AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00750_hinf_reg_100.orf -o00750_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 HI0087 42 threonine synthase (thrC) #2 HI0089 300 aspartokinase I / homoserine dehydrogenase I (thrA) #3 HI0405 72 pyridoxine kinase, putative #4 HI0406 89 acetyl-CoA carboxylase, carboxyl transferase (accA) #5 HI0408 171 ABC transporter, ATP-binding protein (yebM) #6 HI0863 135 pyridoxamine phosphate oxidase (pdxH) #7 HI1167 190 phosphoserine aminotransferase (serC) #8 HI1336 111 dihydropteroate synthase (folP-1) #9 HI1337 37 mrsA protein (mrsA) #10 HI1338 58 conserved hypothetical protein Motif number 1 CGGTTAGTTTACACGAAATTTATTGACTAAG 2 9 1 TTCACGATTT 0.508608 -292 TGCGTAAAGAAATACCGAAATTTCCCGAGCTTG 2 76 0 AAACCGATTT 0.922797 -225 ACAATGAAAAATAACCGCACTTTATCCGTAATC 2 129 1 ATACCGCTTT 0.994154 -172 CATTAGCACGATTACCGCCATTATGATGACCAT 2 161 1 ATACCGCTTA 0.964854 -140 AAGATACAGAAAACCCGCGATTCAACTGAATAG 2 231 1 AACCCGCTTC 0.968504 -70 ATTTATAAAAAAACCCGCTATTCAGTTGAATCG 2 248 0 AACCCGCTTC 0.968504 -53 AGCGGTAAAAATCACCGCTCTTTTAGAATGTTA 3 12 0 ATACCGCTTT 0.994154 -61 AGCGGTGATTTTTACCGCTCTTTTTTGATCTAA 3 26 1 TTACCGCTTT 0.989407 -47 ACCGTAAAAATCGACCGCACTTTATCAAGGAAT 4 50 0 TCACCGCTTT 0.946206 -40 TAAGCGTTTGAATAATGCTTTTTCCATAGGAAT 5 64 0 AAAATGCTTT 0.829368 -108 GGTTGGGGAAAATAACGCATTTTTATAGAATTC 5 126 0 AAAACGCTTT 0.98119 -46 CATTGTTGAAAACACGGCGATTTT 5 158 1 AAACGGCTTT 0.923225 -14 AACAACTCCCTTTAAAATAAATA 7 1 1 AAAACTCTTT 0.802376 -190 TCGTCAAAATTTACCCTCTATTTTATGAATGAT 7 71 1 TTCCCTCTTT 0.752912 -120 AAAATCGATAATCAATGCTTTTTACTGAAATCA 7 118 0 ATAATGCTTT 0.843363 -73 CTCATCAAAGCCTTTCTTCGGAAAGG 8 4 1 ATAAAGCTTC 0.720061 -108 ATTAGGAAAAAATAAAGCCTTTCCGAAGAAAGG 8 21 0 AAAAAGCTTC 0.699042 -91 ACTCTAAAAATTAACCGCATTTT 8 99 1 TTACCGCTTT 0.989407 -13 TTTTTGACCGCACTTAGTAAAGTGCG 10 4 1 TTACCGCTTA 0.937801 -55 TTTATAAAAATAAACCGCACTTTACTAAGTGCG 10 19 0 TAACCGCTTT 0.988282 -40 ** ***** *** Masking position 11 Map Score: 32.1332 Number of sites scoring better than the average of aligned sites = 2264 Number in coding regions = 1630 Number in noncoding regions = 634 Number of orfs with sites within 600 bp upstream = 387 Fraction of orfs with sites within 600 bp upstream = 0.0621587 Motif number 2 CGGTTAGTTTACACGAAATTTAT 2 1 1 CGGTATTTAA 0.984151 -300 CGGGAAATTTCGGTATTTCTTTACGCATTCATT 2 82 1 CGGTTTCTTA 0.960666 -219 GGATAAAGTGCGGTTATTTTTCATTGTGTTTTA 2 123 0 CGGTATTTTA 0.991716 -178 ACTGAATAGCGGGTTTTTTTATAAATTTAAAAA 2 255 1 GGGTTTTTAA 0.940682 -46 TCTAAAAGAGCGGTGATTTTTACCGCTCTTTTT 3 18 1 CGGTATTTTC 