AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00053_bsub_reg_100.orf -o00053_bsub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #2 ycbD 29 similar to aldehyde dehydrogenase #3 ycbE 83 similar to glucarate transporter #4 ycbF 36 similar to glucarate dehydratase #5 yclB 89 similar to phenylacrylic acid decarboxylase #6 yjmC 104 similar to malate dehydrogenase #7 cypA 300 cytochrome P450-like enzyme #8 bioI 68 cytochrome P450-like enzyme #9 bioW 251 6-carboxyhexanoate-CoA ligase #10 yugK 103 similar to NADH-dependent butanol dehydrogenase #11 yugJ 229 similar to NADH-dependent butanol dehydrogenase #12 ywdH 167 alternate gene name: ipa-58r; similar to aldehyde dehydrogenase #13 aldX 142 aldehyde dehydrogenase Motif number 1 CTGATATTTTATAAAAAAGCGGTAAATCACTGTC 1 63 0 AAAAAACGGA 0.949362 -164 ATAAAATATCAGAAAATAAAGATATTGACTTATT 1 85 1 AAAATAAGAA 0.77165 -142 TAATTGTAAGACAAATAAACAATAAGTCAATATC 1 105 0 AAAAAACAAA 0.711415 -122 CTCTACTTTGAAAAGGAGAAGATACT 3 68 1 AAAGAGAGAA 0.972324 -16 AAAAAACTGAAAAGGAAGGAGGCACTTGC 6 86 1 AAGGAGAGGA 0.873594 -19 TCCAAATCCTTAAAAGAGCCGGCATAGAAGTATT 7 80 1 TAAAAGCGGA 0.817114 -221 TCTTTCCCTGATAAAATGGCGAAACTCCTAATAC 7 109 0 AAAATGCGAA 0.876997 -192 CCCCGCATTTTGAAATAAAAGATATGAGACAGTC 7 166 0 TAAAAAAGAA 0.689642 -135 AAGAATCAATAAAAGCAATCGGTATGATGTCGAT 8 11 1 AAAGAACGGA 0.956804 -58 GTTCAAAAATAAAAACAATCGACATCATACCGAT 8 28 0 AAAAAACGAA 0.951628 -41 TTATTTTTGAACAGAAAGGAGAAAATCAC 8 50 1 AAGAAGAGAA 0.859907 -19 CTGTAAAAAGAAATCGAAAAAGACCGTTT 9 6 1 AAAGAACGAA 0.958752 -246 GCAGTTGGTTAAAAGGAAACAAAAAGACCGTTTT 9 46 0 AAAGAACAAA 0.744414 -206 TTCTATTGACAGAAACAGGAGAGAATAATATATT 9 97 1 AAAAAGAGAA 0.967465 -155 AAGTTGACAAAAAAGAAAAAGGGAAGCAGCCAAA 10 29 0 AAAGAAAGGA 0.949362 -75 CAGGAATTTGATAAAATGCAGGAAGACAACATTT 12 31 0 AAAATGAGGA 0.85187 -137 TGCGCGATTGACAAGCAGAAGAGATTTTTCACAT 12 108 1 AAAGAGAGAA 0.972324 -60 ACCATACCTTACAAAAAGGAGAAACGGA 12 150 1 AAAAAGAGAA 0.967465 -18 TAGGTCCGAGAAAAGAAGAAAGCAAATGAGGGGG 13 111 1 AAAGAGAAGA 0.807517 -32 * *** ** *** * Masking position 3 Map Score: 24.5048 Number of sites scoring better than the average of aligned sites = 1274 Number in coding regions = 1035 Number in noncoding regions = 239 Number of orfs with sites within 600 bp upstream = 256 Fraction of orfs with sites within 600 bp upstream = 0.0411179 Motif number 2 TATTTTATAAAAAAGCGGTAAATCACTGTCC 1 62 0 AAAGCGGTAA 0.82498 -165 