AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00330_bsub_reg_100.orf -o00330_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 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #2 ycbD 29 similar to aldehyde dehydrogenase #3 amhX 300 amidohydrolase #4 yclB 89 similar to phenylacrylic acid decarboxylase #5 argC 206 N-acetylglutamate gamma-semialdehyde dehydrogenase #6 carA 70 carbamoyl-phosphate transferase-arginine (subunit A) #7 ykrV 94 similar to aspartate aminotransferase #8 yluA 130 similar to hypothetical proteins #9 yluB 61 similar to hypothetical proteins #10 proS 32 prolyl-tRNA synthetase #11 ynaD 300 similar to hypothetical proteins #12 kdgK 37 2-keto-3-deoxygluconate kinase #13 kdgR 221 transcriptional regulator (LacI family) #14 aspB 22 aspartate aminotransferase #15 ypmA 142 ypmA #16 argG 169 argininosuccinate synthase #17 yugG 147 similar to transcriptional regulator (Lrp/AsnC family) #18 ywiB 300 ywiB #19 ywhG 60 similar to agmatinase #20 ywhF 201 similar to spermidine synthase #21 ywfB 151 alternate gene name: ipa-80d #22 rocA 226 pyrroline-5 carboxylate dehydrogenase #23 ywdH 167 alternate gene name: ipa-58r; similar to aldehyde dehydrogenase #24 aldX 142 aldehyde dehydrogenase #25 rocF 73 arginase #26 rocE 222 amino acid permease #27 rocD 240 ornithine aminotransferase Motif number 1 AGTGATTTACCGCTTTTTTATAAAATATCAGA 1 66 1 CGCTTTTTAA 0.970171 -161 TATCTGTAAGCGCTTTTATTAATTTTTCTTTC 1 170 0 CGCTTTTATA 0.819651 -57 GCCCCTTTCGTGTTTTTTCTGG 2 1 0 TGTTTTTTTG 0.766535 -29 AAATGTCATACGTTTTTTCTTAGGCTGTGTTT 3 111 1 CGTTTTTTTA 0.941925 -190 GCGGTCAGCCTGTTTTTTTATGCGGCTGAAAT 5 12 1 TGTTTTTTAG 0.835524 -195 GCGGGAAATCCGCTTTTAAATAAAACACCATC 15 47 0 CGCTTTTAAA 0.875493 -96 AAGTACGTTTCGTTTTTTCAAGCCTTTTATAA 16 59 0 CGTTTTTTAG 0.953678 -111 CTGTGTCACTCCCTTTTTTTGATGGTTGTATT 17 12 1 CCCTTTTTTA 0.861249 -136 AGTTTCTCCTCGTTTTTTCTTAGCATTCGTCA 17 72 1 CGTTTTTTTA 0.941925 -76 CATTATATCACGTTTTTTGACGAATGCTAAGA 17 89 0 CGTTTTTTAG 0.953678 -59 TATAAGGAAATGCTTTTTATGAGGTTTATCTT 18 175 1 TGCTTTTTTA 0.838367 -126 GCGAATCTTGCGCTTTTTTACAGGAAAGCGAG 19 29 1 CGCTTTTTAA 0.970171 -32 ACGGGTTCCCCCTTTTTTTATGTTTCTACTAT 20 12 1 CCTTTTTTAG 0.858741 -190 AAAAAAAGATCGTTTTTAAACATCGCAGAACA 20 50 1 CGTTTTTAAA 0.8441 -152 TAATTAAAAACCCTTTTTAAAGGGTTTTTTTG 21 31 1 CCCTTTTTAG 0.887376 -121 GAACTGTCAATGTTTTTTGAAAATATTGATAA 21 78 0 TGTTTTTTAA 0.860952 -74 TCCGTTTCTCCTTTTTGTAAGGTATGGTGA 23 148 0 TCCTTTTTTA 0.604987 -20 ATATCCTCTCCGTTTTTTTATAAAATAGAAGC 27 45 0 CGTTTTTTAA 0.961677 -196 ******** * * Masking position 6 Map Score: 20.7853 Number of sites scoring better than the average of aligned sites = 925 Number in