AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -ityrR_hinf_opreg_300.orf -g0.38 -x5 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 = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0286 135 aminotransferase #2 HI0287 116 tryptophan-specific transport protein (mtr) #3 HI0409 171 conserved hypothetical protein #4 HI0410 114 transcriptional regulatory protein (tyrR) #5 HI0468 300 ATP phosphoribosyltransferase (hisG) #6 HI0469 92 histidinol dehydrogenase (hisD) #7 HI0470 68 histidinol-phosphate aminotransferase (hisC) #8 HI0471 111 imidazoleglycerol-phosphate dehydratase / histidinol-phosphatase (hisB) #9 HI0472 65 amidotransferase (hisH) #10 HI0473 35 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA) #11 HI0476 81 H. influenzae predicted coding region HI0476 #12 HI0477 29 tyrosine-specific transport protein (tyrP) #13 HI0528 36 tyrosine-specific transport protein (tyrP) #14 HI0530 231 O-sialoglycoprotein endopeptidase (gcp) #15 HI1288 300 ribosome binding factor A (rbfA) #16 HI1290 59 chorismate mutase / prephenate dehydrogenase (tyrA) #17 HI1547 217 phospho-2-dehydro-3-deoxyheptonate aldolase (phenylalanine repressible) (aroG) #18 HI1549 146 ABC transporter, ATP-binding protein #19 HI1556 59 2-hydroxyacid dehydrogenase #20 HI1560 22 H. influenzae predicted coding region HI1560 #21 HI1561 106 peptide chain release factor 1 (prfA) #22 HI1562 252 H. influenzae predicted coding region HI1562 #23 HI1563 32 conserved hypothetical protein #24 HI1564 32 H. influenzae predicted coding region HI1564 #25 HI1564.1 284 H. influenzae predicted coding region HI1564.1 Motif number 1 TGTCATTAACAATCTGCGGTAGAATATGGC 1 20 0 AATCTGCGGT 0.924146 -116 TTTTTCGAGAAAAGTGCGGTTAATTTACGC 1 90 0 AAAGTGCGGT 0.997627 -46 GTACACAAGGAAAGTGCAATATATTTATAT 2 61 0 AAAGTGCAAT 0.891379 -56 CGATATAAAGTGCGGTCAAAAATGGT 4 7 1 AAAGTGCGGT 0.997627 -108 TTGAAAGAGCGGTTAATTTTTGT 9 4 1 AAAGAGCGGT 0.981626 -62 TGCTTGTTGTAATGTGTGATTTTTATCGAC 15 79 1 AATGTGTGAT 0.799245 -222 GTACAGCACAAAAGTGCGGTATTTTTTTAT 17 19 1 AAAGTGCGGT 0.997627 -199 AGCTCAAGGAAAAGTGTGATAGACTCGTGC 18 75 1 AAAGTGTGAT 0.941333 -72 ATCTGCCGCTAAAGTGCGGTTAAAACGAGT 18 122 1 AAAGTGCGGT 0.997627 -25 ATTTCATCAAAAGTGCGGTTAATTTTGAC 19 10 1 AAAGTGCGGT 0.997627 -50 TTTTATATACAAAGTGCGGTCAAAATTAAC 19 28 0 AAAGTGCGGT 0.997627 -32 ********** Masking position 2 Map Score: 29.5622 Number of