AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i098_bsub_mtub_300.orf -o098_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 resD 80 two-component response regulator #2 resC 135 essential protein similar to cytochrome c biogenesis protein #3 resA 131 essential protein similar to cytochrome c biogenesis protein #4 ypuL 91 similar to hypothetical proteins #5 dacB 122 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5*) #6 ypuI 54 similar to hypothetical proteins from B. subtilis #7 ypuG 280 similar to hypothetical proteins #8 phoP 211 two-component response regulator #9 citH 43 malate dehydrogenase #10 citC 163 isocitrate dehydrogenase #11 citZ 300 citrate synthase II #12 yycF 300 similar to two-component response regulator [YycG] #13 Rv0488 300 hypothetical protein Rv0488 #14 gpm 156 gpm #15 senX3 173 senX3 #16 regX3 227 regX3 Motif number 1 GTTTTCCCCCTGCTTTCCTTCTGTTACT 1 63 0 CCCTGCTTCC 0.924001 -18 AGAAAATTTCCGCTCAGCTCTGCCATGACATCA 2 23 0 CCCAGCCTGC 0.920763 -113 TGCCCCCTTCCCCCTATTGCAGATC 3 117 0 CCCTTCCCCT 0.930665 -15 GGCTTTTTCTCCCGCTTCTGCGCTCCGAGCAAA 7 115 1 CCCTTCGCGC 0.959878 -166 GTCTCTCTTCTCCTTTATGGCTAGT 9 29 0 CCCTTCCCTT 0.771607 -15 TTATTGAAACCTCCCCTCACCGGAGTGCGTCTT 12 60 0 CCCCTCCCGG 0.955063 -241 CCAACTCCTTCTCATCGCGCTGCGC 13 3 0 CCTCGCCTGC 0.930384 -298 TCGCGCTGCGCGCTCTGCATCGTCGTCGGGCTC 13 47 0 CCCTGCTCGT 0.990983 -254 CCAACTCCTTCTCATCGCGCTGCGCGCTCTGCA 13 61 0 CCTCGCCTGC 0.930384 -240 TCGCGCTGCGCGCTCTGCATCGTCGTCGGGCTC 13 105 0 CCCTGCTCGT 0.990983 -196 AGTGCTATTTCTCATCGCGCTGCGCGCTCTGCA 13 119 0 CCTCGCCTGC 0.930384 -182 GCTGGTGGCGCTCACCCCGTTCCGGACTCAGAA 13 182 1 CCCCCCTTCC 0.83683 -119 GCGGTATGAACGCGCTGCGCAGCGGACCGAGGA 14 75 1 CCCTGCCAGC 0.960802 -82 CGCACTCCCGCACTCCTCATCGTGGACCAAAAT 14 118 0 CCCCTCTCGT 0.982563 -39 CTCATCGCTACGCTCTGCATCGTCGTCGGCGCA 16 13 0 CCCTGCTCGT 0.990983 -215 GGGTGGTGCCCCCACCTCATCGCTACGCTCTGC 16 28 0 CCCCTCTCGC 0.993671 -200 TCATCAGCGCCACTCTCCCCCGCAAGCGGGTGG 16 55 0 CCCTCCCCGC 0.994626 -173 CTCATCGCTACGCTCTGCATCGTCGTCGGCGCA 16 90 0 CCCTGCTCGT 0.990983 -138 GGGTGGTGCCCCCACCTCATCGCTACGCTCTGC 16 105 0 CCCCTCTCGC 0.993671 -123 TCATCAGCGCCACTCTCCCCCGCAAGCGGGTGG 16 132 0 CCCTCCCCGC 0.994626 -96 CTCATCGCTACGCTCTGCATCGTCGTCGGCGCA 16 167 0 CCCTGCTCGT 0.990983 -61 GGGTGGTGCCCCCACCTCATCGCTACGCTCTGC 16 182 0 CCCCTCTCGC 0.993671 -46 CAGCGCCACTCTCCCCCGCAAGCGGGTGG 16 209 0 CCCTCCCCGC 0.994626 -19 * * **** **** Masking position 8 Map Score: 57.6758 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 