AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00740_hinf_reg_100.orf -o00740_hinf_100.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 HI0212 44 GTP cyclohydrolase II (ribA) #2 HI0495 218 acid phosphatase (GP:X86971_1) #3 HI0963 34 riboflavin kinase / FMN adenylyltransferase (ribF) #4 HI0964 300 virulence factor (mviN) #5 HI1303 147 riboflavin synthase, beta chain (ribH) #6 HI1336 111 dihydropteroate synthase (folP-1) #7 HI1337 37 mrsA protein (mrsA) #8 HI1338 58 conserved hypothetical protein #9 HI1613 43 riboflavin synthase, alpha chain (ribE) Motif number 1 TTTATTCTTCACTCATAAATAAAAAATGTGAAGTTGA 2 94 1 ATAAAAAAAT 0.951955 -125 CTAATTATTGAATATAAGCTAAAAAATGTATGATCTG 2 157 1 ATTAAAAAAT 0.916463 -62 TTTTCCATTGACAAAAGTATAAAAAATCGGCATATTG 4 52 0 AAAAAAAAAT 0.985467 -249 GCCCATATTGAAAGAGCTTGTAAAAATAACGATACTT 4 123 0 AAATAAAAAT 0.974796 -178 TATTCCGTGAAAAAAAACTGATAAAATCCGCCACACA 4 172 0 AAAATAAAAT 0.869689 -129 AAATTTCTATACAATTAGGCAAAAATTTTAGGGTAGA 4 222 1 AATAAAAATT 0.878832 -79 TTAATGAAGGAAATTTTCCATAAAAATATAGTGTTGG 5 33 1 AATTAAAAAT 0.916402 -115 TATGAACAATAAAATCGCCTTAAAAATGAGTCCTAAA 5 77 1 AATTAAAAAT 0.956632 -71 CCAAGAACAAAATCATTAGGAAAAAATAAAGCCTTTC 6 31 0 ATAAAAAAAT 0.951081 -81 ATCGCCCACCAAAATCACTCTAAAAATTAACCGCATT 6 83 1 AATTAAAAAT 0.95662 -29 TGGTTTTATAACGATAAAAAATTAAAGGAATT 7 6 1 TAAAAAAAAT 0.927138 -32 TTGCTTTCCTAAAAACTTTATAAAAATAAACCGCACT 8 31 0 AAATAAAAAT 0.974795 -28 AAATTTGATATACTGCTAAAAATTTTTAGAAAAG 9 8 1 AAAAAAAATT 0.927024 -36 CTAAAAATTTTTAGAAAAGGAAAAAATT 9 26 1 TAAAAAAAAT 0.927139 -18 * * * ******* Masking position 13 Map Score: 20.8827 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 325 Number in noncoding regions = 186 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 2 TTTGTCTATCAATCAACAGAAATTTTAGGA 4 6 0 AATAACATTT 0.989772 -295 GTCTCACCGAAATCAACACAAATTTTCCATTGACA 4 76 0 AATAACATTT 0.989958 -225 TTGTAAAAATAACGATACTTACTTTCGGTTGTGTC 4 108 0 AACATAATTT 0.777563 -193 CATTAAGGTAAACTATCGGCAATTTTAT 5 4 0 AACATCATTT 0.938602 -144 AGTTTACCTTAATGAAGGAAATTTTCCATAAAAAT 5 25 1 AATAAGATTT 0.950083 -123 ATTAATATTGAATATACGCGATTTT 5 133 1 AATTACATTT 0.939624 -15 TCACTCTAAAAATTAACCGCATTTT 6 97 1 AATAACATTT 0.989971 -15 AACGATAAAAAATTAAAGGAATTTTATT 7 20 1 AATAAAATTT 0.957491 -18 ACTTTATAAAAATAAACCGCACTTTACTAAGTGCG 8 19 0 AATAACATTT 0.989971 -40 *** *** * *** Masking position 11 Map Score: 12.4067 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 126 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 3 TTGATAACAAAAATAACGCGCGCATTCTAA 1 20 1 AAATAACGCG 0.908147 -25 AGAATTTCGGCATTATAGCGAGAAG 3 6 0 CATTATAGCG 0.868389 -29 TTGATAGACAAAATAAAGGGCATCAATATG 4 29 1 AAATAAAGGG 0.958836 -272 TTTTTTCACGGAATATAGCGTAAAAACAAA 4 194 1 GAATATAGCG 0.977973 -107 ATTAGGCAAAAATTTTAGGGTAGAGAAGAA 4 235 1 AATTTTAGGG 0.732304 -66 TTTTCCATAAAAATATAGTGTTGGTGCGGG 5 46 1 AAATATAGTG 0.874451 -102 TATTAATATTGAATATACGCGATTTT 