AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00380_ctra_reg_300.orf -o00380_ctra_300.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -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 = 0.41 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 gatC 200 Glu-tRNA Gln Amidotransferase (C subunit) #2 sucA 300 Oxoglutarate Dehydrogenase #3 dhnA 300 Predicted 1,6-Fructose biphosphate aldolase (dehydrin family) #4 ydaO 153 PP-Loop Superfamily ATPase #5 surE 100 SurE-like Acid Phosphatase #6 ubiA 111 4-hydroxybenzoate octaphenyltransferase #7 CT355 300 hypothetical protein #8 CT421 300 hypothetical protein #9 CT421.1 184 hypothetical protein #10 CT423 132 (CBS Domain) #11 rsbV_1 188 Sigma Regulatory Factor #12 CT425 177 hypothetical protein #13 CT426 196 Fe-S oxidoreductase #14 lpxC 100 UDP-3-O-Acyl GlcNAc Deacetylase #15 cutE 63 Apolipoprotein N-Acetyltransferase #16 yciA 135 Acyl-CoA Thioester Hydrolase #17 CT538 300 hypothetical protein #18 minD 300 chromosome partitioning ATPase-CHLTR plasmid protein homolog GP5D #19 trpS 198 Tryptophanyl tRNA Synthetase #20 hemA 300 Glutamyl tRNA Reductase #21 ygcA 85 rRNA Methyltransferse #22 hctA 300 Histone-Like Developmental Protein Motif number 1 TTAATAAAGTCTTTTTTTGTTCTCTCTATT 1 67 1 CTTTTTTTGT 0.669534 -134 CTGCTCACTTTTTGCTCTGTCTGAGCAAAA 2 63 0 TTTGCTCTGT 0.392648 -238 GCAAACTTTGCTTTTTTTTTAAGTATCGAA 2 209 0 CTTTTTTTTT 0.887716 -92 AAAAGCAAAGTTTGCTTTTTTTGAAAAATA 2 224 1 TTTGCTTTTT 0.519264 -77 AACTATTTTCTCTTTTTAATTTTTA 3 6 1 TTTTCTCTTT 0.841848 -295 CAGAGTCTTTCATTTTCTTTACCTCACCTT 3 100 1 CATTTTCTTT 0.748789 -201 TTTACAAAGCCCTTTTCTGTGCAAAAGAAT 4 11 0 CCTTTTCTGT 0.846099 -143 GTAAAGAAGCTCTTTTCTTTCTAAGACTTA 4 36 1 TCTTTTCTTT 0.826408 -118 TCCTCCTCCCCTTTTTCTTTGGATCTTACC 7 232 0 CTTTTTCTTT 0.948626 -69 TTAACATGCACCTTTTCTTTGAAACTCGTT 8 201 1 CCTTTTCTTT 0.955463 -100 CTAATCATTATCTTCTTTTTAAAAAGAAGG 9 16 1 TCTTCTTTTT 0.725873 -169 CACTAAATTCCCTTCTTTTTAAAAAGAAGA 9 26 0 CCTTCTTTTT 0.922676 -159 AGTAGAGCGCCGTTTTTTTTTCAATAGAGC 9 71 0 CGTTTTTTTT 0.517534 -114 AGAGTTGCTATTTTCTTTTTAAATCCCTTC 9 127 1 TTTTCTTTTT 0.69504 -58 TGTAACATAGCCTTTTCTTTGAAGATCCTC 12 85 1 CCTTTTCTTT 0.955463 -93 CGTATATTATCCTTTTTTTTTTTTAGCAAG 14 58 0 CCTTTTTTTT 0.90182 -43 TAAGGGGATTCTTTTTCTCTCATCTTGAAT 15 19 1 CTTTTTCTCT 0.861405 -45 TTAGGCCTGTTTTGCTTTTTGTAAAAATAC 17 154 1 TTTGCTTTTT 0.519264 -147 CGCCCATATCCCTGTTCTCTACCTACTCTC 17 198 0 CCTGTTCTCT 0.773874 -103 GCCCCTAAAGCCTGCTTTTTAAAAATAGTC 