AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00240_synecho_reg_100.orf -o00240_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 sll1043 127 pnp; polyribonucleotide nucleotidyltransferase. [EC:2.7.7.8] #2 sll1035 234 upp; uracil phosphoribosyltransferase (UMP pyrophosphorylase) #3 slr0965 143 dnaN; DNA polymerase III, beta chain. [EC:2.7.7.7] [SP:DP3B_SYNY3] #4 sll0931 171 hypothetical protein. [EC:2.1.1.45] #5 sll1018 119 pyrC; dihydroorotase. [EC:3.5.2.3] #6 sll1572 55 dnaE; DNA polymerase III alpha subunit. [EC:2.7.7.7] #7 sll1571 100 hypothetical protein. #8 sll1819 77 rplQ, rpl17; 50S ribosomal protein L17. [SP:RL17_SYNY3] #9 sll1818 108 rpoA; DNA-directed RNA polymerase alpha chain (transcriptase alpha #10 sll1789 107 rpoC2; DNA-directed RNA polymerase delta chain. [EC:2.7.7.6] #11 sll1787 85 rpoB; DNA-directed RNA polymerase beta chain (transcriptase beta #12 sll1786 135 hypothetical 29.3 kD protein sll1786. [SP:YH86_SYNY3] #13 slr1237 48 codA; cytosine deaminase. [EC:3.5.4.1] #14 ssl2245 300 hypothetical protein. #15 sll1360 167 dnaX; DNA polymerase III subunit. [EC:2.7.7.7] #16 sll0838 46 pyrF; orotidine 5'-phosphate decarboxylase (OMP decarboxylase). #17 sll0837 107 hypothetical protein. #18 sll1258 252 dcd; deoxycytidine triphosphate deaminase (dctp deaminase). #19 tRNA-Ser-3 146 tRNA-Ser. #20 slr1265 87 rpoC1; DNA-directed RNA polymerase gamma chain. [EC:2.7.7.6] #21 sll1178 129 nodulation protein. [SP:YB78_SYNY3] #22 sll1443 300 pyrG; CTP synthase (UTP--ammonia ligase) (CTP synthetase). #23 slr1164 300 nrdA; ribonucleotide reductase subunit alpha. [EC:1.17.4.1] #24 slr0446 300 dnaX_and_dnaZ; DNA polymerase III subunit. [EC:2.7.7.7] #25 slr0406 72 pyrC; dihydroorotase (DHOase). [EC:3.5.2.3] [SP:PYRC_SYNY3] #26 slr0407 264 hypothetical protein. #27 sll1852 224 ndk, ndkR; nucleoside diphosphate kinase (NDK) (ndp kinase). #28 slr0185 38 umpS; uridine 5-monophosphate synthase. [EC:2.4.2.10 2.7.1.48] #29 sll0154 185 hypothetical 51.0 kD protein sll0154. [SP:Y154_SYNY3] #30 slr0380 113 hypothetical protein. #31 slr0306 71 probable 5'-nucleotidase precursor. [EC:3.1.3.5] #32 sll0286 123 hypothetical protein. #33 slr0707 182 polA; DNA polymerase I. [EC:2.7.7.7] #34 sll0572 300 hypothetical protein. #35 slr0600 143 hypothetical protein. [EC:1.6.4.5] #36 slr0603 198 dnaE; DNA polymerase III alpha subunit. [EC:2.7.7.7] Motif number 1 CCGGAAGTTGGGGCATTGGGAAGGGAAAGGT 