AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00240_aquae_reg_100.orf -o00240_aquae_100.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: serA 27 D-3-phosphoglycerate dehydrogenase putative 27 putative protein Input sequences: #1 pyrD 125 dihydroorotase dehydrogenase #2 rpmJ 60 ribosomal protein L36 #3 secY 44 preprotein translocase SecY #4 nrdA 85 ribonucleotide reductase alpha chain #5 rpsO 58 ribosomal protein S15 #6 aldH2 300 aldehyde dehydrogenase #7 carA 300 carbamoyl phosphate synthetase small subunit #8 trxB 142 thioredoxin reductase #9 thy 300 thymidylate synthase complementing protein #10 pgi 33 glucose-6-phosphate isomerase #11 aq_759 152 hypothetical protein #12 aq_811 66 putative protein #13 dnaQ 230 DNA polymerase III epsilon subunit #14 pyrG 59 CTP synthetase #15 htrA 28 periplasmic serine protease #16 rpoD 38 RNA polymerase sigma factor RpoD #17 dnaG 66 DNA primase #18 nrdF 105 ribonucleotide reductase beta chain #19 mutL 32 DNA mismatch repair protein MutL #20 atpF1 33 ATP synthase F0 subunit b #21 dcd 300 deoxycytidine triphosphate deaminase #22 aq_1625 300 hypothetical protein #23 dnaX 178 DNA polymerase III gamma subunit #24 aq_1873 300 putative protein #25 rplM 45 ribosomal protein L13 #26 dnaN 24 DNA polymerase III beta chain #27 rpoB 212 RNA polymerase beta subunit #28 gatC 297 glutamyl-tRNA (Gln) amidotransferase subunit C #29 aq_2159 49 putative protein Motif number 1 TTAAATTTCAGGAGGTGGTATT 1 3 0 GGAGGTGGTA 0.925759 -123 TTTACTACTCGGCGGTGAAAATTTTTATAA 1 49 1 GGCGGTGAAA 0.791259 -77 TTAAAGGTTAGGAAGTTAAAATAAACTTG 1 107 1 GGAAGTTAAA 0.563535 -19 AAGTTCTCTCGGAGGTAGAAGA 3 3 0 GGAGGTAGAA 0.982081 -42 TTTCTTGAAGAGAGGTAGAATTCTCAAATC 4 66 1 AGAGGTAGAA 0.92056 -20 AAGAAAAGACGGAGGTATATGGGAAG 5 43 1 GGAGGTATAT 0.682037 -16 ACCCAGTCAAGGAAGCGGAATGAAAAGAAA 6 106 1 GGAAGCGGAA 0.569408 -195 TGTACCGTGTGGAGTTAAAACTTCTTCCAT 7 56 1 GGAGTTAAAA 0.880106 -245 TGTACCGTGTGGAGTTAAAACAGGTTTGAG 7 123 1 GGAGTTAAAA 0.880106 -178 TGTACCGTGTGGAGTTAAAACAAGGTTTTG 7 188 1 GGAGTTAAAA 0.880106 -113 TGTACCGTGTGGAGTTAAAACGCAGATTGT 7 253 1 GGAGTTAAAA 0.880106 -48 GAGATTTTTTAGAGGTGGGAACTTGGGTTT 8 25 0 AGAGGTGGGA 0.838189 -118 ACTGTCGCAAGGAGGTACGAAA 8 131 1 GGAGGTACGA 0.756817 -12 TCCTTATTAAGGAGGTGAAAGAATGAGCGA 9 204 0 GGAGGTGAAA 0.98159 -97 AACCTTAATAGGAGGTGGGTAAG 11 140 1 GGAGGTGGGT 0.769361 -13 TTTAGAGTTAGGAGGTAAGAGA 16 27 1 GGAGGTAAGA 0.958224 -12 ATTCATGAAAAGAGGTGTTATAATAAC 18 8 0 AGAGGTGTTA 0.431127 -98 ACAGGAATTTGGAAGTAGAAAATTCATGAA 18 29 0 GGAAGTAGAA 0.905232 -77 CCACCCTTCAGGAGGTAAACCAA 18 93 1 GGAGGTAAAC 0.806858 -13 