AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00340_rpxx_reg_300.orf -o00340_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 Input sequences: #1 RP009 300 UDP-3-O-[3-HYDROXYMYRISTOYL] GLUCOSAMINE N-ACYLTRANSFERASE (lpxD) #2 RP254 225 UDP-3-O-[3-HYDROXYMYRISTOYL] N-ACETYLGLUCOSAMINE DEACETYLASE (lpxC) #3 RP255 300 unknown #4 RP306 217 unknown #5 RP307 130 CATIONIC AMINO ACID TRANSPORTER-1 (atrc1) #6 RP308 80 HISTIDYL-TRNA SYNTHETASE (hisS) #7 RP366 75 APOLIPOPROTEIN N-ACYLTRANSFERASE (lnt) #8 RP680 185 UBIQUINONE/MENAQUINONE BIOSYNTHESIS METHLYTRANSFERASE UBIE (ubiE) #9 RP681 300 unknown #10 RP719 300 unknown Motif number 1 GAGAAATTTAAATTAATAATATTGATTTATTTG 1 87 0 ATTAAATATT 0.856187 -214 TTGAATCTCAAATTTAGTTTAAAATTACTATAT 1 149 1 ATTTATTAAA 0.74034 -152 GCCATATAAAACTTACAATTTTATTGCATAATA 1 228 1 ATTACTTTTA 0.71116 -73 TGATTAAGTCAGTTAAAGTTTAT 1 288 1 ATTAATTTAT 0.921318 -13 TATAATTTGCAATTAAATATTAACATTTAAATA 2 186 1 ATTAAATTAA 0.882328 -40 AAATATTAACATTTAAATATATTTAAACAACCT 2 200 1 ATTAAATATT 0.855667 -26 GTTTATCTAAAATTTCATTTTTTAATTATGGAT 3 13 0 ATTTCTTTTT 0.768714 -288 AAGAGGTGTTATTTAAAGTTTATCTAAAATTTC 3 30 0 ATTAATTTAT 0.921315 -271 ACATTAAAATATTTTCATATTATTTAATTCATT 3 95 1 ATTTCATTAT 0.793467 -206 TTATTATTTAATTTAAAAATAATGAATTAAATA 3 115 0 ATTAAATAAT 0.864878 -186 GAATCTCTTTATTTAATTTTTAAGATAATAATC 3 222 1 ATTAATTTAA 0.874596 -79 TCATAATTATAATTAAGATTATTATCTTAAAAA 3 238 0 ATTAATTATT 0.847034 -63 AATTTTAATTTTTAAAATCTACGT 4 2 1 ATTTATTTTA 0.839119 -216 CGATTATAGCATTTTAATATATTGAAAGATAGT 4 132 1 ATTTAATATT 0.826656 -86 AATTATACTAAATTTATAATTAAATTACAACAC 4 163 0 ATTTAATTAA 0.857731 -55 ATTTAGTATAATTTAATGTTTATTTAAGGTTGA 4 183 1 ATTAATTTAT 0.921315 -35 TTTATTAGGAATTTTAGCATATACGAGAATGGA 5 79 1 ATTTAATATA 0.740346 -52 AACTTCAATTACATTTTTTCATTATTCTT 6 7 1 ATTACTTTTT 0.805206 -74 TTATTTACTCATTATATTTAAACTT 7 3 1 ATTACATTAT 0.826938 -73 ATGTGTCAATATTTTAATTTTTTTTATTATATT 9 85 0 ATTTATTTTT 0.897501 -216 TTAGTGGTGAATTTTAAAATTAATATTACTGAA 9 226 1 ATTTAATTAA 0.857731 -75 AATTTAAAAAAATTAATAATATTTAGTTTAACA 9 270 0 ATTAAATATT 0.856187 -31 AAGATGTAAGAGTTAATAATTATGGGAATTGTA 10 74 1 ATTAAATTAT 0.926412 -227 AATTAACCTCACTTAATTTTATTTCCTGCATTA 10 157 0 ATTAATTATT 0.847028 -144 GAACATTTGCATTTTACGATTATATTAGATAAT 10 227 1 ATTTAATTAT 0.910088 -74 AATATGTTTGACTTTATTTTTAATTGCTGTAAA 10 269 1 ATTTATTTAA 0.84866 -32 AGTTTATGATTTACAGCAATTAA 10 288 0 ATTTAATTTA 0.84866 -13 * **** ***** Masking position 4 Map Score: 31.1608 Number of sites scoring better than the average of aligned sites = 1308 Number