AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00290_bsub_reg_100.orf -o00290_bsub_100.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 ybgE 208 similar to branched-chain amino acid aminotransferase #2 ydaO 300 similar to hypothetical proteins #3 mutT 58 mutator protein #4 ydaP 66 similar to pyruvate oxidase #5 yheM 284 similar to D-alanine aminotransferase #6 pdhA 300 pyruvate dehydrogenase (E1 alpha subunit) #7 ileS 300 isoleucyl-tRNA synthetase #8 ilvD 288 dihydroxy-acid dehydratase #9 yqiS 124 similar to phosphate butyryltransferase #10 valS 300 valyl-tRNA synthetase #11 leuC 49 3-isopropylmalate dehydratase (large subunit) #12 ilvB 300 acetolactate synthase (acetohydroxy-acid synthase) (large subunit) #13 leuS 300 leucyl-tRNA synthetase #14 alsS 154 alpha-acetolactate synthase (pH6) #15 ywaA 140 alternate gene name: ipa-0r; similar to branched-chain amino acid aminotransferase Motif number 1 GGAATCACCTTGGTCCTTTTTAGCGGGAAAA 3 26 1 TGGCCTTTTT 0.877624 -33 CCCCATACCTCCTTTTCCCGCTAAAAA 3 42 0 ACCCCTTTTC 0.864728 -17 AACGTATCCTCCTTTTTCCTTTTTTCA 4 50 0 TCCCCTTTTT 0.989222 -17 AAAAGCCCTCCCTTTTCGAGATGTCC 5 269 0 CCCCCCTTTT 0.930755 -16 ATCTCGCGGTACCACCCTTTTAGAAAAAGCA 7 209 0 ACCCCCTTTT 0.980623 -92 ATAAGCTTTCTCGTCCCTTATGGGATGAGAG 7 238 1 TCGCCCTTAT 0.690923 -63 GTGCATGATCTGCACCTTTTTTATCT 8 6 0 TGCCCTTTTT 0.957213 -283 GTGCAGATCATGCACCTTTTTTATGTGAATT 8 22 1 TGCCCTTTTT 0.957213 -267 TTGTTTCGACTCCGCCTTTTATTATGCAAGT 9 89 0 TCCCCTTTTA 0.952022 -36 CTGTTACCACCTTTCTTGTTTCGACT 9 109 0 ACCCCTTTCT 0.849713 -16 TCTCTCTGCATGCGCCTTTTTTGTACTCTTC 10 46 0 TGCCCTTTTT 0.957213 -255 CTTTCGCGGTACCACCTTTTTTCATGAACTC 10 204 0 ACCCCTTTTT 0.980547 -97 AAAGAGCTTTTCGTCCTTTTACAGGGATGAA 10 231 1 TCGCCTTTTA 0.864149 -70 CTTTTATTTCCTCCCTCTACCTAGAGCTA 11 31 0 TCCCCCTCTA 0.849913 -19 TTTCCGCGGTACCACCCTTGTTTACGGCCTG 12 137 0 ACCCCCTTGT 0.912635 -164 AAAAGCCTTTTCGCCCCTTTTAGCTATCGCA 12 169 1 TCGCCCTTTT 0.967254 -132 TTTAGTTCCTCCTTTTGGATTTTCATC 12 284 0 TCCCCTTTTG 0.955398 -17 TTCCCGCGGTACCACCCTCGTTAGCGCGGCA 13 148 0 ACCCCCTCGT 0.748074 -153 CGAAAGTCTCTCGTCCCTTTTTGGGATGAGG 13 181 1 TCGCCCTTTT 0.967254 -120 AGTAAAAACCTCCTTCTGATTGAATACG 13 283 0 ACCCCTTCTG 0.769803 -18 TTTCTCCTGCTTTTTTCATATGAAT 15 5 1 TCCGCTTTTT 0.843984 -136 *** ******* Masking position 8 Map Score: 30.6492 