AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00120_bsub_reg_300.orf -o00120_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/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 ycbA 300 alternate gene name: yzgA; similar to two-component sensor histidine kinase [YcbB] #2 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #3 ycbD 29 similar to aldehyde dehydrogenase #4 yjlC 300 yjlC #5 yjlD 39 similar to NADH dehydrogenase #6 yjmA 197 similar to glucuronate isomerase #7 yjmB 67 similar to Na+:galactoside symporter #8 yjmC 104 similar to malate dehydrogenase #9 mmgC 27 acyl-CoA dehydrogenase #10 mmgB 149 3-hydroxybutyryl-CoA dehydrogenase #11 mmgA 137 acetyl-CoA acetyltransferase #12 yqiK 78 similar to glycerophosphodiester phosphodiesterase #13 yqiH 300 alternate gene name: yzpA; similar to lipoprotein #14 yraG 248 similar to spore coat protein #15 gbsA 198 glycine betaine aldehyde dehydrogenase #16 yugK 103 similar to NADH-dependent butanol dehydrogenase #17 yugJ 229 similar to NADH-dependent butanol dehydrogenase #18 yusL 267 similar to 3-hydroxyacyl-CoA dehydrogenase #19 yusM 300 similar to proline dehydrogenase #20 ywpB 191 similar to hydroxymyristoyl-(acyl carrier protein) dehydratase #21 ywjF 154 similar to hypothetical proteins #22 ywdH 167 alternate gene name: ipa-58r; similar to aldehyde dehydrogenase #23 aldX 142 aldehyde dehydrogenase Motif number 1 ACATTTTGAAAATAAGCAGTAAGATTTATAAA 1 83 1 AATAGCAGAA 0.971655 -218 TATTTTGGGGAATCGGGAGAAAACCTGCAAAT 1 140 0 AATGGGAGAA 0.723914 -161 ATATTTTATAAAAAAGCGGTAAATCACTGTCC 2 62 0 AAAAGCGGAA 0.966949 -165 CTTTTTTATAAAATATCAGAAAATAAAGATAT 2 78 1 AAAATCAGAA 0.894933 -149 CCCTTTCCAAAAAAATCAGCAAACTGCTTATA 4 262 1 AAAATCAGAA 0.894933 -39 CTATCTTCTGAATGAGGTGAAACC 11 124 1 AATAGGTGAA 0.700955 -14 AATTAGAAAAAATTAGCGGAAAGAAGCAACTT 13 96 0 AATAGCGGAA 0.959318 -205 GATAAAAGCCAAACATCAGGAAGAGGTGGTCA 13 278 1 AAAATCAGAA 0.894933 -23 TATCTTAACGAAACATGAGGAAAAGTCAAAAA 15 68 1 AAAATGAGAA 0.845511 -131 AAAAAGGGGAAATAGCCGTTTG 16 1 1 AAAAGGGGAA 0.94949 -103 GACAAGTCAAAATCAGCAGTATAAAAAACATA 18 52 0 AATAGCAGAT 0.829197 -216 CACAATGGATAATCAGCAGCAATCTCAAATGC 19 189 0 AATAGCAGAA 0.971655 -112 GAAACTATAAAATGAACAGAAACCAAAGGAGG 19 223 0 AATAACAGAA 0.67603 -78 TAGTGTGCCCGAACAGCAGGAATTTAATTATT 21 37 1 GAAAGCAGAA 0.826703 -118 CTTTATCAGTAAAAAGGGGGAATTGGA 21 138 1 AAAAGGGGAA 0.94949 -17 