AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i123_bsub_mtub_300.orf -o123_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 glvA 300 6-phospho-alpha-glucosidase #2 yfiA 64 similar to hypothetical proteins #3 yfiB 105 similar to ABC transporter (ATP-binding protein) #4 yfiD 154 similar to hypothetical proteins #5 yfiF 93 similar to transcriptional regulator (AraC/XylS family) #6 yfiG 174 similar to metabolite transport protein #7 yfiH 26 yfiH #8 yfiJ 123 similar to two-component sensor histidine kinase [YfiK] #9 yfiL 143 similar to ABC transporter (ATP-binding protein) #10 tesA 238 tesA #11 fadD26 286 fadD26 Motif number 1 AGACTGCCCTCCTTTTCGGGAGGGTTTTCG 3 4 1 CTGCCCCCGG 0.893093 -102 CTGCAATCCCCTTGCCGAAATAACGGC 5 1 1 CTGCACCGCG 0.950506 -93 TTGGTGTCGGGTGCTCTGCCATTCTTGAAAGAAGGGG 6 139 1 GTGCCGCCTG 0.956248 -36 ATGAGGGAATGCGCCGCATATGACATAAAGTTCAT 8 9 1 ATGCCGCGCA 0.891636 -115 AGAAAGAAAGGCGTGCGGCATGTAGCGGCAGATAGAA 9 78 0 GCGTCGCACG 0.920937 -66 TCGTCTGTGACTGCACTGGTGGCGCCGGTGTGTCGGG 10 68 1 CTGCCGGGCG 0.990419 -171 CGTGATCTGAGTGGTCGCCCGGGCTCGTCGAATATGA 10 113 0 GTGGCCCCCG 0.872324 -126 TCTACGACACGCGCCCAGCAGGCCGCGTGATCTGAGT 10 138 0 GCGCCGCCCG 0.996117 -101 GTGTCGTAGACCGTTCGGCGGCTGACGGGTGAGCCTA 10 165 1 CCGTCGCGCG 0.990098 -74 CGTTGTCGGCACGCTCGGGCAAGATCGCCCAGACGAC 10 203 0 ACGCCGGACG 0.846214 -36 GGTGTGACGTGTGCGATGCCGGTGACGAATTGGTAG 11 10 0 GTGCAGCGCG 0.982275 -277 CTTCCGCGTGCCGTGCCGCGTCCGCTGTGGTTGGTGT 11 42 0 CCGTCGCGTG 0.914463 -245 CACCACCACCGTGCCCAGGCAACGACGCCGGCCGTCG 11 98 1 GTGCCGGGCG 0.991995 -189 ATGAATAAGGCCGCGCCCGCCCCGACAAATGATTACC 11 156 1 CCGCCCGGCA 0.876322 -131 AACCCCTGCTCCGCTATGCCTAGCCCGCAAATGTAAG 11 192 0 CCGCAGCCCG 0.980529 -95 CGCAGCATGTCTGCGCAGCGCCAGCCGATCTCCCCCT 11 236 0 CTGCCGCGCG 0.99752 -51 **** * ** * ** Masking position 3 Map Score: 24.5756 Number of sites scoring better than the average of aligned sites = 918 Number in coding regions = 847 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 2 TTACAGATTCGAAAATGGGGGAATTTCAT 2 9 0 GAAAAGGGGG 0.992517 -56 ATAATAGAAAGAAAATGGGGGGATCTGAT 2 46 1 GAAAAGGGGG 0.992517 -19 AAACCCTCCCGAAAAGGAGGGCAGTCT 3 7 0 GAAAAGAGGG 0.985404 -99 AGACAATCGAGTAAAAAGGGGTTTGGAGGCT 3 80 1 GTAAAAGGGG 0.962049 -26 TGCCATTCTTGAAAGAAGGGGAAGAAAGCC 6 