AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00480_synecho_reg_300.orf -o00480_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 slr1290 63 hypothetical 21.6 kD protein slr1290. [SP:YC90_SYNY3] #2 sll1201 225 hypothetical protein. #3 slr1291 85 ndhD2; NADH dehydrogenase subunit 4. [EC:1.6.5.3] #4 sll1200 217 hypothetical protein. #5 slr1293 56 hypothetical protein. #6 ssr2142 300 ycf19; hypothetical protein. #7 slr1843 157 zwf; glucose-6-phosphate 1-dehydrogenase (G6PD). [EC:1.1.1.49] #8 slr1844 137 uvrA; excinuclease ABC subunit A. [SP:UVRA_SYNY3] #9 sll1717 93 hypothetical protein. #10 sll1716 134 transposase. #11 sll1714 300 hypothetical protein. #12 slr1238 300 gshB; glutathione synthetase. [EC:6.3.2.3] #13 slr1992 209 glutathione peroxidase. [EC:1.11.1.9] #14 slr1993 101 thl; acetyl coenzyme A acetyltransferase (thiolase). #15 slr1994 60 fabG; 3-oxoacyl-[acyl-carrier protein] reductase (3-ketoacyl-acyl #16 sll1906 60 428 aa (44.5 kD) bacteriochlorophyll synthase subunit. #17 sll1905 68 sensory transduction histidine kinase. #18 slr1998 32 hypothetical protein. #19 slr1999 38 hypothetical protein. #20 slr2000 257 hypothetical protein. #21 slr2001 147 pepE; peptidase E (alpha-aspartyl dipeptidase). [EC:3.4.-.-] #22 slr2002 32 hypothetical protein. #23 sll1902 300 hypothetical protein. #24 slr1269 96 ggt; gamma-glutamyltranspeptidase precursor. [EC:2.3.2.2] #25 slr1270 197 hypothetical protein. #26 slr1271 251 rffM; UDP-N-acetyl-D-mannosaminuronic acid transferase. [EC:2.4.1.-] #27 slr1272 29 hypothetical protein. #28 slr1273 184 hypothetical protein. #29 slr1274 81 pilM; membrane protein. #30 slr1275 39 hypothetical protein. #31 slr1276 80 hypothetical protein. #32 sll1173 66 hypothetical protein. #33 slr1278 49 hypothetical protein. #34 sll1172 282 thrC; threonine synthase. [EC:4.2.99.2] #35 slr1279 71 ndhC; NADH-plastoquinone oxidoreductase chain 3. [EC:1.6.5.3] #36 slr1281 300 ndhJ; NADH-plastoquinone oxidoreductase subunit J (orf 155). #37 slr1171 300 glutathione peroxidase. [EC:1.11.1.9] #38 sll0067 93 gst; glutathione S-transferase. [EC:2.5.1.18] #39 sll0066 99 hypothetical protein. #40 sll0065 181 ilvN; acetolactate synthase. [EC:4.1.3.18] #41 slr0053 64 hypothetical 20.1 kD protein slr0053. [SP:Y053_SYNY3] #42 slr0054 135 dgkA; probable diacylglycerol kinase (DAGK) (diglyceride kinase) #43 slr0055 143 trpG; anthranilate synthase component II. [EC:4.1.3.27] #44 slr0056 146 G4; chlorophyll synthase 33 kD subunit. #45 sll0064 300 hypothetical protein. #46 sll1545 176 gst1; glutathione S-transferase. [EC:2.5.1.18] #47 slr1664 117 hypothetical protein. #48 slr1665 210 dapF; diaminopimelate epimerase. [EC:5.1.1.7] [SP:DAPF_SYNY3] #49 