AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icpxR6_ecoli_hinf_100.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 htrA 129 periplasmic serine protease Do; heat shock protein HtrA #2 ybaU 191 putative protease maturation protein #3 ppiA 270 peptidyl-prolyl cis-trans isomerase A (rotamase A) #4 yihD 69 orf, hypothetical protein #5 yihE 77 orf, hypothetical protein #6 cpxR_b3913 146 cpxR: transcriptional regulator in 2-component system, b3913: orf, hypothetical protein #7 HI0079 102 peptidyl-prolyl cis-trans isomerase B (ppiB) #8 HI0837 53 response regulator (cpxR) #9 HI0839 116 conserved hypothetical protein #10 HI0845 86 conserved hypothetical protein #11 HI1004 272 peptidyl-prolyl cis-trans isomerse, putative #12 HI1259 193 periplasmic serine protease Motif number 1 CACCGAATACAAATAAAAAAGGCACATCAG 2 56 0 AAATAAAAAA 0.961719 -136 CTGCGTTCAAAAATAAAATGGCATAGCGGG 3 18 1 AAATAAAATG 0.879178 -253 TTTGATCACGGAATAAAAAGTGATCGTCAG 3 139 1 GAATAAAAAG 0.959511 -132 TCGTAAAATGAAATAAAAACAAACCGCACT 7 19 1 AAATAAAAAC 0.954186 -84 AGTGTGGTGAAAATAAAAAGA 8 2 0 AAATAAAAAG 0.985586 -52 AATGTTAAAAATAAAAAAAATTTGGCTT 9 9 1 AAATAAAAAA 0.961719 -108 TATTTTTTACGATTAAAAAGGAAATAGCAA 10 46 1 GATTAAAAAG 0.732966 -41 AATAGCAATGAAATAAAAAGGAAATAGCA 10 68 1 AAATAAAAAG 0.985586 -19 GGCAAAATTTAAATCAAAAGCGGCAATATT 11 36 1 AAATCAAAAG 0.915146 -237 CCCTTGTTATAAATATAAAATTTTCCCGAT 11 161 0 AAATATAAAA 0.727777 -112 CAACTAAAAACGATACAGCAA 11 262 0 AACTAAAAAC 0.781441 -11 ATTTTCTAGTCAATAAAAAGGTCAAAAA 12 9 0 CAATAAAAAG 0.927938 -185 TAAGACAAAAAAATAAAAAAAATGTTCAAT 12 138 0 AAATAAAAAA 0.961719 -56 ********** Masking position 7 Map Score: 19.2918 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 92 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 2 TCAAAATCACCTCTTAAAATGCAATTTAGCAAC 3 111 0 CTTAAATGCA 0.954202 -160 ACGATTCAGGCTGCAAACATGCGTCAGGGGGTG 6 55 1 CTAAACTGCG 0.968016 -92 TTTTAAGCTCGTAAAATGAAATAAAAACAA 7 8 1 CTTAAATGAA 0.872259 -95 GGTAAAAGTGCTATAAAAGTGCGGTTTGTTTTT 7 33 0 CTAAAATGCG 0.992339 -70 TGTTTTCCCTCTAAAAAATTAAGGGTTGTATTA 7 78 0 CTAAAATAAG 0.806245 -25 TTTTTTCTTGCTGAAAAAGTGCGGTTATAATTT 9 76 1 CTAAAATGCG 0.992339 -41 AAATTAGCATCTTAAAAAGTGAAAACTCCATCC 11 111 0 CTAAAATGAA 0.955768 -162 AGAATGTTAATTGAAAAAATGCACAATTTAACA 11 195 1 TTAAAATGCA 0.866017 -78 TTTTTATTGACTAGAAAATTGCGCGTATTAGAA 12 20 1 CTAAAATGCG 0.992339 -174 ** **** **** Masking position 7 Map Score: 10.7329 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 137 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 