0.95753 -55 TGATTTTTACCGCTCTTTTTTGATCTAAATATA 3 31 1 CGCTTTTTTA 0.943228 -42 TGATAAAGTGCGGTCGATTTTTACGGTCTTTTT 4 56 1 CGGTGTTTTA 0.977666 -34 TCGATTTTTACGGTCTTTTTAGGATAACAAA 4 69 1 CGGTTTTTAG 0.932866 -21 TCCCTAACCCCGATTTATTTAAACTAAAAAGGT 6 16 0 CGATTTTTAA 0.853243 -120 ATAAAATAGAGGGTAAATTTTGACGATTGATTA 7 64 0 GGGTATTTTA 0.962589 -127 AAAATGCGGTTAATTTTTAGAGTGATTTT 8 93 0 CGGTATTTTA 0.991716 -19 TAGTAAAGTGCGGTTTATTTTTATAAAGTTTTT 10 25 1 CGGTTTTTTA 0.99302 -34 **** * **** * Masking position 8 Map Score: 20.9992 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 164 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 3 TACGGATAAAGTGCGGTTATTTTTCATTGT 2 129 0 GTGCGGTTAT 0.990963 -172 ATGATTAATGGTGCGGGTTAGTGCAGCAAA 2 198 1 GTGCGGGTTA 0.947032 -103 CATTCTAAAAGAGCGGTGATTTTTACCGCT 3 15 1 GAGCGGTGAT 0.939794 -58 GATCAAAAAAGAGCGGTAAAAATCACCGCT 3 26 0 GAGCGGTAAA 0.972531 -47 CCTTGATAAAGTGCGGTCGATTTTTACGGT 4 53 1 GTGCGGTCGA 0.981592 -37 TAAAATGACTGTGCCGTAATTTAGCTTTTT 7 32 1 GTGCCGTAAT 0.895159 -159 AAAATGCGGTTAATTTTTAGAGT 8 99 0 ATGCGGTTAA 0.953472 -13 ACTTTACTAAGTGCGGTCAAAAA 10 4 0 GTGCGGTCAA 0.99426 -55 ACTTAGTAAAGTGCGGTTTATTTTTATAAA 10 22 1 GTGCGGTTTA 0.987101 -37 ********** Masking position 4 Map Score: 12.6191 Number of sites scoring better than the average of aligned sites = 1399 Number in coding regions = 921 Number in noncoding regions = 478 Number of orfs with sites within 600 bp upstream = 305 Fraction of orfs with sites within 600 bp upstream = 0.0489881 Motif number 4 TTTTTCAGAAATTTTCTTAGTCAATAAATTTCG 2 24 0 ATTTTCTGTA 0.96365 -277 TACGCATTCATTTTTCAAGATAAAACACAATGA 2 103 1 TTTTTCAATA 0.80394 -198 AGTGCGGTTATTTTTCATTGTGTTTTATCTTGA 2 117 0 TTTTTCTGTT 0.757188 -184 TATGATGACCATTATTATGATTAATGGTGCGGG 2 182 1 ATTATTTATA 0.888897 -119 ATAGGAATGAATTTTCTTTATAATCTGTAGTCT 5 39 0 ATTTTCTATA 0.969949 -133 AAACGCTTAAATATTCGACATAAGAGAGAAAAT 5 88 1 ATATTCAATA 0.511495 -84 GATGATACGCATATTTCTAATAATTGCAAGAGT 6 74 1 ATATTTTATA 0.834615 -62 GTAATTTAGCTTTTTTTTAATCAATCGTCAAAA 7 47 1 TTTTTTTATA 0.952747 -144 GATAGAAAGAATTTTTTTGATTTCAGTAAAAAG 7 101 1 ATTTTTTATT 0.837768 -90 TTGATTATCGATTTTTGTAGTGATAAAAAAGAC 7 136 1 ATTTTTTGTA 0.960689 -55 AAAAGACATCATTATTTTCATAAAAAGCAAGGA 7 162 1 ATTATTTATA 0.888897 -29 AAGGCTTTATTTTTTCCTAATGATTTTGTTCTT 8 33 1 TTTTTCTATA 0.95628 -79 AATGCGGTTAATTTTTAGAGTGATTTTGGTGGG 8 87 0 ATTTTTGGTA 0.794005 -25 ATTCCTTTAATTTTTTATCGTTATAAAACCA 9 9 0 TTTTTTTGTA 0.943064 -29 TAAAGTGCGGTTTATTTTTATAAAGTTTTTAGG 10 28 1 TTTATTTATA 0.844299 -31 ****** * ** * Masking position 5 Map Score: 13.1402 Number of sites