AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i162_ecoli_mtub_300.orf -o162_ecoli_mtub_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 = 0.58 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 hemL 224 glutamate-1-semialdehyde aminotransferase (aminomutase) #2 hemB 136 5-aminolevulinate dehydratase = porphobilinogen synthase #3 b0370 84 orf, hypothetical protein #4 hemA 213 enzyme in alternate path of synthesis of 5-aminolevulinate #5 hemC 300 porphobilinogen deaminase = hydroxymethylbilane synthase #6 mmpS2 173 mmpS2 #7 hemA 49 hemA #8 cysG 32 cysG #9 hemB 85 hemB #10 hemL 113 hemL #11 cysG2 276 cysG2 #12 Rv2851c 58 hypothetical protein Rv2851c #13 Rv2852c 206 hypothetical protein Rv2852c Motif number 1 TACTCCAAAAGGGGGCGCTCTCTTTTATTG 4 128 1 GGGGGCGCTC 0.954039 -86 TTCCGCCCATCGCGCGGACCTAGTGACCCT 6 147 0 CGCGCGGACC 0.991479 -27 TGTACACCGACACGCCGACCGAGCTGGCAT 9 43 1 CACGCCGACC 0.935915 -43 CGGCCAAAGGGGTGGCGACCCGCGGCGCCC 11 59 1 GGTGGCGACC 0.970929 -218 GGTGGCGACCCGCGGCGCCCGGTCCCCGCG 11 69 1 CGCGGCGCCC 0.999161 -208 CGATCGCAAGCGCGGGGACCGGGCGCCGCG 11 79 0 CGCGGGGACC 0.997411 -198 CATCAGGGCCAGTGGCGATCGCAAGCGCGG 11 94 0 AGTGGCGATC 0.982537 -183 TGGCCCTGATGGTGGCGACCCGCGGCGCCC 11 113 1 GGTGGCGACC 0.970929 -164 GGTGGCGACCCGCGGCGCCCGGTCCCCGCG 11 123 1 CGCGGCGCCC 0.999161 -154 CGATCGCAAGCGCGGGGACCGGGCGCCGCG 11 133 0 CGCGGGGACC 0.997411 -144 CATCAGGGCCAGTGGCGATCGCAAGCGCGG 11 148 0 AGTGGCGATC 0.982537 -129 TGGCCCTGATGGTGGCGACCCGCGGCGCCC 11 167 1 GGTGGCGACC 0.970929 -110 GGTGGCGACCCGCGGCGCCCGGTCCCCGCG 11 177 1 CGCGGCGCCC 0.999161 -100 CGATCGCAAGCGCGGGGACCGGGCGCCGCG 11 187 0 CGCGGGGACC 0.997411 -90 CATCAGGGCCAGTGGCGATCGCAAGCGCGG 11 202 0 AGTGGCGATC 0.982537 -75 TGGCCCTGATGGTGGCGACCCGCGGCGCCC 11 221 1 GGTGGCGACC 0.970929 -56 GGTGGCGACCCGCGGCGCCCGGTCCCCGCG 11 231 1 CGCGGCGCCC 0.999161 -46 CGATCGCAAGCGCGGGGACCGGGCGCCGCG 11 241 0 CGCGGGGACC 0.997411 -36 CGCCAAGCCTAGTGGCGATCGCAAGCGCGG 11 256 0 AGTGGCGATC 0.982537 -21 ATACAGTGGGGGTACCGCCCGCTTGCGGGG 12 26 1 GGTACCGCCC 0.793601 -33 AAGCGCCGCTCTCCCCCGCAA 12 48 0 AGCGCCGCTC 0.971351 -11 CTTCCTTGGCTGCGCCGCTCCCAGGTTATC 13 173 0 TGCGCCGCTC 0.893214 -34 ********** Masking position 7 Map Score: 81.123 Number of sites scoring better than the average