AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00510_synecho_reg_300.orf -o00510_synecho_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/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 slr1118 38 rffM; UDP-N-acetyl-D-mannosaminuronic acid transferase. [EC:2.4.1.-] #2 sll1063 224 hypothetical protein. #3 slr1119 30 hypothetical protein. #4 sll1062 26 hypothetical protein. #5 ssl2069 268 hypothetical protein. #6 ssr1853 209 hypothetical protein. #7 slr1120 150 hofD; type 4 prepilin peptidase. [EC:3.4.99.-] #8 sll1059 79 adk; adenylate kinase. [EC:2.7.4.3] #9 sll1058 86 dapB; dihydrodipicolinate reductase. [EC:1.3.1.26] [SP:DAPB_SYNY3] #10 sll1057 300 trx; thioredoxin M. #11 sll0648 127 lim; lipophilic protein. [EC:2.4.1.-] #12 sll0646 38 cyaA; adenylate cyclase. [EC:4.6.1.1] #13 sll0645 74 hypothetical protein. #14 sll0644 195 esterase. #15 slr0686 254 hypothetical protein. #16 sll0643 300 ureG; urease accessory protein ureG. [SP:UREG_SYNY3] #17 slr1255 176 crtB, pys; phytoene synthase. [EC:2.5.1.-] [SP:CRTB_SYNY3] #18 sll1147 157 hypothetical protein. #19 slr1256 155 ureA; urease gamma subunit (ureA amidohydrolase). [EC:3.5.1.5] #20 tRNA-Glu 219 tRNA-Glu. #21 slr1257 196 hypothetical protein. #22 slr1258 130 hypothetical protein. #23 slr1259 55 hypothetical protein. #24 slr1260 63 hypothetical protein. #25 slr1262 195 hypothetical protein. #26 slr1263 27 hypothetical protein. #27 sll1961 80 hypothetical protein. #28 sll1960 34 hypothetical protein. #29 sll1958 138 hisC; histidinol phosphate aminotransferase. [EC:2.6.1.9] #30 sll1957 300 arsA; arsenical resistance operon repressor. #31 slr1519 109 hglK; HglK. #32 slr1520 167 hypothetical protein. #33 slr1521 170 hflX; GTP-binding protein HflX. #34 slr1522 220 transposase. #35 slr1523 300 transposase. #36 slr1271 251 rffM; UDP-N-acetyl-D-mannosaminuronic acid transferase. [EC:2.4.1.-] #37 slr1272 29 hypothetical protein. #38 slr1273 184 hypothetical protein. #39 slr1274 81 pilM; membrane protein. #40 slr1275 39 hypothetical protein. #41 slr1276 80 hypothetical protein. #42 sll1173 66 hypothetical protein. #43 slr1278 49 hypothetical protein. #44 sll1172 282 thrC; threonine synthase. [EC:4.2.99.2] #45 slr1279 71 ndhC; NADH-plastoquinone oxidoreductase chain 3. [EC:1.6.5.3] #46 slr1281 300 ndhJ; NADH-plastoquinone oxidoreductase subunit J (orf 155). #47 slr1622 263 ppa, ipyR; inorganic pyrophosphatase (pyrophosphate phospho- #48 slr1623 41 hypothetical protein. #49 slr1624 60 hypothetical protein. #50 sll1538 116 bgl; beta-glucosidase. [EC:3.2.1.21] #51 slr1627 118 hypothetical 22.0 kD protein slr1627. [SP:YG27_SYNY3] #52 sll1536 135 moeB; molybdopterin biosynthesis MoeB protein. #53 slr1629 124 hypothetical protein. #54 sll1535 99 rfbP; galactosyl-1-phosphate transferase. #55 sll1533 300 pilT; twitching mobility protein. #56 slr1943 235 dpm1; dolichol phosphate mannose synthase. [EC:2.4.1.83] #57 slr1944 94 hypothetical protein. #58 slr1945 64 yibO; 2,3-bisphosphoglycerate-independent phosphoglycerate mutase. #59 ssr3307 236 ycf47; hypothetical protein. #60 slr1946 160 hypothetical protein. #61 sll1841 210 odhB; dihydrolipoamide acetyltransferase component (E2) of pyruvate #62 slr1949 300 hypothetical protein. #63 slr0926 189 ubiA; 4-hydroxybenzoate-octaprenyl transferase. [EC:2.5.1.