AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00400_tpal_reg_300.orf -o00400_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 TP0218 300 sigma factor SigB regulation protein, putative #5 TP0220 28 anti-sigma F factor antagonist (spoIIAA-1) #6 TP0223 267 aspartate aminotransferase (tpaaT) #7 TP0818 26 T. pallidum predicted coding region TP0818 #8 TP0819 27 conserved hypothetical protein #9 TP0820 95 hypothetical protein #10 TP0821 80 lipoprotein (tpn32) #11 TP0822 87 conserved hypothetical protein #12 TP0823 300 desulfoferrodoxin (rbo) #13 TP0834 86 tyrosyl-tRNA synthetase (tyrS) #14 TP0835 140 ankyrin, putative #15 TP0836 147 T. pallidum predicted coding region TP0836 #16 TP0973 87 phenylalanyl-tRNA synthetase alpha subunit (pheS) Motif number 1 AGCACGAAGTTCGCCTTCGCGCCTAAGTTA 1 57 1 TCGCCTTCGC 0.850329 -244 ATGGTGACGGCCGGGCTCGCGTGCAGACGC 1 117 1 CCGGGCTCGC 0.578297 -184 CTACCGTATCGCGTCTGCACGCGAGCCCGG 1 127 0 GCGTCTGCAC 0.963935 -174 ATACGGTAGCGCGCCCTCGGAGTAAAAGTA 1 148 1 GCGCCCTCGG 0.540097 -153 GGCATAAGTACCGTGCGCACAAAGGCATGA 3 13 0 CCGTGCGCAC 0.901354 -178 AAAGTGTAGAGCACGTGTGCCGTGTAGTGG 3 90 1 GCACGTGTGC 0.766129 -101 AGCCACCACACCGTCTTTGCAGAGGATGCC 3 118 0 CCGTCTTTGC 0.926071 -73 GAGCCCTCCGACCGTGCTCAGTATACG 3 174 0 CCGACCGTGC 0.818022 -17 AAGAGCGCACGCGACCGTGCAGAAAGCGTA 4 35 0 GCGACCGTGC 0.592508 -266 AAACGCCCATCCGCCGTTGCTTGAACTTTC 4 92 1 CCGCCGTTGC 0.849627 -209 TCCTTTTACCCCACGCGCCCCTTTCTGTAG 4 136 0 CCACGCGCCC 0.534391 -165 GATTATTCTCGCGTGCGTGGTGTTTCTTTC 4 164 1 GCGTGCGTGG 0.734257 -137 ATCGTGATGGGTGCGTGTGCTATCTGAGTT 4 221 1 GTGCGTGTGC 0.724157 -80 CAGAGCACACAAGCCCGCGCAGCCACACGG 6 47 0 AAGCCCGCGC 0.649838 -221 GGGTCAGGGGGCGTGTCTACACTGTGAGAC 6 116 1 GCGTGTCTAC 0.584448 -152 CTCTCTGAAGGCGCGCGTGCGTTAAACGCT 6 152 1 GCGCGCGTGC 0.508408 -116 GGAGATAACAGCGCGTGCACCACCGTTCCT 6 190 0 GCGCGTGCAC 0.88554 -78 CCGCGCCTCTGCATTCTGTGCA 6 256 0 GCGCCTCTGC 0.972804 -12 ATATAACGCGCCGTTGCAATACTCCG 7 8 1 GCGCCGTTGC 0.633718 -19 TGCGCGCAGTACGCCCTTGCGTAGGATGCA 11 65 1 ACGCCCTTGC 0.888103 -23 CGCTCCTTCCGAGCCTGTGCTACGCACGAG 12 115 0 GAGCCTGTGC 0.929717 -186 CTCGGAAGGAGCGAGTTTACTGAATGCGTA 12 132 1 GCGAGTTTAC 0.525827 -169 AAAGCGTCACCCACCTGTACGCATTCAGTA 12 149 0 CCACCTGTAC 0.794744 -152 GGTAGAATCAGCGCCTCTGCGGGGCTGTGC 