AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00350_aquae_reg_300.orf -o00350_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 Purged sequences: aq_2087 28 putative protein Input sequences: #1 fabZ 23 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase #2 aq_194 53 putative protein #3 aldH2 300 aldehyde dehydrogenase #4 aq_260 300 hypothetical protein #5 aspC4 80 aminotransferase (AspC family) #6 aspC3 31 aminotransferase (AspC family) #7 mtfB 300 mannosyltransferase B #8 spsK 63 spore coat polysaccharide biosynthesis protein SpsK #9 gsa 24 glutamate-1-semialdehyde aminotransferase #10 ilvC 66 acetohydroxy acid isomeroreductase #11 efp 187 elongation factor P #12 aq_1510 113 putative protein #13 aspC1 260 aspartate aminotransferase #14 hisC 264 histidinol-phosphate aminotransferase #15 pepA_carB2 26 pepA: leucine aminopeptidase, carB2: carbamoyl-phosphate synthase large subunit Motif number 1 TATTTCTTTTCATTCCGCTTCCTTGACTGGG 3 107 0 CTTCCGCTTC 0.791549 -194 ATGACACTTACTATTTCCTCTTTTGAAGGGT 3 268 0 CATTTCCTCT 0.827002 -33 CTTTCTCCTCCTTTATTTAAG 5 1 1 CTTCTCCTCC 0.992925 -80 TCCGCTACCTCCTTTAAAGTTTTTA 5 66 0 CACCTCCTTT 0.900177 -15 CCATACACCACTTTCTCCTTCCAC 7 4 0 CTTCTCCTTC 0.988673 -297 TATCCGATATCATGCTCCTTTGGGACTTGGA 8 12 1 CTGCTCCTTT 0.867226 -52 GTCAAGTCCCCTTTCCCCTCCACTTGAGTTA 11 155 1 CTTCCCCTCC 0.987333 -33 CGCTCTCCTCCGAAAGTAGAG 12 1 1 CCTCTCCTCC 0.963544 -113 ATACCCTTCTCTATCTCCTCGAGCTTCTTTG 13 112 1 CATCTCCTCG 0.9657 -149 ATAGCCTTAGCGAACTCCTCCAAGGACATTC 13 154 1 CAACTCCTCC 0.941846 -107 CCTCCAAGGACATTCCCCTTTCTTCTCTGAT 13 170 1 CTTCCCCTTT 0.950645 -91 CTCTGATCTTCCTTATCCTCTCTCCCACTCC 13 194 1 CTTATCCTCT 0.786025 -67 AATCATGGCTCCACCTCCTCCCTTTTTAATT 13 225 1 CACCTCCTCC 0.973327 -36 GGAAGGTTACCCTTTCCCTTCCAAAGAGCAC 14 58 1 CTTTCCCTTC 0.889707 -207 GCACTTACTACATACTCCTTGGTATAGCTCA 14 85 1 CTACTCCTTG 0.883949 -180 GTTTCTTCCGCTTCTTCCTTGTGTTCCCTTT 14 217 0 CTCTTCCTTG 0.740675 -48 * ********* Masking position 9 Map Score: 20.3095 Number of sites scoring better than the average of aligned sites = 784 Number in coding regions = 712 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 2 CTTTCTCCTCCTTTATTTAAG 5 2 1 TTTCTCCTCC 0.640338 -79 TCCGCTACCTCCTTTAAAGTTT 5 69 0 CGCTACCTCC 0.969517 -12 TGCCATACACCACTTTCTCCTTCCAC 7 7 0 CACTTTCTCC 0.619401 -294 TTCTCGTCCACATCAACTCCACCACAGCCA 7 185 0 CATCAACTCC 0.806376 -116 ATAAATCTGTTATGATCTCCCTGACCTGAT 7 219 0 TATGATCTCC 0.57962 -82 AACCTACCTCCCGACATTATT 10 2 1 ACCTACCTCC 0.719183 -65 GCGTGACCTCCTGAAGGATTT 10 56 0 CGTGACCTCC 0.939543 -11 GATTTGAACCCGCGACCTCCGGGTTATGAG 11 56 1 CGCGACCTCC 0.976161 -132 TCAAGTCCCCTTTCCCCTCCACTTGAGTTA 11 156 1 TTTCCCCTCC 0.800457 -32 GGCTCTTTTGCCCTCTCTCCCAGTGCCAGC 13 19 1 CCCTCTCTCC 0.752472 -242 AGATACCCTTCTCTATCTCCTCGAGCTTCT 13 110 1 CTCTATCTCC 0.921046 -151 