AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00360_hinf_reg_300.orf -o00360_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 HI0195.1 26 conserved hypothetical transmembrane protein (aefA) #2 HI0197 84 penicillin-insensitive murein endopeptidase (mepA) #3 HI0199 46 lipid A biosynthesis (kdo)2-(lauroyl)-lipid IVA acyltransferase (msbB) #4 HI0301 300 hemolysin, putative #5 HI0468 300 ATP phosphoribosyltransferase (hisG) #6 HI0469 92 histidinol dehydrogenase (hisD) #7 HI0470 68 histidinol-phosphate aminotransferase (hisC) #8 HI0916 107 outer membrane protein, putative #9 HI0920 248 conserved hypothetical protein #10 HI1024 49 hexulose-6-phosphate synthase, putative #11 HI1027 58 L-xylulose kinase (lyx) #12 HI1028 30 conserved hypothetical protein #13 HI1030 71 conserved hypothetical transmembrane protein #14 HI1031 175 conserved hypothetical protein #15 HI1062 85 (3R)-hydroxymyristol (acyl carrier protein) dehydrase (fabZ) #16 HI1064 56 conserved hypothetical protein #17 HI1527 84 lipid A biosynthesis lauroyl acyltransferase (htrB) #18 HI1615 160 phosphoribosylaminoimidazole carboxylase, catalytic subunit (purE) #19 HI1616 69 phosphoribosylaminoimidazole carboxylase, ATPase subunit (purK) #20 HI1617 138 aspartate aminotransferase (aspC) Motif number 1 ATTAATTTTAACCGCACTTTTGCGCGCTTT 3 16 0 ACCGCACTTT 0.99907 -31 TGTATTTTTAACCGCACTTTAGGTTTAAAC 4 175 1 ACCGCACTTT 0.99907 -126 ATAAAAAATAACCGCACATTGGGTTTAAAC 4 197 0 ACCGCACATT 0.994142 -104 TTAAATTTTAACCGCACTTTTGCAGCATTT 9 20 1 ACCGCACTTT 0.99907 -229 CTAAAAAACCACCGCACTTTTTATTTCTCT 9 103 0 ACCGCACTTT 0.99907 -146 TTTAGATCTGACCGCACTTTTAAAGTGCGG 19 18 1 ACCGCACTTT 0.99907 -52 GAAAAAAACAACCGCACTTTAAAAGTGCGG 19 29 0 ACCGCACTTT 0.99907 -41 GTAAAAAATGACCGCACTTTTTGATGAATA 20 12 1 ACCGCACTTT 0.99907 -127 ATAAAAATTAACCACGCTTTGATATTTTTA 20 44 0 ACCACGCTTT 0.961039 -95 ********** Masking position 9 Map Score: 38.2108 Number of sites scoring better than the average of aligned sites = 1115 Number in coding regions = 700 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 2 TAAAATGTAATTAATTTTAACCGCACTTTTGCGCGC 3 19 0 TAATACCGCC 0.995733 -28 TAAAAATTGTGTATTTTTAACCGCACTTTAGGTTTA 4 166 1 GATTACCGCC 0.903551 -135 GGAAAATCAATAAAAAATAACCGCACATTGGGTTTA 4 200 0 TAAAACCGCC 0.99802 -101 CAGTGTAAAAGCAATAAATACCCCTCGGAAGGCAAT 5 228 1 GAATACCCCC 0.945601 -73 AAAGTTGAGATAAAAGAAAACCCCTCGAAAATTGCC 