AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00950_aquae_reg_100.orf -o00950_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 fabZ 23 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase #2 aq_260 300 hypothetical protein #3 aspC4 80 aminotransferase (AspC family) #4 aspC3 31 aminotransferase (AspC family) #5 mtfB 300 mannosyltransferase B #6 spsK 63 spore coat polysaccharide biosynthesis protein SpsK #7 aq_1510 113 putative protein #8 aspC1 260 aspartate aminotransferase #9 pepA_carB2 26 pepA: leucine aminopeptidase, carB2: carbamoyl-phosphate synthase large subunit Motif number 1 GTGGAGAATTGTGGAAAACTCAT 2 3 1 GGAGAATTGG 0.690127 -298 GGTTTTCTTTTGAGTAGATTGTGTCGTTATA 2 44 0 TGAGTAGATG 0.817999 -257 CTTAAATAAAGGAGGAGAAAG 3 1 0 GGAGGAGAAG 0.990264 -80 TAAAAACTTTAAAGGAGGTAGCGGA 3 66 1 AAAGGAGGTG 0.948751 -15 GTGGAAGGAGAAAGTGGTGTATGG 5 4 1 GAAGGAGAAG 0.974749 -297 GATGGTTTGGAGAGTATGTAGTGAGCAAAAG 5 76 1 AGAGTATGTG 0.752375 -225 TCCAAGTCCCAAAGGAGCATGATATCGGATA 6 12 0 AAAGGAGCAG 0.833791 -52 CTCTACTTTCGGAGGAGAGCG 7 1 0 GGAGGAGAGG 0.992421 -113 CTCTCCTCCGAAAGTAGAGTGTAATTTTATT 7 13 1 AAAGTAGAGG 0.899008 -101 TATTCATTTTGAAGAAGTGTGTCAAGTTAAT 7 40 1 GAAGAAGTGG 0.795942 -74 CAAAGAAGCTCGAGGAGATAGAGAAGGGTAT 8 112 0 CGAGGAGATG 0.958634 -149 GAATGTCCTTGGAGGAGTTCGCTAAGGCTAT 8 154 0 GGAGGAGTTG 0.980308 -107 AAGGAAGATCAGAGAAGAAAGGGGAATGTCC 8 177 0 AGAGAAGAAG 0.933294 -84 GGAGTGGGAGAGAGGATAAGGAAGATCAGAG 8 194 0 AGAGGATAAG 0.932132 -67 AATTAAAAAGGGAGGAGGTGGAGCCATGATT 8 225 0 GGAGGAGGTG 0.987386 -36 TTAAAGTATATAGTATAAACAGT 9 3 1 AAAGTATATG 0.673492 -24 ********* * Masking position 6 Map Score: 19.6833 Number of sites scoring better than the average of aligned sites = 1084 Number in coding regions = 989 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 2 GTGGAGAATTGTGGAAAACTCATAAGTT 2 9 1 TTGTGGAAAA 0.989305 -292 TACGTTAAAAATGTGGATAAATGTGGAAAA 2 92 1 ATGTGGATAA 0.969244 -209 ATGTGGATAAATGTGGAAAACTTCTTAAGT 2 102 1 ATGTGGAAAA 0.992111 -199 TAAGTTGTTCATGTGGAAAAGTTGTGGAAA 2 186 1 ATGTGGAAAA 0.992111 -115 TGTGGAAAAGTTGTGGAAAGTTTTTCGGGA 2 197 1 TTGTGGAAAG 0.972959 -104 GGTGGAGTTGATGTGGACGAGAAAATAATC 5 192 1 ATGTGGACGA 0.935025 -109 TCGAGCTTCTTTGTGGAAATGCCTATAGCC 8 130 1 TTGTGGAAAT 0.959694 -131 ********** Masking position 7 Map Score: 12.0661 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 24 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 3 GTGTCGTTATATGAACAACTTATGAGTTTTC 2 24 0 ATGAACACTT 0.991789 -277 ACCACGGTGTATAAACTACTTACGTTAAAAA 2 72 1 ATAAACACTT 0.987151 -229 GTTTCGTAGTATGAATAACTTAAGAAGTTTT 2 118 0 ATGAATACTT 0.976088 -183 CTTACGAATTATAAATAACTTAAGTTGTTCA 2 166 1 ATAAATACTT 0.962911 -135 ACTTTTCCACATGAACAACTTAAGTTATTTA 2 177 0 ATGAACACTT 0.991789 -124 ATCTGTTGCCATACACCACTTTCTCCTTCCA 5 12 0 ATACACACTT 0.965628 -289 ****** **** Masking position 5 Map Score: 8.80726 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 14 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 GCTATTTTAACATTTTCAGG 1 1 0 CATTTTCAGG 0.697927 -23 CATTTATCCACATTTTTAACGTAAGTAGTT 2 85 0 CATTTTTAAC 0.887642 -216 ACAATCCGGTGACTTAAAACTTACGAATTA 2 147 1 GACTTAAAAC 0.76989 -154 AAAACCCATTGATTTTCAAGCTTTTCCCGA 2 221 0 GATTTTCAAG 0.857376 -80 ATCTTCTAAAAACTTTAAAGGAGGTAGCGG 3 60 1 AACTTTAAAG 0.806302 -21 TCATTATCCCAACTTTAAACACATGCTCAT 5 124 0 AACTTTAAAC 0.828625 -177 CAGAGCATGGAATTTATAACCCTCTGGGTG 5 253 1 AATTTATAAC 0.859552 -48 CCCTCTGGGTGATTTTTAACTGAATACCTA 5 272 1 GATTTTTAAC 0.9121 -29 TTGAATTTATAGGTATTCAGTTA 5 288 0 AATTTATAGG 0.726767 -13 TAATTTTATTCATTTTGAAGAAGTGTGTCA 7 34 1 CATTTTGAAG 0.713213 -80 GTGTCAAGTTAATTTAAAACACTTTTTGAT 