AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i293_ecoli_bsub_300.orf -o293_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 pcnB 92 poly(A) polymerase I #2 yadB 36 putative tRNA synthetase #3 dksA 177 dnaK suppressor protein #4 rpsB 300 30S ribosomal subunit protein S2 #5 tsf 257 protein chain elongation factor EF-Ts #6 pyrH 146 uridylate kinase #7 frr 291 ribosome releasing factor #8 yaeM 91 putative ATP-binding component of a transport system #9 yaeS 185 orf, hypothetical protein #10 cdsA 120 CDP-diglyceride synthetase #11 yaeT 29 orf, hypothetical protein #12 hlpA 121 histone-like protein, located in outer membrane or nucleoid #13 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #14 dnaE 36 DNA polymerase III, alpha subunit #15 ldcC 98 lysine decarboxylase 2, constitutive #16 yaeR 29 orf, hypothetical protein #17 mesJ 64 cell cycle protein #18 ychF 116 putative GTP-binding protein #19 pth 277 peptidyl-tRNA hydrolase #20 prsA 150 phosphoribosylpyrophosphate synthetase #21 hemM 213 an enzyme in main pathway of synthesis of 5-aminolevulinate, possibly glutamyl-tRNA dehydrogenase #22 yejH 148 putative ATP-dependent helicase #23 rplY 124 50S ribosomal subunit protein L25 #24 folP 44 7,8-dihydropteroate synthase #25 hflB 99 degrades sigma32, integral membrane peptidase, cell division protein #26 ftsJ 125 cell division protein #27 glmU 300 N-acetyl glucosamine-1-phosphate uridyltransferase #28 metS 300 methionyl-tRNA synthetase #29 yabD 78 similar to hypothetical proteins #30 yabE 155 similar to hypothetical proteins #31 yabF 144 similar to hypothetical proteins #32 yabG 161 yabG #33 veg 210 veg #34 sspF 159 small acid-soluble spore protein (alpha/beta-type SASP) #35 yabH 147 similar to hypothetical proteins #36 purR 55 transcriptional regulator #37 spoVG 193 spoVG #38 gcaD 192 UDP-N-acetylglucosamine pyrophosphorylase #39 prs 22 phosphoribosyl pyrophosphate synthetase #40 ctc 84 general stress protein #41 spoVC 106 thermosensitive mutant blocks spore coat formation (stage V sporulation) #42 spoIIE 300 serine phosphatase #43 yabS 84 similar to hypothetical proteins #44 yabT 88 yabT #45 yacA 103 similar to cell-cycle protein #46 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #47 yacB 194 similar to hypothetical proteins #48 yacC 85 similar to hypothetical proteins #49 yacD 