AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_trans1_ctra_reg_100.orf -o199_ctra_100.ace -a/home/amcguire/alignace/lib/ORF_ctra.txt -z/skink1/amcguire/genomes/ctra.fna -g0.41 -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 = 0.41 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RCT00768 16 Chlamydia_trachomatis RCT00769 20 Chlamydia_trachomatis RCT00490 17 Chlamydia_trachomatis Input sequences: #1 RCT00126 206 Chlamydia_trachomatis #2 RCT00300 24 Chlamydia_trachomatis #3 RCT00301 300 Chlamydia_trachomatis #4 RCT00302 31 Chlamydia_trachomatis #5 RCT00303 21 Chlamydia_trachomatis #6 RCT00304 22 Chlamydia_trachomatis #7 RCT00305 105 Chlamydia_trachomatis #8 RCT00306 300 Chlamydia_trachomatis #9 RCT00307 300 Chlamydia_trachomatis #10 RCT00308 300 Chlamydia_trachomatis #11 RCT00377 292 Chlamydia_trachomatis #12 RCT00418 41 Chlamydia_trachomatis #13 RCT00419 49 Chlamydia_trachomatis #14 RCT00420 300 Chlamydia_trachomatis #15 RCT00441 300 Chlamydia_trachomatis #16 RCT00442 69 Chlamydia_trachomatis #17 RCT00472 300 Chlamydia_trachomatis #18 RCT00481 65 Chlamydia_trachomatis #19 RCT00482 20 Chlamydia_trachomatis #20 RCT00483 21 Chlamydia_trachomatis #21 RCT00484 55 Chlamydia_trachomatis #22 RCT00485 22 Chlamydia_trachomatis #23 RCT00488 21 Chlamydia_trachomatis #24 RCT00489 27 Chlamydia_trachomatis #25 RCT00493 16 Chlamydia_trachomatis #26 RCT00495 32 Chlamydia_trachomatis #27 RCT00497 18 Chlamydia_trachomatis #28 RCT00499 23 Chlamydia_trachomatis #29 RCT00502 300 Chlamydia_trachomatis #30 RCT00596 300 Chlamydia_trachomatis #31 RCT00853 300 Chlamydia_trachomatis #32 RCT00754 23 Chlamydia_trachomatis #33 RCT00767 137 Chlamydia_trachomatis Motif number 1 GAACGAAAGGTTCTTATAAAAAAAGCCTTTCCTA 1 60 1 TTCTAAAAAA 0.801122 -147 ATTAAAATCTTTTATCGAAAAAATTTTATACGAC 1 94 1 TTTTAAAAAT 0.667028 -113 TACGACTTCTGTTTCGAAAAAAAATAAAAACTCG 1 122 1 GTTCAAAAAA 0.809304 -85 TGTTAACATTCTAAAAAATAAGGGTGACAA 4 7 1 CATCAAAAAA 0.622459 -25 AAGAAAGTATCTTTTGTAAAAAAACAAGCAGCTT 8 89 1 CTTTAAAAAA 0.924806 -212 TGGGTTTTTGCTTGTAAACAAATTAAAAAAATAT 10 62 1 CTTTACAAAT 0.660107 -239 ATATTTGTTATTCCCGCAAAAACTCAAGAGAGAA 10 92 1 TTCCAAAAAT 0.616805 -209 TGTCAAACAACTTGTCAAAAAACAGAAGGAAAAG 10 138 0 CTTTAAAAAA 0.954516 -163 AGGAGAAGGATTTTTTAAAAAAAAGCTGCAAGAG 11 57 0 TTTTAAAAAA 0.795691 -236 TAAAACAAGCCTTCCCTAAAAATAATTAATAAAA 14 129 0 CTTCAAAAAA 0.962352 -172 CTATAACAATTTTATTAAAAAACATTTCCTCCAA 