AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00051_rpxx_reg_100.orf -o00051_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 RP008 190 (3R)-HYDROXYMYRISTOYL-[ACYL CARRIER PROTEIN] DEHYDRATASE (fabZ) #2 RP060 171 ABC TRANSPORTER ATP-BINDING PROTEIN (abcT1) #3 RP061 60 unknown #4 RP062 34 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE (kdsA) #5 RP379 300 3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE (kdsB) #6 RP410 149 UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE (murD) #7 RP411 74 CELL DIVISION PROTEIN FTSW (ftsW) #8 RP505 184 KPSF PROTEIN (kpsF) #9 RP508 68 ABC TRANSPORTER ATP-BINDING PROTEIN (abcT2) #10 RP509 92 PHOSPHOMANNOMUTASE (exoC) #11 RP825 300 UNDECAPRENYL-PHOSPHATE ALPHA-N-ACETYLGLUCOSAMINYLTRANSFERASE (mraY2) Motif number 1 TTTACTATAACTTTATTGTTGTA 1 1 1 TTACTATATT 0.728384 -190 TGTTGTATGAATCAATTTTTATTGTTATCTCAT 1 27 1 ATAATTTTTT 0.786565 -164 CGGGACCCAATTAAATATATTTTTCTGGATCTA 1 71 0 TTAATATATT 0.902331 -120 AGGTCTCTTGTTTAATATAAATTTGCCTTTATT 1 162 0 TTAATATATT 0.902331 -29 TCTATAACGATTGAATATTTCTTTTTTAGTCTT 2 50 0 TTAATATTTT 0.977134 -122 AATTACAATGTTTAATTTTAAATTTAATGTCTA 2 83 1 TTAATTTTAT 0.916796 -89 AGTATATACATTTATTATTCTATAGACATTAAA 2 105 0 TTATTATTAT 0.90628 -67 AAATTTTGTTTCCTTATTATTTTACACTGCTA 2 150 0 TTCTTATTTT 0.835696 -22 CACAAATATTATTAATTTTATTTGTATGGATAT 3 23 1 ATAATTTTTT 0.786587 -38 ACTCTTATATTTAATTATTGAATGAGACACAAA 4 11 0 TTATTATTAT 0.90628 -24 TTTGAATATATTCAATATTCGATCTGTTTAAAG 5 204 0 TTAATATTAT 0.965058 -97 ACAATTATTTTTTAATTTTAAATATAGGCAGTT 5 277 1 TTAATTTTAT 0.916796 -24 ACTGTATTAATTTCATATTCTTTTTGAAGTCAT 6 88 1 TTCATATTTT 0.935597 -62 TGGTACTCAGTTTACTATTGCTTGAAATAATAT 7 47 1 TTACTATTTT 0.925394 -28 ATTACATATTATTTCAAGCAATAG 7 61 0 TTCATATTTT 0.935597 -14 AACTAACTTGTTAATTTTTATATTACAGATTTA 11 108 1 TTATTTTTAT 0.794149 -193 GTGGTATTTCATTAATATTTTATTAGTCATATG 11 208 0 ATAATATTAT 0.85597 -93 CATAATTAAATTTAATATTTATTATTACTGATC 11 273 0 TTAATATTTT 0.977134 -28 ** ****** ** Masking position 6 Map Score: 21.0254 Number of sites scoring better than the average of aligned sites = 867 Number in coding regions = 537 Number in noncoding regions = 330 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 2 TGTTGTATGAATCAATTTTTATTGTTATCT 1 27 1 ATCAATTTTT 0.592486 -164 ACGGGACCCAATTAAATATATTTTTCTGGA 1 75 0 ATTAAATATA 0.843844 -116 GATTGCATAGAGCAATTTTATCTCTGTTAT 1 119 0 AGCAATTTTA 0.904742 -72 TCGTAATAAAGGCAAATTTATATTAAACAA 1 158 1 GGCAAATTTA 0.684119 -33 TTCTATAGACATTAAATTTAAAATTAAACA 2 91 0 ATTAAATTTA 0.924557 -81 TATACTTAGTAGTAAATATAGCAGTGTAAA 2 132 1 AGTAAATATA 0.877513 -40 CACAAATATTATTAATTTTATTTGTATGGA 3 23 1 ATTAATTTTA 0.843843 -38 TCATTCAATAATTAAATATAAGAGTT 4 19 1 ATTAAATATA 0.843844 -16 CAATATGAAGATCAATTTTAAAAAGAGCAA 5 104 1 ATCAATTTTA 0.877513 -197 TTTAAAGTGCATCAAATATA 6 1 0 ATCAAATATA 0.877513 -149 AGAATTAATTAGCAAATTTTTAAAGTGCAT 6 19 0 AGCAAATTTT 0.813825 -131 TACCAATCTAATCAAATATTCTGAGATTCC 7 22 0 ATCAAATATT 0.592487 -53 GGTGAAAATGAGTAAATTAA 8 175 1 AGTAAATTAA 0.524309 -10 TCTATGCGTTATTAAATTTGTATTTTGGAC 9 32 0 