AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i115_Glycine_Transport_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 opuAA 289 glycine betaine ABC transporter (ATP-binding protein) #2 opuBA 274 choline ABC transporter (ATP-binding protein) #3 opuCB 22 glycine betaine/carnitine/choline ABC transporter (membrane protein) #4 opuCA 263 glycine betaine/carnitine/choline ABC transporter (ATP-binding protein) Motif number 1 TATAGGAGGATTACAGAGCATTTAGAAGCATAAA 1 142 1 TTCAACTTTA 0.952666 -148 GTGTGGGAAGTTACATAAATGTTACGGTAATAAA 1 242 1 TTCAAAGTTA 0.917228 -48 GATGTCAATATACCACATTTTTGATACGGCGAAA 2 30 1 TACAATTTGA 0.709881 -245 AAATCAGCGTTTACACATACTTTATAAATAATAT 2 131 1 TTCAAATTTA 0.984941 -144 TTTACAATTTGTTCATATTATTTATAAAGTATGT 2 145 0 GTCAATTTTA 0.904301 -130 TATGAACAAATTGTAAACTTTTTATTTTATAAAC 2 162 1 TTTAATTTTA 0.961413 -113 AAACTTTTTATTTTATAAACTTTATTCTATAATG 2 176 1 TTTAAATTTA 0.967328 -99 AAATTTAATTTTTCAGACAATTGAATGCTTCCCA 2 208 0 TTCAAATTGA 0.961692 -67 TATATGTTATTTATAGATTATTTATTGTTATGAC 4 141 0 TTTAATTTTA 0.961412 -123 TTTCAACACATTGTAAACTTTTTATTTTACAAAG 4 176 1 TTTAATTTTA 0.961413 -88 AAACTTTTTATTTTACAAAGTTCAAACTATAATA 4 190 1 TTTAAATTCA 0.86062 -74 GGATTATACTTTTCAGAAAATTTAAAGGAAACCT 4 225 1 TTCAAATTTA 0.984942 -39 ** ** * * **** Masking position 7 Map Score: 16.1414 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 194 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 2 CAGTAAAGGAGCAGGAAGTCATAAGAGGAA 1 41 1 GCAGGAAGTC 0.946898 -249 ATAAGAGGAAGGAGGAATTCAATTCCAATA 1 61 1 GGAGGAATTC 0.989435 -229 CAATCATATAGGAGGATTACAGAGCATTTA 1 136 1 GGAGGATTAC 0.978564 -154 CCAGGGGAGGAGCTCTTTTAAG 3 6 1 GGAGGAGCTC 0.988228 -17 AGAGGAAGTGGGAGGTATCCGGAGTAATTG 4 89 1 GGAGGTATCC 0.986835 -175 GTGCACCTCCGCAGGTTTCCTTTAAATTTT 4 241 0 GCAGGTTTCC 0.958123 -23 GGAAACCTGCGGAGGTGCACGGA 4 251 1 GGAGGTGCAC 0.978258 -13 ********** Masking position 3 Map Score: 7.62455 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 152 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 3 TAAGTTGCTTTTTCAACACCCATT 1 5 0 TTTCAACACC 0.966909 -285 CAACTTATTTTTCCAGTAAAGGAGCAGGAA 1 28 1 TTCCAGTAAA 0.878415 -262 AGGAATTCAATTCCAATAAAAGCGTTTTCA 1 73 1 TTCCAATAAA 0.897538 -217 ATAAAAGCGTTTTCAACTAAAGGTAGGAGA 1 88 1 TTTCAACTAA 0.936193 -202 TTTATGTAACTTCCCACACAAACAGCATAT 1 231 0 TTCCCACACA 0.920129 -59 CCTTTCAGCTAACAATTCCGAT 2 3 1 TTTCAGCTAA 0.923664 -272 ATTCAGCTATTTTCAACACCAGGAAGAAAT 4 57 0 TTTCAACACC 0.966909 -207 TAACATATAATTTCAACACATTGTAAACTT 4 166 1 TTTCAACACA 0.983545 -98 GGATTATACTTTTCAGAAAATTTAAAGGAA 4 225 1 TTTCAGAAAA 0.832151 -39 ********** Masking position 2 Map Score: 8.21195 Number of sites scoring better than the average of aligned sites = 550 Number in coding regions = 472 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 4 ATTTTTCTCCTACCTTTAGTTGAAAACGCTTTT 1 90 0 TCCTTAGTTA 0.947142 -200 TTTTATTCTGTACCATTTCTTTATAAACATCCA 1 194 0 TCCTTTCTTA 0.943023 -96 TTACCCGCATTGACGTGTGTTGATCTCCTTATT 2 100 0 TACTGTGTTA 0.957263 -175 ATAAAAAGTTTACAATTTGTTCATATTATTTAT 2 154 0 TCATTTGTTA 0.984379 -121 ATTAAGTTTATTCAATTTGTTCAGTTTAAATTT 2 236 0 TCATTTGTTA 0.984379 -39 ATCATATTTCTTCCTGGTGTTGAAAATAGCTGA 4 52 1 TCCGGTGTTA 0.96301 -212 ATAAAAAGTTTACAATGTGTTGAAATTATATGT 4 168 0 TCATGTGTTA 0.984069 -96 TATTATAGTTTGAACTTTGTAAAATAAAAAGTT 4 191 0 TAATTTGTAA 