AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -ifnr_mthe_opreg_300.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 MTH170 141 phosphoribosylaminoimidazolesuccinocarboxamide synthase #2 MTH420 300 conserved protein #3 MTH700 110 conserved protein #4 MTH702 27 acetyl-CoA synthetase related protein #5 MTH1354 124 NADH oxidase #6 MTH1587 31 histidinol-phosphate aminotransferase #7 MTH1591 30 phosphonopyruvate decarboxylase #8 MTH1592 21 conserved protein #9 MTH1593 205 ribosomal protein S3a #10 MTH1594 72 conserved protein #11 MTH1598 300 conserved protein #12 MTH1707 300 cobalamin biosynthesis protein M Motif number 1 CGGAGTGTGTCCCCTCTGATACGGGGATTGCCGGTG 2 49 0 CCCTCTTGGG 0.952303 -252 CTATCCCCTTCTCCTAGGAGTTATCGGTTA 5 105 0 CCCTTCCGGG 0.96059 -20 GAGTTACATACACCGCCAGTATGGAATACTCTATAA 9 92 0 CCCGCCTGGA 0.991392 -114 GGATAGCACTGGCCTCCTCCAGGGGGAGGAGGTTGA 10 16 1 GCCTCCCGGG 0.996541 -57 GGAGGAGGTTGACCTCCATTTCGGGAGGGCCTCCCA 10 40 1 GCCTCCTGGA 0.992593 -33 GGTTCTCATGGCCCTCCTGTGGGGCGTTATCAG 11 8 0 GCCTCCTGGG 0.996992 -293 GTCTCGGGCACCTTGCCGTTGTGGTGGATGTGAGGT 11 63 0 CTTGCCTGGG 0.845426 -238 GGTCTCCCTCCCGGTGTGCAGCAGGT 11 285 0 GTCTCCCGGG 0.980595 -16 GGTAATAATCCTCCGCCTATCTGGCACATCCCCACC 12 109 0 CCCGCCTGGA 0.991585 -192 GCAATGGTCATCCCTCCGCTCAGGGTGCGATATTAC 12 167 1 TCCTCCTGGT 0.910665 -134 * ***** * ** * Masking position 13 Map Score: 12.9813 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 359 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 2 AGCCCGGAGTGTGTCCCCTCTGATACGGGG 2 59 0 GTGTCCCCTC 0.984373 -242 CCAGGCGGTGTCCCCTGTGTGGTAGTA 4 11 0 GTGTCCCCTG 0.944037 -17 CAAATGGATCGGGACCCCTC 8 12 1 GGGACCCCTC 0.968143 -10 CGAAATGGAGGTCAACCTCCTCCCCCTGGA 10 33 0 GTCAACCTCC 0.898392 -40 AAGGAACTGGGAGGCCCTCCCGAAATGGAG 10 53 0 GAGGCCCTCC 0.972504 -20 AATGGTTCTCATGGCCCTCCTGTGGGGCGT 11 17 0 ATGGCCCTCC 0.856111 -284 ATACCGGATAGAGAACCCCCCTCAATAACT 11 220 1 GAGAACCCCC 0.960593 -81 GGTCTCCCTCCCGGTGTGCAG 11 290 0 GTCTCCCTCC 0.965505 -11 TATACACCCTGAGACCCCCGGCAATGGTCA 12 147 1 GAGACCCCCG 0.970811 -154 CCCGGCAATGGTCATCCCTCCGCTCAGGGT 12 163 1 GTCATCCCTC 0.833724 -138 ********** Masking position 6 Map Score: 7.53214 Number of sites scoring better than the average of aligned sites = 799 Number in coding regions = 752 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 3 GATTCATGCTTCTTAGGGTGAAATA 1 6 0 TCTTAGGGTG 0.967872 -136 GTGGTTGATTTCTCCGGGTGCAGCACCGGC 2 26 1 TCTCCGGGTG 0.928445 -275 TGTCCTTCAGTATCAGGGAATGGATTGCTG 2 255 1 TATCAGGGAA 0.90849 -46 GTGTGGTAGTTATAAGGGAGCATCAAAC 5 9 0 TATAAGGGAG 0.965286 -116 TCTATAATAGGATAAGGGAGTATTTAAATC 9 69 0 GATAAGGGAG 0.967872 -137 CGGTGTTAAAGATTAAGGTGATATA 9 191 1 GATTAAGGTG 0.838914 -15 TTGCCGGGGGTCTCAGGGTGTATAATGGTA 