AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00350_ctra_reg_300.orf -o00350_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 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 yaeT 300 Omp85 Analog #8 CT242 68 (OmpH-Like Outer Membrane Protein) #9 lpxD 27 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase #10 CT355 300 hypothetical protein #11 CT389 181 hypothetical protein #12 aspC 89 Aspartate Aminotransferase #13 CT421 300 hypothetical protein #14 CT421.1 184 hypothetical protein #15 CT423 132 (CBS Domain) #16 rsbV_1 188 Sigma Regulatory Factor #17 CT425 177 hypothetical protein #18 CT426 196 Fe-S oxidoreductase #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 greA 113 Transcription Elongation Factor G #24 tyrB 187 Aromatic AA Aminotransferase #25 ygcA 85 rRNA Methyltransferse #26 hctA 300 Histone-Like Developmental Protein Motif number 1 ACAACTGGTGACAGGGAAACGTGCATAGTAT 2 57 0 AAGGGAAACG 0.563614 -218 CAGAATAAAAATTAAAAAGAGAAAATAGTT 3 10 0 ATAAAAAGAG 0.76862 -291 ATTCTTTTGCACAGAAAAGGGCTTTGTAAAG 4 11 1 AAGAAAAGGG 0.964348 -143 TAAGTCTTAGAAAGAAAAGAGCTTCTTTACA 4 35 0 AAGAAAAGAG 0.929645 -119 TAGGAAGAAAAGAGAACAGAGAGAACTTTGA 7 90 0 AAGAACAGAG 0.616983 -211 TCCAATTACAATAGAGAATCGAGGATAATTT 7 138 0 AAGAGAATCG 0.62394 -163 GTCCCCACATATTAGGAAGAGACTACTCAAG 7 174 0 ATAGGAAGAG 0.565669 -127 CTTCTGACCAAGTAAGAATGGTGCTCTTCCC 7 219 1 ATAAGAATGG 0.451513 -82 AACACTTTTAACAAAAAAGCGTTATATCCTC 10 92 0 AAAAAAAGCG 0.850406 -209 GGTAAGATCCAAAGAAAAAGGGGAGGAGGAA 10 232 1 AAGAAAAAGG 0.866692 -69 TTTAGAGAGCACTGAGAAAAG 12 1 0 ATGAGAAAAG 0.7088 -89 AACGAGTTTCAAAGAAAAGGTGCATGTTAAG 13 200 0 AAGAAAAGGT 0.410481 -101 GGAACGGTCTATAGAAGAGGGTTTTTCTCAC 13 243 0 AAGAAGAGGG 0.641807 -58 TCTTCTTTTTAAAAAGAAGGGAATTTAGTGG 14 26 1 AAAAGAAGGG 0.934151 -159 AGCTCTATTGAAAAAAAAACGGCGCTCTACT 14 70 1 AAAAAAAACG 0.577415 -115 AGGGATTTAAAAAGAAAATAGCAACTCTGCT 14 124 0 AAGAAAATAG 0.558509 -61 TGCCTTCCTGAATGGGAAGGGATTTAAAAAG 14 141 0 ATGGGAAGGG 0.865368 -44 AGAGATTTCTAGAGGGAAGCGAAGACTT 15 8 0 AAGGGAAGCG 0.843098 -125 AAGATTAAGTAGTTAGAAGAGCTGCACTATA 16 153 0 ATTAGAAGAG 0.440781 -36 TTACTCCTATACTGAGAAGGGCTGTAGCGCA 18 50 0 ATGAGAAGGG 0.953981 -147 GCTTGCTAAAAAAAAAAAAGGATAATATACG 