AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iargR_ecoli_bsub_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 carA 300 carbamoyl-phosphate synthetase, glutamine (small) subunit #2 argF 300 ornithine carbamoyltransferase 2, chain F #3 argA 141 N-acetylglutamate synthase; amino acid acetyltransferase #4 argG 300 argininosuccinate synthetase #5 argR 300 repressor of arg regulon; cer-mediated site specific recombination #6 argD 85 acetylornithine delta-aminotransferase #7 pabA 31 p-aminobenzoate synthetase, component II #8 yhfG 104 orf, hypothetical protein #9 ppiA 270 peptidyl-prolyl cis-trans isomerase A (rotamase A) #10 argE_argC 153 argE: acetylornithine deacetylase, argC: N-acetyl-gamma-glutamylphosphate reductase #11 argH 60 argininosuccinate lyase #12 argI 161 ornithine carbamoyltransferase 1 #13 yitV 120 similar to hypothetical proteins #14 yitW 63 similar to hypothetical proteins #15 yitX 54 yitX #16 yitY 57 similar to L-gulonolactone oxydase #17 yitZ 44 similar to multidrug resistance protein #18 argC 206 N-acetylglutamate gamma-semialdehyde dehydrogenase #19 carA 70 carbamoyl-phosphate transferase-arginine (subunit A) #20 ileS 300 isoleucyl-tRNA synthetase #21 ylyA 77 alternate gene name: ylmK; similar to hypothetical proteins from B. subtilis #22 lsp 102 signal peptidase II #23 pyrR 273 transcriptional attenuator and uracil phosphoribosyltransferase activity (minor) #24 pyrP 171 uracil permease #25 pyrB 145 aspartate carbamoyltransferase #26 yodT 300 similar to adenosylmethionine-8-amino-7-oxononanoate aminotransferase #27 ahrC 134 transcriptional regulator #28 yqiE 246 similar to hypothetical proteins #29 yqiC 85 similar to exodeoxyribonuclease VII (small subunit) #30 yqiB 137 similar to exodeoxyribonuclease VII (large subunit) #31 yqhZ 263 similar to transcription termination #32 accB 155 acetyl-CoA carboxylase subunit (biotin carboxyl carrier subunit) #33 spoIIIAC 22 spoIIIAC #34 spoIIIAA 75 spoIIIAA #35 yqhV 144 alternate gene name: yqgE #36 efp 24 elongation factor P #37 yqhS 86 similar to 3-dehydroquinate dehydratase #38 yqhR 226 yqhR #39 argG 169 argininosuccinate synthase #40 moaB 84 molybdopterin precursor biosynthesis protein B #41 ackA 300 acetate kinase #42 rocD 240 ornithine aminotransferase Motif number 1 CCACAAAATAATATAAAAAATCCCGCCATTAAG 1 143 1 AATAAAAACC 0.849064 -158 GCCACTTATTGAATTAAAATTCACTTTATATGT 2 258 0 GATTAAAACA 0.739583 -43 CGAAAAAACAGAATAAAAATACACTAATTTCGA 