AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00340_tpal_reg_300.orf -o00340_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 Purged sequences: TP0244 21 ribosomal protein S7 Input sequences: #1 TP0231 100 conserved hypothetical protein #2 TP0232 99 T. pallidum predicted coding region TP0232 #3 TP0233 30 anti-sigma F factor antagonist, putative #4 TP0234 234 ribosomal protein L33 (rpmG) #5 TP0235 149 preprotein translocase subunit (secE) #6 TP0237 106 ribosomal protein L11 (rplK) #7 TP0240 108 ribosomal protein L7/L12 (rplL) #8 TP0241 262 DNA-directed RNA polymerase, beta subunit (rpoB) #9 TP0243 102 ribosomal protein S12 (rpsL) #10 TP0245 23 T. pallidum predicted coding region TP0245 #11 TP0246 145 T. pallidum predicted coding region TP0246 #12 TP0247 50 N-acetylmuramoyl-L-alanine amidase (amiA) #13 TP0248 66 T. pallidum predicted coding region TP0248 #14 TP0249 78 flagellar filament outer layer protein (flaA-1) #15 TP0250 50 T. pallidum predicted coding region TP0250 #16 TP0251 153 DNA-binding protein II #17 TP0417 26 apolipoprotein N-acyltransferase (cutE) #18 TP0641 140 histidyl-tRNA synthetase (hisS) Motif number 1 CTCTCCTTTCCGTCCCGCACCTATACCAGGCACCGCATACT 1 65 0 CTCCCCCCGC 0.97576 -36 AAAACCACACACCGCCTACCAGAATGCCCTGCTACAGGCAA 2 11 0 ACGCCCACCG 0.679638 -89 GCCAACCAGCCTGCCCCAGAAAGAAAGGCGCGTCAC 4 6 0 CGCCCAAGCC 0.807056 -229 GCACGAAACACCTCCCTAAACAGGCAGCCAACCAGCCTGCC 4 32 0 CTCCCACGCA 0.938329 -203 TATAACGCCTCACCTCACACATCAAGCACGAAACACCTCCC 4 57 0 CCCTCCACCA 0.918846 -178 ACAGACAGGACTCCCCGAGCCGCCCGGAGGCCGGCCCGCAT 4 100 0 CCCCCCCGGC 0.975675 -135 ACCACCCCTCCTCACATCCACAGACGGAAGCTTCC 4 210 0 CCCTCACCGC 0.794914 -25 CTGACCCACAAATCCCCGGAAAACACCAGAAAACCCCGTGC 5 31 0 ATCCCAACGA 0.87449 -119 CCAACGCGTAAGCGGCAGGCAATCATGCGCATTGCAACACT 6 32 0 ACGGCCAGGA 0.450301 -75 AAAACAACAAAACACCCGAAACCAACGCGTAAGCGGCAGGC 6 53 0 ACACCAAGGA 0.464012 -54 AGGAAGACAGCACCCCAGAAGCCTGACCGCCTAACACATAC 7 36 0 CCCCCAGCGC 0.946524 -73 TATGCGAAATAACCCCTATAAACGGACAGGAAGACAGCACC 7 63 0 ACCCCAACGA 0.954872 -46 AGCGCGACGCCCTCCCACACGAAAGGGTGTCAGAGGCACAC 8 47 0 CTCCCCGGGC 0.878236 -216 ACGCGACCCAACCCGCATGCCAAAATGCCGAGAACAAGTAT 8 120 0 ACCGCCCGCA 0.74893 -143 GGGGAGACGCCGTCCCCTCCACTCAAGTGAGGAGAACGCGA 8 155 0 CTCCCCAGGG 0.927722 -108 TACCGTAATACTCCCCACACAGGGGAGACGCCGTCCCCTCC 8 176 0 CCCCCCAGCC 0.992029 -87 CGACACGGTGCTCCCTATACCACACGCTCTACCGTAATACT 8 205 0 CCCCTCCCCA 0.864723 -58 GCACTCCCCCCTCAAGCTGCACCGAACCGACACG 8 239 0 CCCCCCACCG 0.983096 -24 CACCGTAAACCTTGCCGCACACAGCACACGCGGCTAGGATA 9 39 0 CTGCCCACCC 