AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00650_mjan_reg_100.orf -o00650_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: MJ0086 36 unspecified methyltransferase MJ0266 27 pyruvate ferredoxin oxidoreductase, subunit beta (porB) Input sequences: #1 MJ0033 254 succinate dehydrogenase, flavoprotein subunit (sdhA) #2 MJ0050 109 group II decarboxylase #3 MJ0085 134 iron transport periplasmic binding protein, putative (ceuE) #4 MJ0087 23 hemin permease (hemU) #5 MJ0090 80 collagenase (prtC) #6 MJ0091 95 Na+/Ca+ exchanger protein, putative #7 MJ0161 300 acetolactate synthase small subunit (ilvN) #8 MJ0267 21 pyruvate ferredoxin oxidoreductase, subunit alpha (porA) #9 MJ0269 283 pyruvate ferredoxin oxidoreductase, subunit gamma (porG) #10 MJ0276 119 2-ketoglutarate ferredoxin oxidoreductase, subunit alpha (korA) #11 MJ0277 183 acetolactate synthase large subunit (ilvB) #12 MJ0537 276 2-ketoglutarate ferredoxin oxidoreductase, subunit beta (korB) #13 MJ0663 27 acetolactate synthase large subunit (ilvB) #14 MJ1530 178 ribosomal protein S18 alanine acetyltransferase Motif number 1 GAAAATAGTAATATTTTTAATAAGGCACTGGT 1 111 0 ATATTTTATA 0.888856 -144 TTTTCTTGTTCTTTTTTTATTTATACTATGCC 1 138 1 CTTTTTTTTT 0.877845 -117 ATACTATGCCAATTTTTTCATTTAGGATTATT 1 160 1 AATTTTTATT 0.913711 -95 ATTTAGGATTATTTTTTTCATCAAAGCTATTT 1 179 1 ATTTTTTATC 0.795369 -76 TTCATCAAAGCTATTTTGATTTATAAGTTTTA 1 195 1 CTATTTTTTT 0.89208 -60 CTTTTTTCTATTTTTTATATAA 3 1 1 CTTTTTTATT 0.927339 -134 TTTTTAACGATTATTTTTGATAAACTACCGAA 3 53 1 TTATTTTATA 0.747956 -82 ATATGAACAAAAATTTTTAATATCTAATATAT 3 89 0 AAATTTTATA 0.874252 -46 ACTATCACATTTTTTGAATTATT 4 4 0 ATTTTTTATT 0.924128 -20 TCTTTTTTATATAATGAGGTCAT 5 2 1 CTTTTTTATA 0.8793 -79 AAATTTTTTTAAATTTTAAATTATATTTGAAG 5 55 0 AAATTTTATT 0.923468 -26 GATGAACTGAAAATTTTGCTTAAGTTTAAATA 6 21 1 AAATTTTTTA 0.796536 -75 ATCTTAACTTAATTTTTGGTTTCCTA 7 5 0 AATTTTTTTT 0.856372 -296 AAAACTATGAAAATTTTCTTTTAATCTTAACT 7 28 0 AAATTTTTTT 0.872747 -273 AGAGGGTGTTCAATTTTTCATAACTAAATTTA 7 72 0 CAATTTTATA 0.8793 -229 GACAAGGCTTAATTTTTCTTTTGTTAATTAAT 7 170 0 AATTTTTTTT 0.856372 -131 TTTGATTTGCATATTTTTGATAGGATATGACA 7 198 0 ATATTTTATA 0.888856 -103 ATGATACCTGAAATTTTTGATTTGCATATTTT 7 213 0 AAATTTTATT 0.924128 -88 TCTATTTTATTATTTTTAAATCTTACTATAAA 7 274 1 TATTTTTATC 0.556311 -27 CCATGTAAATTAATTTTATTTTTTCTTATGCC 9 168 1 TAATTTTTTT 0.717904 -116 TATGCCTAAACTATTTTCGTTAATTGCTTAAA 9 194 1 CTATTTTTTA 0.825127 -90 CATGCTTCTATTTTTTTAAATTGTTATTTTCT 10 22 1 TTTTTTTATT 0.818823 -98 TTCTTTAATTCTATTTTTTATTTTTAGTCTTT 11 16 1 CTATTTTATT 0.936225 -168 AATACCAACACTTTTTTATATCAAACTTTTTA 11 69 1 CTTTTTTATC 0.802865 -115 TTAGTATAAAAATTTTTATATATGATTTCAAT 11 123 