AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -inagC_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 nagD 47 N-acetylglucosamine metabolism #2 nagA 59 N-acetylglucosamine-6-phosphate deacetylase #3 nagB_nagE 332 nagB: glucosamine-6-phosphate deaminase, nagE: PTS system, N-acetylglucosamine-specific enzyme IIABC #4 manX 300 PTS enzyme IIAB, mannose-specific #5 manY 62 PTS enzyme IIC, mannose-specific #6 glmS 161 L-glutamine:D-fructose-6-phosphate aminotransferase #7 glmU 300 N-acetyl glucosamine-1-phosphate uridyltransferase #8 HI0140 272 N-acetylglucosamine-6-phosphate deacetylase (nagA) #9 HI0141 285 glucosamine-6-phosphate isomerase (nagB) #10 HI0144 45 glucose kinase, putative #11 HI0145 300 conserved hypothetical protein #12 HI0429 111 glucosamine--fructose-6-phosphate aminotransferase (glmS) #13 HI0431 35 conserved hypothetical protein #14 HI0432 66 conserved hypothetical protein #15 HI0433 75 orfG protein #16 HI0439 98 competence protein A (comA) #17 HI0638 128 conserved hypothetical protein #18 HI0639 22 adenylosuccinate lyase (purB) #19 HI0640 271 ribosomal protein L10 (rpL10) #20 HI0641 54 ribosomal protein L7/L12 (rpL7/L12) #21 HI0642 159 UDP-N-acetylglucosamine pyrophosphorylase (glmU) Motif number 1 AAGCCGTATTTTTATTTTGCTGCAAATTGTACTGCC 3 48 1 TTTATTTAAA 0.857796 -285 TCCGACCTGATTTTTTGAATGATAAAATAAGTTTTC 3 223 0 TTTTTTGAAA 0.940685 -110 GTGACAAGGATATTTTACCTTTCGAAATTTCTGCTA 4 97 1 TATTTTTGAA 0.812648 -204 TCGAAAAAATTATTTTATGTGATGAAGATCCGTAAT 4 145 0 TATTTTGGAA 0.794795 -156 ATAAAATAATTTTTTCGATATCTAAAATAAATCGCG 4 163 1 TTTTTCTAAA 0.754988 -138 AAAACTACATTTTTTTCATCGTGAAATGGACAGAGG 7 225 0 TTTTTTGAAA 0.958796 -76 AAAAATGTAGTTTTTTCAAGGTGAAGCGGTTTAAAT 7 247 1 TTTTTTGAAG 0.844604 -54 GGGAGGTAAGTTTTTTCTAATTTAAATAT 9 4 0 TTTTTTTAAA 0.963018 -282 CTCCCCCTGTTTTATTCCGTTACAAACAGAACAGCA 9 35 1 TTTATTTAAA 0.857548 -251 TCTCGAATCCTATTTTGGGGGAGAAAACATACATTT 11 36 0 TATTTTGAAA 0.88289 -265 TTAAATTTGTTTTTTTACTCTTAGAATTGCTCTCGA 11 66 0 TTTTTTTGAA 0.930528 -235 TTTAAAGTGATTTATTCAGATTTAAATGAGGGGTGT 11 272 1 TTTATTTAAA 0.857752 -29 TGCGCAGGGGTTTTTTATTGTGTAAACGCGTGGCAA 12 44 1 TTTTTTTAAA 0.963018 -68 AAAGTGCGGTTATTTTTATGGAGAAAAA 14 49 1 TATTTTGAAA 0.88289 -18 AACTCTAGGCTTTTTTAATGTTCGAGTTCAAAAGCT 17 55 1 TTTTTTTGAG 0.757648 -74 TTCCCATCGGTTTTTTGAATTTTAAAGTGGTTAAAA 21 17 0 TTTTTTTAAA 0.963018 -143 AAACCATCGGTTTTTTCTTATATAAAAGTTTGTTAT 21 51 1 TTTTTTTAAA 0.960064 -109 ****** * *** Masking position 5 Map Score: 18.4899 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 84 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 2 TCATTGATCGAAATAAGAGCAAAAACATCCACC 7 84 1 AAAAGAGCAA 0.898444 -217 CTTCATCTTTATGTAGGGGCGAATTACATTCGC 8 20 1 