AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i226_Glycyl_TRNA_synthase_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 HI0924 300 glycyl-tRNA synthetase, beta chain (glyS) #2 HI0927 265 glycyl-tRNA synthetase, alpha chain (glyQ) Motif number 1 ATCTCCCCTACCCCTCTTTGCTAAAGAGGG 1 61 1 CCCCTCTTTG 0.998968 -240 TTCAAGAATTCCCCTCTTTAGCAAAGAGGG 1 72 0 CCCCTCTTTA 0.998404 -229 AAGATCCAATCCCCTCTTTAGCAAAGAGGG 1 204 1 CCCCTCTTTA 0.998404 -97 ATCGCCCCTACCCCTCTTTGCTAAAGAGGG 1 215 0 CCCCTCTTTG 0.998968 -86 ********** Masking position 5 Map Score: 13.5752 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 1 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 2 CGTTTGAACGTTGCTTTAGCAACGGCAC 1 4 1 TTAATTGTTA 0.930674 -297 AAGCAGATAATTTAATCTCTATTGAAATTAAAATG 1 128 0 TTAATCTTGA 0.903031 -173 TATGTTCTACTTTAACGTTTTTTGAAAGCAGATAA 1 153 0 TTAATTTTGA 0.977703 -148 CTTTGGAGAGTTAAATATTTATGTTCTACTTTAAC 1 172 0 TTAATTTTTT 0.965985 -129 AAAGAGGGGATTGGATCTTTGGAGAGTTAAATATT 1 188 0 TTGATTTGGA 0.840435 -113 TTCTGTAGATTTAAATTCTTATTTTCTCGTTATCA 1 255 0 TTAACTTTTT 0.855544 -46 GTTTCTCTTATTTAAAAATTCTGTAGATTTAAATT 1 273 0 TTAAATTTTA 0.907547 -28 TTTCGATTGTTTAAACCTTTCTATATGATACGCAA 2 61 0 TTAATTTTTA 0.986157 -205 TTAGGTAGATTTTAAGTTTTATTTTAGTATAGTTT 2 116 0 TTAATTTTTT 0.965985 -150 GTAAGTAATTTTGAATATTTAGGTAGATTTTAAGT 2 134 0 TTAATTTGTA 0.978096 -132 TCTAATGTGATTAAAAATGTTGGTATTATACTTGA 2 232 0 TTAATGTGTA 0.902754 -34 ** ** *** * ** Masking position 5 Map Score: 10.2003 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 114 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 3 TGAACGTTGCTTTAGCAACGGCACGAAGTG 1 15 1 TTTAGCAACG 0.985568 -286 AATTCCCCTCTTTAGCAAAGAGGGGTAGGG 1 66 0 TTTAGCAAAG 0.989438 -235 CAATCCCCTCTTTAGCAAAGAGGGGTAGGG 1 210 1 TTTAGCAAAG 0.989438 -91 AGTTAATAAATTTAGTTAGGTTGAAATGAA 2 27 1 TTTAGTTAGG 0.932731 -239 TTGCGTATCATATAGAAAGGTTTAAACAAT 2 61 1 TATAGAAAGG 0.88729 -205 TAAGTTTTATTTTAGTATAGTTTTTTTTGA 2 109 0 TTTAGTATAG 0.927844 -157 ********** Masking position 4 Map Score: 6.541 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 56 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 CGAAGCGAGTAAATCTCCCCTACCCCTCTTTG 1 49 1 AAATCTCCTA 0.972062 -252 TAAAGAGGGGAATTCTTGAATAAATTGATAGT 1 82 1 AATTCTGATA 0.822592 -219 TCTCGTTATCATTTCTGCCAAATCGCCCCTAC 1 234 0 ATTTCTCCAA 0.977627 -67 ATAAGAATTTAAATCTACAGAATTTTTAAATA 1 268 1 AAATCTCAAA 0.962856 -33 CAAGAAATTCATTTCAACCTAACTAAATTTAT 2 32 0 ATTTCACCAA 0.873229 -234 GTTGAAATGAATTTCTTGCGTATCATATAGAA 2 46 1 ATTTCTGCTA 0.906297 -220 TAAACAATCGAAATCTATTAAATTAATCAAAA 2 83 1 AAATCTTTAA 0.736781 -183 ATAAAACTTAAAATCTACCTAAATATTCAAAA 2 129 1 AAATCTCCAA 0.985144 -137 CTTACTTGATATATCTTTATAAAGCCTGATTT 2 164 1 ATATCTTAAA 0.85162 -102 ****** ** ** Masking position 4 Map Score: 5.70218 Number of sites scoring better than the average of aligned sites = 396 Number in coding regions = 341 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 5 TTAGCAAAGAGGGGTAGGGGAGATTTACTC 1 55 0 GGGGTAGGGG 0.998788 -246 TTAGCAAAGAGGGGTAGGGGCGATTTGGCA 1 221 1 GGGGTAGGGG 0.998788 -80 ATCCGTAAAAGGGATAAAGGCGAAAAATGC 2 202 0 GGGATAAAGG 0.97597 -64 ********** Masking position 6 Map Score: 3.32721 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 0 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 ********** No masking Map Score: -1.28365e-12 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 AATGAGCCAGTTACTATCAATTTATTCAAGAATT 1 92 0 TTATTCATTA 0.948582 -209 CATTTACATTTTAATTTCAATAGAGATTAAATTA 1 122 1 TTATTCATAA 0.972839 -179 ATTTAAATTCTTATTTTCTCGTTATCATTTCTGC 1 248 0 TTATTCTGTA 0.941146 -53 CTAACTAAATTTATTAACTTTACAAGGAGTCTAC 2 12 0 TTATACTTAA 0.972969 -254 ATATTCAAAATTACTTACTTGATATATCTTTATA 2 151 1 TTATACTGAA 0.967571 -115 ACCAACATTTTTAATCACATTAGATCAACGATT 2 243 1 TTATACATAA 0.972969 -23 *** * *** ** * Masking position 5 Map Score: 1.86212 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 72 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 8 ********** No masking Map Score: -1.28365e-12 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: -1.28365e-12 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 10 ********** No masking Map Score: -1.28365e-12 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