AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00260_synecho_reg_100.orf -o00260_synecho_100.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 slr1097 57 hypothetical protein. #2 slr1098 67 hypothetical protein. #3 slr1099 300 ubiX; 3-octaprenyl-4-hydroxybenzoate carboxy-lyase. [EC:4.1.1.-] #4 sll1931 300 glyA; serine hydroxymethyltransferase (serine methylase) (SHMT). #5 slr1703 231 serS; seryl-tRNA synthetase (serine--tRNA ligase) (serRS). #6 slr2072 300 ilvA; L-threonine deaminase. [EC:4.2.1.16] #7 sll1760 259 thrB; homoserine kinase (HK). [EC:2.7.1.39] [SP:KHSE_SYNY3] #8 sll1688 300 thrC; threonine synthase. [EC:4.2.99.2] #9 slr0861 164 purT; phosphoribosylglycinamide formyltransferase 2 (gart 2) (GAR #10 sll1908 260 serA; phosphoglycerate dehydrogenase. [EC:1.1.1.95] #11 sll1172 282 thrC; threonine synthase. [EC:4.2.99.2] #12 slr0293 105 gcvP; P protein of glycine cleavage complex. [EC:1.4.4.2] #13 sll0171 168 gcvT; probable aminomethyltransferase (glycine cleavage system T #14 slr0220 175 glyS; glycyl-tRNA synthetase beta chain (glycine--tRNA ligase beta #15 sll0455 127 hom; homoserine dehydrogenase (HDH). [EC:1.1.1.3] [SP:DHOM_SYNY3] #16 slr0638 49 glyQ; glycyl-tRNA synthetase alpha subunit (glycine--tRNA ligase). #17 slr0639 214 hypothetical 33.2 kD protein slr0639. [SP:Y639_SYNY3] #18 sll0078 171 thrS; threonyl-tRNA synthetase (threonine--tRNA ligase) (thrRS). #19 slr0549 59 asd; aspartate beta-semialdehyde dehydrogenese. [EC:1.2.1.11] #20 slr0550 300 dapA; dihydrodipicolinate synthase (DHDPS). [EC:4.2.1.52] #21 slr0657 200 lysC; aspartate kinase. [EC:2.7.2.4] #22 slr1556 152 ddh; 2-hydroxyaciddehydrogenase. [EC:1.1.1.-] Motif number 1 GTGAAAATAGTTGGGGGACAAAGGCTTTAGTGATC 3 184 0 TTGGGGGAGC 0.989101 -117 TCCGGCAAGGTTGGGGGATTTGGACTTACACTTCC 3 225 1 TTGGGGGAAC 0.982523 -76 GTAAACAGTGCTGGGGGCGGAAAGCACCGCGCTTC 4 263 0 CTGGGGGCGC 0.99276 -38 CCGGCCTGTGCTTGGGAAACAGTGAGAAATTATCG 6 202 0 CTTGGGAAGA 0.664286 -99 CCTATATTTATTTGGGAGTTAAAGCCTAGCCA 7 8 0 TTTGGGAGGC 0.555453 -252 CGGGGGTTCAGTGGGGAAGAAACACCCCATTTAAC 8 51 1 GTGGGGAAAC 0.808855 -250 GCTTAATTCCCTTGGGGAAAACCGACCTATTTTAG 8 120 1 CTTGGGGAGA 0.949283 -181 GAGAGATTCCCTGGGGGAAGTTAAAAAGCTCTGGG 9 116 0 CTGGGGGAAA 0.983934 -49 