Number of sites scoring better than the average of aligned sites = 760 Number in coding regions = 466 Number in noncoding regions = 294 Number of orfs with sites within 600 bp upstream = 338 Fraction of orfs with sites within 600 bp upstream = 0.0542885 Motif number 2 TGATACTTTAGGGTACCCTAAGTTTGTATGTATAAAAGG 6 225 1 GGGCCATTTT 0.818596 -76 GTGAGAGTCCGGGATGGCCGGAATCATGTAGATCAGCCC 7 93 1 GGGGGGTCTT 0.932616 -208 CATCCCATAAGGGACGAGAAAGCTTATCTCGCGGTACCA 7 226 0 GGGGAATTTT 0.987508 -75 CGTCCCTTATGGGATGAGAGGGCTTTTTTTATTTTCTGA 7 249 1 GGGGAGTTTT 0.993393 -52 AACAAGGTGAGGGCGGCCTGTATTTATCTTATTTGCAAA 8 185 1 GGGGCGTTTT 0.986576 -104 TCCTTTTACAGGGATGAAGAGCTCTTTTTTCGTTCTCAG 10 244 1 GGGGAACTTT 0.937056 -57 ATAGCTAAAAGGGGCGAAAAGGCTTTTCTTTCCGCGGTA 12 157 0 GGGGAATTTT 0.987508 -144 GGCTGATTGTGGGCGGAAGGGCTTTTTTTATTGAATAAT 12 210 1 GGGGAGTTTT 0.993393 -91 ATCCCAAAAAGGGACGAGAGACTTTCGTTTTCCCGCGGT 13 169 0 GGGGAGTTGT 0.965888 -132 GTCCCTTTTTGGGATGAGGGAGTTTTTTTTAGTTTGGGA 13 193 1 GGGGAGTTTT 0.993393 -108 AAGTATTGACGGGAAGGAGAGGATTATATTCAGAATATT 13 231 0 GGGGGATTTT 0.974774 -70 *** ** * ** * * Masking position 19 Map Score: 16.3929 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 45 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 3 AATTAAAGAAAACAGCCAGTTTTATTCTGGC 1 19 0 AACAGCCGTT 0.80838 -190 GCAAAAAGTATACAGCCTTTCCTTTAATAAT 1 134 0 TACAGCCTTC 0.898729 -75 CCCAACGGCAAAAAGCCGTTCTATT 2 5 0 AAAAGCCTTC 0.98559 -296 CTCCGGGTTTTAAAGCCTTTCTCCTGTGGTA 4 18 1 TAAAGCCTTC 0.939876 -49 AAAAGCCCTCCCTTTTCGAGA 5 274 0 AAAAGCCTCC 0.96074 -11 AATCATGTAGATCAGCCCTTTAGTTTCCTTG 7 114 1 ATCAGCCTTT 0.77712 -187 AGAAAATAAAAAAAGCCCTCTCATCCCATAA 7 255 0 AAAAGCCTCT 0.932718 -46 ATGCAGAGAGAGAAGCCGTTTGCTGAAAGGC 10 66 1 AGAAGCCTTT 0.938874 -235 AGACAACATAAGAAGCCTTTCAGCAAACGGC 10 80 0 AGAAGCCTTC 0.957741 -221 TAAAAGGACGAAAAGCTCTTTCGCGGTACCA 10 221 0 AAAAGCTTTT 0.760655 -80 CCGCGGAAAGAAAAGCCTTTTCGCCCCTTTT 12 159 1 AAAAGCCTTT 0.69607 -142 ATTCAATAAAAAAAGCCCTTCCGCCCACAAT 12 215 0 AAAAGCCTTC 0.98559 -86 ******* *** Masking position 4 Map Score: 16.0661 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 249 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 4 TTTGCCGTTGGGGTGAATCCTTTTTAGGTA 2 24 1 GGGTGAATCC 0.879446 -277 AAAAGGACCAAGGTGATTCCCTTGGTCCTA 3 16 0 AGGTGATTCC 0.940893 -43 