AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00600_synecho_reg_300.orf -o00600_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 Purged sequences: sll1187 27 lgt; prolipoprotein diacylglyceryl transferase. [EC:2.4.99.-] 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 sll1186 97 hypothetical protein. #12 sll1185 222 hemF; coproporphyrinogen III oxidase, aerobic #13 sll1184 134 ho; heme oxygenase. [EC:1.14.99.3] #14 slr1307 89 hypothetical protein. #15 ssr1604 198 rpmB, rpl28; 50S ribosomal protein L28. [SP:RL28_SYNY3] #16 slr0962 52 hypothetical protein. #17 tRNA-Pro-2 129 tRNA-Pro. #18 sll0943 251 hypothetical protein. #19 slr0963 198 sir; sulfite reductase (ferredoxin). [EC:1.8.7.1] [SP:SIR_SYNY3] #20 slr0964 99 hypothetical protein. #21 slr0965 143 dnaN; DNA polymerase III, beta chain. [EC:2.7.7.7] [SP:DP3B_SYNY3] #22 slr0966 155 trpA; tryptophan synthase alpha chain. [EC:4.2.1.20] [SP:TRPA_SYNY3] #23 slr0967 51 hypothetical protein. #24 sll0939 24 hypothetical protein. #25 sll0938 40 aspartate transaminase. [EC:2.6.1.1] #26 ssl1792 33 hypothetical protein. #27 sll0936 83 hypothetical protein. #28 slr0969 102 cbiH; precorrin methylase. #29 slr0971 82 hypothetical protein. #30 sll0934 195 ccmA; carboxysome formation protein. [EC:5.4.99.5] #31 ssl1784 164 rpsO, rps15; 30S ribosomal protein S15. [SP:RS15_SYNY3] #32 sll0932 100 hypothetical protein. #33 sll0931 171 hypothetical protein. [EC:2.1.1.45] #34 sll0930 43 hypothetical protein. #35 sll0928 111 apcD; allophycocyanin-B. #36 sll0927 168 metX; S-adenosylmethionine synthetase. [EC:2.5.1.6] #37 sll0925 266 hypothetical 23.0 kD protein sll0925. [SP:Y925_SYNY3] #38 slr0974 300 infC; translation initiation factor IF-3. [SP:IF3_SYNY3] #39 sll0648 127 lim; lipophilic protein. [EC:2.4.1.-] #40 sll0646 38 cyaA; adenylate cyclase. [EC:4.6.1.1] #41 sll0645 74 hypothetical protein. #42 sll0644 195 esterase. #43 slr0686 254 hypothetical protein. #44 sll0643 300 ureG; urease accessory protein ureG. [SP:UREG_SYNY3] #45 sll0812 300 hypothetical protein. #46 slr1271 251 rffM; UDP-N-acetyl-D-mannosaminuronic acid transferase. [EC:2.4.1.-] #47 slr1272 29 hypothetical protein. #48 slr1273 184 hypothetical protein. #49 slr1274 81 pilM; membrane protein. #50 slr1275 39 hypothetical protein. #51 slr1276 80 hypothetical protein. #52 sll1173 66 hypothetical protein. #53 slr1278 49 hypothetical protein. #54 sll1172 282 thrC; threonine synthase. [EC:4.2.99.2] #55 slr1279 71 ndhC; NADH-plastoquinone oxidoreductase chain 3. [EC:1.6.5.3] #56 slr1281 300 ndhJ; NADH-plastoquinone oxidoreductase subunit J (orf 155). #57 sll0776 77 probable serine/threonine-protein kinase sll0776. [EC:2.7.1.