AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00530_ctra_reg_300.orf -o00530_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 htrB 131 Acyltransferase #2 ybbP 274 hypothetical protein #3 glgX 117 Glycogen Hydrolase (debranching) #4 CT043 300 hypothetical protein #5 leuS 196 Leucyl tRNA Synthetase #6 yaeT 300 Omp85 Analog #7 CT242 68 (OmpH-Like Outer Membrane Protein) #8 lpxD 27 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase #9 dut 36 dUTP Nucleotidohydrolase #10 accD 71 AcCoA Carboxylase/Transferase Beta #11 sodM 131 Superoxide Dismutase (Mn) #12 yhxB 151 Phosphomannomutase #13 CT296 108 hypothetical protein #14 CT406 300 hypothetical protein #15 CT409 101 Amino acid permease #16 pcnB_1 214 PolyA Polymerase #17 lpxB 60 Lipid A Disaccharide Synthase #18 murA 211 UDP-N-Acetylglucosamine Transferase #19 lpxC 100 UDP-3-O-Acyl GlcNAc Deacetylase #20 cutE 63 Apolipoprotein N-Acetyltransferase #21 yciA 135 Acyl-CoA Thioester Hydrolase #22 CT538 300 hypothetical protein #23 glmU 52 UDP-GlcNAc Pyrophosphorylase #24 cpxR 178 HTH Transcriptional Regulatory Protein and Receiver Domain #25 mrsA 245 Phosphoglucomutase #26 murB 132 UDP-N-Acetylenolpyruvoylglucosamine Reductase #27 nusB 300 Transcription termination factor Motif number 1 GTTTTCATTATTTTCAGCAAAACAAGAAGCTGTACCAA 2 218 0 TTTAAAAAAA 0.9421 -57 AAGTTTTGCTATCATACAACAAAAGGAAGAGG 3 5 1 TTTTATAAAA 0.802993 -113 CATAAGCAGGTTTGTTAGTAAATGATTAGAGCCGCGAT 4 236 0 TTTTAAAATA 0.617319 -65 AATTCTTTCCTATAAAAATATAACCAATAGGTG 7 46 0 TTTTAAAAAA 0.961528 -23 ATTGTAATTTTTTTTAACCAATCAATAATAAAA 10 6 0 TTTAAATAAA 0.879411 -66 AACCATCCTCTTTACAAAAAATTGAGCAATAATTTTAT 10 42 0 TTTAAATACA 0.561981 -30 CAGTGAATATTTTATTGATAATCTAGAGGGATCTATCT 11 43 1 TTTTAATAAG 0.741771 -89 GTTAAGCAAGTTTTTTACAAAAACAGAAGCCTGACGTA 12 45 1 TTTTAAAAAA 0.961524 -107 AACTATTTTTTAAGAATACAAAATCTTGAGAGT 13 6 1 TTTTAATAAA 0.896867 -103 ACAGCGGTTACTTATAATCAAAAAATAATTATACTCCG 14 20 1 CTTAAAAAAA 0.852077 -281 ATACCACGGTTTTTATTTTAATGGATAAAATCCTGTGT 14 109 0 TTTTAATAAA 0.911578 -192 TTAGGCGACTTTTGAAAAAAAATCACCACAAATCACAA 14 166 1 TTTAAAAACA 0.741109 -135 CAGGAAAGCTCTTCCTATAATAGAAAAAATTACGTTTA 16 117 0 CTTTATAAAA 0.590663 -98 