AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -isoxS_ecoli_hinf_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 araD 284 L-ribulose-5-phosphate 4-epimerase #2 araB_araC 338 araB: L-ribulokinase, araC: transcriptional regulator for ara operon #3 fumC 142 fumarase C= fumarate hydratase Class II; isozyme #4 zwf 300 glucose-6-phosphate dehydrogenase #5 yeiH 98 orf, hypothetical protein #6 nfo 73 endonuclease IV #7 ompC 300 outer membrane protein 1b (Ib;c) #8 sodA 284 superoxide dismutase, manganese #9 soxS 85 regulation of superoxide response regulon #10 HI0558 75 glucose-6-phosphate 1-dehydrogenase (zwf) #11 HI0559 194 sulfite synthesis pathway protein (cysQ) #12 HI1027 58 L-xylulose kinase (lyx) #13 HI1028 30 conserved hypothetical protein #14 HI1030 71 conserved hypothetical transmembrane protein #15 HI1031 175 conserved hypothetical protein #16 HI1088 248 superoxide dismutase (sodA) #17 HI1398 234 fumarate hydratase, class II (fumC) Motif number 1 GTAGCCGCATCCGGTATGTAACGCCTG 1 6 1 CGCATCGGTT 0.971208 -279 GCGTCAGCGTCGCATCAGGCGTTACATACCGG 1 21 0 CGCATCGGCT 0.998199 -264 GCTGACGCGTCTTATCTGGCCTACACGCTGCG 1 45 1 CTTATCGGCT 0.995374 -240 ATGCGCTTTGCTTATCCGGCCTACAAAATCGC 1 74 0 CTTATCGGCT 0.995374 -211 ATAAGCAAAGCGCATCCGGCATTCAACGCCTG 1 91 1 CGCATCGGCT 0.998199 -194 GCGCCAGCGTCGCATCAGGCGTTGAATGCCGG 1 106 0 CGCATCGGCT 0.998199 -179 GCTGGCGCGTCTTATCAGGCCTACGCGCTGCG 1 130 1 CTTATCGGCT 0.995374 -155 ATGCGCTTTGCTTATCCGGCCTACAAAATCGC 1 159 0 CTTATCGGCT 0.995374 -126 ATAAGCAAAGCGCATCCGGCATTCAACGCCTG 1 176 1 CGCATCGGCT 0.998199 -109 GCGCCAGCGTCGCATCAGGCGTTGAATGCCGG 1 191 0 CGCATCGGCT 0.998199 -94 GCTGGCGCGTCTTATCAGGCCTACACGCTGCG 1 215 1 CTTATCGGCT 0.995374 -70 ATGCGCTTTGCTTATCCGGCCTACAAAATCGC 1 244 0 CTTATCGGCT 0.995374 -41 ATAAGCAAAGCGCATCCGGCACGAAGGAGTCA 1 261 1 CGCATCGGCC 0.98778 -24 AATTATTCCTTATTCGGCTTCCGAGTAATG 10 56 0 CTTATTGGCT 0.929067 -20 ****** *** * Masking position 4 Map Score: 54.3931 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 61 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 2 AATCGCAGCGTGTAGGCCAGATAAGACGCGT 1 49 0 TGTAGGCCGA 0.998023 -236 GCTGCGATTTTGTAGGCCGGATAAGCAAAGC 1 71 1 TGTAGGCCGA 0.998028 -214 CATCAGGCGTTGAATGCCGGATGCGCTTTGC 1 95 0 TGAATGCCGA 0.976946 -190 AATCGCAGCGCGTAGGCCTGATAAGACGCGC 1 134 0 CGTAGGCCGA 0.992616 -151 GCTGCGATTTTGTAGGCCGGATAAGCAAAGC 1 156 1 TGTAGGCCGA 0.998028 -129 CATCAGGCGTTGAATGCCGGATGCGCTTTGC 1 180 0 TGAATGCCGA 0.976946 -105 AATCGCAGCGTGTAGGCCTGATAAGACGCGC 1 219 0 TGTAGGCCGA 0.998026 -66 