AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i072_Fatty_Acid_Bios_+_Butirate_Fermentation_ecoli_hinf_reg_100.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 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 #7 HI0774 205 acetate CoA-transferase, alpha subunit Motif number 1 ATTCACCCGAAACAAAAATGTGATACCAATCAC 1 16 0 AACAAATGGA 0.974769 -285 TTTATGGATCACCAATATTGAAAGTCAGATGTT 1 115 0 ACCAAATGAA 0.989213 -186 TGATCCATAAAACAATATTGAAAATTTCTTTTT 1 137 1 AACAAATGAA 0.991109 -164 TAAGTTCCTCACCAATATTGAAAACACGGCGTA 1 172 0 ACCAAATGAA 0.989213 -129 TGAGGAACTTAACAATATTGAAAGTTGGATTTA 1 194 1 AACAAATGAA 0.991109 -107 AACTTTAATCACCAATATTGAAAATGTCACACG 1 231 0 ACCAAATGAA 0.989213 -70 AACTATTAGCAACAGAAATGTGAAACATCTGGA 2 19 0 AACAGATGGA 0.889588 -266 AACTGCGGAAAACATTAATGCACTGATAAATAA 2 116 1 AACATATGAC 0.826032 -169 TAATTAATTCACGAAAACTGGAATCGTAAAGGT 2 256 1 ACGAAATGAA 0.951712 -29 CGATCGCTAAAACAAAAGTGCAATTTGCGGCAA 3 143 0 AACAAATGAA 0.991109 -158 TTTCCTTGCCAACAATCTTGCAAAAAAAATGCG 3 174 0 AACAACTGAA 0.950339 -127 TTAAACAATTAAGATAACTGTAATTAACAATCA 6 197 1 AAGATATGAA 0.855998 -55 ***** * ** ** Masking position 4 Map Score: 22.2076 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 29 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 2 TGGATCACCAATATTGAAAGTCAGATGTTA 1 114 0 ATATTGAAAG 0.985101 -187 CCATAAAACAATATTGAAAATTTCTTTTTG 1 141 1 ATATTGAAAA 0.982065 -160 TTCCTCACCAATATTGAAAACACGGCGTAG 1 171 0 ATATTGAAAA 0.982065 -130 GAACTTAACAATATTGAAAGTTGGATTTAT 1 198 1 ATATTGAAAG 0.985101 -103 TTAATCACCAATATTGAAAATGTCACACGC 1 230 0 ATATTGAAAA 0.982065 -71 AACTAGATTGATATTAAAAATAGCAAAAAG 7 81 0 ATATTAAAAA 0.937188 -125 CCTAATAACGAGATTAAAAGAAAGAATATC 7 178 0 AGATTAAAAG 0.847358 -28 ********** Masking position 7 Map Score: 11.7928 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 29 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 3 CGTTTTTTCGTTAATTTTGATTAATAATCAG 1 55 1 TTATTTTGAT 0.938851 -246 TATTGAAAATTTCTTTTTGCTACGCCGTGTT 1 152 1 TTTTTTTGCT 0.960761 -149 ATCACGCCCTTTAATTTTGAAATAAAACTTT 1 258 0 TTATTTTGAA 0.810165 -43 TACAAAATTTGTGATTTTACTTAACTATTGT 2 192 1 GTATTTTACT 0.839319 -93 AATGTGATTCGTGTTTTTAATTAATTCACGA 2 239 1 GTTTTTTAAT 0.766111 -46 CCGGCATATATTGTTTTTGCTTGCTCATGG 3 10 0 TTTTTTTGCT 0.960761 -291 AGCGATCGCATTTTTTTTGCAAGATTGTTGG 3 168 1 TTTTTTTGCA 0.871897 -133 TTTAAAAAAAGTGATTTTTATCACAAAGGAA 6 171 0 GTATTTTTAT 0.650051 -81 GCGGGTATAAGTTATTTTGATAGTGTTTTAA 7 20 0 GTATTTTGAT 0.943293 -186 TTTTACGAAATTCTTTTTGCTATTTTTAATA 7 69 1 TTTTTTTGCT 