AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00260_bsub_reg_100.orf -o00260_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 serS 300 seryl-tRNA synthetase #2 purT 230 phosphoribosylglycinamide formyltransferase 2 #3 pssA 195 phosphatidylserine synthase #4 serC 146 phosphoserine aminotransferase #5 yjcI 300 similar to cystathionine gamma-synthase #6 yjmC 104 similar to malate dehydrogenase #7 pdhC 114 pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) #8 yloW 138 similar to phosphoglycerate dehydrogenase #9 ylpA 25 similar to L-serine dehydratase #10 asd 125 aspartate-semialdehyde dehydrogenase #11 dapG 91 aspartokinase I (alpha and beta subunits) #12 tdh 265 threonine 3-dehydrogenase #13 yoaD 300 similar to phosphoglycerate dehydrogenase #14 ilvA 248 threonine dehydratase #15 serA 226 phosphoglycerate dehydrogenase #16 yqjR 75 similar to D-serine dehydratase #17 yqjP 300 yqjP #18 yqiS 124 similar to phosphate butyryltransferase #19 yqhJ 29 similar to glycine dehydrogenase #20 yqhI 300 similar to aminomethyltransferase #21 glyQ 296 glycyl-tRNA synthetase (alpha subunit) #22 yrhA 64 similar to cysteine synthase #23 yrrT 192 yrrT #24 lysC 175 aspartokinase II alpha subunit (aa 1->408) and beta subunit (aa 246->408) #25 thrS 300 threonyl-tRNA synthetase #26 gbsA 198 glycine betaine aldehyde dehydrogenase #27 yugK 103 similar to NADH-dependent butanol dehydrogenase #28 yugJ 229 similar to NADH-dependent butanol dehydrogenase #29 hom 200 homoserine dehydrogenase #30 glyA 206 serine hydroxymethyltransferase #31 thrZ 300 threonyl-tRNA synthetase Motif number 1 CATCCCCATAAAGGGACGAGAGCTCTCGCG 1 233 0 AAGGGACGAG 0.950594 -68 CGTCCCTTTATGGGGATGAGGGCTCTTTTT 1 245 1 TGGGGATGAG 0.737166 -56 TCTTATCGTGAGAGGTGGAGGGACTGGCCC 5 124 1 AGAGGTGGAG 0.877566 -177 AAAAACTGAAAAGGAAGGAGGCACTTGC 6 87 1 AAGGAAGGAG 0.727781 -18 CTCTGGTTCATAAGGAGGAATAGC 8 125 1 TAAGGAGGAA 0.855194 -14 CGAAAAGGGTCAGGAGGAGCCAGTT 9 10 1 TCAGGAGGAG 0.821673 -16 TTCTATCCAGAGAGGTGGAGGGACTGGCCC 13 137 1 AGAGGTGGAG 0.877566 -164 TTGCATAATAAAAGGCGGAGTCGAAACAAG 18 91 1 AAAGGCGGAG 0.845821 -34 CCGTTGATAAAGGGGAGGAATTAG 20 287 1 AGGGGAGGAA 0.834219 -14 CGGTGTAAGCTAAGGATGAGCACGCAACGA 21 107 1 TAAGGATGAG 0.784726 -190 TCTCAGCAACTAGGGTGGAACCGCGGGAGA 