AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00010_synecho_reg_100.orf -o00010_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 slr1124 51 gpmB; phosphoglycerate mutase. [EC:5.4.2.1] #2 slr1125 117 crtX; zeaxanthin glucosyl transferase. #3 slr1097 57 hypothetical protein. #4 slr1098 67 hypothetical protein. #5 slr1099 300 ubiX; 3-octaprenyl-4-hydroxybenzoate carboxy-lyase. [EC:4.1.1.-] #6 sll1196 112 pfkA; phosphofructokinase. [EC:2.7.1.11] #7 sll1275 187 pykF; pyruvate kinase. [EC:2.7.1.40] #8 slr0884 300 gap1; glyceraldehyde 3-phosphate dehydrogenase 1 (gapdh 1) (GAP-1). #9 sll1757 144 hypothetical protein. [EC:2.7.1.69] #10 slr1349 214 pgi; glucose-6-phosphate isomerase (GPI) (phosphoglucose isomerase) #11 slr0942 42 aldehyde reductase. [EC:1.1.1.2] #12 slr0943 121 fda; fructose-bisphosphate aldolase. [EC:4.1.2.13] #13 slr0952 206 fbp; fructose-1,6-bisphosphatase (D-fructose-1,6-bisphosphate 1- #14 slr0394 268 pgk; phosphoglycerate kinase. [EC:2.7.2.3] [SP:PGK_SYNY3] #15 slr1934 123 pyruvate dehydrogenase E1 component, alpha subunit. [EC:1.2.4.1] #16 slr1945 64 yibO; 2,3-bisphosphoglycerate-independent phosphoglycerate mutase. #17 ssr3307 236 ycf47; hypothetical protein. #18 sll1841 210 odhB; dihydrolipoamide acetyltransferase component (E2) of pyruvate #19 sll0325 222 hypothetical protein. #20 sll0018 283 fda; fructose-bisphosphate aldolase. [EC:4.1.2.13] [SP:ALF_SYNY3] #21 sll0891 37 citH; 2-ketoacid dehydrogenase (malate dehydrogenase, lactate #22 ssl1690 300 hypothetical protein. #23 sll0593 206 glk; glucokinase. [EC:2.7.1.2] #24 sll0587 42 pyk1; pyruvate kinase 1. [EC:2.7.1.40] [SP:KPY1_SYNY3] #25 sll0586 300 hypothetical protein. #26 sll0745 111 pfkA; phosphofructokinase. [EC:2.7.1.11] #27 slr0752 192 eno; enolase (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate #28 sll0726 300 pgm; phosphoglucomutase. [EC:5.4.2.2] Motif number 1 TTAAAGTTCACCCCAGGAACATTACCGCCGT 2 17 0 CCCCAGGAAA 0.79969 -101 CTAACCCCGGCCCCTAGCCTAGGGGGGGAAA 3 15 0 CCCCTAGCCA 0.981663 -43 AGATTCTTACCCTCCACCCAACTGTAA 5 7 0 CCTCCACCCA 0.48231 -294 CCAAACTTTGCCCACAGCCGCCGACACTGGG 5 105 1 CCCACAGCCC 0.907245 -196 AAGTCCAAATCCCCCAACCTTGCCGGAGCTT 5 221 0 CCCCCAACCT 0.912565 -80 GGAAAAATTGCCCAAAGCCCAGCCTACCATC 7 41 1 CCCAAAGCCA 0.919083 -147 AATGCCTGGGCCACTAGCCCAAGTGAGGGAC 8 22 0 CCACTAGCCA 0.771373 -279 CAGTCATCGTCCAACAGCCTATGACTTGTCT 8 239 0 CCAACAGCCA 0.57135 -62 GTGAAACTTGCCCCTGCCATCCTCTTGTCTG 12 40 0 CCCCTGCCAC 0.555609 -82 AACACTATTCCCCCCAGAATTGGGGGGCTAG 13 132 1 CCCCCAGAAT 0.817084 -75 TTTTAAAAGCCCCCTAGCCCCCCAATTCTGG 13 145 0 CCCCTAGCCC 0.961178 -62 TTGCGCCGCTCCCCCAGCATA 15 113 1 CCCCCAGCAA 0.973841 -11 CAATTCAGCGCCCCTCGGCGATCATACAGGC 16 13 1 CCCCTCGGCA 0.557054 -52 AAATTCTCCCCCCAGGGCCAATGCCTGACT 17 10 1 CCCCAGGGCA 0.960724 -227 TGTTCAAAGTCCCCCAAACTTGCCGGAGCTT 