AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00550_tpal_reg_300.orf -o00550_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 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 TP0244 21 ribosomal protein S7 #11 TP0245 23 T. pallidum predicted coding region TP0245 #12 TP0246 145 T. pallidum predicted coding region TP0246 #13 TP0247 50 N-acetylmuramoyl-L-alanine amidase (amiA) #14 TP0345 152 phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) #15 TP0382 83 T. pallidum predicted coding region TP0382 #16 TP0383 27 conserved hypothetical protein #17 TP0524 135 ATP-dependent protease LA (lon-2) #18 TP0671 30 sn-1,2-diacylglycerol cholinephosphotransferase, putative #19 TP0672 134 glycyl-tRNA synthetase (glyS) #20 TP0673 177 glutamyl-tRNA synthetase (gltX) #21 TP0933 135 UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase (murE) Motif number 1 TCTCTCCTTTCCGTCCCGCACCTATACCAGGC 1 75 0 CCTCCCGCCC 0.980371 -26 TACCAGAATGCCCTGCTACAGGCAA 2 4 0 CCTGCTACGG 0.649631 -96 CAGCCAACCAGCCTGCCCCAGAAAGAAAGGCG 4 17 0 GCTGCCCCGA 0.897282 -218 ACAGGACTCCCCGAGCCGCCCGGAGGCCGGCC 4 105 0 CCAGCCGCCG 0.938049 -130 GTCAGCGGTTCAATCCCGCTCGGAAGCTTCCG 4 189 1 CATCCCGCCG 0.655119 -46 ACCACCCCTCCTCACATCCACAGACG 4 219 0 CCCTCCTCCA 0.922078 -16 GCGCATTGCAACACTCTCCACCCTGGAAGAAG 6 15 0 ACCTCTCCCC 0.77648 -92 GCGCATGATTGCCTGCCGCTTACGCGTTGGTT 6 43 1 GCTGCCGCTA 0.80436 -64 TTTTTTGCATGCGTCCGGCGCGTCGTTGTGTG 8 20 1 GCTCCGGCCG 0.715061 -243 AAGCGCGACGCCCTCCCACACGAAAGGGTGTC 8 57 0 CCTCCCACCG 0.949626 -206 ATAGAAGCCCACGCTCTACTCAAAAGCGCGAC 8 80 0 ACCTCTACCA 0.448587 -183 AGAACGCGACCCAACCCGCATGCCAAAATGCC 8 132 0 CCACCCGCTG 0.808889 -131 GGGTTGGGTCGCGTTCTCCTCACTTGAGTGGA 8 147 1 GCTTCTCCCA 0.824359 -116 GAGACGCCGTCCCCTCCACTCAAGTGAGGAGA 8 161 0 CCCTCCACCA 0.908742 -102 CTACCGTAATACTCCCCACACAGGGGAGACGC 8 186 0 ACCCCCACCA 0.832928 -77 GCACTCCCCCCTCAAGCTGCACCG 8 249 0 ACCCCCCCCA 0.956019 -14 TTCTGAGTATCCTAGCCGCGTGTGCTGTGTGC 9 32 1 CCAGCCGCTG 0.745249 -71 ACACCGTAAACCTTGCCGCACACAGCACACGC 9 49 0 CCTGCCGCCA 0.972411 -54 ACCAACTCCTCTCCCCAGCCC 10 3 0 CCCTCCCCGC 0.949199 -19 ATTCTCTTGCGCACGCTTCGCATCACAT 12 7 0 GCCGCTTCCA 0.760409 -139 TGGCGATATTCCGTGCTTCAGCGGAAAAAAAA 12 47 0 CCTGCTTCGC 0.555689 -99 