AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i293_bsub_mtub_300.orf -o293_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 metS 300 methionyl-tRNA synthetase #2 yabD 78 similar to hypothetical proteins #3 yabE 155 similar to hypothetical proteins #4 yabF 144 similar to hypothetical proteins #5 yabG 161 yabG #6 veg 210 veg #7 sspF 159 small acid-soluble spore protein (alpha/beta-type SASP) #8 yabH 147 similar to hypothetical proteins #9 purR 55 transcriptional regulator #10 spoVG 193 spoVG #11 gcaD 192 UDP-N-acetylglucosamine pyrophosphorylase #12 prs 22 phosphoribosyl pyrophosphate synthetase #13 ctc 84 general stress protein #14 spoVC 106 thermosensitive mutant blocks spore coat formation (stage V sporulation) #15 spoIIE 300 serine phosphatase #16 yabS 84 similar to hypothetical proteins #17 yabT 88 yabT #18 yacA 103 similar to cell-cycle protein #19 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #20 yacB 194 similar to hypothetical proteins #21 yacC 85 similar to hypothetical proteins #22 yacD 46 similar to protein secretion PrsA homolog #23 cysK 75 cysteine synthetase A #24 pabB 166 para-aminobenzoate synthase (subunit A) #25 sigW 300 RNA polymerase ECF-type sigma factor (sigma-W) #26 ybbP 160 alternate gene name: ybbQ; similar to hypothetical proteins #27 yyaF 126 similar to hypothetical proteins #28 yyaE 300 similar to formate dehydrogenase #29 rplY 216 rplY #30 lpqT 35 lpqT #31 prsA 91 prsA #32 glmU 254 glmU #33 Rv1112 131 hypothetical protein Rv1112 #34 mrsA 124 mrsA #35 rplM 233 rplM #36 Rv3447c 113 hypothetical protein Rv3447c #37 ftsH 66 ftsH #38 Rv3627c 137 hypothetical protein Rv3627c Motif number 1 GGATGTGACCCGGGGGACGTGCTGTTCCC 8 9 1 CCCGGGGGCG 0.949016 -139 AAAAAGTGATCCCGGCTCTCCCAGAATCACT 10 18 0 CCCGGCTCCC 0.955159 -176 TAAGCCTTTTGCCGGCGGTCCTTTTTTAATT 11 50 1 GCCGGCGGCC 0.963131 -143 TAAAAAAACTGCCGGCTGACGCTGGCAGTTT 20 24 1 GCCGGCTGCG 0.813887 -171 TAAAAAAACTCCCGGCGAACCGGGAGTTTTG 24 18 0 CCCGGCGACC 0.99411 -149 CGCCGTGACGCCCGGCTAGGCTAACCCATGG 29 78 0 CCCGGCTAGC 0.959465 -139 AGCCGGGCGTCACGGCGAGGGTGGTCGGCGG 29 92 1 CACGGCGAGG 0.870331 -125 CTGTCGCGACCCTGGCCGTGCCCCCAAACGA 29 169 1 CCTGGCCGGC 0.734331 -48 AGTCGCATCCCGGCTACCCGGCGACAAAT 31 9 1 CCCGGCTACC 0.962876 -83 