AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i220_Ribosomal_Operon_7_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -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 yqeU 22 similar to hypothetical proteins #2 yqeT 24 similar to ribosomal protein L11 methyltransferase #3 dnaJ 199 heat-shock protein #4 dnaK 23 class I heat-shock protein (chaperonin) #5 grpE 71 heat-shock protein #6 hrcA 119 transcriptional regulator #7 hemN 52 coproporphyrinogen III oxidase #8 lepA 133 GTP-binding protein #9 spoIIP 62 spoIIP #10 gpr 203 spore protease Motif number 1 TTCAATGATTAGAAAGTCAAAGTCAGGCAT 3 73 1 AGAAAGTCAA 0.945891 -127 CGGGCAAGAAAAAAAGTCAAAGCCAAGAGA 3 102 0 AAAAAGTCAA 0.72923 -98 CCGGGATAAAAGGAATTGAAAAATCATAAT 3 129 1 AGGAATTGAA 0.863351 -71 GAGAAATTCGGGAGAGTGAAGCGAG 3 185 1 GGAGAGTGAA 0.92887 -15 CCCTCAAAGTGTAAGGAGAAGGACAGGTGC 5 41 0 GTAAGGAGAA 0.848309 -31 TACACTTTGAGGGAGGTGAACACA 5 58 1 GGGAGGTGAA 0.980104 -14 CTTTCTGTAAAGAAGGTGAATCCG 7 39 1 AGAAGGTGAA 0.989498 -14 GTACGTGAAAGAGAAAAGCAACCCA 8 6 1 TGAAAGAGAA 0.913708 -128 ATGTAAAACAAGAAAGAGAAAAGTTCCCTA 8 43 0 AGAAAGAGAA 0.983357 -91 ACAAGCTAGAGGAAGTAGAACTGT 9 5 0 GGAAGTAGAA 0.898924 -58 GTTGTATCTTAGGAGGTGAAACAC 10 5 0 AGGAGGTGAA 0.98137 -199 AAATCATGCTAAAAAGAGAACCTTCAATGA 10 134 0 AAAAAGAGAA 0.901017 -70 ********** Masking position 9 Map Score: 15.7276 Number of sites scoring better than the average of aligned sites = 1205 Number in coding regions = 980 Number in noncoding regions = 225 Number of orfs with sites within 600 bp upstream = 249 Fraction of orfs with sites within 600 bp upstream = 0.0399936 Motif number 2 CAGTTAGTAGGTGTCACAGCGT 1 2 1 ATTAGAGGTG 0.884447 -21 TTATTGGATGAGGAGTTGGTAG 2 1 1 TATTGATGAG 0.966186 -24 GTTCTTTTTAGTGTCAGCCCCGCTTCC 3 6 1 TTTAGGTCAG 0.804549 -194 GACTTTCTAATCATTGAATCAGATTATGAAAT 3 59 0 TATTGATCAG 0.899446 -141 CACATAAATTAGATTGTATCATTTTGAATTAT 3 154 0 AATTGATCAT 0.480502 -46 TTACATAGCAGGAGGTTATTCAA 4 3 1 AATAGAGGAG 0.963172 -21 TTCTCCTTACACTTTGAGGGAGGTGAACACA 5 51 1 ATTTGGGGAG 0.923286 -21 TTTGGCGCTTTTTTTGGGTGAGTTATAATTGA 6 22 1 TTTTGGTGAG 0.929324 -98 GATACTTTTGTTATAGAATTAGCACTCGCTTA 6 71 1 TATAGATTAG 0.692439 -49 ATTTTGCGTTTAATAGTAGGAGTGATAGATT 8 113 1 TATAGAGGAG 0.978657 -21 ACAGGTTGTATCTTAGGAGGTGAAACAC 10 7 0 TTTAGAGGTG 0.930651 -197 AAAGTATTTTTCATTGAAGGTTCTCTTTTTAG 10 124 1 TATTGAGGTT 0.708707 -80 AAGGTTCTCTTTTTAGCATGATTTATTCAGCA 10 140 1 TTTAGATGAT 0.838194 -64 ATAGGTACTTAATGTGAAGGAGGCCCCTGT 10 184 1 ATGTGAGGAG 0.792319 -20 * **** ***** Masking position 6 Map Score: 10.7125 Number of sites scoring better than the average of aligned sites = 1335 Number in coding regions = 1108 Number in noncoding regions = 227 Number of orfs with sites within 600 bp upstream = 245 Fraction of orfs with sites