1 AATTTTTATA 0.858038 -61 CACCTCAAATAATTTTTAATTTATAATGGATA 12 250 0 AATTTTTTTT 0.855125 -27 AATTTTAGTATTATTTTAAATTCTTTTTATAG 14 80 0 TTATTTTATT 0.838675 -99 TTATTAAATTCTATTTTAATTTTAGTATTATT 14 97 0 CTATTTTTTT 0.89208 -82 ******* *** Masking position 6 Map Score: 34.7869 Number of sites scoring better than the average of aligned sites = 2093 Number in coding regions = 1530 Number in noncoding regions = 563 Number of orfs with sites within 600 bp upstream = 406 Fraction of orfs with sites within 600 bp upstream = 0.0652104 Motif number 2 CCCTCATCAGATATTTAAAACTTATAAATCAAAAT 1 207 0 ATTTAACTAT 0.909144 -48 TTTAATCATGATGTTTATCAACTAAAAAAATTAAA 2 83 1 ATTTATATAA 0.674485 -27 TTTTTTATATAATTTTTATGAATATTGATGTATTT 3 21 1 ATTTTAATAT 0.672383 -114 ATATTGATGTATTTTTAACGATTATTTTTGATAAA 3 42 1 ATTTAAATAT 0.972388 -93 ATGAACAAAAATTTTTAATATCTAATATATATTTT 3 84 0 ATTTAATTAA 0.706883 -51 TATAATTTAAAATTTAAAAAAATTTCTAA 5 62 1 ATTAAAATTT 0.728831 -19 AATTTTGCTTAAGTTTAAATATTATTGCAGAATAT 6 32 1 ATTTAAATAT 0.972368 -64 TTCAAAAACAAACTTTAATTAATTTAGTAGGGATA 6 68 1 ATTTAAATTT 0.952352 -28 TTTCATAACTAAATTTAACAACTTTACGAAAAACT 7 54 0 ATTTAAATTT 0.956078 -247 TTTTATAGTAAGATTTAAAAATAATAAAATAGATA 7 272 0 ATTTAAAAAT 0.683991 -29 AGCCGATTTGATTTTTAAACAGCTTTATTGTTGAA 9 45 0 ATTTAAACTT 0.667002 -239 ATCGGCTATTATATTGAAGGAGTTAAAAAAGGAAC 9 73 1 ATTGAAATTA 0.772338 -211 AAAGTTTTGGAGATTTAAGCAATTAACGAAAATAG 9 204 0 ATTTAAATTA 0.922684 -80 TTTATATATTACTTTTAATAATTGTTAATGATTGA 9 236 1 ATTTAAATGT 0.90359 -48 CCTTGTGTTAATATTTAACGACTATAATATAATAG 10 57 0 ATTTAAATAT 0.972377 -63 CTTCTAAGCTACTTTTATATAATATAACCTTGTGT 10 84 0 ATTTATATAT 0.789048 -36 TTGGTATTTAATATTTAATTACTAATCTTAAAGAC 11 42 0 ATTTAAATAA 0.950206 -142 GCATTTGAAGAACTTTAAAAAGTTTGATATAAAAA 11 81 0 ATTTAAATTT 0.956473 -103 AGTAATGATAAAATTGAAATCATATATAAAAATTT 11 132 0 ATTGAACTAT 0.739791 -52 ACCTCAAATAATTTTTAATTTATAATGGATACCCC 12 246 0 ATTTAATTAA 0.70688 -31 CTTTTAAAACATTTTGAAATACTAAGGACCAATAA 14 42 0 ATTGAAATAA 0.844568 -137 TTTTAGTATTATTTTAAATTCTTTTTATAGAGTCT 14 75 0 ATTAAACTTT 0.440878 -104 GCCTTTGAATAATTTTAATCAATGAATGTTGTGTA 14 131 0 ATTTAAATGA 0.836449 -48 * ***** * *** Masking position 5 Map Score: 23.1875 Number of sites scoring better than the average of aligned sites = 708 Number in coding regions = 471 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 214 Fraction of orfs with sites within 600 bp upstream = 0.034372 Motif number 3 ACCTTTTAGTAAAAGGTTCATCAAAACGGAT 1 41 0 AAAAGGTTCT 0.948297 -214 ACCTTTTACTAAAAGGTTCATGTGAAGGAAA 1 55 1 AAAAGGTTCT 0.948297 -200 TGCCTTATTAAAAATATTACTATTTTCTTGT 1 116 1 AAAATATTAT 0.748068 -139 TTTGATGAAAAAAATAATCCTAAATGAAAAA 1 173 0 AAAATAATCT 0.448023 -82 TAGTTTATCAAAAATAATCGTTAAAAATACA 