AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -irpoE_tpal_opreg_100.orf -g0.528 -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 = 0.528 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 TP0091 181 cysteinyl-tRNA synthetase (cysS) #2 TP0092 70 RNA polymerase sigma-24 factor (rpoE) #3 TP0773 300 periplasmic serine protease DO (htrA-1) #4 TP0841 300 periplasmic serine protease DO (htrA-2) Motif number 1 TGCGGACCACGCCCAGCCCCATTGTCGCGC 1 120 0 GCCCAGCCCC 0.947583 -62 GCTTTTAAGAGCACAGGATGATGCAGATTT 2 44 1 GCACAGGATG 0.937715 -27 GACTTGAACTCCCACGCCGGTGAAGGCAC 3 10 1 TCCCACGCCG 0.984617 -291 AAACTATATTTCCCACCATGGAAGGGTTTT 3 86 0 TCCCACCATG 0.977721 -215 AGCTTTCAGGGCACGGGATGCAAAGGCGGC 3 137 1 GCACGGGATG 0.893804 -164 AATACACGCTGCCCGCGGCGCTGCGCGTGG 3 190 1 GCCCGCGGCG 0.994847 -111 TGAGCTAATAGCCCACGGCGCCACGCGCAG 3 210 0 GCCCACGGCG 0.997155 -91 TGTACTATCAGCACACCGCGCACACTT 4 8 0 GCACACCGCG 0.994984 -293 CACAAACTGCTCCCTGCATGTACTATCAGC 4 26 0 TCCCTGCATG 0.913113 -275 CTTACACGCTGCCTACCGTGCACAAACTGC 4 46 0 GCCTACCGTG 0.918185 -255 CTTCACCTGTGCCCGCCACGTACACTTACA 4 70 0 GCCCGCCACG 0.995411 -231 GTTAAAAGCAGCACACAGCGATATGGTTAC 4 113 0 GCACACAGCG 0.945441 -188 ACCCCTACCGACACAGCCCGGGTTAAAAGC 4 134 0 ACACAGCCCG 0.857449 -167 TCCCTCCACGTCCCTGCGCGTACCCAAACC 4 161 0 TCCCTGCGCG 0.981366 -140 TGTTCATGAGTCCCTCCACGTCCCTGCGCG 4 171 0 TCCCTCCACG 0.979941 -130 ********** Masking position 2 Map Score: 28.9205 Number of sites scoring better than the average of aligned sites = 933 Number in coding regions = 852 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 2 GCTTATGCTACAATGGCGCGGTCTTGGCCT 1 38 1 CAATGGCGCG 0.991177 -144 TAGACTGAAGCGCAGGCGGGCAAAGGCGTT 1 89 1 CGCAGGCGGG 0.956887 -93 CGCAGGCGGGCAAAGGCGTTTGCGCGACAA 1 99 1 CAAAGGCGTT 0.955949 -83 GTTTGCGCGACAATGGGGCTGGGCGTGGTC 1 116 1 CAATGGGGCT 0.941439 -66 AAGTTTCTCCCAACCGGGCGCAGAACACGT 1 149 0 CAACCGGGCG 0.907595 -33 GGAGAAACTTCGAAGGGGCGCAC 1 169 1 CGAAGGGGCG 0.967751 -13 CTAGTGCCTTCACCGGCGTGGGAGTTCAAG 3 13 0 CACCGGCGTG 0.975113 -288 GAAAACCCTTCCATGGTGGGAAATATAGTT 3 85 1 CCATGGTGGG 0.891684 -216 GCACGGGATGCAAAGGCGGCGTACTTGACA 3 147 1 CAAAGGCGGC 0.973793 -154 TACACGCTGCCCGCGGCGCTGCGCGTGGCG 3 192 1 CCGCGGCGCT 0.976427 -109 AGCTAATAGCCCACGGCGCCACGCGCAGCG 3 208 0 CCACGGCGCC 0.982088 -93 CATCATGGCTCAGAGGTGGGATTG 3 287 1 CAGAGGTGGG 0.929567 -14 TTTTTTACAGCAGCGGCGTTGCTCGTTTTT 4 248 1 CAGCGGCGTT 0.955898 -53 ********** Masking position 1 Map Score: 18.3281 Number of sites scoring better than the average of aligned sites = 895 Number in coding regions = 804 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 3 CTTATGCTACAATGGCGCGGTCTTGGCCTT 1 39 1 AATGGCGCGG 0.978008 -143 TTTGCGCGACAATGGGGCTGGGCGTGGTCC 1 117 1 AATGGGGCTG 0.811647 -65 TTTCTCCCAACCGGGCGCAGAACACGTGCG 1 146 0 CCGGGCGCAG 0.976287 -36 GAAACTTCGAAGGGGCGCAC 1 172 1 AGGGGCGCAC 0.969848 -10 TAGTGCCTTCACCGGCGTGGGAGTTCAAGT 3 12 0 ACCGGCGTGG 0.946046 -289 GAGCAGCTTTCAGGGCACGGGATGCAAAGG 3 133 1 CAGGGCACGG 0.869834 -168 GGGATGCAAAGGCGGCGTACTTGACAAAAT 3 151 1 GGCGGCGTAC 0.686138 -150 ACACGCTGCCCGCGGCGCTGCGCGTGGCGC 3 193 1 CGCGGCGCTG 0.986882 -108 CGGCGCTGCGCGTGGCGCCGTGGGCTATTA 3 205 1 CGTGGCGCCG 0.961957 -96 CACGCCTTAAAAGGGCGTTGCTCTACCAGC 3 240 0 AAGGGCGTTG 0.939128 -61 TCGAATCCATCATGGCTCAGAGGTGGGATT 3 280 1 CATGGCTCAG 0.73822 -21 ACTATCAGCACACCGCGCACACTT 4 5 0 CACCGCGCAC 0.816408 -296 ATAGTACATGCAGGGAGCAGTTTGTGCACG 