AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i137_Potential_Transporter_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 yiaK 200 putative dehydrogenase #2 yiaM 117 orf, hypothetical protein #3 HI0146 300 conserved hypothetical protein #4 HI1028 30 conserved hypothetical protein #5 HI1030 71 conserved hypothetical transmembrane protein #6 HI1031 175 conserved hypothetical protein Motif number 1 AAAGACATAAAAATCAATTGGTTATAAATTATCTGTC 1 60 0 AAATAAATAA 0.964447 -141 TCGCATATTGAAATTTTAAGCCAAAAAAGCGATCAAA 1 156 1 AAATTTAAAA 0.93367 -45 TCCACACAAAACAATCTTTTATAAGTTGTAATAT 3 8 1 AAAAAAATAA 0.926275 -293 TAATAAGGTTAAATGATGAAAATATAAGCATATTACA 3 37 0 AAATATATAA 0.933648 -264 AAAACACTTCAAAAATATTCTTTAAAATGGCATTTAT 3 82 0 AAAATAAAAA 0.926276 -219 CTCATTTTGGAAATAAAACTCGTAAAACTATTTTAAA 3 139 1 AAATAAAAAA 0.976997 -162 TCTAAGAGTAAAAAAACAAATTTAAAATAGTTTTACG 3 159 0 AAAAACAAAA 0.821238 -142 CAGCAATATGTTTCCAGTAAAACGCCATAATA 5 6 1 ATATTTAAAA 0.741931 -66 ACAATATGAAATATTATCACAAGAAAATAGGATCTAG 6 14 1 ATATATAAAA 0.818137 -162 AATTATTTATAAATCAATATGTTAAAATAATTTTACT 6 62 0 AAATAAAAAA 0.976997 -114 CTCAGTCAATAAATGTAAAATAAATAAATTATTTATA 6 88 0 AAATTAATAA 0.945438 -88 TTTATATAGTAAAATTACGTTTCATAATTTACAAAAA 6 133 0 AAAATAATAA 0.889236 -43 TTACTATATAAAATTAAGAGAGGAAAAA 6 158 1 AAATAAAAAA 0.976997 -18 **** ** **** Masking position 14 Map Score: 13.2913 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 157 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 2 CAAATATATCGATCACTTTTTAACAAGGCA 1 116 0 GATCACTTTT 0.970993 -85 TTGTTTTTTTGATCGCTTTTTTGGCTTAAA 1 170 0 GATCGCTTTT 0.937809 -31 ATGAAAAATAAATGCCATTTTAAAGAATAT 3 75 1 AATGCCATTT 0.892454 -226 ATGAGAAGTTGATCACATTTATGAAAAAAC 3 114 0 GATCACATTT 0.989182 -187 ATTGCTCTCGAATCCTATTTTGGGGGAGAA 3 196 1 AATCCTATTT 0.944047 -105 ATATAAAACGAATCACATTTGTGATAATCA 5 40 1 AATCACATTT 0.972773 -32 ATTTTCTTGTGATAATATTTCATATTGTGA 6 12 0 GATAATATTT 0.822579 -164 TTGTGATCTAGATCCTATTTTCTTGTGATA 6 28 0 GATCCTATTT 0.977358 -148 ********** Masking position 2 Map Score: 8.41534 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 129 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 3 AACAAGGCAATCTGATTGATGAATTTCAAAA 1 94 0 TCTGATTGTG 0.946352 -107 TATTAATAATTCAGGTTGCTGCACATGCGAC 2 62 1 TCAGGTTGTG 0.875207 -56 GAGAAGTTGATCACATTTATGAAAAAACACT 3 111 0 TCACATTTTG 0.974388 -190 GTGATCAACTTCTCATTTTGGAAATAAAACT 3 128 1 TCTCATTTGG 0.955534 -173 TGCTCTCGAATCCTATTTTGGGGGAGAAAAC 3 198 1 TCCTATTTGG 0.928217 -103 AAATTGATTCTCATATTACGGGGTTAATCTA 3 244 1 TCATATTAGG 0.912049 -57 TTTACTGGAAACATATTGCTG 5 1 0 ACATATTGTG 0.875498 -71 ATAAAACGAATCACATTTGTGATAATCAATT 5 42 1 TCACATTTTG 0.974389 -30 TGATAATATTTCATATTGTGAA 6 2 0 TCATATTGGA 0.804669 -174 GACTGAGCTTTCTTATTTTTGTAAATTATGA 