AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00010_ctra_reg_300.orf -o00010_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 Purged sequences: rs11 21 S11 Ribosomal Protein Input sequences: #1 pdhA 221 Pyruvate Dehydrogenase Alpha #2 dut 36 dUTP Nucleotidohydrolase #3 accD 71 AcCoA Carboxylase/Transferase Beta #4 sodM 131 Superoxide Dismutase (Mn) #5 yhxB 151 Phosphomannomutase #6 CT296 108 hypothetical protein #7 tpiS 196 Triosephosphate Isomerase #8 CT330 208 hypothetical protein #9 pykF 96 Pyruvate Kinase #10 pgi 112 Glucose-6-P Isomerase #11 phnP 28 predicted metal dependent hydrolase (histidinic triad) #12 artJ 68 Arginine Binding Protein #13 aroG 136 phospho-2-dehydro-3-deoxyheptonate aldolase #14 CT382.1 182 hypothetical protein #15 sucB_2 245 Dihydrolipoamide Succinyltransferase #16 ribC 300 Riboflavin Synthase #17 gapA 43 Glyceraldehyde-3-P Dehydrogenase #18 rs13 55 S13 Ribosomal Protein #19 secY 22 Translocase #20 rl18 21 L18 Ribosomal Protein #21 rl6 27 L6 Ribosomal Protein #22 rl16 32 L16 Ribosomal Protein #23 rl2 23 L2 Ribosomal Protein #24 rl3 300 L3 Ribosomal Protein #25 CT552 300 hypothetical protein #26 fmu 124 RNA Methyltransferase #27 brnQ 149 Amino Acid (Branched) Transport #28 CT555 174 SWI/SNF family helicase #29 CT556 177 hypothetical protein #30 lpdA 208 Lipoamide Dehydrogenase #31 minD 300 chromosome partitioning ATPase-CHLTR plasmid protein homolog GP5D #32 trpS 198 Tryptophanyl tRNA Synthetase #33 uvrB 24 Exinuclease ABC Subunit B #34 eno 161 Enolase #35 CT691 160 hypothetical protein #36 pgk 127 Phosphoglycerate Kinase #37 pgm 296 Phosphoglycerate Mutase Motif number 1 AGAAGGCCCTCTTTTTGAAGAGCCTCCTATG 2 16 0 TTTTTTAAGA 0.955723 -21 ATTGCTCAATTTTTTGTAAAGAGGATGGTTTT 3 50 1 TTTTGTAAGA 0.827705 -22 CAGGCTTCTGTTTTTGTAAAAAACTTGCTTAA 5 46 0 TTTTGTAAAA 0.730148 -106 AACTATTTTTTAAGAATACAAAATC 6 4 1 TTTTTTAAGA 0.955929 -105 CCTGTGCATGTATTTTGTAAGATAGATCAAAG 7 159 0 TTTTTGAAGA 0.929077 -38 ATTCTTATTTTTTTTAAGAATCATGTTGG 12 8 1 TTTTTTAAGA 0.955866 -61 AATTTAATTTTATTTTTTAAGATCTATTTGTT 14 121 1 TTTTTTAAGA 0.955929 -62 GTCTTTTCTGTGGTTTCAAAAAATGTTTAGTG 15 63 1 TGTTTCAAAA 0.634785 -183 TTGTGGTGATTTTTTTTCAAAAGTCGCCTAAT 16 33 1 TTTTTTAAAA 0.872535 -268 AGGTAGTCAGTGTTTTCGAAAAATTAGCATCA 17 11 0 TTTTTCAAAA 0.859402 -33 TTTTTTCCGCTTTTTTCTAAGATTTCCTGGTT 25 207 1 TTTTTCAAGA 0.949129 -94 CCTGTCCCGTTCTTTCTCAAGAGCTTTTGTTC 25 258 1 TTTTCTAAGA 0.91896 -43 