AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00360_aquae_reg_300.orf -o00360_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 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 aq_2087 28 putative protein #12 pepA 26 leucine aminopeptidase Motif number 1 ATCTTAAATAAAGGAGGAGAAAG 2 1 0 AGGAGGAGAG 0.993584 -80 TCTAAAAACTTTAAAGGAGGTAGCGGA 2 64 1 TAAAGGAGTG 0.95462 -17 GTGGAAGGAGAAAGTGGTGTATGG 4 2 1 TGAAGGAGAG 0.990137 -299 TGGTAACATAAGGAATGAGCATGTGTTTAAAGT 4 110 1 AGAATGAGAG 0.912005 -191 AGTCCAAGTCCCAAAGGAGCATGATATCGGATA 5 12 0 CAAAGGAGAG 0.978041 -52 CACAAAGAAGCTCGAGGAGATAGAGAAGGGTAT 8 112 0 CCGAGGAGTG 0.9654 -149 GGGAATGTCCTTGGAGGAGTTCGCTAAGGCTAT 8 154 0 TGGAGGAGTG 0.98116 -107 AGATCAGAGAAGAAAGGGGAATGTCCTTGGAGG 8 170 0 AAAAGGGGAG 0.947801 -91 TTGGAGTGGGAGAGAGGATAAGGAAGATCAGAG 8 194 0 AAGAGGATAG 0.803245 -67 TAAATTAAAAAGGGAGGAGGTGGAGCCATGATT 8 225 0 AGGAGGAGTG 0.988805 -36 GATAAACAAAAAGAAGGAGGTGGAAA 9 23 1 AGAAGGAGTG 0.989807 -16 AAGTGCTCTTTGGAAGGGAAAGGGTAACCTTCC 10 58 0 TGAAGGGAAG 0.786635 -207 CCTGAGCTATACCAAGGAGTATGTAGTAAGTGC 10 85 0 ACAAGGAGAG 0.986935 -180 CGAAAGGGAACACAAGGAAGAAGCGGAAGAAAC 10 215 1 CCAAGGAAAG 0.87188 -50 * ******* * * Masking position 5 Map Score: 24.1676 Number of sites scoring better than the average of aligned sites = 636 Number in coding regions = 583 Number in noncoding regions = 53 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 0.831032 -79 TCCGCTACCTCCTTTAAAGTTT 2 69 0 CGCTACCTCC 0.980166 -12 TGCCATACACCACTTTCTCCTTCCAC 4 7 0 CACTTTCTCC 0.906911 -294 TTTAAACACATGCTCATTCCTTATGTTACC 4 111 0 TGCTCATTCC 0.564595 -190 TTCTCGTCCACATCAACTCCACCACAGCCA 4 185 0 CATCAACTCC 0.837378 -116 GGCTCTTTTGCCCTCTCTCCCAGTGCCAGC 8 19 1 CCCTCTCTCC 0.90064 -242 AGATACCCTTCTCTATCTCCTCGAGCTTCT 8 110 1 CTCTATCTCC 0.969231 -151 CTTATCCTCTCTCCCACTCCAATCATGGCT 8 205 1 CTCCCACTCC 0.97493 -56 CCAATCATGGCTCCACCTCCTCCCTTTTTA 8 223 1 CTCCACCTCC 0.99218 -38 TTTCCACCTCCTTCTTTTTGT 9 28 0 TTCCACCTCC 0.983583 -11 CTTGCCATAATACCACCTCCT 10 2 0 TACCACCTCC 0.976146 -263 ACAGGAAGGTTACCCTTTCCCTTCCAAAGA 10 55 1 TACCCTTTCC 0.784853 -210 TTCAACTTCTTTTCATCTCCCTGAGCTATA 10 107 0 TTTCATCTCC 0.850987 -158 CAGTTTCTTCCGCTTCTTCCTTGTGTTCCC 10 220 0 CGCTTCTTCC 0.802247 -45 ********** Masking position 8 Map Score: 16.7455 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 0.930157 -66 AAGTAATTATTCTATATCTAGAATAGT 3 7 1 