21 180 1 TAGGGTGGAA 0.791433 -117 GCCGCAAACATAGGGACGAGAGTTCTCCCG 21 203 0 TAGGGACGAG 0.945577 -94 TTTAGAGAAAAACGGAGGAGAACGTTCTCC 22 16 0 AACGGAGGAG 0.886916 -49 CAACCTCTATTAAGGAGGAGGACATAT 22 48 1 TAAGGAGGAG 0.971396 -17 TTGCGGAAAAAAGGGTGGAACCACGATTCC 25 215 1 AAGGGTGGAA 0.807774 -86 CCCCCTATGAAAGGGACGAGGTTGAATAAA 25 246 0 AAGGGACGAG 0.950594 -55 ATAAAAAATCTAAGGAGGAGATGTC 28 215 1 TAAGGAGGAG 0.971396 -15 CAATCAAAAGAAAGGTGGAGTTTTT 29 186 1 AAAGGTGGAG 0.937514 -15 GTCCCGCAGATAGGGACGAGTGTGTGATTA 31 236 0 TAGGGACGAG 0.945577 -65 ********** Masking position 9 Map Score: 23.6483 Number of sites scoring better than the average of aligned sites = 408 Number in coding regions = 265 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 2 TAAATCAATAAAAAAAGGAGTGTTTCGC 1 283 1 AAAAAAGAGG 0.874054 -18 TGCTGTTTAGGAATAGAGAAAGCAGACCGTTA 2 83 1 GAATAGGAAG 0.779421 -148 GTTACCTTTTGAAAAATGAATGCCAATCTTTT 3 22 0 GAAAAAGAAG 0.964464 -174 CATTAACGTGGAAAACAGGGAGAGATCATA 4 127 1 GAAAACGGGG 0.905993 -20 TTTTTATTTTGAAAAGGGAAGGTGTCAGCTAT 5 279 1 GAAAAGGAAG 0.937544 -22 TATCTGTCTTGAAAAATGGGCGGAAATTTTTT 12 150 0 GAAAAAGGGG 0.976356 -116 GATGATCGTAAAATAAAGGGTGTTTTCAACCA 14 58 0 AAATAAGGGG 0.647924 -191 ATAGGGATTTAAAACAAGAAAGGAATCTGTAC 14 227 1 AAAACAGAAG 0.607074 -22 GCTAAAATATGAATAATGAATGAAGACAAGGA 17 271 1 GAATAAGAAG 0.864657 -30 AGGCGGAGTCGAAACAAGAAAGGTGGTAACAG 18 103 1 GAAACAGAAG 0.890836 -22 AACACCTCATGTAAAATGAAGGTTCTCTGTCC 20 222 0 GTAAAAGAAG 0.755315 -79 CTGCGCCGTTGATAAAGGGGAGGAATTAG 20 282 1 GATAAAGGGG 0.717394 -19 ACTTATGAAAGAAAAGTGGAGGTGCTTGAA 21 277 1 GAAAAGGGAG 0.944168 -20 TGTTTTTAGAGAAAAACGGAGGAGAACGTTCT 22 18 0 GAAAAAGGAG 0.968329 -47 TATGACTTGTGAAAGCTGGAGGGTCAAGAC 23 9 0 GAAAGCGGAG 0.595629 -184 TTCAAAGGCGGTAAAGCGAATGGTCCTTAGCT 25 93 0 GTAAAGGAAG 0.630634 -208 TGGCTTTGCGGAAAAAAGGGTGGAACCACGAT 25 210 1 GAAAAAGGGG 0.976356 -91 TTTATATGCAAAAAAAGGAGTGACAAAG 25 283 1 AAAAAAGAGG 0.874054 -18 TGACAAAAAAGAAAAAGGGAAGCAGCCAAACG 27 27 0 GAAAAAGGAG 0.968329 -77 ATGTCTTGTCAAAACAGGAGCGGGCTTATATA 29 100 1 AAAACAGAGG 0.676027 -101 GAGAGGGAAGGAAAGGTGAGAGCTTCCCAGCT 31 79 1 GAAAGGGAGG 0.807137 -222 ATACAACAATGAATAAGGAGTGTTCTAAA 31 282 1 GAATAAGAGG 0.896141 -19 ****** *** * Masking position 8 Map Score: 21.6819 Number of