AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -iarcA_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 AF0396 154 A. fulgidus predicted coding region AF0396 #2 AF0400 84 NADH oxidase (noxA-3) #3 AF0645 232 translation initiation factor eIF-5A (eif5A) #4 AF0647 132 isocitrate dehydrogenase, NADP (icd) #5 AF0681 145 succinate dehydrogenase, flavoprotein subunit A (sdhA) #6 AF0806 113 L-lactate permease (lctP) #7 AF1342 126 thymidine phosphorylase (deoA-2) Motif number 1 ACTGACGATATTTAAATTTTTCTTTAAGATAA 1 43 1 TTAAATTTTC 0.982772 -112 AGCAAATTAGTTTTAAGTTTTTATCTTAAAGA 1 63 0 TTTAATTTTT 0.917779 -92 AATATTGCAATATAAATTTTCCGACGTACAGA 1 119 0 TTAAATTTCC 0.88551 -36 TACCCAAAAATGTTAAGTTTTCGAGCCGTACT 2 17 0 TTTAATTTTC 0.972183 -68 TCAGTCGCATTTTTAACTCTTCTTCAGAAAAA 3 180 1 TTTAATCTTC 0.97162 -53 TTTGCGTTAATTTAAATTTTTCTGAAGAAGAG 3 196 0 TTAAATTTTC 0.982772 -37 TGTGGTAGTTTATAAAATCCTTCCGCTCTTGG 4 101 0 TTAAATCCTT 0.915247 -32 AGGTTTGTTATATAAAATCTTTTTTCTCGTGC 5 23 1 TTAAATCTTT 0.946994 -123 GTTGCCTCTCTTTAAAATTCACTTCGTATGCT 5 71 0 TTAAATTCAC 0.759606 -75 TGTTTAACTCTATTAATCCCTCTATATAAACA 5 114 0 TTTAACCCTC 0.837852 -32 TGTTTTAATTTTTAAAATTTTAATCAAAGATG 6 79 0 TTAAATTTTA 0.818149 -35 GATGTTAAATTGTCGTCAGCTTTA 7 3 1 TTTAATTGTC 0.857139 -124 TGTCGTCAGCTTTAAAACCTTTTCAGGTGAGA 7 21 1 TTAAACCTTT 0.816886 -106 TTGTTTATGTTTAAAAATTCTCACCTGAAAAG 7 39 0 TAAAATTCTC 0.747054 -88 CAACATTATCTATAACTTCTTCACGATAGCGA 7 68 1 TTAACTCTTC 0.876447 -59 TCTGAAAGAATATTAACTTTTTCTCGCTATCG 7 91 0 TTTAATTTTT 0.917779 -36 * **** ***** Masking position 5 Map Score: 18.3153 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 207 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 2 TTCCGACGTACAGAAAAATTCAAGCTACAAACTT 1 99 0 CGAAATCAAG 0.958519 -56 TTTGGGTAAGCTGAAAATAGCAAGCCATATAATA 2 41 1 CGAAAACAAG 0.977758 -44 CTTCTGGAATCCGAGAATTACCAGCTGCCCTGAT 3 26 1 CGAGATCCAG 0.983028 -207 CCCGTGAGGCCAGAGGTAAAGCAGTATTCCGGTA 3 64 1 CGAGTAGCAG 0.972788 -169 CACCATGAAGTAGAACAGAACCAGCCGTCTGATT 3 121 1 TGAAAACCAG 0.877397 -112 AAAAATGCGACTGAGAAGAAAAAGCATGAAGCTC 3 160 0 CGAGAAAAAG 0.954121 -73 CTAATCAATACAAAGCATACGAAGTGAATTTTAA 5 58 1 CAAGAAGAAG 0.890118 -88 GAGGGATTAATAGAGTTAAACAAGGTGGTGTA 5 124 1 TGAGTACAAG 0.932825 -22 AATATTCTTTCAGAGTTTTTGAAGTTCA 7 109 1 CGAGTTGAAG 0.95784 -18 * *** * * **** Masking position 4 Map Score: 5.65967 Number of sites scoring better than the average of aligned sites = 610 Number in coding regions = 578 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 