AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00350_tpal_reg_100.orf -o00350_tpal_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 TP0223 267 aspartate aminotransferase (tpaaT) #2 TP0251 153 DNA-binding protein II #3 TP0417 26 apolipoprotein N-acyltransferase (cutE) Motif number 1 GTTTGTGTAACCATTTGCCGCAGGAAGCTCATCC 1 15 1 CCATTTCGCG 0.794707 -253 CATCCGTGTGGCTGCGCGGGCTTGTGTGCTCTGA 1 44 1 GCTGCGGGCG 0.989746 -224 GGGCTTGTGTGCTCTGAAGTCGGGCTGTCGATTC 1 61 1 GCTCTGGTCG 0.985028 -207 AAATTGACAGGGTCAGGGGGCGTGTCTACACTGT 1 107 1 GGTCAGGGCG 0.952329 -161 GACATGGACCTCTCTGAAGGCGCGCGTGCGTTAA 1 143 1 TCTCTGGGCG 0.970033 -125 TTCAAGAGCAGCGTTTAACGCACGCGCGCCTTCA 1 157 0 GCGTTTCGCG 0.977169 -111 TGGTGCACGCGCTGTTATCTCCTCTTGGTTTGCG 1 198 1 GCTGTTCTCC 0.91772 -70 ATCTCCTCTTGGTTTGCGCGCGTATTTTCCCCAC 1 214 1 GGTTTGCGCA 0.916069 -54 ACCTTTCCGGGCAGCGGTGTCAAGTCGCT 2 6 0 GCAGCGGTCG 0.883267 -148 TGCCCGGAAAGGTGTTTTCGCTAGAAAGGCTGTG 2 27 1 GGTGTTCGCG 0.991117 -127 TACACATTCGGGACTTCTGGCGAGCCACAGCCTT 2 52 0 GGACTTGGCG 0.970562 -102 ACTGTACAACGGTGTGTTCTCTTCACCCGAGGTG 2 87 1 GGTGTGCTCC 0.931184 -67 GAGGTGGTGCGCGTTTGAGGCGGCTGTTTGCCCG 2 115 1 GCGTTTGGCC 0.932903 -39 TTGAGGCGGCTGTTTGCCCGCGTGTGTTTCTTGT 2 129 1 TGTTTGCGCG 0.946431 -25 AAATGCTTTTCTGGCAGGGGAAAGTT 3 5 1 GCTTTTGGCG 0.992944 -22 ****** *** * Masking position 11 Map Score: 21.4732 Number of sites scoring better than the average of aligned sites = 1791 Number in coding regions = 1628 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 2 CAAATGGTTACACAAACACCG 1 2 0 CACAAACACC 0.957519 -266 AACCATTTGCCGCAGGAAGCTCATCCGTGT 1 23 1 CGCAGGAAGC 0.796336 -245 AGCACACAAGCCCGCGCAGCCACACGGATG 1 44 0 CCCGCGCAGC 0.98682 -224 GCCCGACTTCAGAGCACACAAGCCCGCGCA 1 56 0 AGAGCACACA 0.629156 -212 GCGTTTAACGCACGCGCGCCTTCAGAGAGG 1 151 0 CACGCGCGCC 0.956342 -117 ACCGTTCCTTCAAGAGCAGCGTTTAACGCA 1 169 0 CAAGAGCAGC 0.95177 -99 GAGATAACAGCGCGTGCACCACCGTTCCTT 1 189 0 CGCGTGCACC 0.979232 -79 GGAAAATACGCGCGCAAACCAAGAGGAGAT 1 214 0 CGCGCAAACC 0.983173 -54 GCCTTTCTAGCGAAAACACCTTTCCGGGCA 2 27 0 CGAAAACACC 0.960597 -127 TCGGGTGAAGAGAACACACCGTTGTACAGT 2 87 0 AGAACACACC 0.910998 -67 AGCCGCCTCAAACGCGCACCACCTCGGGTG 2 110 0 AACGCGCACC 0.970437 -44 AACACACGCGGGCAAACAGCCGCCTCAAAC 2 127 0 GGCAAACAGC 0.834273 -27 CTTTCCCCTGCCAGAAAAGCATTT 3 5 0 CCAGAAAAGC 0.702161 -22 ********** Masking position 8 Map Score: 15.5442 Number of sites scoring better than the average of aligned sites = 4384 Number in coding regions = 4063 Number in noncoding regions = 321 Number of orfs with sites within 600 bp upstream = 200 Fraction of orfs with sites within 600 bp upstream = 0.0321234 Motif number 3 GCCCGCGCAGCCACACGGATGAGCTTCCTGC 1 34 0 CCACACGGTG 0.969149 -234 AATTTATGCACCCCAGTGAATCGACAGCCCG 1 81 0 CCCCAGTGAT 0.972885 -187 GGTCCATGTCTCACAGTGTAGACACGCCCCC 1 122 0 TCACAGTGAG 0.698802 -146 GAGACATGGACCTCTCTGAAGGCGCGCGTGC 1 141 1 CCTCTCTGAG 0.977708 -127 GCTGTTATCTCCTCTTGGTTTGCGCGCGTAT 1 208 1 CCTCTTGGTT 0.827948 -60 CGCGTATTTTCCCCACGGGATTGTTGCACAG 1 232 1 CCCCACGGAT 0.993064 -36 CCGCGCCTCTGCATTCTGTGCAAC 1 254 0 CGCCTCTGAT 0.947079 -14 AAACGCGCACCACCTCGGGTGAAGAGAACAC 2 100 0 CACCTCGGTG 0.926348 -54 ******** ** Masking position 4 Map Score: 4.08288 Number of sites scoring better than the average of aligned sites = 588 Number in coding regions = 532 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 4 GCGGCAAATGGTTACACAAACACCG 1 6 0 GTTACACAAA 0.937054 -262 GATTCACTGGGGTGCATAAATTGACAGGGT 1 90 1 GGTGCATAAA 0.955217 -178 CCACGGGATTGTTGCACAGAATGCAGAGGC 1 244 1 GTTGCACAGA 0.994105 -24 AGAACACACCGTTGTACAGTCTACACATTC 2 77 0 GTTGTACAGT 0.926796 -77 CACCACCTCGGGTGAAGAGAACACACCGTT 2 94 0 GGTGAAGAGA 0.947254 -60 ********** Masking position 6 Map Score: 0.702251 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 192 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 ********** No masking Map Score: -3.81261e-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 6 ********** No masking Map Score: -3.81261e-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 7 ********** No masking Map Score: -3.81261e-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