AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i340_weak11_mthe_reg_300.orf -o340_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -x5 -e 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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTH00129 300 M.thermo #2 RTH02041 58 M.thermo #3 RTH01062 171 M.thermo #4 RTH01098 51 M.thermo #5 RTH00022 27 M.thermo #6 RTH01487 21 M.thermo #7 RTH01975 73 M.thermo Motif number 1 ATATTGACTGCAGCCCTGTTCCTTGTGGGCCTTTC 1 58 0 CACCGCCTTG 0.987364 -243 GTTTCATCCTCATCGGAGTGCCTGTTTATCTTGGA 1 94 0 CACGGCCTGT 0.994061 -207 AAGGTTTCCGCTTCCAAGGACCTTTCCAGGCACGA 1 134 0 CTCCGCCTTT 0.994577 -167 GACAGGGCAACAACCTGGACCCTGTGGTCAAGGTT 1 163 0 CACCGCCTGT 0.998853 -138 GTCAGGCACTCTCCCCCGGCCCTCTCGATCTTATC 1 217 0 CTCCGCCTCT 0.996487 -84 CGGTGCTGACCATCCCCGTTCCAGTTGAAAAGTCC 3 61 0 CACCGCCAGT 0.994498 -111 GAACTCGGGTCTCCAGCGTTCCGGTGCTGACCATC 3 82 0 CTCAGCCGGT 0.955872 -90 CATCAAATCGAATCCAAGAACCTCTATTTTAATGT 3 132 1 AACCGCCTCT 0.980702 -40 ** ** * ***** Masking position 8 Map Score: 13.821 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 203 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 2 GACTCGAAAGGCCCACAAGGAACAGGGCTG 1 53 1 GCCCACAAGG 0.847505 -248 CGGAAACCTTGACCACAGGGTCCAGGTTGT 1 159 1 GACCACAGGG 0.992785 -142 TGTCTGTGAAAATGACAGGGCAACAACCTG 1 181 0 AATGACAGGG 0.960206 -120 CATTTTCACAGACAGCAAGGGATAAGATCG 1 197 1 GACAGCAAGG 0.89608 -104 ATAAGATCGAGAGGGCCGGGGGAGAGTGCC 1 218 1 GAGGGCCGGG 0.980079 -83 TTATGTTCTTAATGGCCGGGTTCTCTTCAA 1 266 0 AATGGCCGGG 0.978908 -35 GGGACCGTAGGGTAGCTTGGTC 3 3 1 GACCGTAGGG 0.965718 -169 AAACTTCTTCAATGGCTGGGAGGATGGACC 3 29 0 AATGGCTGGG 0.92148 -143 GATTTGATGGGACCGCCGAGATTTGAACTC 3 111 0 GACCGCCGAG 0.958716 -61 TATTCACAGGGTGCATATGTA 6 2 1 ATTCACAGGG 0.82492 -20 ********** Masking position 10 Map Score: 10.4157 Number of sites scoring better than the average of aligned sites = 1211 Number in coding regions = 1141 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 3 TTCTCGTGCCTGGAAAGGTCCTTGGAAGCGGA 1 131 1 TGGAAAGTCT 0.931671 -170 TCCTTGGAAGCGGAAACCTTGACCACAGGGTC 1 149 1 CGGAAACTGA 0.979734 -152 GCCTGACACTCGGAAAAATTGTTGAAGAGAAC 1 245 1 CGGAAAATGT 0.98668 -56 ACTGAATCATTCTACTCTTTAGT 2 46 0 CTGAATCTCT 0.82445 -13 TTGAAAAGTCCGGAAACTTCTTCAATGGCTGG 3 40 0 CGGAAACTTT 0.986673 -132 TGGTCAGCACCGGAACGCTGGAGACCCGAGTT 3 84 1 CGGAACGTGA 0.870319 -88 AAACTCTAGACTGAAAAATAGTGGTTTATTAG 4 14 0 CTGAAAATGT 0.960438 -38 ATATTGAAACTTATTTGAGGTGATA 5 4 1 TTGAAACTTT 0.888347 -24 TATAGGGTGATGGAAAATTTTTAAGGGCGTTA 7 48 1 TGGAAAATTT 0.92159 -26 ******* * ** Masking position 5 Map Score: 5.29774 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 175 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 TGTGGGCCTTTCGAGTCTCCTTGCAACGTC 1 40 0 TCGAGTCTCC 0.915831 -261 