AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00970_tpal_reg_100.orf -o00970_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 TP0015 190 phenylalanyl-tRNA synthetase beta subunit (pheT) #2 TP0091 181 cysteinyl-tRNA synthetase (cysS) #3 TP0162 174 Holliday junction DNA helicase (ruvB) #4 TP0452 278 isoleucyl-tRNA synthetase (ileS) #5 TP0586 88 leucyl-tRNA synthetase (leuS) #6 TP0609 300 asparaginyl-tRNA synthetase (asnS) #7 TP0632 104 tryptophanyl-tRNA synthetase (trsA) #8 TP0641 140 histidyl-tRNA synthetase (hisS) #9 TP0644 30 lysyl-tRNA synthetase (lysS-1) #10 TP0645 58 T. pallidum predicted coding region TP0645 #11 TP0647 49 seryl-tRNA synthetase (serS) #12 TP0651 175 conserved hypothetical integral membrane protein #13 TP0672 134 glycyl-tRNA synthetase (glyS) #14 TP0673 177 glutamyl-tRNA synthetase (gltX) #15 TP0757 40 polypeptide deformylase (def) #16 TP0758 118 ribosomal protein S21 (rpsU) #17 TP0798 32 methionyl-tRNA synthetase (metG) #18 TP0831 22 arginyl-tRNA synthetase (argS) #19 TP0832 66 T. pallidum predicted coding region TP0832 #20 TP0834 86 tyrosyl-tRNA synthetase (tyrS) #21 TP0835 140 ankyrin, putative #22 TP0837 147 threonyl-tRNA synthetase (thrS) #23 TP0973 87 phenylalanyl-tRNA synthetase alpha subunit (pheS) #24 TP0985 143 aspartyl-tRNA synthetase (aspS) #25 TP1017 171 alanyl-tRNA synthetase (alaS) #26 TP1035 152 valyl-tRNA synthetase (valS) #27 TP1041 79 ATP-dependent Clp protease proteolytic component (clpP-2) Motif number 1 CATGCCTTTGTGCGCACGGTACTTATGCCG 1 14 1 TGCGCACGGT 0.882094 -177 AGCGCTCATATGCGCACGGCATAAGTACCG 1 30 0 TGCGCACGGC 0.893325 -161 GCCACTACACGGCACACGTGCTCTACACTT 1 91 0 GGCACACGTG 0.704138 -100 GGCCAGCCACCACACCGTCTTTGCAGAGGA 1 122 0 CACACCGTCT 0.487279 -69 CCGTATACTGAGCACGGTCGGAGGGCTC 1 173 1 AGCACGGTCG 0.517895 -18 AGGCCAAGACCGCGCCATTGTAGCATAAGC 2 38 0 CGCGCCATTG 0.816618 -144 GGTAGACTGAAGCGCAGGCGGGCAAAGGCG 2 87 1 AGCGCAGGCG 0.884749 -95 GCACGTGTTCTGCGCCCGGTTGGGAGAAAC 2 147 1 TGCGCCCGGT 0.946232 -35 GTGCGCCCCTTCGAAGTTTCT 2 171 0 TGCGCCCCTT 0.871182 -11 CAGCTACAGTTGCGCCCTCTT 3 164 1 TGCGCCCTCT 0.921472 -11 CGTGCGATTACGCACACGTGGGGTATCTGG 4 149 1 CGCACACGTG 0.890385 -130 GGAAAGGTGTGGCGCCGGTCATAAGACGTA 4 188 1 GGCGCCGGTC 0.944965 -91 CACCTGGGTGTGCACGGGTTGCAGCCCCT 5 10 0 TGCACGGGTT 0.750775 -79 GCAGAAAGGACGCGCGGGTGAACGATTACC 6 27 0 CGCGCGGGTG 0.930352 -274 GAGCGGCCGAGGCGCGGTCTTCTGTGACCG 6 114 0 GGCGCGGTCT 0.861835 -187 GACGCTTTTTCGCACGGTTCGCTCTCCCCA 6 178 1 CGCACGGTTC 0.77589 -123 