AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -ifruR_aful_opreg_100.orf -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 AF0647 132 isocitrate dehydrogenase, NADP (icd) #2 AF0710 88 phosphoenolpyruvate synthase (ppsA) #3 AF1146 65 3-phosphoglycerate kinase (pgk) #4 AF1499 88 A. fulgidus predicted coding region AF1499 #5 AF1500 45 conserved hypothetical protein Motif number 1 AATTATACCGTAAAAACTTTTGCACATTTTG 1 54 1 TAAAACTTTT 0.968895 -79 TTGCACATTTTGACAATCTTCGACTCAACCA 1 73 1 TACAATCTTC 0.968117 -60 TGGTAGTTTATAAAATCCTTCCGCTCTTGGT 1 100 0 TAAATCCTTC 0.934088 -33 TTATAAACTACCACAACCTTCCGCT 1 118 1 CACAACCTTC 0.987037 -15 TCCGCTCCACCTAAAATTTTTTAAGGCTTTG 2 44 1 CAAAATTTTT 0.921727 -45 AGCAGGTAAATTAAAATTTTCAGAAAGTTTT 3 23 1 TAAAATTTTC 0.967238 -43 AAGGTGAAATTAAAAACTTTCTGAAAATTTT 3 35 0 TAAAACTTTC 0.987338 -31 TGCATTCCCCAACAACTTATTGTTGAAAAC 4 10 1 CACAACTTAT 0.844743 -79 * ********* Masking position 5 Map Score: 8.45853 Number of sites scoring better than the average of aligned sites = 855 Number in coding regions = 733 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 2 GTTTATAAAATCCTTCCGCTCTTGGTTGAG 1 96 0 TCCTTCCGCT 0.978061 -37 AACTACCACAACCTTCCGCT 1 123 1 ACCTTCCGCT 0.978063 -10 CTATGATTTCCTGCTTAATATATCGCTT 2 9 1 TCCTGCTTAA 0.930438 -80 TTACTCACCTCGTTCTGAGTTTGCCAAAG 2 70 0 TCGTTCTGAG 0.932437 -19 ATTTTAATTTACCTGCTCAGAATTGGTTC 3 10 0 ACCTGCTCAG 0.903108 -56 GAAATTAAAAACTTTCTGAAAATTTTAATT 3 31 0 ACTTTCTGAA 0.918247 -35 TTTTAATTTCACCTTCCGAATTGAA 3 51 1 ACCTTCCGAA 0.988354 -15 CAGACTCCTTTCCTTCTTCAACTGCTTGGC 4 54 0 TCCTTCTTCA 0.958599 -35 ********** Masking position 4 Map Score: 7.21919 Number of sites scoring better than the average of aligned sites = 1190 Number in coding regions = 1131 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 AAGCTTTCAGCATCGAAATTCAGG 1 5 1 TTTCAGCATC 0.986889 -128 CAGCATCGAAATTCAGGCTCATGTGAGGCT 1 18 1 ATTCAGGCTC 0.984228 -115 GTATAATTGCTTTAAGCCTCACATGAGCCT 1 32 0 TTTAAGCCTC 0.992523 -101 CCTAAAATTTTTTAAGGCTTTGGCAAACTC 2 53 1 TTTAAGGCTT 0.945834 -36 AAGTTTTTAATTTCACCTTCCGAATTGAA 3 47 1 TTTCACCTTC 0.955314 -19 ********** Masking position 5 Map Score: 3.20347 Number of sites scoring better than the average of aligned sites = 703 Number in coding regions = 659 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 4 TTGTCAAAATGTGCAAAAGTTTTTACGGTA 1 59 0 GTGCAAAAGT 0.912453 -74 TTTAGGTGGAGCGGAATCGCAAGCGATATA 2 29 0 GCGGAATCGC 0.977806 -60 CGTTCTGAGTTTGCCAAAGCCTTAAAAAAT 2 59 0 TTGCCAAAGC 0.963043 -30 ACTATCGAACGCGGCCAAGCAGTTGAAGAA 4 41 1 GCGGCCAAGC 0.98841 -48 AGGAGTCTGCTCGGAAACGCGTAT 4 75 1 TCGGAAACGC 0.988193 -14 ********** Masking position 3 Map Score: 0.518467 Number of sites scoring better than the average of aligned sites = 495 Number in coding regions = 461 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 ********** No masking Map Score: -4.02005e-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 6 ********** No masking Map Score: -4.02005e-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 7 ********** No masking Map Score: -4.02005e-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