AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ityrR_ecoli_hinf_300.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 aroP 300 aromatic amino acid transport protein #2 aroL 182 shikimate kinase II #3 yaiA 49 orf, hypothetical protein #4 aroM 257 protein of aro operon, regulated by aroR #5 aroG 300 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (DAHP synthetase, phenylalanine repressible) #6 ycjX 155 putative EC 2.1 enzymes #7 tyrR 147 transcriptional regulation of aroF, aroG, tyrA and aromatic amino acid transport #8 tyrP 190 tyrosine-specific transport system #9 aroF 170 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (DAHP synthetase, tyrosine repressible) #10 mtr 153 tryptophan-specific transport protein #11 deaD 128 inducible ATP-independent RNA helicase #12 yhbM 108 putative control proteins #13 pnp 177 polynucleotide phosphorylase; cytidylate kinase activity #14 rpsO 148 30S ribosomal subunit protein S15 #15 rbfA 163 ribosome-binding factor A #16 infB 24 protein chain initiation factor IF-2 #17 nusA 27 transcription pausing; L factor #18 yhbC 300 orf, hypothetical protein #19 dnaB 82 replicative DNA helicase; part of primosome #20 alr 52 alanine racemase 1 #21 tyrB 252 tyrosine aminotransferase, tyrosine repressible #22 HI0286 135 aminotransferase #23 HI0287 116 tryptophan-specific transport protein (mtr) #24 HI0409 171 conserved hypothetical protein #25 HI0410 114 transcriptional regulatory protein (tyrR) #26 HI0468 300 ATP phosphoribosyltransferase (hisG) #27 HI0469 92 histidinol dehydrogenase (hisD) #28 HI0470 68 histidinol-phosphate aminotransferase (hisC) #29 HI0471 111 imidazoleglycerol-phosphate dehydratase / histidinol-phosphatase (hisB) #30 HI0472 65 amidotransferase (hisH) #31 HI0473 35 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA) #32 HI0476 81 H. influenzae predicted coding region HI0476 #33 HI0477 29 tyrosine-specific transport protein (tyrP) #34 HI0528 36 tyrosine-specific transport protein (tyrP) #35 HI0530 231 O-sialoglycoprotein endopeptidase (gcp) #36 HI1288 300 ribosome binding factor A (rbfA) #37 HI1290 59 chorismate mutase / prephenate dehydrogenase (tyrA) #38 HI1547 217 phospho-2-dehydro-3-deoxyheptonate aldolase (phenylalanine repressible) (aroG) #39 HI1549 146 ABC transporter, ATP-binding protein #40 HI1556 59 2-hydroxyacid dehydrogenase #41 HI1560 22 H. influenzae