AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00561_bsub_reg_100.orf -o00561_bsub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.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 Input sequences: #1 glpQ 98 glycerophosphoryl diester phosphodiesterase #2 glpT 296 glycerol-3-phosphate permease #3 pssA 195 phosphatidylserine synthase #4 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #5 ycbD 29 similar to aldehyde dehydrogenase #6 phoD 278 phosphodiesterase/alkaline phosphatase D #7 lipA 162 lipase #8 ddlA 174 D-alanyl-D-alanine ligase A #9 phoB 300 alkaline phosphatase III #10 lipB 272 lipase #11 glpF 178 glycerol uptake facilitator #12 glpD 140 glycerol-3-phosphate dehydrogenase #13 phoA 300 alkaline phosphatase A #14 yhdW 233 similar to glycerophosphodiester phosphodiesterase #15 murG 122 UDP-N-acetylglucosamine-N-acetylmuramyl- (pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase #16 yluA 130 similar to hypothetical proteins #17 pgsA 300 phosphatidylglycerophosphate synthase #18 pksF 300 pksF #19 yphC 300 similar to hypothetical proteins #20 bfmBB 22 branched-chain alpha-keto acid dehydrogenase E2 subunit (lipoamide acyltransferase) #21 bfmBAA 73 branched-chain alpha-keto acid dehydrogenase E1 (2-oxoisovalerate dehydrogenase alpha subunit) #22 yqiS 124 similar to phosphate butyryltransferase #23 yqfF 78 yqfF #24 yqfC 56 yqfC #25 yqfB 24 yqfB #26 yqfA 21 yqfA #27 yqeZ 130 yqeZ #28 bltD 168 spermine/spermidine acetyltransferase #29 yraG 248 similar to spore coat protein #30 adhA 300 NADP-dependent alcohol dehydrogenase #31 msmR 217 transcriptional regulator (LacI family) #32 msmE 33 multiple sugar-binding protein #33 gbsA 198 glycine betaine aldehyde dehydrogenase #34 tpi 30 triose phosphate isomerase #35 pgk 300 phosphoglycerate kinase #36 yvfL 39 similar to maltodextrin transport system permease #37 yvfK 140 similar to maltose/maltodextrin-binding protein #38 tagD 300 glycerol-3-phosphate cytidylyltransferase #39 ywnE 242 similar to cardiolipin synthase #40 ywdH 167 alternate gene name: ipa-58r; similar to aldehyde dehydrogenase #41 aldX 142 aldehyde dehydrogenase Motif number 1 GATTTCTCCTCCTTATAGATAAGCACT 1 82 0 CCTCCTTATA 0.639391 -17 GTGTGGCGTGCCTCCTTTCCCGAAAAACAA 2 243 0 CCTCCTTTCC 