AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00620_hinf_reg_300.orf -o00620_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 Purged sequences: HI0180 27 formate acetyltransferase (pfl) HI1739.2 29 glutamate racemase (murI) Input sequences: #1 HI0086 300 cystathionine gamma-synthase (metB) #2 HI0181 300 formate transporter #3 HI0185 122 alcohol dehydrogenase, class III (adhC) #4 HI0318 218 conserved hypothetical protein #5 HI0319 52 conserved hypothetical protein #6 HI0321 93 virulence associated protein B (vapB) #7 HI0323 66 lactoylglutathione lyase (gloA) #8 HI0406 89 acetyl-CoA carboxylase, carboxyl transferase (accA) #9 HI0408 171 ABC transporter, ATP-binding protein (yebM) #10 HI0774 205 acetate CoA-transferase, alpha subunit #11 HI0809 172 phosphoenolpyruvate carboxykinase (pckA) #12 HI0810 144 conserved hypothetical protein #13 HI0811 134 argininosuccinate lyase (argH) #14 HI0812 21 glucosephosphate uridylyltransferase (galU) #15 HI0813 77 carbon storage regulator (csrA) #16 HI0814 187 alanyl-tRNA synthetase (alaS) #17 HI0815 101 universal stress protein A (uspA) #18 HI0817 170 conserved hypothetical protein #19 HI0819 37 galactokinase (galK) #20 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) #21 HI0967 25 H. influenzae predicted coding region HI0967 #22 HI0970 57 3-dehydroquinase (aroQ) #23 HI0971 152 acetyl-CoA carboxylase, biotin carboxyl carrier protein (accB) #24 HI0972 174 acetyl-CoA carboxylase, biotin carboxylase (accC) #25 HI0986 300 2-isopropylmalate synthase (leuA) #26 HI1203 67 phosphate acetyltransferase (pta) #27 HI1204 214 acetate kinase (ackA) #28 HI1210 206 malate dehydrogenase (mdh) #29 HI1231 113 dihydrolipoamide dehydrogenase (lpdA) #30 HI1232 62 dihydrolipoamide acetyltransferase (aceF) #31 HI1233_HI1234 299 HI1233: pyruvate dehydrogenase, E1 component (aceE), HI1234: methylglyoxal synthase (mgsA) #32 HI1245 197 malate oxidoreductase, putative #33 HI1260 193 acetyl-CoA carboxylase carboxyl transferase subunit beta (accD) #34 HI1272 300 ABC transporter, ATP-binding protein #35 HI1274 51 hydroxyacylglutathione hydrolase, putative #36 HI1573 300 pyruvate kinase, type II (pykA) #37 HI1635 274 purine nucleotide synthesis repressor (purR) #38 HI1636 182 phosphoenolpyruvate carboxylase (ppc) #39 HI1649 260 D-lactate dehydrogenase (dld) #40 HI1739.1 211 L-lactate dehydrogenase (lctD) #41 HI1741 260 guanosine-3',5'-bis(diphosphate) 3'- pyrophosphohydrolase (spoT) #42 HI1742 62 DNA-directed RNA polymerase, omega chain (rpoZ) #43 HI1743 249 guanylate kinase (gmk) Motif number 1 ATTCCTTGATAAAGTGCGGTCGATTTTTAC 8 50 1 AAAGTGCGGT 0.998532 -40 ATCAAGACAAAAAGTGCGGAAAAAACCACC 12 96 1 AAAGTGCGGA 0.982021 -49 ATTGAGATAAAAAGTGCGGTGGTTTTTTCC 12 113 0 AAAGTGCGGT 0.998532 -32 CGCTATTTGAGAAGTGCGGTTAAAATTTAA 16 48 0 GAAGTGCGGT 0.993333 -140 ATAGCGTCGTGAAGTGCGGTTTTATTTTGG 16 72 1 GAAGTGCGGT 0.993333 -116 TTTAAAGGAAAAAGTGCGGTTATGAATAAA 23 96 0 AAAGTGCGGT 0.998532 -57 TTTTCCTTTAAAAGTGCGGTTAAAATTTCA 23 114 1 AAAGTGCGGT 0.998532 -39 CGCAACTTATAAAGTGCGGGTTTAAAATTG 25 235 0 AAAGTGCGGG 0.993333 -66 TCCAAAAGTGCGGTGCGTTTTTCC 25 287 0 AAAGTGCGGT 0.998532 -14 