AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -itrpR_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 HI0821 207 galactose operon repressor (galR) #4 HI0822 90 galactose ABC transporter, periplasmic-binding protein (mglB) #5 HI0823 65 galactoside ABC transporter, ATP-binding protein (mglA) #6 HI0825 145 H. influenzae predicted coding region HI0825 #7 HI0830 37 trp operon repressor (trpR) #8 HI1386 300 H. influenzae predicted coding region HI1386 #9 HI1387 105 anthranilate synthase component I (trpE) #10 HI1388.1 48 H. influenzae predicted coding region HI1388.1 #11 HI1389 52 anthanilate phosphoribosyltransferase (trpD) #12 HI1389.1 36 indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomerase (trpC) #13 HI1430 179 short chain dehydrogenase/reductase #14 HI1547 217 phospho-2-dehydro-3-deoxyheptonate aldolase (phenylalanine repressible) (aroG) #15 HI1549 146 ABC transporter, ATP-binding protein #16 HI1556 59 2-hydroxyacid dehydrogenase #17 HI1560 22 H. influenzae predicted coding region HI1560 #18 HI1561 106 peptide chain release factor 1 (prfA) #19 HI1562 252 H. influenzae predicted coding region HI1562 #20 HI1563 32 conserved hypothetical protein #21 HI1564 32 H. influenzae predicted coding region HI1564 #22 HI1564.1 284 H. influenzae predicted coding region HI1564.1 Motif number 1 TGTCATTAACAATCTGCGGTAGAATATGGC 1 20 0 AATCTGCGGT 0.912522 -116 TTTTTCGAGAAAAGTGCGGTTAATTTACGC 1 90 0 AAAGTGCGGT 0.998256 -46 GTACACAAGGAAAGTGCAATATATTTATAT 2 61 0 AAAGTGCAAT 0.896339 -56 GACATCAAAAAGTGCGGTAATTTTTAAC 10 9 1 AAAGTGCGGT 0.998256 -40 TTTCTCCTTTAAAGTGCGGTTAAAAATTAC 10 27 0 AAAGTGCGGT 0.998256 -22 GTACAGCACAAAAGTGCGGTATTTTTTTAT 14 19 1 AAAGTGCGGT 0.998256 -199 AGCTCAAGGAAAAGTGTGATAGACTCGTGC 15 75 1 AAAGTGTGAT 0.896339 -72 ATCTGCCGCTAAAGTGCGGTTAAAACGAGT 15 122 1 AAAGTGCGGT 0.998256 -25 ATTTCATCAAAAGTGCGGTTAATTTTGAC 16 10 1 AAAGTGCGGT 0.998256 -50 TTTTATATACAAAGTGCGGTCAAAATTAAC 16 28 0 AAAGTGCGGT 0.998256 -32 ********** Masking position 5 Map Score: 33.5641 Number of sites scoring better than the average of aligned sites = 1115 Number in coding regions = 700 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 2 CGCAGATTGTTAATGACAAAAAATTTTTTTACAAA 1 32 1 TAATGAAATT 0.768489 -104 TCAATATTGAAAATTCAGCGTAAATTAACCGCACT 1 73 1 AAATTCAAAT 0.678322 -63 AAAATGCCTCTAAAATAAATTTGCAC 2 101 0 AAATGCAAAT 0.667722 -16 ACGATTACATTAATTTATACTAAATTATTGTAAAT 3 38 1 TAATTAAAAT 0.712408 -170 ACAAAATAAGAAAATAAGCAAAATTTTTTATGATT 3 90 1 AAAATCAATT 0.900495 -118 ATGATTACATAAAAAATTATGAATTTGTGATCCAT 4 19 0 AAAAAAAATT 0.935126 -72 