46 similar to protein secretion PrsA homolog #50 cysK 75 cysteine synthetase A #51 pabB 166 para-aminobenzoate synthase (subunit A) #52 sigW 300 RNA polymerase ECF-type sigma factor (sigma-W) #53 ybbP 160 alternate gene name: ybbQ; similar to hypothetical proteins #54 yyaF 126 similar to hypothetical proteins #55 yyaE 300 similar to formate dehydrogenase Motif number 1 GCTATGATTAGCCGCTATTTTTTTGTCCTGA 1 11 1 GCGCTATTTT 0.740448 -82 CCTGCATATGGCCCCCTTTTTCACTTTTATA 5 190 1 GCCCCTTTTT 0.831162 -68 CCCTCAGGCGGCTCCTTTTTGATAA 6 5 0 GCCCTTTTTG 0.947199 -142 CCGCCTGAGGGCGGCTTCTTTTTGTGCCCAT 6 25 1 GCGCTTCTTT 0.900606 -122 GATCTACTGAGCGGCGTTTTTGTCGTTCAAG 8 14 0 GCGCGTTTTT 0.885711 -78 GGATCGGCTGGCGGCGTTTTGCTTTTTATTC 8 50 1 GCGCGTTTTG 0.858081 -42 GTGGTTTTACACGGCTTTTTTTTGTATAGGC 9 118 1 ACGCTTTTTT 0.818118 -68 TCACTTCGGTGGCCCTTTTTTATCGCCACGG 15 34 1 GGCCTTTTTT 0.849629 -65 GTCGTTGTCTGCGGCATTTTTGCCGAGTGCC 18 11 1 GCGCATTTTT 0.661082 -106 CATTTGATACGCAGTTTTTTGTCAAGCGGGG 19 205 1 GCGTTTTTTG 0.898569 -73 ACAGTTTTCGGCAGATTCTTTCCACCAATGG 20 108 1 GCGATTCTTT 0.502626 -43 AAAAGAGAGCGCCCCCTTTTGGAGTAATTGC 21 81 1 GCCCCTTTTG 0.79342 -133 AAATTTTTACGCGCCTATTTGGTGATATATG 26 64 0 GCCCTATTTG 0.585721 -62 CCTTTGGGCGGGAGCTTTTTGACATTCTGAT 28 266 1 GGGCTTTTTG 0.874049 -35 CTTGTCCCTTACAGCGTTTTTCTATAAAAGT 30 39 1 ACGCGTTTTT 0.490583 -117 AAGGGCTTTTTGTTTTGCGCAC 32 2 1 AGGCTTTTTG 0.463045 -160 CCTTGAGAAAGCGCCTTTTTTCGCTGAGTCC 32 95 0 GCCCTTTTTT 0.958322 -67 CTTTCTCAAGGCTCTTTCTTTCATGATGAGG 32 115 1 GCCTTTCTTT 0.643565 -47 GGAGAGCTATGCGGGTTTTTTATTTTACATA 33 29 1 GCGGTTTTTT 0.703091 -182 TACAACACGAGCCCATTTTTGTCAAATAAAA 33 165 0 GCCATTTTTG 0.666748 -46 CCTTTTGTTTACTGCTTTTTGTTTTGCCCTT 34 22 1 ACGCTTTTTG 0.778237 -138 TTTTTGTTTTGCCCTTTTTTGGTTTCCAATA 34 37 1 GCCTTTTTTG 0.849112 -123 ACGAAACAACTCCTTTTTTAGAAGTGATA 34 141 0 ACCCTTTTTT 0.74075 -19 TTTTGCCGGCGGTCCTTTTTTAATTCTGATT 38 56 1 GGCCTTTTTT 0.849629 -137 TCTTGCAGAAGCCGATTTTTTTCATTTTTAG 42 130 1 GCGATTTTTT 0.80147 -171 GCGTCAGCCGGCAGTTTTTTTAGAAAGAAAG 47 15 0 GCGTTTTTTT 0.91906 -180 GCTGACGCTGGCAGTTTTTTTATGTAAATGA 47 38 1 GCGTTTTTTT 0.91906 -157 CACTTCCTACGCGGTTTCTTTCATAAATCAA 48 49 0 GCGTTTCTTT 0.739745 -37 CGGTTCGCCGGGAGTTTTTTTATATTTCGTG 51 27 1 GGGTTTTTTT 0.736166 -140 TTGATCAAAAGGTGTCTTTTTTCTTTTCGGA 52 93 1 GGGTCTTTTT 0.373979 -208 TAGCCGCTTTGCTCTTTTTTTGCGGGCTGAG 53 18 1 