GGCGACAAATCCGGGCGGTGCGCTACGTACC 31 30 1 CCGGGCGGGC 0.98512 -62 CCTGGCGCGCGTCACCCGCGT 32 1 1 CCTGGCGCCG 0.955579 -254 CGCCGGAAAACCCGACGCGGGTGACGCGCGC 32 15 0 CCCGACGCGG 0.914482 -240 AGGTTCGAGTCCTGGCGACGGAGCTTCAAGG 32 227 1 CCTGGCGAGG 0.960149 -28 TCACCGACACGCCGACGAGCGCACACAAACA 34 37 0 GCCGACGACG 0.744835 -88 TTCCGGGCCCCGGAGCGCGCAAC 35 3 1 CCGGGCCCGG 0.623687 -231 CCTGTGTGGTCCCGACGGGGGAGAGCCGTCG 35 39 1 CCCGACGGGG 0.943064 -195 GACCCGAGGTCCCGGCGTACCGCACGCCAAC 35 121 0 CCCGGCGTCC 0.974238 -113 GCGGGTTGGTCTCGGCGAACCGACATTGACC 35 148 0 CTCGGCGACC 0.922093 -86 CCGGGGTGCCCCGGGCGCCGGTCAGGCGTGA 35 182 0 CCGGGCGCGG 0.976471 -52 TCGGGTGGATCCCGGGGTGCCCCGGGCGCCG 35 193 0 CCCGGGGTCC 0.796265 -41 CAACCGAATACCGGGCGATCGAGAACCGGCT 36 44 0 CCGGGCGACG 0.987686 -70 GCTGGGCGACGGTATGCAGCGC 36 102 0 CTGGGCGAGG 0.837742 -12 GCCGAACCGGCCGGGCGACGCTGCCACGGTA 38 88 0 CCGGGCGAGC 0.98541 -50 ******** ** Masking position 4 Map Score: 39.5395 Number of sites scoring better than the average of aligned sites = 454 Number in coding regions = 432 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 2 CGTGAAAGGGCGGTGTCTTAACCGCTTGACCAAC 15 45 0 CGGTGCTCCG 0.979239 -256 TTTATCTAACCTCTGCCTTCACCGGTCTGTATGT 25 276 0 CTCTGCTCCG 0.853891 -25 CGCCGTCTTCTCCTTACCTTCTAT 28 287 0 CGCCGCTCCT 0.891033 -14 GCTCGGATAGCTGTGCCCCAACCGTGCGGACAA 29 10 0 CTGTGCCCCG 0.904767 -207 TGCTGTAGACCGCCGACCACCCTCGCCGTGACGC 29 98 0 CGCCGCCCTC 0.960585 -119 GCTGTCGCGACCCTGGCCGTGCCCCCAAACGAGG 29 168 1 CCCTGCCCCC 0.702834 -49 CCCGGCTACCCGGCGACAAATCCGGGCGGTGCGC 31 19 1 CGGCGCACCG 0.99118 -73 CGCGCTGCCCTCGCCGTTTGGGATCG 31 76 0 CGCTGCCCCG 0.989707 -16 TCGGGTTTTCCGGCGCCTTATCCGGCCCTTTATC 32 31 1 CGGCGCTCCG 0.993278 -224 TCAACGCTGTCGCCGTCTACCCACCGGCCCCACG 32 98 0 CGCCGCTCAC 0.854563 -157 ACGGCGACAGCGTTGACTGTGCTGACGGCGTTGA 32 116 1 CGTTGCTCTG 0.702226 -139 TGACTTTAGACGGTGTCAACGCCGTCAGCACAGT 32 131 0 CGGTGCACCG 0.933721 -124 GTGGTGTAATCGGCAGCACCTCTGATTTTGGTTC 32 184 1 CGGCACACTG 0.640914 -71 CTTGAAGCTCCGTCGCCAGGACTCGAACCTGAAC 32 223 0 CGTCGCACTC 0.671255 -32 GTGAATCGAGCGGTGACTTGCCTGTACCGCCGAC 33 26 1 CGGTGCTCTG 0.914404 -106 TTGCCTGTACCGCCGACCTCGCCCGCTGCGCTGA 33 43 1 CGCCGCCCCC 0.991266 -89 GTGCCGCCTTCGGCGCCATTGCCGGTACGGTCGA 33 83 0 CGGCGCACCG 0.98792 -49 