AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00340_rpxx_reg_100.orf -o00340_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 RP009 300 UDP-3-O-[3-HYDROXYMYRISTOYL] GLUCOSAMINE N-ACYLTRANSFERASE (lpxD) #2 RP254 225 UDP-3-O-[3-HYDROXYMYRISTOYL] N-ACETYLGLUCOSAMINE DEACETYLASE (lpxC) #3 RP307 130 CATIONIC AMINO ACID TRANSPORTER-1 (atrc1) #4 RP308 80 HISTIDYL-TRNA SYNTHETASE (hisS) #5 RP366 75 APOLIPOPROTEIN N-ACYLTRANSFERASE (lnt) #6 RP680 185 UBIQUINONE/MENAQUINONE BIOSYNTHESIS METHLYTRANSFERASE UBIE (ubiE) #7 RP719 300 unknown Motif number 1 ACTAATATAGTAATTTTAAACTAAATTTGAGATTCAAGT 1 147 0 TAATATATTG 0.900232 -154 TATTGCATAATAAAAGCATAACTTATATAATATCGCTAG 1 249 1 TAAGACAATA 0.812095 -52 CTACTGGAAATAATTACAGATACTATATAGTATCTGTAA 2 30 1 TAAAAAAATA 0.798703 -196 GCCTTGAACATAAGGTCCAATTACAGATACTATATAGTA 2 50 0 TAATATAATA 0.967995 -176 TGTTAATATTTAATTGCAAATTATACAAATAATATTTTG 2 172 0 TAAGATAAAA 0.888425 -54 AATTAAATATTAACATTTAAATATATTTAAACAACCTCG 2 196 1 TAATATATTA 0.919582 -30 ACAATTAGAATAAGCTTGAAATGGATATAATTGCCAAAC 3 35 0 TAATATAATA 0.967997 -96 CTAAAATTCCTAATAAAGCAATACAATTAGAATAAGCTT 3 57 0 TAAAATATTA 0.940082 -74 TAATAAAGAATAATGAAAAAATGTAATTGAAGTT 4 6 0 TAAAATATTG 0.928617 -75 ACTCTTGCCATAACTATTTAATCCACATAACACAATAAA 4 52 1 TAAAATAATA 0.976103 -29 TATTATTTTGTAAACAAATAATCGATAAAA 5 56 1 TAAAATAAAA 0.91801 -20 GATTACAAGCTAAAAAAGCAGTGTAGATATATGTCCCAG 7 18 1 TAAAATAATA 0.976529 -283 TAAGTGAGGTTAATTTATCAGTATACAAGGAAAAACAGG 7 175 1 TAATATAAAG 0.869792 -126 TTATCTAATATAATCGTAAAATGCAAATGTTCTTCCGTA 7 220 0 TAAGATAATG 0.960552 -81 TTATATTAGATAATAAAGCAATAAATATGTTTGACTTTA 7 246 1 TAAAATAATG 0.971591 -55 *** * * * * *** Masking position 10 Map Score: 15.7739 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 107 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 2 TATATAAGTTATGCTTTTATTATGCAATAAAATTGTAAGT 1 238 0 ATGTTTGAAA 0.930456 -63 AATGGTGATTATGTAATATTTTGTAACAAAATATTATTTG 2 146 1 ATGATTTAAA 0.981531 -80 ATTCTCGTATATGCTAAAATTCCTAATAAAGCAATACAAT 3 69 0 ATGATTTAAA 0.981531 -62 ATATACGAGAATGGAGATATTACTCACTAAAATAGGAGAA 3 97 1 ATGTTTTAAA 0.974751 -34 TAGTTATGGCAAGAGTATATTTATAATAAAGAATAATGAA 4 28 0 AAGTTTTAAA 0.817235 -53 TGATAGCATGATGTATTATTTTGTAAACAAATAATCGATA 5 43 1 ATGATTTAAA 0.981531 -33 TGATCCACGCATGTAATATTTGCTTACAATA 6 2 0 ATGATTTAAT 0.964991 -184 GTGTAGATATATGTCCCAGTTAGTGAAATTCTTGAAAAGA 7 38 1 ATGATTTATT 0.761488 -263 TCTTGAAAAGATGTAAGAGTTAATAATTATGGGAATTGTA 7 67 1 ATGATTTAAT 0.96499 -234 TTTCGTTTAAATGAGCATATTTCGTAACAAATTTTAATCC 7 110 0 ATGTTTGAAA 0.930453 -191 TAATCGTAAAATGCAAATGTTCTTCCGTATCATTACCTGT 7 209 0 ATGTTTTCAT 0.790358 -92 AGCAATAAATATGTTTGACTTTATTTTTAATTGCTGTAAA 7 262 1 ATGATTTTAA 0.871013 -39 *** * ** * * ** Masking position 1 Map Score: 12.8962 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 118 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 3 TATAAAAATACTAATATAGTAATTTTAAAC 1 165 0 CTAATATAGT 0.83185 -136 CATAACTTATATAATATCGCTAGTGATTAA 1 265 1 ATAATATCGC 0.819353 -36 GCTAAAATTCCTAATAAAGCAATACAATTA 3 