AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00020_synecho_reg_300.orf -o00020_synecho_300.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 Purged sequences: slr0049 25 hypothetical protein. Input sequences: #1 slr1097 57 hypothetical protein. #2 slr1098 67 hypothetical protein. #3 slr1099 300 ubiX; 3-octaprenyl-4-hydroxybenzoate carboxy-lyase. [EC:4.1.1.-] #4 slr1290 63 hypothetical 21.6 kD protein slr1290. [SP:YC90_SYNY3] #5 sll1201 225 hypothetical protein. #6 slr1291 85 ndhD2; NADH dehydrogenase subunit 4. [EC:1.6.5.3] #7 sll1200 217 hypothetical protein. #8 slr1293 56 hypothetical protein. #9 ssr2142 300 ycf19; hypothetical protein. #10 sll1022 146 hypothetical protein. #11 sll1021 39 hypothetical protein. #12 sll1020 95 hypothetical protein. #13 slr1090 44 GTP-binding protein. #14 ssr1789 79 hliA; high light inducible protein. #15 sll1019 60 gloB; probable hydroxyacylglutathione hydrolase (glyoxalase II). #16 sll1018 119 pyrC; dihydroorotase. [EC:3.5.2.3] #17 sll1017 241 putative ammonium transporter sll1017. [SP:YA17_SYNY3] #18 slr1400 119 regulatory components of sensory transduction system. #19 slr0670 117 hypothetical protein. #20 sll0656 130 nucH; extracellular nuclease. #21 sll0654 300 alkaline phosphatase. [EC:3.1.3.1] #22 slr1233 47 frdA; succinate dehydrogenase flavoprotein subunit. [EC:1.3.99.1] #23 ssr2049 51 bchB; protochlorophillide reductase 57 kD subunit. #24 slr1234 45 hypothetical hit-like protein slr1234. [SP:YHIT_SYNY3] #25 slr1235 36 hypothetical protein. #26 slr1236 66 hypothetical protein. #27 ssl2250 221 glycoprotein 64. #28 sll1132 35 hypothetical protein. #29 sll1131 174 hypothetical protein. #30 slr1237 48 codA; cytosine deaminase. [EC:3.5.4.1] #31 ssl2245 300 hypothetical protein. #32 sll1625 293 sdhB; succinate dehydrogenase iron- sulphur protein subunit. #33 sll1623 163 phr; ABC transporter. #34 slr1736 58 phr; hypothetical protein. #35 slr1737 71 phr; hypothetical protein. #36 sll1621 300 phr; membrane protein. [SP:YG21_SYNY3] #37 sll1557 104 sucD; succinyl-CoA synthetase. [EC:6.2.1.5] #38 sll1556 171 hypothetical 37.5 kD protein sll1556. [SP:YF56_SYNY3] #39 sll1555 300 regulatory components of sensory transduction system. #40 slr0018 55 fumC; fumarase. [EC:4.2.1.2] #41 sll0010 192 hypothetical protein. #42 tRNA-Gly-2 198 tRNA-Gly. #43 slr0019 28 hypothetical protein. #44 sll0008 35 hypothetical protein. #45 sll0007 51 hypothetical protein. #46 sll0006 103 aspC; aspartate aminotransferase. [EC:2.6.1.1] #47 sll0005 187 hypothetical 77.3 kD protein sll0005. [SP:Y005_SYNY3] #48 slr0020 100 recG; DNA recombinase. [EC:3.6.1.-] #49 slr0021 65 putative protease slr0021. [EC:3.4.-.-] [SP:Y021_SYNY3] #50 sll0002 226 ponA; penicillin-binding protein 1A. #51 tRNA-Ser-4 225 tRNA-Ser. #52 slr0213 87 guaA; probable GMP synthase (glutamine-hydrolysing) (glutamine #53 sll0210 114 bacA; bacitracin resistance; possibly phosphorylates undecaprenol. #54 slr0216 127 cobU; cobinamide kinase. #55 slr0217 238 hypothetical protein. #56 ssr0349 258 hypothetical protein. #57 sll0209 218 hypothetical protein. #58 sll0208 257 hypothetical protein. #59 sll0207 157 rfbA; glucose-1-phosphate thymidylyltransferase. [EC:2.7.7.24] #60 slr0220 175 glyS; glycyl-tRNA synthetase beta chain (glycine--tRNA ligase beta #61 sll0205 286 