sites scoring better than the average of aligned sites = 1218 Number in coding regions = 776 Number in noncoding regions = 442 Number of orfs with sites within 600 bp upstream = 301 Fraction of orfs with sites within 600 bp upstream = 0.0483456 Motif number 2 CAGATTGTTAATGACAAAAAATTTTTTTACAAAATCTTTTC 1 34 1 AAAAAATTTA 0.672007 -102 AACCGCACTTTTCTCGAAAAATTTATTAGAAACAAAAGGAT 1 99 1 TAAAAATTAA 0.90579 -37 AAAATGCCTCTAAAATAAATTTGCACTATTATAGT 2 92 0 TTAAAATTTA 0.863992 -25 ATCTTGAGAATTCTATAAAAATGCGTTATTTTCCCCAACCA 3 33 0 TAAAAATTAT 0.856047 -139 ACACAATTTTTTTCAAAAAAATTGCTTTTTTTAATTTTAAA 5 30 1 TAAAAATTTT 0.925002 -271 GATCTTATATTGCCTTAAAAATACACTTTAAAATTAAAAAA 5 56 0 TAAAAATCTA 0.848792 -245 TGATGGTAAGTGCAGATAAAATTCATATTGTATATGCTCGC 5 110 0 TTAAAATTTT 0.781433 -191 ATCTTCCGAGTGTAATAAAAATCAGTGTAAAAGCAATAAAT 5 206 1 TAAAAATTTA 0.956341 -95 TTTTCCTTTGTATCCGTAAAATGGATGATAACCCAGCATTT 6 56 0 TTAAAATTAA 0.753861 -37 TTTCGTATTGTTGTATGAAAATTTGACTGCTTACGTGTCGT 7 33 0 TGAAAATATT 0.59857 -36 ATCGGTCGAATTTTGCAAAAATACGACAAAAATTAACCGCT 9 18 0 TAAAAATAAA 0.734124 -48 ACACAGGTGCTTTGGCAAAAATAAAATTTTAAATTGCAATT 14 39 0 TAAAAATATA 0.851344 -193 CCTTTACTTTTTCCCTAAAAATAGATTAGAATTGCGTCCTT 14 99 0 TAAAAATTAA 0.913502 -133 TTCGTCTAAWTCATTTAAAAATGCTTGTTGTAATGTGTGAT 15 58 1 TAAAAATTTT 0.925004 -243 TATTCAAACTTCCGATAAAAATCACTTTACAGAGGGCATAA 15 150 0 TAAAAATTTA 0.956341 -151 CAGGTGTCATTTTATCGAAAAACAGTATTAAGTTGAAAGGG 15 205 1 TGAAAAATTA 0.470742 -96 ATTGAATTTAGCACGCAAAAATCCCTTTCAACTTAATACTG 15 227 0 GAAAAATTTA 0.636294 -74 TCTTACATATATTGTAAAAAATTAATTACAAGGAGATTACT 16 17 0 AAAAAATTAA 0.589818 -43 TTGTAGGTTTTATTCTAAAAAAACATATCGAACTAGTTTAC 17 119 1 TAAAAAATTA 0.657911 -99 ACTAGTTTACTAGTACAAAAATAAGTGTAGATTAGCTACAT 17 150 1 TAAAAATTTA 0.956341 -68 TCAAATCCTGTTTCAGGAAAATGTTTTTCAAGATAACGTT 18 10 0 TGAAAATTTA 0.910146 -137 CGCTGTCAATTTTCCCTAAAATCGGCTAGAATACGCCGATT 21 56 1 TTAAAATCAA 0.439737 -51 TGGGTGTGAAATGATTAAAAATTGAACTATTTAATTAGGAG 22 66 0 AAAAAATATT 0.305103 -187 AGTAGTTACTTGAAAATCTTCAAATTTAAGCT 24 7 0 TGAAAATCAT 0.413412 -26 GCAAGCACGTTTAATCTAAAATTGGTCATATTTAGTCCTAT 25 40 1 TTAAAATTAT 0.63297 -245 TATTTAGTCCTATAAAAAAAATAATAATAATTCTCAAACAT 25 68 1 TAAAAATATT 0.763295 -217 ATCTTTATTGTTGTGAGAAAATACCTTTCTTCATATAATAT 25 107 0 TGAAAATTTT 0.850839 -178 TTTCTTGATTTTTATCAAAAATCAATCTTTATTGTTGTGAG 25 131 0 TAAAAATTTA 0.956341 -154 * ****** * * * Masking position 