AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i255_bsub_mtub_100.orf -o255_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 glnR 110 transcriptional regulator #2 dnaJ 199 heat-shock protein #3 dnaK 23 class I heat-shock protein (chaperonin) #4 grpE 71 heat-shock protein #5 hrcA 119 transcriptional regulator #6 dnaK 226 dnaK #7 dnaJ 35 dnaJ #8 dnaJ2 74 dnaJ2 #9 hrcA 171 hrcA Motif number 1 AGCTCCGGAAGCGGGGCTGACACTAAAAAGAAC 2 11 0 GCGGGGGACC 0.995022 -189 CCGCGTGTCGGCAGGGCACACGCTCGGGGCGTA 6 48 0 GCAGGGCACC 0.990554 -179 CTGCCGACACGCGGGAACAAGACCCGCACGACC 6 67 1 GCGGGAAAGC 0.978175 -160 TCAGTAAGTTGAGTGCATCAGGCTCAGCTCTGA 6 113 1 GAGTGCCAGC 0.754422 -114 TGCCTCGACGGCGGTGTGCTGTCAATTCAGAGC 6 139 0 GCGGTGCTGC 0.978438 -88 GCAAGCTTGAGCGGGGTGCACTCATCATAGTGC 6 169 1 GCGGGGCACC 0.855274 -58 AGGAAGGCGAGAGGGGGTGACGCGAC 7 20 1 GAGGGGGACC 0.935877 -16 CGCTTGAGAAGCGGCATAAAGACGCGGCATAGG 8 42 1 GCGGCAAAGC 0.853723 -33 CATGATCTCGTCGGGCTTCAGCCACTCGGTAGG 9 23 0 TCGGGCCAGC 0.987894 -149 GACACGTTAGTCGGGGCACACGCCCCCTGACCA 9 59 1 TCGGGGCACC 0.991684 -113 CCGTCATCTAGCAGGCGTCTGCCGATGGTCAGG 9 84 0 GCAGGCCTGC 0.948152 -88 CGTAAGAAGTGAGGTGAGCAGTCG 9 158 1 GAGGTGCAGC 0.977639 -14 ****** *** * Masking position 13 Map Score: 20.7086 Number of sites scoring better than the average of aligned sites = 471 Number in coding regions = 418 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 2 CTTCCGGAGCTGACCGAAAAGAACACATTTCATA 2 33 1 TGCCGAGAAC 0.963446 -167 CCTTACACTTTGAGGGAGGTGAACACA 4 55 1 TGGGGGGAAC 0.983755 -17 GCCCCGGTCAAGCCCGGAGAGCAGTGC 6 4 0 AGCCGGGCAG 0.995943 -223 TGTTCCCGCGTGTCGGCAGGGCACACGCTCGGGG 6 52 0 TGCGGGGCAC 0.994403 -175 AATTCAGAGCTGAGCCTGATGCACTCAACTTACT 6 115 0 TGGCCAGCAC 0.858701 -112 GCTTGCCTCGACGGCGGTGTGCTGTCAATTCAGA 6 141 0 ACGCGGGCTG 0.861459 -86 GAGGCAAGCTTGAGCGGGGTGCACTCATCATAGT 6 166 1 TGGCGGGCAC 0.993629 -61 GTTTGTGGATAGCCGCTTGAGAAGCGGCATAAAG 8 29 1 AGCGCGGAAG 0.949118 -46 GGCTTCAGCCACTCGGTAGGGAAGATCCGCCA 9 9 0 ACCGGGGAAG 0.949117 -163 GAGTGGCTGAAGCCCGACGAGATCATGCTGGACA 9 29 1 AGCCGGGATC 0.969064 -143 TGACGGTCAGTGGCCGCCGAGAACGTAAAATGAA 9 111 1 TGCCGGGAAC 0.992503 -61 CGTAAAATGAAGCCGGTCAGGCAGCGTAAGAAGT 9 134 1 AGCGGAGCAG 0.972434 -38 CAGCGTAAGAAGTGAGGTGAGCAGTCG 9 155 1 AGGAGGGCAG 0.945567 -17 ** *** * **** Masking position 11 Map Score: 20.4168 Number of sites scoring better than the average of aligned sites = 747 Number in coding regions = 695 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 3 CCCCGCTTCCGGAGCTGACCGAAAAGAACAC 2 28 1 GGAGCGACCG 0.953521 -172 GTCAAAGCCAAGAGATGCCTGACTTTGACTT 