AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00220_aful_reg_100.orf -o00220_aful_100.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -x5 -e 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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 AF0522 39 acetylornithine deacetylase (argE) #2 AF0883 71 argininosuccinate lyase (argH) #3 AF1147 65 glutamate N-acetyltransferase (argJ) #4 AF1255 27 ornithine carbamoyltransferase (argF) #5 AF1259 36 inosine monophosphate dehydrogenase, putative #6 AF1260 207 phosphoribosylformylglycinamidine synthase I (purQ) #7 AF1280 272 acetylglutamate kinase (argB) #8 AF2071 60 N-acetyl-gamma-glutamyl-phosphate reductase (argC) #9 AF2252 78 argininosuccinate synthetase (argG) #10 AF2289 216 mevalonate kinase (mvk) #11 AF2334 33 spermidine synthase (speE) Motif number 1 TTAAAATTTTCAGAAAGTTTTTAATTTCACCTTC 3 20 0 CGAAGTTTAA 0.978574 -46 TTAATTAACCGGAAATTTTTAACCGGT 4 9 1 CGAAATTTAA 0.982332 -19 ACTTTCAAAGCTGGCAGATCTTTAATT 6 4 0 CGCAGCTTTA 0.978712 -204 GCTGCCGACACGGAAAAAGCTTAAAAGATTGCGG 6 170 1 CGAAACTTAA 0.991925 -38 GGTAGTAGCCTTGAAAAATCTTTAGATTGGAGCG 7 113 0 TGAAACTTTA 0.864902 -160 TTTGGGAATCCAGGCAGTTTTTAACACTTGCCTC 7 199 1 CGCAGTTTAA 0.966271 -74 GCAATGCGGTCTGATAATCCTTAAGTATCCCAAC 7 235 1 CGTAACTTAA 0.950893 -38 TTCGCCATCTCAGAAAACTCTTTATTTTGCCTCT 8 24 1 CGAAACTTTA 0.988916 -37 TCTGAAAACCCAGGAAGTTTTTTAACTTTTGTTT 9 15 1 CGAAGTTTTA 0.970781 -64 TTTGTTTAATCTCAAAAGATTTAAACCTCTCCGC 9 42 1 CCAAATTTAA 0.85534 -37 GATTAGACTACGGGAAAAACTTAAAGAATTTTGT 10 192 0 CGAAACTTAA 0.991925 -25 GTTTATAATCCCGTCAATCCTTTATTAGCTT 11 13 1 CGCAACTTTA 0.982421 -21 * * *** ***** Masking position 6 Map Score: 22.0968 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 123 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 2 GAATTAATAACCTCTGCACAAACTGAGTGC 2 52 1 CCTCGACACG 0.955717 -20 AAAGGAATCAGACCAGCCCCACCAGCTAAAAGAAT 6 85 1 GACCGCCCCG 0.95703 -123 CACCAATGCCCCCCTACCCTTAAGGGCCCGTGGCT 7 17 1 CCCCACCAAG 0.800768 -256 GAAGGCCGTCGCTCTATCCATGCTGAGCCACGGGC 7 42 0 GCTCACCGCG 0.996241 -231 CTTTAGATTGGAGCGGACCCGGCGGGATTTGAACC 7 93 0 GAGCGCCGCG 0.96752 -180 CAGATTGCCTGAGCCATCCACGCCGATTTTGGGAA 7 172 1 GAGCACCGCG 0.969869 -101 TTAACACTTGCCTCCAGCAATGCGGTCTGATAATC 7 219 1 CCTCACAGCG 0.970465 -54 AACCTCTGAAAACCCAGGAAGTTTTTT 9 3 1 CCTCGAACCG 0.89369 -76 GAGAGTATGTCCTCTATCTTTGCCGGTTCCGGCTC 10 32 1 CCTCACTGCG 0.976718 -185 TCCATAATAGCCTCCATCCTCCCAGCCTCCGCTGC 