GCCTTTTTTT 0.878241 -143 ** ******** Masking position 9 Map Score: 30.5795 Number of sites scoring better than the average of aligned sites = 1625 Number in coding regions = 1280 Number in noncoding regions = 345 Number of orfs with sites within 600 bp upstream = 280 Fraction of orfs with sites within 600 bp upstream = 0.0449727 Motif number 2 GAATTTCGCCAAACGTGCCACTGAAGGTTTT 4 33 1 AAAGTGCCAC 0.799555 -268 CTTACTGATGTAAGCTCCCGGGAATTCTCGA 5 63 0 TAACTCCCGG 0.837891 -195 TTATCAAAAAGGAGCCGCCTGAGGGCGG 6 8 1 AAAGAGCCGC 0.900796 -139 ATGGGCACAAAAAGAAGCCGCCCTCAGGCGG 6 25 0 AAAAAGCCGC 0.780188 -122 ATTTGCCCGGTAACGTGCCGGGCATTGCTAC 17 27 1 TAAGTGCCGG 0.807191 -38 GGCACTCGGCAAAAATGCCGCAGACAACGAC 18 11 0 AAAATGCCGC 0.910213 -106 CTTTCGTCTGAAATCTCCCGG 25 1 0 AAACTCCCGG 0.969714 -99 AGAATGTCAAAAAGCTCCCGCCCAAAGGACG 28 263 0 AAACTCCCGC 0.969714 -38 TATGTAAAATAAAAAACCCGCATAGCTCTCC 33 29 0 AAAAACCCGC 0.735234 -182 CTTAAGGCGTAACCCTCCCGCGGTTACGTCT 41 14 1 AACCTCCCGC 0.802394 -93 TCTTTCTAAAAAAACTGCCGGCTGACGCTGG 47 18 1 AAACTGCCGG 0.976148 -177 TTTACATAAAAAAACTGCCAGCGTCAGCCGG 47 35 0 AAACTGCCAG 0.862913 -160 ATTTGTTTACAAATGAGCCGCTGATCGTGTA 47 112 1 AAAGAGCCGC 0.900796 -83 AAAAAGCCAAAACTCCCGGTTCGCCGGGA 51 9 1 AAACTCCCGG 0.969714 -158 GAAATATAAAAAAACTCCCGGCGAACCGGGA 51 24 0 AAACTCCCGG 0.969714 -143 TTAGCAAGTGAAATGTGCCAGCCCTCTCAGC 53 43 0 AAAGTGCCAG 0.799555 -118 *** ******* Masking position 2 Map Score: 18.4014 Number of sites scoring better than the average of aligned sites = 496 Number in coding regions = 445 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 3 ATAAAGCGCGCCGGACTTCCGATCCATTTCGTA 4 138 1 CCGGTCCGAT 0.754541 -163 GGCACATATTCCGGGGTGCCCTTTGGGGTCGGT 4 226 1 CCGGGCCCTT 0.948109 -75 AAATATGAAGGGGGAGAGCCCTTATAGACCAGG 5 135 1 GGGGGCCCTT 0.822092 -123 CCGGTTGCTGCGCGCTGGCCGTGACCAAACTGC 7 94 0 CGCGGCCGTG 0.973392 -198 AAAGCAAAACGCCGCCAGCCGATCCGCAAGGAT 8 42 0 GCCGGCCGAT 0.942902 -50 TCTTACGATTGCGGCAGGCCGTGTTATTATTGT 13 52 1 GCGGGCCGTG 0.974794 -53 GTTACTCGCCCGGAAGCCGCTCTGGCAAG 16 9 0 CCCGGCCGCT 0.962198 -21 CGGCATTTTTGCCGAGTGCCGTGTATAATAGGC 18 22 1 GCCGGCCGTG 0.98366 -95 ATAAGGAAGAGGGGTATTCCCTGTTACAACCCA 19 31 0 GGGGTCCCTG 0.527076 -247 TGGAGTAATTGCCGAAAGCCGTTAGATTCTGGC 21 100 1 GCCGGCCGTT 0.978925 -114 CGGGTCAATGCCCGACCTCCGTTTTTACAGGCA 22 22 0 CCCGTCCGTT 0.930777 -127 GCGCGTGTGACCCGTCCTGAATAG 27 2 1 CGCGGACCCG 