AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -igalR_tpal_opreg_300.orf -g0.528 -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 = 0.528 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 TP0074 300 sugar ABC transporter, periplasmic binding protein (y4oP) #2 TP0075 118 sugar ABC transporter, permease protein (y4oQ) #3 TP0076 39 sugar ABC transporter, permease protein (y4oR) #4 TP0077 40 capsular polysaccharide biosynthesis protein (cap5D) #5 TP0418 26 galactokinase #6 TP0545 84 methylgalactoside ABC transporter, periplasmic galactose-binding protein (mglB-1) #7 TP0547 143 penicillin tolerance protein (lytB) #8 TP0683 92 octaprenyl-diphosphate synthase #9 TP0684 292 methylgalactoside ABC transporter, periplasmic galactose-binding protein (mglB-2) #10 TP0685 119 methylgalactoside ABC transporter, ATP binding protein (mglA) Motif number 1 CCAGAATGCAAACGCGTGTGGGTGCGGTGTAT 1 20 1 ACGCGTGGGG 0.972336 -281 TGGGGTGCGATGCGCGCGGTGGATACGCTCCT 1 158 1 TCGCGCGTGG 0.986427 -143 GGACTGCGTAGGGGCGTGCGTCGATTGGTGTG 1 217 1 GGGCGTGGTC 0.87235 -84 CGTGCGTCGATTGGTGTGGTGCTATGTGTCGT 1 231 1 TGGTGTGTGC 0.716762 -70 GTGGTGCTATGTGTCGTGCTGGTTTGATGTAT 1 246 1 GGTCGTGTGG 0.921526 -55 TATCAGGACTGGGGTGTGAGGGGAAAAACGGA 1 275 1 GGGTGTGGGG 0.988134 -26 TTCTATCTGTGGAGCGCGTTACGTTGGGTAGC 2 81 1 GAGCGCGTAC 0.771378 -38 GTTACGTTGGGTAGCGTAAGAGGGGGAGTGC 2 98 1 GAGCGTAGAG 0.544492 -21 GGGTTGCGTACGGGTTAGATAAGA 3 3 1 GTGCGTAGGG 0.854043 -37 GGATAAACACTCTGCGCGGGTGAGTACGTGCA 4 13 1 TTGCGCGGTG 0.802862 -28 TTTCTATATTCCTCGCGCGGGTATCAGGGTG 6 10 1 TCTCGCGGGG 0.876808 -75 CGCGGGTATCAGGGTGTGAGGGGAAAGAAGTG 6 26 1 AGGTGTGGGG 0.898016 -59 ATGCAAGGGCGCGGCGTGGTGGTGAGTTCTTC 7 56 0 GGGCGTGTGG 0.993796 -88 TTTGGTACACTCGGCGCGCCAGTTTTCTTCCG 7 100 1 TGGCGCGCAG 0.924622 -44 CATAGCATGGGGGGCGTGTAGGAAGGT 8 6 0 GGGCGTGAGG 0.95356 -87 GTGCGAGCACGATGTGTGGGAGCTGTCAGTGT 8 42 0 GTGTGTGGAG 0.827308 -51 GTACCGTTATACGGCGTGTTTGCCTTTTGTGC 8 70 0 AGGCGTGTTG 0.643608 -23 GTCCGTTTCTGTCGCACGGGGTCACCTTTTGT 9 42 0 GCGCACGGGT 0.866613 -251 AAACGGACTGGAGGCACGGCACGACAAGTCGC 9 66 1 GGGCACGCAC 0.541936 -227 CAAACTTCTTTGCGCGTGTCGCGTCTTTCTCA 9 111 0 TCGCGTGCGC 0.89259 -182 TAGTTACAATGGGGCACGCTGTTTCGTGCGAC 9 159 1 GGGCACGTGT 0.777442 -134 GGCACGCTGTTTCGTGCGACGGCGTCAAAAGT 9 171 1 TCGTGCGCGG 0.931892 -122 GGCGTCAAAAGTTTCGCGCGGGCTAAAGTGGG 9 191 1 GTTCGCGGGG 0.894968 -102 AAGTGGGTTGGTCGCGTGTGGGTGCAGCGCGC 9 216 1 GCGCGTGGGG 0.996791 -77 GCGTGTGGGTGCAGCGCGCTGTACTTGTCGCG 9 229 1 GAGCGCGTGT 0.578779 -64 CGCTGTACTTGTCGCGCGTTATTTCGTGCATT 9 245 1 GCGCGCGTAT 0.916238 -48 