AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00010_hinf_reg_100.orf -o00010_hinf_100.ace -a/home/amcguire/genomes/ORF_hinf.txt -z/home/amcguire/genomes/hinf.fna -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HI0185 122 alcohol dehydrogenase, class III (adhC) #2 HI0448 71 PTS system, fructose-specific IIA/FPr component (fruB) #3 HI0449 86 H. influenzae predicted coding region HI0449 #4 HI0451 71 conserved hypothetical protein #5 HI0452 50 conserved hypothetical protein #6 HI0453 26 conserved hypothetical protein #7 HI0454 54 conserved hypothetical protein #8 HI0457 69 conserved hypothetical protein #9 HI0458 70 stationary phase survival protein SurA, putative #10 HI0459 131 pyrimidine operon regulatory protein (pyrR) #11 HI0524 110 fructose-bisphosphate aldolase (fba) #12 HI0525 101 phosphoglycerate kinase (pgk) #13 HI0678 165 triosephosphate isomerase (tpiA) #14 HI0757 175 phosphoglycerate mutase (gpmA) #15 HI0819 37 galactokinase (galK) #16 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) #17 HI0932 120 enolase (eno) #18 HI0982 95 6-phosphofructokinase (pfkA) #19 HI0985 300 DNA processing chain A (dprA) #20 HI1231 113 dihydrolipoamide dehydrogenase (lpdA) #21 HI1232 62 dihydrolipoamide acetyltransferase (aceF) #22 HI1233 299 pyruvate dehydrogenase, E1 component (aceE) #23 HI1573 300 pyruvate kinase, type II (pykA) #24 HI1574 33 replicative DNA helicase (dnaB) #25 HI1576 54 glucose-6-phosphate isomerase (pgi) #26 HI1645 233 fructose-1,6-bisphosphatase (fbp) #27 HI1711 59 PTS system, glucose-specific IIA component (crr) #28 HI1712 79 phosphoenolpyruvate-protein phosphotransferase (ptsI) #29 HI1713 158 phosphocarrier protein HPr (ptsH) Motif number 1 GCAAGTGTTTTTTTATCATTTTTGTTTAAAGGGAAT 1 16 0 TTTTTTTTTT 0.960668 -107 ACCTCAAATTTTTTATGGTTTTATAACATAATTTTG 4 41 0 TTTTTTTTAA 0.938971 -31 GGTCGTTTTCTTTTATATTTTTGAGTA 5 34 1 TTTTTTTTGT 0.894345 -17 ACTTTTCCCTTGTTAGAACTGTGCAT 6 9 0 TTTTTGTTAA 0.859423 -18 TAATTGCCCCTTTTGTTGTTTTTTATTTTCTCTTTC 8 35 1 TTTTTTTTTT 0.960668 -35 TCGTGCTAGGTTGTAACGATTTAGATCAAAGAAATT 12 12 0 TTGTATTTAT 0.728244 -90 ATACAGGTAATTGTAGCTTTTTAGCTCAAGATAATC 13 35 1 TTGTTTTTAT 0.832854 -131 CTGTGAGAATTTTTTTAATTTTATGATCTTCTGCAA 13 77 1 TTTTTTTTAA 0.938971 -89 GATTTGCGAGTTTTACGAATTTAGGATGAATT 14 7 0 TTTTATTTAA 0.892183 -169 CCATCAAACTTTTTCGCCTTTTAACAAATATGATAA 14 43 0 TTTTTTTTAA 0.938971 -133 AACTTTTTCCTTGTTATAATCTATAAATC 16 4 1 TTTTTGTTAA 0.859423 -204 TAAGCAAAATTTTTTATGATTTAGTTCATACTTATG 16 89 0 TTTTATTTAT 0.948006 -119 TCATAAAAAATTTTGCTTATTTTCTTATTTTGTGAC 