TAGCGTATGATAAGTGCGGTCAATTTTTGA 27 20 0 TAAGTGCGGT 0.982021 -195 AAAGACCGTAAAAGTGCGGTCAATATTTTT 29 74 1 AAAGTGCGGT 0.998532 -40 TTGATGAAAACTGCGGTCAAAAAACAT 30 8 1 AAACTGCGGT 0.98859 -55 TGTTCCTTTTAAAGTGCGGTCATAAAACAC 30 39 0 AAAGTGCGGT 0.998532 -24 TAATTATTTGAAAGTGCGGTAATTTTTTTG 31 106 0 AAAGTGCGGT 0.998532 -194 TGTAGAAACAAAACTGCGGTGATAATAAAA 37 18 1 AAACTGCGGT 0.98859 -257 GATTTTTTAAAAAGTGCGGTCTATTTTTGC 38 16 0 AAAGTGCGGT 0.998532 -167 AAATCCCTAAAAAGTGCGGGTCTTTTTTAG 38 41 1 AAAGTGCGGG 0.993333 -142 TCTTTTAAAAGTGCGGTAAAAAATAAA 41 8 1 AAAGTGCGGT 0.998532 -253 AAAATCATCAAAAGTGCGGTGATTTTTTAC 43 176 0 AAAGTGCGGT 0.998532 -74 ********** Masking position 5 Map Score: 81.934 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 AATAAATCACAGAAAATGATGGAAAAATGAAATTTT 1 201 1 AAAAATAAAA 0.941139 -100 AGTAGAAATTAGAAAATTACATAAAATTTCATTTTT 1 223 0 AAAAATAAAA 0.941139 -78 TTGGCACAAAGGAAAAAGTGATAAAAGTAGAAATTA 1 248 0 GAAAAAAAAA 0.774124 -53 CCCTTTCATTGCAAAGAAAAGCAAAAATTATTTCAA 2 169 0 GAAAGAAAAA 0.591754 -132 ATTGACATTGAAAAAGTTGATGAAAATTTAATACTT 2 260 0 AAAAGTAAAA 0.871176 -41 TCATTTTTGTTTAAAGGGAATAAAAA 3 1 0 TAAAGGAAAA 0.417788 -122 TTCCCTTTAAACAAAAATGATAAAAAAACACTTGCT 3 17 1 AAAAAAAAAA 0.96187 -106 ATAGCGGAAAACCAAGAGAGATAAAAAGGTTATTTA 4 61 1 ACAAGAAAAA 0.670938 -158 CAAATCAATCAAAAAAGCAAAGAAAAGTAATAAATA 4 103 1 AAAAAGAAAA 0.886644 -116 AACAAGCGGCATAATATAACAAAAAATCTGATGATA 4 165 0 AAATATAAAA 0.734219 -54 TTGTTATCCTAAAAAGACCGTAAAAATCGACCGCAC 8 63 0 AAAAGAAAAA 0.914304 -27 TAGATTGATATTAAAAATAGCAAAAAGAATTTCGTA 10 72 0 TAAAAAAAAA 0.845487 -134 GCTCTATATCACAATATCACTAAAAAGAGGTAAAGT 11 41 1 AAATATAAAA 0.734219 -132 TAAAGTTCTTAAAAAAATGTTTAAAAATGAGATCTA 11 71 1 AAAAAAAAAA 0.96187 -102 CGATCAAGACAAAAAGTGCGGAAAAAACCACCGCAC 12 94 1 AAAAGTAAAA 0.871176 -51 TAATAATAAAACAAAAATGGACAAAATCTTTCATTT 13 38 0 AAAAAAAAAA 0.96187 -97 TAATTAATTAAAACAAAAAGGAAAAATT 13 117 1 AACAAAAAAA 0.503437 -18 TTTATAAATTTCAAAAATATGCAAAAATAGGGCGAC 16 121 1 TAAAAAAAAA 0.845487 -67 CTTGTTACCCATAATAAAAATAAAAACTAAGTCGCC 16 151 0 AAATAAAAAA 0.813377 -37 TTCGACCACCAAAAATCGAAAAAACCAGTATAA 22 8 1 ACAAAAAAAA 0.828205 -50 AATGTGCCACACAAAAAGGATTAAAA 22 42 1 AAAAAAAAAA 0.96187 -16 AGTCCGCCCGACAAAAATATTGGAAA 24 1 0 AAAAAAGAAA 0.739254 -174 TATTTTTAATATAAAATGCCAAAAAATAGTTTGACA 25 52 1 AAAAATAAAA 0.941139 -249 TTTTTTATCTAAAAAATACAGGAAAAACGCACCGCA 25 267 1 AAAAATAAAA 0.941139 -34 TATTTTATAAATAAAAACTGCCGAAAAATTCGGCAG 26 23 0 AAAAAAGAAA 0.739254 -45 TATGAATAAGAACAAAGAGAAGAAAATATTTATCTC 28 76 1 ACAAAGAAAA 0.599165 -131 TTTTACCTCGTAAAAACGTTAAAAATATTGACCGC 29 89 0 GAAAAAAAAA 0.774124 -25 TGACCGCACTTTAAAAGGAACAAAAA 30 47 1 TAAAAGAAAA 0.629171 -16 GTCCTTTTTGAAAAAAATCTGAAAAAACTTTAAAAC 31 17 1 AAAAAAAAAA 0.96187 -283 TTTGTTCGCTAAAATAACCAGTAAAATATTGCATTC 31 64 0 AAATAAAAAA 0.813377 -236 ATTTTAGCGAACAAAAAAACACAAAAAAATTACCGC 31 85 1 AAAAAAAAAA 0.96187 -215 TCTTTATCTCAAAAAATCTTCTAAAATTTACAAGAT 31 183 1 AAAAATAAAA 0.941139 -117 GGTCTGTAAGACAAAAAAATAAAAAAAATGTTCAAT 33 41 1 AAAAAAAAAA 0.96187 -153 TTTCTAGTCAATAAAAAGGTCAAAAA 33 178 1 AAAAAAAAAA 0.96187 -16 CCGTCAGGCTACCAAGTAGCCAAAAAGTGATTGAAG 34 137 0 ACAAGTAAAA 0.563767 -164 AGTAAGTAATAAAAAAATGGGAACAATCCCTAGCAA 34 214 0 