AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00010_tpal_reg_300.orf -o00010_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 TP0085 80 PTS system, nitrogen regulatory IIA component (ptsN-1) #2 TP0163 174 ABC transporter, periplasmic binding protein (troA) #3 TP0164 147 ABC transporter, ATP-binding protein (troB) #4 TP0168 79 phosphoglycerate mutase (pgm) #5 TP0413 102 phosphoglucomutase #6 TP0475 63 glucose-6-phosphate isomerase (gpi) #7 TP0476 66 acetate kinase (ack) #8 TP0477 60 glucose-6-phosphate 1-dehydrogenase, putative #9 TP0478 72 glucose-6-phosphate 1-dehydrogenase (zwf) #10 TP0479 111 T. pallidum predicted coding region TP0479 #11 TP0505 300 hexokinase (hxk) #12 TP0537 150 triosephosphate isomerase (tpi) #13 TP0662 266 fructose-bisphosphate aldolase (cbbA) #14 TP0755 199 PTS system, nitrogen regulatory IIA component (ptsN-2) #15 TP0757 40 polypeptide deformylase (def) #16 TP0758 118 ribosomal protein S21 (rpsU) #17 TP0818 26 T. pallidum predicted coding region TP0818 #18 TP0819 27 conserved hypothetical protein #19 TP0820 95 hypothetical protein #20 TP0821 80 lipoprotein (tpn32) #21 TP0822 87 conserved hypothetical protein #22 TP0823 300 desulfoferrodoxin (rbo) #23 TP0844 92 glyceraldehyde 3-phosphate dehydrogenase (gap) Motif number 1 GGAGCGGAAAGAGCGTGGGGAGCTTTTCCAAAA 1 20 1 GGGTGGGAGC 0.929217 -61 ATGTAGAGTTGAGTGGGTAGAAGAGCCGTTGGT 3 17 1 GGGGGTGAAG 0.895081 -131 GTGGTGATTAGTGAAGGAGGTGGCGCGCTCACC 3 81 1 GGAGGAGTGG 0.956247 -67 GGTAAGAGCCGTCAGCGGTGAGCGCGCCACCTC 3 97 0 GCGCGGGAGC 0.863335 -51 ATTGAGCGAAAAGAAGGGAGCAGTAT 3 132 1 AGAGGGGCAG 0.897893 -16 TCTTTTTGTATGGGGTGAGGATGCGCCTTT 4 8 1 GAGGGGGAGG 0.988679 -72 TTGTCAGATAAAAGGGGATGTGCAAAACGTATT 4 40 1 AAGGGAGTGC 0.719828 -40 AAACGTATTGTTGAGAGGAGAGGGCC 4 64 1 TGGAGGGAGG 0.582298 -16 CGGGTGTAGGGGCGGGGGAGAGGTAGGA 5 6 0 GCGGGGGAGG 0.977128 -97 AGGAAGTGCAAGGGAGGTGGTGGTCTTGACAGG 5 56 0 AGAGGTGTGG 0.819925 -47 TAGGGCGCGGGTGAAGGAAGTGCAAGGGAGGTG 5 70 0 GGAGGAGTGC 0.944231 -33 GCGCGGAGGATAGGGCGCGGGTGAAGGAAG 5 83 0 GAAGGGGCGG 0.985998 -20 GGGTAGAACGATAAAAGGAGAACGCGCA 6 46 1 AAAAGGGAAC 0.37281 -18 AGAACGTAGCGGGAGAGAGGAGGATGTTCGCCC 8 38 1 GGGAGAGAGG 0.878196 -23 TGCCTTAGGGAGCGGAGAGTCTGCCTGCGG 9 8 1 GGGCGGGAGT 0.798529 -65 