AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i210_trans4_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 b0024 102 orf, hypothetical protein #2 ileS 42 isoleucine tRNA synthetase #3 pnp 177 polynucleotide phosphorylase; cytidylate kinase activity #4 rpsO 148 30S ribosomal subunit protein S15 #5 rbfA 74 ribosome-binding factor A #6 infB 24 protein chain initiation factor IF-2 #7 nusA 27 transcription pausing; L factor #8 yhbC 200 orf, hypothetical protein #9 metY 300 tRNA #10 HI0229 298 polynucleotide phosphorylase (pnp) #11 HI0963 34 riboflavin kinase / FMN adenylyltransferase (ribF) #12 HI0964 300 virulence factor (mviN) #13 HI1282 300 conserved hypothetical protein #14 HI1288 300 ribosome binding factor A (rbfA) #15 HI1324 96 lon protease, putative #16 HI1325 168 3-hydroxydecanoyl-(acyl carrier-protein) dehydratase (fabA) #17 HI1326 233 H. influenzae predicted coding region HI1326 #18 HI1328 135 ribosomal protein S15 (rpS15) Motif number 1 GGATTTGTGCAAATAAGCGCCGTTA 1 88 1 AAATAACGCC 0.909571 -15 TGCGAGTTTCAGAAAAGGGGGCCTGAGTGGC 3 15 1 AGAAAAGGGG 0.707243 -163 CGTCAGCTTGAAAAAAGGGGCCACTCAGGCC 3 34 0 AAAAAAGGGC 0.986211 -144 AAATTAATTTTAAAAAGGGGCTAACAGCCCC 5 32 1 TAAAAAGGGC 0.836527 -43 TTCTCCTGACAAAAAAGGGGCTGTTAGCCCC 5 48 0 AAAAAAGGGC 0.986211 -27 GGGTTCAGTTATATAAAGCCCCGATTTATCG 8 118 1 ATATAAGCCC 0.717074 -83 GTCAGATAACAAAAAACCCCGATAAATCGGG 8 137 0 AAAAAACCCG 0.702024 -64 CCCAAGACATAAAAAAAGGGCCTAAAGCCCA 8 179 0 AAAAAAGGGC 0.986211 -22 GTTTTTTGTAAAATAATGCGCTTAAGGGAGA 9 87 1 AAATAAGCGC 0.944608 -214 CTAATGTAGAAAATAAAGCCCGTGCATTATA 10 153 0 AAATAAGCCC 0.916369 -146 AAATCTTTCGAAAAAATGACCGCACTTTGGG 10 214 0 AAAAAAGACC 0.767306 -85 TTGATAGACAAAATAAAGGGCATCAATATGC 12 29 1 AAATAAGGGC 0.96369 -272 ACAAAAGTATAAAAAATCGGCATATTGATGC 12 48 0 AAAAAACGGC 0.976845 -253 AAAAAAACTGATAAAATCCGCCACACATCGT 12 168 0 ATAAAACCGC 0.862447 -133 TTTCTTATAGAAAAAAACCCCAAAACTGGGG 13 81 0 AAAAAACCCC 0.945702 -220 TCTCAGGCATAAAAAAAGGGTTAGGTTCATA 13 135 0 AAAAAAGGGT 0.780077 -166 TTCCTTATTTATAAAAGCGCCTCATTCTACT 14 275 0 ATAAAACGCC 0.862447 -26 AAAATCCACTAGAAAATCGGCATAAAAACAC 15 50 0 AGAAAACGGC 0.913299 -47 AAGAAAAGCGAAAAAATGCTCGCTTTTCTCT 16 12 0 AAAAAAGCTC 0.767306 -157 ****** **** Masking position 6 Map Score: 25.0903 Number of sites scoring better than the average of aligned sites = 941 Number in coding regions = 645 Number in noncoding regions = 296 Number of orfs with sites within 600 bp upstream = 243 Fraction of orfs with sites within 600 bp upstream = 0.0390299 Motif number 2 CTTCCACCTGAAATTAATTTTAAAAAGGGGCTAAC 5 22 1 AATTTTAAAA 0.935103 -53 CTTTCCCTTAGAGTCCTTTTTCAAATATACTGTG 8 10 1 AATTTTTCAA 0.734616 -191 TCATTACATTATATTTCATATAAAAGAACCTAATT 10 17 1 AAATATAAAA 0.793772 -282 GCGGCTATCAAAAGAAATTTTTAAACGCCCAAAGT 10 187 1 AATTTTTAAA 0.94994 -112 TGTTTTCCTTAAAATTTATATTAAAAACAATGCCT 10 272 0 AAATATTAAA 0.835227 -27 GCCCATATTGAAAGAGCTTGTAAAAATAACGATAC 12 125 0 AATTGTAAAA 0.770988 -176 TATTTTGAGTAAACGACTTTTAAAATCTAGCATTG 12 265 1 AATTTTAAAA 0.935103 -36 AATAGTAAAAAGATAGTTTATTAAATCTCAGGCAT 13 156 0 AATTATTAAA 0.923813 -145 ACACATTACAACAAGCATTTTTAAATGATTAGAC 14 61 0 AATTTTTAAA 0.94994 -240 TATAACTGATATATTTATTTTAAAAGGAACGCAGT 16 112 0 AATTTTAAAA 0.935103 -57 CAAGAATATTATAGATATTTTAAAAATTTATTACA 17 86 0 AATTTTAAAA 0.935103 -148 AGTGGTAAATAAAGTTTATTTTAAAGTTTTTAATA 17 139 1 AAATTTTAAA 0.888053 -95 ATTTTCTATAATAACGTTTATTAAAAACTTTAAAA 17 157 0 AATTATTAAA 0.923813 -77 AAACGTTATTATAGAAAATATTAAATTAATTTCTA 17 173 1 AAATATTAAA 0.835227 -61 * * ******** Masking position 3 Map Score: 13.2663 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 29 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 3 CCTATAACCGCAACTGCGGTCTGGAGCACT 8 90 0 CAACTGCGGT 0.96337 -111 TTAAACGCCCAAAGTGCGGTCATTTTTTCG 10 207 1 AAAGTGCGGT 0.995087 -92 AAAAACCCCAAAACTGGGGTTCTTTTACTG 13 70 0 AAACTGGGGT 0.942634 -231 AGGTTATGATATAGTGCGGTGAATTACACC 13 234 1 ATAGTGCGGT 0.976772 -67 AATTCATACAAAAGTGCGGTGAAAGTTTTT 17 23 1 AAAGTGCGGT 0.995087 -211 TTAATAAGTAAAGGTGCGGTGAAAATCTAG 17 54 0 AAGGTGCGGT 0.984209 -180 TAATGAAAAGTGCGGTAACTTTAATC 18 7 1 AAAGTGCGGT 0.995087 -129 ********** Masking position 5 Map Score: 13.2366 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 18 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 ACGGCGCTTATTTGCACAAATCCATTGACAAAAGAAGGCTAAA 1 68 0 TTTATAAAAA 0.95708 -35 TTTATCGGGGTTTTTTGTTATCTGACTACAGAATAACTGGGCT 8 142 1 TTTATGAGAA 0.646403 -59 AATGTTTTCCTTAAAATTTATATTAAAAACAATGCCTTA 10 270 0 TTCATAAAAA 0.807678 -29 TCCTAAAATTTCTGTTGATTGATAGACAAAATAAAGGGCAT 12 9 1 TTTATAAAAA 0.957053 -292 CAACACAAATTTTCCATTGACAAAAGTATAAAAAATCGGCATA 12 55 0 TTTACAAAAA 0.764712 -246 ATCAGTTTTTTTTCACGGAATATAGCGTAAAAACAAAATTTCT 12 187 1 TTTATAAAAA 0.957064 -114 GAGAAGAATATTTTGAGTAAACGACTTTTAAAATCTAGCATTG 12 257 1 TTTAAAAAAA 0.686035 -44 GTGCGGTGAATTACACCCTATATAGGAGTAGAAATTGGCTACA 13 247 1 TTAATAAGAA 0.849292 -54 CAACAAGCATTTTTAAATGATTAGACGAAAAACTTTGGGCAT 14 45 0 TTTAAAAAA 0.686352 -256 GCAGTCACTCTTAGAAATTATAGAAAAAAAGAAAAGCGAAAAA 16 28 0 TTAATAAGAA 0.849292 -141 TCACCGCACTTTTGTATGAATTAATAAAGAAAAA 17 2 0 TTTATAAAAA 0.956867 -232 ATTTTAAAAATTTATTACAATTTAATAAGTAAAGGTGCGGTGA 17 62 0 TTTATATAAA 0.794553 -172 TAAACTTTATTTACCACTAATAAAATTAAAAAATAACAAGAAT 17 114 0 TTAATAAAAA 0.903124 -120 AAATATTAAATTAATTTCTATTTAAATTATAAATAATATACTA 17 188 1 TTAATATAAA 0.618035 -46 TTATCTTGCATTTGAACTTATTCATCGTTAGAATGCGATTTCC 18 38 1 TTTATAAGAA 0.93094 -98 *** ** * **** Masking position 10 Map