coding regions = 795 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 2 TTCTGATAGAAGGAGGTATTTCTTACC 3 284 1 AGGAGGTTTT 0.881781 -17 TGTAAACATGAGAGGGTCTTTTCACTATTAT 8 31 0 AGAGGGTTTT 0.881781 -100 TCATGTTTACAGGGGGTTTTTTTGTTAATAC 8 51 1 AGGGGGTTTT 0.98332 -80 TTGTAAGAGGATGTTTGTTTAATTCT 11 6 1 AGAGGATTTT 0.704339 -295 GAGGGGTAATATGGGGAATTTATGACAAAAC 11 105 0 ATGGGGATTT 0.866249 -196 AGAGAAGGATAGGGGGATTATTTTGGAGAAT 11 136 1 AGGGGGATAT 0.952074 -165 GACGAATTAGGGGGAGTTCAAG 14 9 1 AGGGGGATTC 0.979755 -14 CCTAAATTTCAGGTGAAGTTTCATAGTATTT 16 17 0 AGGTGAATTT 0.822236 -153 CCTGAAATTTAGGTGAAGTTTTTTTTATAAA 16 35 1 AGGTGAATTT 0.822236 -135 CACGGTTGAGAGGGGATTTTTATC 16 156 1 AGGGGATTTT 0.949567 -14 TGTCAATTCTAGCGGAAGTTTCTCCTCGTTT 17 56 1 AGCGGAATTT 0.877371 -92 TCATAACACGAGGGGGACTACAT 22 214 1 AGGGGGATAC 0.893608 -13 CTGCGTTTTCAGCAGGAATTTGATAAAATGC 23 46 0 AGCAGGATTT 0.7392 -122 AAAGCAAATGAGGGGGATTTTACA 24 129 1 AGGGGGATTT 0.991339 -14 ACAGAAAACAAGGGGGAATTCAAAT 27 226 1 AGGGGGATTC 0.979755 -15 ******* *** Masking position 1 Map Score: 19.4925 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 162 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 3 AGTCGTGCTGATTTTTTTTGAGCGGAATTCC 5 73 1 ATTTTTTTGA 0.900264 -134 TATATTTAATATTTTTATTCATTTATAAATT 5 116 0 ATTTTTATCA 0.963121 -91 GATTGAATTAATTTTTATTCATGTTATAATG 5 148 1 ATTTTTATCA 0.963121 -59 ATAAAAATGAATTTTTATGCCTTTATATCGA 6 18 0 ATTTTTATCC 0.867038 -53 TCATTTCAAGATTTTTTTAGAAGGTGAGAAT 7 72 1 ATTTTTTTGA 0.900264 -23 CACTACTCCTATTCTTATTGCTGCATGATCA 9 35 0 ATTCTTATGC 0.590175 -27 CTTTAAAACTATTCTTATTCAACAATATTGC 11 220 0 ATTCTTATCA 0.910811 -81 TTACCAAAATATTTTCATTCAAGTGATGCTG 13 36 0 ATTTTCATCA 0.867038 -186 TTATCCTAAAATTTTCTTTGAAACCGTTACC 13 62 0 ATTTTCTTGA 0.692675 -160 TACAAAATGTATTTTTATTAAATATAATTTA 16 106 1 ATTTTTATAA 0.800929 -64 AATATAATTTATTTTTATACAAAATAGAAAC 16 126 1 ATTTTTATCA 0.963121 -44 TCCTTTTCACATTTTTTTCAAAATATATGTA 18 79 0 ATTTTTTTAA 0.711182 -222 ATTTTAAGTAAATTTTATCCAGTGGAAATTG 21 109 0 AATTTTATCA 0.69084 -43 TGATTCTTGCATTTTTATTCATATGCGAAGA 22 177 1 ATTTTTATCA 0.963121 -50 GACAACATTTATTTTTTTGGAGGGTGCTTC 23 10 0 ATTTTTTTGA 0.900264 -158 CAAGTGCAAAATTCTTTTGCATATCCTCTCC 27 66 0 ATTCTTTTCA 0.862071 -175 ******** ** Masking position 5 Map Score: 15.2338 Number of sites scoring better than the average of aligned sites = 245 Number in coding regions = 176 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 4 GATTCTGCGCAGCAAAAAAACAGCCTGGTC 1 26 0 AGCAAAAAAA 0.93772 -201 AACACAGCCTAAGAAAAAACGTATGACATT 3 112 0 AAGAAAAAAC 0.739591 -189 GCACGACTCCAGCACAAAAACGTTGATGCG 5 51 0 AGCACAAAAA 0.703683 -156 ATTCCCATTGAACAGAAAATTTATAAATGA 5 99 1 AACAGAAAAT 