sites scoring better than the average of aligned sites = 1006 Number in coding regions = 825 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 3 GAGGGCTCTTTTTATTTTCGATAAATCAATAA 1 262 1 TTTATTTTAT 0.54716 -39 AAAATAAATTTTTATTAAAAAAGATAAAATTA 2 162 0 TTTATTAAAA 0.530306 -69 TTAATAAAAATTTATTTTTCAAATATTTCAGT 2 176 1 TTTATTTTAA 0.951582 -55 AAGATTGGCATTCATTTTTCAAAAGGTAACAA 3 24 1 TTCATTTTAA 0.652655 -172 TTCAAATTCTATTATTATACAACATTTGTTAC 3 49 0 ATTATTATAA 0.421236 -147 ATGAGGTTATTTTATTTTGTGAACATTTCGCA 4 12 1 TTTATTTTGA 0.84819 -135 ATAATTCTAATTTTTTATCAAAAAACTGAATT 4 65 1 TTTTTTATAA 0.421102 -82 AGAAGGGGTTTTTATTTTGAAAAGGGAAGGTG 5 271 1 TTTATTTTAA 0.951582 -30 ACAAACACATTTTATTTACAAATTATTTTAAA 6 30 0 TTTATTTAAA 0.822013 -75 GATTTTACGTTTTATTTTACCATAGAATATGC 10 56 0 TTTATTTTCA 0.675772 -70 TGGGCGGAAATTTTTTTTGAAACGTTTTAGCT 12 134 0 TTTTTTTTAA 0.690931 -132 GAAAACACCCTTTATTTTACGATCATCTTTTT 14 63 1 TTTATTTTGA 0.84819 -186 GACAATTATTTTTATTTAATAATTAAAAAAAT 14 158 0 TTTATTTAAA 0.82215 -91 GATGTTTGCGTTTATTCTGCAAA 18 2 0 TTTATTCTAA 0.700583 -123 GACTCCGCCTTTTATTATGCAAGTTCCATGCC 18 81 0 TTTATTATAA 0.864845 -44 TATATGATCATTTATTATTAAATATGTTGCAG 21 28 1 TTTATTATAA 0.84753 -269 CTTAACGAATTTAATTTTCTAAAGGAAAAGAG 26 18 0 TTAATTTTAA 0.55904 -181 ACATTAAATTTTTATTTAACAAACTTTATTTA 26 161 1 TTTATTTAAA 0.822246 -38 ACCAGATGGTTTTATTTTGCAAGGTGCTGGGA 28 130 0 TTTATTTTAA 0.951587 -100 GACAAGATTCTTTATTTTCTAATTATTTTTGT 29 23 0 TTTATTTTAA 0.951586 -178 AGTCTTTTCTTTTATTTTAAGATAGTGAAATA 30 26 1 TTTATTTTGA 0.84819 -181 GATGTAAAAGATTATTTTTAAAAAATCTAAAT 30 113 0 ATTATTTTAA 0.690921 -94 ******** ** Masking position 6 Map Score: 17.0079 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 208 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 4 CACCAACCATCGGCTCTCTTAGAAAGAGAGGCTCC 1 68 0 CCTCTCGAAA 0.954729 -233 TGTCTGAATCCATCCTTGAGCGAAATGCTGAAGCG 1 121 1 CCCTTGGAAA 0.862289 -180 TCTCGCGTTGCCACCCTGATTGAAAACAAATCAAA 1 205 0 CCCCTGGAAA 0.987619 -96 GTACAATCCTCCTTGAAAAATTCTTGTT 12 248 0 CTCCTCGAAA 0.954729 -18 CTATCAAAAACTGCCCCGTGAGAAACAAGCCACTC 16 31 0 CCCCCGGAAA 0.980235 -45 AAGAGAGCGATACCCCCGGCTGAAAGGTGTTGCGG 17 81 0 TCCCCGGAAA 0.925235 -220 GTGTTGTCTCCTCTCTCCAAGAAAAAATA 19 6 0 CCTCTCGAAA 0.954723 -24 AACAACGAGATAGCCCTCCAAGAAAATGATTTCTT 