155 1 GAAAGAGGGG 0.987438 -20 AGGCAGGTATGATAAGAAGGGAATTGGGTAT 8 89 1 GATAAAAGGG 0.92807 -35 CATAGGGCATGAAAAAAAGGCCTGTAAAAGG 9 47 0 GAAAAAAGGC 0.976841 -97 GCGGCAGATAGAACATAGGGCATGAAAAAAA 9 60 0 GAACAAGGGC 0.950889 -84 CATTGTAGAAGAAAGAAAGGCGTGCGGCATG 9 93 0 GAAAGAAGGC 0.953741 -51 ***** ***** Masking position 9 Map Score: 14.0539 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 145 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 3 ATGAGATAGCTCGTCCCGTAACACGTTTGGC 1 239 0 TCGTCCCGAA 0.741056 -62 ATGACGACCTCCTTGATAACGTTTACAA 1 283 0 CCTCCTTGTA 0.899152 -18 CAAACGAAAACCCTCCCGAAAAGGAGGGCAG 3 14 0 CCCTCCCGAA 0.979514 -92 TTTATCCTCCTTGATAAATGTTATCA 4 139 0 CCTCCTTGTA 0.899152 -16 CTGCAATCCCCTTGCCGAAATAACGGCAGG 5 10 1 CCTTGCCGAA 0.911791 -84 TAAAAAATCCCCCTGCCGTTATTTCGGCAAG 5 21 0 CCCTGCCGTA 0.964368 -73 TTATTTTTGTCCGCCTTGTTATGATGAGAGA 5 49 1 CCGCCTTGTA 0.897322 -45 CAGCAATACCCCTTGTTGTAACCGCTTTCTA 6 84 0 CCTTGTTGAA 0.800648 -91 GGTGCTCTGCCATTCTTGAAAGAAGGGGAAG 6 148 1 CATTCTTGAA 0.531493 -27 TGATAGATTCCTCCTGGTATCTCAGG 7 8 0 TCCTCCTGTA 0.862831 -19 GCTCATCACTCCCGATACCCAATTCCC 8 107 0 CACTCCCGTA 0.884324 -17 GGCCACACCCTCCTGGCATCTTGCAAGA 10 8 1 CCCTCCTGCA 0.963601 -231 CTTGCAAGATCCCTGTTGTTACCAGTGTGCC 10 30 1 CCCTGTTGTA 0.913164 -209 AAGGCCGCGCCCGCCCCGACAAATGATTACC 11 162 1 CCGCCCCGCA 0.916627 -125 ******** ** Masking position 11 Map Score: 13.1337 Number of sites scoring better than the average of aligned sites = 876 Number in coding regions = 727 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 4 TATAAATAATTCGGCATGTATCCGAATCGT 1 33 1 TCGGCATGTA 0.859483 -268 GGTCTTTTTGACGGCAAACGAAAACCCTCC 3 29 0 ACGGCAAACG 0.750707 -77 TGCCGTTATTTCGGCAAGGGGATTGCAG 5 9 0 TCGGCAAGGG 0.92201 -85 TGCCGAAATAACGGCAGGGGGATTTTTTAT 5 23 1 ACGGCAGGGG 0.963124 -71 AAAATGCCCTGAGGCAGGTATGATAAGAAG 8 78 1 GAGGCAGGTA 0.715084 -46 GCGGCATGTAGCGGCAGATAGAACATAGGG 9 71 0 GCGGCAGATA 0.882006 -73 AGAAAGGCGTGCGGCATGTAGCGGCAGATA 9 81 0 GCGGCATGTA 0.920846 -63 CTCAGATCACGCGGCCTGCTGGGCGCGTGT 10 139 1 GCGGCCTGCT 0.816478 -100 AGACCGTTCGGCGGCTGACGGGTGAGCCTA 10 172 1 GCGGCTGACG 0.920494 -67 ACCTACGTTGTCGGCACGCTCGGGCAAGAT 10 215 0 TCGGCACGCT 0.781421 -24 GGCACGGCACGCGGAAGGGACGTTAGACTC 11 62 1 GCGGAAGGGA 0.751912 -225 GACGTTAGACTCGGCTAGCACCACCACCGT 