AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -ipdhR_bsub_opreg_300.orf -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 yfjN 300 similar to hypothetical proteins #2 yfjM 195 yfjM #3 yfjL 29 alternate gene name: yztA #4 acoA 231 acetoin dehydrogenase E1 component (TPP-dependent alpha subunit) #5 pdhA 300 pyruvate dehydrogenase (E1 alpha subunit) #6 pdhC 114 pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) #7 bfmBB 22 branched-chain alpha-keto acid dehydrogenase E2 subunit (lipoamide acyltransferase) #8 bfmBAA 73 branched-chain alpha-keto acid dehydrogenase E1 (2-oxoisovalerate dehydrogenase alpha subunit) #9 yqiS 124 similar to phosphate butyryltransferase #10 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) Motif number 1 CAAAAAGTTCAAAAGCAAGGCCACTAAGAA 1 87 1 AAAAGCAAGG 0.969875 -214 TAAGTGTAAAAGAAGCATGGTCAGTTTTTA 1 228 1 AGAAGCATGG 0.885894 -73 AAAGGCTAACAAAATAAAGGGATTTTTACA 2 30 1 AAAATAAAGG 0.968347 -166 GGATTTACCGAAAATCCAGGTTTATTTTAG 2 70 0 AAAATCCAGG 0.892829 -126 CTGCGTACAAAAAAGACCCGGATTTACCGA 2 89 0 AAAAGACCCG 0.892809 -107 TAAATTAGAGAAAAGACAGGCTGAGTAAAA 2 120 0 AAAAGACAGG 0.985135 -76 TTATTGTAAGAAAATAATGGTATATTTAGT 2 147 1 AAAATAATGG 0.945796 -49 ACATATGAGGAAAAGAGTGGGAAC 3 16 1 AAAAGAGTGG 0.896555 -14 GCATGCAAAAAAAAGACCGGATATCACCCG 4 54 0 AAAAGACCGG 0.973719 -178 TTACGGGCTCAAAAGACTGGCACACTTCTT 4 170 1 AAAAGACTGG 0.974227 -62 CACCAAATAAAGAAGAACCGTCAATCGTTT 5 57 0 AGAAGAACCG 0.824671 -244 ATGACTGTTTAAAAGAAAGGAAGAGGTGAC 5 276 1 AAAAGAAAGG 0.988829 -25 ATGCTTTTAAAAATGAATGGCTTTGCCATC 8 39 0 AAATGAATGG 0.802176 -35 TTTGCAGAATAAACGCAAACATCTG 9 6 1 AGAATAAACG 0.744104 -119 CGGAGTCGAAACAAGAAAGGTGGTAACAG 9 106 1 ACAAGAAAGG 0.962538 -19 AGGAAATGAAAAGATAAAGGGGTTTTCTGA 10 13 0 AAGATAAAGG 0.784568 -140 TTTCCGCTGGACAATAAAGGAAATGAAAAG 10 30 0 ACAATAAAGG 0.898786 -123 ********** Masking position 1 Map Score: 25.0039 Number of sites scoring better than the average of aligned sites = 1205 Number in coding regions = 925 Number in noncoding regions = 280 Number of orfs with sites within 600 bp upstream = 287 Fraction of orfs with sites within 600 bp upstream = 0.046097 Motif number 2 AGTTCAAAAGCAAGGCCACTAAGAAAGACGAAGGTCA 1 92 1 CACCCTAAAG 0.972533 -209 AACAAAAATCAAATCCTTTCATTATGGGATACGGCT 1 275 0 CACCTTAATG 0.990845 -26 GAATTGTGTAAAAATCCCTTTATTTTGTTAGCCTTTT 2 29 0 AACCTTATTG 0.819992 -167 TTTCCTCTCCCCCTTTATATGATATCTCCAC 2 175 0 CCCCCTTATG 0.973032 -21 CCGGATATCACCCGGCCTTTGACAATGATCGACGTAT 4 31 0 CCCCTTAATG 0.991015 -201 TTTGTGCGCCTCCTTCTATTTAGGGTTCACCAT 4 209 0 CCCCTCATAG 0.919498 -23 AAAACTAATACAACACCGCTTAACATGGATTAGTTTA 5 87 0 CACCCTAATG 0.991014 -214 CCCAGTTTGCCAAAACCTTTTATGTAGGATAGTTACA 5 158 0 CACCTTATAG 0.956903 -143 AGTTCTCGACCTCCTAGTTTGATTAAGCAAT 6 94 0 CCCCCCATTG 0.973157 -21 CCGCAGATGGCAAAGCCATTCATTTTTAAAAGCATAA 8 34 1 CACCTTATTT 0.819991 -40 TCAAGCCCCTCCTTTATGCTTTTAAAAA 8 56 0 CACCTCTATG 