2 86 0 AGAGAGCCTG 0.940956 -114 GAGAAGGACAGGTGCTGCCCTTCGATAAAAT 4 25 0 GGTGCGCCCT 0.94568 -47 GAGAGGCCCCGGTCAAGCCCGGAGAGCAGTG 6 12 0 GGTCAGCCCG 0.992744 -215 GGCGTAGCTGGGAGAGGCCCCGGTCAAGCCC 6 23 0 GGAGAGCCCC 0.958442 -204 TGTCGGCAGGGCACACGCTCGGGGCGTAGCT 6 45 0 GCACAGCTCG 0.881923 -182 CACTATGATGAGTGCACCCCGCTCAAGCTTG 6 170 0 AGTGCCCCCG 0.814489 -57 GGTGAATCCTCCTGAATATGT 6 216 0 GGTGATCCTC 0.771104 -11 CTACCGAGTGGCTGAAGCCCGACGAGATCAT 9 24 1 GCTGAGCCCG 0.995137 -148 GTTAGTCGGGGCACACGCCCCCTGACCATCG 9 64 1 GCACAGCCCC 0.97676 -108 CTGACCATCGGCAGACGCCTGCTAGATGACG 9 85 1 GCAGAGCCTG 0.983683 -87 ***** ***** Masking position 8 Map Score: 14.2728 Number of sites scoring better than the average of aligned sites = 911 Number in coding regions = 835 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 4 TTCTTAACTTAGTTTCATTATAGGTGATGTTATATTATG 1 67 0 AGAAAGGGTG 0.996828 -44 CTTTTCGGTCAGCTCCGGAAGCGGGGCTGACACTAAAAA 2 15 0 AGGACGGGTG 0.994496 -185 TCAAAGTGTAAGGAGAAGGACAGGTGCTGCCCTTCGATA 4 29 0 AGAAAGGGTG 0.996828 -43 GCTTATTGAGAGTGCTAACAGAGGTGATGATG 5 98 1 AGAAAGGGTG 0.996828 -22 CAACAAAAGAGGAAGGCGAGAGGGGGTGACGCGAC 7 10 1 AGGAAGGGTG 0.99798 -26 AGCGGCATAAAGACGCGGCATAGGAGAATCAAGC 8 51 1 AGGAAGGGAT 0.949641 -24 ** * * *** * ** Masking position 10 Map Score: 7.82911 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 19 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 TTAAAAATTTCTCCTGGATTTGATGTTAAGAA 1 16 1 CTCCGGTTTG 0.99744 -95 AGTCAGGCATCTCTTGGCTTTGACTTTTTTTC 2 93 1 CTCTGGTTTG 0.983682 -107 TCGCTTCACTCTCCCGAATTTCTCACATAAAT 2 177 0 CTCCGATTTC 0.973954 -23 GCACTGCTCTCCGGGCTTGACCGGGGCCTC 6 9 1 CTCCGGTTGA 0.964667 -218 GGTGAATCCTCCTGAATATGTAGAGCTTCT 6 207 0 CTCCGATATG 0.970134 -20 CGCGCACCTGCTGCAGGGTTTGTGGATAGCCG 8 12 1 CTGCGGTTTG 0.988931 -63 **** ** **** Masking position 9 Map Score: 4.79958 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 146 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 CTCAATTTCCTCCTTTTCTTAACTTAGTTTC 1 90 0 TCTTTTCTTA 0.945269 -21 TGGCTTTGACTTTTTTTCTTGCCCGGGATAA 2 107 1 TTTTTTCTTG 0.945269 -93 AAGTTTTTGGCGCTTTTTTTGGGTGAGTTAT 5 17 1 CCTTTTTTTG 0.952895 -103 TTATAATTGACATTTTTCTTGTGGTTTGATA 5 44 1 CTTTTTCTTG 0.964486 -76 TGTGGTTTGATACTTTTGTTATAGAATTAGC 5 63 1 TCTTTTGTTA 0.922222 -57 TCTCGCCTTCCTCTTTTGTTG 7 1 0 CCTTTTGTTG 0.982199 -35 * ********* Masking position 6 Map Score: 2.50874 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 260 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 7 AGCTCCGGAAGCGGGGCTGACACTAAAAAGA 2 13 0 GCGGGGCGAC 0.99855 -187 