ACGAAGTCAGAGAAGTAGAAGAAGAGTGCC 22 247 1 AGAAGTAGAA 0.668836 -54 TTACTAACCAGGAGGTGTAAA 23 2 0 GGAGGTGTAA 0.94138 -177 AATACCCTCCAGAGGTAATAA 23 168 1 AGAGGTAATA 0.711686 -11 ACGAACTGAGGGAGGTTAAAGTAATCAGAA 24 112 1 GGAGGTTAAA 0.881067 -189 TTGACGCAAAGGAAGTAATAAACTCTCTCA 24 163 1 GGAAGTAATA 0.670482 -138 TAAACTCGGAAGAGGTGAATGGG 25 33 1 AGAGGTGAAT 0.605518 -13 CTTTTGCTCAGGAGGCAGGAACGCTCTGTA 27 36 1 GGAGGCAGGA 0.765482 -177 TACCGGTTAGGGAATTGAAAAAGGAATACT 27 90 1 GGAATTGAAA 0.566001 -123 ATAAAAGAGGAGAGGTATAAAA 27 201 1 AGAGGTATAA 0.769103 -12 ********** Masking position 2 Map Score: 29.8327 Number of sites scoring better than the average of aligned sites = 909 Number in coding regions = 747 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 2 ATAACCTAAGTCCTTGCCTTTTTCAACT 2 9 0 TCCTTGCCTT 0.870467 -52 TCTTCTACCTCCGAGAGAAC 3 1 1 TCTTCTACCT 0.876525 -44 GGTTATTATTTCTTTTCATTCCGCTTCCTT 6 114 0 TCTTTTCATT 0.73626 -187 GTTCGCTCATTCTTTCACCTCCTTAATAAG 9 202 1 TCTTTCACCT 0.855674 -99 TCTTTTCTCTTCTTTCCCCT 10 1 1 TCTTTTCTCT 0.751759 -33 TCTTTTCTCTTCTTTCCCCTTATAATTTTT 10 11 1 TCTTTCCCCT 0.961707 -23 CATAAAAACCTCCTTCCCTTAAATT 13 6 0 TCCTTCCCTT 0.907309 -225 TCCCTCTCTTTTCCTTAAATTTTCCT 19 7 1 TCTTTTCCTT 0.97866 -26 TCTTCTCCTCCGCTAAACAA 20 24 0 TCTTCTCCTC 0.789963 -10 AAGTATAAACTCCTTGCCCTTATAAATGAG 21 101 0 TCCTTGCCCT 0.879371 -200 TCTTTTTGAGTCTTTTCCCTTCCTTTTCTA 21 241 1 TCTTTTCCCT 0.980295 -60 TAATCTTTTCCTTCCCCTCTTTT 22 4 1 TCTTTTCCTT 0.97866 -297 GGGGCACTCTTCTTCTACTTCTCTGACTTC 22 249 0 TCTTCTACTT 0.867442 -52 TATATATCCTTCTTCTACTTTACGGTGAAC 24 84 1 TCTTCTACTT 0.867442 -217 CTCCTTCTTTTCCTTTTCCTTTACA 27 6 1 TCTTTTCCTT 0.97866 -207 ********** Masking position 4 Map Score: 17.5017 Number of sites scoring better than the average of aligned sites = 836 Number in coding regions = 792 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 GTCTATTAAAACGGTGCAGGAACCGCATATTCCCTT 6 45 0 AGGTCAAACC 0.941375 -256 TTAACTCCACACGGTACATTAGAAACAGAACTCTCA 7 38 0 AGGTCAAGAC 0.996079 -263 TTAACTCCACACGGTACATTAGAAACAATAATCAAC 7 105 0 AGGTCAAGAC 0.996079 -196 TTAACTCCACACGGTACATTAGAAACTTCGTCAAGC 7 170 0 AGGTCAAGAC 0.996079 -131 TTAACTCCACACGGTACATTAGAAACCATCTGCAAC 7 235 0 AGGTCAAGAC 0.996079 -66 CTCTGCCCTGAGGGTCCAGAAGCCCCTCTTTCGGCA 13 58 0 AGGTCAAGCC 0.993096 -173 GTTGAACTCGAAGTTTCAGAAGACACCGATCTCAGA 13 156 1 AGTTCAAGAC 0.965947 -75 GTATTTTTTCAGTGTGCAATAGAACCTTTAGGGCTT 24 193 0 ATGTCAAGAC 0.965947 -108 * *** ** *** * Masking position 8 Map Score: 13.0919 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 7 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 AAGTAAACCAAACTATATTTTACTACTCGGCG 