AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00360_aquae_reg_100.orf -o00360_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 aspC4 80 aminotransferase (AspC family) #3 aspC3 31 aminotransferase (AspC family) #4 mtfB 300 mannosyltransferase B #5 spsK 63 spore coat polysaccharide biosynthesis protein SpsK #6 gsa 24 glutamate-1-semialdehyde aminotransferase #7 hemA 38 glutamyl tRNA reductase (delta-aminolevulinate synthase) #8 aspC1 260 aspartate aminotransferase #9 aq_1997 38 hypothetical protein #10 hisC 264 histidinol-phosphate aminotransferase #11 pepA 26 leucine aminopeptidase Motif number 1 CTTTCTCCTCCTTTATTTAAGAT 2 1 1 CTCTCCTCCT 0.994709 -80 TCCGCTACCTCCTTTAAAGTTTTTAGA 2 64 0 CACTCCTTTA 0.962321 -17 CCATACACCACTTTCTCCTTCCAC 4 2 0 CTCTCCTTCA 0.991862 -299 ACTTTAAACACATGCTCATTCCTTATGTTACCA 4 110 0 CTCTCATTCT 0.926379 -191 TATCCGATATCATGCTCCTTTGGGACTTGGACT 5 12 1 CTCTCCTTTG 0.981843 -52 ATACCCTTCTCTATCTCCTCGAGCTTCTTTGTG 8 112 1 CACTCCTCGG 0.971326 -149 ATAGCCTTAGCGAACTCCTCCAAGGACATTCCC 8 154 1 CACTCCTCCA 0.98443 -107 CCTCCAAGGACATTCCCCTTTCTTCTCTGATCT 8 170 1 CTCCCCTTTT 0.956606 -91 CTCTGATCTTCCTTATCCTCTCTCCCACTCCAA 8 194 1 CTATCCTCTT 0.832114 -67 AATCATGGCTCCACCTCCTCCCTTTTTAATTTA 8 225 1 CACTCCTCCT 0.990761 -36 TTTCCACCTCCTTCTTTTTGTTTATC 9 23 0 CACTCCTTCT 0.99159 -16 GGAAGGTTACCCTTTCCCTTCCAAAGAGCACTT 10 58 1 CTTCCCTTCA 0.817388 -207 GCACTTACTACATACTCCTTGGTATAGCTCAGG 10 85 1 CTCTCCTTGT 0.989214 -180 GTTTCTTCCGCTTCTTCCTTGTGTTCCCTTTCG 10 215 0 CTTTCCTTGG 0.892032 -50 * * ******* * Masking position 9 Map Score: 24.3886 Number of sites scoring better than the average of aligned sites = 641 Number in coding regions = 587 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 2 CTTTCTCCTCCTTTATTTAAG 2 2 1 TTTCTCCTCC 0.825257 -79 TCCGCTACCTCCTTTAAAGTTT 2 69 0 CGCTACCTCC 0.979361 -12 TGCCATACACCACTTTCTCCTTCCAC 4 7 0 CACTTTCTCC 0.903428 -294 TTTAAACACATGCTCATTCCTTATGTTACC 4 111 0 TGCTCATTCC 0.554594 -190 TTCTCGTCCACATCAACTCCACCACAGCCA 4 185 0 CATCAACTCC 0.831776 -116 GGCTCTTTTGCCCTCTCTCCCAGTGCCAGC 8 19 1 CCCTCTCTCC 0.896949 -242 AGATACCCTTCTCTATCTCCTCGAGCTTCT 8 110 1 CTCTATCTCC 0.967997 -151 CTTATCCTCTCTCCCACTCCAATCATGGCT 8 205 1 CTCCCACTCC 0.973918 -56 CCAATCATGGCTCCACCTCCTCCCTTTTTA 8 223 1 CTCCACCTCC 0.991859 -38 TTTCCACCTCCTTCTTTTTGT 9 28 0 TTCCACCTCC 0.982914 -11 CTTGCCATAATACCACCTCCT 10 2 0 TACCACCTCC 0.975183 -263 ACAGGAAGGTTACCCTTTCCCTTCCAAAGA 10 55 1 TACCCTTTCC 0.77792 -210 TTCAACTTCTTTTCATCTCCCTGAGCTATA 10 107 0 TTTCATCTCC 0.845767 -158 CAGTTTCTTCCGCTTCTTCCTTGTGTTCCC 10 220 0 CGCTTCTTCC 0.795729 -45 ********** Masking position 8 Map Score: 16.9994 Number of sites scoring better than the average of aligned sites = 1219 Number in coding regions = 1048 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 3 AGAGTTACACTTATCTTAAATAAAGGAGGAG 2 15 0 TTATCTAAAT 0.925776 -66 AAGTAATTATTCTATATCTAGAATAGT 3 7 1 TTATTCATAT 0.914524 -25 ATCATGATCATTATCCCAACTTTAAACACAT 4 130 0 TTATCCAACT 0.94899 -171 TTATCCGATATCATGCTCCTT 5 1 1 TTATCCATAT 0.977562 -63 ACTTGTTATTTTAAATTTAACTTA 6 9 0 TTATTTAAAT 0.740463 -16 CTGATCTTCCTTATCCTCTCTCCCACTCCAA 8 196 1 TTATCCCTCT 0.949763 -65 TTCTTTTTGTTTATCTACAATTATAAT 9 7 0 TTATCTCAAT 0.911418 -32 TTCTGCGAACTTATCCTCTATTATTCCCCTT 10 146 0 TTATCCCTAT 0.97479 -119 CTCACTGTTTATACTATATACTTTAA 11 8 0 TTATACATAT 0.858624 -19 ****** **** Masking position 4 Map Score: 8.55777 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 76 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 4 GTGGAAGGAGAAAGTGGTGTATGGCAACAGA 4 8 1 GAGAAGTTTA 0.759111 -293 ATGGTTTGGAGAGTATGTAGTGAGCAAAAGGCTT 4 77 1 GAGATGTTAG 0.993488 -224 CATAAGGAATGAGCATGTGTTTAAAGTTGGGATA 4 116 1 GAGATGTTAA 0.972139 -185 TAATGATCATGATGATGAGGTCAGGTGGTATGAG 4 148 1 GATATGATAG 0.861809 -153 TGATGTGGACGAGAAAATAATCAGGTCAGGGAGA 4 200 1 GAGAAATTAG 0.861805 -101 AGTCCCAAAGGAGCATGATATCGGATAA 5 5 0 GAGATGATGG 0.97408 -59 GAGAAGAAAGGGGAATGTCCTTGGAGGAGTTCGC 8 163 0 GGGATGTTGG 0.964621 -98 CTATACCAAGGAGTATGTAGTAAGTGCTCTTTGG 10 78 0 GAGATGTTAG 0.993488 -187 *** **** * ** Masking position 5 Map Score: 4.33277 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 136 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 5 CTTTCTCCTCCTTTATTTAAGA 2 2 1 TTTCTCCTCT 0.945064 -79 TACATACTGATATAATCTTCTAAAAACTTTA 2 46 1 TATAATCTCT 0.8012 -35 GCATGGAATTTATAACCCTCTGGGTGATTTT 4 257 1 TATAACCCCT 0.810795 -44 CAAGGTTAATTATATTCCTCTCTGATAAAAT 7 18 0 TATATTCCCT 0.955674 -21 CTCCTCCAAGGACATTCCCCTTTCTTCTCTG 8 168 1 GACATTCCCT 0.586865 -93 TTCCTTATCCTCTCTCCCACTCCAATCATGG 8 202 1 TCTCTCCCCT 0.896807 -59 GGGTCCTGCTTTTCTTCTTCTTGCCATAATA 10 20 0 TTTCTTCTCT 0.968526 -245 TTCAACTTCTTTTCATCTCCCTGAGCTATAC 10 106 0 TTTCATCTCC 0.652553 -159 CCCTTATTAATTTATTCAACTTCTTTTCATC 10 120 0 TTTATTCACT 0.825879 -145 CTTATCCTCTATTATTCCCCTTATTAATTTA 10 137 0 ATTATTCCCT 0.837275 -128 TACATCTGGAGTTCTTCTACTGTAGATTCTG 10 172 0 GTTCTTCTCT 0.921938 -93 GTTTCCTCAGTTTCTTCCGCTTCTTCCTTGT 10 226 0 TTTCTTCCCT 0.983201 -39 ******** ** Masking position 7 Map Score: 7.81745 Number of sites scoring better than the average of aligned sites = 831 Number in coding regions = 780 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 