TCCCCAGTCCTGCGCGGCGTTCCATGCAGA 6 202 1 TGCGCGGCGT 0.820021 -99 ATGCAGATGCCGCGCAGGGCGTGCGCCGTG 6 225 1 CGCGCAGGGC 0.96003 -76 GCGCAGGGCGTGCGCCGTGGCGTCACAGCT 6 236 1 TGCGCCGTGG 0.929619 -65 CTTGCCGGTCCACGCCCTTCCACAAAGAGG 6 267 1 CACGCCCTTC 0.717245 -34 GACGGACACGCACCCGTGATATAGAGGA 7 9 1 CGCACCCGTG 0.950044 -96 GTGCGCCGACCGCGCAGCCCTCCTCTATAT 7 29 0 CGCGCAGCCC 0.937325 -76 CTGCGCGGTCGGCGCACGTGTTCCTGCGCC 7 42 1 GGCGCACGTG 0.886019 -63 GAGAAGGAGATGCACCCTCTAGCAATAGGT 10 31 1 TGCACCCTCT 0.733362 -28 ACCCAAATACCGCACCATCGGCCTCCGCAA 12 20 0 CGCACCATCG 0.628411 -156 GCGAGCGTAACACGCCAGCGGTAATCTGTC 12 105 0 CACGCCAGCG 0.686516 -71 GCGCACTTCTCGCGCCAGCGAGCGTAACAC 12 122 0 CGCGCCAGCG 0.946047 -54 TTCTTCCTCATGCGCACTTCTCGCGCCAGC 12 133 0 TGCGCACTTC 0.775096 -43 ATTCTCAGTTAACGCGGGCTATAGGGAAAA 13 12 1 AACGCGGGCT 0.438937 -123 TCACAGAGATCGCGCCCGCCTTTGAACACA 13 57 0 CGCGCCCGCC 0.90231 -78 GCATACTGTCAGCACCCGCGGCGACCTCAC 13 83 0 AGCACCCGCG 0.793214 -52 GGTGACGCGCCGCTCACCTTCCCCC 13 120 0 CGCGCCGCTC 0.955973 -15 GATGCCGCTTCACGCGGTTGATTGCACAGA 14 29 0 CACGCGGTTG 0.732048 -149 CAGGGATGCTTGCGCCCCGGAGGGGGATGT 14 128 1 TGCGCCCCGG 0.91783 -50 CTCCCCTGCACGCACACCCTACGTGTC 16 8 0 CGCACACCCT 0.73931 -111 TGACACGCGGGGCGACGGTGGGG 20 4 1 CACGCGGGGC 0.811806 -83 CGCACACCCCGATCCAGGGC 20 77 0 CGCACACCCC 0.760453 -10 AGGACGCAACCGCGCAGGCGCGTTCCCATT 21 12 0 CGCGCAGGCG 0.982095 -129 CTGCAGTGACGGCGCAGGCGCACTGGCTCA 22 76 1 GGCGCAGGCG 0.946559 -72 TTTGTCAATGGGCGCCGTTTTGGAGGAAGC 22 108 0 GGCGCCGTTT 0.85852 -40 AACGTATTTTCGCGCCGTTTAGATGTAGGC 23 68 0 CGCGCCGTTT 0.954071 -20 GCGCGGTCTGTGCGCGGCGTAATGGAATCT 24 33 0 TGCGCGGCGT 0.820021 -111 TGCTACACTTCGCGCGCGGTCTGTGCGCGG 24 46 0 CGCGCGCGGT 0.919949 -98 GAAGAGGTTATACGCGCGTTGCTTTGTGGG 27 49 1 TACGCGCGTT 0.578797 -31 ********** Masking position 5 Map Score: 52.9884 Number of sites scoring better than the average of aligned sites = 7654 Number in coding regions = 7108 Number in noncoding regions = 546 Number of orfs with sites within 600 bp upstream = 223 Fraction of orfs with sites within 600 bp upstream = 0.0358175 Motif number 2 CTAAAGTGTAGAGCACGTGTGCCGTGTAGTG 1 88 1 GAGCAGTGTG 0.680803 -103 ACCGTATACTGAGCACGGTCGGAGGGCTC 1 172 1 GAGCAGGTCG 0.529058 -19 AAGCGCAGGCGGGCAAAGGCGTTTGCGCGAC 2 96 1 GGGCAAGGCG 0.977138 -86 GCGCGACAATGGGGCTGGGCGTGGTCCGCAC 2 120 1 GGGGCGGGCG 0.989999 -62 TTCAAGATGTGGGGAAGGGTTTCCTGCCTTC 4 19 1 GGGGAGGGTT 0.900852 -260 GTAATTGGCAGAGCACGTGCGATTACGCACA 4 134 1 GAGCAGTGCG 0.881558 -145 TGGTGCAGGTGGGGAAAGGTGTGGCGCCGGT 4 176 1 