AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifadR_ecoli_hinf_300.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 b1806 39 putative outer membrane protein #5 yeaZ 57 orf, hypothetical protein #6 b1808 83 putative enzyme #7 fadL 300 transport of long-chain fatty acids; sensitivity to phage T2 #8 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 #9 iclR 160 repressor of aceBA operon #10 HI0387 300 ATP-dependent helicase (dinG) #11 HI0389 24 outer membrane protein #12 HI0390.1 42 long chain fatty acid coenzyme A ligase (fadD) #13 HI0401 206 long-chain fatty acid transport protein (fadL) #14 HI1324 96 lon protease, putative #15 HI1325 168 3-hydroxydecanoyl-(acyl carrier-protein) dehydratase (fabA) Motif number 1 ATTATCAAGCTGGTATGATGAGTTAATATTATGTTAACGG 3 119 1 TGTGAGGTTT 0.994109 -86 TTACGGAGTATGGTATGATGCGCGCCTTTTTATTGATCTA 5 15 1 TGTGAGGTTT 0.994109 -43 ACAGGGATTATGTCAGGATGAGGGCGCTTTCGCCAGTTGA 6 34 0 TGCGAGGCTT 0.970513 -50 ATGAACGATGTGCTAAGATGCGGAGACTTAAGGTCAAAAA 8 27 0 TGTGAGGCTA 0.952501 -163 CTGCCGAGCGTGATCAGATCGGCATTTCTTTAATCTTTTG 8 81 1 TGTGACGTTT 0.985014 -109 TCGTACCAGATGAGTCGAAGTGTGTATTTTGTGTTAAAAA 8 129 0 TGGGAGGTTT 0.972371 -61 TCGACTCATCTGGTACGACCAGATCACCTTGCGGATTCAG 8 151 1 TGTGACGCTT 0.983993 -39 TATGCCAGTATGGTTTGTTGAATTTTTATTAAATCTGGGT 9 31 0 TGTGTGATTT 0.767401 -130 ACAAATCTCATGTTGCGTGGTGGTCGCTTTTACCACAGAT 9 76 0 TGTGTGGCTT 0.975099 -85 GTTACTGAACTGATCCGATGAGTTAATGTTGAACAAATCT 9 108 0 TGTGAGGTTT 0.994109 -53 TTCGCAAAACTTGTCGGAGCAGTCACTCTTAGAAATTATA 15 49 0 TTTGACGTTT 0.838165 -120 ** * ** * * * ** Masking position 19 Map Score: 13.3063 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 80 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 TTGCTTGTTTTTAAAGAAAAAGAA 3 5 1 TTGTTTTTAA 0.870514 -200 GCGTCACTATTTATTTTTATCTTTACCGTA 3 65 0 TTATTTTTAT 0.929622 -140 TTGTTTTAGATCATTTTTAAGTGTGATTTC 7 58 0 TCATTTTTAA 0.914225 -243 CCTCAATGATTTATTTTTATACAAACTATG 7 279 0 TTATTTTTAT 0.929622 -22 TTTTGTTTGCATATTTTTAACACAAAATAC 8 116 1 ATATTTTTAA 0.851769 -74 AAGATTTTATTCATTTTAAAACATCTAAAA 10 69 1 TCATTTTAAA 0.666677 -232 TAATGACAAATCATTTTTAACCTTTCTCAT 10 138 1 TCATTTTTAA 0.914225 -163 TACATAGAGGCTATTTTTAAAGAACGGTTA 10 190 0 CTATTTTTAA 0.828479 -111 TAAGCCACCAGTATTTTTATTCTTGATATT 10 224 1 GTATTTTTAT 0.835255 -77 CTAGTAAAACATATTTTTAAAGTAAATAAC 10 281 0 ATATTTTTAA 0.851769 -20 ACTCTATTCCTTATTTTTATTAGAGCTACG 13 125 0 TTATTTTTAT 0.929622 -82 GCCCAGATTTTTATTTATAACAAAGGGTTC 13 184 1 TTATTTATAA 0.69434 -23 ATTAATATACGTGTTTTTATGCCGATTTTC 14 40 1 GTGTTTTTAT 0.59541 -57 ACTGATATATTTATTTTAAAAGGAACGCAG 15 113 0 TTATTTTAAA 0.812952 -56 ********** Masking position 9 Map Score: 13.6968 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 3 ATGCAGAAACAGCGGACCAGCCGCTGTTTC 3 32 0 AGCGGACCAG 0.980758 -173 ATATTAACTCATCATACCAGCTTGATAATT 3 118 0 ATCATACCAG 0.933675 -87 ATTCTGCAAAATCGGATAAGTGACCGAAAT 7 33 1 ATCGGATAAG 0.893161 -268 GAGAGTATAGGTCGGACCAGCTGGAATGTT 7 183 0 GTCGGACCAG 0.994473 -118 CATCTTAGAAATCAGACCAGTGGCGAGAGT 7 207 0 ATCAGACCAG 0.986206 -94 GCCGAGCGTGATCAGATCGGCATTTCTTTA 8 83 1 ATCAGATCGG 0.867195 -107 AGGTGATCTGGTCGTACCAGATGAGTCGAA 8 150 0 GTCGTACCAG 0.972532 -40 ACATTAACTCATCGGATCAGTTCAGTAACT 9 119 1 ATCGGATCAG 0.988409 -42 CGCAAAACTTGTCGGAGCAGTCACTCTTAG 15 57 0 GTCGGAGCAG 0.976336 -112 ********** Masking position 6 Map Score: 12.8878 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 4 AGTTGATGTTTTTTAGTCTGTTGT 2 172 0 TTGTGTTTTT 0.933261 -14 TTGCTTGTTTTTAAAGAAAAAG 3 1 1 TTGTTTTTTT 0.868479 -204 GGACCAGCCGCTGTTTCTTTTTCTTTAAAAAC 3 17 0 CTGTTTTTTT 0.898596 -188 AAGCGCGTCACTATTTATTTTTATCTTTACCG 3 67 0 CTATTTTTTT 0.635695 -138 CTCATGGATTCGGGTGAATTTTGTTTTAGATC 7 76 0 CGGTGATTTT 0.877655 -225 AACCTCAATGATTTATTTTTATACAAACT 7 282 0 ATGTTATTTT 0.820201 -19 TTTTTACCCTTCTGTTTTTTTGACCTTAAG 8 9 1 CTTTGTTTTT 0.894674 -181 GATGAGTCGAAGTGTGTATTTTGTGTTAAAAA 8 129 0 AGTTGATTTT 0.559326 -61 CCAGTATGGTTTGTTGAATTTTTATTAAATCT 9 35 0 TTGTGATTTT 0.948496 -126 TCAATAAGATTTTATTCATTTTAAAACATCTA 10 64 1 TTTTTATTTT 0.79742 -237 TATGAATATTTTTGTGCATTTTATCATTTTTC 13 24 1 TTTTGATTTT 0.892887 -183 GCATTTTATCATTTTTCTTTTTCCCCATAAAT 13 39 1 ATTTTTTTTT 0.610577 -168 ATGGATTGTTTTGTTGAATTTTTGTCATTTAT 13 65 0 TTGTGATTTT 0.948496 -142 TGCCGATTTTCTAGTGGATTTTCACAAGGCTA 14 59 1 CTATGATTTT 0.829541 -38 *** ** ***** Masking position 5 Map Score: 8.4688 Number of sites scoring better than the average of aligned sites = 689 Number in coding regions = 513 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 5 GTGAATTTTGTTTTAGATCATTTTTAAGTGTGATT 7 60 0 TTTGAATTTT 0.964974 -241 GGATCGCGTTTCTTAGATCATATTTGAAAAAAGAT 7 134 1 TTTGAATTTT 0.964974 -167 AGTCTCCGCATCTTAGCACATCGTTCATCCAGAGC 8 39 1 TTTGCATGTT 0.926723 -151 TTTAATCTTTTGTTTGCATATTTTTAACACAAAAT 8 109 1 TTTGCATTTT 0.981861 -81 TATGCGACAATCTTTGCGGTTATTTACTTTAAAAA 10 263 1 TTTGCTTTTT 0.944766 -38 TATCCTAATTTGTTGGAAAATCTTTAAGATTTTAT 12 14 0 TTTGAATTTT 0.964974 -29 TTCTTTNCCTTATATGAATATTTTTGTGCATTTTA 13 12 1 TTAGAATTTT 0.896972 -195 TATACGTGTTTTTATGCCGATTTTCTAGTGGATTT 14 45 1 TTAGCATTTC 0.799858 -52 AGCGAGCATTTTTTCGCTTTTCTTTTTTTCTATAA 15 19 1 TTTGCTTTTT 0.944766 -150 * ** ** ** *** Masking position 11 Map Score: 6.24734 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 55 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 6 TCTTACGGTAAAGATAAAAATAAATAGTGA 3 62 1 AAGATAAAAA 0.906525 -143 TATTTGAAAAAAGATAGAAACATACTTGCA 7 154 1 AAGATAGAAA 0.770698 -147 AAAAAACAGAAGGGTAAAAA 8 1 0 AGGGTAAAAA 0.8984 -189 CGGAGACTTAAGGTCAAAAAAACAGAAGGG 8 17 0 AGGTCAAAAA 0.784764 -173 TCAATGAGAAAGGTTAAAAATGATTTGTCA 10 141 0 AGGTTAAAAA 0.913197 -160 CTAAATATCAAGAATAAAAATACTGGTGGC 10 227 0 AGAATAAAAA 0.752616 -74 