Score: 12.0565 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 53 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 5 GAACACATTTGGGAGTTGGACC 1 2 0 GGGAGTTGAC 0.940622 -101 CTTTTGTCAATGGATTTGTGCAAATAAGCGC 1 77 1 TGGATTTGGC 0.882613 -26 CTATATACTTTGGAGTTTTAAA 4 137 1 TGGAGTTTAA 0.546708 -12 TCAGGTGGAAGGGCTGTTCACG 5 2 0 GGGCTGTTAC 0.924037 -73 GACAAAAAAGGGGCTGTTAGCCCCTTTTTAA 5 41 0 GGGCTGTTGC 0.90915 -34 CGCGGGCTTTTCACCTCATCCAGA 7 14 0 GGGCTTTTAC 0.972298 -14 CCTTCGTAGTGGGATTTGAAAAAATCCTTCT 8 55 1 GGGATTTGAA 0.86217 -146 CAGAATAACTGGGCTTTAGGCCCTTTTTTTA 8 170 1 GGGCTTTAGC 0.838045 -31 ACCGCACTTTGGGCGTTTAAAAATTTCTTTT 10 196 0 GGGCGTTTAA 0.81244 -103 TTGCGGGGGCTGGATTTGAACCAACGACCTT 13 26 0 TGGATTTGAC 0.901377 -275 TAAGTTGAAAGGGATTTTTGCGTGCTAAATT 14 233 1 GGGATTTTGC 0.961429 -68 GATTTTCTAGTGGATTTTCACAAGGCTATTA 15 63 1 TGGATTTTAC 0.907175 -34 ******** ** Masking position 7 Map Score: 8.93055 Number of sites scoring better than the average of aligned sites = 614 Number in coding regions = 538 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 6 AGCGGCAGTATTCTACTCGTAGCGACCTGT 4 30 0 TTCTACTCGT 0.975897 -119 TACTTTTGCCTTCTCCTGCTCTCCCTTAAG 9 107 0 TTCTCCTGCT 0.93789 -194 ACGTGGCAAATTCTACTCGTTTTGGGTAAA 9 275 0 TTCTACTCGT 0.975897 -26 TTCGACAGTATTTTCCTCCTAAAAATTGAT 10 64 0 TTTTCCTCCT 0.907083 -235 TGTAGCCAATTTCTACTCCTATATAGGGTG 13 260 0 TTCTACTCCT 0.981543 -41 AAGCGCCTCATTCTACTGGAAATCATTGAA 14 262 0 TTCTACTGGA 0.780071 -39 TTTTTACTCCTAAAAGGTAGT 18 125 0 TTTTACTCCT 0.935515 -11 ********** Masking position 4 Map Score: 5.09169 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 31 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 CCACCTGAAATTAATTTTAAAAAGGGGCTAA 5 25 1 TTATTTTAAA 0.931533 -50 GTCTTCACAGTATATTTGAAAAAGGACTCTA 8 19 0 TAATTTGAAA 0.878616 -182 ATTAGGTTCTTTTATATGAAATATAATGTAA 10 20 0 TTATATGAAA 0.772838 -279 TTCCTTAAAATTTATATTAAAAACAATGCCT 10 272 0 TTATATTAAA 0.801042 -27 ACAACAATGCTAGATTTTAAAAGTCGTTTAC 12 273 0 TAATTTTAAA 0.920357 -28 AAAAACAGTATTAAGTTGAAAGGGATTTTTG 14 222 1 TTAGTTGAAA 0.787176 -79 AACTGATATATTTATTTTAAAAGGAACGCAG 16 113 0 TTATTTTAAA 0.91113 -56 GAATATTATAGATATTTTAAAAATTTATTAC 17 87 0 GAATTTTAAA 0.685196 -147 GTAAATAAAGTTTATTTTAAAGTTTTTAATA 17 143 1 TTATTTTAAA 0.91113 -91 GTATATTATTTATAATTTAAATAGAAATTAA 17 198 0 TAAATTTAAA 0.631259 -36 AAATGCAAGATAAAGATTAAAGTTACCGCAC 18 20 0 TAAGATTAAA 0.664357 -116 ** ******** Masking position 4 Map Score: 3.88491 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 44 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 8 ATCTTTTATCGGAGACAGGAAGAGTTTAGT 9 55 1 GGAGACAGGA 0.940981 -246 TTTGGTGTACCGAGACGGGACGTAAAATCT 9 225 0 CGAGACGGGA 0.994145 -76 CGAGACGAGACGAGACGAGACGACCAAGAT 14 110 0 