AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -intrC_aquae_opreg_300.orf -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 glnB 196 nitrogen regulatory PII protein #2 folK 300 folate biosynthesis 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase #3 rpsO 58 ribosomal protein S15 #4 aldH2_ntrC3 413 aldH2: aldehyde dehydrogenase, ntrC3: transcriptional regulator (NtrC family) #5 aq_291 28 hypothetical protein #6 pcnB1 300 poly A polymerase #7 aq_1111 216 hypothetical protein #8 icd 113 isocitrate dehydrogenase #9 aq_1515 25 putative protein #10 aq_1516 58 putative protein #11 pycA 23 pyruvate carboxylase c-terminal domain #12 aq_1525 40 putative protein #13 aq_1526 50 hypothetical protein #14 aq_1527 70 hypothetical protein #15 ntrC2 209 transcriptional regulator (NtrC family) Motif number 1 TTTTTACCTCCTTTTTATTGTTGGAATT 1 5 1 TCCTCCTTAT 0.973884 -192 GCTGATTTAGTACCTTTGTTCAATTGTAAACATG 1 74 1 TCCTTTGTAT 0.890862 -123 AAAATTTCCATACCTTTGTAAAAGCGTATTCTGA 1 129 1 TCCTTTGTAG 0.937192 -68 CTTCCTTCCTCCTTGTAAGTTATTATGCA 1 178 0 TCCTCCTTAG 0.985542 -19 TCCGAACTTGTCCCTCTTTACTAGATGGGGATAT 2 22 1 TCCTCTTTAG 0.979711 -279 CTTCCCATATACCTCCGTCTTTTCTTAGAATTG 3 36 0 TCCTCCGTTT 0.880421 -23 AAAGCATTCCTACCTCCATAAGTTTTAAATTTAA 4 17 0 TCCTCCATTT 0.713291 -397 GTTCAATCCATGCCCTTTTAACAGGGTGTTCTTC 4 272 0 TCCCTTTTAG 0.733838 -142 CACTTACTATTTCCTCTTTTGAAGGGTTCGGATT 4 374 0 TCCTCTTTAG 0.979711 -40 AACTTGAGTATACCTTTATAAAATTTCCATCCTT 6 122 1 TCCTTTATAT 0.733915 -179 AGTGGATCTAGGCCTTTGTCTTATAGCACCTGCC 7 96 0 GCCTTTGTAT 0.775344 -121 TTATGACCTCCTTGTTAGGGAATAA 9 8 0 GCCTCCTTAG 0.966467 -18 CTATATTACCTCCTTTAAAGTTT 11 4 0 TCCTCCTTAG 0.985542 -20 GCTTTCCTTTTTCCCTTCTTTTTCTTT 12 4 1 TCCTTTTTTT 0.749314 -37 ACCAGACCTCCTTCAAAGGCTCTCATAA 14 53 0 GCCTCCTTAG 0.966467 -18 * ******* ** Masking position 9 Map Score: 19.0236 Number of sites scoring better than the average of aligned sites = 379 Number in coding regions = 338 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 2 ATGAACTTACCAAAGCTAAAAATTGGAAGG 2 180 0 CAAAGCTAAA 0.727476 -121 TCAGGTGCAATAAAGGAAAGTTCAAGT 2 284 1 TAAAGGAAAG 0.937002 -17 TTTTAAAAGTAAACGGAAAAATGTACGAAG 4 48 1 AAACGGAAAA 0.808103 -366 ATGTACGAAGTAAATGTAAGTCCTGATACG 4 68 1 TAAATGTAAG 0.496291 -346 AGGGTGAAGGTAAAGGAAAAGGAACCCCAA 7 15 0 TAAAGGAAAA 0.902611 -202 CCGTGGGAAAAATAGGAAAGGTAGACATCT 7 68 0 AATAGGAAAG 0.820134 -149 GCAGGAGAGTAAAAGCAAAGTAAAAAAAGC 7 156 1 AAAAGCAAAG 0.975541 -61 