0.944411 -54 GGCTTATTCGCCTTCTTTTCT 7 2 0 CCTTCTTTTC 0.928173 -161 GGCGAATAAGCCTTCTTTTTTTTGGCTTTT 7 20 1 CCTTCTTTTT 0.924997 -143 AATATCCTCCTTTTTTTGTAACAAA 7 148 0 CCTCCTTTTT 0.978632 -15 ATGTCACATCTCCTTTTCAATGCCATTT 8 9 1 TCTCCTTTTC 0.916768 -166 GTGTTCCCTTCCTCCCTTTTCTATAATAAG 10 85 0 CCTCCCTTTT 0.958417 -188 TACGTTTCCTCCTTGTTGTCACGGTAA 12 124 0 CCTCCTTGTT 0.861493 -17 GCCTCCTTTAATGTATTCCGT 13 290 0 CCTCCTTTAA 0.884325 -11 GATCTCGCCTCCTTTTTTGCTATTATA 14 8 1 CCTCCTTTTT 0.978632 -226 TTTCAGCGTTCCTTCTTTTAAAGAGCTGCC 17 52 0 CCTTCTTTTA 0.844675 -249 AGATGACTTTTCTTCCTTTTTATTTACAAT 17 229 0 TCTTCCTTTT 0.587559 -72 AAAAGCTCCATCTCCTTTTGGTCATTGCAA 19 46 0 TCTCCTTTTG 0.587844 -255 AGTACCCTTCCTTTCAATCCAGCCG 19 286 0 CCTTCCTTTC 0.866727 -15 GATTGTATCCTCCCTTACGTCT 20 5 0 CCTCCCTTAC 0.901405 -18 TCAAGCCCCTCCTTTATGCTTTTAAAA 21 57 0 CCTCCTTTAT 0.945467 -17 AGTGTTAGAACCTCCTTTCAAATCATACAC 24 11 1 CCTCCTTTCA 0.877294 -46 ACAAAAAGAACCCCCTTTCATCTCATGTGT 24 37 0 CCCCCTTTCA 0.65007 -20 CAGCGTTCTCCCTTCTTAGAGAGA 25 9 0 TCTCCCTTCT 0.651922 -16 GTGTATCCCTCCTTCCTTTTATAATAAGTG 27 106 0 CCTTCCTTTT 0.861238 -25 ACTACATTCTCCTTTTTTCTTATCCCG 28 152 0 TCTCCTTTTT 0.913134 -17 ATTGATGTAACCTCCTTTTATCAACGTTAC 29 229 0 CCTCCTTTTA 0.952819 -20 CCCATCACCCTTCCTTATTCGCTTACTT 31 9 1 CCTTCCTTAT 0.701455 -209 AGATCTGGGTTCCCCTTTATTTTTCCAACA 31 53 1 TCCCCTTTAT 0.508358 -165 CTTTTCCTCCTTATCATCGTGATGA 32 19 0 CCTCCTTATC 0.808184 -15 ACTGACCCTCTTTTCCTTTAGAAAA 33 6 1 CCCTCTTTTC 0.770522 -193 ATAAGCCTCCTTGACGTAAATAAAG 33 184 0 CCTCCTTGAC 0.71158 -15 ATAATCCTCCCCCTTTATTTGATGTTTC 39 9 1 CCCCCTTTAT 0.818344 -234 TCCGTTTCTCCTTTTTGTAAGGTATG 40 152 0 TCTCCTTTTT 0.913134 -16 TCATTTGCTTTCTTCTTTTCTCGGACCTAT 41 110 0 TCTTCTTTTC 0.74786 -33 ********** Masking position 7 Map Score: 36.1333 Number of sites scoring better than the average of aligned sites = 1085 Number in coding regions = 606 Number in noncoding regions = 479 Number of orfs with sites within 600 bp upstream = 544 Fraction of orfs with sites within 600 bp upstream = 0.0873755 Motif number 2 TAAAAAACGGATGTAAACGGCGTGTTGGAA 1 37 0 ATGTAAACGG 0.900801 -62 TCCGGAGCGAATGTAAACGGGTAATTTTCA 2 106 0 ATGTAAACGG 0.900801 -191 ATGATAATTTAAGAAAGCGCTATCATGATA 2 138 1 AAGAAAGCGC 0.942495 -159 CGGCCTCTATCTGTAAGCGCTTTTATTAAT 4 179 0 CTGTAAGCGC 