AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i222_Ribosomal_Operon_+_Transcription_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 pheS 283 phenylalanine tRNA synthetase, alpha-subunit #2 pheM 122 phenylalanyl-tRNA synthetase (pheST) operon leader peptide #3 rplT 52 50S ribosomal subunit protein L20, and regulator #4 rpmI 96 50S ribosomal subunit protein A #5 thrS 300 threonine tRNA synthetase #6 HI1310 24 H. influenzae predicted coding region HI1310 #7 HI1311 148 phenylalanyl-tRNA synthetase, alpha subunit (pheS) #8 HI1312 33 phenylalanyl-tRNA synthetase, beta subunit (pheT) #9 HI1316 300 H. influenzae predicted coding region HI1316 #10 HI1317 81 conserved hypothetical protein #11 HI1318 267 translation initiation factor 3 (infC) #12 HI1319 138 ribosomal protein L35 (rpL35) #13 HI1320 66 ribosomal protein L20 (rpL20) #14 HI1367 284 threonyl-tRNA synthetase (thrS) Motif number 1 TGAGACAGGCTTTTTATTTTTCAAAACGCGCAT 1 85 0 TTTTTTTTTA 0.766652 -199 CTAGTCTCCCTCTTTTCGTTTCAACGCCATCAA 2 29 1 TCTTTCGTTA 0.982029 -94 ATCGCCGTAGCCTTTTCAATAAAGGTCTTTTGA 2 75 1 CCTTTCATAA 0.619083 -48 GGAGATTGTACCTTTCCGTTTCACATTGATTCG 5 91 0 CCTTTCGTTA 0.979918 -210 CGTTATTCCATTTTTATTTTTGATAAGCCAATG 7 35 1 TTTTTTTTTA 0.766652 -114 TCGCATTATTCTTTTACTTTTTAAGGACTTGGT 7 73 1 CTTTTCTTTA 0.922422 -76 CCCCTGCTTCTCTTTTCTCTATAAAATAAAAAA 7 121 0 TCTTTCTTAA 0.852061 -28 ATTTCATACCCCTTTTCTTCTAACCATTCTTTA 9 76 0 CCTTTCTCTA 0.889954 -225 GGGTACAAGAACTTTGCGGTTTACTCTCAGGCG 9 153 1 ACTTTCGTTA 0.86356 -148 ATGGTTTGATCTTTTGCGCCTGAGAGTAAACCG 9 169 0 CTTTTCGCTA 0.892372 -132 CTTGAATATATTTTTTCGCTTCATCAATGATGA 9 210 0 TTTTTCGTTA 0.96468 -91 ATAGTAAAAATCTTTTCGCTAAAAATAAAAGAT 11 87 0 TCTTTCGTAA 0.92196 -181 AGCGAAAAGATTTTTACTATTAACCAATAGAAG 11 100 1 TTTTTCTTTA 0.930145 -168 GCCGGTGCTTTTTTTACGGTTTTAATAATCGTA 11 136 0 TTTTTCGTTT 0.673945 -132 TTTCAGCAAATCTTTTTGTTTAAGTTTGACTTA 12 27 1 TCTTTTGTTA 0.930953 -112 CATGCAGTTGTCTTTTCATTTAAGTCAAACTTA 12 47 0 TCTTTCATTA 0.893825 -92 GTTATTCTAGCCTTTATTTTTAAGAGATAAAGC 14 43 1 CCTTTTTTTA 0.854432 -242 GGAAATAATGTTTTTCTGACTAAAGGCTTTATC 14 68 0 TTTTTTGCTA 0.696141 -217 ***** ** ** * Masking position 5 Map Score: 17.1419 Number of sites scoring better than the average of aligned sites = 582 Number in coding regions = 474 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 2 CTTTTTTTGTATGCGCGTTTTGAAAAATAAA 1 75 1 ATCGCGTTTT 0.90901 -209 GGAAAGGTACAATCTCCCTTTTTTTAGTGTT 5 107 1 AACTCCCTTT 0.847303 -194 CTGGGATTTCATACCCCTTTTCTTCTAACCA 9 83 0 ATCCCCTTTT 0.883046 -218 TTTGGAGATAATCCGCATTTACGGGTACAAG 9 131 1 ATCGCATTTA 0.825612 -170 TGGGGGCCGCATACGCCTTGTATT 9 287 1 ATCGCCTTGT 0.915521 -14 