AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i316_mixed3_hpyl_reg_100.orf -o316_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 RHP00170 300 AE000511 #2 RHP00636 119 AE000511 #3 RHP00765 42 AE000511 #4 RHP00768 171 AE000511 #5 RHP00950 87 AE000511 #6 RHP00951 74 AE000511 Motif number 1 ATTGTTAGGCGTAACCGCTGTCGCGCAAGTG 1 21 1 GTAACCGCTT 0.974781 -280 GAAACCATTAACAAGCGTTCTCCCCACTTGC 1 45 0 ACAAGCGTTT 0.914039 -256 TGCAGGGGGCACAACCGCTGTAATTATCACA 1 105 1 ACAACCGCTT 0.979612 -196 TTGCGTATTTGAAAGTGCTAGAAAAGTGCTT 1 149 1 GAAAGTGCTG 0.917216 -152 AAAGTGCTAGAAAAGTGCTTTAATGATGAGA 1 160 1 AAAAGTGCTT 0.967258 -141 AAAATAACTTAAAAGAGCTATAAAATAGCCT 2 64 1 AAAAGAGCTT 0.968242 -56 GCTTTGCATAGAAACCGCTTATGCA 4 5 0 GAAACCGCTA 0.951626 -167 ATACCATAAGAAAACCGCTCGCTTGTATTTG 4 75 0 AAAACCGCTG 0.982876 -97 TTCTAAAAAAATAACCGCTATTATACCATAA 4 97 0 ATAACCGCTT 0.973259 -75 TGGATTCAATTAAAGCGCTATTTTTAGCGTT 4 133 0 TAAAGCGCTT 0.96969 -39 GGCTGTGTTAGAAAGCGTTATTCAAGTTTAG 5 16 1 GAAAGCGTTT 0.958615 -72 TTCAGCTTTTAAAATAGCTTTGATTATAACT 5 45 0 AAAATAGCTT 0.799033 -43 ********* * Masking position 4 Map Score: 17.0994 Number of sites scoring better than the average of aligned sites = 1059 Number in coding regions = 956 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 2 ACCCAATGCCTTCTGTGATAATTACAGCGGTT 1 117 0 TTTTGATAAT 0.913615 -184 AACTTCTCTCTTTAAGGAGAATTATCTCAACT 1 228 1 TTAGGAGAAT 0.970552 -73 ACATCCAAAATTAAAGGAGAAAACC 2 4 0 TTAGGAGAAA 0.838594 -116 TTTTGGATGTTTAAAGTATAATAAACTATCTT 2 26 1 TTAGTATAAT 0.953133 -94 AGCGGTTTTCTTATGGTATAATAGCGGTTATT 4 87 1 TTTGTATAAT 0.942882 -85 ATAGCGGTTATTTTTTTAGAATAACCAACGCT 4 107 1 TTTTTAGAAT 0.961819 -65 GTTATTCAAGTTTAGTTATAATCAAAGCTATT 5 32 1 TTATTATAAT 0.940458 -56 GTTATTCTCCTTATGTTAGAATGTTTGATTAT 6 19 1 TTTTTAGAAT 0.96182 -56 ATCCTATGGTTTTATTTAGTATGTTACAATAA 6 47 0 TTATTAGTAT 0.830284 -28 ** * ******* Masking position 8 Map Score: 7.88399 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 67 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 3 GGGCACAACCGCTGTAATTATCACAGAAGG 1 111 1 GCTGTAATTA 0.891136 -190 CATTGGGTTTGCGTATTTGAAAGTGCTAGA 1 141 1 GCGTATTTGA 0.658256 -160 CTAGAAAAGTGCTTTAATGATGAGACGGGC 1 166 1 GCTTTAATGA 0.810547 -135 GCGTTTTTCATAACCCCTAA 1 291 0 GCGTTTTTCA 0.958035 -10 TTGTTTTATCGCGTATTTTAAGGCTATTTT 2 85 0 GCGTATTTTA 0.84751 -35 TGCATAAGCGGTTTCTATGCAAAGCGT 4 8 1 GCGGTTTCTA 0.743272 -164 ATACAAGCGAGCGGTTTTCTTATGGTATAA 4 78 1 GCGGTTTTCT 0.739625 -94 TGGTATAATAGCGGTTATTTTTTTAGAATA 4 100 1 GCGGTTATTT 0.764869 -72 GCTATTTTTAGCGTTGGTTATTCTAAAAAA 4 118 0 GCGTTGGTTA 0.864232 -54 CAATTAAAGCGCTATTTTTAGCGTTGGTTA 4 128 0 GCTATTTTTA 0.827505 -44 TAAAAATAGCGCTTTAATTGAATCCAAAAC 