-] #58 sll0775 222 merR; hypothetical protein. #59 ssr1169 91 ESI3; hypothetical 9.1 kD protein ssr1169. [SP:YB69_SYNY3] #60 slr0698 209 merR; hypothetical protein. #61 slr0699 140 merR; hypothetical protein. #62 slr0700 229 merR; hypothetical protein. #63 slr0701 106 hypothetical 15.7 kD protein slr0701. [SP:Y701_SYNY3] #64 slr0702 300 hypothetical protein. #65 slr1656 300 murG; UDP-N-acetylglucosamine-N-acetylmuramyl-(pentape ptide) Motif number 1 TTTGCCCCCCGGCGATCGCCAAATTGGGGC 2 115 1 GGCGATCGCC 0.499998 -110 TTAACAGCTTGGCGATCGCCCACTGCCCCG 5 96 1 GGCGATCGCC 0.499998 -173 GCCACTTCACGGCGATCGCCCGTCGTCTGG 10 228 1 GGCGATCGCC 0.499998 -73 GCTTATTTAAGCCGATCTCCTAGTCTCGCA 12 104 1 GCCGATCTCC 0.78101 -119 GGCAGATCTCCTTATGATCAG 14 2 1 GCAGATCTCC 0.701626 -88 ATTATGGGCGGGCGATCGCCATTCTCTGGC 14 62 1 GGCGATCGCC 0.499998 -28 AAAAACTACAGCCGATCGCT 15 189 1 GCCGATCGCT 0.862729 -10 CCGGTCAAGCGGCGATCGCCAAATCTGTTT 18 106 1 GGCGATCGCC 0.499998 -146 GGCTAAACCGCCCGATCTCCCAAGTTTGGT 19 148 0 CCCGATCTCC 0.893633 -51 ATTGAGCCATGGCGATCGCCTTTTCCTCGC 23 13 1 GGCGATCGCC 0.499998 -39 CGACCAGGATGGCGATCTCCAACGAGAATT 27 18 0 GGCGATCTCC 0.506071 -66 CGGAGGTGTGGGCGATCGCCTGCCAATCAA 46 97 1 GGCGATCGCC 0.499998 -155 CGGACTTGTGGGCGATCGCCTGGGGGCATT 54 99 1 GGCGATCGCC 0.499998 -184 TCCCGGTCGCCCACGGCAAAA 56 290 0 CCCGGTCGCC 0.835442 -11 TTTGCTCCATGGCGATCGCCTAAGGAAAAC 58 98 1 GGCGATCGCC 0.499998 -125 TTCGTAATTTGGCGATCGCCTACCTAACCC 62 181 1 GGCGATCGCC 0.499998 -49 ********** Masking position 6 Map Score: 62.1054 Number of sites scoring better than the average of aligned sites = 5863 Number in coding regions = 5323 Number in noncoding regions = 540 Number of orfs with sites within 600 bp upstream = 332 Fraction of orfs with sites within 600 bp upstream = 0.0533248 Motif number 2 AGCATTTATACACATTTGCCCCCCGGCGATCGC 2 101 1 CCATTCCCCC 0.989752 -124 ATAATTGCGGCGCATTTGCCCCATCCTATCCCC 2 155 1 CCATTCCCCA 0.958701 -70 CTTGGCGATCGCCCACTGCCCCGGGCCATGGTT 5 103 1 GCCCTCCCCG 0.803239 -166 TGTTTGCCAAGCCCTTTTCCCCCTAATTTCGAC 6 49 1 GCCTTCCCCC 0.975937 -161 GAAACAAGATGCCAATATCCCCGGTATTGTTAG 7 62 0 GCATACCCCG 0.723441 -89 ACAAAAATAACTCATTGTCCCCAGACAACAA 10 9 0 CCATGCCCCA 0.947439 -292 GGAATTTTTCCACAATACCCACCTTCAGATCCA 17 33 0 CCATACCACC 0.75589 -97 GGGCGAGAGATACCATTCCCCCGGTCAAGCGGC 18 86 1 TCCTTCCCCG 0.857755 -166 GTAGGGGCCAGCGTTGCCCTCAATTTTTACC 20 79 0 CGCTTCCCTC 0.668452 -21 AAGGGCGGAAATCCCCATCCCCCAAGGAAATTA 22 80 0 ACCCACCCCC 0.768381 -76 TGAATCTGGAATGATTTGCCCCCCAACGTCTTT 31 19 1 AGATTCCCCC 0.808938 -146 GTAGTTTAGCCTGAGTTGCCCCATACTGCCCCA 35 61 0 CGATTCCCCA 0.868868 -51 GCCCTCCGGCAACATTGACCCCGTTGTAACAGC 38 62 1 ACATGCCCCG 0.770887 -239 CTTTAAAAGCCCCCCTGACCCCCAAATTTAGGG 38 131 1 CCCTGCCCCC 0.992283 -170 AGGACTTTCAGTCAGTTTCCCCCTAAATTTGGG 38 151 0 GCATTCCCCC 0.95944 -150 CTGTTTAATCCCCCCTAGCCCCCCTTAGAAAGG 43 53 1 CCCTACCCCC 0.984298 -202 GGTCTTTTGTAAGAGTTCCCCCCTTTCTAAGGG 43 74 0 AGATTCCCCC 0.808938 -181 TCTTGCCTACCGCCATTACCCCAGCTAACCCCT 44 30 0 CCCTTCCCCA 0.975491 -271 TCGGCCTAACCAACCCTGCCCCGGCAAATCAAC 44 203 1 CACCTCCCCG 0.573076 -98 ATAAATGTAACCCAATTTCCCCCAGCCGTAACC 46 151 1 CCATTCCCCC 0.989752 -101 AACCTTTATCCACAATTTCCCCCGATTATTAAC 46 180 1 CCATTCCCCC 0.989752 -72 CGCCAGCGATTACCGCAACCCCC 48 1 0 TCCCACCCCC 0.729194 -184 TTGGTTTGTTCACCTTGCCCACACCTATTGCTT 49 55 0 CCCTGCCACA 0.723565 -27 TGATCCCTAGCCACCGAACTTTGTT 50 25 0 ACCTACCACC 0.449158 -15 CCGCTGGACCCCCCCTGACCACCATTAGCCGTG 54 28 0 CCCTGCCACC 0.915895 -255 