AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifadR_ecoli_bsub_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 yhfL 116 similar to long-chain fatty-acid-CoA ligase #8 mmgB 149 3-hydroxybutyryl-CoA dehydrogenase #9 lcfA 188 long chain acyl-CoA synthetase #10 yusL 267 similar to 3-hydroxyacyl-CoA dehydrogenase Motif number 1 ATGCAGAAACAGCGGACCAGCCGCTGTTTC 3 32 0 AGCGGACCAG 0.981503 -173 ATATTAACTCATCATACCAGCTTGATAATT 3 118 0 ATCATACCAG 0.915932 -87 ATTCTGCAAAATCGGATAAGTGACCGAAAT 4 33 1 ATCGGATAAG 0.906629 -268 GAGAGTATAGGTCGGACCAGCTGGAATGTT 4 183 0 GTCGGACCAG 0.995815 -118 CATCTTAGAAATCAGACCAGTGGCGAGAGT 4 207 0 ATCAGACCAG 0.984382 -94 GCCGAGCGTGATCAGATCGGCATTTCTTTA 5 83 1 ATCAGATCGG 0.907221 -107 AGGTGATCTGGTCGTACCAGATGAGTCGAA 5 150 0 GTCGTACCAG 0.976256 -40 ACATTAACTCATCGGATCAGTTCAGTAACT 6 119 1 ATCGGATCAG 0.984382 -42 GGCGGCGGAAAACGGACAAGTCAAAATCAG 10 68 0 AACGGACAAG 0.846525 -200 GTAATGCTGAGTCGGACCGGCATCTCCCTT 10 98 1 GTCGGACCGG 0.993335 -170 AGCTATTGAAGTCGAACCGGAAATCTTTTA 10 246 1 GTCGAACCGG 0.935942 -22 ********** Masking position 6 Map Score: 19.1882 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 329 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 2 TGCGTGCTTCAATAAAATAAGGCTTACAGA 1 45 1 AATAAAATAA 0.593016 -24 TAGGCCAGTGAAGAAAAGAATCTCCATCCT 2 58 1 AAGAAAAGAA 0.775611 -128 TTGTTTTTAAAGAAAAAGAAACAGCGGCTG 3 15 1 AGAAAAAGAA 0.974552 -190 TACGGTAAAGATAAAAATAAATAGTGACGC 3 65 1 ATAAAAATAA 0.845504 -140 GAAAAAAGATAGAAACATACTTGCAACATT 4 159 1 AGAAACATAC 0.734826 -142 CATAGTTTGTATAAAAATAAATCATTGAGG 4 279 1 ATAAAAATAA 0.845504 -22 TTAAGGTCAAAAAAACAGAAGGGTAAAAA 5 10 0 AAAAACAGAA 0.936649 -180 TCCATTATAGAGAAACAGAAAAAAACACTC 7 41 0 AGAAACAGAA 0.96566 -76 TCATATTATGAGAAAAAGAAAGATTTACCT 9 96 1 AGAAAAAGAA 0.974552 -93 GGCAAAAAAAAGAAAAAGAAAGGTAAATCT 9 116 0 AGAAAAAGAA 0.974552 -73 CAGCAGTATAAAAAACATAACATGGGACAA 10 41 0 AAAAACATAA 0.902319 -227 ATGGTACGAGAGAAAAAAAATCCGTCTTCA 10 152 0 AGAAAAAAAA 0.832422 -116 GGCTTCATACAAAAAAATAACAAATTAGCT 10 220 1 AAAAAAATAA 0.926362 -48 ********** Masking position 5 Map Score: 16.0273 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 140 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 3 GTCTGTTGTCAAAGCCGCGATTATACCGTA 2 151 0 AAAGCCGCGA 0.92725 -35 AGAAAAAGAAACAGCGGCTGGTCCGCTGTT 3 25 1 ACAGCGGCTG 0.965153 -180 TAAGAATGCAGAAACAGCGGACCAGCCGCT 3 37 0 GAAACAGCGG 0.834865 -168 AATTGCTCAAACAGCCGCCGACGCGGCTTT 8 85 1 ACAGCCGCCG 0.978689 -65 TCCGCACATAAAAGCCGCGTCGGCGGCTGT 8 95 0 AAAGCCGCGT 0.927249 -55 TGTGAATCCAGAGGCCGCGGAGGCAGGA 8 132 1 GAGGCCGCGG 0.989658 -18 AATACTGCTCGCCGCAGCGGGAATCTTTTT 9 43 1 GCCGCAGCGG 0.970072 -146 AAGCAGCCGTGGGAAGCAGCTG 10 3 1 GCAGCCGTGG 0.96704 -265 GCAGCCGTGGGAAGCAGCTGCATTATGATT 10 13 1 GAAGCAGCTG 0.947656 -255 ACTCAGCATTACGGCGGCGGAAAACGGACA 10 80 0 ACGGCGGCGG 0.979522 -188 CGCCGCGCTGACTGCCGCTGAAGACGGATT 