AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00052_bsub_reg_300.orf -o00052_bsub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ybfT 218 similar to glucosamine-6-phosphate isomerase #2 rapJ 122 response regulator aspartate phosphatase #3 ycdF 106 similar to glucose 1-dehydrogenase #4 ycdG 24 similar to oligo-1,6-glucosidase #5 ycnL 164 ycnL #6 mtlA 172 phosphotransferase system (PTS) mannitol-specific enzyme IIABC component #7 treP 192 phosphotransferase system (PTS) trehalose-specific enzyme IIBC component #8 glvA 300 6-phospho-alpha-glucosidase #9 yfiA 64 similar to hypothetical proteins #10 yjlC 300 yjlC #11 yjlD 39 similar to NADH dehydrogenase #12 yjmA 197 similar to glucuronate isomerase #13 yjmB 67 similar to Na+:galactoside symporter #14 yjmC 104 similar to malate dehydrogenase #15 ykvY 300 similar to Xaa-Pro dipeptidase #16 ykvZ 281 similar to transcriptional regulator (LacI family) #17 glcT 62 transcriptional antiterminator (BglG family) #18 ptsG 238 phosphotransferase system (PTS) glucose-specific enzyme IIABC component #19 mobA 136 molybdopterin-guanine dinucleotide biosynthesis protein A #20 moeB 50 molybdopterin biosynthesis protein #21 yknU 223 similar to ABC transporter (ATP-binding protein) #22 yknW 109 yknW #23 fruR 279 transcriptional regulator (DeoR family) #24 yngA 300 yngA #25 ypqE 137 similar to phosphotransferase system enzyme II #26 yqgQ 109 yqgQ #27 yqgP 89 similar to hypothetical proteins #28 yqgO 66 yqgO #29 yqgN 300 similar to 5-formyltetrahydrofolate cyclo-ligase #30 levD 189 phosphotransferase system (PTS) fructose-specific enzyme IIA component #31 levR 300 transcriptional regulator (NifA/NtrC family) #32 pfk 183 6-phosphofructokinase #33 yttI 300 similar to acetyl-CoA carboxylase #34 msmR 217 transcriptional regulator (LacI family) #35 msmE 33 multiple sugar-binding protein #36 ytdA 171 alternate gene name: yzwA; similar to UTP-glucose-1-phosphate uridylyltransferase #37 yugK 103 similar to NADH-dependent butanol dehydrogenase #38 yugJ 229 similar to NADH-dependent butanol dehydrogenase #39 yvfL 39 similar to maltodextrin transport system permease #40 yvfK 140 similar to maltose/maltodextrin-binding protein #41 lacR 179 transcriptional regulator (LacI family) #42 yvfI 300 similar to transcriptional regulator (GntR family) #43 gtaB 245 UTP-glucose-1-phosphate uridylyltransferase #44 sacP 300 phosphotransferase system (PTS) sucrose-specific enzyme IIBC component #45 galK 80 galactokinase #46 ywcC 300 alternate gene name: ipa-33d #47 licB 127 phosphotransferase system (PTS) lichenan-specific enzyme IIB component #48 licR 162 transcriptional regulator (antiterminator) #49 yxzF 28 yxzF #50 yxlJ 128 