AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i020_bsub_mtub_100.orf -o020_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 acoA 231 acetoin dehydrogenase E1 component (TPP-dependent alpha subunit) #2 pdhA 300 pyruvate dehydrogenase (E1 alpha subunit) #3 pdhC 114 pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) #4 odhB 29 2-oxoglutarate dehydrogenase complex (dihydrolipoamide transsuccinylase, E2 subunit) #5 odhA 227 2-oxoglutarate dehydrogenase (E1 subunit) #6 bfmBAA 73 branched-chain alpha-keto acid dehydrogenase E1 (2-oxoisovalerate dehydrogenase alpha subunit) #7 yqiS 124 similar to phosphate butyryltransferase #8 sucA 192 sucA #9 sucB 263 sucB #10 aceE 51 aceE #11 pdhA 258 pdhA #12 sdhA 128 sdhA Motif number 1 ACCCTAAATAGAAGGAGGCGCACAAA 1 216 1 GAGGAGGCGC 0.910222 -16 TTTGCCATCTGCGGCAAGCGCAGCTTCTCCA 6 17 0 GCGCAAGCGC 0.784667 -57 TCACCGACTGCCAGCAGGCGCCGCGCAATGC 8 75 1 CCGCAGGCGC 0.769109 -118 TAGTTGAAGTCCTGCAAGCGCATTGCGCGGC 8 94 0 CCGCAAGCGC 0.968224 -99 ACTTATGTTGGCCACGGCCGCTGTTCGCCTC 8 136 0 GCACGGCCGC 0.946416 -57 AGTCCCGGTGGGCGGAGGTGCG 9 2 0 GGGGAGGTGC 0.944957 -262 CGGGGACATCGGTGCAGTCGGCCGTCCTTGC 9 62 0 GGGCAGTCGG 0.861881 -202 CGAGGTGTCGGCAACGGCCGCCGGGGCCACC 9 94 1 GCACGGCCGC 0.797802 -170 GATGTGTGTCGCTCCGGGCGCAGTGACAGGA 9 141 1 GCCCGGGCGC 0.965598 -123 ACACGGTCGCGCACCGGGTGCGGAACCCAGG 9 188 0 GCCCGGGTGC 0.724433 -76 ATCGTCGGTCGGCGCAGGTCCACCTCTGGCC 9 223 0 GGGCAGGTCC 0.869841 -41 TGAAGAGTCCGGACCGATCGCGAACGCATCG 11 38 0 GGCCGATCGC 0.76461 -221 GGGGCATAATGGAGGAAGCGCCAGTGTTGCG 11 75 1 GGGGAAGCGC 0.97506 -184 CGCCAGTGTTGCGGCGAGCGGAAGCTTTGGT 11 93 1 GCGCGAGCGG 0.983246 -166 CGGAAGCTTTGGTGCGGCCGGCGATCAACTT 11 111 1 GGGCGGCCGG 0.976845 -148 CTGGGAAACCGCTGCGAGCCGAAGTTGATCG 11 132 0 GCGCGAGCCG 0.949352 -127 GGCGGGATGTGCTGTGAGCGCCGCACCACCA 11 162 1 GCGTGAGCGC 0.951604 -97 TAGCGTCGGCGCTGGTGGTGCGGCGCTCACA 11 174 0 GCGGTGGTGC 0.89007 -85 CCACCTCTCCCCCGCAAGCGGGCGGTACCCC 12 38 1 CCGCAAGCGG 0.905181 -91 GCGATGAGGTGGGGGTACCGCCCGCTTGCGG 12 49 0 GGGGTACCGC 0.755364 -80 CCACCTCATCGCTGCGGCCCCCTCGTCGCTT 12 68 1 GCGCGGCCCC 0.953994 -61 TCGCTTCGCGGCTGGGGGTGCCCCCACTGCA 12 93 1 GCGGGGGTGC 0.985075 -36 ** ******** Masking position 10 Map Score: 39.102 Number of sites scoring better than the average of aligned sites = 2855 Number in coding regions = 2642 