AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02010_tpal_reg_100.orf -o02010_tpal_100.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 TP0298 132 exported protein (tpn38b) #9 TP0319 28 membrane lipoprotein (tmpC) #10 TP0321 75 ribose/galactose ABC transporter, ATP-binding protein (rbsA-2) #11 TP0545 84 methylgalactoside ABC transporter, periplasmic galactose-binding protein (mglB-1) #12 TP0547 143 penicillin tolerance protein (lytB) #13 TP0652 175 spermidine/putrescine ABC transporter, ATP-binding protein (potA) #14 TP0655 35 spermidine/putrescine ABC transporter, periplasmic binding protein (potD) #15 TP0684 292 methylgalactoside ABC transporter, periplasmic galactose-binding protein (mglB-2) #16 TP0685 119 methylgalactoside ABC transporter, ATP binding protein (mglA) #17 TP0802 45 T. pallidum predicted coding region TP0802 #18 TP0804 77 sugar ABC transporter, ATP-binding protein (ugpC) #19 TP0821 80 lipoprotein (tpn32) #20 TP0822 87 conserved hypothetical protein #21 TP0823 300 desulfoferrodoxin (rbo) Motif number 1 AAACGCGTGTGGGTGCGGTGTATGTCTTTG 2 29 1 GGGTGCGGTG 0.964856 -272 GGGGTGCGATGCGCGCGGTGGATACGCTCC 2 159 1 GCGCGCGGTG 0.965844 -142 CTGCGTAGGGGCGTGCGTCGATTGGTGTGG 2 220 1 GCGTGCGTCG 0.902541 -81 ATCAGGACTGGGGTGTGAGGGGAAAAACGG 2 276 1 GGGTGTGAGG 0.9587 -25 ACGTTGGGTAGCGTAAGAGGGGGAGTGC 3 101 1 GCGTAAGAGG 0.839429 -18 GCGGTGCACGGCGTGACTTGTACACGCATG 4 43 0 GCGTGACTTG 0.600489 -87 CCTGCAGCACGGGTGCGGTGCACGGCGTGA 4 57 0 GGGTGCGGTG 0.964856 -73 GGGGACCAGGGTCTCTGCAA 4 120 0 GGGGACCAGG 0.670718 -10 GCGGGCGAGTGTACCGAATG 5 1 1 GCGGGCGAGT 0.843465 -109 CTCCTATCCAGGGTGAGGGGTACAGTGCTG 5 52 0 GGGTGAGGGG 0.989007 -58 GTCCCCGGCGGGGAGAGGCT 5 100 1 GGGAGAGGCT 0.531834 -10 CATCAAAGTAGCGGATCACGCAGGAAACGT 6 128 0 GCGGATCACG 0.488232 -47 GATTAGTGAAGGAGGTGGCGCGCTCACCGC 7 86 1 GGAGGTGGCG 0.741384 -62 GTGGTGCAATGCGTTTGGGGGCAGGGGTGA 8 30 1 GCGTTTGGGG 0.734098 -103 TTGGGGGCAGGGGTGAGGAGTAGTGCTCTG 8 44 1 GGGTGAGGAG 0.967599 -89 TTCAGGCTGTGGGTGCCGGTAGGGTGCACC 8 79 1 GGGTGCCGGT 0.84659 -54 TGCACCCTACGCGAGAGAGGGATTTTTGGG 8 103 1 GCGAGAGAGG 0.789348 -30 GGGATTTTTGGGGGGAGGTGTT 8 121 1 GGGGGAGGTG 0.964856 -12 GTCGATAAAGGGGGGAGGATTCTT 9 15 1 GGGGGAGGAT 0.832987 -14 AGTGGGGCGTGTGTCTCGACCCGC 10 5 1 GGGCGTGTGT 0.630929 -71 CTGACCACGGGCGGGTCGAGACACACGCCC 10 15 0 GCGGGTCGAG 0.893297 -61 CGTGGTCAGTGGGTATGGGGACGTCCAGTA 10 36 1 GGGTATGGGG 0.917538 -40 TAATGAACTTGAGGGAGGGGCT 10 64 1 GAGGGAGGGG 0.770262 -12 GCGGGTATCAGGGTGTGAGGGGAAAGAAGT 