AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -iargR_aful_opreg_300.orf -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 AF0079 69 A. fulgidus predicted coding region AF0079 #2 AF0080 27 acetylornithine aminotransferase (argD-1) #3 AF0522 39 acetylornithine deacetylase (argE) #4 AF0883 71 argininosuccinate lyase (argH) #5 AF1255 27 ornithine carbamoyltransferase (argF) #6 AF1259 36 inosine monophosphate dehydrogenase, putative #7 AF1260 207 phosphoribosylformylglycinamidine synthase I (purQ) #8 AF1261 133 medium-chain acyl-CoA ligase (alkK-4) #9 AF1263 74 iron-sulfur cluster binding protein #10 AF1269 300 A. fulgidus predicted coding region AF1269 #11 AF1270 33 transcriptional regulatory protein, ArsR family #12 AF1280 272 acetylglutamate kinase (argB) #13 AF1814 83 A. fulgidus predicted coding region AF1814 #14 AF1815 36 acetylornithine aminotransferase (argD-2) #15 AF2071 60 N-acetyl-gamma-glutamyl-phosphate reductase (argC) #16 AF2252 78 argininosuccinate synthetase (argG) Motif number 1 AAATTTTTTACGGTAACCTTTTTGAGTGTCGGTG 1 22 0 CGAATTTTTG 0.933864 -48 TAACTTATACCTTAAAATTTTTTACGGTAACCTT 1 36 0 CTAATTTTTA 0.809899 -34 CTTAATTACTCAGCAAAATTTTTTCC 2 12 1 CGAATTTTTT 0.96922 -16 TTAATTAACCGGAAATTTTTAACCGGT 5 9 1 CGAATTTTAA 0.952974 -19 TTTTAGCTTGCCGTCATTTTTCTTCTGTA 6 18 1 CGCATTTCTT 0.781482 -19 ACTTTCAAAGCTGGCAGATCTTTAATT 7 4 0 CGCATCTTTA 0.950648 -204 AAGCAATCAACCGCAATCTTTTAAGCTTTTTCCG 7 180 0 CGAATTTTAA 0.952974 -28 TACATCGTAAGTTCATTTTCCAACTTTT 8 5 1 TGAATCATTT 0.460125 -129 CTTAAGAATCCTGAAAGTTTATTTTCAGTTATAA 8 54 0 CGAATTATTT 0.894239 -80 GTAAATTAATTCGAAAAATTATTATGTCGATTAA 8 87 1 TGAATTATTA 0.770446 -47 AACCCTTTAACAGGAAATTTTCTACTGTCTATCC 10 270 0 CGAATTTCTA 0.938171 -31 GGTAGTAGCCTTGAAAAATCTTTAGATTGGAGCG 12 113 0 TGAATCTTTA 0.88321 -160 TTTGGGAATCCAGGCAGTTTTTAACACTTGCCTC 12 199 1 CGCATTTTAA 0.895491 -74 TTCGCCATCTCAGAAAACTCTTTATTTTGCCTCT 15 24 1 CGAATCTTTA 0.978313 -37 TCTGAAAACCCAGGAAGTTTTTTAACTTTTGTTT 16 15 1 CGAATTTTTA 0.986696 -64 * * ** ****** Masking position 6 Map Score: 16.4864 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 216 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 2 ACGGTAACCTTTTTGAGTGTCGGTGGTACTAAT 1 14 0 TTTTGTGCGG 0.987807 -56 CCGCAAATGTATTTATGTTTTGGAGATGATGGC 4 16 0 ATTTGTTTGG 0.943321 -56 CAAAAGTTTTTAGCTTGCCGTCATTTTTCT 6 8 1 TTTTCTTCCG 0.887403 -29 GCTTGCCGTCATTTTTCTTCTGTA 6 23 1 ATTTCTTTGT 0.698104 -14 AAAAGAATTCTTTTAGCTGGTGGGGCTGGTCTG 7 93 0 TTTTCTGTGG 0.980627 -115 CTTTTAAGCTTTTTCCGTGTCGGCAGCGTTGAT 7 164 0 TTTTGTGCGG 0.987807 -44 TTTTTACCTTACGGAGAAGATTGA 10 2 1 TTTTCTTCGG 0.973455 -299 TACGGAGAAGATTGACGTGCCCGAGCAGATAAC 10 20 1 ATTGGTGCCG 0.684666 -281 TTTTCCACCAATTTTGGTGGTGGCC 13 3 0 ATTTGTGTGG 0.973523 -81 