AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i321_bsub_mtub_300.orf -o321_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 csfB 300 alternate gene name: yaaM; sigma-F transcribed gene #2 xpaC 119 xpaC #3 yaaO 81 similar to lysine decarboxylase #4 yaaQ 73 similar to hypothetical proteins #5 metS 300 methionyl-tRNA synthetase #6 yabD 78 similar to hypothetical proteins #7 Rv1008 85 hypothetical protein Rv1008 #8 Rv3644c 85 hypothetical protein Rv3644c Motif number 1 GAGTACAAAAAAAGACCTTTTCAGGT 2 7 0 AAAGACCTTT 0.809167 -113 GAAAACAATCCTTTGAATGTGTCT 3 68 0 ACAATCCTTT 0.92406 -14 TATCCTACTAAAAATCCTTTTAAATCAAGA 5 22 1 AAAATCCTTT 0.973056 -279 CAAATGAAATAAAAAACTTTGGTTCGAAAG 5 52 0 AAAAAACTTT 0.855457 -249 AATTAAAATTAAAAATCTTTAATGAAAATA 5 120 0 AAAAATCTTT 0.83057 -181 GTTACACGTGAAACACCTTTTGTTTATCA 6 10 0 AAACACCTTT 0.983188 -69 ACAATTCGTCGAACACCTTTTGTGTTTCGA 6 38 1 GAACACCTTT 0.959208 -41 AAGTGAAAAACTCCTTTCTTGTCGAAA 6 62 0 AAACTCCTTT 0.976632 -17 ********** Masking position 3 Map Score: 10.2541 Number of sites scoring better than the average of aligned sites = 278 Number in coding regions = 202 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 2 CATTTGTTTGGTGGCGATAGCGAAGA 1 7 1 TTTGGTGGCG 0.960564 -294 AGTTAAGCTCTTCAGCGCCGATGGTAGTCG 1 67 1 TTCAGCGCCG 0.957338 -234 TTTAAGCTTGCTTGGCGGCGTCCTACTCTC 1 112 0 CTTGGCGGCG 0.99228 -189 ATGATTTGCACTTATCGCCGCTCTCGTCCT 5 239 1 CTTATCGCCG 0.967919 -62 CTCCGGAACCCCTGGCGCCG 7 76 1 CCTGGCGCCG 0.995147 -10 TCCGTGATCTTTCGTCGCCATTTGG 8 6 0 TTCGTCGCCA 0.873536 -80 CTGATCGGTATCTGTCGGCGCGGATAGCTA 8 54 1 TCTGTCGGCG 0.985032 -32 GCGGATAGCTACTGTTGCCGATG 8 73 1 ACTGTTGCCG 0.881563 -13 ********** Masking position 7 Map Score: 7.12026 Number of sites scoring better than the average of aligned sites = 909 Number in coding regions = 868 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 GAAGAGGTCACACCCGTTCCCATACCGAACA 1 32 1 CCCCGTTCCC 0.963658 -269 ACCCGTTCCCATACCGAACACGGAAGTTAAG 1 43 1 AACCGAACAC 0.856796 -258 CAGGGGGAAACCCCCGACTACCATCGGCGCT 1 80 0 CCCCGACTAC 0.922973 -221 CTTCTCCACCTCCGTACAGTTAGCCTCCC 1 282 0 CTCCGTACAG 0.893528 -19 TGTCAAAAAGCTCCCGCCCAAAGGACGAGAG 5 259 0 CCCCGCCCAA 0.979746 -42 GGTCGGAGCTCACCCGCACACAATAGGGTGG 7 18 0 CCCCGCACAC 0.99381 -68 GGGTGAGCTCCGACCGCCCAGCCAGACGAGA 7 34 1 CACCGCCCAG 0.989967 -52 CGAGATCCACCGCCCGCTCCGGAACCCCTGG 7 60 1 CCCCGCTCCG 0.987417 -26 GCGCCGACAGATACCGATCAGCGTTCGTTTC 8 44 0 AACCGATCAG 0.856796 -42 * ********* Masking position 5 Map Score: 6.22891 Number of sites scoring better than the average of aligned sites = 499 Number in coding regions = 441 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 AAAAGGTCTAAATAGTGTATACAATATCCGTTT 1 245 1 AATAGTGAAA 0.77816 -56 TTTTATTATTAAGAGTACAAAAAAAGACCTTTT 2 16 0 AAGAGTAAAA 0.940227 -104 TTGTACTCTTAATAATAAAAAGAAGATGAAACT 2 29 1 AATAATAAAA 0.9641 -91 CGTAGTAGATAATAATAATAAAACTGAGTATAG 2 77 1 AATAATATAA 0.940594 -43 CCTGTTTCCCAATAGTTGATATAATAATGTAAA 4 11 1 AATAGTTAAA 0.702974 -63 TATATAATCAAATGAAATAAAAAACTTTGGTTC 5 57 0 AATGAAAAAA 0.806702 -244 AAAAATCTTTAATGAAAATAAAAAAAGTCTGTT 5 107 0 AATGAAATAA 0.711034 -194 CGCCCTGAAAAAGAATAATTAAAATTAAAAATC 5 133 0 AAGAATATAA 0.936739 -168 CTTTAAGATCAAGAATATATACATACGCCCTGA 5 158 0 AAGAATAAAA 0.961708 -143 ATCATAGATAAAGGATAAATATAAATAATATTC 5 202 1 AAGGATAAAA 0.940225 -99 