5 258 0 TAAAACCCCC 0.990854 -43 AAAATCACCTTAAATTTTAACCGCACTTTTGCAGCA 9 11 1 TAATACCGCC 0.995733 -238 AAAAAACAACTAAAAAACCACCGCACTTTTTATTTC 9 106 0 TAAAACCGCC 0.99802 -143 TATTTATAGCTAAAAATAAAACGCACTCAATATAGC 15 11 0 TAAAAACGCC 0.970763 -75 TGGCTTATTCTATAAAATAACCGCTCAAGA 16 37 1 TTAAACCGCC 0.9817 -20 AAACATCTTTAGATCTGACCGCACTTTTAAAGTG 19 9 1 TAGAACCGCC 0.988577 -61 TAAATTTACGAAAAAAACAACCGCACTTTAAAAGTG 19 32 0 AAAAACCGCC 0.984628 -38 TGTAAAAAATGACCGCACTTTTTGATGA 20 3 1 TAAAACCGCC 0.99802 -136 AAAGATTTTATAAAAATTAACCACGCTTTGATATTT 20 47 0 TAAAACCACC 0.975442 -92 * *** ***** * Masking position 10 Map Score: 31.1525 Number of sites scoring better than the average of aligned sites = 741 Number in coding regions = 479 Number in noncoding regions = 262 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 3 TATTTTTCCCTAATCTAAATGGTAAA 1 10 0 TTTTTATCTA 0.301315 -17 TGAATAATGGATTTTTGATTGTGAATTGATCTCGT 4 51 0 ATTTTTTGAA 0.719612 -250 AAATATTCTTATTTTGTTTATATGACGAAAAGTAT 4 105 0 ATTTTAATGA 0.619749 -196 AAATAAGAATATTTTGTTGTCTAGAATTTTCCCCT 4 126 1 ATTTTTTAGA 0.807409 -175 GTTGTCTAGAATTTTCCCCTCTCCGTAAAAATTGT 4 141 1 ATTTTTTCCG 0.456486 -160 TTTTTTATTGATTTTCCTCTTTTCGCGTTTTGCGA 4 219 1 ATTTTTTTCG 0.525362 -82 GCGTTTTGCGATTTTTTCTAAAATATGATAATTTT 4 243 1 ATTTTAAATA 0.584492 -58 AAAAAAAGCAATTTTTTTGAAAAAAATTGTGTTTT 5 27 0 ATTTTAAAAA 0.78073 -274 AAAAATTGCTTTTTTTAATTTTAAAGTGTATTTTT 5 46 1 TTTTTTTAAA 0.680552 -255 AATGTTTTTCCTATTTTAAAGTTGAGATA 5 282 0 TTTTTTTTAA 0.680598 -19 ATAACCCAGCATTTTGAGATATTGATTATTTAAAT 6 35 0 ATTTTTTTGA 0.807409 -58 GTTATCATCCATTTTACGGATACAAAGGAAAATAA 6 65 1 ATTTTAACAA 0.73823 -28 TCTATGCCACATTTTCTATTGTCAAAATGCTGCAA 9 39 0 ATTTTTTCAA 0.878848 -210 CTCCCTATTAATTTTTGCCATTTTACGGTATTCTA 9 70 0 ATTTTATTTA 0.718305 -179 TATTTTTATTATTGAGAGACCTCTAT 9 233 0 ATTTTATGAG 0.437176 -16 CGTTTTTCCTTAAATAATATGAGGAAG 10 33 0 TTTTTAATAA 0.453001 -17 AATAGGCTGGATTTTACATAATAAAAATCCAGCCC 11 13 1 ATTTTATAAA 0.870627 -46 TCTAGATCCTATTTTCTTGTGATAATATTTCATAT 14 17 0 ATTTTTATAA 0.840637 -159 AATTTTACTGATTTTGTGATCTAGATCCTATTTTC 14 36 0 ATTTTTTAGA 0.807409 -140 CAGTAAAATTATTTTAACATATTGATTTATAAATA 14 61 1 ATTTTTTTGA 0.807409 -115 TAATTTATTTATTTTACATTTATTGACTGAGCTTT 14 94 1 ATTTTTATTG 0.461721 -82 ATGAAACGTAATTTTACTATATAAAATTAAGAGAG 14 145 1 ATTTTTTAAA 0.905195 -31 TTTTTCCTCTCTTAATTTTATATAG 14 161 0 TTTTTTTTAA 0.680598 -15 AGTGCGTTTTATTTTTAGCTATAAATATCGTATAA 