AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i115_Glycine_Transport_bsub_reg_300.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 0.954561 -148 GTGTGGGAAGTTACATAAATGTTACGGTAATAAA 1 242 1 TTCAAAGTTA 0.92034 -48 GATGTCAATATACCACATTTTTGATACGGCGAAA 2 30 1 TACAATTTGA 0.718624 -245 AAATCAGCGTTTACACATACTTTATAAATAATAT 2 131 1 TTCAAATTTA 0.985563 -144 TTTACAATTTGTTCATATTATTTATAAAGTATGT 2 145 0 GTCAATTTTA 0.907945 -130 TATGAACAAATTGTAAACTTTTTATTTTATAAAC 2 162 1 TTTAATTTTA 0.962971 -113 AAACTTTTTATTTTATAAACTTTATTCTATAATG 2 176 1 TTTAAATTTA 0.968656 -99 AAATTTAATTTTTCAGACAATTGAATGCTTCCCA 2 208 0 TTCAAATTGA 0.96324 -67 TATATGTTATTTATAGATTATTTATTGTTATGAC 4 141 0 TTTAATTTTA 0.96297 -123 TTTCAACACATTGTAAACTTTTTATTTTACAAAG 4 176 1 TTTAATTTTA 0.962971 -88 AAACTTTTTATTTTACAAAGTTCAAACTATAATA 4 190 1 TTTAAATTCA 0.86568 -74 GGATTATACTTTTCAGAAAATTTAAAGGAAACCT 4 225 1 TTCAAATTTA 0.985565 -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 TTCCTCTTATGACTTCCTGCTCCTTTACTG 1 41 0 GACTTCCTGC 0.941156 -249 TATTGGAATTGAATTCCTCCTTCCTCTTAT 1 61 0 GAATTCCTCC 0.988239 -229 TAAATGCTCTGTAATCCTCCTATATGATTG 1 136 0 GTAATCCTCC 0.976164 -154 CTTAAAAGAGCTCCTCCCCTGG 3 6 0 GAGCTCCTCC 0.986894 -17 CAATTACTCCGGATACCTCCCACTTCCTCT 4 89 0 GGATACCTCC 0.985446 -175 AAAATTTAAAGGAAACCTGCGGAGGTGCAC 4 241 1 GGAAACCTGC 0.953544 -23 TCCGTGCACCTCCGCAGGTTTCC 4 251 0 GTGCACCTCC 0.975821 -13 ********** Masking position 8 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 0.964639 -285 CAACTTATTTTTCCAGTAAAGGAGCAGGAA 1 28 1 TTCCAGTAAA 0.870886 -262 AGGAATTCAATTCCAATAAAAGCGTTTTCA 1 73 1 TTCCAATAAA 0.891046 -217 ATAAAAGCGTTTTCAACTAAAGGTAGGAGA 1 88 1 TTTCAACTAA 0.931964 -202 TTTATGTAACTTCCCACACAAACAGCATAT 1 231 0 TTCCCACACA 0.914933 -59 CCTTTCAGCTAACAATTCCGAT 2 3 1 TTTCAGCTAA 0.918679 -272 ATTCAGCTATTTTCAACACCAGGAAGAAAT 4 57 0 TTTCAACACC 0.964639 -207 TAACATATAATTTCAACACATTGTAAACTT 4 166 1 TTTCAACACA 0.982396 -98 GGATTATACTTTTCAGAAAATTTAAAGGAA 4 225 1 TTTCAGAAAA 0.82237 -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 0.949393 -200 TTTTATTCTGTACCATTTCTTTATAAACATCCA 1 194 0 TCCTTTCTTA 0.94544 -96 TTACCCGCATTGACGTGTGTTGATCTCCTTATT 2 100 0 TACTGTGTTA 0.959098 -175 ATAAAAAGTTTACAATTTGTTCATATTATTTAT 2 154 0 TCATTTGTTA 0.985069 -121 ATTAAGTTTATTCAATTTGTTCAGTTTAAATTT 2 236 0 TCATTTGTTA 0.985069 -39 ATCATATTTCTTCCTGGTGTTGAAAATAGCTGA 4 52 1 TCCGGTGTTA 0.964611 -212 ATAAAAAGTTTACAATGTGTTGAAATTATATGT 4 168 0 TCATGTGTTA 0.984772 -96 TATTATAGTTTGAACTTTGTAAAATAAAAAGTT 4 191 0 TAATTTGTAA 0.729483 -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 0.902039 -140 AAGATTGCTTAATATGGAGGGAAAAT 1 274 1 AATATGGAGG 0.930085 -16 GCCAAATTCTCTTTTGACAGCATTTTCGCC 2 57 0 CTTTTGACAG 0.838298 -218 GTCAAAAGAGAATTTGGCAGGAAATTGGAG 2 69 1 AATTTGGCAG 0.95429 -206 AATAAACTTAATTTTGGAGGTGCGATGT 2 257 1 ATTTTGGAGG 0.965354 -18 CATCAATTGCCATTTGAAGGGATGATCAGC 4 12 0 CATTTGAAGG 0.972888 -252 CTTTTCAGAAAATTTAAAGGAAACCTGCGG 4 233 1 AATTTAAAGG 0.893693 -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 0.983362 -288 ATTGTATTTTACGGGTGATTTTTCTCCTAC 1 110 0 ACGGGTGATT 0.969398 -180 ATGTGGTCACATGGATGTTTATAAAGAAAT 1 183 1 ATGGATGTTT 0.928114 -107 ACCCGCATTGACGTGTGTTGATCTCCTTAT 2 101 0 ACGTGTGTTG 0.933964 -174 TGCCATTTGAAGGGATGATCAGCT 4 5 0 AGGGATGATC 0.899967 -259 CCGAGACGGAAAGGGTGTTCTTACAATTAC 4 112 0 AAGGGTGTTC 0.971029 -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 0.954605 -208 CCCACACAAACAGCATATTCTCTTTTATTC 1 219 0 CAGCATATTC 0.968649 -71 TCTCTTTTGACAGCATTTTCGCCGTATCAA 2 50 0 CAGCATTTTC 0.990258 -225 GCTGATTTACCCGCATTGACGTGTGTTGAT 2 109 0 CCGCATTGAC 0.935053 -166 GCGGGTAAATCAGCGTTTACACATACTTTA 2 125 1 CAGCGTTTAC 0.987111 -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 ATCACCCGTAAAATACAATCATATAGGAGG 1 121 1 AAATACAATC 0.847655 -169 TTATTTTATAAACTTTATTCTATAATGGGA 2 183 1 AACTTTATTC 0.829091 -92 CTGAAAAATTAAATTTAAACTGAACAAATT 2 226 1 AAATTTAAAC 0.935908 -49 CTCCAAAATTAAGTTTATTCAATTTGTTCA 2 246 0 AAGTTTATTC 0.928572 -29 TTATTTTACAAAGTTCAAACTATAATAAGG 4 197 1 AAGTTCAAAC 0.939214 -67 ATTTTCTGAAAAGTATAATCCTTATTATAG 4 216 0 AAGTATAATC 0.928552 -48 ACTTTTCAGAAAATTTAAAGGAAACCTGCG 4 232 1 AAATTTAAAG 0.737347 -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