GAAAAAACACGAAAGGGGCAATGGGC 2 14 1 GAAGGGGCAA 0.895547 -16 TGGTTGTGATAAACCGGGAAAGAGACGCACG 3 27 0 AAACGGGAAA 0.885865 -57 CTCTACTTTGAAAAGGAGAAGATACT 3 68 1 AAAGGAGAAG 0.911802 -16 AGCGCTTTATAAAGGGAGGAAAATGC 4 21 1 AAAGGAGGAA 0.976277 -16 ACATTAATCAAAATGGGGCTAAAAAATTTTC 7 51 1 AAAGGGGCTA 0.875203 -250 TTCCCTGATAAAATGGCGAAACTCCTAATAC 7 109 0 AAAGGCGAAA 0.972262 -192 TTTTATTTCAAAATGCGGGGACGGCATTTTG 7 180 1 AAAGCGGGGA 0.896031 -121 TTTTTGAACAGAAAGGAGAAAATCAC 8 53 1 GAAGGAGAAA 0.953173 -16 TATTGACAGAAACAGGAGAGAATAATATATT 9 100 1 AACGGAGAGA 0.826313 -152 GTTATCAGTGAAAGGGCGAGAAATGATGCAA 9 195 1 AAAGGCGAGA 0.941625 -57 AAAAAGGGGAAATAGCCGTTTG 10 2 1 AAAGGGGAAA 0.990007 -102 GAATTTGATAAAATGCAGGAAGACAACATTT 12 31 0 AAAGCAGGAA 0.939059 -137 TTCCTGCTGAAAACGCAGATATGAGTTTGTT 12 59 1 AAAGCAGATA 0.861772 -109 ATACCTTACAAAAAGGAGAAACGGA 12 153 1 AAAGGAGAAA 0.987882 -15 TAGGTCCGAGAAAAGAAGAAAGCAAATGAGG 13 111 1 AAAGAAGAAA 0.853997 -32 *** ******* Masking position 2 Map Score: 18.3968 Number of sites scoring better than the average of aligned sites = 1021 Number in coding regions = 805 Number in noncoding regions = 216 Number of orfs with sites within 600 bp upstream = 236 Fraction of orfs with sites within 600 bp upstream = 0.0379056 Motif number 3 AGGATATATGGGAAGGAGCGGATGTGAAAG 1 145 1 GGAAGGAGCG 0.946036 -82 TGGTGCTGGAAAGAGGCGTGCGTCTCT 3 8 1 GGAAAGAGGC 0.991103 -76 TGATAAACCGGGAAAGAGACGCACGCCTCT 3 22 0 GGAAAGAGAC 0.945155 -62 GGTTTCGCTTGGAGAGTGCCCAAAAAACTG 6 65 1 GGAGAGTGCC 0.969055 -40 AAACTGAAAAGGAAGGAGGCACTTGC 6 89 1 GGAAGGAGGC 0.991267 -16 ATTTTATCAGGGAAAGAGTTTAGGCAGCAA 7 126 1 GGAAAGAGTT 0.791853 -175 TAACAATTTAGGTGAGAAGCGCTACACGTT 9 160 1 GGTGAGAAGC 0.678852 -92 AAAAAGGGGAAATAGCCGTTTGGCTGC 10 8 1 GGAAATAGCC 0.912757 -96 AAAGAAAAAGGGAAGCAGCCAAACGGCTAT 10 22 0 GGAAGCAGCC 0.966634 -82 TCCATATGAGGGAAGCTGGCCTGCCCTCGC 11 85 1 GGAAGCTGGC 0.886723 -145 CAAGGTGCTGGGAAAGAAGCTGATATAAGC 11 113 0 GGAAAGAAGC 0.93375 -117 TATGCTGATCGGTGAGAGCTGATTGCTTTA 11 161 1 GGTGAGAGCT 0.81477 -69 TTATTTTTTTGGAGGGTGCTTC 12 3 0 GGAGGGTGCT 0.875708 -165 ********** Masking position 2 Map Score: 15.0625 Number of sites scoring better than the average of aligned sites = 737 Number in coding regions = 605 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 4 GATATATGGGAAGGAGCGGATGTGAAAGAAA 1 147 1 AAGGAGCGAT 0.970286 -80 ACACAAATAACAGGAGGTTATGTTG 1 212 1 CAGGAGGTAT 0.770093 -15 CTCCTTTTCAAAGTAGAGAATCATATGCTGG 