AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i222_ecoli_bsub_100.orf -o222_ecoli_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 pheS 283 phenylalanine tRNA synthetase, alpha-subunit #2 rplT 52 50S ribosomal subunit protein L20, and regulator #3 rpmI 96 50S ribosomal subunit protein A #4 thrS 300 threonine tRNA synthetase #5 pheS 300 phenylalanyl-tRNA synthetase (alpha subunit) #6 rplT 31 ribosomal protein L20 #7 infC 171 initiation factor IF-3 #8 thrZ 300 threonyl-tRNA synthetase Motif number 1 AAGAGAAACGGAAAACAGCGCCTGAAAGCC 1 33 1 GAAAACAGCG 0.887564 -251 ACGCGCATACAAAAAAAGCCTCCACTGGGA 1 63 0 AAAAAAAGCC 0.969697 -221 GTTTTGAAAAATAAAAAGCCTGTCTCATCA 1 91 1 ATAAAAAGCC 0.75901 -193 TGAGAATTTCGAGCACAGCCCGGGACCAAA 1 186 1 GAGCACAGCC 0.866352 -98 AAATGGCAAGTAAAATAGCCTGATGGGATA 1 214 1 TAAAATAGCC 0.695513 -70 AAACAAAGGCGAACAAAGCCTGTGAAGCCC 3 43 0 GAACAAAGCC 0.969847 -54 TTAATAAACGAAACAAAGGCGAACAAAGCC 3 53 0 AAACAAAGGC 0.90221 -44 TGTTAACACTAAAAAAAGGGAGATTGTACC 4 112 0 AAAAAAAGGG 0.621056 -189 AGAGCATTTTTAACGCAGCCGGAAATTGGC 5 69 1 TAACGCAGCC 0.804783 -232 TTGGAAAATAAAAAAAACCCGTCCCTTGTA 5 241 0 AAAAAAACCC 0.947567 -60 CCTTTTATGTAAACAAACCGTCATATGTCT 5 271 0 AAACAAACCG 0.892099 -30 GTGGGCATTATAAAACACCCACACTACGAA 7 80 0 TAAAACACCC 0.908636 -92 TCAAATAAAAAAACACACCC 8 1 0 AAACACACCC 0.975651 -300 GTATATAAAAAAACACACCCGTCCCGCAGA 8 256 0 AAACACACCC 0.975651 -45 ********** Masking position 7 Map Score: 14.3794 Number of sites scoring better than the average of aligned sites = 1075 Number in coding regions = 856 Number in noncoding regions = 219 Number of orfs with sites within 600 bp upstream = 210 Fraction of orfs with sites within 600 bp upstream = 0.0337295 Motif number 2 GCGCTGTTTTCCGTTTCTCTTCTCACGCGCTAG 1 21 0 CCGTTCCTCT 0.951903 -263 AAATACGCTCCGGTTTCTCCGCGCTGGCCGTGT 1 146 0 CGGTTCCCCG 0.979761 -138 TCCAACGAACCAGTGTCACCACTGACACAATGA 1 253 1 CAGGTCCCCT 0.902359 -31 TTAATAACTTCCACTTCGCATTGTTAATAAACG 3 73 0 CCATTCCATG 0.679749 -24 TCACATTGATTCGATTCGCAATTCGTTTGTAGT 4 71 0 TCGTTCCATT 0.941602 -230 TTGTACCTTTCCGTTTCACATTGATTCGATTCG 4 86 0 CCGTTCCATG 0.969901 -215 GTTGGCTAGATGGTTTCGCAATGAACTGTTAAT 4 216 1 TGGTTCCATG 0.859185 -85 GATCTTTCGTGTGGGTCACCACTGCAAATAAGG 4 271 1 GTGGTCCCCT 0.737931 -30 AGCCGGAAATTGGCTTCACCTCTTGAGTTGTCG 5 85 1 TGGTTCCCCT 0.960353 -216 GAATCAGATTCCGGTTCACCTTTACGCGCAGTG 5 131 0 CCGTTCCCTT 0.980709 -170 CCGCTTCTCACCTGATTGACACA 7 1 1 CCGTTCCACT 0.991027 -171 TTTCTTCGAATTGATTCACAACTCATTTTGAAT 7 134 0 TTGTTCCACT 0.90273 -38 GGAAAGGTGAGAGCTTCCCAGCTTAGGAATATC 8 88 1 GAGTTCCACT 0.884978 -213 *** *** ** ** Masking position 6 Map Score: 12.1788 Number of sites scoring better than the average of aligned sites = 842 Number in coding regions = 789 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 3 TGGAGGCTTTTTTTGTATGCGCGTTTTGAAAAA 1 69 1 TTTTGTTGCG 