GGCACATCCGGTGTAGGTCGCACCGTTGAAAGA 9 39 1 GGAGGTGCAC 0.841993 -34 CGCACCGTTGAAAGAAGGGGCGGTTT 9 57 1 AAAAGGGCGG 0.749944 -16 CAGCCTTTAGAAAAAGGAGGAGCTC 10 3 0 AAAGGAGAGC 0.789069 -109 CTCTTCGCAAGGAAGGGGGGAGGGC 10 97 1 GAGGGGGAGG 0.988679 -15 TGTTGAGCGAAAAGAGGAGGTGCGTGGGACGCG 11 17 0 AAAGGAGTGC 0.686625 -284 ACTGATTGAAGGAAATGTTGAGCGAAAAGAGGA 11 32 0 GAATGTGAGC 0.531253 -269 CGCCGAACACAACAGGGGCGTAGTAGGGGATTG 11 91 1 ACGGGGGTAG 0.610061 -210 GGAGTGTTCCTTGTAGGGTGAACCCGACGGACC 11 139 0 TGAGGGGAAC 0.574834 -162 AACGAGTACGGCAAACGGAGTGTTCCTTGTAGG 11 155 0 GAACGGGTGT 0.497795 -146 AGGGGTGCCGGCGTATGGGGCAGGGAGTTTATA 11 210 0 GGATGGGCAG 0.767728 -91 CCGTTCCTGCAAAAAAGGGGTGCCGGCGTATGG 11 225 0 AAAAGGGTGC 0.590036 -76 CTGGTCGGCTGCCAGGGTAGCACGGATAGCTCG 11 267 0 GCGGGTGCAC 0.604814 -34 CCTGGCAGCCGACCAGGGAGGGCGCGT 11 284 1 GCAGGGGGGC 0.839295 -17 CCATGCGCTAGAATGCGGCGAGCTGGCGCCTGC 13 44 0 GAGCGGGAGC 0.928127 -223 TCTTGTTACAGAGAAAGGGGAGGTTGGTTTGTC 14 68 1 GGAAGGGAGG 0.960801 -132 TCTCACGATAGAAGAGGTTGCGCGGTACCTGCG 14 110 1 GAAGGTGCGC 0.916871 -90 ATGAGTGGGCGCAAAAGGGGAAGATTCCGTCAG 14 163 1 GAAAGGGAAG 0.748023 -37 TCTTGGGTAAGAGCGGGAAGAGGCG 15 26 1 GGGGGAGAGG 0.977656 -15 GACACGTAGGGTGTGCGTGCAGGGGA 16 4 1 AGAGGGGTGC 0.945785 -115 GGGTGTGCGTGCAGGGGAGGCAGGAGTGCTTTC 16 19 1 GAGGGAGCAG 0.833624 -100 ACTCAAGGATGGGGATGGTGTGGGTGTGTCTTT 19 64 1 GGATGGGTGG 0.894342 -32 AATGCAGGGTGAGTCTTGATGTGC 20 2 1 AGAGGGGAGT 0.820695 -79 ATGGATAGAGGGACAGGGGGAGGCCGAATGAG 20 59 1 GAAGGGGAGG 0.986751 -22 CCTGTTTTTAGGAAGGGGAGCAGGAGATTGGGG 21 25 1 GAGGGGGCAG 0.952321 -63 GTACGCCCTTGCGTAGGATGCAGGC 21 73 1 GGAGGAGCAG 0.895117 -15 CCAAGCTGGCAGGAGCGTAGCGGAAACTACCCA 22 67 1 AGGCGTGCGG 0.621949 -234 AGATAGCGTTGCGCGGGATGTGTGCTCTTTTTA 23 55 1 GGGGGAGTGT 0.753105 -38 GCTCTTTTTAGAGGAGGTTGGGCAA 23 78 1 GGAGGTGGGC 0.811724 -15 * * **** **** Masking position 7 Map Score: 52.0236 Number of sites scoring better than the average of aligned sites = 3512 Number in coding regions = 3070 Number in noncoding regions = 442 Number of orfs with sites within 600 bp upstream = 238 Fraction of orfs with sites within 600 bp upstream = 0.0382268 Motif number 2 AACTGTAGCTGCTTATGCGAGGAAGATCAAAT 2 21 1 GCTTTGCGGG 0.923487 -154 AGAAAACGGCACTCTGGCGCGGACCTCTCGAG 2 70 0 ACTCGGCGGG 0.9592 -105 