AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i144_bsub_mtub_300.orf -o144_bsub_mtub_300.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 qoxB 27 cytochrome aa3 quinol oxidase (subunit I) #2 qoxA 300 cytochrome aa3 quinol oxidase (subunit II) #3 ctaE 157 ctaE #4 ctaD 214 ctaD Motif number 1 CCTCATGGGACCATCAGCGC 3 1 0 CCATCAGCGC 0.939326 -157 TCAACCAACCCCAACCGCGCCCTGAACACG 3 32 1 CCAACCGCGC 0.985665 -126 CTTGCGCTAACCAAACGGCCGGGCGACACG 3 69 1 CCAAACGGCC 0.873391 -89 AACGGCCGGGCGACACGCGGAACTGACTTA 3 82 1 CGACACGCGG 0.961825 -76 CCGAAATTTCCGACCCGGGTAGAGTTCGAC 3 112 1 CGACCCGGGT 0.979591 -46 CGAACGCGTGCTGTCCGGCGGG 4 3 0 CTGTCCGGCG 0.853101 -212 CGGTAGCACTCGGCCAGCCGTCGACCCCGA 4 34 1 CGGCCAGCCG 0.884333 -181 CCAACGCTTTCCGCCCGCGCGAATCGGGGT 4 57 0 CCGCCCGCGC 0.985613 -158 TGGTCTGCAACGGCCCGCCGGCGGAGTCTG 4 84 1 CGGCCCGCCG 0.890135 -131 ACGGTTTGTAGGACCAGGCCTGCCGCCAGC 4 123 1 GGACCAGGCC 0.878013 -92 ACCAGGCCTGCCGCCAGCCTGATCGAGGGC 4 135 1 CCGCCAGCCT 0.9642 -80 ACATCCAGCCCGGACCGGGCCAAAACCCAG 4 182 0 CGGACCGGGC 0.989553 -33 ********** Masking position 7 Map Score: 20.1016 Number of sites scoring better than the average of aligned sites = 1320 Number in coding regions = 1231 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 2 GCAGGCTTCCTCCTTTCCTGATC 1 15 0 GGCTTCCTCC 0.957044 -13 CCGCCGGACAGCACGCGTTCGACGGTAGCA 4 12 1 GCACGCGTTC 0.884031 -203 TTCGACGGTAGCACTCGGCCAGCCGTCGAC 4 29 1 GCACTCGGCC 0.981422 -186 CACTCGGCCAGCCGTCGACCCCGATTCGCG 4 40 1 GCCGTCGACC 0.960038 -175 GCAGACCAACGCTTTCCGCCCGCGCGAATC 4 62 0 GCTTTCCGCC 0.972183 -153 CGTAAATGCCAGACTCCGCCGGCGGGCCGT 4 93 0 AGACTCCGCC 0.895763 -122 GTAGGACCAGGCCTGCCGCCAGCCTGATCG 4 130 1 GCCTGCCGCC 0.974113 -85 AGGCATCTTAGCCCTCGATCAGGCTGGCGG 4 145 0 GCCCTCGATC 0.961285 -70 CGCACTCCTCCAAACATCCAG 4 204 0 GCACTCCTCC 0.990926 -11 ********** Masking position 6 Map Score: 11.8155 Number of sites scoring better than the average of aligned sites = 970 Number in coding regions = 881 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 3 AAAATGAAATTTTTGATTGACCTAAG 2 7 1 AAATTTTTGA 0.928377 -294 TGATTGACCTAAGTTTTTTATTGTGGTAAA 2 24 1 AAGTTTTTTA 0.941368 -277 AAAGTAAAGAAAGATGATGAAGAACTAATT 2 68 0 AAGATGATGA 0.897964 -233 AAATGGGATGAAGTTTATAAAAAAATAAAG 2 189 1 AAGTTTATAA 0.89589 -112 CTAATAAGTGAAGTTTTTGATAGCATAACA 2 219 1 AAGTTTTTGA 0.988206 -82 AAGTAGAGAAAAGATTTTGAGGAAGTATGC 2 249 1 AAGATTTTGA 0.978217 -52 ********** Masking position 5 Map Score: 4.86558 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 209 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 ACTTTATATGCGGAAATAACTAGAAACTTT 2 93 1 CGGAAATAAC 0.972256 -208 CCCATTTTCGCTTAAATGTCATAAAATCGA 2 166 0 CTTAAATGTC 0.922135 -135 GGGCGACACGCGGAACTGACTTACCGAAAT 3 89 1 CGGAACTGAC 0.984308 -69 CTACCCGGGTCGGAAATTTCGGTAAGTCAG 3 104 0 CGGAAATTTC 0.972259 -54 TACAAACCGTCGTAAATGCCAGACTCCGCC 4 103 0 CGTAAATGCC 0.981103 -112 ********** Masking position 5 Map Score: 1.88924 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 270 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 AGTTCTTCATCATCTTTCTTTACTTTATAT 2 72 1 CATCTTTCTT 0.797287 -229 ACTTTATTCACATCTATCGCTTAAGATGAA 2 122 0 CATCTATCGC 0.882421 -179 ATCTGAAGTGCATACTTCCTCAAAATCTTT 2 258 0 CATACTTCCT 0.946646 -43 CATCCTTCCTATTGATGTAA 2 291 0 CATCCTTCCT 0.987273 -10 CCATGAGGATCAACCAACCCCAACCGCGCC 3 23 1 CAACCAACCC 0.886181 -135 TACAAAGCGTCATACTTGCGGAT 3 145 1 CATACTTGCG 0.786423 -13 TATTGAGAGGCATCTTAGCCCTCGATCAGG 4 152 0 CATCTTAGCC 0.906005 -63 CTCCTCCAAACATCCAGCCCGGACCGGGCC 4 191 0 CATCCAGCCC 0.973345 -24 ********** Masking position 2 Map Score: 1.54432 Number of sites scoring better than the average of aligned sites = 1136 Number in coding regions = 964 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 6 AATAAAAAACTTAGGTCAATCAAAAATTTC 2 16 0 TTAGGTCAAT 0.927125 -285 AAATTAAGGTTTACCACAATAAAAAACTTA 2 33 0 TTACCACAAT 0.950846 -268 GTGAATAAAGTTGGAGCAATTTTTGTCGAT 2 141 1 TTGGAGCAAT 0.925517 -160 TTCAGATTTATTACATCAATAGGAAGGATG 2 281 1 TTACATCAAT 0.938037 -20 GGCCGTTTGGTTAGCGCAAGTCGTCGACGT 3 59 0 TTAGCGCAAG 0.965029 -99 CGGAACTGACTTACCGAAATTTCCGACCCG 3 99 1 TTACCGAAAT 0.92242 -59 ********** Masking position 8 Map Score: 0.406462 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 251 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 ********** No masking Map Score: 6.63809e-14 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 8 ********** No masking Map Score: 6.63809e-14 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: 6.63809e-14 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