AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i180_ecoli_bsub_100.orf -o180_ecoli_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 mog 114 required for the efficient incorporation of molybdate into molybdoproteins #2 moaA 300 molybdopterin biosynthesis, protein A #3 moaB 21 molybdopterin biosynthesis, protein B #4 moeA 203 molybdopterin biosynthesis #5 ydiG 125 similar to molybdopterin precursor biosynthesis #6 mobA 136 molybdopterin-guanine dinucleotide biosynthesis protein A #7 moeB 50 molybdopterin biosynthesis protein #8 narQ 245 alternate gene name: narAA Motif number 1 GCCTGTCTGTCACTCCCTTCGCAGTGTATCATTCT 1 57 1 CTCCTTGCGT 0.99349 -58 ATAGCGTGCATCGTCCTTTAGAGGTAGA 2 4 0 TTCTTTGAGT 0.840376 -297 TTTTTACCATCCACACTTTCGCTATGTAATCATGT 2 120 0 CCCTTTGCAT 0.983795 -181 TCAACTGATACGGTGCTTTGGCCGTGACAATGCTC 2 213 1 CTCTTTGCGT 0.989622 -88 GCGAAGTCATTTCTTCCTTCGCCCTGGTGGCAATC 2 253 0 TTCCTTGCCT 0.921007 -48 CTGATCTCTCCTTTTGACGTT 3 2 0 CTCTTTGAGT 0.929818 -20 AAGGGTGGTTCGCCACTTTTGCTATAAATATCAGA 4 25 1 CCCTTTGCAT 0.983795 -179 ACAGACTGTATGCCACCTCGGGCGTAGCGCTGGGT 4 124 0 TCCCTCGGGT 0.841257 -80 GCAAATTCGATTTTGCCTCCGCAGGAGTGTTTTC 4 180 1 TTCCTCGCGG 0.875374 -24 ATTATTTCACCTCTGCTATAATAAGTTAA 5 5 1 TCCCTCGCAT 0.965931 -121 AGTCAGCAAACAATACATTGGCCATATAAGACATA 5 59 1 CTCATTGCAT 0.925197 -67 AGCGTTGAGCCTTTGCTTTTGCTATGCTTTTAACG 6 93 1 CTCTTTGCAT 0.983492 -44 TGTCTCTTCCCCTCCGCAATGTTCCTGCCT 8 226 0 CCCCTCGCAT 0.986178 -20 * * **** ** ** Masking position 8 Map Score: 16.4309 Number of sites scoring better than the average of aligned sites = 881 Number in coding regions = 813 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 2 CTGCGAAGGGAGTGACAGACAGGCTTCAGAAGA 1 48 0 AGAAGACAGG 0.953789 -67 TTTGATATACATCATCAGGGAGGCATAGCGTGC 2 30 0 ATTAGGGAGG 0.979382 -271 ATTTCGCTACAGAATAAGGGAAAATGGCGGTTT 2 66 0 AGTAGGGAAA 0.713885 -235 GTTGACCCAGGTGCAGAGGCTAGAGTGTTTAGT 2 185 0 GTAAGGCTAG 0.72623 -116 TGGATATGGCATGTAAAGGCAGGACCCAGCGCT 4 101 1 ATAAGGCAGG 0.99036 -103 TGGCCATATAAGACATAGAGAAGAAAATAGTGT 5 77 1 AGAAGAGAAG 0.856369 -49 TAGTGTTAACATCATGAGGGAGATGGTTCGA 6 9 0 ATTAGGGAGA 0.891441 -128 TTCCTCTTTAATAAACAGACAAGCAGTAGCGTT 6 66 1 ATAAGACAAG 0.925211 -71 GATGACGGCGGTGTTTAGGCAGGACGCCTAAGC 8 110 0 GTTAGGCAGG 0.967922 -136 GTGTGAAAAAATATAAAGGCAGGAACATTGCGG 8 210 1 ATAAGGCAGG 0.99036 -36 ** * ******* Masking position 7 Map Score: 6.33338 Number of sites scoring better