GGGGAAGGTG 0.968736 -103 AGATGAGGAGCGGCCGAGGCGCGGTCTTCTG 6 120 0 CGGCCAGGCG 0.895273 -181 AGATGCCGCGCAGGGCGTGCGCCGTGGCGTC 6 229 1 CAGGGGTGCG 0.909596 -72 TACCCTCTTTGTGGAAGGGCGTGGACCGGCA 6 269 0 GTGGAGGGCG 0.903613 -32 TCCACAAAGAGGGTAAAAGCGTTAGA 6 285 1 GGGTAAAGCG 0.575667 -16 GCTGCGCGGTCGGCGCACGTGTTCCTGCGCC 7 41 1 CGGCGACGTG 0.57594 -64 CAGTATTCAAGAGTGCAGGCGCAGGAACACG 7 58 0 GAGTGAGGCG 0.797549 -47 TTTTAAAGGTGAGGAAGCGCTC 8 2 0 GAGGAGCGCT 0.598481 -139 GCATTGTAATGGGAAGGTGCTGCTCTGTGCA 8 68 1 GGGAAGTGCT 0.615871 -73 ATAAGTAAGGGGAGAAAGGCGC 11 38 1 GGAGAAGGCG 0.821827 -12 CTCGCTGGCGCGAGAAGTGCGCATGAGGAAG 12 130 1 CGAGAGTGCG 0.678221 -46 GAGGTATGCAGGGGATGTGTTCAAAGGCGGG 13 42 1 GGGGAGTGTT 0.719723 -93 TGCTAGACAGGGGGGAAGGTGAGCGGCGCGT 13 110 1 GGGGGAGGTG 0.965343 -25 CGCCCCGGAGGGGGATGTGCGATAATCGGCC 14 140 1 GGGGAGTGCG 0.988113 -38 AATCGGCCCCCGGGGAGGGCGAGCG 14 163 1 CGGGGGGGCG 0.993676 -15 GGGTAAGAGCGGGAAGAGGCG 15 30 1 GGGAAAGGCG 0.950851 -11 GACACGTAGGGTGTGCGTGCAGGGGAGGC 16 9 1 GGGTGGCGTG 0.737756 -110 GTTTTTTTCAGGGGAGGGTCG 16 108 1 GGGGAGGTCG 0.926181 -11 CGCGGGGCGACGGTGGGGGTGCATCAGCGCG 20 16 1 CGGTGGGGTG 0.889598 -71 CACCCCGATCCAGGGCAGGCGGTTCAGTCCC 20 62 0 CAGGGAGGCG 0.929017 -25 TGCCCTGGATCGGGGTGTGCG 20 76 1 CGGGGGTGCG 0.977981 -11 GTCCTCACGGGAGAGTGGGCGTCTAAAGATT 21 37 1 GAGAGGGGCG 0.914645 -104 ACTGCAGTGACGGCGCAGGCGCACTGGCTCA 22 75 1 CGGCGAGGCG 0.95805 -73 ACTTCGCGCGCGGTCTGTGCGCGGCGTAATG 24 39 0 CGGTCGTGCG 0.748454 -105 GTAAACCAACCGGAACAGGTGGTACACGCTG 24 92 1 CGGAAAGGTG 0.76719 -52 TGGTGTTCATCGGGCAGCGTGTACCACCTGT 24 106 0 CGGGCGCGTG 0.77769 -38 GACCGCAGCAGGGAAAAGGCGATAATACCCT 25 149 1 GGGAAAGGCG 0.950851 -23 ACCTCCTATTCAGGACGGGTTTTTTATGTAT 26 19 1 CAGGAGGGTT 0.550241 -134 CAAAAGCTCTGGGGAGGAGCGGCTGGCAGTG 26 51 1 GGGGAGAGCG 0.953758 -102 ***** ***** Masking position 3 Map Score: 52.8299 Number of sites scoring better than the average of aligned sites = 1970 Number in coding regions = 1728 Number in noncoding regions = 242 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 3 TGACTAAAGTGTAGAGCACGTGTGCCGTGT 1 85 1 GTAGAGCACG 0.468857 -106 CCCTCGAAACGCAAAGAAGGCCAAGACCGC 2 55 0 GCAAAGAAGG 0.841188 -127 CCAACCGGGCGCAGAACACGTGCGGACCAC 2 140 0 GCAGAACACG 0.811135 -42 AGCGGATCACGCAGGAAACGTCAATTTTTC 3 47 1 GCAGGAAACG 0.920324 -128 AGAACTGCGACGAAGGCAGGAAACCCTTCC 4 31 0 CGAAGGCAGG 0.662076 -248 GCAGTAATTGGCAGAGCACGTGCGATTACG 4 131 1 GCAGAGCACG 0.851726 -148 GCGATTCTGAGCAACGGAGGTTGT 4 265 1 GCAACGGAGG 0.753632 -14 GGAACGCCGCGCAGGACTGGGGAGAGCGAA 6 195 0 