AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00550_rpxx_reg_300.orf -o00550_rpxx_300.ace -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -g0.29 -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 = 0.29 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RP409 21 unknown Input sequences: #1 RP246 54 unknown #2 RP247 182 UDP-N-ACETYLMURAMATE--ALANINE LIGASE (murC) #3 RP249 115 D-ALANINE--D-ALANINE LIGASE (ddlB) #4 RP407 300 unknown #5 RP408 148 LIPOPROTEIN SIGNAL PEPTIDASE (lspA) #6 RP410 149 UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE (murD) #7 RP411 74 CELL DIVISION PROTEIN FTSW (ftsW) #8 RP595 166 PHOSPHO-N-ACETYLMURAMOYL-PENTAPEPTIDE- TRANSFERASE (mraY1) #9 RP596 106 UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMYL- 2,6-DIAMINOPIMELATE--D-ALANYL-D-ALANYL LIGASE (murF) #10 RP597 120 UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMATE-- 2,6-DIAMINOPIMELATE LIGASE (murE) #11 RP599 195 unknown #12 RP825 300 UNDECAPRENYL-PHOSPHATE ALPHA-N-ACETYLGLUCOSAMINYLTRANSFERASE (mraY2) Motif number 1 AAAATGTCTTAATATTCTTAAATATATAATTT 1 32 1 ATATTTTAAA 0.761569 -23 TTAAGTTTAATAATTTAAAATTGAATTCGT 2 163 0 ATAATTAAAA 0.884204 -20 TTTTAGTCATACTAATAAAAAAGTAGAAT 3 97 1 ATAATAAAAA 0.912934 -19 AATAATTATATTCACCATTTAC 4 1 1 ATAATATATT 0.819558 -300 AAATAAATATTGTAATGTAAATGGTGAATATA 4 17 0 TTAATTAAAT 0.797634 -284 CATTACAATATTTATTTAAAAAATATTATCAT 4 32 1 TTATTAAAAA 0.764243 -269 TAGTTACATATATATTGAAAATACAAAAAGCA 4 101 1 TTATTAAAAT 0.775387 -200 TCTTATTTATATTAATGAAAATTAACTTATAT 4 143 1 ATAATAAAAT 0.917746 -158 TTGATTTAAAATTAATTAAATATAAGTTAATT 4 162 0 ATAATAAATA 0.870089 -139 TTAATTTTAAATCAATAAAAAACTCATAACCC 4 179 1 ACAATAAAAA 0.724658 -122 CTCATAACCCAGCAATCAAAATTTTACAATTT 4 201 1 ACAATAAAAT 0.737227 -100 TTTACAATTTTTTATTGTAATTTCTTTATATA 4 223 1 TTATTTAATT 0.615206 -78 TATAGTTCATATTATTCATAATCAAAAATTGA 4 253 1 ATATTATAAT 0.799796 -48 AGATAATTAATATATTTATAAATACAAAAAAG 5 127 0 TTATTATAAA 0.692179 -22 TGAGTACCAATCTAATCAAATATTCTGAGATT 7 24 0 TTAATAAATA 0.764418 -51 TCTAGTAATCTTTAATTTTATTACGCAATCAA 8 72 1 TTAATTTATT 0.615027 -95 AAAGTATTTAAGTATTTTTATATAGCTAGAAA 8 129 0 ATATTTTATA 0.692752 -38 CTTAAATACTTTTAATTTAAATCTACAA 8 149 1 TTAATTAAAT 0.797207 -18 ATGTAATTTATCTAATATTATATAAACAACAC 9 36 0 TTAATTTATA 0.60709 -71 CATTTGCTTAAGTAATAAAAATAAAAAACTCT 10 48 1 ATAATAAAAT 0.917535 -73 GTTTTTTTCTATTATTGATAATAAAAGTTAAT 11 17 1 ATATTATAAT 0.799796 -179 TAATTATTCAAGTATTTTAAAATGATTTCGGT 11 85 1 ATATTTAAAA 0.829793 -111 TAGGCTCTATATCATTGAAAATGATGTTCATA 11 120 1 ACATTAAAAT 0.641385 -76 TTATTATTTTAATAATATTATTATAAAAAAAT 11 157 1 ATAATTTATT 0.478075 -39 AACTACTTCAAGTATTGTTATTATCGTCTATC 12 61 1 ATATTTTATT 0.705563 -240 TAATTAAATCTGTAATATAAAAATTAACAAGT 12 113 0 TTAATTAAAA 0.7869 -188 TACAGATTTAATTAATCTTAATAAGAGAAGAA 12 131 1 ATAATTTAAT 0.811035 -170 AGAATTTAACACCAATGAAATATATTAATTTT 12 159 1 ACAATAAATA 0.626709 -142 ATTTTGCTCTAATATTGATATTCATATGACTA 12 186 1 ATATTATATT 0.744625 -115 TATTCATATGACTAATAAAATATTAATGAAAT 12 204 1 ATAATAAATA 0.869993 -97 TGTAATGATCAGTAATAATAAATATTAAATTT 12 267 1 ATAATATAAA 0.859954 -34 * **** ***** Masking position 6 Map Score: 28.3819 Number of sites scoring better than the average of aligned sites = 2447 Number in coding regions = 1487 Number in noncoding regions = 960 Number of orfs with sites within 600 bp upstream = 336 Fraction of orfs with sites within 600 bp upstream = 0.0539672 Motif number 2 AATATTCTTAAATATATAATTTT 1 42 1 ATATAATTTT 0.873527 -13 ATACTATGTAATACTATAATTTTGCTTACTTAT 2 80 0 ATATAATTTT 0.912327 -103 TTAAGTTTAATAATTTAAAATTGAAT 2 167 0 ATAATAATTT 0.917877 -16 ACTTTATCGCAACTTAATATTTTAGTCATACTA 3 78 1 ATAATATTTT 0.650676 -38 ATAGAATATTATGATAATATTTTTTAAATAAAT 4 41 0 ATAATATTTT 0.951335 -260 TATGTAACTAAGAATAATATGTTCTAAAACATC 4 78 0 ATAATATGTT 0.546567 -223 ATTAACTTATATTTAATTAATTTTAAATCAATA 4 163 1 AAATTAATTT 0.544642 -138 ACAATAAAAAATTGTAAAATTTTGATTGCTGGG 4 208 0 ATAAAATTTT 0.919646 -93 TGTATTTATAAATATATTAATTATCT 5 133 1 ATATTAATTA 0.604688 -16 TATTTGATGCACTTTAAAAATTTGCTAATTAAT 6 13 1 ATAAAAATTT 0.86109 -137 TTTTATCTTCACTGTATTAATTTCATATTCTTT 6 78 1 ATATTAATTT 0.913098 -72 TGAATCTAGTAATCTTTAATTTTATTACGCAAT 8 68 1 ATTTAATTTT 0.631204 -99 AAATACTTAAATACTTTTAATTTAAATCTACAA 8 144 1 ATTTTAATTT 0.629604 -23 TACGTGATGATACATAATATTTTTG 9 3 0 TTAATATTTT 0.643989 -104 ATACAAATAGAGTTTTTTATTTTTATTACTTAA 10 55 0 ATTTTATTTT 0.758615 -66 AAAAACTCTATTTGTATTATTTTGGATCACATA 10 71 1 TTATTATTTT 0.759475 -50 TGTTCATAGAACCTTATTATTTTAATAATATTA 11 144 1 ATATTATTTT 0.938657 -52 TAATATTATTATAAAAAAATTTTGCAAGATGTT 11 169 1 AAAAAATTTT 0.565263 -27 GGTGTCGATGATCAGAAAATTTTTCCCATTATG 12 28 1 AGAAAATTTT 0.522481 -273 TTAAATCTGTAATATAAAAATTAACAAGTTAGT 12 109 0 ATAAAAATTA 0.499599 -192 ACACCAATGAAATATATTAATTTTGCTCTAATA 12 167 1 ATATTAATTT 0.747371 -134 GTGTGGTATTTCATTAATATTTTATTAGTCATA 12 