CAACAGCCGATTTAATTAGATTTTAAAAAGTTGTTTTT 18 31 1 TTTTATTAAA 0.645942 -181 TAAAAATAAACTTTGTAGCAAATAATAAAAACAACTTT 18 57 0 CTTTAAAAAA 0.898516 -155 TTTGTTTGTTTTTAAAAACAAATAAAAATAAACTTTGT 18 79 0 TTTAAAAAAA 0.941903 -133 ATAAGATGTTTTTTTTAGAAAAATAAAGTTTTCGTGAA 18 130 1 TTTTAAAAAG 0.864336 -82 AAAATAAAGTTTTCGTGAAAAATAACAGCATACCGGGT 18 149 1 TTTTAAAAAG 0.865032 -63 ATATCGCTTGCTTGCTAAAAAAAAAAAAGGATAATATA 19 48 1 CTTTAAAAAA 0.898447 -53 TCAATAAGACTTTGAATTCAAATGAAAAACTTCTATGT 22 31 0 TTTAAAAAAA 0.939405 -270 TGCAAAAGTATTTTTACAAAAAGCAAAACAGGCCTAAC 22 153 0 TTTAAAAAAA 0.942079 -148 TAGCTTACTATTTATAACCAAACAAAAATTCAAACGGC 25 80 0 TTTAAAAAAA 0.9421 -166 CGATCGAGAGTTTTTTTGAAATAAAAAAATGTTTTGTA 27 125 0 TTTTAATAAA 0.913483 -176 *** * *** * ** Masking position 3 Map Score: 22.3898 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 170 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 TATATATACTAAAAAGAATACTAGAAGTTTTTGAT 2 25 0 AAAAAGAAAA 0.805165 -250 GCTATCATACAACAAAAGGAAGAGGGTCTCTCTTC 3 18 1 AACAAAAAAG 0.808094 -100 TCTAGCTGGTAAGAAAATAAGAAGGCGCAAGCTCG 4 119 0 AAGAAAAAAG 0.808094 -182 TGCTAGGTTTAAAAAAAACAGTACGAAGGAGATTC 4 272 1 AAAAAAAAAG 0.950546 -29 GGATCGCATTAAAAAAAAGATGATGGATTCGCAGA 5 56 1 AAAAAAAAAG 0.950546 -141 AGAAAACCTTAAAAATAACAACAGGTTAGGTGCT 5 173 1 AAAAATAAAG 0.806034 -24 GAAAACAACGAAAAAAAGCCCGAAAAGCAACCCCT 6 57 0 AAAAAAACAA 0.881261 -244 TGATTGGTTAAAAAAAATTACAATAAAATTATTGC 10 20 1 AAAAAAAAAA 0.946544 -52 TGGGATAGGCACAAAAATCCAAAGAA 12 2 0 ACAAAAACAA 0.804113 -150 CGACTTTTGAAAAAAAATCACCACAAATCACAATC 14 171 1 AAAAAAAAAA 0.946544 -130 TCTCTACCAAACAAAAAGGAAAAAAGAGATAATAT 15 36 1 ACAAAAAAAA 0.907352 -66 GTTTTTAAAAACAAATAAAAATAAACTTTGTAGCA 18 75 0 ACAAATAAAA 0.679216 -137 AGTTTTCGTGAAAAATAACAGCATACCGGGTAACG 18 156 1 AAAAATAAAA 0.792884 -56 TTGCTAAAAAAAAAAAAGGATAATATACGGGGTCT 19 59 1 AAAAAAAAAA 0.946544 -42 CTCGATATAGAAGAAAATCAAGAAATTCCTTGGAG 21 13 0 AAGAAAAAAA 0.795048 -123 AAGTATTTTTACAAAAAGCAAAACAGGCCTAACCT 22 151 0 ACAAAAAAAA 0.907352 -150 TCTAAACTTGAAAAAAAGTCTGAAGATATCGGTTT 24 82 1 AAAAAAACAG 0.889582 -97 AAAAACAAAAAAAATAAATCATTTAGTT 25 4 1 AACAAAAAAA 0.795048 -242 TTATAACCAAACAAAAATTCAAACGGCCATTCACT 25 72 0 ACAAAAACAG 0.816715 -174 ATCACACCTAAAAAAGAGTACAACGCTATGCGCCC 