67 0 CTAATAAAGC 0.986433 -64 ATATTACTCACTAAAATAGGAGAAACTA 3 113 1 CTAAAATAGG 0.856145 -18 GAGTATATTTATAATAAAGAATAATGAAAA 4 26 0 ATAATAAAGA 0.827592 -55 TTGATCTATGCTAAAAAAGCTTAATGTGCA 6 105 1 CTAAAAAAGC 0.983338 -81 AAGCATTATCATAAAAAAGCTTGCACATTA 6 126 0 ATAAAAAAGC 0.967781 -60 TGATTACAAGCTAAAAAAGCAGTGTAGATA 7 17 1 CTAAAAAAGC 0.983338 -284 ATTATATTAGATAATAAAGCAATAAATATG 7 245 1 ATAATAAAGC 0.973689 -56 ********** Masking position 6 Map Score: 10.9359 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 94 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 CTAAGTAATCTCTAAATAAAAGAACTACACA 1 28 1 TCAAATAAAA 0.818556 -273 TGTGAGAAATTTAAATTAATAATATTGATTT 1 92 0 TTAATTAATA 0.611488 -209 CATGTTCTACTTCAATTAATAACTTGAATCT 1 126 1 TTAATTAATA 0.611549 -175 ATATTTTGTTACAAAATATTACATAATCACC 2 149 0 ACAAATATTA 0.943739 -77 ATATTTTGTAACAAAATATTATTTGTATAAT 2 161 1 ACAAATATTA 0.943739 -65 ATAATTTGCAATTAAATATTAACATTTAAAT 2 187 1 ATAAATATTA 0.895153 -39 TTTCAGCAAGTTTAAATATAATGAGTAAATA 5 12 0 TTAAATATAA 0.696303 -64 TTATTTGTTTACAAAATAATACATCATGCTA 5 46 0 ACAAATAATA 0.943739 -30 TATTGTAAGCAAATATTACATGCGTGGA 6 8 1 AGAAATATTA 0.911584 -178 GCTCATTTAAACGAAATATTAGTTAATGCAG 7 134 1 ACAAATATTA 0.943739 -167 TAGTTAATGCAGGAAATAAAATTAAGTGAGG 7 153 1 AGAAATAAAA 0.842455 -148 TATGATTTACAGCAATTAAAAATAAAGTCAA 7 276 0 AGAATTAAAA 0.655312 -25 ** ******** Masking position 5 Map Score: 9.07977 Number of sites scoring better than the average of aligned sites = 582 Number in coding regions = 369 Number in noncoding regions = 213 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 5 AAATCAATATTATTAATTTAAATTTCTCACA 1 92 1 TATAATTTAA 0.650947 -209 AGATTCAAGTTATTAATTGAAGTAGAACATG 1 126 0 TATAATTGAA 0.748347 -175 AATACTAATATAGTAATTTTAAACTAAATTT 1 158 0 TAGAATTTTA 0.952919 -143 ATTACTATATTAGTATTTTTATAGTCAAGTC 1 172 1 TAGATTTTTA 0.922658 -129 AGATACTATATAGTATCTGTAATTATTTCCA 2 34 0 TAGATCTGTA 0.880702 -192 AGATACTATATAGTATCTGTAATTGGACCTT 2 47 1 TAGATCTGTA 0.880702 -179 TGTAACAAAATATTATTTGTATAATTTGCAA 2 167 1 TATATTTGTA 0.872882 -59 AACTATGGTGTATCAATTTTACTTAAT 3 7 0 TATAATTTTA 0.880702 -124 CACCATAGTTTGGCAATTATATCCATTTCAA 3 28 1 TGGAATTATA 0.659407 -103 ATTGCTTTATTAGGAATTTTAGCATATACGA 3 74 1 TAGAATTTTA 0.952919 -57 TTAATAATTATGGGAATTGTATTGGGATTAA 7 86 1 TGGAATTGTA 0.926039 -215 *** ******* Masking position 5 Map Score: 8.36295 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 267 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 6 TATCTATGAATACTAAGTAATCTCTAAATAA 1 16 1 TATAAGTAAT 0.841324 -285 AAATTAATAATATTGATTTATTTGAGATTCA 1 80 0 TATGATTTAT 0.927425 -221 AAATCAATATTATTAATTTAAATTTCTCACA 1 92 1 TATAATTTAA 0.426022 -209 GTTATGCTTTTATTATGCAATAAAATTGTAA 1 240 0 TATATGCAAT 0.581284 -61 ATAATATCGCTAGTGATTAAGTCAGTTAAAG 1 275 1 TATGATTAAG 0.85364 -26 ATTTAAATGTTAATATTTAATTGCAAATTAT 2 187 0 TATATTTAAT 0.693508 -39 ATTCTAATTGTATTGCTTTATTAGGAATTTT 3 63 1 TATGCTTTAT 0.846027 -68 TCTCCTATTTTAGTGAGTAATATCTCCATTC 3 105 0 TATGAGTAAT 0.953387 -26 TTTATTGTGTTATGTGGATTAAA 4 68 0 