AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02020_aquae_reg_300.orf -o02020_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 glnB 196 nitrogen regulatory PII protein #2 folK 300 folate biosynthesis 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase #3 ntrC3 300 transcriptional regulator (NtrC family) #4 hksP4 161 histidine kinase sensor protein #5 hksP2_phoB 284 hksP2: histidine kinase sensor protein, phoB: transcriptional regulator (PhoB-like) #6 aq_1111 216 hypothetical protein #7 ntrC2 209 transcriptional regulator (NtrC family) Motif number 1 TCCAACAATAAAAAGGAGGTAAAAA 1 2 0 AAAGGGGAAA 0.851258 -195 GAATACGCTTTTACAAAGGTATGGAAATTTTTCG 1 126 0 TACAAGGAGG 0.66559 -71 AAGCGTATTCTGAAATTGGCACGGAAATTGCATA 1 150 1 TAAATGGAGG 0.922443 -47 ATAATAACTTACAAGGAGGAAGGAAG 1 181 1 AAAGGGGAGA 0.991409 -16 GTAAAGAGGGACAAGTTCGGAAGACCGATAGG 2 9 0 AAAGTCGAGA 0.854906 -292 TACCCATAATTCAAGGCGGAATGGGTGTTGGTAT 2 133 0 TAAGGGGAGG 0.979677 -168 TACCAAAGCTAAAAATTGGAAGGATTGAAGTAGA 2 169 0 AAAATGGAGA 0.966071 -132 GAACACCCTGTTAAAAGGGCATGGATTGAACTTC 3 13 0 TAAAAGGAGG 0.881151 -288 TACCCAGTCAAGGAAGCGGAATGAAAAGAAATAA 3 70 0 AGAAGGGAGA 0.905404 -231 AATTTAAAACTTATGGAGGTAGGAATGCTTTTAA 3 268 0 TATGGGGAGA 0.917858 -33 CAACGAACAAAAATGGAGGTAAGAGT 4 3 0 AATGGGGAGA 0.952445 -159 TTCAGTGTCCAGAAATTGGCACGAAAATTGCAAT 4 42 0 AAAATGGAGA 0.966071 -120 TTAAAAATTCTTACGGTGGAAAGAAATTTTTCCC 4 138 1 TACGGGGAGA 0.945308 -24 TAGGTTTTTGAAAAAGAGGAAGGTTGTAGCGGTT 5 69 0 AAAAGGGAGT 0.903033 -216 CTGCCGTGGGAAAAATAGGAAAGGTAGACATCTC 6 67 0 AAAATGGAGG 0.955194 -150 CGCAGGAATGAAAAAGGGGCTTGACGGAATTATC 7 75 0 AAAAGGGTGA 0.865913 -135 TTGTAAAAGCAAAAGAGCGCAGGAATGAAAAAGG 7 92 0 AAAGACGAGA 0.785998 -118 * **** ** * ** Masking position 9 Map Score: 19.7285 Number of sites scoring better than the average of aligned sites = 694 Number in coding regions = 623 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 2 ATTTTTCGTGTTTACAATTTTGTTAACATG 1 104 0 TTTACAATTT 0.699282 -93 ATAATTCTATCTTAAAATTTGTTTTAAGAT 2 229 0 CTTAAAATTT 0.756521 -72 ACTTGAACTTTCCTTTATTGCACCTGA 2 284 0 CTTTCCTTTA 0.796616 -17 CGTATCAGGACTTACATTTACTTCGTACAT 3 224 1 CTTACATTTA 0.879239 -77 ACATTTACTTCGTACATTTTTCCGTTTACT 3 237 1 CGTACATTTT 0.721625 -64 CTCCATAAGTTTTAAATTTAATTGATA 3 284 1 TTTAAATTTA 0.498084 -17 TTTCAAGTTCCTTAGAATTTCAGTGTCCAG 4 64 0 CTTAGAATTT 0.859246 -98 TTAACCGAAACTTAAAATTTGGGGTTTAAA 5 175 0 CTTAAAATTT 0.756521 -110 TACTAATATACTTAAATTTTCTATTAACAT 5 222 0 CTTAAATTTT 0.890752 -63 TTGGGGTTCCTTTTCCTTTACCTTCACCCT 6 15 1 TTTTCCTTTA 0.555745 -202 GCTTTTTTTACTTTGCTTTTACTCTCCTGC 6 156 0 CTTTGCTTTT 0.896026 -61 