AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -icrp_tpal_opreg_300.orf -g0.528 -x5 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 = 0.528 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 TP0074 300 sugar ABC transporter, periplasmic binding protein (y4oP) #2 TP0075 118 sugar ABC transporter, permease protein (y4oQ) #3 TP0076 39 sugar ABC transporter, permease protein (y4oR) #4 TP0077 40 capsular polysaccharide biosynthesis protein (cap5D) #5 TP0231 100 conserved hypothetical protein #6 TP0232 99 T. pallidum predicted coding region TP0232 #7 TP0233 30 anti-sigma F factor antagonist, putative #8 TP0234 234 ribosomal protein L33 (rpmG) #9 TP0235 149 preprotein translocase subunit (secE) #10 TP0237 106 ribosomal protein L11 (rplK) #11 TP0240 108 ribosomal protein L7/L12 (rplL) #12 TP0241 262 DNA-directed RNA polymerase, beta subunit (rpoB) #13 TP0243 102 ribosomal protein S12 (rpsL) #14 TP0244 21 ribosomal protein S7 #15 TP0245 23 T. pallidum predicted coding region TP0245 #16 TP0246 145 T. pallidum predicted coding region TP0246 #17 TP0247 50 N-acetylmuramoyl-L-alanine amidase (amiA) #18 TP0248 66 T. pallidum predicted coding region TP0248 #19 TP0249 78 flagellar filament outer layer protein (flaA-1) #20 TP0250 50 T. pallidum predicted coding region TP0250 #21 TP0251 153 DNA-binding protein II #22 TP0254 236 transcription termination factor Rho (rho) #23 TP0255 118 ribosomal protein L31 (rpmE) #24 TP0256 44 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (pgsA) #25 TP0257 96 glycerophosphoryldiester phosphodiesterase (glpQ) #26 TP0261 114 catabolite gene activator, putative #27 TP0418 26 galactokinase #28 TP0652 175 spermidine/putrescine ABC transporter, ATP-binding protein (potA) #29 TP0681 88 alanine racemase (alr) #30 TP0682 92 cell division protein (ftsJ) #31 TP0734 81 purine nucleoside phosphorylase (deoD) #32 TP0736 233 hydrogenase, gamma chain (hydG) #33 TP0802 45 T. pallidum predicted coding region TP0802 #34 TP0804 77 sugar ABC transporter, ATP-binding protein (ugpC) #35 TP0840 104 conserved hypothetical integral membrane protein #36 TP0949 275 membrane protein #37 TP0951 119 ribosomal protein L34 (rpmH) #38 TP0952 81 lipase, putative #39 TP0953 86 pheromone shutdown protein (traB) #40 TP0954 71 conserved hypothetical protein #41 TP0955 95 T. pallidum predicted coding region TP0955 #42 TP0976 47 T. pallidum predicted coding region TP0976 #43 TP0979 169 conserved hypothetical protein #44 TP0981 59 sensory transduction histidine kinase, putative Motif number 1 GTTGACAACGGGGAGAAAAGCGTACGAGAATC 1 58 1 GGGGAAAGCG 0.760593 -243 GATATGGGGTGCGATGCGCGCGGTGGATACGC 1 154 1 GCGTGGCGCG 0.972122 -147 TATCAGGACTGGGGTGTGAGGGGAAAAACGGA 1 275 1 GGGTGGAGGG 0.806197 -26 TTCTTCTTGGGGGAAGAGAGGGCAGAAAAGAT 2 19 1 GGGAGGAGGG 0.912432 -100 CGTGTTCTATCTGTGGAGCGCGTTACGTTGGG 2 77 1 CTGGGGCGCG 0.98115 -42 ACGTACTCACCCGCGCAGAGTGTTTATCCCT 4 10 0 CCGGCGAGTG 0.813966 -31 TTTGGTTGACCGGTAGTATGCGGTGCCTGGTA 5 51 1 CGGAGATGCG 0.818857 -50 GCATTCTGGTAGGCGGTGTGTGGTTTTGAGTT 6 25 1 AGGGGGTGTG 0.89635 -75 CTGCCCCAGAAAGAAAGGCGCGTCAC 8 5 0 AAGAAGCGCG 0.730681 -230 GCCGGCCTCCGGGCGGCTCGGGGAGTCCTGTC 8 106 1 GGGGGTCGGG 0.665074 -129 TCTTCTTCCAGGGTGGAGAGTGTTGCAATGCG 10 14 1 GGGGGGAGTG 0.978787 -93 TTTTTTGCATGCGTCCGGCGCGTCGTTGTGTG 12 20 1 GCGCCGCGCG 0.929417 -243 TTTCGTGTGGGAGGGCGTCGCGCTTTTGAGTA 12 