GGAATTTGATAAAATGCAGGAAGACAACATTT 22 31 0 AAATGCAGAA 0.77355 -137 CATACCTTACAAAAAGGAGAAACGGA 22 152 1 AAAAGGAGAA 0.964698 -16 GAAGAAAGCAAATGAGGGGGATTTTACA 23 125 1 AATAGGGGAT 0.682129 -18 *** ***** ** Masking position 2 Map Score: 19.6791 Number of sites scoring better than the average of aligned sites = 702 Number in coding regions = 592 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 2 AAAAAACACGAAAGGGGCAATGGGC 3 15 1 AAAGGGGATG 0.983617 -15 TGCTTATAGTAAAGGAGAATTGGAT 4 286 1 AAAGGAGATG 0.985077 -15 AACATGATGAAAAAGGGGATTTGAATGGAAATC 10 11 1 AAAAGGGATG 0.915859 -139 CTTTGACCAGAATGGAGAATTTGTAAAGACAAC 13 246 0 AATGGAGATG 0.950783 -55 TTTCTAAAGGAAAAGAGGGTCAGT 15 2 0 AAAAGAGGCG 0.847898 -197 AAAAAGGGGAAATAGCCGTTTGGCT 16 3 1 AAAGGGGATG 0.983617 -101 ACAAAAAAGAAAAAGGGAAGCAGCCAAACGGCT 16 24 0 AAAAGGGACG 0.945852 -80 CTTATGTTACAATGGAAAATCTGTTTTTTACCA 16 60 1 AATGGAAACG 0.689869 -44 TTATTTCGACAAAGGATCATTTGTATCTCAATG 19 147 0 AAAGGATATG 0.893068 -154 GGAGGATCACAATGGATAATCAGCAGCAATCTC 19 195 0 AATGGATACG 0.796851 -106 AACAGAAACCAAAGGAGGATCACAATGGATAAT 19 208 0 AAAGGAGACC 0.905277 -93 TTTACTACGGAAAGGAGTGCCGGT 21 2 0 AAAGGAGGCG 0.968502 -153 TTATCAGTAAAAAGGGGGAATTGGA 21 140 1 AAAGGGGATG 0.983617 -15 TACCTTACAAAAAGGAGAAACGGA 22 154 1 AAAGGAGACG 0.990648 -14 ******* * * * Masking position 2 Map Score: 17.6584 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 342 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 3 GTATGATTCTGTAGTCTCCATTATACAGTA 1 39 0 GTAGTCTCCA 0.494087 -262 CAATTTGCAGGTTTTCTCCCGATTCCCCAA 1 138 1 GTTTTCTCCC 0.809833 -163 TTTCACATCCGCTCCTTCCCATATATCCTT 2 144 0 GCTCCTTCCC 0.807194 -83 AGTTTTTTGGGCACTCTCCAAGCGAAACCC 8 64 0 GCACTCTCCA 0.629886 -41 GCAAGTGCCTCCTTCCTTTTCAGTTT 8 89 0 GCCTCCTTCC 0.919816 -16 GCGTCAAACAGCCTCCTTCTAACAACTATT 11 17 0 GCCTCCTTCT 0.767299 -121 GCTGTTTGACGCAGCCTTCTTTTTTCATTC 11 35 1 GCAGCCTTCT 0.777248 -103 ACAATTTCTAGTTGTCTTCTATGAATGTAT 11 85 0 GTTGTCTTCT 0.510373 -53 AAACCCTAAAGTTTTCTCCATTATACTTAT 12 48 0 GTTTTCTCCA 0.702393 -31 ATAAAAAGTTGCTTCTTTCCGCTAATTTTT 13 91 1 GCTTCTTTCC 0.881921 -210 TAGCCGTTTGGCTGCTTCCCTTTTTCTTTT 16 23 1 GCTGCTTCCC 0.904179 -81 ATCTATACATGCATTCTCCATATGAGGGAA 17 69 1 GCATTCTCCA 0.787152 -161 GGGCAGGCCAGCTTCCCTCATATGGAGAAT 17 81 0 GCTTCCCTCA 0.608493 -149 GCTTATATCAGCTTCTTTCCCAGCACCTTG 17 113 1 GCTTCTTTCC 0.881921 -117 TCATAATGCAGCTGCTTCCCACGGCTGCTT 18 11 0 GCTGCTTCCC 