TGTGTGGTCCCGACGGCTCTCCCCCGTCGGGACC 35 46 0 CGACGCTCCC 0.832418 -188 GCGTACCGCACGCCAACCGAGCAGCTTACCGACG 35 104 0 CGCCACCCAG 0.671685 -130 GATCGAGAACCGGCTACCGTTCCGGTGATCCGAG 36 25 0 CGGCTCCCCG 0.951874 -89 GGAAGGACCTGGCCGGCACGGCCGATGATCG 37 46 1 GGCCGCACCG 0.870369 -21 ACCGTGGCAGCGTCGCCCGGCCGGTTCGGCAGAA 38 89 1 CGTCGCCCGG 0.822702 -49 GAGCTCTCCTGCCTTTCCGGTCCCATTCT 38 119 0 CTCCTCCCCG 0.698839 -19 ***** ** *** Masking position 7 Map Score: 28.9701 Number of sites scoring better than the average of aligned sites = 952 Number in coding regions = 914 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 3 TAATCAAATGAAATAAAAAACTTTGGTTCGAA 1 54 0 AAATAAAAAT 0.873409 -247 TCTTTAATGAAAATAAAAAAAGTCTGTTCGTG 1 103 0 AAATAAAAAG 0.851188 -198 AGAATAATTAAAATTAAAAATCTTTAATGAAA 1 123 0 AAATAAAAAC 0.966916 -178 GACGCTCGATATAAGAAAAAGTTTCATGAATA 4 90 1 ATAAAAAAAT 0.533845 -55 CCTCCAAGACAAAATAAAAACTTTTGTATATT 4 118 0 AAAAAAAAAT 0.77957 -27 TGTGGTGCGCAAAACAAAAAGCCCTT 5 5 0 AAAAAAAAAC 0.937426 -157 TCATTCAATGATAAGAAAAAACTTGGACTCAG 5 71 1 ATAAAAAAAC 0.829094 -91 TCATTATGTAAAATAAAAAACCCGCATAGCTC 6 32 0 AAATAAAAAC 0.966916 -179 AAAAAAGGGCAAAACAAAAAGCAGTAAACAAA 7 25 0 AAAAAAAAAC 0.937426 -135 TTTATATCCAAAATAAAAAAACCAGGGAACAG 8 32 0 AAATAAAAAC 0.966916 -116 GGCATAAGGTAAATAAAAAAGTGATCCCGGCT 10 32 0 AAATAAAAAT 0.873409 -162 TGTTGTCTAAAAATGAAAAAAATCGGCTTCTG 15 135 0 AAATAAAAAA 0.677112 -166 CCAATCATTTACATAAAAAAACTGCCAGCGTC 20 41 0 ACATAAAAAC 0.810007 -154 CCCTTTTCTCAAATTAAAAACCCGCTAAAGAG 22 12 0 AAATAAAAAC 0.966916 -35 GATGCACGAAATATAAAAAAACTCCCGGCGAA 24 30 0 ATATAAAAAC 0.904434 -137 GATTTTTCCGAAAAGAAAAAAGACACCTTTTG 25 98 0 AAAAAAAAAG 0.745675 -203 GATATCGTAGAAATGAAAAAACCGCATCCATG 28 81 1 AAATAAAAAC 0.966916 -220 CTTACCTTCTATATGAAAAAGCATGAGTGTCG 28 267 0 ATATAAAAAC 0.904434 -34 **** ***** * Masking position 6 Map Score: 23.4633 Number of sites scoring better than the average of aligned sites = 463 Number in coding regions = 325 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 4 TTATTTGACAAAAATGGGCTCGTGTTGTACAA 6 167 1 AAAGGGCTCG 0.932149 -44 TTGGAAACCAAAAAAGGGCAAAACAAAAAGCA 7 34 0 AAAGGGCAAA 0.818408 -126 ATATAAATACATAATGGGCTGAATATGGATAT 8 57 1 AAAGGGCTGA 0.971609 -91 AAATATTTTAAAAACGAGCAGGATTTCAGAAA 10 116 1 AAAGAGCAGG 0.923297 -78 