AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00620_synecho_reg_100.orf -o00620_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 Purged sequences: slr0361 26 hypothetical protein. Input sequences: #1 sll0712 112 cysM; cysteine synthase. [EC:4.2.99.8] #2 slr1097 57 hypothetical protein. #3 slr1098 67 hypothetical protein. #4 slr1099 300 ubiX; 3-octaprenyl-4-hydroxybenzoate carboxy-lyase. [EC:4.1.1.-] #5 sll1019 60 gloB; probable hydroxyacylglutathione hydrolase (glyoxalase II). #6 sll1018 119 pyrC; dihydroorotase. [EC:3.5.2.3] #7 sll0990 28 formaldehyde dehydrogenase. [EC:1.2.1.1] #8 tRNA-Arg-2 300 tRNA-Arg. #9 sll1298 271 clcD; dienelactone hydrolase. [EC:3.1.1.45] #10 sll1275 187 pykF; pyruvate kinase. [EC:2.7.1.40] #11 slr2132 57 pta; phosphotransacetylase. [EC:2.3.1.8] #12 sll2015 61 hypothetical protein. #13 sll2014 53 sfsA; sugar fermentation stimulation protein. #14 sll2013 159 hypothetical protein. #15 sll1564 300 leuA; alpha-isopropylmalate synthase. [EC:4.1.3.12] #16 sll0920 300 ppc; phosphoenolpyruvate carboxylase. [EC:4.1.1.31] #17 slr1934 123 pyruvate dehydrogenase E1 component, alpha subunit. [EC:1.2.4.1] #18 sll1841 210 odhB; dihydrolipoamide acetyltransferase component (E2) of pyruvate #19 slr0186 84 leuA; 2-isopropylmalate synthase (alpha-isopropylmalate synthase) #20 slr0359 95 hypothetical protein. #21 slr0360 37 hypothetical protein. #22 slr0362 300 hypothetical protein. #23 sll0336 113 accD, zfpA; acetyl-coenzyme A carboxylase carboxyl transferase #24 slr0381 300 gloA; probable lactoylglutathione lyase (methylglyoxalase) #25 slr0435 229 accB; biotin carboxyl carrier protein of acetyl-CoA carboxylase. #26 sll0891 37 citH; 2-ketoacid dehydrogenase (malate dehydrogenase, lactate #27 ssl1690 300 hypothetical protein. #28 sll0542 245 acs; acetyl-coenzyme A synthetase. [EC:6.2.1.1] #29 slr0092 117 hisB; hypothetical protein. #30 sll0587 42 pyk1; pyruvate kinase 1. [EC:2.7.1.40] [SP:KPY1_SYNY3] #31 sll0586 300 hypothetical protein. #32 slr0301 261 ppsA; phosphoenolpyruvate synthase (pyruvate,water dikinase) (PEP #33 sll0728 300 accA; acetyl-CoA carboxylase alpha subunit. [EC:6.4.1.2] Motif number 1 GGCTGATGTAGGGGGAATTTCTGCCGCAAT 1 24 0 GGGGGAATTT 0.939792 -89 TCCTACCCCAGGGAGGATGGGCTGATGTAG 1 43 0 GGGAGGATGG 0.804557 -70 CTAGCCTAGGGGGGGAAATTTC 2 3 0 GGGGGAAATT 0.916652 -55 TCGGCGGCTGTGGGCAAAGTTTGGCATTGC 4 99 0 TGGGCAAAGT 0.652291 -202 AAATAGTTGGGGGACAAAGGCTTTAGTGAT 4 185 0 GGGACAAAGG 0.88887 -116 CGGCAAGGTTGGGGGATTTGGACTTACACT 4 227 1 GGGGGATTTG 0.930786 -74 TAGGATTTTAGGGGGATTTTTGTGCCGTCG 6 77 1 GGGGGATTTT 0.827236 -43 TTTTAACCTCGGGGGAACGACGGCACAAAA 6 