GAAAAATTGGCAGAATGCCCCCAGGCGATCGCC 54 109 0 CGATGCCCCA 0.837267 -174 TGGAACCTCGGGCCATTGCCCCCC 54 269 1 GCCTTCCCCC 0.975937 -14 TGTCCTTGCCTTGCCTGCCCCCCCTATTGTCTT 55 23 0 TGCTGCCCCC 0.820634 -49 AGTTTTAGCTCCCCCTTCCCCCACTGTTGCCAA 56 242 0 CCCTTCCCCA 0.975491 -59 TATTTGCAATCGCACCGCCCCCCAGAAATCTGA 61 114 0 CCACGCCCCC 0.962744 -27 TGGCGATCGCCTACCTAACCCCCAGTAATTTTT 62 190 1 CACTACCCCC 0.834667 -40 AGGGGTTTTGTCCAGCGCCCCCCGAAGGACAGT 64 142 0 TCACGCCCCC 0.763113 -159 ACAATGCCAGCTCCGTTTCCCTGCCCCAACTAA 65 74 0 CCCTTCCCTG 0.673566 -227 GAAACCTTTCCCGAGTTTCCCCCAAGCTTGGGG 65 206 1 CGATTCCCCC 0.964994 -95 AAAATCCAACCTAATTTTCCCCAAGCTTGGGGG 65 224 0 CAATTCCCCA 0.651514 -77 * ** ** ***** Masking position 9 Map Score: 49.0051 Number of sites scoring better than the average of aligned sites = 2870 Number in coding regions = 2516 Number in noncoding regions = 354 Number of orfs with sites within 600 bp upstream = 252 Fraction of orfs with sites within 600 bp upstream = 0.0404754 Motif number 3 CCCGGCGATCGCCAAATTGGGGCAAAAAATTAGATAATT 2 122 1 GCAAGGAAAA 0.963235 -103 GTTCCGATCTGCCAAGTTGGGCGAAACAAGATGCCAATA 7 78 0 GCAAGCAAAA 0.721117 -73 CTTGCCCTGGGTTAACGGTTGCCCAACAATGGAGAGATT 9 22 1 GTAAGCCAAA 0.571136 -65 GGCCAAAGGGAGGACGTTAAAAAAACTTAA 13 2 1 GCAAGGCGAA 0.985581 -133 AAAACCACTGGGTTAACAGGGGACGATAATTTAACAGGA 15 64 0 GGTAGGCGAA 0.88465 -135 TCAATGTTAGGCTAAGGGAAGGAAATTAACCCTGTTTTA 18 158 0 GCAAGGAAAA 0.963235 -94 CGGAACTTTAGGGAAATTATGGCAAGGAA 19 180 1 GGAAGGAAAA 0.905505 -19 ATACGCACGGGAAAAGGGGGGAAAGAAACCCTACCAT 20 9 1 GGAAGGAAAA 0.905505 -91 GGGCAGGCTAGGCTAGGACAAAAAGGAAGGTGGG 21 6 1 GGTAGGCAAA 0.868439 -138 CATAATTTCGGCAAAATTAAGGGCGGAAATCCCCATCCC 22 92 0 GCAAGGCGAA 0.985581 -64 CGTTAACAAAGTTAACAATTGGTCAATAATAATTGCCCA 30 36 1 GTAAGGCAAA 0.931005 -160 TAAAAGCTTAGCTAAAGGTCTGACAGTAAATGCGGACTC 30 127 0 GCAATGCAAA 0.670728 -69 AACCTAGGCTGTAAAGTATTGGGCGATAAATTTCGTTGC 31 121 0 GTAAGGCGAA 0.940039 -44 TTTATTTAGTGCCAAGTTTTGGCCGGGAAACTAAAACTT 33 47 1 GCAAGGCGAA 0.985581 -125 GGGAGAGCGAGTAAATTGCAGGCCGAAAATCCGAGAGAA 37 84 0 GTAAGGCGAA 0.940039 -183 ATCGCCATTGGCTAGCCATGGGAAGCTAAAATACAGGCC 37 165 0 GCAGGGAGAA 0.829793 -102 CGCTGCCTGGGCAGGACAAAGGGCAAAAACAGAGTCATT 41 40 0 GCGGGGCAAA 0.66045 -35 GGGTTAGCTGGGGTAATGGCGGTAGGCAAGAAACTTTCT 44 32 1 GGTAGGAGAA 0.773512 -269 CCCTGCCCCGGCAAATCAACGGAAGAAAATATAAATTAG 44 216 1 GCAAGGAGAA 0.968193 -85 GAAGGGCAAAACCACGGTCACAAAAGAATATTTT 45 6 1 GCAAGGCAAA 0.983287 -295 AGCCCATTGAGCAAAATGCTGGGCAGGAAGGACCCTTGC 45 166 0 GCAAGGCAAA 0.983287 -135 AAGTTTAGTAATGGCCACCAATCCATTGTCC 55 51 0 GTTAGGCAAA 0.805422 -21 TCTACCCTTAGCTGAGGAAGGGAAAGAAAACTTACTTGC 64 252 1 GCGAGGAAAA 0.84395 -49 ATTATCCTCTGCTTAGTTGGGGCAGGGAAACGGAGCTGG 65 62 1 GCTAGGAGAA 0.903266 -239 ** ** ** ** ** Masking position 18 Map Score: 32.1018 Number of sites scoring better than the average of aligned sites = 406 Number in coding regions = 353 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 4 TAGATAATTGCGGCGCATTTGCCCCATCCTATCC 2 152 1 CGCATTTGCC 0.876932 -73 CTTGGCAGATCGGAACTTTTTACCAATCTTTGCG 7 101 1 CGCTTTTTCC 0.935559 -50 TTTTTGTCCTACGACGATTTTCCCTGGTTTAAAA 