AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00272_aful_reg_300.orf -o00272_aful_300.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 AF0409 74 aspartate aminotransferase (aspB-4) #2 AF0410 56 signal-transducing histidine kinase, putative #3 AF0411 30 cysteinyl-tRNA synthetase (cysS) #4 AF1418 49 glycerol-3-phosphate cytidyltransferase (taqD) #5 AF1419 24 ribose-phosphate pyrophosphokinase (prsA-2) #6 AF1420 216 membrane protein #7 AF1421 49 conserved hypothetical protein #8 AF1422 35 aspartate racemase #9 AF1423 112 conserved hypothetical protein Motif number 1 AATATAAACTTTGCTGTTCAGTTAAATAAAAA 2 7 0 TTGGCAGAAA 0.988318 -50 CTGACTTTTCTGGACGATGAATATAAACTTTGCTGT 2 26 0 TGGGGAATAA 0.895261 -31 TGAATTTGGATTGGAGATGAAGAAAAGGGTC 4 29 1 TTGGGAAAAA 0.965965 -21 CCAAATTCAACTGCGGGCTCGGAAAATCTCACGATA 6 15 1 CTGGTCGAAA 0.883079 -202 CCGGGAAGCTTTGAAGCTGAGTGACAGAGTATCGTG 6 44 0 TTGGGAGACA 0.971622 -173 ACGAATAGCCCTGATGGAGTGTGAAATAGACTATCC 6 78 0 CTGGGTGAAA 0.936126 -139 AGTATTGGTAGCACAGCAAACTTTTTAACAT 7 6 1 TGGGCAGAAC 0.95029 -44 TGGATTTTGCTTGAAGTTGAGGTTAAAATTTTTTAG 9 11 1 TTGGGAGTAA 0.978557 -102 TTTTTTAGGTTGGGTGATGCGCTAAATACTTCAAGA 9 39 1 TGGGGCGAAA 0.99323 -74 GATGTTGTTCTGGTTGGGCCGATAAAAATTTACCGC 9 86 0 TGGGCCGAAA 0.986943 -27 *** * *** *** Masking position 6 Map Score: 10.6562 Number of sites scoring better than the average of aligned sites = 702 Number in coding regions = 653 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 2 TACGTTATTCGGGTAAAAGTTGATATATTCG 1 36 1 GGTAAAAGTT 0.978114 -39 ACGGTCATGGGTTTAAAAATT 3 1 0 GTTAAAAATT 0.959052 -30 ATTCAGGTAGGCATAAAAGTTTT 4 3 0 GATAAAAGTT 0.967901 -47 CTGTCACTCAGCTTCAAAGCTTCCCGGATAG 6 53 1 GTTCAAAGCT 0.920459 -164 TGCTTTGAATGTTAAAAAGTTTGCTGTGCTA 7 19 0 GTAAAAAGTT 0.98154 -31 TTGAAGTTGAGGTTAAAATTTTTTAGGTTGG 9 21 1 GTTAAAATTT 0.976359 -92 TGGTTGGGCCGATAAAAATTTACCGCTAAAA 9 81 0 GTAAAAATTT 0.947276 -32 * ********* Masking position 6 Map Score: 7.1492 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 46 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 ATCAACTTTTACCCGAATAACGTAAATATCAGA 1 27 0 ACCGAATACT 0.983954 -48 AATCAAAAAAAGAGGAAGGGCTT 5 1 0 AGAGAAGGCT 0.939549 -24 GAAGCTTTGAAGCTGAGTGACAGAGTATCGTGA 6 43 0 AGCGAGTACG 0.919217 -174 AAGCGTTGCCAGCAGAATAACTTGACAAAACGA 6 110 0 AGCGAATACT 0.992857 -107 CTCATGAAAAACCTTATTAGCCTCTTGTTATTT 6 186 1 ACCTATTGCT 0.846974 -31 TAACATTCAAAGCAGAATTGCATT 7 36 1 AGCGAATGCT 0.995491 -14 AAATAGACTAATCGCCTAACAAGATAA 8 19 0 AGATAATGCT 0.892209 -17 TATCGGCCCAACCAGAACAACATCA 9 98 1 ACCGAACACT 0.963412 -15 *** **** ** * Masking position 6 Map Score: 5.69642 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 265 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 CCTCAAGCTTCTGATATTTACGTTATTCGG 1 18 1 CTGATATTTA 0.662161 -57 TTTTTATTTAACTGAACAGC 2 1 1 TTTTTATTTA 0.848113 -56 AACAGCAAAGTTTATATTCATCGTCCAGAA 2 25 1 TTTATATTCA 0.757649 -32 TTATGCTGACTTTTCTGGACGATGAATAT 2 38 0 CTTTTCTGGA 0.91476 -19 GACCCTTTTCTTCATCTCCAATCC 4 36 0 CTTTTCTTCA 0.904137 -14 AGCCCTTCCTCTTTTTTTGATTC 5 12 1 CTTTTTTTGA 0.800656 -13 TTTCATGAGTTTGATATTGAGATATTGCAG 6 165 0 TTGATATTGA 0.894105 -52 GCTAATAAGGTTTTTCATGAGTTTGATATT 6 177 0 TTTTTCATGA 0.813423 -40 TATTAGCCTCTTGTTATTTATTTGCGT 6 200 1 TTGTTATTTA 0.821225 -17 CCAAAGCTTTATCTTGTTAGGCGATTA 8 8 1 TTTATCTTGT 0.813919 -28 TGGATTTTGCTTGAAGTTGAGGTT 9 5 1 TTTTGCTTGA 0.865981 -108 TGATGTTGTTCTGGTTGGGCCGATA 9 98 0 TTGTTCTGGT 0.706267 -15 ********** Masking position 2 Map Score: 5.56457 Number of sites scoring better than the average of aligned sites = 987 Number in coding regions = 874 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 5 TATCAGAAGCTTGAGGTTCTTGC 1 4 0 TTGAGGTTCT 0.932215 -71 CGGGTAAAAGTTGATATATTCGAAAGCTCC 1 45 1 TTGATATATT 0.919477 -30 ACAGAGTATCGTGAGATTTTCCGAGCCCGC 6 27 0 GTGAGATTTT 0.943145 -190 GAGTTTGATATTGAGATATTGCAGAAAACG 6 159 0 TTGAGATATT 0.978433 -58 GAAGTTGAGGTTAAAATTTTTTAGGTTGGG 9 23 1 TTAAAATTTT 0.756986 -90 AAGGCCTGTCTTGAAGTATTTAGCGCATCA 9 53 0 TTGAAGTATT 0.943481 -60 ********** Masking position 4 Map Score: 1.65421 Number of sites scoring better than the average of aligned sites = 335 Number in coding regions = 294 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 6 TCATCTCCAATCCAAATTCAGGTAGGCATA 4 19 0 TCCAAATTCA 0.992138 -31 CTGTCCAAATTCAACTGCGGGCT 6 4 1 TCCAAATTCA 0.992138 -213 ********** Masking position 5 Map Score: 0.204171 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: 1.49457e-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: 1.49457e-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: 1.49457e-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