ACGAAAATGCGCATCCCCCGCAAAGGTGGCGA 12 73 0 GCTCCCCCCA 0.966401 -73 CCCCTCCTGCGGAACAAACACAA 12 133 0 CCTCCTGCGA 0.878889 -13 GCACATACGTCCACGCACCACA 13 1 0 CCCGCACCCA 0.654969 -50 ACCTGTCCCCTCTCCCTACTCACAATAA 13 33 0 CCCTCTCCTA 0.730933 -18 CTCTCCTGCTGCATCCTTCTCGCTCAGGGACT 14 91 0 GCTCCTTCCG 0.814131 -62 CTCCTCCCTTGCCCTCTCCTGCTGCATCCTTC 14 104 0 GCCTCTCCGC 0.785104 -49 ACGTCCACCCCCCCCCCCCCGACGAGAAAAA 15 10 1 CCCCCCCCCG 0.993319 -74 GATTTCCTACCTTCCCCTATATTTTTC 16 11 0 CCACCTTCCC 0.506256 -17 CGGTATACTGCGCCCCCGCAGGTCGTGCAAGA 17 40 0 CGCCCCGCGG 0.804611 -96 GTTGTTGTCCGCTCTCTGCGCGCGGGGAAA 18 11 1 GCCTCTGCCG 0.940046 -20 ATCTCTGTGAGGTCGCCGCGGGTGCTGACAGT 19 77 1 GGCGCCGCGG 0.632145 -58 GCGCCGCTCACCTTCCCCCCTGTCTAGCATAC 19 107 0 CCTCCCCCTG 0.940758 -28 GGTGACGCGCCGCTCACCTTCCCCCC 19 119 0 ACCGCCGCCA 0.941461 -16 GCGTGAAGCGGCATCCTGCGTGGTAGGAAGGG 20 44 1 GCTCCTGCTG 0.76872 -134 CCTGAAAATTACACTCCTCATGCACCGTGACC 20 90 0 ACCTCCTCTG 0.498763 -88 CGATTATCGCACATCCCCCTCCGGGGCGCAAG 20 136 0 ACTCCCCCCC 0.921689 -42 CGCTCGCCCTCCCCGGGGGCCGATTAT 20 161 0 GCCTCCCCGG 0.952094 -17 TGATTAACTTACACTCCGCCGC 21 1 0 ACCTCCGCGC 0.834593 -135 AACGAGATGGCCTTTCCCCACCGTTTGCGATC 21 46 1 CCTTCCCCCC 0.959198 -90 ** ****** ** Masking position 6 Map Score: 49.9365 Number of sites scoring better than the average of aligned sites = 3493 Number in coding regions = 3066 Number in noncoding regions = 427 Number of orfs with sites within 600 bp upstream = 220 Fraction of orfs with sites within 600 bp upstream = 0.0353357 Motif number 2 CAAAACCACACACCGCCTACCAGAATGCCCTGC 2 20 0 CCGCCTACCG 0.944434 -80 TCCCTAAACAGGCAGCCAACCAGCCTGCCCCAG 4 28 0 GCGCCAACCG 0.953412 -207 TACAATGCGGGCCGGCCTCCGGGCGGCTCGGGG 4 96 1 GCGCCTCCGG 0.996041 -139 ATCCACAGACGGAAGCTTCCGAGCGGGATTGAA 4 197 0 GAGCTTCCGG 0.882859 -38 CATGATTGCCTGCCGCTTACGCGTTGGTTTCGG 6 46 1 TCGCTTACGG 0.598207 -61 CGGACAGGAAGACAGCACCCCAGAAGCCTGACC 7 49 0 GCGCACCCCG 0.992447 -60 AAAGCGCGACGCCCTCCCACACGAAAGGGTGTC 8 57 0 GCTCCCACAG 0.707952 -206 TGGAGGGGACGGCGTCTCCCCTGTGTGGGGAGT 8 175 1 GCTCTCCCCG 0.960725 -88 CCTTGCCGCACACAGCACACGCGGCTAGGATAC 9 38 0 CCGCACACGG 0.926732 -65 ACCAACTCCTCTCCCCAGCCC 10 4 0 CCTCTCCCCG 0.87839 -18 ACGTCCACCCCCCCCCCCCCGACGAGAAAAA 15 9 1 CCCCCCCCCG 0.964904 -75 CTGCGCGGTATACTGCGCCCCCGCAGGTCGTGC 17 44 0 TCGCGCCCCG 0.801355 -92 AAAAGTCAATGCCTCCATTCGAGGCCTTTTAAA 17 85 0 GCCCATTCGG 0.642592 -51 CTAGCATACTGTCAGCACCCGCGGCGACCTCAC 19 83 0 GCGCACCCGG 0.993678 -52 CGCGCCGCTCACCTTCCCCCCTGTCTAGCATAC 19 107 0 ACTCCCCCCG 0.941651 -28 ACCTGTCTGTGCAATCAACCGCGTGAAGCGGCA 20 24 1 GATCAACCGG 0.516718 -154 CGCGTGAAGCGGCATCCTGCGTGGTAGGAAGGG 20 43 1 GCTCCTGCGG 0.852391 -135 CATGCACCGTGACCGCCTCCCTGTCTTCCCCTT 20 71 0 GCGCCTCCCG 0.995287 -107 CCTCCGGGGCGCAAGCATCCCTGTGAGGCCCTG 20 118 0 GAGCATCCCG 0.902188 -60 ATTATCGCACATCCCCCTCCGGGGCGCAAGCAT 20 133 0 ACCCCTCCGG 0.890354 -45 ATGTGCGATAATCGGCCCCCGGGGAGGGCGAGC 20 154 1 ACGCCCCCGG 0.986062 -24 ATCACTAAAAGGCTGTCAACGAGATGGCCTTTC 21 29 1 GCGTCAACGG 0.469727 -107 GTATCTGATTGCACGCCCTCGGGGAACAATCTA 21 100 0 GAGCCCTCGG 0.871877 -36 * * ******* * Masking position 10 Map Score: 30.7069 Number of sites scoring better than the average of aligned sites = 756 Number in coding regions = 660 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 3 ACCGGTAGTATGCGGTGCCTGGTATAGGTGCG 1 59 1 TGGTGCCTGG 0.87834 -42 CATTCTGGTAGGCGGTGTGTGGTTTTGAGTTC 2 26 1 GGGTGTGTGG 0.995495 -74 CTTTCTTTCTGGGGCAGGCTGGTTGGCTGCCT 4 20 1 GGGAGGCTGG 0.867293 -215 TGTTTAGGGAGGTGTTTCGTGCTTGATGTGTG 4 51 1 GGGTTCGTGC 0.954813 -184 GCTTCCGTCTGTGGATGTGAGGAGGGGTGGT 4 214 1 GTGTGTGAGG 0.806881 -21 TGTTACGCACGGGGTTTTCTGGTGTTTTCCGG 5 25 1 GGGTTTCTGG 0.937682 -125 GGTGTTTTCCGGGGATTTGTGGGTCAGTAGCT 5 45 1 GGGTTTGTGG 0.976269 -105 GTTGGTTTCGGGTGTTTTGTTGTTTTTTACGT 6 68 1 GGGTTTGTTG 0.837532 -39 AGGCTTCTGGGGTGCTGTCTTCCTGTCCGTTT 7 53 1 GGGTGTCTTC 0.910138 -56 CGTCCGGCGCGTCGTTGTGTGCCTCTGACACC 8 31 1 GTGTGTGTGC 0.965147 -232 CCTAGCCGCGTGTGCTGTGTGCGGCAAGGTTT 9 42 1 TGGTGTGTGC 0.974639 -61 GGATTTTTTTGGGGAAGTGAGCGAAAAGA 9 84 1 GGGAGTGAGC 0.909442 -19 ATGTGATGCGAAGCGTGCGCAAGAGAAT 12 7 1 TGGAGCGTGC 0.856016 -139 TGTGGTGCGTGGACGTATGTGC 13 1 1 TGGTGCGTGG 0.951782 -50 CGAGTGTAACGGAGCACTGTGCCTTGTGCTAG 14 61 1 GGGACTGTGC 0.848066 -92 CTCGTCGGGGGGGGGGGGGTGGACGT 15 5 0 GGGGGGGTGG 0.889495 -79 GTTGTTGTCCGCTCTCTGCGCG 18 1 1 GTGTGTCCGC 0.702716 -30 GAGGTATGCAGGGGATGTGTTCAAAGGCGGGC 19 42 1 GGGTGTGTTC 0.965146 -93 CGCCCCGGAGGGGGATGTGCGATAATCGGCCC 20 140 1 GGGTGTGCGA 0.818382 -38 ** * ******* Masking position 4 Map Score: 24.9665 Number of sites scoring better than the average of aligned sites = 893 Number in coding regions = 806 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 4 ATCCTCTCTCCTTTCCGTCCCGCACCTAT 1 82 0 CCTTTCCGTC 0.741372 -19 CACACGACACTCTTTCTGTTACCGGCAGAA 2 55 0 TCTTTCTGTT 0.714405 -45 GACGCGCCTTTCTTTCTGGGGCAGGCTGGT 4 13 1 TCTTTCTGGG 0.932659 -222 AGGCTGGTTGGCTGCCTGTTTAGGGAGGTG 4 35 1 GCTGCCTGTT 0.653155 -200 CTCGGGGAGTCCTGTCTGTGTTGCTTCTGT 4 122 1 CCTGTCTGTG 0.964726 -113 CTCGGAAGCTTCCGTCTGTGGATGTGAGGA 4 207 1 TCCGTCTGTG 0.762661 -28 AGGTTCGAGTCCTTCCTGGCCTGAGTGCTT 5 115 1 CCTTCCTGGC 0.976277 -35 TTTTCTTCTTCCAGGGTGGAGAGTGT 6 7 1 TCTTCCAGGG 0.759995 -100 TGGGGTGCTGTCTTCCTGTCCGTTTATAGG 7 60 1 TCTTCCTGTC 0.908338 -49 CGGCGTCTCCCCTGTGTGGGGAGTATTACG 8 184 1 CCTGTGTGGG 0.841493 -79 ATACGCGTCTCTTCCTGGGGCGT 11 10 1 TCTTCCTGGG 0.971903 -14 CCCCTCCTGCGGAACAAACAC 12 135 0 CCCTCCTGCG 0.831754 -11 TACCGGTGCTCCTTCCTGTTCTCCTCCCTT 14 126 0 CCTTCCTGTT 0.947581 -27 TCATAAAAAACCTGTCTGTGCAATCAACCG 20 15 1 CCTGTCTGTG 0.964726 -163 GAAGCGGCATCCTGCGTGGTAGGAAGGGGA 20 48 1 CCTGCGTGGT 0.774667 -130 ACCGTGACCGCCTCCCTGTCTTCCCCTTCC 20 69 0 CCTCCCTGTC 0.908568 -109 TCGCACATCCCCCTCCGGGGCGCAAGCATC 20 132 0 CCCTCCGGGG 0.819925 -46 CGCTCGCCCTCCCCGGGGGCCGATTAT 20 161 0 CCTCCCCGGG 0.896396 -17 ********** Masking position 8 Map Score: 18.5598 Number of sites scoring better than the average of aligned sites = 563 Number in coding regions = 485 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 5 AGGCCATCCCCACTAGCGGT 3 21 0 AGGCCATCCC 0.954156 -10 AGCCGCCCGGAGGCCGGCCCGCATTGTATA 4 94 0 AGGCCGGCCC 0.95558 -141 CTCTAATGGCAGAGCGTCGGTCTCCAAAAC 5 75 1 AGAGCGTCGG 0.731983 -75 GGTATGTGTTAGGCGGTCAGGCTTCTGGGG 7 35 1 AGGCGGTCAG 0.964928 -74 CCCACACGAAAGGGTGTCAGAGGCACACAA 8 45 0 AGGGTGTCAG 0.847738 -218 TTCGTGTGGGAGGGCGTCGCGCTTTTGAGT 8 65 1 AGGGCGTCGC 0.987804 -198 CACAGGGGAGACGCCGTCCCCTCCACTCAA 8 170 0 ACGCCGTCCC 0.963016 -93 ATGTGTTCAAAGGCGGGCGCGATCTCTGTG 19 56 1 AGGCGGGCGC 0.955256 -79 GAAGACAGGGAGGCGGTCACGGTGCATGAG 20 76 1 AGGCGGTCAC 0.981744 -102 TGTAATTTTCAGGGCCTCACAGGGATGCTT 20 109 1 AGGGCCTCAC 0.937508 -69 AATCACTAAAAGGCTGTCAACGAGATGGCC 21 28 1 AGGCTGTCAA 