slr1666 23 degT; pleiotropic regulatory protein. #50 ssr2781 27 hypothetical protein. #51 sll1544 300 regulatory components of sensory transduction system. Motif number 1 GTGGATCTATGGCGATCGCCTTTAGGATT 1 45 1 GGCGATCGCC 0.499999 -19 CCAATTTTCTGGCGATCGCCTGGCGGATCT 2 179 1 GGCGATCGCC 0.499999 -47 AATCTTGGCTGGCGATCGCCATTTACTTAG 7 63 1 GGCGATCGCC 0.499999 -95 TCATCGAGATGGCGATCGCCACATTAACTT 11 261 1 GGCGATCGCC 0.499999 -40 AATCCCCCCCGGCGATCGCCTATGAGGATC 13 93 1 GGCGATCGCC 0.499999 -117 CGGAGGTGTGGGCGATCGCCTGCCAATCAA 26 97 1 GGCGATCGCC 0.499999 -155 CGGACTTGTGGGCGATCGCCTGGGGGCATT 34 99 1 GGCGATCGCC 0.499999 -184 GGGGGGCAATGGCCCGAGGTTCCA 34 269 0 GGCAATGGCC 0.715556 -14 ATTTTAGGACGGCGATCGCCGGGGATAATT 44 11 1 GGCGATCGCC 0.499999 -136 ACTAAAGTCAGGCGATCGCCGTTGGGAATA 47 30 1 GGCGATCGCC 0.499999 -88 ********** Masking position 5 Map Score: 48.9795 Number of sites scoring better than the average of aligned sites = 5646 Number in coding regions = 5126 Number in noncoding regions = 520 Number of orfs with sites within 600 bp upstream = 311 Fraction of orfs with sites within 600 bp upstream = 0.0499518 Motif number 2 TCTCCTAGAGATCCGCCAGGCGATCGCCAGA 2 186 0 ATCCGCCGGC 0.914456 -40 AGCAACTTAAATCCCCCTTGAATAGGATTTG 4 188 1 ATCCCCCTGA 0.917438 -30 AATACTCCCCTTTACCCTGGGTTGTCATAGC 6 109 1 TTTACCCGGG 0.608748 -192 GACAAATAAAATCCCCCTGGCGTAACAGAGG 6 195 1 ATCCCCCGGC 0.985435 -106 AGGACAACTGAGCCGCCGTGCAATGTCCAAA 11 83 1 AGCCGCCTGC 0.867599 -218 AATGCGGATTTGCCCCCTTGGTTGAATAGGG 12 14 0 TGCCCCCTGG 0.966672 -287 AATAAACAAATCCCCCCCGGCGATCGCCTAT 13 85 1 TCCCCCCGGC 0.968882 -125 TACCAATAAAATACCCCGTGCCCAGGGCCGG 13 130 1 ATACCCCTGC 0.654549 -80 TGTTGCAATCTTCACCCCGGCCCTGGGCACG 13 146 0 TTCACCCGGC 0.910209 -64 ATTTAACCTATTTACCCAGGAGTCACC 14 7 0 TTTACCCGGA 0.413238 -95 GATCCGAGTCAGCCCCCAGGGTCAGGGAACC 21 107 1 AGCCCCCGGG 0.979249 -41 AGGTTTTCTTCCCCCTTGCTGGAGTCATT 22 14 0 TTCCCCCTGC 0.976517 -19 TGTAACCCAATTTCCCCCAGCCGTAACCTTT 26 156 1 TTTCCCCAGC 0.689988 -96 ACACCGCTGGACCCCCCCTGACCACCATTAG 34 33 0 ACCCCCCTGA 0.824508 -250 ATTGGCAGAATGCCCCCAGGCGATCGCCCAC 34 106 0 TGCCCCCGGC 0.987645 -177 TCAGGCCGGAAGCCCCCAAGCCCAGGTAGAT 37 179 1 AGCCCCCAGC 0.902841 -122 CTCAAGCACGTCTCCCCAGGGTTGTCCTGAG 39 50 1 TCTCCCCGGG 0.826957 -50 TATCCTACCATGCCCGCCGGGCAAGCTTGCA 40 100 0 TGCCCGCGGG 0.73365 -82 GACCCAGCCTATCACCCTTGGGGCTAGGAAT 43 49 1 ATCACCCTGG 0.771655 -95 ATAGTTTGGCATCCGCCCTGGTAATGGGTTC 45 36 0 ATCCGCCTGG 0.79503 -265 TGCCTAATTATGTCCCCTGGCAGGATTACGG 51 98 0 TGTCCCCGGC 0.950237 -203 CTGTTTTAAAAGCCCCCCTGACCCCCCAAAT 51 142 1 AGCCCCCTGA 0.923444 -159 CCAAAAGTTCTTTCCCCGTGACAAAGTGGGA 51 250 0 TTTCCCCTGA 0.742872 -51 ******* *** Masking position 7 Map Score: 27.8272 Number of sites scoring