CTATAGCCTTAGCGAACTCCTCCAAGGACA 13 152 1 AGCGAACTCC 0.609772 -109 CTTATCCTCTCTCCCACTCCAATCATGGCT 13 205 1 CTCCCACTCC 0.880853 -56 CCAATCATGGCTCCACCTCCTCCCTTTTTA 13 223 1 CTCCACCTCC 0.984815 -38 CTTGCCATAATACCACCTCCT 14 2 0 TACCACCTCC 0.940077 -263 TTCAACTTCTTTTCATCTCCCTGAGCTATA 14 107 0 TTTCATCTCC 0.775982 -158 ********** Masking position 8 Map Score: 13.0283 Number of sites scoring better than the average of aligned sites = 909 Number in coding regions = 758 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 3 TATTAATAATATTTCTACAAGCTTACTTTT 2 32 0 ATTTCTACAA 0.819828 -22 AACTTATGAGTTTTCCACAATTCTCCAC 4 9 0 TTTTCCACAA 0.984888 -292 TTTTCCACATTTATCCACATTTTTAACGTA 4 92 0 TTATCCACAT 0.912544 -209 ACTTAAGAAGTTTTCCACATTTATCCACAT 4 102 0 TTTTCCACAT 0.980464 -199 TTTCCACAACTTTTCCACATGAACAACTTA 4 186 0 TTTTCCACAT 0.980464 -115 TCCCGAAAAACTTTCCACAACTTTTCCACA 4 197 0 CTTTCCACAA 0.967202 -104 GGCTATAGGCATTTCCACAAAGAAGCTCGA 13 130 0 ATTTCCACAA 0.97224 -131 ********** Masking position 7 Map Score: 9.29094 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 45 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 AACGCTATTTTAACATTTTCAGG 1 2 0 TTAACTTTAG 0.566267 -22 ATCCACATTTTTAACGTAAGTAGTTTATACACC 4 77 0 TTAACTAAAG 0.952177 -224 CGTAGTATGAATAACTTAAGAAGTTTTCCACAT 4 112 0 ATAACTAAAG 0.927127 -189 CGAATTATAAATAACTTAAGTTGTTCATGTGGA 4 170 1 ATAACTAATG 0.722107 -131 TCTTATTAATACAAAATAAATAGT 4 287 1 ACAAATAAAG 0.748387 -14 TACACTTATCTTAAATAAAGGAGGAGAAAG 5 8 0 TTAAAAAAAG 0.742633 -73 GCTACCTCCTTTAAAGTTTTTAGAAGATTATAT 5 55 0 TTAAATTTAG 0.640018 -26 GATGTGGACGAGAAAATAATCAGGTCAGGGAGA 7 201 1 AGAAATAAAG 0.748387 -100 TAAGTTAAATTTAAAATAACAAGT 9 11 1 TTAAATAAAG 0.964432 -14 AAAAAGTGTTTTAAATTAACTTGACACACTTCT 12 52 0 TTAAATAATG 0.847049 -62 CCTTAAAATTTTAAATTAAAAAGGGAGGAGGTG 13 236 0 TTAAATAAAG 0.964432 -25 AAGAAGTTGAATAAATTAATAAGGGGAATAATA 14 126 1 ATAAATAAAG 0.945433 -139 TTAAAGTATATAGTATAAACAGT 15 1 1 TTAAATATAG 0.896962 -26 ***** *** ** Masking position 4 Map Score: 8.87592 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 37 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 AATTCCCGAAGAACACCCTGTTAAAAGGGC 3 152 1 GAACACCCTG 0.959916 -149 GTCGTTATATGAACAACTTATGAGTTTTCC 4 23 0 GAACAACTTA 0.951952 -278 TTCGTAGTATGAATAACTTAAGAAGTTTTC 4 117 0 GAATAACTTA 0.719878 -184 TTTTCCACATGAACAACTTAAGTTATTTAT 4 176 0 GAACAACTTA 0.951952 -125 AGTTTTTCGGGAAAAGCTTGAAAATCAATG 4 215 1 GAAAAGCTTG 0.816185 -86 TTATTATAAAGAACAAATTGTAAGATAATA 10 28 0 GAACAAATTG 0.922504 -39 ACGCGGGGTGGAGCAGCCTGGTAGCTCGCC 11 89 0 GAGCAGCCTG 0.911482 -99 GGAAGAAGCGGAAGAAACTGAGGAAACCGA 14 230 1 GAAGAAACTG 0.746594 -35 TGAGGAAACCGAACAACCTGCAACGGA 14 248 1 GAACAACCTG 0.987314 -17 ********** Masking position 5 Map Score: 5.03517 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 151 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 