AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_mixed1_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 HI0004 260 conserved hypothetical protein #2 HI0005 300 fdhD protein (fdhD) #3 HI0016 167 GTP-binding membrane protein (lepA) #4 HI0017 257 conserved hypothetical protein #5 HI0154 255 acyl carrier protein (acpP) #6 HI0156 300 malonyl CoA-acyl carrier protein transacylase (fabD) #7 HI0157 185 beta-ketoacyl-ACP synthase III (fabH) #8 HI0158 22 ribosomal protein L32 (rpL32) #9 HI0159 156 conserved hypothetical protein #10 HI0301 300 hemolysin, putative #11 HI0406 89 acetyl-CoA carboxylase, carboxyl transferase (accA) #12 HI0408 171 ABC transporter, ATP-binding protein (yebM) #13 HI0807 109 conserved hypothetical protein #14 HI0808 151 ribosome releasing factor (rrf) #15 HI0809 172 phosphoenolpyruvate carboxykinase (pckA) #16 HI0810 144 conserved hypothetical protein #17 HI0811 134 argininosuccinate lyase (argH) #18 HI0812 21 glucosephosphate uridylyltransferase (galU) #19 HI0813 77 carbon storage regulator (csrA) #20 HI0814 187 alanyl-tRNA synthetase (alaS) #21 HI0815 101 universal stress protein A (uspA) #22 HI0817 170 conserved hypothetical protein #23 HI0819 37 galactokinase (galK) #24 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) #25 HI0908 79 H. influenzae predicted coding region HI0908 #26 HI0909 124 preprotein translocase SecA subunit (secA) #27 HI0910 64 mutator mutT protein (mutT) #28 HI0911 108 glutathione-regulated potassium efflux system protein (kefC) #29 HI0912 100 H. influenzae predicted coding region HI0912 #30 HI0913 144 ribosomal protein S2 (rpS2) #31 HI0914 132 elongation factor Ts (tsf) #32 HI0916 107 outer membrane protein, putative #33 HI0920 248 conserved hypothetical protein #34 HI1062 85 (3R)-hydroxymyristol (acyl carrier protein) dehydrase (fabZ) #35 HI1064_HI1065 56 HI1064: conserved hypothetical protein, HI1065: uridylate kinase (pyrH) #36 HI1126.1 181 H. influenzae predicted coding region HI1126.1 #37 HI1129 201 conserved hypothetical protein #38 HI1130 30 conserved hypothetical protein #39 HI1136 122 UDP-N-acetylmuramoylalanine--D-glutamate ligase (murD) #40 HI1137 21 cell division protein (ftsW) #41 HI1139 137 UDP-N-acetylmuramate--alanine ligase (murC) #42 HI1140 71 D-alanine--D-alanine ligase (ddlB) #43 HI1143 83 cell division protein (ftsZ) #44 HI1144 38 UDP-3-0-(3-hydroxymyristoyl) N-acetylglucosamine deacetylase (lpxC) #45 HI1260 193 acetyl-CoA carboxylase carboxyl transferase subunit beta (accD) Motif number 1 AATAAGTGCAAAAGTGCGGTTAGAAATTGA 1 221 1 AAAGTGCGGT 0.998829 -40 ATGAAAGGGAAAAGTGCGGTCAAATTTTCA 3 74 0 AAAGTGCGGT 0.998829 -94 TTGTACCTGAAAAGCGCGGAAATCGCTAGG 3 105 0 AAAGCGCGGA 0.898349 -63 TATCCGATTTAAAGTGCGGTCAAAACTCAA 6 17 0 AAAGTGCGGT 0.998829 -284 GTTTAAACCTAAAGTGCGGTTAAAAATACA 10 175 0 AAAGTGCGGT 0.998829 -126 GTTTAAACCCAATGTGCGGTTATTTTTTAT 10 197 1 AATGTGCGGT 0.982145 -104 ATTCCTTGATAAAGTGCGGTCGATTTTTAC 11 50 1 AAAGTGCGGT 0.998829 -40 GTAATCAACAAAAGTGCGGTAAAGATTCT 13 91 1 AAAGTGCGGT 0.998829 -19 TCAGTTACCCAAAGTGCGGTTAATATTTTT 14 22 0 AAAGTGCGGT 0.998829 -130 TTGGGTAACTGAAGTGCGGTCATTTTTTAT 14 40 1 GAAGTGCGGT 0.995669 -112 ATCAAGACAAAAAGTGCGGAAAAAACCACC 16 96 1 AAAGTGCGGA 0.989796 -49 ATTGAGATAAAAAGTGCGGTGGTTTTTTCC 16 113 0 