TAGGGTTAATCTTAGCTTTTTTTACTTTGC 6 170 0 CTTAGCTTTT 0.957652 -47 TCCTGCGCTCTTTTGCTTTTACAAAGCCTA 7 102 1 TTTTGCTTTT 0.733501 -108 AACGAAGCGCCTTACCTTTTCACTGTTTAA 7 154 0 CTTACCTTTT 0.964249 -56 TTATTTTTAATTTAGCTTTTCAAGAACTTT 7 190 0 TTTAGCTTTT 0.878383 -20 ********** Masking position 3 Map Score: 11.3412 Number of sites scoring better than the average of aligned sites = 974 Number in coding regions = 886 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 3 TAAATTCCAACAATAAAAAGGAGGTAAAAA 1 10 0 CATAAAAAGG 0.770659 -187 TTTCCATACCTTTGTAAAAGCGTATTCTGAA 1 133 1 TTGTAAAAGC 0.918514 -64 TTGGTATATCCTGGGAAAAGCTCGCCGGAAG 2 109 0 CGGGAAAAGC 0.968834 -192 CTTTATTGCACCTGATAAAGCTTACTGGACT 2 268 0 CTGATAAAGC 0.673385 -33 GAAGAACACCCTGTTAAAAGGGCATGGATTG 3 19 0 CGTTAAAAGG 0.910121 -282 TTTCCGTTTACTTTTAAAAGCATTCCTACCT 3 255 1 CTTTAAAAGC 0.915373 -46 GGGTGAAGGTAAAGGAAAAGGAACCCCAAGA 6 13 0 AAGGAAAAGG 0.809407 -204 CTCTCCTGCTCGGGTAAAAGGGCAGAAGTAG 6 134 0 CGGTAAAAGG 0.966315 -83 CCCGAGCAGGAGAGTAAAAGCAAAGTAAAAA 6 151 1 AAGTAAAAGC 0.796741 -66 AGAGCGCAGGAATGAAAAAGGGGCTTGACGG 7 82 0 ATGAAAAAGG 0.855344 -128 TCGGATAGGCTTTGTAAAAGCAAAAGAGCGC 7 106 0 TTGTAAAAGC 0.918514 -104 ATCCGAACTTTGTGAAAAAGGTTTTAAACAG 7 131 1 TTGAAAAAGG 0.885048 -79 AGGTTTTAAACAGTGAAAAGGTAAGGCGCTT 7 149 1 CGTGAAAAGG 0.91672 -61 CGAAGAAAGTTCTTGAAAAGCTAAATTAAAA 7 185 1 TTTGAAAAGC 0.812187 -25 * ********* Masking position 7 Map Score: 11.7543 Number of sites scoring better than the average of aligned sites = 814 Number in coding regions = 768 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 4 AATTGAACAAAGGTACTAAATCAGCTTAAT 1 69 0 AGGTACTAAA 0.780961 -128 TTGCAAGAGAAGGTGCTATTGGTGTCGTTT 2 77 0 AGGTGCTATT 0.837761 -224 AAGCTTTATCAGGTGCAATAAAGGAAAGTT 2 276 1 AGGTGCAATA 0.764312 -25 CTACCTCCATAAGTTTTAAATTTAATTGAT 3 280 1 AAGTTTTAAA 0.7302 -21 GAAAAGAATCAGGTGTCAAAAATGACACCT 4 90 1 AGGTGTCAAA 0.914909 -72 TTTGTCACTAAGGTGTCATTTTTGACACCT 4 100 0 AGGTGTCATT 0.706664 -62 TCCTTACTTAAGGTTTTAAACCCCAAATTT 5 161 1 AGGTTTTAAA 0.946143 -124 GGTTAAGGAAATGTTTTAAATTAATGTTAA 5 199 1 ATGTTTTAAA 0.605495 -86 TTCCCACGGCAGGTGCTATAAGACAAAGGC 6 89 1 AGGTGCTATA 0.958415 -128 CCTACCATCTAAGTTTTATAATATTTCCCG 6 196 1 AAGTTTTATA 0.7302 -21 TCGGAATTATAGGTCTTATACTACCGATAA 7 50 1 AGGTCTTATA 0.865292 -160 TTTGTGAAAAAGGTTTTAAACAGTGAAAAG 7 139 1 AGGTTTTAAA 0.946143 -71 ********** Masking position 8 Map Score: 7.99099 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 266 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 TCTAGTAAAGAGGGACAAGTTCGGAAGACCG 2 16 0 AGGGACAAGT 0.952703 -285 AAGATATTCTAAGGAGAGGTTAGTATGAACT 2 203 