3 AACGAATCTGAAGAACACAGCAATTTTGCGTT 1 84 1 AAGAAAAGCA 0.989494 -46 GATTTCCTTAACAAACAGAGCAGAAAAAAAGC 3 247 0 ACAAAAAGCA 0.857203 -24 CTTTTTCAGCAAGAAAAAAGAAATTATTTAGG 9 63 0 AAGAAAAGAA 0.902279 -54 TACGATTAAAAAGGAAATAGCAATGAAATAAA 10 53 1 AAGGAAAGCA 0.987291 -34 ATGAAATAAAAAGGAAATAGCA 10 75 1 AAGGAAAGCA 0.987291 -12 AATTCCTATCAACAAAACACCACCAAATATTG 11 59 0 AACAAAACCA 0.852388 -214 ATCTAAACGTAAAAAATTAGCATCTTAAAAAG 11 125 0 AAAAATAGCA 0.80199 -148 CAACTAAAAACGATACAGCAATCAAACCTA 11 253 0 AACGAAAGCA 0.970397 -20 AATGTTCAATAAGAGGAGAGCAAATTATCTTG 12 116 0 AAGAGAAGCA 0.956532 -78 ***** * **** Masking position 9 Map Score: 6.47092 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 109 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 TATGCCGCGAGCGGGCGATTTTAGGTGATTTT 3 49 1 GCGGGATTTT 0.967925 -222 AATTTCTGCCTCGGAGGTATTTAAACA 6 130 1 TCGGGTATTT 0.899876 -17 CTATAAAAGTGCGGTTTGTTTTTATTTCATTT 7 24 0 GCGGTGTTTT 0.866484 -79 CTGAAAAAGTGCGGTTATAATTTGCGGCAAAT 9 86 1 GCGGATAATT 0.912776 -31 GTTATAATTTGCGGCAAATTTTTCAAAG 9 99 1 GCGGAATTTT 0.978188 -18 AGCGTAAAGTGCGGTCATTTTTTGGCAAAATT 11 13 1 GCGGATTTTT 0.983163 -260 TAAATCAAAAGCGGCAATATTTGGTGGTGTTT 11 45 1 GCGGATATTT 0.983163 -228 TAGATTATAATCGGGAAAATTTTATATTTATA 11 152 1 TCGGAAATTT 0.911169 -121 **** ****** Masking position 11 Map Score: 5.82404 Number of sites scoring better than the average of aligned sites = 587 Number in coding regions = 484 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 5 AGTTTCTGCAAAAGGTAAAAATTTATTGTT 1 30 0 AAAGGTAAAA 0.960654 -100 TATATTTCAGATACGTAAAATTAGGTAAAG 3 175 1 ATACGTAAAA 0.90121 -96 CCCATCATCCGGAAAACATTACGAAT 5 62 0 ATCCGGAAAA 0.766044 -16 TTGCAGCCTGAATCGTAAACTCTCTATCGT 6 41 0 AATCGTAAAC 0.589967 -106 ATTCCACAATCGAGGTAAAAGTGCTATAAA 7 49 0 CGAGGTAAAA 0.653061 -54 TTAATTTTTTAGAGGGAAAACAAA 7 89 1 AGAGGGAAAA 0.897577 -14 AATAAGAATAATTGGTAAAAGGAATCTCCA 8 34 1 ATTGGTAAAA 0.8946 -20 AATGTTAAAAATAAAAAAAA 9 1 1 AATGTTAAAA 0.645565 -116 TTTCCTTTTTAATCGTAAAAAATAGGCAAA 10 40 0 AATCGTAAAA 0.90121 -47 AGCATCTTAAAAAGTGAAAACTCCATCCTC 11 109 0 AAAGTGAAAA 0.694038 -164 ATTATAATCTAAACGTAAAAAATTAGCATC 11 133 0 AAACGTAAAA 0.939292 -140 TTAGATTATAATCGGGAAAATTTTATATTT 11 151 1 ATCGGGAAAA 0.837846 -122 TAGTCAATAAAAAGGTCAAAAA 12 3 0 AAAGGTCAAA 0.793854 -191 ********** Masking position 8 Map Score: 7.39034 Number of sites scoring better than the average of aligned sites = 735 Number in coding regions = 602 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 6 ACAAGACGCAGAAAGTCACCGAATACAAAT 