AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02010_tpal_reg_300.orf -o02010_tpal_300.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 TP0034_TP0035 197 TP0034: ABC transporter, periplasmic binding protein, TP0035: ABC transporter, ATP-binding protein #2 TP0074 300 sugar ABC transporter, periplasmic binding protein (y4oP) #3 TP0075 118 sugar ABC transporter, permease protein (y4oQ) #4 TP0120 129 amino acid ABC transporter, ATP-binding protein (abc) #5 TP0144 109 thiamine ABC transporter, thiamine-binding periplasmic protein, putative #6 TP0163 174 ABC transporter, periplasmic binding protein (troA) #7 TP0164 147 ABC transporter, ATP-binding protein (troB) #8 TP0278 127 T. pallidum predicted coding region TP0278 #9 TP0279 45 ribosomal protein S1 (rpsA) #10 TP0283 177 lipopolysaccharide core biosynthesis protein (kdtB) #11 TP0284 104 T. pallidum predicted coding region TP0284 #12 TP0289 22 T. pallidum predicted coding region TP0289 #13 TP0290 54 conserved hypothetical protein #14 TP0291 36 T. pallidum predicted coding region TP0291 #15 TP0296 85 conserved hypothetical protein #16 TP0298 132 exported protein (tpn38b) #17 TP0319 28 membrane lipoprotein (tmpC) #18 TP0321 75 ribose/galactose ABC transporter, ATP-binding protein (rbsA-2) #19 TP0545 84 methylgalactoside ABC transporter, periplasmic galactose-binding protein (mglB-1) #20 TP0547 143 penicillin tolerance protein (lytB) #21 TP0652 175 spermidine/putrescine ABC transporter, ATP-binding protein (potA) #22 TP0655 35 spermidine/putrescine ABC transporter, periplasmic binding protein (potD) #23 TP0683 92 octaprenyl-diphosphate synthase #24 TP0684 292 methylgalactoside ABC transporter, periplasmic galactose-binding protein (mglB-2) #25 TP0685 119 methylgalactoside ABC transporter, ATP binding protein (mglA) #26 TP0802 45 T. pallidum predicted coding region TP0802 #27 TP0804 77 sugar ABC transporter, ATP-binding protein (ugpC) #28 TP0821 80 lipoprotein (tpn32) #29 TP0822 87 conserved hypothetical protein #30 TP0823 300 desulfoferrodoxin (rbo) Motif number 1 TCCACCCCAAACGGGCGCGTACTCGCACAC 1 157 0 ACGGGCGCGT 0.562959 -41 AACGCGTGTGGGTGCGGTGTATGTCTTTGT 2 30 1 GGTGCGGTGT 0.859678 -271 ATATGGGGTGCGATGCGCGCGGTGGATACG 2 155 1 CGATGCGCGC 0.567253 -146 AGGACTGCGTAGGGGCGTGCGTCGATTGGT 2 216 1 AGGGGCGTGC 0.961598 -85 TGCGTCGATTGGTGTGGTGCTATGTGTCGT 2 233 1 GGTGTGGTGC 0.958935 -68 TGTGGTGCTATGTGTCGTGCTGGTTTGATG 2 245 1 TGTGTCGTGC 0.944141 -56 GTGTTCTATCTGTGGAGCGCGTTACGTTGG 3 78 1 TGTGGAGCGC 0.901982 -41 CGCGTTACGTTGGGTAGCGTAAGAGGGGGA 3 95 1 TGGGTAGCGT 0.555645 -24 TAGCGTAAGAGGGGGAGTGC 3 109 1 GGGGGAGTGC 0.976834 -10 CTGCAGCACGGGTGCGGTGCACGGCGTGAC 4 56 0 GGTGCGGTGC 0.970716 -74 