AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -iglpR_bsub_opreg_100.orf -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 glpQ 98 glycerophosphoryl diester phosphodiesterase #2 glpT 296 glycerol-3-phosphate permease #3 glpF 178 glycerol uptake facilitator #4 glpD 140 glycerol-3-phosphate dehydrogenase #5 fruR 279 transcriptional regulator (DeoR family) #6 yqhL 190 similar to hypothetical proteins #7 yqgP 89 similar to hypothetical proteins #8 yqgO 66 yqgO #9 yqgN 300 similar to 5-formyltetrahydrofolate cyclo-ligase #10 glcR 223 transcriptional regulator (DeoR family) #11 iolR 300 transcriptional regulator (DeoR family) Motif number 1 CCTGTCTTTCATAATAAAAAACGGATGTAAAC 1 49 0 AATAAAAAAC 0.904862 -50 TTTTACTAGTAACATAAAAATCTGGAGGGAGG 2 21 0 AATAAAAATC 0.836 -276 TTCCCGAAAAACAAAAAGAGCCAGAAAACACC 2 225 0 AAAAAGAGCC 0.930338 -72 AGAAGAAGAGAATAAAAAAACCACAACAAACC 3 117 0 AAAAAAAACC 0.979928 -62 CACGGTAAATAGAAAAAGAGACCACAACAGCC 4 100 0 AAAAAGAGAC 0.793337 -41 AATCACTAAACATAAAAAAACCTCATGCATGT 5 20 0 CAAAAAAACC 0.868832 -260 TTCTACTATGAATATAAAAGACTTTTTTCATT 5 51 1 AATAAAAGAC 0.90647 -229 TCATTCAATAACTATCAAAATCTTTCACGTTT 5 169 0 AATCAAAATC 0.68307 -111 TTTAGCATATAAAATCAAAACCCTGCTTCATA 6 155 0 AATCAAAACC 0.933288 -36 GCCTACTGAAAGCAAAAAATCCCGTTTTTCAC 7 17 0 AAAAAAATCC 0.885004 -73 AGCTGTTATAATGAAAAAAAACTATTGGAGCG 7 62 1 AAAAAAAAAC 0.933479 -28 AATAAGGTAGAATAACAAACCCTATTGGCAGG 8 36 1 AAACAAACCC 0.828258 -31 TTTGAGGTGTAAGAAAAAAGCCAGAGCTTTGA 9 238 1 AAAAAAAGCC 0.980294 -63 CCCTCGGAATAGAAAAAAAGCCAGAACCTTTT 9 270 0 AAAAAAAGCC 0.980294 -31 ACATAAATATATAATAAAAACCAAAAGTTAAT 11 249 0 AATAAAAACC 0.970664 -52 * ********* Masking position 7 Map Score: 15.4941 Number of sites scoring better than the average of aligned sites = 786 Number in coding regions = 548 Number in noncoding regions = 238 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 2 GTAAAGAGCTGCTGTGGTCTCCGAGTTCTC 3 61 0 GCTGTGGTCT 0.991308 -118 AAAGCGGTTTGTTGTGGTTTTTTTATTCTC 3 112 1 GTTGTGGTTT 0.9786 -67 ACACTTTGGTGCTGTGGTCTCTCCTCATCT 4 57 0 GCTGTGGTCT 0.991308 -84 CACTTTGGCTGTTGTGGTCTCTTTTTCTAT 4 94 1 GTTGTGGTCT 0.982213 -47 TGACAATCACGCTGTGCTTTACTATAATAG 6 93 1 GCTGTGCTTT 0.947799 -98 CTTTTTCAAAGCTCTGGCTTTTTTCTTACA 9 245 0 GCTCTGGCTT 0.964051 -56 TTTGAAAAAGGTTCTGGCTTTTTTTCTATT 9 265 1 GTTCTGGCTT 0.928491 -36 ********** Masking position 5 Map Score: 9.76163 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 