64 1 GAGGCTCGCG 0.638359 -199 TCGCGCTTTTGAGTAGAGCGTGGGCTTCTATT 12 81 1 GAGAGGCGTG 0.950508 -182 CCACTCAAGTGAGGAGAACGCGACCCAACCCG 12 146 0 GAGAGACGCG 0.874944 -117 GGGAGTATTACGGTAGAGCGTGTGGTATAGGG 12 202 1 CGGAGGCGTG 0.976432 -61 GGTGCAGCTTGAGGGGGGAGTGC 12 250 1 GAGGGGAGTG 0.929687 -13 CTAGCCGCGTGTGCTGTGTGCGGCAAGGTTTA 13 43 1 GTGTGGTGCG 0.835848 -60 GATTTTTTTGGGGAAGTGAGCGAAAAGA 13 85 1 GGGAGGAGCG 0.987662 -18 ATGTGATGCGAAGCGTGCGCAAGAGAATT 16 8 1 GCGAGGTGCG 0.963183 -138 CGCCACCTTTGCGGGGGATGCGCATTTTCGTT 16 74 1 GCGGGATGCG 0.845996 -72 ACGGTGTAGTGAGGGCGGTGTGTTGGACTCTC 18 32 1 GAGGCGTGTG 0.821193 -35 TTGACAAAATAGGCGGTGAGCGTATACTCGAA 19 22 1 AGGGGGAGCG 0.97182 -57 ATCTTATTGTGCGAAAGGAGCGTTTGA 19 62 1 GCGAAGAGCG 0.851808 -17 CCTAGGGAGAGGGGGCGGTGGGGTTCTAGGCG 20 23 1 GGGGCGTGGG 0.877396 -28 TCTTCACCCGAGGTGGTGCGCGTTTGAGGCGG 21 106 1 AGGGGGCGCG 0.990005 -48 TGGTGTATACAGGAACTGTGCGCCTCTTTTAG 22 41 0 AGGACGTGCG 0.858316 -196 GTAGCGTGCACGGTGCTGCGTGCTGTTCAAAC 22 187 1 CGGGCGCGTG 0.970655 -50 ACCTTTTTAAGGGCGCGGCGCGCTGTAGAATG 23 79 1 GGGGCGCGCG 0.994582 -40 CTGTAGAATGGGGAAAGGAGCGATTCAG 23 101 1 GGGAAGAGCG 0.938004 -18 ACGATCTCTGCAGGTGTGCGCGCAGGAGCGCG 26 37 1 CAGTGGCGCG 0.942058 -78 GGTGTGCGCGCAGGAGCGCGTGACGTGAATTC 26 49 1 CAGAGGCGTG 0.922312 -66 GCTCGCTGGCGCGAGAAGTGCGCATGAGGAAG 28 36 0 GCGGAGTGCG 0.907211 -140 AACACATAGCATGGGGGGCGTGTAGGAAGGT 30 72 1 ATGGGGCGTG 0.84246 -21 CGGGTGCTGCATGCGCTGAGCGTACACGCGCG 31 11 1 ATGGCGAGCG 0.720595 -71 CGCGAGGTTACCGAAACGTGTGGGTCTAGGCC 31 39 1 CCGAAGTGTG 0.471189 -43 GGCCCCACGAAGGGAGGGAGTGACG 31 67 1 AGGAGGAGTG 0.835637 -15 GAGAAAAGCAGCGGTCGGCGCGTTAGTTGCCT 32 115 1 GCGTCGCGCG 0.933687 -119 GTATCAGCGGCTGCTGTGCGTGTTGTGTGATC 36 52 1 CTGTGGCGTG 0.753906 -224 ATTCAGAGAACAGACGCGCGCGATCACACAAC 36 73 0 CAGCGGCGCG 0.938235 -203 AGGCAGGAATAGGCCGTGAGTGTGCGTCGCTT 36 116 1 AGGCGGAGTG 0.65496 -160 CTGGTAAAAACGGATCAGCGCGAGCAACAATC 36 168 0 CGGTCGCGCG 0.958178 -108 CAAAAGATGAGGGGAAAGAGCGCGCTGGTAAA 36 192 0 GGGAAGAGCG 0.938004 -84 TAAGGACGTGCTGCAGCACGTGTAAAGTGATG 38 18 1 CTGAGACGTG 0.448996 -64 GAGGGACAGTCGGCAAGGTGCGACTGGTTGAT 39 37 1 CGGAAGTGCG 0.889451 -50 GCCGAGAATTCAGCGACGCGCGGGTGTCGGCA 40 28 1 CAGGAGCGCG 0.938351 -44 GCGCGGGTGTCGGCAGCGTGCGGTACAGGGGG 40 45 1 CGGAGGTGCG 0.977048 -27 AGCTGGGCCGTGCGCGCATGTCCGCG 43 5 1 GGGCGGCGCG 0.988485 -165 ATTGCGGGCACAGGGGCACGCGAACTAGAACG 43 42 0 CAGGGACGCG 0.895308 -128 TACCGCGCGTGTGTGCCGCGCGTTGCGCTTCC 43 95 1 GTGGCGCGCG 0.971427 -75 CGGCGTACCAGGGCGGTACGCGCGAGCGCCTC 43 126 1 GGGGGACGCG 0.979706 -44 *** ** ***** Masking position 3 Map Score: 80.8658 Number of sites scoring better than the average of aligned sites = 3199 Number in coding regions = 2907 Number in noncoding regions = 292 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 2 GGAGCGTATCCACCGCGCGCATCGCACCCC 1 159 0 CACCGCGCGC 0.854698 -142 AGGACTGCGTAGGGGCGTGCGTCGATTGGT 1 216 1 AGGGGCGTGC 0.845453 -85 GTTCTATCTGTGGAGCGCGTTACGTTGGGT 2 80 1 TGGAGCGCGT 0.909013 -39 TAGCGTAAGAGGGGGAGTGC 2 109 1 GGGGGAGTGC 0.921799 -10 TACTCACCCGCGCAGAGTGTTTATCCCT 4 9 0 CGCAGAGTGT 0.805444 -32 CATTCTGGTAGGCGGTGTGTGGTTTTGAGT 6 26 1 GGCGGTGTGT 0.748659 -74 TAGCTCAGTTGGCAGAGCGCAACCATGGTA 8 151 1 GGCAGAGCGC 0.871464 -84 CACCAGAAAACCCCGTGCGTAACAGATATG 9 19 0 CCCCGTGCGT 0.615391 -131 TAGCTCTAATGGCAGAGCGTCGGTCTCCAA 9 72 1 GGCAGAGCGT 0.87734 -78 GTCCTTCCTGGCCTGAGTGCTTTCGAAAAG 9 123 1 GCCTGAGTGC 0.81986 -27 