in coding regions = 755 Number in noncoding regions = 553 Number of orfs with sites within 600 bp upstream = 236 Fraction of orfs with sites within 600 bp upstream = 0.0379056 Motif number 2 TTTTATTTAGAGATTACTTAGTATTCATAGAT 1 17 0 AGATTATTAT 0.81985 -284 ATTTAAATTAATAATATTGATTTATTTGAGAT 1 83 0 ATAATATGAT 0.944638 -218 TTGTTACAAAATATTACATAATCACCATTGTG 2 143 0 ATATTAATAT 0.897658 -83 TATTTAAATGTTAATATTTAATTGCAAATTAT 2 187 0 TTAATATTAT 0.746548 -39 AAGTAATAATATATTTTTTAGTATTTTAAAGA 3 59 0 ATATTTTTAT 0.924358 -242 AAATATTTTCATATTATTTAATTCATTATTTT 3 101 1 ATATTATTAT 0.975939 -200 TGTATATAAATTATTATTTAATTTAAAAATAA 3 126 0 TTATTATTAT 0.851774 -175 CAATTTAGGTATAATAGTTATTAGATTATCAG 3 184 0 ATAATATTAT 0.954123 -117 AATCTTAATTATAATTATGAGTTATATACCAT 3 251 1 ATAATTTGAT 0.837111 -50 TGGTGTATCAATTTTACTTAAT 5 1 0 ATTTTATTAT 0.897658 -130 AGTTTCTCCTATTTTAGTGAGTAATATCTCCA 5 108 0 ATTTTATGAT 0.878 -23 GAGTATATTTATAATAAAGAATAATGAAAAAA 6 24 0 ATAATAAGAT 0.786543 -57 GTATAGTAACATATTTATGATTGATCCACGCA 8 31 0 ATATTTTGAT 0.909304 -155 CAATATTTTAATTTTTTTTATTATATTTTGCT 9 80 0 ATTTTTTTAT 0.72542 -221 TTTAAAATTAATATTACTGAATGAGTTTTTGA 9 238 1 ATATTATGAT 0.970835 -63 AAAAAAATTAATAATATTTAGTTTAACATCAA 9 266 0 ATAATATTAT 0.954119 -35 TTTAAACGAAATATTAGTTAATGCAGGAAATA 10 139 1 ATATTATTAT 0.975946 -162 TTTTACGATTATATTAGATAATAAAGCAATAA 10 238 1 ATATTAATAT 0.897658 -63 ****** *** * Masking position 5 Map Score: 21.576 Number of sites scoring better than the average of aligned sites = 343 Number in coding regions = 215 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 3 AATGTGAGAAATTTAAATTAATAATATTGATT 1 93 0 ATTTAATAAT 0.501332 -208 ATATAGTAATTTTAAACTAAATTTGAGATTCA 1 150 0 TTTAAAAAAT 0.853042 -151 ATGTAATATTTTGTAACAAAATATTATTTGTA 2 156 1 TTGTAAAAAT 0.914102 -70 TTTGTATAATTTGCAATTAAATATTAACATTT 2 182 1 TTGCAAAAAT 0.590816 -44 ATTCATTATTTTTAAATTAAATAATAATTTAT 3 121 1 TTTAAAAAAT 0.834921 -180 GGTAGTCTTATTGTATATAAATTATTATTTAA 3 137 0 TTGTATAAAT 0.804464 -164 TTTATTTAATTTTTAAGATAATAATCTTAATT 3 229 1 TTTTAATAAT 0.905076 -72 TATAATCGTGTTGTTTAATAATTATCAATTTG 4 108 0 TTGTTTTAAT 0.571548 -110 AAAGATAGTGTTGTAATTTAATTATAAATTTA 4 156 1 TTGTAATAAT 0.89895 -62 TGGTGTATCAATTTTACTTAAT 5 1 0 ATTTTATAAT 0.380742 -130 TTCATTATTCTTTATTATAAATATACTCTTGC 6 28 1 TTTATTAAAT 0.461648 -53 TTTCAGCAAGTTTAAATATAATGAGTAAATAA 7 11 0 TTTAAATAAT 0.826121 -65 ATGTATTATTTTGTAAACAAATAATCGATAAA 7 53 1 TTGTAAAAAT 0.914102 -23 TATTGTAAGCAAATATTACATGCG 8 3 1 TTGTAAAAAT 0.914105 -183 GTGCAAGCTTTTTTATGATAATGCTTGCAACG 8 130 1 TTTTATTAAT 0.786826 -56 