AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -ipurR_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 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 PH0437 263 367aa long hypothetical protein #8 PH0438 58 339aa long hypothetical adenylosuccinate synthetase #9 PH1014 60 181aa long hypothetical 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #10 PH1161 150 218aa long hypothetical transcriptional regulator #11 PH1317 58 138aa long hypothetical glycine cleavage system H protein #12 PH1348 131 333aa long hypothetical protein #13 PH1654 185 427aa long hypothetical serine hydroxymethyltransferase #14 PH1922 46 118aa long hypothetical protein #15 PH1953 110 705aa long hypothetical phosphoribosylformylglycinamidine synthase II #16 PH1995 61 449aa long hypothetical glycine dehydrogenase subunit 1 #17 PH1996 150 225aa long hypothetical protein Motif number 1 CTTTTGCCAGATATATGTCTAAAAAATCTTAAAA 1 9 1 ATATATTAAA 0.924502 -48 GTTTATGTAAAAATCATAATACTTTTAAGA 1 37 0 ATAAAATAAT 0.892771 -20 AGTCACTTAAAATAAAATATGGGAATATATAAATAT 3 17 1 AAAAATTAAT 0.783759 -284 TATTAACTCAATTTATAAGTAGTAATATTTATATAT 3 41 0 ATATAATAAT 0.892057 -260 AGGATTTTTTATTTATAATTATTAAAATCCGAGGCG 3 94 1 ATATAATAAA 0.882649 -207 TATCTCACCTAGAATTGATAAATTTATGTGTA 3 279 0 ATAGAATAAA 0.931919 -22 GCTGTTATAAATGGAGATATTATAATCTATAGCAAT 4 71 0 AGAGATTAAT 0.676008 -230 CATTCTTGTCAAGAAAATTTCTCAATTTTCTTCTTT 4 195 0 AAAAATTAAT 0.78338 -106 CCTTTTTAACATAAATATGTTTAAATGATGGACTAT 4 232 0 AAATATTAAT 0.781159 -69 CCCTAATTGACGTATAAATGTTAAAATTTAAATTA 4 276 0 ATATAATAAA 0.930715 -25 CACATATATGTAGAAATATTCGAAGAA 5 2 1 ATATATTAAT 0.88433 -87 TCCCAGGGATAGCTAGAAATCTCAAAT 5 72 1 ATAGAATAAA 0.931913 -17 CACAAAACTGATTTATATTTTCAAAATGTATCTTTA 6 116 1 ATATATTAAA 0.922867 -42 AATTTTTGTAAAATAAATTTTAAAAATTAATCAATC 10 44 0 ATAAATTAAA 0.924502 -107 ATGGAATTTAACAAAAAAGTTATAAAAGAACGCTGA 10 111 1 AAAAAATAAA 0.864285 -40 CCAACATTTCAATGAGAACTTAAAAACCAAGCTATT 12 18 1 AGAGAATAAA 0.786084 -114 GAATATGGTAAAATAAATCTTAAAAATTGCCAATTT 12 81 1 ATAAATTAAA 0.924502 -51 ATTTATTTTGACAAAGAAATGTCAATCACTCACCCT 15 34 0 AAAGAATAAT 0.80203 -77 TTCTTTGTCAAAATAAATCTTAAAAATTTAAAATTT 15 52 1 ATAAATTAAA 0.924502 -59 TGCCAGAAAAATGTAAAAATTTTAAATTTTTAAGAT 15 68 0 ATAAAATAAA 0.930002 -43 CCGGCCCGCCAACAATAACTTTAAAACTTCCACAA 17 126 1 AAATAATAAA 0.864284 -25 * ***** * *** Masking position 10 Map Score: 24.8135 