94 0 GGGGGAACGA 0.640803 -26 GAGCAACAGATGGGGGCTTGCTGACATCAT 8 146 0 TGGGGGCTTG 0.464217 -155 GAATATTTCCGGGGGACAGGGAAAGGATAG 8 221 0 GGGGGACAGG 0.982938 -80 CAAAAAATATGGGAGAATGGAATTGAGTAG 8 274 1 GGGAGAATGG 0.962342 -27 GGCTGGGCTTTGGGCAATTTTTCCCAATAG 10 35 0 TGGGCAATTT 0.524271 -153 GCTGAAATTAGGGGCAGTTAAATATAATAG 10 163 0 GGGGCAGTTA 0.52103 -25 ACTGAAACTAGGGAGATAGTCTATTTTAAC 12 26 0 GGGAGATAGT 0.662917 -36 TTCACCGTTTGGGAGAATGGAATAGTTAAC 17 79 0 GGGAGAATGG 0.962342 -45 TATGCTGGGGGAGCGGCGCAATACGT 17 108 0 GGGGGAGCGG 0.915767 -16 ATTTGTTCGGGGACAGTGGCGATCGCCGG 23 95 0 GGGACAGTGG 0.868824 -19 GCGAGTTGATGGGGGAAAGTACAAAACTTG 24 40 0 GGGGGAAAGT 0.96373 -261 CAGTAAGTTTGGGGGACTGGCAAGACCTGT 24 78 1 GGGGGACTGG 0.987917 -223 GTTTTTGTTAAGGGGACAGGTCTTGCCAGT 24 93 0 AGGGGACAGG 0.621326 -208 CCCCAGTATTGGGGGATTTAGGGGGCAGAA 24 164 0 GGGGGATTTA 0.562842 -137 CCCCAATACTGGGGGACTTTGACTTAGTTT 24 180 1 GGGGGACTTT 0.92337 -121 CCCAAACTTGGGGGGCCAGGGGGGCTTTTC 24 213 1 GGGGGCCAGG 0.775876 -88 AAATGATAGGGGGGGGGTTTACCGAAGTTC 25 171 1 GGGGGGGTTT 0.594657 -59 TGCAAACTTCGGGGCAAAGGACATTTTAAA 25 203 1 GGGGCAAAGG 0.970718 -27 CCCTAGGGGTGGGGGAATTTTTTAGGGTTT 27 82 0 GGGGGAATTT 0.939792 -219 GGGGAATCACTGGGGAAAGTCTGGGGAATG 27 184 1 TGGGGAAAGT 0.80854 -117 GGGGAAAGTCTGGGGAATGGCCTGGGGAGA 27 195 1 TGGGGAATGG 0.943926 -106 TGCCCTCGTTGGGAGACTGGGAAATTAACT 27 276 0 GGGAGACTGG 0.951755 -25 CCGGGTTAATTGGACAGTGGGGAAAAGATC 28 70 0 TGGACAGTGG 0.51283 -176 GTTACAAATCTGGGGAAAGGGGAAAAATTT 28 172 1 TGGGGAAAGG 0.922243 -74 GGTCACAGGAGGGACACTTGT 29 2 0 GGGACACTTG 0.783887 -116 GGGTAAGGCTGGGGCAGTTTGATCAACTCC 29 84 0 GGGGCAGTTT 0.801808 -34 CTGCTCCCCAGGGGGAAAAGTGTGACGCCA 31 65 0 GGGGGAAAAG 0.738742 -236 GTTGGGACGGGGGGCATAGGGTTTTTGCCG 31 184 1 GGGGCATAGG 0.910469 -117 GCACCACCCAGGGACAAATGAAAGACCCAA 33 108 0 GGGACAAATG 0.768014 -193 ********** Masking position 3 Map Score: 42.194 Number of sites scoring better than the average of aligned sites = 4999 Number in coding regions = 4368 Number in noncoding regions = 631 Number of orfs with sites within 600 bp upstream = 532 Fraction of orfs with sites within 600 bp upstream = 0.0854481 Motif number 2 AACATTATCTGCCAACGCCGGGAAAAACGT 9 89 0 GCCAACGCCG 0.937162 -183 GCCGACAGAAGCGATCGCCGTTCTCAGACA 9 197 1 GCGATCGCCG 0.997294 -75 ATTATCCGCCACGATCGCCGTTTCAGTTGC 10 91 0 ACGATCGCCG 0.973066 -97 TCCCTCACCATCCATCGCCC 15 291 1 TCCATCGCCC 0.944792 -10 GACCATCTAGGCGATCGCCCAAAGGAAAAT 18 73 0 GCGATCGCCC 0.994083 -138 TGATCCCCAGGCGATCGCCGCTTTTTTTAA 22 160 1 GCGATCGCCG 0.997294 -141 CCCCGCTTTGGCGATCGCCGGGTTGTCAGG 23 24 0 GCGATCGCCG 0.997294 -90 GGGGACAGTGGCGATCGCCGGGGTAATCCA 23 86 0 GCGATCGCCG 0.997294 -28 