AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i072_Fatty_Acid_Bios_+_Butirate_Fermentation_ecoli_reg_100.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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 fixA 300 probable flavoprotein subunit, carnitine metabolism #2 ydbO 284 orf, hypothetical protein #3 ydiQ 300 putative transport protein #4 atoD 195 acetyl-CoA:acetoacetyl-CoA transferase alpha subunit #5 atoB 30 acetyl-CoA acetyltransferase #6 yqeF 251 putative acyltransferase Motif number 1 TATGGATCACCAATATTGAAAGTCAGATGT 1 116 0 CAATATTGAA 0.990901 -185 ATCCATAAAACAATATTGAAAATTTCTTTT 1 139 1 CAATATTGAA 0.990901 -162 AGTTCCTCACCAATATTGAAAACACGGCGT 1 173 0 CAATATTGAA 0.990901 -128 AGGAACTTAACAATATTGAAAGTTGGATTT 1 196 1 CAATATTGAA 0.990901 -105 CTTTAATCACCAATATTGAAAATGTCACAC 1 232 0 CAATATTGAA 0.990901 -69 AGTTTTATTTCAAAATTAAAGGGCGTGATA 1 260 1 CAAAATTAAA 0.823666 -41 GAAAGTTACACAATAGTTAAGTAAAATCAC 2 202 0 CAATAGTTAA 0.869905 -83 CATGACCGTACAATCTTGCATTCAGTGTAA 3 102 0 CAATCTTGCA 0.963205 -199 ATCGCTAAAACAAAAGTGCAATTTGCGGCA 3 144 0 CAAAAGTGCA 0.913791 -157 TCCTTGCCAACAATCTTGCAAAAAAAATGC 3 175 0 CAATCTTGCA 0.963205 -126 ATTAACAGTGCAATAGTAAATGATTGTTAA 6 220 0 CAATAGTAAA 0.92182 -32 ********** Masking position 3 Map Score: 23.4848 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 83 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 2 TTCACCCGAAACAAAAATGTGATACCAATCA 1 17 0 ACAAAATGTG 0.850486 -284 GTTTCGGGTGAATAGAGGGCGTTTTTTCGTT 1 36 1 AATAAGGGCG 0.968677 -265 ACCAATATTGAAAACACGGCGTAGCAAAAAG 1 164 0 AAAAACGGCG 0.979142 -137 TTATTTCAAAATTAAAGGGCGTGATATCTGT 1 264 1 ATTAAGGGCG 0.847141 -37 ATGATTTATAAAAATAGGGTGCGAAATCCGT 2 148 1 AAAAAGGGTG 0.979371 -137 TAACTTTCATAAAACAATGTGATTCGTGTTT 2 224 1 AAAAAATGTG 0.920868 -61 TATGCCGGATAAAATACGGCGTGTATTGCGG 3 33 1 AAAAACGGCG 0.979142 -268 GATCGCTAAAACAAAAGTGCAATTTGCGGCA 3 144 0 ACAAAGTGCA 0.748694 -157 CAATCTTGCAAAAAAAATGCGATCGCTAAAA 3 164 0 AAAAAATGCG 0.964626 -137 AAATGGCCTGAAAATAGTGTGCGATAGCGGT 3 233 0 AAAAAGTGTG 0.967502 -68 **** ****** Masking position 6 Map Score: 10.5598 Number of sites scoring better than the average of aligned sites = 608 Number in coding regions = 488 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 3 ATAACATCTGACTTTCAATATTGGTGATCC 1 113 1 ACTTTCAATA 0.985164 -188 GCAAAAAGAAATTTTCAATATTGTTTTATG 1 142 0 ATTTTCAATA 0.984003 -159 GCTACGCCGTGTTTTCAATATTGGTGAGGA 1 170 1 GTTTTCAATA 0.965173 -131 GATAAATCCAACTTTCAATATTGTTAAGTT 1 199 0 ACTTTCAATA 0.985164 -102 TGCGTGTGACATTTTCAATATTGGTGATTA 1 229 1 ATTTTCAATA 0.984003 -72 ********** Masking position 5 Map Score: 7.36766 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 29 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 4 TTTTTCGTTAATTTTGATTAATAATCAGTTT 1 58 1 ATTTTATTAA 0.948305 -243 GGGCGTGATATCTGTAATTAACACCACCGAT 1 280 1 TCTGTATTAA 0.865005 -21 TTCGCACCCTATTTTTATAAATCATTATTTA 2 142 0 ATTTTATAAA 0.892425 -143 AAAATTTGTGATTTTACTTAACTATTGTGTA 2 195 1 ATTTTCTTAA 0.82972 -90 CTATTGTGTAACTTTCATAAAACAATGTGAT 2 216 1 ACTTTATAAA 0.899995 -69 GTGATTCGTGTTTTTAATTAATTCACGAAAA 2 242 1 TTTTTATTAA 0.892425 -43 ATTGCCCTCCATTTTGTTTAATTTGTAGATG 6 24 0 ATTTTTTTAA 0.852883 -228 GCATATTTCCTTTGTGATAAAAATCACTTTT 6 165 1 TTTGTATAAA 0.724671 -87 GATAAAAATCACTTTTTTTAAACAATTAAGA 6 180 1 