AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iargR_ecoli_hinf_100.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 argE_argC 153 argE: acetylornithine deacetylase, argC: N-acetyl-gamma-glutamylphosphate reductase #10 argH 60 argininosuccinate lyase #11 argI 161 ornithine carbamoyltransferase 1 #12 HI0596 300 ornithine carbamoyltransferase (arcB) #13 HI0811 134 argininosuccinate lyase (argH) #14 HI1209 206 arginine repressor (argR) #15 HI1727 155 argininosuccinate synthetase (argG) Motif number 1 GTCATCATTGTGAATTAATATGCAAATAAAGTG 1 254 1 TGAATAAATC 0.992286 -47 GCAAATAAAGTGAGTGAATATTCTCTGGAGGGT 1 275 1 TGAGTAAATC 0.928229 -26 GGGTTGCAAATGAATAATTACACATATAAAGTG 2 237 1 TGAATATACC 0.745416 -64 CGCCACTTATTGAATTAAAATTCACTTTATATG 2 259 0 TGAATAAATC 0.992286 -42 GCGAAAAAACAGAATAAAAATACACTAATTTCG 3 95 1 AGAATAAATC 0.901988 -47 CACACCTCTTTGCATGATTATTCGAAATTAGTG 3 117 0 TGCATATATC 0.955905 -25 GCTAATCATGTGAATGAATATCCAGTTCACTTT 4 94 1 TGAATAAATC 0.992286 -207 TCATTTATTTTGCATAAAAATTCAGTGAGAGCG 4 234 1 TGCATAAATC 0.991256 -67 GCTGACTGTTTGCATAAAAATTCATCTGTATGC 5 241 1 TGCATAAATC 0.991256 -60 CCACAAAATATGCATAAAAAATCACTAAATGGC 6 20 0 TGCATAAAAC 0.958346 -66 GCAGTATTTATGAATAAAAATACACTAACGTTG 9 92 0 TGAATAAATC 0.992286 -62 TCATAAATACTGCATGAATATTGATACTATCAT 9 112 1 TGCATAAATG 0.87547 -42 GACTTGCAAATGAATAATCATCCATATAAATTG 11 100 1 TGAATATATC 0.960932 -62 AACGCCTCAATGAATTAAAATTCAATTTATATG 11 122 0 TGAATAAATC 0.992286 -40 TATACATTGGGGAATAAACATACATCATTCGAG 12 256 0 GGAATAAATC 0.931692 -45 TATTGCTTTATGAATAAATATGCACAATAATAG 13 82 1 TGAATAAATC 0.992286 -53 GCATAAGAATTGCATAAAAATTCACTTTCATCA 14 159 0 TGCATAAATC 0.991256 -48 TTTAGCTTTGTGCATAAAAAATCCTAATTT 15 8 0 TGCATAAAAC 0.958346 -148 TCGATTTTTGTGAATAAAAATTCTATAGAGTAT 15 96 0 TGAATAAATC 0.992286 -60 TAATTAGAATTGAATAAATAATCGATTTTTGTG 15 117 0 TGAATAAAAC 0.963105 -39 ***** ** ** * Masking position 5 Map Score: 55.3509 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 22 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 2 ACGAGCAGAAAAAAGTGGACCAAATGGTCAAAATT 1 15 0 AAAATAAAAT 0.971954 -286 GCGCAGCAAGAAGATTGCATGAAATAAAAACGAGC 1 44 0 AAGATAAAAT 0.883616 -257 TGAGCCACAAAATAATATAAAAAATCCCGCCATTA 1 139 1 AATATAAAAT 0.875514 -162 TATGGGCGCTAAAAGTCAACTTAATGGCGGGATTT 1 160 0 AAAATATAAT 0.690908 -141 AAAACAGAATAAAAATACACTAATTTCGAATAATC 3 100 1 AAAATAAATT 0.918584 -42 GATTAGCAATAAACGTTGACAAAATGTGGCGTGGA 4 66 0 AAACTAAAAT 0.768141 -235 TGTCTCCGATAAAAGATGATTAAATGAAAACTCAT 4 203 1 AAAAAAAAAT 0.868883 -98 CCGTTCAGCCAAAACAACATCAATTTGATAACAAT 5 98 1 AAAAAAAATT 0.68329 -203 AATTCTGCTTAAAAGTAAATTAATTGTTATCAAAT 5 120 0 AAAATAAATT 0.918584 -181 TCTCAATAACGAAATTTGATAAAATCCCGCTCTTT 5 179 1 GAAATAAAAT 0.786089 -122 