than the average of aligned sites = 422 Number in coding regions = 353 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 3 ATCAAAGTAAAACCGCCATTTTCCCTTATT 2 57 1 AACCGCCATT 0.955854 -244 CATAACCACTAAACACTCTAGCCTCTGCAC 2 178 1 AAACACTCTA 0.806177 -123 AAAAGTGGCGAACCACCCTTAATGGACGAA 4 15 0 AACCACCCTT 0.933231 -189 TATGTCAGAAAAACGCCACAGACTGTATGC 4 146 0 AAACGCCACA 0.914579 -58 GAAAACACTCCTGCGGAGGCAA 4 192 0 AAACACTCCT 0.944276 -12 ATTAAAACGCTCCTTAAACAGATC 5 112 0 AAACGCTCCT 0.980999 -14 GCAAATACTGAACAGCTATTCCTCTTTAAT 6 48 1 AACAGCTATT 0.757939 -89 AGCAAAGGCTCAACGCTACTGCTTGTCTGT 6 80 0 CAACGCTACT 0.860115 -57 CACATCCTGTAAAAGCCCTTTATATAGAGG 8 142 1 AAAAGCCCTT 0.908834 -104 ********** Masking position 2 Map Score: 4.80761 Number of sites scoring better than the average of aligned sites = 1163 Number in coding regions = 1033 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 4 ACCGACTTCCCGGTCACGCTAAGAATGA 1 9 0 CGGTCACGCT 0.974903 -106 ACCGGGAAGTCGGTCACGCTACCTCTTCTG 1 25 1 CGGTCACGCT 0.974903 -90 CATGTATATAGCGTCATGATCGTGCTATTT 2 95 0 GCGTCATGAT 0.820427 -206 GAGTGTTTAGTGGTTATGCCGATACTAGCG 2 166 0 TGGTTATGCC 0.915345 -135 GCGTAGCGCTGGGTCCTGCCTTTACATGCC 4 108 0 GGGTCCTGCC 0.989423 -96 GCAGGACCCAGCGCTACGCCCGAGGTGGCA 4 119 1 GCGCTACGCC 0.860439 -85 GCGGGGTTTGTCGACACGCTGAGACACCTC 8 24 0 TCGACACGCT 0.838867 -222 AAATGCTTAGGCGTCCTGCCTAAACACCGC 8 106 1 GCGTCCTGCC 0.986932 -140 CCCTCCGCAATGTTCCTGCCTTTATATTTT 8 217 0 TGTTCCTGCC 0.816192 -29 ********** Masking position 8 Map Score: 3.56244 Number of sites scoring better than the average of aligned sites = 2114 Number in coding regions = 1996 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 5 TTTAAACAGTCTCGTTAAACAGAATGATACAC 1 80 0 CTCTTAACAG 0.891897 -35 CAAGATTTTTCCGTTTAAACAGTCTCGTTAAA 1 93 0 CCGTTAACAG 0.572394 -22 CGCTATATACATGATTACATAGCGAAAGTGTG 2 112 1 ATGTTAATAG 0.783616 -189 ATTAAAACGCTCCTTAAACAGATCATACACT 5 105 0 CTCTTAACAG 0.891897 -21 AGTCCTTTATACAGAGGTGTCTCA 8 3 1 TCCTTAACAG 0.969784 -243 CCTGTAAAAGCCCTTTATATAGAGGGCTCTTT 8 147 1 CCCTTAATAG 0.982221 -99 *** *** **** Masking position 6 Map Score: 3.49209 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 56 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 GGAGGCGAAGTCATTTCTTCCTTCGCCCTG 2 262 0 TCATTTCTTC 0.924371 -39 CTGATCTCTCCTTTTGACGTT 3 11 0 TGATCTCTCC 0.941704 -11 ATTATTTCACCTCTGCTATAA 5 2 1 TTATTTCACC 0.872958 -124 