AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i263_hypothetical_ecoli_hinf_reg_100.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 ybeB 300 orf, hypothetical protein #2 leuS 234 leucine tRNA synthetase #3 HI0033 53 conserved hypothetical protein #4 HI0034 124 conserved hypothetical protein Motif number 1 CAGCCAGACTTTTTCCGCCAGACACGA 1 4 1 CCGACTTTTG 0.985588 -297 TTTCCGCCAGACACGACTTTGTAGAAATTGTTTT 1 22 1 ACCGACTTTG 0.86059 -279 CCGCAGATTGCATCGCCATTTTTGTAAAACAATT 1 47 0 CACGCCATTG 0.908709 -254 GTAAAGCACTCCAGGATTTTGTTATCGACAAAAT 1 210 1 CCGGATTTTA 0.849195 -91 CCTTTGAGGTCATCAATTTTGTCGATAACAAAAT 1 225 0 CACAATTTTG 0.909392 -76 GCGATGATGTCCTGACCTTTGAGGTCATCAATTT 1 240 0 CCGACCTTTG 0.987488 -61 GTCAGGACATCATCGCCTTAGACGTTCAGGGCAA 1 258 1 CACGCCTTAG 0.951074 -43 TTATTTTTTACCGCACTTTACTAAAAT 3 4 0 CCCACTTTAA 0.915212 -50 TAAAAAATAACCGCACTTTTTAGATAAGGATGAC 3 28 1 CCCACTTTTA 0.977527 -26 GCGAAATTAACCGCGCTTTTTATGTCTAAATTGA 4 22 0 CCCGCTTTTG 0.995774 -103 TGATAGAATTCCGCACCTTTATTGCTAAGTGAGA 4 96 1 CCCACCTTTG 0.995765 -29 ** ******* * Masking position 9 Map Score: 14.0098 Number of sites scoring better than the average of aligned sites = 1354 Number in coding regions = 1230 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 2 ATGACCTCAAAGGTCAGGACATCATCGCCT 1 246 1 AGGTCAGGAC 0.878239 -55 TGAACGTCTAAGGCGATGATGTCCTGACCT 1 256 0 AGGCGATGAT 0.799182 -45 CGTATTAGCAAAGCAAGGAACAAAGAACGT 2 50 0 AAGCAAGGAA 0.860468 -185 CGTTGAAATGATGCCCGGATTATTCATACA 2 101 0 ATGCCCGGAT 0.890784 -134 ATTTTAGTAAAGTGCGGTAAAAAATAACC 3 10 1 AAGTGCGGTA 0.97349 -44 CTTATCTAAAAAGTGCGGTTATTTTTTACC 3 26 0 AAGTGCGGTT 0.972996 -28 TAGACATAAAAAGCGCGGTTAATTTCGCGC 4 28 1 AAGCGCGGTT 0.959511 -97 CGCAAAAAATAAGCGCGAAATTAACCGCGC 4 40 0 AAGCGCGAAA 0.957059 -85 TTAGCAATAAAGGTGCGGAATTCTATCATT 4 94 0 AGGTGCGGAA 0.985279 -31 CTTTATTGCTAAGTGAGAACAAA 4 112 1 AAGTGAGAAC 0.832298 -13 ********** Masking position 1 Map Score: 8.21622 Number of sites scoring better than the average of aligned sites = 2033 Number in coding regions = 1882 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 3 TGCAATCTGCGGCGCGGGGTGGGATGATAG 1 69 1 GGCGCGGGGT 0.940962 -232 GGCTTTCGAAAGTGGGCTATCATCCCACCC 1 85 0 AGTGGGCTAT 0.8688 -216 TTCAACGTCGAGTGCGCGAAAGGCTGTTTT 2 124 1 AGTGCGCGAA 0.969389 -111 ATTTTAGTAAAGTGCGGTAAAAAATAACCG 3 11 1 AGTGCGGTAA 0.989565 -43 TTATCTAAAAAGTGCGGTTATTTTTTACCG 3 25 0 AGTGCGGTTA 0.976336 -29 AGACATAAAAAGCGCGGTTAATTTCGCGCT 4 29 1 AGCGCGGTTA 0.975868 -96 GCAAAAAATAAGCGCGAAATTAACCGCGCT 4 39 0 AGCGCGAAAT 0.884246 -86 TAGCAATAAAGGTGCGGAATTCTATCATTG 4 93 0 GGTGCGGAAT 0.96638 -32 ********** Masking position 6 Map Score: 6.57977 Number of sites scoring better than the