AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02010_mpneu_reg_300.orf -o02010_mpneu_300.ace -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -g0.40 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 E07_orf586 23 ugpC; sn-glycerol-3-phosphate transport ATP-binding protein. #2 E07_orf301 300 ugpB; sn-glycerol-3-phosphate transport lipoprotein. #3 D09_orf560L 300 potA; spermidine/putrescine transport ATP-binding protein potA #4 C12_orf157 54 pmsR; peptide methionine sulfoxide reductase. #5 C12_orf456 300 eno; enolase (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate #6 A05_orf317 30 putative cobalt transport permease protein. #7 A05_orf409 37 pgk; phosphoglycerate kinase. [EC:2.7.2.3] [SP:PGK_MYCPN] #8 A05_orf290 184 yidA; #9 A05_orf370 130 hypothetical protein. #10 A05_orf241a 51 glpQ; glycerophosphoryl diester phosphodiesterase. [EC:3.1.4.46] #11 A05_orf900 300 alaS; alanyl-tRNA synthetase (alanine--tRNA ligase) (alaRS). #12 A05_orf380V 250 P37; high affinity transport system protein P37 precursor. #13 A05_orf493 300 hypothetical protein. #14 A65_orf251b 300 hypothetical protein. #15 G07_orf389a 275 oppB; oligopeptide transport system permease protein oppB. #16 G07_orf1030 104 hypothetical protein. #17 G07_orf294 300 rpsB; 30S ribosomal protein S2. [SP:RS2_MYCPN] #18 VXpSPT7_orf108 93 rpsJ; 30S ribosomal protein S10. [SP:RS10_MYCPN] #19 VXpSPT7_orf112 246 hypothetical protein. #20 VXpSPT7_orf320 121 hypothetical protein. #21 VXpSPT7_orf445 153 hypothetical protein. #22 VXpSPT7_orf424 25 hlyC; #23 VXpSPT7_orf617 280 infB; initiation factor IF-2. [SP:IF2_MYCPN] Motif number 1 TAAAACTACTTAAATTGCTAAAAATTAACCGTTT 2 115 1 TATGCAAAAA 0.81701 -186 TTGGCCTAATTTTGACCCTAAAACTAATTCAAAA 2 147 0 TTCCCAAAAC 0.887394 -154 TGGTTCAAAATTTAGTCCAAAAACAGTCAAATTT 3 124 1 TTTCCAAAAC 0.905826 -177 TTGCAGTTAAATTTGTGCTAAAAATTTGACTGTT 3 145 0 ATTGCAAAAA 0.912725 -156 TAGCACAAATTTAACTGCAAAAACTGTTCAAAAA 3 159 1 TTTGCAAAAC 0.965696 -142 TGGGATAAATTTTCTTGCAAAAAAATGATTGCAA 3 204 0 TTTGCAAAAA 0.763484 -97 TTGACCCCGCTTGCCCCCTAAAACTGGGATAAAT 3 228 0 TTCCCAAAAC 0.887394 -73 CGTTGTTTTGATAAATGCTTAAACTTTTCAAAAA 5 82 1 ATTGCTAAAC 0.685312 -219 TTAATCCGGTTAGCTTGCCAAAAAATAAATTAGA 9 57 1 TATGCAAAAA 0.816994 -74 TTTGCAATAAATGTATGCCAAAAACGTTTTTCTA 9 87 0 ATTGCAAAAA 0.912356 -44 CCAGCTTGCTTTAAATCCTTAAAAAGGGTATTAA 11 154 1 TTTCCTAAAA 0.675765 -147 