CGAACATCCTCCTCTCTCCCGCTACGTTCTAG 8 36 0 CCTCCTCCGC 0.680347 -25 TAGGCGTTTAGCGCGCGCCGTCAAGTTTTTCT 10 48 1 GCGCCGCCTC 0.8454 -64 ACGCGCCCTCCCTGGTCGGCTGCC 11 287 0 GCGCCTCCTG 0.716376 -14 GCAGAGACATACCCTCGCCAGGAGATCTCGCC 12 47 0 ACCCCGCCGG 0.946947 -104 CGGCGAGCTGGCGCCTGCGAGGCGTTAGGGGT 13 30 0 GCGCTGCGGG 0.988312 -237 GCTTGTCAAACCTCCCGCGTGGTACCTGTCCA 13 84 1 CCTCCGCGGG 0.966669 -183 TTGAGTCCACACGCAGGCGTTGGAACGGCAGC 13 125 0 ACGCGGCGTG 0.778382 -142 CTACCATGCCCCTCTTGCCGAGGGTGGCACGC 13 195 1 CCTCTGCCAG 0.948903 -72 TGCGTAGAAATCTCACGCCTGGCGTGTATCAC 14 11 0 TCTCCGCCGG 0.954195 -189 CGCGCAGTACGCCCTTGCGTAGGATGCAGGC 21 67 1 GCCCTGCGAG 0.962419 -21 TTTCCGCTACGCTCCTGCCAGCTTGGATTCCT 22 61 0 GCTCTGCCGC 0.96726 -240 GTCAAGGTATACTCGTGCGTAGCACAGGCTCG 22 104 1 ACTCTGCGAG 0.941162 -197 CAGTAAACTCGCTCCTTCCGAGCCTGTGCTAC 22 122 0 GCTCTTCCAG 0.83617 -179 TAGAATCAGCGCCTCTGCGGGGCTGTGCTCTG 22 199 1 GCCTTGCGGG 0.847488 -102 GCGGGGCTGTGCTCTGGCGCGGGCGGTTTCCG 22 215 1 GCTCGGCGGG 0.985959 -86 CGGGCGGTTTCCGCACGCGGAGGCACGACAGG 22 234 1 CCGCCGCGAG 0.956279 -67 CTGATTTTGTTCTCGTGCGGACGCCTGTCGTG 22 257 0 TCTCTGCGAC 0.70273 -44 **** **** ** Masking position 8 Map Score: 22.5076 Number of sites scoring better than the average of aligned sites = 1442 Number in coding regions = 1308 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 3 TATCCTGGGAGCGGAAAGAGCGTGGGGAGCTTTT 1 13 1 GCGGAGCGTG 0.934808 -68 GTAGCGGATCACGCAGGAAACGTCAATTTTTCAG 2 117 0 ACGCAACGTC 0.898712 -58 AGAGCCGTCAGCGGTGAGCGCGCCACCTCCTTCA 3 92 0 GCGGTGCGCC 0.793382 -56 CGTAGCATACACGCAAAATGCGCCACTTTC 7 7 0 ACGCAACGCC 0.899071 -60 GCCTTAGGGAGCGGAGAGTCTGCCTGCGGCACAT 9 12 1 GCGGAGTGCC 0.811579 -61 ACTTGACGGCGCGCGCTAAACGCCTAATAATTGC 10 40 0 GCGCGACGCC 0.992393 -72 AAAAGAGGAGGTGCGTGGGACGCGACGATA 11 7 0 GTGCGGCGCG 0.916957 -294 GGTTTCCTAAACGAGCTATCCGTGCTACCCTGGC 11 256 1 ACGAGACGTG 0.536167 -45 GGAGCTATCGGCGGGGTGTTTGTGGTGTGAACGA 12 105 1 GCGGGGTGTG 0.894581 -46 CAAACCTCCCGCGTGGTACCTGTCCAAATCGTCT 13 90 1 GCGTGATGTC 0.632423 -177 GTGATACACGCCAGGCGTGAGATTTCTAC 14 6 1 ACACGACGTG 0.729507 -194 CACTTGGGGTACGCATCATGCGTTGCGTAGAAAT 14 32 0 ACGCAACGTT 0.368853 -168 AGAAGAGGTTGCGCGGTACCTGCGAATTTCTGAA 14 119 1 GCGCGATGCG 0.946293 -81 GACACGTAGGGTGTGCGTGCAGGGGAGGC 16 6 1 GTAGGGCGTG 0.499222 -113 