AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i014_bsub_mtub_100.orf -o014_bsub_mtub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 tpi 30 triose phosphate isomerase #2 pgk 300 phosphoglycerate kinase #3 gap 46 glyceraldehyde-3-phosphate dehydrogenase #4 yvbQ 297 yvbQ #5 gap 300 gap Motif number 1 CCCTTCCCTTGTCCGCTTTCATTATAGCGC 2 38 0 GTCCGCTTTC 0.979275 -263 AAGGGAGTCCGTCCCCTTCCCTTGTCCGCT 2 51 0 GTCCCCTTCC 0.982408 -250 AGGGGACGGACTCCCTTTCCCTTTTTCCAT 2 64 1 CTCCCTTTCC 0.91749 -237 CTCTATCACAGAGCGTTTTCTGAAAGCCGG 2 99 0 GAGCGTTTTC 0.913647 -202 GCAGCTTTGCCGGCGCTTTCGCCTAAGGCC 2 146 1 CGGCGCTTTC 0.992031 -155 TTTCGCCTAAGGCCGCTGCCCTGGCTTTTA 2 162 1 GGCCGCTGCC 0.832732 -139 TTTAATGAAACAGCCCTTTCTACGGGAAGG 4 17 1 CAGCCCTTTC 0.971164 -281 CCAATATAAACAGCCCTTCCCGTAGAAAGG 4 31 0 CAGCCCTTCC 0.98428 -267 ATGCACCATTTGGCGCTTTCTGTATAAGAT 4 62 1 TGGCGCTTTC 0.941699 -236 TGGGGAACATGAGCCCCGCCGCACCGGGCC 5 62 1 GAGCCCCGCC 0.872527 -239 CGCCGCACCGGGCCGTTTCCAAATGGTGAC 5 78 1 GGCCGTTTCC 0.981526 -223 CGATCCCAGCCGCCGCGTCCCTACCGCGGA 5 138 0 CGCCGCGTCC 0.974737 -163 CAGTGACACCCGCCGCCTTCGGCCGGTAAG 5 214 0 CGCCGCCTTC 0.980406 -87 ********** Masking position 4 Map Score: 22.0845 Number of sites scoring better than the average of aligned sites = 1484 Number in coding regions = 1367 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 2 TCTCAAAACTGCTATAAGGAAGTGGAACAG 1 9 1 CCTAAGGTGA 0.985207 -22 GAAAGCCGGTCTTCATGGAAAAAGGGAAAGGGAGTCCG 2 70 0 CCAGAAGGGA 0.955054 -231 GCCGGCAAAGCTGCTTAAAACGCGGTCGTTTCTCTATC 2 122 0 CCTAAAGGTG 0.965439 -179 CAGGGCAGTTCGTCTAAAAGCCAGGGCAGCGGCCTTAG 2 168 0 CCTAAGGGGA 0.990672 -133 GGTTTGCATACAGCACGAAAAACGTGAAACCGTCTGTT 2 249 0 CCAAAAGTGA 0.98459 -52 CTAGGAGATCCTCCTTCAAAATGGTTTGCATACAGCAC 2 271 0 CCTAAAGTTG 0.946001 -30 GATTGTTTCCTCCTTTAAATAAGTGAGAGATATTTAT 3 20 0 CCTAAAGTGG 0.990211 -27 TAAAACGACGCGGCATGAAAACTCTGCGAATATTGTCG 4 121 1 CCAAAACTGG 0.909566 -177 ATATAATGTCCAGCAAAAAAGGAAGGAACGTTTGAGTC 4 270 1 CCAAAAAGGA 0.908997 -28 GAGCGCCCGGCTTCTCAAAGCGAGGGGAGCCCCGGGAC 5 175 1 CCTAAGGGGA 0.990672 -126 * ** *** *** * Masking position 9 Map Score: 10.3788 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 261 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 3 GGCGCTTTCGCCTAAGGCCGCTGCCCTGGC 2 157 1 CCTAAGGCCG 0.937148 -144 TCGTCTAAAAGCCAGGGCAGCGGCCTTAGG 2 167 0 GCCAGGGCAG 0.990643 -134 TCTTTTTCGGCACAGGGCAGTTCGTCTAAA 2 188 0 CACAGGGCAG 0.976675 -113 CGATAACTCCGCTAGGGCAGATCGCAGTCT 2 215 0 GCTAGGGCAG 0.988722 -86 GCCTAGGAGATCCTCCTTCAA 2 290 0 CCTAGGAGAT 0.792143 -11 AGCCCCGCCGCACCGGGCCGTTTCCAAATG 5 73 1 CACCGGGCCG 0.873574 -228 CGCGTCCCTACCGCGGACATTGCGCTGGCT 5 125 0 CCGCGGACAT 0.856246 -176 GCTTCTCAAAGCGAGGGGAGCCCCGGGACT 5 184 1 GCGAGGGGAG 0.981872 -117 CTCTTACCGGCCGAAGGCGGCGGGTGTCAC 5 212 1 CCGAAGGCGG 0.926529 -89 TGGCCGTCAGCCTAGATCAGTGACACCCGC 5 231 0 CCTAGATCAG 0.664486 -70 AACAAATAAGCCGAGGAGAGACAA 5 287 1 CCGAGGAGAG 0.975145 -14 ********** Masking position 6 Map Score: 9.10765 Number of sites scoring better than the average of aligned sites = 738 Number in coding regions = 640 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 4 TAGGGCAGATCGCAGTCTTTTTCGGCACAGGGCAGTT 2 196 0 CGCTTTCGCA 0.946954 -105 TTGGCTATGACGGGACGTTTTTTGTCATAGCGGGACA 4 234 1 CGGCTTTGCA 0.992929 -64 TTTGTCATAGCGGGACATATAATGTCCAGCAAAAAAG 