predicted coding region HI1560 #42 HI1561 106 peptide chain release factor 1 (prfA) #43 HI1562 252 H. influenzae predicted coding region HI1562 #44 HI1563 32 conserved hypothetical protein #45 HI1564 32 H. influenzae predicted coding region HI1564 #46 HI1564.1 284 H. influenzae predicted coding region HI1564.1 Motif number 1 CCTATAACCGCAACTGCGGTCTGGAGCACT 18 190 0 CAACTGCGGT 0.952377 -111 TGTCATTAACAATCTGCGGTAGAATATGGC 22 20 0 AATCTGCGGT 0.931 -116 TTTTTCGAGAAAAGTGCGGTTAATTTACGC 22 90 0 AAAGTGCGGT 0.996454 -46 CGATATAAAGTGCGGTCAAAAATGGT 25 7 1 AAAGTGCGGT 0.996454 -108 TTGAAAGAGCGGTTAATTTTTGT 30 4 1 AAAGAGCGGT 0.977924 -62 GTACAGCACAAAAGTGCGGTATTTTTTTAT 38 19 1 AAAGTGCGGT 0.996454 -199 ATCTGCCGCTAAAGTGCGGTTAAAACGAGT 39 122 1 AAAGTGCGGT 0.996454 -25 ATTTCATCAAAAGTGCGGTTAATTTTGAC 40 10 1 AAAGTGCGGT 0.996454 -50 TTTTATATACAAAGTGCGGTCAAAATTAAC 40 28 0 AAAGTGCGGT 0.996454 -32 ********** Masking position 2 Map Score: 23.4379 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 4 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 2 AGAAACCGTTTGTAAAGCTCAGCCTCAACCCCTCTCAA 1 77 0 TGTAAATCAA 0.706649 -224 ACTTCTTTGATGTAAACAAATTAATACAACAAACGGAA 1 213 1 TGTAAATACA 0.955299 -88 GTGATGCGTGTGTAAGTTTGCAATTCCGTTTGTTGTAT 1 236 0 TGTAAGTCCG 0.75371 -65 AAGAATGAAGTGTAAATAATAAATTACAT 2 2 0 TGTAAATACA 0.610182 -181 CAATTTCGATTGTAAAGAAAAAATTCCACTTAAAGTGA 2 78 0 TGTAAATCCA 0.946638 -105 CCGTTCATAGTGTAAAACCCCGTTTACACATTCTGACG 5 213 1 TGTAAATACA 0.499902 -88 TTACATATGGTGTAAATATAAATGTACAATAAAAAGCA 8 82 0 TGTAAATACA 0.622857 -109 AGGGAGTGTAAATTTATCTATACAGAGGTAAGGG 9 7 1 TGTAAATACA 0.622857 -164 AAATTGCCTGTGTAAATAAAAATGTACGAAATATGGAT 9 59 1 TGTAAATACG 0.922183 -112 TAACACATAAAGTAAAGTTTTCAATCCATATTTCGTAC 9 82 0 AGTAAATCCA 0.795848 -89 GAACACAATCTGTAAAATAATATATACAGCCCCGATTT 10 26 1 TGTAAATACA 0.622857 -128 TTTTACCTTATGTAAAATAATATTTACACTTTGTTGTA 25 42 1 TGTAAATACA 0.499902 -73 TTACATATATTGTAAAAAATTAATTACAAGGAGATTAC 37 18 0 TGTAAATACA 0.610182 -42 TTACAATATATGTAAGATAAAAATTACAG 37 41 1 TGTAAGTACA 0.593027 -19 TTGTACTCTCTGTAAAGAGAGTACAACACCCAGTATAC 43 107 0 TGTAAAAACA 0.865188 -146 ****** **** Masking position 5 Map Score: 22.5032 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 5 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 3 GCGACCTATTGGGGAAAACCCACG 2 169 1 GGAAAACCCA 0.777548 -14 TCCGTTCATAGTGTAAAACCCCGTTTACACAT 5 212 1 GTAAAACCCC 0.790888 -89 