better than the average of aligned sites = 2528 Number in coding regions = 2219 Number in noncoding regions = 309 Number of orfs with sites within 600 bp upstream = 272 Fraction of orfs with sites within 600 bp upstream = 0.0436878 Motif number 3 CCTTGTTAAATTTTTGCCAATTTTCTGGCGATC 2 163 1 TTTTGCCATT 0.827603 -63 CAATGAACAATTTCTCCCCATCTTAACCCGACC 5 34 1 TTTCCCCACT 0.891676 -23 TGTTCTGGGTTTTAAGCCTATTTCTAAGTAAAT 7 83 0 TTTAGCCATT 0.795772 -75 ATTTTCCATTCTTCACCCTACTTTTCAAACACG 10 81 0 CTTCCCCATT 0.896982 -54 AGAATAAAATTTTCACCATAATTA 10 121 1 TTTCCCAATT 0.917911 -14 ATAATCTTTTTTTAACCAAACTTGCTGAGATTG 12 260 1 TTTACCAATT 0.707873 -41 TCCTAATTTTCTCCTCCCTAATTCTGGGGAGAT 15 16 0 CTCCCCCATT 0.851714 -45 ACACAAAATATTTCTCCCAAATTTCTTATTTTG 23 250 1 TTTCCCCATT 0.96662 -51 CAGTCTAGTATTCTCCCAGAATTGCCGGAGTTT 25 80 1 TTCTCCAATT 0.663227 -118 AGCCGTAACCTTTATCCACAATTTCCCCCGATT 26 174 1 TTTACCAATT 0.707873 -78 CCTAAATTTCAGCCAATTTATCCATAGTT 33 7 1 TTTCGCCATT 0.947315 -43 TAATCATTTCTCCCCAGCTAAACTATGGA 33 31 0 TTTCCCCACT 0.891676 -19 GCCTGGGGGCATTCTGCCAATTTTTCTGATTAT 34 116 1 ATTCGCCATT 0.576409 -167 CACAAAAATATTCCCCCAAAGTTTTCAGTCCAT 36 210 1 TTCCCCAATT 0.880616 -91 CCGACGGAGATTTTGCCCAATTTGGCCCTCCAA 37 102 0 TTTTCCCATT 0.88547 -199 CCTATCGAGGTTTCCGCAAATTTATCTACCTGG 37 200 0 TTTCGCAATT 0.874106 -101 TCTGACCCCATTCCTGCAAAATTTTGCCTACTA 37 275 0 TTCCGCAATT 0.820794 -26 GGCGATAACTTTTTTGCAAAACTCTGCTGGGGA 38 11 1 TTTTGCAACT 0.34509 -83 TACGGCGTATTTCTGCCCCAATTCGCCTAAATA 42 26 1 TTCTCCCATT 0.836067 -110 CCTTGACCGACTTAGGCCGAATTGAGAGGAAAG 43 118 1 CTTAGCCATT 0.539508 -26 TTCACTCAGTTTCCCCCCAAATTTGGGGGGTCA 51 160 0 TTCCCCCATT 0.950255 -141 **** *** * ** Masking position 2 Map Score: 19.6664 Number of sites scoring better than the average of aligned sites = 618 Number in coding regions = 448 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 4 GAAATGTAAAGAAAATTTCCCCACTGTCCTTT 4 15 0 GAAAATTTCC 0.619779 -203 CTATCGATATCACCATTGCCACT 5 2 0 CACCATTGAC 0.556178 -55 GATAGCAATGAACAATTTCTCCCCATCTTAAC 5 29 1 AACAATTTCC 0.892159 -28 GATTAGGAAGAAAAATTTAGCCGAGTCTCAAC 6 71 1 AAAAATTTCC 0.722421 -230 GCCCCGCTTGCCAAATTAATCCCCATAATTGA 13 27 0 CCAAATTACC 0.701875 -183 TCAACATTTTCAACATTTAACCTATTTACCCA 14 20 0 CAACATTTCC 0.820392 -82 GCAAGATCTCCACAATTAGTCCCTTTAGTTCA 14 74 0 CACAATTACC 0.822441 -28 TACAAATTGGCCCGTTGGTGTTT 17 56 0 ACAAATTGCC 0.735017 -13 AGCCAATAAAACCAATTATCCCTAAACG 18 7 0 ACCAATTACC 0.742915 -26 GTTCGCTGTGAACAATTGATCCGAGTCAGCCC 21 90 1 AACAATTGCC 0.845137 -58 GCCAATCAACACCAATTTAGACGGCGATACCT 26 118 1 ACCAATTTAC 0.636207 -134 ATAAATGTAACCCAATTTCCCCCAGCCGTAAC 26 151 1 CCCAATTTCC 0.971922 -101 AACCTTTATCCACAATTTCCCCCGATTATTAA 26 180 1 CACAATTTCC 0.955406 -72 ATTCTTCAAACAAAATTGGCCCTTTATGCAGT 