AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00190_bsub_reg_100.orf -o00190_bsub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ndhF 300 NADH dehydrogenase (subunit 5) #2 ctaC 239 cytochrome caa3 oxidase (subunit II) #3 ctaD 32 cytochrome caa3 oxidase (subunit I) #4 fliH 117 flagellar assembly protein #5 qcrA 142 menaquinol:cytochrome c oxidoreductase (iron-sulfur subunit) #6 yrhE 300 similar to formate dehydrogenase #7 sdhA 33 succinate dehydrogenase (flavoprotein subunit) #8 sdhC 292 succinate dehydrogenase (cytochrome b558 subunit) #9 yteU 21 similar to hypothetical proteins from B. subtilis #10 yteQ 94 similar to sugar transport protein #11 yteP 215 similar to hypothetical proteins from B. subtilis #12 yufT 300 similar to NADH dehydrogenase #13 atpC 23 ATP synthase (subunit epsilon) #14 atpD 25 ATP synthase (subunit beta) #15 atpG 76 ATP synthase (subunit gamma) #16 atpF 162 ATP synthase (subunit b) #17 atpE 45 ATP synthase (subunit c) #18 atpI 300 ATP synthase (subunit i) Motif number 1 TTGAAGTTGTCGGCTTTTTTGTTGGAAAAA 1 182 1 CGGCTTTTTT 0.771872 -119 TCTAAATTCTCCCTTTTTTAAAACTCAT 1 283 0 CTCCCTTTTT 0.974362 -18 GCCGCCTTGACCTCTTGTTTAATCAGGCGG 2 68 1 CCTCTTGTTT 0.798706 -172 TTCACCCAACCCCTTTTCTGGTCAATACA 2 221 0 CCCCTTTTCT 0.959745 -19 CCCCCAATATCTCCCTTTCTTCC 3 4 0 CTCCCTTTCT 0.954762 -29 TGTAATCCTCCCCCCTGTTTGAGCTATAAT 8 37 0 CCCCCTGTTT 0.971146 -256 GTTTTCTTGACGCCCTTTTGAGGGAGGAGT 8 172 1 CGCCCTTTTG 0.861207 -121 TACTTTACCCCCTGTTTGATAAGTGCG 8 276 0 CCCCCTGTTT 0.971146 -17 GGCGCCCCCTCCTTTTTTGCA 9 4 0 CTCCTTTTTT 0.964185 -18 CATATGATCACATCCTGTTTTATCCCTTTA 11 127 0 CATCCTGTTT 0.604433 -89 ATACAAATAACCTCTTTTTTGTTAGACTTA 12 45 1 CCTCTTTTTT 0.877223 -256 AAGATAAGACCTCCTTTTCTCGTTCTCAAT 12 201 0 CTCCTTTTCT 0.937306 -100 GCTATTTTATCGCCTTTTTTATTTGCTTTT 12 248 1 CGCCTTTTTT 0.971957 -53 TTCTCTTTTTCTCTCTTTTTACGCAGATGA 15 36 1 CTCTCTTTTT 0.667641 -41 AGATTTCACCACCTTTTCTCTTCATCTGC 15 58 0 CACCTTTTCT 0.866737 -19 GAATGATCTTCGCCATTTTTAGTTCATATA 16 23 0 CGCCATTTTT 0.845292 -140 ********** Masking position 6 Map Score: 19.7123 Number of sites scoring better than the average of aligned sites = 943 Number in coding regions = 674 Number in noncoding regions = 269 Number of orfs with sites within 600 bp upstream = 296 Fraction of orfs with sites within 600 bp upstream = 0.0475426 Motif number 2 CATTTTGAGTAAAAAAACTCATAATTTAAGAGAAG 2 120 1 AACTCATAAT 0.979035 -120 AAACACTTACATTTCCTTATAAACAATATTTTG 5 9 1 AACTTATAAA 0.929874 -134 CAATAACTCTAGACACCCTCATAATATATGAATCT 5 64 0 AACTCATAAT 0.979036 -79 CGATATTGCCTTATAAAGGCTTTTCCC 6 3 1 AACTTATAAA 0.929874 -298 TTTTCCTGCCATATTGTATTATAATAAATATCACA 6 70 1 AAATTATAAT 0.835048 -231 