scoring better than the average of aligned sites = 407 Number in coding regions = 294 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 5 TTCATTTTTCAAGATAAAACACAATGAAAAA 2 109 1 AAGATAAACA 0.961959 -192 CAGCAAAAACAAGATACAGAAAACCCGCGAT 2 221 1 AAGATAAGAA 0.93955 -80 TTTTGATCTAAATATACAACAAAGGAGAAAA 3 48 1 AATATAAACA 0.828933 -25 CCCTAAAATAAAAAAGTTTTCAGCA 5 5 1 AAAATAAAAA 0.94563 -167 TATTCGACATAAGAGAGAAAATCTTGAGAAT 5 99 1 AAGAGAAAAA 0.878523 -73 ATGGTTGGGGAAAATAACGCATTTTTATAGA 5 130 0 AAAATACGCA 0.78381 -42 CAATTTTCATAAAATATAAAACTCAAATGCA 6 111 0 AAAATAAAAA 0.94563 -25 AACTCCCTTTAAAATAAATAAAATGACTGTG 7 14 1 AAAATAATAA 0.864263 -177 GTAGTGATAAAAAAGACATCATTATTTTCAT 7 152 1 AAAAGAATCA 0.766323 -39 TCATTAGGAAAAAATAAAGCCTTTCCGAAGA 8 25 0 AAAATAAGCC 0.78381 -87 TGGTTTTATAACGATAAAAAATTAAAGGAAT 9 11 1 ACGATAAAAA 0.780151 -27 ****** **** Masking position 6 Map Score: 4.84894 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 264 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 6 TAATGGTGCGGGTTAGTGCAGCAAAAACAA 2 203 1 GGTTAGTGCA 0.952082 -98 GGTTTTCACTGGTTGGGCAAGC 4 3 0 GGTTGGGCAA 0.987286 -87 TTTCAACAATGGTTGGGGAAAATAACGCAT 5 139 0 GGTTGGGGAA 0.995219 -33 AATAAATCGGGGTTAGGGAACCCGAGGTTG 6 30 1 GGTTAGGGAA 0.992624 -106 ********** Masking position 4 Map Score: 2.6849 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 8 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 TTTAATCTGATTTCATCTATTTAAATTAAC 1 11 0 TTTCATCTAT 0.757861 -32 GTGACAAATTTTTCAGAAATTTTCTTAGTC 2 35 0 TTTCAGAAAT 0.939992 -266 TAGCGGGTTTTTTTATAAATTTAAAAACAC 2 261 1 TTTTATAAAT 0.572951 -40 ATAAAAAAGTTTTCAGCATTCAGACTACAG 5 18 1 TTTCAGCATT 0.690306 -154 ATCGCCGTGTTTTCAACAATGGTTGGGGAA 5 149 0 TTTCAACAAT 0.815287 -23 TCGTCAATTTTCATAAAATATAAAACTC 6 118 0 TTTCATAAAA 0.883539 -18 TTAGCTTTTTTTTAATCAATCGTCAAAATT 7 52 1 TTTAATCAAT 0.675862 -139 TCTTTCTATCATTCATAAAATAGAGGGTAA 7 81 0 ATTCATAAAA 0.652611 -110 ATTTTTTTGATTTCAGTAAAAAGCATTGAT 7 111 1 TTTCAGTAAA 0.727805 -80 ACATCATTATTTTCATAAAAAGCAAGGAAA 7 167 1 TTTCATAAAA 0.883539 -24 TTTGCTTTCCTAAAAACTTTATAAA 10 44 0 TTTCCTAAAA 0.742401 -15 ********** Masking position 3 Map Score: 5.0644 Number of sites scoring better than the average of aligned sites = 724 Number in coding regions = 595 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 8 ********** No masking Map Score: -7.50743e-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 9 ********** No masking Map Score: -7.50743e-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: -7.50743e-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