AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i087_PTS_sugar_Utilization_hinf_reg_100.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -x5 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 = 0 Input sequences: #1 HI0448 71 PTS system, fructose-specific IIA/FPr component (fruB) #2 HI0449 86 H. influenzae predicted coding region HI0449 #3 HI0451 71 conserved hypothetical protein #4 HI0452 50 conserved hypothetical protein #5 HI0453 26 conserved hypothetical protein #6 HI0454 54 conserved hypothetical protein #7 HI0457 69 conserved hypothetical protein #8 HI0458 70 stationary phase survival protein SurA, putative #9 HI0459 131 pyrimidine operon regulatory protein (pyrR) #10 HI1009 158 glycerol-3-phosphate regulon repressor (glpR) #11 HI1711 59 PTS system, glucose-specific IIA component (crr) #12 HI1712 79 phosphoenolpyruvate-protein phosphotransferase (ptsI) #13 HI1713 158 phosphocarrier protein HPr (ptsH) Motif number 1 CATCCGCAGCTTTCTTTTTAAATTATTAAGGAG 1 44 1 TTTTTTTTAT 0.890077 -28 AAGTGCGGTAAATTTTTATCCATTTCTCTACAA 3 11 1 AATTTTATAT 0.583848 -61 TTAACCTCAAATTTTTTATGGTTTTATAACATA 3 47 0 ATTTTTATTT 0.967765 -25 GTGCGGTCGTTTTCTTTTATATTTTTGAGTA 4 30 1 TTTTTTTATT 0.841374 -21 AATTATTTTTCCTTATGCCTAAGG 6 41 0 ATTTTTTTTT 0.960329 -14 AAGCCCCTTTATTTTTGATACTTTG 7 3 0 ATTTTGATTT 0.95742 -67 AATTGCCCCTTTTGTTGTTTTTTATTTTCTCTT 7 36 1 TTTTTGTTTT 0.965567 -34 TTATTTTCTCTTTCTTATAGCTT 7 57 1 TTTTTATATT 0.520019 -13 TTGCACCATTTTTCTTGTTCGTTATACTATCCA 9 38 0 TTTTTGTTTT 0.965567 -94 TTAGGCGTATTTTCTTTATACTTTGTGCATTGA 9 84 1 TTTTTTATTT 0.978933 -48 AAAAAATAACATTTTTTATCATTCTGTGATCTA 10 83 0 ATTTTTATTT 0.967112 -76 AAAAATGTTATTTTTTGTTAATTTTAGTGATAA 10 100 1 TTTTTGTTTT 0.965567 -59 TTTTATGGCTATTGTTTATTTATTACTTTGTTA 12 38 1 ATTTTTATAT 0.866498 -42 TATTTATTACTTTGTTAATTGTTTCGGAAGGTA 12 54 1 TTTTTAATTT 0.904676 -26 AGCTAAATAGTTTATTTATTATTCACAATCTCA 13 15 0 TTTTTTATTT 0.978921 -144 CTATTTAGCTTATTTTTATGATTTAATTCAGGC 13 38 1 TATTTTATTT 0.909422 -121 TTTAGTGTTTATTCTTGATTATTTTGCTTTGAA 13 73 1 ATTTTGATTT 0.957333 -86 TTTCTGGTTTTATATTTTTAATTATTGATTAGT 13 124 1 TATTTTTTTT 0.890077 -35 *** ***** ** Masking position 6 Map Score: 29.3394 Number of sites scoring better than the average of aligned sites = 596 Number in coding regions = 408 Number in noncoding regions = 188 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 2 CCTTTAGACAGTATAATGGCGGCGTTTTATTAACTTTAAT 2 52 1 GTATTTTTAT 0.878222 -35 AAGTGCGGTAAATTTTTATCCATTTCTCTACAAAATT 3 8 1 GAATATTTCT 0.842706 -64 ATTTTTTATGGTTTTATAACATAATTTTGTAGAGAAATGG 3 30 0 GTTTTTTTGT 0.971468 -42 