ATTATAATAAATATCACATTATAATAAAAGCAGTG 6 87 1 AAATTATAAT 0.835049 -214 ATGTGTGTTTACACCTTCTTAGAATTAAGGGCAGG 6 218 1 AACTTAGAAT 0.859297 -83 TTTTGAGGTCAAAAGAACTCATAAAAATCCATTAC 12 75 1 AACTCATAAA 0.954845 -226 AAAGCTATGAAAACCTTCTCATAATACCCTCGTTT 18 56 0 AACTCATAAT 0.979036 -245 ATTCGCTTAAATAAATCCTCATAATACGGGTTTGC 18 126 0 AACTCATAAT 0.979036 -175 * * ******** Masking position 9 Map Score: 9.7183 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 29 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 3 ACTCATTATTGGTCAAAAGACCTTTCAATC 1 259 0 GGTCAAAAGA 0.906636 -42 CCTTTTGCAGGCTGAAGAGAACCCGGAGCG 4 95 1 GCTGAAGAGA 0.981976 -23 GACTTAGAGGGGGGAGAAGAG 5 132 1 GGGGAGAAGA 0.736261 -11 AGTGAAATGTCCTGAGGGGAACCGGGAAAA 6 31 0 CCTGAGGGGA 0.788246 -270 CTCAAAAGGGCGTCAAGAAAACGCGTACAT 8 164 0 CGTCAAGAAA 0.478346 -129 GAAAGAAGTGGGGGAAGAGATTTAGCACAT 8 244 1 GGGGAAGAGA 0.908658 -49 AGCCGGTCCACCTGAAAAAAAGACACCGAT 11 84 0 CCTGAAAAAA 0.753848 -132 TGCAAGAATCCGTGAAAGGAGGCTAGGAAA 11 194 1 CGTGAAAGGA 0.860686 -22 TCCTGATCAAGCTGAAGGAAAG 12 3 0 GCTGAAGGAA 0.895313 -298 CTTATTTTGAGGTCAAAAGAACTCATAAAA 12 71 1 GGTCAAAAGA 0.906636 -230 AGATGTAAGAGCTGCAAAGATAAGACCTCC 12 217 0 GCTGCAAAGA 0.825017 -84 CTCGAATGCTGATGAGAGAAAAAGGTT 15 8 1 GCTGATGAGA 0.832976 -69 TTTTTACGCAGATGAAGAGAAAAGGTGGTG 15 51 1 GATGAAGAGA 0.89354 -26 CGCCTTGCCGGCTGAAAAGAGACAAGTGCG 16 94 1 GCTGAAAAGA 0.976763 -69 AGAAAAACCTGCAGAAGGGAGTTGCCGTAG 16 140 1 GCAGAAGGGA 0.747841 -23 ATACGGGTTTGCTGAGAGGATTTACATTGA 18 108 0 GCTGAGAGGA 0.906774 -193 CCGTTTTGCCGGTCAAAAAAGGTCTTCTAC 18 211 1 GGTCAAAAAA 0.70554 -90 TCTGTCTCCTGATGAAAAAATAATGTATAG 18 275 0 GATGAAAAAA 0.615067 -26 ********** Masking position 10 Map Score: 13.1238 Number of sites scoring better than the average of aligned sites = 2179 Number in coding regions = 1935 Number in noncoding regions = 244 Number of orfs with sites within 600 bp upstream = 252 Fraction of orfs with sites within 600 bp upstream = 0.0404754 Motif number 4 TATTGGTGATAGGTTGGATGGCGATAGATTT 2 172 1 AGGTGGATGG 0.726048 -68 GTCAATACAAAGGCGGAAAGCGGATCGAAAT 2 199 0 AGGGGAAAGC 0.66176 -41 AGGGAGATATTGGGGGAGGTCACAT 3 18 1 TGGGGAGGTC 0.609428 -15 CACCTTTTGCAGGCTGAAGAGAACCCGGAGC 4 93 1 AGGTGAAGAG 0.879967 -25 GGGGTGACTTAGAGGGGGGAGAAGAG 5 127 1 AGAGGGGGAG 0.938104 -16 TAAACACACATGGCGGAATAGTTCACTAGCA 6 198 0 TGGGGAATAG 0.784525 -103 CTTGAAAGAAAGATGGAGGGGAATATGAAT 6 281 1 AGAGGAGGGG 0.935973 -20 AGATTACTAGAGGGAGAGGGGCTATC 7 18 1 AGGAGAGGGG 0.816284 -16 TACGCAGGAGAGAGGGGAGACAGAT 8 5 0 AGAGGGAGAC 0.859674 -288 TAGCTCAAACAGGGGGGAGGATTACAGAATG 8 41 1 AGGGGGAGGA 0.841653 -252 GACGCCCTTTTGAGGGAGGAGTAAAATGAAA 8 180 1 TGAGGAGGAG 0.808112 -113 TTGAAAGAAGTGGGGGAAGAGATTTAGCACA 8 242 1 TGGGGAAGAG 0.93911 -51 