AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00860_aquae_reg_100.orf -o00860_aquae_100.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 ctaA 300 heme O oxygenase #2 nirB 120 nitrite reductase (NAD(P)H) large subunit #3 hemC 300 porphobilinogen deaminase #4 dcuP 157 uroporphyrinogen decarboxylase #5 gsa 24 glutamate-1-semialdehyde aminotransferase #6 glyQ 290 glycyl-tRNA synthetase alpha subunit #7 proA 30 gamma-glutamyl phosphate reductase #8 gltX 279 glutamyl-tRNA synthetase #9 cysG 161 siroheme synthase #10 hemA 38 glutamyl tRNA reductase (delta-aminolevulinate synthase) #11 ssf 300 Na(+):solute symporter (Ssf family) Motif number 1 TGGTGTTCATGCTCTCCTCCTTT 1 3 0 GCTCTCTCCT 0.774975 -298 TGAGTATAGCCTTCCTTTCCGCATTCTTTAC 1 152 1 CTTCCTTCCG 0.941363 -149 GCTCTCCTCCTTTTAATCTTT 1 290 0 GCTCTCTCCT 0.774975 -11 CTTTCACTCCTCCTGAGGAAA 2 110 0 CTTTCCTCCT 0.702596 -11 CGAACAAGACCCGCTTTTTCCAGTTCTCTCA 3 78 0 CCGCTTTTCC 0.722564 -223 AATTATAATTCCTTTGTTTCGTTTTTCATAC 3 225 0 CCTTTTTTCG 0.481591 -76 GTTTCCAGCGCCGCGCCTTCGACCGCTCGGC 3 277 0 CCGCGCTTCG 0.955633 -24 TCTGCCAGTTCCGCCACTCCGGCTTACCTAA 4 50 0 CCGCCCTCCG 0.99589 -108 GGGCGTGCGGGTTCGACTCCCGCCTCCGGCA 4 112 1 GTTCGCTCCC 0.737339 -46 ACGTGTTTATCCTTCGCACCCA 6 2 0 CCTTCCACCC 0.834911 -289 TGACCCAGTACCTGCCCTCCGGAGTACCTAT 6 133 0 CCTGCCTCCG 0.955631 -158 GCTTTGCGTGCTTCCGCTTCGTTTGGCACCC 6 224 0 CTTCCCTTCG 0.962196 -67 ATGGGTTGAACCTCCACTCCCTGTTTTTGTA 8 32 1 CCTCCCTCCC 0.993468 -248 TCTATTTCTTCCGCTTCACCGTCAATTTCAA 8 80 1 CCGCTCACCG 0.925209 -200 GTGAACTCCTCCGCGTTTTCCAGAGCCACTT 9 16 0 CCGCGTTTCC 0.718532 -146 AATCTCCAGAGCGCCTCTTCGTGAGGTAAAG 9 63 0 GCGCCCTTCG 0.95516 -99 ATCGCCTTTCCCTTCTCACCCTTAATCTTAT 9 100 0 CCTTCCACCC 0.834911 -62 ATGGCTTACTCCTCCACTCCGTATTTTTTAT 11 126 0 CCTCCCTCCG 0.996376 -175 ACGTAAAACTCTTCCGCTTCGGTCGCCCTGT 11 222 0 CTTCCCTTCG 0.962196 -79 TCAGCGGCTACTGCCATTCCGTTCCAGAAGG 11 272 0 CTGCCTTCCG 0.933992 -29 ***** ***** Masking position 10 Map Score: 28.5817 Number of sites scoring better than the average of aligned sites = 1362 Number in coding regions = 1258 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 2 AGTCAAGACAACCGAGGCGAGAACTAACGTCTTCAGGGGA 1 47 0 ACCGAAATCT 0.745352 -254 CAAAACTATAAGGGCTACTACAATTTTCTTCGCAGTACTG 1 114 0 AGCTAAATCT 0.804088 -187 TGAAAGTTATACGTATACGGGAGGTAACCT 2 1 0 AGCGGAGTCT 0.979201 -120 TATAGTTTAACAGAGCTCGGTAAAAGTCTTGAAGAAATAT 3 146 1 CGCGGAAACT 0.983039 -155 CCTCATGCGGATGCCCTCTGGAAAAAACTTCAGGAAGAAT 6 67 1 