AAAGTGCGGT 0.998829 -32 CGCTATTTGAGAAGTGCGGTTAAAATTTAA 20 48 0 GAAGTGCGGT 0.995669 -140 ATAGCGTCGTGAAGTGCGGTTTTATTTTGG 20 72 1 GAAGTGCGGT 0.995669 -116 TGAACAATCAAAGTGCGGTGATTTTTCAC 27 10 1 AAAGTGCGGT 0.998829 -55 AGGTATGAAAAAGGTGCGGTGAAAAATCAC 27 28 0 AAGGTGCGGT 0.987883 -37 TTTATACCATAAAGTGCGGTTAAAAACCAG 30 21 0 AAAGTGCGGT 0.998829 -124 TTTTTATCTAAAAGTGCGGTCAAAATAAAC 31 87 1 AAAGTGCGGT 0.998829 -46 TCCTCTGTCGAAAATGCGGTTTATTTTGAC 31 105 0 AAAATGCGGT 0.969983 -28 AAATGCTGCAAAAGTGCGGTTAAAATTTAA 33 20 0 AAAGTGCGGT 0.998829 -229 AGAGAAATAAAAAGTGCGGTGGTTTTTTAG 33 103 1 AAAGTGCGGT 0.998829 -146 AACTCAACTAAAAGTGCGGTTAAAATTCGC 41 91 0 AAAGTGCGGT 0.998829 -47 ********** Masking position 2 Map Score: 102.246 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 TAAGTGCAAAAGTGCGGTTAGAAATTGAAAA 1 223 1 AGTGCGGTAG 0.986781 -38 GAAAGGGAAAAGTGCGGTCAAATTTTCAAAC 3 71 0 AGTGCGGTAA 0.99805 -97 TCCGATTTAAAGTGCGGTCAAAACTCAAAAT 6 14 0 AGTGCGGTAA 0.99805 -287 TTAAACCTAAAGTGCGGTTAAAAATACACAA 10 172 0 AGTGCGGTAA 0.99805 -129 TTAAACCCAATGTGCGGTTATTTTTTATTGA 10 199 1 TGTGCGGTAT 0.945527 -102 TCCTTGATAAAGTGCGGTCGATTTTTACGGT 11 52 1 AGTGCGGTGA 0.993914 -38 AATCAACAAAAGTGCGGTAAAGATTCT 13 93 1 AGTGCGGTAA 0.99805 -17 AGTTACCCAAAGTGCGGTTAATATTTTTAGT 14 19 0 AGTGCGGTAA 0.99805 -133 GGGTAACTGAAGTGCGGTCATTTTTTATCTG 14 42 1 AGTGCGGTAT 0.995895 -110 CAAGACAAAAAGTGCGGAAAAAACCACCGCA 16 98 1 AGTGCGGAAA 0.972002 -47 TGAGATAAAAAGTGCGGTGGTTTTTTCCGCA 16 110 0 AGTGCGGTGT 0.987248 -35 CTATTTGAGAAGTGCGGTTAAAATTTAAGTT 20 45 0 AGTGCGGTAA 0.99805 -143 AGCGTCGTGAAGTGCGGTTTTATTTTGGAGT 20 74 1 AGTGCGGTTT 0.951187 -114 GAACAATCAAAGTGCGGTGATTTTTCACCGC 27 12 1 AGTGCGGTAT 0.995895 -53 GTATGAAAAAGGTGCGGTGAAAAATCACCGC 27 25 0 GGTGCGGTAA 0.981906 -40 TATACCATAAAGTGCGGTTAAAAACCAGTTT 30 18 0 AGTGCGGTAA 0.99805 -127 TTTATCTAAAAGTGCGGTCAAAATAAACCGC 31 89 1 AGTGCGGTAA 0.99805 -44 ATGCTGCAAAAGTGCGGTTAAAATTTAAGGT 33 17 0 AGTGCGGTAA 0.99805 -232 AGAAATAAAAAGTGCGGTGGTTTTTTAGTTG 33 105 1 AGTGCGGTGT 0.987248 -144 CTCAACTAAAAGTGCGGTTAAAATTCGCAAC 41 88 0 AGTGCGGTAA 0.99805 -50 ******** ** Masking position 3 Map Score: 76.9037 Number of sites scoring better than the average of aligned sites = 842 Number in coding regions = 496 Number in noncoding regions = 346 Number of orfs with sites within 600 bp upstream = 239 Fraction of orfs with sites within 600 bp upstream = 0.0383874 Motif number 3 TAGTAGCTAGATTATGTTGATTTCGTTAAAATAATACTCTC 2 98 1 ATTAATTTAA 0.594557 -203 ATGTCATTTGATTATGGATTTATCGTTAAAAAATCGTTACT 2 184 0 ATTATTATAA 0.685853 -117 TGTTAAATTATTTTTATATTTATGATCTAGATCACAATATT 2 236 0 TTTTTTATAA 0.902269 -65 TGCGGTCAAATTTTCAAACTTTTTAGATAAAACAAAACCCC 3 49 0 TTTTTTTTAA 0.94812 -119 CGCCAGTTAAATTTAATGATTTTTGAGAAAAACAATCTTTT 3 137 1 ATTTTTTTAA 0.930679 -31 ATTAATAAGTTTTTATTCATTATAAACAAAAACATTCATTC 4 22 1 TTTTTTATAA 0.854752 -236 TTTTAATTAATTTTTATAAATTTGATCTAAATTAAAATTCA 4 118 0 TTTTATTTAA 0.850997 -140 ATTTCAAATTATTTTATATTTATTTGATAAAGAGCAGGTTA 4 162 0 ATTTTTATAA 0.878086 -96 TGTTTTTCCTATTTGTTAGTTTTAACTCATAAAAGAGTGGT 5 224 0 ATTTTTTTAA 0.934516 -32 AGGGAACCCAATTTGTTCTTTATCCGATTTAAAGTGCGGTC 6 26 0 ATTTTTATTA 0.597602 -275 TTTTTTCCTTTTTAATCGCTTATCTTATTGAGT 7 163 1 TTTATTATTA 0.365861 -23 AAGAGGCGTGATTATAGCAATTTTTGTTATAGTTCCAACCT 9 30 1 ATTAATTTAA 0.594579 -127 