16 106 1 TTTTATTTTT 0.929261 -102 ATAAAGCTATTTTAGATTTTTTCTTGTAAAAAATG 17 34 0 TTTTTTTTT 0.223471 -87 TCAAACTATTTTTTGGCATTTTATATTAAAAATAAA 19 28 1 TTTTTTTTAT 0.971347 -273 AATATGCTAATTTTATTAAGTTTATTAGTTAAATGT 19 87 0 TTTTAGTTTT 0.839228 -214 TCTTATTGGATTTTTTACATTTTCAAAATAAGAAAA 19 153 1 TTTTATTTTA 0.856362 -148 ATAAGAAAAATTTTGCAATTTTTTATTCATTAAAAA 19 180 1 TTTTTTTTTT 0.960668 -121 ATTTTTTCCTTTTTATTTGAAAATCTAG 19 283 0 TTTTTTTTAT 0.971347 -18 GTTTTAAAGTTTTTTCAGATTTTTTTCAAAAAGGAC 22 17 0 TTTTATTTTT 0.929261 -283 GCGGTAATTTTTTTGTGTTTTTTTGTTCGCTAAAAT 22 85 0 TTTTTTTTTT 0.960668 -215 TTTGTTTACTTTTTTGCCAGTTATATCGGGTTTTAA 23 139 0 TTTTAGTTAT 0.878717 -162 TTTTTACCTTTTGGCTTAATAAAGTG 26 1 1 TTTTTTTTGT 0.894345 -233 TTTGAATAAATTTTGGAGTGTTTTTATGCATTTGCG 26 66 0 TTTTTGTTTA 0.81498 -168 ATTTAGCTTATTTTTATGATTTAATTCAGGCTTTTT 29 40 1 TTTTATTTAT 0.948006 -119 AATTTTCTGGTTTTATATTTTTAATTATTGATTAGT 29 121 1 TTTTTTTTAT 0.971334 -38 **** ***** * Masking position 11 Map Score: 40.2159 Number of sites scoring better than the average of aligned sites = 687 Number in coding regions = 479 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 2 TAAAAGAAAACGACCGCACTTTGCGACCGTTT 5 17 0 CACCGCATTT 0.976955 -34 GCCTAAAAAGCGACGGCATTTGCACCATTTTT 10 58 0 CACGGCATTG 0.843183 -74 TTTGTATTGATGATGGCATTTTTGATGCCACC 11 39 0 TATGGCATTT 0.962403 -72 TAGCAAAATTTGACGGGATTTTGATCTACA 18 9 0 TACGGGATTT 0.963269 -87 TCAAACTATTTTTTGGCATTTTATATTAAAAA 19 28 1 TTTGGCATTT 0.805151 -273 CAAATTTTTCTTATTGGATTTTTTACATTTTC 19 145 1 TATTGGATTT 0.725425 -156 TTAAAAATATTGACCGCACTTTTACGGTCTTT 20 74 0 TACCGCATTT 0.990861 -40 CAATGTTTTTTGACCGCAGTTTTCATCAA 21 8 0 TACCGCATTT 0.990854 -55 TTGTGTTTTATGACCGCACTTTAAAAGGAACA 21 37 1 TACCGCATTT 0.990861 -26 CACAAAAAAATTACCGCACTTTCAAATAATTA 22 104 1 TACCGCATTT 0.990861 -196 TCACTGCATTTTTTGAACAGAG 25 1 1 TACTGCATTT 0.97884 -54 TTTCTGGAATTTTTATTAGGGA 25 43 0 TTCTGGATTT 0.643699 -12 TGGGCTACCATAACCGCACTTTATTAAGCCAA 26 21 0 TACCGCATTT 0.990818 -213 TTCACATTTATTACTGCAATTTTTAGAAACTA 26 111 0 TACTGCATTT 0.978751 -123 GTGTAAACTCTAATGGCAGATTATCAGAATGA 26 161 0 TATGGCAATT 0.686504 -73 AAAAAGGATACTAGGGCAATTTTCTGGTTTTA 29 104 1 CAGGGCATTT 0.818478 -55 * ****** *** Masking position 8 Map Score: 23.0127 Number of sites scoring better than the average of aligned sites = 1362 Number in coding regions = 900 Number in noncoding regions = 462 Number of orfs with sites within 600 bp upstream = 307 Fraction of orfs with sites within 600 bp upstream = 0.0493093 Motif number 3 TAAAGCAAGTGTTTTTTTATCATTTTTGTTTAA 