0.943078 -48 ACAGGATATGCAGAAAACGCGTCATTCAGC 6 112 1 CAGAAAACGC 0.742356 -167 TGTGAACTGATTGTAAGCGCTGAACATTAA 6 190 0 TTGTAAGCGC 0.760469 -89 ATTGTTCAAGATGTAAGCGGGTTGCTTCTA 9 41 1 ATGTAAGCGG 0.968966 -260 GTATCAGTGCATGAAAGCGGTG 11 3 0 ATGAAAGCGG 0.975469 -176 TTATGTAAAAATGAAAGCGGCTGGATTGAA 19 269 1 ATGAAAGCGG 0.975469 -32 TACACATGAGATGAAAGGGGGTTCTTTTTG 24 36 1 ATGAAAGGGG 0.757 -21 CGTAAATGTGAAGTAAGCGAATAAGGAAGG 31 19 0 AAGTAAGCGA 0.589671 -199 TATCATATAAAAGTAAGCGGTTACAATAAT 31 138 0 AAGTAAGCGG 0.936138 -80 AAGCGCTATAATGAAAGCGGACAAGGGAAG 35 36 1 ATGAAAGCGG 0.975469 -265 GACCGGCTTTCAGAAAACGCTCTGTGATAG 35 97 1 CAGAAAACGC 0.742356 -204 TTCGGTAGGAATGAAAGCGCTTTAAAGATA 37 108 0 ATGAAAGCGC 0.972152 -33 CAAATTCCTGCTGAAAACGCAGATATGAGT 40 55 1 CTGAAAACGC 0.859886 -113 ********** Masking position 5 Map Score: 21.1965 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 368 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 3 GATTTCTCCTCCTTATAGATAAG 1 86 0 TTCTCCTCCT 0.966277 -13 GGATTCCTGGCTCTCCTCATCTCCATCCAA 2 178 0 CTCTCCTCAT 0.98217 -119 AAGATCCCCTCTCTCCTCATTGATCGTCTC 6 257 0 CTCTCCTCAT 0.98217 -22 GTGCTGTGGTCTCTCCTCATCTCAGGACCG 12 49 0 CTCTCCTCAT 0.98217 -92 ATAACCACAGCTCTCCTCGAATATACTTTA 13 73 0 CTCTCCTCGA 0.78583 -228 GATCTCGCCTCCTTTTTTGCTAT 14 4 1 CTCGCCTCCT 0.845871 -230 TTAAGATGACTTTTCTTCCTTTTTATTTAC 17 232 0 TTTTCTTCCT 0.529568 -69 ATAATGCGCTCTCTCCTCAAGGGATTATTT 18 57 0 CTCTCCTCAA 0.905305 -244 ATAACTTCTCCTCGTTTCTAT 26 7 0 TTCTCCTCGT 0.937407 -15 AATAAGTGCCTTCTCTTCATACGTAACAAA 27 84 0 TTCTCTTCAT 0.86656 -47 TTGGCGCAAATTCTCCTAATTGTTCTC 30 8 0 TTCTCCTAAT 0.688269 -293 CGAACCTATCCTTTCTTCATCATAAGTGTT 30 280 0 CTTTCTTCAT 0.68396 -21 CTTTTCCTCCTTATCATCGTG 32 23 0 TTTTCCTCCT 0.871202 -11 TCTTTTTGACTTTTCCTCATGTTTCGTTAA 33 72 0 TTTTCCTCAT 0.902072 -127 TGGAATGTTTTTCTCCTCATGAGTACTTAA 38 129 1 TTCTCCTCAT 0.975013 -172 ********** Masking position 7 Map Score: 18.2474 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 139 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 4 ATAAAAATCTGGAGGGAGGCTGTTTAAAG 2 10 0 GGAGGGAGGC 0.895297 -287 AGGATATATGGGAAGGAGCGGATGTGAAAG 4 145 1 GGAAGGAGCG 0.972162 -82 CGATCAATGAGGAGAGAGGGGATCTTGA 6 261 1 GGAGAGAGGG 0.985324 -18 GTATTACGTTGGAAAGAGGTATTGT 9 6 0 GGAAAGAGGT 0.690947 -295 