27 275 0 AAAAAGAAAG 0.817716 -26 ******* * * * Masking position 7 Map Score: 18.9247 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 107 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 GCTTAAACACAAAAGGAAGAGAGACCCTCTTCCTTTTG 3 30 0 AGAAGACCCT 0.804386 -88 CGAAGAAATGAAGAGAAGAGAGGGGCTTAAACACAAAA 3 54 0 AGAGAGGCTT 0.862257 -64 CACCAGCCTCGATAGGAAGGCCTTGCCTAACAGCAAAT 4 192 1 GGAAGGGCCT 0.978372 -109 AAAAAAAACAGTACGAAGGAGATTCCCTC 4 282 1 GGAGGACCCT 0.939101 -19 CAAGGCGGTTGTAAGGAGAGAAAACCTTAAAAATAACA 5 155 1 GGAGAGCCTT 0.972729 -42 ACGAAAAAAAGCCCGAAAAGCAACCCCTCTAGCAGGTT 6 47 0 GGAAAGCCCT 0.98566 -254 CTCCGAGACCGCCCGTAGAGAAAACCTTTCTAAGAAGA 14 53 1 GGAGAGCCTT 0.972729 -248 CTTCAGAAATGAAAGAAAGAGGTAGCTTGGGGGATCTA 14 220 0 GGAAGAGCTT 0.707518 -81 TTCCTTTTTGTTTGGTAGAGAGATCCTTGAAAGAAAGA 15 19 0 TGAGAGCCTT 0.719046 -83 AGCTGTTGATGATCAAAAAGACGTGCCTTATATATGGT 16 29 1 GAAAAGGCCT 0.753224 -186 TTTTTCTATTATAGGAAGAGCTTTCCTGGAGAGAACTC 16 127 1 AGAGAGCCTG 0.807354 -88 ATTCAAGATGAGAGAAAAAGAATCCCCTTAGAAGTTAC 20 11 0 AAAAAGCCCT 0.675053 -53 TTGAATGTAAGCTAGTAAGGGAGCCCCTTTA 20 43 1 GGAAGGCCCT 0.9889 -21 GAGATGACTGGGGAGTAGAGGTGGGCCTGTAACTCTGA 21 64 1 GGAGAGGCCT 0.978372 -72 CCCATGCTCTAGGGGTAGGGGCATCCTGAATCGACTAC 22 112 0 AGAGGGCCTG 0.844521 -189 ACAGGGATATGGGCGGAAAGGCTTCCCTTTAGAAGGAG 22 213 1 GGAAAGCCCT 0.98566 -88 TAGGGCGCCAAAATGGAAGGAAGGCCCGAGTATATATG 27 204 0 AGAAGGCCCG 0.912794 -97 CCCTAAGAAAGGAGGAAAGGCTGAGCCTTCGTATTACA 27 237 1 GGAAGGGCCT 0.978372 -64 * * **** **** Masking position 7 Map Score: 19.2301 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 133 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 4 TTTTCAACTGAAACAGCGTTTTATATAAAGA 1 26 1 AAACACGTTT 0.421817 -106 CGTTTTATATAAAGAAGCTTTTACGTAGAGC 1 42 1 AAAGAGCTTT 0.760352 -90 TTTGTGATCGAGACAGGCTCTACGTAAAAGC 1 58 0 AGACAGCTCT 0.873702 -74 GTAGTTACAGAAAGAAGCTTTGTGATCGAGA 1 76 0 AAAGAGCTTT 0.760352 -56 CCAGTTGTTAAAACAGCCCTTTTCCACAAAA 2 80 1 AAACACCCTT 0.72527 -195 GGAAGGTCTTAAGAAGGCCTTTGGGAAAGGA 2 152 0 AAGAAGCCTT 0.697437 -123 AACCGAAGTCAAGGAAGGTCTTAAGAAGGCC 2 164 0 AAGGAGGTCT 0.80069 -111 CAAAAGGAAGAGAGACCCTCTTCCTTTTGTT 3 28 0 AGAGACCTCT 0.853668 -90 TACGCTTCTAAAACACGCTTTAGTTTCGGTA 