AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00310_mjan_reg_300.orf -o00310_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: MJ0086 36 unspecified methyltransferase MJ0806 81 X-pro aminopeptidase (pepQ) Input sequences: #1 MJ0081 300 methyl coenzyme M reductase II, subunit beta (mrtB) #2 MJ0084 261 CODH nickel-insertion accessory protein (cooC) #3 MJ0085 134 iron transport periplasmic binding protein, putative (ceuE) #4 MJ0087 23 hemin permease (hemU) #5 MJ0090 80 collagenase (prtC) #6 MJ0260 94 signal sequence peptidase I, SEC11 #7 MJ0261 161 conserved hypothetical protein #8 MJ0652 300 conserved hypothetical protein #9 MJ1530 178 ribosomal protein S18 alanine acetyltransferase #10 MJ1597 226 serine hydroxymethyltransferase (glyA) Motif number 1 TTTAAAATCTTTAAAAAAATTTTGAATTCCTCA 1 136 0 TTAAAATTTT 0.900613 -165 TTTTAAAGATTTTAAAGATTTTTTTAATTTTAT 1 153 1 TTTAATTTTT 0.965396 -148 AATTTTATCATTTTAATATTATTATTTTAACAT 1 178 1 TTTTATTATT 0.925745 -123 ATATTATTATTTTAACATTTTTTAGTAATTTTT 1 193 1 TTTAATTTTT 0.965396 -108 ATTATCTTATTTTAAGTTTTATTTTTTGGACTT 2 16 1 TTTAATTATT 0.965395 -246 TTTTTTGGACTTTATTTTTAATTTTAAAATTTT 2 37 1 TTTATTAATT 0.559221 -225 GTCTCTTCCATTAATATTATTTTATCTAAAACT 2 110 0 TTAATATTTT 0.755449 -152 CTCAGTCTGATTTAAATTTAATTAAAACCTAAT 2 231 0 TTTAATAATT 0.788209 -31 CTTTTTTCTATTTTTTATATAATTT 3 3 1 TTTTTTTTTT 0.809525 -132 TTTATATAATTTTTATGAATATTGATGTATTTT 3 24 1 TTTTAATATT 0.888847 -111 TTGATGTATTTTTAACGATTATTTTTGATAAAC 3 45 1 TTTAATTATT 0.965395 -90 ATTTTTAATATCTAATATATATTTTTCGGTAGT 3 76 0 TCTAAATATT 0.791072 -59 TATATTAGATATTAAAAATTTTTGTTCATATCA 3 90 1 ATTAATTTTT 0.734829 -45 ACTATCACATTTTTTGAATTATT 4 1 0 TTTTTTTATT 0.809525 -23 GTCATATTGGTTATTGCTATTTTATACTTCAAA 5 29 1 TTATTATTTT 0.579903 -52 TTTTTTAAATTTTAAATTATATTTGAAGTATAA 5 50 0 TTTAAATATT 0.947076 -31 TAATTTAAAATTTAAAAAAATTTCTAA 5 64 1 TTTAAAATTT 0.704764 -17 TGATTCCACCTCATATATTTATTCCATAATGTT 6 25 0 TCATATTATT 0.571871 -70 ACAACATCTTTTTTACTGATTTTTAGGTTAATG 6 56 0 TTTTAATTTT 0.888847 -39 TAACTTGAATTTATAAATTTATTGATATATTGT 7 38 0 TTATATTATT 0.863258 -124 TCAAGTTATCATTATATATTATTATTTGTGAAA 7 63 1 ATTATTTATT 0.485816 -99 GATGTTTAACTTATATATATTTTATTTGCAAAT 7 110 1 TTATAATTTT 0.801952 -52 AGCCTCATAGTTTATTATTTTTTATCAATATTT 8 142 1 TTTATTTTTT 0.90486 -159 AGTTAAGTTTTTTATTAAATATTGATAAAAAAT 8 158 0 TTTATATATT 0.859164 -143 CATACCTTACATTAACTATTTTTAATCTTAATA 8 238 1 ATTAATTTTT 0.734829 -63 TTACTGTAAATTTATTATATATTATTAAGATTA 