3 96 1 GATAAAAACA 0.965184 -46 CATTTATTTTGCATAAAAATTCAGTGAGAGCGG 4 235 1 GATAAAAACA 0.965184 -66 CTGACTGTTTGCATAAAAATTCATCTGTATGCA 5 242 1 GATAAAAACA 0.965184 -59 CACAAAATATGCATAAAAAATCACTAAATGGCA 6 19 0 GATAAAAACA 0.965184 -67 CAAACAGAGCAGAAAAAAAGCAAGTGAAGAGAT 9 235 0 AAAAAAAAAA 0.623975 -36 AACGTTGAGCGTAATAAAACCCACCAGCCGTAA 10 66 0 GAATAAAACA 0.750253 -88 CAGTATTTATGAATAAAAATACACTAACGTTGA 10 91 0 GATAAAAACA 0.965184 -63 ACGCCTCAATGAATTAAAATTCAATTTATATGG 12 121 0 GATTAAAACA 0.739583 -41 AACAAAAAAGGACAGCCTGACATG 15 2 1 AAAAAAAGCA 0.744698 -53 CCTTTCAGCTGTAAAAAAGGACAGCCTCACATG 15 31 0 GAAAAAAGCA 0.891213 -24 CATTTCAGCCGCATAAAAAAACAGGCTGACCGC 18 12 0 GATAAAAACA 0.965184 -195 GGAATTCCGCTCAAAAAAAATCAGCACGACTCC 18 71 0 TAAAAAAACA 0.662077 -136 ATTATAACATGAATAAAAATTAATTCAATCGTA 18 145 0 GATAAAAAAA 0.815019 -62 CGATATAAAGGCATAAAAATTCATTTTTATAAT 19 19 1 GATAAAAACA 0.965184 -52 TTTTCAGAAAATAAAAAAAGCCCTCTCATCCCA 20 258 0 AAAAAAAACC 0.856121 -43 CACTCTTGGCACAAAAAAAGCCCGGCTTTTACG 21 26 0 AAAAAAAACC 0.856121 -52 GTTCATATAGAAGAAAAAACCCCTCCTGCCAGA 23 235 0 AGAAAAAACC 0.624395 -39 ATGCCTCTTTGCGTAAAAAAGCAAAGAGGTTTT 24 92 1 GGTAAAAACA 0.885648 -80 CTCAATGACTGTATAAAAAAACCTCTTTGCTTT 24 109 0 GATAAAAACC 0.940473 -63 ACTTAAGGCTGAAAAAAAACCCCGGTCTAAGAT 25 102 0 GAAAAAAACC 0.94354 -44 GACGTTAAAAGAAAAAAAAGCAGATGTACCGG 27 10 1 AAAAAAAACA 0.912594 -125 GAATCATATAACATAAAAGAACAGATAAGCTTG 27 95 1 AATAAAAGCA 0.733874 -40 AATCTCAGACATAAAAAAAGACAAACGCGCTTT 28 155 0 AAAAAAAACA 0.912594 -92 CAGACGTGAAAAAAAATGAAACATGACATT 29 8 1 GAAAAAAAAA 0.823337 -78 AGGGTAACGTGTAAAAAAACCAAAGGGCCGCCC 31 36 0 GAAAAAAAAA 0.823337 -228 TTCGGTAATAGGGTAAAAAAACCTTGATTTCAA 31 160 1 GGTAAAAACC 0.815289 -104 GAATGAGGGAAAAAAGCCCGCTAAACAAG 32 7 1 GGAAAAAACC 0.823597 -149 GTAGTAACCTATAAAAAAAGAAATTTCATACAT 32 119 1 AAAAAAAAAA 0.623975 -37 TGAAATGTCAATAAAAAAGCTCACACTTTTTGG 38 174 0 AAAAAAAGCA 0.744698 -53 AAATTATATTTAATAAAAATACATTTTGTATGT 39 103 0 TATAAAAACA 0.649399 -67 TTTCTATTTTGTATAAAAATAAATTATATTTAA 39 123 0 GATAAAAAAA 0.815019 -47 TCATGCATCAACAAAAAAGCACATTCAAGAGAA 40 27 0 AAAAAAAGCA 0.744698 -58 GATATTCACCGGGAAAAAAGTACGAAAAACGAA 41 245 1 GGAAAAAAAC 0.425958 -56 * ******* ** Masking position 7 Map Score: 45.2213 Number of sites scoring better than the average of aligned sites = 493 Number in coding regions = 330 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 2 CTCGCCATGTTCTCCGCCATTTTAGAAGCATAA 2 39 1 TTCCCCTTTT 0.83594 -262 