CATCCTTTATTCTTTCCAAAGAACTTCTGTGA 27 77 1 TTTTCCAAGA 0.499785 -73 CAACATCCCCTTGTTTGCAAGACGATACCCCT 29 88 0 TGTTTGAAGA 0.788435 -90 CTAACAATCATCTTTCTAAAGATGATGTTACA 32 24 1 TTTTCTAAGA 0.742712 -175 TGAATCAGACTATTTTTAAAAAGCAGGCTTTA 32 63 1 TTTTTTAAAA 0.87242 -136 TAGGGGCTTATTTTTCGTAAAAATCCAGAGAT 32 93 1 TTTTCGAAAA 0.675331 -106 GGCGGGACCCTGTTTGGGAAAAAACCTCGCTC 32 164 0 TTTTGGAAAA 0.738565 -35 ACAATGGATAGTTGTTAAGATTTT 33 5 0 TGTTGTAAGA 0.809216 -20 AATTTTTTGTTTTTTTCTAAGATTTTTCACGC 35 47 0 TTTTTCAAGA 0.949129 -114 AGGTAAAAAATCTTTGCAAAGATAATCCGCAA 37 228 1 TTTTGCAAGA 0.497563 -69 * ***** **** Masking position 5 Map Score: 27.9936 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 174 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 AGATTCTCTTGGATAAAGGGTTCC 1 208 0 TTCTCTTGAT 0.816274 -14 CTTTAGAAGCTTCTCTTGCCTTGTATGAAGA 8 91 1 TTCTCTTGCT 0.949547 -118 TCATTAAACGTTCTCTTCTCTTCAAGAGAAG 13 13 1 TTCTCTTCCT 0.982064 -124 GAAAAAAACGCCCTCTTCTCTTGAAGAGAAG 13 27 0 CCCTCTTCCT 0.975365 -110 TCTATTTCTTTTCTCTTCCCTGTGTGTATGA 13 71 1 TTCTCTTCCT 0.982064 -66 TCCTTGTTTCTTCTCTTAACTCATGAACAGC 13 105 0 TTCTCTTACT 0.901111 -32 AGAGAGAAAACCCTCTTCGTTAAAAGATCT 15 10 0 CCCTCTTCTT 0.90335 -236 AGAGGGTTTTCTCTCTTCGTTTTCTTTAAGG 15 25 1 CTCTCTTCTT 0.924913 -221 GTTATTCTTCTCTTCCTTCTTTA 23 6 0 TTCTCTTCTT 0.928191 -18 TAACCCTTTTTTCTCTTAACTCTCTATCTAA 25 159 1 TTCTCTTACT 0.901111 -142 TTCCTTTTCGCTTCCATCATCT 26 2 1 TCCTTTTCCT 0.838867 -123 CGATAGTTTATTCTCTTCCCCAATAGGAGAA 26 45 1 TTCTCTTCCC 0.853073 -80 AAGAGCATCCCTCTCTTGGCTCGAAGGACCG 26 101 1 CTCTCTTGCT 0.947188 -24 TGAAGGACCTCTCTTTTCCTTTCCTAGAAAG 30 104 1 CTCTTTTCTT 0.606841 -105 GGAAGGAGAATCCTCTTCCCTCAGATAATCA 30 139 1 TCCTCTTCCT 0.976496 -70 AACATTTCCTCTTCAATGAGTGTTTAG 30 192 0 TCCTCTTCAT 0.907475 -17 CTCCAGATACCTCTTTTCTATATTATTGGGT 31 149 0 CTCTTTTCAT 0.606841 -152 GCCAGTCCTCTTGTCTTTCGACTGCT 37 6 1 TCCTCTTGCT 0.934558 -291 ACACCGGGAACTCTCTTAGATTCAAGGGTAA 37 93 1 CTCTCTTAAT 0.672129 -204 ******** ** Masking position 6 Map Score: 27.593 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 201 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 TCTATGCTACAAAAAAAAACTTTTCGGCACTA 1 49 0 AAAAAAACTT 0.670452 -173 AGATTCTCTTGGATAAAGGGTTCCTGAAAAAT 1 200 0 GGAAAAGGTT 0.719568 -22 TTTTTTAAGAATACAAAATCTTGAGAGTCAAT 6 16 1 ATAAAAACTT 0.690574 -93 TTATTTCCGCCTATAAAAACCCGATTGACTCT 6 39 0 CTAAAAACCC 0.482286 -70 CGATTTCTTGCAAGGAAGGCTTATTTTTATAT 7 118 0 CAAGAAGCTT 0.658372 -79 AAACGTGGAAAAAATCTCTTTTGAAGAC 