GGCGTATCAGATACGCCCTTAATCTACGACT 10 15 0 ATCGCCCTTA 0.958396 -67 GGCGTATCTGATACGCCCTTTGTTATCTCTG 10 29 1 ATCGCCCTTT 0.988053 -53 AGGCAAATTAAATCGCCTTTTCAAAAGCAGT 12 101 0 AACGCCTTTT 0.972578 -38 AGGCTAGAATAACCGCACTTTTAAATACCCA 14 25 0 AACGCACTTT 0.948851 -260 TATAAAAATTAACCGCACTTTTGCCCTACTT 14 206 0 AACGCACTTT 0.948851 -79 ** ******** Masking position 9 Map Score: 10.1781 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 234 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 3 GAAAGCCTCCCAGTGGAGGCTTTTTTTGTA 1 56 1 CAGTGGAGGC 0.984947 -228 CTCATTGTGTCAGTGGTGACACTGGTTCGT 1 257 0 CAGTGGTGAC 0.991115 -27 GTAGCACTGTCTGTGGAGCCTTCGGGCTTC 4 20 1 CTGTGGAGCC 0.984742 -77 CGAACAAAGCCTGTGAAGCCCGAAGGCTCC 4 34 0 CTGTGAAGCC 0.908963 -63 TCCTTATTTGCAGTGGTGACCCACACGAAA 5 275 0 CAGTGGTGAC 0.991115 -26 TTTCCTTATACAGTGGTCACCCATACGAAA 14 260 0 CAGTGGTCAC 0.962374 -25 ********** Masking position 4 Map Score: 6.38643 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 110 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 CAGGCTATTTTACTTGCCATTTTGGTCCCGGGC 1 203 0 TATTCATTTT 0.618025 -81 GCCGTTAACGTTTTTAACTTTTTAATTAGAATA 3 11 1 TTTTCTTTTT 0.918214 -42 TTCACAGGCTTTGTTCGCCTTTGTTTCGTTTAT 4 47 1 TTTTCCTTTG 0.82526 -50 TTTATATCCTTATTTGCAGTGGT 5 288 0 TTATCCTTAT 0.683514 -13 AAGCCAATGATTTTTCGCATTATTCTTTTACTT 7 59 1 TTTTCATTAT 0.853883 -90 TTCGCATTATTCTTTTACTTTTTAAGGACTTGG 7 72 1 TCTTCTTTTT 0.639091 -77 CATTACTCGGTTTTTTATTTTATAGAGAAAAGA 7 111 1 TTTTTTTTAT 0.558767 -38 TTGTTGTTATCCTTTTAATTCAAATC 8 18 0 TTTTCCTTTT 0.972073 -16 TCTCTGCACCTTATTTATCTTTTAAAATAGGAA 10 54 1 TTTTTCTTTT 0.852788 -28 GTTTATTCCTATTTTAAAAGATAAA 10 67 0 TTTTTATTTT 0.589313 -15 CAATCCCTGCTTGTTCACCATTTTGGTCAATTA 11 222 0 TTTTCCATTT 0.761137 -46 AAAGGCGATTTAATTTGCCTTATGATGGAAATG 12 112 1 TATTCCTTAT 0.815738 -27 CAGAAAAACATTATTTCCTTTTTGTAAAATATG 14 83 1 TTTTCTTTTT 0.918214 -202 TCGCCACGCATTTTTTGCCTAATTTCGCTCGTT 14 154 1 TTTTCCTAAT 0.683514 -131 TGTTTTTTCCTTATACAGTGGTCA 14 271 0 GTTTCCTTAT 0.761958 -14 ** ** ****** Masking position 5 Map Score: 5.72593 Number of sites scoring better than the average of aligned sites = 657 Number in coding regions = 451 Number in noncoding regions = 206 Number of orfs with sites within 600 bp upstream = 221 Fraction of orfs with sites within 600 bp upstream = 0.0354963 Motif number 5 CAGGAGGCTAGCGCGTGAGAAGAGAAACGG 1 14 1 GCGCGTGAGA 0.988733 -270 ACGGAAAACAGCGCCTGAAAGCCTCCCAGT 1 40 1 GCGCCTGAAA 0.993473 -244 ACATCACGGTGCGTCTGAAAGGTT 5 5 0 GCGTCTGAAA 0.974563 -296 TTGATCTTTTGCGCCTGAGAGTAAACCGCA 9 167 0 GCGCCTGAGA 0.99576 -134 ********** Masking position 6 Map Score: 3.85028 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 