15 20 1 ATTTTTTAAA 0.905227 -66 TTGAGCGGTTATTTTATAGAATAAGCCAATTTTTT 16 30 0 ATTTTATAAG 0.743151 -27 AATCGCCACAATTTTGGTTATTCAAATAGAGAGAT 17 17 0 ATTTTATCAA 0.836363 -68 CCTAAGCACAATTTTTATAAGAATAGGTCAAATT 18 10 0 ATTTTAAATA 0.584541 -151 TTAGGATAAAATTTTATCCTTAAAGTTGCAATGGT 18 40 1 ATTTTTAAAG 0.6938 -121 TTGCAATGGTATTTTCCTATAAAAGCCATTTAGCA 18 65 1 ATTTTTAAAG 0.693797 -96 TATTTTCTCAATTTTCTAATTAAAAACGTGGCGTA 18 134 0 ATTTTTAAAA 0.840636 -27 TGCGGTTGTTTTTTTCGTAAATTTAACGAGAAATA 19 43 1 TTTTTATTTA 0.362389 -27 ACGCTTTGATATTTTTAAATATTCATCAAAAAGTG 20 26 0 ATTTTTTTCA 0.72042 -113 ATCAAGAAAGATTTTATAAAAATTAACCACGCTTT 20 54 0 ATTTTAATTA 0.584541 -85 TACTTCAGTCATTTTATTTTATCAAGAAAGATTTT 20 74 0 ATTTTTTCAA 0.878847 -65 ***** * **** Masking position 5 Map Score: 25.4469 Number of sites scoring better than the average of aligned sites = 1369 Number in coding regions = 945 Number in noncoding regions = 424 Number of orfs with sites within 600 bp upstream = 331 Fraction of orfs with sites within 600 bp upstream = 0.0531642 Motif number 4 TCCTGTACCTAGGGTAGTATACTCTAGGTTA 2 11 1 AGGTAGTATA 0.564588 -74 GTTTTGCTGTAGGTAAGTATATCCTAGGTTC 2 58 0 AGGAAGTATA 0.748786 -27 GAAAAGAGGAAAATCAATAAAAAATAACCGC 4 212 0 AAACAATAAA 0.925373 -89 GTGTATTTTTAAGGCAATATAAGATCTAATA 5 71 1 AAGCAATATA 0.937411 -230 GTATGTTTGGAAGATAATAAAATATCTTCCG 5 183 1 AAGTAATAAA 0.837947 -118 AATCAGTGTAAAAGCAATAAATACCCCTCGG 5 225 1 AAACAATAAA 0.925373 -76 ACGGATACAAAGGAAAATAAACA 6 80 1 AGGAAATAAA 0.887405 -13 ATTAATAGGGAGAGAAATAAAAAGTGCGGTG 9 93 1 AGAAAATAAA 0.788212 -156 AATTCATAGCAAGCCAATATAACTTATGATA 9 184 1 AAGCAATATA 0.937411 -65 TAATATGAGGAAGGCAGTATAATTCTGTCTT 10 15 0 AAGCAGTATA 0.908517 -35 CTAGATCACAAAATCAGTAAAATTATTTTAA 14 47 1 AAACAGTAAA 0.891565 -129 AATAAATGTAAAATAAATAAATTATTTATAA 14 87 0 AAAAAATAAA 0.848778 -89 TAAGAAAGCTCAGTCAATAAATGTAAAATAA 14 102 0 CAGCAATAAA 0.792984 -74 TACAAAAAATAAACAAATAAAATCTATCGGA 15 55 0 AAAAAATAAA 0.848778 -31 *** ******* Masking position 6 Map Score: 10.6194 Number of sites scoring better than the average of aligned sites = 451 Number in coding regions = 339 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 5 AATAAAATGTAATTAATTTTAACCGCAC 3 29 0 AAAATTATTT 0.747839 -18 AATTCACAATCAAAAATCCATTATTCACAAGTTAT 4 59 1 CAAAATCTTT 0.640524 -242 TCATATAAACAAAATAAGAATATTTTGTTGTCTAG 4 115 1 AAAATAGTTT 0.841763 -186 CCCTCTCCGTAAAAATTGTGTATTTTTAACCGCAC 