CAGAGGTAAGGGTTGAAAGCGCGACTAAATTG 9 33 1 GGGAAAGCGC 0.890058 -138 ACAAAAGACAGAAAAAAAGCCCCGATGGTAAA 10 63 0 GAAAAAGCCC 0.915937 -91 ATTTTTCACTGGAGAGAAGCCCTC 10 140 1 GGAGAAGCCC 0.960187 -14 CGTCCTGCCCGGTTAAAAGCCCCCCGCCGCAG 12 30 0 GGAAAAGCCC 0.993991 -79 ATCAGGTCAACGTGAACAGCCCTTCCACCTGA 15 90 1 CGAACAGCCC 0.89612 -74 TTTAAAAAGGGGCTAACAGCCCCTTTTTTGTC 15 129 1 GGAACAGCCC 0.979598 -35 GTCTGGATGAGGTGAAAAGCCCGCG 17 13 1 GGAAAAGCCC 0.993989 -15 ATAAAAAAAGGGCCTAAAGCCCAGTTATTCTG 18 270 0 GGTAAAGCCC 0.970996 -31 GGTTTCAACTGGTTAAAACCGCTTAAACAGGG 35 169 1 GGAAAACCGC 0.942428 -63 CGCTTAAACAGGGTAAAATCGCGCAACATTTT 35 188 1 GGAAAATCGC 0.879011 -44 GAATTTAGCACGCAAAAATCCCTTTCAACTTA 36 233 0 CGAAAATCCC 0.820743 -68 GTTTTTTGGTGGGCTAAAGCCCACCCTACAAC 46 249 0 GGTAAAGCCC 0.952751 -36 ** ******** Masking position 8 Map Score: 15.9158 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 215 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 4 ACAAAGACGGAAAAACGGGCACTTCGGCGT 7 41 0 AAAAACGGGC 0.948519 -107 CCGATGGTAAAAATCGGGGCTGTATATATT 10 44 0 AAATCGGGGC 0.938197 -110 CGAGTTTCAGAAAAGGGGGCCTGAGTGGCC 13 17 1 AAAAGGGGGC 0.970799 -161 GTCAGCTTGAAAAAAGGGGCCACTCAGGCC 13 34 0 AAAAAGGGGC 0.993021 -144 AATTAATTTTAAAAAGGGGCTAACAGCCCC 15 122 1 AAAAAGGGGC 0.993021 -42 TCTCCTGACAAAAAAGGGGCTGTTAGCCCC 15 137 0 AAAAAGGGGC 0.993021 -27 AAACCCCGATAAATCGGGGCTTTATATAAC 18 225 0 AAATCGGGGC 0.938197 -76 CCAAGACATAAAAAAAGGGCCTAAAGCCCA 18 279 0 AAAAAAGGGC 0.925547 -22 TGACAACATTACAAAGGGGACTAAATGTCC 23 20 1 ACAAAGGGGA 0.804998 -97 TTATATCGATAAAAAGGGGACATTTAGTCC 23 37 0 AAAAAGGGGA 0.956372 -80 TTTGTATATAAAAAAGGAGCAATTA 40 45 1 AAAAAGGAGC 0.918109 -15 ********** Masking position 3 Map Score: 17.2811 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 54 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 GTTTTTCGCGACAATCTGGCGTTTTTCTTGCTAATTCC 5 166 1 AAATCTTTTT 0.970631 -135 AATCTGCGGTAGAATATGGCTAATTTTTT 22 2 0 AAATCATTTT 0.87731 -134 CAAAGGGGACTAAATGTCCCCTTTTTATCGATATAAAT 23 31 1 TAATCTTTTT 0.748193 -86 GTGTACTACTATAATAGTGCAAATTTATTTTAGAGGCA 23 85 1 AAATCATTTT 0.87731 -32 ATGGTTGGGGAAAATAACGCATTTTTATAGAATTCTCA 24 32 1 AAATCTTTTT 0.922758 -140 ACATAAGGTAAAAATGCGACCATTTTTGACCGCACTTT 25 17 0 AAATCTTTTG 0.950702 -98 TTATCCTTTTACAATCGGTCGAATTTTGCAAAAATACG 30 34 0 AAATCATTTG 0.871001 -32 GATTTCCAGTAGAATGAGGCGCTTTTATAAATAAGGAA 36 268 1 AAATCTTTTT 0.970631 -33 AAAAGATAAAAAAATACCGCACTTTTGTGCTGTACTCT 