0 AAGGAGAGGT 0.988745 -98 CTGGGTAATAAGGGAGAGGTTGAGACTTACC 3 185 0 AGGGAGAGGT 0.996167 -116 TAAGAGGCAGAAAGAGAGGGTAATTAGTAGG 5 99 0 AAAGAGAGGT 0.931474 -186 TCCGAAGGTCAGGGTGAAGGTAAAGGAAAAG 6 24 0 AGGGTGAAGT 0.955901 -193 GCAGAAGTAGAGGGAGTGGATCTAGGCCTTT 6 113 0 AGGGAGTGGT 0.98465 -104 ********* * Masking position 1 Map Score: 4.57969 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 233 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 AAGTTATTATGCAATTTCCGTGCCAATTTC 1 161 0 GCAATTTCCG 0.962954 -36 AAAGCTTACTGGACTTTACGTTCAATAATT 2 253 0 GGACTTTACG 0.865832 -48 AACCATCGAGGGAATTCCCGAAGAACACCC 3 39 0 GGAATTCCCG 0.968948 -262 AGCTCCTCACAGGATTTCCGTCTATTAAAA 3 109 1 AGGATTTCCG 0.867272 -192 GGAGAGGTTGAGACTTACCGGGACGAAGTT 3 174 0 AGACTTACCG 0.894982 -127 TGTATTTATTGCAATTTTCGTGCCAATTTC 4 35 1 GCAATTTTCG 0.910399 -127 CAAGTTCCTTAGAATTTCAGTGTCCAGAAA 4 61 0 AGAATTTCAG 0.846332 -101 TTCAATATTCGGAATTATAGGTCTTATACT 7 42 1 GGAATTATAG 0.803715 -168 GGGGCTTGACGGAATTATCGGTAGTATAAG 7 64 0 GGAATTATCG 0.954115 -146 ********** Masking position 5 Map Score: 4.40227 Number of sites scoring better than the average of aligned sites = 398 Number in coding regions = 373 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 CGGTCTTCCGAACTTGTCCCTCTTTACTAG 2 16 1 AACTTGTCCC 0.844421 -285 CACCAATAGCACCTTCTCTTGCAACGCTTC 2 83 1 ACCTTCTCTT 0.858267 -218 CCCAGGATATACCAACACCCATTCCGCCTT 2 125 1 ACCAACACCC 0.782252 -176 AGTTCATACTAACCTCTCCTTAGAATATCT 2 203 1 AACCTCTCCT 0.963603 -98 GGTAAGTCTCAACCTCTCCCTTATTACCCA 3 185 1 AACCTCTCCC 0.98545 -116 CCTACTAATTACCCTCTCTTTCTGCCTCTT 5 99 1 ACCCTCTCTT 0.925963 -186 CTTTTCCTTTACCTTCACCCTGACCTTCGG 6 24 1 ACCTTCACCC 0.961233 -193 AAAGGCCTAGATCCACTCCCTCTACTTCTG 6 113 1 ATCCACTCCC 0.90752 -104 ********** Masking position 1 Map Score: 3.09056 Number of sites scoring better than the average of aligned sites = 435 Number in coding regions = 397 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 8 TTATCAGGTGCAATAAAGGAAAGTTCAAGT 2 281 1 CAATAAGGAA 0.928531 -20 TGTCAGTACCCAGTCAAGGAAGCGGAATGAA 3 79 0 CAGTAAGGAA 0.988233 -222 TCTATTAAAACGGTGCAGGAACCGCATATTC 3 129 1 CGGTCAGGAA 0.989116 -172 AGTTCGGATGCGGTAAGGGAATATGCGGTTC 3 147 0 CGGTAGGGAA 0.989116 -154 TTTTAAGTTTCGGTTAAGGAAATGTTTTAAA 5 188 1 CGGTAAGGAA 0.995993 -97 GTCAGGGTGAAGGTAAAGGAAAAGGAACCCC 6 17 0 AGGTAAGGAA 0.974651 -200 **** ****** Masking position 4 Map Score: 7.32907 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 = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 GCCTGTTCCACAGCGGAAACGACACCAATAG 2 61 1 CAGCGGAAAG 0.987144 -240 CCTTATTACCCAGAGGAGAGGCGTATCAGGA 3 203 1 