3 55 0 AAGTAGAAAT 0.789657 -29 CTACTTTGAAAAGGAGAAGATACT 3 70 1 AAGGAGAGAT 0.982954 -14 AAGGTATGATAAGGAGGCGCTTTCTT 5 6 0 AAGGAGGGCT 0.980914 -84 ACTGAAAAGGAAGGAGGCACTTGC 6 91 1 AAGGAGGACT 0.974553 -14 TTTGAACAGAAAGGAGAAAATCAC 8 55 1 AAGGAGAAAT 0.977257 -14 TTGACAGAAACAGGAGAGAATAATATATTCT 9 102 1 CAGGAGAAAT 0.937076 -150 GAAATGATGCAAGAAGAAACTTTTTATAGTG 9 214 1 AAGAAGAACT 0.844864 -38 GGTGCTGGGAAAGAAGCTGATATAAGCGAGG 11 109 0 AAGAAGCGAT 0.834179 -121 TAAAAAATCTAAGGAGGAGATGTC 11 216 1 AAGGAGGGAT 0.984246 -14 ACCTTACAAAAAGGAGAAACGGA 12 155 1 AAGGAGAACG 0.858526 -13 ******* *** Masking position 5 Map Score: 16.1182 Number of sites scoring better than the average of aligned sites = 335 Number in coding regions = 210 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 5 TATATCCATATGAAAAATATCTATTAAATCTA 5 51 0 TGAAAAATTT 0.962589 -39 CAATATAATATAAAGAATATTTAAAATAATTT 6 11 1 TAAAGAATTT 0.820068 -94 TTTAAGGATTTGGAAAATTTTTTAGCCCCATT 7 62 0 TGGAAAATTT 0.976083 -239 CACTGATAACTGAAGAACGTGTAGCGCTTCTC 9 173 0 TGAAGAACTT 0.915543 -79 TATGTTACAATGGAAAATCTGTTTTTTACCAG 10 62 1 TGGAAAATTT 0.976084 -42 TGTGACATATTGGAGAATCTATACATGCATTC 11 53 1 TGGAGAATTT 0.984788 -177 TTCCCTCATATGGAGAATGCATGTATAGATTC 11 67 0 TGGAGAATCT 0.945038 -163 ATTTATTATGTGAAAAATCTCTTCTGCTTGTC 12 117 0 TGAAAAATTT 0.962589 -51 ******** * * Masking position 6 Map Score: 6.80409 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 104 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 6 GCATTTTCCTCCCTTTATAAAGCG 4 23 0 CTTTTCTCCT 0.987684 -14 GAAAGCGCCTCCTTATCATACCTTTTAGGTATT 5 13 1 CTTATCTCCT 0.934942 -77 AGTCATTAATCATTTTGCTGCCTAAACTCTTTC 7 137 0 CTTTTGTCCT 0.984789 -164 GCGGGGACGGCATTTTGGCCCTTATCATGAATA 7 194 1 CTTTTGCCTT 0.921564 -107 TGAAAACGGTCTTTTTGTTTCCTTTTAACCAAC 9 44 1 CTTTTGTCCT 0.984789 -208 GGGAAATAGCCGTTTGGCTGCTTCCCTTTTTCT 10 17 1 CTTTGGTCTT 0.960908 -87 GGCTGCTTCCCTTTTTCTTTTTTGTCAACTTAT 10 32 1 CTTTTCTTTT 0.859282 -72 GATGGTTCACCGTTGTCTTTCTTACAGAAAAGG 13 65 1 CTTGTCTCTT 0.943001 -78 AAATCCCCCTCATTTGCTTTCTTCTTTTCTCGG 13 116 0 CTTTGCTCTT 0.9682 -27 * ***** * *** Masking position 4 Map Score: 7.70053 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 198 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 7 CAGCCGGCTGACCAGGCTGTTTTTTTGCTGCGC 1 17 1 AAGGTGTTTT 0.930695 -210 ATACACAAATAACAGGAGGTTATGTTG 1 210 1 AAGGGGTTAT 0.916983 -17 TAAATATAAAATCAGGACGATTTGTAAAATGAT 7 240 0 AAGGCGATTT 