AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i107_TRK_operon_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 ACTCTCACATGGGGAAACCCCACACTACCATCG 1 38 0 GGAAACCCAC 0.998704 -263 ACCTGGCGGTGCCCTACTCTCACATGGGGAAAC 1 53 0 GCTACCTCAC 0.977893 -248 ATTCCCAAAAGCTAAAACCCCATATCTTTCGAC 1 130 0 GCAAACCCAT 0.991802 -171 TATTAGCTGTGCTATAATCCCACTAAAATTCTA 1 257 1 GCTAACCCAC 0.998721 -44 AATGATTGCTGGCTAAAGCCCACCCTACGTT 2 9 0 GGAAACCCAC 0.998723 -84 AAAAACGGTGGGCTTAAGCCCACCCTACTTCCT 2 45 1 GGTAACCCAC 0.998723 -48 ** *** ***** Masking position 6 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 0.966304 -266 ATGTGAGAGTAGGGCACCGCCAGGTTACCA 1 61 1 AGGGCACCGC 0.975374 -240 TAAAAACAGAAGGACCCCGTGTCGAAAGAT 1 110 1 AGGACCCCGT 0.965887 -191 TGCTGGCTAAAGCCCACCCTACGTT 2 6 0 AGCCCACCCT 0.998524 -87 GGTGGGCTTAAGCCCACCGTTTTTTGAAAT 2 39 0 AGCCCACCGT 0.99871 -54 GGTGGGCTTAAGCCCACCCTACTTCCTATC 2 51 1 AGCCCACCCT 0.998524 -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 ATGGGGAAACCCCACACTACCATCGGCATT 1 33 0 CCCACACTAC 0.997406 -268 CTGGCTAAAGCCCACCCTACGTT 2 4 0 CCCACCCTAC 0.999346 -89 TGGGCTTAAGCCCACCGTTTTTTGAAATGA 2 37 0 CCCACCGTTT 0.982692 -56 TGGGCTTAAGCCCACCCTACTTCCTATCAA 2 53 1 CCCACCCTAC 0.999346 -40 ********** Masking position 4 Map Score: 9.40138 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 4 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 TCCTTCTGTTTTTATTTAACTTAGATAAGTATT 1 91 0 TTTATTAATA 0.955844 -210 GGGTTTTAGCTTTTGGGAATTTATTCATTATTT 1 143 1 TTTTGGAATA 0.981336 -158 TTATTCATTATTTAATCAAATAAGTGTCTAATT 1 163 1 TTTAATAATA 0.841243 -138 AATTACTTACTTATTGAAAATTAAAATTAGACA 1 187 0 TTATTGAATA 0.92843 -114 TAAGTAAGTAATTTTTCAACTCATATGAAGTCA 1 207 1 ATTTTTAATA 0.916028 -94 AAGCCCACCGTTTTTTGAAATGATTGCTGGCTA 2 27 0 TTTTTTAATA 0.944054 -66 ATGTTCTACGTTATGGTAATTGATAGGAAGTAG 2 69 0 TTATGGAATA 0.957454 -24 ****** ** * * Masking position 8 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 GTGTGGGGTTTCCCCATGTGAGAGTAGGGC 1 46 1 TCCCCATGTG 0.971868 -255 AAACAGAAGGACCCCGTGTCGAAAGATATG 1 113 1 ACCCCGTGTC 0.989805 -188 AAAAGCTAAAACCCCATATCTTTCGACACG 1 127 0 ACCCCATATC 0.993522 -174 TAGGAATGTGACTTCATATGAGTTGAAAAA 1 218 0 ACTTCATATG 0.954002 -83 AGCCCACCCTACTTCCTATCAATTACCATA 2 61 1 ACTTCCTATC 0.946584 -32 ********** Masking position 7 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 TTAACTTAGATAAGTATTTGGTAACCTGGCGG 1 77 0 TAAGTATTGT 0.951425 -224 CTTATTTGATTAAATAATGAATAAATTCCCAA 1 155 0 TAAATAAGAT 0.889413 -146 TTTAATCAAATAAGTGTCTAATTTTAATTTTC 1 173 1 TAAGTGTTAT 0.988267 -128 TAATTTTCAATAAGTAAGTAATTTTTCAACTC 1 197 1 TAAGTAATAT 0.966341 -104 CACATTCCTATAAATGTTTTATTAGCTGTGCT 1 238 1 TAAATGTTAT 0.966057 -63 CTCTTGTTTTTAAGGGTAGAATTTTAGTGGGA 1 274 0 TAAGGGTGAT 0.962312 -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