AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_mixed1_hinf_reg_100.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 HI0016 167 GTP-binding membrane protein (lepA) #3 HI0154 255 acyl carrier protein (acpP) #4 HI0156 300 malonyl CoA-acyl carrier protein transacylase (fabD) #5 HI0157 185 beta-ketoacyl-ACP synthase III (fabH) #6 HI0301 300 hemolysin, putative #7 HI0406 89 acetyl-CoA carboxylase, carboxyl transferase (accA) #8 HI0408 171 ABC transporter, ATP-binding protein (yebM) #9 HI0807 109 conserved hypothetical protein #10 HI0808 151 ribosome releasing factor (rrf) #11 HI0913 144 ribosomal protein S2 (rpS2) #12 HI0914 132 elongation factor Ts (tsf) #13 HI0916 107 outer membrane protein, putative #14 HI0920 248 conserved hypothetical protein #15 HI1062 85 (3R)-hydroxymyristol (acyl carrier protein) dehydrase (fabZ) #16 HI1064_HI1065 56 HI1064: conserved hypothetical protein, HI1065: uridylate kinase (pyrH) #17 HI1139 137 UDP-N-acetylmuramate--alanine ligase (murC) #18 HI1140 71 D-alanine--D-alanine ligase (ddlB) #19 HI1143 83 cell division protein (ftsZ) #20 HI1144 38 UDP-3-0-(3-hydroxymyristoyl) N-acetylglucosamine deacetylase (lpxC) #21 HI1260 193 acetyl-CoA carboxylase carboxyl transferase subunit beta (accD) Motif number 1 AATAAGTGCAAAAGTGCGGTTAGAAATTGA 1 221 1 AAAGTGCGGT 0.998646 -40 ATGAAAGGGAAAAGTGCGGTCAAATTTTCA 2 74 0 AAAGTGCGGT 0.998646 -94 TATCCGATTTAAAGTGCGGTCAAAACTCAA 4 17 0 AAAGTGCGGT 0.998646 -284 GTTTAAACCTAAAGTGCGGTTAAAAATACA 6 175 0 AAAGTGCGGT 0.998646 -126 GTTTAAACCCAATGTGCGGTTATTTTTTAT 6 197 1 AATGTGCGGT 0.984403 -104 ATTCCTTGATAAAGTGCGGTCGATTTTTAC 7 50 1 AAAGTGCGGT 0.998646 -40 GAATTCTATAAAAATGCGTTATTTTCCCCA 8 126 1 AAAATGCGTT 0.79551 -46 GTAATCAACAAAAGTGCGGTAAAGATTCT 9 91 1 AAAGTGCGGT 0.998646 -19 TCAGTTACCCAAAGTGCGGTTAATATTTTT 10 22 0 AAAGTGCGGT 0.998646 -130 TTGGGTAACTGAAGTGCGGTCATTTTTTAT 10 40 1 GAAGTGCGGT 0.989423 -112 TTTATACCATAAAGTGCGGTTAAAAACCAG 11 21 0 AAAGTGCGGT 0.998646 -124 TTTTTATCTAAAAGTGCGGTCAAAATAAAC 12 87 1 AAAGTGCGGT 0.998646 -46 TCCTCTGTCGAAAATGCGGTTTATTTTGAC 12 105 0 AAAATGCGGT 0.986595 -28 AAATGCTGCAAAAGTGCGGTTAAAATTTAA 14 20 0 AAAGTGCGGT 0.998646 -229 AGAGAAATAAAAAGTGCGGTGGTTTTTTAG 14 103 1 AAAGTGCGGT 0.998646 -146 AACTCAACTAAAAGTGCGGTTAAAATTCGC 17 91 0 AAAGTGCGGT 0.998646 -47 ********** Masking position 5 Map Score: 80.4782 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 GAGTAAATTAGCGGTAAACATAAATTATGTAA 1 91 1 GCGGTAAATA 0.981212 -170 GTGCAAAAGTGCGGTTAGAAATTGAAAAGAAT 