AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00020_ecoli_reg_300.orf -o00020_ecoli_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 lpdA 300 lipoamide dehydrogenase (NADH); component of 2-oxodehydrogenase and pyruvate complexes; L-protein of glycine cleavage complex #2 acnB 300 aconitate hydrase B #3 prpC 41 putative citrate synthase; propionate metabolism? #4 citC 291 citrate lyase synthetase (citrate (pro-3S)-lyase ligase #5 gltA_sdhC 600 gltA: citrate synthase, sdhC: succinate dehydrogenase, cytochrome b556 #6 BIME45 63 BIME #7 sucC 85 succinyl-CoA synthetase, beta subunit #8 icdA 201 isocitrate dehydrogenase, specific for NADP+ #9 acnA 300 aconitate hydrase 1 #10 fumC 142 fumarase C= fumarate hydratase Class II; isozyme #11 fumA 198 fumarase A = fumarate hydratase Class I; aerobic isozyme #12 mdh 300 malate dehydrogenase #13 pckA 300 phosphoenolpyruvate carboxykinase #14 fumB 77 fumarase B= fumarate hydratase Class I; anaerobic isozyme #15 dcuB 300 anaerobic dicarboxylate transport #16 frdA 294 fumarate reductase, anaerobic, flavoprotein subunit Motif number 1 GCGAATAGACAAATCGGTTGCCGTTTGTTGTTT 1 51 1 ATCGGTGCCG 0.805325 -250 CATACCCGTCGTCTTTCAGGCCGCAGCGGCGTT 1 248 0 GTTTCGGCCG 0.801012 -53 GGTGATAATCACCTTTCTCAACGAATCCCAAGA 2 54 0 ATTTCCAACG 0.509777 -247 AGCGTGAAGAGAATCGCCTGCCGCACTATGACA 2 257 1 GTCGCTGCCG 0.967024 -44 AAATAAATCAAAATTTCACGCCGAAATACTCCT 4 213 1 ATTTCCGCCG 0.932742 -79 TGGAAGCAGTGTTTTGCATGACGCGCAGTTATA 5 30 0 GTTGCTGACG 0.951147 -571 CCCGTTTTTTATTTGGCTCGCCGCTCTGTGAAA 5 503 0 ATGGCCGCCG 0.963843 -98 AATAACGCGCATCTTTCATGACGGCAAACAATA 8 49 1 ATTTCTGACG 0.910686 -153 TAAAGCATCCGTATCGCAGGACGCAAACGCATA 8 129 1 GTCGCGGACG 0.832067 -73 GATAACACAAACATCGCGTAACGATTTGATAAC 9 220 0 ATCGCTAACG 0.798367 -81 AGTGAGCTAAAAGTTGCTTAACGAAAGCAAAAC 10 86 1 ATTGCTAACG 0.84356 -57 TTTTAAGCAGAATTTGCATGCCGTGACGCAGGC 12 14 0 ATTGCTGCCG 0.986285 -287 ATAAACGCTAAACTTGCGTGACTACACATTCTT 12 185 1 ATTGCTGACT 0.649503 -116 ATGCACTTTGCGTGCCGCCCGTGACTA 14 5 1 ATTGCTGCCG 0.986285 -73 TGTTATTCGAAAATGGCGTGCCGCGTAGTCACG 14 30 0 ATGGCTGCCG 0.975729 -48 CCTGCGTAAAATTTGTCTCGCCGTCGCGTTGCG 16 21 0 ATGTCCGCCG 0.885753 -274 * **** ***** Masking position 4 Map Score: 17.9418 Number of sites scoring better than the average of aligned sites = 1003 Number in coding regions = 947 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 2 GGATAGAACGACCCGGTGGTGGTTAGGGTATT 1 116 1 ACCGGTGTGG 0.885091 -185 CGTGAAGCTAACGCCGCTGCGGCCTGAAAGAC 1 239 1 ACGCGCGCGG 0.961721 -62 TCCGAGTATAAAGAGGCGGTAGTTTAAATTTT 2 16 1 AAGGGCGTAG 0.819435 -285 TGTTCCGGAGACCTGGCGGCAGTATAGGCTGT 5 111 1 ACCGGCGCAG 0.942233 -490 CCCCTCTTTCACAGAGCGGCGAGCCAAATAAA 