AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i056_bsub_mtub_300.orf -o056_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 ycnL 164 ycnL #2 mtlA 172 phosphotransferase system (PTS) mannitol-specific enzyme IIABC component #3 mtlD 52 mannitol-1-phosphate dehydrogenase #4 ycsA 107 similar to 3-isopropylmalate dehydrogenase #5 ilvD 288 dihydroxy-acid dehydratase #6 ypgR 59 similar to hypothetical proteins #7 bsaA 300 glutathione peroxidase #8 leuC 49 3-isopropylmalate dehydratase (large subunit) #9 ilvB 300 acetolactate synthase (acetohydroxy-acid synthase) (large subunit) #10 alsS 154 alpha-acetolactate synthase (pH6) #11 ilvD 147 ilvD #12 leuD 24 leuD #13 leuC 71 leuC #14 serA 29 serA #15 ilvC 37 ilvC #16 ilvB 300 ilvB #17 leuA 256 leuA Motif number 1 AAACGAAACAGAAGGGACTCTGGTATAATAGAC 1 114 1 GAGACTCTGG 0.737593 -51 TATGCGGCCCAAGGATGCGCTCGCCGCGGCACG 11 117 0 AGGGCGCTCG 0.905339 -31 TTCATTCGTTCGCGACTCGCTGGTCATCTCAAA 13 34 0 CCGTCGCTGG 0.855451 -38 GAGAGATTCAGCGGTGGCACTAGAG 15 23 1 GGGGCACTAG 0.652996 -15 GTGGGCGTCGAGTTCGCGAGCGTAAC 16 4 1 GCGGAGTTCG 0.943763 -297 TTTTCGCGGTGGCGTTACGCTCGCGAACTCGAC 16 17 0 GCGACGCTCG 0.985205 -284 ATTTCGCAGTGCCGTCACGCTCGCGGATCAAGA 16 60 1 GCGACGCTCG 0.985212 -241 TATGGACAAGGCCGGAAAGCCCGGGATGCTCGT 16 144 1 GCGAAGCCCG 0.947518 -157 GTAGTAATTGGTCGGCGCGTTGGTGCCTGACTA 16 175 1 GCGGCGTTGG 0.990449 -126 CTGCTGCACGAGGGTCGCGTTGGTGCTCGCTTG 16 211 0 AGGGCGTTGG 0.79897 -90 CCCTCGTGCAGCAGCTGAGCTGGCGAGGGTTTT 16 230 1 GAGGAGCTGG 0.962281 -71 TATTGCTCTGGAAGTCTCGTTGGTGGACAAGAA 16 263 0 GAGTCGTTGG 0.793677 -38 GTCCAGAATAGGGGGCGCGCCGGCCTGCGCTGA 17 42 1 GGGGCGCCGG 0.994213 -215 TCCCGTGGTGGACGCAGAGTCAGCGCAGGCCGG 17 61 0 GCGGAGTCAG 0.796099 -196 CGGCGTCCGAGGAGGAGCACCCGCTGCACATGA 17 143 0 GAGGCACCCG 0.89772 -114 ATCAGACCCCGTCGCGGCGTCCGAGGAGGAGCA 17 157 0 GCGGCGTCCG 0.988565 -100 AACGTCCCGCGACGGGAAGCCGGTCTGGATCAG 17 185 0 GCGAAGCCGG 0.962388 -72 GCGGGACGTTCGCGATGCGCCGGTCTGAGGTTC 17 208 1 CCGGCGCCGG 0.983539 -49 GGTAGTTGCTCCGGGATGGTGAGA 17 243 0 GAGGCTCCGG 0.925582 -14 * ** ******* Masking position 4 Map Score: 25.7112 Number of sites scoring better than the average of aligned sites = 1237 Number in coding regions = 1164 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 2 