0.720381 -73 * ** ****** * Masking position 13 Map Score: 5.63515 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 216 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 ATTTTTCTCCTACCTTTAGTTGAAAACGCT 1 93 0 TACCTTTAGT 0.866461 -197 TTTTATTCTGTACCATTTCTTTATAAACAT 1 197 0 TACCATTTCT 0.962474 -93 ATAAAAAGTTTACAATTTGTTCATATTATT 2 157 0 TACAATTTGT 0.983385 -118 ATTAAGTTTATTCAATTTGTTCAGTTTAAA 2 239 0 TTCAATTTGT 0.935907 -36 AGGGTGTTCTTACAATTACTCCGGATACCT 4 101 0 TACAATTACT 0.943121 -163 ATAAAAAGTTTACAATGTGTTGAAATTATA 4 171 0 TACAATGTGT 0.955835 -93 ********** Masking position 6 Map Score: 3.4795 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 44 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 GATTACAGAGCATTTAGAAGCATAAATAAG 1 150 1 CATTTAGAAG 0.896263 -140 AAGATTGCTTAATATGGAGGGAAAAT 1 274 1 AATATGGAGG 0.924886 -16 GCCAAATTCTCTTTTGACAGCATTTTCGCC 2 57 0 CTTTTGACAG 0.827988 -218 GTCAAAAGAGAATTTGGCAGGAAATTGGAG 2 69 1 AATTTGGCAG 0.950796 -206 AATAAACTTAATTTTGGAGGTGCGATGT 2 257 1 ATTTTGGAGG 0.962674 -18 CATCAATTGCCATTTGAAGGGATGATCAGC 4 12 0 CATTTGAAGG 0.970941 -252 CTTTTCAGAAAATTTAAAGGAAACCTGCGG 4 233 1 AATTTAAAGG 0.886212 -31 ********** Masking position 5 Map Score: 2.87308 Number of sites scoring better than the average of aligned sites = 642 Number in coding regions = 554 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 7 AATGGGTGTTGAAAAAGCAAC 1 2 1 ATGGGTGTTG 0.984649 -288 ATTGTATTTTACGGGTGATTTTTCTCCTAC 1 110 0 ACGGGTGATT 0.971734 -180 ATGTGGTCACATGGATGTTTATAAAGAAAT 1 183 1 ATGGATGTTT 0.933386 -107 ACCCGCATTGACGTGTGTTGATCTCCTTAT 2 101 0 ACGTGTGTTG 0.938836 -174 TGCCATTTGAAGGGATGATCAGCT 4 5 0 AGGGATGATC 0.907097 -259 CCGAGACGGAAAGGGTGTTCTTACAATTAC 4 112 0 AAGGGTGTTC 0.973245 -152 ********** Masking position 6 Map Score: 2.16484 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 177 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 8 ATTCCAATAAAAGCGTTTTCAACTAAAGGT 1 82 1 AAGCGTTTTC 0.959876 -208 CCCACACAAACAGCATATTCTCTTTTATTC 1 219 0 CAGCATATTC 0.972337 -71 TCTCTTTTGACAGCATTTTCGCCGTATCAA 2 50 0 CAGCATTTTC 0.991426 -225 GCTGATTTACCCGCATTGACGTGTGTTGAT 2 109 0 CCGCATTGAC 0.942459 -166 GCGGGTAAATCAGCGTTTACACATACTTTA 2 125 1 CAGCGTTTAC 0.988653 -150 ********** Masking position 6 Map Score: 3.0781 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 231 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 CCTCCTATATGATTGTATTTTACGGGTGAT 1 121 0 GATTGTATTT 0.853319 -169 TCCCATTATAGAATAAAGTTTATAAAATAA 2 183 0 GAATAAAGTT 0.835312 -92 AATTTGTTCAGTTTAAATTTAATTTTTCAG 2 226 0 GTTTAAATTT 0.93853 -49 TGAACAAATTGAATAAACTTAATTTTGGAG 2 246 1 GAATAAACTT 0.93147 -29 CCTTATTATAGTTTGAACTTTGTAAAATAA 4 197 0 GTTTGAACTT 0.94171 -67 CTATAATAAGGATTATACTTTTCAGAAAAT 4 216 1 GATTATACTT 0.931449 -48 CGCAGGTTTCCTTTAAATTTTCTGAAAAGT 4 232 0 CTTTAAATTT 0.745888 -32 ********** Masking position 7 Map Score: 0.762974 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 280 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 10 ********** No masking Map Score: -7.72059e-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 11 ********** No masking Map Score: -7.72059e-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 12 ********** No masking Map Score: -7.72059e-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