AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i267_hypothetical12_hpyl_reg_100.orf -o267_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 RHP00088 297 AE000511 #2 RHP00089 82 AE000511 Motif number 1 AATTTTTAAAAATTTTCATACTCTCATTTA 1 73 0 AATTTTCATA 0.844164 -225 CATTTTTGTAAATTTTTAAAAATTTTCATA 1 83 0 AATTTTTAAA 0.967938 -215 TGTTCTTTCTCATTTTTGTAAATTTTTAAA 1 93 0 CATTTTTGTA 0.917953 -205 TAAAAGGGGATATTTTTATATAATATGTAA 1 215 1 TATTTTTATA 0.941764 -83 ATGTAAAAAGCATTCTTAAATCTAAAAATG 1 239 1 CATTCTTAAA 0.968232 -59 AACATTGTAGCATTTTTAGATTTAAGAATG 1 249 0 CATTTTTAGA 0.981022 -49 CTACAATGTTTATCTTTAAAACGAAAGGGC 1 269 1 TATCTTTAAA 0.831154 -29 TAATTTTTAGCGTTTTTAAGA 2 2 1 AATTTTTAGC 0.853966 -81 TATAACTAATCATTCTTAAAAACGCTAAAA 2 15 0 CATTCTTAAA 0.968232 -68 ********** Masking position 6 Map Score: 10.1148 Number of sites scoring better than the average of aligned sites = 508 Number in coding regions = 389 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 2 AGTATCTCCTTTGTGTTGGTTT 1 3 1 TATCTCCTTT 0.975001 -295 TTACTTTTTCATTATCATTTATGCTATAAT 1 46 0 ATTATCATTT 0.923889 -252 AAATTTTCATACTCTCATTTACTTTTTCAT 1 64 0 ACTCTCATTT 0.972488 -234 GCCGGTGTTCTTTCTCATTTTTGTAAATTT 1 98 0 TTTCTCATTT 0.983676 -200 TTTTTACCTAATTCTCATTAAATAGATTTT 1 160 0 ATTCTCATTA 0.942163 -138 TATATAAAAATATCCCCTTTTAACCCCCTA 1 207 0 TATCCCCTTT 0.963295 -91 GGTTAAATTGCCCTTTCGTTTTAAAG 1 282 0 ATTGCCCTTT 0.935977 -16 ********** Masking position 3 Map Score: 7.04257 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 218 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 3 ATTATCATTTATGCTATAATTATGGGACAA 1 36 0 ATGCTATAAT 0.966882 -262 ATAGATTTTTATGATAAAATCTAAGCTTTA 1 139 0 ATGATAAAAT 0.94829 -159 TGTAAAAAGCATTCTTAAATCTAAAAATGC 1 240 1 ATTCTTAAAT 0.855488 -58 AAATCTAAAAATGCTACAATGTTTATCTTT 1 256 1 ATGCTACAAT 0.983084 -42 ATTCTTAAAAACGCTAAAAATTA 2 4 0 ACGCTAAAAA 0.946294 -79 AACAACACTCAAGCTAAAATCTATTAAGGA 2 56 1 AAGCTAAAAT 0.97952 -27 ********** Masking position 5 Map Score: 5.94114 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 211 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 4 CTTGATAAAGCTTAGATTTTATCATAAAAA 1 134 1 CTTAGATTTT 0.981372 -164 ATTCTCATTAAATAGATTTTTATGATAAAA 1 150 0 AATAGATTTT 0.983263 -148 TTGTAGCATTTTTAGATTTAAGAATGCTTT 1 245 0 TTTAGATTTA 0.933641 -53 TGATTTCCTTAATAGATTTTAGCTTGAGTG 2 61 0 AATAGATTTT 0.983263 -22 ********** Masking position 6 Map Score: 3.0028 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 44 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 TTGATGCCAACCCCTTTTTTTTACCTAATT 1 177 0 CCCCTTTTTT 0.987958 -121 CCCTTTTAACCCCCTATTGATGCCAACCCC 1 193 0 CCCCTATTGA 0.988825 -105 ATAAAAATATCCCCTTTTAACCCCCTATTG 1 204 0 CCCCTTTTAA 0.987958 -94 GGTTAAATTGCCCTTTCGTTTTAAAGATA 1 279 0 GCCCTTTCGT 0.979986 -19 ********** Masking position 5 Map Score: 2.05428 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 194 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 6 AATGATAATGAAAAAGTAAATGAGAGTATG 1 57 1 AAAAAGTAAA 0.908048 -241 AGTAAATGAGAGTATGAAAATTTTTAAAAA 1 71 1 AGTATGAAAA 0.91531 -227 TTTAATGAGAATTAGGTAAAAAAAAGGGGT 1 168 1 ATTAGGTAAA 0.964151 -130 ATTTTTATATAATATGTAAAAAGCATTCTT 1 226 1 AATATGTAAA 0.97011 -72 GCTAAAATCTATTAAGGAAATCAGT 2 68 1 ATTAAGGAAA 0.950116 -15 ********** Masking position 4 Map Score: 0.914789 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 47 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 ********** No masking Map Score: 2.36911e-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 8 ********** No masking Map Score: 2.36911e-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 9 ********** No masking Map Score: 2.36911e-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