AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i346_weak7_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 HI0372 39 ferredoxin (fdx-1) #2 HI0374 50 H. influenzae predicted coding region HI0374 #3 HI0376 56 conserved hypothetical protein #4 HI0377 59 iscU protein (iscU) #5 HI0378 60 nifS protein (nifS) #6 HI0379 52 conserved hypothetical protein #7 HI0380 300 conserved hypothetical protein Motif number 1 CAAATTACATTTGCCCCCACAT 2 3 0 TTGCCCCCAC 0.987836 -48 CAAATGTAATTTGCCCCTACGAGATGTGAA 2 20 1 TTGCCCCTAC 0.926277 -31 GCGGTCAAAATTGACCGCACTTTTTCACAT 3 13 0 TTGACCGCAC 0.980622 -44 GCGGTCAATTTTGACCGCATTTTTAGCGGT 3 25 1 TTGACCGCAT 0.886302 -32 CTATCCCCCAACACCGCTAAAA 3 45 0 ATCCCCCAAC 0.9432 -12 TATGCTAAATATAACCGCACTTTTTTATTA 5 33 0 ATAACCGCAC 0.973425 -28 GACTGAGCTAACGACCCCACTGTATTAAAT 7 13 0 ACGACCCCAC 0.992793 -288 CGAATCCTTCACGACCCACCACTCTCTGAT 7 81 1 ACGACCCACC 0.981851 -220 AACTGAGCTAACAACCCAACTGGACAACTA 7 112 0 ACAACCCAAC 0.973588 -189 CTAGTCTCTCACAACCCACCATTTTTATTA 7 180 1 ACAACCCACC 0.958485 -121 AATGATACCCGACTAAAATTTAAG 7 287 0 ATACCCGACT 0.67456 -14 ********** Masking position 5 Map Score: 16.8634 Number of sites scoring better than the average of aligned sites = 627 Number in coding regions = 442 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 2 ATATTAAATAATTTTGAGGAAAGTATT 1 23 1 ATTTTGAGGA 0.944479 -17 AGTGCGGTCAATTTTGACCGCATTTTTAGC 3 22 1 ATTTTGACCG 0.930486 -35 TTTTGACCGCATTTTTAGCGGTGTTGGGGG 3 33 1 ATTTTTAGCG 0.992749 -24 AAGTGCGGTTATATTTAGCATAATTTAGGA 5 41 1 ATATTTAGCA 0.831545 -20 TGCGCAATTAATTTTTAGGGATTCTTT 6 36 1 ATTTTTAGGG 0.991033 -17 AGAAATTTAAAATATTAGGGATGAATAATA 7 205 0 AATATTAGGG 0.901378 -96 AATAGTCAAGAATTTAAGCTAATTAAAGAA 7 231 0 AATTTAAGCT 0.802063 -70 ATTCTTGACTATTTTTAGCGGTTATTGTGG 7 248 1 ATTTTTAGCG 0.992749 -53 ACCCGACTAAAATTTAAGGGTATTCTACCA 7 275 0 AATTTAAGGG 0.961864 -26 ********** Masking position 5 Map Score: 11.3563 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 241 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 3 ACTTACATATCTGACTAATTTAG 6 2 0 CTACTAATTA 0.903102 -51 AGCTAACGACCCCACTGTATTAAATGG 7 6 0 CCACTGTTTA 0.977939 -295 CGCTGCTCTACCGACTGAGCTAACGACCCCAC 7 23 0 CCACTGACTA 0.995245 -278 GAACCTTCGACCAACGGATTAAAAGTCCGCTG 7 50 0 CCACGGATAA 0.986906 -251 CGACCCACCACTCTCTGATTTAGTTGTCCAGT 7 92 1 CTTCTGATTA 0.937333 -209 AGCTAACAACCCAACTGGACAACTAAATCAGA 7 105 0 CCACTGGCAA 0.975693 -196 CGCTACTCTACCAACTGAGCTAACAACCCAAC 7 122 0 CCACTGACTA 0.995245 -179 GAACTCTCGACTGACGGATTAAGAGTCCGCTA 7 149 0 CTACGGATAA 0.967172 -152 ** ***** *** Masking position 12 Map Score: 9.93529 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 55 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 4 TATTTAGTTGCCATTATCTGACAATGGCATT 4 9 1 TCATTTCTGA 0.887646 -51 AAGTCCGCTGCTCTACCGACTGAGCTAACGACC 7 27 0 CCACCACTGA 0.99775 -274 GATTCGAACCTTCGACCAACGGATTAAAAGTCC 7 54 0 TCACCACGGA 0.991099 -247 CTTCACGACCCACCACTCTCTGATTTAGTTGTC 7 87 1 CCACTTCTGA 0.993428 -214 GAGTCCGCTACTCTACCAACTGAGCTAACAACC 7 126 0 CCACCACTGA 0.99775 -175 GACTAGAACTCTCGACTGACGGATTAAGAGTCC 