similar to DNA-3-methyladenine glycosidase #51 galE 114 UDP-glucose 4-epimerase #52 yxkA 129 similar to hypothetical proteins #53 bglP 300 phosphotransferase system (PTS) beta-glucoside-specific enzyme IIABC component Motif number 1 AATCACTTAAAAGCGTTAACATTCAGCACATC 2 30 0 AACGTTACAT 0.950266 -93 CTCTATGTTAAAACGCTTACAGTCCCTATACA 6 78 0 AACGCTACAG 0.876466 -95 CACTTTTTTATAGCGCTTTCATCCTAGTCTGG 7 90 0 TACGCTTCAT 0.921664 -103 ATGGAATTGTAAACGTTATCAAGGAGGTCGTC 8 277 1 AACGTTTCAA 0.841092 -24 AATGAAATGTTAACGCTGTCATAAACATAAAA 12 75 0 TACGCTTCAT 0.921664 -123 TTCAAAATGTTAACGTTAACATTTTGATTTGT 12 153 0 TACGTTACAT 0.840107 -45 CTTCCAGTTTAACCGTTTACATTTGCCCTTTT 18 143 0 AACGTTACAT 0.950266 -96 ACGCCTGTGAATTCGTTGTCATGATTTTTAGC 18 179 1 ATCGTTTCAT 0.885702 -60 TATGTAGAATAAACGCTTACAGAAAATCATTG 21 82 0 AACGCTACAG 0.876466 -142 AAACCGAAAATAGCGTTTACAATGAAATTGTA 23 223 1 TACGTTACAA 0.55293 -57 TTCAAAATGAATACGTTTTCATTAGGAGGTGA 23 255 1 ATCGTTTCAT 0.885702 -25 GTCAAGAAGAAAACGCTGACAAAAAAGCCAGC 26 31 0 AACGCTACAA 0.895376 -79 TAACTATCATAAGCGTATTCATAAGGAAGCGG 26 66 0 AACGTATCAT 0.558242 -44 CAGTTGTGTTAAGCGTTTTCATTGTTATTTCA 30 110 0 AACGTTTCAT 0.957421 -80 TTATTTTTGAATGCGCTGTCAACCTTGTCGTT 33 15 1 ATCGCTTCAA 0.776326 -286 TTTTTTTGTCAAACGCTGTCATCCTCAATTCG 33 107 0 AACGCTTCAT 0.977162 -194 ACCCTTCCTTATTCGCTTACTTCACATTTACG 34 17 1 ATCGCTACTT 0.564705 -201 CAATTATTGTAACCGCTTACTTTTATATGATA 34 136 1 AACGCTACTT 0.79011 -82 ATTATCTTTAAAGCGCTTTCATTCCTACCGAA 40 106 1 AACGCTTCAT 0.977162 -35 TAGTTGACGAAAACGCTATCATGATTTATGAT 44 130 1 AACGCTTCAT 0.977162 -171 CAGATTAAGAATACGCTTTCATCATAAATCAT 44 150 0 ATCGCTTCAT 0.936487 -151 CATATTATGAAATCGCTTTCATAAACACTCAG 47 51 0 AACGCTTCAT 0.977162 -77 TAACAAATTGTTACGTTTACATGCGTATTTGT 52 40 1 TTCGTTACAT 0.644217 -90 CCAAAAATGAAAGCGTTGACATCTCACGAATC 53 52 1 AACGTTACAT 0.950266 -249 ** **** **** Masking position 5 Map Score: 31.7967 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 195 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 2 TATGGTCTCAATGAAAAAGAACGGATTGCA 1 31 0 ATGAAAAAGA 0.597479 -188 TGAAAACAGCACAAAAAAAGCAGAGAACCT 3 29 0 ACAAAAAAAG 0.825051 -78 AAGACAAAACAGGGGGATTGCGG 4 4 1 ACAAAACAGG 0.893175 -21 TAAGTGGATGATAAAAAATGTGAAAATGTG 5 71 1 ATAAAAAATG 0.581327 -94 CAGCAACAAAACGAAACAGAAGGGACTCTG 5 106 1 ACGAAACAGA 0.609041 -59 ACAGCGACAAACAAAACAGGGAGGGTTTAT 6 151 1 ACAAAACAGG 0.893175 -22 TCTGGAATATATGAAACAGACAAGGTTACC 7 65 0 ATGAAACAGA 0.403598 -128 CTTTAAGATTACAAAAAAGGTAAAAAAACC 8 128 1 ACAAAAAAGG 0.948292 -173 TGTCATAAACATAAAAAAAGACATTGCCAG 12 61 0 ATAAAAAAAG 0.671985 -137 CATTTCATTTTCAAAAAAGAGATTGATCCC 12 98 1 TCAAAAAAGA 0.646532 -100 TAGAAATAAAAAAGGACTTTGTTCT 16 6 1 ATAAAAAAGG 0.888477 -276 TTTAATGCAGATAAAAAAGGACGATGTCGA 16 