CAAGGACTGCTGAAAGGGCTGACATAAGCCTT 11 26 1 TAAGGGCTGA 0.941408 -167 AACAGCTTGGTAAAGGGGCCAATGGAATT 17 70 1 TAAGGGCCAA 0.731483 -19 TGTCCTCCTCACAATGAGCAGGTATTTTAAAG 18 80 0 AAAGAGCAGG 0.923297 -24 TTCTTAACCCTAAAAGGGCTGGAATTGATTTA 21 25 1 TAAGGGCTGG 0.970551 -61 TTAATTTGAGAAAAGGGGCTGAAAGCAGGT 22 27 1 AAAGGGCTGA 0.971609 -20 CAGCCCGCAAAAAAAGAGCAAAGCGGCTAACG 26 15 0 AAAGAGCAAA 0.515487 -146 TTTTGCGGGCTGAGAGGGCTGGCACATTTCAC 26 35 1 TAGGGGCTGG 0.806931 -126 GAAATGTGGTATAATGGGCTCGCTATGTAAAG 26 77 1 AAAGGGCTCG 0.932149 -84 AAAGGGCCGGATAAGGCGCCGGAAAACCCGAC 32 30 0 AAAGCGCCGG 0.874707 -225 GCCGGACCGGATAAAGGGCCGGATAAGGCGCC 32 42 0 AAAGGGCCGG 0.984996 -213 CACTCTGATCTGAAGGAGCCGACGC 38 4 0 TAAGAGCCGA 0.780083 -134 AGTGCATGGGACAACGGGCAGGTCCAATGCGT 38 32 1 AAAGGGCAGG 0.980766 -106 * ** ******* Masking position 3 Map Score: 18.2603 Number of sites scoring better than the average of aligned sites = 467 Number in coding regions = 409 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 5 TCCTTTGGGCGGGAGCTTTTTGACATTCTG 1 265 1 GGGAGCTTTT 0.702187 -36 TCGACAAGAAAGGAGTTTTTCACTT 2 64 1 AGGAGTTTTT 0.723068 -15 AAAAAACGCTAGCGGGTTTTGTAAGAGCTT 3 12 1 AGCGGGTTTT 0.970182 -144 TTATGTATTCAGAGGGTTTTGCGCCCTCTG 4 18 1 AGAGGGTTTT 0.700113 -127 AGCTCTCCTATGCAGGTTTTCAACTG 6 7 0 TGCAGGTTTT 0.940274 -204 AGGAGAGCTATGCGGGTTTTTTATTTTACA 6 28 1 TGCGGGTTTT 0.956941 -183 TTTAAAAACGAGCAGGATTTCAGAAAAAAT 10 122 1 AGCAGGATTT 0.678452 -72 CCTCACAATGAGCAGGTATTTTAAAGATAT 18 76 0 AGCAGGTATT 0.678452 -28 AGCGTCAGCCGGCAGTTTTTTTAGAAAGAA 20 17 0 GGCAGTTTTT 0.924762 -178 GGCTGACGCTGGCAGTTTTTTTATGTAAAT 20 37 1 GGCAGTTTTT 0.924762 -158 TTGGCTCAGCTGCGGCTTTTACAATCATCC 20 69 1 TGCGGCTTTT 0.855965 -126 GCTCTTTAGCGGGTTTTTAATTTGAGA 22 8 1 AGCGGGTTTT 0.970182 -39 CCGGTTCGCCGGGAGTTTTTTTATATTTCG 24 26 1 GGGAGTTTTT 0.77797 -141 TCCGCATGGATGCGGTTTTTTCATTTCTAC 28 87 0 TGCGGTTTTT 0.898285 -214 CGTCACCCGCGTCGGGTTTTCCGGCGCCTT 32 20 1 GTCGGGTTTT 0.711867 -235 ********** Masking position 9 Map Score: 11.6546 Number of sites scoring better than the average of aligned sites = 791 Number in coding regions = 627 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 6 GTAACCGCGGGAGGGTTACGCCTTAAGCTA 14 10 0 GAGGGTACGC 0.753119 -97 GCCCTTTCACGGCGGTAACACGGGTTCGAAT 15 68 1 GGCGGTACAC 