TTCTGAGTACCCGATCGCCGATTGTTTTTG 24 116 0 CCGATCGCCG 0.989954 -185 GGCCGCTGTGGCGATCGCCTTCTATGATAA 25 27 1 GCGATCGCCT 0.969876 -203 TATTTTTCTGGCGATCGCCGCCTGGGGAAT 27 31 0 GCGATCGCCG 0.997294 -270 TTACACGCAGCCCATAGCCCATTCACTCGG 28 22 0 CCCATAGCCC 0.6821 -224 TCTTCTATCCTAGATCGCCCCCAGGGTAAA 28 117 1 TAGATCGCCC 0.71699 -129 TTTGATCAACTCCATAGCCGGTTTGGATAA 29 67 0 TCCATAGCCG 0.813414 -51 ********** Masking position 4 Map Score: 38.1982 Number of sites scoring better than the average of aligned sites = 6510 Number in coding regions = 5938 Number in noncoding regions = 572 Number of orfs with sites within 600 bp upstream = 366 Fraction of orfs with sites within 600 bp upstream = 0.0587857 Motif number 3 TAGGTTATCCTACCCCAGGGAGGATGGGCT 1 50 0 TACCCCAGGG 0.805542 -63 GAAATTTCCCCCCCTAGGCTAGGGGCCGG 2 10 1 CCCCCTAGGC 0.474082 -48 TAGGACGGACTAACCCCGGCCCCTAGCCTA 2 25 0 TAACCCCGGC 0.909859 -33 TCCTTTCCCTGTCCCCCGGAAATATTCCAT 8 224 1 GTCCCCCGGA 0.655274 -77 TTCATTACGTTACCCCTGGTTTTGACGGGA 14 24 1 TACCCCTGGT 0.421737 -136 CAGCAAACCTCACCCCTGGAATAAAAGGAA 14 128 1 CACCCCTGGA 0.872529 -32 TTTAAAATTTTTGCCCAGGAATAGTAAAAA 15 223 1 TTGCCCAGGA 0.658152 -78 TACCTTCGTCAAACCCTGGAAACTTTAGCT 16 30 1 AAACCCTGGA 0.493693 -271 TGTCTTCTTCCTCCCCCTGCTCCAGGGGTT 16 132 1 CTCCCCCTGC 0.721637 -169 GGCAGAAAAAAACCCCTGGAGCAGGGGGAG 16 142 0 AACCCCTGGA 0.757017 -159 CCTCACTCCGCATCCCAGGCTACAGCCAGC 16 199 0 CATCCCAGGC 0.486289 -102 TATTGCGCCGCTCCCCCAGCATA 17 111 1 CTCCCCCAGC 0.721637 -13 TCCTTAACTAACCCCCCGGCAGAAATCTGA 18 112 1 ACCCCCCGGC 0.965787 -99 CGGTGACAGTTACGCCAGGCTAAGTCGGAT 19 60 0 TACGCCAGGC 0.780176 -25 ATTATGGCTGATCCCCAGGCGATCGCCGCT 22 152 1 ATCCCCAGGC 0.941483 -149 TGTAGCCCTGACAACCCGGCGATCGCCAAA 23 18 1 ACAACCCGGC 0.195504 -96 GTATTCTGGATTACCCCGGCGATCGCCACT 23 80 1 TTACCCCGGC 0.937457 -34 GTTTGAAAAGCCCCCCTGGCCCCCCAAGTT 24 217 0 CCCCCCTGGC 0.972427 -84 TCCACCATCAACACCCCGGAGGGTGCC 26 21 1 ACACCCCGGA 0.734405 -17 TTTTCTGGGATTCCCCAGGCGGCGATCGCC 27 22 1 TTCCCCAGGC 0.967365 -279 AGCGGATTTTATCCCCAGGAGGTTAAGGTT 27 149 0 ATCCCCAGGA 0.834313 -152 CCCCAGGCCATTCCCCAGACTTTCCCCAGT 27 192 0 TTCCCCAGAC 0.410409 -109 TGGCTAGTTTCTCCCCAGGCCATTCCCCAG 27 204 0 CTCCCCAGGC 0.972488 -97 CCTCTGCTGTTTACCCTGGGGGCGATCTAG 28 126 0 TTACCCTGGG 0.638843 -120 CCTGAAACTGCCGCCCTGGAGCAAAGCCAG 29 30 1 CCGCCCTGGA 0.696113 -88 GCCCTGGAGCAAAGCCAGGAAAAGTTTATC 29 42 1 AAAGCCAGGA 0.158745 -76 GTTGATCAAACTGCCCCAGCCTTACCCCTA 29 87 1 CTGCCCCAGC 0.349806 -31 GTCACACTTTTCCCCCTGGGGAGCAGATAA 31 69 1 TCCCCCTGGG 0.859894 -232 CACACCACACTCCGCCTGGATGATGTTCGG 31 110 0 TCCGCCTGGA 0.622025 -191 ATACGGAACTCCCCACCGGCAAAAACCCTA 31 200 0 CCCCACCGGC 0.592905 -101 TTAAAGGGGCTTCGCCCGGCAAAACC 