5 132 1 GAATATACGC 0.646535 -16 CATTAGGAAAAAATAAAGCCTTTCCGAAGA 6 25 0 AAATAAAGCC 0.925986 -87 TTTGGTGGGCGATTATAGCGAAATACATCC 6 66 0 GATTATAGCG 0.946495 -46 ATCACTCTAAAAATTAACCGCATTTT 6 96 1 AAATTAACCG 0.835359 -16 AACTTTATAAAAATAAACCGCACTTTACTA 8 25 0 AAATAAACCG 0.953378 -34 ********** Masking position 2 Map Score: 7.55526 Number of sites scoring better than the average of aligned sites = 521 Number in coding regions = 412 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 4 CATTTTTTATTTATGAGTGAAGAATAAATCTA 2 90 0 TTTGAGGAAG 0.979591 -129 AAATCAGCGTTTGTGAGGAAAGGCA 2 204 1 TTTGAGAAAG 0.992432 -15 GAGAAGAATATTTTGAGTAAACGACTTTTAAA 4 257 1 TTTGAGAAAC 0.967691 -44 ATCAAAGCCTTTCTTCGGAAAGGCTTTATTTT 6 14 1 TTTTCGAAAG 0.968035 -98 TTTTATAAAGTTTTTAGGAAAGCAAA 8 43 1 TTTTAGAAAG 0.988007 -16 CTGCTAAAAATTTTTAGAAAAGGAAAAAATT 9 23 1 TTTTAGAAAG 0.986504 -21 ** **** **** Masking position 4 Map Score: 7.30414 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 15 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 GTTGTTCGTTATATGGCGACAAATTGATTAA 2 36 1 ATATGGCGAA 0.975392 -183 AATTTCGGCATTATAGCGAGAAG 3 3 0 TTATAGCGAA 0.990859 -32 GAGCTTGTAAAAATAACGATACTTACTTTCG 4 116 0 AAATAACGAA 0.900365 -185 TTTTCACGGAATATAGCGTAAAAACAAAATT 4 196 1 ATATAGCGTA 0.963955 -105 TGGTGGGCGATTATAGCGAAATACATCCAAG 6 63 0 TTATAGCGAA 0.990859 -49 TGGTTTTATAACGATAAAAAATTAAA 7 6 1 TTATAACGAA 0.973425 -32 ********* * Masking position 4 Map Score: 5.74045 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 39 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 GCCATATAACGAACAACTTTTCACTTTATA 2 23 0 GAACAACTTT 0.92965 -196 TATTTTGAGTAAACGACTTTTAAAATCTAG 4 265 1 AAACGACTTT 0.945346 -36 TTCAATATTAATAAGGCTTTACCCTATTTT 5 115 0 ATAAGGCTTT 0.890376 -33 CCTTTCCGAAGAAAGGCTTTGATGAG 6 7 0 GAAAGGCTTT 0.98669 -105 CCTTTCTTCGGAAAGGCTTTATTTTTTCCT 6 21 1 GAAAGGCTTT 0.98669 -91 TTTGCTTTCCTAAAAACTTTATAAAAATAA 8 39 0 TAAAAACTTT 0.800489 -20 ********** Masking position 3 Map Score: 2.9701 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 143 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 GCGACAAATTGATTAAATTCAAGAGGGAAAT 2 51 1 GATAAATTCA 0.918399 -168 CTCAAAATATGATCAACTTCACATTTTTTAT 2 112 0 GACAACTTCA 0.924121 -107 GGTTGTGTCTCACCGAAATCAACACAAATTT 4 86 0 CACGAAATCA 0.957848 -215 GGGTTATGAACAATAAAATCGCCTTAAAAAT 5 73 1 CATAAAATCG 0.884768 -75 ATACATCCAAGAACAAAATCATTAGGAAAAA 6 43 0 GACAAAATCA 0.984164 -69 TATAATCGCCCACCAAAATCACTCTAAAAAT 6 79 1 CACAAAATCA 0.984164 -33 ** ******** Masking position 6 Map Score: 1.15782 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 202 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 ********** No masking Map Score: -1.43286e-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: -1.43286e-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: -1.43286e-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