TATGTGTTAT 0.889563 -13 AGTTTAAATATAATGAGTAAATAA 5 4 0 TATGAGTAAA 0.820872 -72 TAGGTAAAACTATTGATCTATGCTAAAAAAG 6 93 1 TATGATCTAT 0.86579 -93 TAAAAAAGCTTAATGTGCAAGCTTTTTTATG 6 116 1 TATGTGCAAG 0.649855 -70 TTTCCTTGTATACTGATAAATTAACCTCACT 7 177 0 TATGATAAAT 0.681358 -124 CAAACATATTTATTGCTTTATTATCTAATAT 7 248 0 TATGCTTTAT 0.846027 -53 ** ******** Masking position 2 Map Score: 7.18972 Number of sites scoring better than the average of aligned sites = 510 Number in coding regions = 342 Number in noncoding regions = 168 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 7 ATTGATTTATTTGAGATTCATCTTTGAATAG 1 69 0 TTGAGTTCAT 0.874888 -232 TAAACTAAATTTGAGATTCAAGTTATTAATT 1 139 0 TTGAGTTCAA 0.922275 -162 AAGTGGTGTTGTATGCTTCAAGACGTCTAGC 2 103 0 GTATGTTCAA 0.84832 -123 AATCACCATTGTGAGCATCAATAAGTGGTGT 2 125 0 GTGAGATCAA 0.978856 -101 TGCCAAACTATGGTGTATCAATTTTACTTAA 3 12 0 TGGTGATCAA 0.85759 -119 AATATTACATGCGTGGATCAATCATAAATAT 6 22 1 GCGTGATCAA 0.939063 -164 AGTATAAACAGTGTGAATCAAGTACTTTAAC 6 161 0 GTGTGATCAA 0.980366 -25 ATAAAATTAAGTGAGGTTAATTTATCAGTAT 7 168 1 GTGAGTTAAT 0.671856 -133 ***** ***** Masking position 10 Map Score: 2.67789 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 37 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 TCACATTACATGTTCTACTTCAATTAATAA 1 118 1 TGTTCTACTT 0.912064 -183 ATATTATATAAGTTATGCTTTTATTATGCA 1 252 0 AGTTATGCTT 0.68287 -49 GCTTATGTTATGTTCTGCCTTGAACATAAG 2 75 0 TGTTCTGCCT 0.969736 -151 TTATTCTAATTGTATTGCTTTATTAGGAAT 3 61 1 TGTATTGCTT 0.723985 -70 TAGTTTCTCCTATTTTAGTGA 3 120 0 AGTTTCTCCT 0.743365 -11 ATAGATCAATAGTTTTACCTACATAACATT 6 84 0 AGTTTTACCT 0.915935 -102 TATCATTACCTGTTTTTCCTTGTATACTGA 7 192 0 TGTTTTTCCT 0.954107 -109 AAAATGCAAATGTTCTTCCGTATCATTACC 7 212 0 TGTTCTTCCG 0.826424 -89 GCAATAAATATGTTTGACTTTATTTTTAAT 7 263 1 TGTTTGACTT 0.737572 -38 ********** Masking position 3 Map Score: 0.966045 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 160 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 AACTACACAAAAACCTTAGCTATTCAAAGAT 1 50 1 AAACCTTACT 0.846539 -251 GTTCTACTTCAATTAATAACTTGAATCTCAA 1 129 1 AATTAATACT 0.773807 -172 CTAATATAGTAATTTTAAACTAAATTTGAGA 1 154 0 AATTTTAACT 0.68232 -147 ATAAACTTTAACTGACTTAATCA 1 288 0 AAACTTTACT 0.867742 -13 AGGCAGAACATAACATAAGCTAGACGTCTTG 2 85 1 TAACATAACT 0.748225 -141 TTTAGCTTGTAATCAATACCT 7 1 0 AATCAATACT 0.915242 -300 CAATTCCCATAATTATTAACTCTTACATCTT 7 74 0 AATTATTACT 0.915814 -227 TGTTCTTCCGTATCATTACCTGTTTTTCCTT 7 201 0 TATCATTACT 0.915254 -100 AATTGCTGTAAATCATAAACT 7 290 1 AATCATAACT 0.947139 -11 ******** ** Masking position 8 Map Score: 2.70618 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 166 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 10 ********** No masking Map Score: -3.03101e-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 11 ********** No masking Map Score: -3.03101e-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 12 ********** No masking Map Score: -3.03101e-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