35 0 ATAAAAAAGG 0.888477 -247 TGAATGCATTGAAAAAAGGTTTGACGTGC 17 10 1 TGAAAAAAGG 0.451012 -53 TCTTATTTTAATGAAAAAAGTCTTTTATAT 23 62 0 ATGAAAAAAG 0.520395 -218 TAAAATATGAACAAAACATGAAAAAGCGGG 24 232 0 ACAAAACATG 0.593036 -69 CATAATCTGGTTAAAAAAGGCGGTGGCGAT 25 12 0 TTAAAAAAGG 0.693133 -126 GAAAACGCTGACAAAAAAGCCAGCTTCCTT 26 25 0 ACAAAAAAGC 0.484826 -85 AGCTGTTATAATGAAAAAAAACTATTGGAG 27 62 1 ATGAAAAAAA 0.276252 -28 AGCCAGAGCTTTGAAAAAGGTTCTGGCTTT 29 256 1 TTGAAAAAGG 0.544694 -45 CCCTCGGAATAGAAAAAAAGCCAGAACCTT 29 272 0 AGAAAAAAAG 0.426972 -29 AACACTTAAAACGAAAAAAATAAACCTGTA 30 58 0 ACGAAAAAAA 0.467707 -132 ATATGGATGTACAAAACAGGAAAGGAGCAA 30 165 1 ACAAAACAGG 0.893175 -25 ATAATCAATGACAAAAAATGAATCTTATAG 31 31 0 ACAAAAAATG 0.761696 -270 AAGGAATGTCACAAAAAATAAACGTGAGCC 32 28 0 ACAAAAAATA 0.529278 -156 ACAGCGTTTGACAAAAAAAGTACAATAGTT 33 120 1 ACAAAAAAAG 0.825051 -181 GGATATATTCACGAAAAAGAAAAAGTATGC 33 235 1 ACGAAAAAGA 0.773599 -66 CAATATCCTATTAAAAAAGGGCTGGTTCGT 36 47 1 TTAAAAAAGG 0.693133 -125 ACATAAGTTGACAAAAAAGAAAAAGGGAAG 37 37 0 ACAAAAAAGA 0.865797 -67 TTTTACCTAAATAAAAAATGACTTAGTGTC 40 22 0 ATAAAAAATG 0.581327 -119 TTGGCGGCCCACAAAACAGAGTATAATAGA 42 47 1 ACAAAACAGA 0.746273 -254 ATTTGCGTAAATGAAAAAGGATCGCTGTGT 44 223 1 ATGAAAAAGG 0.808412 -78 TTTTATTTAAACAAAAAAGACCTAAAATTC 44 268 0 ACAAAAAAGA 0.865797 -33 AATAAGGGGAATAAAAAATAAAAACCAGAA 45 49 1 ATAAAAAATA 0.328157 -32 TTGTTACCGTTCAAAAAAGGAGGGCCAACC 50 12 0 TCAAAAAAGG 0.8387 -117 CCGAAGCAGATCAAAAAAAACGGCTGTTTT 50 65 0 TCAAAAAAAA 0.319891 -64 CACTATATAATGAAAACAGGTCATTTTTTA 51 81 1 TGAAAACAGG 0.272485 -34 AGCATTTGATACAAAAAAAGCTGGTGAAAG 53 233 1 ACAAAAAAAG 0.825051 -68 ********** Masking position 5 Map Score: 29.712 Number of sites scoring better than the average of aligned sites = 1696 Number in coding regions = 1269 Number in noncoding regions = 427 Number of orfs with sites within 600 bp upstream = 433 Fraction of orfs with sites within 600 bp upstream = 0.0695471 Motif number 3 TTCATTCTCCCCATTCTGTATGCAATC 1 6 1 TTCCCCTTCT 0.901356 -213 CGGTCTGCCTCCTTCCTCCTGCTACTA 2 106 0 TCCTCCTCCT 0.871187 -17 AACTACAGGTTCTCTGCTTTTTTTGTGCTGTT 3 23 1 TTCTGCTTTT 0.751961 -84 ATGAAATTCCCCCATTTTCGAATCTGTA 9 7 1 TCCCCCTTTT 0.965327 -58 ATCAGATCCCCCCATTTTCTTTCTATTA 9 47 0 TCCCCCTTTT 0.965327 -18 GCAAGTGCCTCCTTCCTTTTCAGTTTT 14 88 0 TCCTCCTCCT 0.871187 -17 ATCACATGGGTTTCTTCATTTTAATTGGGTTA 16 159 0 TTCTTCTTTT 0.573655 -123 AGATTCCCTTCTTTCTAAATCCCCTT 16 266 0 TCCTTCTTCT 0.765755 -16 TTGAGCGGTATACCCGCTTTTTCATGTTTTGT 24 220 1 TCCCGCTTTT 0.862236 -81 TGTATTTTCTCCCTTCTCATTCACTTC 25 121 0 TTCTCCTTCT 0.923325 -17 AACAAATGATTACCTCCCTTTTGTGAAGGGTT 33 200 0 TCCTCCTTTT 0.973469 -101 CAAACGGCTATTTCCCCTTTTT 37 1 0 TTCCCCTTTT 0.910974 -103 