AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00300_tpal_reg_300.orf -o00300_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 TP0382 83 T. pallidum predicted coding region TP0382 #18 TP0383 27 conserved hypothetical protein #19 TP0417 26 apolipoprotein N-acyltransferase (cutE) #20 TP0644 30 lysyl-tRNA synthetase (lysS-1) #21 TP0645 58 T. pallidum predicted coding region TP0645 #22 TP0647 49 seryl-tRNA synthetase (serS) #23 TP0651 175 conserved hypothetical integral membrane protein #24 TP0933 135 UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase (murE) #25 TP1041 79 ATP-dependent Clp protease proteolytic component (clpP-2) Motif number 1 CGCACCTATACCAGGCACCGCATACTACCGGT 1 59 0 CCGCACCGCA 0.896481 -42 TCTCTCCTTTCCGTCCCGCACCTATACCAGGC 1 75 0 CCTCCGCACC 0.959659 -26 GAACTCAAAACCACACACCGCCTACCAGAATG 2 26 0 CCCCACCGCC 0.976706 -74 AGGCAGCCAACCAGCCTGCCCCAGAAAGAAAG 4 20 0 CCGCTGCCCC 0.899627 -215 TTGTATAACGCCTCACCTCACACATCAAGCAC 4 69 0 CCCCCTCACA 0.972175 -166 ACCACCCCTCCTCACATCCACAGACG 4 219 0 CCCCCTCACA 0.972175 -16 GCGCATTGCAACACTCTCCACCCTGGAAGAAG 6 15 0 ACCCTCCACC 0.973193 -92 ACTGGCCTCTCCTTATGACGTA 6 95 0 ACGCCTCTCC 0.780816 -12 ATAGAAGCCCACGCTCTACTCAAAAGCGCGAC 8 80 0 ACCCTACTCA 0.736798 -183 GAGACGCCGTCCCCTCCACTCAAGTGAGGAGA 8 161 0 CCCCCACTCA 0.96339 -102 CTACCGTAATACTCCCCACACAGGGGAGACGC 8 186 0 ACCCCACACA 0.949479 -77 GCACTCCCCCCTCAAGCTGCACCG 8 249 0 ACCCCCCTCA 0.96809 -14 ACACCGTAAACCTTGCCGCACACAGCACACGC 9 49 0 CCTCCGCACA 0.930717 -54 GCACATACGTCCACGCACCACA 12 1 0 CCCCACCACA 0.980935 -50 ACCTGTCCCCTCTCCCTACTCAC 12 38 0 CCGCCCCTCT 0.881159 -13 AACACACCGCCCTCACTACACCGTACAATGCT 13 24 0 CCCCTACACC 0.969221 -43 CTTCGAGTATACGCTCACCGCCTATTTTGTCA 14 23 0 ACCCACCGCC 0.933594 -56 GCGCCTAGAACCCCACCGCCCCCTCTCCCTAG 15 24 0 CCCCCGCCCC 0.987219 -27 ACACCGTTGTACAGTCTACACATTCGGGACTT 16 70 0 ACGCTACACA 0.685612 -84 GCCGCCTCAAACGCGCACCACCTCGGGTGAAG 16 107 0 ACCCACCACC 0.968305 -47 ACGTCCACCCCCCCCCCCCCGACGAG 17 5 1 CCCCCCCCCC 0.995176 -79 GCGCCTTTCTCCCCTTACTTATTCT 22 35 0 CCTCTCCCCT 0.606527 -15 AACGAGATGGCCTTTCCCCACCGTTTGCGATC 24 46 1 CCTCCCCACC 0.984504 -90 ** * ******* Masking position 6 Map Score: 39.6441 Number of sites scoring better than the average of aligned sites = 799 Number in coding regions = 658 