8 260 0 TTTATATATT 0.859164 -41 AAATAGTTTTTAATTTTATTACTGTAAATT 8 281 0 TTTTATTATT 0.925745 -20 TATAGAGTCTTTTAAAACATTTTGAAATACTAA 9 52 0 TTTAAATTTT 0.947076 -127 TAGTATTATTTTAAATTCTTTTTATAGAGTCTT 9 74 0 TTAAATTTTT 0.933895 -105 TCTATTTTAATTTTAGTATTATTTTAAATTCTT 9 87 0 TTTTATTATT 0.925745 -92 GTGTAATTTATTAAATTCTATTTTAATTTTAGT 9 103 0 TTAAATATTT 0.653325 -76 ACTGGTTACTTCAAAATGTTTTTGAAAGACACT 10 37 0 TCAAATTTTT 0.749322 -190 AGGAAGGCATTTAAATATTTATTGTCAAATATT 10 90 1 TTAAATTATT 0.933894 -137 ATATTTATTGTCAAATATTTATTAATAAACTTT 10 104 1 TCAAATTATT 0.749321 -123 ATTAATAAACTTTAATTAATTTTGAAGACAGTA 10 124 1 TTTAAATTTT 0.947076 -103 ACAGTATAGTTTAAAGATATTTTTAAGTATTAA 10 151 1 TTAAAATTTT 0.900613 -76 ***** ***** Masking position 12 Map Score: 50.0019 Number of sites scoring better than the average of aligned sites = 3159 Number in coding regions = 2249 Number in noncoding regions = 910 Number of orfs with sites within 600 bp upstream = 549 Fraction of orfs with sites within 600 bp upstream = 0.0881786 Motif number 2 TCAAAATTTTTTTAAAGATTTTAAAGATTTTT 1 144 1 TTTAAATTTT 0.832434 -157 TTTAAAGATTTTTTTAATTTTATCATTTTAAT 1 163 1 TTTTTATTTA 0.895233 -138 AATATTATTATTTTAACATTTTTTAGTAATTT 1 192 1 TTTTAATTTT 0.877511 -109 TAACATTTTTTAGTAATTTTTAGGATAAAATA 1 205 1 TAGTAATTTA 0.70731 -96 TAGGATAAAATAGAAAATTTTATATACCTATT 1 225 1 TAGAAATTTA 0.63068 -76 TATTATCTTATTTTAAGTTTTATTTTTTGGAC 2 15 1 TTTTAATTTA 0.954305 -247 TATTTTTAATTTTAAAATTTTAATTGGAGGGC 2 49 1 TTTAAATTTA 0.935409 -213 TCTTATTTAGTATAAATCTTTTTCTAACAAGT 2 198 0 TATAAATTTT 0.811988 -64 CTAAATAAGATATTAGGTTTTAATTAAATTTA 2 220 1 TATTAGTTTA 0.563468 -42 TTCTATTTTTTATATAATTTTTATGAATATTG 3 16 1 TATATATTTT 0.638608 -119 ATTGATGTATTTTTAACGATTATTTTTGATAA 3 44 1 TTTTAAATTA 0.747829 -91 GAACAAAAATTTTTAATATCTAATATATATTT 3 85 0 TTTTAATCTA 0.854491 -50 TTAGAAATTTTTTTAAATTTTAAATTATATTT 5 59 0 TTTTAATTTA 0.954305 -22 ATAACTTGAATTTATAAATTTATTGATATATT 7 40 0 TTTATATTTA 0.855605 -122 AAGTTATCATTATATATTATTATTTGTGAAAT 7 65 1 TATATAATTA 0.421321 -97 ATGTTTAACTTATATATATTTTATTTGCAAAT 7 111 1 TATATATTTT 0.638585 -51 CCTGCTAAGATTTTAACCTCTATCGATTCCTA 8 56 1 TTTTAATCTA 0.854503 -245 TATTATTTTTTATCAATATTTAATAAAAAACT 8 154 1 TATCAATTTA 0.683672 -147 ACATTAGATATATATACCTTTAAAATCATACC 8 212 1 TATATATTTA 0.837433 -89 ACATTAACTATTTTTAATCTTAATAATATATA 8 246 1 TTTTTACTTA 0.567072 -55 AAATAGTTTTTAATTTTATTACTGTAAA 8 283 0 TTTTTATTTA 0.895233 -18 TATAGAGTCTTTTAAAACATTTTGAAATACTA 9 53 0 