11 27 1 GGGTGTGAGG 0.9587 -58 GGTCATGCAAGGGCGCGGCGTGGTGGTGAG 12 62 0 GGGCGCGGCG 0.984159 -82 AAGAAAACTGGCGCGCCGAGTGTACCAAAG 12 99 0 GCGCGCCGAG 0.920859 -45 AATGCGTAAGACGGGGTGGTCCT 13 4 1 GCGTAAGACG 0.772885 -172 CGCGAGAAGTGCGCATGAGGAAGAAAGGAC 13 29 0 GCGCATGAGG 0.79961 -147 ACGCTCGCTGGCGCGAGAAGTGCGCATGAG 13 40 0 GCGCGAGAAG 0.914599 -136 GCGCCAGCGAGCGTAACACGCCAGCGGTAA 13 56 1 GCGTAACACG 0.555531 -120 GTCAAGGCTCGCGGTTGGGGTACGCAAGGC 13 110 0 GCGGTTGGGG 0.739824 -66 GTCTTCTTCCGGGCGACTTGTCGTGCCGTG 15 80 0 GGGCGACTTG 0.607555 -213 ACTTCTTTGCGCGTGTCGCGTCTTTCTCAA 15 110 0 GCGTGTCGCG 0.940967 -183 TGGGTTGGTCGCGTGTGGGTGCAGCGCGCT 15 219 1 GCGTGTGGGT 0.91533 -74 ACGAAATAACGCGCGACAAGTACAGCGCGC 15 242 0 GCGCGACAAG 0.797299 -51 CCGCTTTCGCGCGCGAGAGGAGTGATAGTT 16 97 1 GCGCGAGAGG 0.969936 -23 TCCCCCACGAGGGTATGGAGAGGAA 17 6 0 GGGTATGGAG 0.786938 -40 TACGCAAACGGGAGGTGGTGTTGTCATG 18 9 0 GGAGGTGGTG 0.566127 -69 AATGCAGGGTGAGTCTTGATGTGCGC 19 7 1 GGGTGAGTCT 0.593155 -74 TAGAGGGACAGGGGGAGGCCGAATGAG 19 64 1 GGGGGAGGCC 0.671027 -17 TCTTTCCGCAGGGCACGTAGAAACTCCTCA 21 32 1 GGGCACGTAG 0.448052 -269 GCGTACAGGTGGGTGACGCTTTACCCACGG 21 157 1 GGGTGACGCT 0.77717 -144 GTGCTCTGGCGCGGGCGGTTTCCGCACGCG 21 223 1 GCGGGCGGTT 0.820959 -78 GGCGGTTTCCGCACGCGGAGGCACGACAGG 21 236 1 GCACGCGGAG 0.670158 -65 GCACGCGGAGGCACGACAGGCGTCCGCACG 21 246 1 GCACGACAGG 0.431797 -55 ********** Masking position 1 Map Score: 51.6547 Number of sites scoring better than the average of aligned sites = 4457 Number in coding regions = 3963 Number in noncoding regions = 494 Number of orfs with sites within 600 bp upstream = 247 Fraction of orfs with sites within 600 bp upstream = 0.0396723 Motif number 2 ACAAAGACATACACCGCACCCACACGCGTT 2 30 0 ACACCGCACC 0.922701 -271 TCCACCGCGCGCATCGCACCCCATATCGAT 2 151 0 GCATCGCACC 0.76066 -150 ACCAATCGACGCACGCCCCTACGCAGTCCT 2 216 0 GCACGCCCCT 0.747024 -85 ACGACACATAGCACCACACCAATCGACGCA 2 233 0 GCACCACACC 0.990146 -68 CATCAAACCAGCACGACACATAGCACCACA 2 245 0 GCACGACACA 0.967359 -56 CCAACGTAACGCGCTCCACAGATAGAACAC 3 78 0 GCGCTCCACA 0.925166 -41 TCCCCCTCTTACGCTACCCAACGTAACGCG 3 95 0 ACGCTACCCA 0.560071 -24 GCACTCCCCCTCTTACGCTA 3 109 0 GCACTCCCCC 0.977943 -10 GTCACGCCGTGCACCGCACCCGTGCTGCAG 4 56 1 GCACCGCACC 0.989664 -74 CAAGACAGCAGCACTGTACCCCTCACCCTG 5 44 1 GCACTGTACC 0.841992 -66 TCAGCGGTGAGCGCGCCACCTCCTTCACTA 7 89 0 GCGCGCCACC 0.981418 -59 CAAACGCATTGCACCACCCAGAGAGAAGGA 8 17 0 GCACCACCCA 0.952572 -116 AAAGACCAGAGCACTACTCCTCACCCCTGC 8 50 0 