AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -icpxR9_rpxx_opreg_300.orf -g0.290 -x5 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 = 0 Input sequences: #1 RP025 90 unknown #2 RP069 266 DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE (dcd) #3 RP070 196 PROTEIN-EXPORT PROTEIN SECB (secB) #4 RP071 196 TRANSCRIPTIONAL ACTIVATOR PROTEIN CZCR (czcR) #5 RP122 98 HFLK PROTEIN (hflK) #6 RP123 143 HFLC PROTEIN (hflC) #7 RP124 30 PROBABLE PERIPLASMIC SERINE PROTEASE DO-LIKE PRECURSOR (htrA) #8 RP427 121 PETR PROTEIN (ompR) #9 RP780 245 unknown #10 RP782 175 unknown #11 RP784 254 VIRB4 PROTEIN PRECURSOR (virB4) #12 RP785 112 unknown #13 RP822 300 unknown Motif number 1 ATTTTGCTTCTATTATAAAGTATATATTTTTA 1 9 1 TATTATAATA 0.752591 -82 CAATTTTATTTCAATAAAAATATATACTTTATAA 1 23 0 TATAAAAATA 0.821088 -68 TATTGTAGAATGGTTAATAGTCAAAAGGAATAAA 1 66 1 TTTAATAGAA 0.833708 -25 ATTTATTATTTAAATAATATGGAATTATTAAA 2 9 0 TATAATATAA 0.892549 -258 TTCTGCAAAGTATATTATATTTTAGCGTAGTTGA 2 81 0 TATTATATTA 0.747383 -186 AAACTTTATTTAATTAATAAACTAATGATTATAA 2 238 0 TTTAATAATA 0.910201 -29 AATAGGTTCCTACATAAAAAAGAAG 3 2 0 TATAAAAAAA 0.694612 -195 TAAAAATTTTTAATTATTAGGCAAAATAAAATTG 3 128 1 TTTATTAGAA 0.53317 -69 AAAAATCCTTATTAAAAATTTAACATAATTTT 3 175 0 TTTAAAAATA 0.797691 -22 AATTATAAAATTTTTACTATTAAATTCTACCTTT 4 52 0 TTTACTATAA 0.527687 -145 CTTTATACGTTCATTAATAATATAAGTAAAGAAT 4 95 0 TTTAATAATA 0.938939 -102 TATAAAGCACTAGATAAAAAATTATAATTTAGTT 4 122 1 TATAAAAATA 0.815068 -75 ATTTAGTTAATAATTATTAACTAAATTATAATTT 4 140 0 TTTATTAAAA 0.642123 -57 AAATTCAATTTTGATAATAATTTAGTTAATAATT 4 159 0 TATAATAATA 0.92896 -38 TATTTTTCTCCATAAAATTCAATTTTGATAAT 4 175 0 TATAAAATAA 0.683167 -22 AGTGATTATATATATAATAGTATATAACGTCAAG 5 48 0 TATAATAGTA 0.918058 -51 TTGCTTTTTTATATTATTTTAAGATTAAGTG 5 78 0 TATATTATTA 0.788447 -21 TCCTTATTATTTTATAATATCATACTAAAAAAGC 6 113 0 TATAATATTA 0.942408 -31 TAAGTTATATTTATATTAGATTAGAAACTCATC 8 10 1 TATATTAGTA 0.71941 -112 GGGTTCAAAATTATTAATATCATAGTTGTTTTTG 8 65 0 TTTAATATTA 0.934883 -57 AATTTTTTGTGATTTTTATATTAAATTTTTAAA 9 10 1 TTTTTTATTA 0.406894 -236 GAACCAAAGATCCATAATATAAAAAGCTGAAGCT 9 111 1 TATAATATAA 0.892551 -135 CAGATATACTTGTTTAATATGAAAAATTGATACC 10 38 1 TTTAATATAA 0.879351 -138 TTATTATTTATATTTAATAAAGAA 11 1 0 TTTAATAAAA 0.859791 -254 TTATTAAATATAAATAATAAGGTAAAGTTTTTTG 11 15 1 TATAATAATA 0.945825 -240 TAAAGTTTTTTGTATAATAGTTTAATGTAAAATT 11 37 1 TATAATAGTA 0.918408 -218 AATTATAGATTTTTTACTATATTATTGCACCGAT 11 216 0 TTTACTATTA 0.687586 -39 AAATAACCTGATTTAAATTATAGATTTTTTAC 11 233 0 TTTTAAATTA 0.438735 -22 GTTTTTATAATTCATAATAAACTATCGTCATCCC 12 66 0 TATAATAATA 0.931039 -47 GAGTTTTTTTTGCTTTATAATGTACTCATTGTGT 