0.917043 -64 TTTTCGCTCACTTCCCCAAAAAAATCCTCAACACCGTAAAC 9 70 0 CTCCCAACCA 0.971838 -33 ACGCCCCAGGAAGAGACGCGTAT 10 2 0 CCCCCAAGGA 0.985955 -22 CGAAAATGCGCATCCCCCGCAAAGGTGGCGATATTCCGTGC 11 63 0 CTCCCCAGCA 0.977111 -83 ACCTGTCCCCTCTCCCTACTCACAATAAGCACATA 12 26 0 GCCCCCCCCA 0.872213 -25 GAGTCCAACACACCGCCCTCACTACACCGTACAATGCTGCC 13 21 0 CCCGCCACGA 0.971021 -46 ACCGCCCCCTCTCCCTAGGAAGACTACTGCA 15 1 0 CCCCTAACGA 0.840337 -50 GCCCCGCGCCTAGAACCCCACCGCCCCCTCTCCCT 15 26 0 CCGCCAACGC 0.947879 -25 GCGAAAACACCTTTCCGGGCAGCGGTGTCAAGTCGCT 16 7 0 CTTCCCAGCA 0.596447 -147 GCGGGCAAACAGCCGCCTCAAACGCGCACCACCTCGGGTGA 16 109 0 ACCGCAACCA 0.785639 -45 GAGCGCTTCCTCACCTTTAAAAGTACTGGACTATTTACGG 18 10 1 CCACCAACGA 0.86483 -131 AGAGCAGCACCTTCCCATTACAATGCCCCTCTATCCTGTGG 18 53 0 CTCCCACCCC 0.956153 -88 * **** ** * * * Masking position 6 Map Score: 41.0646 Number of sites scoring better than the average of aligned sites = 1989 Number in coding regions = 1727 Number in noncoding regions = 262 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 2 AGCAGGATAACACGGAGTACATCTACTCGC 1 12 0 CACGGAGTAC 0.82976 -89 GCACCTATACCAGGCACCGCATACTACCGG 1 60 0 CAGGCACCGC 0.935691 -41 AACTCAAAACCACACACCGCCTACCAGAAT 2 27 0 CACACACCGC 0.961606 -73 TTACCATGGTTGCGCTCTGCCAACTGAGCT 4 152 0 TGCGCTCTGC 0.685464 -83 GGGATTGAACCGCTGACCTCAACCTTACCA 4 176 0 CGCTGACCTC 0.731602 -59 TTTGGAGACCGACGCTCTGCCATTAGAGCT 5 73 0 GACGCTCTGC 0.824422 -77 CGCATTGCAACACTCTCCACCCTGGAAGAA 6 16 0 CACTCTCCAC 0.977157 -91 AATAGAAGCCCACGCTCTACTCAAAAGCGC 8 83 0 CACGCTCTAC 0.983302 -180 CCCTATACCACACGCTCTACCGTAATACTC 8 204 0 CACGCTCTAC 0.983302 -59 ACCGAACCGACACGGTGCTCCCTATACCAC 8 223 0 CACGGTGCTC 0.777206 -40 ACTCCCCCCTCAAGCTGCACCGAACCGACA 8 241 0 CAAGCTGCAC 0.698528 -22 AACCTTGCCGCACACAGCACACGCGGCTAG 9 43 0 CACACAGCAC 0.880012 -60 TCTTTTCGCTCACTTCCCCAAAAAAA 9 87 0 CGCTCACTTC 0.838628 -16 TTCTCTTGCGCACGCTTCGCATCACAT 11 8 0 CACGCTTCGC 0.906649 -138 CACATACGTCCACGCACCACA 12 2 0 CACGCACCAC 0.99455 -49 CAACACACCGCCCTCACTACACCGTACAAT 13 27 0 CCCTCACTAC 0.770195 -40 TTCGAGTATACGCTCACCGCCTATTTTGTC 14 24 0 CGCTCACCGC 0.975372 -55 CCGCCTCAAACGCGCACCACCTCGGGTGAA 16 108 0 CGCGCACCAC 0.992096 -46 ********** Masking position 10 Map Score: 21.9766 Number of sites scoring better than the average of aligned sites = 1965 Number in coding regions = 1799 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 3 CGTGTTATCCTGCTGTTTGCGTGTTTGGTT 1 28 1 TGCTGTTTGC 0.950204 -73 CGGTAGTATGCGGTGCCTGGTATAGGTGCG 1 61 1 CGGTGCCTGG 0.856111 -40 TTCTGGTAGGCGGTGTGTGGTTTTGAGTTC 2 28 1 CGGTGTGTGG 