AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i093_Galactoside_Transport_hinf_reg_100.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 HI0821 207 galactose operon repressor (galR) #2 HI0822 90 galactose ABC transporter, periplasmic-binding protein (mglB) #3 HI0823 65 galactoside ABC transporter, ATP-binding protein (mglA) Motif number 1 CTGTTTTTTATCAATGTAAACGATTACATTA 1 19 1 TCATGTAAAC 0.943897 -189 TTAGTATAAATTAATGTAATCGTTTACATTG 1 30 0 TTATGTAATC 0.988854 -178 TTATACTAAATTATTGTAAATAAACCGTGAT 1 52 1 TTTTGTAAAT 0.985889 -156 CGCTTTCAATTTATCGTAAATTATTTATGAT 1 148 1 TTTCGTAAAT 0.971552 -60 AACTTTTTCCTTGTTATAATCTATAAATCTT 1 187 0 TTTTATAATC 0.943117 -21 TTCATAATTTTTTATGTAATCATTTTCATTT 2 31 1 TTATGTAATC 0.988854 -60 ATCATTTTCATTTTTGCAAATTTGCTCATAG 2 49 1 TTTTGCAAAT 0.942273 -42 AAATAAATTATCGTAATTAATCTATGAG 2 73 0 TTTCGTAATT 0.976786 -18 CCATCAATTTTTGTTGTAATCTAAGGGGAAG 3 15 1 TTTTGTAATC 0.994122 -51 ** ******** Masking position 8 Map Score: 16.3068 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 185 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 2 GTAAACGATTACATTAATTTATACTAAATTAT 1 34 1 ACATAATTAT 0.954858 -174 CGGTTTATTTACAATAATTTAGTATAAATTAA 1 47 0 ACATAATTAG 0.929856 -161 GTGATCTTTGTCACAAAATAAGAAAATAAGCA 1 78 1 TCAAAAATAG 0.958881 -130 ATGAACTAAATCATAAAAAATTTTGCTTATTT 1 101 0 TCAAAAAATT 0.855221 -107 TATATTTTGATCATAAATAATTTACGATAAAT 1 156 0 TCAAAATATT 0.909246 -52 TTATTTATGATCAAAATATAAGATTTATAGAT 1 168 1 TCAAATATAG 0.747665 -40 GTGACATGGATCACAAATTCATAATTTTTTAT 2 14 1 TCAAAATTAT 0.984411 -77 GAAAATGATTACATAAAAAATTATGAATTTGT 2 26 0 ACAAAAAATT 0.832522 -65 GCAAATTTGCTCATAGATTAATTACGATAATT 2 64 1 TCAAGATTAT 0.922433 -27 TAGATTAATTACGATAATTTATTT 2 77 1 ACGTAATTAT 0.799382 -14 TTAGATTACAACAAAAATTGATGGGAAA 3 7 0 ACAAAATTAT 0.981526 -59 *** ***** ** Masking position 2 Map Score: 10.9247 Number of sites scoring better than the average of aligned sites = 709 Number in coding regions = 585 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 3 ATAATTTAGTATAAATTAATGTAATCGTTT 1 36 0 ATAAATTAAT 0.937503 -172 TTAATTTATACTAAATTATTGTAAATAAAC 1 47 1 CTAAATTATT 0.928278 -161 TTGTCACAAAATAAGAAAATAAGCAAAATT 1 85 1 ATAAGAAAAT 0.766781 -123 GAACTAAATCATAAAAAATTTTGCTTATTT 1 101 0 ATAAAAAATT 0.95934 -107 TATTTTGATCATAAATAATTTACGATAAAT 1 156 0 ATAAATAATT 0.978211 -52 TATAAGATTTATAGATTATAACAAGGAAAA 1 184 1 ATAGATTATA 0.810276 -24 AAATGATTACATAAAAAATTATGAATTTGT 2 26 0 ATAAAAAATT 0.95934 -65 AAATTTGCTCATAGATTAATTACGATAATT 2 66 1 ATAGATTAAT 0.93251 -25 ATTAATTACGATAATTTATTT 2 80 1 ATAATTTATT 0.90802 -11 ********** Masking position 3 Map Score: 10.8358 Number of sites scoring better than the average of aligned sites = 433 Number in coding regions = 314 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 4 GTAATCGTTTACATTGATAAAAAACAGGAG 1 16 0 ACATTGATAA 0.987916 -192 GAAAGCGGTTACTTTCATAAGTATGAACTA 1 125 0 ACTTTCATAA 0.838297 -83 AATTTACGATAAATTGAAAGCGGTTACTTT 1 140 0 AAATTGAAAG 0.947914 -68 ATAGATTATAACAAGGAAAAAGTT 1 194 1 ACAAGGAAAA 0.913551 -14 TTTGTGACATGGATCACAAATTCATA 2 7 1 ACATGGATCA 0.934388 -84 CATGGATCACAAATTCATAATTTTTTATGT 2 18 1 AAATTCATAA 0.948021 -73 CAAATTTGCAAAAATGAAAATGATTACATA 2 43 0 AAAATGAAAA 0.921663 -48 ATTACAACAAAAATTGATGGGAAA 3 5 0 AAATTGATGG 0.899823 -61 ********** Masking position 7 Map Score: 4.61089 Number of sites scoring better than the average of aligned sites = 654 Number in coding regions = 547 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 5 CGATAAATTGAAAGCGGTTACTTTCATAAG 1 134 0 AAAGCGGTTA 0.950741 -74 TGTTGTAATCTAAGGGGAAGTGGATCTTCC 3 26 1 TAAGGGGAAG 0.98382 -40 ACCTCTTTAAAAAGGGGAAGATCCACTTCC 3 41 0 AAAGGGGAAG 0.993533 -25 TCCCCTTTTTAAAGAGGTTGGAT 3 53 1 AAAGAGGTTG 0.982514 -13 ********** Masking position 3 Map Score: 1.79355 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 76 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 ********** No masking Map Score: -3.31523e-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: -3.31523e-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: -3.31523e-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