AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i343_weak4_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 gbsA 198 glycine betaine aldehyde dehydrogenase #2 sbo 300 subtilosin A #3 ywiA 133 similar to hypothetical proteins Motif number 1 ACTGACCCTCTTTTCCTTTAGAAAATTA 1 1 1 AACCCTTTTT 0.938514 -198 TTTCTTTTTGACTTTTCCTCATGTTTCGTTAAGATAAA 1 66 0 ATCCCATGTG 0.727579 -133 TTAAACTGTCAAAGTCCCATTTTGATTTTTCTTTTTGA 1 93 0 ATCCTTTTGT 0.99045 -106 TAACAACCTTAATCTAACATATGGTTTTTAAACTGTCA 1 120 0 ATACTATGGT 0.680412 -79 GGTTGTTAAAAACATTAAATTTTTATTTAACAAACTTT 1 150 1 ATAATTTTTT 0.718988 -49 TTTTCATCATTCCACTTTGACTTGAATAGTATA 2 6 1 ATCCCTTTGT 0.98704 -295 ACCTTTAGGAAATGTTACATTTTTCCGAAATCTATCAT 2 161 1 ATACTTTTTA 0.720263 -140 AATTGAATCCTCCCTTTTTTTGTTTTTCTAGCAG 2 277 0 ATCCTTTTTT 0.990271 -24 TAGTAGAATGACTATGCCCTTTTGGGAGATCC 3 5 0 ATCCTTTTGG 0.972934 -129 TAGTCATTCTACTATGCCCTTTTTAAGTAAATTACAAT 3 29 1 ATCCTTTTTT 0.990271 -105 CTTTTTAAGTAAATTACAATTTTTAACTAAAATCTACC 3 47 1 ATCATTTTTT 0.927523 -87 TTTTAACTAAAATCTACCTCTTGGATATACATACACAA 3 67 1 ATCCCTTGGT 0.97465 -67 GGATATACATACACAACCGTTTTTCATTTGAATCATAT 3 89 1 AACCTTTTTT 0.953871 -45 * * ** ***** * Masking position 1 Map Score: 14.7228 Number of sites scoring better than the average of aligned sites = 1241 Number in coding regions = 976 Number in noncoding regions = 265 Number of orfs with sites within 600 bp upstream = 284 Fraction of orfs with sites within 600 bp upstream = 0.0456152 Motif number 2 TTTAATTTTCTAAAGGAAAAGAGGGTCAGT 1 11 0 TAAAGGAAAA 0.96998 -188 ATAAAGAACATAAAGAAATAACTTAACGAA 1 41 0 TAAAGAAATA 0.673162 -158 TCATGTTTCGTTAAGATAAAGAACATAAAG 1 56 0 TTAAGATAAA 0.896737 -143 TTAACGAAACATGAGGAAAAGTCAAAAAGA 1 72 1 ATGAGGAAAA 0.92083 -127 GGAAAAGTCAAAAAGAAAAATCAAAATGGG 1 86 1 AAAAGAAAAA 0.958139 -113 TAAAGTTTGTTAAATAAAAATTTAATGTTT 1 159 0 TAAATAAAAA 0.73351 -40 ATAAGCCTCCTTGACGTAAATAAAGTTTGT 1 179 0 TTGACGTAAA 0.482375 -20 TCAAAGTGGAATGATGAAAA 2 1 0 ATGATGAAAA 0.555243 -300 TCATCAGATTTGAAGATAAACCTCATAAAA 2 91 1 TGAAGATAAA 0.697594 -210 TCTCTTCTATATAAGGAAATGCTTTTTATG 2 114 0 ATAAGGAAAT 0.907133 -187 CCTTATATAGAAGAGAAAATCATATCACTA 2 128 1 AAGAGAAAAT 0.835285 -173 TAACATTTCCTAAAGGTAATTAGTGATATG 2 148 0 TAAAGGTAAT 0.857389 -153 AAAAAATGTGAAAAGGAAATGATAGATTTC 2 187 0 AAAAGGAAAT 0.925599 -114 TTTGATAGTTTTAAGATAAAAGTACAACAT 2 243 1 TTAAGATAAA 0.896737 -58 ATCTGCTAGAAAAACAAAAAAAGGGAGGAT 2 275 