2 70 0 GGGCATGGGA 0.981484 -165 CTTGGCCGTTGGGGAACCGAAAAATGGGCTA 2 171 0 GGGGAACGAA 0.928874 -64 AAAAGGAAGGTGGGATTGGGATCATCTCCCT 3 31 1 TGGGATGGGA 0.683874 -113 AATTAAGCTGGGGGAGCCGGACTTTCTGCAA 4 121 0 GGGGAGCGGA 0.922309 -51 AGGGGAAGGCAAAATACAGGGA 7 89 0 GGGGAAGCAA 0.955051 -12 AGTTTTTCAGGAGGATGGCGATCGCCTAGGG 10 31 1 GAGGATGCGA 0.532154 -77 GCAATTAAGGGGGCAGGAGGATTAGACCCTA 10 57 0 GGGCAGAGGA 0.864956 -51 TGAGATTAGGGGGCAAGGCAATTAAGGGGGC 10 74 0 GGGCAAGCAA 0.94744 -34 TGCGGTGGTTGGGGTTAGGGAAGGCCGGGGA 11 40 0 GGGGTTGGGA 0.881999 -46 TTGTCGTCCCGGGCAAAGGGCTTATCTAATA 14 40 1 GGGCAAGGGC 0.912753 -261 AGTTATGGCAGAGGAATGGGAAAATTCGAGC 16 13 0 GAGGAAGGGA 0.900407 -34 TGAGATCCTGGGGGGAGGGGAAGCTTTTGAA 22 85 1 GGGGGAGGGA 0.974485 -216 TTTAAATATTGGGCGACGGAAACCGTTTTGC 23 127 0 GGGCGAGGAA 0.944532 -174 CAGAACCCTAGGGGAAAAGAAGATCAAGGAT 27 71 0 GGGGAAAGAA 0.892535 -154 TACATGGTTTGGGCATCGGGATTATGAATGG 27 150 0 GGGCATGGGA 0.981484 -75 GTTGGGGATTGGGATTCTAAGCAC 28 4 1 GGGGATGGGA 0.984247 -35 AACGCATTAAGGGGAAACCAATCGCTACCGA 29 104 0 GGGGAACCAA 0.788413 -82 GGAGAAGAAAGGGCAATGGGACGATAAAGCA 29 146 0 GGGCAAGGGA 0.99175 -40 GGAAGCAGAGGGGGAGAAGAAAGGGCAATGG 29 158 0 GGGGAGAGAA 0.798701 -28 GGGCTAGGGAAGCAGAGGGGG 29 175 0 GGGCTAGGAA 0.883146 -11 AGATTCACCAGGGGGAAGCGATCAAAGCTTA 32 11 1 GGGGGAGCGA 0.915946 -113 AAAACGGTGGGGGCAATGAAAATGGTGATAA 32 62 0 GGGCAAGAAA 0.736051 -62 GTATTACCTTGGGCAGTGGAGAATTTTTAAG 33 127 1 GGGCAGGGAG 0.724261 -56 GGGGGGCAGGGCAATGGAAGTGTGATCAA 36 9 1 GGGCAAGGAA 0.984418 -190 ****** **** Masking position 3 Map Score: 34.8059 Number of sites scoring better than the average of aligned sites = 2068 Number in coding regions = 1829 Number in noncoding regions = 239 Number of orfs with sites within 600 bp upstream = 256 Fraction of orfs with sites within 600 bp upstream = 0.0411179 Motif number 2 GGTGGACAAGGCCCATTTCCCCGGTGATCAACCT 1 23 1 GCCATTTCCG 0.936945 -105 GTGGGATTGGGATCATCTCCCTGGAACGGACAGA 3 40 1 GTCATCTCCG 0.603933 -104 TAGTCCCATGGCCAATCCCCAAAGGATTTGCTCA 3 118 1 GCAATCCCCG 0.859905 -26 TTTTTGTGCCGTCGTTCCCCCGAGGTTAAAAGGT 5 93 1 GCGTTCCCCG 0.98102 -27 TCAGGAGGATGGCGATCGCCTAGGGTCTAATCCT 10 37 1 GCGATCGCCG 0.99018 -71 TTACCAGGGGGGCGATACCCCCAGA 11 2 0 GCGATACCCG 0.878568 -84 GCACCGTCCTTTCCCTTGGGAAGGCCAAA 12 6 1 GCCTTTCCCG 0.902504 -130 CCAAAAACCAGAGGTTTTCCCCAGCTAGAATACC 12 77 0 GGGTTTTCCG 0.711492 -59 TAATGCCGTGGGCGATCTCCAAAGTAACCAAAAA 12 104 0 GCGATCTCCG 0.988091 -32 