Number in noncoding regions = 213 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 2 GCTTTGCCATCTGCGGCAAGCGCAGCTTCTC 6 19 0 CTGCGGCAAC 0.949187 -55 TGCCCGGTCTCTCTGGCGAATCGCTGGCAAA 8 18 1 CTCTGGCGAT 0.654831 -175 TCTGGCGAATCGCTGGCAAAGCGTTAGCCTT 8 29 1 CGCTGGCAAG 0.618206 -164 CGAACAGCGGCCGTGGCCAACATAAGTTCAC 8 140 1 CCGTGGCCAC 0.92063 -53 CGCACCTCCGCCCACCGGGACTTGCT 9 6 1 CTCCGCCCAC 0.807092 -258 CCGGGACTTGCTGTTGCAACCAGTCGCCCAA 9 25 1 CTGTTGCAAC 0.442943 -239 GTCGCCCAAACCGTAGCAAGGACGGCCGACT 9 47 1 CCGTAGCAAG 0.837913 -217 GGACGGCCGACTGCACCGATGTCCCCGCCGA 9 66 1 CTGCACCGAG 0.942471 -198 GCACCGATGTCCCCGCCGAGGTGTCGGCAAC 9 78 1 CCCCGCCGAG 0.955276 -186 GCAACGGCCGCCGGGGCCACCAACTCGCCGC 9 104 1 CCGGGGCCAC 0.926296 -160 CACATCCAGGGCGCGGCGAGTTGGTGGCCCC 9 116 0 GCGCGGCGAT 0.702524 -148 GTCACTGCGCCCGGAGCGACACACATCCAGG 9 137 0 CCGGAGCGAA 0.765136 -127 AGAGGTGGACCTGCGCCGACCGACGATCGAT 9 227 1 CTGCGCCGAC 0.977687 -37 CGCAAGCGAACCCGACCGAGTTCGGGTGATC 10 22 1 CCCGACCGAT 0.558001 -30 GGGCGCAGATCCCCCGCGACACGGTTGCGAT 11 11 1 CCCCCGCGAA 0.800255 -248 CCCCGCGACACGGTTGCGATGCGTTCGCGAT 11 22 1 CGGTTGCGAG 0.703265 -237 TGTGAAGAGTCCGGACCGATCGCGAACGCAT 11 40 0 CCGGACCGAC 0.930116 -219 AGCGCCAGTGTTGCGGCGAGCGGAAGCTTTG 11 91 1 TTGCGGCGAC 0.731085 -168 TGATCGCCGGCCGCACCAAAGCTTCCGCTCG 11 107 0 CCGCACCAAG 0.920147 -152 GCCTGGGAAACCGCTGCGAGCCGAAGTTGAT 11 134 0 CCGCTGCGAC 0.97467 -125 GCCGCACCACCAGCGCCGACGCTAAGGATGG 11 181 1 CAGCGCCGAG 0.926776 -78 CGCCACCTCTCCCCCGCAAGCGGGCGGTACC 12 36 1 CCCCCGCAAC 0.873225 -93 GACGAGGGGGCCGCAGCGATGAGGTGGGGGT 12 64 0 CCGCAGCGAG 0.988358 -65 GGGGCACCCCCAGCCGCGAAGCGACGAGGGG 12 86 0 CAGCCGCGAG 0.866564 -43 CGCCGCCGCCGACGATGCAGTGGG 12 115 0 CGCCGCCGAG 0.930999 -14 ********* * Masking position 9 Map Score: 25.8291 Number of sites scoring better than the average of aligned sites = 2570 Number in coding regions = 2370 Number in noncoding regions = 200 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 3 TCAAGCCCCTCCTTTATGCTTTT 6 61 0 AGCCCCTCCT 0.507439 -13 TACCTGGTATGACAGCACCCTTAAGAGCTG 7 52 1 GACAGCACCC 0.676827 -73 TTCTTGTTTCGACTCCGCCTTTTATTATGC 7 93 0 GACTCCGCCT 0.651712 -32 ACTTATGTTGGCCACGGCCGCTGTTCGCCT 8 137 0 GCCACGGCCG 0.911931 -56 CGCACCTCCGCCCACCGGGACTT 9 4 1 ACCTCCGCCC 0.843965 -260 AAGGACGGCCGACTGCACCGATGTCCCCGC 9 64 1 GACTGCACCG 0.909255 -200 