0.644761 -233 GCTATAGCCAAGCGGTAAGGCAACGGACTTT 25 12 1 AGCGGTAGGC 0.851053 -289 AAAGAGCAAAGCGGCTAACGCGCT 26 4 0 GCGGCTACGC 0.762825 -157 TTTGTGTTTTACGTGTTACGCATATGTACTT 26 106 0 ACGTGTACGC 0.413708 -55 TACCTCGTTTGGGGGCACGGCCAGGGTCGCG 29 173 0 GGGGGCCGGC 0.872548 -44 AAAACCCGACGCGGGTGACGCGCGCCAGG 32 9 0 GCGGGTACGC 0.930568 -246 CGGCCCTTTATCCGGTCCGGCCACATCAACA 32 53 1 TCCGGTCGGC 0.781576 -202 GCGGTGACTTGCCTGTACCGCCGACCTCGCC 33 35 1 GCCTGTCCGC 0.892119 -97 CGGCGCCATTGCCGGTACGGTCGACGTGTGT 33 76 0 GCCGGTCGGT 0.909732 -56 TTTAAGGCGAGGCGGTGCCGCCTTCGGCGCC 33 100 0 GGCGGTCCGC 0.975818 -32 TGCCCCGGGCGCCGGTCAGGCGTGAACGGCG 35 176 0 GCCGGTAGGC 0.623037 -58 GAAGGACCTGGCCGGCACGGCCGATGATCG 37 47 1 GCCGGCCGGC 0.936814 -20 CCCTAGTCGAGCCGGTACCGTGGCAGCGTCG 38 73 1 GCCGGTCCGT 0.923607 -65 GCGTCGCCCGGCCGGTTCGGCAGAATGGGAC 38 98 1 GCCGGTCGGC 0.861098 -40 GCAGAATGGGACCGGAAAGGCAGGAGAGCTC 38 117 1 ACCGGAAGGC 0.589827 -21 ****** **** Masking position 10 Map Score: 18.3382 Number of sites scoring better than the average of aligned sites = 724 Number in coding regions = 674 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 7 GACTTTCGAACCAAAGTTTTTTATTTCATT 1 50 1 CCAAAGTTTT 0.797987 -251 TGATAAACAAAAGGTGTTTCACGTGTA 2 8 1 CAAAAGGTGT 0.970029 -71 TGTCGAAACACAAAAGGTGTTCGACGAATT 2 40 0 CAAAAGGTGT 0.970029 -39 CATGAATATACAAAAGTTTTTATTTTGTCT 4 114 1 CAAAAGTTTT 0.911443 -31 AAGCAGTAAACAAAAGGTTCACTGCCCG 7 9 0 CAAAAGGTTC 0.819557 -151 GGACCGCCGGCAAAAGGCTTATGTCAGCCC 11 41 0 CAAAAGGCTT 0.944971 -152 CATTCTAGCACAAAAGACGTAACCGCGGGA 14 29 0 CAAAAGACGT 0.749318 -78 AGAAACTATTCAAAAGTGGTGATAGAGG 20 177 1 CAAAAGTGGT 0.785805 -18 CACCTTTGATCAAAAGGTGTCTTTTTTCTT 25 88 1 CAAAAGGTGT 0.970029 -213 AGCTTCGTTTCAAAAGGTTTCAATTTTTTT 25 241 0 CAAAAGGTTT 0.960188 -60 ATCATTCAGGCCAAAGTCTTTATCCGCCAA 28 54 0 CCAAAGTCTT 0.73771 -247 ********** Masking position 5 Map Score: 8.63702 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 95 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 TAAGGCGTAACCCTCCCGCGGTTACGTCTT 14 16 1 CCCTCCCGCG 0.739552 -91 GATCCCCTCCGCCGCTACCATATT 15 5 1 CCCTCCGCCG 0.861632 -296 TATCAAGGCAGAAACCGTCGAAGATTTCTT 15 193 1 GAAACCGTCG 0.695355 -108 AACGGACTTTGACTCCGTCATGCGTTGGTT 25 33 1 GACTCCGTCA 0.792739 -268 CACTGTGAGAGCATCCCTCACACTTAATTC 