AGCCCCGCTTCCGGAGCTGACCGAAAAGAAC 2 26 1 CCGGAGCGAC 0.96241 -174 GGGCACACGCTCGGGGCGTAGCTGGGAGAGG 6 37 0 TCGGGGCTAG 0.933412 -190 CCGCGTGTCGGCAGGGCACACGCTCGGGGCG 6 50 0 GCAGGGCCAC 0.990194 -177 GCAAGCTTGAGCGGGGTGCACTCATCATAGT 6 169 1 GCGGGGTCAC 0.992906 -58 AGGAAGGCGAGAGGGGGTGACGCGAC 7 20 1 GAGGGGGGAC 0.970367 -16 GACACGTTAGTCGGGGCACACGCCCCCTGAC 9 59 1 TCGGGGCCAC 0.99773 -113 TTTTACGTTCTCGGCGGCCACTGACCGTCAT 9 110 0 TCGGCGGCAC 0.972823 -62 ******* *** Masking position 10 Map Score: 11.4911 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 111 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 TTGAATAACCTCCTGCTATGTAA 3 4 0 CCTCCTGCAG 0.989123 -20 TGTGTTCACCTCCCTCAAAGTGTAAGGAGA 4 52 0 CCTCCCTCAG 0.989123 -20 GAGCGTGTGCCCTGCCGACACGCGGGAACAAG 6 56 1 CCTGCCGAAG 0.973202 -171 CCCGCTCAAGCTTGCCTCGACGGCGGTGTGCT 6 152 0 CTTGCCTCAG 0.953815 -75 ACGCGCACCTGCTGCAGGGTTTGTGGATA 8 8 1 CCTGCTGCGG 0.983792 -67 GCGGATCTTCCCTACCGAGTGGCTGAAGCCCG 9 13 1 CCTACCGATG 0.895433 -159 ******** * * Masking position 3 Map Score: 1.83085 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 239 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 AAAATGTCAATTATAACTCACCCAAAAAAAG 5 29 0 TTATAACTCC 0.936069 -91 TGTTATAGAATTAGCACTCGCTTATTGAGAG 5 79 1 TTAGCACTCC 0.995692 -41 ATCACCTCTGTTAGCACTCTCAATAAGCGAG 5 95 0 TTAGCACTCC 0.995692 -25 ACGACCAGCGTTAGCATGCTCAGTAAGTTGA 6 94 1 TTAGCATGCC 0.971529 -133 ********* * Masking position 6 Map Score: 0.906038 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 3 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 10 AACATCAAATCCAGGAGAAATTTTTAAAAA 1 13 0 CCAGGAGAAA 0.856961 -98 TTTATCCCGGGCAAGAAAAAAAGTCAAAGC 2 109 0 GCAAGAAAAA 0.829811 -91 TTTTTCTTGCCCGGGATAAAAGGAATTGAA 2 119 1 CCGGGATAAA 0.963139 -81 CCCAAAAAAAGCGCCAAAAACTTCATTGC 5 10 0 GCGCCAAAAA 0.919115 -110 CTGCCGACACGCGGGAACAAGACCCGCACG 6 67 1 GCGGGAACAA 0.962324 -160 TCATCATAGTGCAGGAAAGAAGCTCTACAT 6 190 1 GCAGGAAAGA 0.955129 -37 CGCTTGAGAAGCGGCATAAAGACGCGGCAT 8 42 1 GCGGCATAAA 0.978445 -33 GCATAAAGACGCGGCATAGGAGAATCAAGC 8 55 1 GCGGCATAGG 0.872244 -20 ********** Masking position 6 Map Score: 2.53436 Number of sites scoring better than the average of aligned sites = 1437 Number in coding regions = 1340 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 11 ********** No masking Map Score: -8.50219e-13 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: -8.50219e-13 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 13 ********** No masking Map Score: -8.50219e-13 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