AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00280_bsub_reg_300.orf -o00280_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 ybgA 218 similar to transcriptional regulator (GntR family) #2 ybgB 33 ybgB #3 ybgE 208 similar to branched-chain amino acid aminotransferase #4 ycbA 300 alternate gene name: yzgA; similar to two-component sensor histidine kinase [YcbB] #5 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #6 ycbD 29 similar to aldehyde dehydrogenase #7 yheM 284 similar to D-alanine aminotransferase #8 ykvY 300 similar to Xaa-Pro dipeptidase #9 ykvZ 281 similar to transcriptional regulator (LacI family) #10 glcT 62 transcriptional antiterminator (BglG family) #11 ptsG 238 phosphotransferase system (PTS) glucose-specific enzyme IIABC component #12 ptsH 97 histidine-containing phosphocarrier protein of the phosphotransferase system (PTS) (HPr protein) #13 splA 90 transcriptional regulator #14 splB 77 spore photoproduct lyase #15 mcpC 134 methyl-accepting chemotaxis protein #16 ykwC 136 similar to 3-hydroxyisobutyrate dehydrogenase #17 pksF 300 pksF #18 yngG 250 similar to hydroxymethylglutaryl-CoA lyase #19 yngI 43 similar to long-chain acyl-CoA synthetase #20 yngJ 90 similar to butyryl-CoA dehydrogenase #21 ynzE 270 ynzE #22 yngK 135 alternate gene name: yotA; similar to hypothetical proteins #23 yngL 110 yngL #24 ppsD 24 peptide synthetase #25 ppsB 24 peptide synthetase #26 ppsA 300 peptide synthetase #27 yqjC 201 similar to hypothetical proteins #28 yqjB 51 similar to hypothetical proteins #29 yqjA 70 yqjA #30 yqiY 80 similar to amino acid ABC transporter (permease) #31 yqiX 268 similar to amino acid ABC transporter (binding protein) #32 yqiW 162 similar to hypothetical proteins from B. subtilis #33 bfmBB 22 branched-chain alpha-keto acid dehydrogenase E2 subunit (lipoamide acyltransferase) #34 bfmBAA 73 branched-chain alpha-keto acid dehydrogenase E1 (2-oxoisovalerate dehydrogenase alpha subunit) #35 yqiS 124 similar to phosphate butyryltransferase #36 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) #37 blt 116 multidrug-efflux transporter #38 bltD 168 spermine/spermidine acetyltransferase #39 yusL 267 similar to 3-hydroxyacyl-CoA dehydrogenase #40 yusM 300 similar to proline dehydrogenase #41 ywdH 167 alternate gene name: ipa-58r; similar to aldehyde dehydrogenase #42 dltA 300 D-alanyl-D-alanine carrier protein ligase (Dcl) #43 dltE 90 alternate gene name: ipa-1r #44 ywaA 140 alternate gene name: ipa-0r; similar to branched-chain amino acid aminotransferase #45 yxjD 78 similar to 3-oxoadipate CoA-transferase #46 yxjC 153 similar to hypothetical proteins from B. subtilis #47 yxjB 300 similar to hypothetical proteins #48 iolA 300 methylmalonate-semialdehyde dehydrogenase #49 aldX 142 aldehyde dehydrogenase Motif number 1 