AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i072_Fatty_Acid_Bios_+_Butirate_Fermentation_ecoli_reg_300.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 atoS 214 sensor protein AtoS for response regulator AtoC #5 atoD 195 acetyl-CoA:acetoacetyl-CoA transferase alpha subunit #6 atoB 30 acetyl-CoA acetyltransferase #7 yqeF 251 putative acyltransferase Motif number 1 ATTCACCCGAAACAAAAATGTGATACCAATCAC 1 16 0 AACAAATGGA 0.948505 -285 TTTATGGATCACCAATATTGAAAGTCAGATGTT 1 115 0 ACCATATGAA 0.985294 -186 TGATCCATAAAACAATATTGAAAATTTCTTTTT 1 137 1 AACATATGAA 0.989159 -164 TAAGTTCCTCACCAATATTGAAAACACGGCGTA 1 172 0 ACCATATGAA 0.985294 -129 TGAGGAACTTAACAATATTGAAAGTTGGATTTA 1 194 1 AACATATGAA 0.989159 -107 AACTTTAATCACCAATATTGAAAATGTCACACG 1 231 0 ACCATATGAA 0.985294 -70 AACTATTAGCAACAGAAATGTGAAACATCTGGA 2 19 0 AACAAATGGA 0.948505 -266 AACTGCGGAAAACATTAATGCACTGATAAATAA 2 116 1 AACATATGAC 0.939988 -169 TAATTAATTCACGAAAACTGGAATCGTAAAGGT 2 256 1 ACGAAATGAA 0.930566 -29 CGATCGCTAAAACAAAAGTGCAATTTGCGGCAA 3 143 0 AACAAATGAA 0.983137 -158 TTTCCTTGCCAACAATCTTGCAAAAAAAATGCG 3 174 0 AACATCTGAA 0.935027 -127 TATACCGGACAAGACTAGTGGATTTCAGC 4 196 1 AAGATATGAT 0.767896 -19 TTAAACAATTAAGATAACTGTAATTAACAATCA 7 197 1 AAGAAATGAA 0.948057 -55 **** ** ** ** Masking position 4 Map Score: 23.2879 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 54 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 2 GTTTCGGGTGAATAGAGGGCGTTTTTTCGTT 1 36 1 AATAAGGGCG 0.963454 -265 ACCAATATTGAAAACACGGCGTAGCAAAAAG 1 164 0 AAAAACGGCG 0.980225 -137 TTATTTCAAAATTAAAGGGCGTGATATCTGT 1 264 1 ATTAAGGGCG 0.825307 -37 ATGATTTATAAAAATAGGGTGCGAAATCCGT 2 148 1 AAAAAGGGTG 0.963975 -137 TAACTTTCATAAAACAATGTGATTCGTGTTT 2 224 1 AAAAAATGTG 0.850072 -61 TATGCCGGATAAAATACGGCGTGTATTGCGG 3 33 1 AAAAACGGCG 0.980225 -268 CAATCTTGCAAAAAAAATGCGATCGCTAAAA 3 164 0 AAAAAATGCG 0.952595 -137 AAATGGCCTGAAAATAGTGTGCGATAGCGGT 3 233 0 AAAAAGTGTG 0.943756 -68 CAGAGAAGAGAGAACATTGCGGTAACACGCT 4 114 0 AGAAATTGCG 0.907599 -101 GCGGCTATGCAGAAAATTGCGCACTGTGCAA 5 35 0 AGAAATTGCG 0.907599 -161 **** ****** Masking position 6 Map Score: 10.4263 Number of sites scoring better than the average of aligned sites = 430 Number in coding regions = 354 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 3 TAACATCTGACTTTCAATATTGGTGATCCA 1 114 1 CTTTCAATAT 0.982498 -187 CAAAAAGAAATTTTCAATATTGTTTTATGG 1 141 0 TTTTCAATAT 0.981135 -160 CTACGCCGTGTTTTCAATATTGGTGAGGAA 1 171 1 TTTTCAATAT 0.981135 -130 ATAAATCCAACTTTCAATATTGTTAAGTTC 1 198 0 CTTTCAATAT 0.982498 -103 GCGTGTGACATTTTCAATATTGGTGATTAA 1 230 1 TTTTCAATAT 0.981135 -71 TTAAAGTTTTATTTCAAAATTAAAGGGCGT 1 256 1 