4 60 0 AAACAGCTTT 0.760676 -241 ATTTGCTGTTAGGCAAGGCCTTCCTATCGAG 4 199 0 AGGCAGGCCT 0.763199 -102 TGCTAGTGACCAGCACCCCCTCTGAGTTCTC 6 11 1 CAGCACCCCT 0.507488 -290 AAAGCCCGAAAAGCAACCCCTCTAGCAGGTT 6 47 0 AAGCACCCCT 0.925004 -254 GTGAAAGGAGAAGGATGCTCTCCTTCTCCTT 7 18 0 AAGGAGCTCT 0.936624 -51 GGCTCTTCAAAAAGAGGGCCTTCT 9 23 1 AAAGAGGCCT 0.691027 -14 AAAACCATCCTCTTTACAAAAAA 10 59 0 AACCACCTCT 0.552188 -13 CCGCCCGTAGAGAAAACCTTTCTAAGAAGAG 14 61 1 AGAAACCTTT 0.481941 -240 CTTGTGTTGAAAAGAACCTCTTCTTAGAAAG 14 78 0 AAAGACCTCT 0.877374 -223 AGTTCTCTCCAGGAAAGCTCTTCCTATAATA 16 133 0 AGGAAGCTCT 0.836949 -82 GTCCTTGAGCAAGAAGGCTTTTAGAGTTCTC 16 157 0 AAGAAGCTTT 0.701819 -58 ATGAGAGAAAAAGAATCCCCTTAGAAGTTAC 20 11 0 AAGAACCCCT 0.838859 -53 TAAGCTAGTAAGGGAGCCCCTTTA 20 50 1 AGGGACCCCT 0.908207 -14 CTCCTTCTAAAGGGAAGCCTTTCCGCCCATA 22 220 0 AGGGAGCCTT 0.815601 -81 CTAGGTATTTAAACACCCTCTGGGGTT 23 7 0 AAACACCTCT 0.877681 -46 TTGATGTTTGAGGAAAGGTCTTAAGAAGGCG 25 130 1 AGGAAGGTCT 0.581295 -116 ***** ***** Masking position 11 Map Score: 18.73 Number of sites scoring better than the average of aligned sites = 520 Number in coding regions = 520 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 5 TATCATACAACAAAAGGAAGAGGGTCTCTCTTCC 3 20 1 CAAGAAGGGG 0.781514 -98 GGCTTAAACACAAAAGGAAGAGAGACCCTCTTCC 3 35 0 CAAGAAGGAG 0.645893 -83 AAAAATCTAACCGAAGAAATGAAGAGAAGAGAGG 3 69 0 CCAGAATAAG 0.664025 -49 AAAAACTAGAACAAGTAAGTTTAATAAAA 3 99 0 CTAAAAGAAG 0.931814 -19 TTTTTTAAACCTAGCATAAGCAGGTTTGTTAGTA 4 254 0 CTCAAAGAGG 0.761307 -47 GCAGAGATCTCTGTAAAGATTGGGGAAAGGGAAG 5 13 1 CTAAGATGGG 0.344689 -184 GGTGCTCTTCCCAGAAAGAGTAAGAATAAAACTT 6 238 1 CCAAGAGAAG 0.809961 -63 GCAGACTTTTCTAGATAAAGGAAGTAATA 6 282 1 CTATAAGAAG 0.612834 -19 AATCCGAAAGGAGAAGGAGAGCATCCT 7 4 1 CCAAGAGAGG 0.893141 -65 ATAGGAGGCTCTTCAAAAAGAGGGCCTTCT 9 17 1 CTAAAAGGGG 0.936795 -20 AGCCATCCTAAAAAATAAGGTTACTATCCT 11 112 0 CCAAAATAGG 0.766304 -20 AGTTTATTCGCCTAAATAAGTGAGT 13 94 1 CCAAAAGGAG 0.886259 -15 GGATTTTGTCCTTGAGCAAGAAGGCTTTTAGAGT 16 161 0 CTAGAAGAGG 0.96871 -54 CCTTTTTTTTTTTTAGCAAGCAAGCGATATCAAA 19 44 0 TTAGAAGAAG 0.403182 -57 TGTAAAAATACTTTTGCAAGGAAGTGAGAGTAGG 22 173 1 CTTGAAGAAG 0.766132 -128 GAAAGGCTTCCCTTTAGAAGGAGGCTGGTGATTA 