AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00260_ecoli_reg_100.orf -o00260_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 thrL 189 thr operon leader peptide #2 thrA 81 aspartokinase I, homoserine dehydrogenase I #3 lpdA 300 lipoamide dehydrogenase (NADH); component of 2-oxodehydrogenase and pyruvate complexes; L-protein of glycine cleavage complex #4 betI 128 probably transcriptional repressor of bet genes #5 lolA 108 periplasmic protein effects translocation of lipoproteins from inner membrane to outer #6 serS 90 serine tRNA synthetase; also charges selenocystein tRNA with serine #7 serC 198 3-phosphoserine aminotransferase #8 solA 114 sarcosine oxidase-like protein #9 tynA 247 copper amine oxidase (tyramine oxidase) #10 rspA 205 starvation sensing protein #11 thrS 300 threonine tRNA synthetase #12 sdaA 183 L-serine deaminase #13 purT 133 phosphoribosylglycinamide formyltransferase 2 #14 gatD 47 galactitol-1-phosphate dehydrogenase #15 gatB 30 galactitol-specific enzyme IIB of phosphotransferase system #16 gatZ 28 putative tagatose 6-phosphate kinase 1 #17 gatY 197 tagatose-bisphosphate aldolase 1 #18 pdxB 98 erythronate-4-phosphate dehyrogenase #19 dsdX 217 transport system permease (serine?) #20 glyA 300 serine hydroxymethyltransferase #21 pssA 110 phosphatidylserine synthase; phospholipid synthesis #22 sdaC 300 probable serine transporter #23 sdaB 57 L-serine dehydratase (deaminase), L-SD2 #24 gcvP 118 glycine decarboxylase, P protein of glycine cleavage system #25 gcvT 300 aminomethyltransferase (T protein; tetrahydrofolate-dependent) of glycine cleavage system #26 serA 255 D-3-phosphoglycerate dehydrogenase #27 yhaP 119 putative L-serine dehydratase #28 yhaQ 65 putative L-serine dehydratase #29 tdcE 33 probable formate acetyltransferase 3 #30 tdcC 21 anaerobically inducible L-threonine, L-serine permease #31 tdcB 98 threonine dehydratase, catabolic #32 tdcA 188 transcriptional activator of tdc operon #33 asd 192 aspartate-semialdehyde dehydrogenase #34 glyQ 300 glycine tRNA synthetase, alpha subunit #35 kbl 274 2-amino-3-ketobutyrate CoA ligase (glycine acetyltransferase) #36 ilvM 300 acetolactate synthase II, valine insensitive, small subunit #37 ilvD 95 dihydroxyacid dehydratase #38 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #39 metB 276 cystathionine gamma-synthase #40 lysC 300 aspartokinase III, lysine sensitive #41 psd 96 phosphatidylserine decarboxylase; phospholipid synthesis #42 yjeQ 64 orf, hypothetical protein #43 serB 105 3-phosphoserine phosphatase Motif number 1 TCGAAAAAAAAAGCCCGCACTGTCAGGTGCGGGCTTTTT 2 30 