AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00670_aquae_reg_100.orf -o00670_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 oppB 300 transporter (OppBC family) #2 thy 300 thymidylate synthase complementing protein #3 metF 80 5,10-methylenetetrahydrofolate reductase #4 gcvT 144 aminomethyltransferase (glycine cleavage system T protein) #5 dmt 27 dolichol-phosphate mannosyltransferase #6 aq_1974 37 putative protein Motif number 1 CAGTCGGGTATCCTGTCCTTTTCTTCTATG 1 161 0 TCCTGTCCTT 0.777111 -140 TGTTTTTCCTTCACGTACTTGATTACCTTG 1 221 0 TCACGTACTT 0.954423 -80 TTCGTTTCCTTAAAGTACCTGTCTATCTCC 1 257 0 TAAAGTACCT 0.842503 -44 TAATTAGCTATAAAGAACTTCGTTTCCTTA 1 275 0 TAAAGAACTT 0.941433 -26 CCGGACCAGCTACACTCCTTCTCAAGAAAG 2 46 0 TACACTCCTT 0.93751 -255 ATGAACGTGGTCATGTACTTCACCGGACCA 2 68 0 TCATGTACTT 0.876176 -233 GCTCATTCTTTCACCTCCTTAATAAGGAGT 2 206 1 TCACCTCCTT 0.950117 -95 TCTTATATATTAAACTCCTTATTAAGGAGG 2 219 0 TAAACTCCTT 0.974597 -82 ACGGAACTTATAAAATACTTTCT 2 288 1 TAAAATACTT 0.939385 -13 ATAAAAAGTGTAAAAAACTTTCAAGGGAGG 3 17 0 TAAAAAACTT 0.855193 -64 AGTCCACCTTTAAAATACTTCCTT 3 67 1 TAAAATACTT 0.939385 -14 ACTATGTCCATAAACACCTGAAGGCAAAGT 4 43 1 TAAACACCTG 0.784977 -102 AAGGCAAAGTTCACGAACTTCGCAGGCTGG 4 63 1 TCACGAACTT 0.888643 -82 GCTCTTCCCTTACAGCCCTTACTTCTTCTA 4 121 0 TACAGCCCTT 0.781084 -24 CAAATTAAGATAAAATACTTCTTCTA 5 12 1 TAAAATACTT 0.939385 -16 TTTTAACCTCCTGAGTTTTACTT 6 25 0 TAACCTCCTG 0.863986 -13 ********** Masking position 1 Map Score: 18.6783 Number of sites scoring better than the average of aligned sites = 773 Number in coding regions = 698 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 2 GAAACTCGCAAAAGTCCCTCCCACCATGGAGT 1 17 1 AAATCCCTCC 0.97549 -284 TCTGGACGCCAAACTCCTCTTCAGGATACTCT 1 65 1 AAATCCTCTC 0.967381 -236 GAGCTGCTGTAAAATCTTCCCTTGCCTCCTCA 1 119 0 AAATCTTCCT 0.770283 -182 TCGTTTCCTTAAAGTACCTGTCTATCTCCTCT 1 254 0 AAATACCTTC 0.915938 -47 CGGACCAGCTACACTCCTTCTCAAGAAAGGCG 2 43 0 ACATCCTTTC 0.947844 -258 CTTATATATTAAACTCCTTATTAAGGAGGTGA 2 216 0 AAATCCTTTT 0.980632 -85 CGGAACTTATAAAATACTTTCT 2 289 1 AAATACTTCT 0.961481 -12 GTCCACCTTTAAAATACTTCCTT 3 68 1 AAATACTTCT 0.961485 -13 TACTTTATGCAAACTCCCCTTTACTATGTCCA 4 21 1 AAATCCCCTT 0.952065 -124 CTCTTCCCTTACAGCCCTTACTTCTTCTATTA 4 118 0 ACACCCTTCT 0.830824 -27 AAATTAAGATAAAATACTTCTTCTA 5 13 1 AAATACTTTT 0.948982 -15 *** ***** ** Masking position 3 Map Score: 11.1081 Number of sites scoring better than the average of aligned sites = 720 Number in coding regions = 666 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 3 CCTCACTCAGGTCAAAGTTAGGGTCGGAGAGT 1 92 0 GTAAAGTAGG 0.968967 -209 TGACCTGAGTGAGGAGGCAAGGGAAGATTTTA 1 110 1 GAGAGGCAGG 0.978372 -191 TTTCTTCTATGAAGTACCAAAGAGCTGCTGTA 1 140 0 GAGTACCAAG 0.74435 -161 CTTCATAGAAGAAAAGGACAGGATACCCGACT 1 158 1 GAAAGGAAGG 0.939738 -143 ACACAAAGAGGAGATAGACAGGTACTTTAAGG 1 248 1 GAATAGAAGG 0.943614 -53 AGCAGCAGCGGTTGAAGCGAGGAAGAAAGCAG 2 104 1 GTGAAGCAGG 0.979816 -197 GGTGTTTATGGACATAGTAAAGGGGAGTTTGC 