22 228 1 CCTAAAGAGG 0.849427 -73 CATTAAGCAACTGAAAAAAGTAAGGATAAGT 22 280 1 CTAAAAGAAG 0.931816 -21 CACATTTCTTCTTATGGAAGAAGGAGTGAAGTTT 27 72 0 CTTGAAGAGG 0.865334 -229 ATTTTGGCGCCCTAAGAAAGGAGGAAAGGCTGAG 27 228 1 CCAGAAGAGG 0.970372 -73 GCTATGCGCCCTGTAATACGAAGGCTCAGCCTTT 27 252 0 CTAAACGAGG 0.729285 -49 ** ** *** *** Masking position 14 Map Score: 13.4788 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 243 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 GAATACTAGAAGTTTTTGATTTGGAGAGCC 2 15 0 AGTTTTTGAT 0.960139 -260 TTCTTCGGTTAGATTTTTATTAAACTTACT 3 85 1 AGATTTTTAT 0.821105 -33 CCTATTGGTTATATTTTTATAGGAAAGAAT 7 48 1 ATATTTTTAT 0.741446 -21 GAGTATAATTATTTTTTGATTATAAGTAAC 14 26 0 ATTTTTTGAT 0.937692 -275 CTAGGTAGTAATTTTTTGATATCGCTTGCT 19 30 1 ATTTTTTGAT 0.937692 -71 CCTCCAAGGAATTTCTTGATTTTCTTCTAT 21 12 1 ATTTCTTGAT 0.720942 -124 TCGACATAGAAGTTTTTCATTTGAATTCAA 22 28 1 AGTTTTTCAT 0.799462 -273 TGCTTTATCTAGTTTTTGATCGAAAAATTT 24 19 0 AGTTTTTGAT 0.960139 -160 TAAATCATTTAGTTTTCGATAATTATTTTC 25 25 1 AGTTTTCGAT 0.805258 -221 CGAATTGCAAAGATTTTGATAAAAATAGGG 25 159 1 AGATTTTGAT 0.925886 -87 ATACCTATATTTTTATCTTTAGCATT 26 7 1 ATATTTTTAT 0.741446 -126 CATACAAAACATTTTTTTATTTCAAAAAAA 27 123 1 ATTTTTTTAT 0.846839 -178 ********** Masking position 9 Map Score: 9.39656 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 75 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 CTATATAAGATAACCCTAGCAGTTGAA 2 258 0 AAGAAACCCT 0.923502 -17 CGAGGCTGGTGCGACATCCCTCTTCGGAGTT 4 172 0 GCGAATCCCT 0.892831 -129 GTTGTAAGGAGAGAAAACCTTAAAAATAACA 5 162 1 GAGAAACCTT 0.975303 -35 AAAGAGAACAGAGAGAACTTTGAAAACAACG 6 82 0 GAGAAACTTT 0.917654 -219 AGGCTAGCTAGATAGATCCCTCTAGATTATC 11 59 0 GATAATCCCT 0.628633 -73 AAGACAACCTTCCGATCAGAA 12 141 0 AAGAAACCTT 0.917646 -11 ACCGCCCGTAGAGAAAACCTTTCTAAGAAGA 14 60 1 GAGAAACCTT 0.975303 -241 TTGTTTGGTAGAGAGATCCTTGAAAGAAAGA 15 19 0 GAGAATCCTT 0.947044 -83 AGCTTTCCTGGAGAGAACTCTAAAAGCCTTC 16 145 1 GAGAAACTCT 0.923508 -70 GTTATTTTTCACGAAAACTTTATTTTTCTAA 18 144 0 ACGAAACTTT 0.57483 -68 **** ****** Masking position 6 Map Score: 7.02339 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 96 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 