11 Map Score: 24.3607 Number of sites scoring better than the average of aligned sites = 658 Number in coding regions = 460 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 3 TTTCGAGAAAAGTGCGGTTAATTTACGCTGA 1 87 0 AGTGCGGTAA 0.996624 -49 CGATATAAAGTGCGGTCAAAAATGGTCGC 4 9 1 AGTGCGGTAA 0.996624 -106 GATGATGGTAAGTGCAGATAAAATTCATATT 5 122 0 AGTGCAGAAA 0.855235 -179 TTGAAAGAGCGGTTAATTTTTGTCGT 9 6 1 AGAGCGGTAA 0.981448 -60 ACAGCACAAAAGTGCGGTATTTTTTTATCTT 17 21 1 AGTGCGGTTT 0.904585 -197 CTGCCGCTAAAGTGCGGTTAAAACGAGTAAA 18 124 1 AGTGCGGTAA 0.996624 -23 TTTCATCAAAAGTGCGGTTAATTTTGACCGC 19 12 1 AGTGCGGTAA 0.996624 -48 TTATATACAAAGTGCGGTCAAAATTAACCGC 19 25 0 AGTGCGGTAA 0.996624 -35 ******** ** Masking position 1 Map Score: 19.5936 Number of sites scoring better than the average of aligned sites = 611 Number in coding regions = 351 Number in noncoding regions = 260 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 4 AGGGGACATTTAGTCCCCTTTGTAATGTTGTCAAA 2 18 0 TATCCTGTAA 0.872916 -99 AGGGGACTAAATGTCCCCTTTTTATCGATATAAAT 2 34 1 ATTCCTTTAT 0.891382 -83 ATGGTCGCATTTTTACCTTATGTAAAATAATATTT 4 32 1 TTTCCTGTAA 0.971302 -83 TTTTCAAAAAAATTGCTTTTTTTAATTTTAAAGTG 5 39 1 AATCTTTTAA 0.560739 -262 ATAATAAAATATCTTCCGAGTGTAATAAAAATCAG 5 196 1 ATTCCTGTAA 0.952593 -105 AATGTTTTTCCTATTTTAAAGTTGAGATA 5 282 0 TTTCCTTTAA 0.958801 -19 TTATTTAGTTTTATACTGTTTGTATAAAGCAAATG 8 46 1 TTTCTTGTAT 0.901445 -66 ATTTTTCTCCGTGTATGTTATATGAA 8 96 0 TTTCTTGTAT 0.901459 -16 TTTTGCAAAATTCGACCGATTGTAAAAGGATAAAA 9 39 1 TTGCCTGTAA 0.801148 -27 TGTTGCGCGATTTTACCCTGTTTAAGCGGTTTTAA 14 181 0 TTTCCTTTAA 0.958798 -51 TGATTTTCTTAATTTATTACCTAAAAT 14 215 0 ATTCTTTTAT 0.788819 -17 AWTCATTTAAAAATGCTTGTTGTAATGTGTGATTT 15 66 1 AATCTTGTAA 0.649925 -235 CTTGCATAAATTATGCCCTCTGTAAAGTGATTTTT 15 140 1 TTTCCTGTAA 0.971302 -161 AGTTATTCCTTATTTATAAAAGCGCCT 15 284 0 TTTCCTTTAT 0.932523 -17 TTTTTACTCGTTTTAACCGCACTTTA 18 131 0 TTTCTTTTAA 0.913737 -16 TAATTGCTCCTTTTTTATATACAAAGTG 19 42 0 TTCCCTTTAT 0.751714 -18 ATCGGCTAGAATACGCCGATTTTATTTTCGGTGAC 21 76 1 ATCCCTTTAT 0.642575 -31 TTATGCTTTGTTGTACTCTCTGTAAAGAGAGTACA 22 120 0 TTTCTTGTAA 0.939044 -133 TATTCTTATTATTTTCTGTATTTAAACCTGCTTGT 25 179 1 ATTCTTTTAA 0.862829 -106 ** * ** ***** Masking position 11 Map Score: 22.2524 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 141 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 5 