hypothetical protein. #62 sll0204 136 gidA; glucose inhibited division protein A. #63 sll0202 129 gidA; glucose inhibited division protein A. [SP:GIDA_SYNY3] #64 sll0200 300 transposase. #65 sll0401 193 gltA; citrate synthase. [EC:4.1.3.7] [SP:CISY_SYNY3] #66 sll0400 62 hypothetical protein. [SP:Y400_SYNY3] #67 slr0440 93 hypothetical protein. #68 ssr0102 74 ycf40; hypothetical protein. #69 sll0072 31 hypothetical protein. #70 sll0071 93 hypothetical protein. #71 sll0070 90 purU; formyltetrahydrofolate deformylase (formyl-fh(4) hydrolase). #72 sll0069 26 hypothetical protein. #73 sll0068 157 hypothetical protein. #74 sll0067 93 gst; glutathione S-transferase. [EC:2.5.1.18] #75 sll0066 99 hypothetical protein. #76 sll0065 181 ilvN; acetolactate synthase. [EC:4.1.3.18] #77 slr0053 64 hypothetical 20.1 kD protein slr0053. [SP:Y053_SYNY3] #78 slr0054 135 dgkA; probable diacylglycerol kinase (DAGK) (diglyceride kinase) #79 slr0055 143 trpG; anthranilate synthase component II. [EC:4.1.3.27] #80 slr0056 146 G4; chlorophyll synthase 33 kD subunit. #81 sll0064 300 hypothetical protein. #82 sll0823 166 sdhB; succinate dehydrogenase iron-sulfur protein. [EC:1.3.99.1] #83 sll0822 163 hypothetical protein. #84 slr0846 61 hypothetical protein. #85 sll0821 300 hypothetical protein. #86 slr0665 229 acnB; aconitate hydratase 2 (citrate hydro-lyase 2) (aconitase 2). #87 slr0666 300 hypothetical protein. Motif number 1 GTGGATCTATGGCGATCGCCTTTAGGATT 4 45 1 GGCGATCGCC 0.499998 -19 CCAATTTTCTGGCGATCGCCTGGCGGATCT 5 179 1 GGCGATCGCC 0.499998 -47 CCCTATCAGTAGCGATCGCCGTTGATCCCC 10 12 0 AGCGATCGCC 0.532913 -135 GCTGTCCGTTGGCGATCGCCAGCACCGATT 21 233 1 GGCGATCGCC 0.499998 -68 GGATTTTAGGGGCGATCGCCTTGGGAATTT 32 119 1 GGCGATCGCC 0.499998 -175 AACTGAGTTTGGCGATCGCCTGATATTCTG 39 168 1 GGCGATCGCC 0.499998 -133 TCGCATAGAAGGCGATCGCCGCAAAAGGAG 42 53 1 GGCGATCGCC 0.499998 -146 ATTCCTGACTGCCGATCGCC 51 1 0 GCCGATCGCC 0.539858 -225 CCCCTAGAATTGTGATCGCCCCACCGTTGC 53 17 0 TGTGATCGCC 0.871189 -98 GTGTTTGCTGTTCGATCGCCTTTGAGTAGA 55 199 0 TTCGATCGCC 0.846056 -40 AGTTAACGACTCCGATCGCCATAAAGCTTT 57 155 0 TCCGATCGCC 0.922685 -64 GCTTAAAAGATGCGATCGCCAAAACGCAGA 64 86 0 TGCGATCGCC 0.539025 -215 GAGTTTGCCGGCCCATCGCCTCTAACTTCC 66 23 1 GCCCATCGCC 0.879097 -40 ATTTTAGGACGGCGATCGCCGGGGATAATT 80 11 1 GGCGATCGCC 0.499998 -136 CCCGATCGCCTAACAATTAA 84 1 1 CCCGATCGCC 0.899132 -61 GCATTGGTTAGGTGATCGCCAACGTGGTCT 87 114 0 GGTGATCGCC 0.534742 -187 ********** Masking position 5 Map Score: 54.4882 Number of sites scoring better than the average of aligned sites = 5990 Number in coding regions = 5444 Number in noncoding regions = 546 Number of orfs with sites within 600 bp upstream = 338 Fraction of orfs with sites within 600 bp upstream = 0.0542885 Motif number 2 CTTGAACAATGCCTGGGCCAGGAACCGTTGC 7 62 0 GCCGGGCCAG 0.97359 -156 CAATTTGCCGGCCCGGGAAAAGCAGTACTCT 17 118 0 GCCGGGAAAA 0.946217 -124 TAAATCAACTCCCTGGAAAAGTGAAATTTTT 17 212 0 CCCGGAAAAG 0.3909 -30 TCAATCTTGACCAAGGGCCAATGGGTTTAGA 18 77 0 CCAGGGCCAA 0.904552 -43 GCGTTACCCTGCAGGGGAAAAATTTAGCCCC 29 75 1 GCAGGGAAAA 0.91589 -100 TAAGCCCTTTGCCCGGGACGACAAGCTAAAG 31 33 0 GCCGGGACGA 0.912387 -268 GGGTTAATGCCCAGGGGGCAGCGAATGATTT 32 54 0 CCAGGGGCAG 0.814295 -240 AGGAAATACCCTGGGAAAAGCAATATGGG 32 275 0 CCCGGGAAAA 0.856876 -19 AACCCAGGTAGCCAGGGCCAACCCATTCTCG 47 37 1 GCCGGGCCAA 