272 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 2 CGCGTATGGCCCCGCCGAAGATTGGGACAGC 2 84 0 CCCGCCGAGA 0.980478 -52 TATCTTTATTCCCGCGTATGGCCCCGCCGAA 2 96 0 CCCGCGTTGG 0.791989 -40 CAGAGCACTGGCGGATCACGGTAAAAACGCT 3 18 1 GCGGATCCGG 0.813515 -114 CTTCTTTGAACCGGCCGCAGGGCCGGTTCTC 12 14 0 CCGGCCGAGG 0.552308 -287 TTAGGTCGAGCCCGACGACGATGCAGAGCGC 13 40 1 CCCGACGCGA 0.987414 -261 TTAGGTCGAGCCCGACGACGATGCAGAGCGC 13 98 1 CCCGACGCGA 0.987414 -203 GGTCAAGACGCCCGCCGGTGATGGGCTGGTG 13 158 1 CCCGCCGTGA 0.969061 -143 TCACCCCGTTCCGGACTCAGAAATTCGCGAT 13 193 1 CCGGACTAGA 0.806564 -108 CGATACATGGGCGGCCTACGAGGTGG 14 6 0 GCGGCCTCGA 0.960547 -151 GCGCTGCGCAGCGGACCGAGGAGAATTCGGG 14 86 1 GCGGACCAGG 0.826152 -71 TGAGATCCCACCTGCCGGCGGTTTCGGCGGC 15 16 1 CCTGCCGCGG 0.886851 -158 GGCGGTTTCGGCGGCTGATGGTGTGCTTTGG 15 32 1 GCGGCTGTGG 0.84733 -142 TTTTGGCCTTGCCGCGCTAGGGCGACGTTCA 15 131 1 GCCGCGCAGG 0.786959 -43 CCTGCGCCGACGACGATGCAGAGCGT 16 6 1 GCCGACGCGA 0.982922 -222 GGGGGCACCACCCGCTTGCGGGGGAGAGTGG 16 48 1 CCCGCTTCGG 0.968825 -180 GATGACCTGCGCCGACGACGATGCAGAGCGT 16 83 1 GCCGACGCGA 0.982922 -145 GGGGGCACCACCCGCTTGCGGGGGAGAGTGG 16 125 1 CCCGCTTCGG 0.968825 -103 GATGACCTGCGCCGACGACGATGCAGAGCGT 16 160 1 GCCGACGCGA 0.982922 -68 GGGGGCACCACCCGCTTGCGGGGGAGAGTGG 16 202 1 CCCGCTTCGG 0.968825 -26 ******* *** Masking position 4 Map Score: 35.0321 Number of sites scoring better than the average of aligned sites = 946 Number in coding regions = 857 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 AAAGAAAATTTCCGCTCAGCTCTGCCATGACA 2 26 0 TCGCTCACTC 0.865368 -110 GCTCGACCTAACCGCCCAACTCCTTCTCATCG 13 19 0 ACGCCCACTC 0.992369 -282 GACGATGCAGAGCGCGCAGCGCGATGAGAAGG 13 56 1 ACGCGCACGC 0.962575 -245 GCTCGACCTAACCGCCCAACTCCTTCTCATCG 13 77 0 ACGCCCACTC 0.992369 -224 GACGATGCAGAGCGCGCAGCGCGATGAGAAAT 13 114 1 ACGCGCACGC 0.962575 -187 GAACGGGGTGAGCGCCACCAGCCCATCACCGG 13 172 0 ACGCCACAGC 0.908659 -129 CCCCCACCTCATCGCTACGCTCTGCATCGTCG 16 21 0 ACGCTACCTC 0.99064 -207 GCAGGTCATCAGCGCCACTCTCCCCCGCAAGC 16 61 0 ACGCCACCTC 0.995984 -167 CCCCCACCTCATCGCTACGCTCTGCATCGTCG 16 98 0 ACGCTACCTC 0.99064 -130 GCAGGTCATCAGCGCCACTCTCCCCCGCAAGC 16 138 0 ACGCCACCTC 0.995984 -90 CCCCCACCTCATCGCTACGCTCTGCATCGTCG 16 175 0 ACGCTACCTC 0.99064 -53 CAGCGCCACTCTCCCCCGCAAGC 16 215 0 ACGCCACCTC 0.995984 -13 * ****** *** Masking position 5 Map Score: 29.8098 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 70 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 4 