210 0 TTAATATTTT 0.757839 -91 AACATAATTAAATTTAATATTTATTATTACTGA 12 275 0 ATAATATTTA 0.757125 -26 * ********* Masking position 12 Map Score: 23.0985 Number of sites scoring better than the average of aligned sites = 995 Number in coding regions = 589 Number in noncoding regions = 406 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 3 TACCTATGTTATAAAGTATAATAATTGATGCACTAC 2 115 0 ATAAATAATT 0.832103 -68 TGAATTCGTCATAAAGATCATTACCTATGTTATAAA 2 136 0 ATAAAATATT 0.704568 -47 TTAAGTTTAATAATTTAAAATTGAATTCGTCATAA 2 158 0 ATAATTAATA 0.591905 -25 TTAAGTTGCGATAAAGTAATATCAGTATGTTTGAAA 3 59 0 ATAAATATTT 0.880123 -57 GAATATTATGATAATATTTTTTAAATAAATATTGTA 4 35 0 ATAATTTTTT 0.682384 -266 AAATATTATCATAATATTCTATTTATGATGTTTTAG 4 52 1 ATAATTTTTT 0.680631 -249 TTTCATTAATATAAATAAGATTTATAACTATGCTTT 4 127 0 ATAAAAAATA 0.704566 -174 TTAATTAAATATAAGTTAATTTTCATTAATATAAAT 4 147 0 ATAAGTATTT 0.604601 -154 TAACTTATATTTAATTAATTTTAAATCAATAAAAAA 4 165 1 TTAATAATTT 0.514375 -136 AGAAATTACAATAAAAAATTGTAAAATTTTGATTGC 4 212 0 ATAAAAATTA 0.779213 -89 CATATTATTCATAATCAAAAATTGATTCAAATAATC 4 260 1 ATAATAAATT 0.908633 -41 GTCCATTTTGATAATTAACATTCCTTTTTTGTATTT 5 104 1 ATAATAAATT 0.909043 -45 TACAGTGAAGATAAAAAACTGTGACTTAATACCTCC 6 58 0 ATAAAAATTT 0.930405 -92 GATATTCTTAATAATCATGTGTCTCTCAATGTCATT 8 20 1 ATAATATTTT 0.796428 -147 CTAATATTATATAAACAACACTACGTGATGATACAT 9 21 0 ATAAAAAATT 0.900248 -86 ATCTAGTGTCATAATGTAATTTATCTAATATTATAT 9 45 0 ATAATTATTT 0.890476 -62 AGTAATAAAAATAAAAAACTCTATTTGTATTATTTT 10 58 1 ATAAAAATTT 0.930351 -63 TAATATTATTATAAAAAAATTTTGCAAGATGTTATA 11 169 1 ATAAAAATTA 0.779341 -27 ATTCATATGACTAATAAAATATTAATGAAATACCAC 12 205 1 CTAATAATTT 0.610872 -96 ATGATCAGTAATAATAAATATTAAATTTAATTATGT 12 271 1 ATAATAAATT 0.90902 -30 ***** ** * * * Masking position 12 Map Score: 17.6441 Number of sites scoring better than the average of aligned sites = 629 Number in coding regions = 361 Number in noncoding regions = 268 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 4 AGTAAAAATGTCTTAATATTCTTAAATATA 1 28 1 TCTTAATATT 0.585953 -27 ATATTCTTAAATATATAATTTT 1 43 1 ATATATAATT 0.671758 -12 GTAAGCAAAATTATAGTATTACATAGTATT 2 84 1 TTATAGTATT 0.773572 -99 TTATAGTATTACATAGTATTTGTAGTGCAT 2 94 1 ACATAGTATT 0.846622 -89 CTTTATCGCAACTTAATATTTTAGTCATAC 3 79 1 ACTTAATATT 0.565259 -37 AAAAATATTATCATAATATTCTATTTATGA 4 50 1 TCATAATATT 0.928852 -251 ATGTTTTAGAACATATTATTCTTAGTTACA 4 79 1 ACATATTATT 0.908034 -222 TAAATCTTATTTATATTAATGAAAATTAAC 4 139 1 TTATATTAAT 0.690181 -162 TATATATAGTTCATATTATTCATAATCAAA 4 249 1 TCATATTATT 0.914869 -52 AAACATCAATTTATAAAATTGA 5 3 0 TTATAAAATT 0.730185 -146 GTATTTATAAATATATTAATTATCT 5 134 1 ATATATTAAT 0.671767 -15 CCTCCAGTTCTTATAGAATTAATTAGCAAA 6 33 0 TTATAGAATT 0.554642 -117 TGTATTAATTTCATATTCTTTTTGAAGTCA 6 90 1 TCATATTCTT 0.48327 -60 CTAAGGAATCTCAGAATATTTGATTAGATT 7 18 1 TCAGAATATT 0.686426 -57 ATTACATATTATTTCAAGCAATA 7 62 0 ACATATTATT 0.908034 -13 TTTTCTAGCTATATAAAAATACTTAAATAC 8 128 1 ATATAAAAAT 0.475435 -39 ACGTGATGATACATAATATTTTTG 9 5 0 ACATAATATT 0.923045 -102 AGTGTTGTTTATATAATATTAGATAAATTA 9 35 1 ATATAATATT 0.872137 -72 GTTAAGGATGTCATATTATTT 10 110 1 TCATATTATT 0.914869 -11 CAAAATTTTTTTATAATAATATTATTAAAA 11 163 0 TTATAATAAT 0.730185 -33 GTGTCGATGATCAGAAAATTTTTCCCATTA 12 29 1 TCAGAAAATT 0.443817 -272 TAAATCTGTAATATAAAAATTAACAAGTTA 12 111 0 ATATAAAAAT 0.475435 -190 CACCAATGAAATATATTAATTTTGCTCTAA 12 168 1 ATATATTAAT 0.671767 -133 ********** Masking position 10 Map Score: 22.3845 Number of sites scoring better than the average of aligned sites = 823 Number in coding regions = 546 Number in noncoding regions = 277 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 5 ATATTTAAGAATATTAAGACATTTTTACTTTAA 1 24 0 ATATTAGAAT 0.859888 -31 ATAACAAGATCAATTTTGAAACTCTCAAGGAAT 2 24 1 CAATTTGAAT 0.781514 -159 ATTCAATTTTAAATTATTAAACTTAA 2 167 1 AAATTTTAAT 0.704484 -16 GGCTTTTCAAACATACTGATATTACTTTATCGC 3 55 1 ACATATGAAT 0.893022 -61 CATAAATAGAATATTATGATAATATTTTTTAAA 4 46 0 ATATTTGAAT 0.954482 -255 TTAGTTACATATATATTGAAAATACAAAAAGCA 4 100 1 ATATATGAAT 0.839111 -201 TTACAATAAAAAATTGTAAAATTTTGATTGCTG 4 210 0 AAATTTAAAT 0.485463 -91 TATGAACTATATATAAAGAAATTACAATAAAAA 4 231 0 ATATAAGAAT 0.604169 -70 TTACTATTGTCCATTTTGATAATTAACATTCCT 5 96 1 CCATTTGAAT 0.89341 -53 ATTAATTAGCAAATTTTTAAAGTGCATCAAATA 6 13 0 AAATTTTAAT 0.704332 -137 ATCTAATCAAATATTCTGAGATTCCTTAGTAAA 7 14 0 ATATTTGAAT 0.954461 -61 ATACATTAGGATATTCTTAATAATC 8 3 1 ACATTGGAAT 0.91383 -164 TGCGGGAATGACATTGAGAGACACATGATTATT 8 29 0 ACATTAGAAA 0.456695 -138 TAGATAAATTACATTATGACACTAGATGCTTTT 9 54 1 ACATTTGAAT 0.971071 -53 TAACCATTCTACATTGGGAAAGTTCTATTAACT 11 42 0 ACATTGGAAT 0.913826 -154 TTTTATAATAATATTATTAAAATAATAAGGTTC 11 152 0 ATATTTTAAT 0.777013 -44 ***** *** * * Masking position 9 Map Score: 15.0839 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 114 