CAGAGGAGAG 0.987144 -98 TATCGTTCTTCAGCTGAGAGGGATTGTTCAC 5 38 1 CAGCTGAGAG 0.989965 -247 GGACACATAACAGCCGAGATGTCTACCTTTC 6 52 1 CAGCCGAGAG 0.992826 -165 ********* * Masking position 7 Map Score: 1.25306 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 11 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 GTAAACACGAAAAATTTCCATACCTTTGTAA 1 119 1 AAATTTCCAT 0.928568 -78 ATTCTATCTTAAAATTTGTTTTAAGATATTC 2 225 0 AAATTTGTTT 0.828638 -76 CTTTACGTTCAATAATTCTATCTTAAAATTT 2 239 0 AAAATTCTAT 0.800425 -62 CTCGATGGTTATTATTTCTTTTCATTCCGCT 3 59 1 ATATTTCTTT 0.83929 -242 GGGAAAAATTTCTTTCCACCGTAAG 4 147 0 AAATTTCTTT 0.961753 -15 ATTAATTTAAAACATTTCCTTAACCGAAACT 5 193 0 AAATTTCCTT 0.944218 -92 TAATATACTTAAATTTTCTATTAACATTAAT 5 218 0 AATTTTCTAT 0.800425 -67 ** ******** Masking position 1 Map Score: 0.158727 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 85 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 11 ********** No masking Map Score: -9.35484e-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 CAGGCTACAGATATCCCCATCTAGTAAAGA 2 36 0 ATATCCCCAT 0.793271 -265 AATTATGGGTATATCTACTTCAATCCTTCC 2 156 1 ATATCTACTT 0.856308 -145 GTTCATACTAACCTCTCCTTAGAATATCTT 2 204 1 ACCTCTCCTT 0.936884 -97 CAGGAACCGCATATTCCCTTACCGCATCCG 3 144 1 ATATTCCCTT 0.893275 -157 ATCAGGACTTACATTTACTTCGTACATTTT 3 227 1 ACATTTACTT 0.856309 -74 AAATTACAACATCCGCTTTCTTTAAAAT 5 9 1 ACATCCGCTT 0.926254 -276 CCTTCATCTCACACCTCCTTACTTAAGGTT 5 146 1 ACACCTCCTT 0.936884 -139 TTAATTTAAAACATTTCCTTAACCGAAACT 5 193 0 ACATTTCCTT 0.956228 -92 ********** Masking position 1 Map Score: 2.36596 Number of sites scoring better than the average of aligned sites = 399 Number in coding regions = 371 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 13 ********** No masking Map Score: -9.35484e-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 14 ********** No masking Map Score: -9.35484e-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 15 CTGAAGTTCAATCCATGCCC 3 1 1 CTGAAGTTCA 0.861769 -300 GAGGGAATTCCCGAAGAACACCCTGTTAAA 3 32 0 CCGAAGAACA 0.956754 -269 CTTACCGCATCCGAACTTCGTCCCGGTAAG 3 161 1 CCGAACTTCG 0.96713 -140 TCCCTCTCAGCTGAAGAACGATATTTTAAA 5 31 0 CTGAAGAACG 0.928292 -254 TGTTATGTGTCCGAAGGTCAGGGTGAAGGT 6 34 0 CCGAAGGTCA 0.941136 -183 ACCTATAATTCCGAATATTGAAAGGATAAC 7 34 0 CCGAATATTG 0.793037 -176 CAAAGCCTATCCGAACTTTGTGAAAAAGGT 7 123 1 CCGAACTTTG 0.889216 -87 GCGCTTCGTTCCGAAGAAAGTTCTTGAAAA 7 174 1 CCGAAGAAAG 0.897497 -36 ********** Masking position 5 Map Score: 1.83701 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 200 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863