10 134 1 ACTGCCGCTG 0.933467 -134 ********** Masking position 5 Map Score: 11.3063 Number of sites scoring better than the average of aligned sites = 2454 Number in coding regions = 2373 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 4 CCCAACGAAAAGGTTGCGAAGCGCGTCACT 3 87 0 AGGTTGCGAA 0.971323 -118 TCATCATACCAGCTTGATAATTACCCAACG 3 110 0 AGCTTGATAA 0.73643 -95 CGCATTTTAGAGGTGAAGAA 3 195 1 AGGTGAAGAA 0.7909 -10 CAGAATTAACAACTGGAGCAGCACTTTC 4 9 0 AACTGGAGCA 0.857786 -292 CAAAATTTGGAGGTGGCGCACTCATGGATT 4 98 0 AGGTGGCGCA 0.988363 -203 AACGCGATCCAGCTGGCAAAATTTGGAGGT 4 114 0 AGCTGGCAAA 0.94815 -187 AAATCATGGTAGCTGGCGCAGGTCAGATGG 8 48 1 AGCTGGCGCA 0.992813 -102 TAGATGGAAAAGCTTGCGAAAATACTGCTC 9 23 1 AGCTTGCGAA 0.982177 -166 ********** Masking position 1 Map Score: 5.96762 Number of sites scoring better than the average of aligned sites = 1618 Number in coding regions = 1546 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 5 TTCTTTTCTTCACTGGCCTAAAAAGCTGATATTC 2 44 0 CAGGTAAAAA 0.951923 -142 GCGGCTTTGACAACAGACTAAAAAACATCAACT 2 163 1 CAAGTAAAAA 0.984697 -23 GTCAAAAAAACAGAAGGGTAAAAA 5 1 0 CAAGTAAAAA 0.984697 -189 GATGCGGAGACTTAAGGTCAAAAAAACAGAAGGG 5 17 0 CTAGCAAAAA 0.949587 -173 AATATGCAAACAAAAGATTAAAGAAATGCCGATC 5 97 0 CAAGTAAAGA 0.951923 -93 GAAAAAAACACTCAAGAGCAAAAAGCCCTGAGTG 7 20 0 CTAGCAAAAA 0.949589 -97 AAGTCAAAATCAGCAGTATAAAAAACATAACATG 10 47 0 CAAGTAAAAA 0.984697 -221 ** ** ****** Masking position 10 Map Score: 5.52502 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 39 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 CGCGATTATACCGTAACCGGCACTACAGCAC 2 135 0 CCGTAACCGC 0.840217 -51 CGGCTGGTCCGCTGTTTCTGCATTCTTACGG 3 39 1 GCTGTTTCGC 0.81769 -166 ACTTCGCGCTCCTGTTACAGCACGTAACATA 4 252 1 CCTGTTACGC 0.868674 -49 GTCAGTCTCCTGAATCCGCAAGGTGATCT 5 171 0 CCTGAATCGC 0.913519 -19 TGAAGCCAAGCTTTCTTCTCCATTATAGAGA 7 58 0 CTTTCTTCCC 0.646105 -59 ATTCAAATCCCCTTTTTCATCATGTT 8 6 0 CCTTTTTCTC 0.732121 -144 CCCCATCTGACCTGCGCCAGCTACCATGATT 8 49 0 CCTGCGCCGC 0.952661 -101 TCCTGCCTCCGCGGCCTCTGGA 8 138 0 CCTGCCTCGC 0.969492 -12 TTTGACTTGTCCGTTTTCCGCCGCCGTAATG 10 73 1 CCGTTTTCGC 0.958167 -195 CTGAGTCGGACCGGCATCTCCCTTTACGCTC 10 104 1 CCGGCATCCC 0.95813 -164 GAAAAAAAATCCGTCTTCAGCGGCAGTCAGC 10 140 0 CCGTCTTCGC 0.981717 -128 CGTACCATTCCCTTCACCTCCGGGCTTAAGT 10 174 1 CCTTCACCCC 0.915863 -94 ******** ** Masking position 8 Map Score: 6.00515 Number of sites scoring better than the average of aligned sites = 3409 Number in coding regions = 3260 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 7 TCCGACCTATACTCTCGCCACTGGTCTGAT 4 197 1 ACTCTCGCCA 0.960605 -104 CGATCTGATCACGCTCGGCAGAAATCACGC 5 72 0 ACGCTCGGCA 0.973075 -118 TTGAGCAATTCCGCTCCCCATCTGACCTGC 8 65 0 CCGCTCCCCA 0.992339 -85 TGCGAAAATACTGCTCGCCGCAGCGGGAAT 9 37 1 CTGCTCGCCG 0.985295 -152 CATAATGCAGCTGCTTCCCACGGCTGCTT 