AAACAAGGTGAGGGCGGCCTGTATTTATCTTAT 5 184 1 AGCGGCCTGA 0.90351 -105 TCGCCTCAGAGTGCCAGTCTGAAATGACAGTAG 9 34 1 GGCAGTCTGA 0.743843 -267 AGTATCTCTGGAGATGGCGAGTAA 11 2 0 GGTGGCGAGA 0.983152 -146 CCCTGCTTTCGGGTTGGCGAGTATCTCTGGAGA 11 21 0 GGTGGCGAGA 0.983152 -127 TGGCAACCGTGCCGCGGCGAGCGCATCCTTGGG 11 110 1 GCCGGCGAGG 0.931308 -38 CTCGTATTTTGAGATGACCAGCGAGTCGCGAAC 13 27 1 GGTGACCAGG 0.90351 -45 GTGGGCGTCGAGTTCGCGAGCGTAACGCCACC 16 10 1 GGTCGCGAGG 0.952665 -291 GGTCGCGTTGGTGCTCGCTTGGGCTAGTCAGGC 16 199 0 GGTCGCTTGG 0.692067 -102 TGCAGCAGCTGAGCTGGCGAGGGTTTTTTCTTG 16 236 1 GGTGGCGAGG 0.989434 -65 AATAGGGGGCGCGCCGGCCTGCGCTGACTCTGC 17 48 1 GGCGGCCTGG 0.99233 -209 GGTGGACGCAGAGTCAACGTGTAAAGTGCTTCA 17 113 1 GGCAACGTGA 0.601782 -144 CCGCGACGGGAAGCCGGTCTGGATCAGACCCCG 17 179 0 AGCGGTCTGA 0.708236 -78 CGTTCGCGATGCGCCGGTCTGAGGTTCCTTCTC 17 214 1 GGCGGTCTGG 0.971048 -43 TAGTTGCTCCGGGATGGTGAGAAGGAACCTCAG 17 232 0 GGTGGTGAGA 0.937994 -25 * * ******* * Masking position 11 Map Score: 13.8118 Number of sites scoring better than the average of aligned sites = 639 Number in coding regions = 576 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 3 CATTGTGTCACGGGTGGTCGGTTATTGATTA 4 18 0 CGGTGGTCGG 0.883753 -90 AACAAAACAAGGTGAGGGCGGCCTGTATTTA 5 180 1 GGGAGGGCGG 0.930681 -109 GAGTATCTCTGGAGATGGCGAGTAA 11 5 0 GGGATGGCGA 0.951891 -143 GCCCTGCTTTCGGGTTGGCGAGTATCTCTGG 11 24 0 CGGTTGGCGA 0.993636 -124 GTGGGCGTCGAGTTCGCGAGCGTAACGCC 16 9 1 CGGTTCGCGA 0.971063 -292 TGCGAATTTTCGCGGTGGCGTTACGCTCGCG 16 25 0 CGGGTGGCGT 0.895942 -276 AGTCTTGATCCGCGAGCGTGACGGCACTGCG 16 64 0 CGGAGCGTGA 0.880494 -237 AATTGGTCGGCGCGTTGGTGCCTGACTAGCC 16 180 1 CGGTTGGTGC 0.975623 -121 GCACGAGGGTCGCGTTGGTGCTCGCTTGGGC 16 208 0 CGGTTGGTGC 0.975623 -93 CTCTGGAAGTCTCGTTGGTGGACAAGAAAAA 16 260 0 CTGTTGGTGG 0.807061 -41 CTGCGTCCACCGTGTGGGCTACTCGCACATT 17 93 0 CGGTGGGCTA 0.902122 -164 GTAGTTGCTCCGGGATGGTGAGAAGGAACCT 17 235 0 CGGATGGTGA 0.976565 -22 ** ******** Masking position 4 Map Score: 12.1157 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 TCATACACCCTCTTCATTAAGATCTA 1 4 1 TCACCCTCTA 0.905142 -161 TCAACACATTTTCACATTTTTTATCATCCACTT 1 72 0 TCACATTTTA 0.944681 -93 AGGGTATTCCTCACTTTCTATTCCATCTGT 1 145 0 TCTCACTTTA 0.719379 -20 GTCAGTTCACCTCGTTGAAATGGCGATC 3 35 0 TCACCTCGTA 0.790438 -18 