AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -ifruR_aful_opreg_300.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 AF0645 232 translation initiation factor eIF-5A (eif5A) #2 AF0647 132 isocitrate dehydrogenase, NADP (icd) #3 AF0710 88 phosphoenolpyruvate synthase (ppsA) #4 AF1146 65 3-phosphoglycerate kinase (pgk) #5 AF1499 88 A. fulgidus predicted coding region AF1499 #6 AF1500 45 conserved hypothetical protein Motif number 1 CTCTTCTTCAGAAAAATTTAAATTAACGCAA 1 196 1 GAAAAATTTA 0.965582 -37 CAAAATGTGCAAAAGTTTTTACGGTATAATT 2 54 0 AAAAGTTTTA 0.944612 -79 TGGTTGAGTCGAAGATTGTCAAAATGTGCAA 2 73 0 GAAGATTGTA 0.964021 -60 ACCAAGAGCGGAAGGATTTTATAAACTACCA 2 100 1 GAAGGATTTA 0.978962 -33 AGCGGAAGGTTGTGGTAGTTTATAA 2 118 0 GAAGGTTGTG 0.918628 -15 CCAAAGCCTTAAAAAATTTTAGGTGGAGCGG 3 45 0 AAAAAATTTA 0.824798 -44 AAAACTTTCTGAAAATTTTAATTTACCTGCT 4 23 0 GAAAATTTTA 0.97828 -43 AAAATTTTCAGAAAGTTTTTAATTTCACCTT 4 35 1 GAAAGTTTTA 0.985671 -31 ********* * Masking position 3 Map Score: 7.90857 Number of sites scoring better than the average of aligned sites = 364 Number in coding regions = 294 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 2 GAATTACCAGCTGCCCTGATTTGGCCCGTGAGGCCA 1 40 1 CTGCCCTGCC 0.975625 -193 TACCGGAATACTGCTTTACCTCTGGCCTCACGGGCC 1 62 0 CTGCTTTTGC 0.978078 -171 ACCTTGCTGCCTAATTTTGCGTTAATTTAAAT 1 211 0 CTGCCTTGGT 0.992584 -22 TAAAATCCTTCCGCTCTTGGTTGAGTCGAAGATTGT 2 85 0 CCGCTCTGGT 0.994436 -48 CTATGATTTCCTGCTTAATATATCGCTTGCGATTCC 3 11 1 CTGCTTTTGC 0.978076 -78 TTTAATTTACCTGCTCAGAATTGGTTC 4 2 0 CTGCTCTGTT 0.976158 -64 AACTGCTTGGCCGCGTTCGATAGTGTTTTCAACAAT 5 29 0 CCGCGTTGGT 0.976262 -60 GGAAAGGAGTCTGCTCGGAAACGCGTAT 5 71 1 CTGCTCAGGT 0.982558 -18 ****** * * ** Masking position 4 Map Score: 6.40501 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 205 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 3 CTATAATTACTCCTGAAAGCACCATGAAGT 1 102 1 TCCTGAAAGC 0.981223 -131 TGAATTTCGATGCTGAAAGCTT 2 3 0 TGCTGAAAGC 0.995633 -130 ACGGTATAATTGCTTTAAGCCTCACATGAG 2 35 0 TGCTTTAAGC 0.89694 -98 AATAAGTTGTTGGGGAATGCA 5 2 0 TGGGGAATGC 0.933872 -87 AACAACTTATTGTTGAAAACACTATCGAAC 5 21 1 TGTTGAAAAC 0.950965 -68 CTTTTATTGCTGGTGATAAC 6 36 1 TGGTGATAAC 0.928829 -10 ********** Masking position 1 Map Score: 2.42331 Number of sites scoring better than the average of aligned sites = 536 Number in coding regions = 503 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 4 GGCCTCACGGGCCAAATCAGGGCAGCTGGT 1 45 0 GCCAAATCAG 0.983741 -188 ATGAAGCTCGCAAAAATCAGACGGCTGGTT 1 139 0 CAAAAATCAG 0.958596 -94 TTAAATTAACGCAAAATTAGGCAGCAAGGT 1 213 1 GCAAAATTAG 0.962551 -20 CTTTCAGCATCGAAATTCAGGCTCATGTGA 2 14 1 CGAAATTCAG 0.92995 -119 TAAGGCTTTGGCAAACTCAGAACGAGGTGA 3 65 1 GCAAACTCAG 0.987463 -24 ********** Masking position 5 Map Score: 1.63875 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 103 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 GAAAGCACCATGAAGTAGAACAGAACCAGC 1 116 1 TGAAGTAGAA 0.973895 -117 AATGCGACTGAGAAGAAAAAGCATGAAGCT 1 161 0 AGAAGAAAAA 0.845922 -72 TAAATTTTTCTGAAGAAGAGTTAAAAATGC 1 186 0 TGAAGAAGAG 0.976993 -47 AAGCGATATATTAAGCAGGAAATCATAG 3 9 0 TTAAGCAGGA 0.91958 -80 GCCAAGCAGTTGAAGAAGGAAAGGAGTCTG 5 54 1 TGAAGAAGGA 0.990268 -35 ********** Masking position 4 Map Score: 0.997702 Number of sites scoring better than the average of aligned sites = 471 Number in coding regions = 443 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 ********** No masking Map Score: -9.70439e-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: -9.70439e-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 8 ********** No masking Map Score: -9.70439e-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