GCAGGACTGG 0.545355 -106 CGCGGCATCTGCATGGAACGCCGCGCAGGA 6 209 0 GCATGGAACG 0.574424 -92 TTGCGTACCTGTAAGGAAGGATC 9 18 1 GTAAGGAAGG 0.793801 -13 AATAAGTAAGGGGAGAAAGGCGC 11 37 1 GGGAGAAAGG 0.432292 -13 GTGCGCATGAGGAAGAAAGGACCACCCCGT 12 146 1 GGAAGAAAGG 0.917375 -30 AATGCGTAAGACGGGGTGGTCCTTT 12 161 0 GTAAGACGGG 0.628725 -15 CGGGCTATAGGGAAAAGAGGTATGCAGGGG 13 26 1 GGAAAAGAGG 0.735001 -109 AAAGAGGTATGCAGGGGATGTGTTCAAAGG 13 39 1 GCAGGGGATG 0.508069 -96 CTGACAGTATGCTAGACAGGGGGGAAGGTG 13 101 1 GCTAGACAGG 0.728819 -34 CATCCTGCGTGGTAGGAAGGGGAAGACAGG 14 55 1 GGTAGGAAGG 0.547863 -123 GGTAGGAAGGGGAAGACAGGGAGGCGGTCA 14 65 1 GGAAGACAGG 0.951278 -113 GGTAAGAGCGGGAAGAGGCG 15 31 1 GGAAGAGGCG 0.793673 -10 GGGTGTGCGTGCAGGGGAGGCAGGAGTGCT 16 19 1 GCAGGGGAGG 0.954183 -100 GAGTGCTTTCGGAAGAAACGATTGACAGGG 16 42 1 GGAAGAAACG 0.906815 -77 GTAGGCTAGCGCAAAAGACGTCCCCTGTCA 16 64 0 GCAAAAGACG 0.803957 -55 TTAAATCAGAGTAGGAAACGCT 17 21 1 GTAGGAAACG 0.639644 -12 TATATTTTTTGCAAGGCGGGGATAAGGGAC 19 45 1 GCAAGGCGGG 0.936463 -22 ACACCCCGATCCAGGGCAGGCGGTTCAGTC 20 64 0 CCAGGGCAGG 0.699291 -23 GCAGTCTGTAGGAAGGGACGTGGTATGTAG 22 50 0 GGAAGGGACG 0.938942 -98 CTAGCCTCTCGCAAGACAGTTTCGCACCCT 25 34 0 GCAAGACAGT 0.615023 -138 ACCGCAGCAGGGAAAAGGCGATAATACCCT 25 150 1 GGAAAAGGCG 0.448526 -22 GGCAGTGACGGCAAGAAACTTGCATGTACC 26 75 1 GCAAGAAACT 0.443281 -78 TATTTTGCCTGCAATAAACGAAGAGGTTAT 27 30 1 GCAATAAACG 0.383486 -50 CACCCACAAAGCAACGCGCGTATAACCTCT 27 51 0 GCAACGCGCG 0.571752 -29 ********** Masking position 10 Map Score: 23.4726 Number of sites scoring better than the average of aligned sites = 1471 Number in coding regions = 1323 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 4 ATGCTACAATGGCGCGGTCTTGGCCTTCTT 2 42 1 GGCGCGGTCT 0.988083 -140 AATGGGGCTGGGCGTGGTCCGCACGTGTTC 2 127 1 GGCGTGGTCC 0.994889 -55 CTCCCAACCGGGCGCAGAACACGTGCGGAC 2 143 0 GGCGCAGAAC 0.638016 -39 TGACGTTTCCTGCGTGATCCGCTACTTTGA 3 40 0 TGCGTGATCC 0.75616 -135 ACGGCACTCTGGCGCGGACCTCTCGAGCTA 3 99 1 GGCGCGGACC 0.994344 -76 TAGATGTACCGGCGTGTACAATGCCCTCTG 5 52 1 GGCGTGTACA 0.829146 -37 GAGTCTTATAGGCGCGGTAATCGTTCACCC 6 12 1 GGCGCGGTAA 0.931867 -289 TATGTCGTACGGCGTGGTCCCGGTCACAGA 6 94 1 GGCGTGGTCC 0.994889 -207 GAGCGGCCGAGGCGCGGTCTTCTGTGACCG 6 114 0 GGCGCGGTCT 0.988083 -187 TGCCGCGCAGGGCGTGCGCCGTGGCGTCAC 6 232 1 GGCGTGCGCC 0.639084 -69 TTTGTGGAAGGGCGTGGACCGGCAAGCAGC 6 263 0 GGCGTGGACC 0.9901 -38 AGAGGAGGGCTGCGCGGTCGGCGCACGTGT 7 33 1 TGCGCGGTCG 0.766054 -72 GATTACCGCTGGCGTGTTACGCTCGCTGGC 12 109 1 GGCGTGTTAC 0.924177 -67 