19 70 0 CCTGCTTTTT 0.849742 -129 TCGCTCCTTGCTTTTTCTTTAATTCTTAAT 19 140 0 CTTTTTCTTT 0.948626 -59 TCGGTTGGCTCATTCTCTTTGTTTCGTATT 20 245 0 CATTCTCTTT 0.794754 -56 AGCATACAATCTTTTTCTTTAGAAAGGGA 20 282 1 CTTTTTCTTT 0.948626 -19 TATTTTAGCGCTTTCTCTTTTTTATAGAGG 21 11 1 CTTTCTCTTT 0.95998 -75 CTCATTGATCCCTTCTCTTTTTT 21 73 1 CCTTCTCTTT 0.965361 -13 AAGAAAGGAGCTTGTTCTCTTGTTAGAAGA 22 14 0 CTTGTTCTCT 0.746554 -287 GAACAAGCTCCTTTCTTTCTTTTCTAAACA 22 27 1 CTTTCTTTCT 0.775636 -274 ********** Masking position 6 Map Score: 32.3702 Number of sites scoring better than the average of aligned sites = 452 Number in coding regions = 452 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 Motif number 2 ACTTCAACGTACTTTTTTCAGCAAGAAAAG 6 31 1 ACTTTTTTCA 0.97018 -81 ATTTTTCTGGAATTTTTTCACTTAAATATC 7 40 0 AATTTTTTCA 0.953111 -261 CCGTCAGAACACTTTTAACAAAAAAGCGTT 7 100 0 ACTTTTAACA 0.575767 -201 TTACACCAAAAATTTTTTCAGGACCACACA 12 60 0 AATTTTTTCA 0.953111 -118 GCGAAAGCAAAATTTTTACAGATAAAGGAC 12 125 1 AATTTTTACA 0.805888 -53 ACTAGGTAGTAATTTTTTGATATCGCTTGC 14 29 1 AATTTTTTGA 0.664918 -72 CTCGACATAGAAGTTTTTCATTTGAATTCA 17 27 1 AAGTTTTTCA 0.865264 -274 CAAGCTCATTACGTTTTTCAATAAGACTTT 17 56 0 ACGTTTTTCA 0.911336 -245 ACTTATCCTTACTTTTTTCAGTTGCTTAAT 17 281 0 ACTTTTTTCA 0.97018 -20 GAGCTTTCTTACTTTATTCATCTCCTTTAA 18 179 1 ACTTTATTCA 0.775897 -122 CAGACTACAAAATTTTTTCAATGCAGAGAA 20 185 1 AATTTTTTCA 0.953111 -116 TATAGAGGGCACTTTTATCAACAGGGCCCT 21 33 1 ACTTTTATCA 0.869195 -53 GTTTTAAACTATTTTTTTCAGTTTTAATTT 22 259 0 ATTTTTTTCA 0.80843 -42 ********** Masking position 1 Map Score: 14.5976 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 36 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 Motif number 3 CTTATGCAGAATAAAATCCTTCGTACTTTTT 1 151 0 AAAAATCCTT 0.877875 -50 GAGTCTTTAGTTAAGATCTTTGAGAAGGTGA 3 123 0 TAAGATCTTT 0.766189 -178 GGCTTTGTAAAGAAGCTCTTTTCTTTCTAAG 4 30 1 AAAGCTCTTT 0.923892 -124 TTTCAGCAAGAAAAGCTCCTTCTGATTACAA 6 46 1 AAAGCTCCTT 0.983864 -66 TGATTACAATACAAGATCTTTTACACCTATA 6 68 1 AAAGATCTTT 0.895824 -44 TTTTTAGAATATAAGCTGCTTTGTTTGGGTG 7 179 1 AAAGCTGCTT 0.910103 -122 GTTTTTAGGTAGAAAAACCTTAAGAATTTTG 7 268 0 AAAAAACCTT 0.555073 -33 AGCAGAGGACTGAAGATCCTTGTGTCGTCGG 8 98 0 TAAGATCCTT 0.942726 -203 AAATAACCCAACAAGATCCTTCTGCCTTCCT 9 163 0 AAAGATCCTT 0.977372 -22 TATCACGATCAAAAGCACCTTTTCGTAATCT 11 93 0 AAAGCACCTT 0.913661 -96 GCCTTTTCTTTGAAGATCCTCTGTAAAGCAT 12 94 1 TAAGATCCTC 0.690715 -84 ATGTCGAGCAAGAAAATCATTTCT 17 4 0 