GCGTTTTTACCGTGATCCGCCAGTGCTCTG 3 18 0 CGTGATCCGC 0.869484 -114 CATAACTGATGGACATGCGCATAAACTTGT 5 75 1 GGACATGCGC 0.945637 -48 ACCACCACAAGGACGTGAGCAAAC 5 109 1 GGACGTGAGC 0.956465 -14 AAATAGTATTGGACGAGAGCTTTTTGGTGG 7 199 1 GGACGAGAGC 0.826365 -82 GCGATGAGAAGGAGTTGGGCGGTTAGGTCG 13 18 1 GGAGTTGGGC 0.85903 -283 TGGGCGGTTAGGTCGAGCCCGACGACGATG 13 33 1 GGTCGAGCCC 0.926229 -268 GCGATGAGAAGGAGTTGGGCGGTTAGGTCG 13 76 1 GGAGTTGGGC 0.85903 -225 TGGGCGGTTAGGTCGAGCCCGACGACGATG 13 91 1 GGTCGAGCCC 0.926229 -210 GACGCCCGCCGGTGATGGGCTGGTGGCGCT 13 164 1 GGTGATGGGC 0.971353 -137 ATACCGCCGAGGTGGTCGGCACCGTAACGG 14 52 0 GGTGGTCGGC 0.987258 -105 CGCTCTGCATCGTCGTCGGCGCAGG 16 6 0 CGTCGTCGGC 0.966103 -222 CCCGCAAGCGGGTGGTGCCCCCACCTCATC 16 40 0 GGTGGTGCCC 0.977517 -188 CGTCGGCGCAGGTCATCAGCGCCACTCTCC 16 70 0 GGTCATCAGC 0.868112 -158 CGCTCTGCATCGTCGTCGGCGCAGGTCATC 16 83 0 CGTCGTCGGC 0.966103 -145 CCCGCAAGCGGGTGGTGCCCCCACCTCATC 16 117 0 GGTGGTGCCC 0.977517 -111 CGTCGGCGCAGGTCATCAGCGCCACTCTCC 16 147 0 GGTCATCAGC 0.868112 -81 CGCTCTGCATCGTCGTCGGCGCAGGTCATC 16 160 0 CGTCGTCGGC 0.966103 -68 CCCGCAAGCGGGTGGTGCCCCCACCTCATC 16 194 0 GGTGGTGCCC 0.977517 -34 ********** Masking position 2 Map Score: 31.8346 Number of sites scoring better than the average of aligned sites = 348 Number in coding regions = 316 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 GCACATTAAAGGAGGAAGCACC 7 1 0 GGGGAGCACC 0.983732 -280 GCGTTTTTTCGGGGAAATCACAGAATGGAAAA 11 30 1 GGGAATCACA 0.89045 -271 CCGGCCGCAGGGCCGGTTCTCCCT 12 3 0 GGCGGTCTCC 0.985283 -298 CCGGCCCTGCGGCCGGTTCAAAGAAGAAGACG 12 19 1 GGCGGTCAAA 0.855953 -282 ACTCCGGTGAGGGGAGGTTTCAATAAAGTTAT 12 67 1 GGGAGTTTCA 0.646021 -234 GCACCGTAACGGCCGGTTCACCAAGGCCGATA 14 32 0 GGCGGTCACC 0.99213 -125 ACCGCCGGCAGGTGGGATCTCAAACAA 15 6 0 GGGGGTCTCA 0.982862 -168 GGCCAAAATCGGACAAGTCACACACTACGCCA 15 107 0 GGCAATCACA 0.854881 -67 TGCCGCGCTAGGGCGACGTTCACCGGATTTGT 15 140 1 GGCGAGTTCA 0.690382 -34 GTAGCGATGAGGTGGGGGCACCACCCGCTTGC 16 35 1 GGGGGGCACC 0.991631 -193 GTAGCGATGAGGTGGGGGCACCACCCGCTTGC 16 112 1 GGGGGGCACC 0.991631 -116 GTAGCGATGAGGTGGGGGCACCACCCGCTTGC 16 189 1 GGGGGGCACC 0.991631 -39 ** *** ***** Masking position 2 Map Score: 17.1139 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 186 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 6 ATTTCACATTTCTTACTTTTTGAAGGTTATG 3 61 0 TCTTCTTTTT 0.946965 -71 TCAAGTATTATCTTACTTTTTTCAACCTTAA 4 61 0 TCTTCTTTTT 0.946965 -31 CGTTTACTCTCCCTTTTTCAGGGAGAGT 5 8 1 TCTCCTTTTT 0.980552 -115 