10 35 1 AGGATTTTCC 0.750127 -266 CCCGATCTGGACGTAGATTTGACCTTGGACATCA 10 128 1 AGGATTTGCC 0.773541 -173 ATCAAACATCCTGAACGTTTTCCCCTAGTTTGTA 10 161 1 CGCGTTTTCC 0.889655 -140 CCTGTTAACCCAGTGGTTTTACCCCCCAATGGCA 15 83 1 CGGTTTTACC 0.94983 -116 TTCTGCTCCTCTGTGGATTTGTCCATGGGAAGCT 15 140 1 CGGATTTGCC 0.956949 -59 GGATTAACCACGGACGATTTTCCCGTCGATTACA 18 23 0 CGGATTTTCC 0.951304 -229 CTTGGGAGATCGGGCGGTTTAGCCGACGGAACTT 19 154 1 CGGGTTTACC 0.913149 -45 GTCCGTTGACCGGGAGTATTTTCCA 28 2 0 CGGTATTTCC 0.891151 -101 AAAAAAAGGCCCGCTGGTTTTTCCGTCGGGCCTG 29 44 0 CGGGTTTTCC 0.96176 -39 TACTTTACAGCCTAGGTTTTTTCCACAGAGACT 31 142 1 CTGTTTTTCC 0.834737 -23 GGTAAAAATGACTCTGTTTTTGCCCTTTGTCCTG 41 34 1 ATGTTTTTCC 0.436997 -41 TCCATAGCCAAAGCTGGTTTATCCCCAGTTTAAG 42 67 1 AGGGTTTACC 0.617694 -129 GAGAGAGATACAGAACTTTTGCCCATAAATAAAT 44 162 1 CGCTTTTGCC 0.942919 -139 TCTTTTGTGACCGTGGTTTTGCCCTTC 45 4 0 CGGTTTTGCC 0.980963 -297 ACAAGTCGCTCTGAAGTATTGGCCTCCATTGCCA 56 59 1 CGGTATTGCC 0.903058 -242 GCCTTTTTTTCTGTTGTTTTAACCGATTGAAAAT 56 169 1 CGGTTTTACC 0.94983 -132 GATAAATTTTCTTCCGTTTTTCCCTTTGCTCCAT 58 74 1 CTGTTTTTCC 0.834737 -149 AGGGTTCCAGCAGGGGTTTTGTCCAGCGCCCCCC 64 152 0 CGGTTTTGCC 0.980963 -149 ACTGCTTACCCAGGACTATTTTCCCTAGATTGGT 65 23 1 CGCTATTTCC 0.7241 -278 * * ****** ** Masking position 9 Map Score: 28.5829 Number of sites scoring better than the average of aligned sites = 580 Number in coding regions = 528 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 5 TACCCGCCCGACCCTAGGACATCATCCC 2 8 0 ACCTAGGACA 0.863134 -217 AAATTTTCCAATGCCGGGGGACTTTAAGTTT 6 91 0 AGCCGGGGGA 0.928668 -119 GGCAACCGTTAACCCAGGGCAAGCACTGGAT 9 14 0 ACCCAGGGCA 0.922095 -73 AATTCGGATAAAGCTGGGGCAATT 9 73 1 AGCTGGGGCA 0.950277 -14 GATTCAGTACAAACTAGGGGAAAACGTTCAG 10 171 0 AACTAGGGGA 0.870268 -130 GGGCTAGCAAAACCAAGGGGATCAGTTGGGA 10 256 1 ACCAAGGGGA 0.818066 -45 ATTAATCCCCAGCCTAAGGCAGAAGTGAATA 11 18 0 ACCTAAGGCA 0.83719 -80 AATAATTGCGAGACTAGGAGATCGGCTTAAA 12 109 0 AACTAGGAGA 0.63615 -114 GGTCAATGTTAGGCTAAGGGAAGGAAATTAA 18 168 0 AGCTAAGGGA 0.88722 -84 CTTGATTAAGAGGCTAGGAGAACTGAGATAC 19 11 1 AGCTAGGAGA 0.906049 -188 GGGCAGGCTAGGCTAGGACAAAAAGGAAGG 21 10 1 AGCTAGGACA 0.873822 -134 AGGCAGAGTCAGCCCAGGGGACAAAAACTTC 32 64 0 ACCCAGGGGA 0.942643 -37 CAACAAAATTAAGCTGGGGGAGCCGGACTTT 33 127 0 AGCTGGGGGA 0.963785 -45 ATACCCTCTCATCCTGAGGCAGTGTACTTTT 35 24 0 ACCTGAGGCA 0.787242 -88 GAGGGTATTTAGCCTGGGGCAGTATGGGGCA 35 47 1 ACCTGGGGCA 0.945654 -65 AAGCCAGAGTACCCTAGGGGAGAGCGAGTAA 37 109 0 ACCTAGGGGA 0.971129 -158 TCAAAAATTGAAGCTAGGGCGCAAGGCACAC 45 100 1 AGCTAGGGCG 0.688783 -201 ATAAAGGTTACGGCTGGGGGAAATTGGGTTA 46 158 0 CGCTGGGGGA 0.689124 -94 GCGGTGTTGCACCCCAAGGGATTACACCTGG 54 57 1 ACCCAAGGGA 0.777628 -226 GGGGCAGGCAAGGCAAGGACAATGGATTGGT 55 35 1 AGCAAGGACA 0.480297 -37 ATTGCCAATAATCCCAAGACAAGCTCCTGAA 56 86 1 ACCCAAGACA 0.396106 -215 GGTGGCAAGAACGCTAAGGGAGGTAAGCCTT 56 132 0 AGCTAAGGGA 0.88722 -169 TACTGATAAGAAACTGGGAGAAAATCGTCCT 62 97 0 AACTGGGAGA 0.55704 -133 AGTTTCCCCCAAGCTTGGGGAAAATTAGGTT 65 219 1 AGCTTGGGGA 0.74823 -82 * ********* Masking position 4 Map Score: 27.4039 Number