1 23 0 GTTTTTTTAT 0.961386 -100 CTTTTTAGGCGTATTTTCTTTATACTTTGTGCA 10 80 1 GATTTTCTAT 0.835962 -52 AATTGGTTATTTTTTATTGGTTCCATA 13 5 1 GTTATTTTAT 0.913151 -161 CTTTCTGTGAGAATTTTTTTAATTTTATGATCT 13 73 1 GATTTTTTAT 0.938043 -93 TAAAGCTAAGGATTTTTTGCTATAAAATGTGCG 14 121 1 GTTTTTTCAT 0.888207 -55 AGAATCTCCTAATTTTTTCAAATAAAAAGAACG 14 152 0 ATTTTTTAAT 0.718311 -24 ATTTATCGTAAATTATTTATGATCAAAATATAA 16 40 0 ATTATTTTAT 0.767856 -168 AAATAAGCAAAATTTTTTATGATTTAGTTCATA 16 95 0 ATTTTTTTAT 0.886782 -113 AAAGATCACGGTTTATTTACAATAATTTAGTAT 16 142 1 GTTATTTCAT 0.770391 -66 CAAAGCATACGCATTTTTTACAAGAAAAAATCT 17 23 1 GATTTTTAAA 0.511245 -98 GTGTAAGTAGGTTTATTTTTAATATAAAATGCC 19 42 0 GTTATTTTAT 0.913151 -259 CCTAATCAACAAATTTTTCTTATTGGATTTTTT 19 136 1 AATTTTTTAT 0.826478 -165 TTTTCTTATTGGATTTTTTACATTTTCAAAATA 19 150 1 GATTTTTAAT 0.831341 -151 AAAAATTGCAAAATTTTTCTTATTTTGAAAATG 19 170 0 AATTTTTTAT 0.826478 -131 TCATTAAAAAGAATTTTTGCGATCTGCATCGCA 19 206 1 GATTTTTCAT 0.828515 -95 TTTGTTTTAAAGTTTTTTCAGATTTTTTTCAAA 22 23 0 ATTTTTTAAT 0.718311 -277 TAAAGATAGTGAATTTTCATCAAATCATCATAT 22 156 0 GATTTTCTAA 0.519568 -144 AATTTTAGAAGATTTTTTGAGATAAAGATAGTG 22 178 0 GTTTTTTAAT 0.89018 -122 TTGAACACAAGTATTTTTCTTAAAACCCGATAT 23 120 1 GATTTTTTAA 0.762634 -181 AGAAACTATCGCTTATTTTTGAATAAATTTTGG 26 86 0 GTTATTTTAA 0.69052 -148 AATAAATGTGAATTTTTTGTGATAAAGATCTCA 26 131 1 ATTTTTTTAT 0.886782 -103 ATTTCCTTTTAGTTTTTCATAATACGTTGATCA 26 210 0 ATTTTTCTAT 0.725004 -24 AAGCTAAATAGTTTATTTATTATTCACAATCTC 29 16 0 GTTATTTTAT 0.913151 -143 GCTTTTTAGTGTTTATTCTTGATTATTTTGCTT 29 69 1 GTTATTCTAT 0.77969 -90 * ****** * ** Masking position 7 Map Score: 24.6478 Number of sites scoring better than the average of aligned sites = 539 Number in coding regions = 389 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 4 TACGTAAGGCAACTTTGTCAATGAATTAAG 1 93 1 AACTTTGTCA 0.767271 -30 TTTTCCCAGCTTTATCAATAGTATTTC 10 115 0 AGCTTTATCA 0.96283 -17 TGATTTCCTGATCTTTAGCAAAAAATAACC 14 77 0 ATCTTTAGCA 0.923605 -99 ATAGCAAAAAATCCTTAGCTTTAAAAGTTA 14 114 0 ATCCTTAGCT 0.684815 -62 CTCCCTCTTTAGCTTTAGCAAAGAGGG 15 21 1 AGCTTTAGCA 0.941818 -17 ATAAACCGTGATCTTTGTCACAAAATAAGA 16 128 0 ATCTTTGTCA 0.940759 -80 GTATGCTTTGATCTTTATCTAT 17 3 0 ATCTTTATCT 0.909187 -118 ATCTYAAAATAGCTTTATCATATCGCCTGT 17 52 1 AGCTTTATCA 0.96283 -69 ATATCAAATCAGCTTTGCCATAAATAATTA 22 130 0 AGCTTTGCCA 0.832752 -170 AAAATTCACTATCTTTATCTCAAAAAATCT 22 172 1 ATCTTTATCT 0.909187 -128 ATTCGTGTTTAGCCTTGTCTAAACTAATAT 22 253 1 AGCCTTGTCT 0.79297 -47 TCAGAATGAGATCTTTATCACAAAAAATTC 26 140 0 ATCTTTATCA 