GTTTAATGAATCGCGCTTTTTCATCATCATA 6 13 1 TCGCCTTTTT 0.936041 -42 CGGGCGTTCTTTTTTCCTTTTATCCCTTCTA 7 46 0 TTTTCCTTTT 0.910071 -235 CATCTCACCATTTTCAAGTATCA 7 268 0 TCTCCCATTT 0.895893 -13 AGCAAGCCTTTCTCTCTTTTTA 8 2 0 TCTCCTTTTT 0.980552 -210 TAATACAGCCTTTCTCTTTTTACTATAAATG 8 33 1 TTTCCTTTTT 0.969153 -179 CATTCCGACAATTCGCCTTTTACATCATTTT 8 97 0 ATTCCCTTTT 0.842826 -115 CGACATCCTATTTCTCTATTTTATGTCATCT 8 165 0 TTTCCTATTT 0.854981 -47 AAATGTAAGCATTTTCTTTTTGGGGGAGAGA 11 195 1 ATTTCTTTTT 0.676152 -106 AATACTTGCATCGTGCTTTTTAAGTAAGCCT 11 226 1 TCGTCTTTTT 0.838261 -75 TTTCAATAAATTTCCCCTTTAAGAGTGTTGT 11 266 0 TTTCCCTTTA 0.842826 -35 AAAACACATGTTTCACCTTTATCGCCAGTTG 12 138 0 TTTCCCTTTA 0.842826 -163 **** ****** Masking position 9 Map Score: 15.3575 Number of sites scoring better than the average of aligned sites = 827 Number in coding regions = 650 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 7 GTTTTCCCCCTGCTTTCCTTC 1 70 0 TTTTCCCCCT 0.84965 -11 TTTTTTTATGTTTGCTTCCAGAAATATAAT 5 38 1 TTTGCTTCCA 0.779915 -85 GGTGCTTCCTCCTTTAATGT 7 1 1 GGTGCTTCCT 0.952445 -280 GCTGTGCCTCCAGTATTATAAT 8 200 0 TGTGCCTCCA 0.978027 -12 CCGCAGGGCCGGTTCTCCCT 12 1 0 GGTTCTCCCT 0.900119 -300 CATTTTGATTTTCCTCCTGCCGAATGAC 12 283 0 TTTTCCTCCT 0.779915 -18 AGCGTTCCGCTGTGCCTCTTCAGGTGTTTG 13 267 1 TGTGCCTCTT 0.795453 -34 GCAAGCGGGTGGTGCCCCCACCTCATCGCT 16 37 0 GGTGCCCCCA 0.991242 -191 GCAAGCGGGTGGTGCCCCCACCTCATCGCT 16 114 0 GGTGCCCCCA 0.991242 -114 GCAAGCGGGTGGTGCCCCCACCTCATCGCT 16 191 0 GGTGCCCCCA 0.991242 -37 ********** Masking position 3 Map Score: 12.6608 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 220 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 8 TTTCTTTATGCGGCCTTTCTTGTGTATTTAA 2 51 1 CGGCTTTCTT 0.8467 -85 GAAATTTAGAAAGCGTTTTTACCGTGATCCG 3 29 0 AAGCTTTTTA 0.888921 -103 AAACGGCGTTTTTTTTAGATTTGG 4 4 1 CGGCTTTTTT 0.908085 -88 CTTAACAAACAAGCTTTTTCAAATTCCTATG 4 35 0 AAGCTTTTCA 0.902631 -57 CCAGAAGCAAAGGCTTTTTCTCCCGCTTCTG 7 104 1 AGGCTTTTCT 0.953426 -177 TGTATTAAGCAAGCCTTTCTCTCTTTTTA 8 9 0 AAGCTTTCTC 0.875541 -203 TTGCTTAATACAGCCTTTCTCTTTTTACTAT 8 28 1 CAGCTTTCTC 0.797275 -184 GGCTAGTTTTAGGCTTTTTCCTTGC 9 5 0 AGGCTTTTCC 0.944089 -39 CCGCAAATAAAGGCGTTTTTTCGGGGAAATC 11 18 1 AGGCTTTTTT 0.946444 -283 ATTTAAGTTTAAGCCTATTCTCATTATAAAC 11 102 0 AAGCTATTCT 0.798368 -199 AAATTTTTATAAGCTTATTTAAGTTTAAGCC 11 118 0 AAGCTATTTA 0.641965 -183 AGTAAAATGTAAGCATTTTCTTTTTGGGGGA 11 191 1 AAGCTTTTCT 0.946443 -110 **** ****** Masking position 6 Map Score: 8.87699 Number of sites