within 600 bp upstream = 0.0393511 Motif number 3 TCTTTTTAGTGTCAGCCCCGCTTCCGGAGCTG 3 13 1 GTCGCCCCCT 0.984206 -187 GTTCTTTTCGGTCAGCTCCGGAAGCGGGGCTG 3 25 0 GTCGCTCCGA 0.927895 -175 TTTATCGAAGGGCAGCACCTGTCCTTCTCCTT 5 27 1 GGCGCACCGT 0.993561 -45 AAGCCGCCGCAGTCTTGTACTGC 7 2 1 AGCGCCGCGT 0.99302 -51 CTTTACAGAAAGAAGCCGCAGTACAAGACTGC 7 19 0 AGAGCCGCGT 0.979623 -34 TTAATGTGAAGGAGGCCCCTGT 10 192 1 GGAGCCCCGT 0.996262 -12 *** ***** ** Masking position 6 Map Score: 4.01445 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 247 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 GCGGGGCTGACACTAAAAAGAAC 3 4 0 CACTAAAAAG 0.784578 -196 TTATCCCGGGCAAGAAAAAAAGTCAAAGCC 3 108 0 CAAGAAAAAA 0.940034 -92 TATCAAACCACAAGAAAAATGTCAATTATA 6 45 0 CAAGAAAAAT 0.893638 -75 CAATGTAAAACAAGAAAGAGAAAAGTTCCC 8 45 0 CAAGAAAGAG 0.914467 -89 TGTAAAGATTCAATGTAAAACAAGAAAGAG 8 55 0 CAATGTAAAA 0.868677 -79 ACTCTATGAACAAGCTAGAGGAAGTAGAAC 9 14 0 CAAGCTAGAG 0.912888 -49 ATTTATATTGCAATCTAAAGGTGTGTTTGA 10 92 0 CAATCTAAAG 0.938582 -112 CTTTAGATTGCAATATAAATGTAAAGTATT 10 102 1 CAATATAAAT 0.840473 -102 AGAGAACCTTCAATGAAAAATACTTTACAT 10 120 0 CAATGAAAAA 0.868677 -84 CTGAATAAATCATGCTAAAAAGAGAACCTT 10 140 0 CATGCTAAAA 0.707793 -64 ********** Masking position 7 Map Score: 5.79489 Number of sites scoring better than the average of aligned sites = 1039 Number in coding regions = 840 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 200 Fraction of orfs with sites within 600 bp upstream = 0.0321234 Motif number 5 CGGATTCACCTTCTTTACAGAAAGAAGCC 7 34 0 CTTCTTTACA 0.984461 -19 TTTTACATTGAATCTTTACAATCCTATTGA 8 65 1 AATCTTTACA 0.919832 -69 AAGGTTAAATCTTCTTCACAATAGAACAAA 10 52 1 CTTCTTCACA 0.981317 -152 CTATCAAACACACCTTTAGATTGCAATATA 10 89 1 CACCTTTAGA 0.89367 -115 TCAATGAAAAATACTTTACATTTATATTGC 10 111 0 ATACTTTACA 0.894432 -93 ACAGGGGCCTCCTTCACATTAAGTACCT 10 186 0 CTCCTTCACA 0.982669 -18 ********** Masking position 5 Map Score: 4.4602 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 164 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 6 CTTTTTTTGGGTGAGTTATAATTGACATTTT 6 29 1 GGAGTTATAA 0.965901 -91 CTCTCAATAAGCGAGTGCTAATTCTATAACA 6 79 0 GGAGTGCTAA 0.994288 -41 CTCGCTTATTGAGAGTGCTAACAGAGGTGAT 6 95 1 GGAGTGCTAA 0.994288 -25 GTTTAATAGTAGGAGTGATAGATT 8 120 1 AGAGTGATAG 0.943232 -14 * ********* Masking position 6 Map Score: 0.505256 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 7 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 ********** No masking Map Score: -2.7468e-13 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 8 ********** No masking Map Score: -2.7468e-13 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 9 ********** No masking Map Score: -2.7468e-13 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