24 28 0 TCCCTCGAAA 0.971347 -148 TATAAAAACCCCGCCCCCTATGAAAGGGACGAGGT 25 254 0 CCCCCCGAAA 0.988471 -47 TTTCTTTTGATTGTCCTCTTGGAAAAGACAATTGT 29 164 0 TTCCTCGAAA 0.839324 -37 CTCACCTTTCCTTCCCTCTCTGAAAACCGTAACTA 31 64 0 CCCCTCGAAA 0.99274 -237 * ***** **** Masking position 13 Map Score: 12.3363 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 41 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 ATCAAAGACTCGTTTTCCACTTTCAAACATAAC 1 178 0 CTTTCCCTTT 0.864165 -123 GAGAGCTCTCGCGTTGCCACCCTGATTGAAAAC 1 213 0 GGTTCCCCCT 0.813848 -88 ACGCTTGCTGGATTTAGCACCTTGGCGCTTTGC 5 188 0 GTTTGCCCTT 0.960301 -113 GCAAGTGCCTCCTTCCTTTTCAGT 6 91 0 CAGTCCCCTT 0.770731 -14 GCTATTCCTCCTTATGAACCAGA 8 126 0 GTATCCCCTT 0.874395 -13 AGAGAGCAGGCTGATAGCGCCTTACTCTCTTCT 11 36 0 CGATGCCCTT 0.879607 -56 TTTTTGAAACGTTTTAGCTCATTTCTGATTTTG 12 120 0 GTTTGCCATT 0.721949 -146 CAATTGGCTCCTTTTGGTTCTAA 14 1 1 CATTGCCCTT 0.952185 -248 AAAACCTAAACGTTTCCCGCGTTACGGGGA 17 8 0 CTTTCCCGTT 0.842451 -293 CCTTTCGCTCCTTGTCTTCATTC 17 288 0 CTTTGCCCTT 0.979439 -13 CTGTTACCACCTTTCTTGTTTCG 18 112 0 CGTTCCCCTT 0.975186 -13 ATTCACTCCGCAGTTTGCTCCTTCGGCGCCTGT 20 78 0 CGTTGCCCTT 0.969312 -223 TATGCCATCTCATATTGCGCATTGACCGCAAAA 23 55 0 CTATGCCATT 0.541858 -138 GTATTACCACCCTTTACATTTTG 24 163 0 GATTCCCCCT 0.733783 -13 AGGACCATTCGCTTTACCGCCTTTGAACTTCAG 25 98 1 GTTTCCCCTT 0.967842 -203 AGCCAAACGGCTATTTCCCCTTTTT 27 3 0 CATTCCCTTT 0.726741 -101 GGGAAATAGCCGTTTGGCTGCTTCCCTTTTTCT 27 17 1 CTTTGCGCTT 0.767316 -87 TTAGGAATATCATTTACCGCCTTGGAGCAGCAT 31 110 1 CTTTCCCCTT 0.983408 -191 * *** ** **** Masking position 5 Map Score: 15.2559 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 257 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 6 TTTAGGAATAGAGAAAGCAGACCGTTATTT 2 88 1 GAGAAAGCAG 0.473563 -143 TTTTATTTTGAAAAGGGAAGGTGTCAGCTA 5 280 1 AAAAGGGAAG 0.815005 -21 CCAAAAAACTGAAAAGGAAGGAGGCACTTG 6 84 1 GAAAAGGAAG 0.873046 -21 CTGCATAATCGAGAGGGAAGATGAACGTTT 7 16 1 GAGAGGGAAG 0.985783 -99 TTTTTTCTTGGAGAGAGGAGACAACAC 19 13 1 GAGAGAGGAG 0.921623 -17 GCGAATGACAGCAAGGGGAGAGACCTGACC 20 34 1 GCAAGGGGAG 0.912099 -267 GCGCCGTTGATAAAGGGGAGGAATTAG 20 284 1 TAAAGGGGAG 0.717981 -17 GTTGCAGTGAGAGAAAGAAGTACTTGCGTT 21 53 1 GAGAAAGAAG 0.676594 -244 GGCAAGCATAGAGACGGGAGTTTTTTGGTT 21 234 1 