14 173 0 TTTTAAAAAA 0.860184 -128 GAAATAACCCCTTGCAAACAAAGATATTCTTATT 14 233 1 CTTCACAAAA 0.879023 -68 TCGATTCAACCTCTCTTACAAACAGGGAAATATA 14 268 0 CTCCACAAAA 0.827382 -33 AGGAAAATAGCTCTTTGAAAAAGAAGAGTTTAAA 15 23 0 CTCTAAAAAA 0.93263 -278 GACTCTTATGCTTTTCAAAAAAAAAACTCTCGTG 17 110 0 CTTTAAAAAA 0.954488 -191 AGAATCCTTGCTTCCTAAAAAAGAAGTTGACTGT 17 144 1 CTTCAAAAAA 0.962352 -157 AACACTCTCTCCTAAAAATTA 20 2 0 CTCCAAAAAT 0.84591 -20 AAAAACTCTTCTTATTTAAAAAATCTCA 30 5 0 CTTTAAAAAT 0.872249 -296 CCTTATTTTATTCCTTAAAAAACATCGCCTCGCT 30 156 0 TTCTAAAAAA 0.802333 -145 TTACTGTTCACTTTTTGAAAAAAAGTTACTGAAA 33 23 1 CTTTAAAAAA 0.952897 -115 TTGAAAAAAAGTTACTGAAAAATAATCAGTTTCG 33 37 1 GTTCAAAAAA 0.80931 -101 *** * ***** * Masking position 8 Map Score: 23.2493 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 154 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 2 GATTTTAATTAGGAAAGGCTTTTTTTATAAGAACC 1 68 0 AGGAAGTTTT 0.972352 -139 AGTTACCCGCAAAAGCTGCTTGTTTTTTTACAAAA 8 100 0 AAAAGGTTTT 0.530915 -201 AATCAACCAAAGAAAAAGCTTGTTACTTTACCGAA 8 275 0 AGAAAGTTTA 0.824929 -26 GACAAGTTTAAGGTATTGGGTTTTTGCTTGTAAAC 10 46 1 AGGTAGTTTT 0.750741 -255 AAAAAACAGAAGGAAAAGTATCTTTTGACATTCTC 10 121 0 AGGAAGTTTT 0.972361 -180 CGGAAACTCGAGAGAGCGATTATATCGACTAAACA 10 177 0 AGAGAGTTAT 0.810634 -124 GCTGGGATCAAGAGATAGAATGTTTTTTAGGTTTT 10 269 1 AGAGAGTTTT 0.945005 -32 GAAAGAAGAGAGGAGAAGGATTTTTTAAAAAAAAG 11 66 0 AGGAGGTTTT 0.956138 -227 AACATCTCTTAGAAATGGTGTTTATGCCATAACAG 11 153 0 AGAAAGTTAT 0.866285 -140 AGAAATACGAAGAGGTTGAGTTTAT 13 35 1 AGAGGGTTAT 0.726102 -15 AATTATTTTTAGGGAAGGCTTGTTTTAAGAAAATC 14 136 1 AGGGAGTTTT 0.958716 -165 AATCTTTTGGAGGAAATGTTTTTTAATAAAATTGT 14 167 1 AGGAAGTTTA 0.864203 -134 AAAGCGAATTAGAAAACGATTTATTCCTCGGACTA 15 148 0 AGAAAGTATT 0.747735 -153 TTCCTAAAAAAGAAGTTGACTGTCTAAAAACCCCG 17 155 1 AGAAGGTTCT 0.64417 -146 TTTCTTGGTTAGAGACGGGGTTTTTAGACAGTCAA 17 170 0 AGAGAGTTTT 0.943385 -131 TCTCTAACCAAGAAAACGATATTTTTCTTCCCCTC 17 190 1 AGAAAGATTT 0.615709 -111 GTTTGCTTTAAGGAGCCGCGTTTTCTTTGTCGTGG 29 170 1 AGGAGGTTTC 0.698025 -131 TTTTTTAAATAAGAAGAGTTTTTTTAGCACTGAGA 30 16 1 AAGAAGTTTT 0.711532 -285 AGTGAGGAAAAGGGTAAATTTTGTTCCTC 31 5 1 AGGAAGTAAT 0.499235 -296 CTTGTCCGGTAGGAGGAGGCTGTTTTGCTAGGGGC 31 198 1 AGGAGGTTTT 0.956138 -103 CTCTTAAAAAAGAGACTGATTCTTACTACACCCTC 31 259 0 AGAGAGTTTA 0.75658 -42 TCCATGTTATCGAAACTGATTATTTTTCAGTAACT 33 46 0 CGAAAGTTTT 0.703689 -92 ***** * * *** Masking position 8 Map Score: 18.2389 Number of sites scoring better than the average of aligned sites = 245 Number in coding regions = 245 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 3 AGAGGAATACTAAGGTAGAGTAGGGTTGAA 7 85 1 TAAGGTAGAG 0.739764 -21 TTAGGTAACTGAAAGAAGAATTCGCTTATG 8 32 1 GAAAGAAGAA 0.773479 -269 TCAAAAAACAGAAGGAAAAGTATCTTTTGA 10 128 0 GAAGGAAAAG 0.744108 -173 GGCTCTTGCTTAAGGAAGATGAATAAAGCA 11 13 0 TAAGGAAGAT 0.666952 -280 AAGGATTTTTTAAAAAAAAGCTGCAAGAGC 11 56 0 TAAAAAAAAG 0.439577 -237 TTACTCTTAAGAAAGAAGAGAGGAGAAGGA 11 81 0 GAAAGAAGAG 0.97161 -212 TCCCTAAACCTAAAGAAAAGAAATACGAAG 13 17 1 TAAAGAAAAG 0.808186 -33 AATAATTAATAAAAAAAGAGTTAAATCCTT 14 113 0 AAAAAAAGAG 0.676168 -188 AGCTCTTTGAAAAAGAAGAGTTTAAAGTTG 15 19 0 AAAAGAAGAG 0.918142 -282 CAAGTCTTCAGCAAGAAGAGAGGTAAAAGC 15 178 0 GCAAGAAGAG 0.802916 -123 AAAGAGTTGCGAAGGAAGAGCCCTAAACTT 15 249 1 GAAGGAAGAG 0.956088 -52 GACTCCTAGTTAAAGAAGATGATAAGAAAA 15 277 0 TAAAGAAGAT 0.758902 -24 TTCCTCATCTTAAAGACGAGGAACACGTGA 16 24 0 TAAAGACGAG 0.779666 -46 CCTTGCTTCCTAAAAAAGAAGTTGACTGTC 17 149 1 TAAAAAAGAA 0.369472 -152 AGGGTAAAGTAGAGTCGAACT 23 5 1 TAAAGTAGAG 0.817123 -17 TAAAGAAGGAAGAGAAGAATAAC 28 5 1 GAAGGAAGAG 0.956088 -19 GATTTTTTAAATAAGAAGAGTTTTTTTAGC 30 14 1 ATAAGAAGAG 0.473927 -287 CTTGGGCTCTTAAAAAAGAGACTGATTCTT 31 270 0 TAAAAAAGAG 0.854502 -31 ********** Masking position 3 Map Score: 14.3799 Number of sites scoring better than the average of aligned sites = 435 Number in coding regions = 435 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 4 CATTTCCCTATTTAGTCTCTCTGTGATCTCT 3 243 0 TTTATCTCTC 0.749664 -58 ACTTTTTCGTTTTTCCCCCTCGTTTTGAGAG 7 58 1 TTTTCCCCTC 0.971096 -48 ATCTCGCTTATTTACCCACTCAATCTTCTTA 8 148 0 TTTACCACTC 0.937151 -153 CGAACTTTTTTGCCTCTCACACACGAAT 12 24 0 TTTTCCTCTC 0.971652 -18 CTCTTCTCGATTCAACCTCTCTTACAAACAG 14 277 0 TTCACCTCTC 0.973778 -24 TCTAATTCGCTTTTACCTCTCTTCTTGCTGA 15 170 1 TTTTCCTCTC 0.971652 -131 GGGACGTACTTTCGACCACTCAGTCATCTTT 17 35 1 TTCGCCACTC 0.930522 -266 CTCGTGTAAATTTATCCCTTCGGAGCTTTTT 17 85 0 TTTACCCTTC 0.745887 -216 AACGATATTTTTCTTCCCCTCCCCTTTCCTC 17 204 1 TTCTCCCCTC 0.973261 -97 AGCAAAGGGTTTCGACCTCTCCCAAAGATGT 30 249 0 TTCGCCTCTC 0.96854 -52 **** ****** Masking position 2 Map Score: 9.43737 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 59 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 5 GCGAGCTCTCCTAAGACTTTA 3 290 0 GCGAGCTCCC 