0.978258 -151 CGGTGGATAGGCACGGGAAGGCCGAATTTGG 50 204 0 GCAGGGAAGG 0.750183 -23 TCTATGGAAAGCACGGGGAAATATTGACTAC 56 66 0 GCAGGGGAAA 0.899433 -193 CTTCCCGTTGGCATGGGCCAGCTTCCTAAAA 57 99 0 GCAGGGCCAG 0.958012 -120 ACATTTTAAAGCAGGGGACAGTCTACCGCCC 62 80 0 GCAGGGACAG 0.940079 -57 AATTGCGCCGGCCCGGGCCAGCCTGTCCCCA 65 120 0 GCCGGGCCAG 0.97359 -74 AGAACCGTTGGCCGGGGCAAATAATTACCGA 73 112 0 GCCGGGCAAA 0.962387 -46 CTCAGGACAACCCTGGGGAGACGTGCTTGAG 75 50 0 CCCGGGGAGA 0.623372 -50 AAAATCTATGGCAAGGGCAAAAACAATCGTT 76 12 1 GCAGGGCAAA 0.940605 -170 GCTAGGAATGCCATGGAACAATGGGGGTAAC 79 71 1 CCAGGAACAA 0.460212 -73 GACGGCGATCGCCGGGGATAATTGACCAACC 80 18 1 GCCGGGATAA 0.670812 -129 ATGGAATTTTGCCGGGACCAGGAATAAAAAT 82 80 1 GCCGGACCAG 0.828273 -87 TTACGGAAGGGCCGGGGGCAATAATTTTTAT 82 103 0 GCCGGGGCAA 0.962136 -64 AAGCAGGGTAGCAAGGAGCAAAAGAGTCAAC 83 79 1 GCAGGAGCAA 0.672963 -85 GAATTGGTAAGCAAGGGAAGATTAGTCGAAG 83 115 0 GCAGGGAAGA 0.785651 -49 AACCATGGCTGCAAGGGCAAACCTTAAAATT 85 155 0 GCAGGGCAAA 0.940605 -146 *** ******* Masking position 6 Map Score: 32.8221 Number of sites scoring better than the average of aligned sites = 1740 Number in coding regions = 1612 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 3 ACTAACCCCGGCCCCTAGCCTAGGGGGGGAA 1 16 0 GCCCCTACCT 0.817344 -42 TAAGTCCAAATCCCCCAACCTTGCCGGAGCT 3 222 0 TCCCCCACCT 0.962535 -79 ATTCCCCCACTCCCCTTTATTTA 6 3 1 TCCCCCATCC 0.962535 -83 GGTGGTTAGAGGCCCCAACCTCCAGTTCCAC 9 248 0 GGCCCCACCT 0.969088 -53 ATCTCTGCAGGCCTCCACCTTCCCCT 10 131 1 GCCTCCACTT 0.537627 -16 ATGATATTTGGGCTCCAATCTAGTGGAACGA 17 86 0 GGCTCCATCT 0.763783 -156 ACGATCACTTGGCCCCGCTCCAGTTTTTCAT 21 181 0 GGCCCCGTCC 0.787044 -120 TTGAAGGTTTTGCCCCACTTTTTCCTGATTG 21 261 1 TGCCCCATTT 0.874972 -40 TGACTACTTTTCACCCAGTCCTAGAGCATA 32 10 0 TCACCCATCC 0.546451 -284 ACCATTTTCCTGCCCTAATCCAGAGCAAAGG 33 69 1 TGCCCTATCC 0.850614 -95 TGATGAAAAATGCTCCATCCCCTCAGAAAAA 36 251 1 TGCTCCACCC 0.871276 -50 TGTGGCTTGATGCCCTACTCCGCAGCTATCG 37 62 0 TGCCCTATCC 0.850614 -43 ACCACAATATGCCCCCACCTTAATCCTGGGT 38 76 1 GCCCCCACTT 0.887313 -96 TTTAAGTTATTGCTCCACTCCCTCCAGTTGA 38 111 1 TGCTCCATCC 0.825402 -61 TTAAAGTTGCTCCCCTACTCCCAAAAACTTG 39 69 1 TCCCCTATCC 0.82045 -232 GTCCTGCCCCATTCTATTAATAAAT 40 5 1 TGCCCCATCT 0.957192 -51 AAAGACGGTTTTCCCCATCCTAACCCAGGTA 47 16 1 TTCCCCACCT 0.87276 -172 CCAGGACTGTTTCTCCAGTCCCTAATCTGCA 50 67 1 TTCTCCATCC 0.503198 -160 GCAATTTTCCGCCCCCATCTTAGCGCAGATT 51 181 0 GCCCCCACTT 0.887313 -45 CATAAATAAATTCCCCAATTTTTAAGCAACG 52 49 0 TTCCCCATTT 0.599903 -39 CCAGCCAGTGTCCCCCAGTCTACTCAAAGGC 55 181 1 TCCCCCATCT 0.947213 -58 CTGTGGGTTTTTCCCTATTCTGGAGTGCTTT 57 71 1 TTCCCTATCT 0.460067 -148 AAAATCTCTATGCCCCATCTCAACTTGCCTG 59 69 0 TGCCCCACTC 0.934835 -89 TGAGTGAAAGTCCCCCAGTATTGCCGGAGCT 60 110 0 TCCCCCATAT 0.55719 -66 TGTCCTCCTGGCCTCCAATTTGGGGGGAAAC 60 141 0 GCCTCCATTT 0.44816 -35 CCAAGGAGAAGGCCCCATCTCCTGAAGAATG 62 51 0 GGCCCCACTC 0.933548 -86 CTAACCCCATGGCCCCATCATAGTTTATTTT 73 38 1 GGCCCCACAT 0.687345 -120 ACTCTTCAGCTTCCCTAACTCTAGTGAGGAA 76 59 1 TTCCCTACTC 0.353454 -123 TGCACGACTGGGCCCTAACCCAGACCG 76 165 1 GGCCCTACCC 0.888685 -17 GGCGTATTTCTGCCCCAATTCGCCTAAATAC 78 29 1 TGCCCCATTC 0.909253 -107 CCAAAAACACTGACCCAGCCTATCACCCTTG 79 38 1 TGACCCACCT 0.600216 -106 AAAAATTATTGCCCCCGGCCCTTCCGTAATA 82 105 1 GCCCCCGCCC 0.809394 -62 ******* *** Masking position 5 Map Score: 29.2913 Number of sites scoring