AAATAAATTATCGTAATTAATCTATGAG 4 73 0 TAAATCAATT 0.848255 -18 GCAATCTTAATAAAATGAATGAAAAGTGGGCAAAT 6 18 1 TAAAAAAAAA 0.518826 -128 TAGATAAAACAAAAGTGGACAAATTTGCCCACTTT 6 40 0 AAAAGAAATT 0.94253 -106 GATTATTGCATAAATATCCTTAATTCAGAATTGAA 6 75 0 TAAATCAATT 0.848254 -71 TGATTAACTCAAAATATACTTAATATAAGGCAAAA 8 75 0 AAAATCAATA 0.606462 -226 TTTGGCTATTAAAAGCGTACAAAATCAAACTTATC 8 264 1 AAAAGAAAAT 0.921035 -37 TTTTTAATCAAAAAGTATAAAAAATAAAAATCAGG 9 20 1 AAAAGAAAAT 0.921035 -86 TGCACTAGTTTAATAGTACAAAATTTTCCAAAAGG 9 71 1 TAATACAATT 0.605304 -35 TAAAATATAGAAAATTAACAAATCC 11 1 1 TAAAAAAAAT 0.86361 -52 TTTAATTTTAAAAATGTCATTAAATGAATTAATTT 13 81 0 AAAATAAAAT 0.924468 -99 GACATTTTTAAAATTAAAATGAAATTGCTTGCAAT 13 98 1 AAATTAAAAT 0.800411 -82 TTAAGTAAATAAAAGATAAAAAAATACCGCACTTT 14 29 0 AAAAGAAAAT 0.921034 -189 GCAAGCTGAATAAAACGAAATAATTAAGTAAATAA 14 52 0 TAAAAAAATT 0.899028 -166 TTTTTTAGAATAAAACCTACAAATTCCCTATTAAA 14 106 0 TAAAAAAATT 0.899028 -112 CTTTGTATATAAAAAAGGAGCAATTA 16 44 1 AAAAAAAATT 0.935123 -16 TTAAGACTGAAAAAAGTGAGCAATTTTGATCACTT 19 18 0 AAAAAAAATT 0.93512 -235 ACTGGGTGTGAAATGATTAAAAATTGAACTATTTA 19 74 0 AAATGAAATT 0.842581 -179 TTGGCAAATCAAAAACACACTAAAACAAGGCGACA 19 181 0 AAAAAAAAAA 0.635781 -72 TCTTCAAGAAAAAATTGAAGCAATTAAAGAAGAAT 19 226 1 AAAATAAATT 0.945084 -27 TTTATAGGACTAAATATGACCAATTTTAGATTAAA 22 49 0 TAAATAAATT 0.914022 -236 TCCTATAAAAAAAATAATAATAATTCTCAAACATA 22 75 1 AAAATAAATT 0.945087 -210 TGATTTTTGATAAAAATCAAGAAATAAAAACTATT 22 148 1 TAAAAAAAAT 0.86361 -137 TTAAATACAGAAAATAATAAGAATAGTTTTTATTT 22 169 0 AAAATAAATA 0.745598 -116 ***** * **** Masking position 12 Map Score: 30.4977 Number of sites scoring better than the average of aligned sites = 1095 Number in coding regions = 753 Number in noncoding regions = 342 Number of orfs with sites within 600 bp upstream = 263 Fraction of orfs with sites within 600 bp upstream = 0.0422422 Motif number 3 ATGCACTAGTTTAATAGTGTAAAATGGG 7 7 1 TGTTTATAGT 0.934484 -31 GTTGGTTGGTTGGTTGGTTGGTTCATCAGTAT 8 136 0 TGTTGGTGGT 0.992504 -165 GTTGGTTGGTTGGTTGGTTGGTTGGTTGGTTG 8 148 0 TGTTGGTGGT 0.992504 -153 GTTGGTTGGTTGGTTGGTTGGTTGGTTGGTTG 8 160 0 TGTTGGTGGT 0.992504 -141 GTTGGTTGGTTGGTTGGTTGGTTGGTTGGTTG 8 172 0 TGTTGGTGGT 0.992504 -129 TTATTTTGGTTGGTTGGTTGGTTGGTTGGTTG 8 184 0 TGTTGGTGGT 0.992504 -117 CCTTTTGCACTAGTTTAATAGTACAAAATTTT 9 66 1 TGTTTATAGT 0.934484 -40 GTTGTAAAGATAGTTTAATAGGGAATTTGTAG 14 93 1 TGTTTATAGG 0.831744 -125 CATATCGAACTAGTTTACTAGTACAAAAATAA 14 142 1 TGTTTATAGT 0.934484 -76 GAGCCGTTGATTGTTGATTAGTAGTTGTAGGG 22 226 1 TGTTGATAGT 0.969241 -59 TGATTAGTAGTTGTAGGGTGGGCTTTAGCCCA 22 240 1 TGTAGGTGGG 