AGATTTTGCTCTGGGGGAACAGTAACCAGGGCAAT 10 54 1 CTGGGGGAAA 0.983934 -207 TTCCCTGGGACTGGGGGGGCCAAACCATAGGGAGT 10 157 0 CTGGGGGGAC 0.990579 -104 TTCTAGCGGCTTGGGGGATAACCGTTAGCAATATT 10 197 0 TTGGGGGAGT 0.955404 -64 TAATGGTGGTCAGGGGGGGTCCAGCGGTGTTGCAC 11 34 1 CAGGGGGGGC 0.950783 -249 GGTGTAATCCCTTGGGGTGCAACACCGCTGGACCC 11 50 0 CTTGGGGTAC 0.755007 -233 GGGCGATCGCCTGGGGGCATTCTGCCAATTTTTCT 11 108 1 CTGGGGGCGC 0.99276 -175 TCCCCCAGTATTGGGGGCTAGGGGACTTTCAATAC 13 29 0 TTGGGGGCGA 0.952783 -140 GCCCCCAATACTGGGGGAATCAGATTCGATAATCC 13 46 1 CTGGGGGAAT 0.973052 -123 TGAAGAGATTTAGGGGGCTGAACAAAACTGCTAAA 14 71 0 TAGGGGGCAA 0.587077 -105 TCCGGCAATACTGGGGGACTTTCACTCAGTTTCCC 14 113 1 CTGGGGGAAC 0.993505 -63 GGCCTCCAATTTGGGGGGAAACTGAGTGAAAGTCC 14 128 0 TTGGGGGGGA 0.961531 -48 CATGGTCTCAGTGGGGGATGATAATCGAGGGAGAA 17 133 0 GTGGGGGAAT 0.9043 -82 CTTCAACCCAGTGGGGGGCGGGAGCGGATCAAGTA 18 94 1 GTGGGGGGGC 0.977997 -78 GGTAAAGAACTTGGGGATAAATATTCGATTAACC 20 277 0 CTTGGGGAAT 0.87239 -24 ******** ** Masking position 6 Map Score: 36.0296 Number of sites scoring better than the average of aligned sites = 1491 Number in coding regions = 1292 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 2 CGGCCCCTAGCCTAGGGGGGGAAATTTC 1 8 0 CCTAGGGGGG 0.833204 -50 GCTCGGTGCGCCATGGTTGGGATTAGCCGTT 3 153 0 CCATGGTGGG 0.929094 -148 TAAAGCTCCGGCAAGGTTGGGGGATTTGGAC 3 219 1 GCAAGGTGGG 0.985934 -82 ATCACACTCTGAAAGACGGGGTTTTAGACCC 4 202 1 GAAAGAGGGG 0.921829 -99 ACGATTTGATGCAGTGATGGGT 5 220 1 GCAGTGTGGG 0.876088 -12 AAATATTCTTGCTAGATTGGCAGGTTCATCG 6 13 1 GCTAGATGGC 0.902375 -288 CCCATTACTAGCACGAATGGGGCAAAAAA 6 282 1 GCACGATGGG 0.950501 -19 GGCAGTAATGGAATTAATGGGAGTAAAATAT 7 73 0 GAATTATGGG 0.847282 -187 CTACCTGAATGAATGATTGGGCAGTAATGGA 7 92 0 GAATGATGGG 0.936585 -168 TGGGCCAGAGGCAATAGTGGCTTGACCCAGA 7 186 0 GCAATATGGC 0.879116 -74 TTTTTACCCAGCATTGATGGGAAGACTCGGC 8 165 0 GCATTGTGGG 0.935334 -136 GATTCCCTGGGACTGGGGGGGCCAAACCATA 10 163 0 GACTGGGGGG 0.596836 -98 CCCCCAAGCCGCTAGAATGGGCTACGGAGAT 10 215 1 GCTAGATGGG 0.971486 -46 TCTCTAAAATGCTAGACTGAGAAACTGTAGT 12 31 0 GCTAGATGAG 0.542 -75 CCCCTAGCCCCCAATACTGGGGGAATCAGAT 13 40 1 CCAATATGGG 0.900675 -129 TTAGTGAAGAGATTTAGGGGGCTGAACAAAA 14 79 0 GATTTAGGGG 0.53739 -97 TAAAGCTCCGGCAATACTGGGGGACTTTCAC 14 107 1 GCAATATGGG 0.963911 -69 