CAGGGTGAGGGGTACAGTGCTGCTGTCTTG 5 44 0 GGTACAGTGC 0.724365 -66 GTAGCTCGAGAGGTCCGCGCCAGAGTGCCG 6 66 1 AGGTCCGCGC 0.851249 -109 GGTCGGCTGTACGGCAGCGCCTGTTCACGA 7 50 1 ACGGCAGCGC 0.703232 -98 TAGTGAAGGAGGTGGCGCGCTCACCGCTGA 7 89 1 GGTGGCGCGC 0.992595 -59 ATGTGGGGAAGGGAGTGCGCTGGTGATCAG 8 55 1 GGGAGTGCGC 0.519979 -73 AGACAACAGACGAGGAGCGCAAACAGTCTC 8 83 1 CGAGGAGCGC 0.687489 -45 GAGGAGAAGCGTTCGCGCCGTGCGGTGC 10 9 1 GCGTTCGCGC 0.831026 -169 GCGTTCGCGCCGTGCGGTGCGCACGTTGTG 10 19 1 CGTGCGGTGC 0.92444 -159 AACGTGAGGGGTTGCCGTGC 10 168 1 GTTGCCGTGC 0.878984 -10 AGTGATCTTCGGGGCTGTGCTTTTAAAGTT 11 56 1 GGGGCTGTGC 0.936564 -49 AGTTGCCGTGTTGTTTTTTGG 13 2 1 GTTGCCGTGT 0.573092 -53 AGAGGGCAGTGCTTTTTTAGGG 14 3 1 AGGGCAGTGC 0.894892 -34 CACTTGAGGACGGTGCGTGTTTGACGTTAC 15 57 1 CGGTGCGTGT 0.631535 -29 TCCTTCTCTCTGGGTGGTGCAATGCGTTTG 16 17 1 TGGGTGGTGC 0.831104 -116 GCAGGGGTGAGGAGTAGTGCTCTGGTCTTT 16 50 1 GGAGTAGTGC 0.788241 -83 TGTGGGTGCCGGTAGGGTGCACCCTACGCG 16 86 1 GGTAGGGTGC 0.683151 -47 AGTGGGGCGTGTGTCTCGACCC 18 3 1 TGGGGCGTGT 0.822317 -73 CCGGAAGAAAACTGGCGCGCCGAGTGTACC 20 103 0 ACTGGCGCGC 0.869764 -41 GTTTTCTTCCGGTTTAGTGCCCCAGTGAGT 20 121 1 GGTTTAGTGC 0.852215 -23 ACAGATTACCGCTGGCGTGTTACGCTCGCT 21 61 0 GCTGGCGTGT 0.844223 -115 GGTACGCAAGGCGTCCGTGTGTCCTTGCTG 21 92 0 GCGTCCGTGT 0.533995 -84 ACATAGCATGGGGGGCGTGTAGGAAGGT 23 9 0 GGGGGCGTGT 0.958196 -84 GGCGACTTGTCGTGCCGTGCCTCCAGTCCG 24 69 0 CGTGCCGTGC 0.977708 -224 CTTCTTTGCGCGTGTCGCGTCTTTCTCAAG 24 109 0 CGTGTCGCGT 0.865619 -184 TGGGGCACGCTGTTTCGTGCGACGGCGTCA 24 168 1 TGTTTCGTGC 0.773977 -125 CGGCGTCAAAAGTTTCGCGCGGGCTAAAGT 24 190 1 AGTTTCGCGC 0.794355 -103 GTCGCGTGTGGGTGCAGCGCGCTGTACTTG 24 226 1 GGTGCAGCGC 0.97853 -67 GCGCGCTGTACTTGTCGCGCGTTATTTCGT 24 242 1 CTTGTCGCGC 0.680546 -51 GTTCTAAGGTGGTTTAGCGCTT 24 281 1 GGTTTAGCGC 0.866753 -12 ACCTCGCACCGCTTTCGCGCGCGAGAGGAG 25 89 1 GCTTTCGCGC 0.825198 -31 AGGAAAGTAGTGTGTTGCGCACCCGTGTTT 27 39 1 TGTGTTGCGC 0.694164 -39 GGGTGTAGTGCTCTCCTGTTT 29 2 1 GGTGTAGTGC 0.966059 -86 GCGCCTCTGCGGGGCTGTGCTCTGGCGCGG 30 207 1 GGGGCTGTGC 0.936564 -94 CGTGCGGACGCCTGTCGTGCCTCCGCGTGC 30 246 0 CCTGTCGTGC 0.884047 -55 ********** Masking position 7 Map Score: 53.4484 Number of sites scoring better than the average of aligned sites = 3084 Number in coding regions = 2809 Number in noncoding regions = 275 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 2 AGGGGCTTCCACCCCAAACGGGCGCGTACTC 1 163 0 ACCCCAACGG 0.763115 -35 ACATACACCGCACCCACACGCGTTTGCATTC 2 23 0 CACCCACCGC 0.966105 -278 AGGAGCGTATCCACCGCGCGCATCGCACCCC 2 159 0 CCACCGCCGC 0.968853 -142 TCCGTTTTTCCCCTCACACCCCAGTCCTGAT 2 276 0 CCCTCACCCC 0.970232 -25 ATCTTTTCTGCCCTCTCTTCCCCCAAGAAGA 3 20 0 CCCTCTCTCC 0.679196 -99 GCACTCCCCCTCTTACGCTACCCAACGT 3 101 0 