-] #64 slr0927 124 psbD2; photosystem II D2 protein. #65 slr0930 22 hypothetical protein. #66 sll0899 242 glmU; UDP-N-acetylglucosamine pyrophosphorylase. [EC:2.7.7.23] #67 ssr1562 65 clpP; hypothetical protein. #68 sll0897 106 dnaJ; DnaJ. #69 sll0895 300 cysQ; ammonium transport protein. #70 sll1550 181 hypothetical protein. #71 sll1549 300 hypothetical protein. #72 slr1656 300 murG; UDP-N-acetylglucosamine-N-acetylmuramyl-(pentape ptide) Motif number 1 TTTGCCCCCCGGCGATCGCCAAATTGGGGC 2 115 1 GGCGATCGCC 0.499996 -110 TTAACAGCTTGGCGATCGCCCACTGCCCCG 5 96 1 GGCGATCGCC 0.499996 -173 GCCACTTCACGGCGATCGCCCGTCGTCTGG 10 228 1 GGCGATCGCC 0.499996 -73 GAAACATCGGGGCGATCGCCTTTGTTCGCT 17 42 1 GGCGATCGCC 0.499996 -135 CATGGAGATATGCCATGGCCAAACTGCCAA 29 11 0 TGCCATGGCC 0.689766 -128 CGTTAGCAGGCGATCGCCGGGGAGACGC 32 9 1 GGCGATCGCC 0.499996 -159 CGGAGGTGTGGGCGATCGCCTGCCAATCAA 36 97 1 GGCGATCGCC 0.499996 -155 CGGACTTGTGGGCGATCGCCTGGGGGCATT 44 99 1 GGCGATCGCC 0.499996 -184 TGGAACCTCGGGCCATTGCCCCCC 44 269 1 GGCCATTGCC 0.644325 -14 GCTGGATTCTTGCCATTGCCTGGTGACCGA 47 67 0 TGCCATTGCC 0.911669 -197 CTCGATTTGAGCCCATAGCCCCCCAAATTA 47 182 1 GCCCATAGCC 0.857876 -82 TGATCATATTGGCGATCGCCATTTTCCTGG 51 43 1 GGCGATCGCC 0.499996 -76 CTCCCCCCAGGGCCAATGCCTGACTCTCCA 59 16 1 GGCCAATGCC 0.90656 -221 TTTTCCTTTGGGCGATCGCCTAGATGGTCG 61 74 1 GGCGATCGCC 0.499996 -137 GTTTCCATCTTGCCAATGCCTTCAATTGAT 62 137 1 TGCCAATGCC 0.704963 -164 AATTTTCTCTCCCGATCGCCGACCCATGGT 63 46 1 CCCGATCGCC 0.925085 -144 ATCTTACCCAGCCCAACGCCTGGAGTGGTT 69 234 1 GCCCAACGCC 0.94284 -67 TGCCCTTCCTCCCCATGGCCATCACGGGCA 70 103 0 CCCCATGGCC 0.744038 -79 CCTGAAGTTGTCCGATCGCCGTTGGTCAAT 71 139 1 TCCGATCGCC 0.931849 -162 ********** Masking position 5 Map Score: 49.9749 Number of sites scoring better than the average of aligned sites = 6207 Number in coding regions = 5638 Number in noncoding regions = 569 Number of orfs with sites within 600 bp upstream = 348 Fraction of orfs with sites within 600 bp upstream = 0.0558946 Motif number 2 TTATACACATTTGCCCCCCGGCGATCGCCA 2 106 1 TTGCCCCCCG 0.952241 -119 AACCAATCGTTTGTCCCCAACCATGGCCCG 5 124 0 TTGTCCCCAA 0.907797 -145 TGCCAAGCCCTTTTCCCCCTAATTTCGACG 6 53 1 TTTTCCCCCT 0.758884 -157 AAAAAACTTAAAGTCCCCCGGCATTGGAAA 6 88 1 AAGTCCCCCG 0.889425 -122 AAATAACTCATTGTCCCCAGACAACAA 10 8 0 TTGTCCCCAG 0.869663 -293 TAATCCCCCCTAGCCCCCCTTAGAAAGGGG 15 58 1 TAGCCCCCCT 0.875113 -197 CGCTGAAAAAAAGCCCCCAACCGTTGTAGG 17 111 0 AAGCCCCCAA 0.931198 -66 TCACCCAAACAATTCCCCAAGAAGTTTAAA 20 147 0 AATTCCCCAA 0.798873 -73 AAAAGTGTCGATTTCCCCATTGATTGTAGT 25 68 1 ATTTCCCCAT 0.689057 -128 AGCCAAATTCTTGCCCCCAAAAAGTAAAAT 30 80 0 TTGCCCCCAA 0.947847 -221 ATTTGGCTACATTTCCCCAGCATCTAACCC 30 102 1 ATTTCCCCAG 0.804682 -199 GTAATGTTCCTTTCCCCCAATAGAGTAGAG 35 143 1 TTTCCCCCAA 0.907797 -158 ATGTAACCCAATTTCCCCCAGCCGTAACCT 36 155 1 ATTTCCCCCA 0.907756 -97 TTTATCCACAATTTCCCCCGATTATTAACC 36 184 1 ATTTCCCCCG 0.869608 -68 AATTGGCAGAATGCCCCCAGGCGATCGCCC 44 108 0 ATGCCCCCAG 0.933503 -175 ACACAAAAATATTCCCCCAAAGTTTTCAGT 46 209 1 ATTCCCCCAA 0.918178 -92 CCTGGCCCTAAAGCCCCCCTCCTATTAGTT 47 144 0 AAGCCCCCCT 0.888723 -120 TTTGAGCCCATAGCCCCCCAAATTAAGAAG 47 187 1 TAGCCCCCCA 0.950551 -77 CTATTAAATAATGTCCCCAATGTCCCCATT 55 169 1 ATGTCCCCAA 0.918178 -132 AAATTCTCCCCCCAGGGCCAATGC 