GTATGCAATCCGTTCTTTTTCATTGAGACCATA 1 179 0 CTTCTTTTCT 0.926368 -40 TTGATCACATCCTCGCTTTTTATTTTGGGGAAT 4 159 0 CTCGTTTTTT 0.519837 -142 TTCTATGTGCTTTCCAGTTTTATTCCTGTATAC 7 108 0 TTCCGTTTTT 0.561991 -177 TCTCTTGATCTTTCTGTTTTTCAGCTTGTCCAA 7 195 1 TTCTTTTTTA 0.459275 -90 AAAAGCCCTCCCTTTTCGAGATGTCCCTG 7 266 0 CTCCTTTTCA 0.924218 -19 TTTCACGACGCCTTCATTTTCTAATGCATTTTA 8 206 0 CTTCTTTTCA 0.876744 -95 TTCTCGACATCGTCCTTTTTTATCTGCATTAAA 9 32 1 CTCCTTTTTT 0.965958 -250 CGAGAATGAACTTCCCGTTTTTTTCCCTCAATC 11 68 0 CTCCGTTTTT 0.815965 -171 CAATTTTGCTCATGCCTTTTTGTTGTGTAAAAG 11 115 1 CTGCTTTTTT 0.906158 -124 AAGAATTGACCTCCTCTTTTTACTAGTCTGAC 11 217 0 CTCCCTTTTA 0.80309 -22 ATTTTTTGATTATTCATTTTTCAAACGAAAGGG 15 84 1 TTTCTTTTTA 0.730303 -51 TATCATTTTTCCTTCATTTTCTAGACTACCATA 16 71 0 CTTCTTTTCA 0.876744 -66 ACGATCGGGATTTCCATTTTCATCGATTCCAAA 18 114 0 TTCCTTTTCT 0.86192 -137 ACAAAGTCGCCTTCCTTTTTTTTGACTTCTTTT 18 168 0 CTCCTTTTTT 0.965958 -83 CTTTCTAAGTCGTCTTTTTTTAAAAAGTGATTT 21 27 1 CTCTTTTTTA 0.745876 -244 GTGAATCTCACCTTTGTTTTTTAAAAAATTCAG 21 85 0 CTTTTTTTTA 0.631254 -186 TCTCTGTCCGTCTTTCTTTTTGTATCAAGAATG 23 35 1 TTTTTTTTTT 0.467009 -76 ATGATAACATCATCCTTTTTCTTGGAGGCTTCT 23 86 1 CTCCTTTTCT 0.955694 -25 CTTTATTTTTCGTTTCTTTTTTTATCAAATTTC 26 97 0 CTTTTTTTTT 0.751727 -204 TTGTCATTTTTCTGCTTTTTTCTACATTTTCTT 26 246 1 TTGCTTTTTT 0.73645 -55 GGCGCCTGCTTTTTTATCGTTATAGAA 27 5 1 CTGCTTTTTT 0.906158 -197 AAGCTCCTCCTTTTTCATTAGGTTGACC 28 34 0 CTCCTTTTCT 0.955694 -18 CGGCCAGCCTTCTTCTTTTTTATATT 29 4 0 TTTCTTTTTT 0.82727 -67 GCTGGCCGCCTCTTCTTTTTTATTGAAGAAACA 29 29 1 TTTCTTTTTT 0.82727 -42 TACAACTGCTCCTTTATTTTCCTTCTGGTTATA 32 12 1 CTTTTTTTCT 0.697123 -151 TTTGCTTCGCCGTGCACTTTTTTTGGCCTCTTC 32 73 0 CTGCCTTTTT 0.710543 -90 TGAAGACCTCTCCTTTTTCATCATCTGTTCT 32 142 0 TTCCTTTTCT 0.86192 -21 ATGGCAAAGCCATTCATTTTTAAAAGCATAAAG 34 40 1 CTTCTTTTTA 0.90345 -34 ACTACATTCTCCTTTTTTCTTATCCCGGTA 38 149 0 TTCCTTTTTT 0.89144 -20 GATTTTGACTTGTCCGTTTTCCGCCGCCGTAAT 39 70 1 TTCCTTTTCG 0.468436 -198 AGGAAGACAACATTTATTTTTTTGGAGGGTGCT 41 13 0 CTTTTTTTTT 0.751727 -155 CAAAAATTCCCTTCCCGTTTTTTCGACAATCAC 42 109 0 CTCCGTTTTT 0.815965 -192 TTTCTCCTGCTTTTTTCATATGAATTTC 44 6 1 CTGCTTTTTA 0.845189 -135 ATTGATGCCCCTTTCGTTTTCTTCTACACTAGA 45 56 0 CTTCTTTTCT 0.926368 -23 AAAAAAGGAGCTTTCCTTTTTTAATCGGAATAG 46 30 1 CTTCTTTTTA 0.90345 -124 CGGCTGTTTCCGTCCCCTTTCCATATGTACGAG 46 76 0 CTCCCTTTCA 0.756118 -78 TTTATTTGTCTATGCCTTTTTCATTTATCTAAA 47 252 1 TTGCTTTTTA 0.612387 -49 ACACCCCATTCATTCATTTTTAGATAAATGAAA 47 270 0 CTTCTTTTTG 0.700284 -31 ATGCATCCGCCATTTATTTTTTTGGTGTTTTTG 48 175 1 CTTTTTTTTT 0.751727 -126 TTCATATCAATATCCACTTTTCAGCAAGCCAAG 48 221 0 TTCCCTTTTA 0.541335 -80 AAATCCCCCTCATTTGCTTTCTTCTTTTCTCGG 49 116 0 CTTTCTTTCT 0.369132 -27 * *** ***** * Masking position 8 Map Score: 38.427 Number of sites scoring better than the average of aligned sites = 1847 