ATTTCAAAAT 0.829305 -45 ********** Masking position 6 Map Score: 9.42438 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 4 AATTTCTTTTTGCTACGCCGTGTTTTCAAT 1 159 1 TGCTACGCCG 0.986263 -142 ATTGAAAATGTCACACGCAGATAAATCCAA 1 218 0 TCACACGCAG 0.823292 -83 TTTCCGCAGTTGCTATACAGATCGCATAGT 2 97 0 TGCTATACAG 0.947347 -188 CTCTGGAATATGATACACCGCCGAGAAATC 4 140 1 TGATACACCG 0.966145 -75 CTGATAATCGTCATATACCGGACAAGACTA 4 183 1 TCATATACCG 0.917073 -32 CACCAAAACTTGCTATGCAGAAATTTGCAC 5 11 1 TGCTATGCAG 0.966146 -185 GAGAATGAGCGGCTATGCAGAAAATTGCGC 5 44 0 GGCTATGCAG 0.941727 -152 TATCCCTCTTGCATACACCGTTGTGGGTAC 5 172 0 GCATACACCG 0.908534 -24 ********** Masking position 5 Map Score: 5.00652 Number of sites scoring better than the average of aligned sites = 395 Number in coding regions = 361 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 5 ATTAACGAAAAAACGCCCTCTATTCACCCGAA 1 38 0 AAACCCTCTA 0.715954 -263 CTAATAGTTAAATCGCGAATCATAAAAAGCAA 2 43 1 AATCCAATCA 0.836188 -242 AATTAATTAAAAACACGAATCACATTGTTTTA 2 233 0 AAACCAATCA 0.780817 -52 GCGGTTGTATAACCGCAATACACGCCGTATTT 3 44 0 AACCCATACA 0.881033 -257 CTCCGTCGAAAACCCCGCACCGCTATCGCACA 3 215 1 AACCCCACCG 0.961104 -86 CCGCTACCTTAACCACACTCCATCGGTCACCT 4 78 0 AACCCCTCCA 0.990633 -137 TCTCCTTATAAATCCCCATCCAATTTATCCCT 5 70 1 AATCCATCCA 0.962857 -126 GTTTATGGTAAATTGCCCTCCATTTTGTTTAA 7 34 0 AATTCCTCCA 0.78316 -218 TAAGGTTTGCAACCACTAACCCACCAATAGAG 7 102 0 AACCCAACCC 0.939375 -150 AACCTCGCACCAATTAACAGTG 7 240 0 AACCCCACCA 0.990633 -12 **** * ***** Masking position 2 Map Score: 5.78999 Number of sites scoring better than the average of aligned sites = 546 Number in coding regions = 486 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 6 CTCCAGATGTTTCACATTTCTGTTGCTAAT 2 18 1 TTCACATTTC 0.930971 -267 GATCGCATAGTTAACATTTCGTTAAAAGAT 2 78 0 TTAACATTTC 0.917818 -207 AAATCATTATTTATCAGTGCATTAATGTTT 2 125 0 TTATCAGTGC 0.908175 -160 TGCGAAATCCGTCACAGTTCAAACATACAA 2 167 1 GTCACAGTTC 0.910594 -118 CAGAGAAGAGAGAACATTGCGGTAACACGC 4 115 0 AGAACATTGC 0.792926 -100 TGCAGAAATTTGCACAGTGCGCAATTTTCT 5 26 1 TGCACAGTGC 0.974819 -170 CTCGCACCAATTAACAGTGCAATAGTAAAT 7 229 0 TTAACAGTGC 0.979441 -23 ********** Masking position 6 Map Score: 2.39922 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 160 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 TTTCGTTAATTTTGATTAATAATCAGTTTG 1 60 1 TTTGATTAAT 0.806941 -241 GCGTGATATCTGTAATTAACACCACCGAT 1 282 1 TGTAATTAAC 0.950681 -19 AATTTGTGATTTTACTTAACTATTGTGTAA 2 197 1 TTTACTTAAC 0.833876 -88 GATTCGTGTTTTTAATTAATTCACGAAAAC 2 244 1 TTTAATTAAT 0.896151 -41 TTGCATTCAGTGTAAATAATCTTGTTTAGC 3 87 0 TGTAAATAAT 0.803245 -214 