AGCTGAAACT 0.910924 -224 ACAGGTTTCACAGGACACGGGAATTCTCCTTGTTGAAATT 8 103 0 CGCGGAATCT 0.995227 -177 CCTCACGAAGAGGCGCTCTGGAGATTGCCTTTATAAGATT 9 68 1 AGCTGAGTCT 0.928143 -94 GATAAGTGCACAGCTTTCGGTAATTACCTTTGTTGTGGAG 11 52 1 CGCGGAATCT 0.995213 -249 CATTCCGTTCCAGAAGGCGGGAATTCTCATACCGGTACGT 11 249 0 CGCGGAATCT 0.995227 -52 TCATCCAGTCAGCGGCTACTGCCATTCCGTTCCAG 11 276 0 CGCGGTATCT 0.967014 -25 * * *** ** * * * Masking position 20 Map Score: 10.4131 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 84 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 3 TCAAAACTATAAGGGCTACTACAATTTTCT 1 125 0 AAGGGCTACT 0.717276 -176 AGAGGCTTGAACGTGCAAGGGAAACAAATC 1 230 1 ACGTGCAAGG 0.910107 -71 CACGCCCGTAAAGGGCACCGTCCCCTCAAG 4 89 0 AAGGGCACCG 0.980574 -69 CAACCCATAGAAGGGCAAATATTCACCGA 8 10 0 AAGGGCAAAT 0.942967 -270 TAAACATAAGGAGGGCACAGGTTTCACAGG 8 129 0 GAGGGCACAG 0.8873 -151 CCCTGAAGAAAAGGTCAAGGAGCCTGTACT 8 191 0 AAGGTCAAGG 0.89296 -89 GGAGGAGTTCACGGGAAAGGTTTACAAGCT 9 35 1 ACGGGAAAGG 0.942613 -127 TAAGGGTGAGAAGGGAAAGGCGATTGTGGA 9 107 1 AAGGGAAAGG 0.963271 -55 GGACGCACTCACGGGAAAAGTTGTAAAATT 9 134 1 ACGGGAAAAG 0.91194 -28 ACTACTGGATAAGTGCACAGCTTTCGGTAA 11 45 1 AAGTGCACAG 0.865494 -256 TCGCCATAAAAAGGGCAACTATTCCAAAGA 11 180 0 AAGGGCAACT 0.952304 -121 ********** Masking position 3 Map Score: 9.58361 Number of sites scoring better than the average of aligned sites = 767 Number in coding regions = 723 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 4 GCTCTCCTCCTTTTAATCTTTCTT 1 287 0 TCCTCCTTTT 0.72921 -14 TGTTAAACTATATTCCACTCTCGGCGGAAT 3 128 0 TATTCCACTC 0.908606 -173 GTCTGCCAGTTCCGCCACTCCGGCTTACCT 4 52 0 TCCGCCACTC 0.950313 -106 TGCTTTGCGTGCTTCCGCTTCGTTTGGCAC 6 226 0 GCTTCCGCTT 0.930384 -65 TATGGGTTGAACCTCCACTCCCTGTTTTTG 8 31 1 ACCTCCACTC 0.935306 -249 CCTTTCTATTTCTTCCGCTTCACCGTCAAT 8 76 1 TCTTCCGCTT 0.982818 -204 TCCCGTGAACTCCTCCGCGTTTTCCAGAGC 9 21 0 TCCTCCGCGT 0.950058 -141 AGGTTAATTATATTCCTCTCTGATAAAATA 10 17 0 TATTCCTCTC 0.841981 -22 CATGGCTTACTCCTCCACTCCGTATTTTTT 11 128 0 TCCTCCACTC 0.989214 -173 TACGTAAAACTCTTCCGCTTCGGTCGCCCT 11 224 0 TCTTCCGCTT 0.982818 -77 ********** Masking position 5 Map Score: 8.92582 Number of sites scoring better than the average of aligned sites = 450 Number in coding regions = 420 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 AACTAACGTCTTCAGGGGACTACTTTTGAG 1 36 0 TTCAGGGGAC 0.949752 -265 ACTTAAAACATCCAGAAAACAGGGAGTACT 1 194 1 TCCAGAAAAC 0.659612 -107 CTTTTAACATTTCAACGGACTCTTTTATGG 1 