AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i093_Galactoside_Transport_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 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 ATGTAATCGTTTACATTGATAAAAAACAGGAG 1 16 0 TTACATGATA 0.980538 -192 ATGTAAACGATTACATTAATTTATACTAAATT 1 32 1 TTACATAATT 0.969569 -176 CACGGTTTATTTACAATAATTTAGTATAAATT 1 49 0 TTACAAAATT 0.981831 -159 TCTTATTTTGTGACAAAGATCACGGTTTATTT 1 69 0 TGACAAGATA 0.973569 -139 CATAAATAATTTACGATAAATTGAAAGCGGTT 1 145 0 TTACGAAAAT 0.924405 -63 TTATAGATTATAACAAGGAAAAAGTT 1 192 1 TAACAAGAAA 0.888478 -16 TTTGTGACATGGATCACAAATTCATA 2 5 1 TGACATGATA 0.956005 -86 ATGAAAATGATTACATAAAAAATTATGAATTT 2 28 0 TTACATAAAA 0.969568 -63 ATGAGCAAATTTGCAAAAATGAAAATGATTAC 2 46 0 TTGCAAAATA 0.945236 -45 CATAGATTAATTACGATAATTTATTT 2 75 1 TTACGAAATT 0.954002 -16 TCCCCTTAGATTACAACAAAAATTGATGGGAA 3 12 0 TTACAAAAAA 0.981831 -54 ****** *** * Masking position 9 Map Score: 17.2412 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 201 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 2 TGTTTTTTATCAATGTAAACGATTACATTA 1 20 1 CAATGTAAAC 0.915861 -188 TAGTATAAATTAATGTAATCGTTTACATTG 1 30 0 TAATGTAATC 0.984994 -178 TATACTAAATTATTGTAAATAAACCGTGAT 1 53 1 TATTGTAAAT 0.962386 -155 GCTTTCAATTTATCGTAAATTATTTATGAT 1 149 1 TATCGTAAAT 0.9357 -59 ACTTTTTCCTTGTTATAATCTATAAATCTT 1 187 0 TGTTATAATC 0.887022 -21 TCATAATTTTTTATGTAATCATTTTCATTT 2 32 1 TTATGTAATC 0.941916 -59 AAATAAATTATCGTAATTAATCTATGAG 2 73 0 TATCGTAATT 0.958903 -18 CATCAATTTTTGTTGTAATCTAAGGGGAAG 3 16 1 TGTTGTAATC 0.986067 -50 ********** Masking position 7 Map Score: 9.4858 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 244 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 3 AAATAAGAAAATAAGCAAAATTTTTTATGAT 1 93 1 ATAACAAAAT 0.982224 -115 TTTCATAAGTATGAACTAAATCATAAAAAAT 1 112 0 ATGACTAAAT 0.988548 -96 TAAATTATTTATGATCAAAATATAAGATTTA 1 164 1 ATGACAAAAT 0.995251 -44 TAATTAATCTATGAGCAAATTTGCAAAAATG 2 57 0 ATGACAAATT 0.988633 -34 **** ****** Masking position 4 Map Score: 4.55431 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 25 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 CGATAAATTGAAAGCGGTTACTTTCATAAG 1 134 0 AAAGCGGTTA 0.952538 -74 TGTTGTAATCTAAGGGGAAGTGGATCTTCC 3 26 1 TAAGGGGAAG 0.984548 -40 ACCTCTTTAAAAAGGGGAAGATCCACTTCC 3 41 0 AAAGGGGAAG 0.993827 -25 TCCCCTTTTTAAAGAGGTTGGAT 3 53 1 AAAGAGGTTG 0.983297 -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 5 ACTCCTGTTTTTTATCAATGTAAACGATTA 1 15 1 TTTATCAATG 0.765551 -193 AACGATTACATTAATTTATACTAAATTATT 1 37 1 TTAATTTATA 0.90381 -171 GCTTATTTTCTTATTTTGTGACAAAGATCA 1 79 0 TTATTTTGTG 0.902823 -129 AATAAGCAAAATTTTTTATGATTTAGTTCA 1 102 1 ATTTTTTATG 0.936541 -106 TTTATCGTAAATTATTTATGATCAAAATAT 1 157 1 ATTATTTATG 0.970232 -51 TTTCCTTGTTATAATCTATAAATCTTATAT 1 183 0 ATAATCTATA 0.869962 -25 TAAAAAATTATGAATTTGTGATCCATGTCA 2 15 0 TGAATTTGTG 0.810566 -76 CAAATTCATAATTTTTTATGTAATCATTTT 2 27 1 ATTTTTTATG 0.936541 -64 ATTATCGTAATTAATCTATGAGCAAATTTG 2 65 0 TTAATCTATG 0.971408 -26 ATTAATTACGATAATTTATTT 2 80 1 ATAATTTATT 0.841986 -11 ********** Masking position 5 Map Score: 10.8164 Number of sites scoring better than the average of aligned sites = 603 Number in coding regions = 480 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 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