1 226 1 GCGGTAGAAT 0.899652 -35 AGGGAAAAGTGCGGTCAAATTTTCAAACTTTT 2 67 0 GCGGTAATTT 0.991658 -101 GATTTAAAGTGCGGTCAAAACTCAAAATATT 4 10 0 GCGGTAAACT 0.968388 -291 AACCTAAAGTGCGGTTAAAAATACACAATTTT 6 168 0 GCGGTAAAAT 0.981212 -133 AACCCAATGTGCGGTTATTTTTTATTGATTTT 6 202 1 GCGGTATTTT 0.978401 -99 TTGATAAAGTGCGGTCGATTTTTACGGTCTTT 7 55 1 GCGGTGATTT 0.967407 -35 CAACAAAAGTGCGGTAAAGATTCT 9 96 1 GCGGTAAATT 0.994878 -14 TACCCAAAGTGCGGTTAATATTTTTAGTATTT 10 15 0 GCGGTAAATT 0.994878 -137 TAACTGAAGTGCGGTCATTTTTTATCTGTTTT 10 45 1 GCGGTATTTT 0.978401 -107 ACCATAAAGTGCGGTTAAAAACCAGTTTATTT 11 14 0 GCGGTAAAAC 0.89174 -131 ATCTAAAAGTGCGGTCAAAATAAACCGCATTT 12 92 1 GCGGTAAATA 0.981212 -41 CTGCAAAAGTGCGGTTAAAATTTAAGGTGATT 14 13 0 GCGGTAAATT 0.994878 -236 AATAAAAAGTGCGGTGGTTTTTTAGTTGTTTT 14 108 1 GCGGTGTTTT 0.918772 -141 TCTTGAGCGGTTATTTTATAGAATAAGC 16 39 0 GCGGTATTTA 0.924129 -18 AACTAAAAGTGCGGTTAAAATTCGCAACGTTT 17 84 0 GCGGTAAATT 0.994878 -54 ***** ** *** Masking position 5 Map Score: 36.0602 Number of sites scoring better than the average of aligned sites = 541 Number in coding regions = 320 Number in noncoding regions = 221 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 3 AGAGCGAGAGATTTGAGGTTTTGTGTTGATTAAGGAAATAGC 1 20 1 ATTTTTTATA 0.906757 -241 AAATAGCGTGATTTGTCTCTTTGTACGTTAAAAATAGAGTAA 1 55 1 ATTTTTTTAA 0.879379 -206 TGCGGTCAAATTTTCAAACTTTTTAGATAAAACAAAACCCCG 2 48 0 TTTTTTTAAA 0.945692 -120 ATCCCTAGCGATTTCCGCGCTTTTCAGGTACAATCCGCCAGT 2 102 1 ATTTTTTTAA 0.879379 -66 CGCCAGTTAAATTTAATGATTTTTGAGAAAAACAATCTTTT 2 137 1 ATTTTTTAAA 0.926189 -31 TTGTTTTTCCTATTTGTTAGTTTTAACTCATAAAA 3 231 0 TTTTTTTTTA 0.886854 -25 AAGGGAACCCAATTTGTTCTTTATCCGATTTAAAGTGCGGTC 4 26 0 AATTTTTTTA 0.660573 -275 GGTTCCCTTCTTTTCCACCTTTGTGGAATTGAATTTGTAGGA 4 59 1 TTTTTTTTTA 0.886854 -242 ATTTTTTCCTTTTTAATCGCTTATCTTATTGAGT 5 162 1 TTTTTTTTTA 0.886854 -24 AAAAATCCATTATTCACAAGTTATCCACAACATAGATACTTT 6 70 1 TATTTTTAAA 0.857204 -231 GACAACAAAATATTCTTATTTTGTTTATATGACGAAAAGTAT 6 105 0 TATTTTTATA 0.823056 -196 TCTTTTCGCGTTTTGCGATTTTTTCTAAAATATGATAATTTT 6 236 1 TTTTTTTAAA 0.945714 -65 TGCGGTCGATTTTTACGGTCTTTTTAGGATAACAAA 7 64 1 TTTTTTTATA 0.931022 -26 AATTCTCAAGATTTTCTCTCTTATGTCGAATATTTAAGCGTT 8 89 0 ATTTTTTAAA 0.926222 -83 GTGCGGTCATTTTTTATCTGTTTTCAAGCTGATAAATGTATT 10 53 1 TTTTTTTCTA 0.771182 -99 TTTTACTGGATTTTTTTAAATTTTTGAATACATTTATCAGCT 10 79 0 TTTTTTTTAA 0.910063 -73 TAAATTGAACTTTTTTCTTCATCAGAACTCAAAA 13 3 1 AATTTTTATA 0.770184 -105 ATTTTTGCCATTTTACGGTATTCTATGCCACATTTTCTATTG 