3 TTAAGATAAAAACTTAAAACTAATTTGCTT 1 66 1 AACTTAAAAC 0.94883 -89 TCAAGCTACAAACTTAAAAAGCAAATTAGT 1 84 0 AACTTAAAAA 0.762216 -71 ACGTACAGAAAAATTCAAGCTACAAACTTA 1 98 0 AAATTCAAGC 0.977503 -57 GAAGCTCGCAAAAATCAGACGGCTGGTTCT 3 137 0 AAAATCAGAC 0.761654 -96 AGAAAAATTTAAATTAACGCAAAATTAGGC 3 205 1 AAATTAACGC 0.913045 -28 TTCAGCATCGAAATTCAGGCTCATGTGAGG 4 16 1 AAATTCAGGC 0.960945 -117 AACAAACCTAAACTTCAAGCG 5 2 0 AACTTCAAGC 0.979199 -144 AAAATTTTAAAAATTAAAACATGGAGGTGA 6 90 1 AAATTAAAAC 0.944798 -24 TTATGTTTAAAAATTCTCACCTGAAAAGGT 7 37 0 AAATTCTCAC 0.761654 -90 TGAACTTCAAAAACTCTGAAAG 7 115 0 AACTTCAAAA 0.88251 -12 ********** Masking position 5 Map Score: 9.70987 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 203 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 AAGTTTTTATCTTAAAGAAAAATTTAAATA 1 51 0 CTTAAAGAAA 0.943141 -104 AAGATAAAAACTTAAAACTAATTTGCTTTT 1 68 1 CTTAAAACTA 0.802771 -87 ATAATTACTCCTGAAAGCACCATGAAGTAG 3 104 1 CTGAAAGCAC 0.978391 -129 AATTTCGATGCTGAAAGCTT 4 1 0 CTGAAAGCTT 0.966524 -132 TCATGTGAGGCTTAAAGCAATTATACCGTA 4 36 1 CTTAAAGCAA 0.980036 -97 TTCAAAAACTCTGAAAGAATATTAACTTTT 7 102 0 CTGAAAGAAT 0.947923 -25 ********** Masking position 5 Map Score: 3.41129 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 162 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 GCACAGTAGCAGTGCGGAGGGGATAGG 1 8 0 AGTGCGGAGG 0.877431 -147 TGTGAGCAAGTGGCAATATT 1 145 0 TGTGAGCAAG 0.784899 -10 AAAATGCGACTGAGAAGAAAAAGCATGAAG 3 163 0 TGAGAAGAAA 0.767163 -70 TTTAAATTTTTCTGAAGAAGAGTTAAAAAT 3 188 0 TCTGAAGAAG 0.908247 -45 ATTGTCAAAATGTGCAAAAGTTTTTACGGT 4 60 0 TGTGCAAAAG 0.937122 -73 GACTCAACCAAGAGCGGAAGGATTTTATAA 4 94 1 AGAGCGGAAG 0.905843 -39 TTAGTACGCACGAGAAAAAAGATTTTATAT 5 32 0 CGAGAAAAAA 0.7662 -114 TCACATGTGAACAGCAAAGGTTATCTAACG 6 32 0 ACAGCAAAGG 0.701472 -82 AAAATTCTCACCTGAAAAGGTTTTAAAGCT 7 28 0 CCTGAAAAGG 0.860413 -99 TTCTCGCTATCGTGAAGAAGTTATAGATAA 7 73 0 CGTGAAGAAG 0.975793 -54 TTCACGATAGCGAGAAAAAGTTAATATTCT 7 87 1 CGAGAAAAAG 0.955101 -40 ********** Masking position 8 Map Score: 4.39093 Number of sites scoring better than the average of aligned sites = 2191 Number in coding regions = 2073 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 6 ********** No masking Map Score: 2.34722e-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 7 ********** No masking Map Score: 2.34722e-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 8 ********** No masking Map Score: 2.34722e-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