TCAAACCAAAATCAATGCCTAAAATGTACTGCA 11 278 1 ATTGCTAAAA 0.689789 -23 GCTGAATTTTCTATATGCAAAAAACGATAAAAAG 12 160 0 CTTGCAAAAA 0.761901 -91 TCAGCATTTATTAAGCTCAAAAAATAAGAAAAGC 12 189 1 TTCTCAAAAA 0.803749 -62 CAACTTAATCTTCCGTTCAAACACCCACGTGGCC 13 86 0 TTTTCAACAC 0.544571 -215 TGGCGTTAGGTTTAATGCAAAAACTCAATGTTGA 14 47 1 TTTGCAAAAC 0.964355 -254 TTTCTGTGTGATTGTTGCCAACAAGGCTTATGAC 14 150 1 ATTGCAACAA 0.718938 -151 TGCGCCAGCTTTTTGTGCAAAAAATCTTGCAAAC 14 221 1 TTTGCAAAAA 0.742371 -80 CTTGTTCTCTTAAACCTTATTTAAC 14 286 0 TTCTCTAAAC 0.459797 -15 AAACAGCATTTTAGTCGCTAAAAACATTGTTAGT 15 51 0 TTCGCAAAAA 0.95917 -225 GTGACACAATAAGATCGCCAAAAAGCGGGGTTAC 19 106 1 AACGCAAAAA 0.571448 -141 GGAAACTAATTTCTACCCTAAAAAGACTACTTAA 20 18 0 TTCCCAAAAA 0.889448 -104 AGGGTAGAAATTAGTTTCCAAAAACGGTTTTAAA 20 33 1 TTTTCAAAAA 0.833301 -89 TACGGGTGGATTTAGCGCAAACACTACCAGGTCG 23 120 1 TTCGCAACAC 0.84916 -161 ** *** ***** Masking position 11 Map Score: 23.8114 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 188 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 2 TTCTTTTTTTAAAAAATCTCTACTTTTTACCCCCTAAAT 2 190 1 AAAAATTTTA 0.801672 -111 TCTTGATAAAAAGAAAGGGAATCTTTTAACAAGAAAAAA 3 47 0 AAAAATTTTA 0.920053 -254 TCTTTTTATCAAGAAAATCTCTTTTTTTATGTCTTAAAA 3 72 1 AAAAATTTTA 0.917529 -229 TTTTGAACCAAAATAAAGACCACTTTTAAGACATAAAAA 3 95 0 AATAATTTTA 0.920108 -206 AAATTGCTACAATAAATACCGTTTTTTCTTTAAAAATTA 3 262 1 AAAAATTTTT 0.888453 -39 GGTTTATTAAAACTAGGGGACTTTTTTGAAAAGTTTAAG 5 99 0 AATAGTTTTA 0.864812 -202 AATCCTCTAATTAGTTTATATTTTACTACT 6 9 1 AATAGTTTAT 0.550203 -22 ACTTAATTAAGCTTAATTTTTTTAACTGAACCG 8 162 0 AATAATTTTT 0.891394 -23 TTGTGGAACTAATAAAAACCCGCTTTAATGTACCAGTAA 11 38 0 AAAAATTTAT 0.574547 -263 CATTTAAAAAGTTCTTTTAAAACAAATTTG 12 2 1 ATTAATTTTA 0.593321 -249 GGATTCAAGAAATAAATTTCTTGTTTATTGTGAAAAATT 12 50 1 AAAAATTTAT 0.451525 -201 TGAAAAATTCAAAAAAGCAACAATTTTTAAAGTGATTTC 12 80 1 AAAAATTTTA 0.801672 -171 TTCAAAGCAAAATTAAAAAAGCTTTTTATCGTTTTTTGC 12 139 1 AATAATTTTT 0.916535 -112 TTTTGAGCTTAATAAATGCTGAATTTTCTATATGCAAAA 12 172 0 AAAAATTTTT 0.888453 -79 TAATTCAATTATGAAATTGCTGCTTTTCTTATTTTTTGA 12 205 0 ATAAATTTTT 0.591298 -46 AAAGCAAACCAAAAAGTCACCTGTTTTTAACGGGTGGCT 17 121 1 AAAAGTTTTA 0.862495 -180 TTCTTTTAACAATTAAATGGGTCTTTTAAAGTGACACAA 19 76 1 AATAATTTTA 0.92036 -171 AACGGTTTTAAATTAGAGGCTTATTTTTAAAAATTCAAA 20 55 1 AATAGTTTTA 0.864805 -67 AAGGTAAATAATTTAGCTTTTTGTTTAATCAGCA 21 6 1 AATAATTTTT 0.917686 -148 