AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i232_formulase_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0622 300 polypeptide deformylase (def) #2 HI0623 92 methionyl-tRNA formyltransferase (fmt) Motif number 1 CGATGGTAGTGTGGGGTTTCCCCATGTGAGAGT 1 38 1 GTGGGTTTCC 0.998753 -263 GTTTCCCCATGTGAGAGTAGGGCACCGCCAGGT 1 53 1 GTGAGGTAGC 0.978731 -248 GTCGAAAGATATGGGGTTTTAGCTTTTGGGAAT 1 130 1 ATGGGTTTGC 0.992117 -171 TAGAATTTTAGTGGGATTATAGCACAGCTAATA 1 257 0 GTGGGTTAGC 0.99877 -44 AACGTAGGGTGGGCTTTAGCCAGCAATCATT 2 9 1 GTGGGTTTCC 0.998772 -84 AGGAAGTAGGGTGGGCTTAAGCCCACCGTTTTT 2 45 0 GTGGGTTACC 0.998772 -48 ***** *** ** Masking position 8 Map Score: 14.0112 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 15 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 2 TGCCGATGGTAGTGTGGGGTTTCCCCATGT 1 35 1 AGTGTGGGGT 0.969683 -266 TGGTAACCTGGCGGTGCCCTACTCTCACAT 1 61 0 GCGGTGCCCT 0.977357 -240 ATCTTTCGACACGGGGTCCTTCTGTTTTTA 1 110 0 ACGGGGTCCT 0.968995 -191 AACGTAGGGTGGGCTTTAGCCAGCA 2 6 1 AGGGTGGGCT 0.998624 -87 ATTTCAAAAAACGGTGGGCTTAAGCCCACC 2 39 1 ACGGTGGGCT 0.998831 -54 GATAGGAAGTAGGGTGGGCTTAAGCCCACC 2 51 0 AGGGTGGGCT 0.998624 -42 ********** Masking position 10 Map Score: 11.8116 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 20 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 3 AATGCCGATGGTAGTGTGGGGTTTCCCCAT 1 33 1 GTAGTGTGGG 0.997551 -268 AACGTAGGGTGGGCTTTAGCCAG 2 4 1 GTAGGGTGGG 0.999382 -89 TCATTTCAAAAAACGGTGGGCTTAAGCCCA 2 37 1 AAACGGTGGG 0.983641 -56 TTGATAGGAAGTAGGGTGGGCTTAAGCCCA 2 53 0 GTAGGGTGGG 0.999382 -40 ********** Masking position 7 Map Score: 9.40138 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 3 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 4 AATACTTATCTAAGTTAAATAAAAACAGAAGGA 1 91 1 TATTAATAAA 0.946712 -210 AAATAATGAATAAATTCCCAAAAGCTAAAACCC 1 143 0 TATTCCAAAA 0.976944 -158 AATTAGACACTTATTTGATTAAATAATGAATAA 1 163 0 TATTATTAAA 0.822308 -138 TGTCTAATTTTAATTTTCAATAAGTAAGTAATT 1 187 1 TATTCAATAA 0.927296 -114 TGACTTCATATGAGTTGAAAAATTACTTACTTA 1 207 0 TATTAAAAAT 0.89785 -94 TAGCCAGCAATCATTTCAAAAAACGGTGGGCTT 2 27 1 TATTAAAAAA 0.946594 -66 CTACTTCCTATCAATTACCATAACGTAGAACAT 2 69 1 TATTCCATAA 0.948017 -24 * * ** ****** Masking position 3 Map Score: 3.85239 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 160 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 5 GCCCTACTCTCACATGGGGAAACCCCACAC 1 46 0 CACATGGGGA 0.97326 -255 CATATCTTTCGACACGGGGTCCTTCTGTTT 1 113 0 GACACGGGGT 0.990318 -188 CGTGTCGAAAGATATGGGGTTTTAGCTTTT 1 127 1 GATATGGGGT 0.993849 -174 TTTTTCAACTCATATGAAGTCACATTCCTA 1 218 1 CATATGAAGT 0.956239 -83 TATGGTAATTGATAGGAAGTAGGGTGGGCT 2 61 0 GATAGGAAGT 0.949162 -32 ********** Masking position 4 Map Score: 2.65202 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 21 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 CACCGCCAGGTTACCAAATACTTATCTAAG 1 75 1 TTACCAAATA 0.8204 -226 AATGAATAAATTCCCAAAAGCTAAAACCCC 1 142 0 TTCCCAAAAG 0.976245 -159 TAATTTTAATTTTCAATAAGTAAGTAATTT 1 191 1 TTTCAATAAG 0.91332 -110 TGAAGTCACATTCCTATAAATGTTTTATTA 1 232 1 TTCCTATAAA 0.965129 -69 CCAGCAATCATTTCAAAAAACGGTGGGCTT 2 30 1 TTTCAAAAAA 0.906183 -63 CCCACCCTACTTCCTATCAATTACCATAAC 2 63 1 TTCCTATCAA 0.897979 -30 TTCCTATCAATTACCATAACGTAGAACATT 2 73 1 TTACCATAAC 0.928089 -20 ********** Masking position 6 Map Score: 2.22129 Number of sites scoring better than the average of aligned sites = 445 Number in coding regions = 360 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 7 ********** No masking Map Score: 4.92707e-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: 4.92707e-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: 4.92707e-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