GAGACGGGAG 0.882545 -63 CCGGCTCAAAGAGAGGGAAGCCCTGGTGCA 25 55 1 GAGAGGGAAG 0.985783 -246 CGCCCCCTATGAAAGGGACGAGGTTGAATA 25 248 0 GAAAGGGACG 0.837307 -53 ACAAAAAAGAAAAAGGGAAGCAGCCAAACG 27 27 0 AAAAGGGAAG 0.815005 -77 GCTGATATAAGCGAGGGCAGGCCAGCTTCC 28 95 0 GCGAGGGCAG 0.888937 -135 ACGGTTTTCAGAGAGGGAAGGAAAGGTGAG 31 69 1 GAGAGGGAAG 0.985783 -232 GAGAGGGAAGGAAAGGTGAGAGCTTCCCAG 31 79 1 GAAAGGTGAG 0.686228 -222 ********** Masking position 4 Map Score: 14.4595 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 236 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 7 ATAGGATAATTGTATTATTTTATACATTAACG 4 103 1 TGTTTTTTTA 0.949613 -44 ATTTTCTGATTGTTTTATATTAGCGCAATTCA 5 79 0 TGTTTTATTA 0.667288 -222 TCTATTCTTATGTCTGCTTTTAAGTGCGGCAG 8 27 1 TGTTGTTTTA 0.93261 -112 TATGATTTTACGTTTTATTTTACCATAGAATA 10 59 0 CGTTTTTTTA 0.748272 -67 GGACATAGTCTGTATTTTTTTAATTATTAAAT 14 145 1 TGTTTTTTTA 0.949613 -104 TAAAAATAATTGTCTTATTTTTTGAATATTCA 14 176 1 TGTTTTTTTT 0.793784 -73 TACAGATTCCTTTCTTGTTTTAAATCCCTATT 14 226 0 TTTTTTTTTA 0.597582 -23 TTCGTGCAGATGTTTGCGTTTATTCTGCAAA 18 10 0 TGTTGGTTTA 0.685805 -115 TGTCCTTTTTTGTATGTTTTTTAGCTGCGCCG 20 258 1 TGTTGTTTTT 0.738666 -43 GCCAGTCTTTTCTTTTATTTTAAGATAGTGAA 30 23 1 TCTTTTTTTA 0.801997 -184 CGTATCCTGTTCTTTGTTTTTACCATCACTAT 30 165 0 TCTTGTTTTA 0.748379 -42 GGGTGTGTTTTTTTATTTGAATTGA 31 4 1 TGTTTTTTTA 0.949613 -297 GCGGGACGGGTGTGTTTTTTTATATACAACAA 31 259 1 TGTTTTTTTA 0.949613 -42 *** ** ***** Masking position 5 Map Score: 7.97455 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 81 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 8 TGGCCCTTAGAAACCTCAGCAACCGGCTTGTTT 5 148 1 AAACCTCCAC 0.936702 -153 AAGAAGCGTTAAACCCCTTCTTCTTATGAAGAA 5 242 1 AAACCCCCTC 0.98129 -59 TTCAAAATAAAAACCCCTTCTTCATAAGAAGAA 5 259 0 AAACCCCCTC 0.98129 -42 TCTCCAAGCGAAACCCCTACAAACACATTTTAT 6 47 0 AAACCCCCAA 0.880489 -58 CTGTAAAACTCCTTCCGCCAATCAGCTT 10 108 0 AAACTCCCCC 0.968318 -18 TGGCCCTATGAAACCTCGGCAACATTATTGTGC 13 161 1 AAACCTCCAC 0.936702 -140 GCTGAGAACAAAATCCCAGCCTCTTTTTTAAAA 21 154 0 AAATCCCCCC 0.938334 -143 AGCAACCAAAAAACTCCCGTCTCTATGCTTGCC 21 234 0 AAACTCCTCC 0.749768 -63 TTGCATATAAAAACCCCGCCCCCTATGAAAGGG 25 261 0 AAACCCCCCC 0.993599 -40 ******* ** * Masking position 3 Map Score: 6.23033 