0.615599 -299 GGATGTGACCCGGGGGACGTGCTGTTCCCTG 35 9 1 CCCGGACGTG 0.922537 -139 AAAAGTGATCCCGGCTCTCCCAGAATCACTTTT 37 15 0 CCGGTCCCAG 0.610561 -179 GATCCCCTCCGCCGCTACCATATTTG 42 4 1 CCCCGCCGCT 0.819728 -297 TAAAAAAACTGCCGGCTGACGCTGGCAGTTTTT 47 24 1 GCCGGACGCT 0.846898 -171 GCCAAAACTCCCGGTTCGCCGGGAGTTTTTTTA 51 16 1 CCGGGCCGGG 0.913846 -151 AGCGCGTTAGCCGCTTTGCTCTTTT 53 3 1 CGCGGCCGCT 0.961808 -158 **** ****** Masking position 10 Map Score: 13.9966 Number of sites scoring better than the average of aligned sites = 1961 Number in coding regions = 1864 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 4 GACCATCGTCACGCCTTTTGTCTGCAGAAA 27 146 0 ACGCCTTTTG 0.976004 -155 TACACGTGAAACACCTTTTGTTTATCA 29 8 0 ACACCTTTTG 0.980123 -71 AATTCGTCGAACACCTTTTGTGTTTCGACA 29 40 1 ACACCTTTTG 0.980123 -39 AGACAAAATAAAAACTTTTGTATATTCATG 31 114 0 AAAACTTTTG 0.737027 -31 CGGGCAGTGAACCTTTTGTTTACTGCTT 34 9 1 GAACCTTTTG 0.854312 -151 GGGCTGACATAAGCCTTTTGCCGGCGGTCC 38 41 1 AAGCCTTTTG 0.953921 -152 TCCCGCGGTTACGTCTTTTGTGCTAGAATG 41 29 1 ACGTCTTTTG 0.819558 -78 AAGAAAAAAGACACCTTTTGATCAAAGGTG 52 88 0 ACACCTTTTG 0.980123 -213 AAAAAAATTGAAACCTTTTGAAACGAAGCT 52 241 1 AAACCTTTTG 0.961683 -60 ********** Masking position 6 Map Score: 9.16419 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 34 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 CGTTCCATCACGTTTACCACAGGCGGGAA 2 18 1 CGTCAGGGGA 0.975427 -19 AAATAGTTCGAGTTGCAGAAAGGCGGCAAGCTCGAGAA 5 32 1 AGTAAGGGGA 0.785534 -226 ATCTGCGGCGCGAAATATGAAGGGGGAGAGCCCTTATA 5 123 1 CGAAAGGGGG 0.943851 -135 CACAAAAAGAAGCCGCCCTCAGGCGGCTCCTTTTTGAT 6 13 0 AGCCAGGGGT 0.690548 -134 TTAACACAAAAGCAGATATCAGGCGATACTTCAGCAAA 10 22 0 AGACAGGGAA 0.64098 -99 GTTACAATGGCGAACCCCACCGGCGGCAACAGAAACAA 10 80 0 CGACCGGGGA 0.960491 -41 CGCAATCGTAAGAATGAGACAGGCCGTAAAGTTTGGCG 13 27 0 AGACAGGCGA 0.838458 -78 CTCATTCTTACGATTGCGGCAGGCCGTGTTATTATTGT 13 47 1 CGTCAGGCGG 0.775745 -58 TGATTAAGGAAGGATTTTCCAGGAGGAACAC 15 78 1 AGACAGGGGA 0.972973 -21 ATCTGCTTTGCGTATGCAAAAGCGGGCGAGATTCTATA 23 44 0 CGAAAGCGGG 0.802582 -81 TCGAAAATGGCGCTTTCGTCAGCGGGGATAATCCGTTA 27 174 1 CGTCAGCGGA 0.905662 -127 TCTATTATAACGAAAAAAACAGAGGGCGCAAAACCCTC 31 29 0 CGACAGAGGG 0.793073 -116 GTTAAGACACCGCCCTTTCACGGCGGTAACACGGGTTC 42 57 1 CGCACGGGGA 0.672188 -244 TGACAGGCAACGAATATAACAGGTGGGAGATGAGAGGA 42 273 1 CGACAGGGGA 0.990491 -28 