AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00440_aquae_reg_100.orf -o00440_aquae_100.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 GAAAACTCATAAGTTGTTCATATAACGACA 1 24 1 AAGTTGTTCA 0.986964 -277 TTTTTAACGTAAGTAGTTTATACACCGTGG 1 73 0 AAGTAGTTTA 0.877049 -228 ATAACTTAAGAAGTTTTCCACATTTATCCA 1 105 0 AAGTTTTCCA 0.883024 -196 AAAACTTCTTAAGTTATTCATACTACGAAA 1 118 1 AAGTTATTCA 0.945404 -183 TGAACAACTTAAGTTATTTATAATTCGTAA 1 167 0 AAGTTATTTA 0.901034 -134 TAAATAACTTAAGTTGTTCATGTGGAAAAG 1 177 1 AAGTTGTTCA 0.986964 -124 TCATGTGGAAAAGTTGTGGAAAGTTTTTCG 1 194 1 AAGTTGTGGA 0.901145 -107 AAGTTGTGGAAAGTTTTTCGGGAAAAGCTT 1 204 1 AAGTTTTTCG 0.847245 -97 TGGAAGGAGAAAGTGGTGTATGGCAACAGA 2 12 1 AAGTGGTGTA 0.958874 -289 CTTGGACTTGCAGTGGTGTAACTGATCTAA 3 37 1 CAGTGGTGTA 0.800101 -27 CATTTTGAAGAAGTGTGTCAAGTTAATTTA 4 44 1 AAGTGTGTCA 0.838372 -70 AAAAATCAAAAAGTGTTTTAAATTAACTTG 4 62 0 AAGTGTTTTA 0.94078 -52 ********** Masking position 2 Map Score: 14.8573 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 194 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 2 AACTACTTACGTTAAAAATGTGGATAAATG 1 85 1 GTTAAAAATG 0.852912 -216 TAATTCGTAAGTTTTAAGTCACCGGATTGT 1 147 0 GTTTTAAGTC 0.93138 -154 TGGAAAAGTTGTGGAAAGTTTTTCGGGAAA 1 199 1 GTGGAAAGTT 0.841657 -102 CTATTTTCATGTGACAAATTTCAAAACCCA 1 243 0 GTGACAAATT 0.917519 -58 ATGAGCATGTGTTTAAAGTTGGGATAATGA 2 124 1 GTTTAAAGTT 0.943091 -177 CACCCAGAGGGTTATAAATTCCATGCTCTG 2 253 0 GTTATAAATT 0.949604 -48 TAGGTATTCAGTTAAAAATCACCCAGAGGG 2 272 0 GTTAAAAATC 0.939547 -29 TTGAAGAAGTGTGTCAAGTTAATTTAAAAC 4 48 1 GTGTCAAGTT 0.907254 -66 ATCAAAAAGTGTTTTAAATTAACTTGACAC 4 58 0 GTTTTAAATT 0.938437 -56 TTTGATTTTTGTTATAAATCTCTAGAGGTA 4 82 1 GTTATAAATC 0.939234 -32 ********** Masking position 6 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 0.981836 -293 TTACGTTAAAAATGTGGATAAATGTGGAAA 1 91 1 AATGTGGATA 0.962683 -210 AATGTGGATAAATGTGGAAAACTTCTTAAG 1 101 1 AATGTGGAAA 0.992017 -200 TTAAGTTGTTCATGTGGAAAAGTTGTGGAA 1 185 1 CATGTGGAAA 0.978465 -116 ATGTGGAAAAGTTGTGGAAAGTTTTTCGGG 1 196 1 GTTGTGGAAA 0.951844 -105 TTTTCGGGAAAAGCTTGAAAATCAATGGGT 1 218 1 AAGCTTGAAA 0.814307 -83 CCATCGCTCGAAGGTTGAAAAGAAGCTCTC 2 51 0 AAGGTTGAAA 0.958002 -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 AAACTCATAAGTTGTTCATATAACGACACA 1 26 1 GTTGTTCATA 0.986916 -275 TTTAACGTAAGTAGTTTATACACCGTGGTT 1 71 0 GTAGTTTATA 0.962563 -230 AACTTCTTAAGTTATTCATACTACGAAACA 1 120 1 GTTATTCATA 0.97958 -181 AACAACTTAAGTTATTTATAATTCGTAAGT 1 165 0 GTTATTTATA 0.968262 -136 AATAACTTAAGTTGTTCATGTGGAAAAGTT 1 179 1 GTTGTTCATG 0.965012 -122 GACAGAGCATGGAATTTATAACCCTCTGGG 2 251 1 GGAATTTATA 0.85671 -50 ********** Masking position 5 Map Score: 5.61653 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 19 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 GTGGAAGGAGAAAGTGGTGTATGG 2 5 1 AAGGAGAAAG 0.919403 -296 TAACATAAGGAATGAGCATGTGTTTAAAGT 2 113 1 AATGAGCATG 0.989179 -188 AAGTTGGGATAATGATCATGATGATGAGGT 2 139 1 AATGATCATG 0.91538 -162 GATTTATTGGACAGAGCATGGAATTTATAA 2 242 1 ACAGAGCATG 0.970001 -59 CCAAGTCCCAAAGGAGCATGATATCGGATA 3 12 0 AAGGAGCATG 0.994744 -52 ********** Masking position 5 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 6 CTTTTGAGTAGATTGTGTCGTTATATGAAC 1 39 0 GATTGTGTCG 0.971723 -262 TAAGTCACCGGATTGTTTCGTAGTATGAAT 1 133 0 GATTGTTTCG 0.920709 -168 AACTTAAGTTGTTCATGTGGAAAAGTTGTG 1 182 1 GTTCATGTGG 0.949585 -119 ACCTTCGAGCGATGGTTTGGAGAGTATGTA 2 66 1 GATGGTTTGG 0.980414 -235 TAATGATCATGATGATGAGGTCAGGTGGTA 2 148 1 GATGATGAGG 0.958748 -153 CTGTGGTGGAGTTGATGTGGACGAGAAAAT 2 188 1 GTTGATGTGG 0.98058 -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 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