0.944038 -11 CGCTTATGGGGCAAGATCACCGAAGAAAATT 8 54 1 GCAAGATCCC 0.971542 -247 TGCTTACCATGCAAGTGCTCTACCACTGAGC 9 203 0 GCAAGTGCCT 0.912113 -98 TCTTCCTTAAGCAAGAGCCTCTTGAAAAAGG 11 24 1 GCAAGAGCTC 0.927464 -269 AAAAAAAGCTGCAAGAGCCCCTTTTTCAAGA 11 43 0 GCAAGAGCCC 0.984833 -250 GAGTTGCGAAGGAAGAGCCCTAAACTTTTCT 15 252 1 GGAAGAGCCT 0.932897 -49 GGTTGGTAAAGGAAGCTCTCTCGGCCAGGTT 17 260 0 GGAAGCTCCT 0.903944 -41 TTTCTTCCAAGGAAGCTCCACTAGTAAAACC 29 23 1 GGAAGCTCAC 0.834539 -278 CCTCCATCCTGCAAGAGCGATTTCCACGACA 29 197 0 GCAAGAGCAT 0.82449 -104 GTTGTTGAACGCGAGTTCCCCGCGCTTGACA 30 108 0 GCGAGTTCCC 0.850749 -193 TCGATAACATGGAAGCGCTTCTTATAGAGTA 33 68 1 GGAAGCGCTC 0.905598 -70 ******** ** Masking position 4 Map Score: 8.35675 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 84 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 6 AAGGTTCTTATAAAAAAAGCCTTTCCTAATT 1 66 1 TAAAAAAGCC 0.7185 -141 CAGCTAGGACAAAACAGAGCCTATCCAATGC 3 187 0 AAAACAAGCC 0.948109 -114 ATCTTTTGTAAAAAAACAAGCAGCTTTTGCG 8 97 1 AAAAAAAAGC 0.553748 -204 CATTCAAACAAAAAAACAGGCTTGGGCACCC 10 239 0 AAAAAAAGGC 0.945338 -62 GATTTTTTAAAAAAAAGCTGCAAGAGCCCCT 11 52 0 AAAAAACTGC 0.665575 -241 GTTGCATCATCAAAAACCGGCTGCCCTACTA 11 185 1 CAAAAACGGC 0.888153 -108 GTCAAAATAAAAAACATAGCCAAGTCTTCAG 15 197 0 AAAACAAGCC 0.948109 -104 CTTTCCAACGAAACAACCGGCCCAAAAAGCT 17 62 1 AAACAACGGC 0.820332 -239 ACAACCGGCCCAAAAAGCTCCGAAGGGATAA 17 74 1 CAAAAACTCC 0.538536 -227 AAAAATCGCAAAAACAAAGCCTGAAAAATCG 29 59 0 AAAACAAGCC 0.948109 -242 CTCCTTAAAGCAAACAAAGGCGGCGAATGGG 29 154 0 CAAACAAGGC 0.888153 -147 TATTCCTTAAAAAACATCGCCTCGCTAACTT 30 151 0 AAAACACGCC 0.943241 -150 ACAGAATTGCAAACAAGAGCCTTCCCGGATA 31 58 0 AAACAAAGCC 0.853605 -243 TTGGGCTCTTAAAAAAGAGACTGATTCTTAC 31 268 0 AAAAAAAGAC 0.691664 -33 ****** **** Masking position 6 Map Score: 9.34113 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 103 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 7 GAAGTCGTATAAAATTTTTTCGATAAAAGAT 1 100 0 AAATTTTTTC 0.553704 -107 AAGAATACACAGAATTTCTTATTC 7 4 0 AAATTTCTTA 0.694893 -102 CTTTCTTAAGAAATTTTCTTCGGTGATCTTG 8 65 0 AATTTTCTTC 0.929303 -236 TTTACAAAAGATACTTTCTTAAGAAATTTTC 8 78 0 AACTTTCTTA 0.57191 -223 GTCGAGACCGAGATTATCTTCAGTTGTATTC 9 51 1 AATTATCTTC 0.513568 -250 GGAATAACAAATATTTTTTTAATTTGTTTAC 10 75 0 AATTTTTTTA 0.77658 -226 AATGTTTTTTAGGTTTTTTTAGGA 10 287 1 AGTTTTTTTA 0.740585 -14 AGAGAGGAGAAGGATTTTTTAAAAAAAAGCT 11 64 0 AGATTTTTTA 0.415189 -229 TGCTGATAAAATGTTTTCTTCGAATACTGTT 14 83 0 AGTTTTCTTC 0.915228 -218 TTCCTCCAAAAGATTTTCTTAAAACAAGCCT 14 151 0 AATTTTCTTA 0.901559 -150 TTGCAAACAAAGATATTCTTATTCTATATTT 14 244 1 AATATTCTTA 0.423826 -57 AAGAGCCCTAAACTTTTCTTATCATCTTCTT 15 264 1 ACTTTTCTTA 0.760423 -37 GACCAACCCTAAATTTTTTTCTAGCGTGTTG 18 22 0 AATTTTTTTC 0.833025 -44 AGCGTTATAAGTTTTCTTCCAAGGAAGCT 29 9 1 AGTTTTCTTC 0.915228 -292 GGAAAAGGGTAAATTTTGTTCCTCTAGTTGT 31 16 1 AATTTTGTTC 0.605535 -285 AAAACCATAAAAGTTTTCTTACAGTGATCTC 31 131 0 AGTTTTCTTA 0.882657 -170 ATTTTTCAGTAACTTTTTTTCAAAAAGTGAA 33 29 0 ACTTTTTTTC 0.633568 -109 * ********* Masking position 7 Map Score: 10.0361 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 229 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 8 TATCCCCTATCCTGTCATTAGTA 1 4 1 CCCCTATCCT 0.96057 -203 ATTCAACCCTACTCTACCTTAGTAT 7 91 0 ACCCTACTCT 0.564614 -15 AAATCCTTCTCCTCTCTTCTTTCTTAAGAG 11 78 1 CCTCTCTTCT 0.950045 -215 TTCGCTTTTACCTCTCTTCTTGCTGAAGAC 15 175 1 CCTCTCTTCT 0.950045 -126 TATTTTTCTTCCCCTCCCCTTTCCTCTTGA 17 209 1 CCCCTCCCCT 0.975296 -92 GATATATTCCCCTATACCCTAACCTGGCCG 17 240 1 CCTATACCCT 0.731214 -61 AACACTCTCTCCTAAAAATTA 20 9 0 ACTCTCTCCT 0.919526 -13 AACCTGTCTCCTTATGAC 27 7 0 CCTGTCTCCT 0.905696 -12 ACGGCCATGCCCTCCATCCTGCAAGAGCGA 29 208 0 CCTCCATCCT 0.873428 -93 ********** Masking position 10 Map Score: 3.30952 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 146 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 9 ATTTTCCATCTATTGTGTGGATTTAGCTCTTCGA 8 226 1 TTTTGGGATT 0.930841 -75 CATAGTAACTTCAGACGCGGATTATTATCAAGCT 9 12 0 TAGCGGGATA 0.683652 -289 AACTAATTTTTAATTTGAGGATTTTTGAG 9 282 1 TATTGGGATT 0.859046 -19 TCCTCGTCTTTAAGATGAGGAACTAGTTCATTCT 16 32 1 TAGTGGGAAT 0.90724 -38 TTTTGCGATTTTTGGTGTGGGATTTCTTAGCGTC 29 77 1 TTGTGGGGAT 0.902795 -224 AAGAAAAATCTCTTGTGTGGATGTCGCAGGTCAT 29 111 1 TTTTGGGATT 0.930841 -190 CCGCGTTTTCTTTGTCGTGGAAATCGCTCTTGCA 29 185 1 TTGCGGGAAT 0.938946 -116 GGTTTTTAGTTGTGCTGCGGATTTTATAGCAAAA 31 156 1 TTGTGGGATT 0.979461 -145 AAGTATTTTATGTGGTGAGGGTGTAGTAAGAATC 31 243 1 TTGTGGGGTT 0.953512 -58 TCTGACGGGGATTTACTGTTCACT 33 1 1 TTGCGGGATT 0.971399 -137 * ** ** **** * Masking position 1 Map Score: 5.41268 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 50 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 10 ACACTTGTTGGAGAGAAGTTA 2 14 1 GAGAGAAGTT 0.795677 -11 TTAGGTAACTGAAAGAAGAATTCGCTTATG 8 32 1 GAAAGAAGAA 