GTTTTATTTTAATAGTTGAAAAT 9 2 1 TTTTATTAAT 0.776328 -299 CAAGTACTAGTTTTTATAAAATGTGTCAATAT 9 106 0 TTTTTAAAAT 0.806762 -195 AGTGGTGAATTTTAAAATTAATATTACTGAAT 9 228 1 TTTAAATAAT 0.826121 -73 AATCTCCAAATTTAAAAAAATTAATAATATT 9 280 0 ATTTAAAAAT 0.54992 -21 GGATTAAAATTTGTTACGAAATATGCTCATTT 10 110 1 TTGTTAAAAT 0.804581 -191 AATATGCTCATTTAAACGAAATATTAGTTAAT 10 129 1 TTTAAAAAAT 0.853403 -172 TATGTTTGACTTTATTTTTAATTGCTGTAAAT 10 271 1 TTTATTTAAT 0.417184 -30 ****** **** Masking position 2 Map Score: 24.3187 Number of sites scoring better than the average of aligned sites = 763 Number in coding regions = 478 Number in noncoding regions = 285 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 4 GTGAGAAATTTAAATTAATAATATTGATTTAT 1 90 0 TAATAATAAT 0.826137 -211 ATAAAAATACTAATATAGTAATTTTAAACTAA 1 162 0 TAATAGTAAT 0.758133 -139 TAATATTTTGTAACAAAATATTATTTGTATAA 2 159 1 TAAAAATATT 0.923888 -67 GTATAATTTGCAATTAAATATTAACATTTAAA 2 185 1 CAAAAATATT 0.591 -41 TTATCCATAATTAAAAAATGAAATTTTAG 3 8 1 TAAAAAAAAT 0.853429 -293 TATTTTAATGTAAGAAAGTAATAATATATTTT 3 74 0 TAAAAGTAAT 0.922249 -227 TAAAAATAATGAATTAAATAATATGAAAATAT 3 103 0 GAAAAATAAT 0.681583 -198 AATTATTATTTAATTTAAAAATAATGAATTAA 3 118 0 TAATAAAAAT 0.606092 -183 ATTTAATTTTTAAGATAATAATCTTAATTATA 3 232 1 TAATAATAAT 0.826137 -69 AAATTAAGTATTTGCTAAACAT 3 289 0 AAAAAGTATT 0.61905 -12 ACATCAACCTTAAATAAACATTAAATTATACT 4 187 0 TAAAAACATT 0.861775 -31 CTAAAATTCCTAATAAAGCAATACAATTAGAA 5 64 0 TAAAAGCAAT 0.859004 -67 TAATAAAGAATAATGAAAAAATGTAATTGAAG 6 13 0 TAAAAAAAAT 0.853429 -68 TATTATTTTGTAAACAAATAATCGATAAAA 7 56 1 TAAAAATAAT 0.947317 -20 TATTGTAAGCAAATATTACATGCGTGG 8 6 1 TAAAAATATT 0.923888 -180 CTAAAACACGTAAATAAATTTTGCAGTAAAAC 9 146 1 TAAAAATTTT 0.439123 -155 AATTTTGCAGTAAAACAAAAATAAACGTCTAT 9 162 1 TAACAAAAAT 0.409382 -139 TTTTGATGTTAAACTAAATATTATTAATTTTT 9 264 1 AAAAAATATT 0.711268 -37 GATTACAAGCTAAAAAAGCAGTGTAGATATAT 10 18 1 TAAAAGCAGT 0.490034 -283 ATGCTCATTTAAACGAAATATTAGTTAATGCA 10 132 1 AAAAAATATT 0.711268 -169 TTATATTAGATAATAAAGCAATAAATATGTTT 10 246 1 TAAAAGCAAT 0.859004 -55 *** ******* Masking position 12 Map Score: 15.6485 Number of sites scoring better than the average of aligned sites = 828 Number in coding regions = 538 Number in noncoding regions = 290 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 5 CTTGACTATAAAAATACTAATATAGTAATTTT 1 169 0 AAATATAATA 0.822248 -132 ACAATTTTATTGCATAATAAAAGCATAACTTA 1 242 1 TGATATAAAA 0.827079 -59 TTAACATTTAAATATATTTAAACAACCTCGT 2 205 1 AAATATTAAA 0.809578 -21 ACACCTCTTTAAAATACTAAAAAATATATTAT 3 54 1 