CCCTCTTCGC 0.677424 -18 GTCACGCCGTGCACCGCACCCGTGCTGCAGG 4 56 1 GCACCGCCCC 0.804646 -74 GCATTCGGTACACTCGCCCGC 5 1 0 CACTCGCCGC 0.886685 -109 GCAGCACTGTACCCCTCACCCTGGATAGGAG 5 51 1 ACCCCTCCCC 0.985575 -59 AGCCTCTCCCCGCCGGGGACTA 5 98 0 GCCTCTCCCG 0.817881 -12 TCTGGCGCGGACCTCTCGAGCTACATGATAA 6 59 0 ACCTCTCAGC 0.548969 -116 AAGAAAACGGCACTCTGGCGCGGACCTCTCG 6 72 0 CACTCTGCGC 0.584648 -103 CACAACGTGCGCACCGCACGGCGCGAACGCT 10 18 0 GCACCGCCGG 0.732071 -160 CACTCCGTCAACTCCTCGCGGAAAATCGGTG 10 79 0 ACTCCTCCGG 0.908711 -99 TTTATATTCGCACCCACTCCGTCAACTCCTC 10 93 0 CACCCACCCG 0.894503 -85 GCACGGCAACCCCTCACGTTGTTCAGGAA 10 159 0 ACCCCTCCGT 0.851512 -19 TCTTTCTCCTTCTCTCTGGGTGGTGCAA 16 8 1 CCTTCTCCTG 0.416281 -125 CTCACCCCTGCCCCCAAACGCATTGCACCAC 16 30 0 CCCCCAACGC 0.949589 -103 CCAGAGCACTACTCCTCACCCCTGCCCCCAA 16 44 0 ACTCCTCCCC 0.937524 -89 GCGTAGGGTGCACCCTACCGGCACCCACAGC 16 84 0 CACCCTACGG 0.688906 -49 CCCCAAAAATCCCTCTCTCGCGTAGGGTGCA 16 103 0 CCCTCTCCGC 0.987071 -30 AACACCTCCCCCCAAAAATCCC 16 121 0 ACACCTCCCC 0.929579 -12 AAGAATCCTCCCCCCTTTATCGAC 17 15 0 AATCCTCCCC 0.716843 -14 AGCCCCTCCCTCAAGTTCATTA 18 64 0 GCCCCTCCTC 0.833808 -12 CACTTCTTTCCCCTCACACCCTGATACCCGC 19 27 0 CCCTCACCCC 0.970232 -58 GAAGAACTCACCACCACGCCGCGCCCTTGCA 20 56 1 CCACCACCCG 0.90663 -88 CCTCATGCGCACTTCTCGCGCCAGCGAGCGT 21 39 1 ACTTCTCCGC 0.865871 -137 CGCCTTGCGTACCCCAACCGCGAGCCTTGAC 21 109 1 ACCCCAACGC 0.878816 -67 TCGTGCCGTGCCTCCAGTCCGTTTCTGTCGC 24 59 0 CCTCCAGCCG 0.546757 -234 CAGCGCGCTGCACCCACACGCGACCAACCCA 24 219 0 CACCCACCGC 0.966105 -74 GGGTCTACCGACCTCGCACCGCTTTCGCGCG 25 79 1 ACCTCGCCCG 0.841568 -41 CGCAACTATCACTCCTCTCGCGCGCGAAAGC 25 99 0 ACTCCTCCGC 0.957281 -21 AGGGGGGCATCCCCCACGAGGGTATGGAGAG 26 14 0 CCCCCACAGG 0.756508 -32 CATGACAACACCACCTCCCGTTTGCGTAAGG 27 11 1 CCACCTCCGT 0.742125 -67 CATTCGGCCTCCCCCTGTCCCTCTATCCATC 28 58 0 CCCCCTGCCC 0.950969 -23 CGCAAATATGCCCCCAATCTCCTGCTCCCCT 29 38 0 CCCCCAACTC 0.643295 -50 CCGCGTGCGGAAACCGCCCGCGCCAGAGCAC 30 223 0 AAACCGCCGC 0.668908 -78 GCCTGTCGTGCCTCCGCGTGCGGAAACCGCC 30 236 0 CCTCCGCTGC 0.594208 -65 ******* *** Masking position 5 Map Score: 51.0978 Number of sites scoring better than the average of aligned sites = 2283 Number in coding regions = 1947 Number in noncoding regions = 336 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 3 AGAGTGTGCGAGTACGCGCCCGTTTGGGGTGG 1 154 1 ATACGCCCCG 0.807654 -44 TATGGGGTGCGATGCGCGCGGTGGATACGCTC 2 156 1 GTGCGCCGGT 0.847615 -145 GCGCGCGGTGGATACGCTCCTTCTCGACTGAG 2 169 1 GTACGCCCTT 0.927372 -132 TTTACCGTAGGATGCGCACTCGTGGTCC 4 7 0 GTGCGCCTCG 0.986564 -123 GTCACGCCGTGCACCGCACCCGTGCTGCAGGA 4 56 1 GACCGCCCCG 0.774068 -74 AGCAGCTACAGTTGCGCCCTCTT 6 2 0 GTGCGCCTCT 0.936709 -173 TAGCTCGAGAGGTCCGCGCCAGAGTGCCGTTT 6 67 1 