28 157 0 GCATCCCTCA 0.819257 -144 CAGCTTGTCGGCCTCCGTCGATAACGGTGT 29 142 0 GCCTCCGTCG 0.982733 -75 ATGGCAGCCGTCATCCTTGAGGG 30 4 1 GCAGCCGTCA 0.936525 -32 ATCCTTGAGGGCATCCGGCGGGC 30 23 1 GCATCCGGCG 0.968968 -13 CGCGCTGCCCTCGCCGTTTGGGA 31 79 0 GCTGCCCTCG 0.737445 -13 CATCGATGTGCAATCCGTCGTGGTGTAATC 32 165 1 CAATCCGTCG 0.804979 -90 GTGTGTCAGCGCAGCGGGCGAGGTCGGCGG 33 52 0 GCAGCGGGCG 0.741643 -80 GCGAGGCGGTGCCGCCTTCGGCGCCATTGC 33 95 0 GCCGCCTTCG 0.820456 -37 GGATATGTGCGCAGCCGTCAACTGTGAAAG 34 96 1 GCAGCCGTCA 0.936525 -29 TGCAGCGCGAGAATCCGCCGCAAGTCGCTT 36 80 0 GAATCCGCCG 0.847493 -34 ********** Masking position 5 Map Score: 8.84436 Number of sites scoring better than the average of aligned sites = 797 Number in coding regions = 750 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 9 ATATTTGTTTGGCCCGTTGGTCAAGCGGTTA 15 30 1 GGCCGTTGGT 0.981947 -271 GTTTGCGTGGGGCCGGTGGGTAGACGGCGAC 32 93 1 GGCCGTGGGT 0.969608 -162 CCAAGTTTAAGGCGAGGCGGTGCCGCCTTCG 33 105 0 GGCGGGCGGT 0.977169 -27 TGCGCTCGTCGGCGTGTCGGTGAACCAACAG 34 45 1 GGCGGTCGGT 0.992864 -80 GCAGCGAATATGCCTGTTGGTTCACCGACAC 34 58 0 TGCCGTTGGT 0.914606 -67 CCTGCGTGGATGCTCGTCGGTAAGCTGCTCG 35 90 1 TGCTGTCGGT 0.840013 -144 AGGCGTGAACGGCGGGTTGGTCTCGGCGAAC 35 159 0 GGCGGTTGGT 0.981946 -75 GGACACCCTAGTCGAGCCGGTACCGTGGCAG 38 68 1 GTCGGCCGGT 0.897941 -70 TGGCAGCGTCGCCCGGCCGGTTCGGCAGAAT 38 93 1 GCCCGCCGGT 0.928731 -45 **** ****** Masking position 11 Map Score: 7.09566 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 82 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 10 CACTTTGTCTATTATAACGAAAAAAACAGAGG 4 42 0 ATTATCGAAA 0.901179 -103 AATGATACATAATTTACCGAAACTTGCGGAAC 6 59 1 AATTTCGAAA 0.819795 -152 GAATCATAGAATTTTGTCAAAATAATTTTATT 6 100 1 ATTTTCAAAA 0.936208 -111 GTTTCCAATAATTTTAACGAAAGTTCCATCTG 7 58 1 ATTTTCGAAA 0.966506 -102 ACTATATCCTATTTTTTCAAAAAATATTTTAA 10 95 1 ATTTTCAAAA 0.936208 -99 CACAGATAGGATTTTGTCAAAAGAAGGTAACA 15 229 0 ATTTTCAAAA 0.936208 -72 GTTGCCTGTCATTATAGCGAAAGCACAGATAG 15 252 0 ATTATCGAAA 0.901179 -49 AGTTGGAATGATTTTTCCGAAAAGAAAAAAGA 25 107 0 ATTTTCGAAA 0.966506 -194 TGATAAACTTATTTTATAAAAAAATTGAAACC 25 224 1 ATTTTAAAAA 0.589219 -77 ***** ***** Masking position 5 Map Score: 5.2513 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 