AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i057_ecoli_mtub_300.orf -o057_ecoli_mtub_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 = 0.58 maxlen = 30 weight = 0.8 exclude = 1 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 #16 aroA 54 aroA Motif number 1 TGTAATTTATTATTTACACTTCATTCTTGAATATT 1 12 1 TATTTCCTCT 0.638364 -171 GGTGTATTGAGATTTTCACTTTAAGTGGAATTTTT 1 63 1 GATTTCCTTG 0.843727 -120 CGTGGGTTTTCCCCAATAGGTCGCAATGCG 1 163 0 GTTTTCCATG 0.894589 -20 CTTAACGTGGTTTATCCGCTAAAAGCATAGTCAAC 2 87 0 TTTATCCTAG 0.947751 -34 TTTTATGCTCTTAACGTGGTTTATCC 2 105 0 TTTATCCTAG 0.947751 -16 GCAAGCCACATTTTTGCCCTCAACGGTTTTACTCA 3 63 1 TTTTTCCTAG 0.988866 -136 GCCCTCAACGGTTTTACTCATTGCGATGTGTGTCA 3 78 1 GTTTTCCATG 0.894589 -121 CAGCAATTCGTTGTTTCACTCAGGGGATTTCCATG 5 126 0 TTGTTCCTAG 0.933367 -175 TTTTTTAACATTTTTCCGCTTCGCTACCTCGCCCC 5 195 1 TTTTTCCTCT 0.896294 -106 TTTTTCCACAGAAAGGAATTGTCGT 6 1 1 TTTTTCCAAG 0.966116 -99 TTTTTACCCTTTCTGCACGCGGTCA 8 16 0 TTTTTCCTTG 0.981261 -15 AGCGGTAATGTTTTTACGCTGAACGTGTTTCATCT 14 22 1 TTTTTCCTAG 0.988866 -178 TTTGCTGTCTTTTTTACGCTAATCTTACCCGGTGA 14 160 1 TTTTTCCTAT 0.94647 -40 ***** * ** * * Masking position 5 Map Score: 14.9501 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 CAAAAGAATCTCTCGGATTATTAGCAAAAAGCCGATGT 3 19 0 TCCGGAGCAA 0.975225 -180 AATCGATTGACCGCGGGTTAATAGCAACGCAACGTGGT 3 163 1 CCCGGAGCAC 0.994907 -36 CACAGGCTGGCTGTGGGGATTAAGCAAAATTTCGGCA 4 10 0 CTTGGAGCAA 0.923115 -61 TACTATTAGCTCACGGTTATAAATCAACATATTGATTT 5 83 1 TCCGGATCAC 0.964211 -218 AAAAAGCCCATCGTGGGAGATGGGCAAAGACTACACAC 5 160 0 TCTGGGGCAA 0.975225 -141 TTTTAAAGCACCTTTGCTAAGTAGAACCT 6 81 1 CCTTGAGAAC 0.72759 -19 AGATGATTTTCCCTGGGTACATGGCATAAAGTTTATGT 7 121 0 CCTGGGGCAA 0.984376 -100 TTTTTACCCTTTCTGCACGCGGTCAGCCTG 8 4 0 TTCTGGTCAC 0.603308 -27 GACAAATCCCCCTCTGATTGACAGCATCACTGACCAAT 12 62 1 CCCTGAGCAC 0.977335 -68 TAAATCATCATCATGGAACGCAGGCAGCGAAGAGCACC 14 107 0 TCTGGGGCAC 0.991873 -93 CGCTCTGGCGATAAATCACCGGGTAAGATT 14 180 0 CTTGGATCAC 0.891509 -20 TCGGCGGGTGTCGTGGGTACCAGGCACCATAGGAAGC 16 10 0 TCTGGGGCAC 0.991873 -45 ** *** **** * Masking position 16 Map Score: 12.1856 Number of sites scoring better than the average of aligned sites = 1114 Number in coding regions = 1069 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 3 GCAATGCGGCGAAAGCCGGTGTCATGAGAA 1 141 0 GAAAGCCGGT 0.836383 -42 TAGTCGTACGGAAAGCGCGCAATAATACGG 2 13 1 GAAAGCGCGC 0.897679 -108 AATCGATTGCGACCACAGGTAATACATTAT 3 141 0 GACCACAGGT 0.873461 -58 GCAATCGATTGACCGCGGGTTAATAGCAAC 3 161 1 GACCGCGGGT 0.991653 -38 TCTTCAAGCCGTCAGCAGGCTGATAATGTT 5 269 1 GTCAGCAGGC 0.93717 -32 CAGGCTGACCGCGTGCAGAAAGGGTA 8 7 1 GACCGCGTGC 0.91648 -24 ATATACACTCGTCTGCGGGTACAGTAATTA 13 21 1 GTCTGCGGGT 0.942781 -36 CATCATCATGGAACGCAGGCAGCGAAGAGC 14 110 0 GAACGCAGGC 0.956844 -90 GCCTTTATACTACCGCGCGTTTGTTTATAA 15 20 0 TACCGCGCGT 0.865147 -49 ATCCTGCCGTGTCGGCGGGTGTCGTGGGTA 16 29 0 GTCGGCGGGT 0.960796 -26 ********** Masking position 6 Map Score: 7.56565 Number of sites