AGTTTTAGAAGGAAAGAGCGATAGTACTAA 9 135 0 GGAAAGAGCG 0.961147 -166 TATAGAAAAGGGAGGAAGGGAACACAACCG 10 90 1 GGAGGAAGGG 0.975541 -183 GTGACAACAAGGAGGAAACGTA 12 129 1 GGAGGAAACG 0.62054 -12 AATCCCTTGAGGAGAGAGCGCATTATGGAT 18 61 1 GGAGAGAGCG 0.978365 -240 GAAACCCTTCAGAGGAAGGGCTTAACTCAT 19 194 0 AGAGGAAGGG 0.692949 -107 TATTATAAAAGGAAGGAGGGATACACCGCC 27 110 1 GGAAGGAGGG 0.981078 -21 TTTTCTAAAGGAAAAGAGGGTCAGT 33 6 0 GAAAAGAGGG 0.675129 -193 CGGTCTTCATGGAAAAAGGGAAAGGGAGTC 35 72 0 GGAAAAAGGG 0.939232 -229 AGCGGCCTTAGGCGAAAGCGCCGGCAAAGC 35 149 0 GGCGAAAGCG 0.72083 -152 TTTAACATTAGGAAGGAGCGTTTCTTTAA 38 282 1 GGAAGGAGCG 0.972162 -19 CTTACAAAAAGGAGAAACGGA 40 157 1 GGAGAAACGG 0.718234 -11 ********** Masking position 7 Map Score: 16.9452 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 269 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 5 TAATAATTATCCCCCTTTGCTGTTTG 2 281 0 TTATCCCCCT 0.711775 -16 CAACATAACCTCCTGTTATTTGTG 4 213 0 ATAACCTCCT 0.969539 -14 AATATCCTCCTTTTTTTGTAA 7 152 0 ATATCCTCCT 0.949409 -11 CTGGATAACCTCCTAAATATAGAT 9 287 0 ATAACCTCCT 0.969539 -14 TATTAACAAAAAAACCCCCTGTAAACATGA 16 51 0 AAAACCCCCT 0.928312 -80 AAGAACCTCCTCTTGAAACAT 23 68 0 AGAACCTCCT 0.976173 -11 AGTGTTAGAACCTCCTTTCAAATCAT 24 7 1 AGAACCTCCT 0.976173 -50 ACAAAAAGAACCCCCTTTCATCTCAT 24 41 0 AGAACCCCCT 0.974569 -16 ATTGATGTAACCTCCTTTTATCAACG 29 233 0 GTAACCTCCT 0.869074 -16 GCCTAGGAGATCCTCCTTCAAAATGGT 35 284 0 AGATCCTCCT 0.960255 -17 TGTAAAATCCCCCTCATTTGCTTT 41 129 0 AAATCCCCCT 0.884192 -14 ********** Masking position 3 Map Score: 15.7595 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 18 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 6 GTTACCTTTTGAAAAATGAATGCCAATCTT 3 24 0 GAAAAATGAA 0.906627 -172 TCTGCGCAGCAAAAAAACAGCCTGGTCAGC 4 23 0 AAAAAAACAG 0.342448 -204 CCAGAAAAAACACGAAAGGGGCA 5 4 1 GAAAAAACAC 0.746039 -26 TAAAAAGCCAAAAAAAAGAAGGCTTATTCG 7 22 0 AAAAAAAGAA 0.761001 -141 TATTATATATAAAAAATCAATATCGTTACT 10 215 0 AAAAAATCAA 0.64894 -58 TCATATATCGGAAAAATGAGTGATAAAGTA 13 50 1 GAAAAATGAG 0.791532 -251 AGATTTTTCTGAAAAATGAATGCTTTACAT 13 153 1 GAAAAATGAA 0.906627 -148 GCGTATAACTAAAAAAAGACACTCAGCGTA 14 100 0 AAAAAAAGAC 0.761718 -134 TAGACTGGGGGAAAAAAGAA 15 113 1 GAAAAAAGAA 0.874932 -10 AAGGAACGCTGAAAAAAGACGAAACCTATA 17 68 1 GAAAAAAGAC 0.875363 -233 