AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00061_ecoli_reg_100.orf -o00061_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -x5 -e 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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #2 dnaE 36 DNA polymerase III, alpha subunit #3 fabA 68 beta-hydroxydecanoyl thioester dehydrase, trans-2-decenoyl-ACP isomerase #4 b0955 185 putative ATP-dependent protease #5 plsX 110 glycerolphosphate auxotrophy in plsB background #6 fabH 67 3-oxoacyl-[acyl-carrier-protein] synthase III; acetylCoA ACP transacylase #7 acpP 210 acyl carrier protein #8 fabF 87 3-oxoacyl-[acyl-carrier-protein] synthase II #9 fabI 300 enoyl-[acyl-carrier-protein] reductase (NADH) #10 ydbO 284 orf, hypothetical protein #11 atoD 195 acetyl-CoA:acetoacetyl-CoA transferase alpha subunit #12 atoB 30 acetyl-CoA acetyltransferase #13 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #14 fabB 98 3-oxoacyl-[acyl-carrier-protein] synthase I #15 yqeF 251 putative acyltransferase #16 accB 300 acetylCoA carboxylase, BCCP subunit; carrier of biotin #17 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 Motif number 1 ACAATAATAACACGGCCTGCCGCAATCGTAAGAA 1 51 0 CACGCCGCGA 0.992299 -54 GCTTTAACGCCCATGCCAGGAGTATTGTCGGTGC 4 92 1 CCAGCCGGGA 0.958283 -94 CTTGACACGTCTAACCCTGGCGTTAGATGTC 5 90 1 CTACCCGGGT 0.594397 -21 GCGGTCGAACGACCGCCTGGAGATGTTCAC 8 7 0 GACGCCGGGT 0.908617 -81 ATCATTTTTTCCCTCCCTGGAGGACAAAC 8 69 1 CCCCCCGGGA 0.991325 -19 GGGAAAAGCGCCCCCCCTGCCGCAGCCTGCTCCG 9 144 1 CCCCCCGCGA 0.992837 -157 TAGTTGCCAGGTCCGACCGGAGCAGGCTGCGGCA 9 161 0 GTCGACGGGA 0.840023 -140 TATAGCTACTCACAGCCAGGTTGATTATAATAAC 9 193 1 CACGCCGGTA 0.943267 -108 CCTGACTGTACCCACAACGGTGTATGCAAGAGGG 11 165 1 CCCCAAGGGA 0.732568 -31 CCAGTTATGTCTCTGACTGCTGCTCAGGCATATT 15 138 1 CTCGACGCGT 0.808583 -114 GTCTAACATTGACACTCTGGGGCAAAATAGACCG 16 161 1 GACCTCGGGA 0.874493 -140 AGACCGGCGTCCCGGCCTGCTGGAATTTATCGCT 16 189 1 CCCGCCGCGA 0.991325 -112 AAAGCGTATGCCCCGACAGCTGTATGCATAGCGA 16 218 0 CCCGACGCGA 0.981043 -83 ACAGGCGTTTCACCGCCGTCTGTAAAGCGTATGC 16 241 0 CACGCCTCGA 0.862688 -60 CGGCAGAAATCACGCTCTGGATGAACGATGTGCT 17 53 0 CACCTCGGTA 0.741901 -137 CCGATCTGATCACGCTCGGCAGAAATCACGCTCT 17 69 0 CACCTCGCGA 0.957216 -121 *** *** ** * * Masking position 7 Map Score: 19.4087 Number of sites scoring better than the average of aligned sites = 1870 Number in coding regions = 1755 