32 7 0 TTCGCCCGGC 0.894903 -255 TGTCAAAGACTTGCCCTGGCAATCATCCAA 32 90 1 TTGCCCTGGC 0.849664 -172 TAAAGGTTTTTAACCCTTGCCCAAAATGAA 32 124 1 TAACCCTTGC 0.206696 -138 CTATCTAGCACCACCCAGGGACAAATGAAA 33 115 0 CCACCCAGGG 0.713732 -186 TCCTTCACCCTTAGCCCGGCTAATCCATCC 33 275 1 TTAGCCCGGC 0.727151 -26 ********** Masking position 5 Map Score: 26.9068 Number of sites scoring better than the average of aligned sites = 5938 Number in coding regions = 5463 Number in noncoding regions = 475 Number of orfs with sites within 600 bp upstream = 454 Fraction of orfs with sites within 600 bp upstream = 0.07292 Motif number 4 GCTTTTCTGGCGGCAATGCCAAACTTTGCC 4 87 1 CGGCAATGCC 0.722024 -214 TCTAGCTTAACGGCTAATCCCAACCATGGC 4 145 1 CGGCTAATCC 0.842576 -156 TCCCTCTGGGAGCCTAAATCCAGCAGACGT 9 120 1 AGCCTAAATC 0.559469 -152 TTTGGAGGGCAAAATCAAGGTAATTC 11 7 1 GGGCAAAATC 0.852051 -51 CCATTGATCCCGTCAAAACCAGGGGTAACG 14 31 0 CGTCAAAACC 0.930378 -129 TCCTCTCCGTGGCCAAATCCTGGAACTTAT 15 50 1 GGCCAAATCC 0.679818 -251 AAATTTGGTCAGCCAAAGTCTTGATACCAA 15 181 1 AGCCAAAGTC 0.743287 -120 CCACTACCTTCGTCAAACCCTGGAAACTTT 16 26 1 CGTCAAACCC 0.735931 -275 GGACACTAAAAGCCAAAATCACCGCAACCA 16 94 0 AGCCAAAATC 0.760957 -207 CAGTTACGCCAGGCTAAGTCGGATTAATTG 19 54 0 AGGCTAAGTC 0.716998 -31 GGGGAAACTAAGTCAAAGTCCCCCAGTATT 24 184 0 AGTCAAAGTC 0.692209 -117 CTATCCCTAGCGTCAAAACCCTAAAAAATT 27 67 1 CGTCAAAACC 0.930378 -234 CTCCCAACGAGGGCAAAACC 27 291 1 GGGCAAAACC 0.929069 -10 GGTTCTCCGTCAAAGTCTTTAATGGCT 28 229 0 CGTCAAAGTC 0.842374 -17 AACTCCCCACCGGCAAAAACCCTATGCCCC 31 194 0 CGGCAAAAAC 0.748318 -107 GGGCTTCGCCCGGCAAAACC 32 1 0 CGGCAAAACC 0.974184 -261 TTGCCGACTAAGGCTAAACCATAAATACAG 32 227 0 AGGCTAAACC 0.863672 -35 ACCCTTAGCCCGGCTAATCCATCCCTAGTT 33 281 1 CGGCTAATCC 0.842576 -20 ********** Masking position 6 Map Score: 14.8993 Number of sites scoring better than the average of aligned sites = 1396 Number in coding regions = 1278 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 5 CCCCCTACATCAGCCCATCCTCCCTGGGGTA 1 39 1 CAGCCCACCT 0.796749 -74 CCTGTTAGGTTATCCTACCCCAGGGAGGATG 1 54 0 TATCCTACCC 0.817738 -59 CCCCGCTTGACCGCCTTACCTCAACTCAGC 1 93 1 CCGCCTTCCT 0.870912 -20 GCAAATAGGACGGACTAACCCCGGCCCCTAG 2 29 0 CGGACTACCC 0.567818 -29 GGCTTGCTGACATCATTACCCCGTTCCTTTT 8 131 0 CATCATTCCC 0.467328 -170 AGCTGTCAACTATCCTTTCCCTGTCCCCCGG 8 212 1 TATCCTTCCC 0.772376 -89 TTAACACCGAAATCCTAGCCCCAAAAAATAT 8 253 1 AATCCTACCC 0.878012 -48 GGAAATAATAACTCCTAGCCTATCTCAAAAT 9 242 0 ACTCCTACCT 0.728628 -30 AAATTGCCCAAAGCCCAGCCTACCATCGTTG 10 45 1 AAGCCCACCT 0.491672 -143 GGACAAAAATCCTGCTACCCTAATTCTAGAT 15 257 0 CCTGCTACCT 0.460186 -44 ACTACGGGATTATCCCTACCTCACTCCGCAT 16 216 0 