GCCGTTTGGCTGCTTCCCTTTTTCTTTTTTGT 37 25 1 TCTTCCTTTT 0.618254 -79 TGTATCTGCCTCCATTATTCAGCTCGCA 41 162 0 TCCTCCTTAT 0.882269 -18 GTCTTTTCCTGCTTTCTTTCATGATTG 44 6 1 TCCTGCTTCT 0.880462 -295 CTATTTCTCCCCCTTTTATTTAAACAA 44 284 0 TTCCCCTTTT 0.910974 -17 GACTTGCCATTCTCTCCATTATAGAATTTATA 48 65 1 TTCTCCTTAT 0.733641 -98 TGGTTGGCCCTCCTTTTTTGAACGGTAA 50 7 1 GCCTCCTTTT 0.795531 -122 GTGTATACCTCCTTTTTATGGGGGGAC 53 284 0 TCCTCCTTTT 0.973469 -17 * ***** **** Masking position 9 Map Score: 19.2656 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 255 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 4 CAAAAAAGGTAAAAAAACCAAATCTCTCAGAC 8 139 1 AAAAAACAAA 0.874479 -162 CTCTATGGGAAAAAACACTAAAGTTGATCAAA 8 195 1 AAAAAACAAA 0.874479 -106 TGAAAATAGCAAACACAAAAAACTCCAATTCG 10 59 0 AAACAAAAAA 0.726394 -242 ACGCTGTCATAAACATAAAAAAAGACATTGCC 12 63 0 AAACAAAAAA 0.726394 -135 GGTAAAATAAAAACAAATCAAAATGTTAACGT 12 141 1 AAACAATAAA 0.818276 -57 CCTCTCAACCAAAAACATGAAATTAAACCCTT 16 88 0 AAAAAATAAA 0.812777 -194 CCTTTCAGCTAAAAACACAAAAAGATATCTGG 16 196 1 AAAAAACAAA 0.874479 -86 AATTTATTAGAAAAACATGAAACTTTTTGATA 22 44 1 AAAAAATAAA 0.812777 -66 AGAAATCACTAAACATAAAAAAACCTCATGCA 23 23 0 AAACAAAAAA 0.726394 -257 CTATATTTCTAAAAAGACCAAACGCAACAATC 29 124 1 AAAAAACAAA 0.874479 -177 TCATTGCCCTAAAAACAATGAAAAGGGATCTC 32 119 0 AAAAAAAGAA 0.500227 -65 GCTGCCATGTAAAAAGACTGAACCATTTGCGG 41 70 0 AAAAAACGAA 0.731492 -110 ATTGAAATATAAACAGATTAAAACAAAAAAAT 42 116 1 AAACAATAAA 0.818276 -185 AAATGTGTAAAAACATATTGAAAAGGGTAAAT 43 172 1 AAACAATGAA 0.637785 -74 TATTTAAACAAAAAAGACCTAAAATTCGCCAA 44 263 0 AAAAAACTAA 0.547329 -38 GCTAAAAAATATGAAAAAACTATTAA 51 5 1 AAAAAATAAA 0.812777 -110 GTATACCTACAAACAAATAAAACGACCCGTCA 53 94 1 AAACAATAAA 0.818276 -207 AAAAGAGAATAAAAAAACCTAAATGACACAGA 53 189 0 AAAAAACTAA 0.547329 -112 ***** ** *** Masking position 7 Map Score: 13.5908 Number of sites scoring better than the average of aligned sites = 466 Number in coding regions = 334 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 5 AACAAAACAGGGAGGGTTTATAT 6 160 1 GGAGGGTTTA 0.853807 -13 TTGGATGTTTTATATAAATGAT 8 3 1 GGATGTTTTA 0.874185 -298 TAATCGAATTGGAGTTTTTTGTGTTTGCTA 10 55 1 GGAGTTTTTT 0.618481 -246 TTTTTGGTTGAGAGGTTTTACAGCAAGACA 16 105 1 AGAGGTTTTA 0.569757 -177 CTTCAATATTGAAGGTTTTTGGAAATTTAT 22 21 1 GAAGGTTTTT 0.618481 -89 ATATTCTCAAGGAGGTTTTGAA 22 98 1 GGAGGTTTTG 0.870028 -12 GCAACATGCATGAGGTTTTTTTATGTTTAG 23 17 1 TGAGGTTTTT 0.63557 -263 CGCATTGAACGGCTGTTTTTTGTGTCTGAA 24 163 0 GGCTGTTTTT 0.858506 -138 CGTTCAATGCGGCTGTTTTTTTCAAGAGTA 24 182 1 GGCTGTTTTT 0.858506 -119 AGCATCATTTGGAGGTTTTACT 37 92 1 GGAGGTTTTA 0.956054 -12 GGAATAGGTAGGTGGTTTTTCCTTCAGTTT 46 71 0 GGTGGTTTTT 0.784499 -230 TCCCGGCTGTTTTTTTATAGGTCA 48 5 1 