CGAGACGAGA 0.990973 -191 TTTATGCAAGCGAGACGAGACGAGACGAGA 14 120 0 CGAGACGAGA 0.990973 -181 ********** Masking position 5 Map Score: 2.63955 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 5 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 TTTAGCCTTCTTTTGTCAATGGATTTGTGCA 1 68 1 TTTTGTCAAG 0.893661 -35 ACAGCCCCTTTTTTGTCAGGAGAATTTATT 5 55 1 TTTTGTCAGA 0.893668 -20 TAAAGCCCCGATTTATCGGGGTTTTTTGTTA 8 131 1 ATTTATCGGG 0.733564 -70 TTTAATCATCTTTTATCGGAGACAGGAAGAG 9 48 1 TTTTATCGGG 0.962787 -253 CCACGCCACATTTTGTCAACGTTTATTGCTA 9 177 0 TTTTGTCAAG 0.893661 -124 AGTGCGGTCATTTTTTCGAAAGATTTCTTTT 10 219 1 TTTTTTCGAA 0.512955 -80 TTTTTTATACTTTTGTCAATGGAAAATTTGT 12 63 1 TTTTGTCAAG 0.893661 -238 GTGTGGCGGATTTTATCAGTTTTTTTTCACG 12 173 1 TTTTATCAGT 0.703898 -128 TGTTTGCGGAGTTTATCAGCAGATGCCCAAA 14 23 1 GTTTATCAGA 0.643624 -278 AATGTGTGATTTTTATCGACAATCTTGGTCG 14 89 1 TTTTATCGAA 0.882148 -212 GTAAAGTGATTTTTATCGGAAGTTTGAATAT 14 161 1 TTTTATCGGA 0.932957 -140 TCAGGTGTCATTTTATCGAAAAACAGTATTA 14 204 1 TTTTATCGAA 0.882037 -97 TTTTTATCATTGAGTGACGTGG 15 2 1 TTTTATCATG 0.703898 -95 TATTTTTTAATTTTATTAGTGGTAAATAAAG 17 122 1 TTTTATTAGG 0.56443 -112 ********* * Masking position 6 Map Score: 7.98948 Number of sites scoring better than the average of aligned sites = 479 Number in coding regions = 400 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 10 TTCAAGCTGACGGCAGCAATTCACTGGAAAC 3 53 1 CGGCAGAATT 0.935432 -125 CGACGTTAAGCGGCAGTATTCTACTCGTAGC 4 37 0 CGGCAGATTC 0.937895 -112 CCTTTTTTGTCAGGAGAATTTATT 5 61 1 CAGGAGATTT 0.872293 -14 GAGCACTTTCCAGAAGGATTTTTTCAAATCC 8 66 0 CAGAAGATTT 0.938128 -135 CAGGAGAAGGCAAAAGTATTCAACAAATGAA 9 119 1 CAAAAGATTC 0.871294 -182 CACCAAATCCCAGCAGTATTTGCATTTTTTA 9 248 1 CAGCAGATTT 0.967522 -53 ATCATTGTTTCGACAGTATTTTCCTCCTAAA 10 71 0 CGACAGATTT 0.930072 -228 GTGCGGCTATCAAAAGAAATTTTTAAACGCC 10 185 1 CAAAAGAATT 0.866566 -114 TTGCGACTAGCAAAAGAAATCTTTCGAAAAA 10 230 0 CAAAAGAATC 0.82219 -69 GTCTATCAATCAACAGAAATTTTAGGA 12 7 0 CAACAGAATT 0.927323 -294 ****** **** Masking position 5 Map Score: 7.25299 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 256 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 11 TTAGGCCCTTTTTTTATGTCTTGGGG 8 185 1 TTTTTATGTC 0.777022 -16 TCTCACTGAATTTTTATGCAAAATAAATGA 9 11 1 TTTTTATGCA 0.856729 -290 ATATGCCGATTTTTTATACTTTTGTCAATG 12 54 1 TTTTTATACT 0.662141 -247 AGAAATTTTGTTTTTACGCTATATTCCGTG 12 200 0 TTTTTACGCT 0.936748 -101 CCTAACCCTTTTTTTATGCCTGAGATTTAA 13 141 1 TTTTTATGCC 0.96895 -160 AATATACGTGTTTTTATGCCGATTTTCTAG 15 43 1 TTTTTATGCC 0.96895 -54 AAAGCGAGCATTTTTTCGCTTTTCTTTTTT 16 17 1 TTTTTTCGCT 0.726327 -152 TTTTTACTCCTAAAAGGTAG 18 126 0 TTTTTACTCC 0.79869 -10 ********** Masking position 5 Map Score: 3.17794 Number of sites