AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i194_dna_replication_hpyl_reg_300.orf -o194_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 RHP00146 68 AE000511 #2 RHP00147 207 AE000511 #3 RHP00340 155 AE000511 Motif number 1 TGACTTAAAACTAGCCCCTTT 1 1 0 CTACCCCTTT 0.924929 -68 TGTAATCCTTAAAACTCATTTAGGAGTATTG 1 42 0 AAACTCATTT 0.838222 -27 ACTTATTCTTAAACGCCACTAAGAGCGCTAA 2 21 1 AAAGCCACTA 0.968855 -187 GAAAATTTAAAAACCCCATTTTTTAGCGCTC 2 43 0 AAACCCATTT 0.978512 -165 AATTTTCGCGCAAAGCCATTGTGTATCATCA 2 67 1 CAAGCCATTG 0.927188 -141 TTAGGGTTTAAAACGACCTTTATAAATAAAA 2 104 0 AAAGACCTTT 0.710988 -104 TAAAATTTTAAAATACCATTTTTGAATGATT 2 132 1 AAAACCATTT 0.905965 -76 TAAAATTGAGATAGCACATTATAACACTTCC 3 20 1 ATACACATTA 0.72178 -136 AATAATATGAAAAAGCGCTTAATGAAGCGTT 3 56 0 AAAGCGCTTA 0.913934 -100 TTATTTAATTAAACCCCCTTTTAAAAAACAA 3 82 1 AAACCCCTTT 0.979549 -74 AAAAAACAATAAAAGCCCTTTTAGTGGCTTT 3 104 1 AAAGCCCTTT 0.889385 -52 AACTTGACTTGAAAGCCACTAAAAGGGCTTT 3 115 0 GAAGCCACTA 0.866858 -41 *** ******* Masking position 3 Map Score: 15.8465 Number of sites scoring better than the average of aligned sites = 2355 Number in coding regions = 2045 Number in noncoding regions = 310 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 2 AGGGGCTAGTTTTAAGTCATTTTGCATTAC 1 13 1 TTTAAGTCAT 0.853411 -56 TTTAGGAGTATTGTAATGCAAAATGACTTA 1 25 0 TTGTAATGCA 0.79009 -44 ATTGATTGTAATCCTTAAAACTCAT 1 54 0 TTGTAATCCT 0.786354 -15 AAACCCCATTTTTTAGCGCTCTTAGTGGCG 2 34 0 TTTTAGCGCT 0.977945 -174 GGTTTTTAAATTTTCGCGCAAAGCCATTGT 2 59 1 TTTTCGCGCA 0.768842 -149 ATAAATAAAAATTAAATGATGATACACAAT 2 84 0 ATTAAATGAT 0.734411 -124 TAAAGGTCGTTTTAAACCCTAAAATTTTAA 2 113 1 TTTAAACCCT 0.940673 -95 AAATACCATTTTTGAATGATTGGTTTGTAT 2 142 1 TTTGAATGAT 0.882344 -66 TTTAGCTTATTTTGAGTGAAAGGATTAAGC 2 185 1 TTTGAGTGAA 0.800313 -23 AACACTTCCATTTAAACGCTTCATTAAGCG 3 42 1 TTTAAACGCT 0.976024 -114 TAAACGCTTCATTAAGCGCTTTTTCATATT 3 54 1 ATTAAGCGCT 0.931293 -102 ********** Masking position 2 Map Score: 7.66632 Number of sites scoring better than the average of aligned sites = 4495 Number in coding regions = 4098 Number in noncoding regions = 397 Number of orfs with sites within 600 bp upstream = 263 Fraction of orfs with sites within 600 bp upstream = 0.0422422 Motif number 3 TAAAACTCATTTAGGAGTATTGTAATGCAA 1 34 0 TTAGGAGTAT 0.881301 -35 AAATGAGTTTTAAGGATTACAATCAAT 1 52 1 TAAGGATTAC 0.969528 -17 TAAGAATAAGTTAAGATTAAC 2 2 0 TTAAGATTAA 0.932383 -206 TTAGTGGCGTTTAAGAATAAGTTAAGATTA 2 13 0 TTAAGAATAA 0.94179 -195 CCTTTATAAATAAAAATTAAATGATGATAC 2 89 0 TAAAAATTAA 0.84384 -119 ATTTTGAGTGAAAGGATTAAGCAAG 2 193 1 AAAGGATTAA 0.947529 -15 ATCTCAATTTTAAGGAATAAC 3 2 0 TAAGGAATAA 0.979001 -154 ********** Masking position 6 Map Score: 5.49871 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 174 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 4 TTTTTTAGCGCTCTTAGTGGCGTTTAAGAA 2 26 0 CTCTTAGTGG 0.988836 -182 GGTTTGTATGGTGTTGGTAGTTTTTAGCTT 2 163 1 GTGTTGGTAG 0.902939 -45 ACTAAAAGGGCTTTTATTGTTTTTTAAAAG 3 99 0 CTTTTATTGT 0.900077 -57 AATAAAAGCCCTTTTAGTGGCTTTCAAGTC 3 111 1 CTTTTAGTGG 0.990591 -45 TCTGTTAGTATATCAAACTTA 3 145 0 CTGTTAGTAT 0.969902 -11 ********** Masking position 5 Map Score: 1.41101 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 162 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 ********** No masking Map Score: -7.57849e-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: -7.57849e-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: -7.57849e-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