4 30 1 CAGGGAGCAG 0.851606 -271 TGTAAGTGTACGTGGCGGGCACAGGTGAAG 4 70 1 CGTGGCGGGC 0.795071 -231 GCTGCTTTTAACCCGGGCTGTGTCGGTAGG 4 131 1 ACCCGGGCTG 0.456755 -170 GGGTACGCGCAGGGACGTGGAGGGACTCAT 4 166 1 AGGGACGTGG 0.662191 -135 TTTTTACAGCAGCGGCGTTGCTCGTTTTTA 4 249 1 AGCGGCGTTG 0.961217 -52 ********** Masking position 5 Map Score: 16.7405 Number of sites scoring better than the average of aligned sites = 2733 Number in coding regions = 2501 Number in noncoding regions = 232 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 4 CCCCATTGTCGCGCAAACGCCTTTGCCCGCCT 1 102 0 GCCAAACCCT 0.99607 -80 TGCGGACCACGCCCAGCCCCATTGTCGCGCAA 1 118 0 GCCAGCCCAT 0.915154 -64 GCCGGTGAAGGCACTAGCACCTGAAGCTAGCG 3 26 1 GCCTAGCCCT 0.989326 -275 CCTGAAAGCTGCTCTAATCCCTTGACTAGAAA 3 115 0 GCCTAATCCT 0.970483 -186 TGCATCCCGTGCCCTGAAAGCTGCTCTAATCC 3 127 0 GCCTGAAGCT 0.919638 -174 AAAGGGCGTTGCTCTACCAGCTGAGCTAATAG 3 229 0 GCCTACCGCT 0.990552 -72 TGCCTACCGTGCACAAACTGCTCCCTGCATGT 4 35 0 GCCAAACGCT 0.993623 -266 CCCTGCGCGTACCCAAACCCCTACCGACACAG 4 148 0 ACCAAACCCT 0.965878 -153 ** ***** *** Masking position 12 Map Score: 9.67394 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 212 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 ATTGTAGCATAAGCGCGTGAAATCGTATAT 1 22 0 AAGCGCGTGA 0.865564 -160 TGGGCGTGGTCCGCACGTGTTCTGCGCCCG 1 135 1 CCGCACGTGT 0.9575 -47 GCGCCGCGGGCAGCGTGTATTGGAATTGGC 3 181 0 CAGCGTGTAT 0.973653 -120 GCCCGCGGCGCTGCGCGTGGCGCCGTGGGC 3 200 1 CTGCGCGTGG 0.938378 -101 AAACTGCTCCCTGCATGTACTATCAGCACA 4 23 0 CTGCATGTAC 0.970041 -278 GCACGGTAGGCAGCGTGTAAGTGTACGTGG 4 55 1 CAGCGTGTAA 0.973734 -246 CTCCACGTCCCTGCGCGTACCCAAACCCCT 4 158 0 CTGCGCGTAC 0.991396 -143 CTGCGGCATACCGCATGTACCCCACACACA 4 217 0 CCGCATGTAC 0.972172 -84 ********** Masking position 8 Map Score: 9.20087 Number of sites scoring better than the average of aligned sites = 730 Number in coding regions = 671 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 6 GGCGGGCAAAGGCGTTTGCGCGACAATGGGG 1 103 1 GGCGTTTGGC 0.979757 -79 GCTAGCTTCAGGTGCTAGTGCCTTCACCGGC 3 26 0 GGTGCTAGGC 0.971257 -275 TTCTAGTCAAGGGATTAGAGCAGCTTTCAGG 3 116 1 GGGATTAGGC 0.956321 -185 GCGCAGCGCCGCGGGCAGCGTGTATTGGAAT 3 185 0 GCGGGCAGGT 0.89954 -116 TATTAGCTCAGCTGGTAGAGCAACGCCCTTT 3 230 1 GCTGGTAGGC 0.979157 -71 CATGCAGGGAGCAGTTTGTGCACGGTAGGCA 4 36 1 GCAGTTTGGC 0.961263 -265 TGTGTCGGTAGGGGTTTGGGTACGCGCAGGG 4 149 1 GGGGTTTGGT 0.972536 -152 ******** ** Masking position 8 Map Score: 2.19443 Number of sites scoring better than the average of aligned sites = 356 Number in coding regions = 323 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 7 ACGCAAAGAAGGCCAAGACCGCGCCATTGT 1 47 0 GGCCAAGACC 0.965088 -135 GTGCGGACCACGCCCAGCCCCATTGTCGCG 1 121 0 CGCCCAGCCC 0.968706 -61 CTAGCGTGTCTGCCAATTCCACCATCGAGG 3 52 1 TGCCAATTCC 0.983298 -249 ATTGGCATTTTGTCAAGTACGCCGCCTTTG 3 157 0 TGTCAAGTAC 0.901068 -144 CTTGACAAAATGCCAATTCCAATACACGCT 3 170 1 TGCCAATTCC 0.983298 -131 CACCTGTGCCCGCCACGTACACTTACACGC 4 67 0 CGCCACGTAC 0.958744 -234 ********** Masking position 4 Map Score: 2.66914 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 68 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 ********** No masking Map Score: 1.48747e-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: 1.48747e-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: 1.48747e-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