AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifadR_ecoli_hinf_100.orf -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 fabA 68 beta-hydroxydecanoyl thioester dehydrase, trans-2-decenoyl-ACP isomerase #2 b0955 185 putative ATP-dependent protease #3 fadD 204 acyl-CoA synthetase, long-chain-fatty-acid--CoA ligase #4 fadL 300 transport of long-chain fatty acids; sensitivity to phage T2 #5 fadB 189 4-enzyme protein: 3-hydroxyacyl-CoA dehydrogenase; 3-hydroxybutyryl-CoA epimerase; delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase; enoyl-CoA hydratase #6 iclR 160 repressor of aceBA operon #7 HI0387 300 ATP-dependent helicase (dinG) #8 HI0389 24 outer membrane protein #9 HI0390.1 42 long chain fatty acid coenzyme A ligase (fadD) #10 HI0401 206 long-chain fatty acid transport protein (fadL) #11 HI1325 168 3-hydroxydecanoyl-(acyl carrier-protein) dehydratase (fabA) Motif number 1 TTGCTTGTTTTTAAAGAAAAAGAA 3 5 1 TTGTTTTTAA 0.856867 -200 GCGTCACTATTTATTTTTATCTTTACCGTA 3 65 0 TTATTTTTAT 0.946142 -140 TTGTTTTAGATCATTTTTAAGTGTGATTTC 4 58 0 TCATTTTTAA 0.950398 -243 CCTCAATGATTTATTTTTATACAAACTATG 4 279 0 TTATTTTTAT 0.946142 -22 TTTTGTTTGCATATTTTTAACACAAAATAC 5 116 1 ATATTTTTAA 0.903988 -74 AAGATTTTATTCATTTTAAAACATCTAAAA 7 69 1 TCATTTTAAA 0.79648 -232 TAATGACAAATCATTTTTAACCTTTCTCAT 7 138 1 TCATTTTTAA 0.950398 -163 TACATAGAGGCTATTTTTAAAGAACGGTTA 7 190 0 CTATTTTTAA 0.887836 -111 TAAGCCACCAGTATTTTTATTCTTGATATT 7 224 1 GTATTTTTAT 0.785613 -77 CTAGTAAAACATATTTTTAAAGTAAATAAC 7 281 0 ATATTTTTAA 0.903988 -20 ACTCTATTCCTTATTTTTATTAGAGCTACG 10 125 0 TTATTTTTAT 0.946142 -82 GCCCAGATTTTTATTTATAACAAAGGGTTC 10 184 1 TTATTTATAA 0.799807 -23 ACTGATATATTTATTTTAAAAGGAACGCAG 11 113 0 TTATTTTAAA 0.885743 -56 ********** Masking position 9 Map Score: 14.8673 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 121 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 2 GAAACAGCGGCTGGTCCGCTGTTTCTGCAT 3 32 1 CTGGTCCGCT 0.984413 -173 AATTATCAAGCTGGTATGATGAGTTAATAT 3 118 1 CTGGTATGAT 0.945773 -87 ATTTCGGTCACTTATCCGATTTTGCAGAAT 4 33 0 CTTATCCGAT 0.911957 -268 AACATTCCAGCTGGTCCGACCTATACTCTC 4 183 1 CTGGTCCGAC 0.995534 -118 ACTCTCGCCACTGGTCTGATTTCTAAGATG 4 207 1 CTGGTCTGAT 0.988838 -94 TAAAGAAATGCCGATCTGATCACGCTCGGC 5 83 0 CCGATCTGAT 0.889998 -107 TTCGACTCATCTGGTACGACCAGATCACCT 5 150 1 CTGGTACGAC 0.977705 -40 AGTTACTGAACTGATCCGATGAGTTAATGT 6 119 0 CTGATCCGAT 0.990624 -42 CTAAGAGTGACTGCTCCGACAAGTTTTGCG 11 57 1 CTGCTCCGAC 0.980814 -112 ********** Masking position 5 Map Score: 14.0474 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 180 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 3 CGCGGCTTTGACAACAGACTAAAAAACATCAACT 2 162 1 AAACGAAAAA 0.683615 -24 AATCACACTTAAAAATGATCTAAAACAAAATTCAC 4 60 1 AAAAGAAAAA 0.931969 -241 ATCATATTTGAAAAAAGATAGAAACATACTTGCAA 4 150 1 AAAAGAAAAC 0.892247 -151 ATGCGGAGACTTAAGGTCAAAAAAACAGAAGGGTA 5 15 0 TAAGTCAAAA 0.584859 -175 AAATATGCAAACAAAAGATTAAAGAAATGCCGATC 5 97 0 AAAAGAAAGA 0.892247 -93 CAGATTTAATAAAAATTCAACAAACCATACTGGCA 6 34 1 AAAATCAAAC 0.916042 -127 GCTATCTATGAAAAACTCAATAAGATTTTATTCAT 