59 5 1 TCTCCCCCCA 0.766897 -232 ATGGTGTTCAAAGTCCCCCAAACTTGCCGG 59 174 0 AAGTCCCCCA 0.922294 -63 TTTGAACACCATTCCCCCCAGAATTGGGGG 59 192 1 ATTCCCCCCA 0.947823 -45 AATGCTCCCCTAGCCCCCCAATTCTGGGGG 59 206 0 TAGCCCCCCA 0.950551 -31 TTGTTTGGAAAAGTCCCCCAACTCGTTCGG 60 32 1 AAGTCCCCCA 0.922294 -129 CCCGAAAGGAAATCCCCCAAAACCGAACGA 60 54 0 AATCCCCCAA 0.879981 -107 TAATACAGCAAAGCCCCCCTTTGTTTGTAT 66 50 0 AAGCCCCCCT 0.888723 -193 TGGCTGGTAGTTTTCCCCCTGAATTTGCCT 66 173 1 TTTTCCCCCT 0.758884 -70 TAGCAAACTCTCGCCCCCAGATGGTTGCCC 68 32 0 TCGCCCCCAG 0.71771 -75 CTTTCCCGAGTTTCCCCCAAGCTTGGGGAA 72 211 1 TTTCCCCCAA 0.907797 -90 TCCAACCTAATTTTCCCCAAGCTTGGGGGA 72 223 0 TTTTCCCCAA 0.842114 -78 ********** Masking position 5 Map Score: 47.1218 Number of sites scoring better than the average of aligned sites = 1634 Number in coding regions = 1354 Number in noncoding regions = 280 Number of orfs with sites within 600 bp upstream = 215 Fraction of orfs with sites within 600 bp upstream = 0.0345326 Motif number 3 TTTAGTTTATCGGGGATAGGATGGGGCAAATGCGC 2 164 0 CGGATATGGG 0.832436 -61 CCACTGCCCCGGGCCATGGTTGGGGACAAACGATT 5 115 1 GGGATGGGGG 0.704705 -154 TACCTGGCATAGGTATTAATGGGGGACCCCACCGC 5 194 1 AGGTTAGGGG 0.876559 -75 TTTTTCCCGTCGTCGAAATTAGGGGGAAAAGGGCT 6 58 0 CGTAAAGGGG 0.881387 -152 GCAGTCAATAAGGATAAAATTGGGCTTTTCAAAAG 6 183 0 AGGAAAGGGC 0.654057 -27 TTGAGCAATTCGGATAAAGCTGGGGCAATT 9 67 1 CGGAAAGGGG 0.977083 -20 ATTAAGATTCAGTACAAACTAGGGGAAAACGTTCA 10 172 0 AGTAAAGGGG 0.889902 -129 GGCTAAGCACCGTACAAATATGGGGTAAACTTTAT 11 73 1 CGTAAAGGGG 0.881387 -55 ACTAAAGCTCCGGCAATACTGGGGGTCTTTTGTAA 15 95 0 CGGATAGGGG 0.97552 -160 AGCTTTAGTGAGGAGATTTAGGGGGCAGAATAAAA 15 121 1 AGGATTGGGG 0.960642 -134 ATTCCGAAGTAGGGGTTAGCTGGGGTAATGGCGGT 16 20 1 AGGTTAGGGG 0.876559 -281 TATTTTCTTCCGTTGATTTGCCGGGGCAGGGTTGG 16 212 0 CGTATTCGGG 0.489239 -89 TCTTCACCTAAGGGGAAACATCGGGGCGATCGCCT 17 28 1 AGGAAACGGG 0.919087 -149 TAAACTTCTTGGGGAATTGTTTGGGTGAGCAACAA 20 149 1 GGGATTTGGG 0.612368 -71 ATGATGAAGCAGGGCAAAGAACGGGCAATGGAACC 25 13 1 AGGAAACGGG 0.919087 -183 GGCGACGTCTAGGAAAAAACAGGGGAAAGAATGCC 29 79 0 AGGAAAGGGG 0.978893 -60 CGTTAGCAGGCGATCGCCGGGGAGACGCTGTT 32 8 1 AGGATCGGGG 0.821318 -160 AGCTCGATTTCGGTATAATGTCGGGTAATGTTCCT 35 119 1 CGGTAACGGG 0.631085 -182 ATGTTCCAGGGGTTAATAATCGGGGGAAATTGTGG 36 189 0 GGTATAGGGG 0.796846 -63 AAAATTATTAAGGAGTAAGGATGGGAGGGAGAGAA 38 44 1 AGGTAATGGG 0.486414 -141 AAATAGGAGAAGACAATAGGGGGGGCAGGCAAGGC 45 14 1 AGAATAGGGG 0.734447 -58 TAAGGACATAGGGACAAACGTGGGGAAACAAATGC 55 88 1 GGGAAAGGGG 0.960124 -213 CTCCTTTCCAAGGTAAATCATGGGGGTAGTGAGAC 56 186 1 AGGAATGGGG 0.963118 -50 AGCTTTAGTGAGGAGATTTAGGGGGCGGGTCATAG 59 139 0 AGGATTGGGG 0.960642 -98 ACTAAAGCTCCGGCAAGTTTGGGGGACTTTGAACA 59 165 1 CGGAGTGGGG 0.752752 -72 TCCCAACAACGGGCAAAACCATGGGTCGGCGATCG 63 58 0 GGGAAATGGG 0.750103 -132 GATTGGGGCAAGGCAAATTCAGGGGGAAAACTACC 66 178 0 AGGAATGGGG 0.963118 -65 ATCACTCCACAGTGGATTCACGGGGAAATTTTTTC 69 29 0 AGTATTGGGG 0.809669 -272 GCAGTGGCATCGAAAATTAAAGGGGCGATTCTAAT 69 266 0 CGAATTGGGG 0.588764 -35 ATTTAGCCCTAGGATAATTGCCGGGATTAAATGAA 71 250 1 AGGAATCGGG 0.864791 -51 *** *** **** Masking position 13 Map Score: 37.401 Number of sites scoring better than the average of aligned sites = 1272 Number in coding regions = 1079 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 