260 0 TTCAACGGAC 0.669611 -41 CTCTTTGAAGTTGAGAGAACCTCT 3 5 0 TTGAGAGAAC 0.872123 -296 TTCTCTCAACTTCAAAGAGCTATACCCGGA 3 16 1 TTCAAAGAGC 0.847808 -285 TACCAAACAATTGAGAGAACTGGAAAAAGC 3 67 1 TTGAGAGAAC 0.872123 -234 GGCCGAGCGGTCGAAGGCGCGGCGCTGGAA 3 276 1 TCGAAGGCGC 0.645276 -25 ACGCGCCGTCTTGAGGGGACGGTGCCCTTT 4 80 1 TTGAGGGGAC 0.914342 -78 TGAAGTTTTTTCCAGAGGGCATCCGCATGA 6 69 0 TCCAGAGGGC 0.988097 -222 ACATAGGTACTCCGGAGGGCAGGTACTGGG 6 131 1 TCCGGAGGGC 0.923719 -160 GCGGAAGAAATAGAAAGGGCTATAGATTTT 8 64 0 TAGAAAGGGC 0.636091 -216 GGGCACAGGTTTCACAGGACACGGGAATTC 8 117 0 TTCACAGGAC 0.829007 -163 AAAGGCAATCTCCAGAGCGCCTCTTCGTGA 9 70 0 TCCAGAGCGC 0.956892 -92 GCCATTCCGTTCCAGAAGGCGGGAATTCTC 11 261 0 TCCAGAAGGC 0.906029 -40 ********** Masking position 1 Map Score: 10.3196 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 387 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 CTCTTTAAAAAGTACTCCCTGTTTTCTGGATGTTTTAA 1 196 0 AGATCTGCTG 0.912968 -105 ATTTCTTCAAGACTTTTACCGAGCTCTGTTAAACTATA 3 146 0 GATTCCGCTG 0.981325 -155 TTTCAACAAGGAGAATTCCCGTGTCCTGTGAAACCTGT 8 105 1 GAATCCGCTG 0.996062 -175 CTACTATATTCGGATTCCCCGCTCACTACTGGATAAGT 11 21 1 CGATCCGCTA 0.939565 -280 CCACAACAAAGGTAATTACCGAAAGCTGTGCACTTATC 11 52 0 GGATCCGCTG 0.998091 -249 GTACCGGTATGAGAATTCCCGCCTTCTGGAACGGAATG 11 251 1 GAATCCGCTG 0.996004 -50 GGAACGGAATGGCAGTAGCCGCTGACTGGATGA 11 278 1 GGATCCGCTG 0.998091 -23 ** * * *** *** Masking position 6 Map Score: 6.45694 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 7 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 7 TCTGTAAGGACTTACAAAACATAACTACCCG 2 51 1 CTTACAAAAA 0.949193 -70 TTGCAAAAAACGTGCCAAAAAGTTCCGGGTA 2 76 0 CGTGCCAAAA 0.969502 -45 TGAGGAAACTCTTGCAAAAAACGTGCCAAAA 2 87 0 CTTGCAAAAA 0.96708 -34 AAAAAAAATGCTTACCAAACAATTGAGAGAA 3 55 1 CTTACCAAAA 0.982235 -246 TACTTGCCAAATAAAGGGCTTTT 4 3 1 CTTGCCAAAA 0.988629 -155 GCCACTCCGGCTTACCTAAGATTTTTATTTT 4 38 0 CTTACCTAAA 0.931695 -120 ********* * Masking position 8 Map Score: 4.94531 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 5 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 GGTGATTCCGGGTATAGCTCTTTGAAGTTG 3 22 0 GGTATAGCTC 0.727619 -279 GGTTATAGACGGTAAGCTTGCATTCGTGGG 6 195 1 GGTAAGCTTG 0.734542 -96 GCCTGTACTTTGTATGGTTTGTAAAAACTT 8 170 0 TGTATGGTTT 0.539325 -110 TCATGAACATGGTAAGGCTTCAATTAATAT 8 222 0 GGTAAGGCTT 0.932865 -58 GGAGTTCACGGGAAAGGTTTACAAGCTTTA 9 38 1 GGAAAGGTTT 0.946399 -124 CTCTTCGTGAGGTAAAGCTTGTAAACCTTT 9 50 0 GGTAAAGCTT 0.879602 -112 CGCACTCACGGGAAAAGTTGTAAAATTCTT 9 137 1 GGAAAAGTTG 0.936725 -25 AGTAAGCCATGGAATGGTTGGGTTACGTAA 11 147 1 GGAATGGTTG 0.965703 -154 AATAGTCTTTGGAATAGTTGCCCTTTTTAT 11 175 1 GGAATAGTTG 0.936725 -126 CGACCGAAGCGGAAGAGTTTTACGTACCGG 11 228 1 GGAAGAGTTT 0.772435 -73 CTTCTGGAACGGAATGGCAGTAGCCGCTGA 11 273 1 GGAATGGCAG 0.769893 -28 ********** Masking position 4 Map Score: 5.34419 Number of sites scoring better than the average of aligned sites = 627 Number in coding regions = 583 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 9 AGGAAGGCTATACTCAAAACTATAAGGGCT 1 138 0 TACTCAAAAC 0.949131 -163 CGTTTACAACTACTTAAAACATCCAGAAAA 1 183 1 TACTTAAAAC 0.957457 -118 ACCTCCCGTATACGTATAACTTTCATTTTA 2 16 1 TACGTATAAC 0.897231 -105 CAGAACTTCATACTTAAAGCCGTATTCTTC 6 100 0 TACTTAAAGC 0.949131 -191 GAAGCGGAAGCACGCAAAGCAATAGAGGAG 6 235 1 CACGCAAAGC 0.898924 -56 CTCATACCGGTACGTAAAACTCTTCCGCTT 11 234 0 TACGTAAAAC 0.972519 -67 ********** Masking position 6 Map Score: 2.58051 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 57 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 TGTTTTAAGTAGTTGTAAACGGTAAAGAAT 1 174 0 AGTTGTAAAC 0.952057 -127 TCCTTACAGAGGTTGTAAAATGAAAGTTAT 2 31 0 GGTTGTAAAA 0.965965 -90 ACTTTGACGTTGTAGTAAACATAAGGAGGG 8 144 0 TGTAGTAAAC 0.805056 -136 ACTTTGTATGGTTTGTAAAAACTTTGACGT 8 164 0 GTTTGTAAAA 0.812356 -116 GTGAGGTAAAGCTTGTAAACCTTTCCCGTG 9 44 0 GCTTGTAAAC 0.911023 -118 TCACGGGAAAAGTTGTAAAATTCTTCAAGA 9 142 1 AGTTGTAAAA 0.926711 -20 TCGGTCGCCCTGTTGTAAATAGCTATCGCC 11 205 0 TGTTGTAAAT 0.833446 -96 ********** Masking position 7 Map Score: 1.8678 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 117 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 11 GGAGAGCATGAACACCAACCTCAAAAGTAG 1 17 1 AACACCAACC 0.851151 -284 ATATACCTTTCACCCCAACGGTGCATGGCG 3 190 0 CACCCCAACG 0.978087 -111 GCGGGAGTCGAACCCGCACGCCCGTAAAGG 4 105 0 AACCCGCACG 0.973358 -53 CTTCGTTTGGCACCCCCACGAATGCAAGCT 6 209 0 CACCCCCACG 0.992487 -82 TATAAAGTTAAACCCCCTCCTCTATTGCTT 6 251 0 AACCCCCTCC 0.964269 -40 CTATGGGTTGAACCTCCACTCCCTGTTTTT 8 30 1 AACCTCCACT 0.861193 -250 ********** Masking position 2 Map Score: 1.40365 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 52 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 12 TACTGCTCATAACCTTTTTAAATTATAACG 1 89 0 AACCTTTTTA 0.943161 -212 TGCACGTTCAAGCCTCTTTAAAAAGTACTC 1 217 0 AGCCTCTTTA 0.95844 -84 TTCATTTTACAACCTCTGTAAGGACTTACA 2 37 1 AACCTCTGTA 0.976403 -84 TTTAACTTTATACCTTTTTATAATCTTTAA 6 