AAATATAAAA 0.92072 -247 ATTTAATTTAAAAATAATGAATTAAATAATAT 3 111 0 AAATATGAAT 0.593058 -190 ACTATCTTTCAATATATTAAAATGCTATAATC 4 133 0 AAATATAAAA 0.92072 -85 TTTATAATAAAGAATAATGAAAAAATGTAATT 6 17 0 AGATATGAAA 0.935795 -64 TTATGGCAAGAGTATATTTATAATAAAGAATA 6 33 0 AGATATTATA 0.662338 -48 TTATTAGCAAAATATAATAAAAAAAATTAAAA 9 75 1 AAATATAAAA 0.92072 -226 AAAAAAAATTAAAATATTGACACATTTTATAA 9 93 1 AAATATGACA 0.746176 -208 AGTACTTGCTTGCATACTAAAACACGTAAATA 9 130 1 TGATATAAAA 0.827079 -171 TGTTTTTCCTTGTATACTGATAAATTAACCTC 10 180 0 TGATATGATA 0.673634 -121 ** *** ***** Masking position 6 Map Score: 5.0071 Number of sites scoring better than the average of aligned sites = 412 Number in coding regions = 258 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 6 ATAAAAATACTAATATAGTAATTTTAAACTA 1 163 0 TAAATAGTAA 0.740248 -138 TAATATTTTGTAACAAAATATTATTTGTATA 2 159 1 TAAAAAATAT 0.789269 -67 TATTTTAATGTAAGAAAGTAATAATATATTT 3 75 0 TAAAAAGTAA 0.90687 -226 AATTAAATAATATGAAAATATTTTAATGTAA 3 93 0 TATAAAATAT 0.53009 -208 TATCAGCTTTTAATCCAGTATGGTAGTCTTA 3 159 0 TAACCAGTAT 0.599025 -142 TAAAAGCTGATAATCTAATAACTATTATACC 3 178 1 TAACTAATAA 0.636099 -123 ATTTAATTTTTAAGATAATAATCTTAATTAT 3 232 1 TAAATAATAA 0.733159 -69 GGTGACCGTATATTACAACAAATTGATAATT 4 90 1 TATACAACAA 0.508137 -128 CTAAAATTCCTAATAAAGCAATACAATTAGA 5 65 0 TAAAAAGCAA 0.854776 -66 AGTATATTTATAATAAAGAATAATGAAAAAA 6 24 0 TAAAAAGAAT 0.532041 -57 TTAATCCACATAACACAATAAA 6 69 1 TAAACAATAA 0.85018 -12 TATTATTTTGTAAACAAATAATCGATAAAA 7 56 1 TAACAAATAA 0.856586 -20 TATTGTAAGCAAATATTACATGCGTG 8 6 1 TAACAAATAT 0.70439 -180 TATTTTCAACTATTAAAATAAAAC 9 4 0 TATAAAATAA 0.73874 -297 TAGCAAAATATAATAAAAAAAATTAAAATAT 9 79 1 TAAAAAAAAA 0.733159 -222 CGTGTTTTAGTATGCAAGCAAGTACTAGTTT 9 125 0 TATCAAGCAA 0.530041 -176 AATTTTGCAGTAAAACAAAAATAAACGTCTA 9 162 1 TAAACAAAAA 0.624167 -139 TTATATTAGATAATAAAGCAATAAATATGTT 10 246 1 TAAAAAGCAA 0.854776 -55 *** ******* Masking position 1 Map Score: 9.56565 Number of sites scoring better than the average of aligned sites = 905 Number in coding regions = 578 Number in noncoding regions = 327 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 7 GATTACTTAGTATTCATAGATACGATA 1 7 0 TATTCAAGAT 0.934151 -294 GTAGTTCTTTTATTTAGAGATTACTTAGTAT 1 25 0 TATTTAAGAT 0.970582 -276 AAACCTTAGCTATTCAAAGATGAATCTCAAA 1 60 1 TATTCAAGAT 0.934151 -241 CTACTGGAAATAATTACAGATACTATATAGT 2 30 1 TAATTAAGAT 0.951107 -196 ACATAAGGTCCAATTACAGATACTATATAGT 2 51 0 CAATTAAGAT 0.785561 -175 TTTCATTTTTTAATTATGGATAA 3 3 0 TAATTAGGAT 0.881879 -298 AAAGAGGTGTTATTTAAAGTTTATCTAAAAT 