ATCATCTCACCTCTAGTTTCG 6 126 0 TCATCTCACC 0.990665 -11 ATCTTTTATGTCATCTTATCATGTTATTGC 7 15 0 TCATCTTATC 0.912593 -36 AACACCGCCGTCATCACATCCTGTAAAAGC 8 128 1 TCATCACATC 0.943342 -118 ********** Masking position 4 Map Score: 1.59818 Number of sites scoring better than the average of aligned sites = 424 Number in coding regions = 382 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 7 TCCCTTATTCTGTAGCGAAATAGCACGATCATGACGCTA 2 78 1 TGTGAAACGT 0.824397 -223 GTACACCTTTCCAGATACGGGAGGCGAAGTCATTTC 2 275 0 TTTGAAAGGG 0.979574 -26 ACTCATTCAATTTTTGAATATAGAAAGATGGATATGGCA 4 73 1 TTTAAAAAGT 0.688522 -131 TCTGTGGCGTTTTTCTGACATAATAGGCAAATTCGATTT 4 154 1 TTTGAAAGGA 0.824609 -50 ATTTCACCTCTGCTATAATAAGTTAAGTGTAGCTTATGA 5 14 1 TGCAAAAAGG 0.950348 -112 TTGCTATGCTTTTAACGAAACTAGAGGTGAGATGAT 6 111 1 TTTGAAAGGG 0.979574 -26 CATGATAAGATGACATAAAAGATAAGGAGAACAGGTTTG 7 22 1 TGAAAAAGGG 0.895772 -29 AGCACCAATGTGCATTGACAACGAACGCGGGGTTTGTCG 8 41 0 TGCGAAACGG 0.962117 -205 GGTGCTCACGTGTTATAAAAGGAACGGCGGCTAAATGCT 8 74 1 TGTAAACGGG 0.891692 -172 TTTTGTCGAATTCTGAGACACAAAAAGAGCCCTCTATAT 8 163 0 TTCGAAAAGG 0.950348 -83 TGTCTCAGAATTCGACAAAATCCGAGGAGTGTGAAAAAA 8 182 1 TTCAAAAGGG 0.965542 -64 ATCCGAGGAGTGTGAAAAAATATAAAGGCAGGAACATTG 8 201 1 TGTAAAAAGC 0.748347 -45 *** ** * *** * Masking position 10 Map Score: 5.06956 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 307 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 8 ACATCATCAGGGAGGCATAGCGTGCATCGT 2 25 0 GGAGGCATAG 0.98863 -276 CCTTCGCCCTGGTGGCAATCTTTACGAGCA 2 243 0 GGTGGCAATC 0.898535 -58 TCCAGATACGGGAGGCGAAGTCATTTCTTC 2 272 0 GGAGGCGAAG 0.988805 -29 CACCCTTAATGGACGAATACT 4 2 0 GGACGAATAC 0.74292 -202 TTATAGCAAAAGTGGCGAACCACCCTTAAT 4 22 0 AGTGGCGAAC 0.901257 -182 CTACGCCCGAGGTGGCATACAGTCTGTGGC 4 132 1 GGTGGCATAC 0.978457 -72 ACACTCCTGCGGAGGCAAAATCGAATTTGC 4 180 0 GGAGGCAAAA 0.953554 -24 TGTTTATTAAAGAGGAATAGCTGTTCAGTA 6 53 0 AGAGGAATAG 0.796616 -84 GGAACATTGCGGAGGGGAAGAGACA 8 231 1 GGAGGGGAAG 0.944413 -15 ********** Masking position 5 Map Score: 7.3976 Number of sites scoring better than the average of aligned sites = 973 Number in coding regions = 889 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 9 ********** No masking Map Score: -2.12209e-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: -2.12209e-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: -2.12209e-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