TATTAGATAAGCCCTTTGCCCGGGACGACAAGCT 14 37 0 GCCTTTGCCG 0.902504 -264 GGGAGACTGTAACGTTCCCCCACGACGGCTCAAA 17 74 1 ACGTTCCCCG 0.859153 -34 CTGCATCAATGGCGATCGCCGACGGGAATAATTT 18 191 0 GCGATCGCCG 0.99018 -62 GCATAAGCCTGACCATCTCCGTCGGCAAACTCGA 22 117 0 GCCATCTCCG 0.970279 -184 ATGCCATGTTGGCGGTTCCCAGAGAAAAATTAAT 22 147 1 GCGGTTCCCG 0.930177 -154 GCAGAGGCAAAACGGTTTCCGTCGCCCAATATTT 23 121 1 ACGGTTTCCG 0.564011 -180 CAACAAGGCAGTGGATTTCCAGGGTAAATCCGCC 24 108 1 GGGATTTCCG 0.827915 -193 TTACTATTCCGCCGATTTCCTCTTTGCTCTCCGT 26 90 1 GCGATTTCCT 0.612405 -175 GTTCTGGAACAGCGATCGCCAGGGTGGTTTTCCC 27 96 1 ACGATCGCCG 0.922481 -129 GCAAAATCTTGGCGATCGCCCTTGGCTTTATCTT 30 52 1 GCGATCGCCG 0.99018 -62 AAAATTAGTGGACTTTCGCCCTAGCCCGCCGGGA 35 103 0 GCTTTCGCCG 0.75882 -41 * ******** * Masking position 6 Map Score: 28.3668 Number of sites scoring better than the average of aligned sites = 2765 Number in coding regions = 2507 Number in noncoding regions = 258 Number of orfs with sites within 600 bp upstream = 252 Fraction of orfs with sites within 600 bp upstream = 0.0404754 Motif number 3 GGTGATCAACCTTTGGTCGGCCCAGGGTTCG 1 45 1 CTTTGGCGGC 0.896018 -83 TCTGCCATACTTTGGGCAGGGATTTCCCCCA 2 37 0 TTTGGGAGGG 0.786969 -198 TAGTGCCAAGTTTTGGCCGGGAAACTAAAAC 4 53 1 TTTTGGCGGG 0.93946 -119 TTAACTGTACTTTTGGGTTGAGCCAATCAGC 5 13 0 TTTTGGTTGA 0.434659 -107 GGTTGCCCAACTTTGCTAGGATTTTAGGGGG 5 61 1 CTTTGCAGGA 0.944857 -59 TTGACAGCATTTTTGGCCGGATTTTTCAGAC 7 23 1 TTTTGGCGGA 0.912763 -78 CGTCCTTTCCCTTGGGAAGGCCAAATGGTTG 12 15 1 CTTGGGAGGC 0.672275 -121 ATATGATTAGCTTTGGCCGGACTGACTGCC 13 29 1 CTTTGGCGGA 0.967413 -20 TAGATAAGCCCTTTGCCCGGGACGACAAGCT 14 37 0 CTTTGCCGGG 0.982404 -264 AGAAAATAGTCTTTGGTCGGATAGAAGACAT 14 179 0 CTTTGGCGGA 0.967413 -122 TCAGTATCTATTTTGCACTGGTTCATCATTG 14 212 1 TTTTGCCTGG 0.807095 -89 AATGATTAGGTTTTGCTTTGGGTAAGCTGGG 17 46 1 TTTTGCTTGG 0.591171 -62 CGTATAATAACTTGGGTTGGGAACTAGACCG 21 56 0 CTTGGGTGGG 0.888379 -74 CCAACATTCCCTTTGGTCAGGATAGTTTAAC 21 109 1 CTTTGGCAGG 0.660263 -21 ATTGTCCCAACTTGTCCCTGACGCAATAGAA 22 51 0 CTTGTCCTGA 0.507654 -250 AAGCCATTAATTTTTCTCTGGGAACCGCCAA 22 155 0 TTTTTCCTGG 0.507516 -146 GTCCAGGAATCTTTGGATGGGATTGTGATAT 23 61 0 CTTTGGTGGG 0.938337 -240 AACTCCCACTCTTGTCCAGGAATCTTTGGAT 23 74 0 CTTGTCAGGA 0.688216 -227 CAAAATTACCCTTTTCAAGGAAATTTGCCAC 23 196 1 CTTTTCAGGA 0.808445 -105 ATAAACGCACCTTTTCAAGGGTGAAAAAGAC 29 12 1 CTTTTCAGGG 0.862248 -174 ATCGCCAAGATTTTGCTAGGATCTGCCTGTT 30 37 0 TTTTGCAGGA 0.857937 -77 TTGGCTTTATCTTTTCCAGGATCTGGTGGTG 30 73 1 CTTTTCAGGA 0.808444 -41 CAAGACCAAATTTGTCTCGGATCTAGCCCCT 33 51 0 TTTGTCCGGA 0.630894 -132 TGTTACAATACTTTGCCTGGGAACCTTCTCC 34 124 0 CTTTGCTGGG 0.950731 -177 TTTTCTCTTGCTTTGCATTGATCCCCGGTTG 34 204 0 CTTTGCTTGA 0.734486 -97 ****** **** Masking position 3 Map Score: 25.3342 Number of sites scoring better than the average of aligned sites = 1559 Number in coding regions = 1395 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 4 AGGGGAAGGCAAAATACAGGGAGTTCTTGCTT 7 79 0 GGAAATCGGA 0.971683 -22 AAAACTAACGGGAAAAATGGTTGGGA 10 2 0 GGAAATGGGG 0.9822 -106 AGAAGTCTCCGGAAATTTGCGGTGGTTGGGGTTAG 11 53 0 GGAATTCTGG 0.779637 -33 GGCAAAGTTGAGGAGTTATGGCAGA 16 32 0 GGAAATGGAG 0.85555 -15 GGGCAAAGTTCAGGGAAATAAAGCGG 18 237 0 GGAAATCGGA 0.971683 -16 TGGTATCTCCGGTAAAATGGGCGGGGATTTAAGCG 22 254 1 GGAAATGGGG 0.9822 -47 CCTTGAAAAGGGTAATTTTGACGGATTTTTTCTGA 23 181 0 GGAATTGGGA 0.871527 -120 TAGGATCCGTGGCAAATTTCCTTGAAAAGGGTAAT 23 200 0 GGAAATCTGA 0.935236 -101 GGATTTCCAGGGTAAATCCGCCGGAAACAAATAAG 24 120 1 GGAAACGGGA 0.959393 -181 TCCAAACGGGTAAAGTGGAGTGAAAATTATTAA 25 50 0 GGAAATGTGA 0.94269 -23 CATCGATAGGGGAAAACCACCCTGGCGATCGCTGT 27 104 0 GGAAACCTGG 0.924936 -121 GTGGACAAACGGAAAAACGGTGGGGGCAATGAAAA 32 71 0 GGAAACGGGG 0.97089 -53 GAGTAAGTGAGGAAAAGTGGATTAATAATCAAAGT 34 20 1 GGAAATGTAA 0.638418 -281 TTTTGATGGAGAAAAACCGCTAGGATATGGCAAAT 34 59 0 GAAAACCGGA 0.690054 -242 CAAAGCAAGAGAAAAAATACCCTGGTTAATCATAT 34 220 1 GAAAATCTGG 0.686339 -81 ** *** * * *** Masking position 5 Map Score: 16.3076 Number of sites scoring better than the average of aligned sites = 922 Number in coding regions = 803 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 5 TTCTTCTCAGCAGATCCTAACACCATTGACG 1 74 0 CAATCCTAAC 0.924397 -54 GAGAAGAAGAAACGTCATAGCACATAAGGAA 1 97 1 AAGTCATAGC 0.787919 -31 ACGGTGAGACCACGTCCTAACTTTTAGCCCA 2 147 1 CAGTCCTAAC 0.896967 -88 AAATCCCCCTAAAATCCTAGCAAAGTTGGGC 5 65 0 AAATCCTAGC 0.924397 -55 AATTTATTCACAAATCATAGTATTAAAATTT 18 65 1 CAATCATAGT 0.725056 -188 CTGACAGTTCCATATCATAGCAAACAATGAC 19 123 0 CAATCATAGC 0.967932 -24 AAATTTGCCACGGATCCTAGCCTTGTTGGCA 23 216 1 CGATCCTAGC 0.93651 -85 CACTAATTTTCAAGTCATAGCAGTTGGGAAA 26 150 1 CAGTCATAGC 0.955538 -115 GGTCAACAGGCAGATCCTAGCAAAATCTTGG 30 33 1 CAATCCTAGC 0.986059 -81 TTAAATTTGCCATATCCTAGCGGTTTTTCTC 34 55 1 CAATCCTAGC 0.986059 -246 ** ******** Masking position 5 Map Score: 10.9412 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 