AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00970_tpal_reg_300.orf -o00970_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 TP0010 300 T. pallidum predicted coding region TP0010 #2 TP0011 33 tpr protein B (tprB) #3 TP0015 190 phenylalanyl-tRNA synthetase beta subunit (pheT) #4 TP0091 181 cysteinyl-tRNA synthetase (cysS) #5 TP0162 174 Holliday junction DNA helicase (ruvB) #6 TP0452 278 isoleucyl-tRNA synthetase (ileS) #7 TP0586 88 leucyl-tRNA synthetase (leuS) #8 TP0609 300 asparaginyl-tRNA synthetase (asnS) #9 TP0629 170 T. pallidum predicted coding region TP0629 #10 TP0630 169 chemotaxis protein methyltransferase (cheR) #11 TP0631 46 protein-glutamate methylesterase (cheB) #12 TP0632 104 tryptophanyl-tRNA synthetase (trsA) #13 TP0641 140 histidyl-tRNA synthetase (hisS) #14 TP0644 30 lysyl-tRNA synthetase (lysS-1) #15 TP0645 58 T. pallidum predicted coding region TP0645 #16 TP0647 49 seryl-tRNA synthetase (serS) #17 TP0651 175 conserved hypothetical integral membrane protein #18 TP0672 134 glycyl-tRNA synthetase (glyS) #19 TP0673 177 glutamyl-tRNA synthetase (gltX) #20 TP0757 40 polypeptide deformylase (def) #21 TP0758 118 ribosomal protein S21 (rpsU) #22 TP0798 32 methionyl-tRNA synthetase (metG) #23 TP0831 22 arginyl-tRNA synthetase (argS) #24 TP0832 66 T. pallidum predicted coding region TP0832 #25 TP0834 86 tyrosyl-tRNA synthetase (tyrS) #26 TP0835 140 ankyrin, putative #27 TP0836_TP0837 147 TP0836: T. pallidum predicted coding region TP0836, TP0837: threonyl-tRNA synthetase (thrS) #28 TP0973 87 phenylalanyl-tRNA synthetase alpha subunit (pheS) #29 TP0985 143 aspartyl-tRNA synthetase (aspS) #30 TP1017 171 alanyl-tRNA synthetase (alaS) #31 TP1035 152 valyl-tRNA synthetase (valS) #32 TP1041 79 ATP-dependent Clp protease proteolytic component (clpP-2) Motif number 1 GGGGTTCTCTCGCACAGTGCCGGTTGCCCC 1 11 1 CGCACAGTGC 0.839009 -290 GATACGGTAGCGCGCCCTCGGAGTAAAAGT 1 147 1 CGCGCCCTCG 0.968797 -154 CATGCCTTTGTGCGCACGGTACTTATGCCG 3 14 1 TGCGCACGGT 0.885582 -177 AGCGCTCATATGCGCACGGCATAAGTACCG 3 30 0 TGCGCACGGC 0.929426 -161 GCCACTACACGGCACACGTGCTCTACACTT 3 91 0 GGCACACGTG 0.570964 -100 GGCCAGCCACCACACCGTCTTTGCAGAGGA 3 122 0 CACACCGTCT 0.544157 -69 TATACGATTTCACGCGCTTATGCTACAATG 4 23 1 CACGCGCTTA 0.483928 -159 ATGCTACAATGGCGCGGTCTTGGCCTTCTT 4 42 1 GGCGCGGTCT 0.822843 -140 CAAACGCCTTTGCCCGCCTGCGCTTCAGTC 4 91 0 TGCCCGCCTG 0.693206 -91 GTGCGGACCACGCCCAGCCCCATTGTCGCG 4 121 0 CGCCCAGCCC 0.671081 -61 GCACGTGTTCTGCGCCCGGTTGGGAGAAAC 4 147 1 TGCGCCCGGT 0.949314 -35 GTGCGCCCCTTCGAAGTTTCT 4 171 0 TGCGCCCCTT 0.881149 -11 CAGCTACAGTTGCGCCCTCTT 5 164 1 TGCGCCCTCT 0.932387 -11 CGTGCGATTACGCACACGTGGGGTATCTGG 6 149 1 CGCACACGTG 0.803204 -130 GGAAAGGTGTGGCGCCGGTCATAAGACGTA 6 188 1 GGCGCCGGTC 0.861537 -91 CACCTGGGTGTGCACGGGTTGCAGCCCCT 7 10 0 TGCACGGGTT 0.720008 -79 GAGGGCATTGTACACGCCGGTACATCTACG 7 50 0 TACACGCCGG 0.568346 -39 GCAGAAAGGACGCGCGGGTGAACGATTACC 8 27 0 