7 48 1 AAAATCAAGA 0.916042 -253 TAGTCAGGCTAAAAGTGCGGTAAAAATTTTAGATG 7 90 0 AAAGGCAAAA 0.925652 -211 ATGATAAAATCTTAAAGATTTTCCAACA 9 4 1 AAAATCAAGA 0.916042 -39 AGAAAAATGATAAAATGCACAAAAATATTCATATA 10 22 0 TAAAGCAAAA 0.920213 -185 CATAAATGACAAAAATTCAACAAAACAATCCATTA 10 64 1 AAAATCAAAA 0.947508 -143 AAACAATCCATTAAATGCAAAAAGCTCCTGCTAAC 10 86 1 TAAAGCAAGC 0.808202 -121 ATAGAAAAAAAGAAAAGCGAAAAAATGCTCGCTTT 11 17 0 AAAAGCAAAA 0.977217 -152 AGTCACTCTTAGAAATTATAGAAAAAAAGAAAAGC 11 34 0 AAAATAAAAA 0.852182 -135 TTATTTTAAAAGGAACGCAGTAAACTGTAAATAGC 11 98 0 AGAAGCAAAC 0.778649 -71 * *** ** **** Masking position 4 Map Score: 11.9614 Number of sites scoring better than the average of aligned sites = 768 Number in coding regions = 619 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 4 ATTTTATTGAAGCACGCAGGATAGCTAACACGTG 1 29 0 ACACGCATAG 0.988743 -40 TGTGAGCTTTAACGCCCATGCCAGGAGTATTGTC 2 87 1 ACGCCCACAG 0.92886 -99 GATGACGACGAACACGCATTTTAGAGGTGAAGAA 3 181 1 ACACGCATAG 0.988743 -24 TGCCAGCTGGATCGCGTTTCTTAGATCATATTTG 4 126 1 ACGCGTTTAG 0.96108 -175 CTGTAACAGGAGCGCGAAGTGTAGGGTCTGAGGT 4 238 0 ACGCGAATAG 0.963894 -63 CTCCTGTTACAGCACGTAACATAGTTTGTATAAA 4 260 1 ACACGTATAG 0.977025 -41 TGCCGATCTGATCACGCTCGGCAGAAATCACGCT 5 71 0 ACACGCTCAG 0.947938 -119 AACCGTGTATTCTAGAACCAGTTTT 7 2 1 ACGTGTATAG 0.882801 -299 * ****** *** Masking position 13 Map Score: 5.0246 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 130 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 TTCTCTGTAAGCCTTATTTTATTGAAGCACG 1 47 0 GCTTATTTTA 0.51465 -22 TTGCTTGTTTTTAAAGAAAAAG 3 2 1 TCTTGTTTTT 0.777778 -203 GACCAGCCGCTGTTTCTTTTTCTTTAAAAAC 3 17 0 TTTTCTTTTT 0.943766 -188 AGCGCGTCACTATTTATTTTTATCTTTACCG 3 67 0 TTTTATTTTT 0.953272 -138 CAAGTATGTTTCTATCTTTTTTCAAATATGA 4 151 0 TTATCTTTTT 0.774153 -150 AACCTCAATGATTTATTTTTATACAAACTA 4 281 0 GTTTATTTTT 0.876088 -20 ATCTTTTGTTTGCATATTTTTAACACAAAAT 5 113 1 TCATATTTTT 0.75367 -77 GCCACCAGTATTTTTATTCTTGATATTTAGC 7 227 1 TTTTATTCTT 0.762901 -74 CATTTTATCATTTTTCTTTTTCCCCATAAAT 10 40 1 TTTTCTTTTT 0.943766 -167 GCAACTCTATTCCTTATTTTTATTAGAGCTA 10 127 0 TCTTATTTTT 0.937422 -80 ATTGCCCAGATTTTTATTTATAACAAAGGGT 10 181 1 TTTTATTTAT 0.68464 -26 CATTTTTTCGCTTTTCTTTTTTTCTATAATT 11 25 1 CTTTCTTTTT 0.759646 -144 ATAACTGATATATTTATTTTAAAAGGAACGC 11 115 0 TTTTATTTTA 0.806452 -54 * ********* Masking position 5 Map Score: 8.12324 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 154 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 6 GGATGGAGATTCTTTTCTTCACTGGCCTAAA 2 56 0 TCTTTTCTCA 0.683301 -130 GCCGCTGTTTCTTTTTCTTTAAAAACAAGCA 3 12 0 CTTTTTCTTA 0.545494 -193 TTTATTTTTATCTTTACCGTAAGAATGCAGA 3 55 0 TCTTTACCTA 0.95823 -150 TTTTTACCCTTCTGTTTTTTT 5 1 1 TTTTTACCTT 0.712842 -189 CCTTCTGTTTTTTTGACCTTAAGTCTCCGCA 5 18 1 TTTTGACCTA 0.786289 -172 TGTTTGCATATTTTTAACACAAAATACACAC 5 119 1 TTTTTAACCA 0.601752 -71 GTGGTGGTCGCTTTTACCACAGATGCGTTTA 6 69 0 CTTTTACCCA 0.913472 -92 ACATCTAAAATTTTTACCGCACTTTTAGCCT 7 89 1 TTTTTACCCA 0.95823 -212 AAATGATTTGTCATTACCTTATCTTTTGCTA 7 123 0 TCATTACCTA 0.69305 -178 TTTTTATCCTAATTTGTTGGA 9 32 0 TTTTTATCTA 