AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02060_hinf_reg_300.orf -o02060_hinf_300.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 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 HI1711 59 PTS system, glucose-specific IIA component (crr) #11 HI1712 79 phosphoenolpyruvate-protein phosphotransferase (ptsI) #12 HI1713 158 phosphocarrier protein HPr (ptsH) #13 HI1714 70 conserved hypothetical protein Motif number 1 ACCAGCAGCTTATTGAAAAACAA 1 1 0 TATAAAAAAA 0.840771 -71 GCTCCTTAATAATTTAAAAAGAAAGCTGCGGAT 1 45 0 AATAAAAAAA 0.942217 -27 TTTGTAGAGAAATGGATAAAAATTTACCGCACT 3 12 0 AATATAAAAT 0.813914 -60 TTATGTTATAAAACCATAAAAAATTTGAGGTTA 3 46 1 AAAATAAAAA 0.985331 -26 TACTCAAAAATATAAAAGAAAACGACCGCA 4 31 0 AAATAAAAAA 0.822458 -20 GCCTTAGGCATAAGGAAAAATAATT 6 40 1 TAAAAAAAAA 0.946038 -15 CAAAGTATCAAAAATAAAGGGGCT 7 2 1 AAAATCAAAA 0.971831 -68 AAGAAAGAGAAAATAAAAAACAACAAAAGGGGC 7 40 0 AAAAAAAAAA 0.981864 -30 CTCATCCAAAAAAGAGTCAATAACGTTGGTTAG 8 48 0 AAAGTCAAAA 0.889525 -23 TTGGATAGTATAACGAACAAGAAAAATGGTGCA 9 37 1 TAAAACAAAA 0.900045 -95 TTCAATGCACAAAGTATAAAGAAAATACGCCTA 9 85 0 AAAATAAAAA 0.985331 -47 TTAACAAAGTAATAAATAAACAATAGCCATAAA 11 39 0 AATATAAAAA 0.952899 -41 ATACCTTCCGAAACAATTAACAAAGTAATAAAT 11 55 0 AAAATTAAAA 0.868612 -25 TTGAGATTGTGAATAATAAATAAACTATTTAGC 12 14 1 GAAATAAAAA 0.907393 -145 AGCCTGAATTAAATCATAAAAATAAGCTAAATA 12 39 0 AAAATAAAAT 0.935575 -120 TTTCAAAGCAAAATAATCAAGAATAAACACTAA 12 74 0 AAAATCAAAA 0.971831 -85 GACTAATCAATAATTAAAAATATAAAACCAGAA 12 125 0 TAAAAAAAAT 0.791115 -34 TGTTTTTGGTAAAATGAAAAAAATTTTTGCATA 13 25 0 AAAGAAAAAA 0.926662 -46 *** ***** ** Masking position 9 Map Score: 27.7231 Number of sites scoring better than the average of aligned sites = 727 Number in coding regions = 482 Number in noncoding regions = 245 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 0.989093 -31 AAATGGATAAAAATTTACCGCACTT 3 2 0 AAATCGCACT 0.979678 -70 AATATAAAAGAAAACGACCGCACTTTGCGACCGT 4 19 0 AAAGCGCACT 0.995269 -32 TATCAAAAATAAAGGGGCTTAATTGCCCCTTTTG 7 16 1 AAAGCTAATT 0.925027 -54 ATACGCCTAAAAAGCGACGGCATTTGCACCATTT 9 60 0 AAAGCGCATT 0.99516 -72 CAATAGCCATAAAATTTCACAATTTTATGGCTAA 11 18 0 AAATCCAATT 0.890271 -62 AATAAACACTAAAAAGCCTGAATTAAATCATAAA 12 52 0 AAAGCGAATT 0.988243 -107 AACAAGGGAAAAAACGACCGCACTTTT 13 54 1 AAAGCGCACT 0.995269 -17 *** * * ***** Masking position 3 Map Score: 12.6914 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 0.952299 -85 ACTTTTCCCTTGTTAGAACTGT 5 15 0 TTTTCCCTTG 0.984425 -12 AATTATTTTTCCTTATGCCTAAGGCT 6 39 0 TTTTCCTTAT 0.727796 -16 AATTTGGTTTCCTTTGATGGAATGTT 