26 228 0 CAAAATTGCC 0.816382 -24 CTAAATTTCAGCCAATTTATCCATAGTTTAGC 33 12 1 GCCAATTTCC 0.893295 -38 GCCGTGAGGAGACCATTGGCCCT 34 2 0 GACCATTGCC 0.69847 -281 GGAGATTTTGCCCAATTTGGCCCTCCAACTGG 37 98 0 CCCAATTTCC 0.971922 -203 ACTAACAAAGACCAATTTGAACGCTTAAAGGC 37 247 0 ACCAATTTAC 0.636207 -54 CCCATTCCTGCAAAATTTTGCCTACTAACAAA 37 270 0 CAAAATTTCC 0.8708 -31 CGTATTTCTGCCCCAATTCGCCTAAATACTGA 42 31 1 CCCCAATTCC 0.568659 -105 TCCCCGTCCACATTTGACCGTAAAGGAGC 42 117 0 CCACATTTCC 0.880666 -19 ACCAAGTTACCCCCATTGTTCCATGGCATTCC 43 75 0 CCCCATTGCC 0.939301 -69 ATAATTGACCAACCATTTCTCCCATTGAATAG 44 35 1 AACCATTTCC 0.848635 -112 CCGAACAATACCCAATTTGAACCCATTACCAG 45 18 1 CCCAATTTAC 0.819133 -283 ******** ** Masking position 7 Map Score: 22.1336 Number of sites scoring better than the average of aligned sites = 1685 Number in coding regions = 1475 Number in noncoding regions = 210 Number of orfs with sites within 600 bp upstream = 209 Fraction of orfs with sites within 600 bp upstream = 0.0335689 Motif number 5 AAAGGCGATCGCCATAGATCCACCAAAGGACGTG 1 34 0 GCATACCACC 0.852911 -30 CGAGCCTATCGCATTTACTCCACCAAATCAATTG 4 107 0 GCTTCCCACC 0.971744 -111 CCACCAATCAGATTTTTAGCCACCGGAATTATGT 6 274 1 GATTACCACC 0.607435 -27 AAAGTTAAGAGCCTTGTCTCCCCCT 7 2 0 GCTTCCCCCC 0.990798 -156 TACTCTGTCTGCCTTTACCTCCCCGATGGAAGGA 12 52 1 GCTTCTCCCC 0.949016 -249 TGAGCTTGTTGCAATCTTCACCCCGGCCCTGGGC 13 149 0 GCATTACCCC 0.640273 -61 GACTTAATCGGCGTTGAATGCCCCGACGAAATTA 20 125 1 GCTTAGCCCC 0.971866 -133 AGGTTTTCTTCCCCCTTGCTGGAGT 22 18 0 GGTTTCCCCC 0.877759 -15 CATTGTCCTTGCCTTGCCTGCCCCCCCTATTGTC 35 25 0 GCTTCGCCCC 0.982171 -47 ACCTCCCTTAGCGTTCTTGCCACCATCAAAGCCT 36 139 1 GCTTTCCACC 0.955684 -162 ATCAAAATTAGTTTTAGCTCCCCCTTCCCCCACT 36 250 0 GTTTCCCCCC 0.931618 -51 TTGTTCCATGGCATTCCTAGCCCCAAGGGTGATA 43 58 0 GCTTTGCCCC 0.971866 -86 CACGTCATAGGCCTTAAAATCCCCGGCCCGGCGT 45 92 0 GCTTATCCCC 0.921089 -209 GCCCAACACCGCTATTTTTCCACCCCATAACTAG 48 23 0 GCATTCCACC 0.852911 -188 TTAACAGCCTGTTTTAAAAGCCCCCCTGACCCCC 51 134 1 GTTTAGCCCC 0.813803 -167 ** ** * ***** Masking position 5 Map Score: 16.1341 Number of sites scoring better than the average of aligned sites = 471 Number in coding regions = 420 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 6 CTGATTGGTGGTTAGAGGCCCCAACCTCCAGT 6 253 0 GTAGAGGCCC 0.811594 -48 CCATAATTGAGCTGGAGGCGGAGTTA 13 5 0 GTGGAGGCGA 0.893397 -205 AACAGTTTCAGTCAGAGGCCTAGCTTGAGAAT 21 61 0 GCAGAGGCCA 0.969162 -87 GAGAATACTAGACTGAGTCCCATCCCTCTGGA 25 63 0 GCTGAGTCCA 0.871967 -135 CTGTAATCCAGTCGGAGGGCAATCAACAAAGC 28 163 1 GCGGAGGGCA 0.970292 -22 GTCTGTCCTGGTTGGAGTCCTATAATCAGAAA 34 138 0 GTGGAGTCCA 0.908849 -145 GATTATTGGCAATGGAGGCCAATACTTCAGAG 36 67 0 ATGGAGGCCA 0.839377 -234 ACTACCCCCAGTTGGAGGGCCAAATTGGGCAA 