0.904179 -257 CATGAAATGCGCTTTTTTCATCGCGAGCAA 19 100 1 GCTTTTTTCA 0.65959 -201 AATCTCAAATGCCGCCTTCCGTTATTTCGA 19 171 0 GCCGCCTTCC 0.922471 -130 TCATTTTATAGTTTCCTTCAGACTGGGAGT 19 240 1 GTTTCCTTCA 0.805423 -61 GAAGCACCCTCCAAAAAAATAAA 22 4 1 GCACCCTCCA 0.784283 -164 AAAAATAAATGTTGTCTTCCTGCATTTTAT 22 25 1 GTTGTCTTCC 0.783846 -143 CCCCTCATTTGCTTTCTTCTTTTCTCGGAC 23 114 0 GCTTTCTTCT 0.797864 -29 ********** Masking position 9 Map Score: 14.315 Number of sites scoring better than the average of aligned sites = 2204 Number in coding regions = 1949 Number in noncoding regions = 255 Number of orfs with sites within 600 bp upstream = 257 Fraction of orfs with sites within 600 bp upstream = 0.0412785 Motif number 4 ACCAAACAGCCGGCTGACCAGGCTG 2 5 1 AAAGCCGGCT 0.975159 -222 GCAGCAAAAAAACAGCCTGGTCAGCCGGCTG 2 17 0 AAAGCCTGGT 0.835603 -210 GCAAGTGCCTCCTTCCTTTTCAG 8 92 0 AATGCCTCCT 0.979248 -13 GAATTGCTCAAACAGCCGCCGACGCGGCTTT 10 84 1 AAAGCCGCCG 0.926347 -66 ATCCGCACATAAAAGCCGCGTCGGCGGCTGT 10 95 0 AAAGCCGCGT 0.939351 -55 GGCTGCGTCAAACAGCCTCCTTCTAACAACT 11 20 0 AAAGCCTCCT 0.983313 -118 AATTTTTTCTAATTGGCGCCTCAATTAGAGC 13 114 1 AATGGCGCCT 0.855212 -187 ATCGAGTGCCTCCTATAAAACCAT 14 4 1 GATGCCTCCT 0.873616 -245 ATAAGCCTCCTTGACGTAAAT 15 188 0 ATAGCCTCCT 0.859834 -11 CGAGAGAAAAAAAATCCGTCTTCAGCGGCAG 18 145 0 AAATCCGTCT 0.661337 -123 CAGCAATCTCAAATGCCGCCTTCCGTTATTT 19 174 0 AATGCCGCCT 0.984955 -127 GTCAATAATTAAATTCCTGCTGTTCGGGCAC 21 41 0 AATTCCTGCT 0.848504 -114 GCATTTTATCAAATTCCTGCTGAAAACGCAG 22 46 1 AATTCCTGCT 0.848504 -122 TGTAAAATCCCCCTCATTTGCTTT 23 129 0 AAATCCCCCT 0.811213 -14 ** ******** Masking position 7 Map Score: 12.2726 Number of sites scoring better than the average of aligned sites = 659 Number in coding regions = 543 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 5 TGTTTAATTGTAAGACAAATAAACAATAAGTCAATA 2 107 0 TGAAAAAAAA 0.931621 -120 AAGGAGCGGATGTGAAAGAAAAATTAATAAAAGCGC 2 157 1 TGAAAAAATA 0.632202 -70 CAGATAGAGGCCGTATACACAAATAACAGGAGGTTA 2 196 1 CTAAAAAAAA 0.485055 -31 TCTCTGAAAATAGCAAACACAAAAAACTCCAATTCG 4 59 0 TCAAAAAAAA 0.638235 -242 AATTGTTTATTTTTAGATAAAAATAATACTGAATAT 4 118 1 TTAAAAAAAA 0.903523 -183 TCATGCACAATCATTTACAAAAATAAATGTTTACTA 4 173 0 TTTAAAAAAA 0.885184 -128 GTTAACGCTGTCATAAACATAAAAAAAGACATTGCC 6 63 0 TTAAAAAAAA 0.903551 -135 ACGTTAACATTTTGAAATAGAATGAAAGACGGTGAG 6 169 1 TGAAAAATAA 0.782626 -29 ATTCTCAAATTTTTTAAAATGAATAAAAAGTTGCTT 