8 7 1 GGAAAAACTC 0.910644 -202 TTTGAAGACGCTATGAAACGTTTGGAAGAGAT 8 30 1 CTAGAAAGTT 0.43908 -179 TATCCGAAATGAAAGAAGCCTTCAACTATACA 9 33 0 GAAGAAGCTT 0.761073 -64 ATTTTTCAATGAAAAAAACGCCCTCTTCTCTT 13 36 0 GAAAAAAGCC 0.306476 -101 CATTGAAGACAAAGAAAAACTTTTGTTAAAAT 14 54 0 AAAAAAACTT 0.670452 -129 GAAAACGAAGAGAGAAAACCCTCTTCGTTAAA 15 17 0 AGAAAAACCT 0.674651 -229 TTATTTTAATGGATAAAATCCTGTGTCTTGTG 16 95 1 GGAAAAACCT 0.782198 -206 GACCGCCCGTAGAGAAAACCTTTCTAAGAAGA 16 139 0 AGAAAAACTT 0.846965 -162 ACTAGATACACGAAAAAGCCCTCTCCGGATCT 16 221 0 CGAAAAGCCT 0.648809 -80 GAGCTTCCTTGGAAGAAAACTTATAACGCT 24 9 0 GGAGAAACTT 0.910644 -292 TTTCTTGACGCTAAGAAATCCCACACCAAAAA 24 85 0 CTAGAAACCC 0.497605 -216 AGTGGTAAGCATACGAAGACTCATTAAAAGAA 25 47 0 ATAGAAGCTC 0.682052 -254 CAACCTCGTGCGACAAAAACTTTTTCTAACCC 25 133 1 CGAAAAACTT 0.852921 -168 AGAGTTAAGAGAAAAAAGGGTTAGAAAAAGTT 25 150 0 GAAAAAGGTT 0.485393 -151 AACTCTCTATCTAAGAAATCTTTAGCGGACTT 25 176 1 CTAGAAACTT 0.713167 -125 AGAAAAAAGCGGAAAAAAAGTCCGCTAAAGAT 25 193 0 GGAAAAAGTC 0.762387 -108 CCTGGTTGTTAGAGAAAGTCTTTTTTCCTGTC 25 232 1 AGAAAAGCTT 0.82474 -69 TACGCAATCCGAACAAAAGCTCTTGAGAAAGA 25 268 0 GAAAAAACTC 0.789308 -33 AGGATGAATTAGAAGAAACGTCCGTTAGCCCT 27 51 0 AGAGAAAGTC 0.663267 -99 GTAAAAAGAAGAATAAAAGGTCAATCATTTCT 29 15 0 GAAAAAAGTC 0.541169 -163 TATGGAAGCCATAAAAAGGCCCAAAGACTGTT 29 142 1 ATAAAAGCCC 0.430507 -36 ACATCTGGGTGGATAAAATCTCAATGAGGAGA 30 49 0 GGAAAAACTC 0.910644 -160 TTTTCCTTTCCTAGAAAGGCTTGGAAGGAGAA 30 117 1 CTAAAAGCTT 0.66537 -92 CACTCATTGAAGAGGAAATGTT 30 197 1 AGAGAAAGTT 0.649442 -12 GATGAATAAAGTAAGAAAGCTCTCCAGATACC 31 169 0 GTAGAAACTC 0.813761 -132 CCCTTGTAGGGGAGGAAGCCTCGCTCCTTTTT 31 261 0 GGAGAAGCTC 0.902087 -40 ACCCTGTTTGGGAAAAAACCTCGCTCCTTGCT 32 158 0 GGAAAAACTC 0.910644 -41 TGTGGCACTGAGATAAAGGCTTGAGTTTTCCT 36 62 1 AGAAAAGCTT 0.82474 -66 AGGCCTAAGCAAAGGAAAACTCAAGCCTTTAT 36 74 0 AAAGAAACTC 0.696955 -54 AAGCGACTATCTAAGAAACCTTCTCTCCGAAA 37 59 1 CTAGAAACTT 0.713167 -238 AGAGGCTCACAAATGAAGAGTTCCCCCCCTCC 37 190 1 AAAGAAGGTT 0.366707 -107 CCCTTATAAGGTAAAAAATCTTTGCAAAGATA 37 220 1 GTAAAAACTT 0.794462 -77 CAAACAAGGAAGATGAAGCCTTTCGTAATCAT 37 257 1 AGAGAAGCTT 0.833426 -40 *** **** *** Masking position 6 Map Score: 31.351 Number of sites scoring better than the average of aligned sites = 742 Number in coding regions = 742 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 CCTCTTTTTGAAGAGCCTCCTATGATCTT 2 9 0 AAGAGCTCCT 0.798971 -28 GCTCTTCAAAAAGAGGGCCTTCT 