GTCCGCCCAG 0.925979 -108 CGCGCCGTGCGGTGCGCACGTTGTGTAGCTAG 10 24 1 GTGCGCCGTT 0.950494 -154 TTGTTTTTTGGGTGTGCACTTGTTCAAGTTCA 13 21 1 GTGTGCCTTG 0.919828 -34 CGTGTTTGACGTTACGCTCTCGCT 15 72 1 GTACGCCTCG 0.971732 -14 CGTGTGTCTCGACCCGCCCGTGGTCAGTGGGT 18 18 1 GCCCGCCGTG 0.935046 -58 CTCACACCCTGATACCCGCGCGAGGAATATAG 19 14 0 GTACCCCGCG 0.925786 -71 TCACCACCACGCCGCGCCCTTGCATGACCTGG 20 63 1 GCGCGCCTTG 0.967391 -81 CCGCTGGCGTGTTACGCTCGCTGGCGCGAGAA 21 51 0 GTACGCCGCT 0.907236 -125 GATCACAAAAGGTGACCCCGTGCGACAGAAAC 24 38 1 GTGACCCGTG 0.506702 -255 CAACGAACAGGACGTGCACCAGGAACAGCAGC 25 39 0 GCGTGCCCAG 0.730204 -81 CCTCGTGGGGGATGCCCCCCTGTGTACGCTTC 26 24 1 GTGCCCCCTG 0.972062 -22 AAAGTAGTGTGTTGCGCACCCGTGTTTCAAAA 27 42 1 GTGCGCCCCG 0.99324 -36 GGTGAGTCTTGATGTGCGCTTTTTCTTTGGAC 28 18 1 GTGTGCCTTT 0.698023 -63 CTCATTCGGCCTCCCCCTGTCCCTCTATC 28 62 0 GCCTCCCCTG 0.470741 -19 ATTTGCGCGCAGTACGCCCTTGCGTAGGATGC 29 62 1 ATACGCCTTG 0.659102 -26 GGTAGTTTCCGCTACGCTCCTGCCAGCTTGGA 30 66 0 GTACGCCCTG 0.984462 -235 CCGAGCCTGTGCTACGCACGAGTATACCTTGA 30 105 0 GTACGCCGAG 0.923199 -196 TGGGTAAAGCGTCACCCACCTGTACGCATTCA 30 152 0 GCACCCCCTG 0.877183 -149 CCTCTGCGGGGCTGTGCTCTGGCGCGGGCGGT 30 210 1 GTGTGCCTGG 0.769073 -91 * ***** **** Masking position 7 Map Score: 38.1628 Number of sites scoring better than the average of aligned sites = 1175 Number in coding regions = 1089 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 4 CCTTTGAAGGGGCTTCCACCCCAAACGGGCG 1 170 0 GGCTTCCCCC 0.882716 -28 TTCTCGTACGCTTTTCTCCCCGTTGTCAACA 2 57 0 CTTTTCTCCC 0.982112 -244 AGCACGTACAGTTTGCTCCCCCTTCAACCTA 2 98 0 GTTTGCTCCC 0.825293 -203 GCGGTGGATACGCTCCTTCTCGACTGAGGTC 2 173 1 CGCTCCTCTC 0.83131 -128 CCTGTCCGTTTTTCCCCTCACACCCCA 2 284 0 CGTTTTTCCC 0.938804 -17 TATCCAGCATCTTTTCTGCCCTCTCTTCCCC 3 28 0 CTTTTCTCCC 0.982112 -91 CCACCAACGGCTCTTCTACCCACTCAACTCT 7 21 0 CTCTTCTCCC 0.984818 -127 CACCGCTGACGGCTCTTACCCGATTGAGCGA 7 110 1 GGCTCTTCCC 0.871819 -38 CACCAGCGCACTCCCTTCCCCACATGGACTG 8 49 0 CTCCCTTCCC 0.714104 -79 CTTCCGTTTTCTGCCCTGTACTTCCC 9 6 1 GTTTTCTCCC 0.970045 -40 TCCCTTCTTCGTTTTTCACCCCT 9 33 1 GTTTTTCCCC 0.66216 -13 ACGGCGCGAACGCTTCTCCTC 10 1 0 CGCTTCTCTC 0.885662 -177 TGATTTGACACTTCTTTCCCCTCACACCCTG 19 35 0 CTTCTTTCCC 0.768678 -50 CGGCGCGCCAGTTTTCTTCCGGTTTAGTGCC 20 111 1 GTTTTCTCCG 0.899321 -33 CGGGGTGGTCCTTTCTTCCTCATGCGCACTT 21 22 1 CTTTCTTCTC 0.562045 -154 GCCTCCAGTCCGTTTCTGTCGCACGGGGTCA 24 50 0 CGTTTCTTCG 0.5431 -243 TCTTTCTCAAGTCTTCTTCCGGGCGACTTGT 24 89 0 GTCTTCTCCG 0.913448 -204 TTGCTTTTTTCTTTTCTTTCCGCAGGGCACG 30 18 1 CTTTTCTTCC 0.818904 -283 TCAGTAAACTCGCTCCTTCCGAGCCTGTGCT 30 124 0 CGCTCCTCCG 0.915599 -177 ******* *** Masking position 7 Map Score: 17.3213 Number of sites scoring better than the average