AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -icpxR6_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 RP822 300 unknown Motif number 1 CAATAAAAATATATACTTTATAATAGAAGCAA 1 14 0 ATATATTATA 0.810378 -77 ATTCCATATTATTTAAATAATAAATTTACTAT 2 18 1 ATTTATAATA 0.93122 -249 AGAAACTATTAAATTCTTAATTTTAAGTATAT 2 124 1 AAATTTAATT 0.909252 -143 TTCCATAAATATAGTGGTAATAATACAACGCT 2 156 0 ATAGTTAATA 0.764569 -111 TCAAAACTTTATTTAATTAATAAACTAATGAT 2 243 0 ATTTATAATA 0.93122 -24 TTATTCAAAAAACTTCATAATTTCTCACTTAA 3 70 0 AACTTTAATT 0.736202 -127 TAAGATAAACATCTTATTAATTTTTGCTTTAA 3 99 1 ATCTTTAATT 0.878584 -98 TTTGCTTTAAAAATTTTTAATTATTAGGCAAA 3 121 1 AAATTTAATT 0.909252 -76 AAATTATGTTAAATTTTTAATAAGGATTTTT 3 176 1 AAATTTAATA 0.932339 -21 ATTATTGGATAATTAGGTAATTTT 4 3 0 AATTATAATT 0.480052 -194 TAATAGTAAAAATTTTATAATTTGATTAAATA 4 64 1 AATTTTAATT 0.809086 -133 TTCTTTACTTATATTATTAATGAACGTATAAA 4 96 1 ATATTTAATG 0.848984 -101 AAAAATTATAATTTAGTTAATAATTATTAACT 4 138 1 ATTTATAATA 0.93122 -59 TTTGATAATAATTTAGTTAATAATTATTAACT 4 152 0 ATTTATAATA 0.93122 -45 ATAAAATTCAATTTTGATAATAATTTAGTTAA 4 164 0 ATTTTTAATA 0.951389 -33 TTAAGTGATTATATATATAATAGTATATAACG 5 53 0 ATATATAATA 0.961389 -46 CTTTAGCATGATATATCTAATT 6 1 0 ATATATAATT 0.946252 -143 TTAATATTCCTTATTATTTTATAAT 6 129 0 ATATTTTATT 0.82209 -15 TAAGTTATATTTATATTAGATTAGAAAC 8 7 1 ATATTTATTA 0.696879 -115 AACAACTATGATATTAATAATTTTGAACCCGT 8 69 1 ATATTTAATT 0.964183 -53 TATTATCTTTATATAGTTTATATAATGTACCT 9 81 1 ATATATTATA 0.810378 -220 CTCATTGTGTATATTAGTACTAATACCCGTGG 9 214 1 ATATTTACTA 0.773111 -87 ***** ***** Masking position 8 Map Score: 24.9138 Number of sites scoring better than the average of aligned sites = 1181 Number in coding regions = 738 Number in noncoding regions = 443 Number of orfs with sites within 600 bp upstream = 212 Fraction of orfs with sites within 600 bp upstream = 0.0340508 Motif number 2 GTGTATCAATTTTATTTCAATAAAAATATATACTTTA 1 26 0 TTTATTAAAT 0.624402 -65 CTAAAAGTTTATTTTGTATAGTAAATTTATTATTTAA 2 30 0 ATTTTTAAAT 0.851953 -237 ATAGCGTTGTATTATTACCACTATATTTATGGAAGTA 2 154 1 ATTATAATAT 0.735129 -113 TAGTTTTAGATTTTTTAAAGAAAAATTTTGTATTGTA 2 189 1 TTTTTAAAAT 0.943753 -78 ATCAAAACTTTATTTAATTAATAAACTAATGATTATA 2 239 0 TATTTAAAAT 0.631598 -28 CTTCTTTTTTATGTAGGAACCTATTCGCGATC 3 6 1 TTTTTTAACT 0.82378 -191 TAAAAAGATTTTAATTAGCTTTAAAATTAAGATCGCG 3 36 0 TTAATAAAAT 0.479117 -161 AATTAAAATCTTTTTAAGTGAGAAATTATGAAGTTTT 3 57 1 TTTTTAAAAT 0.943753 -140 ATTATGAAGTTTTTTGAATAAGATAAACATCTTATTA 3 81 1 TTTTTAATAA 0.492815 -116 TAATTAAAAATTTTTAAAGCAAAAATTAATAAGATGT 3 107 0 TTTTTAAAAT 0.943753 -90 GTTCGCAATTTTATTTTGCCTAATAATTAAAAATTTT 3 130 0 TTATTTATAT 0.601694 -67 TTATGTTAAATTTTTAATAAGGATTTTT 3 179 1 TTTTTAATTT 0.629195 -18 AAATTATAAAATTTTTACTATTAAATTCTACCTTTAA 4 50 0 ATTTTAAAAT 0.660109 -147 TATTTTTCTCCATAAAATTCAATTTTGAT 4 178 0 TTTTTTAAAT 0.906717 -19 AGATTAAGTGATTATATATATAATAGTATATAACGTC 5 51 0 ATTATTATAT 0.597492 -48 ATCTTTGCTCTTTTTGAAGTTGATCTTCTTACAAGGC 6 78 1 TTTTTAATCT 0.870669 -66 CTTACAAGGCTTTTTTAGTATGATATTATAAAATAAT 6 105 1 TTTTTAATAT 0.947666 -39 CGGGTTCAAAATTATTAATATCATAGTTGTTTTTGGC 8 63 0 ATTATAATAT 0.710314 -59 ATAATATACTTTTTGCACTGTGATACTGCCTCAGCTT 9 50 0 TTTTGAATAT 0.683621 -251 ATCTTTTATTATTTTTTGTAAAAAAGTTGCTATTACT 9 134 0 ATTTTTAAAT 0.797504 -167 ACTATAGAGTTTTTTTTGCTTTATAATGTACTCATTG 9 184 1 TTTTTTATAT 0.797442 -117 GTATCCAGTCTTTTTTATGGACAACCTGATCAATCTA 9 257 1 TTTTTAAACT 0.889427 -44 ***** * *** * Masking position 13 Map Score: 22.0784 Number of sites scoring better than the average of aligned sites = 1051 Number in coding regions = 652 Number in noncoding regions = 399 Number of orfs with sites within 600 bp upstream = 187 Fraction of orfs with sites within 600 bp upstream = 0.0300353 Motif number 3 AATTTATTATTTAAATAATATGGAATTATTA 2 13 0 TTAAATAATT 0.858888 -254 ATTTACTATACAAAATAAACTTTTAGATTAG 2 41 1 CAAAATAAAT 0.872486 -226 GATTAGTTAATTAAATCAACTACGCTAAAAT 2 66 1 TTAAATCAAT 0.736176 -201 TCAACTACGCTAAAATATAATATACTTTGCA 2 81 1 TAAAATATAT 0.872439 -186 AAATTTTTCTTTAAAAAATCTAAAACTACTT 2 186 0 TTAAAAAATT 0.811871 -81 AGTTTATTAATTAAATAAAGTTTTGATT 2 249 1 TTAAATAAAT 0.844547 -18 TAAAGCTAATTAAAATCTTTTTAAGTGAGAA 3 50 1 TAAAATCTTT 0.797389 -147 AATTTTTGCTTTAAAAATTTTTAATTATTAG 3 117 1 TTAAAAATTT 0.793897 -80 AATTATTAGGCAAAATAAAATTGCGAACAGG 3 139 1 CAAAATAAAT 0.872486 -58 CGAACAGGCTCTAAAAATTATGTTAAATTTT 3 162 1 CTAAAAATTT 0.774758 -35 TATAATTTGATTAAATATTCTTTACTTATAT 4 79 1 TTAAATATTT 0.844547 -118 AAGCACTAGATAAAAAATTATAATTTAGTTA 4 126 1 TAAAAAATTT 0.844546 -71 CACTTAATCTTAAAATAATATAAAAAAGCAA 5 78 1 TAAAATAATT 0.895665 -21 TCCAATGAGATAAAATCTTATCCTAAATGAT 6 48 0 TAAAATCTTT 0.797389 -96 CCACGAAAGCCAAAAACAACTATGATATTAA 8 55 1 CAAAAACAAT 0.713611 -67 AACTTTTTTACAAAAAATAATAAAAGATCCT 9 143 1 CAAAAAATAT 0.812391 -158 CATTATAAAGCAAAAAAAACTCTATAGTCAA 9 181 0 CAAAAAAAAT 0.829098 -120 ********* * Masking position 5 Map Score: 16.8255 Number of sites scoring better than the average of aligned sites = 1523 Number in coding regions = 1026 Number in noncoding regions = 497 Number of orfs with sites within 600 bp upstream = 228 Fraction of orfs with sites within 600 bp upstream = 0.0366206 Motif number 4 TGGCTTTCGTGGTCAAACCACGGGATGAGTTTCT 8 33 0 GTCAACACGG 0.998743 -89 TTGAACCCGTGGTCAAACCACGAGATGTAAAATG 8 91 1 GTCAACACGG 0.998743 -31 GGATACCGGTGGTCAAGCCACGGGTATTAGTACT 9 229 0 GTCAACACGG 0.998743 -72 TGGACAACCTGATCAATCTACGTGGTGACACAAA 9 274 1 GTCAACACGG 0.998743 -27 * **** * *** * Masking position 6 Map Score: 7.62513 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 5 AGTAGTTTTAGATTTTTTAAAGAAAAATTT 2 187 1 GATTTTTTAA 0.515128 -80 CTTCTTTTTTATGTAGGAACCT 3 3 1 TCTTTTTTAT 0.922075 -194 CTAATTAAAATCTTTTTAAGTGAGAAATTA 3 55 1 TCTTTTTAAG 0.863865 -142 AAGATAAACATCTTATTAATTTTTGCTTTA 3 100 1 TCTTATTAAT 0.368268 -97 CCTTTTTAAAGCTCTTTAAGCTGGTAACTT 