AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00600_rpxx_reg_100.orf -o00600_rpxx_100.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 Input sequences: #1 RP046 198 PROLIPOPROTEIN DIACYLGLYCERYL TRANSFERASE (lgt) #2 RP410 149 UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE (murD) #3 RP411 74 CELL DIVISION PROTEIN FTSW (ftsW) #4 RP825 300 UNDECAPRENYL-PHOSPHATE ALPHA-N-ACETYLGLUCOSAMINYLTRANSFERASE (mraY2) Motif number 1 ATTTTACCTATTATTATTATTATAAAATA 1 1 1 ATTTTCTATA 0.93989 -198 AATACAAATCATTTTTTTATTATTACTAAGAATTTTATT 1 36 1 ATTTTTTTTA 0.94079 -163 TATTACTAAGAATTTTATTTTTATCAATAATTTTAACTC 1 56 1 AATTTTTATA 0.987254 -143 CAGTATTTATATTTGCTTAGTAATACCAAATGCTTTTGA 1 93 0 ATTTGTTATA 0.911671 -106 AAACTGTATTAATTACTTTGTAATTTCCAGCAACTTAG 1 171 1 AATTATTATA 0.964959 -28 GCACTTTAAAAATTTGCTAATTAATTCTATAAGAACTGG 2 21 1 AATTTTTAAA 0.891805 -129 TCACTGTATTAATTTCATATTCTTTTTGAAGTCATCTCT 2 86 1 AATTTTTTTA 0.96134 -64 TAATGGGAAAAATTTTCTGATCATCGACACCTAAACGTT 4 20 0 AATTTTTATA 0.987254 -281 ACAATACTTGAAGTAGTTCATAATGGGAAAAATTTTCTG 4 40 0 AAGTATTATA 0.812852 -261 TATATTACAGATTTAATTAATCTTAATAAGAGAAGAATT 4 126 1 ATTTATTTTA 0.849592 -175 GAAATATATTAATTTTGCTCTAATATTGATATTCATATG 4 175 1 AATTTCTATA 0.960739 -126 TTTCATTAATATTTTATTAGTCATATGAATATCAATATT 4 196 0 ATTTTTTATA 0.980195 -105 AACATAATTAAATTTAATATTTATTATTACTGATCATTA 4 269 0 AATTTTTATA 0.987251 -32 ***** * * ** * Masking position 1 Map Score: 18.6768 Number of sites scoring better than the average of aligned sites = 410 Number in coding regions = 265 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 2 TTGTATTTTATAATAATAATAATAGGTAAAA 1 12 0 TAATAAAATA 0.936856 -187 AAATTCTTAGTAATAATAAAAAAATGATTTG 1 40 0 TAATAAAAAA 0.957409 -159 AAATTATTGATAAAAATAAAATTCTTAGTAA 1 58 0 TAAAAAAAAA 0.741522 -141 ATTTGCTTAGTAATACCAAATGCTTTTGAGT 1 91 0 TAATACAAAT 0.842392 -108 ATTACTAAGCAAATATAAATACTGTCATTAC 1 108 1 AAATATAATA 0.706893 -91 TTAATACAGTGAAGATAAAAAACTGTGACTT 2 67 0 GAAGATAAAA 0.893272 -83 ACTTCAAAAAGAATATGAAATTAATACAGTG 2 87 0 GAATATAAAT 0.87391 -63 GTTTAGTATCTAAGACAAATAGATAGAGATG 2 118 0 TAAGACAATA 0.830537 -32 TGATAGACGATAATAACAATACTTGAAGTAG 4 63 0 TAATAAAATA 0.94471 -238 ATTAAATCTGTAATATAAAAATTAACAAGTT 4 112 0 TAATATAAAA 0.957585 -189 CTTCTCTTATTAAGATTAATTAAATCTGTAA 4 130 0 TAAGATAATT 0.783441 -171 TTAGTCATATGAATATCAATATTAGAGCAAA 4 188 0 GAATATAATA 0.926406 -113 ATATTCATATGACTAATAAAATATTAATGAA 4 203 1 GACTAAAAAA 0.707469 -98 TAATGATCAGTAATAATAAATATTAAATTTA 4 269 1 TAATAAAAAT 0.904179 -32 ****** **** Masking position 5 Map Score: 15.0858 Number of sites scoring better than the average of aligned sites = 933 Number in coding regions = 583 Number in noncoding regions = 350 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 3 ATTTTACCTATTATTATTATTATA 1 3 1 TTTACCATAT 0.828514 -196 ATGATTTGTATTTTATAATAATAATAATAGGT 1 16 0 TTTTATATAT 0.396045 -183 TTTTTTTATTATTACTAAGAATTTTATTTTTA 1 47 1 ATTACTAGAT 0.941759 -152 TTGAGTTAAAATTATTGATAAAAATAAAATTC 1 65 0 ATTATTATAA 0.564799 -134 AGCATTTGGTATTACTAAGCAAATATAAATAC 1 98 1 ATTACTAGAA 0.961838 -101 AAATACTGTCATTACAAAACAACTAAGCCATT 1 124 1 ATTACAAAAA 0.646602 -75 GTTGCTGGAAATTACAAAGTAATTAATACAGT 1 173 0 ATTACAAGAA 0.922148 -26 TTCTTATAGAATTAATTAGCAAATTTTTAAAG 2 24 0 ATTAATAGAA 0.782934 -126 TTATTTACTAAGGAATCTCAGAATA 