AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -ipurR_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 PH0239_PH0240 56 PH0239: 238aa long hypothetical phosphoribosylaminoimidazole-succinocarboxamide synthase, PH0240: 449aa long hypothetical amidophosphoribosyltransferase #2 PH0307 112 486aa long hypothetical inosine-5'-monophosphate dehydrogenase #3 PH0316 300 334aa long hypothetical phosphoribosylformylglycinamide cyclo-ligase #4 PH0318 300 433aa long hypothetical phosphoribosylglycinamide formyl transferase #5 PH0320 88 177aa long hypothetical phosphoribosylaminoimidazole carboxylase catalytic subunit #6 PH0322_PH0323 157 PH0322: 219aa long hypothetical protein, PH0323: 438aa long hypothetical phosphoribosylamide--glycine ligase #7 PH0434 185 336aa long hypothetical protein #8 PH0437 263 367aa long hypothetical protein #9 PH0438 58 339aa long hypothetical adenylosuccinate synthetase #10 PH1014 60 181aa long hypothetical 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #11 PH1161 150 218aa long hypothetical transcriptional regulator #12 PH1317 58 138aa long hypothetical glycine cleavage system H protein #13 PH1348 131 333aa long hypothetical protein #14 PH1654 185 427aa long hypothetical serine hydroxymethyltransferase #15 PH1922 46 118aa long hypothetical protein #16 PH1953 110 705aa long hypothetical phosphoribosylformylglycinamidine synthase II #17 PH1995 61 449aa long hypothetical glycine dehydrogenase subunit 1 #18 PH1996 150 225aa long hypothetical protein Motif number 1 CTTTTGCCAGATATATGTCTAAAAAATCTTAA 1 2 1 TTATAATTAA 0.763405 -55 ATCTTAAAAGTATTATGATTTTTACATAAAC 1 36 1 TTATTATAAC 0.91073 -21 CTTGTCGACCTATGGGAAGGTAAAATTTAAATATACATTTT 2 31 0 TTATAATAAA 0.962372 -82 AATATTTATATATTCCCATATTTTATTTTAAGTGACTAATT 3 13 0 TTATTTTTAA 0.670799 -288 TCGCCTCGGATTTTAATAATTATAAATAAAAAATCCTACGA 3 90 0 TTATAATAAA 0.953695 -211 TAGTCCATCATTTAAACATATTTATGTTAAAAAGGCTTAAA 4 233 1 TTATTATAAA 0.96314 -68 ATAATTTAAATTTTAACATTTATACGTCAATTAGGG 4 275 1 TTATAATAAT 0.78355 -26 TCGAAGAAACTTTTTAAATATTGACATTAAATTGCTAGGGT 5 30 1 TTATTATAAA 0.978728 -59 TTTATATCACCATATTTAAGTCAAAATTATAAGGT 6 5 1 TTATTATAAA 0.978728 -153 TTAACTTTTTTGTTAACACGTTTATGTAAACAAAAACCATT 6 49 0 TTATTATAAC 0.910731 -109 GTTATACTACTCTCTGTAGGTTATCTTAAAATCCCTCTTTT 7 48 1 TTATTTTAAA 0.941691 -138 AAAATCCCTCTTTTAAAAGTTTCTCGTTAAATCAAACTGGA 7 75 1 TTATTTTAAA 0.688799 -111 AAACTGGAGATTTCTGTAGAATAAATTAAAACCTTCTGTGA 7 