CGCGCGGGTG 0.586449 -274 GAGCGGCCGAGGCGCGGTCTTCTGTGACCG 8 114 0 GGCGCGGTCT 0.822843 -187 GACGCTTTTTCGCACGGTTCGCTCTCCCCA 8 178 1 CGCACGGTTC 0.871938 -123 TCCCCAGTCCTGCGCGGCGTTCCATGCAGA 8 202 1 TGCGCGGCGT 0.886225 -99 ATGCAGATGCCGCGCAGGGCGTGCGCCGTG 8 225 1 CGCGCAGGGC 0.934254 -76 GCGCAGGGCGTGCGCCGTGGCGTCACAGCT 8 236 1 TGCGCCGTGG 0.930451 -65 CTTGCCGGTCCACGCCCTTCCACAAAGAGG 8 267 1 CACGCCCTTC 0.844678 -34 CTGGTTATTTTGCGCGCTCCACAGCAGCAC 9 22 1 TGCGCGCTCC 0.950001 -149 CACTCTCCTTTGCGCGCCTGCACCGTGCTG 9 46 0 TGCGCGCCTG 0.89816 -125 TTGACAGAAGTACCCGCTCCCTTCTAGAGT 9 94 1 TACCCGCTCC 0.517825 -77 ACGCTCCTGACACACCGTGCGGCGCGTGCA 10 37 1 CACACCGTGC 0.710618 -133 CCCTTGAAGGTGCACGCGCCGCACGGTGTG 10 47 0 TGCACGCGCC 0.901102 -123 CCTGGCACCTCGCGCGCCGACACGGTCTGC 10 78 0 CGCGCGCCGA 0.872475 -92 CGAGGTGCCAGGCACGCTTCCGTAAGACAC 10 96 1 GGCACGCTTC 0.782401 -74 ACTGTCGTTGTACACCCGGTAGCAATTACC 10 139 1 TACACCCGGT 0.600403 -31 CCTGCACACGGGGTAATTGCTA 10 158 0 TGCACACGGG 0.805723 -12 GGTAGTCTGTGGCCCCCTGCCTGTATACGC 11 25 0 GGCCCCCTGC 0.799574 -22 GACGGACACGCACCCGTGATATAGAGGA 12 9 1 CGCACCCGTG 0.908012 -96 AGAGGAGGGCTGCGCGGTCGGCGCACGTGT 12 33 1 TGCGCGGTCG 0.908486 -72 GAGAAGGAGATGCACCCTCTAGCAATAGGT 15 31 1 TGCACCCTCT 0.850331 -28 TTCTTCCTCATGCGCACTTCTCGCGCCAGC 17 133 0 TGCGCACTTC 0.868461 -43 AAGAAAGGACCACCCCGTCTTACGCATT 17 158 1 CACCCCGTCT 0.416907 -18 TCACAGAGATCGCGCCCGCCTTTGAACACA 18 57 0 CGCGCCCGCC 0.948401 -78 ATACTGTCAGCACCCGCGGCGACCTCACAG 18 81 0 CACCCGCGGC 0.707102 -54 GGTGACGCGCCGCTCACCTTCCCCC 18 120 0 CGCGCCGCTC 0.931588 -15 GATGCCGCTTCACGCGGTTGATTGCACAGA 19 29 0 CACGCGGTTG 0.708545 -149 ACACTCCTCATGCACCGTGACCGCCTCCCT 19 82 0 TGCACCGTGA 0.568337 -96 CAGGGATGCTTGCGCCCCGGAGGGGGATGT 19 128 1 TGCGCCCCGG 0.944814 -50 TGCGATAATCGGCCCCCGGGGAGGGCGAGC 19 157 1 GGCCCCCGGG 0.773797 -21 CTCCCCTGCACGCACACCCTACGTGTC 21 8 0 CGCACACCCT 0.764266 -111 TGACACGCGGGGCGACGGTGGGG 25 4 1 CACGCGGGGC 0.859054 -83 AACGCGCTGATGCACCCCCACCGTCGCCCC 25 19 0 TGCACCCCCA 0.582338 -68 CGCACACCCCGATCCAGGGC 25 77 0 CGCACACCCC 0.846599 -10 AGGACGCAACCGCGCAGGCGCGTTCCCATT 26 12 0 CGCGCAGGCG 0.878465 -129 AATCTTTAGACGCCCACTCTCCCGTGAGGA 26 38 0 CGCCCACTCT 0.710842 -103 TACGCTTTTACACACACTGTACAGACGCGG 26 96 1 CACACACTGT 0.4913 -45 TTTGTCAATGGGCGCCGTTTTGGAGGAAGC 27 31 1 GGCGCCGTTT 0.767533 -117 TGACGGCGCAGGCGCACTGGCTCAGTGCTT 27 57 0 GGCGCACTGG 0.836186 -91 CCAGTGCGCCTGCGCCGTCACTGCAGTCTG 27 67 1 TGCGCCGTCA 0.72561 -81 AACGTATTTTCGCGCCGTTTAGATGTAGGC 28 68 0 CGCGCCGTTT 0.910135 -20 GCGCGGTCTGTGCGCGGCGTAATGGAATCT 29 33 0 TGCGCGGCGT 0.886225 -111 TGCTACACTTCGCGCGCGGTCTGTGCGCGG 29 46 0 CGCGCGCGGT 0.968257 -98 GAACAGGTGGTACACGCTGCCCGATGAACA 29 104 1 TACACGCTGC 0.685698 -40 AAGACAGTTTCGCACCCTTAAAAAATATAA 30 22 0 CGCACCCTTA 0.677439 -150 ACAGAATTCGCACACACCTCTAGCCTCTCG 30 53 0 CACACACCTC 0.422437 -119 GAAGAGGTTATACGCGCGTTGCTTTGTGGG 32 49 1 TACGCGCGTT 0.658506 -31 ********** Masking position 5 Map Score: 66.5373 Number of sites scoring