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 2 GAATATCAGCTTTTTAGGCCAGTGAAGAAA 4 44 1 TTTTTAGGCC 0.695458 -142 GAGTTTTATCTTTTTGTCCCACTAGAATCA 8 43 1 TTTTTGTCCC 0.953943 -45 ACTAGAATCATTTTTTCCCTCCCTGGAGGA 8 63 1 TTTTTTCCCT 0.725573 -25 TGTGCAAATATTGTTACCCCAGCAACAAAC 9 73 0 TTGTTACCCC 0.937801 -228 TTGTTGATGCTTGTTGTGCCTGAAAATCAG 9 267 0 TTGTTGTGCC 0.855572 -34 TTTTTATCCCTCTTGCATAC 11 186 0 TTTTTATCCC 0.883852 -10 CATAATGCCATTTTTGCCCCCAACAGACCA 13 83 0 TTTTTGCCCC 0.98656 -73 CCTGACGCAGTTTTTGCGCTGCGGAAAAGG 16 56 1 TTTTTGCGCT 0.92374 -245 AAATATACCTTCGTTGCGCCAATGTCACCT 16 83 0 TCGTTGCGCC 0.782806 -218 ACGCCGGTCTATTTTGCCCCAGAGTGTCAA 16 169 0 ATTTTGCCCC 0.894764 -132 TTTTTACCCTTCTGTTTTTT 17 1 1 TTTTTACCCT 0.896895 -189 CCCTTCTGTTTTTTTGACCTTAAGTCTCCG 17 17 1 TTTTTGACCT 0.725573 -173 ********** Masking position 5 Map Score: 9.24544 Number of sites scoring better than the average of aligned sites = 658 Number in coding regions = 567 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 3 ACATGAGCATTTTGTGCAAATCGCGG 7 7 0 TTTGTGCAAA 0.804391 -204 AATGTTGAAAAATTTGCAACTAAATCCCGG 7 137 0 AATTTGCAAC 0.85353 -74 AGGGGACCGTATTGTGCAAATATTGTTACC 9 85 0 ATTGTGCAAA 0.943494 -216 TAGCAACAGAAATGTGAAACATCTGGAGAG 10 16 0 AATGTGAAAC 0.85353 -269 TTACTTAACTATTGTGTAACTTTCATAAAA 10 208 1 ATTGTGTAAC 0.799209 -77 AAAATTGCGCACTGTGCAAATTTCTGCATA 11 24 0 ACTGTGCAAA 0.882885 -172 GTTATGTTTTAATGTGCAACATTCATGGTC 13 58 1 AATGTGCAAC 0.985228 -98 AAACTTACTCTATGTGCGACTTACAGAGGT 14 74 1 TATGTGCGAC 0.863976 -25 AAATCGTTATAATGTGCGACCTCGTCCTCC 16 27 1 AATGTGCGAC 0.962405 -274 CTTGACGGACATTGTGCAGCGATCTGCTGC 16 132 0 ATTGTGCAGC 0.895604 -169 TTGTGTTAAAAATATGCAAACAAAAGATTA 17 111 0 AATATGCAAA 0.681627 -79 ********** Masking position 5 Map Score: 8.19824 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 257 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 4 GAGATTAAGTAAACCGGAATCTGAAG 2 21 1 AAACGGATCA 0.97295 -16 ACTCTTAAATTTCCTATCAAAACTCGCTTTC 7 190 0 AATTCCATCA 0.85371 -21 CTAATAGTTAAATCGCGAATCATAAAAAGCAAAG 10 43 1 AATCCGATCA 0.956627 -242 AATTAATTAAAAACACGAATCACATTGTTTTATG 10 231 0 AAACCGATCA 0.985875 -54 TAATTCACGAAAACTGGAATCGTAAAGGTGATGA 10 260 1 AAACGGATCA 0.97295 -25 TTCTCCTTATAAATCCCCATCCAATTTATCCCTT 11 69 1 AAATCCATCA 0.948632 -127 CCCAAAGATAAAACTGGCATCGAACCAGGTTCAG 13 117 1 AAACGGATCA 0.97295 -39 GACGGCGGTGAAACGCCTGTCACAATCACACTAA 16 255 1 AAACCCGTCA 0.929404 -46 