CAACCTGGACCCTGTGGTCAAGGTTTCCGC 1 158 0 CCTGTGGTCA 0.935243 -143 ATCGAGAGGGCCGGGGGAGAGTGCCTGACA 1 223 1 CCGGGGGAGA 0.92216 -78 AACAATTTTTCCGAGTGTCAGGCACTCTCC 1 238 0 CCGAGTGTCA 0.966162 -63 ACCAAGCTACCCTACGGTCCC 3 2 0 CCTACGGTCC 0.932664 -170 CTCCAGCGTTCCGGTGCTGACCATCCCCGT 3 77 0 CCGGTGCTGA 0.93209 -95 AGATTTGAACTCGGGTCTCCAGCGTTCCGG 3 93 0 TCGGGTCTCC 0.965321 -79 AGTTCAAATCTCGGCGGTCCCATCAAATCG 3 112 1 TCGGCGGTCC 0.983754 -60 ********** Masking position 2 Map Score: 3.59103 Number of sites scoring better than the average of aligned sites = 1178 Number in coding regions = 1114 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 5 CATCCCAGGAAGGCGCAGCAATCTGGAAGG 1 10 1 AAGGCGAGCA 0.949304 -291 GCAATCTGGAAGGACGTTGCAAGGAGACTCG 1 28 1 AGGACGTGCA 0.991702 -273 CACTCCGATGAGGATGAAACAGTTCTCGTGC 1 109 1 AGGATGAACA 0.962517 -192 CACAGGGTCCAGGTTGTTGCCCTGTCATTTT 1 172 1 AGGTTGTGCC 0.923402 -129 AATGGCTGGGAGGATGGACCAAGCTACCCTA 3 18 0 AGGATGACCA 0.955032 -154 AGGAATTTATAGGGTGATGGAAAATTTTTAA 7 41 1 AGGGTGTGGA 0.972746 -33 AAAATTTTTAAGGGCGTTAAAAT 7 61 1 AGGGCGTAAA 0.907634 -13 ****** **** Masking position 1 Map Score: 1.46621 Number of sites scoring better than the average of aligned sites = 559 Number in coding regions = 535 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 CAGCAAGGGATAAGATCGAGAGGGCCGGGG 1 209 1 TAAGATCGAG 0.895515 -92 CTTTAGTTTATAAAATAAAAATATATAAAG 2 23 0 TAAAATAAAA 0.804569 -36 TTTTATTTTATAAACTAAAGAGTAGAATGA 2 33 1 TAAACTAAAG 0.911954 -26 TCCGGACTTTTCAACTGGAACGGGGATGGT 3 58 1 TCAACTGGAA 0.88577 -114 GGCGGTCCCATCAAATCGAATCCAAGAACC 3 124 1 TCAAATCGAA 0.945092 -48 AGAAAAACATTAAAATAGAGGTTCTTGGAT 3 143 0 TAAAATAGAG 0.930972 -29 CACCTCATAATAAACTCTAGACTGAAAAAT 4 27 0 TAAACTCTAG 0.894363 -25 TCTATCACCTCAAATAAGTTTCAA 5 14 0 TCACCTCAAA 0.802668 -14 ********** Masking position 3 Map Score: 0.50774 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 196 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 AACAGGGCTGCAGTCAATATATCCAAGATA 1 73 1 CAGTCAATAT 0.934853 -228 CCAAGATAAACAGGCACTCCGATGAGGATG 1 95 1 CAGGCACTCC 0.970126 -206 AGGACCTTTCCAGGCACGAGAACTGTTTCA 1 123 0 CAGGCACGAG 0.991253 -178 TTCCGAGTGTCAGGCACTCTCCCCCGGCCC 1 230 0 CAGGCACTCT 0.982257 -71 CACTATTTTTCAGTCTAGAGTTTATTATGA 4 23 1 CAGTCTAGAG 0.857332 -29 GGACATTCACGATTATCAATCAA 7 4 1 CATTCACGAT 0.911744 -70 ********** Masking position 2 Map Score: 2.24736 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 170 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 ********** No masking Map Score: 7.27186e-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 9 ********** No masking Map Score: 7.27186e-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 10 ********** No masking Map Score: 7.27186e-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