CCCAAGTCCAGATAGAATGGGGAGCCGATCG 15 67 1 GATAGATGGG 0.927744 -61 TGGTGTAGGGGACAGGCTGGGCGGTAATTTA 16 14 1 GACAGGTGGG 0.859856 -36 AACCTTCAACCCAGTGGGGGGCGGGAGCGGA 18 91 1 CCAGTGGGGG 0.513403 -81 GGGCAAGTAACCATGGATGGGTTGGGAAAAA 19 37 1 CCATGGTGGG 0.929089 -23 GAATGTATATGCTAGAATGGCATGAACTTAA 20 66 0 GCTAGATGGC 0.90214 -235 CGATACCAGTCAAAGAATGGCAGTCACAAGC 20 205 0 CAAAGATGGC 0.71222 -96 TGAATGCTTTGAACTACTGGCTGAGCTGATC 21 109 0 GAACTATGGC 0.423112 -92 ****** **** Masking position 9 Map Score: 22.4981 Number of sites scoring better than the average of aligned sites = 2094 Number in coding regions = 1834 Number in noncoding regions = 260 Number of orfs with sites within 600 bp upstream = 262 Fraction of orfs with sites within 600 bp upstream = 0.0420816 Motif number 3 GACTAACCCCGGCCCCTAGCCTAGGGGGGGAAATT 1 13 0 GGCCTCCAGG 0.920906 -45 GCACAGGCCGGAGCCGTAACCAGGGCCAGAAATTA 6 226 1 GAGCTCCGGG 0.983781 -75 GGAATACAGTGACCAAAACCCAGAGCTTTTTAACT 9 98 1 GACCACCGAG 0.748302 -67 CTTCCCTAAGGAGAGATTCCCTGGGGGAAGTTAAA 9 126 0 GAGATCCGGG 0.976884 -39 TGCTCTGGGGGAACAGTAACCAGGGCAATTTTAAG 10 60 1 GAACTCCGGG 0.937596 -201 CCAAACCATAGGGAGTTTTCCCTAGAAAGCCTAGA 10 138 0 GGGATCCTAG 0.938562 -123 TAGTATCCTGGGCCGATCTCCGTAGCCCATTCTAG 10 226 0 GGCCTCCTAG 0.943091 -35 TGCACCCCAAGGGATTACACCTGGGTCAAGCTTAC 11 64 1 GGGAACCGGG 0.96887 -219 CCGGACTTGTGGGCGATCGCCTGGGGGCATTCTGC 11 98 1 GGGCTCCGGG 0.992803 -185 GGGGGGCAATGGCCCGAGGTTCCATTCT 11 265 0 GGGCTCCGAG 0.96507 -18 AAAAAAGCACAAAAAATCCCCCTGGTTAAAGGAGG 13 79 0 AAAATCCTGG 0.542901 -90 GGGACGAGGTGGCAAAAATCCTTGGGTACCAGATG 17 26 1 GGCAACCTGG 0.949157 -189 CCAGAGATGAAGGAAAACGCCTTGGATTATAACCT 18 18 1 AGGAACCTGG 0.779315 -154 CTTGGATTATAACCTGTTCCCATGGGCCAGATTTC 18 38 1 AACCTCCTGG 0.838747 -134 AAGGGCAGCGGGCAAGTAACCATGGATGGGTTGGG 19 28 1 GGCATCCTGG 0.98295 -32 ACACTGGGCAGGGATTTAGCCATGGAGTTGATGGT 20 139 1 GGGATCCTGG 0.98706 -162 AATCAATTGGGAAACTTGACCTTGGCGATACCAGT 20 226 0 GAAATCCTGG 0.892561 -75 **** * ** *** Masking position 15 Map Score: 23.5291 Number of sites scoring better than the average of aligned sites = 2124 Number in coding regions = 1937 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 220 Fraction of orfs with sites within 600 bp upstream = 0.0353357 Motif number 4 TCGGCGGCTGTGGGCAAAGTTTGGCATTGC 