Number in coding regions = 1432 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 447 Fraction of orfs with sites within 600 bp upstream = 0.0717957 Motif number 2 ATATTTTATAAAAAAGCGGTAAATCACTGTCCG 5 61 0 AAAAACGAAA 0.721447 -166 CTTTTTTATAAAATATCAGAAAATAAAGATATT 5 78 1 AAATACAAAA 0.771658 -149 GATGTGAAAGAAAAATTAATAAAAGCGCTTACA 5 165 1 AAAAATAAAA 0.842972 -62 CCAGAAAAAACACGAAAGGGGCAATGG 6 5 1 AAAAACAAAA 0.956057 -25 CATTAAATAAAAAAATCATCAAATGTTCGAAAG 9 58 1 AAAAACAAAA 0.956057 -224 CCTTTCAGCTAAAAACACAAAAAGATATCTGGT 9 196 1 AAAAAACAAA 0.821056 -86 CCTTACAGCTAAAAATCATGACAACGAATTCAC 11 185 0 AAAAACAACA 0.885091 -54 TTACTTATGAAAAAAACCAGACAGGCCGGAGGC 13 28 0 AAAAACCACA 0.847097 -63 TTATAAAATAAAAAATCCCCAAACAAATGATGT 16 28 0 AAAAACCAAA 0.939935 -109 ATATACCTATAAAAATCATTAAAATAATCCCTT 17 36 1 AAAAACAAAA 0.956057 -265 AACTAGTACTAAATAAAAATAAAATCGAAGAGA 21 167 1 AAATAAAAAA 0.497707 -104 AAATAAACGAAAAAAGTCCTAAAGCATGTTGTG 22 19 0 AAAAATCAAA 0.794288 -117 AAAAGAAACGAAAAATAAAGAAATAATACTATA 26 110 1 AAAAAAAAAA 0.864485 -191 AAAGTACAATAAAAAACATTAAATTTTTATAAC 26 155 0 AAAAACAAAA 0.956057 -146 AAAATGTAGAAAAAAGCAGAAAAATGACAATAA 26 243 0 AAAAACAAAA 0.956057 -58 TTGAAAGAATAAAAACTCCCAAAATCACGATCA 27 62 1 AAAAATCAAA 0.794288 -140 ATAAATATTCAAATACACCAAAAGTAATGAATA 31 231 1 AAATAACAAA 0.416122 -38 TCAGCAGTATAAAAAACATAACATGGGACAATC 39 39 0 AAAAACAACA 0.885091 -229 GCTTCATACAAAAAAATAACAAATTAGCTATTG 39 221 1 AAAAATAAAA 0.842972 -47 GGTTTGTCAGAAAAAATAACAAACTCATATCTG 41 74 0 AAAAATAAAA 0.842972 -94 AACCATACATAAAAAACAAAACAAGCAGTATCA 42 217 0 AAAAACAACA 0.885091 -84 ATTCATATGAAAAAAGCAGGAGAAA 44 3 0 AAAAACAAGA 0.686284 -138 TTAATATAATAAAAATAATGAAAAAATGTAGTG 48 45 1 AAAAAAAAAA 0.864485 -256 AAACGCTTTCAAAAACACCAAAAAAATAAATGG 48 184 0 AAAAAACAAA 0.821056 -117 ***** ** *** Masking position 5 Map Score: 26.3188 Number of sites scoring better than the average of aligned sites = 361 Number in coding regions = 283 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 3 AGAACCACCATTCCCTTCTTAAAACACATT 2 14 0 TTCCCTTCTT 0.703615 -20 TTCTTTCACATCCGCTCCTTCCCATATATC 5 147 0 TCCGCTCCTT 0.921531 -80 TTTGGGAATTTCCGCTCCTTTTATCGGGAT 8 69 0 TCCGCTCCTT 0.921531 -232 ACCCATGTGATCTTCTCCTTTCAGCTAAAA 9 180 1 TCTTCTCCTT 0.86226 -102 AGATTCCCTTCTTTCTAAATCCC 9 269 0 TTCCCTTCTT 0.703615 -13 ACTATCCCTCCTAGCCATGTTAT 13 78 0 ATCCCTCCTA 0.513835 -13 ACCAATCCCCTCCTAATTTCTATAT 15 120 0 TCCCCTCCTA 0.818675 -15 TTCGAGCAGTACGTCTCCTTCATTTACAAA 18 196 0 ACGTCTCCTT 0.683402 -55 TCATTGTTCCTCCTTTCTTAATGAT 19 29 0 GTTCCTCCTT 0.855192 -15 ATCGTTTCCTCCTTCACATCTTTG 20 77 0 TTTCCTCCTT 0.877906 -14 AGACATGATTTTCTCTCCTTAAACAATCTG 27 117 1 TTCTCTCCTT 0.902309 -85 AAGCTCCTCCTTTTTCATTAGG 28 40 0 GCTCCTCCTT 0.913393 -12 AAGGCTGGCCGCCTCTTCTTTTTTATTGAA 29 26 1 GCCTCTTCTT 0.629293 -45 AGCCTTTGTCTCCTTTTCTTACAGG 30 66 0 TTGTCTCCTT 0.743027 -15 