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 97 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 2 GTTTATGTAAAAATCATAATACT 1 44 0 TTTATGTAAA 0.974379 -13 CATATTTTATTTTAAGTGACTAATTGG 3 6 0 TTTAAGTACA 0.727432 -295 AACCAACGTTTTTAAGTACACATAAATTTATC 3 263 1 TTTAAGTCAA 0.727432 -38 TTTTCTTCTTTTCAAGTGAATAGGGATGGAAA 4 174 0 TTCAAGTAAA 0.900516 -127 GGACTATCCATTCTTGTCAAGAAAATTTCTCA 4 207 0 TTCTTGTAAA 0.900516 -94 TTTAAACATATTTATGTTAAAAAGGCTTAAAT 4 243 1 TTTATGTAAA 0.97443 -58 CCCTAGCAATTTAATGTCAATATTTAAAAAGT 5 38 0 TTAATGTAAA 0.815621 -51 TATCACCATATTTAAGTCAAAATTATAAGGTA 6 15 1 TTTAAGTAAA 0.951617 -143 TGTTAACACGTTTATGTAAACAAAAACCATTA 6 48 0 TTTATGTAAA 0.974482 -110 GTAATTAACTTTTTTGTTAACACGTTTATGTA 6 62 0 TTTTTGTAAA 0.951568 -96 AGTTGACAAATTTTTGTAAAATAAATTTTAAA 10 56 0 TTTTTGTAAT 0.786752 -95 TTTTATAACTTTTTTGTTAAATTCCATAACCT 10 106 0 TTTTTGTAAT 0.78679 -45 TATCACCATGTTCATGTTAAAAATTGGCAATT 12 105 0 TTCATGTAAA 0.946164 -27 AAGGTTTAAATTTAAGTTAAGCAAATATTAGC 13 151 1 TTTAAGTAAC 0.756241 -35 GATTGACATTTCTTTGTCAAAATAAATCTTAA 15 43 1 TCTTTGTAAA 0.727324 -68 ******* ** * Masking position 7 Map Score: 16.1187 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 18 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 3 CTCTTACTCATGATTGTGTAAAAATGT 2 5 1 TCCAGATTGT 0.842414 -108 CTTCCTCTCCTCCTCACCCTTTTTTATGAACTA 2 90 0 TCCACCTTTT 0.986725 -23 TCTTTTTCTTTTCGTAGGATTTTTTATTTATAA 3 79 1 TCTAGATTTT 0.856617 -222 TTCACTCTTTTACTTTGGCTTTTTTCGTTTGAA 3 131 0 TCTTGCTTTT 0.858431 -170 TAGCTTCTAATTCTCTTGCTTGTGTTAAGAACA 4 108 0 TCCTGCTTGT 0.844375 -193 TGGAAAAATATCCCCAGCATTTTATCTGACAAA 4 147 0 TCCACATTTT 0.942557 -154 CACATAATACTCCTCATACTTTTCGATTGGAGT 7 90 0 TCCAACTTTT 0.892479 -174 TACCTTAAAATGCTTACCCTTTTGACAGGG 8 8 0 TCTACCTTTT 0.978921 -51 GGTACCCCTTTACTTACCCTTTGGTAAGGAGT 8 37 1 TCTACCTTTG 0.888548 -22 TTTGTTAAATTCCATAACCTTGTTATAATTATG 10 93 0 TCTACCTTGT 0.962912 -58 TGTTAACTCCCCAGCCTTTTTACTGTAAAG 11 8 1 TCCACCTTTT 0.986725 -51 AATGTTCAGTTACATAACCTTTTTAAGGAAGTA 13 39 0 TCTACCTTTT 0.978921 -147 * * ** ****** Masking position 10 Map Score: 14.9371 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 156 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 TATGGGAAGGTAAAATTTAAATATACATTTT 2 31 0 TAAAATTTAA 0.761487 -82 TAAATATAATTTAAATTTTAACATTTATACG 4 270 1 TTAAATTTAA 0.681813 -31 AATATTGACATTAAATTGCTAGGGTATCCCA 5 46 1 TTAAATTGTA 0.935623 -43 ATGACTACTTAAATTGCAACTTTATAAAC 