AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i231_protease_clp_hpyl_reg_100.orf -o231_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 RHP00218 17 AE000511 #2 RHP00219 111 AE000511 #3 RHP00768 171 AE000511 #4 RHP00770 300 AE000511 #5 RHP00771 41 AE000511 Motif number 1 TTTTTTAAATTTTTGAAAACTAGAATTA 2 5 1 TTAAATTTAA 0.958401 -107 TCATTATAGCTTAATTTGTTTTAATTCCAGTTTA 2 52 0 TTAATTTGAA 0.916216 -60 GGCTAAAAAATTAAATTTTTGTATCATTATAGCT 2 75 0 TTAAATTTAT 0.958404 -37 AACCGCTCGCTTGTATTTGCAAAAACACCGATGC 3 60 0 TTGTATTTAA 0.91291 -112 ATAATAGCGGTTATTTTTTTAGAATAACCAACGC 3 104 1 TTATTTTTAA 0.958393 -68 CTAGCGAAAATTGATTTTACCAAAATTGTTTG 4 9 0 TTGATTTTAA 0.95207 -292 CAACTCCTTATTATATTTTATAATGATTCGGTTA 4 83 0 TTATATTTAT 0.943618 -218 GATTTGTGGTTTTATTTTGCTCATTCCTCAACTC 4 111 0 TTTATTTTAT 0.83334 -190 TTTACTGGGATTATTTTTCTTGATTTGTGGTTTT 4 132 0 TTATTTTTAT 0.958404 -169 GCGGCTGGGCTTGATTTGGAGAAATGGTGCTGAC 4 199 1 TTGATTTGAA 0.873176 -102 TAACTCATGGTTATTTTTTCTTATCTTTCTTATT 4 246 0 TTATTTTTAT 0.958404 -55 TCTTATAAAGTTAAATTTTTGAATAACTCATGGT 4 269 0 TTAAATTTAT 0.958404 -32 ******** ** Masking position 13 Map Score: 16.4364 Number of sites scoring better than the average of aligned sites = 556 Number in coding regions = 406 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 2 TTTTTTAAATTTTTGAAAACTAGA 2 5 1 TTAAATTTTT 0.949023 -107 TCATTATAGCTTAATTTGTTTTAATTCCAG 2 56 0 TTAATTTGTT 0.938627 -56 ATACAAAAATTTAATTTTTTAGCCATTAAG 2 85 1 TTAATTTTTT 0.972651 -27 ATAATAGCGGTTATTTTTTTAGAATAACCA 3 104 1 TTATTTTTTT 0.981158 -68 CAACTCCTTATTATATTTTATAATGATTCG 4 87 0 TTATATTTTA 0.811447 -214 ATTTGTGGTTTTATTTTGCTCATTCCTCAA 4 114 0 TTATTTTGCT 0.940976 -187 TTTACTGGGATTATTTTTCTTGATTTGTGG 4 136 0 TTATTTTTCT 0.973737 -165 TTATTTTTTCTTATCTTTCTTATTCCCACC 4 240 0 TTATCTTTCT 0.919409 -61 TAACTCATGGTTATTTTTTCTTATCTTTCT 4 250 0 TTATTTTTTC 0.92405 -51 TCTTATAAAGTTAAATTTTTGAATAACTCA 4 273 0 TTAAATTTTT 0.949023 -28 ********** Masking position 6 Map Score: 15.0362 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 240 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 3 ACGGCTAAAAAGGAGAG 1 1 1 ACGGCTAAAA 0.981146 -17 TAGAATTAAAACCGCTTTTTATAAACTGGA 2 31 1 ACCGCTTTTT 0.880902 -81 TTTTTCCTTAATGGCTAAAAAATTAAATTT 2 91 0 ATGGCTAAAA 0.889511 -21 TTGCATAGAAACCGCTTATGCA 3 3 0 ACCGCTTATG 0.946197 -169 TAAAAAAATAACCGCTATTATACCATAAGA 3 95 0 ACCGCTATTA 0.982804 -77 TAGAATAACCAACGCTAAAAATAGCGCTTT 3 123 1 AACGCTAAAA 0.957904 -49 CGCTAAAAATAGCGCTTTAATTGAATCCAA 3 135 1 