1 31 1 AATATTTTTA 0.585364 -95 CTCGGCGGTGAAAATTTTTATAAAAATTTCGT 1 56 1 AAATTTTATA 0.808922 -70 TTTTTATAAAAATTTCGTTATATATACATAAA 1 70 1 AATTCTTATA 0.922146 -56 CAAGTTTATTTTAACTTCCTAAC 1 113 0 AATTTTTTTA 0.85023 -13 CCTCCGAGAGAACTTTATTATATTAAAATCTT 3 18 1 AATTTTTATA 0.923614 -27 TTATTATATTAAAATCTTTTAAC 3 32 1 AAATCTTTAA 0.405361 -13 AAATTCCTTATAATATTTATTT 5 1 1 AATTCTTATA 0.922146 -58 TTTTTATTTTAATTTCTTTTTACAATCTGCGT 7 272 0 AATTCTTTTA 0.847583 -29 TTAACAAATTCTTTAAACCCAAGTTCC 8 6 1 AATTCTTAAA 0.805713 -137 GATGATTTTAAACATTCTTATATATTAAACTC 9 232 0 AAATTTTATA 0.808922 -69 AGAAAGTATTTTATAAGTTCCGTTT 9 286 0 AATATTTATA 0.750434 -15 AATTATTGCAAAAATTTTTAAAAGGAATATAA 11 94 1 AAATTTTAAA 0.597137 -59 GTTTACATATAATTTTATTATATTCCTTTTAA 11 111 0 AATTTTTATA 0.923614 -42 TTAAATAGAGAACTACATTTTAAACAGGAGGG 12 39 1 AATACTTTTA 0.580348 -28 CTAACTCTAAAAATTTATTAAAGTTAA 16 6 0 AATTTTTAAA 0.808922 -33 AAGTTTGTTATACTAATTCTCC 26 1 1 AATTTTTATA 0.923614 -24 ** *** ***** Masking position 8 Map Score: 12.7076 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 78 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 5 GTTTTAACTCCACACGGTACATTAGAAACA 7 47 0 CACACGGTAC 0.991035 -254 GTTTTAACTCCACACGGTACATTAGAAACA 7 114 0 CACACGGTAC 0.991035 -187 GTTTTAACTCCACACGGTACATTAGAAACT 7 179 0 CACACGGTAC 0.991035 -122 GTTTTAACTCCACACGGTACATTAGAAACC 7 244 0 CACACGGTAC 0.991035 -57 TCTTTTATGTCACACTTGACAACATCCGCT 22 173 0 CACACTTGAC 0.844126 -128 TGGGGGAGTTCACCCTGTCCCGCCGCAGGG 23 83 0 CACCCTGTCC 0.879585 -96 TAGGACCCTGCGCACGGGACGGCGGGCTTA 23 133 0 CGCACGGGAC 0.963495 -46 TAGCTTTCTCCACACTTTCCTCTTTGAGTA 24 226 0 CACACTTTCC 0.844126 -75 GAGGCAGGAACGCTCTGTACGTAAATGGAA 27 47 1 CGCTCTGTAC 0.831322 -166 ********** Masking position 5 Map Score: 12.3 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 16 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 TGACTGGGTACTGACAGCTCCTCACAGGATTTCCGTCTATTAAA 6 71 0 CTCTCTCGCC 0.982879 -230 TAATAACCATCGAGGGAATTCCCGAAGAACACCCTGTTAAAAGG 6 136 1 CGGTCCAGCC 0.925876 -165 CTTCTTCCATGGGACGTATGCTTTCCGCAACGCCTTTCTTGAGA 9 13 1 GGCTCTCGCC 0.99272 -288 TATGTAGAGGGGATCTCTTACTCCCTGAAGGTCCTTCTTTTTGA 21 206 1 GGCTCTCGCC 0.992789 -95 TTCTACTTCTCTGACTTCGTCTTCCAGTCCTTCCGGGACTATCA 22 223 0 CTCGCTCGCC 0.922912 -78 GGACGGCGGGCTTACCCTTGCTCCCTTTCGGGCCTGGGGGAGTT 23 103 0 CTCTCTCTCC 0.833766 -76 GTGGGTCGCGGGTTCGAGTCCCGCCCGGCTCACCATATAACTAT 28 71 0 GGCTCCCGCC 0.995458 -227 CTTAAAAGGCCGTTGCTCTACCAACTGAGCTACCGGCTCTTAGC 28 117 1 CGGTCCCGCC 0.993087 -181 GGAGGTCGGGGGTTCGAGTCCCCTCCGCTCCACCAGTTGAGCTG 28 160 0 GGCTCCCGCC 0.995462 -138 CATGCCATATCGGCGCTCTCCCAGCTGAGCTACCGCCCCTACTG 