ACGGACGGGTTTGCCTCCACCTTTGTAAGAAAG 2 192 1 TGCCCCCCTT 0.882083 -109 AATTATTCATTTGCAACCCCATTTCACAATTCT 2 223 0 TGCACCCATT 0.649971 -78 CATAACATTATTTCAGCCTTCTTCAGGGCTGAC 5 214 1 TTCACCTCTT 0.938436 -87 AATAATGTTGTATCAACCACCATATCGGGTGAC 5 276 1 TTCACCCCAT 0.757379 -25 ACCACTGACATTGCCTCCACCTTTGTGACAAAG 12 55 1 TGCCCCCCTT 0.882083 -107 AATGTGCCCCTCCTTAGGATAACCA 13 106 0 TTGCCCCCTT 0.778368 -15 TTTGTGATAATGTCAGCCATTTTAATTTGTTTT 17 17 0 TTCACCTTTT 0.928067 -28 TGACTGTCCCTTTCAACCGTTTTTTCATCTGAA 20 25 0 TTCACCTTTT 0.928067 -276 AGAAACCCTCTGTCAACCGTTTTTTCTGAGGTT 23 81 0 TTCACCTTTT 0.928067 -193 CCGTTATCCTTCTCAGCCTCTCTGGACTGTTTT 23 150 0 TTCACCCTCT 0.944687 -124 GTGCACCTCTTTGCAACCTCTCTGGATTGCTTA 24 24 0 TGCACCCTCT 0.898653 -148 TACATGCTGTTTTCATCCTTTCTTATCACGATA 26 40 0 TTCACCTTCT 0.877088 -261 TTAATTATTGTTGGAGCCGCTTTTATTTGCTAG 26 149 1 TGGACCCTTT 0.796238 -152 GATACAATGCTCTCAAGCCCTTTCATCGCTTCT 29 44 0 TTCAGCCTTT 0.788031 -42 TACCGAATATTTTCACACACCTTAATATGATTA 31 134 0 TTCAACCCTT 0.616909 -130 TTCTTTCTCCTTTGATCCTCTTTATCCGCTTGT 31 240 0 TTGACCCTTT 0.88272 -24 ATTATCAACCTGCCTATTTCTTTAG 38 3 1 TTCACCGCCT 0.663282 -224 CGTTTCGTTTTTTCAAGCCTTTTATAAAAAAAA 39 53 0 TTCAGCTTTT 0.608352 -117 AAAAATCCCCTCTCAACCGTGTTTCTATTTTGT 39 144 0 TTCACCTGTT 0.688942 -26 TGTATGAACCTCCCTCAATTATTTT 42 3 1 TTGACCCCCT 0.831036 -238 * *** ** **** Masking position 1 Map Score: 14.2644 Number of sites scoring better than the average of aligned sites = 541 Number in coding regions = 462 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 3 AAAACGAGCAGAAAAAAGTGGACCAAATGGTC 1 21 0 GAAAAAGGGA 0.791693 -280 AATAATGTTATGAAAGAGCGGGATTTTATCAA 5 194 0 TGAAAAGGGG 0.955216 -107 TAAATTCAGATGAAAAAACGGTTGAAAGGGAC 20 21 1 TGAAAAAGGT 0.606392 -280 GTTCAGCAAGGAAACTAAAGGGCTGATCTACA 20 119 0 GAAACAAGGG 0.895877 -182 CGGGGTATGGTTAAATAGAGGGCAGCATTGAA 25 65 0 TTAAAAGGGG 0.767427 -81 GCCTTAAGTTGAAAAGAGAGGGGAAAGAAC 25 126 1 GAAAAAGGGG 0.970347 -20 AGATAAGCTTGGAAATAGAGGTGCTTAC 27 117 1 GGAAAAGGGT 0.757372 -18 TTTAGGAGCCTGAAGAAGCGGGTATCGTGCTC 30 57 0 TGAAGAGGGG 0.770861 -81 GGCTTAACACGAAACCAAGGGGAGGGCGGCCC 31 13 1 GAAACAAGGG 0.895877 -251 CTTCATGCTTTGAAATAAAGGGTAACGTGTAA 31 55 0 TGAAAAAGGG 0.929896 -209 AAAAGCCCGCTAAACAAGCGGGCTTTTTGCGT 32 22 1 TAAACAGGGG 0.916528 -134 GCATATCATATAAAAAAATGGGAGGTTGGGAG 35 117 1 TAAAAAAGGG 0.941691 -28 AGTAAAATTTGAAAATAACGGGTATAATGCAT 38 134 0 GAAAAAAGGG 0.953161 -93 ACAGAAAACATAAAAGAGGTGGGCCA 40 69 1 TAAAAAGTGG 0.578536 -16 