4 TCCTAGGGTCGGGCGGGTAAAATCAAAACCAA 2 20 1 GGGGGGTAAA 0.695734 -205 AGGGGGAAAAGGGCTTGGCAAACACCACCTTA 6 41 0 GGGTTGGAAA 0.937082 -169 AAAGTCCCCCGGCATTGGAAAATTTAAATTTA 6 97 1 GGCTTGGAAA 0.941943 -113 GGGCAAAGATGGGATTGGGAAGGGTTTAGGAT 11 106 0 GGGTTGGAAG 0.886767 -22 AACGCTGCCTGGGCAGGACAAAGGGCAAAAAC 13 49 0 GGGAGGAAAA 0.773703 -26 AACCAGCTTTGGCTATGGAAAAGTCTCTGTAC 14 54 0 GGCATGGAAA 0.941943 -142 CAGAGTAACAGCCTTGGTAAAATTTTCAGATA 22 108 1 GCCTGGTAAA 0.436901 -23 ACAGATTGATGGGTAGGGCAAATTAGCTAACT 25 130 0 GGGAGGGAAA 0.975051 -66 TAATTGGGAAGGTGTTGGAAAATTTTGTCGGC 27 45 1 GGTTTGGAAA 0.856388 -36 GGTGCCCAGGGAAAAAACAGATAAA 31 4 1 GCCAGGGAAA 0.87198 -106 CTATCATTGTGGGTAGGATAAAATGGAGAAGA 33 121 0 GGGAGGAAAA 0.773703 -50 CAGTGTAGGTGGGAAGGTAAAATAATTGGAGC 34 56 1 GGGAGGTAAA 0.816578 -165 TAAAGGTTACGGCTGGGGGAAATTGGGTTACA 36 156 0 GGCGGGGAAA 0.956269 -96 TGAAGCAATAGGTGTGGGCAAGGTGAACAAAC 39 53 1 GGTTGGGAAG 0.891634 -29 TCGGTCACCAGGCAATGGCAAGAATCCAGCCA 47 67 1 GGCATGGAAG 0.895081 -197 GGGGCTTTAGGGCCAGGGGAAGACCCTCGATT 47 157 1 GGCAGGGAAG 0.95724 -107 AGACGGCATGGAGAAGGCAATTAATG 55 5 1 GGCTGGAAAG 0.661983 -296 GGTATTGGAAAAATAGTTGGAA 56 1 1 GGTTTGGAAA 0.856388 -235 GTAGGGGGATGGAAAAGCGCTAAAAT 58 49 0 GGGATGGAAA 0.937082 -16 ATCAATTGAAGGCATTGGCAAGATGGAAACCT 62 135 0 GGCTTGGAAG 0.895081 -166 TAGTGACGATGGTTGTGGAAAAATGCACAGTG 62 219 1 GGTGTGGAAA 0.753866 -82 CGGCTAGGGCAAAAGAAAAAGGA 64 2 1 GGCAGGGAAA 0.977051 -123 ATCGTGATTGGGGCAAGGCAAATTCAGGGGGA 66 186 0 GGGAAGGAAA 0.633038 -57 TCCAGGCGTTGGGCTGGGTAAGATTGTGTTTA 69 226 0 GGGTGGGAAG 0.953597 -75 GGAAGTAATCGGCTTGGTGAAACCATCTATCT 70 17 1 GGCTGGTAAA 0.829053 -165 ATAGGCAACAGCCAAGGGAAAAACAATGCCCT 70 127 0 GCCAGGGAAA 0.87198 -55 CGCTTTTCATGGTCTGGGCAAATTAAAACCAT 71 60 1 GGTTGGGAAA 0.939932 -241 TGCTTAGTTGGGGCAGGGAAACGGAGCTGGCA 72 71 1 GGGAGGGAAC 0.77279 -230 TGATTTGGGAGGTGTTGGCAAAGTTCGGGTTT 72 153 1 GGTTTGGAAA 0.856388 -148 TTTCCCCCAAGCTTGGGGAAAATTAGGTTGGA 72 221 1 GCTGGGGAAA 0.56252 -80 *** **** *** Masking position 10 Map Score: 36.8951 Number of sites scoring better than the average of aligned sites = 1641 Number in coding regions = 1436 Number in noncoding regions = 205 Number of orfs with sites within 600 bp upstream = 221 Fraction of orfs with sites within 600 bp upstream = 0.0354963 Motif number 5 TAATCCTTTGGTGGATGACCTCTGTTAACCAATC 5 146 0 GTGATGACCG 0.636353 -123 ACCATCCAGTGCTTGCCCTGGGTTAACGGTTG 9 9 1 GTGTTGCCCG 0.946308 -78 CATTGAAAATATGTTTTACCAGAGCGTTTTTAAA 10 62 0 ATGTTTACCG 0.920206 -239 AACATCCTGAACGTTTTCCCCTAGTTTGTACTGA 10 165 1 ACGTTTCCCG 0.700428 -136 GATCGCCCCGATGTTTCCCCTTAGGTGAAGAGAA 17 25 0 ATGTTCCCCG 0.881089 -152 TATAGCGATAAAGATTGATCACTGTCAACCCTAG 19 54 1 AAGTTGATCG 0.567786 -102 ACGGTATTATAAGTTTTACCAGGGT 21 182 1 AAGTTTACCG 0.892573 -15 TAACCGATGAATGATTGATCTTTGTTGGTTTTCG 22 45 0 ATGTTGATCG 0.645809 -86 AAACAGGGGAAAGAATGCCCTTTGTTTGGGCTAT 29 64 0 AAGATGCCCG 0.826699 -75 GAGGTGGTATATGGTTGCCCTACGTGAAGCAAAA 33 73 0 ATGTTGCCCG 0.978083 -98 GCTTTGTTGATTGCCCTCCGACTGGATTAC 38 165 0 TTGTTGCCCG 0.917435 -20 CAAGTCCGGTAAGCTTGACCCAGGTGTAATCCCT 44 73 0 AAGTTGACCG 0.955589 -210 CCTGAACTATATGTTTAACCTATGCTTATTAATC 44 175 1 ATGTTAACCG 0.762228 -108 CCTCTAAATTTTGTTTGCCCCCGGACTTCTTAAT 47 208 0 TTGTTGCCCG 0.917435 -56 TACCAGCGCTATGGTTTCCCAGAGTATTGCTTGA 49 29 0 ATGTTTCCCG 0.945153 -32 