AAATATGCATAAAAAATCACTAAATGGCAATCAGA 6 13 0 AAAAAAAAAT 0.868883 -73 CCTCTTCATCAAAAATAAACTAAAACATATTTTCG 12 37 1 AAAATAAAAA 0.805664 -264 TTTGATTTCTAATAGTAGATGAATTTAAACGAAAA 12 66 0 AATATAAATT 0.69602 -235 ATCTACTATTAGAAATCAAACAAATAACAATAAAG 12 81 1 AGAATAAAAT 0.907843 -220 TAGTATTATTAGAATTTAATAAAATAATCTAACTC 12 115 0 AGAATAAAAT 0.907843 -186 TACCAGTTGAAAAACGACAACAAATTTCATTTTAC 12 183 1 AAAAGAAAAT 0.795381 -118 CTAATACAAATAAAATGGACAAAATGAAAGATTTT 13 17 1 TAAATAAAAT 0.813855 -118 ATAATAAAACAAAAATGGACAAAATCTTTCATTTT 13 37 0 AAAATAAAAT 0.971954 -98 AAATATGCACAATAATAGAATAATTAATTAAAACA 13 97 1 AATATAAATT 0.696002 -38 AATTTGCATAAGAATTGCATAAAAATTCACTTTCA 14 162 0 AGAATAAAAA 0.540958 -45 TACTAATAATTAGAATTGAATAAATAATCGATTTT 15 121 0 TAGATAAAAT 0.489233 -35 **** * * **** Masking position 9 Map Score: 16.6374 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 121 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 3 CCGCCATTAAGTTGACTTTTAGCGCCCATAT 1 165 1 GTGACTTTTA 0.694343 -136 ACACATATAAAGTGAATTTTAATTCAATAAG 2 256 1 ATGAATTTTA 0.878261 -45 GTGAATATAAAAAGAATGTTTACCGTTTATT 3 13 0 AAGAATGTTT 0.754574 -129 ATTCGAAATTAGTGTATTTTTATTCTGTTTT 3 100 0 ATGTATTTTT 0.835807 -42 TTCCGCTCTCACTGAATTTTTATGCAAAATA 4 239 0 ATGAATTTTT 0.949828 -62 CTTCTTCAGGGCTGACTGTTTGCATAAAAAT 5 231 1 GTGACTGTTT 0.782758 -70 TGTGCATACAGATGAATTTTTATGCAAACAG 5 246 0 GTGAATTTTT 0.953567 -55 ATTGCCATTTAGTGATTTTTTATGCATATTT 6 17 1 ATGATTTTTT 0.668283 -69 CCAGCCGTAAGGTGAATGTTTTACGTTTAAC 9 45 0 GTGAATGTTT 0.925448 -109 GCTCAACGTTAGTGTATTTTTATTCATAAAT 9 89 1 ATGTATTTTT 0.835807 -65 ATCCATATAAATTGAATTTTAATTCATTGAG 11 119 1 ATGAATTTTA 0.878261 -43 ATGCCAGTATGTAGAATTTTATTGCGAGATT 12 152 0 GAGAATTTTA 0.67787 -149 TATCTCGAATGATGTATGTTTATTCCCCAAT 12 253 1 GTGTATGTTT 0.769468 -48 AGTTGATGAAAGTGAATTTTTATGCAATTCT 14 156 1 ATGAATTTTT 0.949828 -51 GTTATACTCTATAGAATTTTTATTCACAAAA 15 93 1 AAGAATTTTT 0.835804 -63 * ********* Masking position 7 Map Score: 16.1972 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 139 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 4 GACCATTTGGTCCACTTTTTTCTGCTCGTTTTT 1 21 1 TCCACTTTTT 0.918944 -280 AGGCCAATCATTCTCATTTCTGACTCGACCTGG 2 90 1 TTCTCTTTTA 0.782199 -211 CGGGTTTGCCTCCACCTTTGTAAGAAAGAATTG 2 197 1 TCCACTTTTA 0.899006 -104 GCAACCCCATTTCACAATTCTTTCTTACAAAGG 2 211 0 TTCACATTTT 0.767193 -90 GAATATCCAGTTCACTTTCATTTGTTGAATACT 4 109 1 TTCACTTCTT 0.938592 -192 TGGTTATAATTTCACATTTGTTTATGCGTAACA 6 50 1 TTCACTTTTT 0.953303 -36 CGGGGCTATTCACCTTCTTATGTCTGGTTGC 9 9 1 TTCACTTCTT 0.938592 -145 AACTCTGTTTCCTTATTTTGAAATTCAATGC 10 40 0 TTCCTATTTA 0.394365 -21 TGACATTGCCTCCACCTTTGTGACAAAGATTTA 11 60 1 TCCACTTTTA 0.899006 -102 GATAGACACATTCCTCTTCATCAAAAATAAACT 12 25 1 TTCCTTTCTA 