TGAGAATCCTCGTATTCTCCAGGAGGAATGAAT 43 62 1 CGACAGGGGA 0.990491 -23 TTGAACCTAGAGCAATTATAAGGAGGTTCACTGGAAAA 54 55 0 AGAAAGGGGT 0.662515 -72 CGCATCCATGCGGAGCGAACAGCTGGAAAATTATACGC 55 103 1 CGACAGCGGA 0.96182 -198 ** * **** ** * Masking position 12 Map Score: 12.3795 Number of sites scoring better than the average of aligned sites = 587 Number in coding regions = 538 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 6 TTTCAATCCCAACGTAAGCAAAAAATACG 26 5 0 AAAAAAAAAA 0.918027 -121 GTATATAATCAAATGAAATAAAAAACTTTGGTTCG 28 56 0 AAAAAAAAAA 0.918027 -245 AAAAATCTTTAATGAAAATAAAAAAAGTCTGTTCG 28 105 0 AAAAAAAAAA 0.918027 -196 GAAAAAGAATAATTAAAATTAAAAATCTTTAATGA 28 125 0 AAAATAAAAA 0.67758 -176 CACTTTGTCTATTATAACGAAAAAAACAGAGGGCG 31 39 0 ATAAAAAAAA 0.823997 -106 TATTTCCTCCAAGACAAAATAAAAACTTTTGTATA 31 120 0 AAAATAAAAA 0.677581 -25 CCTTTCATTCAATGATAAGAAAAAACTTGGACTCA 32 67 1 AATAAAAAAA 0.524319 -95 ATGTATCATTATGTAAAATAAAAAACCCGCATAGC 33 34 0 ATAAAAAAAA 0.823997 -177 ATGTATTTATATCCAAAATAAAAAAACCAGGGAAC 35 34 0 ATAAAAAAAA 0.823997 -114 TTTCGGGCATAAGGTAAATAAAAAAGTGATCCCGG 37 34 0 AAAAAAAAAA 0.918027 -160 AAAATAACCAAAAAGCAAGGACTGC 38 1 1 AAAAAAAAAG 0.620301 -192 AGTTTGAAAAATCAGAATTAAAAAAGGACCGCCGG 38 61 0 ATAAAAAAAA 0.823997 -132 TTTACAATTAAAAACAAGTAAAAAAGAAAATAGAG 51 131 1 AAAAAAAAAA 0.918027 -36 GAGAATTTGAAAGAAAACTAAAAAAAGTACTAGTC 55 202 1 AAAAAAAAAA 0.918027 -99 ** ** ****** Masking position 7 Map Score: 12.6345 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 32 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 CTCCGGTGCAAATGGGATGGTAAGGAGTTT 12 99 1 AATGGGATGG 0.87804 -23 ATTTGACAAAAATGGGCTCGTGTTGTACAA 33 169 1 AATGGGCTCG 0.958 -42 ATAAATACATAATGGGCTGAATATGGATAT 35 59 1 AATGGGCTGA 0.961833 -89 AGGACTGCTGAAAGGGCTGACATAAGCCTT 38 28 1 AAAGGGCTGA 0.950869 -165 CTTAACCCTAAAAGGGCTGGAATTGATTTA 48 27 1 AAAGGGCTGG 0.980203 -59 AATTTGAGAAAAGGGGCTGAAAGCAGGT 49 29 1 AAGGGGCTGA 0.919045 -18 TTGCGGGCTGAGAGGGCTGGCACATTTCAC 53 37 1 AGAGGGCTGG 0.929332 -124 AATGTGGTATAATGGGCTCGCTATGTAAAG 53 79 1 AATGGGCTCG 0.958 -82 ********** Masking position 1 Map Score: 6.29542 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 134 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 GTGATATATGGGAGATGGCGGTAGAATGACC 26 43 0 GGAGATGGGG 0.949771 -83 TGATCTTAAAGGCTAAGATGGTATCATAGAT 28 180 1 GGCTAAGAGG 0.740081 -121 TATCCTATGAGGAGAAGAAAGCATGTAGAAC 