AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i187_lipoic_acid_Biosynthesis_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 lipA 208 lipoate synthesis, sulfur insertion? #2 ybeF 300 putative transcriptional regulator LYSR-type #3 lipB 166 protein of lipoate biosynthesis #4 ybeD 109 orf, hypothetical protein #5 dacA 138 D-alanyl-D-alanine carboxypeptidase, fraction A; penicillin-binding protein 5 #6 mrdA 30 cell elongation, e phase; peptidoglycan synthetase; penicillin-binding protein 2 #7 ybeB 300 orf, hypothetical protein #8 HI0026 53 lipoate biosynthesis protein A (lipA) #9 HI0028 55 conserved hypothetical protein #10 HI0030 51 lipoprotein, putative #11 HI0033 53 conserved hypothetical protein #12 HI0034 124 conserved hypothetical protein #13 HI0035 205 conserved hypothetical protein Motif number 1 GAGAATGAGTAAAAGTGGGGGAAAAGTATA 3 66 0 AAAAGTGGGG 0.992161 -101 ATGGAATTAAAAAAGTGCCCTACTATAGCA 5 97 0 AAAAGTGCCC 0.977745 -42 ATTGTTTTACAAAAATGGCGATGCAATCTG 7 48 1 AAAAATGGCG 0.859235 -253 ATCGGCTTTCGAAAGTGGGCTATCATCCCA 7 88 0 GAAAGTGGGC 0.892165 -213 TTTCCTAAATAAAAATGCCCAAATTGGGCA 8 29 0 AAAAATGCCC 0.859235 -25 AAATAAATCAAAAAGTGCGGTCAATTTTCA 9 19 0 AAAAGTGCGG 0.997265 -37 ATTTTAGTAAAGTGCGGTAAAAAATAA 11 8 1 TAAAGTGCGG 0.978871 -46 TCCTTATCTAAAAAGTGCGGTTATTTTTTA 11 28 0 AAAAGTGCGG 0.997265 -26 TTTAGACATAAAAAGCGCGGTTAATTTCGC 12 26 1 AAAAGCGCGG 0.984275 -99 ACTTAGCAATAAAGGTGCGGAATTCTATCA 12 96 0 AAAGGTGCGG 0.984275 -29 CATCCGAGATAAAAGTGCGGTGAAAAATAA 13 19 1 AAAAGTGCGG 0.997265 -187 CCCTTTTACAAAAAGTGCGGTTATTTTTCA 13 39 0 AAAAGTGCGG 0.997265 -167 ********** Masking position 3 Map Score: 31.5672 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 219 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 2 AATTGGAGTAAGTGCGTGGATAGTAATAATC 2 143 1 AGTGCGTGAT 0.92309 -158 AATGAGTAAAAGTGGGGGAAAAGTATATCAC 3 62 0 AGTGGGGGAA 0.966145 -105 TAAATCAAAAAGTGCGGTCAATTTTCAAATT 9 15 0 AGTGCGGTAA 0.996727 -41 ATTTTAGTAAAGTGCGGTAAAAAATAACCGC 11 11 1 AGTGCGGTAA 0.996726 -43 TTATCTAAAAAGTGCGGTTATTTTTTACCGC 11 24 0 AGTGCGGTAT 0.994759 -30 AGACATAAAAAGCGCGGTTAATTTCGCGCTT 12 29 1 AGCGCGGTAA 0.987786 -96 CCGAGATAAAAGTGCGGTGAAAAATAACCGC 13 22 1 AGTGCGGTAA 0.996727 -184 TTTTACAAAAAGTGCGGTTATTTTTCACCGC 13 35 0 AGTGCGGTAT 0.994759 -171 ******** ** Masking position 10 Map Score: 19.8501 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 42 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 3 AAAAGTATTGTTACAGCCAGA 1 2 1 AAAGTATTGT 0.695408 -207 CGAAAATGTAAAATTGTTGTTGGATTGTGC 1 55 0 AAATTGTTGT 0.975947 -154 GTTAATTCAAAAATAGTTGATAATTACAAC 1 134 1 AAATAGTTGA 0.882126 -75 TCAATTCAATAGATTGTTGTAATTATCAAC 1 149 0 AGATTGTTGT 0.933622 -60 TAACCTATTGAAATAGTTGATTATGGTGAG 2 44 1 AAATAGTTGA 0.882126 -257 ATTAGACATAAGATTATTGTAATTTTTTAA 2 92 1 AGATTATTGT 0.821721 -209 GTAAGGTTGTAAATATTTGTGGTTTACCTT 2 207 0 AAATATTTGT 0.767423 -94 TATCAGGATAAAATTCTTGTCCGCCAGCTC 3 114 1 AAATTCTTGT 0.886386 -53 GACTTTGTAGAAATTGTTTTACAAAAATGG 7 36 1 AAATTGTTTT 0.849205 -265 GTTATCGACAAAATTGATGACCTCAAAGGT 7 230 1 AAATTGATGA 