0 ACCCCAGGTG 0.988899 -52 CCTCAAATTACGTCACTCCCGATCGGGAGTTCCCTCTAC 5 76 0 CCCCCGGGAG 0.968028 -33 GGCACACCTGCCAAACAACCTGGCAGGTGCAGGCAATCC 9 129 1 CCACCAGGTG 0.952435 -119 TTTTAGTGTTAACATCGCTCAACCGGGTGGAAGGTGAGA 11 128 1 ACCCCGGGTG 0.982662 -173 CAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAA 11 178 0 ATCCCAGGTA 0.854408 -123 TACTGGAAGTCCAGTCACCTTGTCAGGAGTATTATC 12 158 1 CCCTCAGGAG 0.689712 -26 GTTAAGGGGGATAACCTCCCCCTCAGGTAAAAA 14 5 0 ACCCCAGGTA 0.956486 -43 GGGAGGTTATCCCCCTTAACAATCAGGAGTTTTT 14 24 1 CTACCAGGAG 0.733571 -24 GCACTTTGCTACGGCTTCCCTATCGGGAGGCCGTTTTTT 17 58 1 ATCCCGGGAG 0.886277 -140 CAAGTGTGCCATAATCTCGCGGCCAGGCATACTTGCGAA 18 34 0 ACCCCAGGCA 0.917331 -65 GTCCGGTTAACTCTCGTCTCATACAGGTAACACAAAC 18 72 1 CGCCCAGGTA 0.689987 -27 AAGCTGAATTATTTGCATTCCTCCAGGAGAAATAG 22 276 1 ACTCCAGGAG 0.75137 -25 AAATAATCCACCTGTCTGTCTTGCAGGTGTCGGTTACGG 31 33 1 CCGCCAGGTG 0.900203 -66 CGTACTGTATATCTTCCATCCAGCGGGTATACTGATCCC 34 236 1 ACACCGGGTA 0.751889 -65 GTAAACCCGCATAGTTTACCGTACAGGCGTTACCGTGAC 39 76 1 ATACCAGGCG 0.72237 -201 AATTATATGCATTATCACGCCGACAGGTGCATTACACGA 39 116 0 ACCCCAGGTG 0.988899 -161 ATCACCTCGGCGATGCACCCCCTCAGGTGTTATCACAGG 40 72 0 CCCCCAGGTG 0.989294 -229 TTGTCACCAGAAGCGTTCGCAGTCGGGCGTTTCGCAAGT 40 161 1 ATCCCGGGCG 0.884243 -140 * * * * ****** Masking position 14 Map Score: 16.6801 Number of sites scoring better than the average of aligned sites = 731 Number in coding regions = 672 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 2 TTCTTTCCTCAAGCTGATTATTAGCCTGGAATAGAGA 5 39 1 AGATTTAGCT 0.658511 -70 TGTGTGATGCAAGCCACATTTTTGCCCTCAACGGTTT 7 55 1 AGCATTTGCC 0.924523 -144 ATGAAGGGCAACGGCGAATAGTTGCCCTTTTATTTCA 9 18 1 AGAAGTTGCC 0.770529 -230 ATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGT 10 87 0 AGTATTTGCC 0.887323 -119 GCGCAGTATAAACGAAAACGTTTGCGTGTGTCTTTAT 13 81 0 ACAATTTGCT 0.88743 -53 CCCTATCGGGAGGCCGTTTTTTTGCCTTTCACTCCTC 17 75 1 AGTTTTTGCT 0.798203 -123 GAATTGAGATATGGTTCACTTTAGCTCATCTCATAGC 19 60 0 AGCATTAGCC 0.622989 -158 CAGGCTGACAAACGATAAAATTTGCCTTTCACATGAG 19 140 0 ACAATTTGCT 0.887671 -78 GAATGTGATGAAGTGAAAAATTTGCATCACAAACCTG 20 82 1 AGAATTTGCT 0.961179 -219 GCGTAGCCTGAAGGTAATCGTTTGCGTAAATTCCTTT 20 166 1 AGATTTTGCT 0.935406 -135 AAGAGAATTTAAGGGCAATATTTGCCCATTAAACGAC 22 36 0 AGAATTTGCC 0.969383 -265 ACTGGCTAAAAGCTGAATTATTTGCATTCCTCCAGGA 22 267 1 ACATTTTGCT 0.824525 -34 AGTGAGGGTGAGGCATAAATTTTCCTCACCCTGATCC 24 37 0 AGAATTTCCC 0.66986 -82 CCCCAACGCAATCGTTCTCTTTTGCCTGAACTTACCA 25 189 0 ACCTTTTGCT 0.647603 -112 ATATTCATCCAAGAATTACCTTTGCGTGATATTTCCT 26 124 1 AGTATTTGCT 0.86954 -132 ATATTGCGGCAATATGAACGTTTGCGTCGCGATGTTG 26 161 0 