ATAGGGGCAA 0.959005 -253 TCTTGTTGAGATTATAGGGCGAATGTAATTCGC 8 38 0 ATTAGGGCAA 0.950613 -235 CCTATAATCTCAACAAGAGCTAAAAGTGAAAAC 8 53 1 CAAAGAGCAA 0.602972 -220 CTTCATCTTTATGTAGGGGCGAATTACATTCGC 8 156 1 ATAGGGGCAA 0.959005 -117 ATTGTTTGTGATTATAGGGCGAATGTAATTCGC 8 174 0 ATTAGGGCAA 0.950613 -99 ATCACAAACAATCATAGGGCAAATTGTCCTTAC 8 195 1 ATTAGGGCAA 0.950613 -78 CTGTCGTAAATTATTGGAGCAAAAGAATTTCTT 9 146 1 TTTGGAGCAA 0.840078 -140 TGCGGTTATTTTTATGGAGAAAAA 14 53 1 TTTGGAGAAA 0.4878 -14 TACAATTCTGGAGCAAACATTT 18 5 1 ATTGGAGCAA 0.962574 -18 AATATTGTTGAAAAAAGAGCCAAATTC 19 5 0 AAAAGAGCAA 0.898444 -267 CAGGCGCAGGATTATAGAGAAAAGCTATGTTCT 19 45 0 ATTAGAGAAA 0.793247 -227 ATCGGAGTGTATTCAGGAGCTAAAAGCCA 19 253 1 ATAGGAGCAA 0.962574 -19 GTTATTGATGAATAAAGAGAAAATTT 21 144 1 AAAAGAGAAA 0.615959 -16 ** ****** ** Masking position 12 Map Score: 14.5576 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 99 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 3 TCACAAAAGACACGCGTTTAATTTGCGATAC 3 142 0 CCGCGTTTAA 0.93215 -191 GTTATTATCACTCCCTTTTACTGGCTAAACC 3 191 1 CCCCTTTTAC 0.926163 -142 ATATGTTTAACTCCCGTTTAACAACCATGGA 4 17 0 CCCCGTTTAA 0.968716 -284 TGTACTTCTCCTGTTTACGTAAGACTTA 5 45 0 CCCTGTTTAC 0.985288 -18 AACCTGTATGCCCGTTTTTTCGGGCGCCCCG 6 108 0 CCGTTTTTTC 0.7782 -54 ATATAAAACCCCCCTGTTTTCCTGTTTATTC 7 55 1 CCCTGTTTTC 0.978608 -246 AACTTACCTCCCCCTGTTTTATTCCGTTACA 9 28 1 CCCTGTTTTA 0.951272 -258 CACTTTCCTTCCCCTGTTTACGGGGGAAGGT 9 81 1 CCCTGTTTAC 0.985288 -205 TTACATTTGCCACGCGTTTACACAATAAAAA 12 55 0 CCGCGTTTAC 0.969873 -57 TATAATCCTGCGCCTGTGTTAGTCAATCTAA 19 62 1 CCCTGTGTTA 0.802811 -210 * ********* Masking position 7 Map Score: 12.3849 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 202 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 4 TAGCCAGTAAAAGGGAGTGATAATAACGATATTT 3 184 0 AAGGGATGAT 0.606334 -149 ATTCGTTTGCAAAGGAAGGTAAATCTTTGCCAAA 4 63 0 AAAGGAGGAT 0.964856 -238 AGCCTTGTAGAGAGTGGGGTTATTTTTATAGTTA 6 74 0 AGAGTGGGAT 0.948202 -88 ATTGCTCTTAAACGTAAGGACAATTTGCCCTATG 8 207 0 AACGTAGGAT 0.909091 -66 GGAATAAAACAGGGGGAGGTAAGTTTTTTCTAAT 9 19 0 AGGGGGGGAT 0.945919 -267 CCCCGTAAACAGGGGAAGGAAAGTGCTTGCTGAC 9 72 0 AGGGGAGGAT 0.916164 -214 AGGATCATTATAAGTGCGGCAATTTTCTATCTTG 9 187 0 TAAGTGGGAT 0.791348 -99 GGTCAATAATAAAGGAAGGCTAAT 9 272 1 AAAGGAGGAT 0.964856 -14 TTATTGTGTAAACGCGTGGCAAATGTAAAAACAA 12 58 1 AACGCGGGAT 0.831221 -54 CGCACTTTCAAAAGTGCGGTCATTATAAATCTTC 14 23 0 AAAGTGGGAT 0.970365 -44 CGCACTTTTGAAAGTGCGGTTATTTTTATGGAGA 14 39 1 AAAGTGGGAT 0.970365 -28 TACTTGAGAGAAAGTATCGGGAATAATACGCTTA 15 38 0 AAAGTACGAT 0.704939 -38 ****** ** * * Masking position 12 Map Score: 7.51572 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 146 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 