3 99 0 TGGGCAAAGT 0.919681 -202 AGTTTCCGTCTGGGAAGAAATTGTCAAGAG 4 77 0 TGGGAAGAAA 0.859286 -224 CGTTTTTGTTTGGGCAAAGTAACGATTTGA 5 199 1 TGGGCAAAGT 0.919681 -33 CCTGCCAATCTAGCAAGAATATTTGC 6 7 0 TAGCAAGAAT 0.615051 -294 GCCGTAACCAGGGCCAGAAATTAGGGTAAC 6 238 1 GGGCCAGAAA 0.711152 -63 TAGCACGAATGGGGCAAAAAA 6 290 1 GGGGCAAAAA 0.857803 -11 ATTTTCGCCTTGGCAAAAATCAATCGTATC 7 141 1 TGGCAAAAAT 0.884945 -119 GGGGTTCAGTGGGGAAGAAACACCCCATTT 8 53 1 GGGGAAGAAA 0.795294 -248 CCAGCATTGATGGGAAGACTCGGCAGGGAG 8 159 0 TGGGAAGACT 0.733398 -142 ATGCTAACACGGGGCAAAATGGGCGTCAAT 8 247 0 GGGGCAAAAT 0.952447 -54 GGGGCAAAGTCCTAAATTTC 8 291 0 GGGGCAAAGT 0.879297 -10 ATCAGAAAAATTGGCAGAATGCCCCCAGGC 11 116 0 TTGGCAGAAT 0.665296 -167 GTGCTTTTTTTAGGAAAAATCTATTATGCA 13 104 1 TAGGAAAAAT 0.796534 -65 TGGGACGAGGTGGCAAAAATCCTTGGGTAC 17 25 1 TGGCAAAAAT 0.884945 -190 CTGATAAAGATGGGCAGAATAACTAAGTTT 17 104 1 TGGGCAGAAT 0.970286 -111 ATGGATGGGTTGGGAAAAATT 19 49 1 TGGGAAAAAT 0.951332 -11 CTCGCCCCGTTAGCCAAAATACAAAATAAC 21 54 0 TAGCCAAAAT 0.712717 -147 GCTTCATTTTTAGGAAAAATATCTGGTAAT 22 80 1 TAGGAAAAAT 0.796534 -73 ********** Masking position 6 Map Score: 17.972 Number of sites scoring better than the average of aligned sites = 1788 Number in coding regions = 1542 Number in noncoding regions = 246 Number of orfs with sites within 600 bp upstream = 257 Fraction of orfs with sites within 600 bp upstream = 0.0412785 Motif number 5 CGGTAAAATGTCGGCGAAAGCCTACAAAAGTT 6 172 0 TGCGAAAGCC 0.916664 -129 GCTTGACCCAGAGGCGATCGCTTGGCGGATAC 7 166 0 GGCGATCGCT 0.984611 -94 CTGTATTCCGTTGTCGAAATCCTCAGGATCTG 9 75 0 TGCGAAATCC 0.89522 -90 TTAGTATCCTGGGCCGATCTCCGTAGCCCATT 10 230 0 GGCGATCTCC 0.989862 -31 ACCGGACTTGTGGGCGATCGCCTGGGGGCATT 11 97 1 TGCGATCGCC 0.984611 -186 AAGGATTAATGAGGCGATCTCTAAAATGCTAG 12 47 0 GGCGATCTCT 0.980275 -59 TCCTTCACAAGTGACGATCTCTCTAGGATAAA 12 74 1 GGCGATCTCT 0.980275 -32 ATAGAATGGGGAGCCGATCGCCAGTAACCTAA 15 78 1 GGCGATCGCC 0.992108 -50 CCCATGCTGCTGGTCGAAATCTGGCCCATGGG 18 56 0 TGCGAAATCT 0.813036 -116 * * ******** Masking position 7 Map Score: 10.6539 Number of sites scoring better than the average of aligned sites = 3113 Number in coding regions = 2844 Number in noncoding regions = 269 Number of orfs with sites within 600 bp upstream = 256 Fraction