AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -iarcA_aful_opreg_100.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 AF0396 154 A. fulgidus predicted coding region AF0396 #2 AF0400 84 NADH oxidase (noxA-3) #3 AF0647 132 isocitrate dehydrogenase, NADP (icd) #4 AF0681 145 succinate dehydrogenase, flavoprotein subunit A (sdhA) #5 AF0806 113 L-lactate permease (lctP) #6 AF1342 126 thymidine phosphorylase (deoA-2) Motif number 1 TATCTTAAAGAAAAATTTAAATATCGTCAGTG 1 42 0 AAAATTAAAT 0.96328 -113 CTTTAAGATAAAAACTTAAAACTAATTTGCTT 1 64 1 AAAATTAAAC 0.981755 -91 CGACGTACAGAAAAATTCAAGCTACAAACTTA 1 98 0 AAAATTAAGC 0.949106 -57 TGTACGTCGGAAAATTTATATTGCAATATTGC 1 121 1 AAAATTTATT 0.793229 -34 GTACGGCTCGAAAACTTAACATTTTTGGGTAA 2 18 1 AAAATTACAT 0.955715 -67 CAAAATGTGCAAAAGTTTTTACGGTATAATTG 3 53 0 AAAATTTTAC 0.907156 -80 ATAACAAACCTAAACTTCAAGCG 4 2 0 TAAATTAAGC 0.822621 -144 CGCACGAGAAAAAAGATTTTATATAACAAACC 4 24 0 AAAAATTTAT 0.536975 -122 TGCCTCTCTTTAAAATTCACTTCGTATGCTTT 4 69 0 TAAATTACTT 0.691696 -77 TCCCTCTATATAAACATTATACTAACTGTTGC 4 98 0 TAAAATATAC 0.633156 -48 AACGATGCAAAAAAGATAAATCATA 5 4 0 AAAAATAATC 0.848343 -110 TTTAATTTTTAAAATTTTAATCAAAGATGGTA 5 76 0 AAAATTAATC 0.957436 -38 TTAAAATTTTAAAAATTAAAACATGGAGGTGA 5 88 1 AAAATTAAAC 0.981755 -26 AAAGCTGACGACAATTTAACATC 6 2 0 ACAATTACAT 0.732393 -125 GTTTATGTTTAAAAATTCTCACCTGAAAAGGT 6 37 0 AAAATTTCAC 0.939389 -90 GATAGCGAGAAAAAGTTAATATTCTTTCAGAG 6 92 1 AAAATTATAT 0.93153 -35 **** ** **** Masking position 7 Map Score: 17.6502 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 176 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 2 CGATATTTAAATTTTTCTTTAAGATAAAAACTTAAAACTA 1 48 1 ATTTCAAAAA 0.933548 -107 TGTAGCTTGAATTTTTCTGTACGTCGGAAAATTTATATTG 1 104 1 ATTTCTGAAA 0.948234 -51 AAAACTTAACATTTTTGGGTAAGCTGAAAATAGCAAGCCA 2 28 1 ATTTGCAAAA 0.942993 -57 TTGAGTCGAAGATTGTCAAAATGTGCAAAAGTTTTTACGG 3 61 0 GTTTCTAAAA 0.984772 -72 AGCGGAAGGTTGTGGTAGTTTATAAAATCCTTCCGCT 3 106 0 GTTTGTAAAA 0.981165 -27 CATTATACTAACTGTTGCCTCTCTTTAAAATTCACTTCGT 4 76 0 ATGTGTAAAA 0.96869 -70 GAACAGCAAAGGTTATCTAACGATGCAAAAAAGATAAATC 5 14 0 GTTTCTAAAA 0.984772 -100 GATGTTAAATTGTCGTCAGCTTTAAAACCTTTTCAGG 6 8 1 ATTTCTAAAA 0.987405 -119 AGTTATAGATAATGTTGTTTATGTTTAAAAATTCTCACCT 6 45 0 ATGTGTAAAA 0.96869 -82 * ** ** * **** Masking position 6 Map Score: 7.36267 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 45 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 3 CCTATCCCCTCCGCACTGCTACTGTG 1 7 1 CCCTCCGCAC 0.960735 -148 CAATATTGCCACTTGCTCACA 1 144 1 ACTTGCTCAC 0.912439 -11 TACCGTAAAAACTTTTGCACATTTTGACAA 3 59 1 ACTTTTGCAC 0.978014 -74 TTTATAAAATCCTTCCGCTCTTGGTTGAGT 3 95 0 CCTTCCGCTC 0.960124 -38 TATATAAAATCTTTTTTCTCGTGCGTACTA 4 31 1 CTTTTTTCTC 0.693978 -115 TCGTTAGATAACCTTTGCTGTTCACATGTG 5 31 1 ACCTTTGCTG 0.900705 -83 CAGCTTTAAAACCTTTTCAGGTGAGAATTT 6 27 1 ACCTTTTCAG 0.8967 -100 ATTATCTATAACTTCTTCACGATAGCGAGA 6 72 1 ACTTCTTCAC 0.971319 -55 AAGAATATTAACTTTTTCTCGCTATCGTGA 6 88 0 ACTTTTTCTC 0.96557 -39 ********** Masking position 4 Map Score: 6.52461 Number of sites scoring better than the average of aligned sites = 1062 Number in coding regions = 993 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 4 ATTTTTCTTTAAGATAAAAACTTAAAACTAAT 1 58 1 AGATAAAACT 0.929109 -97 AGAAAAATTCAAGCTACAAACTTAAAAAGCAA 1 90 0 AGCTCAAACT 0.959143 -65 ATTTTTGGGTAAGCTGAAAATAGCAAGCCATA 2 38 1 AGCTAAAATA 0.882011 -47 CTGAATTTCGATGCTGAAAGCTT 3 2 0 AGCTAAAGCT 0.975228 -131 GGCTCATGTGAGGCTTAAAGCAATTATACCGT 3 33 1 AGCTAAAGCA 0.969844 -100 AGGTTATCTAACGATGCAAAAAAGATAAATCA 5 13 0 AGATCAAAAA 0.766346 -101 CTTTGATTAAAATTTTAAAAATTAAAACATGG 5 82 1 ATTTAAAAAT 0.485825 -32 AATGTTGTTTATGTTTAAAAATTCTCACCTGA 6 43 0 AGTTAAAAAT 0.831091 -84 AACTTCAAAAACTCTGAAAGAATATTAACTTT 6 103 0 ATCTAAAGAA 0.799798 -24 * *** ****** Masking position 5 Map Score: 2.45484 Number of sites scoring better than the average of aligned sites = 550 Number in coding regions = 483 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 5 ********** No masking Map Score: 6.91659e-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 6 ********** No masking Map Score: 6.91659e-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 7 ********** No masking Map Score: 6.91659e-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