ATAATTTGCT 0.602627 -95 GAAGGCGGTGACGTCGATTTTTTGCTCGCCGGTGTTA 34 72 0 AGATTTTGCC 0.949505 -229 TTTGACGCGGATGGCCATTTTTTGCATCTTTCCATGC 34 175 1 AGATTTTGCT 0.94041 -126 TGCATATCAAATGGTTAATTTTTGCACAGGACTGGTG 38 132 1 AGAATTTGCC 0.969329 -108 * * ** ***** * Masking position 12 Map Score: 15.4125 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 192 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 3 CACCCAAAAGGCACCTCACCGGTGCCTTTA 8 26 1 GCACCTCACC 0.679547 -89 AAGGGAGATTGTACCTTTCCGTTTCACATT 11 97 0 GTACCTTTCC 0.921339 -204 TTAAGGGGGATAACCTCCCCCTCAGGTAAA 14 13 0 TAACCTCCCC 0.561159 -35 ATCTCACCTTCCCCTGTGATTAA 19 205 0 TCACCTTCCC 0.845185 -13 TAACTTGTGTGTATCTTTCCGCCCTCAAAT 22 161 1 GTATCTTTCC 0.752253 -140 TTACGGTCAGGCACCTTCCCGGGCTGAACT 22 240 1 GCACCTTCCC 0.979169 -61 TCTGACGGGGGAACCTCCCCCGTTAAAAAA 26 11 1 GAACCTCCCC 0.916734 -245 GCCATTTTTTGCATCTTTCCATGCGTTAAG 34 188 1 GCATCTTTCC 0.82883 -113 TGCCATTGTCGAACCATCCCTAACCGTTGG 36 32 0 GAACCATCCC 0.790421 -269 TGGTTTCGCTGTATCGTTCCTGAAAAAACA 36 67 0 GTATCGTTCC 0.755741 -234 GGGACGGTGCGTGCCGTCCCATTTTTTGTA 37 12 0 GTGCCGTCCC 0.814172 -84 GGGACGGCACGCACCGTCCCATTTACGAGA 37 22 1 GCACCGTCCC 0.979548 -74 GTATGCCTAAGTACCGTTCCGCCACCACCA 37 73 1 GTACCGTTCC 0.922688 -23 ACCGTCGTTAGAATCGTCCCCTTTTTTTCA 41 22 1 GAATCGTCCC 0.863386 -75 ********** Masking position 5 Map Score: 9.97576 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 243 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 CAGGAAACACAGAAAAAAGCCCGCACCTGAC 2 17 1 AAAAAAAGCC 0.948595 -65 CTTTGGTCGAAAAAAAAAGCCCGCACTGTCA 2 44 0 AAAAAAAGCC 0.948595 -38 TCGGATTATTAGCAAAAAGCCGATGTTTTTA 7 14 0 ACAAAAAGCC 0.932506 -185 GGAGTGATCACAAAAAAAGGCGTATATTTGC 10 99 0 CAAAAAAGGC 0.648025 -107 GTATAAAGATCGAAAAAAGCCGGAGTGATCA 10 120 0 CAAAAAAGCC 0.911095 -86 TGAGTACACCAGCAAAACGCTTAAAGAACAA 11 41 0 ACAAAACGCT 0.795272 -260 AGTGAAAGGCAAAAAAACGGCCTCCCGATAG 17 77 0 AAAAAACGGC 0.858362 -121 GATAACGATCACAAAAACGACAATATGAAAA 17 118 0 AAAAAACGAC 0.79666 -80 TGCATCTTATAAAAAATAGCCCTGCAATGTA 20 25 1 AAAAATAGCC 0.865968 -276 TCTTTGCAGGAAAAAAACGCTT 33 181 1 AAAAAACGCT 0.838405 -12 ACCGGCGAGCAAAAAATCGACGTCACCGCCT 34 76 1 AAAAATCGAC 0.578367 -225 GGAAAGATGCAAAAAATGGCCATCCGCGTCA 34 177 0 AAAAATGGCC 0.631819 -124 CTCAGTTGGTATCAAAACGCTACCCACTAAT 35 21 0 ACAAAACGCT 0.795272 -254 TTGTCTTATGCCAAAAACGCCACGTGTTTAC 38 13 1 CAAAAACGCC 0.949324 -227 CAGATATAAAAGCAAAACGCCACGTAAACAC 38 36 0 ACAAAACGCC 0.961913 -204 TTGAGCAAATCCCAAATAGCCGTTAAAATTA 39 150 0 CCAAATAGCC 0.728733 -127 * ********* Masking position 6 Map Score: 10.6042 Number of sites scoring better than the average of aligned sites = 870 