23 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 CTCTGAGCCTCACATATTTTGCCATAGTCCCAT 3 94 1 CACTATTGCC 0.644351 -50 TTGTTGTTATTGGGAATTTTCCCCTTTTCT 4 152 1 TGGAATTCCC 0.900398 -20 CCCCAGAATCCGGAAAGGTTGCCCAACTTTGCT 5 45 1 CGGAATTGCC 0.831285 -75 GGAACGACGGCACAAAAATCCCCCTAAAATCCT 5 78 0 CACAATCCCC 0.804145 -42 GTTGATCGCCCGGTTACCTTGCC 15 155 1 CGGTATTGCC 0.831403 -13 AAGCTCGAATTTTCCCATTCCTCTGC 16 4 1 CTCAATTCCC 0.875954 -43 AGCTGGGAGACTGTAACGTTCCCCCACGACGGC 17 70 1 CTGAATTCCC 0.806396 -38 TAATGATTGCCGCTTTATTTCCCTGAACTTTGC 18 228 1 CGCTTTTCCC 0.94028 -25 GATTGGCGATCGGTCTAGTTCCCAACCCAAGTT 21 46 1 CGGCTTTCCC 0.65949 -84 TTGACAGCGACACCAACATTCCCTTTGGTCAGG 21 97 1 CACAATTCCC 0.901914 -33 CTACAAAGTGCGCTTAAATCCCCGCCCATTTTA 22 266 0 CGCTATCCCC 0.949867 -35 GAGGAAATGATGCTTAGTTTCCCTTGAAGGTCG 23 251 0 TGCTATTCCC 0.939741 -50 CCTTTTGCGCCTGTTTTGTCCCCATTGTCAGGG 24 222 1 CTGTTTCCCC 0.408332 -79 ACGGTTCCAATGCTAAGCCTCCCTGACAATGGG 24 242 0 TGCAACTCCC 0.636267 -59 CCATTGGTTTTGCCTATCTTCCCAGCAATTAAT 26 18 0 TGCTATTCCC 0.939743 -247 TTGGAGCTTGTGCTTAGAATCCCAATCCCCAAC 28 11 0 TGCTAATCCC 0.541336 -28 TAAACAGCAACGGGATTATTCCCAGAACCTTTG 34 153 0 CGGATTTCCC 0.902212 -148 TCTCTTGCTTTGCATTGATCCCCGGTTGCTTTT 34 199 0 TGCTTTCCCC 0.72097 -102 AGCAGAAATTTACTAAATTTCCCC 35 2 0 TACAATTCCC 0.771668 -142 *** ** ***** Masking position 12 Map Score: 12.2199 Number of sites scoring better than the average of aligned sites = 1168 Number in coding regions = 1030 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 7 TTTAATTAATCAGCATCAAAAAATCCCTCAAG 6 7 1 TAACACACAA 0.948684 -49 AAAAAAGCTGTTAGCAAAAAATTTAACTGTC 9 6 0 TTACAAAAAA 0.840388 -103 ATCTCCAAAGTAACCAAAAACCAGAGGTTTTCCCCA 12 88 0 TAACAAACAG 0.794147 -48 AGAAGACATATTAGCAGAAAAGTAAACAATTCGTGG 14 152 0 TTACAAAAAA 0.840388 -149 GTTGGATTTTTTAACACCAACGTCAAGTCTCCGAAT 19 35 1 TTACACACAA 0.930696 -112 AGCCAATAACTAAACCTAACCTCCAATTGAGTACTG 22 219 0 TAACCAACAA 0.794147 -82 ACTTAATGGTTAATCATCACCGCCAAATAATCGGGT 26 202 1 TAACACACAA 0.948684 -63 TTAAGTTTTTTTAACAGAAAAAGCAAAAGGAGGTTG 27 197 1 TTACAAAAAA 0.840388 -28 ATTGGGATTCTAAGCACAAGCTCCAAAAATT 28 18 1 TAACAAACAA 0.957397 -21 ACACTAGGTTTAAGCACAAGACCAAATTTGTCTCGG 33 62 0 TAACAAAAAA 0.878763 -121 TTTCTACCTTTTATCATAAACAGCAACGGGATTATT 34 166 0 TTACAAACAA 0.942277 -135 TTTTCAACCTTAAACACCAGCTCGAAATATGATTAA 34 245 0 TAACACACAA 0.948684 -56 *** ** ** * ** Masking position 9 Map Score: 6.78053 