AAGTTAAATTAGGTTTAAATTTTAT 22 1 0 AATAGTTTTT 0.864756 -25 ** *** **** * Masking position 14 Map Score: 19.9357 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 87 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 3 TGATGTATGGCAAGACCGCCGAAAAATTACAA 2 9 0 CAAACCGCAA 0.889029 -292 TTTTTTAAAAAAAGAAAGCGGGAAATTGGCCTAA 2 172 0 AAAAAAGCAA 0.829187 -129 AAAAGGAACCAAAGAAAACCGTAACTCGTTGTTT 5 56 1 AAAAAAACAA 0.606315 -245 TTTAATAAACCAACCACGCTTAACGCTACAAACG 5 127 1 CAACACGCAC 0.917417 -174 ACCTTTCCTTAAAGCCAACTAGAATAATCTAGTA 8 42 0 AAACCAACAA 0.404261 -143 GGAACTAATAAAAACCCGCTTTAATGTACCAGTA 11 39 0 AAACCCGCAA 0.734902 -262 TTTTGTACCGCAAACACGCGGAAGGGACTTGGAA 11 205 1 CAACACGCAG 0.805603 -96 GTGAAAAATTCAAAAAAGCAACAATTTTTAAAGT 12 79 1 CAAAAAGCAA 0.947869 -172 TTCACGAACACAATAACGCGATACAGCACCGTGG 14 12 0 CAAAACGCAC 0.89552 -289 TTGTTGGCAACAATCACACAGAAAAACAAGCTAC 14 140 0 CAACACACAA 0.906457 -161 AAACATTCTACAAAAAAACGATACTAGTAAGTAC 15 11 0 CAAAAAACAC 0.677221 -265 ATTTTGTTAGCAATAACACCAAAATCCACATCTA 17 88 1 CAAAACACAA 0.882027 -213 ATCCACATCTAAAGCAAACCAAAAAGTCACCTGT 17 111 1 AAACAAACAA 0.666233 -190 TTAACTAGCGCAAACAAGTCCCAATGCTTTTAGC 19 16 1 CAACAAGTAA 0.67329 -231 TTACTAACAGCAAAAAAGCTCCAAGCTAAAAGCA 19 40 0 CAAAAAGCAA 0.947869 -207 TAAACAACTTCAAAAAAGTAGTAACCCCGCTTTT 19 126 0 CAAAAAGTAA 0.613905 -121 AGCACTGTTACAAAAACGCTTAAAGGTAAGCTGT 23 205 1 CAAAACGCAA 0.959293 -76 CCCTTTCCTTTAAACAAGCAATAATGTGATCTAG 23 251 0 TAACAAGCAA 0.608178 -30 *** ***** ** Masking position 3 Map Score: 11.8554 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 190 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 4 AATTAACCGTTTTTGAATTAGTTTTAGGGTC 2 137 1 TTTGAATTAG 0.816047 -164 ACCGTAGTTAGTTCAATTTAGGTAAAG 2 284 1 GTTAATTTAG 0.832496 -17 CAGTTTTTGCAGTTAAATTTGTGCTAAAAAT 3 154 0 AGTAAATTTG 0.675114 -147 TTAAATCAGGTTAGATTTTGCAATAGTGCA 8 10 1 GTTGATTTTG 0.825865 -175 ATCCTTTTTATTTCAAATTTGTTTTAAAAGA 12 23 0 TTTAAATTTG 0.782481 -228 TAAAAAGCTTTTTTAATTTTGCTTTGAAAAA 12 136 0 TTTAATTTTG 0.75987 -115 AGTCTTCTTGGGTGGAATTAGATGAAGTTCC 13 18 0 GGTGAATTAG 0.918058 -283 TTGCAATTCAGGTCAATTTAGTAA 16 4 0 GGTAATTTAG 0.900844 -101 TGATAACTTATTTTGATTTTGTTAGCAATAA 17 73 1 TTTGATTTTG 0.774407 -228 TTGCTTTAGATGTGGATTTTGGTGTTATTGC 17 97 0 TGTGATTTTG 0.862544 -204 AGTTCTTAAGGGTGAAATTTGATGGTCAAAA 18 68 0 GGTAAATTTG 0.900844 -26 CCAAAAACGGTTTTAAATTAGAGGCTTATTT 20 50 1 TTTAAATTAG 0.803514 -72 AAGTTAAATTAGGTTTAAATTT 