TTTAAAATTT 0.413635 -126 TTTAGTATTATTTTAAATTCTTTTTATAGAGT 9 77 0 TTTTAATCTT 0.668283 -102 TTGTGTAATTTATTAAATTCTATTTTAATTTT 9 106 0 TATTAATCTA 0.836191 -73 AAGGAAGGCATTTAAATATTTATTGTCAAATA 10 89 1 TTTAAATTTA 0.935401 -138 CTTCAAAATTAATTAAAGTTTATTAATAAATA 10 119 0 AATTAATTTA 0.465501 -108 AAATATACCGTATTAATACTTAAAAATATCTT 10 164 0 TATTAACTTA 0.735666 -63 TTATCCCTCTTATTAACGTTTAATAGAAATAG 10 203 0 TATTAATTTA 0.947797 -24 ****** **** Masking position 11 Map Score: 29.459 Number of sites scoring better than the average of aligned sites = 2067 Number in coding regions = 1350 Number in noncoding regions = 717 Number of orfs with sites within 600 bp upstream = 469 Fraction of orfs with sites within 600 bp upstream = 0.0753293 Motif number 3 TTTCTTTATGATTCAAAAAAATGCGTAAGT 1 82 1 ATTCAAAAAA 0.847169 -219 TCTTTAAAATCTTTAAAAAAATTTTGAATT 1 141 0 CTTTAAAAAA 0.847156 -160 AAAATGATAAAATTAAAAAAATCTTTAAAA 1 162 0 AATTAAAAAA 0.900916 -139 TTTTAGGATAAAATAGAAAATTTTATATAC 1 222 1 AAATAGAAAA 0.777956 -79 ATTACTACAGCTATAGAAAATGATAGTAAT 1 254 0 CTATAGAAAA 0.681119 -47 ACTTAAAATAAGATAATAAAGA 2 3 0 AGATAATAAA 0.60069 -259 TAAAATTTTAAAATTAAAAATAAAGTCCAA 2 41 0 AAATTAAAAA 0.741602 -221 CATAAAAATTATATAAAAAATAGAAAAAAG 3 11 0 ATATAAAAAA 0.944573 -124 TATATATTAGATATTAAAAATTTTTGTTCA 3 88 1 ATATTAAAAA 0.831702 -47 AATAATTCAAAAAATGTGATAGT 4 5 1 ATTCAAAAAA 0.847169 -19 TGACCTCATTATATAAAAAAGA 5 3 0 ATATAAAAAA 0.944573 -78 ATAATTTAAAATTTAAAAAAATTTCTAA 5 63 1 ATTTAAAAAA 0.939952 -18 TTAACCTAAAAATCAGTAAAAAAGATGTTG 6 58 1 AATCAGTAAA 0.42576 -37 TATATCAATAAATTTATAAATTCAAGTTAT 7 42 1 AATTTATAAA 0.631747 -120 ATTCCTATTCCTTTTAAAAAGCTTCCTCTC 8 81 1 CTTTTAAAAA 0.615903 -220 TATTGATAAAAAATAATAAACTATGAGGCT 8 142 0 AAATAATAAA 0.865565 -159 TTTTATCAATATTTAATAAAAAACTTAACT 8 161 1 ATTTAATAAA 0.910607 -140 TCTTAATAATATATAATAAATTTACAGTAA 8 263 1 ATATAATAAA 0.917268 -38 TACAGTAATAAAATTAAAAACTATTT 8 285 1 AAATTAAAAA 0.741602 -16 TTAAAATAGAATTTAATAAATTACACAACA 9 110 1 ATTTAATAAA 0.910607 -69 CTCACTTAACCTTTAGTAAAGCCTTTGAAT 9 156 0 CTTTAGTAAA 0.560779 -23 GAAAGACACTATATAAAAAAGTTTTTGGTG 10 17 0 ATATAAAAAA 0.944573 -210 ATAGAAATAGAAACAATAAATATACCGTAT 10 183 0 AAACAATAAA 0.695069 -44 ********** Masking position 8 Map Score: 26.781 Number of sites scoring better than the average of aligned sites = 2543 Number in coding regions = 1920 Number in noncoding regions = 623 Number of orfs with sites within 600 bp upstream = 433 Fraction of orfs with sites