29 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 3 GATTTCTCCTCCTTATAGATAAGC 1 85 0 TCTCCTCCTT 0.982065 -14 GATTCCTGGCTCTCCTCATCTCCATCCAAG 2 177 0 TCTCCTCATC 0.962344 -120 TTTTTTATTCTCTTCTTCTCTATCATGCTT 3 130 1 TCTTCTTCTC 0.834229 -49 TGCTGTGGTCTCTCCTCATCTCAGGACCGT 4 48 0 TCTCCTCATC 0.962344 -93 TACGTTTCCTCCTTGTTGTCACGG 4 127 0 TTTCCTCCTT 0.904453 -14 TACGACATTTTCTTCTTATTTTAATGAAAA 5 75 0 TCTTCTTATT 0.856883 -205 GTCGTACAATTGTCCTTATTTTTGTCGAAT 5 99 1 TGTCCTTATT 0.815428 -181 CTTTCACGTTTCTCCATATTAACGTATGTC 5 150 0 TCTCCATATT 0.794383 -130 TGTGATTCTACTCCTTTAGCATATAA 6 175 0 TCTACTCCTT 0.915129 -16 ACTAAAATCATTTACTTATTCAGACTTATA 9 33 0 TTTACTTATT 0.508606 -268 ATAAAAAACTCCTTCTTGAATCTTTAC 11 284 0 ACTCCTTCTT 0.838308 -17 ********** Masking position 3 Map Score: 7.74425 Number of sites scoring better than the average of aligned sites = 803 Number in coding regions = 528 Number in noncoding regions = 275 Number of orfs with sites within 600 bp upstream = 302 Fraction of orfs with sites within 600 bp upstream = 0.0485063 Motif number 4 CTTTAAACAGCCTCCCTCCAGATTTTTATG 2 11 1 CCTCCCTCCA 0.859922 -286 TCCTGGCTCTCCTCATCTCCATCCAAGCTA 2 174 0 CCTCATCTCC 0.974499 -123 GTGTGGCGTGCCTCCTTTCCCGAAAAACAA 2 243 0 CCTCCTTTCC 0.929449 -54 TGTGGTCTCTCCTCATCTCAGGACCGTTCT 4 45 0 CCTCATCTCA 0.960148 -96 CCTCATGCAACATGCATGAG 5 1 1 CCTCATGCAA 0.918288 -279 CATAAAAAAACCTCATGCATGTTGCATGAG 5 12 0 CCTCATGCAT 0.857615 -268 GATATCCCTCCTGCCAATAGGGTTTG 8 51 0 CCTCCTGCCA 0.978852 -16 CTCTCATCCCCCTCGGAATAG 9 290 0 TCTCATCCCC 0.922075 -11 CGGATCTTCGCATCATCCCCTCAAAATTGA 10 51 1 CATCATCCCC 0.922075 -173 GCCCTCATTCCTTTTCTCAGCA 10 212 0 CCTCATTCCT 0.956819 -12 ********** Masking position 3 Map Score: 6.73239 Number of sites scoring better than the average of aligned sites = 406 Number in coding regions = 322 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 5 TTCCAACACGCCGTTTACATCCGTTTTTTA 1 37 1 CCGTTTACAT 0.983801 -62 TGAAAATTACCCGTTTACATTCGCTCCGGA 2 106 1 CCGTTTACAT 0.983801 -191 CACCGCTTTCATGCACTGATAC 3 3 1 CCGCTTTCAT 0.945902 -176 GTCGAATTTACAGTTTACAAACCCTATAGA 5 122 1 CAGTTTACAA 0.828574 -158 ACCGAAAATAGCGTTTACAATGAAATTGTA 5 225 1 GCGTTTACAA 0.89083 -55 CAAAATGAATACGTTTTCATTAGGAGGTGA 5 257 1 ACGTTTTCAT 0.893125 -23 ACCTTCCTTACCGTTTTAATAGAATCAGTT 6 17 1 CCGTTTTAAT 0.880045 -174 GGTCATAGAGCCGTTTTCGACAAATACTAT 6 119 0 CCGTTTTCGA 0.934175 -72 AAAGCCAGAACCTTTTTCAAAGCTCTGGCT 9 256 