GCAAGAATTACCAGCGCTATGGTTTC 49 45 0 AAGATTACCG 0.552113 -16 ATTTACCCAATTGATTGACCTTCG 51 105 1 TTGTTGACCG 0.881462 -14 GTCTGCATCAAAGGTTTACCGGGGGTTAGCTGTG 55 246 1 AAGTTTACCG 0.892573 -55 CACTACCCCCATGATTTACCTTGGAAAGGAGAAA 56 183 0 ATGTTTACCG 0.920206 -53 TATGATCGGTGTGATTAACCCAAGAGCTTGTCTA 59 100 1 GTGTTAACCG 0.558702 -137 GACTGGCTGGTAGTTTTCCCCCTGAATTTGCCTT 66 170 1 TAGTTTCCCG 0.755581 -73 TCGCCCCCAGATGGTTGCCCAGAAATCCCCACCT 68 18 0 ATGTTGCCCA 0.731514 -89 CATTATTTAGAAGTTTGCCCGTGATGGCCATGGG 70 88 1 AAGTTGCCCA 0.662504 -94 GCACCTTTTGAAGATTGACCAACGGCGATCGGAC 71 148 0 AAGTTGACCG 0.955589 -153 AACCTTTCCCGAGTTTCCCCCAAGCTTGGGGAAA 72 208 1 GAGTTCCCCG 0.678285 -93 *** ****** * Masking position 6 Map Score: 23.4459 Number of sites scoring better than the average of aligned sites = 610 Number in coding regions = 531 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 6 TAAAGCTCTAACAATACCGGGGATATTGGCATCTTGTTT 7 55 1 AATGGAATGG 0.906227 -96 TGCCCTTGTTATTTTTTCGCAAAGATTGGTAAAAAGTTC 7 113 0 ATTGCAATGG 0.718331 -38 CAAAGTCTTTACTGCCTGGGTAACAGTGGCTAAGCACCG 11 46 1 ATCGGAATGG 0.979205 -82 TTAACTTCAAAATCTGTTGGACATAATGGCGTAACTTAA 14 96 0 ATTGGAATGG 0.949631 -100 TCTCCTCACTAAAGCTCCGGCAATACTGGGGGTCTTTTG 15 98 0 AACGGAATGG 0.960218 -157 TCATAAAGTGAGTCCTTAGCCTACAACGGTTGGGGGCTT 17 92 1 ATCGCAACGG 0.752653 -85 AGATCTTTTAATTATCAGGGAAAATACGGACAGAGTAAC 22 78 1 ATTGGATCGG 0.853402 -53 CATTGATTGTAGTTCTTCGGTTACTTTGGCAAAATTGCC 25 85 1 ATCGGATTGG 0.968188 -111 GTGTTGGAAAATTTTGTCGGCAATATCGGCAATAA 27 56 1 ATTGGAACGG 0.900068 -25 CTTATTTTCCAGTCCGTTGGTCATTTTGGTTGAGGAGTG 36 18 0 ATCGGATTGG 0.968188 -234 CAGGGGTTAATAATCGGGGGAAATTGTGGATAAAGGTTA 36 179 0 TACGGATTGG 0.688424 -73 TCTCCCCAGCTAAACTATGGATAAATTGGCTGAAATTTA 43 13 0 TACGGAATGG 0.77368 -37 CAAAGTTTTCAGTCCATTGGCAACAGTGGGGGAAGGGGG 46 226 1 ATCGGAATGG 0.979205 -75 GGGCAAACAAAATTTAGAGGATTTACCGGTTCAGTTAGC 47 222 1 ATTGGTACGG 0.560563 -42 TAACCGGTCGAATTCAATGGGGACATTGGGGACATTATT 55 175 0 ATCGGAATGG 0.979205 -126 TCTCCTCACTAAAGCTCCGGCAAGTTTGGGGGACTTTGA 59 158 1 AACGGATTGG 0.93976 -79 AATGTTATCCATTGTAAAGGAAATTCTGGGAATCTGCCA 63 131 1 ATTGGATTGG 0.924159 -59 AATCATTATCATAGCATGGGCTTTTCTGGAATTTTTTAG 70 47 0 AACGGTTTGG 0.688424 -135 * * * ** * * *** Masking position 9 Map Score: 16.2609 Number of sites scoring better than the average of aligned sites = 515 Number in coding regions = 453 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 7 CAATCGTTTGTCCCCAACCATGGCCCGGGGCA 5 119 0 TCCCCAACAG 0.782335 -150 ACATTCCTTCGCCGAGACCAGC 6 1 0 GCCGAGACAC 0.764889 -209 GGTTTTGCTAGCCCAGACGACGGGCGATCGCC 10 238 0 GCCCAGACAG 0.984501 -63 TGGACTGGGAGCGCAAACAATGCCTTTTATTG 21 99 0 GCGCAAACAG 0.830814 -98 CTAAAAAATAGCCCAAACAAAGGGCATTCTTT 29 57 1 GCCCAAACAG 0.983209 -82 GATTGGTGCGGCCAAAACGACGGTATTGCAAA 31 40 1 GCCAAAACAG 0.807749 -70 TTGGATTATTGCCCAAACGATTAATAAGCATA 44 195 0 GCCCAAACAT 0.794106 -88 CGGGACTATGGCCGCAACGAACCTATCATTTT 52 88 0 GCCGCAACAC 0.764889 -48 TGCGGCCATAGTCCCGACGATGATTTTCCGTG 52 104 1 GTCCCGACAG 0.880904 -32 CTCAGCCCATGCCGAGACAAGGGACTTTGACT 62 259 1 GCCGAGACAG 0.947667 -42 TCTCATTTTTGTCCCAACAACGGGCAAAACCA 63 72 0 GTCCCAACAG 0.872097 -118 AATTTGCCTTGCCCCAATCACGATATACTCAA 66 194 1 GCCCCAATAG 0.782335 -49 CCAAATGGTAGCCCAGACAAAGGCAGAACAAG 69 117 0 GCCCAGACAG 0.984501 -184 GTTTTAATTTGCCCAGACCATGAAAAGCGAAC 