CTAGTTGATTAGGAAACTCCGAAGAGGGAT 4 158 1 AGGAAACTCC 0.951271 -143 GAGGGAATCTCCTTCGTACTGT 4 289 0 GGGAATCTCC 0.738161 -12 AAAGCCCGAAAAGCAACCCCTCTAGCAGGT 6 48 0 AAGCAACCCC 0.916062 -253 ACATATTAGGAAGAGACTACTCAAGACCTA 6 169 0 AAGAGACTAC 0.663567 -132 CCAATCTCATAGGCGTCCCCACATATTAGG 6 189 0 AGGCGTCCCC 0.89745 -112 CCTCTTTTTGAAGAGCCTCCTATGATCTT 9 10 0 AAGAGCCTCC 0.894272 -27 GAATTTTAGGAGGAATCTCCC 14 290 1 AGGAATCTCC 0.942619 -11 AACCCTGACAAAGAGACCCCGTATATTATC 19 77 0 AAGAGACCCC 0.957652 -24 ATGAGAGAAAAAGAATCCCCTTAGAAGTTA 20 12 0 AAGAATCCCC 0.942619 -52 GAAGAAAATCAAGAAATTCCTTGGAGGA 21 9 0 AAGAAATTCC 0.651538 -127 CTCTATCCCTAAGAATATCCTTTGGCTCAA 25 224 0 AAGAATATCC 0.611415 -22 AGAGTAAGGGAAGCGACTCCGTCCAAGATA 26 60 1 AAGCGACTCC 0.938903 -73 ********** Masking position 10 Map Score: 6.11773 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 200 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 TCCGTAATAAGTTTCAAGGAGTTGGTACAG 2 197 1 GTTTCAAGGA 0.84784 -78 TTTCTTTCATTTCTGAAGGGCCTATCGTAG 14 240 1 TTCTGAAGGG 0.748661 -61 AAAATTCTTTCTTTCAAGGATCTCTCTACC 15 14 1 CTTTCAAGGA 0.911146 -88 TATAGGGTAATTTTCAAGGAATTTTAGTTT 15 68 1 TTTTCAAGGA 0.967307 -34 TTTCTAAAAATTTTCAAGGGTTTAGAGGAC 16 65 0 TTTTCAAGGG 0.967897 -150 AAAAATTACGTTTACAAGGGCAAAATCACC 16 101 0 TTTACAAGGG 0.914671 -114 TTTTAGAGTTCTCTCCAGGAAAGCTCTTCC 16 140 0 CTCTCCAGGA 0.62054 -75 AAAGCCTTCTTGCTCAAGGACAAAATCCTC 16 167 1 TGCTCAAGGA 0.825141 -48 TAAAAATACTTTTGCAAGGAAGTGAGAGTA 22 175 1 TTTGCAAGGA 0.86054 -126 AAGGCTTCCCTTTAGAAGGAGGCTGGTGAT 22 230 1 TTTAGAAGGA 0.673072 -71 AAAAATAGTTTTTTCAAAGAGCCTCAGAAA 24 119 0 TTTTCAAAGA 0.660883 -60 AAAAGTTGACTGTTCAAGGGAAGCGACACA 26 99 0 TGTTCAAGGG 0.904991 -34 AGCGGACCTGTTTACCAGGGGCGATCGAGA 27 154 0 TTTACCAGGG 0.772031 -147 ********** Masking position 7 Map Score: 6.39266 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 102 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 AACAACTGGTGACAGGGAAACGTGCATAGT 2 59 0 GACAGGGAAA 0.796791 -216 AAAGATTGGGGAAAGGGAAGTGTATACCAG 5 27 1 GAAAGGGAAG 0.965939 -170 TGGATTCGCAGACTGGAGAGGACTTGATTT 5 79 1 GACTGGAGAG 0.818178 -118 CAAGGCGGTTGTAAGGAGAGAAAACCTTAA 5 155 1 GTAAGGAGAG 0.848884 -42 AATCCGAAAGGAGAAGGAGAGCATC 7 6 1 GAAAGGAGAA 