AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02060_bsub_reg_300.orf -o02060_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/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 ycnL 164 ycnL #2 mtlA 172 phosphotransferase system (PTS) mannitol-specific enzyme IIABC component #3 ydhM 218 similar to cellobiose phosphotransferase system enzyme II #4 treP 192 phosphotransferase system (PTS) trehalose-specific enzyme IIBC component #5 ykvY 300 similar to Xaa-Pro dipeptidase #6 ykvZ 281 similar to transcriptional regulator (LacI family) #7 glcT 62 transcriptional antiterminator (BglG family) #8 ptsG 238 phosphotransferase system (PTS) glucose-specific enzyme IIABC component #9 ptsH 97 histidine-containing phosphocarrier protein of the phosphotransferase system (PTS) (HPr protein) #10 mobA 136 molybdopterin-guanine dinucleotide biosynthesis protein A #11 moeB 50 molybdopterin biosynthesis protein #12 yknU 223 similar to ABC transporter (ATP-binding protein) #13 yknW 109 yknW #14 fruR 279 transcriptional regulator (DeoR family) #15 levD 189 phosphotransferase system (PTS) fructose-specific enzyme IIA component #16 levR 300 transcriptional regulator (NifA/NtrC family) #17 licB 127 phosphotransferase system (PTS) lichenan-specific enzyme IIB component #18 licR 162 transcriptional regulator (antiterminator) #19 yxzF 28 yxzF #20 yxlJ 128 similar to DNA-3-methyladenine glycosidase #21 bglP 300 phosphotransferase system (PTS) beta-glucoside-specific enzyme IIABC component Motif number 1 TGTATAGGGACTGTAAGCGTTTTAACATAGA 2 78 1 CTGTAAGCGT 0.972981 -95 ATAATAATCAATGTAAGCGTTTTAATAACAG 3 186 1 ATGTAAGCGT 0.986608 -33 CCAGACTAGGATGAAAGCGCTATAAAAAAGT 4 90 1 ATGAAAGCGT 0.986608 -103 AAAAGGGCAAATGTAAACGGTTAAACTGGAA 8 143 1 ATGTAAACGT 0.969173 -96 CAATGATTTTCTGTAAGCGTTTATTCTACAT 12 82 1 CTGTAAGCGT 0.972981 -142 TACAATTTCATTGTAAACGCTATTTTCGGTT 14 224 0 TTGTAAACGT 0.849264 -56 TGTATTCAAAATGAATACGTTTTCATTAGGA 14 251 1 ATGAATACGT 0.815627 -29 TGAAATAACAATGAAAACGCTTAACACAACT 15 110 1 ATGAAAACGT 0.969173 -80 CTGAGTGTTTATGAAAGCGATTTCATAATAT 17 51 1 ATGAAAGCGT 0.986608 -77 AACACCAAAAATGAAAGCGTTGACATCTCAC 21 48 1 ATGAAAGCGT 0.986608 -253 ********* * Masking position 5 Map Score: 17.2489 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 51 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 2 TACCAGAGTCCCTTCTGTTTCGTTTTGTTGCTGT 1 105 0 CCTTCTGTTT 0.937799 -60 ATAAACCCTCCCTGTTTTGTTTGTCGCTGTAAGA 2 147 0 CCTGTTTTTT 0.97472 -26 AGAGGCTCACCCTGCTTTTTAATGTCATATTCAA 4 11 1 CCTGCTTTTG 0.893753 -182 CCCTCCGTATCCGTTTTTATAACTTGTATATACA 4 163 0 CCGTTTTTTT 0.940825 -30 AGAACAAAGTCCTTTTTTATTTCTA 6 2 0 CCTTTTTTTT 0.959964 -280 TCGACATCGTCCTTTTTTATCTGCATTAAATAAA 6 35 1 CCTTTTTTTC 0.764886 -247 AGATTCCCTTCTTTCTAAATCCCCTTGATC 6 262 0 CCTTCTTTTT 0.97472 -20 AATGAACTTCCCGTTTTTTTCCCTCAATCACTGA 8 63 0 CCGTTTTTTT 0.940825 -176 TTTGCTCATGCCTTTTTGTTGTGTAAAAGGGCAA 8 119 1 CCTTTTTGTT 0.752522 -120 TTGCTCCTTTCCTGTTTTGTACATCCATATATAA 15 161 0 CCTGTTTTTT 0.97472 -29 CGCATAAAAGCCAGCTTTGTCAATCTGCTATAGA 16 193 1 CCAGCTTTTT 0.932846 -108 TTTGTAATGTCCTGCTGTTGCTATCATCATATTA 17 76 0 CCTGCTGTGT 0.85823 -52 TCCCGGCTGTTTTTTTATAGGTCAGT 18 3 1 CCGGCTGTTT 0.941437 -160 TTTAAAACAGCCGTTTTTTTTGATCTGCTTCGGG 20 62 1 CCGTTTTTTT 0.940825 -67 TTAGGTTTTGCCTGCTTTCGCAGTAACAATCCTG 21 124 0 CCTGCTTTGT 0.939324 -177 CCGCCTTTCACCAGCTTTTTTTGTATCAAATGCT 21 233 0 CCAGCTTTTT 0.932846 -68 ******** * * Masking position 6 Map Score: 15.6783 Number of sites scoring better than the average of aligned sites = 501 Number in coding regions = 386 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 3 ATATGACATTAAAAAGCAGGGTGAGCCTCT 4 11 0 AAAAAGCAGG 0.729886 -182 TTCATCCCGATAAAAGGAGCGGAAATTCCC 5 66 1 TAAAAGGAGC 0.926906 -235 CAGTATACAGGAAGAGGAGCAGGAAATAAA 5 180 1 GAAGAGGAGC 0.723128 -121 AATGCAGATAAAAAAGGACGATGTCGAGAA 6 32 0 AAAAAGGACG 0.729886 -250 TGTTTTTAGCTGAAAGGAGAAGATCACATG 6 183 0 TGAAAGGAGA 0.885538 -99 AAGGGGATTTAGAAAGAAGGGAATCT 6 266 1 AGAAAGAAGG 0.696719 -16 AGACTAGTAAAAAGAGGAGGTCAATTCTT 8 220 1 AAAGAGGAGG 0.889448 -19 AGCTTTAAGTTAAAAGGAGAATGATAAAA 9 79 1 TAAAAGGAGA 0.859942 -19 GATAAATGTTGGAAAGGTGCTGGAT 12 209 1 GGAAAGGTGC 0.695809 -15 GTACAAAACAGGAAAGGAGCAATAGAT 15 173 1 GGAAAGGAGC 0.929477 -17 GTGAATAGGCAGAAAGGATGATGAAGGGAT 18 107 0 AGAAAGGATG 0.696719 -56 TTACCGTTCAAAAAAGGAGGGCCAACCA 20 9 0 AAAAAGGAGG 0.969899 -120 CAAAAATCGGTAAAAGGAGAGGTCGATTC 20 110 1 TAAAAGGAGA 0.859942 -19 AAAAAGCTGGTGAAAGGCGGCCACCTTTCA 21 247 1 TGAAAGGCGG 0.836397 -54 GACTGCTGGATGAAAGGTGGCCGCCTTTCA 21 257 0 TGAAAGGTGG 0.858805 -44 GTCCCCCCATAAAAAGGAGGTATACAC 21 284 1 AAAAAGGAGG 0.969899 -17 ********** Masking position 5 Map Score: 13.5711 Number of sites scoring better than the average of aligned sites = 967 Number in coding regions = 524 Number in noncoding regions = 443 