0.946068 -18 CTTGTTTCGACTCCGCCTTTTATTATGCAAGTTCCAT 9 84 0 CCCCTTAATG 0.991015 -41 CCCGATACCCCTTTGTATGAAAAAATTTG 10 134 0 CACCCTTATG 0.972534 -19 * * ** ** * *** Masking position 7 Map Score: 19.0873 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 358 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 3 TACCAACGCAAAATAATTGCCCTGTTA 1 8 0 AAATAATTGC 0.649041 -293 AAAAAGTTCAAAAGCAAGGCCACTAAGAAA 1 88 1 AAAGCAAGGC 0.943679 -213 TATAGATTGATAAGAAATGCTTTCGCATGC 1 196 1 TAAGAAATGC 0.554019 -105 CGTATCCCATAATGAAAGGATTTGATTTTT 1 278 1 AATGAAAGGA 0.578874 -23 TTTTTTGAATCAAGCACTGCTG 2 3 0 CAAGCACTGC 0.575089 -193 GTGCTTGATTCAAAAAAGGCTAACAAAATA 2 16 1 CAAAAAAGGC 0.682004 -180 AAGGCTAACAAAATAAAGGGATTTTTACAC 2 31 1 AAATAAAGGG 0.637453 -165 TTATTTTAGTCAAGAATTGTGTAAAAATCC 2 49 0 CAAGAATTGT 0.700545 -147 GATTTACCGAAAATCCAGGTTTATTTTAGT 2 69 0 AAATCCAGGT 0.590261 -127 GATTTTCGGTAAATCCGGGTCTTTTTTGTA 2 84 1 AAATCCGGGT 0.294855 -112 AAATTAGAGAAAAGACAGGCTGAGTAAAAG 2 119 0 AAAGACAGGC 0.954032 -77 TATTGTAAGAAAATAATGGTATATTTAGTG 2 148 1 AAATAATGGT 0.740631 -48 CATGCAAAAAAAAGACCGGATATCACCCGG 4 53 0 AAAGACCGGA 0.63392 -179 TACGGGCTCAAAAGACTGGCACACTTCTTG 4 171 1 AAAGACTGGC 0.899523 -61 ATTATAAATGCAAGAAGTGTGCCAGTCTTT 4 181 0 CAAGAAGTGT 0.611531 -51 CGCTGATTTTCAATAAATGTATTCGCTTTA 5 23 0 CAATAAATGT 0.648158 -278 TGTATGTATAAAAGGAATGCACGTCTAATG 5 249 1 AAAGGAATGC 0.600401 -52 TGACTGTTTAAAAGAAAGGAAGAGGTGACT 5 277 1 AAAGAAAGGA 0.91994 -24 TGCTTTTAAAAATGAATGGCTTTGCCATCT 8 38 0 AATGAATGGC 0.6735 -36 GGAGTCGAAACAAGAAAGGTGGTAACAG 9 107 1 CAAGAAAGGT 0.944985 -18 TTCCGCTGGACAATAAAGGAAATGAAAAGA 10 29 0 CAATAAAGGA 0.774778 -124 ********** Masking position 2 Map Score: 8.39197 Number of sites scoring better than the average of aligned sites = 3338 Number in coding regions = 2845 Number in noncoding regions = 493 Number of orfs with sites within 600 bp upstream = 462 Fraction of orfs with sites within 600 bp upstream = 0.0742049 Motif number 4 AGGTTGGAATCCTTTTTATCCAAAAAGTTC 1 67 1 CCTTTTTATC 0.817741 -234 CGCTGACCTTCGTCTTTCTTAGTGGCCTTG 1 102 0 CGTCTTTCTT 0.918616 -199 GATTATCTACCCTATTTTTTATATTCTGGT 1 139 0 CCTATTTTTT 0.546197 -162 CAATGATCGACGTATTTATTTCCTTGGAAA 4 16 0 CGTATTTATT 0.825107 -216 TCAGTCTTCTCATCTTCACTTTGGAGACAG 4 138 0 CATCTTCACT 0.815763 -94 ATTCGCTTTACATTTTCATCAA 5 3 0 CATTTTCATC 0.801535 -298 AACCGTCAATCGTTTTCATCGCTGATTTTC 5 42 0 CGTTTTCATC 0.911755 -259 ATTGACGGTTCTTCTTTATTTGGTGTAAAC 5 62 1 CTTCTTTATT 0.651224 -239 ACTAAGTCACCTCTTCCTTTCTTTTAAAC 5 282 0 CCTCTTCCTT 0.944263 -19 GGAAAACGTTCATCTTCCCTCTCGATTATG 6 19 0 CATCTTCCCT 0.805481 -96 GGAAGATGAACGTTTTCCCTCTATTATATA 6 31 1 CGTTTTCCCT 0.86916 -84 TATGTTACCACGTTTTCTTCTCTTGACAAA 10 66 0 CGTTTTCTTC 0.765533 -87 AATTTGCACACCTATTTATTCCGTTGCAAT 10 110 0 CCTATTTATT 0.792047 -43 ********** Masking position 5 Map Score: 4.27678 Number of sites scoring better than the average of aligned sites = 1934 Number in coding regions = 1648 Number in noncoding regions = 286 Number of orfs with sites within 600 bp upstream = 288 Fraction of orfs with sites within 600 bp upstream = 0.0462576 Motif number 5 AGGATTCCAACCTAAATAGAATATCATATGA 1 49 0 CCTAAATAAA 0.974621 -252 CGCCAGTTAACCAGAATATAAAAAATAGGGT 1 130 1 CCAGAATAAA 0.910716 -171 AACCTTTATCCCAAATTAAAAACTGACCATG 1 243 0 CCAAATTAAA 0.87313 -58 CAATTCTTGACTAAAATAAACCTGGATTTTC 2 60 1 CTAAAATAAC 0.832605 -136 TGATATCTCCACTAAATATACCATTATTTTC 2 156 0 ACTAAATAAC 0.708322 -40 AATGGTGAACCCTAAATAGAAGGAGGCGCAC 4 208 1 CCTAAATAAA 0.974621 -24 GTGTAACTATCCTACATAAAAGGTTTTGGCA 5 157 1 CCTACATAAA 0.910716 -144 TGGGGATCGGCTAAAATATAATACGACTTAC 5 191 1 CTAAAATAAA 0.897787 -110 ******** ** Masking position 8 Map Score: 2.91552 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 174 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 6 GGTCTTTTTTGTACGCAGCTTTTACTCAGCC 2 101 1 GTACGCAGTT 0.922705 -95 TCCCTCTCGATTATGCAGTTTGA 6 3 0 TTATGCAGTT 0.969664 -112 CCTAGTTTGATTAAGCAATTTTAAAGTTTAC 6 82 0 TTAAGCAATT 0.921376 -33 CCGCCTTTTATTATGCAAGTTCCATGCCAGC 9 78 0 TTATGCAATT 0.974719 -47 TAACATAGGGTTGTGCAAATTATTGCAACGG 10 89 1 TTGTGCAATT 0.969664 -64 GAATAAATAGGTGTGCAAATTTTTTCATACA 10 119 1 GTGTGCAATT 0.963636 -34 ******** ** Masking position 7 Map Score: 2.18752 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 67 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 TTTGGATAAAAAGGATTCCAACCTAAATAGAATATC 1 55 0 AAATTCACAA 0.970786 -246 TAGGGTAGATAATCATCCCACGTGAAATCTTCAAAA 1 155 1 AAATCCATAA 0.911738 -146 CTTCTTTTACACTTATCGCATGCGAAAGCATTTCTT 1 207 0 ACATCCACAA 0.791453 -94 AAAGATTTCCAAGGAAATAAATACGTC 4 2 1 AATTTCAGAA 0.945745 -230 ATTTGGTGTAAACTAATCCATGTTAAGCGGTGTTGT 5 79 1 AAAATCATAA 0.86976 -222 TACAACTTCGAAATAATACAGTTCAAAGCAGAGTGT 5 125 1 AAAATCATAA 0.86976 -176 AAGCAATTTTAAAGTTTACATCGTAAGCATTGAAAA 6 65 0 AATTTCAGAA 0.945745 -50 GGGTTGTGCAAATTATTGCAACGGAATAAATAGGTG 10 96 1 AAATTCAGAA 0.970786 -57 TAGGTGTGCAAATTTTTTCATACAAAGGGGTATCGG 10 126 1 AATTTCACAA 0.945745 -27 ** *** ** * ** Masking position 10 Map Score: 1.9473 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 136 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 8 ACAAATGAATCAGTTTGAGACAAAACGAGA 4 95 1 CAGTTTGAGA 0.988601 -137 ACTTTGGAGACAGTTTGAGACGTGTGTCTC 4 121 0 CAGTTTGAGA 0.988601 -111 AGCCGATCCCCAGTTTGCCAAAACCTTTTA 5 173 0 CAGTTTGCCA 0.949945 -128 AGCAATTGGAGAAGCTGCGCTT 8 3 1 CAATTGGAGA 0.927561 -71 ********** Masking position 5 Map Score: 0.518415 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 18 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 ********** No masking Map Score: -2.86816e-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 ********** No masking Map Score: -2.86816e-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: -2.86816e-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