AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i107_TRK_operon_hinf_reg_100.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 0.998792 -263 GTTTCCCCATGTGAGAGTAGGGCACCGCCAGGT 1 53 1 GTGAGGTAGC 0.979404 -248 GTCGAAAGATATGGGGTTTTAGCTTTTGGGAAT 1 130 1 ATGGGTTTGC 0.99237 -171 TAGAATTTTAGTGGGATTATAGCACAGCTAATA 1 257 0 GTGGGTTAGC 0.99881 -44 AACGTAGGGTGGGCTTTAGCCAGCAATCATT 2 9 1 GTGGGTTTCC 0.998812 -84 AGGAAGTAGGGTGGGCTTAAGCCCACCGTTTTT 2 45 0 GTGGGTTACC 0.998812 -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 ACATGGGGAAACCCCACACTACCATCGGCA 1 35 0 ACCCCACACT 0.9704 -266 ATGTGAGAGTAGGGCACCGCCAGGTTACCA 1 61 1 AGGGCACCGC 0.977769 -240 TAAAAACAGAAGGACCCCGTGTCGAAAGAT 1 110 1 AGGACCCCGT 0.96965 -191 TGCTGGCTAAAGCCCACCCTACGTT 2 6 0 AGCCCACCCT 0.998644 -87 GGTGGGCTTAAGCCCACCGTTTTTTGAAAT 2 39 0 AGCCCACCGT 0.998857 -54 GGTGGGCTTAAGCCCACCCTACTTCCTATC 2 51 1 AGCCCACCCT 0.998644 -42 ********** Masking position 1 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 ATGCCGATGGTAGTGTGGGGTTTCCCCATG 1 34 1 TAGTGTGGGG 0.992815 -267 AACGTAGGGTGGGCTTTAGCCAGC 2 5 1 TAGGGTGGGC 0.999321 -88 CATTTCAAAAAACGGTGGGCTTAAGCCCAC 2 38 1 AACGGTGGGC 0.995419 -55 TGATAGGAAGTAGGGTGGGCTTAAGCCCAC 2 52 0 TAGGGTGGGC 0.999321 -41 ********** Masking position 6 Map Score: 9.40138 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 4 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 4 TTTTATTTAACTTAGATAAGTATTTGGTAAC 1 84 0 CTTAATAAGT 0.849639 -217 AATGAATAAATTCCCAAAAGCTAAAACCCCA 1 141 0 TTCCAAAAGC 0.961414 -160 TCATTATTTAATCAAATAAGTGTCTAATTTT 1 167 1 ATCAATAAGT 0.907007 -134 TAATTTTAATTTTCAATAAGTAAGTAATTTT 1 191 1 TTTCATAAGT 0.979156 -110 GGAATGTGACTTCATATGAGTTGAAAAATTA 1 215 0 TTCAATGAGT 0.9353 -86 TGAAGTCACATTCCTATAAATGTTTTATTAG 1 232 1 TTCCATAAAT 0.979157 -69 CCAGCAATCATTTCAAAAAACGGTGGGCTTA 2 30 1 TTTCAAAAAC 0.791954 -63 CCCACCCTACTTCCTATCAATTACCATAACG 2 63 1 TTCCATCAAT 0.935299 -30 **** ****** Masking position 6 Map Score: 3.65601 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 268 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 5 TGCCGATGGTAGTGTGGGGTTTCCCCATGT 1 35 1 AGTGTGGGGT 0.958116 -266 GCCCTACTCTCACATGGGGAAACCCCACAC 1 46 0 CACATGGGGA 0.968835 -255 CATATCTTTCGACACGGGGTCCTTCTGTTT 1 113 0 GACACGGGGT 0.985299 -188 CGTGTCGAAAGATATGGGGTTTTAGCTTTT 1 127 1 GATATGGGGT 0.992842 -174 AATGTGACTTCATATGAGTTGAAAAATTAC 1 214 0 CATATGAGTT 0.615709 -87 AACGTAGGGTGGGCTTTAGC 2 1 1 AACGTAGGGT 0.969236 -92 TAATTGATAGGAAGTAGGGTGGGCTTAAGC 2 56 0 GAAGTAGGGT 0.947603 -37 ********** Masking position 8 Map Score: 3.37456 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 119 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 TTAACTTAGATAAGTATTTGGTAACCTGGCGG 1 77 0 TAAGTATTGT 0.943681 -224 CTTATTTGATTAAATAATGAATAAATTCCCAA 1 155 0 TAAATAAGAT 0.873101 -146 TTTAATCAAATAAGTGTCTAATTTTAATTTTC 1 173 1 TAAGTGTTAT 0.986312 -128 TAATTTTCAATAAGTAAGTAATTTTTCAACTC 1 197 1 TAAGTAATAT 0.960878 -104 CACATTCCTATAAATGTTTTATTAGCTGTGCT 1 238 1 TAAATGTTAT 0.960549 -63 CTCTTGTTTTTAAGGGTAGAATTTTAGTGGGA 1 274 0 TAAGGGTGAT 0.956223 -27 ******* * ** Masking position 3 Map Score: 1.14225 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 42 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 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