5 497 1 ACAAGCGCGA 0.815414 -104 CGCATATGCAACGTGGTGGCAGACGAGCAAAC 8 156 1 ACGGGTGCAG 0.814165 -46 CTGATCCTTGACCCCGCTGCGGCGGGGTTGTC 9 144 1 ACCCGCGCGG 0.952042 -157 CTCCTTAATGACAGGGTTGCGAAGCCCTGATT 9 274 0 ACAGGTGCGA 0.729937 -27 CTCGCTTTTAACAGGGCAACGGAACACCCGCC 11 140 1 ACAGGCACGG 0.576146 -59 GCATAACCAAACCAGGCAGTAAGTGAGAGAAC 11 176 1 ACCGGCGTAA 0.837606 -23 GCAACATTCCAACAGGTGGTGACAATATACCC 12 92 0 AACGGTGTGA 0.517034 -209 TGGATTAAGGTCGCGGCAGCGGAGCAACATAT 12 248 1 TCGGGCGCGG 0.88092 -53 CATATTGGCTAAGGAGCAGTGAA 13 288 1 AAGAGCGTGA 0.742512 -13 TGGCTGATTAAAGCAGCGGCAAATTTATGCAC 15 137 0 AAGAGCGCAA 0.499075 -164 TTTAGCAAATACCTCACAGTGAATATTGGCTG 15 163 0 ACCCACGTGA 0.426436 -138 ACAAAACAGAACGTGACTGTGATCTATTCAGC 15 244 1 ACGGACGTGA 0.823795 -57 TCTACTCGCAACGCGACGGCGAGACAAATTTT 16 15 1 ACGGACGCGA 0.877561 -280 CGCAGGAATCAAACAGCGGTGGGCAGTGACTA 16 48 1 AAAAGCGTGG 0.594472 -247 TGTACCTATAAAGGAGCAGTGGAATAGCGTTC 16 202 1 AAGAGCGTGG 0.849738 -93 ACCCTGAAGTACGTGGCTGTGGGATAAAAACA 16 258 1 ACGGGCGTGG 0.987199 -37 *** *** **** Masking position 1 Map Score: 16.2381 Number of sites scoring better than the average of aligned sites = 3884 Number in coding regions = 3703 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 3 GATTTCTGGGTGCAGCAAGGTAGCAAGCGC 1 165 1 TGCAGCAAGG 0.76739 -136 TCTTTCAGGCCGCAGCGGCGTTAGCTTCAC 1 240 0 CGCAGCGGCG 0.921931 -61 TGCCCAGTACCGCAACGGGCAGAATAGCAG 2 199 0 CGCAACGGGC 0.950341 -102 ATTGTCATAGTGCGGCAGGCGATTCTCTTC 2 262 0 TGCGGCAGGC 0.949272 -39 TCTTTCACAGAGCGGCGAGCCAAATAAAAA 5 501 1 AGCGGCGAGC 0.753168 -100 GCATCCGTATCGCAGGACGCAAACGCATAT 8 133 1 CGCAGGACGC 0.850152 -69 ACAACCCCGCCGCAGCGGGGTCAAGGATCA 9 145 0 CGCAGCGGGG 0.986616 -156 GGATTAAGGTCGCGGCAGCGGAGCAACATA 12 249 1 CGCGGCAGCG 0.938729 -52 GGGTGTTAACCGCGACAAGGCTCATAGATT 13 230 0 CGCGACAAGG 0.919637 -71 CGTAGTCACGGGCGGCACGCAAAGTGCAT 14 10 0 GGCGGCACGC 0.874664 -68 CCCGTGACTACGCGGCACGCCATTTTCGAA 14 28 1 CGCGGCACGC 0.981782 -50 CTACTCGCAACGCGACGGCGAGACAAATTT 16 16 1 CGCGACGGCG 0.927567 -279 TTTTTTAGTGCGCAAGAGGGCTAAATTATC 16 128 0 CGCAAGAGGG 0.810228 -167 ********** Masking position 3 Map Score: 11.4247 Number of sites scoring better than the average of aligned sites = 2705 Number in coding regions = 2581 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 4 TTTACAAAATTGTTAACAATTTTTAAACAAC 1 77 0 TGTTACAATT 0.817479 -224 GGTGTTAATCTGTTTACAAAAAAGCAACATA 2 157 0 TGTTACAAAA 0.913827 -144 CAGTATAGGCTGTTCACAAAATCATTACAAT 5 130 1 TGTTACAAAA 0.913827 -471 GTTTCTCCTCTTTTATCAATTTGGGTTGTTA 9 193 1 TTTTTCAATT 0.649047 -108 CAATTTGGGTTGTTATCAAATCGTTACGCGA 9 209 1 TGTTTCAAAT 0.959271 -92 ACCAAACATTTGTTATCAAATGGTAAATAAT 10 54 1 TGTTTCAAAT 0.959271 -89 