19 57 1 AAAAAAAAGG 0.729486 -44 TATTAGACTCATATAGAAGGGTGAT 21 121 1 AATAGAAGGG 0.726931 -15 TCAAAGTCTTATTGAAAAACGTAATGAGCTT 22 54 1 ATGAAAAACG 0.666295 -247 GAGAGTAGGTAGAGAACAGGGATATGGGCGG 22 198 1 AAGAACAGGG 0.767306 -103 CCATTAAGCAACTGAAAAAAGTAAGGATAAG 22 279 1 ATGAAAAAAG 0.658119 -22 ACGCCGAATAACAAAAAAGAGCAATATTACA 23 64 0 AAAAAAAGAG 0.845696 -50 ATATTTCCGGACTAAAAAGGGGAGCCATC 23 95 1 ATAAAAAGGG 0.871796 -19 AGTGCCCTCTATAAAAAAGAGAAAGCGCTAA 25 15 0 AAAAAAAGAG 0.845696 -71 AGAAGGGATCAATGAGAAGAGGAAAGAGGGC 25 58 0 ATGAGAAGAG 0.910126 -28 AAAAAAGAGAAGGGATCAATGAGA 25 72 0 AAGAGAAGGG 0.971592 -14 TGTTTAGAAAAGAAAGAAAGGAGCTTGTTCT 26 26 0 AAAAGAAAGG 0.773232 -275 GGTTTCTTTTAATAGAAAGCGCTGAACCTTG 26 55 0 ATAGAAAGCG 0.516523 -246 * ********* Masking position 8 Map Score: 29.2861 Number of sites scoring better than the average of aligned sites = 543 Number in coding regions = 543 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 GAAACAGCGTTTTATATAAAGAAGCTTTTACGT 1 35 1 TTAAAAAGAA 0.864181 -97 TTTGCTAGTAGTTACAGAAAGAAGCTTTGTGAT 1 81 0 GTAAAAAGAA 0.93537 -51 CTTTGAGAAGGTGAGGTAAAGAAAATGAAAGAC 3 104 0 GTAGAAAGAA 0.913995 -197 ACAGAAAAGGGCTTTGTAAAGAAGCTCTTTTCT 4 21 1 GCTGAAAGAA 0.857356 -133 ATCCAGGTAAGTCTTAGAAAGAAAAGAGCTTCT 4 40 0 GTTAAAAGAA 0.940914 -114 GGTTATATTTTTATAGGAAAGAATT 8 54 1 TTTGAAAGAA 0.839601 -15 GCAGCTTATATTCTAAAAAAGAACCTACCCTCG 10 165 0 TTTAAAAGAA 0.876058 -136 ATTTTTAAACGAGTTTCAAAGAAAAGGTGCATG 13 205 0 GATTAAAGAA 0.758324 -96 AATTCCCTTCTTTTTAAAAAGAAGATAATGATT 14 18 0 TTTAAAAGAA 0.876412 -167 AATGGGAAGGGATTTAAAAAGAAAATAGCAACT 14 129 0 GATAAAAGAA 0.871436 -56 AAAAGCCAGCTCCTGTAAAAGAAATTATTGGGA 15 98 0 TCTTAAAGAA 0.62426 -35 AACAGACGAGTAGAAATAAAGAAGTCATGAAGG 18 18 0 TAAAAAAGAA 0.726785 -179 AGCGACTGCTGTCAGAAAAAGAAGTCTTGTCCC 18 140 1 GTAAAAAGAA 0.935369 -57 CATTCAAGATGAGAGAAAAAGAATCCCCTTAGA 20 17 0 GAAAAAAGAA 0.858159 -47 AAGGAGGCTGGTGATTAAAAGAAGAATCAGTTT 22 245 1 GTATAAAGAA 0.87012 -56 GCTGAACCTTGTTTAGAAAAGAAAGAAAGGAGC 26 33 0 GTTGAAAGAA 0.922517 -268 TTCAGCGCTTTCTATTAAAAGAAACCCTATTCA 26 60 1 TCATAAAGAA 0.597924 -241 ** * * ****** Masking position 8 Map Score: 15.0165 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 141 