114 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 11 CCGCTACATAGGCTAGAGAAGGACCTTTCATTC 5 44 1 GCTAAGAGGA 0.672876 -118 AAAAAAACCAGGGAACAGCACGTCCCCCGGGTC 8 17 0 GGAAAGCCGT 0.784359 -131 CTTTTATATAGGGAAAAGGTGGTGAACTACT 10 173 1 GGAAAGGGGT 0.975797 -21 GGAGTTATGTGACTAAGGGAGGATTCGCC 14 88 1 GCTAGGGGGA 0.728237 -19 TGTTACCGCCGTGAAAGGGCGGTGTCTTAACCG 15 55 0 GGAAGGGGGT 0.963942 -246 ATAGGATTTTGTCAAAAGAAGGTAACAATACCA 15 223 0 GCAAAGAGGT 0.894042 -78 CGCGTAGGAAGTGTATAGGAGGTTTAGTA 21 67 1 GGTAAGGGGT 0.968368 -19 TTTTTAATTTGAGAAAAGGGGCTGAAAGCAGGT 22 24 1 GGAAAGGGCT 0.784359 -23 ATTTTTGGCAGGGTGTAGATGGTAATTCGTGAA 25 190 0 GGTGAGAGGT 0.818932 -111 TCCATGCGGAGCGAACAGCTGGAAAATTATACG 28 107 1 GGAAAGCGGA 0.928281 -194 GTGGTCGGCGGTCTACAGCAGGCCGGCAGAACA 29 112 1 GCTAAGCGGC 0.703304 -105 GTATCGGTTTGCGTGGGGCCGGTGGGTAGACGG 32 87 1 GGTGGGCGGT 0.854906 -168 CCGGTCAGGCGTGAACGGCGGGTTGGTCTCGGC 35 163 0 GGAAGGCGGT 0.963942 -71 ATCCACCCGAGAGAAAAGAAGGTAAGCGCT 35 214 1 GGAAAGAGGT 0.953532 -20 * *** *** *** Masking position 8 Map Score: 7.40046 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 272 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 12 TATTTCCTCCAAGACAAAATAAAA 4 131 0 TCCTCCAAGA 0.978846 -14 TTATTGGCCTCCAATATCCCTTTTAT 11 177 0 GCCTCCAATA 0.88222 -16 TCGGCAGCCTGCTTCCGAGATGGTTATTGT 19 11 1 GCTTCCGAGA 0.895833 -87 AGTGAATTTCTCTTCCAAGAATAACATTCG 24 81 0 TCTTCCAAGA 0.943595 -86 TTCCTCGTCCTCCAAGATTTCAGTCAT 26 144 0 TCCTCCAAGA 0.978846 -17 AAAGTCTTTATCCGCCAAGACCCTTCACCT 28 42 0 TCCGCCAAGA 0.969828 -259 AGGCATATTCGCTGCCAAGAGTGGATATGT 34 74 1 GCTGCCAAGA 0.9495 -51 ********** Masking position 8 Map Score: 5.22117 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 60 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 13 CGGTAACACGGGTTCGAATCCCGTACGGGT 15 80 1 GGTTCGAATC 0.883331 -221 GTCATGCGTTGGTTCGAATCCAGCTAGCCC 25 49 1 GGTTCGAATC 0.883331 -252 CAGCTCACAAGGATCGAATTTCCCCAATGC 29 43 1 GGATCGAATT 0.948663 -174 TCGCCGTTTGGGATCGAATTGGATTACCCA 31 62 0 GGATCGAATT 0.948663 -30 AGATAGTTCAGGTTCGAGTCCTGGCGACGG 32 218 1 GGTTCGAGTC 0.953039 -37 ********** Masking position 4 Map Score: 2.55401 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 11 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 14 