of aligned sites = 597 Number in coding regions = 529 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 GCACTCCCCCTCTTACGCTACCCAACG 3 102 0 CCCTCTTACG 0.892152 -17 ACCACGAGTGCGCATCCTACGGTAAAAATGC 4 13 1 CGCTCCTACG 0.985631 -117 GAAAAATTGACGTTTCCTGCGTGATCCGCTA 6 119 1 CGTTCCTGCG 0.97971 -56 GAGAAGCGTTCGCGCCGTGCGGTGCGCACGT 10 14 1 CGCCCGTGCG 0.968194 -164 GATATTCCTGCGTATCTTGCGCTGA 15 5 0 CGTTCTTGCG 0.962107 -81 GCCGGTAGGGTGCACCCTACGCGAGAGAGGG 16 93 1 TGCCCCTACG 0.959382 -40 AGACACGTTGCTTTTCCTGCGCGA 20 4 0 CTTTCCTGCG 0.90585 -140 AAAGGACCACCCCGTCTTACGCATT 21 5 0 CCCTCTTACG 0.892152 -171 GCTTTGCTCCTTACGAGATTGTTTG 22 21 0 TGCCCTTACG 0.927672 -15 TGGGGCACGCTGTTTCGTGCGACGGCGTCAA 24 168 1 TGTTCGTGCG 0.776503 -125 CAACACACTACTTTCCTTACGCAAACGGGAG 27 25 0 CTTCCTTACG 0.819899 -53 CACATCAAGACTCACCCTGCATT 28 3 0 CTCCCCTGCA 0.646137 -78 GCCTGCATCCTACGCAAGGGCGTA 29 74 0 TGCTCCTACG 0.94408 -14 GGAGTTTCTACGTGCCCTGCGGAAAGAAAAG 30 28 0 CGTCCCTGCG 0.985351 -273 TCAGTAAACTCGCTCCTTCCGAGCCTGTGCT 30 124 0 CGCCCTTCCG 0.935194 -177 *** ******* Masking position 8 Map Score: 19.3719 Number of sites scoring better than the average of aligned sites = 637 Number in coding regions = 578 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 6 AGAAGGAGCGTATCCACCGCGCGCATCGCACC 2 161 0 TATCCACGCC 0.788189 -140 CGGGCGAGTGTACCGAATGCACTCCCTTTGAG 5 12 1 TACCGAAGCC 0.946937 -98 CATCAAAATTCACCCAAGGAGTGTCAC 6 158 1 CACCCAAGAT 0.741922 -17 ACGGCTCTTCTACCCACTCAACTCTACATTCC 7 14 0 TACCCACCAC 0.77752 -134 TACAGCCGACCACCAACGGCTCTTCTACCCAC 7 29 0 CACCAACGCC 0.911995 -119 GCGCGCTCACCGCTGACGGCTCTTACCCGATT 7 103 1 CGCTGACGCC 0.680141 -45 CTACACAACGTGCGCACCGCACGGCGCGAACG 10 20 0 TGCGCACGCC 0.804963 -158 TTTATATTCGCACCCACTCCGTCAACTCCTCG 10 92 0 CACCCACCCT 0.748885 -86 AACAAGTGCACACCCAAAAAACAACACGGCAA 13 13 0 CACCCAAAAC 0.41494 -42 ACCCTACCGGCACCCACAGCCTGAAAAGACCA 16 72 0 CACCCACGCT 0.953885 -61 GACGTCCCCATACCCACTGACCACGGGCGGGT 18 29 0 TACCCACGAC 0.96038 -47 GCGCCGAGTGTACCAAAGGCACCCAGGTCATG 20 85 0 TACCAAAGCC 0.829589 -59 GCGGTTGGGGTACGCAAGGCGTCCGTGTGTCC 21 98 0 TACGCAAGCT 0.599948 -78 TGACAGAACATACCCAAATACCGCACCATCGG 21 136 1 TACCCAATAC 0.535338 -40 CTATGTGTTACACTGACAGCTCCCACACATCG 23 33 1 CACTGACGCC 0.876114 -60 CACCTTAGAACGCTCAATGCACGAAATAACGC 24 260 0 CGCTCAAGCC 0.733737 -33 GAACAGCAGCTACCCAACGCACGTCCAAACCC 25 17 0 TACCCAAGCC 0.978426 -103 AGGTAGGGTCTACCGACCTCGCACCGCTTTCG 25 74 1 TACCGACTCC 0.76536 -46 GGAGCGAGTTTACTGAATGCGTACAGGTGGGT 30 139 1 TACTGAAGCT 0.415812 -162 GGTGACGCTTTACCCACGGACCTGATTTAGGT 30 168 1 TACCCACGAC 0.96038 -133 ******* ** * Masking position 6 Map Score: 16.2191 Number of sites scoring better than the average of aligned sites = 827 Number in coding regions = 