TCAGCGTAAATTAACCGCACTTTTCTCGAA 1 87 1 TTAACCGCAC 0.996227 -49 GCGACCATTTTTGACCGCACTTTATATCG 4 10 0 TTGACCGCAC 0.994403 -105 AATATGAATTTTATCTGCACTTACCATCAT 5 122 1 TTATCTGCAC 0.87669 -179 ACGACAAAAATTAACCGCTCTTTCAA 9 7 0 TTAACCGCTC 0.982083 -59 TTTACTCGTTTTAACCGCACTTTAGCGGCA 18 125 0 TTAACCGCAC 0.996227 -22 GCGGTCAAAATTAACCGCACTTTTGATGAA 19 13 0 TTAACCGCAC 0.996227 -47 GCGGTTAATTTTGACCGCACTTTGTATATA 19 25 1 TTGACCGCAC 0.994403 -35 ********** Masking position 2 Map Score: 17.0084 Number of sites scoring better than the average of aligned sites = 390 Number in coding regions = 243 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 6 ATTGAAAAGATTTTGTAAAAAAATTTTTTGTC 1 46 0 TTTGTAAAAA 0.837903 -90 CTAATAAATTTTTCGAGAAAAGTGCGGTTAAT 1 96 0 TTTGAAAAAG 0.801754 -40 AATATATTTATATCGATAAAAAGGGGACATTT 2 42 0 TATGAAAAAA 0.797021 -75 AAAGCAATTTTTTTGAAAAAAATTGTGTTTTT 5 26 0 TTTGAAAAAA 0.964182 -275 TGATTGTATGTTTGGAAGATAATAAAATATCT 5 178 1 TTTGAGATAA 0.557085 -123 ATCGGTCGAATTTTGCAAAAATACGACAAAAA 9 27 0 TTTGCAAAAT 0.635627 -39 CACACAGGTGCTTTGGCAAAAATAAAATTTTA 14 49 0 CTTGGAAAAA 0.619876 -183 CTAATCTATTTTTAGGGAAAAAGTAAAGGATA 14 111 1 TTTGGAAAAA 0.938999 -121 CGCGCAACATTTTAGGTAATAAATTAAGAAAA 14 207 1 TTTGGAATAA 0.672631 -25 TTTTAAATGATTAGACGAAAAACTTTGGGCA 15 46 0 TTGAGAAAA 0.137607 -255 CGACCAAGATTGTCGATAAAAATCACACATTA 15 88 0 TGTGAAAAAA 0.767461 -213 ATATTCAAACTTCCGATAAAAATCACTTTACA 15 160 0 TTCGAAAAAA 0.756673 -141 TAATACTGTTTTTCGATAAAATGACACCTGAT 15 203 0 TTTGAAAAAT 0.917084 -98 ATCTTACATATATTGTAAAAAATTAATTACAA 16 27 0 TATGTAAAAA 0.424236 -33 GATATGTTTTTTTAGAATAAAACCTACAAATT 17 116 0 TTTGATAAAA 0.70345 -102 TTAACCGCACTTTTGATGAAAT 19 1 0 TTTGAGAAAT 0.789847 -59 TCTAGCCGATTTTAGGGAAAATTGACAGCGAA 21 54 0 TTTGGAAAAT 0.859992 -53 ATCTTTATTGTTGTGAGAAAATACCTTTCTTC 25 116 0 TTGGAAAAAT 0.553694 -169 AAAGATTGATTTTTGATAAAAATCAAGAAATA 25 142 1 TTTGAAAAAA 0.959882 -143 *** ** ***** Masking position 9 Map Score: 13.5964 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 387 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 7 CAATCTGCGGTAGAATATGGCTAATTTTTT 1 4 0 TAAATGCTTT 0.976656 -132 TTTCAATATTGAAAATTCAGCGTAAATTAACCGCACT 1 71 1 GAAATGCAAT 0.60481 -65 TGTGTACTACTATAATAGTGCAAATTTATTTTAGAGG 2 84 1 TAAATGCTTT 0.976656 -33 AACCATTGTTGAAAACACGGCGATTTT 3 1 0 GAAACGCTTT 0.941473 -171 AATGGTTGGGGAAAATAACGCATTTTTATAGAATTCT 3 31 1 GAAATGCTTT 0.968965 -141 TAAAATGGATGATAACCCAGCATTTTGAGATATTGAT 6 44 0 GAAACGCTTG 0.656924 -49 TTTATCCTTTTACAATCGGTCGAATTTTGCAAAAATA 9 36 0 TAAATTCTTT 0.806738 -30 ATTTATTACCTAAAATGTTGCGCGATTTTACCCTGTT 14 194 0 TAAATGCATT 0.93126 -38 TGATTTCCAGTAGAATGAGGCGCTTTTATAAATAAGG 15 267 1 TAAATGCTTT 0.976654 -34 TAAAAGATAAAAAAATACCGCACTTTTGTGCTGTACT 17 18 0 AAAATGCTTT 0.828098 -200 AAAAGTGTGATAGACTCGTGCAAGTTTTTGATGGTGT 18 84 1 TAACTGCTTT 0.832788 -63 TAAAATCGGCTAGAATACGCCGATTTTATTTTCGGTG 21 72 1 TAAATCCTTT 0.7782 -35 TTACAGAGAGTACAACAAAGCATAATTGGCAACTAGG 22 130 1 TAAACGCATT 0.874346 -123 AAAAACACACTAAAACAAGGCGACAATATGCTTGCTA 22 169 0 TAAACGCAAT 0.51217 -84 ATTTTTTCTTGAAGATCAGGCTGTTTTGGCAAATCAA 22 204 0 GAGATGCTTT 0.788533 -49 TATAATCTTGCGGTTTTTTAGGAGTCG 23 1 1 TAAATGCTTT 0.976656 -32 ACGTTTAATCTAAAATTGGTCATATTTAGTCCTATAA 25 46 1 TAAATTCTTT 0.806737 -239 ** *** ** *** Masking position 2 Map Score: 18.65 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 139 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 8 TATTCGACATAAGAGAGAAAATCTTGAGAA 3 64 0 AAGAGAGAAA 0.874652 -108 TGTATAAAGCAAATGATAAACCTCATACCA 8 66 1 AAATGATAAA 0.861414 -46 ACCGATTGTAAAAGGATAAAAAA 9 53 1 AAAGGATAAA 0.77875 -13 AGGCAATATTAAGTGAGCAATTAGAAGATT 11 21 1 AAGTGAGCAA 0.94483 -61 ACCTGTGTGTAAATGACAAATTTAATAAAG 14 72 1 AAATGACAAA 0.694447 -160 TTAAGTAAATAAAAGATAAAAAAATACCGC 17 34 0 AAAAGATAAA 0.765289 -184 ATTTGAAAGCAAGAGAGTAATGT 17 205 1 AAGAGAGTAA 0.752201 -13 TGTATATAAAAAAGGAGCAATTA 19 47 1 AAAGGAGCAA 0.878441 -13 TGGCAGAAAGTGATCAAAATTGCTCAC 22 8 1 AAGTGATCAA 0.914814 -245 AGACTGAAAAAAGTGAGCAATTTTGATCAC 22 20 0 AAGTGAGCAA 0.94483 -233 ACTGGGTGTGAAATGATTAAAAATTGAACT 22 79 0 AAATGATTAA 0.730023 -174 ********** Masking position 6 Map Score: 5.81392 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 129 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 9 TTTGTAATGTTGTCAAAGCATTCA 2 5 0 TGTCAAAGCA 0.973517 -112 TAAAAATCAGTGTAAAAGCAATAAATACCC 5 221 1 TGTAAAAGCA 0.826942 -80 TTAAATGGCGAGTCAAAGCTCGCACTACAT 6 11 0 AGTCAAAGCT 0.768964 -82 GATATTGAATTGCCCAAACAAATCTTCTAA 11 41 0 TGCCCAAACA 0.933099 -41 ATTTTATTTTTGCCAAAGCACCTGTGTGTA 14 53 1 TGCCAAAGCA 0.98679 -179 GTTTTTGATTTGCCAAAACAGCCTGATCTT 22 200 1 TGCCAAAACA 0.953939 -53 TTGCCGTTAGCCCAAGCATAACGGAATA 25 9 1 AGCCCAAGCA 0.956999 -276 ********** Masking position 6 Map Score: 3.82403 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 