ACGAAACCTATAAAAAAGACATAACTGATC 17 86 1 TAAAAAAGAC 0.671341 -215 AATCTGAAAATAAAAATCAACGGTAAGGTT 17 151 1 TAAAAATCAA 0.541533 -150 TGGTCATTGCAAAAAAAGACAGGTGCTCCC 19 28 0 AAAAAAAGAC 0.761718 -273 AAAATTTATGTAAAAATGAAAGCGGCTGGA 19 264 1 TAAAAATGAA 0.738494 -37 TTTATGCTTTTAAAAATGAATGGCTTTGCC 21 42 0 TAAAAATGAA 0.738494 -32 AGGCGGAGTCGAAACAAGAAAGGTGGTAAC 22 103 1 GAAACAAGAA 0.701913 -22 TAAGCAATCATAAAAATGACCCGATAACGG 23 30 0 TAAAAATGAC 0.739255 -49 ACCTCCTCTTGAAACATCAAGCCCATAAGC 23 55 0 GAAACATCAA 0.577527 -24 TTTTATGTATAAAAAAAGACATCTCTCTTA 27 35 0 AAAAAAAGAC 0.761718 -96 TTTATACATAAAAAAATGAAACCTTTGATA 27 52 1 AAAAAATGAA 0.81548 -79 TTATCTTAACGAAACATGAGGAAAAGTCAA 33 67 1 GAAACATGAG 0.561024 -132 AAGTCAAAAAGAAAAATCAAAATGGGACTT 33 90 1 GAAAAATCAA 0.802421 -109 TTACCTAAATAAAAAATGACTTAGTGTCCT 37 20 0 AAAAAATGAC 0.816073 -121 CGTGAAGCTTGAAACATCAAATAAAGGGGG 39 19 0 GAAACATCAA 0.577527 -224 ********** Masking position 6 Map Score: 20.035 Number of sites scoring better than the average of aligned sites = 1465 Number in coding regions = 1133 Number in noncoding regions = 332 Number of orfs with sites within 600 bp upstream = 331 Fraction of orfs with sites within 600 bp upstream = 0.0531642 Motif number 7 CGGAGACCACAGCAGCTCTTTACGGCAAATGT 11 68 1 ACAGCTCTTA 0.800601 -111 GCTAAGTCAGCTCCTCGTATGGGCATT 14 217 0 GCAGCTCCTG 0.98903 -17 AAGGCATCAGACAGCTCCTGGATTTGAGTGC 17 10 1 GCAGCTCCTG 0.98903 -291 GCGATGAAGTGGCAGCTCTTTAAAAGAAGGAA 17 42 1 GCAGCTCTTA 0.972936 -259 TGTCTACAGAGTCAGCTCCTAGCTCAACTAAC 18 177 0 GCAGCTCCTG 0.98903 -124 CAAGTTCCATGCCAGCTCTTAAGGGTGCTGTC 22 62 0 GCAGCTCTTA 0.972936 -63 ACATTTACGAGACAGATCTGGGTTCCCCTTTA 31 40 1 GCAGATCTGG 0.84368 -178 CCAATCATTAGACAGATCTTAGATATATGTAC 41 22 1 GCAGATCTTG 0.954507 -121 * ******** * Masking position 4 Map Score: 6.43994 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 111 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 CGAAAAACAAAAAGAGCCAGAAAACACCCCTTG 2 220 0 AAAACAGAAA 0.828862 -77 ATTGTAAGACAAATAAACAATAAGTCAATATCT 4 104 0 AAAACAATAA 0.849774 -123 ATGATCTTAAAAAGAAGCAAAAACACCGAGCCA 6 42 0 AAAACAAAAA 0.905606 -237 CCTGCTGCTGAAACATGCCGAAAGCTGGCTGAA 6 136 0 AAAACCGAAA 0.900042 -143 TATTGGTCCTAAAAAGCCAAAAAAAAGAAGGCT 7 28 0 AAAACAAAAA 0.905606 -135 ATTTCTTTAAAAATAAGCCAAAATTACCCTTTA 7 80 1 