108 1 TTAATATAAA 0.756738 -78 GTTGACAAATTTTTGTAAAATAAATTTTAAAAATTAATCAA 11 46 0 TTATAATAAA 0.962127 -105 TTCAGCGTTCTTTTATAACTTTTTTGTTAAATTCCATAACC 11 107 0 TTATTTTAAA 0.688799 -44 TTGCATAGAATATGGTAAAATAAATCTTAAAAATTGCCAAT 13 74 1 TTATAATAAA 0.962368 -58 TCTGATATCACCATGTTCATGTTAAAAATTGGCAAT 13 106 0 TTATTATAAA 0.978972 -26 CATGCTAATATTTGCTTAACTTAAATTTAAACCTTGTGCAT 14 145 0 TTATTATAAA 0.978972 -41 TTGACATTTCTTTGTCAAAATAAATCTTAAAAATTTAAAAT 16 45 1 TTATAATAAA 0.962127 -66 CGACTAAAAATTTAGTAAGATTATAATAAATACCTTTCCTA 17 21 0 TTATTTTAAT 0.695645 -41 * * * ** * * *** Masking position 17 Map Score: 35.536 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 27 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 2 CTTTTGCCAGATATATGTCTAAAAA 1 2 1 TTTTGATATA 0.785038 -55 ATTGTGTAAAAATGTATATTTAAATTTTACCTTC 2 23 1 AATGTATAAA 0.764714 -90 CTTGTCGACCTATGGGAAGGTAAAATTTAAATAT 2 38 0 TATGGATAAA 0.946784 -75 TAAAATAAAATATGGGAATATATAAATATTACTA 3 24 1 TATGGATATA 0.894666 -277 AATATATAAATATTACTACTTATAAATTGAGTTA 3 40 1 TATTAATATA 0.795307 -261 TCGCCTCGGATTTTAATAATTATAAATAAAAAAT 3 97 0 TTTTAATATA 0.692346 -204 TTGATAAATTTATGTGTACTTAAAAACGTTGGTT 3 263 0 TATGTATAAA 0.892923 -38 TAAATGGAGATATTATAATCTATAGCAATTTCCA 4 66 0 TATTAATATA 0.796369 -235 CAAGCAAGAGAATTAGAAGCTAAATCTCTTTGTC 4 119 1 AATTAATAAA 0.760154 -182 ATAATTTAAATTTTAACATTTATACGTCAATTAG 4 275 1 TTTTAATATA 0.694295 -26 TTTCTTCGAATATTTCTACATATATGTG 5 5 0 TATTTATATA 0.747339 -84 TTGACTTAAATATGGTGATATAAA 6 1 0 TATGGATAAA 0.946776 -157 AATACCTTATAATTTTGACTTAAATATGGTGATA 6 15 0 AATTTATAAA 0.706449 -143 ATTAATGGTTTTTGTTTACATAAACGTGTTAACA 6 46 1 TTTGTATAAA 0.82885 -112 CAAAAAAGTTAATTACTAAATAAAGTAGTGTCCA 6 78 1 AATTAATAAA 0.760148 -80 AAAGATACATTTTGAAAATATAAATCAGTTTTGT 6 117 0 TTTGAATAAA 0.865307 -41 GTGCCCTCCCTATTGTAAGCTAAAATTACCTCCA 7 14 1 TATTGATAAA 0.929427 -172 GTTGACAAATTTTTGTAAAATAAATTTTAAAAAT 11 53 0 TTTTGATAAA 0.884374 -98 TTTTACAAAAATTTGTCAACTAAACACATAATTA 11 67 1 ATTTGATAAA 0.747444 -84 CCAACATTTCAATGAGAACTTAAAAACCAAGCTA 13 18 1 AATGAATAAA 0.810624 -114 TTGCATAGAATATGGTAAAATAAATCTTAAAAAT 13 74 1 TATGGATAAA 0.946776 -58 TTGACATTTCTTTGTCAAAATAAATCTTAAAAAT 16 45 1 TTTGTATAAA 0.829881 -66 ***** * **** Masking position 11 Map Score: 25.0084 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 140 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 3 GTTTATGTAAAAATCATAATACTTTTAAGATTTTT 1 32 0 AAATAATTTT 0.745545 -25 TCTTGTCAAGAAAATTTCTCAATTTTCTTCTTTTCAA 