GATAATTTCCTTTATTGAGTTATCCAATAAAAAATGTGATT 9 83 1 TTTATTATAA 0.736662 -74 AAATATTCTTATTTTGTTTATATGACGAAAAGTATCTATGT 10 99 0 ATTTATATAA 0.709387 -202 TGCGGTTATTTTTTATTGATTTTCCTCTTTTCGCGTTTTGC 10 211 1 TTTTTTTTTT 0.437336 -90 ACGGCGAAAAATTATCATATTTTAGAAAAAATCGCAAAACG 10 244 0 ATTATTTTAA 0.80891 -57 GCGGTCGATTTTTACGGTCTTTTTAGGATAACAAA 11 65 1 TTTATTTTTA 0.533346 -25 ATTCTCAAGATTTTCTCTCTTATGTCGAATATTTAAGCGTT 12 89 0 TTTTTTATAA 0.902267 -83 TGCGGTCATTTTTTATCTGTTTTCAAGCTGATAAATGTATT 14 54 1 TTTTTTTTTA 0.79037 -98 TTTACTGGATTTTTTTAAATTTTTGAATACATTTATCAGCT 14 79 0 TTTTTTTTAA 0.94812 -73 GTAGATCTCATTTTTAAACATTTTTTTAAGAACTTTACCTC 15 67 0 TTTTATTTAA 0.861118 -106 CCACAGTTAAATTTTAATCTTATATATTAGAGGTGACTT 15 144 1 ATTTTTATAA 0.878107 -29 TGATCGTTTTATTTAAGTGTTTTTGCTTATAAATAGGTGGC 16 59 0 ATTTTTTTAA 0.934516 -86 AAATCTTTCATTTTGTCCATTTTATTTGTATTAGTGCTAT 17 10 0 TTTTTTTTTT 0.437336 -125 GATTTTGTCCATTTTTGTTTTATTATTAATATAGAATATTG 17 46 1 ATTTTTATAA 0.878106 -89 GTTTTAATTAATTATTCTATTATTGTGCATATTTATTCATA 17 90 0 ATTATTATAA 0.685906 -45 AATTTTTCCTTTTTGTTTTAATTAATTATTCT 17 113 0 ATTTTTTTAT 0.746316 -22 GTGCGGTTTTATTTTGGAGTTTTGGCAAAAAGCCTTTTTAT 20 85 1 ATTTTTTTAA 0.934491 -103 GCAAAAAGCCTTTTTATAAATTTCAAAAATATGCAAAAATA 20 109 1 TTTTATTTAA 0.8609 -79 AACTTTTTCCTTGTTATAATCTATAAATCTTATAT 24 5 1 TTTTTTATAA 0.902269 -203 ATAAGCAAAATTTTTTATGATTTAGTTCATACTTATGAAAG 24 85 0 TTTTATTTAA 0.861119 -123 AATTTTGCTTATTTTCTTATTTTGTGACAAAGATCACGGTT 24 114 1 ATTTTTTTAA 0.934484 -94 TCACGGTTTATTTACAATAATTTAGTATAAATTAATGTAAT 24 147 1 TTTAATTTAA 0.645087 -61 TTTTTCTGTTTTTTGTGAAGAATATTGCTAT 26 1 1 TTTTTTTTAA 0.948156 -124 AATTTCTCTTTTTAAATATATAAGTTAAATAGTTAAATG 26 96 0 TTTTATATAA 0.757694 -29 TGGCGAGTATATTAAAAAGTTATATGTGATAAATCATACTA 28 44 0 ATTATTATAA 0.685906 -65 TCGCCAAAATATTTGTATTTTTTGCATTATTGGAGTCATT 28 79 1 ATTTTTTTAT 0.74632 -30 AGAAGTTAAAATTTAATATTTTTATAGATAAAAAATAATT 29 10 0 ATTTTTTTTA 0.74632 -91 TAAAATAAAAATTTACGTGATTTAAATCACTCAAAAGTAAA 29 61 0 ATTTATTTAT 0.49935 -40 TTAACCGCACTTTTGCAGCATTTTGACAATAGAAAATGTGG 33 27 1 TTTTATTTAA 0.861118 -222 TCCCTATTAATTTTTGCCATTTTACGGTATTCTATGCCACA 33 63 0 TTTTTTTTAT 0.790346 -186 TGCGGTGGTTTTTTAGTTGTTTTTTACAATAAATTTTCAAT 33 117 1 TTTTTTTTAA 0.948156 -132 TTTACAATAAATTTTCAATTTTTGCAGAACAGATTAGAACA 33 139 1 ATTTTTTTAA 0.934516 -110 CAAAATTGAATTTAAAGATTTTTATAAGATTTGTGACTTGT 36 84 0 TTTATTTTAT 0.533347 -98 TTTGTGGAGATTTTTAGAGATTTTCTAAAAATAAGTTCAAT 37 157 1 TTTTATTTAA 0.8609 -45 AATGATATAATTTTAAAATTTATAGCAATTAAGAAGAAAGA 39 90 1 TTTTTTATTA 0.655558 -33 TTGAACATTTTTTTTATTTTTTTGTCTTACAGACCACGTTA 45 35 0 TTTTTTTTAA 0.948157 -159 TTTTTGACCTTTTTATTGACTAGAAAATTGC 45 173 0 TTTTTTTTAT 0.79037 -21 **** **** * * Masking position 11 Map Score: 59.158 Number of sites scoring better than the average of aligned sites = 795 Number in coding regions = 506 Number in noncoding regions = 289 Number of orfs with sites within 600 bp upstream = 248 Fraction of orfs with sites within 600 bp upstream = 0.039833 Motif number 4 GAGTAAATTAGCGGTAAACATAAATTATGTAA 1 91 1 GCGGTAAATA 0.932806 -170 AGGGAAAAGTGCGGTCAAATTTTCAAACTTTT 3 67 0 GCGGTAATTT 0.984665 -101 GATTTAAAGTGCGGTCAAAACTCAAAATATT 6 10 0 GCGGTAAACT 0.88431 -291 AACCTAAAGTGCGGTTAAAAATACACAATTTT 10 168 0 GCGGTAAAAT 0.837592 -133 AACCCAATGTGCGGTTATTTTTTATTGATTTT 10 202 1 GCGGTATTTT 0.976471 -99 TTGATAAAGTGCGGTCGATTTTTACGGTCTTT 11 55 1 GCGGTGATTT 0.958939 -35 CAACAAAAGTGCGGTAAAGATTCT 13 96 1 GCGGTAAATT 0.984665 -14 TACCCAAAGTGCGGTTAATATTTTTAGTATTT 14 15 0 GCGGTAAATT 0.984665 -137 TAACTGAAGTGCGGTCATTTTTTATCTGTTTT 14 45 1 GCGGTATTTT 0.976471 -107 GATAAAAAGTGCGGTGGTTTTTTCCGCACTTT 16 106 0 GCGGTGTTTT 0.937867 -39 TTTGAGAAGTGCGGTTAAAATTTAAGTTATTT 20 41 0 GCGGTAAATT 0.984665 -147 GTCGTGAAGTGCGGTTTTATTTTGGAGTTTTG 20 77 1 GCGGTTTTTT 0.791632 -111 CAATCAAAGTGCGGTGATTTTTCACCGCACCT 27 15 1 GCGGTATTTT 0.976471 -50 ATCTAAAAGTGCGGTCAAAATAAACCGCATTT 31 92 1 GCGGTAAATA 0.932806 -41 CTGCAAAAGTGCGGTTAAAATTTAAGGTGATT 33 13 0 GCGGTAAATT 0.984665 -236 AATAAAAAGTGCGGTGGTTTTTTAGTTGTTTT 33 108 1 GCGGTGTTTT 0.937867 -141 TCTTGAGCGGTTATTTTATAGAATAAGC 35 39 0 GCGGTATTTA 0.899724 -18 AACTAAAAGTGCGGTTAAAATTCGCAACGTTT 41 84 0 GCGGTAAATT 0.984665 -54 ***** ** *** Masking position 5 Map Score: 39.8099 Number of sites scoring better than the average of aligned sites = 506 Number in coding regions = 290 Number in noncoding regions = 216 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 5 TCTCTTTGTACGTTAAAAATAGAGTAAATT 1 70 1 CGTTAAAAAT 0.578691 -191 ATGTTGATTTCGTTAAAATAATACTCTCTA 2 111 1 CGTTAAAATA 0.578691 -190 ATGGATTTATCGTTAAAAAATCGTTACTCT 2 182 0 CGTTAAAAAA 0.758686 -119 TAGATCATAAATATAAAAATAATTTAACAG 2 248 1 ATATAAAAAT 0.731477 -53 ATTAATTTTTAAATAAAATTTATATCAATA 4 89 0 AAATAAAATT 0.686776 -169 ATTTGATCTAAATTAAAATTCATTAATTTT 4 110 0 AATTAAAATT 0.526687 -148 TATAAAAATTAATTAAAAAAATAACCTGCT 4 141 1 AATTAAAAAA 0.853618 -117 TATCAAATAAATATAAAATAATTTGAAATA 4 174 1 ATATAAAATA 0.731478 -84 AAGAATTTTCAATTAAAAAACAATAGGACA 6 274 1 AATTAAAAAA 0.853618 -27 TTGAGTTATCCAATAAAAAATGTGATTTCC 9 97 1 CAATAAAAAA 0.889904 -60 AGAGGAAAATCAATAAAAAATAACCGCACA 10 209 0 CAATAAAAAA 0.889904 -92 CCCTAAAATAAAAAAGTTTTCAGCA 12 6 1 AAATAAAAAA 0.919921 -166 CTTGAGAATTCTATAAAAATGCGTTATTTT 12 121 1 CTATAAAAAT 0.657151 -51 GCTTGAAAACAGATAAAAAATGACCGCACT 14 52 0 AGATAAAAAA 0.897982 -100 GTATTCAAAAATTTAAAAAAATCCAGTAAA 14 90 1 ATTTAAAAAA 0.759915 -62 ATGGATGTCAATATAAAAAAATGTTAAGTA 15 105 0 ATATAAAAAA 0.861788 -68 ACATTTTGAGCAATAAAAAACTGTGTACTA 21 33 0 CAATAAAAAA 0.889904 -69 AAACCTTTGTAAATAAAAAAGCCATCGCTT 22 118 0 AAATAAAAAA 0.919921 -53 ATATTTTTATAGATAAAAAATAATT 29 6 0 AGATAAAAAA 0.897982 -95 TTAAACGAGAAGTTAAAATTTAATATTTTT 29 28 0 AGTTAAAATT 0.460289 -73 TATTGCCTTAAAATAAAAATTTACGTGATT 29 80 0 AAATAAAAAT 0.833852 -21 TGTTGTTAGTAATTAAAAAACTGCTTTTGA 30 72 0 AATTAAAAAA 0.853618 -73 CCGCACTTTTAGATAAAAATATAGGGGCTA 31 76 0 AGATAAAAAT 0.793625 -57 TTGGCTTATTCTATAAAATAACCGCTCAAG 35 36 1 CTATAAAATA 0.657151 -21 TCAATAAAATTTTATGAAAAA 37 2 1 CAATAAAATT 0.606729 -200 ATTTTTATCAAAATAAAAAAGCCGTTTGAA 37 50 0 AAATAAAAAA 0.919921 -152 GCACTTTTGGATATAAAAAATACTTATGAC 41 39 0 ATATAAAAAA 0.861788 -99 GTAGATGAAAAATTAAAATAA 43 2 0 AATTAAAATA 0.718124 -82 CTGACTAAATATATAAAATATAAATTCCCT 43 37 0 ATATAAAATA 0.731478 -47 TAAGACAAAAAAATAAAAAAAATGTTCAAT 45 47 1 AAATAAAAAA 0.919921 -147 ********** Masking position 5 Map Score: 26.2951 Number of sites scoring better than the average of aligned sites = 623 Number in coding regions = 373 Number in noncoding regions = 250 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 6 ATAAAAACTTATTAATAGGATAAAATA 4 4 0 ATAAAGTAAA 