AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -ifruR_mpneu_opreg_300.orf -g0.400 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 fruA 300 fructose-permease IIBC component; similar to Swiss-Prot Accession Number P20966, from E. coli #2 1673758 182 putative lipoprotein, MG040 homolog, from M. genitalium #3 mtlA 300 PTS system mannitol-specific component IIA (EIIA-MTL); similar to Swiss-Prot Accession Number P28008, from S. carnosus #4 yfiB 86 hypothetical protein (yfiB) homolog; similar to Swiss-Prot Accession Number P27712, from S. citri #5 tim 52 triosephosphate isomerase; similar to Swiss-Prot Accession Number P00943, from E. coli #6 1674088 300 putative lipoprotein, MG307 homolog, from M. genitalium #7 dnaK 55 heat shock protein DnaK; similar to GenBank Accession Number A49230, from E. rhusiopathiae #8 cbiO 157 abc transport ATP-binding protein; similar to Swiss-Prot Accession Number Q05596, from S. typhimurium #9 gap 30 glycerladehyde-3-phosphate dehydrogenase; similar to GenBank Accession Number S34254, from C. pasteurianum #10 1674235 206 MG211 homolog, from M. genitalium #11 1674237 48 H10_orf220L Protein #12 1674238 38 H10_orf206 Protein Motif number 1 TTTATAAAAATTTTTGCGTTTTCTTTTATT 1 4 0 TTTTTCTTTT 0.794796 -297 GTGGTCTGCTTTTTTATTGCGCTTTTTGTTAACAAGA 1 98 0 TTTTCTTTTT 0.909016 -203 TTAAATGTTTTTTAAAAAACCACTTTTTCAGCTCTGC 2 79 0 TTTACCTTTT 0.975778 -104 AATAAGTTACTATTACGCATATTTTTTAGAAAGGGTG 2 149 1 TATATTTTTT 0.736913 -34 AAGTTCACATTCAGTCTTTGGATTCATTG 3 3 1 GTTACTCTTT 0.794025 -298 TGACGATGCCGATTATTGGCATCTTTATTGCTTGGGG 3 50 1 GATACCTTTA 0.551763 -251 GCTTGGGGACTTTTAGCTTCTTTTTTTATTCCATCTG 3 79 1 TTTACTTTTT 0.975685 -222 CCACCACGTATTTCATAAATCTTTTTACCACCAAAAA 3 189 0 TTTATTTTTA 0.83456 -112 AATGCTTCGGTTTGACCAGCAGCTATTACAGCAATGG 3 246 0 TTTACCTATT 0.722098 -55 TACTGATTTTTGACCAACAATTTTTGTAAATGCTT 3 276 0 TTTACTTTTT 0.975685 -25 ATTCCAAGTCCTCCTTTTTCATCATTTT 4 69 0 TTCACCTTTT 0.793862 -18 AAACTTACAATTTCAAACGTTTTTTTTTTTTTTTTGA 6 98 0 TTTATTTTTT 0.939374 -203 TTTTCTTACTTATCAATACTTATTTTTAGGTAAAAAC 6 213 1 TATATTTTTT 0.736913 -88 ATTTTGGCACTTTAAAAGCTAGTTTTTACCTAAAAAT 6 234 0 TTTATTTTTT 0.939373 -67 CTCTCTAAAGGTTAAATTTTTGCTTTATTTTGGCACT 6 260 0 GTTATCTTTA 0.724471 -41 AAAAGAGCAGTTTAACTGCCCTCTTTTTATTGATCTA 8 23 0 TTTACCTTTT 0.975778 -135 TGTAATAATGGTTTATAGACGTCTTTAAGCACTTTTT 8 78 1 GTTACCTTTA 0.871948 -80 CTTTAAGCACTTTTTAAACCATTTTTTCAATTAGTCT 8 100 1 TTTTCTTTTT 0.909016 -58 TTTAAGTTTTTATTTTTAAATTTTAAA 8 141 0 TTTATTTTTT 0.939374 -17 AAATCATCGTTTTTAACTTCAATCTTTGGCA 10 5 0 TTTACTCTTT 0.881306 -202 GGCCGTTATTTTACATTTTTAAAATTAAGCT 12 18 0 GTTTCTTTTA 0.628083 -21 *** * * ***** Masking position 16 Map Score: 22.8019 Number of sites scoring better than the average of aligned sites = 504 Number in coding regions = 396 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 2 