AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i087_PTS_sugar_Utilization_hinf_reg_300.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) #14 HI1714 70 conserved hypothetical protein Motif number 1 TTGTTTTTCAATAAGCTGCTGGT 1 1 1 TTTTTTTATA 0.731535 -71 ATCCGCAGCTTTCTTTTTAAATTATTAAGGAGC 1 45 1 TTTTTTTATT 0.900469 -27 AGTGCGGTAAATTTTTATCCATTTCTCTACAAA 3 12 1 ATTTTATATT 0.779809 -60 TAACCTCAAATTTTTTATGGTTTTATAACATAA 3 46 0 TTTTTATTTT 0.980664 -26 GCGGTCGTTTTCTTTTATATTTTTGAGTA 4 32 1 TCTTTATTTT 0.836048 -19 AATTATTTTTCCTTATGCCTAAGGC 6 40 0 TTTTTTTTTA 0.911595 -15 AGCCCCTTTATTTTTGATACTTTG 7 2 0 TTTTGATTTT 0.967753 -68 GCCCCTTTTGTTGTTTTTTATTTTCTCTTTCTT 7 40 1 TTTTTTTTTT 0.97162 -30 CTAACCAACGTTATTGACTCTTTTTTGGATGAG 8 48 1 TTTTGACTTT 0.751091 -23 TGCACCATTTTTCTTGTTCGTTATACTATCCAA 9 37 0 TTTTGTTTTA 0.859191 -95 TAGGCGTATTTTCTTTATACTTTGTGCATTGAA 9 85 1 TTTTTATTTT 0.980664 -47 AAAAATAACATTTTTTATCATTCTGTGATCTAG 10 82 0 TTTTTATTTC 0.926813 -77 AAAATGTTATTTTTTGTTAATTTTAGTGATAAA 10 101 1 TTTTGTTTTT 0.952959 -58 TTTATGGCTATTGTTTATTTATTACTTTGTTAA 12 39 1 TTTTTATATT 0.930565 -41 ATTTATTACTTTGTTAATTGTTTCGGAAGGTAT 12 55 1 TTTTAATTTT 0.822781 -25 GCTAAATAGTTTATTTATTATTCACAATCTCAA 13 14 0 TTTTTATTTC 0.926813 -145 TATTTAGCTTATTTTTATGATTTAATTCAGGCT 13 39 1 ATTTTATTTT 0.930565 -120 TTAGTGTTTATTCTTGATTATTTTGCTTTGAAA 13 74 1 TTTTGATTTT 0.967753 -85 TTCTGGTTTTATATTTTTAATTATTGATTAGTC 13 125 1 ATTTTTTTTA 0.731521 -34 CTATGCAAAAATTTTTTTCATTTTACCAAAAAC 14 24 1 ATTTTTTTTT 0.900469 -47 ** ***** *** Masking position 5 Map Score: 32.9461 Number of sites scoring better than the average of aligned sites = 770 Number in coding regions = 523 Number in noncoding regions = 247 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 2 TAAAGTTAATAAAACGCCGCCATTATACTGTCTA 2 56 0 AAAGCCCATT 0.988217 -31 AAATGGATAAAAATTTACCGCACTT 3 2 0 AAATCGCACT 0.978061 -70 AATATAAAAGAAAACGACCGCACTTTGCGACCGT 4 19 0 AAAGCGCACT 0.994888 -32 TATCAAAAATAAAGGGGCTTAATTGCCCCTTTTG 7 16 1 AAAGCTAATT 0.91995 -54 ATACGCCTAAAAAGCGACGGCATTTGCACCATTT 9 60 0 AAAGCGCATT 0.994801 -72 CAATAGCCATAAAATTTCACAATTTTATGGCTAA 12 18 0 AAATCCAATT 0.882395 -62 AATAAACACTAAAAAGCCTGAATTAAATCATAAA 13 52 0 AAAGCGAATT 0.987299 -107 AACAAGGGAAAAAACGACCGCACTTTT 14 54 1 AAAGCGCACT 0.994888 -17 *** * * ***** Masking position 3 Map Score: 11.3831 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 187 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 3 CATTTGCCTAGATAAGCCTTA 2 2 1 ATTTGCCTAG 0.917466 -85 ACTTTTCCCTTGTTAGAACTGT 5 15 0 TTTTCCCTTG 0.984052 -12 AATTATTTTTCCTTATGCCTAAGGCT 6 39 0 TTTTCCTTAT 0.757424 -16 AATTTGGTTTCCTTTGATGGAATGTT 9 7 1 GTTTCCTTTG 0.912453 -125 TGATGGAATGTTTTGGATAGTATAACGAAC 9 25 1 TTTTGGATAG 0.85143 -107 TCTTTATACTTTGTGCATTGAAATACTATT 9 96 1 TTGTGCATTG 0.919068 -36 TTCTTGATTATTTTGCTTTGAAAAAGGATA 13 84 1 TTTTGCTTTG 0.979841 -75 TGAAAAAAATTTTTGCATAGGATACCTGAT 14 14 0 TTTTGCATAG 0.975232 -57 TGCGGTCGTTTTTTCCCTTGTTTTTGGTAA 