AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i222_Ribosomal_Operon_+_Transcription_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 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 Motif number 1 ATCCAGGAGGCTAGCGCGTGAGAAG 1 6 1 GGAGGCTAGC 0.977097 -278 GCCTCCACTGGGAGGCTTTCAGGCGCTGTT 1 46 0 GGAGGCTTTC 0.991309 -238 GCCTCCCAGTGGAGGCTTTTTTTGTATGCG 1 60 1 GGAGGCTTTT 0.989177 -224 ACCTGATGAGACAGGCTTTTTATTTTTCAA 1 94 0 ACAGGCTTTT 0.920153 -190 CGGAGAAACCGGAGCGTATTTAAGTACGTG 1 158 1 GGAGCGTATT 0.85983 -126 GCCTATCCCATCAGGCTATTTTACTTGCCA 1 217 0 TCAGGCTATT 0.793587 -67 CGTTGGACTTAGAGCCTATCCCATCAGGCT 1 230 0 AGAGCCTATC 0.950201 -54 ACGAAAAGAGGGAGACTAGCTCCCTCTTTC 2 18 0 GGAGACTAGC 0.847837 -105 TTTTATCGCCGTAGCCTTTTCAATAAAGGT 2 71 1 GTAGCCTTTT 0.874533 -52 CACTGTCTGTGGAGCCTTCGGGCTTCACAG 4 24 1 GGAGCCTTCG 0.907488 -73 TTCGGGCTTCACAGGCTTTGTTCGCCTTTG 4 40 1 ACAGGCTTTG 0.885937 -57 ********** Masking position 3 Map Score: 10.1509 Number of sites scoring better than the average of aligned sites = 660 Number in coding regions = 575 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 2 AAGAGAAACGGAAAACAGCGCCTGAAAGCC 1 33 1 GAAAACAGCG 0.971003 -251 ACGCGCATACAAAAAAAGCCTCCACTGGGA 1 63 0 AAAAAAAGCC 0.980785 -221 GTTTTGAAAAATAAAAAGCCTGTCTCATCA 1 91 1 ATAAAAAGCC 0.901451 -193 TGAGAATTTCGAGCACAGCCCGGGACCAAA 1 186 1 GAGCACAGCC 0.934139 -98 GCGTTGAAACGAAAAGAGGGAGACTAGCTC 2 26 0 GAAAAGAGGG 0.917924 -97 AAACAAAGGCGAACAAAGCCTGTGAAGCCC 4 43 0 GAACAAAGCC 0.987556 -54 TTAATAAACGAAACAAAGGCGAACAAAGCC 4 53 0 AAACAAAGGC 0.968505 -44 TGTTAACACTAAAAAAAGGGAGATTGTACC 5 112 0 AAAAAAAGGG 0.950699 -189 ********** Masking position 5 Map Score: 6.81366 Number of sites scoring better than the average of aligned sites = 646 Number in coding regions = 511 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 3 AGGCGCTGTTTTCCGTTTCTCTTCTCACGC 1 26 0 TTCCGTTTCT 0.986225 -258 GTCTCCCTCTTTTCGTTTCAACGCCATCAA 2 32 1 TTTCGTTTCA 0.978851 -91 TTCGCCTTTGTTTCGTTTATTAACAATGCG 4 60 1 TTTCGTTTAT 0.956016 -37 TCGATTCGCAATTCGTTTGTAGTGAGTACA 5 64 0 ATTCGTTTGT 0.936005 -237 GATTGTACCTTTCCGTTTCACATTGATTCG 5 91 0 TTCCGTTTCA 0.974601 -210 GGTTAATGTCTTTCATTTGTGTACCTGATT 5 167 1 TTTCATTTGT 0.901688 -134 ********** Masking position 6 Map Score: 5.27309 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 57 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 TCGTTTATTAACAATGCGAAGTGGAAGTTA 4 72 1 ACAATGCGAA 0.973772 -25 CACTACAAACGAATTGCGAATCGAATCAAT 5 70 1 GAATTGCGAA 0.952029 -231 GCGAATCGAATCAATGTGAAACGGAAAGGT 5 85 1 TCAATGTGAA 0.947303 -216 TTTGTGTACCTGATTGCGAACCAATTTAGC 5 182 1 TGATTGCGAA 0.980448 -119 TATTAACAGTTCATTGCGAAACCATCTAGC 5 220 0 TCATTGCGAA 0.992616 -81 ********** Masking position 5 Map Score: 3.25055 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 101 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 CTTTTTATTTTTCAAAACGCGCATACAAAA 1 79 0 TTCAAAACGC 0.984476 -205 GTTTTGAAAAATAAAAAGCCTGTCTCATCA 1 91 1 ATAAAAAGCC 0.757439 -193 TCTCACGTACTTAAATACGCTCCGGTTTCT 1 161 0 TTAAATACGC 0.796235 -123 TTTCAACGCCATCAAAACATTGACTTTTAT 2 47 1 ATCAAAACAT 0.79417 -76 AAGACCTTTATTGAAAAGGCTACGGCGATA 2 74 0 TTGAAAAGGC 0.921498 -49 TTTGGTACTCTTCAAAAGACCTTTATTGAA 