71 57 0 GCCCAGACAG 0.984501 -244 CCGTTTCCCTGCCCCAACTAAGCAGAGGATAA 72 63 0 GCCCCAACAG 0.984501 -238 ******** * * Masking position 7 Map Score: 16.4679 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 155 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 CGCCAAATTGGGGCAAAAAATTAGATAATT 2 131 1 GGGCAAAAAA 0.961893 -94 TCACTTAGGGTAAAAATTAACACTCAA 8 8 1 GGGTAAAAAT 0.854999 -72 AATCGTCGTAGGACAAAAATAACTCATTGT 10 24 0 GGACAAAAAT 0.916745 -277 GGGCAAAGATGGGATTGGGA 11 118 0 GGGCAAAGAT 0.958167 -10 TTGTTATCTTGGGTAAAAATGACTCTGTTT 13 23 1 GGGTAAAAAT 0.854999 -52 GCAGGACAAAGGGCAAAAACAGAGTCATTT 13 39 0 GGGCAAAAAC 0.885936 -36 ATTTATTTATGGGCAAAAGTTCTGTATCTC 16 166 0 GGGCAAAAGT 0.905889 -135 GGGATAAAAAATACAAAAGGA 18 2 1 GGATAAAAAA 0.490703 -156 AGAGCCTCAAGGACAAAGAACTACGCCCCT 20 20 1 GGACAAAGAA 0.789146 -200 TGATGAAGCAGGGCAAAGAACGGGCAATGG 25 14 1 GGGCAAAGAA 0.933414 -182 TACTTTTTGGGGGCAAGAATTTGGCTACAT 30 84 1 GGGCAAGAAT 0.839497 -217 CAGGCTGATTGGGCAAAGATTCCGTTCAAA 30 142 0 GGGCAAAGAT 0.958167 -159 AAAATTTAGTGGACAAAAATAATATAA 42 8 0 GGACAAAAAT 0.916745 -59 TTAATCGTTTGGGCAATAATCCAATTCTGA 44 203 1 GGGCAATAAT 0.779201 -80 AGAAGTCCGGGGGCAAACAAAATTTAGAGG 47 212 1 GGGCAAACAA 0.799249 -52 CCCGTTGTTGGGACAAAAATGAGAAAGAAC 63 80 1 GGACAAAAAT 0.916745 -110 CGGCTAGGGCAAAAGAAAAAGGAGAG 64 7 1 GGGCAAAAGA 0.854888 -118 ********** Masking position 5 Map Score: 16.13 Number of sites scoring better than the average of aligned sites = 614 Number in coding regions = 519 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 9 ATTTACCAAACCGGGGGTTAACAGCTTGGCG 5 79 1 CCGGGGTTAA 0.965535 -190 CCAGTGCTTGCCCTGGGTTAACGGTTGCCCA 9 16 1 CCTGGGTTAA 0.945956 -71 CGACGATTTTCCCTGGTTTAAAAACGCTCTG 10 46 1 CCTGGTTTAA 0.849523 -255 CAACTGATCCCCTTGGTTTTGCTAGCCCAGA 10 253 0 CCTGGTTTTG 0.900359 -48 GGTCAACAGGCCTGGGGTTTAACGGTAAAAA 19 106 1 CCGGGGTTTA 0.965535 -50 TAGCTGTGTTCCTGGGGTTTATTTTCTCGGT 21 53 0 CCGGGGTTTA 0.965535 -144 GGTTTTAAGCCGTTGGGTTTGGCCGTAGATG 32 74 1 CGTGGGTTTG 0.857568 -94 TGGAAATGTTCCAGGGGTTAATAATCGGGGG 36 198 0 CCGGGGTTAA 0.965535 -54 GGCGGCACTACCATGGTTTTGGTGTGAAGAT 52 45 0 CCTGGTTTTG 0.900359 -91 CAAAGGTTTACCGGGGGTTAGCTGTGCCACA 55 254 1 CCGGGGTTAG 0.978185 -47 AGATTTCTGCCGGGGGGTTAGTTAAGGAGCA 61 109 0 CGGGGGTTAG 0.905986 -102 GATCGCCGACCCATGGTTTTGCCCGTTGTTG 63 59 1 CCTGGTTTTG 0.900359 -131 ** ******** Masking position 8 Map Score: 13.5925 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 223 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 10 AGTTTTTTAGATTTTTTTAAGAGGGT 4 11 0 ATTTTTTTTT 0.796284 -16 GCGTTAGAACTTATTTGAAAAGTTTTATTCTGCCCC 15 142 0 TATTTATTTT 0.762897 -113 AGGGAGTTCAAAATTTCTGGAGTTTTCTCAGCGACT 16 103 1 AATTTTTTTT 0.762897 -198 TAACAGTTCGTTATTTCAGACGTTTTTAAATATAGC 19 24 1 TATTTATTTT 0.762897 -132 CTTCTTTTCGTTTTTTCTTTTTTTTTAA 20 202 1 TTTTTTTTTT 0.826041 -18 CGCTTAAGTTTGTTTTTAATAATTTTAAATTTAGTG 24 22 1 TTTTTATTTT 0.796284 -42 AAGGTAGCACTGTTTTGTCAAATTTTGTACAAAATC 30 37 1 TTTTTTTTTT 0.826041 -264 ATATTAAAAATAATTTATGCGATTTTCTTGCGGATA 30 253 0 TATTTTTTTT 0.796284 -48 TGCAAAGGTCAGTTTTTATTGTTTTTATCAGAGTTG 31 66 1 ATTTTATTTT 0.762897 -44 TTTAGTTGCTTAATTTGACTGGTTTTAAGCCGTTGG 32 54 1 TATTTATTTT 0.762897 -114 CGACATATTAAATTTTATTAACTTTTGCGGCTTATT 36 51 0 ATTTTTTTTT 0.796284 -201 ATCAAAGCCTTTTTTTCTGTTGTTTTAACCGATTGA 46 163 1 