better than the average of aligned sites = 10769 Number in coding regions = 9944 Number in noncoding regions = 825 Number of orfs with sites within 600 bp upstream = 298 Fraction of orfs with sites within 600 bp upstream = 0.0478638 Motif number 2 AGCACCGCTTGGGGCAACCGGCACTGTGCGA 1 20 0 GGGGCAACGG 0.876233 -281 TTTCGAGGGAGGGTAGACTGAAGCGCAGGCG 4 76 1 GGGTAGACGA 0.612383 -106 AAGCGCAGGCGGGCAAAGGCGTTTGCGCGAC 4 96 1 GGGCAAAGCG 0.814441 -86 GCGCGACAATGGGGCTGGGCGTGGTCCGCAC 4 120 1 GGGGCTGGCG 0.599457 -62 GGTGCAGGTGGGGAAAGGTGTGGCGCCGGTC 6 177 1 GGGAAAGGGT 0.716217 -102 TAAGACGTATGGGGAAAAGGAAGGACGAAAA 6 209 1 GGGGAAAAGA 0.703928 -70 GCGCAGGACTGGGGAGAGCGAACCGTGCGAA 8 186 0 GGGGAGAGGA 0.975398 -115 TGCAGATGCCGCGCAGGGCGTGCGCCGTGGC 8 226 1 GCGCAGGGGT 0.627967 -75 GGGGAGACTGTAAATCAAGGT 12 94 0 GGGGAGACGT 0.961763 -11 GAATAAGTAAGGGGAGAAAGGCGC 16 36 1 GGGGAGAAGG 0.969253 -14 CCTTCTCATTGCGGAGGCCGATGGTGCGGTA 17 12 1 GCGGAGGCGA 0.845729 -164 GCGGGCTATAGGGAAAAGAGGTATGCAGGGG 18 25 1 GGGAAAAGGG 0.896103 -110 GCTAGACAGGGGGGAAGGTGAGCGGCGCGTC 18 111 1 GGGGAAGGGA 0.933324 -24 TGGTAGGAAGGGGAAGACAGGGAGGCGGTCA 19 64 1 GGGAAGACGG 0.959178 -114 ATCGGCCCCCGGGGAGGGCGAGCG 19 164 1 GGGGAGGGGA 0.980614 -14 GGGTAAGAGCGGGAAGAGGCG 20 30 1 GGGAAGAGCG 0.924921 -11 TGTGCGTGCAGGGGAGGCAGGAGTGCTTTCG 21 22 1 GGGGAGGCGG 0.992904 -97 GTTTTTTTCAGGGGAGGGTCG 21 108 1 GGGGAGGGCG 0.986552 -11 TTTGCAAGGCGGGGATAAGGGACGT 24 52 1 GGGGATAAGG 0.733807 -15 TGACACGCGGGGCGACGGTGGGGGTGCAT 25 9 1 GGGGCGACGT 0.854394 -78 CCCCGATCCAGGGCAGGCGGTTCAGTCCCGA 25 60 0 GGGCAGGCGT 0.898496 -27 GGACGCAACCGCGCAGGCGCGTTCCCATTT 26 10 0 GCGCAGGCCG 0.686825 -131 TGCGTCCTCACGGGAGAGTGGGCGTCTAAAG 26 34 1 CGGGAGAGGG 0.877392 -107 GACCGCAGCAGGGAAAAGGCGATAATACCCT 30 149 1 GGGAAAAGCG 0.773201 -23 CAAAAGCTCTGGGGAGGAGCGGCTGGCAGTG 31 51 1 GGGGAGGACG 0.940819 -102 ******** ** Masking position 3 Map Score: 31.6897 Number of sites scoring better than the average of aligned sites = 923 Number in coding regions = 765 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 3 GCGTCTGCACGCGAGCCCGGCCGTCACCATT 1 116 0 GCGACCCGGC 0.946266 -185 TACACGGCACACGTGCTCTACACTTTAGTCA 3 85 0 ACGTCTCTAC 0.788698 -106 CCGTGTAGTGGCATCCTCTGCAAAGACGGTG 3 109 1 GCATCTCTGC 0.948888 -82 CGTGGTCCGCACGTGTTCTGCGCCCGGTTGG 4 139 1 ACGTTTCTGC 0.862125 -43 TGAAAAATTGACGTTTCCTGCGTGATCCGCT 5 47 0 ACGTTCCTGC 0.954955 -128 ATGTGGGGAAGGGTTTCCTGCCTTCGTCGCA 6 25 1 GGGTTCCTGC 0.832888 -254 GCGTAATCGCACGTGCTCTGCCAATTACTGC 6 131 0 ACGTCTCTGC 0.945714 -148 ACTGGGGAGAGCGAACCGTGCGAAAAAGCGT 8 179 0 GCGACCGTGC 0.802021 -122 GTCCTGCGCGGCGTTCCATGCAGATGCCGCG 8 208 1 GCGTCCATGC 0.911851 -93 ACGCCACGGCGCACGCCCTGCGCGGCATCTG 8 228 0 GCACCCCTGC 0.93147 -73 TCTTACGGAAGCGTGCCTGGCACCTCGCGCG 10 92 0 GCGTCCTGGC 0.736003 -78 TATCACGGGTGCGTGTCCGTC 12 1 0 GCGTTCCGTC 0.690363 -104 GCTAGAGGGTGCATCTCCTTCTCAGATTCCT 15 23 0 GCATTCCTTC 0.678049 -36 GCCTTTGAACACATCCCCTGCATACCTCTTT 18 39 0 ACATCCCTGC 0.937647 -96 