11 80 1 TCGGCTAGCA 0.85547 -207 TTTCTTAGCGACGGCCGGCGTCGTTGCCTG 11 113 0 ACGGCCGGCG 0.957615 -174 TAGGGGGAGATCGGCTGGCGCTGCGCAGAC 11 235 1 TCGGCTGGCG 0.971078 -52 ********** Masking position 4 Map Score: 10.7165 Number of sites scoring better than the average of aligned sites = 2185 Number in coding regions = 2022 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 5 AGATTCGAAAATGGGGGAATTTCAT 2 6 0 ATGGGGGAAT 0.833563 -59 TAGAAAGAAAATGGGGGGATCTGAT 2 50 1 ATGGGGGGAT 0.889086 -15 CCCTCCTTTTCGGGAGGGTTTTCGTTTGCC 3 17 1 CGGGAGGGTT 0.942295 -89 ATCGAGTAAAAAGGGGTTTGGAGGCTTTTA 3 85 1 AAGGGGTTTG 0.658312 -21 AACATTTATCAAGGAGGATAAA 4 143 1 AAGGAGGATA 0.69977 -12 GTTATTTCGGCAAGGGGATTGCAG 5 5 0 CAAGGGGATT 0.741983 -89 GAAATAACGGCAGGGGGATTTTTTATTTTT 5 27 1 CAGGGGGATT 0.979271 -67 CGGTTACAACAAGGGGTATTGCTGAAGGAG 6 91 1 AAGGGGTATT 0.912473 -84 GGTATTGCTGAAGGAGGGATGCATTGGCTT 6 105 1 AAGGAGGGAT 0.95707 -70 CCTGAGATACCAGGAGGAATCTATCA 7 11 1 CAGGAGGAAT 0.957179 -16 AATTGGGTATCGGGAGTGATGAGC 8 110 1 CGGGAGTGAT 0.814508 -14 GGATCAAAAAAAGGAGTGAGACGAC 9 129 1 AAGGAGTGAG 0.799424 -15 TGCAAGATGCCAGGAGGGTGTGGCC 10 6 0 CAGGAGGGTG 0.959654 -233 CATAGCGGAGCAGGGGTTTTAGTCTAGGGG 11 211 1 CAGGGGTTTT 0.859642 -76 ********** Masking position 6 Map Score: 12.1706 Number of sites scoring better than the average of aligned sites = 797 Number in coding regions = 462 Number in noncoding regions = 335 Number of orfs with sites within 600 bp upstream = 365 Fraction of orfs with sites within 600 bp upstream = 0.0586251 Motif number 6 ATTGGAAGGGCGTATATTCACTTAAAATTCAC 1 85 1 CGATATTACT 0.871465 -216 CCCCCATTTTCGAATCTGTAATTGTATATAAT 2 19 1 CGATCTGAAT 0.966116 -46 TTACATTTTACGAAAATGAAATAAAAGTACTA 4 52 0 CGAAATGAAT 0.975185 -103 GGGAATGCGCCGCATATGACATAAAGTTCATA 8 15 1 CGATATGCAT 0.966116 -109 AAATAAAAACCGCATATGAACTTTATGTCATA 8 29 0 CGATATGACT 0.983815 -95 TTCAGAGAAGCGTATATGCAAAACGTCATATG 9 11 0 CGATATGAAA 0.957056 -133 CCGGGCTCGTCGAATATGAAATTGTGTCCCGA 10 100 0 CGATATGAAT 0.990771 -139 ATGCCTAGCCCGCAAATGTAAGGTAATCATTT 11 182 0 CGAAATGAAG 0.923526 -105 ** ***** *** Masking position 4 Map Score: 7.44653 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 105 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 ATGACGACCTCCTTGATAACGTTTA 1 286 0 