9 7 1 GTTTCCTTTG 0.890452 -125 TGATGGAATGTTTTGGATAGTATAACGAAC 9 25 1 TTTTGGATAG 0.798479 -107 TCTTTATACTTTGTGCATTGAAATACTATT 9 96 1 TTGTGCATTG 0.864539 -36 TTCTTGATTATTTTGCTTTGAAAAAGGATA 12 84 1 TTTTGCTTTG 0.968358 -75 AAACCAGAAAATTGCCCTAGTATCCTTTTT 12 104 0 ATTGCCCTAG 0.806401 -55 TGAAAAAAATTTTTGCATAGGATACCTGAT 13 14 0 TTTTGCATAG 0.968332 -57 TGCGGTCGTTTTTTCCCTTGTTTTTGGTAA 13 46 0 TTTTCCCTTG 0.984425 -25 ********** Masking position 8 Map Score: 8.74622 Number of sites scoring better than the average of aligned sites = 331 Number in coding regions = 283 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 4 GATAAAAATTTACCGCACTT 3 1 0 TACCGCACTT 0.992972 -71 AAAAGAAAACGACCGCACTTTGCGACCGTT 4 18 0 GACCGCACTT 0.998201 -33 CCTAAAAAGCGACGGCATTTGCACCATTTT 9 59 0 GACGGCATTT 0.981424 -73 GGGAAAAAACGACCGCACTTTT 13 59 1 GACCGCACTT 0.998201 -12 ********** Masking position 7 Map Score: 7.02521 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 TAATTTAAAAAGAAAGCTGCGGATGAAACA 1 39 0 AGAAAGCTGC 0.930064 -33 ATAATTTTGTAGAGAAATGGATAAAAATTT 3 20 0 AGAGAAATGG 0.87 -52 TGAACCTTCAATAGAATTGTTACTCTAACC 8 24 1 ATAGAATTGT 0.801481 -47 AAAAGAGTCAATAACGTTGGTTAGAGTAAC 8 42 0 ATAACGTTGG 0.824843 -29 ATAACGAACAAGAAAAATGGTGCAAATGCC 9 46 1 AGAAAAATGG 0.931932 -86 AATACTATTGATAAAGCTGGGAAAA 9 117 1 ATAAAGCTGG 0.931356 -15 TTACTTAGCCATAAAATTGTGAAATTTTAT 11 14 1 ATAAAATTGT 0.891992 -66 AACAATAGCCATAAAATTTCACAATTTTAT 11 24 0 ATAAAATTTC 0.645959 -56 ATATAAAACCAGAAAATTGCCCTAGTATCC 12 109 0 AGAAAATTGC 0.959937 -50 ********** Masking position 3 Map Score: 2.78986 Number of sites scoring better than the average of aligned sites = 661 Number in coding regions = 553 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 6 CCATTTCTCTACAAAATTATGTTATAAAAC 3 30 1 ACAAAATTAT 0.960056 -42 TACTCAAAAATATAAAAGAAAAC 4 38 0 TCAAAAATAT 0.805676 -13 TAGGCATAAGGAAAAATAATT 6 44 1 GAAAAATAAT 0.790442 -11 ACAAAATTATTTGATTTTAC 10 1 1 ACAAAATTAT 0.960056 -59 GAAACAATTAACAAAGTAATAAATAAACAA 11 49 0 ACAAAGTAAT 0.850531 -31 CTTTTTCAAAGCAAAATAATCAAGAATAAA 12 80 0 GCAAAATAAT 0.966755 -79 GGTATCCTATGCAAAAATTTTTTTCATTTT 13 18 1 GCAAAAATTT 0.773746 -53 ********** Masking position 5 Map Score: 2.6239 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 344 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 7 ********** No masking Map Score: -1.26233e-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: -1.26233e-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 9 ********** No masking Map Score: -1.26233e-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