better than the average of aligned sites = 2902 Number in coding regions = 2621 Number in noncoding regions = 281 Number of orfs with sites within 600 bp upstream = 300 Fraction of orfs with sites within 600 bp upstream = 0.048185 Motif number 4 GTTGAGACTCGGCTAAATTTTTCTTCCTAATCC 9 70 0 GCTATTTTTC 0.950886 -231 ACTAAAAATAGACTTCAATTTTCCGAATAGCCT 12 40 1 GCTAATTTTC 0.961025 -56 TTCAGCCTAATACTCAATTTTTCTAACTCCCAT 26 11 0 TCTATTTTTC 0.904203 -56 TGCAAATAGGGGCTAAATTTTTCCCCTGCAGGG 29 81 0 GCTATTTTTC 0.950886 -94 AACCAAAAGAGTTTTAAATTTTCAACATTATCT 31 247 0 GTTAATTTTC 0.725783 -54 CTATCTAAACGACTAAATTTTTCTGAGGGGATG 36 266 0 GCTATTTTTC 0.950886 -35 AATCTTATTTTCCTTAAATTTTCCGTAATCTCT 39 34 1 TCTAATTTTC 0.923202 -267 GATTTGCCCTTACTGAAATTTTCCTTGACATAA 50 103 1 TCTAATTTTC 0.923202 -124 TGAGAAGGATTTCTGCAATTTTCCGCCCCCATC 51 193 0 TCTAATTTTC 0.923202 -33 AGGAGGAAACTTCTGGATTTTTCAGGAGTATTA 54 17 0 TCTATTTTTC 0.904203 -111 CAAAGTGTTCTACTTCAATTTTCATGGCATCGG 61 115 0 TCTAATTTTC 0.923202 -172 ATCTCCTGAAGAATGGAATTTTCCTTGTCTTGA 62 33 0 GATAATTTTC 0.600155 -104 TCTCTAACTATTTTTGAATTTTCAAAGTTCCCT 62 114 1 TTTAATTTTC 0.563385 -23 TAGGATATAAGGCTGGATTTATCAACGAATTTC 76 124 1 GCTATTTATC 0.623579 -58 TTGATATCCCGCCTTTATTTTTCGATCAA 84 43 1 GCTATTTTTC 0.950886 -19 CCTTAAGTCTGGCTCAAATTTTCTAACTATCCC 86 19 0 GCTAATTTTC 0.961025 -211 * ** ******* Masking position 7 Map Score: 18.3665 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 34 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 5 GCGGCTGTGGGCAAAGTTTGGCATTGCCGCCA 3 94 0 GCAAAGTTGC 0.914582 -207 AAACTATTTACCAATGCTTGCCACTGTTGGAG 7 142 0 CCAATGTTGC 0.785379 -76 GCGCTGATTGGCTCAACCCAAA 16 1 1 GCGCTGTTGC 0.745401 -119 CCCAGAATCCGGAAAGGTTGCCCAACTTTGCT 16 46 1 GGAAAGTTGC 0.866788 -74 AATTTTTTGGGGCCGGTTTGCCGTAGGTGCAA 27 113 0 GGCCGGTTGC 0.752509 -109 TGATTTAGTTTGCCAGTTTGCCGTTGCATCAA 29 19 1 TGCCAGTTGC 0.5873 -156 TCCACTGGCTGGCCGCAAATATG 30 2 1 CCACTGCTGC 0.650896 -47 AGCTTTGGCCGGACTGACTGCC 30 37 1 GGACTGCTGC 0.851299 -12 ATAATGATCCGCACTGTTTGGCTATAGTCTAT 36 104 1 GCACTGTTGC 0.95571 -197 GCATTTTTCATCAATGCTTGCCCTCTTTTCTC 36 232 0 TCAATGTTGC 0.788735 -69 GGGACATTTTGCTCTGGTTGACGATACAGTGA 37 11 1 GCTCTGTTGC 0.663909 -94 AGTGAAGCTTGGACTGGTTGACCCCGATAGCT 37 38 1 GGACTGTTGC 0.928851 -67 GGACCTGTCAGCAAAGTCTGCCAAACAAATTC 42 23 1 GCAAAGCTGC 0.825337 -176 CTCAAGTCGCGGACTGCTTGGCAATAACGCTG 42 133 1 GGACTGTTGC 0.928835 -66 GCCATGGTTGCCATAGGTTCCA 46 1 1 GCCATGTTGC 0.944759 -103 TGACGGCAAGGCCATGGTCGTCAACAATCCCC 51 107 1 GCCATGTCGC 0.590932 -119 ATTTTTGATTGCCAAGGCTGGCCAATAGATTA 55 44 0 GCCAAGCTGC 0.789599 -195 CTTGTCTTGATCAATGTTTGACCTTGGAACCC 62 11 0 TCAATGTTGC 0.78874 -126 ATGGATATGGGGACAGGCTGGCCCGGGCCGGC 65 113 1 GGACAGCTGC 0.768759 -81 AGCACGTCTCCCCAGGGTTGTCCTGAGCTCTT 75 54 1 CCCAGGTTGC 0.460411 -46 TTTTGCAAAATGCAAGCTTGCCCGGCGGGCAT 76 90 1 TGCAAGTTGC 0.527316 -92 AGATGATTCAAAGGTTGACTAGCGTACCC 79 8 1 TCAAAGTTGC 0.684352 -136 ATTAGTCGAAGGAATGGTTGACTCTTTTGCTC 83 94 0 GGAATGTTGC 0.918278 -70 TGCCCTTGCAGCCATGGTTGCCAAAGGGATAA 85 167 1 GCCATGTTGC 0.944759 -134 ****** *** * Masking position 6 Map Score: 18.9428 Number of sites scoring better than the average of aligned sites = 579 Number in coding regions = 523 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 6 GAAATTTCCCCCCCTAGGCTA 1 2 1 AAATTTCCCC 0.854603 -56 AATGTAAAGAAAATTTCCCCACTGTCCTTT 7 15 0 