12 141 0 TCTCAGGGTG 0.984182 -160 TCATCCCTCCGCTCAGGGTGCGATATTACC 12 174 1 GCTCAGGGTG 0.985382 -127 ATTACCACAATATAAGGGAAACCGAAGATT 12 198 1 TATAAGGGAA 0.827791 -103 ATTAAAAAAAGATTAAGGAGGCGAATAGC 12 282 1 GATTAAGGAG 0.838914 -19 ********** Masking position 3 Map Score: 10.6034 Number of sites scoring better than the average of aligned sites = 927 Number in coding regions = 883 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 4 TATTTAAGTTTTTGTGGTTGATTTCTCCGGG 2 13 1 TTTGTGGTGA 0.972824 -288 TGAGCATAGATTTTTGGTTAAATGCTGCATA 2 129 0 TTTTTGGTAA 0.715923 -172 CGGTGTCCCCTGTGTGGTAGTA 4 2 0 TGTGTGGTGT 0.989141 -26 TCAATAGATCTGTGTGGTAGTTATAAGGGAG 5 19 0 TGTGTGGTGT 0.989141 -106 TTTGGGGTGCTGTGTGGTCATGAATATGAAC 9 26 0 TGTGTGGTAT 0.982884 -180 TTGTGGTGGATGTGAGGTCATGTTTAATCAT 11 50 0 TGTGAGGTAT 0.911435 -251 GCACCTTGCCGTTGTGGTGGATGTGAGGTCA 11 61 0 GTTGTGGTGA 0.916768 -240 TTTCCCTTATATTGTGGTAATATCGCACCCT 12 188 0 ATTGTGGTAT 0.882578 -113 ******** ** Masking position 8 Map Score: 6.85649 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 61 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 CACCCTAAGAAGCATGAATCTGATTTCGCAA 1 16 1 ACATGAATCT 0.96041 -126 GTGTCCCTGTATCATGGATTTATCTGTCAGT 2 93 0 ACATGGATTT 0.960412 -208 GTGTTCTGTGAGCATAGATTTTTGGTTAAAT 2 137 0 ACATAGATTT 0.961166 -164 CCTTCCCTTTACCATAGATCTCTGGTCCCGG 2 208 0 ACATAGATCT 0.960412 -93 AGATCATAAATCTAGGAAGGTGG 7 3 1 ACATAAATCT 0.961166 -28 TAACCAGTTAAATATGAATTTTTTGAATTTA 9 139 1 ATATGAATTT 0.734317 -67 AGCTGGATTTAACATAAATTCAAAAAATTCA 9 153 0 ACATAAATTC 0.870246 -53 GGTGATATTGATCATAAACTTAAGATGCACA 11 257 0 ACATAAACTT 0.870246 -44 * ********* Masking position 4 Map Score: 4.01493 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 39 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 GCCGGTGCTGCACCCGGAGAAATCAACCAC 2 26 0 CACCCGGAGA 0.808104 -275 TCACAGAACACTGCAGCACTGATATGAGTA 2 157 1 CTGCAGCACT 0.700669 -144 TTCCCTGATACTGAAGGACAGATAATCACA 2 245 0 CTGAAGGACA 0.673365 -56 GAATGGATTGCTGGCGCAGACAGAAGGGCT 2 272 1 CTGGCGCAGA 0.963431 -29 TTAATTTTTCCTGACGCTGATGAGGTGTAA 3 89 1 CTGACGCTGA 0.857346 -22 CCAGGCGGTGTCCCCTGTGTG 4 17 0 CAGGCGGTGT 0.97297 -11 GTATTCCATACTGGCGGTGTATGTAACTCT 9 99 1 CTGGCGGTGT 0.982558 -107 CCTCCTCCCCCTGGAGGAGGCCAGTGCTAT 10 18 0 CTGGAGGAGG 0.928586 -55 CCCTCCCGAAATGGAGGTCAACCTCCTCCC 10 39 0 ATGGAGGTCA 0.465306 -34 CTTTACTTCTCAGGCGCTCTCTATCTCTTT 11 180 0 CAGGCGCTCT 0.882112 -121 TCCCGGTGTGCAGCAGGTGATATTGATCAT 11 273 0 CAGCAGGTGA 0.908304 -28 GGTCTCCCTCCCGGTGTGCAGCAGGTG 11 284 0 CTCCCGGTGT 0.865316 -17 ATGTGCCAGATAGGCGGAGGATTATTACCA 12 116 1 TAGGCGGAGG 0.600032 -185 ********** Masking position 6 Map Score: 5.28184 Number of sites scoring better than the