GTGCATGATCTGCACCTTTTTTATCT 5 4 0 TCACCTTTTA 0.985714 -285 GTGCAGATCATGCACCTTTTTTATGTGAATTCA 5 22 1 TCACCTTTTA 0.985714 -267 TTTATGTGAATTCACTTTTTATAAAAATTATTT 5 41 1 TCACTTTTTA 0.922645 -248 TTAATTGATGTTTACATTTTGAATTGCGATTTA 7 234 1 TTACATTTTA 0.681726 -67 TGCTGATTATTTTACCTTTTTTAAATCGCAATT 7 255 0 TTACCTTTTA 0.897233 -46 CTGAGGCGAGTTCACCTTGTAAAGCTTCGCCG 9 10 0 TCACCTTGTA 0.959262 -291 CTTTTGGATTTTCATCCTTTAAAGATCATCTTT 9 267 0 TCATCCTTTA 0.769449 -34 TTTAGTTCCTCCTTTTGGATTTTCATCCT 9 282 0 TCTCCTTTTA 0.933746 -19 AGTTTCACTATACACTCTTTGGAAATTGACCTC 10 80 0 TCACTCTTTA 0.897465 -75 * ******** * Masking position 13 Map Score: 12.101 Number of sites scoring better than the average of aligned sites = 504 Number in coding regions = 399 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 5 TCCGTCTCTAAAATCCTCTACGCTTAAATAGAT 1 32 0 AAATCCTCGC 0.992846 -133 AATGGCGATCAAATCTTCTTCGCTTTAGCGGAG 3 12 0 AAATCTTCGC 0.939388 -41 AGTATAATAGAAAGCGCTTACGATAACAGGGGA 4 79 1 AAAGCGTCGA 0.853444 -29 CAAATAAGATAAATACAGGCCGCCCTCACCTTG 5 187 0 AAATACGCGC 0.930355 -102 CGCGGAAAGAAAAGCCTTTTCGCCCCTTTTAGC 9 160 1 AAAGCCTCGC 0.994435 -141 TTCAATAAAAAAAGCCCTTCCGCCCACAATCAG 9 212 0 AAAGCCTCGC 0.994435 -89 GGTCATCTCAAAATACGAGACGCTATGATCTCT 13 13 0 AAATACGCGC 0.930355 -59 TCGTCAATTACAGCCGATACGCTATCGGC 14 10 1 ACAGCCTCGC 0.976607 -20 CGGCACTGCGAAATCCCATGCGAATTTTCGCGG 16 41 0 AAATCCTCGA 0.964701 -260 ****** * *** Masking position 3 Map Score: 10.0416 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 146 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 TCAACACATTTTCACATTTTTTATCATCCA 1 75 0 TTCACATTTT 0.93213 -90 GTCAGTTCACCTCGTTGAAATGGCG 3 38 0 TTCACCTCGT 0.920458 -15 GTGCATGATCTGCACCTTTTTTATCT 5 7 0 TGCACCTTTT 0.967052 -282 GTGCAGATCATGCACCTTTTTTATGTGAAT 5 22 1 TGCACCTTTT 0.967052 -267 TTTATGTGAATTCACTTTTTATAAAAATTA 5 41 1 TTCACTTTTT 0.886216 -248 ACAGGCCGCCCTCACCTTGTTTTGTTCTTT 5 176 0 CTCACCTTGT 0.920458 -113 TTAATTGATGTTTACATTTTGAATTGCGAT 7 234 1 TTTACATTTT 0.730052 -67 TGCTGATTATTTTACCTTTTTTAAATCGCA 7 258 0 TTTACCTTTT 0.922021 -43 CTGAGGCGAGTTCACCTTGTAAAGCTTCGC 9 13 0 TTCACCTTGT 0.980209 -288 ********** Masking position 4 Map Score: 8.33727 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 208 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 