AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i142_Cytochrome_Oxidase_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 ctaB 300 cytochrome caa3 oxydase assembly factor #2 ctaC 239 cytochrome caa3 oxidase (subunit II) #3 ctaD 32 cytochrome caa3 oxidase (subunit I) Motif number 1 ATTTTCCAGAAGCCGTCATTCTATTATATT 1 58 0 AGCCGTCATT 0.956993 -243 TTTCTATCAGACCCGGCATGAATAATCAAG 1 93 0 ACCCGGCATG 0.962178 -208 GCAATCTCCAAATCGGCATTGCGTTTACCT 1 125 0 AATCGGCATT 0.95713 -176 TTAAACGACAAACAGGAATTTATTTGTGAA 1 183 0 AACAGGAATT 0.869297 -118 CAAGAGGTCAAGGCGGCATTTACTAGTTGT 2 55 0 AGGCGGCATT 0.996657 -185 TTGTTTAATCAGGCGGCTTTACTTTTATAC 2 82 1 AGGCGGCTTT 0.979166 -158 TTTTATACATAGATGGCATTTTGAGTAAAA 2 104 1 AGATGGCATT 0.881098 -136 AATTTAAGAGAAGAGGAAATGTAAGTGCTT 2 142 1 AAGAGGAAAT 0.734085 -98 GTCAATACAAAGGCGGAAAGCGGATCGAAA 2 200 0 AGGCGGAAAG 0.937861 -40 ********** Masking position 1 Map Score: 7.01495 Number of sites scoring better than the average of aligned sites = 1743 Number in coding regions = 1624 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 2 TCCAGAAGCCGTCATTCTATTATATTTTTG 1 54 0 GTCATTCTAT 0.84426 -247 ATTCCTGTTTGTCGTTTAATATTTAATAGG 1 194 1 GTCGTTTAAT 0.945244 -107 TTAATAGGATGTTTTTTTACAAGATGTTAT 1 216 1 GTTTTTTTAC 0.946253 -85 AGAGTTGCAGGTTATTTTATTCTCCTGCGT 1 256 1 GTTATTTTAT 0.963184 -45 AGATATGATGCTTGTTTTATCGCTTCAAAA 2 16 1 CTTGTTTTAT 0.961379 -224 GCCTTGACCTCTTGTTTAATCAGGCGGCTT 2 71 1 CTTGTTTAAT 0.915451 -169 TAAATTATGAGTTTTTTTACTCAAAATGCC 2 118 0 GTTTTTTTAC 0.946253 -122 ********** Masking position 9 Map Score: 3.98145 Number of sites scoring better than the average of aligned sites = 494 Number in coding regions = 336 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 3 AGCGAATATGTGTTTTGTGGCAATTC 1 7 1 TATGTGTTTT 0.982467 -294 GTGAACTTTTTATGAATTTTACCAAAGATG 1 158 0 TATGAATTTT 0.972706 -143 GGAATTTATTTGTGAACTTTTTATGAATTT 1 169 0 TGTGAACTTT 0.915281 -132 ACAAGCATCATATCTATTTT 2 1 0 TATCTATTTT 0.890972 -239 TCTCTTAAATTATGAGTTTTTTTACTCAAA 2 123 0 TATGAGTTTT 0.982469 -117 AGAGGAAATGTAAGTGCTTTATTGGTGATA 2 153 1 TAAGTGCTTT 0.918249 -87 ********** Masking position 8 Map Score: 3.88272 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 155 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 ATATGTGTTTTGTGGCAATTCCCAGAGCCT 1 16 1 TGTGGCAATT 0.869903 -285 ATAATAGAATGACGGCTTCTGGAAAATGTA 1 61 1 GACGGCTTCT 0.93527 -240 TACCAAAGATGAAGGCAATCTCCAAATCGG 1 139 0 GAAGGCAATC 0.845875 -162 AAGAGGTCAAGGCGGCATTTACTAGTTGTC 2 54 0 GGCGGCATTT 0.990631 -186 TGTTTAATCAGGCGGCTTTACTTTTATACA 2 83 1 GGCGGCTTTA 0.968116 -157 TTTATACATAGATGGCATTTTGAGTAAAAA 2 105 1 GATGGCATTT 0.981945 -135 TGATAGGTTGGATGGCGATAGATTTCGATC 2 178 1 GATGGCGATA 0.907519 -62 ********** Masking position 5 Map Score: 3.18161 Number of sites scoring better than the average of aligned sites = 1149 Number in coding regions = 1045 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 5 CAATCTCCAAATCGGCATTGCGTTTACCTTA 1 123 0 ATCGGCATTC 0.957277 -178 AACGTAAACCTCCCTTACAAACCTAACG 1 283 0 ACCTCCCTTC 0.984159 -18 ATAGATTTCGATCCGCTTTCCGCCTTTGTAT 2 195 1 ATCCGCTTTC 0.986434 -45 TTCACCCAACCCCTTTTCTGGTCAATAC 2 222 0 AACCCCTTTC 0.9767 -18 CTCCCCCAATATCTCCCTTTCTTCC 3 5 0 ATCTCCCTTC 0.990647 -28 ********* * Masking position 8 Map Score: 1.22482 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 145 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 6 TATCTTGTATGATAGAGTTGCAGGTTATTT 1 243 1 GATAGAGTTG 0.98007 -58 ATTCTCCTGCGTTAGGTTTGTAAGGGAGGT 1 274 1 GTTAGGTTTG 0.97284 -27 AAAATAGATATGATGCTTGTTT 2 3 1 AATAGATATG 0.863921 -237 CTTTATTGGTGATAGGTTGGATGGCGATAG 2 169 1 GATAGGTTGG 0.981509 -71 GTTGGATGGCGATAGATTTCGATCCGCTTT 2 184 1 GATAGATTTC 0.96694 -56 ********** Masking position 4 Map Score: 1.19717 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 87 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 TGTTTTGTGGCAATTCCCAGAGCCTTTTGT 1 21 1 CAATTCCCAG 0.95035 -280 ATCAAGTGTACATTTTCCAGAAGCCGTCAT 1 69 0 CATTTTCCAG 0.977032 -232 TGTCGTTTAATATTTAATAGGATGTTTTTT 1 203 1 TATTTAATAG 0.802229 -98 GTCAAGGCGGCATTTACTAGTTGTCATCGT 2 49 0 CATTTACTAG 0.979396 -191 TCCGCCTTTGTATTGACCAGAAAAGGGGTT 2 213 1 TATTGACCAG 0.955537 -27 ********** Masking position 4 Map Score: 0.517822 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 265 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 TTCTATTATATTTTTGTGAACAAAAGGCTC 1 40 0 TTTTTGTGAA 0.976585 -261 ATTTGTGAACTTTTTATGAATTTTACCAAA 1 162 0 TTTTTATGAA 0.888755 -139 AACAGGAATTTATTTGTGAACTTTTTATGA 1 173 0 TATTTGTGAA 0.983547 -128 GTAAGTGCTTTATTGGTGATAGGTTGGATG 2 162 1 TATTGGTGAT 0.95149 -78 GAAAGGGAGATATTGGGGGAGGTCACAT 3 15 1 TATTGGGGGA 0.929057 -18 ********** Masking position 4 Map Score: 1.62007 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 147 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 9 ********** No masking Map Score: 1.15351e-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: 1.15351e-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: 1.15351e-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