CTGCACCGATGTCCCCGCCGAGGTGTCGGC 9 76 1 GTCCCCGCCG 0.981552 -188 GCGAGTTGGTGGCCCCGGCGGCCGTTGCCG 9 102 0 GGCCCCGGCG 0.934583 -162 CACACATCCAGGGCGCGGCGAGTTGGTGGC 9 119 0 GGGCGCGGCG 0.651577 -145 CTGTCACTGCGCCCGGAGCGACACACATCC 9 140 0 GCCCGGAGCG 0.939078 -124 TGGGTTCCGCACCCGGTGCGCGACCGTGTG 9 190 1 ACCCGGTGCG 0.688798 -74 CCAGAGGTGGACCTGCGCCGACCGACGATC 9 225 1 ACCTGCGCCG 0.961144 -39 AGCGCAAGCGAACCCGACCGAGTTCGGGTG 10 20 1 AACCCGACCG 0.817094 -32 GTCGCGGGGGATCTGCGCCC 11 1 0 ATCTGCGCCC 0.622407 -258 AATGTGAAGAGTCCGGACCGATCGCGAACG 11 43 0 GTCCGGACCG 0.905623 -216 GTTGATCGCCGGCCGCACCAAAGCTTCCGC 11 110 0 GGCCGCACCA 0.772574 -149 CCGCCTGGGAAACCGCTGCGAGCCGAAGTT 11 137 0 AACCGCTGCG 0.72295 -122 GGGATGTGCTGTGAGCGCCGCACCACCAGC 11 165 1 GTGAGCGCCG 0.535866 -94 GCGCCGCACCACCAGCGCCGACGCTAAGGA 11 179 1 ACCAGCGCCG 0.952591 -80 AGCGGGCGGTACCCCCACCTCATCGCTGCG 12 54 1 ACCCCCACCT 0.866205 -75 GCGACGAGGGGGCCGCAGCGATGAGGTGGG 12 67 0 GGCCGCAGCG 0.930221 -62 CAGTGGGGGCACCCCCAGCCGCGAAGCGAC 12 92 0 ACCCCCAGCC 0.845687 -37 GGCTGGGGGTGCCCCCACTGCATCGTCGGC 12 102 1 GCCCCCACTG 0.800846 -27 CGCCGCCGCCGACGATGCAGT 12 118 0 GCCGCCGCCG 0.945201 -11 ********** Masking position 9 Map Score: 24.5977 Number of sites scoring better than the average of aligned sites = 3402 Number in coding regions = 3144 Number in noncoding regions = 258 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 4 AAAAAAGACCGGATATCACCCGGCCTTTGACA 1 44 0 GGTTCACCCG 0.905657 -188 TTATATTTTAGCCGATCCCCAGTTTGCCAAAA 2 180 0 GCGTCCCCAG 0.981906 -121 TTTTTCATTTCCCCCTTAGTTTTTGC 4 14 0 TCTTCCCCCT 0.78543 -16 CGCGCGTTGCCCGGTCTCTCTGG 8 2 1 GCCTTGCCCG 0.971366 -191 CGCTTTGCCAGCGATTCGCCAGAGAGACCGGG 8 20 0 GCATCGCCAG 0.858359 -173 AGTCCTGCAAGCGCATTGCGCGGCGCCTGCTG 8 86 0 GCCTTGCGCG 0.753728 -107 GACCAGCCATTCGTTTTGCCCGAATGGTGAAC 8 165 0 TCTTTGCCCG 0.872523 -28 ACCTATCCTGTCACTGCGCCCGGAGCGACACA 9 145 0 TCCGCGCCCG 0.791682 -119 TCCACCTCTGGCCTATCACACGGTCGCGCACC 9 204 0 GCTTCACACG 0.791068 -60 GTCGGTCGGCGCAGGTCCACCTCTGGCCTATC 9 219 0 GCGTCCACCT 0.650446 -45 ACCCTCGCGGATCACCCGAACTCGGTCG 10 34 0 GCGTCACCCG 0.990055 -18 GGGCGCAGATCCCCCGCGACACGGTT 11 5 1 GCGTCCCCCG 0.997174 -254 TCGGCTCGCAGCGGTTTCCCAGGCGGGATGTG 11 141 1 GCGTTCCCAG 0.921631 -118 TGATCACGCCACCTCTCCCCCGCAAGCGGGCG 12 30 1 ACTTCCCCCG 0.935566 -99 GATGAGGTGGGGGTACCGCCCGCTTGCGGGGG 12 46 0 GGTCCGCCCG 