6 GCTCTCAATAAGCCATCTGTTGCCATACAC 4 27 0 AGCCATCTGT 0.989278 -274 ATACTCTCCAAACCATCGCTCGAAGGTTGA 4 63 0 AACCATCGCT 0.926133 -238 ACTCCACCACAGCCATCTCTCATACCACCT 4 170 0 AGCCATCTCT 0.992708 -131 CGGGCTCTTTTGCCCTCTCTCCCAGTGCCA 8 17 1 TGCCCTCTCT 0.953905 -244 TCCCAGTGCCAGCCACCTGTAATCCACGTT 8 36 1 AGCCACCTGT 0.972632 -225 GTCTGGAGATACCCTTCTCTATCTCCTCGA 8 104 1 ACCCTTCTCT 0.941382 -157 ********** Masking position 10 Map Score: 4.36106 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 38 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 ACTACATACTCTCCAAACCATCGCTCGAAG 4 68 0 CTCCAAACCA 0.845205 -233 TTCCTTATGTTACCAAGCCTTTTGCTCACT 4 95 0 TACCAAGCCT 0.820871 -206 TCTCTCATACCACCTGACCTCATCATCATG 4 155 0 CACCTGACCT 0.988485 -146 TGTTATGATCTCCCTGACCTGATTATTTTC 4 212 0 TCCCTGACCT 0.987137 -89 AGAAGGGTATCTCCAGACCTTGTGACGCTA 8 92 0 CTCCAGACCT 0.978728 -169 TCTTTTCATCTCCCTGAGCTATACCAAGGA 10 100 0 TCCCTGAGCT 0.936519 -165 ACTCCAGATGTACCTGACCAAACCCGAAAG 10 191 1 TACCTGACCA 0.968677 -74 ********** Masking position 4 Map Score: 4.54107 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 101 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 GGCTTATTGAGAGCTTCTTTTCAACCTTCG 4 43 1 GAGCTTCTTT 0.975962 -258 AATCTGTTATGATCTCCCTGACCTGATTAT 4 216 0 GATCTCCCTG 0.887728 -85 CTATCTCCTCGAGCTTCTTTGTGGAAATGC 8 122 1 GAGCTTCTTT 0.975962 -139 TTTCTTCTCTGATCTTCCTTATCCTCTCTC 8 188 1 GATCTTCCTT 0.983372 -73 TTAATTTATTCAACTTCTTTTCATCTCCCT 10 115 0 CAACTTCTTT 0.886107 -150 GTTTCTTCCGCTTCTTCCTTGTGTTCCCTT 10 218 0 CTTCTTCCTT 0.884071 -47 ********** Masking position 5 Map Score: 2.2462 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 279 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 AGCTCTCAATAAGCCATCTGTTGCCATACA 4 28 0 AAGCCATCTG 0.989819 -273 CATACTCTCCAAACCATCGCTCGAAGGTTG 4 64 0 AAACCATCGC 0.862776 -237 TTATGTTACCAAGCCTTTTGCTCACTACAT 4 91 0 AAGCCTTTTG 0.787946 -210 GCCATCTCTCATACCACCTGACCTCATCAT 4 159 0 ATACCACCTG 0.870611 -142 AACTCCACCACAGCCATCTCTCATACCACC 4 171 0 CAGCCATCTC 0.976819 -130 CTCCCAGTGCCAGCCACCTGTAATCCACGT 8 35 1 CAGCCACCTG 0.984962 -226 ********** Masking position 5 Map Score: 0.691276 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 91 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 ********** No masking Map Score: 2.10564e-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 11 ********** No masking Map Score: 2.10564e-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 12 ********** No masking Map Score: 2.10564e-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