0.960761 -137 ** ******** Masking position 6 Map Score: 7.60251 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 289 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 4 TGTGATTGGTATCACATTTTTGTTTCGGGT 1 15 1 ATCACATTTT 0.93812 -286 TGCTATACAGATCGCATAGTTAACATTTCG 2 87 0 ATCGCATAGT 0.93671 -198 AAAAACACGAATCACATTGTTTTATGAAAG 2 227 0 ATCACATTGT 0.948207 -58 ATTGCCGCAAATTGCACTTTTGTTTTAGCG 3 142 1 ATTGCACTTT 0.863002 -159 TGTTTTAGCGATCGCATTTTTTTTGCAAGA 3 162 1 ATCGCATTTT 0.974864 -139 CCGCACCGCTATCGCACACTATTTTCAGGC 3 229 1 ATCGCACACT 0.893401 -72 AAATCCAATAATCTCATTCTGGCACTCCCC 4 126 1 ATCTCATTCT 0.832614 -70 TGTGATAAAAATCACTTTTTTTAAACAATT 6 177 1 ATCACTTTTT 0.705005 -75 ATCATTTACTATTGCACTGTTAATTGGTGC 6 226 1 ATTGCACTGT 0.883817 -26 ********** Masking position 2 Map Score: 5.18328 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 243 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 5 CACATTTTTGTTTCGGGTGAATAGAGGGCGTTTTTTCGTT 1 27 1 TCGGAAAGGG 0.945425 -274 ACAATATTGAAAGTTGGATTTATCTGCGTGTGACATTTTC 1 205 1 ATGGTTTCGG 0.669398 -96 TAATTCACGAAAACTGGAATCGTAAAGGTGATGAC 2 260 1 ACGGTCAGGG 0.977552 -25 AAAACAATATATGCCGGATAAAATACGGCGTGTATTGCGG 3 24 1 ACGGAAAGGG 0.989761 -277 TACGGCGTGTATTGCGGTTATACAACCGCGTTTAGCGAGA 3 47 1 AGGGATACGG 0.918481 -254 TGCGATAGCGGTGCGGGGTTTTCGACGGAGCAAGCTGTTT 3 205 0 GCGGTTAGGG 0.983112 -96 GGGATAAATTGGATGGGGATTTATAAGGAGAATGAGCGGC 4 61 0 GTGGTTAGGG 0.930143 -135 TTGTGGGTACAGTCAGGCAATAGCAAGGGGAGTGCCAGAA 4 142 0 ACGGATAGGG 0.991672 -54 ATTTACCATAAACCAGGTTAAGTATGGGAGATTAACGCCC 6 53 1 ACGGAATGGG 0.96412 -199 TAACCCACCAATAGAGGGGTAGATAGGGCGTTAATCTCCC 6 78 0 AGGGTAAGGG 0.971591 -174 * * ** ** * ** * Masking position 7 Map Score: 5.98806 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 312 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 6 TAACGAAAAAACGCCCTCTATTCACCCGAAA 1 37 0 ACGCCCTTAT 0.98901 -264 TCTTTTTGCTACGCCGTGTTTTCAATATTGG 1 163 1 ACGCCGTTTT 0.986063 -138 TACAGATATCACGCCCTTTAATTTTGAAATA 1 265 0 ACGCCCTTAA 0.949196 -36 GACGGATTTCGCACCCTATTTTTATAAATCA 2 149 0 GCACCCTTTT 0.968576 -136 ACCGCAATACACGCCGTATTTTATCCGGCAT 3 34 0 ACGCCGTTTT 0.986082 -267 CACCGCTATCGCACACTATTTTCAGGCCATT 3 232 1 GCACACTTTT 0.799917 -69 TGGGAGATTAACGCCCTATCTACCCCTCTAT 6 77 1 ACGCCCTTCT 0.986952 -175 ******* *** Masking position 7 Map Score: 5.05339 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 158 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 TTTTTACTCACAACAGAGCATAACAAACTG 1 83 0 CAACAGAGCA 0.90317 -218 ATTGAAAACACGGCGTAGCAAAAAGAAATT 