AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i056_bsub_mtub_100.orf -o056_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 ycsA 107 similar to 3-isopropylmalate dehydrogenase #2 ilvD 288 dihydroxy-acid dehydratase #3 leuC 49 3-isopropylmalate dehydratase (large subunit) #4 ilvB 300 acetolactate synthase (acetohydroxy-acid synthase) (large subunit) #5 alsS 154 alpha-acetolactate synthase (pH6) #6 ilvD 147 ilvD #7 leuD 24 leuD #8 leuC 71 leuC #9 serA 29 serA #10 ilvC 37 ilvC #11 ilvB 300 ilvB #12 leuA 256 leuA Motif number 1 CACTCTGAGGCGAGTTCACCTTGTAAAGCTTCG 4 14 0 CGAGTTCCTG 0.584535 -287 CGTGCCGCGGCGAGCGCATCCTTGGGCCGCATA 6 117 1 CGAGCGCCCT 0.9197 -31 TTTGAGATGACCAGCGAGTCGCGAACGAATGAA 8 34 1 CCAGCGACGG 0.870638 -38 CTCTAGTGCCACCGCTGAATCTCTC 10 23 0 CTAGTGCCCC 0.766451 -15 GTTACGCTCGCGAACTCGACGCCCAC 11 4 0 CGAACTCCGC 0.971816 -297 GTCGAGTTCGCGAGCGTAACGCCACCGCGAAAA 11 17 1 CGAGCGTCGC 0.986582 -284 TCTTGATCCGCGAGCGTGACGGCACTGCGAAAT 11 60 0 CGAGCGTCGC 0.986618 -241 ACTGACACCGCGGATTTGACTGCTGAGCTGTGT 11 92 1 CGGATTTCTC 0.426756 -209 ACGAGCATCCCGGGCTTTCCGGCCTTGTCCATA 11 144 0 CGGGCTTCGC 0.970765 -157 TAGTCAGGCACCAACGCGCCGACCAATTACTAC 11 175 0 CCAACGCCGC 0.990245 -126 CAAGCGAGCACCAACGCGACCCTCGTGCAGCAG 11 211 1 CCAACGCCCT 0.79552 -90 AAAACCCTCGCCAGCTCAGCTGCTGCACGAGGG 11 230 0 CCAGCTCCTC 0.973634 -71 TTCTTGTCCACCAACGAGACTTCCAGAGCAATA 11 263 1 CCAACGACTC 0.805275 -38 TCAGCGCAGGCCGGCGCGCCCCCTATTCTGGAC 12 42 0 CCGGCGCCCC 0.993898 -215 CCGGCCTGCGCTGACTCTGCGTCCACCACGGGA 12 61 1 CTGACTCCGC 0.875661 -196 TCATGTGCAGCGGGTGCTCCTCCTCGGACGCCG 12 143 1 CGGGTGCCTC 0.963167 -114 TGCTCCTCCTCGGACGCCGCGACGGGGTCTGAT 12 157 1 CGGACGCCGC 0.992624 -100 CTGATCCAGACCGGCTTCCCGTCGCGGGACGTT 12 185 1 CCGGCTTCGC 0.970765 -72 GAACCTCAGACCGGCGCATCGCGAACGTCCCGC 12 208 0 CCGGCGCCGG 0.987943 -49 TCTCACCATCCCGGAGCAACTACC 12 243 1 CCGGAGCCTC 0.888216 -14 ******* ** * Masking position 10 Map Score: 31.121 Number of sites scoring better than the average of aligned sites = 1718 Number in coding regions = 1624 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 2 AAACAAGGTGAGGGCGGCCTGTATTTATCTTAT 2 184 1 AGCGGCCTGA 0.927199 -105 TCGCCTCAGAGTGCCAGTCTGAAATGACAGTAG 4 34 1 GGCAGTCTGA 0.779928 -267 AGTATCTCTGGAGATGGCGAGTAA 6 2 0 GGTGGCGAGA 0.986936 -146 CCCTGCTTTCGGGTTGGCGAGTATCTCTGGAGA 6 21 0 GGTGGCGAGA 0.986936 -127 TGGCAACCGTGCCGCGGCGAGCGCATCCTTGGG 6 110 1 GCCGGCGAGG 0.976689 -38 CTCGTATTTTGAGATGACCAGCGAGTCGCGAAC 8 27 1 GGTGACCAGG 0.918056 -45 GTGGGCGTCGAGTTCGCGAGCGTAACGCCACC 11 10 1 GGTCGCGAGG 0.96432 -291 GGTCGCGTTGGTGCTCGCTTGGGCTAGTCAGGC 11 199 0 GGTCGCTTGG 0.750751 -102 TGCAGCAGCTGAGCTGGCGAGGGTTTTTTCTTG 11 236 1 GGTGGCGAGG 