0.887174 -83 CCTCATCGCTGCGGCCCCCTCGTCGCTTCGCG 12 71 1 GCGCCCCTCG 0.852198 -58 ** * ******* Masking position 9 Map Score: 12.9086 Number of sites scoring better than the average of aligned sites = 1103 Number in coding regions = 1021 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 5 ATTTCGAAGTTGTAAAAAACTAATACAACACCGCT 2 104 0 TTAAAAAAAA 0.854718 -197 TAAGTTTGTATGTATAAAAGGAATGCACGTCTAAT 2 243 1 TTTAAAAAAG 0.939062 -58 GTCTAATGACTGTTTAAAAGAAAGGAAGAGGTGAC 2 271 1 TTTAAAAAAG 0.939061 -30 CTCGCAAAAACTAAGGGGGAAATGAA 4 2 1 TGAAAAAAAG 0.960366 -28 ATTTAATCATTCGAAAAAACAAACGCCAAAAAGCA 5 23 0 TGAAAAAAAG 0.960366 -205 AAAAAACCTTTATAAAAAACAAAAAATTTAATCAT 5 48 0 TTAAAAAAAA 0.854718 -180 TTTACTATTTTGTGAACAATCAAGGTAGAATCAAA 5 80 1 TTAACAAAAG 0.936034 -148 GTGTCAAAATTATGTAATAAAAACGCTTCCAACGA 5 135 0 TTTAATAAAG 0.684376 -93 TCCTTTATGCTTTTAAAAATGAATGGCTTTGCCAT 6 40 0 TTAAAAAAAG 0.971454 -34 AAAGGCGGAGTCGAAACAAGAAAGGTGGTAACAG 7 101 1 TGAACAAAAG 0.912427 -24 * * ***** ** * Masking position 9 Map Score: 7.83356 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 195 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 6 TCTCGTTTTGTCTCAAACTGATTCATTTGT 1 95 0 TCTCAAACTG 0.927305 -137 GAGACACACGTCTCAAACTGTCTCCAAAGT 1 121 1 TCTCAAACTG 0.927305 -111 TAAAAGGTTTTGGCAAACTGGGGATCGGCT 2 173 1 TGGCAAACTG 0.950191 -128 ATCGTAAGCATTGAAAACAGATATATAATA 3 52 0 TTGAAAACAG 0.693285 -63 TAGAATCAAATTGCAAACAGTGGTAAAATA 5 105 1 TTGCAAACAG 0.962786 -123 TGCAGAATAAACGCAAACATCTGCACGAAT 7 13 1 ACGCAAACAT 0.723634 -112 AGAAGAATCGAGGCGAACAGCGGCCGTGGC 8 127 1 AGGCGAACAG 0.844665 -66 GGACTTGCTGTTGCAACCAGTCGCCCAAAC 9 28 1 TTGCAACCAG 0.858052 -236 AACTCAAACAGCGCAAGCGAA 10 2 1 ACTCAAACAG 0.89425 -50 CGCGTTGTGATCGCGAGCTGAGGAGACGGT 11 239 1 TCGCGAGCTG 0.819554 -20 ********** Masking position 6 Map Score: 4.16 Number of sites scoring better than the average of aligned sites = 651 Number in coding regions = 605 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 7 CGATCATTGTCAAAGGCCGGGTGATATCCG 1 37 1 CAAAGGCCGG 0.945766 -195 GCATGCAAAAAAAAGACCGGATATCACCCG 1 54 0 AAAAGACCGG 0.978616 -178 TTACGGGCTCAAAAGACTGGCACACTTCTT 1 170 1 AAAAGACTGG 0.956819 -62 ATGACTGTTTAAAAGAAAGGAAGAGGTGAC 2 276 1 AAAAGAAAGG 0.752784 -25 ATGCTTTTAAAAATGAATGGCTTTGCCATC 6 39 0 AAATGAATGG 0.695938 -35 CGATTCGCCAGAGAGACCGGGCAACGCGCG 