9 9 1 TTAAATTGAA 0.960532 -52 CAAAGATTGATTAATTTTTAAAATTTATTTT 10 40 1 TTAATTTTAA 0.851003 -111 AAGGTTGCTGCTAAATTGGAAG 11 47 1 CTAAATTGAA 0.904482 -12 TTTGCTTAACTTAAATTTAAACCTTGTGCAT 13 145 0 TTAAATTTAA 0.945127 -41 GAACCTTAATTTTATATACTTGCTTT 14 6 1 TTAATTTTTA 0.794187 -41 TGTAAAAATTTTAAATTTTTAAGATTTATTT 15 62 0 TTAAATTTTA 0.867027 -49 TATAATCTTACTAAATTTTTAGTCGGGGATT 16 37 1 CTAAATTTTA 0.8544 -25 AGAAAAGGCTTTAAATTGAAAGCGTAATAAA 17 26 0 TTAAATTGAA 0.960532 -125 ******** ** Masking position 4 Map Score: 11.5062 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 36 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 5 TTTAGCTTCTAATTCTCTTGCTTGTGTTAA 4 113 0 AATTCTCTTG 0.966778 -188 AAAATTTCTCAATTTTCTTCTTTTCAAGTG 4 188 0 AATTTTCTTC 0.972533 -113 AAAATTGAGAAATTTTCTTGACAAGAATGG 4 202 1 AATTTTCTTG 0.948735 -99 AATATTTAAAAAGTTTCTTCGAATATTTCT 5 22 0 AAGTTTCTTC 0.928298 -67 CCTGGTAGAGATTTCTCTTCTTATCGACAT 7 12 0 ATTTCTCTTC 0.932136 -252 GAGTCTCCTTAATTCTCTTCTCAAACTCTT 7 64 0 AATTCTCTTC 0.982356 -200 ********** Masking position 6 Map Score: 4.59647 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 49 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 TTCCCATAGGTCGACAAGTTTTTTATACCCCT 2 54 1 TCGCAAGTTT 0.903333 -59 TATTTATATATTCCCATATTTTATTTTAAGTG 3 20 0 TTCCATATTT 0.756676 -281 TCAAGAAAATTTCTCAATTTTCTTCTTTTCAA 4 191 0 TTCCAATTTC 0.677268 -110 TAGCAATTTAATGTCAATATTTAAAAAGTTTC 5 35 0 ATGCAATTTT 0.554173 -54 ACCAGGGATCTCCTCAAAATATTAGGTGAAGA 7 36 1 TCCCAAATAT 0.698559 -228 CTTAATTCTCTTCTCAAACTCTTCACCTAATA 7 55 0 TTCCAAATCT 0.838735 -209 CACATAATACTCCTCATACTTTTCGATTGGAG 7 91 0 TCCCATATTT 0.790768 -173 TCAGTAAACCTTCTCAATGTTTATAAAGTTGC 9 26 0 TTCCAATTTT 0.939272 -35 TGCCTTTGTTTTGTCAAAGATTGATTAATTTT 10 26 1 TTGCAAAATT 0.731907 -125 ATGTGTTTAGTTGACAAATTTTTGTAAAATAA 10 64 0 TTGCAAATTT 0.940228 -87 ATGTTAAAAATTGGCAATTTTTAAGATTTATT 12 92 0 TTGCAATTTT 0.931405 -40 ATCCCTCGCCAAAATTTGGTTGCCTTA 13 6 1 TCGCAAATTT 0.950292 -180 AACTGAACATTCGACAATAATTCAAGAAATTG 13 61 1 TCGCAATATT 0.741204 -125 AGGATAAAACTCCACAATTTCTTGAATTATTG 13 75 0 TCCCAATTCT 0.845111 -111 TGCCCAAAAATGCACAAGGTTTAAATTTAAGT 13 136 1 TGCCAAGTTT 0.671738 -50 *** **** *** Masking position 6 Map Score: 6.89104 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 209 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 7 CATAAAAAAGGGTGAGGAGGAGAGGAAG 2 95 1 GGTGAGGAGG 0.974963 -18 