AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iompR_ecoli_bsub_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 ompF 300 outer membrane protein 1a (Ia;b;F) #2 ompC 300 outer membrane protein 1b (Ib;c) #3 fadL 300 transport of long-chain fatty acids; sensitivity to phage T2 #4 yrpD 300 similar to hypothetical proteins from B. subtilis Motif number 1 CAAAAAGAAAAAATATGTAACCAAAAGTAAAATTT 1 97 0 AAAATGTAAA 0.913806 -204 GTTTGAATGGAAAGATGCCTGCAGACACATAAAGA 1 179 1 AAAATGCAGA 0.966144 -122 CGGAATGGCGAAATAAGCACCTAACATCAAGCAAT 2 71 0 AAAAAGCAAC 0.926125 -230 ATTTATCGCTATAGATGTTTCAAAATGTAAATGCA 2 128 0 ATAATGTAAA 0.684078 -173 AATCCAACACGAATATGATACTAAAACTTTTAAGA 2 169 0 GAAATGAAAA 0.82039 -132 CATTCTCCCCAAAAATGCAGAATAATCCAACACGA 2 192 0 AAAATGCTAA 0.805286 -109 GCAGTGGCATAAAAAAGCAAATAAAGGCATATAAC 2 262 1 AAAAAGCAAA 0.96129 -39 AATCACACTTAAAAATGATCTAAAACAAAATTCAC 3 60 1 AAAATGAAAA 0.966622 -241 ATCTTTTTTCAAATATGATCTAAGAAACGCGATCC 3 134 0 AAAATGAAGA 0.955087 -167 ATCATATTTGAAAAAAGATAGAAACATACTTGCAA 3 150 1 AAAAAGAAAC 0.903304 -151 GAGGGGGGAGAAATAAGAGGGGAAAGAGAGAAAAC 4 45 0 AAAAAGAAAA 0.948731 -256 ATTCCATAATAAACATGCACATAGATACAGAATTT 4 208 0 AAAATGCAGA 0.966144 -93 ATGTTTTATAATACAAGATGATAGCGTTTTCTAAT 4 253 1 ATAAAGAAGC 0.583513 -48 *** **** *** Masking position 5 Map Score: 11.7795 Number of sites scoring better than the average of aligned sites = 360 Number in coding regions = 281 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 2 ATAGATTAAAATTGCTGTAAATATCATCACGT 1 29 1 ATGCGTAAAT 0.969145 -272 GTGTTCACAAAGTTCCTTAAATTTTACTTTTG 1 79 1 ATTCTTAAAT 0.817885 -222 TCTCATCAATAGTTCCGTAAATTTTTATTGAC 1 222 1 ATTCGTAAAT 0.96755 -79 GCCGTCAATAAGTTCTGTCAATAAAAATTTAC 1 238 0 ATTCGTCAAT 0.980711 -63 GACACCTGCCACTGCCGTCAATAAGTTCTGTC 1 251 0 ATGCGTCAAT 0.973506 -50 TTGACATTCAGTGCTGTCAAATACTTAAGAA 2 10 1 ATGCGTCAAA 0.945054 -291 TCCAGTTGTTAATTCTGCAAAATCGGATAAGT 3 22 1 ATTCGCAAAA 0.823085 -279 TTTAAGTGTGATTTCGGTCACTTATCCGATTT 3 41 0 ATTCGTCACT 0.957766 -260 TAGCTTTTCTATTTCAATAAAACACAAGTCTC 4 84 1 ATTCATAAAA 0.68617 -217 ATAATGTGTAAATTCTGTATCTATGTGCATGT 4 199 1 ATTCGTATCT 0.748797 -102 * *** ****** Masking position 3 Map Score: 9.26277 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 159 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 3 ACTAACGTTTCGCTACCGTGAAAGTGCTAC 1 151 0 CGCTACCGTG 0.944468 -150 TTCGCCATTCCGCAATAATCTTAAAAAGTT 2 94 1 CGCAATAATC 0.803082 -207 TTGGAGGTGGCGCACTCATGGATTCGGGTG 3 92 0 CGCACTCATG 0.980442 -209 ATCTAAGAAACGCGATCCAGCTGGCAAAAT 3 122 0 CGCGATCCAG 0.944637 -179 CCCTACACTTCGCGCTCCTGTTACAGCACG 3 246 1 CGCGCTCCTG 0.98303 -55 ACGGTCGATTCGCAATCGTGAAAAATCTCC 4 150 0 CGCAATCGTG 0.984326 -151 AATTAGAAAACGCTATCATCTTGTATTATA 4 259 0 CGCTATCATC 0.956403 -42 ********** Masking position 3 Map Score: 3.63244 Number of sites scoring better than the average of aligned sites = 568 Number in coding regions = 531 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 ATGTAACCAAAAGTAAAATTTAAGGAACTTTGTGA 1 83 0 AAAAAATTAG 0.976843 -218 AAGTTCTGTCAATAAAAATTTACGGAACTATTGAT 1 226 0 AAAAAATTAG 0.976915 -75 TCAAATACTTAAGAATAAGTTATTGATTTTAACCT 2 27 1 AAATAATTAG 0.96348 -274 AACATCAAGCAATAATAATTCAAGGTTAAAATCAA 2 49 0 AAATAATCAG 0.962769 -252 AAATGATCTAAAACAAAATTCACCCGAATCCATGA 3 72 1 AAAAAATCAC 0.87287 -229 TAGTTTGTATAAAAATAAATCATTGAGGTT 3 281 1 AAATAATCAG 0.962769 -20 TTTTATTGAAATAGAAAAGCTATAGAGAGGGGGGA 4 71 0 ATAAAACTAG 0.804507 -230 ACAAGTCTCGATTGAAAAGTTATCGTAACATTTAC 4 107 1 ATAAAATTAG 0.939372 -194 ** **** *** * Masking position 8 Map Score: 3.78485 