average of aligned sites = 1747 Number in coding regions = 1638 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 7 GGATTGCCGGTGCTGCACCCGGAGAAATCA 2 31 0 TGCTGCACCC 0.973562 -270 ACACACTCCGGGCTGCAGACTGACAGATAA 2 75 1 GGCTGCAGAC 0.691364 -226 AATCTATGCTCACAGAACACTGCAGCACTG 2 148 1 CACAGAACAC 0.916834 -153 TTCATGACCACACAGCACCCCAAACCACCA 9 33 1 CACAGCACCC 0.964297 -173 CAATATCACCTGCTGCACACCGGGAGGGAG 11 278 1 TGCTGCACAC 0.987109 -23 TGTGCATTGTCGCTGAACACATAAAGACAT 12 62 1 CGCTGAACAC 0.983821 -239 ********** Masking position 7 Map Score: 2.69067 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 110 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 GTGGAACTTAAACATTTAAGATGAGAAACTT 3 21 1 AAATTTAAGA 0.757003 -90 AGAGACATTTATCATTAATAATCATTATTAA 3 62 1 ATATTAATAA 0.904089 -49 AGCGTCAGGAAAAATTAATAATGATTATTAA 3 76 0 AAATTAATAA 0.872568 -35 ATAATTCAGATATATTTATAAATTTGGATAC 5 51 0 TAATTTATAA 0.708832 -74 ATATATCTGAATTATTTATAAAATGAAGAAG 5 67 1 ATATTTATAA 0.904089 -58 CCCACCTTCCTAGATTTATGATCT 7 4 0 TAATTTATGA 0.603921 -27 AACCATTGAGATGATTAAACATGACCTCACA 11 40 1 ATATTAAACA 0.615361 -261 TCATGTGGAGATTATTTAAGAAAAGAGATAG 11 159 1 ATATTTAAGA 0.810916 -142 TTAATGATTTATAATGATGTTTTT 12 4 1 ATATTTATAA 0.904089 -297 TAGATTCCATAAAATTAAAAACATCATTATA 12 20 0 AAATTAAAAA 0.832606 -281 ATCCCCACCATTTATTAAAAAGGTCCATGTC 12 87 0 TTATTAAAAA 0.708802 -214 GGTTGAAGTGATTATTACTAATCTTCGGTTT 12 216 0 ATATTACTAA 0.61806 -85 ** ******** Masking position 4 Map Score: 3.10673 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 53 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 9 TCACATCCTTACCTTCCCTTTACCATAGAT 2 220 0 ACCTTCCCTT 0.822999 -81 CGCCAGCAATCCATTCCCTGATACTGAAGG 2 258 0 CCATTCCCTG 0.922709 -43 TGATAAATGTCTCTTCCCTTAATAAAGTTT 3 46 0 CTCTTCCCTT 0.889417 -65 CCAGGCGGTGTCCCCTGTGTGGTAGTA 4 11 0 GTGTCCCCTG 0.830178 -17 GTTTGATGCTCCCTTATAACTACCA 5 6 1 ATGCTCCCTT 0.874098 -119 CTATCCCCTTCTCCTAGGAG 5 115 0 CTATCCCCTT 0.957717 -10 CAAGATTTAAATACTCCCTTATCCTATTAT 9 66 1 ATACTCCCTT 0.924588 -140 TATATCACCTTAATCTTTAAC 9 195 0 ATATCACCTT 0.763081 -11 AGGTCAACCTCCTCCCCCTGGAGGAGGCCA 10 25 0 CCTCCCCCTG 0.787066 -48 TTTATGATCAATATCACCTGCTGCACACCG 11 270 1 ATATCACCTG 0.812112 -31 TATTACCATTATACACCCTGAGACCCCCGG 12 138 1 ATACACCCTG 0.802336 -163 ********** Masking position 9 Map Score: 2.95111 Number of sites scoring better than the average of aligned sites = 1324 Number in coding regions = 1244 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 10 ********** No masking Map Score: -2.85395e-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: -2.85395e-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: -2.85395e-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