TGCAAAAAAGGAGGGGGCGCC 9 9 1 AGGGGGGGCG 0.942333 -13 AGATTTTGTCAGGAGGGATAGCG 14 13 1 AGGGGGATAG 0.929094 -13 TCAGCCGGCAAGGCGGGATGCTTATCAGACA 16 78 0 AGGGGGATGC 0.890241 -85 ATTTACATTGAGGATGAGGACTATAATGAAA 18 88 0 AGGTGAGGAC 0.824711 -213 *** ******* Masking position 6 Map Score: 10.4397 Number of sites scoring better than the average of aligned sites = 1285 Number in coding regions = 1009 Number in noncoding regions = 276 Number of orfs with sites within 600 bp upstream = 260 Fraction of orfs with sites within 600 bp upstream = 0.0417604 Motif number 5 CATTCTCACCTTTTGCAGGCTGAAGAGAAC 4 87 1 TTTTGCAGGC 0.971793 -31 TTATAAAGGCTTTTCCCGGTTCCCCTCAGG 6 21 1 TTTTCCCGGT 0.896944 -280 TCGGTGTCTTTTTTTCAGGTGGACCGGCTG 11 85 1 TTTTTCAGGT 0.749303 -131 TAATCAAGGGTTCAGCCGGTCCACCTGAAA 11 97 0 TTCAGCCGGT 0.955345 -119 GTAGACGGACTTTTGCCTGCTGCGCTACAG 11 160 1 TTTTGCCTGC 0.883181 -56 TATCGCACTTTTCTGCAAGCTGCCACGCTT 12 119 0 TTCTGCAAGC 0.832019 -182 CTTGTCTCTTTTCAGCCGGCAAGGCGGGAT 16 90 0 TTCAGCCGGC 0.964966 -73 GGCAACTCCCTTCTGCAGGTTTTTCTTTGC 16 136 0 TTCTGCAGGT 0.971754 -27 AACAGGCCCGTTTTGCCGGTCAAAAAAGGT 18 204 1 TTTTGCCGGT 0.981338 -97 ********** Masking position 2 Map Score: 8.05714 Number of sites scoring better than the average of aligned sites = 664 Number in coding regions = 619 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 6 TTCAATTTTTATTTATCTCTATTTTTTTCCAAC 1 202 0 ATTTTCTATT 0.712017 -99 TTTGTCTATTATTTATTTCAATTTTTATTTATC 1 218 0 ATTTTCAATT 0.874278 -83 CAATCAGATCATATTTGTCTATTATTTATTTCA 1 231 0 AATTTCTATT 0.87428 -70 ATTGGTCAAAAGACCTTTCAATCAGATCATATT 1 249 0 AACTTCAATC 0.758469 -52 CTAAAATAGAAAATATTGCAATAACTCTAGACA 5 84 0 AATTGCAATA 0.662118 -59 TGATAAAATAAAATTTTTCAATCAACTAATCAA 8 113 1 AATTTCAATC 0.948166 -180 CTCTTCCCCCACTTCTTTCAATTGTAAGCACTT 8 230 0 ATTTTCAATT 0.874278 -63 GAGATTTAGCACATTTCGCACTTATCAAACAGG 8 260 1 AATTGCACTT 0.652439 -33 ATTATTGACAATATCTATCAATCTTTGGATTAA 11 40 0 AATTTCAATC 0.948166 -176 TATACATAGCGCATTTTTCAATTGAGAACGAGA 12 181 1 GATTTCAATT 0.770528 -120 TGCAGCTCTTACATCTTGCTATTTTATCGCCTT 12 231 1 AATTGCTATT 0.795406 -70 ATAGCCCCTAACATGTGTCAATCTGTTTAAAGT 18 15 0 AATTTCAATC 0.948166 -286 * ** * ****** Masking position 6 Map Score: 4.29478 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 180 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 TATGTTTTCATTTCCTTTAATATAGTCCTGATTATCAAA 1 31 0 TTTCTTATAT 0.854979 -270 ATTATTGGTCTTTACTTTATGCTATGTTTTCATTTCCTT 1 53 0 TTTCTTAGCT 0.742345 -248 ATCAGGCGGCTTTACTTTTATACATAGATGGCATTTTGA 2 89 1 TTTCTTTTAT 0.954974 -151 AGCACTTACATTTCCTCTTCTCTTAAATTATGAGTTTTT 2 132 0 TTTCTTTTCT 0.980276 -108 GTATAGAAAGTTTTCTTTTTTCCTTTTGTGGAGAAATAG 4 31 0 TTTCTTTTCT 0.980276 -87 