GCCGGGTTTGGACGTGCGTTGGGTAGCTGCTG 10 14 1 GCGTGCGTGG 0.984323 -106 CAACGAACAGGACGTGCACCAGGAACAGCAGC 10 39 0 GCGTGCACAG 0.503961 -81 GCGCGCGAAAGCGGTGCGAGGTCGGTAGACCC 10 79 0 GGGTGCGGGT 0.930634 -41 TCGCACCGCTTTCGCGCGCGAGAGGAGTGATA 10 92 1 TCGCGCGGAG 0.963015 -28 * ****** *** Masking position 6 Map Score: 48.9871 Number of sites scoring better than the average of aligned sites = 4074 Number in coding regions = 3727 Number in noncoding regions = 347 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 2 TCGTACGCTTTTCTCCCCGTTGTCAACAAAG 1 54 0 TCTCCCCGTT 0.954145 -247 CGTACGAGAATCTGCCCCGTTAGGTTGAAGG 1 78 1 TTGCCCCGTT 0.709343 -223 ACGTACAGTTTGCTCCCCCTTCAACCTAACG 1 95 0 TCTCCCCCTT 0.982726 -206 GCGGTGGATACGCTCCTTCTCGACTGAGGTC 1 173 1 CCTCCTTCTC 0.896005 -128 CCTGTCCGTTTTTCCCCTCACACCCCAGT 1 282 0 TTTTCCCCTC 0.962817 -19 AAAGTCTCTTCTTCTTGGGGGAAGAG 2 6 1 CCTTCTTCTT 0.590388 -113 CAGCATCTTTTCTGCCCTCTCTTCCCCCAAG 2 24 0 TTGCCCTCTC 0.878259 -95 CACGTCATTCTGTTTCCGCTCATATCCAGCA 2 50 0 TTTTCCGCTC 0.951388 -69 GCACTCCCCCTCTTACGCTACC 2 107 0 CCTCCCCCTC 0.986657 -12 GCTATCTGCTCCTGCTCTTATCTAACC 3 23 0 TCTCCTGCTC 0.971673 -17 CTGCTGCACGTACTCACCCGCGCAGAGTGTT 4 18 0 TCTCACCCGC 0.763496 -23 ATTTGACACTTCTTTCCCCTCACACCCTGAT 6 33 0 TTTTCCCCTC 0.962817 -52 ATTTCCTCCTCATGTTCACCA 6 74 0 ATTCCTCCTC 0.604279 -11 GACACGTTGCTTTTCCTGCGCGA 7 3 0 TTTCCTGCGC 0.849159 -141 TGGTGGTGAGTTCTTCTTCTTTTATTTATTT 7 41 0 TCTTCTTCTT 0.751061 -103 CGCGCCAGTTTTCTTCCGGTTTAGTGCCCCA 7 114 1 TCTTCCGGTT 0.877422 -30 TTCTCAAGTCTTCTTCCGGGCGACTTGTCGT 9 86 0 TCTTCCGGGC 0.896868 -207 GTTCCTGGTGCACGTCCTGTTCGTTGAATAG 10 45 1 CCGTCCTGTT 0.364572 -75 CAACTATCACTCCTCTCGCGCGCGAAAGCGG 10 97 0 TCTCTCGCGC 0.709296 -23 * ********* Masking position 6 Map Score: 18.0636 Number of sites scoring better than the average of aligned sites = 2029 Number in coding regions = 1796 Number in noncoding regions = 233 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 3 AAGACATACACCGCACCCACACGCGTTTGC 1 27 0 CCGCACCCAC 0.987427 -274 AAGATTACATGAGCACGTACAGTTTGCTCC 1 110 0 GAGCACGTAC 0.948926 -191 AGCGTATCCACCGCGCGCATCGCACCCCAT 1 157 0 CCGCGCGCAT 0.615154 -144 ACACCAATCGACGCACGCCCCTACGCAGTC 1 218 0 ACGCACGCCC 0.94041 -83 GCTATCTGCTCCTGCTCTTATCTAA 3 25 0 CTGCTCCTGC 0.73626 -15 ATCTGCTGCACGTACTCACCCGCGC 4 26 0 CTGCACGTAC 0.985676 -15 ACCTTCCTACACGCCCCCCATGCTAT 8 7 1 CTACACGCCC 0.869715 -86 GTTACACTGACAGCTCCCACACATCGTGCT 8 39 1 CAGCTCCCAC 0.954058 -54 CCCACACATCGTGCTCGCACAAAAGGCAAA 8 54 1 GTGCTCGCAC 0.829168 -39 CAGAAACGGACTGGAGGCACGGCACGACAA 9 63 1 CTGGAGGCAC 0.697154 -230 GTACAGCGCGCTGCACCCACACGCGACCAA 