2 72 0 GAAAGTCACC 0.946273 -120 GCGTGAGGTACACAGTCATCTACAGCGGAG 2 160 1 CACAGTCATC 0.947168 -32 AAACAGATCACAAAATCACCTAAAATCGCC 3 62 0 CAAAATCACC 0.977954 -209 ATTCCGTGATCAAAATCACCTCTTAAAATG 3 123 0 CAAAATCACC 0.977954 -148 CCTTCAAGAACAAGGCCATCCCTTTACCTA 3 196 0 CAAGGCCATC 0.923337 -75 GCGGCGCCACCAAAATCATCGTGAAATGAT 5 21 1 CAAAATCATC 0.965764 -57 TCCATCCTCACAAAGCCAGCTAATAGCAAT 11 88 0 CAAAGCCAGC 0.958331 -185 ********** Masking position 8 Map Score: 5.43783 Number of sites scoring better than the average of aligned sites = 356 Number in coding regions = 340 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 TCTACAGCGGAGTGTTGTTACACC 2 178 1 AGTGTTGTTA 0.908559 -14 GTGCTATAAAAGTGCGGTTTGTTTTTATTT 7 29 0 AGTGCGGTTT 0.972606 -74 TTCTTATTGTAGTGTGGTGAAAATAAAAAG 8 12 0 AGTGTGGTGA 0.968168 -42 TTGCTGAAAAAGTGCGGTTATAATTTGCGG 9 83 1 AGTGCGGTTA 0.991513 -34 GAAGCGTAAAGTGCGGTCATTTTTTGGCA 11 10 1 AGTGCGGTCA 0.985612 -263 ********** Masking position 3 Map Score: 3.93233 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 60 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 GTATTTCAGTCTCGATTAACAGA 1 117 0 TTTCAGTCTC 0.963579 -13 ATTCGGTGACTTTCTGCGTCTTGTGGGCTG 2 78 1 TTTCTGCGTC 0.963882 -114 CCTGCTAACGTGTCTGTCTCAAGAGTAAGG 4 41 1 TGTCTGTCTC 0.975132 -29 TCCCAAAATCTTTCTGTCGCGATTCAACGA 6 15 1 TTTCTGTCGC 0.975132 -132 GATGACGTAATTTCTGCCTCGGAGGTATTT 6 122 1 TTTCTGCCTC 0.98947 -25 ********** Masking position 3 Map Score: 3.23214 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 86 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 GTATTTCAGTCTCGATTAACAGATAACGCAAAATTG 1 104 0 CCGATTGTAA 0.992443 -26 ATCTTTCTGTCGCGATTCAACGATAGAGAGTTTACG 6 22 1 CCGATTGTAG 0.990899 -125 GCACTTTTACCTCGATTGTGGAATAATACAACCCTT 7 55 1 CCGATTATAA 0.970637 -48 GCTTATGATACCCGATTATTTGGTAGAACCTAAATA 9 35 1 CCGATTGTAG 0.990899 -82 ATAAAATTTTCCCGATTATAATCTAAACGTAAAAAA 11 141 0 CCGATTTTAA 0.98259 -132 TTTGTACTGCTCCGATTTCCTTTTAAACAAGATAAT 12 89 1 TCGATTTTAA 0.900177 -105 * ***** * *** Masking position 7 Map Score: 2.11721 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 12 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 GTAAAGACGAACAATAAATTTTTACCTTTTG 1 21 1 ACATAAATTT 0.88588 -109 CCTGCGTTCAAAAATAAAATGGCATAGCGGG 3 17 1 AAATAAAATG 0.858387 -254 TGTTAAAAATAAAAAAAATTTGGCTTATGAT 9 13 1 AAAAAAATTT 0.839773 -104 CCTTGTTATAAATATAAAATTTTCCCGATTA 11 159 0 AAATAAAATT 0.912279 -114 AATCAAACCTAAGATAAATTTAGAAATCTTT 11 233 0 AAATAAATTT 0.966646 -40 CGCGTATTAGAACATAAATTTATAGAATTTG 12 41 1 