AAAGGCGGGCGCGATCTCTGTGAGGTCGCCG 18 64 1 GCGACTCTGT 0.670769 -71 TCCCCTGCACGCACACCCTACGTGTC 21 6 0 GCACCCCTAC 0.747147 -113 AAGCACTCCTGCCTCCCCTGCACGCACACCC 21 19 0 GCCTCCCTGC 0.950907 -100 AGCGCAAAAGACGTCCCCTGTCAATCGTTTC 21 56 0 ACGTCCCTGT 0.861957 -63 AGCGTTTCCTACTCTGATTTAA 22 21 0 GCGTTCCTAC 0.950037 -12 GTGTGTAAAAGCGTATCCTACCGGTTTCGGC 26 80 0 GCGTTCCTAC 0.950037 -61 AAAACAGAAAGCATCCTCTACTATACCCTAC 27 115 0 GCATCTCTAC 0.799127 -33 AGAGGTGTGTGCGAATTCTGTCAAGGATCTT 30 62 1 GCGATTCTGT 0.422392 -110 **** ****** Masking position 2 Map Score: 22.5891 Number of sites scoring better than the average of aligned sites = 1169 Number in coding regions = 1083 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 4 TTATGCTACAATGGCGCGGTCTTGGCCTTC 4 40 1 ATGGCGCGGT 0.84035 -142 CAGGTGGGGAAAGGTGTGGCGCCGGTCATA 6 181 1 AAGGTGTGGC 0.792827 -98 AGGAGCGGCCGAGGCGCGGTCTTCTGTGAC 8 116 0 GAGGCGCGGT 0.948548 -185 CTCTCTAGATGAGGAGCGGCCGAGGCGCGG 8 127 0 GAGGAGCGGC 0.993778 -174 GTGGAAGGGCGTGGACCGGCAAGCAGCTGT 8 260 0 GTGGACCGGC 0.907237 -41 GACCACAAACGAGGAGCGCCGCTGCCACTC 9 120 0 GAGGAGCGCC 0.930612 -51 CCTCTATCCTGTGGTGCCGTAAATAGTCCA 13 37 0 GTGGTGCCGT 0.873606 -104 TTGTAATGGGAAGGTGCTGCTCTGTGCAAT 13 71 1 AAGGTGCTGC 0.889778 -70 GGAATCTGAGAAGGAGATGCACCCTCTAGC 15 24 1 AAGGAGATGC 0.520657 -35 GCGGAGGCCGATGGTGCGGTATTTGGGTAT 17 22 1 ATGGTGCGGT 0.902877 -154 AATCAACCGCGTGAAGCGGCATCCTGCGTG 19 36 1 GTGAAGCGGC 0.859822 -142 AGCTTGGTATGAGGTGAGGCA 23 12 1 GAGGTGAGGC 0.941299 -11 CCTCCTGAGTATGGTGCCGCGTCTGTACAG 26 112 0 ATGGTGCCGC 0.924934 -29 CCATACTCAGGAGGATCCGCTGC 26 128 1 GAGGATCCGC 0.75194 -13 AAGCTCTGGGGAGGAGCGGCTGGCAGTGAC 31 54 1 GAGGAGCGGC 0.993778 -99 ********** Masking position 3 Map Score: 14.8859 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 430 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 CTCGCGTGCAGACGCGATACGGTAGCGCGC 1 132 1 GACGCGATAC 0.667768 -169 TTACTCCGAGGGCGCGCTACCGTATCGCGT 1 143 0 GGCGCGCTAC 0.958092 -158 ATGCTACAATGGCGCGGTCTTGGCCTTCTT 4 42 1 GGCGCGGTCT 0.986674 -140 AATGGGGCTGGGCGTGGTCCGCACGTGTTC 4 127 1 GGCGTGGTCC 0.990278 -55 CTCCCAACCGGGCGCAGAACACGTGCGGAC 4 143 0 GGCGCAGAAC 0.479172 -39 TGACGTTTCCTGCGTGATCCGCTACTTTGA 5 40 0 TGCGTGATCC 0.709363 -135 ACGGCACTCTGGCGCGGACCTCTCGAGCTA 5 99 1 GGCGCGGACC 0.984751 -76 TAGATGTACCGGCGTGTACAATGCCCTCTG 7 52 1 GGCGTGTACA 0.522246 -37 GAGTCTTATAGGCGCGGTAATCGTTCACCC 8 12 1 GGCGCGGTAA 0.950412 -289 TATGTCGTACGGCGTGGTCCCGGTCACAGA 8 94 1 GGCGTGGTCC 0.990278 -207 GAGCGGCCGAGGCGCGGTCTTCTGTGACCG 8 114 0 GGCGCGGTCT 0.986674 -187 GCGCACGCCCTGCGCGGCATCTGCATGGAA 8 221 0 TGCGCGGCAT 0.562378 -80 TGCCGCGCAGGGCGTGCGCCGTGGCGTCAC 8 232 1 GGCGTGCGCC 0.653751 -69 TTTGTGGAAGGGCGTGGACCGGCAAGCAGC 8 263 0 GGCGTGGACC 0.965521 -38 CTGGTTATTTTGCGCGCTCCACAGCAGCAC 9 22 1 TGCGCGCTCC 0.875885 -149 CACACCGTGCGGCGCGTGCACCTTCAAGGG 10 47 1 GGCGCGTGCA 0.652737 -123 AGAGGAGGGCTGCGCGGTCGGCGCACGTGT 12 33 1 TGCGCGGTCG 0.841509 -72 GCGGTCGGCGCACGTGTTCCTGCGCCTGCA 