14 53 0 TTTTTTTCAA 0.813118 -196 GTGCGGTGGTTTTTTAGTTGTTTTTTACAATAAATTTTCAAT 14 116 1 TTTTTTTAAA 0.945714 -133 TTTTACAATAAATTTTCAATTTTTGCAGAACAGATTAGAACA 14 138 1 AATTTTTAAA 0.812258 -111 TGGCTTAAAAAATTGGCTTATTCTATAAAATAACCGCTCAAG 16 24 1 AATTTTTAAA 0.812258 -33 TTATTTTTCCTTTTCTCCCAATGACAAAACTCAA 17 114 0 ATTTTTTATA 0.906757 -24 ATTGAACATTTTTTTTATTTTTTTGTCTTACAGACCACGTTA 21 35 0 TTTTTTTTAA 0.910063 -159 TTTTTGACCTTTTTATTGACTAGAAAATTGCG 21 172 0 TTTTTTTACA 0.717662 -22 **** ** * ** * Masking position 11 Map Score: 28.8671 Number of sites scoring better than the average of aligned sites = 592 Number in coding regions = 363 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 220 Fraction of orfs with sites within 600 bp upstream = 0.0353357 Motif number 4 CTAACCGCACTTTTGCACTTATTGAATACA 1 214 0 TTTTGCACTT 0.659507 -47 CTCCTAAATTCTTTTCAATTTCTAACCGCA 1 235 0 CTTTTCAATT 0.764032 -26 TCGGGGTTTCTTTTTTCATTCAAACTGAAA 2 11 0 TTTTTTCATT 0.91671 -157 TTTGACCGCACTTTTCCCTTTCATCCCTAG 2 80 1 CTTTTCCCTT 0.873737 -88 TTGTTTTTCCTATTTGTTAGTTT 3 243 0 TTTTTCCTAT 0.664379 -13 TTTTTGCTTACTTTTTCTTTGGCGAAGCAA 4 196 1 CTTTTTCTTT 0.898672 -105 GGCGAGCTTACTTTTTCTTTGCTTCGCCAA 4 214 0 CTTTTTCTTT 0.898672 -87 TGTCCTATTGTTTTTTAATTGAAAATTCTT 4 274 0 TTTTTTAATT 0.862236 -27 TTTTTTACTTATAGGTGTTC 5 1 1 TTTTTTACTT 0.88381 -185 AGTCCATAGATTTTTTCCTTTTTAATCGCT 5 153 1 TTTTTTCCTT 0.930441 -33 TGCTGAAAACTTTTTTATTTTAGGG 8 6 0 TTTTTTATTT 0.875187 -166 TTGAATAATGCTTTTTCCATAGGAATGAAT 8 60 0 CTTTTTCCAT 0.682279 -112 TTTACTGGATTTTTTTAAATTTTTGAATAC 10 90 0 TTTTTTAAAT 0.582806 -62 TGCATTGTCCTTTTTAATTGATGAAAGTT 10 133 0 CTTTTTAATT 0.818237 -19 GCCCCGCTGTTTTTGCCTTTCAAAAGCAGT 11 53 1 TTTTGCCTTT 0.758447 -92 TCAAAAGCAGTTTTTTAATTACTAACAACA 11 72 1 TTTTTTAATT 0.862236 -73 CCCTATTAATTTTTGCCATTTTACGGTATT 14 73 0 TTTTGCCATT 0.737023 -176 AACCACCGCACTTTTTATTTCTCTCCCTAT 14 97 0 CTTTTTATTT 0.83453 -152 TGTTTTTTCCTTCTGGCTTAAA 16 3 1 TTTTTTCCTT 0.930441 -54 GTCATAAGTATTTTTTATATCCAAAAGTGC 17 39 1 TTTTTTATAT 0.610148 -99 TTTAGTTGAGTTTTGTCATTGGGAGAAAAG 17 109 1 TTTTGTCATT 0.795775 -29 TTATTTTTCCTTTTCTCCCAATG 17 125 0 TTTTTCCTTT 0.898672 -13 ATTGAACATTTTTTTTATTTTTTTGTCTTA 21 47 0 TTTTTTATTT 0.875187 -147 ********** Masking position 4 Map Score: 26.0745 Number of sites scoring better than the average of aligned sites = 832 Number in coding regions = 599 Number in noncoding regions = 233 Number of orfs with sites within 600 bp upstream = 209 Fraction of orfs with sites within 600 bp upstream = 