2 89 0 TTCAAAAGAC 0.92132 -34 TTTGAAGAGTACCAAAAGGTAACGCAAGCA 2 103 1 ACCAAAAGGT 0.783407 -20 AATTAAAAAGTTAAAAACGTTAACGGC 3 8 0 TTAAAAACGT 0.890399 -45 TGAGTACACCAGCAAAACGCTTAAAGAACA 5 42 0 AGCAAAACGC 0.93184 -259 ********** Masking position 5 Map Score: 2.51342 Number of sites scoring better than the average of aligned sites = 1376 Number in coding regions = 1207 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 6 CAGGAGGCTAGCGCGTGAGAAGAGAAACGGA 1 14 1 GCGCTGAGAA 0.97428 -270 ACGGAAAACAGCGCCTGAAAGCCTCCCAGTG 1 40 1 GCGCTGAAAG 0.990514 -244 GCGTATTTAAGTACGTGAGAATTTCGAGCAC 1 171 1 GTACTGAGAA 0.755963 -113 GCCAGTTGAAAGAGGGAGCTAG 2 2 1 CCAGTGAAAG 0.968558 -121 ACATCACGGTGCGTCTGAAAGGTT 5 4 0 GCGTTGAAAG 0.952399 -297 CACCTTCCACCCGGTTGAGCGATGTTAACAC 5 133 0 CCGGTGAGCG 0.953671 -168 CAACCGGGTGGAAGGTGAGAGGTTAATGTCT 5 147 1 GAAGTGAGAG 0.911592 -154 CAGTGGTGACCCACACGAAAGATCACATACA 5 264 0 CCACCGAAAG 0.91487 -37 **** ****** Masking position 8 Map Score: 2.456 Number of sites scoring better than the average of aligned sites = 1021 Number in coding regions = 946 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 7 TCATTGTGTCAGTGGTGACACTGGTTCGTT 1 256 0 AGTGGTGACA 0.980388 -28 TCCACTTCGCATTGTTAATAAACGAAACAA 4 67 0 ATTGTTAATA 0.826154 -30 TTAAAGAACAACTGATAACATCACGGTGCG 5 22 0 ACTGATAACA 0.938197 -279 CCCTTTTTTTAGTGTTAACATCGCTCAACC 5 122 1 AGTGTTAACA 0.982412 -179 TTCGCAATGAACTGTTAATAAACAAATTTT 5 230 1 ACTGTTAATA 0.928378 -71 CCTTATTTGCAGTGGTGACCCACACGAAAG 5 274 0 AGTGGTGACC 0.94814 -27 ********** Masking position 6 Map Score: 1.64621 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 102 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 TCTCTTCTCACGCGCTAGCCTCCTGGAT 1 9 0 CGCGCTAGCC 0.997791 -275 CCGGTTTCTCCGCGCTGGCCGTGTCCAGTC 1 140 0 CGCGCTGGCC 0.995296 -144 GTTGAAAGAGGGAGCTAGTCTCCCTCTTTT 2 15 1 GGAGCTAGTC 0.924979 -108 TGACTTTTATCGCCGTAGCCTTTTCAATAA 2 67 1 CGCCGTAGCC 0.980288 -56 CATTGCGAAACCATCTAGCCAACAAATGCT 5 209 0 CCATCTAGCC 0.941845 -92 ********** Masking position 6 Map Score: 2.39889 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 270 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 GGAGGCTTTTTTTGTATGCGCGTTTTGAAA 1 70 1 TTTGTATGCG 0.93589 -214 CCGTGTCCAGTCTGGCTGCGACAATTACAC 1 122 0 TCTGGCTGCG 0.953741 -162 TTTTCCTCATTGTGTCAGTGGTGACACTGG 1 262 0 TGTGTCAGTG 0.932691 -22 TTCAAGTAGCACTGTCTGTGGAGCCTTCGG 4 15 1 ACTGTCTGTG 0.9315 -82 TATCAGTTGTTCTTTAAGCGTTTTGCTGGT 5 35 1 TCTTTAAGCG 0.87327 -266 CAATCTCCCTTTTTTTAGTGTTAACATCGC 5 116 1 TTTTTTAGTG 0.697339 -185 CAAATTTTTCTTTGTATGTGATCTTTCGTG 5 252 1 TTTGTATGTG 0.937081 -49 TTATATCCTTATTTGCAGTGGTGACCCACA 5 280 0 ATTTGCAGTG 0.713677 -21 ********** Masking position 3 Map Score: 0.993989 Number of sites scoring better than the average of aligned sites = 1522 Number in coding regions = 1392 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 10 ********** No masking Map Score: 1.87173e-13 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 11 ********** No masking Map Score: 1.87173e-13 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 12 ********** No masking Map Score: 1.87173e-13 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