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 2 CCTGCTGTTTGCGTGTTTGGTTGACCGGTAGTA 1 36 1 GCGGTTTGTG 0.898716 -65 GTGCGAAACCGCTAGTGGGGATGGCCT 3 14 1 GCTGTGGGAG 0.532878 -17 GTGACGCGCCTTTCTTTCTGGGGCAGGC 4 6 1 GCGCTTTCTC 0.303359 -229 TCTGGGGCAGGCTGGTTGGCTGCCTGTTTAGGG 4 27 1 GCTGTTGGTC 0.740402 -208 CGCCCGGAGGCCGGCCCGCATTGTATAACGCCT 4 88 0 CCGCCCGCTG 0.64433 -147 CGGCCTCCGGGCGGCTCGGGGAGTCCTGTCTGT 4 108 1 GCGCTCGGGG 0.954183 -127 ACGGAAGCTTCCGAGCGGGATTGAACCGCTGAC 4 189 0 CCGGCGGGTG 0.944296 -46 CCGCTCGGAAGCTTCCGTCTGTGGATGTGAGGA 4 204 1 GCTCCGTCGG 0.596743 -31 TCGAGTCCTTCCTGGCCTGAGTGCTTTCGAAAA 5 119 1 CCTGCCTGGG 0.779526 -31 AGGCGGTCAGGCTTCTGGGGTGCTGTCTTCCTG 7 45 1 GCTCTGGGTC 0.666043 -64 CATGCGTCCGGCGCGTCGTTGTGTGCCTCTGAC 8 27 1 GCGGTCGTGG 0.862691 -236 TGACACCCTTTCGTGTGGGAGGGCGTCGCGCTT 8 56 1 TCGGTGGGGG 0.914455 -207 TGGGAGGGCGTCGCGCTTTTGAGTAGAGCGTGG 8 71 1 TCGGCTTTGG 0.309034 -192 ATTTTGGCATGCGGGTTGGGTCGCGTTCTCCTC 8 135 1 GCGGTTGGTG 0.955342 -128 GGGGACGGCGTCTCCCCTGTGTGGGGAGTATTA 8 179 1 TCTCCCTGGG 0.409712 -84 TTACGGTAGAGCGTGTGGTATAGGGAGCACCGT 8 209 1 GCGGTGGTTG 0.81863 -54 ATAGGGAGCACCGTGTCGGTTCGGTGCAGCTTG 8 228 1 CCGGTCGGTG 0.916385 -35 CACAGCACACGCGGCTAGGATACTCAGAATAGC 9 28 0 GCGCTAGGTC 0.434145 -75 ATACGCGTCTCTTCCTGGGGCGT 10 10 1 TCTCCTGGGG 0.563531 -14 TGGCGATATTCCGTGCTTCAGCGGAAAAAAAAC 11 46 0 CCGGCTTCGG 0.698372 -100 AAACACCTTTCCGGGCAGCGGTGTCAAGTCGCT 16 11 0 CCGGCAGCGG 0.55569 -143 CCGAGGTGGTGCGCGTTTGAGGCGGCTGTTTGC 16 113 1 GCGGTTTGGC 0.850119 -41 GGCTGTTTGCCCGCGTGTGTTTCTTGTC 16 136 1 CCGGTGTGTC 0.676114 -18 ATGTTCTTTTTCTCGTCGGGGGGGGGGGGGTGG 17 15 0 TCTGTCGGGG 0.756308 -69 TTCTGTCAAGGCTCGCGGTTGGGGTACGCAAGG 23 53 1 GCTGCGGTGG 0.778291 -123 GGTACGCAAGGCGTCCGTGTGTCCTTGCTGGAC 23 75 1 GCGCCGTGGC 0.831415 -101 ACAGATTACCGCTGGCGTGTTACGCTCGCTGGC 23 106 1 GCTGCGTGTC 0.703417 -70 GGCGTGTTACGCTCGCTGGCGCGAGAAGTGCGC 23 119 1 GCTGCTGGGG 0.943307 -57 CGCGGGTCTGATTGTATCTGATTG 24 122 0 GCGGTCTGTG 0.920003 -14 GAGGTTATACGCGCGTTGCTTTGTGGGTGTAGA 25 52 1 GCGGTTGCTG 0.867702 -28 *** ***** * * Masking position 2 Map Score: 32.231 Number of sites scoring better than the average of aligned sites = 3919 Number in coding regions = 3547 Number in noncoding regions = 372 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 3 AAACCACACACCGCCTACCAGAATGCCCTG 