0.97675 -215 AATGTCTTTCATTTGTGTACCTGATTGCGAACC 4 171 1 ATTTGTTACG 0.866652 -130 CCAATTTAGCATTTGTTGGCTAGATGGTTTCGC 4 202 1 ATTTGTGGCG 0.990781 -99 TCACCTCTTGAGTTGTCGCCGGGACCGCGTACA 5 100 1 AGTTGTGCCG 0.986289 -201 ACAAGGGACGAGTTGTGGCCGCGGTACCACCCT 5 209 0 AGTTGTGCCG 0.986289 -92 GACACATGCATGTAGTTGGCAGGTTGACCGTAC 7 28 1 TGTAGTGGCG 0.968304 -144 TGCCCACACTTTTTGTTTGCCTGCAAAATGCAT 7 103 1 TTTTGTTGCG 0.97675 -69 ACAAATACTATGTTGTCGGCTCGGTGCTGTAAC 8 178 0 TGTTGTGGCG 0.994168 -123 ****** *** * Masking position 6 Map Score: 9.34237 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 120 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 4 GAAAACAGCGCCTGAAAGCCTCCCAGTGGAGGCTTTT 1 43 1 CCTGTCCCGT 0.974835 -241 GGTTTTCCTCATTGTGTCAGTGGTGACACTGGT 1 261 0 CCTGTCAGGG 0.986141 -23 GGCCTTCAAGTAGCACTGTCTGTGGAGCC 3 3 1 CCTGGCACGT 0.997306 -94 GTCTGTGGAGCCTTCGGGCTTCACAGGCTTTGTTCGC 3 28 1 CCTGTCACGG 0.996506 -69 AACCTTTCAGACGCACCGTGATGTTATCA 4 3 1 CCTGGCACGT 0.995688 -298 GGAGATTGTACCTTTCCGTTTCACATTGATTCGATTC 4 87 0 CCTGTCACTT 0.96302 -214 TCATTTACCGCCTTGGAGCAGCATTGGGGAACTGAAG 8 119 1 CCTGGCATGG 0.984478 -182 CACACTCGTCCCTATCTGCGGGACGGGTGTGTTTTTT 8 242 1 CCTGGGACGG 0.989328 -59 *** * **** ** Masking position 3 Map Score: 11.4769 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 92 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 TTTTGTATGCGCGTTTTGAAAAATAAAAAG 1 79 1 GCGTTTTGAA 0.975925 -205 AGAAACCGGAGCGTATTTAAGTACGTGAGA 1 161 1 GCGTATTTAA 0.840379 -123 GCCGTTAACGTTTTTAACTTTTTAATT 2 8 1 ACGTTTTTAA 0.880495 -45 CTTCCACTTCGCATTGTTAATAAACGAAAC 3 69 0 GCATTGTTAA 0.909818 -28 TGTTCTTTAAGCGTTTTGCTGGTGTACTCA 4 42 1 GCGTTTTGCT 0.828922 -259 ACCCGGTTGAGCGATGTTAACACTAAAAAA 4 126 0 GCGATGTTAA 0.693608 -175 CTGACTGAGAGCATTTTTAACGCAGCCGGA 5 62 1 GCATTTTTAA 0.959122 -239 GGTTGACCGTACATTTTTATTGATACAGAT 7 49 1 ACATTTTTAT 0.562231 -123 CATTTTGAATGCATTTTGCAGGCAAACAAA 7 114 0 GCATTTTGCA 0.916179 -58 GATTCACAACTCATTTTGAATGCATTTTGC 7 125 0 TCATTTTGAA 0.739491 -47 ********** Masking position 7 Map Score: 4.87497 Number of sites scoring better than the average of aligned sites = 833 Number in coding regions = 730 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 6 CTGAAAGCCTCCCAGTGGAGGCTTTTTTTG 1 54 1 CCCAGTGGAG 0.971749 -230 TCCTCATTGTGTCAGTGGTGACACTGGTTC 1 259 0 GTCAGTGGTG 0.964254 -25 AAGTAGCACTGTCTGTGGAGCCTTCGGGCT 3 18 1 GTCTGTGGAG 0.96229 -79 GGCGAACAAAGCCTGTGAAGCCCGAAGGCT 3 36 0 GCCTGTGAAG 0.917382 -61 TCACCTTCCACCCGGTTGAGCGATGTTAAC 4 135 0 CCCGGTTGAG 0.737076 -166 ATTCCGTTATGTCAATGAAGCTGACGACAG 5 160 1 GTCAATGAAG 0.786335 -141 ACTTCAGTTCCCCAATGCTGCTCCAAGGCG 8 127 0 CCCAATGCTG 0.874939 -174 AACCAATGCCGTCTATGCTGCGTTACAGCA 8 157 1 GTCTATGCTG 0.837912 -144 ATGTTGTCGGCTCGGTGCTGTAACGCAGCA 8 172 0 CTCGGTGCTG 0.932186 -129 ********** Masking position 6 Map Score: 4.13168 Number of sites