3 33 0 TATTTAAGTT 0.89114 -268 CATTTTAATATATTGAAAGATAGTGTTGTAA 4 141 1 TATTGAAGAT 0.885171 -77 TGTTGTAATTTAATTATAAATTTAGTATAAT 4 164 1 TAATTAAAAT 0.605171 -54 ATTTAATGTTTATTTAAGGTTGATGTGATTA 4 193 1 TATTTAGGTT 0.758562 -25 CACCACTAAGTTTTTATAGATACGTGATAAT 9 204 0 TTTTTAAGAT 0.8074 -97 ****** **** Masking position 6 Map Score: 7.0495 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 93 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 TTTTAAAATCTACGTGTATTGTTGTATGGA 4 20 1 TACGTGTATT 0.978393 -198 GGTATGACACTGCGTGTATTTTCACTCCAT 4 45 0 TGCGTGTATT 0.953268 -173 TATGTTACTATACGTGTCTTGACCTAAATA 8 50 1 TACGTGTCTT 0.974398 -136 AAAATTTATTTACGTGTTTTAGTATGCAAG 9 138 0 TACGTGTTTT 0.978393 -163 TCCGTATCATTACCTGTTTTTCCTTGTATA 10 196 0 TACCTGTTTT 0.927852 -105 ********** Masking position 5 Map Score: 3.16223 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 5 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 AGCTATTCAAAGATGAATCTCAAATAAATCAA 1 67 1 AATGAATCCA 0.929505 -234 TCAATTAATAACTTGAATCTCAAATTTAGTTT 1 137 1 ATTGAATCCA 0.929506 -164 ACAAAATATTACATAATCACCATTGTGAGCAT 2 138 0 AATAATCACA 0.54994 -88 AAATTAATCACATCAACCTTAA 4 206 0 AATTAATCCA 0.930807 -12 TGCCATAACTATTTAATCCACATAACACAATA 6 57 1 ATTAATCCCA 0.812406 -24 ACGTTAAAGTACTTGATTCACACTGTTTATAC 8 159 1 ATTGATTCCA 0.900063 -27 TCTATCTTATAGATTATTAGCAAAATATAATA 9 62 1 AATTATTACA 0.721649 -239 AATAATATTTAGTTTAACATCAAAAACTCATT 9 257 0 ATTTAACACA 0.80439 -44 TTCGTAACAAATTTTAATCCCAATACAATTCC 10 98 0 ATTTAATCCA 0.930807 -203 GTATACTGATAAATTAACCTCACTTAATTTTA 10 169 0 AATTAACCCA 0.935792 -132 * ******* ** Masking position 6 Map Score: 2.90087 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 73 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 10 ACATAATCACCATTGTGAGCATCAATAAGTGG 2 128 0 CTTGTAGCAT 0.975248 -98 CAATTATATCCATTTCAAGCTTATTCTAATTG 5 41 1 CTTTCAGCTT 0.975641 -90 GCACATTAAGCTTTTTTAGCATAGATCAATAG 8 102 0 CTTTTAGCAT 0.979392 -84 AGTACTTTAACGTTGCAAGCATTATCATAAAA 8 140 0 CTTGCAGCAT 0.984115 -46 ATCTACACTGCTTTTTTAGCTTGTAATCAATA 10 14 0 CTTTTAGCTT 0.962224 -287 ACTCTTACATCTTTTCAAGAATTTCACTAACT 10 55 0 CTTTCAGAAT 0.920373 -246 * **** ***** Masking position 8 Map Score: 2.64959 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 25 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 11 ********** No masking Map Score: -2.42052e-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: -2.42052e-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: -2.42052e-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