0.841651 -45 TATCTCTCGATTGTTTTTTGGTGGGCTAAAGC 22 261 0 TGTTTTTGGT 0.886027 -24 * ***** **** Masking position 4 Map Score: 22.1947 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 104 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 ACTGATGAACCAACCAACCAACCAACCAAC 8 138 1 CAACCAACCA 0.997502 -163 ACCAACCAACCAACCAACCAACCAACCAAC 8 150 1 CAACCAACCA 0.997502 -151 ACCAACCAACCAACCAACCAACCAACCAAC 8 162 1 CAACCAACCA 0.997502 -139 ACCAACCAACCAACCAACCAACCAACCAAC 8 174 1 CAACCAACCA 0.997502 -127 ACCAACCAACCAACCAACCAACCAAAATAA 8 186 1 CAACCAACCA 0.997502 -115 ACAGAGAGTACAACAAAGCATAATTGGCAA 19 132 1 CAACAAAGCA 0.934048 -121 ********** Masking position 6 Map Score: 17.5429 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 81 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 CTACCGCAGATTGTTAATGACAAAAAATTTTTTTACA 1 28 1 TTTATAAAAA 0.884738 -108 TACGCTGAATTTTCAATATTGAAAAGATTTTGTAAAA 1 58 0 TTAAAAAAAA 0.947833 -78 CTCGAAAAATTTATTAGAAACAAAAGGATTTCACT 1 111 1 TTTAAAAAAG 0.960662 -25 GTGCAATATATTTATATCGATAAAAAGGGGACATTTA 2 41 0 TTTACAAAAG 0.768156 -76 AATGTAATCGTTTACATTGATAAAAAACAGGAGTCAA 3 12 0 TTCATAAAAA 0.727879 -196 GATTTATAGATTATAACAAGGAAAAAGTT 3 189 1 TTAAAAAAAG 0.9454 -19 ATGAGCAAATTTGCAAAAATGAAAATGATTACATAAA 4 41 0 TTAAAAAAAG 0.9454 -50 TTAATTCAGAATTGAATAGATAAAACAAAAGTGGACA 6 54 0 ATAAAAAAAA 0.593388 -92 CGCCACCATTTTCATAGAGAGAAAAAA 6 129 1 TTTAAAAAAA 0.962433 -17 TTATAATACCTTGATTAACTCAAAATATACTTAATAT 8 84 0 TTTTAAAAAA 0.647067 -217 AATCAAGGTATTATAAAAATGAAAAGGATCTATACTG 8 105 1 TTAAAAAAAG 0.9454 -196 GTACAAAATTTTCCAAAAGGATAAATAAAT 9 86 1 TTAAATAAAA 0.565206 -20 TTTAATGACATTTTTAAAATTAAAATGAAATTGCTTG 13 92 1 TTTAAAAAAG 0.960624 -88 GAATTTGTAGGTTTTATTCTAAAAAAACATATCGAAC 14 115 1 GTTATAAAAA 0.626319 -103 TCGAACTAGTTTACTAGTACAAAAATAAGTGTAGATT 14 146 1 TTTATAAAAA 0.885298 -72 TTGACCGCACTTTGTATATAAAAAAGGAGCAATTA 16 35 1 TTTAAAAAAG 0.960662 -25 TCAGGCTGTTTTGGCAAATCAAAAACACACTAAAACA 19 189 0 TTCAAAAAAA 0.898799 -64 GTCATATTTAGTCCTATAAAAAAAATAATAATAATTC 22 64 1 GTTAAAAAAA 0.848808 -221 AACAAGCAGGTTTAAATACAGAAAATAATAAGAATAG 22 178 0 TTAAAAAAAA 0.947833 -107 ** ** * **** * Masking position 2 Map Score: 18.0993 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 182 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 6 TTGGTTGGTTGGTTGGTTGGTTCATCAGTA 8 137 0 GGTTGGTTGG 0.998428 -164 TTGGTTGGTTGGTTGGTTGGTTGGTTGGTT 8 149 0 GGTTGGTTGG 0.998428 -152 TTGGTTGGTTGGTTGGTTGGTTGGTTGGTT 8 161 0 GGTTGGTTGG 0.998428 -140 TTGGTTGGTTGGTTGGTTGGTTGGTTGGTT 8 173 0 GGTTGGTTGG 0.998428 -128 TATTTTGGTTGGTTGGTTGGTTGGTTGGTT 8 185 0 GGTTGGTTGG 