13 69 1 TTTAAGAAAA 0.599592 -232 AAAACAGCGATTCTTAAAACAAAAAATGATACCGAG 14 156 1 TTTAAAAAAA 0.885184 -93 GACCCTCTTTTCCTTTAGAAAATTAAATTCGTTAAG 15 14 1 TTTAAAATAA 0.670817 -185 TCCTCATGTTTCGTTAAGATAAAGAACATAAAGAAA 15 53 0 TTTAAAAAAA 0.885181 -146 GTAAATAAAGTTTGTTAAATAAAAATTTAATGTTTT 15 158 0 TGTAAAAAAT 0.432077 -41 AAGGGAATGGTACGAGAGAAAAAAAATCCGTCTTCA 18 152 0 TGAAAAAAAA 0.931622 -116 TTTATAGGCTTCATACAAAAAAATAACAAATTAGCT 18 214 1 TTAAAAAAAA 0.903552 -54 AGATTATCTTTATGATAAATAATGAATGAGTGTTCA 21 72 0 TGAAAAATAA 0.782626 -83 TCGCGCAAGGTTTGTCAGAAAAAATAACAAACTCAT 22 79 0 TGTAAAAATA 0.585905 -89 GCAGAAGAGATTTTTCACATAATAAATCACCATACC 22 122 1 TTTAAAATAA 0.670355 -46 TGGTACCTTTTCTGTAAGAAAGACAACGGTGAACCA 23 67 0 TGTAAAGAAA 0.530003 -76 TTATAATAGGTCCGAGAAAAGAAGAAAGCAAATGAG 23 105 1 TGAAAGAAAA 0.726687 -38 * ** * * *** ** Masking position 9 Map Score: 12.6283 Number of sites scoring better than the average of aligned sites = 525 Number in coding regions = 348 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 6 TTTATGTTGATCACATCCTCGCTTTTTATTTTGG 1 164 0 TCACATCCCT 0.969683 -137 AATTTTTCTTTCACATCCGCTCCTTCCCATATAT 2 148 0 TCACATCCCT 0.969683 -79 CAACATAACCTCCTGTTATTTGTGTATAC 2 208 0 TAACCTCCTT 0.924106 -19 CGTATATCCTCCGTCCTTTATATCAATT 5 22 0 TATCCTCCCT 0.943891 -18 CGTTTCACCTCAAACCCTAAAGTTTTCT 12 61 0 TCACCTCACT 0.940912 -18 ATTGATGTAACCTCCTTTTATCAACGTTACA 14 228 0 TAACCTCCTT 0.924106 -21 GACATCTCCTCCTTAGATTTTTTATTAT 17 212 0 TCTCCTCCGT 0.907985 -18 ACCATTCCCTTCACCTCCGGGCTTAAGTTGCCCG 18 177 1 TCACCTCCCT 0.993881 -91 AAAAGACACCTCCAATCATTAGACAGATC 23 6 1 ACACCTCCCT 0.962414 -137 ******** * * Masking position 6 Map Score: 5.94265 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 66 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 7 CCGATTCCCCAAAATAAAAAGCGAGGATGT 1 156 1 AAAATAAAAA 0.942858 -145 GGATGTGATCAACATAAAACTGGAACGGTT 1 180 1 AACATAAAAC 0.713187 -121 AAAATATCAGAAAATAAAGATATTGACTTA 2 87 1 AAAATAAAGA 0.894457 -140 GAAAATAGCAAACACAAAAAACTCCAATTC 4 60 0 AACACAAAAA 0.739184 -241 TTTTTATCTAAAAATAAACAATTGAATAAG 4 111 0 AAAATAAACA 0.706481 -190 CGCTGTCATAAACATAAAAAAAGACATTGC 6 64 0 AACATAAAAA 0.91903 -134 ATATAAAGGTAAAATAAAAACAAATCAAAA 6 134 1 AAAATAAAAA 0.942858 -64 CAATATAATATAAAGAATATTTAAAA 8 7 1 AATATAAAGA 0.474203 -98 AGCGATTCTTAAAACAAAAAATGATACCGA 14 161 1 AAAACAAAAA 0.804689 -88 TAAGATAAAGAACATAAAGAAATAACTTAA 