of sites scoring better than the average of aligned sites = 1078 Number in coding regions = 912 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 6 CAAGGAAAATCTTGCCGAAGTTACCAACAA 3 8 1 ATTTGCCGAG 0.977895 -23 TTGAGTGTTAATTTTTACCCTAAGTGA 8 5 0 ATTTACCCAA 0.651712 -75 ACATCCTGAACGTTTTCCCCTAGTTTGTACTGA 10 166 1 CTTTCCCCAG 0.729878 -135 GATCAGACCCAAAATTCCCCAAGATTGATTGGC 12 146 1 AATTCCCCAG 0.791929 -77 TTCCGCCCTTAATTTTGCCGAAATTATGCTTCT 22 103 1 ATTTGCCGAA 0.878317 -53 TTACTATATCACGTTTGCCGGAGGGCTCCTTTC 31 82 0 AGTTGCCGAG 0.906469 -83 AAAGCCCTTTAATATTGTCGGAGCTTTTATTTA 33 22 1 ATTTGTCGAG 0.649236 -150 CAACGGGGTCAATGTTGCCGGAGGGCCGCACAA 38 55 0 ATTTGCCGAG 0.977895 -246 AAAGTCCTCTAGTATTGCCGGAGCTTTAGTGAG 38 176 1 ATTTGCCGAG 0.977895 -125 GTGCTTAGCCACTGTTACCCAGGCAGTAAAGAC 39 50 0 ATTTACCCGG 0.775192 -78 AAACAGAGTCATTTTTACCCAAGATAACAAACT 41 20 0 ATTTACCCAG 0.919796 -55 AAAGACCCCCAGTATTGCCGGAGCTTTAGTGAG 43 100 1 ATTTGCCGAG 0.977895 -155 TTAAATCTTGATGTTTCCCGTGGGAAAAATTGA 52 37 0 AGTTCCCGGG 0.639012 -30 TCAGAATTGGATTATTGCCCAAACGATTAATAA 54 200 0 ATTTGCCCAA 0.878317 -83 TCAACACAAAAATATTCCCCCAAAGTTTTCAGT 56 206 1 ATTTCCCCAA 0.814288 -95 TTTGATGTTTAATTTTGCCGTGGGCGACCGGGA 56 278 1 ATTTGCCGGG 0.930077 -23 AACTTATAGGAATATTACCCTAGTTTTACGAAA 58 174 0 ATTTACCCAG 0.919796 -49 ATCGCAGATTAAAGTTGCCGGAGAAGAGATTGA 61 60 0 AATTGCCGAG 0.862364 -81 ACCTTTCCCGAGTTTCCCCCAAGCTTGGGGAAA 65 209 1 ATTCCCCCAG 0.729878 -92 AATCCAACCTAATTTTCCCCAAGCTTGGGGGAA 65 222 0 ATTTCCCCAG 0.964123 -79 * * ****** ** Masking position 5 Map Score: 21.5886 Number of sites scoring better than the average of aligned sites = 517 Number in coding regions = 428 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 7 AATCAAAACCAATGGGATGGATTGTAACGA 2 40 1 AATGGGATGG 0.794802 -185 TCTCGCAATTATTGGGATGGATCAGACCCA 12 127 1 ATTGGGATGG 0.614851 -96 GATAACGCAGAATGGAAAGGTGAACTTCTC 15 27 0 AATGGAAAGG 0.791657 -172 TTTACCCCCCAATGGCAAGGAGCAGGAACC 15 100 1 AATGGCAAGG 0.9388 -99 TCCAAATTAGTATGGCAAGGGTTAGG 17 7 0 TATGGCAAGG 0.903739 -123 AATGTTAGGCTAAGGGAAGGAAATTAACCC 18 165 0 TAAGGGAAGG 0.791796 -87 TTAGGGAAATTATGGCAAGGAA 19 187 1 TATGGCAAGG 0.903739 -12 AGTTAGTACGGTTGGCAAGGCTTAAAAGAA 22 132 0 GTTGGCAAGG 0.838519 -24 ACTAAAAGGCAAAGGAATAAAACT 24 5 1 AAAGGCAAAG 0.658523 -20 TCCATCACGAAAAGGGAAAGTTATCGACAA 31 54 0 AAAGGGAAAG 0.70583 -111 CCCTTTTCGTGATGGAAAGGAGCCCTCCGG 31 68 1 GATGGAAAGG 0.757332 -97 GAATCGGTAAAATGGCAAAGTCAGCATTTT 37 57 0 AATGGCAAAG 0.855562 -210 GTACTCTGGCTTTGGGAAAGGGTAAATGGG 37 128 1 TTTGGGAAAG 0.65023 -139 ATTAGACAAATTTGGCAAGGCAG 37 254 1 TTTGGCAAGG 0.794637 -13 CAAAGATGGGATTGGGAAGGGTTTAGGATA 39 105 0 ATTGGGAAGG 0.887212 -23 CAGCTTTGGCTATGGAAAAGTCTCTGTACA 42 53 0 TATGGAAAAG 0.47313 -143 AAGGAGTAAGGATGGGAGGGAGAGAATATC 48 53 1 GATGGGAGGG 0.774481 -132 AAAATTAGTCAATGGGATAGCATAGTCA 58 9 0 AATGGGATAG 0.599305 -214 TTAAAACCAGAAAGGGAGGGTTTGTC 63 7 0 AAAGGGAGGG 0.576503 -100 CTTAGCTGAGGAAGGGAAAGAAAACTTACT 64 258 1 GAAGGGAAAG 0.663377 -43 TTTGGGAGGTGTTGGCAAAGTTCGGGTTTG 65 156 1 GTTGGCAAAG 0.667235 -145 ********** Masking position 7 Map Score: 15.1622 Number of