CCAAACGGTCGCAAAGTGCGGTCGTTTTCTTTTATATTTT 4 15 1 GAATTTTTCT 0.974362 -36 AAAATAAAGGGGCTTAATTGCCCCTTTTGTTGTTTTTTAT 7 21 1 GTTATTTTGT 0.812252 -49 CCCTTTTGTTGTTTTTTATTTTCTCTTTCTTATAGCTT 7 42 1 GTTTCTTTCT 0.941193 -28 AAAAAGCGACGGCATTTGCACCATTTTTCTTGTTCGTTAT 9 46 0 GATTTTTTCT 0.978376 -86 AAATGCCGTCGCTTTTTAGGCGTATTTTCTTTATACTTTG 9 69 1 GTTTTTTTCT 0.987137 -63 CTATTTTAACGTAAAATCAAATAATTTTGT 11 1 0 GAATTTTTGT 0.942254 -59 ATTTAATTCAGGCTTTTTAGTGTTTATTCTTGATTATTTT 13 58 1 GTTTTATTCT 0.906986 -101 CTTTGAAAAAGGATACTAGGGCAATTTTCTGGTTTTATAT 13 99 1 GTATTTTTCT 0.984736 -60 * ** * ****** Masking position 17 Map Score: 9.96434 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 134 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 TACTGTCTAAAGGGGATTAAGCAAGGAAGC 2 35 0 AGGGGATTAA 0.994074 -52 TCAAAAATAAAGGGGCTTAATTGCCCCTTT 7 18 1 AGGGGCTTAA 0.989939 -52 AAGATCTATTAGGAGATTAAAA 10 3 0 AGGAGATTAA 0.990863 -156 TTGAATGGATAGGAGATTAAA 11 49 1 AGGAGATTAA 0.990863 -11 ********** Masking position 7 Map Score: 6.34451 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 1 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 4 TTAGAGTAACAATTCTATTGAAGGTTCACA 8 22 0 AATTCTATTG 0.917523 -49 TACTCTAACCAACGTTATTGACTCTTTTTT 8 44 1 AACGTTATTG 0.934735 -27 CCTTTGATGGAATGTTTTGGATAGTATAAC 9 21 1 AATGTTTTGG 0.893317 -111 TGTGCATTGAAATACTATTGATAAAGCTGG 9 107 1 AATACTATTG 0.73294 -25 AATGATAAAAAATGTTATTTTTTGTTAATT 10 93 1 AATGTTATTT 0.765556 -66 ATTTTTTGTTAATTTTAGTGATAAAACGTT 10 109 1 AATTTTAGTG 0.843641 -50 TTAGTGATAAAACGTTATGAGCTCATAATC 10 123 1 AACGTTATGA 0.691271 -36 AAAATTTCACAATTTTATGGCTAAGTAAGA 12 12 0 AATTTTATGG 0.976336 -68 AAAATTGTGAAATTTTATGGCTATTGTTTA 12 26 1 AATTTTATGG 0.976336 -54 ATACTAGGGCAATTTTCTGGTTTTATATTT 13 111 1 AATTTTCTGG 0.906013 -48 ********** Masking position 6 Map Score: 6.262 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 262 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 CATTTGCCTAGATAAGCCTTAC 2 3 1 TTTGCCTAGA 0.966615 -84 ACTTTTCCCTTGTTAGAACTGTG 5 14 0 TTTCCCTTGT 0.976839 -13 AATTTGGTTTCCTTTGATGGAATGTTT 9 8 1 TTTCCTTTGA 0.964057 -124 TCTTGATTATTTTGCTTTGAAAAAGGATAC 13 85 1 TTTGCTTTGA 0.94849 -74 AACCAGAAAATTGCCCTAGTATCCTTTTTC 13 103 0 TTGCCCTAGT 0.92987 -56 ********** Masking position 7 Map Score: 1.61821 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 76 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 ********** No masking Map Score: -1.99419e-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: -1.99419e-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: -1.99419e-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