Number in coding regions = 669 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 5 GTAGCAAGCGCCAGAATCCCCAGGAGCTTACATA 3 184 1 CAGAATCAGG 0.824107 -117 AGGGGATTGCCTGCACCTGCCAGGTTGTTTGGCA 9 137 0 CGCACCCAGG 0.874693 -111 TTGAAATCGAAAACAAACGACAGGAT 17 182 1 AACAAACAGG 0.821202 -16 TCACAATTCACTGCACGTTTCAGGAACCATCGCT 24 94 1 CGCACGCAGG 0.927776 -25 TTAGAGCAATCGACAATTGCCTGGTAAAAGCGTG 26 71 0 CACAATCTGG 0.614326 -185 TTTTTTTGACAAAAATCAGGGTTTATGCTG 32 7 1 TACAAACAGG 0.722579 -182 AGAAAGTCCGCGGCAATTATCAGGGAATTTGAGT 33 12 0 CGCAATCAGG 0.974138 -181 TGGAAGCGTTATGCAAGGATCAGGCGGCAAAACG 34 35 1 AGCAAGCAGG 0.849615 -266 CAGTACGAAACGGGAAAAAGCAGGGCTTAACGCA 34 209 0 CGGAAACAGG 0.96302 -92 GTTAACACTTCTGCAAAATTCAGGATAAATAACG 35 182 0 CGCAAACAGG 0.98812 -93 AACACATCACCCGGAAAGACCAGGTTGAAGCGGC 36 154 1 CGGAAACAGG 0.963018 -147 CATAACATGCCAGCAAATTCCAGGAATTTTCCTA 38 93 0 CGCAAACAGG 0.988122 -147 GACATTTCACCGACAAAGCCCAGGGAACTTCATC 39 251 1 CACAAACAGG 0.970637 -26 * ***** **** Masking position 5 Map Score: 10.913 Number of sites scoring better than the average of aligned sites = 493 Number in coding regions = 450 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 6 GCAGCAAGGTAGCAAGCGCCAGAATCCCCAG 3 176 1 AGCAGCGCCA 0.922664 -125 GAGGGCGTGAAGCTAACGCCGCTGCGGCCTG 3 234 1 AGCAACGCCG 0.981109 -67 ATAGTGTAAGAGGGAACGCGGCGACTGGCTT 12 109 0 AGGAACGCGG 0.902139 -75 TAAATGATTAAGCCATCGCCGATAGACAGAT 22 202 1 AGCATCGCCG 0.940388 -99 GTTAAAACGGAGGAAGCGCCGCCCGAAAGCG 23 23 0 AGGAGCGCCG 0.986093 -35 TTCCATATTCAACGAACGCAGAGGATCAA 34 9 0 AACAACGCAG 0.61173 -292 TCCTCATGTTAGCCAGCGCCTTCGGCATCCA 36 118 1 AGCAGCGCCT 0.954621 -183 TTCCTAACATCGCCAGCGCGGCATTAAGATT 38 68 0 CGCAGCGCGG 0.971962 -172 CACGATGTCACGGTAACGCCTGTACGGTAAA 39 90 0 CGGAACGCCT 0.830246 -187 CCTGCGCTAGCGCAGGCCAGAAGAG 40 5 1 CGCAGCGCAG 0.957285 -296 CTCCAAAGGCCAGCAGCGCCGC 42 53 1 CAGAGCGCCG 0.910834 -12 *** ******* Masking position 5 Map Score: 7.41912 Number of sites scoring better than the average of aligned sites = 1324 Number in coding regions = 1252 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 7 TTACTGTATCCCTGTGGTCGCAGGCTGTGGC 6 33 1 CCTGTGGCGC 0.969859 -58 TAATGTATTACCTGTGGTCGCAATCGATTGA 7 142 1 CCTGTGGCGC 0.969859 -57 TTTGTCAAGACCTGTTATCGCACAATGATTC 20 200 1 CCTGTTACGC 0.786961 -101 GCGCTTCCTCCGTTTTAACGCGATGTATTTC 23 35 1 CGTTTTACGC 0.598184 -23 AAGAACACTTCGGCCTGTCGCACGATGTCGA 27 53 1 CGGCCTGCGC 0.927083 -67 GTGCCGGTCTCCTCTTGGCACATCTTTCACC 33 134 0 CCTCTTGCAC 0.820647 -59 GGTGTTATAACGTTTTGCCGCCTGATCCTTG 34 48 0 CGTTTTGCGC 0.906219 -253 AACTTGAGAACGTCTGGCCGCTGGTGCCGCC 36 244 1 CGTCTGGCGC 0.979397 -57 