of aligned sites = 584 Number in coding regions = 568 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 2 ACATCCCTACCCTGCTTCAGGTATACT 2 120 1 CCGCTCGGTT 0.522006 -17 TTGTCATCCCTCCTCAGGGACGTAATAAGTT 3 8 1 CCTCTCGGGC 0.925387 -77 CTAGCGTTACCGTCCGCTATCGTCTATGTTCAAG 4 57 1 CGCCCTTCGC 0.933069 -157 AAAGAGAGCGCCCCCTTTTGGAGTAATTGCCGAA 4 119 0 CCCCTTGGAT 0.557497 -95 GTAACCGTTACCACTTTTCGCGCCTGGTTTTTTT 5 37 1 CCCTTTGCGC 0.823616 -264 CCTCGTGTTCCGCCCATCGCGCGGACCTAGTGA 6 151 0 CCCCATGCGG 0.787944 -23 CACCACCTGGCCAGCTCCCTCGACTACCCCAGTA 7 21 0 CCGCCCTCGC 0.983362 -29 TGGCCCACCCTCGTCAGGTGAGCGTGCG 9 5 1 CCCCTCTCAG 0.422887 -81 ACGCAAAATGCCAGCTCGGTCGGCGTGTCGGTGT 9 46 0 CCGCCGTCGC 0.832102 -40 TGGCATTTTGCGTACGCTCGCGGCTACGA 9 67 1 CGACCTGCGC 0.834 -19 AACTCGTGGACCGGCCGCGGCATCAAGCAAACCT 10 22 1 CCGCGCGCAC 0.940054 -92 CCGCGGGTCGCCACCCCTTTGGCCGCGAATGTAA 11 50 0 CCCCCTTGGC 0.9532 -227 AAAGGGGTGGCGACCCGCGGCGCCCGGTCCCCGC 11 64 1 CGCCGCGCGC 0.986426 -213 GCGCCCGGTCCCCGCGCTTGCGATCGCCACTGGC 11 83 1 CCGCCTGCGT 0.976642 -194 CCGCGGGTCGCCACCATCAGGGCCAGTGGCGATC 11 104 0 CCCCTCGGGC 0.992386 -173 CTGATGGTGGCGACCCGCGGCGCCCGGTCCCCGC 11 118 1 CGCCGCGCGC 0.986426 -159 GCGCCCGGTCCCCGCGCTTGCGATCGCCACTGGC 11 137 1 CCGCCTGCGT 0.976642 -140 CCGCGGGTCGCCACCATCAGGGCCAGTGGCGATC 11 158 0 CCCCTCGGGC 0.992386 -119 CTGATGGTGGCGACCCGCGGCGCCCGGTCCCCGC 11 172 1 CGCCGCGCGC 0.986426 -105 GCGCCCGGTCCCCGCGCTTGCGATCGCCACTGGC 11 191 1 CCGCCTGCGT 0.976642 -86 CCGCGGGTCGCCACCATCAGGGCCAGTGGCGATC 11 212 0 CCCCTCGGGC 0.992386 -65 CTGATGGTGGCGACCCGCGGCGCCCGGTCCCCGC 11 226 1 CGCCGCGCGC 0.986426 -51 GCGCCCGGTCCCCGCGCTTGCGATCGCCACTAGG 11 245 1 CCGCCTGCGT 0.976642 -32 CCCGCGCCGGCGACGATACAGTGG 12 1 1 CCGCCCGCGC 0.997367 -58 GCGCCGCTCTCCCCCGCAAGCGGGCGGTACCCCC 12 33 0 CCCCCAGCGG 0.578659 -26 ACGATGACGTCCGCCTCCTGGGCCAGTAACCCTG 13 124 0 CCCCCCGGGC 0.996464 -83 ACGGTTGGTTCCTTCCTTGGCTGCGCCGCTCCCA 13 180 0 CCTCTTGCTC 0.475284 -27 ** ** ** *** * Masking position 1 Map Score: 59.9915 Number of sites scoring better than the average of aligned sites = 4304 Number in coding regions = 4137 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 3 CGTTACCACTTTTCGCGCCTGGTTTTTTTAGT 5 42 1 TTTCGCCTGG 0.67601 -259 ATTCAGGATTTCACGTACCCAGCTTTGCGCGT 6 17 0 TCACACCCAG 