ATTAAATTTG 0.593308 -37 TAAAATTATTAGTAGATTTACGTGGTCAAG 10 45 0 AGTAGATTTA 0.620292 -48 CACGGAATCAAGTAAAATTATTAGTAGATT 10 57 0 AGTAAAATTA 0.811084 -36 TCAATATTAGAGCAAAATTAATATATTTCA 11 174 0 AGCAAAATTA 0.850566 -127 TCATATGAATATCAATATTAGAGCAAAATT 11 185 0 ATCAATATTA 0.654357 -116 TGTAATGATCAGTAATAATAAATATTAAAT 11 267 1 AGTAATAATA 0.454978 -34 AATAATAAATATTAAATTTAATTATGTTAC 11 280 1 ATTAAATTTA 0.924557 -21 ********** Masking position 4 Map Score: 20.2142 Number of sites scoring better than the average of aligned sites = 998 Number in coding regions = 711 Number in noncoding regions = 287 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 3 AAAAATTGATTCATACAACAATAAAGTTATAG 1 15 0 TCAACAAAAT 0.821343 -176 CATTGTAATTTCTATAACGATTGAATATTTCT 2 61 0 TCTTAACATT 0.642823 -111 ATATGTCTTTTACACAAATATTATTAATT 3 8 1 TTTACACAAT 0.935984 -53 GTGGTTTTGTTACCAATATCCATACAA 3 44 0 TTTTTACAAT 0.620152 -17 TTTGTGTCTCATTCAATAATTAAATATAAG 4 9 1 TCATCAAAAT 0.821343 -26 AAAAGGCTAATCTGTCAACAATTATTTTTTAA 5 260 1 TCTTCAAAAT 0.953529 -41 TAGTTTAGTATCTAAGACAAATAGATAGAGAT 6 119 0 TCTAGACAAT 0.952634 -31 TACTAAGGAATCTCAGAATATTTGATTAGATT 7 16 1 TCTAGAAATT 0.763963 -59 GCTTAAAACTTCTTACAATAATGGTC 8 5 0 TCTACAAAAT 0.953529 -180 GTTTTTTGACCATTGGCTCTATGC 9 55 0 TTTTGACATT 0.697549 -14 GTTATTATCGTCTATCACTAATAAAGACGTAA 11 77 1 TCTTCACAAT 0.978416 -224 AAGAGAAGAATTTAACACCAATGAAATATATT 11 153 1 TTTACACAAT 0.935984 -148 *** **** *** Masking position 7 Map Score: 5.63456 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 130 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 TTCTGGATCTAATGGTTAAACCATGAGATA 1 52 0 AATGGTTAAA 0.591547 -139 TATCTAGGTCTCTTGTTTAATATAAATTTG 1 170 0 TCTTGTTTAA 0.601461 -21 TTACAATGTTTAATTTTAAATTTAATGTCT 2 85 1 TAATTTTAAA 0.62834 -87 AACTCTTTGCTCTTTTTAAAATTGATCTTC 5 110 0 TCTTTTTAAA 0.925614 -191 CAATATTCGATCTGTTTAAAGAATGGCTAC 5 195 0 TCTGTTTAAA 0.898578 -106 AAGTAAAACATATTTTTGAATATATTCAAT 5 221 0 TATTTTTGAA 0.866735 -80 TGTCAACAATTATTTTTTAATTTTAAATAT 5 272 1 TATTTTTTAA 0.807864 -29 AAACTGCCTATATTTAAAATTAAAAAAT 5 283 0 TATATTTAAA 0.70453 -18 TTAATTAGCAAATTTTTAAAGTGCATCAAA 6 15 0 AATTTTTAAA 0.841266 -135 AATTTCATATTCTTTTTGAAGTCATCTCTA 6 96 1 TCTTTTTGAA 0.858805 -54 CATGTACCTTAATGTTTAAAGTGTGGTATT 11 233 0 AATGTTTAAA 0.79051 -68 ********** Masking position 9 Map Score: 4.43581 Number of sites scoring better than the average of aligned sites = 564 Number in coding regions = 329 Number in noncoding regions = 235 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 5 ATCCAGAAAAATATATTTAATTGGGTCCCGT 1 74 1 ATATATTAAT 0.970664 -117 AATGAATATATTAAATTATAAAAGCT 2 6 1 ATATATAAAT 0.779791 -166 TAATAAATGTATATACTTAGTAGTAAATATA 2 121 1 ATATATTAGT 0.906541 -51 ATCCATACAAATAAAATTAATAATATTTGTG 3 23 0 ATAAATTAAT 0.879265 -38 AACTCTTATATTTAATTATTGAATGA 4 19 0 TTATATTAAT 0.767516 -16 TCATATTGCTACATATTTAAGAGCTCGTAGC 5 81 0 ACATATTAAG 0.827966 -220 ATATTTTTGAATATATTCAATATTCGATCTG 5 211 0 ATATATCAAT 0.840531 -90 TCCAGTTCTTATAGAATTAATTAGCAAATTT 6 30 0 ATAGATTAAT 0.920256 -120 TATATCTAGTACATATTTAGTATTAGGAGTA 8 131 