37 91 1 GTGGAGGGCA 0.93911 -210 CCGGCCAGCAGTCGGAGGCTAAAAATAAATAC 37 142 1 GCGGAGGCTA 0.922925 -159 CGCCAATCAGGCCGGAAGCCCCCAAGCCCAGG 37 173 1 GCGGAAGCCC 0.776573 -128 AACGCTTAAAGGCTGAGGCCGAGGCTCCCTAT 37 228 0 GCTGAGGCCA 0.983232 -73 GGGGAGACGTGCTTGAGGCCAATGGATATCAA 39 35 0 GTTGAGGCCA 0.965144 -65 AACCTTGACCGACTTAGGCCGAATTGAGAGGA 43 116 1 GCTTAGGCCA 0.781153 -28 CCATTACCAGGGCGGATGCCAAACTATTAATT 45 40 1 GCGGATGCCA 0.922925 -261 * ******** * Masking position 6 Map Score: 12.9057 Number of sites scoring better than the average of aligned sites = 387 Number in coding regions = 364 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 ACCTTGTTAAATTTTTGCCAATTTTCTGGCGAT 2 162 1 ATTTTGCCTT 0.388025 -64 CTATTTACCAATGCTTGCCACTGTTGGAGCCGA 4 138 0 ATGTTGCCTG 0.746856 -80 ATGGTTCACAAATCTTCCCTCTGTTACGCCAGG 6 210 0 AATTTCCCTG 0.878213 -91 ATCTAAAGTCACTGTTGACCGGGTCGCACCGGA 8 80 0 ACTTTGACGG 0.618589 -58 AGCTTGTTGCAATCTTCACCCCGGCCCTGGGCA 13 148 0 AATTTCACCG 0.307093 -62 TAATTGTGGAGATCTTGCCACTGT 14 88 1 GATTTGCCTG 0.724778 -14 GCCCACAAAAACTCTTGGCATGGACTTTTTTTC 20 72 0 ACTTTGGCGG 0.718328 -186 TCTGACTGAAACTGTTCGCTGTGAACAATTGAT 21 77 1 ACTTTCGCTG 0.554726 -71 TTTGTTGCTTATTGTTGACAGTGTGCGCCAGAA 28 101 0 ATTTTGACTG 0.680452 -84 TAAATTTTCAATTTTTCCCACGGGAAACATCAA 32 30 1 ATTTTCCCGG 0.893385 -37 TTGTCTTGGGATTATTGGCAATGGAGGCCAATA 36 75 0 ATTTTGGCTG 0.770028 -226 CCCTTCCCCCACTGTTGCCAATGGACTGAAAAC 36 230 0 ACTTTGCCTG 0.921308 -71 TTTGATGTTTAATTTTGCCGTGGGCGACCGGGA 36 278 1 AATTTGCCGG 0.936554 -23 AATTGTCTCCATTGTTGCCCTGGTTTTTGCTCG 37 26 1 ATTTTGCCGG 0.94298 -275 TTAAACGATTGTTTTTGCCCTTGCCATAGATTT 40 13 0 GTTTTGCCTG 0.746856 -169 TTGACCAACCATTTCTCCCATTGAATAGTAAAA 44 39 1 ATTCTCCCTG 0.599185 -108 TTTCTTGGTAAATGTTCCCGGGGATTATGCCGT 45 162 1 AATTTCCCGG 0.882068 -139 ACTTTAAACAAAGTTTGCCTTCGATTGTACACC 46 135 1 AAGTTGCCCG 0.547895 -42 TAGTTTCTTTATTATTCCCAACGGCGATCGCCT 47 39 0 ATTTTCCCCG 0.788035 -79 TTTCTTAAGGAATGTTGCCAATGGGAAAGAGAT 48 167 0 AATTTGCCTG 0.934347 -44 GTCAGACCGTAATCCTGCCAGGGGACATAATTA 51 92 1 AATCTGCCGG 0.732009 -209 *** ***** ** Masking position 6 Map Score: 12.2601 Number of sites scoring better than the average of aligned sites = 1224 Number in coding regions = 1074 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 8 AAATAAAATCCCCCTGGCGTAACAGAGGGA 6 198 1 CCCCTGGCGT 0.658674 -103 GTGGTTAGAGGCCCCAACCTCCAGTTCCAC 6 248 0 GCCCCAACCT 0.63289 -53 TAAATGGCGATCGCCAGCCAAGATTAGCAA 7 58 0 TCGCCAGCCA 0.575163 -100 TTTTTCTTGATCCCTGACCTTTTTTGTTCC 12 188 0 TCCCTGACCT 0.613485 -113 AAACAAATCCCCCCCGGCGATCGCCTATGA 13 88 1 CCCCCGGCGA 0.925916 -122 TGCAATCTTCACCCCGGCCCTGGGCACGGG 13 144 0 ACCCCGGCCC 0.594374 -66 GGCGTTGAATGCCCCGACGAAATTACAATT 20 134 1 GCCCCGACGA 0.861459 -124 