AAAAAAACAA 0.503437 -87 TATAACTGGCAAAAAAGTAAACAAAACCAGCTTAAA 36 150 1 AAAAAGAAAA 0.886644 -151 CATTCTAGCAAGAATAATACGAAAAAATCACTTCTT 37 169 1 AAATAAAAAA 0.813377 -106 CGCACTTTTTAAAAAATCCCTAAAAAGTGCGGGTCT 38 28 1 AAAAATAAAA 0.941139 -155 AAGAAAAGCTAAAAAATAGCTAAAAAAGACCCGCAC 38 54 0 AAAAATAAAA 0.941139 -129 AGAAATTTTGAAAATAATCAAGAAAAGCTAAAAAAT 38 73 0 AAATAAAAAA 0.813377 -110 GTTGAAACCTTTAAAGATAGAGAAAAATATTATTTA 39 47 0 TAAAGAAAAA 0.698278 -214 AAAATCACCTATAAAATTAGGAAAAATTGTGAATTT 40 41 0 AAAAATAAAA 0.941139 -171 ACACTATTTTAACAAATTCAATAAAAATCATAATTA 40 138 0 ACAAATAAAA 0.75343 -74 CTCTTATTCAATAAAATAGTGAGAAACCTGAGAGGT 40 180 0 AAAAATGAAA 0.642476 -32 ACTATTTTATTGAATAAGAGGTAAAA 40 196 1 TAATAAAAAA 0.485967 -16 TCTTTTAAAAGTGCGGTAAAAAATAAAGGTA 41 6 1 TAAAGTAAAA 0.594631 -255 CATTAGAATGAAAAAGTACCGTAAAAAATCACCGCA 43 156 1 AAAAGTAAAA 0.871176 -94 GATTTCTCTATAAAAAATCATCAAAAGTGCGGTGAT 43 183 0 TAAAAAAAAA 0.845487 -67 * ***** **** Masking position 15 Map Score: 67.6025 Number of sites scoring better than the average of aligned sites = 735 Number in coding regions = 503 Number in noncoding regions = 232 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 3 AAGGTTTGTTTAATTAAAGACAAAATTCCCATAT 2 117 0 TAATTACAAA 0.386768 -184 TTTTCCTCTTAATTCATTGACAAAGTTGCCTTAC 3 96 0 AATTCACAAA 0.545068 -27 AAAGTAATAAATATTCAAAATAAAGGCTTTTTTG 4 126 1 ATATTATAAA 0.807144 -93 GCCACAGTTTAATTCCTTGATAAAGTGCGGTCGA 8 39 1 AATTCATAAA 0.666709 -51 TCTTTTTGCTATTTTTAATATCAATCTAGTTCCT 10 80 1 ATTTTATCAA 0.600264 -126 TATTTAAGTGTTTTTGCTTATAAATAGGTGGCAC 12 57 0 TTTTTATAAA 0.796361 -88 GCAATATTCTATATTAATAATAAAACAAAAATGG 13 54 0 ATATTATAAA 0.807144 -81 TTATTGTGCATATTTATTCATAAAGCAATATTCT 13 78 0 TATTTATAAA 0.724878 -57 TTGTAATGACATTTTTATTATAAATAATGGC 18 8 0 ATTTTATAAA 0.912763 -163 AGCGATGGCTTTTTTATTTACAAAGGTTTACACT 18 119 1 TTTTTACAAA 0.705306 -52 TAAATCTTATATTTTGATCATAAATAATTTACGA 20 34 1 ATTTTATAAA 0.912763 -174 TGATCATAAATAATTTACGATAAATTGAAAGCGG 20 48 1 TAATTATAAA 0.512911 -160 CTTATTTTCTTATTTTGTGACAAAGATCACGGTT 20 121 1 TATTTACAAA 0.612143 -87 TTATACTAAATTATTGTAAATAAACCGTGATCTT 20 143 0 TTATTATAAA 0.625679 -65 AAATTCTGTGAATTTCGCCAAAAATACTCGATTT 23 13 0 AATTTAAAAA 0.733481 -140 TAATTTTTTCAAATTTGCGATAAAATTCTGTGAA 23 35 0 AAATTATAAA 0.724957 -118 TTTAGTCCGTATTTCATATACAAACAATTAGAGC 24 36 1 ATTTCACAAA 0.655464 -139 AAGTAGGTTTATTTTTAATATAAAATGCCAAAAA 25 43 1 ATTTTATAAA 0.912763 -258 AACGTTTTCCATATTACGAATAAAAAACTGGCTG 25 86 0 ATATTATAAA 0.807144 -215 TTTTTCCTGTATTTTTTAGATAAAAAACCCGCAA 25 260 0 ATTTTATAAA 0.912763 -41 TAATATGTATATTTTATAAATAAAAACTGCCGAA 26 34 0 ATTTTATAAA 0.912763 -34 TTTTAAGTCTATTTTTAGTAAAAATAGTTTAATT 27 50 1 ATTTTAAAAA 0.802963 -165 AAAATAGTTTAATTTTTCAAAAAATACGATAAAG 27 70 1 AATTTAAAAA 0.733481 -145 CGATGAATTTATTTTATTCATCAAAAGGTGTATT 27 122 1 ATTTTATCAA 0.600264 -93 TCTAGTTCACATTTCTGAGATAAATATTTTCTTC 28 94 0 ATTTCATAAA 0.760553 -113 GTTTTTTCAGATTTTTTTCAAAAAGGACTCAGCA 31 11 0 ATTTTAAAAA 0.802963 -289 TTTACTGGTTATTTTAGCGAACAAAAAAACACAA 31 75 1 ATTTTAACAA 0.385179 -225 TTTTAGAAGATTTTTTGAGATAAAGATAGTGAAT 31 175 0 TTTTTATAAA 0.796361 -125 AAAAGGTAGGATTTTCGCAACAAAAGCATAAAGG 32 19 0 ATTTTACAAA 0.862443 -179 