0.709134 -71 GTCTAAATTGAAATTATTTTTA 12 3 0 AAATTATTTT 0.645133 -122 ACAATACCGAAAATTTTTGACCCTTTTACA 13 59 0 AAATTTTTGA 0.828014 -147 ********** Masking position 3 Map Score: 8.23362 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 248 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 4 AAAAGTATTGTTACAGCCAGATCACAGCGC 1 11 1 TTACAGCCAG 0.88744 -198 GTGATATACTTTTCCCCCACTTTTACTCAT 3 62 1 TTTCCCCCAC 0.846474 -105 ATAAAATTCTTGTCCGCCAGCTCGGTCTTC 3 121 1 TGTCCGCCAG 0.962937 -46 CCAGCTCGGTCTTCAGCCTTACGAGCCAAT 3 137 1 CTTCAGCCTT 0.758352 -30 CAGTAAAAAACTCCCGCCTTCTGGCGGGAG 4 58 1 CTCCCGCCTT 0.911344 -52 TAAATAGCAACTCCCGCCAGAAGGCGGGAG 4 68 0 CTCCCGCCAG 0.985047 -42 GGCATCTGACTTTCCGCGTGACTTTGTTAA 5 52 0 TTTCCGCGTG 0.916793 -87 AGCAAATGCACTACCGGCAGGCATCTGACT 5 71 0 CTACCGGCAG 0.850046 -68 AGCCAGACTTTTTCCGCCAGACACGACTTT 7 12 1 TTTCCGCCAG 0.992028 -289 CCCTGCAAGTTTTCCCCCTGGGTGAATCAA 7 181 0 TTTCCCCCTG 0.957902 -120 ********** Masking position 4 Map Score: 7.39486 Number of sites scoring better than the average of aligned sites = 3115 Number in coding regions = 2990 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 5 TTATTCATGGAAAAATAATATTTAAAAAAT 2 113 0 AAAAATAATA 0.908648 -188 TTTCTTTCCTAAAAATAAAATAAATCAAAA 9 36 0 AAAAATAAAA 0.928325 -20 TTAAGAAAGAAAAAATGAAA 10 1 0 AAAAATGAAA 0.963964 -51 TAAAGAAAGAATAAATGAAAAGCGTTAATA 10 28 1 ATAAATGAAA 0.847409 -24 TAAAAATAATTTCAATTTAGA 12 2 1 AAAAATAATT 0.673727 -123 ACCAAACTCAAAAAATGATACGTTCGTCAC 13 120 0 AAAAATGATA 0.953582 -86 TTGACCCCTTAAAAATGAAATTTAACTCCT 13 185 0 AAAAATGAAA 0.963964 -21 ********** Masking position 5 Map Score: 6.0974 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 53 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 6 AGCAGAAAGTCGTCAGAAGGTAAACCACAA 2 191 1 CGTCAGAAGG 0.987189 -110 CTTCAAAAATAGTCAGAAGGTTAAGATCAA 2 243 0 AGTCAGAAGG 0.979832 -58 TAGCAACTCCCGCCAGAAGGCGGGAGTTTT 4 64 0 CGCCAGAAGG 0.986933 -46 GAAATTGACACATCAGATGCCTGCTTTACG 5 11 0 CATCAGATGC 0.90845 -128 TCACGCGGAAAGTCAGATGCCTGCCGGTAG 5 61 1 AGTCAGATGC 0.941193 -78 AGTATACCTGAACCAGAGGCGATTTCGGGA 7 131 0 AACCAGAGGC 0.904627 -170 GTGGATTTTGCGCAAGAGGGTATTCAATGA 12 69 1 CGCAAGAGGG 0.874886 -56 ACTTGGATATAATCCGAAGGAGTTAAATTT 13 168 1 AATCCGAAGG 0.834547 -38 ********** Masking position 7 Map Score: 4.74932 Number of sites scoring better than the average of aligned sites = 682 Number in coding regions = 640 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 7 AACGACTGGCAGTATATCATTGAAACGGACCT 1 105 0 AGTATATCAG 0.953636 -104 GTGGGGGAAAAGTATATCACAGCGAGGAGAGG 3 50 0 AGTATATCAG 0.953636 -117 CACTTTTTTAATTCCATCACGGATGTCGTAGT 5 110 1 ATTCCATCAG 0.97026 -29 GACAAAATTGATGACCTCAAAGGTCAGGACAT 7 236 1 ATGACCTCAG 0.833503 -65 CTCAAAGGTCAGGACATCATCGCCTTAGACGT 7 251 1 AGGACATCAG 0.94865 -50 AAGGTGCGGAATTCTATCATTGAATACCCTCT 12 83 0 ATTCTATCAG 0.953636 -42 AAATATTCCATCCGAGATAAAAGTGC 13 5 1 ATTCCATCCG 0.94865 -201 ACTCCTTCGGATTATATCCAAGTTGTTTTTTG 13 159 0 ATTATATCCG 0.922377 -47 ********* * Masking position 1 Map Score: 3.31855 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 