AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i128_Transmembrane_Transport_2_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 yaeC 39 putative lipoprotein #2 abc 187 ATP-binding component of a transporter #3 HI0620 300 28 kDa outer membrane protein (hlpA) #4 HI0621 175 ABC transporter, ATP-binding protein Motif number 1 ACCTTATTCCTTCTTCAATTATTTATGTTGTGTTGAACG 1 8 0 TTTATTATGG 0.982968 -32 CTTTTATAGCTCCTTAATAAGGCATGTGACGCTAGTATCGC 2 10 1 CTTATGATGG 0.983112 -178 CGTTGCCCGTTTCAGGCATTCGAGATGCCACGACTAACTTAA 2 137 1 TTGATGATGG 0.989733 -51 CAAATTGTTCGTAAATTCTATTTGTCAGAAGCTCTACCT 3 8 1 TTTATTTTGA 0.735215 -293 GTCACTTTAGTTGGTTATTCTGCAATGGCAGGAACACAAGGG 3 80 1 TTTTTGATGG 0.983948 -221 ACCATTATTATTGTGCTATTCGTTATGATTAGCCAAAAACTC 3 195 1 TTGATGATGG 0.984486 -106 AGGATTTCCTTCCTGTTTAAGTTAAGAGTTGCGTTTAATTA 3 270 0 TTTTTGAAGG 0.896119 -31 ATAGATAATTTTTGTCAATTTGACATGTATAAAAGGTAAGAG 4 12 0 TTTATGATGA 0.958917 -164 TTAGTTATGACTTATATTTGCTAATTGCTTGGATTAAATAGA 4 49 0 CTTTTTTTGG 0.755252 -127 TTTAAATCTGTTTTGGTATTCTAGATGTCTAGATTGCTATGT 4 121 0 TTGATTATGG 0.976266 -55 ** * ** * *** * Masking position 9 Map Score: 8.19549 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 192 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 2 GATTTAGACGTCTGGATGCCTTAACATCCA 2 95 1 TCTGGATGCC 0.964473 -93 TTTCAGGCATTCGAGATGCCACGACTAACT 2 146 1 TCGAGATGCC 0.981043 -42 GTTCGTAAATTCTATTTGTCAGAAGCTCTA 3 17 1 TCTATTTGTC 0.952858 -284 GGCGTATATCGCAATATGCCTTATGTAACT 3 156 1 GCAATATGCC 0.957328 -145 ATAATTTTTGTCAATTTGACATGTATAAAA 4 20 0 TCAATTTGAC 0.888884 -156 GATTGCTATGTCAATATGTCAGATTATCTT 4 102 0 TCAATATGTC 0.978929 -74 GTTTTGGTATTCTAGATGTCTAGATTGCTA 4 124 0 TCTAGATGTC 0.982489 -52 ********** Masking position 7 Map Score: 6.85353 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 111 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 3 GGCAACGCCGTCAATGAAATGGATGTTAAGGC 2 112 0 TCATGAAAGG 0.924619 -76 GCATCTCGAATGCCTGAAACGGGCAACGCCGT 2 133 0 TGCTGAAAGG 0.988352 -55 GGCGATACACTGGCTAAAAAAGTGGATCATCG 3 237 1 TGCTAAAAAG 0.984739 -64 ACGCAACTCTTAACTTAAACAGGAAGGAAATC 3 277 1 TACTTAAAAG 0.904164 -24 CAATTTGACATGTATAAAAGGTAAGAGA 4 7 0 TGATAAAAGT 0.878135 -169 GCTAATTGCTTGGATTAAATAGATAATTTTTG 4 40 0 TGATTAAAAG 0.956148 -136 ATAACTAATCTGTCTAAAAAAGATAATCTGAC 4 83 1 TGCTAAAAAG 0.984739 -93 TTAAAAACAATAAATAAAAAGGGCTTAT 4 158 1 TAATAAAAGG 0.946245 -18 ** ****** ** Masking position 7 Map Score: 6.52116 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 178 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 4 GCATGTGACGCTAGTATCGCATGTTTCGACC 2 32 1 CTGTATCGCA 0.968638 -156 ATGCCTGAAACGGGCAACGCCGTCAATGAAA 2 125 0 CGGCAACGCC 0.991063 -63 GACTAGCGTAAGAGTAACGCCATTAATTAGC 3 52 0 AGGTAACGCC 0.989292 -249 CAACTACGGGCGTATATCGCAATATGCCTTA 3 148 1 CGATATCGCA 0.968638 -153 TTTTTTAGCCAGTGTATCGCCGAGTTTTTGG 3 227 0 AGGTATCGCC 0.993698 -74 ** ******** Masking position 6 Map Score: 3.5431 Number of sites scoring better than the average of aligned sites = 460 Number in coding regions = 440 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 ATAAGGCATGTGACGCTAGTATCGCATGTT 2 27 1 TGACGCTAGT 0.992283 -161 ATTATCGTCATTAAGTTAGTCGTGGCATCT 2 159 0 TTAAGTTAGT 0.851748 -29 ACTAACTTAATGACGATAATAAATAATCA 2 169 1 TGACGATAAT 0.934916 -19 GAAGCTCTACCTACGCTAATTAATGGCGTT 3 38 1 CTACGCTAAT 0.959696 -263 GGCGTTACTCTTACGCTAGTCACTTTAGTT 3 62 1 TTACGCTAGT 0.991674 -239 ********** Masking position 7 Map Score: 2.52464 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 43 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 ATCCATTTCATTGACGGCGTTGCCCGTTTC 2 120 1 TTGACGGCGT 0.983856 -68 CACGACTAACTTAATGACGATAATAAATAA 2 165 1 TTAATGACGA 0.970854 -23 CCTACGCTAATTAATGGCGTTACTCTTACG 3 47 1 TTAATGGCGT 0.981279 -254 ACGCCCGTAGTTGATAGCGAGGCTACCTAA 3 131 0 TTGATAGCGA 0.939424 -170 TTGCGTTTAATTAACGATGATCCACTTTTT 3 253 0 TTAACGATGA 0.873254 -48 ********** Masking position 4 Map Score: 1.2529 Number of sites scoring better than the average of aligned sites = 790 Number in coding regions = 744 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 7 TCAACACAACATAAATAATTGAAGAAGGAA 1 14 1 ATAAATAATT 0.903523 -26 AATGACGATAATAAATAATCA 2 177 1 ATAAATAATC 0.979953 -11 TCAAATTGACAAAAATTATCTATTTAATCC 4 31 1 AAAAATTATC 0.911688 -145 AATATAAGTCATAACTAATCTGTCTAAAAA 4 73 1 ATAACTAATC 0.956565 -103 TCTGTCTAAAAAAGATAATCTGACATATTG 4 91 1 AAAGATAATC 0.938904 -85 ********** Masking position 6 Map Score: 2.02325 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 111 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 8 ********** No masking Map Score: -5.16264e-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 9 ********** No masking Map Score: -5.16264e-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 10 ********** No masking Map Score: -5.16264e-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