0.54151 -269 GGCTTAGCACAAAAGAGGAAGCAACCTAAT 9 167 0 AAAAGAGGAA 0.820573 -134 GCAAAAACTCAAGAGAGAATGTCAAAAGAT 10 107 1 AAGAGAGAAT 0.598306 -194 CTTAAGAAAGAAGAGAGGAGAAGGATTTTT 11 76 0 AAGAGAGGAG 0.921599 -217 CACCATTTCTAAGAGATGTTGCATCATCAA 11 168 1 AAGAGATGTT 0.699947 -125 CCCTGTTTGTAAGAGAGGTTGAATCGAGAA 14 275 1 AAGAGAGGTT 0.937807 -26 AGCTCTTTGAAAAAGAAGAGTTTAAAGTTG 15 19 0 AAAAGAAGAG 0.738579 -282 ATTGATCCCTAAGAGAAGATCATGTTACCA 15 107 0 AAGAGAAGAT 0.939278 -194 CTTCAGCAAGAAGAGAGGTAAAAGCGAATT 15 173 0 AAGAGAGGTA 0.911501 -128 TGCTTCCTAAAAAAGAAGTTGACTGTCTAA 17 152 1 AAAAGAAGTT 0.783746 -149 TAAAGAAGGAAGAGAAGAATAAC 28 10 1 AAGAGAAGAA 0.913537 -14 ********** Masking position 6 Map Score: 4.90078 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 290 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 11 GAATATTTTTGGCTTTGGATTTTCCATCTATTG 8 208 1 GGCTGGATTT 0.955533 -93 TTTTGTCTGCGGCTGAGGGATTGAGAAAACTAG 9 90 1 GGCTGGGTTG 0.909176 -211 TAGTTCAGGCTGGTTGAGAGTTTGATTGCGGGA 9 120 1 TGGTAGATTT 0.670197 -181 GCAAAAACATTCCTTGGGGGTTTGAGAAGTAAG 11 233 1 TCCTGGGTTT 0.860477 -60 CCTCTCTTCTTGCTGAAGACTTGGCTATGTTTT 15 185 1 TGCTAGATTG 0.765681 -116 TTATAGCTAAGGAGTTTGGG 19 5 1 AGCTGGATTT 0.887363 -16 TTGCGATTTTTGGTGTGGGATTTCTTAGCGTCA 29 79 1 TGGTGGGTTT 0.927197 -222 TTTTTAGTTGTGCTGCGGATTTTATAGCAAAAG 31 158 1 TGCTGGATTT 0.977759 -143 GAGGCTGTTTTGCTAGGGGCTCTCATTTCTAAG 31 213 1 TGCTGGGTCT 0.908531 -88 GCAAGGTCAATGCTTAGGAGTTTTTA 33 122 1 TGCTGGATTT 0.977759 -16 **** *** *** Masking position 4 Map Score: 2.95959 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 76 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 12 TTTTTTTTCGAAACAGAAGTCGTATAAAAT 1 116 0 AAACAGAAGT 0.953565 -91 TTGGCATCGCAAACAGAATATTTCTGTTGC 3 80 1 AAACAGAATA 0.913108 -221 TGTGATCTCTAAACAGGAATACGACAGATG 3 223 0 AAACAGGAAT 0.591354 -78 GAATAAGAATACACAGAATTTCTTATTC 7 9 0 ACACAGAATT 0.84772 -97 ACTTGTCAAAAAACAGAAGGAAAAGTATCT 10 133 0 AAACAGAAGG 0.882473 -168 TATATCGACTAAACAGAAAATGTCAAACAA 10 162 0 AAACAGAAAA 0.84922 -139 TAGCTCTTTGAAAAAGAAGAGTTTAAAGTT 15 20 0 AAAAAGAAGA 0.742363 -281 TTGCTTCCTAAAAAAGAAGTTGACTGTCTA 17 151 1 AAAAAGAAGT 0.780218 -150 GTGGCCCTAAAAACAGAATAGCGAGACGTT 30 210 1 AAACAGAATA 0.913108 -91 CACGCTCCATACACAGAATTGCAAACAAGA 31 71 0 ACACAGAATT 0.84772 -230 ********** Masking position 5 Map Score: 3.39058 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 95 