3 4 1 TTTACTAGAA 0.942114 -71 ATTACATATTATTTCAAGCAAT 3 63 0 ATTACAATAT 0.917363 -12 ATGGGAAAAATTTTCTGATCATCGACACCTAA 4 25 0 TTTTCTATAT 0.82178 -276 ATCAGAAAATTTTTCCCATTATGAACTACTTC 4 38 1 TTTTCCATAT 0.593162 -263 ATTATCGTCTATCACTAATAAAGACGTAAACT 4 80 1 ATCACTATAA 0.882655 -221 TAATTTTTATATTACAGATTTAATTAATCTTA 4 119 1 ATTACAATTA 0.565827 -182 TGTTAAATTCTTCTCTTATTAAGATTAATTAA 4 138 0 TTCTCTATAA 0.624952 -163 TGATATTCATATGACTAATAAAATATTAATGA 4 201 1 ATGACTATAA 0.811356 -100 AATACCACACTTTAAACATTAAGGTACATGAT 4 233 1 TTTAAAATAA 0.61408 -68 AATATTTATTATTACTGATCATTACATTATCA 4 261 0 ATTACTATAT 0.958654 -40 ****** ** ** Masking position 2 Map Score: 15.5741 Number of sites scoring better than the average of aligned sites = 991 Number in coding regions = 692 Number in noncoding regions = 299 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 4 TATTATAAAATACAAATCATTTTTTTATTA 1 28 1 TACAAATCAT 0.59728 -171 CATTTGGTATTACTAAGCAAATATAAATAC 1 100 1 TACTAAGCAA 0.95672 -99 ATACTGTCATTACAAAACAACTAAGCCATT 1 126 1 TACAAAACAA 0.879672 -73 TAAGCCATTGCATCAATCTATAAAAAACTG 1 147 1 CATCAATCTA 0.612498 -52 TGCTGGAAATTACAAAGTAATTAATACAGT 1 173 0 TACAAAGTAA 0.661992 -26 TTGTCTTAGATACTAAACTACAATGACTA 2 131 1 TACTAAACTA 0.832038 -19 TTATTTACTAAGGAATCTCAGAATA 3 6 1 TACTAAGGAA 0.948768 -69 GTAAACTGAGTACCAATCTAATCAAATATT 3 32 0 TACCAATCTA 0.886199 -43 CCACAAAAGAACGTTTAGGTG 4 2 1 CACAAAAGAA 0.861993 -299 TATCGTCTATCACTAATAAAGACGTAAACT 4 82 1 CACTAATAAA 0.729501 -219 AAGAATTTAACACCAATGAAATATATTAAT 4 158 1 CACCAATGAA 0.934975 -143 ACTAATAAAATATTAATGAAATACCACACT 4 214 1 TATTAATGAA 0.773029 -87 ACACTTTAAACATTAAGGTACATGATAATG 4 239 1 CATTAAGGTA 0.635129 -62 ********** Masking position 5 Map Score: 7.51423 Number of sites scoring better than the average of aligned sites = 450 Number in coding regions = 319 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 5 TAAGCAAATATAAATACTGTCATTACAAAA 1 113 1 TAAATACTGT 0.947569 -86 ATCAATCTATAAAAAACTGTATTAATTACT 1 158 1 AAAAAACTGT 0.976323 -41 ATTAATTCTATAAGAACTGGAGGTATTAAG 2 40 1 TAAGAACTGG 0.923481 -110 CAGTGAAGATAAAAAACTGTGACTTAATAC 2 62 0 AAAAAACTGT 0.976323 -88 TTAAGATTAATTAAATCTGTAATATAAAAA 4 122 0 TTAAATCTGT 0.846053 -179 ********** Masking position 3 Map Score: 1.44598 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 56 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 AAAAATGATTTGTATTTTATAATAATAATA 1 22 0 TGTATTTTAT 0.918323 -177 TGACAGTATTTATATTTGCTTAGTAATACC 1 105 0 TATATTTGCT 0.872848 -94 TATATTTGATGCACTTTAAA 2 1 1 TATATTTGAT 0.962749 -149 GGAATCTCAGAATATTTGATTAGATTGGTA 3 22 1 AATATTTGAT 0.952035 -53 CAATACTTGAAGTAGTTCATAATGGGAAAA 4 48 0 AGTAGTTCAT 0.837856 -253 GCAAAATTAATATATTTCATTGGTGTTAAA 4 163 0 TATATTTCAT 0.962749 -138 GTATTTCATTAATATTTTATTAGTCATATG 4 208 0 AATATTTTAT 0.898056 -93 TTTAAAGTGTGGTATTTCATTAATATTTTA 4 219 0 GGTATTTCAT 0.919432 -82 ********** Masking position 4 Map Score: 7.04521 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 143 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 7 ********** No masking Map Score: -2.95996e-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 8 ********** No masking Map Score: -2.95996e-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: -2.95996e-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