ATACAACTGCTCCTTTATTTTCCTT 32 6 1 ACTGCTCCTT 0.650751 -157 TGAAGACCTCTCCTTTTTCATCATC 32 148 0 ACCTCTCCTT 0.873342 -15 TCAAGCCCCTCCTTTATGCTTTTA 34 60 0 GCCCCTCCTT 0.965263 -14 TCCGTTTCTCCTTTTTGTAAGGT 41 155 0 GTTTCTCCTT 0.742211 -13 TCTTATTGCCTCCTTCATTAGTAAA 48 286 0 TTGCCTCCTT 0.855719 -15 ********** Masking position 6 Map Score: 15.7489 Number of sites scoring better than the average of aligned sites = 655 Number in coding regions = 354 Number in noncoding regions = 301 Number of orfs with sites within 600 bp upstream = 345 Fraction of orfs with sites within 600 bp upstream = 0.0554128 Motif number 4 AGGAAAAAATAAACTCCTTTCCGCTATAGA 7 165 1 AAACTCCTTT 0.81692 -120 CAAACGGAACAACCCCCCTGCGATTGAACG 8 143 1 AACCCCCCTG 0.806931 -158 CTTCTTTCTAAATCCCCTTGATCTGGAATG 9 255 0 AATCCCCTTG 0.860965 -27 TTTTATCATTCTCCTTTTAACTTAAAG 12 81 0 ATTCTCCTTT 0.847574 -17 CTGGTTATATAATCCCCTTTTTCTGTAAGC 32 36 1 AATCCCCTTT 0.917699 -127 GATTGTATCCTCCCTTACGTCT 33 7 0 ATCCTCCCTT 0.789607 -16 CTTCAGAAAACCCCTTTATCTTTTCAT 36 8 1 AAACCCCTTT 0.852578 -145 CCCGATACCCCTTTGTATGAAAAA 36 139 0 ATACCCCTTT 0.788936 -14 AAAAACCTCCTTGACTATACGGT 37 4 1 AACCTCCTTG 0.797181 -113 CTGAATTCCCCTTTTACTCAATTG 37 103 0 ATTCCCCTTT 0.878152 -14 ACTACATTCTCCTTTTTTCTTATCC 38 154 0 ATTCTCCTTT 0.847574 -15 ATCCATTGTGATCCTCCTTTGGTTTCTGTT 40 211 1 ATCCTCCTTT 0.82061 -90 TTTTTTCCCTAATCTCCCTCAAATTAATAT 42 43 0 AATCTCCCTC 0.672002 -258 GGTCAATCTCCCTGCTGTTAAATT 44 127 0 AATCTCCCTG 0.796742 -14 ATTGATGCCCCTTTCGTTTTCTTC 45 65 0 ATGCCCCTTT 0.75603 -14 TAAAAAAGGAAAGCTCCTTTTTTCGGAGCT 46 23 0 AAGCTCCTTT 0.787201 -131 ATCATGAAAAAAACTCCCTTTCTGCTGTAT 47 144 0 AAACTCCCTT 0.785446 -157 TGTAAAATCCCCCTCATTTGCTTTC 49 128 0 AATCCCCCTC 0.726433 -15 ********** Masking position 9 Map Score: 15.9822 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 193 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 218 Fraction of orfs with sites within 600 bp upstream = 0.0350145 Motif number 5 TATTATGGTCTCAATGAAAAAGAACGGATTG 1 176 1 TAATGAAAAA 0.698185 -43 GGCGTATTATTAAAGGAAAGGCTGTATACTT 3 129 1 TAAGGAAAGG 0.628963 -80 GGAGCGGATGTGAAAGAAAAATTAATAAAAG 5 159 1 TAAAGAAAAA 0.567449 -68 CAGTCAAGTATACAGGAATAAAACTGGAAAG 7 101 1 TCAGGAATAA 0.506416 -184 ATGTCAGATTTTAAGGAAAAAATAAACTCCT 7 152 1 TAAGGAAAAA 0.952193 -133 ACTGTCAGTATACAGGAAGAGGAGCAGGAAA 8 175 1 TCAGGAAGAG 0.636905 -126 CATCAGTGATTGAGGGAAAAAAACGGGAAGT 11 61 1 TAGGGAAAAA 0.804357 -178 GTAACGTTAGTAAAGGAAAAGGATGTGGCAT 14 56 1 TAAGGAAAAG 0.937938 -22 GTCTAGAAAATGAAGGAAAAATGATAAATTT 16 78 1 TAAGGAAAAA 0.952193 -59 TCTCACTAAATAAACGAAAAAAGTCCTAAAG 22 28 0 TAACGAAAAA 0.872547 -108 GGTTGACCAATGAAGGAAGAGCTCATGCGAA 28 11 0 TAAGGAAGAG 0.846078 -41 ATAAAAAGGCTCAACGAAAAAGTTGAGCCGC 30 17 0 TAACGAAAAA 0.872547 -64 CTCCTTTTCTTACAGGAAAAAAGTTTCCTAT 30 51 0 TCAGGAAAAA 0.864054 -30 AAAATACAAATTAACGAATAAATATTCAAAT 31 214 