AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00130_aquae_reg_300.orf -o00130_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 aq_134 201 putative protein #2 aq_260 300 hypothetical protein #3 nuoG 139 NADH dehydrogenase I chain G #4 mtfB 300 mannosyltransferase B #5 spsK 63 spore coat polysaccharide biosynthesis protein SpsK #6 nuoD1 43 NADH dehydrogenase I chain D #7 frdB1 35 fumarate reductase iron-sulfur subunit #8 stpK 30 ser/thr protein kinase #9 trpE 300 anthranilate synthase component I #10 glgP 110 glycogen phosphorylase #11 dhaT 25 1,3 propanediol dehydrogenase #12 aq_1148 300 putative protein #13 nuoA2 300 NADH dehydrogenase I chain A #14 dnaG 66 DNA primase #15 aq_1510 113 putative protein #16 carB2 26 carbamoyl-phosphate synthase large subunit Motif number 1 GTAAACAACGAAGTTGTCCCTCTTTATGTA 1 48 1 AAGTTGTCCC 0.915035 -154 TATCACCGGGAAGTTTCCCAAGTCCCAGGG 1 80 1 AAGTTTCCCA 0.917048 -122 GTCCCAGGGGAAGTTTTTCAAAGAACAGGA 1 101 1 AAGTTTTTCA 0.977011 -101 AACAACTTATGAGTTTTCCACAATTCTCCA 2 12 0 GAGTTTTCCA 0.9715 -289 GAAAACTCATAAGTTGTTCATATAACGACA 2 24 1 AAGTTGTTCA 0.951356 -277 ATAACTTAAGAAGTTTTCCACATTTATCCA 2 105 0 AAGTTTTCCA 0.988659 -196 AAAACTTCTTAAGTTATTCATACTACGAAA 2 118 1 AAGTTATTCA 0.896696 -183 TAAATAACTTAAGTTGTTCATGTGGAAAAG 2 177 1 AAGTTGTTCA 0.951356 -124 AACTTTCCACAACTTTTCCACATGAACAAC 2 189 0 AACTTTTCCA 0.887194 -112 AAGTTGTGGAAAGTTTTTCGGGAAAAGCTT 2 204 1 AAGTTTTTCG 0.861101 -97 TCTGGGGGATAAATTTTTCAAACGGAATT 7 10 0 AAATTTTTCA 0.820203 -26 TGTTGCCCTTAAGTTTTCAAGCTCCTCTTC 9 113 1 AAGTTTTCAA 0.896883 -188 ACCATTCAAAGAATTTTCCATAGTCCCCTC 9 256 1 GAATTTTCCA 0.785363 -45 GGAGTTCAGGGAGTTTTCAAACCCCGAAGA 12 149 1 GAGTTTTCAA 0.772787 -152 CTGAGCCTCTAAGTTATCCAATATTTCTAC 12 204 0 AAGTTATCCA 0.946822 -97 GTTTTTGATTAAGTTTTTCCAATTCCTTCT 13 150 0 AAGTTTTTCC 0.919414 -151 ********** Masking position 5 Map Score: 24.0633 Number of sites scoring better than the average of aligned sites = 432 Number in coding regions = 404 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 2 CATTGATTTTCAAGCTTTTCCCGAAAAACT 2 215 0 CAAGCTTTTC 0.884674 -86 ATCAACCTCCTTAAAACACCAT 3 128 0 CAACCTCCTT 0.951905 -12 CTTATGTTACCAAGCCTTTTGCTCACTACA 4 92 0 CAAGCCTTTT 0.791656 -209 ACTTTAAACACATGCTCATTCCTTATGTTA 4 113 0 CATGCTCATT 0.835125 -188 TTATAAATTCCATGCTCTGTCCAATAAATC 4 242 0 CATGCTCTGT 0.821258 -59 TATCCGATATCATGCTCCTTTGGGACTTGG 5 12 1 CATGCTCCTT 0.970363 -52 ATTTGTGCTTCAAGCTCTTTTATCTTCTTC 9 51 1 CAAGCTCTTT 0.985624 -250 TTCTCCAGAGCAAGCTTCTTCGCAATCAGG 9 78 1 