AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00950_hpyl_reg_100.orf -o00950_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HP1067 290 chemotaxis protein (cheY) #2 HP1376 171 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase (fabZ) #3 HP1483 26 gerC2 protein (gerC2) #4 HP1490 103 hemolysin Motif number 1 GGATGGTTTGAAAAAAGAAAGACAAGGATT 1 21 0 AAAAAAGAAA 0.950523 -270 TTTAAAAGTAATAAAATAACTCTTTGAGTG 1 66 0 ATAAAATAAC 0.733409 -225 ATTTTTTTACAAATAAGAACGCTCATTGAA 1 120 1 AAATAAGAAC 0.919786 -171 AATCATTGGCTAAATGGAGCGTTCAATGAG 1 141 0 TAAATGGAGC 0.731229 -150 AAATCGTTCCAAATAATAGCATGTTTTGAT 1 193 0 AAATAATAGC 0.894262 -98 TAACGCCTTATAATAATAAATCGTTCCAAA 1 210 0 TAATAATAAA 0.837972 -81 TTTGGCTGTTTAAAAAGAGCCTAATTTAAA 1 247 1 TAAAAAGAGC 0.976832 -44 AATGCAATCTTAAAAGGAGAAGCACT 1 275 1 TAAAAGGAGA 0.877526 -16 GGTTATTCTAAAAAAATAACCGCTATTATA 2 103 0 AAAAAATAAC 0.962758 -69 TAACCAACGCTAAAAATAGCGCTTTAATTG 2 128 1 TAAAAATAGC 0.968272 -44 ACAAGCCATGAAAAAAGAAAAGTC 3 13 1 AAAAAAGAAA 0.950523 -14 AGCCTAACTTTAAAAATCAAGCCTTCAAAA 4 14 0 TAAAAATCAA 0.717576 -90 AACCTAACGATAAATATAAAATATATAAAA 4 70 0 TAAATATAAA 0.766903 -34 ********** Masking position 3 Map Score: 14.3681 Number of sites scoring better than the average of aligned sites = 1691 Number in coding regions = 1411 Number in noncoding regions = 280 Number of orfs with sites within 600 bp upstream = 208 Fraction of orfs with sites within 600 bp upstream = 0.0334083 Motif number 2 TTACTTGTAAAATCCTTGTCTTTCTTTT 1 9 1 AAAATCCTTG 0.879513 -282 AACCATCCAATGACCCTTTATCGCACTCAA 1 43 1 TGACCCTTTA 0.872378 -248 AGTAATAAAATAACTCTTTGAGTGCGATAA 1 60 0 TAACTCTTTG 0.954256 -231 AAAGCGTCTCTAACGCCTTATAATAATAAA 1 220 0 TAACGCCTTA 0.951912 -71 AAGGCGTTAGAGACGCTTTGGCTGTTTAAA 1 231 1 AGACGCTTTG 0.975431 -60 CTTTGCATAGAAACCGCTTATGCA 2 5 0 AAACCGCTTA 0.913901 -167 AAGCTTCAAGAAACGCTTTGCATAGAAACC 2 20 0 AAACGCTTTG 0.983825 -152 TACCATAAGAAAACCGCTCGCTTGTATTTG 2 75 0 AAACCGCTCG 0.84535 -97 ACGCTAAAAATAGCGCTTTAATTGAATCCA 2 134 1 TAGCGCTTTA 0.783987 -38 AAAATAAACTCCTTGTTTTGGATTC 2 157 0 AAACTCCTTG 0.979335 -15 GGTTTTTGAAGGCTTGATTTTTAAAG 4 7 1 TGAAGGCTTG 0.791002 -97 ********** Masking position 8 Map Score: 10.6651 Number of sites scoring better than the average of aligned sites = 1627 Number in coding regions = 1485 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 3 TGCTATGATAATCGTTTAAAAGTAATAAAA 1 80 0 ATCGTTTAAA 0.713051 -211 GCGTTCAATGAGCGTTCTTATTTGTAAAAA 1 123 0 AGCGTTCTTA 0.956154 -168 