GGGTAGGCTAGCGCAAAAGACGTCCCCTGTCAAT 16 62 0 GCGCAACGTC 0.977846 -57 CCTTGAGTATGCAGAAGAACCGTCAGGACTGGGT 19 38 0 GCAGAACGTC 0.800031 -58 GGGCATATTTGCGCGCAGTACGCCCTTGCGTAGG 21 56 1 GCGCGGCGCC 0.990736 -32 AATCAGGTCCGTGGGTAAAGCGTCACCCACCTGT 22 161 0 GTGGGACGTC 0.921742 -140 GTGCCTCCGCGTGCGGAAACCGCCCGCGCCAGAG 22 226 0 GTGCGACGCC 0.952489 -75 GCACGCGGAGGCACGACAGGCGTCCGCACGAGAA 22 246 1 GCACGACGTC 0.95231 -55 AGATAGCGTTGCGCGGGATGTGTGCTCTTTTTAG 23 55 1 GCGCGATGTG 0.946092 -38 ***** * **** Masking position 12 Map Score: 28.082 Number of sites scoring better than the average of aligned sites = 1922 Number in coding regions = 1792 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 4 GCGGAAAGAGCGTGGGGAGCTTTTCCAAAA 1 23 1 CGTGGGGAGC 0.792513 -58 AGCCGTTGGTGGTCGGCTGTACGGCAGCGC 3 40 1 GGTCGGCTGT 0.968334 -108 AATCAGGTGTGGTCGGGTGTAGGGGCGGGG 5 22 0 GGTCGGGTGT 0.972617 -81 ACAGACATATCGCCGGCTGTT 6 2 0 CGCCGGCTGT 0.974546 -62 CGTTCTACCCCGTAGGGTTTACCTACAGAC 6 26 0 CGTAGGGTTT 0.894659 -38 TCACTGGGTCCGTCGGGTTCACCCTACAAG 11 133 1 CGTCGGGTTC 0.845288 -168 CGGCGTATGGGGCAGGGAGTTTATACCTAA 11 205 0 GGCAGGGAGT 0.849316 -96 CGCCCTCCCTGGTCGGCTGCCAGGGTAGCA 11 278 0 GGTCGGCTGC 0.944389 -23 TGGAGCTATCGGCGGGGTGTTTGTGGTGTG 12 104 1 GGCGGGGTGT 0.965624 -47 TGAGTCCACACGCAGGCGTTGGAACGGCAG 13 126 0 CGCAGGCGTT 0.675219 -141 GACACGTAGGGTGTGCGTGCAGGG 16 5 1 CGTAGGGTGT 0.975119 -114 GCCTACCCCTGGTAGGCTGTGTTTTTTTCA 16 88 1 GGTAGGCTGT 0.963501 -31 GTCAGGACTGGGTAGGTTTTAAACGGAAAG 19 21 0 GGTAGGTTTT 0.425949 -75 TACGCCCTTGCGTAGGATGCAGGC 21 74 1 CGTAGGATGC 0.810814 -14 TGTGCTCTGGCGCGGGCGGTTTCCGCACGC 22 222 1 CGCGGGCGGT 0.89972 -79 GATAGCGTTGCGCGGGATGTGTGCTCTTTT 23 56 1 CGCGGGATGT 0.876083 -37 ********** Masking position 5 Map Score: 21.747 Number of sites scoring better than the average of aligned sites = 384 Number in coding regions = 339 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 5 ATATCCTGGGAGCGGAAAGAGCGTGGGGAG 1 12 1 AGCGGAAAGA 0.993922 -69 TACCCGATTGAGCGAAAAGAAGGGAGCAGT 3 126 1 AGCGAAAAGA 0.965837 -22 TGCCTTAGGGAGCGGAGAGTCTGCCTGCGG 9 11 1 AGCGGAGAGT 0.915093 -62 GGAAATGTTGAGCGAAAAGAGGAGGTGCGT 11 25 0 AGCGAAAAGA 0.965837 -276 ACAGGGCCTATGCGGAACGAGTACGGCAAA 11 173 0 TGCGGAACGA 0.939185 -128 CTTGGGTAAGAGCGGGAAGAGGCG 15 27 1 AGCGGGAAGA 0.971515 -14 GTAGGTTTTAAACGGAAAGAACTTGCACC 19 10 0 AACGGAAAGA 0.934589 -86 CTACGTGCCCTGCGGAAAGAAAAGAAAAAA 22 22 0 TGCGGAAAGA 0.986676 -279 GCAGGAGCGTAGCGGAAACTACCCAAATGG 22 75 1 AGCGGAAACT 0.932519 -226 TGCCTCCGCGTGCGGAAACCGCCCGCGCCA 22 229 0 TGCGGAAACC 0.840239 -72 ********** Masking position 3 Map Score: 13.6565 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 67 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 TCACCACGTCGTGAACAGGCGCTGCCGTACA 3 57 0 GTGAAAGGCG 0.974015 -91 ACCCGATTGAGCGAAAAGAAGGGAGCAGTAT 3 127 1 GCGAAAGAAG 0.557623 -21 TTTGTATGGGGTGAGGATGCGCCTTTTGTCA 4 15 1 GTGAGATGCG 0.640869 -65 GTGTGGTCGGGTGTAGGGGCGGGGGAGAGGT 5 15 0 GTGTAGGGCG 0.831653 -88 GGTGAAGGAAGTGCAAGGGAGGTGGTGGTCT 5 63 0 GTGCAGGGAG 0.972272 -40 GCGCGGAGGATAGGGCGCGGG 5 92 0 GCGCGAGGAT 0.813424 -11 CCCCTTCCTTGCGAAGAGGAGTATGCCAAAC 10 84 0 GCGAAAGGAG 0.967874 -28 AAAAGAGGAGGTGCGTGGGACGCGACGATA 11 10 0 GTGCGGGGAC 0.843673 -291 ACGAAAGGATGTGCTAAGGAGGGGAT 12 135 1 GTGCTAGGAG 0.915627 -16 GTTAGGGGTGGTGAAAAGGAGTTTGCGA 13 8 0 GTGAAAGGAG 0.958754 -259 CTAGAATGCGGCGAGCTGGCGCCTGCGAGGC 13 39 0 GCGAGTGGCG 0.918636 -228 GTCAACCGAAGCGCGAAGGCTTGAGTCCACA 13 146 0 GCGCGAGGCT 0.875474 -121 GCATGGTAGGGCGATCGGGACGCTCTAGTCA 13 173 0 GCGATGGGAC 0.575744 -94 CGTACCGTGTATGAGTGGGCGCAAAAGGGGA 14 153 1 ATGAGGGGCG 0.78465 -47 GGGTAAGAGCGGGAAGAGGCG 15 30 1 GGGAAAGGCG 0.928526 -11 TAGGGTGTGCGTGCAGGGGAGGCAGGAGTGC 16 17 1 GTGCAGGGAG 0.972272 -102 TTTTAGGAAGGGGAGCAGGAGATTGGGGGCA 21 30 1 GGGAGAGGAG 0.901637 -58 CCTGCATCCTACGCAAGGGCGTACTGCGCGC 21 66 0 ACGCAGGGCG 0.857874 -22 GAGCACAGCCCCGCAGAGGCGCTGATTCTAC 22 198 0 CCGCAAGGCG 0.830257 -103 CTGCGGGGCTGTGCTCTGGCGCGGGCGGTTT 22 213 1 GTGCTTGGCG 0.781396 -88 ***** ***** Masking position 3 Map Score: 23.3497 Number of sites scoring better than the average of aligned sites = 1025 Number in coding regions = 925 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 7 GACACTCCTTGGGTGAATTTTGATGCATCAAAGTAG 2 147 0 GGGTGATAGC 0.603586 -28 TGATTAGTGAAGGAGGTGGCGCGCTCACCGCTGACG 3 85 1 AGGAGTGGTC 0.722799 -63 ATCTGACAAAAGGCGCATCCTCACCCCATACAAAAA 4 13 0 AGGCGATACC 0.506335 -67 GTCAGATAAAAGGGGATGTGCAAAACGTATTGTTGA 4 42 1 AGGGGTGAAC 0.876991 -38 AGCGGGAGAGAGGAGGATGTTCGCCC 8 45 1 AGGAGATGCC 0.890423 -16 GAGCGAAAAGAGGAGGTGCGTGGGACGCGACGATA 