48 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 CTTTTTATTTTTCAAAACGCGCATACAAAA 1 79 0 TTCAAAACGC 0.749814 -205 TGAGTACACCAGCAAAACGCTTAAAGAACA 5 42 0 AGCAAAACGC 0.981454 -259 AAATCCCAGAAGTAAGCCGCGCCTACTTTG 9 105 1 AGTAAGCCGC 0.935716 -196 TGCGCCTGAGAGTAAACCGCAAAGTTCTTG 9 158 0 AGTAAACCGC 0.979299 -143 AAGCACCGGCAGTAAATCGCCCAAACCGTA 11 159 1 AGTAAATCGC 0.968337 -109 CATAAGGCAAATTAAATCGCCTTTTCAAAA 12 106 0 ATTAAATCGC 0.892966 -33 CCGTTATTTAAGCAAAACGTACGATTAGTT 13 12 1 AGCAAAACGT 0.87284 -55 ********** Masking position 5 Map Score: 3.5095 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 342 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 GGCTTTGTTCGCCTTTGTTTCGTTTATTAA 4 53 1 GCCTTTGTTT 0.939284 -44 GAGTGTGTTGGCGGTTGGTTGAAGACTAAA 9 37 0 GCGGTTGGTT 0.913636 -264 ATGAAGGCAAGCCGTTCTTTGCATGGATAA 9 252 1 GCCGTTCTTT 0.942908 -49 GCCGTTATTTAAGCAAAACG 13 1 1 GCCGTTATTT 0.98171 -66 ATTTAAAAGTGCGGTTATTCTAGCCTTTAT 14 30 1 GCGGTTATTC 0.94161 -255 GGTTATTCTAGCCTTTATTTTTAAGAGATA 14 42 1 GCCTTTATTT 0.964689 -243 AAGAGATAAAGCCTTTAGTCAGAAAAACAT 14 64 1 GCCTTTAGTC 0.883198 -221 TAAAATATGGGCATTTATTTAACAATACTT 14 107 1 GCATTTATTT 0.808663 -178 GGGCAAAAGTGCGGTTAATTTTTATAGAAT 14 211 1 GCGGTTAATT 0.872598 -74 ********** Masking position 5 Map Score: 6.7652 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 231 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 8 TTTTACTTGCCATTTTGGTCCCGGGCTGTGCT 1 197 0 CTTTGGTCCC 0.98311 -87 TGTGATCTTTCGTGTGGGTCACCACTGCAAAT 5 268 1 CTTGGGTCAC 0.991023 -33 CATGGATAAACTTCTGGGGGCCGCATACGCCT 9 273 1 CTTGGGGGCC 0.975406 -28 GCTTGTTCACCATTTTGGTCAATTAAACGAAC 11 215 0 CTTTGGTCAA 0.915694 -53 AAGACAACTGCATGTTGGGCACACTACGCAGC 12 66 1 CTTTGGGCAC 0.98311 -73 CGTCACCTTTCGTATGGGTGACCACTGTATAA 14 253 1 CTTGGGTGAC 0.982965 -32 * * ******** Masking position 5 Map Score: 2.78414 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 33 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 9 CTTTTCAATAAAGGTCTTTTGAAGAGTACCAAAA 2 86 1 AAGTTTGAAG 0.837708 -37 ACTCACTACAAACGAATTGCGAATCGAATCAATG 5 67 1 AAGTGCGAAT 0.986218 -234 CAAGAAAAAATGGAATAGCGAATACGTTATTCC 7 10 1 ATGTGCGAAT 0.946275 -139 GCCTTCATCTAATGATTCTTGAATATATTTTTTC 9 226 0 AAGTTTGAAT 0.943742 -75 AGGAACGAGCAAAGTCTCGCGAATTCTATAGTAT 11 34 0 AAGTGCGAAT 0.986218 -234 TTCTAGGGCTTGTTGAATAGAAACAATC 11 250 0 AGGTTTGAAT 0.859822 -18 TTAGGCAAAAAATGCGTGGCGAATTCTATCACTT 14 142 0 AAGTGCGAAT 0.986218 -143 ** * * ****** Masking position 12 Map Score: 2.40626 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 79 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 ACTTAGAGCCTATCCCATCAGGCTATTTTA 1 224 0 TATCCCATCA 