0.519311 -108 CAACAGTATTAACAAAAAAACCCCCTGTAA 8 57 0 AACAAAAAAA 0.952629 -74 GAAAAGAGTCAACGAAAAAATAATGAATTG 13 98 1 AACGAAAAAA 0.705356 -124 AAACCGTTACAACAAAAGAATACCATAATT 13 162 0 AACAAAAGAA 0.824358 -60 TAATACAACCATCAAAAAAAGGGAGTGACA 17 15 0 ATCAAAAAAA 0.699633 -133 GACGAATGCTAAGAAAAAACGAGGAGAAAC 17 73 0 AAGAAAAAAC 0.739591 -75 CTGCTAGAAAAACAAAAAAAGG 18 3 0 AACAAAAAAA 0.952629 -298 TAATAGTAGAAACATAAAAAAAGGGGGAAC 20 16 0 AACATAAAAA 0.681533 -186 TTCCCATACAAACAAAAAAACCCTTTAAAA 21 45 0 AACAAAAAAA 0.952629 -107 TTGCTCTTTACGCAAAAAACAAATGCAAAA 22 34 0 CGCAAAAAAC 0.637123 -193 TTGCGTAAAGAGCAAAAAACGCAAAATAAA 22 49 1 AGCAAAAAAC 0.936504 -178 AAGTTTTTTCAGCAAAAGACAAGAAAATGG 22 145 1 AGCAAAAGAC 0.774888 -82 ATAAATTTACAACAGAAAAATCAGCACTCC 26 45 1 AACAGAAAAA 0.894765 -178 AACATGTTGAAACAGAAAACAAGGGGGAAT 27 215 1 AACAGAAAAC 0.892807 -26 ********** Masking position 6 Map Score: 13.479 Number of sites scoring better than the average of aligned sites = 861 Number in coding regions = 634 Number in noncoding regions = 227 Number of orfs with sites within 600 bp upstream = 211 Fraction of orfs with sites within 600 bp upstream = 0.0338901 Motif number 5 TTCAATATAAATAAAGTAAAGAAGGTAAAAAT 3 249 1 ATAAGAAAGA 0.918244 -52 GGTTAAATGAAAAAAGTAAAGAAAAATTTGGG 7 22 0 AAAAGAAAGA 0.936674 -73 ACAATAGATAATAGTGAAAAGACCCTCTCATG 8 24 1 ATAGGAAAGA 0.881619 -107 TTTAGGATAAATAGTGAAAAGAGTCAACGAAA 13 83 1 ATAGGAAAGA 0.881619 -139 CAACGAAAAAATAATGAATTGACATATTATTA 13 107 1 ATAAGATTGA 0.751309 -115 AACCATCAAAAAAAGGGAGTGACACAGA 17 7 0 AAAAGAGTGA 0.7698 -141 AAAACGTGATATAATGTCATGAGATTTCTTGA 17 105 1 ATAAGCATGA 0.823727 -43 AAAAAATGTGAAAAGGAAATGATAGATTTCGG 18 93 1 AAAAGAATGA 0.951171 -208 TCTCTTCTATATAAGGAAATGCTTTTTATGAG 18 166 1 ATAAGAATGC 0.683311 -135 TATTCAAGTCAAAGTGGAATGATGAAAAGGAC 18 271 1 AAAGGAATGA 0.928143 -30 GATGGCGGGGAAAAAGTAAAGATGCGTCCTGT 20 79 0 AAAAGAAAGA 0.936674 -123 TCACCTAAGGAAAAAGTATAGAGGATGGCGGG 20 102 0 AAAAGATAGA 0.751309 -100 TACAGCCTCGAAAGGGAGATGACAA 20 187 1 AAAGGGATGA 0.689186 -15 AAAAGACAAGAAAATGGCATGATTCTTGCATT 22 158 1 AAAAGCATGA 0.860222 -69 **** * ***** Masking position 3 Map Score: 9.36765 Number of sites scoring better than the average of aligned sites = 342 Number in coding regions = 274 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 6 CATGTTTACAGGGGGTTTTTTTGTTAATACT 8 52 1 GGGGGTTTTT 0.89525 -79 AGGGGTAATATGGGGAATTTATGACAAAACT 11 104 0 TGGGGATTTA 0.893507 -197 GAGAAGGATAGGGGGATTATTTTGGAGAATC 11 137 1 GGGGGATATT 0.934154 -164 CCTAACCAAGGGGGAAATATA 13 1 0 GGGGAATATA 0.898378 -221 GACGAATTAGGGGGAGTTCAAG 14 10 1 GGGGGATTCA 0.986032 -13 ACGGTTGAGAGGGGATTTTTATC 16 157 1 GGGGATTTTA 0.841912 -13 