0.816883 -63 ACCAATAGGTGAAAGGAGAAGGATGCTCTC 7 27 0 GAAAGGAGAA 0.816883 -42 TGTAGTAATCGATAGGGGAGAAGAATTTTC 17 31 0 GATAGGGGAG 0.90806 -30 TTACAGAGATGACTGGGGAGTAGAGGTGGG 21 59 1 GACTGGGGAG 0.933117 -77 TACCCCTAGAGCATGGGGAGGTTAGGCCTG 22 133 1 GCATGGGGAG 0.905463 -168 AGCCTCCTTCTAAAGGGAAGCCTTTCCGCC 22 224 0 TAAAGGGAAG 0.797583 -77 GAATGACAGAGTAAGGGAAGCGACTCCGTC 26 53 1 GTAAGGGAAG 0.88743 -80 AGTTGACTGTTCAAGGGAAGCGACACAAGC 26 96 0 TCAAGGGAAG 0.62884 -37 ********** Masking position 9 Map Score: 6.90217 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 169 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 11 CTGTTCTCTTTTCTTCCTATATTTGTAGGG 6 102 1 TTCTTCCTAT 0.928398 -199 CTTGAGTAGTCTCTTCCTAATATGTGGGGA 6 174 1 CTCTTCCTAA 0.745811 -127 CTTTGGATTTTTGTGCCTATCCCACTTTCT 12 13 1 TTGTGCCTAT 0.871421 -139 TTAAGATTATTTCCGCCTATAAAAACCCGA 13 47 0 TTCCGCCTAT 0.97067 -62 GGGAGATTCCTCCTAAAATTCAAATA 14 285 0 TTCCTCCTAA 0.935651 -16 TCCAGGAAAGCTCTTCCTATAATAGAAAAA 16 127 0 CTCTTCCTAT 0.832674 -88 TTCAGTTCCTTCTATTGCATTTCTT 18 197 0 TTCCTTCTAT 0.660226 -15 CGTAATGAGCTTGTGCCTAACGGAAAATCA 22 73 1 TTGTGCCTAA 0.799803 -228 AGGGAAGCCTTTCCGCCCATATCCCTGTTC 22 211 0 TTCCGCCCAT 0.86173 -90 TTATCAAGTATTGCGCCTAAAACTTCACTC 27 53 1 TTGCGCCTAA 0.883685 -248 GGCTCAGCCTTTCCTCCTTTCTTAGGGCGC 27 234 0 TTCCTCCTTT 0.758073 -67 ********** Masking position 2 Map Score: 5.26659 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 113 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 ACGTAAAAGCTTCTTTATATAAAACGCTGTTT 1 36 0 TTTTTATATA 0.472334 -96 ATCACAAAGCTTCTTTCTGTAACTACTAGCAA 1 81 1 TTTTTCTGTA 0.667628 -51 GTACAGCTTCTTGTTTTGCTGAAAATAATGAA 2 221 1 TTTTTTGCTA 0.568198 -54 TGTTTGACGCTTATTTCTCTCTAAGTGCAAGG 5 128 1 TTTTTCTCTT 0.693724 -69 TTTGTGGTGATTTTTTTTCAAAAGTCGCCTAA 14 166 0 TTTTTTTCAA 0.610223 -135 CAAAAAATTCTTTCTTTCAAGGATCTCTC 15 8 1 TTTTTCTTTA 0.56495 -94 GTAAACGTAATTTTTTCTATTATAGGAAGAGC 16 116 1 TTTTTCTATA 0.823681 -99 AAATCGGCTGTTGTTTTTATTTAATTTGTAGT 18 12 0 TTTTTTTATT 0.783949 -200 TTTTAAAAAGTTGTTTTTATTATTTGCTACAA 18 51 1 TTTTTTTATA 0.900944 -161 GCTACAAAGTTTATTTTTATTTGTTTTTAAAA 18 76 1 TTTTTTTATT 0.783949 -136 AGACATTTGTTTGTTTTTAAAAACAAATAAAA 18 90 0 TTTTTTTAAA 0.56297 -122 