1 AAAACAAAAA 0.79168 -26 TATGCCCTTTTTAAGTAAATTACAATTTTT 3 41 1 TTAAGTAAAT 0.549969 -93 CATATGATTCAAATGAAAAACGGTTGTGTA 3 98 0 AAATGAAAAA 0.647688 -36 ********** Masking position 8 Map Score: 14.1978 Number of sites scoring better than the average of aligned sites = 4818 Number in coding regions = 3981 Number in noncoding regions = 837 Number of orfs with sites within 600 bp upstream = 757 Fraction of orfs with sites within 600 bp upstream = 0.121587 Motif number 3 AAAGAAAAATCAAAATGGGACTTTGACAGT 1 97 1 CAAAATGGGA 0.974208 -102 TTTGTTAAATAAAAATTTAATGTTTTTAAC 1 154 0 AAAAATTTAA 0.660847 -45 CTATTCAAGTCAAAGTGGAATGATGAAAA 2 10 0 CAAAGTGGAA 0.900036 -291 GTAACATTTCCTAAAGGTAATTAGTGATAT 2 149 0 CTAAAGGTAA 0.73716 -152 TAGATTTCGGAAAAATGTAACATTTCCTAA 2 165 0 AAAAATGTAA 0.957089 -136 ATATTTTGAAAAAAATGTGAAAAGGAAATG 2 196 0 AAAAATGTGA 0.956259 -105 TAGAAAAACAAAAAAAGGGAGGATTCAATT 2 281 1 AAAAAAGGGA 0.87861 -20 GGATCTCCCAAAAGGGCATAGTCATTCT 3 9 1 CAAAAGGGCA 0.955335 -125 TAATTTACTTAAAAAGGGCATAGTAGAATG 3 33 0 AAAAAGGGCA 0.951789 -101 ATTTTAGTTAAAAATTGTAATTTACTTAAA 3 50 0 AAAATTGTAA 0.778569 -84 ********** Masking position 4 Map Score: 9.14471 Number of sites scoring better than the average of aligned sites = 1386 Number in coding regions = 1143 Number in noncoding regions = 243 Number of orfs with sites within 600 bp upstream = 252 Fraction of orfs with sites within 600 bp upstream = 0.0404754 Motif number 4 AAGAAATAACTTAACGAATTTAATTTTCTAAAGG 1 25 0 TTACGAATAT 0.964667 -174 ACTTTGACAGTTTAAAAACCATATGTTAGATTAA 1 116 1 TTTAAAACAT 0.894361 -83 TTTAATGTTTTTAACAACCTTAATCTAACATATG 1 135 0 TTACAACTAT 0.927569 -64 AAATTTTTATTTAACAAACTTTATTTACGTCAAG 1 166 1 TTACAAATAT 0.979681 -33 GCAGTTGAAGTTTACAAACCGAATGATTATACTA 2 37 0 TTTCAAACAT 0.986982 -264 ATGAGGTTTATCTTCAAATCTGATGAGCAATGAT 2 83 0 TCTCAAACAT 0.95269 -218 ATGTTACATTTTTCCGAAATCTATCATTTCCTTT 2 172 1 TTTCGAATAT 0.977679 -129 TTTCACATTTTTTTCAAAATATATGTATTGAATT 2 204 1 TTTCAAATAT 0.987237 -97 *** **** * ** Masking position 7 Map Score: 7.30235 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 152 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 5 ********** No masking Map Score: 6.2771e-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 6 ********** No masking Map Score: 6.2771e-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: 6.2771e-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