GTCAGCCAAATCGCCGAGTGCGCCAATCATC 7 186 0 TGCCGAGTGC 0.993049 -71 CCGTCGTGGCGTGCCGAGAACCTGGTCCGGT 8 105 0 GGCCGAGAAC 0.912626 -46 CGGCCACCGATCACAGAGGGCAGC 8 137 1 TACAGAGGGC 0.78557 -14 * ********* Masking position 4 Map Score: 28.4975 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 303 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 TGGACAAGGAGAGCCTGGGATAAACGTGCAG 3 76 0 GAGCTGGGAT 0.984792 -65 CGCCCCCGTAGCTCAGGGGATAGAGCGTCTG 5 168 0 GCTCGGGGAT 0.984334 -133 AACCACCTCAGCCCATAGGATGGACGTTC 5 282 1 GCCCTAGGAT 0.9369 -19 CGGCTCCGCCGCGCTTGCGATCGCCA 6 6 0 GCGCTGCGAT 0.997551 -212 CGGCTCCGCCGCGCTTGCGATCGCCACCCAA 6 63 0 GCGCTGCGAT 0.997551 -155 CGGCTCCGCCGCGCTTGCGATCGCCACCCAA 6 120 0 GCGCTGCGAT 0.997551 -98 CGGCTCCGCCGCGCTTGCGATCGCCACCCAA 6 177 0 GCGCTGCGAT 0.997551 -41 TTGCTGGACGGCTCCGAGGATAGCCCGCTTC 7 48 0 GCTCGAGGAT 0.925222 -209 TACGTATGCAGATGCTGCGATTGCTGGACGG 7 68 0 GATGTGCGAT 0.820005 -189 **** ****** Masking position 10 Map Score: 18.9583 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 152 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 ATCCACAAATTGTGGACAACGCTAATAAAGAAG 1 37 0 TTGGACACGT 0.963226 -120 GTCCACAATTTGTGGATAACGCTTGTTTTATTA 1 53 1 TTGGATACGT 0.953151 -104 GTTTTATTGTTGTGAATAAGGAGTTTGGTCAGA 1 133 1 TTGAATAGGG 0.927878 -24 CTAGCCCTATTATGGACAAGGAGAGCCTGGGAT 3 86 0 TTGGACAGGG 0.994116 -55 ATTGAAATGCTTTTGACTGGGGTTAATCACTAT 4 59 1 TTTGACGGGT 0.915638 -67 GTCGGCACGGTTTGGATTGGGTGGCGATCGCAA 6 47 1 TTGGATGGGG 0.994116 -171 GTCGGCACGGTTTGGATTGGGTGGCGATCGCAA 6 104 1 TTGGATGGGG 0.994116 -114 GTCGGCACGGTTTGGATTGGGTGGCGATCGCAA 6 161 1 TTGGATGGGG 0.994116 -57 CAATTCTTCTTGTGGACGAGGTTCGCCGTATTC 7 123 1 TTGGACAGGT 0.988505 -134 * ***** *** * Masking position 6 Map Score: 15.1589 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 65 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 AGCCAACTATGCGGCCGCCCTCGCGGGTGG 5 48 1 GCGGCCGCCC 0.98957 -253 CAACAATGTGATCGGCGCCACCCGCGAGGG 5 65 0 ATCGGCGCCA 0.396264 -236 CAGGATTCGAACCTGCGGCCTTCTGCTCCG 5 134 1 ACCTGCGGCC 0.959939 -167 GGCCTTCTGCTCCGGAGGCAGACGCTCTAT 5 150 1 TCCGGAGGCA 0.314961 -151 CAACGTGTCGTCGTGCGCCCCCGTAGCTCA 5 184 0 TCGTGCGCCC 0.94548 -117 AAGCCCAACCACCTCAGCCCATAGGATGGA 5 276 1 ACCTCAGCCC 0.885441 -25 CGCACCCGGCTCCGCCGCGCTTGCGATCGC 6 13 0 TCCGCCGCGC 0.991579 -205 ACCGTGCCGACCCGCCGCACCCGGCTCCGC 6 28 0 CCCGCCGCAC 0.99001 -190 CGCACCCGGCTCCGCCGCGCTTGCGATCGC 6 70 0 TCCGCCGCGC 0.991579 -148 ACCGTGCCGACCCGCCGCACCCGGCTCCGC 6 85 0 CCCGCCGCAC 0.99001 -133 CGCACCCGGCTCCGCCGCGCTTGCGATCGC 6 127 0 TCCGCCGCGC 0.991579 -91 ACCGTGCCGACCCGCCGCACCCGGCTCCGC 6 142 0 CCCGCCGCAC 0.99001 -76 CGCACCCGGCTCCGCCGCGCTTGCGATCGC 6 184 0 TCCGCCGCGC 0.991579 -34 GCGTGCCGACCCGCCGCACCCGGCTCCGC 6 199 0 CCCGCCGCAC 0.99001 -19 GGGTTTGCTTGCTTCCGGCCAGGAAGCGGG 7 26 1 GCTTCCGGCC 0.635718 -231 GCATCTGCATACGTACTGCCTTGCCGCTAG 7 84 1 ACGTACTGCC 0.107285 -173 ACACCGAGATGCGTGCGGACATTCCCGGCG 