TTTTCTAAAAGGGTGGTACCGCGAGATAAG 7 213 1 GGGTGGTACC 0.99584 -88 GAAACAAGAAAGGTGGTAACAG 9 113 1 AGGTGGTAAC 0.912691 -12 AACGGATAACGGGTGTTTCCCGAATTTCTC 10 155 0 GGGTGTTTCC 0.958495 -146 TCATGAAAAAAGGTGGTACCGCGAAAGAGC 10 208 1 AGGTGGTACC 0.98943 -93 CCGTAAACAAGGGTGGTACCGCGGAAAGAA 12 141 1 GGGTGGTACC 0.99584 -160 GCGCTAACGAGGGTGGTACCGCGGGAAAAC 13 152 1 GGGTGGTACC 0.99584 -149 ********** Masking position 4 Map Score: 15.5292 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 16 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 AAGCGTTCGTGAGAGGAGATGAATGAAACCT 2 95 1 GAGAGAGATG 0.673576 -206 CCTTTTTAGCGGGAAAAGGAGGTATGGGG 3 40 1 GGGAAAGGAG 0.78156 -19 TTTAAAAGAAAGGAAGAGGTGACTTAGT 6 283 1 AGGAGAGGTG 0.78171 -18 CATCCCATAAGGGACGAGAAAGCTTATCTCG 7 234 0 GGGAGAGAAA 0.94367 -67 CGTCCCTTATGGGATGAGAGGGCTTTTTTTA 7 249 1 GGGAGAGAGG 0.9886 -52 TCCCTGTAAAAGGACGAAAAGCTCTTTCGCG 10 227 0 AGGAGAAAAG 0.779942 -74 TCCTTTTACAGGGATGAAGAGCTCTTTTTTC 10 244 1 GGGAGAAGAG 0.965224 -57 TCTAGGTAGAGGGAGGAAATAAAAG 11 35 1 GGGAGAAATA 0.805814 -15 GTGGTACCGCGGAAAGAAAAGCCTTTTCGCC 12 153 1 GGAAGAAAAG 0.779942 -148 ATAGCTAAAAGGGGCGAAAAGGCTTTTCTTT 12 165 0 GGGGGAAAAG 0.827973 -136 GGCTGATTGTGGGCGGAAGGGCTTTTTTTAT 12 210 1 GGGCGAAGGG 0.854541 -91 ATCCCAAAAAGGGACGAGAGACTTTCGTTTT 13 177 0 GGGAGAGAGA 0.957414 -124 GTCCCTTTTTGGGATGAGGGAGTTTTTTTTA 13 193 1 GGGAGAGGGA 0.953376 -108 AGTATTGACGGGAAGGAGAGGATTATATTCA 13 238 0 GGAAGAGAGG 0.909685 -63 **** ****** Masking position 7 Map Score: 13.2156 Number of sites scoring better than the average of aligned sites = 504 Number in coding regions = 408 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 6 AAAGCTTATCTCGCGGTACCACCCTTTTAG 7 217 0 TCGCGGTACC 0.96651 -84 TAAATACAGGCCGCCCTCACCTTGTTTTGT 8 181 0 CCGCCCTCAC 0.937358 -108 AAAAGCTCTTTCGCGGTACCACCTTTTTTC 10 212 0 TCGCGGTACC 0.96651 -89 GCTTTTCTTTCCGCGGTACCACCCTTGTTT 12 145 0 CCGCGGTACC 0.992137 -156 ACAATCAGCCGCGCAGTAACTGCGATAGCT 12 190 0 GCGCAGTAAC 0.880451 -111 AAGTTTGTTTCCGAACTCACCTCAGAGTTG 13 59 1 CCGAACTCAC 0.71436 -242 GCGGCATACGCCGCACTCACTTGATACTTT 13 124 0 CCGCACTCAC 0.962279 -177 GCGGCGTATGCCGCGCTAACGAGGGTGGTA 13 140 1 CCGCGCTAAC 0.987519 -161 TTTCGTTTTCCCGCGGTACCACCCTCGTTA 13 156 0 CCGCGGTACC 0.992137 -145 ********** Masking position 7 Map Score: 10.916 