0.977478 -72 GTGACGCGCCTTTCTTTCTGGGGC 4 5 1 CGCGCCTTTC 0.659933 -230 TTACCATGGTTGCGCTCTGCCAACTGAGCT 4 152 0 TGCGCTCTGC 0.639701 -83 CTGTTACGCACGGGGTTTTCTGGTGTTTTC 5 24 1 CGGGGTTTTC 0.938756 -126 CGGGGTTTTCTGGTGTTTTCCGGGGATTTG 5 34 1 TGGTGTTTTC 0.928474 -116 CGTTGGTTTCGGGTGTTTTGTTGTTTTTTA 6 67 1 GGGTGTTTTG 0.797564 -40 GCTTCTGGGGTGCTGTCTTCCTGTCCGTTT 7 55 1 TGCTGTCTTC 0.87889 -54 TCCGGCGCGTCGTTGTGTGCCTCTGACACC 8 33 1 CGTTGTGTGC 0.84633 -230 GGGAGGGCGTCGCGCTTTTGAGTAGAGCGT 8 72 1 CGCGCTTTTG 0.753151 -191 ACGGCGTCTCCCCTGTGTGGGGAGTATTAC 8 183 1 CCCTGTGTGG 0.718949 -80 TAGCCGCGTGTGCTGTGTGCGGCAAGGTTT 9 44 1 TGCTGTGTGC 0.968487 -59 TGTGGTGCGTGGACGTATGTGC 12 3 1 TGGTGCGTGG 0.882854 -48 GTAGTGAGGGCGGTGTGTTGGACTCTCTTG 13 37 1 CGGTGTGTTG 0.967239 -30 ATGCAGGGGTGTTGACAAAATAGG 14 5 1 AGGGGTGTTG 0.680488 -74 TCAAACGCTCCTTTCGCACAATAAG 14 64 0 CGCTCCTTTC 0.788931 -15 CTGCCCGGAAAGGTGTTTTCGCTAGAAAGG 16 26 1 AGGTGTTTTC 0.804 -128 GACTGTACAACGGTGTGTTCTCTTCACCCG 16 86 1 CGGTGTGTTC 0.979402 -68 CGTTTGAGGCGGCTGTTTGCCCGCGTGTGT 16 126 1 GGCTGTTTGC 0.90317 -28 GGGAAGGTGCTGCTCTGTGCAATGCTCACA 18 78 1 TGCTCTGTGC 0.90785 -63 ********** Masking position 8 Map Score: 22.4632 Number of sites scoring better than the average of aligned sites = 1402 Number in coding regions = 1297 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 4 GCTCTAATGGCAGAGCGTCGGTCTCCAAAACCGAAT 5 74 1 CAGCCGTTCC 0.985142 -76 CAATCATGCGCATTGCAACACTCTCCACCCTGGAAG 6 18 0 CAGCCCTTCC 0.99751 -89 CTCTACTCAAAAGCGCGACGCCCTCCCACACGAAAG 8 63 0 AAGCCCCTCC 0.991338 -200 CAAGTGAGGAGAACGCGACCCAACCCGCATGCCAAA 8 137 0 GAGCCCACCC 0.927676 -126 CTACACCGTACAATGCTGCCCCATCCCCTA 13 5 0 CAGCCCCTCC 0.999016 -62 CAAGAGAGTCCAACACACCGCCCTCACTACACCGTA 13 31 0 CAACCCCTCA 0.907832 -36 CCTAGAACCCCACCGCCCCCTCTCCCTAGGAAGACT 15 17 0 CAGCCTCCCC 0.982438 -34 CTTCCCATTACAATGCCCCTCTATCCTGTGGTGCCG 18 48 0 CAGCCCTTCC 0.99751 -93 GAGCATTGCACAGAGCAGCACCTTCCCATTACAATG 18 69 0 CAGCCCCTCC 0.999021 -72 ** ** * ** *** Masking position 2 Map Score: 15.7839 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 61 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 TCCCTAAACAGGCAGCCAACCAGCCTGCCCCAGA 4 27 0 GGCGCCCCAC 0.963764 -208 CGAGCCGCCCGGAGGCCGGCCCGCATTGTATAAC 4 92 0 GGAGCCCCCC 0.993795 -143 ATCCACAGACGGAAGCTTCCGAGCGGGATTGAAC 4 196 0 GGAGCTCGAC 0.965594 -39 ATTCGGTTTTGGAGACCGACGCTCTGCCATTAGA 5 76 0 GGAACCCGCC 0.973561 -74 ACTCAGGCCAGGAAGGACTCGAACCTTCAACATT 5 107 0 GGAGGACGAC 0.882734 -43 ACAGCACCCCAGAAGCCTGACCGCCTAACACATA 7 37 0 AGAGCCACCC 0.792015 -72 