0.950747 -94 ********** Masking position 1 Map Score: 13.2889 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 89 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 TATGTTATAAAACCATAAAAAATTTGAGGTT 4 47 1 AACCAAAAAA 0.973831 -25 AGAAAATAAAAAACAACAAAAGGGGCAATTA 8 35 0 AAACACAAAA 0.712794 -35 TAGTATAACGAACAAGAAAAATGGTGCAAAT 10 42 1 AACAAAAAAA 0.78782 -90 TTATCCCGCTAAACATAAAAAGGAAACACAA 11 88 1 AAACAAAAAA 0.929472 -23 ACCTGTATGGAACCAATAAAAAATAACCAAT 13 12 0 AACCATAAAA 0.950412 -154 GTATGAACTAAATCATAAAAAATTTTGCTTA 16 94 1 AATCAAAAAA 0.85148 -114 TAGCATATTTAACCAATACAACCCTAATCAA 19 114 1 AACCATACAA 0.708508 -187 TCGCTAAAATAACCAGTAAAATATTGCATTC 22 64 0 AACCATAAAA 0.950412 -236 GCGAACAAAAAAACACAAAAAAATTACCGCA 22 91 1 AAACAAAAAA 0.929472 -209 GCTACATATTAGCCAGATAAAAAATCGGTGC 23 231 0 AGCCAATAAA 0.554594 -70 ACGTATTATGAAAAACTAAAAGGAAATT 26 216 1 AAAAATAAAA 0.403776 -18 TTCTTACTTAGCCATAAAATTGTGAAATTT 28 10 1 AGCCAAAAAT 0.783497 -70 AATAAACAATAGCCATAAAATTTCACAATTT 28 27 0 AGCCAAAAAT 0.783497 -53 GCCTGAATTAAATCATAAAAATAAGCTAAAT 29 40 0 AATCAAAAAA 0.85148 -119 AATCAAGAATAAACACTAAAAAGCCTGAATT 29 62 0 AAACATAAAA 0.871589 -97 AAAAATATAAAACCAGAAAATTGCCCTAGTA 29 112 0 AACCAAAAAT 0.902482 -47 ***** ***** Masking position 5 Map Score: 13.1379 Number of sites scoring better than the average of aligned sites = 348 Number in coding regions = 276 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 6 TCATTTTTGTTTAAAGGGAATAAAAA 1 7 0 TTAAAGGGAA 0.957464 -116 TGTCAATGAATTAAGAGGAAAAACA 1 108 1 TTAAGAGGAA 0.906408 -15 CCTTAATAATTTAAAAAGAAAGCTGCGGAT 2 45 0 TTAAAAAGAA 0.859214 -27 ATTATACTGTCTAAAGGGGATTAAGCAAGG 3 39 0 CTAAAGGGGA 0.839278 -48 CATCAATATGTTATAGAGGAAAAGTGCGG 11 10 0 TTATAGAGGA 0.401951 -101 CCGCTAAACATAAAAAGGAAACACAAGT 11 93 1 TAAAAAGGAA 0.907763 -18 GCTTTAAAAGTTAAAAGGGATGATTTCCTG 14 97 0 TTAAAAGGGA 0.957464 -79 TTGCTAAAGCTAAAGAGGGAGACTGACTAT 15 12 0 TAAAGAGGGA 0.695411 -26 TTTTTATTCATTAAAAAGAATTTTTGCGAT 19 199 1 TTAAAAAGAA 0.859214 -102 GATTTTCAAATAAAAAGGAAAAAAT 19 286 1 TAAAAAGGAA 0.907763 -15 TGACCGCACTTTAAAAGGAACAAAAA 21 47 1 TTAAAAGGAA 0.968409 -16 CGTTGATCAATTATAGGGAATCTGGAGTGT 26 189 0 TTATAGGGAA 0.821347 -45 TTATGAAAAACTAAAAGGAAATT 26 221 1 CTAAAAGGAA 0.906408 -13 ********** Masking position 3 Map Score: 11.9129 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 94 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 7 CGTAAGGCAACTTTGTCAATGAATTAAGAG 1 95 1 CTTTGTCAAT 0.794417 -28 TTTTCCCAGCTTTATCAATAGTATTTCAA 10 113 0 CTTTATCAAT 0.909648 -19 ATTTTATGATCTTCTGCAAAGAATAGGGGC 13 