TTATTCATAT 0.919488 -25 ATCATGATCATTATCCCAACTTTAAACACAT 4 130 0 TTATCCAACT 0.952072 -171 TTATCCGATATCATGCTCCTT 5 1 1 TTATCCATAT 0.978754 -63 ACTTGTTATTTTAAATTTAACTTA 6 9 0 TTATTTAAAT 0.752862 -16 CTGATCTTCCTTATCCTCTCTCCCACTCCAA 8 196 1 TTATCCCTCT 0.952801 -65 TTCTTTTTGTTTATCTACAATTATAAT 9 7 0 TTATCTCAAT 0.91657 -32 TTCTGCGAACTTATCCTCTATTATTCCCCTT 10 146 0 TTATCCCTAT 0.976351 -119 CTCACTGTTTATACTATATACTTTAA 12 8 0 TTATACATAT 0.866375 -19 ****** **** Masking position 4 Map Score: 8.40154 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 0.785639 -293 ATGGTTTGGAGAGTATGTAGTGAGCAAAAGGCTT 4 77 1 GAGATGTTAG 0.994395 -224 CATAAGGAATGAGCATGTGTTTAAAGTTGGGATA 4 116 1 GAGATGTTAA 0.97595 -185 TAATGATCATGATGATGAGGTCAGGTGGTATGAG 4 148 1 GATATGATAG 0.878833 -153 TGATGTGGACGAGAAAATAATCAGGTCAGGGAGA 4 200 1 GAGAAATTAG 0.878828 -101 AGTCCCAAAGGAGCATGATATCGGATAA 5 5 0 GAGATGATGG 0.977632 -59 GAGAAGAAAGGGGAATGTCCTTGGAGGAGTTCGC 8 163 0 GGGATGTTGG 0.969429 -98 CTATACCAAGGAGTATGTAGTAAGTGCTCTTTGG 10 78 0 GAGATGTTAG 0.994395 -187 *** **** * ** Masking position 5 Map Score: 4.21308 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 0.942406 -79 TACATACTGATATAATCTTCTAAAAACTTTA 2 46 1 TATAATCTCT 0.793105 -35 GCATGGAATTTATAACCCTCTGGGTGATTTT 4 257 1 TATAACCCCT 0.802995 -44 CAAGGTTAATTATATTCCTCTCTGATAAAAT 7 18 0 TATATTCCCT 0.953504 -21 CTCCTCCAAGGACATTCCCCTTTCTTCTCTG 8 168 1 GACATTCCCT 0.574676 -93 TTCCTTATCCTCTCTCCCACTCCAATCATGG 8 202 1 TCTCTCCCCT 0.89208 -59 GGGTCCTGCTTTTCTTCTTCTTGCCATAATA 10 20 0 TTTCTTCTCT 0.966963 -245 TTCAACTTCTTTTCATCTCCCTGAGCTATAC 10 106 0 TTTCATCTCC 0.641116 -159 CCCTTATTAATTTATTCAACTTCTTTTCATC 10 120 0 TTTATTCACT 0.818561 -145 CTTATCCTCTATTATTCCCCTTATTAATTTA 10 137 0 ATTATTCCCT 0.830338 -128 TACATCTGGAGTTCTTCTACTGTAGATTCTG 10 172 0 GTTCTTCTCT 0.918257 -93 GTTTCCTCAGTTTCTTCCGCTTCTTCCTTGT 10 226 0 TTTCTTCCCT 0.982354 -39 ******** ** Masking position 7 Map Score: 7.60909 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 0.988297 -274 ATACTCTCCAAACCATCGCTCGAAGGTTGA 4 63 0 AACCATCGCT 0.919653 -238 ACTCCACCACAGCCATCTCTCATACCACCT 4 170 0 AGCCATCTCT 0.992344 -131 CGGGCTCTTTTGCCCTCTCTCCCAGTGCCA 8 17 1 TGCCCTCTCT 0.949409 -244 TCCCAGTGCCAGCCACCTGTAATCCACGTT 8 36 1 AGCCACCTGT 0.969911 -225 GTCTGGAGATACCCTTCTCTATCTCCTCGA 8 104 1 ACCCTTCTCT 0.935755 -157 ********** Masking position 10 Map Score: 4.25236 