AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i057_Chorismate_Biosynthes_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 aroL 182 shikimate kinase II #2 ycaP 120 orf, hypothetical protein #3 serC 198 3-phosphoserine aminotransferase #4 aroA 70 5-enolpyruvylshikimate-3-phosphate synthetase #5 b1689 300 orf, hypothetical protein #6 b1690 99 putative transport system permease protein #7 b1691 220 putative amino acid/amine transport protein #8 aroD 30 3-dehydroquinate dehydratase #9 aroC 34 chorismate synthase #10 yrdD 62 putative DNA topoisomerase #11 smf_2 53 orf, fragment 2 #12 smf_1 129 orf, fragment 1 #13 aroB 56 3-dehydroquinate synthase #14 aroK 199 shikimate kinase I #15 yrfD 68 orf, hypothetical protein Motif number 1 TGTAATTTATTATTTACACTTCATTCTTGAATATT 1 12 1 TATTTCCTCT 0.654818 -171 GGTGTATTGAGATTTTCACTTTAAGTGGAATTTTT 1 63 1 GATTTCCTTG 0.852988 -120 CGTGGGTTTTCCCCAATAGGTCGCAATGCG 1 163 0 GTTTTCCATG 0.901189 -20 CTTAACGTGGTTTATCCGCTAAAAGCATAGTCAAC 2 87 0 TTTATCCTAG 0.951204 -34 TTTTATGCTCTTAACGTGGTTTATCC 2 105 0 TTTATCCTAG 0.951204 -16 GCAAGCCACATTTTTGCCCTCAACGGTTTTACTCA 3 63 1 TTTTTCCTAG 0.989631 -136 GCCCTCAACGGTTTTACTCATTGCGATGTGTGTCA 3 78 1 GTTTTCCATG 0.901189 -121 CAGCAATTCGTTGTTTCACTCAGGGGATTTCCATG 5 126 0 TTGTTCCTAG 0.937708 -175 TTTTTTAACATTTTTCCGCTTCGCTACCTCGCCCC 5 195 1 TTTTTCCTCT 0.902799 -106 TTTTTCCACAGAAAGGAATTGTCGT 6 1 1 TTTTTCCAAG 0.968396 -99 TTTTTACCCTTTCTGCACGCGGTCA 8 16 0 TTTTTCCTTG 0.98254 -15 AGCGGTAATGTTTTTACGCTGAACGTGTTTCATCT 14 22 1 TTTTTCCTAG 0.989631 -178 TTTGCTGTCTTTTTTACGCTAATCTTACCCGGTGA 14 160 1 TTTTTCCTAT 0.950004 -40 ***** * ** * * Masking position 5 Map Score: 15.271 Number of sites scoring better than the average of aligned sites = 399 Number in coding regions = 334 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 2 TCGATTGTAAAGAAAAAATTCCACTTAAAGTG 1 79 0 AGAAAAATCC 0.959876 -104 CCATCAAACTAGTACAATTTCGATTGTAAAGA 1 98 0 AGACAATTCG 0.818897 -85 AGCGCCTTTGAGATAAAACCCGTATTATTGCG 2 30 0 AGTAAAACCG 0.903918 -91 TCGGATTATTAGCAAAAAGCCGATGTTTTTAC 3 13 0 AGAAAAACCG 0.985263 -186 GTGGGGATTAAGCAAAATTTCGGCA 4 4 0 AGAAAATTCG 0.959972 -67 CTACAACAGAAATAAAAACCCCACAGGCTGGC 4 37 0 AAAAAAACCC 0.896226 -34 ATCTGATCGACGCAAAAAGTCCGTATGCCTAC 5 54 1 CGAAAAATCC 0.818353 -247 GAAAAATGTTAAAAAAAAGCCCATCGTGGGAG 5 179 0 AAAAAAACCC 0.896226 -122 GCGCTAACTAAGGAAAATCGCGATCAAAAACA 7 63 1 AGAAAATGCG 0.915365 -158 CTTCTATTCTAGACAAATCCCCCTCTGATTGA 12 51 1 AGCAAATCCC 0.907733 -79 TAAAAAAGACAGCAAAATGCCGCCTGAATGAT 14 144 0 AGAAAATCCG 0.982527 -56 ** ***** *** Masking position 6 Map Score: 9.04897 Number of sites scoring better than the average of aligned sites = 475 Number in coding regions = 372 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 3 GATAAAACCGATAGCCACAGGAATAATGTA 3 119 1 ATAGCCACAG 0.950606 -80 ATTTTGCTTAATCCCCACAGCCAGCCTGTG 4 18 1 ATCCCCACAG 0.994512 -53 