7 GAGTCCCTTCTGTTTCGTTTTGTTGCTGTTC 1 103 0 TGTTCGTTTT 0.513647 -62 AGGGTATTCCTCACTTTCTATTCCATC 1 148 0 TTCTCACTTT 0.879909 -17 CAGAGAATGATGCTTCCCTTTGACTCTATGT 2 102 0 TGCTCCCTTT 0.986128 -71 CGATCAAATCTTCTTCGCTTTAGCGGAGA 3 9 0 TTCTCGCTTT 0.952348 -44 CTTTTATTTCCTCCCTCTACCTAGAGCT 8 32 0 TTCTCCCTCT 0.931897 -18 GAAAAGCCTTTTCGCCCCTTTTAGCTATCGC 9 168 1 TTCCCCCTTT 0.931897 -133 CTTTTGGATTTTCATCCTTTAAAGATCATCT 9 269 0 TTCTCCTTTA 0.722607 -32 TTTAGTTCCTCCTTTTGGATTTTCAT 9 285 0 TTCTCCTTTT 0.948753 -16 TCAATATGCATTCCTTTCCATAGGTTA 10 7 1 TGCTTCCTTT 0.861316 -148 TGTTTCCCTTTCCGGGGAAGA 17 1 1 TGTTCCCTTT 0.924748 -256 *** ******* Masking position 9 Map Score: 5.71756 Number of sites scoring better than the average of aligned sites = 694 Number in coding regions = 529 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 187 Fraction of orfs with sites within 600 bp upstream = 0.0300353 Motif number 8 TCGCCTCAGAGTGCCAGTCTGAAATGACAG 9 34 1 GTGCCAGTCT 0.984955 -267 CAAATCCGCGGTGTCAGTCTTGATCCGCGA 16 80 0 GTGTCAGTCT 0.910145 -221 CGGCGCGTTGGTGCCTGACTAGCCCAAGCG 16 187 1 GTGCCTGACT 0.918603 -114 AATAGGGGGCGCGCCGGCCTGCGCTGACTC 17 48 1 GCGCCGGCCT 0.984825 -209 CCGCGACGGGAAGCCGGTCTGGATCAGACC 17 182 0 AAGCCGGTCT 0.899507 -75 CGTTCGCGATGCGCCGGTCTGAGGTTCCTT 17 214 1 GCGCCGGTCT 0.993716 -43 ********** Masking position 10 Map Score: 2.98107 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 9 TATAAACCCTCCCTGTTTTGTTTGTCGCTG 2 152 0 CCCTGTTTTG 0.98073 -21 TCTCCTTCCCCTGTTATCGTAAGCGCTT 4 90 0 CCCTGTTATC 0.960038 -18 GCCGCCCTCACCTTGTTTTGTTCTTTCGTG 5 172 0 CCTTGTTTTG 0.952139 -117 GTAAGTCCCTCCTATGTCCTTGGTGC 7 285 0 CCCTCCTATG 0.835387 -16 GCGGTACCACCCTTGTTTACGGCCTGTTAA 9 133 0 CCTTGTTTAC 0.686648 -168 CCTCACTCCTTATTATGCATTTTAAAC 10 138 0 CCTTATTATG 0.806491 -17 CATGCCTGGGCCCTGCTTTCGGGTTGGCGA 11 34 0 CCCTGCTTTC 0.946564 -114 CCGGCGCGCCCCCTATTCTGGACCTGTCTC 17 35 0 CCCTATTCTG 0.862153 -222 ********** Masking position 4 Map Score: 1.7743 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 178 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 10 TGTTTTGTTTGTCGCTGTAAGATACAAAAAT 2 138 0 GTCGCTGAAG 0.974075 -35 TTCTATCATAGTCGCTCCAAGCCTTCTA 6 8 0 GTCGCTCAAG 0.895994 -52 TAGAGCTAAGACCGCTTAACGTAAGCTG 8 8 0 ACCGCTTACG 0.904878 -42 CAAGGGTGGTACCGCGGAAAGAAAAGCCTTT 