AAGATTAAAGAAATGCCGATCTGATCACGCTCGG 17 84 0 AAATCCATCA 0.948632 -106 **** ** *** * Masking position 10 Map Score: 7.76829 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 33 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 ACCGTGTAACTCTTTACAGAATATCAGCTT 4 26 1 TCTTTACAGA 0.790219 -160 TTCCGCAGTTGCTATACAGATCGCATAGTT 10 96 0 GCTATACAGA 0.98246 -189 ACCAAAACTTGCTATGCAGAAATTTGCACA 11 12 1 GCTATGCAGA 0.991694 -184 AGAATGAGCGGCTATGCAGAAAATTGCGCA 11 43 0 GCTATGCAGA 0.991694 -153 GGAATTTATCGCTATGCATACAGCTGTCGG 16 210 1 GCTATGCATA 0.939549 -91 CGGGGCATACGCTTTACAGACGGCGGTGAA 16 237 1 GCTTTACAGA 0.968255 -64 ATCTGATCACGCTCGGCAGAAATCACGCTC 17 70 0 GCTCGGCAGA 0.943209 -120 ********** Masking position 8 Map Score: 7.9972 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 51 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 CCCCAGTTGCCTGGGGAAAATCCTCACTAA 5 33 0 CTGGGGAAAA 0.990031 -78 CCCCAGGCAACTGGGGAAAGACCAAACCGG 5 47 1 CTGGGGAAAG 0.991729 -64 CTGTTTGTTGCTGGGGTAACAATATTTGCA 9 71 1 CTGGGGTAAC 0.916927 -230 CCTCGCCCCTCTGGGGAGAGGGTTAGGGTG 9 112 1 CTGGGGAGAG 0.969562 -189 CCGGAGCAGGCTGCGGCAGGGGGGGCGCTT 9 149 0 CTGCGGCAGG 0.929455 -152 TGTATAGCAACTGCGGAAAACATTAATGCA 10 108 1 CTGCGGAAAA 0.983882 -177 AGTTTTTGCGCTGCGGAAAAGGTGACATTG 16 64 1 CTGCGGAAAA 0.983882 -237 CATTGACACTCTGGGGCAAAATAGACCGGC 16 167 1 CTGGGGCAAA 0.985257 -134 ********** Masking position 2 Map Score: 12.0335 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 109 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 GCTCATACAGCCCCTAACCCTTTCATGGCG 9 41 0 CCCCTAACCC 0.991349 -260 ACAATACGGTCCCCTCGCCCCTCTGGGGAG 9 100 1 CCCCTCGCCC 0.994998 -201 CCTCACCCTAACCCTCTCCCCAGAGGGGCG 9 115 0 ACCCTCTCCC 0.973415 -186 GGGCGCTTTTCCCCTCACCCTAACCCTCTC 9 127 0 CCCCTCACCC 0.99706 -174 GGAAAAGCGCCCCCCCTGCCGCAGCCTGCT 9 145 1 CCCCCCTGCC 0.952022 -156 AGGTTTGCAACCACTAACCCACCAATAGAG 15 102 0 CCACTAACCC 0.946605 -150 ********** Masking position 4 Map Score: 6.54766 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 29 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 GGGGAAAGACCAAACCGGGCGGCGACGATA 5 59 1 CAAACCGGGC 0.94762 -52 TTGACACGTCTAACCCTGGCGTTAGATGTC 5 91 1 TAACCCTGGC 0.799746 -20 AATTTCCTATCAAAACTCGCTTTCGCGATG 7 184 0 CAAAACTCGC 0.915948 -27 TGGGACGGTTCAGACCTTGCCGAAT 9 6 0 CAGACCTTGC 0.936948 -295 CTGCTCCGGTCGGACCTGGCAACTATAGCT 9 170 1 CGGACCTGGC 0.939479 -131 GTTATTATAATCAACCTGGCTGTGAGTAGC 9 197 0 TCAACCTGGC 