11 10 0 AGGAGTGGAC 0.86822 -291 GGGGCGTAGTAGGGGATTGACTGTGCAGTCACTGGG 11 105 1 AGGGGTTGGC 0.989138 -196 GGTACCACGCGGGAGGTTTGACAAGCTATTTCTCCA 13 74 0 GGGAGTTAGC 0.87365 -193 CCTCGGCAAGAGGGGCATGGTAGGGCGATCGGGACG 13 182 0 AGGGGATGGC 0.987847 -85 CAGAGAAAGGGGAGGTTGGTTTGTCCGAAGAAATTC 14 76 1 GGAGGTGGCC 0.774355 -124 TCACGATAGAAGAGGTTGCGCGGTACCTGCGAATTT 14 112 1 AGAGGTGGAC 0.760352 -88 ACAGCCTACCAGGGGTAGGCTAGCGCAAAAGACGTC 16 72 0 AGGGGAGGGC 0.989303 -47 GGATGGATAGAGGGACAGGGGGAGGCCGAATGAG 20 57 1 AGGGAAGAGC 0.61318 -24 GCAGGAGATTGGGGGCATATTTGCGCGCAGTACGCC 21 44 1 GGGGGATGGC 0.982411 -44 TGGATTCCTGAGGAGTTTCTACGTGCCCTGCGGAAA 22 34 0 AGGAGTTGGC 0.966759 -267 CTCTGGCGCGGGCGGTTTCCGCACGCGGAGGCACGA 22 226 1 GGCGGTTAGC 0.66138 -75 CCTACAGCAAAGAGGGATTGACGTGCCGATCTTTTT 23 17 1 AGAGGATGGC 0.925935 -76 ***** ** * ** Masking position 2 Map Score: 13.2399 Number of sites scoring better than the average of aligned sites = 612 Number in coding regions = 557 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 8 AGCTAAAAACTCTCAAAGGAAAAGTCAAGCTT 1 52 0 TTCAAGGAAA 0.804991 -29 CCGTAGGGTTTACCTACAGACATATCGCCGGC 6 15 0 TCCACAGACA 0.912774 -49 AGGGAGTTTATACCTAAAGACAGGGCCTATGC 11 190 0 TCCAAAGACA 0.964897 -111 TAGGAAACCGTTCCTGCAAAAAAGGGGTGCCG 11 233 0 TCCGCAAAAA 0.72056 -68 GAGGTTGGTTTGTCCGAAGAAATTCTCACGAT 14 87 1 TTCGAAGAAA 0.900409 -113 GCAGGAGTGCTTTCGGAAGAAACGATTGACAG 16 38 1 TTCGAAGAAA 0.943486 -81 CTTCTTTCAAAAGACACACCCACACC 19 80 0 TTCAAAGACA 0.952611 -16 ATCCTGTCAATGTCCAAAGAAAAAGCGCACAT 20 29 0 TTCAAAGAAA 0.951221 -52 CCTGCTCCCCTTCCTAAAAACAGGAGAGCACT 21 17 0 TCCAAAAACA 0.87204 -71 CTACGTGCCCTGCGGAAAGAAAAGAAAAAAGC 22 20 0 TCGAAAGAAA 0.774569 -281 CGCGCAACGCTATCTGAAAAAAGATCGGCACG 23 38 0 TTCGAAAAAA 0.835261 -55 * ** ******* Masking position 10 Map Score: 5.71519 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 71 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 9 GGAGCGGAAAGAGCGTGGGGAGCTTTTCCA 1 20 1 GAGCGTGGGG 0.72116 -61 CATGTAGCTCGAGAGGTCCGCGCCAGAGTG 2 63 1 GAGAGGTCCG 0.801225 -112 AGGTCCGCGCCAGAGTGCCGTTTTCTTTTC 2 76 1 CAGAGTGCCG 0.670306 -99 TTTGATGCATCAAAGTAGCGGATCACGCAG 2 135 0 CAAAGTAGCG 0.838037 -40 TAAGAGCCGTCAGCGGTGAGCGCGCCACCT 3 98 0 CAGCGGTGAG 0.763347 -50 ACGTATTGTTGAGAGGAGAGGGCC 4 66 1 