GCAAAGTAAAAAAAGCTAAGATTAACCCTA 7 170 1 AAAAGCTAAG 0.957892 -47 ATTTATAACAAAAATCAAAAAGTGTTTTAA 8 34 1 AAAATCAAAA 0.742704 -80 AAAGAAGGGAAAAAGGAAAGC 12 2 0 AAAAGGAAAG 0.978871 -39 TAAAAATTTTAAAAGAAAAAGAAGGGAAAA 12 19 0 AAAAGAAAAA 0.763241 -22 TAGGCTTTGTAAAAGCAAAAGAGCGCAGGA 15 102 0 AAAAGCAAAA 0.96132 -108 TTAAACAGTGAAAAGGTAAGGCGCTTCGTT 15 154 1 AAAAGGTAAG 0.963535 -56 AAAGTTCTTGAAAAGCTAAATTAAAAATAA 15 190 1 AAAAGCTAAA 0.934103 -20 ********** Masking position 8 Map Score: 15.4759 Number of sites scoring better than the average of aligned sites = 850 Number in coding regions = 779 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 3 GAATTTAAATAAACATTTTAGCTCAACTCAA 1 34 1 AAAATTTTAG 0.795179 -163 GTTCAATTGTAAACATGTTAACAAAATTGTA 1 91 1 AAAATGTTAA 0.782165 -106 ATATCTTAAAACAAATTTTAAGATAGAATTA 2 227 1 ACAATTTTAA 0.795178 -74 TTGAGCAAATAAATATTATAAGGAATTT 3 8 0 AAAATTATAA 0.940221 -51 TCCTACCTCCATAAGTTTTAAATTTAATTGA 4 13 0 ATAGTTTTAA 0.657937 -401 AAAAACATTCTAAGTTAAAATTA 5 16 0 AAAATTCTAA 0.851875 -13 TCAAGGATGGAAATTTTATAAAGGTATACTC 6 127 0 AAATTTATAA 0.688778 -174 GGCCTTATTTAAACATTATAATCATAAAACA 6 277 1 AAAATTATAA 0.940222 -24 GCGGGAAATATTATAAAACTTAGATG 7 201 0 AAAATTATAA 0.940221 -16 ACTTAAAGATTTTACCTCTAGAGAT 8 5 1 AAAATTTTAC 0.795179 -109 AAAAATCAAAAAGTGTTTTAAATTAACTTGA 8 43 1 AAGGTTTTAA 0.725017 -71 TTTAAAAATTTTAAAAGAAAAAGA 12 27 0 AAAATTTTAA 0.960959 -14 GCGAAGTTGCAAAGGTTATAAACGAAACCTG 13 14 1 AAAGTTATAA 0.920315 -37 ACTTTGTGAAAAAGGTTTTAAACAGTGAAAA 15 137 1 AAAGTTTTAA 0.947574 -73 *** ******* Masking position 10 Map Score: 12.023 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 109 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 4 CCTATCGGTCTTCCGAACTTGTCCCTCTT 2 9 1 TCTCCGAACT 0.968626 -292 GAGGAGAGGCGTATCAGGACTTACATTTACT 4 76 0 GTTCAGGACT 0.905126 -338 TTCCCTTACCGCATCCGAACTTCGTCCCGGT 4 134 0 GCTCCGAACT 0.987498 -280 CGGGCTGGCAGTATCCGCACTGGGGAACCTG 4 308 0 GTTCCGCACT 0.965082 -106 CTTCCACTATTTGTCCGGGCTGGCAGTATCC 4 323 0 TTTCCGGGCT 0.969113 -91 CCTGCTGAGGGCTTTCGGGCTCCTTGGCAAT 6 247 0 GCTTCGGGCT 0.95316 -54 CTCGTGTCTTTCTTTCGGACTCTTTTTGTTT 10 18 1 TCTTCGGACT 0.906046 -41 CTCAGGTCTCCGAGCTTATAAAACAA 10 43 0 GTTCCGAGCT 0.980621 -16 TTTACAAAGCCTATCCGAACTTTGTGAAAAA 15 119 1 CTTCCGAACT 0.933632 -91 ** ******** Masking position 4 Map Score: 8.20207 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 85 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 ATGTTTATTTAAATTCCAACAATAAAAAGGAGG 1 17 0 AATTCAACAT 