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 42 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 CTTCTTCTTATCTTCCAAGCATAAAAAACG 5 218 0 TCTTCCAAGC 0.776956 -83 GCAAGCGGGCGCGTTACAGCGCTGCCGCAC 8 50 0 GCGTTACAGC 0.898169 -89 TGCTTTCCTATCTTTCAAGCTAGCGCTTGC 13 202 0 TCTTTCAAGC 0.646644 -99 CCGTCTCTATGCTTGCCAGCCGCAAACATA 21 221 0 GCTTGCCAGC 0.836739 -76 GAAAATGATTTCTTGACAGCCTTACATTTA 24 12 0 TCTTGACAGC 0.866941 -164 CCTGGTGCAAGCTTCCCAGCTAAGGACCAT 25 76 1 GCTTCCCAGC 0.979416 -225 AGGACCATTCGCTTTACCGCCTTTGAACTT 25 98 1 GCTTTACCGC 0.808863 -203 CTTTTCAAGAGGTTCACAGCTGAAGTTCAA 25 120 0 GGTTCACAGC 0.855287 -181 AAAGGTGAGAGCTTCCCAGCTTAGGAATAT 31 90 1 GCTTCCCAGC 0.979416 -211 CGTCTATGCTGCGTTACAGCACCGAGCCGA 31 166 1 GCGTTACAGC 0.898169 -135 ********** Masking position 4 Map Score: 5.47233 Number of sites scoring better than the average of aligned sites = 454 Number in coding regions = 410 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 10 ATTTTTTATCAAAAAACTGAATTTTTGTGAT 4 74 1 AAAAACTGAA 0.88372 -73 GCTAATATAAAACAATCAGAAAATTGAAATC 5 87 1 AACAACAGAA 0.757869 -214 GAGAGTGCCCAAAAAACTGAAAAGGAAGGAG 6 76 1 AAAAACTGAA 0.88372 -29 CTCCTAAATTGACAAACTAAATATCTGATAA 15 195 0 GACAACTAAA 0.887109 -32 TCGCGGTTAGGAAAACCTAAACGTTTCCCGC 17 21 0 GAAAACTAAA 0.871525 -280 CATAATGAACAACAAACTAAAACGAGAACCA 17 158 0 AACAACTAAA 0.933582 -143 CAAGACCGAGAAAAAGCTAAAATATGAATAA 17 256 1 AAAAACTAAA 0.923863 -45 AGTCAAAAAGAAAAATCAAAATGGGACTTTG 26 91 1 AAAAACAAAA 0.811821 -108 TAATGTTTTTAACAACCTTAATCTAACATAT 26 136 0 AACAACTTAA 0.689039 -63 CTGCATAATAAAAAATCTAAGGAGGAGATGT 28 208 1 AAAAACTAAG 0.675647 -22 TTTCCAAGAGGACAATCAAAAGAAAGGTGGA 29 174 1 GACAACAAAA 0.736412 -27 ATTATTTTTAAAAAATCTAAATTTTTATTGG 30 104 0 AAAAACTAAA 0.923863 -103 ***** ***** Masking position 5 Map Score: 5.355 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 201 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 11 AAATCTTTTAAATTCTTAAACGAAAGCAGACAA 2 116 0 AATTTAAACA 0.860193 -115 CCAAACCTCCAATTGTAAAACCATCTATATTAT 3 166 0 AATTTAAACA 0.860185 -30 AAAAAATTAGAATTATCAAAAGAAATTGACGGA 4 48 0 AATTTAAAAA 0.893344 -99 TAATATAAAGAATATTTAAAATAATTTGTAAAT 6 16 1 AATATAAAAA 0.841397 -89 GAAATGTTATAATTCTTACAAAATATC 13 5 0 AATTTACAAA 0.725788 -296 TGATAACGTCAATTCTGAAAAAAAGAGATTGAC 