TGCGTAAGACGGGGTGGTCCTTTCTTCCTC 12 154 0 GGGGTGGTCC 0.923812 -22 TTCAAAGGCGGGCGCGATCTCTGTGAGGTC 13 61 1 GGCGCGATCT 0.937744 -74 GAAGGTGAGCGGCGCGTCACC 13 124 1 GGCGCGTCAC 0.790328 -11 CAACCGCGCAGGCGCGTTCCCATTT 21 6 0 GGCGCGTTCC 0.990523 -135 ACATCTAAACGGCGCGAAAATACGTT 23 72 1 GGCGCGAAAA 0.559675 -16 CTACACTTCGCGCGCGGTCTGTGCGCGGCG 24 44 0 CGCGCGGTCT 0.859345 -100 TTCATCGGGCAGCGTGTACCACCTGTTCCG 24 102 0 AGCGTGTACC 0.591191 -42 ********** Masking position 4 Map Score: 36.0689 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 277 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 CAATTTTTCAGTACCCTTTCAGGAAAAGAAAA 3 68 1 GTACCCTCAG 0.912651 -107 GTTCACCCGCGCGTCCTTTCTGCGGGAGTGTT 6 34 1 GCGTCCTCTG 0.990938 -267 AGGCGTCCGTGTGTCCTTGCTGGACAGATTAC 12 83 1 GTGTCCTCTG 0.975714 -93 AGCACCCGCGGCGACCTCACAGAGATCGCGCC 13 71 0 GCGACCTCAG 0.933297 -64 CCCCTGTCTAGCATACTGTCAGCACCCGCGGC 13 91 0 GCATACTCAG 0.839003 -44 GCGTGAAGCGGCATCCTGCGTGGTAGGAAGGG 14 44 1 GCATCCTGTG 0.904905 -134 CTGCGCGGTTGCGTCCTCACGGGAGAGTGGGC 21 25 1 GCGTCCTCGG 0.986592 -116 GTGTAAAAGCGTATCCTACCGGTTTCGGCGAT 21 77 0 GTATCCTCGG 0.952708 -64 CAGTGCGCCTGCGCCGTCACTGCAGTCTGTAG 22 69 0 GCGCCGTCTG 0.845939 -79 GTATCCTCCCAGAGGTTAAAAA 24 1 1 GTATCCTCAG 0.960474 -143 CGTACACTTTTCATCCTATCTGCTGTGAAATG 26 116 1 TCATCCTCTG 0.865237 -37 ******* *** Masking position 7 Map Score: 9.6758 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 88 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 GCTCATGCCTTTGTGCGCACGGTACTT 1 7 1 GCCTTGTGCG 0.913493 -184 TATGCCGTGCGCATATGAGCGCTCAGTTTAA 1 37 1 GCATTGAGCG 0.943135 -154 CGCCATTGTAGCATAAGCGCGTGAAATCGTA 2 25 0 GCATAGCGCG 0.951446 -157 GCGGGCAAAGGCGTTTGCGCGACAATGGGGC 2 104 1 GCGTTGCGCG 0.994441 -78 AGGTACACCTGGGTGTGCACGGGTTGCAGCC 5 14 0 GGGTTGCACG 0.93052 -75 TCCACAAAGAGGGTAAAAGCGTTAGA 6 285 1 GGGTAAAGCG 0.62209 -16 GATATAGAGGAGGGCTGCGCGGTCGGCGCAC 7 28 1 AGGGTGCGCG 0.880578 -77 CGCCCCGGAGGGGGATGTGCGATAATCGGCC 14 140 1 GGGGTGTGCG 0.944501 -38 AGTTTCTCTTGGGTAAGAGCGGGAAGAGGCG 15 20 1 GGGTAGAGCG 0.966769 -21 GACACGTAGGGTGTGCGTGCAGGGGAGGC 16 9 1 GGGTTGCGTG 0.93052 -110 CGGTGGGGGTGCATCAGCGCGTTTTGTCTTT 20 26 1 GCATAGCGCG 0.951446 -61 AAATGGGAACGCGCCTGCGCGGTTGCGTCCT 21 11 1 GCGCTGCGCG 0.965772 -130 TTTCTGTTTTGGATGTGAGCGC 22 2 0 GGATTGAGCG 0.956416 -146 TTCGCGCGCGGTCTGTGCGCGGCGTAATGGA 24 37 0 GTCTTGCGCG 0.846851 -107 GAGAGGCTAGAGGTGTGTGCGAATTCTGTCA 25 54 1 AGGTTGTGCG 0.862888 -118 **** ****** Masking position 11 Map Score: 19.5811 Number of sites scoring better than