0.822748 -157 CTCGTTGCGTTAGCTAGCGTAGACGCTACCGT 6 63 0 TAGCGCGTAG 0.795966 -111 TGAAATGTCCTAACGTGCGTAGTAATCGGATG 6 96 0 TAACGCGTAG 0.707677 -78 GGCAGCACCACCTGGCCAGCTCCCTCGAC 7 31 0 CCACGGCCAG 0.841409 -19 ACTAGTGTTCCAGCCTGCCCAGGTCGCTCAAC 10 88 0 CAGCGCCCAG 0.956728 -26 CCACTGCGAATTTCCGGCCCGGCTTTTCGCAG 11 16 0 TTTCGCCCGG 0.935895 -261 CGCAGTGGCGTTACATTCGCGGCCAAAGGGGT 11 40 1 TTACTCGCGG 0.722503 -237 CCAGTGGCGATCGCAAGCGCGGGGACCGGGCG 11 84 0 TCGCGCGCGG 0.995542 -193 CTTGCGATCGCCACTGGCCCTGATGGTGGCGA 11 99 1 CCACGCCCTG 0.975773 -178 CCAGTGGCGATCGCAAGCGCGGGGACCGGGCG 11 138 0 TCGCGCGCGG 0.995542 -139 CTTGCGATCGCCACTGGCCCTGATGGTGGCGA 11 153 1 CCACGCCCTG 0.975773 -124 CCAGTGGCGATCGCAAGCGCGGGGACCGGGCG 11 192 0 TCGCGCGCGG 0.995542 -85 CTTGCGATCGCCACTGGCCCTGATGGTGGCGA 11 207 1 CCACGCCCTG 0.975773 -70 CTAGTGGCGATCGCAAGCGCGGGGACCGGGCG 11 246 0 TCGCGCGCGG 0.995542 -31 CACTGTATCGTCGCCGGCGCGGG 12 2 0 TCGCGCGCGG 0.994741 -57 GGGGTACCGCCCGCTTGCGGGGGAGAGCGGCG 12 34 1 CCGCGCGGGG 0.957399 -25 CTGCACAGGGTTACTGGCCCAGGAGGCGGACG 13 119 1 TTACGCCCAG 0.956713 -88 **** ****** Masking position 4 Map Score: 36.0026 Number of sites scoring better than the average of aligned sites = 1942 Number in coding regions = 1860 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 4 CAACTTATTACGTCCCTGAGGAGGGATGACAA 3 11 0 CGTCCCTGGA 0.870237 -74 CCTCGTGTTCCGCCCATCGCGCGGACCTAGT 6 153 0 CCGCCCATCG 0.902815 -21 GTCGAGGGAGCTGGCCAGGTGGTGCTGCC 7 31 1 CTGGCCAGGG 0.929233 -19 GTGTTCCAGCCTGCCCAGGTCGCTCAACTACA 10 84 0 CTGCCCAGCG 0.985326 -30 CGATCGCCACTGGCCCTGATGGTGGCGACCCG 11 103 1 TGGCCCTGGG 0.994747 -174 CGATCGCCACTGGCCCTGATGGTGGCGACCCG 11 157 1 TGGCCCTGGG 0.994747 -120 CGATCGCCACTGGCCCTGATGGTGGCGACCCG 11 211 1 TGGCCCTGGG 0.994747 -66 TCCGCACTATCCGCCCAGTCCGGTTCTTCTTG 13 21 0 CCGCCCAGCG 0.980979 -186 CCACAATGTGCGTCCCTGGCCGCCATAGAATC 13 51 0 CGTCCCTGCG 0.7878 -156 ACAGGGTTACTGGCCCAGGAGGCGGACGTCAT 13 123 1 TGGCCCAGGG 0.993018 -84 ******** ** Masking position 6 Map Score: 17.3725 Number of sites scoring better than the average of aligned sites = 489 Number in coding regions = 459 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 AAATGAGGTCTGGCAGTGGATCCTGACAGG 5 206 0 TGGCAGTGGA 0.639807 -95 AAGAAGTGACTGGGAGTGACAATC 8 19 1 TGGGAGTGAC 