GAGAGGAGAG 0.767986 -14 GAAAGTGGCGCATTTTGCGT 7 1 1 GAAAGTGGCG 0.858452 -66 AACGACACTAGAACGTAGCGGGAGAGAGGA 8 29 1 GAACGTAGCG 0.958635 -32 TGCCTTAGGGAGCGGAGAGTCTGCCTGCG 9 10 1 GAGCGGAGAG 0.90006 -63 CCCCTTCTTTCAACGGTGCGACCTACACCG 9 47 0 CAACGGTGCG 0.923499 -26 GAGAAAAACTTGACGGCGCGCGCTAAACGC 10 51 0 TGACGGCGCG 0.616054 -61 TATCGTCGCGTCCCACGCAC 11 1 1 TATCGTCGCG 0.457276 -300 CGGTTGACTAGAGCGTCCCGATCGCCCTAC 13 169 1 GAGCGTCCCG 0.936772 -98 GCGAATTTCTGAACGTACCGTGTATGAGTG 14 140 1 GAACGTACCG 0.864731 -60 CGGAGTATTGCAACGGCGCGTTATAT 17 7 0 CAACGGCGCG 0.959542 -20 AAGCTGGCAGGAGCGTAGCGGAAACTACCC 22 69 1 GAGCGTAGCG 0.978888 -232 GCACAGGCTCGGAAGGAGCGAGTTTACTGA 22 125 1 GGAAGGAGCG 0.718874 -176 CACAGCCCCGCAGAGGCGCTGATTCTACCT 22 196 0 CAGAGGCGCT 0.434967 -105 TTTTTTCAGATAGCGTTGCGCGGGATGTGT 23 48 1 TAGCGTTGCG 0.844785 -45 ********** Masking position 5 Map Score: 15.8855 Number of sites scoring better than the average of aligned sites = 1408 Number in coding regions = 1282 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 10 CGTGGGGAGCTTTTCCAAAAAGCTTGACTTTT 1 33 1 TTTTCCAAAG 0.914632 -48 TGCCGTTTTCTTTTCCTGAAAGGGTACTGAAA 2 91 1 TTTTCCTAAG 0.980897 -84 GAGCTCCTCCTTTTTCTAAAGGCTGCGAGGCA 10 11 1 TTTTTCTAAG 0.945784 -101 CGCCGTCAAGTTTTTCTCACCGTTTGGCATAC 10 63 1 TTTTTCTACG 0.921501 -49 TGCAGGAACGGTTTCCTAAACGAGCTATCCGT 11 247 1 GTTTCCTAAG 0.97202 -54 GGTGCCCACTTTTCCTGACGGAATCTTCCCC 14 179 0 TTTTCCTACG 0.972021 -21 GAAGGAGCGAGTTTACTGAATGCGTACAGGTG 22 136 1 GTTTACTAAG 0.8694 -165 ******* ** * Masking position 9 Map Score: 2.89274 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 16 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 11 AGGGAGCGGAGAGTCTGCCTGCGGCACATCCG 9 17 1 GAGTTCCTGC 0.923945 -56 ACGGCAAACGGAGTGTTCCTTGTAGGGTGAAC 11 149 0 GAGTTCCTTG 0.993146 -152 GGTGCCGTGAGATTTTCCCTTGGGTTGGGGCG 12 19 1 GATTTCCTTG 0.957296 -132 TGCGTACCCCAAGTGTGTCTTGTTACAGAGAA 14 51 1 AAGTTTCTTG 0.883378 -149 GCGGGTATGAGTTTCTCTTGGGTAAGAGCG 15 9 1 GAGTTTCTTG 0.979985 -32 TGCTACGCACGAGTATACCTTGACCATTTGGG 22 96 0 GAGTTCCTTG 0.993145 -205 **** * ***** Masking position 6 Map Score: 2.59426 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 6 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 12 CATAAGCAGCTACAGTTGCGCCCTCTT 2 3 0 