AAAACCAAAA 0.946911 -83 AGAAGAGAATAAAAAAACCACAACAAACCGCTT 11 113 0 AAAACCACAA 0.897103 -66 GTAAATAGAAAAAGAGACCACAACAGCCAAAGT 12 95 0 AAAACCACAA 0.897103 -46 ATAAGCTGAGAAACAGTCAGTAATTAATGCAGA 30 130 0 AAAACAGTAA 0.740637 -171 TCGTTATGTTGAAGACACCATAAAACATAAATA 30 228 1 GAAACCATAA 0.768648 -73 ATTGTTTTCGAAATATTCCATAATATTTACTAA 31 107 0 AAAACCATAA 0.913167 -111 GAAACATGAGGAAAAGTCAAAAAGAAAAATCAA 33 77 1 GAAACAAAAA 0.751923 -122 ATGAGGAGAAAAACATTCCAAAATATGTAATTA 38 116 0 AAAACCAAAA 0.946911 -185 *** * ****** Masking position 5 Map Score: 7.20935 Number of sites scoring better than the average of aligned sites = 322 Number in coding regions = 241 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 9 GATGGTTTTACAATTGGAGGTTTGGTTACA 3 174 1 CAATTGGAGG 0.981851 -22 TAACGTAATACAATTGGAGAATTTGTTACA 7 127 1 CAATTGGAGA 0.954848 -36 CTAAAGAAATAAATTGGAGGAATAGATACT 9 109 0 AAATTGGAGG 0.982205 -192 ATATAATAGGAAATTGGTGGTATGAAAATT 10 237 1 AAATTGGTGG 0.908184 -36 TCCGAGTATGAAATTGGAGGGGCTTT 17 285 1 AAATTGGAGG 0.982205 -16 AGCAATTGGAGAAGCTGCGCTT 21 3 1 CAATTGGAGA 0.954848 -71 TGGTATCATTAAATTGGATGACCAGTAAAA 29 37 0 AAATTGGATG 0.877441 -212 TTCAATTGTAAAATTGGAAACATATTTAAA 38 42 0 AAATTGGAAA 0.736738 -259 ********** Masking position 3 Map Score: 6.03312 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 12 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 AATCTTAAAATTTCTTTAAAAATAAGCCAAAA 7 71 1 TTTCTTAAAA 0.828054 -92 TATCCTCCTTTTTTTGTAACAAATTCTCCAAT 7 139 0 TTTTTTAAAA 0.903699 -24 AATGGTTATTCTTTTATGAGAAGTTTTAGAAG 9 154 0 CTTTTTGAAA 0.827465 -147 CTTCCTCCCTTTTCTATAATAAGGGGAATAGG 10 76 0 TTTCTTAAAA 0.828054 -197 TCGTTACTATTTTTTCTGAAAATTAAATTTAA 10 191 0 TTTTTTGAAA 0.921409 -82 GAGGTAAAGATTTTTCTGAAAAATGAATGCTT 13 146 1 TTTTTTGAAA 0.921409 -155 ATTTCATTCACTTTTATGAAAAGAAACCCTTC 19 214 0 CTTTTTGAAA 0.824632 -87 CGGTTGAAAATTTATGTAAAAATGAAAGCGGC 19 258 1 TTTATTAAAA 0.754997 -43 TCCCTCCTTCCTTTTATAATAAGTGCCTTCTC 27 99 0 CTTTTTAAAA 0.789233 -32 TTTTAAATGGTTTTTTTAAAAAACCCTTGCCT 30 175 1 TTTTTTAAAA 0.786047 -126 ACCGCTTACTTTTATATGATAATATCAATTTA 31 147 1 TTTATTGAAA 0.797478 -71 TTAACTCATCTGTTTTTGATAAATTGATATTA 31 166 0 TGTTTTGAAA 0.753912 -52 AAAAATTTAATGTTTTTAACAACCTTAATCTA 33 142 0 TGTTTTAAAA 0.708521 -57 ACATTAAATTTTTATTTAACAAACTTTATTTA 33 161 1 