of orfs with sites within 600 bp upstream = 0.0411179 Motif number 6 AGGCTAGGGGCCGGGGTTAGTCCGTCCTATTTGC 1 26 1 CGGGTTGTCG 0.848219 -32 CCAACCTTGCCGGAGCTTTAGTGAAAATAGTTGG 3 205 0 CGAGTTAGTA 0.745144 -96 GACTTACCCTCAGAGCCTAAGTAAATCCG 3 282 1 CGAGCTAGTA 0.824835 -19 AAAGAAAGGGCCTGACCTTAGTAGCTCCTCGCCA 6 73 0 CTGACTAGTG 0.659434 -228 TTCAGGTAGCCATGGTCTAAGTAAACTATTTTCG 7 114 1 CTGGCTAGTA 0.917939 -146 CATTATCGGGCTTGGTCTGGGCCAGAGGCAATAG 7 200 0 CTGGCTGGCA 0.942845 -60 CTAGGGTTTTCGGGGGTTCAGTGGGGAAGAAACA 8 41 1 CGGGTTAGTG 0.965956 -260 TTAAAAAGCTCTGGGTTTTGGTCACTGTATTCCG 9 97 0 CGGGTTGGTA 0.965956 -68 TACGGGGGCTGAGTAAAGTTGGCTAA 10 3 1 CGGGCTAGTA 0.97242 -258 TTCTGATTCCCTGGGACTGGGGGGGCCAAACCAT 10 164 0 CGGGCTGGGG 0.917721 -97 ACATATAGTTCAGGGCTTGGTCTGTCCTGGTTGG 11 155 0 CGGGTTGTCG 0.848219 -128 CCAGTATTGCCGGAGCTTTAGTGAAGAGATTTAG 14 93 0 CGAGTTAGTA 0.745144 -83 CCCATTCTATCTGGACTTGGGCAGGGAAAAGAAT 15 54 0 CGGATTGGCG 0.848219 -74 GTTAATTGTCCTGGGACGAGGTGGCAAAAATCCT 17 14 1 CGGGCGGGTG 0.869166 -201 GAATTTCCCCCATGGTCTCAGTGGGGGATGATAA 17 144 0 CTGGCTAGTG 0.935475 -71 CGACACTGGGCAGGGATTTAGCCATGGAGTTGAT 20 137 1 CGGGTTAGCA 0.961404 -164 AATTGGGAAACTTGACCTTGGCGATACCAGTCAA 20 223 0 CTGACTGGCA 0.687809 -78 GTCTATCTTCCTTGGGTTAATCGAATATTTATCC 20 263 1 CTGGTTATCA 0.51349 -38 * *** ** *** * Masking position 1 Map Score: 15.2322 Number of sites scoring better than the average of aligned sites = 1928 Number in coding regions = 1785 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 7 CCAAACTTTGCCCACAGCCGCCGACACTGG 3 105 1 CCCACAGCCG 0.84191 -196 AGAAAAACCGCCCAGTGTCGGCGGCTGTGG 3 116 0 CCCAGTGTCG 0.979021 -185 AGGACTTACCCTCAGAGCCTAAGTAAATCC 3 280 1 CTCAGAGCCT 0.60985 -21 TCAGGTAGACCTCAGTGTCCGGATCTCGAA 4 111 1 CTCAGTGTCC 0.870335 -190 CTTTTGACAACTCAGTGTCACAACGGCTTC 4 144 1 CTCAGTGTCA 0.890066 -157 CAACGGATAACCCACCGCCAACAAACTTTC 5 160 0 CCCACCGCCA 0.754698 -72 GGAGCGGCAACTCAGTGGCGAGGAGCTACT 6 58 1 CTCAGTGGCG 0.965953 -243 AGTGGCTTGACCCAGAGGCGATCGCTTGGC 7 172 0 CCCAGAGGCG 0.959889 -88 CTCAAAATTGCCCAGCCTCACTAGGGTTTT 8 21 1 CCCAGCCTCA 0.753776 -280 GCCAACTTTACTCAGCCCCCGTA 10 4 0 CTCAGCCCCC 0.656498 -257 GTTTGGCCCCCCCAGTCCCAGGGAATCAGA 10 167 1 CCCAGTCCCA 0.886294 -94 CCCCCATGGTCTCAGTGGGGGATGATAATC 17 142 0 CTCAGTGGGG 0.835983 -73 