5 CTTATTCCCCCTACGAGAACCCTAT 3 6 1 TCCCCCTACG 0.969421 -327 AGATGCCTAATCCGCCAACGGCTTACATTT 3 295 1 TCCGCCAACG 0.715958 -38 GCAAAAACATCCACCTGACGCTTAAATTAA 7 102 1 CCACCTGACG 0.877097 -199 ACGGATTATCCCCGCTGACGAAAGCGCCAT 7 180 0 CCCGCTGACG 0.918178 -121 GAATGTAATTCGCCCCTACATAAAGATGAA 8 21 0 CGCCCCTACA 0.940337 -252 GAATGTAATTCGCCCCTACATAAAGATGAA 8 157 0 CGCCCCTACA 0.940337 -116 ATAGAAGTTGCCCCCTTCCGCCCTTCGGGC 9 112 0 CCCCCTTCCG 0.91519 -174 GGACTTTAGCCCACCCTACACCAAAGGATC 9 215 0 CCACCCTACA 0.935897 -71 GGGCTAAAGTCCAGCCTACGATATGAATAG 9 233 1 CCAGCCTACG 0.958259 -53 ATTAAGATTACTCCCCTACGGTCTTGGATG 19 128 0 CTCCCCTACG 0.953442 -144 ********** Masking position 5 Map Score: 7.64379 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 280 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 6 ACGGCTTACATTTTACTTATTGAGGTGAAT 3 312 1 TTTTACTTAT 0.905105 -21 AACCCCCCTGTTTTCCTGTTTATTCATTGA 7 61 1 TTTTCCTGTT 0.708797 -240 CCGTGAAATATTTTACTGAATTAGAAGGCG 8 85 1 TTTTACTGAA 0.797085 -188 AGATCTCTATTTATCCTGATAATCCGTACC 8 123 0 TTATCCTGAT 0.938518 -150 AGTTGCTATGTTAAACTGATGTTGATATTA 8 243 1 TTAAACTGAT 0.642629 -30 AACTTATCCTTATAGTGTAAAGT 10 33 0 TTATCCTTAT 0.929466 -13 TTTTCATCATTTAACCTTATTATATGAAAA 11 191 0 TTAACCTTAT 0.746986 -110 AAGTTTTCCTTATTTATTCTATT 12 99 0 TTTTCCTTAT 0.947756 -13 GCTGAATCTTTTATACTTAACAGCCAAATC 16 58 0 TTATACTTAA 0.711245 -41 AACGGAAACGTTTTCCTGATATTTACTA 17 111 1 TTTTCCTGAT 0.954575 -18 AACCATCGGTTTTTTCTTATATAAAAGTTT 21 52 1 TTTTTCTTAT 0.701764 -108 TTGTTATAGTTTTTACTTAAAAACTTACCA 21 80 1 TTTTACTTAA 0.772263 -80 ********** Masking position 7 Map Score: 7.3304 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 169 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 7 ACCCCCGATTTTAAAAAATATTGCCCTGAG 2 36 0 TTAAAAAATA 0.752209 -24 CTACATAAAGATGAAGAATAGATCT 8 6 0 ATGAAGAATA 0.925217 -267 CTACATAAAGATGAAGAATAGATCTCTATT 8 142 0 ATGAAGAATA 0.925217 -131 AAATGCCATTTTAAAGAATATTTTTGAAGT 11 159 0 TTAAAGAATA 0.939085 -142 ACCTTATTATATGAAAAATAAATGCCATTT 11 178 0 ATGAAAAATA 0.708981 -123 TCTCGCTTCGTTAATGAATATTCTTGTCAA 16 19 1 TTAATGAATA 0.829689 -80 GATTCAGCCTTTAAAGAATAGGAAAGAAT 16 80 1 TTAAAGAATA 0.939085 -19 CTATGTTCTTGTAAAGAATATTGTTGAAAA 19 24 0 GTAAAGAATA 0.849327 -248 CCCGTTGTTATTGATGAATAAAGAGAAAAT 21 138 1 TTGATGAATA 0.862485 -22 ********** Masking position 4 Map Score: 5.66863 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 102 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 8 ACTCCCGTTTAACAACCATGGAGTATAG 4 9 0 AACAACCATG 0.72784 -292 GCTACAACCAAAAACCCCTGCGTTTCGCGA 4 194 0 AAAACCCCTG 0.97694 -107 CTATAAAAATAACCCCACTCTCTACAAGGC 6 77 1 AACCCCACTC 0.763876 -85 GCTGATATAAAACCCCCCTGTTTTCCTGTT 7 51 1 