AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00940_ecoli_reg_100.orf -o00940_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -x5 -e 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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 mhpA 76 3-(3-hydroxyphenyl)propionate hydroxylase #2 bglX 195 beta-D-glucoside glucohydrolase, periplasmic #3 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #4 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #5 cvpA 165 membrane protein required for colicin V production #6 pepP 25 proline aminopeptidase P II #7 ygfB 161 orf, hypothetical protein Motif number 1 TCGCCACCACAAGGAGTGGAAA 2 1 0 AAGGAGGAAA 0.975676 -195 ACTCCTTGTGGTGGCGAAAAAATATCACAAAC 2 16 1 GTGGCGAAAA 0.984239 -180 CATAAGCATGATGGAGAGAGAAAAAGAATGCT 2 111 0 ATGGAGAGAA 0.909765 -85 GGCAGCGAAAATGGTGCAAAAACCGTAGTTTG 2 144 0 ATGGTGAAAA 0.935438 -52 GTTGCCCGACGTGGCAGCGAAAATGGTGCAAA 2 156 0 GTGGCAGAAA 0.947142 -40 TCGGGCAACAAAGGAAGAAAAATCCAT 2 179 1 AAGGAAAAAA 0.895588 -17 GATGTGGCTTAACGAGGAAAAAGACGT 4 20 1 AACGAGAAAA 0.786437 -17 CGATGCCGCAAAGGCATAAAAAGTCGATGGCG 5 21 1 AAGGCAAAAA 0.942243 -145 TAAAAAGTCGATGGCGTTGAATATTTTTTCAG 5 37 1 ATGGCGGAAT 0.966657 -129 ATCAATAAAAATGGCGCTGAAAAAATATTCAA 5 53 0 ATGGCGGAAA 0.992331 -113 ACAGGATGACAGGGCGTAAAATCGTGGGACAC 5 142 1 AGGGCGAAAT 0.869238 -24 TTGGGCCCTGGTGGACCAGAAAAGGGCTTGTC 7 100 0 GTGGACGAAA 0.846773 -62 ****** **** Masking position 11 Map Score: 13.5197 Number of sites scoring better than the average of aligned sites = 2037 Number in coding regions = 1823 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 215 Fraction of orfs with sites within 600 bp upstream = 0.0345326 Motif number 2 ATATTTTTTCGCCACCACAAGGAGTGGAAA 2 8 0 GCCACACAGA 0.894735 -188 CATTTTCGCTGCCACGTCGGGCAACAAAGGAAG 2 163 1 GCCACTCGCA 0.990984 -33 TGCCAGACCGGCACCCTCAGCGAAGGCA 3 6 0 GCACCTCAGA 0.972844 -89 CCGAAATCCTGCAAAGTCTGCCTGCAAGTCTGA 3 58 1 GCAAATCTCT 0.681187 -37 AAATAGTTGCCCTGTCAGACTTGCAGGCAGA 3 74 0 GCCCTTCACT 0.960796 -21 TCCTCGTTAAGCCACATCTCAGAGCAC 4 5 0 GCCACTCTGA 0.976583 -32 TTATGCCTTTGCGGCATCGGGCAATGCGT 5 7 0 GCGGCTCGCA 0.963129 -159 CCTGTTCGGGGCGCATTCTAACAGAAAAAGAAA 5 114 0 GCGCATCTCA 0.965897 -52 ACGATTTTACGCCCTGTCATCCTGTTCGGGGCG 5 134 0 GCCCTTCACT 0.960787 -32 GACGAAGGCAGCGCAGTCAATCAGCAGGAAGGT 7 14 0 GCGCATCACA 0.978465 -148 CTATAGTGTCGCCCCTTCGCAGACCATGGGTCT 7 50 0 GCCCCTCGGA 0.993533 -112 ***** *** ** Masking position 8 Map Score: 11.6116 Number of sites scoring better than the average of aligned sites = 1558 Number in coding regions = 1232 Number in noncoding regions = 326 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 3 GGCAGCGAAAATGGTGCAAAAACCGTAGTT 2 146 0 ATGGTGCAAA 0.974841 -50 GCCTTCGCTGAGGGTGCCGGTCTGGCACCC 3 12 1 AGGGTGCCGG 0.965952 -83 