17 169 0 CCCCCAAACT 0.615741 -68 AACACCATTCCCCCCAGAATTGGGGGGCTAG 17 196 1 CCCCCAGAAT 0.817084 -41 TTTAAATGCTCCCCTAGCCCCCCAATTCTGG 17 209 0 CCCCTAGCCC 0.961178 -28 TAGGCGATCGCCCAAAGGAAAATGTCAAAAT 18 65 0 CCCAAAGGAA 0.421666 -146 CTTAACTAACCCCCCGGCAGAAATCTGATAG 18 114 1 CCCCCGGCAA 0.979765 -97 ACTTCCCTTTCCCCAGGGCTTGAAGCTGTGT 19 164 0 CCCCAGGGCT 0.950291 -59 ATATCTCTTCCCCCCGGCAATAGGCGATCGG 20 23 0 CCCCCGGCAT 0.974254 -261 AACTTGATTACCCAAAACCTTCCCCCATCCT 20 62 1 CCCAAAACCT 0.4541 -222 CGTATTTTTACCCCCACCCTAGTCTATGGCT 20 108 0 CCCCCACCCA 0.954919 -176 TTTTGTCCTGCCCCAAGGAATTTGTGCTAGG 20 154 0 CCCCAAGGAT 0.793375 -130 TTCTGGGATTCCCCAGGCGGCGATCGCCAGA 22 24 1 CCCCAGGCGC 0.858576 -277 CTAAAAAATTCCCCCACCCCTAGGGTGCCCA 22 87 1 CCCCCACCCT 0.943036 -214 CCCTAGGGTGCCCACGGCCCAGTCAGGGTTA 22 104 1 CCCACGGCCA 0.964921 -197 CGGATTTTATCCCCAGGAGGTTAAGGTTTTT 22 146 0 CCCCAGGAGT 0.611667 -155 GCTAGTTTCTCCCCAGGCCATTCCCCAGACT 22 201 0 CCCCAGGCCT 0.987309 -100 CGGTTAATTTCCTCTGGCCCAGGTGGAGGAA 23 56 1 CCTCTGGCCA 0.753842 -151 GGCCCCAAAGCCATTGAAAAACTA 23 193 0 CCCAAAGCCT 0.898754 -14 CTTATCTGCTCCCCAGGGGGAAAAGTGTGAC 25 69 0 CCCCAGGGGA 0.763354 -232 AACCCTATGCCCCCCGTCCCAACCTGTACAA 25 176 0 CCCCCGTCCA 0.840744 -125 ACGGAACTCCCCACCGGCAAAAACCCTATGC 25 197 0 CCACCGGCAA 0.753178 -104 TTTTAAAGTTCCCCTAGCCCAAGGGTTGGGG 27 166 0 CCCCTAGCCA 0.981663 -27 TTAAGCAACTCCCCTGAACGTTAACACAATC 28 81 1 CCCCTGAACT 0.439114 -220 GCCAAAGTTACCCCAGGCCATACACGGCCCA 28 182 0 CCCCAGGCCT 0.987309 -119 ********* * Masking position 2 Map Score: 51.4754 Number of sites scoring better than the average of aligned sites = 4741 Number in coding regions = 4269 Number in noncoding regions = 472 Number of orfs with sites within 600 bp upstream = 439 Fraction of orfs with sites within 600 bp upstream = 0.0705108 Motif number 2 CCCATTTGTTCCCTAACTCTTGTTTGCT 1 3 0 CCCTACTTGG 0.939985 -49 GAAATTTCCCCCCCTAGGCTAGGGGCCGGGGTT 3 8 1 CCCCCCTGCG 0.621799 -50 GTCCAAATCCCCCAACCTTGCCGGAGCTTTAGTGAA 5 214 0 CCCACCTGCG 0.995187 -87 TAGGGTTTGTCCCTCACTTGGGCTAGTGGCCCAGGC 8 14 1 CCCTACTGGG 0.975044 -287 ACTTGCCCCTGCCATCCTCTTGTCTGACTTTACCCT 12 30 0 GCCACCTTGG 0.878134 -92 TTCAAAGTCCCCCAAATTTGCCGGAGCTTTAGTGAA 13 98 0 CCCAATTGCG 0.96747 -109 CCCCCTAGCCCCCCAATTCTGGGGGGAATAGTGTTC 13 131 0 CCCCATTTGG 0.778806 -76 CAGGGCCAATGCCTGACTCTCCAACGACGGAGAGAA 17 23 1 GCCTACTTCG 0.767296 -214 TTCAAAGTCCCCCAAACTTGCCGGAGCTTTAGTGAG 17 162 0 CCCAACTGCG 0.993773 -75 TCCCCTAGCCCCCCAATTCTGGGGGGAATGGTGTTC 17 195 0 CCCCATTTGG 0.778806 -42 TGGAAAAGCTCCCAAACTTGGCAAAAATGAGAACTA 19 112 1 CCCAACTGCA 0.881825 -111 AAAACCTTCCCCCATCCTGGACTTGGTTAACTCAGC 20 75 1 CCCACCTGCG 0.99513 -209 TATTTTTACCCCCACCCTAGTCTATGGCTGAGTTAA 20 101 0 CCCACCTGCG 0.983673 -183 TATTTCTTAACCCTGACTGGGCCGTGGGCACCCTAG 22 106 0 CCCTACTGCG 0.982855 -195 CAGGCCATTCCCCAGACTTTCCCCAGTGATTCCCCC 22 183 0 CCCAACTTCG 