CATAACACGAGGGGGACTACAT 22 215 1 GGGGGATACA 0.973706 -12 AAGCAAATGAGGGGGATTTTACA 24 130 1 GGGGGATTTA 0.988451 -13 CAGAAAACAAGGGGGAATTCAAAT 27 227 1 GGGGGATTCA 0.986032 -14 ****** **** Masking position 8 Map Score: 9.95191 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 56 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 7 ATATGTGCTATATTATATACAGCCTATCTTC 3 214 1 TATTATATAA 0.466725 -87 ACCTTTTAGGTATTAATTATAGATTTAATAG 4 32 1 TATTAATTAA 0.604707 -58 GATATATCCATATGAAAAATATCTATTAAAT 4 54 0 TATGAAAAAA 0.902448 -36 TGAATAAAAATATTAAATATACGATTGAATT 5 126 1 TATTAAATAA 0.904784 -81 TAATCAACAGTATTAACAAAAAAACCCCCTG 8 60 0 TATTAACAAA 0.554389 -71 ATTGACATATTATTAAAAAAACTCTTCCCAA 13 124 1 TATTAAAAAA 0.894803 -98 GTTTCAAATATATGAGATACAGGAGCACTTG 13 200 1 TATGAGATAA 0.721471 -22 GGAAATCCGCTTTTAAATAAAACACCATCCT 15 45 0 TTTTAAATAA 0.59059 -98 TCAAGCCTTTTATAAAAAAAACTTCACCTAA 16 43 0 TATAAAAAAA 0.678991 -127 AATGTATTTTTATTAAATATAATTTATTTTT 16 111 1 TATTAAATAA 0.904784 -59 ATACATATATTTTGAAAAAAATGTGAAAAGG 18 78 1 TTTGAAAAAA 0.58282 -223 TTTCTACTATTATGAGAAAAAAAGATCGTTT 20 34 1 TATGAGAAAA 0.698071 -168 TATCTTCGCATATGAATAAAAATGCAAGAAT 22 179 0 TATGAATAAA 0.615951 -48 CCCCTCGTGTTATGAAATATATCTTCGCATA 22 198 0 TATGAAATAA 0.912058 -29 GTGAATTTTATATTAAATAGATAGAGACTCT 26 125 1 TATTAAATAA 0.905318 -98 ATAGAAGCAATATTAAGAAAATAATTGAGGG 27 22 0 TATTAAGAAA 0.554389 -219 TCCGTTTTTTTATAAAATAGAAGCAATATTA 27 38 0 TATAAAATAA 0.703495 -203 ********* * Masking position 5 Map Score: 7.8466 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 193 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 8 TTTCTTTCACATCCGCTCCTTCCCATATATC 1 147 0 ATCCCTCCTT 0.975741 -80 ATTTCGATCCATCCCCTCTGTTTGAAAATAT 3 162 1 ATCCCTCTGT 0.79445 -139 CTATTCTCACCTTCTAAAAAAAT 7 82 0 ATTCCACCTT 0.94249 -13 TTGATTCACACCTTTGCAATGTCA 17 134 0 ATTCCACCTT 0.94249 -14 AAAGCGCAAGATTCGCTCCTGCGCCATACCT 19 14 0 ATTCCTCCTG 0.879511 -47 ATCCGCACCATGGCGGGATAT 26 1 1 ATCCCACCAT 0.838846 -222 ATGGCGGGATATTCACTTCGTTTGTATAAAT 26 20 1 ATTCCTTCGT 0.857752 -203 TTAATATAAAATTCACTTCTTCTCATAAAGA 26 110 0 ATTCCTTCTT 0.860178 -113 TCTTTTGCATATCCTCTCCGTTTTTTTATAA 27 54 0 ATCCCTCCGT 0.975263 -187 **** ****** Masking position 2 Map Score: 5.00647 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 124 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 9 ATATATGGTTAAATGAAAAAAGTAAAGAAA 7 30 0 AAATGAAAAA 0.667978 -65 TCCTGTAAAAAAGCGCAAGATTCGCTCCTG 19 24 0 AAGCGCAAGA 0.903541 -37 CGCAAAAAACAAATGCAAAATTATTTTGCG 22 24 0 AAATGCAAAA 0.96231 -203 AAAGAGCAAAAAACGCAAAATAAATTTGCG 22 55 1 AAACGCAAAA 0.941149 -172 ATATGAATAAAAATGCAAGAATCATGCCAT 22 171 0 AAATGCAAGA 0.959805 -56 GAATTTGATAAAATGCAGGAAGACAACATT 