15 45 0 AACATAAAGA 0.853582 -154 GGAAAAGTCAAAAAGAAAAATCAAAATGGG 15 86 1 AAAAGAAAAA 0.804689 -113 TAAAGTTTGTTAAATAAAAATTTAATGTTT 15 159 0 TAAATAAAAA 0.555301 -40 AAGTTGACAAAAAAGAAAAAGGGAAGCAGC 16 33 0 AAAAGAAAAA 0.804689 -71 AGCACCTTGCAAAATAAAACCATCTGGTAT 17 134 1 AAAATAAAAC 0.783307 -96 GACATTCTGCATAATAAAAAATCTAAGGAG 17 202 1 ATAATAAAAA 0.700324 -28 TTCATACAAAAAAATAACAAATTAGCTATT 18 223 1 AAAATAACAA 0.783307 -45 TTCATTATTTATCATAAAGATAATCTTATA 21 82 1 ATCATAAAGA 0.452257 -73 TTTGTCAGAAAAAATAACAAACTCATATCT 22 75 0 AAAATAACAA 0.783307 -93 ********** Masking position 6 Map Score: 12.6727 Number of sites scoring better than the average of aligned sites = 1198 Number in coding regions = 828 Number in noncoding regions = 370 Number of orfs with sites within 600 bp upstream = 374 Fraction of orfs with sites within 600 bp upstream = 0.0600707 Motif number 8 CGGTGAACTGAAATTTTATCCCCTCAATGA 1 264 1 AAATTTTATC 0.697939 -37 TTTGTTCAAAAAGTGTTATCATATAGAAGG 4 25 1 AAGTGTTATC 0.845707 -276 TTACAAAAATAAATGTTTACTACCCAGTTT 4 165 0 AAATGTTTAC 0.851243 -136 TTTGAAAATGAAATGTTAACGCTGTCATAA 6 83 0 AAATGTTAAC 0.95867 -115 AAACAAATCAAAATGTTAACGTTAACATTT 6 151 1 AAATGTTAAC 0.95867 -47 TTCTATTTCAAAATGTTAACGTTAACATTT 6 161 0 AAATGTTAAC 0.95867 -37 CCAAAAAAATAAATGTTGTCTTCCTGCATT 22 21 1 AAATGTTGTC 0.866905 -147 ********** Masking position 2 Map Score: 3.23587 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 11 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 TTTGTCGTATTTTGTATGATTCTGTAGTCTCC 1 50 0 TTTGATGTTC 0.901891 -251 TCAAAAGCAATTTGCAGGTTTTCTCCCGATTC 1 131 1 TTTGAGGTTT 0.760615 -170 AGTAAAGGATTTTGACTTATTCAATTGTTTAT 4 96 1 TTTGCTTTTC 0.880353 -205 ACGTTAACATTTTGATTTGTTTTTATTTTACC 6 141 0 TTTGTTTTTT 0.569229 -57 GCTACCATGATTTGTTTGATTTCCATTCAAAT 10 29 0 TTTGTTGTTT 0.758456 -121 TTATACTTATTTTGTCGGCTCCACTCTAGGAT 12 26 0 TTTGCGGTCC 0.928884 -53 GAGTGTATTTTCTGTATGCTTCAACTTCATTT 14 189 1 TCTGATGTTC 0.555016 -60 GATTTTTCTTTTTGACTTTTCCTCATGTTTCG 15 76 0 TTTGCTTTCC 0.870002 -123 AAAGTCCCATTTTGATTTTTCTTTTTGACTTT 15 89 0 TTTGTTTTCT 0.545845 -110 GAAATAGCCGTTTGGCTGCTTCCCTTTTTCTT 16 19 1 TTTGCTGTTC 0.9459 -85 ACCAGCATCATTTGGAGGTTTTACT 16 89 1 TTTGAGGTTT 0.760615 -15 TACTGCTGATTTTGACTTGTCCGTTTTCCGCC 18 63 1 TTTGCTTTCC 0.870002 -205 TATCATAACTTTTGACGGCTCTCATTGACAGT 20 51 1 TTTGCGGTCT 0.846075 -141 CATTTATTTTTTTGGAGGGTGCTTC 22 4 0 TTTGAGGTGC 0.611589 -164 