4 138 1 GCTTTAATTG 0.660686 -34 GTGTTAGAAAGCGTTATTCAAGTTTAGTTA 5 20 1 GCGTTATTCA 0.945459 -68 TTTTAAAATAGCTTTGATTATAACTAAACT 5 40 0 GCTTTGATTA 0.874854 -48 AAGCTGAATAGCTATAGTTATTAGGATGCG 5 68 1 GCTATAGTTA 0.610333 -20 TTATCCTATGGTTTTATTTAGTATGTTACA 6 51 0 GTTTTATTTA 0.462179 -24 GCTTTTATCCTATGGTTTTA 6 65 0 GCTTTTATCC 0.629672 -10 ********** Masking position 1 Map Score: 6.6159 Number of sites scoring better than the average of aligned sites = 3320 Number in coding regions = 2971 Number in noncoding regions = 349 Number of orfs with sites within 600 bp upstream = 214 Fraction of orfs with sites within 600 bp upstream = 0.034372 Motif number 4 GTTGGCATGATAACTTCTCTCTTTAAGGAGAATT 1 217 1 TAATTCTTTT 0.93621 -84 TCATAACCCCTAATCTTATTGTGTTAATTTCTTG 1 270 0 TAACTTTTGT 0.977495 -31 TAAAGTATAATAAACTATCTTTTTAAAAAAATAA 2 37 1 TAACTCTTTT 0.977494 -83 ATAGCTCTTTTAAGTTATTTTTTTAAAAAGATAG 2 51 0 TAATTTTTTT 0.946532 -69 AAAATAAACTCCTTGTTTTGGATTCAAT 4 154 0 TAACTTTTTT 0.981269 -18 AATTGATTGTTATTCTCCTTATGTTAGAATGTTT 6 11 1 TATCTTTTGT 0.914643 -64 *** ** ** *** Masking position 6 Map Score: 1.51833 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 46 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 AAGGAAACCATTAACAAGCGTTCTCCCCAC 1 49 0 TTAACAAGCG 0.806692 -252 TTCTAGCACTTTCAAATACGCAAACCCAAT 1 142 0 TTCAAATACG 0.878779 -159 ATTAGGGGTTATGAAAAACGC 1 290 1 ATGAAAAACG 0.9623 -11 TAAAATAGCCTTAAAATACGCGATAAAACA 2 84 1 TTAAAATACG 0.896104 -36 AGCGGTTTCTATGCAAAGCGTTTCTTGAAG 4 17 1 ATGCAAAGCG 0.954006 -155 AAAAACACCGATGCATTGCGCCATAAGCTT 4 44 0 ATGCATTGCG 0.873893 -128 ATAACTAAACTTGAATAACGCTTTCTAACA 5 21 0 TTGAATAACG 0.935313 -67 ********** Masking position 2 Map Score: 0.5627 Number of sites scoring better than the average of aligned sites = 531 Number in coding regions = 472 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 ********** No masking Map Score: -1.61761e-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 7 TTGTGGGGAGTGTTGCAGGGGGCACAACCGCTG 1 92 1 TGTTGCGGGC 0.992178 -209 AGTGCTTTAATGATGAGACGGGCGAAGTCAATT 1 173 1 TGATGAGGGC 0.995197 -128 TCAATTTGCCTGATGAAGTTGGCATGATAACTT 1 200 1 TGATGATGGC 0.99259 -101 AAGCGTTTCTTGAAGCTTATGGCGCAATGCATC 4 32 1 TGAAGCTGGC 0.987953 -140 ****** **** Masking position 1 Map Score: 0.0711556 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 20 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 ********** No masking Map Score: -1.61761e-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: -1.61761e-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 10 ********** No masking Map Score: -1.61761e-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