0.998428 -116 ********** Masking position 4 Map Score: 18.6877 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 7 TTGGTTGGTTGGTTGGTTGGTTCATCAGTA 8 137 0 GGTTGGTTGG 0.998514 -164 TTGGTTGGTTGGTTGGTTGGTTGGTTGGTT 8 149 0 GGTTGGTTGG 0.998514 -152 TTGGTTGGTTGGTTGGTTGGTTGGTTGGTT 8 161 0 GGTTGGTTGG 0.998514 -140 TTGGTTGGTTGGTTGGTTGGTTGGTTGGTT 8 173 0 GGTTGGTTGG 0.998514 -128 TATTTTGGTTGGTTGGTTGGTTGGTTGGTT 8 185 0 GGTTGGTTGG 0.998514 -116 ********** Masking position 4 Map Score: 18.6877 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 8 TACTGATGAACCAACCAACCAACCAACCAA 8 137 1 CCAACCAACC 0.998809 -164 AACCAACCAACCAACCAACCAACCAACCAA 8 149 1 CCAACCAACC 0.998809 -152 AACCAACCAACCAACCAACCAACCAACCAA 8 161 1 CCAACCAACC 0.998809 -140 AACCAACCAACCAACCAACCAACCAACCAA 8 173 1 CCAACCAACC 0.998809 -128 AACCAACCAACCAACCAACCAACCAAAATA 8 185 1 CCAACCAACC 0.998809 -116 ********** Masking position 4 Map Score: 18.6877 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 9 GTAATCGTTTACATTGATAAAAAACAGGAGT 3 15 0 ACATGATAAA 0.732588 -193 TCTTTGTCACAAAATAAGAAAATAAGCAAAA 3 82 1 AAAAAAGAAA 0.575922 -126 ATGAACTAAATCATAAAAAATTTTGCTTATT 3 102 0 TCATAAAAAT 0.413392 -106 TATATTTTGATCATAAATAATTTACGATAAA 3 157 0 TCATAATAAT 0.37454 -51 ATAGATTATAACAAGGAAAAAGTT 3 194 1 ACAAGAAAAA 0.870394 -14 GAAAATGATTACATAAAAAATTATGAATTTG 4 27 0 ACATAAAAAT 0.704138 -64 CAAATTTGCAAAAATGAAAATGATTACATAA 4 42 0 AAAAGAAAAT 0.702828 -49 CCCTTAGATTACAACAAAAATTGATGGGAAA 5 11 0 ACAAAAAAAT 0.832145 -55 AGGTATTATAAAAATGAAAAGGATCTATACT 8 110 1 AAAAGAAAAG 0.843237 -191 CCAACCAACCAAAATAATAAAACCGTTGCGG 8 199 1 AAAAAATAAA 0.746905 -102 AATGCTTACATGGATAAGTTTGATTTTG 8 283 0 ACATGATAAG 0.815422 -18 ATACAATTTTTAATCAAAAAGTATAAAAAAT 9 14 1 TAATAAAAAG 0.44324 -92 AAAAGTATAAAAAATAAAAATCAGGCTTGAC 9 30 1 AAAAAAAAAT 0.711182 -76 AACTAGTGCAAAAGGAATAAGTCAAGCCTGA 9 50 0 AAAGAATAAG 0.495545 -56 AAAATTTTCCAAAAGGATAAATAAAT 9 90 1 AAAAGATAAA 0.739206 -16 GACATCAAAAAGTGCGGTAATT 10 2 1 ACATAAAAAG 0.844065 -47 AAATCCATATACAAAGAAAAACAGGAATAGA 11 30 1 ACAAGAAAAA 0.870394 -23 TTTATACGCCACAATAAGAAGAAAA 12 22 1 ACAAAAGAAG 0.815126 -15 ATTAAGTAAATAAAAGATAAAAAAATACCGC 14 34 0 TAAAGATAAA 0.456312 -184 GTTTACTAGTACAAAAATAAGTGTAGATTAG 14 154 1 ACAAAATAAG 0.905491 -64 AAATTTAAGCTCAAGGAAAAGTGTGATAGAC 15 68 1 TCAAGAAAAG 0.762285 -79 GGGAAAATTGACAGCGAAAAGGAAATTAAGA 18 41 0 ACAGGAAAAG 0.690926 -66 AGCCTGATCTTCAAGAAAAAATTGAAGCAAT 19 219 1 TCAAAAAAAA 0.674308 -34 TCCTATAAAAAAAATAATAATAATTCTCAAA 22 75 1 AAAAAATAAT 0.676624 -210 GTATTTTCTCACAACAATAAAGATTGATTTT 22 124 1 ACAAAATAAA 0.855937 -161 TTTTTGATAAAAATCAAGAAATAAAAACTAT 