13 190 1 TTTTATAATA 0.726752 -111 * ******* ** Masking position 9 Map Score: 32.5755 Number of sites scoring better than the average of aligned sites = 790 Number in coding regions = 474 Number in noncoding regions = 316 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 2 ATTTTTCTTTAAAAAATCTAAAACTACTTCCA 2 183 0 AAAAATCTAA 0.915571 -84 TTTTTTAAAGAAAAATTTTGTATTGTAAATAA 2 199 1 AAAAATTTTA 0.97478 -68 TTCTCACTTAAAAAGATTTTAATTAGCTTTAA 3 49 0 AAAAGTTTAA 0.891019 -148 ATCTTATTCAAAAAACTTCATAATTTCTCACT 3 73 0 AAAAATTCTA 0.839868 -124 CCTAATAATTAAAAATTTTTAAAGCAAAAATT 3 117 0 AAAAATTTAA 0.948254 -80 ATTTAATAGTAAAAATTTTATAATTTGATTAA 4 61 1 AAAAATTTTA 0.97478 -136 TAATTTGATTAAATATTCTTTACTTATATTAT 4 81 1 AAATATCTTA 0.620712 -116 AGCACTAGATAAAAAATTATAATTTAGTTAAT 4 127 1 AAAAATTAAA 0.747357 -70 ATCATACTAAAAAAGCCTTGTAAGAAGATCAA 6 97 0 AAAAGCTTTA 0.659402 -47 CGTATAATTTAAAAATTTAATATAAAAATCAC 9 19 0 AAAAATTATA 0.86188 -227 ATAGAACTCCAAAAATTTGCTAAGTCATCCTA 9 176 0 AAAAATTGTA 0.906123 -70 GAAATATGATAAAAGCTTTCTATACTCAGATA 9 205 0 AAAAGTTTTA 0.945228 -41 CAATTATTAAAAAAGGTTTATAATATTCAGAT 10 11 1 AAAAGTTTTA 0.945228 -165 GGAAAAGAATAAAAACGCTGTAAATTAAAAAT 11 140 1 AAAAAGCTTA 0.719547 -115 GTAATCCAGTAAAAATTTTTAATTTACAGCGT 11 154 0 AAAAATTTAA 0.948254 -101 ATAATATAGTAAAAAATCTATAATTTAAATCA 11 225 1 AAAAATCTTA 0.958046 -30 TTATTCACGTAAAAAATTTTAACTTCTACAAA 12 29 1 AAAAATTTAA 0.948105 -84 ATTTTTTGTAAAAAAGTTGCTATTACTTCCAC 13 129 0 AAAAATTGTA 0.906123 -172 ATAAAGCAAAAAAAACTCTATAGTCAAACTAT 13 176 0 AAAAATCTTA 0.958107 -125 ***** *** ** Masking position 3 Map Score: 26.4475 Number of sites scoring better than the average of aligned sites = 389 Number in coding regions = 229 Number in noncoding regions = 160 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 3 TTTAATAATTCCATATTATTT 2 2 1 TTAATAATTC 0.58812 -265 GTATAGTAAATTTATTATTTAAATAATATG 2 22 0 TTTATTATTT 0.859663 -245 AACTATTAAATTCTTAATTTTAAGTATATA 2 127 1 TTCTTAATTT 0.729538 -140 ATTATAACGCATAATTATTTACAATACAAA 2 215 0 ATAATTATTT 0.424997 -52 CCTATTCGCGATCTTAATTTTAAAGCTAAT 3 30 1 ATCTTAATTT 0.388345 -167 TTCAAAAAACTTCATAATTTCTCACTTAAA 3 69 0 TTCATAATTT 0.897888 -128 GATAAACATCTTATTAATTTTTGCTTTAAA 3 102 1 TTATTAATTT 0.713421 -95 TAGTAAAAATTTTATAATTTGATTAAATAT 4 67 1 TTTATAATTT 0.940595 -130 TATACGTTCATTAATAATATAAGTAAAGAA 4 96 0 TTAATAATAT 0.668946 -101 TATTAACTAAATTATAATTTTTTATCTAGT 4 130 0 ATTATAATTT 0.788453 -67 TTCAATTTTGATAATAATTTAGTTAATAAT 4 160 0 ATAATAATTT 0.656394 -37 TTGCTTTTTTATATTATTTTAAGA 5 85 0 TTTTTTATAT 0.318745 -14 TCCTTATTATTTTATAATATCATACTAAAA 6 117 0 TTTATAATAT 0.797669 -27 AACTATGATATTAATAATTTTGAACCCGTG 8 72 1 TTAATAATTT 0.890305 -50 TTAAAAAAGGTTTATAATATTCAGATATAC 10 17 1 TTTATAATAT 0.797669 -159 CTATCTACTTTTCATTATTTACTTATT 10 159 1 TTCATTATTT 0.772825 -17 CCAGTAAAAATTTTTAATTTACAGCGTTTT 11 151 0 TTTTTAATTT 0.829267 -104 TAGTAAAAAATCTATAATTTAAATCAGGTT 11 231 1 TCTATAATTT 0.590604 -24 GCTCGTTGTTTTTATAATTCATAATAAACT 12 77 0 TTTATAATTC 0.735843 -36 ATGATGATTTATTATTTGGTACTGTAT 13 8 1 TTTATTATTT 0.859663 -293 TATAGGATCTTTTATTATTTTTTGTAAAAA 13 147 0 TTTATTATTT 0.859663 -154 TTTTTTTTGCTTTATAATGTACTCATTGTG 13 193 1 TTTATAATGT 0.639767 -108 ********** Masking position 5 Map Score: 24.7438 Number of sites scoring better than the average of aligned sites = 909 Number in coding regions = 597 Number in noncoding regions = 312 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 4 AGAAACTCATCCCGTGGTTTGACCACGAAAGCCAA 8 33 1 CCGTGTTGCA 0.998024 -89 CATTTTACATCTCGTGGTTTGACCACGGGTTCAAA 8 90 0 CCGTGTTGCA 0.998024 -32 ACTCTTTTATCTCGTAACTTATTCACGTAAAAAAT 12 11 1 CCGTATTACA 0.937386 -102 ATTCTTGATGCTCGTTGTTTTTATAATTCATAATA 12 81 0 CCGTGTTTTA 0.937387 -32 AGTACTAATACCCGTGGCTTGACCACCGGTATCCA 13 229 1 CCGTGTTGCA 0.998024 -72 TTTGTGTCACCACGTAGATTGATCAGGTTGTCCAT 13 273 0 CCGTGTTGCA 0.998024 -28 * *** * *** ** Masking position 9 Map Score: 7.32521 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 2 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 AGAGTGTATCAATTTTATTTCAATAAAAATATATA 1 31 0 AATTTATATA 0.905218 -60 TTTTGTATAGTAAATTTATTATTTAAATAATATGG 2 21 0 TAATTTTTTA 0.698618 -246 AACTAATCTAAAAGTTTATTTTGTATAGTAAATTT 2 39 0 AAGTTTTTTA 0.710819 -228 AATAAACTTTTAGATTAGTTAATTAAATCAACTAC 2 54 1 TAATTATATA 0.848734 -213 TTAAATTCTTAATTTTAAGTATATAGCGTTGTATT 2 132 1 AATTTATTTA 0.913617 -135 AATCAAAACTTTATTTAATTAATAAACTAAT 2 246 0 AATTTATATA 0.905197 -21 TTGCTTTAAAAATTTTTAATTATTAGGCAAAATAA 3 122 1 AATTTTTATA 0.779925 -75 CTCTAAAAATTATGTTAAATTTTTAATAAGGATTT 3 170 1 TAGTTATTTA 0.797308 -27 AAAATTACCTAATTATCCAATAATA 4 1 1 AAATTATATA 0.905218 -196 TTATTAACTAAATTATAATTTTTTATCTAGTGCTT 4 126 0 AATATATTTA 0.585302 -71 AATTAAATTTCCTTTTTAAAGCTCTTTA 5 4 1 TAATTTTTTA 0.699743 -95 ATATTATTTTAAGATTAAGTGATTATATATATAAT 5 64 0 AAATTATATA 0.905218 -35 TAAGTTATATTTATATTAGATTAGA 8 1 1 TAGTTATTTA 0.797308 -121 TTGTGATTTTTATATTAAATTTTTAAATTATACGT 9 17 1 TAATTATTTA 0.862578 -229 CATATTAAACAAGTATATCTGAATATTATAAACCT 10 24 0 AATATATATA 0.560345 -152 TTATACAAAAAACTTTACCTTATTATTTATATTTA 11 19 0 AATTTATATA 0.905218 -236 AGTTTAATGTAAAATTAGCTATGTAGTAGCAATCA 11 55 1 AAATTATTTA 0.913617 -200 CAAAACTGATAATTTTTGATGACTAGGTATCGGTG 11 188 1 AATTTTTATA 0.779925 -67 GTGCAAAAAGTATATTATCTTTATATAGTTTATAT 13 69 1 TAATTATTTA 0.862643 -232 ** **** * * ** Masking position 6 