7 58 1 AATTTAAAAC 0.859449 -56 TACCTCTAGAGATTTATAACAAAAATCAAA 7 82 0 GATTTATAAC 0.868856 -32 TTTAATTTAAAATTTTAAGGAA 8 249 1 AATTTTAAGG 0.8063 -12 ********** Masking position 8 Map Score: 6.60496 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 362 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 5 GTGTATGGCAACAGATGGCTTATTGAGAGC 5 27 1 ACAGATGGCT 0.989511 -274 TCAACCTTCGAGCGATGGTTTGGAGAGTAT 5 63 1 AGCGATGGTT 0.928126 -238 AGGTGGTATGAGAGATGGCTGTGGTGGAGT 5 170 1 AGAGATGGCT 0.991437 -131 TAAAAATCACCCAGAGGGTTATAAATTCCA 5 260 0 CCAGAGGGTT 0.892383 -41 TGGCACTGGGAGAGAGGGCAAAAGAGCCCG 8 17 0 AGAGAGGGCA 0.956039 -244 AACGTGGATTACAGGTGGCTGGCACTGGGA 8 36 0 ACAGGTGGCT 0.967307 -225 TCGAGGAGATAGAGAAGGGTATCTCCAGAC 8 104 0 AGAGAAGGGT 0.915996 -157 ********** Masking position 4 Map Score: 4.43202 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 65 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 ATCTCTCATACCACCTGACCTCATCATCAT 5 156 0 CCACCTGACC 0.960252 -145 CACATCAACTCCACCACAGCCATCTCTCAT 5 177 0 CCACCACAGC 0.978296 -124 CTGTTATGATCTCCCTGACCTGATTATTTT 5 213 0 CTCCCTGACC 0.960252 -88 TAGATCAGTTACACCACTGCAAGTCCAAGT 6 36 0 ACACCACTGC 0.874577 -28 TTTGCCCTCTCTCCCAGTGCCAGCCACCTG 8 25 1 CTCCCAGTGC 0.978296 -236 CTTATCCTCTCTCCCACTCCAATCATGGCT 8 205 1 CTCCCACTCC 0.978296 -56 ********** Masking position 5 Map Score: 2.42022 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 107 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 CCTGAAAATGTTAAAATAGCGTT 1 5 1 AAAATTAAAT 0.644882 -19 GAATTGTGGAAAACTCATAAGTTGTTCATATAA 2 16 1 AAACTTAGTT 0.872657 -285 CACGGTGTATAAACTACTTACGTTAAAAATGTG 2 74 1 AAACTTACGT 0.900886 -227 TAAATGTGGAAAACTTCTTAAGTTATTCATACT 2 109 1 AAACTTAAGT 0.961328 -192 GAAAAGCTTGAAAATCAATGGGTTTTGAAATTT 2 225 1 AAAATAGGGT 0.766352 -76 AATCTTCTAAAAACTTTAAAGGAGGTAGCGGA 3 59 1 AAACTAAGGA 0.748099 -22 TGTGGACGAGAAAATAATCAGGTCAGGGAGATC 5 203 1 AAAATTAGGT 0.967256 -98 ATTTATAACAAAAATCAAAAAGTGTTTTAAATT 7 68 0 AAAATAAAGT 0.916119 -46 TTTTGTTATAAATCTCTAGAGGTAAAATCTTTA 7 88 1 AATCTAAGGT 0.748099 -26 CTCTAGAGGTAAAATCTTTAAGT 7 101 1 AAAATTAAGT 0.94878 -13 TTCCTTAAAATTTTAAATTAAAAAGGGAG 8 242 0 AAAATTAATT 0.762014 -19 ***** * **** Masking position 2 Map Score: 4.94696 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 188 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 TCCACATTTTTAACGTAAGTAGTTTATACACC 2 77 0 TAACGTAAAG 0.952696 -224 GTAGTATGAATAACTTAAGAAGTTTTCCACAT 2 112 0 TAACTTAAAG 0.982102 -189 GAATTATAAATAACTTAAGTTGTTCATGTGGA 2 171 1 TAACTTAATG 0.927739 -130 ACACTTATCTTAAATAAAGGAGGAGAAAG 3 8 0 TAAATAAAAG 0.896491 -73 AAAAGTGTTTTAAATTAACTTGACACACTTCT 7 52 0 TAAATTAATG 0.947028 -62 CTTAAAATTTTAAATTAAAAAGGGAGGAGGTG 8 236 0 TAAATTAAAG 0.9723 -25 ******** ** Masking position 7 Map Score: 3.12417 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 8 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 9 GGCTTATTGAGAGCTTCTTTTCAACCTTCG 5 43 1 GAGCTTCTTT 0.981992 -258 AATCTGTTATGATCTCCCTGACCTGATTAT 5 216 0 GATCTCCCTG 0.949402 -85 CTATCTCCTCGAGCTTCTTTGTGGAAATGC 8 122 1 GAGCTTCTTT 0.981992 -139 TTTCTTCTCTGATCTTCCTTATCCTCTCTC 8 188 1 GATCTTCCTT 0.981992 -73 ********** Masking position 5 Map Score: 0.851797 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 52 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 ********** No masking Map Score: -7.50743e-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 11 ********** No masking Map Score: -7.50743e-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 12 ********** No masking Map Score: -7.50743e-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