9 148 1 ACCGCGGAAG 0.955793 -153 GGATGCGCTCGCCGCGGCACGGTTGCCAAAT 11 107 0 GCCGCGGACG 0.995882 -41 AATTTTCGCGGTGGCGTTACGCTCGCGAACT 16 21 0 GTGGCGTACG 0.888835 -280 CGCCAGCTCAGCTGCTGCACGAGGGTCGCGT 16 224 0 GCTGCTGACG 0.951865 -77 CCGGCTTCCCGTCGCGGGACGTTCGCGATGC 17 195 1 GTCGCGGACG 0.993484 -62 ******* *** Masking position 9 Map Score: 5.89813 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 318 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 11 CTATACAATTGAAAGTAAAGAGGACTTTGGCAC 2 52 0 GAAGAAAAGG 0.805629 -121 TGTTTGATTGGATTTTATTTTGACAATTTTCAG 5 241 0 GATTATTTGA 0.529989 -48 TCAAACAATTGAAAGAATTTAGGAGGATCACC 5 267 1 GAAGATTAGG 0.694301 -22 CGTATAGATAGATTGAAAATTGGCGTGAAAATT 7 14 0 GATGAAATGG 0.95204 -287 CGAGCCATATGAATTGATAATGAACTGACGCTC 7 176 1 GATTATATGA 0.819644 -125 TTTGAATTGCGATTTAAAAAAGGTAAAATAATC 7 251 1 GATTAAAAGG 0.824972 -50 CTATGGAAAGGAATGCATATTGA 10 1 0 GATGATATGA 0.941543 -154 ATCATAAGGCGAATCGATATTGGAGGTCAATTT 10 58 1 GATCATATGG 0.878872 -97 AATTTCCAAAGAGTGTATAGTGAAACTTATCAC 10 86 1 GATGATATGA 0.941543 -69 AGTCGCGAACGAATGAATAGAGGCACTTCGAG 13 50 1 GATGATAAGG 0.973609 -22 TTCCGGGGAAGATTGGAGACAGGTCCAGAATAG 17 20 1 GATGAGAAGG 0.907396 -237 ** ** *** *** Masking position 7 Map Score: 3.80998 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 233 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 12 ATTTCAGACTGGCACTCTGAGGCGAGTTCAC 9 28 0 GGCACTTGAG 0.879789 -273 AAACAAGGGTGGTACCGCGGAAAGAAAAGCC 9 145 1 GGTACCCGGA 0.940742 -156 AATGAATAGAGGCACTTCGAG 13 61 1 GGCACTCGAG 0.969695 -11 CTCTAGTGCCACCGCTGAATCTCTCCTT 15 20 0 GCCACCCTGA 0.892445 -18 CGAGCGTAACGCCACCGCGAAAATTCGCATG 16 27 1 GCCACCCGAA 0.979097 -274 CGAGCGTGACGGCACTGCGAAATCCCATGCG 16 52 0 GGCACTCGAA 0.982611 -249 GATCAAGACTGACACCGCGGATTTGACTGCT 16 85 1 GACACCCGGA 0.979606 -216 GCTACCGTCGGACACTATGGACAAGGCCGGA 16 129 1 GACACTTGGA 0.873848 -172 ****** **** Masking position 4 Map Score: 3.97184 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 158 Number in noncoding regions = 20 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: -1.19128e-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: -1.19128e-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: -1.19128e-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