12 46 1 CACGTGTTCC 0.201378 -59 GGAGGCCGATGGTGCGGTATTTGGGTATGT 17 24 1 GGTGCGGTAT 0.489777 -152 GATTACCGCTGGCGTGTTACGCTCGCTGGC 17 109 1 GGCGTGTTAC 0.914482 -67 TGCGTAAGACGGGGTGGTCCTTTCTTCCTC 17 154 0 GGGGTGGTCC 0.816963 -22 TTCAAAGGCGGGCGCGATCTCTGTGAGGTC 18 61 1 GGCGCGATCT 0.923571 -74 GAAGGTGAGCGGCGCGTCACC 18 124 1 GGCGCGTCAC 0.883204 -11 AGCGGCATCCTGCGTGGTAGGAAGGGGAAG 19 50 1 TGCGTGGTAG 0.470372 -128 CAACCGCGCAGGCGCGTTCCCATTT 26 6 0 GGCGCGTTCC 0.984163 -135 ACACTGTACAGACGCGGCACCATACTCAGG 26 109 1 GACGCGGCAC 0.768535 -32 TGTAGGAAGGGACGTGGTATGTAGGGTATA 27 95 1 GACGTGGTAT 0.56505 -53 ACATCTAAACGGCGCGAAAATACGTT 28 72 1 GGCGCGAAAA 0.462353 -16 CTACACTTCGCGCGCGGTCTGTGCGCGGCG 29 44 0 CGCGCGGTCT 0.879658 -100 ********** Masking position 4 Map Score: 42.2889 Number of sites scoring better than the average of aligned sites = 755 Number in coding regions = 674 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 6 GGACAGAAAACATATACGATTT 4 2 1 GACAGAAACA 0.742826 -180 CGCCGTACGACATAGAAAACCAGATGCAAGT 8 77 0 CATAGAAACC 0.953465 -224 TGGTCCCGGTCACAGAAGACCGCGCCTCGGC 8 108 1 CACAGAAACC 0.982385 -193 GGCAGGGGGCCACAGACTACCGT 11 34 1 CACAGACACC 0.981187 -13 GTCCTTGCTGGACAGATTACCGCTGGCGTGT 17 95 1 GACAGATACC 0.878253 -81 TCTTTCATAAAAAACCTGTCTGTGCA 19 6 1 CATAAAAACC 0.868571 -172 CTGAAAAAAACACAGCCTACCAGGGGTAGGC 21 88 0 CACAGCCACC 0.907593 -31 GGCGCCCATTGACAAACCACCCATAAGGTCT 27 16 0 GACAAACACC 0.923912 -132 GACTATGCAGCACAGTAAACCAACCGGAACA 29 78 1 CACAGTAACC 0.876329 -66 GAAAGACTACCTCCTATTCAG 31 1 1 GAAAGACACC 0.807827 -152 CTTTTGGATACATAAAAAACCCGTCCTGAAT 31 26 0 CATAAAAACC 0.868571 -127 GCATGTACCGGATAAAAAACCGTACACTTTT 31 96 1 GATAAAAACC 0.826701 -57 ******* *** Masking position 4 Map Score: 9.94839 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 49 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 AATGCCCTCTGCATACACAGAGGGGATT 7 71 1 GCATACACAG 0.806445 -18 CGTGCGCCGTGGCGTCACAGCTGCTTGCCG 8 244 1 GGCGTCACAG 0.95848 -57 AAAGAGCAATGGCTTGACAGAAGTACCCGC 9 81 1 GGCTTGACAG 0.927052 -90 CACCTCGCGCGCCGACACGGTCTGCTCCCT 10 73 0 GCCGACACGG 0.953168 -97 CCAACCGCGAGCCTTGACAGAACATACCCA 17 45 0 GCCTTGACAG 0.952504 -131 TGTCCAGCAAGGACACACGGACGCCTTGCG 17 79 0 GGACACACGG 0.820388 -97 CACCCGCGGCGACCTCACAGAGATCGCGCC 18 71 0 GACCTCACAG 0.781243 -64 GCTGACAGTATGCTAGACAGGGGGGAAGGT 18 100 1 TGCTAGACAG 0.412651 -35 GCGGTTGATTGCACAGACAGGTTTTTTATG 19 16 0 GCACAGACAG 0.853652 -162 AGACAGGGAGGCGGTCACGGTGCATGAGGA 19 78 1 GCGGTCACGG 0.836524 -100 TAATTTTCAGGGCCTCACAGGGATGCTTGC 19 111 1 GGCCTCACAG 0.95848 -67 GCGCGGTTGCGTCCTCACGGGAGAGTGGGC 26 27 1 GTCCTCACGG 0.794834 -114 CCTACAGACTGCAGTGACGGCGCAGGCGCA 27 71 0 GCAGTGACGG 0.924733 -77 TGCGACAAGATCCTTGACAGAATTCGCACA 30 69 0 TCCTTGACAG 0.682803 -103 GGAGCGGCTGGCAGTGACGGCAAGAAACTT 31 66 1 GCAGTGACGG 0.924733 -87 ********** Masking position 7 Map Score: 10.4457 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 163 