AGCGCTTTAA 0.929102 -37 GACGCCACCTACCGCTAAAATGAGATTTAC 4 161 0 ACCGCTAAAA 0.993247 -140 ********** Masking position 1 Map Score: 8.94486 Number of sites scoring better than the average of aligned sites = 727 Number in coding regions = 656 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 CTCTCCTTTTTAGCCGT 1 3 0 CTTTTTAGCC 0.862375 -15 ATTCCAGTTTATAAAAAGCGGTTTTAATTC 2 33 0 ATAAAAAGCG 0.703345 -79 ATTTTTGTATCATTATAGCTTAATTTGTTT 2 65 0 CATTATAGCT 0.727877 -47 AAAAATTTAATTTTTTAGCCATTAAGGAAA 2 89 1 TTTTTTAGCC 0.735525 -23 TGTTTTTGCAAATACAAGCGAGCGGTTTTC 3 67 1 AATACAAGCG 0.924193 -105 TTTCTTATGGTATAATAGCGGTTATTTTTT 3 93 1 TATAATAGCG 0.862417 -79 TTAAAGCGCTATTTTTAGCGTTGGTTATTC 3 125 0 ATTTTTAGCG 0.94482 -47 TTTTGGATTCAATTAAAGCGCTATTTTTAG 3 137 0 AATTAAAGCG 0.944819 -35 GATTATATCCAAAACTAGCGAAAATTGATT 4 27 0 AAAACTAGCG 0.891728 -274 CAGTAAATCTCATTTTAGCGGTAGGTGGCG 4 159 1 CATTTTAGCG 0.95992 -142 CCATTTCTCCAAATCAAGCCCAGCCGCACC 4 196 0 AAATCAAGCC 0.785135 -105 ********** Masking position 7 Map Score: 6.63068 Number of sites scoring better than the average of aligned sites = 2092 Number in coding regions = 1884 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 5 CTTTAATTGAATCCAAAACAAGGAGTTTAT 3 149 1 ATCCAAAACA 0.971342 -23 TTGGGATTATATCCAAAACTAGCGAAAATT 4 31 0 ATCCAAAACT 0.875571 -270 TTTGGATATAATCCCAATAACTTAACCATG 4 44 1 ATCCCAATAA 0.969016 -257 ATGGAAGTTTAACCGAATCATTATAAAATA 4 74 1 AACCGAATCA 0.938533 -227 AAGAAAAATAATCCCAGTAAATCTCATTTT 4 145 1 ATCCCAGTAA 0.905865 -156 AGCACCATTTCTCCAAATCAAGCCCAGCCG 4 200 0 CTCCAAATCA 0.981283 -101 TTCTTATTCCCACCAAATAATGTCAGCACC 4 224 0 CACCAAATAA 0.916965 -77 ********** Masking position 6 Map Score: 4.31105 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 236 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 6 ACGGCTAAAAAGGAGAG 1 8 1 AAAAGGAGAG 0.946898 -10 TGAATCCAAAACAAGGAGTTTATTTT 3 156 1 ACAAGGAGTT 0.98873 -16 ATAAAATATAATAAGGAGTTGAGGAATGAG 4 96 1 ATAAGGAGTT 0.969844 -205 ACCTACCGCTAAAATGAGATTTACTGGGAT 4 155 0 AAAATGAGAT 0.946141 -146 AGAAAAAATAACCATGAGTTATTCAAAAAT 4 259 1 ACCATGAGTT 0.94605 -42 ********** Masking position 4 Map Score: 2.15289 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 35 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 7 ********** No masking Map Score: -1.32628e-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: -1.32628e-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: -1.32628e-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