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 104 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 TGAACAACAAAAAACACAGAGGCAAACGGAT 2 151 0 AAACACAGAG 0.662647 -150 CAGAGACATCATAGCAGAAAGGACTATCATC 2 203 1 AAGCAGAAAG 0.969937 -98 ATGAGAAATTAAAAGGGGAAGACATCG 2 284 1 AAAGGGGAAG 0.761447 -17 TTTCAATACCACAGGAGAAAGGCTTTAAAAC 4 24 0 AAGGAGAAAG 0.937359 -43 GGTATTGAAAAAAGGAAAAAGGAGGATACGT 4 45 1 AAGGAAAAAG 0.654374 -22 ATAATGCTGTACAGCAGGCAGCTTATGAAGA 5 42 1 AAGCAGGCAG 0.834372 -243 ATAAAACTGGAAAGCACATAGAAAATTTGTC 5 118 1 AAGCACATAG 0.695315 -167 CAAGAGATCTATAGCGGAAAGGAGTTTATTT 5 171 0 AAGCGGAAAG 0.969329 -114 GACAAGCTGAAAAACAGAAAGATCAAGAGAT 5 194 0 AAACAGAAAG 0.903693 -91 AATACAGTTCAAAGCAGAGTGTAACTATCCT 6 139 1 AAGCAGAGTG 0.669651 -162 ACGATGCTCAAGAGGAAAAAGTGTATGCTTG 7 180 1 AAGGAAAAAG 0.654374 -121 CTTGCATAATAAAAGGCGGAGTCGAAACAAG 9 90 1 AAAGGCGGAG 0.400541 -35 ACACCTGCTTAGAACGGGAAGAGTACAAAAA 10 29 1 AAACGGGAAG 0.873129 -272 ACTCGTTACTAAAGCGGATAGAAATATCCAT 12 91 1 AAGCGGATAG 0.8869 -210 CAAGGGTGGTACCGCGGAAAGAAAAGCCTTT 12 148 1 ACGCGGAAAG 0.800319 -153 AAACAATTTAACAGCAGGGAGATTGACC 15 123 1 AAGCAGGGAG 0.946631 -18 * ********* Masking position 1 Map Score: 9.66664 Number of sites scoring better than the average of aligned sites = 1243 Number in coding regions = 1068 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 8 AAGTATACAGCCTTTCCTTTAATAATACGCC 1 129 0 CCTTTCCTTA 0.931882 -80 AATCAGCACACCTTTCACATAATTGTTTAAA 1 185 0 CCTTTCAATA 0.756999 -24 TGATGATAGTCCTTTCTGCTATGATGTCTCT 2 204 0 CCTTTCTCTA 0.943403 -97 GGTTTTAAAGCCTTTCTCCTGTGGTATTGAA 4 23 1 CCTTTCTCTG 0.884671 -44 AAAATAAACTCCTTTCCGCTATAGATCTCTT 5 170 1 CCTTTCCCTA 0.971773 -115 GTCACCTCTTCCTTTCTTTTAAACAGTCATT 6 275 0 CCTTTCTTTA 0.868832 -26 CATGACTGTCCCTTTCAACCGTTTTTTCATC 7 29 0 CCTTTCACCG 0.923254 -272 TCGATTTGAACCCTCCAACTATTAATATTGT 8 117 0 CCCTCCACTA 0.754517 -172 ACATAAGAAGCCTTTCAGCAAACGGCTTCTC 10 75 0 CCTTTCACAA 0.898304 -226 TCCCGGGCGACCTTCCAATCAGACAACATAA 10 100 0 CCTTCCATCA 0.873225 -201 CCTTTTCGCCCCTTTTAGCTATCGCAGTTAC 12 174 1 CCTTTTACTA 0.659204 -127 TAAAAAAAGCCCTTCCGCCCACAATCAGCCG 12 209 0 CCTTCCGCCA 0.842111 -92 ATAATCCTCTCCTTCCCGTCAATACTTGAAC 13 243 1 CCTTCCCTCA 0.881832 -58 AATATGCATTCCTTTCCATAGGTTAATAATT 14 13 1 CCTTTCCTAG 0.63637 -142 ******* *** Masking position 4 Map Score: 8.57906 Number of