0.868415 -254 ACATTCATTCAATAAAAAGTTAAATTAATGTTAA 4 53 1 ATAAAGTAAA 0.868415 -205 GAAAATAATAATAAAACTGTACAAATTTTATCAA 4 214 0 AAAACGACAA 0.795346 -44 GTTAAAACTAACAAATAGGAAAAACAA 5 239 1 AAAAAGAAAA 0.950032 -17 ATTCAATTCCACAAAGGTGGAAAAGAAGGGAACC 6 59 0 AAAAGGAAAA 0.769849 -242 ATGGAACAAAGGAAACAAGGAAAAGTAGGGGCGC 6 157 1 GAAAAGAAAA 0.744538 -144 AAGATAAGCGATTAAAAAGGAAAAAATCTATGGA 7 155 0 ATAAAGAAAA 0.915633 -31 TTGATCTCGTAAAAAGAGGGCAAAGATCCTTATC 10 27 0 AAAAAGCAAA 0.706847 -274 CATATTTTAGAAAAAATCGCAAAACGCGAAAAGA 10 236 0 AAAATGAAAA 0.550833 -65 ACTTTCATCAATTAAAAAGGACAATGCA 14 134 1 ATAAAGACAA 0.926521 -18 TAAAGTTCTTAAAAAAATGTTTAAAAATGAGATC 15 71 1 AAAAAGTTAA 0.51419 -102 AAAACACTTAAATAAAACGATCAAGACAAAAAGT 16 77 1 ATAAAGTCAA 0.884629 -68 CACTAATACAAATAAAATGGACAAAATGAAAGAT 17 15 1 ATAAAGACAA 0.926521 -120 TAATAATAAAACAAAAATGGACAAAATCTTTCAT 17 40 0 AAAAAGACAA 0.956691 -95 TGCTTTATGAATAAATATGCACAATAATAGAATA 17 85 1 AAAAAGACAA 0.956691 -50 ATTAATTAAAACAAAAAGGAAAAATT 17 119 1 AAAAAGAAAA 0.950032 -16 ATAAATGCAAACTAAGGAGATAAAAG 19 62 1 ATAAGGTAAA 0.537269 -16 TATAAATTTCAAAAATATGCAAAAATAGGGCGAC 20 123 1 AAAAAGAAAA 0.950032 -65 CACAAAATAAGAAAATAAGCAAAATTTTTTATGA 24 106 0 GAAAAGAAAA 0.744538 -102 TATTCTTCACAAAAAACAGAAAAA 26 1 0 AAAACGAAAA 0.769849 -124 GTTCTGATGAAGAAAAAAGTTCAATTTA 32 5 0 AAAAAGTCAA 0.930714 -103 GAGATTTTCTAAAAATAAGTTCAATTTTTAAGGC 37 173 1 AAAAAGTCAA 0.930714 -29 AAGTATCATCAGTAAGAAGAAAAACAGGATAGAA 42 47 1 ATAAAGAAAA 0.915633 -25 CAAAAAAATAAAAAAAATGTTCAATAAGAGGAGA 45 52 1 AAAAAGTCAA 0.930714 -142 TTTTCTAGTCAATAAAAAGGTCAAAAA 45 177 1 ATAAAGTCAA 0.884629 -17 * *** * * **** Masking position 5 Map Score: 28.0397 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 165 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 7 ACAAAGAGACAAATCACGCTATTTCCTTAATCAAC 1 44 0 AAACCATTTC 0.65997 -217 GTTTACCGCTAATTTACTCTATTTTTAACGTACAA 1 75 0 AATTCATTTT 0.800003 -186 TAAACCTACCAATCCCCTAAATTTAGATTACATAA 1 115 0 AATCCATTTA 0.475971 -146 ATTATTGTATAATTCCCCTCATTTTTACACATACA 1 149 1 AATCCATTTT 0.947718 -112 TCCGCCAGTTAAATTTAATGATTTTTGAGAAAAAC 3 135 1 AAATAATTTT 0.463523 -33 TTTTATTTAAAAATTAATGAATTTTAATTTAGATC 4 101 1 AAATAATTTT 0.407129 -157 AAGTGCGGTCAAAACTCAAAATATT 6 1 0 AAACCATATT 0.555044 -300 AGTGCGGTTAAAAATACACAATTTTTACGGAGAGG 10 158 0 AAATCATTTT 0.591502 -143 ATTTTTATAGAATTCTCAAGATTTTCTCTCTTATG 12 106 0 AATCCATTTT 0.948012 -66 GAATTCTATAAAAATGCGTTATTTTCCCCAACCAT 12 126 1 AAATCATTTT 0.589759 -46 AAAATCGCCGTGTTTTCAACAATGGT 12 156 0 AAACCGTTTT 0.676775 -16 TATAGAGCAAAAATCCCGACATTGTGTCGGGATTG 15 14 0 AAACCATTGT 0.781308 -159 AGTGCGGAAAAAACCACCGCACTTTTTATCTCAAT 16 108 1 AAACCACTTT 0.840821 -37 TAAAATGGACAAAATGAAAGATTTTGTCCATTTTT 17 27 1 AAATAATTTT 0.462004 -108 AATAAAAACTAAGTCGCCCTATTTTTGCATATTTT 20 134 0 AAGCCATTTT 0.757906 -54 AATCATAAAAAATTTTGCTTATTTTCTTATTTTGT 24 104 1 AATTGATTTT 0.389151 -104 TTTCCGTTACAATACACGCAATTTTCATAATAAAC 25 45 1 AATCCATTTT 0.942404 -35 ATTGCTATTGAAATAGCGATATTTTAAAAAATTAT 26 34 1 AAAACATTTT 0.511259 -91 GTGCGGTGAAAAATCACCGCACTTTGATTGTTCA 27 10 0 AAACCACTTT 0.816028 -55 TGAGTGATTTAAATCACGTAAATTTTTATTTTAAG 29 69 1 AAACCAATTT 0.582402 -32 GTGCGGTTAAAAACCAGTTTATTTTGT 30 3 0 AAACGATTTT 0.804759 -142 CTCTGTCGAAAATGCGGTTTATTTTGACCGCACTT 31 98 0 AATCGATTTT 0.741445 -35 AACAACTAAAAAACCACCGCACTTTTTATTTCTCT 