TCTTCCAGGGTGGAGAGTGTTGCAATGCGC 10 17 1 TGGAGAGTGT 0.713907 -90 TTTGCATGCGTCCGGCGCGTCGTTGTGTGC 12 23 1 TCCGGCGCGT 0.962992 -240 CGTGTGGGAGGGCGTCGCGCTTTTGAGTAG 12 67 1 GGCGTCGCGC 0.481341 -196 AGTATTACGGTAGAGCGTGTGGTATAGGGA 12 205 1 TAGAGCGTGT 0.614409 -58 GCAGCTTGAGGGGGGAGTGC 12 253 1 GGGGGAGTGC 0.921799 -10 TGAGTATCCTAGCCGCGTGTGCTGTGTGCG 13 35 1 AGCCGCGTGT 0.815978 -68 GTGTAGTGAGGGCGGTGTGTTGGACTCTCT 18 35 1 GGCGGTGTGT 0.748659 -32 ACAAAATAGGCGGTGAGCGTATACTCGAAG 19 25 1 CGGTGAGCGT 0.836094 -54 TCACCCGAGGTGGTGCGCGTTTGAGGCGGC 21 109 1 TGGTGCGCGT 0.916386 -45 GCGGCTGTTTGCCCGCGTGTGTTTCTTGTC 21 134 1 GCCCGCGTGT 0.958761 -20 GCCAATTTAGGTGAGAGTGTTCTTGGGCGT 22 122 1 GTGAGAGTGT 0.363008 -115 GAGAGTGTTCTTGGGCGTGTACTCGTTGGA 22 134 1 TTGGGCGTGT 0.718764 -103 GCGTGCACGGTGCTGCGTGCTGTTCAAACC 22 190 1 TGCTGCGTGC 0.902429 -47 GTCGGTTACACCCGGCGTGTACGAGCCTTC 23 31 1 CCCGGCGTGT 0.965025 -88 TTTTTAAGGGCGCGGCGCGCTGTAGAATGG 23 82 1 CGCGGCGCGC 0.977138 -37 CGCATATCTCCACTGAGCGCTGATCCTACC 25 18 0 CACTGAGCGC 0.546821 -79 AGTGGAGATATGCGGCGTGCTACTATGCAC 25 34 1 TGCGGCGTGC 0.958222 -63 CGTCACGCGCTCCTGCGCGCACACCTGCAG 26 44 0 TCCTGCGCGC 0.908641 -71 CTTCTCGCGCCAGCGAGCGTAACACGCCAG 28 50 1 CAGCGAGCGT 0.635176 -126 ACAGATTACCGCTGGCGTGTTACGCTCGCT 28 61 0 GCTGGCGTGT 0.524351 -115 TGGGTAAGAATAGGGAGCGTAGGCGCCTGT 29 11 1 TAGGGAGCGT 0.655499 -78 AGTACCGTTATACGGCGTGTTTGCCTTTTG 30 11 1 TACGGCGTGT 0.836496 -82 ACATAGCATGGGGGGCGTGTAGGAAGGT 30 75 1 GGGGGCGTGT 0.974064 -18 GTGCTGCATGCGCTGAGCGTACACGCGCGA 31 14 1 CGCTGAGCGT 0.857562 -68 TTCGGTAACCTCGCGCGTGTACGCTCAGCG 31 24 0 TCGCGCGTGT 0.915129 -58 AAAAGCAGCGGTCGGCGCGTTAGTTGCCTT 32 118 1 GTCGGCGCGT 0.879889 -116 TCAGCGGCTGCTGTGCGTGTTGTGTGATCG 36 55 1 CTGTGCGTGT 0.591617 -221 TGTTGTGTGATCGCGCGCGTCTGTTCTCTG 36 72 1 TCGCGCGCGT 0.900325 -204 CAGGAATAGGCCGTGAGTGTGCGTCGCTTG 36 119 1 CCGTGAGTGT 0.757369 -157 ATCCGTTTTTACCAGCGCGCTCTTTCCCCT 36 185 1 ACCAGCGCGC 0.717891 -91 GTATGCCTATGAGAGCGTGCGAGTACATGG 36 256 1 GAGAGCGTGC 0.734529 -20 GGCAAACGGAGCGGGCGTGTAAGCGGCGGC 38 61 1 GCGGGCGTGT 0.968098 -21 CGCTGCCGACACCCGCGCGTCGCTGAATTC 40 33 0 ACCCGCGCGT 0.800084 -39 CGCGGGTGTCGGCAGCGTGCGGTACAGGGG 40 46 1 GGCAGCGTGC 0.939192 -26 AGCTGGGCCGTGCGCGCATGTCCGCGT 43 8 1 CCGTGCGCGC 0.921231 -162 TCCGCAAATACCGCGCGTGTGTGCCGCGCG 43 87 1 CCGCGCGTGT 0.938019 -83 CGCGCGTGTGTGCCGCGCGTTGCGCTTCCG 43 98 1 TGCCGCGCGT 0.954297 -72 AGGGCGGTACGCGCGAGCGCCTCACAGCAC 43 135 1 GCGCGAGCGC 0.695003 -35 GGGCTAATATCCTGAGTGCTGTGAGGCGC 43 151 0 TCCTGAGTGC 0.713006 -19 ********** Masking position 7 Map Score: 66.132 Number of sites scoring better than the average of aligned sites = 4192 Number in coding regions = 3857 Number in noncoding regions = 335 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 3 TCTTTTCTGCCCTCTCTTCCCCCAAGAAGA 2 20 0 CCTCTCTTCC 0.400815 -99 ATCCTCTCTCCTTTCCGTCCCG 5 89 0 CCTCTCTCCT 0.842178 -12 AAGCACGAAACACCTCCCTAAACAGGCAGC 8 45 0 CACCTCCCTA 0.705482 -190 CATTGTATAACGCCTCACCTCACACATCAA 8 73 0 CGCCTCACCT 0.854835 -162 ACCACCCCTCCTCACATCCACAGA 8 221 0 CCCCTCCTCA 0.936863 -14 ACTGGCCTCTCCTTATGACGTAAAA 10 92 0 CCTCTCCTTA 0.608247 -15 GGGTCGCGTTCTCCTCACTTGAGTGGAGGG 12 152 1 CTCCTCACTT 0.456295 -111 GAGACGCCGTCCCCTCCACTCAAGTGAGGA 12 163 0 CCCCTCCACT 0.946684 -100 GAGGGGACGGCGTCTCCCCTGTGTGGGGAG 12 177 1 CGTCTCCCCT 0.934759 -86 GCACTCCCCCCTCAAGCTGCACCGAAC 12 246 0 CCCCTCAAGC 0.400295 -17 ACCAACTCCTCTCCCCAGCCC 14 