AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i251_chemotaxis_hpyl_reg_300.orf -o251_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 = 0.39 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RHP01329 56 AE000511 #2 RHP01332 22 AE000511 #3 RHP01335 28 AE000511 #4 RHP01336 120 AE000511 #5 RHP01340 80 AE000511 #6 RHP00471 290 AE000511 Motif number 1 TTTACAATTTTATAAAAAGAA 1 1 0 TATAAAAAAA 0.959448 -56 TTCTCATGCTTTTAAAATCACTCT 3 4 0 TTTAAAATAC 0.880773 -25 GAAAATTTTCTTTAAAAAAACCGCTAATTGT 4 19 1 TTTAAAAAAC 0.97056 -102 TACAAAATCGTTTAAAAACTAACAATTAGCG 4 40 0 TTTAAAAATA 0.890597 -81 ACTGCCTTACTATAAAATAAATATAAAATCC 4 98 0 TATAAAATAA 0.840541 -23 ATAATACAACTTTAATAAAAGAAAAACCTTA 5 28 0 TTTAATAAAG 0.939975 -53 ATTATAGCTTTTTAAAAATAAAATATAAGGA 5 54 1 TTTAAAAAAA 0.989594 -27 AGACAAGGATTTTACAAGTAA 6 1 0 TTTACAAGAA 0.940305 -290 CATTGGATGGTTTGAAAAAAGAAAGACAAGG 6 24 0 TTTGAAAAAG 0.888888 -267 ATGATAATCGTTTAAAAGTAATAAAATAACT 6 75 0 TTTAAAAGAA 0.984392 -216 ACTGAATTTTTTTACAAATAAGAACGCTCAT 6 115 1 TTTACAAAAA 0.959605 -176 TCAAGGTAATTTTAATCAAAACATGCTATTA 6 179 1 TTTAATCAAA 0.761827 -112 TCTAACGCCTTATAATAATAAATCGTTCCAA 6 211 0 TATAATAAAA 0.85473 -80 GCTTTGGCTGTTTAAAAAGAGCCTAATTTAA 6 245 1 TTTAAAAAAG 0.984395 -46 AAGAGCCTAATTTAAATGCAATCTTAAAAGG 6 261 1 TTTAAATGAA 0.85224 -30 TAAATGCAATCTTAAAAGGAGAAGCACT 6 273 1 CTTAAAAGAG 0.841389 -18 ******** ** Masking position 3 Map Score: 22.5868 Number of sites scoring better than the average of aligned sites = 1098 Number in coding regions = 799 Number in noncoding regions = 299 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 2 CGTTTGAGATAAGAGTATTTTACAATTTTATA 1 18 0 AAGATATTTA 0.835218 -39 ACTAACAATTAGCGGTTTTTTTAAAGAAAATT 4 22 0 AGCGTTTTTT 0.92615 -99 TTAGTTTTTAAACGATTTTGTAAGCCAAAAAA 4 49 1 AACGTTTTTA 0.981288 -72 TAAAATCCTTAAGGGTATTGTATCCTTTTTTG 4 74 0 AAGGTATTTA 0.987168 -47 CAATACCCTTAAGGATTTTATATTTATTTTAT 4 86 1 AAGGTTTTTA 0.989238 -35 GCTCCCTTTTAAGGTTTTTCTTTTATTAAAGT 5 19 1 AAGGTTTTTT 0.976924 -62 TTATTTTTAAAAAGCTATAATACAACTTTAAT 5 43 0 AAAGTATATA 0.757088 -38 AAAGAAAGACAAGGATTTTACAAGTAA 6 6 0 AAGGTTTTCA 0.935577 -285 TCGCACTCAAAGAGTTATTTTATTACTTTTAA 6 63 1 AGAGTATTTA 0.8851 -228 GCGTTCAATGAGCGTTCTTATTTGTAAAAAAA 6 121 0 AGCGTCTTTT 0.876575 -170 ATTGTCGGTCAAGGTAATTTTAATCAAAACAT 6 171 1 AAGGAATTTA 0.891821 -120 TATTATTTGGAACGATTTATTATTATAAGGCG 6 205 1 AACGTTTATA 0.916362 -86 GCATTTAAATTAGGCTCTTTTTAAACAGCCAA 6 248 0 TAGGTCTTTT 0.719802 -43 **** **** ** Masking position 8 Map Score: 14.3968 Number of sites scoring better than the average of aligned sites = 1298 Number in coding regions = 1116 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 3 TTAAAACCCCTTTTTAGCGTTTGAGATAAGA 1 36 0 CTTTTTGCTT 0.99047 -21 AATTCTTCTTTATGGCTATTCT 2 4 0 CTTTATGCAT 0.945138 -19 GTATTGTATCCTTTTTTGGCTTACAAAATCGT 4 60 0 CTTTTTGGTT 0.985984 -61 GGATACAATACCCTTAAGGATTTTATATTTAT 4 81 1 CCCTTAGGTT 0.898825 -40 GCTTTTTTGCTCCCTTTTAAGGT 5 2 1 CTTTTTGCCC 0.92466 -79 TTTTTGCTCCCTTTTAAGGTTTTTCTTTTATT 5 14 1 CTTTTAGGTT 0.979613 -67 TCCAATGACCCTTTATCGCACTCAAAGAGTTA 6 48 1 CTTTATGCCT 0.963831 -243 TATTTTATTACTTTTAAACGATTATCATAGCA 6 78 1 CTTTTAACAT 0.81793 -213 GCCAAAGCGTCTCTAACGCCTTATAATAATAA 6 221 0 CTCTAAGCTT 0.932528 -70 AGTGCTTCTCCTTTTAAGATTGCATTTAAAT 6 270 0 CCTTTTAGTT 0.839462 -21 ****** ** ** Masking position 4 Map Score: 8.28929 Number of sites scoring better than the average of aligned sites = 1536 Number in coding regions = 1395 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 4 AATTCTTCTTTATGGCTATT 2 13 0 AATTCTTCTT 0.749859 -10 TAACGATCCTTATATTTTATT 5 70 0 AACGATCCTT 0.915486 -11 CAAACCATCCAATGACCCTTTATCGCACTC 6 41 1 AATGACCCTT 0.837469 -250 ATTACTTTTAAACGATTATCATAGCAAACA 6 84 1 AACGATTATC 0.89839 -207 TACAAATAAGAACGCTCATTGAACGCTCCA 6 127 1 AACGCTCATT 0.930723 -164 ACGCTCATTGAACGCTCCATTTAGCCAATG 6 138 1 AACGCTCCAT 0.960592 -153 CCATTTAGCCAATGATTATTGTCGGTCAAG 6 154 1 AATGATTATT 0.744768 -137 TATTATTTGGAACGATTTATTATTATAAGG 6 205 1 AACGATTTAT 0.69522 -86 AGTGCTTCTCCTTTTAAGAT 6 281 0 AGTGCTTCTC 0.777417 -10 ********** Masking position 1 Map Score: 3.9704 Number of sites scoring better than the average of aligned sites = 1383 Number in coding regions = 1242 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 5 ********** No masking Map Score: 1.34536e-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 6 ********** No masking Map Score: 1.34536e-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 7 ********** No masking Map Score: 1.34536e-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