AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00680_hinf_reg_100.orf -o00680_hinf_100.ace -a/home/amcguire/genomes/ORF_hinf.txt -z/home/amcguire/genomes/hinf.fna -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HI0185 122 alcohol dehydrogenase, class III (adhC) #2 HI0889 123 serine hydroxymethyltransferase (serine methylase) (glyA) #3 HI0928 265 catalase (hktE) #4 HI1444 300 5,10 methylenetetrahydrofolate reductase (metF) Motif number 1 TTTATTCCCTTTAAACAAAAATGATAAAAA 1 13 1 TTAAACAAAA 0.939029 -110 TTTTCATCACTTAAATGAAATTAATTCATC 2 24 0 TTAAATGAAA 0.939011 -100 GGATAAAAATTTAATTAAAATTTCATTCCT 2 57 0 TTAATTAAAA 0.933879 -67 AAAACTATACTAAAATAAAACTTAAAATCT 3 142 0 TAAAATAAAA 0.933872 -124 ATCTATTAAATTAATCAAAAAAAACTATAC 3 162 0 TTAATCAAAA 0.877003 -104 TAAATGCGTGTTAAATAAATACAATAGATT 4 31 0 TTAAATAAAT 0.861713 -270 GCATTTATCTTTCTATAAAAATACACAAAA 4 54 1 TTCTATAAAA 0.815106 -247 TACCCCATTTTACAACGAAAAAGAAAGTGC 4 91 0 TACAACGAAA 0.832583 -210 ATAATTATTGTTCAATAATAACTAATTTTT 4 167 0 TTCAATAATA 0.817673 -134 TTATTAATAATTCAATAAATGGATAATTAT 4 189 0 TTCAATAAAT 0.895933 -112 TTTCAATTTATTCATTAAAAGTATGATTAT 4 218 0 TTCATTAAAA 0.95125 -83 TTTTAATGAATAAATTGAAATTGACTCATA 4 228 1 TAAATTGAAA 0.767492 -73 ATAGTATTTGTACAATAAAATAGGTTTTAA 4 258 0 TACAATAAAA 0.951243 -43 ********** Masking position 8 Map Score: 16.2791 Number of sites scoring better than the average of aligned sites = 849 Number in coding regions = 615 Number in noncoding regions = 234 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 2 TAAAATTTCATTCCTAAATTTTCATCACTTAA 2 40 0 TTCCAATTTT 0.935293 -84 AATGAAATTTTAATTAAATTTTTATCCATAAA 2 60 1 TAATAATTTT 0.716896 -64 TCAAGTATAATACCAACATTTTTAATCACATT 3 23 0 TACCACTTTT 0.955403 -243 CCTGATTTTCAACCGCATTTTTCGCCTTTATC 3 67 0 AACCCATTTT 0.939975 -199 ACTTAAAATCTACCTAAATATTCAAAATTACT 3 121 0 TACCAATATT 0.935293 -145 CATTTCAACCTAACTAAATTTATTAACTTTAC 3 232 1 TAACAATTTA 0.901559 -34 CACAAAAAATTACCGCACTTTCTTTTTCGTTG 4 77 1 TACCCATTTC 0.967277 -224 AGCAATGATTTACCCCATTTTACAACGAAAAA 4 99 0 TACCCATTTA 0.972352 -202 TACTCAAAACTACCGCACTTTTGTTAGCAATG 4 124 0 TACCCATTTT 0.991095 -177 TGTTCAATAATAACTAATTTTTAGATCAACAC 4 157 0 TAACAATTTT 0.966648 -144 **** ** **** Masking position 9 Map Score: 10.9713 Number of sites scoring better than the average of aligned sites = 737 Number in coding regions = 496 Number in noncoding regions = 241 Number of orfs with sites within 600 bp upstream = 183 Fraction of orfs with sites within 600 bp upstream = 0.0293929 Motif number 3 TTTTTCCTCTTAATTCATTGACAAAGTTGC 1 101 0 TAATTCATTG 0.917364 -22 TAAATGAAATTAATTCATCATAATGATATG 2 13 0 TAATTCATCA 0.943882 -111 TTAATCACATTAGATCAACGATT 3 4 0 TAGATCAACG 0.850736 -262 TTTTTTTGATTAATTTAATAGATTTCGATT 3 169 1 TAATTTAATA 0.798091 -97 TCTATTGTATTTATTTAACACGCATTTATC 4 33 1 TTATTTAACA 0.660274 -268 TAAAATGGGGTAAATCATTGCTAACAAAAG 4 109 1 TAAATCATTG 0.834614 -192 AACTAATTTTTAGATCAACACATACTCAAA 4 148 0 TAGATCAACA 0.88895 -153 TGGATAATTATTGTTCAATAATAACTAATT 4 170 0 TTGTTCAATA 0.88079 -131 TTATTATTAATAATTCAATAAATGGATAAT 4 192 0 TAATTCAATA 0.957747 -109 CAATTTCAATTTATTCATTAAAAGTATGAT 4 221 0 TTATTCATTA 0.875892 -80 ********** Masking position 5 Map Score: 7.09631 Number of sites scoring better than the average of