AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -intrC_aquae_opreg_100.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 TAAATTCCAACAATAAAAAGGAGGTAAAAA 1 5 0 CATAGGAGGA 0.980656 -192 AACATGTTTACAATTGAACAAAGGTACTAAATCAGC 1 74 0 CATAAAAGGA 0.93998 -123 TTTCAGAATACGCTTTTACAAAGGTATGGAAATTTT 1 129 0 CCTAAAAGGA 0.961807 -68 ATTGCATAATAACTTACAAGGAGGAAGGAAG 1 176 1 ACTAGGAGGA 0.982698 -21 AGATATCCCCATCTAGTAAAGAGGGACAAGTTCGGA 2 22 0 ACTAAGAGGA 0.977689 -279 TATCTGTAGCCTGTTCCACAGCGGAAACGACACCAA 2 53 1 CGTAAGCGGA 0.796965 -248 AGATATACCCATAATTCAAGGCGGAATGGGTGTTGG 2 136 0 AAAAGGCGGA 0.712877 -165 AAGCTTTATCAGGTGCAATAAAGGAAAGTTCAAGT 2 276 1 AGTAAAAGGA 0.824305 -25 CTCAATTCTAAGAAAAGACGGAGGTATATGGGAAG 3 34 1 AAAAGGAGGA 0.914076 -25 AATTAAATTTAAAACTTATGGAGGTAGGAATGCTTT 4 15 1 AAAAGGAGGA 0.914076 -399 CCGAAGAACACCCTGTTAAAAGGGCATGGATTGAAC 4 270 1 CCTAAAGGGA 0.761545 -144 AAAATCCGAACCCTTCAAAAGAGGAAATAGTAAGTG 4 372 1 CCTAAGAGGA 0.98435 -42 TCAAGGATGGAAATTTTATAAAGGTATACTCAAGTT 6 122 0 AATAAAAGGA 0.916046 -179 ACGGCAGGTGCTATAAGACAAAGGCCTAGATCCACT 7 94 1 CATAAAAGGC 0.841874 -123 TTATTCCCTAACAAGGAGGTCATAA 9 6 1 CCTAGGAGGC 0.965173 -20 AAACTTTAAAGGAGGTAATATAG 11 2 1 ACTAGGAGGA 0.982698 -22 TAAAAGAAAAAGAAGGGAAAAAGGAAAGC 12 4 0 AAAAAAAGGA 0.766702 -37 AATTATGAGAGCCTTTGAAGGAGGTCTGGT 14 51 1 GCTAGGAGGC 0.801063 -20 * ** * ***** * Masking position 8 Map Score: 20.7252 Number of sites scoring better than the average of aligned sites = 397 Number in coding regions = 353 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 2 ATGAACTTACCAAAGCTAAAAATTGGAAGG 2 180 0 CAAAGCTAAA 0.747667 -121 TCAGGTGCAATAAAGGAAAGTTCAAGT 2 284 1 TAAAGGAAAG 0.958067 -17 GGAATGCTTTTAAAAGTAAACGGAAAAATG 4 41 1 TAAAAGTAAA 0.685916 -373 ATGTACGAAGTAAATGTAAGTCCTGATACG 4 68 1 TAAATGTAAG 0.682693 -346 AGGGTGAAGGTAAAGGAAAAGGAACCCCAA 7 15 0 TAAAGGAAAA 0.941808 -202 CCGTGGGAAAAATAGGAAAGGTAGACATCT 7 68 0 AATAGGAAAG 0.733652 -149 GCAGGAGAGTAAAAGCAAAGTAAAAAAAGC 7 156 1 AAAAGCAAAG 0.963524 -61 GCAAAGTAAAAAAAGCTAAGATTAACCCTA 7 170 1 AAAAGCTAAG 0.947099 -47 ATTTATAACAAAAATCAAAAAGTGTTTTAA 8 34 1 AAAATCAAAA 0.72221 -80 TCCGAGCTTATAAAACAAAAAGAGTCCGAA 10 31 0 TAAAACAAAA 0.738817 -28 AAAGAAGGGAAAAAGGAAAGC 12 2 0 AAAAGGAAAG 0.967834 -39 TTAAAAATTTTAAAAGAAAAAGAAGGGAAA 12 20 0 TAAAAGAAAA 0.763154 -21 TAGGCTTTGTAAAAGCAAAAGAGCGCAGGA 15 