scoring better than the average of aligned sites = 1615 Number in coding regions = 1529 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 7 ATCCAGGAGGCTAGCGCGTGAGAAGAGA 1 6 1 GGGCAGCGCG 0.99606 -278 CCAGACTGGACACGGCCAGCGCGGAGAAACCGG 1 137 1 CAGCAGCGCG 0.969686 -147 CTTGAGTTGTCGCCGGGACCGCGTACACTGCGC 5 106 1 CGGGACCGCG 0.953804 -195 TCTGAAATAAGGGTGGTACCGCGGCCACAACTC 5 200 1 GGGGACCGCG 0.998097 -101 TCGGGAACTTGGGTGGAACCACGGGTTAATCAC 8 210 1 GGGGACCACG 0.990479 -91 ** ** ****** Masking position 8 Map Score: 3.10195 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 92 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 CAGTGGAGGCTTTTTTTGTATGCGCGTTTT 1 66 1 TTTTTTTGTA 0.843683 -218 TCGCCTTTGTTTCGTTTATTAACAATGCGA 3 61 1 TTCGTTTATT 0.895407 -36 CGATTCGCAATTCGTTTGTAGTGAGTACAC 4 63 0 TTCGTTTGTA 0.772547 -238 ACAATCTCCCTTTTTTTAGTGTTAACATCG 4 115 1 TTTTTTTAGT 0.783231 -186 CAAAGAAAAATTTGTTTATTAACAGTTCAT 4 236 0 TTTGTTTATT 0.945986 -65 AGGGACGGGTTTTTTTTATTTTCCAAAGAC 5 245 1 TTTTTTTATT 0.931524 -56 CATATGACGGTTTGTTTACATAAAAGGAGG 5 274 1 TTTGTTTACA 0.790608 -27 GGGTGTGTTTTTTTATTTGAATTGAAT 8 8 1 TTTTTTTATT 0.931524 -293 GACGGGTGTGTTTTTTTATATACAACAATG 8 263 1 TTTTTTTATA 0.916955 -38 ********** Masking position 5 Map Score: 6.1769 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 87 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 9 AGACATTAACCTCTCACCTTCCACCCGGTT 4 148 0 CTCTCACCTT 0.911814 -153 GCGGCCACAACTCGTCCCTTGTACAAGGGA 5 220 1 CTCGTCCCTT 0.991477 -81 ATAAAAAAAACCCGTCCCTTGTACAAGGGA 5 234 0 CCCGTCCCTT 0.992932 -67 CTCTCACCTTTCCTTCCCTCTCTGAAAACC 8 71 0 TCCTTCCCTC 0.879728 -230 AGCTGGGAAGCTCTCACCTTTCCTTCCCTC 8 81 0 CTCTCACCTT 0.911814 -220 TAATCACACACTCGTCCCTATCTGCGGGAC 8 236 1 CTCGTCCCTA 0.972497 -65 AAAAAACACACCCGTCCCGCAGATAGGGAC 8 249 0 CCCGTCCCGC 0.972852 -52 ********** Masking position 7 Map Score: 4.80137 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 127 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 10 CGTGTCCAGTCTGGCTGCGACAATTACACC 1 121 0 CTGGCTGCGA 0.973319 -163 ATTTGTGTACCTGATTGCGAACCAATTTAG 4 181 1 CTGATTGCGA 0.954575 -120 GAAAATGCCGCTGACTGAGAGCATTTTTAA 5 52 1 CTGACTGAGA 0.986845 -249 CAGCATCAGTCTGTCTGAAATAAGGGTGGT 5 187 1 CTGTCTGAAA 0.958738 -114 CGCTTCTCACCTGATTGACACATGCATGTA 7 12 1 CTGATTGACA 0.904359 -160 CTTTCCTTCCCTCTCTGAAAACCGTAACTA 8 64 0 CTCTCTGAAA 0.841961 -237 ********** Masking position 6 Map Score: 1.23016 Number of sites scoring better than the average of aligned sites = 422 Number in coding regions = 383 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 11 ********** No masking Map Score: 8.47978e-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: 8.47978e-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 13 ********** No masking Map Score: 8.47978e-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