Map Score: 19.0757 Number of sites scoring better than the average of aligned sites = 538 Number in coding regions = 282 Number in noncoding regions = 256 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 6 ATAATACAACGCTATATACTTAAAATTAAGA 2 138 0 GCTATATACT 0.840685 -129 ATTTTAATTAGCTTTAAAATTAAGATCGCGA 3 35 0 GCTTTAAAAT 0.962844 -162 ATTAATTTTTGCTTTAAAAATTTTTAATTAT 3 114 1 GCTTTAAAAT 0.962844 -83 TTGCGAACAGGCTCTAAAAATTATGTTAAAT 3 159 1 GCTCTAAAAT 0.88863 -38 TTTATCTAGTGCTTTATACGTTCATTAATAA 4 109 0 GCTTTATACT 0.962145 -88 AGCTTAAAGAGCTTTAAAAAGGAAATTTAAT 5 12 0 GCTTTAAAAG 0.936218 -87 TACTGCCTCAGCTTTATACATGTTATATACA 13 33 0 GCTTTATACT 0.962146 -268 AGTTTTTTTTGCTTTATAATGTACTCATTGT 13 191 1 GCTTTATAAG 0.936241 -110 ********* * Masking position 6 Map Score: 7.77849 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 49 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 CTATTAACCATTCTACAATAAGAGTGTATCA 1 55 0 TTTACAATAA 0.842605 -36 ATACAACGCTATATACTTAAAATTAAGAATT 2 135 0 ATTACTTAAA 0.486207 -132 ATCTAAAACTACTTCCATAAATATAGTGGTA 2 169 0 ACTCCATAAA 0.71488 -98 GCGAATAGGTTCCTACATAAAAAAGAAG 3 8 0 TCTACATAAA 0.913773 -189 GATGTTTATCTTATTCAAAAAACTTCATAAT 3 81 0 TTTTCAAAAA 0.739698 -116 AATTACCTAATTATCCAATAATATTGTTGTT 4 13 1 TTTCCAATAA 0.861096 -184 TATTTTTCTCCATAAAATTCAATTTT 4 181 0 TTTCCATAAA 0.943559 -16 TTTTATAATATCATACTAAAAAAGCCTTGTA 6 107 0 TCTACTAAAA 0.79717 -37 ATTTGCTAAGTCATCCTAAAAAAGTACGCAG 9 163 0 TCTCCTAAAA 0.820286 -83 CATTAAACTATTATACAAAAAACTTTACCTT 11 33 0 TTTACAAAAA 0.939405 -222 ACATAGCTAATTTTACATTAAACTATTATAC 11 48 0 TTTACATTAA 0.822221 -207 ATAGCAACTTTTTTACAAAAAATAATAAAAG 13 138 1 TTTACAAAAA 0.930852 -163 ATTGATCAGGTTGTCCATAAAAAAGACTGGA 13 260 0 TTTCCATAAA 0.943559 -41 ** ******** Masking position 10 Map Score: 9.27482 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 99 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 TTAGAAACTCATCCCGTGGTTTGACCACGA 8 31 1 ATCCCGTGGT 0.988006 -91 AATAATTTTGAACCCGTGGTCAAACCACGA 8 84 1 AACCCGTGGT 0.991247 -38 CTCATTTTACATCTCGTGGTTTGACCACGG 8 97 0 ATCTCGTGGT 0.944877 -25 TTAGTACTAATACCCGTGGCTTGACCACCG 13 227 1 TACCCGTGGC 0.976286 -74 AAAGACTGGATACCGGTGGTCAAGCCACGG 13 240 0 TACCGGTGGT 0.96291 -61 ********** Masking position 7 Map Score: 3.5375 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 1 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 TAGTAAATTTATTATTTAAATAATATGGAAT 2 18 0 ATTATTAAAT 0.930342 -249 TTTTAGATTAGTTAATTAAATCAACTACGCT 2 61 1 GTTATTAAAT 0.648943 -206 TCATTAGTTTATTAATTAAATAAAGTTTTGA 2 244 1 ATTATTAAAT 0.92266 -23 AAAATTACCTAATTATCCAATAAT 4 4 1 ATTACTAATT 0.633624 -193 TTAAATATTCTTTACTTATATTATTAATGAA 