752 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 7 GCGCCAGAGTGCCGTTTTCTTTTCCTGAAAGGGT 6 82 1 GCGTCTTTTC 0.940492 -93 ATACTGCTCCCTTCTTTTCGCTCAATCGG 7 129 0 GCCTCTTTTC 0.991873 -19 CTGATCACCAGCGCACTCCCTTCCCCACATGGAC 8 51 0 GCCTCCTTCC 0.935048 -77 TCCGTTTTCTGCCCTGTACTTCCCTTCTTCGTTT 9 13 1 GCCTCTTCCC 0.940976 -33 GGAGAACCTTGCTCAAAACTTTTCTGAACTTTAA 11 78 0 GCCACTTTTC 0.97137 -27 GAGGAGTAGTGCTCTGGTCTTTTCAGGCTGTGGG 16 58 1 GCCGCTTTTC 0.966121 -75 TTTGAAAAAGACACGTTGCTTTTCCTGCGCGA 20 9 0 ACCTCTTTTC 0.949504 -135 ACTTTAGCCCGCGCGAAACTTTTGACGCCGTCGC 24 186 0 GCCACTTTTG 0.798475 -107 TGGGTGCAGCGCGCTGTACTTGTCGCGCGTTATT 24 234 1 GCCTCTTGTC 0.962198 -59 CGGGTGCGCAACACACTACTTTCCTTACGCAAAC 27 30 0 ACCTCTTTCC 0.921734 -48 CTATCTTTTGCTTTTTTCTTTTCTTTCCGCAGG 30 10 1 GCTTCTTTTC 0.914262 -291 ** * * ****** Masking position 11 Map Score: 10.341 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 128 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 GGTGCGATGCGCGCGGTGGATACGCTCCTTC 2 161 1 GCGCGGTGAT 0.752451 -140 TCTCGACTGAGGTCGCAAGATTTTGTAGGAC 2 190 1 GGTCGCAGAT 0.765525 -111 AGCTGCTTATGCGAGGAAGATCAAATGCTTC 6 27 1 GCGAGGAGAT 0.943308 -148 GCGAAAAGAAGGGAGCAGTAT 7 137 1 GGGAGCATAT 0.853343 -11 GAACACTCATGGGCGGATGATGGA 8 114 1 GGGCGGAGAT 0.974256 -14 GCGCCGTGCGGTGCGCACGTTGTGTAGCTAG 10 25 1 GTGCGCAGTT 0.5986 -153 ACAAAAAACAGGCAGCACTATTTATATTCGC 10 113 0 GGCAGCATAT 0.648923 -65 GGGGGCAGGGGTGAGGAGTAGTGCTCTGGTC 16 46 1 GTGAGGATAG 0.596384 -87 TGTCGATAAAGGGGGGAGGATTCTT 17 14 1 GGGGGGAGAT 0.815481 -15 TGATACCCGCGCGAGGAATATAGAAA 19 6 0 GCGAGGATAT 0.804137 -79 GGCGCGAGAAGTGCGCATGAGGAAGAAAGGA 21 30 0 GTGCGCAGAG 0.950746 -146 TGCCTTTTGTGCGAGCACGATGTGTGGGAGC 23 51 0 GCGAGCAGAT 0.95932 -42 ACGACAAGTCGCCCGGAAGAAGACTTGAGAA 24 86 1 GCCCGGAGAA 0.604353 -207 CACCGCTTTCGCGCGCGAGAGGAGTGATAGT 25 95 1 GCGCGCGGAG 0.862153 -25 GACAGGGGGAGGCCGAATGAG 28 70 1 GGCCGAAGAG 0.568045 -11 TTTTAGGAAGGGGAGCAGGAGATTGGGGGCA 29 30 1 GGGAGCAGAG 0.958507 -58 GGGCATATTTGCGCGCAGTACGCCCTTGCGT 29 56 1 GCGCGCATAC 0.713648 -32 CACGACAGGCGTCCGCACGAGAACAAAATCA 30 257 1 GTCCGCAGAG 0.859785 -44 ******* *** Masking position 5 Map Score: 12.2465 Number of sites scoring better than the average of aligned sites = 896 Number in coding regions = 820 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 9 GCTGCACAATGCAAATTGTCTCTCTACCATGG 1 69 1 GCAAATTTCC 0.862026 -129 GCGCGTACTCGCACACTCTCTGCAAAATATGC 1 141 0 GCACACTTCG 0.682531 -57 CAGGGTCTCTGCAAATAGGTACGTGTGTCAAC 4 102 0 GCAAATAGTC 0.690702 -28 AGTGCATTCGGTACACTCGCCCGC 5 3 0 GTACACTGCC 0.840617 -107 TCACCACGTCGTGAACAGGCGCTGCCGTACAG 7 56 0 GTGAACAGCC 0.804373 -92 GAAGACTGTGGCAAATAAGCGGCAGTCCATGT 8 27 1 GCAAATAGCG 0.91415 -101 GACGAGGAGCGCAAACAGTCTCAGAACACTCA 