AAAAATCATT 0.499687 -297 TCCGTTAGGCACAAGCTCATTACGTTTTTCA 17 66 0 AAAGCTCATT 0.894424 -235 TAACAAGAGAACAAGCTCCTTTCTTTCTTTT 22 19 1 AAAGCTCCTT 0.983864 -282 AGATGTCAAATAAAGCTGCTTTAGGATCCTT 22 177 1 TAAGCTGCTT 0.794153 -124 * ********* Masking position 4 Map Score: 13.0687 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 276 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 4 GAACAAATACTTTGGAATGAGTATTTTATTAG 2 124 0 TTTGAAGAGT 0.784179 -177 AAAATAAAAATTTTGCTATGGGAATTTTCTAA 2 248 1 TTTGCTTGGG 0.658934 -53 ATAACTGATCTTTAGAACGGGGAAAAATCGCA 3 70 1 TTTGAAGGGG 0.933241 -231 GGAAAGATCGTTTATCTTGAGGTTTTCTCCTA 3 156 1 TTTTCTGAGG 0.881088 -145 TTTTGTTTCCTTTGGCTTGAGGATATAACGCT 7 74 1 TTTGCTGAGG 0.929736 -227 GAAGAGGGTTTTTCTCACGAGGAATTTTTAAA 8 229 0 TTTTCAGAGG 0.939866 -72 GCGCCGTTTTTTTTTCAATAGAGCTATGAGTC 9 63 0 TTTTCATAGA 0.37231 -122 GTAACAGCTGTTTTGATAGGGTCTTTCCTACT 13 77 1 TTTGATGGGT 0.504782 -120 GGCCACATCCTTTAGATAGGGGTCTTCCTAGT 13 106 0 TTTGATGGGG 0.868891 -91 TAGCAAGTGTTTTAGAACTAGGTAGTAATTTT 14 13 1 TTTGAATAGG 0.853564 -88 AAGGCTTCCCTTTAGAAGGAGGCTGGTGATTA 17 230 1 TTTGAAGAGG 0.959388 -71 GTTTATCACGAGGTGAAGCCCTT 18 288 0 TTTTCAGAGG 0.939866 -13 TAACATCATCTTTAGAAAGATGATTGTTAGGA 19 22 0 TTTGAAGATG 0.510461 -177 TTACATTATTTTTCTAAAGAGAGCATAACTAT 20 37 0 TTTTAAGAGA 0.670469 -264 AATCTTTTTCTTTAGAAAGGGA 20 289 1 TTTGAAGGGA 0.682549 -12 CGCTTTCTCTTTTTTATAGAGGGCACTTTTAT 21 19 1 TTTTATGAGG 0.862475 -67 AGAGGGCACTTTTATCAACAGGGCCCTCTTTC 21 36 1 TTTTCACAGG 0.585076 -50 TACCGCTCTGTTTATCAATAGGTTATTTTTCC 22 140 0 TTTTCATAGG 0.794087 -161 TCAGTTTTAATTTTTAATTAGTTTGTTTGTTC 22 240 0 TTTTAATAGT 0.334234 -61 *** *** **** Masking position 3 Map Score: 14.2279 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 272 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 AGAATAAAATCCTTCGTACTTTTTTACACTAAAA 1 141 0 CCTCACTTTT 0.883402 -60 TTTGTTTATGCCTGCTCACTTTTTGCTCTGTCTG 2 70 0 CCTCACTTTT 0.883402 -231 AATACCCTAGCCTCCTGACTTCTTACAAAAGCTA 2 177 0 CCTCACTCTT 0.820775 -124 TGTTCTGACGGCTGGGTCCCTCCTCCCCTATAGC 7 119 1 GCTGCCTCCT 0.8377 -182 TAAAAAAGAACCTACCCTCGTCCTAGGTAAAAGC 7 151 0 CCTCTCTCCT 0.914963 -150 TTGGGTTGTTCCTCCTCCCCTTTTTCTTTGGATC 7 237 0 CCTCCCTTTT 0.974396 -64 CCAACAAGATCCTTCTGCCTTCCTGAATGGGAAG 9 153 0 CCTCCCTCCT 0.976473 -32 TGCAAGTAAGCCTCGAGTCTTTTTGTGGACTCTC 10 66 1 CCTGTCTTTT 0.845136 -67 CGTCTGTTGCGCTACAGCCCTTCTCAGTATAGGA 13 43 1 GCTCCCTTCT 0.93916 -154 CCTTTAACCTCATTCGTCCATGCTTATGGACAAA 18 202 1 CATCCCTGCT 0.812898 -99 GGGGAGGAAGCCTCGCTCCTTTTTAGTTGCTTTA 18 251 0 CCTGCCTTTT 0.954651 -50 TGGGAAAAAACCTCGCTCCTTGCTTTTTCTTTAA 19 148 0 CCTGCCTGCT 0.923079 -51 AGAGAAGAAGCATACAATCTTTTTCTTTAGAAAG 20 274 1 CATCTCTTTT 0.663954 -27 TTCCTCTTCTCATTGATCCCTTCTCTTTTTT 21 65 1 CATGCCTTCT 0.883819 -21 AAGAGAACAAGCTCCTTTCTTTCTTTTCTAAACA 22 23 1 GCTCTCTTCT 0.800068 -278 TTTGACATCTCCTTGTACCGCTCTGTTTATCAAT 22 153 0 CCTGCCCTCT 0.818897 -148 TGTTCAAATTCATGCAACCATTTTCTAGAATCTA 22 211 0 CATCCCTTTT 0.884012 -90 *** * ** **** Masking position 3 Map Score: 17.6619 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 129 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 Motif number 6 CTTTTAATCTTTTTTGCAATTTAATAAAGTC 1 47 1 TTTTTGCATT 0.825312 -154 TTAAAGATGCGTTTTGCTGTCGCAAAAGACG 1 95 1 GTTTTGCTTC 0.717678 -106 GCCTGCTCACTTTTTGCTCTGTCTGAGCAAA 2 64 0 TTTTTGCTTG 0.611858 -237 AACTATTTTCTCTTTTTAATTTTT 3 4 1 TATTTTCTTT 0.500647 -297 AAATCGCAGAGTCTTTCATTTTCTTTACCTC 3 94 1 GTCTTTCATT 0.659905 -207 GTGTTTTGCTCTTAGTTACCCCT 7 3 1 GTTTTGCTTT 0.91591 -298 TTTTCTGGAATTTTTTCACTTAAATATCGAA 7 37 0 TTTTTTCATT 0.860449 -264 TTTAAAGCGGGTATTTCTCTAGAATAGCCCC 8 157 0 GTATTTCTTA 0.279395 -144 AGCGCCGTTTTTTTTTCAATAGAGCTATGAG 9 65 0 TTTTTTCATA 0.571376 -120 GCAGAGTTGCTATTTTCTTTTTAAATCCCTT 9 125 1 TATTTTCTTT 0.500647 -60 ATCTGTAAAAATTTTGCTTTCGCATGCTTTA 12 117 0 ATTTTGCTTC 0.261008 -61 CAGTTTGTGAGTTTTGCTTTTCACGGGGACA 13 167 0 GTTTTGCTTT 0.91591 -30 CGACATAGAAGTTTTTCATTTGAATTCAAAG 17 29 1 GTTTTTCATT 0.908617 -272 AGCTCATTACGTTTTTCAATAAGACTTTGAA 17 53 0 GTTTTTCATA 0.682505 -248 GGTTAGGCCTGTTTTGCTTTTTGTAAAAATA 17 152 1 GTTTTGCTTT 0.91591 -149 TTATCCTTACTTTTTTCAGTTGCTTAATGGC 17 278 0 TTTTTTCATT 0.860449 -23 GTAAGGCGTAGTATTTCTTTTAGTCTTCTGT 20 65 1 GTATTTCTTT 0.642009 -236 TTTTTTAACGGTTTTTCTATTTTCGTCTCCA 20 156 1 GTTTTTCTTT 0.934275 -145 GACTACAAAATTTTTTCAATGCAGAGAACGA 20 187 1 TTTTTTCATG 0.590001 -114 ACAAGCTCCTTTCTTTCTTTTCTAAACAAGG 22 29 1 TTCTTTCTTT 0.632383 -272 TTTATAAAAAATTTTTCTATTAACAGAGGAA 22 113 1 ATTTTTCTTT 0.663869 -188 TTTAAACTATTTTTTTCAGTTTTAATTTTTA 22 256 0 TTTTTTCATT 0.860449 -45 ******** ** Masking position 5 Map Score: 14.7971 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 271 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 Motif number 7 CCTTCGTACTTTTTTACACTAAAAACACTCTTAC 1 131 0 TTTTTAAAAA 0.919751 -70 AAAGTTTGCTTTTTTTGAAAAATAAAAATTTTGC 2 230 1 TTTTTTAAAA 0.802581 -71 CTATTAGATCTTTTTAAAATAATAAGAAAAATAA 5 59 0 TTTTTAAAAA 0.921377 -42 TTCAACGTACTTTTTTCAGCAAGAAAAGCTCCTT 6 33 1 TTTTTTAAAA 0.837977 -79 AATACAAGATCTTTTACACCTATAATCCCATAAT 6 75 1 CTTTTAATAA 0.38769 -37 TTTTCTGGAATTTTTTCACTTAAATATCGAAAAG 7 34 0 TTTTTTATAA 0.613425 -267 CGTCAGAACACTTTTAACAAAAAAGCGTTATATC 7 95 0 CTTTTACAAA 0.560271 -206 GGTAGGTTCTTTTTTAGAATATAAGCTGCTTTGT 7 169 1 TTTTTAAATA 0.441976 -132 TCTTAAGGTTTTTCTACCTAAAAACTACAAATCA 7 274 1 TTTCTACAAA 0.558819 -27 ATTCCCTTCTTTTTAAAAAGAAGATAATGATTAG 9 16 0 TTTTAAAAAA 0.418958 -169 GAGCGCCGTTTTTTTTTCAATAGAGCTATGAGTC 9 63 0 TTTTTTCTAA 0.492138 -122 ACGATAAAAATTTTTATCGATATAGAGATTTCTA 10 28 0 TTTTTACTAA 0.690016 -105 TCGATAAAAATTTTTATCGTAACATGCAAGTAAG 10 42 1 TTTTTACAAA 0.877756 -91 ACACCAAAAATTTTTTCAGGACCACACAACTTTG 12 54 0 TTTTTTAACA 0.489083 -124 GAAAGCAAAATTTTTACAGATAAAGGACTTCCTG 12 127 1 TTTTTAATAA 0.782196 -51 CCTGTTTTGCTTTTTGTAAAAATACTTTTGCAAG 17 159 1 TTTTTGAAAA 0.57558 -142 AGGAGCGAGGTTTTTTCCCAAACAGGGTCCCGCC 19 162 1 TTTTTTCAAA 0.761761 -37 AGTTATGCTCTCTTTAGAAAAATAATGTAAGGCG 20 39 1 TCTTTAAAAA 0.495477 -262 TTGTTTCGTATTTTTATACCAATATTTTTGAGAC 20 223 0 TTTTTAAAAA 0.921148 -78 TCCCTTTCTAAAGAAAAAGATTGTATGC 20 283 0 TTTCTAAAAA 0.673268 -18 ATAGAAAAATTTTTTATAAAACTATGTGCTGCAT 22 99 0 TTTTTAAACA 0.68392 -202 TTATAAAAAATTTTTCTATTAACAGAGGAAAAAT 22 114 1 TTTTTCAAAA 0.607897 -187 ****** * ** * Masking position 3 Map Score: 10.3355 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 253 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 Motif number 8 GTTTATCTTGAGGTTTTCTCCTACGAAATAAA 3 165 1 AGGTTTCCCT 0.832198 -136 TTCTGACGGCTGGGTCCCTCCTCCCCTATAGC 7 121 1 TGGGCCCCCT 0.882569 -180 GGACGAGGGTAGGTTCTTTTTTAGAATATAAG 7 162 1 AGGTCTTTTT 0.49991 -139 CTGTTTTGATAGGGTCTTTCCTACTAGGAAGA 13 84 1 AGGGCTTCCT 0.972717 -113 TCCTTTAGATAGGGGTCTTCCTAGTAGGAAAG 13 99 0 AGGGTCTCCT 0.928699 -98 TAAAGGGGCTCCCTTACTAGCTTAC 15 49 0 AGGGCTCCTT 0.974704 -15 TATGGGCGGAAAGGCTTCCCTTTAGAAGGAGG 17 220 1 AAGGTTCCTT 0.615405 -81 CTCCCCTACAAGGGCTTCACCTCGTGATAAAC 18 279 1 AGGGTTCCCT 0.972476 -22 AGCAGGCTTTAGGGGCTTATTTTTCGTAAAAA 19 84 1 AGGGCTTTTT 0.87796 -115 TTTCCCAAACAGGGTCCCGCCTCGTGAGTCAG 19 175 1 AGGGCCCCCT 0.984785 -24 TTTTATCAACAGGGCCCTCTTTCCTCTTCTCA 21 45 1 AGGGCCTTTT 0.855465 -41 GGGTCTGAATAGGGTTTCTTTTAATAGAAAGC 22 66 0 AGGGTTCTTT 0.87797 -235 **** *** *** Masking position 12 Map Score: 6.59569 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 81 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 Motif number 9 GATAAACGATCTTTCCTGGAGTCTTTAGTT 