AAATTTTTATAAATTGTTTGCAACAGCAAA 1 28 1 AAATTGTTTG 0.979704 -273 TTCTCAATATAAATTGTAAGCAGACCATCA 1 135 0 AAATTGTAAG 0.952088 -166 GCATTTACAAAAATTGTTGGTCAAAAATCA 3 278 1 AAATTGTTGG 0.981179 -23 AGATTTACTTAAATAGTTAGATAAAAGCAG 6 44 1 AAATAGTTAG 0.928851 -257 TTTTTGAAAGAAATTGATTGCTTTAACTAA 6 75 0 AAATTGATTG 0.883844 -226 AAAAAAAAAAAAAACGTTTGAAATTGTAAG 6 102 1 AAAACGTTTG 0.809321 -199 AAAACGTTTGAAATTGTAAGTTTGTCATGC 6 112 1 AAATTGTAAG 0.952088 -189 TATTATAAACAAATCGTTAGCACTTTTAGC 7 20 0 AAATCGTTAG 0.972669 -36 AGGTAATTTTAAATTGTTGGTT 11 3 0 AAATTGTTGG 0.981179 -46 ********** Masking position 3 Map Score: 10.8574 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 32 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 3 CAATTTATAAAAATTTTTGCGTTTTCTTTTATT 1 10 0 AATTTTTGCT 0.686276 -291 AGCTCTGCAAAACTTTAAACGATAAAAGCATCGG 2 53 0 AATTTAAACA 0.624122 -130 TTTTTTAAAAAACATTTAACTCTTATTTAAATAC 2 97 1 AAATTTAACT 0.904045 -86 AAAATTACACCCTTTCTAAAAAAT 2 169 0 AAATTACACT 0.668927 -14 ATTGCTTGGGGACTTTTAGCTTCTTTTTTTATTC 3 76 1 GATTTTAGCT 0.866574 -225 AATAAATATTAAATTTAAGCCTGTTAGCAATTGG 4 34 1 AATTTAAGCT 0.96438 -53 ACAAACTTACAATTTCAAACGTTTTTTTTTTTTT 6 103 0 AATTCAAACT 0.711046 -198 ATTAAGCCAAGAGATTAAGCTAGTTGCACCAGTG 6 165 1 GAATTAAGCT 0.866575 -136 AAATAAAGCAAAAATTTAACCTTTAGAGAGCAAA 6 267 1 AAATTTAACT 0.906644 -34 AAATCGTTAGCACTTTTAGCGTTTGAGTG 7 6 0 CATTTTAGCT 0.779208 -50 ATTTGTTTATAATATTTAGCACATAAACAT 7 36 1 AAATTTAGCT 0.939784 -20 AGTAGTAAAATATAAACTAATTAGAGGATT 9 8 1 AATATAAACT 0.624118 -23 AGCTTTAAAAAAGTTTAAACGGGTTTCGCTAGAA 10 48 1 AATTTAAACT 0.944042 -159 TTACATTTTTAAAATTAAGCTCATCAAG 12 5 0 AAATTAAGCT 0.953612 -34 ** ******* * Masking position 2 Map Score: 7.64445 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 91 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 4 GGGTGTCCTCTTAACCACTTGAGTACGCTC 1 229 1 TTAACCACTT 0.62925 -72 TGTTTTTTAAAAAACCACTTTTTCAGCTCT 2 81 0 AAAACCACTT 0.918301 -102 ATTCCTGTTTTAATCCGCTTATCACCAATT 6 14 0 TAATCCGCTT 0.906219 -287 TTGCTTTAACTAACCTGCTTTTATCTAACT 6 58 0 TAACCTGCTT 0.933801 -243 ATAAGTAAGAAAAACTGCTTTAGTGCCCAC 6 196 0 AAAACTGCTT 0.943413 -105 TTAGAGAGCAAAAACCGCGTTA 6 289 1 AAAACCGCGT 0.895242 -12 AGAGGGCAGTTAAACTGCTCTTTTTTTATG 8 36 1 TAAACTGCTC 0.78863 -122 AAATGGTTTAAAAAGTGCTTAAAGACGTCT 8 94 0 AAAAGTGCTT 0.798865 -64 AAGCACTTTTTAAACCATTTTTTCAATTAG 8 104 1 TAAACCATTT 0.672971 -54 ATTTCTAGCGAAACCCGTTTAAACTTTTTT 10 54 0 AAACCCGTTT 0.808294 -153 TAAAATTACCTAACGCGCTTGCGCTTAAAA 11 22 1 TAACGCGCTT 0.900595 -27 ********** Masking position 3 Map Score: 5.07249 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 456 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 5 TCTTCTAAAAATTCCGTTTCTTTCTTGTTA 1 76 1 ATTCCGTTTC 0.934977 -225 ATAAATTTAGATTCCAGTTCCTGGGAGCGT 1 253 0 ATTCCAGTTC 0.982217 -48 CACATATTGGATTCCTATTCCACCATTAAA 3 141 0 ATTCCTATTC 0.960806 -160 ATTCCAAGTCCTCCTTTTTC 4 77 0 ATTCCAAGTC 0.942843 -10 AAGTAAATCTATTCCTGTTTTAATCCGCTT 6 24 0 ATTCCTGTTT 0.877514 -277 ATAAACCATTATTACAGGTCAAATAAGACA 8 64 0 ATTACAGGTC 0.828205 -94 ACGCAAGCGCATTCCTTTTCGAAGGTGGTA 10 109 0 ATTCCTTTTC 0.960806 -98 ********** Masking position 1 Map Score: 3.54604 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 41 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 AATAAAAGAAAACGCAAAAATTTTTATAAA 1 10 1 AAACGCAAAA 0.98171 -291 TGTTAACAAAAAGCGCAATAAAAAAGCAGAC 1 101 1 AAGCGCATAA 0.950642 -200 GCAAAACTTTAAACGATAAAAGCATCGGCGT 2 50 0 AAACGAAAAA 0.924681 -133 GCAATTGGCAAAATGATGAAAAAGGAGGACT 4 60 1 AAATGAGAAA 0.763551 -27 CTAGCTTTTAAAGTGCCAAAATAAAGCAAAA 6 249 1 AAGTGCAAAA 0.953629 -52 CACTCAAACGCTAAAAGTGCTAACGA 7 6 1 AAACGCAAAA 0.98171 -50 ATGGTTTAAAAAGTGCTTAAAGACGTCTATA 8 91 0 AAGTGCTAAA 0.835351 -67 TGCGCAGAAGAAACGCCGTAAGTTTCGTAAT 10 153 1 AAACGCGTAA 0.929689 -54 ****** **** Masking position 2 Map Score: 4.7123 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 108 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 AATAAAAGAAAACGCAAAAA 1 1 1 AATAAAAGAA 0.759015 -300 TTTTTGTTAACAAGAAAGAAACGGAATTTT 1 83 0 CAAGAAAGAA 0.722119 -218 AAAAGCGCAATAAAAAAGCAGACCACTGAT 1 109 1 TAAAAAAGCA 0.741362 -192 AACTTTAAACGATAAAAGCATCGGCGTGTC 2 47 0 GATAAAAGCA 0.962275 -136 CATCGTCATTGATGAAAGCAATGAATCCAA 3 28 0 GATGAAAGCA 0.907319 -273 CAGATGGAATAAAAAAAGAAGCTAAAAGTC 3 86 0 AAAAAAAGAA 0.695855 -215 TTGAACACCTGATAAAAACCTAGCTTTAAT 3 117 1 GATAAAAACC 0.664661 -184 TTTTTACCACCAAAAAAACAATTATGGTCG 3 175 0 CAAAAAAACA 0.871315 -126 GTGATAAGCGGATTAAAACAGGAATAGATT 6 19 1 GATTAAAACA 0.618989 -282 TAAATAGTTAGATAAAAGCAGGTTAGTTAA 6 53 1 GATAAAAGCA 0.962275 -248 CAATTTCTTTCAAAAAAAAAAAAAAAACGT 6 89 1 CAAAAAAAAA 0.753987 -212 TCAAATAAGACATAAAAAAAGAGCAGTTTA 8 46 0 CATAAAAAAA 0.808399 -112 ********** Masking position 5 Map Score: 5.41824 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 166 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 8 TTTAGAAGAGCTCGCTTAATTCCGGAATTT 1 55 0 CTCGCTTAAT 0.92763 -246 GCTTTTTTATTGCGCTTTTTGTTAACAAGA 1 98 0 TGCGCTTTTT 0.586772 -203 TGATAAAAACCTAGCTTTAATGGTGGAATA 3 126 1 CTAGCTTTAA 0.90254 -175 CAATTGCTAACAGGCTTAAATTTAATATTT 4 37 0 CAGGCTTAAA 0.570272 -50 GCTTAATCTCTTGGCTTAATTTTGTACATT 6 155 0 TTGGCTTAAT 0.867677 -146 ACTGGTGCAACTAGCTTAATCTCTTGGCTT 6 168 0 CTAGCTTAAT 0.928963 -133 TAGGTAAAAACTAGCTTTTAAAGTGCCAAA 6 239 1 CTAGCTTTTA 0.696764 -62 AGGTTAAATTTTTGCTTTATTTTGGCACTT 6 259 0 TTTGCTTTAT 0.669209 -42 TGATTTAGAGTTAGCTTTAAAAAAGTTTAA 10 36 1 TTAGCTTTAA 0.873428 -171 CTAACGCGCTTGCGCTTAAAAAATCGCT 11 31 1 TGCGCTTAAA 0.851255 -18 CTTGATGAGCTTAATTTTAAAAATG 12 6 1 TGAGCTTAAT 0.874027 -33 ********** Masking position 6 Map Score: 3.825 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 225 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 