2 21 0 CCGCCTACCA 0.831649 -79 AGGCCATCCCCACTAGCGGTT 3 20 0 GGCCATCCCC 0.886774 -11 CAGCCAACCAGCCTGCCCCAGAAAGAAAGG 4 19 0 GCCTGCCCCA 0.633209 -216 ACCATGGTTGCGCTCTGCCAACTGAGCTAC 4 150 0 CGCTCTGCCA 0.943567 -85 CACCAGAAAACCCCGTGCGTAACAGATATG 5 19 0 CCCCGTGCGT 0.706232 -131 TGGAGACCGACGCTCTGCCATTAGAGCTAC 5 71 0 CGCTCTGCCA 0.943567 -79 AAAAGCGCGACGCCCTCCCACACGAAAGGG 8 61 0 CGCCCTCCCA 0.989789 -202 GCGACCCAACCCGCATGCCAAAATGCCGAG 8 129 0 CCGCATGCCA 0.861959 -134 ACAGGGGAGACGCCGTCCCCTCCACTCAAG 8 169 0 CGCCGTCCCC 0.980856 -94 ACACGGTGCTCCCTATACCACACGCTCTAC 8 214 0 CCCTATACCA 0.653472 -49 GCACTCCCCCCTCAAGCTGCA 8 252 0 CACTCCCCCC 0.685108 -11 CAACGAAAATGCGCATCCCCCGCAAAGGTG 11 77 0 GCGCATCCCC 0.773441 -69 ACCTGTCCCCTCTCCCTACTCACAATA 12 34 0 CCCTCTCCCT 0.972731 -17 TACAATGCTGCCCCATCCCCTA 13 3 0 CCCCATCCCC 0.985396 -64 TCCAACACACCGCCCTCACTACACCGTACA 13 29 0 CGCCCTCACT 0.721576 -38 CCCCACCGCCCCCTCTCCCTAGGAAGACTA 15 16 0 CCCTCTCCCT 0.972731 -35 GCCCCGCGCCTAGAACCCCAC 15 40 0 CCCCGCGCCT 0.89327 -11 ACGTCCACCCCCCCCCCCCCGACGAGAA 17 9 1 CCCCCCCCCC 0.989821 -75 AACTTTCCCCTGCCAGAAAAGCATT 19 12 0 TCCCCTGCCA 0.805398 -15 ACCGCACCATCGGCCTCCGCAATGAGAAGG 23 12 0 CGGCCTCCGC 0.810017 -164 ********** Masking position 8 Map Score: 21.5013 Number of sites scoring better than the average of aligned sites = 1378 Number in coding regions = 1120 Number in noncoding regions = 258 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 4 TCTGGTAGGCGGTGTGTGGTTTTGAGTTCT 2 29 1 GGTGTGTGGT 0.914538 -71 ACCGCTAGTGGGGATGGCCT 3 21 1 GGGATGGCCT 0.623406 -10 TGTTTAGGGAGGTGTTTCGTGCTTGATGTG 4 51 1 GGTGTTTCGT 0.936736 -184 TGATGTGTGAGGTGAGGCGTTATACAATGC 4 74 1 GGTGAGGCGT 0.797803 -161 CGGGCGGCTCGGGGAGTCCTGTCTGTGTTG 4 115 1 GGGGAGTCCT 0.912763 -120 TGTTACGCACGGGGTTTTCTGGTGTTTTCC 5 25 1 GGGGTTTTCT 0.95713 -125 GGGGTTTTCTGGTGTTTTCCGGGGATTTGT 5 35 1 GGTGTTTTCC 0.852476 -115 GGTGTTTTCCGGGGATTTGTGGGTCAGTAG 5 45 1 GGGGATTTGT 0.828384 -105 GTTGGTTTCGGGTGTTTTGTTGTTTTTTAC 6 68 1 GGTGTTTTGT 0.955605 -39 TCAGGCTTCTGGGGTGCTGTCTTCCTGTCC 7 51 1 GGGGTGCTGT 0.949728 -58 ATCCTAGCCGCGTGTGCTGTGTGCGGCAAG 9 40 1 CGTGTGCTGT 0.711297 -63 TAGTGAGGGCGGTGTGTTGGACTCTCTTGC 13 38 1 GGTGTGTTGG 0.947954 -29 ATGCAGGGGTGTTGACAAAATAGGC 14 6 1 GGGGTGTTGA 0.873837 -73 TGCCCGGAAAGGTGTTTTCGCTAGAAAGGC 16 27 1 