8 26 0 GCGTGCGGAC 0.644553 -125 GCACGCCACGACGGGCGGCCACCGATCACA 8 122 1 ACGGGCGGCC 0.96984 -29 CTGGCTTACCGACGCCCGAACTGTGCA 9 8 1 ACCGACGCCC 0.985087 -82 CCTAACGCGAACCGACGCCCGTCCTGTACC 9 43 0 ACCGACGCCC 0.985087 -47 ********** Masking position 7 Map Score: 41.9299 Number of sites scoring better than the average of aligned sites = 1384 Number in coding regions = 1286 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 8 GGGGCACAAGGGTTGATCTAGCCTCACGCATG 5 99 0 GGTGATCTGC 0.941264 -202 GGCACGGTTTGGATTGGGTGGCGATCGCAAGC 6 50 1 GGTTGGGTGC 0.99053 -168 GGCACGGTTTGGATTGGGTGGCGATCGCAAGC 6 107 1 GGTTGGGTGC 0.99053 -111 GGCACGGTTTGGATTGGGTGGCGATCGCAAGC 6 164 1 GGTTGGGTGC 0.99053 -54 AAGGTTGCGGGGGTTTGCTTGCTTCCGGCCAG 7 16 1 GGTTTGCTGC 0.990766 -241 AAGAATTGGTGGCTGTCCTAGCGGCAAGGCAG 7 99 0 GGTGTCCTGC 0.985373 -158 ACGTCATACGGGGTTTTGTTGCAGTCAGCCAA 7 208 0 GGTTTTGTGC 0.966963 -49 GGATTTCCTTTCCTTCCCCCGC 7 245 0 GGTTTCCTTC 0.888988 -12 GGGTGATAGCGGTTGACCTGGCATAATCGATG 8 59 1 GGTGACCTGC 0.973036 -92 ** ****** ** Masking position 4 Map Score: 15.084 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 76 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 ACGCAAAAACGGGGTGAACGG 2 56 1 GGGGTGAAGG 0.858327 -11 ACAAAGCACGGAGAGGAACGGTGGGGACCG 3 121 1 GAGAGGAAGG 0.210153 -20 CAGGAAAACAGAGGTGAAGACC 4 114 1 GAGGTGAAAC 0.738437 -12 TTCTGCTCCGGAGGCAGACGCTCTATCCCCT 5 154 1 GAGGCAGAGC 0.724773 -147 CGAATCCGTTGCGGTGGTCAGTGGGTAGCCG 5 245 0 GCGGTGGTAG 0.870326 -56 CCTATGGGCTGAGGTGGTTGGGCTTCGAATC 5 270 0 GAGGTGGTGG 0.905636 -31 GATCGCAAGCGCGGCGGAGCCGGGTGCGGCG 6 15 1 GCGGCGGACC 0.988529 -203 TTTGGATTGGGTGGCGATCGCAAGCGCGGCG 6 57 1 GTGGCGATGC 0.965837 -161 GATCGCAAGCGCGGCGGAGCCGGGTGCGGCG 6 72 1 GCGGCGGACC 0.988529 -146 TTTGGATTGGGTGGCGATCGCAAGCGCGGCG 6 114 1 GTGGCGATGC 0.965837 -104 GATCGCAAGCGCGGCGGAGCCGGGTGCGGCG 6 129 1 GCGGCGGACC 0.988529 -89 TTTGGATTGGGTGGCGATCGCAAGCGCGGCG 6 171 1 GTGGCGATGC 0.965837 -47 GATCGCAAGCGCGGCGGAGCCGGGTGCGGCG 6 186 1 GCGGCGGACC 0.988529 -32 CCGCAAGGTTGCGGGGGTTTGCTTGCTTCCG 7 12 1 GCGGGGGTTG 0.686626 -245 GTATGCAGATGCTGCGATTGCTGGACGGCTC 7 65 0 GCTGCGATGC 0.863162 -192 ATCGCCATCAGCGGCGAATACGGCGAACCTC 7 140 0 GCGGCGAAAC 0.966323 -117 CGACTTTGCAACGGTGATCGCCATCAGCGGC 7 156 0 ACGGTGATGC 0.705378 -101 GACGTGATCAGCGGGGGAAGGAAAGGAAATC 7 235 1 GCGGGGGAGG 0.971278 -22 CTCGGTGTTTGGGGTGATAGCGGTTGACCTG 8 48 1 GGGGTGATGC 0.920984 -103 ******** ** Masking position 6 Map Score: 32.8933 Number of sites scoring better than the average of aligned sites = 1536 Number in coding regions = 1378 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 10 ********** No masking Map Score: 2.07722e-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 11 ********** No masking Map Score: 2.07722e-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 12 ********** No masking Map Score: 2.07722e-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