0.984607 -118 TGCCCCCCGTCCCAACCTGTACAATGAAGAGGGCGG 25 164 0 CCCACCTTCG 0.988082 -137 CGAAGTAACCCCAACCCTTGGGCTAGGGGAACTTTA 27 158 1 CCAACCTGGG 0.861359 -35 ATTTGTGCTCCCCATCTTGGCGCTGGGCCGTGTATG 28 159 1 CCCACTTGGG 0.961192 -142 **** *** * * * Masking position 8 Map Score: 34.4877 Number of sites scoring better than the average of aligned sites = 506 Number in coding regions = 440 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 3 TAGGGAACAAATGGGGGGATAATTGGCTAT 1 24 1 ATGGGGGGAT 0.909135 -28 GGTAATGTTCCTGGGGTGAACTTTAAAATA 2 22 1 CTGGGGTGAA 0.688886 -96 TTACAGTTGGGTGGAGGGTAAGAATC 5 7 1 TTGGGTGGAG 0.623706 -294 TGCGCCATGGTTGGGATTAGCCGTTAAGCT 5 148 0 TTGGGATTAG 0.184582 -153 GTGAAAATAGTTGGGGGACAAAGGCTTTAG 5 189 0 TTGGGGGACA 0.898953 -112 TCCGGCAAGGTTGGGGGATTTGGACTTACA 5 225 1 TTGGGGGATT 0.746277 -76 TCCGGCAAATTTGGGGGACTTTGAACACTA 13 109 1 TTGGGGGACT 0.971153 -98 CCCCCCAATTCTGGGGGGAATAGTGTTCAA 13 129 0 CTGGGGGGAA 0.92038 -78 CCCCCCAGAATTGGGGGGCTAGGGGGCTTT 13 141 1 TTGGGGGGCT 0.984836 -66 CCAGTATCATCTAGGGGAAT 14 259 1 CTAGGGGAAT 0.729691 -10 CGTTCACCGTTTGGGAGAATGGAATAGTTA 15 81 0 TTGGGAGAAT 0.820312 -43 GTAGGGGGATGGAAAAGCGC 16 55 0 GTAGGGGGAT 0.648186 -10 GGCATTGGCCCTGGGGGGAGAATTT 17 6 0 CTGGGGGGAG 0.964397 -231 GTGAGGAGATTTAGGGGGCGGGTCATAGCC 17 137 0 TTAGGGGGCG 0.827212 -100 TCCGGCAAGTTTGGGGGACTTTGAACACCA 17 173 1 TTGGGGGACT 0.971153 -64 CCCCCCAATTCTGGGGGGAATGGTGTTCAA 17 193 0 CTGGGGGGAA 0.92038 -44 CCCCCCAGAATTGGGGGGCTAGGGGAGCAT 17 205 1 TTGGGGGGCT 0.984836 -32 GGTAATCAAGTTGGGGTTCTATATCTCTTC 20 44 0 TTGGGGTTCT 0.729426 -240 CAAGTCCAGGATGGGGGAAGGTTTTGGGTA 20 70 0 ATGGGGGAAG 0.762562 -214 GCAATAGAACTTAGGAGGATTT 20 272 1 TTAGGAGGAT 0.511813 -12 CACCCTAGGGGTGGGGGAATTTTTTAGGGT 22 84 0 GTGGGGGAAT 0.889168 -217 AATCCGCTAACTGGGGGAATCACTGGGGAA 22 171 1 CTGGGGGAAT 0.957763 -130 TTACAAAATTTTGGGGTTATGTAACAATTT 22 244 1 TTGGGGTTAT 0.745704 -57 TTTGCCCTCGTTGGGAGACTGGGAAATTAA 22 278 0 TTGGGAGACT 0.807578 -23 AAAGGGATTTTTGGGGTGATTAGATCCATT 25 244 1 TTGGGGTGAT 0.931186 -57 TGGCGATAGATTGGGGTTCGATTTTGACCA 26 31 1 TTGGGGTTCG 0.625373 -81 ********** Masking position 2 Map Score: 35.7517 Number of sites scoring better than the average of aligned sites = 2699 Number in coding regions = 2313 Number in noncoding regions = 386 Number of orfs with sites within 600 bp upstream = 298 Fraction of orfs with sites within 600 bp upstream = 0.0478638 Motif number 4 ATGTTCCTGGGGTGAACTTTAAAATATTTCTTGAAATTCT 2 26 1 GGATAAAATC 0.752763 -92 ATATGTAAAGGGAAATAATTAAAAATTAACTAAAAATCAA 4 17 0 GGATAAATTC 0.942186 -51 TAAGGATTGAGGACAATTTTAAGAATTCTCACAAAGAAGT 6 26 1 GGATAAATTC 0.918618 -87 AAACTGTGCAGACTATTGGGAAAAATTGCCCAAAGCCCAG 7 23 1 GAAGAAATTC 0.776524 -165 CGATCGTGGCGGATAATGAGAATATTTCCCTAACACCGCT 7 104 1 GGAGAAATTC 0.961014 -84 GTTGATCGGCGGTCATGGTAAAAATTCCACTAATTCAAAA 8 60 0 GGAAAAATCC 0.671872 -241 ATCAAGCCCAGGAAAATCAGAGCAGTCATCGTCCAACAGC 8 252 0 GGAGAGATCC 0.87471 -49 GGCAAATTTGGGGGACTTTGAACACTATTCCCCCCAGAAT 13 112 1 GGAGAAATAC 0.936539 -95 TAGTTTTCGGGGAAAGTTGGCATAATAAACTATTCCTAGC 14 15 1 GGAGCAATAC 0.841073 -254 GCACAGGGGGTAGGAGGAAAAATAGGCAGTTAATCGA 15 8 1 GGAGAAATAC 0.976957 -116 TTCACCGTTTGGGAGAATGGAATAGTTAACCGTGGGAGTT 15 69 0 GGGGAAATTC 0.904117 -55 GGCAAGTTTGGGGGACTTTGAACACCATTCCCCCCAGAAT 17 176 1 GGAGAAACAC 0.855977 -61 TCCCAAACTTGGCAAAAATGAGAACTACTCATCACAAAAT 19 121 1 GGAGAGATAC 0.91168 -102 TTGACGCTAGGGATAGTAGGAATATTTTTCTGGCGATCGC 22 43 0 GGAGAAATTC 0.985299 -258 AACGGGTTAGGCATAAAAATTCCCACAGTTCACC 27 5 1 GGATAAATTC 0.942233 -188 CCAAATCCCTGGTCATAGAGAAAAAATTGCCAAAGTTACC 28 201 0 GGAGAAAATC 0.928082 -100 ** * *** * ** * Masking position 14 Map Score: 18.1504 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 114 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 GGGAACAAATGGGGGGATAATTGGCTATGG 1 26 1 GGGGGGATAA 0.932045 -26 CCTAGCCTAGGGGGGGAAATTTC 3 4 0 GGGGGGAAAT 0.844436 -54 GAAAATAGTTGGGGGACAAAGGCTTTAGTG 5 187 0 GGGGGACAAA 0.661333 -114 CCCATCACTAGGGCGGATAGCAAAATACCA 8 128 0 GGGCGGATAG 0.969749 -173 CCAAATGGAAGGTCGGACAGATTTTGTTTA 10 27 1 GGTCGGACAG 0.811386 -188 AATTGTTAATGGTGGACCAGGTAATCGCGG 10 180 0 GGTGGACCAG 0.689478 -35 TTATCGCAGAGGGAAGAAAGC 11 2 0 GGGAAGAAAG 0.444191 -41 CCCAATTCTGGGGGGAATAGTGTTCAAAGT 13 126 0 GGGGGAATAG 0.975294 -81 CCCCAGAATTGGGGGGCTAGGGGGCTTTTA 13 143 1 GGGGGGCTAG 0.979884 -64 AATGAAAAACGGGAGGACAGATTTTCATCC 14 111 1 GGGAGGACAG 0.871539 -158 CATTGGCCCTGGGGGGAGAATTT 17 4 0 GGGGGGAGAA 0.855019 -233 CCCCAATTCTGGGGGGAATGGTGTTCAAAG 17 191 0 GGGGGGAATG 0.882298 -46 CCCCAGAATTGGGGGGCTAGGGGAGCATTT 17 207 1 GGGGGGCTAG 0.979884 -30 TCGCCTAGATGGTCGAAAAGTGCTCCTTAA 18 89 1 GGTCGAAAAG 0.699972 -122 GATTTCTGCCGGGGGGTTAGTTAAGGAGCA 18 109 0 GGGGGGTTAG 0.903236 -102 TTTGACCAAGGGTGGAAAAGCTCCCAAACT 19 100 1 GGTGGAAAAG 0.894268 -123 CCTATTGCCGGGGGGAAGAGATATAGAACC 20 30 1 GGGGGAAGAG 0.944364 -254 CTGCTCCCCAGGGGGAAAAGTGTGACGCCA 25 65 0 GGGGGAAAAG 0.975294 -236 GGTTGGGACGGGGGGCATAGGGTTTTTGCC 25 183 1 GGGGGCATAG 0.912931 -118 ACCGTACCATGGTGAGAAAGCCTATCTG 28 9 0 GGTGAGAAAG 0.647525 -292 AGTGCTCCTTGGCCGGATAGCTTCCGGCCT 28 114 1 GGCCGGATAG 0.715213 -187 ********** Masking position 2 Map Score: 26.6485 Number of sites scoring better than the average of aligned sites = 1401 Number in coding regions = 1192 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 6 GGAACAAATGGGGGGATAATTGGCTATGGACA 1 27 1 GGGGGATTTG 0.75218 -25 GCCCAGTGTCGGCGGCTGTGGGCAAAGTTTGG 5 105 0 GGCGGCTGGG 0.767432 -196 CCCCAACCTTGCCGGAGCTTTAGTGAAAATAG 5 209 0 GCCGGAGTTA 0.957631 -92 CGGCAAGGTTGGGGGATTTGGACTTACACTTC 5 227 1 GGGGGATGGA 0.878161 -74 CGGCGATCGTGGCGGATAATGAGAATATTTCC 7 101 1 GGCGGATTGA 0.951244 -87 ATACTCTAACGCCGGAGATTCAACTTTGTTGG 13 33 0 GCCGGAGTCA 