CAGGTAAGGTTCCCTGACCCTGGGGGCTGA 21 115 0 TCCCTGACCC 0.831109 -33 GGCCCTAACGCTCGTTTCCCT 27 19 0 GCCCTAACGC 0.709041 -11 TGTCTTATTATCGCCAGCGATTACCGCAAC 28 15 0 TCGCCAGCGA 0.385547 -170 TGATCCCTAGCCACCGAACTTTG 30 27 0 TCCCTAGCCA 0.913205 -13 TAATCATTTCTCCCCAGCTAAACTATGGAT 33 30 0 TCCCCAGCTA 0.613121 -20 CGCTGGACCCCCCCTGACCACCATTAGCCG 34 30 0 CCCCTGACCA 0.839379 -253 GGCAGAATGCCCCCAGGCGATCGCCCACAA 34 104 0 CCCCAGGCGA 0.769752 -179 TTGGATTATTGCCCAAACGATTAATAAGCA 34 197 0 GCCCAAACGA 0.576589 -86 GGCCGGAAGCCCCCAAGCCCAGGTAGATAA 37 182 1 CCCCAAGCCC 0.741803 -119 AGGCCGAGGCTCCCTATCGAGGTTTCCGCA 37 215 0 TCCCTATCGA 0.419487 -86 GGGATCGGTTTCCCAAGCCAGGACAACATC 38 40 1 TCCCAAGCCA 0.819489 -54 GATTGTTTTTGCCCTTGCCATAGATTTTT 40 10 0 GCCCTTGCCA 0.409323 -172 CTCTTCAGCTTCCCTAACTCTAGTGAGGAA 40 60 1 TCCCTAACTC 0.273326 -122 GCACGACTGGGCCCTAACCCAGACCG 40 166 1 GCCCTAACCC 0.767885 -16 TCCCCGTCCACATTTGACCG 42 126 0 TCCCCGTCCA 0.659018 -10 CAAGGTTTAACCCCCAACCAAGTTACCCCC 43 93 0 CCCCCAACCA 0.8738 -51 TGGTCAATTATCCCCGGCGATCGCCGTCCT 44 16 0 TCCCCGGCGA 0.931163 -131 GGCCTTAAAATCCCCGGCCCGGCGTAGAAA 45 87 0 TCCCCGGCCC 0.941161 -214 TTTTATCTGGGCCCAAGCGAACTAATTGCG 45 223 1 GCCCAAGCGA 0.732555 -78 TTTAAAAGCCCCCCTGACCCCCCAAATTTG 51 146 1 CCCCTGACCC 0.801356 -155 TGAGTGAAAGTCCCCAACAACAAGTCAACA 51 185 1 TCCCCAACAA 0.308646 -116 AGGGAATGTCTCCCTAGCGTCCCACTTTGT 51 231 1 TCCCTAGCGT 0.658512 -70 ********** Masking position 4 Map Score: 24.6008 Number of sites scoring better than the average of aligned sites = 4319 Number in coding regions = 3934 Number in noncoding regions = 385 Number of orfs with sites within 600 bp upstream = 376 Fraction of orfs with sites within 600 bp upstream = 0.0603919 Motif number 9 CTACCTTGTCACAGAAAACATCCCGTATTCT 16 38 0 ACAGAAAACT 0.756757 -23 TGATCAGAGAACTGAACCCCTAAGAGTTGAC 20 12 0 ACTGAACCCT 0.921852 -246 TAGGCCTCTGACTGAAACTGTTCGCTGTGAA 21 71 1 ACTGAAACTT 0.910368 -77 ACCAACAGTCACTGAAACCTTCTCGGAATAA 23 167 1 ACTGAAACCT 0.97798 -134 CTAAGCTTCAACTGAAACCTTACTGTAATCC 28 141 1 ACTGAAACCT 0.97798 -44 GCCATACTCCACTGAAACCATCCC 29 4 0 ACTGAAACCT 0.97798 -78 TTGCCAATGGACTGAAAACTTTGGGGGAATA 36 218 0 ACTGAAAACT 0.945535 -83 CCCATAGGAGACTGAAAATGTTCTAAAACGG 45 191 0 ACTGAAAATT 0.798824 -110 ********* * Masking position 6 Map Score: 6.63537 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 16 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 ATTAAATAAAGGGGAGTGGGGGAAT 3 5 0 GGGAGTGGGG 0.972952 -81 GGGAAAAGGACAGTGGGGAAATTTTCTT 4 8 1 GGAAGTGGGG 0.946054 -210 TGACAACCCAGGGTAAAGGGGAGTATTACCA 6 105 0 GGGAAAGGGG 0.85487 -196 CAGTGGAACTGGAGGTTGGGGCCTCTAACCA 6 246 1 GGAGTTGGGG 0.823254 -55 GTCACCATAAGGGTATTGCGGCCATTGACTG 10 17 0 GGGATTGCGG 0.960198 -118 GGTGAAGAATGGAAAATGGTGAAAAGAATAA 