22 14 0 AGTAAATTAG 0.702582 -12 TTTTGCGTCTTGTAAAATTAGAGCATCAACT 23 90 1 TGTAAATTAG 0.882012 -191 ATCAACTACGGGTGGATTTAGCGCAAACACT 23 114 1 GGTGATTTAG 0.907881 -167 *** ******* Masking position 6 Map Score: 9.37491 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 63 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 AACTACGGTGAACAATTTAGATAAATTTACATTAA 2 258 0 AAATTAGAAA 0.877194 -43 ATTAAAGTAAAGAGTAAAACTAAGTAAGCAGGT 7 15 0 AAAGTAAAAA 0.934904 -23 CTTGCCAAAAAATAAATTAGAAAAACGTTTTTGGC 9 70 1 AAAATAGAAA 0.529637 -61 CATTTATTGCAAAAAGTGAGAGGAAAACCGTAT 9 108 1 AAAGTAGAAA 0.896706 -23 TACCCTTTTTAAGGATTTAAAGCAAGCTGGTTATG 11 149 0 AAATTAAAAA 0.92198 -152 GTTTATTGTGAAAAATTCAAAAAAGCAACAATTTT 12 72 1 AAATTAAAAG 0.615881 -179 GATTTGATGTAACCAGTCCAACTAAAAGTGCAGAT 15 129 0 AAAGTCAAAA 0.660859 -147 AATACTAATAAAAAAGAAAAAGGAACCTGGTTCTC 15 201 0 AAAGAAAAAA 0.567989 -75 TTAAAAACTTAAATATTGAAATGAAAAAAGACTAG 16 63 0 AAATTAAAAA 0.92198 -42 AGTAAAAATTGGTTAAATTAAAAACTTAAAT 16 84 0 AAGGTAAAAA 0.858603 -21 AGACCCATTTAATTGTTAAAAGAAACTTACTAACA 19 65 0 AAGTTAAAAA 0.833233 -182 ATTTTCCCATAATCATTGAAATTAAACAACTTCAA 19 147 0 AAATTAAAAA 0.92198 -100 GCTTATTTTTAAAAATTCAAAATAAGCAAATATAA 20 73 1 AAATTAAAAA 0.92198 -49 TCACCTGGCAAACAATTTAAAGTTAATGCCAT 21 132 1 AAATTAAATA 0.519646 -22 GCATAGTGTGAAATGGTTAGATTAACGA 23 4 0 AAGGTAGAAA 0.785886 -277 ** *** *** ** Masking position 11 Map Score: 7.29847 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 78 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 GTTGTAGGCTAAAAGAAGGGGAATTAACAAA 3 9 0 AAAGAAGGGA 0.98302 -292 AACAAGAAAAAAGAGAAGTTGTAGGCTAAAAGA 3 26 0 AAAGAATTGA 0.802983 -275 TTTCTTGATAAAAAGAAAGGGAATCTTTTAACA 3 55 0 AAAGAAGGGA 0.98302 -246 TAACGCTACAAACGGAAAGGGTAGTAACCAACC 5 147 1 AAGGAAGGGA 0.982682 -154 AAACACGCGGAAGGGACTTGGAAAGCGGTCAAT 11 216 1 AAGGACTGGA 0.904779 -85 TTTTGGTTTGAAGAGAATTGGTACAGCACTAGT 11 256 0 AAAGAATGGA 0.973332 -45 GCTCCAAGCTAAAAGCATTGGGACTTGTTTGCG 19 24 0 AAAGCATGGA 0.90649 -223 TTGCTTGTTTAAAGGAAAGGGAAAGCG 23 264 1 AAGGAAGGGA 0.982682 -17 ** **** *** * Masking position 2 Map Score: 4.92214 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 22 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 AGTCAAATTTTTAGCACAAATTTAACTGCAAAAACTGT 3 148 1 TTCAAATATG 0.699755 -153 ACTAGGGGACTTTTTTGAAAAGTTTAAGCATTTATCAA 5 89 0 TTGAAAGTAG 0.747183 -212 TATTAACGGCTTGTTGCAAATTATTTTGTACCGCAAAC 11 182 1 TTCAAATTTG 