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 AGCACGAAGTTCGCCTTCGCGCCTAAGTTA 1 57 1 TCGCCTTCGC 0.946854 -244 AGCCACCACACCGTCTTTGCAGAGGATGCC 3 118 0 CCGTCTTTGC 0.936169 -73 GCGGTCTTGGCCTTCTTTGCGTTTCGAGGG 4 55 1 CCTTCTTTGC 0.935035 -127 TTCAGTCTACCCTCCCTCGAAACGCAAAGA 4 68 0 CCTCCCTCGA 0.834227 -114 ACGCCTTTGCCCGCCTGCGCTTCAGTCTAC 4 88 0 CCGCCTGCGC 0.907205 -94 TGTCGCGCAAACGCCTTTGCCCGCCTGCGC 4 98 0 ACGCCTTTGC 0.816775 -84 AAGCATTTGATCTTCCTCGCATAAGCAGCT 5 139 1 TCTTCCTCGC 0.781659 -36 GGGTTTCCTGCCTTCGTCGCAGTTCTGATG 6 35 1 CCTTCGTCGC 0.942391 -244 ACAACCTCCGTTGCTCAGAATCGC 6 265 0 CCTCCGTTGC 0.97909 -14 CGCCGGTACATCTACGTTGCAAGGTACACC 7 36 0 TCTACGTTGC 0.540407 -53 TTTTTCTCACTCTCCTTTGCGCGCCTGCAC 9 53 0 TCTCCTTTGC 0.935035 -118 GAGATCGCGCCCGCCTTTGAACACATCCCC 18 52 0 CCGCCTTTGA 0.855613 -83 AGCACTCCTGCCTCCCCTGCACGCACACCC 21 19 0 CCTCCCCTGC 0.849013 -100 TGATGCACCCCCACCGTCGCCCCGCGTGTC 25 12 0 CCACCGTCGC 0.899524 -75 ********** Masking position 5 Map Score: 11.8064 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 344 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 9 CGCTTGGGGCAACCGGCACTGTGCGAGAGA 1 16 0 AACCGGCACT 0.965195 -285 CGGTTGCCCCAAGCGGTGCTACGGGTAGCA 1 31 1 AAGCGGTGCT 0.842305 -270 CAGGAAAAGAAAACGGCACTCTGGCGCGGA 5 87 1 AAACGGCACT 0.97631 -88 CCTGGAAATGAAACGACGCTTTTTCGCACG 8 164 1 AAACGACGCT 0.963685 -137 TCTAGAGTGGCAGCGGCGCTCCTCGTTTGT 9 116 1 CAGCGGCGCT 0.927166 -55 CGACAGTGAGAACCGACACTGTGTCTTACG 10 116 0 AACCGACACT 0.900879 -54 TGTACAAGAAAAACGACACTC 16 2 0 AAACGACACT 0.931066 -48 GCTTCCTCCAAAACGGCGCCCATTGACAAA 27 31 0 AAACGGCGCC 0.955567 -117 GCCTACATCTAAACGGCGCGAAAATACGTT 28 68 1 AAACGGCGCG 0.955567 -20 ********** Masking position 2 Map Score: 8.76262 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 98 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 TCGTGTTTATGAAAGGGTCATAATGG 2 6 1 TTTATGAAGG 0.661473 -28 ATTTTCAAGATGTGGGGAAGGGTTTCCTGCC 6 16 1 TGTGGGAAGG 0.904086 -263 GGTACACCTGGGTGTGCACGGGTTGCAGCCC 7 13 0 GGTGTGACGG 0.873553 -76 ATCCCCTCTGTGTATGCAGAGGGCATTGTAC 7 67 0 TGTATGAGAG 0.793346 -22 TTTGCGTACCTGTAAGGAAGGATC 14 17 1 TGTAAGAAGG 0.846569 -14 TCGCGGTTGGGGTACGCAAGGCGTCCGTGTG 17 65 1 GGTACGAAGG 0.92878 -111 AGGGAAAAGAGGTATGCAGGGGATGTGTTCA 18 34 1 GGTATGAGGG 0.98593 -101 CATCCTGCGTGGTAGGAAGGGGAAGACAGGG 19 55 1 GGTAGGAGGG 0.985649 -123 CACTGCAGTCTGTAGGAAGGGACGTGGTATG 27 85 1 TGTAGGAGGG 0.977309 -63 GAAGGGACGTGGTATGTAGGGTATAGTAGAG 27 100 1 GGTATGAGGG 0.98593 -48 ****** **** Masking position 8 Map Score: 6.58153 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 93 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 TAACACTAGACGCATGCATACAGTAGTGTAC 1 194 1 CGCATGCATC 0.658288 -107 TTAAACTGAGCGCTCATATGCGCACGGCATA 3 37 0 CGCTCATATC 0.75864 -154 TACGATTTCACGCGCTTATGCTACAATGGCG 4 25 1 CGCGCTTATC 0.297592 -157 CAAACGCCTTTGCCCGCCTGCGCTTCAGTCT 4 90 0 TGCCCGCCTC 0.614352 -92 GTGCGGACCACGCCCAGCCCCATTGTCGCGC 4 120 0 CGCCCAGCCC 0.705732 -62 