8 91 1 GCAAACATCC 0.971437 -37 GAGCGTAACGTCAAACACGCACCGTCCTCAAG 15 59 0 TCAAACAGCC 0.886302 -27 TAAACCGGAAGAAAACTGGCGCGCCGAGTGTA 20 105 0 GAAAACTGCC 0.868542 -39 CTACTTTCTGCAAACAATCTCGTAAGGAGCA 22 10 1 GCAAACATCC 0.971437 -26 CGCACAAAAGGCAAACACGCCGTATAACGGTA 23 69 1 GCAAACAGCG 0.973719 -24 CGTACTGCGCGCAAATATGCCCCCAATCTCCT 29 46 0 GCAAATAGCC 0.9708 -42 TACGCATTCAGTAAACTCGCTCCTTCCGAGCC 30 130 0 GTAAACTGCC 0.943484 -171 ******* ** * Masking position 5 Map Score: 9.37057 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 317 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 10 TCTCTGAGAAAAAAGAGACCACAGCTGCACA 1 46 1 AAAGAGACCA 0.900752 -152 CAGTCCTGATACATCAAACCAGCACGACACA 2 255 0 ACACAAACCA 0.784846 -46 GCGCTGCCGTACAGCCGACCACCAACGGCTC 7 39 0 ACACCGACCA 0.979552 -109 TGGTGATCAGACAACAGACGAGGAGCGCAAA 8 75 1 ACACAGACGA 0.950436 -53 TTGTTCAGGAACATGCGGCGAACTACACAAA 10 139 0 ACAGCGGCGA 0.877222 -39 CACCTTCAGTACATGCGACGCGGTAAAG 24 8 0 ACAGCGACGC 0.877222 -285 CGCTGCACCCACACGCGACCAACCCACTTTA 24 214 0 ACAGCGACCA 0.983427 -79 CTTCCTAAAAACAGGAGAGCACTACACCC 29 9 0 ACAGAGAGCA 0.870077 -79 CACGAGAACAAAATCAGACCAACATAGGAGA 30 272 1 AAACAGACCA 0.87991 -29 *** ******* Masking position 3 Map Score: 3.20478 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 35 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 TGGGGTGCGATGCGCGCGGTGGATACGCTCC 2 158 1 TGCGCGGGTG 0.878247 -143 GAGCGGAAACAGAATGACGTGTTCTATCTGT 3 60 1 AGAATGCGTG 0.854646 -59 ACGGGTGCGGTGCACGGCGTGACTTGTACAC 4 48 0 TGCACGCGTG 0.969075 -82 TTCACTAATCACCACGTCGTGAACAGGCGCT 7 65 0 ACCACGCGTG 0.899327 -83 TGGTGATTAGTGAAGGAGGTGGCGCGCTCAC 7 82 1 TGAAGGGGTG 0.711351 -66 TAAGCGGCAGTCCATGTGGGGAAGGGAGTGC 8 42 1 TCCATGGGGG 0.824421 -86 ATTGCATGAGCTGAGTATGTGAT 11 3 1 TGCATGGCTG 0.964351 -102 TCAAGTGTTCAGAATGTGCTGAACACCCGAT 15 33 0 AGAATGGCTG 0.875197 -53 ATACCCACTGACCACGGGCGGGTCGAGACAC 18 21 0 ACCACGGCGG 0.830596 -55 GTGTCAAATCAGAATGCGCTGGTGAACATGA 19 55 1 AGAATGGCTG 0.875197 -30 GCCGCGCCCTTGCATGACCTGGGTGCCTTTG 20 73 1 TGCATGCCTG 0.94488 -71 TGTAACACATAGCATGGGGGGCGTGTAGGAA 23 14 0 AGCATGGGGG 0.942762 -79 CTTTTGTGCGAGCACGATGTGTGGGAGCTGT 23 48 0 AGCACGTGTG 0.828994 -45 CTGTTCCTGGTGCACGTCCTGTTCGTTGAAT 25 43 1 TGCACGCCTG 0.959488 -77 ****** **** Masking position 6 Map Score: 11.9866 Number of sites scoring better than the average of aligned sites = 686 Number in coding regions = 625 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 12 TAGGTACGTGTGTCAACACTACGGTATGCG 4 89 0 TGTCAACACT 0.801717 -41 TCGTCTGTTGTCTGATCACCAGCGCACTCC 8 66 0 TCTGATCACC 0.938048 -62 GCAAACAGTCTCAGAACACTCATGGGCGGA 8 101 1 TCAGAACACT 0.838614 -27 AGAGAGCTCGCGTGAACACCGATTTTCCGC 10 63 1 CGTGAACACC 0.954398 -115 GCCGCATGTTCCTGAACAACGTGAGGGGTT 