AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00471_hpyl_reg_300.orf -o00471_hpyl_300.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 HP0493 124 phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) #2 HP0549 37 glutamate racemase (glr) #3 HP0550 263 transcription termination factor Rho (rho) #4 HP0624 119 solute-binding signature and mitochondrial signature protein (aspB) Motif number 1 GGATAGAAGCTTATTTTAATTTTTAGGAATCTT 1 13 0 TTTTTAATTT 0.978823 -112 CTATTCATGCTATTTTTAAGTAAATCAATTTGC 1 50 1 TTTTTAATAA 0.952409 -75 ACAATTTTCTTTTTTCTAAATTTCAAGCATGGC 1 86 1 TTTCTAATTT 0.927179 -39 GACACTATTTTTAATTTAATGGGATTAA 2 20 0 TTTTTAATTA 0.91736 -18 AAGTATCCTTTATTTTTAAATTTAAACTTAAAA 3 12 1 TTTTTAATTT 0.913939 -252 ACTTATGCTATAATTTTAAGTTTAAATTTAAAA 3 25 0 TTTTTAATTT 0.983228 -239 AACTTTAGAGTGGTTTTAATTTATTATGACTTA 3 53 0 TTTTTAATTA 0.985843 -211 AAAGTCAAATTTTATTTAACTTTAGAGTGGTTT 3 70 0 TATTTAATTT 0.89603 -194 GCTATCATAATTTTTTTAACAAAGTCAAATTTT 3 90 0 TTTTTAAAAA 0.929834 -174 GGTTACACTAATTTTTTAAGAATGCTTTAGCTT 3 181 1 ATTTTAAAAT 0.66921 -83 TAGCTTTTTGTATTTTTATCTTAATTGCAACAA 3 208 1 TTTTTATTTA 0.882144 -56 TAAATTTCCTTTTAACAAAAAGAGATTTC 3 245 0 TTTTTAAAAA 0.937965 -19 ATTAACTATTCCATTTTAAGATTAAAGTAGCCC 4 96 1 CTTTTAAATT 0.866664 -24 * ****** *** Masking position 8 Map Score: 22.7485 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 273 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 2 AATAAGCTTCTATCCTACCCTATTCATGCTATTT 1 31 1 TATCTATATT 0.881845 -94 CAATTTGCGCTACAATTTTCTTTTTTCTAAATTT 1 75 1 TACATTTTTT 0.96082 -50 CAAGTATCCTTTATTTTTAAATTTAAAC 3 5 1 TATCTTTTTT 0.981419 -259 TATTATGACTTATGCTATAATTTTAAGTTTAAAT 3 31 0 TATCTATTTT 0.981461 -233 TTTGCTATGCTATCATAATTTTTTTAACAAAGTC 3 97 0 TATATATTTT 0.957689 -167 ATCTTTTGGTTACACTAATTTTTTAAGAATGCTT 3 174 1 TACCTATTTT 0.98288 -90 ATTTTTTAAGAATGCTTTAGCTTTTTGTATTTTT 3 191 1 AATCTTCTTT 0.806758 -73 TCTTATGCGCTATTATACTCTTTCTTGGTGGTTT 4 33 1 TATATATTTC 0.825195 -87 TTCATACCATAACGCTTAAATTTTAGGTAAGATT 4 65 1 AACCTTTTTT 0.96275 -55 AGGTAAGATTAACTATTCCATTTTAAGATTAAAG 4 89 1 AACATTTTTT 0.917386 -31 *** *** **** Masking position 6 Map Score: 9.9016 Number of sites scoring better than the average of aligned sites = 372 Number in coding regions = 291 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 3 AAAAGATTCCTAAAAATTAAAATA 1 2 1 AAAGCCTAAA 0.961869 -123 GATTTACTTAAAAATAGCATGAATAGGGTAGGA 1 43 0 AAAACATGAA 0.952361 -82 AAAATCCCCTAAAATCGCCATGC 1 112 0 AAAACCTAAA 0.982455 -13 TAATAAATTAAAACCACTCTAAAGTTAAATAAA 3 60 1 AAACTCTAAA 0.883058 -204 CAATTAAGATAAAAATACAAAAAGCTAAAGCAT 3 202 0 AAAACAAAAA 0.928182 -62 GAAAGAGTATAATAGCGCATAAGAATTTAACTG 4 24 0 AATACATAAG 0.774403 -96 TTATGGTATGAAACCACCAAGAAAGAGTATAAT 4 44 0 AAACCAAGAA 0.898351 -76 TGGAATAGTTAATCTTACCTAAAATTTAAGCGT 4 76 0 AATCCCTAAA 0.961173 -44 **** ****** Masking position 2 Map Score: 1.93807 Number of sites scoring better than the average of aligned sites = 1115 Number in coding regions = 963 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 4 GAAATTTAGAAAAAAGAAAATTGTAGCGCAA 1 79 0 AAAAGAAAAT 0.782787 -46 GCATGGCGATTTTAGGGGATTTT 1 112 1 TTTAGGGATT 0.863961 -13 TAATGGGATTAATTAGGGATT 2 1 0 AATTGGGATT 0.656705 -37 TATTTTTAATTTAATGGGATTAATTAGGGAT 2 12 0 TTAAGGGATT 0.933447 -26 ACTCTAAAGTTAAATAAAATTTGACTTTGTT 3 75 1 TAAAAAAATT 0.751497 -189 TTTGACTTTGTTAAAAAAATTATGATAGCAT 3 94 1 TTAAAAAATT 0.673805 -170 ATAGCAAAGAATTACGAAATTCAACACTTGT 3 123 1 ATTAGAAATT 0.887658 -141 TCCTTTTAACAAAAAGAGATTTCTAGTTTGT 3 237 0 AAAAGAGATT 0.965215 -27 TCTTTTTGTTAAAAGGAAATTTA 3 251 1 AAAAGAAATT 0.96242 -13 CTTTAATCTTAAAATGGAATAGTTAATCTTA 4 92 0 AAAAGGAATA 0.796071 -28 **** ****** Masking position 9 Map Score: 3.80067 Number of sites scoring better than the average of aligned sites = 1282 Number in coding regions = 1075 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 5 CCTAAAAATTAAAATAAGCTTCTATCCTAC 1 19 1 AAAATAAGCT 0.897604 -106 AATTAGTGTAACCAAAAGATGCTAATAAGT 3 164 0 ACCAAAAGAT 0.970875 -100 AGATAAAAATACAAAAAGCTAAAGCATTCT 3 199 0 ACAAAAAGCT 0.988765 -65 TTTCCTTTTAACAAAAAGAGATTTCTAGTT 3 240 0 ACAAAAAGAG 0.970913 -24 ********** Masking position 6 Map Score: 0.111908 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 106 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 ********** No masking Map Score: 4.50646e-14 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: 4.50646e-14 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: 4.50646e-14 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