0 CCTTTTTCAA 0.856216 -45 ********** Masking position 5 Map Score: 6.71326 Number of sites scoring better than the average of aligned sites = 633 Number in coding regions = 580 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 6 AAGACACATAAAAGATTAATAGTTTTCCAAC 1 13 1 AAGATTAATA 0.91043 -86 GCATTTAGTAAAAGGATAATATTCACTTCCC 2 63 1 AAGGATAATA 0.830193 -234 CGCTATCATGATAAGTTAATAGCTTGGATGG 2 155 1 AAAGTTAATA 0.937563 -142 TACAATTGCACTAGGTTAATACATTGTGATG 3 30 1 CAGGTTAATA 0.938117 -149 TATAATGGTTACAAGTTAATAAGAACGGTCC 4 24 1 AAAGTTAATA 0.937563 -117 CCCTATAGACATACGTTAATATGGAGAAACG 5 143 1 AACGTTAATA 0.941894 -137 TGATTTTATTCAACATTAATAAGTGATTTTA 10 151 0 CACATTAATA 0.721979 -73 TACTTGATTAAAAGATTAATATAATAAAAAT 11 146 0 AAGATTAATA 0.91043 -155 AATAAAAACCAAAAGTTAATCAATAGTTGCT 11 238 0 AAAGTTAATC 0.778193 -63 * ********* Masking position 7 Map Score: 4.92315 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 27 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 ACTACCTGTCTTTCATAATAAAAAACGGAT 1 55 0 TTTCATAATA 0.855096 -44 AAAAGACTTTTTTCATTAAAATAAGAAGAA 5 66 1 TTTCATTAAA 0.850372 -214 TTGAATACAATTTCATTGTAAACGCTATTT 5 230 0 TTTCATTGTA 0.897936 -50 AATATTTTAGTTCCATTATAGATGACAATC 6 71 1 TTCCATTATA 0.949388 -120 AATAGTTTTTTTTCATTATAACAGCTGGCG 7 58 0 TTTCATTATA 0.970493 -32 CGTCCATTATAGTGGTATTAT 9 2 1 GTCCATTATA 0.833019 -299 CACTACATTTTTTCATTATTTTTATTATAT 11 129 1 TTTCATTATT 0.855984 -172 AACTTTTGGTTTTTATTATATATTTATGTT 11 252 1 TTTTATTATA 0.786589 -49 ********** Masking position 5 Map Score: 4.26353 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 67 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 8 TATCCTTTTACTAAATGCAATTATATTTTT 2 51 0 CTAAATGCAA 0.745466 -246 ACATCCAGCACAAACAGCAAAGGGGGATAA 2 271 1 CAAACAGCAA 0.941174 -26 AAGTCACGATTAAAAAGCATGATAGAGAAG 3 144 0 TAAAAAGCAT 0.637931 -35 ACCACAGCACCAAAGTGTAAGCATGCACTT 4 69 1 CAAAGTGTAA 0.810527 -72 CCACAACAGCCAAAGTGCATGCTTACACTT 4 81 0 CAAAGTGCAT 0.885002 -60 CCTCATGCAACATGCATGAGGTTTTTT 5 8 1 CAACATGCAT 0.719048 -272 ATAGGGTTTGTAAACTGTAAATTCGACAAA 5 119 0 TAAACTGTAA 0.489787 -161 AAATTGTATTCAAAATGAATACGTTTTCAT 5 247 1 CAAAATGAAT 0.756599 -33 TCTTACACCTCAAACAGCAAAGCTGTTATT 9 222 0 CAAACAGCAA 0.941174 -79 CCTAAGTAGGCAAAAAGAAAGAACCAGTCT 10 91 0 CAAAAAGAAA 0.816061 -133 AAGAAATGACCAAAAAGTAACCTGTTGTGC 11 57 0 CAAAAAGTAA 0.864078 -244 ********** Masking position 3 Map Score: 2.58758 Number of sites scoring