0.952655 -119 TGAATCCTTTTTATTTCAAATTTGTTTTAAAAGAACTT 12 19 0 TTCAAATTTT 0.590795 -232 GCTGGTAGTTTTGTTTCAAAGTCATAAGCCTTGTTGGC 14 166 0 TTCAAATTAG 0.965157 -135 TGAACACATTTTAAGTGAAATTTCTTAGGTTAAATAAG 14 258 1 TTGAAATTAG 0.934087 -43 GTTGGACTGGTTACATCAAATCTTTCAGGTAACCAGAA 15 142 1 TTCAAACTAG 0.914025 -134 AACACCATTTTTGTGCCAAAGTGTTAAGCCAAACATTG 17 211 0 TTCAAATTAG 0.965157 -90 GTGTATCCACTTCGACCAAAGCCTTAAGATTGTAGCAA 18 15 0 TTCAAACTAG 0.914025 -79 ATTTCAATGATTATGGGAAAATAATAAGGCCTGCAAGC 19 160 1 TTGAAATTAG 0.934087 -87 ATTCCTTATCTTTTTCCAAACTAGTTTGCCGCTTGCAG 19 190 0 TTCAAATTTG 0.952655 -57 CAATGTTTAGTTACCAGAAAGTCTTTTGCTAAGCCGCT 23 50 1 TTGAAATTTG 0.911459 -231 ** **** * * ** Masking position 9 Map Score: 7.60194 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 28 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 TGTGCACTAAATTTTGACACCTTGGTTTTG 2 57 0 ATTTTGACAC 0.85988 -244 AATTGGCCTAATTTTGACCCTAAAACTAAT 2 153 0 ATTTTGACCC 0.972602 -148 TTTGGACTAAATTTTGAACCAAAATAAAGA 3 115 0 ATTTTGAACC 0.957008 -186 TTTGTGAGATTTTTTGAACAGTTTTTGCAG 3 173 0 TTTTTGAACA 0.832856 -128 ATTGTAGCAATTTTTGACCCCGCTTGCCCC 3 245 0 TTTTTGACCC 0.949036 -56 TACTTAAATTATATTGACCAATAAATTTAG 4 32 1 ATATTGACCA 0.680682 -23 CTAGGGGACTTTTTTGAAAAGTTTAAGCAT 5 96 0 TTTTTGAAAA 0.462565 -205 GTTGCAAATTATTTTGTACCGCAAACACGC 11 194 1 ATTTTGTACC 0.758003 -107 TTTGTAGAATGTTTTGAACCACTAACAATG 15 31 1 GTTTTGAACC 0.872587 -245 AAGCGTAGTCATTTTGACCATCAAATTTCA 18 57 1 ATTTTGACCA 0.938079 -37 ********** Masking position 5 Map Score: 5.00072 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 74 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 GTTACTACCCTTTCCGTTTGTAGCGTTAAG 5 145 0 TTTCCGTTTG 0.850221 -156 TTAGTGGGTATTTTAGTTTGAGCTTTAACT 5 204 0 TTTTAGTTTG 0.94472 -97 TAGGCATTGATTTTGGTTTGAAGAGAATTG 11 269 0 TTTTGGTTTG 0.977639 -32 TTTAAAGTGATTTCGCTTTGATTACAGACC 12 105 1 TTTCGCTTTG 0.882915 -146 GCTTTTTTAATTTTGCTTTGAAAAATGGTC 12 131 0 TTTTGCTTTG 0.930151 -120 CCATCTGCACTTTTAGTTGGACTGGTTACA 15 127 1 TTTTAGTTGG 0.799715 -149 TTCTTAAACGTTTGGGTTTGGCAGTGTTAG 15 254 1 TTTGGGTTTG 0.930808 -22 ACAGGTGACTTTTTGGTTTGCTTTAGATGT 17 115 0 TTTTGGTTTG 0.977639 -186 GTCCCAATGCTTTTAGCTTGGAGCTTTTTT 19 33 1 TTTTAGCTTG 0.799715 -214 ********** Masking position 3 Map Score: 4.93908 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 54 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 10 AAAAAAAGAAAGCGGGAAATTGGCCTAATTTTG 