4 157 1 AAAAATGTTT 0.946094 -144 GATTTTTTCTAAAATATGATAATTTTTCGCCGTCA 4 252 1 AAAATTGATT 0.885113 -49 TTTTTTTGAAAAAAATTGTGTTTTTAGTACATTTT 5 16 0 AAAAATGTTT 0.634842 -285 TTTTTTTCAAAAAAATTGCTTTTTTTAATTTTAAA 5 36 1 AAAAATGTTT 0.855038 -265 TTGTTGTATGAAAATTTGACTGCTTACGTGTCGTG 7 32 0 AAAATTGTTT 0.975213 -37 TCTGTTCTGCAAAAATTGAAAATTTATTGTAAAAA 9 137 0 AAAAATGATT 0.809776 -112 TTGATTATCACAAATGTGATTCGTTTTATATTATG 13 36 0 CAAATTGTTT 0.923067 -36 TTCACAATATGAAATATTATCACAAGAA 14 4 1 ACAATTGATT 0.714904 -172 TCTAGATCACAAAATCAGTAAAATTATTTTAACAT 14 46 1 AAAATAGATT 0.764133 -130 TTCTGGCTTAAAAAATTGGCTTATTCTATAAAATA 16 21 1 AAAAATGTTT 0.965907 -36 TTTAAAATCTCTCTATTTGAATAACCAA 17 4 1 AAAATTCTTT 0.847365 -81 ***** ** * ** Masking position 4 Map Score: 14.3139 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 165 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 6 CTTAAAAATACACTTTAAAATTAAAAAAAGCA 5 52 0 CCTTAAAATT 0.943693 -249 ATTTTCTCTGCCCAATTAAATTAGGCAGAGAA 8 51 0 CCATTAAATT 0.902863 -57 AAAATCACCTTAAATTTTAACCGCACT 9 6 1 CCTTAAATTT 0.973701 -243 TTATTTCTCTCCCTATTAATTTTTGCCATTTT 9 81 0 CCATTAATTT 0.953547 -168 AAAACCACCGCACTTTTTATTTCTCTCCCTAT 9 97 0 CCTTTTATTT 0.780628 -152 AGTTGTTTTTTACAATAAATTTTCAATTTTTG 9 131 1 TCATAAATTT 0.724182 -118 ATTGAGAGACCTCTATAAATTTGGTGGTAAAC 9 217 0 CCATAAATTT 0.967796 -32 TTTTTCCTCTCTTAATTTTATATAGTAA 14 158 0 CCCTTAATTT 0.902411 -18 AAAACAACCGCACTTTAAAAGTGCGGTCAGAT 19 23 0 CCTTAAAAGT 0.777582 -47 AATATTTCTCGTTAAATTTACGAAAAAAA 19 51 0 CCTTAAATTT 0.973702 -19 * * ******** Masking position 6 Map Score: 6.63972 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 134 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 CCAATGTGCGGTTATTTTTTATTGATTTTCC 4 205 1 GTTATTTTTA 0.751962 -96 CTTTTACACTGATTTTTATTACACTCGGAAG 5 208 0 GATTTTATTA 0.956485 -93 AGCATTTTGAGATATTGATTATTTAAATGGC 6 32 0 GATATTATTA 0.948711 -61 GATATTAATTATAGATCTAAG 7 1 1 GATATTATTA 0.948708 -68 TTTAATTAAGGATATTTATCAA 8 96 1 GATATTATCA 0.776955 -12 TATAACTTATGATATAGTTTACCACCAAATT 9 201 1 GATATATTTA 0.560592 -48 TATTTTTATTATTGAGAGACC 9 238 0 TATTTTATTA 0.633952 -11 CGTTTTTCCTTAAATAATATGA 10 38 0 GTTTTTCTTA 0.751737 -12 TTATGGGCTGGATTTTTATTATGTAAAATCC 11 21 0 GATTTTATTA 0.956485 -38 AATGTGATTCGTTTTATATTATGGCGTTTTA 13 28 0 GTTTTAATTA 0.762786 -44 TCTACGCCACGTTTTTAATTAGAAAATTGAG 18 132 1 GTTTTTATTA 0.928366 -29 ****** **** Masking