10 92 1 CCTCACCCCG 0.995742 -125 ACCGTCTACACCTCCGACCCCGCAGCGGAGGCTGG 10 113 0 CCTCGCCGCG 0.997265 -104 **** * ** ** * Masking position 4 Map Score: 14.1045 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 491 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 3 AAAGCCCAGTATATAAGCCTGATTC 1 6 0 ATATAAGCCT 0.83514 -34 GCGGTAAGAATTAATAACCTCTGCACAAAC 2 45 1 TTAATAACCT 0.834815 -27 GAAGGTGAAATTAAAAACTTTCTGAAAATT 3 20 1 TTAAAAACTT 0.758623 -46 TAACCGGAAATTTTTAACCGGT 4 16 1 TTTTTAACCG 0.874322 -12 CAAAAGTTTTTAGCTTGCCGTCATTT 5 7 1 TTTTTAGCTT 0.902835 -30 AACCTAAACTTTCAAAGCTGGCAGATCTTT 6 15 0 TTCAAAGCTG 0.729298 -193 GAAAAGAATTCTTTTAGCTGGTGGGGCTGG 6 97 0 CTTTTAGCTG 0.687292 -111 AACCGCAATCTTTTAAGCTTTTTCCGTGTC 6 176 0 TTTTAAGCTT 0.902835 -32 AGCGACGGCCTTCTAAGCCGTAGATCGCGG 7 64 1 TTCTAAGCCG 0.902222 -209 GAGGCAAGTGTTAAAAACTGCCTGGATTCC 7 203 0 TTAAAAACTG 0.701769 -70 TTTATTTTGCCTCTTAACCTTTTCCTC 8 44 1 CTCTTAACCT 0.707718 -17 CCCAGGAAGTTTTTTAACTTTTGTTTAATC 9 23 1 TTTTTAACTT 0.852473 -56 ATCTCAAAAGATTTAAACCTCTCCGCATGA 9 50 1 ATTTAAACCT 0.731136 -29 CAGCTCCTCCATAATAGCCTCCATCCTCCC 10 85 1 ATAATAGCCT 0.703998 -132 ATTGACGGGATTATAAACCT 11 1 0 TTATAAACCT 0.914998 -33 CGTCAATCCTTTATTAGCTT 11 24 1 TTATTAGCTT 0.914998 -10 ********** Masking position 6 Map Score: 12.9255 Number of sites scoring better than the average of aligned sites = 656 Number in coding regions = 547 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 4 TTTCCGTGTCGGCAGCGTTGATGTTCTGCA 6 156 0 GGCAGCGTTG 0.968229 -52 TTAAGGGTAGGGGGGCATTGGTGTTTATA 7 10 0 GGGGGCATTG 0.98813 -263 GAGCGGACCCGGCGGGATTTGAACCCGCGA 7 88 0 GGCGGGATTT 0.957161 -185 TCCCAAAATCGGCGTGGATGGCTCAGGCAA 7 176 0 GGCGTGGATG 0.836683 -97 AGGATTATCAGACCGCATTGCTGGAGGCAA 7 226 0 GACCGCATTG 0.940496 -47 CTCTCCGCATGACGGGATTGT 9 68 1 GACGGGATTG 0.990276 -11 GAGGGATTACGAGGTCGTTGAGCCGGAACC 10 56 0 GAGGTCGTTG 0.873127 -161 AGCGGAGGCTGGGAGGATGGAGGCTATTAT 10 95 0 GGGAGGATGG 0.8464 -122 ATAAAGGATTGACGGGATTATAAACCT 11 8 0 GACGGGATTA 0.919175 -26 ********** Masking position 1 Map Score: 5.72351 Number of sites scoring better than the average of aligned sites = 896 Number in coding regions = 844 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 GCACTCAGTTTGTGCAGAGGTTATTA 2 56 0 AGTTTGTGCA 0.907285 -16 GAACCAATTCTGAGCAGGTAAATTAA 3 50 0 ATTCTGAGCA 0.976789 -16 GGCAGCGTTGATGTTCTGCACTCTTTAGTG 6 146 0 ATGTTCTGCA 0.906095 -62 CGCTCTATCCATGCTGAGCCACGGGCCCTT 7 