0.939664 -60 AGGGGTATGAAATCCCAGAAGTAAGCCGCG 9 96 1 AATCCCAGAA 0.753231 -205 AACCATCCCTTATTTCATCATTGATGAAGC 9 196 1 TATTTCATCA 0.669779 -105 CCCAGAAGTTTATCCATGCAAAGAACGGCT 9 261 0 TATCCATGCA 0.736356 -40 CGCCCTTTGTTATCTCTGCACCTTATTTAT 10 42 1 TATCTCTGCA 0.949076 -40 TTAATAATCGTATTCCTTCTATTGGTTAAT 11 118 0 TATTCCTTCT 0.61882 -150 CTTTTACACGAATCTCTTCATTGATACGGT 11 183 0 AATCTCTTCA 0.891165 -85 GAATAGAAACAATCCCTGCTTGTTCACCAT 11 234 0 AATCCCTGCT 0.838336 -34 TTTGCTGAAAAATCTCAGCAAAATTC 12 7 0 AATCTCAGCA 0.866289 -132 TTTTATTCCTTAACTGGGTATTT 14 4 1 TATTCCTTAA 0.618425 -281 CTAAAGGCTTTATCTCTTAAAAATAAAGGC 14 52 0 TATCTCTTAA 0.774778 -233 ********** Masking position 2 Map Score: 2.77844 Number of sites scoring better than the average of aligned sites = 979 Number in coding regions = 857 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 11 ATCCAGGAGGCTAGCGCGTGAGAAG 1 6 1 GGAGGCTAGC 0.994621 -278 GCCTCCACTGGGAGGCTTTCAGGCGCTGTT 1 46 0 GGAGGCTTTC 0.979189 -238 GCCTCCCAGTGGAGGCTTTTTTTGTATGCG 1 60 1 GGAGGCTTTT 0.917137 -224 ACGAAAAGAGGGAGACTAGCTCCCTCTTTC 2 18 0 GGAGACTAGC 0.972821 -105 ATCATTAGATGAAGGCAAGCCGTTCTTTGC 9 244 1 GAAGGCAAGC 0.915454 -57 ********** Masking position 3 Map Score: 1.37231 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 54 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 12 ATCCAGGAGGCTAGCGCGTGAGAAGAGA 1 9 1 GGCTAGCGCG 0.995256 -275 GACTGGACACGGCCAGCGCGGAGAAACCGG 1 140 1 GGCCAGCGCG 0.991749 -144 TTATTGAAAAGGCTACGGCGATAAAAGTCA 2 67 0 GGCTACGGCG 0.987315 -56 TCATTGATACGGTTTGGGCGATTTACTGCC 11 166 0 GGTTTGGGCG 0.954513 -102 ********** Masking position 8 Map Score: 0.789789 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 78 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 13 ********** No masking Map Score: 2.70249e-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: 2.70249e-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 ATTCTTTTACTTTTTAAGGACTTGGTATTA 7 80 1 TTTTTAAGGA 0.844941 -69 GGTTTTTTATTTTATAGAGAAAAGAGAAGC 7 119 1 TTTATAGAGA 0.789557 -30 CTAACCATTCTTTATAACGATTAGAGTGTG 9 60 0 TTTATAACGA 0.822144 -241 TTTATTCCTATTTTAAAAGATAAATAAGGT 10 61 0 TTTTAAAAGA 0.907431 -21 AAATCTTTTATTTTTAGCGAAAAGATTTTT 11 85 1 TTTTTAGCGA 0.934815 -183 AACGAACTTCTTTTACACGAATCTCTTCAT 11 192 0 TTTTACACGA 0.73511 -76 TAGCCTTTATTTTTAAGAGATAAAGCCTTT 14 50 1 TTTTAAGAGA 0.906011 -235 GTGCGGTTAATTTTTATAGAATTTTAAATG 14 219 1 TTTTTATAGA 0.747382 -66 TTTTATAGAATTTTAAATGAACACGTCACC 14 230 1 TTTTAAATGA 0.749338 -55 ********** Masking position 3 Map Score: 0.566658 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 106 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084