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 TTTGTAAAGAAGCTCTTTTCTTTCTAAGAC 4 33 1 AGCTCTTTTC 0.630211 -121 GTTCTCTCTGTTCTCTTTTCTTCCTATATT 7 95 1 TTCTCTTTTC 0.823185 -206 GTAAGAATGGTGCTCTTCCCAGAAAGAGTA 7 230 1 TGCTCTTCCC 0.87879 -71 GATGCTCTCCTTCTCCTTTCGGATT 8 6 0 TTCTCCTTTC 0.828443 -63 GAGAGCATCCTTCTCCTTTCACCTATTGGT 8 27 1 TTCTCCTTTC 0.828443 -42 TCTTAGTTACCCCTCTTTTCGATATTTAAG 10 20 1 CCCTCTTTTC 0.929546 -281 ACGGCTGGGTCCCTCCTCCCCTATAGCTTT 10 126 1 CCCTCCTCCC 0.948446 -175 TTTGGGTTGTTCCTCCTCCCCTTTTTCTTT 10 242 0 TCCTCCTCCC 0.899689 -59 GACACTCGAGCGCTCTTCTCCTAAAAATCT 11 108 1 CGCTCTTCTC 0.934801 -74 CTTGTTTTTTCTCTACTTCCGAGTTATAAC 11 136 1 CTCTACTTCC 0.59495 -46 GTGAGAAAAACCCTCTTCTATAGACCGTTC 13 243 1 CCCTCTTCTA 0.444045 -58 ACAGCAGAGTTGCTATTTTCTTTTTAAATC 14 122 1 TGCTATTTTC 0.435359 -63 AAGTCTTCGCTTCCCTCTAGAAATC 15 6 1 TTCGCTTCCC 0.41246 -127 CTTCAACTCGCTCTCTTTTCAAGTGATGCG 17 17 1 CTCTCTTTTC 0.90521 -161 ACAGGCCCACCTCTACTCCCCAGTCATCTC 21 64 0 CTCTACTCCC 0.655615 -72 CCGCCCATATCCCTGTTCTCTACCTACTCT 22 199 0 CCCTGTTCTC 0.589162 -102 ATCAACAGGGCCCTCTTTCCTCTTCTCATT 25 49 1 CCCTCTTTCC 0.931903 -37 CAAGAGAACAAGCTCCTTTCTTTCTTTTCT 26 22 1 AGCTCCTTTC 0.638688 -279 ********** Masking position 7 Map Score: 11.8442 Number of sites scoring better than the average of aligned sites = 487 Number in coding regions = 485 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 4 GCTCTACGTAAAAGCTTCTTTATATAAAAC 1 43 0 AAAGCTTCTT 0.959553 -89 TCTCGATCACAAAGCTTCTTTCTGTAACTA 1 76 1 AAAGCTTCTT 0.959553 -56 AGGAGTTGGTACAGCTTCTTGTTTTGCTGA 2 213 1 ACAGCTTCTT 0.964889 -62 TAGAAAGAAAAGAGCTTCTTTACAAAGCCC 4 29 0 AGAGCTTCTT 0.863035 -125 TTCAGCAAGAAAAGCTCCTTCTGATTACAA 6 47 1 AAAGCTCCTT 0.968276 -65 ACACCCAAACAAAGCAGCTTATATTCTAAA 10 181 0 AAAGCAGCTT 0.861843 -120 ATCACGATCAAAAGCACCTTTTCGTAATCT 16 93 0 AAAGCACCTT 0.861825 -96 TATAGGAGTAACAGCTGTTTTGATAGGGTC 18 70 1 ACAGCTGTTT 0.717405 -127 CAGTAAGATGACAGCTTGTTGTCCTAAATC 24 123 0 ACAGCTTGTT 0.745061 -65 TCTATAGCGCACTGCTGCTTACTGTCTTTT 24 157 0 ACTGCTGCTT 0.790142 -31 AACAAGAGAACAAGCTCCTTTCTTTCTTTT 26 20 1 CAAGCTCCTT 0.828099 -281 GCTTTATTTGACATCTCCTTGTACCGCTCT 26 163 0 ACATCTCCTT 0.699734 -138 GATGTCAAATAAAGCTGCTTTAGGATCCTT 26 178 1 AAAGCTGCTT 