sites scoring better than the average of aligned sites = 645 Number in coding regions = 528 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 8 TTACTGCTAAAACATTAGGGATAAAATAGT 1 19 1 AACATTAGGG 0.738984 -20 TTTAGCCAAAAGATTTAGAGGATAAACAAA 7 29 0 AGATTTAGAG 0.592208 -122 GGTCCTTCCTAGCTTTGGTGCTACCATTTA 18 214 1 AGCTTTGGTG 0.713817 -38 TATTGGGAGAAAAATTAGGGTCCTGCCAAC 19 67 0 AAAATTAGGG 0.663587 -132 TAGCCGACGGAACTTTAGGGAAATTATGGC 19 173 1 AACTTTAGGG 0.946058 -26 CCAATGGTAAAAATTGAGGGCAACGCTGGC 20 74 1 AAATTGAGGG 0.753157 -26 AATTTCGGCAAAATTAAGGGCGGAAATCCC 22 98 0 AAATTAAGGG 0.527996 -58 CCTGACCCCCAAATTTAGGGGGAAACTGAC 38 144 1 AAATTTAGGG 0.924354 -157 GTATTGCCGGAGCTTTAGTGAGGAGATTTA 38 187 1 AGCTTTAGTG 0.872737 -114 TTTAGTGAGGAGATTTAGGGGGCAGAATAA 38 200 1 AGATTTAGGG 0.956613 -101 GTATTGCCGGAGCTTTAGTGAGGAGATTTA 43 111 1 AGCTTTAGTG 0.872737 -144 TTTAGTGAGGAGATTTAGGGGGCAGAATAA 43 124 1 AGATTTAGGG 0.956613 -131 AAGGGAAACGAGCGTTAGGGCC 47 18 1 AGCGTTAGGG 0.811097 -12 GAAAAATTGAAAATTTAGTGGACAAAAATA 52 17 0 AAATTTAGTG 0.725877 -50 ATGGACTGAAAACTTTGGGGGAATATTTTT 56 213 0 AACTTTGGGG 0.864481 -88 AAGGACAGTTAGATTTAGGGGATGAATTGC 64 121 0 AGATTTAGGG 0.956613 -180 ATTTTCCCCAAGCTTGGGGGAAACTCGGGA 65 214 0 AGCTTGGGGG 0.74187 -87 ********** Masking position 5 Map Score: 14.2042 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 207 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 9 TCAAGGGTTTAAGGTGGTGTTTGCCAAGCCCTTTT 6 32 1 AAGGTTTGCC 0.960622 -178 GATTGGTAAAAAGTTCCGATCTGCCAAGTTGGGCG 7 94 0 AAGTTTTGCC 0.984511 -57 CCTGTCGGCAAAGTTTTAGTTTCCCGGCCAAAACT 33 61 0 AAGTTTTCCC 0.881275 -111 AGCTTTGTTGAAGGTCTTGTTTGCCCAATAGCCTT 36 87 1 AAGGTTTGCC 0.960622 -82 GGTGTTTGGAAAGTTTTATTCTGCCCCCTAAATCT 38 210 0 AAGTTTTGCC 0.984511 -91 GTTAATTTTAAAGTTAAATTTTGCCATTAAGCTTG 42 130 1 AAGTTTTGCC 0.984511 -66 CCTTTTTAAAAAGTTGAGTTTTGGCTGTTTAATCC 43 29 1 AAGTTTTGGC 0.938069 -226 CTTATTTGAAAAGTTTTATTCTGCCCCCTAAATCT 43 134 0 AAGTTTTGCC 0.984511 -121 AAGTTTAGTAATGGCCACCAATCCA 55 57 0 AAGTTATGGC 0.658072 -15 ACTAATTTTGATGTTTAATTTTGCCGTGGGCGACC 56 272 1 ATGTTTTGCC 0.889822 -29 GGTGTTGGCAAAGTTCGGGTTTGCCCTTAAATCGA 65 163 1 AAGTTTTGCC 0.984511 -138 ***** * **** Masking position 1 Map Score: 15.1634 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 12 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 GCGCATTTGCCCCATCCTATCCCCGATAAACTA 2 164 1 CCCTCCTCCC 0.99084 -61 GTACTTGTTTCCCATCTTAATCCTTTGGTGGAT 5 164 0 CCCTCTTTCC 0.824083 -105 ACCATCCAGTGCTTGCCCTGGGTTAACG 9 6 1 CCATGCTCCC 0.660478 -81 AATTGCCCCAGCTTTATCCGAATTGCTCA 9 68 0 CCCGCTTTCC 0.596769 -19 GAGGACTGATCCCAACTGATCCCCTTGGTTTTG 10 263 0 CCCACTGCCC 0.708666 -38 AAATTATCGTCCCCTGTTAACCCAGTGGTTTTA 15 71 1 CCCTGTTCCC 0.881381 -128 GGGTTAATTTCCTTCCCTTAGCCTAACATTGAC 18 165 1 CCTCCCTGCC 0.60008 -87 CATTTATCGCCTCCTCCTCCTCCA 18 238 1 CTCTCCTTCC 0.587736 -14 GGGTTTCTTTCCCCCCTTTTCCCGTGCGTAT 20 9 0 CCCCCTTCCC 0.975732 -91 TGGCGATCGCCTTTTCCTCGCCCAACTCCAGTC 23 22 1 CTTTCCTCCC 0.662248 -30 AAGCTTTTAACCCTCCCTGTCCCAACCTATCGA 30 157 1 CCCCCCTCCC 0.992236 -39 CCTGAGTTGCCCCATACTGCCCCAGGCTAAATA 35 52 0 