position 11 Map Score: 7.12798 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 107 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 8 ATGTGCGGTTATTTTTTATTGATTTTCCTC 4 208 1 ATTTTTTATT 0.651349 -93 CGCGTTTTGCGATTTTTTCTAAAATATGAT 4 242 1 GATTTTTTCT 0.617678 -59 GTTTTTAGTACATTTTTACTA 5 2 0 CATTTTTACT 0.732096 -299 CTTTTACACTGATTTTTATTACACTCGGAA 5 209 0 GATTTTTATT 0.916502 -92 TAAATTGAACTTTTTTCTTCATCAGAACT 8 10 1 CTTTTTTCTT 0.638471 -98 AAGTGCGGTGGTTTTTTAGTTGTTTTTTAC 9 114 1 GTTTTTTAGT 0.862968 -135 TTTTTTAGTTGTTTTTTACAATAAATTTTC 9 125 1 GTTTTTTACA 0.760838 -124 TTATGGGCTGGATTTTTATTATGTAAAATC 11 22 0 GATTTTTATT 0.916502 -37 ATTCTCCTTAGTTTTTTATGGGCTGGATTT 11 37 0 GTTTTTTATG 0.802773 -22 AATGTGATTCGTTTTATATTATGGCGTTTT 13 29 0 GTTTTATATT 0.828844 -43 TGTTTTTTCCTTCTGGCTTAA 16 2 1 GTTTTTTCCT 0.904933 -55 TCTACGCCACGTTTTTAATTAGAAAATTGA 18 132 1 GTTTTTAATT 0.716165 -29 GTGATGAATAGTTTTATACTTCAGTCATTT 20 95 0 GTTTTATACT 0.848708 -44 ********** Masking position 5 Map Score: 4.095 Number of sites scoring better than the average of aligned sites = 514 Number in coding regions = 366 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 9 TGTGGATAACTTGTGAATAATGGATTTTTG 4 69 0 TTGTGAATAA 0.851809 -232 AGTATCTATGTTGTGGATAACTTGTGAATA 4 80 0 TTGTGGATAA 0.782574 -221 AAAGCAATTTTTTTGAAAAAAATTGTGTTT 5 28 0 TTTTGAAAAA 0.645173 -273 TATTTTAAAGTTGAGATAAAAGAAAACCCC 5 270 0 TTGAGATAAA 0.828685 -31 ACATTTTCTATTGTCAAAATGCTGCAAAAG 9 36 0 TTGTCAAAAT 0.638821 -213 TGAAAATTTATTGTAAAAAACAACTAAAAA 9 126 0 TTGTAAAAAA 0.669296 -123 TCTATAAATTTGGTGGTAAACTATATCATA 9 208 0 TGGTGGTAAA 0.696931 -41 CGAATCACATTTGTGATAATCAATTGGAGG 13 48 1 TTGTGATAAT 0.919969 -24 TCCTATTTTCTTGTGATAATATTTCATATT 14 16 0 TTGTGATAAT 0.919969 -160 TAAATTTGAGTTGTGGTAAAATCGCCACAA 17 41 0 TTGTGGTAAA 0.924239 -44 AATTAGAAAATTGAGAAAATAGC 18 148 1 TTGAGAAAAT 0.772174 -13 ********** Masking position 9 Map Score: 3.31254 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 435 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 10 GTGATAAGGATCTTTGCCCTCTTTTTACGAGATC 4 25 1 TCTTGCCTTT 0.991926 -276 TTGATTTTCCTCTTTTCGCGTTTTGCGATTTTTT 4 226 1 TCTTTCGTTT 0.813346 -75 AAAACAACGTTCTCTGCCTAATTTAATTGGGCAG 8 42 1 TCTTGCCTTT 0.991926 -66 TTTACGGTATTCTATGCCACATTTTCTATTGTCA 9 50 0 TCTTGCCTTT 0.991926 -199 TCCCTATTAATTTTTGCCATTTTACGGTATTCTA 9 70 0 TTTTGCCTTA 0.824208 -179 GATGTGCTATTCTACGCCACGTTTTTAATTAGAA 