AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iglpR_ecoli_bsub_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 glpT_glpA 272 glpT: sn-glycerol-3-phosphate permease, glpA: sn-glycerol-3-phosphate dehydrogenase (anaerobic), large subunit #2 glpG 44 protein of glp regulon #3 glpE_glpD 189 glpE: protein of glp regulon, glpD: sn-glycerol-3-phosphate dehydrogenase (aerobic) #4 glpK 22 glycerol kinase #5 glpF 300 facilitated diffusion of glycerol #6 glpQ 98 glycerophosphoryl diester phosphodiesterase #7 glpT 296 glycerol-3-phosphate permease #8 glpF 178 glycerol uptake facilitator #9 glpD 140 glycerol-3-phosphate dehydrogenase #10 fruR 279 transcriptional regulator (DeoR family) #11 yqhL 190 similar to hypothetical proteins #12 yqgP 89 similar to hypothetical proteins #13 yqgO 66 yqgO #14 yqgN 300 similar to 5-formyltetrahydrofolate cyclo-ligase #15 glcR 223 transcriptional regulator (DeoR family) #16 iolR 300 transcriptional regulator (DeoR family) Motif number 1 ACATTATTAAATAAGATTTACAAAATGTTCAAAATGA 1 121 0 AAATACAAAG 0.873702 -152 TTATGTCACCAGGAGAAGGATGAAAAGTGTGGCAAAC 5 33 0 AAAAATAAAG 0.832581 -268 ATCATGTACAATCAGATGGAATAAATGGCGCGATAAC 5 127 1 AAATAAAAAG 0.906681 -174 AAAAAATATAATTGCATTTAGTAAAAGGATAATATTC 7 50 1 AGATAGAAAG 0.862077 -247 CCACACATCCAGCACAAACAGCAAAGGGGGATAATTA 7 267 1 AAAAAGAAAG 0.96983 -30 GATAGAGAAGAAGAGAATAAAAAAACCACAACAAACC 8 117 0 AAAAAAAAAC 0.810707 -62 CCTTGTTGTCACGGTAAATAGAAAAAGAGACCACAAC 9 104 0 AGAAAGAAAG 0.946955 -37 ATTTACCGTGACAACAAGGAGGAAACGTA 9 122 1 AAAAAGAAAG 0.96983 -19 TTTTTTCATTAAAATAAGAAGAAAATGTCGTACAATT 10 73 1 AAAAAGAAAG 0.96983 -207 CGAAACGCCTACTGAAAGCAAAAAATCCCGTTTTTCA 12 18 0 AGAAAAAAAC 0.704006 -72 TAACTATATTTCTAAAAAGACCAAACGCAACAATCCA 14 121 1 TAAAACAAAG 0.761307 -180 CTCATCCCCCTCGGAATAGAAAAAAAGCCAGAACCTT 14 272 0 TGATAAAAAG 0.465529 -29 ATGCGATTAGAATATAACCAAGAAATGACCAAAAAGT 16 69 0 AAAAAAAAAG 0.965218 -232 TAATATAATAAAAATAATGAAAAAATGTAGTGTTTAT 16 124 0 AAAAAAAAAG 0.965218 -177 TTAATCAAGTAAGAGAAGTAAGAGAAGGCCGTCCAAT 16 166 1 AAAAAAAGAG 0.778723 -135 ACATAAATATATAATAAAAACCAAAAGTTAATCAATA 16 244 0 AAAAACAAAG 0.951826 -57 * * ** ** *** * Masking position 10 Map Score: 13.0703 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 148 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 2 GTGAGAGAACCTGCCGTTTCTTGAGTTGCCG 1 202 0 CTGCCGTTTT 0.952435 -71 CGTTGCTGTCGCTTATTCCACACAAA 2 29 0 CTGTCGCTTT 0.972436 -16 GTATAACATTATGGCGTTTATCTGCCGCTTC 3 116 1 ATGGCGTTTT 0.816831 -74 TGGCGTTTATCTGCCGCTTCGACGTAAACTG 3 127 1 CTGCCGCTTG 0.935966 -63 TAAGCACTACCTGTCTTTCATAATAAAAAAC 6 59 0 CTGTCTTTCT 0.879302 -40 GGTTGGATTCCTGGCTCTCCTCATCTCCATC 7 181 0 CTGGCTCTCT 0.976894 -116 GGGGTGTTTTCTGGCTCTTTTTGTTTTTCGG 7 223 1 CTGGCTCTTT 0.985402 -74 ATTATAACAGCTGGCGCTCCGAAACGCCTAC 12 43 0 CTGGCGCTCG 0.962792 -47 CTTTCCTGTCCCTTATTCGAGAATAA 13 6 1 CTGTCCCTTT 0.889979 -61 TTTCAAAGCTCTGGCTTTTTTCTTACACCTC 14 241 0 CTGGCTTTTT 0.972596 -60 GAAAAAGGTTCTGGCTTTTTTTCTATTCCGA 14 268 1 CTGGCTTTTT 0.972596 -33 ********* * Masking position 8 Map Score: 11.3211 Number of sites scoring better than the average of aligned sites = 832 Number in coding regions = 771 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 3 CGTTGCTGTCGCTTATTCCACACA 2 31 0 GCTGTCGCTT 0.875804 -14 ATTTTCGATTGATGTGGATTATGTCACCAG 5 58 0 GATGTGGATT 0.832807 -243 GTTTACATTCGCTCCGGACTATGATAATTT 7 118 1 GCTCCGGACT 0.797612 -179 GTAAAGAGCTGCTGTGGTCTCCGAGTTCTC 8 61 0 GCTGTGGTCT 0.982939 -118 AAAGCGGTTTGTTGTGGTTTTTTTATTCTC 8 112 1 GTTGTGGTTT 0.952809 -67 ACACTTTGGTGCTGTGGTCTCTCCTCATCT 9 57 0 GCTGTGGTCT 0.982939 -84 CACTTTGGCTGTTGTGGTCTCTTTTTCTAT 9 94 1 GTTGTGGTCT 0.949704 -47 TGACAATCACGCTGTGCTTTACTATAATAG 11 93 1 GCTGTGCTTT 0.877966 -98 AATTCAACGCGGTCTGGATTGTTGCGTTTG 14 142 0 GGTCTGGATT 0.811398 -159 CTTTTTCAAAGCTCTGGCTTTTTTCTTACA 14 245 0 GCTCTGGCTT 0.972368 -56 TTTGAAAAAGGTTCTGGCTTTTTTTCTATT 14 265 1 GTTCTGGCTT 0.92021 -36 ********** Masking position 3 Map Score: 8.53645 Number of sites scoring better than the average of aligned sites = 423 Number in coding regions = 389 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 4 GCTGCCCTCATTCACTTTCGTTAAA 3 6 1 CCTCATTCAC 0.943009 -184 AACAAACATGCATCATGTACAATCAGATGG 5 116 1 CATCATGTAC 0.659206 -185 TCCTGGCTCTCCTCATCTCCATCCAAGCTA 7 174 0 CCTCATCTCC 0.97157 -123 GTGTGGCGTGCCTCCTTTCCCGAAAAACAA 7 243 0 CCTCCTTTCC 0.863955 -54 TGTGGTCTCTCCTCATCTCAGGACCGTTCT 9 45 0 CCTCATCTCA 0.918035 -96 CCTCATGCAACATGCATGAG 10 1 1 CCTCATGCAA 0.918035 -279 CATAAAAAAACCTCATGCATGTTGCATGAG 10 12 0 CCTCATGCAT 0.886576 -268 GATATCCCTCCTGCCAATAGGGTTTG 13 51 0 CCTCCTGCCA 0.921261 -16 CTCTCATCCCCCTCGGAATAG 14 290 0 TCTCATCCCC 0.879939 -11 CGGATCTTCGCATCATCCCCTCAAAATTGA 15 51 1 CATCATCCCC 0.934769 -173 GCCCTCATTCCTTTTCTCAGCA 15 212 0 CCTCATTCCT 0.911512 -12 ********** Masking position 6 Map Score: 7.55942 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 253 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 5 CATCAATCGAAAATGTTAATAAATTTGTTGC 5 74 1 AAAGTTAATA 0.963188 -227 AAGACACATAAAAGATTAATAGTTTTCCAAC 6 13 1 AAAATTAATA 0.880705 -86 GCATTTAGTAAAAGGATAATATTCACTTCCC 7 63 1 AAAGATAATA 0.786399 -234 CGCTATCATGATAAGTTAATAGCTTGGATGG 7 155 1 ATAGTTAATA 0.932089 -142 TACAATTGCACTAGGTTAATACATTGTGATG 8 30 1 CTAGTTAATA 0.855106 -149 TATAATGGTTACAAGTTAATAAGAACGGTCC 9 24 1 ACAGTTAATA 0.889514 -117 CCCTATAGACATACGTTAATATGGAGAAACG 10 143 1 ATAGTTAATA 0.932089 -137 TGATTTTATTCAACATTAATAAGTGATTTTA 15 151 0 CAAATTAATA 0.760444 -73 