AACCCCCCTG 0.985644 -250 ATAACGGATTATCCCCGCTGACGAAAGCGC 7 183 0 ATCCCCGCTG 0.869319 -118 ATAACACCCCTCATTTAAATCT 11 289 0 AACACCCCTC 0.962053 -12 TACACAATAAAAAACCCCTGCGCAATCGAC 12 38 0 AAAACCCCTG 0.97694 -74 TAAAATTCAAAAAACCGATGGGAAACCATC 21 29 1 AAAACCGATG 0.895113 -131 TATATAAGAAAAAACCGATGGTTTCCCATC 21 45 0 AAAACCGATG 0.895113 -115 ********** Masking position 9 Map Score: 5.32405 Number of sites scoring better than the average of aligned sites = 426 Number in coding regions = 376 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 9 TTGTTATCCCTGCCCTGGCTCCTTGCTC 2 9 1 CCTGCCCTGG 0.957928 -51 CAAAGATTTACCTTCCTTTGCAAACGAATG 4 68 1 CCTTCCTTTG 0.88144 -233 AAAAAACTTACCTCCCCCTGTTTTATTCCG 9 24 1 CCTCCCCCTG 0.988154 -262 CAAGCACTTTCCTTCCCCTGTTTACGGGGG 9 77 1 CCTTCCCCTG 0.993017 -209 CCTTCGGGCACCTTCCCCCGTAAACAGGGG 9 91 0 CCTTCCCCCG 0.98463 -195 TCTCTATAATCCTGCGCCTGTGTTAGTCAA 19 58 1 CCTGCGCCTG 0.971325 -214 ********** Masking position 3 Map Score: 4.36122 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 75 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 10 AAAGGTAAAATATCCTTGTCACATTCGTTTGCAA 4 85 0 TATCCTTAAT 0.954618 -216 TTAAATTACGGATCTTCATCACATAAAATAATTT 4 141 1 GATCTTTAAT 0.887126 -160 TGTACTTCTCCTGTTTACGTAAGACTTAAG 5 43 0 TCTCCTTAGT 0.748157 -20 GATTATGTTATCTCCTCATCCCATGTGACCGGGT 6 24 0 TCTCCTTCAT 0.906317 -138 CGTTCACATAGATCCTGCTGATATAAAACCCCCC 7 35 1 GATCCTTAAT 0.960579 -266 GGATGTTTTTGCTCTTATTTCGATCAATGAATAA 7 80 0 GCTCTTTCAT 0.783297 -221 TTGAACAATTTATCCTCTGTCCATTTCACGATGA 7 212 1 TATCCTGCAT 0.802979 -89 TTCACTTTTAGCTCTTGTTGAGATTATAGGGCGA 8 49 0 GCTCTTTAAT 0.866054 -224 TGACCGTGATGATCCTATTCATATCGTAGGCTGG 9 243 0 GATCCTTAAT 0.960579 -43 TTTCATCATTTAACCTTATTATATGAAAAATAAA 11 186 0 TAACCTTAAT 0.709002 -115 TAATCTTAATTATCCTACGTAGATGGTGAACAGA 19 148 1 TATCCTGAAT 0.879376 -124 TACCATTTGCTATCTTTCTAAGATAGAATATTAC 21 105 1 TATCTTTAAT 0.871544 -55 ****** * * ** Masking position 6 Map Score: 5.39038 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 35 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 11 TTGACAACAATAAGCGCCACTATAAAAGCA 1 13 0 TAAGCGCCAC 0.798579 -35 CCCGCTGACGAAAGCGCCATTTTCGACCAT 7 170 0 AAAGCGCCAT 0.92991 -131 ACTGAATTAGAAGGCGCGGTTGCTGGTACG 8 99 1 AAGGCGCGGT 0.950761 -174 AGGATCATTATAAGTGCGGCAATTTTCTAT 9 191 0 TAAGTGCGGC 0.90381 -95 CGCACTTTCAAAAGTGCGGTCATTATAAAT 14 27 0 AAAGTGCGGT 0.96978 -40 CGCACTTTTGAAAGTGCGGTTATTTTTATG 14 39 1 AAAGTGCGGT 0.96978 -28 ACTGGAAAAAAAAGCGCGATAAGCGTATTA 15 19 1 AAAGCGCGAT 0.969564 -57 ********** Masking position 2 Map Score: 3.64736 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 303 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 12 CTTTTGTGAGTTTTGTCACCAAATATCGTTATT 3 