GGGCGTGGTCCGCACGTGTTCTGCGCCCGGT 4 136 1 CGCACGTGTC 0.738005 -46 TGTGCGTAATCGCACGTGCTCTGCCAATTAC 6 134 0 CGCACGTGCC 0.865191 -145 GCGCGGTAATCGTTCACCCGCGCGTCCTTTC 8 23 1 CGTTCACCCC 0.472563 -278 TCGCACGGTTCGCTCTCCCCAGTCCTGCGCG 8 187 1 CGCTCTCCCA 0.450494 -114 GACGCCACGGCGCACGCCCTGCGCGGCATCT 8 229 0 CGCACGCCCG 0.847237 -72 TGCCGGTCCACGCCCTTCCACAAAGAGGGTA 8 269 1 CGCCCTTCCC 0.922714 -32 TCTAACGCTTTTACCCTCTTTGTGGA 8 285 0 CGCTTTTACC 0.451964 -16 GCGCGGTCGGCGCACGTGTTCCTGCGCCTGC 12 44 1 CGCACGTGTC 0.738005 -61 CGTGTTCCTGCGCCTGCACTCTTGAATACTG 12 58 1 CGCCTGCACC 0.83317 -47 GCGCCTTTCTCCCCTTACTTAT 16 38 0 CGCCTTTCTC 0.434564 -12 ACAGAGATCGCGCCCGCCTTTGAACACATCC 18 54 0 CGCCCGCCTT 0.641655 -81 GGTGACGCGCCGCTCACCTTCCCCCCTGTCT 18 114 0 CGCTCACCTC 0.932464 -21 CCCTCCGGGGCGCAAGCATCCCTGTGAGGCC 19 121 0 CGCAAGCATC 0.455947 -57 GGCCGATTATCGCACATCCCCCTCCGGGGCG 19 140 0 CGCACATCCC 0.930379 -38 CGCTCGCCCTCCCCGGGGGCC 19 167 0 CGCTCGCCCC 0.985338 -11 CGCCTCTTCCCGCTCTTACCCAAGAGAAACT 20 20 0 CGCTCTTACC 0.84901 -21 CTGCCTCCCCTGCACGCACACCCTACGTGTC 21 11 0 TGCACGCACC 0.609113 -108 ACGTCTTTTGCGCTAGCCTACCCCTGGTAGG 21 73 1 CGCTAGCCTC 0.653011 -46 CGCACACCCCGATCCAGGGCA 25 76 0 CGCACACCCG 0.721923 -11 AATCTTTAGACGCCCACTCTCCCGTGAGGAC 26 37 0 CGCCCACTCC 0.648653 -104 CGGTAGGATACGCTTTTACACACACTGTACA 26 88 1 CGCTTTTACC 0.451964 -53 GCGCTCACATCCAAAACAGAAA 27 136 0 CGCTCACATC 0.870881 -12 TGACAGAATTCGCACACACCTCTAGCCTCTC 30 54 0 CGCACACACT 0.450518 -118 CACTGCCAGCCGCTCCTCCCCAGAGCTTTTG 31 51 0 CGCTCCTCCC 0.753527 -102 ********* * Masking position 2 Map Score: 22.2471 Number of sites scoring better than the average of aligned sites = 2317 Number in coding regions = 2125 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 12 GGTTCTCTCGCACAGTGCCGGTTGCCCCAA 1 13 1 CACAGTGCCG 0.959246 -288 AGGTCCGCGCCAGAGTGCCGTTTTCTTTTC 5 90 0 CAGAGTGCCG 0.955011 -85 CCTCTGCATACACAGAGGGGATT 7 76 1 CACAGAGGGG 0.639326 -13 TCCACAGCAGCACGGTGCAGGCGCGCAAAG 9 39 1 CACGGTGCAG 0.961848 -132 GCCACTCTAGAAGGGAGCGGGTACTTCTGT 9 97 0 AAGGGAGCGG 0.598472 -74 TGGTCTTGTACACGCAGGAGGTCAGAACGA 9 145 1 CACGCAGGAG 0.778491 -26 GTGCACCTTCAAGGGAGCAGACCGTGTCGG 10 62 1 AAGGGAGCAG 0.676728 -108 AGGTGCCAGGCACGCTTCCGTAAGACACAG 10 98 1 CACGCTTCCG 0.622334 -72 TTCCGTAAGACACAGTGTCGGTTCTCACTG 10 113 1 CACAGTGTCG 0.571149 -57 AGAGCGTATACAGGCAGGGGGCCACAGACT 11 22 1 CAGGCAGGGG 0.692946 -25 CAGGGGGCCACAGACTACCGT 11 36 1 CAGACTACCG 0.403492 -11 GACGGACACGCACCCGTGATATAGAG 12 7 1 CACGCACCCG 0.642151 -98 TCCAGTATTCAAGAGTGCAGGCGCAGGAAC 12 61 0 AAGAGTGCAG 0.56461 -44 GTGAGCATTGCACAGAGCAGCACCTTCCCA 13 77 0 CACAGAGCAG 0.89397 -64 TCCTACCACGCAGGATGCCGCTTCACGCGG 19 42 0 CAGGATGCCG 0.769922 -136 AAGGGGAAGACAGGGAGGCGGTCACGGTGC 19 71 1 CAGGGAGGCG 0.910059 -107 GGGAGGCGGTCACGGTGCATGAGGAGTGTA 19 83 1 CACGGTGCAT 0.540769 -95 TCCCTTCCTACAGACTGCAGTGACGGCGCA 27 77 0 CAGACTGCAG 0.869274 -71 ACAGGTGGTACACGCTGCCCGATGAACACC 29 106 1 CACGCTGCCC 0.69699 -38 ********** Masking position 