TACTTGATTAAAAGATTAATATAATAAAAAT 16 146 0 AAAATTAATA 0.880705 -155 AATAAAAACCAAAAGTTAATCAATAGTTGCT 16 238 0 AAAGTTAATC 0.84512 -63 *** ******* Masking position 7 Map Score: 5.92076 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 34 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 TAAAGCTCATAAATGTTCGTTATCGAACATATTAG 3 32 1 AACGTTATCG 0.955615 -158 CCTCGTCATAAAATGAGCGTTATCGCGCCATTTAT 5 147 0 AACGTTATCG 0.955615 -154 GCATGCTGTAAACTTATCGTTAACGAGCAAAAACG 5 209 0 AACGTTAACG 0.955615 -92 ATAGTTTTCCAACACGCCGTTTACATCCGTTTTTT 6 31 1 AACGTTTACA 0.966771 -68 CCAATTTGAAAATTACCCGTTTACATTCGCTCCGG 7 100 1 AACGTTTACA 0.966771 -197 ATGATAATTTAAGAAAGCGCTATCATGATAAGTTA 7 138 1 AACGCTATCA 0.805613 -159 ATTTTTGTCGAATTTACAGTTTACAAACCCTATAG 10 116 1 AAAGTTTACA 0.717664 -164 GCCTAAACCGAAAATAGCGTTTACAATGAAATTGT 10 219 1 AACGTTTACA 0.966771 -61 TGTATTCAAAATGAATACGTTTTCATTAGGAGGTG 10 251 1 ATCGTTTTCA 0.88996 -29 AAACAAGGTCATAGAGCCGTTTTCGACAAATACTA 11 120 0 ATCGTTTTCG 0.897564 -71 ** ******** Masking position 11 Map Score: 5.7024 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 153 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 TATGGCTAAATGGTAAAAAACGAACTTCAG 1 21 0 TGGTAAAAAA 0.794665 -252 CATTTAGCCATAGTAAAAACATGAATTGTT 1 39 1 TAGTAAAAAC 0.860802 -234 CTGTCTTTCATAATAAAAAACGGATGTAAA 6 50 0 TAATAAAAAA 0.943447 -49 TTTATGTTACTAGTAAAAAAATATAATTGC 7 35 1 TAGTAAAAAA 0.924527 -262 GAGAAGAAGAGAATAAAAAAACCACAACAA 8 120 0 GAATAAAAAA 0.72461 -59 CTTCTTATTTTAATGAAAAAAGTCTTTTAT 10 64 0 TAATGAAAAA 0.924527 -216 CTTCACCTCCTAATGAAAACGTATTCATTT 10 259 0 TAATGAAAAC 0.860802 -21 CCAGCTGTTATAATGAAAAAAAACTATTGG 12 60 1 TAATGAAAAA 0.924527 -30 ATTGCCCACGTGATAAAAAATCTACGTTAC 14 180 1 TGATAAAAAA 0.840522 -121 GTTTGAGGTGTAAGAAAAAAGCCAGAGCTT 14 237 1 TAAGAAAAAA 0.741191 -64 CCCCTCGGAATAGAAAAAAAGCCAGAACCT 14 273 0 TAGAAAAAAA 0.586582 -28 ATAATAAAAATAATGAAAAAATGTAGTGTT 16 127 0 TAATGAAAAA 0.924527 -174 CATAAATATATAATAAAAACCAAAAGTTAA 16 250 0 TAATAAAAAC 0.893862 -51 ********** Masking position 6 Map Score: 12.2521 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 87 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 8 TGTTTGATTTCGCGCATATTCGCTCATAAT 1 65 1 CGCGCATATT 0.950554 -208 CGCGCATATTCGCTCATAATTCGAAAGTGA 1 75 1 CGCTCATAAT 0.885677 -198 TGAATTGCCGCACACATTATTAAATAAGAT 1 141 0 CACACATTAT 0.841366 -132 TGTTCGTTATCGAACATATTAGCAAAGAAT 3 45 1 CGAACATATT 0.721406 -145 GCAAATTTACCGCACAGTTTACGTCGAAGC 3 142 0 CGCACAGTTT 0.908092 -48 GGCGCGATAACGCTCATTTTATGACGAGGC 5 153 1 CGCTCATTTT 0.952239 -148 TGACGAGGCACACACATTTTAAGTTCGATA 5 174 1 CACACATTTT 0.894831 -127 GTAATATTAACGCGCATTATTTTCCCTCCA 14 64 0 CGCGCATTAT 0.950554 -237 ********** Masking position 6 Map Score: 2.94488 Number of sites scoring better than