AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00330_rpxx_reg_100.orf -o00330_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 RP064 249 DEOXYGUANOSINETRIPHOSPHATE TRIPHOSPHOHYDROLASE (dgtP) #2 RP091 174 ASPARTATE AMINOTRANSFERASE A (aatA) #3 RP153 300 GLUTAMYL-tRNA AMIDOTRANSFERASE SUBUNIT C (gatC) #4 RP254 225 UDP-3-O-[3-HYDROXYMYRISTOYL] N-ACETYLGLUCOSAMINE DEACETYLASE (lpxC) #5 RP384 141 PROLYL-TRNA SYNTHETASE (proS) #6 RP541 62 3-OCTAPRENYL-4-HYDROXYBENZOATE CARBOXY-LYASE (ubiX) Motif number 1 ATTACCTTGTAAAAATCTTATAAATTATAT 1 16 1 AAAAATCTTA 0.942502 -234 CACCATCTTGAAAAATATTAAGATATATTA 1 45 0 AAAAATATTA 0.958427 -205 TTTTATCTTTAAAATTCTTGTATTTTAAGT 1 156 1 AAAATTCTTG 0.850716 -94 TTTTATTTAAAAATTTATTAAGATATGCTT 2 49 0 AAATTTATTA 0.935924 -126 TAATCTCAATAAAATTATTTTATTTAAAAA 2 66 0 AAAATTATTT 0.944438 -109 AAATAGGTAAAAAAATCTTAAGATCATTAT 3 15 1 AAAAATCTTA 0.942502 -286 GTAGACATTTAAAAGTATTTGAATCAATCT 3 57 1 AAAAGTATTT 0.789443 -244 TGTTTTAATTAAAAATAATATCTTGTAGTT 3 105 0 AAAAATAATA 0.839846 -196 AACAGTCGTTAAATTTCTTTTTTATGTTTT 3 129 0 AAATTTCTTT 0.867438 -172 ATTTTTACGTAAAAATAATAAAACT 3 286 1 AAAAATAATA 0.839846 -15 TATTTTGTTACAAAATATTACATAATCACC 4 149 0 CAAAATATTA 0.840319 -77 TATTTTGTAACAAAATATTATTTGTATAAT 4 162 1 CAAAATATTA 0.840319 -64 ATTAACATTTAAATATATTTAAACAACCTC 4 204 1 AAATATATTT 0.49646 -22 TGAAATAATAAAATTTATTAGATTGCTTCA 5 64 1 AAATTTATTA 0.935924 -78 TAATAATAGGAAAATTATTAAACTAAAACA 5 117 1 AAAATTATTA 0.962688 -25 AAAATTGTTTTAGTTTAATA 5 132 0 AAAATTGTTT 0.727673 -10 ATATAAATATATTTTATATTGTTT 6 5 1 AAATATATTT 0.49646 -58 ATTATATACTAAATTTAATGAATTAAAGAA 6 37 1 AAATTTAATG 0.518866 -26 TTAAATTTCTTTAATTCATTAA 6 51 0 AAATTTCTTT 0.867438 -12 ********** Masking position 6 Map Score: 25.5874 Number of sites scoring better than the average of aligned sites = 1344 Number in coding regions = 920 Number in noncoding regions = 424 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 2 ATATTAAGATATATTATATAATTTATAAGATTTTTAC 1 24 0 ATTTTTTTAA 0.947722 -226 CAAGATGGTGTTGTTTTGTAGTTTAGAAATTGCCATA 1 65 1 TTTTTTTTAA 0.970596 -185 CTAGATAATCAACTTTTATCTTTAAAATTCTTGTATT 1 143 1 AATTTTTAAA 0.814481 -107 AATTCTTGTATTTTAAGTTGCTTTATACTGTGATTAA 1 168 1 TTTGTTTTAA 0.776522 -82 AGTTATCCTTTGTTTTGTAAGGCATTGCC 1 231 0 TTTTTTTTGA 0.954546 -19 TTAATTACTAAATTCATATTATTTACACTATAATAAA 2 14 1 AATTTTTTAA 0.888812 -161 AATCTCAATAAAATTATTTTATTTAAAAATTTATTAA 2 58 0 AATTTTTTAA 0.888811 -117 TGAATTCGGATTCTTATATACTTTAGAATAACATTAA 2 120 0 TTTTTTTTAA 0.970595 -55 AACTTCTGTCATATAATGATCTTAAGATTTTTTTACC 3 20 0 ATTTATTAAA 0.556698 -281 ATTAAAAATAATATCTTGTAGTTTATATTCATTGATA 3 91 0 ATTTTTTTAA 0.947722 -210 AATTTCTTTTTTATGTTTTAATTAAAAATAATATCTT 3 111 0 TTTTTTTAAA 0.946483 -190 AAAAGCTAATTAGTTATTTTTCTAAAACTATCTTAAT 3 165 0 TATTTCTAAA 0.609332 -136 GATACAGTTGTTATACTATATTCTATATCCTATTTTA 3 216 0 TTTTTTCTAA 0.865616 -85 TGTATCCAAGTTCTAATTTTATCAGAATTACACAAGC 3 247 1 TTTTTTCAGA 0.47128 -54 CTAGCTTATGTTATGTTCTGCCTTGAACATAAGGTCC 4 71 0 TTTTTCTTGA 0.803848 -155 ACAATGGTGATTATGTAATATTTTGTAACAAAATATT 4 144 1 TTTATTTTGA 0.600394 -82 AACAAAATATTATTTGTATAATTTGCAATTAAATATT 4 170 1 TATTTTTTGA 