CACGAAAACTTTATTTTTCTAAAAAAAACATC 18 134 0 TTTTTTTCTA 0.917039 -78 ATATTATCCTTTTTTTTTTTTAGCAAGCAAGC 19 53 0 TTTTTTTTTA 0.716577 -48 TCTAAGGGGATTCTTTTTCTCTCATCTTGAAT 20 17 1 TTTTTTTCTT 0.815154 -47 AAACTGATTCTTCTTTTAATCACCAGCCTCCT 22 246 0 TTTTTTAATA 0.422139 -55 AAGATATCGGTTTTTTTTCTGAGGCTCTTTGA 24 104 1 TTTTTTTCTA 0.917039 -75 AAATGATTTATTTTTTTTGTTTTT 25 3 0 TTTTTTTGTT 0.609407 -243 ATATGAGTCATTATTTTTATGAAAGAGCGGAC 27 177 0 TTTTTTTATA 0.900943 -124 ** ******* * Masking position 6 Map Score: 9.80987 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 239 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 ACGTAGAGCCTGTCTCGATCACAAAGCTTC 1 64 1 TGTCTCGATC 0.926586 -68 ATGTCGCACCAGCCTCGATAGGAAGGCCTT 4 186 1 AGCCTCGATA 0.964526 -115 AAATGATTAGAGCCGCGATCAGGTGATTTG 4 225 0 AGCCGCGATC 0.967125 -76 AATGGATAGTAGTCTCGATATAGAAGAAAA 21 31 0 AGTCTCGATA 0.945319 -105 TGAGTCTAATAGCCTCTATCTTGACTAGTC 21 102 0 AGCCTCTATC 0.925642 -34 TTTCAAAAAAACTCTCGATCGCCCCTGGTA 27 142 1 ACTCTCGATC 0.921464 -159 ********** Masking position 8 Map Score: 0.345531 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 22 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 GTTAATGGCAAAGTATTTTGTGGAAAAGGGCT 2 94 0 AAGATTTTTG 0.922186 -181 AAAATTGAGCAATAATTTTATTGTAATTTTTT 10 31 0 AATATTTTTT 0.813552 -41 CTCGGAGTATAATTATTTTTTGATTATAAGTA 14 28 0 AATATTTTTG 0.898228 -273 AATCACAATCAAGAATTGTGTTACTAGATCCC 14 196 1 AAGATTGTTT 0.711996 -105 CCTTGAAAGAAAGAATTTTTTG 15 1 0 AAGATTTTTG 0.921512 -101 AGAACTAGGTAGTAATTTTTTGATATCGCTTG 19 26 1 AGTATTTTTG 0.6026 -75 TCCTCCAAGGAATTTCTTGATTTTCTTC 21 7 1 AAGAATTTTT 0.599765 -129 AGAAATGATTTTCTTGCTCGACATA 22 4 1 AATATTTTTT 0.91001 -297 TCGAAAACTAAATGATTTATTTTTTTTGTTTT 25 12 0 AATATTTATT 0.553855 -234 AGTTTTCGATAATTATTTTCTTACTTCTTATT 25 35 1 AATATTTTTT 0.895237 -211 TTTTGAGCCAAAGGATATTCTTAGGGATAGAG 25 222 1 AAGATATTTT 0.599765 -24 CCTTCATACAAAACATTTTTTTATTTCAAAAA 27 119 1 AAAATTTTTT 0.689762 -182 *** ***** ** Masking position 5 Map Score: 1.38934 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 91 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 ********** No masking Map Score: 8.31578e-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