0.874286 -180 AAACACGAAAAATTTCCATACCTTTGTAAAAGC 1 121 1 AATTCATACT 0.91774 -76 TGGGTATATCTACTTCAATCCTTCCAATTTTTA 2 161 1 TATTCATCCT 0.947102 -140 GGGGAACCTGAAGTTCAATCCATGCCCTTTTAA 4 285 0 AATTCATCCT 0.990088 -129 TTCTGAGTAAAAATCCGAACCCTTCAAAAGAGG 4 363 1 AATCCAACCT 0.942992 -51 CAACTTATTAAACTTCTAACCTTCACGAAATGA 6 58 1 AATTCAACCT 0.984191 -243 ACCTTTATAAAATTTCCATCCTTGATTTTCAAT 6 133 1 AATTCATCCT 0.990089 -168 TCCATCCTTGATTTTCAATCCCTTTAACCCTAT 6 147 1 ATTTCATCCT 0.947102 -154 ** *** **** * Masking position 8 Map Score: 7.49625 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 26 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 TTTTTACCTCCTTTTTATTGTT 1 2 1 TTTACCTCCT 0.951898 -195 CTTCCTTCCTCCTTGTAAGTTAT 1 184 0 TCTTCCTCCT 0.910242 -13 GAAACGACACCAATAGCACCTTCTCTTGCAA 2 76 1 CATAGCACCT 0.902008 -225 GAACTTTCCTTTATTGCACCTGATAAAGCTT 2 276 0 TATTGCACCT 0.803358 -25 TTAAAAGCATTCCTACCTCCATAAGTTTTAA 4 23 0 TCTACCTCCA 0.825603 -391 GACTGGGTACTGACAGCTCCTCACAGGATTT 4 196 0 TACAGCTCCT 0.893978 -218 GCTGAGGGCTTTCGGGCTCCTTGGCAATTGA 6 244 0 TCGGGCTCCT 0.888534 -57 GGCCTTTGTCTTATAGCACCTGCCGTGGGAA 7 89 0 TATAGCACCT 0.942744 -128 TTATGACCTCCTTGTTAGGGAA 9 14 0 TTGACCTCCT 0.948736 -12 GAAAGAAAGACACGAGCACCTCC 10 3 0 CCGAGCACCT 0.917238 -56 CTATATTACCTCCTTTAAAGTTT 11 10 0 TTTACCTCCT 0.951898 -14 ACCAGACCTCCTTCAAAGGCTC 14 59 0 CAGACCTCCT 0.943174 -12 * ********* Masking position 7 Map Score: 8.08109 Number of sites scoring better than the average of aligned sites = 348 Number in coding regions = 282 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 7 TTTCAGAATACGCTTTTACAAAGGTATGGA 1 135 0 CGCTTTTACA 0.833409 -62 CCGAACTTGTCCCTCTTTACTAGATGGGGA 2 23 1 CCCTCTTTAC 0.790139 -278 CTTCCCATATACCTCCGTCTTTT 3 46 0 CCCATATACC 0.893464 -13 CTCAACCTCTCCCTTATTACCCAGAGGAGA 4 100 0 CCCTTATTAC 0.919193 -314 GTGCAGGAACCGCATATTCCCTTACCGCAT 4 151 0 CGCATATTCC 0.712748 -263 TCAATCCATGCCCTTTTAACAGGGTGTTCT 4 274 0 CCCTTTTAAC 0.940938 -140 GATTTTCAATCCCTTTAACCCTATTGCATC 6 156 1 CCCTTTAACC 0.893152 -145 GACCTATCCACCCTTATTCAATTGCCAAGG 6 227 1 CCCTTATTCA 0.943247 -74 TCTACTTCTGCCCTTTTACCCGAGCAGGAG 7 133 1 CCCTTTTACC 0.986333 -84 GCTTTCCTTTTTCCCTTCTTTTTC 12 5 1 TCCTTTTTCC 0.886727 -36 TCCGTCAAGCCCCTTTTTCATTCCTGCGCT 15 81 1 CCCTTTTTCA 0.969738 -129 ACTGTTTAAAACCTTTTTCACAAAGTTCGG 15 133 0 ACCTTTTTCA 0.716306 -77 ********** Masking position 3 Map Score: 11.5498 Number of sites scoring better than the average of aligned sites = 742 Number