TCATGGCCTC 0.934933 -172 CAATTATTAGGCGTTTAGCGCGCGCCGTCAAGTTT 10 41 1 GGTTGGCGGC 0.949031 -71 TGACTGTGCAGTCACTGGGTCCGTCGGGTTCACCC 11 122 1 GCATGTCCTC 0.820629 -179 ACATACCCTCGCCAGGAGATCTCGCCCCAACCCAA 12 38 0 GCAGGTCTGC 0.696628 -113 CGAGAAACTGTTCTATAGAGCCACCGCAGAGACAT 12 69 0 TCTTGGCCCC 0.97033 -82 CGCGCTTCGGTTGACTAGAGCGTCCCGATCGCCCT 13 162 1 TGATGGCGCC 0.887782 -105 TCACGAAATAGAGAAGCGTGCCACCCTCGGCAAGA 13 207 0 GGAGGGCCCC 0.942368 -60 GTGCAGGGGAGGCAGGAGTGCTTTCGGAAGAAACG 16 27 1 GCAGGGCTTC 0.919651 -92 GACAGGGGACGTCTTTTGCGCTAGCCTACCCCTGG 16 65 1 GCTTGGCTGC 0.976562 -54 GGGTGTAGTGCTCTCCTGTTTTTAG 21 1 1 GGTTGGCTTC 0.922929 -87 TGCGGGGCTGTGCTCTGGCGCGGGCGGTTTCCGCA 22 214 1 TCTTGGCGGC 0.941957 -87 TCGTGCGGACGCCTGTCGTGCCTCCGCGTGCGGAA 22 242 0 GCTTGGCCCC 0.987995 -59 AATCCCTCTTTGCTGTAGGGCTCCC 23 1 0 TCTTGGCTCC 0.953506 -92 * ** * * *** ** Masking position 11 Map Score: 10.665 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 281 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 13 GTAAGAGCCGTCAGCGGTGAGCGCGCCACCT 3 98 0 TCAGCGTGAG 0.372993 -50 CAGGATGAAATCAGGTGTGGTCGGGTGTAGG 5 29 0 TCAGGTTGGT 0.733504 -74 TGAAGGAAGTGCAAGGGAGGTGGTGGTCTTG 5 61 0 GCAAGGAGGT 0.801521 -42 CTAGTGTCGTTCAAGGCTCGGCATTACCG 8 9 0 TCAAGGTCGG 0.927549 -52 TGCCTTAGGGAGCGGAGAGTCTGCC 9 5 1 TTAGGGGCGG 0.814006 -68 ACTCCTCTTCGCAAGGAAGGGGGGAGGGC 10 93 1 GCAAGGAGGG 0.919376 -19 CTGCGAGGCGTTAGGGGTGGTGAAAAGGAGT 13 17 0 TTAGGGTGGT 0.874285 -250 GAAACGATTGACAGGGGACGTCTTTTGCGCT 16 56 1 ACAGGGACGT 0.641271 -63 ACACAGCCTACCAGGGGTAGGCTAGCGCAAA 16 79 0 CCAGGGTAGG 0.663708 -40 TGTGTTTTTTTCAGGGGAGGGTCG 16 105 1 TCAGGGAGGG 0.98745 -14 AGAAGAACCGTCAGGACTGGGTAGGTTTTAA 19 29 0 TCAGGATGGG 0.931996 -67 TTCTGCATACTCAAGGATGGGGATGGTGTGG 19 56 1 TCAAGGTGGG 0.965612 -40 TCTCCTGTTTTTAGGAAGGGGAGCAGGAGAT 21 22 1 TTAGGAGGGG 0.548435 -66 TTTTCTTTCCGCAGGGCACGTAGAAACTCCT 22 29 1 GCAGGGACGT 0.876579 -272 ****** **** Masking position 3 Map Score: 4.59819 Number of sites scoring better than the average of aligned sites = 540 Number in coding regions = 466 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 14 ********** No masking Map Score: -6.85431e-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: -6.85431e-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