0.916999 -174 CCCCAAATTTGCCGGAGCTTTAGTGAAGACAT 13 93 0 GCCGGAGTTA 0.957631 -114 TATGCTGGGGGAGCGGCGCAATACGTTC 15 106 0 GGGGGAGGCG 0.832686 -18 CCCCAAACTTGCCGGAGCTTTAGTGAGGAGAT 17 157 0 GCCGGAGTTA 0.957631 -80 TCAGATTTCTGCCGGGGGGTTAGTTAAGGAGC 18 110 0 GCCGGGGTTA 0.767283 -101 CTTGGAATACAGCGGATTAGGACTGCGGAAGA 18 156 0 AGCGGATGGA 0.609131 -55 GGTTGACTCCGGCGGAGCCGTAAAATCGCATA 19 48 1 GGCGGAGGTA 0.979315 -175 ACATCATCCAGGCGGAGTGTGGTGTGAGGAGT 25 114 1 GGCGGAGTGG 0.97441 -187 CAATGAAGAGGGCGGAGACGTAAGTTTCCGTT 25 147 0 GGCGGAGGTA 0.979326 -154 TAAACCGCCGGATTAGGGATTGGCGATA 26 7 1 GCCGGATGGG 0.93841 -105 ******* *** Masking position 5 Map Score: 14.9034 Number of sites scoring better than the average of aligned sites = 1023 Number in coding regions = 924 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 7 AACAAATGGGGGGATAATTGGCTATGGACA 1 29 1 GGGATAATTG 0.506474 -23 TAGCCTAGGGGGGGAAATTTC 3 2 0 GGGGAAATTT 0.909311 -56 CGGCAAGGTTGGGGGATTTGGACTTACACT 5 227 1 GGGGGATTTG 0.764528 -74 AGTCGATTATGAGGGAAGTGTAAGTCCAAA 5 243 0 GAGGGAAGTG 0.809683 -58 GAGGATGGCAGGGGCAAGTTTCACCGTGTT 12 47 1 GGGGCAAGTT 0.644582 -75 CGGCAAATTTGGGGGACTTTGAACACTATT 13 111 1 GGGGGACTTT 0.90546 -96 CCCAATTCTGGGGGGAATAGTGTTCAAAGT 13 126 0 GGGGGAATAG 0.87575 -81 GTTAGTTTTCGGGGAAAGTTGGCATAATAA 14 13 1 GGGGAAAGTT 0.90593 -256 ATATCGCCCCGAGAAAAGTGCATCAATAAC 14 81 0 GAGAAAAGTG 0.394154 -188 TTCACCGTTTGGGAGAATGGAATAGTTAAC 15 79 0 GGGAGAATGG 0.937452 -45 TGGCCCTGGGGGGAGAATTT 17 1 0 GGGAGAATTT 0.898581 -236 CGGCAAGTTTGGGGGACTTTGAACACCATT 17 175 1 GGGGGACTTT 0.90546 -62 CCCAATTCTGGGGGGAATGGTGTTCAAAGT 17 190 0 GGGGGAATGG 0.976061 -47 TTCAAGCCCTGGGGAAAGGGAAGTCCGGCT 19 171 1 GGGGAAAGGG 0.942165 -52 CCTATTGCCGGGGGGAAGAGATATAGAACC 20 30 1 GGGGGAAGAG 0.871294 -254 AGTCCAGGATGGGGGAAGGTTTTGGGTAAT 20 68 0 GGGGGAAGGT 0.947008 -216 CCCTAGGGGTGGGGGAATTTTTTAGGGTTT 22 82 0 GGGGGAATTT 0.960163 -219 GGGAATCACTGGGGAAAGTCTGGGGAATGG 22 185 1 GGGGAAAGTC 0.623101 -116 GGGGAAAGTCTGGGGAATGGCCTGGGGAGA 22 195 1 TGGGGAATGG 0.822834 -106 TGCCCTCGTTGGGAGACTGGGAAATTAACT 22 276 0 GGGAGACTGG 0.856232 -25 TTGCTGAAACGGGAGAATTTTAGCTTTTTG 23 111 1 GGGAGAATTT 0.898581 -96 TTAGGTCACCGAGGAAAGGGTCACCAAGCA 23 139 0 GAGGAAAGGG 0.577387 -68 GCTCCCCAGGGGGAAAAGTGTGACGCCAAC 25 63 0 GGGAAAAGTG 0.885812 -238 TGGATTTCACTGGAAAATGGATCTAATCAC 25 259 0 TGGAAAATGG 0.415283 -42 CCTTGGGCTAGGGGAACTTTAAAACACTTT 27 173 1 GGGGAACTTT 0.799369 -20 TACTATTAATTGGAAAATTGTGTTAAGCAA 28 59 1 TGGAAAATTG 0.479175 -242 ACCAGGGATTTGGAGACTTTTTCTTTTATC 28 228 1 TGGAGACTTT 0.28625 -73 ********** Masking position 6 Map Score: 33.8824 Number of sites scoring better than the average of aligned sites = 3813 Number in coding regions = 3302 Number in noncoding regions = 511 Number of orfs with sites within 600 bp upstream = 433 Fraction of orfs with sites within 600 bp upstream = 0.0695471 