AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i087_bsub_mtub_300.orf -o087_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 ycnL 164 ycnL #2 mtlA 172 phosphotransferase system (PTS) mannitol-specific enzyme IIABC component #3 mtlD 52 mannitol-1-phosphate dehydrogenase #4 ykvY 300 similar to Xaa-Pro dipeptidase #5 ykvZ 281 similar to transcriptional regulator (LacI family) #6 glcT 62 transcriptional antiterminator (BglG family) #7 ptsG 238 phosphotransferase system (PTS) glucose-specific enzyme IIABC component #8 ptsH 97 histidine-containing phosphocarrier protein of the phosphotransferase system (PTS) (HPr protein) #9 mobA 136 molybdopterin-guanine dinucleotide biosynthesis protein A #10 moeB 50 molybdopterin biosynthesis protein #11 yknU 223 similar to ABC transporter (ATP-binding protein) #12 yknW 109 yknW #13 fruR 279 transcriptional regulator (DeoR family) #14 crh 23 catabolite repression HPr-like protein #15 yvcL 22 similar to hypothetical proteins #16 yvcJ 24 similar to hypothetical proteins #17 yvcI 300 similar to mutator MutT protein Motif number 1 TTATACCAGAGTCCCTTCTGTTTCGTTTTGTTG 1 109 0 GCCCTTTTTT 0.937802 -56 AACCAGGAGCCTTTTTATTTTTAAAAAATTG 2 9 1 GCTTTTATTT 0.510136 -164 TGTGCCAAAGTCCTCTTTACTTTCAATTGTATA 2 51 1 TCTCTTATTT 0.809517 -122 GAATGATGCTTCCCTTTGACTCTATGTTAAAAC 2 96 0 TCCTTTATCT 0.587953 -77 TCTCTGAACATATTTTTGTATCTTACAGCGACA 2 127 1 TTTTTTTTCT 0.786082 -46 GAAGATGGTGGGCTTTTATTATTACAGCTCTAT 4 36 0 GCTTTTTATT 0.623414 -265 GGGAATTTCCGCTCCTTTTATCGGGATGAAGAT 4 63 0 GTCCTTTTCG 0.562701 -238 GAGAACAAAGTCCTTTTTTATTTCTA 5 4 0 TCTTTTTTTT 0.920825 -278 CTCGACATCGTCCTTTTTTATCTGCATTAAATA 5 34 1 TCTTTTTTCT 0.879414 -248 AACATTTGATGATTTTTTTATTTAATGCAGATA 5 52 0 GTTTTTTTTT 0.754986 -230 GATCACATGGGTTTCTTCATTTTAATTGGGTTA 5 159 0 GTTCTTATTT 0.529629 -123 GTACCAGATATCTTTTTGTGTTTTTAGCTGAAA 5 198 0 TTTTTTTTTT 0.854231 -84 AGATTCCCTTCTTTCTAAATCCCCTT 5 266 0 TCCCTTTTCT 0.947315 -16 AAATTCAGTTTATCCTTATAACGTGTTACTGAT 7 19 1 TTCCTTTACG 0.398476 -220 GAGAATGAACTTCCCGTTTTTTTCCCTCAATCA 7 67 0 TCCCGTTTTT 0.78955 -172 ATTTTGCTCATGCCTTTTTGTTGTGTAAAAGGG 7 117 1 TCCTTTTTTG 0.783051 -122 AGAATTGACCTCCTCTTTTTACTAGTCTGACCT 7 215 0 TCTCTTTACT 0.809023 -24 TTTTATCATTCTCCTTTTAACTTAAAGCTTTA 8 76 0 TTCCTTTACT 0.710359 -22 TCAACGCTACTGCTTGTCTGTTTATTAAAGAGG 9 68 0 TCTTGTTTTT 0.603436 -69 CAAACCTGTTCTCCTTATCTTTTATGTCATCT 10 29 0 TTCCTTTTTT 0.935269 -22 CGAAATAAATTTCTATTATTTTTCAAAATTTCA 11 156 0 TCTATTTTTT 0.553105 -68 ATGCATGAGGTTTTTTTATGTTTAGTGATTTCT 13 22 1 TTTTTTTTTT 0.854231 -258 GAATATAAAAGACTTTTTTCATTAAAATAAGAA 13 60 1 GCTTTTTATT 0.623414 -220 TTGTACGACATTTTCTTCTTATTTTAATGAAAA 13 75 0 TTTCTTTATT 0.772936 -205 GTCGTACAATTGTCCTTATTTTTGTCGAATTTA 13 99 1 TTCCTTTTTT 0.935269 -181 AAGATCTCCCCTTTTCTTTACGG 14 5 0 TCCCTTTTTT 0.966301 -19 CAGTTATCCGTGTCCTTTTTTTGTCCATAAATA 17 134 1 TTCCTTTTTG 0.796026 -167 GTAACTGGAATTCTCTTTTATTTATGGACAAAA 17 152 0 TCTCTTTTTT 0.961474 -149 ATTGACAATCTTTTCTTCTATTTTACAGCATAT 17 212 0 TTTCTTTTTT 0.926335 -89 * ***** * *** Masking position 7 Map Score: 25.4887 Number of sites scoring better than the average of aligned sites = 2956 Number in coding regions = 2328 Number in noncoding regions = 628 Number of orfs with sites within 600 bp upstream = 579 Fraction of orfs with sites within 600 bp upstream = 0.0929971 Motif number 2 GCAGGAAATAAAATGCATTAGAAAATGAAGGC 4 198 1 AAATGCATTA 0.819941 -103 ATTAAATAAAAAAATCATCAAATGTTCGAAAG 5 59 1 AAAATCATCA 0.923376 -223 CCTCTCAACCAAAAACATGAAATTAAACCCTT 5 88 0 AAAAACATGA 0.916261 -194 ATATTGTATGAAACGCATTCCAGATCAAGGGG 5 240 1 AAACGCATTA 0.870954 -42 CTTACAGCTAAAAATCATGACAACGAATTCAC 7 185 0 AAAATCATGA 0.946101 -54 TAGTTTCGTTAAAAGCATAGCAAAAGCAAAGG 9 102 0 AAAAGCATAA 0.875707 -35 ACGCTTACAGAAAATCATTGTATGCTGAGGAT 11 70 0 AAAATCATTA 0.961019 -154 TATGAAAAGCCTTCAATATTGAAGGT 12 5 1 AAAAGCCTTA 0.925489 -105 ATAAATTTCCAAAAACCTTCAATATTGAAGGC 12 19 0 AAAAACCTTA 0.82921 -91 AATTTATTAGAAAAACATGAAACTTTTTGATA 12 44 1 AAAAACATGA 0.916261 -66 TTAGGCAACTAAAATCATTCAAATTCATTCAA 13 193 0 AAAATCATTA 0.961019 -87 ATCATAACCGAAAAGCATTACACATGTGTTAC 17 45 0 AAAAGCATTA 0.975195 -256 CAGTTACAGCAAAATCATCTGAATTAAGGAAT 17 178 1 AAAATCATCA 0.923376 -123 ********* * Masking position 3 Map Score: 13.485 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 311 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 3 TCATACACCCTCTTCATTAAGATCTA 1 5 1 ACACCCCTCA 0.93132 -160 TCCGTCTCTAAAATCCTCTACGCTTAAATAGA 1 33 0 AAATCCCTCG 0.896275 -132 AATGGCGATCAAATCTTCTTCGCTTTAGCGGA 3 13 0 AAATCTCTCG 0.712955 -40 AAGGAAACCCGCTGCACAGCCTATGA 4 5 1 AAACCCCTCA 0.988502 -296 CAAACGGAACAACCCCCCTGCGATTGAACGTT 4 143 1 AACCCCCTCG 0.87254 -158 AACACCGGTAAAACCTGTTACAATGGAAGACA 4 243 1 AAACCTTTCA 0.90079 -58 ACATGAAATTAAACCCTTTCGAACATTTGATG 5 74 0 AAACCCTTGA 0.952419 -208 TAAAATGAAGAAACCCATGTGATCTTCTCCTT 5 168 1 AAACCCTGGA 0.75945 -114 ATATTGTATGAAACGCATTCCAGATCAAGGGG 5 240 1 AAACGCTTCA 0.755118 -42 CCTTCTTTCTAAATCCCCTTGATCTGGAATGC 5 254 0 AAATCCCTGA 0.915589 -28 TTCAAAACCTCCTTGAGAATATCTAA 12 94 0 AAACCTCTGA 0.939978 -16 AAACATAAAAAAACCTCATGCATGTTGCATGA 13 13 0 AAACCTATCA 0.829536 -267 TACAGTTTACAAACCCTATAGACATACGTTAA 13 130 1 AAACCCATGA 0.914736 -150 ****** ** ** Masking position 1 Map Score: 9.07525 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 351 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 4 TTAAATAGATCTTAATGAAGAGGGTGTATGA 1 7 0 CAAGAGAGGT 0.979049 -158 TAAGATCTATTTAAGCGTAGAGGATTTTAGAGACG 1 28 1 TAGGAGAGAT 0.97377 -137 TCTCCGCTAAAGCGAAGAAGATTTGATCGCCA 3 8 1 TAGGAGAGAT 0.97377 -45 CTCCTTTTATCGGGATGAAGATGGTGGGCTTTTAT 4 50 0 CGAGAGAGGT 0.958058 -251 GTGTTTTTAGCTGAAAGGAGAAGATCACATGGGTT 5 179 0 CAAGAGAGAT 0.982655 -103 GTGTTAACATCATGAGGGAGATGGTTCGA 9 5 0 CGAGAGAGGT 