ATTTTTACTCAGAAGTGCATAGGCTTCCAC 3 234 0 AGAAGTGCAT 0.807181 -67 TTTTCTTTTGAGTAGATTGTGTCGTTATAT 4 43 0 AGTAGATTGT 0.791752 -258 TTTTAACGTAAGTAGTTTATACACCGTGGT 4 72 0 AGTAGTTTAT 0.895466 -229 TAAAGTTTTTAGAAGATTATATCAGTATGT 5 47 0 AGAAGATTAT 0.842261 -34 GGAAGGAGAAAGTGGTGTATGGCAACAGAT 7 13 1 AGTGGTGTAT 0.934607 -288 AAAATCACCCAGAGGGTTATAAATTCCATG 7 258 0 AGAGGGTTAT 0.804084 -43 TTGGACTTGCAGTGGTGTAACTGATCTAAG 8 38 1 AGTGGTGTAA 0.667887 -26 CTCCTCCGAAAGTAGAGTGTAATTTTATTC 12 15 1 AGTAGAGTGT 0.899082 -99 TTCATTTTGAAGAAGTGTGTCAAGTTAATT 12 42 1 AGAAGTGTGT 0.934607 -72 GAGGAGATAGAGAAGGGTATCTCCAGACCT 13 102 0 AGAAGGGTAT 0.93107 -159 ********** Masking position 1 Map Score: 4.36256 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 155 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 TTTAAAGGCTATTATAAAAGTGT 2 4 0 ATTATAAAAG 0.631259 -50 CTTATTAATAATATTTCTACAAG 2 41 0 ATTAATAATA 0.770634 -13 ATTTCCGTCTATTAAAACGGTGCAGGAACC 3 57 0 ATTAAAACGG 0.761075 -244 AAACTTACGAATTATAAATAACTTAAGTTG 4 163 1 ATTATAAATA 0.770634 -138 TTTATTTTGTATTAATAAGAATAATAATAG 4 277 0 ATTAATAAGA 0.895783 -24 TGAAGGATTTATTATAAAGAACAAATTGTA 10 36 0 ATTATAAAGA 0.895783 -31 GCGTTGCCAAATTATTAATATATAGAAAAA 11 115 1 ATTATTAATA 0.731695 -73 AAAATTTTAAATTAAAAAGGGAGGAGGTGG 13 235 0 ATTAAAAAGG 0.931664 -26 AGTTGAATAAATTAATAAGGGGAATAATAG 14 130 1 ATTAATAAGG 0.917123 -135 ********** Masking position 4 Map Score: 2.33529 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 106 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 CCGCATATTCCCTTACCGCATCCGAACTTCGTC 3 26 0 CCTTACCATC 0.81172 -275 GCGGATACTGCCAGCCCGGACAAATAGTGGAAG 3 208 1 CCAGCCCACA 0.953011 -93 TCTCATACCACCTGACCTCATCATCATGATCAT 7 150 0 CCTGACCATA 0.985545 -151 TTATGATCTCCCTGACCTGATTATTTTCTCGTC 7 207 0 CCTGACCATA 0.985545 -94 AACCTACCTCCCGACATTATTATCTTACAATT 10 10 1 CCCGACAATA 0.863235 -57 GGGTTCAAATCCCGCCCCCGCAACCATATCACC 11 34 0 CCCGCCCGCA 0.94671 -154 AAGGGTATCTCCAGACCTTGTGACGCTACGCTC 13 87 0 CCAGACCGTA 0.9539 -174 TCCAGATGTACCTGACCAAACCCGAAAGGGAAC 14 193 1 CCTGACCACC 0.974255 -72 ******* ** * Masking position 6 Map Score: 2.76434 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 34 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 CCTGTTAAAAGGGCATGGATTGAACTTCAGG 3 168 1 GGGCATGGAT 0.965619 -133 ATGGTTTGGAGAGTATGTAGTGAGCAAAAGG 7 77 1 GAGTATGTAT 0.960069 -224 CATAAGGAATGAGCATGTGTTTAAAGTTGGG 7 116 1 GAGCATGTGT 0.969747 -185 TTATTGGACAGAGCATGGAATTTATAACCCT 7 245 1 GAGCATGGAT 0.987149 -56 AGTCCCAAAGGAGCATGATATCGGATAA 8 8 0 GAGCATGATT 0.895391 -56 CTATACCAAGGAGTATGTAGTAAGTGCTCTT 14 81 0 GAGTATGTAT 0.960069 -184 ********* * Masking position 6 Map Score: 1.91829 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 15 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 GGAAGCGGAATGAAAAGAAATAATAACCAT 