TATCCCTCCT 0.357424 -85 GCCTATTTTTCCTCCTACCCCCTGTGC 17 7 0 CCTCCTACCC 0.971803 -117 GGATCTGGATAATCCTAACCCATTTTGACAT 18 44 1 AATCCTACCC 0.878012 -167 TGCTAAACCCCCTCCCATCCCC 19 2 0 CCTCCCACCC 0.947072 -83 GAAAAATATTCCTACTATCCCTAGCGTCAAA 27 53 1 CCTACTACCC 0.857011 -248 GGCCATTCCCCAGACTTTCCCCAGTGATTCC 27 186 0 CAGACTTCCC 0.758755 -115 CAAACTGCCCCAGCCTTACCCCTAACTAACT 29 93 1 CAGCCTTCCC 0.947604 -25 CTATGCCCCCCGTCCCAACCTGTACAATGAA 31 172 0 CGTCCCACCT 0.601707 -129 CGGGATGTCAAAGACTTGCCCTGGCAATCAT 32 85 1 AAGACTTCCC 0.43695 -177 CATTTTAACCCCTCCTTACCCTTGGAATTGA 32 177 1 CCTCCTTCCC 0.963052 -85 AAATACAGCCCCTTCTTTCCCGCTGGTTCAA 32 204 0 CCTTCTTCCC 0.579434 -58 ******* *** Masking position 9 Map Score: 17.2186 Number of sites scoring better than the average of aligned sites = 1572 Number in coding regions = 1329 Number in noncoding regions = 243 Number of orfs with sites within 600 bp upstream = 256 Fraction of orfs with sites within 600 bp upstream = 0.0411179 Motif number 6 GGTGTGTTGATTTTTAGTTAATTTTTAA 3 9 1 GATTTTTAGT 0.80295 -59 AACTTTGCTAGGATTTTAGGGGGATTTTTG 6 69 1 GGATTTTAGG 0.951861 -51 GATTTTAGGGGGATTTTTGTGCCGTCGTTC 6 80 1 GGATTTTTGT 0.92574 -40 ATTTGGGTGTGAATTTTTGTATCTTTCGCC 8 90 0 GAATTTTTGT 0.820791 -211 GGGATTATACGGTTTTTAGGCCATTGATCC 14 51 0 GGTTTTTAGG 0.912067 -109 TAGGGTAGCAGGATTTTTGTCCGTATCCCT 15 266 1 GGATTTTTGT 0.92574 -35 CGGTGATTTTGGCTTTTAGTGTCCTAGTCC 16 100 1 GGCTTTTAGT 0.866769 -201 CCTATCATTTGAGTTTTAGTGGAGCCATTT 25 151 0 GAGTTTTAGT 0.705034 -79 AGGAGGTTAAGGTTTTTAGGCTATTTCTTA 27 133 0 GGTTTTTAGG 0.912067 -168 TGGAATTTTAGTCCAACTTACT 30 31 0 GAATTTTAGT 0.88595 -12 TTTTTTAAAGGGATTTTTGGGGTGATTAGA 31 238 1 GGATTTTTGG 0.921001 -63 ********** Masking position 5 Map Score: 9.15336 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 143 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 AATGCCAAACTTTGCCCACAGCCGCCGACACTGG 4 101 1 TTGCCCACGG 0.978062 -200 GCTTTTTCATGGGGCCCACAAGCGGAATTAGTAG 9 164 1 GGGCCCACAG 0.976577 -108 AGCGGAATTAGTAGCCGACAGAAGCGATCGCCGT 9 184 1 GTGCCGACGG 0.97219 -88 CCCATCAAACTGTGCAGACTATTGGGAAAAATTG 10 17 1 TGGCAGACAG 0.852043 -171 TTTGTTTAACTGGGCCCACCGAGGAAATCGTCTT 13 26 0 TGGCCCACGG 0.994475 -28 TAGTAGATAGTGTGCCGACGGAGGGAGAATTCAA 15 115 0 TGGCCGACGG 0.993417 -186 AATGGAAAGCTGAGCCGACTGGTCGCCGACATAC 20 25 1 TGGCCGACGC 0.972944 -71 CCACCCCTAGGGTGCCCACGGCCCAGTCAGGGTT 27 100 1 GGGCCCACGC 0.975675 -201 TTTAATGGCTTGGGCCCAACGTTGATGATTGTCG 28 205 0 TGGCCCAAGG 0.934129 -41 TGGTGTTTATTTTGCCGACTAAGGCTAAACCATA 32 234 0 TTGCCGACAG 0.902527 -28 AGACCCAATCGGAGCACGCTGCAGGGTATGCACA 33 82 0 GGGCACGCGG 0.830028 -219 ** ****** * * Masking position 5 Map Score: 11.2127 