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 13 GATAGTATTTGTCGGATGGACAAGTGTATAGAG 3 138 1 GGGATGACAA 0.96475 -163 GTCTGCGGCTGAGGGATTGAGAAAACTAGTTCA 9 94 1 GGGATTAGAA 0.975076 -207 TTGAGTTTTTGCGGGAATAACAAATATTTTTTT 10 86 0 GGGAATACAA 0.948628 -215 AACATTCCTTGGGGGTTTGAGAAGTAAGAATGT 11 238 1 GGGTTTAGAA 0.906118 -55 ATATTCTTGAGTAGGATTCACAACAACTTTCAT 14 19 1 GGGATTACAA 0.986814 -282 CCCGGATAAAGGAGGATTAACAACTAGAGGAAC 31 33 0 GGGATTACAA 0.986816 -268 * ***** **** Masking position 10 Map Score: 0.929967 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 4 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 AGCCGACAATACTTTTGGAGGCCATATAAAAT 1 161 0 ACTTGGAGGC 0.80858 -46 TTCTAAGTTTAAAGAGGAAAA 5 7 1 GTTTAGAGGA 0.902486 -15 TTTCCCCCTCGTTTTGAGAGGAATACTAAGGT 7 69 1 GTTTAGAGGA 0.902504 -37 GAAGTATTGAGTCTAAGGAGGACAAGTTTAAG 10 26 1 GTCTGGAGGA 0.908485 -275 GCTCTCTCGAGTTTCCGGAGGACAACAGGTGC 10 195 1 GTTTGGAGGA 0.951996 -106 AGAGGCTCTTGCTTAAGGAAGATGAATAAAGC 11 14 0 GCTTGGAAGA 0.818212 -279 AAGAGCCCCTTTTTCAAGAGGCTCTTGCTTAA 11 30 0 TTTTAGAGGC 0.849695 -263 TTGTGAATATTCTTGAGTAGGATTCACAACAA 14 13 1 TCTTGTAGGA 0.639684 -288 TTTAAGAAAATCTTTTGGAGGAAATGTTTTTT 14 159 1 TCTTGGAGGA 0.955005 -142 GTCAACTTCTTTTTTAGGAAGCAAGGATTCTG 17 143 0 TTTTGGAAGC 0.70967 -158 GGGGAATATATCCTCAAGAGGAAAGGGGAGGG 17 220 0 TCCTAGAGGA 0.635173 -81 CTTATATTACTTTAAGGGAGGCCCTTCGT 21 37 1 TTTAGGAGGC 0.670826 -19 **** ****** Masking position 9 Map Score: 3.50544 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 248 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 CACACAATAGATGGAAAATCCAAAGCCAAAA 8 214 0 ATGAAAATCC 0.767737 -87 CTCAAAAATCCTCAAATTAAA 9 290 0 CTCAAAATCC 0.89664 -11 TCCTAAAAAAACCTAAAAAACAT 10 288 0 CTAAAAAACC 0.78903 -13 TAAAAAAAAGCTGCAAGAGCCCCTTTTTCAA 11 45 0 CTGAAGAGCC 0.772348 -248 CAGCTTTTTTTTAAAAAATCCTTCTCCTCTC 11 63 1 TTAAAAATCC 0.674561 -230 AAAACAAAGCCTGAAAAATCGTTCTAGGTTT 29 49 0 CTGAAAATCG 0.815441 -252 TTTCTTGACGCTAAGAAATCCCACACCAAAA 29 86 0 CTAGAAATCC 0.956873 -215 GGTATATGACCTGCGACATCCACACAAGAGA 29 119 0 CTGGACATCC 0.880653 -182 CACTGAGAATCTAGGAAATCCGTTGTAGAAA 30 43 1 CTAGAAATCC 0.956873 -258 AAACCCTTTGCTGAGAAAGCCCAATCCTCCG 30 268 1 CTGGAAAGCC 0.938325 -33 TACCCTTTTGCTATAAAATCCGCAGCACAAC 31 164 0 CTAAAAATCC 0.959555 -137 *** ******* Masking position 6 Map Score: 3.64855 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 101 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