2 24 1 AAGAGGCCTT 0.607178 -13 AGTAAAAAGAAAGAAGGTCTCTCGTATCACA 10 73 1 AAGAAGTCTC 0.862041 -40 TGCTTTTAAGAGCCTCGCAATCATTTTG 14 8 1 AAGAGCTCGC 0.884061 -175 CCTTTCTAAGAAGAGGTTCTTTTCAACACAA 16 122 0 AAGAGGTCTT 0.566223 -179 ACGAAGGGCCTCCCTTAAAGTAAT 18 42 0 AAGGGCTCCC 0.96725 -14 GCGTACTTTAAAGAGCATCCCTCTCTTGGCT 26 91 1 AAGAGCTCCC 0.975717 -34 TTCCGGGCAAAAGAACATCCCTTACTTATTC 28 48 0 AAGAACTCCC 0.89706 -127 TATTTGTCTGAAGGACCTCTCTTTTCCTTTC 30 96 1 AAGGACTCTC 0.799702 -113 CCTCCCCTACAAGGGCTTCACCTCGTGATAA 31 278 1 AAGGGCTCAC 0.873109 -23 TTTTTTCCCAAACAGGGTCCCGCCTCGTGAG 32 172 1 AACAGGTCCC 0.759102 -27 CTTTTCTACTAAGGGAATCTCCCTCCGAGCC 34 47 1 AAGGGATCTC 0.708765 -115 CTACTATTTGAAGGGGACCTCGAGCGTGAAA 35 24 1 AAGGGGCCTC 0.894652 -137 GAGAGTCCAGAAGAAGTTCTCCTCTCAAAGA 37 162 1 AAGAAGTCTC 0.847872 -135 TCTCCTCTCAAAGAGGCTCACAAATGAAGAG 37 179 1 AAGAGGTCAC 0.900508 -118 CTCACAAATGAAGAGTTCCCCCCCTCCCTTA 37 195 1 AAGAGTCCCC 0.637195 -102 ****** **** Masking position 2 Map Score: 12.9649 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 141 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 TTGCTTTAAAGTAGGGAGGATATCGCTCTCT 25 12 0 GTAGGGAGGT 0.831936 -289 TCGAGCCAAGAGAGGGATGCTCTTTAAAGTA 26 94 0 AGAGGGATGT 0.755665 -31 CTGTGACTTGGGAAGGATGATATGCCCTCTT 27 103 1 GGAAGGATGT 0.951245 -47 TAGGCAGAAAGGAACGAGTGTTTAGGAGTAG 28 113 0 GGAACGAGTT 0.813369 -62 TTTCCTCCTAGGAACTATAATTCGGGAGGGG 29 62 1 GGAACTATAT 0.465143 -116 AGAAAGGCTTGGAAGGAGAATCCTCTTCCCT 30 129 1 GGAAGGAGAT 0.951414 -80 CTTTTCTACCGGAGGGATACTGTACCCAATA 31 126 1 GGAGGGATAT 0.964323 -175 CAACTAAAAAGGAGCGAGGCTTCCTCCCCTA 31 256 1 GGAGCGAGGT 0.972448 -45 ATGATTGTTAGGAAGGATTATAGA 32 4 0 GGAAGGATTT 0.841832 -195 GAAAAAGCAAGGAGCGAGGTTTTTTCCCAAA 32 153 1 GGAGCGAGGT 0.972448 -46 GAGAAGGCTCGGAGGGAGATTCCCTTAGTAG 34 52 0 GGAGGGAGAT 0.977407 -110 TATATATGAAGGAGGTATATTTTGGGAGCAT 35 110 1 GGAGGTATAT 0.789714 -51 ********* * Masking position 7 Map Score: 8.58775 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 119 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 TCTTTCAAATAAATCTTTTGAATTTCACTCTGG 1 158 0 AAATTTTTGT 0.958553 -64 GCTTTGATATAAATCTCTTGGATATGCTAATCT 7 70 0 AAATTCTTGT 0.95019 -127 TGCGGTTGCTAAATATTTTGTATAGTTGAAGGC 9 15 1 AAATTTTTGT 0.958553 -82 ACTTTTGTTAAAATTTTTTCGCTATACCGCAAA 14 35 0 AAATTTTTCT 0.77066 -148 TGGTTTCAAAAAATGTTTAGTGTAACATAGGGA 15 73 1 AAATTTTAGT 0.784751 -173 GCGTCAAGAAAAATCTCTTGTGTGGATGTCGCA 24 106 1 AAATTCTTGT 0.95019 -195 AAAAATCCAGAGATGTCTTGCATCGATAAATTA 32 111 1 AGATTCTTGT 0.81675 -88 CTAAGAACCAAAATTTTTTGTTTTTTTCTAAGA 35 57 0 AAATTTTTGT 0.958553 -104 TGCAGACTAAAAATGTTTTGTCTGAGTGATTCT 36 26 1 AAATTTTTGT 0.958553 -102 **** ***** * Masking position 6 Map Score: 5.86184 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 40 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 GGACCTTTCCGGTTACTTTTCCGCGCCGGCCTT 1 119 1 GGTTCTTTCG 0.975155 -103 TTCTCTCTTCGTTTTCTTTAAGGTTTAAGCGTC 15 33 1 GTTTCTTTGG 0.954017 -213 TCTTAGAAAGGTTTTCTCTACGGGCGGTCTCGG 16 142 1 GTTTCTCTGG 0.81227 -159 CGCCGCCTTTGTTTGCTTTAAGGAGCCGCGTTT 24 160 1 GTTTCTTTGG 0.954017 -141 AAGGAGCCGCGTTTTCTTTGTCGTGGAAATCGC 24 179 1 GTTTCTTTCG 0.943661 -122 TAAAAGAATTCGTTGCTTTAAAGTAGGGAGGAT 25 22 0 CGTTCTTTAG 0.667896 -279 TGTCGCACGAGGTTGCTTTTTCCTACGATAGAT 25 115 0 GGTTCTTTCC 0.945693 -186 GCAGCTACACGGTTGCTTTCTCCTATTGGGGAA 26 60 0 GGTTCTTTCC 0.945693 -65 GCGTTTTTTGGGTTGCTTTCCGGGCAAAAGAAC 28 63 0 GGTTCTTTGG 0.979845 -112 CCTAAACACTCGTTCCTTTCTGCCTAGGTCATG 28 118 1 CGTTCTTTGC 0.85224 -57 **** **** ** Masking position 7 Map Score: 6.97993 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 41 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 TTATATTACTTTAAGGGAGGCCCTTCGT 18 38 1 TTAAGGGAGG 0.939704 -18 TTTGGAAAGAATAAAGGATGAATTAGAAGA 27 67 0 ATAAAGGATG 0.730004 -83 TACTTATTCAGTAAGGGATGGCTTCAAACA 28 27 0 GTAAGGGATG 0.975234 -148 TACTGAATAAGTAAGGGATGTTCTTTTGCC 28 44 1 GTAAGGGATG 0.975234 -131 TGAAGCCCTTGTAGGGGAGGAAGCCTCGCT 31 268 0 GTAGGGGAGG 0.9577 -33 TTTTTACCTTATAAGGGAGGGGGGGAACTC 37 207 0 ATAAGGGAGG 0.96489 -90 ********** Masking position 3 Map Score: 2.56781 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 15 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 TTCAAATAAATCTTTTGAATTTCACTCTGG 1 158 0 TCTTTTGAAT 0.606841 -64 AGAAGGCCCTCTTTTTGAAGAGCCTCCTAT 2 17 0 CTTTTTGAAG 0.720385 -20 GGAAAAAATCTCTTTTGAAGACGCTATGAA 8 17 1 TCTTTTGAAG 0.951429 -192 ACCAACCACGTCTTTAGAAGCTTCTCTTGC 8 80 1 TCTTTAGAAG 0.886348 -129 GATTCTCCTTTTGAGGAAATGTGATA 10 97 0 CCTTTTGAGG 0.960091 -16 AACGCCCTCTTCTCTTGAAGAGAAGAGAAC 13 22 0 TCTCTTGAAG 0.786664 -115 GCCTCGCAATCATTTTGCGGTATAGCGAAA 14 22 1 CATTTTGCGG 0.619936 -161 ATAAAAAATGCCTTTTGAGGGTTTAATAAC 15 144 0 CCTTTTGAGG 0.960091 -102 ATCTAAGAAATCTTTAGCGGACTTTTTTTC 25 184 1 TCTTTAGCGG 0.736872 -117 CCAAAAAACGCCTTTAGAAGACACCTATCT 28 85 1 CCTTTAGAAG 0.91004 -90 GACTGCTTAATATTTTGAAGTTCACTAATA 37 30 1 TATTTTGAAG 0.772022 -267 ********** Masking position 5 Map Score: 4.15183 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 181 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 10 TAGTGCCGAAAAGTTTTTTTTTGTAGCATAG 1 49 1 AAGTTTTTTT 0.534844 -173 AGAAGGCCCTCTTTTTGAAGAGCCT 2 22 0 GGCCTCTTTT 0.647996 -15 ACTATACGTCAGGCTTCTGTTTTTGTAAAAA 5 56 0 AGGCTCTGTT 0.810413 -96 CTTGCAAGGAAGGCTTATTTTTATATGATTT 7 113 0 AGGCTATTTT 0.877735 -84 ACGTCTTTAGAAGCTTCTCTTGCCTTGTATG 8 87 1 AAGCTCTCTT 0.472817 -122 GTATAGTTGAAGGCTTCTTTCATTTCGGATA 9 34 1 AGGCTCTTTC 0.687739 -63 CAAGAGAAGAGGGCGTTTTTTTCATTGAAAA 13 35 1 GGGCTTTTTT 0.946272 -102 TTTAAGGTTTAAGCGTCTTTTCTGTGGTTTC 15 49 1 AAGCTCTTTT 0.894268 -197 ATGTTACACTAAACATTTTTTGAAACCACAG 15 70 0 AAACTTTTTT 0.459177 -176 AACCCTCAAAAGGCATTTTTTATCTGTAAAA 15 151 1 AGGCTTTTTT 0.963897 -95 TGCAGATATTAGGCGACTTTTGAAAAAAAAT 16 41 0 AGGCACTTTT 0.585551 -260 ACGATTTTTCAGGCTTTGTTTTTGCGATTTT 24 58 1 AGGCTTGTTT 0.718493 -243 AACTTTTTCTAACCCTTTTTTCTCTTAACTC 25 150 1 AACCTTTTTT 0.567742 -151 AATCTTTAGCGGACTTTTTTTCCGCTTTTTT 25 192 1 GGACTTTTTT 0.591935 -109 TTGTTAGAGAAAGTCTTTTTTCCTGTCCCGT 25 237 1 AAGTTTTTTT 0.534844 -64 TCTTTCTCAAGAGCTTTTGTTCGGATTGCGT 25 268 1 GAGCTTTGTT 0.570294 -33 TGTCTTCTAAAGGCGTTTTTTGGGTTGCTTT 28 77 0 AGGCTTTTTT 0.963897 -98 AACAGTCTTTGGGCCTTTTTATGGCTTCCAT 29 143 0 GGGCTTTTTA 0.544383 -35 CAGGCTTTAGGGGCTTATTTTTCGTAAAAAT 32 86 1 GGGCTATTTT 0.825654 -113 TATATGAAGGAGGTATATTTTGGGAGCATTT 35 112 1 AGGTTATTTT 0.444649 -49 ATAAGCCTTTTTTAATTGTCTTT 35 148 0 AAGCTTTTTT 0.911579 -13 **** ****** Masking position 10 Map Score: 10.0003 Number of sites scoring better than the average of aligned sites = 362 Number in coding regions = 362 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 TTGGATATGCTAATCTTCTTGTCTTACTTT 7 56 0 TAATCTTCTT 0.889748 -141 TTCTAGAAGATATTCTACTCACTAATACCG 9 65 1 TATTCTACTC 0.818371 -32 AGCCAGTTGATAATCTTCTTCTCATATTGA 15 181 1 TAATCTTCTT 0.889748 -65 GTTATTCTTCTCTTCCTTCTTT 23 12 0 TATTCTTCTC 0.955953 -12 ATTGACCTTTTATTCTTCTTTTTACGTATT 29 22 1 TATTCTTCTT 0.913105 -156 TTCCCTCAGATAATCATCTCATATGGATCG 30 154 1 TAATCATCTC 0.878801 -55 TTTCTTACTTTATTCATCTCCTTTAACCTC 31 183 1 TATTCATCTC 0.904228 -118 ********** Masking position 2 Map Score: 2.55388 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 23 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 12 CATCTCTATCCATTTTTCTGGGTAGTGCCGA 1 27 1 CATTTTTCTG 0.792362 -195 GACATTCTAGAATTTTTCAGGAACCCTTTAT 1 189 