GACCTCCTTG 0.919866 -15 AACAAAAAAAGACCTCTGTGCAGGACAAAG 4 13 0 GACCTCTGTG 0.936317 -142 TTTATCCTCCTTGATAAATGTTA 4 142 0 ATCCTCCTTG 0.715737 -13 TTTTATTTTTGTCCGCCTTGTTATGATGAG 5 47 1 GTCCGCCTTG 0.925326 -47 TGATAGATTCCTCCTGGTATCTCAGG 7 10 0 TTCCTCCTGG 0.823682 -17 TGCCTGGTGTTTCGTCTGTGACTGCACTGG 10 57 1 TTCGTCTGTG 0.904445 -182 CTGCACTGGTGGCGCCGGTGTGTCGGGACA 10 78 1 GGCGCCGGTG 0.948226 -161 GATCTGAGTGGTCGCCCGGGCTCGTCGAAT 10 117 0 GTCGCCCGGG 0.974838 -122 GTGAGCCTACGTCGTCTGGGCGATCTTGCC 10 193 1 GTCGTCTGGG 0.969216 -46 TGACGTGTGCGATGCCGGTGACGAATTGGT 11 13 0 GATGCCGGTG 0.682203 -274 GCCGTGCCGCGTCCGCTGTGGTTGGTGTGA 11 40 0 GTCCGCTGTG 0.940728 -247 AGCGACGGCCGGCGTCGTTGCCTGGGCACG 11 107 0 GGCGTCGTTG 0.920763 -180 AAGGTAATCATTTGTCGGGGCGGGCGCGGC 11 165 0 TTTGTCGGGG 0.582432 -122 ********** Masking position 6 Map Score: 6.71336 Number of sites scoring better than the average of aligned sites = 1003 Number in coding regions = 933 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 8 CTGAGAGATTTGGTTTTTTTACCTTTTTTGTAATC 1 134 0 TTTTTTACCT 0.90747 -167 CCCCCCATTTTCTTTCTATTATATACAATTACAGA 2 33 0 TTTTTTATAA 0.642551 -32 ATTGTCTCTTTCTTTACTTTACTATGGCGGTCTTT 3 52 0 TTTCTTACTT 0.717484 -54 CACAGAGGTCTTTTTTTGTTACAGTTTTATAGTAC 4 23 1 TTTTTTACAT 0.979178 -132 AGTTTTATAGTACTTTTATTTCATTTTCGTAAAAT 4 45 1 TTTTTTTCAT 0.881141 -110 TTACGTCAAGTAATTTTGTTACATTTTACGAAAAT 4 67 0 TTTTTTACAT 0.979178 -88 GCGAGAAATCTCGTTGTCTTATAATCTTTTTAGAA 6 54 1 TTTTTTATAT 0.878713 -121 TCATATGCGGTTTTTATTTTCCAGAAACTCCTGTC 8 42 1 TTTTTTCCAA 0.833808 -82 CGCACGCCTTTCTTTCTTCTACAATGGCAATGGAT 9 98 1 TTTTCTACAT 0.90747 -46 GTCTCACTCCTTTTTTTGATCCATTGCCATTGTAG 9 116 0 TTTTATCCAT 0.739938 -28 CCCCGACAAATGATTACCTTACATTTGCGGGCTAG 11 175 1 TTTCTTACAT 0.947503 -112 * ** * ***** * Masking position 10 Map Score: 3.25277 Number of sites scoring better than the average of aligned sites = 385 Number in coding regions = 281 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 9 TCAGCAATACCCCTTGTTGTAACCGCTTTC 6 86 0 CCCTTGTTGT 0.915031 -89 CATTGGCTTATGCTTGGTGTCGGGTGCTCT 6 126 1 TGCTTGGTGT 0.987415 -49 TCTTGCAAGATCCCTGTTGTTACCAGTGTG 10 29 1 TCCCTGTTGT 0.962695 -210 GTTACCAGTGTGCCTGGTGTTTCGTCTGTG 10 47 1 TGCCTGGTGT 0.988331 -192 GCGTCCGCTGTGGTTGGTGTGACGTGTGCG 11 32 0 TGGTTGGTGT 