0.902532 -56 ATTTGCAATTAAATATTAACATTTAAATATATTTAAA 4 190 1 AATTATTTAA 0.502111 -36 AGTTTAATAATTTTCCTATTATTATAAGGAAAAACCA 5 104 0 TTTTTTTATA 0.758324 -38 TAAATATATTTTATATTGTTTTTATTATATACTAAAT 6 14 1 TTTTTTTATA 0.75866 -49 ** * * * **** * Masking position 4 Map Score: 17.6213 Number of sites scoring better than the average of aligned sites = 1198 Number in coding regions = 747 Number in noncoding regions = 451 Number of orfs with sites within 600 bp upstream = 219 Fraction of orfs with sites within 600 bp upstream = 0.0351751 Motif number 3 TAAATTCATATTATTTACACTATAATAAAGCA 2 22 1 TTATTAACTA 0.962492 -153 TAAAATAATTTTATTGAGATTAAAATTGCTGT 2 74 1 TTATTAATTA 0.837236 -101 TTATCGTTTATTATTAATGTTATTCTAAAGTA 2 107 1 TTATTAGTTA 0.832764 -68 ATTAGTTATTTTTCTAAAACTATCTTAATTAT 3 162 0 TTTCTAACTA 0.879547 -139 TTTCATTAAGTCATAAAAGCTAATTAGTTATT 3 184 0 TCATAAGCTA 0.851902 -117 TTTATCAGAATTACACAAGCAAATTTTTACGT 3 264 1 TTACAAGCAA 0.895215 -37 CTGGAAATAATTACAGATACTATATAGTATCT 4 33 1 TTACAAACTA 0.976254 -193 TAAGGTCCAATTACAGATACTATATAGTATCT 4 47 0 TTACAAACTA 0.976254 -179 AGGCAGAACATAACATAAGCTAGACGTCTTGA 4 85 1 TAACAAGCTA 0.86754 -141 ACAACACCACTTATTGATGCTCACAATGGTGA 4 122 1 TTATTAGCTC 0.806176 -104 TAATTGCAAATTATACAAATAATATTTTGTTA 4 169 0 TTATAAATAA 0.536776 -57 CTAAATTGTGTTACTCATACTAGAGACAAATC 5 24 0 TTACTAACTA 0.972621 -118 ATATTGTTTTTATTATATACTAAATTTAATGA 6 26 1 TATTAAACTA 0.576447 -37 ***** * **** Masking position 7 Map Score: 6.42843 Number of sites scoring better than the average of aligned sites = 440 Number in coding regions = 308 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 4 TAGCTCCAATTTTTATTGCAGCTTAATCAC 1 197 0 TTTTATTGCA 0.96551 -53 AATAAAATTATTTTATTTAAAAATTTATTA 2 59 0 TTTTATTTAA 0.930978 -116 AATAAAATAATTTTATTGAGATTAAAATTG 2 72 1 TTTTATTGAG 0.734891 -103 AAGATATTATTTTTAATTAAAACATAAAAA 3 111 1 TTTTAATTAA 0.844069 -190 CTATATCCTATTTTATTTCATTAAGTCATA 3 201 0 TTTTATTTCA 0.962742 -100 ACAAATAATATTTTGTTACAAAATATTACA 4 157 0 TTTTGTTACA 0.770697 -69 AATGTTAATATTTAATTGCAAATTATACAA 4 183 0 TTTAATTGCA 0.873696 -43 TAATAAATTTTATTATTTCATGAGATTGCT 5 54 0 TATTATTTCA 0.766608 -88 AAACCATTAGTTTTGATGAAGCAATCTAAT 5 80 0 TTTTGATGAA 0.786031 -62 AAAATTGTTTTAGTTTAATAATTTTCCT 5 124 0 TTTAGTTTAA 0.678197 -18 TTAAATTTCTTTAATTCATTAAATTTAG 6 45 0 CTTTAATTCA 0.659759 -18 ********** Masking position 7 Map Score: 5.18695 Number of sites scoring better than the average of aligned sites = 668 Number in coding regions = 480 Number in noncoding regions = 188 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 5 CTTGAAAAATATTAAGATATATTATATAAT 1 39 0 ATTAAGATAT 0.939373 -211 TTAAGCTGCAATAAAAATTGGAGCTACATG 1 201 1 ATAAAAATTG 0.672359 -49 TTAAAAATTTATTAAGATATGCTTTATTAT 2 43 0 ATTAAGATAT 0.939373 -132 TTTTATTGAGATTAAAATTGCTGTATTATC 2 82 1 ATTAAAATTG 0.941693 -93 ACTAAAATAGGTAAAAAAAT 3 1 1 ACTAAAATAG 0.817656 -300 ATATAATGATCTTAAGATTTTTTTACCTAT 3 17 0 CTTAAGATTT 0.710603 -284 ATTATTTTTAATTAAAACATAAAAAAGAAA 3 116 1 ATTAAAACAT 0.729235 -185 TGTTTTGATAATTAAGATAGTTTTAGAAAA 3 155 1 ATTAAGATAG 0.954114 -146 GACTTAATGAAATAAAATAGGATATAGAAT 3 204 1 AATAAAATAG 0.842147 -97 