within 600 bp upstream = 0.0695471 Motif number 4 TAATATTAAAATGATAAAATTAAAAAAATC 1 169 0 ATGATAAAAT 0.923352 -132 TTACTAAAAAATGTTAAAATAATAATATTA 1 191 0 ATGTTAAAAT 0.745054 -110 AGTAATTTTTAGGATAAAATAGAAAATTTT 1 216 1 AGGATAAAAT 0.925138 -85 ACCAACCTTTTTGTTAATATATTACTACAG 1 274 0 TTGTTAATAT 0.774963 -27 TTTATTTTTAATTTTAAAATTTTAATTGGA 2 47 1 ATTTTAAAAT 0.404161 -215 TCTAAAACTTTTGATAAAATGTTTGAATCT 2 89 0 TTGATAAAAT 0.934013 -173 TCAAAAGTTTTAGATAAAATAATATTAATG 2 105 1 TAGATAAAAT 0.643766 -157 ACGATTATTTTTGATAAACTACCGAAAAAT 3 59 1 TTGATAAACT 0.628488 -76 TGAACAAAAATTTTTAATATCTAATATATA 3 88 0 TTTTTAATAT 0.37254 -47 TTATATTTGAAGTATAAAATAGCAATAACC 5 37 0 AGTATAAAAT 0.690858 -44 TGTTGTTGAGTGGATAATATTC 6 83 1 TGGATAATAT 0.867363 -12 AATTTCACAAATAATAATATATAATGATAA 7 68 0 ATAATAATAT 0.513931 -94 GAATCGATAGAGGTTAAAATCTTAGCAGGG 8 55 0 AGGTTAAAAT 0.852312 -246 TTATTAAATATTGATAAAAAATAATAAACT 8 150 0 TTGATAAAAA 0.533037 -151 GTTTCGTCTCAGGATAACATTAGATATATA 8 196 1 AGGATAACAT 0.679253 -105 ATTTTTAATCTTAATAATATATAATAAATT 8 255 1 TTAATAATAT 0.547165 -46 CAACATTCATTGATTAAAATTATTCAAAGG 9 135 1 TGATTAAAAT 0.581611 -44 ********** Masking position 5 Map Score: 11.4033 Number of sites scoring better than the average of aligned sites = 936 Number in coding regions = 773 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 5 TTTGCTATTGATGATACTTTTAGGCTTTCTTTATGA 1 57 1 AGAATTAGGT 0.924245 -244 GCTATAGAAAATGATAGTAATAGGTATATAAAATTT 1 239 0 AGAATTAGGA 0.980067 -62 ATATTAATGGAAGAGACTTTGAGATAGAGAATCAAG 2 126 1 AGAATGAGAA 0.97172 -136 TTAAATTTAAATCAGACTGAGGGAGAGGT 2 243 1 ACAATGGGAA 0.633739 -19 TTGTGATTAAAACACATTAAGAGGGATTATT 7 6 0 ACAATGAGGA 0.96155 -156 ACTTTTCTCAATGATAATCCGAGGTAGTATAAAAGC 8 20 1 AGAATGAGGA 0.989421 -281 AGTTATAAAGAAGAAAATCGTAGAGAGGAAGCTTTT 8 97 0 AGAATTAGAA 0.94755 -204 GATAAAAAATAATAAACTATGAGGCTCATGATAGAA 8 132 0 ATAATGAGGT 0.694648 -169 GTTTCGTCTCAGGATAACATTAGATATATATACCTT 8 196 1 AGAACTAGAA 0.772839 -105 GTATAGTTTAAAGATATTTTTAAGTATTAATACGGT 10 154 1 AGAATTAAGA 0.794848 -73 TTTCTATTAAACGTTAATAAGAGGGATAAAA 10 206 1 AGTATGAGGA 0.92238 -21 * ** * * **** * Masking position 6 Map Score: 5.41758 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 247 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 GTAATAGGTATATAAAATTTTCTATTTTAT 1 229 0 TATAAAATTT 0.5916 -72 TCTTTATTATCTTATTTTAAGTTTTAT 2 8 1 TATCTTATTT 0.803138 -254 TAAAACCTAATATCTTATTTAGTATAAATC 2 212 0 TATCTTATTT 0.803138 -50 TTCTATTTTTTATATAATTTTTATGAATAT 