TATTGCAATATTTTCTATTTTAGTCAGTTTGCAGGGGTG 5 94 1 TTTCTTTTAT 0.954974 -49 GATTGAAAAATTTTATTTTATCAATATATATTTCTTGCT 8 97 0 TTTATTTTCT 0.812807 -196 TCAATAATCATTTTCTAATATCGGTGTCTTTTTTTCAGG 11 65 1 TTTCTATTCT 0.874893 -151 GCTCTTACATCTTGCTATTTTATCGCCTTTTTTATTTGC 12 235 1 CTTCTTTTAT 0.815606 -66 GCCTTTTTTATTTGCTTTTATCATTCCCTTCTTGGCAAA 12 259 1 TTTCTTTTCT 0.980276 -42 *** ** ** ** * Masking position 6 Map Score: 4.42263 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 133 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 8 TTATTTTGAAGCGATAAAACAAGCATCATA 2 19 0 GCGATAAAAC 0.979067 -221 CATAAAATGCGGGATATAAATCAGCGTCTG 10 21 0 GGGATATAAA 0.811146 -74 ACAAACGAAAGCGATACAACAATGACCCAA 10 53 0 GCGATACAAC 0.964836 -42 TGATTATAAAGGGATAAAACAGGATGTGAT 11 121 1 GGGATAAAAC 0.960706 -95 GCAGAAAAGTGCGATATAATTTGGACTAGG 12 133 1 GCGATATAAT 0.935442 -168 AATAAAAAAGGCGATAAAATAGCAAGATGT 12 241 0 GCGATAAAAT 0.954052 -60 ********** Masking position 5 Map Score: 2.99241 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 51 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 AGCCGACAATTTTCAGGATTCAATGATCTAACATA 1 135 1 TTCAGTAATG 0.783718 -166 ATTATGAGGGTGTCTAGAGTTATTGCAATATTTTC 5 74 1 TTCTGTATTG 0.96262 -69 ATACATGGCTTTTTTTGACTTCTTGAAAGAAAGAT 6 260 1 TTTTGTCTTG 0.919986 -41 TCAATATATATTTCTTGCTTAATTTTTCATAAGAA 8 81 0 TTCTGTATTT 0.816575 -212 GTAAGCACTTTATTAAGATTTATTGACAATTTCAT 8 205 0 TTTAGTATTG 0.941685 -88 CCGCATTTTATGTCTTGGGTCATTGTTGTATCGCT 10 39 1 TTCTGTATTG 0.96262 -56 TATCTATCAATCTTTGGATTAATTGTATTAAGGTG 11 27 0 TTTTGTATTG 0.941686 -189 CCTAGCCTCCTTTCACGGATTCTTGCATTCACTGT 11 186 0 TTCAGTCTTG 0.948282 -30 TGTAATGGATTTTTATGAGTTCTTTTGACCTCAAA 12 76 0 TTTAGTCTTT 0.665287 -225 GATTGACACATGTTAGGGGCTATTGTATGCTAAAC 18 25 1 TTTAGCATTG 0.77105 -276 * *** * * **** Masking position 3 Map Score: 3.99538 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 131 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 10 TAATCAGGACTATATTAAAGGAAATGAAAAC 1 36 1 TATATTAAAG 0.7186 -265 TTTATCGCTTCAAAATAAACGATGACAACTA 2 31 1 CAAAATAAAG 0.757476 -209 TAAAAAAACTCATAATTTAAGAGAAGAGGAA 2 129 1 CATAATTTAG 0.768054 -111 TAGACACCCTCATAATATATGAATCTCTCAG 5 59 0 CATAATATAG 0.903342 -84 CATATTGTATTATAATAAATATCACATTATA 6 79 1 TATAATAAAA 0.612917 -222 AATATCACATTATAATAAAAGCAGTGTTGAT 6 96 1 TATAATAAAG 0.952602 -205 CTGTTTGAGCTATAATATACGCAGGAGAGAG 8 22 0 TATAATATAG 0.944151 -271 TTCGGAAAATTATAATTTATGTACGCGTTTT 8 146 1 TATAATTTAG 0.83639 -147 TTTATCCCTTTATAATCAAGGGTTCAGCCGG 11 108 0 TATAATCAAG 0.842225 -108 GCGCTATGTATAAAATATACGGTCAAACGAC 12 162 0 TAAAATATAG 0.80756 -139 GGATGAGGACTATAATGAAAGCTATGAAAAC 18 77 0 TATAATGAAG 0.842225 -224 ********* * Masking position 4 Map Score: 3.21821 