GATAAATATAAATAATATTCATATATGATTTGC 5 215 1 AATAATATAA 0.940351 -86 ******* * * * Masking position 11 Map Score: 6.45451 Number of sites scoring better than the average of aligned sites = 278 Number in coding regions = 205 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 5 CCCATACCGAACACGGAAGTTAAGCTCTTC 1 50 1 ACACGGAAGT 0.936794 -251 CGTCCTACTCTCACAGGGGGAAACCCCCGA 1 94 0 TCACAGGGGG 0.86802 -207 ACAAATACAAACACCGAGGGCTTATATAGC 1 192 1 ACACCGAGGG 0.95224 -109 CTGAGTATAGACACAGGAGTCGATTATCTC 2 100 1 ACACAGGAGT 0.936383 -20 TGATAAACAAAAGGTGTTTCACGT 6 5 1 AAACAAAAGG 0.87148 -74 TCTTGTCGAAACACAAAAGGTGTTCGACGA 6 43 0 ACACAAAAGG 0.983798 -36 TTGTGTTTCGACAAGAAAGGAGTTTTTCAC 6 57 1 ACAAGAAAGG 0.820238 -22 GCTCACCCGCACACAATAGGGTGGTGTCGA 7 12 0 ACACAATAGG 0.937424 -74 ********** Masking position 3 Map Score: 3.5831 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 234 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 6 GTGGCGATAGCGAAGAGGTCACACCCGTTC 1 21 1 CGAAGAGGTC 0.985115 -280 CCATCGGCGCTGAAGAGCTTAACTTCCGTG 1 61 0 TGAAGAGCTT 0.866868 -240 TTTAAAGTTTCAAAAAGGTCTAAATAGTGT 1 233 1 CAAAAAGGTC 0.964254 -68 ACCTGAAAAGGTCTTTTTTTGTA 2 4 1 TGAAAAGGTC 0.980683 -116 ATCAGAATGTCAAAAAGCTCCCGCCCAAAG 5 267 0 CAAAAAGCTC 0.964254 -34 AAGTGAAAAACTCCTTTCTTGTC 6 66 0 TGAAAAACTC 0.887058 -13 ********** Masking position 6 Map Score: 3.39045 Number of sites scoring better than the average of aligned sites = 322 Number in coding regions = 267 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 AGGACGCCGCCAAGCAAGCTTAAACCCAGC 1 118 1 CAAGCAAGCT 0.935433 -183 AAGCAAGCTTAAACCCAGCTTAATGAGCTG 1 129 1 AAACCCAGCT 0.972607 -172 AGTAAACAAAAAACCCAGCTCATTAAGCTG 1 144 0 AAACCCAGCT 0.972607 -157 GACAGAACTTAAAGCCAGACTTACTGGTAA 3 11 0 AAAGCCAGAC 0.981031 -71 AAATCCTTTTAAATCAAGACTTTCGAACCA 5 33 1 AAATCAAGAC 0.814762 -268 CTCCGACCGCCCAGCCAGACGAGATCCACC 7 41 1 CCAGCCAGAC 0.940038 -45 ********** Masking position 7 Map Score: 1.15826 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 375 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 8 GTGTGACCTCTTCGCTATCGCCACCAAACA 1 15 0 TTCGCTATCG 0.9047 -286 GAGCTTAACTTCCGTGTTCGGTATGGGAAC 1 47 0 TCCGTGTTCG 0.929309 -254 TTGTTTGATTTTCTCGATCTTGAGTAAACA 1 166 0 TTCTCGATCT 0.955656 -135 TATGTATATATTCTTGATCTTAAAGGCTAA 5 166 1 TTCTTGATCT 0.962957 -135 TTTATATTTATCCTTTATCTATGATACCAT 5 197 0 TCCTTTATCT 0.932488 -104 TCGCGACAATTCCGTGATCTTTCGTCGCCA 8 16 0 TCCGTGATCT 0.98468 -70 ********** Masking position 8 Map Score: 2.69672 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 155 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 TCTTCGCTATCGCCACCAAACAAATG 1 7 0 CGCCACCAAA 0.965128 -294 CGACAAAATTCGACACGAACAGACTTTTTT 5 90 1 CGACACGAAC 0.995065 -211 TTTTGTGTTTCGACAAGAAAGGAGTTTTTC 6 55 1 CGACAAGAAA 0.944899 -24 TTCGACACCACCCTATTGTGTG 7 3 1 CGACACCACC 0.984217 -83 GGAATTGTCGCGAAACGAACGCTGATCGGT 8 33 1 CGAAACGAAC 0.974772 -53 ********** Masking position 5 Map Score: 2.9836 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 41 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 10 ********** No masking Map Score: 3.44146e-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: 3.44146e-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 12 ********** No masking Map Score: 3.44146e-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