30 68 0 GGAGAAGAAG 0.960778 -88 ATGTTTAGATGGAGAAGTAGGTGAAAGCT 35 129 1 GGAGAAGTGG 0.922771 -19 TTTTATATAGGGAAAAGGTGGTGAACTACT 37 174 1 GGAAAAGGGG 0.805731 -20 ATAACAGGTGGGAGATGAGAGGA 42 288 1 GGAGATGAAG 0.907039 -13 AATTTCTTCTGGCGAAGATGGGAATATATGA 43 28 1 GGCGAAGAGG 0.97023 -57 TTTTTGGCAGGGTGTAGATGGTAATTCGTGA 52 191 0 GGTGTAGAGG 0.728047 -110 CATACAGACCGGTGAAGGCAGAGGTTAGATA 52 277 1 GGTGAAGGAG 0.846427 -24 TTTATATAGAGGAGATGAAAGA 54 115 1 GGAGATGAAG 0.907039 -12 TAGAAGGTAAGGAGAAGACGGCG 55 288 1 GGAGAAGAGG 0.985223 -13 ******** ** Masking position 7 Map Score: 6.39307 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 283 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 CCATCTTGTAAATTCAGCTAACCCTTGTGGGGC 6 52 1 AATTCGCTAC 0.807985 -95 GGATAATCCGGCTACAGAGAGTCGCGC 9 5 1 AATCCGCTAG 0.964681 -181 TTAGCAGAATAATCTACCTACGCGAGACC 22 130 1 AATCTCCTAC 0.500659 -19 CTCTTAAATTAATCCTGCTACAGGCGACCCAGC 23 94 0 AATCCGCTAG 0.964681 -31 CTTGAAACCTCCTAATCAGAATGTCAA 28 284 0 AAACCCCTAC 0.910318 -17 AGCTCTTACAAAACCCGCTAGCGTTTTTTG 30 8 0 AAACCGCTAG 0.952017 -148 TGAATCTGAGAATCCTCGTATTCTCCAGGAGGA 43 56 1 AATCCCGTAC 0.750198 -29 ACAATCATCCAATTCTGGTATCGATTTGTTTAC 47 89 1 AATTCGGTAG 0.474888 -106 TACTAAACCTCCTATACACTTCCTACG 48 69 0 AAACCCCTAC 0.910318 -17 CTCAAATTAAAAACCCGCTAAAGAGC 49 4 0 AAACCGCTAG 0.952017 -43 CGTTGGTTCGAATCCAGCTAGCCCAGTCACAGA 52 55 1 AATCCGCTAC 0.964681 -246 AAAAAAGAGCAAAGCGGCTAACGCGCT 53 5 0 AAAGCGCTAG 0.719821 -156 ***** **** * Masking position 10 Map Score: 5.51082 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 65 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 GGCCACCGAAGTGACCCTTTTTCAGAACTTTTGC 15 14 0 GTCTTTTTCA 0.718781 -85 ATAGTATGCCATGGATCTTTTTCCCTTGAGGGAT 22 97 0 ATCTTTTTCC 0.718781 -52 TGGCGGTAGAATGACCCGTTTTCAATCCCAACGT 26 25 0 ATCGTTTTCA 0.824678 -101 GATGAAAAAAATGTAGTTTTTTCAAGGTGAAGCG 27 241 1 ATTTTTTTCA 0.916095 -60 TTTAATTTTAATTATTCTTTTTCAGGGCGTATGT 28 137 1 ATCTTTTTCA 0.946009 -164 TTGTATATTCATGAAACTTTTTCTTATATCGAGC 31 93 0 ATCTTTTTCT 0.632962 -52 TTGAGGAATCATAGAATTTTGTCAAAATAATTTT 33 95 1 ATTTTTGTCA 0.868413 -116 ATCAACGTTAATAAGACGTTGTCAATAAAATTAT 33 121 0 ATCGTTGTCA 0.7398 -90 GTGTAACTATATCCTATTTTTTCAAAAAATATTT 37 90 1 ATTTTTTTCA 0.916095 -104 TCCTTTTTTAATTCTGATTTTTCAAACTTAGTTG 38 68 1 ATATTTTTCA 0.661777 -125 GAAAGCACAGATAGGATTTTGTCAAAAGAAGGTA 42 232 0 