AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i111_bsub_mtub_300.orf -o111_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 mobA 136 molybdopterin-guanine dinucleotide biosynthesis protein A #2 moeB 50 molybdopterin biosynthesis protein #3 yknU 223 similar to ABC transporter (ATP-binding protein) #4 yknW 109 yknW #5 ytrD 29 similar to cytochrome c oxidase subunit #6 ytrA 300 similar to transcriptional regulator (GntR family) #7 Rv0986 300 hypothetical protein Rv0986 Motif number 1 AAACCGGACGGCATTTCAGCCG 3 2 1 AACCGGCGGC 0.991517 -222 AATACAGAAAAACCGGACGGCTGAAATGCCG 3 19 0 AACCGGCGGC 0.991517 -205 GCCAATGCTGATTGCGGCATCTGTGATCGCT 6 172 1 ATTGCGCATC 0.767038 -129 TGCCATTCAAAACCGATCATCACAAGAACAA 6 216 0 AACCGACATC 0.894291 -85 GGCAACGGCGATCCCAGCGTCGTGGCCATTG 7 62 0 ATCCCACGTC 0.951145 -239 ACAGCACCGGATCCCGGCAGCGTCAGCTCCC 7 96 0 ATCCCGCAGC 0.993353 -205 AGTCAAGGGCATCCCGTCAACAAACAACAGC 7 122 0 ATCCCGCAAC 0.98637 -179 GTGTGCGCGTAACCGGCCGGTCGGGAACGCG 7 165 1 AACCGGCGGT 0.901758 -136 GCCGGTCGGGAACGCGGCGACGGATGGCGCG 7 180 1 AACGCGCGAC 0.974882 -121 TGTCCTGGCCACCGCGCCATCCGTCGCCGCG 7 192 0 ACCGCGCATC 0.938429 -109 TCGAGATGACATCACGCCAACAACGCCTTCA 7 227 1 ATCACGCAAC 0.889881 -74 ****** **** Masking position 1 Map Score: 12.5614 Number of sites scoring better than the average of aligned sites = 832 Number in coding regions = 751 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 2 CGGCTGAAATGCCGTCCGGTTT 3 3 0 GCCGTCCGGT 0.944779 -221 CGGCATTTCAGCCGTCCGGTTTTTCTGTAT 3 19 1 GCCGTCCGGT 0.944779 -205 CGGCCGGCAGTCCGCGAGTGGAACAC 7 7 1 GCAGTCCGCG 0.981791 -294 AGCACCGGATCCCGGCAGCGTCAGCTCCCC 7 95 0 CCCGGCAGCG 0.845756 -206 CGCGCACACCACGGTCAGCGAAGTCAAGGG 7 144 0 ACGGTCAGCG 0.940091 -157 TGTGCGCGTAACCGGCCGGTCGGGAACGCG 7 166 1 ACCGGCCGGT 0.499592 -135 CGCCAACAACGCCTTCAGCTGTGAGCGATC 7 241 1 GCCTTCAGCT 0.917678 -60 TCAGCTGTGAGCGATCCGGGCTAGACTACC 7 255 1 GCGATCCGGG 0.950217 -46 ********** Masking position 6 Map Score: 8.31258 Number of sites scoring better than the average of aligned sites = 586 Number in coding regions = 560 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 3 TAGCGTTGAGCCTTTGCTTTTGCTATGCTTTTAA 1 92 1 CCTTTCTTGT 0.96372 -45 CAAACCTGTTCTCCTTATCTTTTATGTC 2 33 0 CCTGTCTTTT 0.994138 -18 TGATATCCTTCCCGTACTATTTGTTAGATATTCT 4 71 1 CCCGTCTTTT 0.984129 -39 TCTGTGATCGCTTGTTCTTTTTTTCTTGTTCTTG 6 191 1 CTTGTCTTTT 0.978841 -110 TTCTTTTTTTCTTGTTCTTGTGATGATCGGTTTT 6 205 1 CTTGTCTTGT 0.982415 -96 ATTGACACCACCTGGTCTAGTTTTTCTAGGTGTT 7 32 0 CCTGGCTTTT 0.981196 -269 CTGCCGGGATCCGGTGCTGTTGTTTGTTGACGGG 7 107 1 CCGGTCTTGT 0.986821 -194 ***** ** ** * Masking position 8 Map Score: 6.776 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 84 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 TTAATAAACAGACAAGCAGTAGCGTTGAGC 1 73 1 GACAAGCAGT 0.845931 -64 CCGGACGGCTGAAATGCCGTCCGGTTT 3 8 0 GAAATGCCGT 0.952968 -216 AACGCTTACAGAAAATCATTGTATGCTGAG 3 73 0 GAAAATCATT 0.958359 -151 AAAAATAATAGAAATTTATTTCGGGTATCG 3 166 1 GAAATTTATT 0.84036 -58 TATGAAAAGCCTTCAATATTGAA 4 4 1 GAAAAGCCTT 0.972813 -106 AAGGTTTTTGGAAATTTATTAGAAAAACAT 4 32 1 GAAATTTATT 0.84036 -78 GAAATGCCTTAGGTTTGGAG 5 1 1 GAAATGCCTT 0.972813 -29 GACACTAATATAAAATCATTTATATATTGA 6 93 1 TAAAATCATT 0.719894 -208 ********** Masking position 4 Map Score: 4.44006 Number of sites scoring better than the average of aligned sites = 753 Number in coding regions = 640 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 5 GTAGAATAAACGCTTACAGAAAATCATTGT 3 81 0 CGCTTACAGA 0.925932 -143 AAAGAACAAGCGATCACAGATGCCGCAATC 6 181 0 CGATCACAGA 0.969313 -120 GTGTTCCACTCGCGGACTGCCGGCCG 7 7 0 CGCGGACTGC 0.961328 -294 ATGGCAACGGCGATCCCAGCGTCGTGGCCA 7 65 0 CGATCCCAGC 0.961283 -236 CCCTTGACTTCGCTGACCGTGGTGTGCGCG 7 144 1 CGCTGACCGT 0.925749 -157 CGGCCGGTTACGCGCACACCACGGTCAGCG 7 154 0 CGCGCACACC 0.957289 -147 GATGTCATCTCGATCACTGTCCTGGCCACC 7 210 0 CGATCACTGT 0.932162 -91 TAGCCCGGATCGCTCACAGCTGAAGGCGTT 7 248 0 CGCTCACAGC 0.995836 -53 ********** Masking position 7 Map Score: 7.22113 Number of sites scoring better than the average of aligned sites = 431 Number in coding regions = 416 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 CGGGGCAATAACATGATAAGATGACATAA 2 10 1 AACATGATAA 0.91465 -41 GCCAATGAAATACAGAAAAACCGGACGGCT 3 28 0 TACAGAAAAA 0.807932 -196 CGATATAGTGAAGATGATAAATGTTGGAAA 3 194 1 AAGATGATAA 0.791295 -30 TTATTAGAAAAACATGAAACTTTTTGATAT 4 47 1 AACATGAAAC 0.886042 -63 ATCCTTTTTTTACAAAAAAACG 6 3 0 TACAAAAAAA 0.833463 -298 GCAGTTATGAAACATAAAAAACGAAACAAA 6 134 1 AACATAAAAA 0.948601 -167 TCATCACAAGAACAAGAAAAAAAGAACAAG 6 201 0 AACAAGAAAA 0.927192 -100 GAACCTTTTATAGATAAAAATGATCAATTA 6 255 0 TAGATAAAAA 0.802768 -46 ********** Masking position 4 Map Score: 2.34572 Number of sites scoring better than the average of aligned sites = 760 Number in coding regions = 537 Number in noncoding regions = 223 Number of orfs with sites within 600 bp upstream = 223 Fraction of orfs with sites within 600 bp upstream = 0.0358175 Motif number 7 AGTAAGAGACTCACTCCATAATTAGACTGAA 3 129 1 TCCTCCATAA 0.930071 -95 ATCCAGCACCTTTCCAACATTTATCATCT 3 205 0 CCTTCCAACA 0.90402 -19 CTCACTTCCCTCCAAACCTAAGGCATT 5 13 0 TCCTCCAAAC 0.953646 -17 GTCAAGGGCATCCCGTCAACAAACAACAGCA 7 121 0 TCCGTCAACA 0.946989 -180 GTCCTGGCCACCGCGCCATCCGTCGCCGCGT 7 191 0 CCCGCCATCC 0.977032 -110 CGAGATGACATCACGCCAACAACGCCTTCAG 7 228 1 TCCGCCAACA 0.991391 -73 ** ******** Masking position 8 Map Score: 0.516601 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 217 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 TAACATCATGAGGGAGATGGTTCGA 1 6 0 AGGGAGATGG 0.969438 -131 CGAAACTAGAGGTGAGATGAT 1 126 1 GGTGAGATGA 0.869419 -11 CGGGGCAATAACATGATAAGA 2 2 1 GGGGCAATAA 0.816219 -49 TTAGGTTTGGAGGGAAGTGAG 5 19 1 AGGGAAGTGA 0.963136 -11 ATTGACATTAAGGGAGGCAGTTATGAAACA 6 118 1 AGGGAGGCAG 0.871824 -183 TATAGAAAGTAGGGAAGTAA 6 291 1 AGGGAAGTAA 0.910814 -10 CCGTTGCCATGGGGAGCTGACGCTGCCGGG 7 85 1 GGGGAGCTGA 0.967856 -216 GGCGACGGATGGCGCGGTGGCCAGGACAGT 7 195 1 GGCGCGGTGG 0.918781 -106 ********** Masking position 4 Map Score: 1.05754 Number of sites scoring better than the average of aligned sites = 654 Number in coding regions = 460 Number in noncoding regions = 194 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261 Motif number 9 ********** No masking Map Score: -2.10788e-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: -2.10788e-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: -2.10788e-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