0.829106 -104 CACCAAAACTTGCTATGCAGAAA 11 4 1 CAAAACTTGC 0.960302 -192 CTGTTGGGGGCAAAAATGGCATTATGCGTC 13 87 1 CAAAAATGGC 0.825306 -69 TCCCCAAAGATAAAACTGGCATCGAACCAG 13 115 1 TAAAACTGGC 0.935628 -41 ATTGTGCATTCGAAACTTACTCTATGTGCG 14 62 1 CGAAACTTAC 0.563312 -37 TTAGTGGTTGCAAACCTTACGTGCCAGTTA 15 115 1 CAAACCTTAC 0.843249 -137 CAGTCAGAGACATAACTGGCACGTAAGGTT 15 127 0 CATAACTGGC 0.902578 -125 ********** Masking position 10 Map Score: 6.85475 Number of sites scoring better than the average of aligned sites = 1159 Number in coding regions = 1083 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 9 CCAGGCAACTGGGGAAAGACCAAACCGGGCG 5 49 1 GGGAAAGACC 0.978267 -62 GCGTTATTGGGGGGTAAGGCCTCAAAATAAC 7 85 1 GGGTAAGGCC 0.969387 -126 ACGTAAAATCGTGGTAAGACCTGCCGGGATT 7 114 1 GGGTAAGACC 0.990428 -97 AACTCAGGCGGTCGAACGACCGCCTGGAGAT 8 17 0 GCGAACGACC 0.947019 -71 CTATAGTTGCCAGGTCCGACCGGAGCAGGCT 9 167 0 CGGTCCGACC 0.970567 -134 AAGTAACTCCGCGGTTCGACCACTTTTTTAT 13 12 1 GGGTTCGACC 0.981387 -144 TTCGACTCATCTGGTACGACCAGATCACCTT 17 150 1 CGGTACGACC 0.989033 -40 * ********* Masking position 4 Map Score: 6.51414 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 81 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 CGTTCCATCTTTTGTTCGCCAAACTTT 1 8 1 TCTTTTGTTC 0.899238 -97 GCAACATGAGCATTTTGTGCAAATCGCGG 7 10 0 CATTTTGTGC 0.834809 -201 TTTATATTCCTTCTGTTTGTAGGGGTGC 12 13 0 CCTTCTGTTT 0.934017 -18 AATTGCCCTCCATTTTGTTTAATTTGTAGA 15 26 0 CATTTTGTTT 0.940334 -226 AACGAAGGTATATTTTGTTTTTTGCCGGAG 16 98 1 TATTTTGTTT 0.908559 -203 TTTTTACCCTTCTGTTTTTTTGACCTT 17 8 1 CCTTCTGTTT 0.934017 -182 ATTTCTTTAATCTTTTGTTTGCATATTTTT 17 104 1 TCTTTTGTTT 0.940334 -86 TCGAAGTGTGTATTTTGTGTTAAAAATATG 17 125 0 TATTTTGTGT 0.84909 -65 ********** Masking position 6 Map Score: 4.32182 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 49 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 11 AACCGAAAAGTGACTGAGCGTAC 6 55 1 TGCTGACGAC 0.991366 -13 AATAACCGTTTATCTGTTCGTACTGTTTACTAA 9 221 1 TACTGTCGAC 0.96753 -80 TCACAAATTTTGTATGTTTGAACTGTGACGGAT 10 173 0 TGATGTTGAC 0.847054 -112 CCCTTGCTATTGCCTGACTGTACCCACAACGGT 11 153 1 TGCTGATGAC 0.982329 -43 TAGGGACCTTTCTGTCTGAACCTGGTTCGAT 13 135 0 TTCTGTTGAC 0.89104 -21 CTCTATTAAATGGCTGATCGGACTTGTTCGGCG 14 15 1 TGCTGACGAC 0.991366 -84 TATCTGAACGTATCATCTACAAA 15 1 1 TACTGACGAT 0.834238 -251 ** **** ** ** Masking position 12 Map Score: 2.29415 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 