average of aligned sites = 1347 Number in coding regions = 1253 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 4 TTACAAAAATGGCGATGCAATCTGCGGCGC 1 54 1 GGCGATGCAA 0.993607 -247 GAACGTCTAAGGCGATGATGTCCTGACCTT 1 255 0 GGCGATGATG 0.990715 -46 GCAGTCGGTGATGCTGGATTTGCCCT 1 285 0 GGTGATGCTG 0.983743 -16 TAACGACCCGGGAGATGAAACG 2 3 0 GGAGATGAAA 0.945541 -232 CGGACGTTTGGGCTATGCTATGCGGATCTG 2 158 1 GGCTATGCTA 0.977105 -77 ********** Masking position 5 Map Score: 5.00933 Number of sites scoring better than the average of aligned sites = 645 Number in coding regions = 617 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 TGGCGGAAAAAGTCTGGCTG 1 1 0 AGTCTGGCTG 0.969021 -300 TACAAAGTCGTGTCTGGCGGAAAAAGTCTG 1 15 0 TGTCTGGCGG 0.962864 -286 CCCGAAATCGCCTCTGGTTCAGGTATACTG 1 132 1 CCTCTGGTTC 0.969008 -169 GCAAGTTTTCCCCCTGGGTGAATCAAATAG 1 177 0 CCCCTGGGTG 0.972963 -124 GAAAACAGGACCACTGGCTGCC 2 223 1 CCACTGGCTG 0.989287 -12 CATTGAATACCCTCTTGCGCAAAATCCACG 4 68 0 CCTCTTGCGC 0.954346 -57 ********** Masking position 5 Map Score: 2.05857 Number of sites scoring better than the average of aligned sites = 1849 Number in coding regions = 1758 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 6 TTCGGGACAATTGTCGCCGAATCGGCTTTC 1 108 0 TTGTCGCCGA 0.980179 -193 GTCCTGACCTTTGAGGTCATCAATTTTGTC 1 236 0 TTGAGGTCAT 0.907655 -65 TTTACAGAGTTTGTGGGCGTATTAGCAAAG 2 67 0 TTGTGGGCGT 0.982739 -168 AAAGGCTGTTTTGACGCGGACGTTTGGGCT 2 142 1 TTGACGCGGA 0.966533 -93 AAATGTAGCGTTGAGGTGGTTTTTCAGATC 2 182 0 TTGAGGTGGT 0.972527 -53 AACGCTACATTTGTAGCCGTATTGAAAACA 2 200 1 TTGTAGCCGT 0.974629 -35 ********** Masking position 2 Map Score: 2.73691 Number of sites scoring better than the average of aligned sites = 548 Number in coding regions = 514 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 7 TTGCTTTGCTAATACGCCCACAAACTCTGT 2 64 1 AATACGCCCA 0.987422 -171 ATGTATGAATAATCCGGGCATCATTTCAAC 2 100 1 AATCCGGGCA 0.984864 -135 TCCTGTTTTCAATACGGCTACAAATGTAGC 2 203 0 AATACGGCTA 0.863899 -32 TGCGGTAAAAAATAACCGCACTTTTTAGAT 3 23 1 AATAACCGCA 0.935124 -31 CCACGCAAAAAATAAGCGCGAAATTAACCG 4 43 0 AATAAGCGCG 0.948868 -82 TCTTGCGCAAAATCCACGCAAAAAATAAGC 4 56 0 AATCCACGCA 0.959776 -69 ********** Masking position 3 Map Score: 1.7113 Number of sites scoring better than the average of aligned sites = 1024 Number in coding regions = 933 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 8 ********** No masking Map Score: -2.95996e-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 9 ********** No masking Map Score: -2.95996e-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 10 ********** No masking Map Score: -2.95996e-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