3 49 0 AAAATAATCT 0.448023 -86 TAGATATTAAAAATTTTTGTTCATATCATAT 3 95 1 AAATTTTTGT 0.766938 -40 GGATGAACTGAAAATTTTGCTTAAGTTTAAA 6 20 1 AAAATTTTGT 0.929658 -76 CTAAATTAATTAAAGTTTGTTTTTGAATATA 6 64 0 TAAAGTTTGT 0.628721 -32 AAAAACTATGAAAATTTTCTTTTAATCTTAA 7 30 0 AAAATTTTCT 0.849093 -271 ATTGGCATCTAAATTATTGGTTTTTGCAAAT 7 141 0 AAATTATTGT 0.734692 -160 ATGATACCTGAAATTTTTGATTTGCATATTT 7 214 0 AAATTTTTGT 0.766938 -87 TCTTTCTCTAAAAATGATGTTGTATTTATTT 9 128 0 AAAATGATGT 0.867614 -156 CTATTTTTTTAAATTGTTATTTTCTTCTCTA 10 29 1 AAATTGTTAT 0.717676 -91 TTGATATAAAAAAGTGTTGGTATTTAATATT 11 62 0 AAAGTGTTGT 0.810935 -122 AAGAACTTTAAAAAGTTTGATATAAAAAAGT 11 78 0 AAAAGTTTGT 0.937062 -106 CAATCACCAAAAAATGTTAAGGGTAAAGTAA 11 162 0 AAAATGTTAG 0.733462 -22 AACCTTTTAGAAAAGGTTGATCAAAACTTAG 12 102 0 AAAAGGTTGT 0.977313 -175 AACCTTTTCTAAAAGGTTGTTCGAGTAACCT 12 115 1 AAAAGGTTGT 0.977313 -162 ACCTTTTAGTAAAAGGTTACTCGAACAACCT 12 128 0 AAAAGGTTAT 0.920008 -149 ACCTTTTACTAAAAGGTTGGGAGCAATGTTT 12 142 1 AAAAGGTTGG 0.920706 -135 AAAAATATTGATTTAAACGGTG 13 16 0 AAAATATTGT 0.917504 -12 AAGGCTTTACTAAAGGTTAAGTGAGAAC 14 161 1 TAAAGGTTAG 0.260675 -18 ********* * Masking position 8 Map Score: 21.7078 Number of sites scoring better than the average of aligned sites = 920 Number in coding regions = 771 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 4 AACCTCAAATAAATGTTTAGTATATTGTATTATAT 2 16 1 AATTATATAT 0.800704 -94 ATGATTAAATTTATAAGTATTTAATGCGTTCTTAG 2 57 0 TATTATTAAT 0.860384 -53 ACATCAATATTCATAAAAATTATATAAAAAATAGA 3 17 0 TATAATATAT 0.681502 -118 TAATATATATTTTTCGGTAGTTTATCAAAAATAAT 3 62 0 TTTTATTTAT 0.896129 -73 CAAAAATTTTTAATATCTAATATATATTTTTCGGT 3 79 0 TATTATATAT 0.963822 -56 GTCATATTGGTTATTGCTATTTTATACTTCAAATA 5 29 1 TATTATTTAT 0.963823 -52 AATTTTCAGTTCATCCATATTGTAT 6 1 0 TATTATGTAT 0.861589 -95 TCTTATCCCTACTAAATTAATTAAAGT 6 79 0 TATTATAAAT 0.860386 -17 ATTATGTCCTTTATCTTTAGAATATTTGCAAAAAC 7 118 1 TATTAAATAT 0.681439 -183 ATTTCAGGTATCATAATTATTATATGGTGAGTTCT 7 231 1 TATTATATAT 0.963718 -70 GAGTTCTACTAAATATCTATTTTATTATTTTTAAA 7 259 1 AATTATTTAT 0.800785 -42 TTAACAATTATTAAAAGTAATATATAAAGTTTTGG 9 229 0 TAATATATAT 0.681444 -55 ATTGTTATTTTCTTCTCTATTATATTATAGTCGTT 10 41 1 TTTTATATAT 0.896129 -79 AAAGTGTTGGTATTTAATATTTAATTACTAATCTT 11 48 0 TTTTATTAAT 0.666172 -136 GATTTCAATTTTATCATTACTTTACCCTTAACATT 11 146 1 TATTATTTAC 0.760283 -38 CCACCTCAAATAATTTTTAATTTATAATGGATACC 12 248 0 TATTATTTAT 0.963823 -29 AATCAATGAATGTTGTGTAATTTATTAAATTCTAT 14 115 0 TTTTATTTAT 0.896129 -64 * ** ** ***** Masking position 9 Map Score: 16.3276 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 256 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 5 TTTTGATGAACCTTTTACTAAAAGGTTCATGT 