AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00190_hinf_reg_300.orf -o00190_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 HI0124 234 inorganic pyrophosphatase (ppa) #2 HI0478 29 ATP synthase F1, subunit epsilon (atpC) #3 HI0483 49 ATP synthase F0, subunit b (atpF) #4 HI0484 55 ATP synthase F0, subunit c (atpE) #5 HI0485 36 ATP synthase F0, subunit a (atpB) #6 HI0485.1 125 H. influenzae predicted coding region HI0485.1 #7 HI0486 139 glucose-inhibited division protein (gidB) #8 HI0487 115 H. influenzae predicted coding region HI0487 #9 HI0835 181 fumarate reductase, flavoprotein subunit (frdA) Motif number 1 AGTAATAAGGTGCGCTATTTTACATCATAAAAACGATAAG 1 42 1 TTTTTTCAAA 0.988714 -193 GATGGATCTATTTGCTGATTTTCTCTACAAATGAGACTGC 1 142 1 TTATTTCAAA 0.98038 -93 CTATACTTGTTGCGTTTTTTAACTTGATAAAATGAAGGAA 1 200 1 TTTTTACAAA 0.962446 -35 TCACTTCAAGTCATTTGAAGGAGAACAAA 2 6 1 TTATTTAAAA 0.928332 -24 TCACCTTATTTGCTTATCAACGTAAAACAA 3 1 1 TTATTTCTAA 0.935994 -49 CTTTGGGTTATTCTTCTTCAGAACAAAGGATCG 5 4 1 TTTTCTCAAA 0.962163 -33 ATAACACTTTTTATGTGTTTTTAAGTTGAATCTAAAGCCA 6 54 1 TTTTTTATAA 0.867639 -72 ACCGAATCAATGTCCAGTTTTACACCATAAATTGAATGCA 7 23 0 TATTTTCAAA 0.91757 -117 AGTAATTTGATGAATTATTTACCGAATCAATGTCCAGTTT 7 43 0 TTTTTACTAA 0.882377 -97 CTTTGAAAAATTACGCTATTTTACTTAAAAGTGCGGTAAA 7 99 0 TCATTTAAAA 0.867359 -41 TACAAATTTTTTTACCATTTTGCTACAAAACTGTGATCTA 8 22 1 TCTTTTCAAA 0.977855 -94 AGTATCGGATTTTGTGATCTACCTCAAAAAAGCTAAGAT 9 37 0 TTATCTCAAA 0.935495 -145 TCCGATACNTTTCCATCTTTAGACATAAAANACGTTATTA 9 67 1 TTTTTAAAAA 0.865822 -115 GTGTGGGCATTGTGCCATTTTTCGTTACAAATTAATAACG 9 99 0 TCTTTTCAAA 0.977889 -83 * * **** * * ** Masking position 19 Map Score: 17.1105 Number of sites scoring better than the average of aligned sites = 518 Number in coding regions = 406 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 2 ATCGTTTTTATGATGTAAAATAGCGCACCTTATTACT 1 42 0 TGGAAAATGA 0.993376 -193 GTCTCATTTGTAGAGAAAATCAGCAAATAGATCCATC 1 142 0 TAGAAATCGA 0.938566 -93 TCCTTTGTTCTGAAGAAGAATAACCCAAAG 5 4 0 TGGAGAATAA 0.857805 -33 ATTCAATTTATGGTGTAAAACTGGACATTGATTCGGT 7 26 1 TGGAAAACGA 0.993365 -114 TACTTAAAAGTGCGGTAAATTTCCTTAATGTTTTTAG 7 81 0 TGGAAATTCA 0.86934 -59 TACCGCACTTTTAAGTAAAATAGCGTAATTTTTCAAA 7 101 1 TTGAAAATGA 0.940127 -39 ATCACAGTTTTGTAGCAAAATGGTAAAAAAATTTGTA 8 22 0 TGGAAAATGA 0.993761 -94 CGCACTTTACTGAAATAAAACAGTGCATAGATCACAG 8 52 0 TGAAAAACGA 0.921978 -64 TTCAGTAAAGTGCGGTAAATTAGCGAACAAATTTTGA 8 75 1 TGGAAATTGA 0.988284 -41 TTAGCTTTTTTGAGGTAGATCACAAAATCCGATACNT 9 40 1 TGGAGATCCA 0.900623 -142 TATTAATTTGTAACGAAAAATGGCACAATGCCCACAC 9 102 1 TAGAAAATGA 0.964769 -80 ** * ***** * * Masking position 9 Map Score: 14.2095 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 128 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 3 TTACTTCCAATTTTTTACTTAACTTCAAGG 1 17 0 TTTTTTACTT 0.971742 -218 CTTGTTGCGTTTTTTAACTTGATAAAATGA 1 205 1 TTTTTAACTT 0.895094 -30 TTTGTTTCCTTCATTTTATC 1 225 0 TTTGTTTCCT 0.760494 -10 AATTTATCTATTTGTTACTTT 6 2 0 TTTGTTACTT 0.969843 -124 TTTTTATGTGTTTTTAAGTTGAATCTAAAG 6 61 1 TTTTTAAGTT 0.832559 -65 AAAATTACGCTATTTTACTTAAAAGTGCGG 7 103 0 TATTTTACTT 0.813758 -37 CCTTACAAATTTTTTTACCATTTTGCTACA 8 19 1 TTTTTTACCA 0.73238 -97 TAGTTCAAAATTTGTTCGCTAATTTACCGC 8 86 0 TTTGTTCGCT 0.834633 -30 TTGTTTTTGTTAGTTCAAAATTTGT 8 101 0 TTTGTTAGTT 0.949345 -15 GCATTGTGCCATTTTTCGTTACAAATTAAT 9 103 0 ATTTTTCGTT 0.681325 -79 TAGGGGATTTATTTTTACTTTCTATTGATT 9 152 1 ATTTTTACTT 0.895094 -30 ********** Masking position 5 Map Score: 9.18036 Number of sites scoring better than the average of aligned sites = 557 Number in coding regions = 445 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 4 TGGAAGTAATAAGGTGCGCTATTTTACATC 1 38 1 AAGGTGCGCT 0.953782 -197 TATTTAGGATAAAGTGCGGTCAAAATTATG 1 101 1 AAAGTGCGGT 0.995218 -134 GTTCGCAGAAAARCTGCTATACTTGTTGCG 1 184 1 AARCTGCTAT 0.933141 -51 TTATTTTCTAAAAGTGTGATTTATATAACA 6 30 1 AAAGTGTGAT 0.985384 -96 AAACACATAAAAAGTGTTATATAAATCACA 6 44 0 AAAGTGTTAT 0.939097 -82 ATTTTACTTAAAAGTGCGGTAAATTTCCTT 7 92 0 AAAGTGCGGT 0.995218 -48 TTTTGCTACAAAACTGTGATCTATGCACTG 8 39 1 AAACTGTGAT 0.959762 -77 TTATTTCAGTAAAGTGCGGTAAATTAGCGA 8 71 1 AAAGTGCGGT 0.995218 -45 ********** Masking position 2 Map Score: 15.8708 Number of sites scoring better than the average of aligned sites = 1219 Number in coding regions = 777 Number in noncoding regions = 442 Number of orfs with sites within 600 bp upstream = 303 Fraction of orfs with sites within 600 bp upstream = 0.0486669 Motif number 5 TTTAGGATAAAGTGCGGTCAAAATTATGAA 1 103 1 AGTGCGGTCA 0.996105 -132 TTTACTTAAAAGTGCGGTAAATTTCCTTAA 7 90 0 AGTGCGGTAA 0.99678 -50 ATTTCAGTAAAGTGCGGTAAATTAGCGAAC 8 73 1 AGTGCGGTAA 0.99678 -43 ********** Masking position 1 Map Score: 4.7127 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 119 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 6 AGTGTTCCTTGAAGTTAAGTAAAAAA 1 6 1 TCCTTAAGTT 0.952067 -229 CGCACCTTATTACTTCCAATTTTTTACTTAA 1 25 0 TACTTCAATT 0.939887 -210 TTTGTTTCCTTCATTTTATCAAGTTAA 1 218 0 TCCTTATTTT 0.86197 -17 TTTGTTCTCCTTCAAATGACTTGAAGTG 2 12 0 TCCTTAAATG 0.947634 -18 AACGTCCTCCTTACTATGCTTGTTTTAC 3 32 0 TCCTTCTATG 0.949824 -18 GCGGTAAATTTCCTTAATGTTTTTAGTAATT 7 76 0 TCCTTATGTT 0.944467 -64 TACGCTATTTTACTTAAAAGTGCGGTAAATT 7 97 0 TACTTAAAGT 0.762904 -43 TTTTACATCCTTACAAATTTTTTTACCA 8 8 1 TCCTTCAAAT 0.895291 -108 GATTTATTTTTACTTTCTATTGATTGGAGGA 9 157 1 TACTTCTATT 0.926966 -25 ***** ***** Masking position 5 Map Score: 5.46468 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 115 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 7 CGTTTGCGTGAGTTTTATTTAGGATAAAGT 1 86 1 AGTTTTATTT 0.858943 -149 GTTATGAGATGGATCTATTTGCTGATTTTC 1 135 1 GGATCTATTT 0.872348 -100 AACAAATAGATAAATTATTTTCTAAAAGTG 6 16 1 TAAATTATTT 0.815667 -110 TCTAAAAGTGTGATTTATATAACACTTTTT 6 36 1 TGATTTATAT 0.847608 -90 TCGGCGGGCTAAAATTATTTTGTAAAAGTG 6 106 1 AAAATTATTT 0.703258 -20 AGTAATTTGATGAATTATTTACCGAATCAA 7 53 0 TGAATTATTT 0.950853 -87 ATCTATGCACTGTTTTATTTCAGTAAAGTG 8 57 1 TGTTTTATTT 0.919108 -59 CCCTTTTAGGGGATTTATTTTTACTTTCTA 9 146 1 GGATTTATTT 0.962581 -36 ********** Masking position 7 Map Score: 4.20591 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 229 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 8 TATTACTTCCAATTTTTTACTTAACTTCAA 1 19 0 AATTTTTTAC 0.743581 -216 AACTATTCATAATTTTGACCGCACTTTATC 1 108 0 AATTTTGACC 0.952908 -127 ATAGAAGTTAAGTTTTAGCCCTAGAGCCGG 4 25 0 AGTTTTAGCC 0.955315 -31 AATTTTCTCCAATAGAAGTT 4 46 0 AATTTTCTCC 0.916634 -10 TTTACAAAATAATTTTAGCCCGCCGATTAT 6 102 0 AATTTTAGCC 0.974197 -24 ATCAATGTCCAGTTTTACACCATAAATTGA 7 28 0 AGTTTTACAC 0.893127 -112 TTAGCGAACAAATTTTGAACTAACAAAAAC 8 94 1 AATTTTGAAC 0.887763 -22 ATGCCCACACAATATTACCCTTTTAGGGGA 9 129 1 AATATTACCC 0.871232 -53 ********** Masking position 1 Map Score: 2.82546 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 324 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 9 ********** No masking Map Score: 9.97192e-13 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: 9.97192e-13 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: 9.97192e-13 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