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 252 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 CGGTCAAGCGGGGGTTAAAACCCTGTTAGGT 1 75 0 GGGGTAAAAC 0.772118 -38 CCTAGCCTAGGGGGGGAAATTTC 2 3 0 GGGGGAAATT 0.82153 -55 AGTTGGGTGGAGGGTAAGAATCTGTAGAACA 4 15 1 AGGGTAGAAT 0.456453 -286 GAAAATAGTTGGGGGACAAAGGCTTTAGTGA 4 186 0 GGGGGCAAAG 0.673842 -115 TCCGGATTCTGGGGGTTAACTGTACTTTTGG 6 28 0 GGGGGTAACT 0.751899 -92 TTAGGCTCCCAGAGGGAAAACATTATCTGCC 9 106 0 AGAGGAAAAC 0.552893 -166 TTTGGAGGGCAAAATCAAGGTAATT 11 5 1 GAGGGAAAAT 0.808734 -53 ATTTATTCGGAGAGTTAAAATAGACTATCTC 12 13 1 AGAGTAAAAT 0.387474 -49 GTGTGCCGACGGAGGGAGAATTCAAGCGACG 15 109 0 GGAGGAGAAT 0.883513 -192 TGGAGCAGGGGGAGGAAGAAGACAATGGACT 16 125 0 GGAGGAGAAG 0.720549 -176 ACAGGGGGTAGGAGGAAAAATAGGCAGTTAA 17 13 1 GGAGGAAAAT 0.947631 -111 GGGGGATTTAGGGGGCAGAATCAGACTTTAT 24 153 0 GGGGGAGAAT 0.960035 -148 CCCCAAGTTTGGGGGGAAACTAAGTCAAAGT 24 195 0 GGGGGAAACT 0.960035 -106 TTAACCTCCTGGGGATAAAATCCGCTAACTG 27 153 1 GGGGAAAAAT 0.842316 -148 GGAATGGCCTGGGGAGAAACTAGCCAAAAAT 27 208 1 GGGGAAAACT 0.691263 -93 GTCTCCCAACGAGGGCAAAACC 27 289 1 GAGGGAAAAC 0.589735 -12 CCATTCACTCGGAGGATAAATCT 28 3 0 GGAGGTAAAT 0.695393 -243 ATCTGGGGAAAGGGGAAAAATTTTTGCGACA 28 179 1 AGGGGAAAAT 0.920132 -67 TCAGGTCACAGGAGGGACACTTGT 29 4 0 GGAGGACACT 0.474484 -114 TCTGCTCCCCAGGGGGAAAAGTGTGACGCCA 31 65 0 AGGGGAAAAG 0.796605 -236 AGGGTAAGGAGGGGTTAAAATGCAGTCAATA 32 168 0 GGGGTAAAAT 0.908815 -94 ***** ***** Masking position 9 Map Score: 15.1482 Number of sites scoring better than the average of aligned sites = 2236 Number in coding regions = 1922 Number in noncoding regions = 314 Number of orfs with sites within 600 bp upstream = 293 Fraction of orfs with sites within 600 bp upstream = 0.0470607 Motif number 9 TGTAAAGATATGTAAAGGGAAATAATTAAA 3 34 0 TGTAAAGGGA 0.966431 -34 TTGCCACAATTTTAAAGGGATCAAGCCAAA 22 48 1 TTTAAAGGGA 0.947782 -253 TTTTTTATTATGTTAAGGGTCTTTATAAAG 22 95 1 TGTTAAGGGT 0.890037 -206 CGATTGTTTTTGTTAAGGGGACAGGTCTTG 24 98 0 TGTTAAGGGG 0.82602 -203 CAAAGGACATTTTAAAGGGACCT 25 217 1 TTTAAAGGGA 0.947782 -13 ATGGGCTGCGTGTAAAGGGTCCGATGTTTT 28 37 1 TGTAAAGGGT 0.956728 -209 TGTTAAGTTTTTTAAAGGGATTTTTGGGGT 31 231 1 TTTAAAGGGA 0.947782 -70 TCATCCAAAATTTAAAGGTTTTTAACCCTT 32 112 1 TTTAAAGGTT 0.608852 -150 ********** Masking position 5 Map Score: 5.76584 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 34 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 AACCACCTCCCGTCAGCTTTTCTGGCGGCAA 4 72 1 CGTCGCTTTT 0.938648 -229 CGCCCAGTGTCGGCGGCTGTGGGCAAAGTTT 4 107 0 CGGCGCTGTG 0.96072 -194 CGCCGACACTGGGCGGTTTTTCTCTAGCTTA 4 123 1 GGGCGTTTTT 0.813522 -178 TTTGGTCAGCTTTTTAAAATACTT 