AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00440_aquae_reg_300.orf -o00440_aquae_300.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -x5 -e 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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 aq_260 300 hypothetical protein #2 mtfB 300 mannosyltransferase B #3 spsK 63 spore coat polysaccharide biosynthesis protein SpsK #4 aq_1510 113 putative protein #5 carB2 26 carbamoyl-phosphate synthase large subunit Motif number 1 TGGAGAATTGTGGAAAACTCATAAGTTGTT 1 12 1 TGGAAAACTC 0.878553 -289 TGTCGTTATATGAACAACTTATGAGTTTTC 1 24 0 TGAACAACTT 0.983714 -277 CCACGGTGTATAAACTACTTACGTTAAAAA 1 73 1 TAAACTACTT 0.790961 -228 TGGATAAATGTGGAAAACTTCTTAAGTTAT 1 105 1 TGGAAAACTT 0.978662 -196 TTTCGTAGTATGAATAACTTAAGAAGTTTT 1 118 0 TGAATAACTT 0.966937 -183 TTACGAATTATAAATAACTTAAGTTGTTCA 1 167 1 TAAATAACTT 0.92077 -134 CTTTTCCACATGAACAACTTAAGTTATTTA 1 177 0 TGAACAACTT 0.983714 -124 GTTGTTCATGTGGAAAAGTTGTGGAAAGTT 1 189 1 TGGAAAAGTT 0.899763 -112 AAGCTTTTCCCGAAAAACTTTCCACAACTT 1 204 0 CGAAAAACTT 0.897891 -97 TCTGTTGCCATACACCACTTTCTCCTTCCA 2 12 0 TACACCACTT 0.821859 -289 AATGGACTTAGATCAGTTACACCACTGC 3 46 0 TAGATCAGTT 0.606189 -18 TAAATTAACTTGACACACTTCTTCAAAATG 4 44 0 TGACACACTT 0.878553 -70 CAAGTTAATTTAAAACACTTTTTGATTTTT 4 62 1 TAAAACACTT 0.947987 -52 ********** Masking position 7 Map Score: 15.0258 Number of sites scoring better than the average of aligned sites = 402 Number in coding regions = 375 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 2 CATTTATCCACATTTTTAACGTAAGTAGTT 1 85 0 CATTTTTAAC 0.836222 -216 ACAATCCGGTGACTTAAAACTTACGAATTA 1 147 1 GACTTAAAAC 0.922897 -154 TTTCCCGAAAAACTTTCCACAACTTTTCCA 1 199 0 AACTTTCCAC 0.823954 -102 TGGGTTTTGAAATTTGTCACATGAAAATAG 1 243 1 AATTTGTCAC 0.907363 -58 TCATTATCCCAACTTTAAACACATGCTCAT 2 124 0 AACTTTAAAC 0.935865 -177 CAGAGCATGGAATTTATAACCCTCTGGGTG 2 253 1 AATTTATAAC 0.943156 -48 CCCTCTGGGTGATTTTTAACTGAATACCTA 2 272 1 GATTTTTAAC 0.931905 -29 GTTTTAAATTAACTTGACACACTTCTTCAA 4 48 0 AACTTGACAC 0.895978 -66 GTGTCAAGTTAATTTAAAACACTTTTTGAT 4 58 1 AATTTAAAAC 0.930711 -56 TACCTCTAGAGATTTATAACAAAAATCAAA 4 82 0 GATTTATAAC 0.931632 -32 ********** Masking position 5 Map Score: 9.78656 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 154 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 3 GTGGAGAATTGTGGAAAACTCATAAGT 1 8 1 ATTGTGGAAA 0.982959 -293 TTACGTTAAAAATGTGGATAAATGTGGAAA 1 91 1 AATGTGGATA 0.964947 -210 AATGTGGATAAATGTGGAAAACTTCTTAAG 1 101 1 AATGTGGAAA 0.992515 -200 TTAAGTTGTTCATGTGGAAAAGTTGTGGAA 1 185 1 CATGTGGAAA 0.979791 -116 ATGTGGAAAAGTTGTGGAAAGTTTTTCGGG 1 196 1 GTTGTGGAAA 0.954734 -105 TTTTCGGGAAAAGCTTGAAAATCAATGGGT 1 218 1 AAGCTTGAAA 0.823926 -83 CCATCGCTCGAAGGTTGAAAAGAAGCTCTC 2 51 0 AAGGTTGAAA 0.960538 -250 ********** Masking position 8 Map Score: 8.42795 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 130 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 CCATACACCACTTTCTCCTTCCAC 2 5 0 CTTTCTCCTT 0.917411 -296 ACTTTAAACACATGCTCATTCCTTATGTTA 2 113 0 CATGCTCATT 0.989048 -188 ACCTCATCATCATGATCATTATCCCAACTT 2 139 0 CATGATCATT 0.915477 -162 TTATAAATTCCATGCTCTGTCCAATAAATC 2 242 0 CATGCTCTGT 0.969218 -59 TATCCGATATCATGCTCCTTTGGGACTTGG 3 12 1 CATGCTCCTT 0.994613 -52 ********** Masking position 6 Map Score: 4.52197 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 40 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 CTTTTGAGTAGATTGTGTCGTTATATGAAC 1 39 0 GATTGTGTCG 0.975041 -262 TAAGTCACCGGATTGTTTCGTAGTATGAAT 1 133 0 GATTGTTTCG 0.929579 -168 AACTTAAGTTGTTCATGTGGAAAAGTTGTG 1 182 1 GTTCATGTGG 0.955381 -119 ACCTTCGAGCGATGGTTTGGAGAGTATGTA 2 66 1 GATGGTTTGG 0.98273 -235 TAATGATCATGATGATGAGGTCAGGTGGTA 2 148 1 GATGATGAGG 0.963531 -153 CTGTGGTGGAGTTGATGTGGACGAGAAAAT 2 188 1 GTTGATGTGG 0.982877 -113 ********** Masking position 6 Map Score: 3.55387 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 53 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 ATTGTGTCGTTATATGAACAACTTATGAGT 1 28 0 TATATGAACA 0.798697 -273 ATTGTTTCGTAGTATGAATAACTTAAGAAG 1 122 0 AGTATGAATA 0.959293 -179 AAACTTACGAATTATAAATAACTTAAGTTG 1 163 1 ATTATAAATA 0.807085 -138 ATTTTGTATTAATAAGAATAATAATAGGCG 1 274 0 AATAAGAATA 0.855121 -27 TTATTAATACAAAATAAATAGT 1 289 1 AAAATAAATA 0.856897 -12 ACACTTCTTCAAAATGAATAAAATTACACT 4 30 0 AAAATGAATA 0.925194 -84 TAAAGTATATAGTATAAACAGTGAG 5 6 0 AGTATAAACA 0.884676 -21 ********** Masking position 4 Map Score: 1.65457 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 45 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 ********** No masking Map Score: -4.73059e-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: -4.73059e-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 9 ********** No masking Map Score: -4.73059e-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