0.751253 -276 AAAGATTTTGTCCATTTTTGTTTTATTATTAAT 13 43 1 TCCATTTTTT 0.811419 -92 AATTTTTCCTTTTTGTTTTAATTAATTA 13 117 0 TTCCTTTTTT 0.837066 -18 TATGATCTAGTTCACATTTCTGAGATAAATATT 14 95 1 TTCACTTTTA 0.941276 -112 CTTCTCTTTGTTCTTATTCATATTTCAGTTGAT 14 130 1 TTCTTTTCTT 0.565165 -77 TGCATAAAAATTCACTTTCATCAACTGAAATAT 14 149 0 TTCACTTCTA 0.923083 -58 AACCGCACTTTTCCTCTTTGTCTAGTGTTTTGT 15 63 0 TTCCTTTTTT 0.837066 -93 ***** *** * * Masking position 8 Map Score: 15.0366 Number of sites scoring better than the average of aligned sites = 355 Number in coding regions = 267 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 5 TGAATTAATATGCAAATAAAGTGAGTGAAT 1 264 1 TGCAAATAAA 0.908259 -37 GAAATGGGGTTGCAAATGAATAATTACACA 2 231 1 TGCAAATGAA 0.867707 -70 ACTTGCACCCTGCGAAAAAACAGAATAAAA 3 84 1 TGCGAAAAAA 0.786644 -58 CGCATTATTTTACAAAAAACACACTAAACT 4 168 1 TACAAAAAAC 0.52553 -133 TGAATTTTTATGCAAAATAAATGAGTTTTC 4 228 0 TGCAAAATAA 0.932164 -73 GCTGACTGTTTGCATAAAAATTCATCTGTA 5 241 1 TGCATAAAAA 0.949361 -60 TTCATCTGTATGCACAATAATGTTGTATCA 5 261 1 TGCACAATAA 0.909831 -40 CCACAAAATATGCATAAAAAATCACTAAAT 6 23 0 TGCATAAAAA 0.949361 -63 GCGGCTCCGGTACAAAAGAACCGCGCTATT 7 11 0 TACAAAAGAA 0.770239 -21 GGCATTGAATTTCAAAATAAGGAAACAGAG 10 39 1 TTCAAAATAA 0.595959 -22 GCTTTAGACTTGCAAATGAATAATCATCCA 11 94 1 TGCAAATGAA 0.867707 -68 ATAGCACTAATACAAATAAAATGGACAAAA 13 11 1 TACAAATAAA 0.603606 -124 TGAATAAATATGCACAATAATAGAATAATT 13 92 1 TGCACAATAA 0.909831 -43 GCATAAGAATTGCATAAAAATTCACTTTCA 14 162 0 TGCATAAAAA 0.949361 -45 AGTCAAAATTTGCATAAGAATTGCATAAAA 14 173 0 TGCATAAGAA 0.925435 -34 TTTAGCTTTGTGCATAAAAAATCCTAATTT 15 11 0 TGCATAAAAA 0.949361 -145 TTGCTTTTAATGCACAAAACACTAGACAAA 15 50 1 TGCACAAAAC 0.840965 -106 AGAATTTTTATTCACAAAAATCGATTATTT 15 105 1 TTCACAAAAA 0.721515 -51 ********** Masking position 1 Map Score: 22.9336 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 229 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 6 ATCTCCAGAATGCCGCCGTTTGCCAGAAATT 1 194 1 TGCCCCGTTT 0.96086 -107 TAATCGTATCTGCCTCCGATTCTCTGCAGAA 2 152 0 TGCCCCGATT 0.960881 -149 CGGACGGGTTTGCCTCCACCTTTGTAAGAAA 2 193 1 TGCCCCACCT 0.979085 -108 AAACTCTTCCTGTCTCCGATAAAAGATGATT 4 193 1 TGTCCCGATA 0.716679 -108 TAGGGTATATTGTCACCACCTGTTGGAATGT 5 67 0 TGTCCCACCT 0.902131 -234 TTGAGAAACATGCCTGCGTCACGGCATGCAA 5 154 0 TGCCGCGTCA 0.911932 -147 CGGGCAAGATTGCCCGCGCGAGAAATCA 8 8 0 TGCCGCGCGA 0.916405 -97 CGGGCAATCTTGCCCGCGCTTCTGCTCTCCC 8 23 1 TGCCGCGCTT 0.978906 -82 CCACTGACATTGCCTCCACCTTTGTGACAAA 11 56 1 TGCCCCACCT 0.979085 -106 **** ****** Masking position 1 Map Score: 6.46223 Number of sites scoring better than the average of aligned sites = 1033 Number in coding regions = 989 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 