GCACTACTCC 0.857848 -83 CGCGTAGGGTGCACCCTACCGGCACCCACA 8 86 0 GCACCCTACC 0.852522 -47 GGGTCGAGACACACGCCCCACT 10 3 0 ACACGCCCCA 0.672581 -73 ACTCACTGGGGCACTAAACCGGAAGAAAAC 12 121 0 GCACTAAACC 0.889043 -23 GAGGAAGAAAGGACCACCCCGTCTTACGCA 13 13 0 GGACCACCCC 0.770095 -163 CGGACTGGAGGCACGGCACGACAAGTCGCC 15 69 1 GCACGGCACG 0.932455 -224 CTTGAGAAAGACGCGACACGCGCAAAGAAG 15 109 1 ACGCGACACG 0.536399 -184 TGACGCCGTCGCACGAAACAGCGTGCCCCA 15 168 0 GCACGAAACA 0.748609 -125 CAAGTACAGCGCGCTGCACCCACACGCGAC 15 226 0 GCGCTGCACC 0.979874 -67 AAGCGCTAAACCACCTTAGAAC 15 281 0 GCGCTAAACC 0.836961 -12 AAACACGGGTGCGCAACACACTACTTTCCT 18 39 0 GCGCAACACA 0.788981 -39 AAACAGGAGAGCACTACACCC 20 2 0 GCACTACACC 0.987615 -86 CCGCGCCAGAGCACAGCCCCGCAGAGGCGC 21 207 0 GCACAGCCCC 0.927421 -94 ********** Masking position 9 Map Score: 37.8588 Number of sites scoring better than the average of aligned sites = 1143 Number in coding regions = 1032 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 3 TCCACCCCAAACGGGCGCGTACTCGCACACT 1 156 0 ACGGGGCGTA 0.983906 -42 CGTTAGGTTGAAGGGGGAGCAAACTGTACGT 2 95 1 AAGGGGAGCA 0.953913 -206 CCTCAGTCGAGAAGGAGCGTATCCACCGCGC 2 171 0 GAAGGGCGTA 0.937976 -130 TTCTTGGGGGAAGAGAGGGCAGAAAAGATGC 3 22 1 AAGAGGGGCA 0.911425 -97 GGACCACGAGTGCGCATCCTACGGTA 4 6 1 ACGAGGCGCA 0.986802 -124 CACCCGTGCTGCAGGATCGCATACCGTAGTG 4 72 1 GCAGGTCGCA 0.83825 -58 GCGGGCGAGTGTACCGAATGC 5 1 1 GCGGGGAGTG 0.814224 -109 GTCTTGCTCAAAGGGAGTGCATTCGGTACAC 5 19 0 AAGGGGTGCA 0.836236 -91 AAGAGGGCGCAACTGTAGCTG 6 1 1 AAGAGGCGCA 0.964888 -174 TTGAGCGAAAAGAAGGGAGCAGTAT 7 133 1 AGAAGGAGCA 0.762322 -15 CCCACTGACCACGGGCGGGTCGAGACACACG 10 18 0 ACGGGGGGTC 0.719705 -58 CCCAGGTCATGCAAGGGCGCGGCGTGGTGGT 12 65 0 GCAAGGCGCG 0.938006 -79 CGCTGGCGCGAGAAGTGCGCATGAGGAAGAA 13 34 0 AGAAGGCGCA 0.91686 -142 GAAGCGTACACAGGGGGGCATCCCCCACGA 17 26 0 ACAGGGGGCA 0.983478 -20 CTTTTGAAACACGGGTGCGCAACACACTACT 18 44 0 ACGGGGCGCA 0.994862 -34 TGTCCAAAGAAAAAGCGCACATCAAGACTCA 19 20 0 AAAAGGCACA 0.472905 -61 CTTCCTAAAAACAGGAGAGCACTACACCC 20 9 0 ACAGGGAGCA 0.978829 -79 CTGTTTTTAGGAAGGGGAGCAGGAGATTGGG 20 26 1 GAAGGGAGCA 0.933023 -62 TGCATCCTACGCAAGGGCGTACTGCGCGCAA 20 64 0 GCAAGGCGTA 0.940787 -24 ATCCAAGCTGGCAGGAGCGTAGCGGAAACTA 21 65 1 GCAGGGCGTA 0.976273 -236 CTGAATGCGTACAGGTGGGTGACGCTTTACC 21 151 1 ACAGGGGGTG 0.849644 -150 ***** ***** Masking position 5 Map Score: 29.3645 Number of sites scoring better than the average of aligned sites = 1215 Number in coding regions = 1134 