38 16 0 AAATCTTTTT 0.922758 -202 AAAATCGGCTAGAATACGCCGATTTTATTTTCGGTGAC 42 73 1 AAATCTTTTT 0.971366 -34 GAAAGTGATCAAAATTGCTCACTTTTTTCAGTCTTAAG 43 16 1 AAATCTTTTT 0.971784 -237 GAAATGATTAAAAATTGAACTATTTAATTAGGAGGGAA 43 62 0 AAATCTTTAT 0.74819 -191 TTTTTTCTTGAAGATCAGGCTGTTTTGGCAAATCAAAA 43 202 0 AGATCTTTTG 0.709779 -51 TATAATCTTGCGGTTTTTTAGGAGTCGAT 44 2 1 AAATCTTTTT 0.970631 -31 CGTTTAATCTAAAATTGGTCATATTTAGTCCTATAAAA 46 47 1 AAATCATTTG 0.870997 -238 ATTTTTATCAAAAATCAATCTTTATTGTTGTGAGAAAA 46 127 0 AAATCTATTT 0.747538 -158 * *** * **** * Masking position 5 Map Score: 19.7436 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 27 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 6 CACAGGCAATTTAGTCGCGCTTTCAACCCT 9 41 0 TTAGTCGCGC 0.784953 -130 CGGGGGGCTTTTAACCGGGCAGGACGCCTT 12 36 1 TTAACCGGGC 0.917135 -73 AAGCCTCTCATTAGCCGCGCGAACCTCTGC 13 116 0 TTAGCCGCGC 0.973845 -62 TCAGCGTAAATTAACCGCACTTTTCTCGAA 22 87 1 TTAACCGCAC 0.987296 -49 GCGACCATTTTTGACCGCACTTTATATCG 25 10 0 TTGACCGCAC 0.97435 -105 ACGACAAAAATTAACCGCTCTTTCAA 30 7 0 TTAACCGCTC 0.950427 -59 TTTACTCGTTTTAACCGCACTTTAGCGGCA 39 125 0 TTAACCGCAC 0.987296 -22 GCGGTCAAAATTAACCGCACTTTTGATGAA 40 13 0 TTAACCGCAC 0.987296 -47 GCGGTTAATTTTGACCGCACTTTGTATATA 40 25 1 TTGACCGCAC 0.97435 -35 ********** Masking position 2 Map Score: 14.0863 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 102 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 TCCCTTCCGAGCAGTCTGATGCGG 4 2 0 GCGTTGTGCG 0.88533 -256 TATCTGCGGCGCAGGTTAAGGCATAACGGCTGC 8 135 0 GCGGTAGGCA 0.977483 -56 AGGGTTCCATGCGGGATAAGGCGTTTACGCTGC 15 18 1 GCGGTAGGCG 0.985685 -146 GGCAATCCATGCCGGATGCAGCGTAAACGCCTT 15 35 0 GCGGTGAGCG 0.988411 -129 CGTTTCAGGCGCGGGGTGGAGCAGCCTGGTAGC 18 25 1 GCGGTGAGCA 0.981742 -276 AACCGCAACTGCGGTCTGGAGCACTTTCCAGAA 18 182 0 GCGTTGAGCA 0.924806 -119 GATTGTCTGTGCCGGATGCGGCGTGAATGCCTT 21 27 1 GCGGTGGGCG 0.994355 -226 GATTTTATTGGCCGGATAAGGCATTCACGCCGC 21 44 0 GCGGTAGGCA 0.977483 -209 ** ** ** **** Masking position 7 Map Score: 9.29467 Number of sites scoring better than the average of aligned sites = 599 Number in coding regions = 270 Number in noncoding regions = 329 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 8 TAAGTGGAATTTTTTCTTTACAATCGAAATTGT 2 84 1 TTTTTTACAA 0.697521 -99 AGAGATCTCGTTTTTCGCGACAATCTGGCGTTT 5 157 1 TTTTTCACAA 0.963389 -144 AGCAGGAAGGTTTCTGTCAACAATCATTGACAC 7 69 0 TTTCTCACAA 