AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -imodE_pyro_opreg_300.orf -g0.419 -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 = 0.419 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 PH0114 40 316aa long hypothetical molybdenum cofactor biosynthesis protein #2 PH0115 298 296aa long hypothetical protein #3 PH0154 55 248aa long hypothetical transport system protein #4 PH0184 54 149aa long hypothetical molybdopterinconverting factor, subunit #5 PH0514 300 352aa long hypothetical protein #6 PH0521 154 226aa long hypothetical protein #7 PH0522 53 248aa long hypothetical protein #8 PH0523 71 173aa long hypothetical molybdenum cofactor biosynthesis protein #9 PH1359 300 639aa long hypothetical protein #10 PH1811 84 159aa long hypothetical molybdenum cofactor biosynthesis protein Motif number 1 AAGCCTTTGAAATAGCATCCCTTGACCCCTTTGCAATTTC 2 13 1 ATACTTGACT 0.984597 -286 CTGATCCTTCTCAACTTCTCCTTCAACTCTGCAACCCCAA 2 87 1 TAACTTCACT 0.831676 -212 AAGTTGAAGGATTTTCTCCGCTTCACTTTTCTTGGCTTTT 2 209 0 ATTCTTCATT 0.953145 -90 AAAAACATTCTGTTAAGTAACTTCACTTATCCG 3 4 0 TTTCTTCAAT 0.75439 -52 AATGTTTTTAAGTTAACAATCTTGAGGATTA 3 35 1 ATTCTTGATT 0.962206 -21 ATCCCAACATATTTAAGTTCCTTGAAATTTAAGATTAGCG 4 20 0 ATTCTTGATT 0.962962 -35 CGAGCTATAGATTAGGAAAGCTTGACGACTTTGGATTGGT 5 64 0 ATACTTGACT 0.982903 -237 TCGCGCTTTCAATATCCATCCTTGCGAACTTTGCTATCTC 5 101 1 ATACTTGCCT 0.960667 -200 ACCCACCTATAGTACCTCATCTTCAGCTCTACGGCCCTTA 5 151 1 ATACTTCACT 0.980396 -150 TGGTGAGTAAATTACTAGCCCTTGAAGCTTATCCAAAGCT 5 214 0 ATACTTGATT 0.953305 -87 AATTATAATAACTTCTAGCCCTTCCATACTAAGAGGGGAG 6 121 1 ATTCTTCCCT 0.961399 -34 TGAGGTTTTATTAGGCTACAAAACTAGCACCTAAG 7 29 0 TTTCTACACT 0.76931 -25 TTGATGAGACTCTTGACTATTTAGGAGGAGA 9 2 1 TATCTTGATT 0.719794 -299 CCATGAAGTCTGTTAAATTCCTTGATAACTCTCTCAAGCT 9 55 0 TTTCTTGACT 0.980325 -246 TCGGATTAAAAATAAAACCAGTTGAGATCTTGGAAAGCGA 9 223 1 ATAGTTGACT 0.833547 -78 GTACCTCCCCTTTTCAAAATCTTCCTCGCTTTCCAAGATC 9 248 0 TTTCTTCCCT 0.938437 -53 * ** ***** ** Masking position 12 Map Score: 17.3335 Number of sites scoring better than the average of aligned sites = 321 Number in coding regions = 291 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 2 TCCCTTGACCCCTTTGCAATTTCTGGAATCAAA 2 30 1 CTTTGCAATC 0.938988 -269 TCTGGAATCAAATTTTCAAAGTCTCGGTGGGAA 2 51 1 ATTTTCAATC 0.945072 -248 AATCTCTGATCCTTCTCAACTTCTCCTTCAACT 2 82 1 CTTCTCAATC 0.980838 -217 AAAATCCTTCAACTTTTAAAATCTCAAAACCTG 2 234 1 ACTTTTAATC 0.90071 -65 CTCATCCCAACATATTTAAGTTCCTTGAAATTT 4 30 0 CTATTTAATC 0.845189 -25 CTATAGCTCGCGCTTTCAATATCCATCCTTGCG 5 94 1 CCTTTCAATC 0.987081 -207 GTTATAACACCTCTCTTAAAATTTCTA 8 55 1 CCTCTTAATT 0.794963 -17 CAAGCTTTTCCATTTTTAATCTCCTCCTAAATA 9 28 0 CTTTTTAATC 0.97725 -273 TCCTTGATAACTCTCTCAAGCTTTTCCATTTTT 9 44 0 CCTCTCAATT 0.880591 -257 ACGTACCTCCCCTTTTCAAAATCTTCCTCGCTT 9 257 0 CTTTTCAATC 0.987879 -44 TTTACTTGAAAGTTTTTAAGTTCTAAACTTTTC 10 19 0 ATTTTTAATC 0.914114 -66 * ******* ** Masking position 8 Map Score: 11.5929 Number of sites scoring better than the average of aligned sites = 408 Number in coding regions = 374 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 3 TGAAGAGGCGATATGGGGAGGCCTCGGGGTT 2 169 1 AATGGGGAGG 0.991227 -130 GGCCTATAAGAGATGGGGATTACGTT 2 283 1 AATGGGGATT 0.965329 -16 GAACTTAAATATGTTGGGATGAGGG 4 40 1 AGTTGGGATG 0.926559 -15 GGGGTGAGAAAAGTGGTGAGTAAATTACTAG 5 236 0 AGTGGTGAGT 0.950271 -65 ATGACGATCTAAATGGTGATGAA 6 3 0 AATGGTGATG 0.951055 -152 CTTCCATACTAAGAGGGGAGGGGC 6 141 1 AGAGGGGAGG 0.991127 -14 TTGACTATTTAGGAGGAGATTAAAAATGGAA 9 23 1 AGAGGAGATT 0.809842 -278 GAAGATTTTGAAAAGGGGAGGTACGTTGTAA 9 264 1 AAAGGGGAGG 0.986 -37 * ********* Masking position 9 Map Score: 7.85327 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 242 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 GATCCTTCTCAACTTCTCCTTCAACTCTGC 2 89 1 AACTTCTCCT 0.962695 -210 ATATTAATTTAACTTCTTTTGCTTAAATAA 2 131 0 AACTTCTTTT 0.839833 -168 TTCTCCGCTTCACTTTTCTTGGCTTTTACC 2 206 0 CACTTTTCTT 0.970821 -93 TCTCTTATAGGCCTTCTCTTTCCATCTAAC 2 266 0 GCCTTCTCTT 0.920793 -33 AACGTAATCCCCATCTCTTATAGGCCTTC 2 280 0 CCCATCTCTT 0.888798 -19 TCTGTTAAGTAACTTCACTTATCCG 3 6 0 AACTTCACTT 0.89412 -50 TAACCCATGTCACTTCTCCTCACGACCAAT 5 40 1 CACTTCTCCT 0.980658 -261 ATTTACTCACCACTTTTCTCACCCCTCAAG 5 242 1 CACTTTTCTC 0.874032 -59 AGTGTTATAACACCTCTCTTAAAATTTCTA 8 52 1 CACCTCTCTT 0.964974 -20 TTAAGTTCTAAACTTTTCTTTTAACC 10 7 0 AACTTTTCTT 0.94424 -78 ********** Masking position 5 Map Score: 9.83026 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 299 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 AGATATTGTTAAAAATATAAGTCATGCGCT 1 18 0 AAAAATATAA 0.94854 -23 TATGGAAGAGAAAATTATAATAACTTCTAG 6 109 1 AAAATTATAA 0.792838 -46 GCACCTAAGGAAAAATAAATTAAAGGA 7 8 0 AAAAATAAAT 0.83287 -46 CTTACTATACAAAAATAAAAAACTAGACCT 8 15 0 AAAAATAAAA 0.960006 -57 ATTTCGGATTAAAAATAAAACCAGTTGAGA 9 220 1 AAAAATAAAA 0.960006 -81 AGGTACGTTGTAAAATATAAAGTTGAAAG 9 282 1 TAAAATATAA 0.889107 -19 GGTTAAAAGAAAAGTTTAGAACT 10 4 1 TAAAAGAAAA 0.762645 -81 ********** Masking position 4 Map Score: 4.10804 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 33 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 6 