12 197 1 GCGCCTCTGC 0.972804 -104 CGTGCGGAAACCGCCCGCGCCAGAGCACAG 12 221 0 CCGCCCGCGC 0.532414 -80 TGTCGTGCCTCCGCGTGCGGAAACCGCCCG 12 234 0 CCGCGTGCGG 0.764108 -67 GGCACGACAGGCGTCCGCACGAGAACAAAA 12 255 1 GCGTCCGCAC 0.955468 -46 TGATGCACCCCCACCGTCGCCCCGCGTGTC 13 12 0 CCACCGTCGC 0.494675 -75 CGGGACTGAACCGCCTGCCCTGGATCGGGG 13 61 1 CCGCCTGCCC 0.960942 -26 AAATGGGAACGCGCCTGCGCGGTTGCGTCC 14 11 1 GCGCCTGCGC 0.652903 -130 CTGCGCGGTTGCGTCCTCACGGGAGAGTGG 14 25 1 GCGTCCTCAC 0.911463 -116 GTATGGTGCCGCGTCTGTACAGTGTGTGTA 14 104 0 GCGTCTGTAC 0.946363 -37 CTGAGCCAGTGCGCCTGCGCCGTCACTGCA 15 62 1 GCGCCTGCGC 0.652903 -86 ********** Masking position 10 Map Score: 57.5234 Number of sites scoring better than the average of aligned sites = 4104 Number in coding regions = 3805 Number in noncoding regions = 299 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 2 CGGGCTCGCGTGCAGACGCGATACGGTAGC 1 128 1 TGCAGACGCG 0.954013 -173 ACTTTTACTCCGAGGGCGCGCTACCGTATC 1 147 0 CGAGGGCGCG 0.763958 -154 AGTATAAAAATGCACGAGCCTAACACTAGA 1 174 1 TGCACGAGCC 0.881219 -127 CATGCCTTTGTGCGCACGGTACTTATGCCG 3 14 1 TGCGCACGGT 0.596132 -177 AGCGCTCATATGCGCACGGCATAAGTACCG 3 30 0 TGCGCACGGC 0.773291 -161 CACTACACGGCACACGTGCTCTACACTTTA 3 89 0 CACACGTGCT 0.588232 -102 CCGCTAAGAGCGCACGCGACCGTGCAGAAA 4 40 0 CGCACGCGAC 0.95572 -261 ATCCTTTTACCCCACGCGCCCCTTTCTGTA 4 137 0 CCCACGCGCC 0.699884 -164 AGAAACACCACGCACGCGAGAATAATCCTT 4 161 0 CGCACGCGAG 0.925271 -140 CTCATCCTGCGACACACGAGAAAGAAACAC 4 183 0 GACACACGAG 0.666006 -118 ACTCAGATAGCACACGCACCCATCACGATG 4 220 0 CACACGCACC 0.766174 -81 GACTTCAGAGCACACAAGCCCGCGCAGCCA 6 52 0 CACACAAGCC 0.742228 -216 TCACAGTGTAGACACGCCCCCTGACCCTGT 6 113 0 GACACGCCCC 0.729048 -155 CAGCGTTTAACGCACGCGCGCCTTCAGAGA 6 153 0 CGCACGCGCG 0.538088 -115 GGAACGGTGGTGCACGCGCTGTTATCTCCT 6 191 1 TGCACGCGCT 0.960769 -77 GTGGGGAAAATACGCGCGCAAACCAAGAGG 6 218 0 TACGCGCGCA 0.760225 -50 GCACAGAATGCAGAGGCGCGG 6 257 1 CAGAGGCGCG 0.899725 -11 AATCCAAGCTGGCAGGAGCGTAGCGGAAAC 12 64 1 GGCAGGAGCG 0.880435 -237 GAGCCTGTGCTACGCACGAGTATACCTTGA 12 105 0 TACGCACGAG 0.556879 -196 TCGTGCGTAGCACAGGCTCGGAAGGAGCGA 12 116 1 CACAGGCTCG 0.773326 -185 CACAGCCCCGCAGAGGCGCTGATTCTACCT 12 196 0 CAGAGGCGCT 0.724656 -105 TGTGCTCTGGCGCGGGCGGTTTCCGCACGC 12 222 1 CGCGGGCGGT 0.925015 -79 