Motif number 8 TTTTAGACGGCGGTAATGTTCCTGGG 2 7 1 ACGGCGGTAA 0.738671 -111 TGCAACTGAAACGGCGATCGTGGCGGATAA 7 90 1 ACGGCGATCG 0.982404 -98 CAACAGTTGATCGGCGGTCATGGTAAAAAT 8 75 0 TCGGCGGTCA 0.965995 -226 TCAGCGCCCCTCGGCGATCATACAGGCTTT 16 17 1 TCGGCGATCA 0.980456 -48 TTCGACCATCTAGGCGATCGCCCAAAGGAA 18 76 0 TAGGCGATCG 0.97223 -135 CCCCCGGCAATAGGCGATCGGGGATCAAAC 20 14 0 TAGGCGATCG 0.97223 -270 GATTCCCCAGGCGGCGATCGCCAGAAAAAT 22 30 1 GCGGCGATCG 0.979135 -271 GGATTAGGGATTGGCGATAGATTGGGGTTC 26 20 1 TTGGCGATAG 0.819532 -92 ********** Masking position 8 Map Score: 7.03755 Number of sites scoring better than the average of aligned sites = 3892 Number in coding regions = 3544 Number in noncoding regions = 348 Number of orfs with sites within 600 bp upstream = 325 Fraction of orfs with sites within 600 bp upstream = 0.0522004 Motif number 9 AGGGGCCGGGGTTAGTCCGTCCTATTTGCAAAC 3 31 1 GTAGCCTCCT 0.565881 -27 TGTGGGCAAAGTTTGGCATTGCCGCCAGAAAAG 5 88 0 GTTGCATGCC 0.91096 -213 GGTTTTCCTTGCCGATATAGTTC 6 100 0 GTTTCCTGCC 0.972987 -13 CCATAGGGTTTGTCCCTCACTTGGGCTAGT 8 8 1 GTTGCCTCAC 0.801643 -293 ATTAGTGGAATTTTTACCATGACCGCCGATCAA 8 66 1 TTTTCCTGAC 0.687639 -235 TAGTTGTCCTCCTTGTCCCTGGTATTTTGCTAT 8 109 1 CTTGCCTGGT 0.668853 -192 AGTTAGTCTAGATTTACCGGGGTAATAAAGTAA 8 205 0 GTTTCCGGGT 0.835458 -96 TGACTGCTCTGATTTTCCTGGGCTTGATAACTT 8 264 1 GTTTCCGGGC 0.923968 -37 ATTATTTCCATTTTGCCATTGCCC 9 2 0 TTTGCATGCC 0.716263 -143 AAGCGGCCAAGGTTTGCCGTGCCTAGGAATTAA 10 74 1 GTTTCCTGCC 0.972987 -141 ACACGGTGAAACTTGCCCCTGCCATCCTCTTGT 12 43 0 ATTGCCTGCC 0.744032 -79 GACCTCAAACGATTTGCAGTGATTAAGTAAA 13 186 1 GTTTCATGAT 0.444041 -21 AGTGAAAAAAGTTATCCCGTGGTCCAGTCTGCA 14 204 1 GTATCCTGGT 0.763542 -65 TTATTTTAGCGCTTTTCCATCCCCCTAC 16 47 1 GTTTCCTCCC 0.924849 -18 TAACGATCTTTTTTGTCCTGCCCCAAGGAATTT 20 162 0 TTTGCCGCCC 0.5476 -122 GGTTTTGCCCTCGTTGGGAGACTG 22 287 0 GTTTCCTCGT 0.852284 -14 ATTTTGTGTAGTTTTTCAATGGCTTTGGGGCC 23 185 1 GTTTCATGGC 0.896474 -22 CAAGACTTAATTTTTCCCATGGTTACCCTACCG 27 44 0 TTTTCCTGGT 0.806452 -149 CAAAAGAACCTGTTGGCAATGGTTTGATTATCT 27 123 1 TTTGCATGGT 0.542025 -70 TTTGCCCATGGATAGCCCTTGGCTAGTTAACCC 28 260 1 GTAGCCTGGC 0.911079 -41 * *** ** **** Masking position 3 Map Score: 11.7609 Number of sites scoring better than the average of aligned sites = 2580 Number in coding regions = 2335 Number in noncoding regions = 245 Number of orfs with sites within 600 bp upstream = 269 Fraction of orfs with sites within 600 bp upstream = 0.0432059 Motif number 10 CACCGAGCGATCACTAAAGCCTTTGTCCCC 5 176 1 TCACTAAAGC 0.987746 -125 CCAACTATTTTCACTAAAGCTCCGGCAAGG 5 205 1 TCACTAAAGC 0.987746 -96 AAACTACCCATCACTAGGGCGGATAGCAAA 8 134 0 TCACTAGGGC 0.942133 -167 CCAAATGTCTTCACTAAAGCTCCGGCAAAT 13 89 1 TCACTAAAGC 0.987746 -118 CTAAATCTCCTCACTAAAGCTCCGGCAAGT 17 153 1 TCACTAAAGC 0.987746 -84 ********** Masking position 5 Map Score: 