23 32 0 AAATGCAGGA 0.901619 -136 TTCCTGCTGAAAACGCAGATATGAGTTTGT 23 59 1 AAACGCAGAT 0.603629 -109 AACGGAGAGGATATGCAAAAGAATTTTGCA 27 63 1 ATATGCAAAA 0.782242 -178 AAATTTCAGCAAGTGCAAAATTCTTTTGCA 27 76 0 AAGTGCAAAA 0.941148 -165 TTCGAGGACAAGGTGCAAAAACATTCTGAT 27 117 0 AGGTGCAAAA 0.769324 -124 CCCTTTATATAAATGCAAGTTCTGTGCCAA 27 175 0 AAATGCAAGT 0.855582 -66 ********** Masking position 7 Map Score: 4.68396 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 243 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 10 ATAAGTCAATATCTTTATTTTCTGATATTT 1 88 0 ATCTTTATTT 0.85614 -139 TATTGACTTATTGTTTATTTGTCTTACAAT 1 107 1 TTGTTTATTT 0.853612 -120 ATATATCCTTTTGTTTAATTGTAAGACAAA 1 124 0 TTGTTTAATT 0.717253 -103 AATTTTTACCTTCTTTACTTTATTTATATT 3 252 0 TTCTTTACTT 0.927967 -49 CCCCAAATTTTTCTTTACTTTTTTCATTTA 7 21 1 TTCTTTACTT 0.927967 -74 AAGAGGATGTTTGTTTAATTCTTACATATT 11 15 1 TTGTTTAATT 0.717253 -286 AATATACTTAATCTTTATTTCAATATGAAG 11 264 0 ATCTTTATTT 0.85614 -37 AATATGTCAATTCATTATTTTTTCGTTGAC 13 105 0 TTCATTATTT 0.649041 -117 AACAGGACGCATCTTTACTTTTTCCCCGCC 20 78 1 ATCTTTACTT 0.853656 -124 AACACACGAATTCTTGATTTGGCACAGAAC 27 157 1 TTCTTGATTT 0.732688 -84 ********** Masking position 5 Map Score: 3.82577 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 261 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 11 GCCTGGTCAGCCGGCTGTTTGGT 1 4 0 CCGGCTGTTT 0.914095 -223 GCCGGCTGACCAGGCTGTTTTTTTGCTGCG 1 19 1 CAGGCTGTTT 0.975647 -208 CTTACAGATAGAGGCCGTATACACAAATAA 1 192 1 GAGGCCGTAT 0.890971 -35 CGTTTTTTCTTAGGCTGTGTTTCGGCTGCT 3 121 1 TAGGCTGTGT 0.889011 -180 AACAGGAAGATAGGCTGTATATAATATAGC 3 220 0 TAGGCTGTAT 0.931765 -81 CGCGGTCAGCCTGTTTTTTTATGCGG 5 7 1 CAGCCTGTTT 0.868949 -200 TTGTAAGAGGATGTTTGTTTAATTCT 11 7 1 GAGGATGTTT 0.817309 -294 TCTCCCTTTCGAGGCTGTATTCATTTATTG 20 176 0 GAGGCTGTAT 0.968521 -26 ********** Masking position 8 Map Score: 3.30608 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 183 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 12 CTTTTTTATAAAATATCAGAAAATAAAGATA 1 78 1 AAATATCAGA 0.962898 -149 AAACAAAAGGATATATGGGAAGGAGCGGATG 1 138 1 ATATATGGGA 0.590201 -89 CCGTATACACAAATAACAGGAGGTTATGTTG 1 206 1 AAATAACAGA 0.865579 -21 AAGCAATCATAAATAAGAGGACATAGGCGTC 3 71 1 AAATAAGAGA 0.789586 -230 GGATGGATCGAAATATGAGTATGCCAGCAGC 3 145 0 AAATATGAGA 0.93798 -156 TTTCATATGGATATATCAGGAGTATGATTGA 4 68 1 ATATATCAGA 0.865579 -22 TCCGCTCAAAAAAAATCAGCACGACTCCAGC 5 68 0 AAAAATCAGA 0.865579 -139 CATAATTTTAAAATTTGGGAAGAGTTTTTTT 13 138 0 AAATTTGGGA 0.590201 -84 TTTACAACAGAAAAATCAGCACTCCCTATTT 26 50 1 AAAAATCAGA 0.865579 -173 TTTCGAGCGAAAATTTCAGCAAGTGCAAAAT 27 85 0 AAATTTCAGA 0.865579 -156 TTTTCGCTCGAAATATCAGAATGTTTTTGCA 