AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -ipurR_mthe_opreg_100.orf -g0.495 -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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH141 102 conserved protein #2 MTH147 23 phenylacrylic acid decarboxylase #3 MTH148 47 conserved protein #4 MTH150 75 conserved protein #5 MTH170 141 phosphoribosylaminoimidazolesuccinocarboxamide synthase #6 MTH615 173 adenylosuccinate synthetase #7 MTH648 65 ribosomal protein L37 #8 MTH649 300 conserved protein #9 MTH661 119 ammonium transporter #10 MTH662 61 nitrogen regulatory protein P-II #11 MTH663 205 ammonium transporter #12 MTH710 102 GMP synthetase, subunit B #13 MTH784 83 ribose-phosphate pyrophosphokinase #14 MTH997 31 carbamoyl-phosphate synthase, large subunit #15 MTH1202 236 proteasome, beta subunit #16 MTH1203 69 cleavage and polyadenylation specificity factor #17 MTH1204 46 phosphoribosylformylglycinamidine cyclo-ligase #18 MTH1375 22 isoleucyl-tRNA synthetase #19 MTH1376 65 conserved protein #20 MTH1380 167 serine hydroxymethyltransferase #21 MTH1393 141 phosphoribosylaminoimidazole carboxylase #22 MTH1445 64 glycinamide ribonucleotide synthetase #23 MTH1537 300 adenylosuccinate lyase #24 MTH1864 109 phosphoribosylformylglycinamidine synthase II related protein #25 MTH1865 37 conserved protein Motif number 1 CTAGCACAGCACCTTTTTATACCTTTCTTT 1 10 0 ACCTTTTATA 0.869289 -93 TCTATAACCTCCTGGTAAAAATCATGG 1 86 0 ACCTCCTGTA 0.955816 -17 CAGGACAGAAACCTCCTGGAACAGATTAACG 3 18 1 ACCTCCTGAA 0.961629 -30 GGTGTGAAAAACCCCTTGAAAACTTGGAGGG 6 77 1 ACCCCTTAAA 0.951305 -97 TTTATTGGATACCCCTTAATATATGAGAGGC 6 131 1 ACCCCTTATA 0.94402 -43 GTTCTAATCCTCCTTAAAATCAGTTAAT 7 48 0 TCCTCCTAAA 0.935031 -18 GCACTGCAGTACCTCTTCAAATCCATTCCAG 8 171 0 ACCTCTTAAA 0.97481 -130 TTTAATAAGGACCTCCTGTTATATATTGGTA 15 96 1 ACCTCCTTTA 0.844837 -141 ATGGGTTAACCCCATCAAATCCTTTATCC 20 9 1 ACCCCATAAA 0.777825 -159 CAGTACACCTTCTGATACTCTGTAACT 21 7 1 ACCTTCTATA 0.885108 -135 TCCCTTCGTCTCCTCTTCAAAGTACCTTACA 23 184 0 TCCTCTTAAA 0.925507 -117 CTGTAGCAGATCCTTTTTAAAAGTTTCCAAG 24 29 0 TCCTTTTAAA 0.712104 -81 ACCTCTTTGTATCGTTTAGGT 24 99 0 ACCTCTTGTA 0.949173 -11 ******* *** Masking position 11 Map Score: 12.9628 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 252 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 2 CATGATTTTTACCAGGAGGTTATAGA 1 87 1 ACCAGGAGGT 0.984713 -16 GTTAATCTGTTCCAGGAGGTTTCTGTCCTG 3 18 0 TCCAGGAGGT 0.956583 -30 TCATCACAGAACCTGGATGGAATTCGGCTG 