4 191 0 AAATCAATTC 0.879121 -110 ATTTAATGTCAATATTTAAAAAGTTTCTTCGAATATT 5 25 0 AAATAAATTC 0.817548 -64 GCCTTCACATAATACTCCTCATACTTTTCGATTGGAG 8 91 0 AAATCATTTT 0.840937 -173 CAATTTCAGTAAACCTTCTCAATGTTTATAAAGTTGC 10 26 0 AACTCAATTT 0.67428 -35 ATAAATTTTAAAAATTAATCAATCTTTGACAAAACAA 11 31 0 AAATCAATTT 0.971874 -120 AATTTAGCAGCAACCTTTAAAATCTTTACAGTAAAAA 12 27 0 CACTAAATTT 0.716214 -32 AATAAATCTTAAAAATTGCCAATTTTTAACATGAACA 13 92 1 AAATCAATTT 0.499615 -40 ATCCCTCGCCAAAATTTGGTTGCCTTA 14 1 1 ATCTCAATTT 0.762007 -185 TATGTAACTGAACATTCGACAATAATTCAAGAAATTG 14 56 1 AAATCAAATT 0.840617 -130 CACAGAGGATAAAACTCCACAATTTCTTGAATTATTG 14 75 0 AAATCAATCT 0.816098 -111 TGAGTTTTCAAAACGTCTAAAAGGATTGCCCAAAAAT 14 110 1 AACTAAAATT 0.609896 -76 AGGATTGCCCAAAAATGCACAAGGTTTAAATTTAAGT 14 131 1 AAATCAATTT 0.958318 -55 AATAAATCTTAAAAATTTAAAATTTTTACATTTTTCT 16 63 1 AAATAAATTT 0.498801 -48 TAATCAACCTTAGGAAAGGTATTTATTATAAT 17 6 1 AACTAAATAT 0.6533 -56 TATTTATTATAATCTTACTAAATTTTTAGTCGGGGAT 17 30 1 AACTAAATTT 0.954837 -32 TTTAAATTGAAAGCGTAATAAAGGTTTCGGTGATAAA 18 11 0 AACTAAATTT 0.956417 -140 ** * * *** *** Masking position 11 Map Score: 15.3882 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 104 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 4 TAGTTCATAAAAAAGGGTGAGGAGGAGAGGAAG 2 90 1 AAAAGGTGAA 0.980118 -23 TTATAAATAAAAAATCCTACGAAAAGAAAAAGATTTAT 3 74 0 AAAATCTGAA 0.694002 -227 TTCAAACGAAAAAAGCCAAAGTAAAAGAGTGAACAAAA 3 131 1 AAAAGCAGAA 0.973862 -170 TGTTCTTAACACAAGCAAGAGAATTAGAAGCTAAATCT 4 108 1 ACAAGCAGAA 0.91536 -193 TTTTCAAGTGAATAGGGATGGAAAAATATCCCCAGCAT 4 160 0 AATAGGAGAA 0.829115 -141 GTCATAGGTTGAAGGGAAAGGGATAAAAAGGTTTAGTT 7 156 0 GAAGGGAGAA 0.868159 -30 AGTATTATGTGAAGGCTAGAGAAGCGGAGTGGAAGCGC 8 112 1 GAAGGCAGAA 0.832688 -152 CCCTGTCAAAAGGGTAAGCATTTTAAGGTACCCCT 9 8 1 AAAAGGTGAA 0.980118 -51 TTGACAAAACAAAGGCAATTGGAGGGGAAAGG 11 5 0 AAAGGCAGAA 0.944891 -146 CATAATTATAACAAGGTTATGGAATTTAACAAAAAAGT 11 93 1 ACAAGGTGAA 0.934679 -58 CTTTACAGTAAAAAGGCTGGGGAGTTAACA 12 3 0 AAAAGGTGAA 0.980118 -56 TACTTCCTTAAAAAGGTTATGTAACTGAACATTCGACA 14 39 1 AAAAGGTGAA 0.980118 -147 TGAGTAGAGAAAAAGCAAGTATATAAAATTAAGGTTC 15 10 0 AAAAGCAAAA 0.81229 -37 CGGCCCTCAGAAAAGGCTTTAAATTGAAAGCGTAATAA 18 27 0 AAAAGGTAAA 0.851313 -124 ****** * * * * Masking position 13 Map Score: 13.7594 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 167 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 TAGTTCATAAAAAAGGGTGAGGAGGAGAGG 