102 0 AAAAGCAAAA 0.949269 -108 TTAAACAGTGAAAAGGTAAGGCGCTTCGTT 15 154 1 AAAAGGTAAG 0.953256 -56 AAAGTTCTTGAAAAGCTAAATTAAAAATAA 15 190 1 AAAAGCTAAA 0.926912 -20 ********** Masking position 4 Map Score: 15.7059 Number of sites scoring better than the average of aligned sites = 1092 Number in coding regions = 1013 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 3 GAATTTAAATAAACATTTTAGCTCAACTCAA 1 34 1 AAAATTTTAG 0.814772 -163 GTTCAATTGTAAACATGTTAACAAAATTGTA 1 91 1 AAAATGTTAA 0.802694 -106 ATATCTTAAAACAAATTTTAAGATAGAATTA 2 227 1 ACAATTTTAA 0.814771 -74 TTGAGCAAATAAATATTATAAGGAATTT 3 8 0 AAAATTATAA 0.946867 -51 TCCTACCTCCATAAGTTTTAAATTTAATTGA 4 13 0 ATAGTTTTAA 0.685465 -401 AAAAACATTCTAAGTTAAAATTA 5 16 0 AAAATTCTAA 0.866952 -13 TCAAGGATGGAAATTTTATAAAGGTATACTC 6 127 0 AAATTTATAA 0.714899 -174 GGCCTTATTTAAACATTATAATCATAAAACA 6 277 1 AAAATTATAA 0.946867 -24 GCGGGAAATATTATAAAACTTAGATG 7 201 0 AAAATTATAA 0.946867 -16 ACTTAAAGATTTTACCTCTAGAGAT 8 5 1 AAAATTTTAC 0.814772 -109 AAAAATCAAAAAGTGTTTTAAATTAACTTGA 8 43 1 AAGGTTTTAA 0.749205 -71 TTTAAAAATTTTAAAAGAAAAAGA 12 27 0 AAAATTTTAA 0.965384 -14 GCGAAGTTGCAAAGGTTATAAACGAAACCTG 13 14 1 AAAGTTATAA 0.929006 -37 ACTTTGTGAAAAAGGTTTTAAACAGTGAAAA 15 137 1 AAAGTTTTAA 0.953442 -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 ACACGAAAAATTTCCATACCTTTGTAAAAGC 1 123 1 TTTCCAACCT 0.8471 -74 CCTATCGGTCTTCCGAACTTGTCCCTCTTT 2 10 1 CTTCCGACTT 0.967362 -291 GGTATATCTACTTCAATCCTTCCAATTTTTA 2 163 1 CTTCAACCTT 0.893195 -138 AGGAGAGGCGTATCAGGACTTACATTTACTT 4 75 0 TATCAGACTT 0.839849 -339 TCCCTTACCGCATCCGAACTTCGTCCCGGTA 4 133 0 CATCCGACTT 0.955614 -281 GGGCTGGCAGTATCCGCACTGGGGAACCTGA 4 307 0 TATCCGACTG 0.761371 -107 ACTTATTAAACTTCTAACCTTCACGAAATGA 6 60 1 CTTCTACCTT 0.853722 -241 CTTTATAAAATTTCCATCCTTGATTTTCAAT 6 135 1 TTTCCACCTT 0.962386 -166 CATCCTTGATTTTCAATCCCTTTAACCCTAT 6 149 1 TTTCAACCCT 0.714449 -152 CACTAAGACCTATCCACCCTTATTCAATTGC 6 221 1 TATCCACCTT 0.948943 -80 ACTCCCTCTACTTCTGCCCTTTTACCCGAGC 7 127 1 CTTCTGCCTT 0.9033 -90 TTACAAAGCCTATCCGAACTTTGTGAAAAAG 15 120 1 TATCCGACTT 0.948943 -90 ****** **** Masking position 3 Map Score: 9.80487 Number of sites scoring better than the average of aligned sites = 459 Number in coding regions = 424 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 5 AACAATAAAAAGGAGGTAAAAA 1 3 0 AGGAGGTAAA 0.842068 -194 ATAACTTACAAGGAGGAAGGAAG 1 184 1 AGGAGGAAGG 0.957043 -13 CCATAATTCAAGGCGGAATGGGTGTTGGTA 2 134 0 AGGCGGAATG 0.905751 -167 TAAGAAAAGACGGAGGTATATGGGAAG 3 42 1 CGGAGGTATA 0.739853 -17 TTAAAACTTATGGAGGTAGGAATGCTTTTA 4 23 1 TGGAGGTAGG 0.704175 -391 CCTTATTACCCAGAGGAGAGGCGTATCAGG 4 89 0 CAGAGGAGAG 0.77232 -325 CCAGTCAAGGAAGCGGAATGAAAAGAAATA 4 221 1 AAGCGGAATG 0.635342 -193 AACCCTTCAAAAGAGGAAATAGTAAGTGTC 4 380 1 AAGAGGAAAT 0.645909 -34 CTTTTACCCGAGCAGGAGAGTAAAAGCAAA 7 145 1 AGCAGGAGAG 0.820716 -72 ACTCTACTTTCGGAGGAGAGCG 8 102 1 CGGAGGAGAG 0.949265 -12 TTCCCTAACAAGGAGGTCATAA 9 14 1 AGGAGGTCAT 0.74569 -12 AAACTTTAAAGGAGGTAATATAG 11 10 1 AGGAGGTAAT 0.884259 -14 GAGCCTTTGAAGGAGGTCTGGT 14 59 1 AGGAGGTCTG 0.906089 -12 AGCAAAAGAGCGCAGGAATGAAAAAGGGGC 15 89 0 CGCAGGAATG 0.8137 -121 ********** Masking position 5 Map Score: 6.87752 Number of sites scoring better than the average of aligned sites = 1256 Number in coding regions = 1090 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 6 CTTTACTAGATGGGGATATCTGTAGCCTGTT 2 37 1 TGGGGAATCT 0.755104 -264 AGTATCCGCACTGGGGAACCTGAAGTTCAAT 4 299 0 CTGGGGACCT 0.837248 -115 TTTTGAAGGGTTCGGATTTTTACTCAGAAGT 4 361 0 TTCGGATTTT 0.865863 -53 GCTGAGGGCTTTCGGGCTCCTTGGCAATTGA 6 244 0 TTCGGGTCCT 0.975296 -57 ACTCTTGGGGTTCCTTTTCCTTTAC 7 5 1 TTGGGGTCCT 0.945992 -212 CACCCTGACCTTCGGACACATAACAGCCGAG 7 39 1 TTCGGAACAT 0.936726 -178 GTGTCTTTCTTTCGGACTCTTTTTGTTTTAT 10 21 1 TTCGGATCTT 0.937988 -38 GTTTTATAAGCTCGGAGACCTGAG 10 45 1 CTCGGAACCT 0.942146 -14 TTACGTGATTTGCGGAGTTATCCTTTCAATA 15 18 1 TGCGGATTAT 0.79908 -192 CCTTTCAATATTCGGAATTATAGGTCTTATA 15 39 1 TTCGGATTAT 0.902434 -171 ****** **** Masking position 11 Map Score: 3.52774 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 323 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 CTGATTTAGTACCTTTGTTCAATTGTAAACA 1 75 1 ACCTTTTTCA 0.919676 -122 AGACCTATCCACCCTTATTCAATTGCCAAGG 6 226 1 ACCCTTTTCA 0.986669 -75 TTAATTTAAAACACTTTTTGATTTTTGTTAT 8 38 0 ACACTTTTGA 0.946756 -76 TTAACTTGACACACTTCTTCAAAATGAATAA 8 65 1 ACACTTTTCA 0.966589 -49 TAAACCGTTATTGATTCCGTAACA 14 4 1 ACCGTTTTGA 0.950483 -67 TTCCGTCAAGCCCCTTTTTCATTCCTGCGCT 15 80 1 CCCCTTTTCA 0.951592 -130 CACTGTTTAAAACCTTTTTCACAAAGTTCGG 15 133 0 AACCTTTTCA 0.944221 -77 CGTTCCGAAGAAAGTTCTTGAAAAGCTAAAT 15 180 1 AAAGTTTTGA 0.631834 -30 ****** **** Masking