AAATTTCCCC 0.854603 -203 CAACTTTGGTAATACTCCCCTTTACCCTGG 9 99 1 AATACTCCCC 0.729844 -202 CCTGGACAAATAAAATCCCCCTGGCGTAAC 9 191 1 TAAAATCCCC 0.919786 -110 ACGACGGCACAAAAATCCCCCTAAAATCCT 16 78 0 AAAAATCCCC 0.970641 -42 TTCCCACAAGTAATATCCCCACTCCTAATT 19 21 1 TAATATCCCC 0.799077 -97 ACATATACGAAAAAATCCCCACCTCTGCAA 19 51 0 AAAAATCCCC 0.970641 -67 GTCAAAAATCTCCTCCAATAGTA 20 118 0 AAAAATCTCC 0.580409 -13 AAATTCTGCGAAAAATCCTCGGCGGGATCG 21 14 0 AAAAATCCTC 0.720147 -287 AACGGACAGCAAAATTCCCCATCGGTGAAG 21 213 0 AAAATTCCCC 0.94428 -88 AGCCTGCCACTAAAATTCCCAAGGCGATCG 32 131 0 TAAAATTCCC 0.471599 -163 GTTTTCCTTTAATAATCCCCCC 37 93 1 AATAATCCCC 0.902981 -12 TGCCGCCCAGAAAACTCCCCTAACAAAAAA 39 196 1 AAAACTCCCC 0.905629 -105 CATGGTCGTCAACAATCCCCGTATTCTACC 51 119 1 AACAATCCCC 0.807424 -107 AAGACATAAATAAATTCCCCAATTTTTAAG 52 54 0 TAAATTCCCC 0.854603 -34 CTGCCATCCAAATTTTCCCCTTTAGAACAC 61 223 0 AATTTTCCCC 0.623306 -64 AGTCAGAAAAATTCCCTGGGGGCACT 71 7 1 AAAAATTCCC 0.720147 -84 TGCATTTTGCAAAATTCCTCACTAGAGTTA 76 74 0 AAAATTCCTC 0.568789 -108 ATGGTTGGTCAATTATCCCCGGCGATCGCC 80 21 0 AATTATCCCC 0.763485 -126 TCATAGGCCTTAAAATCCCCGGCCCGGCGT 81 92 0 TAAAATCCCC 0.919786 -209 ********** Masking position 6 Map Score: 21.0391 Number of sites scoring better than the average of aligned sites = 820 Number in coding regions = 667 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 7 TTAACCTTTTAACCTCGGGGGAACGACGGCAC 16 98 0 ACCTCGGGGA 0.854462 -22 AACCGCCATTGTCAACGGGGAACGAAAAAGCT 21 71 0 GCAACGGGGA 0.861297 -230 ATCGTCCTTCACCGATGGGGAATTTTGCTGTC 21 207 1 ACGATGGGGA 0.84494 -94 AGATTAACTTACCAACGGGGCTAAG 23 37 1 ACAACGGGGT 0.924377 -15 ATCAACCCCAAACCATAGGGGA 25 25 1 ACCATAGGGA 0.88289 -12 TTCATTATGCATCAACAGGGCAGAAAAAACAA 27 143 0 ACAACAGGGA 0.899926 -79 CTTCCATCACACCAATGGGCTACAAA 28 5 0 ACAATGGGCA 0.70516 -31 AAAAAAAGCCAGCAACGGGGTCTTAATCTAAA 32 226 1 ACAACGGGGC 0.817202 -68 AAAACCAAAAAACATTAGGGATTTCGATTTCA 38 31 0 ACATTAGGGT 0.587461 -141 ACCATCGTAAAACATTAGGGGAACTTCGCCTA 41 22 1 ACATTAGGGA 0.767512 -171 AAAACAATTAATCAATGGGGAACTATTCTAAC 48 37 1 ACAATGGGGA 0.971869 -64 TCAGAACAATGGGGAAGACATAAATA 52 72 0 ACAATGGGGA 0.971869 -16 ATAGCGGTCTAACCATAGGGAACACCTATCCA 58 99 0 ACCATAGGGA 0.88289 -159 ACTATGATGGGGCCATGGGGTTAGGGTTTCCC 73 30 0 GCCATGGGGT 0.691762 -128 CCAGCCTATCACCCTTGGGGCTAGGAATGCCA 79 52 1 ACCTTGGGGT 0.754903 -92 AATGCCATGGAACAATGGGGGTAACTTGGTTG 79 77 1 ACAATGGGGT 0.937112 -67 AATTCCATAGATCAATGGGGAATTGTAGGAGG 82 56 0 ACAATGGGGA 0.971869 -111 GTATGAGGAAATCAACAGGGCAAAAAAGGCTC 82 144 0 ACAACAGGGA 0.899926 -23 * ******** * Masking position 8 Map Score: 15.9552 Number of sites scoring better than the average of aligned sites = 571 Number in coding regions = 477 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 8 TTTAGTGAAAATAGTTGGGGGACAAAGGCTT 3 192 0 ATATTGGGGG 0.796211 -109 TCCAAATCCTATTCAAGGGGGATTTAAGTTG 7 190 0 ATTAAGGGGG 0.90298 -28 ATCTTCCCTCATTATTGGGGGCTTTGGTGAT 10 54 0 ATTTTGGGGG 0.923081 -93 ACCTTTCCGGATTCTGGGGGTTAACTGTACT 16 33 0 ATTTGGGGGT 0.719165 -87 CTTTGCTAGGATTTTAGGGGGATTTTTGTGC 16 71 1 ATTTAGGGGG 0.973945 -49 TTTAGATTGGATTTTAGGGGCGATCGCCTTG 32 111 1 ATTTAGGGGC 0.887006 -183 CGCCTTGGGAATTTTAGTGGCAGGCTTAGTG 32 135 1 ATTTAGTGGC 0.46681 -159 AATAGGCACAATTCTAGGGGGTTCTCGACAA 32 197 1 ATTTAGGGGG 0.973945 -97 TGGGAAAAGCAATATGGGCGGAGGCTACCTC 32 262 0 AATTGGGCGG 0.518192 -32 