0.992811 -65 AATAGGGGGCGCGCCGGCCTGCGCTGACTCTGC 12 48 1 GGCGGCCTGG 0.995411 -209 GGTGGACGCAGAGTCAACGTGTAAAGTGCTTCA 12 113 1 GGCAACGTGA 0.68072 -144 ATCAGACCCCGTCGCGGCGTCCGAGGAGGAGCA 12 157 0 GCCGGCGTCG 0.799792 -100 CCGCGACGGGAAGCCGGTCTGGATCAGACCCCG 12 179 0 AGCGGTCTGA 0.750411 -78 CGTTCGCGATGCGCCGGTCTGAGGTTCCTTCTC 12 214 1 GGCGGTCTGG 0.980844 -43 TAGTTGCTCCGGGATGGTGAGAAGGAACCTCAG 12 232 0 GGTGGTGAGA 0.946905 -25 * * ******* * Masking position 11 Map Score: 18.8902 Number of sites scoring better than the average of aligned sites = 779 Number in coding regions = 703 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 3 TAATCAATAACCGACCACCCGTGACACAATG 1 18 1 CCGACCACCG 0.922274 -90 TAAATACAGGCCGCCCTCACCTTGTTTTGTT 2 180 0 CCGCCCTCCC 0.954452 -109 TTACTCGCCATCTCCAGAGATACTC 6 5 1 TCGCCATCCC 0.968634 -143 CCAGAGATACTCGCCAACCCGAAAGCAGGGC 6 24 1 TCGCCAACCG 0.995913 -124 GGCGTTACGCTCGCGAACTCGACGCCCAC 11 9 0 TCGCGAACCG 0.981265 -292 CGCGAGCGTAACGCCACCGCGAAAATTCGCA 11 25 1 ACGCCACCCG 0.93074 -276 CGCAGTGCCGTCACGCTCGCGGATCAAGACT 11 64 1 TCACGCTCCG 0.919996 -237 GGCTAGTCAGGCACCAACGCGCCGACCAATT 11 180 0 GCACCAACCG 0.984244 -121 GCCCAAGCGAGCACCAACGCGACCCTCGTGC 11 208 1 GCACCAACCG 0.984244 -93 TTTTTCTTGTCCACCAACGAGACTTCCAGAG 11 260 1 CCACCAACAG 0.867175 -41 AATGTGCGAGTAGCCCACACGGTGGACGCAG 12 93 1 TAGCCCACCG 0.935003 -164 AGGTTCCTTCTCACCATCCCGGAGCAACTAC 12 235 1 TCACCATCCG 0.984858 -22 ******** ** Masking position 8 Map Score: 16.3817 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 240 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 GCGAGATAGTAAAAAAAGCCCGTGACATTG 1 44 0 AAAAAAAGCC 0.981678 -64 AATATTGTTGAAAAATATCCGAAAACTATT 2 76 1 AAAAATATCC 0.925185 -213 TCTTATTTGCAAAAACAGCCCATAAATAAA 2 211 1 AAAAACAGCC 0.942813 -78 AAATTGTCAAAATAAAATCCAATCAAACAA 2 245 1 AATAAAATCC 0.875201 -44 TAAAGCGGATAGAAATATCCATGAGACGGC 4 100 1 AGAAATATCC 0.875036 -201 GTACCGCGGAAAGAAAAGCCTTTTCGCCCC 4 156 1 AAGAAAAGCC 0.968092 -145 ATTATTCAATAAAAAAAGCCCTTCCGCCCA 4 219 0 AAAAAAAGCC 0.981678 -82 TCTTTAAAGGATGAAAATCCAAAAGGAGGA 4 275 1 ATGAAAATCC 0.798841 -26 TTGGTGGACAAGAAAAAACCCTCGCCAGCT 11 247 0 AGAAAAAACC 0.853243 -54 ********** Masking position 5 Map Score: 8.56553 Number of sites scoring better than the average of aligned sites = 523 Number in coding regions = 368 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 5 CTGTCATTTCAGACTGGCACTCTGAGGCGA 4 34 0 AGACTGGCAC 0.989832 -267 TCGCGGATCAAGACTGACACCGCGGATTTG 11 80 1 AGACTGACAC 0.937743 -221 CGCTTGGGCTAGTCAGGCACCAACGCGCCG 11 187 0 AGTCAGGCAC 0.943763 -114 GAGTCAGCGCAGGCCGGCGCGCCCCCTATT 12 48 0 AGGCCGGCGC 0.988583 -209 GGTCTGATCCAGACCGGCTTCCCGTCGCGG 12 182 1 AGACCGGCTT 