6.85657 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 11 GAAATTTCCCCCCCTAGGCTAGGGGCCGGGG 3 11 1 CCCCTAGGCA 0.862891 -47 GTTTGTCCCTCACTTGGGCTAGTGGCCCAGG 8 18 1 CACTTGGGCA 0.784929 -283 AAACTCACAATGCCTGGGCCACTAGCCCAAG 8 30 0 TGCCTGGGCA 0.876507 -271 GTCCTCCTTGTCCCTGGTATTTTGCTATCCG 8 114 1 TCCCTGGTAT 0.349808 -187 TGCTCTGATTTTCCTGGGCTTGATAACTTAA 8 268 1 TTCCTGGGCT 0.84531 -33 TGTTTATGGATTCATGGGCTATAAAGCGGCC 10 51 1 TTCATGGGCA 0.707885 -164 AGCAATTCGGTTCCTGGTCAATGGCAACGTG 10 138 0 TTCCTGGTCA 0.88931 -77 CAGCCGCGATTACCTGGTCCACCATTAACAA 10 177 1 TACCTGGTCA 0.860533 -38 AAAAAGTTATCCCGTGGTCCAGTCTGCAAAC 14 209 1 CCCGTGGTCA 0.867716 -60 TATGATTGTGCTCCTGATCGATTAACTGCCT 15 34 0 CTCCTGATCA 0.550829 -90 CAATTCAGCGCCCCTCGGCGATCATACAGGC 16 13 1 CCCCTCGGCA 0.903172 -52 AAATTCTCCCCCCAGGGCCAATGCCTGACT 17 10 1 CCCCAGGGCA 0.947335 -227 ACCCCCTCCATCCCTGATCCTTAAGAGAAGT 19 20 0 TCCCTGATCT 0.500214 -203 AGCTTTTCCACCCTTGGTCAAACCGTCATAG 19 91 0 CCCTTGGTCA 0.917916 -132 ACTTCCCTTTCCCCAGGGCTTGAAGCTGTGT 19 164 0 CCCCAGGGCT 0.861855 -59 GCAGTTCCTCCACCTGGGCCAGAGGAAATTA 23 60 0 CACCTGGGCA 0.959561 -147 CAATAGCTGACCCATGGTCAAAATCGAACCC 26 44 0 CCCATGGTCA 0.917916 -68 GTAACCCCAACCCTTGGGCTAGGGGAACTTT 27 162 1 CCCTTGGGCA 0.956388 -31 AGTCTCCAAATCCCTGGTCATAGAGAAAAAA 28 215 0 TCCCTGGTCT 0.927844 -86 CCAAGGGCTATCCATGGGCAAAGAGATAAAA 28 251 0 TCCATGGGCA 0.917916 -50 ********* * Masking position 3 Map Score: 22.2574 Number of sites scoring better than the average of aligned sites = 2028 Number in coding regions = 1859 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 12 CAGTTAAAAGTAGGTTAAGGATTGAGGAC 6 9 1 AGAGGTTAAG 0.891015 -104 GTTTTGCTAAAGGGGGTTAACTAAACATAAA 8 160 1 AGGGGTTAAC 0.953853 -141 GAATGATATTAAAGGGTAAAGTCAGACAAGA 12 18 1 AAGGGTAAAG 0.779987 -104 AAAATGTCAAAATGGGTTAGGATTATCCAGA 18 47 0 AAGGGTTAGG 0.967978 -164 CTTGGAATACAGCGGATTAGGACTGCGGAAG 18 157 0 AGGGATTAGG 0.819173 -54 TCAGGGATGGAGGGGGTTGACTCCGGCGGAG 19 34 1 AGGGGTTGAC 0.8117 -189 TTTTATCCCCAGGAGGTTAAGGTTTTTAGGC 22 142 0 AGAGGTTAAG 0.891015 -159 TTAACCGTTAAATGGGTTACGATCAAAGCTG 23 32 0 AAGGGTTACG 0.895673 -175 GGATAAATTAAGGGGGTTTGGT 26 100 1 AGGGGTTTGG 0.889988 -12 AACGGGTTAGGCATAAAAATT 27 1 1 AAGGGTTAGG 0.967978 -192 TCCTAGCCAAAAAGGGTTAACTAGCCAAGGG 28 275 0 AAGGGTTAAC 0.915737 -26 ** ******** Masking position 1 Map Score: 6.12888 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 207 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 13 ATTTGATATGGGTAAGAATTTCAAGAAATATT 2 48 0 GGTAGATTTC 0.744022 -70 TTGGGTGGAGGGTAAGAATCTGTAGAACAAAC 5 17 1 GGTAGATCTG 0.914201 -284 AACCACCTCCCGTCAGCTTTTCTGGCGGCAAT 5 72 1 CGTAGTTTTC 0.643237 -229 ATGGAAGGTCGGACAGATTTTGTTTATGGATT 10 31 1 GGAAGTTTTG 0.923599 -184 TTCCCTCTGCGATAAGTTTCTGTAATATCTTA 11 17 1 GATAGTTCTG 0.693672 -26 AGGTTAGTTTTCGGGGAAAGTTG 14 2 1 GGTAGTTTCG 0.930019 -267 