Number of orfs with sites within 600 bp upstream = 499 Fraction of orfs with sites within 600 bp upstream = 0.0801478 Motif number 4 CTGTAATAATAAAAGCCCACCATCTTCATCCC 5 42 1 AAAACCCCCA 0.826411 -259 ATTAAATAAAAAAATCATCAAATGTTCGAAAG 6 59 1 AAAACATAAA 0.899891 -223 CCTCTCAACCAAAAACATGAAATTAAACCCTT 6 88 0 AAAACATAAA 0.899891 -194 GTCTTGCTGTAAAACCTCTCAACCAAAAACAT 6 102 0 AAAACTCCAA 0.734523 -180 CCTTTCAGCTAAAAACACAAAAAGATATCTGG 6 196 1 AAAACACAAA 0.765779 -86 ATATTGTATGAAACGCATTCCAGATCAAGGGG 6 240 1 AAACCATCCA 0.86637 -42 CTTACAGCTAAAAATCATGACAACGAATTCAC 8 185 0 AAAACATACA 0.906989 -54 TAGTTTCGTTAAAAGCATAGCAAAAGCAAAGG 10 102 0 AAAACATGCA 0.826585 -35 ACGCTTACAGAAAATCATTGTATGCTGAGGAT 12 70 0 AAAACATGTA 0.521582 -154 TATGAAAAGCCTTCAATATTGAAGGT 13 5 1 AAAACCTCAA 0.923466 -105 ATAAATTTCCAAAAACCTTCAATATTGAAGGC 13 19 0 AAAACCTCAA 0.923466 -91 AATTTATTAGAAAAACATGAAACTTTTTGATA 13 44 1 AAAACATAAA 0.899891 -66 TTAGGCAACTAAAATCATTCAAATTCATTCAA 14 193 0 AAAACATCAA 0.942634 -87 TTTGTTGTTGAAACACTTAAAACGAAAAAAAT 15 67 0 AAACCTTAAA 0.60216 -123 ATAACAATGAAAACGCTTAACACAACTGTGTT 15 114 1 AAACCTTACA 0.621488 -76 GAGAAAAACCTCCTAACTAGTAGAT 18 148 0 AAAACCTCTA 0.749614 -15 CGGCTGTTTTAAAATCTTTCCATTCAGGGAAT 20 43 0 AAAACTTCCA 0.891917 -86 **** *** *** Masking position 3 Map Score: 12.2127 Number of sites scoring better than the average of aligned sites = 599 Number in coding regions = 470 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 5 TGAAAATGTGTTGAACAGCAACAAAACGAAACAG 1 91 1 TTAACGAAAA 0.954861 -74 TTATAAAACGGTGAACCGGAAAAAAATATGATTA 3 110 1 GTAACGAAAA 0.725057 -109 TTCCGCTCCTTTTATCGGGATGAAGATGGTGGGC 5 56 0 TTATCGATAA 0.756893 -245 ATAACTGCTTTTCGTCTGAAAAAATTCATCAGCA 5 111 1 TTGTCGAAAA 0.723732 -190 ATCGTCCTTTTTTATCTGCATTAAATAAAAAAAT 6 40 1 TTATCGATAA 0.787507 -242 GGTTGAGAGGTTTTACAGCAAGACAGCTGCCACC 6 110 1 TTTACGAAAC 0.586847 -172 CATAACCCAATTAAAATGAAGAAACCCATGTGAT 6 157 1 TTAAAGAGAA 0.872432 -125 ATGTAAACGGTTAAACTGGAAGACTTACGCCTGT 8 153 1 TTAACGAAAC 0.840806 -86 AGTCTCTTACTTTATAGGGAGTAACATATGTAGA 12 106 0 TTATAGAGAA 0.842084 -118 TTTCTTCTTATTTTAATGAAAAAAGTCTTTTATA 14 63 0 TTTAAGAAAA 0.734965 -217 TAGACATACGTTAATATGGAGAAACGTGAAAGAT 14 148 1 TTATAGAGAA 0.842084 -132 TTAATACAGGTTCATATGAAAAAACTGTTT 15 7 0 TTATAGAAAA 0.889874 -183 GTTGAAACACTTAAAACGAAAAAAATAAACCTGT 15 59 0 TTAAAGAAAA 0.911256 -131 GCCAGTCCCCTTCAAAAGTAATAATCAGTAAACA 16 95 0 TTAAAGAAAA 0.911515 -206 