ATAACCCAGGATTAAGGTGGGGGCATATTGT 38 79 0 ATTAGGTGGG 0.573627 -93 GTCAAATTCCATACTAGGCGGCGGTAAAAAG 39 109 0 ATATAGGCGG 0.693098 -192 CTTTGAAGACATAGTGGGGGGCGGCGACCTG 41 93 0 ATATGGGGGG 0.94038 -100 GGCGATCACAATTCTAGGGGACAGTTTAAAA 53 27 1 ATTTAGGGGA 0.776987 -88 TAGTGAAGAGATTTAGGGGGCTGAACAAAAC 60 78 0 ATTAGGGGGC 0.716978 -98 AGCTCCGGCAATACTGGGGGACTTTCACTCA 60 110 1 ATATGGGGGA 0.595165 -66 CCTGGCCTCCAATTTGGGGGGAAACTGAGTG 60 135 0 AATTGGGGGG 0.852847 -41 TTTTAAGCTAATATTTGGGGGACAGCTTTTG 67 31 0 ATATTGGGGG 0.796211 -63 GCTAAGAACCATTCTAGGCGGTGCTATACCA 68 40 1 ATTTAGGCGG 0.874003 -35 TGGGGATAAAATTTAAGGGGGACATCCTCCT 82 31 1 ATTAAGGGGG 0.90298 -136 TCAATGGGGAATTGTAGGAGGATGTCCCCCT 82 46 0 ATTTAGGAGG 0.635824 -121 GCCGTAAAATTATGGTGGGCCTTTTATGG 86 211 0 ATTTGGTGGG 0.843831 -19 *** ******* Masking position 1 Map Score: 16.8292 Number of sites scoring better than the average of aligned sites = 690 Number in coding regions = 539 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 9 CAAATAGGACGGACTAACCCCGGCCCCTAG 1 29 0 GGACTAACCC 0.95734 -29 TGGGGGATTTGGACTTACACTTCCCTCATA 3 236 1 GGACTTACAC 0.664433 -65 CTCATCAGAAGGACTTACCCTCAGAGCCTA 3 271 1 GGACTTACCC 0.944568 -30 GGTTAGGCGAGGAAAAACCTAGGTCAAAGA 5 135 0 GGAAAAACCT 0.74833 -91 AATAGGATTTGGAATTACCC 7 208 1 GGAATTACCC 0.924932 -10 GAGATAGACCGGAAAAACCAGGACTCAGCA 10 106 0 GGAAAAACCA 0.74833 -41 AGGAAATACCCTGGGAAAAGC 32 283 0 GGAAATACCC 0.941952 -11 GGGAATAACACTGCCTTGTTT 35 61 0 GGAATAACAC 0.653666 -11 TTGCCCAGAGGGACTTACCCATCAAAAATC 36 37 0 GGACTTACCC 0.944568 -264 GGTGCTGCTAGGAAAAACCAAAAAACATTA 38 46 0 GGAAAAACCA 0.74833 -126 CTGGGACGATGGACATTCCCCATGTATCTC 48 78 1 GGACATTCCC 0.688371 -23 TGGTTAAAAAGGACAAACCTAACAGCTAAA 50 177 0 GGACAAACCT 0.804234 -50 TCCAGAATAGGGAAAAACCCACAGATCCTA 57 65 0 GGAAAAACCC 0.955299 -154 CCCTGAGCCTGGATAAACCCTTAGTAAATT 81 256 1 GGATAAACCC 0.792675 -45 ********** Masking position 3 Map Score: 10.1311 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 252 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 10 GACTAACCCCGGCCCCTAGCCTAGGGGGGGA 1 17 0 GGCCCCTACC 0.83238 -41 GTCAGAGAATGGGCTCTATCCATGTGAATAA 5 102 1 GGGCTCTACC 0.974661 -124 TGGAGGTTGGGGCCTCTAACCACCAATCAGA 9 255 1 GGCCTCTACC 0.955111 -46 TTTGGTGATGGGGGTCTACCCCCCTATCAGT 10 32 0 GGGGTCTACC 0.96523 -115 GCGCTGATTGGCTCAACCCAAAAGTACAG 16 9 1 TGGCTCAACC 0.800641 -111 GCAAACGGTGGGGATCAACCCCAAACCATAG 25 12 1 GGGATCAACC 0.950991 -25 TACTTTTGCCGGGGTCTACCCCCTATAGCCC 27 61 0 GGGGTCTACC 0.96523 -161 CTGCCCCCTGGGCATTAACCCATGGAAAGTA 32 64 1 GGCATTAACC 0.501295 -230 CGCAGCTATCGGGGTCAACCAGTCCAAGCTT 37 42 0 GGGGTCAACA 0.743525 -63 TGCGGAGTAGGGCATCAAGCCACAGTTTTCC 37 69 1 GGCATCAACC 0.915054 -36 CCCATAGCAGTGCATCTACCCGTTGGTATGG 41 146 0 TGCATCTACC 0.473041 -47 TTGCTGAGGCGAGATCAAGCCAGTGCCGGTC 46 42 1 GAGATCAACC 0.507637 -62 GAGGATCATAGCGGTCTAACCATAGGGAACA 58 107 0 GCGGTCTACC 0.685053 -151 GACCAGTACTGGGCTCAATCCAGGGGTGAAG 65 49 1 GGGCTCAACC 0.977316 -145 GATATCCATTGGCCTCAAGCACGTCTCCCCA 75 37 1 GGCCTCAACA 0.68961 -63 TTGCACGACTGGGCCCTAACCCAGACCG 76 164 1 GGGCCCTACC 0.89977 -18 AACTTGGTTGGGGGTTAAACCTTGACCGACT 79 99 1 GGGGTTAACC 0.74354 -45 ******** ** Masking position 8 Map Score: 14.6644 Number of sites scoring better than the average of aligned sites = 325 Number in coding regions = 273 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 11 ATCCCCCAACCTTGCCGGAGCTTTAGTGAAAAT 