AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -imodE_pyro_opreg_100.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 GAAATTGCAAAGGGGTCAAGGGATGCTATTTCAAAGGCTT 2 13 0 AGTCAAGTAT 0.982757 -286 TTGGGGTTGCAGAGTTGAAGGAGAAGTTGAGAAGGATCAG 2 87 0 AGTGAAGTTA 0.814999 -212 AAAAGCCAAGAAAAGTGAAGCGGAGAAAATCCTTCAACTT 2 209 1 AATGAAGAAT 0.947747 -90 CGGATAAGTGAAGTTACTTAACAGAATGTTTTT 3 4 1 ATTGAAGAAA 0.732519 -52 TAATCCTCAAGATTGTTAACTTAAAAACATT 3 35 0 AATCAAGAAT 0.957975 -21 CGCTAATCTTAAATTTCAAGGAACTTAAATATGTTGGGAT 4 20 1 AATCAAGAAT 0.958647 -35 ACCAATCCAAAGTCGTCAAGCTTTCCTAATCTATAGCTCG 5 64 1 AGTCAAGTAT 0.981248 -237 GAGATAGCAAAGTTCGCAAGGATGGATATTGAAAGCGCGA 5 101 0 AGGCAAGTAT 0.956289 -200 TAAGGGCCGTAGAGCTGAAGATGAGGTACTATAGGTGGGT 5 151 0 AGTGAAGTAT 0.978065 -150 AGCTTTGGATAAGCTTCAAGGGCTAGTAATTTACTCACCA 5 214 1 AATCAAGTAT 0.947924 -87 CTCCCCTCTTAGTATGGAAGGGCTAGAAGTTATTATAATT 6 121 0 AGGGAAGAAT 0.956909 -34 CTTAGGTGCTAGTTTTGTAGCCTAATAAAACCTCA 7 29 1 AGTGTAGAAA 0.748331 -25 TCTCCTCCTAAATAGTCAAGAGTCTCATCAA 9 2 0 AATCAAGATA 0.696083 -299 AGCTTGAGAGAGTTATCAAGGAATTTAACAGACTTCATGG 9 55 1 AGTCAAGAAA 0.977986 -246 TCGCTTTCCAAGATCTCAACTGGTTTTATTTTTAATCCGA 9 223 0 AGTCAACTAT 0.817015 -78 GATCTTGGAAAGCGAGGAAGATTTTGAAAAGGGGAGGTAC 9 248 1 AGGGAAGAAA 0.931466 -53 ** ***** ** * Masking position 9 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 TTTGATTCCAGAAATTGCAAAGGGGTCAAGGGA 2 30 0 GATTGCAAAG 0.934592 -269 TTCCCACCGAGACTTTGAAAATTTGATTCCAGA 2 51 0 GATTGAAAAT 0.942206 -248 AGTTGAAGGAGAAGTTGAGAAGGATCAGAGATT 2 82 0 GATTGAGAAG 0.979391 -217 CAGGTTTTGAGATTTTAAAAGTTGAAGGATTTT 2 234 0 GATTAAAAGT 0.894974 -65 AAATTTCAAGGAACTTAAATATGTTGGGATGAG 4 30 1 GATTAAATAG 0.835221 -25 CGCAAGGATGGATATTGAAAGCGCGAGCTATAG 5 94 0 GATTGAAAGG 0.986099 -207 TAGAAATTTTAAGAGAGGTGTTATAAC 8 55 0 AATTAAGAGG 0.782594 -17 TATTTAGGAGGAGATTAAAAATGGAAAAGCTTG 9 28 1 GATTAAAAAG 0.97554 -273 AAAAATGGAAAAGCTTGAGAGAGTTATCAAGGA 9 44 1 AATTGAGAGG 0.872559 -257 AAGCGAGGAAGATTTTGAAAAGGGGAGGTACGT 9 257 1 GATTGAAAAG 0.986962 -44 GAAAAGTTTAGAACTTAAAAACTTTCAAGTAAA 10 19 1 GATTAAAAAT 0.908101 -66 ** ******* * Masking position 2 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 0.990936 -130 GGCCTATAAGAGATGGGGATTACGTT 2 283 1 AATGGGGATT 0.964211 -16 GAACTTAAATATGTTGGGATGAGGG 4 40 1 AGTTGGGATG 0.924288 -15 GGGGTGAGAAAAGTGGTGAGTAAATTACTAG 5 236 0 AGTGGTGAGT 0.948692 -65 ATGACGATCTAAATGGTGATGAA 6 3 0 AATGGTGATG 0.9495 -152 CTTCCATACTAAGAGGGGAGGGGC 6 141 1 AGAGGGGAGG 0.990833 -14 TTGACTATTTAGGAGGAGATTAAAAATGGAA 9 23 1 AGAGGAGATT 0.804722 -278 GAAGATTTTGAAAAGGGGAGGTACGTTGTAA 9 264 1 AAAGGGGAGG 0.985538 -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 GTAAGCCTTTGAAATAGCATCCCT 2 4 1 ACCTTTGAAA 0.790996 -295 CATCCCTTGACCCCTTTGCAATTTCTGGAAT 2 28 1 CCCTTTGCAA 0.968668 -271 TTTCTGGAATCAAATTTTCAAAGTCTCGGTG 2 49 1 CAATTTTCAA 0.737427 -250 GGAATCTCTGATCCTTCTCAACTTCTCCTTC 2 80 1 ACCTTCTCAA 0.71892 -219 ACTTCTCCTTCAACTCTGCAACCCCAAAATG 2 100 1 CACTCTGCAA 0.949544 -199 CTCCCCATATCGCCTCTTCAAAAGGGCAATA 2 158 0 CCCTCTTCAA 0.986298 -141 GAAAATCCTTCAACTTTTAAAATCTCAAAAC 2 233 1 CACTTTTAAA 0.821865 -66 CTCCTTCCCGCTAATCTTAAATTTCAAGGAA 4 12 1 CAATCTTAAA 0.737427 -43 CCTATAGTACCTCATCTTCAGCTCTACGGCC 5 156 1 CCATCTTCAG 0.751135 -145 TGTTATAACACCTCTCTTAAAATTTCTA 8 54 1 CTCTCTTAAA 0.74809 -18 CATTTTTAATCTCCTCCTAAATAGTCAAGAG 9 20 0 CCCTCCTAAA 0.907972 -281 TTATCACTTCATCATCTGAAAAGCGTAATAT 9 114 0 ACATCTGAAA 0.697314 -187 ATTTACGGGTAGCTTCTGCAAAACCTGTGGC 9 149 1 ACTTCTGCAA 0.597234 -152 CAACGTACCTCCCCTTTTCAAAATCTTCCTC 9 261 0 CCCTTTTCAA 0.971421 -40 * ********* Masking position 10 Map Score: 11.3476 Number of sites scoring better than the average of aligned sites = 844 Number in coding regions = 775 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 5 GATCCTTCTCAACTTCTCCTTCAACTCTGC 2 89 1 AACTTCTCCT 0.956221 -210 ATATTAATTTAACTTCTTTTGCTTAAATAA 2 131 0 AACTTCTTTT 0.816109 -168 TTCTCCGCTTCACTTTTCTTGGCTTTTACC 2 206 0 CACTTTTCTT 0.965706 -93 TCTCTTATAGGCCTTCTCTTTCCATCTAAC 2 266 0 GCCTTCTCTT 0.907744 -33 AACGTAATCCCCATCTCTTATAGGCCTTC 2 280 0 CCCATCTCTT 0.871215 -19 TCTGTTAAGTAACTTCACTTATCCG 3 6 0 AACTTCACTT 0.877263 -50 TAACCCATGTCACTTCTCCTCACGACCAAT 5 40 1 CACTTCTCCT 0.977228 -261 ATTTACTCACCACTTTTCTCACCCCTCAAG 5 242 1 CACTTTTCTC 0.854496 -59 AGTGTTATAACACCTCTCTTAAAATTTCTA 8 52 1 CACCTCTCTT 0.958878 -20 TTAAGTTCTAAACTTTTCTTTTAACC 10 7 