3 142 0 CTTTCCTGGA 0.972151 -159 CTTTCTAAGACTTACCTGGATTTCTAATTC 4 52 1 CTTACCTGGA 0.96057 -102 ACAATGTAGTCCTCCATGGACAAAATTAGG 4 115 1 CCTCCATGGA 0.855125 -39 TCCTTTCCTAGATTTAAATAAA 5 3 1 CTTTCCTAGA 0.944139 -98 GATCTTACCGCCTCCCTAGAGATGTGGCAA 7 211 0 CCTCCCTAGA 0.956583 -90 GATCCTTCTGCCTTCCTGAATGGGAAGGGA 9 150 0 CCTTCCTGAA 0.845388 -35 CTTTAGGATCCTTACCTAGATTCTAGAAAA 22 195 1 CTTACCTAGA 0.921845 -106 ********** Masking position 10 Map Score: 2.63346 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 42 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 Motif number 10 CGCTTCAGTAAGAGTGTTTTTAGTGTAAAA 1 124 1 AGAGTGTTTT 0.921603 -77 ATAGATCAGGAGAGATTTTGGCTAATAAAA 2 103 1 AGAGATTTTG 0.777776 -198 GCTCTGACGGAGAGTGTGTTGCGCTTTTTT 3 245 1 AGAGTGTGTT 0.869399 -56 AATTTAGAGAGTTCTCCGTCAAAAC 8 6 1 AGAGAGTTCT 0.938493 -295 AATGGCGTTTAGAGAGTTTTGACGGAGAAC 8 21 0 AGAGAGTTTT 0.964311 -280 GGTCTATAGAAGAGGGTTTTTCTCACGAGG 8 239 0 AGAGGGTTTT 0.908095 -62 TTATCGATATAGAGATTTCTAGAGGGAAGC 10 19 0 AGAGATTTCT 0.775438 -114 CAACAGCTACAGAGAGTGTGATTTACTAGT 11 34 0 AGAGAGTGTG 0.896536 -155 ********** Masking position 3 Map Score: 2.31668 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 76 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 11 TCGAAGATGCTCCTATTTTAAATA 3 287 0 AGATGCTCCT 0.839058 -14 GAGCTTCTTTACAAAGCCCTTTTCTGTGCAA 4 17 0 AAAAGCCCTT 0.885266 -137 GGGCTTTGTAAAGAAGCTCTTTTCTTTCTAA 4 29 1 AGAAGCTCTT 0.899162 -125 TTTTCAGCAAGAAAAGCTCCTTCTGATTACA 6 45 1 GAAAGCTCCT 0.621134 -67 TCGAGTAACCAGGAAGTCCTTTATCTGTAAA 12 139 0 AGAAGTCCTT 0.711977 -39 TAAAGAAGTCATGAAGGCCTTATT 13 4 0 AGAAGGCCTT 0.872456 -193 ATGAGAGAAAAAGAATCCCCTTAGAAGTTAC 15 11 0 AGAATCCCCT 0.857087 -53 TAAGCTAGTAAGGGAGCCCCTTTA 15 50 1 AGGAGCCCCT 0.937058 -14 TAGTCGATTCAGGATGCCCCTACCCCTAGAG 17 113 1 AGATGCCCCT 0.952576 -188 TTATCACGAGGTGAAGCCCTTGTAGGGGAGG 18 278 0 GGAAGCCCTT 0.910277 -23 AGATGATGTTACATAGCCCCTGAATCAGACT 19 43 1 AATAGCCCCT 0.698667 -156 TTTTACGAAAAATAAGCCCCTAAAGCCTGCT 19 84 0 ATAAGCCCCT 0.896078 -115 GAGAAGAGGAAAGAGGGCCCTGTTGATAAAA 21 45 0 AGAGGGCCCT 0.76787 -41 CTAACAAGAGAACAAGCTCCTTTCTTTCTTT 22 18 1 ACAAGCTCCT 0.768131 -283 * ********* Masking position 11 Map Score: 6.44774 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 110 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 Motif number 12 CAGTTATATTAAAATAACCTTGGTGTTCAA 3 47 0 AAAATAACCT 0.936294 -254 AATAATAAGAAAAATAAACCAAGTATTATG 5 46 0 AAAATAAACC 0.730208 -55 