GGCTGTTTTT 0.858506 -158 CTACTAGTTAGGAGGTTTTTCTC 48 150 1 GGAGGTTTTT 0.966274 -13 CAAAAAAAACGGCTGTTTTAAAATCTTTCC 50 54 0 GGCTGTTTTA 0.821657 -75 TCATTTTTTAGGAGGGTTTACATC 51 101 1 GGAGGGTTTA 0.853807 -14 ********** Masking position 7 Map Score: 9.73901 Number of sites scoring better than the average of aligned sites = 370 Number in coding regions = 245 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 6 AGTAGCAGGAGGAAGGAGGCAGACCG 2 107 1 GGAAGAGGCG 0.693936 -16 AAAAGCGTGAGACAGGGAGAGGCACTACCCTT 10 235 1 GACAGGAGAG 0.744331 -66 TTCATCCCGATAAAAGGAGCGGAAATTCCCAA 15 66 1 TAAAGGAGCG 0.907454 -235 CAGTATACAGGAAGAGGAGCAGGAAATAAAAT 15 180 1 GAAGGGAGCG 0.868791 -121 TGTTTTTAGCTGAAAGGAGAAGATCACATGGG 16 181 0 TGAAGGAGAG 0.860878 -101 GATAAATGTTGGAAAGGTGCTGGAT 21 209 1 GGAAGGTGCG 0.969672 -15 GTGGAATATGGAAAGGAAGCTGGCTTTTTTGT 26 13 1 GAAAGAAGCG 0.883376 -97 TTAAGTTCAAGAAATGGTGAGGAAA 26 95 1 GAAAGGTGAG 0.90736 -15 GTACAAAACAGGAAAGGAGCAATAGAT 30 173 1 GGAAGGAGCA 0.791469 -17 AAGCGAATAAGGAAGGGTGATGGG 34 3 0 GGAAGGTGAG 0.93359 -215 ATTCTCCATATGAGGGAAGCTGGCCTGCCCTC 38 81 1 TGAGGAAGCG 0.467218 -149 CAAGGTGCTGGGAAAGAAGCTGATATAAGCGA 38 111 0 GGAAGAAGCG 0.915767 -119 GGTTTTATTTTGCAAGGTGCTGGGAAAGAAGC 38 123 0 TGCAGGTGCG 0.720594 -107 CATTCCTACCGAAAGGGTGACAATCA 40 125 1 GAAAGGTGAA 0.477235 -16 TGAATAGGCAGAAAGGATGATGAAGGGATGCG 48 104 0 GAAAGATGAG 0.72337 -59 CAAAAATCGGTAAAAGGAGAGGTCGATTC 50 110 1 TAAAGGAGAG 0.81172 -19 AGGCAAAACCTAAATGGTGCAGGTGCAGGAGG 53 145 1 TAAAGGTGCG 0.885044 -156 **** ***** * Masking position 6 Map Score: 8.00563 Number of sites scoring better than the average of aligned sites = 899 Number in coding regions = 784 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 7 CTTTTAAGGCATAAGAATAAGGATTGTGAA 10 210 0 ATAAGAATAA 0.621191 -91 GTAACACGTTATAAGGATAAACTGAATTTA 18 18 0 ATAAGGATAA 0.850856 -221 GACATAAAAGATAAGGAGAACAGGTTTG 20 33 1 ATAAGGAGAA 0.952873 -18 TTTCATTAAAATAAGAAGAAAATGTCGTAC 23 76 1 ATAAGAAGAA 0.853197 -204 TTCGACAAAAATAAGGACAATTGTACGACA 23 98 0 ATAAGGACAA 0.899705 -182 ACATACGTTAATATGGAGAAACGTGAAAGA 23 151 1 ATATGGAGAA 0.903477 -129 AATTAATAAAATATGAACAAAACATGAAAA 24 238 0 ATATGAACAA 0.544154 -63 GGCTTATCTAATAAGGACAAAGG 31 288 1 ATAAGGACAA 0.899705 -13 CATCACGATGATAAGGAGGAAAAG 35 20 1 ATAAGGAGGA 0.761281 -14 AGCTTCCCTCATATGGAGAATGCATGTATA 38 72 0 ATATGGAGAA 0.903477 -158 ACAAAAAAATATATGAAGAAGTAGCGGATG 42 138 1 ATATGAAGAA 0.729038 -163 CTATGAAGAAATAAGGGGAATAAAAAATAA 45 40 1 ATAAGGGGAA 0.864641 -41 CCGGTGTAAGATAAGGGTAATCATTACCGC 46 269 1 ATAAGGGTAA 0.643158 -32 ********** Masking position 3 Map Score: 8.0421 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 94 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 