5 4 1 GGTCGCTTTT 0.963308 -57 TAGTTAAGGCCGTCTGCTTTTAAGCGGTGTT 10 135 0 CGTCGCTTTT 0.938648 -53 TGGGGGGCCAGGGGGGCTTTTCAAACACGCT 24 221 1 GGGGGCTTTT 0.853615 -80 GAAAAGATCAGGGCCGCTGTGGCGATCGCCT 25 16 1 GGGCGCTGTG 0.976728 -214 GCGTGTAAAGGGTCCGATGTTTTCTTGATCT 28 44 1 GGTCGATGTT 0.754788 -202 TATTTCTTTGCCTCTGCTGTTTACCCTGGGG 28 135 0 CCTCGCTGTT 0.705683 -111 CTTTGCTCCAGGGCGGCAGTTTCAGGTCACA 29 25 0 GGGCGCAGTT 0.894896 -93 TGAATTTATTGGGCAGCTTTGAGATGCCTTG 33 34 1 GGGCGCTTTG 0.969016 -267 **** ****** Masking position 10 Map Score: 7.05742 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 243 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 11 CCCTAGGCTAGGGGCCGGGGTTAGTCCGTC 2 22 1 GGGGCCGGGG 0.962735 -36 TTACAGTTGGGTGGAGGGTAAGAATCT 4 8 1 TGGGTGGAGG 0.890092 -293 GAAAAGCTGACGGGAGGTGGTTAATTGATA 4 64 0 CGGGAGGTGG 0.94895 -237 CAGTGCACATCGGGACTGGGCAAAAGAGCA 8 171 0 CGGGACTGGG 0.751557 -130 TGCCCTAATCTGGGAGGGGCATCGACAAAT 16 168 1 TGGGAGGGGC 0.965187 -133 GGGGATGGGAGGGGGTTTAGCAACA 19 6 1 TGGGAGGGGG 0.991478 -79 CTCAAATGATAGGGGGGGGGTTTACCGAAG 25 168 1 AGGGGGGGGG 0.898287 -62 GGGCACCCTAGGGGTGGGGGAATTTTTTAG 27 87 0 GGGGTGGGGG 0.976228 -214 TAACCCTGACTGGGCCGTGGGCACCCTAGG 27 105 0 TGGGCCGTGG 0.927916 -196 TTGTACAGGTTGGGACGGGGGGCATAGGGT 31 176 1 TGGGACGGGG 0.985465 -125 CATTTGTCCCTGGGTGGTGCTAGATAGAGC 33 118 1 TGGGTGGTGC 0.829825 -183 ********** Masking position 4 Map Score: 11.6219 Number of sites scoring better than the average of aligned sites = 626 Number in coding regions = 589 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 12 CTACATCAGCCCATCCTCCCTGGGGTAGGA 1 43 1 CCATCCTCCC 0.965382 -70 CAGATTCTTACCCTCCACCCAACTGTAA 4 9 0 CCCTCCACCC 0.94239 -292 CGGAAATATTCCATTAACACCGAAATCCTA 8 240 1 CCATTAACAC 0.867517 -61 CTACTCAATTCCATTCTCCCATATTTTTTG 8 274 0 CCATTCTCCC 0.936152 -27 GCCATTGATCCCGTCAAAACCAGGGGTAAC 14 32 0 CCGTCAAAAC 0.296741 -128 GTTAACTATTCCATTCTCCCAAACGGTGAA 17 79 1 CCATTCTCCC 0.936152 -45 GTACTTTCCCCCATCAACTCGCCAAATTTC 24 48 1 CCATCAACTC 0.941918 -253 CTTTTCTCCACCATCAACACCCCGGAGGGT 26 15 1 CCATCAACAC 0.925675 -23 AGCCCATAGCCCATTCACTCGGAGGATAAA 28 14 0 CCATTCACTC 0.95869 -232 ACGTAAGTTTCCGTTCACTCCTCACACCAC 31 132 0 CCGTTCACTC 0.908915 -169 CCAAAATGAACCATCCACTCTTAATATTGA 32 144 1 CCATCCACTC 0.977847 -118 ********** Masking position 4 Map Score: 8.94309 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 268 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 13 GGGGTTAAAACCCTGTTAGGTTATCCTACC 1 66 0 CCCTGTTAGG 0.744778 -47 GCTCGGTGCGCCATGGTTGGGATTAGCCGT 4 154 0 CCATGGTTGG 0.957542 -147 TAAAGCTCCGGCAAGGTTGGGGGATTTGGA 4 219 1 GCAAGGTTGG 0.657924 -82 AACGTTTTTCCCGGCGTTGGCAGATAATGT 