0.855205 -79 TGACAAAAAATTTTTTTACAAAATCTTTTCAAT 22 45 1 TTTTTAAAAA 0.789068 -91 TTCTAATAAATTTTTCGAGAAAAGTGCGGTTAA 22 97 0 TTTTTAAAAA 0.87237 -39 CTCGAAAAATTTATTAGAAACAAAAGGATTTCA 22 111 1 TTATTAACAA 0.761139 -25 CTATGATAATTTCTTTACAACAAAGTGTAAATA 25 62 0 TTCTTCACAA 0.789041 -53 AAAAACACAATTTTTTTCAAAAAAATTGCTTTT 26 26 1 TTTTTCAAAA 0.512203 -275 ATTAGTTTTTAAACACAACATTATAAGG 34 6 1 TTTTTAACAA 0.927425 -31 TATCCTTTACTTTTTCCCTAAAAATAGATTAGA 35 110 0 TTTTTCAAAA 0.931022 -122 TTTTCTTAATTTATTACCTAAAATGTTGCGCGA 35 206 0 TTATTCAAAA 0.783783 -26 TAATGTGTGATTTTTATCGACAATCTTGGTCGT 36 88 1 TTTTTCACAA 0.962998 -213 CTTAATACTGTTTTTCGATAAAATGACACCTGA 36 204 0 TTTTTAAAAA 0.87237 -97 TTTGTAGGTTTTATTCTAAAAAAACATATCGAA 38 118 1 TTATTAAAAA 0.632527 -100 AATTGCTCCTTTTTTATATACAAAGTGCGGTCA 40 36 0 TTTTTAACAA 0.927425 -24 AGAAAGGTATTTTCTCACAACAATAAAGATTGA 46 118 1 TTTCTCACAA 0.86028 -167 TATTTCTTGATTTTTATCAAAAATCAATCTTTA 46 141 0 TTTTTCAAAA 0.607657 -144 ***** * **** Masking position 5 Map Score: 16.2513 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 62 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 9 ACTATACCAATAAATATTCAAGAATGAAGTGTAA 2 25 0 TAAATTAAAA 0.735021 -158 TTCATCCCGTGAAATAAGGAAGAACG 3 34 1 GAAATAAAAA 0.854916 -16 TAGAAAAACATGAATTATGAAAAATGTGACGCAG 4 58 0 TGAATAAAAA 0.757024 -200 AGAGAATCTTGAAATAATTAACAAACAAAGGAGT 5 104 1 GAAATAAAAA 0.854916 -197 GATTAATCCTGGAATTAGCAAGAAAAACGCCAGA 5 180 0 GGAATAAAAA 0.681854 -121 AACCTTCACCTGAAAAAAGAACAATTAATATGAT 7 121 0 TGAAAAAAAA 0.634804 -27 GGTGTAAATATAAATGTACAATAAAAAGCATTCA 8 78 0 TAAATTAAAA 0.73502 -113 AATAAAATCCTAAAAATTCAATAAGTTGATGTTC 21 68 1 TAAAATAAAA 0.607471 -185 AAATACACTTTAAAATTAAAAAAAGCAATTTTTT 26 45 0 TAAAATAAAA 0.607471 -256 ATCTCAACTTTAAAATAGGAAAAACATT 26 283 1 TAAAAAAAAA 0.826966 -18 ACTCGCCATTTAAATAATCAATATCTCAAAATGC 27 28 1 TAAATAAAAT 0.563792 -65 TTTTAGGTAATAAATTAAGAAAATCA 35 216 1 TAAATAAAAT 0.563792 -16 GGCGCTTTTATAAATAAGGAATAACT 36 285 1 TAAATAAAAA 0.895465 -16 ATTAAGTAAATAAAAGATAAAAAAATACCGCACT 38 31 0 TAAAAAAAAA 0.826966 -187 TGGGTAAATCACAAATAAAGCGTCTGAG 42 5 1 TAAATAAAAA 0.895465 -102 TACTGGGTGTGAAATGATTAAAAATTGAACTATT 43 76 0 GAAATAAAAA 0.854916 -177 TTTAAATACAGAAAATAATAAGAATAGTTTTTAT 46 171 0 GAAAAAAAAA 0.766767 -114 ***** * ** ** Masking position 10 Map Score: 9.71357 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 70 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 