CCCTACTCCC 0.819036 -60 AAATTTTAGCCCTTTCCGTTCCCGTACCAGGGA 36 16 1 CCTTCCGCCC 0.833391 -153 GCTTTAAAAGCCCCCCTGACCCCCAAATTTAGG 38 130 1 CCCCCTGCCC 0.907579 -171 CCTTCCCAATCCCATCTTTGCCC 39 115 1 CCCTCTTCCC 0.971454 -13 GGCTGTTTAATCCCCCCTAGCCCCCCTTAGAAA 43 51 1 TCCCCCTCCC 0.815669 -204 ACCGCCATTACCCCAGCTAACCCCTACTTCGGA 44 22 0 CCCAGCTCCC 0.873616 -279 ATCGGCCTAACCAACCCTGCCCCGGCAAATCAA 44 202 1 CCACCCTCCC 0.913243 -99 TTCTCTCCCTCCCATCCTTACTCCTTAATAATT 48 46 0 CCCTCCTCTC 0.789265 -139 TTGCTTCACTCCTCTCCTTGTCCGATGCCATAC 49 28 0 CCTTCCTTCC 0.738166 -54 CACCGCTGGACCCCCCCTGACCACCATTAGCCG 54 30 0 CCCCCCTCCA 0.815669 -253 ATTGTCCTTGCCTTGCCTGCCCCCCCTATTGTC 55 25 0 CCTGCCTCCC 0.866136 -47 TTAGTTTTAGCTCCCCCTTCCCCCACTGTTGCC 56 244 0 CTCCCCTCCC 0.924449 -57 GGAAACCTTTCCCGAGTTTCCCCCAAGCTTGGG 65 205 1 CCCAGTTCCC 0.684997 -96 *** **** *** Masking position 12 Map Score: 31.8076 Number of sites scoring better than the average of aligned sites = 1173 Number in coding regions = 1012 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 11 AAACTTAAAGTCCCCCGGCATTGGAAAATT 6 91 1 TCCCCCGGCA 0.904695 -119 TGGACCGAAGTGCTCCGGAACACTCATATT 19 93 0 TGCTCCGGAA 0.933483 -106 TGGAAAGGAGCCCTCCGGCAAACGTGATAT 31 80 1 CCCTCCGGCA 0.94339 -85 ACTAAATAAAAGCTCCGACAATATTAAAGG 33 27 0 AGCTCCGACA 0.898314 -145 ACTTGTGCGGCCCTCCGGCAACATTGACCC 38 53 1 CCCTCCGGCA 0.94339 -248 TCCTCACTAAAGCTCCGGCAATACTAGAGG 38 181 0 AGCTCCGGCA 0.984513 -120 TCCTCACTAAAGCTCCGGCAATACTGGGGG 43 105 0 AGCTCCGGCA 0.984513 -150 TAACCAACCCTGCCCCGGCAAATCAACGGA 44 209 1 TGCCCCGGCA 0.955007 -92 TCCCAAGACAAGCTCCTGAAAAGCAACTAC 56 97 1 AGCTCCTGAA 0.50177 -204 AATCAATCTCTTCTCCGGCAACTTTAATCT 61 58 1 TTCTCCGGCA 0.861731 -83 TTACGAATATTGCTCCGAAACTGACCACAT 62 158 0 TGCTCCGAAA 0.661036 -72 GAGTAGGAAAAGCACCGGCAATTCATCCCC 64 104 1 AGCACCGGCA 0.899454 -197 ********** Masking position 10 Map Score: 13.6609 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 256 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 12 TTTATACACATTTGCCCCCCGGCGATCGCC 2 105 1 TTTGCCCCCC 0.916558 -120 TTATCTAATTTTTTGCCCCAATTTGGCGAT 2 129 0 TTTTGCCCCA 0.537156 -96 TTGCGGCGCATTTGCCCCATCCTATCCCCG 2 159 1 TTTGCCCCAT 0.660066 -66 TAACCAATCGTTTGTCCCCAACCATGGCCC 5 125 0 TTTGTCCCCA 0.840384 -144 TGCCAAGCCCTTTTCCCCCTAATTTCGACG 6 53 1 TTTTCCCCCT 0.814443 -157 TAGTTTCCATTATGGCCCCTCTACCAAAGA 11 54 0 TATGGCCCCT 0.905697 -44 CTGTTTATACTTTGGCCCTTGTCAGCGGTA 18 130 1 TTTGGCCCTT 0.630266 -122 GTAGGGTTTCTTTCCCCCCTTTTCCCGTGC 20 15 0 TTTCCCCCCT 0.928518 -85 TGAGGGCAACGCTGGCCCCTAC 20 88 1 GCTGGCCCCT 0.856408 -12 TCTGGAATGATTTGCCCCCCAACGTCTTTG 31 23 1 TTTGCCCCCC 0.916558 -142 TCAGGAAGTTTTTGTCCCCTGGGCTGACTC 32 60 1 TTTGTCCCCT 0.94589 -41 CAATTTACTCGCTCTCCCCTAGGGTACTCT 37 105 1 GCTCTCCCCT 0.443564 -162 GCCTTCATTCTATGGCCCCACACCATTGCG 37 219 0 TATGGCCCCA 0.743099 -48 CGCACAAGTTTTCGGCCCCTGTCCTAGAAT 38 32 0 TTCGGCCCCT 0.795212 -269 AAAGTTTTATTCTGCCCCCTAAATCTCCTC 38 206 0 TCTGCCCCCT 0.957617 -95 AAGACTTTGGTATGGCCCCTAGAATTTGGC 39 25 0 TATGGCCCCT 0.905697 -103 TTTTGTAAGAGTTCCCCCCTTTCTAAGGGG 43 73 0 GTTCCCCCCT 0.796154 -182 