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 4 ACACGCGTTTGCATTCTGGCACAGGGAA 2 9 0 GCATTCTGGC 0.527825 -292 GAATGCAAACGCGTGTGGGTGCGGTGTATG 2 23 1 GCGTGTGGGT 0.703987 -278 GGTGCGATGCGCGCGGTGGATACGCTCCTT 2 161 1 GCGCGGTGGA 0.951991 -140 TTGTAGGACTGCGTAGGGGCGTGCGTCGAT 2 212 1 GCGTAGGGGC 0.574083 -89 GTGCTATGTGTCGTGCTGGTTTGATGTATC 2 249 1 TCGTGCTGGT 0.770838 -52 AGTCTCTTCTTCTTGGGGGAAGAGAGGGCA 3 13 1 TCTTGGGGGA 0.582067 -106 CGATCCTGCAGCACGGGTGCGGTGCACGGC 4 61 0 GCACGGGTGC 0.640028 -69 CAAAGGGAGTGCATTCGGTACACTCGCCCG 5 12 0 GCATTCGGTA 0.506063 -98 AAAGAAAACGGCACTCTGGCGCGGACCTCT 6 74 0 GCACTCTGGC 0.713671 -101 AAGTAGCGGATCACGCAGGAAACGTCAATT 6 123 0 TCACGCAGGA 0.681495 -52 TCTATATTCCTCGCGCGGGTATCAGGGTGT 11 13 1 TCGCGCGGGT 0.965241 -72 AAATCAGAATGCGCTGGTGAACATGAGGAG 11 60 1 GCGCTGGTGA 0.518511 -25 TCGCGCAGGAAAAGCAACGT 12 1 1 TCGCGCAGGA 0.874637 -143 CAAGGGCGCGGCGTGGTGGTGAGTTCTTCT 12 55 0 GCGTGGTGGT 0.819594 -89 ATCACTCACTGGGGCACTAAACCGG 12 129 0 TCACTGGGGC 0.662234 -15 GGCGTGTTACGCTCGCTGGCGCGAGAAGTG 13 48 0 GCTCGCTGGC 0.820913 -128 TTCTGTCAAGGCTCGCGGTTGGGGTACGCA 13 114 0 GCTCGCGGTT 0.682292 -62 CGTTTCTGTCGCACGGGGTCACCTTTTGTG 15 41 0 GCACGGGGTC 0.879441 -252 TTACAATGGGGCACGCTGTTTCGTGCGACG 15 162 1 GCACGCTGTT 0.615854 -131 GTCAAAAGTTTCGCGCGGGCTAAAGTGGGT 15 194 1 TCGCGCGGGC 0.931213 -99 TGGGTTGGTCGCGTGTGGGTGCAGCGCGCT 15 219 1 GCGTGTGGGT 0.703987 -74 TGTGGGTGCAGCGCGCTGTACTTGTCGCGC 15 232 1 GCGCGCTGTA 0.913452 -61 GCTGTACTTGTCGCGCGTTATTTCGTGCAT 15 246 1 TCGCGCGTTA 0.53603 -47 GTTTGGACGTGCGTTGGGTAGCTGCTGTTC 16 19 1 GCGTTGGGTA 0.646598 -101 CGCACCGCTTTCGCGCGCGAGAGGAGTGAT 16 93 1 TCGCGCGCGA 0.457281 -27 CTCCATACCCTCGTGGGGGATGCCCCCCTG 17 16 1 TCGTGGGGGA 0.929424 -30 GGGCATATTTGCGCGCAGTACGCCCTTGCG 20 56 1 GCGCGCAGTA 0.845472 -32 CCACCTGTACGCATTCAGTAAACTCGCTCC 21 139 0 GCATTCAGTA 0.123603 -162 GGCTGTGCTCTGGCGCGGGCGGTTTCCGCA 21 219 1 TGGCGCGGGC 0.716582 -82 TCGTGCCTCCGCGTGCGGAAACCGCCCGCG 21 232 0 GCGTGCGGAA 0.815651 -69 GATTTTGTTCTCGTGCGGACGCCTGTCGTG 21 257 0 TCGTGCGGAC 0.668985 -44 ********** Masking position 2 Map Score: 25.8661 Number of sites scoring better than the average of aligned sites = 4322 Number in coding regions = 4002 Number in noncoding regions = 320 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 5 AGAGACAGTAGTGTTGCATTCATAAAAATAGAG 1 18 0 GTGTTGTTAT 0.690288 -180 TTGTGCAGCTGTGGTCTCTTTTTTCTCAGAGAC 1 45 0 GTGGTCTTTT 0.964019 -153 CAAACTGTACGTGCTCATGTAATCTTTGTTTTC 2 114 1 GTGCTCGTAT 0.952164 -187 GCTATGTGTCGTGCTGGTTTGATGTATCAGGAC 