GTTGCAAGTCAGGGTGCCAGACCGGCACCC 3 23 0 AGGGTGCCAG 0.966395 -72 GCATTGCCCGATGCCGCAAAGGCATAAAAA 5 13 1 ATGCCGCAAA 0.942646 -153 TAAAAAGTCGATGGCGTTGAATATTTTTTC 5 37 1 ATGGCGTTGA 0.922802 -129 ATCAATAAAAATGGCGCTGAAAAAATATTC 5 55 0 ATGGCGCTGA 0.980979 -111 ACAGGATGACAGGGCGTAAAATCGTGGGAC 5 142 1 AGGGCGTAAA 0.973037 -24 CTGGTCCACCAGGGCCCAAAGTGGTAGCAT 7 113 1 AGGGCCCAAA 0.963118 -49 ********** Masking position 1 Map Score: 7.57463 Number of sites scoring better than the average of aligned sites = 1444 Number in coding regions = 1321 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 4 GTACTGTGCGCGCAACGACATTTTGTCCGA 1 41 1 CGCAACGACA 0.907448 -36 CGCCACCACAAGGAGTGGAAA 2 2 0 AGGAGTGGAA 0.798463 -194 AAGCATGATGGAGAGAGAAAAAGAATGCTC 2 110 0 GAGAGAGAAA 0.723863 -86 TGCCCGACGTGGCAGCGAAAATGGTGCAAA 2 156 0 GGCAGCGAAA 0.797229 -40 CACGTCGGGCAACAAAGGAAGAAAAATCCA 2 175 1 AACAAAGGAA 0.807462 -21 CGGCACCCTCAGCGAAGGCA 3 1 0 AGCGAAGGCA 0.958084 -94 GTCAGGGTGCCAGACCGGCACCCTCAGCGA 3 16 0 CAGACCGGCA 0.751547 -79 TGCCCGATGCCGCAAAGGCATAAAAAGTCG 5 17 1 CGCAAAGGCA 0.961889 -149 TATTGATGCGCGGGAAGGAAATCCCTACGC 5 78 1 CGGGAAGGAA 0.943899 -88 GCGCCCCGAACAGGATGACAGGGCGTAAAA 5 133 1 CAGGATGACA 0.688329 -33 TGGGTCTAAAGACGAAGGCAGCGCAGTCAA 7 27 0 GACGAAGGCA 0.89902 -135 TGGTCTGCGAAGGGGCGACACTATAGCTAC 7 57 1 AGGGGCGACA 0.934425 -105 TACCCTGATGAGAAGAGACAAGCCCTTTTC 7 84 1 AGAAGAGACA 0.614132 -78 TCGTCGTCAAAGGGAGGAATATTCATGAT 7 143 0 AAGGGAGGAA 0.891061 -19 ********** Masking position 10 Map Score: 8.12507 Number of sites scoring better than the average of aligned sites = 6163 Number in coding regions = 5776 Number in noncoding regions = 387 Number of orfs with sites within 600 bp upstream = 422 Fraction of orfs with sites within 600 bp upstream = 0.0677803 Motif number 5 TTTAACAAAATAAGTTGCGCTGTACTGTGC 1 20 1 TAAGTTGCGC 0.972159 -57 CGGACAAAATGTCGTTGCGCGCACAGTACA 1 40 0 GTCGTTGCGC 0.978896 -37 TTTTTCTTCCTTTGTTGCCCGACGTGGCAG 2 171 0 TTTGTTGCCC 0.947608 -25 AAATAGTTGCCCTGTCAGACTT 3 83 0 ATAGTTGCCC 0.977749 -12 CGCATCAATAAAAATGGCGCTGAAAAAATA 5 58 0 AAAATGGCGC 0.832684 -108 CGCCATTTTTATTGATGCGCGGGAAGGAAA 5 69 1 ATTGATGCGC 0.932522 -97 TGTCATCCTGTTCGGGGCGCATTCTAACAG 5 123 0 TTCGGGGCGC 0.959758 -43 CAGGGTAGCTATAGTGTCGCCCCTTCGCAG 7 61 0 ATAGTGTCGC 0.931481 -101 ********** Masking position 8 Map Score: 4.72537 Number of sites scoring better than the average of aligned sites = 1616 Number in coding regions = 1493 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 6 ********** No masking Map Score: -1.51102e-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 7 ********** No masking Map Score: -1.51102e-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 8 ********** No masking Map Score: -1.51102e-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