3 211 0 CTTGCCGGGT 0.972911 -90 CTTTTTGCCGGGAAATAAGCTGATTT 14 4 1 TTTGCCGGAT 0.944896 -76 AATCTCAGTGTTTGCCTGCAAGTATTTTAAAAA 15 21 0 TTTGCCTGAT 0.64805 -40 AAAATTTCACTTTTCCAGGGAGTTGATTTAGTA 17 213 1 TTTTCCAGGT 0.665819 -29 GCTAAAAATGCTTGCCAGGGAGTATGGCTCTAA 20 23 0 CTTGCCAGGT 0.898599 -108 ACAAGTTACTTTTGCCGGGGTCTACCCCCTATA 27 65 0 TTTGCCGGGT 0.974152 -157 TTGGGGCCGGTTTGCCGTAGGTGCAAAGGCTAG 27 106 0 TTTGCCGTGG 0.701486 -116 AAGGACTTTTCCGTAAATTTTGAGAGAAG 27 203 0 TTTTCCGTAT 0.695043 -19 AGTTTGCCAGTTTGCCGTTGCATCAATTCAGGG 29 25 1 TTTGCCGTGT 0.958968 -150 ATTTTCCATACTTTCCATGGGTTAATGCCCAGG 32 70 0 CTTTCCATGT 0.54074 -224 GGCAAGCAATTTTGCCATCAACTGGAGGGAGTG 38 126 0 TTTGCCATAT 0.724118 -46 GGCAAAATTGCTTGCCGGTATTTGTAATGTAAT 38 143 1 CTTGCCGGAT 0.942354 -29 TTTCCTTAAATTTTCCGTAATCTCTTCTTAAAG 39 42 1 TTTTCCGTAT 0.695043 -259 CGACCATGGCCTTGCCGTCAGTTAGACCCAGAA 51 94 0 CTTGCCGTAT 0.910212 -132 TTAGCGCAGATTTGCCGTGGGTTATTCTGGGCT 51 160 0 TTTGCCGTGT 0.958968 -66 AAATGTAAACCTTTCCGTTACATTCTAATCTAT 55 19 1 CTTTCCGTAT 0.684737 -220 CCAGGCAGATTTTGCCTGTGATTCTCGGGCATC 55 114 1 TTTGCCTGGT 0.801801 -125 GTCCCCCAGTATTGCCGGAGCTTTAGTGAAGAG 60 99 0 ATTGCCGGGT 0.800426 -77 TCTGCTTGAGTTTGCCGGCCCATCGCCTCTAAC 66 16 1 TTTGCCGGCT 0.800317 -47 TGTTTTTGCCCTTGCCATAGATTTTT 76 4 0 CTTGCCATGT 0.846046 -178 ******** * * Masking position 3 Map Score: 15.4102 Number of sites scoring better than the average of aligned sites = 686 Number in coding regions = 604 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 12 GAAATTTCCCCCCCTAGGCTAGGGGCC 1 8 1 CCCCCCCTAG 0.690889 -50 GACGGACTAACCCCGGCCCCTAGCCTAGGG 1 22 0 CCCCGGCCCC 0.913461 -36 GTCCACAATTTGCCGGCCCGGGAAAAGCAG 17 124 0 TGCCGGCCCG 0.957778 -118 TGTCGATCCCGCCGAGGATTTTTCGC 21 7 1 TCCCGCCGAG 0.779384 -294 CAGCGAATGTTGCCGCACCGATGTTAG 36 8 0 TGCCGCACCG 0.711662 -293 TCCTTTTTACCGCCGCCTAGTATGGAATTT 39 107 1 CGCCGCCTAG 0.904624 -194 CCTGATATTCTGCCGCCCAGAAAACTCCCC 39 186 1 TGCCGCCCAG 0.946017 -115 TAATCCAGGTCGCCGCCCCCCACTATGTCT 41 88 1 CGCCGCCCCC 0.921285 -105 GAATTGTGATCGCCCCACCGTTGCAACTCC 53 11 0 CGCCCCACCG 0.564183 -104 TCCCGGCTAGAAATATCTTC 57 1 1 TCCCGGCTAG 0.774007 -218 CCTCCCCCCCAGCAACTTAGAC 58 3 1 TCCCCCCCAG 0.805053 -255 CAAAAAATTGCGCCGGCCCGGGCCAGCCTG 65 126 0 CGCCGGCCCG 0.982652 -68 TGCTTGAGTTTGCCGGCCCATCGCCTCTAA 66 18 1 TGCCGGCCCA 0.708873 -45 AGTGGTATAGCACCGCCTAGAATGGTTCTT 68 43 0 CACCGCCTAG 0.481823 -32 TAATTATTTGCCCCGGCCAACGGTTCTAGG 73 116 1 CCCCGGCCAA 0.809053 -42 GCCTTAAAATCCCCGGCCCGGCGTAGAAAC 81 86 0 CCCCGGCCCG 0.984514 -215 AAATTATTGCCCCCGGCCCTTCCGTAATAG 82 107 1 CCCCGGCCCT 0.794656 -60 ACCGCTTAATCCCCGCCGAGTCAAAAC 85 284 1 CCCCGCCGAG 0.898202 -17 ********** Masking position 4 Map Score: 14.4194 Number of sites scoring better than the average of aligned sites = 1162 Number in coding regions = 1112 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 13 TTAGTGAAAATAGTTGGGGGACAAAGGCTT 3 192 0 TAGTTGGGGG 0.876108 -109 AGCTCCGGCAAGGTTGGGGGATTTGGACTT 3 222 1 AGGTTGGGGG 0.696144 -79 AAAATCTTTCTGATTGGGCGCAAAGGATCT 9 13 1 TGATTGGGCG 0.827535 -288 GCTAAAAATCTGATTGGTGGTTAGAGGCCC 9 264 0 TGATTGGTGG 0.833666 -37 CGATCGCTACTGATAGGGGGGTAGACCCCC 10 24 1 TGATAGGGGG 0.830551 -123 TCTTCCCTCATTATTGGGGGCTTTGGTGAT 10 54 0 TTATTGGGGG 0.907743 -93 TTTGCTAGGATTTTAGGGGGATTTTTGTGC 16 72 1 TTTTAGGGGG 0.559595 -48 TCCCCTATGGTTTGGGGTTGATCCCCA 25 20 0 