GCCGCTGGTGCCGCCTGGCGCCAGTAATTCA 36 260 1 CCGCCTGCGC 0.9141 -41 GGTGATTGAACGGCTGGCCACGTTCATCATC 40 105 1 CGGCTGGCAC 0.872594 -196 GAGCGGAAGACGGGTGGGCGCAGAGCGATAC 40 233 0 CGGGTGGCGC 0.972892 -68 ******* *** Masking position 9 Map Score: 6.36033 Number of sites scoring better than the average of aligned sites = 677 Number in coding regions = 651 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 8 CACGGCAGGTAACCAGTTCAGAAGCTGCTAT 1 73 0 AACCAGTTCG 0.670644 -117 TTTCGCCACTCCATTCATCAGCGG 4 115 0 CGCCACTCCT 0.815638 -14 CCTCAAATTACGTCACTCCCGATCGGGAGTT 5 84 0 CGTCACTCCG 0.815634 -25 ACCCAAAAGGCACCTCACCGGTGCCTTTACC 8 27 1 CACCTCACCG 0.683384 -88 GATTATGGCACACTTGTCCGGTTAACTCTCG 18 57 1 CACTTGTCCG 0.590907 -42 CCGCATCTCCTGACTCAGCTAA 20 289 0 CGCATCTCCG 0.784245 -12 GCAATAATAACACCAGTCCCGATTAAGTGGT 21 31 0 CACCAGTCCG 0.96653 -80 TTCAGCTTTTAGCCAGTTCAGCCCGGGAAGG 22 253 0 AGCCAGTTCG 0.836713 -48 CCTCACCCTGATCCTCTCCCGCAGAAGAGGA 24 20 0 ATCCTCTCCG 0.657059 -99 CCAGCATCGGAGCCACTCCCGGTCCCCAACG 25 218 0 AGCCACTCCG 0.9626 -83 GTTCCAAACCCACCAGTCCTGTGCAAAAATT 38 148 0 CACCAGTCCG 0.966532 -92 GTCACGGTAACGCCTGTACGGTAAACTATGC 39 84 0 CGCCTGTACG 0.813026 -193 TTGGGCAACGCGCCTCTTCTGGCCTGCGCTA 40 18 0 CGCCTCTTCG 0.916576 -283 GTGTTGGAGGAGCCAGTCCTGTGATAACACC 40 55 1 AGCCAGTCCG 0.9626 -246 ********* * Masking position 9 Map Score: 7.07685 Number of sites scoring better than the average of aligned sites = 1236 Number in coding regions = 1163 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 9 CCTGACTAAACCGCCCACAGAGCGCGGTTGC 9 195 1 CCGCCCACAA 0.920669 -53 GGGAGGTTATCCCCCTTAACAATCAGGAGTT 14 24 1 CCCCCTTAAA 0.788772 -24 TCCAACAGGACCGCCTATAAAGGCCAAAAAT 20 251 1 CCGCCTATAA 0.876923 -50 GTGTATCTTTCCGCCCTCAAATTATTACGGC 22 169 1 CCGCCCTCAA 0.966817 -132 TAATCATTTACCGCCGTAATAATTTGAGGGC 22 181 0 CCGCCGTAAA 0.949587 -120 GGGGGAGGTTCCCCCGTCAGA 26 1 0 CCCCCGTCAA 0.964151 -255 GGGGGAACCTCCCCCGTTAAAAAAATTCTCT 26 17 1 CCCCCGTTAA 0.931921 -239 GGATTTGCATCCGCCTTTCAACATATCAAAA 26 202 0 CCGCCTTTCA 0.788605 -54 AATAAACCCGCCGCCGACAGAGTAATAGGTT 27 15 0 CCGCCGACAA 0.964916 -105 ATCGACGTCACCGCCTTCGAACAGTTCCAGG 34 91 1 CCGCCTTCGA 0.879942 -210 ATTAAGCTAACCGTCGTTAGAATCGTCCCCT 41 13 1 CCGTCGTTAA 0.734688 -84 ********* * Masking position 11 Map Score: 4.59239 Number of sites scoring better than the average of aligned sites = 402 Number in coding regions = 378 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 10 GACATATTGCCCGTTGCAGTCAGAATGAAAAGC 1 12 0 CCGTTGCCAG 0.925306 -178 ATAGACAAATCGGTTGCCGTTTGTTGTTTAAAA 3 55 1 CGGTTGCTTG 0.889742 -246 GAAGCTAACGCCGCTGCGGCCTGAAAGACGACG 3 242 1 CCGCTGCCTG 0.966292 -59 