0.677296 -14 GCCAGCTCGGTCGGCGTGTCGGTGTACAGA 9 41 0 TCGGCGTGTC 0.569088 -45 TCGTAGCCGCGAGCGTACGC 9 76 0 TCGTAGCCGC 0.722266 -10 ACTCGTGGACCGGCCGCGGCATCAAGCAAA 10 23 1 CGGCCGCGGC 0.993009 -91 AAACCTCTGGTGGCTGCGGCAAACTCTTAC 10 50 1 TGGCTGCGGC 0.978017 -64 GCCCGGCTTTTCGCAGTGCCG 11 2 0 TCGCAGTGCC 0.799164 -275 GGCCGGAAATTCGCAGTGGCGTTACATTCG 11 29 1 TCGCAGTGGC 0.906344 -248 GCCACCCCTTTGGCCGCGAATGTAACGCCA 11 45 0 TGGCCGCGAA 0.805663 -232 GCGCCGCGGGTCGCCACCCCTTTGGCCGCG 11 57 0 TCGCCACCCC 0.68197 -220 GCGCGGGGACCGGGCGCCGCGGGTCGCCAC 11 70 0 CGGGCGCCGC 0.980131 -207 GCGCGGGGACCGGGCGCCGCGGGTCGCCAC 11 124 0 CGGGCGCCGC 0.980131 -153 GCGCGGGGACCGGGCGCCGCGGGTCGCCAC 11 178 0 CGGGCGCCGC 0.980131 -99 GCGCGGGGACCGGGCGCCGCGGGTCGCCAC 11 232 0 CGGGCGCCGC 0.980131 -45 CACTGTATCGTCGCCGGCGCGGG 12 4 0 TCGCCGGCGC 0.896208 -55 TGTGCGTCCCTGGCCGCCATAGAATCCGCA 13 47 0 TGGCCGCCAT 0.701547 -160 TGTCTTGGGTTGGCTGCCCCGCGCTGCACA 13 96 1 TGGCTGCCCC 0.947699 -111 GTTCCTTCCTTGGCTGCGCCGCTCCCAGGT 13 177 0 TGGCTGCGCC 0.948171 -30 ********** Masking position 3 Map Score: 25.596 Number of sites scoring better than the average of aligned sites = 4169 Number in coding regions = 4034 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 6 GTTGGTATTATTTCCCGCAGAC 4 202 1 TTTCCCGCAG 0.987852 -12 ACATACGAAATATCCCGAATG 5 2 0 TATCCCGAAT 0.879755 -299 CGTTACCACTTTTCGCGCCTGGTTTTTTTA 5 42 1 TTTCGCGCCT 0.871302 -259 GTTTTTTTAGTTTCACGACGAAAAAATGGT 5 63 1 TTTCACGACG 0.956894 -238 CTGACAGGCGTTTCACGCCGTTGTAATAAG 5 184 0 TTTCACGCCG 0.972394 -117 GGTGTAAGAGTTTGCCGCAGCCACCAGAGG 10 53 0 TTTGCCGCAG 0.93091 -61 CCAAGACAATTACCCCGAAGCCCACAATGT 13 74 0 TACCCCGAAG 0.894709 -133 GCTCCCAGGTTATCCCGACGGGTGTTAACA 13 157 0 TATCCCGACG 0.980674 -50 ********** Masking position 1 Map Score: 5.48433 Number of sites scoring better than the average of aligned sites = 805 Number in coding regions = 760 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 7 AACTTGAACATAGACGATAGCGGACGGTAACG 4 61 0 TAGACGAGCG 0.990455 -153 TGGTGAAACGTAGACGCCTGCGCAAACCGTAA 5 235 0 TAGACGCGCG 0.996754 -66 TTAGCTAGCGTAGACGCTACCGTTGACAGGCT 6 54 0 TAGACGCCCG 0.985992 -120 TTTACTGGGGTAGTCGAGGGAGCTGGCCAGGT 7 19 1 TAGTCGAGAG 0.918054 -31 TCGTAGCCGCGAGCGTACGCAAAAT 9 71 0 TAGCCGCGCG 0.994474 -15 