1 46 1 CCTTTTTAAA 0.962576 -209 ATTTTCTTGTTCTTTTTTTATTTATACTATGC 1 137 1 TCTTTTTATT 0.719416 -118 ATAATAAATGTCTTTCGATAGAGGGTGTTCAA 7 91 0 TCTTTCTAGA 0.787628 -210 GCTTAATTTTTCTTTTGTTAATTAATTGGCAT 7 164 0 TCTTTTTAAT 0.947975 -137 TCCTTTTTATAGTAAGATTTAAA 7 288 0 CCTTTTTAGT 0.942347 -13 TATAGCAGTTCCTTTTTTAACTCCTTCAATAT 9 83 0 CCTTTTAACT 0.751106 -201 GATTACATAGTCTTTCTCTAAAAATGATGTTG 9 137 0 TCTTTCTAAA 0.880616 -147 TTTATATATTACTTTTAATAATTGTTAATGAT 9 236 1 ACTTTTTAAT 0.765466 -48 TATAATATAACCTTGTGTTAATATTTAACGAC 10 70 0 CCTTGTTAAT 0.798696 -50 TTTCTTTCTTTAATTCTATTTTTT 11 3 1 TCTTTCTAAT 0.893453 -181 ACTCGAACAACCTTTTAGAAAAGGTTGATCAA 12 109 0 CCTTTTAAAA 0.873661 -168 GTTCGAGTAACCTTTTACTAAAAGGTTGGGAG 12 133 1 CCTTTTTAAA 0.962576 -144 TTTTATAGAGTCTTTTAAAACATTTTGAAATA 14 56 0 TCTTTTAACA 0.60582 -123 TATTTTAAATTCTTTTTATAGAGTCTTTTAAA 14 69 0 TCTTTTTAGA 0.89841 -110 TTTAGTAAAGCCTTTGAATAATTTTAATCAAT 14 143 0 CCTTTGTAAT 0.833884 -36 ****** **** Masking position 10 Map Score: 9.24868 Number of sites scoring better than the average of aligned sites = 557 Number in coding regions = 458 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 6 GAGGCACTGCCGAGCGTAGCGAGGC 1 1 1 GAGCATCCGC 0.998925 -254 CATCAAAACGGATGCACTGCCTCGCTACGCTCGGC 1 19 0 GAGCATCCGC 0.998925 -236 CTATGCTAAGAGGCATTACCGAGCGTAGCGAGGT 12 10 1 GAGCATCCGC 0.998925 -267 GATCAAAACAGATGCATTACCTCGCTACGCTCGGT 12 28 0 GAGCATCCGC 0.998925 -249 ** *** * ** ** Masking position 8 Map Score: 6.52598 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 7 AGGCACTGCCGAGCGTAGCGAGGCAGTGCATCC 1 12 1 GAGCTAGCAG 0.997265 -243 GAAGGAAATAGAGCATAGGAAAGAATTAGGATT 1 78 1 GAGCTAGGAG 0.990437 -177 AGGCATTACCGAGCGTAGCGAGGTAATGCATCT 12 21 1 GAGCTAGCAG 0.997265 -256 TATCCCAATAGGGCGAAGCTATGGTGCGTTGAT 12 60 0 GGGCAAGCAG 0.980365 -217 AGCAATGTTTGAGCTTAGCCATGCGGTAGTTAT 12 163 1 GAGCTAGCAG 0.997265 -114 **** **** * * Masking position 7 Map Score: 6.49813 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 1 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 AAAATAGTAATATTTTTAATAAGGCACTGG 1 112 0 TATTTTTAAT 0.808642 -143 GAGGGTATCCTATTTTTGGTGATAAAAA 1 237 1 TATTTTTGGT 0.964704 -18 ACTAAACATTTATTTGAGGTTTAATT 2 7 0 TATTTGAGGT 0.91235 -103 CCTTTAATTTTTTTAGTTGATAAACAT 2 93 0 TTTTTTTAGT 0.610056 -17 TTTTAACGATTATTTTTGATAAACTACCGA 3 54 1 TATTTTTGAT 0.887086 -81 TTTTAAATTATATTTGAAGTATAAAATAGC 5 44 0 TATTTGAAGT 0.84846 -37 ATCTTAACTTAATTTTTGGTTTCCTA 7 7 0 AATTTTTGGT 0.74415 -294 TTGATTTGCATATTTTTGATAGGATATGAC 7 199 0 TATTTTTGAT 0.887086 -102 TTCTATTTTTTATTTTTAGTCTTTAAGATT 11 24 1 TATTTTTAGT 0.936311 -160 ACTCTATCTCTATTTGGGGTATCCATTATA 12 231 1 TATTTGGGGT 0.824225 -46 AATTAAAAATTATTTGAGGTGGTAAA 12 