94 1 CTTCTGCAAA 0.643514 -72 ATTTCCTGATCTTTAGCAAAAAATAACCAT 14 75 0 CTTTAGCAAA 0.958382 -101 CCCTCTTTAGCTTTAGCAAAGAGGG 15 23 1 CTTTAGCAAA 0.958382 -15 AAACCGTGATCTTTGTCACAAAATAAGAAA 16 126 0 CTTTGTCACA 0.870615 -82 ATGCTTTGATCTTTATCTAT 17 1 0 CTTTATCTAT 0.672818 -120 CTYAAAATAGCTTTATCATATCGCCTGTTT 17 54 1 CTTTATCATA 0.815252 -67 AAAGAATCTGCTCTAGCAAAATTTGACGGG 18 24 0 CTCTAGCAAA 0.784116 -72 CCTACTTACACTTCATCAAATATACATTTA 19 64 1 CTTCATCAAA 0.908318 -237 AATTCACTATCTTTATCTCAAAAAATCTTC 22 174 1 CTTTATCTCA 0.781701 -126 AGAATGAGATCTTTATCACAAAAAATTCAC 26 138 0 CTTTATCACA 0.94604 -96 CCCTAGTATCCTTTTTCAAAGCAAAATAAT 29 90 0 CTTTTTCAAA 0.886122 -69 ********** Masking position 2 Map Score: 8.71482 Number of sites scoring better than the average of aligned sites = 316 Number in coding regions = 279 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 TGCTTACTATACCAAAATTTCGCCCCTATT 13 115 0 ACCAAAATTT 0.952613 -51 TAAGAAAATAAGCAAAATTTTTTATGATTT 16 103 0 AGCAAAATTT 0.961391 -105 AATCTGCTCTAGCAAAATTTGACGGGATTT 18 20 0 AGCAAAATTT 0.961391 -76 AAATCCAATAAGAAAAATTTGTTGATTAGG 19 136 0 AGAAAAATTT 0.709398 -165 AATAAAAAATTGCAAAATTTTTCTTATTTT 19 177 0 TGCAAAATTT 0.973302 -124 CCCGATGGAATGCAATATTTTACTGGTTAT 22 57 1 TGCAATATTT 0.836858 -243 CAAAAAATCTTCTAAAATTTACAAGATTTG 22 192 1 TCTAAAATTT 0.742619 -108 GTTTTTGATTTCCAAAAGTTTTAAGCGTAT 23 196 1 TCCAAAAGTT 0.859902 -105 CGTCAATAATTACAAAATTTTAAAGGTGTT 23 272 0 TACAAAATTT 0.849392 -29 ATAAAAACACTCCAAAATTTATTCAAAAAT 26 75 1 TCCAAAATTT 0.967139 -159 ********** Masking position 5 Map Score: 7.45224 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 151 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 9 AATGAATTAAGAGGAAAAACA 1 112 1 GAGGAAAAAA 0.903896 -11 CAGTTCTAACAAGGGAAAAGT 6 16 1 AAGGGAAAAT 0.707286 -11 CCTTAGGCATAAGGAAAAATAATT 7 41 1 AAGGAAAAAA 0.964461 -14 CATTCCATCAAAGGAAACCAAATT 10 4 0 AAGGAAACCA 0.867084 -128 TAAACATAAAAAGGAAACACAAGT 11 97 1 AAGGAAACAA 0.938163 -14 AGATTATAACAAGGAAAAAGTT 16 2 0 AAGGAAAAAT 0.933666 -206 TAACTTAATTGAGGAAAATAAAA 17 108 1 GAGGAAAATA 0.723336 -13 TTCAAATAAAAAGGAAAAAAT 19 290 1 AAGGAAAAAT 0.933666 -11 CGCACTTTAAAAGGAACAAAAA 21 51 1 AAGGAACAAA 0.823284 -12 AAAACAGATTAAGGAAAACCT 22 289 1 AAGGAAAACT 0.858199 -11 ACTGGCAAAAAAGTAAACAAAACCAGCTTAA 23 154 1 AAGTAAACAA 0.678245 -147 ATATGTAGCGAAGTAAAATAACACCTTTAAA 23 253 1 AAGTAAAATA 0.511754 -48 ********* * Masking position 6 Map Score: 6.62796 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 182 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 10 