AAAGAAACAAATTTAGCTGACGGAGGAATATTT 13 48 0 ATTTCTGCGG 0.983292 -36 AAATAAAGAGTTTTCTGAGATGGCGAAAGTTGA 15 18 0 TTTTGAGTGG 0.854288 -43 CCAGGAAGTTTTTTAACTTTTGTTTAATCTCAA 16 24 1 TTTTCTTTGT 0.760958 -55 **** *** *** Masking position 3 Map Score: 12.6595 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 199 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 3 AAAAAATTTTGCTGAGTAATTAAGT 2 6 0 GCTGAGTAAT 0.922298 -22 GTTATAATCTGCTGAAAAACAAAAAAGTTG 8 31 0 GCTGAAAAAC 0.870939 -103 AATCTGTAATGCTGCCCAATCCAAAAAGCT 10 136 0 GCTGCCCAAT 0.963983 -165 GCGACGGAGAGCTGCACCATTCTTCTCTGT 10 191 0 GCTGCACCAT 0.97434 -110 TATACTTTGCGCTGCAAAATATAGGCGACG 10 215 0 GCTGCAAAAT 0.913293 -86 AAGTTGCACCGTTGCGCAACCAAACA 11 18 1 GTTGCGCAAC 0.495488 -16 CTCTATCCATGCTGAGCCACGGGCCCTTAA 12 36 0 GCTGAGCCAC 0.983813 -237 CAGGCAATCTGCTGAGCAATTGTAAAGCTG 12 153 0 GCTGAGCAAT 0.988925 -120 CAGCAGATTGCCTGAGCCATCCACGCCGAT 12 169 1 CCTGAGCCAT 0.916443 -104 ********** Masking position 3 Map Score: 8.79165 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 287 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 AATTACTCAGCAAAATTTTTTCC 2 15 1 CAAATTTTTC 0.658172 -13 CGCAAATGTATTTATGTTTTGGAGATGATGGC 4 16 0 TTATTTTTGG 0.677899 -56 GCTTTGAAAGTTTAGGTTTTTCTTTTTTTACT 7 27 1 TTAGTTTTTC 0.952079 -181 GGTTTTTCTTTTTTTACTTTTCCCTAGACAGG 7 41 1 TTTTCTTTTC 0.798523 -167 CCGCAATCTTTTAAGCTTTTTCCGTGTCGGCA 7 172 0 TAAGTTTTTC 0.895508 -36 TTTTCCAACTTTTTTGTTTTTCAGCAGATTAT 8 26 1 TTTTTTTTTC 0.841108 -108 TTAATCGACATAATAATTTTTCGAATTAATTT 8 89 0 TATATTTTTC 0.476301 -45 TATATAAATCTATAGCATTTGCGATATTGTTA 9 18 1 TTAGATTTGC 0.672658 -57 GCTTTCACCTCATAGCCTTTTCTCCACAAATT 9 53 0 CTAGCTTTTC 0.910972 -22 TAAACTAGCACATAGTCTTTTGTGGTTATCTG 10 45 0 CTAGCTTTTG 0.595994 -256 CTCTCCGTCGCCTATATTTTGCAGCGCAAAGT 10 210 1 CTATTTTTGC 0.909431 -91 GTCAAGGAGATTTATACTTTGCGCTGCAAAAT 10 225 0 TTATCTTTGC 0.916174 -76 CGCTCCAATCTAAAGATTTTTCAAGGCTACTA 12 113 1 TAAGTTTTTC 0.895493 -160 AATAAATCATTAAATATTTTTCCT 14 3 0 TAATTTTTTC 0.875787 -34 ATGATTTATTTCTATTTTTTGC 14 25 1 TTATTTTTGC 0.935888 -12 CTCAGAAAACTCTTTATTTTGCCTCTTAACCT 15 32 1 TTTTTTTTGC 0.825388 -29 TATTTTGCCTCTTAACCTTTTCCTC 15 46 1 CTAACTTTTC 0.770303 -15 * *** ****** Masking position 8 Map Score: 14.2408 Number of sites scoring better than the average of aligned sites = 467 Number in coding regions = 333 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 5 CAAAAGTTTTTAGCTTGCCGTCATTTTTCT 6 11 1 TAGCTTGCCG 0.947008 -26 AGAATTCTTTTAGCTGGTGGGGCTGGTCTG 7 93 0 TAGCTGGTGG 0.963458 -115 TTGCGGTTGATTGCTTACCG 7 198 1 TTGCTTACCG 0.880711 -10 TTTTTACCTTACGGAGAAGATTGA 10 5 1 TACCTTACGG 0.812702 -296 CTGCAAAATATAGGCGACGGAGAGCTGCAC 10 204 0 TAGGCGACGG 0.876001 -97 TGTTTGGTTGCGCAACGGTGCAA 11 21 0 TTGGTTGCGC 0.780989 -13 TCAGACCGCATTGCTGGAGGCAAGTGTTAA 12 219 0 TTGCTGGAGG 0.923875 -54 TCCACCAATTTTGGTGGTGGCC 13 3 0 TTGGTGGTGG 0.916866 -81 GAAACAAATTTAGCTGACGGAGGAATATTT 13 48 0 TAGCTGACGG 0.983242 -36 ********** Masking position 1 Map Score: 3.67804 Number of sites scoring better than the average of aligned sites = 545 Number in coding regions = 514 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 GCAATTAGTACCACCGACACTCAAAAAGG 1 9 1 TACCACCGCA 0.734118 -61 GCTCTGCCATCATCTCCAAAAC 4 2 1 CTCTGCCACA 0.939375 -70 AAATTGATGCCGTTACTAGCACTAAAGAGTG 7 127 1 CGTTACTACA 0.628553 -81 AGAACATCAACGCTGCCGACACGGAAAAAGC 7 159 1 CGCTGCCGCA 0.968829 -49 AAAGCTCAAGGGCTTCCATCATCCTAACTAA 10 111 0 GGCTTCCACA 0.977481 -190 GATTTTTCAAGGCTACTACCATTCAGCAGCT 12 127 1 GGCTACTACA 0.882384 -146 TTTTAACACTTGCCTCCAGCAATGCGGTCTG 12 217 1 TGCCTCCACA 0.960929 -56 GGCCACCACCAAAATTGGTGG 13 1 1 GGCCACCACA 0.979149 -83 TATAGCCCTACTTTTCCACCAATTTTGGTGG 13 16 0 CTTTTCCACA 0.763664 -68 TATATAAATATTCCTCCGTCAGCTAAATTTG 13 43 1 TTCCTCCGCA 0.874703 -41 ******** ** Masking position 11 Map Score: 3.34848 Number of sites scoring better than the average of aligned sites = 918 Number in coding regions = 866 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 AATCGTAGCTCTTAAAAGCCCAGTATATA 3 21 0 CTCTAAAAGC 0.973115 -19 AACGGCATCAATTTGAAAAGAATTCTTTTAG 7 110 0 ATTTAAAAGA 0.818182 -98 ACACGGAAAAAGCTTAAAAGATTGCGGTTGA 7 177 1 AGCTAAAAGA 0.936446 -31 AGCAGATTATAACTGAAAATAAACTTTCAGG 8 48 1 AACTAAAATA 0.694553 -86 ATGCTGCCCAATCCAAAAAGCTCAAGGGCTT 10 127 0 ATCCAAAAGC 0.944374 -174 GTTTCTTTACAACTGAAAAGC 13 73 1 AACTAAAAGC 0.965285 -11 AACCTCTGAAAACCCAGGAAGTTT 16 4 1 CTCTAAAACC 0.874345 -75 CTTTTGTTTAATCTCAAAAGATTTAAACCTC 16 40 1 ATCTAAAAGA 0.975786 -39 **** ****** Masking position 6 Map Score: 1.81767 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 148 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 GCACTCAGTTTGTGCAGAGGTTAT 4 58 0 TCAGTTTGTG 0.764183 -14 AATTCTTTTAGCTGGTGGGGCTGGTCTGAT 7 91 0 GCTGGTGGGG 0.973227 -117 TTTGTGGTTATCTGCTCGGGCACGTCAATC 10 29 0 TCTGCTCGGG 0.936382 -272 TTGACGATCCTCTGGTTGGGATAGACAGTA 10 252 1 TCTGGTTGGG 0.993031 -49 TGTTTGGTTGCGCAACGGTGCA 11 22 0 TTTGGTTGCG 0.916947 -12 GTGTCCAGATTCAGGTTGGGATACTTAAGG 12 253 0 TCAGGTTGGG 0.984125 -20 TTCCACCAATTTTGGTGGTGGCC 13 4 0 TTTGGTGGTG 0.915894 -80 ********** Masking position 6 Map Score: 3.59426 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 215 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 ********** No masking Map Score: -3.15948e-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 10 ********** No masking Map Score: -3.15948e-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: -3.15948e-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