AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i138_Transmembrane_Transport_11_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 HI0118 300 conserved hypothetical protein #2 HI0119 177 conserved hypothetical protein #3 HI0408 171 ABC transporter, ATP-binding protein (yebM) Motif number 1 TCAGTGGCATCAGATCGCAATATTATCCCATCTGGTT 1 90 1 CAAGCTTATC 0.981503 -211 CGATATAAGTCAAAGTGATGACCTTTCACTGCACCGC 1 217 0 CAAGACTTTC 0.958752 -84 TAGAGCAGGACATATTGCAGGGCTTTCAAAACACTAC 1 266 1 CAAGCCTTTC 0.987632 -35 TCATTCAATAAAAAATGCACATTTATGGTCAATGTGC 2 26 0 AAAGCTTATG 0.873751 -152 TTATAGTAAAAAGAGGGAAAATTTTTCATTTTCAAAG 2 73 0 AAAGATTTTC 0.986883 -105 AAAGGGAAAAAAGAGTACGCCTTTTTATATAAATTGC 2 117 0 AAAACTTTTA 0.82978 -61 CCCTAAAATAAAAAAGTTTTCAGCATTCAGA 3 5 1 AAAAATTTTC 0.955015 -167 ATGCTTTTTCCATAGGAATGAATTTTCTTTATAATCT 3 46 0 CAAAATTTTC 0.95456 -126 AGAATTCTATAAAAATGCGTTATTTTCCCCAACCATT 3 125 1 AAAGCTTTTC 0.971412 -47 AAAATCGCCGTGTTTTCAACAATGGTT 3 155 0 AAAGCTTTTC 0.992266 -17 ** * ** ***** Masking position 4 Map Score: 11.7973 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 193 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 2 GCCACTTGGATCATTTTTAAAGAATACATAAG 1 16 0 TCATTTTAAG 0.846262 -285 CCAGTTTCCGTTATTATCAATGTCGGGTACTT 1 142 0 TTATTTCAAG 0.976078 -159 CTCTACCGTAGTGTTTTGAAAGCCCTGCAATA 1 278 0 GTGTTTGAAG 0.895017 -23 TGGTCAATGTGCATTTTCAAGAGGTGA 2 6 0 GCATTTCAAA 0.971053 -172 AAATGCACATTTATGGTCAATGTGCATTTTCA 2 19 0 TTATGTCAAG 0.946086 -159 GGAAAATTTTTCATTTTCAAAGTCAATAGGTT 2 63 0 TCATTTCAAG 0.980116 -115 TTGTTGGTAGTAATTCTCAAAGGGAAAAAAGA 2 140 0 TAATTTCAAG 0.969086 -38 TCTGTAGTCTGAATGCTGAAAACTTTTTTATT 3 17 0 GAATGTGAAA 0.736432 -155 CATTTTTATAGAATTCTCAAGATTTTCTCTCT 3 110 0 GAATTTCAAA 0.955225 -62 AAAATCGCCGTGTTTTCAACAATGGTTGGGG 3 151 0 GTGTTTCAAA 0.922749 -21 ***** **** * Masking position 7 Map Score: 8.46935 Number of sites scoring better than the average of aligned sites = 350 Number in coding regions = 303 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 3 AGTGGCAAAGTGAAAGGCTCTGCGGGCGTT 1 42 1 TGAAAGGCTC 0.834127 -259 CTGATGCCACTGAAGCCATTGCTACAAGAG 1 73 0 TGAAGCCATT 0.942631 -228 CTACATCAAGTGCAACCATTAAGTGTAATT 1 187 0 TGCAACCATT 0.980557 -114 CAGGACATATTGCAGGGCTTTCAAAACACT 1 271 1 TGCAGGGCTT 0.95783 -30 TTATATAAATTGCAACGATTTTATAGTAAA 2 100 0 TGCAACGATT 0.985128 -78 AAAGCATTATTCAAACGCTTAAATATTCGA 3 76 1 TCAAACGCTT 0.94234 -96 CGTTATTTTCCCCAACCATTGTTGAAAACA 3 142 1 CCCAACCATT 0.867514 -30 ********** Masking position 4 Map Score: 2.44017 Number of sites scoring better than the average of aligned sites = 456 Number in coding regions = 417 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 4 AGAACCAGATGGGATAATATTGCGATCTGA 1 99 0 GGGATAATAT 0.972634 -202 AGTAAAAAGAGGGAAAATTTTTCATTTTCA 2 76 0 GGGAAAATTT 0.978849 -102 AATTCTCAAAGGGAAAAAAGAGTACGCCTT 2 131 0 GGGAAAAAAG 0.954229 -47 CGACATAAGAGAGAAAATCTTGAGAATTCT 3 103 1 GAGAAAATCT 0.929297 -69 ACAATGGTTGGGGAAAATAACGCATTTTTA 3 134 0 GGGAAAATAA 0.978849 -38 ********** Masking position 6 Map Score: 2.04805 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 113 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 ********** No masking Map Score: 1.69352e-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 6 ********** No masking Map Score: 1.69352e-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: 1.69352e-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