1 TAACGAATAA 0.52497 -55 CTGTAAGCAGTAAACGAAGAGGCCAAAAAAA 32 58 1 TAACGAAGAG 0.653905 -105 CGCTGGACAATAAAGGAAATGAAAAGATAAA 36 25 0 TAAGGAAATG 0.533524 -128 TTGAGGGAGATTAGGGAAAAAATGAAACTTT 42 51 1 TAGGGAAAAA 0.804357 -250 AATAAAGGAAAAACATGCTGGAT 47 3 1 TAAGGAAAAA 0.952193 -298 CATTTTTAGATAAATGAAAAAGGCATAGACA 47 258 0 TAATGAAAAA 0.698185 -43 * ********* Masking position 1 Map Score: 11.6151 Number of sites scoring better than the average of aligned sites = 491 Number in coding regions = 417 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 6 ATCAAACAGCCAGAATAAAACTG 3 4 1 AAACAGCCAG 0.965895 -205 AAATTAAAGAAAACAGCCAGTTTTATTCTG 3 21 0 AAACAGCCAG 0.965895 -188 ACCAAACAGCCGGCTGACCAGGC 5 4 1 AAACAGCCGG 0.978038 -223 CGCAGCAAAAAAACAGCCTGGTCAGCCGGC 5 19 0 AAACAGCCTG 0.951842 -208 GCATCTTCATAAGCTGCCTGCTGTACAGCA 7 46 0 AAGCTGCCTG 0.837448 -239 CGGATGCTCAAAGCAGCCCGGGTTTTTTTG 31 23 1 AAGCAGCCCG 0.931986 -246 AAGCAGCCGTGGGAAGCAGC 39 1 1 AAGCAGCCGT 0.803997 -267 AAGGGGACGGAAACAGCCGATGCGGACAGG 46 90 1 AAACAGCCGA 0.832581 -64 AGGTGTAGACAAACTGCCAGACCTGGCCAA 47 203 1 AAACTGCCAG 0.899495 -98 ********** Masking position 2 Map Score: 7.6984 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 245 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 AAAAATTAATAAAAGCGCTTACAGATAGAG 5 175 1 AAAAGCGCTT 0.899349 -52 TCAAATGTTCGAAAGGGTTTAATTTCATGT 9 76 1 GAAAGGGTTT 0.870557 -206 CCTTGATCTGGAATGCGTTTCATACAATAT 9 240 0 GAATGCGTTT 0.936387 -42 TTAATGATAGGAAAGCGTTTACATTT 19 7 0 GAAAGCGTTT 0.975326 -37 AAAACTGATGAAAAGCGTTTTGATCGTGAT 27 85 0 AAAAGCGTTT 0.924358 -117 CTGCGCCATGAAATGCGCTTTTTTCATCGC 40 94 1 AAATGCGCTT 0.766554 -207 CCGCGAACTAGAAAGCGTTTACAAAAACCT 46 117 0 GAAAGCGTTT 0.975326 -37 TGGTGTTTTTGAAAGCGTTTAATTCTTGGC 48 197 1 GAAAGCGTTT 0.975326 -104 ********** Masking position 3 Map Score: 7.4117 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 57 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 8 CACCTATAAATTTCAGAATATTCTTTAGGATCATC 3 88 0 TTTCATTTCT 0.856368 -121 TTTTGTATGATTCTGTAGTCTCCATTATACAGTAA 4 38 0 TTCTATTCCT 0.764758 -263 CATCCGCTCCTTCCCATATATCCTTTTGTTTAATT 5 134 0 TTCCTTTCCT 0.622811 -93 GTAAGCGCTTTTATTAATTTTTCTTTCACATCCGC 5 162 0 TTATATTTCT 0.293838 -65 TCTTTCTGTTTTTCAGCTTGTCCAATATGGTAGAA 7 203 1 TTTCCTTCCA 0.635018 -82 AGCCCTCCCTTTTCGAGATGTCCCTGATGTCATTC 7 257 0 TTTCGTTCCT 0.580252 -28 TATAATTTATTTTTTGATTATTCATTTTTCAAACG 15 76 1 TTTTATTTCT 0.705671 -59 TTTATCATTTTTCCTTCATTTTCTAGACTACCATA 16 71 0 TTCCCTTTCA 0.56395 -66 ATAGGTATATTTTCATAATATTCAAACTTTTATTT 17 11 0 TTTCATTTCA 0.492821 -290 CAGTTTTAATTTTCAGACTTTTCTTGTCAGGGAAT 20 13 1 TTTCATTTCT 0.856368 -78 GATGTTATCATTCCCAAGTGTCCCTTATCCATTCT 23 62 0 TTCCATTCCT 0.889921 -49 ATAGTATTATTTCTTTATTTTTCGTTTCTTTTTTT 26 107 0 TTCTATTTCT 0.70649 -194 TTTCTGCTTTTTTCTACATTTTCTTATCCTCTTAT 26 254 1 TTTCCTTTCT 0.887697 -47 