0.973498 -61 AAGAAATCGAAAAAGACCGTTTTGTGTGAAAAC 9 18 1 AAGACGTTTT 0.967216 -234 AAAGGAAACAAAAAGACCGTTTTCACACAAAAC 9 36 0 AAGACGTTTT 0.967216 -216 TCAATAGAAGAAAGGATCGATTTATGGCAGTTG 9 73 0 AGGACGATTT 0.832484 -179 TACCAGCATCATTTGGAGGTTTTACT 10 88 1 ATGGGGTTTT 0.926263 -16 CGATCAGCATACCAGATGGTTTTATTTTGCAAG 11 139 0 AAGAGGTTTT 0.972736 -91 AAGAAAGCAAATGAGGGGGATTTTACA 13 126 1 AAGGGGATTT 0.973524 -17 * *** ****** Masking position 11 Map Score: 7.43369 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 124 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 8 CAATAAGTCAATATCTTTATTTTCTGATATTTTATAAA 1 82 0 ATATTTTTAT 0.829732 -145 TACGGCCTCTATCTGTAAGCGCTTTTATTAATTTTTCT 1 173 0 ATCTTATTAT 0.977388 -54 TCTATAATTAATACCTAAAAGGTATGATAAGGAGGCGC 5 17 0 ATACTATTAT 0.878653 -73 TATGAAAAATATCTATTAAATCTATAATTAATACCTAA 5 37 0 ATCTTATTAT 0.97738 -53 TTTCATATGGATATATCAGGAGTATGATTGAA 5 68 1 ATATTATTAT 0.964543 -22 TCCTGATTTTATATTTAAAGATTATCATAACCTTTCAA 7 256 1 ATATTATTAT 0.964618 -45 ATATGTCACAATCTATAACTGTTTTAATAATTCATGGA 11 25 0 ATCTTATTAT 0.977399 -205 CCGTACATATATCTAAGATCTGTCTAATGATTGGAGGT 13 18 0 ATCTAATTAT 0.885226 -125 **** * * * * ** Masking position 17 Map Score: 3.39549 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 40 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 ********** No masking Map Score: 5.18939e-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 10 CGGTTTATCACAACCAGCATATGATTCTCT 3 42 1 CAACCAGCAT 0.952305 -42 TCATTCGACCTCCATCTTTGAAAGG 7 286 0 CGACCTCCAT 0.954904 -15 TAAAAAGTTTCTTCTTGCATCATTTCTCGC 9 210 0 CTTCTTGCAT 0.82134 -42 AATCTGTTTTTTACCAGCATCATTTGGAGG 10 77 1 TTACCAGCAT 0.661865 -27 GTTTTGCAACCTCCTCCATGAATTATTAA 11 10 1 CCTCCTCCAT 0.934105 -220 TCTATACATGCATTCTCCATATGAGGGAAG 11 70 1 CATTCTCCAT 0.887898 -160 CAGCTCTCACCGATCAGCATACCAGATGGT 11 152 0 CGATCAGCAT 0.875993 -78 GTGGTGAGGACATTCTGCATAATAAAAAAT 11 194 1 CATTCTGCAT 0.938909 -36 TAAATGTTGTCTTCCTGCATTTTATCAAAT 12 30 1 CTTCCTGCAT 0.979121 -138 ********** Masking position 9 Map Score: 4.18495 Number of sites scoring better than the average of aligned sites = 658 Number in coding regions = 603 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 11 ********** No masking Map Score: 5.18939e-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: 5.18939e-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: 5.18939e-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