in coding regions = 690 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 8 ATTCCGCCTTGAATTATGGGTATATCTACTT 2 145 1 GAATTATGGT 0.978271 -156 GGCATGGATTGAACTTCAGGTTCCCCAGTGC 4 292 1 GAACTTCGGT 0.973414 -122 CAAGTTTGCAGAACTTCAGGTTAGCGGAAAT 6 97 0 GAACTTCGGT 0.973414 -204 TCAATATTCGGAATTATAGGTCTTATACTAC 15 43 1 GAATTATGGT 0.978271 -167 GGGCTTGACGGAATTATCGGTAGTATAAGAC 15 62 0 GAATTATGGT 0.978271 -148 ******* *** Masking position 5 Map Score: 2.55251 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 = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 9 TCATACTAACCTCTCCTTAGAATATCTTAA 2 206 1 CTCTCCTTAG 0.962677 -95 ATACCTCCGTCTTTTCTTAGAATTGAGCAA 3 31 0 CTTTTCTTAG 0.684294 -28 CCTGATACGCCTCTCCTCTGGGTAATAAGG 4 89 1 CTCTCCTCTG 0.923739 -325 GAAGCCTATGCACTTCTGAGTAAAAATCCG 4 350 1 CACTTCTGAG 0.58051 -64 GATCCACTCCCTCTACTTCTGCCCTTTTAC 7 122 1 CTCTACTTCT 0.675232 -95 TTTGCTTTTACTCTCCTGCTCGGGTAAAAG 7 145 0 CTCTCCTGCT 0.94805 -72 CGCTCTCCTCCGAAAGTAGAGT 8 102 0 CTCTCCTCCG 0.977975 -12 GTGCTCGTGTCTTTCTTTCGGACTCTTTTT 10 15 1 CTTTCTTTCG 0.711004 -44 GCTTTCCTTTTTCCCTTCTTT 12 2 1 CTTTCCTTTT 0.684294 -39 GCCCCTTTTTCATTCCTGCGCTCTTTTGCT 15 89 1 CATTCCTGCG 0.884696 -121 ********** Masking position 4 Map Score: 2.70016 Number of sites scoring better than the average of aligned sites = 675 Number in coding regions = 636 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 10 GGAATTTAAATAAACATTTTAGCTCAACTC 1 33 1 TAAACATTTT 0.959098 -164 TGTTCAATTGTAAACATGTTAACAAAATTG 1 90 1 TAAACATGTT 0.94086 -107 ATTGAGCAAATAAATATTATAAGGAATTT 3 10 0 TAAATATTAT 0.663223 -49 GGGCCTTATTTAAACATTATAATCATAAAA 6 276 1 TAAACATTAT 0.911394 -25 ACTTAAAGATTTTACCTCTAGAG 8 4 1 TAAAGATTTT 0.870103 -110 TTTAAAAATTTTAAAAGAAAAA 12 29 0 TAAAAATTTT 0.818935 -12 AAATTTAATTTAAACAGGTTTCGTTTATAA 13 29 0 TAAACAGGTT 0.830405 -22 ********** Masking position 6 Map Score: 1.14574 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 9 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 11 CTTTACTAGATGGGGATATCTGTAGCCTGTT 2 37 1 TGGGATATCT 0.987262 -264 TGGTATATCCTGGGAAAAGCTCGCCGGAAGC 2 108 0 TGGGAAAGCT 0.895981 -193 GGAATGGGTGTTGGTATATCCTGGGAAAAGC 2 119 0 TTGGATATCC 0.905446 -182 CCTTGAATTATGGGTATATCTACTTCAATCC 2 151 1 TGGGATATCT 0.987261 -150 TAACCTCTCCTTAGAATATCTTAAAACAAAT 2 212 1 TTAGATATCT 0.898471 -89 TCTGCAAACTTGAGTATACCTTTATAAAATT 6 116 1 TGAGATACCT 0.921858 -185 **** ****** Masking position 6 Map Score: 0.0962732 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 