TGGTTTGGGG 0.756464 -17 GAAAAAACAATTTTTTGGGGCCGGTTTGCC 27 123 0 TTTTTTGGGG 0.308567 -99 CATGATTTTTTTGTTAGGGGAGTTTTCTGG 39 202 0 TTGTTAGGGG 0.689888 -99 CTAGTCTAAGTTGCTGGGGGGGAGG 58 6 0 TTGCTGGGGG 0.766637 -252 CCTGATATGTTTATTGGTGGTGGCTTTTGC 59 43 0 TTATTGGTGG 0.714703 -115 TGATCTTTTCTAGTAGGGCGGTGTCTGTCA 61 76 0 TAGTAGGGCG 0.300295 -211 GTTACTGGACTGACTGGTGGTTGCTTAGTC 61 161 0 TGACTGGTGG 0.481174 -126 TTTAAGCTAATATTTGGGGGACAGCTTTTG 67 31 0 TATTTGGGGG 0.670258 -63 ATAAACTACATGATTGGTGGAAGTGCGAAT 73 79 1 TGATTGGTGG 0.833666 -79 GGGGGTAACTTGGTTGGGGGTTAAACCTTG 79 93 1 TGGTTGGGGG 0.972617 -51 AACCGCTTAATTGTTAGGCGATCGGG 84 7 0 TTGTTAGGCG 0.351596 -55 GGGTCTTGGGTTGTTGGTCGTTACAACGAG 85 245 1 TTGTTGGTCG 0.52421 -56 GCTTCGGTGATGATAAGGGGTGAATTAAAT 86 159 1 TGATAAGGGG 0.380493 -71 TAGCAATAAATGTTTGGTGGTTTACAGTGA 87 77 0 TGTTTGGTGG 0.722182 -224 ********** Masking position 7 Map Score: 9.69867 Number of sites scoring better than the average of aligned sites = 1462 Number in coding regions = 1317 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 14 TATTTTCACTAAAGCTCCGGCAAGGTTGGG 3 210 1 AAAGCTCCGG 0.904117 -91 GGACAAATAAAATCCCCCTGGCGTAACAGA 9 194 1 AATCCCCCTG 0.55321 -107 CTACAACTTTTATCCTCCGGAGGCACACC 11 21 1 TATCCTCCGG 0.85515 -19 TTAACCTTTTAACCTCGGGGGAACGACGG 16 101 0 TAACCTCGGG 0.642166 -19 TCCATGGGTTAATGCCCAGGGGGCAGCGAA 32 60 0 AATGCCCAGG 0.743736 -234 CCCTCTGGGCAAACCTCAGGAACCATGGGT 36 55 1 AAACCTCAGG 0.880903 -246 CTTGGGCTGAAAAGCTCCGGTCTAAGCAGA 42 101 1 AAAGCTCCGG 0.904117 -98 TTAACACTTAAATCCTCTGGGGAGTGAAGT 45 30 1 AATCCTCTGG 0.664158 -22 GGTGAGGGCGAATCCCCAGGCACACCTCAG 51 41 1 AATCCCCAGG 0.875902 -185 AGACCGCTATGATCCTCCGGGATTTGCATT 58 121 1 GATCCTCCGG 0.775934 -137 GTTAAGAAATTAACCCCCGGTTGTCTTTAT 58 168 0 TAACCCCCGG 0.879233 -90 TCTCTTCACTAAAGCTCCGGCAATACTGGG 60 98 1 AAAGCTCCGG 0.904117 -78 CCCGGCGTAGAAACCTCAGGCGATTTTCAA 81 70 0 AAACCTCAGG 0.880903 -231 ATAGGCCTTAAAATCCCCGGCCCGGCGTAG 81 90 0 AAATCCCCGG 0.662174 -211 AAAACGGCATAATCCCCGGGAACATTTACC 81 168 0 AATCCCCGGG 0.854046 -133 ********** Masking position 2 Map Score: 9.16225 Number of sites scoring better than the average of aligned sites = 629 Number in coding regions = 542 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 15 TCTATTTTTAGTCAGAATTAACAGGAAGTA 12 22 0 GTCAGAATTA 0.806787 -74 AGATTAATCAGACAAAAAAATT 15 49 1 GACAAAAAAA 0.718163 -12 GCAAAGGCTAGACAGAATTACAAGTTACTT 27 87 0 GACAGAATTA 0.782817 -135 GCATCAACAGGGCAGAAAAAACAATTTTTT 27 137 0 GGCAGAAAAA 0.7251 -85 GGGGGTTCTCGACAAAAAAAGCCAGCAACG 32 213 1 GACAAAAAAA 0.718163 -81 ATGGAGAAAGGTCAGAATTATCTACAACAT 39 262 1 GTCAGAATTA 0.806787 -39 TGATAATAGTCAGAATAAATAGGGGAAG 57 201 0 GTCAGAATAA 0.825991 -18 TCGATACAAAGTCAAAATTAAGGAGCAATC 61 43 1 GTCAAAATTA 0.695518 -244 ACCAATGATGGACAAAAAAAATATCGTCAA 61 189 1 GACAAAAAAA 0.718163 -98 CAAACTAATGGACAAAAAAATCGCATCTCG 64 115 0 GACAAAAAAA 0.718163 -186 AGTCAGAAAAATTCCCTGGGG 71 2 1 GTCAGAAAAA 0.843657 -89 TATTTTTATAGTCAAAATAAACTACATGAT 73 63 1 GTCAAAATAA 0.721971 -95 GGCGAATTGGGGCAGAAATACGCCGTAGCC 78 23 0 GGCAGAAATA 0.69882 -113 TAAATGAATAGTCAAAATTAAGGTGAGCCA 86 184 1 GTCAAAATTA 0.695518 -46 GGACTAAAGGGACAGAAATAGATCGCCTAT 87 155 1 GACAGAAATA 0.803825 -146 ********** Masking position 6 Map Score: 8.12419 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 138 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405