28 206 1 CGGTCCCGCC 0.992324 -92 ** * * ** * * ** Masking position 11 Map Score: 12.39 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 38 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 ATAGAAAATTGCATAGCTTAGAGGGAACATATAGATG 8 59 0 GAAGTAGGAA 0.785043 -84 CTCCTTCTCAAGAAAGGCGTTGCGGAAAGCATACGTC 9 25 0 AAAGGGGGAA 0.971053 -276 TTGAAGCGAGGAAGAAAGCAGATGGAAGTCTCTTAGG 9 115 1 GAAACAGGAA 0.771787 -186 GACCCTCAGGGCAGAGCCGTTGAGGAGATGTTAAAGG 13 78 1 GAAGGGGGAG 0.902127 -153 CAGAATTGGCATAGAAAAGGAAGGGAAAAGACTCAAA 21 245 0 AAAAGAGGAA 0.947625 -56 AAGATTTATGAAAAAGAGGGGAAGGAAAAGATTA 22 8 0 AAAGGAGGAA 0.966621 -293 AGGTTTACAAGAACAGGGGAGACGGAATAGCGGATGT 22 145 1 GAAGGAGGAA 0.978881 -156 GTCAAGTGTGACATAAAAGACGAGGAAGATCACTGCT 22 183 1 AAAAGGGGAA 0.954461 -118 TTCAACGATAATAGAACCGCTGGGGCACTCTTCTTCT 22 263 0 AAAAGGGGCA 0.797858 -38 AAAGTAATCAGAAAAGCCGAAAAGGAACATTCTTTTG 24 129 1 GAAGGAGGAA 0.978881 -172 TGCCTCCTGAGCAAAAGTGTAAAGGAAAAGGAAAAGA 27 16 0 GAAAGAGGAA 0.966621 -197 TTTAAGAAACATAAAAGAGGAGAGGTATAAAA 27 191 1 AAAAGGGGTA 0.727006 -22 * * ** * * **** Masking position 5 Map Score: 9.24507 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 212 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 TTCGGATGCGGTAAGGGAATATGCGGTTCCT 6 33 1 GTAAGGGAAA 0.767157 -268 GAAGCGGAATGAAAAGAAATAATAACCATCG 6 117 1 GAAAAGAAAA 0.797468 -184 TTGATTTTGTGAAATGGAAGAAGTTTTAACT 7 68 0 GAAATGGAAA 0.873804 -233 CAAAAATTTTTAAAAGGAATATAATAAAATT 11 102 1 TAAAAGGAAA 0.950694 -51 TGAGGAGATGTTAAAGGAAAACGGCTTTAAC 13 98 1 TTAAAGGAAA 0.860924 -133 ATAAGGAAAATTTAAGGAAAAGAGAGGGA 19 9 0 TTTAAGGAAA 0.55837 -24 CGGATAAGGAAAATTTAAGGAAA 19 20 0 GATAAGGAAA 0.924299 -13 AATTGGCATAGAAAAGGAAGGGAAAAGACTC 21 248 0 GAAAAGGAAG 0.904112 -53 GACCTCCTTTGAAAAAGAAAAAAGATTTATG 22 35 0 GAAAAAGAAA 0.797468 -266 CAGAAAAGCCGAAAAGGAACATTCTTTTGAC 24 137 1 GAAAAGGAAA 0.983547 -164 AAGTGTAAAGGAAAAGGAAAAGAAGGAG 27 8 0 GAAAAGGAAA 0.983547 -205 TAGGGAATTGAAAAAGGAATACTTGACAGTG 27 97 1 AAAAAGGAAA 0.854239 -116 AACCTTCATTTAAAAGGATTATAATTTCTAT 28 255 0 TAAAAGGATA 0.672336 -43 ********* * Masking position 4 Map Score: 10.2413 Number of sites scoring better than the average of aligned sites = 874 Number in coding regions = 799 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 9 TTATTATTACCCTTACGAGCTTCATAAAAA 13 28 0 CCTTACGAGC 0.843506 -203 GGCTTCTGGACCCTCAGGGCAGAGCCGTTG 13 70 1 CCCTCAGGGC 0.969867 -161 AAAAGAAGGACCTTCAGGGAGTAAGAGATC 21 217 0 CCTTCAGGGA 0.967476 -84 GTCTTCCAGTCCTTCCGGGACTATCATCCA 22 219 0 CCTTCCGGGA 0.979068 -82 ACCCTTGCTCCCTTTCGGGCCTGGGGGAGT 23 104 0 CCTTTCGGGC 0.983983 -75 TGCAATAGAACCTTTAGGGCTTTGAGAGAG 