GATCCATTTCCCCCGTATTCATTACTTTTGGT 31 247 0 TTCCCTTTCT 0.888089 -22 CGTGCACTTTTTTTGGCCTCTTCGTTTACTGCTTA 32 61 0 TTTTCTTTCT 0.760683 -102 CAACCCTATGTTACCACGTTTTCTTCTCTTGACAA 36 67 0 TTACCTTTCT 0.578388 -86 AATTGAACCCTTTTTACCTATCCTTTTCGCTTGAA 37 73 0 TTTTCTTCCT 0.811069 -44 TTAAGTACCTTTTCTTATTGTGCCTAACCAGGGGC 38 51 0 TTTCATTGCT 0.484639 -118 ACTACATTCTCCTTTTTTCTTATCCCGGTAT 38 148 0 TTCTTTTTCT 0.32959 -21 ATACTGCTGATTTTGACTTGTCCGTTTTCCGCCGC 39 62 1 TTTTCTTCCT 0.811069 -206 TTTCTGTTCATTTTATAGTTTCCTTCAGACTGGGA 40 233 1 TTTTATTCCT 0.764047 -68 GTTTCATTTTTTCCCTAATCTCCCTCAAATTAATA 42 44 0 TTCCATTCCT 0.889921 -257 GCTGTATGGGTTTCCCCGTTTCCATCATACAACAA 47 116 0 TTTCCTTCCT 0.914352 -185 **** * * *** * Masking position 9 Map Score: 13.9179 Number of sites scoring better than the average of aligned sites = 597 Number in coding regions = 507 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 9 TTTTAAAGCTGCAAAAAGTATACAGCCTTTCCTTTAATA 3 136 0 GCAAAACGCT 0.720494 -73 GAGAGGTTTTACAGCAAGACAGCTGCCACCGAGAACAGT 9 114 1 ACAGAACGCC 0.960772 -168 AGCTAAAAACACAAAAAGATATCTGGTACGTCCATATCA 9 202 1 ACAAAACGGC 0.980051 -80 GCCCTTTTACACAACAAAAAGGCATGAGCAAAATTGGGT 11 112 0 ACAAAACTGC 0.763918 -127 TGTACAAAAACCAGACGGCCTCCGGCCTGTCT 13 4 1 ACAAAACGCC 0.987265 -87 TCCGAACAGCACAAAAAATAATGTGGCACCTAACCAGAC 21 236 0 ACAAAAGGGC 0.905791 -35 TGTTTCTATAACGATAAAAAAGCAGGCGCC 27 2 0 ACGAAACGGC 0.885695 -200 AAATTTATGCACAAAAAAACCCGGGCTGCTTTGAGCATC 31 25 0 ACAAAAGGCC 0.938166 -244 ATAACATGGGACAATCATAATGCAGCTGCTTCCCACGGC 39 16 0 ACAACACGCC 0.9244 -252 AAACGTTAAAGCAAGAACTCGACCGCGTCGGACACATGC 40 42 0 GCAAAACGCC 0.975085 -259 ACAAATCTTAGCAGGAAATATGCAGCCGCGTCCTATGAG 43 15 0 GCAGAACGCC 0.925174 -76 GAAAGCGTTTACAAAAACCTGTCCGCATCGGCTGTTTCC 46 98 0 ACAAAACGCC 0.987265 -56 TTTCCATCATACAACAAATATCCAGGAGCTGGAACCTTA 47 94 0 ACAAAACGGC 0.980051 -207 **** ** * ** * Masking position 7 Map Score: 11.3051 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 148 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 GAATTTAGCACCGCCCTTATCAAACTGTCAAT 1 80 1 CCGCCTTTCA 0.976636 -139 CAGTATATATCCGTCTTTTTCAATAAACCGTT 4 203 0 CCGTCTTTCA 0.974704 -98 GCCAGCGGCACCGTAATCAGCATGAGGGCCAG 4 232 0 CCGTATCGCA 0.793416 -69 GTCATTCAAGCTGTCATTATCACTAATTCTAC 7 232 0 CTGTCTTTCA 0.805299 -53 TAATAAAAGCCCACCATCTTCATCCCGATAAA 8 48 1 CCACCTCTCA 0.698278 -253 TTGTTCCTCCCTGCCATTTGCAATGCATTGTT 8 276 0 CTGCCTTGCA 0.730607 -25 TGTTAGTACGCCGTGCTTGTCAGATGACAAGT 12 14 1 CCGTGTTTCA 0.803835 -84 TATCATACAACCGTACTTGTCATCTGACAAGC 12 28 0 CCGTATTTCA 0.874778 -70 AAATCTGTGTCCGTCTAATTCAGGAAGCACCT 17 131 0 CCGTCAATCA 0.593145 -170 ACTTAGAAAGCCGTCCTTCTCATTTC 21 5 0 CCGTCTTTCA 0.974704 -266 AAGCTCCTCCTTTTTCATTAGGTTGAC 28 35 0 CCTCCTTTCA 0.71787 -17 GCTGCGCTTGCCGCAGATGGCAAAGCCATTCA 34 24 1 CCGCAATGCA 0.551907 -50 GAAAAAAAATCCGTCTTCAGCGGCAGTCAGCG 39 139 0 CCGTCTCGCG 0.741888 -129 CTCCCTCCCGCCGTCATCTTCAAAACACCTGT 40 275 0 CCGTCTCTCA 0.972259 -26 TGCTGGTATCCCGCCAACATCATATCAGCATA 47 37 0 CCGCCACTCA 0.910896 -264 ***** ** *** Masking position 11 Map Score: 6.56309 Number of sites scoring better than the average of aligned sites = 871 Number in coding regions = 803 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 11 ATGCTGATTACGGTGCCGCTGGCCGGTGAACT 4 241 1 CGGTCCGCGG 0.830902 -60 AAAAAACAGCCTGGTCAGCCGGCTGTTTGGT 5 10 0 CTGGCAGCGG 0.966237 -217 CGGTAAATCACTGTCCGGCCGGGATTCTGCGC 5 46 0 CTGTCGGCGG 0.93922 -181 CTACATAATGCTGTACAGCAGGCAGCTTATGA 7 38 1 CTGTCAGCGG 0.986769 -247 GATCTTTCTGTTTTTCAGCTTGTCCAATATGG 7 201 1 TTTTCAGCTG 0.673901 -84 CTATCATAGGCTGTGCAGCGGGTTTCCTT 8 8 0 CTGTCAGCGG 0.986769 -293 GGTTGAGAGGTTTTACAGCAAGACAGCTGCCA 9 110 1 TTTTCAGCAG 0.784672 -172 GACAAAATATTTTTTCCGCTGGACAATAAAGG 36 40 0 TTTTCCGCGG 0.900776 -113 TCATATCTGCGTTTTCAGCAGGAATTTGATAA 41 51 0 GTTTCAGCGG 0.914204 -117 GACATGTCCACTTGACAGCGGGTTTTTCATAC 42 167 0 CTTGCAGCGG 0.961103 -134 ATATAAACAATTTAACAGCAGGGAGATTGACC 44 119 1 TTTACAGCGG 0.768961 -22 TCAATATCCACTTTTCAGCAAGCCAAGAATTA 48 216 0 CTTTCAGCAG 0.90841 -85 **** **** ** Masking position 6 Map Score: 7.05046 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 341 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 12 AGCTGACCCGGAATTCTTCATTG 4 288 0 GCTGACGGAA 0.947248 -13 AAACGAAAGGGCCGATATAGAAATTAGGAGGG 15 106 1 GCCGATAGAA 0.746934 -29 CGATTTGGTCGCCGGCTTTGACGTGGACTTTC 18 60 0 GCCGGTTGAC 0.781078 -191 AAAGTCATTTGCCGATATGGACGTTTCCTTGC 32 103 1 GCCGATGGAC 0.976772 -60 ACCCTTAAGAGCTGGCATGGAACTTGCATAAT 35 68 1 GCTGGTGGAA 0.876948 -57 TTTTTATACTGCTGATTTTGACTTGTCCGTTT 39 57 1 GCTGATTGAC 0.838829 -211 CCGCCGTAATGCTGAGTCGGACCGGCATCTCC 39 93 1 GCTGACGGAC 0.966257 -175 AGCTATTGAAGTCGAACCGGAAATCTTTTAAG 39 246 1 GTCGACGGAA 0.714424 -22 TCAATGACATGCTGAACTGGAATTTGCTCGCG 40 121 0 GCTGATGGAA 0.943099 -180 GACGGAAACAGCCGATGCGGACAGGTTTTTGT 46 95 1 GCCGACGGAC 0.978548 -59 ***** ***** Masking position 11 Map Score: 4.57055 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 230 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 13 ATTGCATACAGAATGGGGAGAATGAA 1 203 1 GAATGGGAGA 0.812314 -16 TTATTTTGGGGAATCGGGAGAAAACCTGCAA 4 142 0 GAATGGGAGA 0.812314 -159 GAAAAAACACGAAAGGGGCAATGGGC 6 14 1 GAAAGGGCAA 0.863597 -16 GGGACATCTCGAAAAGGGAGGGCTTTT 7 268 1 GAAAGGGAGG 0.693387 -17 TTTTGTTGTGTAAAAGGGCAAATGTAAACGG 11 132 1 TAAAGGGCAA 0.592183 -107 TTTTTCAAACGAAAGGGCCGATATAGAAATT 15 100 1 GAAAGGCCGA 0.92559 -35 CGACCAAATCGAAAAGGGCCAGGAGGTAGCC 18 81 1 GAAAGGGCCA 0.740401 -170 TCCCGGGCTATAAAAGGGTGATTAACAGAAT 22 64 0 TAAAGGGTGA 0.546835 -72 TGAAAGTGATGTAATGGGGGAGAAGAAACAG 22 114 1 GTAAGGGGGA 0.87748 -22 AGCGTGTTTTGAATGGGCGGACAAGCGATAT 27 157 1 GAATGGCGGA 0.799342 -45 ACTGCTTACAGAAAAAGGGGATTATATAACC 32 38 0 GAAAAGGGGA 0.870549 -125 