scoring better than the average of aligned sites = 1423 Number in coding regions = 1347 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 4 TACATTATTCCTGTGGCTATCGGTTTTATC 3 119 0 CTGTGGCTAT 0.944152 -80 CACAGGCTGGCTGTGGGGATTAAGCAAAAT 4 18 0 CTGTGGGGAT 0.993757 -53 CACAGCCAGCCTGTGGGGTTTTTATTTCTG 4 33 1 CTGTGGGGTT 0.975168 -38 CGTTGTTTCACTCAGGGGATTTCCATGCTT 5 123 0 CTCAGGGGAT 0.975167 -178 CTGAACACATCTCTGGAGATTT 12 3 0 CTCTGGAGAT 0.975593 -127 CGCTCTGGCGATAAATCACCGG 14 188 0 CTCTGGCGAT 0.990929 -12 ********** Masking position 2 Map Score: 7.18818 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 5 ACAAAAGAATCTCTCGGATTATTAGCAAAAAGC 3 25 0 CTTCGGTTTT 0.848497 -174 ATTCCTGTGGCTATCGGTTTTATCATTCAGTGA 3 110 0 CTTCGGTTAT 0.968994 -89 CTACTATTAGCTCACGGTTATAAATCAACATAT 5 82 1 CTACGGTAAA 0.968994 -219 TATCAGCCTGCTGACGGCTTGAAGAGAGTCACA 5 261 0 CTACGGTTAA 0.968985 -40 CATGCAAGATCTTACGGATAAATAACTCTTTCT 7 30 1 CTACGGTAAT 0.988421 -191 AGCGAAGGGCCTCACTGGTTAATAAAACAAGGT 11 22 1 CTACTGTTAT 0.95128 -32 AAAATGCCGCCTGAATGATAAATCATCATCATG 14 130 0 CTAATGTAAT 0.685562 -70 TCTGACGGGTATATCAATGCGTCT 15 55 0 CTACGGTAAT 0.988421 -14 ** **** ** ** Masking position 9 Map Score: 6.25905 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 6 TAAATATTCAAGAATGAAGTGTAAATAATAA 1 18 0 AAATGAAGTG 0.738809 -165 ATTTATTGGTATAGTAAGGGGTGTATTGAGA 1 44 1 AAGTAAGGGG 0.785738 -139 CCAATAGGTCGCAATGCGGCGAAAGCCGGTG 1 150 0 GAATGCGGCG 0.777222 -33 GCAACGCAACGTGGTGAGGGGAA 3 186 1 GGGTGAGGGG 0.959954 -13 GAGGGGCGAGGTAGCGAAGCGGAAAAATGTT 5 201 0 GAGCGAAGCG 0.971239 -100 ATTATTGGAAAGAGTGAGGGGCGAGGTAGCG 5 216 0 AAGTGAGGGG 0.978966 -85 TGTTACAACAATAATGAACGGATGCTGACAC 6 36 1 AAATGAACGG 0.681047 -64 GGTGCTTTAAAAAGTGAAGCGATGTTGTGTC 6 62 0 AAGTGAAGCG 0.975715 -38 GGAATCCGGGAAGCGAAGGGCCTCACTGGT 11 10 1 GAGCGAAGGG 0.976652 -44 TGGAACGCAGGCAGCGAAGAGCACCAACTCT 14 101 0 GAGCGAAGAG 0.866151 -99 CCGACACGGCAGGATGAAGCG 16 44 1 AGATGAAGCG 0.849971 -11 * ********* Masking position 11 Map Score: 5.30343 Number of sites scoring better than the average of aligned sites = 869 Number in coding regions = 747 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 7 ATGTAATTTATTATTTACACTTCATTCTT 1 10 1 ATTATTTACA 0.811706 -173 AGTGGAATTTTTTCTTTACAATCGAAATTG 1 86 1 TTTCTTTACA 0.873413 -97 GAACTCAACTCTCTACAACAGAAATAA 4 54 0 ACTCTCTACA 0.964294 -17 CCTGTCGCAAATTCTTTACAGTTTTTAAAC 5 13 1 ATTCTTTACA 0.97079 -288 CTCGCCCCTCACTCTTTCCAATAATGTTGC 5 222 1 ACTCTTTCCA 0.947588 -79 AGATACTGTGACTCTCTTCAAGCCGTCAGC 5 255 1 ACTCTCTTCA 0.935377 -46 TGCAATATTCTTTTCAGGTCATGCAA 7 7 1 ATTCTTTTCA 0.946844 -214 ********** Masking position 10 Map Score: 4.28056 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 AGCGCCTTTGAGATAAAACCCGTATTATTGCG 2 30 0 AGAAAACCCG 0.986116 -91 TCGGATTATTAGCAAAAAGCCGATGTTTTTAC 3 13 0 AGAAAAGCCG 0.977606 -186 CTACAACAGAAATAAAAACCCCACAGGCTGGC 4 37 0 AAAAAACCCC 0.950921 -34 ATTTATAAGCATGGAAATCCCCTGAGTGAAAC 5 117 1 ATAAATCCCC 0.916578 -184 GAAAAATGTTAAAAAAAAGCCCATCGTGGGAG 