2 251 1 GTGCTGTTAT 0.952288 -50 GAGGGGTACAGTGCTGCTGTCTTGCTCAAAGGG 5 35 0 GTGCTGGTTT 0.98037 -75 CCGCGCCAGAGTGCCGTTTTCTTTTCCTGAAAG 6 80 1 GTGCCGTTTT 0.871795 -95 ATACTGCTCCCTTCTTTTCGCTCAAT 7 132 0 CTGCTCTTTT 0.797866 -16 GTGAGGAGTAGTGCTCTGGTCTTTTCAGGCTGT 8 56 1 GTGCTCGTTT 0.977271 -77 GCGCGGCGTGGTGGTGAGTTCTTCTTCTTTTAT 12 47 0 GTGGTGTTTT 0.968867 -97 GTAAGACGGGGTGGTCCTTTCTTCCTCATGCGC 13 16 1 GTGGTCTTTT 0.964019 -160 GCGGAGGCCGATGGTGCGGTATTTGGGTATGTT 13 142 0 ATGGTGGTTT 0.72119 -34 CAAACGGGAGGTGGTGTTGTCATG 18 2 0 GTGGTGGTAT 0.943468 -76 GGGTGTAGTGCTCTCCTGTTTTTAGGAAGG 20 8 1 GTGCTCCTTT 0.907906 -80 ****** ** ** Masking position 10 Map Score: 13.5588 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 71 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 AGTACGCGCCCGTTTGGGGTGGAAGCCCCTTC 1 164 1 CGTTGGGGGG 0.990606 -34 AATGCAAACGCGTGTGGGTGCGGTGTATGTCT 2 24 1 CGTTGGGTCG 0.964603 -277 CGCTCCTTCTCGACTGAGGTCGCAAGATTTTG 2 183 1 CGATGAGGCG 0.957906 -118 GGGCGTGCGTCGATTGGTGTGGTGCTATGTGT 2 228 1 CGATGGTGGG 0.692064 -73 TCAGGACTGGGGTGTGAGGGGAAAAACGGACA 2 277 1 GGTTGAGGGA 0.926128 -24 CGTTGGGTAGCGTAAGAGGGGGAGTGC 3 102 1 CGTAGAGGGG 0.795015 -17 TGGTGCAATGCGTTTGGGGGCAGGGGTGAGGA 8 31 1 CGTTGGGGCA 0.98821 -102 GTGGTCAGTGGGTATGGGGACGTCCAGTAATG 10 37 1 GGTTGGGGCG 0.993335 -39 CGGGTATCAGGGTGTGAGGGGAAAGAAGTGTC 11 28 1 GGTTGAGGGA 0.926128 -57 CAAGGCTCGCGGTTGGGGTACGCAAGGCGTCC 13 106 0 GGTGGGGTCG 0.770803 -70 CCGTTTCTGTCGCACGGGGTCACCTTTTGTGA 15 40 0 CGCCGGGGCA 0.848227 -253 CGACAGAAACGGACTGGAGGCACGGCACGACA 15 60 1 GGATGGAGCA 0.711351 -233 CACGCTGTTTCGTGCGACGGCGTCAAAAGTTT 15 173 1 CGTCGACGCG 0.715348 -120 GGGTTGGTCGCGTGTGGGTGCAGCGCGCTGTA 15 220 1 CGTTGGGTCA 0.922975 -73 GCGCGAAAGCGGTGCGAGGTCGGTAGACCCTA 16 77 0 GGTCGAGGCG 0.956127 -43 CCCCCACGAGGGTATGGAGAGGAA 17 3 0 GGTTGGAGGG 0.898535 -43 GGGGAGCAGGAGATTGGGGGCATATTTGCGCG 20 39 1 AGATGGGGCA 0.719403 -49 *** ***** ** Masking position 6 Map Score: 17.4217 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 337 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 7 CCTTTGAAGGGGCTTCCACCCCAAACGGGCG 1 170 0 GGCTTCCCCC 0.917339 -28 TTCTCGTACGCTTTTCTCCCCGTTGTCAACA 2 57 0 CTTTTCTCCC 0.969736 -244 AGCACGTACAGTTTGCTCCCCCTTCAACCTA 2 98 0 GTTTGCTCCC 0.528498 -203 CGAGAAGGAGCGTATCCACCGCGCGCATCGC 2 164 0 CGTATCCCCG 0.638192 -137 CCTGTCCGTTTTTCCCCTCACACCCCA 2 284 0 CGTTTTTCCC 0.616753 -17 TTTCTGCCCTCTCTTCCCCCAAGAAGAAGAG 3 16 0 CTCTTCCCCA 0.844901 -103 TATCCAGCATCTTTTCTGCCCTCTCTTCCCC 3 