AGAAATGGATAAAAATTTACCGCACTT 4 7 0 AAAAATTTAC 0.812912 -65 TGGAACCAATAAAAAATAACCAATT 13 5 0 AAAAAATAAC 0.860297 -161 AGCTAAAAAGCTACAATTACCTGTATGGAAC 13 30 0 CTACAATTAC 0.680203 -136 CATAAAATTAAAAAAATTCTCACAGAAAGAT 13 71 0 AAAAAATTCC 0.812668 -95 TCCATAGTTGATAAAATTAACTTGCTTACTA 13 136 0 ATAAAATTAC 0.892735 -30 GATCTTTAGCAAAAAATAACCATCAAACTTT 14 67 0 AAAAAATAAC 0.860297 -109 TTTTTATTTGAAAAAATTAGGAGATTCTT 14 157 1 AAAAAATTAG 0.575401 -19 TTCATCAAATATACATTTAACTAATAAACTT 19 75 1 ATACATTTAC 0.574952 -226 AATAAACTTAATAAAATTAGCATATTTAACC 19 97 1 ATAAAATTAC 0.892735 -204 TTTTTGTTCGCTAAAATAACCAGTAAAATAT 22 71 0 CTAAAATAAC 0.572827 -229 AAAAAACACAAAAAAATTACCGCACTTTCAA 22 98 1 AAAAAATTAC 0.941723 -202 TGCTTTTCACAAACATTTAACAAATCTTGTA 22 211 0 AAACATTTAC 0.724243 -89 AAAATTTATTCAAAAATAAGCGATAGTTTCT 26 88 1 CAAAAATAAC 0.722504 -146 TCTTTATCACAAAAAATTCACATTTATTACT 26 128 0 AAAAAATTCC 0.812668 -106 ATACCTTCCGAAACAATTAACAAAGTAATAA 28 57 0 AAACAATTAC 0.907129 -23 ********* * Masking position 5 Map Score: 11.6944 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 246 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 11 ACGCCGCCATTATACTGTCTAAAGGGGATTAAG 3 44 0 TATCTCTAAA 0.548403 -43 TCTTGTTCGTTATACTATCCAAAACATTCCATC 10 26 0 TATCTCCAAA 0.903489 -106 AATTGTAGCTTTTTAGCTCAAGATAATCATCTT 13 43 1 TTTATCAAGA 0.667702 -123 ATTTCGCCCCTATTCTTTGCAGAAGATCATAAA 13 96 0 TATCTGCAGA 0.812559 -70 TGTGCGTTCTTTTTATTTGAAAAAATTAGGAGA 14 148 1 TTTATGAAAA 0.649741 -28 TCGTAAATTATTTATGATCAAAATATAAGATTT 16 35 0 TTTTTCAAAA 0.47028 -173 AATGTAATCGTTTACATTGATAAAAAACAGGAG 16 180 1 TTTCTGATAA 0.41357 -28 TGCAATTTTTTATTCATTAAAAAGAATTTTTGC 19 193 1 TATCTAAAAA 0.448506 -108 TTAAAAGCATTTTGCGATGCAGATCGCAAAAAT 19 218 0 TTTCTGCAGA 0.855439 -83 ATTTTTTCCTTTTTATTTGAAAATCTAGTATGG 19 278 0 TTTATGAAAA 0.649741 -23 TCTAAACTAATATTCACTCAAAACAGATTAAGG 22 270 1 TATCTCAAAA 0.902078 -30 CTGAGCCGTTTTTGATTTCCAAAAGTTTTAAGC 23 189 1 TTTATCCAAA 0.740794 -112 CGGTGCACATTATACGCTTAAAACTTTTGGAAA 23 204 0 TATCTTAAAA 0.454993 -97 TTTTTATGCATTTGCGCTCCAAATAAACTTGGG 26 49 0 TTTCTCCAAA 0.927304 -185 GCCATTAGAGTTTACACTCCAGATTCCCTATAA 26 176 1 TTTCTCCAGA 0.900339 -58 TTTAATCTCCTATCCATTCAAGATGGTTGCTAT 27 37 0 TATCTCAAGA 0.867975 -23 TCTTGATTATTTTGCTTTGAAAAAGGATACTAG 29 85 1 TTTCTGAAAA 0.793403 -74 *** * ****** Masking position 8 Map Score: 7.16548 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 196 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 12 TCTTCAAATTGTGGGCTTATCCCGCTAAACATA 11 72 1 GTGGGCATCC 0.906673 -39 AACGGGTTAGGCGAGCCTAAAACAGGCGATATG 17 