6 17 1 ACCTGGATGG 0.915395 -157 CCCCTTGAAAACTTGGAGGGTTAATGATGA 6 88 1 ACTTGGAGGG 0.849237 -86 ACTGGGACCTGAAGGTACCCACCCTA 12 7 1 ACCTGAAGGT 0.939531 -96 ATTGTTAATTACCGGAAGGTGATTTTTC 13 66 1 ACCGGAAGGT 0.941522 -18 AGATGGGGCTTCCTGAGGGGTTGAAGAACG 15 46 0 TCCTGAGGGG 0.713766 -191 ACCAATATATAACAGGAGGTCCTTATTAAA 15 96 0 AACAGGAGGT 0.931133 -141 ATTTCTCCTGAACTGGATGTATATACTTAT 19 12 1 AACTGGATGT 0.743717 -54 GCGTGTTGATAGCTGGGGGGATTCCGAATC 20 73 0 AGCTGGGGGG 0.891664 -95 GTTACAGAGTATCAGAAGGTGTACTG 21 7 0 ATCAGAAGGT 0.795374 -135 AAATGGTCCCTGCGGGAGGTGCCATCTATT 21 81 1 TGCGGGAGGT 0.847738 -61 TCTCTCAGTAATCTGGAGGTCCTTCAGTTT 23 30 1 ATCTGGAGGT 0.957744 -271 ********** Masking position 5 Map Score: 11.0938 Number of sites scoring better than the average of aligned sites = 1185 Number in coding regions = 1115 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 3 AATCATGGAATGAATATCCCAAGAAACATG 1 64 0 TGAATATCCC 0.806096 -39 TCCCACCTCATCATTAACCCTCCAAGTTTT 6 95 0 TCATTAACCC 0.632297 -79 AAACTTTTATTGGATACCCCTTAATATATG 6 126 1 TGGATACCCC 0.813168 -48 GGTGATTCTCCCTAAAATTTCT 6 162 0 TGATTCTCCC 0.919524 -12 TCTGTAAAGTTGATCCACCCTTCCCCTTAC 7 19 0 TGATCCACCC 0.944311 -47 GTCCGCCCTGGGATCCCCCCATCCATGAGA 8 140 0 GGATCCCCCC 0.96686 -161 ATCCATTCCAGGGTCCGCCCTGGGATCCCC 8 152 0 GGGTCCGCCC 0.925919 -149 GGATAACCGTTCTTCAACCCCTCAGGAAGC 15 39 1 TCTTCAACCC 0.466331 -198 TATGTCCATGGGGACAGCCCTTTGCAGGGT 15 136 1 GGGACAGCCC 0.814167 -101 GTGTTTCTCCCTCAGCTGGAT 18 12 0 TGTTTCTCCC 0.760577 -11 CTTATTTATATCATCACCCCAAAACCATAA 19 37 1 TCATCACCCC 0.832945 -29 ATGGGTTAACCCCATCAAATCC 20 3 1 GGGTTAACCC 0.489389 -165 AATCGGATTCGGAATCCCCCCAGCTATCAA 20 68 1 GGAATCCCCC 0.891447 -100 TTTAATAGATGGCACCTCCCGCAGGGACCA 21 84 0 GGCACCTCCC 0.731648 -58 TAACACTCCTTGATCATCCCGAAAATCTGA 23 279 0 TGATCATCCC 0.93669 -22 ********** Masking position 8 Map Score: 10.0417 Number of sites scoring better than the average of aligned sites = 966 Number in coding regions = 891 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 4 TCAACTCTCCAATACTTATATAGGTGTAAAT 5 84 0 ATACTTATAT 0.896241 -58 ACTATCACTTTTAAAGAATTTGAG 5 128 0 ACACTTTTAA 0.734043 -14 TGAGGTGGGAAAAACTTTTATTGGATACCCC 6 115 1 AAACTTTTAT 0.950719 -59 GCAGTGCAAGAAAACTTATATATTAGTAGAA 8 195 1 AAACTTATAT 0.936102 -106 GGTTCACAGAAGTACTTATAAGAAATCCGGT 10 27 1 ATACTTATAA 0.716547 -35 AAATTAAACAATTATTTTTATTTAACATATT 11 12 1 ATATTTTTAT 0.843051 -194 CTATATCCGAAAGATTTATATATCAGCATCA 11 99 1 AGATTTATAT 0.647569 -107 TTTCTCTCCAACAATTTATATCATAGTCGGA 