14 46 0 TTTTCCCTTG 0.984052 -25 ********** Masking position 4 Map Score: 7.22094 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 284 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 4 AAGTGCGGTAAATTTTTATC 3 1 1 AAGTGCGGTA 0.990931 -71 AACGGTCGCAAAGTGCGGTCGTTTTCTTTT 4 18 1 AAGTGCGGTC 0.997686 -33 AAAATGGTGCAAATGCCGTCGCTTTTTAGG 9 59 1 AAATGCCGTC 0.976089 -73 AAAAGTGCGGTCGTTTTTTCCC 14 59 0 AAGTGCGGTC 0.997686 -12 ********** Masking position 4 Map Score: 6.39186 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 317 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 5 AAATTATGTTATAAAACCATAAAAAATTTGA 3 43 1 ATAAAACCAA 0.965131 -29 ATTTAACCTCAAATTTTTTAT 3 61 0 ATTTAACCTA 0.650083 -11 GATACAATAAATTAAATCTGAGATCTAGATC 10 58 1 ATTAAATCTA 0.901516 -101 AATTTTAGTGATAAAACGTTATGAGCTCATA 10 119 1 ATAAAACGTA 0.88825 -40 CTATTTTAACGTAAAATCAAATAATTTTGT 11 10 0 GTAAAATCAA 0.913109 -50 AACAATAGCCATAAAATTTCACAATTTTATG 12 23 0 ATAAAATTTA 0.693578 -57 AAAAGCCTGAATTAAATCATAAAAATAAGCT 13 44 0 ATTAAATCAA 0.918552 -115 AATTAAAAATATAAAACCAGAAAATTGCCCT 13 116 0 ATAAAACCAA 0.965131 -43 CTTGTTTTTGGTAAAATGAAAAAAATTTTTG 14 29 0 GTAAAATGAA 0.788046 -42 ********* * Masking position 6 Map Score: 3.65386 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 249 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 6 GCTTCCTTGCTTAATCCCCTTTAGACAGTA 2 35 1 TTAATCCCCT 0.992957 -52 AAAGGGGCAATTAAGCCCCTTTATTTTTGA 7 18 0 TTAAGCCCCT 0.988053 -52 TTTTAATCTCCTAATAGATCTT 10 3 1 TTAATCTCCT 0.989148 -156 TTTAATCTCCTATCCATTCAA 11 49 0 TTAATCTCCT 0.989148 -11 ********** Masking position 4 Map Score: 6.09722 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 7 TCCCCTTTAGACAGTATAATGGCGGCGTTT 2 49 1 ACAGTATAAT 0.878697 -38 CCATTTCTCTACAAAATTATGTTATAAAAC 3 30 1 ACAAAATTAT 0.958321 -42 GATCTAGATCACAGAATGATAAAAAATGTT 10 79 1 ACAGAATGAT 0.907137 -80 ACAAAATTATTTGATTTTAC 11 1 1 ACAAAATTAT 0.958321 -59 ATAAAATTTCACAATTTTATGGCTAAGTAA 12 14 0 ACAATTTTAT 0.70759 -66 GAAACAATTAACAAAGTAATAAATAAACAA 12 49 0 ACAAAGTAAT 0.900479 -31 CTTTTTCAAAGCAAAATAATCAAGAATAAA 13 80 0 GCAAAATAAT 0.883925 -79 ********** Masking position 3 Map Score: 2.34557 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 142 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 TTATTTTTCCTTATGCCTAAGGCTTGAACG 6 33 0 TTATGCCTAA 0.876147 -22 TCATAACGTTTTATCACTAAAATTAACAAA 10 113 0 TTATCACTAA 0.89555 -46 TTTCACAATTTTATGGCTAAGTAAGAA 12 8 0 TTATGGCTAA 0.943431 -72 TTGTGAAATTTTATGGCTATTGTTTATTTA 12 30 1 TTATGGCTAT 0.962843 -50 ********** Masking position 4 Map Score: 0.552958 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 33 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 ********** No masking Map Score: 2.12695e-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: 2.12695e-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 11 ********** No masking Map Score: 2.12695e-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