ATTTTTGTCA 0.868413 -69 TGGAAGAGAAATTCACTTTTTTCACTAACAACAT 51 94 1 ATTTTTTTCA 0.916095 -73 CAAGCTGAAAATGCTTTTTTGTCAGCTTGTCTTT 54 24 1 ATTTTTGTCA 0.868413 -103 CTCCGCATGGATGCGGTTTTTTCATTTCTACGAT 55 84 0 ATTTTTTTCA 0.916095 -217 TAGGCCGACACTCATGCTTTTTCATATAGAAGGT 55 262 1 CTCTTTTTCA 0.718781 -39 ** ******** Masking position 9 Map Score: 7.01935 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 58 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 ACTTGACAACTGTGTGAGGAAAAGCGTATTTGCGCA 3 48 0 TTGTGAAGCG 0.914442 -130 CGGAAAAGCATCTGCTATTTATAGCGGCCTCATTTT 3 107 1 TTGCTAAGCG 0.876925 -71 TTCGACGTCTGATGCTGTACACAGCGCCAACAATTA 4 77 1 GTGCAAAGCG 0.970751 -224 CCACGACGTATTTGTGGTATAAAGCGCGCCGGACTT 4 120 1 TTGTAAAGCG 0.92853 -181 CCCTTGTGGGGCTGCGCTGAAAAGCGACGTACAATG 6 73 1 GTGCGAAGCG 0.964668 -74 ACAGTGGAAGTGTGCTAAGTATAGCCCTGATTAAAC 7 219 0 TTGCGAAGCC 0.879184 -73 TACTGAAGCCTATACAAAAAAAAGCCGTGTAAAACC 9 120 0 TTACAAAGCC 0.528124 -66 CTTTCCAGGCGGTGTATTAAAGAGCGCGATGCAACG 20 55 0 GTGTAAAGCG 0.905123 -96 TGAACTGTTGTCTGCCCAGTATAGCGGTCTAATAAC 22 61 1 TTGCGAAGCG 0.97381 -88 AAGTTTGAAAGATGCTGGATATAGAGTATCCTGACG 25 29 1 GTGCAAAGAG 0.686128 -71 TTATTACAACTGTGTTAAAAACAGCGTCAGGATACT 25 53 0 TTGTAAAGCG 0.92853 -47 AAAATCGGCTTCTGCAAGAGAAACCGATTTGTTAGG 42 113 0 TTGCAAACCG 0.815235 -188 GTTACGCATATGTACTTTACATAGCGAGCCCATTAT 53 87 0 TTACAAAGCG 0.851161 -74 * *** * * **** Masking position 11 Map Score: 7.88427 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 240 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 12 CTCGGAGATGTGATCTGCCCGGCATTAAACC 5 228 0 TGACTGCCCG 0.901022 -30 GAGGATGGCGAGCACTGCCCGGGGCCAAAAT 7 144 1 AGCCTGCCCG 0.926346 -148 TGCAGTTCTTTGCGTGGCCCGGCGATCTTAT 12 66 0 TGCTGGCCCG 0.985951 -56 ACAGTAGCAATGCCCGGCACGTTACCGGGCA 17 30 0 TGCCGGCACG 0.976227 -35 GAAAGGATCATGCCTGGCCCGCACAGTTTTC 20 86 1 TGCTGGCCCG 0.985951 -65 AAACAAAAGGTTCACTGCCCG 34 1 0 TTCCTGCCCG 0.886842 -159 TAGCCATTCGTGCACGTCACGATAATATGTG 34 112 0 TGCCGTCACG 0.820976 -48 CTACCATATTTGTTTGGCCCGTTGGTCAAGC 42 25 1 TGTTGGCCCG 0.901022 -276 *** ******* Masking position 8 Map Score: 3.69692 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 243 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 13 GCTATTTTTTTGTCCTGAATGATGTTTGACAC 1 24 1 TGCCTGATGA 0.936599 -69 TTTGCGCACGCGACCAGAATGTAAATTAACCA 3 24 0 CGCCAGATGT 0.941193 -154 