ACACTCAGGGTTTTTCCGCAGCAACGGAAAAAAG 17 25 0 TTTTCGAGAA 0.741243 -103 CCCTCCTTTTTTGAACGGTAACAATATTCCCTGA 20 18 1 TTAACGAAAA 0.954762 -111 ** *** * ** ** Masking position 10 Map Score: 9.4917 Number of sites scoring better than the average of aligned sites = 551 Number in coding regions = 459 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 6 CCTTTTTATTTTTAAAAAATTGTCACAGTCATGTGC 2 20 1 TTTAAAGCAC 0.898157 -153 CTGTAAGCGTTTTAACATAGAGTCAAAGGGAAGCAT 2 88 1 TTTAAAGCAA 0.974169 -85 CATATTTTTGTATCTTACAGCGACAAACAAAACAGG 2 135 1 TATCAAGCAA 0.937405 -38 CATAGAAAAATTTATAAAACGGTGAACCGGAAAAAA 3 99 1 TTTAAAGGAA 0.845782 -120 TAGTCTGGAATATATGAAACAGACAAGGTTACCCTA 4 62 0 TATAAAGCAA 0.968392 -131 GCTATTCCTCTTTAATAAACAGACAAGCAGTAGCGT 10 62 1 TTTAAAGCAA 0.974191 -75 AAAAGGTCTCTATAGCAGATTGACAAAGCTGGCTTT 16 199 0 TATAAAGCAA 0.968392 -102 GTTAATGGCTTATCTAATAAGGACAAAGG 16 282 1 TATCAAGCAA 0.937405 -19 CATGTTTAAGGAAGAGGCAATCAGGGGA 19 5 1 TTTAGAGCAA 0.898158 -24 **** * * * *** Masking position 9 Map Score: 3.61325 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 60 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 ACAAACAAAACAGGGAGGGTTTATAT 2 157 1 CAGGGAGGGT 0.974165 -16 GTTTTAATAACAGGGGGGATAGCAG 3 204 1 CAGGGGGGAT 0.986022 -15 CGTTCAATCGCAGGGGGGTTGTTCCGTTTG 5 143 0 CAGGGGGGTT 0.990204 -158 TTGCAAATGGCAGGGAGGAACAAGAA 5 285 1 CAGGGAGGAA 0.917134 -16 CATTCCAGATCAAGGGGATTTAGAAAGAAG 6 255 1 CAAGGGGATT 0.840863 -27 TAGATATTCTCAAGGAGGTTTTGAA 13 95 1 CAAGGAGGTT 0.955988 -15 ********** Masking position 2 Map Score: 3.08151 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 20 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 AACAAAACAGGGAGGGTTTATAT 2 160 1 GGAGGGTTTA 0.569057 -13 TTTAATAACAGGGGGGATAGCAG 3 206 1 GGGGGGATAG 0.863484 -13 AAACGGATACGGAGGGGTTGGC 4 181 1 GGAGGGGTTG 0.969553 -12 GTTCAATCGCAGGGGGGTTGTTCCGTTTGC 5 142 0 AGGGGGGTTG 0.629909 -159 GTATACAGGAAGAGGAGCAGGAAATAAAAT 5 182 1 AGAGGAGCAG 0.687472 -119 CAAATGGCAGGGAGGAACAAGAA 5 288 1 GGAGGAACAA 0.529488 -13 ATATTCTCAAGGAGGTTTTGAA 13 98 1 GGAGGTTTTG 0.727966 -12 GTTTTCATTAGGAGGTGAAGC 14 269 1 GGAGGTGAAG 0.849412 -11 GCTCAGTTCTGGAGGGCCAGTCCCCTTCAA 16 114 0 GGAGGGCCAG 0.971904 -187 ATGAACATCCGGAGGACTAGAGGGAAAACT 18 34 0 GGAGGACTAG 0.859118 -129 GTTCAAAAAAGGAGGGCCAACCA 20 4 0 GGAGGGCCAA 0.862475 -125 CCTAAATGGTGCAGGTGCAGGAGGAGACTC 21 153 1 GCAGGTGCAG 0.689916 -148 TTCTCTTTTAGGAGGTGATGCAGCATTTGA 21 