TGTATCCCTGTGGTCGCAGGCTGTGGCCACATC 6 37 1 TGGTCGCCTG 0.764015 -54 TTGTACCTTTCCGTTTCACATTGATTCGATTCG 11 86 0 CCGTTTCTTG 0.907876 -215 CGGTTAACTCTCGTCTCATACAGGTAACACAAA 18 75 1 TCGTCTCCAG 0.584325 -24 GAAAAGAAATCCGTTTCCGGTTGCAAGCTCTTT 20 118 1 CCGTTTCTTG 0.907872 -183 GACAATAAACCCGCCGCCGACAGAGTAATAGGT 27 16 0 CCGCCGCCAG 0.893135 -104 CTTGCGACTTTGGCTGCTTTTTGTATGGTGAAA 33 108 1 TGGCTGCTTG 0.594399 -85 ATAAATGTGCCGGTCTCCTCTTGGCACATCTTT 33 138 0 CGGTCTCTTG 0.805738 -55 CTGCTTTTTCCCGTTTCGTACTGTATATCTTCC 34 220 1 CCGTTTCCTG 0.956086 -81 GTGTCGAGTGCCGCTTCAACCTGGTCTTTCCGG 36 164 0 CCGCTTCCTG 0.947111 -137 ******* *** Masking position 7 Map Score: 4.06092 Number of sites scoring better than the average of aligned sites = 1284 Number in coding regions = 1217 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 11 CTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC 1 46 1 TAAAAAGGTC 0.890586 -144 ATGTTAACACTAAAAAAAGGGAGATTGTACCTTTC 11 108 0 TAAAAAGGAT 0.781602 -193 CGCTTAAGTGTAAAAAAATAGCGGCAAAATTTCAG 19 26 1 TAAAAAGGGC 0.970005 -192 GGTTAAAAAATGCAAAAATCGCGACAGAATAAAAA 25 103 0 TAAAAAGGAC 0.978458 -198 CTTGTCCTCATTGAATAAGCGGGGCTGACAACTTT 25 276 0 TAATAAGGGC 0.804269 -25 GACAATTGCCTGGTAAAAGCGTGACACATGTCACC 26 59 0 TTAAAAGGAC 0.852314 -197 GTATCGTTCCTGAAAAAACAGTTGCTGCCATTGTC 36 52 0 TAAAAAGTGC 0.71816 -249 ATACAAAAAATGGGACGGCACGCACC 37 2 1 TAAAAAGGAC 0.978458 -94 ATCCTCTTCGTCAATAAATTGAGACCAGACCACAC 39 21 1 TATAAAGGAC 0.852314 -256 TGCCGGATCCTGAAAAAAAGGGGACGATTCTAACG 41 27 0 TAAAAAGGAC 0.978458 -70 CTTCCACCCTTTGAAAATTTGAGACTTAATGTTGC 43 11 1 TAAAATGGAC 0.852314 -95 * ***** * *** Masking position 7 Map Score: 4.69391 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 57 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 12 CATCATGCATAATGTGACAACGTCACAAAACTTAGT 9 54 0 AATTAAGTAC 0.626373 -194 AAGAACACAACATCTGACGAGGTTAATA 9 230 1 CATTAAGTAA 0.918782 -18 CGCACCTGCCATTTAACAAGGAAAAAAC 16 10 1 CATTAAGAAA 0.89151 -19 AATTCACCTTCATTTTTAGATGTAAATCACTCCATT 19 92 1 CATTTAGTAA 0.717084 -126 TTTTTTGTCCAATATCATCAGGTTAATCACAGGGGA 19 183 1 AATTAAGTAA 0.907112 -35 TTTCAGAAAGAATGTGATGAAGTGAAAAATTTGCAT 20 73 1 AATTAAGTAA 0.907112 -228 TGAGAAAGTCAATTTGAATAAGACAATATTAAGAGC 25 28 0 AATTAAGAAA 0.876449 -273 TCGTGGTGATAATTTCACCATGAAAAAGTTGTCAGC 25 252 1 AATTAAGAAA 0.876449 -49 CATGTCACCAAATTTAATGAAGAGAATTTTTTTAAC 26 32 0 AATTAAGAAA 0.876449 -224 AATACCTTTAAATATCAACAAGTTAAAGTATAAAAA 32 42 0 AATTAAGTAA 0.907112 -147 ATACAGCACACATCTTTGCAGGAAAAAAACGCTT 33 169 1 CATTTAGAAA 0.64803 -24 ATGCAATTTGCATATCAAATGGTTAATTTTTGCACA 38 124 1 CATTATGTAA 0.567154 -116 *** * * * ** ** Masking position 2 Map Score: 