2 90 1 AAAAGGGTGA 0.89263 -23 CCACAATCATAGAAGGCTGGACTATATTCT 3 203 0 AGAAGGCTGG 0.957972 -98 TGTGTACTTAAAAACGTTGGTTTTACGGTG 3 255 0 AAAACGTTGG 0.781237 -46 TTGTGTTAAGAACAGGCTGTTATAAATGGA 4 92 0 AACAGGCTGT 0.657034 -209 TTTGTCAGATAAAATGCTGGGGATATTTTT 4 147 1 AAAATGCTGG 0.68089 -154 ATTTATGTTAAAAAGGCTTAAATATAATTT 4 252 1 AAAAGGCTTA 0.95082 -49 ACTTTATCACAGAAGGTTTTAATTTATTCT 7 125 0 AGAAGGTTTT 0.810733 -61 GAAAGGGATAAAAAGGTTTAGTTGACTTTA 7 149 0 AAAAGGTTTA 0.92316 -37 GGTATATAATATAAGGTTTGCTCTCAATAG 8 217 0 ATAAGGTTTG 0.658432 -47 CCCTGTCAAAAGGGTAAGCATTTTAAG 9 8 1 AAAAGGGTAA 0.62079 -51 ATAAACATTGAGAAGGTTTACTGAAATTGG 10 34 1 AGAAGGTTTA 0.879256 -27 AAGTTATAAAAGAACGCTGAAGAGTGGGGT 11 127 1 AGAACGCTGA 0.718009 -24 CTTTACAGTAAAAAGGCTGGGGAGTTAACA 12 11 0 AAAAGGCTGG 0.974166 -48 TACTTCCTTAAAAAGGTTATGTAACTGAAC 14 39 1 AAAAGGTTAT 0.662898 -147 CAAAACGTCTAAAAGGATTGCCCAAAAATG 14 118 1 AAAAGGATTG 0.748931 -68 CCAAAAATGCACAAGGTTTAAATTTAAGTT 14 139 1 ACAAGGTTTA 0.67388 -47 CGGCCCTCAGAAAAGGCTTTAAATTGAAAG 18 35 0 AAAAGGCTTT 0.919155 -116 ********** Masking position 4 Map Score: 11.1496 Number of sites scoring better than the average of aligned sites = 513 Number in coding regions = 442 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 6 CATAATACTTTTAAGATTTTTTAGACATATA 1 22 0 TAAGATTTTT 0.912571 -35 AAAATTTAAATATACATTTTTACACAATCAT 2 20 0 TTACATTTTT 0.791092 -93 AATTTAAATTTTAACATTTATACGTCAATTA 4 277 1 TAACATTTAT 0.876014 -24 ATTTGAGATTTCTAGCTATCCCT 5 76 0 TGAGATTTCT 0.971586 -13 TAAATCAAACTGGAGATTTCTGTAGAATAAA 7 102 1 TGAGATTTCT 0.971586 -84 AGATCCCTGGTAGAGATTTCTCTTCTTATCG 8 16 0 TGAGATTTCT 0.971586 -248 TTGGCAATTTTTAAGATTTATTTTACCATAT 13 83 0 TAAGATTTAT 0.912571 -49 GGGTGAGTGATTGACATTTCTTTGTCAAAAT 16 35 1 TGACATTTCT 0.958585 -76 TTTTAAATTTTTAAGATTTATTTTGACAAAG 16 54 0 TAAGATTTAT 0.912571 -57 ATTTAAAATTTTTACATTTTTCTGGCAAATA 16 77 1 TTACATTTTT 0.791092 -34 * ********* Masking position 6 Map Score: 9.32173 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 32 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 CTTTTGCCAGATATATGTCTA 1 2 1 TTTTGCCAGA 0.912079 -55 AGCTAAATCTCTTTGTCAGATAAAATGCTG 4 136 1 CTTTGTCAGA 0.93584 -165 TAATTAACTTTTTTGTTAACACGTTTATGT 6 63 0 TTTTGTTAAC 0.746023 -95 ATTGCCTTTGTTTTGTCAAAGATTGATTAA 11 24 1 TTTTGTCAAA 0.962241 -127 GTTGACAAATTTTTGTAAAATAAATTTTAA 11 57 0 TTTTGTAAAA 0.748494 -94 TTTTACAAAAATTTGTCAACTAAACACATA 11 67 1 ATTTGTCAAC 0.848213 -84 