AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i215_Ribosomal_Operon_2_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0877 27 GTP-binding protein (yhbZ) #2 HI0878 80 conserved hypothetical protein #3 HI0880 212 ribosomal protein L21 (rpL21) Motif number 1 TAAAACTTCTCCAAAATAAACCGCA 1 13 0 AAAACTTCAA 0.989688 -15 CTATTCCATTGAAACGCCCTACAATTTTKTGGGG 2 19 1 GAAACGCCAA 0.987018 -62 TAAAAAAGACAAAACGCCCCAAAAATTGTAGGG 2 35 0 AAAACGCCAA 0.993612 -46 CAGAAAGTCTGAAAATTCGGGTAAAATGCACCGC 3 36 0 GAAAATTCAA 0.973291 -177 AATAAAATAAAAAAATTCCCTTCATTTGCGGATT 3 75 0 AAAAATTCCA 0.951924 -138 AATTCTACGGAAAAATCCTACCTATGGCAAGATT 3 117 0 AAAAATCCTA 0.9633 -96 GTCCACACTTAAAAATTCATATAAATAGGTCGCA 3 151 0 AAAAATTCAA 0.986763 -62 GTGGACTGCTAAAAAGCAGGAAAACACAATTAAG 3 179 1 AAAAAGCAAA 0.922141 -34 AAATACTCCGCTTAATTGTGTTTTC 3 198 0 AATACTCCAA 0.967454 -15 ******** ** Masking position 4 Map Score: 12.8308 Number of sites scoring better than the average of aligned sites = 380 Number in coding regions = 285 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 2 AACTTCTCCAAAATAAACCGCACT 1 3 0 AAATACCGCA 0.992533 -25 CGCCCCAAAAATTGTAGGGCGTTTCAATGGA 2 23 0 AATTAGGGCG 0.979234 -58 AATTCGGGTAAAATGCACCGCACTTTTAACTG 3 25 0 AAATACCGCA 0.992533 -188 ATCAATCCGCAAATGAAGGGAATTTTTTTATT 3 72 1 AAATAGGGAA 0.977867 -141 ATAGGTCGCAAATTCTACGGAAAAATCCTACC 3 129 0 AATTACGGAA 0.984829 -84 AAATTCATATAAATAGGTCGCAAATTCTACGG 3 141 0 AAATGTCGCA 0.94487 -72 AGGAAAACACAATTAAGCGGAGTATTT 3 196 1 AATTGCGGAG 0.967099 -17 **** ****** Masking position 2 Map Score: 7.22031 Number of sites scoring better than the average of aligned sites = 667 Number in coding regions = 476 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 3 TGTAGGGCGTTTCAATGGAATAGATTTTAA 2 12 0 TTCAATGGAA 0.885485 -69 CCCCAAAAATTGTAGGGCGTTTCAATGGA 2 23 0 TTGTAGGGCG 0.981399 -58 CCCTACAATTTTKTGGGGCGTTTTGTCTTT 2 35 1 TTKTGGGGCG 0.965843 -46 CAATCCGCAAATGAAGGGAATTTTTTTATT 3 74 1 ATGAAGGGAA 0.908958 -139 AGGTCGCAAATTCTACGGAAAAATCCTACC 3 129 0 TTCTACGGAA 0.942929 -84 GAAAACACAATTAAGCGGAGTATTT 3 198 1 TTAAGCGGAG 0.95893 -15 ********** Masking position 2 Map Score: 1.06423 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 149 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 4 TTTCAATGGAATAGATTTTAAA 2 3 0 ATAGATTTTA 0.941062 -78 TTTTGTCTTTTTTAATTTCACATAAGCGAG 2 55 1 TTTAATTTCA 0.954441 -26 TCATTTGCGGATTGATTTCAGAAAGTCTGA 3 58 0 ATTGATTTCA 0.984285 -155 AAGGGAATTTTTTTATTTTATTATAAATAA 3 87 1 TTTTATTTTA 0.936694 -126 ********** Masking position 5 Map Score: 0.443455 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 263 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 5 AGTGCGGTTTATTTTGGAGA 1 1 1 AGTGCGGTTT 0.995442 -27 AAAAATTGTAGGGCGTTTCAATGGAATAG 2 19 0 AGGGCGTTTC 0.95904 -62 ATCAGTTAAAAGTGCGGTGCATTTTACCCG 3 23 1 AGTGCGGTGC 0.988411 -190 ATTCCCTTCATTTGCGGATTGATTTCAGAA 3 65 0 TTTGCGGATT 0.910785 -148 TGAATTTTTAAGTGTGGACTGCTAAAAAGC 3 166 1 AGTGTGGACT 0.946882 -47 ACTCCGCTTAATTGTGTTTTCCTGCTTTTT 3 189 0 ATTGTGTTTT 0.898161 -24 ********** Masking position 6 Map Score: 3.41877 Number of sites scoring better than the average of aligned sites = 1573 Number in coding regions = 1120 Number in noncoding regions = 453 Number of orfs with sites within 600 bp upstream = 305 Fraction of orfs with sites within 600 bp upstream = 0.0489881 Motif number 6 ********** No masking Map Score: 2.58227e-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: 2.58227e-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 8 ********** No masking Map Score: 2.58227e-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