22 151 1 AAATAAGAAA 0.394659 -134 TTAAATACAGAAAATAATAAGAATAGTTTTT 22 173 0 AAAAAATAAG 0.826355 -112 **** ****** Masking position 7 Map Score: 16.8339 Number of sites scoring better than the average of aligned sites = 987 Number in coding regions = 714 Number in noncoding regions = 273 Number of orfs with sites within 600 bp upstream = 241 Fraction of orfs with sites within 600 bp upstream = 0.0387086 Motif number 10 TATAAATATATTGCACTTTCCTTGTGTACT 2 62 1 TTGCACTTTC 0.741741 -55 CACTTTCCTTGTGTACTACTATAATAGTGC 2 75 1 GTGTACTACT 0.696192 -42 TAAAATAAATTTGCACTATTATAGTAGTAC 2 87 0 TTGCACTATT 0.968537 -30 TGCTCCCATTTTACACTATTAAACTAGTGC 7 13 0 TTACACTATT 0.652032 -25 AAGTTTGATTTTGTACGCTTTTAATAGCCA 8 266 0 TTGTACGCTT 0.817865 -35 CTTATTCCTTTTGCACTAGTTTAATAGTAC 9 60 1 TTGCACTAGT 0.914299 -46 TTGGAAAATTTTGTACTATTAAACTAGTGC 9 72 0 TTGTACTATT 0.976702 -34 CAAAATTTATTTGTACTACTTTAATAGTAC 13 133 1 TTGTACTACT 0.935604 -47 TTGAGCTTATTTGTACTATTAAAGTAGTAC 13 145 0 TTGTACTATT 0.976702 -35 CACTTTTGTGCTGTACTCTCGAAA 14 5 0 CTGTACTCTC 0.762998 -213 ACACTTATTTTTGTACTAGTAAACTAGTTC 14 148 0 TTGTACTAGT 0.935604 -70 TGATTAAAAATTGAACTATTTAATTAGGAG 19 66 0 TTGAACTATT 0.855046 -187 ATACTGGGTGTTGTACTCTCTTTACAGAGA 19 109 1 TTGTACTCTC 0.953296 -144 TTATGCTTTGTTGTACTCTCTGTAAAGAGA 19 125 0 TTGTACTCTC 0.953296 -128 ********** Masking position 5 Map Score: 13.5347 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 39 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 ATTCAGCGTAAATTAACCGCACTTTTCTCG 1 85 1 AATTAACCGC 0.982508 -51 AATTATTGTAAATAAACCGTGATCTTTGTC 3 60 1 AATAAACCGT 0.899772 -148 ATACTTATGAAAGTAACCGCTTTCAATTTA 3 131 1 AAGTAACCGC 0.953569 -77 AACCAAAATAATAAAACCGTTGCGGTAGTG 8 205 1 ATAAAACCGT 0.745899 -96 GTGCGGTAATTTTTAACCGCACTTTAAAGG 10 22 1 TTTTAACCGC 0.903012 -27 AAAAGATAAAAAAATACCGCACTTTTGTGC 14 24 0 AAAATACCGC 0.817516 -194 TTTTTACTCGTTTTAACCGCACTTTAGCGG 15 127 0 TTTTAACCGC 0.903012 -20 GTGCGGTCAAAATTAACCGCACTTTTGATG 16 15 0 AATTAACCGC 0.982508 -45 ATCGACTCCTAAAAAACCGCAAGATTATA 20 10 0 AAAAAACCGC 0.966008 -23 ********** Masking position 6 Map Score: 7.71613 Number of sites scoring better than the average of aligned sites = 372 Number in coding regions = 236 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 12 TAAAAAAATTTTTTGTCATTAACAATCTGCGG 1 31 0 TTTTTCTTAA 0.769483 -105 GACAAAAAATTTTTTTACAAAATCTTTTCAAT 1 46 1 TTTTTAAAAA 0.461486 -90 TTAACCGCACTTTTCTCGAAAAATTTATTAGA 1 97 1 TTTTTCAAAA 0.912516 -39 ACCGCTTTCAATTTATCGTAAATTATTTATGA 3 146 1 ATTTTCTAAA 0.752694 -62 AATCTTATATTTTGATCATAAATAATTTACGA 3 161 0 TTTGTCTAAA 