position 11 Map Score: 5.20062 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 63 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 8 TCTAGTAAAGAGGGACAAGTTCGGAAGACCG 2 16 0 AGGGACAAGT 0.952322 -285 TGGTATATCCTGGGAAAAGCTCGCCGGAAGC 2 108 0 TGGGAAAAGT 0.859202 -193 AAGATATTCTAAGGAGAGGTTAGTATGAACT 2 203 0 AAGGAGAGGT 0.92569 -98 CTGGGTAATAAGGGAGAGGTTGAGACTTACC 4 106 1 AGGGAGAGGT 0.991115 -308 CCCTGTTAAAAGGGCATGGATTGAACTTCAG 4 280 1 AGGGCATGGT 0.858839 -134 TCCGAAGGTCAGGGTGAAGGTAAAGGAAAAG 7 24 0 AGGGTGAAGT 0.935901 -193 GCAGAAGTAGAGGGAGTGGATCTAGGCCTTT 7 113 0 AGGGAGTGGT 0.976098 -104 GGTTTTAAACAGTGAAAAGGTAAGGCGCTTC 15 150 1 AGTGAAAAGT 0.791779 -60 ********* * Masking position 11 Map Score: 2.95212 Number of sites scoring better than the average of aligned sites = 443 Number in coding regions = 408 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 9 AGGGACAAGTTCGGAAGACCGATAGG 2 7 0 TCGGAAGACC 0.833713 -294 CGAGGGAATTCCCGAAGAACACCCTGTTAA 4 259 1 CCCGAAGAAC 0.940795 -155 TGCCAAGGAGCCCGAAAGCCCTCAGCAGGG 6 249 1 CCCGAAAGCC 0.944915 -52 CTGTTATGTGTCCGAAGGTCAGGGTGAAGG 7 35 0 TCCGAAGGTC 0.978027 -182 CGCTCTCCTCCGAAAGTAGAGTGTAATT 8 96 0 TCCGAAAGTA 0.916451 -18 ACAAAAAGAGTCCGAAAGAAAGACACGAGC 10 17 0 TCCGAAAGAA 0.916451 -42 AAAGGATAACTCCGCAAATCACGTAAAGAA 15 14 0 TCCGCAAATC 0.824532 -196 GGCGCTTCGTTCCGAAGAAAGTTCTTGAAA 15 173 1 TCCGAAGAAA 0.916451 -37 ********** Masking position 6 Map Score: 1.95114 Number of sites scoring better than the average of aligned sites = 340 Number in coding regions = 319 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 10 GAGTTGAGCTAAAATGTTTATTTAAATTCC 1 33 0 AAAATGTTTA 0.957261 -164 CAATTTTGTTAACATGTTTACAATTGAACA 1 90 0 AACATGTTTA 0.938216 -107 AAATTCCTTATAATATTTATTTGCTCAAT 3 10 1 ATAATATTTA 0.65276 -49 TTTTATGATTATAATGTTTAAATAAGGCCC 6 276 0 ATAATGTTTA 0.907561 -25 CTCTAGAGGTAAAATCTTTAAGT 8 4 0 AAAATCTTTA 0.864774 -110 TTTTTCTTTTAAAATTTTTAAA 12 29 1 AAAATTTTTA 0.811951 -12 TTATAAACGAAACCTGTTTAAATTAAATTT 13 29 1 AACCTGTTTA 0.823745 -22 ********** Masking position 1 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 ********** 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 Motif number 12 ********** 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 Motif number 13 ********** 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