0.958058 -132 TTAACGAAACTAGAGGTGAGATGAT 9 122 1 TAGTAGAGAT 0.879668 -15 CGGGTATCGATATAGTGAAGATGATAAATGTTGGA 11 187 1 TAGGAGAGAT 0.97377 -37 ATATTCATTCCTTAATTCAGATGATTTTGCTGTAA 17 181 0 CAATAGAGAT 0.917736 -120 * ** * *** *** Masking position 9 Map Score: 7.49008 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 104 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 5 GGAAATAAAATGCATTAGAAAATGAAGGCGTCGT 4 201 1 TCATTAAAAG 0.970925 -100 TGTTCTGTCTTCCATTGTAACAGGTTTTACCGGT 4 246 0 TCATTGAAAG 0.977266 -55 GACAGAACAATGCATTGCAAATGGCAGGGAGGAA 4 271 1 TCATTGAATG 0.931437 -30 CATGGGTTTCTTCATTTTAATTGGGTTATGTCTC 5 153 0 TCATTTAATG 0.722414 -129 ATGCGTTTCATACAATATGATATGGACGTACCAG 5 224 0 TCAATAGAAG 0.769878 -58 TGAATGCATTGAAAAAAGGTTTGACGTG 6 5 1 TCATTGAAAG 0.977268 -58 AAAGACTTTTTTCATTAAAATAAGAAGAAAATGT 13 67 1 TCATTAAAAG 0.970903 -213 TGAATACGTTTTCATTAGGAGGTGAAGC 13 262 1 TCATTAGAGG 0.863296 -18 AAAAAGTGTATTCATTATAAAAAGGGGGTCAATT 17 86 0 TCATTAAAAG 0.970922 -215 TCAATGTCTCTTCATTGTGGGAGGCATCTTGAAG 17 240 1 TCATTGGGAG 0.864568 -61 * ***** ** * * Masking position 6 Map Score: 7.54767 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 94 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 TCGTTTTGTTGCTGTTCAACACATTTTCACA 1 89 0 GCTGTTCACA 0.897867 -76 TTTGTTTGTCGCTGTAAGATACAAAAATATG 2 135 0 GCTGTAAATA 0.94495 -38 AAGGAAACCCGCTGCACAGCCTATGATAGAG 4 11 1 GCTGCACGCC 0.924514 -290 CAGCTGTCTTGCTGTAAAACCTCTCAACCAA 5 108 0 GCTGTAAACC 0.977279 -174 ATGATTTTTAGCTGTAAGGTCAGACTAGTAA 7 199 1 GCTGTAAGTC 0.966042 -40 AAGAGGAATAGCTGTTCAGTATTTGCATATT 9 43 0 GCTGTTCGTA 0.852088 -94 AAACCGGACGGCTGAAATGCCGTCCGGTTT 11 10 0 GCTGAAAGCC 0.909242 -214 TTTTAATTCCGCTGTAACACATGTGTAATGC 17 32 1 GCTGTAAACA 0.970996 -269 GAATGAATATGCTGTAAAATAGAAGAAAAGA 17 206 1 GCTGTAAATA 0.94495 -95 ******* *** Masking position 3 Map Score: 6.09923 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 237 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 AGCGACAAACAAAACAGGGAGGGTTTATAT 2 153 1 AACAGGGAGG 0.981941 -20 TTTGATCGCCATTTCAACGAGGTGAACTGAC 3 32 1 ATCAACGAGG 0.920848 -21 GTAACGTTCAATCGCAGGGGGGTTGTTCCGTT 4 145 0 ATCAGGGGGG 0.993418 -156 TGCATTGCAAATGGCAGGGAGGAACAAGAA 4 281 1 ATCAGGGAGG 0.992063 -20 TTGTTAGATATTCTCAAGGAGGTTTTGAA 12 91 1 TTCAAGGAGG 0.926273 -19 AAAGACAAGTCAGGGGGGAGAAAG 16 7 1 AACAGGGGGG 0.984999 -18 TGTATTCATTATAAAAAGGGGGTCAATTACTT 17 82 0 ATAAAGGGGG 0.904571 -219 ** ******** Masking position 6 Map Score: 5.79089 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 30 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 TCCACTTACTTGTCTCCGTCTCTAAAATCCTCTA 1 45 0 TGTCTCGTTA 0.853113 -120 ATAAAAAATGTGAAAATGTGTTGAACAGCAACAA 1 81 1 TGAAATGTTA 0.873584 -84 CACATGACTGTGACAATTTTTTAAAAATAAAAAG 2 21 0 TGACATTTTA 0.742065 -152 GTATAGGGACTGTAAGCGTTTTAACATAGAGTCA 2 79 1 TGTAACGTTA 0.946059 -94 AAAGGGCAAATGTAAACGGTTAAACTGGAAGACT 7 