GCAATTAAATATTAACATTTAAATATATTT 4 194 1 ATTAACATTT 0.787376 -32 CTCATGAAATAATAAAATTTATTAGATTGC 5 60 1 AATAAAATTT 0.769875 -82 ********** Masking position 5 Map Score: 6.17402 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 193 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 6 AGATATATTATATAATTTATAAGATTTTTAC 1 24 0 TATATTTATA 0.634487 -226 GGTGTTGTTTTGTAGTTTAGAAATTGCCATA 1 71 1 TGTATTTAGA 0.924215 -179 ACTAAATTCATATTATTTACACTATAATAAA 2 20 1 TATTTTTACA 0.802365 -155 CGGATTCTTATATACTTTAGAATAACATTAA 2 120 0 TATATTTAGA 0.960184 -55 AATAATATCTTGTAGTTTATATTCATTGATA 3 91 0 TGTATTTATA 0.788101 -210 GTTGTTATACTATATTCTATATCCTATTTTA 3 216 0 TATATCTATA 0.852001 -85 ATATTATTTGTATAATTTGCAATTAAATATT 4 176 1 TATATTTGCA 0.851831 -50 ATATAAATATATTTTATATTGTTTTTAT 6 8 1 TATATTTATA 0.925564 -55 **** ****** Masking position 11 Map Score: 6.00545 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 74 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 7 TATCTTAATATTTTTCAAGATGGTGTTGTT 1 50 1 TTTTTCAAGA 0.922092 -200 AAATACAAGAATTTTAAAGATAAAAGTTGA 1 151 0 ATTTTAAAGA 0.76632 -99 TATTTAAAAATTTATTAAGATATGCTTTAT 2 46 0 TTTATTAAGA 0.836525 -129 AACTATCTTAATTATCAAAACAGTCGTTAA 3 147 0 ATTATCAAAA 0.928175 -154 AAGTTCTAATTTTATCAGAATTACACAAGC 3 254 1 TTTATCAGAA 0.879455 -47 AGACAAATCGATTATCAAGATT 5 3 0 ATTATCAAGA 0.970664 -139 ATTAGATTGCTTCATCAAAACTAATGGTTT 5 80 1 TTCATCAAAA 0.773763 -62 TTTTCCTATTATTATAAGGAAAAACCATTA 5 101 0 ATTATAAGGA 0.836366 -41 ********** Masking position 7 Map Score: 2.24419 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 317 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 8 ACTGTATCTAGTGTTTTAAGCCAAGGTATA 1 107 0 GTGTTTTAAG 0.980963 -143 TAAAATTCTTGTATTTTAAGTTGCTTTATA 1 165 1 GTATTTTAAG 0.970857 -85 GTTATCCTTTGTTTTGTAAGGCATTGCCCA 1 229 0 GTTTTGTAAG 0.965055 -21 TCCGAATTCAGTATTTTAAGATTCTCAAAG 2 147 1 GTATTTTAAG 0.970857 -28 CGTTAAATTTCTTTTTTATGTTTTAATTAA 3 123 0 CTTTTTTATG 0.803684 -178 TCAATAAGTGGTGTTGTATGCTTCAAGACG 4 109 0 GTGTTGTATG 0.958153 -117 ********** Masking position 5 Map Score: 4.86515 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 30 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 TAAAAATCTTATAAATTATATAATATATCT 1 25 1 ATAAATTATA 0.840012 -225 ATGGCAATTTCTAAACTACAAAACAACACC 1 71 0 CTAAACTACA 0.832894 -179 GCCTTACAAAACAAAGGATAACT 1 237 1 ACAAAGGATA 0.783791 -13 TTACACTATAATAAAGCATATCTTAATAAA 2 36 1 ATAAAGCATA 0.893966 -139 AACATTAATAATAAACGATAATACAGCAAT 2 98 0 ATAAACGATA 0.921953 -77 TAATGTTATTCTAAAGTATATAAGAATCCG 2 121 1 CTAAAGTATA 0.930523 -54 ATCAATGAATATAAACTACAAGATATTATT 3 92 1 ATAAACTACA 0.910688 -209 AGGATATAGAATATAGTATAACAACTGTAT 3 222 1 ATATAGTATA 0.812008 -79 TAAAAACAATATAAAATATATTTATAT 6 8 0 ATAAAATATA 0.840012 -55 ********** Masking position 5 Map Score: 3.33321 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 174 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 10 ********** No masking Map Score: -1.50392e-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: -1.50392e-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: -1.50392e-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