7 TTTTGTCGCTTAATGCCTGTAAAACATGCAT 1 109 1 TAATGCCTGA 0.972775 -192 AAAGTCAACTTAATGGCGGGATTTTTTATAT 1 153 0 TAATGGCGGA 0.964719 -148 AATTTCTGGCAAACGGCGGCATTCTGGAGAT 1 194 0 AAACGGCGGA 0.808932 -107 TTTTTATCAGTAATGCCGTGAATATAAAAAG 3 30 0 TAATGCCGTA 0.8997 -112 TGGATCACTATAATGCCTGCAGATTTTACGT 4 39 0 TAATGCCTGA 0.973534 -262 CAAATCCGGGTTACGCCGGGAGAGCAGAAGC 8 40 0 TTACGCCGGA 0.921514 -65 TTTTGAAATTCAATGCCGGAAAGCTGCGCCT 10 25 0 CAATGCCGGA 0.961504 -36 CTCCTGTGGCTAACGCCTCAATGAATTAAAA 11 135 0 TAACGCCTCA 0.833403 -27 TTTCAACTGGTAATGCCAGTATGTAGAATTT 12 164 0 TAATGCCAGA 0.920856 -137 ********* * Masking position 3 Map Score: 5.72826 Number of sites scoring better than the average of aligned sites = 534 Number in coding regions = 496 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 8 GTCCACTTTTTTCTGCTCGTTTTTATTTCA 1 30 1 TTCTGCTCGT 0.884893 -271 TTTTGCCTTCTCCTGCTCTCCCTTAAGCGC 4 141 1 TCCTGCTCTC 0.968645 -160 CACTAAACTCTTCCTGTCTCCGATAAAAGA 4 189 1 TTCCTGTCTC 0.824899 -112 GAGCCTGGATTTCCGCTCTCACTGAATTTT 4 250 0 TTCCGCTCTC 0.986453 -51 TTTGATAAAATCCCGCTCTTTCATAACATT 5 193 1 TCCCGCTCTT 0.968645 -108 TTGCCCGCGCTTCTGCTCTCCCGGCGTAAC 8 32 1 TTCTGCTCTC 0.978682 -73 AATTTCATTTTACCTCTCTTATAATGCAAC 12 205 1 TACCTCTCTT 0.815742 -96 GATAAATATTTTCTTCTCTTTGTTCTTATT 14 118 1 TTCTTCTCTT 0.91879 -89 ********** Masking position 7 Map Score: 5.60314 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 159 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 TTCTACAACCAGGTCGAGTCAGAAATGAGA 2 101 0 AGGTCGAGTC 0.940747 -200 TTTCTTACAAAGGTGGAGGCAAACCCGTCC 2 194 0 AGGTGGAGGC 0.995518 -107 AAGGGAGAGCAGGAGAAGGCAAAAGTATTC 4 135 0 AGGAGAAGGC 0.928244 -166 ACATTCCAACAGGTGGTGACAATATACCCT 5 67 1 AGGTGGTGAC 0.944418 -234 TTTGTCACAAAGGTGGAGGCAATGTCAGTG 11 57 0 AGGTGGAGGC 0.995518 -105 ********** Masking position 1 Map Score: 2.81219 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 56 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 GTCAACTTAATGGCGGGATTTTTTATATTAT 1 150 0 TGGGGGATTT 0.95842 -151 GAATATTCTCTGGAGGGTGTT 1 290 1 TGGGGGTGTT 0.932801 -11 CTGCTGGGATTTGGTGTACCGA 4 2 1 TGCGGGATTT 0.966161 -299 ACTGATGATGAGCCTGGATTTCCGCTCTCAC 4 258 0 AGCTGGATTT 0.797081 -43 CAGTTAATTAAGCAGGGTGTTATTTT 4 285 1 AGCGGGTGTT 0.954905 -16 GTTATGAAAGAGCGGGATTTTATCAAATTTC 5 189 0 AGCGGATTTT 0.809471 -112 AATAGCGCGGTTCTTTTGTACCGG 7 4 1 AGCCGGTTCT 0.778016 -28 ACCTTACGGCTGGTGGGTTTTATTACGCTCA 9 63 1 TGGGGGTTTT 0.965984 -91 CGTTAGCCACAGGAGGGATCT 11 151 1 AGGGGGATCT 0.932799 -11 *** ******* Masking position 11 Map Score: 3.89865 Number of sites scoring better than the average of aligned sites = 452 Number in coding regions = 356 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 