1 AATTTTTCAG 0.805086 -33 GAAATAGAAAGATTTTTCAATGAAAAAAACG 13 48 0 GATTTTTCAT 0.805086 -89 AACCTAGAACGATTTTTCAGGCTTTGTTTTT 24 50 1 GATTTTTCAG 0.969553 -251 CCACACAAGAGATTTTTCTTGACGCTAAGAA 24 100 0 GATTTTTCTG 0.952038 -201 TTAACTATACGATTTTTCTTCCCATGGTAGT 31 45 1 GATTTTTCTC 0.792362 -256 TTTTTTCTAAGATTTTTCACGCTCGAGGTCC 35 38 0 GATTTTTCAG 0.969553 -123 TTGTCTGAGTGATTCTTCATGTGGCACTGAG 36 43 1 GATTCTTCAG 0.894269 -85 ********* * Masking position 2 Map Score: 2.33514 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 35 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 AAGGCCGGACCTTTCCGGTTACTTTTCCGCGCC 1 113 1 CTTTCCGTCT 0.807978 -109 CTTTCGTGATCTTTCGCGATTCCATTTTTGTAG 10 32 0 CTTTCGGTCC 0.944306 -81 ATCTGCAGGACGCTCAAGATACCACGGTTTTTA 16 65 1 CGCTCAGTCC 0.964934 -236 CTTCACAGACCGCCCCCGGTGCCTAATTACACT 24 246 0 CGCCCCGTCC 0.977632 -55 CCTATTTTTTCTCTCCTGCTACCACTTCTCCTC 30 23 1 CTCTCCGTCC 0.991661 -186 AGTAAGAAAGCTCTCCAGATACCTCTTTTCTAT 31 159 0 CTCTCCGTCC 0.991661 -142 AGATTTTTCACGCTCGAGGTCCCCTTCAAATAG 35 27 0 CGCTCGGTCC 0.986852 -134 ****** * * ** Masking position 10 Map Score: 3.12599 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 17 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 TTCAAACCAACTTCATCTCTATCCATTTTTC 1 14 1 CTTCTCTCTA 0.912096 -208 AAAACCATCCTCTTTACAAAAAATTG 3 56 0 CATCTCTTTA 0.963961 -16 CTATCCTCGCCACCTTCTCTATTTTCTACAG 4 88 0 CACCTCTCTA 0.938944 -44 TTTTCGCTTCCATCATCTCTACATTTTGCTC 26 15 1 CATCTCTCTA 0.976776 -110 TTACTTTATTCATCTCCTTTAACCTCATTCG 31 187 1 CATCCCTTTA 0.907236 -114 GGCTATGTAACATCATCTTTAGAAAGATGAT 32 30 0 CATCTCTTTA 0.963961 -169 **** ****** Masking position 8 Map Score: 1.40212 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 17 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 ATCCACATCTTTACGTACTGATG 4 2 0 TTACGTACAT 0.939058 -130 TGGATGAGTGTTTCGTTCTGATCGGAAGGTTG 5 126 1 TTTCGTTCAT 0.961143 -26 CTTATAGAACTTACGTTCTTATCCTACTCTTT 25 77 1 TTACGTTCAT 0.961124 -224 TCTCAAGAGCTTTTGTTCGGATTGCGTAAAAG 25 272 1 TTTTGTTCAT 0.734162 -29 TCAATCTCTGTTACGTTCCCATGCTTGCGCAT 28 148 0 TTACGTTCAT 0.961143 -27 CACTCTTACGTTCCTATTTTTTCTCTC 30 6 1 TTACGTTCAT 0.961124 -203 GGGGCTTATTTTTCGTAAAAATCCAGAGATGT 32 95 1 TTTCGTAAAT 0.77905 -104 AGATGAAGCCTTTCGTAATCATCCTTAAATCT 37 267 1 TTTCGTAAAT 0.779093 -30 ******** ** Masking position 11 Map Score: 3.04364 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 14 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