10 97 1 GGAAATGGTG 0.853795 -38 GGATTAATTTGGCAAGCGGGGCATTGGAAAT 13 37 1 GGCAGCGGGG 0.681573 -173 TCGCAAAAAGGGGAAACGCTGTTCGCTAAAT 24 41 1 GGGAACGCTG 0.623284 -56 ACAATTCTTAGGGCAATGCGGTAAGTTATTT 24 68 0 GGGAATGCGG 0.97267 -29 CCATCCCTCTGGACAATGCGGAGGGAAATGA 25 45 0 GGAAATGCGG 0.945512 -153 TTACGGCTGGGGGAAATTGGGTTACATTTAT 26 151 0 GGGAATTGGG 0.750336 -101 AATAATCGGGGGAAATTGTGGATAAAGGTTA 26 179 0 GGAATTGTGG 0.604042 -73 GGGGGTTGCGGTAATCGCTGG 28 1 1 GGGGTTGCGG 0.840893 -184 GTCTCCTCACGGCTAATGGTGGTCAGGGGGG 34 21 1 GGCAATGGTG 0.740562 -262 GGCAACAGTGGGGGAAGGGGGAGCTAAAACT 36 244 1 GGGAAGGGGG 0.897228 -57 CAGTATTTAGGCGAATTGGGGCAGAAATACG 42 31 0 GCGATTGGGG 0.762212 -105 GAATGCCATGGAACAATGGGGGTAACTTGGT 43 76 1 GAAAATGGGG 0.608715 -68 AATCTGGAAGGGAAATTGCTGTTTTTATTTG 51 15 1 GGAATTGCTG 0.686465 -286 *** ******* Masking position 1 Map Score: 13.4869 Number of sites scoring better than the average of aligned sites = 1725 Number in coding regions = 1582 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 11 TTAACTTAAGCCAACTAAGGGCTGTTG 11 284 1 CCAACTAAGG 0.978354 -17 TTGCCCTATTCAACCAAGGGGGCAAATCC 12 10 1 TCAACCAAGG 0.770619 -291 AACTGAACGCCCAACTAATAATCTTTTTTT 12 243 1 CCAACTAATA 0.782526 -58 CGTATTCTAACCAACTAAGGCCTAGCAAGA 16 16 0 CCAACTAAGG 0.978354 -45 TGATGAGGAGCCAACTGAGGAAAGG 17 6 0 CCAACTGAGG 0.951062 -63 TTAAACCTATCCAACTAATAATTGTAATTT 20 153 0 CCAACTAATA 0.782526 -105 AAAAAATCAGCCAAGTAATGAAATCGGGCT 23 35 0 CCAAGTAATG 0.62283 -266 TTATAGGACTCCAACCAGGACAGACCAAGC 34 145 1 CCAACCAGGA 0.702184 -138 ATTTGGCCCTCCAACTGGGGGTAGTGGCCC 37 86 0 CCAACTGGGG 0.89312 -215 GCTAATCTGTTCAACTAAGGGACGGCCATG 48 84 0 TCAACTAAGG 0.886534 -127 ********** Masking position 4 Map Score: 4.12017 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 233 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 12 CAAATAACTAACGACCATGCAGCAGGTGCGA 9 46 0 ACACCATGCA 0.681172 -48 TTTTTTGTTCCATACCATACCATTATCTAAA 12 168 0 CAACCATACC 0.677857 -133 CAAAGAAAAAAAGTCCATGCCAAGAGTTTTT 20 68 1 AATCCATGCC 0.917835 -190 GCAAGGTGAACAAACCAAGCCG 29 70 1 CAACCAAGCC 0.967025 -12 CCAACCAGGACAGACCAAGCCCTGAACTATA 34 155 1 CAACCAAGCC 0.967025 -128 GTTCTTGCCACCATCAAAGCCTTTTTTTCTG 36 151 1 CCTCAAAGCC 0.672262 -150 AGCCTTATATCCTACCATGCCCGCCGGGCAA 40 107 0 CCACCATGCC 0.971405 -75 TGTTCCATGGCATTCCTAGCCCCAAGGGTGA 43 60 0 CATCCTAGCC 0.740828 -84 ATTGAATAGTAAAACCAAGCCCGGTCTACTC 44 58 1 AAACCAAGCC 0.929944 -89 AAAAGCGTGCAATTCCAAGCCCAGGAAGCTA 44 95 0 AATCCAAGCC 0.917835 -52 CAACTAAGGGACGGCCATGCCCTAGAATTTG 48 72 0 ACGCCATGCC 0.825525 -139 TAGCCGCCCACCATCCATGCAGTAGCTGGAA 48 110 1 CCTCCATGCA 0.798873 -101 ** ******** Masking position 5 Map Score: 5.07761 Number of sites scoring better than the average of aligned