TTAATTTCTGAAAATTTGTTATAAAAGAAGGATACA 1 91 0 AAAATGTTAA 0.832771 -128 AGTGGATGATAAAAAATGTGAAAATGTGTTGAACAG 5 73 1 AAAATGTAAG 0.71282 -92 GTAAGATACAAAAATATGTTCAGAGAATGATGCTTC 6 117 0 AAAATGTAAA 0.944493 -56 ATCCGTTTTTATAACTTGTATATACAACTTATAATC 7 153 0 ATAATGTAAA 0.876745 -40 TTAAGATTACAAAAAAGGTAAAAAAACCAAATCTCT 8 130 1 AAAAGGTAAA 0.831623 -171 AATTTTGTTCAAAAAGTGTTATCATATAGAAGGTAA 10 22 1 AAAATGTTAA 0.832771 -279 AATATTTAAAATAATTTGTAAATAAAATGTGTTTGT 14 26 1 ATAATGTAAA 0.876745 -79 ACATCATTAAAAAAATTGTGTATAGAAACTTTTGGA 24 41 1 AAAATGTAAA 0.944493 -260 ATACAATTAAATAAATTGTTTTTAAATAAAATTTAA 32 56 0 ATAATGTTAA 0.675511 -128 CATGCCTGAGAAAATGTGTAAACAAACTATTTACTT 40 66 0 AAAATGTAAA 0.944493 -75 TATTAAGGATAAAGCTTGTTTAAAAATGGTTTATCC 43 126 1 AAAGTGTAAA 0.71282 -120 CGATATCATAAAAATGTGTAAAAACATATTGAAAAG 43 161 1 AAAATGTAAA 0.944493 -85 ATAGTTTGATATAACATGTAGACAAAAATTCGTAAA 44 81 0 ATAATGTAAA 0.876745 -220 GCAGCAACGGAAAAAAGGTATATACAGGCTG 47 6 0 AAAAGGTAAA 0.831623 -122 **** *** * * * Masking position 3 Map Score: 8.57478 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 55 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 9 GTGACACCCCCTCAAAGAGATAGACAAG 1 201 0 ACCCCCTAGA 0.870305 -18 ATGACGACCTCCTTGATAACGTTTACAAT 8 282 0 ACCTCCTAAA 0.974426 -19 CAATTCGATTACCTTCTATATGATAACACTTTT 10 33 0 ACCTTCTAGA 0.845907 -268 TTCAAAACCTCCTTGAGAATATCTAACAA 22 91 0 ACCTCCTAAA 0.974426 -19 GCTTCACCTCCTAATGAAAACGTATTCA 23 262 0 ACCTCCTTAA 0.828805 -18 ATCGAACACTAACTCCTCCAAAAGTTTCTATAC 24 60 0 AACTCCTAAA 0.86819 -241 CACCTGAGCTCCTTTACAAGATTACTGGT 36 7 1 AGCTCCTAAA 0.847005 -165 GTTTTGCAACCTCCTCCATGAATTATTAAAA 38 9 1 ACCTCCTAGA 0.972702 -221 TAAACGATTAAACTTCTTAAAAATGGATGTGGA 51 37 1 AACTTCTAAA 0.503659 -78 GATGTAAACCCTCCTAAAAAATGACCTGTTT 51 94 0 CCCTCCTAAA 0.877681 -21 ATGCTGCATCACCTCCTAAAAGAGAATAAAAAA 53 205 0 ACCTCCTAGA 0.972702 -96 ******* * ** Masking position 13 Map Score: 6.17571 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 23 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 10 TCTCACTTTCTCAAGATGTGCTGAATGTTAACGCT 2 16 1 TAATTGCTAA 0.7452 -107 ACCCTCTTCATTAAGATCTATTTAAGCGTAGAGGA 5 17 1 TAATTATTAA 0.867656 -148 ATAAAAAATGTGAAAATGTGTTGAACAGCAACAAA 5 81 1 TAATTGTTAA 0.902508 -84 TGCTTCCCTTTGACTCTATGTTAAAACGCTTACAG 6 88 0 TACTTGTTAA 0.635479 -85 ATTCACGTTCAAATTTTGTTCAAAAAGTGTTAT 10 9 1 TAATTGTTAA 0.902507 -292 GCGTTTACAATGAAATTGTATTCAAAATGAATACG 23 235 1 TAATTATTAA 0.867682 -45 CATATTTTATTAATTGTTTATTCAACACTGTCCGC 24 253 1 TATTTATTAA 0.732717 -48 GAAGCAAAATTGAAAGTGTGGTTAAATAGTGGTGA 25 69 1 TAATTGGTAA 0.745198 -69 TTTTTTCATATGAACCTGTATTAAATGGAACACCA 30 17 1 TAATTATTAA 0.867683 -173 ACGAAAAAAATAAACCTGTATTAAAATGGTGTTCC 30 43 0 TAATTATTAA 0.867683 -147 GTGACATTCCTTAAATTTTATTTAAAAACAATTTA 