CAAGCTTCTT 0.967431 -223 CTTAAGTTTTCAAGCTCCTCTTCCAGTTTT 9 120 1 CAAGCTCCTC 0.96962 -181 GAACTTCATACAACCTCTTTTAAGCGAAAA 9 153 0 CAACCTCTTT 0.936502 -148 ATTTCTTCCACTAGCTCCATGAGCTCAGTT 12 26 0 CTAGCTCCAT 0.723891 -275 ACCAAACGATCTAGCTTTTTCTGTAGCT 13 9 0 CTAGCTTTTT 0.832194 -292 ********** Masking position 5 Map Score: 12.5067 Number of sites scoring better than the average of aligned sites = 327 Number in coding regions = 301 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 3 CTCCCATACCTTAAATTTTAGTGT 1 188 1 TTAAATTTTT 0.816446 -14 TCAAAACCCATTGATTTTCAAGCTTTTCCCGAAA 2 219 0 TTGATTTTCT 0.748836 -82 CTTTTTATTATTAAATTTTATAATGGTGTTTTAA 3 106 1 TTAAATTTTT 0.816446 -34 TTGAATTTATAGGTATTCAGTTAA 4 287 0 TTGAATTTAT 0.817223 -14 CCCCTCTCCATTAAATTTTAAAATTTTTTGT 9 280 1 TTAAATTTTT 0.816446 -21 TACTTGTATTTTATAGTAAATCCGCGG 10 94 0 TTGTATTTTT 0.940589 -17 CCTTCTCCTTTTATATTTATTCCTT 11 11 1 TTATATTTAT 0.61881 -15 TTAACCCTCATTGTTTTTTTCACTCTTTTAAGTA 12 242 1 TTGTTTTTTT 0.947362 -59 ACTCATTATTTTGTTTTTGTCTTTATAGTAAGTC 13 44 1 TTGTTTTTGT 0.772175 -257 TATTTAGCTTTTGTTGTTTACTTTATATACTGGC 13 83 1 TTGTTGTTTT 0.828521 -218 CAGCTCTGTTTTATTGTTTTTGATTAAGTTTTTC 13 161 0 TTATTGTTTT 0.606784 -140 AACAGAGCTGTTGTATTTTCCCCTTTGTTTTTTA 13 185 1 TTGTATTTTT 0.940589 -116 ATTTTCCCCTTTGTTTTTTAGCCTTTCTTCACCA 13 199 1 TTGTTTTTTT 0.947362 -102 AATTTGATTTTACAGGTATTTCTTCAG 14 4 1 TTGATTTTAT 0.835602 -63 AAAACACTTTTTGATTTTTGTTATAAATCTCTAG 15 73 1 TTGATTTTTT 0.940589 -41 ********* * Masking position 7 Map Score: 10.6421 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 161 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 ATCGTCCTTGTTATAATCGGACTCCTTCTCCTGTTCTTTGAA 1 117 0 TTATAGTTCT 0.969365 -85 CGTAAGTAGTTTATACACCGTGGTTTTCTTTTGAGTAGATTG 2 54 0 TTATAGTTTT 0.977993 -247 CTTAAGTTATTTATAATTCGTAAGTTTTAAGTCACCGGATTG 2 148 0 TTATAGTTAT 0.888443 -153 ATAAGAATAATAATAGGCGGCTATTTTCATGTGACAAATTTC 2 251 0 TAATAGTTTT 0.84955 -50 TTTTAGTCTGGGGGATAAATTTTTCAAACGGA 7 14 0 TTTTAGTATT 0.692229 -22 AACGGGATAATTATAAGTAGTATTTTTTCCCTCTGAGTCCTT 9 207 1 TTATAGTTCT 0.969365 -94 AGATACGCGGTTTTAGCCCGCGGATTTACTATAAAATACAAG 10 77 1 TTTTAGTTTT 0.946528 -34 GTTTTTGTCTTTATAGTAAGTCTTATTTATTTAGCTTTTGTT 13 56 1 TTATAGTTTT 0.977993 -245 GTTGTTTACTTTATATACTGGCTTATTGATGTAAGGCAAATG 13 95 1 TTATAGTTTT 0.977993 -206 AATTCCTTCTTTATATCGTGCAACATTTGCCTTACATCAATA 13 118 0 TTATAGTTCT 0.969365 -183 TTTCTTCACCATTTAAGTTGGCTCGTTTTTCTTGACACAATT 13 222 1 ATTTAGTTTT 0.692229 -79 ***** * ** * * Masking position 5 Map Score: 8.57805 