sites scoring better than the average of aligned sites = 360 Number in coding regions = 264 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 9 ATAGCAGAAAGGACTATCATCAACATGTGAG 2 213 1 GGATATCATC 0.922483 -88 CGGCCATCCCGGACTCTCACCATCTCCGGGT 7 82 0 GGATCTCACC 0.968252 -219 CAGTAGGTTAGGACGTTCATCACGTTACGAT 7 154 1 GGAGTTCATC 0.956285 -147 AAAGAATTTAGGAGGATCACC 8 278 1 GGAGATCACC 0.958979 -11 TCCTCCTTTTGGATTTTCATCCTTTAAAGAT 12 274 0 GGATTTCATC 0.970159 -27 CAAACTTGATTGACTTTCACCAGCCGTCAAC 13 35 0 TGATTTCACC 0.906757 -266 ATGCGTCAGCGGCTTTTCACCGCTGCAACTC 13 83 0 GGCTTTCACC 0.958623 -218 TACACTCTTTGGAAATTGACCTCCAATATCG 14 72 0 GGAATTGACC 0.92882 -83 TTAACAGCAGGGAGATTGACC 15 130 1 GGAATTGACC 0.911779 -11 *** ******* Masking position 7 Map Score: 5.82805 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 144 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 10 TTCCTTTAATAATACGCCGCTTCACACCTA 1 117 0 AATACGCCGC 0.966089 -92 CCCCAACGGCAAAAAGCCGTTCTATT 2 7 0 AAAAAGCCGT 0.81051 -294 ATAAGATAAATACAGGCCGCCCTCACCTTG 8 187 0 TACAGGCCGC 0.951593 -102 ACGGCCTGTTAATCGGCCGTCTCATGGATA 12 115 0 AATCGGCCGT 0.948058 -186 ACGGCCGATTAACAGGCCGTAAACAAGGGT 12 125 1 AACAGGCCGT 0.972298 -176 TTCCGCCCACAATCAGCCGCGCAGTAACTG 12 198 0 AATCAGCCGC 0.937282 -103 GATTGACTTTCACCAGCCGTCAACTCTCTG 13 29 0 CACCAGCCGT 0.925314 -272 GTTAGCGCGGCATACGCCGCACTCACTTGA 13 130 0 CATACGCCGC 0.950423 -171 ACTTGAACCATACACGCCGTATTCAATCAG 13 266 1 TACACGCCGT 0.938534 -35 ********** Masking position 2 Map Score: 5.45271 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 313 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 AAGAAAACAGCCAGTTTTATTCTGGCTGTTTGAT 1 11 0 CGTTTTTTCG 0.98174 -198 ACATCGAACACAGGTTTCATTCATCTCCTCTCAC 2 103 0 CGTTTCTTCT 0.973623 -198 TATGTGCTTTCCAGTTTTATTCCTGTATACTTGA 5 104 0 CGTTTTTTCT 0.978033 -181 AAGGGACAGTCATGTTTCCTTCAGGCCTTCATAG 7 46 1 CGTTTCTTCG 0.978058 -255 CCGCCCTCACCTTGTTTTGTTCTTTCGTGTTTTT 8 167 0 CGTTTTTTCT 0.978033 -122 GAAAGTCAATCAAGTTTGTTTCCGAACTCACCTC 13 48 1 CGTTTGTTCG 0.96035 -253 TTTCTCCTGCTTTTTTCATATGAATTTCT 15 6 1 CGCTTTTTCT 0.931971 -135 * ***** *** * Masking position 7 Map Score: 4.84101 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 100 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 12 TTTTTAAAGCTGCAAAAAGTATACAGCCTTTCCTT 1 141 0 