8 11 0 GAGAGACCGG 0.962123 -182 CGGGCAAAACGAATGGCTGGTCGAAGAG 8 175 1 GAATGGCTGG 0.815807 -18 GCTCCGGGCGCAGTGACAGGATAGGTTTCG 9 151 1 CAGTGACAGG 0.818262 -113 CCCAAATGTGAAGAGTCCGGACCGATCGCG 11 47 0 AAGAGTCCGG 0.886837 -212 ********** Masking position 2 Map Score: 3.5911 Number of sites scoring better than the average of aligned sites = 610 Number in coding regions = 518 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 8 ATCTTCCCTCTCGATTATGCAGTTTGA 3 8 0 TCGATTATGC 0.97721 -107 ACCTCCTAGTTTGATTAAGCAATTTTAAAG 3 87 0 TTGATTAAGC 0.828897 -28 TGTTTGCAATTTGATTCTACCTTGATTGTT 5 94 0 TTGATTCTAC 0.774617 -134 TCAAGCCCCTCCTTTATGCTTTTAAAAAT 6 55 0 TCCTTTATGC 0.800647 -19 GATGTTTGCGTTTATTCTGCAAA 7 4 0 TTTATTCTGC 0.899531 -121 GACTCCGCCTTTTATTATGCAAGTTCCATG 7 83 0 TTTATTATGC 0.901326 -42 GCTGTTCGCCTCGATTCTTCTGCTAGTTGA 8 118 0 TCGATTCTTC 0.844996 -75 TGGCGCTTCCTCCATTATGCCCCCAAATGT 11 68 0 TCCATTATGC 0.957285 -191 ********** Masking position 5 Map Score: 2.10988 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 294 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 9 CTACATAAAAGGTTTTGGCAAACTGGGGAT 2 168 1 GGTTTTGGCA 0.820874 -133 TCTGCACGAATGTTTCGGTATACCTGGTAT 7 32 1 TGTTTCGGTA 0.788794 -93 CCACCTTTCTTGTTTCGACTCCGCCTTTTA 7 99 0 TGTTTCGACT 0.531133 -26 TTGGGCGACTGGTTGCAACAGCAAGTCCCG 9 26 0 GGTTGCAACA 0.641337 -238 TCCTTGCTACGGTTTGGGCGACTGGTTGCA 9 39 0 GGTTTGGGCG 0.943739 -225 TCCCCGCCGAGGTGTCGGCAACGGCCGCCG 9 87 1 GGTGTCGGCA 0.967022 -177 TGACAGGATAGGTTTCGACATCCACCTGGG 9 164 1 GGTTTCGACA 0.944171 -100 CCCGCGACACGGTTGCGATGCGTTCGCGAT 11 23 1 GGTTGCGATG 0.889157 -236 GAAGCGCCAGTGTTGCGGCGAGCGGAAGCT 11 89 1 TGTTGCGGCG 0.972943 -170 TCGGCGCTGGTGGTGCGGCGCTCACAGCAC 11 170 0 TGGTGCGGCG 0.872485 -89 GCAGCGATGAGGTGGGGGTACCGCCCGCTT 12 53 0 GGTGGGGGTA 0.711733 -76 CTGCATCGTCGGCGGCGGCG 12 119 1 GGCGGCGGCG 0.922238 -10 ********** Masking position 2 Map Score: 7.1148 Number of sites scoring better than the average of aligned sites = 1247 Number in coding regions = 1166 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 10 ********** No masking Map Score: 5.07571e-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 11 ********** No masking Map Score: 5.07571e-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: 5.07571e-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