122 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 ATTTTTATAGAATTCTCAAGATTTTCTCTCTTAT 3 52 1 ATTCTAAATT 0.344434 -120 AGGAATGAATTTTCTTTATAATCTGTAGTCTGAA 3 123 1 TTCTTATATT 0.901357 -49 ATCATAGCCATATCTTAATTATCTCCATTCCCTG 4 88 1 TTCTTATATT 0.901358 -27 CATCATCACCACACCTGATTATCTTTCAGGCGTG 5 146 1 AACCTATATT 0.830308 -155 CACTCGGAAGATATTTTATTATCTTCCAAACATA 5 184 0 AATTTATATT 0.599507 -117 AAACAGTATAAAACTAAATAATCTCGAATCGCTC 8 33 0 AACTAATATT 0.600875 -79 TGATCCTGTATGACTATATGATCTAGTGA 10 6 0 TACTAATATT 0.745915 -30 TTTTGTTTCCTTATGATGTAATAAAAAAT 12 11 0 TTCCTATATT 0.922137 -19 AAAATTGTCCTTATAATGTTGTGTTTAAA 13 18 0 TTCCTATATT 0.922137 -19 GAATGCCAATTCACCTTAATATTTGTGGTTTCAA 14 143 1 TACCTAAATT 0.673603 -89 ACAACAAGCATTTTTAAATGATTAGACGAAAAA 15 55 0 TTTTAATAT 0.0241157 -246 CGATAAAATGACACCTGATAATTTGTTTGAATAT 15 188 0 AACCTATATT 0.830278 -113 TATCTTTTATTTACTTAATTATTTCGTTTTATTC 17 46 1 TACTTATATT 0.880455 -172 TCAAATGTTGTGTTTAAATTATGTAGCTAATCTA 17 177 0 TTTTAATATT 0.593427 -41 AAATAGTTCAATTTTTAATCATTTCACACCCAGT 22 75 1 ATTTTATATT 0.652216 -178 AGTAGTTACTTGAAAATCTTCAAATTTAA 24 14 0 TACTTAAATT 0.614243 -19 AAAATACCTTTCTTCATATAATATGTTTGAGAAT 25 97 0 TTTCAATATT 0.654075 -188 AAATAAAAACTATTCTTATTATTTTCTGTATTTA 25 169 1 TTTCTATATT 0.825839 -116 * **** ** ** * Masking position 12 Map Score: 10.5485 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 327 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 11 TGACAAAAAATTTTTTTACAAAATCTTTTCA 1 45 1 TTTTTTTAAA 0.566062 -91 TAACCGCACTTTTCTCGAAAAATTTATTAGA 1 98 1 TTTCTCGAAA 0.793172 -38 AGGAATGAATTTTCTTTATAATCTGTAGTCT 3 123 1 TTTCTTTAAA 0.940613 -49 GCTATGATAATTTCTTTACAACAAAGTGTAA 4 65 0 TTTCTTTAAA 0.940613 -50 AGATCTTATATTGCCTTAAAAATACACTTTA 5 67 0 TTGCCTTAAA 0.922505 -234 CCCTCGAAAATTGCCTTCCGAGGGGTATTTA 5 242 0 TTGCCTTCGA 0.439535 -59 GGTTTATCATTTGCTTTATACAAACAGTATA 8 57 0 TTGCTTTAAC 0.675328 -55 TCACTTAATATTGCCTGACAATTTTC 11 6 0 TTGCCTGAAA 0.900108 -76 TTTTGTTTCCTTATGATGTAATAAAA 12 14 0 TTTCCTTAGA 0.856561 -16 AAAATTGTCCTTATAATGTTGTGTTT 13 21 0 TGTCCTTAAA 0.690178 -16 TCCTTTACTTTTTCCCTAAAAATAGATTAGA 14 110 0 TTTCCCTAAA 0.856553 -122 CCTATTAAACTATCTTTACAACTCTCTTGCA 17 84 0 TATCTTTAAA 0.691666 -134 GTTCGATATGTTTTTTTAGAATAAAACCTAC 17 121 0 TTTTTTTAAA 0.566067 -97 CATTACTCTCTTGCTTTCAAATGTTGTGTTT 17 196 0 TTGCTTTCAA 0.675328 -22 AACGTTATCTTGAAAAACATTTTCCT 18 6 1 