AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i039_Mannose_Metabolism_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 HI0870.1 300 H. influenzae predicted coding region HI0870.1 #2 HI1334 126 cell division protein (ftsJ) #3 HI1335 90 cell division protein (ftsH) #4 HI1336 111 dihydropteroate synthase (folP-1) #5 HI1337 37 mrsA protein (mrsA) Motif number 1 GATAAGATAAGATAAGATAAGATA 1 5 0 GATAAGATAA 0.983389 -296 GATAAGATAAGATAAGATAAGATAAGATAA 1 15 0 GATAAGATAA 0.983389 -286 AAAAAGATAAGATAAGATAAGATAAGATAA 1 25 0 GATAAGATAA 0.983389 -276 TAGAACAATGAAAAAGATAAGATAAGATAA 1 35 0 AAAAAGATAA 0.88713 -266 GGATAAGAGAGATAAAATCAAAATATCCCT 1 117 0 GATAAAATCA 0.983389 -184 ATACCCACCCGAAAAAATCATAATATACTA 1 154 0 GAAAAAATCA 0.978479 -147 CAGAATATTGGACAAAATAATAATAAACCC 1 231 0 GACAAAATAA 0.978403 -70 AAAAAACATTGAGAAAATCAACCGCTCTTT 2 27 0 GAGAAAATCA 0.963859 -100 AAATCATTAGGAAAAAATAAAGCCTTTCCG 4 29 0 GAAAAAATAA 0.976726 -83 TACATCCAAGAACAAAATCATTAGGAAAAA 4 43 0 AACAAAATCA 0.894567 -69 ********** Masking position 5 Map Score: 21.5373 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 176 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 2 ATCTTATCTTTTTCATTGTTCTAGTGCTTTATATCTGC 1 42 1 TTTCGTTAGT 0.923173 -259 TTATTACTTTCTTTTTTGATTTTAAGATAAGGGATATT 1 88 1 CTTTGTTTGT 0.959366 -213 CTTATCCGCTATTTTAGTATATTATGATTTTTTCGGGT 1 140 1 ATTTTTTTGT 0.878394 -161 ATTATGATTTTTTCGGGTGGGTATAGAGTATTTGTATG 1 160 1 TTTCTGTAGG 0.829018 -141 TAGAGAAAACCTTTATATAGTTTAAGGTATTAATTTTC 1 265 0 CTTTTGTTGT 0.980613 -36 TTTTTACTGATTTCAATTAGCTTCGGCTTGAATTTGAC 2 52 1 TTTCTGTTGT 0.977612 -75 TTTGTAGTCGTTTCGCCTATATTTGGGTACAATCTGTC 2 87 0 TTTCTTTTGT 0.970184 -40 GCTTTGATAGCTTTTCATTGCTAATGATGTGTAGTATC 3 13 1 CTTTTGTAGT 0.96756 -78 ATGATTTTGTTCTTGGATGTATTTCGCTATAATCGCCC 4 52 1 TCTTTTTTGT 0.867592 -60 TGCGGTTAATTTTTAGAGTGATTTTGGTGGGCGATTAT 4 80 0 TTTTGGTTGT 0.966937 -32 AATAAAATTCCTTTAATTTTTTATCGTTATAAAACCA 5 10 0 CTTTTTTAGT 0.956944 -28 **** * * ** * * Masking position 12 Map Score: 8.87536 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 238 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 3 CATATATAGAGAAAACCTTTATATAGTTTA 1 279 0 GAAAACCTTT 0.979501 -22 CATTAGCAATGAAAAGCTATCAAAGCAA 3 9 0 GAAAAGCTAT 0.980772 -82 CCTTTCCGAAGAAAGGCTTTGATGAG 4 7 0 GAAAGGCTTT 0.994941 -105 CCTTTCTTCGGAAAGGCTTTATTTTTTCCT 4 21 1 GAAAGGCTTT 0.994941 -91 ********** Masking position 4 Map Score: 5.31977 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 9 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 4 ATCTTATCTTTTTCATTGTTCTAGTGCTTT 1 42 1 