GGTGTTTTCG 0.852476 -127 ACTGTACAACGGTGTGTTCTCTTCACCCGA 16 87 1 GGTGTGTTCT 0.985475 -67 GCGGTATTTGGGTATGTTCTGTCAAGGCTC 23 37 1 GGTATGTTCT 0.855766 -139 GCAAGGCGTCCGTGTGTCCTTGCTGGACAG 23 80 1 CGTGTGTCCT 0.863259 -96 TGCGTAAGACGGGGTGGTCCTTTCTTCCTC 23 154 0 GGGGTGGTCC 0.880775 -22 ********** Masking position 2 Map Score: 19.0308 Number of sites scoring better than the average of aligned sites = 470 Number in coding regions = 420 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 GAGCCGCCCGGAGGCCGGCCCGCATTGTATA 4 94 0 GAGGCCGCCC 0.958702 -141 TTCGGTTTTGGAGACCGACGCTCTGCCATTA 5 78 0 GAGACCACGC 0.983223 -72 CAAAACACCCGAAACCAACGCGTAAGCGGCA 6 56 0 GAAACCACGC 0.973504 -51 AAACGGACAGGAAGACAGCACCCCAGAAGCC 7 54 0 GAAGACGCAC 0.894399 -55 TTTTTTGCATGCGTCCGGCGCGTCGTTGTGT 8 20 1 GCGTCCGCGC 0.688818 -243 AAAAGAAATAGAAGCCCACGCTCTACTCAAA 8 88 0 GAAGCCACGC 0.985892 -175 CCACTCAAGTGAGGAGAACGCGACCCAACCC 8 147 0 GAGGAGACGC 0.967739 -116 ATGTGATGCGAAGCGTGCGCAAGAGAATTT 11 10 1 GAAGCGGCGC 0.982534 -136 ATTAGCAAGAGAGTCCAACACACCGCCCTCA 13 41 0 GAGTCCACAC 0.867543 -26 CACCTCGGGTGAAGAGAACACACCGTTGTAC 16 90 0 GAAGAGACAC 0.781299 -64 GACAAGAAACACACGCGGGCAAACAG 16 138 0 GAAACAACGC 0.878569 -16 TAAGTAAGGGGAGAAAGGCGC 22 39 1 GAGAAAGCGC 0.880724 -11 TCGCTGGCGCGAGAAGTGCGCATGAGGAAGA 23 131 1 GAGAAGGCGC 0.956036 -45 ****** **** Masking position 9 Map Score: 15.8831 Number of sites scoring better than the average of aligned sites = 491 Number in coding regions = 441 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 CACCGCATACTACCGGTCAACCAAACACGCAAACAGC 1 39 0 TAGTCCAACA 0.901151 -62 ACACCTCCCTAAACAGGCAGCCAACCAGCCTGCCCCA 4 29 0 AAGGCCAACA 0.983381 -206 TTTCGAAAGCACTCAGGCCAGGAAGGACTCGAACCTT 5 114 0 ACGGCGAAGA 0.885168 -36 AACCAACGCGTAAGCGGCAGGCAATCATGCGCATTGC 6 38 0 TAGGCCAACA 0.983381 -69 TTATAGGGGTTATTTCGCATACAAGGAGAAGATAAT 7 83 1 TACGCCAAGA 0.943241 -26 CGAAAGGGTGTCAGAGGCACACAACGACGCGCCGGAC 8 32 0 TCGGCCAAGA 0.984936 -231 TCAGCTTGTAAAATAGGTACACAACGAAAATGCGCAT 11 91 0 AAGGTCAAGA 0.847587 -55 GACAAGAAACACACGCGGGCAAACAGCCGCCTCAA 16 129 0 ACCGCCAACA 0.92952 -25 CGCCAGCGGTAATCTGTCCAGCAAGGACACACGGACG 23 86 0 AAGTCCAAGA 0.915777 -90 AGTTAATCACTAAAAGGCTGTCAACGAGATGGCCTTT 24 24 1 TAGGCCAAGA 0.985999 -112 AGATTGTTCCCCGAGGGCGTGCAATCAGATACAATCA 24 101 1 CCGGCCAACA 0.95291 -35 ** *** *** ** Masking position 13 Map Score: 10.2344 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 44 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 TGCGGTGCCTGGTATAGGTGCGGGACGGAAAG 1 69 1 GGTATAGGTG 0.940472 -32 TGCCTGTTTAGGGAGGTGTTTCGTGCTTGATG 4 47 1 GGGAGGTGTC 0.911729 -188 ACCATGGTAAGGTTGAGGTCAGCGGTTCAATC 4 172 1 GGTTGAGGTG 0.909207 -63 GTGTTTTCCGGGGATTTGTGGGTCAGTAGCTC 5 46 1 GGGATTTGTG 0.821747 -104 TTCAACATTCGGTTTTGGAGACCGACGCTCTG 5 84 0 GGTTTTGGAC 0.598685 -66 GCGGTTGTTGTAACTTAGTTACGG 7 3 1 GGTTGTTGTC 0.774058 -106 TTAGTTACGGGGTATGTGTTAGGCGGTCAGGC 7 25 1 GGTATGTGTG 0.95699 -84 TTTGGCATGCGGGTTGGGTCGCGTTCTCCTCA 8 137 1 GGGTTGGGTC 0.968309 -126 TAGAGCGTGTGGTATAGGGAGCACCGTGTCGG 8 215 1 GGTATAGGGC 0.824989 -48 CAAGCTGATCGGTTTGTGTTTGTTCCGCAGGA 11 120 1 GGTTTGTGTG 0.950511 -26 TAGGGGATGGGGCAGCATTGTACGG 13 4 1 GGGATGGGGG 0.934424 -63 AACCGGCAACGGTATGGGTGACAATGTTCTTT 17 39 0 GGTATGGGTC 0.979677 -45 CAAGGCTCGCGGTTGGGGTACGCAAGGCGTCC 23 59 1 GGTTGGGGTG 0.972596 -117 ********* * Masking position 8 Map Score: 11.9995 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 202 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 TCCCCACTAGCGGTTTCGCACACT 3 2 0 CTTTCGCAAC 0.972963 -29 GAAACACCTTTTCGAAAGCACTCAGGCCA 5 131 0 CTTTCGAAGC 0.815036 -19 TTTATAGGGGTTATTTCGCATACAAGGAGAAGA 7 82 1 TTTTCGCAAC 0.972458 -27 TGTCTGGTTTTTTTTGCATGCGTCCGGCGCG 8 9 1 TTTTTGCAGC 0.824894 -254 TTGTTCTCGGCATTTTGGCATGCGGGTTGGGTC 8 124 1 CTTTGGCAGC 0.876767 -139 ACACCGTAAACCTTGCCGCACACAGCACACGCG 9 48 0 CTGCCGCAAC 0.823036 -55 TCTTTTCGCTCACTTCCCCAAAA 9 90 0 TTTTCGCTAC 0.918948 -13 GCGCAAAATTCTCTTGCGCACGCTTCGCATCAC 11 13 0 CTTGCGCAGC 0.939872 -133 TTGCGCGTTTTTTTTCCGCTGAAGCACGGAATA 11 40 1 TTTCCGCTAA 0.72818 -106 CGGTTTGTGTTTGTTCCGCAGGAGGGG 11 129 1 TTTCCGCAGA 0.930981 -17 TCAAACGCTCCTTTCGCACAATAAGATAACC 14 58 0 TTTTCGCAAA 0.910079 -21 CCCGGAAAGGTGTTTTCGCTAGAAAGGCTGTGG 16 29 1 TTTTCGCTGA 0.858333 -125 GGGTGGTCCTTTCTTCCTCATGCGCACTTCTCG 23 140 0 TTTCCTCAGC 0.78057 -36 * ******* ** Masking position 4 Map Score: 8.06211 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 376 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 9 CAACCAAACACGCAAACAGCAGGATAACACGG 1 27 0 CGCACAGCAG 0.953238 -74 CCTCACCTCACACATCAAGCACGAAACACCTC 4 59 0 CACAAAGCAC 