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 12 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 TCTCCTGTTCTTTGAAAAACTTCCCCTGGG 1 103 0 TTTGAAAAAC 0.753838 -99 ATCAACCTCCTTAAAACACCATTATAAAA 3 121 0 CTTAAAACAC 0.976149 -19 ATTATCCCAACTTTAAACACATGCTCATTC 4 122 0 CTTTAAACAC 0.8947 -179 GATAAAAGAGCTTGAAGCACAAATTGAGAC 9 45 0 CTTGAAGCAC 0.904109 -256 TCTCTTTTCGCTTAAAAGAGGTTGTATGAA 9 149 1 CTTAAAAGAG 0.809979 -152 CAAGATTCATTTTAAAAAACTGCTTACACA 10 24 1 TTTAAAAAAC 0.695306 -87 TTTAAAAATACTTAAAAGAGTGAAAAAAAC 12 254 0 CTTAAAAGAG 0.809979 -47 GCTCGTTTTTCTTGACACAATTTTAAAACA 13 242 1 CTTGACACAA 0.75063 -59 TTGACACAATTTTAAAACACTGGTATATCT 13 253 1 TTTAAAACAC 0.92958 -48 ATTTCTTCAGCTTGACACAGATCAGAAATA 14 28 1 CTTGACACAG 0.922835 -39 TTTAAATTAACTTGACACACTTCTTCAAAA 15 46 0 CTTGACACAC 0.968459 -68 GTCAAGTTAATTTAAAACACTTTTTGATTT 15 60 1 TTTAAAACAC 0.92958 -54 ********** Masking position 5 Map Score: 8.67973 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 176 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 AAATCGCGGTAGTTATGGGAATGTAAACAA 1 26 1 AGTTATGGGA 0.958283 -176 CTAAAATTTAAGGTATGGGAGAGATAGGGA 1 179 0 AGGTATGGGA 0.939237 -23 GAAAATAATCAGGTCAGGGAGATCATAACA 4 212 1 AGGTCAGGGA 0.975206 -89 ATCATAACAGATTTATTGGACAGAGCATGG 4 233 1 ATTTATTGGA 0.778261 -68 TAAAGGTTTAATTTCAGGGAGGAAGAGA 6 26 1 ATTTCAGGGA 0.958067 -18 AAATTTTAAAATTTAATGGAGAGGGGACTA 9 276 0 ATTTAATGGA 0.849183 -25 AACGAAACTGAGCTCATGGAGCTAGTGGAA 12 21 1 AGCTCATGGA 0.893096 -280 ATGGTTAGGGAGTTCAGGGAGTTTTCAAAC 12 141 1 AGTTCAGGGA 0.983179 -160 ********** Masking position 1 Map Score: 5.70422 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 215 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 GTTGTTTACATTCCCATAACTACCGCGATT 1 27 0 TTCCCATAAC 0.818401 -175 TTCCCTATCTCTCCCATACCTTAAATTTTA 1 178 1 CTCCCATACC 0.976721 -24 CCACAGCCATCTCTCATACCACCTGACCTC 4 164 0 CTCTCATACC 0.91965 -137 CTGTTATGATCTCCCTGACCTGATTATTTT 4 213 0 CTCCCTGACC 0.985196 -88 TCTCTTCCTCCCTGAAATTAAACCTTT 6 27 0 CTCCCTGAAA 0.877273 -17 TAACGCTCAGAACGAAACTGAGC 12 4 1 CGCTCAGAAC 0.857618 -297 GGTTTGAAAACTCCCTGAACTCCCTAACCA 12 142 0 CTCCCTGAAC 0.982178 -159 ********** Masking position 8 Map Score: 4.05015 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 195 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 TAATCGGACTCCTTCTCCTGTTCTTTGAAA 1 116 0 CCTTCTCCTG 0.982409 -86 CCATACACCACTTTCTCCTTCCAC 4 5 0 CTTTCTCCTT 0.8952 -296 GTTATGATCTCCCTGACCTGATTATTTTCT 4 211 0 CCCTGACCTG 0.822868 -90 TCTTTTATCTTCTTCTCCAGAGCAAGCTTC 