CAGAAATAAAAACCCCACAGGCTGGCTGTG 4 33 0 AACCCCACAG 0.97812 -38 AAGCATGGAAATCCCCTGAGTGAAACAACG 5 123 1 ATCCCCTGAG 0.978119 -178 AAATCTCCAGAGATGTGTTCAG 12 3 1 ATCTCCAGAG 0.978481 -127 CCGGTGATTTATCGCCAGAGCG 14 188 1 ATCGCCAGAG 0.992022 -12 ********** Masking position 9 Map Score: 7.34713 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 64 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 GCTTTTTGCTAATAATCCGAGAGATTCTTTTGT 3 25 1 AAAACCGAAG 0.873009 -174 TCACTGAATGATAAAACCGATAGCCACAGGAAT 3 110 1 ATAACCGAAG 0.974594 -89 ATATGTTGATTTATAACCGTGAGCTAATAGTAG 5 82 0 TTTACCGTAG 0.974594 -219 TGTGACTCTCTTCAAGCCGTCAGCAGGCTGATA 5 261 1 TTAACCGTAG 0.974583 -40 AGAAAGAGTTATTTATCCGTAAGATCTTGCATG 7 30 0 ATTACCGTAG 0.990546 -191 ACCTTGTTTTATTAACCAGTGAGGCCCTTCGCT 11 22 0 ATAACAGTAG 0.959947 -32 CATGATGATGATTTATCATTCAGGCGGCATTTT 14 130 1 ATTACATTAG 0.727978 -70 AGACGCATTGATATACCCGTCAGA 15 55 1 ATTACCGTAG 0.990547 -14 ** ** **** ** Masking position 5 Map Score: 6.46243 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 165 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 GCAATGCGGCGAAAGCCGGTGTCATGAGAA 1 141 0 GAAAGCCGGT 0.863241 -42 TAGTCGTACGGAAAGCGCGCAATAATACGG 2 13 1 GAAAGCGCGC 0.926109 -108 AATCGATTGCGACCACAGGTAATACATTAT 3 141 0 GACCACAGGT 0.891697 -58 GCAATCGATTGACCGCGGGTTAATAGCAAC 3 161 1 GACCGCGGGT 0.989829 -38 TCTTCAAGCCGTCAGCAGGCTGATAATGTT 5 269 1 GTCAGCAGGC 0.929079 -32 CAGGCTGACCGCGTGCAGAAAGGGTA 8 7 1 GACCGCGTGC 0.906284 -24 ATATACACTCGTCTGCGGGTACAGTAATTA 13 21 1 GTCTGCGGGT 0.911084 -36 CATCATCATGGAACGCAGGCAGCGAAGAGC 14 110 0 GAACGCAGGC 0.967872 -90 GCCTTTATACTACCGCGCGTTTGTTTATAA 15 20 0 TACCGCGCGT 0.881697 -49 ********** Masking position 6 Map Score: 5.58867 Number of sites scoring better than the average of aligned sites = 1282 Number in coding regions = 1214 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 6 ATTTATTGGTATAGTAAGGGGTGTATTGAGA 1 44 1 AAGTAAGGGG 0.898509 -139 GCAACGCAACGTGGTGAGGGGAA 3 186 1 GGGTGAGGGG 0.977465 -13 GAGGGGCGAGGTAGCGAAGCGGAAAAATGTT 5 201 0 GAGCGAAGCG 0.986609 -100 ATTATTGGAAAGAGTGAGGGGCGAGGTAGCG 5 216 0 AAGTGAGGGG 0.98556 -85 GGTGCTTTAAAAAGTGAAGCGATGTTGTGTC 6 62 0 AAGTGAAGCG 0.967258 -38 GGAATCCGGGAAGCGAAGGGCCTCACTGGT 11 10 1 GAGCGAAGGG 0.992956 -44 TGGAACGCAGGCAGCGAAGAGCACCAACTCT 14 101 0 GAGCGAAGAG 0.964302 -99 * ********* Masking position 7 Map Score: 5.427 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 175 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 AAGAATGAAGTGTAAATAATAAATTACAT 1 10 0 TGTAAATAAT 0.808073 -173 CAATTTCGATTGTAAAGAAAAAATTCCACT 1 86 0 TGTAAAGAAA 0.870782 -97 TTATTTCTGTTGTAGAGAGTTGAGTTC 4 54 1 TGTAGAGAGT 0.963473 -17 GTTTAAAAACTGTAAAGAATTTGCGACAGG 5 13 0 TGTAAAGAAT 0.970113 -288 GCAACATTATTGGAAAGAGTGAGGGGCGAG 5 222 0 TGGAAAGAGT 0.946404 -79 GCTGACGGCTTGAAGAGAGTCACAGTATCT 5 255 0 TGAAGAGAGT 0.933937 -46 TTGCATGACCTGAAAAGAATATTGCA 