GGGCGGTTTCCGCACGCGGAGGCACGACAG 12 235 1 CGCACGCGGA 0.840933 -66 TTTGTTCTCGTGCGGACGCCTGTCGTGCCT 12 254 0 TGCGGACGCC 0.891768 -47 TGACACGCGGGGCGACGGTGG 13 2 1 GACACGCGGG 0.93401 -85 CCCGATCCAGGGCAGGCGGTTCAGTCCCGA 13 60 0 GGCAGGCGGT 0.868533 -27 CGCACACCCCGATCCAGGGC 13 77 0 CGCACACCCC 0.827726 -10 GACGCAACCGCGCAGGCGCGTTCCCATTT 14 10 0 CGCAGGCGCG 0.950218 -131 GTTGCGTCCTCACGGGAGAGTGGGCGTCTA 14 32 1 CACGGGAGAG 0.518506 -109 ACACACACTGTACAGACGCGGCACCATACT 14 105 1 TACAGACGCG 0.907939 -36 GCAGTGACGGCGCAGGCGCACTGGCTCAGT 15 61 0 CGCAGGCGCA 0.958192 -87 ********** Masking position 3 Map Score: 36.8982 Number of sites scoring better than the average of aligned sites = 6381 Number in coding regions = 5926 Number in noncoding regions = 455 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 3 CTGCAAAGACGGTGTGGTGGCTGGCCCTTGT 3 126 1 GGTGGGTGGC 0.986065 -65 TACTGAGCACGGTCGGAGGGCTC 3 178 1 GGTCGAGGGC 0.987813 -13 TGTGTCGCAGGATGAGTTGGCTTCATCGTGA 4 197 1 GATGGTTGGC 0.869558 -104 CATCGTGATGGGTGCGTGTGCTATCTGAGTT 4 220 1 GGTGGTGTGC 0.987176 -81 CATCCGTGTGGCTGCGCGGGCTTGTGTGCTC 6 44 1 GCTGGCGGGC 0.93298 -224 AAATTGACAGGGTCAGGGGGCGTGTCTACAC 6 107 1 GGTCGGGGGC 0.997184 -161 GGATGGGGATGGTGTGGGTGTGTCTTTTGAA 9 70 1 GGTGGGGTGT 0.975503 -26 ATGGATAGAGGGACAGGGGGAGGCCGAATGA 10 59 1 GGACGGGGGA 0.863466 -22 ACCTAAATCAGGTCCGTGGGTAAAGCGTCAC 12 169 0 GGTCGTGGGT 0.97092 -132 GCGGGGCGACGGTGGGGGTGCATCAGCGCGT 13 17 1 GGTGGGGTGC 0.994487 -70 GCCTGCCCTGGATCGGGGTGTGCG 13 73 1 GATCGGGTGT 0.847807 -14 CGTCCTCACGGGAGAGTGGGCGTCTAAAGAT 14 36 1 GGAGGTGGGC 0.979898 -105 TTCTGTTTTGGATGTGAGCGC 15 137 1 GATGGAGCGC 0.804039 -11 **** ****** Masking position 6 Map Score: 20.0174 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 302 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 4 ACCGTATCGCGTCTGCACGCGAGCCCGGCC 1 125 0 GTCTGCACGC 0.592052 -176 GACGCGATACGGTAGCGCGCCCTCGGAGTA 1 142 1 GGTAGCGCGC 0.906341 -159 AACACTCTTAAACTGAGCGCTCATATGCGC 3 45 0 AACTGAGCGC 0.685142 -146 AAAGGTATTGGTGCGTATTCCAACTA 4 7 1 ATTGGTGCGT 0.42637 -294 GGCTACAGAAAGGGGCGCGTGGGGTAAAAG 4 134 1 AGGGGCGCGT 0.879666 -167 TCATCCGTGTGGCTGCGCGGGCTTGTGTGC 6 43 1 GGCTGCGCGG 0.900023 -225 GGACCTCTCTGAAGGCGCGCGTGCGTTAAA 6 148 1 GAAGGCGCGC 0.963018 -120 AAGAGGAGATAACAGCGCGTGCACCACCGT 6 194 