GGCTAAATGGAGCGTTCAATGAGCGTTCTT 1 134 0 AGCGTTCAAT 0.904972 -157 ATAATAATAAATCGTTCCAAATAATAGCAT 1 201 0 ATCGTTCCAA 0.735594 -90 AAACAGCCAAAGCGTCTCTAACGCCTTATA 1 228 0 AGCGTCTCTA 0.837495 -63 TGCATAAGCGGTTTCTATGCAAAGCG 2 7 1 AGCGGTTTCT 0.9004 -165 TTCTATGCAAAGCGTTTCTTGAAGCTTATG 2 23 1 AGCGTTTCTT 0.972733 -149 GGCGCAATGCATCGGTGTTTTTGCAAATAC 2 52 1 ATCGGTGTTT 0.785995 -120 AATACAAGCGAGCGGTTTTCTTATGGTATA 2 77 1 AGCGGTTTTC 0.912841 -95 ATGGTATAATAGCGGTTATTTTTTTAGAAT 2 99 1 AGCGGTTATT 0.95499 -73 CGCTATTTTTAGCGTTGGTTATTCTAAAAA 2 119 0 AGCGTTGGTT 0.866755 -53 CGCTAAAAATAGCGCTTTAATTGAATCCAA 2 135 1 AGCGCTTTAA 0.827479 -37 ********** Masking position 1 Map Score: 8.23717 Number of sites scoring better than the average of aligned sites = 3077 Number in coding regions = 2781 Number in noncoding regions = 296 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 4 AGACAAGGATTTTACAAGTAA 1 1 0 TTTACAGTAA 0.961842 -290 ATGATAATCGTTTAAAAGTAATAAAATAACT 1 75 0 TTTAAAGTAA 0.980976 -216 ACTGAATTTTTTTACAAATAAGAACGCTCAT 1 115 1 TTTACAATAA 0.924254 -176 GTCAAGGTAATTTTAATCAAAACATGCTATT 1 178 1 TTTTAACAAA 0.789178 -113 AAGAGCCTAATTTAAATGCAATCTTAAAAGG 1 261 1 TTTAAAGCAA 0.931931 -30 GCGGTTATTTTTTTAGAATAACCAACGCTAA 2 110 1 TTTTAGATAA 0.825479 -62 AAGGCTTGATTTTTAAAGTTAGGCTTAATCT 4 19 1 TTTTAAGTTA 0.868395 -85 AATCTCAGAATTTTAACATAAAAGATTAAGC 4 41 0 TTTTAAATAA 0.952796 -63 AACTTTAAACCTAAAACCTAACGA 4 90 0 TTTAAACTAA 0.964226 -14 ****** **** Masking position 3 Map Score: 7.73671 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 222 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 5 TTATCATAGCAAACAAACTGAATTTTTTTAC 1 99 1 AAAAAACTGA 0.944128 -192 AACGCTTTGCATAGAAACCGCTTATGCA 2 8 0 ATAAAACCGC 0.979228 -164 TTGTATTTGCAAAAACACCGATGCATTGCGC 2 53 0 AAAACACCGA 0.957716 -119 ATTATACCATAAGAAAACCGCTCGCTTGTAT 2 78 0 AAGAAACCGC 0.98589 -94 TTATTCTAAAAAAATAACCGCTATTATACCA 2 100 0 AAATAACCGC 0.979228 -72 AACCAACGCTAAAAATAGCGCTTTAATTGAA 2 129 1 AAAATAGCGC 0.915035 -43 AAAATAAACTCCTTGTTTTGGA 2 160 0 AAAAAACTCC 0.922532 -12 *** ******* Masking position 7 Map Score: 4.75061 Number of sites scoring better than the average of aligned sites = 470 Number in coding regions = 429 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 ********** No masking Map Score: 1.76458e-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 ********** No masking Map Score: 1.76458e-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: 1.76458e-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