TTCTATTTTATAAAAAAACGGAGAGGATATGC 42 47 1 TAAAAAAGGA 0.652264 -194 TGTTGAAACAGAAAACAAGGGGGAATTCAAAT 42 219 1 GAAAAAAGGG 0.953161 -22 ***** ** *** Masking position 7 Map Score: 12.5912 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 204 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 4 CCTGTTCTGGAAAACGCTTGCGCAGCAAGAA 1 67 0 AAACGCTTGC 0.488661 -234 AAATAATATAAAAAATCCCGCCATTAAGTTG 1 148 1 AAAATCCCGC 0.794912 -153 GTGGATCACTATAATGCCTGCAGATTTTACG 4 40 0 ATATGCCTGC 0.705075 -261 GTTATTGAGAAACATGCCTGCGTCACGGCAT 5 158 0 AACTGCCTGC 0.598249 -143 AGCGCGGGCAAGATTGCCCGCGCGAGAAATC 8 12 0 AGATGCCCGC 0.926658 -93 AAATCACCTAAAATCGCCCGCTCGCGGCATA 9 49 0 AAACGCCCGC 0.956381 -222 AAGAGATTCTAAATAGCCTTCAAGAACAAGG 9 211 0 AAAAGCCTTC 0.889172 -60 TATGAAAAAGAAATTGCTTGCATTCGCGCT 16 38 1 AAATGCTTGC 0.535471 -20 CAGAAAATAAAAAAAGCCCTCTCATCCCATA 20 256 0 AAAAGCCCTC 0.934758 -45 TGCAAAAGAGCCCGGCGTAAAAGCC 21 5 1 AAAAGCCCGG 0.913585 -73 CTTGGCACAAAAAAAGCCCGGCTTTTACGCC 21 24 0 AAAAGCCCGG 0.913585 -54 TGAAATTTCAAAAGAGCCTTCCTTATTAGGA 26 186 1 AAAAGCCTTC 0.889172 -115 TTTCACATAAAAAGAGCCTTCCTAATAAGGA 26 205 0 AAAAGCCTTC 0.889172 -96 CTTTTTGAAGAGAGAGTCCGCCGA 28 4 0 AGAAGTCCGC 0.765541 -243 CCATAACTAAAGAAAACCCGCCCTGGCTTTA 30 85 0 AGAAACCCGC 0.649326 -53 CAAAGCATGAAGAAAGCCGGCTTACATAGCC 31 75 1 AGAAGCCGGC 0.830478 -189 GAATGAGGGAAAAAAGCCCGCTAAACAAGCG 32 11 1 AAAAGCCCGC 0.98874 -145 ACAGCAACGCAAAAAGCCCGCTTGTTTAGCG 32 29 0 AAAAGCCCGC 0.98874 -127 GAGGCTTGTCATAAAGTCTGCCTCACATCAT 34 14 1 ATAAGTCTGC 0.381882 -62 TTGGGCACAAAAAAAGCCTGCTCCCATTTGG 35 33 0 AAAAGCCTGC 0.980068 -112 *** ******* Masking position 1 Map Score: 22.8166 Number of sites scoring better than the average of aligned sites = 754 Number in coding regions = 659 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 5 GGACACGTTCAGGGAGGCATCAA 8 92 1 AGGGAGGCAT 0.65382 -13 CAGCCTCACATGTCAGGCTGTCCTTTTTTG 15 13 0 TGTCAGGCTG 0.900247 -42 CAGCCTGACATGTGAGGCTGTCCTTTTTTA 15 23 1 TGTGAGGCTG 0.946353 -32 CCGCATAAAAAAACAGGCTGACCGCG 18 7 0 AAACAGGCTG 0.629545 -200 AAAACAGTCCAGAGAGGCTGAGAAGGATAA 23 150 1 AGAGAGGCTG 0.978856 -124 TAAGCAATCCAGAGAGGTTGCAAAGAGGTG 24 24 1 AGAGAGGTTG 0.91087 -148 ATGAAAGTCCAGAGAGGCTTGGAAGGGTTA 25 20 1 AGAGAGGCTT 0.91087 -126 AGAGAGGCTTGTCATAAAGT 34 1 1 AGAGAGGCTT 0.91087 -75 AAATGTATGATGTGAGGCAGACTTTATGAC 34 21 0 TGTGAGGCAG 0.798077 -55 TATAAAAAAATGGGAGGTTGGGAGAGTGCT 35 125 1 TGGGAGGTTG 0.859614 -20 CTAAAGAAATAGGCAGGTTGATAAT 38 6 0 AGGCAGGTTG 0.811766 -221 ACCTCTAGATTGACAGGCTGAAAAAATTGC 38 84 1 TGACAGGCTG 0.945068 -143 ********** Masking position 5 Map Score: 8.71163 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 206 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 6 TTCTACAACCAGGTCGAGTCAGAAATGAGA 2 101 0 AGGTCGAGTC 0.820912 -200 TTTCTTACAAAGGTGGAGGCAAACCCGTCC 2 194 0 AGGTGGAGGC 0.955445 -107 AAGGGAGAGCAGGAGAAGGCAAAAGTATTC 4 135 0 AGGAGAAGGC 0.92373 -166 TTTGTCACAAAGGTGGAGGCAATGTCAGTG 12 57 0 AGGTGGAGGC 0.955445 -105 CGTTAGCCACAGGAGGGATCT 12 151 1 AGGAGGGATC 0.76633 -11 GAGGGGTTTTAGGACAAGGTGCGCGCCTAT 23 200 0 AGGACAAGGT 0.721361 -74 ATGCTCTGGCAGGAGGGGTTTTTTCTTCTA 23 231 1 AGGAGGGGTT 0.903952 -43 AGGGGTTTTGAGGTGGGAGC 26 291 1 AGGTGGGAGC 0.819889 -10 TCCTAAAGCCAGGGCGGGTTTTCTTTAGTT 30 82 1 AGGGCGGGTT 0.697271 -56 CACGAAACCAAGGGGAGGGCGGCCCTTTGG 31 20 1 AGGGGAGGGC 0.894149 -244 ATCGGTAGAAAGGAGGAGGCTCTG 34 62 1 AGGAGGAGGC 0.961304 -14 CCTCGCGAAAAGGAGAGATTGT 37 75 1 AGGAGAGATT 0.498569 -12 CCTAAATTTCAGGTGAAGTTTCATAGTATT 39 18 0 AGGTGAAGTT 0.801712 -152 CCTGAAATTTAGGTGAAGTTTTTTTTATAA 39 35 1 AGGTGAAGTT 0.801712 -135 ACAATTTTCGAGGACAAGGTGCAAAAACAT 42 123 0 AGGACAAGGT 0.721361 -118 ACAGAAAACAAGGGGGAATTCAAAT 42 226 1 AGGGGGAATT 0.597162 -15 ********** Masking position 1 Map Score: 10.7313 Number of sites scoring better than the average of aligned sites = 495 Number in coding regions = 418 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 7 CGATAAAAGATGATTAAATGAAAACTCATTTA 4 209 1 TGTTAAATGA 0.901548 -92 ATGCAAATTCTGCTTAAAAGTAAATTAATTGT 5 128 0 TGTTAAAAGA 0.71108 -173 TTTTGTGATCTGTTTAAATGTTTTATTGCAAT 9 77 1 TGTTAAATGT 0.711171 -194 CAAAATCACCTCTTAAAATGCAATTTAGCAAC 9 111 0 TCTAAAATGA 0.824649 -160 ACAATAAAGATGGTAAAAAGCTACACTGTAAG 13 52 0 TGTAAAAAGT 0.634684 -69 TCCTTTCAGCTGTAAAAAAGGACAGCCTCACA 15 33 0 TGAAAAAAGA 0.634684 -22 AATAATTAATTATAAAAATGAATTTTTATGCC 19 28 0 TAAAAAATGA 0.449796 -43 TTTTATTTTCTGAAAAAATGCAGTGGAGGAAT 20 275 1 TGAAAAATGA 0.865974 -26 TGCTTTTTATTGATAAAATGCATAATGGATTA 22 54 1 TGTAAAATGA 0.960047 -49 CATTGAGTCATCCTAAAATGAAAGTCAACAAT 24 135 1 TCTAAAATGA 0.824649 -37 CAACAATAATTAATAAAATGAACAAGACAACA 26 130 0 TATAAAATGA 0.752496 -171 CACGAGGGTATGGTAAAATGTAAGCAGTTTAT 28 106 1 TGTAAAATGA 0.960047 -141 TTTTCCAGTATGATAAAATGTTCACGAGAAGT 37 21 1 TGTAAAATGT 0.865975 -66 GAAACGTACTTGTTAAAGTGTATACATACAAA 39 80 1 TGTAAAGTGA 0.765277 -90 GACATGACAATGTTTAAATGGAAAAGTCAGAT 41 194 1 TGTTAAATGA 0.901547 -107 ** ******* * Masking