GATTTAGTTATTTAACTAATTGAATATGAA 5 101 0 TTTAACTAAT 0.831982 -95 TTAAGATAACTGTAATTAACAATCATTTAC 7 205 1 TGTAATTAAC 0.950681 -47 ********** Masking position 8 Map Score: 1.34567 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 43 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 8 ATTCTGTGATTGGTATCACATTTT 1 5 1 TGTGATTGGT 0.955882 -296 CTTTGCTTTTTATGATTCGCGATTTAACTA 2 47 0 TATGATTCGC 0.957649 -238 CATAAAACAATGTGATTCGTGTTTTTAATT 2 231 1 TGTGATTCGT 0.983074 -54 GATTTCTCCTGTGAGTCGCATACGGAACC 3 282 0 TGTGAGTCGC 0.981378 -19 ********** Masking position 5 Map Score: 0.178884 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 17 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 ********** No masking Map Score: 2.53196e-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 TTTTGAAATAAAACTTTAATCACCAATATT 1 245 0 AAACTTTAAT 0.638947 -56 AAGGGCGTGATATCTGTAATTAACACCACC 1 278 1 TATCTGTAAT 0.901791 -23 TAGGGTGCGAAATCCGTCACAGTTCAAACA 2 162 1 AATCCGTCAC 0.649026 -123 AACTATTGTGTAACTTTCATAAAACAATGT 2 214 1 TAACTTTCAT 0.805132 -71 TAATTCACGAAAACTGGAATCGTAAAGGTG 2 260 1 AAACTGGAAT 0.909101 -25 CGCCGTATTTTATCCGGCATATATTGTTTT 3 24 0 TATCCGGCAT 0.909418 -277 ATGACCGTACAATCTTGCATTCAGTGTAAA 3 101 0 AATCTTGCAT 0.818196 -200 TGTTCTCTCTTCTCTGGAATATGATACACC 4 129 1 TCTCTGGAAT 0.753315 -86 GTCAGAGACATAACTGGCACGTAAGGTTTG 7 125 0 TAACTGGCAC 0.909427 -127 ACAATTAAGATAACTGTAATTAACAATCAT 7 201 1 TAACTGTAAT 0.901791 -51 ********** Masking position 9 Map Score: 1.14703 Number of sites scoring better than the average of aligned sites = 1063 Number in coding regions = 912 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 11 ********** No masking Map Score: 2.53196e-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 ATGCTCTGTTGTGAGTAAAAAATAACATCTGA 1 92 1 GGAGAAAAAA 0.959618 -209 ATTGTTTTATGAAAGTTACACAATAGTTAAGT 2 210 0 GAAGTACACA 0.904952 -75 CCATGAGCAAGCAAAAACAATATATGCC 3 7 1 GAAGAAAAAC 0.858256 -294 CGCGTTTAGCGAGAGCTAAACAAGATTATTTA 3 73 1 GGAGTAAACA 0.973935 -228 AAGATTGTTGGCAAGGAAAACAGCTTGCTCCG 3 188 1 GAAGAAAACA 0.959618 -113 CATCTCCGATGGAAGGTAAAAATGGCCTGAAA 3 251 0 GAAGTAAAAA 0.962439 -50 GTGTATGCAAGAGGGATAAAAA 5 184 1 GGGGTAAAAA 0.904952 -12 * *** ****** Masking position 8 Map Score: 0.770046 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 135 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 13 ********** No masking Map Score: 2.53196e-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 14 ********** No masking Map Score: 2.53196e-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 15 ********** No masking Map Score: 2.53196e-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