TAAAGTATCA 0.889258 -68 CATTTTTGAATGCAAATCGCATACAGAGACATCAT 2 180 1 TAAAGCATCA 0.956614 -121 AATGAGAAATTAAAAGGGGAAGACATCG 2 283 1 TAAGGAAGCA 0.839804 -18 ATACATAGGTTGTAAACATAAGGCATCTTCATAAG 5 63 0 TAAATAAGCA 0.812922 -222 TATACAGGAATAAAACTGGAAAGCACATAGAAAAT 5 109 1 TAACGAAACA 0.772163 -176 TTGATGAAAATGTAAAGCGAATACATTTATTGAAA 6 11 1 TAAAGAATCA 0.980921 -290 TTCGAAGTTGTAAAAAACTAATACAACACCGCTTA 6 102 0 TAAATAATCA 0.898888 -199 AGTTTGTATGTATAAAAGGAATGCACGTCTAATGA 6 245 1 TAAAGAATCA 0.980925 -56 ACCACCCTTTTAGAAAAAGCAAGCATACACTTTTT 7 195 0 TAAAGCAACA 0.874807 -106 ATAATTTTTATAAAAAGTGAATTCACATAAAAAAG 8 37 0 TAAAGAATCA 0.980926 -252 CTGAAAATTGTCAAAATAAAATCCAATCAAACAAT 8 241 1 TAAAAAATCA 0.83448 -48 * *** **** ** Masking position 5 Map Score: 4.29927 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 184 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 13 ********** No masking Map Score: 3.98147e-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 CTGATGATCCTAAAGAATATTCTGAAATTTATAGG 1 86 1 TAAAATTTGA 0.963583 -123 ACTGAATATTTAAACAATTATGTGAAAGGTGTGCT 1 177 1 TAAAATATGA 0.9531 -32 GGGGATCGGCTAAAATATAATACGACTTACTGCTG 6 192 1 TAAATTATGA 0.808392 -109 TCCTTTCTTTTAAACAGTCATTAGACGTGCATTCC 6 262 0 TAAAATATGA 0.953098 -39 TCACTTTTTATAAAAATTATTTCGAATATTGTTGA 8 52 1 TAAAATTTGA 0.963526 -237 TTACTTACTATAAATAGTTTTCGGATATTTTTCAA 8 83 0 TAAAATTTGA 0.963585 -206 TAAGTTTCACTATACACTCTTTGGAAATTGACCTC 14 80 0 TATAATTTGA 0.846 -75 **** * * ** ** Masking position 4 Map Score: 1.36822 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 38 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 15 TTGAACTGTATTATTTCGAAGTTGTAAAAAA 6 120 0 TTATTTCGAG 0.782505 -181 TTTATAAAAATTATTTCGAATATTGTTGAAA 8 58 1 TTATTTCGAT 0.921214 -231 TTATATAGCTTTCTTTCGATTTGAACCCTCC 8 132 0 TTCTTTCGAT 0.977201 -157 CCTTGTTTTGTTCTTTCGTGTTTTTATATTT 8 161 0 TTCTTTCGTT 0.884808 -128 TCCTCCTAAATTCTTTCAATTGTTTGATTGG 8 263 0 TTCTTTCAAT 0.943676 -26 ACCACCTTTCTTGTTTCGACTCCGCCTTTTA 9 99 0 TTGTTTCGAT 0.907645 -26 TTCTCTACTCTTCTTTCAAGAAATTATGCTC 10 129 0 TTCTTTCAAA 0.776702 -172 TCATATGAATTTCTTACAAATTTGAGCAAAC 15 26 1 TTCTTACAAT 0.750155 -115 ********* * Masking position 5 Map Score: 0.621261 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 160 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159