24 185 0 CCTTTAGGGC 0.97504 -116 ********** Masking position 4 Map Score: 3.68932 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 73 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 10 CTTAAATTTCAGGAGGTGGTATT 1 4 0 AGGAGGTGGT 0.968381 -122 AACTGTCGCAAGGAGGTACGAAA 8 130 1 AGGAGGTACG 0.919148 -13 AAACCTTAATAGGAGGTGGGTAAG 11 139 1 AGGAGGTGGG 0.973675 -14 CATTTTAAACAGGAGGGGCTAAA 12 54 1 AGGAGGGGCT 0.993372 -13 ATAATGCCGAAAGAGGGGCTTCTGGACCCT 13 54 1 AAGAGGGGCT 0.951088 -177 GAAAATAAATAGGAGGGGCTTGA 24 288 1 AGGAGGGGCT 0.993372 -13 CTATTCTGTCAGTAGGGGCGGTAGCTCAGC 28 229 0 AGTAGGGGCG 0.959153 -69 ********** Masking position 4 Map Score: 8.06231 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 32 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 11 TTCCGCTATTGTGGAGGTTCGGT 2 48 1 GGGAGGTCGG 0.973948 -13 GACTTACCGGGACGAAGTTCGGATGCGGTAAG 6 16 1 GCGAAGTCGG 0.958765 -285 ACCTTAATAGGAGGTGGGTAAG 11 141 1 GGGTGGTAAG 0.788369 -12 CTTTAATTTTGCCATGGCTCAGACCTCCTTTG 22 55 0 GCATGGTCAG 0.551348 -246 CATAAAAGACGAGGAAGATCACTGCTGGATGA 22 194 1 GGGAAGTCAC 0.89998 -107 TTTCGGGCCTGGGGGAGTTCACCCTGTCCCGC 23 90 0 GGGGAGTCAC 0.915725 -89 CTAAAAGTCCGCCGAAGGTAGGATTACTTACT 24 35 0 GCGAAGTAGG 0.74631 -266 GGCCTTTTAAGCCGTGGGTCGCGGGTTCGAGT 28 96 0 GCGTGGTCGC 0.940529 -202 CTGCTAAGAGCCGGTAGCTCAGTTGGTAGAGC 28 131 0 CGGTAGTCAG 0.900438 -167 AGCAGCTCAACTGGTGGAGCGGAGGGGACTCG 28 158 1 CGGTGGGCGG 0.844081 -140 GATATGGCATGTCGGAGGTCGGGGGTTCGAGT 28 185 0 GCGGAGTCGG 0.96561 -113 GGTAGCTCAGCTGGGAGAGCGCCGATATGGCA 28 208 0 CGGGAGGCGC 0.666434 -90 GTCAGTAGGGGCGGTAGCTCAGCTGGGAGAGC 28 220 0 GGGTAGTCAG 0.966542 -78 * ***** **** Masking position 7 Map Score: 5.03852 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 245 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 12 ATACTAAGATATTCCGCTATTGTGGAGGTTC 2 37 1 ATTCCCTATT 0.88885 -24 TTTGAGAATTCTACCTCTCTTCAAGAAAATT 4 63 0 CTACCCTCTT 0.758382 -23 CTTCCCATATACCTCCGTCTT 5 48 0 CTTCCATATA 0.550519 -11 AGTGCATAGGCTTCCACTATTTGTCCGGGCT 6 220 0 CTTCCCTATT 0.975709 -81 AAAAATCTCTCTTCATCTATATGTTCCCTCT 8 46 1 CTTCACTATA 0.787329 -97 CATCTGCTTTCTTCCTCGCTTCAACCGCTGC 9 108 0 CTTCCCGCTT 0.937066 -193 GACTTTGTCCCATACACTATTTTGCTAAAGA 11 32 0 CATACCTATT 0.459278 -121 TCTCGTAATCCTCTATTAACGGGTTGA 13 214 0 AATCCCTATT 0.719664 -17 CTCTCGGAAACTTCCCCGATAACTCCTCAAA 21 40 1 CTTCCCGATA 0.903729 -261 TAATCTTTTCCTTCCCCTCTTTTTCATAAAT 22 11 1 CTTCCCTCTT 0.967208 -290 CACTTGACAACATCCGCTATTCCGTCTCCCC 22 160 0 CATCCCTATT 0.928034 -141 TCTTCGAGTTCTTCAACGATAATAGAACCGC 22 280 0 CTTCACGATA 0.651435 -21 CCCATTCACCTCTTCCGAGTTTAA 25 32 0 ATTCACTCTT 