scoring better than the average of aligned sites = 880 Number in coding regions = 694 Number in noncoding regions = 186 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 9 GTCTTTCACCTCAAGTATTATCTTACTTT 4 73 0 ACCTCAGTTT 0.947748 -19 AGAACGCCCGGCCTCTAGTGCTTCTTAGAAAG 7 67 1 GCCTCTGTCT 0.980012 -214 AAAAGCCTTTGCTTCTGGTTTTCCTTTCTAAG 7 90 0 GCTTCTGTTT 0.951936 -191 CCGAGCAAACACCTCTTGTGTTTTGAATATTC 7 139 1 ACCTCTGTTT 0.959358 -142 GCTGTGCCTCCAGTATTATAATTCCCC 8 195 0 GCCTCCGTTT 0.975004 -17 AATGAGGTTAGCCTCTTGTTCAGACATCAAAA 10 37 1 GCCTCTGTCA 0.897825 -127 TTTTAAGTAAGCCTCATGTTTTTACAACACTC 11 243 1 GCCTCAGTTT 0.985185 -58 CCGCTGTGCCTCTTCAGGTGTTTGTCGGCTTC 13 273 1 TCTTCAGTTT 0.701762 -28 ****** ** ** Masking position 4 Map Score: 4.65163 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 40 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 GAGAACTGTGTCGCTTTCAAAGGA 1 5 0 TCGCTTTCAA 0.724879 -76 CACGGTAAAAACGCTTTCTAAATTTCACAT 3 34 1 ACGCTTTCTA 0.681385 -98 TTATATCATTGCACGTTCATTTCACATTTC 3 80 0 GCACGTTCAT 0.901863 -52 ACTAGAGGCCGGGCGTTCTTTTTTCCTTTT 7 56 0 GGGCGTTCTT 0.91705 -225 GTTTATGATAGCGCTTTCATTTATAGTAAA 8 51 0 GCGCTTTCAT 0.968477 -161 TCATCGCGCTGCGCGCTCTGCATCGTCGTC 13 53 0 GCGCGCTCTG 0.968586 -248 TCATCGCGCTGCGCGCTCTGCATCGTCGTC 13 111 0 GCGCGCTCTG 0.968586 -190 ATCACAATTTGCGCGTTCAAGTCATTGGCA 13 222 1 GCGCGTTCAA 0.9863 -79 CCGCTGCGCAGCGCGTTCATACCGCCGAGG 14 70 0 GCGCGTTCAT 0.989445 -87 ********** Masking position 7 Map Score: 6.9209 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 310 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 11 GCGCTTTTTCATCATCATAAGATATAAGGAAGAAGCTATC 6 25 1 ATAAAAAAAA 0.97424 -30 CTTTTACATCATTTTTAAAAGAAATAAAGACGTTTATGAT 8 72 0 ATAAAAAAAA 0.97424 -140 GGGAAATCACAGAATGGAAAAAAAAAATTATAGGTAAACA 11 41 1 ATGAAAAAAA 0.909463 -260 GTTTAAGCCTATTCTCATTATAAACAATAATCAGACATTT 11 87 0 ATATAAAAAA 0.871425 -214 AAAGTTGACCAGCATGACAATAGATAAACAACTGGCGATA 12 110 1 ATAAAAAAAA 0.97424 -191 AAAAAAATAAAGGTTTAGAAAAAAAACACATGTTTCACCT 12 151 0 ATAAAAAACA 0.909463 -150 ATAACGGTTTAAGGTCAAAAGATAAAAAAAATAAAGGTTT 12 175 0 ATAAAAAAAA 0.97424 -126 TTGACCTTAAACCGTTATAATAGACAAGGACCCATTCTTT 12 197 1 ATAAAAAAAA 0.97424 -104 * * * ** * * ** * Masking position 10 Map Score: 3.28498 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 81 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 12 TTTTTAAAAGAAATAAAGACGTTTATGATAGCGC 8 67 0 AAATAAGTTT 0.82989 -145 TCTTATATAGAAAATAAAATGATTTTTCCTAACA 10 91 0 AAAAAAGATT 0.861382 -73 CTATATAAGAAAAATAAAATGTTTTCTAAATATG 10 115 1 AAAAAAGTTT 0.971949 -49 ATGGAAAAAAAAAATTATAGGTAAACATTTAACA 11 54 1 AAAAAAGTAA 0.575595 -247 ATGTTCTTTCAAAAGCAAAGGGTTTTAGTTCCAG 11 152 1 AAAAAAGGTT 0.902057 -149 CTCTCCCCCAAAAAGAAAATGCTTACATTTTACT 11 191 0 AAAAAAGCTT 0.902057 -110 AAATTTATTGAAAAGGAGATGTTATAT 11 284 1 AAAAAAGTTA 0.906006 -17 ACTTTTTTTAAAAAAGATAACTTTATTGAAACCT 12 81 0 AAAAAACTTT 0.817268 -220 GGTTTAGAAAAAAAACACATGTTTCACCTTTATC 12 146 0 AAAAAAGTTT 0.971949 -155 AAAAGATAAAAAAAATAAAGGTTTAGAAAAAAAA 12 165 0 AAAAAAGTTT 0.971273 -136 **** * * **** Masking position 7 Map Score: 6.0308 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 120 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 13 CTTTTTCAGGGAGAGTTTTTTTATGTTTGCT 5 23 1 GAGAGTTTTT 0.923382 -100 GATAGCTTCTTCCTTATATCT 6 44 0 GATAGTTCTT 0.721034 -11 GCCCGGCCTCTAGTGCTTCTTAGAAAGGAAA 7 72 1 TAGTGTTCTT 0.685017 -209 AGTATTGGACGAGAGCTTTTTGGTGGCTTAT 7 203 1 GAGAGTTTTT 0.923382 -78 CCGGCAATGAGAGTGATACTTGAAAATGGTG 7 255 1 GAGTGTACTT 0.958695 -26 ATTACATACTGGGAGGTTTTTATT 10 150 1 GGGAGTTTTT 0.737936 -14 TTTTGGGGGAGAGAAATACTTGCATCGTGCT 11 212 1 GAGAATACTT 0.684286 -89 CCCCTCACCGGAGTGCGTCTTTATCAATGAC 12 50 0 GAGTGGTCTT 0.945314 -251 TGACCTCCACGAGTGCTATTTCTCATCGCGC 13 132 0 GAGTGTATTT 0.895119 -169 GCGGGAGTGCGTGAGAGACTTGCCGGT 14 140 1 GTGAGGACTT 0.827766 -17 CTGTGGCGTAGTGTGTGACTTGTCCGATTTT 15 104 1 GTGTGGACTT 0.801761 -70 ***** ***** Masking position 10 Map Score: 3.47327 Number of sites scoring better than the average of aligned sites = 350 Number in coding regions = 288 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 14 CCATTGGAGGCTGGCTTGCGTCAATGAGGTTA 10 15 1 CGGTTGCGTC 0.958156 -149 CCTCCCCTCACCGGAGTGCGTCTTTATCAATG 12 52 0 CGGGTGCGTC 0.995737 -249 CAGCCCATCACCGGCGGGCGTCTTGACCTCCA 13 154 0 CGGGGGCGTC 0.990586 -147 TGTGCCTCTTCAGGTGTTTGTCGGCTTCGTTG 13 277 1 CGGGTTTGTC 0.8014 -24 ATGAGGAGTGCGGGAGTGCGTGAGAGACTTGC 14 131 1 CGGGTGCGTG 0.994725 -26 TCCTACAAATCCGGTGAACGTCGCCCTAGCGC 15 144 0 CGGGAACGTC 0.963078 -30 CACCCGCTTGCGGGGGAGAGTGGCGCTGATGA 16 56 1 CGGGAGAGTG 0.986615 -172 CACCCGCTTGCGGGGGAGAGTGGCGCTGATGA 16 133 1 CGGGAGAGTG 0.986615 -95 CACCCGCTTGCGGGGGAGAGTGGCGCTG 16 210 1 CGGGAGAGTG 0.986615 -18 * ** ******* Masking position 11 Map Score: 15.4837 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 30 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 15 ********** No masking Map Score: 2.34012e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0