0.700601 -108 CGGTGGGGAAAGGCCATCTCGTTGACAGCC 21 39 0 AGGCCATCTC 0.839946 -97 ATCTGATTGCACGCCCTCGGGGAACAATCT 21 101 0 ACGCCCTCGG 0.809177 -35 ********** Masking position 1 Map Score: 12.1498 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 125 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 GTTATACAATGCGGGCCGGCCTCCGGGCGG 4 92 1 GCGGGCCGGC 0.54356 -143 TACCATGGTTGCGCTCTGCCAACTGAGCTA 4 151 0 GCGCTCTGCC 0.920824 -84 CTTTTCGAAAGCACTCAGGCCAGGAAGGAC 5 123 0 GCACTCAGGC 0.944117 -27 TATGTGTTAGGCGGTCAGGCTTCTGGGGTG 7 37 1 GCGGTCAGGC 0.955896 -72 CTACTCAAAAGCGCGACGCCCTCCCACACG 8 67 0 GCGCGACGCC 0.809244 -196 GCACTCCCCCCTCAAGCTGC 8 253 0 GCACTCCCCC 0.855146 -10 TGCATCCTTCTCGCTCAGGGACTAGCACAA 14 84 0 TCGCTCAGGG 0.886985 -69 GCGGTATACTGCGCCCCCGCAGGTCGTGCA 17 43 0 GCGCCCCCGC 0.803479 -93 TCCGCTCTCTGCGCGCGGGGAAA 18 18 1 GCGCGCGGGG 0.892511 -13 CTCACAGAGATCGCGCCCGCCTTTGAACAC 19 58 0 TCGCGCCCGC 0.74449 -77 AGACAGGGAGGCGGTCACGGTGCATGAGGA 20 78 1 GCGGTCACGG 0.906756 -100 CTGATTGCACGCCCTCGGGGAACAATCTAT 21 99 0 GCCCTCGGGG 0.846105 -37 ********** Masking position 2 Map Score: 10.8691 Number of sites scoring better than the average of aligned sites = 1479 Number in coding regions = 1370 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 7 GGTGCGGGACGGAAAGGAGAGAGGAT 1 85 1 GGAAAGGAGA 0.882198 -16 GTGGATGTGAGGAGGGGTGGT 4 224 1 GGAGGGGTGG 0.971328 -11 TCACTTGAGTGGAGGGGACGGCGTCTCCCC 8 166 1 GGAGGGGACG 0.987238 -97 ACGCCCCAGGAAGAGACGCGTAT 11 6 0 GGAAGAGACG 0.968032 -18 CGCATCCCCCGCAAAGGTGGCGATATTCCG 12 66 0 GCAAAGGTGG 0.89366 -80 GAAGGATGCAGCAGGAGAGGGCAAGGGAGG 14 104 1 GCAGGAGAGG 0.964964 -49 GCAGGAGAGGGCAAGGGAGGAGAACAGGAA 14 114 1 GCAAGGGAGG 0.992395 -39 AAAATATAGGGGAAGGTAGGAAATC 16 13 1 GGAAGGTAGG 0.936607 -15 TAGTATCCAGGCAAGGGACGAAAAGTCAAT 17 108 0 GCAAGGGACG 0.985241 -28 CGGGCTATAGGGAAAAGAGGTATGCAGGGG 19 26 1 GGAAAAGAGG 0.944486 -109 AAAGAGGTATGCAGGGGATGTGTTCAAAGG 19 39 1 GCAGGGGATG 0.903784 -96 GGTAGGAAGGGGAAGACAGGGAGGCGGTCA 20 65 1 GGAAGACAGG 0.862909 -113 CAAACGGTGGGGAAAGGCCATCTCGTTGAC 21 43 0 GGAAAGGCCA 0.419112 -93 ********** Masking position 3 Map Score: 17.5392 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 304 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 8 