AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i341_weak2_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 ybiT 218 putative ATP-binding component of a transport system #2 ygiM 241 orf, hypothetical protein #3 cca 63 tRNA nucleotidyl transferase #4 HI1603 207 conserved hypothetical protein #5 HI1604 24 phosphate permease, putative #6 HI1605 65 conserved hypothetical protein Motif number 1 GTTAAGCGAGATTTTGTGCCTGGC 1 2 1 TTAGCGATTT 0.98739 -217 AGTGTAGACCTTAAGCGAGGAGCAGGATCTTCT 1 142 1 TTAGCGAAGC 0.887843 -77 ACTTATGGCATAATGCGCGGTTTGTCATATCTC 1 180 1 TAAGCGCTTT 0.971327 -39 CTTATGTGACATAACCGATAAGTAAAGGCC 2 8 0 ATACCGAAGT 0.811745 -234 ACGGCGAACTTAATGCGATCTTTTTTGTCAGTA 2 50 1 TAAGCGATTT 0.976233 -192 TTCTCGCTTTTAAAGCGAAAAGTGTATTGAGTT 4 29 1 TAAGCGAAGT 0.946731 -179 CGTGCGCATATTACCCGATTTTTGTTGATAGTT 4 151 0 TTACCGATTT 0.984428 -57 GCGGTTAAAATTAACCGCACTTTTTATTGAGAT 6 14 0 TTACCGCTTT 0.981183 -52 GCGGTTAATTTTAACCGCACTTTTGTTGTGATG 6 29 1 TTACCGCTTT 0.981183 -37 *** **** *** Masking position 3 Map Score: 9.36915 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 185 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 2 AGCCAAAGGCAAAAAATGTGATTTCGTACA 1 110 0 AAAAAATGTG 0.954593 -109 TCTACTGACAAAAAAGATCGCATTAAGTTC 2 55 0 AAAAAGATCG 0.953219 -187 TTGACGGGCGTAAAAGTTTGAAGCAGTGGC 2 121 1 TAAAAGTTTG 0.922877 -121 TTTAAAAGCGAGAAAATTTGAAAGGTAAAA 4 13 0 AGAAAATTTG 0.870781 -195 AAATTTTTCAAAAAAATTTGTAAGAAAAAA 4 120 0 AAAAAATTTG 0.961952 -88 TTAACTATCAACAAAAATCGGGTAATATGC 4 149 1 ACAAAAATCG 0.807839 -59 ATTAAGGGGTTAAAAATTCGTGCGCATATT 4 172 0 TAAAAATTCG 0.948204 -36 TGATCTCAATAAAAAGTGCGGTTAATTTTA 6 12 1 AAAAAGTGCG 0.981543 -54 AACATCACAACAAAAGTGCGGTTAAAATTA 6 34 0 CAAAAGTGCG 0.94229 -32 ********** Masking position 5 Map Score: 8.45163 Number of sites scoring better than the average of aligned sites = 442 Number in coding regions = 354 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 3 TTCTCAACCCAATGGCCTGCCAGGCACAAAATCTCGCTT 1 14 0 ATGCTAGCAA 0.989578 -205 ATGTCACATAAGTGACGATGAACGGCGAACTTAATGCGA 2 29 1 ATGCAAGGAA 0.989949 -213 TTTGCGCCAAATTGCCATGCAACGGGCAATTTGACGGGC 2 91 1 ATGCTAGCAA 0.989502 -151 GGGCAATTTGACGGGCGTAAAAGTTTGAAGCAGTGGCAA 2 114 1 AGGCTATGAA 0.942367 -128 TGACACAGAGGATTCCGATTGATGTCGAATGCTTTGCGT 2 157 1 GTTCAAGGAA 0.856852 -85 GGCTGTCGTTATTGTCATGGAAAGTGGAACGATAGTAGT 2 211 0 ATGCTAGGAA 0.996281 -31 TCTTCGTTGCACTGTCTTATTATTAGGAATTGTGTATTT 3 18 1 ATGCTATGAA 0.984016 -46 AATATTACCCAGTTGCTTACTTAGTCGAAGATAAACCTT 4 83 1 ATTCTTGGAA 0.916884 -125 * ** * * * * *** Masking position 18 Map Score: 5.1403 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 167 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 4 CTGGCAGGCCATTGGGTTGAGAATATTAGAGTATT 1 30 1 ATTGGGAAAA 0.963044 -189 ATATTAGAGTATTGGAAGCGCATTATAAGTTCATT 1 52 1 ATTGGCGATA 0.915097 -167 GTGAAATCAGATGTGTACGAAATCACATTTTTTGC 1 97 1 ATGTGGAATA 0.924374 -122 TTGCATGGCAATTTGGCGCAAAATACTATCTACTG 2 78 0 ATTTGCAAAA 0.951022 -164 GCAACGGGCAATTTGACGGGCGTAAAAGTTTGAAG 2 109 1 ATTTGGGGTA 0.922955 -133 AAGCGAGAAAATTTGAAAGGTAAAAAA 4 3 0 ATTTGGGAAA 0.978298 -205 TTTCAAAAAAATTTGTAAGAAAAAAGGTTTATCTT 4 110 0 ATTTGGAAAA 0.978507 -98 TAACCCCTTAATTTGGAGTAAATCACTT 4 190 1 ATTTGTAATA 0.876836 -18 ***** ** ** * Masking position 1 Map Score: 2.53644 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 98 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 TGACATAACCGATAAGTAAAGGCC 2 5 0 GATAAGTAAA 0.979377 -237 GAGAAAATTTGAAAGGTAAAAAA 4 4 0 GAAAGGTAAA 0.967091 -204 AGTGTGGTAAGATAAGTAACTCAATACACT 4 49 0 GATAAGTAAC 0.961003 -159 GATTTTTGTTGATAGTTAAAATTTTTCAAA 4 138 0 GATAGTTAAA 0.948843 -70 ********** Masking position 4 Map Score: 0.816934 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 41 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 CGTACACATCTGATTTCACTGTGAGCTGGAAT 1 84 0 TGTTTACTGT 0.877764 -135 TTTTTGCCTTTGGCTTGAGTGTAGACCTTAAG 1 125 1 TGCTTAGTGT 0.985419 -94 CCGCGCATTATGCCATAAGTCTGAAAGAAGAT 1 168 0 TGCATAGTCT 0.979623 -51 ATGCGCGGTTTGTCATATCTCTTTTCAGGATA 1 192 1 TGCATTCTCT 0.895528 -27 ACGATAGTAGTGGCATCAGTGTCGCTACGCAA 2 190 0 TGCATAGTGT 0.989782 -52 CAGGCTGTCGTTATTGTCATGGAAAGT 2 225 0 TGCGTATTGT 0.934656 -17 ** *** ***** Masking position 6 Map Score: 0.81641 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 80 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 ********** No masking Map Score: -7.29427e-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 8 ********** No masking Map Score: -7.29427e-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: -7.29427e-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