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 86 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 11 GCATAAAGTAAAGACCAATAATAAGGTAGC 1 70 1 AAGACCAATA 0.816213 -231 GAAAGGTCTTTTGACCAATAATGAGTTTTA 1 263 1 TTGACCAATA 0.837263 -38 CATCCAACCTATCACCAATAAAGCACTTAC 2 162 0 ATCACCAATA 0.763165 -78 AACCCCTTTTCTGGTCAATACAAAGGCGGA 2 213 0 CTGGTCAATA 0.870961 -27 AAAGGTGAGAATGATCAATACGCACCTCTT 4 70 0 ATGATCAATA 0.944562 -48 ATCTCTCAGCAAGGTCAATATAGCCAAAAT 5 38 0 AAGGTCAATA 0.873925 -105 AAAATTTTATTTTATCAATATATATTTCTT 8 100 0 TTTATCAATA 0.709146 -193 GTAAAATGAAATTGTCAATAAATCTTAATA 8 200 1 ATTGTCAATA 0.895555 -93 ATTGATAGATATTGTCAATAATCATTTTCT 11 51 1 ATTGTCAATA 0.895555 -165 ********** Masking position 7 Map Score: 1.59606 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 219 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 12 CTATATTAAAGGAAATGAAAACATAGCATA 1 45 1 GGAAATGAAA 0.972672 -256 TAAGAGAAGAGGAAATGTAAGTGCTTTATT 2 146 1 GGAAATGTAA 0.95019 -94 TTGTTTATAAGGAAATGTAAGTGTTT 5 7 0 GGAAATGTAA 0.95019 -136 AATGATAAAAGCAAATAAAAAAGGCGATAA 12 254 0 GCAAATAAAA 0.742135 -47 TTGCCAAGAAGGGAATGATAAAAGCAAATA 12 267 0 GGGAATGATA 0.879223 -34 ATTTATTTAAGCGAATGAAACAGCATCCCT 18 145 1 GCGAATGAAA 0.93911 -156 ********** Masking position 5 Map Score: 1.14423 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 141 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 13 GCTATATTGACCTTGCTGAGAGATTCATAT 5 44 1 CCTTGCTGAG 0.966113 -99 ATTTTAGTCAGTTTGCAGGGGTGACTTAGA 5 110 1 GTTTGCAGGG 0.93708 -33 ACGGACTTTTGCCTGCTGCGCTACAGTGAA 11 164 1 GCCTGCTGCG 0.875824 -52 AAGCGTGGCAGCTTGCAGAAAAGTGCGATA 12 119 1 GCTTGCAGAA 0.83243 -182 GAGGTCTTATCTTTGCAGCTCTTACATCTT 12 218 1 CTTTGCAGCT 0.820557 -83 GCAGGTTTTTCTTTGCTGATCCAGCAGCCG 16 122 0 CTTTGCTGAT 0.846643 -41 CATAATACGGGTTTGCTGAGAGGATTTACA 18 112 0 GTTTGCTGAG 0.952813 -189 CATCCGCAAGCCTTGCAGGGATGCTGTTTC 18 161 0 CCTTGCAGGG 0.845243 -140 ********** Masking position 4 Map Score: 2.01197 Number of sites scoring better than the average of aligned sites = 348 Number in coding regions = 317 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 14 CTCTTGTATAGAAAGTTTTCTTTTTTCCTT 4 45 0 GAAAGTTTTC 0.891027 -73 GATGAGAGAAAAAGGTTCTCTTTTTCTCTC 15 21 1 AAAGGTTCTC 0.961834 -56 AAGCAATGGCGAAGGTTCTCTTGGAATGAT 16 46 0 GAAGGTTCTC 0.982146 -117 GGTATTATGAGAAGGTTTTCATAGCTTTCA 18 63 1 GAAGGTTTTC 0.972008 -238 GCCGGTCAAAAAAGGTCTTCTACTAAGGGT 18 218 1 AAAGGTCTTC 0.911525 -83 ********** Masking position 6 Map Score: 1.66246 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 48 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 15 ********** No masking Map Score: -2.10731e-13 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