33 103 0 AAACCACTTT 0.840821 -146 AATATCGTATAATCCGATAGATTTTATTTGTTTAT 34 43 1 AATCAATTTT 0.746224 -43 ATTCCACATTAAAGCAACTGATTTTTATCAAAATA 37 65 0 AAACAATTTT 0.788315 -137 GTGCGGTTAAAATTCGCAACGTTTTTATTTCTAAT 41 73 0 AATCCGTTTT 0.712372 -65 ATAAAATATAAATTCCCTTTATTGTAGATGAAAAA 43 20 0 AATCCATTGT 0.712431 -64 TTTATGTTCTAATACGCGCAATTTTCTAGTCAATA 45 156 1 AATCCATTTT 0.942404 -38 *** * * ***** Masking position 2 Map Score: 22.5168 Number of sites scoring better than the average of aligned sites = 531 Number in coding regions = 399 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 8 TGTGTTGATTAAGGAAATAGCGTGATTTGT 1 41 1 AAGGAAATAG 0.671025 -220 CATTAGTTAAATGTAAAAAGTCTGTTAAAT 2 269 0 ATGTAAAAAG 0.729059 -32 TTCAGTTTGAATGAAAAAAGAAACCCCGAA 3 12 1 ATGAAAAAAG 0.729059 -156 CTAGGGATGAAAGGGAAAAGTGCGGTCAAA 3 80 0 AAGGGAAAAG 0.751438 -88 AAGAAAAAGTAAGCAAAAAGAAAGGCGCCC 6 185 0 AAGCAAAAAG 0.899244 -116 TTGCTTCGCCAAAGAAAAAGTAAGCAAAAA 6 196 0 AAAGAAAAAG 0.781298 -105 TTGGCGAAGCAAAGAAAAAGTAAGCTCGCC 6 214 1 AAAGAAAAAG 0.781298 -87 GAACACCTATAAGTAAAAAA 7 1 0 AAGTAAAAAA 0.551568 -185 AGCGATTAAAAAGGAAAAAATCTATGGACT 7 153 0 AAGGAAAAAA 0.860688 -33 ATTCATTCCTATGGAAAAAGCATTATTCAA 12 60 1 ATGGAAAAAG 0.93111 -112 TTAAAACAAAAAGGAAAAATT 17 124 1 AAGGAAAAAT 0.825926 -11 TTTCAAAAATATGCAAAAATAGGGCGACTT 20 129 1 ATGCAAAAAT 0.413203 -59 AGATTATAACAAGGAAAAAGTT 24 3 0 AAGGAAAAAG 0.966113 -205 GACTCCAATAATGCAAAAAATACAAATATT 28 86 0 ATGCAAAAAA 0.478326 -23 AGTTCTGATGAAGAAAAAAGTTCAATTTA 32 10 0 AAGAAAAAAG 0.850208 -98 ATAGGGAGAGAAATAAAAAGTGCGGTGGTT 33 97 1 AAATAAAAAG 0.415625 -152 TTTAAGCCAGAAGGAAAAAACA 35 3 0 AAGGAAAAAA 0.860688 -54 ATAAAATTTTATGAAAAAAGCCGTTTGAAT 37 14 1 ATGAAAAAAG 0.729059 -188 ATTGGGAGAAAAGGAAAAATAA 41 126 1 AAGGAAAAAT 0.825926 -12 ********** Masking position 6 Map Score: 15.859 Number of sites scoring better than the average of aligned sites = 378 Number in coding regions = 286 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 9 CATTCAATAAAAAGTTAAATTAATGTTAAAT 4 58 1 AAATTAAATT 0.811593 -200 AAGTTAAATTAATGTTAAATTATTGATATAA 4 69 1 AATTTAAATT 0.840309 -189 ATCATTTTAATATTTCAAATTATTTTATATT 4 183 0 TATTCAAATT 0.621509 -75 CCCATAAATCAATGTCAAATT 5 1 0 AATTCAAATT 0.716816 -255 ACCGAAGAAGAATTTTCAATTAAAAAACAAT 6 267 1 AATTTCAATT 0.771266 -34 TAATCTGAAATAACTTAAATTTTAACCGCAC 20 34 1 TAATTAAATT 0.735785 -154 GGTTTACACTAATTTCAAATTTACTCAGGAA 22 143 1 AATTCAAATT 0.65344 -28 ATAATCTATAAATCTTATATTTTGATCATAA 24 26 1 AATTTATATT 0.615326 -182 AATGTGGTTTAAAGTTATATTAAAAGATTTA 28 15 1 AAATTATATT 0.56476 -94 TATCTATAAAAATATTAAATTTTAACTTCTC 29 21 1 AATTTAAATT 0.815111 -80 GATGAAGAAAAAAGTTCAATTTA 32 3 0 AAATTCAATT 0.732704 -105 TTTTACAATAAATTTTCAATTTTTGCAGAAC 33 138 1 AATTTCAATT 0.771266 -111 AACTATATCATAAGTTATATTGGCTTGCTAT 33 189 0 TAATTATATT 0.456152 -60 TAAAAATCTTTAAATTCAATTTTGATTTGAC 36 101 1 TAATTCAATT 0.639212 -81 GGCTGTATTCTATTTCAAATTACGTCAAATC 36 124 0 TATTCAAATT 0.621509 -58 TTTCTAAAAATAAGTTCAATTTTTAAGGCGT 37 178 1 TAATTCAATT 0.639212 -24 GTAGTACTTTTATCTTAAATTT 38 19 1 TATTTAAATT 0.775502 -12 TTAGTAAAGGAAATTTATATTTCCATCAATG 39 63 1 AAATTATATT 0.563683 -60 *** ******* Masking position 5 Map Score: 9.6534 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 181 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 