aligned sites = 724 Number in coding regions = 631 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 4 AACAAAAATGATAAAAAAACACTTGCTTTAG 1 26 1 ATAAAAAACA 0.657075 -97 TTTAGAGTTCACTCTAAAGCAAGTGTTTTTT 1 39 0 ACTCTAAACA 0.939036 -84 TTTAGAGTGAACTCTAAAGTGTAAACTGTTG 1 52 1 ACTCTAAATG 0.881947 -71 CTACCTAAATATTCAAAATTACTTACTTGAT 3 113 0 ATTCAAAATA 0.938603 -153 AAAAAAAACTATACTAAAATAAAACTTAAAA 3 145 0 ATACTAAATA 0.912603 -121 ATAAAAATACACAAAAAATTACCGCACTTTC 4 68 1 ACAAAAAATA 0.912603 -233 ATCAACACATACTCAAAACTACCGCACTTTT 4 134 0 ACTCAAAATA 0.972843 -167 TATGTGTTGATCTAAAAATTAGTTATTATTG 4 154 1 TCTAAAAATA 0.68265 -147 TAGTATTTGTACAATAAAATAGGTTTTAATA 4 256 0 ACAATAAATA 0.912603 -45 TTCCTTTAGGATTCTAAAATAGTATTTGTAC 4 275 0 ATTCTAAATA 0.938603 -26 ******** ** Masking position 6 Map Score: 8.17013 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 188 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 5 CATTTTTGTTTAAAGGGAATAAAAA 1 3 0 TAAAGGAAAA 0.95883 -120 TGTCAATGAATTAAGAGGAAAAACA 1 108 1 TTAAGGAAAA 0.980497 -15 TTAATTTCATTTAAGTGATGAAAATTTAGGAAT 2 30 1 TTAAGGTAAA 0.95885 -94 GTGATGAAAATTTAGGAATGAAATTTTAATTAA 2 44 1 TTTAGATAAA 0.736068 -80 AGTTTAACTGTTTATGGATAAAAATTTAATTAA 2 69 0 TTTATGTAAA 0.866385 -55 TGTTATGTAATTTATGGCAGATAGTTTAACTGT 2 91 0 TTTATGAATA 0.627306 -33 ATCGTTGATCTAATGTGATTAAAAATGTTGGTA 3 12 1 TAATGGTAAA 0.534452 -254 CTTGAATCCGTAAAAGGGATAAAGGCGAAAAAT 3 50 1 TAAAAGAAAA 0.820787 -216 ATCTATTAAATTAATCAAAAAAAACTATACTAA 3 159 0 TTAATAAAAA 0.717625 -107 AGACTCCTTGTAAAGTTAATAAATTTAGTTAGG 3 240 0 TAAAGTAAAA 0.647289 -26 AGATTTGTTTTTTAGCGCAAAAAAT 4 3 0 TTTAGGAAAA 0.976474 -298 TAATCATACTTTTAATGAATAAATTGAAATTGA 4 219 1 TTTAAGAAAA 0.799838 -82 TAAAACCTATTTTATTGTACAAATACTATTTTA 4 259 1 TTTATGAAAA 0.934105 -42 ***** * * *** Masking position 11 Map Score: 12.0818 Number of sites scoring better than the average of aligned sites = 651 Number in coding regions = 502 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 6 TACTTGATATATCTTTATAAAGCCTGATTTT 3 90 0 ATCTTATAAA 0.908003 -176 AAAACTTAAAATCTACCTAAATATTCAAAAT 3 125 0 ATCTACTAAA 0.972934 -141 GATTGTTTAAACCTTTCTATATGATACGCAA 3 195 1 ACCTTCTATA 0.974877 -71 ATTCATTTCAACCTAACTAAATTTATTAACT 3 229 1 ACCTACTAAA 0.974877 -37 ACACGCATTTATCTTTCTATAAAAATACACA 4 50 1 ATCTTCTATA 0.972934 -251 ***** ***** Masking position 4 Map Score: 1.99945 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 19 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 AAGGCGAAAAATGCGGTTGAAAATCAGGCT 3 71 1 ATGCGGTTGA 0.951102 -195 ATTTTTTGCGCTAAAAAACAAATCT 4 6 1 TTGCGCTAAA 0.905135 -295 GAAAAAGAAAGTGCGGTAATTTTTTGTGTA 4 75 0 GTGCGGTAAT 0.984614 -226 TCGTTGTAAAATGGGGTAAATCATTGCTAA 4 103 1 ATGGGGTAAA 0.943933 -198 GCTAACAAAAGTGCGGTAGTTTTGAGTATG 4 128 1 GTGCGGTAGT 0.985731 -173 ********** Masking position 7 Map Score: 0.31718 Number of sites scoring better than the average of aligned sites = 835 Number in coding regions = 582 Number in noncoding regions = 253 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 8 ********** No masking Map Score: -3.03101e-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: -3.03101e-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: -3.03101e-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