AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -ioxyR_hpyl_opreg_300.orf -g0.389 -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 = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP0243 205 neutrophil activating protein (napA) (bacterioferritin) #2 HP0246 188 flagellar basal-body P-ring protein (flgI) Motif number 1 TTTAATATTATTTAATCTTTTTAAAATTTTG 1 53 0 TTTAACTTTT 0.961148 -153 AATAAGATCAAAAAAATTTTTTATTAACTCT 1 113 1 AAAAATTTTT 0.489865 -93 AAAATTTTTTATTAACTCTTTTGGTGTAGGA 1 125 1 ATTAATCTTT 0.919227 -81 AGGATAGCGATCAAGGTTTTTATGAAAATAA 1 152 1 TCAAGTTTTT 0.948273 -54 TTAAAATTGTTTTAGGCTTTTATTTTCATAA 1 171 0 TTTAGCTTTT 0.978604 -35 CAAAAGTCCTTTTTTTAAAATT 1 194 0 AAAAGCCTTT 0.730104 -12 TTAGCCTTTTATTAGCTTTTTATAAAGTTTC 2 37 0 ATTAGTTTTT 0.962165 -152 AGATTTTAATTTTAGCCTTTTATTAGCTTTT 2 48 0 TTTAGCTTTT 0.978604 -141 AAGGCTAAAATTAAAATCTTTGATTTAAAGT 2 60 1 TTAAATCTTT 0.953742 -129 TTTAAAGTTTATAAGATTTTTGAGTATAGCA 2 83 1 ATAAGTTTTT 0.842091 -106 TCAATTAGGTTTAAAGTTTTTATAAAAGGCT 2 125 1 TTAAATTTTT 0.96253 -64 TTATTTTAGCATAAGCCTTTTATAAAAACTT 2 138 0 ATAAGCTTTT 0.778789 -51 TCAAACCCTTTCTTATTCCCT 2 178 0 TCAAACCTTT 0.916193 -11 ***** ***** Masking position 4 Map Score: 23.6625 Number of sites scoring better than the average of aligned sites = 1284 Number in coding regions = 1066 Number in noncoding regions = 218 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 2 AAATTTTGTTTTATAGTAAAACTCATTTTTA 1 30 0 TTATATAAAA 0.677642 -176 TATTATTTAATCTTTTTAAAATTTTGTTTTA 1 48 0 TCTTTTAAAA 0.875129 -158 TTTGATCTTATTTTTGTCAAATATTGATAAA 1 94 0 TTTTTTCAAA 0.889284 -112 ACCAAAAGAGTTAATAAAAAATTTTTTTGAT 1 119 0 TTAATAAAAA 0.701068 -87 GCGATCAAGGTTTTTATGAAAATAAAAGCCT 1 158 1 TTTTTTGAAA 0.889284 -48 CAAAAGTCCTTTTTTTAAAATTGTTTTAGG 1 186 0 TTTTTTAAAA 0.569012 -20 ATACCTCAATTTAATTTGAAACTTTATAAAA 2 20 1 TTAATTGAAA 0.903649 -169 TTTTATTAGCTTTTTATAAAGTTTCAAATTA 2 31 0 TTTTTTAAAG 0.875129 -158 TCTTATAAACTTTAAATCAAAGATTTTAATT 2 68 0 TTTAATCAAA 0.788583 -121 AGGTTTAAAGTTTTTATAAAAGGCTTATGCT 2 131 1 TTTTTTAAAA 0.569012 -58 TATAAAAGGCTTATGCTAAAATAATTAGAAT 2 145 1 TTATGTAAAA 0.901931 -44 ***** ***** Masking position 9 Map Score: 15.4189 Number of sites scoring better than the average of aligned sites = 1160 Number in coding regions = 904 Number in noncoding regions = 256 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 3 TATTATTTAATCTTTTTAAAATTTTGTTTT 1 49 0 TCTTTTTAAA 0.670298 -157 GATCAAAAAAATTTTTTATTAACTCTTTTG 1 118 1 ATTTTTTATT 0.586632 -88 TAGCGATCAAGGTTTTTATGAAAATAAAAG 1 156 1 GGTTTTTATG 0.952565 -50 AATTGTTTTAGGCTTTTATTTTCATAAAAA 1 168 0 GGCTTTTATT 0.969999 -38 CAAAAGTCCTTTTTTTAAAATTGTTT 1 190 0 TCCTTTTTTT 0.77942 -16 CCTTTTATTAGCTTTTTATAAAGTTTCAAA 2 34 0 GCTTTTTATA 0.97782 -155 TTTAATTTTAGCCTTTTATTAGCTTTTTAT 2 45 0 GCCTTTTATT 0.987117 -144 TTAAATCAAAGATTTTAATTTTAGCCTTTT 2 58 0 GATTTTAATT 0.730785 -131 TAATTGAGCGTATTTTTATGCTATACTCAA 2 102 0 TATTTTTATG 0.809699 -87 TTTAGCATAAGCCTTTTATAAAAACTTTAA 2 135 0 GCCTTTTATA 0.979493 -54 ********** Masking position 5 Map Score: 9.04199 Number of sites scoring better than the average of aligned sites = 1097 Number in coding regions = 931 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 4 TATAGTAAAACTCATTTTTAAGGGGGATAGT 1 19 0 CTCATTTTAA 0.956603 -187 ATAAACCCCATTCAATTTAATATTATTTAAT 1 68 0 TTCAATTTAT 0.92849 -138 TTTTTTTGATCTTATTTTTGTCAAATATTGA 1 98 0 CTTATTTTGT 0.958321 -108 GTTTTAGGCTTTTATTTTCATAAAAACCTTG 1 163 0 TTTATTTTAT 0.939061 -43 CAAAAGTCCTTTTTTTAAAATTGTTTTAG 1 187 0 CTTTTTTTAA 0.730307 -19 AGATTCATACCTCAATTTAATTTGAAACTTT 2 14 1 CTCAATTTAT 0.968573 -175 AATCAAAGATTTTAATTTTAGCCTTTTATTA 2 54 0 TTTAATTTAG 0.773509 -135 CCTAATTGAGCGTATTTTTATGCTATACTCA 2 103 0 CGTATTTTAT 0.9166 -86 TAAAAATACGCTCAATTAGGTTTAAAGTTTT 2 114 1 CTCAATTAGT 0.791062 -75 ******** ** Masking position 6 Map Score: 5.80548 Number of sites scoring better than the average of aligned sites = 742 Number in coding regions = 606 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 5 ********** No masking Map Score: 7.34864e-14 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 6 ********** No masking Map Score: 7.34864e-14 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 7 ********** No masking Map Score: 7.34864e-14 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