TAAACGGACAGGAAGACAGCACCCCAGAAGCCTG 7 52 0 GGAGACCACC 0.887324 -57 CTTTCGTGTGGGAGGGCGTCGCGCTTTTGAGTAG 8 63 1 GGAGGCCGCC 0.996698 -200 GAAAAGAAATAGAAGCCCACGCTCTACTCAAAAG 8 86 0 AGAGCCCGCC 0.986188 -177 TGAGTGGAGGGGACGGCGTCTCCCCTGTGTGGGG 8 171 1 GGAGGCCTCC 0.940914 -92 CGTTTGAGGCGGCTGTTTGCCCGCGTGTGTTTCT 16 126 1 GGCGTTCCCC 0.794751 -28 CATTGTAATGGGAAGGTGCTGCTCTGTGCAATGC 18 69 1 GGAGGTTGCC 0.871587 -72 *** *** *** * Masking position 14 Map Score: 13.2187 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 267 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 CCGCCTACCAGAATGCCCTGCTACAGGCAA 2 10 0 GAATGCCTGC 0.815639 -90 AAATTCACACGACACTCTTTCTGTTACCGGC 2 59 0 GACACTCTTC 0.415847 -41 GAGCCGCCCGGAGGCCGGCCCGCATTGTATA 4 94 0 GAGGCCGCCC 0.941745 -141 TTCGGTTTTGGAGACCGACGCTCTGCCATTA 5 78 0 GAGACCGCGC 0.976947 -72 TTCCAGGGTGGAGAGTGTTGCAATGCGCATG 6 19 1 GAGAGTGTGC 0.734543 -88 CAAAACACCCGAAACCAACGCGTAAGCGGCA 6 56 0 GAAACCACGC 0.864558 -51 CGGACAGGAAGACAGCACCCCAGAAGCCTGA 7 51 0 GACAGCACCC 0.556073 -58 TTTTTTGCATGCGTCCGGCGCGTCGTTGTGT 8 20 1 GCGTCCGCGC 0.858563 -243 GTGTGCCTCTGACACCCTTTCGTGTGGGAGG 8 47 1 GACACCCTTC 0.792893 -216 TTTCGTGTGGGAGGGCGTCGCGCTTTTGAGT 8 64 1 GAGGGCGCGC 0.955916 -199 AAAAGAAATAGAAGCCCACGCTCTACTCAAA 8 88 0 GAAGCCCCGC 0.973493 -175 ACACAGGGGAGACGCCGTCCCCTCCACTCAA 8 170 0 GACGCCGCCC 0.949453 -93 ACGAAAATGCGCATCCCCCGCAAAGGTGGCG 11 74 0 GCATCCCCGC 0.742873 -72 ACGGTGTAGTGAGGGCGGTGTGTTGGACTCT 13 32 1 GAGGGCGTGT 0.455003 -35 CGGTGTGTTGGACTCTCTTGCTAATAATTG 13 47 1 GACTCTCTGC 0.767903 -20 CTATTTTGTCAACACCCCTGCAT 14 3 0 AACACCCTGC 0.629302 -76 AGCGACTTGACACCGCTGCCCGGAAAGGT 16 9 1 GACACCGTGC 0.977127 -145 GACAAGAAACACACGCGGGCAAACAG 16 138 0 GAAACACCGC 0.656969 -16 ATTGTAATGGGAAGGTGCTGCTCTGTGCAAT 18 70 1 GAAGGTGTGC 0.670603 -71 ******* *** Masking position 1 Map Score: 15.195 Number of sites scoring better than the average of aligned sites = 1319 Number in coding regions = 1212 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 7 AATTCACACGACACTCTTTCTGTTACCGGC 2 59 0 ACACTCTTTC 0.951946 -41 ACCACCCCTCCTCACATCCAC 4 224 0 CCACCCCTCC 0.921258 -11 GAAACACCTTTTCGAAAGCACTC 5 137 0 ACACCTTTTC 0.974552 -13 TGTGCCTCTGACACCCTTTCGTGTGGGAGG 8 48 1 ACACCCTTTC 0.988979 -215 CGGAATATCGCCACCTTTGCGGGGGATGCG 11 66 1 CCACCTTTGC 0.954885 -80 GGTGTGTTGGACTCTCTTGCTAATAATTG 13 48 1 ACTCTCTTGC 0.785364 -19 TATTTTGTCAACACCCCTGCAT 14 3 0 ACACCCCTGC 0.987647 -76 AGCGACTTGACACCGCTGCCCGGAAAGGT 16 10 1 ACACCGCTGC 0.965503 -144 TCTAGCGAAAACACCTTTCCGGGCAGCGGT 16 22 0 ACACCTTTCC 0.962645 -132 CTGGCGAGCCACAGCCTTTCTAGCGAAAAC 