TAACCTTCAACCCAGTGGGGGGCGGGAGCG 18 90 1 CCCAGTGGGG 0.915175 -82 TAAATCCCTGCCCAGTGTCGATGATTTCTC 20 127 0 CCCAGTGTCG 0.979021 -174 ********** Masking position 4 Map Score: 11.4737 Number of sites scoring better than the average of aligned sites = 1032 Number in coding regions = 963 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 8 CCCTAGGCTAGGGGCCGGGGTTAGTCCGTC 1 22 1 GGGGCCGGGG 0.931617 -36 AAATAGTTGGGGGACAAAGGCTTTAGTGAT 3 185 0 GGGACAAAGG 0.772474 -116 CAAATTCAGGGTCAGTGGTAACATAGAA 4 9 1 GGGTCAGTGG 0.978305 -292 TAGATTGGCAGGTTCATCGGTTCAGGGAGG 6 25 1 GGTTCATCGG 0.515233 -276 GGCTTGGTCTGGGCCAGAGGCAATAGTGGC 7 196 0 GGGCCAGAGG 0.982121 -64 GGTTTTCGGGGGTTCAGTGGGGAAGAAACA 8 45 1 GGTTCAGTGG 0.899777 -256 GGGGCAAAGTCCTAAATTTC 8 291 0 GGGGCAAAGT 0.538529 -10 AGGGCCAATGGTCTCCTCACG 11 2 1 GGGCCAATGG 0.958455 -281 CGGCTAATGGTGGTCAGGGGGGGTCCAGCG 11 30 1 TGGTCAGGGG 0.796223 -253 GGTCAGGGGGGGTCCAGCGGTGTTGCACCC 11 41 1 GGTCCAGCGG 0.945044 -242 GGGGGGCAATGGCCCGAGGTTC 11 271 0 GGGGCAATGG 0.958455 -12 CCAGTATTGGGGGCTAGGGGACTTTCAATA 13 30 0 GGGCTAGGGG 0.850505 -139 TCAACGAAAAAGGGCAGCGGGCAAGTAACC 19 19 1 AGGGCAGCGG 0.861065 -41 ********** Masking position 2 Map Score: 8.44217 Number of sites scoring better than the average of aligned sites = 1708 Number in coding regions = 1521 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 188 Fraction of orfs with sites within 600 bp upstream = 0.030196 Motif number 9 TTATGAGGGAAGTGTAAGTCCAAATCCCCC 3 237 0 AGTGTAAGTC 0.931281 -64 TTAGGCTCTGAGGGTAAGTCCTTCTGATGA 3 272 0 AGGGTAAGTC 0.86884 -29 GTTCATTATTAGTGAAAGTTTGTTGGCGGT 5 147 1 AGTGAAAGTT 0.807849 -85 GGGATAGGAAAATGAAACTCGGTCATTATT 6 114 0 AATGAAACTC 0.817878 -187 AACTTCCCCCAGGGAATCTCTCCTTAGGGA 9 129 1 AGGGAATCTC 0.72736 -36 TAAAACCTGTATTGAAAGTCCCCTAGCCCC 13 21 1 ATTGAAAGTC 0.847622 -148 GGGGAAACTGAGTGAAAGTCCCCCAGTATT 14 119 0 AGTGAAAGTC 0.977213 -57 GGAAAAGAATACTGAAACTCTTTGATTGTT 15 34 0 ACTGAAACTC 0.869383 -94 CATCTTTATCAGTGAAACTCCGGTAATTGA 17 86 0 AGTGAAACTC 0.971928 -129 ********** Masking position 6 Map Score: 4.22029 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 41 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 10 ATTTTTAATTATTTCCCTTTACATATCTTT 2 31 1 ATTTCCCTTT 0.602247 -37 TGTAAGTCCAAATCCCCCAACCTTGCCGGA 3 225 