4 254 1 CGGCATTGCC 0.988606 -44 ATAGCCGTATCGAGTTCCTTTTCGACCATCGGCTCAA 5 11 1 CGATTTCGCC 0.959456 -290 TTTCGACCATCGGCTCAATTGTCAGCATCCTATGGGG 5 30 1 CGGCTTCACA 0.96854 -271 CCCGGTGCGGCGGGGCTCATGTTCCCCATAGGATGCT 5 53 0 CGGCATTCCC 0.934657 -248 CGGCTGGGATCGGTGGGGTGAGCGCCCGGCTTCTCAA 5 156 1 CGGGTGCGCC 0.966193 -145 AGGGGAGCCCCGGGACTCTTACCGGCCGAAGGCGGCG 5 197 1 CGGCTTCGCC 0.998062 -104 TGTCTCTCCTCGGCTTATTTGTTGTCATCCTTGTTGG 5 273 0 CGGTTTTGCA 0.98211 -28 *** * ** ** ** Masking position 16 Map Score: 7.69899 Number of sites scoring better than the average of aligned sites = 466 Number in coding regions = 433 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 TCCCTTGTCCGCTTTCATTATAGCGCTTCTAT 2 32 0 GCTTTCTATA 0.970127 -269 ATGAAGACCGGCTTTCAGAAAACGCTCTGTGA 2 92 1 GCTTTCGAAA 0.991553 -209 CTTTGCCGGCGCTTTCGCCTAAGGCCGCTGCC 2 150 1 GCTTTCCTAA 0.9009 -151 CGTTTTTCGTGCTGTATGCAAACCATTTTGAA 2 263 1 GCTGTAGAAA 0.90786 -38 AAACGCTTTAATGAAACAGCCCTTTC 4 5 1 GCTTTATAAA 0.953193 -293 ACCATTTGGCGCTTTCTGTATAAGATAAAGAT 4 66 1 GCTTTCGATA 0.980793 -232 AATCATTTCTGCTTTCTTTAATTATTTTAACA 4 198 0 GCTTTCTAAT 0.939387 -100 ****** * *** Masking position 5 Map Score: 4.01253 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 298 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 6 TTCTCTATCACAGAGCGTTTTCTGAAAGCC 2 101 0 CAGAGCGTTT 0.703501 -200 TCCCGTAGAAAGGGCTGTTTCATTAAAGCG 4 14 0 AGGGCTGTTT 0.917776 -284 TTCTACGGGAAGGGCTGTTTATATTGGGAT 4 34 1 AGGGCTGTTT 0.917776 -264 GTTTTCATGCCGCGTCGTTTTATCCAGCAA 4 113 0 CGCGTCGTTT 0.881771 -185 TTGGCTATGACGGGACGTTTTTTGTCATAG 4 234 1 CGGGACGTTT 0.994751 -64 TTTGTCATAGCGGGACATATAATGTCCAGC 4 254 1 CGGGACATAT 0.854701 -44 CAAAAAAGGAAGGAACGTTTGAGTC 4 283 1 AGGAACGTTT 0.902372 -15 CCCGGTGCGGCGGGGCTCATGTTCCCCATA 5 60 0 CGGGGCTCAT 0.787123 -241 CCCGCCGCACCGGGCCGTTTCCAAATGGTG 5 76 1 CGGGCCGTTT 0.995649 -225 AGGGGAGCCCCGGGACTCTTACCGGCCGAA 5 197 1 CGGGACTCTT 0.941329 -104 ********** Masking position 10 Map Score: 8.59757 Number of sites scoring better than the average of aligned sites = 1002 Number in coding regions = 920 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 7 AAGCGCTATAATGAAAGCGGACAAGGGAAG 2 36 1 ATGAAAGCGG 0.903234 -265 CACGAAAAACGTGAAACCGTCTGTTCAAGC 2 244 0 GTGAAACCGT 0.987033 -57 GCGCTGGCTTGTGACACCGTTGTGACGTCA 5 104 0 GTGACACCGT 0.987976 -197 CCCTCGCTTTGAGAAGCCGGGCGCTCACCC 5 171 0 GAGAAGCCGG 0.959157 -130 GCCTAGATCAGTGACACCCGCCGCCTTCGG 5 222 0 GTGACACCCG 0.981338 -79 ********** Masking position 4 Map Score: 1.4223 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 248 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 8 GCTGTATGCAAACCATTTTGAAGGAGGATC 2 273 1 AACCATTTTG 0.963008 -28 TATTGGGATGCACCATTTGGCGCTTTCTGT 4 55 1 CACCATTTGG 0.993209 -243 GTTGTGACGTCACCATTTGGAAACGGCCCG 5 86 0 CACCATTTGG 0.993209 -215 TGGCTTGTGACACCGTTGTGACGTCACCAT 5 100 0 CACCGTTGTG 0.959358 -201 ********** Masking position 6 Map Score: 2.59573 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 42 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 ********** No masking Map Score: 2.54618e-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: 2.54618e-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 11 ********** No masking Map Score: 2.54618e-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