2.84633 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 37 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 13 AGTAGCTCAGTTGCGTAGATTTCATGCATCACGACAA 10 160 1 TTGCGATTGC 0.961727 -46 GTGTACCTGATTGCGAACCAATTTAGCATTTGTTGGC 11 185 1 TTGCGAATGC 0.982299 -116 TAACAGTTCATTGCGAAACCATCTAGCCAACAAATGC 11 210 0 TTGCGAATGC 0.982299 -91 CCAGGCATACTTGCGAAGATTTCAGGTATAAGGATAC 18 14 0 TTGCGATTGT 0.687046 -85 GTCCTTTCGCGCCGCTTTCGGGCGGCGCTTCCT 23 7 1 TCGCGCTTGC 0.884962 -51 CGTCGCGATGTTGAGGAAATATCACGCAAAGGTAATT 26 137 0 TTGAGAATGC 0.939969 -119 AACTTATAGGTCGCGACGAGATAACGCGTTAACACTT 35 206 0 TCGCGCATGC 0.944412 -69 CAACTGTTTTTTCAGGAACGATACAGCGAAACCACCC 36 63 1 TTCAGAATGC 0.669699 -238 CTAAACTTCTTTGCGTATAGATTGAGCAAATCCCAAA 39 165 0 TTGCGAATGC 0.982299 -112 CTTTGAAAATTTGAGACTTAATGTTGCCAGAAGCAAT 43 19 1 TTGAGCATGC 0.917686 -87 ***** * ** ** Masking position 12 Map Score: 4.04948 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 150 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 14 GCACTGTCAGGTGCGGGCTTTTTTCTGTGT 2 23 0 GTGCGGGCTT 0.938299 -59 GCACCTGACAGTGCGGGCTTTTTTTTTCGA 2 39 1 GTGCGGGCTT 0.938299 -43 TTTATTGCTGATGTTGATTTCTCAACCGAA 13 56 0 ATGTTGATTT 0.515526 -78 AGTGGCTCCGATGCTGGGTTTCGTGGTGAT 25 232 1 ATGCTGGGTT 0.765635 -69 TTGGATGAATATGCTGGTTTAGAGGATTTA 26 106 0 ATGCTGGTTT 0.913919 -150 GAAATGTTGTGTGCGGATTTGCATCCGCCT 26 217 0 GTGCGGATTT 0.931828 -39 ATCAGGGTTTATGCTGATTTTTATACTTTA 32 25 1 ATGCTGATTT 0.843844 -164 TGCTGGATACGTGTGGATTTAAAGGAAGGG 34 272 0 GTGTGGATTT 0.729112 -29 ACGGTAAACTATGCGGGTTTACGGTCAGTA 39 68 0 ATGCGGGTTT 0.954253 -209 ********** Masking position 2 Map Score: 2.39376 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 209 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 15 AAAGTATTTAGTGACCTAAGTCAATAAAATTTTAAT 1 109 0 GTGAAGTCAA 0.854395 -81 TTATCATTCAGTGACACACATCGCAATGAGTAAAAC 7 88 0 GTGAAATCCA 0.969066 -111 AACACTACTTGAGACAATCATCGCAATATTAGTTAA 12 35 1 GAGATATCCA 0.750698 -149 TGTCGTTTTTGTGATCGTTATCTCGATATTTAAAAA 17 127 1 GTGATATCCA 0.955357 -71 ATGAGCTAAAGTGAACCATATCTCAATTCACCTTCA 19 68 1 GTGAAATCCA 0.969057 -150 CATCAATGGAGTGATTTACATCTAAAAATGAAGGTG 19 96 0 GTGAAATCAA 0.844143 -122 GTATCTATCAGTGATCTTGATCTCAAATACAATAAT 22 124 0 GTGATATCCA 0.955355 -177 TGGTAAAAGCGTGACACATGTCACCAAATTTAATGA 26 48 0 GTGAAGTCCA 0.97138 -208 TTTTTGTATGGTGAAAGATGTGCCAAGAGGAGACCG 33 125 1 GTGAAGTGCA 0.831423 -68 GCACTTCTGGGTGAAAATAGTAGCGAAGTATCGCTC 40 206 1 GTGATGTACA 0.694465 -95 **** * *** * * Masking position 11 Map Score: 2.99585 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 87 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899