the average of aligned sites = 367 Number in coding regions = 321 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 9 AGCCTGATTCAGTGAGAGAACCTGCCGTTT 1 214 0 AGTGAGAGAA 0.759958 -59 CTTATCTATAAGGAGGAGAAATC 6 86 1 AGGAGGAGAA 0.984762 -13 TTGGGCCTTAGGGAAGTGAATATTATCCTT 7 74 0 GGGAAGTGAA 0.835545 -223 CAAACAGCAAAGGGGGATAATTATTA 7 281 1 AGGGGGATAA 0.755903 -16 CATGATAGAGAAGAAGAGAATAAAAAAACC 8 127 0 AAGAAGAGAA 0.763289 -52 CGTTTTCATTAGGAGGTGAAGC 10 268 1 AGGAGGTGAA 0.953318 -12 TATATGCTAAAGGAGTAGAATCACA 11 176 1 AGGAGTAGAA 0.863674 -15 GATAGATAACGGGAGGAGCAGGGGTG 15 7 0 GGGAGGAGCA 0.880674 -217 AAGTAAGAGAAGTAAGAGAAGGCCGTCCAA 16 172 1 AGTAAGAGAA 0.866255 -129 ********** Masking position 10 Map Score: 2.52841 Number of sites scoring better than the average of aligned sites = 341 Number in coding regions = 287 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 10 CGCGATGTTAAGAAAACATTCATAAATTAA 1 174 0 AGAAAACATT 0.899467 -99 TATGTTCGATAACGAACATTTATGAGCTTT 3 33 0 AACGAACATT 0.801396 -157 GGTAACATTGAAAAAACATTTTAGAGTGAT 3 84 1 AAAAAACATT 0.891981 -106 CGAATGATCTAACAAACATGCATCATGTAC 5 106 1 AACAAACATG 0.801415 -195 TCACGCATACAACAAACATTAACTCTTCAG 5 272 1 AACAAACATT 0.950856 -29 TATAATGAAAAAAAACTATTGGAGCGGTAA 12 68 1 AAAAACTATT 0.657743 -22 CGTTGAATTTAAAAAATATTGCCCACGTGA 14 163 1 AAAAAATATT 0.699687 -138 TCCTTTTCTCAGCAATCATTTATAAGTAAT 15 196 0 AGCAATCATT 0.813166 -28 TTTACATACAAGCAACCATTTCATGCACAA 16 33 1 AGCAACCATT 0.945334 -268 ATCATTTTTAAGCAACTATTGATTAACTTT 16 228 1 AGCAACTATT 0.829911 -73 ********** Masking position 5 Map Score: 3.14607 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 182 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 11 TGTTATCCCTCTGAAGTTCGTTTTTTA 1 6 1 TCCCTCGAAT 0.977633 -267 GTTATACATATCACTCTAAAATGTTTTTTCAA 3 91 0 TCACTCAAAT 0.923782 -99 ATAATCCACATCAATCGAAAATGTTAATAAAT 5 66 1 TCAATCAAAT 0.704723 -235 TTAAACAGCCTCCCTCCAGATTTTTATGTTAC 7 13 1 TCCCTCAGAT 0.962828 -284 CCGTTTACATTCGCTCCGGACTATGATAATTT 7 116 1 TCGCTCGGAT 0.804204 -181 TCTCCTCATCTCCATCCAAGCTATTAACTTAT 7 165 0 TCCATCAAGT 0.709132 -132 CGCATTATTTTCCCTCCAAACTAAAATCATTT 14 50 0 TCCCTCAAAT 0.981478 -251 CTCTCATCCCCCTCGGAATAGAAAAAAAGC 14 281 0 CCCCTCGAAA 0.771064 -20 TTCGCATCATCCCCTCAAAATTGACCAGTCGA 15 57 1 CCCCTCAAAT 0.962828 -167 ****** *** * Masking position 5 Map Score: 1.95332 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 44 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 12 TGAATTTGAATGATTTTAGTTGCCTAAACC 10 198 1 TGATTTTAGT 0.943343 -82 TTTGATAAACTGATTCTATTAAAACGGTAA 11 24 0 TGATTCTATT 0.927468 -167 AGCAGGGTTTTGATTTTATATGCTAAAGGA 11 160 1 TGATTTTATA 0.791889 -31 TGTGATTCTACTCCTTTAGCAT 11 179 0 TGATTCTACT 0.882361 -12 AATAAGTAAATGATTTTAGTTTGGAGGGAA 14 43 1 