212 1 GGAGGTGATG 0.810717 -89 TCCTTTTTATGGGGGGACTGCTGGATGAAA 21 272 0 GGGGGGACTG 0.884888 -29 ********** Masking position 5 Map Score: 4.00533 Number of sites scoring better than the average of aligned sites = 744 Number in coding regions = 574 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 9 AGGGAAGCATCATTCTCTGAACATATTTTTG 2 114 1 CATTCCTGAA 0.920311 -59 GTCCATATCATATTGTATGAAACGCATTCCA 6 231 1 TATTGATGAA 0.914328 -51 TTTTGATAGTTATTGAATGAATTTGAATGAT 14 181 1 TATTGATGAA 0.914328 -99 AACAAATTGCTATTGGCTGAAATAACAATGA 15 93 1 TATTGCTGAA 0.96931 -97 CCTTTCTGCCTATTCACTGAATCCCTGCATC 18 120 1 TATTCCTGAA 0.969311 -43 ACGGTAACAATATTCCCTGAATGGAAAGATT 20 32 1 TATTCCTGAA 0.969311 -97 ***** ***** Masking position 4 Map Score: 2.61557 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 29 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 ATATTGTATTCCTGTATATACAGGTAGTCAA 4 122 0 CCTGTATTAC 0.981989 -71 GTTTTTATAACTTGTATATACAACTTATAAT 4 154 0 CTTGTATTAC 0.89401 -39 TTCATATGAACCTGTATTAAATGGAACACCA 15 21 1 CCTGTATAAA 0.90804 -169 AAAAAATAAACCTGTATTAAAATGGTGTTCC 15 43 0 CCTGTATAAA 0.90804 -147 CAGCCTGTATATACCTTTTTTCCG 17 4 1 CCTGTATTAC 0.981989 -124 TCACTGAATCCCTGCATCTACTAGTTAGGAG 18 133 1 CCTGCATTAC 0.952236 -30 ******* *** Masking position 6 Map Score: 2.42905 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 16 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 AGCATCATTCTCTGAACATATTTTTGTATCTTAC 2 119 1 TTACATATTT 0.935321 -54 ATAAAATAAATATAATCATATTTTTTTCCGGTTC 3 122 0 TTACATATTT 0.935321 -97 ATATACAACTTATAATCATATTGTATTCCTGTAT 4 136 0 TTACATATTT 0.935321 -57 TTATAAGTTGTATATACAAGTTATAAAAACGGAT 4 155 1 TTTCAAGTTT 0.671266 -38 CGAAAGGGTTTAATTTCATGTTTTTGGTTGAGAG 6 85 1 TATCATGTTT 0.671266 -197 AGCTGTTCAGTATTTGCATATTGTAGTGTTAACA 10 31 0 TTTCATATTT 0.945008 -106 TTTTATGTCATCTTATCATGTTATTGCCCCG 11 8 0 TTACATGTTT 0.931148 -43 TGTACGACATTTTCTTCTTATTTTAATGAAAAAA 14 73 0 TTTCTTATTT 0.685876 -207 ATCTTTCACGTTTCTCCATATTAACGTATGTCTA 14 148 0 TTTCATATTA 0.810022 -132 TATGCGTATATGTTTACATGTTGAATCATTTGCA 16 165 0 TTTCATGTTA 0.799498 -136 CTGCTGTTGCTATCATCATATTATGAAATCGCTT 17 65 0 TTACATATTT 0.935321 -63 * * * ****** * Masking position 11 Map Score: 4.26109 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 104 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 12 AACGGTTTTGGGAATTTCCGCTCCTTTTAT 5 75 0 GGAATTTCCG 0.775591 -226 ATCGCAGGGGGGTTGTTCCGTTTGCTGATG 