27 103 1 AAATATCAGA 0.962898 -138 ********* * Masking position 3 Map Score: 6.98708 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 194 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 13 TCCATCCCCTCTGTTTGAAAATATTAATTA 3 169 1 CTGTTTGAAA 0.932073 -132 GCCTATCTTCCTGTTTCAATATAAATAAAG 3 235 1 CTGTTTCAAT 0.845631 -66 ATTTTGGTAACGGTTTCAAAGAAAATTTTA 13 57 1 CGGTTTCAAA 0.965917 -165 GTTTTGAAATCGGTTTCAAATATATGAGAT 13 188 1 CGGTTTCAAA 0.965917 -34 TTTCATCCTCCAGTTTGAACAAATATTGTT 15 121 0 CAGTTTGAAC 0.818254 -22 TATAATCATTCGGTTTGTAAACTTCAACTG 18 240 0 CGGTTTGTAA 0.817497 -61 CCCTTGTTTTCTGTTTCAACATGTTATCCT 27 210 0 CTGTTTCAAC 0.937272 -31 ********** Masking position 9 Map Score: 1.33095 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 154 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 14 CGGACAGTGATTTACCGCTTTTTTATAAAA 1 61 1 TTTACCGCTT 0.507046 -166 GCCCATTGCCCCTTTCGTGTTTTT 2 16 0 ATTGCCCCTT 0.89096 -14 AACAAGTTCACCCTCTTGGTCTTTG 5 192 0 GTTCACCCTC 0.75292 -15 AATTCCCCATATTACCCCTCAGAGAAGGAT 11 116 1 ATTACCCCTC 0.865228 -185 TATATTTCCCCCTTGGTTAGGATT 13 5 1 TTTCCCCCTT 0.96292 -217 TAAAAGCGGATTTCCCGCTCTGTGATACTA 15 61 1 TTTCCCGCTC 0.899972 -82 AACGGGTTCCCCCTTTTTTTATGTT 20 6 1 GTTCCCCCTT 0.976298 -196 ATGTAGTCCCCCTCGTGTTATGAA 22 213 0 AGTCCCCCTC 0.879341 -14 TACAGAAAAGGTACCACCTTATAATAGGTC 24 87 1 GTACCACCTT 0.512422 -56 TGTAAAATCCCCCTCATTTGCTTTC 24 128 0 AATCCCCCTC 0.831 -15 CTGTGATTCCACCTCAACATTTAAG 25 59 0 ATTCCACCTC 0.922948 -15 CCATGCAGATGTTCCAGCTTAGATCCAATA 26 179 1 GTTCCAGCTT 0.752723 -44 TCAGAATGTTTTTGCACCTTGTCCTCGAAA 27 118 1 TTTGCACCTT 0.591307 -123 ATTTGAATTCCCCCTTGTTTTCTGTT 27 225 0 ATTCCCCCTT 0.974372 -16 ********** Masking position 9 Map Score: 11.2426 Number of sites scoring better than the average of aligned sites = 443 Number in coding regions = 282 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 182 Fraction of orfs with sites within 600 bp upstream = 0.0292323 Motif number 15 TTTGTTTAATTGTAAGACAAATAAACAATAA 1 114 0 TGTAGACAAA 0.947619 -113 GGAGCGGATGTGAAAGAAAAATTAATAAAAG 1 159 1 TGAAGAAAAA 0.887408 -68 TATTGCCTCTTGCTAGAACAACTCAAGGATT 11 195 0 TGCAGAACAA 0.850968 -106 AACATAGATCTGCTAGAAAAACAAAAAAAGG 18 11 0 TGCAGAAAAA 0.955551 -290 TTTCTACTATTATGAGAAAAAAAGATCGTTT 20 34 1 TATAGAAAAA 0.781065 -168 GGTGATCACCTGTTAGACAAATTTCTGTTCG 22 107 1 TGTAGACAAA 0.947618 -120 GCGCAAGGTTTGTCAGAAAAAATAACAAACT 23 82 0 TGTAGAAAAA 0.969649 -86 GTACCTTTTCTGTAAGAAAGACAACGGTGAA 24 70 0 TGTAGAAAGA 0.894576 -73 *** ******* Masking position 5 Map Score: 2.63463 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 137 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652