2 167 0 AGGGGAATGG 0.709406 -134 TCCCAGTTTTAGGGGGCAAGCGGGGTCAAAAAT 3 233 1 AGGGGAAGGG 0.961393 -68 GCTTTGGTTAGTGGTTTTAGTGGGTATTTTAGT 5 217 0 GTGTTTAGGG 0.866404 -84 TACTTGACTGGTAGTGGAAGTGGGGAAAGCCAA 11 98 1 GTGTGAAGGG 0.958307 -203 GGTCTTTTAAGGTGGTGTAGAGGGAGCCCTTAC 13 175 0 GGGGTTAGGG 0.961393 -126 CCCCGCATTGGGCGTGTAAGGGGTCACGGGTTG 13 219 0 GGGTGAAGGG 0.987873 -82 CGTGGCCTGCAGTGGGGTAGCGGGTCCTGATGC 14 87 1 AGGGGTAGGG 0.961393 -214 TTAGACATAGGTTGTGTTAAGGGATTTTTAGGA 17 21 1 GTGTGTAAGG 0.692618 -280 AAAATAATAAGGCCTGCAAGCGGCAAACTAGTT 19 177 1 GGCTGAAGGG 0.913406 -70 CGATAGTATAGGGGTTCTAGGGGAGTTAATTTG 21 76 1 GGGTTTAGGG 0.958307 -78 ** *** *** ** Masking position 9 Map Score: 5.34663 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 68 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 TCTTGCAAAAAAATGATTGCAATTTTGTGAG 3 195 0 AATGATTGCA 0.684077 -106 TATTACAAGTACTAGTTTGCCAAAGACAAGT 8 105 0 ACAGTTTGCC 0.940806 -80 TTTTTGCAATAAATGTATGCCAAAAACGTTT 9 92 0 AATGTATGCC 0.888113 -39 GTTTAATTGTAAATGTTTGCCTTAAACCAAG 10 13 1 AATGTTTGCC 0.977921 -39 AAATGTGTTCAACTGTTTGCAAGATTTTTTG 14 238 0 AATGTTTGCA 0.923564 -63 AAGCATTGGGACTTGTTTGCGCTAGTTAAGC 19 14 0 ACTGTTTGCG 0.908713 -233 CTTTTTCCAAACTAGTTTGCCGCTTGCAGGC 19 188 0 ACAGTTTGCC 0.940806 -59 ATTAACTTTAAATTGTTTGCCAGGTGAAACA 21 128 0 AATGTTTGCC 0.977921 -26 ** ******** Masking position 1 Map Score: 5.35411 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 18 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 12 TTGCCATACATCAATTAAATGCTTGATCAA 2 30 1 TCAATTAAAT 0.750566 -271 TAACTACCCAACACTTAAAAGTTTTATACG 5 179 0 ACACTTAAAA 0.926434 -122 CATGAGCGGTTCAGTTAAAAAAATTAAGCT 8 156 1 TCAGTTAAAA 0.708444 -29 GCAAACATTTACAATTAAACCA 10 3 0 ACAATTAAAC 0.677156 -49 CAAAGCGAAATCACTTTAAAAATTGTTGCT 12 95 0 TCACTTTAAA 0.808471 -156 CTAAGAAATTTCACTTAAAATGTGTTCAAC 14 256 0 TCACTTAAAA 0.913775 -45 TTGCAGTTCCACAATTAAAAAGCCACCCGT 17 150 0 ACAATTAAAA 0.887602 -151 GTTTCTTTTAACAATTAAATGGGTCTTTTA 19 74 1 ACAATTAAAT 0.781457 -173 TCTTATTGTGTCACTTTAAAAGACCCATTT 19 90 0 TCACTTTAAA 0.808471 -157 CACCTGGCAAACAATTTAAAGTTAATGCCA 21 133 1 ACAATTTAAA 0.758773 -21 TAAAGCAGCTACACTTAAATAATACCCCCG 23 152 0 ACACTTAAAT 0.850797 -129 ********** Masking position 3 Map Score: 5.64381 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 55 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 13 CTTTACCTAAATTGAACTAAC 2 290 0 TTTACCTAAA 