AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00750_hinf_reg_300.orf -o00750_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 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 HI1334 126 cell division protein (ftsJ) #9 HI1335 90 cell division protein (ftsH) #10 HI1336 111 dihydropteroate synthase (folP-1) #11 HI1337 37 mrsA protein (mrsA) #12 HI1338 58 conserved hypothetical protein Motif number 1 CAAGCTCGGGAAATTTCGGTATTTCTTTACGCA 2 76 1 AAATTCGGTT 0.86822 -225 GATTACGGATAAAGTGCGGTTATTTTTCATTGT 2 129 0 AAAGGCGGTT 0.996226 -172 ATGGTCATCATAATGGCGGTAATCGTGCTAATG 2 161 0 TAATGCGGTT 0.958999 -140 CTATTCAGTTGAATCGCGGGTTTTCTGTATCTT 2 231 0 GAATGCGGGT 0.933984 -70 CGATTCAACTGAATAGCGGGTTTTTTTATAAAT 2 248 1 GAATGCGGGT 0.933984 -53 TAACATTCTAAAAGAGCGGTGATTTTTACCGCT 3 12 1 AAAGGCGGTT 0.996226 -61 TTAGATCAAAAAAGAGCGGTAAAAATCACCGCT 3 26 0 AAAGGCGGTA 0.995198 -47 ATTCCTTGATAAAGTGCGGTCGATTTTTACGGT 4 50 1 AAAGGCGGTA 0.995198 -40 GAATTCTATAAAAATGCGTTATTTTCCCCAACC 5 126 1 AAAAGCGTTT 0.819911 -46 AAAATCGCCGTGTTTTCAACAATG 5 158 0 AAATGCCGTT 0.907086 -14 TATTTATTTTAAAGGGAGTTGTT 7 1 0 AAAGGAGTTT 0.724345 -190 ATCATTCATAAAATAGAGGGTAAATTTTGACGA 7 71 0 AAATGAGGGA 0.792463 -120 TCCTAATAAAAAAGAGCGGTTGATTTTCTCAAT 8 17 1 AAAGGCGGTA 0.995198 -110 AAAATGCGGTTAATTTTTAGAGT 10 99 0 AAAAGCGGTA 0.972847 -13 CGCACTTTACTAAGTGCGGTCAAAAA 12 4 0 TAAGGCGGTA 0.974932 -55 CGCACTTAGTAAAGTGCGGTTTATTTTTATAAA 12 19 1 AAAGGCGGTA 0.995198 -40 **** ***** * Masking position 3 Map Score: 35.2107 Number of sites scoring better than the average of aligned sites = 1763 Number in coding regions = 1209 Number in noncoding regions = 554 Number of orfs with sites within 600 bp upstream = 344 Fraction of orfs with sites within 600 bp upstream = 0.0552522 Motif number 2 ATTGTGTTTTATCTTGAAAAATGAATGCGTAAAGAAAT 2 96 0 AAAAAAATGC 0.903846 -205 AAGATAAAACACAATGAAAAATAACCGCACTTTATCCG 2 119 1 AAAAAACCGC 0.997384 -182 GTGTTTTTAAATTTATAAAAAAACCCGCTATTCAGTTG 2 253 0 AAAAACCCGC 0.984953 -48 ATCAAAAAAGAGCGGTAAAAATCACCGCTCTTTTAGAA 3 17 0 AAAAAACCGC 0.997384 -56 TCCTAAAAAGACCGTAAAAATCGACCGCACTTTATCAA 4 55 0 AAAAAACCGC 0.997384 -35 CGATTTATTTAAACTAAAAAGGTACAAC 6 1 0 AAAAAACAAC 0.916934 -135 CGATTTTTGTAGTGATAAAAAAGACATCATTATTTTCA 7 144 1 AAAAAACATC 0.916934 -47 AGTAAAAAACATTGAGAAAATCAACCGCTCTTTTTTAT 8 22 0 AAAAAACCGC 0.997384 -105 GAACAAAATCATTAGGAAAAAATAAAGCCTTTCCGAAG 10 26 0 AAAAAAAAGC 0.968678 -86 CACCAAAATCACTCTAAAAATTAACCGCATTTT 10 89 1 AAAAAACCGC 0.997384 -23 TGGTTTTATAACGATAAAAAATTAAAGGAATTTTATT 11 11 1 AAAAAAAAGG 0.766839 -27 TCCTAAAAACTTTATAAAAATAAACCGCACTTTACTAA 12 24 0 TAAAAACCGC 0.97786 -35 * **** ***** Masking position 9 Map Score: 23.4543 Number of sites scoring better than the average of aligned sites = 640 Number in coding regions = 437 Number in noncoding regions = 203 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 3 TACGGATAAAGTGCGGTTATTTTTCATTGTG 2 128 0 GTGCGGTATT 0.994884 -173 CATTCTAAAAGAGCGGTGATTTTTACCGCTC 3 15 