70 0 GCGAGCAAAC 0.963234 -51 TCATTAATCGGTGGGCTTAAAGCCCACCTACAG 20 12 0 GTGGGCAAAC 0.9908 -102 GAAATCTTTGGTGGGCAGAAACCCATCCTATAA 20 43 1 GTGGGCAAAC 0.990798 -71 GATGAAAACTGCGGTCAAAAAACATTGTGTTTT 21 13 1 GCGGTCAAAC 0.982801 -50 CTTTTAAAGTGCGGTCATAAAACACAATGTTTT 21 31 0 GCGGTCAAAC 0.982801 -32 ****** *** * Masking position 9 Map Score: 2.37318 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 13 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 13 GGGGCTTAATTGCCCCTTTTGTTGTTTTTTAT 8 29 1 TGCCCTTTGT 0.908221 -41 CCAACGTTATTGACTCTTTTTTGGATGAG 9 52 1 TGATCTTTTT 0.945321 -19 CGACGGCATTTGCACCATTTTTCTTGTTCGTT 10 48 0 TGCCCTTTTT 0.962664 -84 ACTTGTGTTTCCTTTTTATGTTTAGCG 11 94 0 TGTTCTTTTT 0.810073 -17 CTATAAAATGTGCGTTCTTTTTATTTGAAAAA 14 140 1 TGCTTTTTTT 0.809432 -36 TTTGACTCCTGTTTTTTATCAATG 16 194 0 TGATCTGTTT 0.765026 -14 ATCGTTTCTCTCCCTCGTTTTTTCCATACTAG 19 255 1 TCCTCTTTTT 0.763016 -46 TGCTGAGTCCTTTTTGAAAAAAATC 22 4 1 TGATCTTTTT 0.945321 -296 CTTAAATAACTGAGCCGTTTTTGATTTCCAAA 23 180 1 TGACCTTTTT 0.941753 -121 GCGTATAATGTGCACCGATTTTTTATCTGGCT 23 220 1 TGCCCATTTT 0.766143 -81 GTAATAAATGTGAATTTTTTGTGATAAAGATC 26 129 1 TGATTTTTGT 0.505498 -105 *** ** ***** Masking position 10 Map Score: 4.81281 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 145 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 14 CTTTAAACAAAAATGATAAAAAAACACTTGCTTT 1 21 1 AAGATAAAAA 0.693067 -102 TTGCTCCTTAATAATTTAAAAAGAAAGCTGCGGA 2 46 0 AATTTAAAAA 0.834813 -26 ACCCGATTAAAGTTAATAAAACGCCGCCATT 3 66 0 TAGTTAATAA 0.74818 -21 TATCCTCTTGTTAAGTTAAAATTAAAATTAAAAT 12 74 0 TAGTTAAAAA 0.964729 -28 CAGAAGATCATAAAATTAAAAAAATTCTCACAGA 13 76 0 TAATTAAAAA 0.822013 -90 CCTTAGCTTTAAAAGTTAAAAGGGATGATTTCCT 14 98 0 AAGTTAAAAG 0.869444 -78 CATTTTCAATTATGGTTAAAAGTAGGTAAATT 18 74 1 TTGTTAAAAA 0.748294 -22 TTTTGGCATTTTATATTAAAAATAAACCTACTTA 19 38 1 TAATTAAAAA 0.776634 -263 AGAGAAACGATTAATTTAAAAGCATTTTGCGATG 19 232 0 TATTTAAAAA 0.866716 -69 TACCTCGTAAAAACGTTAAAAATATTGACCGCAC 20 87 0 AAGTTAAAAA 0.958226 -27 AAATCTGAAAAAACTTTAAAACAAAGCCCGATGG 22 31 1 AATTTAAAAA 0.835041 -269 ATACTTGTGTTCAAGTTAAAAATATCTATAATCA 23 100 0 TAGTTAAAAA 0.967644 -201 AACAATCTAAATATGTTAAAATAAAAGAGCG 24 13 1 AAGTTAAAAA 0.954515 -21 TTATTTGATTTTACGTTAAAATAGCAACCATCTT 27 17 1 TAGTTAAAAG 0.897537 -43 * * ******* * Masking position 8 Map Score: 11.3923 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 60 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 15 ********** No masking Map Score: 1.08027e-11 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