5 0 CCTCTCCCCA 0.969527 -17 AACGAAAATGCGCATCCCCCGCAAAGGTGG 16 76 0 CGCATCCCCC 0.572206 -70 CCCCTCCTGCGGAACAAACA 16 136 0 CCCCTCCTGC 0.86418 -10 ACCTGTCCCCTCTCCCTACTCACAATAA 17 33 0 CCTCTCCCTA 0.899076 -18 ACAATGCTGCCCCATCCCCTA 18 2 0 CCCATCCCCT 0.878559 -65 GAGTCCAACACACCGCCCTCACTACACCGT 18 32 0 CACCGCCCTC 0.483436 -35 CCCACCGCCCCCTCTCCCTAGGAAGACTAC 20 15 0 CCTCTCCCTA 0.899076 -36 GCCCCGCGCCTAGAACCCCAC 20 40 0 CCCCGCGCCT 0.874407 -11 TTCTACAGCGCGCCGCGCCCTTAAAAAGGT 23 79 0 CGCCGCGCCC 0.562793 -40 CTGAATCGCTCCTTTCCCCATTCTACAGCG 23 99 0 CCTTTCCCCA 0.466704 -20 AAACTTCTCTCCTCCCCTGTTATAGAAT 25 79 0 CTCCTCCCCT 0.951255 -18 GTTTCGGTAACCTCGCGCGTGTACGCTCAG 31 26 0 CCTCGCGCGT 0.469597 -56 CGTCACTCCCTCCCTTCGTGGGGCCT 31 66 0 TCCCTCCCTT 0.518092 -16 TTCCTCTCCATACCCTCGTGGG 33 3 1 CCTCTCCATA 0.514684 -43 ATGACAACACCACCTCCCGTTTGCGTAAGG 34 12 1 CACCTCCCGT 0.836067 -66 TTTCTCCCCCTCACCTATTTCTCCTC 35 7 1 CCCCTCACCT 0.958173 -98 CGCGCTCTTTCCCCTCATCTTTTGCCTTCG 36 200 1 CCCCTCATCT 0.799703 -76 GCTGACGCGGCTCCTCCCGAGGAGCCGGTT 37 15 1 CTCCTCCCGA 0.791263 -105 GCGTCAAGATCCCCTCTTGTAGGGGGAACC 37 41 0 CCCCTCTTGT 0.458559 -79 CGATTTCTCCTCCCCCTGCTAAGAAC 37 104 0 CTCCTCCCCC 0.933494 -16 CTGAGCACTGCCTCGCCCCTGAGCATGGAA 41 16 0 CCTCGCCCCT 0.945302 -80 GCTCAGCTGGCGTCTCCACTCGCACAGAAA 41 40 1 CGTCTCCACT 0.630403 -56 ********** Masking position 6 Map Score: 29.3776 Number of sites scoring better than the average of aligned sites = 1123 Number in coding regions = 898 Number in noncoding regions = 225 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 4 CCTGCTGTTTGCGTGTTTGGTTGACCGGTAGTAT 5 36 1 GCTGTGGTGA 0.671316 -65 TTCTGGGGCAGGCTGGTTGGCTGCCTGTTTAGGG 8 26 1 GGTGTGGTGC 0.93177 -209 CGAGCCGCCCGGAGGCCGGCCCGCATTGTATAAC 8 92 0 GGGGCGCCGC 0.829314 -143 GTTGCAATGCGCATGATTGCCTGCCGCTTACGCG 10 35 1 GCTGTGCTGC 0.863754 -72 TAGGCGGTCAGGCTTCTGGGGTGCTGTCTTCCTG 11 44 1 GGTTTGGTGC 0.765379 -65 CTTTCGTGTGGGAGGGCGTCGCGCTTTTGAGTAG 12 63 1 GGGGCTCCGC 0.67991 -200 CTTGTTCTCGGCATTTTGGCATGCGGGTTGGGTC 12 123 1 GCTTTGCTGC 0.919998 -140 CGTTTGAGGCGGCTGTTTGCCCGCGTGTGTTTCT 21 126 1 GGTGTGCCGC 0.990491 -28 TTTCTTTCCAGGGTTGTAGCGTGCACGGTGCTGC 22 172 1 GGTTTGCTGC 0.934037 -65 TCGTCACCGTGCATAGTAGCACGCCGCATATCTC 25 38 0 GCTATGCCGC 0.797502 -59 AACGATCTCTGCAGGTGTGCGCGCAGGAGCGCGT 26 36 1 GCGGGGCCGC 0.913564 -79 GGCGTGTTACGCTCGCTGGCGCGAGAAGTGCGCA 28 44 0 GCCGTGCCGA 0.70574 -132 ATGGATCAATGCCTGATTGCATGCCACAGGCGCC 29 32 0 GCTGTGCTGC 0.976382 -57 CGGCGCCGATGGCGTTTTGCTTGAATGAGGACTG 32 53 1 GGGTTGCTGA 0.733371 -181 TTTGCTTGAATGAGGACTGCACGCAAAACCTGCC 32 68 1 TGGGCGCCGC 0.796821 -166 TTTCCGTTGTGGAAGACAGCTTGCGGCGTATCAG 36 25 1 GGAGCGCTGC 0.850085 -251 TGTGCGTGTTGTGTGATCGCGCGCGTCTGTTCTC 36 66 1 GTTGTGCCGC 0.872463 -210 GGTATTTAGTGGATTGTTGCTCGCGCTGATCCGT 36 157 1 GGTTTGCCGC 0.961396 -119 GCCGTCTTGGGCGCCACCGTGTGT 39 1 1 GCGTTGGCGC 0.838851 -86 AGGTGCGACTGGTTGATGGCGTGAGTCTCGGGTA 39 52 1 GGTGTGCTGA 0.913846 -35 AGCTGGGCCGTGCGCGCATGTCCGC 43 2 1 GCGGCGTCGC 0.684337 -168 CGTCGGCCGTTCTAGTTCGCGTGCCCCTGTGCCC 43 35 1 TCAGTGCTGC 0.383224 -135 GGCGTACCAGGGCGGTACGCGCGAGCGCCTCACA 43 127 1 GGGGAGCCGA 0.619241 -43 ** ** * ** *** Masking position 13 Map Score: 26.6759 Number of sites scoring better than the average of aligned sites = 834 Number in coding regions = 759 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 5 CAGAATGCAAACGCGTGTGGGTGCGGTGTAT 1 21 1 ACCGTGTGGG 0.979431 -280 GCGTGCGTCGATTGGTGTGGTGCTATGTGTC 1 230 1 ATGGTGTGGT 0.859395 -71 TGGTGTGGTGCTATGTGTCGTGCTGGTTTGA 1 242 1 CTTGTGTCGT 0.80515 -59 GGTGCCTGGTATAGGTGCGGGACGGAAAGGA 5 72 1 ATGGTGCGGG 0.884043 -29 TTCTGGTAGGCGGTGTGTGGTTTTGAGTTCT 6 28 1 CGTGTGTGGT 0.750393 -72 TCTGACACCCTTTCGTGTGGGAGGGCGTCGC 12 54 1 TTCGTGTGGG 0.806768 -209 ACGGCGTCTCCCCTGTGTGGGGAGTATTACG 12 183 1 CCTGTGTGGG 0.973128 -80 GTATAGGGAGCACCGTGTCGGTTCGGTGCAG 12 226 1 CACGTGTCGG 0.949826 -37 ACGTGAAGTTAAGGGTGTCGTCTTCTGTTTT 22 72 1 AAGGTGTCGT 0.707706 -165 TGCTGTTCAAACCGGTGTCGGTAATCTCGGT 22 207 1 ACGGTGTCGG 0.960285 -30 GGAGACTGGAACGTGTGTCGGTTACACCCGG 23 15 1 ACTGTGTCGG 0.937916 -104 TGTGCGAGCACGATGTGTGGGAGCTGTCAGT 30 39 1 CGTGTGTGGG 0.916878 -54 GAGGTTACCGAAACGTGTGGGTCTAGGCCCC 31 42 1 AACGTGTGGG 0.945931 -40 ATGAACAGATATACGTGTCGGGGAGGTTTAC 32 11 0 ATCGTGTCGG 0.952234 -223 CTCTCCATACCCTCGTGGGGGATGCCCCCCT 33 14 1 CCCGTGGGGG 0.906766 -32 CAGAGGAGAAATAGGTGAGGGGGAGAAA 35 8 0 ATGGTGAGGG 0.657404 -97 CATCTTTTGCCTTCGTGCCGTTATTATCCGA 36 215 1 CTCGTGCCGT 0.748418 -61 TTGGGCGCCACCGTGTGTGGGAGGGACAGTC 39 17 1 CCTGTGTGGG 0.973128 -70 TCAGCGACGCGCGGGTGTCGGCAGCGTGCGG 40 37 1 GCGGTGTCGG 0.83451 -35 CGGGTGTCGGCAGCGTGCGGTACAGGGGGTC 40 48 1 CACGTGCGGT 0.723039 -24 ** ******** Masking position 6 Map Score: 19.0753 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 328 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 GGGGAGAAAAGCGTACGAGAATCTGCCCCG 1 67 1 GCGTACGAGA 0.943856 -234 TATCCACCGCGCGCATCGCACCCCATATCG 1 153 0 GCGCATCGCA 0.729935 -148 ACGTTGGGTAGCGTAAGAGGGGGAGTGC 2 101 1 GCGTAAGAGG 0.943856 -18 ACCACACACCGCCTACCAGAATGCCCTGCT 6 19 0 GCCTACCAGA 0.760445 -81 AAAACCCCGTGCGTAACAGATATGACGACA 9 13 0 GCGTAACAGA 0.934336 -137 CGAAACCAACGCGTAAGCGGCAGGCAATCA 10 48 0 GCGTAAGCGG 0.891583 -59 AAGCCTGACCGCCTAACACATACCCCGTAA 11 29 0 GCCTAACACA 0.697711 -80 TGCGAAGCGTGCGCAAGAGAATTTTGCGCG 16 17 1 GCGCAAGAGA 0.944344 -129 CAACGAAAATGCGCATCCCCCGCAAAGGTG 16 77 0 GCGCATCCCC 0.776026 -69 CGCCTCAAACGCGCACCACCTCGGGTGAAG 21 107 0 GCGCACCACC 0.946987 -47 GCAGGTGTGCGCGCAGGAGCGCGTGACGTG 26 46 1 GCGCAGGAGC 0.847224 -69 AATGCGTAAGACGGGGTGGTCCT 28 4 1 GCGTAAGACG 0.935241 -172 CGCGAGAAGTGCGCATGAGGAAGAAAGGAC 28 29 0 GCGCATGAGG 0.903734 -147 GCGCCAGCGAGCGTAACACGCCAGCGGTAA 28 56 1 GCGTAACACG 0.935241 -120 CGGACGCCTTGCGTACCCCAACCGCGAGCC 28 105 1 GCGTACCCCA 0.876006 -71 AGAATAGGGAGCGTAGGCGCCTGTGGCATG 29 17 1 GCGTAGGCGC 0.694735 -72 AAACACGGGTGCGCAACACACTACTTTCCT 34 39 0 GCGCAACACA 0.935802 -39 ACAGCTTGCGGCGTATCAGCGGCTGCTGTG 36 40 1 GCGTATCAGC 0.873876 -236 CTCGCAGTATGCCTATGAGAGCGTGCGAGT 36 250 1 GCCTATGAGA 0.557801 -26 ACACGGTGGCGCCCAAGACGGC 39 3 0 GCCCAAGACG 0.764815 -84 TACCATAGCCGCGTACGAGCAGTTTCTGTG 41 62 0 GCGTACGAGC 0.945757 -34 TTTCCTTGTTGCGCAAGGGAACAGGTGGTG 42 25 0 GCGCAAGGGA 0.870096 -23 GCGGACATGCGCGCACGGCCCAGCT 43 6 0 GCGCACGGCC 0.875794 -164 TACGCCGGAAGCGCAACGCGCGGCACACAC 43 103 0 GCGCAACGCG 0.871822 -67 TGCGCTTCCGGCGTACCAGGGCGGTACGCG 43 118 1 GCGTACCAGG 0.952067 -52 TACGCTTCCGGCGTACCCCAACTTACT 44 43 1 GCGTACCCCA 0.876006 -17 ********** Masking position 5 Map Score: 35.2837 Number of sites scoring better than the average of aligned sites = 1405 Number in coding regions = 1316 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 7 CCTCTCTTCCCCCAAGAAGAAGAGACTTT 2 10 0 CCCAAGAAGA 0.779805 -109 AACCAGCCTGCCCCAGAAAGAAAGGCGCGT 8 14 0 CCCCAGAAAG 0.793553 -221 