0 AACAGCGCGT 0.960006 -74 TCTCCTCTTGGTTTGCGCGCGTATTTTCCC 6 215 1 GTTTGCGCGC 0.899315 -53 CACAGAATGCAGAGGCGCGG 6 258 1 AGAGGCGCGG 0.888108 -10 GGAGTATTGCAACGGCGCGTTATAT 7 6 0 AACGGCGCGT 0.983715 -21 TGTCCAAAGAAAAAGCGCACATCAAGACTC 10 21 0 AAAAGCGCAC 0.4 -60 TTGGGGGCATATTTGCGCGCAGTACGCCCT 11 52 1 ATTTGCGCGC 0.915875 -36 TTTAGGTAGAATCAGCGCCTCTGCGGGGCT 12 193 1 ATCAGCGCCT 0.7492 -108 GTGGGGGTGCATCAGCGCGTTTTGTCTTTT 13 28 1 ATCAGCGCGT 0.953959 -59 ACGCAACCGCGCAGGCGCGTTCCCATTT 14 9 0 GCAGGCGCGT 0.790944 -132 CTTCCTCCAAAACGGCGCCCATTGACAAAC 15 30 0 AACGGCGCCC 0.940897 -118 CCTACATCTAAACGGCGCGAAAATACGTT 16 69 1 AACGGCGCGA 0.915433 -19 ********** Masking position 5 Map Score: 14.2909 Number of sites scoring better than the average of aligned sites = 2233 Number in coding regions = 2068 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 5 GCGACCGTGCAGAAAGCGTAGTTGGAATACG 4 24 0 AGAAAGCGAG 0.917054 -277 ATTTCTCAAGAGGAAGGGGAAAACGCCCATC 4 72 1 AGGAAGGGAA 0.885184 -229 AGTAGGCTACAGAAAGGGGCGCGTGGGGTAA 4 130 1 AGAAAGGGCG 0.910978 -171 CGTGTGTCGCAGGATGAGTTGGCTTCATCGT 4 195 1 AGGATGAGTG 0.711355 -106 GCCATACAAAGGGAACGGTAG 4 290 1 GGGAACGGAG 0.940405 -11 CTGCTCTTGAAGGAACGGTGGTGCACGCGCT 6 180 1 AGGAACGGGG 0.922487 -88 ATTGTTGCACAGAATGCAGAGGCGCGG 6 251 1 AGAATGCAAG 0.652922 -17 AGAACCGTCAGGACTGGGTAGGTTTTAAACG 9 26 0 GGACTGGGAG 0.693599 -70 TGCATACTCAAGGATGGGGATGGTGTGGGTG 9 59 1 AGGATGGGAT 0.858225 -37 GGACATTGACAGGATGGATAGAGGGACAGGG 10 46 1 AGGATGGAAG 0.95865 -35 TCCTGTTTTTAGGAAGGGGAGCAGGAGATTG 11 24 1 AGGAAGGGAG 0.992714 -64 TGCGTAGCACAGGCTCGGAAGGAGCGAGTTT 12 119 1 AGGCTCGGAG 0.950989 -182 CCGCACGCGGAGGCACGACAGGCGTCCGCAC 12 244 1 AGGCACGAAG 0.842649 -57 CATACTCAGGAGGATCCGCTGC 14 129 1 AGGATCCGTG 0.856425 -12 GCCGTTTTGGAGGAAGCACTGAGCCAGTGCG 15 44 1 AGGAAGCATG 0.780197 -104 TGCAGTCTGTAGGAAGGGACGTGGTATGTAG 15 88 1 AGGAAGGGCG 0.979263 -60 ******** ** Masking position 2 Map Score: 13.6616 Number of sites scoring better than the average of aligned sites = 609 Number in coding regions = 534 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 6 GCACCGCTTGGGGCAACCGGCACTGTGCGAG 1 19 0 GGGCAACGGC 0.91224 -282 GCGGTGCTACGGGTAGCACGAAGTTCGCCTT 1 43 1 GGGTAGACGA 0.967229 -258 TCACCATTTCGGGGAGTACTCGTCTTACTTG 1 93 0 GGGGAGACTC 0.962042 -208 GTCATAATACGCGTAACACTCTTAAACTGAG 3 58 0 GCGTAAACTC 0.781563 -133 TCAAGAGGAAGGGGAAAACGCCCATCCGCCG 4 77 1 GGGGAAACGC 0.984173 -224 GGGGCGCGTGGGGTAAAAGGATTATTCTCGC 4 145 1 GGGTAAAGGA 0.864046 -156 AGGCGCGCGTGCGTTAAACGCTGCTCTTGAA 6 160 1 GCGTTAACGC 0.609962 -108 AGAGGGACAGGGGGAGGCCGAATGAG 10 65 1 GGGGAGCCGA 0.973835 -16 CCTAAAAACAGGAGAGCACTACACCC 11 6 0 GGAGAGACTA 0.38257 -82 TTTTTAGGAAGGGGAGCAGGAGATTGGGGGC 11 29 1 GGGGAGAGGA 0.962404 -59 GCATATTTGCGCGCAGTACGCCCTTGCGTAG 11 58 1 GCGCAGACGC 0.949287 -30 GTACGCCCTTGCGTAGGATGCAGGC 11 73 1 GCGTAGATGC 0.78457 -15 GCCTCCGCGTGCGGAAACCGCCCGCGCCAGA 12 227 0 GCGGAACCGC 0.868324 -74 CCCCGATCCAGGGCAGGCGGTTCAGTCCCGA 13 60 0 GGGCAGCGGT 0.683345 -27 ****** **** Masking position 1 Map Score: 10.831 Number of sites scoring better than the average of aligned sites = 815 Number in coding regions = 740 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 7 CGGCACTGTGCGAGAGAACCCC 1 1 0 CGAGAGACCC 0.966508 -300 CCAAGTAAGACGAGTACTCCCCGAAATGGTGA 1 92 1 CGAGTACCCC 0.897847 -209 CCCTTCCTCTTGAGAAATCTCCGCTAAGAGCG 4 58 0 TGAGAAACCC 0.982726 -243 TCAAGAGGAAGGGGAAAACGCCCATCCGCCGT 4 77 1 GGGGAAACCC 0.931891 -224 ACCACGCACGCGAGAATAATCCTTTTACCCCA 4 153 0 CGAGAATACC 0.914774 -148 CTGCGACACACGAGAAAGAAACACCACGCACG 4 175 0 CGAGAAAAAC 0.912222 -126 GGTTCAGTCCCGAGAAAAAGACAAAACGCGCT 13 41 0 CGAGAAAAAC 0.912222 -46 AAATGGGAACGCGCCTGCGCGGTTG 14 4 1 TGGGAACCCC 0.937744 -137 CGGCGCCCATTGACAAACCACCCATAAGGTCT 15 16 0 TGACAAACCC 0.902764 -132 AACGAAAAATTGAGAAACAGCCTACATCTAAA 16 49 1 TGAGAAAACC 0.968352 -39 ******* * ** Masking position 12 Map Score: 6.17632 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 118 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 GTACTAAACTGTGGTGAAAACACGGTACAC 1 219 0 GTGGTGAAAA 0.932674 -82 AAAGGGGCGCGTGGGGTAAAAGGATTATTC 4 142 1 GTGGGGTAAA 0.956845 -159 CTTTTAAACTGTGGGAAGAAAACTCAGATA 4 241 0 GTGGGAAGAA 0.932302 -60 CAACAATCCCGTGGGGAAAATACGCGCGCA 6 228 0 GTGGGGAAAA 0.990724 -40 AATCAGGTCCGTGGGTAAAGCGTCACCCAC 12 165 0 GTGGGTAAAG 0.917384 -136 TCTGTACAGTGTGTGTAAAAGCGTATCCTA 14 91 0 GTGTGTAAAA 0.907788 -50 ATCTGCCGTAGTGTGGAGAAATAG 16 5 0 GTGTGGAGAA 0.951468 -83 ********** Masking position 9 Map Score: 5.57762 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 66 