3 116 1 TGAAAAGAAA 0.966455 -185 CACAATCTACTCAAAAGAAAACCACGGTGT 4 52 1 TCAAAAGAAA 0.847067 -249 GGGAAAAGCTTGAAAATCAATGGGTTTTGA 4 223 1 TGAAAATCAA 0.715482 -78 GCTCGAAGGTTGAAAAGAAGCTCTCAATAA 7 46 0 TGAAAAGAAG 0.972061 -255 AAGGAAGATCAGAGAAGAAAGGGGAATGTC 13 178 0 AGAGAAGAAA 0.794094 -83 GGCAAGAAGAAGAAAAGCAGGACCCAAGTA 14 26 1 AGAAAAGCAG 0.910594 -239 CTCAGGGAGATGAAAAGAAGTTGAATAAAT 14 112 1 TGAAAAGAAG 0.972061 -153 ********** Masking position 5 Map Score: 2.56901 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 202 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 11 ACTATTCTAGATATAGAATAATTACTT 6 7 0 ATATAGATAA 0.970592 -25 AAGGAGCATGATATCGGATAA 8 1 0 ATATCGATAA 0.922994 -63 AATTATTAATATATAGAAAAAATCTTATCTC 11 124 1 ATATAGAAAA 0.891089 -64 TTGGAGTGGGAGAGAGGATAAGGAAGATCAG 13 196 0 AGAGAGATAA 0.909533 -65 AAGGGGAATAATAGAGGATAAGTTCGCAGAA 14 146 1 ATAGAGATAA 0.964865 -119 TTAAAGTATATAGTATAAACAGTGAG 15 8 1 ATATAGATAA 0.968358 -19 ****** **** Masking position 8 Map Score: 2.40656 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 4 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 12 ACATGAAAATAGCCGCCTATTATTATTCTT 4 261 1 AGCCGCCTAT 0.962143 -40 GCTCTCAATAAGCCATCTGTTGCCATACAC 7 27 0 AGCCATCTGT 0.987072 -274 ACTCCACCACAGCCATCTCTCATACCACCT 7 170 0 AGCCATCTCT 0.976215 -131 TCCCAGTGCCAGCCACCTGTAATCCACGTT 13 36 1 AGCCACCTGT 0.991605 -225 ********** Masking position 8 Map Score: 0.801691 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 8 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 13 TAAGGGAATATGCGGTTCCTGCACCGTTTTAA 3 44 1 TGGGTTCTGC 0.977175 -257 GTATCCGCACTGGGGAACCTGAAGTTCAATCC 3 184 0 TGGGAACTGA 0.973718 -117 GGTTCCCCAGTGCGGATACTGCCAGCCCGGAC 3 197 1 TGGGATCTGC 0.977215 -104 GGACTTGCAGTGGTGTAACTGATCTAAGTCCA 8 40 1 TGTGTACTGA 0.93613 -24 CCAAGGAGTATGTAGTAAGTGCTCTTTGGAAG 14 75 0 TGAGTAGTGC 0.793727 -190 GTTCTTCTACTGTAGATTCTGCGAACTTATCC 14 161 0 TGAGATCTGC 0.935453 -104 GAAGAACTCCAGATGTACCTGACCAAACCCGA 14 186 1 AGTGTACTGA 0.724239 -79 CGGAAGAAACTGAGGAAACCGAACAACCTGCA 14 238 1 TGGGAACCGA 0.919828 -27 ** **** **** Masking position 5 Map Score: 0.860568 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 86 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 14 TGTGACAAATTTCAAAACCCATTGATTTTC 4 234 0 TTCAAAACCC 0.934863 -67 CCACTGCAAGTCCAAGTCCCAAAGGAGCAT 8 23 0 TCCAAGTCCC 0.970505 -41 AGGTCGCGGGTTCAAATCCCGCCCCCGCAA 11 44 0 TTCAAATCCC 0.979262 -144 ATCTTATCTCGTCAAGTCCCCTTTCCCCTC 11 145 1 GTCAAGTCCC 0.970504 -43 TCAACTTCTTTTCATCTCCCTGAGCTATAC 14 106 0 TTCATCTCCC 0.923449 -159 ********** Masking position 4 Map Score: 0.6656 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 51 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 15 ********** No masking Map Score: -6.88273e-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