0.0335689 Motif number 5 GTACAAAGAGACAAATCACGCTATTTCCTTAATCAA 1 45 0 AAAACCATTT 0.682894 -216 ATGTTTACCGCTAATTTACTCTATTTTTAACGTACA 1 76 0 CAATTCATTT 0.71554 -185 AATAAACCTACCAATCCCCTAAATTTAGATTACATA 1 116 0 CAATCCATTT 0.947655 -145 TTATTATTGTATAATTCCCCTCATTTTTACACATAC 1 147 1 AAATCCATTT 0.966052 -114 TCTAGACAACAAAATATTCTTATTTTGTTTATATGA 6 115 0 AAATTCTTTT 0.514667 -186 AGTGCGGTTAAAAATACACAATTTTTACGGAGAGGG 6 157 0 AAATCCTTTT 0.958706 -144 TTGACGGCGAAAAATTATCATATTTTAGAAAAAATC 6 252 0 AAATACTTTT 0.646044 -49 CCCTAAAATAAAAAAGTTTTCAGCATTCAG 8 5 1 AAATAATTTT 0.601118 -167 GCATTTTTATAGAATTCTCAAGATTTTCTCTCTTAT 8 107 0 AAATCCATTT 0.966049 -65 AAAATCGCCGTGTTTTCAACAATGGT 8 156 0 AAATGCTTTT 0.743382 -16 ACAAAATAAACTGGTTTTTAACCGCACT 11 3 1 AAATACTTTT 0.888535 -142 AAGTGCGGTCAAAATAAACCGCATTTTCGACAGAGG 12 98 1 AAATACATTT 0.900868 -35 TAAATATCGTATAATCCGATAGATTTTATTTGTTTA 15 41 1 AAATCAATTT 0.841172 -45 GTTATTTTATAGAATAAGCCAATTTTTTAAGCCAGA 16 22 0 AAATACTTTT 0.849858 -35 AAGTGCGGTTAAAATTCGCAACGTTTTTATTTCTAA 17 74 0 AAATCCGTTT 0.854882 -64 TGATACTTTTCTAATACTAAGATTTTCAATCAATCC 18 19 0 CAATCATTTT 0.750376 -53 TTACAAGTAGCAAATTCTATAAATTTATGTTCTAAT 21 133 1 CAATCAATTT 0.77085 -61 AATTTATGTTCTAATACGCGCAATTTTCTAGTCAAT 21 154 1 CAATCCATTT 0.947539 -40 * *** * * **** Masking position 14 Map Score: 19.4894 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 183 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 6 GTCTGGTCGCACCACAAAATAGGCAATGTGA 3 154 0 ACACAAAATA 0.869265 -102 GTGCGACCAGACCATAAAATAGTTGCAAGTT 3 173 1 ACATAAAATA 0.807393 -83 GTTGCAAGTTACTAAAAAATACATACACTAA 3 194 1 ACAAAAAATA 0.900546 -62 GTGCGGTCAAAACTCAAAATATT 4 3 0 AATCAAAATA 0.773735 -298 TTTCGTCATATAAACAAAATAAGAATATTTT 6 110 1 TAACAAAATA 0.812937 -191 AAAATTCTAGACAACAAAATATTCTTATTTT 6 125 0 ACACAAAATA 0.869265 -176 GAGGAAAATCAATAAAAAATAACCGCACATT 6 207 0 AAAAAAAATA 0.893015 -94 TTAAAAATACTAAAAATATTAACCGCAC 10 8 1 TATAAAAATA 0.767537 -144 CCGCACTTTTAGATAAAAATATAGGGGCTAA 12 75 0 AGTAAAAATA 0.641235 -58 GGTCTCTCAATAATAAAAATA 14 238 1 TATAAAAATA 0.767537 -11 CGATATTTATAGCTAAAAATAAAACGCACTC 15 19 0 AGTAAAAATA 0.641235 -67 GTTGATACCTTACAAAAAATAAACAAATAAA 15 65 0 TAAAAAAATA 0.855455 -21 ATTGGCTTATTCTATAAAATAACCGCTCAAG 16 35 1 TCATAAAATA 0.748241 -22 CACTTTTGGATATAAAAAATACTTATGACTG 17 37 0 TAAAAAAATA 0.855448 -101 TGTAGATGAAAAATTAAAATAA 19 2 0 AATTAAAATA 0.683129 -82 GCTGACTAAATATATAAAATATAAATTCCCT 19 37 0 TAATAAAATA 0.732249 -47 GGTCTGTAAGACAAAAAAATAAAAAAAATGT 21 41 1 ACAAAAAATA 0.900546 -153 ** ******** Masking position 6 Map Score: 14.1858 Number of sites scoring better than the average of aligned sites = 396 Number in coding regions = 262 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 7 GGGCTTATGACCACTTTTGTATGTGTAAAAATGAG 1 166 0 CCCTTGTATG 0.888035 -95 GAAAATTTGACCGCACTTTTCCCTTTCATCCCTAG 2 75 1 CCCTTTTCCT 0.709532 -93 CATACACTAACCACTCTTTTATGAGTTAAAACTAA 3 215 1 CCCTTTTATG 0.94516 -41 AAATTGGGTTCCCTTCTTTTCCACCTTTGTGGAAT 4 53 1 CCTTTTTCCC 0.912959 -248 AGAAAGGCGCCCCTACTTTTCCTTGTTTCCTTTGT 4 162 0 CCTTTTTCCG 0.958342 -139 AGGATCTTTGCCCTCTTTTTACGAGATCAATTCAC 6 31 1 CCTTTTTACG 0.969069 -270 ACCATTTGCGCCACAGTTTAATTCCTTGATAAAGT 7 30 1 CCCTTTAATC 0.595888 -60 GTTTTGTCTGCCTTTATTTTATTAGGTATGCAAAT 9 36 1 CCTTTTTATG 0.934129 -74 AGTTAGAACGCCGTGATTTTACTGGATTTTTTTAA 10 102 0 CCTTTTTACG 0.969068 -50 TAAATTTTAACCGCACTTTTGCAGCATTTTGACAA 14 21 1 CCCTTTTGCC 0.783569 -228 CGAATTTTAACCGCACTTTTAGTTGAGTTTTGTCA 17 92 1 CCCTTTTAGG 0.92062 -46 ATATAAATTCCCTTTATTGTAGATGAAAAATTAAA 19 15 0 CCTTTGTAGG 0.81452 -69 TCTACTACCTTCATTTACTAGGTATTTTCTGA 20 17 0 CCTTTTACTG 0.661483 -22 ACTTGTAAGACCGTTTTTGTACTGCTCCGATTTCC 21 106 0 CCTTTGTACC 0.867959 -88 ** * ****** * Masking position 8 Map Score: 9.15286 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 181 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 8 ATAATAAACCTACCAATCCCCTAAATTTAGA 1 123 0 TACCAACCCC 0.934016 -138 TTTATTATTGTATAATTCCCCTCATTTTTAC 1 146 1 TATAATCCCC 0.941712 -115 TTTTAGATAAAACAAAACCCCGAATAACTTC 2 39 0 AACAAACCCC 0.905218 -129 GCTTTTCAGGTACAATCCGCCAGTTAAATTT 2 120 1 TACAATCGCC 0.923028 -48 TTTTATTGCTTAGAAATCCCCCATAAATCAA 3 20 0 TAGAAACCCC 0.952109 -236 CACTTTATGGTATAAATCGCCCCGCTGTTTT 11 35 1 TATAAACGCC 0.964445 -110 TGAGGCTATTTATAAAACGCCACAACCC 17 8 0 TATAAACGCC 0.964445 -130 ATATATAAAATATAAATTCCCTTTATTGTAG 19 28 0 TATAAATCCC 0.831315 -56 ****** **** Masking position 5 Map Score: 3.89668 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 22 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 AATAAAATCATAGCCAAAGATTTTAGATAA 3 44 1 TAGCCAAAGA 0.776181 -212 TCGTAAAAAGAGGGCAAAGATCCTTATCAC 6 25 0 AGGGCAAAGA 0.92227 -276 AAAAATGCGAAAGGCAGACAGTTTTGTCTG 9 16 1 AAGGCAGACA 0.957661 -94 TAATAAAATAAAGGCAGACAAAACTGTCTG 9 30 0 AAGGCAGACA 0.957661 -80 CTGCTTTTGAAAGGCAAAAACAGCGGGGCG 11 52 0 AAGGCAAAAA 0.764234 -93 CCAATTAAATTAGGCAGAGAACGTTGTTTT 13 42 0 TAGGCAGAGA 0.981686 -66 CTAATTTAATTGGGCAGAGAAAATATTAAA 13 59 1 TGGGCAGAGA 0.968106 -49 CAAAAATTAATAGGGAGAGAAATAAAAAGT 