38 0 ATGCTGAGCC 0.960311 -235 CTCAGGCAATCTGCTGAGCAATTGTAAAGC 7 155 0 CTGCTGAGCA 0.960311 -118 AACTTAAAGAATTTTGTGCAAACATTCTCT 10 179 0 ATTTTGTGCA 0.963981 -38 ********** Masking position 5 Map Score: 1.81172 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 122 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 TCAGAAAGTTTTTAATTTCACCTTCCGAATTG 3 13 0 TTTATTTACC 0.944296 -53 TTCTGAAAATTTTAATTTACCTGCTCAGAATT 3 39 1 TTTATTTCCT 0.982815 -27 CAAAAGTTTTTAGCTTGCCGTCATTTTTCT 5 9 1 TTTACTTCCG 0.955859 -28 TTTTTCTTTTTTTACTTTTCCCTAGACAGGAC 6 43 1 TTTATTTCCC 0.988822 -165 CAGAAAACTCTTTATTTTGCCTCTTAACCTTT 8 34 1 TTTATTTCCT 0.982815 -27 **** *** *** Masking position 7 Map Score: 1.63423 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 30 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 7 GGGCTTTTAAGAGCTACGATT 1 29 1 GAGCTACGAT 0.861815 -11 AATTAAAGATCTGCCAGCTTTGAAAGT 6 8 1 GATCTGCCAG 0.782982 -200 TAGACAGGACGATCTTAGAGAAAGGAATCA 6 65 1 GATCTTAGAG 0.681301 -143 TATCCATGCTGAGCCACGGGCCCTTAAGGG 7 33 0 GAGCCACGGG 0.981334 -240 AGCATGGATAGAGCGACGGCCTTCTAAGCC 7 53 1 GAGCGACGGC 0.967181 -220 TTGAACCCGCGATCTACGGCTTAGAAGGCC 7 70 0 GATCTACGGC 0.968441 -203 TATTATGGAGGAGCTGAGGGATTACGAGGT 10 71 0 GAGCTGAGGG 0.971047 -146 CTCCCAGCCTCCGCTGCGGGGTCGGAGGTG 10 110 1 CCGCTGCGGG 0.839722 -107 AGACGGTGTAGAACTTCGGGTGAAAAACGA 10 141 1 GAACTTCGGG 0.930173 -76 GCTAATAAAGGATTGACGGGATTATAAACC 11 12 0 GATTGACGGG 0.811407 -22 ********** Masking position 2 Map Score: 3.29039 Number of sites scoring better than the average of aligned sites = 885 Number in coding regions = 833 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 8 TGGAGCGGACCCGGCGGGATTTGAACCCGC 7 90 0 CCGGCGGGAT 0.923204 -183 TTGTAAAGCTGCTGAATGGTAGTAGCCTTG 7 134 0 GCTGAATGGT 0.870982 -139 ATCCCGTCATGCGGAGAGGTTTAAATCTTT 9 56 0 GCGGAGAGGT 0.984566 -23 TTATGGAGGAGCTGAGGGATTACGAGGTCG 10 69 0 GCTGAGGGAT 0.983217 -148 CGCAGCGGAGGCTGGGAGGATGGAGGCTAT 10 98 0 GCTGGGAGGA 0.917596 -119 CCCAGCCTCCGCTGCGGGGTCGGAGGTGTA 10 112 1 GCTGCGGGGT 0.994684 -105 ********** Masking position 4 Map Score: 2.15713 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 341 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 ********** No masking Map Score: 3.36387e-13 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: 3.36387e-13 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: 3.36387e-13 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