TTGGTTTTACGGTGTGGAATTCTCCATAAC 3 239 0 GGTGTGGAAT 0.801549 -62 CAAAATATTAGGTGAAGAGTTTGAGAAGAG 7 50 1 GGTGAAGAGT 0.971043 -214 AATCGAAAAGTATGAGGAGTATTATGTGAA 7 95 1 TATGAGGAGT 0.846909 -169 CTTACCCTTTGGTAAGGAGT 8 49 1 GGTAAGGAGT 0.942436 -10 ATAAAAGAACGCTGAAGAGTGGGGTAACG 10 132 1 GCTGAAGAGT 0.946024 -19 CAGTAAAAAGGCTGGGGAGTTAACA 11 6 0 GCTGGGGAGT 0.980976 -53 GCCTAGCCTGGATGGGGCGTCGGCCTTCGG 17 68 1 GATGGGGCGT 0.89852 -83 ********** Masking position 3 Map Score: 3.21142 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 175 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 AATCATAATACTTTTAAGATTTTTTAGACATA 1 24 0 CTTAAGATTT 0.819319 -33 TCTTTTTCTTTTCGTAGGATTTTTTATTTATA 3 79 1 TTCAGGATTT 0.549196 -222 CCAGAGCTTCCTGCAGGTATTTCTGACCCCGG 4 37 0 CTGGGTATTT 0.808774 -264 AGATAAAATGCTGGGGATATTTTTCCATCCCT 4 153 1 CTGGATATTT 0.825674 -148 TAAAAAGTTTCTTCGAATATTTCTACATATAT 5 14 0 CTTAATATTT 0.547647 -75 TAGCAATTTAATGTCAATATTTAAAAAGTTTC 5 35 0 ATGAATATTT 0.577034 -54 AGGAGATCCCTGGTAGAGATTTCTCTTCTTAT 7 18 0 TGGGAGATTT 0.8415 -246 ATTCTATTCATTGCAGGGATTTAGTGCTTCCC 7 183 0 TTGGGGATTT 0.928748 -81 TTTATAAACATTGAGAAGGTTTACTGAAATTG 9 31 1 TTGAAGGTTT 0.619326 -30 AGCCTTTTTACTGTAAAGATTTTAAAGGTTGC 11 23 1 CTGAAGATTT 0.939728 -36 AAATTGGCAATTTTTAAGATTTATTTTACCAT 12 85 0 TTTAAGATTT 0.788635 -47 ATTCAAGAAATTGTGGAGTTTTATCCTCTGTG 13 80 1 TTGGAGTTTT 0.555357 -106 AAGAATCACCATGCTAATATTTGCTTAACTTA 13 163 0 ATGAATATTT 0.577034 -23 TCAGTTTCAGTTGATAGGATTTAGGGTGAGTG 15 12 1 TTGAGGATTT 0.919716 -99 AAATTTTAAATTTTTAAGATTTATTTTGACAA 15 56 0 TTTAAGATTT 0.788635 -55 CTAAATTTTTAGTCGGGGATTTGCA 16 47 1 AGTGGGATTT 0.354512 -15 GTTGGCGGGCCGGCCGGGATTTGAACCCGGGA 17 107 0 CGGGGGATTT 0.85211 -44 *** ******* Masking position 10 Map Score: 8.41547 Number of sites scoring better than the average of aligned sites = 361 Number in coding regions = 300 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 9 AACTTGTCGACCTATGGGAAGGTAAAATTTAAAT 2 40 0 CCGGGAGGTA 0.926819 -73 AAAAAAGGGTGAGGAGGAGAGGAAG 2 98 1 GAGGAGGGAA 0.982558 -15 CTTTTCAAGTGAATAGGGATGGAAAAATATCCCC 4 165 0 GAGGGAGGAA 0.948332 -136 GAAGGCTAGAGAAGCGGAGTGGAAGCGCCTAAGA 7 122 1 GAGGAGGGAA 0.982558 -142 AAAACAAAGGCAATTGGAGGGGAAAGG 10 4 0 CAGGAGGGAA 0.986666 -147 TAATCAACCTTAGGAAAGGTATTTATTATAA 16 8 1 CCGGAAGGTA 0.949548 -54 GGGGCGTCGGCCTTCGGAGCCGAAGGTCCCGGGT 17 81 1 CCGGAGCGAA 0.944989 -70 ** **** **** Masking position 14 