AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00930_hpyl_reg_300.orf -o00930_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 HP0243 205 neutrophil activating protein (napA) (bacterioferritin) #2 HP0246 188 flagellar basal-body P-ring protein (flgI) Motif number 1 TAATATTATTTAATCTTTTTAAAATTTTGTT 1 51 0 TAATCTTTTA 0.963474 -155 TAAGATCAAAAAAATTTTTTATTAACTCTTT 1 115 1 AAAATTTTTA 0.826861 -91 GGATAGCGATCAAGGTTTTTATGAAAATAAA 1 153 1 CAAGGTTTTA 0.987032 -53 TAAAATTGTTTTAGGCTTTTATTTTCATAAA 1 170 0 TTAGGTTTTA 0.984363 -36 TAGCCTTTTATTAGCTTTTTATAAAGTTTCA 2 36 0 TTAGCTTTTA 0.977088 -153 GATTTTAATTTTAGCCTTTTATTAGCTTTTT 2 47 0 TTAGCTTTTA 0.977088 -142 AACTTTAAATCAAAGATTTTAATTTTAGCCT 2 61 0 CAAAGTTTTA 0.968788 -128 ATCTTTGATTTAAAGTTTATAAGATTTTTGA 2 75 1 TAAAGTTATA 0.896374 -114 CAATTAGGTTTAAAGTTTTTATAAAAGGCTT 2 126 1 TAAAGTTTTA 0.935272 -63 TATTTTAGCATAAGCCTTTTATAAAAACTTT 2 137 0 TAAGCTTTTA 0.990288 -52 CCCTAAATTCTAATTATTTTAGCATAAGCCT 2 151 0 TAATTTTTTA 0.901461 -38 AGGGAATAAGAAAGGGTTTGA 2 178 1 AAAGGTTTGA 0.894415 -11 ***** ***** Masking position 3 Map Score: 21.7297 Number of sites scoring better than the average of aligned sites = 968 Number in coding regions = 801 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 2 ATAGTAAAACTCATTTTTAAGGGGGATAGTT 1 18 0 TCATTTTAAG 0.780604 -188 AAAATGAGTTTTACTATAAAACAAAATTTTA 1 32 1 TTACTATAAA 0.851253 -174 TATTATTTAATCTTTTTAAAATTTTGTTTTA 1 48 0 TCTTTTTAAA 0.952765 -158 TTTGATCTTATTTTTGTCAAATATTGATAAA 1 94 0 TTTTTGTAAA 0.960503 -112 TAATAAAAAATTTTTTTGATCTTATTTTTGT 1 108 0 TTTTTTTATC 0.769799 -98 TCAAAAAAATTTTTTATTAACTCTTTTGGTG 1 120 1 TTTTTATAAC 0.970496 -86 GCGATCAAGGTTTTTATGAAAATAAAAGCCT 1 158 1 TTTTTATAAA 0.950344 -48 CAAAAGTCCTTTTTTTAAAATTGTTTTAGG 1 186 0 TTTTTTTAAA 0.829198 -20 ATACCTCAATTTAATTTGAAACTTTATAAAA 2 20 1 TTAATTTAAA 0.854533 -169 TTTTATTAGCTTTTTATAAAGTTTCAAATTA 2 31 0 TTTTTATAAG 0.966937 -158 TCTTATAAACTTTAAATCAAAGATTTTAATT 2 68 0 TTTAAATAAA 0.585779 -121 AGGTTTAAAGTTTTTATAAAAGGCTTATGCT 2 131 1 TTTTTATAAA 0.848867 -58 ******* *** Masking position 9 Map Score: 15.9893 Number of sites scoring better than the average of aligned sites = 1554 Number in coding regions = 1237 Number in noncoding regions = 317 Number of orfs with sites within 600 bp upstream = 218 Fraction of orfs with sites within 600 bp upstream = 0.0350145 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 CCCCCTTAAAAATGAGTTTTACTATAAAAC 1 24 1 AATGAGTTTT 0.967577 -182 TCTTTTTAAAATTTTGTTTTATAGTAAAAC 1 39 0 ATTTTGTTTT 0.801054 -167 TATTAAATTGAATGGGGTTTATCAATATTT 1 77 1 AATGGGGTTT 0.975485 -129 TAGGATAGCGATCAAGGTTTTTATGAAAAT 1 151 1 ATCAAGGTTT 0.890463 -55 TTCAAATTAAATTGAGGTATGAATCTCCC 2 10 0 ATTGAGGTAT 0.956126 -179 AAATACGCTCAATTAGGTTTAAAGTTTTTA 2 117 1 AATTAGGTTT 0.975126 -72 ********** Masking position 8 Map Score: 2.87393 Number of sites scoring better than the average of aligned sites = 325 Number in coding regions = 266 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 5 ATAGTAAAACTCATTTTTAAGGGGGATAGT 1 19 0 TCATTTTTAA 0.921127 -187 TATTATTTAATCTTTTTAAAATTTTGTTTT 1 49 0 TCTTTTTAAA 0.921127 -157 TAAACCCCATTCAATTTAATATTATTTAAT 1 68 0 TCAATTTAAT 0.97594 -138 AAAGCCTAAAACAATTTTAAAAAAAGGACT 1 182 1 ACAATTTTAA 0.842794 -24 GATTCATACCTCAATTTAATTTGAAACTTT 2 15 1 TCAATTTAAT 0.97594 -174 TTCCCTAAATTCTAATTATTTTAGCATAAG 2 154 0 TCTAATTATT 0.568841 -35 ********** Masking position 6 Map Score: 1.73053 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 155 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 6 TAAAAATGAGTTTTACTATAAAACAAAATT 1 30 1 TTTTACTATA 0.905605 -176 TTATTAACTCTTTTGGTGTAGGATAGCGAT 1 133 1 TTTTGGTGTA 0.942913 -73 AAGATTTTAATTTTAGCCTTTTATTAGCTT 2 50 0 TTTTAGCCTT 0.90496 -139 TTATAAGATTTTTGAGTATAGCATAAAAAT 2 91 1 TTTGAGTATA 0.971959 -98 TTTAAACCTAATTGAGCGTATTTTTATGCT 2 110 0 ATTGAGCGTA 0.935596 -79 ATTCTAATTATTTTAGCATAAGCCTTTTAT 2 146 0 TTTTAGCATA 0.985013 -43 ********** Masking position 3 Map Score: 1.70324 Number of sites scoring better than the average of aligned sites = 428 Number in coding regions = 347 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 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 Motif number 8 ********** 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 9 ********** 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