10 GAAACCTCGTGCGGTGGTTGTTTTTTT 1 284 0 CGTGCGGTGG 0.8147 -17 ATGCCGTGCACGTCTGCTGCTACGCTTTTT 4 151 1 CGTCTGCTGC 0.91864 -107 ATTTCAAGATTCTCTGCTGCGTTTCATAAC 5 89 0 TCTCTGCTGC 0.879511 -212 TGCTGTCCTGTGCTGCTCTGAAGACC 6 140 0 CCTGTGCTGC 0.978644 -16 AGCATTCAGTCCTGCGCTGGCGCAAAGTCT 8 56 0 CCTGCGCTGG 0.913429 -135 TATGCCTTAACCTGCGCCGCAGATATCACT 8 143 1 CCTGCGCCGC 0.977891 -48 TGCCATTTGCCCTCCGCTGCGGCGGGGGGC 12 14 1 CCTCCGCTGC 0.978862 -95 TATTTGATTGTCTGTGCCGGATGCGGCGTG 21 22 1 TCTGTGCCGG 0.857506 -231 AAAGGTCGTGCCTCTGGCGGATGTACGTTT 21 116 1 CCTCTGGCGG 0.882263 -137 ********** Masking position 3 Map Score: 4.48048 Number of sites scoring better than the average of aligned sites = 591 Number in coding regions = 573 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 11 CGGGTGCATTCGCTGCCGCATACCATTATT 1 148 1 CGCTGCCGCA 0.97496 -153 TTTCAAGATTCTCTGCTGCGTTTCATAACC 5 88 0 CTCTGCTGCG 0.793965 -213 TTCAGTCCTGCGCTGGCGCAAAGTCTTCAT 8 52 0 CGCTGGCGCA 0.975313 -139 TGCATAACAACGCAGTCGCACTATTTTTCA 10 118 1 CGCAGTCGCA 0.916599 -36 ATTTGCCCTCCGCTGCGGCGGGGGGCTTTT 12 18 1 CGCTGCGGCG 0.783898 -91 CCTGATGTGACGCTGGCGCGTCTTATCAGG 15 66 1 CGCTGGCGCG 0.979849 -98 TGCTCCAGACCGCAGTTGCGGTTATAGGGT 18 192 1 CGCAGTTGCG 0.679236 -109 ********** Masking position 5 Map Score: 3.82818 Number of sites scoring better than the average of aligned sites = 1036 Number in coding regions = 935 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 12 AATTTTGTGATTTTTAATTCAATTAAAACGAATTTAA 1 26 1 TTTTTCATTA 0.9054 -275 GACGGAAGTCTTTTTGTAACAATTCAAACTTCTTTGA 1 186 1 TTTTACATTA 0.45023 -115 CTGAATGCTTTTTATTGTACATTTATATTTACACCAT 8 77 1 TTATTCATTA 0.420062 -114 TTTCAATCCATATTTCGTACATTTTTATTTACACAGG 9 65 0 TTTTTCATTA 0.905402 -106 ATCGGGGCTTTTTTTCTGTCTTTTGTACTCGTGTACT 10 69 1 TTTTGCTTTA 0.734843 -85 AAGTTGATGTTCTTTCATGCTCTTATAAAGGTCGTGC 21 90 1 TTTTTCTTTA 0.922326 -163 AAAAATTGTGTTTTTAGTACATTTTTACTA 26 4 0 TTTTTCATTA 0.905402 -297 TTAAAGTGTATTTTTAAGGCAATATAAGATCTAATAA 26 66 1 TTTTGCATAA 0.340661 -235 ACTCGGAAGATATTTTATTATCTTCCAAACATACAAT 26 180 0 TTTTTATTTA 0.542288 -121 TTTACACTGATTTTTATTACACTCGGAAGATATTTTA 26 200 0 TTTTTCATCA 0.564952 -101 TTCCGAGGGGTATTTATTGCTTTTACACTGATTTTTA 26 221 0 TTTTTCTTTA 0.922326 -80 ACATATTTCGTATTGTTGTATGAAAATTTG 28 49 0 TTTTTTTTTA 0.542288 -20 TTTTTTATCCTTTTACAATCGGTCGAA 30 49 0 TTTTTCTTTA 0.922326 -17 TGTGTTTGATCCTGTATGACTATATGATC 31 17 0 TTTTTCTTAA 