better than the average of aligned sites = 1014 Number in coding regions = 891 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 9 TTTTTAATCGTGACTTTAGGAGGAATGTGC 3 158 1 TGACTTTAGG 0.832705 -21 TGAATTTGAATGATTTTAGTTGCCTAAACC 5 198 1 TGATTTTAGT 0.965337 -82 TTTGATAAACTGATTCTATTAAAACGGTAA 6 24 0 TGATTCTATT 0.909332 -167 AGCAGGGTTTTGATTTTATATGCTAAAGGA 6 160 1 TGATTTTATA 0.813759 -31 TGTGATTCTACTCCTTTAGCAT 6 179 0 TGATTCTACT 0.854713 -12 AATAAGTAAATGATTTTAGTTTGGAGGGAA 9 43 1 TGATTTTAGT 0.965337 -258 CATTAATAAGTGATTTTAAGTAAAAATGCG 10 139 0 TGATTTTAAG 0.825076 -85 AGTTTTTATTTGATTTTATTCAACATTAAT 10 162 0 TGATTTTATT 0.946556 -62 ********** Masking position 3 Map Score: 3.62337 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 204 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 10 TAAACAGCCTCCCTCCAGATTTTTATGTTA 2 14 1 CCCTCCAGAT 0.96078 -283 CGTTTACATTCGCTCCGGACTATGATAATT 2 117 1 CGCTCCGGAC 0.978955 -180 TAACAGCTGGCGCTCCGAAACGCCTACTGA 7 40 0 CGCTCCGAAA 0.954676 -50 GTTTACCGCTCCAATAGTTTTTTTTC 7 74 0 CGCTCCAATA 0.757623 -16 GCATTATTTTCCCTCCAAACTAAAATCATT 9 51 0 CCCTCCAAAC 0.975186 -250 AATATAGTTACGCTCACGACATTCAGTGCA 9 101 0 CGCTCACGAC 0.825597 -200 CTCTCATCCCCCTCGGAATAGAAAAAAAG 9 282 0 CCCTCGGAAT 0.873742 -19 TCGCATCATCCCCTCAAAATTGACCAGTCG 10 58 1 CCCTCAAAAT 0.872091 -166 ********** Masking position 4 Map Score: 1.69426 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 210 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 11 GCCTCCTTTCCCGAAAAACAAAAAGAGCCA 2 234 0 CCGAAAAACA 0.852228 -63 TAAACATTTGCCGTAAAGAGCTGCTGTGGT 3 73 0 CCGTAAAGAG 0.960747 -106 GTTTATGCACCCGTAAAGCGGTTTGTTGTG 3 98 1 CCGTAAAGCG 0.967273 -81 CTTGTTGTCACGGTAAATAGAAAAAGAGAC 4 110 0 CGGTAAATAG 0.752594 -31 GTTGCCTAAACCGAAAATAGCGTTTACAAT 5 216 1 CCGAAAATAG 0.873156 -64 AATCCCGTGAAAAACGGGATTTTT 7 5 1 CCGTGAAAAA 0.880771 -85 CTACGTTACACCGTGAAACAAAATAACAGC 9 201 1 CCGTGAAACA 0.899202 -100 ********** Masking position 6 Map Score: 0.046092 Number of sites scoring better than the average of aligned sites = 453 Number in coding regions = 422 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 12 ********** No masking Map Score: -4.47399e-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 13 ********** No masking Map Score: -4.47399e-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 14 ********** No masking Map Score: -4.47399e-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