TATATTCTAAAAAAGAACCTACCCTCGTCC 7 162 0 AAAAGAACCT 0.734593 -139 GTATTTCTCTAGAATAGCCCCGTGTATGGC 8 148 0 AGAATAGCCC 0.737141 -153 AAAATAACCCAACAAGATCC 9 175 0 AAAATAACCC 0.93218 -10 TTTTTGGTGTAACATAGCCTTTTCTTTGAA 12 78 1 AACATAGCCT 0.749915 -100 CTTATCCCTAAAAATAGACTTTTCTACCGG 18 108 1 AAAATAGACT 0.75819 -193 CTGCTTTTTAAAAATAGTCTGATTCAGGGG 19 59 0 AAAATAGTCT 0.640027 -140 ATTTTTACGAAAAATAAGCCCCTAAAGCCT 19 87 0 AAAATAAGCC 0.694646 -112 TAACAGAGGAAAAATAACCTATTGATAAAC 22 133 1 AAAATAACCT 0.936294 -168 GAAAAAATATCCTCTAGTTGTTG 22 288 0 AAAATATCCT 0.753138 -13 ********** Masking position 6 Map Score: 3.21735 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 47 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 Motif number 13 TTGGCTCTCAGGGGGTTTCC 2 1 0 GGGGGTTTCC 0.817706 -300 TTTATCTTGAGGTTTTCTCCTACGAAATAA 3 166 1 GGTTTTCTCC 0.935971 -135 CGCTTTTTTGGGTTTTCACCATATTTAAAA 3 266 1 GGTTTTCACC 0.672839 -35 TCTGACGGCTGGGTCCCTCCTCCCCTATAG 7 122 1 GGGTCCCTCC 0.958816 -179 GCTTTGTTTGGGTGTTTGCCACATCTCTAG 7 196 1 GGTGTTTGCC 0.73026 -105 TAAGAATTTTGGGTTGTTCCTCCTCCCCTT 7 249 0 GGGTTGTTCC 0.901218 -52 CTATAGAAGAGGGTTTTTCTCACGAGGAAT 8 236 0 GGGTTTTTCT 0.711369 -65 TGTTTTGATAGGGTCTTTCCTACTAGGAAG 13 85 1 GGGTCTTTCC 0.955582 -112 CCTTTAGATAGGGGTCTTCCTAGTAGGAAA 13 100 0 GGGGTCTTCC 0.947243 -97 AAAGGAGCGAGGCTTCCTCCCCTACAAGGG 18 263 1 GGCTTCCTCC 0.860242 -38 CAAGGAGCGAGGTTTTTTCCCAAACAGGGT 19 160 1 GGTTTTTTCC 0.926578 -39 TTCCCAAACAGGGTCCCGCCTCGTGAGTCA 19 176 1 GGGTCCCGCC 0.899197 -23 ********** Masking position 9 Map Score: 5.70221 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 89 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 Motif number 14 ********** No masking Map Score: -1.3476e-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 Motif number 15 GAGAGCCAATTTACTTGCTTCCTACCAAGG 2 22 1 TTACTTGCTT 0.953096 -279 GACTCGAGGCTTACTTGCATGTTACGATAA 10 55 0 TTACTTGCAT 0.784551 -78 AATTTTGCTTTCGCATGCTTTACAGAGGAT 12 109 0 TCGCATGCTT 0.765843 -69 TTTTTTGATATCGCTTGCTTGCTAAAAAAA 14 41 1 TCGCTTGCTT 0.948054 -60 AGGGGCTCCCTTACTAGCTTACATTCAAGA 15 41 0 TTACTAGCTT 0.784552 -23 CTACCTACTCTCACTTCCTTGCAAAAGTAT 17 180 0 TCACTTCCTT 0.842133 -121 CTTACTTTTTTCAGTTGCTTAATGGCAAAC 17 274 0 TCAGTTGCTT 0.919375 -27 TCGCTCCTTTTTAGTTGCTTTAATTCCTTT 18 243 0 TTAGTTGCTT 0.877888 -58 ********** Masking position 1 Map Score: 1.30032 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 53 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