AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i289_moxr_protein_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 yeaB 300 alternate gene name: ydxT; similar to cation efflux system membrane protein #2 yeaC 152 similar to methanol dehydrogenase regulation #3 yeaD 300 similar to hypothetical proteins from B. subtilis Motif number 1 ACAAAACACTACAAATTTGAAATAAGCTGGTAT 1 7 0 ACAAATGAGC 0.968601 -294 CATTTTTTCCACACATTCGCTGAAAGCGCAAACAAAA 1 38 0 ACACATGCGC 0.99163 -263 TGTAAATATTACGCAAAATCACACAGCGAATAAAAAA 1 80 0 ACGCAATCGC 0.938895 -221 AAACCCAAGGACACCAGTGCTTCTCGCATTCTATCGA 1 119 0 ACACCAGCGC 0.98877 -182 ACAAAACCTCCTCTCGCTCACATTTTC 1 284 0 ACAAAATCGC 0.985499 -17 GCCAAAACACACAAAAAAGCTTCCTGTGACAGGAAGC 2 15 0 ACAAAAGCGT 0.987179 -138 AATCTGTATAAAAAAAACGATTCTAGCAAATTGTTAC 2 63 0 AAAAAAGAGC 0.906521 -90 TAACTTTACCACAAAAAAGCAATCTGTATAAAAAAAA 2 83 0 ACAAAAGCGT 0.986616 -70 GGCATACAAGACAAAAGGGAGAAACGCGTAAAACAAA 3 40 0 ACAAAAGAGC 0.991066 -261 AATGGATAAAACACAATTGCATGCGGGGGACAGGCTG 3 123 1 ACACAAGCGG 0.986017 -178 ****** ** ** Masking position 1 Map Score: 13.1077 Number of sites scoring better than the average of aligned sites = 580 Number in coding regions = 520 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 2 CAATTTATTTGCTCCGCCAAAAATCCCATCA 1 155 0 GCTCCGCAAA 0.98384 -146 TACCAATAAAGCTGGCCAAAACACACAAAAA 2 35 0 GCTGGCCAAA 0.979988 -118 AGCTGACAAAGCCGCCCTGAAACAT 3 5 0 GCCGCCCGAA 0.988261 -296 AAGGCCAACAGCCCGGCATACAAGACAAAAG 3 60 0 GCCCGGCTAC 0.962328 -241 CGGGGGACAGGCTGGGCGTAACGGTTACGCT 3 146 1 GCTGGGCTAA 0.98764 -155 ATTGAAGATTGCCTGCCAGAAGGTATCGAGT 3 215 1 GCCTGCCGAA 0.941504 -86 CGAGACGGAGGCCGCGCCAAACGGCTCGTTT 3 254 1 GCCGCGCAAA 0.992174 -47 CGTCATGCTCCGTTTAAACCAAGGAAA 3 284 0 GCTCCGTTAA 0.871819 -17 ******* *** Masking position 10 Map Score: 8.18853 Number of sites scoring better than the average of aligned sites = 479 Number in coding regions = 446 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 3 GAATGTGTGGAAAAAATGTTTCGTTTTTTATTCG 1 57 1 AAAAAAGCGT 0.949701 -244 TAAATATTACGCAAAATCACACAGCGAATAAAAA 1 81 0 GCAAAACCAG 0.817156 -220 TGGATGAGAGAAAAAGTGTTCCTTCGTCACTATT 1 184 1 AAAAAGGCTT 0.908243 -117 CAAAACACACAAAAAAGCTTCCTGTGACAGGAAG 2 16 0 AAAAAACCTG 0.985879 -137 ATCTGTATAAAAAAAACGATTCTAGCAAATTGTT 2 65 0 AAAAAAGCTA 0.901175 -88 ACTTTACCACAAAAAAGCAATCTGTATAAAAAAA 2 84 0 AAAAAACCTG 0.985977 -69 AAACCAGCTGACAAAGCCGCCCTGAAACAT 3 7 0 ACAAAGCCTG 0.955609 -294 AACGCGTAAAACAAAAACCAGCTGACAAAGCCGC 3 21 0 ACAAAACCTG 0.980417 -280 TGAAGCCTGAAAAGAACGGAGCGGATACAAGGCC 3 85 0 AAAGAAGCGG 0.923638 -216 TTAAACCAAGGAAAAACGAGCCGTTTGGCGCGGC 3 264 0 GAAAAAGCGT 0.890988 -37 ****** * *** Masking position 5 Map Score: 6.43791 Number of sites scoring better than the average of aligned sites = 1426 Number in coding regions = 1126 Number in noncoding regions = 300 Number of orfs with sites within 600 bp upstream = 258 Fraction of orfs with sites within 600 bp upstream = 0.0414391 Motif number 4 TTTTCCACACATTCGCTGAAAGCGCAAACAAA 1 39 0 ATTCGCTGAG 0.946806 -262 TTCGTTTTTTATTCGCTGTGTGATTTTGCGTA 1 76 1 ATTCGCTGGG 0.993765 -225 TTACAATTCGATAGAATGCGAGAAGCACTGGT 1 112 1 ATAGAATGGG 0.906452 -189 GAGCAAATAAATTGGATGAGAGAAAAAGTGTT 1 172 1 ATTGGATGGG 0.990138 -129 TACAAAGCTGATCCGCAGTGGGTCTACAGAAA 1 240 0 ATCCGCAGGG 0.901841 -61 ATAAAACACAATTGCATGCGGGGGACAGGCTG 3 128 1 ATTGCATGGG 0.983669 -173 CATGCGGGGGACAGGCTGGGCGTAACGGTTAC 3 142 1 ACAGGCTGGG 0.966392 -159 CAATCACCATATACCATCAGCGGAAATGGCAG 3 187 0 ATACCATCGG 0.818721 -114 GTGATTGAAGATTGCCTGCCAGAAGGTATCGA 3 212 1 ATTGCCTGCG 0.952562 -89 ******** * * Masking position 1 Map Score: 5.98837 Number of sites scoring better than the average of aligned sites = 449 Number in coding regions = 392 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 5 TTCACCCGCCACAGAAAAATAGTGACGAAG 1 205 0 ACAGAAAAAT 0.965597 -96 CAGTGGGTCTACAGAAACATGATTCACCCG 1 227 0 ACAGAAACAT 0.959335 -74 TAAGATAATAATAGGAAAATGTGAGCGAGA 1 270 1 ATAGGAAAAT 0.92377 -31 GCTTCCTGTGACAGGAAGCTCCA 2 4 0 ACAGGAAGCT 0.990619 -149 GCTTCCTGTCACAGGAAGCTTTTTTGTGTG 2 15 1 ACAGGAAGCT 0.990619 -138 ********** Masking position 6 Map Score: 3.71599 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 127 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 TTTGTTTGCGCTTTCAGCGAATGTGTGGAAA 1 39 1 CTTCAGCGAA 0.959101 -262 TACGCAAAATCACACAGCGAATAAAAAACGA 1 77 0 CAACAGCGAA 0.832882 -224 AACACTTTTTCTCTCATCCAATTTATTTGCT 1 173 0 CTTCATCCAA 0.907328 -128 TTTCTGTAGACCCACTGCGGATCAGCTTTGT 1 240 1 CCACTGCGGA 0.820285 -61 AAAACAAAAACCAGCTGACAAAGCCGCCCTG 3 17 0 CCGCTGACAA 0.926952 -284 GGCCAACAGCCCGGCATACAAGACAAAAGGG 3 58 0 CCGCATACAA 0.928172 -243 TTCTTTTCAGGCTTCAGGCAAATGGATAAAA 3 103 1 GCTCAGGCAA 0.893949 -198 CAGCCTGTCCCCCGCATGCAATTGTGTTTTA 3 129 0 CCGCATGCAA 0.966813 -172 TCACCATATACCATCAGCGGAAATGGCAGCT 3 185 0 CCTCAGCGGA 0.968479 -116 TCGATACCTTCTGGCAGGCAATCTTCAATCA 3 213 0 CTGCAGGCAA 0.97088 -88 ** ******** Masking position 11 Map Score: 6.16614 Number of sites scoring better than the average of aligned sites = 1439 Number in coding regions = 1334 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 7 CAAGGACACCAGTGCTTCTCGCATTCTATCGAATT 1 116 0 AGTTCTCATT 0.946321 -185 ACGAAGGAACACTTTTTCTCTCATCCAATTTATTT 1 176 0 ACTTCTCATC 0.876923 -125 AAAAAGTGTTCCTTCGTCACTATTTTTCTGTGGCG 1 194 1 CCTTCACTTT 0.95824 -107 ACAAAACCTCCTCTCGCTCACATTTTCCTATTAT 1 277 0 CCTGCTCATT 0.982794 -24 TTTTGTTTTACGCGTTTCTCCCTTTTGTCTTGTAT 3 39 1 CGCTCTCTTT 0.962815 -262 TTTGGCGCGGCCTCCGTCTCGATTTAATGACTCGA 3 240 0 CCTTCTCTTT 0.991034 -61 CGTCATGCTCCGTTTAAACCAAGGA 3 286 0 CGTGCTCTTT 0.982646 -15 *** **** *** Masking position 14 Map Score: 1.48486 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 165 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 8 ********** No masking Map Score: -1.79524e-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 9 ********** No masking Map Score: -1.79524e-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 10 ********** No masking Map Score: -1.79524e-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