CCCCACTGTATCGTCGCCGGCGCGGG 12 5 0 TCGTCGCGCG 0.9874 -54 ******* *** Masking position 1 Map Score: 5.83568 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 115 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 ATTTGAAACATTACGCTTTGCAAAGGATTTTCATGG 1 66 0 TTGTTCAAGG 0.944038 -159 ATTCGGGATATTTCGTATGTCAAAGGTAACCGTTAC 5 12 1 TTGTGCAAGG 0.983549 -289 GCCTGGTTTTTTTAGTTTCACGACGAAAAAATGGTC 5 58 1 TTGTCCACGA 0.552911 -243 TCTCTGTAAATTCCTTATTACAACGGCGTGAAACGC 5 171 1 TTTTTCACGG 0.678282 -130 AGACCTCATTTTACGGTTTGCGCAGGCGTCTACGTT 5 225 1 TTGTTCCAGG 0.940392 -76 GGCAAGGATGTTAGGATGGACCACGG 5 285 1 TTGGGCACGG 0.981718 -16 TCCTGAATTCTTCAGCCTGTCAACGGTAGCGTCTAC 6 41 1 TTGTGCACGG 0.989565 -133 TTCAGGAGGTATCGGGAGGCCTAAGGGTCACTAGGT 6 124 1 ATGGGCAAGG 0.811383 -50 GTCCCCGCGCTTGCGATCGCCACTGGCCCTGATGGT 11 90 1 TTGCGCCTGG 0.972542 -187 GTCCCCGCGCTTGCGATCGCCACTGGCCCTGATGGT 11 144 1 TTGCGCCTGG 0.972542 -133 GTCCCCGCGCTTGCGATCGCCACTGGCCCTGATGGT 11 198 1 TTGCGCCTGG 0.972542 -79 ** * ** * **** Masking position 2 Map Score: 7.43529 Number of sites scoring better than the average of aligned sites = 378 Number in coding regions = 358 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 9 ACTTGAACATAGACGATAGCGGACGGTAACG 4 61 0 AGACGAAGCG 0.942703 -153 GGTGAAACGTAGACGCCTGCGCAAACCGTAA 5 235 0 AGACGCTGCG 0.973169 -66 TAGCTAGCGTAGACGCTACCGTTGACAGGCT 6 54 0 AGACGCACCG 0.981179 -120 TCGTAGCCGCGAGCGTACGCAAAAT 9 71 0 AGCCGCAGCG 0.996673 -15 GTTTGCTTGATGCCGCGGCCGGTCCACGAGT 10 23 0 TGCCGCGCCG 0.946923 -91 AGTTTGCCGCAGCCACCAGAGGTTTGCTTGA 10 44 0 AGCCACAGAG 0.791412 -70 CCCACTGTATCGTCGCCGGCGCGGG 12 5 0 CGTCGCGGCG 0.875795 -54 CGCCGCTCTCCCCCGCAAGCGGGCGGTACCC 12 35 0 CCCCGCAGCG 0.971285 -24 ****** **** Masking position 4 Map Score: 4.67226 Number of sites scoring better than the average of aligned sites = 1633 Number in coding regions = 1525 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 10 TACTGGTGCAATCCTGATTTCTTAGAGTAT 1 115 0 ATCCTGATTT 0.857323 -110 GATCTTACGCATCCTGTATGATGCAAGCAG 4 157 1 ATCCTGTATG 0.84893 -57 CATACGAAATATCCCGAATG 5 1 0 ATCCCGAATG 0.946686 -300 CTGGCAGTGGATCCTGACAGGCGTTTCACG 5 197 0 ATCCTGACAG 0.966756 -104 CCGTGGTCCATCCTAACATCCTTGCCAGA 5 282 0 ATCCTAACAT 0.671849 -19 GGTACGTGAAATCCTGAATTCTTCAGCCTG 