0 AATCCCCCAA 0.744472 -76 CCAGAGCATTAATCCCCATTTTCCCTGCTA 7 234 1 AATCCCCATT 0.723103 -26 TACGGGGCTTAATTCCCTTGGGGAAAACCG 8 114 1 AATTCCCTTG 0.768734 -187 ATGTTCTTAAATTTCCCCTGATTCCCTAAC 9 32 1 ATTTCCCCTG 0.940023 -133 CTTTTTTTTTAAACCCCCTTTAGCCAACTT 10 26 0 AAACCCCCTT 0.775893 -235 CAAAACTTAAAATTGCCCTGGTTACTGTTC 10 70 0 AATTGCCCTG 0.696466 -191 ATCGAATCTGATTCCCCCAGTATTGGGGGC 13 46 0 ATTCCCCCAG 0.885819 -123 CAGATTCGATAATCCTCCTTTAACCAGGGG 13 66 1 AATCCTCCTT 0.682007 -103 AAGCACAAAAAATCCCCCTGGTTAAAGGAG 13 80 0 AATCCCCCTG 0.979452 -89 GTTCCATACAATTTCCCCTTACCATCTGGT 17 53 0 ATTTCCCCTT 0.907648 -162 AAATTCAGTCATTCCCCCTAATTACTTAGT 17 172 1 ATTCCCCCTA 0.904267 -43 ********** Masking position 1 Map Score: 6.37852 Number of sites scoring better than the average of aligned sites = 1365 Number in coding regions = 1186 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 182 Fraction of orfs with sites within 600 bp upstream = 0.0292323 Motif number 11 GACAATTTCTTCCCAGACGGAAACTGTACTCAG 4 82 1 TCCACGGAAA 0.839622 -219 GACCTCAGTGTCCGGATCTCGAATATCTTTTGA 4 118 1 TCCGCTCGAA 0.819301 -183 TTTGTAGATATCACACTCTGAAAGACGGGGTTT 4 193 1 TCAACTGAAA 0.935966 -108 TGGTCATAGGCTCAAAATTGCCCAGC 8 4 1 TCAACTCAAA 0.894935 -297 GTCGAAATCCTCAGGATCTGAAAATTTTCCGCA 9 62 0 TCAGCTGAAA 0.951492 -103 TGGGCAATAATCCAATTCTGAAACGATTCACAT 11 212 1 TCCACTGAAA 0.965278 -71 AATGGTTCCAGGAATCAAAAATCAAAGAA 13 150 0 TCCGATCAAA 0.770085 -19 GCAATAAGGTTCAAGGAATGAAAATGACTCATA 14 28 0 TCAGATGAAA 0.751362 -148 TTAAATGTCCTCCTGGCCTCCAATTTGGGGGGA 14 144 0 TCCGCTCCAA 0.819301 -32 TTCGATTCCGTCCAAACCTGAATAGATAATCCA 20 18 0 TCCACTGAAT 0.779364 -283 AGAATGGCAGTCACAAGCTGAAATGATCTTTGA 20 190 0 TCAACTGAAA 0.935966 -111 *** * ****** Masking position 12 Map Score: 2.83858 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 149 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 12 CTAATCTCTTTTTTTGATTGAACTCCAAAC 5 89 1 TTTTTGATTG 0.929881 -143 TAAACCACCGTTTTTGTTTGGGCAAAGTAA 5 191 1 TTTTTGTTTG 0.910591 -41 ATGGGAGGTATCTTTGTTAGTTACCCTAAT 6 257 0 TCTTTGTTAG 0.813674 -44 CTTAGGGAAGTTTTTGTTTGTCTG 9 151 1 TTTTTGTTTG 0.910591 -14 CTTGCTGATTTCTTTGATTTTTGATTCCTG 13 141 1 TCTTTGATTT 0.78035 -28 ATACTGAAACTCTTTGATTGTTCAAAACGC 15 26 0 TCTTTGATTG 0.964776 -102 TGACTGCCATTCTTTGACTGGTATCGCCAA 