5 179 0 AAAAAAGCCC 0.922534 -122 GCGCTAACTAAGGAAAATCGCGATCAAAAACA 7 63 1 AGAAATCGCG 0.921595 -158 CTTCTATTCTAGACAAATCCCCCTCTGATTGA 12 51 1 AGAAATCCCC 0.986113 -79 TAAAAAAGACAGCAAAATGCCGCCTGAATGAT 14 144 0 AGAAATGCCG 0.977605 -56 ** ******** Masking position 6 Map Score: 7.39071 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 140 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 9 GAGATTTTCACTTTAAGTGGAATTTTTTCT 1 71 1 CTTTAAGTGG 0.716398 -112 GTTGACTATGCTTTTAGCGGATAAACCACG 2 87 1 CTTTTAGCGG 0.951159 -34 GGCATACGGACTTTTTGCGTCGATCAGATT 5 53 0 CTTTTTGCGT 0.896302 -248 ACGACAATTCCTTTCTGTGGAAAAA 6 6 0 CTTTCTGTGG 0.942292 -94 ATAAATAACTCTTTCTGCGCTAACTAAGGA 7 47 1 CTTTCTGCGC 0.980004 -174 ACGAAATTATCTTTCAGCAAGGAGCT 7 205 1 CTTTCAGCAA 0.804298 -16 TTTTTACCCTTTCTGCACGCGGTCAGCC 8 13 0 CTTTCTGCAC 0.9181 -18 AGATGAAACACGTTCAGCGTAAAAACATTA 14 27 0 CGTTCAGCGT 0.893794 -173 ********** Masking position 4 Map Score: 2.82242 Number of sites scoring better than the average of aligned sites = 1111 Number in coding regions = 1051 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 10 TGTCATGAGAATAGCGATCATACCATCAAA 1 122 0 ATAGCGATCA 0.956278 -61 CTTTCGCCGCATTGCGACCTATTGGGGAAA 1 156 1 ATTGCGACCT 0.976545 -27 GGTTTTACTCATTGCGATGTGTGTCACTGA 3 87 1 ATTGCGATGT 0.916344 -112 CGGTCAATCGATTGCGACCACAGGTAATAC 3 146 0 ATTGCGACCA 0.983516 -53 ACTAAGGAAAATCGCGATCAAAAACAAACT 7 69 1 ATCGCGATCA 0.970077 -152 ********** Masking position 7 Map Score: 2.16401 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 11 GCATCACACAAAAGAATCTCTCGGATTATT 3 35 0 AAAGAATCTC 0.808879 -164 TAAAATATAAATAACATTATCAGCCTGC 5 283 0 AAATAACATT 0.677991 -18 TTCACTTTTTAAAGCACCTTTGCTAAGTAG 6 75 1 AAAGCACCTT 0.915833 -25 CATGACCTGAAAAGAATATTGCA 7 4 0 AAAGAATATT 0.784691 -217 TACCCAGGGAAAATCATCTTCAGTATAGTA 7 140 1 AAATCATCTT 0.95153 -81 TACGGTAACGAAATTATCTTTCAGCAAGGA 7 198 1 AAATTATCTT 0.831668 -23 AGAATAGAAGAAATAATCTTTCTAACTCCT 12 31 0 AAATAATCTT 0.942051 -99 CCTGAATGATAAATCATCATCATGGAACGC 14 124 0 AAATCATCAT 0.778668 -76 ********** Masking position 6 Map Score: 1.00313 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 138 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 12 AATATTTATTGGTATAGTAAGGGGTGTATT 1 41 1 GGTATAGTAA 0.930623 -142 TTTAGTCGTACGGAAAGCGCGCAATA 2 7 1 CGTACGGAAA 0.962538 -114 AATCATCTTCAGTATAGTAATTATGTAAAC 7 151 1 AGTATAGTAA 0.831021 -70 GAGAACAATACGTACGGTAACGAAATTATC 7 186 1 CGTACGGTAA 0.979567 -35 AGGCTGACCGCGTGCAGAAAGGGTAAAAA 8 12 1 CGTGCAGAAA 0.918911 -19 CTCGTCTGCGGGTACAGTAATTAAGGTGGA 13 28 1 GGTACAGTAA 0.975429 -29 ********** Masking position 3 Map Score: 1.22857 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 129 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 13 ********** No masking Map Score: 2.60302e-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: 2.60302e-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 ********** No masking Map Score: 2.60302e-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