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 70 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 GTTGAGCAAATCCTTTGGGG 3 134 0 GTTGAGCAAA 0.969334 -10 GTACTTTTGGGTTGAGCCAATCAGCGC 5 8 0 GTTGAGCCAA 0.972294 -112 TCCTAGCAAAGTTGGGCAACCTTTCCGGAT 5 52 0 GTTGGGCAAC 0.781262 -68 TAACAGCTTTTTTGAGCAAATCGTAATTTC 9 29 1 TTTGAGCAAA 0.736368 -80 GATCAATACAGTTGACCAAAAATATTGCAA 12 43 0 GTTGACCAAA 0.919717 -93 TCAGGGACAAGTTGGGACAATTATTGAGAT 22 61 1 GTTGGGACAA 0.868034 -240 CCACTGCCTTGTTGACCAAAATAAACTGCG 24 92 0 GTTGACCAAA 0.919717 -209 AGTCATAGCAGTTGGGAAAATGATCATTCT 26 162 1 GTTGGGAAAA 0.858363 -103 GGATCTGCCTGTTGACCCAACTTAGATCAT 30 20 0 GTTGACCCAA 0.93922 -94 CCCAATCTTGGTTCGGCCAAAAAATTGCCC 34 95 0 GTTCGGCCAA 0.831283 -206 ********** Masking position 3 Map Score: 7.27452 Number of sites scoring better than the average of aligned sites = 454 Number in coding regions = 412 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 9 CATTTCCCCGGTGATCAACCTTTGGTCGGCC 1 36 1 GTGATAACCT 0.836041 -92 ATCTTAGGCAATGATGAACCAGTGCAAAATA 14 220 0 ATGATAACCA 0.980487 -81 GATCAATGAAATGATTAATCAGGAGAAAAAC 18 139 0 ATGATAATCA 0.866981 -114 ATGGCTTTACACGATCAACCAATCTTGCTAG 22 179 1 ACGATAACCA 0.966048 -122 TTTGGCGGTGATGATTAACCATTAAGTAATA 26 198 0 ATGATAACCA 0.980487 -67 GGGCAATGGGACGATAAAGCAAATTACTCCT 29 136 0 ACGATAAGCA 0.845445 -50 AGCTCGAAATATGATTAACCAGGGTATTTTT 34 232 0 ATGATAACCA 0.980487 -69 CTGTTGCTAAGTGATGAACCAGAAATGAAAA 36 125 0 GTGATAACCA 0.966049 -74 ***** ***** Masking position 7 Map Score: 5.77018 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 21 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 CGTGGTCTCACCGTCGGTAACAATTCACCG 2 131 0 CCGTCGGTAA 0.968327 -104 ACGCGAGGGCCTGTCGGCAAAGTTTTAGTT 4 75 0 CTGTCGGCAA 0.915006 -97 ATGGCGATCGCCGACGGGAATAATTTGAGC 18 187 0 CCGACGGGAA 0.983107 -66 CTGACCATCTCCGTCGGCAAACTCGACTTC 22 113 0 CCGTCGGCAA 0.988133 -188 TAAATATTGGGCGACGGAAACCGTTTTGCC 23 126 0 GCGACGGAAA 0.878537 -175 CAGGGTAAATCCGCCGGAAACAAATAAGAC 24 127 1 CCGCCGGAAA 0.983091 -174 TCGCCCTAGCCCGCCGGGAAACCAAGTTTG 35 92 0 CCGCCGGGAA 0.988997 -52 ********** Masking position 9 Map Score: 5.26163 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 246 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 AGTCCGGCTCCCCCAGCTTAATTTTGTTGT 4 129 1 CCCCAGCTTA 0.797367 -43 GGAAAGGTTGCCCAACTTTGCTAGGATTTT 5 56 1 CCCAACTTTG 0.726023 -64 GCCCCCTAATCTCAATCTTGGAGCGTT 10 91 1 CTCAATCTTG 0.839804 -17 CAGAGGTTTTCCCCAGCTAGAATACCAGTT 