AAATAAATTT 0.966646 -153 CCTTTTAAACAAGATAATTTGCTCTCCTCTT 12 107 1 AAATAATTTG 0.74803 -87 AAATACTCCAAAATAAATTTCAGATAACGT 12 174 0 AAATAAATTT 0.960031 -20 ** ******** Masking position 6 Map Score: 6.24686 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 24 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 11 TATTGTTCGTCTTTACAAAAGCCTGG 1 5 0 CTTTCAAAAC 0.778474 -125 ACGTATCGATGCGCGCAAAGGCCTATTGTGAC 2 127 0 GCGCCAAAGC 0.973998 -65 GATTGGCCTGCGTTCAAAAATAAAATGGCAT 3 10 1 GCGTCAAAAT 0.827556 -261 CATTTAAACAGATCACAAAATCACCTAAAATC 3 65 0 GATCCAAAAC 0.926249 -206 TTTTTATTCCGTGATCAAAATCACCTCTTAAA 3 126 0 GTGACAAAAC 0.870693 -145 ATTCTAAATAGCCTTCAAGAACAAGGCCATCC 3 205 0 GCCTCAAGAC 0.85431 -66 TGTAAGCGGCGCCACCAAAATCATCGTGAAAT 5 16 1 GCCACAAAAC 0.938977 -62 TTGCTCCCAAAATCTTTCTGTCGC 6 3 1 GCTCCAAAAC 0.982093 -144 AAAACTCCATCCTCACAAAGCCAGCTAATAGC 11 91 0 CCTCCAAAGC 0.912886 -182 GAAATCGGAGCAGTACAAAAACGGTCTTACAA 12 76 0 CAGTCAAAAC 0.847892 -118 **** ***** * Masking position 7 Map Score: 1.2098 Number of sites scoring better than the average of aligned sites = 884 Number in coding regions = 773 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 12 CAGCAATTTTGCGTTATCTGTTAATCGAGA 1 101 1 GCGTTATCTG 0.924084 -29 TGAGACAGACACGTTAGCAGGGTCAATCCC 4 32 0 ACGTTAGCAG 0.980946 -38 CCCCTGACGCATGTTTGCAGCCTGAATCGT 6 55 0 ATGTTTGCAG 0.810232 -92 GGCAGAAATTACGTCATCAGACGTCGCTAA 6 110 0 ACGTCATCAG 0.957827 -37 TTATAACCGCACTTTTTCAGCAAGAAAAAA 9 76 0 ACTTTTTCAG 0.837403 -41 CTTACAGACCACGTTATCTGAAATTTATTT 12 164 1 ACGTTATCTG 0.970837 -30 ********** Masking position 4 Map Score: 0.574104 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 408 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 13 GGAACTTCAGGCTATAAAACGAATCTGAAG 1 67 1 GCTATAAAAC 0.969062 -63 GCAACCGATTGCAATAAAACATTTAAACAG 3 86 0 GCAATAAAAC 0.976138 -185 TTTTGATCACGGAATAAAAAGTGATCGTCA 3 138 1 GGAATAAAAA 0.828277 -133 TGCGTCAGGGGGTGTAAAACAACGTAAAGT 6 74 1 GGTGTAAAAC 0.880381 -73 AGGTAAAAGTGCTATAAAAGTGCGGTTTGT 7 37 0 GCTATAAAAG 0.878212 -66 CCTCGATTGTGGAATAATACAACCCTTAAT 7 64 1 GGAATAATAC 0.866153 -39 AAACGATACAGCAATCAAACCTAAGATAAA 11 246 0 GCAATCAAAC 0.926475 -27 ********** Masking position 7 Map Score: 2.82394 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 149 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 14 ********** No masking Map Score: 1.2743e-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 15 ********** No masking Map Score: 1.2743e-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