AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i196_mixed_replication_rec__hpyl_reg_100.orf -o196_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 RHP01073 165 AE000511 #2 RHP01276 248 AE000511 #3 RHP01277 24 AE000511 Motif number 1 AGATATTTGATTTTAGTCAAGCAAAGGGTG 1 28 1 TTTTAGTCAA 0.979681 -138 GGTTTTTATGGTTTAATGAATCGTTTAGTC 1 88 1 GTTTAATGAA 0.983544 -78 TTAATGAATCGTTTAGTCAAAATTCTATGC 1 100 1 GTTTAGTCAA 0.975491 -66 TGTTTATACCTATTAATGAATGATTGTAGC 1 128 0 TATTAATGAA 0.919505 -38 AAACGCATCGTTTAAGTGAAAAATTAGCTT 2 31 1 TTTAAGTGAA 0.949675 -218 CTACGAGCACTTTTAAAGAAGTGAAACGAT 2 75 0 TTTTAAAGAA 0.963622 -174 TTCTGCATGTTTTTAAACATTATCGCTCCC 2 182 1 TTTTAAACAT 0.87126 -67 CTCCTAGCGTGTTTAAGCAAGTATTTATTT 2 221 0 GTTTAAGCAA 0.9369 -28 TTCCTTTTATTTTAAATGAT 3 1 0 TTTAAATGAT 0.878582 -24 ********** Masking position 5 Map Score: 9.97269 Number of sites scoring better than the average of aligned sites = 772 Number in coding regions = 649 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 2 TCAAATATCTATGCAAAGGATGCAAAC 1 8 0 ATGCAAAGGA 0.833093 -158 GCTTGACTAAAATCAAATATCTATGCAAAG 1 20 0 AATCAAATAT 0.910201 -146 GATTTTAGTCAAGCAAAGGGTGTTCCAACT 1 36 1 AAGCAAAGGG 0.982101 -130 CAGCGTTAAAAATCAAAGAGTTGGAACACC 1 54 0 AATCAAAGAG 0.930794 -112 GAACGCCTTTAATAAAATGTTTATACCTAT 1 145 0 AATAAAATGT 0.917123 -21 TGATTATAGCAAGAAAAGCTAATTTTTCAC 2 46 0 AAGAAAAGCT 0.945797 -203 GCAGAATATTAAGAAATGGTGTGCTCGGAG 2 158 0 AAGAAATGGT 0.866999 -91 TAGCGTGTTTAAGCAAGTATTTATTTTACC 2 217 0 AAGCAAGTAT 0.790646 -32 AATCAAATCTCCTAGCGTGT 2 239 0 AATCAAATCT 0.916261 -10 ATCATTTAAAATAAAAGGAATCAT 3 10 1 AATAAAAGGA 0.904697 -15 ********** Masking position 5 Map Score: 8.86708 Number of sites scoring better than the average of aligned sites = 868 Number in coding regions = 772 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 3 AAAATTCTATGCTACAATCATTCATTAATA 1 118 1 GCTACAATCA 0.991392 -48 AGCTTTTCTTGCTATAATCATCGTTTCACT 2 56 1 GCTATAATCA 0.974947 -193 ATTCAGCTGAGCTACGAGCACTTTTAAAGA 2 86 0 GCTACGAGCA 0.990391 -163 GCAACCTGTTGCTCTATTCAGCTGAGCTAC 2 101 0 GCTCTATTCA 0.937874 -148 GGTTTGAATCCCTCCGAGCACACCATTTCT 2 147 1 CCTCCGAGCA 0.973795 -102 AAACATTATCGCTCCCATTATGGTAAAATA 2 196 1 GCTCCCATTA 0.942639 -53 ********** Masking position 3 Map Score: 5.201 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 168 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 TATCTATGCAAAGGATGCAAAC 1 3 0 AAGGATGCAA 0.982761 -163 ATTTTGACTAAACGATTCATTAAACCATAA 1 93 0 AACGATTCAT 0.985449 -73 TTTTCACTTAAACGATGCGTTTTTTCTATT 2 23 0 AACGATGCGT 0.979631 -226 AAAGAAGTGAAACGATGATTATAGCAAGAA 2 61 0 AACGATGATT 0.834647 -188 GTGTGCTCGGAGGGATTCAAACCCCCGACC 2 140 0 AGGGATTCAA 0.930468 -109 TTTAAAATAAAAGGAATCAT 3 15 1 AAGGAATCAT 0.943834 -10 ********** Masking position 5 Map Score: 3.61471 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 86 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 CAAAGAGTTGGAACACCCTTTGCTTGACTA 1 41 0 GAACACCCTT 0.988904 -125 CTTTGATTTTTAACGCTGTTATGGTTTTTA 1 66 1 TAACGCTGTT 0.891152 -100 GGAACGCCTTTAATAAAATGT 1 155 0 GAACGCCTTT 0.990693 -11 GCTGAGCTACGAGCACTTTTAAAGAAGTGA 2 81 0 GAGCACTTTT 0.95498 -168 ATCCCTCCGAGCACACCATTTCTTAATATT 2 154 1 GCACACCATT 0.964433 -95 ********** Masking position 9 Map Score: 1.25708 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 220 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 ********** No masking Map Score: -3.88366e-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: -3.88366e-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: -3.88366e-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