7 153 0 CCACTACGGA 0.995449 -148 * * *** ***** Masking position 5 Map Score: 8.83557 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 17 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 AACTGCAGTCAGATATTAAATAATTT 1 7 1 AGTCAGATAT 0.985725 -33 TGAATGCCATTGTCAGATAATGGCAACTAA 4 14 0 TGTCAGATAA 0.870837 -46 CTAAATTAGTCAGATATGTAAGTATTG 6 8 1 AGTCAGATAT 0.985725 -45 ACGGATTAAAAGTCCGCTGCTCTACCGACT 7 39 0 AGTCCGCTGC 0.969477 -262 ACGGATTAAGAGTCCGCTACTCTACCAACT 7 138 0 AGTCCGCTAC 0.988619 -163 CTTAAATTTTAGTCGGGTATCATT 7 287 1 AGTCGGGTAT 0.959605 -14 ********** Masking position 3 Map Score: 5.08303 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 15 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 CTATCCCCCAACACCGCTAAAAATGCGG 3 39 0 CCAACACGCT 0.972284 -18 AGCTAACGACCCCACTGTATTAAATGG 7 7 0 CCCACTGATT 0.952944 -294 CGCTGCTCTACCGACTGAGCTAACGACCCCA 7 24 0 CCGACTGGCT 0.995821 -277 AGCTAACAACCCAACTGGACAACTAAATCAG 7 106 0 CCAACTGACA 0.982085 -195 CGCTACTCTACCAACTGAGCTAACAACCCAA 7 123 0 CCAACTGGCT 0.997544 -178 ******* *** Masking position 4 Map Score: 3.16871 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 23 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 TCATGTGAAAAAGTGCGGTCAATTTTG 3 8 1 AAAAAGTGCG 0.994763 -49 CCAACACCGCTAAAAATGCGGTCAAAATTG 3 30 0 TAAAAATGCG 0.962441 -27 TTTTTTAATAAAAAAGTGCGGTTATATTTA 5 28 1 AAAAAGTGCG 0.994763 -33 ATCCCTAAAAATTAATTGCGCAATACTTAC 6 28 0 ATTAATTGCG 0.836899 -25 ACCAACGGATTAAAAGTCCGCTGCTCTACC 7 43 0 TAAAAGTCCG 0.958921 -258 GATGAATAATAAAAATGGTGGGTTGTGAGA 7 186 0 AAAAATGGTG 0.826656 -115 ********** Masking position 5 Map Score: 4.04452 Number of sites scoring better than the average of aligned sites = 1373 Number in coding regions = 929 Number in noncoding regions = 444 Number of orfs with sites within 600 bp upstream = 301 Fraction of orfs with sites within 600 bp upstream = 0.0483456 Motif number 8 AAAAAATATACTGCTTATCTTTT 5 4 0 CTGCTTATCT 0.916296 -57 GATTAAAAGTCCGCTGCTCTACCGACTGAG 7 36 0 CCGCTGCTCT 0.996111 -265 CCTTCACGACCCACCACTCTCTGATTTAGT 7 86 1 CCACCACTCT 0.978253 -215 GATTAAGAGTCCGCTACTCTACCAACTGAG 7 135 0 CCGCTACTCT 0.996729 -166 ********** Masking position 8 Map Score: 2.14811 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 5 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 CTCAAAATTATTTAATATCTGACTGCAGTT 1 11 0 TTTAATATCT 0.947454 -29 ACTTTCCTTTTTTCAATTCTAGTGAATGCC 4 36 0 TTTCAATTCT 0.951136 -24 TGCGCAATACTTACATATCTGACTAATTTA 6 12 0 TTACATATCT 0.931432 -41 CCCTAATATTTTAAATTTCTTTAATTAGCT 7 215 1 TTAAATTTCT 0.947302 -86 CTTTAATTAGCTTAAATTCTTGACTATTTT 7 233 1 CTTAAATTCT 0.890384 -68 ********** Masking position 5 Map Score: 1.0327 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 146 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 10 ********** No masking Map Score: 1.24588e-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: 1.24588e-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 12 ********** No masking Map Score: 1.24588e-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