10 151 1 CCTGAACAAC 0.735819 -27 TTCAGAATGTGCTGAACACCCGATATTCCT 15 27 0 GCTGAACACC 0.936327 -59 TTCAGCACATTCTGAACACTTGAGGACGGT 15 41 1 TCTGAACACT 0.942659 -45 GGTCACCTTTTGTGATCACCTTCAGTACAT 24 25 0 TGTGATCACC 0.837919 -268 CATGACAACACCACCTCCCGTT 27 3 1 TGACAACACC 0.795866 -75 ********** Masking position 5 Map Score: 2.78444 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 86 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 13 GCAAACTGTACGTGCTCATGTAATCTTTGT 2 113 1 CGTGCTCATG 0.894798 -188 AAAATGCATGCGTGTACAAGTCACGCCGTG 4 37 1 CGTGTACAAG 0.683747 -93 GTGCTGCTGTCTTGCTCAAAGGGAGTGCAT 5 28 0 CTTGCTCAAA 0.936599 -82 GCAGGAGAACCTTGCTCAAAACTTTTCTGA 11 85 0 CTTGCTCAAA 0.936599 -20 TGGGTGTGCACTTGTTCAAGTTCAGAGGTG 13 29 1 CTTGTTCAAG 0.730145 -26 AAACACGCACCGTCCTCAAGTGTTCAGAAT 15 49 0 CGTCCTCAAG 0.943958 -37 AGCCCCTCCCTCAAGTTCATTACTG 18 61 0 CTCCCTCAAG 0.876499 -15 AGCAACGTGTCTTTTTCAAAATAAATAAAA 20 23 1 CTTTTTCAAA 0.392876 -121 GTGGTCCTTTCTTCCTCATGCGCACTTCTC 21 26 1 CTTCCTCATG 0.821051 -150 ACACATCGTGCTCGCACAAAAGGCAAACAC 23 57 1 CTCGCACAAA 0.647116 -36 CGTGTCGCGTCTTTCTCAAGTCTTCTTCCG 24 99 0 CTTTCTCAAG 0.900443 -194 ACGAACAGGACGTGCACCAGGAACAGCAGC 25 39 0 CGTGCACCAG 0.698375 -81 ********** Masking position 7 Map Score: 6.96326 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 237 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 14 TACTCGCACACTCTCTGCAAAATATGCAAT 1 138 0 CTCTCTGCAA 0.787929 -60 ACGTCATTCTGTTTCCGCTCATATCCAGCA 3 50 0 GTTTCCGCTC 0.954496 -69 GGGGACCAGGGTCTCTGCAAATAGGTACGT 4 110 0 GTCTCTGCAA 0.893325 -20 TTCTGAGACTGTTTGCGCTCCTCGTCTGTT 8 87 0 GTTTGCGCTC 0.730904 -41 CGCACCATCGGCCTCCGCAATGAGAAGGA 21 157 1 GCCTCCGCAA 0.927334 -19 CTACTTTCTGCAAACAATCTCGT 22 4 1 CTTTCTGCAA 0.818327 -32 TTTTTCTTTTCTTTCCGCAGGGCACGTAGA 30 23 1 CTTTCCGCAG 0.853742 -278 CATTTGGGTAGTTTCCGCTACGCTCCTGCC 30 74 0 GTTTCCGCTA 0.942172 -227 GGCGCGGGCGGTTTCCGCACGCGGAGGCAC 30 230 1 GTTTCCGCAC 0.978869 -71 GGCACGACAGGCGTCCGCACGAGAACAAAA 30 255 1 GCGTCCGCAC 0.859727 -46 ********** Masking position 4 Map Score: 4.68078 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 116 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 15 TTTTTAGGATGTTGAACGGGAATTTCTTCG 1 105 0 GTTGAACGGG 0.943123 -93 GATGGCTCCTTTGAAGGGGCTTCCACCCC 1 179 0 TTTGAAGGGG 0.960687 -19 GCCCCGTTAGGTTGAAGGGGGAGCAAACTG 2 91 1 GTTGAAGGGG 0.986361 -210 GTTTGTCGATAAAGGGGGGAGGATTCT 17 8 1 GATAAAGGGG 0.917952 -21 TAATGAACTTGAGGGAGGGGCT 18 64 1 GAGGGAGGGG 0.956375 -12 CTCCTGTTTTTAGGAAGGGGAGCAGGAGAT 29 23 1 TAGGAAGGGG 0.952961 -65 ********** Masking position 6 Map Score: 2.13956 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 83 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678