28 0 CTTTTCTCCC 0.969736 -91 AGCCTCTCCCCGCCGGGGACTATA 5 96 0 CTCTCCCGCC 0.805138 -14 GAAAAATTGACGTTTCCTGCGTGATCCGCTA 6 119 1 CGTTTCCGCG 0.894449 -56 CCACCAACGGCTCTTCTACCCACTCAACTCT 7 21 0 CTCTTCTCCC 0.978992 -127 TCTGATTTGACACTTCTTTCCCCTCACACCC 11 37 0 CACTTCTTCC 0.634721 -48 AGACACGTTGCTTTTCCTGCGCGA 12 4 0 CTTTTCCGCG 0.881625 -140 CGGCGCGCCAGTTTTCTTCCGGTTTAGTGCC 12 111 1 GTTTTCTCCG 0.887346 -33 TCCTCATGCGCACTTCTCGCGCCAGCGAGCG 13 38 1 CACTTCTGCG 0.761809 -138 GCCTCCAGTCCGTTTCTGTCGCACGGGGTCA 15 50 0 CGTTTCTTCG 0.84393 -243 TCTTTCTCAAGTCTTCTTCCGGGCGACTTGT 15 89 0 GTCTTCTCCG 0.919714 -204 TTGCTTTTTTCTTTTCTTTCCGCAGGGCACG 21 18 1 CTTTTCTTCC 0.842087 -283 GTTTCCGCTACGCTCCTGCCAGCTTGGATTC 21 63 0 CGCTCCTCCA 0.735241 -238 TCAGTAAACTCGCTCCTTCCGAGCCTGTGCT 21 124 0 CGCTCCTCCG 0.941398 -177 ******* *** Masking position 10 Map Score: 17.5732 Number of sites scoring better than the average of aligned sites = 656 Number in coding regions = 591 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 8 CACTCCCCCTCTTACGCTACCCAACGTAACGCGC 3 94 0 CTATACCCAA 0.946037 -25 TCACCGCTGACGGCTCTTACCCGATTGAGCGAAA 7 109 1 CGCTACCCGA 0.980523 -39 CACCCACAGCCTGAAAAGACCAGAGCACTACTCC 8 60 0 CGAGACCAGA 0.865616 -73 AACTGGCGCGCCGAGTGTACCAAAGGCACCCAGG 12 90 0 CGATACCAAA 0.977183 -54 CGAGCCTTGACAGAACATACCCAAATACCGCACC 13 129 1 CGATACCCAA 0.993671 -47 GCACCAGGAACAGCAGCTACCCAACGCACGTCCA 16 22 0 CGCTACCCAA 0.988877 -98 AGGAGCGTAGCGGAAACTACCCAAATGGTCAAGG 21 77 1 CGATACCCAA 0.993671 -224 CGCAGAGGCGCTGATTCTACCTAAATCAGGTCCG 21 184 0 CGATACCTAA 0.960454 -117 * ** ******* Masking position 9 Map Score: 8.20699 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 7 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 AGAGACAATTTGCATTGTGCAGCTGTGGTCT 1 61 0 TGCATTGGCA 0.720744 -137 TTGCATATTTTGCAGAGAGTGTGCGAGTACG 1 139 1 TGCAGAGGTG 0.847098 -59 CGCGTGTGGGTGCGGTGTATGTCTTTGTTGA 2 32 1 TGCGGTGATG 0.932731 -269 CGATATGGGGTGCGATGCGCGCGGTGGATAC 2 153 1 TGCGATGGCG 0.935055 -148 GTGTTCTATCTGTGGAGCGCGTTACGTTGGG 3 78 1 TGTGGAGGCG 0.925129 -41 GCAGCACGGGTGCGGTGCACGGCGTGACTTG 4 53 0 TGCGGTGACG 0.97936 -77 AAGAGCCGTCAGCGGTGAGCGCGCCACCTCC 7 96 0 AGCGGTGGCG 0.960152 -52 ATCCCTCTCTCGCGTAGGGTGCACCCTACCG 8 95 0 CGCGTAGGTG 0.765787 -38 AATGCGTAAGACGGGGTGGTCCT 13 3 1 TGCGTAAACG 0.711322 -173 TCCTTCTCATTGCGGAGGCCGATGGTGCGGT 13 155 0 TGCGGAGCCG 0.966256 -21 CGTTATTTCGTGCATTGAGCGTTCTAAGGTG 15 261 1 TGCATTGGCG 0.929833 -32 GGTTTGGACGTGCGTTGGGTAGCTGCTGTTC 16 18 1 TGCGTTGGTA 0.843916 -102 CGCGCGCGAAAGCGGTGCGAGGTCGGTAGAC 16 81 0 AGCGGTGGAG 0.633558 -39 AGGAAAGTAGTGTGTTGCGCACCCGTGTTTC 18 39 1 TGTGTTGGCA 0.622924 -39 AGTACGCCCTTGCGTAGGATGCAGGC 20 72 1 TGCGTAGATG 0.885014 -16 GGTATACTCGTGCGTAGCACAGGCTCGGAAG 21 109 1 TGCGTAGACA 0.836266 -192 TGCCTCCGCGTGCGGAAACCGCCCGCGCCAG 21 228 0 TGCGGAACCG 0.72744 -73 ******* *** Masking position 2 Map Score: 16.2191 Number of sites scoring better than the average of aligned sites = 1300 Number in coding regions = 1180 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 10 GCATTGTGCAGCTGTGGTCTCTTTTTTCTC 1 51 0 GCTGTGGTCT 0.898844 -147 ATTCTCGTACGCTTTTCTCCCCGTTGTCAA 2 59 0 GCTTTTCTCC 0.797102 -242 TACAAGTCACGCCGTGCACCGCACCCGTGC 4 51 1 GCCGTGCACC 0.918085 -79 GGGGACTATAGCATAGCTCTAGAGCTCCTA 5 76 0 GCATAGCTCT 0.830704 -34 GCCCCCAAACGCATTGCACCACCCAGAGAG 8 22 0 GCATTGCACC 0.926811 -111 GGGGTGAGGAGTAGTGCTCTGGTCTTTTCA 8 53 1 GTAGTGCTCT 0.923325 -80 GCTTTGCTCCTTACGAGATT 14 26 0 GCTTTGCTCC 0.975653 -10 GGGTGTAGTGCTCTCCTGTTTTTA 20 5 1 GTAGTGCTCT 0.923325 -83 CCTCTGCGGGGCTGTGCTCTGGCGCGGGCG 21 210 1 GCTGTGCTCT 0.983911 -91 ********** Masking position 9 Map Score: 5.43665 Number of sites scoring better than the average of aligned sites = 319 Number in coding regions = 289 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 11 TCATATCCAGCATCTTTTCTGCCCTCTCTTCC 3 30 0 CACTTTCTGC 0.926217 -89 GGGGACCAGGGTCTCTGCAAATAGGTAC 4 112 0 CAGGCTCTGC 0.975497 -18 AGCCGACCACCAACGGCTCTTCTACCCACTCA 7 26 0 CACGCTCTTC 0.983531 -122 GGCTGTACGGCAGCGCCTGTTCACGACGTGGT 7 54 1 CACGCTGTTC 0.968563 -94 ACTCGGCGCGCCAGTTTTCTTCCGGTTTAGTG 12 108 1 CCGTTTCTTC 0.741648 -36 GCGTCTTTCTCAAGTCTTCTTCCGGGCGACTT 15 91 0 CAGTTTCTTC 0.924735 -202 GTGCGTTGGGTAGCTGCTGTTCCTGGTGCACG 16 27 1 TACTCTGTTC 0.701139 -93 GTTCCTGGTGCACGTCCTGTTCGTTGAATAGG 16 45 1 CAGTCTGTTC 0.950787 -75 TAGGTAGAATCAGCGCCTCTGCGGGGCTGTGC 21 195 1 CACGCTCTGC 0.980124 -106 ** ** ****** Masking position 8 Map Score: 4.05682 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 141 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 CCTGTCCGTTTTTCCCCTCACAC 2 288 0 GTCCGTTTTT 0.904844 -13 CTGCAAATAGGTACGTGTGTCAACACTACG 4 96 0 GTACGTGTGT 0.95784 -34 CCCGCCCGTGGTCAGTGGGTATGGGGACGT 10 30 1 GTCAGTGGGT 0.949584 -46 TACGCAAGGCGTCCGTGTGTCCTTGCTGGA 13 90 0 GTCCGTGTGT 0.993237 -86 CGTGCCTCCAGTCCGTTTCTGTCGCACGGG 15 54 0 GTCCGTTTCT 0.933747 -239 CCTAAATCAGGTCCGTGGGTAAAGCGTCAC 21 169 0 GTCCGTGGGT 0.991853 -132 ********** Masking position 6 Map Score: 