AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -icpxR9_aquae_opreg_300.orf -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 phoB 284 transcriptional regulator (PhoB-like) #2 xanB 33 mannose-6-phosphate isomerase/mannose-1-phosphate guanyl transferase #3 aq_592 96 hypothetical protein #4 motA 42 flagellar motor protein MotA #5 htrA 28 periplasmic serine protease Motif number 1 TATTAGTATAAGATTTCAAGACTTATTAAT 1 32 0 AGATTTCAAG 0.940889 -253 ATGTTAATAGAAAATTTAAGTATATTAGTA 1 54 0 AAAATTTAAG 0.916365 -231 GGTTAAGGAAATGTTTTAAATTAATGTTAA 1 77 0 ATGTTTTAAA 0.930768 -208 TTTAAACCCCAAATTTTAAGTTTCGGTTAA 1 101 0 AAATTTTAAG 0.987321 -184 TCCTTACTTAAGGTTTTAAACCCCAAATTT 1 115 0 AGGTTTTAAA 0.968042 -170 CTGAAGAACGATATTTTAAAGAAAGCGGAT 1 255 1 ATATTTTAAA 0.969008 -30 AGGGGATAATTTTAAACTGCTAAAAT 2 7 1 TAATTTTAAA 0.910016 -27 TAAACTGCTAAAATTCTAAGT 2 23 1 AAATTCTAAG 0.941992 -11 GAGAAAGATTTTAAAGGATTTGGTG 3 82 0 AGATTTTAAA 0.986004 -15 AATTTAAATTTTAAAAAGGAAATCC 4 6 1 AAATTTTAAA 0.986277 -37 ********** Masking position 5 Map Score: 17.5217 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 119 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 2 TAATATATTACTATGTTCGAGCTTT 1 4 0 CATGTTGAGC 0.931973 -281 CCTTAAGTAAGGAGGTGTGAGATGAAGGTCTT 1 132 1 GAGGTGGAGA 0.988184 -153 GGTGTGAGATGAAGGTCTTAGCAGTCAGGAAT 1 145 1 GAGGTCTAGC 0.995486 -140 AGGGTAATTAGTAGGTTTTTGAAAAAGAGGAA 1 192 1 GAGGTTTTGA 0.949137 -93 TGAAAAAGAGGAAGGTTGTAGCGGTTGTGAAC 1 211 1 GAGGTTTAGC 0.996255 -74 GCGTAGCTCAGCTGGTCAGAGCGGGGATCTCA 3 14 1 GTGGTCGAGC 0.989523 -83 GTCCCAGGTCGGAGGTTCGAGTCCTCCCGCCG 3 49 1 GAGGTTGAGT 0.990591 -48 * ***** **** Masking position 6 Map Score: 8.328 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 95 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 3 TAGCAGTCAGGAATAAGAGGCAGAAAGAGA 1 163 1 GAATAAGAGG 0.978214 -122 ATAAGAGGCAGAAAGAGAGGGTAATTAGTA 1 175 1 GAAAGAGAGG 0.993768 -110 GTAGGTTTTTGAAAAAGAGGAAGGTTGTAG 1 202 1 GAAAAAGAGG 0.993276 -83 CGATATTTTAAAGAAAGCGGATGTTGTAAT 1 263 1 AAGAAAGCGG 0.94716 -22 AGCTCAGCTGGTCAGAGCGGGGATCTCATA 3 18 1 GTCAGAGCGG 0.968447 -79 ********** Masking position 6 Map Score: 4.23576 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 129 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 TCATCTCACACCTCCTTACTTAAGGTTTTA 1 127 0 CCTCCTTACT 0.977066 -158 TCTGCCTCTTATTCCTGACTGCTAAGACCT 1 157 0 ATTCCTGACT 0.8335 -128 ATTACCCTCTCTTTCTGCCTCTTATTCCTG 1 170 0 CTTTCTGCCT 0.970099 -115 ACCGCTACAACCTTCCTCTTTTTCAAAAAC 1 206 0 CCTTCCTCTT 0.876802 -79 AGGACTCGAACCTCCGACCTGGGACTTATG 3 44 0 CCTCCGACCT 0.976634 -53 AGGTTCGAGTCCTCCCGCCGCCACCAAATC 3 61 1 CCTCCCGCCG 0.991112 -36 ********** Masking position 3 Map Score: 0.92732 Number of sites scoring better than the average of aligned sites = 822 Number in coding regions = 731 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 ACATTTCCTTAACCGAAACTTAAAATTTGG 1 93 1 AACCGAAACT 0.954698 -192 TAAGGTTTTAAACCCCAAATTTTAAGTTTC 1 107 0 AACCCCAAAT 0.925881 -178 GATTGTTCACAACCGCTACAACCTTCCTCT 1 217 0 AACCGCTACA 0.989847 -68 GATAATTTTAAACTGCTAAAATTCTAAGT 2 15 1 AACTGCTAAA 0.945367 -19 TAAAAAGGAAATCCGATAAATTTATTTAGA 4 22 1 ATCCGATAAA 0.924145 -21 ********** Masking position 8 Map Score: 0.349212 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 198 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 ********** No masking Map Score: -6.37056e-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 7 ********** No masking Map Score: -6.37056e-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: -6.37056e-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