9 88 1 CCGGCGTTGG 0.827078 -184 GCCCAGCCTACCATCGTTGGCCCTGTAAGC 10 57 1 CCATCGTTGG 0.700127 -131 GCTAAAGTTTCCAGGGTTTGACGAAGGTAG 16 29 0 CCAGGGTTTG 0.676974 -272 GATCGTTGACCCCGCTTTGGCGATCGCCGG 23 33 0 CCCGCTTTGG 0.921082 -81 CCCTGGCCCCCCAAGTTTGGGGGGAAACTA 24 204 0 CCAAGTTTGG 0.793113 -97 TTCTGCTTGACCCTGGTTCGAGATACCGTT 25 79 0 CCCTGGTTCG 0.880071 -151 GGTTTTGCCCTCGTTGGGAGACTGGGA 27 284 0 CCCTCGTTGG 0.956803 -17 CAACTCCATAGCCGGTTTGGATAAACTTTT 29 61 0 GCCGGTTTGG 0.833859 -57 CCCTGTATGGAAAAATATCG 31 1 1 CCCTGTATGG 0.760513 -300 TTTCATTTGTCCCTGGGTGGTGCTAGATAG 33 115 1 CCCTGGGTGG 0.922119 -186 ********** Masking position 2 Map Score: 7.03269 Number of sites scoring better than the average of aligned sites = 924 Number in coding regions = 848 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 14 TATCTTTACAAACCAATCGACGTA 3 54 1 ACCAACGACG 0.933528 -14 TTTTGGGTTGAGCCAATCAGCGC 6 2 0 ACCAACAGCG 0.933528 -118 AGCCGATGCAACTGAAACGGCGATCGTGGCGG 10 84 1 ATGAACGGCG 0.939761 -104 CGGAGGGAGAATTCAAGCGACGTTCAAGTGTG 15 99 0 ATCAACGACG 0.89852 -202 GAGAATCTTAAAAAAAGCGGCGATCGCCTGGG 22 165 0 AAAAACGGCG 0.754026 -136 CCCTTAACAAAAACAATCGGCGATCGGGTACT 24 109 1 AACAACGGCG 0.964852 -192 CCCATAGCCCATTCACTCGGAGGATAAATCT 28 10 0 ATCACCGGAG 0.771508 -236 CCCGAACATCATCCAGGCGGAGTGTGGTGTGA 31 109 1 ACCAGCGGAG 0.84266 -192 TACCCTTGGAATTGAACCAGCGGGAAAGAAGG 32 193 1 ATGAACAGCG 0.729502 -69 CAAATGAAAGACCCAATCGGAGCACGCTGCAG 33 92 0 ACCAACGGAG 0.958198 -209 * **** ***** Masking position 5 Map Score: 1.54494 Number of sites scoring better than the average of aligned sites = 406 Number in coding regions = 384 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 15 TTAATTTTTAATTATTTCCCTTTACATATC 3 28 1 ATTATTTCCC 0.947992 -40 GTGTTAATGGAATATTTCCGGGGGACAGGG 8 230 0 AATATTTCCG 0.670163 -71 TTGGCAGATAATGTTTTCCCTCTGGGAGCC 9 104 1 ATGTTTTCCC 0.825345 -168 GCTAGGAGTTATTATTTCCGGGTAGTTT 9 254 1 ATTATTTCCG 0.796643 -18 GGCTTTGGGCAATTTTTCCCAATAGTCTGC 10 30 0 AATTTTTCCC 0.928646 -158 GGATAATGAGAATATTTCCCTAACACCGCT 10 114 1 AATATTTCCC 0.904342 -74 AAACTTTAAAATTTTTGCCCAGGAATAGTA 15 219 1 ATTTTTGCCC 0.811596 -82 CAAAATAACGATTTTTTACCGGGGATGAAG 20 67 0 ATTTTTTACC 0.64292 -29 CAGTTAGCGGATTTTATCCCCAGGAGGTTA 27 154 0 ATTTTATCCC 0.744015 -147 TGTTTTCTTGATCTTTTCCCCACTGTCCAA 28 61 1 ATCTTTTCCC 0.825345 -185 TTGTCGCAAAAATTTTTCCCCTTTCCCCAG 28 181 0 AATTTTTCCC 0.928646 -65 TGATGTAGCCATTACTTCCCATAATTTTCT 32 52 1 ATTACTTCCC 0.75782 -210 ********** Masking position 1 Map Score: 6.9578 Number of sites scoring better than the average of aligned sites = 656 Number in coding regions = 566 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617