the average of aligned sites = 792 Number in coding regions = 729 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 7 TATGCGCACGGCATAAGTACCGTGCGCACAA 1 21 0 GCATAAGACC 0.802796 -170 CACCGTCTTTGCAGAGGATGCCACTACACGG 1 109 0 GCAGAGGTGC 0.979741 -82 GATCTTCCTCGCATAAGCAGCTACAGTTGCG 3 147 1 GCATAAGAGC 0.838351 -28 GTATTCGATTGCAGAAGGTGTAATGTGGGGC 4 76 1 GCAGAAGTGT 0.589938 -203 CACACGTGGGGTATCTGGTGCAGGTGGGGAA 4 161 1 GTATCTGTGC 0.413683 -118 GCTCAGAATCGCATAAGGAGCGTAAGGCATT 4 246 0 GCATAAGAGC 0.869687 -33 ACCTTGCAACGTAGATGTACCGGCGTGTACA 5 41 1 GTAGATGACC 0.852505 -48 GGCGTTCCATGCAGATGCCGCGCAGGGCGTG 6 217 1 GCAGATGCGC 0.921708 -84 TACTTTTAAAGGTGAGGAAGCGCTC 8 5 0 GGTGAGGAGC 0.690493 -136 AATCTGAGAAGGAGATGCACCCTCTAGCAAT 10 26 1 GGAGATGACC 0.859481 -33 CATTGCGGAGGCCGATGGTGCGGTATTTGGG 12 18 1 GCCGATGTGC 0.930482 -158 CTGTGAGGTCGCCGCGGGTGCTGACAGTATG 13 81 1 GCCGCGGTGC 0.858128 -54 GACAAAACGCGCTGATGCACCCCCACCGTCG 20 23 0 GCTGATGACC 0.852367 -64 GCAGCGGATCCTCCTGAGTAT 21 130 0 GCAGCGGTCC 0.89883 -11 GTAGGGTATAGTAGAGGATGCTTTCTGTTTT 22 23 0 GTAGAGGTGC 0.906472 -125 CCACACTACGGCAGATGTACCCTGATGCAGA 23 19 1 GCAGATGACC 0.969518 -69 ******* *** Masking position 7 Map Score: 11.6198 Number of sites scoring better than the average of aligned sites = 722 Number in coding regions = 685 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 8 ACAACCTCCGTTGCTCAGAATCGCATAAG 4 260 0 GTTGCTCAGA 0.965534 -19 TTTTGTGAGCATTGCACAGAGCAGCACCTT 8 81 0 ATTGCACAGA 0.967583 -60 GTGTGTCCTTGCTGGACAGATTACCGCTGG 12 91 1 GCTGGACAGA 0.934461 -85 CACGCGGTTGATTGCACAGACAGGTTTTTT 14 19 0 ATTGCACAGA 0.967583 -159 TTTTACACACACTGTACAGACGCGGCACCA 21 101 1 ACTGTACAGA 0.747648 -40 CGCGCGAAGTGTAGCACAGACTATGCAGCA 24 60 1 GTAGCACAGA 0.965537 -84 CACAGACTATGCAGCACAGTAAACCAACCG 24 74 1 GCAGCACAGT 0.830873 -70 TTGTCGCAAGGTTGCTCAGAGAGTCCCCGT 25 91 1 GTTGCTCAGA 0.965534 -81 ********** Masking position 8 Map Score: 5.87236 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 90 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 AGTATACGGTCAAAAAAAGGACACCACAAGGGCC 1 148 0 CAAAAAACAC 0.919045 -43 AGTACCCTTTCAGGAAAAGAAAACGGCACTCTGG 3 77 1 CGAAAAAAAC 0.975453 -98 GAGTAAGTTCCCTGGAAATGAAACGACGCTTTTT 6 154 1 CGGAAAAAAC 0.9244 -147 CCTGTGAGGCCCTGAAAATTACACTCCTCATGCA 14 98 0 CGAAAAACAC 0.990259 -80 CGACCCTCCCCTGAAAAAAACACAGCCTACCAG 16 96 0 CGAAAAACAC 0.990259 -23 GGTTCAGTCCCGAGAAAAAGACAAAACGCGCTGA 20 39 0 CGAAAAACAA 0.958767 -48 TGACCCTAAACGGGAAAAAGAAACGGGGACTCTC 25 109 0 CGAAAAAAAC 0.975453 -63 