14 88 1 TAGGGAGAGA 0.898702 -161 ********** Masking position 6 Map Score: 4.39268 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 64 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 CTTTGTTCCATTGAATTTGCCTTAACGGAA 4 138 0 TTGAATTTGC 0.906904 -163 ATTACCGAAGAAGAATTTTCAATTAAAAAA 4 264 1 AAGAATTTTC 0.906063 -37 TTTTGTTGTCTAGAATTTTCCCCTCTCCGT 6 137 1 TAGAATTTTC 0.93837 -164 TTCCATAGGAATGAATTTTCTTTATAATCT 8 46 0 ATGAATTTTC 0.860892 -126 CGCATTTTTATAGAATTCTCAAGATTTTCT 8 114 0 TAGAATTCTC 0.889561 -58 GTTTTTTACAATAAATTTTCAATTTTTGCA 14 135 1 ATAAATTTTC 0.586123 -114 AAAGTGCGGTTAAAATTCGCAACGTTTTTA 17 81 0 TAAAATTCGC 0.668506 -57 CATAAATTTATAGAATTTGCTACTTGTAAG 21 132 0 TAGAATTTGC 0.939712 -62 ********** Masking position 5 Map Score: 2.05141 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 139 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 11 GGTTTTGTGTTGATTAAGGAAATAGCGTGAT 1 36 1 TGATAAGGAA 0.957831 -225 TCAGTTTGAATGAAAAAAGAAACCCCGAAGT 2 13 1 TGAAAAAGAA 0.643803 -155 TATTTTCCGATGTTAAAGGAATGCAGATAGT 5 90 0 TGTTAAGGAA 0.877718 -96 AGATAAGCGATTAAAAAGGAAAAAATCTATG 5 157 0 TTAAAAGGAA 0.934728 -29 CGACCGCACTTTATCAAGGAATTAAACTGTG 7 41 0 TTATAAGGAA 0.94636 -49 AGACTACAGATTATAAAGAAAATTCATTCCT 8 39 1 TTATAAGAAA 0.776493 -133 CTTTCATCAATTAAAAAGGACAATGCA 10 135 1 TTAAAAGGAC 0.769896 -17 TTTTGAGTTCTGATGAAGAAAAAAGTTCAAT 13 14 0 TGATAAGAAA 0.817277 -94 AATTATCTTGTTTAAAAGGAAATCGGAGCAG 21 89 1 TTTAAAGGAA 0.819015 -105 **** ****** Masking position 6 Map Score: 2.18366 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 81 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 12 TGAATTTGTAGGAAATTTTCGTCTGTTTGA 4 88 1 GGAAATTTTC 0.690132 -213 TTGCCTTAACGGAAATTTTCTGAACTCGCT 4 122 0 GGAAATTTTC 0.690132 -179 TTTAACATCGGAAAATAATCCGGTGTGGTC 5 104 1 GAAAATAATC 0.821815 -82 TTTATATGACGAAAAGTATCTATGTTGTGG 6 94 0 GAAAAGTATC 0.925874 -207 ATTGACGGCGAAAAATTATCATATTTTAGA 6 259 0 AAAAATTATC 0.753932 -42 CTTAGTATTAGAAAAGTATCATCAGTAAGA 18 34 1 GAAAAGTATC 0.925874 -38 TAAGAGGAGAGCAAATTATCTTGTTTAAAA 21 76 1 GCAAATTATC 0.900747 -118 ********** Masking position 5 Map Score: 0.38742 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 82 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 13 ********** No masking Map Score: -3.82029e-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 14 ********** No masking Map Score: -3.82029e-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: -3.82029e-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