sites = 673 Number in coding regions = 633 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 13 GTAAACTTTTGAGAATTTTTTTTGAGATTTTCCC 2 61 1 GAGATTTTTG 0.876493 -165 CCTATTCAAGGGGGATTTAAGTTGCTGTTGTTAA 4 180 0 GGGATTTTTG 0.961073 -38 GTTACGCCAGGGGGATTTTATTTGTCCAGGTTAC 6 187 0 GGGATTTTTG 0.961073 -114 AATTTGCTCCGAAAATTTCACTTGCACGGCCTAG 11 127 0 GAAATTTTTG 0.442115 -174 GCTCAATTATGGGGATTAATTTGGCAAGCGGGGC 13 25 1 GGGATTATGG 0.798016 -185 CCTGGGCACGGGGTATTTTATTGGTAAAAATCCG 13 122 0 GGGATTTTGG 0.971518 -88 GAACCACTCCGATCATTTTGGTTGAATTAGAAAC 23 108 1 GATATTTTTG 0.722787 -193 CCAGTCCGTTGGTCATTTTGGTTGAGGAGTGTTC 26 15 0 GGTATTTTTG 0.900703 -237 AGGGTAATTTTGCTGGTAGATTATCG 31 65 0 GGTATTTTGG 0.926102 -16 CTGATGACTTGGCTATTTCGCTGGGAATCGAGCA 37 53 0 GGCATTTTGG 0.849522 -248 GACCGTAAAGGAGCATTCCAGTTGATTCTGGTCA 42 97 0 GAGATTCTTG 0.549202 -39 GAACAATGGGGGTAACTTGGTTGGGGGTTAAACC 43 86 1 GGTACTTTGG 0.664048 -58 AGTCTCCTATGGGATTTTATCTGGGCCCAAGCGA 45 209 1 GGGTTTTTGG 0.784014 -92 *** **** *** Masking position 7 Map Score: 4.29441 Number of sites scoring better than the average of aligned sites = 534 Number in coding regions = 471 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 14 ATTCCCCCACTCCCCTTTATTTA 3 4 1 CCCCCACTCC 0.892171 -82 AGGTGCGATATGCTCACTCCTCTTAGAAAG 9 24 0 TGCTCACTCC 0.837518 -70 TAACTCCGCCTCCAGCTCAATTA 13 4 1 CTCCGCCTCC 0.823716 -206 GAGCTAAAATCGCTCACACTGGTTAATTGA 20 234 0 CGCTCACACT 0.52157 -24 GGCAGGCGATCGCCCACACCTCCGGTTACG 26 91 0 CGCCCACACC 0.95215 -161 GATAGATATTCTCTCCCTCCCATCCTTACT 28 57 0 CTCTCCCTCC 0.957678 -128 TTGTTCACCTTGCCCACACCTATTGCTTCA 29 53 0 TGCCCACACC 0.848819 -29 TTAGTTTTAGCTCCCCCTTCCCCCACTGTT 36 247 0 CTCCCCCTTC 0.759192 -54 TAACATGACTCTCTCCCTCCCTGGAGCAAC 46 99 0 CTCTCCCTCC 0.957678 -78 ACTTCTCCCACCATCAATCATC 49 12 0 TTCTCCCACC 0.813469 -12 ********** Masking position 7 Map Score: 2.38783 Number of sites scoring better than the average of aligned sites = 683 Number in coding regions = 621 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 15 CTAAAAATCTGATTGGTGGTTAGAGGCCCCAA 6 261 0 GTGGTGGTTA 0.965382 -40 ACGATGGGATGATGGGTGGTTAAAGGTGCTGA 25 164 0 GTGGTGGTTA 0.965382 -34 TAAAAACAAAGTTCGGTGGCTAGGGATCA 30 21 1 GTGGTGGCTA 0.986177 -19 AAGGACAATGGATTGGTGGCCATTACTAAACT 35 49 1 GTGGTGGCCA 0.949872 -23 GCCTCCGACTGCTGGCCGGCTACGACCCGACG 37 129 0 GTGCCGGCTA 0.907313 -172 ATCTACCTGGGCTTGGGGGCTTCCGGCCTGAT 37 178 0 GTGGGGGCTT 0.913787 -123 GGGGTAACTTGGTTGGGGGTTAAACCTTGACC 43 94 1 GTGGGGGTTA 0.958539 -50 CTGCATGGATGGTGGGCGGCTAATCTGTTCAA 48 100 0 GTGGCGGCTA 0.983374 -111 * * ******** Masking position 3 Map Score: 5.45783 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 29 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185