0.957049 -255 ********** Masking position 5 Map Score: 1.65299 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 65 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 TGCTTGGTGTCGGGTGCTCTGCCATTCTTG 6 136 1 CGGGTGCTCT 0.75833 -39 AGATGCCAGGAGGGTGTGGCC 10 2 0 AGGGTGTGGC 0.876157 -237 AGTGGTCGCCCGGGCTCGTCGAATATGAAA 10 111 0 CGGGCTCGTC 0.96092 -128 CGGCGGCTGACGGGTGAGCCTACGTCGTCT 10 180 1 CGGGTGAGCC 0.977952 -59 CGATCTTGCCCGAGCGTGCCGACAACGTAG 10 213 1 CGAGCGTGCC 0.929802 -26 CCAACCACAGCGGACGCGGCACGGCACGCG 11 45 1 CGGACGCGGC 0.987519 -242 TTTGTCGGGGCGGGCGCGGCCTTATTCATG 11 155 0 CGGGCGCGGC 0.998759 -132 CTTACATTTGCGGGCTAGGCATAGCGGAGC 11 192 1 CGGGCTAGGC 0.977457 -95 GGGAGATCGGCTGGCGCTGCGCAGACATGC 11 239 1 CTGGCGCTGC 0.939692 -48 ********** Masking position 4 Map Score: 9.59168 Number of sites scoring better than the average of aligned sites = 465 Number in coding regions = 436 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 TGAGAGATTTGGTTTTTTTACCTTTTTTGTA 1 137 0 GGTTTTTTAC 0.427778 -164 TTACTATGGCGGTCTTTTTGACGGCAAACGA 3 38 0 GGTTTTTTGA 0.756102 -68 AAATCCCCCTGCCGTTATTTCGGCAAGGGGA 5 17 0 GCCTTATTTC 0.804521 -77 CGGGTGCTCTGCCATTCTTGAAAGAAGGGGA 6 146 1 GCCTTCTTGA 0.952358 -29 GGCTTTCTTCCCCTTCTTTCA 6 164 0 GGCTTCTTCC 0.967972 -11 CCTGCCTCAGGGCATTTTTGACAGGAGTTTC 8 65 0 GGCTTTTTGA 0.960787 -59 TCTCTGAAAAGGCCTTTTACAGGCCTTTTTT 9 35 1 GGCTTTTACA 0.720591 -109 CCTTTTACAGGCCTTTTTTTCATGCCCTATG 9 47 1 GCCTTTTTTC 0.904403 -97 CATGCCGCACGCCTTTCTTTCTTCTACAATG 9 93 1 GCCTTCTTTC 0.924127 -51 TTGATCCATTGCCATTGTAGAAGAAAGAAAG 9 105 0 GCCTTGTAGA 0.680916 -39 ACGTCGTCTGGGCGATCTTGCCCGAGCGTGC 10 201 1 GGCATCTTGC 0.861896 -38 AGCGACGGCCGGCGTCGTTGCCTGGGCACGG 11 106 0 GGCTCGTTGC 0.828609 -181 GGGCGGGCGCGGCCTTATTCATGAAGTCAAC 11 147 0 GGCTTATTCA 0.84599 -140 *** ******* Masking position 8 Map Score: 5.14422 Number of sites scoring better than the average of aligned sites = 1696 Number in coding regions = 1521 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 12 ********** No masking Map Score: 3.42725e-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 13 ********** No masking Map Score: 3.42725e-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: 3.42725e-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