AAATAACTGGAGGATAGAAA 11 15 1 AGGATAGAAA 0.936284 -10 ATGATAAAATCTTAAAGATT 12 1 1 ATGATAAAAT 0.802133 -42 CCAACAAATTAGGATAAAAA 12 33 1 AGGATAAAAA 0.976959 -10 AAAAAGAAAAATGATAAAATGCACAAAAAT 13 31 0 ATGATAAAAT 0.802133 -176 TTCCCCATAAATGACAAAAATTCAACAAAA 13 59 1 ATGACAAAAA 0.862469 -148 ACGTCACTCAATGATAAAAA 14 1 0 ATGATAAAAA 0.947629 -96 ********** Masking position 6 Map Score: 13.3217 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 212 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 7 CACGTGTTAGCTATCCTGCGTGCTTCAATAAAAT 1 29 1 CTATGCGTGT 0.989681 -40 GACAATACTCCTGGCATGGGCGTTAAAGCTCACA 2 87 0 CTGTGGGCGT 0.852624 -99 TTCTTCACCTCTAAAATGCGTGTTCGTCGTCATC 3 181 0 CTATGCGTGT 0.989681 -24 CAAATATGATCTAAGAAACGCGATCCAGCTGGCA 7 126 0 CTAAACGCGT 0.936312 -175 ACCTCAGACCCTACACTTCGCGCTCCTGTTACAG 7 238 1 CTATTCGCGT 0.941434 -63 TTTATACAAACTATGTTACGTGCTGTAACAGGAG 7 260 0 CTATACGTGT 0.979926 -41 AGCGTGATTTCTGCCGAGCGTGATCAGATCGGCA 8 71 1 CTGAGCGTGT 0.919766 -119 TGAACAAATCTCATGTTGCGTGGTGGTCGCTTTT 9 85 0 TCATGCGTGT 0.775666 -76 AAAACTGGTTCTAGAATACACGGTT 10 2 0 CTATACACGT 0.822083 -299 GGTAACTGCATTAATATACGTGTTTTTATGCCGA 14 31 1 TTATACGTGT 0.894054 -66 *** ****** * Masking position 14 Map Score: 5.6046 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 270 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 8 AAAATAAGGCTTACAGAGAAC 1 58 1 TTACAGAGAA 0.888972 -11 GATCTCAATGTTACCGTGTAACTCTTTACA 2 14 1 TTACCGTGTA 0.933586 -172 GTGTAACTCTTTACAGAATATCAGCTTTTT 2 29 1 TTACAGAATA 0.921292 -157 GTAGTGCCGGTTACGGTATAATCGCGGCTT 2 140 1 TTACGGTATA 0.959946 -46 TTCTGCATTCTTACGGTAAAGATAAAAATA 3 54 1 TTACGGTAAA 0.912477 -151 TTTGTTACGGAGTATGGTATGATG 5 5 1 TTACGGAGTA 0.966601 -53 TGTTAGCTATTTACAGTTTACTGCGTTCCT 15 93 1 TTACAGTTTA 0.857793 -76 ********** Masking position 3 Map Score: 2.47872 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 40 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 AGCGATCTCAATGTTACCGT 2 1 1 AGCGATCTCA 0.965676 -185 AAGTGGTGACGGCGACCTCACATT 6 5 0 GGCGACCTCA 0.991606 -79 AACTGGCGAAAGCGCCCTCATCCTGACATA 6 36 1 AGCGCCCTCA 0.99189 -48 ATTTGGAGGTGGCGCACTCATGGATTCGGG 7 94 0 GGCGCACTCA 0.970757 -207 CTGTGGTAAAAGCGACCACCACGCAACATG 9 78 1 AGCGACCACC 0.939005 -83 ********** Masking position 4 Map Score: 2.26673 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 21 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 GGTGCGACTCCTTTTTTTCTCAGGGCAT 4 22 0 CCCTTTTTTT 0.883133 -18 GTATGATGCGCGCCTTTTTATTGATCTAAGC 5 27 1 CCCTTTTTAT 0.837704 -31 AGGGCGCTTTCGCCAGTTGAAGTGGTGACGG 6 23 0 CCCAGTTGAA 0.83535 -61 ACTACCCCCTGTTGATTTGAACAGGG 6 68 0 CCCTGTTGAT 0.96098 -16 GAAAGTGCTGCTCCAGTTGTTAATTCTGCAA 7 11 1 CCCAGTTGTT 0.981406 -290 TTTTTACCCTTCTGTTTTTTTGACCTTAA 8 9 1 CTCTGTTTTT 0.792493 -181 TGTATTCTAGAACCAGTTTTTGGGATAAGCA 10 16 1 ACCAGTTTTT 0.917102 -285 AATCTTAAGCCACCAGTATTTTTATTCTTGA 