TCGTTTATTGCAGGCAAAATACAATAGGTTGTAT 27 17 0 CGCAAAACAA 0.877373 -63 * ***** **** Masking position 7 Map Score: 5.79173 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 21 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 ACTTGCATCTGGTTTTCTATGTCGTACGGC 6 77 1 GGTTTTCTAT 0.953004 -224 TGCACAGACAGGTTTTTTATGAAAGA 14 7 0 GGTTTTTTAT 0.971887 -171 ATTCAGGACGGGTTTTTTATGTATCCAAAA 26 26 1 GGTTTTTTAT 0.971887 -127 AAAAGTGTACGGTTTTTTATCCGGTACATG 26 97 0 GGTTTTTTAT 0.971887 -56 ********** Masking position 5 Map Score: 2.88834 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 2 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 GACGCCACGGCGCACGCCCTGCGCGGCATCTG 6 228 0 CGCACGCCGC 0.962445 -73 CGCAGGAACACGTGCGCCGACCGCGCAGCCCT 7 38 0 CGTGCGCCCC 0.894203 -67 GGTTGGGGTACGCAAGGCGTCCGTGTGTCCTT 12 69 1 CGCAAGGCCC 0.880477 -107 GGTGACGCGCCGCTCACCTTCCCCCCTGTCTA 13 113 0 CGCTCACCCC 0.982597 -22 CCCTCCGGGGCGCAAGCATCCCTGTGAGGCCC 14 120 0 CGCAAGCACC 0.973862 -58 GGCCGATTATCGCACATCCCCCTCCGGGGCGC 14 139 0 CGCACATCCC 0.872954 -39 CGCTCGCCCTCCCCGGGGGCCG 14 166 0 CGCTCGCCCC 0.99301 -12 CTGCCTCCCCTGCACGCACACCCTACGTGTC 16 10 0 TGCACGCACC 0.89515 -109 TCGTTTCTTCCGAAAGCACTCCTGCCTCCCCT 16 31 0 CGAAAGCACC 0.727777 -88 ACGTCTTTTGCGCTAGCCTACCCCTGGTAGGC 16 73 1 CGCTAGCCCC 0.976098 -46 GCGCTCACATCCAAAACAGAAAG 22 2 1 CGCTCACACA 0.666708 -146 TCCATTACGCCGCGCACAGACCGCGCGCGAAG 24 37 1 CGCGCACACC 0.9618 -107 TGACAGAATTCGCACACACCTCTAGCCTCTCG 25 53 0 CGCACACATC 0.78705 -119 ******** ** Masking position 2 Map Score: 14.5047 Number of sites scoring better than the average of aligned sites = 553 Number in coding regions = 510 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 12 TGCAGAGGATGCCACTACACGGCACACGTG 1 101 0 GCCACTACAC 0.932992 -90 ACAAGGGCCAGCCACCACACCGTCTTTGCA 1 127 0 GCCACCACAC 0.723915 -64 GTGACACTCCTTGGGTGAATTT 3 3 1 GACACTCCTT 0.845026 -172 TCCTGCGTGATCCGCTACTTTGATGCATCA 3 33 0 TCCGCTACTT 0.781995 -142 TATGACCGGCGCCACACCTTTCCCCACCTG 4 181 0 GCCACACCTT 0.906155 -98 TATAATGCCTTACGCTCCTTATGCGATTCT 4 243 1 TACGCTCCTT 0.69348 -36 CCGCGCCTCGGCCGCTCCTCATCTAGAGAG 6 127 1 GCCGCTCCTC 0.992697 -174 ACAGCTGCTTGCCGGTCCACGCCCTTCCAC 6 260 1 GCCGGTCCAC 0.874916 -41 GAGCGCTTCCTCACCTTTAAAAGTACT 8 8 1 TCCTCACCTT 0.478178 -133 GTGTACCAGAGCCACTACACTG 8 129 1 GCCACTACAC 0.932992 -12 CACGCAGGATGCCGCTTCACGCGGTTGATT 14 36 0 GCCGCTTCAC 0.871357 -142 CCCTGAAAATTACACTCCTCATGCACCGTG 14 93 0 TACACTCCTC 0.799659 -85 TGCCTCACCTCATACCAAGCT 18 12 0 GCCTCACCTC 0.908939 -11 GTCACTGCCAGCCGCTCCTCCCCAGAGCTT 