0.968297 -123 ********** Masking position 9 Map Score: 12.3506 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 196 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 GTGTTTTCATTATTTTCAGCAAAACAAGAAGCTG 2 224 0 TATTTCAGAA 0.866728 -51 ATTCTTTTGCACAGAAAAGGGCTTTGT 4 4 1 CTTTTCACAA 0.82593 -150 TTCAACGTACTTTTTTCAGCAAGAAAAGCTCCTT 6 33 1 TTTTTCAGAA 0.963191 -79 AATACAAGATCTTTTACACCTATAATCCCATAAT 6 75 1 CTTTTCACAA 0.825971 -37 TTTCTTCCTATATTTGTAGGGCTAGTCAAATTAT 7 111 1 TATTTTAGCA 0.45996 -190 CTAGCGCAGACTTTTCTAGATAAAGGAAGTAATA 7 277 1 CTTTTTAGAA 0.828976 -24 TTTTCTGGAATTTTTTCACTTAAATATCGAAAAG 10 34 0 TTTTTCACAA 0.923879 -267 ATTCTTAAGGTTTTTCTACCTAAAAACTACAAAT 10 272 1 TTTTTTACAA 0.851529 -29 ACGATAAAAATTTTTATCGATATAGAGATTTCTA 15 28 0 TTTTTTCGAA 0.761052 -105 TCGATAAAAATTTTTATCGTAACATGCAAGTAAG 15 42 1 TTTTTTCGAA 0.761082 -91 ACACCAAAAATTTTTTCAGGACCACACAACTTTG 17 54 0 TTTTTCAGCA 0.875392 -124 GAAAGCAAAATTTTTACAGATAAAGGACTTCCTG 17 127 1 TTTTTCAGAA 0.963107 -51 TATCCTTTTTTTTTTTTAGCAAGCAAGCGATATC 19 47 0 TTTTTTAGAC 0.618016 -54 CTTGCAAAAGTATTTTTACAAAAAGCAAAACAGG 22 159 0 TATTTTACAA 0.513784 -142 TTACTGTCTTTTTTTCCAGTAAGATGACAGCTTG 24 135 0 TTTTTCAGAA 0.963075 -53 TTTAAACTATTTTTTTCAGTTTTAATTTTTAATT 26 253 0 TTTTTCAGTA 0.720326 -48 ***** *** * * Masking position 5 Map Score: 7.59302 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 139 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 AAGTTTTTGATTTGGAGAGCCAAAT 2 6 0 TTTGGAGAGC 0.789419 -269 CAGCGTAATTTTTAGAGAGCACTGAGAAAA 12 12 0 TTTAGAGAGC 0.947301 -78 AATTTAGAGAGTTCTCCGTCAA 13 3 1 TTTAGAGAGT 0.920767 -298 GCTAATGGCGTTTAGAGAGTTTTGACGGAG 13 24 0 TTTAGAGAGT 0.920767 -277 CGCATTACAAGTTATAGAGGATTTAGCTAT 13 279 1 GTTATAGAGG 0.784595 -22 GATATAGAGATTTCTAGAGGGAAGCGAAGA 15 14 0 TTTCTAGAGG 0.801337 -119 TTTCGCATGCTTTACAGAGGATCTTCAAAG 17 101 0 TTTACAGAGG 0.954295 -77 GGCCACATCCTTTAGATAGGGGTCTTCCTA 18 108 0 TTTAGATAGG 0.82301 -89 AGCAGTGCGCTATAGAGAGGTTTTATT 24 171 1 TATAGAGAGG 0.882334 -17 CTTTCTCTTTTTTATAGAGGGCACTTTTAT 25 21 1 TTTATAGAGG 0.95084 -65 AATTTTTCTATTAACAGAGGAAAAATAACC 26 122 1 TTAACAGAGG 0.726251 -179 ********** Masking position 6 Map Score: 5.30296 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 