0.733094 -19 AAAAGTGCGGTATTTTTTTATCTTTTATTTACTTAAT 38 28 1 TTTTTATTTA 0.542288 -190 TAATTGCTCCTTTTTTATATACAAAGT 40 43 0 TATTTCTTTA 0.47331 -17 AAATTGGTCATATTTAGTCCTATAAAAAAAATAATAA 46 58 1 TTTTTCTTAA 0.733095 -227 CTATTCTTATTATTTTCTGTATTTAAACCTGCTTGTT 46 178 1 TTTTTTATTA 0.488477 -107 * *** * ** ** * Masking position 5 Map Score: 6.54677 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 73 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 13 GCTACGCTTTTTGTCATTTGTAGCACAAGTA 4 169 1 TTGTCATTGT 0.92167 -89 ACTGCCCGTGTTGTCATCGACCGGCGAACTC 6 54 0 TTGTCATCAC 0.733275 -102 GGTTGCCATTTGCCCTCCGCTGC 12 3 1 TTGCCATTGC 0.967418 -106 TGGGTTAGGGTTGTCATTAGTCGCGAGG 13 160 1 TTGTCATTGT 0.92167 -18 GGATGTACGTTTGTCATGAGTCTCACTCTGT 21 134 1 TTGTCATGGT 0.733275 -119 CTGTTGCTAATTGCCGTTCGCTCCTGAACAT 21 161 1 TTGCCGTTGC 0.927363 -92 AAAAAATTTTTTGTCATTAACAATCTGCGGT 22 30 0 TTGTCATTAC 0.92167 -106 GGTATGAGGTTTATCATTTGCTTTATACAAA 29 64 0 TTATCATTGC 0.78464 -48 TTTATTAAATTTGTCATTTACACACAGGTGC 35 70 0 TTGTCATTAC 0.92167 -162 TTGCCGTTAGCCCAAGCATAA 46 1 1 TTGCCGTTGC 0.927363 -284 ******** ** Masking position 7 Map Score: 2.94688 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 240 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 14 TACAAAAAGACTTCCGTCAGATCAAGAATA 1 174 0 CTTCCGTCAG 0.983211 -127 CGGATAACCTCTTCCAACAGTGCATTTGCA 5 23 1 CTTCCAACAG 0.899814 -278 CAATCTATATCTTCCGTCAGAATGTGTAAA 5 235 0 CTTCCGTCAG 0.983211 -66 CAGTGAATTGCTGCCGTCAGCTTGAAAAAA 13 49 0 CTGCCGTCAG 0.90157 -129 GTGAACAGCCCTTCCACCTGAAATTAATTT 15 101 1 CTTCCACCTG 0.858097 -63 GACAAACGTACATCCGCCAGAGGCACGACC 21 119 0 CATCCGCCAG 0.946578 -134 ********** Masking position 5 Map Score: 1.49186 Number of sites scoring better than the average of aligned sites = 412 Number in coding regions = 400 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 15 GCATAACGGCTGCTTCGTCAAACCGACGTTA 8 117 0 TGCTTGTCAA 0.922124 -74 TGAATGCTTTGACAACATTACAAAG 23 5 1 TGCTTGACAA 0.922124 -112 TTAGAAGATTTGTTTGGGCAATTCAATATCA 32 41 1 TGTTTGGCAA 0.954296 -41 TACACACAGGTGCTTTGGCAAAAATAAAATT 35 52 0 TGCTTGGCAA 0.984075 -180 AAGATCAGGCTGTTTTGGCAAATCAAAAACA 43 199 0 TGTTTGGCAA 0.954296 -54 TATTCCGTTATGCTTGGGCTAACGGCAA 46 8 0 TGCTTGGCTA 0.938441 -277 ***** ***** Masking position 5 Map Score: 2.41724 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 22 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617