TTGTCGCTTCCGTCCAGTCTGTGTATACGAAA 4 164 0 CGCCAGTTGT 0.878745 -137 TGTGACTGTCTGGTCTGACTGAGACAAGTTTT 7 256 1 TGTCTGATGA 0.806509 -36 GTTTTTTTGTCCTGAGTGTGTACATAACT 19 259 0 TGCCTGATGT 0.97026 -19 ACGCGTCCTGACTGTAATTTGAGAA 27 286 0 CGCCTGATGT 0.972487 -15 GAAAGCTTTATGACCTAATTGTGTAACTATAT 37 70 1 TGCCTAATGT 0.740282 -124 AACTTCTAACTGTTCAGTCTGTATAATAATTT 52 135 1 TGTCAGTTGT 0.653666 -166 CTGCCTTCACCGGTCTGTATGTATACGAGCTT 52 266 0 CGTCTGTTGT 0.818705 -35 ATAAAGACTTTGGCCTGAATGATATCGTAGAA 55 61 1 TGCCTGATGA 0.936599 -240 ** ***** *** Masking position 10 Map Score: 3.45367 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 298 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 14 GTGAGATTGTCGCTTCCGTCCAGTCTGTGT 4 172 0 CGCTTCCGTC 0.97545 -129 CACGGCCTGCCGCAATCGTAAGAATGAGAC 13 45 0 CGCAATCGTA 0.695579 -60 CGTTACCGTCCGCTATCGTCTATGTTCAAG 21 144 0 CGCTATCGTC 0.970255 -70 TTAATGCTAGCGTTACCGTCCGCTATCGTC 21 154 0 CGTTACCGTC 0.852454 -60 TCGAAAATGGCGCTTTCGTCAGCGGGGATA 27 174 1 CGCTTTCGTC 0.961613 -127 CACTTATCGCCGCTCTCGTCCTTTGGGCGG 28 247 1 CGCTCTCGTC 0.936282 -54 TCCCCTCCGCCGCTACCATATTTGTTTGGC 42 13 1 CGCTACCATA 0.693099 -288 CGCTTCCGTATAAATCAAAT 43 1 1 CGCTTCCGTA 0.939509 -84 ********** Masking position 9 Map Score: 3.39783 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 241 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 15 GCTGTGTACAGCATCAGACGTCGAATTTTC 4 72 0 GCATCAGACG 0.857656 -229 CATATTTCGCGCCGCAGATGCGTTATCTTC 5 112 0 GCCGCAGATG 0.921961 -146 CGGCCAGCGCGCAGCAACCGGAGCGTACAA 7 106 1 GCAGCAACCG 0.95918 -186 AACACGGCCTGCCGCAATCGTAAGAATGAG 13 47 0 GCCGCAATCG 0.803546 -58 CGGCAAAAATGCCGCAGACAACGAC 18 6 0 GCCGCAGACA 0.835774 -111 GTCAAGCGGGGCCGCAACCAGTAAACTACG 19 225 1 GCCGCAACCA 0.814173 -53 GTTCCCGCATCAGATGACTGTATTTG 24 7 1 GCATCAGATG 0.660256 -38 CGTCTAATAAGCAGAAAATGCACTTTGTCT 31 64 0 GCAGAAAATG 0.46799 -81 GGTTTCTCTTGCAGAAGCCGATTTTTTTCA 42 124 1 GCAGAAGCCG 0.919742 -177 GAATATCAAGGCAGAAACCGTCGAAGATTT 42 190 1 GCAGAAACCG 0.838377 -111 AAAACTGCCAGCGTCAGCCGGCAGTTTTTT 47 26 0 GCGTCAGCCG 0.779063 -169 GATTGTAAAAGCCGCAGCTGAGCCAATCAT 47 65 0 GCCGCAGCTG 0.957393 -130 ********** Masking position 6 Map Score: 4.24853 Number of sites scoring better than the average of aligned sites = 2329 Number in coding regions = 2045 Number in noncoding regions = 284 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651