164 1 TTTGTCAAAA 0.681741 -169 ATTCTGTTCCTAATATCAACATCA 8 259 0 TTTGTTCAAT 0.808383 -14 AAACATACATTTTTGGCCTAAATTGATTCTCAT 11 15 0 TTTGGCCAAT 0.835762 -286 TTTACGAGTTTTATTTCCAAAATGAGAAGTTGA 11 108 1 TTTTTCCAAT 0.957484 -193 TTTTGAAGTGTTTTTTCATAAATGTGATCAACT 11 135 0 TTTTTCAAAT 0.933821 -166 CTTATTTCCTTAATTCGTAAGAGT 13 22 0 TTTTTCCAAT 0.957493 -14 AATTATGTCCTAAATACTTGAGAGA 15 61 0 TTTGTCCAAT 0.960636 -15 AATTTGGCTCTTTTTTCAACAATATTCTTTACA 19 12 1 TTTTTCAAAT 0.933842 -260 CTAACTTTATTTATTTTAGGAATTGATTGTT 20 34 1 TTTTTTAAAT 0.709455 -21 AAATTTTCTCTTTATTCATCAATAACAACGGGT 21 137 0 TTATTCAAAT 0.665273 -23 ** ***** *** Masking position 11 Map Score: 3.86693 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 43 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 AATTACATTCGCCCTATAATCTCAACAAGA 8 41 1 GCCCTATAAT 0.98296 -232 AATTACATTCGCCCTATAATCACAAACAAT 8 177 1 GCCCTATAAT 0.98296 -96 AGGACAATTTGCCCTATGATTGTTTGTGAT 8 195 0 GCCCTATGAT 0.988913 -78 CTTGTCAAGAGACCTATGATTTGGCTGTTA 16 41 1 GACCTATGAT 0.957367 -58 ********** Masking position 5 Map Score: 2.62256 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 2 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 Motif number 14 TGTGCTTTTATAGTGGCGCTTATTGTTG 1 6 1 TTTTAGTGCG 0.816388 -42 GTGGGGTTATTTTTATAGTTACTGCTTGTGGGA 6 62 0 TTTTAGTTCT 0.857461 -100 CGTAAAACTATTTTAAATTTGTTTTTTTACTCT 11 81 0 TTTTATTTTT 0.672967 -220 TAAAGAATATTTTTGAAGTGTTTTTTCATAAAT 11 145 0 TTTTAGTGTT 0.962753 -156 ATTAAATTAATTTTAAAGTGATTTATTCAGATT 11 261 1 TTTTAGTGTT 0.962753 -40 TGCGCAGGGGTTTTTTATTGTGTAAACGCGTGG 12 44 1 TTTTATTGGT 0.691746 -68 TCGCGCTTTTTTTTCCAGTGCTTTATA 15 5 0 TTTTAGTGTT 0.962753 -71 ACCAGAAATTTGTTAGATTGACTAACACAGGCG 19 72 0 TGTTATTGCT 0.721186 -200 GTTTTTTGAATTTTAAAGTGGTTAAAATAGAAA 21 11 0 TTTTAGTGTT 0.962753 -149 TATAAAAGTTTGTTATAGTTTTTACTTAAAAAC 21 71 1 TGTTAGTTTT 0.758215 -89 **** **** ** Masking position 7 Map Score: 3.16038 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 88 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 15 ATAAAGATGAAGAATAGATCT 8 1 0 AGAATAGTCT 0.957219 -272 ATAAAGATGAAGAATAGATCTCTATTTATCC 8 137 0 AGAATAGTCT 0.957219 -136 TTGGAGCAAAAGAATTTCTTTTTAAAAACAA 9 159 1 AGAATTTTTT 0.849771 -127 TTTTACTCTTAGAATTGCTCTCGAATCCTAT 11 59 0 AGAATTGTCT 0.933067 -242 AAACAAATTTAAAATAGTTTTACGAGTTTTA 11 90 1 AAAATAGTTT 0.615672 -211 GCCATTTTAAAGAATATTTTTGAAGTGTTTT 11 154 0 AGAATATTTT 0.898423 -147 GTTCTTGTAAAGAATATTGTTGAAAAAAGAG 19 19 0 AGAATATGTT 0.706914 -253 GAACAGAATAAGAATTTTTCTTGCTTCTGGG 19 175 1 AGAATTTTCT 0.867655 -97 ******* *** Masking position 4 Map Score: 1.44617 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 65 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234