TTTATTAAAA 0.757589 -38 AGTTTGTTATTTTTTCTGACAAACCTTGCGCG 40 82 1 TTTTTTGAAA 0.924576 -86 GGTGGTACCTTTTCTGTAAGAAAGACAACGGT 41 73 0 TTTCTTAAAA 0.830899 -70 ***** *** ** Masking position 7 Map Score: 12.593 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 178 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 11 ATATAATTGCATTTAGTAAAAGGATAATAT 2 55 1 ATTTAGTAAA 0.925579 -242 TACCAAATTAATTAAGTAAAGGGTAATTTT 7 99 0 ATTAAGTAAA 0.869531 -64 TTTACTAAATATTTAGTAAATGATGTGATT 31 85 0 ATTTAGTAAA 0.925579 -133 TTTACTAAATATTTAGTAAATATTATGGAA 31 95 1 ATTTAGTAAA 0.925579 -123 CCTCTCATCTATTTAGTAAAATATTAACTC 31 191 0 ATTTAGTAAA 0.925579 -27 AATTTACTCTATGAAGTAAATAGTTTGTTT 37 53 1 ATGAAGTAAA 0.709078 -88 ********** Masking position 5 Map Score: 2.42184 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 8 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 12 CGAATAGCGTTACAGGAAAAATTTTTCTCCA 3 121 0 TACAGAAAAA 0.842256 -75 AGAGGCCGTATACACAAATAACAGGAGGTTA 4 201 1 TACAAAATAA 0.82542 -26 GCGATAGTACTAAAGAAATAAATTGGAGGAA 9 117 0 TAAAAAATAA 0.834865 -184 AAACTTCTCATAAAAGAATAACCATTATTTA 9 160 1 TAAAGAATAA 0.871541 -141 AGATTGGATTTACAAGAATAATGAACTGGCA 9 195 0 TACAGAATAA 0.863852 -106 ATAAAGGAAATAAATGAAAAACTTTCGGGGT 13 15 1 TAAAGAAAAA 0.850954 -286 TATGTTTGTTTAAATAAAAAAACTGCGGATA 13 100 0 TAAAAAAAAA 0.809684 -201 TCTTTTTTTATACATAAAAAAATGAAACCTT 27 46 1 TACAAAAAAA 0.799146 -85 ATAAAGAACATAAAGAAATAACTTAACGAAT 33 40 0 TAAAAAATAA 0.834865 -159 TTTTTTTACCTAAATAAAAAATGACTTAGTG 37 24 0 TAAAAAAAAA 0.809684 -117 ACTCACATTTTAAAAGAATAAAGAGCGGCGA 39 132 0 TAAAGAATAA 0.871541 -111 **** ****** Masking position 7 Map Score: 6.31584 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 165 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 13 GGTTTTACAATTGGAGGTTTGGTTACACT 3 177 1 TTGGGGTTTG 0.841884 -19 TGAAGAAAAATAGGCCGAATGGGCGGCTTGC 6 76 1 TAGGCGAATG 0.871949 -203 TGGCCGTGGATAGGCGGACTGAAATCTGCTA 9 79 0 TAGGGGACTG 0.92677 -222 AAGAAATAAATTGGAGGAATAGATACTGGCC 9 105 0 TTGGGGAATA 0.903943 -196 TAATAGGAAATTGGTGGTATGAAAATTTTTT 10 240 1 TTGGGGTATG 0.962472 -33 TGAAAATTTTTTGGGGGAATAAAC 10 259 1 TTGGGGAATA 0.903943 -14 ATCGTGACTTTAGGAGGAATGTGCT 11 164 1 TAGGGGAATG 0.976272 -15 TAACCTTTTTTAGGCGGTATGCTATAATTAA 38 156 1 TAGGGGTATG 0.962472 -145 **** ****** Masking