7 7 0 TGAAAAGAAT 0.945644 -214 ********** Masking position 6 Map Score: 4.466 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 60 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 TGTCATGAGAATAGCGATCATACCATCAAA 1 122 0 ATAGCGATCA 0.962502 -61 CTTTCGCCGCATTGCGACCTATTGGGGAAA 1 156 1 ATTGCGACCT 0.979945 -27 GGTTTTACTCATTGCGATGTGTGTCACTGA 3 87 1 ATTGCGATGT 0.927825 -112 CGGTCAATCGATTGCGACCACAGGTAATAC 3 146 0 ATTGCGACCA 0.98592 -53 ACTAAGGAAAATCGCGATCAAAAACAAACT 7 69 1 ATCGCGATCA 0.974391 -152 ********** Masking position 7 Map Score: 2.29645 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 95 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 ATAAATCAATATGTTGATTTATAACCGTGA 5 93 0 ATGTTGATTT 0.91321 -208 TACTATACTGAAGATGATTTTCCCTGGGTA 7 140 0 AAGATGATTT 0.963748 -81 TCCTTGCTGAAAGATAATTTCGTTACCGTA 7 198 0 AAGATAATTT 0.804368 -23 ATAACAACTTATGCTGAATTAAAGAAATGA 10 11 0 ATGCTGAATT 0.856291 -52 ACCGTGAACAGTGCTGATTTCGCCATAACA 10 35 0 GTGCTGATTT 0.898284 -28 AGGAGTTAGAAAGATTATTTCTTCTATTCT 12 31 1 AAGATTATTT 0.804421 -99 GCGTTCCATGATGATGATTTATCATTCAGG 14 124 1 ATGATGATTT 0.971925 -76 ********** Masking position 7 Map Score: 1.72843 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 248 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 10 AGAAAAAATTCCACTTAAAGTGAAAATCTC 1 71 0 CCACTTAAAG 0.733232 -112 TTTAGTCGTACGGAAAGCGCGCAATAA 2 8 1 GTACGGAAAG 0.717464 -113 CGTGGTTTATCCGCTAAAAGCATAGTCAAC 2 87 0 CCGCTAAAAG 0.919075 -34 GCGATGTGTGTCACTGAATGATAAAACCGA 3 100 1 TCACTGAATG 0.632636 -99 AATCTGATCGACGCAAAAAGTCCGTATGCC 5 53 1 ACGCAAAAAG 0.803588 -248 TTTTTCCACAGAAAGGAATTGTCGT 6 6 1 CCACAGAAAG 0.952331 -94 TCCTTAGTTAGCGCAGAAAGAGTTATTTAT 7 47 0 GCGCAGAAAG 0.979086 -174 AGCTCCTTGCTGAAAGATAATTTCGT 7 205 0 TTGCTGAAAG 0.878385 -16 GGCTGACCGCGTGCAGAAAGGGTAAAAA 8 13 1 GTGCAGAAAG 0.929622 -18 TAATGTTTTTACGCTGAACGTGTTTCATCT 14 27 1 ACGCTGAACG 0.856751 -173 ********** Masking position 7 Map Score: 2.73816 Number of sites scoring better than the average of aligned sites = 1791 Number in coding regions = 1702 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 11 CCAATAGGTCGCAATGCGGCGAAAGCCGGTG 1 150 0 GCAAGCGGCG 0.993612 -33 CAGTTCATCGGCATGGCGGCGGTGATAGCGC 2 57 0 GCATGCGGCG 0.979285 -64 TAATAGCAACGCAACGTGGTGAGGGGAA 3 181 1 GCAAGTGGTG 0.984603 -18 AGAGTGAGGGGCGAGGTAGCGAAGCGGAAAA 5 206 0 GCGAGTAGCG 0.975092 -95 AAAAAGTGAAGCGATGTTGTGTCAGCATCCG 6 54 0 GCGAGTTGTG 0.945578 -46 **** ****** Masking position 6 Map Score: 0.842873 Number of sites scoring better than the average of aligned sites = 547 Number in coding regions = 527 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 12 ********** No masking Map Score: 5.26755e-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: 5.26755e-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: 5.26755e-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