4 29 0 GAATAGTAAG 0.86011 -116 CTCAATAATAGAAGAAGTAAGGGCTGTAAGGG 4 113 1 GAGAAGTAGG 0.987119 -32 TAAATTTTAAGTAAAACTCAGGAGGTTAAAA 6 17 1 GTAAACTAGG 0.904858 -21 ** ***** *** Masking position 10 Map Score: 6.89487 Number of sites scoring better than the average of aligned sites = 520 Number in coding regions = 485 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 4 AGCTCTTTGGTACTTCATAGAAGAAAAGGAC 1 146 1 TACTTCATAA 0.936127 -155 TTTGTGTTTTTCCTTCACGTACTTGATTACC 1 224 0 TCCTTCACGA 0.87501 -77 TCCTTCTTCCATGGGACGTAT 2 1 1 TCCTTCTTCA 0.982783 -300 CCAGCTACACTCCTTCTCAAGAAAGGCGTTG 2 40 0 TCCTTCTCAG 0.960762 -261 CGTGGTCATGTACTTCACCGGACCAGCTACA 2 62 0 TACTTCACCG 0.940561 -239 TATATTAAACTCCTTATTAAGGAGGTGAAAG 2 213 0 TCCTTATTAG 0.744254 -88 CTTTTTATTTTATTTCTTAAAAATTCTTAGT 3 39 1 TATTTCTTAA 0.73265 -42 TTACAGCCCTTACTTCTTCTATTATTGAGGT 4 111 0 TACTTCTTCA 0.977944 -34 TAAGATAAAATACTTCTTCTA 5 17 1 TACTTCTTCA 0.977944 -11 ********* * Masking position 5 Map Score: 6.81232 Number of sites scoring better than the average of aligned sites = 636 Number in coding regions = 596 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 5 GCGTCCAGAATCAGGTTTCTGACGTACTCC 1 44 0 TCAGGTTTCT 0.961038 -257 AAACTCCTCTTCAGGATACTCTCCGACCCT 1 75 1 TCAGGATACT 0.968142 -226 GGTTCCCATGTTAGGATACTGGGACGACTA 1 191 1 TTAGGATACT 0.911257 -110 TGGAAGTCTCTTAGGATTTTCGGGACCTGT 2 137 1 TTAGGATTTT 0.940707 -164 ACCTCCTTAATAAGGAGTTTAATATATAAG 2 218 1 TAAGGAGTTT 0.915719 -83 AACTTTGCCTTCAGGTGTTTATGGACATAG 4 44 0 TCAGGTGTTT 0.961038 -101 TAAGTAAAACTCAGGAGGTTAAAA 6 24 1 TCAGGAGGTT 0.962324 -14 ********** Masking position 3 Map Score: 5.56052 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 183 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 AAGTACCAAAGAGCTGCTGTAAAATCTTCC 1 131 0 GAGCTGCTGT 0.979535 -170 TCAACCGCTGCTGCTGCTGACATGAACGTG 2 89 0 CTGCTGCTGA 0.988775 -212 TCAGCAGCAGCAGCGGTTGAAGCGAGGAAG 2 99 1 CAGCGGTTGA 0.970466 -202 GAACAACAACAAGCTGCTGATCTTGTAATC 2 176 0 AAGCTGCTGA 0.987893 -125 ********** Masking position 8 Map Score: 0.500047 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 5 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 CTTTGACCTGAGTGAGGAGGCAAGGGAAGA 1 107 1 AGTGAGGAGG 0.98616 -194 TGCTGCTGACATGAACGTGGTCATGTACTT 2 78 0 ATGAACGTGG 0.847765 -223 TAAACTCCTTATTAAGGAGGTGAAAGAATG 2 209 0 ATTAAGGAGG 0.966992 -92 AAAACTTTCAAGGGAGGTGTGCC 3 4 0 AGGGAGGTGT 0.952292 -77 TTCTTCTATTATTGAGGTGTACTGGAGTGG 4 99 0 ATTGAGGTGT 0.957088 -46 TTTAAGTAAAACTCAGGAGGTTAAAA 6 22 1 ACTCAGGAGG 0.934845 -16 ********** Masking position 5 Map Score: 0.623191 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 263 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 8 ********** No masking Map Score: 1.43062e-12 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: 1.43062e-12 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 10 ********** No masking Map Score: 1.43062e-12 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