3 16 1 TATATAATTT 0.936378 -119 AAATTTTTAATATCTAATATATATTTTTCG 3 81 0 TATCTAATAT 0.606058 -54 TCTTTTTTATATAATGAGGTCATATTG 5 8 1 TATATAATGA 0.862441 -73 TTATACTTCAAATATAATTTAAAATTTAAA 5 50 1 AATATAATTT 0.591599 -31 AATTTATTGATATATTGTGATTAAAACACA 7 26 0 TATATTGTGA 0.432067 -136 CAAATAATAATATATAATGATAACTTGAAT 7 61 0 TATATAATGA 0.862441 -101 AAATAAAATATATATAAGTTAAACATCAAA 7 107 0 TATATAAGTT 0.682234 -55 TTCTATTCGCTAAATAATTTGCAAATAAAA 7 129 0 TAAATAATTT 0.591573 -33 AAGGTATATATATCTAATGTTATCCTGAGA 8 202 0 TATCTAATGT 0.90863 -99 AAATTTATTATATATTATTAAGATTAAAAA 8 256 0 TATATTATTA 0.720051 -45 AAAACTTTTTTATATAGTGTCTTTCAAAAA 10 22 1 TATATAGTGT 0.813199 -205 ********** Masking position 2 Map Score: 5.87294 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 277 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 7 ATCAATAGCAAATAGAGTATAGCCTCTGCGT 1 38 0 AATAGGTATA 0.835905 -263 AATGTTTTAAAAGACTCTATAAAAAGAATTT 9 64 1 AAGACCTATA 0.975345 -115 ATGTTTTTGAAAGACACTATATAAAAAAGTT 10 24 0 AAGACCTATA 0.975345 -203 ATTAATTTTGAAGACAGTATAGTTTAAAGAT 10 138 1 AAGACGTATA 0.978706 -89 TTTAAGTATTAATACGGTATATTTATTGTTT 10 172 1 AATACGTATA 0.889236 -55 ***** ***** Masking position 4 Map Score: 1.61222 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 11 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 CACAGAGGTGAGCCCTATTCAATAGAACTT 1 108 0 AGCCCTATTC 0.931916 -193 AAAATTTTATATACCTATTACTATCATTTT 1 238 1 ATACCTATTA 0.919127 -63 AATAATCCCTCTTAATGTGTTTTA 7 5 1 ATCCCTCTTA 0.973982 -157 ACCTCTATCGATTCCTATTCCTTTTAAAAA 8 71 1 ATTCCTATTC 0.943228 -230 TATTGTTTCTATTTCTATTAAACGTTAATA 10 195 1 ATTTCTATTA 0.756117 -32 TTTTATCCCTCTTATTAACGTTTA 10 213 0 ATCCCTCTTA 0.973982 -14 ********** Masking position 6 Map Score: 0.894215 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 57 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 9 TCCCACAATGGAACTTACGCAGAGGCTATA 1 22 1 GAACTTACGC 0.990714 -279 CTATTCAATAGAACTTACGCATTTTTTTGA 1 94 0 GAACTTACGC 0.990714 -207 ACAAGTGGAGGAACATACACTGGTCTGAAA 2 174 0 GAACATACAC 0.956854 -88 ********** Masking position 7 Map Score: 0.344751 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 1 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 10 ********** No masking Map Score: -2.9179e-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: -2.9179e-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: -2.9179e-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