1 159 0 CGGCGTAGCA 0.986892 -142 ACTATGCGATCTGTATAGCAACTGCGGAAA 2 97 1 CTGTATAGCA 0.928648 -188 GCGGGGTTTTCGACGGAGCAAGCTGTTTTC 3 203 0 CGACGGAGCA 0.954735 -98 GTGCAAATTTCTGCATAGCAAGTTTTGGTG 4 11 0 CTGCATAGCA 0.988253 -185 GCGCAATTTTCTGCATAGCCGCTCATTCTC 4 44 1 CTGCATAGCC 0.968516 -152 ********** Masking position 7 Map Score: 2.75805 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 0.934213 -267 ATCTTTTAACGAAATGTTAACTATGCGATC 2 78 1 GAAATGTTAA 0.900308 -207 AAACATTAATGCACTGATAAATAATGATTT 2 125 1 GCACTGATAA 0.912033 -160 TTGTATGTTTGAACTGTGACGGATTTCGCA 2 167 0 GAACTGTGAC 0.938899 -118 AGAAAATTGCGCACTGTGCAAATTTCTGCA 4 26 0 GCACTGTGCA 0.960259 -170 ATTTACTATTGCACTGTTAATTGGTGCGAG 6 229 1 GCACTGTTAA 0.976758 -23 ********** Masking position 5 Map Score: 2.12271 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 TTGGTGATCCATAAAACAATATTGAAAATT 1 133 1 ATAAAACAAT 0.866081 -168 TTGGTGAGGAACTTAACAATATTGAAAGTT 1 190 1 ACTTAACAAT 0.919178 -111 ATGATTCGCGATTTAACTATTAGCAACAGA 2 36 0 ATTTAACTAT 0.913305 -249 TTGTGATTTTACTTAACTATTGTGTAACTT 2 200 1 ACTTAACTAT 0.837391 -85 TGTAACTTTCATAAAACAATGTGATTCGTG 2 222 1 ATAAAACAAT 0.866081 -63 GGATTTAGTTATTTAACTAATTGAATATGA 4 102 0 ATTTAACTAA 0.745456 -94 TCATCTACAAATTAAACAAAATGGAGGGCA 6 23 1 ATTAAACAAA 0.866085 -229 AATCACTTTTTTTAAACAATTAAGATAACT 6 186 1 TTTAAACAAT 0.866085 -66 AGATAACTGTAATTAACAATCATTTACTAT 6 208 1 AATTAACAAT 0.806561 -44 TTGATAGTGTTTTAAACAATCCTT 7 5 0 TTTAAACAAT 0.866085 -201 ********** Masking position 5 Map Score: 5.9462 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 130 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 10 CGTGATATCTGTAATTAACACCACCGAT 1 283 1 GTAATAACAC 0.882836 -18 ATTGTTTTATGAAAGTTACACAATAGTTAAG 2 211 0 GAAATTACAC 0.969988 -74 CTATATTGCCGCAAATTGCACTTTTGTTTTA 3 138 1 GCAATTGCAC 0.967796 -163 TTGCTATGCAGAAATTTGCACAGTGCGCAAT 4 20 1 GAAATTGCAC 0.98524 -176 CGGCTATGCAGAAAATTGCGCACTGTGCAAA 4 34 0 GAAATTGCGC 0.982249 -162 CTGGTTTATGGTAAATTGCCCTCCATTTTGT 6 38 0 GTAATTGCCC 0.941575 -214 TTAAGTATGGGAGATTAACGCCCTATCTACC 6 70 1 GAGATAACGC 0.781958 -182 **** ****** Masking position 4 Map Score: 2.68286 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 180 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 11 ********** No masking Map Score: 1.28851e-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: 1.28851e-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 13 ********** No masking Map Score: 1.28851e-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