0.929456 -75 AAGGAACCTCAGACCGGCGCATCGCGAACG 12 214 0 AGACCGGCGC 0.995729 -43 ********** Masking position 1 Map Score: 5.11313 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 97 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 CAGCTTACGTTAAGCGGTCTTAGCTCT 3 8 1 CGTTAAGCGG 0.952005 -42 AAAGGCTTTTCTTTCCGCGGTACCACCCTT 4 149 0 CTTTCCGCGG 0.980674 -152 ATTTGGCAACCGTGCCGCGGCGAGCGCATC 6 107 1 CGTGCCGCGG 0.997822 -41 ACGCGACCCTCGTGCAGCAGCTGAGCTGGC 11 224 1 CGTGCAGCAG 0.952384 -77 TGTTTCCCTTTCCGGGGAAGATTGGAG 12 8 1 CTTTCCGGGG 0.947238 -249 AAGTGCTTCATGTGCAGCGGGTGCTCCTCC 12 136 1 TGTGCAGCGG 0.952384 -121 CCTCGGACGCCGCGACGGGGTCTGATCCAG 12 164 1 CGCGACGGGG 0.907822 -93 GCATCGCGAACGTCCCGCGACGGGAAGCCG 12 196 0 CGTCCCGCGA 0.935618 -61 ********** Masking position 7 Map Score: 7.29377 Number of sites scoring better than the average of aligned sites = 405 Number in coding regions = 375 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 TCTCCTTCCCCTGTTATCGTAAGCG 1 93 0 TTCCCCTGTT 0.897085 -15 GTGCATGATCTGCACCTTTTTTATCT 2 7 0 TGCACCTTTT 0.912605 -282 GTGCAGATCATGCACCTTTTTTATGTGAAT 2 22 1 TGCACCTTTT 0.912605 -267 TTTATGTGAATTCACTTTTTATAAAAATTA 2 41 1 TTCACTTTTT 0.927371 -248 CCTAAATTCTTTCAATTGTTTGATTGGATT 2 260 0 TTCAATTGTT 0.571449 -29 CTGAGGCGAGTTCACCTTGTAAAGCTTCGC 4 13 0 TTCACCTTGT 0.820577 -288 GTGAACTTGATTCACTCGTTACTAAAGCGG 4 78 1 TTCACTCGTT 0.941262 -223 CTTTTGGATTTTCATCCTTTAAAGATCATC 4 270 0 TTCATCCTTT 0.901919 -31 TTTAGTTCCTCCTTTTGGATTTTCA 4 286 0 TTCCTCCTTT 0.779214 -15 AGTTTCACTATACACTCTTTGGAAATTGAC 5 83 0 TACACTCTTT 0.729818 -72 AGTGCCTCTATTCATTCGTTCGCGACTCGC 8 47 0 TTCATTCGTT 0.81889 -25 ********** Masking position 1 Map Score: 6.53745 Number of sites scoring better than the average of aligned sites = 895 Number in coding regions = 732 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 192 Fraction of orfs with sites within 600 bp upstream = 0.0308384 Motif number 8 CAATCTAGTATAATAGAAAGCGCTTACGAT 1 73 1 TAATAGAAAG 0.873931 -35 CCTTCCCCTGTTATCGTAAGCGCTTTCTAT 1 85 0 TTATCGTAAG 0.973709 -23 GAAATAATTTTTATAAAAAGTGAATTCACA 2 45 0 TTATAAAAAG 0.812978 -244 CGAAAACTATTTATAGTAAGTAACAATATT 2 95 1 TTATAGTAAG 0.935402 -194 TGGAGGGTTCAAATCGAAAGAAAGCTATAT 2 131 1 AAATCGAAAG 0.760657 -158 CTAAGACCGCTTAACGTAAGCTG 3 4 0 TTAACGTAAG 0.86908 -46 TATTACATATTAATCATAAGGCGAATCGAT 5 46 1 TAATCATAAG 0.900264 -109 ATAGTGAAACTTATCACAAGATATTTAAAA 5 102 1 TTATCACAAG 0.867078 -53 ********** Masking position 3 Map Score: 2.07747 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 194 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 9 AGGTAAGGAGAGATTCAGCGGTGGCACTAG 10 16 1 AGATTCAGCG 0.986399 -22 