scoring better than the average of aligned sites = 370 Number in coding regions = 266 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 12 ATAGCAACAATACATTAGTTTCCAGTGAATTGCTGCC 3 64 0 TTAGTTCAGG 0.908855 -114 CTGGGATCGCTGAATTAGAGATCGGCGTCCTTTCATT 4 100 1 TTAGGACGGG 0.981079 -49 CTTTATTTTCTACATTAGCGTGCGGCTATCAAAAGAA 10 166 1 TTAGGTCGGT 0.940534 -133 AATGGAAAATTTGTGTTGATTTCGGTGAGACACAACC 12 80 1 TTTGTTCGGG 0.982351 -221 TTACTGAACTTATTATTGGTTGCGGGGGCTGGATTTG 13 39 0 TTTGTTCGGG 0.982351 -262 TTCATAAGGTTATGATATAGTGCGGTGAATTACACCC 13 228 1 TTATGTCGGG 0.940534 -73 GCGGCATCAAGTTGTTTGCGGAGTTTATCAGCA 14 7 1 TTTGTTCGGG 0.982351 -294 TTGTCATCGCTGAGTTAGAGATCGGCGAATGATGTAT 18 81 1 TTAGGACGGG 0.981079 -55 * *** ** *** * Masking position 6 Map Score: 4.05605 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 79 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 13 TCATTAGCCGCGCGAACCTCTGCAACGGAAG 3 108 0 CGCAACCTCT 0.941822 -70 AATGAAAGGACGCCGATCTCTAATTCAGCGA 4 106 0 CGCGATCTCT 0.985796 -43 GCTATAATGCCGAAATTCTCTTATTTTC 11 17 1 CGAATTCTCT 0.87384 -18 AAAAAATGCTCGCTTTTCTCTA 16 2 0 CGCTTTCTCT 0.978207 -167 AGCATTTTTTCGCTTTTCTTTTTTTCTATAA 16 23 1 CGCTTTCTTT 0.874121 -146 ATACATCATTCGCCGATCTCTAACTCAGCGA 18 87 0 CGCGATCTCT 0.985796 -49 *** ******* Masking position 9 Map Score: 0.825225 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 120 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 14 CCTCGCGACTAATGACAACCCTAACCCAGCTC 3 156 0 TATGACAACT 0.914869 -22 TTAAAATTTATATTAAAAACAATGCCTTATTTC 10 266 0 TATAAAAACT 0.950888 -33 ATATAAATTTTAAGGAAAACATT 10 286 1 TAGGAAAACT 0.914869 -13 AGAACTAACAACAATGCTAGATTTT 12 286 0 AATAACAACT 0.797568 -15 AAATGATTAGACGAAAAACTTTGGGCATCTGC 14 41 0 GAGAAAAACT 0.85379 -260 GGTGAAAATCTAGGAAAAACTTTCACCGCACTT 17 34 0 TAGAAAAACT 0.949945 -200 TAATAACGTTTATTAAAAACTTTAAAATAAACT 17 151 0 TATAAAAACT 0.950888 -83 GCGAATGATGTATTAACAACACTACCTTTTAGG 18 105 1 TATAACAACT 0.949945 -31 ** ******* * Masking position 6 Map Score: 0.652507 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 37 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 15 ATTATTTTACAAAAAACACACTAAACTCTT 9 74 0 AAAAAACACA 0.87913 -227 AAGAGCTTGTAAAAATAACGATACTTACTT 12 119 0 AAAAATAACG 0.826039 -182 ATATTCCGTGAAAAAAAACTGATAAAATCC 12 180 0 AAAAAAAACT 0.778839 -121 GATTGTCGATAAAAATCACACATTACAACA 14 83 0 AAAAATCACA 0.943564 -218 AACTTCCGATAAAAATCACTTTACAGAGGG 14 155 0 AAAAATCACT 0.943564 -146 TTTAGCACGCAAAAATCCCTTTCAACTTAA 14 232 0 AAAAATCCCT 0.837252 -69 AATAAAATTAAAAAATAACAAGAATATTAT 17 109 0 AAAAATAACA 0.890051 -125 ********** Masking position 5 Map Score: 1.40891 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 106 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837