AATCTTTAATGAAAATAAAAAAAGTCTGTT 1 107 0 GAAAATAAAA 0.558571 -194 TTTGTGTTTCGACAAGAAAGGAGTTTTTCA 2 56 1 GACAAGAAAG 0.910419 -23 ATCCTATGAGGAGAAGAAAGCATGTAGAAC 3 68 0 GAGAAGAAAG 0.960136 -88 TTCATTCAATGATAAGAAAAAACTTGGACT 5 70 1 GATAAGAAAA 0.568875 -92 CCTTATGCCCGAAATGAAAGCTTTATGACC 10 55 1 GAAATGAAAG 0.882391 -139 TAACAGGTGGGAGATGAGAGGA 15 289 1 GAGATGAGAG 0.822488 -12 AAGTAAAAAAGAAAATAGAGGAATGATACA 24 146 1 GAAAATAGAG 0.621829 -21 TGATTTTTCCGAAAAGAAAAAAGACACCTT 25 101 0 GAAAAGAAAA 0.864053 -200 AAGACAAGCTGACAAAAAAGCATTTTCAGC 27 27 0 GACAAAAAAG 0.444685 -100 TTATATAGAGGAGATGAAAGA 27 116 1 GAGATGAAAG 0.909654 -11 TGATATCGTAGAAATGAAAAAACCGCATCC 28 80 1 GAAATGAAAA 0.726551 -221 TTATGATTCCGAGAAGAGAATTTGAAAGAA 28 187 1 GAGAAGAGAA 0.79696 -114 CCACCCGAGAGAAAAGAAGGTAAGCGCT 35 216 1 GAAAAGAAGG 0.723608 -18 CCGGTGATCCGAGAATAAAGGGGGAGA 36 8 0 GAGAATAAAG 0.827439 -106 ********** Masking position 4 Map Score: 5.04734 Number of sites scoring better than the average of aligned sites = 730 Number in coding regions = 601 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 15 GAGCTTGTCCCTTACAGCGTTTTTCTATAA 3 36 1 CTTACAGCGT 0.428349 -120 CAAAAGGCTTATGTCAGCCCTTTCAGCAGT 11 31 0 ATGTCAGCCC 0.715037 -162 CATAAAAAAACTGCCAGCGTCAGCCGGCAG 20 32 0 CTGCCAGCGT 0.936219 -163 TCATAAATCAATTCCAGCCCTTTTAGGGTT 21 30 0 ATTCCAGCCC 0.589672 -56 ACCTGCTTTCAGCCCCTTTTCTCAA 22 32 0 CTTTCAGCCC 0.704538 -15 CAAGTGAAATGTGCCAGCCCTCTCAGCCCG 26 40 0 GTGCCAGCCC 0.960182 -121 AAAAGCATGAGTGTCGGCCTATTTATGAAG 28 253 0 GTGTCGGCCT 0.927193 -48 TAACGGTGTTCTGCCGGCCTGCTGTAGACC 29 121 0 CTGCCGGCCT 0.959248 -96 TCGCGACAGCTTGTCGGCCTCCGTCGATAA 29 148 0 TTGTCGGCCT 0.744543 -69 CGCGTCGGGTTTTCCGGCGCCTTATCCGGC 32 27 1 TTTCCGGCGC 0.640399 -228 GTTGACTGTGCTGACGGCGTTGACACCGTC 32 127 1 CTGACGGCGT 0.803166 -128 CGGTCGACGTGTGTCAGCGCAGCGGGCGAG 33 60 0 GTGTCAGCGC 0.905934 -72 TTGACCCGAGGTCCCGGCGTACCGCACGCC 35 124 0 GTCCCGGCGT 0.742646 -110 ATCATCGGCCGTGCCGGCCAGGTCCTTCCC 37 45 0 GTGCCGGCCA 0.813131 -22 AGCCGGTACCGTGGCAGCGTCGCCCGGCCG 38 82 1 GTGGCAGCGT 0.743431 -56 ********** Masking position 2 Map Score: 6.44801 Number of sites scoring better than the average of aligned sites = 964 Number in coding regions = 899 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454