position 10 Map Score: 2.14943 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 98 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 14 GATGAGGAGAGCCAGGAATCCAACCCCTTTTGAC 2 187 1 GCCAGGACCC 0.902231 -110 TTGATTATCAGCAGGGAATGTAACCTTTTTGGGT 16 93 1 GCAGGGAGTC 0.904779 -38 AAATCGGGTTGCAGGGGGAGCACCTGTCTTTTTT 19 13 1 GCAGGGGGCC 0.987646 -288 AGCTATTCCATCAAGGATCGCCTCAAGATTTTTA 19 79 0 TCAAGGAGCC 0.846365 -222 GCCATCTGCGGCAAGCGCAGCTTCTCCAATTGCT 21 11 0 GCAAGCGGCC 0.925329 -63 TCATTTGGATGCAGGGAATGCCCCTGGTTAGGCA 28 32 1 GCAGGGAGCC 0.989788 -137 GAACTTTCATCCCGGGATCGCAGCATGATTACAG 30 94 1 CCCGGGAGCC 0.953482 -207 AGGCGAAAGCGCCGGCAAAGCTGCTTAAAACGCG 35 136 0 GCCGGCAGCC 0.973996 -165 TCGTCTAAAAGCCAGGGCAGCGGCCTTAGGCGAA 35 163 0 GCCAGGGGCC 0.980484 -138 ******* ** * Masking position 2 Map Score: 3.57541 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 150 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 15 CGGACAGTGATTTACCGCTTTTTTATAAAATAT 4 61 1 TTTACCTTTT 0.756676 -166 GTCATTGAGATTCATCTATATTTAGGAGGTTAT 9 274 1 TTCATCTTTT 0.769877 -27 AATATACTTTATCACTCATTTTTCCGATATATG 13 51 0 ATCACTTTTT 0.3966 -250 CAGAAAAATCTTTACCTCTCTGTCTTTGCATGA 13 131 0 TTTACCTTGT 0.738798 -170 TTACAAGGCTTTCATTATTGTTTACATGATCAA 13 222 1 TTCATTTTTT 0.401204 -79 GCAGAAAAAATTCACCAGTTTGTATCGCGGTGC 14 158 1 TTCACCTTGT 0.951886 -76 AGAGGGTCTTTTCACTATTATCTATTGTACATA 16 19 0 TTCACTTTCT 0.708908 -112 TGAAGTATTAATCACCAATATTTGCGAGGTGCT 18 105 1 ATCACCTTTT 0.766458 -196 TCGTGATAATTTCAGCTCTGTCTACAGAGTCAG 18 194 0 TTCAGCTTCT 0.523146 -107 CCTCAGCTAATTCACCGATGTTTTTCACCCCGG 18 272 0 TTCACCTTTT 0.956047 -29 AATCATTTCATTCACTTTTATGAAAAGAAACCC 19 217 0 TTCACTTTGA 0.374149 -84 GTTTCCATACTTCACCCTTATTTCAGATTTAAG 29 92 1 TTCACCTTTT 0.956047 -157 GACTTTAAGGTTTATCGTTATGTTGAAGACACC 30 214 1 TTTATCTTGT 0.303153 -87 CAGATCTGGGTTCCCCTTTATTTTTCCAACATA 31 52 1 TTCCCCTTTT 0.733933 -166 CGTTTTCACCTCTCTTACAATACAAAT 36 23 0 TTCACCTTTA 0.766458 -17 TCCGTTTCTCCTTTTTGTAAGGTATGGT 40 150 0 TTCTCCTTGT 0.628641 -18 GTATAGATGGTTCACCGTTGTCTTTCTTACAGA 41 60 1 TTCACCTTCT 0.924013 -83 ****** * *** Masking position 9 Map Score: 4.00764 Number of sites scoring better than the average of aligned sites = 829 Number in coding regions = 642 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052