ATCCCCCTCATTTGCTTTCTTCTTTTCTCGGA 23 115 0 TTTGTTTTTC 0.758456 -28 **** *** *** Masking position 3 Map Score: 7.27869 Number of sites scoring better than the average of aligned sites = 721 Number in coding regions = 657 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 10 CCCCATCTGACCTGCGCCAGCTACCATGATT 10 49 0 CCTGCCCAGC 0.968627 -101 GGATTCACATCATACATCCGCACATAAAAGC 10 110 0 CATACTCCGC 0.907255 -40 TCCTGCCTCCGCGGCCTCTGGA 10 138 0 CCTGCTCCGC 0.993135 -12 AACTTGCTCGCCTGCATTCGCGTTGTCTTTA 13 225 1 CCTGCTTCGC 0.976102 -76 AGAATCTATACATGCATTCTCCATATGAGGG 17 66 1 CATGCTTCTC 0.549686 -164 GGGAAGCTGGCCTGCCCTCGCTTATATCAGC 17 94 1 CCTGCCTCGC 0.977901 -136 GAAAAAAAATCCGTCTTCAGCGGCAGTCAGC 18 140 0 CCGTCTCAGC 0.769782 -128 CCGACTCCCTCCCGCCGTCAT 19 290 0 CCGACCCCTC 0.820048 -11 CTTGACATCTCCTTCATCTGCATTAGTATGT 20 168 0 CCTTCTCTGC 0.815157 -24 ACCGCGATCCCCTACCCCCGAATCTGTATAA 21 107 0 CCTACCCCGA 0.842674 -48 ***** ***** Masking position 5 Map Score: 3.0582 Number of sites scoring better than the average of aligned sites = 747 Number in coding regions = 663 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 11 AGCAGTAAGATTTATAAAAACCTCATGTTCTGG 1 97 1 TTTTAAAACT 0.661996 -204 TCCTCCGTCCTTTATATCAATTTGAATCTGAGA 5 11 0 TTTTACAATT 0.792935 -29 TTCCGAGTGCTTTCTGGCAATGTCTTTTTTTAT 6 48 1 TTTTGCAATT 0.705747 -150 TTTTTTTATGTTTATGACAGCGTTAACATTTCA 6 72 1 TTTTGCAGCT 0.906983 -126 AAACAGCCTCCTTCTAACAACTATTCATTTT 11 9 0 CTTTACAACA 0.686579 -129 GCTCGTTATCTTTCTAACAACAGGAAATGATCG 13 164 1 TTTTACAACG 0.83828 -137 ATGTAACCTCCTTTTATCAACGTTACATTTCCC 14 222 0 CTTTACAACT 0.939644 -27 AAATTTAATGTTTTTAACAACCTTAATCTAACA 15 139 0 TTTTACAACT 0.961325 -60 CCCTTTTTCTTTTTTGTCAACTTATGTTACAAT 16 40 1 TTTTGCAACT 0.939643 -64 GAAAATCTGTTTTTTACCAGCATCATTTGGAGG 16 74 1 TTTTACAGCT 0.939643 -30 CCTGCCCTCGCTTATATCAGCTTCTTTCCCAGC 17 104 1 CTTTACAGCT 0.906983 -126 *** ** **** * Masking position 9 Map Score: 4.44154 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 162 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 12 TTTCAGTTCACCGGCCAGCGGCACCGTAATCAGC 1 243 0 CGCCAGCGGC 0.984923 -58 GGATAGTGATCCGCTCAGCGATACTGAGCGGACA 7 16 0 CGTCAGCGAC 0.95524 -52 ACGGGTGGGTCAGCCAAGCGTAACCTTTTAAAGG 13 16 0 CGCAAGCGTC 0.958634 -285 TAAGCGAGGGCAGGCCAGCTTCCCTCATATGGAG 17 84 0 CGCCAGCTTC 0.978246 -146 TCAGCTCTCACCGATCAGCATACCAGATGGTTTT 17 149 0 CGTCAGCATC 0.982147 -81 