TTAAATAACATTTTGGGGTTGCAGAGTTGA 2 109 0 TTTTGGGGTT 0.859763 -190 TATGGGGAGGCCTCGGGGTTGGTTGGGGTA 2 180 1 CCTCGGGGTT 0.94727 -119 AAGTTAACAATCTTGAGGATTA 3 44 1 TCTTGAGGAT 0.975424 -12 TTTGGATTGGTCGTGAGGAGAAGTGACATG 5 45 0 TCGTGAGGAG 0.900886 -256 GGTGGGTTCCCCTTGAGGAGATAGCAAAGT 5 128 0 CCTTGAGGAG 0.987085 -173 TTTAACGTTTCCTTGAGGGGTGAGAAAAGT 5 253 0 CCTTGAGGGG 0.959214 -48 CGTTAAATATCTTTGGGGACTATATTAATA 5 276 1 CTTTGGGGAC 0.923258 -25 TTTACGATTACTTCGAGGATATATCCTGGG 9 181 1 CTTCGAGGAT 0.925883 -120 TTTACTGTACTCTTGGGGATTCTT 10 71 1 TCTTGGGGAT 0.980805 -14 ********** Masking position 5 Map Score: 7.66002 Number of sites scoring better than the average of aligned sites = 411 Number in coding regions = 380 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 GTAAGCCTTTGAAATAGCATCCCTTGAC 2 7 1 CTTTGAAAGC 0.959769 -292 AATATTGCCCTTTTGAAGAGGCGATATGGGGA 2 156 1 TTTTGAGGGC 0.973616 -143 AGCTTGACGACTTTGGATTGGTCGTGAGGAGA 5 54 0 CTTTGATGGT 0.936589 -247 TATCCTTAAGCTTTGGATAAGCTTCAAGGGCT 5 206 1 CTTTGATAGC 0.978027 -95 GTATAATAATCTTTTTCTGGGCTTAGGTATAT 6 43 1 CTTTTCTGGC 0.878059 -112 AGCGTAATATCTTTGCCTGGGCCTCACTCCCA 9 92 0 CTTTGCTGGC 0.984729 -209 AGGCCACAGGTTTTGCAGAAGCTACCCGTAAA 9 150 0 TTTTGAGAGC 0.935167 -151 GCGAGGAAGATTTTGAAAAGGGGAGGTACGTT 9 259 1 TTTTGAAGGG 0.820989 -42 ***** ** *** Masking position 4 Map Score: 3.14516 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 179 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 8 CGACCAATCCAAAGTCGTCAAGCTTTCCTAAT 5 62 1 AAGTCGTCAG 0.829721 -239 GCTTAAGGATATAGACTTCAGGCTGCTAAGGG 5 185 0 AAGACTTCAG 0.985064 -116 TAAGCTTTGGATAAGCTTCAAGGGCTAGTAAT 5 212 1 AAAGCTTCAG 0.751878 -89 CTTCCATACCAAAGAATTAAGGGATATTTAGA 6 85 0 AAGAATTAAG 0.775276 -70 TAGAAATTTTAAGAGAGGTGTTA 8 59 0 AAAATTTTAG 0.775981 -13 AAGGAATTTAACAGACTTCATGGGAGTGAGGC 9 72 1 AAGACTTCAG 0.985064 -229 AGGCCCAGGCAAAGATATTACGCTTTTCAGAT 9 100 1 AAGATATTAG 0.759544 -201 TGAAGTGATAATAGAATTTACGGGTAGCTTCT 9 134 1 AAGAATTTAG 0.933255 -167 TATTTACTTGAAAGTTTTTAAGTTCTAAACTT 10 22 0 AAGTTTTTAG 0.863612 -63 GTAAAGGATTAAAGACTTTTAGTATTTACTTG 10 44 0 AAGACTTTTG 0.878192 -41 * ******** * Masking position 8 Map Score: 2.74839 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 182 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 9 ********** No masking Map Score: -3.25896e-12 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 10 ********** No masking Map Score: -3.25896e-12 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 11 ********** No masking Map Score: -3.25896e-12 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