CTACACACTTTTTTAACAAAAACTGAGACTA 11 99 0 TTTTACAAAA 0.702841 -100 GTAAATTAATTGTTATCAAATTGATGTTGTT 12 47 1 TGTTTCAAAT 0.959271 -254 GTGTGGAAAATGTTCTCAAAAGGTTAAATCT 13 111 0 TGTTTCAAAA 0.93954 -190 TCACGGAGTTTTTTGTCAAATATGAATTTCT 13 188 1 TTTTTCAAAT 0.801781 -113 **** ****** Masking position 4 Map Score: 9.24191 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 40 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 CAACATTTTAATTACATCCGTCAAAGAGGCTCGGG 4 30 0 ATTAATTAAA 0.956432 -262 AATTTTATTCATTAAATCAATTAAATCACTTAAAC 4 101 1 ATTAATTAAA 0.954732 -191 TCATTTCGTAATTACATTAATTAAAAAACTTAAAA 4 143 1 ATTAATTAAA 0.956368 -149 ACTTAAAATCATTAAATAAATAAAAAACCACTAAC 4 170 1 ATTAATTAAA 0.956126 -122 TGATTGTCAAATTAGATGATTAAAAATTAAATAAA 5 222 0 ATTAATTAAA 0.956126 -379 GATTACGGCAATTAAATGCATAAACGCTAAACTTG 12 166 1 ATTAATTAAC 0.955578 -135 TAAACTCCTTATTATATTGATAAACTAAGATATGT 12 274 0 ATTAATTAAC 0.955589 -27 AAGATGATTAATTTAATTACTAAACCATCAGATCG 16 89 0 ATTTATTAAC 0.793818 -206 **** ** * *** Masking position 6 Map Score: 5.41975 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 18 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 GGGAAACAATCTCTAGACCATCCTTAACGATTC 2 113 1 CTCAGACACC 0.963531 -188 GTCAAAGAGGCTCGGGACAACCCGCAAGGAAAA 4 13 0 CTCGGAAACC 0.987619 -279 GCCGCCAGGTCTCCGGAACACCCTGCAATCCCG 5 98 0 CTCGGACACC 0.987372 -503 AATTCATAATCTCTGAAAATACC 8 1 0 CTCGAAATCC 0.948484 -201 CAAAAAATTGCTCTAAAGCATCCGTATCGCAGG 8 116 1 CTCAAACACC 0.943365 -86 TGCGATTCCACTCACAATATTCCCGCCATATAA 13 74 1 CTCCAAATCC 0.905866 -227 GAGTCTTTCTCTCTGAAAAAGCCGCTTATCACA 15 104 1 CTCGAAAACC 0.980504 -197 GTGTGAACCCTCGCGATAATCCTATTTAAATT 15 279 0 CTCCGAAACC 0.976578 -22 *** *** ** ** Masking position 7 Map Score: 6.80971 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 34 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 CGTTCTATCCGTCGGTATTTTACAAAATTG 1 96 0 GTCGGTATTT 0.947426 -205 AGTATAAAGAGGCGGTAGTTTAAATTTTGA 2 20 1 GGCGGTAGTT 0.961605 -281 CATATAGTTTGTCGGGTTTTATCCTGAACA 5 168 1 GTCGGGTTTT 0.965913 -433 AAGTTATGAAGTCGGTATTTCACCTAAGAT 5 306 1 GTCGGTATTT 0.947426 -295 GTCCTGGATGGGCGCGTTTTCTCTGTCGAT 9 78 1 GGCGCGTTTT 0.918375 -223 CGCCCTTCGGGGCGGTTTTTTTACATGGCA 10 18 1 GGCGGTTTTT 0.979783 -125 TTATGCTCTGGGCGGGTGTTCCGTTGCCCT 11 152 0 GGCGGGTGTT 0.975237 -47 ********** Masking position 9 Map Score: 5.66813 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 186 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 8 TTTCGCATCTGGAAGCAGTGTTTTGCATGA 5 42 0 GGAAGCAGTG 0.925048 -559 AGCGGGGTCAAGGATCAGTGAGTAATGATC 9 132 0 AGGATCAGTG 0.971226 -169 CACCCTGAAGAGAATCAGGGCTTCGCAACC 9 262 1 AGAATCAGGG 0.904357 -39 TAATCAGGTGAGGAGCAGGTC 10 132 1 AGGAGCAGGT 