0.859247 -47 AAATACAATTTTTAATCAAAAAGTATAAAAAA 9 12 1 TTTATCAAAA 0.891498 -94 TTTTTCTCCTAAATCTTGAGCTT 13 167 0 TTTTTCTAAA 0.93756 -13 ATTTGTAGGTTTTATTCTAAAAAAACATATCG 14 117 1 TTTATCAAAA 0.891498 -101 TCGCTGTCAATTTTCCCTAAAATCGGCTAGAA 18 55 1 TTTTCCAAAA 0.847613 -52 ATTGCTTCAATTTTTTCTTGAAGATCAGGCTG 19 218 0 TTTTTCTGAA 0.8317 -35 GGCAAGCACGTTTAATCTAAAATTGGTCATAT 22 39 1 TTTATCAAAA 0.891498 -246 ATTTCTTGATTTTTATCAAAAATCAATCTTTA 22 141 0 TTTTTCAAAA 0.912516 -144 **** ** **** Masking position 11 Map Score: 9.72995 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 183 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 13 GACAACATTACAAAGGGGACTAAATGTCCC 2 21 1 CAAAGGGGAC 0.887119 -96 TATATCGATAAAAAGGGGACATTTAGTCCC 2 36 0 AAAAGGGGAC 0.978623 -81 AACCTCTTTAAAAAGGGGAAGATCCACTTC 5 42 0 AAAAGGGGAA 0.766614 -24 AAAATGAATGAAAAGTGGGCAAATTTGTCC 6 29 1 AAAAGTGGGC 0.98195 -117 TAGATAAAACAAAAGTGGACAAATTTGCCC 6 45 0 AAAAGTGGAC 0.966219 -101 CTCTCTATGAAAATGGTGGCGCAATTATAC 6 120 0 AAATGGTGGC 0.583295 -26 TAATAGTGTAAAATGGGAGCATAATT 7 22 1 AAATGGGAGC 0.86287 -16 AATTGAAATAAAAATTGGGCAGATTATATC 13 25 1 AAAATTGGGC 0.930917 -155 TTTGTATATAAAAAAGGAGCAATTA 16 45 1 AAAAAGGAGC 0.733561 -15 TAAGACTGAAAAAAGTGAGCAATTTTGATC 19 22 0 AAAAGTGAGC 0.946081 -231 GAAATGATTAAAAATTGAACTATTTAATTA 19 70 0 AAAATTGAAC 0.695603 -183 CGTTTAATCTAAAATTGGTCATATTTAGTC 22 47 1 AAAATTGGTC 0.636084 -238 ********** Masking position 3 Map Score: 10.4092 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 164 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 14 GTTAATGACAAAAAATTTTTTTACAAAATCTT 1 40 1 AAAAATTTTT 0.709353 -96 AATTTTTTTACAAAATCTTTTCAATATTGAAA 1 53 1 CAAAATTTTC 0.780528 -83 CTATAATAGTGCAAATTTATTTTAGAGGCATT 2 93 1 GCAAATTTTT 0.807987 -24 AGAAAATAAGCAAAATTTTTTATGATTTAGTT 3 98 1 CAAAATTTTA 0.722696 -110 GATTAATTACGATAATTTATTT 4 79 1 GATAATTTTT 0.756959 -12 TTATGCAATAGAAAATATTTTTGG 8 3 0 GAAAATTTTT 0.701887 -298 TAATATAAGGCAAAATATGTTTTGATAAGATT 8 58 0 CAAAATTTTT 0.951318 -243 TTGATTAACTCAAAATATACTTAATATAAGGC 8 79 0 CAAAATTCTT 0.876832 -222 TGCTTGCAATCAAAATTTATTTGTACTACTTT 13 123 1 CAAAATTTTT 0.953545 -57 CCTGTTTCAGGAAAATGTTTTTCAAGATAACG 15 13 0 GAAAATTTTT 0.946749 -134 AAAACAAGGCGACAATATGCTTGCTAATCCTA 19 163 0 GACAATTCTT 0.615361 -90 ATTGTTGTGAGAAAATACCTTTCTTCATATAA 22 110 0 GAAAATCTTT 0.807688 -175 ****** * *** Masking position 5 Map Score: 7.65914 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 76 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 15 ********** No masking Map Score: 4.54991e-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