0 AACTTTTCTT 0.93478 -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 6 AGCGCATGACTTATATTTTTAACAATATCT 1 18 1 TTATATTTTT 0.943502 -23 CTAGAAGTTATTATAATTTTCTCTTCCATA 6 109 0 TTATAATTTT 0.77615 -46 TCCTTTAATTTATTTTTCCTTAGGTGC 7 8 1 ATTTATTTTT 0.818669 -46 AGGTCTAGTTTTTTATTTTTGTATAGTAAG 8 15 1 TTTTATTTTT 0.956038 -57 TCTCAACTGGTTTTATTTTTAATCCGAAAT 9 220 0 TTTTATTTTT 0.956038 -81 CTTTCAACTTTATATTTTACAACGTACCT 9 282 0 TTATATTTTA 0.878994 -19 AGTTCTAAACTTTTCTTTTAACC 10 4 0 TTTTCTTTTA 0.74431 -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 7 GTAAGCCTTTGAAATAGCATCC 2 3 1 AAGCCTTTGA 0.926408 -296 GTTGGGGTAAAAGCCAAGAAAAGTGAAGCG 2 201 1 AAGCCAAGAA 0.820767 -98 TGGAAAGAGAAGGCCTATAAGAGATGGGGA 2 272 1 AGGCCTATAA 0.824437 -27 ACTTAACAGAATGTTTTTAAGTTAACAATC 3 26 1 ATGTTTTTAA 0.52961 -30 TAGCAGCCTGAAGTCTATATCCTTAAGCTT 5 189 1 AAGTCTATAT 0.619702 -112 CTATATCCTTAAGCTTTGGATAAGCTTCAA 5 203 1 AAGCTTTGGA 0.866643 -98 ATATATACCTAAGCCCAGAAAAAGATTATT 6 47 0 AAGCCCAGAA 0.871583 -108 TTTGTATAGTAAGTCTAGAAAGTGTTATAA 8 32 1 AAGTCTAGAA 0.957478 -40 ATATCCTGGGATGCCTTGGATTTCGGATTA 9 201 1 ATGCCTTGGA 0.833311 -100 GTTAAAAGAAAAGTTTAGAACTTAAAAACT 10 12 1 AAGTTTAGAA 0.878976 -73 ATTTACTTGAAAGTTTTTAAGTTCTAAACT 10 23 0 AAGTTTTTAA 0.81942 -62 TAAATACTAAAAGTCTTTAATCCTTTACTG 10 48 1 AAGTCTTTAA 0.933637 -37 ********** Masking position 1 Map Score: 5.67874 Number of sites scoring better than the average of aligned sites = 659 Number in coding regions = 609 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 8 TTTAAGTTAACAATCTTGAGGATTA 3 41 1 CTCTTGAGGA 0.959348 -15 GACTTTGGATTGGTCGTGAGGAGAAGTGACAT 5 46 0 TTCGTGAGGA 0.95861 -255 ATAGGTGGGTTCCCCTTGAGGAGATAGCAAAG 5 129 0 TCCTTGAGGA 0.894621 -172 ATATTTAACGTTTCCTTGAGGGGTGAGAAAAG 5 254 0 TCCTTGAGGG 0.979889 -47 AAACGTTAAATATCTTTGGGGACTATATTAAT 5 273 1 TCTTTGGGGA 0.96678 -28 GCCTTTACGATTACTTCGAGGATATATCCTGG 9 178 1 TCTTCGAGGA 0.930102 -123 TCCTTTACTGTACTCTTGGGGATTCTT 10 68 1 TTCTTGGGGA 0.971288 -17 * ********* Masking position 8 Map Score: 4.44417 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 204 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 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