TATCTTGAAA 0.629923 -141 TGAAAAACATTTTCCTGAAACAGGATTTGAA 18 21 1 TTTCCTGAAC 0.74561 -126 CGCTGTCAATTTTCCCTAAAATCGGCTAGAA 21 56 1 TTTCCCTAAA 0.856553 -51 GCTTCAATTTTTTCTTGAAGATCAGGCTGTT 22 216 0 TTTCTTGAGA 0.793181 -37 AGTAGTTACTTGAAAATCTTCAAATT 24 17 0 TTACTTGAAA 0.541878 -16 ******** ** Masking position 1 Map Score: 10.0026 Number of sites scoring better than the average of aligned sites = 506 Number in coding regions = 367 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 12 TTATTCAAACGCTTAAATATTCGACATAAG 3 81 0 GCTTAAATAT 0.9287 -91 TTTTCCTTGAGCTTAAATTTCAATACACCT 18 58 0 GCTTAAATTT 0.970511 -89 TTCTTTAATTGCTTCAATTTTTTCTTGAAG 22 227 0 GCTTCAATTT 0.950751 -26 AGCTTAAATTTGAAGATTTTC 24 2 1 GCTTAAATTT 0.970511 -31 ********** Masking position 6 Map Score: 0.855474 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 12 Number in noncoding regions = 6 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: 3.15071e-13 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 TCAATATTGAAAATTCAGCGTAAATTAACC 1 73 1 AAATTCAGCG 0.826732 -63 CCATTGTTGAAAACACGGCGATTTT 3 6 0 AAACACGGCG 0.92611 -166 TGGTTGGGGAAAATAACGCATTTTTATAGA 3 33 1 AAATAACGCA 0.655699 -139 CTTTAAAATTAAAAAAAGCAATTTTTTTGA 5 42 0 AAAAAAAGCA 0.653255 -259 GAGTGTAATAAAAATCAGTGTAAAAGCAAT 5 213 1 AAAATCAGTG 0.347722 -88 AATTTTGCAAAAATACGACAAAAATTAACC 9 21 0 AAATACGACA 0.576182 -45 TATCATCGTAAAATACAGTGAAACT 11 67 1 AAATACAGTG 0.693846 -15 ATTAGTTTTTAAACACAACATTATAAGGAC 13 11 1 AAACACAACA 0.682004 -26 ATCTGCTGATAAACTCCGCAAACAACTTGA 15 17 0 AAACTCCGCA 0.781037 -284 CATTTTATCGAAAAACAGTATTAAGTTGAA 15 212 1 AAAAACAGTA 0.591311 -89 AAAGATAAAAAAATACCGCACTTTTGTGCT 17 23 0 AAATACCGCA 0.904845 -195 TACATAATTTAAACACAACATTTGAAAGCA 17 186 1 AAACACAACA 0.682004 -32 GGTAAATCACAAATAAAGCGTCTGAGATTC 21 13 1 AAATAAAGCG 0.746901 -94 CACCGAAAATAAAATCGGCGTATTCTAGCC 21 79 0 AAAATCGGCG 0.717917 -28 AAACACACTAAAACAAGGCGACAATATGCT 22 174 0 AAACAAGGCG 0.715114 -79 TCGACTCCTAAAAAACCGCAAGATTATA 23 9 0 AAAAACCGCA 0.873538 -24 AAGCAGGTTTAAATACAGAAAATAATAAGA 25 182 0 AAATACAGAA 0.440808 -103 ********** Masking position 3 Map Score: 7.39549 Number of sites scoring better than the average of aligned sites = 760 Number in coding regions = 646 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 15 ********** No masking Map Score: 3.15071e-13 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