Map Score: 1.16239 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 115 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 AGATTATAATATCTCCATTTATAACAGCCT 4 79 1 ATCTCCATTT 0.928594 -222 TTTATATCACCATATTTAAGTCAAA 6 6 1 ATCACCATAT 0.949068 -152 CCAGTACGGTATCTTCATGTCGTAAAGCTT 7 155 0 ATCTTCATGT 0.908264 -109 TCTGATATCACCATGTTCATGTTAAA 12 116 0 ATCACCATGT 0.986673 -16 TAAGAATCACCATGCTAATATTTGC 13 171 0 ATCACCATGC 0.97089 -15 ********** Masking position 7 Map Score: 0.734117 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 19 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 11 AAAAAATCTTAAAAGTATTATGATTTTTAC 1 31 1 AAAAGTATTA 0.546559 -26 ACATAATATAAAAATGATTGTTTGTGTTCT 3 168 0 AAAATGATTG 0.897057 -133 TTTGTCAGATAAAATGCTGGGGATATTTTT 4 147 1 AAAATGCTGG 0.928555 -154 ATTTATGTTAAAAAGGCTTAAATATAATTT 4 252 1 AAAAGGCTTA 0.970531 -49 GGGGTACCTTAAAATGCTTACCCTTTTGAC 8 15 0 AAAATGCTTA 0.943702 -44 CTTTACAGTAAAAAGGCTGGGGAGTTAACA 11 11 0 AAAAGGCTGG 0.962314 -48 TATTCTATGCAAAATACTTAGTTTTAGCAT 12 56 0 AAAATACTTA 0.651789 -76 CAAAACGTCTAAAAGGATTGCCCAAAAATG 13 118 1 AAAAGGATTG 0.944815 -68 CGGCCCTCAGAAAAGGCTTTAAATTGAAAG 17 35 0 AAAAGGCTTT 0.909167 -116 ********** Masking position 4 Map Score: 5.36198 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 111 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 12 GTAGAATATAGTCCAGCCTTCTATGATTGTG 3 201 1 GCCAGCCTTC 0.982012 -100 GTATTTCTGACCCCGGCTTTAATATTATCAC 4 22 0 CCCGGCTTTA 0.795178 -279 GGAAAAATATCCCCAGCATTTTATCTGACAA 4 148 0 CCCAGCATTT 0.841708 -153 CACTCCGCTTCTCTAGCCTTCACATAATACT 7 112 0 CCTAGCCTTC 0.946152 -152 TTACCCCACTCTTCAGCGTTCTTTTATAACT 10 128 0 CTCAGCGTTC 0.871547 -23 TGTTAACTCCCCAGCCTTTTTACTGTAAA 11 9 1 CCCAGCCTTT 0.976188 -50 CAGGCTAGGCCACCGGCCCTCAGAAAAGGCT 17 47 0 CCCGGCCCTC 0.991212 -104 CTGGATGGGGCGTCGGCCTTCGGAGCCGAAG 17 75 1 CTCGGCCTTC 0.978466 -76 TTCAAATCCCGGCCGGCCCGCCAACAATAAC 17 114 1 GCCGGCCCGC 0.88922 -37 * ********* Masking position 7 Map Score: 4.69161 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 182 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 13 ********** No masking Map Score: -4.90742e-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 14 ********** No masking Map Score: -4.90742e-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 15 ********** No masking Map Score: -4.90742e-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