AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00580_hinf_reg_100.orf -o00580_hinf_100.ace -a/home/amcguire/genomes/ORF_hinf.txt -z/home/amcguire/genomes/hinf.fna -g0.38 -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 HI0645 54 lysophospholipase L2 (pldB) #2 HI0646 158 aspartate-semialdehyde dehydrogenase (asd) #3 HI0686 292 glycerol-3-phosphatase transporter (glpT) #4 HI0687 99 conserved hypothetical protein #5 HI0688 94 H. influenzae predicted coding region HI0688 Motif number 1 TACGCCCTTTTCATTAAAAAATT 1 42 1 TCATTAAAAA 0.958841 -13 AAAGTGTGGTTAATTTAAAAGAAAATTTAA 2 27 0 TAATTTAAAA 0.905687 -132 GAAAGAAATTAAATAAAAAAGTGTGGTTAA 2 44 0 AAATAAAAAA 0.961849 -115 AGATCAATTTTCATTAAAAATACTTGATTT 2 79 1 TCATTAAAAA 0.958841 -80 CGCTATCTTGTAATTAATAATGCTATTCAA 2 115 1 TAATTAATAA 0.842035 -44 TCCCAAAATGTAAGAAAAAATAATATAAAA 3 25 1 TAAGAAAAAA 0.927698 -268 TAAGAAAAAATAATATAAAAAGTGTAATCA 3 35 1 TAATATAAAA 0.892405 -258 AGTGCGGCCAAAATTAACAACATTTTGAGT 3 74 1 AAATTAACAA 0.821642 -219 AAAGTAAAAAAAATCAAAAATGTGAAGTGT 3 178 0 AAATCAAAAA 0.885815 -115 AAAAAATAAGAAAGTAAAAAAAATCAAAAA 3 188 0 AAAGTAAAAA 0.894492 -105 TCATAAAAGAAAATAAAAAATAAGAAAGTA 3 202 0 AAATAAAAAA 0.961849 -91 GATTTGCGAATCATAAAAGAAAATAAAAAA 3 212 0 TCATAAAAGA 0.746838 -81 AGATGACACATAATTAAAAAGTTGGAGAAA 3 268 1 TAATTAAAAA 0.980773 -25 ATCATAAGAATAATAAAAAGATAAGTATCA 4 62 1 TAATAAAAAG 0.86574 -38 ********** Masking position 7 Map Score: 19.7936 Number of sites scoring better than the average of aligned sites = 681 Number in coding regions = 447 Number in noncoding regions = 234 Number of orfs with sites within 600 bp upstream = 192 Fraction of orfs with sites within 600 bp upstream = 0.0308384 Motif number 2 GTAGTAAATACGCCCTTTGTAGTGAAAGTA 1 15 0 CGCCCTTTGT 0.987928 -40 GTATTTACTACGCCCTTTTCATTAAAAAAT 1 34 1 CGCCCTTTTC 0.984162 -21 TTAATTTAATCACTCTTTTT 2 1 0 CACTCTTTTT 0.971487 -158 TTAAATTAACCACACTTTTTTATTTAATTT 2 39 1 CACACTTTTT 0.93096 -120 ACAATGATTACACTTTTTATATTATTTTTT 3 39 0 CACTTTTTAT 0.863918 -254 ATCACAAAATCGCTTTCTTTTACACTCAAA 3 97 0 CGCTTTCTTT 0.925165 -196 ATTTGCCCACCGCCTTTTTTAAGCTAA 4 8 0 CGCCTTTTTT 0.992667 -92 ATTGCTTAGTCGCCTTTTTTGTAACTATCA 4 36 1 CGCCTTTTTT 0.992667 -64 GAATTGCTAACGCCCTTAATAAAACCAATT 5 62 0 CGCCCTTAAT 0.938831 -33 ********** Masking position 6 Map Score: 14.5902 Number of sites scoring better than the average of aligned sites = 590 Number in coding regions = 408 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 3 ATTTTACTTTCACTACAAAGGGCGTAT 1 8 1 TTTCACTACA 0.865466 -47 ACTACGCCCTTTTCATTAAAAAATT 1 40 1 TTTCATTAAA 0.820804 -15 AAAATTGATCTTTCGCGAAAGAAATTAAAT 2 60 0 TTTCGCGAAA 0.497379 -99 AAAGATCAATTTTCATTAAAAATACTTGAT 2 77 1 TTTCATTAAA 0.820804 -82 TTTACCCCCGATTCCCAAAATGTAAGAAAA 3 13 1 ATTCCCAAAA 0.942101 -280 TTGTGATCAATATCACAAAATCGCTTTCTT 3 108 0 TATCACAAAA 0.92502 -185 TAATTTTCGCATTCGCTCAAACGGTGTAAA 3 138 1 ATTCGCTCAA 0.7577 -155 ATGTGAAGTGTTTCACAAATCTTTACACCG 3 159 0 TTTCACAAAT 0.932419 -134 AAGTAAAAAAAATCAAAAATGTGAAGTGTT 3 177 0 AATCAAAAAT 0.223823 -116 TTCTTTTATGATTCGCAAATCCCTTACTGT 3 221 1 ATTCGCAAAT 0.86537 -72 TTTTACTTTTCCCAAAAATGATACTTA 4 83 0 TTTCCCAAAA 0.961373 -17 ********** Masking position 3 Map Score: 6.01036 Number of sites scoring better than the average of aligned sites = 875 Number in coding regions = 744 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 4 AAAAAGAGTGATTAAATTAAATTTTCTT 2 9 1 TGATTAAATT 0.939255 -150 TAAAAAAGTGTGGTTAATTTAAAAGAAAAT 2 31 0 TGGTTAATTT 0.975335 -128 CTTTCGCGAAAGATCAATTTTCATTAAAAA 2 69 1 AGATCAATTT 0.847108 -90 ACTCAAAATGTTGTTAATTTTGGCCGCACT 3 74 0 TTGTTAATTT 0.815402 -219 AAAATTATTGTGATCAATATCACAAAATCG 3 115 0 TGATCAATAT 0.730936 -178 CTGTTTCAAAAGGGTAAATTTAGATGACAC 3 247 1 AGGGTAAATT 0.891341 -46 AAAAAGGCGGTGGGCAAATTGCTTAGTCGC 4 19 1 TGGGCAAATT 0.956453 -81 GTTAAATATCTGGTTCAATTGGTTTTATTA 5 46 1 TGGTTCAATT 0.913122 -49 ********** Masking position 7 Map Score: 3.90558 Number of sites scoring better than the average of aligned sites = 796 Number in coding regions = 632 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 5 ATTTTTTCTTACATTTTGGGAATCGGGGGT 3 16 0 ACATTTTGGG 0.981518 -277 AAAATTAACAACATTTTGAGTGTAAAAGAA 3 83 1 ACATTTTGAG 0.980079 -210 AAATCTTTACACCGTTTGAGCGAATGCGAA 3 143 0 ACCGTTTGAG 0.980367 -150 CCCTTTTGAAACAGTAAGGGATTTGCGAAT 3 231 0 ACAGTAAGGG 0.934993 -62 ACATAATTAAAAAGTTGGAGAAAAAATT 3 275 1 AAAGTTGGAG 0.925706 -18 ********** Masking position 5 Map Score: 0.906465 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 45 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 ********** No masking Map Score: 1.57984e-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: 1.57984e-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: 1.57984e-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