TCCCCGAGCCGCCCGGAGGCCGGCCCGCAT 8 100 0 GCCCGGAGGC 0.885957 -135 GTTCAATCCCGCTCGGAAGCTTCCGTCTGT 8 196 1 GCTCGGAAGC 0.746973 -39 ACCCACAAATCCCCGGAAAACACCAGAAAA 9 39 0 CCCCGGAAAA 0.952132 -111 AAGCACTCAGGCCAGGAAGGACTCGAACCT 9 115 0 GCCAGGAAGG 0.961457 -35 ACACTCTCCACCCTGGAAGAAGAAAA 10 7 0 CCCTGGAAGA 0.882383 -100 GAAGACAGCACCCCAGAAGCCTGACCGCCT 11 45 0 CCCCAGAAGC 0.919768 -64 CCTATAAACGGACAGGAAGACAGCACCCCA 11 60 0 GACAGGAAGA 0.389353 -49 CACAACGACGCGCCGGACGCATGCAAAAAA 12 20 0 CGCCGGACGC 0.757861 -243 ACGCCCCAGGAAGAGACGCGTAT 15 10 0 CCCAGGAAGA 0.971013 -14 AATGCGCATCCCCCGCAAAGGTGGCGATAT 16 70 0 CCCCGCAAAG 0.789818 -76 GTGTTTGTTCCGCAGGAGGGG 16 135 1 CGCAGGAGGG 0.764852 -11 GCCCCCTCTCCCTAGGAAGACTACTGCA 20 9 0 CCTAGGAAGA 0.691187 -42 TGACACCGCTGCCCGGAAAGGTGTTTTCGC 21 18 1 GCCCGGAAAG 0.936776 -136 AGACTAGAACACCAGGAAAACAGAAGACGA 22 89 0 ACCAGGAAAA 0.372533 -148 CACGCTACAACCCTGGAAAGAAAAACCGAC 22 165 0 CCCTGGAAAG 0.821432 -72 GCACGCCTTTTCCAGGAAAGGTGG 26 5 0 TCCAGGAAAG 0.520452 -110 GGGTCTAGGCCCCACGAAGGGAGGGAGTGA 31 60 1 CCCACGAAGG 0.791446 -22 CGCAAAACCTGCCAGGAAACAATGATGAGA 32 89 1 GCCAGGAAAC 0.893244 -145 GCCGCTGATACGCCGCAAGCTGTCTTCCAC 36 33 0 CGCCGCAAGC 0.771881 -243 CGCCCTGGTACGCCGGAAGCGCAACGCGCG 43 111 0 CGCCGGAAGC 0.970362 -59 AGTTGGGGTACGCCGGAAGCGTACGTTTTT 44 36 0 CGCCGGAAGC 0.970362 -24 ********** Masking position 7 Map Score: 20.5136 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 343 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 8 CCACACGCGTTTGCATTCTGGCACAGGGAA 1 10 0 TTGCTTCTGG 0.94906 -291 TGGTGCTATGTGTCGTGCTGGTTTGATGTAT 1 247 1 TGTCTGCTGG 0.735329 -54 GCCTGTAGCAGGGCATTCTGGTAGGCGGTGT 6 13 1 GGGCTTCTGG 0.993536 -87 TTTCTTTCTGGGGCAGGCTGGTTGGCTGCCT 8 21 1 GGGCGGCTGG 0.921765 -214 GTTACGCACGGGGTTTTCTGGTGTTTTCCGG 9 26 1 GGGTTTCTGG 0.968355 -124 GTGTTTTCCGGGGATTTGTGGGTCAGTAGCT 9 46 1 GGGATTGTGG 0.825256 -104 GAAGGTTCGAGTCCTTCCTGGCCTGAGTGCT 9 113 1 GTCCTCCTGG 0.811042 -37 CTCGGCATTTTGGCATGCGGGTTGGGTCGCG 12 129 1 TGGCTGCGGG 0.817239 -134 CTACACATTCGGGACTTCTGGCGAGCCACAG 21 56 0 GGGATTCTGG 0.968355 -98 TCTGTTTTCCTGGTGTTCTAGTCTTTAGCCA 22 95 1 TGGTTTCTAG 0.536771 -142 CGGCGTGTACGAGCCTTCTGGAAGAGGGTGG 23 43 1 GAGCTTCTGG 0.923726 -76 AGCGCGTGACGTGAATTCTGGAAAAAGACTT 26 63 1 GTGATTCTGG 0.907177 -52 AAATGCTTTTCTGGCAGGGGAAAG 27 13 0 TGCTTTCTGG 0.85539 -14 GCGTCCGTGTGTCCTTGCTGGACAGATTACC 28 81 0 GTCCTGCTGG 0.937937 -95 TCCTCTTGGTTTCCGTTGTGGAAGACAGCTT 36 16 1 TTCCTTGTGG 0.59424 -260 TGTCCGCGTCGGCCGTTCTAGTTCGCGTGCC 43 29 1 GGCCTTCTAG 0.886503 -141 **** ****** Masking position 11 Map Score: 8.79169 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 176 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 CTGCCCCGTTAGGTTGAAGGGGGAGCAAACT 1 89 1 AGGTTGAAGG 0.488004 -212 TTGCCTGTAGCAGGGCATTCTGGTA 6 5 1 CTGTAGCAGG 0.868944 -95 AGCCTGCCCCAGAAAGAAAGGCGCGTCAC 8 9 0 AGAAAGAAGG 0.677853 -226 GTTGGCAGAGCGCAACCATGGTAAGGTTGAG 8 158 1 CGCAACCAGG 0.691823 -77 TTTTTTTCCGCTGAAGCACGGAATATCGCCA 16 48 1 CTGAAGCAGG 0.903401 -98 GTGTTTGTTCCGCAGGAGGGG 16 135 1 CGCAGGAGGG 0.742719 -11 AAGGTGTTTTCGCTAGAAAGGCTGTGGCTCG 21 35 1 CGCTAGAAGG 0.921343 -119 AATGTGTAGACTGTACAACGGTGTGTTCTCT 21 78 1 CTGTACAAGG 0.711478 -76 GCGCGGCGCGCTGTAGAATGGGGAAAGGAGC 23 91 1 CTGTAGAAGG 0.916457 -28 GGTACATTTTCGATAGAACGGTCATGCACTT 26 94 0 CGATAGAAGG 0.881642 -21 AGTGCGCATGAGGAAGAAAGGACCACCCCGT 28 21 0 AGGAAGAAGG 0.920674 -155 