11 164 0 AAATTTATAT 0.873704 -42 TAATAAATCAATCATTTTTATTCG 12 89 1 ACATTTTTAT 0.816621 -14 CCGGTAATTAACAATTTTTATATAGATAACT 13 50 0 AAATTTTTAT 0.90109 -34 ATATTGGTACAGAACTTTTATGTCCATGGGG 15 118 1 AAACTTTTAT 0.950719 -119 CTGGTTTTTTATTATTTTTATTAGAGGTGTA 15 213 1 ATATTTTTAT 0.843051 -24 TTCAGCTAGTGAAACTTATATTATATGGTAT 23 58 1 GAACTTATAT 0.80961 -243 GGAGGACTTGGAAACTTTTAAAAAGGATCTG 24 23 1 GAACTTTTAA 0.621063 -87 * ********* Masking position 4 Map Score: 7.6998 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 35 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 5 GTCTTGCCCCGTTAATCTGTTCCAGGAG 3 30 0 CCGTTAATCT 0.800755 -18 AACTAACGAGCTGAAAATCTTCCAATCAGA 8 241 0 CTGAAAATCT 0.955646 -60 TAACCTACTTCCGAAAATCTACCAACATTA 9 42 0 CCGAAAATCT 0.978022 -78 ATACATTTATCTGAAACTATATCCGAAAGA 11 83 1 CTGAAACTAT 0.77142 -123 TTCTGATACTCTGTAACTCTCTATTGGTAG 21 20 1 CTGTAACTCT 0.918823 -122 GACGAAGGGACCGAAACTCACACCGGAACA 23 205 1 CCGAAACTCA 0.917738 -96 CTTGATCATCCCGAAAATCTGAGTACAAGG 23 271 0 CCGAAAATCT 0.978022 -30 ********** Masking position 6 Map Score: 4.09583 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 33 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 GGCTCCATGAATATATACTAGAAGCACCATAGT 4 19 1 ATATATATGA 0.829296 -57 TTTCGCAAGATTATATAACTGAATCGCAATATA 5 39 1 TTATATACGA 0.963802 -103 TCTCCAATACTTATATAGGTGTAAATTCTATTA 5 77 0 TTATATAGGA 0.775231 -65 GCAAGAAAACTTATATATTAGTAGAATAGAAAA 8 200 1 TTATATATGA 0.904146 -101 TACCAACATTATAAATATCATGAGAATAAAAAA 9 20 0 ATAAATACTA 0.645836 -100 CTTAAATATCCTTAACCGGATTTC 10 48 0 TTAAATACTA 0.779766 -14 TCCGAAAGATTTATATATCAGCATCATCTTACT 11 104 1 TTATATACGA 0.963815 -102 TTCTGTACCAATATATAACAGGAGGTCCTTATT 15 99 0 ATATATACGA 0.932057 -138 TGAAAACCCTTTATATACCATAAAAACACAATG 15 170 1 TTATATACTA 0.949612 -67 GGCTAACTATTTAGATAACCTTAAACTATTCTT 17 11 1 TTAGATACTA 0.74848 -36 GTATATACTTATTTATATCATCACCCCAAAACC 19 30 1 ATTTATACTA 0.627774 -36 TTAACACCAATTTTATATTGTCATTGCAACTAT 20 138 1 TTTTATATTA 0.536965 -30 TAGAATCCCCTTATATACTGTTATGAAGACCTG 21 47 1 TTATATATTA 0.869822 -95 TTCCTATAAAATATATACTTTCAAATAA 22 47 1 ATATATATTA 0.774845 -18 ATAAAGCTTATTATATCTCTGCAGATACCATAT 23 80 0 TTATATCCGA 0.783265 -221 ******* * * * Masking position 5 Map Score: 10.0283 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 20 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 AATATATACTAGAAGCACCATAGTTCTAATA 4 28 1 AGAACACCAT 0.948317 -48 CTGAGGTGTGAAAAACCCCTTGAAAACTTGG 6 73 1 AAAACCCCTT 0.971829 -101 AACTTTTATTGGATACCCCTTAATATATGAG 6 127 1 GGATCCCCTT 0.852402 -47 GAAAAATCACCTTCCGGTAATTA 13 71 0 AAAACACCTT 0.946116 -13 CAACCCCTCAGGAAGCCCCATCTATTATAAA 15 53 1 GGAACCCCAT 0.967464 -184 AGGGTTAAATGAAAACCCTTTATATACCATA 15 161 1 GAAACCCTTT 0.760628 -76 TATATACCATAAAAACACAATGGGATCCAGG 15 181 1 AAAACACAAT 0.614127 -56 CTCTATTGGTAGAATCCCCTTATATACTGTT 21 38 1 AGAACCCCTT 0.97798 -104 TTTGCCATGAAAAATCACCATAAGTTTGATG 23 114 0 AAAACACCAT 0.934435 -187 **** ****** Masking position 3 Map Score: 4.95676 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 153 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 8 TCATGTGGGTAACATTCAGAAGA 2 10 0 ATGTGGTAAA 0.89203 -14 TAAAGTTATTATGTCAGTAAAACTATTAGAAC 4 50 0 ATGTCATAAA 0.932832 -26 TATAAATATCATGAGAATAAAAAAAGTAGAGA 9 12 0 ATGAGATAAA 0.957618 -108 CTCCTTTTGGATGTGCCTAACATATCTGCAAT 9 92 0 ATGTGCTAAA 0.938289 -28 ACTTCCGACAATGAGAGTAAGATGATGCTGAT 11 120 0 ATGAGATAAA 0.957618 -86 AATAGTTGCAATGACAATATAAAATTGGTGTT 20 140 0 ATGACATATA 0.71337 -28 TATAGGAAATATGTCATTAATAATAATGACAG 22 23 0 ATGTCATAAA 0.932832 -42 GGTAGTTGTGATGAGCATAATACTGGCAGTGT 23 235 1 ATGAGCTAAA 0.938289 -66 ****** *** * Masking position 9 Map Score: 3.49032 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 17 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 TGGATTTGAAGAGGTACTGCAGTGCAAGAAA 8 177 1 GAGTACTGCA 0.953534 -124 ACATTAAATAGATGTCCTGCAAGATAATAAA 12 65 1 GAGTCCTGCA 0.992518 -38 ATACTGTTATGAAGACCTGTAAATGGTCCCT 21 61 1 GAGACCTGTA 0.916657 -81 CAGTAATCTGGAGGTCCTTCAGTTTCAGCTA 23 35 1 GAGTCCTTCA 0.962148 -266 AAGTACCTTACAAGACCTGCACCGCTGGGTG 23 165 0 CAGACCTGCA 0.973794 -136 TAAAAGTTTCCAAGTCCTCCACTTCAATTGT 24 12 0 CAGTCCTCCA 0.95167 -98 ** ******** Masking position 8 Map Score: 2.39824 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 105 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 CTAGCACAGCACCTTTTTATACCTTTCTTT 1 11 0 ACCTTTTTAT 0.688808 -92 AATTATCATATCATGTTTCTTGGGATATTC 1 53 1 TCATGTTTCT 0.898533 -50 GAAATCAGATTCATGCTTCTTAGGGTGAAA 5 13 0 TCATGCTTCT 0.77266 -129 ATCAGATACTTCATTTTTCTATTCTACTAA 8 217 0 TCATTTTTCT 0.848093 -84 GATGCCGGTAACCTACTTCCGAAAATCTAC 9 50 0 ACCTACTTCC 0.779471 -70 GAAGTTACCTTCCTATTTCCGACTATGATA 11 147 1 TCCTATTTCC 0.916274 -59 AATAAATCAATCATTTTTATTCG 12 90 1 TCATTTTTAT 0.580349 -13 TGCAGTAAACACCTGTTTACTGATATTCCC 16 30 1 ACCTGTTTAC 0.824915 -40 AAATCCTTTATCCTTTTTCTAACTTACATA 20 27 1 TCCTTTTTCT 0.913932 -141 ATTATTAATGACATATTTCCTATAAAATAT 22 31 1 ACATATTTCC 0.828826 -34 