142 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 8 GGGGTGAGTTACGGAGCAAGGCGTGGC 2 7 0 ACGGAGCAGG 0.962276 -294 GAGCCGGGTAACGGAGAAGCGAG 3 3 0 ACGGAGAGCG 0.974145 -164 GTTACCCGACCAGGAGCCGGGTAACGGAGAA 3 16 0 CAGGAGCGGG 0.977433 -151 ATATCACAGCGAGGAGAGGGGAGTTACCCGA 3 38 0 GAGGAGAGGG 0.944231 -129 CTCATTCTCCACGGAGATGCCGTTTTGTATC 3 87 1 ACGGAGAGCC 0.958606 -80 AAGGCTGAAGACCGAGCTGGCGGACAAGAAT 3 126 0 ACCGAGCGGC 0.95874 -41 TTACGTTACGCCGGAGCTGAC 4 99 1 CCGGAGCGAC 0.947388 -11 GATGCAATCTGCGGCGCGGGGTGGGATGATA 7 67 1 GCGGCGCGGG 0.980506 -234 ******* *** Masking position 6 Map Score: 3.85177 Number of sites scoring better than the average of aligned sites = 951 Number in coding regions = 891 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 9 ATATACTGCCAGTCGTTAATTCAAAAATAGT 1 120 1 AGTCGTAATT 0.953264 -89 ATTCAAAAATAGTTGATAATTACAACAATCT 1 138 1 AGTTGTAATT 0.972962 -71 TGCGTGTTCCAGTTGCGAATTACGAAGGAAA 1 184 0 AGTTGGAATT 0.905362 -25 CTATTGAAATAGTTGATTATGGTGAGCAAAA 2 48 1 AGTTGTTATG 0.94001 -253 ACAGGGTTCAATTTGATTATTACTATCCACG 2 157 0 ATTTGTTATT 0.755503 -144 TTCTGGCGGGAGTTGCTATTTAATTACGTTA 4 76 1 AGTTGTATTT 0.929529 -34 GCAGTCGGTGATGCTGGATTTGC 7 288 0 AGTCGTGATG 0.838834 -13 ATTATATCCAAGTTGTTTTTTGAAAACCTTA 13 150 0 AGTTGTTTTT 0.910154 -56 ***** ***** Masking position 1 Map Score: 2.31885 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 99 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 10 ATTGAAACGCTTTCCTTCGTAATTCGCAACTG 1 174 1 TTTCCTCTAA 0.980571 -35 AGTATTTTCCTAAATAAAAATGCCCAA 8 37 0 TTTCCTATAA 0.90594 -17 TTTCTTTCCTAAAAATAAAATA 9 44 0 TTTCTTCTAA 0.979247 -12 TTTCATTTTTTCTTTCTTAAAGAAAGAATA 10 9 1 TTTCTTCTAA 0.979247 -43 CGTCACATTTTTTCTTGCGAAATTGAGCATAG 13 94 0 TTTCTTCAAA 0.921267 -112 ****** * *** Masking position 6 Map Score: 1.03829 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 10 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 TATCGTTCTGCGCTGTGATCTGGCTGTAACA 1 19 0 CGCTGTGATT 0.981715 -190 TTTCGCTGCATTAACGATCCCTTT 2 287 0 CGCTGCATTA 0.91928 -14 CCCCTCTCCTCGCTGTGATATACTTTTCCCC 3 48 1 CGCTGTGATT 0.981715 -119 CCGCTGCGTTTTCTACTCAAAG 6 19 0 CGCTGCGTTT 0.988294 -12 ACAAAAATGGCGATGCAATCTGCGGCGCGGG 7 56 1 CGATGCAATT 0.911405 -245 ********* * Masking position 4 Map Score: 0.24327 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 240 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 12 GCAGTATATCATTGAAACGGACCTGAAAGC 1 99 0 ATTGAAACGG 0.983714 -110 AATCTATTGAATTGAAACGCTTTCCTTCGT 1 164 1 ATTGAAACGC 0.957507 -45 CTTATGTCTAATTGGAACGGAACGCTTTTG 2 74 0 ATTGGAACGG 0.989411 -227 TGCTTAGTATATGGGGACGGAAATTACACT 4 27 0 ATGGGGACGG 0.969833 -83 ********** Masking position 7 Map Score: 0.217124 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 30 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 13 ********** No masking Map Score: -5.52559e-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: -5.52559e-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: -5.52559e-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