32 46 1 TAATTATTAA 0.865364 -138 AGGGCAATGATCATGTTATGTTTAATCATATATGT 32 141 1 TATTTGTTAA 0.794657 -43 AAAAGGGAGGTAATCATTTGTTAAAGGATATATTC 33 210 1 TATTTGTTAA 0.794658 -91 TAATATTTACTAAATATTTAGTAAATGATGTGATT 34 85 0 TAATTAGTAA 0.674452 -133 ACAGATGAGTTAATATTTTACTAAATAGATGAGAG 34 185 1 TATTTACTAA 0.464116 -33 * ** * **** ** Masking position 3 Map Score: 5.50823 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 72 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 11 TGAAAGATTTGTATCCTTCTTTTATAACAAAT 1 82 1 GATCCTCTTT 0.921355 -137 ATCGGTCTCACTTTCTCAAGATGTGC 2 5 1 GCTCATTTCT 0.722715 -118 CCACTTACTTGTCTCCGTCTCTAAAATCCTCT 5 46 0 GCTCCTCTCT 0.957813 -119 TCAAAGGGAAGCATCATTCTCTGAACATATTT 6 110 1 GATCATCTCT 0.959615 -63 CAACCCCTCCGTATCCGTTTTTATAACTTGTA 7 169 0 GATCCTTTTT 0.643478 -24 TATTCCTTTGGGATCAATCTCTTTTTTGAAAA 12 105 0 GATCATCTCT 0.959615 -93 GGGTATCCCTCTCATCTATTTAGT 34 204 0 GATCCTCTCA 0.88779 -14 AACCATTTGCGGCTCAGTCTCAGTTGTTCGTA 41 50 0 GCTCATCTCA 0.807609 -130 AGCCGCAAATGGTTCAGTCTTTTTACATGGCA 41 68 1 GTTCATCTTT 0.610055 -112 ATCTTACACCGGATCAATCTTTAGCGGTATTT 46 249 0 GATCATCTTT 0.897225 -52 ATGAATCCCTCTCTCTATTTTCTC 52 116 0 GATCCTCTCT 0.969593 -14 * **** ***** Masking position 8 Map Score: 4.20026 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 99 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 12 CTTATGCCTTAAAAGCGTGAGACAGGGAGA 10 225 1 AAAAGCGTGA 0.915671 -76 CCTCTCAACCAAAAACATGAAATTAAACCC 16 90 0 AAAAACATGA 0.606316 -192 ATTGAGGGAAAAAAACGGGAAGTTCATTCT 18 69 1 AAAAACGGGA 0.95372 -170 TGAAATACAGAAAAACCGGACGGCTGAAAT 21 23 0 AAAAACCGGA 0.894444 -201 AATTTATTAGAAAAACATGAAACTTTTTGA 22 44 1 AAAAACATGA 0.606316 -66 GTTAATATGGAGAAACGTGAAAGATTTTGA 23 157 1 AGAAACGTGA 0.63614 -123 CAAAACATGAAAAAGCGGGTATACCGCTCA 24 221 0 AAAAGCGGGT 0.633335 -80 AATCCCGTGAAAAACGGGATTTTTTGCTT 27 10 1 AAAAACGGGA 0.95372 -80 GGTGTAAGAAAAAAGCCAGAGCTTTGAAAA 29 243 1 AAAAGCCAGA 0.700784 -58 GGAATAGAAAAAAAGCCAGAACCTTTTTCA 29 267 0 AAAAGCCAGA 0.700784 -34 ATAAACGTGAAGCCTTTGGC 32 1 1 ATAAACGTGA 0.748776 -183 GTCACAAAAAATAAACGTGAGCCAAAGGCT 32 21 0 ATAAACGTGA 0.748776 -163 AAAAAGGGGAAATAGCCGTT 37 1 1 AAAAAGGGGA 0.760792 -103 CTTAATCTGAATAAGCGGGATTGTGACTGG 44 173 1 ATAAGCGGGA 0.84443 -128 TTGTTTAAATAAAAGGGGGAGAAATAG 44 284 1 AAAAGGGGGA 0.757017 -17 AATAAAAAATAAAAACCAGAAAGGTGATTG 45 58 1 AAAAACCAGA 0.705092 -23 ********** Masking position 4 Map Score: 7.03069 Number of sites scoring better than the average of aligned sites = 497 Number in coding regions = 446 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 13 TGAGAAACAGAGGAGGATATCAAGT 3 92 1 AGGAGGATAT 0.786771 -15 CAGGAAGAGGAGCAGGAAATAAAATGCATT 15 187 1 AGCAGGAAAT 0.763939 -114 