0.927597 -11 ATATTGGCTAAGGAGCAGTGAA 13 289 1 AGGAGCAGTG 0.990088 -12 GTACCTATAAAGGAGCAGTGGAATAGCGTT 16 203 1 AGGAGCAGTG 0.990088 -92 ********** Masking position 4 Map Score: 4.3084 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 48 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 9 AATACTCCTTAGGATGTATAGCGAAAGGAGAAA 4 237 1 AGTGTAAGCG 0.906603 -55 TTTTGTGAACAGCCTATACTGCCGCCAGGTCTC 5 118 0 AGTATATGCC 0.982226 -483 TACCAGGAAAAGCATATAATGCGTAAAAGTTAT 5 280 1 AGTATATGCG 0.982219 -321 TTGCCGGAGAAGGCGATAATGCCTTATCCGGTC 6 36 0 AGGATATGCC 0.936216 -28 GCGCGTTATTAGGCTATAATGCGGCAATTCATA 8 26 0 AGTATATGCG 0.982226 -176 GCTGAACGGTAGGGTATATTGTCACCACCTGTT 12 81 1 AGTATATGTC 0.860551 -220 CTCCTTAGCCAATATGTATTGCCTGAATAGTAA 13 271 0 AATGTATGCC 0.85813 -30 ATGGGTTTATAGTTTGTACTGCGCAGATGTTAA 15 64 0 AGTGTATGCG 0.981873 -237 ** **** **** Masking position 8 Map Score: 3.17165 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 20 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 AAAATTGTTAACAATTTTTAAACAACAAACGGCA 1 69 0 ACAATTAACA 0.803746 -232 TAATCTGTTTACAAAAAAGCAACATAAAAAAGTG 2 149 0 ACAAAAAACA 0.962705 -152 AAATCATTAAATAAATAAAAAACCACTAACTCTA 4 175 1 ATAAAAAACC 0.731867 -117 CAAAATCATTACAATTAACCTACATATAGTTTGT 5 146 1 ACAATATACA 0.591296 -455 ATCTAATTTGACAATCATTCAACAAAGTTGTTAC 5 240 1 ACAATTAACA 0.803746 -361 CAAGCCAATTACAAATCATTAACAAAAAATTGCT 8 94 1 ACAAAAAACA 0.962705 -108 TTATCTCAACACAAAATAATAACCGTTAAGGGTG 9 12 1 ACAAAAAACC 0.971943 -289 CGCCATATAAACCAAGATTTAACCTTTTGAGAAC 13 97 1 ACCAATAACC 0.722103 -204 TGAGAACAAAAAATAGACCGATAAATATC 15 6 1 ACAAAAGACC 0.87841 -295 ATAACAGCAAACAAAACATTAACATCTGCGCAGT 15 46 1 ACAAAAAACA 0.962705 -255 TCTGCGCAGTACAAACTATAAACCCATCGCCAGA 15 70 1 ACAAAAAACC 0.971943 -231 ***** * **** Masking position 4 Map Score: 4.61901 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 56 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 11 ATACCCTAACCACCACCGGGTCGTTCTATCC 1 116 0 CACCACGGGT 0.64771 -185 CTGCCCGTTGCGGTACTGGGCATTTACCCTA 2 207 1 CGGTACGGGC 0.919366 -94 TCCGTCAAAGAGGCTCGGGACAACCCGCAAG 4 18 0 AGGCTCGGAC 0.701786 -274 ACCTGGATCACTGTTCAGGATAAAACCCGAC 5 178 0 CTGTTCGGAT 0.82296 -423 TATTTCGTATCGCTTCCGGGCATTGTCGGTC 7 15 0 CGCTTCGGGC 0.982081 -71 TCTGTCGATGCTCTTCTGGGCCGAACTCCTC 9 99 1 CTCTTCGGGC 0.977047 -202 CTGGGCCGAACTCCTCTGGATCATTACTCAC 9 114 1 CTCCTCGGAT 0.88127 -187 AGCCCTGATTCTCTTCAGGGTGAATATTAAA 9 253 0 CTCTTCGGGT 0.957201 -48 ACAGAGCCGCCCTTCGGGGCGGTTTTTTTA 10 10 1 CCCTTCGGGC 0.939633 -133 CGACTTTTTGCGGCTCCAGGTTACTTCCCGT 11 65 0 CGGCTCAGGT 0.718681 -134 TGGTTTGGTTATGCTCTGGGCGGGTGTTCCG 11 159 0 ATGCTCGGGC 0.880654 -40 ****** **** Masking position 6 Map Score: 4.28711 Number