0.538971 -14 ***** ***** Masking position 10 Map Score: 7.1294 Number of sites scoring better than the average of aligned sites = 498 Number in coding regions = 469 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 13 TTAATATAATAAAGTTCTCTCGGAGGTAGAA 3 13 0 AAAGTCTCTC 0.968551 -32 AAAATGCTGTCTTATGAATAA 4 1 1 AAAATCTGTC 0.857964 -85 GTTAATAGAAAAAGCTCTCGGTTCTTCTG 7 9 1 AAAAACTCTC 0.969155 -292 TACATTAGAAACAGAACTCTCAGAAGAACCG 7 29 0 ACAGACTCTC 0.891069 -272 CTTTACCTCAAAAGTCCTCTCAAACCTGTTT 7 140 0 AAAGTCTCTC 0.968551 -161 CCCACCTCTAAAAAATCTCTCTTCATCTATA 8 36 1 AAAAACTCTC 0.969155 -107 CGGAACTTATAAAATACTTTCT 9 289 1 AAAATCTTTC 0.802973 -12 CAAAGGAAGTAATAAACTCTCTCAAAGCCCT 24 169 1 AATAACTCTC 0.849189 -132 ***** ***** Masking position 1 Map Score: 3.50891 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 54 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 14 AAGGTTAGGAAGTTAAAATAAACTTG 1 110 1 AGTTAAAATA 0.668494 -16 AAGAACACCCTGTTAAAAGGGCATGGATTG 6 160 1 TGTTAAAAGG 0.683391 -141 TACCGTGTGGAGTTAAAACTTCTTCCATTT 7 58 1 AGTTAAAACT 0.523924 -243 TACCGTGTGGAGTTAAAACAGGTTTGAGAG 7 125 1 AGTTAAAACA 0.896218 -176 TACCGTGTGGAGTTAAAACAAGGTTTTGAA 7 190 1 AGTTAAAACA 0.896218 -111 TACCGTGTGGAGTTAAAACGCAGATTGTAA 7 255 1 AGTTAAAACG 0.853773 -46 TGGGAACTTGGGTTTAAAGAATTTGTTAA 8 10 0 GGTTTAAAGA 0.44868 -133 TATATCAATATGTTAAAAGATAGAAAATTG 8 85 0 TGTTAAAAGA 0.764746 -58 TTTTTAGATGATTTTAAACATTCTTATATA 9 240 0 ATTTTAAACA 0.675768 -61 TTGCAAAAATTTTTAAAAGGAATATAATAA 11 99 1 TTTTAAAAGG 0.544704 -54 GTAGTTCTCTATTTAAAATATTCACTAACT 12 25 0 ATTTAAAATA 0.527799 -42 AGAGAACTACATTTTAAACAGGAGGGGCTA 12 45 1 ATTTTAAACA 0.675768 -22 ACCTCTTCCGAGTTTAAAGCAAGATTGTAA 25 19 0 AGTTTAAAGC 0.660866 -27 TTTGGTTTAAATTTAAAAGATCAGTTAATG 27 134 1 ATTTAAAAGA 0.878864 -79 TGACAGCAAGATTTAAAAGCTATATACTAA 28 32 0 ATTTAAAAGC 0.715462 -266 TGAAACCTTCATTTAAAAGGATTATAATTT 28 259 0 ATTTAAAAGG 0.827907 -39 GGGCGTATATATTTTAAAGAC 29 2 0 ATTTTAAAGA 0.757789 -48 ********** Masking position 6 Map Score: 7.99854 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 = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 15 CGGTACATTAGAAACTTCGTCAAGCTTTAC 7 165 0 GAAACTTCGT 0.949272 -136 GGTGTCTTCTGAAACTTCGAGTTCAACAAC 13 153 0 GAAACTTCGA 0.881038 -78 ACTTGTCCGTTAAACCTCGTTGTAGGATAA 14 31 1 TAAACCTCGT 0.975036 -29 CCTGTTCTTGTAAACCTCGGGAACTCTATC 22 132 0 TAAACCTCGG 0.958177 -169 TTAATAAATATAAACCTCGTGAAATTTCCT 23 49 0 TAAACCTCGT 0.975036 -130 ********** Masking position 4 Map Score: 0.529166 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 52 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701