20 210 1 TCTTTGACTG 0.89393 -91 ********** Masking position 5 Map Score: 1.78693 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 149 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 13 CACCGAGCGATCACTAAAGCCTTTGTCCCC 3 176 1 TCACTAAAGC 0.984582 -125 CCAACTATTTTCACTAAAGCTCCGGCAAGG 3 205 1 TCACTAAAGC 0.984582 -96 CTAAATCTCTTCACTAAAGCTCCGGCAATA 14 93 1 TCACTAAAGC 0.984582 -83 ********** Masking position 6 Map Score: 1.30208 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 14 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 14 CAGAAAAGCTGACGGGAGGTGGTTAATTGAT 3 65 0 GCGGGAGGTG 0.919658 -236 AGTAATGAGAGGCGCCAGTTGTGTAGTGGTT 4 37 0 GCGCCAGTTG 0.719156 -264 CGGCAACTCAGTGGCGAGGAGCTACTAAGGT 6 62 1 GGGCGAGGAG 0.991524 -239 ACCACCATTAGCCGTGAGGAGACCATTGGCC 11 13 0 GCGTGAGGAG 0.922309 -270 ACGGCTAATGGTGGTCAGGGGGGGTCCAGCG 11 29 1 GGGTCAGGGG 0.935635 -254 CCCAGTATTGGGGGCTAGGGGACTTTCAATA 13 30 0 GGGCTAGGGG 0.924118 -139 CCCCAAATTGGAGGCCAGGAGGACATTTAAA 14 147 1 GGGCCAGGAG 0.989523 -29 TAATTGTCCTGGGACGAGGTGGCAAAAATCC 17 16 1 GGACGAGGTG 0.864336 -199 CAACCCAGTGGGGGGCGGGAGCGGATCAAGT 18 97 1 GGGGCGGGAG 0.874507 -75 TTTGGCTAACGGGGCGAGAAGTAAGCAGAAC 21 66 1 GGGCGAGAAG 0.9198 -135 * ********* Masking position 8 Map Score: 5.2336 Number of sites scoring better than the average of aligned sites = 503 Number in coding regions = 401 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 15 GAAATTTCCCCCCCTAGGCTAGGGG 1 5 1 TTTCCCCCCT 0.887667 -53 TTTTTAATTATTTCCCTTTACATATCTTTAC 2 32 1 TTTCCCTTAC 0.869449 -36 TTAATCCCCATTTTCCCTGCTATTTGCC 7 242 1 TTTTCCCTCT 0.935205 -18 TGTTCTTAAATTTCCCCTGATTCCCTAACTG 9 33 1 TTTCCCCTAT 0.968961 -132 TTCAGTATTCTTTTCCCTGCCCAAGTCCAGA 15 48 1 TTTTCCCTCC 0.939894 -80 TTCCATACAATTTCCCCTTACCATCTGGTAC 17 51 0 TTTCCCCTAC 0.971282 -164 AATTCAGTCATTCCCCCTAATTACTTAGTAA 17 173 1 TTCCCCCTAT 0.86685 -42 ATCCAAGGCGTTTTCCTTCATCTCTGGTTTT 18 14 0 TTTTCCTTAT 0.724009 -158 AATTCAGCCCTTTCCCATGATACTTGATCCG 18 118 0 TTTCCCATAT 0.777085 -54 AATTTTTCCCAACCCATCCATGGT 19 46 0 TTTTCCCACC 0.711406 -14 ******** ** Masking position 2 Map Score: 3.20582 Number of sites scoring better than the average of aligned sites = 967 Number in coding regions = 831 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412