AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00760_pyro_reg_100.orf -o00760_pyro_100.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 = 0.42 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 PH0013 43 300aa long hypothetical quinolinate synthetase #2 PH0014 34 395aa long hypothetical protein #3 PH0016 300 475aa long hypothetical protein #4 PH0183 54 318aa long hypothetical protein #5 PH0999 300 180aa long hypothetical pyrazinamidase/nicotinamidase Motif number 1 TAATCCGTTGATGGGGATGTTGAA 1 30 1 ATGGAGTTGA 0.98276 -14 CGATTCCCCCAGAGAGATATTGAAAAACATACC 3 107 0 AGGGAATTGA 0.942147 -194 CTCGCCCTGAAGGGTGATGTTTTCGAAGAGAAA 3 168 0 AGGGAGTTTT 0.910839 -133 ATCACCCTTCAGGGCGAGGTAGATCACTTGGAG 3 183 1 AGGGAGTAGA 0.995744 -118 ATTTAAGATTAGCGGGAAGGAGA 4 42 1 AGGGAGGAGA 0.995658 -13 AGCTTATCCAATGGAGAAGTATATAGAAGGAAT 5 129 1 ATGGAGTATA 0.972786 -172 CTTTACAGGGTGAGCGAGGGAGAAGAGGAGCAT 5 195 1 TGGGAGGAGA 0.976244 -106 GGAGCATAGGATAGTGAGGGATATCCACGTTAT 5 221 1 ATGGAGGATA 0.972251 -80 ** * ** ***** Masking position 7 Map Score: 10.3883 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 228 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 2 ATATAAATTTTTGAAGTAGCTCTCCTCACGA 3 137 0 TTGAAGAGCT 0.9897 -164 CTCTGGAAGCTTGGAGCAATTGAAAGCTAAC 3 220 1 TTGGAGAATT 0.93697 -81 AATCTTAAATTTCAAGGAACTTAAATATGTT 4 21 0 TTCAAGAACT 0.944354 -34 TACTTCTCCATTGGATAAGCTAAAAGCTGGG 5 119 0 TTGGATAGCT 0.977775 -182 TAGGCCGTGGCTGGAGGAGCTTGGATTTAAG 5 161 1 CTGGAGAGCT 0.990474 -140 AAGCTAAAAATTCGAGAAGCTCTAGTTATCC 5 269 1 TTCGAGAGCT 0.993317 -32 ****** **** Masking position 5 Map Score: 5.79846 Number of sites scoring better than the average of aligned sites = 278 Number in coding regions = 259 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 AATGGGGCAAGTAGCTCTCTTGCC 3 5 0 GTAGCTCTCT 0.98716 -296 AATTTTTGAAGTAGCTCTCCTCACGATTCC 3 133 0 GTAGCTCTCC 0.905277 -168 TCAGGGCGAGGTAGATCACTTGGAGTGCTC 3 191 1 GTAGATCACT 0.962684 -110 ACTTAATAACGTGGATATCCCTCACTATCC 5 229 0 GTGGATATCC 0.953242 -72 TAGTTATCCTGGGGATCTCT 5 291 1 GGGGATCTCT 0.879227 -10 ********** Masking position 6 Map Score: 3.79108 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 51 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 4 AAGAAAATTGGAAATCTTTGCTACGCTGAT 3 77 1 GAAATCTTTG 0.907945 -224 AGTGCTCTCTGGAAGCTTGGAGCAATTGAA 3 214 1 GGAAGCTTGG 0.992826 -87 CAAAGCTTTCGAACGCTTGATAATATAACC 5 49 0 GAACGCTTGA 0.916833 -252 TCAAGCGTTCGAAAGCTTTGCCGATGTACT 5 59 1 GAAAGCTTTG 0.896521 -242 TGGATAAGCTAAAAGCTGGGAACACGAAAA 5 109 0 AAAAGCTGGG 0.959862 -192 CCGTGGCTGGAGGAGCTTGGATTTAAGGTT 5 165 1 AGGAGCTTGG 0.952448 -136 ********** Masking position 7 Map Score: 3.19768 Number of sites scoring better than the average of aligned sites = 406 Number in coding regions = 389 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 GTGAACTTTCTAAAGAAAATTGGAAATCTTTGC 3 65 1 TAAAGATTGG 0.968762 -236 TTAGTCATATTTAAAAGTATTGGGATAAATTTT 3 273 0 TTAAAATTGG 0.976999 -28 TTCAAGGAACTTAAATATGTTGGGATGAGGG 4 9 0 TTAAAGTTGG 0.93951 -46 TCCTTGAAATTTAAGATTAGCGGGAAGGAGA 4 34 1 TTAAGAGCGG 0.974429 -21 TGAACCCCTCTTAAGTACATCGGCAAAGCTTTC 5 69 0 TTAAGATCGG 0.990496 -232 ATCCACGTTATTAAGTTCATTCGATAAAGCTAA 5 243 1 TTAAGATTCG 0.966469 -58 ***** ***** Masking position 4 Map Score: 2.07266 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 82 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 6 GGAGCAATTGAAAGCTAACACTAGTATTTT 3 232 1 AAAGCTAACA 0.977368 -69 ATTTTGAAGAAAAGGCAAAATACTAGTGTT 3 248 0 AAAGGCAAAA 0.941553 -53 CTCCATTGGATAAGCTAAAAGCTGGGAACA 5 115 0 TAAGCTAAAA 0.966818 -186 TTCATTCGATAAAGCTAAAAATTCGAGAAG 5 258 1 AAAGCTAAAA 0.986599 -43 ********** Masking position 7 Map Score: 1.42656 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 50 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 TATATGCATGCAAATTAATCCGTTGATGGG 1 15 1 CAAATTAATC 0.977561 -29 TCACACATGCCAAAGTAATAGATCATCCTG 3 39 0 CAAAGTAATA 0.897018 -262 AGCTACTTCAAAAATTTATATTTTCTCTTC 3 147 1 AAAATTTATA 0.856918 -154 CCTTTTCTTCAAAATTTATCCCAATACTTT 3 263 1 AAAATTTATC 0.931005 -38 CCAAATTAGTCATATTTAAAA 3 290 0 CAAATTAGTC 0.951517 -11 ********** Masking position 6 Map Score: 0.389007 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 46 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 ********** No masking Map Score: 5.35339e-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: 5.35339e-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: 5.35339e-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