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 CTTCGAGCGATGGTTTGGAGAGTATGTAGT 4 68 1 TGGTTTGGAG 0.845831 -233 AGTGAGCAAAAGGCTTGGTAACATAAGGAA 4 95 1 AGGCTTGGTA 0.821574 -206 CATGATGATGAGGTCAGGTGGTATGAGAGA 4 155 1 AGGTCAGGTG 0.98854 -146 GAAAATAATCAGGTCAGGGAGATCATAACA 4 212 1 AGGTCAGGGA 0.987197 -89 TAGCGTCACAAGGTCTGGAGATACCCTTCT 8 92 1 AGGTCTGGAG 0.978827 -169 TCCTTGGTATAGCTCAGGGAGATGAAAAGA 10 100 1 AGCTCAGGGA 0.936804 -165 CTTTCGGGTTTGGTCAGGTACATCTGGAGT 10 191 0 TGGTCAGGTA 0.968822 -74 ********** Masking position 7 Map Score: 4.41425 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 TCGAAGGTTGAAAAGAAGCTCTCAATAAGC 4 44 0 AAAAGAAGCT 0.98546 -257 GTCCAAGTCCCAAAGGAGCATGATATCGGA 5 14 0 CAAAGGAGCA 0.916745 -50 GGCATTTCCACAAAGAAGCTCGAGGAGATA 8 123 0 CAAAGAAGCT 0.982514 -138 TAGATAAACAAAAAGAAGGAGGTGGAAA 9 21 1 AAAAGAAGGA 0.931274 -18 CAGGGAGATGAAAAGAAGTTGAATAAATTA 10 114 1 AAAAGAAGTT 0.967824 -151 TATAACCGCTAAAATAAGTTTTT 11 16 1 AAAATAAGTT 0.823103 -13 ********** Masking position 4 Map Score: 3.19552 Number of sites scoring better than the average of aligned sites = 280 Number in coding regions = 259 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 9 TGTATGGCAACAGATGGCTTATTGAGAGCT 4 28 1 CAGATGGCTT 0.989124 -273 CAACCTTCGAGCGATGGTTTGGAGAGTATG 4 64 1 GCGATGGTTT 0.854663 -237 ATGTAGTGAGCAAAAGGCTTGGTAACATAA 4 91 1 CAAAAGGCTT 0.776555 -210 ATGATGAGGTCAGGTGGTATGAGAGATGGC 4 159 1 CAGGTGGTAT 0.862888 -142 GGTGGTATGAGAGATGGCTGTGGTGGAGTT 4 171 1 GAGATGGCTG 0.975258 -130 ACGTGGATTACAGGTGGCTGGCACTGGGAG 8 35 0 CAGGTGGCTG 0.98398 -226 ********** Masking position 6 Map Score: 0.582577 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 CCTGAAAATGTTAAAATAGCGTT 1 8 1 ATGTTAAAAT 0.822271 -16 CTCTTACATACTGATATAATCTTCTAAAAA 2 42 1 CTGATATAAT 0.962241 -39 TCCAATAAATCTGTTATGATCTCCCTGACC 4 223 0 CTGTTATGAT 0.943284 -78 ATATTCCTCTCTGATAAAATATTGGAT 7 8 0 CTGATAAAAT 0.946749 -31 CTTATTTTAGCGGTTATAATTAA 11 4 0 CGGTTATAAT 0.943758 -25 ********** Masking position 5 Map Score: 0.451223 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 8 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 ********** No masking Map Score: -2.07235e-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: -2.07235e-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 13 ********** No masking Map Score: -2.07235e-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