TGTTTAGGGAGGTGTTTCGTGCTTGATGTGT 4 51 1 GGTGTTTCTG 0.823854 -184 GGGGTTTTCTGGTGTTTTCCGGGGATTTGTG 5 35 1 GGTGTTTTCG 0.981327 -115 GGTGTTTTGTTGTTTTTTACGTCATAAGGAG 6 78 1 TGTTTTTTCG 0.954183 -29 CCGTTTATAGGGGTTATTTCGCATACAAGGA 7 79 1 GGGTTATTCG 0.861015 -30 TGTCTGGTTTTTTTTGCATGCGTCCG 8 6 1 GGTTTTTTTG 0.969229 -257 CCCTGTGTGGGGAGTATTACGGTAGAGCGTG 8 193 1 GGAGTATTCG 0.839945 -70 ACGGTGTTGAGGATTTTTTTGGGGAAGTGAG 9 74 1 GGATTTTTTG 0.908707 -29 ATTTTGCGCGTTTTTTTTCCGCTGAAGCACG 12 37 1 TTTTTTTTCG 0.645326 -109 GATCGGTTTGTGTTTGTTCCGCAGGAGGGG 12 126 1 TGTTTGTTCG 0.846895 -20 TGCACAGACAGGTTTTTTATGAAAGA 20 6 0 GGTTTTTTTG 0.969229 -172 ******** ** Masking position 5 Map Score: 3.71575 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 149 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 AAAAACTATTGAAATTCACACGACACTCTT 2 71 0 GAAATTCACA 0.584856 -29 GCCCCAGAAAGAAAGGCGCGTCAC 4 5 0 GAAAGGCGCG 0.972699 -230 GAGGCGTTATACAATGCGGGCCGGCCTCCG 4 87 1 ACAATGCGGG 0.77583 -148 GGAGAGTGTTGCAATGCGCATGATTGCCTG 6 28 1 GCAATGCGCA 0.973226 -79 CAGCGGAAAAAAAACGCGCAAAATTCTCTT 12 31 0 AAAACGCGCA 0.840115 -115 GTACACAACGAAAATGCGCATCCCCCGCAA 12 82 0 AAAATGCGCA 0.93494 -64 ACGCGCTCAAGAAATGCACGCTCGTACCCA 14 18 0 GAAATGCACG 0.948721 -135 AGGGACTAGCACAAGGCACAGTGCTCCGTT 14 68 0 ACAAGGCACA 0.902249 -85 TAGTATCCAGGCAAGGGACGAAAAGTCAAT 17 108 0 GCAAGGGACG 0.772328 -28 ********** Masking position 4 Map Score: 1.88654 Number of sites scoring better than the average of aligned sites = 611 Number in coding regions = 573 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 10 AGTGTGCGAAACCGCTAGTGG 3 2 1 GTGTGCGAAA 0.985247 -29 TCTTCTCCTTGTATGCGAAATAACCCCTAT 7 85 0 GTATGCGAAA 0.97703 -24 CGCGCCGGACGCATGCAAAAAAAACCAGAC 8 12 0 GCATGCAAAA 0.927632 -251 GACCCAACCCGCATGCCAAAATGCCGAGAA 8 127 0 GCATGCCAAA 0.949998 -136 TTTTGGGGAAGTGAGCGAAAAGA 9 90 1 GTGAGCGAAA 0.942863 -13 GTGATGCGAAGCGTGCGCAAGAGAATTTTG 12 13 1 GCGTGCGCAA 0.974639 -133 ********** Masking position 9 Map Score: 3.67461 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 46 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 11 TGTTTGGTTGACCGGTAGTATGCGGTGCCT 1 49 1 ACCGGTAGTA 0.99134 -52 TCTTTCTGTTACCGGCAGAACTCAAAACCA 2 45 0 ACCGGCAGAA 0.96373 -55 