10 10 0 CTGCTTCCCA 0.871326 -258 ATCTCCCTTTACGCTCGCCGCGCTGACTGC 10 119 1 ACGCTCGCCG 0.992361 -149 ********** Masking position 5 Map Score: 4.0477 Number of sites scoring better than the average of aligned sites = 715 Number in coding regions = 694 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 8 TTTTATTGAAGCACGCAGGATAGCTAACACGTG 1 29 0 GCCGAGATAG 0.995628 -40 GGGCGTTAAAGCTCACAGGATGGAGATTCTTTT 2 71 0 GCCAAGATGG 0.930099 -115 TAACGCCCATGCCAGGAGTATTGTCGGTGCTTT 2 96 1 GCAGAGATTG 0.970841 -90 TGTAACAGGAGCGCGAAGTGTAGGGTCTGAGGT 4 238 0 GCCGAGGTAG 0.985929 -63 TCCTGTTACAGCACGTAACATAGTTTGTATAAA 4 261 1 GCCGAAATAG 0.967253 -40 GGGGACGGAGAATAGATGGAAAAGC 9 3 1 GGCGAGATAG 0.977668 -186 TCCCGCTGCGGCGAGCAGTATTTTCGCAAGCTT 9 32 0 GCAGAGATTT 0.81198 -157 ** ** ** **** Masking position 7 Map Score: 2.42088 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 141 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 AGCTGGTATGATGAGTTAATATTATGTTAAC 3 126 1 ATGAGTTAAA 0.964335 -79 ACACTTAAAAATGATCTAAAACAAAATTCAC 4 64 1 ATGATCTAAA 0.938401 -237 TTTTTCAAATATGATCTAAGAAACGCGATCC 4 134 0 ATGATCTAAA 0.938401 -167 TGGATGAACGATGTGCTAAGATGCGGAGACT 5 39 0 ATGTGCTAAA 0.960465 -151 AGTGTGTATTTTGTGTTAAAAATATGCAAAC 5 120 0 TTGTGTTAAA 0.709468 -70 AACTGATCCGATGAGTTAATGTTGAACAAAT 6 110 0 ATGAGTTAAG 0.892701 -51 TAACTATTGCATTAGCTAACAATAAAA 6 144 1 ATTAGCTAAA 0.878693 -17 ********* * Masking position 8 Map Score: 0.840529 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 59 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 10 TTGCTTGTTTTTAAAGAAAAAG 3 3 1 GCTTGTTTTT 0.77171 -202 TCATTTTTAAGTGTGATTTCGGTCACTTAT 4 48 0 GTGTGATTTC 0.974381 -253 TCATGGATTCGGGTGAATTTTGTTTTAGAT 4 77 0 GGGTGAATTT 0.79816 -224 CTCGCCACTGGTCTGATTTCTAAGATGTAC 4 210 1 GTCTGATTTC 0.897126 -91 TTCATCCAGAGCGTGATTTCTGCCGAGCGT 5 62 1 GCGTGATTTC 0.96926 -128 ATGAGTCGAAGTGTGTATTTTGTGTTAAAA 5 130 0 GTGTGTATTT 0.845486 -60 TTTTGCTCTTGAGTGTTTTTTTCTGTTTCT 7 31 1 GAGTGTTTTT 0.819595 -86 ACCATGATTTGTTTGATTTCCATTCAAATC 8 28 0 GTTTGATTTC 0.912091 -122 ********** Masking position 4 Map Score: 2.08161 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 322 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 11 GATATTCTGTAAAGAGTTACACGGTAACAT 2 21 0 AAAGAGTTAC 0.94239 -165 CAATTAACAAAAAGATTCCCGCTGCGGCGA 9 51 0 AAAGATTCCC 0.961981 -138 TGAGAAAAAGAAAGATTTACCTTTCTTTTT 9 104 1 AAAGATTTAC 0.96538 -85 CTTAAAAGATTTCCGGTTCGACTT 10 254 0 AAAGATTTCC 0.97734 -14 ********** Masking position 5 Map Score: 0.329483 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 27 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 12 ********** No masking Map Score: 3.76831e-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: 3.76831e-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: 3.76831e-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