6 118 1 TCTTATTTTG 0.953188 -58 ******** ** Masking position 6 Map Score: 7.16168 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 256 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 4 AAAATGGCATTTATTTTTCATATAATAAGG 3 66 0 TTATTTTTCA 0.947023 -235 TTTAAATTTGTTTTTTTACTCTTAGAATTG 3 170 1 TTTTTTTACT 0.837114 -131 TTTCTTGTGATAATATTTCATATTGTGAA 6 10 0 TAATATTTCA 0.762075 -166 TATGTTAAAATAATTTTACTGATTTTGTGA 6 52 0 TAATTTTACT 0.966305 -124 AATAATTTATTTATTTTACATTTATTGACT 6 92 1 TTATTTTACA 0.966305 -84 CTGAGCTTTCTTATTTTTGTAAATTATGAA 6 120 1 TTATTTTTGT 0.774605 -56 TTATGAAACGTAATTTTACTATATAAAATT 6 143 1 TAATTTTACT 0.966305 -33 TTTCCTCTCTTAATTTTATATAGTAAAATT 6 154 0 TAATTTTATA 0.788123 -22 ********** Masking position 6 Map Score: 4.61427 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 204 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 5 TAATTTATAACCAATTGATTTTTATGTCTT 1 66 1 CCAATTGATT 0.985429 -135 TTTAACAAGGCAATCTGATTGATGAATTTC 1 98 0 CAATCTGATT 0.895596 -103 ATTTTTGGCCTAAATTGATTCTCATATTAC 3 233 1 TAAATTGATT 0.923108 -68 TACACCTCCAATTGATTATCACAAATG 5 55 0 CCAATTGATT 0.985429 -17 ATTATTTTAACATATTGATTTATAAATAAT 6 68 1 CATATTGATT 0.950105 -108 ********** Masking position 6 Map Score: 2.98465 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 57 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 CTATGTCTGTCATAATTCAAGTCGCATGTG 2 83 0 CATAATTCAA 0.961699 -35 TCCACACAAAACAATCTTTTATAA 3 5 1 CACAAAACAA 0.794452 -296 AAAATATAAGCATATTACAACTTATAAAAG 3 26 0 CATATTACAA 0.881812 -275 CTTATATTTTCATCATTTAACCTTATTATA 3 46 1 CATCATTTAA 0.820041 -255 ATTTATTTTTCATATAATAAGGTTAAATGA 3 58 0 CATATAATAA 0.824681 -243 TGGAAAGGGGCATAGATTAACCCCGTAATA 3 257 0 CATAGATTAA 0.829671 -44 AGTAAAACGCCATAATATAAAACGAATCAC 5 26 1 CATAATATAA 0.940584 -46 ATAAATTATTTATAAATCAATATGTTAAAA 6 72 0 TATAAATCAA 0.666444 -104 AATTACGTTTCATAATTTACAAAAATAAGA 6 128 0 CATAATTTAC 0.820041 -48 ********** Masking position 2 Map Score: 2.38069 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 171 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 7 CTTTTTAACAAGGCAATCTGATTGATGAAT 1 101 0 AGGCAATCTG 0.931254 -100 CAAAAAAACAAGGAAGCCTGGG 1 189 1 AGGAAGCCTG 0.993 -12 CGTCTACGCCAGAACGCCTGGGTAATGTTA 2 20 1 AGAACGCCTG 0.981756 -98 CCTTGTGTTAAGAAAGTCTGTT 4 3 0 AGAAAGTCTG 0.98342 -28 ********** Masking position 9 Map Score: 0.461059 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 124 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 ********** No masking Map Score: -1.51813e-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 9 ********** No masking Map Score: -1.51813e-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: -1.51813e-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