269 1 TACCTTTTTA 0.775017 -22 TGTGAGTAACATCTGTATATATTAAAA 7 8 1 AACATCTGTA 0.842881 -23 AGTTTATTTTAACCTTTGAATTACAATAAA 8 257 0 AACCTTTGAA 0.806205 -23 CGTTTTCCAGAGCCACTTTAGCG 9 4 0 AGCCACTTTA 0.827223 -158 ********** Masking position 10 Map Score: 0.885318 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 223 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 13 AAAGTAGTCCCCTGAAGACGTTAGTTCTCG 1 40 1 CCTGAAGACG 0.979295 -261 CTTAAAACATCCAGAAAACAGGGAGTACTT 1 195 1 CCAGAAAACA 0.737548 -106 TTTCACTCCTCCTGAGGAAACTCTTGCAAA 2 100 0 CCTGAGGAAA 0.961144 -21 CGGTAAAAGTCTTGAAGAAATATTCAACGC 3 163 1 CTTGAAGAAA 0.822452 -138 GGCACCGTCCCCTCAAGACGGCGCGTCTGC 4 76 0 CCTCAAGACG 0.834154 -82 CATTGAGAAACCAGAAGAATAACGTGTTTA 6 24 0 CCAGAAGAAT 0.848536 -267 AGGGCATCCGCATGAGGACATGTAGGACAC 6 54 0 CATGAGGACA 0.826821 -237 GAAGTTTTTTCCAGAGGGCATCCGCATGAG 6 68 0 CCAGAGGGCA 0.947404 -223 CATAGGTACTCCGGAGGGCAGGTACTGGGT 6 132 1 CCGGAGGGCA 0.890283 -159 ATTAATATACCCTGAAGAAAAGGTCAAGGA 8 200 0 CCTGAAGAAA 0.967813 -80 TCTTGAAGAATTTTACAACTT 9 151 0 CTTGAAGAAT 0.594127 -11 CCATTCCGTTCCAGAAGGCGGGAATTCTCA 11 260 0 CCAGAAGGCG 0.939722 -41 ********** Masking position 5 Map Score: 9.11687 Number of sites scoring better than the average of aligned sites = 717 Number in coding regions = 684 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 14 ACATAACTACCCGGAACTTTTTGGCACGTT 2 69 1 CCGGAACTTT 0.904151 -52 AGAGCTATACCCGGAATCACCCAAAAAAAA 3 31 1 CCGGAATCAC 0.946498 -270 AAAAGTCTATCCGGAAATTCCGCCGAGAGT 3 112 1 CCGGAAATTC 0.918371 -189 ACTCCCGCCTCCGGCACCACAAAATCCCTT 4 127 1 CCGGCACCAC 0.972362 -31 GTACCTATGTCCAGAACTTCATACTTAAAG 6 111 0 CCAGAACTTC 0.952013 -180 TCCGCGTTTTCCAGAGCCACTTTAGCG 9 8 0 CCAGAGCCAC 0.905646 -154 AAAGCGGGAACTACTATATTCGGA 11 5 1 CGGGAACTAC 0.947929 -296 ********** Masking position 4 Map Score: 1.73361 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 202 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 15 CCTTTTAATCTTTCTTTTAACATTTCAACG 1 273 0 TTTCTTTTAA 0.871406 -28 ACCTAAGATTTTTATTTTATAAAAAAGCCC 4 26 0 TTTATTTTAT 0.820553 -132 TTGATTATTTTAAGGGATTTTGT 4 145 0 ATTATTTTAA 0.849254 -13 ACTTGTTATTTTAAATTTAACTTA 5 11 0 GTTATTTTAA 0.893057 -14 CATGATAAGTTTTATTGTAATTCAAAGGTT 8 247 1 TTTATTGTAA 0.871406 -33 GAGAGTTTATTTTAACCTTTGAATT 8 265 0 TTTATTTTAA 0.948716 -15 ********** Masking position 5 Map Score: 0.68437 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 13 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665