AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i211_transcription_translation_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 ykgM 300 putative ribosomal protein #2 trxA 76 thioredoxin 1 #3 rhoL 140 rho operon leader peptide #4 rho 84 transcription termination factor Rho; polarity suppressor #5 rpmE 202 50S ribosomal subunit protein L31 #6 HI0295 246 transcription termination factor (rho) #7 HI0758 176 ribosomal protein L31 (rpL31) Motif number 1 GAGGAATACACGCTGTCAGGTAATCAATCA 1 32 1 CGCTGTCAGG 0.811721 -269 TGCCAGAGTTCCCCGTTGCGAAAATTCCAC 1 191 1 CCCCGTTGCG 0.924719 -110 AACACTCAATCCCTGTGACTCTTTGTGGAT 1 221 0 CCCTGTGACT 0.914303 -80 TGTTCGGGTGCCCCGTCGCTAAAAACTGGA 3 21 1 CCCCGTCGCT 0.967508 -120 ACTGGACGCCCGGCGTGAGTCATGCTAACT 3 45 1 CGGCGTGAGT 0.984118 -96 AGTGGTGTGAGTTCTTAAACTT 4 73 0 TGGTGTGAGT 0.791769 -12 ACTTTTAACATCGCGTGGTGTCTGGCGTTA 5 143 1 TCGCGTGGTG 0.78044 -60 GCGTGGTGTCTGGCGTTAGGGCTGGAAGAG 5 155 1 TGGCGTTAGG 0.766546 -48 CGGTTTAAGGCCGCGTCGCTCTTCCAGCCC 5 173 0 CCGCGTCGCT 0.980811 -30 TCTCCCCACACCGCGTGAGTGAATAATACG 7 117 0 CCGCGTGAGT 0.98665 -60 GTTCCTATAGCGGCGTGGCTTCATTTTGAG 7 149 1 CGGCGTGGCT 0.988101 -28 ********** Masking position 6 Map Score: 9.89281 Number of sites scoring better than the average of aligned sites = 3204 Number in coding regions = 3089 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 2 ATCGGCCAGTAAAGTGGAGATAACCTCCATT 1 76 1 AAAGTGGAGT 0.959707 -225 GGATTTTTCGAGAATGGAGGTTATCTCCACT 1 88 0 AGAATGGAGT 0.943837 -213 GGTTTTGCTGAGAGTATGGATTTTTCGAGAA 1 105 0 AGAGTATGGT 0.900553 -196 TTGCCGTAGAAGAGTGCGGATCAGTTTGCAT 5 52 1 AGAGTGCGGT 0.984408 -151 CGCGATGTTAAAAGTATAGCTTCAATACGAT 5 127 0 AAAGTATAGT 0.808849 -76 ATTTTTAATTAGAATACGGACAATTTGTAAG 6 38 0 AGAATACGGC 0.766726 -209 AAAGCTAGACAGCGTAGGGTTTTAGTGGTAA 6 152 1 AGCGTAGGGT 0.834625 -95 AAAAAGAAAAGTGCGGTTAAAAATGCTG 7 8 1 AAAGTGCGGT 0.979187 -169 AGTGCGGTTAAAAATGCTGATGATTTTACAC 7 20 1 AAAATGCTGT 0.792821 -157 ATTTTACACGAAAATAGAGCTTGTTTATCTG 7 42 1 AAAATAGAGT 0.868145 -135 TTATACTGAAAAAATGCAGATAAACAAGCTC 7 58 0 AAAATGCAGT 0.939436 -119 ********* * Masking position 1 Map Score: 8.0857 Number of sites scoring better than the average of aligned sites = 453 Number in coding regions = 407 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 3 TTATATCCGTGGGAGAGGAATACACGCTGTCAGGT 1 18 1 GGGAGGAACC 0.808027 -283 CCACTTTACTGGCCGATAATTTATCGCAGTATGAT 1 58 0 GGGATAATAC 0.942077 -243 GATGAGTGATTGATGATGGTTTTGCTGAGAGTATG 1 118 0 TGGATGGTTC 0.784005 -183 CGTCACCAATGGCTGCTAACAATGCCAGAGTTCCC 1 169 1 GGGCTAAATC 0.922119 -132 GACTCTTTGTGGATGTGGAATTTTCGCAACGGGGA 1 200 0 GGGTGGATTC 0.85978 -101 GAAATGATCCGGATGAGCATGTATCTTTATGGTTA 1 251 1 GGGAGCATAC 0.889321 -50 CGTAGAAGAGTGCGGATCAGTTTGCATACGCTGGT 5 56 1 TGGATCATTC 0.923245 -147 CTTAAGTGCTTATTGATAACCTTACAAATTGTCCG 6 18 1 TAGATAATTC 0.756896 -229 TAACAATCTAGACGGCTAAACTTCCAAAATAAGTT 6 77 1 GAGCTAATTC 0.763696 -170 CGGTTAAAAATGCTGATGATTTTACACGAAAATAG 7 24 1 TGGATGATTC 0.958355 -153 ACTGAAAAAATGCAGATAAACAAGCTCTATTTTCG 7 50 0 TGGATAAAAC 0.801988 -127 GCACCAAATAGGTTGCGAATTATACTGAAAAAATG 7 73 0 GGGCGAAATC 0.923459 -104 TCACGCGGTGTGGGGAGAAAGTTCCTATAGCGGCG 7 129 1 TGGAGAATTC 0.96165 -48 ** ***** ** * Masking position 15 Map Score: 5.76792 Number of sites scoring better than the average of aligned sites = 1358 Number in coding regions = 1249 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 4 TAATTTATCGCAGTATGATTGATTACCTGA 1 47 0 CAGTATGATT 0.882729 -254 CCATAAACGCCTGGATGAGTGATTGATGAT 1 136 0 CTGGATGAGT 0.98417 -165 TTGAAATGATCCGGATGAGCATGTATCTTT 1 249 1 CCGGATGAGC 0.977797 -52 GTAAACAGGCATGGATGATCCTGCCATACC 4 13 1 ATGGATGATC 0.913048 -72 AATTTCAAGTCAGGATGATGCT 5 3 0 CAGGATGATG 0.941796 -200 TGGTTAATTTCTGTATGATTTCGCGCCTTC 5 87 1 CTGTATGATT 0.933531 -116 GGCGTTAGGGCTGGAAGAGCGACGCGGCCT 5 166 1 CTGGAAGAGC 0.953042 -37 ********** Masking position 5 Map Score: 4.54575 Number of sites scoring better than the average of aligned sites = 599 Number in coding regions = 542 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 5 AATGGAGGTTATCTCCACTTTACTGGCCGA 1 77 0 ATCTCCACTT 0.911084 -224 ATGCAAACTGATCCGCACTCTTCTACGGCA 5 53 0 ATCCGCACTC 0.962082 -150 AAGGTTATCAATAAGCACTTAAGGGAAATT 6 11 0 ATAAGCACTT 0.921658 -236 TCTAGCTTTTATTAGCATTTAATATAAAAA 6 131 0 ATTAGCATTT 0.851114 -116 CAGCATTTTTAACCGCACTTTTCTTTTT 7 9 0 AACCGCACTT 0.944077 -168 GTGTAAAATCATCAGCATTTTTAACCGCAC 7 21 0 ATCAGCATTT 0.973539 -156 GAGCTTGTTTATCTGCATTTTTTCAGTATA 7 58 1 ATCTGCATTT 0.959555 -119 ********** Masking position 7 Map Score: 3.90478 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 269 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 6 ACTTTACTGGCCGATAATTTATCGCAGTAT 1 61 0 CCGATAATTT 0.965467 -240 CATGCTCATCCGGATCATTTCAACACTCAA 1 242 0 CGGATCATTT 0.984373 -59 TAGAAGAGTGCGGATCAGTTTGCATACGCT 5 58 1 CGGATCAGTT 0.950939 -145 TAGCTTCAATACGATCATTTCGTACGAAGG 5 112 0 ACGATCATTT 0.906935 -91 AATTAGAATACGGACAATTTGTAAGGTTAT 6 33 0 CGGACAATTT 0.895862 -214 TAAAAAAAGTGCGATGATTTTTATATTAAA 6 114 1 GCGATGATTT 0.90839 -133 GTTAAAAATGCTGATGATTTTACACGAAAA 7 26 1 CTGATGATTT 0.915859 -151 ********** Masking position 4 Map Score: 3.5464 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 204 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 CGGATCATTTCAACACTCAATCCCTGTGACT 1 231 0 CAACACTAAT 0.955343 -70 GAAATAAAGTCAACCTTTAGTTGGTTA 2 60 1 CAACCTTAGT 0.97258 -17 AATACGAAGTCAACACTAAGTTAGCATGACT 3 62 0 CAACACTAGT 0.988372 -79 ATACCATTCACAACATTAAGTTCGAGATTTA 4 38 1 CAACATTAGT 0.987459 -47 TTATTAATTCCAACATTTATTCATT 6 232 1 CAACATTATT 0.951963 -15 ******* *** Masking position 7 Map Score: 3.36651 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 14 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 AGTAAAGTGGAGATAACCTCCATTCTCGAA 1 83 1 AGATAACCTC 0.864648 -218 ATGCTCATCCGGATCATTTCAACACTCAAT 1 241 0 GGATCATTTC 0.780327 -60 TTAAACTTGGGGTAAATCTCGAACTTAATG 4 51 0 GGTAAATCTC 0.95975 -34 TGCATACGCTGGTTAATTTCTGTATGATTT 5 78 1 GGTTAATTTC 0.898648 -125 GGGAAAACCTCGGTTTAAGGC 5 192 0 GGAAAACCTC 0.984645 -11 AATCTAGACGGCTAAACTTCCAAAATAAGT 6 81 1 GCTAAACTTC 0.845379 -166 AGAAAAACCTCAAAATGAAGC 7 166 0 GAAAAACCTC 0.908409 -11 ********** Masking position 6 Map Score: 0.669122 Number of sites scoring better than the average of aligned sites = 672 Number in coding regions = 612 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 9 ********** No masking Map Score: -3.62844e-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 10 ********** No masking Map Score: -3.62844e-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 11 ********** No masking Map Score: -3.62844e-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