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 TGGGGCAACCGGCACTGTGCGAGAGAACCC 1 12 0 GGCACTGTGC 0.960315 -289 GCTCATGCCTTTGTGCGCACGGTACT 3 7 1 GCCTTTGTGC 0.856788 -184 GGGTGTAGTGCTCTCCTGTTT 11 2 1 GGTGTAGTGC 0.947886 -86 CCTACGCAAGGGCGTACTGCGCGCAAATAT 11 60 0 GGCGTACTGC 0.861206 -28 GCGCCTCTGCGGGGCTGTGCTCTGGCGCGG 12 207 1 GGGGCTGTGC 0.964671 -94 CAGGGCAGGCGGTTCAGTCCCGAGAAAAAG 13 53 0 GGTTCAGTCC 0.864496 -34 GGCGTCTAAAGATTCTGTGCCTTATCGCCG 14 54 1 GATTCTGTGC 0.833333 -87 CAGGCGCACTGGCTCAGTGCTTCCTCCAAA 15 49 0 GGCTCAGTGC 0.987595 -99 ********** Masking position 8 Map Score: 2.37964 Number of sites scoring better than the average of aligned sites = 389 Number in coding regions = 357 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 10 GGGGTTCTCTCGCACAGTGCCGG 1 2 1 GGGTCTCCGC 0.984354 -299 GGTGACGGCCGGGCTCGCGTGCAGACGCGATA 1 119 1 GGGCCGCTGC 0.960667 -182 TTTGTGCGCACGGTACTTATGCCGTGCGCATA 3 20 1 CGGTCTTTGC 0.977384 -171 TGCCACTACACGGCACACGTGCTCTACACTTT 3 90 0 CGGCCACTGC 0.979604 -101 TCATCGTGATGGGTGCGTGTGCTATCTGAGTT 4 219 1 GGGTCGTTGC 0.933297 -82 ACGGCGCTCCCGAACTTTTCCTC 5 16 0 CGGCCTCCGA 0.941655 -13 GTGCGTTAAACGCTGCTCTTGAAGGAACGGTG 6 168 1 CGCTCTCTGA 0.860314 -100 GAAGGAACGGTGGTGCACGCGCTGTTATCTCC 6 188 1 TGGTCACCGC 0.839073 -80 CCAGTCCTGACGGTTCTTCTGCATACTCAAGG 9 40 1 CGGTCTTTGC 0.977384 -56 TCAGTAAACTCGCTCCTTCCGAGCCTGTGCTA 12 123 0 CGCTCTTCGA 0.72567 -178 CTCGTGCGGACGCCTGTCGTGCCTCCGCGTGC 12 246 0 CGCCGTCTGC 0.642473 -55 GCGACGGTGGGGGTGCATCAGCGCGTTTTGTC 13 22 1 GGGTCATAGC 0.745981 -65 GCAGCGGATCCTCCTGAGTATGGTGCC 14 124 0 GGATCTCTGA 0.539512 -17 ACTGCAGTGACGGCGCAGGCGCACTGGCTCAG 15 62 0 CGGCCAGCGC 0.863899 -86 TTCTGCATCAGGGTACATCTGCCGTAGTGTGG 16 19 0 GGGTCATTGC 0.954277 -69 **** *** *** Masking position 2 Map Score: 13.1195 Number of sites scoring better than the average of aligned sites = 753 Number in coding regions = 697 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 11 CATGCATACAGTAGTGTACCGTGTTTTCACC 1 206 1 GTAGGTACCG 0.987361 -95 CAAGTCTCAAGTAGGCTACAGAAAGGGGCGC 4 121 1 GTAGCTACAG 0.954093 -180 ACGCCCTTGCGTAGGATGCAGGC 11 75 1 GTAGATGCAG 0.881915 -13 CAAGCTGGCAGGAGCGTAGCGGAAACTACCC 12 68 1 GGAGGTAGCG 0.927293 -233 GTGTAAAAGCGTATCCTACCGGTTTCGGCGA 14 78 0 GTATCTACCG 0.927983 -63 