26 54 0 GCCGCTCCTC 0.992697 -99 ********** Masking position 3 Map Score: 12.4307 Number of sites scoring better than the average of aligned sites = 402 Number in coding regions = 358 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 13 GAATACGAAAAAGGCATCATCAGAACTGCG 4 52 0 AAGGCATCAT 0.79812 -227 GGTGTAATGTGGGGCATTATTGCATACGTA 4 92 1 GGGGCATTAT 0.963861 -187 TAAGGAGCGTAAGGCATTATATCATTTTCG 4 234 0 AAGGCATTAT 0.915342 -45 GTGTATGCAGAGGGCATTGTACACGCCGGT 5 59 0 AGGGCATTGT 0.979535 -30 ACAGGATAGAGGGGCATTGTAATGGGAAGG 8 55 1 GGGGCATTGT 0.969886 -86 CGTGGTATGTAGGGTATAGTAGAGGATGCT 22 32 0 AGGGTATAGT 0.763099 -116 GGAGGGTATTATCGCCTTTTCC 25 160 0 AGGGTATTAT 0.915342 -12 ********** Masking position 6 Map Score: 2.4905 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 27 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 GGCGTGGTCCCGGTCACAGAAGACCGCGCC 6 104 1 CGGTCACAGA 0.906057 -197 GTGCGCCGTGGCGTCACAGCTGCTTGCCGG 6 245 1 GCGTCACAGC 0.93864 -56 GGGTGCATCTCCTTCTCAGATTCCTATTCA 10 18 0 CCTTCTCAGA 0.803229 -41 CAACCGCGAGCCTTGACAGAACATACCCAA 12 44 0 CCTTGACAGA 0.933336 -132 TCCTCATGCACCGTGACCGCCTCCCTGTCT 14 78 0 CCGTGACCGC 0.954071 -100 TGCGCCTGCGCCGTCACTGCAGTCTGTAGG 22 68 0 CCGTCACTGC 0.975734 -80 GCGACAAGATCCTTGACAGAATTCGCACAC 25 68 0 CCTTGACAGA 0.933336 -104 AAGTTTCTTGCCGTCACTGCCAGCCGCTCC 26 66 0 CCGTCACTGC 0.975734 -87 ********** Masking position 4 Map Score: 4.8114 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 51 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 15 TTCTTTGCGTTTCGAGGGAGGGTAGACTGA 2 67 1 TTCGAGGGAG 0.859764 -115 TAGCTGCTTATGCGAGGAAGATCAAATGCT 3 140 0 TGCGAGGAAG 0.98412 -35 ATTTTCAAGATGTGGGGAAGGGTTTCCTGC 4 16 1 TGTGGGGAAG 0.908805 -263 TCATCAGAACTGCGACGAAGGCAGGAAACC 4 36 0 TGCGACGAAG 0.923832 -243 AGGTGTACCTTGCAACGTAGATGTACCGGC 5 35 1 TGCAACGTAG 0.639173 -54 ACCCTCTTTGTGGAAGGGCGTGGACCGGCA 6 269 0 TGGAAGGGCG 0.784019 -32 TACTTTTAAAGGTGAGGAAGCGCTC 8 6 0 GGTGAGGAAG 0.832641 -135 TTTGCGTACCTGTAAGGAAGGATC 9 17 1 TGTAAGGAAG 0.910507 -14 GCGCGATCTCTGTGAGGTCGCCGCGGGTGC 13 72 1 TGTGAGGTCG 0.818592 -63 GCATCCTGCGTGGTAGGAAGGGGAAGACAG 14 54 1 TGGTAGGAAG 0.830651 -124 AGGGTGTGCGTGCAGGGGAGGCAGGAGTGC 16 18 1 TGCAGGGGAG 0.818063 -101 GGGCGCCGTTTTGGAGGAAGCACTGAGCCA 22 99 0 TTGGAGGAAG 0.874239 -49 CCGTCCTGAATAGGAGGTAGTCTTTC 26 7 0 TAGGAGGTAG 0.640943 -146 ********** Masking position 7 Map Score: 5.30361 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 260 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912