0.965736 -176 ACAGAAGCAACACAGACAGGACTCCCCGAGCC 4 120 0 CACACAGGAC 0.977577 -115 TAAACGGACAGGAAGACAGCACCCCAGAAGCC 7 54 0 GGAACAGCAC 0.800561 -55 GCACTCCCCCCTCAAGCTGCACCGAACCGACA 8 241 0 CTCACTGCAC 0.879965 -22 TAAACCTTGCCGCACACAGCACACGCGGCTAG 9 43 0 CGCACAGCAC 0.992923 -60 TCTCCCTACTCACAATAAGCACATACGTCCAC 12 19 0 CACAAAGCAC 0.965736 -32 GTACAGTCTACACATTCGGGACTTCTGGCGAG 16 62 0 CACACGGGAC 0.930626 -92 AGAACATACCCAAATACCGCACCATCGGCCTC 23 25 0 CAAACCGCAC 0.896614 -151 **** ****** Masking position 4 Map Score: 5.55952 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 269 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 10 CCGGTAACAGAAAGAGTGTCGTGTGAATTT 2 60 1 AAAGAGTGTC 0.927888 -40 CTCCCACACGAAAGGGTGTCAGAGGCACAC 8 47 0 AAAGGGTGTC 0.985326 -216 TTTTCGCTAGAAAGGCTGTGGCTCGCCAGA 16 41 1 AAAGGCTGTG 0.965242 -113 TTAATCACTAAAAGGCTGTCAACGAGATGG 24 26 1 AAAGGCTGTC 0.989868 -110 AACGGTGGGGAAAGGCCATCTCGTTGACAG 24 41 0 AAAGGCCATC 0.893829 -95 ********** Masking position 3 Map Score: 1.54526 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 15 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 11 CTGTGTTGCTTCTGTAGCTCAGTTGGCAGA 4 137 1 TCTGTAGCTC 0.972601 -98 GATTTGTGGGTCAGTAGCTCTAATGGCAGA 5 58 1 TCAGTAGCTC 0.961201 -92 CGAAAGGGTGTCAGAGGCACACAACGACGC 8 39 0 TCAGAGGCAC 0.9287 -224 TTTTTTTTCCGCTGAAGCACGGAATATCGC 11 47 1 GCTGAAGCAC 0.949145 -99 CGCTAGAAAGGCTGTGGCTCGCCAGAAGTC 16 45 1 GCTGTGGCTC 0.976397 -109 ********** Masking position 4 Map Score: 0.52892 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 26 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 12 GTGTGAATTTCAATAGTTTTTCTCTAGGGT 2 80 1 CAATAGTTTT 0.911687 -20 CACCCTCTAGCAATAGGTTTCATGCT 21 43 1 CAATAGGTTT 0.965604 -16 AAAGCATTGACAATAGATTGTTCCCCGAGG 24 87 1 CAATAGATTG 0.896833 -49 AGGCAAAATACAATAGGTTGTATCATAGG 25 10 0 CAATAGGTTG 0.973957 -70 ********** Masking position 5 Map Score: 0.145643 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 2 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 13 ********** No masking Map Score: 8.62189e-13 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 14 ********** No masking Map Score: 8.62189e-13 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: 8.62189e-13 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