AATCCTACCTTTTTTGCTGAAAAATGAAAAGTCT 32 40 1 TTTTTAAAAA 0.433716 -158 GCATCAAAAAAATTTTGTTATAAAGTTGTAAAAG 32 86 1 AATTTATAAA 0.868379 -112 GTTCGTCACAATTTTTTGAATAAAAAACAGATAT 32 126 1 ATTTTATAAA 0.912763 -72 TTTATTGCAAATTTTTTATAAAAAGAAGTGATTT 37 193 0 ATTTTAAAAA 0.802963 -82 AAAGATGACTAAATTCTCAACAAACCTTTATAAT 37 224 1 AAATTACAAA 0.61221 -51 TATGTAGAGCAATTCCAAAAAAAACACCGATTAA 39 161 1 AATTCAAAAA 0.45497 -100 ATAAGTAGAAAAATCACCTATAAAATTAGGAAAA 40 52 0 AAATCATAAA 0.444186 -160 TATATGTCACTTTTTTAAAATAAATTGTGATCTA 40 94 1 TTTTTATAAA 0.796361 -118 CTATTTTAACAAATTCAATAAAAATCATAATTAT 40 137 0 AAATTAAAAA 0.523791 -75 TTCAATAGAGTAATTTTTGACAAATCGGAGTAAA 42 37 1 TAATTACAAA 0.386768 -26 ***** ***** Masking position 10 Map Score: 32.3242 Number of sites scoring better than the average of aligned sites = 788 Number in coding regions = 509 Number in noncoding regions = 279 Number of orfs with sites within 600 bp upstream = 251 Fraction of orfs with sites within 600 bp upstream = 0.0403148 Motif number 4 CGGTTAGACAATTTTTTTAAATCTGTAATT 1 147 0 ATTTTTTTAA 0.679044 -154 TAAAGCAAGTGTTTTTTTATCATTTTTGTT 3 26 0 GTTTTTTTAT 0.859878 -97 ACTTTTCTTTGCTTTTTTGATTGATTTGTC 4 101 0 GCTTTTTTGA 0.743415 -118 CAAAATAAAGGCTTTTTTGTGCCATATCAT 4 141 1 GCTTTTTTGT 0.845831 -78 CATATCATCAGATTTTTTGTTATATTATGC 4 163 1 GATTTTTTGT 0.818321 -56 ATAATTCTGATTTTTTATTTTACTTATG 7 9 1 GATTTTTTAT 0.840738 -58 AATGCTGAAAACTTTTTTATTTTAGGG 9 8 0 ACTTTTTTAT 0.80761 -164 GGAAAATAACGCATTTTTATAGAATTCTCA 9 123 0 GCATTTTTAT 0.723702 -49 ATTTTTAAACATTTTTTTAAGAACTTTACC 11 69 0 ATTTTTTTAA 0.679044 -104 TCTACTTAACATTTTTTTATATTGACATCC 11 103 1 ATTTTTTTAT 0.800249 -70 CTATTTTTGCATATTTTTGAAATTTATAAA 16 121 0 ATATTTTTGA 0.423744 -67 TCTTGTAATGACATTTTTATTATAAATAAT 18 14 0 ACATTTTTAT 0.630991 -157 TCAAGCGATGGCTTTTTTATTTACAAAGGT 18 116 1 GCTTTTTTAT 0.865412 -55 AAATAAGCAAAATTTTTTATGATTTAGTTC 20 98 0 AATTTTTTAT 0.775094 -110 TTTCCAATATTTTTGTCGGGCGGACT 24 7 1 ATATTTTTGT 0.582014 -168 AGATAGACGTGAATTTTTATGTAGGCTCTT 24 137 0 GAATTTTTAT 0.682579 -38 ACATCTGACTGTTTTTTTATCCACAACTTA 25 198 0 GTTTTTTTAT 0.859878 -103 TGATGAAAGTGAATTTTTATGCAATTCTTA 28 39 0 GAATTTTTAT 0.682579 -168 AGTGCGGTCAATATTTTTAACGTTTTTACG 29 86 1 ATATTTTTAA 0.462892 -28 ATTTTTTTGTGTTTTTTTGTTCGCTAAAAT 31 85 0 GTTTTTTTGT 0.839641 -215 AAGTGCGGTAATTTTTTTGTGTTTTTTTGT 31 95 0 ATTTTTTTGT 0.773667 -205 AATTTTAGAAGATTTTTTGAGATAAAGATA 31 181 0 GATTTTTTGA 0.704026 -119 TTATAACAAAATTTTTTTGATGCGAGGCAT 32 79 0 ATTTTTTTGA 0.643517 -119 AGTTCGTCACAATTTTTTGAATAAAAAACA 32 125 1 AATTTTTTGA 0.608287 -73 CATTTTTTTTATTTTTTTGTCTTACAGACC 33 41 0 ATTTTTTTGT 0.773667 -153 GGATCCGCAAGAATTTTTAACAAAGAAATG 34 93 0 GAATTTTTAA 0.531752 -208 GATTGTTCCCATTTTTTTATTACTTACTGA 34 222 1 ATTTTTTTAT 0.800249 -79 GTGATTATAGATATTTTTAACTTGAACACA 36 99 1 ATATTTTTAA 0.462892 -202 AATGTGCACCGATTTTTTATCTGGCTAATA 36 226 1 GATTTTTTAT 0.840738 -75 CTTTATTGCAAATTTTTTATAAAAAGAAGT 37 198 0 AATTTTTTAT 0.775094 -77 ACTTTTTAGGGATTTTTTAAAAAGTGCGGT 38 26 0 GATTTTTTAA 0.735996 -157 TCTATATGTCACTTTTTTAAAATAAATTGT 40 92 1 ACTTTTTTAA 0.689137 -120 TATAGCACGAGCATTTTTATAAAACTATAA 43 91 1 GCATTTTTAT 0.723702 -159 AAACCCTACTACTTTTTTGTGATCTATATC 43 119 1 ACTTTTTTGT 