13 41 1 AATTTAAAAA 0.893344 -260 AAAGGCATGATATAATGAAACCAATTAGAACCA 14 25 0 TATATAAACA 0.557954 -224 ATTTTTATTTAATAATTAAAAAAATACAGACTA 14 150 0 AATATAAAAA 0.842622 -99 TTATAACATGAATATTCAAAAAATAAGACAATT 14 183 0 AATATAAAAA 0.842594 -66 TAATTTAACATATTCTCAAAAGAGTGTCAACGT 15 165 0 TATTTAAAAA 0.727757 -62 CTCATTCTGCAATAATGACACAAGACCGAGAAA 17 236 1 AATATACACA 0.553987 -65 CTCCTCCATGAATTATTAAAACAGTTATAGATT 28 21 1 AATTTAAAAA 0.893344 -209 TGTAAAAGATTATTTTTAAAAAATCTAAATTTT 30 110 0 TATTTAAAAA 0.689238 -97 **** * **** * Masking position 8 Map Score: 6.67232 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 105 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 12 CGAATCGGTGAAAGATGCTGTCTGAATCCA 1 103 1 AAAGATGCTG 0.851339 -198 TATTTTGAAAAGGGAAGGTGTCAGCTAT 5 283 1 AGGGAAGGTG 0.811543 -18 CATAATCGAGAGGGAAGATGAACGTTTTCC 7 19 1 AGGGAAGATG 0.743948 -96 AAATCAATTCAATGAAGCTGATTGGCGGAA 10 94 1 AATGAAGCTG 0.898233 -32 TAAAACAAGAAAGGAATCTGTAC 14 236 1 AAGGAATCTG 0.762817 -13 GCCAGCTCTTAAGGGTGCTGTCATACCAGG 18 54 0 AAGGGTGCTG 0.776996 -71 CAATTTTAAAAAAGAGGCTGGGATTTTGTT 21 151 1 AAAGAGGCTG 0.860764 -146 TATTTACGTCAAGGAGGCTTAT 26 187 1 AAGGAGGCTT 0.611202 -12 AAAAAGAAAAAGGGAAGCAGCCAAACGGCT 27 24 0 AGGGAAGCAG 0.810285 -80 AAAACCTCCAAATGATGCTGGTAAAAAACA 27 81 0 AATGATGCTG 0.799863 -23 TCTCCATATGAGGGAAGCTGGCCTGCCCTC 28 83 1 AGGGAAGCTG 0.973597 -147 AGGTGCTGGGAAAGAAGCTGATATAAGCGA 28 111 0 AAAGAAGCTG 0.926725 -119 ********** Masking position 1 Map Score: 4.67378 Number of sites scoring better than the average of aligned sites = 745 Number in coding regions = 672 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 13 AGACCACCACACCGACAGGAGGCATCCC 2 7 0 ACGAAGGAGG 0.968173 -224 ATGGTTTGGAACAGATAGGAGGGGCAAAG 2 212 1 ACGAAGGAGG 0.968173 -19 TATTTCTTATCGTGAGAGGTGGAGGGACTGGC 5 120 1 CGGAAGGTGG 0.940609 -181 AAAAAACTGAAAAGGAAGGAGGCACTTGC 6 86 1 AAGGAGGAGG 0.805519 -19 CGAAAAGGGTCAGGAGGAGCCAGTT 9 6 1 AGGTAGGAGG 0.868482 -20 TATTTTCTATCCAGAGAGGTGGAGGGACTGGC 13 133 1 CCGAAGGTGG 0.951497 -168 GGAGTCGAAACAAGAAAGGTGGTAACAG 18 107 1 CAGAAGGTGG 0.944243 -18 ATTTTTTCTTGGAGAGAGGAGACAACAC 19 12 1 GGGAAGGAGA 0.500557 -18 GCAAAGACGTCCCCAAAGGTGGTTTGCGCATC 20 163 0 CCCAAGGTGG 0.751716 -138 TCAACTTATGAAAGAAAAGTGGAGGTGCTTGA 21 274 1 