AGTGTGCGAAACCGCTAGTGGGGATGGCCT 3 11 1 ACCGCTAGTG 0.961611 -20 AGGAAGGAGCACCGGTAGTAGTTG 14 139 1 ACCGGTAGTA 0.99134 -14 ********** Masking position 7 Map Score: 0.739759 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 7 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 12 TGCTGTTTGCGTGTTTGGTTGACCGGTAGTATGCG 1 38 1 GTGTTGGTCG 0.975247 -63 GTAGTATGCGGTGCCTGGTATAGGTGCGGGACGGA 1 63 1 GTGCTGGTGT 0.70673 -38 CTGGTAGGCGGTGTGTGGTTTTGAGTTCTGCCGGT 2 30 1 GTGTTGGTGG 0.975247 -70 GGTTGGCTGCCTGTTTAGGGAGGTGTTTCGTGCTT 4 40 1 CTGTTAGGGG 0.433611 -195 CGTGCTTGATGTGTGAGGTGAGGCGTTATACAATG 4 68 1 GTGTAGGTGG 0.864129 -167 ACTCCCCGAGCCGCCCGGAGGCCGGCCCGCATTGT 4 97 0 CCGCCGGACG 0.786071 -138 GTGTTGCAATGCGCATGATTGCCTGCCGCTTACGC 6 33 1 GCGCTGATCG 0.773546 -74 TACGGGGTATGTGTTAGGCGGTCAGGCTTCTGGGG 7 30 1 GTGTAGGCCG 0.481258 -79 AGGCGGTCAGGCTTCTGGGGTGCTGTCTTCCTGTC 7 45 1 GCTTTGGGCG 0.781605 -64 CATGCGTCCGGCGCGTCGTTGTGTGCCTCTGACAC 8 27 1 GCGCTCGTGG 0.920756 -236 TGACACCCTTTCGTGTGGGAGGGCGTCGCGCTTTT 8 56 1 TCGTTGGGGG 0.612584 -207 TTACGGTAGAGCGTGTGGTATAGGGAGCACCGTGT 8 209 1 GCGTTGGTGG 0.981553 -54 TCCTAGCCGCGTGTGCTGTGTGCGGCAAGGTTTAC 9 41 1 GTGTCTGTCG 0.579627 -62 GTGCGGCAAGGTTTACGGTGTTGAGGATTTTTTTG 9 60 1 GTTTCGGTGG 0.746165 -43 TGATCGGTTTGTGTTTGTTCCGCAGGAGGGG 12 125 1 GTGTTGTTCG 0.610404 -21 TGTGGTGCGTGGACGTATGTGCTTATTGT 13 5 1 GTGCTGGAAG 0.687258 -46 AGGCTCCTGGGTACGAGCGTGCATTTC 14 3 1 GCTCTGGGGG 0.852447 -150 AAAAATATACCTGCGCGGTATACTGCGCCCCCGCA 17 52 0 CTGCCGGTCG 0.916216 -84 AGGGCGCCTAGTATCCAGGCAAGGGACG 17 118 0 GCGCTAGTCG 0.914988 -18 TTTCCCCGCGCGCAGAGAGCGGACAACAAC 18 9 0 GCGCCAGACG 0.653834 -22 AAGCGGCATCCTGCGTGGTAGGAAGGGGAAGACAG 20 49 1 CTGCTGGTAG 0.682738 -129 AGGGATGCTTGCGCCCCGGAGGGGGATGTGCGATA 20 129 1 GCGCCCGGGG 0.839153 -49 **** **** * * Masking position 15 Map Score: 13.0198 Number of sites scoring better than the average of aligned sites = 1783 Number in coding regions = 1637 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 13 ********** No masking Map Score: 2.91566e-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 14 ********** No masking Map Score: 2.91566e-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: 2.91566e-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