position 6 Map Score: 8.42868 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 119 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 8 TGAATTAATATGCAAATAAAGTGAGTGAATATTCTC 1 264 1 TGCAAAAGAT 0.980485 -37 AGTAATGCCGTGAATATAAAAAGAATGTTTACCGTT 3 17 0 TGAAAAAGAT 0.88559 -125 ACTTGCACCCTGCGAAAAAACAGAATAAAAATACAC 3 84 1 TGCAAAAGAT 0.980485 -58 TGAATTTTTATGCAAAATAAATGAGTTTTCATTTAA 4 222 0 TGCATAAGAT 0.853363 -79 CCACAAAATATGCATAAAAAATCACTAAATGGCAAT 6 17 0 TGCAAAACAT 0.945771 -69 GCAGTATTTATGAATAAAAATACACTAACGTTGAGC 10 89 0 TGAAAAACAT 0.728766 -65 TGAATAATCATCCATATAAATTGAATTTTAATTCAT 12 110 1 TCCAAAAGAT 0.84235 -52 TACGTTATACTGTAGAAAAAAGGAGTGAGGGAAC 14 40 1 TGTAAAAGAT 0.814459 -24 TATGCCTCTTTGCGTAAAAAAGCAAAGAGGTTTTTT 24 91 1 TGCAAAACAA 0.796234 -81 TGTACATGAATGCAGAAAAAAGGAATAATAGCGCCC 27 50 0 TGCAAAAGAT 0.980485 -85 GCTTTTTTTGTGCCCAAAAACAGAATCTTTCTTTTA 35 47 1 TGCAAAAGAT 0.980485 -98 AGTTAAAGTGTGCCCAAAAAATGAAATGTCAATAAA 38 192 0 TGCAAAAGAA 0.918416 -35 *** * *** ** * Masking position 9 Map Score: 10.5814 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 28 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 9 AATTTGATAAAATCCCGCTCTTTCATAACA 5 191 1 AATCCCGCTC 0.942275 -110 GTTCAATGGGAATTCCGCTCAAAAAAAATC 18 82 0 AATTCCGCTC 0.852526 -125 AAAATAAAAAAAGCCCTCTCATCCCATAAG 20 254 0 AAGCCCTCTC 0.970964 -47 CTTGTCCTAAAACCCCTCTATGCTCTGGCA 23 212 1 AACCCCTCTA 0.684003 -62 GCTGAAAAAAAACCCCGGTCTAAGATAGAC 25 98 0 AACCCCGGTC 0.912143 -48 CAATGCTCTCAAGCCCTTTCATCGCTTCTT 29 43 0 AAGCCCTTTC 0.822891 -43 GTCTAAAAACTCCTCTCCTAAGCATTC 30 121 0 AACTCCTCTC 0.858329 -17 TGAGGGAAAAAAGCCCGCTAAACAAGCGGG 32 14 1 AAGCCCGCTA 0.922736 -142 GCAACGCAAAAAGCCCGCTTGTTTAGCGGG 32 27 0 AAGCCCGCTT 0.870161 -129 TTGAATTCACAAGTCCGCTCCTGTAAGATG 32 70 1 AAGTCCGCTC 0.970964 -86 AGGAAAAAAGAAGTCTGTTCCCAAATGGGA 35 13 1 AAGTCTGTTC 0.350496 -132 GGCACAAAAAAAGCCTGCTCCCATTTGGGA 35 31 0 AAGCCTGCTC 0.916411 -114 GATAAAAATCCCCTCTCAACCGTGTTT 39 153 0 ATCCCCTCTC 0.627397 -17 TCAATTCGTCAAGTCCGGTCTTCAAAAGCA 41 23 0 AAGTCCGGTC 0.877853 -278 ********** Masking position 1 Map Score: 11.8826 Number of sites scoring better than the average of aligned sites = 321 Number in coding regions = 261 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 10 TAATGCGCTTAAGGGAGAGCAGGAGAAGGC 4 145 0 AAGGGAGAGC 0.979729 -156 CATAAAAATTCAGTGAGAGCGGAAATCCAG 4 246 1 CAGTGAGAGC 0.964578 -55 TTATGCGTAACAGGGTGATCATGAG 6 71 1 CAGGGTGATC 0.849231 -15 CCGGGTTACGCCGGGAGAGCAGAAGCGCGG 