1 GAGCGGTATT 0.986147 -58 CCTTGATAAAGTGCGGTCGATTTTTACGGTC 4 53 1 GTGCGGTGAT 0.995259 -37 TAAAATGACTGTGCCGTAATTTAGCTTTTTT 7 32 1 GTGCCGTATT 0.969865 -159 TAATAAAAAAGAGCGGTTGATTTTCTCAATG 8 20 1 GAGCGGTGAT 0.987154 -107 AAAATGCGGTTAATTTTTAGAGTG 10 98 0 ATGCGGTAAT 0.972095 -14 ACTTTACTAAGTGCGGTCAAAAA 12 3 0 GTGCGGTAAA 0.982427 -56 ACTTAGTAAAGTGCGGTTTATTTTTATAAAG 12 22 1 GTGCGGTTAT 0.987173 -37 ******* *** Masking position 7 Map Score: 14.2478 Number of sites scoring better than the average of aligned sites = 691 Number in coding regions = 442 Number in noncoding regions = 249 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 4 GTTAATTTAAATAGATGAAATCA 1 2 1 TAATTAAATA 0.864926 -41 ATAGATGAAATCAGATTAAAAACGGATTAAAT 1 21 1 TAGATAAAAA 0.966308 -22 GGTTTTTTTATAAATTTAAAAACACAATATCT 2 266 1 TAATTAAAAA 0.962697 -35 TGTTGTATATTTAGATCAAAAAAGAGCGGTAA 3 37 0 TAGATAAAAA 0.966308 -36 CCCTAAAATAAAAAAGTTTTCAGCA 5 4 1 TAAATAAAAA 0.968419 -168 TTGTACCTTTTTAGTTTAAATAAATCGGGGTT 6 12 1 TAGTTAAATA 0.856906 -124 TCAATTTTCATAAAATATAAAACTCAAATGCA 6 111 0 TAAATTAAAA 0.79578 -25 CAACTCCCTTTAAAATAAATAAAATGACTGTG 7 13 1 TAAATAATAA 0.795688 -178 ATTTTGACGATTGATTAAAAAAAAGCTAAATT 7 49 0 TGATTAAAAA 0.829334 -142 TGCTTTTTACTGAAATCAAAAAAATTCTTTCT 7 104 0 TAAATAAAAA 0.968423 -87 CTACCTTTCCTAAGTTAAAAAATTTCGTCACA 9 52 0 TAGTTAAAAA 0.960189 -39 * **** ***** Masking position 9 Map Score: 13.0568 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 146 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 5 AAGTGACAAATTTTTCAGAAATTTTCTTAGT 2 36 0 TTTTTCGAAA 0.948128 -265 ACGCATTCATTTTTCAAGATAAAACACAATG 2 104 1 TTTTCAGATA 0.732329 -197 ATGATGACCATTATTATGATTAATGGTGCGG 2 183 1 TTATTAGATT 0.775159 -118 TTTTACGGTCTTTTTAGGATAACAAA 4 74 1 TTTTTAGATA 0.935601 -16 AGACTACAGATTATAAAGAAAATTCATTCCT 5 39 1 TTATAAGAAA 0.915264 -133 TGAGTTTTATATTTTATGAAAATTGACGA 6 117 1 ATTTTAGAAA 0.833172 -19 TTTACCCTCTATTTTATGAATGATAGAAAGA 7 80 1 ATTTTAGAAT 0.63622 -111 AATCAATGCTTTTTACTGAAATCAAAAAAAT 7 111 0 TTTTACGAAA 0.905404 -80 ATTTCCTTGCTTTTTATGAAAATAATGATGT 7 167 0 TTTTTAGAAA 0.968601 -24 CCGCTCTTTTTTATTAGGAATCCTT 8 5 0 TTATTAGAAT 0.880141 -122 TCTCAATGTTTTTTACTGATTTCAATTAGCT 8 43 1 TTTTACGATT 0.612934 -84 ATCAAAGCCTTTCTTCGGAAAGGCTTTATTT 10 14 1 TTCTTCGAAA 0.795946 -98 AAGAACAAAATCATTAGGAAAAAATAAAGCC 10 35 0 TCATTAGAAA 0.726758 -77 TGGTGGGCGATTATAGCGAAATACATCCAAG 10 63 0 TTATAGGAAA 0.649656 -49 TGGTTTTATAACGATAAAAAATTAAA 11 6 1 TTATAAGATA 0.835294 -32 TTTTATAAAGTTTTTAGGAAAGCAAA 12 43 1 TTTTTAGAAA 0.968661 -16 ****** **** Masking position 4 Map Score: 13.9496 Number of sites scoring better than the average of aligned sites = 560 Number in coding regions = 403 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 6 CTTTTTCCATAGGAATGAATTTTCTTTATAAT 5 48 0 AGAATGATTT 0.846169 -124 TAAGCGTTTGAATAATGCTTTTTCCATAGGAA 5 65 0 ATAATGCTTT 0.939851 -107 TATGTCGAATATTTAAGCGTTTGAATAATGCT 5 78 0 ATTAAGCTTT 0.90405 -94 GGTTGGGGAAAATAACGCATTTTTATAGAATT 5 127 0 