120 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 AAATATGGTGAAAACCCAAAAAAGCGCAACAC 3 260 0 AAACCAAAAA 0.926168 -41 AACAACGAAAAAAAGCCCGAAAAGCAACCCCT 7 57 0 AAACCCGAAA 0.866013 -244 AGGGGTAACTAAGAGCAAAACAC 10 2 0 AAACAAAACA 0.883989 -299 AGATGTGGCAAACACCCAAACAAAGCAGCTTA 10 190 0 AAACCAAACA 0.943928 -111 GGGAGGCGGTAAGATCCAAAGAAAAAGGGGAG 10 225 1 AAACCAAAGA 0.794232 -76 GGGGAGGAGGAACAACCCAAAATTCTTAAGGT 10 251 1 AAACCCAAAA 0.887091 -50 AAAATAACCCAACAAGATCCTTCT 14 171 0 AAACCCAACA 0.913372 -14 GCAAAACCCTGACAAAGAGACCCC 19 87 0 AAACCTGACA 0.685845 -14 GATATAGAAGAAAATCAAGAAATTCCTTGGAG 21 13 0 AAACAAGAAA 0.823668 -123 TATTTTTACAAAAAGCAAAACAGGCCTAACCT 22 151 0 AAACAAAACA 0.883989 -150 TTACATCACAAAAAACAAGAAAAATTTTATTA 23 37 0 AAACAAGAAA 0.823668 -77 ATATACGCCGAATAACAAAAAAGAGCAATATT 23 67 0 AAACAAAAAA 0.850256 -47 ** * ******* Masking position 4 Map Score: 8.50322 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 43 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 GGAAGGTCTTAAGAAGGCCTTTGGGAAAGGA 2 152 0 AAGAAGCCTT 0.947037 -123 ACCGAAGTCAAGGAAGGTCTTAAGAAGGCCT 2 163 0 AGGAAGTCTT 0.898121 -112 CTATATAAGATAACCCTAGCAGTTGAA 2 258 0 AAGATACCCT 0.670058 -17 TCGAAGATGCTCCTATTTTAAATA 3 287 0 AAGATGTCCT 0.793089 -14 GGGCTTTGTAAAGAAGCTCTTTTCTTTCTAA 4 29 1 AAGAAGTCTT 0.837693 -125 TGAAAGGAGAAGGATGCTCTCCTTCTCCTTT 8 17 0 AGGATGTCTC 0.510453 -52 TCGAGTAACCAGGAAGTCCTTTATCTGTAAA 17 139 0 AGGAAGCCTT 0.924286 -39 TAAAGAAGTCATGAAGGCCTTATT 18 4 0 ATGAAGCCTT 0.764852 -193 CTTTCCTACTAGGAAGACCCCTATCTAAAGG 18 99 1 AGGAAGCCCC 0.934011 -98 ATGAGAGAAAAAGAATCCCCTTAGAAGTTAC 20 11 0 AAGAATCCCT 0.654445 -53 TAAGCTAGTAAGGGAGCCCCTTTA 20 50 1 AGGGAGCCCT 0.895593 -14 GAAGAAAATCAAGAAATTCCTTGGAGGA 21 8 0 AAGAAATCCT 0.494027 -128 TAGTCGATTCAGGATGCCCCTACCCCTAGAG 22 113 1 AGGATGCCCT 0.943444 -188 CTCCTTCTAAAGGGAAGCCTTTCCGCCCATA 22 220 0 AGGGAACCTT 0.575696 -81 GAGAAGAGGAAAGAGGGCCCTGTTGATAAAA 25 45 0 AAGAGGCCCT 0.860955 -41 ****** **** Masking position 1 Map Score: 9.85585 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 TGACTTTGCTAGTAGTTACAGAAAGAAGCT 1 88 0 AGTAGTTACA 0.786987 -44 CCCTGTCACCAGTTGTTAAAACAGCCCTTT 2 72 1 AGTTGTTAAA 0.684845 -203 TCCCTAGTTTAGCTGGAAGACAGTTAATGG 2 