9 223 0 CTGCACCCAC 0.988045 -70 CAGCTACCCAACGCACGTCCAAACCCGGCT 10 13 0 ACGCACGTCC 0.869303 -107 GCACCAGGAACAGCAGCTACCCAACGCACG 10 26 0 CAGCAGCTAC 0.776363 -94 GCTGTTCCTGGTGCACGTCCTGTTCGTTGA 10 42 1 GTGCACGTCC 0.954143 -78 AGGGTCTACCGACCTCGCACCGCTTTCGCG 10 78 1 GACCTCGCAC 0.626427 -42 ********** Masking position 10 Map Score: 16.531 Number of sites scoring better than the average of aligned sites = 2235 Number in coding regions = 2077 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 4 AAAGACATACACCGCACCCACACGCGTTTG 1 28 0 ACCGCACCCA 0.995387 -273 GAGCGTATCCACCGCGCGCATCGCACCCCA 1 158 0 ACCGCGCGCA 0.977762 -143 TCACCACCACGCCGCGCCCTTGCATGACCT 7 63 1 GCCGCGCCCT 0.969047 -81 GAGTGTACCAAAGGCACCCAGGTCATGCAA 7 82 0 AAGGCACCCA 0.950572 -62 ACCTTCCTACACGCCCCCCATGCTATGTGT 8 11 1 ACGCCCCCCA 0.943608 -82 TGTTACACTGACAGCTCCCACACATCGTGC 8 38 1 ACAGCTCCCA 0.955616 -55 AGTACAGCGCGCTGCACCCACACGCGACCA 9 224 0 GCTGCACCCA 0.97341 -69 ********** Masking position 5 Map Score: 4.87536 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 156 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 GTGAGGGGAAAAACGGACAGG 1 290 1 AAACGGACAG 0.957242 -11 ATATGAGCGGAAACAGAATGACGTGTTCTA 2 56 1 AAACAGAATG 0.977832 -63 AGAAGTGTCAAATCAGAATGCGCTGGTGAA 6 51 1 AATCAGAATG 0.93059 -34 CGTGCGACAGAAACGGACTGGAGGCACGGC 9 56 1 AAACGGACTG 0.986605 -237 CCGTCGCACGAAACAGCGTGCCCCATTGTA 9 163 0 AAACAGCGTG 0.943509 -130 ********** Masking position 2 Map Score: 1.00055 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 17 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 AAACCAGCACGACACATAGCACCACACCAA 1 241 0 GACACATAGC 0.947374 -60 AGGGATAAACACTCTGCGCGGGTGAGT 4 8 1 AACACTCTGC 0.769766 -33 TTTTGAAAAAGACACGTTGCTTTTCCTGCG 7 14 0 GACACGTTGC 0.972351 -130 AGAACTCACCACCACGCCGCGCCCTTGCAT 7 58 1 ACCACGCCGC 0.965058 -86 CTGTCAGTGTAACACATAGCATGGGGGGCG 8 22 0 AACACATAGC 0.937177 -71 TGACAGCTCCCACACATCGTGCTCGCACAA 8 46 1 CACACATCGT 0.68954 -47 CTTTACCGCGTCGCATGTACTGAA 9 5 1 ACCGCGTCGC 0.928209 -288 GGCACGGCACGACAAGTCGCCCGGAAGAAG 9 78 1 GACAAGTCGC 0.924525 -215 ********** Masking position 3 Map Score: 1.23018 Number of sites scoring better than the average of aligned sites = 386 Number in coding regions = 358 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 7 ********** No masking Map Score: 2.06301e-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 8 ********** No masking Map Score: 2.06301e-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 9 ********** No masking Map Score: 2.06301e-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