ACTTTTTTAA 0.862654 -72 AATTAAGATAACTGTAATTAACAATCATTTA 6 203 1 ACTGTATTAA 0.934 -49 ***** ***** Masking position 5 Map Score: 5.97043 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 115 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 5 GTTTGAACTGTGACGGATTTCGCACCCTATTTTTA 2 156 0 TGGATTCGCC 0.968002 -129 TCACATTGTTTTATGAAAGTTACACAATAGTTAAG 2 211 0 TTGAATTACC 0.908745 -74 ATAACTATATTGCCGCAAATTGCACTTTTGTTTTA 3 134 1 TGGAATTGCC 0.997032 -167 AAACTTGCTATGCAGAAATTTGCACAGTGCGCAAT 4 16 1 TGGAATTGCC 0.997032 -180 TGAGCGGCTATGCAGAAAATTGCGCACTGTGCAAA 4 34 0 TGGAATTGCC 0.997032 -162 TAACCTGGTTTATGGTAAATTGCCCTCCATTTTGT 6 38 0 TAGAATTGCC 0.984703 -214 ** * ** **** * Masking position 7 Map Score: 5.58336 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 87 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 TTTTGAAATAAAACTTTAATCACCAATATTG 1 244 0 AAACTTAATC 0.702618 -57 CTAATAGTTAAATCGCGAATCATAAAAAGCA 2 43 1 AATCCGAATC 0.956817 -242 AATTAATTAAAAACACGAATCACATTGTTTT 2 234 0 AAACCGAATC 0.982451 -51 TAATTCACGAAAACTGGAATCGTAAAGGTGA 2 260 1 AAACGGAATC 0.927728 -25 CTCCGTCGAAAACCCCGCACCGCTATCGCAC 3 215 1 AACCCGCACC 0.986214 -86 TAAGGTTTGCAACCACTAACCCACCAATAGA 6 103 0 AACCCTAACC 0.966667 -149 AACCTCGCACCAATTAACAGT 6 241 0 AACCCGCACC 0.986214 -11 **** ****** Masking position 9 Map Score: 4.28268 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 166 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 TTTTTACTCACAACAGAGCATAACAAACTG 1 83 0 CAACAGAGCA 0.912489 -218 ATTGAAAACACGGCGTAGCAAAAAGAAATT 1 159 0 CGGCGTAGCA 0.988259 -142 ACTATGCGATCTGTATAGCAACTGCGGAAA 2 97 1 CTGTATAGCA 0.935689 -188 GCGGGGTTTTCGACGGAGCAAGCTGTTTTC 3 203 0 CGACGGAGCA 0.959314 -98 GTGCAAATTTCTGCATAGCAAGTTTTGGTG 4 11 0 CTGCATAGCA 0.989479 -185 GCGCAATTTTCTGCATAGCCGCTCATTCTC 4 44 1 CTGCATAGCC 0.971742 -152 ********** Masking position 7 Map Score: 3.60227 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 266 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 ATTAGCAACAGAAATGTGAAACATCTGGAG 2 18 0 GAAATGTGAA 0.94634 -267 ATCTTTTAACGAAATGTTAACTATGCGATC 2 78 1 GAAATGTTAA 0.918136 -207 AAACATTAATGCACTGATAAATAATGATTT 2 125 1 GCACTGATAA 0.927933 -160 TTGTATGTTTGAACTGTGACGGATTTCGCA 2 167 0 GAACTGTGAC 0.950208 -118 AGAAAATTGCGCACTGTGCAAATTTCTGCA 4 26 0 GCACTGTGCA 0.96775 -170 ATTTACTATTGCACTGTTAATTGGTGCGAG 6 229 1 GCACTGTTAA 0.9812 -23 ********** Masking position 5 Map Score: 2.96693 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 100 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 TATTGTGTAACTTTCATAAAACAATGTGAT 2 217 1 CTTTCATAAA 0.785262 -68 ACCGTACAATCTTGCATTCAGTGTAAATAA 3 98 0 CTTGCATTCA 0.955084 -203 TGCCAACAATCTTGCAAAAAAAATGCGATC 3 171 0 CTTGCAAAAA 0.95941 -130 AGCTGTTTTCCTTGCCAACAATCTTGCAAA 3 183 0 CTTGCCAACA 0.962378 -118 TTTTATCCCTCTTGCATACACCGTTGTGGG 4 175 0 CTTGCATACA 0.985907 -21 GCACGTAAGGTTTGCAACCACTAACCCACC 6 109 0 TTTGCAACCA 0.829801 -143 ********** Masking position 3 Map Score: 1.50299 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 49 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 10 ********** No masking Map Score: -1.68155e-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: -1.68155e-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: -1.68155e-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