9 TCGAATCCCACCGCTTCCGCCATAAAAATT 1 164 0 CCGCTTCCGC 0.959616 -137 GTCCTCTTAACCACTTGAGTACGCTCCCAG 1 233 1 CCACTTGAGT 0.926062 -68 TAGGTATTTCCCGCTGGGGTTAATCAATAA 5 12 1 CCGCTGGGGT 0.962893 -41 GCTTTAGTGCCCACTGGTGCAACTAGCTTA 6 180 0 CCACTGGTGC 0.851522 -121 AGCACTTTTAGCGTTTGAGTG 7 2 0 GCGTTTGAGT 0.819302 -54 GAAAAGGAATGCGCTTGCGTGAAAAGCGAA 10 119 1 GCGCTTGCGT 0.973993 -88 ATTACCTAACGCGCTTGCGCTTAAAAAATC 11 26 1 GCGCTTGCGC 0.831437 -23 ********** Masking position 5 Map Score: 2.38941 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 52 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 CGCAATAAAAAAGCAGACCACTGATGGTCT 1 114 1 AAGCAGACCA 0.980846 -187 TATAAATTGTAAGCAGACCATCAGTGGTCT 1 128 0 AAGCAGACCA 0.980846 -173 CGTGGGTTCGAATCCCACCGCTTCCGCCAT 1 171 0 AATCCCACCG 0.940608 -130 CCAATATGTGATTCCGACCATAATTGTTTT 3 161 1 ATTCCGACCA 0.939631 -140 TAATGACAGCAATCACACCACCACGTATTT 3 213 0 AATCACACCA 0.970209 -88 ********** Masking position 7 Map Score: 1.55756 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 13 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 11 ATAAATTGTTTGCAACAGCAAATTCCGGAAT 1 36 1 TGCAACGCAA 0.942054 -265 GTACGCTCCCAGGAACTGGAATCTAAATTTA 1 251 1 AGGAACGGAA 0.959483 -50 GCTTTAATGGTGGAATAGGAATCCAATATGT 3 139 1 TGGAATGGAA 0.960254 -162 CAGCTATTACAGCAATGGCAATAATGACAGC 3 233 0 AGCAATGCAA 0.943138 -68 TAAGCCTGTTAGCAATTGGCAAAATGATGAA 4 49 1 AGCAATGGCA 0.893926 -38 ATGAAAAAGGAGGACTTGGAAT 4 75 1 AGGACTGGAA 0.865175 -12 AAAAAACGTTTGAAATTGTAAGTTTGTCATG 6 110 1 TGAAATGTAA 0.672641 -191 ATTGATCTACTGCAACAGTAA 8 1 0 TGCAACGTAA 0.913121 -157 ****** **** Masking position 4 Map Score: 0.79862 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 61 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 12 TGTTAGATCGTTCTACGGTGCGTGGGTTCG 1 191 0 TTCTACGGTG 0.971873 -110 GAGGACACCCTGCTAAGGTGTTAGATCGTT 1 209 0 TGCTAAGGTG 0.989144 -92 CGCATTCCTTTTCGAAGGTGGTATTCGTGA 10 102 0 TTCGAAGGTG 0.971873 -105 ATAAAACTGGTAAGGTGCTAGTAACTA 10 190 0 TGGTAAGGTG 0.97142 -17 ********** Masking position 5 Map Score: 0.287344 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 4 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 13 AACGGAATTTTTAGAAGAGCTCGCTTAATT 1 64 0 TTAGAAGAGC 0.949691 -237 CGTTTAAAGTTTTGCAGAGCTGAAAAAGTG 2 66 1 TTTGCAGAGC 0.966887 -117 AATGCTTCGGTTTGACCAGCAGCTATTACA 3 253 0 TTTGACCAGC 0.977021 -48 TACTGATTTTTGACCAACAATTTTTGTA 3 283 0 TTTGACCAAC 0.890587 -18 AATTCGCCGTTTAGCACAGCGTCACGAATA 10 81 1 TTAGCACAGC 0.967408 -126 ********** Masking position 8 Map Score: 0.169332 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 33 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 14 ********** No masking Map Score: 4.92649e-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 15 ********** No masking Map Score: 4.92649e-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