0.781741 -131 CACTTTTGATGATTTTTTATAGAGAAATCT 43 190 1 GATTTTTTAT 0.840738 -60 ********** Masking position 5 Map Score: 36.0486 Number of sites scoring better than the average of aligned sites = 686 Number in coding regions = 420 Number in noncoding regions = 266 Number of orfs with sites within 600 bp upstream = 200 Fraction of orfs with sites within 600 bp upstream = 0.0321234 Motif number 5 TCTTTCTTAGGCGGGTATAAGTTATTTTGA 10 31 0 GCGGGTATAA 0.816974 -175 TTTGAGAAGTGCGGTTAAAATTTAAGTTAT 16 43 0 GCGGTTAAAA 0.909062 -145 GTCGTGAAGTGCGGTTTTATTTTGGAGTTT 16 77 1 GCGGTTTTAT 0.717612 -111 TAAATTGAAAGCGGTTACTTTCATAAGTAT 20 68 1 GCGGTTACTT 0.548889 -140 AGGAAAAAGTGCGGTTATGAATAAACTTAC 23 91 0 GCGGTTATGA 0.631825 -62 CTTTAAAAGTGCGGTTAAAATTTCAATCTT 23 119 1 GCGGTTAAAA 0.909062 -34 CTTATAAAGTGCGGGTTTAAAATTGGGTAT 25 230 0 GCGGGTTTAA 0.556856 -71 TTTATAAGTTGCGGGTTTTTTATCTAAAAA 25 252 1 GCGGGTTTTT 0.423101 -49 TATGATAAGTGCGGTCAATTTTTGAGGTGT 27 15 0 GCGGTCAATT 0.876402 -200 CCGTAAAAGTGCGGTCAATATTTTTAACGT 29 79 1 GCGGTCAATA 0.887036 -35 GATGAAAACTGCGGTCAAAAAACATTGTGT 30 13 1 GCGGTCAAAA 0.92395 -50 CTTTTAAAGTGCGGTCATAAAACACAATGT 30 34 0 GCGGTCATAA 0.92395 -29 ATTTGAAAGTGCGGTAATTTTTTTGTGTTT 31 101 0 GCGGTAATTT 0.699151 -199 AAACAAAACTGCGGTGATAATAAAAAGTTG 37 23 1 GCGGTGATAA 0.811262 -252 TTTAAAAAGTGCGGTCTATTTTTGCTAAGT 38 11 0 GCGGTCTATT 0.666239 -172 TTTTAAAAGTGCGGTAAAAAATAAAGGTAT 41 13 1 GCGGTAAAAA 0.799268 -248 ATACCTACCCGCGGTAAAATACCTTTATTT 41 31 0 GCGGTAAAAT 0.782399 -230 AATTTTATCTGCGGGCAAATACCCTTGAAT 41 220 0 GCGGGCAAAT 0.830473 -41 CATCAAAAGTGCGGTGATTTTTTACGGTAC 43 171 0 GCGGTGATTT 0.714993 -79 ********** Masking position 4 Map Score: 12.8354 Number of sites scoring better than the average of aligned sites = 989 Number in coding regions = 640 Number in noncoding regions = 349 Number of orfs with sites within 600 bp upstream = 234 Fraction of orfs with sites within 600 bp upstream = 0.0375843 Motif number 6 ACAGAAAATGATGGAAAAATGAAATTTTAT 1 209 1 ATGGAAAAAT 0.763017 -92 TTTTGGCACAAAGGAAAAAGTGATAAAAGT 1 256 0 AAGGAAAAAG 0.978329 -45 AACTATTGACATTGAAAAAGTTGATGAAAA 2 270 0 ATTGAAAAAG 0.725595 -31 ATTCATTCCTATGGAAAAAGCATTATTCAA 9 60 1 ATGGAAAAAG 0.954336 -112 ATAGGCAATAAAGGAACTAGATTGATATTA 10 95 0 AAGGAACTAG 0.744441 -111 TTAAAACAAAAAGGAAAAATT 13 124 1 AAGGAAAAAT 0.874291 -11 AGATTATAACAAGGAAAAAGTT 20 3 0 AAGGAAAAAG 0.978329 -205 CGCACTTTTAAAGGAAAAAGTGCGGTTATG 23 102 0 AAGGAAAAAG 0.978329 -51 TATTCGTAATATGGAAAACGTTTTACACAG 25 98 1 ATGGAAAACG 0.868467 -203 ATTCATCGGTAAGGAAAAAATACAAACTTT 27 100 0 AAGGAAAAAA 0.874291 -115 CGCACTTTAAAAGGAACAAAAA 30 51 1 AAGGAACAAA 0.687231 -12 TCTTGTTTAAAAGGAAATCGGAGCAGTACA 33 94 1 AAGGAAATCG 0.744441 -100 TCATCATTAGAATGAAAAAGTACCGTAAAA 43 152 1 AATGAAAAAG 0.851009 -98 ********** Masking position 5 Map Score: 9.70241 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 95 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 TTTGTTATCCTAAAAAGACCGTAAAAATCGACCGC 8 65 0 CCTAAAGTAA 0.973273 -25 AGAGACCTCCTAATAACGAGATTAAAAGAAAG 10 184 0 CCTAAAGAAT 0.945164 -22 ATTTGATCCTTATAAAAGTGAGAAT 21 8 1 CCTAAAGAAA 0.977413 -18 TTCGACCACCAAAAATCGAAAAAACCAGTATA 22 6 1 CCAAAAGAAA 0.846113 -52 ACGTTCTTCCTAAAAAGATTGAAATTTTAACCGCA 23 128 0 CCTAAAGAAT 0.945164 -25 AGAAACCCATCCTATAAAGACCGTAAAAGTGCGGTCA 29 59 1 CCTAAAGTAA 0.973273 -55 TTTTACCTCGTAAAAACGTTAAAAATATTGAC 29 92 0 CCTAAAGTAA 0.973273 -22 GCTCCGATTTCCTTTTAAACAAGATAATTTGCTCTCC 33 81 0 CCTAACGAAA 0.8907 -113 ACCCGATATAACTGGCAAAAAAGTAAACAAAACCAGC 36 144 1 ACTAAAGTAA 0.741552 -157 TCCGTTGAAACCTTTAAAGATAGAGAAAAATATTATT 39 49 0 CCTAAAGAAA 0.977413 -212 ATTATAACGCCCTTTCAATAGAGTAATTTTTGACAAA 42 24 1 CCTAAAGTAT 0.935503 -39 *** ** * ** ** Masking position 8 Map Score: 8.67502 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 16 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 CGGGATTTTTGCTCTATATCACAATATCACTAA 11 31 1 GTCTAATCAA 0.928003 -142 ATAGCACTAATACAAATAAAATGGAC 13 4 1 GACTATACAA 0.77132 -131 AAAAAACTGTGTACTAGATCACAATTTAAACAT 17 16 0 GACTAATCAA 0.97607 -86 TCATAAGTATGAACTAAATCATAAAAAATTTTG 20 88 1 GACTAATCAA 0.97607 -120 TCAGAAATGTGAACTAGATCATAGAATGATATT 28 110 1 GACTAATCAA 0.97607 -97 AAAATTGCGCGTATTAGAACATAAATTTATAGA 33 148 0 GATTAAACAA 0.677166 -46 AGAATTAATAGCACTATAACAGAATAATTCCCA 39 218 0 GACTAAACAA 0.95535 -43 ATTATTTTGAGAACTAGATCACAATTTATTTTA 40 109 0 GACTAATCAA 0.97607 -103 ACTTTTTTGTGATCTATATCAAATCATCATTAG 43 129 1 GTCTAATCAA 0.928003 -121 * **** **** * Masking position 6 Map Score: 7.69298 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 5 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 AAGCAAGAAGATCAAATTACCGTTGTT 6 5 0 ATCAAATACT 0.950613 -89 TTAAAACACTATCAAAATAACTTATACCCGCCT 10 20 1 ATCAAATACT 0.950613 -186 TGTCTGATTTTTCAAACCATCTTAGATGATGGA 27 159 1 TTCAAACACT 0.898214 -56 AAATCATCATATCAAATCAGCTTTGCCATAAAT 31 135 0 ATCAAACACT 0.980096 -165 GTGAATTTTCATCAAATCATCATATCAAATCAG 31 148 0 ATCAAACACT 0.980096 -152 ATAAGAGGAGAGCAAATTATCTTGTTTAAAAGG 33 75 1 AGCAAATACT 0.836398 -119 CAATCTTTTAATCAAACCAACTTTTTATTATCA 37 37 0 ATCAAACACT 0.980096 -238 TGTGATCTATATCAAATCATCATTAGAATGAAA 43 136 1 ATCAAACACT 0.980096 -114 ****** ** * * Masking position 6 Map Score: 6.65611 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 10 TTTCTACTTTTATCACTTTTTCCTTTGTGCCAAAA 1 251 1 TATCTTTTTT 0.362184 -50 GTTGAAATAATTTTTGCTTTTCTTTGCAATGAAAG 2 168 1 TTTGTTTTTT 0.417841 -133 CAAGTGTTTTTTTATCATTTTTGTTTAAAGGGAAT 3 16 0 TTTCTTTTTT 0.916466 -107 TGTTTTTCCTCTTAATTCATTGACAAA 3 106 0 TTTCTCTTTT 0.88145 -17 TTTTGAATATTTATTACTTTTCTTTGCTTTTTTGA 4 111 0 TTAATTTTTT 0.121148 -108 CAACGGTAATTTGATCTTCTTGCTTGCATACAGCA 6 13 1 TTGCTCTTTT 0.896249 -81 ATAATTCTGATTTTTTATTTTACTTATGACATAAT 7 11 1 TTTTTTTTTT 0.662499 -56 TGGTTTGTCCTTTTTTAGTTGAGTTAAAC 7 48 0 TTGCTTTTGT 0.504472 -19 TACTTATTTGTTGATATTCTTTCTTTTAATCTCGT 10 166 1 TTGATCTTTT 0.402047 -40 ACTTTTTGTCTTGATCGTTTTATTTAAGTGTTTTT 12 76 0 TTGCTTTTTT 0.927255 -69 ATCTTTCATTTTGTCCATTTTATTTGTATTAGTGC 13 14 0 TTGCTTTTTT 0.927255 -121 ATGAAAGATTTTGTCCATTTTTGTTTTATTATTAA 13 40 1 TTGCTTTTTT 0.927255 -95 TATTCTATTATTGTGCATATTTATTCATAAAGCAA 13 84 0 TTGCTATTTT 0.629772 -51 AATTTTTCCTTTTTGTTTTAATTAATTA 13 117 0 TTTCTTTTTT 0.916466 -18 CTTTTATCTCCTTAGTTTGCATTTATT 15 61 0 TTTCCCTTTT 0.363208 -17 CAAACTATTTTTTGGCATTTTATATTAAAAATAAA 25 50 0 TTTCTTTTAT 0.371548 -251 AAATACAAACTTTATCGTATTTTTTGAAAAATTAA 