AAAAACGGGAGGACAGATTTTCATCCATCTTC 14 115 1 GGAAGTTTTC 0.806011 -154 CCATCTTCCCGGTTAATTTCTGAGGAGTTTTT 14 139 1 GGTAATTCTG 0.693695 -130 TCCAGGATGGGGGAAGGTTTTGGGTAATCAAG 20 64 0 GGGAGTTTTG 0.876228 -220 TCTCATCTTAGGCTAGTTTCTGCGCCTTGACA 20 200 0 GGCAGTTCTG 0.959924 -84 TCTTATTTTTGGCTAGTTTCTCCCCAGGCCAT 22 211 0 GGCAGTTCTC 0.891689 -90 AGGGCGGAGACGTAAGTTTCCGTTCACTCCTC 25 139 0 CGTAGTTCCG 0.720579 -162 GATAGATTGGGGTTCGATTTTGACCATGGGTC 26 35 1 GGTCGTTTTG 0.811756 -77 TTTGACCATGGGTCAGCTATTGAAAGAGTTAG 26 53 1 GGTAGTATTG 0.744207 -59 CTCCTTGGCCGGATAGCTTCCGGCCTGTTTAC 28 118 1 GGAAGTTCCG 0.845764 -183 AACCCTTTTTGGCTAGGATTTGG 28 288 1 GGCAGATTTG 0.825401 -13 *** ** ***** Masking position 9 Map Score: 7.77472 Number of sites scoring better than the average of aligned sites = 581 Number in coding regions = 478 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 14 CGATCACTAAAGCCTTTGTCCCCCAACTATT 5 183 1 AGCCTTTGCC 0.96999 -118 ATCGTCCAACAGCCTATGACTTGTCTCAGTT 8 234 0 AGCCTATGCT 0.754891 -67 AAATCAGAGCAGTCATCGTCCAACAGCCTAT 8 248 0 AGTCATCGCC 0.7296 -53 ATTTCCATTTTGCCATTGCCC 9 1 0 TGCCATTGCC 0.939947 -144 AGGCGAATTAAGCCAACGTCTGTCAAATTAT 9 39 0 AGCCAACGCT 0.864994 -106 TATAACACGTTGCCATTGACCAGGAACCGAA 10 133 1 TGCCATTGCC 0.943832 -82 TTGGAGAGTCAGGCATTGGCCCTGGGGGGAG 17 16 0 AGGCATTGCC 0.724769 -221 CTTGTCTAAAAGGCTATGACCCGCCCCCTAA 17 126 1 AGGCTATGCC 0.847634 -111 TGGTTAACTCAGCCATAGACTAGGGTGGGGG 20 98 1 AGCCATAGCT 0.529247 -186 ACCCCTAGGGTGCCCACGGCCCAGTCAGGGT 22 102 1 TGCCCACGCC 0.818885 -199 ACCGGCAAAAACCCTATGCCCCCCGTCCCAA 25 185 0 ACCCTATGCC 0.722427 -116 GCCCATGGATAGCCCTTGGCTAGTTAACCCT 28 263 1 AGCCCTTGCT 0.696888 -38 ******** ** Masking position 4 Map Score: 4.88647 Number of sites scoring better than the average of aligned sites = 1300 Number in coding regions = 1205 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 15 TCGACTCATCAGAAGGACTTACCCTCAGAG 5 267 1 AGAAGGACTT 0.83955 -34 TTTTATTTGTAGAAGCAAATCGAATCAGCA 6 68 0 AGAAGCAAAT 0.819134 -45 ACCAGGGACAAGGAGGACAACTAACATCAA 8 102 0 AGGAGGACAA 0.890707 -199 GAGGCGCAATTTCAGCTTTGG 9 134 0 AGGCGCAATT 0.742196 -11 GGCTGAATTCAGAAGCAATTCGGTTCCTGG 10 152 0 AGAAGCAATT 0.839915 -63 CACAGGGGGTAGGAGGAAAAATAGGCAGTT 15 12 1 AGGAGGAAAA 0.875549 -112 TTAATCGATCAGGAGCACAATCATAAACAA 15 40 1 AGGAGCACAA 0.904455 -84 AACGACGGAGAGAAGGAAATCTGAATATGT 17 45 1 AGAAGGAAAT 0.795879 -192 GGGTTAGTTAAGGAGCACTTTTCGACCATC 18 96 0 AGGAGCACTT 0.954834 -115 GGATAGAGGAGCAAAATTTAGAACAG 19 207 0 AGGAGCAAAA 0.890971 -16 AATAGAACTTAGGAGGATTT 20 274 1 AGGAGGATTT 0.737952 -10 CAACTTACTGAGGAGGAATTAAGGGAATG 24 10 0 AGGAGGAATT 0.940171 -33 TATCCGGCCAAGGAGCACTCAGATTGTGTT 28 103 0 AGGAGCACTC 0.831655 -198 ********** Masking position 7 Map Score: 9.9372 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 160 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577