TTTAGCTGAAAGGAGAAGATCACATGGGTT 16 179 0 AGGAGAAGAT 0.671171 -103 TAGTAAAAAGAGGAGGTCAATTCTT 18 224 1 AGGAGGTCAA 0.750692 -15 CGTTTTCATTAGGAGGTGAAGC 23 268 1 AGGAGGTGAA 0.894857 -12 CACGATGATAAGGAGGAAAAG 35 23 1 AGGAGGAAAA 0.886949 -11 AAAAAATCTAAGGAGGAGATGTC 38 217 1 AGGAGGAGAT 0.96604 -13 CATGAAAGAAAGCAGGAAAAGAC 44 4 0 AGCAGGAAAA 0.731423 -297 TTTAAATAAAAGGGGGAGAAATAG 44 287 1 AGGGGGAGAA 0.804285 -14 TGATAGCAACAGCAGGACATTACAAAATTG 47 84 1 AGCAGGACAT 0.777455 -44 GTGCAGGTGCAGGAGGAGACTCTCGCAATC 53 161 1 AGGAGGAGAC 0.897467 -140 ATTCTCTTTTAGGAGGTGATGCAGCATTTG 53 211 1 AGGAGGTGAT 0.91002 -90 ********** Masking position 9 Map Score: 4.37913 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 147 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 14 GTGACAATTTTTTAAAAATAAAAAGGCTCCTG 6 14 0 TAAAAATAAA 0.915664 -159 ATTATTTTTATCTAAAAATAAACAATTGAATA 10 113 0 TAAAAATAAA 0.915762 -188 CACAATCATTTACAAAAATAAATGTTTACTAC 10 172 0 TAAAAATAAA 0.915764 -129 ATGATAGAGCTGTAATAATAAAAGCCCACCAT 15 33 1 TAATAATAAA 0.637006 -268 GACTGAAATTTTGAAAAATAATAGAAATTTAT 21 153 1 TAAAAATAAT 0.72999 -71 TCTGAAAACATACAAATATAAACGGAGTGTTA 24 137 0 TAAATATAAA 0.637014 -164 CACTTAAAACGAAAAAAATAAACCTGTATTAA 30 54 0 GAAAAATAAA 0.613281 -136 AATGTAATGATGTCAAAATAATCAATGACAAA 31 46 0 TCAAAATAAT 0.403011 -255 AAGGAATGTCACAAAAAATAAACGTGAGCCAA 32 26 0 AAAAAATAAA 0.653593 -158 TGACAGCGCATTCAAAAATAATGTT 33 4 0 TAAAAATAAT 0.72999 -297 TGATTTATGTTGGAAAAATAAAGGGGAACCCA 34 58 0 TAAAAATAAA 0.915764 -160 TCCCAGCACCTTGCAAAATAAAACCATCTGGT 38 130 1 TCAAAATAAA 0.730789 -100 GTGAATTGCATTGAAATATAAACAGATTAAAA 42 107 1 TAAATATAAA 0.637006 -194 AATAAGGGGAATAAAAAATAAAAACCAGAAAG 45 49 1 AAAAAATAAA 0.653593 -32 GGACCTTATTTATAATAATAAACAATTAAATA 46 127 1 TAATAATAAA 0.637006 -174 CATAACCGTTTAAAGAAATAAATACCGCTAAA 46 230 1 TAGAAATAAA 0.579601 -71 * ********* Masking position 8 Map Score: 4.57211 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 88 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 15 GCATACAGAATGGGGAGAATGAA 1 3 0 TGGGAGAATG 0.963117 -216 TTTCTCAAGATGTGCTGAATGTTAACGCTTT 2 22 1 TGGCTGAATG 0.938128 -101 GTGGTTAAATAGTGGTGAATGAAGGGATAAC 25 86 1 AGGGTGAATG 0.886972 -52 GGATAACGGTTGAAGTGAATGAGAAGGGAGA 25 110 1 TGAGTGAATG 0.962031 -28 TACTTTGGCTTGCACTGAATGTCGTGAGCGT 29 91 1 TGACTGAATG 0.885287 -210 TATATGTTGCTGAGGTGAATGGAGA 32 169 1 TGGGTGAATG 0.980307 -15 GCTTCCCTCATATGGAGAATGCATGTATAGA 38 70 0 TAGGAGAATG 0.719098 -160 AATTCTATAATGGAGAGAATGGCAAGTCAAT 48 62 0 TGAGAGAATG 0.930026 -101 ATGGATAACTTGCAGTGAAGGAGATATTTC 52 10 0 TGAGTGAAGG 0.855488 -120 ** ******** Masking position 8 Map Score: 3.29333 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 86 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172