AAAGTTTTATTCTGCCCCCTAAATCTCCTC 43 130 0 TCTGCCCCCT 0.957617 -125 TTATATTATTTTTGTCCACTAAATTTTCAA 52 11 1 TTTGTCCACT 0.422431 -56 TAATCATTTCTCCCCAGCTAAACTAT 53 34 0 TTTCTCCCCA 0.608557 -16 ********** Masking position 6 Map Score: 17.1527 Number of sites scoring better than the average of aligned sites = 863 Number in coding regions = 733 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 13 GGGGACTTTAAGTTTTTTCCCGTCGTCGAAAT 6 74 0 AGTTTTTCCG 0.973501 -136 TTAAAGGTTGAGTTTTTGCTGGACTTTATCGA 8 49 0 AGTTTTGCTG 0.881257 -31 TAAAATCACCAGTTTTTCCTGGATAAGTTGTC 12 24 0 AGTTTTCCTG 0.835932 -199 TAGAGTTGCCAGTTTTTCTCCGTCTGTTTAGA 12 72 1 AGTTTTCTCG 0.819515 -151 GATCGGCTGTAGTTTTTGTTGGTATCCCAGAC 15 174 0 AGTTTTGTTG 0.680845 -25 TTTAGTGCCAAGTTTTGGCCGGGAAACTAAAA 33 51 1 AGTTTTGCCG 0.95835 -121 GTGTTTGGAAAGTTTTATTCTGCCCCCTAAAT 38 212 0 AGTTTTTTCG 0.913495 -89 TATTTCCTTTAGTTTTCTCCGGTGG 40 4 0 AGTTTTTCCG 0.973501 -35 TTTTCTATTAAGTTTTATCAAGCTTAATGGCA 42 151 0 AGTTTTTCAG 0.782682 -45 TTATTTGAAAAGTTTTATTCTGCCCCCTAAAT 43 136 0 AGTTTTTTCG 0.913495 -119 CTATCTTCATATTTTTTTCCTGTTAGTACCAT 44 271 1 ATTTTTTCCG 0.707581 -30 TTCCAGCAGGGGTTTTGTCCAGCGCCCCCCGA 64 150 0 GGTTTTTCCG 0.85282 -151 ATAGTGATCAAGTTTTATCTTGATTTGGGAGG 65 133 1 AGTTTTTCTG 0.922175 -168 ****** *** * Masking position 6 Map Score: 9.45645 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 140 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 14 ACCTGGCTTGTTAAAGGCCACTTCACGGCGATCGC 10 212 1 TTAAGCATTA 0.779156 -89 CTCCGTCTGTTTAGAGCTTATTTAAGCCGATCTCC 12 89 1 TTAAGTATTA 0.944178 -134 CCAACAGATTTTGAAGTTAATTTTAAAGTTAAATT 42 115 1 TTGAGTATTA 0.879142 -81 ACTACTAGCGTTAGAACTTATTTGAAAAGTTTTAT 43 150 0 TTAAATATTA 0.596452 -105 TGACTGTCGGTTAAAGTTTACTTAAGTCTTTGAAC 43 183 0 TTAAGTATTA 0.944178 -72 AAGGTTTCAGTTGAAGCTTAGTTAACACTTTGTTG 48 127 0 TTGAGTATTA 0.879142 -58 AGCTACTAATTTATAGCTAATTTAATTAATTATGA 56 17 0 TTAAGTATTA 0.944178 -284 GTTTTTTACAGTTCAATTGATTGAATTAAA 57 6 1 TTAAGTATTA 0.944188 -72 ATTGATTGAATTAAAGTTGAATTTAAGTATTTCAA 57 26 1 TTAAGTATTA 0.944188 -52 GGTAGTACTGTTAAAGTTAATTTCACCAAAATTAG 58 31 0 TTAAGTATTA 0.944178 -192 *** ** * * ** * Masking position 10 Map Score: 6.57895 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 7 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 15 TTGATTTTACCCGCCCGACCCTAGGACATCA 2 15 0 CCGCCGACCC 0.892795 -210 GGCGGTTTAGCCGACGGAACTTTAGGGAAAT 19 166 1 CCGCGGAACT 0.946179 -33 ATCTACTATTCCGTCAGGACTTGT 26 4 0 CCGCAGGACT 0.969695 -30 GCTGGTTTTTCCGTCGGGCCTGGTTTAATCT 29 35 0 CCGCGGGCCT 0.989743 -48 GACGGAAAAACCAGCGGGCCTTTTTTTGTTG 29 51 1 CCACGGGCCT 0.943462 -32 ATTATTTTGACCAACAGGACTGGGCAATTAT 30 64 0 CCACAGGACT 0.846893 -132 TCCGCATTTACTGTCAGACCTTTAGCTAAGC 30 130 1 CTGCAGACCT 0.736531 -66 TAAAACTTTGCCGACAGGCCCTCGCGTTATC 33 78 1 CCGCAGGCCC 0.981612 -94 GGGTGCAACACCGCTGGACCCCCCCTGACCA 54 40 0 CCGTGGACCC 0.719301 -243 GGATCTCATTCCGTCAGGACTCTTTTATTAA 58 142 0 CCGCAGGACT 0.969695 -81 *** ******* Masking position 10 Map Score: 6.09734 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 224 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863