5 137 0 GGTTGTTCCG 0.96105 -164 CATTGTAACAGGTTTTACCGGTGTTTGCCT 5 238 0 GGTTTTACCG 0.972132 -63 TTGGTTGAGAGGTTTTACAGCAAGACAGCT 6 108 1 GGTTTTACAG 0.86987 -174 TCAGCCGTCCGGTTTTTCTGTATTTCATTG 12 26 1 GGTTTTTCTG 0.964407 -198 AAACACTCAGGGTTTTTCCGCAGCAACGGA 17 31 0 GGTTTTTCCG 0.987683 -97 CTAGTTAGGAGGTTTTTCTC 18 153 1 GGTTTTTCTC 0.838943 -10 ********** Masking position 6 Map Score: 3.62927 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 242 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 13 TTTCACATTTTTTATCATCCACTTACTTGTCT 1 64 0 TTATCATCAC 0.954356 -101 TTCACAATATTATATCATACAACCGTACTTGT 9 40 0 TTATCATCAA 0.876009 -58 TTTTATCATTCTCCTTTTAACTT 9 85 0 TTATCATCTC 0.975007 -13 CTTTCCAACATTTATCATCTTCACTATATCGA 12 193 0 TTATCATTTC 0.857857 -31 CAGTAAACAGTTTATCATTCTCGGGGAATGTA 16 72 0 TTATCATCTC 0.975007 -229 GAACTGAGCATCTATCATACTAATATGAGGTG 16 135 1 TTATCATCTA 0.929488 -166 * ****** *** Masking position 7 Map Score: 1.48582 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 21 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 GATTTTAGAGACGGAGACAAGTAAGTGGATG 1 50 1 ACGGAGACAG 0.947098 -115 ACACTCATCAACGGAAACGAATCAATTAAAT 3 46 0 ACGGAAACAA 0.767945 -173 AAGGAAACCCGCTGCACAGCC 5 1 1 AAGGAAACCG 0.728732 -300 GACAGCTGCCACCGAGAACAGTGAGACATAA 6 131 1 ACCGAGAAAG 0.928357 -151 TTTTAGCTGAAAGGAGAAGATCACATGGGTT 6 179 0 AAGGAGAAAT 0.583067 -103 CTATGCTTTTAACGAAACTAGAGGTGAGATG 10 114 1 AACGAAACAG 0.906156 -23 CATAAAAGATAAGGAGAACAGGTTTG 11 35 1 AAGGAGAAAG 0.934491 -16 TTCTTATTTTAATGAAAAAAGTCTTTTATAT 14 62 0 AATGAAAAAG 0.664263 -218 AGTTGCCTAAACCGAAAATAGCGTTTACAAT 14 215 1 ACCGAAAAAG 0.932687 -65 AAACACTTAAAACGAAAAAAATAAACCTGTA 15 58 0 AACGAAAAAA 0.640919 -132 TTCCGCAGCAACGGAAAAAAGGTATATACAG 17 15 0 ACGGAAAAAG 0.953423 -113 ******** ** Masking position 5 Map Score: 3.37371 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 239 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 15 TATTATACCAGAGTCCCTTCTGTTTCGTTT 1 114 0 GAGTCCCTTC 0.97325 -51 AGAGAATGATGCTTCCCTTTGACTCTATGT 2 102 0 GCTTCCCTTT 0.899565 -71 AGATTCCCTTCTTTCTAAATC 6 271 0 GATTCCCTTC 0.977419 -11 TATACATTTCGCATCCCTTCATCATCCTTT 18 95 1 GCATCCCTTC 0.978999 -68 CCTATTCACTGAATCCCTGCATCTACTAGT 18 128 1 GAATCCCTGC 0.951105 -35 ********** Masking position 4 Map Score: 0.637855 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 47 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987