118 0 AGCTGGAAGA 0.784792 -157 AGTTTCAAGGAGTTGGTACAGCTTCTTGTT 2 206 1 AGTTGGTACA 0.93813 -69 TAGATAGCTCAGCTGGTAGAGCAGAGGACT 13 118 0 AGCTGGTAGA 0.953159 -183 CCTAAGATTAAGTAGTTAGAAGAGCTGCAC 16 157 0 AGTAGTTAGA 0.897499 -32 AGGAAGTGAGAGTAGGTAGAGAACAGGGAT 22 191 1 AGTAGGTAGA 0.957265 -110 GTATTAGCTCAGTTGGTAGAGCGCAACAAT 24 59 0 AGTTGGTAGA 0.972926 -129 ********** Masking position 8 Map Score: 3.03951 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 46 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 TGAACCGAAGTCAAGGAAGGTCTTAAGAAG 2 167 0 TCAAGGAAGG 0.902229 -108 AACTAAAGACTCCAGGAAAGATCGTTTATC 3 142 1 TCCAGGAAAG 0.977997 -159 GAATTAGAAATCCAGGTAAGTCTTAGAAAG 4 52 0 TCCAGGTAAG 0.942104 -102 CCTAATTTTGTCCATGGAGGACTACATTGT 4 115 0 TCCATGGAGG 0.704358 -39 TTTATTTAAATCTAGGAAAGGA 5 3 0 TCTAGGAAAG 0.971851 -98 ACTTCCTTTATCTAGAAAAGTCTGCGCTAG 7 277 0 TCTAGAAAAG 0.751019 -24 GTTATATTTTTATAGGAAAGAATT 8 55 1 TATAGGAAAG 0.771932 -14 TTGCCACATCTCTAGGGAGGCGGTAAGATC 10 211 1 TCTAGGGAGG 0.954917 -90 TCCCTTCCCATTCAGGAAGGCAGAAGGATC 14 150 1 TTCAGGAAGG 0.825206 -35 TTTTCTAGAATCTAGGTAAGGATCCTAAAG 26 195 0 TCTAGGTAAG 0.926682 -106 ********** Masking position 4 Map Score: 5.86186 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 70 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 AAGTATTTTGTGGAAAAGGGCTGTTTTAACAA 2 84 0 TGGAAAGGCT 0.966705 -191 AGAAGGCCTTTGGGAAAGGACTCATCCCTAGT 2 140 0 TGGGAAGGCT 0.990692 -135 TCTATTGTAATTGGATAGGTCTTGAGTAGTCT 7 154 1 TTGGAAGGCT 0.966705 -147 TAATGCGTTTTTGGAACGGTCTATAGAAGAGG 13 254 0 TTGGACGGCT 0.951308 -47 GGAATTTAGTGGGAACCAGACTCATAGCTCTA 14 45 1 GGGAACAGCT 0.781965 -140 TGGGATAGGGCTCCTAAGATTA 16 177 0 TGGGAAGGCT 0.990692 -12 TGCTTTTCACGGGGACAAGACTTCTTTTTCTG 18 152 0 GGGGAAAGCT 0.951308 -45 ***** *** ** Masking position 5 Map Score: 2.63309 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 19 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 TTATATAAAGAAGCTTTTACGTAGAGCCTGTCTC 1 46 1 AAGTTTTTAG 0.930881 -86 AGAATACTAGAAGTTTTTGATTTGGAGAGCCAAA 2 12 0 AAGTTTTTTG 0.849173 -263 GAAGTCAAGGAAGGTCTTAAGAAGGCCTTTGGGA 2 157 0 AAGTCTTAAG 0.586578 -118 AGATTGTCTATAAATCTTTCTTAGCATGCAAACA 3 197 0 TAATCTTTAG 0.68952 -104 