27 78 0 TTTCTATTTT 0.594172 -137 ACGATAAAGTTTGTATTTTTTCCTTACCGATGAAT 27 95 1 TTGTTTTTTT 0.695179 -120 AGATAAATATTTTCTTCTCTTTGTTCTTATTCATA 28 76 0 TTTTTCTTTT 0.570871 -131 GGTAATTTTTTTGTGTTTTTTTGTTCGCTAAAATA 31 84 0 TTGTTTTTTT 0.695179 -216 TCTCCTCTTATTGAACATTTTTTTTATTTTTTTGT 33 51 0 TTGCTTTTTT 0.927255 -143 TTTTTGACCTTTTTATTGACTAGAAAA 33 177 0 TTTCTTTTTT 0.916466 -17 TGTTGAGAATTTAGTCATCTTTATTGCAAATTTTT 37 211 0 TTACTCTTTT 0.545504 -64 AACTGACAAATTTTATTTTTTACTTTTAGGAGTTC 38 156 1 TTTTTTTTTT 0.662499 -27 TTTTACCTCTTATTCAATAAAATAG 40 197 0 TTTCTCTTTC 0.363208 -15 AGATTTTCACCTTTTATTTAAGTTAAACA 43 5 1 TTTCTTTTTT 0.916466 -245 *** * **** ** Masking position 10 Map Score: 19.2695 Number of sites scoring better than the average of aligned sites = 372 Number in coding regions = 275 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 11 CTTTGTACTCTTTTAATTATGCTCAAAAATCTGTCG 4 20 1 TTTTAAGTAA 0.829584 -199 ATAACGCATTTTTATAGAATTCTCAAGATTTTCTCT 9 112 0 TTTAAATTAA 0.861999 -60 AAGGATTGTTTAAAACACTATCAAAATAACTTAT 10 9 1 TTTAAATTAA 0.861999 -197 AGAAATTGTTTTTTGAATAATCTGAAATAACTTAAA 16 17 1 TTTTAATTAA 0.83556 -171 GCAAAAAGCCTTTTTATAAATTTCAAAAATATGCAA 16 109 1 TTTTAATTAA 0.879792 -79 AATGCTAACATTTTGAGCAATAAAAAACTGTGTACT 17 34 0 TTTTAATAAA 0.711811 -68 TTTACAAAGGTTTACACTAATTTCAAATTTACTCAG 18 135 1 TTTAAATTAA 0.772473 -36 TGACTCCTGTTTTTTATCAATGTAAACGATTACATT 20 180 0 TTTTAATTAA 0.83556 -28 CTTTATTTTTCAATAGTCAAAATTTGCATAAG 28 7 1 TTTTAATAAA 0.470135 -200 ATTTTTAACGTTTTTACGAGGTAAAA 29 98 1 TTTTAAGAAA 0.671164 -16 TGAATATTAGTTTAGACAAGGCTAAACACGAATACG 31 250 0 TTTAAAGTAA 0.806501 -50 CCGTTTTTGATTTCCAAAAGTTTTAAGCGTATAATG 36 194 1 TTTCAATTAA 0.662598 -107 TCAACAAACCTTTATAATAGGAAAAATTTTTAGGGA 37 240 1 TTTAAAGAAA 0.566386 -35 CACGAGCATTTTTATAAAACTATAAACCCTACTACT 43 96 1 TTTAAATTAA 0.772473 -154 **** * * * * ** Masking position 9 Map Score: 6.21599 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 88 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 12 AGCAAAAATTATTTCAACAAACTTTGATAT 2 156 0 ATTTCAACAA 0.792724 -145 AAATTTAATACTTTTAACAAGTTTACGACT 2 243 0 CTTTTAACAA 0.670344 -58 AAGTATTAAATTTTCATCAACTTTTTCAAT 2 260 1 TTTTCATCAA 0.92392 -41 TTTTTATTCCCTTTAAACAAAAATGATAAA 3 11 1 CTTTAAACAA 0.670427 -112 AATCGCCGTGTTTTCAACAATGGTTGGGGA 9 150 0 TTTTCAACAA 0.959381 -22 TTTGATAGTGTTTTAAACAATCCTT 10 6 0 TTTTAAACAA 0.848217 -200 TGACTCCTGTTTTTTATCAATGTAAACGAT 20 186 0 TTTTTATCAA 0.741303 -22 ATAGTTTAATTTTTCAAAAAATACGATAAA 27 73 1 TTTTCAAAAA 0.65637 -142 TAAAAATTCACTTTCATCAACTGAAATATG 28 50 1 CTTTCATCAA 0.815399 -157 TTGACCGCAGTTTTCATCAA 30 1 0 TTTTCATCAA 0.92392 -62 TTTCAGATTTTTTTCAAAAAGGACTCAGCA 31 11 0 TTTTCAAAAA 0.65637 -289 AGATAGTGAATTTTCATCAAATCATCATAT 31 156 0 TTTTCATCAA 0.92392 -144 GACTTTTCATTTTTCAGCAAAAAAGGTAGG 32 43 0 TTTTCAGCAA 0.788886 -155 TCCGATTTCCTTTTAAACAAGATAATTTGC 33 86 0 TTTTAAACAA 0.848217 -108 TCCGCAAGAATTTTTAACAAAGAAATGCCT 34 90 0 TTTTTAACAA 0.841818 -211 ACTTTCAATCTTTTAATCAAACCAACTTTT 37 45 0 TTTTAATCAA 0.741394 -230 GATGACTAAATTCTCAACAAACCTTTATAA 37 227 1 TTCTCAACAA 0.715274 -48 TTATAACACTATTTTAACAAATTCAATAAA 40 149 0 ATTTTAACAA 0.474413 -63 TAGGCGATATTTTTCAACGATAAGTAGGTC 