144 1 TGTAACGGTA 0.631229 -95 CTAAAAATCATGACAACGAATTCACAGGCGTAAG 7 176 0 TGACACGATA 0.677156 -63 CGCTACTGCTTGTCTGTTTATTAAAGAGGAATAG 9 63 0 TGTCTTTTTA 0.415541 -74 TTATCTTTTATGTCATCTTATCATGTTATTGCCC 10 13 0 TGTCACTTTT 0.820669 -38 AATGATTTTCTGTAAGCGTTTATTCTACATATGT 11 83 1 TGTAACGTTT 0.916539 -141 TAGAAAAACATGAAACTTTTTGATATCCTTCCCG 12 51 1 TGAAATTTTT 0.50556 -59 GCGTTTACAATGAAATTGTATTCAAAATGAATAC 13 235 1 TGAAATGTTA 0.868956 -45 CACCTCCTAATGAAAACGTATTCATTTTGAATAC 13 252 0 TGAAACGTTA 0.551206 -28 AAGAAAAGATTGTCAATGTCTCTTCATTGTGGGA 17 228 1 TGTCATGTTT 0.892887 -73 ACCTTCGTCCTGTCATCGTCTCTTTATTATACCG 17 274 0 TGTCACGTTT 0.946389 -27 ***** *** * * Masking position 11 Map Score: 5.97548 Number of sites scoring better than the average of aligned sites = 609 Number in coding regions = 518 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 9 GTCAGTTCACCTCGTTGAAATGGCG 3 38 0 TTCACCTCGT 0.855361 -15 TTTTGGGAATTTCCGCTCCTTTTATCGGGA 4 70 0 TTCCGCTCCT 0.95673 -231 GCATTTTATTTCCTGCTCCTCTTCCTGTAT 4 184 0 TCCTGCTCCT 0.874797 -117 TCTCGTTCTTTTGCGCACCCAATTTTGCTC 7 96 1 TTGCGCACCC 0.70786 -143 AAGAATTGACCTCCTCTTTTTACTA 7 224 0 TTGACCTCCT 0.954493 -15 ATCCAGCACCTTTCCAACATT 11 213 0 TCCAGCACCT 0.874797 -11 GCTTCACCTCCTAATGAAAACG 13 268 0 TTCACCTCCT 0.976019 -12 CTTTCTCCCCCCTGACTTGTCT 16 13 0 TTCTCCCCCC 0.853455 -12 AATAAAGTAATTGACCCCCTTTTTATAATG 17 78 1 TTGACCCCCT 0.933837 -223 ********** Masking position 1 Map Score: 2.54042 Number of sites scoring better than the average of aligned sites = 530 Number in coding regions = 374 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 10 TGTATGAAACGCATTCCAGATCAAGGGGATT 5 244 1 GATTCCAGAT 0.904334 -38 ACAGGCGTAAGTCTTCCAGTTTAACCGTTTA 7 156 0 GCTTCCAGTT 0.985927 -83 CGGCTGAAATGCCGTCCGGTTT 11 2 0 GCGTCCGGTT 0.987902 -222 CGGCATTTCAGCCGTCCGGTTTTTCTGTATT 11 19 1 GCGTCCGGTT 0.987902 -205 AAATAAAAGAGAATTCCAGTTACAGCAAAAT 17 162 1 GATTCCAGTT 0.968848 -139 * ********* Masking position 5 Map Score: 1.52884 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 41 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 11 TCTATGTTAAAACGCTTACAGTCCCTATAC 2 79 0 AACGCTTACA 0.971093 -94 TTCCAGTTTAACCGTTTACATTTGCCCTTT 7 144 0 ACCGTTTACA 0.979648 -95 ATGTAGAATAAACGCTTACAGAAAATCATT 11 83 0 AACGCTTACA 0.971093 -141 TGTCGAATTTACAGTTTACAAACCCTATAG 13 121 1 ACAGTTTACA 0.90219 -159 AACCGAAAATAGCGTTTACAATGAAATTGT 13 224 1 AGCGTTTACA 0.963176 -56 ********** Masking position 6 Map Score: 2.20609 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 45 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 12 ********** No masking Map Score: 3.31356e-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 13 ********** No masking Map Score: 3.31356e-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 14 ********** No masking Map Score: 3.31356e-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