12 73 0 CCCCAGCTAG 0.863864 -63 TACACGATCAACCAATCTTGCTAGCAAGTT 22 186 1 ACCAATCTTG 0.839805 -115 CTTAGAAACTCCCACTCTTGTCCAGGAATC 23 81 0 CCCACTCTTG 0.865014 -220 GCATCATTTCCTCAAGCTTGTGAACAAGTT 23 271 1 CTCAAGCTTG 0.924723 -30 AATAACTAGCCCCAAGATTGTTCTTGCTGA 24 275 0 CCCAAGATTG 0.886583 -26 CGTTTGTCCACCCCAGCTTGTTCTTGAACG 32 95 1 CCCCAGCTTG 0.98037 -29 GAACCTTCTCCCCAATCTTGGTTCGGCCAA 34 105 0 CCCAATCTTG 0.971452 -196 CCGCCGGGAAACCAAGTTTGACGGGCTGTC 35 82 0 ACCAAGTTTG 0.679855 -62 ********** Masking position 8 Map Score: 6.1915 Number of sites scoring better than the average of aligned sites = 507 Number in coding regions = 427 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 12 GTGCTATGACGTTTCTTCTTCTCAGCAGATCCTAACA 1 83 0 GTTTCTAGCA 0.587115 -45 GCATTGGGAAGGGAAAGGTTTTCTGCCATACTTTGGG 2 52 0 GGTTTTTGCC 0.9021 -183 GGTGAGACCACGTCCTAACTTTTAGCCCATTTTTCGG 2 149 1 CTCTTTAGCC 0.641949 -86 AACCAACAATAAGCCTTGCTCTGAGCCTCACATATTT 3 76 1 AGCTCTAGCC 0.7288 -68 TAAGCTGGGGGAGCCGGACTTTCTGCAATCCAATGCC 4 112 0 GGCTTTTGCA 0.846609 -60 CTAGGATTTTAGGGGGATTTTTGTGCCGTCGTTCCCC 5 76 1 AGTTTTTGCC 0.479228 -44 ATTAACAACAGGGGGTTACTCTAAGGCAAGCAGCAGT 8 31 0 GGCTCTAGGC 0.809724 -47 ACCATTTTTCCCGTTAGTTTTTCAGGAGGATGGCGAT 10 16 1 CGTTTTAGGA 0.441108 -92 TAACCTCTCCCCGGCCTTCCCTAACCCCAACCACCGC 11 33 1 CGCCCTACCC 0.355907 -53 CCGCAAATTTCCGGAGACTTCTGAGCCACC 11 66 1 CGTTCTAGCC 0.916146 -20 TTCATTCTAAGCGTCTTACCCTTTGCCTTTAGCACCC 15 50 1 GGCCCTTGCC 0.75571 -118 GATCAACAGACAGGGGGATTCTCAGCCTAACTCCAAA 15 125 0 CGTTCTAGCC 0.916146 -43 CGATCAATGTTTTGAGCCGTCGTGGGGG 17 90 0 GTTTTTAGCC 0.739089 -18 TTTTGCAGTTGCGGCTGTTTTTTTGGAATAAACAGGA 20 20 0 GGTTTTTGGA 0.411115 -68 GTTTATCCAGCCGTTTAACTTTTTGCAGTTGCGGCTG 20 40 0 CGCTTTTGCA 0.736606 -48 TTTTGATCTGGGTGAAATCTTCTGCACAAACCCTGG 23 10 1 GGTCTTTGCA 0.531021 -291 CTGGACAAGAGTGGGAGTTTCTAAGCCTATACTTTGC 23 86 1 GGTTCTAGCC 0.955678 -215 GCTTGACAATGGGCACCACTTTCAGCACAATAGAATA 27 20 0 GGCTTTAGCA 0.924894 -205 GTTGGGGATTGGGATTCTAAGCACAAGCTCCAA 28 7 1 GTTTCTAGCA 0.587115 -32 CAGAATCTATCTGTGTCTTTTTCACCCTTGAAAAGGT 29 20 0 CGTTTTACCC 0.622277 -166 TTTTGTGACAAACTTTCAGCAACAACTTAAT 33 162 0 GGCTTTAGCA 0.924894 -21 CCTAGGATAGGGGGCATTCTTTTAGCAGAAATTTACT 35 21 0 GGCTTTAGCA 0.924894 -123 CAAGTTTGACGGGCTGTCTTTTGACCCTTGAACGTTA 35 63 0 GGTTTTACCC 0.764781 -81 * * **** **** Masking position 12 Map Score: 14.0236 Number of sites scoring better than the average of aligned sites = 1151 Number in