5 21 1 GCTCTTTAAG 0.889643 -78 TTGCTTTTTTATATTATTTTAA 5 87 0 GCTTTTTTAT 0.967509 -12 TTGGATCTTTGCTCTTTTTGAAGTTGATCT 6 74 1 GCTCTTTTTG 0.780538 -70 TTCTTACAAGGCTTTTTTAGTATGATATTA 6 103 1 GCTTTTTTAG 0.971826 -41 TTTACTGTCGTCTTTATTTGGAGTAT 7 15 1 TCTTTATTTG 0.473354 -16 ATGATGATTTATTATTTGGTACTGT 9 6 1 GATTTATTAT 0.655562 -295 AACTATATAGGATCTTTTATTATTTTTTGT 9 152 0 GATCTTTTAT 0.749548 -149 AGTTTTTTTTGCTTTATAATGTACTCATTG 9 191 1 GCTTTATAAT 0.815693 -110 CGGTATCCAGTCTTTTTTATGGACAACCTG 9 255 1 TCTTTTTTAT 0.922075 -46 ********** Masking position 7 Map Score: 7.70599 Number of sites scoring better than the average of aligned sites = 731 Number in coding regions = 556 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 6 TCGTGGTCAAACCACGGGATGAGTTTCTAA 8 31 0 ACCACGGGAT 0.991056 -91 TCGTGGTTTGACCACGGGTTCAAAATTATT 8 84 0 ACCACGGGTT 0.993204 -38 CCGTGGTCAAACCACGAGATGTAAAATGAG 8 97 1 ACCACGAGAT 0.962 -25 CGGTGGTCAAGCCACGGGTATTAGTACTAA 9 227 0 GCCACGGGTA 0.984232 -74 CCGTGGCTTGACCACCGGTATCCAGTCTTT 9 240 1 ACCACCGGTA 0.975233 -61 ********** Masking position 4 Map Score: 5.74613 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 7 TCTATTATAAAGTATATATTTTTATTGAAA 1 19 1 AGTATATATT 0.705837 -72 AATTCTGCAAAGTATATTATATTTTAGCGT 2 87 0 AGTATATTAT 0.941085 -180 CTTAATTTTAAGTATATAGCGTTGTATTAT 2 139 1 AGTATATAGC 0.730446 -128 AATTTTGTATTGTAAATAATTATGCGTTAT 2 212 1 TGTAAATAAT 0.745266 -55 TATATATAATAGTATATAACGTCAAGTTAC 5 44 0 AGTATATAAC 0.930329 -55 TAAGTGATTATATATATAATAGTATATAAC 5 54 0 TATATATAAT 0.657262 -45 TTGCTTTTTTATATTATTTTAAGATTA 5 82 0 TTTATATTAT 0.718115 -17 TATTTGGTACTGTATATAACATGTATAAAG 9 23 1 TGTATATAAC 0.934996 -278 CAGTGCAAAAAGTATATTATCTTTATATAG 9 67 1 AGTATATTAT 0.941085 -234 CTTTATATAGTTTATATAATGTACCTTATG 9 87 1 TTTATATAAT 0.700838 -214 ATACACAATGAGTACATTATAAAGCAAAAA 9 196 0 AGTACATTAT 0.759046 -105 GTACTCATTGTGTATATTAGTACTAATACC 9 211 1 TGTATATTAG 0.796306 -90 ********** Masking position 6 Map Score: 6.33927 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 171 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 8 TAATAAATTTACTATACAAAATAAACTTTT 2 35 1 ACTATACAAA 0.931406 -232 ATAATTATTTACAATACAAAATTTTTCTTT 2 205 0 ACAATACAAA 0.946484 -62 AGTTTTTTGAATAAGATAAACATCTTATTA 3 88 1 ATAAGATAAA 0.828302 -109 CGTATAAAGCACTAGATAAAAAATTATAAT 4 120 1 ACTAGATAAA 0.931409 -77 TAATCTTAAAATAATATAAAAAAGCAA 5 82 1 ATAATATAAA 0.877231 -17 CATTATATAAACTATATAAAGATAATATAC 9 78 0 ACTATATAAA 0.952397 -223 CACAATGAGTACATTATAAAGCAAAAAAAA 9 193 0 ACATTATAAA 0.845118 -108 ********** Masking position 6 Map Score: 3.62896 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 64 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 9 ********** No masking Map Score: -1.93024e-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: -1.93024e-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: -1.93024e-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