of sites scoring better than the average of aligned sites = 955 Number in coding regions = 901 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 12 TTTGTAAAATACCGACGGATAGAACGACCC 1 100 1 ACCGACGGAT 0.674878 -201 CAAGGTAGCAAGCGCCAGAATCCCCAGGAG 1 180 1 AGCGCCAGAA 0.83491 -121 GACGGGTATGACCGCCGGAGATAAATATAT 1 271 1 ACCGCCGGAG 0.982147 -30 ATTGCGTAAGACTGCCGGAACTTAAATTTG 5 560 0 ACTGCCGGAA 0.946389 -41 TTCAATTGCCGGAGAAGGCGATAA 6 50 0 ATTGCCGGAG 0.966178 -14 CCAGAAGAGCATCGACAGAGAAAACGCGCC 9 88 0 ATCGACAGAG 0.812028 -213 TATGCATTTAATTGCCGTAATCAGGAACCT 12 158 0 ATTGCCGTAA 0.638412 -143 GCCAATATGTATTGCCTGAATAGTAAAGTC 13 267 0 ATTGCCTGAA 0.735879 -34 CTATAAACCCATCGCCAGAGAGTCTTTCTC 15 85 1 ATCGCCAGAG 0.956405 -216 ********** Masking position 9 Map Score: 2.35864 Number of sites scoring better than the average of aligned sites = 1381 Number in coding regions = 1218 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 13 GATTTAATGAATAAAATTTGCCACGATCATAA 4 87 0 AAAATTTGCC 0.896669 -205 ACTGCCGGAACTTAAATTTGCCTTCGCACATC 5 548 0 CAAATTTGCC 0.985288 -53 AAATCATTAACAAAAAATTGCTCTAAAGCATC 8 106 1 CAAAATTGCT 0.908828 -96 AATAAGTGAGCTAAAAGTTGCTTAACGAAAGC 10 82 1 CAAAGTTGCT 0.893342 -61 GACCTTAATCCACAAAATTGCCGTTTACAATG 12 228 0 CAAAATTGCC 0.973269 -73 TATCACAGTGCATAAATTTGCCGCTGCTTTAA 15 130 1 CAAATTTGCC 0.985485 -171 ATGGATAAGTCTGAAATTTGACGAGATCGATT 16 157 0 CAAATTTGAC 0.898184 -138 * ********* Masking position 6 Map Score: 3.06185 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 67 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 14 TTCACGCTCCTGTGAGACAGCAGTTTGTAGGG 2 233 0 TGTGGACGCA 0.962211 -68 GCCAGGTTGATGTGCGAAGGCAAATTTAAGTT 5 540 1 TGTGGAAGCA 0.963615 -61 TAGGCTATAATGCGGCAATTCATAATCTCTGA 8 18 0 TGCGCAATCA 0.897447 -184 AACAAAAAATTGCTCTAAAGCATCCGTATCGC 8 114 1 TGCTTAAGCA 0.666868 -88 GGAGAAACCTTGTGGCAAAGCAAATGACAACC 9 169 0 TGTGCAAGCA 0.948875 -132 CATGCCTGCGTCACGGCATGCAAATTCT 12 7 1 TGCGCACGCA 0.957534 -294 GTTGGAATGTTGCGCTAATGCATAAGCGACTG 12 111 1 TGCGTAAGCA 0.926738 -190 ACGCTAAACTTGCGTGACTACACATTCTTGAG 12 189 1 TGCGGACACA 0.886362 -112 **** *** *** Masking position 7 Map Score: 2.40463 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 250 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 15 CTGGGCATTTACCCTACAAACTGCTGTCTC 2 222 1 ACCCTACAAA 0.981188 -79 ACAATCTCGACCCTACAAATGATAACAAT 3 10 1 ACCCTACAAA 0.981188 -32 TCTCCGGAACACCCTGCAATCCCGAGCCAC 5 92 0 ACCCTGCAAT 0.923715 -509 TCAGGATAAAACCCGACAAACTATATGTAG 5 165 0 ACCCGACAAA 0.96835 -436 ********** Masking position 8 Map Score: 0.0871398 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 3 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467