41 156 1 TTTTCAACGA 0.715285 -105 ********** Masking position 4 Map Score: 15.4738 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 255 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 13 TATTTCAACAAACTTTGATATTTTGCAAGGTTTG 2 143 0 AATTAATTTT 0.719362 -158 AACTTGTTAAAAGTATTAAATTTTCATCAACTTT 2 250 1 AATTAATTTT 0.719374 -51 AATTCTATAAAAATGCGTTATTTTCCCCAACCAT 9 127 1 AATCTATTTT 0.620672 -45 AAAATGGACAAAATGAAAGATTTTGTCCATTTTT 13 28 1 AATAAATTTT 0.804289 -107 ACTAGATCACAATTTAAACATTTTTA 17 3 0 AATAAATTTT 0.804397 -99 TATAATCTATAAATCTTATATTTTGATCATAAAT 20 25 1 AATTAATTTT 0.719361 -183 ATTTCGCCAAAAATACTCGATTTTC 23 2 0 AATCCATTTT 0.936103 -151 GTGCGGTTAAAATTTCAATCTTTTTAGGAAGAAC 23 127 1 AATCACTTTT 0.818581 -26 AGTCAGATGTAAATACCCAATTTTAAACCCGCAC 25 218 1 AATCCATTTT 0.936167 -83 TTTTTTGAAAAATTAAACTATTTTTACTAAAAAT 27 60 0 AATACATTTT 0.810085 -155 AAGCCCGATGGAATGCAATATTTTACTGGTTATT 31 54 1 GATCAATTTT 0.599897 -246 GATTTGATGAAAATTCACTATCTTTATCTCAAAA 31 163 1 AATCCATCTT 0.608563 -137 TTTGTTGCGAAAATCCTACCTTTTTTGCTGAAAA 32 29 1 AATCACTTTT 0.818582 -169 AATTGTGACGAACTGCAAACTTTTACAACTTTAT 32 105 0 AATCACTTTT 0.818583 -93 AATAAGTGCTCCATTTTCTTGAAACAG 32 181 0 AATCCATTTT 0.936166 -17 CTCCGTCAATAATTACAAAATTTTAAAGGTGTTA 36 271 0 AATCAATTTT 0.933948 -30 GAGGAGAACAAAATGAGCGATTTTGGTTATGCAA 37 118 0 AATACATTTT 0.80911 -157 ATCTATCGCCAACTGACAAATTTTATTTTTTACT 38 146 1 AATAAATTTT 0.804397 -37 TGATATTGATAAATTCACAATTTTTCCTAATTTT 40 31 1 AATCCATTTT 0.936096 -181 ** * * * ***** Masking position 4 Map Score: 17.6095 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 53 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 14 CCTCGTTTCCCGCTCCAATTCGTGGCGTGT 1 12 0 CGCTCCAATT 0.868203 -289 CCGTAAAATGCGCACCAATAACAGCGAATG 1 100 0 CGCACCAATA 0.671813 -201 AGAGTAAAATAGCACCAATTATAGAAGTAT 2 209 1 AGCACCAATT 0.865894 -92 GGGCTTTAAGCCCACCGATTAATGAAATCT 29 20 1 CCCACCGATT 0.849446 -94 GTTTTTGTACTGCTCCGATTTCCTTTTAAA 33 99 0 TGCTCCGATT 0.940292 -95 AAGAAATGCCTGCACCAAGTAAAGAACCAA 34 71 0 TGCACCAAGT 0.755819 -230 CTCGCACGATTGCACCGATTGAACTGCCAC 34 260 1 TGCACCGATT 0.972051 -41 GCGTATAATGTGCACCGATTTTTTATCTGG 36 220 1 TGCACCGATT 0.972051 -81 TTCCAAAAAAAACACCGATTAAAGCCTAAA 39 173 1 AACACCGATT 0.7487 -88 AATTTACTCCGATTTGTCAAAAAT 42 49 0 TACTCCGATT 0.75616 -14 ********** Masking position 8 Map Score: 2.8416 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 120 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 15 ACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGA 1 43 0 CAAGTGGGTC 0.990146 -258 CCGACCTTGGCAAGGTCGTGCTCTACCAACTGA 1 57 1 CAAGTGTGTC 0.958302 -244 AATCCCGACACAATGTCGGGATTTTTGCTCTAT 11 15 1 CAAGTGGGTT 0.91817 -158 AACCTCAATCAAATATAGGGTTCCT 27 200 1 AAAATGGGTC 0.840169 -15 TCCCTAGCAACAACATCGGGATCAATTGAATTA 34 191 0 CAAATGGGTC 0.958302 -110 ACCACCTTGACATGGTGGGGGTCACTGGTTCGA 36 24 0 CATGTGGGTC 0.947387 -277 CCCACCATGTCAAGGTGGTGCTCTAACCAACTG 36 38 1 CAAGTGTGTC 0.958302 -263 AAAATCCCTAAAAAGTGCGGGTCTTTTTTAGCT 38 40 1 AAAGTCGGTC 0.791829 -143 *** ** *** ** Masking position 2 Map Score: 1.95789 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 14 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493