AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i029_Glycolate_Oxidase_hpyl_reg_100.orf -o029_hpyl_100.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 RHP01426 203 AE000511 #2 RHP00088 297 AE000511 #3 RHP00089 82 AE000511 #4 RHP00098 37 AE000511 Motif number 1 TAGCGTTGGGTATTTTCTTTTTAATCAATCCGTA 1 17 0 TTTTCTTTTA 0.976427 -187 GGCCTTGTTTTTATAGCTTTATGAAGCGCGTTTT 1 95 0 TTAGCTTATA 0.986222 -109 GGCTTTAAACTTGTATCGTTTTTCTTTAATGGCT 1 130 1 TTATCTTTTC 0.929719 -74 CTCTCATTTACTTTTTCATTATCATTTATGCTAT 2 49 0 CTTTCTTATA 0.930451 -249 TATGATAAAATCTAAGCTTTATCAAGCCATTAGC 2 126 0 TAAGCTTATA 0.909569 -172 AAGATAAACATTGTAGCATTTTTAGATTTAAGAA 2 251 0 TTAGCTTTTA 0.9895 -47 GGTTAAATTGCCCTTTCGTTTTAAAGATAAACAT 2 274 0 CTTTCTTTTA 0.940821 -24 TAATTTTTAGCGTTTTTAAGAATGATTA 3 5 1 TTAGCTTTTA 0.988236 -78 TGAGTGTTGTTAGTAGCGTTATTATAACTAATCA 3 33 0 TTAGCTTATA 0.9852 -50 ACTGATTTCCTTAATAGATTTTAGCT 3 67 0 TTTTCTTAAA 0.815777 -16 TTTATATCCTTTTTAAGCTGATTGT 4 23 0 TTATCTTTTA 0.985797 -15 * **** **** * Masking position 9 Map Score: 17.3127 Number of sites scoring better than the average of aligned sites = 401 Number in coding regions = 312 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 2 AGATAAAACCATTTATGAGAAACCACCATGC 1 58 1 ATTTATGAAA 0.807798 -146 AGCGCGTTTTATTGATGCATGGTGGTTTCTC 1 74 0 ATTGATGCTG 0.889912 -130 TGGCCTTGTTTTTATAGCTTTATGAAGCGCG 1 99 0 TTTATAGCTT 0.612385 -105 ACGATACAAGTTTAAAGCCTGGCCTTGTTTT 1 118 0 TTTAAAGCTG 0.925825 -86 AACATAAGCCATTAAAGAAAAACGATACAAG 1 139 0 ATTAAAGAAA 0.822068 -65 GCAGTTGTTTAATGCCTTCAATCAAATC 1 186 0 TTTAATGCTT 0.833004 -18 TTTCATTATCATTTATGCTATAATTATGGGA 2 39 0 ATTTATGCAT 0.835606 -259 TTAAATAGATTTTTATGATAAAATCTAAGCT 2 142 0 TTTTATGAAA 0.807788 -156 TAAAAATCTATTTAATGAGAATTAGGTAAAA 2 158 1 TTTAATGAAA 0.783933 -140 TTAACCCCCTATTGATGCCAACCCCTTTTTT 2 187 0 ATTGATGCAA 0.859896 -111 GCATTTTTAGATTTAAGAATGCTTTTTACAT 2 239 0 ATTTAAGATG 0.875767 -59 AAAGATAAACATTGTAGCATTTTTAGATTTA 2 255 0 ATTGTAGCTT 0.565801 -43 GCCCTTTCGTTTTAAAGATAAACATTGTAGC 2 268 0 TTTAAAGAAA 0.822091 -30 TTTTTAGCGTTTTTAAGAATGATTAGTTATA 3 14 1 TTTTAAGATG 0.875767 -69 TCCTTAATAGATTTTAGCTTGAGTGTTGTTA 3 55 0 ATTTTAGCTG 0.782416 -28 TTTATATCCTTTTTAAGCTGATTGTATCCAA 4 17 0 TTTTAAGCGA 0.744668 -21 ******** ** Masking position 3 Map Score: 10.8091 Number of sites scoring better than the average of aligned sites = 2789 Number in coding regions = 2448 Number in noncoding regions = 341 Number of orfs with sites within 600 bp upstream = 251 Fraction of orfs with sites within 600 bp upstream = 0.0403148 Motif number 3 AGTATCTCCTTTGTGTTGGTTT 2 3 1 TATCTCCTTT 0.990907 -295 GCCGGTGTTCTTTCTCATTTTTGTAAATTT 2 98 0 TTTCTCATTT 0.900833 -200 CTATTGATGCCAACCCCTTTTTTTTACCTA 2 180 0 CAACCCCTTT 0.939234 -118 TATATAAAAATATCCCCTTTTAACCCCCTA 2 207 0 TATCCCCTTT 0.994198 -91 AAGCTGATTGTATCCAATTTCGT 4 4 0 TATCCAATTT 0.899569 -34 TTTATATCCTTTTTAAGCTGAT 4 26 0 TATATCCTTT 0.944003 -12 ********** Masking position 8 Map Score: 4.80304 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 239 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 4 ATGCATGGTGGTTTCTCATAAATGGTTTTA 1 61 0 GTTTCTCATA 0.864144 -143 TATTTTATTAGTATAACATAAGCCATTAAA 1 154 0 GTATAACATA 0.897977 -50 TGTCCCATAATTATAGCATAAATGATAATG 2 37 1 TTATAGCATA 0.854911 -261 AAAGCTTAGATTTTATCATAAAAATCTATT 2 140 1 TTTTATCATA 0.941536 -158 CAACCCCTTTTTTTTACCTAATTCTCATTA 2 170 0 TTTTTACCTA 0.902451 -128 AAAGGGGATATTTTTATATAATATGTAAAA 2 217 1 TTTTTATATA 0.795863 -81 TTAAGAATGCTTTTTACATATTATATAAAA 2 228 0 TTTTTACATA 0.967744 -70 ********** Masking position 10 Map Score: 1.67381 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 197 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 ********** No masking Map Score: -9.14168e-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: -9.14168e-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: -9.14168e-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