11 TTTTCCAGAACAGGTTAGATGATCTTTTTGT 1 84 1 CAGTTAGATG 0.909704 -217 AATATTCACTCACTTTATTTGCATATTAATT 1 266 0 CATTTATTTG 0.946652 -35 TGTTCTCCGCCATTTTAGAAGCATAATCCTT 2 46 1 CATTTAGAAG 0.872072 -255 AATTAAAATTCACTTTATATGTGTAATTATT 2 249 0 CATTTATATG 0.970465 -52 AATTAAAATTCAATTTATATGGATGATTATT 11 112 0 CATTTATATG 0.967385 -50 TCATTTTGTCCATTTTATTTGTATTAGTGCT 13 13 0 CATTTATTTG 0.940683 -122 ** ******** Masking position 6 Map Score: 1.70863 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 14 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 12 AATCATGCAAAGAGGTGTGCC 3 131 1 AGAGGTGTGC 0.985297 -11 TATCATGACCAGAGGTGTGTCAACA 9 139 1 AGAGGTGTGC 0.985297 -15 CAGGACATTAAGAGGAATGAGCC 11 3 0 AGAGGAATGG 0.967985 -159 AGGCAATGTCAGTGGTGTGTGACAATAAGAG 11 40 0 AGTGGTGTGG 0.967395 -122 TTTTTGATGAAGAGGAATGTGTCTATCTATA 12 21 0 AGAGGAATGG 0.967985 -280 ********* * Masking position 8 Map Score: 1.52209 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 4 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 13 TTTCATGCAATCTTCTTGCTGCGCAAGCGTT 1 55 1 TCTTTTGCTG 0.815728 -246 GGTTAGATGATCTTTTTGTCGCTTAATGCCT 1 96 1 TCTTTTGTCG 0.900666 -205 TCAATGCAAATCTGCTTACCGACGAATTTCT 1 218 0 TCTGTTACCG 0.918863 -83 TTAAGCAGAATTTGCATGCCGTGACGCAGGC 5 143 1 TTTGATGCCG 0.806084 -158 TTTCTGATTGCCATTTAGTGATT 6 3 1 TCTGTTGCCA 0.975395 -83 CCTTCTTATGTCTGGTTGCCAGGTTAAACGT 9 23 1 TCTGTTGCCA 0.975395 -131 GTTTTGTTGGCCGGAGGCGCAGC 10 3 1 TTTGTGGCCG 0.860354 -58 CTGCCGATACTCTTATTGTCACACACCACTG 11 31 1 TCTTTTGTCA 0.779939 -131 **** ****** Masking position 3 Map Score: 0.912192 Number of sites scoring better than the average of aligned sites = 936 Number in coding regions = 874 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 14 ********** No masking Map Score: -4.82215e-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 Motif number 15 TTACAGGCATTAAGCGACAAAAAGATCATC 1 101 0 TAAGCGACAA 0.894575 -200 ATATGGGCGCTAAAAGTCAACTTAATGGCG 1 166 0 TAAAAGTCAA 0.730733 -135 CTAATAAACGGTAAACATTCTTTT 3 5 1 TAAACGGTAA 0.770207 -137 AAAAGATGATTAAATGAAAACTCATTTATT 4 213 1 TAAATGAAAA 0.731905 -88 AAATTCTGCTTAAAAGTAAATTAATTGTTA 5 126 0 TAAAAGTAAA 0.629869 -175 AAAAAATCACTAAATGGCAATCAGAAA 6 8 0 TAAATGGCAA 0.810149 -78 GCCACAAGTATAAGCGGCAAATCCGGGTTA 8 58 0 TAAGCGGCAA 0.892672 -47 GTTGCCAGGTTAAACGTAAAACATTCACCT 9 37 1 TAAACGTAAA 0.89625 -117 TCATCAAAAATAAACTAAAACATATTTTCG 12 42 1 TAAACTAAAA 0.522079 -259 TAGATGAATTTAAACGAAAATATGTTTTAG 12 56 0 TAAACGAAAA 0.932722 -245 TACCAGTTGAAAAACGACAACAAATTTCAT 12 183 1 AAAACGACAA 0.737478 -118 ********** Masking position 3 Map Score: 3.01483 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 310 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432