AATGCTGAGTCGGACCGGCATCTCCCTTTACGCT 18 100 1 CGCCGGCATC 0.972193 -168 GAGCAAATTCCAGTTCAGCATGTCATTGAGATAC 19 124 1 CGTCAGCATC 0.982147 -177 * * ******* * Masking position 8 Map Score: 2.63569 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 107 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 13 ATCTTACTGCTTATTTTCAAAATGTTTTTGT 1 77 0 TTATTTCAAA 0.813952 -224 ATTCACGTTCAAATTTTGTTCAA 4 3 1 TCACTTCAAA 0.95687 -298 TCATGCACAATCATTTACAAAAATAAATGTT 4 178 0 TCATTACAAA 0.860649 -123 TCTCAGATTCAAATTGATATAAA 5 3 1 TCAGTTCAAA 0.923395 -37 CGTTAACATTTCATTTTCAAAAAAGAGATTG 6 92 1 TCATTTCAAA 0.975111 -106 AACTTTTTATTCATTTTAAAAAATTTGAGAA 13 70 0 TCATTTAAAA 0.793424 -231 GCAAGTTCCATGATTTTCAAAAGGGCTATAC 13 201 0 TGATTTCAAA 0.866387 -100 TGCATCATGATCACTATCAAAGAATATTAAA 19 14 0 TCACATCAAA 0.777647 -287 CCTCCCGCCGTCATCTTCAAAACACCTGTAT 19 273 0 TCATTTCAAA 0.975111 -28 **** ****** Masking position 3 Map Score: 4.7875 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 169 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 14 TTTTTATTTTGGGGAATCGGGAGAAAACCT 1 146 0 GGGGAATCGG 0.984672 -155 AAACACGAAAGGGGCAATGGGC 3 18 1 GGGGCAATGG 0.957554 -12 TTATAGTAAAGGAGAATTGGAT 4 289 1 GGAGAATTGG 0.978824 -12 TGACCAGAATGGAGAATTTGTAAAGACAAC 13 246 0 GGAGAATTTG 0.877312 -55 AAAAAGGGGAAATAGCCGTTTGGCT 16 6 1 GGGGAAATAG 0.918977 -98 CAGTAAAAAGGGGGAATTGGA 21 144 1 GGGGAATTGG 0.989634 -11 CTTACAAAAAGGAGAAACGGA 22 157 1 GGAGAAACGG 0.959819 -11 ********** Masking position 6 Map Score: 6.05075 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 87 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 15 AAAACCTGCAAATTGCTTTTGACCCAGAAC 1 123 0 AATTGCTTTT 0.807984 -178 GAGGGGATAAAATTTCAGTTCACCGGCCAG 1 259 0 AATTTCAGTT 0.483077 -42 CTCTATCTGTAAGCGCTTTTATTAATTTTT 2 175 0 AAGCGCTTTT 0.943089 -52 CTTTGGGATCAATCTCTTTTTTGAAAATGA 6 102 0 AATCTCTTTT 0.808554 -96 TAGAAATTGTAAGCGCTGTCTATCTTCTGA 11 105 1 AAGCGCTGTC 0.833068 -33 TTTCAGATTTAAGTGCAGTTTAGTCCATGT 14 112 1 AAGTGCAGTT 0.780131 -137 TTGTTTTAAGAATCGCTGTTTTTGCTCGTT 14 148 0 AATCGCTGTT 0.943089 -101 GCGATGAAAAAAGCGCATTTCATGGCGCAG 19 94 0 AAGCGCATTT 0.896304 -207 ATTATGAATTAATCTCTTTTTCAACCGCGC 20 96 0 AATCTCTTTT 0.808554 -96 ********** Masking position 2 Map Score: 1.35373 Number of sites scoring better than the average of aligned sites = 591 Number in coding regions = 509 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577