ATCCTCCTGAGTATGGTGCCGCGTCTGTACA 14 113 0 GTATGTGCCG 0.967671 -28 GGTATGTAGGGTATAGTAGAGGATGCTTTCT 15 110 1 GTATGTAGAG 0.922073 -38 TACATCTGCCGTAGTGTGGAGAAATAG 16 7 0 GTAGGTGGAG 0.967398 -81 **** ****** Masking position 3 Map Score: 4.40928 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 76 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 12 AGCCCGGCCGTCACCATTTCGGGGAGTACT 1 104 0 TCACCATTTC 0.93615 -197 GCAGCCATTATGACCCTTTCATAAACACGA 2 11 0 TGACCCTTTC 0.983033 -23 TTACCCCACGCGCCCCTTTCTGTAGCCTAC 4 131 0 CGCCCCTTTC 0.923053 -170 GGTGTTTGTGTAACCATTTGCCGCAGGAAG 6 12 1 TAACCATTTG 0.694021 -256 ACACGCCCCCTGACCCTGTCAATTTATGCA 6 102 0 TGACCCTGTC 0.974991 -166 TCATTCGGCCTCCCCCTGTCCCTCTATCCA 10 60 0 TCCCCCTGTC 0.932028 -21 GAGTATACCTTGACCATTTGGGTAGTTTCC 12 88 0 TGACCATTTG 0.922099 -213 ********** Masking position 7 Map Score: 2.40722 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 40 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 13 ********** No masking Map Score: 7.19312e-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 CATGCCTTTGTGCGCACGGTACTTATGCCGTG 3 14 1 TGCGCAGGAC 0.790693 -177 CCGTCTTTGCAGAGGATGCCACTACACGGCAC 3 106 0 AGAGGAGCAC 0.969662 -85 ACGGTCAAAAAAAGGACACCACAAGGGCCAGC 3 145 0 AAAGGAACAC 0.830959 -46 CTCCGCTAAGAGCGCACGCGACCGTGCAGAAA 4 40 0 AGCGCAGCAC 0.946419 -261 GTGCGCTCTTAGCGGAGATTTCTCAAGAGGAA 4 55 1 AGCGGAATTC 0.687177 -246 GCGCAAACCAAGAGGAGATAACAGCGCGTGCA 6 201 0 AGAGGAATAC 0.870405 -67 GTAGGTTTTAAACGGAAAGAACTTGCACC 9 8 0 AACGGAAGAC 0.876565 -88 CTTCCTAAAAACAGGAGAGCACTACACCC 11 8 0 ACAGGAAGAC 0.678847 -80 CTACGTGCCCTGCGGAAAGAAAAGAAAAAAGC 12 20 0 TGCGGAAGAA 0.588183 -281 GCAGGAGCGTAGCGGAAACTACCCAAATGGTC 12 75 1 AGCGGAACAC 0.990967 -226 TGCCTCCGCGTGCGGAAACCGCCCGCGCCAGA 12 227 0 TGCGGAACGC 0.887301 -74 CACTCTCCCGTGAGGACGCAACCGCGCAGGCG 14 22 0 TGAGGAGCAC 0.930369 -119 TGTGTGTAAAAGCGTATCCTACCGGTTTCGGC 14 80 0 AGCGTACCAC 0.771899 -61 GCAGCGGATCCTCCTGAGTATGGT 14 127 0 AGCGGACCCC 0.888985 -14 ****** ** ** Masking position 6 Map Score: 6.66496 Number of sites scoring better than the average of aligned sites = 331 Number in coding regions = 298 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 15 ********** No masking Map Score: 7.19312e-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