261 1 TATTTGAGGT 0.91235 -16 ATTTTAGTATTATTTTAAATTCTTTTTATA 14 81 0 TATTTTAAAT 0.686689 -98 AATTCTATTTTAATTTTAGTATTATTTTAA 14 93 0 TAATTTTAGT 0.610056 -86 ********** Masking position 5 Map Score: 13.0187 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 179 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 9 GGCAGTGCATCCGTTTTGATGAACCTTTTA 1 33 1 CCGTTTTGAT 0.971699 -222 TAAATCAAAATAGCTTTGATGAAAAAAATA 1 188 0 TAGCTTTGAT 0.868062 -67 CTTAATCTCCCAGCTTTCAT 9 1 0 CAGCTTTCAT 0.935434 -283 AATATAATAGCCGATTTGATTTTTAAACAG 9 58 0 CCGATTTGAT 0.931453 -226 GGTAATGCATCTGTTTTGATCAACGCACCA 12 42 1 CTGTTTTGAT 0.896285 -235 CTATTTAACTAAGTTTTGATCAACCTTTTC 12 94 1 AAGTTTTGAT 0.880642 -183 TGAATTTTGAACGCTTTCATAAAGGGGGTG 14 11 1 ACGCTTTCAT 0.885027 -168 ********** Masking position 9 Map Score: 1.31605 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 37 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 ********** No masking Map Score: -2.88948e-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 11 ********** No masking Map Score: -2.88948e-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 12 TTAGGTATAAATATAATACAATATACTAAA 2 31 0 ATATAATACA 0.644289 -79 ATATTCATAAAAATTATATAAAAAATAGAA 3 16 0 AAATTATATA 0.56071 -119 AATTTTTAATATCTAATATATATTTTTCGG 3 80 0 ATCTAATATA 0.687536 -55 ATTTTTGTTCATATCATATAGCCTAAAATG 3 107 1 ATATCATATA 0.75385 -28 TATACTTCAAATATAATTTAAAATTTAAAA 5 51 1 ATATAATTTA 0.844578 -30 AACAAACTTTAATTAATTTAGTAGGGATAA 6 74 1 AATTAATTTA 0.74092 -22 TTGCAAAAACCAATAATTTAGATGCCAATT 7 143 1 CAATAATTTA 0.623831 -158 TTTAGATGCCAATTAATTAACAAAAGAAAA 7 159 1 AATTAATTAA 0.455621 -142 TAAGATTTAAAAATAATAAAATAGATATTT 7 269 0 AAATAATAAA 0.778283 -32 GAAAAAATAAAATTAATTTACATGGATTAC 9 163 0 AATTAATTTA 0.74092 -121 CAATTATTAAAAGTAATATATAAAGTTTTG 9 230 0 AAGTAATATA 0.714398 -54 TATTTAACGACTATAATATAATAGAGAAGA 10 51 0 CTATAATATA 0.739071 -69 AGCTACTTTTATATAATATAACCTTGTGTT 10 83 0 ATATAATATA 0.913427 -37 GATAAAATTGAAATCATATATAAAAATTTT 11 131 0 AAATCATATA 0.776861 -53 TTAAAATAGAATTTAATAAATTACACAACA 14 110 1 ATTTAATAAA 0.588392 -69 ********** Masking position 6 Map Score: 2.9854 Number of sites scoring better than the average of aligned sites = 810 Number in coding regions = 537 Number in noncoding regions = 273 Number of orfs with sites within 600 bp upstream = 253 Fraction of orfs with sites within 600 bp upstream = 0.040636 Motif number 13 ********** No masking Map Score: -2.88948e-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 14 ********** No masking Map Score: -2.88948e-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 ********** No masking Map Score: -2.88948e-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