4.30774 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 20 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 13 GTTTGATGTATCAGGACTGGGGTGTGAGGGGAAA 2 267 1 TCAGACGGTG 0.712848 -34 TGTACCGAATGCACTCCCTTTGAGCAAGACAGCA 5 20 1 GCATCCTGAG 0.862151 -90 GTGACACTCCTTGGGTGAATTTTGATG 6 158 0 ACATCCGGTG 0.889102 -17 CCGCGCCCTTGCATGACCTGGGTGCCTTTGGTAC 12 74 1 GCAGACGGTG 0.96201 -70 AGCGAGCGTAACACGCCAGCGGTAATCTGTCCAG 13 61 1 ACAGCCGGTA 0.81404 -115 AAGGACACACGGACGCCTTGCGTACCCCAACCGC 13 96 1 GGAGCCCGTA 0.916259 -80 TTCTCATTGCGGAGGCCGATGGTGCGGTATTTGG 13 149 0 GGAGCCGGTG 0.992796 -27 ACACAGGGGGGCATCCCCCACGAGGGTATGGAGA 17 15 0 GCACCCCGAG 0.892079 -31 AGGGACAGGGGGAGGCCGAATGAG 19 67 1 GGAGCCTGAG 0.948941 -14 CTGCCAGCTTGGATTCCTGAGGAGTTTCTACGTG 21 45 0 GGATCCGGAG 0.958206 -256 GTTCTCGTGCGGACGCCTGTCGTGCCTCCGCGTG 21 247 0 GGAGCCCGTG 0.986115 -54 *** *** **** Masking position 3 Map Score: 5.89492 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 189 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 14 ATTTTGCAGAGAGTGTGCGAGTACGCGCCC 1 145 1 GAGTGTGCGA 0.8992 -53 CCTCAGTCGAGAAGGAGCGTATCCACCGCG 2 172 0 GAAGGAGCGT 0.76416 -129 ACGTGGTGATTAGTGAAGGAGGTGGCGCGC 7 79 1 TAGTGAAGGA 0.326452 -69 GCTCTTACCCGATTGAGCGAAAAGAAGGGA 7 121 1 GATTGAGCGA 0.926167 -27 GCACCACCCAGAGAGAAGGAGAAAGA 8 7 0 GAGAGAAGGA 0.847272 -126 CACCCTACGCGAGAGAGGGATTTTTGGGGG 8 105 1 GAGAGAGGGA 0.96978 -28 TAATGAACTTGAGGGAGGGGCT 10 64 1 GAGGGAGGGG 0.970058 -12 TGCGGAGGCCGATGGTGCGGTATTTGGGTA 13 146 0 GATGGTGCGG 0.778774 -30 TGACAGGATGGATAGAGGGACAGGGGGAGG 19 52 1 GATAGAGGGA 0.926167 -29 CACAGGCTCGGAAGGAGCGAGTTTACTGAA 21 126 1 GAAGGAGCGA 0.947591 -175 ********** Masking position 2 Map Score: 3.61264 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 194 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 15 GACCACGAGTGCGCATCCTACGGTAAAAATG 4 12 1 GCGCACCTAC 0.983149 -118 AGGCGCTGCCGTACAGCCGACCACCAACGGC 7 41 0 GTACACCGAC 0.973505 -107 CTCGCGTAGGGTGCACCCTACCGGCACCCAC 8 87 0 GTGCACCTAC 0.983454 -46 ATCACCTTCAGTACATGCGACGCGGTAAAG 15 10 0 GTACAGCGAC 0.939447 -283 CGCGCTGCACCCACACGCGACCAACCCACTT 15 216 0 CCACAGCGAC 0.84333 -77 TGCGAGGTCGGTAGACCCTACCTATTCAACG 16 66 0 GTAGACCTAC 0.91371 -54 GCCTGCATCCTACGCAAGGGCGT 20 75 0 CTGCACCTAC 0.95467 -13 CAGGAGCGTAGCGGAAACTACCCAAATGGTC 21 76 1 GCGGAACTAC 0.761508 -225 ***** ***** Masking position 5 Map Score: 3.3038 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 82 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172