TTTTTTTTTT 0.826041 -138 AACGAACCTATCATTTTAGTCTTTTTGGCGGCGGCA 52 69 0 TATTTATTTT 0.762897 -67 ATTCAGCTCCTAATTTAATTAATTTTCGAGCCTTCC 53 24 1 TATTTATTTT 0.76289 -101 TAGGTTAAAGACTTTTTTCTGTTTTTCGTCAGTTGT 55 136 0 ATTTTTTTTT 0.796284 -165 GTAGTGAGACAATTTTTAGACTTTTTAAACAGACT 56 211 1 ATTTTATTTT 0.762897 -25 TACAGGCTTTTTATTTTAGCGCTTTTCCATCCCCCT 58 37 1 TATTTATTTT 0.762897 -28 AAAAAATCAAAATTTTCTCAAGTTTT 60 145 1 ATTTTTTTTT 0.796284 -16 ATTCACGGGGAAATTTTTTCACTTTTGAACAATCCA 69 13 0 AATTTTTTTT 0.76289 -288 CGAGCCAAATTTTTTCTCTTTTTATAATCCTCT 71 8 1 ATTTTTTTTT 0.796284 -293 * **** * **** Masking position 6 Map Score: 13.7296 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 219 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 11 GGGATGATGTCCTAGGGTCGGGCGGGT 2 3 1 GAAGTCCGGG 0.816726 -222 GCCCCAATTTGGCGATCGCCGGGGGGCAAATGTGT 2 110 0 GGACGCCGGG 0.649367 -115 CTTGGCGATCGCCCACTGCCCCGGGCCATGGTTGG 5 103 1 GCATGCCGGG 0.957393 -166 CAGCATCGGAGCCAAATTCTAGGGGCCATACCAAA 11 15 1 GCATTCTGGG 0.755204 -113 CTCTCTCAATGCTTTGTCGCAAGGGCTTTTAGTCG 16 134 0 GCTTCGCGGG 0.852175 -167 ATTTTCTTCCGTTGATTTGCCGGGGCAGGGTTGGT 16 211 0 GTATTGCGGG 0.662558 -90 TTTTTCTACGGTCAACAGGCCTGGGGTTTAACGGT 19 97 1 GTAAGGCGGG 0.360435 -59 TAAACTTCTTGGGGAATTGTTTGGGTGAGCAACAA 20 149 1 GGATTGTGGG 0.439412 -71 CCTTGGACTAGCTGTGTTCCTGGGGTTTATTTTCT 21 57 0 GCTTTCCGGG 0.952462 -140 GGTTACTTTGGCAAAATTGCCGGGGACAGTTAGCT 25 103 1 GCATTGCGGG 0.907939 -93 CTAGGGAGTGGGTTAGATGCTGGGGAAATGTAGCC 30 106 0 GGAATGCGGG 0.643418 -195 TGTGGATAAAGGTTACGGCTGGGGGAAATTGGGTT 36 159 0 GGAGGCTGGG 0.513806 -93 TTATGCAGTGGAAATGTTCCAGGGGTTAATAATCG 36 202 0 GATTTCCGGG 0.86485 -50 ATTAAATCTTGATGTTTCCCGTGGGAAAAATTGAA 42 36 0 GATTCCCGGG 0.81488 -31 CTTGACCCAGGTGTAATCCCTTGGGGTGCAACACC 44 59 0 GTATCCCGGG 0.763546 -224 GGACTTGTGGGCGATCGCCTGGGGGCATTCTGCCA 44 100 1 GCTGCCTGGG 0.516226 -183 TAGGAGGGGGGCTTTAGGGCCAGGGGAAGACCCTC 47 150 1 GCTGGGCGGG 0.825353 -114 GGAGAGTCAGGCATTGGCCCTGGGGGGAGAATTT 59 10 0 GCTGCCCGGG 0.890754 -227 AACCCATTTTGACATTTTCCTTTGGGCGATCGCCT 61 60 1 GATTTCCTGG 0.181373 -151 AATTCTATCAGATTTCTGCCGGGGGGTTAGTTAAG 61 114 0 GATTGCCGGG 0.859119 -97 GTCCTAATCCGCTGTATTCCAAGGGATCTACAAGA 61 165 1 GCTTTCCGGG 0.952462 -46 CGAGAATATAGGCAACAGCCAAGGGAAAAACAATG 70 131 0 GGAAGCCGGG 0.804348 -51 ATAATTTGTTGGCTAATTCCTAGGGT 70 166 1 GGATTCCGGG 0.93474 -16 TTTAATCCCGGCAATTATCCTAGGGCTAAATAGGA 71 246 0 GCTATCCGGG 0.857846 -55 ** * **** *** Masking position 14 Map Score: 18.2366 Number of sites scoring better than the average of aligned sites = 2074 Number in coding regions = 1856 Number in noncoding regions = 218 Number of orfs with sites within 600 bp upstream = 241 Fraction of orfs with sites within 600 bp upstream = 0.0387086 Motif number 12 CGGTATTGTTAGAGCTTTAGCCAAAAGATT 7 44 0 AGAGCTTTAG 0.861685 -107 CAGTATTGCCGGAGCTTTAGTGAGGAGATT 15 109 1 GGAGCTTTAG 0.984508 -146 GCTTTAGTGAGGAGATTTAGGGGGCAGAAT 15 122 1 GGAGATTTAG 0.97001 -133 TGTTGATAGAGGCGCTTTAGTTGCTTAATT 32 39 1 GGCGCTTTAG 0.944067 -129 CGAGCTGGCTGAAGATTTAGATTATGCTCA 35 95 0 GAAGATTTAG 0.760243 -206 TAATAGGAGGGGGGCTTTAGGGCCAGGGGA 47 147 1 GGGGCTTTAG 0.944067 -117 GCTTTAGTGAGGAGATTTAGGGGGCGGGTC 59 143 0 GGAGATTTAG 0.97001 -94 CAAACTTGCCGGAGCTTTAGTGAGGAGATT 59 156 0 GGAGCTTTAG 0.984508 -81 TTATTATTTTGGAGATTTTGCGCC 63 5 0 GGAGATTTTG 0.836035 -185 ********** Masking position 6 Map Score: 8.2898 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 44 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 13 TACTTGTTTCCCATCTTAATCCTTTGGTGGATGACCTCTG 5 156 0 CAAATTGGGG 0.978648 -113 CGTTTTTAAACCAGGGAAAATCGTCGTAGGACAAAAATAA 10 32 0 CAAATCGTGG 0.904591 -269 CCAGATCGGGCCAATAAAAATGATTGGCGGTTGGCTCAAT 10 98 0 CAAATTGGGG 0.978678 -203 TTAGTCCGAGCAATATTAATGATTTGGAGGCAGAGTAACT 18 86 1 CAAATTGGGG 0.978683 -72 AAAGAAAAAACGAAAAGAAGTTCTTCGGGGCTTCTTTTTT 20 182 0 CAAATTCGGG 0.963969 -38 GGCACTCCTCTAAAAACAAAGTTCGGTGGCTAGGGATCA 40 10 1 CACATCGGGG 0.92057 -30 GCAGGCAAGGCAAGGACAATGGATTGGTGGCCATTACTAA 45 38 1 CAAATTGGGG 0.978682 -34 AAGAGTAATTCTAAACAAATTTGTCCGGGGTCGGTCACCA 47 37 1 CAAATCCGGG 0.972902 -227 CCATAGCCCCCCAAATTAAGAAGTCCGGGGGCAAACAAAA 47 194 1 CAAATCCGGG 0.972902 -70 GAAATCCCCCAAAACCGAACGAGTTGGGGGACTTTTCCAA 60 36 0 AAAATTGGGG 0.783428 -125 AAACACCAATCTAGGGAAAATAGTCCTGGGTAAGCAGTCA 72 21 0 CAAATCCTGG 0.846889 -280 * * ** **** ** Masking position 9 Map Score: 8.69441 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 57 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 14 ATGTCCTAGGGTCGGGCGGGTAAAATCAAA 2 17 1 GTCGGGCGGG 0.604169 -208 TTTGGCGATCGCCGGGGGGCAAATGTGTAT 2 108 0 GCCGGGGGGC 0.94178 -117 CATGGCCCGGGGCAGTGGGCGATCGCCAAG 5 103 0 GGCAGTGGGC 0.952179 -166 ATTTCTGCTCAGCGGTGGGGTCCCCCATTA 5 210 0 AGCGGTGGGG 0.638295 -59 AAAAATGATTGGCGGTTGGCTCAATGACAT 10 93 0 GGCGGTTGGC 0.838683 -208 CTGGGGTAATGGCGGTAGGCAAGAAACTTT 16 39 1 GGCGGTAGGC 0.901649 -262 TTCTATCAGTGTAGGTGGGAAGGTAAAATA 34 50 1 GTAGGTGGGA 0.610763 -171 TAAAGGTTACGGCTGGGGGAAATTGGGTTA 36 158 0 GGCTGGGGGA 0.738961 -94 CTGTAATCCAGTCGGAGGGCAATCAACAAA 38 163 1 GTCGGAGGGC 0.79454 -22 GCTAATGGTGGTCAGGGGGGGTCCAGCGGT 44 32 1 GTCAGGGGGG 0.79774 -251 CAACAGTGGGGGAAGGGGGAGCTAAAACTA 46 246 1 GGAAGGGGGA 0.696793 -55 TCAACTAATAGGAGGGGGGCTTTAGGGCCA 47 142 1 GGAGGGGGGC 0.976138 -122 AAATTAAGAAGTCCGGGGGCAAACAAAATT 47 206 1 GTCCGGGGGC 0.812064 -58 GACCATAACTGGAGGGAGGCTTAACACT 48 9 0 GGAGGGAGGC 0.80321 -33 TGGCGGTGGGAGTCCTCAGTT 54 2 1 GGCGGTGGGA 0.959709 -98 GATGCGGAGGTGGGGATTTCTGGGC 68 6 1 GGAGGTGGGG 0.903122 -101 AACCACTCCAGGCGTTGGGCTGGGTAAGAT 69 234 0 GGCGTTGGGC 0.811023 -67 ACTTCAGGCAGGCAGGGGGCATTATTTGAA 71 117 0 GGCAGGGGGC 0.97292 -184 ********** Masking position 8 Map Score: 15.7353 Number of sites scoring better than the average of aligned sites = 1239 Number in coding regions = 1148 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 15 TAATGAGCTGGCCGGTCAGGGCGG 19 142 0 GAGCTGGCCG 0.973543 -14 AAGAAGCGGGGAGCTTGTCGAGGGAAACAG 20 90 0 GAGCTTGTCG 0.956626 -130 AATACATCCAGAGCTTTTCGGTGGTTATCC 30 228 1 GAGCTTTTCG 0.792217 -73 TACCGAAATCGAGCTGGCTGAAGATTTAGA 35 104 0 GAGCTGGCTG 0.878721 -197 CTGATTTTCAGAGCTTTCCTCTCTACATTT 35 266 0 GAGCTTTCCT 0.792217 -35 TGCTTTTCAGGAGCTTGTCTTGGGATTATT 46 92 0 GAGCTTGTCT 0.903959 -209 ATTAACCCAAGAGCTTGTCTAAAAGGCTAT 59 113 1 GAGCTTGTCT 0.903959 -124 GGCATGGGCTGAGTTTGCCGCCACTGTGCA 62 242 0 GAGTTTGCCG 0.818685 -59 TTTTATTAAGGAGCTTGCTG 71 291 1 GAGCTTGCTG 0.910522 -10 CAGGGAAACGGAGCTGGCATTGTTTTTCCC 72 84 1 GAGCTGGCAT 0.636839 -217 ********** Masking position 5 Map Score: 5.17325 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 99 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665