9 66 1 TCTTCTCCAG 0.899257 -235 TTCCATAGTCCCCTCTCCATTAAATTTTAA 9 271 1 CCCTCTCCAT 0.966714 -30 CCTTCTCCTTTTATATTTAT 11 1 1 CCTTCTCCTT 0.977467 -25 CGTTTCCAAACTTTATCCTGTAAGTTGCGT 12 73 0 CTTTATCCTG 0.715533 -228 TCCCTGAACTCCCTAACCATAATCGCGAGG 12 131 0 CCCTAACCAT 0.777012 -170 TTTTAGCCTTTCTTCACCATTTAAGTTGGC 13 214 1 TCTTCACCAT 0.784341 -87 ********** Masking position 4 Map Score: 3.71946 Number of sites scoring better than the average of aligned sites = 613 Number in coding regions = 571 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 9 ACCGTGGTTTTCTTTTGAGTAGATTGTGTC 2 50 0 TCTTTTGAGT 0.974073 -251 TAAGGATTTATCTCTTGAGGAATTACTAAA 9 15 0 TCTCTTGAGG 0.962013 -286 TCATACAACCTCTTTTAAGCGAAAAGAGAA 9 148 0 TCTTTTAAGC 0.822989 -153 TTAAAATGAATCTTGTGAGGTCACTCAA 10 9 0 TCTTGTGAGG 0.924008 -102 TTTTTTTCACTCTTTTAAGTATTTTTAAAA 12 255 1 TCTTTTAAGT 0.911471 -46 TTTGTTTTTGTCTTTATAGTAAGTCTTATT 13 53 1 TCTTTATAGT 0.681988 -248 TAAAATAAATTCTTTTGAGTG 14 56 1 TCTTTTGAGT 0.974073 -11 TTGTTATAAATCTCTAGAGGTAAAATCTTT 15 90 1 TCTCTAGAGG 0.886437 -24 ********** Masking position 8 Map Score: 5.209 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 68 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 GGTGATATATACATAAAGAGGGACAACTTC 1 57 0 ACATAAAGAG 0.690965 -145 AAAGCTTGAAAATCAATGGGTTTTGAAATT 2 227 1 AATCAATGGG 0.889338 -74 GTTAAAAATCACCCAGAGGGTTATAAATTC 4 262 0 ACCCAGAGGG 0.870604 -39 TAATGAAAGGACTCAGAGGGAAAAAATACT 9 225 0 ACTCAGAGGG 0.88895 -76 AGAGTGAAAAAAACAATGAGGGTTAAGCGG 12 238 0 AAACAATGAG 0.917854 -63 AAAAGATAACAAACATAGGGGAGGTGAATT 12 281 1 AAACATAGGG 0.869662 -20 GACAAAAACAAAATAATGAGTGCTTCACCA 13 35 0 AAATAATGAG 0.68752 -266 AAAGGCTAAAAAACAAAGGGGAAAATACAA 13 195 0 AAACAAAGGG 0.964344 -106 TATATAGTATAAACAGTGAG 16 1 0 AAACAGTGAG 0.916332 -26 ********** Masking position 5 Map Score: 2.28658 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 160 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 GAACAACTTATGAGTTTTCCACAATTCTCC 2 13 0 TGAGTTTTCC 0.663673 -288 GGAAAACTCATAAGTTGTTCATATAACGAC 2 23 1 TAAGTTGTTC 0.903365 -278 GAAAACTTCTTAAGTTATTCATACTACGAA 2 117 1 TAAGTTATTC 0.774126 -184 ATAAATAACTTAAGTTGTTCATGTGGAAAA 2 176 1 TAAGTTGTTC 0.903365 -125 GATGGCTTATTGAGAGCTTCTTTTCAACCT 4 40 1 TGAGAGCTTC 0.808916 -261 TTAGTCTCAATTTGTGCTTCAAGCTCTTTT 9 42 1 TTTGTGCTTC 0.354544 -259 TTTTTCCCTCTGAGTCCTTTCATTAAACCA 9 230 1 TGAGTCCTTT 0.494591 -71 ATTGGTTCTTTAATTTCTTCCACTAGCTCC 12 38 0 TAATTTCTTC 0.687708 -263 AGGTTGCTAAAGAGTTCTTCCTTCAAAGGT 12 104 0 AGAGTTCTTC 0.871117 -197 GCTGCATTTTTGAGTTCTTCGGGGTTTGAA 12 164 0 TGAGTTCTTC 0.983147 -137 AACAAAATAATGAGTGCTTCACCAAACGAT 13 29 0 TGAGTGCTTC 0.973374 -272 TGTTTTTGATTAAGTTTTTCCAATTCCTTC 13 151 0 TAAGTTTTTC 0.858026 -150 ********** Masking position 8 Map Score: 4.58591 Number of sites scoring better than the average of aligned sites = 574 Number in coding regions = 552 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 TCAAAGAACAGGAGAAGGAGTCCGATTATAACAAGGA 1 118 1 GGAGAGCCGT 0.905601 -84 TAATTCGTAAGTTTTAAGTCACCGGATTGTTTCGTAG 2 140 0 GTAGTCCCGT 0.995135 -161 TCGCCGGTTCGAGTCCCGTCGCCCGCTCCAAATTTTT 3 25 0 GTCGTCCCCT 0.974928 -115 TGCTTCCCAAGCAGGAGGTCGCCGGTTCGAGTCCCGT 3 43 0 GGAGTCCCGT 0.994135 -97 TTACACAGGCGGCTTCTGTCCCCGTATCATAGATACG 10 47 1 GTCGTCCCGT 0.994138 -64 ATAACTTAGAGGCTCAGGTCTCCGCTTAACCCTCATT 12 217 1 GTAGTCCCGT 0.995135 -84 * * * *** *** * Masking position 17 Map Score: 1.85098 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 13 AAGAAGCTCTCAATAAGCCATCTGTTGCCA 4 32 0 CAATAAGCCA 0.983857 -269 TGAGTCCTTTCATTAAACCATTCAAAGAAT 9 240 1 CATTAAACCA 0.891558 -61 ATTAAAGAACCAATAAGAAACGCAACTTAC 12 54 1 CAATAAGAAA 0.838274 -247 TGCCTTACATCAATAAGCCAGTATATAAAG 13 103 0 CAATAAGCCA 0.983857 -198 TAATCAAAAACAATAAAACAGAGCTGTTGT 13 169 1 CAATAAAACA 0.923108 -132 ********** Masking position 5 Map Score: 1.08784 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 4 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 14 CCCATAACTACCGCGATTTTGCTCAGCCTC 1 15 0 CCGCGATTTT 0.973997 -187 AGTTTATACACCGTGGTTTTCTTTTGAGTA 2 59 0 CCGTGGTTTT 0.973997 -242 TATCATAGATACGCGGTTTTAGCCCGCGGA 10 71 1 ACGCGGTTTT 0.973997 -40 CGGTTTTAGCCCGCGGATTTACTATAAAAT 10 84 1 CCGCGGATTT 0.983305 -27 ********** Masking position 8 Map Score: 0.942025 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 15 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 15 TAGGGAAAGTATTGATTTTCTTCGGTATCG 1 155 0 ATTGATTTTC 0.885 -47 TTCAAAACCCATTGATTTTCAAGCTTTTCC 2 224 0 ATTGATTTTC 0.885 -77 ACTATTTATTTTGTATTAATAAG 2 288 0 ATTTATTTTG 0.912158 -13 ATTTATAGGTATTCAGTTAAAAATCACCCA 4 277 0 ATTCAGTTAA 0.502411 -24 ACCTCACAAGATTCATTTTAAAAAACTGCT 10 18 1 ATTCATTTTA 0.912158 -93 AGTAAGTCTTATTTATTTAGCTTTTGTTGT 13 70 1 ATTTATTTAG 0.79173 -231 ACTCAAAAGAATTTATTTTATTTCTGATCT 14 46 0 ATTTATTTTA 0.868488 -21 GTGTAATTTTATTCATTTTGAAGAAGTGTG 15 31 1 ATTCATTTTG 0.942291 -83 ********** Masking position 5 Map Score: 0.636264 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 29 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604