16 40 0 ACAGCCTTTC 0.905151 -114 TGAAGAGAACACACCGTTGTACAGTCTACA 16 82 0 ACACCGTTGT 0.782545 -72 TGGCTCTGGTACACTTTTTCAAGACATGCA 18 113 0 ACACTTTTTC 0.894224 -28 ********** Masking position 8 Map Score: 17.1912 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 202 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 CTGCTGTTTGCGTGTTTGGTTGACCGGTAGT 1 37 1 CGGTTTGGTT 0.95164 -64 GTGACGCGCCTTTCTTTCTGGGGCAGG 4 7 1 CGCTTTCTTT 0.753329 -228 GAGTCCTGTCTGTGTTGCTTCTGTAGCTCAG 4 128 1 TGGTTGCTTC 0.875686 -107 CTGCCGCTTACGCGTTGGTTTCGGGTGTTTT 6 55 1 CGGTTGGTTT 0.98023 -52 TTTTGGCATGCGGGTTGGGTCGCGTTCTCCT 8 136 1 CGGTTGGGTC 0.971427 -127 TAGGGAGCACCGTGTCGGTTCGGTGCAGCTT 8 229 1 CGGTCGGTTC 0.974779 -34 ATACGCGTCTCTTCCTGGGGCGT 10 4 1 CGGTCTCTTC 0.948412 -20 GAGAATTTTGCGCGTTTTTTTTCCGCTGAAG 11 33 1 CGGTTTTTTT 0.855829 -113 CTGATCGGTTTGTGTTTGTTCCGCAGGAGGG 11 124 1 TGGTTTGTTC 0.926559 -22 GCTGTTTGCCCGCGTGTGTTTCTTGTC 16 137 1 CGGTGTGTTT 0.923986 -17 ** ******** Masking position 5 Map Score: 7.29286 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 = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 CCTGGTATAGGTGCGGGACGGAAAGGAGAGA 1 76 1 GTGCGGACGG 0.971444 -25 AGTGTGCGAAACCGCTAGTGGGGA 3 4 1 GTGCGAACCG 0.994669 -27 TCAGTTGGCAGAGCGCAACCATGGTAAGGTT 4 155 1 GAGCGAACCA 0.928921 -80 AGAAAACCCCGTGCGTAACAGATATGACGAC 5 14 0 GTGCGAACAG 0.991641 -136 GATGCGAAGCGTGCGCAAGAGAATTTTGCGC 11 15 1 GTGCGAAGAG 0.986473 -131 CCCCTCCTGCGGAACAAACACAAACCG 11 129 0 CTGCGAACAA 0.884736 -17 TTATCTTATTGTGCGAAAGGAGCGTTTGA 14 60 1 GTGCGAAGGA 0.968526 -19 ACTTTTAAAGGTGAGGAAGCGCTC 18 4 0 GTGAGAAGCG 0.927564 -137 ***** ***** Masking position 8 Map Score: 8.35285 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 129 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 GTGTGGTTTTGAGTTCTGCCGGTAACAGAAAG 2 42 1 GAGTCTGCGG 0.995271 -58 ATGCGGGCCGGCCTCCGGGCGGCTCGGGGAGT 4 100 1 GCCTCGGCGG 0.938138 -135 GCGGCTCGGGGAGTCCTGTCTGTGTTGCTTCT 4 118 1 GAGTCTGCTG 0.982858 -117 TTGAAGGTTCGAGTCCTTCCTGGCCTGAGTGC 5 111 1 GAGTCTTCTG 0.965253 -39 TTCCTGGCCTGAGTGCTTTCGAAAAGGTGTTT 5 127 1 GAGTCTTCGA 0.965275 -23 ACACATTCGGGACTTCTGGCGAGCCACAGCCT 16 53 0 GACTCTGCGA 0.977634 -101 AAAAGTACTGGACTATTTACGGCACCACAGGA 18 29 1 GACTTTTCGG 0.909607 -112 **** *** *** Masking position 4 Map Score: 3.42363 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 57 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 GGCGAGTAGATGTACTCCGTG 1 1 1 GGCGAGAGAT 0.858331 -100 GGGACGGAAAGGAGAGAGGAT 1 90 1 GGAGAGGGAT 0.970208 -11 TCTGGTAGGCGGTGTGTGGTTTTGAGTTCTG 