0.624239 -11 TTTCTTTNCCTTATATGAATATT 10 3 1 TCTTTNCCTA 0.95823 -204 TATCATTTTTCTTTTTCCCCATAAATGACAA 10 45 1 CTTTTTCCCA 0.857575 -162 TGAGTGCAACTCTATTCCTTATTTTTATTAG 10 132 0 TCTATTCCTA 0.562896 -75 TCGCTTTTCTTTTTTTCTATAATTTCTAAGA 11 32 1 TTTTTTCTTA 0.722841 -137 ******** ** Masking position 4 Map Score: 7.502 Number of sites scoring better than the average of aligned sites = 609 Number in coding regions = 498 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 7 TGTTAGCTATCCTGCGTGCTTCAATAAAAT 1 33 1 CCTGCGTGCT 0.908801 -36 ACTCATCATACCAGCTTGATAATTACCCAA 3 112 0 CCAGCTTGAT 0.985966 -93 CCAAATTTTGCCAGCTGGATCGCGTTTCTT 4 118 1 CCAGCTGGAT 0.983121 -183 ATAGGTCGGACCAGCTGGAATGTTGCAAGT 4 177 0 CCAGCTGGAA 0.934934 -124 TCGTTCATCCAGAGCGTGATTTCTGCCGAG 5 59 1 AGAGCGTGAT 0.899319 -131 TGATTTCTGCCGAGCGTGATCAGATCGGCA 5 75 1 CGAGCGTGAT 0.982976 -115 ********** Masking position 5 Map Score: 2.6413 Number of sites scoring better than the average of aligned sites = 700 Number in coding regions = 678 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 TTGCAGAATTAACAACTGGAGCAGCACTTT 4 12 0 AACAACTGGA 0.93021 -289 TCCAGCTGGCAAAATTTGGAGGTGGCGCAC 4 107 0 AAAATTTGGA 0.750972 -194 GAATTTTTATTAAATCTGGGTTGAGCGTGT 6 22 0 TAAATCTGGG 0.800483 -139 TGCTTATCCCAAAAACTGGTTCTAGAATAC 7 17 0 AAAAACTGGT 0.958709 -284 TCAAGAATAAAAATACTGGTGGCTTAAGAT 7 220 0 AAATACTGGT 0.806239 -81 GTTTAAATAACTGGAGGATAGAAA 8 6 1 AATAACTGGA 0.89994 -19 GTTATAAATAAAAATCTGGGCAATTATAAA 10 175 0 AAAATCTGGG 0.957243 -32 TATATCAGTTATAAACTGGATTTATCATAT 11 134 1 ATAAACTGGA 0.885892 -35 ********** Masking position 7 Map Score: 2.44603 Number of sites scoring better than the average of aligned sites = 605 Number in coding regions = 564 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 9 GCCAGCTGGATCGCGTTTCTTAGATCATAT 4 127 1 TCGCGTTTCT 0.993977 -174 ACCCTACACTTCGCGCTCCTGTTACAGCAC 4 245 1 TCGCGCTCCT 0.971007 -56 TCTTGATATTTAGCGTTTCTATGCGACAAT 7 244 1 TAGCGTTTCT 0.969348 -57 GAAAAAATGCTCGCTTTTCTCTA 11 4 0 TCGCTTTTCT 0.986531 -165 GAGCATTTTTTCGCTTTTCTTTTTTTCTAT 11 22 1 TCGCTTTTCT 0.986531 -147 ********** Masking position 7 Map Score: 5.84612 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 42 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 TAAGCCTTATTTTATTGAAGCACGCAGGAT 1 41 0 TTTATTGAAG 0.836137 -28 CGTGTAACTCTTTACAGAATATCAGCTTTT 2 28 1 TTTACAGAAT 0.89703 -158 CTTATCCGATTTTGCAGAATTAACAACTGG 4 23 0 TTTGCAGAAT 0.913168 -278 TTGTTGAATTTTTATTAAATCTGGGTTGAG 6 27 0 TTTATTAAAT 0.719533 -134 GCCAGTATGGTTTGTTGAATTTTTATTAAA 6 38 0 TTTGTTGAAT 0.952423 -123 TTGAATAGATTTTACTCAATGAGAAAGGTT 7 156 0 TTTACTCAAT 0.82116 -145 AATGGATTGTTTTGTTGAATTTTTGTCATT 10 68 0 TTTGTTGAAT 0.952423 -139 ********** Masking position 8 Map Score: 0.668279 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 118 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 11 ********** No masking Map Score: 5.84309e-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: 5.84309e-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: 5.84309e-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