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 ATTCTACTTTTTTATTAGTATGACTA 3 100 0 CTTTTTTATT 0.772839 -16 ATAACTATGCTTTTTGTATTTTCAATATAT 4 110 0 TTTTTGTATT 0.891722 -191 TGGGTTATGAGTTTTTTATTGATTTAAAAT 4 182 0 GTTTTTTATT 0.936861 -119 AAATTTTACAATTTTTTATTGTAATTTCTT 4 219 1 ATTTTTTATT 0.801891 -82 TAACATTCCTTTTTTGTATTTATAAATATA 5 119 1 TTTTTGTATT 0.891722 -30 TTAAGTCACAGTTTTTTATCTTCACTGTAT 6 65 1 GTTTTTTATC 0.862516 -85 AGTCATTGTAGTTTAGTATCTAAGACAAAT 6 129 0 GTTTAGTATC 0.63859 -21 TTGGTACTCAGTTTACTATTGCTTGAAATA 7 46 1 GTTTACTATT 0.806916 -29 GATTTACGTGTTGTTCTATTGCTTTTAAAA 9 84 0 TTGTTCTATT 0.657775 -23 GTTTTATTATGCAGAGAAAAA 10 2 1 TTTTATTATG 0.589412 -119 TACAAATAGAGTTTTTTATTTTTATTACTT 10 57 0 GTTTTTTATT 0.936861 -64 AAAACTCTATTTGTATTATTTTGGATCACA 10 72 1 TTGTATTATT 0.679917 -49 ATTTACGTTTTTTTCTATTATTGATAATA 11 10 1 TTTTTCTATT 0.891722 -186 TTCTATTAACTTTTATTATCAATAATAGAA 11 23 0 TTTTATTATC 0.793737 -173 TCTTGCAAAATTTTTTTATAATAATATTAT 11 168 0 TTTTTTTATA 0.63451 -28 AACTTGTTAATTTTTATATTACAGATTTAA 12 112 1 TTTTTATATT 0.674566 -189 TAAATTTAATATTTATTATTACTGATCATT 12 270 0 ATTTATTATT 0.69309 -31 ********** Masking position 4 Map Score: 11.8843 Number of sites scoring better than the average of aligned sites = 805 Number in coding regions = 518 Number in noncoding regions = 287 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 7 CTTGTTATAATTATAACGTTT 2 1 0 TTATACGTTT 0.851591 -182 TTTTGCTTACTTATTAAGTATATGCCTTATC 2 63 0 TTATAAGTAT 0.938595 -120 ATTACCTATGTTATAAAGTATAATAATTGAT 2 122 0 TTATAAGTAT 0.938595 -61 GTAATGATCTTTATGACGAATTCAATTTTAA 2 148 1 TTATACGAAT 0.896436 -35 AATATTCTATTTATGATGTTTTAGAACATAT 4 64 1 TTATATGTTT 0.87376 -237 AATCAATTTTTGATTATGAATAATATGAACT 4 256 0 TGATATGAAT 0.685278 -45 AGACACATGATTATTAAGAATATCCTAATGT 8 13 0 TTATAAGAAT 0.912594 -154 CAAAAATATTATGTATCATCACGTAG 9 6 1 ATATATGTAT 0.6826 -101 AATTCTTCTCTTATTAAGATTAATTAAATCT 12 134 0 TTATAAGATT 0.825408 -167 GATCATTACATTATCATGTACCTTAATGTTT 12 246 0 TTATATGTAC 0.761211 -55 **** ****** Masking position 6 Map Score: 5.07312 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 110 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 8 ********** No masking Map Score: 3.36387e-13 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 9 ********** No masking Map Score: 3.36387e-13 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: 3.36387e-13 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