AACAGATGATGAAAAAGGAGAGGTCTTCA 32 144 1 GAAAAGGAGA 0.727694 -19 ACTTGCATAATAAAAGGCGGAGTCGAAACAA 35 89 1 TAAAGGCGGA 0.818248 -36 TTCAATTGAGTAAAAGGGGAATTCAG 37 101 1 TAAAGGGGAA 0.696181 -16 CGCGGCGAGCGTAAAGGGAGATGCCGGTCCG 39 110 0 GTAAGGGAGA 0.739989 -158 AAAGGGGACGGAAACAGCCGATGCGGACAGG 46 89 1 GAAAAGCCGA 0.609174 -65 CTAGTTCGCGGAAACGGGGGATGTGTGT 46 136 1 GAAAGGGGGA 0.981708 -18 TTGTATGATGGAAACGGGGAAACCCATACAG 47 119 1 GAAAGGGGAA 0.909015 -182 ACCAAAAAAATAAATGGCGGATGCATATTTA 48 170 0 TAAAGGCGGA 0.818248 -131 **** ****** Masking position 3 Map Score: 14.4567 Number of sites scoring better than the average of aligned sites = 573 Number in coding regions = 437 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 14 AAAGAAGGATACAAATCTTTCATATTGGGAGGG 1 136 1 ACAACTTCAT 0.752591 -83 CAGCTATTATACACCACATTCATTGTCAGATGA 3 56 0 ACACCTTCAT 0.974752 -153 TTTTATTATTACAGCTCTATCATAGGCTGTGCA 8 23 0 ACACCATCAT 0.905473 -278 TTTGCCTTTCACGACGCCTTCATTTTCTAATGC 8 212 0 ACGCCTTCAT 0.960282 -89 GATATCTGGTACGTCCATATCATATTGTATGAA 9 219 1 ACGCAATCAT 0.509117 -63 AAAAATCATGACAACGAATTCACAGGCGTAAGT 11 175 0 ACACATTCAC 0.719214 -64 TTCGAGCAGTACGTCTCCTTCATTTACAAAGTC 18 193 0 ACGCCTTCAT 0.960286 -58 AAATGTCCAAACACCGCCTCCATATTCATGTGA 21 114 0 ACACCTCCAT 0.879086 -157 CTCCCCCATTACATCACTTTCACTATTCGCTAT 22 103 0 ACACCTTCAC 0.936777 -33 GGTTTTTCATACAGCTGTTTCATTAATTGCAGC 42 146 0 ACACGTTCAT 0.848702 -155 GATAAAAAACACCCCATTCATTCATTTTTAG 47 280 0 ACACCTTCAT 0.974752 -21 *** * * ***** Masking position 12 Map Score: 6.8382 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 50 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 15 GTCAGATTTTAAGGAAAAAATAAACTCCTT 7 154 1 AAGGAAAAAA 0.751799 -131 ACCCAATTAAAATGAAGAAACCCATGTGAT 9 161 1 AATGAAGAAA 0.789275 -121 TGAATGCATTGAAAAAAGGTTTGACGT 10 8 1 ATTGAAAAAA 0.521118 -55 TCAGTGATTGAGGGAAAAAAACGGGAAGTT 11 63 1 AGGGAAAAAA 0.865129 -176 TTAAAAGGAGAATGATAAAA 12 88 1 AATGATAAAA 0.465224 -10 CTTTCCGCCTAGTGAGAAAAGTAACGTTAG 14 36 1 AGTGAGAAAA 0.66541 -42 CAAAGATGTGAAGGAGGAAACGAT 20 77 1 AAGGAGGAAA 0.54665 -14 CCGGATATAAAGTGATAAAAGTATTGTTTT 26 68 0 AGTGATAAAA 0.648168 -233 TAGCGAAAGCAGGGATGAAA 27 192 1 AGGGATGAAA 0.702863 -10 CTTCTTTTTTATTGAAGAAACAAATAGAAA 29 40 1 ATTGAAGAAA 0.578269 -31 TATTTTGTCAAGAGAAGAAAACGTGGTAAC 36 63 1 AGAGAAGAAA 0.759579 -90 GAATGGTACGAGAGAAAAAAAATCCGTCTT 39 154 0 AGAGAAAAAA 0.714884 -114 GAGGGAGATTAGGGAAAAAATGAAACTTTT 42 53 1 AGGGAAAAAA 0.865129 -248 GGAACCTTATAGTGAAGAAAAATCAGTACT 47 73 0 AGTGAAGAAA 0.888041 -228 TAATAAAAATAATGAAAAAATGTAGTGTTT 48 51 1 AATGAAAAAA 0.74827 -250 AGGTCCGAGAAAAGAAGAAAGCAAATGAGG 49 112 1 AAAGAAGAAA 0.598699 -31 ********** Masking position 5 Map Score: 7.09662 Number of sites scoring better than the average of aligned sites = 605 Number in coding regions = 503 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709