TCAACCTGTTTCCCCAAATCAAT 25 25 0 ACCTGTTTCC 0.950052 -13 ********** Masking position 4 Map Score: 4.26202 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 281 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 11 TTTTTAATTTATCTAGCACAGCACCTTTTTA 1 22 0 ATCTAGCAAG 0.87545 -81 CCTGGTAAAAATCATGGAATGAATATCCCAA 1 72 0 ATCATGGATG 0.82462 -31 GGATCCCCCCATCCATGAGAGATGCATGTGG 8 129 0 ATCCATGAAG 0.798647 -172 CCCAGGGCGGACCCTGGAATGGATTTGAAGA 8 158 1 ACCCTGGATG 0.936048 -143 CTAAATTTTAATCTAGGATAG 8 290 1 ATCTAGGAAG 0.912157 -11 TTTTCATTTAACCCTGCAAAGGGCTGTCCCC 15 145 0 ACCCTGCAAG 0.90832 -92 ACACAATGGGATCCAGGACTGGTTTTTTATT 15 195 1 ATCCAGGATG 0.978448 -42 TATCCAGCTGAGGGAGAAACAC 18 2 1 ATCCAGCTAG 0.828897 -21 AGACACTTCCACCCAGCGGTGCAGGTCTTGT 23 156 1 ACCCAGCGTG 0.836393 -145 TTTCGGGATGATCAAGGAGTGTTAAG 23 285 1 ATCAAGGATG 0.912157 -16 ******** ** Masking position 1 Map Score: 3.00632 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 244 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 12 AAGGGGTTTTTCACACCTCAGGATGAACGC 6 64 0 TCACACCTCA 0.987494 -110 TAAAAGTTTTTCCCACCTCATCATTAACCC 6 105 0 TCCCACCTCA 0.99188 -69 TACTCCCACCTCATTCCTTTTAA 15 4 1 TCCCACCTCA 0.99188 -233 GGACCGAAACTCACACCGGAACAGGTAGTT 23 212 1 TCACACCGGA 0.945039 -89 ********** Masking position 5 Map Score: 2.16687 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 20 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 13 TCCTTAAAATCAGTTAATCTGTAAAGTTGATCCA 7 32 0 CAGTTTTTAA 0.877118 -34 AAAATTTAGCCGGATTATATTTAAATCTAACTAA 8 265 0 CGGATTTTAA 0.953451 -36 TATCCTTAACCGGATTTCTTATAAGTACTTCTGT 10 32 0 CGGATCTTAA 0.964897 -30 TCAGTAATTGAGGTTATTATCTAAACTTGTTTTA 11 43 1 AGGTTTTTAA 0.439136 -163 AAGATCACTTCTAAAAAACAGGGA 16 56 0 AAGATCTTAA 0.856066 -14 AGTACACCTTCTGATACTCTGTAACTCTCTATTG 21 12 1 CTGATTTTAA 0.837541 -130 ATAATAATGACAGATTCCGTTCAAG 22 2 0 CAGATCTCAA 0.879085 -63 TTATTAATGACATATTTCCTATAAAATATATACT 22 32 1 CATATCTTAA 0.752591 -33 TATATCTCTGCAGATACCATATAATATAAGTTTC 23 68 0 CAGATCTTAA 0.974751 -233 TAATCTGTAGCAGATCCTTTTTAAAAGTTTCCAA 24 30 0 CAGATTTTAA 0.966407 -80 GGATCTGCTACAGATTATAGATAATACAGGTGCA 24 47 1 CAGATTGTAA 0.844178 -63 ***** * * *** Masking position 13 Map Score: 4.71239 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 33 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 14 ********** No masking Map Score: -1.26944e-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: -1.26944e-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