CTAGGCCCCACGAAGGGAGGGAGTGACG 31 64 1 CGAAGGGAGG 0.713071 -18 TGCGACAGAGCTGAAGAAAGGCTTTTCTTTG 32 149 1 CTGAAGAAGG 0.939291 -85 ACCAAACTCTCGGAGGGATGGATGATAGTAC 32 197 0 CGGAGGGAGG 0.932009 -37 GTTTGGTCGAAGGAGGCATGGCT 32 221 1 AGGAGGCAGG 0.840063 -13 AGTTTAAGGACGGAGGAAAGGCTCTACAGAG 35 34 0 CGGAGGAAGG 0.977472 -71 CGGCAGCGTGCGGTACAGGGGGTCGGT 40 55 1 CGGTACAGGG 0.683124 -17 ******** ** Masking position 10 Map Score: 11.6991 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 275 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 10 TGAGGGGAAAAACGGACAGG 1 291 1 AACGGACAGG 0.95041 -10 ATAGGTGCGGGACGGAAAGGAGAGAGGAT 5 82 1 GACGGAAAGG 0.941414 -19 GTATGTGTTAGGCGGTCAGGCTTCTGGGGT 11 36 1 GGCGGTCAGG 0.919425 -73 AACCCCTATAAACGGACAGGAAGACAGCAC 11 64 0 AACGGACAGG 0.95041 -45 GAGTAGGGAGAGGGGACAGGT 17 40 1 AGGGGACAGG 0.985254 -11 CGCTGTAGAATGGGGAAAGGAGCGATTCAG 23 99 1 TGGGGAAAGG 0.89655 -20 ACTCACCTAGGGGAAAGACGTAATGGTA 24 27 0 AGGGGAAAGA 0.881662 -18 CTTTTCTGGCAGGGGAAAGTT 27 2 0 AGGGGAAAGT 0.881662 -25 GTTTAAGGACGGAGGAAAGGCTCTACAGAG 35 34 0 GGAGGAAAGG 0.862179 -71 GCAAAAGATGAGGGGAAAGAGCGCGCTGGT 36 195 0 AGGGGAAAGA 0.881662 -81 GTGACGGTAAGGACGTGCTGCA 38 3 1 GACGGTAAGG 0.766464 -79 CCGTGTGTGGGAGGGACAGTCGGCAAGGTG 39 27 1 GAGGGACAGT 0.825732 -60 TTGTTGCGCAAGGGAACAGGTGGTGCGTAG 42 20 0 AGGGAACAGG 0.814842 -28 ********** Masking position 8 Map Score: 11.3568 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 178 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 11 GACTGGGGTGTGAGGGGAAAAACGGACAGG 1 281 1 TGAGGGAAAA 0.842721 -20 TTTTGAGTTCTGCCGGTAACAGAAAGAGTGT 6 48 1 TGCGGTAACA 0.764244 -52 CATGCCAAAATGCCGAGAACAAGTATGAAAA 12 115 0 TGCGAGAACA 0.985005 -148 TCCACTCAAGTGAGGAGAACGCGACCCAACC 12 148 0 TGAGAGAACG 0.955813 -115 CCACCTCGGGTGAAGAGAACACACCGTTGTA 21 91 0 TGAGAGAACA 0.97186 -63 CGCGCACACCTGCAGAGATCGTTCGCACGCC 26 28 0 TGCGAGATCG 0.839421 -87 CAGGAAACAATGATGAGAAAAGCAGCGGTCG 32 101 1 TGAGAGAAAA 0.895341 -133 CAGCGGTAAATTCAGAGAACAGACGCGCGCG 36 83 0 TTCGAGAACA 0.838076 -193 AGGCAAAAGATGAGGGGAAAGAGCGCGCTGG 36 196 0 TGAGGGAAAG 0.770426 -80 CTCCTCCCCCTGCTAAGAACACGAGGGTCCA 37 93 0 TGCAAGAACA 0.838073 -27 GCGCGGTATTTGCGGAGAACAAAGCAACCAT 43 72 0 TGCGAGAACA 0.985005 -98 *** ******* Masking position 8 Map Score: 8.51474 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 115 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 12 AAAGACATACACCGCACCCACACGCGTTTGC 1 27 0 ACCCACCCAC 0.979552 -274 GACACATAGCACCACACCAATCGACGCACGC 1 230 0 ACCCACCAAT 0.686125 -71 ACCACCCCTCCTCACATCCAC 8 224 0 ACCCCCCTCC 0.940239 -11 TGCTCCCTATACCACACGCTCTACCGTAATA 12 207 0 ACCCACGCTC 0.835917 -56 CTCAAGCTGCACCGAACCGACACGGTGCTCC 12 232 0 ACCAACCGAC 0.848309 -31 GCACTCCCCCCTCAAGCTGCACC 12 250 0 ACTCCCCCTC 0.756408 -13 AAGAGAGTCCAACACACCGCCCTCACTACAC 18 35 0 AACCACCGCC 0.898686 -32 CGCGCCTAGAACCCCACCGCCCCCTCTCCCT 20 26 0 ACCCACCGCC 0.991976 -25 GGAAGAAAGGACCACCCCGTCTTACGCATT 28 10 0 ACCCCCCGTC 0.984643 -166 ATACCCAAATACCGCACCATCGGCCTCCGCA 28 145 1 ACCCACCATC 0.968219 -31 GTAAACCTCCCCGACACGTATATCT 32 5 1 ACCCCCCGAC 0.984643 -229 CATGACAACACCACCTCCCGTTTGC 34 5 1 ACACACCACC 0.791994 -73 *** ******* Masking position 1 Map Score: 9.87585 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 127 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 13 TGAGCACGTACAGTTTGCTCCCCCTTCAAC 1 101 0 CAGTTTGCTC 0.678792 -200 ACACGTCATTCTGTTTCCGCTCATATCCAG 