0.528294 -11 CTAACTAATATTTACTTAAATTATATTGAC 4 20 1 TTTACTTAAA 0.548327 -35 AGTTTTACTCTTTACTTTAAT 7 27 1 TTTACTTTAA 0.790056 -11 ATTATTCTAGTTGGCTTTAAGGAAAGGTTT 8 48 1 TTGGCTTTAA 0.779067 -137 GTTAAAAAAATTAAGCTTAATTAAGT 8 169 1 TTAAGCTTAA 0.487541 -16 ATTGTAAATGTTTGCCTTAAACCAAGGATG 10 18 1 TTTGCCTTAA 0.841044 -34 TTCTTATTTTTTGAGCTTAATAAATGCTGA 12 189 0 TTGAGCTTAA 0.663589 -62 CATAATTGAATTAAGTTTAATTCGCTAGTA 12 231 1 TTAAGTTTAA 0.749192 -20 TGAAATGGCGTTAGGTTTAATGCAAAAACT 14 42 1 TTAGGTTTAA 0.875678 -259 GTGAAATTTCTTAGGTTAAATAAGGTTTAA 14 272 1 TTAGGTTAAA 0.69708 -29 GATGACAATGTTTGGCTTAACACTTTGGCA 17 206 1 TTTGGCTTAA 0.829536 -95 ATGGCATTAACTTTAAATTGTTTGCC 21 138 0 TTAACTTTAA 0.814247 -16 AAGTTAAATTAGGTTTAAATTTTAT 22 8 0 TTAGGTTTAA 0.875678 -18 ********** Masking position 9 Map Score: 5.47902 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 271 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 14 TGGTTTTGATCAAGCATTTAATTGATGTATGG 2 33 0 CAAGCTTTAT 0.874076 -268 TTGCCAAAGACAAGTGGTTGGTGCAACTAGTT 8 88 0 CAAGTGTTGT 0.872068 -97 GGATTTAAAGCAAGCTGGTTATGAATTAGTGC 11 140 0 CAAGCGGTAT 0.944819 -161 TAATTTGCAACAAGCCGTTAATACCCTTTTTA 11 173 0 CAAGCGTTAT 0.962186 -128 ATTGGAAAACCAAGCAGTTGGTAGCTTGTTTT 14 120 1 CAAGCGTTGT 0.981327 -181 GTTTCTAGAGCCAGCTGGTAGTTTTGTTTCAA 14 185 0 CCAGCGGTGT 0.959672 -116 ACGAATTGCGCCAGCTTTTTGTGCAAAAAATC 14 215 1 CCAGCTTTGT 0.906077 -86 ***** *** ** Masking position 3 Map Score: 1.26153 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 60 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 15 TTAGAGTAAAACTACTTAAATTGCTAAAAA 2 109 1 ACTACTTAAA 0.865094 -192 TTTAACTACTTAATTTTTAAAGAA 3 287 0 ACTACTTAAT 0.614057 -14 AATTATATTGACCAATAAATTTAGGAA 4 38 1 ACCAATAAAT 0.663241 -17 AACTAAAATACCCACTAAAACCACTAACCA 5 216 1 CCCACTAAAA 0.802708 -85 GTACAACTGGACCAATAAAAAACTCACTAA 5 274 0 ACCAATAAAA 0.888114 -27 CCCCATAATTACCACTAAAATAATGGCGTA 9 27 0 ACCACTAAAA 0.955762 -104 AGTTTGTGGAACTAATAAAAACCCGCTTTA 11 50 0 ACTAATAAAA 0.855384 -251 AATGTTTTGAACCACTAACAATGTTTTTAG 15 38 1 ACCACTAACA 0.802708 -238 ACTTTCGAATACTAATAAAAAAGAAAAAGG 15 213 0 ACTAATAAAA 0.855384 -63 TTCAATTGTGACTGCTAAAAGC 19 235 1 ACTGCTAAAA 0.751972 -12 CCCTAAAAAGACTACTTAAAAGAACC 20 7 0 ACTACTTAAA 0.865094 -115 ********** Masking position 8 Map Score: 5.47418 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 94 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911