2 Map Score: 11.4473 Number of sites scoring better than the average of aligned sites = 994 Number in coding regions = 908 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 13 CGGGCTCGCGTGCAGACGCGATACGGTAGC 1 128 1 TGCAGACGCG 0.862319 -173 GCGCCATTGTAGCATAAGCGCGTGAAATCG 4 27 0 AGCATAAGCG 0.364463 -155 TAGACTGAAGCGCAGGCGGGCAAAGGCGTT 4 89 1 CGCAGGCGGG 0.979489 -93 TGATCTTCCTCGCATAAGCAGCTACAGTTG 5 146 1 CGCATAAGCA 0.771974 -29 CGTATTCGATTGCAGAAGGTGTAATGTGGG 6 75 1 TGCAGAAGGT 0.785602 -204 GGGTATCTGGTGCAGGTGGGGAAAGGTGTG 6 169 1 TGCAGGTGGG 0.847028 -110 TGCTCAGAATCGCATAAGGAGCGTAAGGCA 6 248 0 CGCATAAGGA 0.850331 -31 GAAACACTCCCGCAGAAAGGACGCGCGGGT 8 38 0 CGCAGAAAGG 0.52437 -263 ATACTCTACTTGCATCTGGTTTTCTATGTC 8 70 1 TGCATCTGGT 0.216565 -231 AGCAGCACGGTGCAGGCGCGCAAAGGAGAG 9 44 1 TGCAGGCGCG 0.937816 -127 GTCTTGTACACGCAGGAGGTCAGAACGAGG 9 147 1 CGCAGGAGGT 0.942347 -24 TATTCAAGAGTGCAGGCGCAGGAACACGTG 12 56 0 TGCAGGCGCA 0.869341 -49 GCGAGAAGTGCGCATGAGGAAGAAAGGACC 17 139 1 CGCATGAGGA 0.928436 -37 GCGGTCACGGTGCATGAGGAGTGTAATTTT 19 88 1 TGCATGAGGA 0.868717 -90 ACGGTGGGGGTGCATCAGCGCGTTTTGTCT 25 25 1 TGCATCAGCG 0.778971 -62 GACGCAACCGCGCAGGCGCGTTCCCATTT 26 10 0 CGCAGGCGCG 0.966823 -131 CGGCACCATACTCAGGAGGATCCGCTGC 26 123 1 CTCAGGAGGA 0.537026 -18 TGACAAACCACCCATAAGGTCTCACGA 27 8 0 CCCATAAGGT 0.172585 -140 GCAGTGACGGCGCAGGCGCACTGGCTCAGT 27 61 0 CGCAGGCGCA 0.928587 -87 TTTTTCGTTCTGCATCAGGGTACATCTGCC 28 28 0 TGCATCAGGG 0.859877 -60 AGATGTTGACCGCAGCAGGGAAAAGGCGAT 30 142 1 CGCAGCAGGG 0.960448 -30 ********** Masking position 4 Map Score: 21.9807 Number of sites scoring better than the average of aligned sites = 1245 Number in coding regions = 1170 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 14 CGTCTTACTTGGGGCATTAACTTAGGCGCG 1 74 0 GGGGCATTAA 0.915716 -227 GAATACGAAAAAGGCATCATCAGAACTGCG 6 52 0 AAGGCATCAT 0.784371 -227 GGTGTAATGTGGGGCATTATTGCATACGTA 6 92 1 GGGGCATTAT 0.98125 -187 TAAGGAGCGTAAGGCATTATATCATTTTCG 6 234 0 AAGGCATTAT 0.922009 -45 GTGTATGCAGAGGGCATTGTACACGCCGGT 7 59 0 AGGGCATTGT 0.966845 -30 ACAGGATAGAGGGGCATTGTAATGGGAAGG 13 55 1 GGGGCATTGT 0.972387 -86 GGAGGGTATTATCGCCTTTTCC 30 160 0 AGGGTATTAT 0.848969 -12 ********** Masking position 6 Map Score: 2.81262 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 22 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 15 ATGCGCACGGCATAAGTACCGTGCGCACAA 3 21 0 CATAAGTACC 0.83294 -170 CGTGCACACCCAGGTGTACCTTGCAACGTA 7 24 1 CAGGTGTACC 0.964524 -65 CCTTGCAACGTAGATGTACCGGCGTGTACA 7 42 1 TAGATGTACC 0.93183 -47 AATGGCTTGACAGAAGTACCCGCTCCCTTC 9 88 1 CAGAAGTACC 0.974644 -83 ATCTGAGAAGGAGATGCACCCTCTAGCAAT 15 27 1 GAGATGCACC 0.931661 -32 ACAAAACGCGCTGATGCACCCCCACCGTCG 25 23 0 CTGATGCACC 0.925059 -64 CACACTACGGCAGATGTACCCTGATGCAGA 28 20 1 CAGATGTACC 0.988809 -68 ********** Masking position 8 Map Score: 3.84607 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 14 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467