10 TTTCAAACTTTTTAGATAAAACAAAACCCC 3 49 0 TTTAGATAAA 0.379353 -119 TTAATGATTTTTGAGAAAAACAATCTTTT 3 149 1 TTGAGAAAAA 0.90139 -19 TGTTAAATTATTGATATAAATTTTATTTAA 4 81 1 TTGATATAAA 0.744359 -177 TTAGATCAAATTTATAAAAATTAATTAAAA 4 129 1 TTTATAAAAA 0.767634 -129 TTATATTTATTTGATAAAGAGCAGGTTATT 4 160 0 TTGATAAAGA 0.782041 -98 TTAAAATGATTTGATAAAATTTGTACAGTT 4 204 1 TTGATAAAAT 0.756498 -54 TATCTTTCCTTGTTAAAAAAAGAGGCGTG 9 10 1 TTGTTAAAAA 0.517986 -147 ATTATCATATTTTAGAAAAAATCGCAAAAC 10 245 0 TTTAGAAAAA 0.7427 -56 GTTTAATTCCTTGATAAAGTGCGGTCGATT 11 45 1 TTGATAAAGT 0.436876 -45 TTATTCCTAATTGAGATAAAAAGTGCGGTG 16 122 0 TTGAGATAAA 0.66387 -23 ATTTTTGAAATTTATAAAAAGGCTTTTTGC 20 109 0 TTTATAAAAA 0.767634 -79 ATCGTTTACATTGATAAAAAACAGGAGTCA 24 186 1 TTGATAAAAA 0.933765 -22 AATATTTTTATAGATAAAAAATAATT 29 7 0 TAGATAAAAA 0.670416 -94 ACCGCACTTTTAGATAAAAATATAGGGGCT 31 77 0 TAGATAAAAA 0.670416 -56 TTGATAAATATCCTTAATTA 32 98 0 TTGATAAATA 0.698658 -10 CTTTTTTATTTTGATAAAAATCAGTTGCTT 37 59 1 TTGATAAAAA 0.933765 -143 TGAACTTATTTTTAGAAAATCTCTAAAAAT 37 166 0 TTTAGAAAAT 0.385413 -36 GTTGTGGCGTTTTATAAATAGCCTCAGTCA 41 13 1 TTTATAAATA 0.419638 -125 ********** Masking position 1 Map Score: 8.79084 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 282 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 11 AACCTACCAATCCCCTAAATTTAGATTACAT 1 117 0 TCCCTAAATT 0.731873 -144 TCTATTCTCCTAAATTCTTTTCAATT 1 245 0 TCCCTAAATT 0.731873 -16 GTCTGGTCGCACCACAAAATAGGCAATGTGA 5 154 0 ACACAAAATA 0.851594 -102 GTGCGACCAGACCATAAAATAGTTGCAAGTT 5 173 1 ACATAAAATA 0.695146 -83 TGGCTATACTCCTAAATTTAAT 8 5 0 ACCCTAAATT 0.810308 -18 AAAATTCTAGACAACAAAATATTCTTATTTT 10 125 0 ACACAAAATA 0.851594 -176 CATTATTCAAACGCTTAAATATTCGACATAA 12 80 1 ACCTTAAATA 0.785716 -92 ATAAGCAAAAACACTTAAATAAAACGATCAA 16 70 1 ACCTTAAATA 0.785716 -75 TTTTGCCAAAACTCCAAAATAAAACCGCACT 20 84 0 ACCCAAAATA 0.935235 -104 TTTAATATACTCGCCAAAATATTTGTATTTT 28 69 1 TCCCAAAATA 0.902222 -40 ATTGGCTTATTCTATAAAATAACCGCTCAAG 35 35 1 TCATAAAATA 0.59301 -22 TCAATAAAATTTTATGAAAAA 37 1 1 TCATAAAATT 0.40282 -201 AAATACTCCAAAATAAATTTCAGAT 45 5 1 ACCCAAAATA 0.935235 -189 ** ******** Masking position 7 Map Score: 5.12025 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 132 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 12 AATCCCCTAAATTTAGATTACATAATTTAT 1 110 0 ATTTAGATTA 0.617628 -151 CTACTAAACGAATTTTATTACTATCTATAA 2 74 0 AATTTTATTA 0.640993 -227 TTTAAATAAAATTTATATCAATAATTTAAC 4 82 0 ATTTATATCA 0.795874 -176 ATGAATTTTAATTTAGATCAAATTTATAAA 4 117 1 ATTTAGATCA 0.721083 -141 TTTTTAATTAATTTTTATAAATTTGATCTA 4 130 0 ATTTTTATAA 0.609917 -128 AAACTGTACAAATTTTATCAAATCATTTTA 4 205 0 AATTTTATCA 0.74078 -53 CTTAGTTTTTATTTTTATTATGGGTAACAA 20 156 1 ATTTTTATTA 0.810284 -32 TTGTAATGACATTTTTATTATAAATAATGG 22 12 0 ATTTTTATTA 0.810284 -159 TGACCAATTAAATTAGATTAAGAGGCTGGT 22 89 0 AATTAGATTA 0.403071 -82 TAAATCTTATATTTTGATCATAAATAATTT 24 34 1 ATTTTGATCA 0.819259 -174 TATTTTTATTATTGAGAGACC 33 238 0 ATTTTTATTA 0.810284 -11 GAATTTAAAGATTTTTATAAGATTTGTGAC 36 88 0 ATTTTTATAA 0.609917 -94 AAAGCAACTGATTTTTATCAAAATAAAAAA 37 60 0 ATTTTTATCA 0.872384 -142 TAAATTTTAAAATTATATCATTGATGGAAA 39 82 0 AATTATATCA 0.619759 -41 ********** Masking position 7 Map Score: 6.5921 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 150 