8 36 0 CCGGGAGAGC 0.968469 -69 ATAAAAACAGCAGGGAGAGCACTATGAAAA 16 16 1 CAGGGAGAGC 0.990082 -42 AGCTGCCAAAAAGTGTGAGCTTTTTTATTG 38 169 1 AAGTGTGAGC 0.851537 -58 CATTTATATAAAGGGAAAGCAGGATAACAT 42 190 1 AAGGGAAAGC 0.862431 -51 ********** Masking position 8 Map Score: 4.31409 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 95 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 CGGACGGGTTTGCCTCCACCTTTGTAAGAA 2 193 1 TGCCTCCACC 0.985309 -108 TGAATACTTTTGCCTTCTCCTGCTCTCCCT 4 134 1 TGCCTTCTCC 0.957739 -167 CCACTGACATTGCCTCCACCTTTGTGACAA 12 56 1 TGCCTCCACC 0.985309 -106 TTTCATTCCTCCACTGCATTTTTTC 20 286 0 TTCCTCCACT 0.857067 -15 GCATTGAAGCTTCCTTCTCTTCATAACCCT 25 43 0 TTCCTTCTCT 0.669547 -103 CTCCTAAGCATTCCTGCACCATAACTAAAG 30 104 0 TTCCTGCACC 0.931984 -34 CAGAGCCTCCTCCTTTCTACCGA 34 63 0 AGCCTCCTCC 0.960865 -13 GCACAAAAAAAGCCTGCTCCCATTTGGGAA 35 30 0 AGCCTGCTCC 0.927709 -115 ********** Masking position 5 Map Score: 4.66911 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 113 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 12 CAATGATGACGTAAATCAATGCAAATCTGCTTACC 1 229 0 GAATAATCAA 0.611673 -72 CACTTTATTTGCATATTAATTCACAATGATGACGT 1 252 0 GTATAATCAA 0.94119 -49 CGAAAAAACAGAATAAAAATACACTAATTTCGAAT 3 96 1 GTAAAATCAT 0.812177 -46 CACTAATTTCGAATAATCATGCAAAGAGGTGTGCC 3 117 1 GTAACATCAA 0.886435 -25 AAAGTGAACTGGATATTCATTCACATGATTAGCAA 4 92 0 GTATCATCAA 0.916729 -209 CATTTATTTTGCATAAAAATTCAGTGAGAGCGGAA 4 235 1 GTAAAATCAT 0.812177 -66 CTGACTGTTTGCATAAAAATTCATCTGTATGCACA 5 242 1 GTAAAATCAC 0.660782 -59 CATATTTTGTGGTTATAATTTCACATTTGTTTATG 6 41 1 GTATATTCAA 0.707149 -45 CAGTATTTATGAATAAAAATACACTAACGTTGAGC 10 89 0 GTAAAATCAT 0.812177 -65 ACTTGCAAATGAATAATCATCCATATAAATTGAAT 12 101 1 GTAACATCAA 0.886435 -61 CGATATAAAGGCATAAAAATTCATTTTTATAATTA 19 19 1 GTAAAATCAT 0.812177 -52 AATACGTTCATAAATTCAGATGAAAAAACG 20 6 1 GCATAATCAA 0.862225 -295 ATTCAGCTTCGTTTATTATTTCAGAAAAGAAACCC 23 106 0 GTATATTCAA 0.707149 -168 ACCGTACCCAGAGTATCCATACATGCTGTTTTCAT 26 57 0 GTATCATCAG 0.653967 -244 TCTGCACATTGTACATGAATGCAGAAAAAAGGAAT 27 60 0 GCATAATCAA 0.862225 -75 ACTTGTTAAAGTGTATACATACAAAATGTATTTTT 39 87 1 GTATCATCAA 0.916729 -83 AATTGTAAGCGTTCATCAATACAAAACCTATAGTG 41 93 1 GCATAATCAA 0.862225 -208 * *** *** ** * Masking position 10 Map Score: 11.7895 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 43 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 13 GCAAGTGTAAATTTTATGCGAGAGCGACTT 3 60 0 ATTTTATGCG 0.947369 -82 GCTAAATTGCATTTTAAGAGGTGATTTTGA 9 114 1 ATTTTAAGAG 0.813669 -157 TCAGCCTGTTTTTTTATGCGGCTGAAATGC 18 16 1 TTTTTATGCG 0.739418 -191 AATATGTCGAATTTGAAGCGCCGCTTCCCG 23 28 1 ATTTGAAGCG 0.91554 -246 GATATACGACATTTTATGCGGGCCAAGTCC 26 14 0 ATTTTATGCG 0.947369 -287 CTTTTACCATATTGTATGAGTGTCCAAATG 26 263 0 ATTGTATGAG 0.745133 -38 AACGATCCTAATTTGAAGCGGCTGCACGAG 28 82 1 ATTTGAAGCG 0.91554 -165 AAAACCGCAAATTGTAAGCGTTCATCAATA 41 84 1 ATTGTAAGCG 0.948165 -217 ACGACTTCTTATTGTAAGCGTTATCAATAC 41 144 1 ATTGTAAGCG 0.948165 -157 ********** Masking position 6 Map Score: 5.85187 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 29 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 14 TGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGC 1 28 1 TTTCGTCTTT 0.815446 -273 AGGCCAATCATTCTCATTTCTGACTCGACCTGGTT 2 90 1 TTTCTTCGAT 0.826526 -211 TGTGTGAAAATAATCGTATCTGCCTCCGATTCTCT 2 158 0 TATCTTCGCT 0.725725 -143 TTTTAGGTGATTTTGTGATCTGTTTAAATGTTTTA 9 67 1 TTTGGTCGTT 0.874178 -204 CACTTGCTTTTTTTCTGCTCTGTTTGTTAAGGAAA 9 242 1 TTTCGTCGTT 0.956884 -29 AAGATTTTTCCTTTCGTTCTAAAGGATGTC 21 58 0 TTTCTTCTTT 0.857494 -20 TCTGAGATTATTGTCAGCTCGGCATGCAAAAGACA 28 179 1 TTTCGTCGCT 0.948073 -68 TAACATATTTTTTTCGTATCCGCATATTGAAATCA 31 184 0 TTTCTTCGCT 0.961336 -80 AAAAAATATGTTATGATCTCTTTGTGGCTTAACGA 31 206 1 TTTGTTCTTT 0.653225 -58 TGAAGTAGTCTTGTCATTTCCGTATAAAAGAAAGA 35 72 0 TTTCTTCGTT 0.967973 -73 CCCACCTCTTTTATGTTTTCTGTCTGTCACTATCA 40 57 0 TTTGTTCGTT 0.904413 -28 CATTTAAACATTGTCATGTCGGCTTTTCAAGTCAA 41 179 0 TTTCTTCGCT 0.961336 -122 ATTCTTTTGCATATCCTCTCCGTTTTTTTATAAAA 42 52 0 ATTCTTCGTT 0.762829 -189 ** ** * ** ** * Masking position 9 Map Score: 7.54996 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 58 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 15 GAATAATCATGCAAAGAGGTGTGCC 3 127 1 GCAAAGAGGT 0.976612 -15 AAATAAAATGGCATAGCGGGATATGCCGCGAG 9 28 1 GCATAGCGGT 0.97615 -243 TCCTGCCAGAGCATAGAGGGGTTTTAGGACAA 23 213 0 GCATAGAGGT 0.976612 -61 CAGAGAGGTTGCAAAGAGGTGCACAACAAAGG 24 33 1 GCAAAGAGGC 0.917293 -139 GCTTTTTTACGCAAAGAGGCATACAAAGACCT 24 82 0 GCAAAGAGGT 0.976612 -90 GCGTAAAAAAGCAAAGAGGTTTTTTTATACAG 24 102 1 GCAAAGAGGT 0.976612 -70 AAGCCCGCTTGTTTAGCGGGCTTTTTTCCCTC 32 15 0 GTTTAGCGGT 0.774121 -141 CAATCTAGAGGTTTAGCGGTGTTTCCTGTACA 38 64 0 GTTTAGCGGT 0.77412 -163 ********* * Masking position 5 Map Score: 3.98584 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 37 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274