coding regions = 1021 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 13 TTTGGTCAACTGTATTGATCAACTGGTATT 12 53 1 TGTATTGATC 0.94614 -83 GATTAATCATTTCATTGATCAGATCAATTC 18 150 1 TTCATTGATC 0.940132 -103 GAGCTAGTCTTGAATTGATCTGATCAATGA 18 161 0 TGAATTGATC 0.924583 -92 AAGTTTTTAATGATCTAAGTTGGGT 30 6 1 TTTAATGATC 0.751246 -108 TCTCTTGCTTTGCATTGATCCCCGGTTGCT 34 202 0 TGCATTGATC 0.949908 -99 GTGAAGGCGATTTATTGATCACACTTCCAT 36 24 0 TTTATTGATC 0.935678 -175 TCCTCAGTCATTAATTGATCTGAATGTAGG 36 91 1 TTAATTGATC 0.91033 -108 ********** Masking position 4 Map Score: 3.47956 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 46 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 14 TACCCGACACCCGGTGGACAAGGCC 1 6 1 GACACCCGGT 0.739314 -122 CCAATGCCCCAACTTCCGGTAACCCGATCT 2 82 1 AACTTCCGGT 0.904333 -153 TCCAAGCAAGAACTCCCTGTATTTTGCCTT 7 76 1 AACTCCCTGT 0.906295 -25 GCCTTAGAGTAACCCCCTGTTGTTAATTTT 8 41 1 AACCCCCTGT 0.961155 -37 AGCTGGGGAAAACCTCTGGTTTTTGGTTAC 12 85 1 AACCTCTGGT 0.614342 -51 AGGTCAAGTTAACAGCCGGTGACGGGGGTG 15 82 0 AACAGCCGGT 0.861586 -86 TAGGCTGAGAATCCCCCTGTCTGTTGATCG 15 133 1 ATCCCCCTGT 0.919709 -35 CTGTCTGTTGATCGCCCGGTTACCTTGCC 15 149 1 ATCGCCCGGT 0.899805 -19 TTGTGATATTAACCTCCGTTAGTCCAGGGT 23 40 0 AACCTCCGTT 0.82778 -261 AAACTTAACAATCACCCTGTATTTTACATG 27 175 0 ATCACCCTGT 0.817435 -50 GGCAACCTCCTTTTGCTTTTTCT 27 212 0 AACCTCCTTT 0.721444 -13 TTTTGCTAGGATCTGCCTGTTGACCCAACT 30 28 0 ATCTGCCTGT 0.613021 -86 CCTACAGGGCAACGTCCGTTCAATCAAATT 34 279 0 AACGTCCGTT 0.657582 -22 ********** Masking position 10 Map Score: 4.7369 Number of sites scoring better than the average of aligned sites = 525 Number in coding regions = 478 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 15 TGTCCTAGCCTAGCCTGCCC 3 1 0 TAGCCTGCCC 0.95721 -143 TCCGTGTAAATAGCTTGACCGACGCTATCT 9 68 0 TAGCTTGACC 0.931015 -41 CACCGGCTGTTAACTTGACCTCTTTTTTTT 15 91 1 TAACTTGACC 0.917873 -77 CTTGGGTTGGGAACTAGACCGATCGCCAAT 21 47 0 GAACTAGACC 0.836959 -83 GTTAAACTATCCTGACCAAAGGGAATG 21 113 0 TATCCTGACC 0.885214 -17 AACATGGCATAAGCCTGACCATCTCCGTCG 22 127 0 AAGCCTGACC 0.782955 -174 TTCCCCAATAACTAGCCCCAAGATTGTT 24 283 0 TAACTAGCCC 0.921125 -18 TTATGAATGGTAACCAGCCCCCATCGATAG 27 130 0 TAACCAGCCC 0.93764 -95 ATTTGTCTCGGATCTAGCCCCTTGCCTTGA 33 43 0 GATCTAGCCC 0.776659 -140 ********** Masking position 2 Map Score: 2.8026 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 187 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529