ATAGGTGTAAAAGATCTTGTATTGTAATCAGAAG 6 64 0 AAGTCTTTTG 0.836624 -48 TGTAATTGGATAGGTCTTGAGTAGTCTCTTCCTA 7 159 1 TAGTCTTTAG 0.924526 -142 TCCTCCCCTATAGCTTTTACCTAGGACGAGGGTA 10 139 1 TAGTTTTTAG 0.930881 -162 GGACGAGGGTAGGTTCTTTTTTAGAATATAAGCT 10 162 1 AGGTCTTTAG 0.641178 -139 CCTTGATTTGTAGTTTTTAGGTAGAAAAACCTTA 10 277 0 TAGTTTTTAG 0.930881 -24 GAGAAAAAACAAGATTTTTAGGAGAAGAGCGCTC 11 115 0 AAGTTTTGAG 0.8097 -67 CTGTCCAGCGTAATTTTTAGAGAGCACTGAGAAA 12 13 0 TAATTTTGAG 0.435473 -77 TGGTGTAACATAGCCTTTTCTTTGAAGATCCTCT 17 82 1 TAGCTTTTTG 0.450936 -96 CTCGACATAGAAGTTTTTCATTTGAATTCAAAGT 22 27 1 AAGTTTTTTG 0.849173 -274 TTTTCAGTTTTAATTTTTAATTAGTTTGTTTGTT 26 241 0 TAATTTTTAG 0.709443 -60 *** **** *** Masking position 7 Map Score: 3.13618 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 175 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 CTGCCATGTCGCATCCGCTCTGACGGAGAGT 3 229 1 GCACCGCTCT 0.966814 -72 CTAGTGACCAGCACCCCCTCTGAGTTCTCCC 7 13 1 GCACCCCTCT 0.992191 -288 AGCCCGAAAAGCAACCCCTCTAGCAGGTTCG 7 45 0 GCACCCCTCT 0.992191 -256 TTTGCTCTTAGTTACCCCTCTTTTCGATATT 10 15 1 GTTCCCCTCT 0.90672 -286 AGCTAGTAAGGGAGCCCCTTTA 20 52 1 GGACCCCTTT 0.967184 -12 GATGGCTCCCCTTTTTAGTCCGGA 23 100 0 GGCCCCCTTT 0.929963 -14 *** ******* Masking position 9 Map Score: 2.00449 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 24 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 14 TAAGGCTAGTATGACTTTGCTAGTAGTTACAGAA 1 95 0 ATACTTGCGT 0.970854 -37 TTTTAGTATATATACTATGCACGTTTCCCTGTCA 2 46 1 TAACTTGCGT 0.733654 -229 TTTTCCACAAAATACTTTGCCATTAACTGTCTTC 2 99 1 AAACTTGCTT 0.851339 -176 AAGAAAATGAAAGACTCTGCGATTTTTCCCCGTT 3 85 0 AAACTTGCTT 0.851339 -216 GAAATCCAGAATGAGTATGCTTGTTGGTTAGTTA 11 35 0 ATAGTTGCGT 0.976295 -147 TGGCCATCCCATGAGTATGCGGGTATGTCCGCTA 13 50 0 ATAGTTGCGT 0.976336 -251 AGTAGTTATCAGTTTGTGAGTTTTGCTTTTC 18 176 0 ATAGTTGTGT 0.890407 -21 TAAAAGAAGAATCAGTTTGCCATTAAGCAACTGA 22 260 1 ATAGTTGCTT 0.931141 -41 TTAATTTTTAATTAGTTTGTTTGTTCAAATTCAT 26 232 0 ATAGTTGTGT 0.890407 -69 ** *** *** ** Masking position 8 Map Score: 2.63179 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 19 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: 9.63739e-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