2 29 1 GGTGTGGGTT 0.938523 -71 GTGACGCGCCTTTCTTTCTGGGG 4 3 1 GACGCGCTTT 0.610264 -232 TGATGTGTGAGGTGAGGCGTTATACAATGCG 4 74 1 GGTGAGCGTT 0.971111 -161 GTAAGGTTGAGGTCAGCGGTTCAATCCCGCT 4 178 1 GGTCAGGGTT 0.8973 -57 CTTCCAGGGTGGAGAGTGTTGCAATGCGCAT 6 18 1 GGAGAGGTTG 0.776349 -89 GCATGCGTCCGGCGCGTCGTTGTGTGCCTCT 8 26 1 GGCGCGCGTT 0.960605 -237 CTTTGCGGGGGATGCGCATTTTCGTTGTGTA 11 80 1 GATGCGATTT 0.493949 -66 TGTGGTGCGTGGACGTATGTGCTT 12 4 1 GGTGCGGGAC 0.946757 -47 TTGTGAGTAGGGAGAGGGGACAGGT 12 36 1 GGAGAGGGAC 0.911414 -15 CAAAATAGGCGGTGAGCGTATACTCGAAGAG 14 26 1 GGTGAGGTAT 0.951363 -53 GCGTATACTCGAAGAGTGGTTATCTTATTGT 14 41 1 GAAGAGGGTT 0.911901 -38 CACCCGAGGTGGTGCGCGTTTGAGGCGGCTG 16 110 1 GGTGCGGTTT 0.972181 -44 ****** **** Masking position 6 Map Score: 11.9655 Number of sites scoring better than the average of aligned sites = 602 Number in coding regions = 534 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 12 CTGTGTTGCTTCTGTAGCTCAGTTGGCAGA 4 137 1 TCTGTAGCTC 0.969336 -98 GATTTGTGGGTCAGTAGCTCTAATGGCAGA 5 58 1 TCAGTAGCTC 0.969336 -92 CGAAAGGGTGTCAGAGGCACACAACGACGC 8 39 0 TCAGAGGCAC 0.934548 -224 TTTTTTTTCCGCTGAAGCACGGAATATCGC 11 47 1 GCTGAAGCAC 0.934548 -99 CGCTAGAAAGGCTGTGGCTCGCCAGAAGTC 16 45 1 GCTGTGGCTC 0.987367 -109 CAGTGTAGTGGCTCTGGTACACTT 18 127 0 GTAGTGGCTC 0.923614 -14 ********** Masking position 4 Map Score: 3.31031 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 87 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 13 AGGCCATCCCCACTAGCGGTTTCGCAC 3 14 0 CCCCACTAGC 0.97328 -17 ACCACCCCTCCTCACATCCACAGA 4 221 0 CCCCTCCTCA 0.911397 -14 GAGAACGCGACCCAACCCGCATGCCAAAAT 8 135 0 CCCAACCCGC 0.908402 -128 GAGACGCCGTCCCCTCCACTCAAGTGAGGA 8 163 0 CCCCTCCACT 0.950476 -100 GCACTCCCCCCTCAAGCTGCACCGAAC 8 246 0 CCCCTCAAGC 0.960708 -17 CCCCTCCTGCGGAACAAACA 11 136 0 CCCCTCCTGC 0.988332 -10 ACCTGTCCCCTCTCCCTACTCACAAT 12 35 0 CCCCTCTCCC 0.993713 -16 TACAATGCTGCCCCATCCCCTA 13 3 0 CCCCATCCCC 0.924722 -64 ACCCCACCGCCCCCTCTCCCTAGGAAGACT 15 17 0 CCCCTCTCCC 0.993713 -34 CATTACAATGCCCCTCTATCCTGTGGTGCC 18 49 0 CCCCTCTATC 0.93908 -92 ********** Masking position 3 Map Score: 15.703 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 220 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 14 ********** No masking Map Score: 3.42725e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 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 ********** No masking Map Score: 3.42725e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 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