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 13 TGTTGAAGCTAATGTCATTTGATTATGGAT 2 206 0 AATGTCATTT 0.831822 -95 TTCAACAAATATTGTGATCTAGATCATAAA 2 229 1 ATTGTGATCT 0.808733 -72 AATTTTTATAAATTTGATCTAAATTAAAAT 4 121 0 AATTTGATCT 0.573149 -137 TCCAATAAAAAATGTGATTTCCCTTTGACT 9 105 1 AATGTGATTT 0.927 -52 AATGTTTAAAAATGAGATCTACTTAACATT 15 86 1 AATGAGATCT 0.808733 -87 TGTAAAATCCAATGTGATCTCTAAGTTATA 16 18 0 AATGTGATCT 0.944572 -127 AAATGTTTAAATTGTGATCTAGTACACAGT 21 14 1 ATTGTGATCT 0.808733 -88 TAGATCTTGTAATGACATTTTTATTATAAA 22 18 0 AATGACATTT 0.551011 -153 AATCTAAACTAATGTCATTTACTGGGGGCA 25 17 0 AATGTCATTT 0.831822 -63 AATAAATGTGGTTTAAAGTTATAT 28 5 1 AATGTGGTTT 0.705136 -104 GTTAAAATTTAAGGTGATTTT 33 2 0 AAGGTGATTT 0.705136 -247 ********** Masking position 1 Map Score: 3.96346 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 43 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 14 TTTGTGTTGATTAAGGAAATAGCGTGATTT 1 39 1 TTAAGGAAAT 0.595089 -222 GCTAGGGATGAAAGGGAAAAGTGCGGTCAA 3 81 0 AAAGGGAAAA 0.687231 -87 GAATTTGCCTTAACGGAAATTTTCTGAACT 6 126 0 TAACGGAAAT 0.83531 -175 TAAGCGATTAAAAAGGAAAAAATCTATGGA 7 155 0 AAAAGGAAAA 0.874291 -31 GATAACTCAATAAAGGAAATTATCCGCTAA 9 77 0 TAAAGGAAAT 0.941364 -80 GAAGATAGTCAAAGGGAAATCACATTTTTT 9 111 0 AAAGGGAAAT 0.852199 -46 CTACAGATTATAAAGAAAATTCATTCCTAT 12 42 1 TAAAGAAAAT 0.513956 -130 AATTAAAACAAAAAGGAAAAATT 17 122 1 AAAAGGAAAA 0.874291 -13 GCGTGTATTGTAACGGAAATCTAAACTAAT 25 34 0 TAACGGAAAT 0.83531 -46 TAAATCACTCAAAAGTAAATACTTAAACGA 29 50 0 AAAAGTAAAT 0.545885 -51 GAATAGGTATAAAAGCAAAT 36 1 0 AAAAGCAAAT 0.640499 -181 TTTACGTTAGTAAAGGAAATTTATATTTCC 39 57 1 TAAAGGAAAT 0.941364 -66 TCATTGGGAGAAAAGGAAAAATAA 41 124 1 AAAAGGAAAA 0.874291 -14 TCATCTACAATAAAGGGAATTTATATTTTA 43 24 1 TAAAGGGAAT 0.685361 -60 TATCTTGTTTAAAAGGAAATCGGAGCAGTA 45 92 1 AAAAGGAAAT 0.948053 -102 ********** Masking position 3 Map Score: 11.2727 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 149 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 15 TACAATCCGCCAGTTAAATTTAATGATTTT 3 130 1 CAGTTAAATT 0.65659 -38 TGATAAAGAGCAGGTTATTTTTTTAATTAA 4 149 0 CAGGTTATTT 0.530496 -109 AAGACCACACCGGATTATTTTCCGATGTTA 7 106 0 CGGATTATTT 0.795486 -80 TTTTAGTTAGCGGATAATTTCCTTTATTGA 9 71 1 CGGATAATTT 0.733889 -86 ACCCAATGTGCGGTTATTTTTTATTGATTT 10 203 1 CGGTTATTTT 0.809473 -98 ATTTGCGCCACAGTTTAATTCCTTGATAAA 11 33 1 CAGTTTAATT 0.729486 -57 ACCCAAAGTGCGGTTAATATTTTTAGTATT 14 16 0 CGGTTAATAT 0.578448 -136 TAATAAGCCACAGTTAAATTTTAATCTTAT 15 137 1 CAGTTAAATT 0.65659 -36 TTGTCTTGATCGTTTTATTTAAGTGTTTTT 16 76 0 CGTTTTATTT 0.775022 -69 TCATTTTGTCCATTTTATTTGTATTAGTGC 17 14 0 CATTTTATTT 0.543503 -121 TCGTGAAGTGCGGTTTTATTTTGGAGTTTT 20 78 1 CGGTTTTATT 0.659907 -110 AAATTGAAAGCGGTTACTTTCATAAGTATG 24 69 1 CGGTTACTTT 0.713642 -139 ACAAAGATCACGGTTTATTTACAATAATTT 24 140 1 CGGTTTATTT 0.960152 -68 GGTTAAAAACCAGTTTATTTTGT 30 4 0 CAGTTTATTT 0.892793 -141 GTCGAAAATGCGGTTTATTTTGACCGCACT 31 99 0 CGGTTTATTT 0.960152 -34 ATATTGAGTGCGTTTTATTTTTAGCTATAA 34 14 1 CGTTTTATTT 0.775022 -72 TCTTGAGCGGTTATTTTATAGAATAAG 35 40 0 CGGTTATTTT 0.809473 -17 ********** Masking position 5 Map Score: 10.2775 Number of sites scoring better than the average of aligned sites = 458 Number in coding regions = 311 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678