4 89 1 TTTATTATAT 0.495678 -108 GTTAATAATTATTAACTAAATTATAATTTTT 4 138 0 ATTACTAAAT 0.948834 -59 GTTAATAATTATTAACTAAATTATTATCAAA 4 153 1 ATTACTAAAT 0.948834 -44 TAACTAAATTATTATCAAAATTGAATTTTAT 4 165 1 ATTACAAAAT 0.752949 -32 GTTATATACTATTATATATATAATCACTTAA 5 54 1 ATTAATATAT 0.829141 -45 AATTAGATATATCATGCTAAAG 6 2 1 ATTAATATAT 0.829361 -142 CGGGTTCAAAATTATTAATATCATAGTTGTT 8 69 0 ATTATAATAT 0.634031 -53 ACTTTACCTTATTATTTATATTTAATAAAGA 11 12 0 ATTATTATAT 0.914668 -243 TTAATGTAAAATTAGCTATGTAGTAGCAATC 11 58 1 ATTACTATGT 0.66806 -197 TAAAAAATCTATAATTTAAATCAGGTTATTT 11 234 1 ATAATTAAAT 0.538486 -21 CAAAAAGTATATTATCTTTATATAGTTTATA 13 72 1 ATTACTTTAT 0.558937 -229 CATAAGGTACATTATATAAACTATATAAAGA 13 86 0 ATTAATAAAC 0.439626 -215 **** ****** Masking position 4 Map Score: 9.03373 Number of sites scoring better than the average of aligned sites = 392 Number in coding regions = 250 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 10 GTTAATTAAATCAACTACGCTAAAATATAATATAC 2 71 1 TCAATGAAAA 0.82974 -196 TTTCTTATTGTCAATTCTGCAAAGTATATTATATT 2 94 0 TCAATGAAGT 0.932614 -173 TTGTTGTTTTTCAATTAAAGGTAGAATTTAATAGT 4 36 1 TCAATATAGA 0.840795 -161 CGTTCATTAATAATATAAGTAAAGAATATTTAATC 4 87 0 TAATTGAAGA 0.773904 -110 TCCATAAAATTCAATTTTGATAATAATTTAGTTAA 4 164 0 TCAATGAATA 0.829538 -33 GATGTTCACATCATTTAGGATAAGATTTTATCTCA 6 39 1 TCATTGAAGA 0.956346 -105 TGTAAGAAGATCAACTTCAAAAAGAGCAAAGATCC 6 76 0 TCAATAAAGA 0.974969 -68 AGTGTATACCTCAAATAAATGAAGAGTAGTATAAG 9 61 1 TCAATAAAGA 0.976505 -185 AGTATAAGAATCAACTTCAGAAAGAACCAAAGATC 9 88 1 TCAATAAAGA 0.976465 -158 TATCAATTTTTCATATTAAACAAGTATATCTGAAT 10 35 0 TCATTAAAGT 0.803953 -141 GTACATTATATAAACTATATAAAGATAATATACTT 13 76 0 TAAATAAAGA 0.86493 -225 **** * * **** Masking position 3 Map Score: 7.75028 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 57 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 11 AAAAATTTTTAAAGCAAAAATTAATAAGAT 3 109 0 AAAGCAAAAA 0.968136 -88 AACTTCAAAAAGAGCAAAGATCCAATGAGA 6 69 0 AGAGCAAAGA 0.93661 -75 TTTGACCACGAAAGCCAAAAACAACTATGA 8 50 1 AAAGCCAAAA 0.931913 -72 GCAGTATCACAGTGCAAAAAGTATATTATC 13 58 1 AGTGCAAAAA 0.908834 -243 AGTACATTATAAAGCAAAAAAAACTCTATA 13 186 0 AAAGCAAAAA 0.968136 -115 ********** Masking position 7 Map Score: 1.4382 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 39 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 12 ********** No masking Map Score: -6.29951e-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 13 ********** No masking Map Score: -6.29951e-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 14 ********** No masking Map Score: -6.29951e-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