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 40 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 AAAAAAACCATGAGGGTAATAAATA 1 286 1 TGAGGGTAAT 0.842308 -15 GACTGATTAATGAGGGTTAATCAGTATGCA 2 235 1 TGAGGGTTAA 0.962587 -66 GGCATATAACAGAGGGTTAATAAC 2 287 1 AGAGGGTTAA 0.971016 -14 CACTCATGGATTCGGGTGAATTTTGTTTTA 3 80 0 TTCGGGTGAA 0.829519 -221 GGGAGAAATAAGAGGGGAAAGAGAGAAAAC 4 45 0 AGAGGGGAAA 0.975878 -256 AAAGCTATAGAGAGGGGGGAGAAATAAGAG 4 61 0 AGAGGGGGGA 0.965574 -240 AATTATAATGATAGGGGGAAATAATG 4 285 1 ATAGGGGGAA 0.961339 -16 ********** Masking position 5 Map Score: 3.42579 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 247 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 6 GAAAAAATATGTAACCAAAAGTAAAATTTAAGGA 1 92 0 GTCCAAAGTA 0.945541 -209 TAAAGATTTGGTTTCAAAAAGAAAAAATATGTAA 1 112 0 GTCAAAAGAA 0.986722 -189 TACCGTGAAAGTGCTACAAAGATAAAGATTTGGT 1 134 0 GTTAAAAGAA 0.866532 -167 CACTTTCACGGTAGCGAAACGTTAGTTTGAATGG 1 155 1 GTCGAACGTA 0.894591 -146 GATGCCTGCAGACACATAAAGACACCAAACTCTC 1 192 1 GACAAAAGAA 0.953826 -109 GCAGTGGCAGGTGTCATAAAAAAAACCATGAGGG 1 268 1 GTCAAAAAAA 0.927779 -33 CGCTATAGATGTTTCAAAATGTAAATGCAAGGGA 2 123 0 GTCAAATGTA 0.930154 -178 TCAGTATGCAGTGGCATAAAAAAGCAAATAAAGG 2 255 1 GTCAAAAAAG 0.728193 -46 TCGCGCTCCTGTTACAGCACGTAACATAGTTTGT 3 255 1 GTCACACGTA 0.883386 -46 CCGTTTGCCAGATGCACAAAGTCATAATGTGTAA 4 176 1 GACAAAAGTA 0.953826 -125 ** ** ***** * Masking position 9 Map Score: 3.98418 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 255 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 7 GACGTGATGATATTTACAGCAATTTTAATC 1 32 0 TATTTACAGC 0.92901 -269 TGTCAATAAAAATTTACGGAACTATTGATG 1 225 0 AATTTACGGA 0.695622 -76 CGTAAATTTTTATTGACAGAACTTATTGAC 1 237 1 TATTGACAGA 0.958718 -64 TGACAGAACTTATTGACGGCAGTGGCAGGT 1 250 1 TATTGACGGC 0.969955 -51 ATTCTTAAGTATTTGACAGCACTGAATGTC 2 13 0 ATTTGACAGC 0.951801 -288 CACCTCCAAATTTTGCCAGCTGGATCGCGT 3 113 1 TTTTGCCAGC 0.961216 -188 CGAATCGACCGTTTGCCAGATGCACAAAGT 4 168 1 GTTTGCCAGA 0.843881 -133 ********** Masking position 4 Map Score: 2.29614 Number of sites scoring better than the average of aligned sites = 641 Number in coding regions = 583 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 8 TTCCGCAATAATCTTAAAAAGTTCCCTTGC 2 101 1 ATCTTAAAAA 0.967819 -200 TAAATGAAACATCTTAAAAGTTTTAGTATC 2 158 1 ATCTTAAAAG 0.93155 -143 CTTAAAAATGATCTAAAACAAAATTCACCC 3 67 1 ATCTAAAACA 0.905082 -234 TTCAAATATGATCTAAGAAACGCGATCCAG 3 132 0 ATCTAAGAAA 0.958071 -169 TCTGAGGTACATCTTAGAAATCAGACCAGT 3 216 0 ATCTTAGAAA 0.970348 -85 ********** Masking position 6 Map Score: 1.75608 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 15 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 9 TTTTTTTTATGACACCTGCCACTGCCGTCA 1 263 0 GACACCTGCC 0.91961 -38 TTGCAGAATTAACAACTGGAGCAGCACTTT 3 12 0 AACAACTGGA 0.804823 -289 CCATGAGTGCGCCACCTCCAAATTTTGCCA 3 101 1 GCCACCTCCA 0.957659 -200 TCCAAATTTTGCCAGCTGGATCGCGTTTCT 3 117 1 GCCAGCTGGA 0.583659 -184 TATAGGTCGGACCAGCTGGAATGTTGCAAG 3 178 0 ACCAGCTGGA 0.768781 -123 TCGACCGTTTGCCAGATGCACAAAGTCATA 4 172 1 GCCAGATGCA 0.950973 -129 ********** Masking position 4 Map Score: 1.40473 Number of sites scoring better than the average of aligned sites = 1353 Number in coding regions = 1314 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 10 ********** No masking Map Score: 1.08246e-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: 1.08246e-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 12 ********** No masking Map Score: 1.08246e-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