AAGAAAGTGG 0.67291 -23 TTGGTTCGTGCGGGTGAGGAGAAAGAGCGCTT 24 134 0 CGGTAGGAGA 0.540299 -42 TAATTTTCTAAAGGAAAAGAGGGTCAGT 26 7 0 AAGAAAGAGG 0.723767 -192 CATAATAAAAAATCTAAGGAGGAGATGTC 28 211 1 AACTAGGAGG 0.521477 -19 AGGACAATCAAAAGAAAGGTGGAGTTTTT 29 182 1 AAGAAGGTGG 0.953745 -19 AGAACAGGATACGGATAGGAGAGGATCTCGCT 30 184 1 ACGAAGGAGA 0.868284 -23 TCAGAGAGGGAAGGAAAGGTGAGAGCTTCCCA 31 76 1 AAGAAGGTGA 0.817125 -225 ** ** ****** Masking position 7 Map Score: 11.3028 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 196 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 14 AGTTTTTTGGGCACTCTCCAAGCGAAACCC 6 64 0 GCACTCTCCA 0.934208 -41 AACAAATAAAGCATTCTCAACCTGTTTGCG 12 12 1 GCATTCTCAA 0.9226 -254 AACGTATTCTTCATTCTGAAAATTACATAC 13 99 1 TCATTCTGAA 0.692112 -202 TCTGAAAATTACATACTCAATATTTTCTAT 13 113 1 ACATACTCAA 0.749582 -188 AGGTTTGTTCTCATTCTGCAATAATGACAC 17 227 1 TCATTCTGCA 0.810445 -74 ATCCGCACAAACACTCTCCAGAGTTGCGTC 20 136 0 ACACTCTCCA 0.89952 -165 AGTTTACTTTGCATACGCAAAGACGTCCCC 20 181 0 GCATACGCAA 0.645669 -120 ATTTGTCACACTCCATATTTAATAA 23 178 0 TCACACTCCA 0.73251 -15 ATCTATACATGCATTCTCCATATGAGGGAA 28 69 1 GCATTCTCCA 0.957755 -161 TGTGGTGAGGACATTCTGCATAATAAAAAA 28 193 1 ACATTCTGCA 0.847728 -37 TTAAGCGTTTACATTCGCAAAATTCAGCCT 29 66 1 ACATTCGCAA 0.742549 -135 ********** Masking position 3 Map Score: 2.42999 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 202 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 15 CTCGCGTTGCCACCCTGATTGAAAACAAATC 1 208 0 CACCCTGTTG 0.984986 -93 TATGATCTCTCCCTGTTTTCCACGTTAAT 4 128 0 CTCCCTGTTT 0.627815 -19 GAAACCTCAGCAACCGGCTTGTTTTGCATTT 5 157 1 CAACCGGTTG 0.877678 -144 AAAGCATTCTCAACCTGTTTGCGTAATGCAA 12 19 1 CAACCTGTTG 0.952496 -247 AAATGAAAAACAACCTGTTTGCATTACGCAA 12 37 0 CAACCTGTTG 0.952496 -229 GAAACCTCGGCAACATTATTGTGCCAATTCC 13 170 1 CAACATTTTG 0.68361 -131 GAATGAGAACAAACCTTTTTGAAAAAGCTAT 17 212 0 AAACCTTTTG 0.658839 -89 CTGTTACCACCTTTCTTGTTTCGACTCC 18 107 0 CACCTTTTTG 0.77579 -18 CCCGCGGTTCCACCCTAGTTGCTGAGAACAA 21 176 0 CACCCTATTG 0.910866 -121 ATCGTGGTTCCACCCTTTTTTCCGCAAAGCC 25 211 0 CACCCTTTTT 0.859184 -90 ******* *** Masking position 9 Map Score: 2.12178 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 163 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467