115 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 CGTTCCATCTTTTGTTCGCCAA 1 2 1 GTTCATCTTT 0.939268 -103 TCGCCGCCCGGTTTGGTCTTTCCCCAGTTGC 5 53 0 GTTTGTCTTT 0.939268 -58 GACCGCCTGAGTTTTATCTTTTTGTCCCACT 8 35 1 GTTTATCTTT 0.976904 -53 AGCTTTAATCCTTATTGTTGATG 9 288 0 CTTTATCCTT 0.88991 -13 TTCGATGCCAGTTTTATCTTTGGGGACGCAT 13 110 0 GTTTATCTTT 0.976904 -46 ATCGGCATTTCTTTAATCTTTTGTTTGCATA 17 98 1 CTTTATCTTT 0.956724 -92 **** ****** Masking position 7 Map Score: 2.16359 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 16 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 CCAGCGAACTCGCAGTTTGCAAGTGACGGT 6 21 1 CGCAGTTTGC 0.982662 -47 CCGCGATTTGCACAAAATGCT 7 2 1 CGCGATTTGC 0.970365 -209 TCATGTTGCGCGCAGTCTGCGTGGTTATGA 7 31 1 CGCAGTCTGC 0.982318 -180 CCCCCCCTGCCGCAGCCTGCTCCGGTCGGA 9 154 1 CGCAGCCTGC 0.936531 -147 CTTGCTATGCAGAAATTTGCACAGTGCGCA 11 19 1 AGAAATTTGC 0.716235 -177 TTGCACAGTGCGCAATTTTCTGCATAGCCG 11 35 1 CGCAATTTTC 0.865902 -161 ACGATTTCGTAGCAATTGGCAGC 16 4 0 AGCAATTGGC 0.857208 -297 GACATTGTGCAGCGATCTGCTGCTATCCTC 16 125 0 AGCGATCTGC 0.926175 -176 ********** Masking position 2 Map Score: 4.67464 Number of sites scoring better than the average of aligned sites = 911 Number in coding regions = 864 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 14 GTGCTTCAATAAAATAAGGCTTACAGAGAA 3 48 1 AAAATAAGGC 0.931977 -21 CAAAAAGATAAAACTCAGGCGGTCGAACGA 8 29 0 AAACTCAGGC 0.948094 -59 TACCCCAGCAACAAACAGGCTCATACAGCC 9 59 0 ACAAACAGGC 0.940224 -242 GTTGTGCCTGAAAATCAGGCGATTCGTCGT 9 255 0 AAAATCAGGC 0.975931 -46 ACAAGCATCAACAATAAGGATTAAAGCT 9 283 1 ACAATAAGGA 0.769204 -18 CGTTGTGGGTACAGTCAGGCAATAGCAAGG 11 154 0 ACAGTCAGGC 0.966354 -42 ********** Masking position 7 Map Score: 1.6866 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 201 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 15 AGACCTGCCGGGATTTAGTTGCAAATTTTT 7 130 1 GGATTTAGTT 0.923754 -81 CTTTCGCGATGGTTTTCGTAGTGTATAAAA 7 165 0 GGTTTTCGTA 0.950126 -46 GGCGATTCGTCGTTTTAGTAAACAGTACGA 9 238 0 CGTTTTAGTA 0.863619 -63 GAACTGTGACGGATTTCGCACCCTATTTTT 10 157 0 GGATTTCGCA 0.928555 -128 TGAGATTATTGGATTTAGTTATTTAACTAA 11 112 0 GGATTTAGTT 0.923754 -84 CACATTATAACGATTTCGTAGCAATTGGCA 16 13 0 CGATTTCGTA 0.948923 -288 ********** Masking position 5 Map Score: 0.586767 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 53 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678