6 30 1 ATCCTGAATT 0.951852 -144 CTCCCGATACCTCCTGAAATGTCCTAACGT 6 112 0 CTCCTGAAAT 0.801293 -62 CTCCCAGGTTATCCCGACGGGTGTTAACAC 13 156 0 ATCCCGACGG 0.906188 -51 ********** Masking position 2 Map Score: 0.883903 Number of sites scoring better than the average of aligned sites = 503 Number in coding regions = 448 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 11 GTTTCACGACGAAAAAATGGTCTAAAACGT 5 72 1 GAAAAAATGG 0.931659 -229 AATTTACAGAGAATAAACGGTGCTACACTT 5 153 0 GAATAAACGG 0.86694 -148 ACCGGTACGCGCAAAGCTGGGTACGTGAAA 6 11 1 GCAAAGCTGG 0.937761 -163 GACTACCCCAGTAAAACTGGTGT 7 4 0 GTAAAACTGG 0.9246 -46 CGGCACTGCGAAAAGCCGGGCCGGAAATT 11 10 1 GAAAAGCCGG 0.981341 -267 TACCTCCCAAGAAGAACCGGACTGGGCGGA 13 14 1 GAAGAACCGG 0.966191 -193 ********** Masking position 5 Map Score: 0.635085 Number of sites scoring better than the average of aligned sites = 557 Number in coding regions = 529 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 12 TTATACTCTAAGAAATCAGGATTGCACCAG 1 113 1 AGAAATCAGG 0.975528 -112 AATACTCGTCAAACATCAGGCTGCTTGTAC 1 142 0 AAACATCAGG 0.920694 -83 CACTTTTTCTACGAATCAGGAACCCTCC 1 207 1 ACGAATCAGG 0.935798 -18 GTGAAACTAAAAAAACCAGGCGCGAAAAGT 5 49 0 AAAAACCAGG 0.904059 -252 GACAGGCTGAAGAATTCAGGATTTCACGTA 6 32 0 AGAATTCAGG 0.955288 -142 GCACGTTAGGACATTTCAGGAGGTATCGGG 6 110 1 ACATTTCAGG 0.866557 -64 ********** Masking position 8 Map Score: 0.163966 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 69 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 13 ********** No masking Map Score: -6.21482e-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: -6.21482e-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 TTATTGGTCATACAAATAAGATGACGGCATTTTAC 1 22 1 TAAAGATGAC 0.974095 -203 TTGCTGTTTCTATTAAAAAGATGTCCTGGCCTCTC 2 44 1 TAAAGATGTC 0.974095 -93 ATCAGCAAGGTGTTAAATTGATCACGTTTTAGACC 5 90 0 TGAAGATCAC 0.931306 -211 CTAACATCCTTGCCAGAGTGATGTCAGTGTTGTGG 5 264 0 TGAGGATGTC 0.955791 -37 CTAACGTGCGTAGTAATCGGATGTCTCGTTGCGTT 6 84 0 TAAAGATGTC 0.974095 -90 TCCCGACGGGTGTTAACACGATGACGTCCGCCTCC 13 140 0 TGAAGATGAC 0.983369 -67 ** ** ****** Masking position 5 Map Score: 0.486584 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 21 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617