TTTATAACTTTTTTGTTAAATTCCATAACC 11 107 0 TTTTGTTAAA 0.856384 -44 ATTGACATTTCTTTGTCAAAATAAATCTTA 16 44 1 CTTTGTCAAA 0.946432 -67 ACACCTCCTTATTTGCCAGAAAAATGTAAA 16 87 0 ATTTGCCAGA 0.821664 -24 ********** Masking position 4 Map Score: 3.78609 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 36 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 CCGGGGTCAGAAATACCTGCAGGAAGCTCT 4 37 1 AAATACCTGC 0.892854 -264 TATTTTGAGGAGATCCCTGGTAGAGATTTC 8 27 0 AGATCCCTGG 0.968412 -237 GGGAAGCACTAAATCCCTGCAATGAATAGA 8 183 1 AAATCCCTGC 0.981774 -81 TGCAAATCCCCGACTAAAAATTT 17 49 0 AAATCCCCGA 0.888301 -13 TCGGAGCCGAAGGTCCCGGGTTCAAATCCC 18 94 1 AGGTCCCGGG 0.92367 -57 TCCCGGGTTCAAATCCCGGCCGGCCCGCCA 18 107 1 AAATCCCGGC 0.983093 -44 ********** Masking position 4 Map Score: 1.37928 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 55 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 9 CCTCTCCTCCTCACCCTTTTTTATGAACTA 2 90 0 TCACCCTTTT 0.883374 -23 TTTATATCACCATATTTAAGTCAAAA 6 7 1 TCACCATATT 0.943864 -151 AGGAGAGTCACCTGGTTAAAGATACAT 6 141 0 TCACCTGGTT 0.910315 -17 TTAAATTCCATAACCTTGTTATAATTATGT 11 92 0 TAACCTTGTT 0.912471 -59 AAGATTTATTTTACCATATTCTATGCAAAA 13 72 0 TTACCATATT 0.722312 -60 TCTGATATCACCATGTTCATGTTAAAA 13 115 0 TCACCATGTT 0.9803 -17 TTCAGTTACATAACCTTTTTAAGGAAGTAT 14 38 0 TAACCTTTTT 0.778886 -148 TAAGAATCACCATGCTAATATTTGCT 14 170 0 TCACCATGCT 0.92966 -16 ********** Masking position 3 Map Score: 2.44918 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 67 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 10 CTTCCTCTCCTCCTCACCCTTT 2 101 0 TCCTCTCCTC 0.945408 -12 TAATAAATCTTTTTCTTTTCGTAGGATTTT 3 72 1 TTTTCTTTTC 0.713505 -229 AATTTCTCAATTTTCTTCTTTTCAAGTGAA 4 186 0 TTTTCTTCTT 0.839686 -115 TGGTAGAGATTTCTCTTCTTATCGACATA 8 10 0 TTCTCTTCTT 0.950496 -254 GTCTCCTTAATTCTCTTCTCAAACTCTTCA 8 62 0 TTCTCTTCTC 0.985991 -202 GCGCTTCCACTCCGCTTCTCTAGCCTTCAC 8 120 0 TCCGCTTCTC 0.935787 -144 TACTTGCTTTTTCTCTACTCAATTTTGGTT 15 27 1 TTCTCTACTC 0.945545 -20 ********** Masking position 6 Map Score: 2.31304 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 270 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 ********** No masking Map Score: -5.90218e-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 12 ********** No masking Map Score: -5.90218e-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 13 ********** No masking Map Score: -5.90218e-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