2 52 0 CTGTTTCCGC 0.947326 -67 TGTTATCCTGCTGTTTGCGTGTTTGGTTGA 5 30 1 CTGTTTGCGT 0.933197 -71 TTTGAGGCGGCTGTTTGCCCGCGTGTGTTT 21 128 1 CTGTTTGCCC 0.980973 -26 GTGTCGTCTTCTGTTTTCCTGGTGTTCTAG 22 86 1 CTGTTTTCCT 0.778566 -151 GTTATACGGCGTGTTTGCCTTTTGTGCGAG 30 17 1 GTGTTTGCCT 0.759937 -76 ACACCACCTCCCGTTTGCGTAAGGAAAGTA 34 18 1 CCGTTTGCGT 0.908645 -60 TACCAGCGCGCTCTTTCCCCTCATCTTTTG 36 194 1 CTCTTTCCCC 0.802975 -82 TCCCGAGGAGCCGGTTCCCCCTACAAGAGG 37 29 1 CCGGTTCCCC 0.823923 -91 CACGCCCGCTCCGTTTGCCCGTGACTGCTC 38 50 0 CCGTTTGCCC 0.973481 -32 CTGTTTCCTTGTTGCGCAAG 42 38 0 CTGTTTCCTT 0.807573 -10 ********** Masking position 5 Map Score: 5.4342 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 143 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 14 CTGATACATCAAACCAGCACGACACATAGC 1 251 0 AAACCAGCAC 0.419521 -50 TCAGCGGTTCAATCCCGCTCGGAAGCTTCC 8 190 1 AATCCCGCTC 0.700962 -45 AGCGGCAGGCAATCATGCGCATTGCAACAC 10 33 0 AATCATGCGC 0.6875 -74 AAAACACCCGAAACCAACGCGTAAGCGGCA 10 56 0 AAACCAACGC 0.665428 -51 AAAGAAATAGAAGCCCACGCTCTACTCAAA 12 88 0 AAGCCCACGC 0.920667 -175 ATGTGATGCGAAGCGTGCGCAAGAGAATTT 16 11 1 AAGCGTGCGC 0.863379 -135 TCAGCGGAAAAAAAACGCGCAAAATTCTCT 16 32 0 AAAAACGCGC 0.741207 -114 CAGCCGCCTCAAACGCGCACCACCTCGGGT 21 111 0 AAACGCGCAC 0.870684 -43 GACAAGAAACACACGCGGGCAAACAG 21 138 0 AAACACACGC 0.821101 -16 CACCGGTTTGAACAGCACGCAGCACCGTGC 22 194 0 AACAGCACGC 0.498221 -43 AACATACCCAAATACCGCACCATCGGCCTC 28 142 1 AATACCGCAC 0.575985 -34 GCATCAGTACAATCGCGCGCA 35 94 1 AATCGCGCGC 0.977944 -11 CGTGTTGTGTGATCGCGCGCGTCTGTTCTC 36 70 1 GATCGCGCGC 0.824341 -206 GATGAGGGGAAAGAGCGCGCTGGTAAAAAC 36 189 0 AAGAGCGCGC 0.878663 -87 CCATGTACTCGCACGCTCTCATAGGC 36 260 0 ACTCGCACGC 0.770879 -16 CACGCTGCCGACACCCGCGCGTCGCTGAAT 40 35 0 ACACCCGCGC 0.912329 -37 CGCGCAAACCTACGCACCACCTGTT 42 6 1 AAACCTACGC 0.787725 -42 GTTCTCCGCAAATACCGCGCGTGTGTGCCG 43 83 1 AATACCGCGC 0.910483 -87 ACCGCGTGAAAAACGTACGCTTCCGGCGTA 44 28 1 AAACGTACGC 0.787725 -32 ********** Masking position 8 Map Score: 15.6997 Number of sites scoring better than the average of aligned sites = 1376 Number in coding regions = 1290 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 15 CGCGGTGGATACGCTCCTTCTCGACTGAGG 1 172 1 ACGCTCCTTC 0.940984 -129 CAATCGACGCACGCCCCTACGCAGTCCTAC 1 214 0 ACGCCCCTAC 0.842222 -87 AATTCACACGACACTCTTTCTGTTACCGGC 6 59 0 ACACTCTTTC 0.873775 -41 GAAACACCTTTTCGAAAGCACTC 9 137 0 ACACCTTTTC 0.825427 -13 TGTGCCTCTGACACCCTTTCGTGTGGGAGG 12 48 1 ACACCCTTTC 0.948023 -215 GGTGTGTTGGACTCTCTTGCTAATAATTG 18 48 1 ACTCTCTTGC 0.451323 -19 TATTTTGTCAACACCCCTGCAT 19 3 0 ACACCCCTGC 0.938417 -76 TCAAACGCTCCTTTCGCACAATAA 19 65 0 ACGCTCCTTT 0.457345 -14 AGCGACTTGACACCGCTGCCCGGAAAGGT 21 10 1 ACACCGCTGC 0.765953 -144 TCTAGCGAAAACACCTTTCCGGGCAGCGGT 21 22 0 ACACCTTTCC 0.471018 -132 CTGGCGAGCCACAGCCTTTCTAGCGAAAAC 21 40 0 ACAGCCTTTC 0.737872 -114 GATCGTTCGCACGCCTTTTCCAGGAAAGGT 26 13 0 ACGCCTTTTC 0.8963 -102 TTCACGTCACGCGCTCCTGCGCGCACACCT 26 48 0 GCGCTCCTGC 0.725269 -67 GGACCAGATTACGCCGCATCAGTACAATCG 35 79 1 ACGCCGCATC 0.435845 -26 TTTTACCAGCGCGCTCTTTCCCCTCATCTT 36 191 1 GCGCTCTTTC 0.759596 -85 GTTGCACGGCTTTTCAAACCGCGTG 44 6 1 ACGGCTTTTC 0.57154 -54 ********** Masking position 2 Map Score: 6.44676 Number of sites scoring better than the average of aligned sites = 597 Number in coding regions = 537 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701