18 122 1 TCTCGCCTTT 0.978222 -39 *** **** *** Masking position 3 Map Score: 1.44548 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 32 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 CTCCGTAAAAATTGTGTATTTTTAACCGCAC 4 161 1 ATTGTGTTTT 0.968702 -140 TTTGAAAAAAATTGTGTTTTTAGTACATTTT 5 16 0 ATTGTGTTTT 0.968702 -285 TTTCAAAAAAATTGCTTTTTTTAATTTTAAA 5 40 1 ATTGCTTTTT 0.871919 -261 TTAATTTTAAAGTGTATTTTTAAGGCAATAT 5 60 1 AGTGTATTTT 0.762443 -241 TTCAGGCGTGATTGTATGTTTGGAAGATAAT 5 170 1 ATTGTATTTT 0.932143 -131 ATTTTGAGATATTGATTATTTAAATGGCGAG 6 29 0 ATTGATTTTT 0.821208 -64 AGGCAGTATAATTCTGTCTTTAAT 10 4 0 ATTCTGTTTT 0.818087 -46 ATAGATTTTATTTGTTTATTTTTTGTAAGGT 15 59 1 TTTGTTTTTT 0.821208 -27 TTAAAGTGCGGTTGTTTTTTTCGTAAATTTA 19 37 1 GTTGTTTTTT 0.871919 -33 ******* *** Masking position 7 Map Score: 2.76264 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 71 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 TGAAGTTTGATGTGATAAGGATCTTTGCCCTC 4 14 1 TGTGTAGGAT 0.980105 -287 GAAAAGTATCTATGTTGTGGATAACTTGTGAA 4 82 0 TATGTTGGAT 0.92279 -219 GATAATCAGGTGTGGTGATGATGGTAAGTGCA 5 137 0 TGTGTATGAT 0.918487 -164 CCCAGCATTTTGAGATATTGATTATTTAAATG 6 34 0 TGAGTTTGAT 0.686368 -59 CTTAGTTTTTTATGGGCTGGATTTTTATTATG 11 29 0 TATGGTGGAT 0.853844 -30 AAAGTCTCCTTGTGTTAAGAAAGTCTGTT 12 8 0 TGTGTAGAAA 0.604626 -23 TTACTGATTTTGTGATCTAGATCCTATTTTCT 14 35 0 TGTGTTAGAT 0.887295 -141 TTATAAAAATTGTGCTTAGGATAAAATTTTAT 18 25 1 TGTGTAGGAT 0.980105 -136 ATGTATGTGTTGTGTGATGAATAGTTTTATAC 20 106 0 TGTGGTGAAT 0.853844 -33 **** * ***** Masking position 11 Map Score: 2.26482 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 105 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 13 ACGAAAAGTATCTATGTTGTGGATAACTTGT 4 85 0 TTATGTTGTG 0.950687 -216 GAACGTTGTTTTTGAGTTCTGATGAAGAAAA 8 23 0 TTGAGTTCTG 0.946459 -85 TTATCGTAAATTTGAGTTGTGGTAAAATCGC 17 46 0 TTGAGTTGTG 0.984188 -39 GCCTGATATATGTAAGATGTGCTATTCTACG 18 107 1 TTAAGATGTG 0.893575 -54 TTTCCTTATGTATGTGTTGTGTGATGAATAG 20 114 0 TTGTGTTGTG 0.977496 -25 * ********* Masking position 8 Map Score: 0.184823 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 = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 14 ********** No masking Map Score: -4.85057e-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 15 ********** No masking Map Score: -4.85057e-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