TTTCATTGTT 0.963492 -259 TGCTTATTACTTTCTTTTTTGATTTTAAGA 1 85 1 TTTCTTTTTT 0.962922 -216 AAAATCAACCGCTCTTTTTTATTAGGAATC 2 14 0 GCTCTTTTTT 0.912822 -113 CGGTTGATTTTCTCAATGTTTTTTACTGAT 2 33 1 TCTCAATGTT 0.77435 -94 AATCTTCTATTTTTTGTAGTCGTTT 2 112 0 TCTATTTTTT 0.915988 -15 TTTGATAGCTTTTCATTGCTAATGATGTGT 3 15 1 TTTCATTGCT 0.860456 -76 TCGGAAAGGCTTTATTTTTTCCTAATGATT 4 28 1 TTTATTTTTT 0.929668 -84 AAAATGCGGTTAATTTTTAGAGTGATTT 4 94 0 GTTAATTTTT 0.888397 -18 ATAAAATTCCTTTAATTTTTTATCGTTATA 5 17 0 TTTAATTTTT 0.942147 -21 ********** Masking position 7 Map Score: 8.56339 Number of sites scoring better than the average of aligned sites = 641 Number in coding regions = 467 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 5 TGTTCTAGTGCTTTATATCTGCTTCCTTGCT 1 58 1 CTTTATATCG 0.892431 -243 CTCTCTTATCCGCTATTTTAGTATATTATGA 1 136 1 CGCTATTTTG 0.936066 -165 CTAATGTTAGCTATATATTTGGTAGGGTTTA 1 207 1 CTATATATTG 0.972751 -94 ATACCTTAAACTATATAAAGGTTTTCTCTAT 1 273 1 CTATATAAAG 0.915354 -28 TAAAGGTTTTCTCTATATATGTA 1 288 1 CTCTATATAG 0.975128 -13 GTCGTTTCGCCTATATTTGGGTACAATCTGT 2 88 0 CTATATTTGG 0.900177 -39 GGATGTATTTCGCTATAATCGCCCACCAAAA 4 66 1 CGCTATAATG 0.938213 -46 ********* * Masking position 5 Map Score: 2.33481 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 45 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 ATACTCTATACCCACCCGAAAAAATCATAA 1 161 0 CCCACCCGAA 0.990378 -140 TAATAATAAACCCTACCAAATATATAGCTA 1 214 0 CCCTACCAAA 0.986777 -87 TATTAATTTTCCCTCCAGAATATTGGACAA 1 246 0 CCCTCCAGAA 0.980328 -55 AAAAATAAAGCCTTTCCGAAGAAAGGCTTT 4 17 0 CCTTTCCGAA 0.948109 -95 CGCTATAATCGCCCACCAAAATCACTCTAA 4 76 1 GCCCACCAAA 0.92555 -36 ********** Masking position 9 Map Score: 1.72589 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 39 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 AGTATATTATGATTTTTTCGGGTGGGTATAGA 1 155 1 GATTTTTCGG 0.88782 -146 TGGGTATAGAGTATTTGTATGAAAATTACTCT 1 177 1 GTTTTGTAGA 0.955839 -124 TTTTCTCAATGTTTTTTACTGATTTCAATTAG 2 40 1 GTTTTTACGA 0.975836 -87 GCTTCGGCTTGAATTTGACAGATTGTACCCAA 2 71 1 GATTTGACGA 0.984496 -56 AGGTAGGTTAGACTTTGAACGAT 3 78 1 GATTTGAAGA 0.975836 -13 TGGTTTTATAACGATAAAAAATTA 5 3 1 GTTTATAAGA 0.863659 -35 ** ****** ** Masking position 5 Map Score: 0.951027 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 62 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 ********** No masking Map Score: -1.70998e-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: -1.70998e-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: -1.70998e-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