0 ACATATTAGT 0.898457 -54 TATGTACTAGATATAGTTAATAAACCACGGT 8 147 1 ATATATTAAT 0.970664 -38 TGTCCAAAATACAAATTTAATAACGCATAGA 9 31 1 ACAAATTAAT 0.871441 -38 TTTTTATATTACAGATTTAATTAATCTTAAT 11 122 1 ACAGATTAAT 0.913452 -179 AGCAAAATTAATATATTTCATTGGTGTTAAA 11 163 0 ATATATTCAT 0.83 -138 AGTAACATAATTAAATTTAATATTT 11 286 0 ACATATTAAA 0.764547 -15 ***** ***** Masking position 5 Map Score: 14.6009 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 145 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 6 TATAACTTTATTGTTGTATGAATCAATTTTT 1 16 1 TTGTTTATGA 0.715317 -175 AATCAACGCGTTCTCGTAATAAAGGCAAATT 1 145 1 TTCTCTAATA 0.943918 -46 AATGGCTACGTTGTCTTAATAAAGTTTGTAG 5 173 0 TTGTCTAATA 0.956723 -128 TATCAACAAATACTCCTAATACTAAATATGT 8 121 1 TACTCTAATA 0.879795 -64 ATGTGTTAGGTTGTCATATTATGCTTGACCA 10 22 1 TTGTCTATTA 0.966426 -71 TGTTAAATTCTTCTCTTATTAAGATTAATTA 11 139 0 TTCTCTATTA 0.956362 -162 AATATTTTATTAGTCATATGAATATCAATAT 11 197 0 TAGTCTATGA 0.893918 -104 ***** ***** Masking position 8 Map Score: 2.24183 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 49 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 GATATTGGTAACAAAACCAC 3 51 1 ACAAAACCAC 0.85441 -10 TTAATTATTGAATGAGACACAAA 4 4 0 AATGAGACAC 0.770638 -31 TGCTCTACCAACTGAGCTACGAGCTCTTAA 5 66 1 ACTGAGCTAC 0.936264 -235 AGCTTAACACAAAAAACTACAAACTTTATT 5 157 1 AAAAAACTAC 0.859321 -144 TGTCTTAGATACTAAACTACAATGACTA 6 132 1 ACTAAACTAC 0.942379 -18 AGATATAGTTAATAAACCACGGTGAAAATG 8 155 1 AATAAACCAC 0.942379 -30 TTTTTCCCATTATGAACTACTTCAAGTATT 11 47 1 TATGAACTAC 0.825871 -254 ATAAAATATTAATGAAATACCACACTTTAA 11 218 1 AATGAAATAC 0.858225 -83 ********** Masking position 5 Map Score: 1.69535 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 47 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 GACCCAATTAAATATATTTTTCTGGATCTA 1 71 0 AATATATTTT 0.614947 -120 CTGTTATTCAATTATTTATTCACGGGACCC 1 96 0 ATTATTTATT 0.805508 -95 ATAACGATTGAATATTTCTTTTTTAGTCTT 2 50 0 AATATTTCTT 0.830761 -122 TAAAATTAATAATATTTGTGTAAAAGACAT 3 13 0 AATATTTGTG 0.772253 -48 TATATTCAAAAATATGTTTTACTTTATCGC 5 227 1 AATATGTTTT 0.899379 -74 TCTGTCAACAATTATTTTTTAATTTTAAAT 5 270 1 ATTATTTTTT 0.850007 -31 GGAATCTCAGAATATTTGATTAGATTGGTA 7 22 1 AATATTTGAT 0.873133 -53 TGCTTGAAATAATATGTAAT 7 65 1 AATATGTAAT 0.67879 -10 AATTCCTAAGATTATGTGTTACTCAGTGCG 8 65 1 ATTATGTGTT 0.901498 -120 TAGTATTAGGAGTATTTGTTGATACCTAAA 8 115 0 AGTATTTGTT 0.833962 -70 GCTATGTTATTATGTGTTAGGTTGTCAT 10 9 1 ATTATGTGTT 0.901498 -84 GTATTTCATTAATATTTTATTAGTCATATG 11 208 0 AATATTTTAT 0.778141 -93 AATTAAATTTAATATTTATTATTACTGATC 11 273 0 AATATTTATT 0.867781 -28 ********** Masking position 4 Map Score: 8.95504 Number of sites scoring better than the average of aligned sites = 516 Number in coding regions = 352 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 9 ********** No masking Map Score: 2.1909e-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 10 ********** No masking Map Score: 2.1909e-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: 2.1909e-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