TGGTGGACGCAGAGTCAGCGCAGGCCGGCG 12 59 0 AGAGTCAGCG 0.994975 -198 CGGTGGACGCAGAGTCAACGTGTAAAGTGC 12 112 1 AGAGTCAACG 0.986416 -145 ********** Masking position 7 Map Score: 0.761832 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 6 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 CCGTGACACAATGTCACGGGCTTTTTTTACT 1 36 1 AGTCACGGGC 0.809452 -72 ACTCGCCTCAGAGTGCCAGTCTGAAATGACA 4 32 1 GGTGCCAGTC 0.879866 -269 AGAAATATCCATGAGACGGCCGATTAACAGG 4 110 1 AGAGACGGCC 0.941263 -191 TCGCCAACCCGAAAGCAGGGCCCAGGCATGC 6 34 1 GAAGCAGGGC 0.7141 -114 TGATCCGCGAGCGTGACGGCACTGCGAAATC 11 59 0 GGTGACGGCA 0.810309 -242 ATTACTACGAGCATCCCGGGCTTTCCGGCCT 11 152 0 GATCCCGGGC 0.908707 -149 TCAGGCACCAACGCGCCGACCAATTACTACG 11 174 0 AGCGCCGACC 0.886352 -127 AGAATAGGGGGCGCGCCGGCCTGCGCTGACT 12 46 1 GGCGCCGGCC 0.992965 -211 TCCCGCGACGGGAAGCCGGTCTGGATCAGAC 12 183 0 GAAGCCGGTC 0.947807 -74 GACGTTCGCGATGCGCCGGTCTGAGGTTCCT 12 212 1 AGCGCCGGTC 0.977393 -45 * ********* Masking position 7 Map Score: 3.15971 Number of sites scoring better than the average of aligned sites = 1233 Number in coding regions = 1141 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 11 AATGTCACGGGCTTTTTTTACTATCTCGCA 1 45 1 GCTTTTTTTA 0.861077 -63 CATGATCTGCACCTTTTTTATCT 2 4 0 ACCTTTTTTA 0.964797 -285 CAGATCATGCACCTTTTTTATGTGAATTCA 2 25 1 ACCTTTTTTA 0.964797 -264 GGCCGCCCTCACCTTGTTTTGTTCTTTCGT 2 173 0 ACCTTGTTTT 0.872951 -116 AGGCGAGTTCACCTTGTAAAGCTTCGCCG 4 10 0 ACCTTGTAAA 0.587878 -291 CGCGGTACCACCCTTGTTTACGGCCTGTTA 4 134 0 CCCTTGTTTA 0.937143 -167 GGGCGGAAGGGCTTTTTTTATTGAATAATC 4 220 1 GCTTTTTTTA 0.861077 -81 ********** Masking position 5 Map Score: 1.11667 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 249 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 12 CCCCTGTTATCGTAAGCGCTTTCTATTATAC 1 80 0 CGAAGCGCTT 0.961074 -28 CTAAAAGGGGCGAAAAGGCTTTTCTTTCCGC 4 161 0 CGAAAGGCTT 0.95208 -140 TGATTGTGGGCGGAAGGGCTTTTTTTATTGA 4 213 1 CGAAGGGCTT 0.992274 -88 GCCGATAGCGTATCGGCTGTAATTGACGA 9 11 0 CGATCGGCTG 0.945274 -19 CGCGAAAATTCGCATGGGATTTCGCAGTGCC 11 42 1 CGATGGGATT 0.95593 -259 CGTTGGTGCTCGCTTGGGCTAGTCAGGCACC 11 196 0 CGTTGGGCTA 0.956732 -105 CTGCGTCCACCGTGTGGGCTACTCGCACATT 12 93 0 CGGTGGGCTA 0.97039 -164 ** ******** Masking position 10 Map Score: 3.24744 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 125 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 ********** No masking Map Score: 2.95118e-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 14 ********** No masking Map Score: 2.95118e-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 15 ********** No masking Map Score: 2.95118e-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