10 219 1 CCCAGTATTT 0.900051 -82 TTTCTATCCTCCAGTTATTTAAAC 11 6 0 CCCAGTTATT 0.930003 -19 TATATGATAAATCCAGTTTATAACTGATATA 15 134 0 ACCAGTTTAT 0.883132 -35 * ********* Masking position 7 Map Score: 4.99065 Number of sites scoring better than the average of aligned sites = 950 Number in coding regions = 885 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 11 AGCGTACACGTGTTAGCTATCCTGCGTGCT 1 23 1 TGTTAGCTAT 0.967778 -46 ATCTCCATCCTGTGAGCTTTAACGCCCATG 2 77 1 TGTGAGCTTT 0.888609 -109 TGTTGCGTGGTGGTCGCTTTTACCACAGAT 9 76 0 TGGTCGCTTT 0.936138 -85 TTTTATTGTTAGCTAATGCAATAGTT 9 145 0 TGTTAGCTAA 0.916634 -16 AGCGAAAAAATGCTCGCTTTTCTCTA 15 7 0 TGCTCGCTTT 0.936138 -162 AGCGAGCATTTTTTCGCTTTTCTTTTTTTC 15 19 1 TTTTCGCTTT 0.841769 -150 AGCTAACACTTGTTCGCAAAACTTGTCGGA 15 71 0 TGTTCGCAAA 0.757482 -98 TGCGAACAAGTGTTAGCTATTTACAGTTTA 15 83 1 TGTTAGCTAT 0.967778 -86 ********** Masking position 1 Map Score: 3.4034 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 215 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 12 TTAACATAATATTAACTCATCATACCAGCTT 3 125 0 ATTACTCATC 0.965902 -80 CCATACTGGCATAAACGCATCTGTGGTAAAA 9 58 1 ATAACGCATC 0.962196 -103 TTTGTTCAACATTAACTCATCGGATCAGTTC 9 111 1 ATTACTCATC 0.965902 -50 ATGATTTGTCATTACCTTATCTTTTGCTAGT 10 121 0 ATTACTTATC 0.786067 -180 AACCGCAAAGATTGTCGCATAGAAACGCTAA 10 253 0 ATTGCGCATA 0.897082 -48 TTTAAAGTAAATAACCGCAAAGATTGTCGCA 10 265 0 ATAACGCAAA 0.718978 -36 ATTATCGCATATTTAATAGCC 14 86 0 ATTACGCATA 0.965903 -11 **** ****** Masking position 9 Map Score: 1.50258 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 266 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 13 CTTTTTATTGATCTAAGCACGAAGACCC 5 40 1 ATCTAAGCAC 0.931032 -18 TTCAAATATGATCTAAGAAACGCGATCCAG 7 132 0 ATCTAAGAAA 0.951553 -169 TCTGAGGTACATCTTAGAAATCAGACCAGT 7 216 0 ATCTTAGAAA 0.951553 -85 AAGTCTCCGCATCTTAGCACATCGTTCATC 8 38 1 ATCTTAGCAC 0.931031 -152 TAAGCAAGCTATCTATGAAAAACTCAATAA 10 41 1 ATCTATGAAA 0.828929 -260 GGAGCAGTCACTCTTAGAAATTATAGAAAA 15 44 0 CTCTTAGAAA 0.877775 -125 ********** Masking position 4 Map Score: 1.48402 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 9 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 14 ********** No masking Map Score: -1.26944e-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 ACGTGTTAGCTATCCTGCGTGCTTCAATAAA 1 30 1 TATCTGCGTG 0.968935 -39 TCTTCACCTCTAAAATGCGTGTTCGTCGTCA 3 183 0 TAAATGCGTG 0.966102 -22 CGGAGTATGGTATGATGCGCGCCTTTTTATT 5 18 1 TATATGCGCG 0.951084 -40 TTATACAAACTATGTTACGTGCTGTAACAGG 7 262 0 TATTTACGTG 0.926129 -39 GAACAAATCTCATGTTGCGTGGTGGTCGCTT 9 87 0 CATTTGCGTG 0.930973 -74 GTAACTGCATTAATATACGTGTTTTTATGCC 14 32 1 TAAATACGTG 0.905928 -65 *** ******* Masking position 6 Map Score: 0.0297053 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 91 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911