AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i346_weak7_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 HI0372 39 ferredoxin (fdx-1) #2 HI0374 50 H. influenzae predicted coding region HI0374 #3 HI0376 56 conserved hypothetical protein #4 HI0377 59 iscU protein (iscU) #5 HI0378 60 nifS protein (nifS) #6 HI0379 52 conserved hypothetical protein #7 HI0380 300 conserved hypothetical protein Motif number 1 ATGTGGGGGCAAATGTAATTTG 2 3 1 GTGGGGGCAA 0.98817 -48 TTCACATCTCGTAGGGGCAAATTACATTTG 2 20 0 GTAGGGGCAA 0.92818 -31 ATGTGAAAAAGTGCGGTCAATTTTGACCGC 3 13 1 GTGCGGTCAA 0.981151 -44 ACCGCTAAAAATGCGGTCAAAATTGACCGC 3 25 0 ATGCGGTCAA 0.889113 -32 TTTTAGCGGTGTTGGGGGATAG 3 45 1 GTTGGGGGAT 0.944693 -12 TAATAAAAAAGTGCGGTTATATTTAGCATA 5 33 1 GTGCGGTTAT 0.974145 -28 ATTTAATACAGTGGGGTCGTTAGCTCAGTC 7 13 1 GTGGGGTCGT 0.992992 -288 ATCAGAGAGTGGTGGGTCGTGAAGGATTCG 7 81 0 GGTGGGTCGT 0.982347 -220 TAGTTGTCCAGTTGGGTTGTTAGCTCAGTT 7 112 1 GTTGGGTTGT 0.974304 -189 TAATAAAAATGGTGGGTTGTGAGAGACTAG 7 180 0 GGTGGGTTGT 0.959593 -121 CTTAAATTTTAGTCGGGTATCATT 7 287 1 AGTCGGGTAT 0.680723 -14 ********** Masking position 5 Map Score: 16.8634 Number of sites scoring better than the average of aligned sites = 627 Number in coding regions = 442 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 2 CCCCCAACACCGCTAAAAATGCGGTCAAAA 3 33 0 CGCTAAAAAT 0.965538 -24 AGTTGCCATTATCTGACAATGGCATTCACT 4 16 1 ATCTGACAAT 0.824269 -44 AAAGAATCCCTAAAAATTAATTGCGCA 6 36 0 CCCTAAAAAT 0.888357 -17 CTACCGACTGAGCTAACGACCCCACTGTAT 7 18 0 AGCTAACGAC 0.964166 -283 AAGTCCGCTGCTCTACCGACTGAGCTAACG 7 30 0 CTCTACCGAC 0.96197 -271 CTACCAACTGAGCTAACAACCCAACTGGAC 7 117 0 AGCTAACAAC 0.982157 -184 GAGTCCGCTACTCTACCAACTGAGCTAACA 7 129 0 CTCTACCAAC 0.981046 -172 GAGTTCTAGTCTCTCACAACCCACCATTTT 7 175 1 CTCTCACAAC 0.965665 -126 CCACAATAACCGCTAAAAATAGTCAAGAAT 7 248 0 CGCTAAAAAT 0.965538 -53 ********** Masking position 4 Map Score: 10.1479 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 141 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 3 AACTGCAGTCAGATATTAAATAATTTT 1 7 1 AGTCAGTATT 0.945585 -33 CTAAATTAGTCAGATATGTAAGTATTGC 6 8 1 AGTCAGTATG 0.802663 -45 GGGGTCGTTAGCTCAGTCGGTAGAGCAGCGG 7 25 1 GCTCAGCGGT 0.922395 -276 ACGGATTAAAAGTCCGCTGCTCTACCGACTG 7 38 0 AGTCCGTGCT 0.97808 -263 GCGGACTTTTAATCCGTTGGTCGAAGGTTCG 7 52 1 AATCCGTGGT 0.98081 -249 TGGACAACTAAATCAGAGAGTGGTGGGTCGT 7 91 0 AATCAGGAGT 0.901795 -210 TGGGTTGTTAGCTCAGTTGGTAGAGTAGCGG 7 124 1 GCTCAGTGGT 0.954522 -177 ACGGATTAAGAGTCCGCTACTCTACCAACTG 7 137 0 AGTCCGTACT 0.971764 -164 GCGGACTCTTAATCCGTCAGTCGAGAGTTCT 7 151 1 AATCCGCAGT 0.956352 -150 ****** **** Masking position 3 Map Score: 5.96635 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 106 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 4 GGCATTCACTAGAATTGAAAAAAGGAAAGT 4 36 1 AGAATTGAAA 0.874006 -24 TTGAAAAAAGGAAAGTTAAA 4 50 1 GAAAGTTAAA 0.940221 -10 AAAAGATAAGCAGTATATTT 5 1 1 AAAAGATAAG 0.880376 -60 GCTAATTAAAGAAATTTAAAATATTAGGGA 7 214 0 GAAATTTAAA 0.949929 -87 AAAATAGTCAAGAATTTAAGCTAATTAAAG 7 233 0 AGAATTTAAG 0.967566 -68 ATACCCGACTAAAATTTAAGGGTATTCTAC 7 277 0 AAAATTTAAG 0.972961 -24 ********** Masking position 4 Map Score: 1.99481 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 134 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 5 CTACGAGATGTGAATAAATAACACT 2 36 1 TGAATAAATA 0.899177 -15 TCATGTGAAAAAGTGCGGTCAATTT 3 6 1 TGAAAAAGTG 0.986182 -51 TCACTAGAATTGAAAAAAGGAAAGTTAAA 4 41 1 TGAAAAAAGG 0.967515 -19 CACTTTTTTATTAAAAAATATACTGCTTAT 5 16 0 TTAAAAAATA 0.880746 -45 TATTTTTTAATAAAAAAGTGCGGTTATATT 5 26 1 TAAAAAAGTG 0.947267 -35 ********** Masking position 6 Map Score: 0.43416 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 248 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 6 ********** No masking Map Score: 1.24588e-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: 1.24588e-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: 1.24588e-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