ATAACGCTTT 0.875603 -45 ATTGCAAGAGTCGATTGCATTTGAGTTTTATA 6 96 1 TGATTGCTTT 0.821262 -40 ACTGTGCCGTAATTTAGCTTTTTTTTAATCAA 7 39 1 ATTTAGCTTT 0.830127 -152 TTATGAATGATAGAAAGAATTTTTTTGATTTC 7 93 1 TGAAAGATTT 0.768353 -98 AAAATCGATAATCAATGCTTTTTACTGAAATC 7 119 0 ACAATGCTTT 0.913153 -72 TTGCTTTGATAGCTTTTCATTGCTAAT 9 6 1 TGATAGCTTT 0.886273 -85 TAGGAAAGGTAGGTTAGACTTTGAACGAT 9 72 1 AGTTAGATTT 0.632396 -19 CTCATCAAAGCCTTTCTTCGGAAAG 10 4 1 ACAAAGCTTT 0.946902 -108 ATTAGGAAAAAATAAAGCCTTTCCGAAGAAAG 10 22 0 ATAAAGCTTT 0.963638 -90 * ****** *** Masking position 10 Map Score: 7.13987 Number of sites scoring better than the average of aligned sites = 433 Number in coding regions = 372 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 7 TAATGGTGCGGGTTAGTGCAGCAAAAACAA 2 203 1 GGTTAGTGCA 0.94777 -98 GGTTTTCACTGGTTGGGCAAGC 4 3 0 GGTTGGGCAA 0.986096 -87 TTTCAACAATGGTTGGGGAAAATAACGCAT 5 139 0 GGTTGGGGAA 0.994768 -33 AATAAATCGGGGTTAGGGAACCCGAGGTTG 6 30 1 GGTTAGGGAA 0.991929 -106 ********** Masking position 4 Map Score: 2.02642 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 8 ATTCATTTTTCAAGATAAAACACAATGAAAAA 2 108 1 CAAGAAAACA 0.890219 -193 GCAGCAAAAACAAGATACAGAAAACCCGCGAT 2 220 1 CAAGAAAGAA 0.916796 -81 ATATTTAGATCAAAAAAGAGCGGTAAAAATCA 3 31 0 CAAAAAAGCG 0.523863 -42 AAATATACAACAAAGGAGAAAATATA 3 57 1 CAAAGAAAAA 0.930631 -16 CGCACTTTATCAAGGAATTAAACTGTGGCGCA 4 36 0 CAAGGATAAA 0.850186 -54 CCCTAAAATAAAAAAGTTTTCAG 5 2 1 CCTAAAAAAA 0.724653 -170 ATGCTTTTTCCATAGGAATGAATTTTCTTTAT 5 51 0 CATAGATGAA 0.683805 -121 AAATATTCGACATAAGAGAGAAAATCTTGAGA 5 96 1 CATAAAAGAA 0.836398 -76 TCAATTTTCATAAAATATAAAACTCAAATGCA 6 111 0 TAAAAAAAAA 0.636797 -25 TCATAAAAAGCAAGGAAATACA 7 179 1 CAAGGATACA 0.774278 -12 AAGGATTCCTAATAAAAAAGAGCGGTTGA 8 8 1 CCTAAAAAAA 0.724653 -119 GAAACGACTACAAAAAATAGAAGATT 8 111 1 CAAAAAAGAA 0.930631 -16 AATTTCGTCACAAGATACTACACATCATTAGC 9 32 0 CAAGAATACA 0.806817 -59 CGAAATACATCCAAGAACAAAATCATTAGGAA 10 46 0 CCAAGAAAAA 0.850124 -66 TTTATAACGATAAAAAATTAAAGGAATTTTAT 11 15 1 TAAAAATAAA 0.474514 -23 ***** * **** Masking position 7 Map Score: 6.00853 Number of sites scoring better than the average of aligned sites = 935 Number in coding regions = 727 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261 Motif number 9 GTTTTTAATCTGATTTCATCTATTTAAATT 1 14 0 TGATTTCATC 0.947614 -29 AAAATAAAAAAGTTTTCAGCATTCAGACTA 5 15 1 AGTTTTCAGC 0.912785 -157 AAAATCGCCGTGTTTTCAACAATGGTTGGG 5 152 0 TGTTTTCAAC 0.957009 -20 AGAATTTTTTTGATTTCAGTAAAAAGCATT 7 108 1 TGATTTCAGT 0.956329 -83 TGTTTTTTACTGATTTCAATTAGCTTCGGC 8 49 1 TGATTTCAAT 0.934024 -78 ********** Masking position 5 Map Score: 0.78753 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 101 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 ********** No masking Map Score: 2.14117e-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: 2.14117e-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: 2.14117e-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