TGATTTTAGT 0.943343 -258 AGTTTTTATTTGATTTTATTCAACATTAAT 15 162 0 TGATTTTATT 0.939113 -62 ********** Masking position 5 Map Score: 1.97949 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 38 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 13 GAAATCAAACAATTCATGTTTTTACTATGGC 1 45 0 AATTCATGTT 0.405925 -228 GAATTGTTTGATTTCGCGCATATTCGCTCAT 1 61 1 ATTTCGCGCT 0.552232 -212 GTGAAACGTGATTTCATGCGTCATTTTGAAC 1 101 1 ATTTCATGCT 0.904233 -172 AGGTCCGTGACTTTCACGCATACAACAAACA 5 259 1 CTTTCACGCT 0.942415 -42 AACTATTAATCTTTTATGTGTCTTTC 6 6 0 CTTTTATGTT 0.615079 -93 AATTATCCCCCTTTGCTGTTTGTGCTGGATG 7 272 0 CTTTGCTGTT 0.731892 -25 CACCGCTTTCATGCACTGATACAATT 8 6 1 CTTTCATGCC 0.942415 -173 CTCTTCTTCTCTATCATGCTTTTTAATCGTG 8 139 1 CTATCATGCT 0.772246 -40 CTATCAAAATCTTTCACGTTTCTCCATATTA 10 159 0 CTTTCACGTT 0.910913 -121 CTTTCCTGTCCCTTATTCGAG 13 1 1 CTTTCCTGTC 0.86494 -66 AAAATAACAGCTTTGCTGTTTGAGGTGTAAG 14 220 1 CTTTGCTGTT 0.731892 -81 ACAAGCAACCATTTCATGCACAACAGGTTAC 16 40 1 ATTTCATGCC 0.840728 -261 ********* * Masking position 4 Map Score: 1.22185 Number of sites scoring better than the average of aligned sites = 617 Number in coding regions = 551 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 14 CAGGCTGTTAATCATAAATAAGACCACGGG 1 238 1 ATCATAAATA 0.880246 -35 CCTGTCTTTCATAATAAAAAACGGATGTAA 6 51 0 ATAATAAAAA 0.849804 -48 TTTTACTAGTAACATAAAAATCTGGAGGGA 7 23 0 AACATAAAAA 0.897275 -274 AGAGAAGAAGAGAATAAAAAAACCACAACA 8 121 0 AGAATAAAAA 0.791984 -58 GAAATCACTAAACATAAAAAAACCTCATGC 10 24 0 AACATAAAAA 0.897275 -256 CCCTTATTCGAGAATAAATAAGGTAGAATA 13 20 1 AGAATAAATA 0.722265 -47 GATTTTATTCAACATTAATAAGTGATTTTA 15 151 0 AACATTAATA 0.431194 -73 CCATAAGTCAATCATAAACACTACATTTTT 16 111 1 ATCATAAACA 0.768048 -190 AAAGATTAATATAATAAAAATAATGAAAAA 16 137 0 ATAATAAAAA 0.849804 -164 ACATAAATATATAATAAAAACCAAAAGTTA 16 251 0 ATAATAAAAA 0.849804 -50 ATCTTTACGTAACATAAATATATAATAAAA 16 262 0 AACATAAATA 0.856449 -39 ********** Masking position 4 Map Score: 6.9546 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 121 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 15 AATTAAATGTGAATTGCCGCACACATTATT 1 150 0 GAATTGCCGC 0.910114 -123 GCCGTTTCTTGAGTTGCCGCGATGTTAAGA 1 191 0 GAGTTGCCGC 0.937506 -82 TTATGGCGTTTATCTGCCGCTTCGACGTAA 3 124 1 TATCTGCCGC 0.803684 -66 TAATCTGCAAGGCGTGCCGC 5 1 0 GGCGTGCCGC 0.988971 -300 TGCAGATTACGGTTTGCCACACTTTTCATC 5 22 1 GGTTTGCCAC 0.910115 -279 ACTTAAAATGTGTGTGCCTCGTCATAAAAT 5 168 0 TGTGTGCCTC 0.884509 -133 CTGGATGTGTGGCGTGCCTCCTTTCCCGAA 7 249 0 GGCGTGCCTC 0.968028 -48 ********** Masking position 5 Map Score: 0.140501 Number of sites scoring better than the average of aligned sites = 743 Number in coding regions = 695 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714