44 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 12 AATTTCCGTGCCAATTTCAGAATACGCTTT 1 149 0 CCAATTTCAG 0.88033 -48 GTAAAGAGGGACAAGTTCGGAAGACCGATA 2 13 0 ACAAGTTCGG 0.956079 -288 CTTACCGGGACGAAGTTCGGATGCGGTAAG 4 131 1 CGAAGTTCGG 0.989734 -283 CTTCAGGTTCCCCAGTGCGGATACTGCCAG 4 305 1 CCCAGTGCGG 0.94952 -109 GTTATGTGTCCGAAGGTCAGGGTGAAGGTA 7 33 0 CGAAGGTCAG 0.922718 -184 ACCTTTTTCACAAAGTTCGGATAGGCTTTG 15 123 0 CAAAGTTCGG 0.972526 -87 ********** Masking position 4 Map Score: 0.257802 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 81 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 13 CTTAAAATTTGTTTTAAGATATTCTAAGGA 2 219 0 GTTTTAAGAT 0.777685 -82 AGTCCAGTAAGCTTTATCAGGTGCAATAAA 2 268 1 GCTTTATCAG 0.8224 -33 GGTAGGAATGCTTTTAAAAGTAAACGGAAA 4 37 1 CTTTTAAAAG 0.488677 -377 TTCCTGCACCGTTTTAATAGACGGAAATCC 4 172 1 GTTTTAATAG 0.835935 -242 AATCCATGCCCTTTTAACAGGGTGTTCTTC 4 272 0 CTTTTAACAG 0.748952 -142 AAAAAATAACGTTTTATCAGCAACTTATTA 6 38 1 GTTTTATCAG 0.960827 -263 AAGGTTAGAAGTTTAATAAGTTGCTGATAA 6 51 0 GTTTAATAAG 0.761123 -250 ATATGTTTTATGATTATAATGTTT 6 287 0 GTTTTATGAT 0.80698 -14 TACCATCTAAGTTTTATAATATTTCCCGC 7 198 1 GTTTTATAAT 0.860254 -19 GACTCTTTTTGTTTTATAAGCTCGGAGACC 10 35 1 GTTTTATAAG 0.95824 -24 TTTAAAAATTTTAAAAGAAAAAGAAGG 12 24 0 ATTTTAAAAG 0.463421 -17 ********** Masking position 6 Map Score: 5.53468 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 168 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 14 GAAATTAAGCTGATTTAGTACCTTTGTTCAAT 1 66 1 TGATTTATAC 0.770377 -131 TTGTAAGTTATTATGCAATTTCCGTGCCAATT 1 163 0 TTATGCATTC 0.864057 -34 ATTCCTTATAATATTTATTTGCTCAATTCTAA 3 13 1 ATATTTATTC 0.601544 -46 CAGGAACCGCATATTCCCTTACCGCATCCGAA 4 146 0 ATATTCCTTC 0.846492 -268 TCGATGGTTATTATTTCTTTTCATTCCGCTTC 4 230 0 TTATTTCTTC 0.890892 -184 AATGAAATCATGATGCAATAGGGTTAAAGGGA 6 165 0 TGATGCATAG 0.455094 -136 TATTGCATCATGATTTCATTTCATCACATCAT 6 177 1 TGATTTCTTC 0.884208 -124 CTATCCACCCTTATTCAATTGCCAAGGAGCCC 6 230 1 TTATTCATTC 0.943055 -71 GAGTGTAATTTTATTCATTTTGAAGAAGTGTG 8 74 0 TTATTCATTG 0.797837 -40 TTATTCCCTAACAAGGAGGTCA 9 1 1 TTATTCCTAC 0.929096 -25 AAACCGTTATTGATTCCGTAACATTTAAACCT 14 12 1 TGATTCCTAC 0.924554 -59 ******* ** * Masking position 3 Map Score: 1.91375 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 204 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 15 ********** No masking Map Score: 5.4955e-13 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