GCTGCGATTTTGTAGGCCGGATAAGCAAAGC 1 241 1 TGTAGGCCGA 0.998028 -44 ******** ** Masking position 4 Map Score: 25.5215 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 12 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 3 TATCCGGCCTACAAAATCGCAGCGTGTAGG 1 64 0 ACAAAATCGC 0.961758 -221 AGGCCGGATAAGCAAAGCGCATCCGGCATT 1 84 1 AGCAAAGCGC 0.980243 -201 TATCCGGCCTACAAAATCGCAGCGCGTAGG 1 149 0 ACAAAATCGC 0.961758 -136 AGGCCGGATAAGCAAAGCGCATCCGGCATT 1 169 1 AGCAAAGCGC 0.980243 -116 TATCCGGCCTACAAAATCGCAGCGTGTAGG 1 234 0 ACAAAATCGC 0.961758 -51 AGGCCGGATAAGCAAAGCGCATCCGGCACG 1 254 1 AGCAAAGCGC 0.980243 -31 AGCATTCTGTAACAAAGCGGGACCAAAGCC 2 132 1 AACAAAGCGG 0.84635 -207 CAAAGCCATGACAAAAACGCGTAACAAAAG 2 155 1 ACAAAAACGC 0.967622 -184 CACTCCATCCAAAAAAACGGGTATGGAGAA 2 314 0 AAAAAAACGG 0.76841 -25 GTGCCATGTAAAAAAACCGCCCCGAAGGGC 3 19 0 AAAAAACCGC 0.721808 -124 GCTTAACGAAAGCAAAACAGAAAGAAAAAA 3 101 1 AGCAAAACAG 0.646159 -42 CGTGTTAATGACAAAAGCAGATAAAAAAGT 4 58 1 ACAAAAGCAG 0.79175 -243 TGCGATTACGGGAAAAGCGCGCAAAGTGCG 4 164 0 GGAAAAGCGC 0.854896 -137 CGAGATGTGAAGCAAATCACCCACTTAATG 8 128 0 AGCAAATCAC 0.796146 -157 ATATGTTTCCAGTAAAACGCCATAATATAA 14 16 1 AGTAAAACGC 0.859233 -56 GATCTAGATCACAAAATCAGTAAAATTATT 15 44 1 ACAAAATCAG 0.632477 -132 GACATAGATCATAAAAGCGCGGTGGATTTT 17 115 0 ATAAAAGCGC 0.916252 -120 GTGGAACGTAACAAAAACGTTAAAAATCAG 17 151 0 ACAAAAACGT 0.645288 -84 TTGAATGAAAATTAAAACGCAAGTGATTTT 17 199 0 ATTAAAACGC 0.545856 -36 ********** Masking position 5 Map Score: 19.3945 Number of sites scoring better than the average of aligned sites = 1092 Number in coding regions = 932 Number in noncoding regions = 160 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 4 TGATGCGACGCTGACGCGTCTTATCTGGCCTA 1 36 1 CTGCGCGTTT 0.987017 -249 TGATGCGACGCTGGCGCGTCTTATCAGGCCTA 1 121 1 CTGCGCGTTT 0.987237 -164 TGATGCGACGCTGGCGCGTCTTATCAGGCCTA 1 206 1 CTGCGCGTTT 0.987237 -79 GCGTCTTTTACTGGCTCTTCTCGCTAACCCAA 2 79 1 CTGCTCTTTC 0.892597 -260 AGACACTTTTGTTACGCGTTTTTGTCATGGCT 2 158 0 GTTCGCGTTT 0.767177 -181 CGGATCCTACCTGACGCTTTTTATCGCAACTC 2 274 1 CTGCGCTTTT 0.979736 -65 ACCACTACATCTTGCTCCTGTTAACCCGCTAT 6 11 1 CTTCTCCTTT 0.770192 -63 AAAAATCGTGCTGTCGATTAACCTTTCGCCTG 8 63 1 CTGCGATTAC 0.768657 -222 GTCGATTAACCTTTCGCCTGTTGCCGCCGTTG 8 75 1 CTTCGCCTTT 0.928203 -210 TATTGTCGGGCGGCCGATTGTTAATGCCGCGT 8 251 0 CGGCGATTTT 0.714092 -34 AAATCTGCCTCTTTTCAGTGTTCAGT 9 70 0 CTGCTCTTTC 0.892597 -16 CCTTATTCGGCTTCCGAGTAATGTCGAAAATA 10 47 0 CTTCGAGTAT 0.791091 -29 AATACTGTCACTTTCTATTTTCCCTCTGTAAT 16 12 0 CTTCTATTTC 0.581552 -237 GATTTTAACACTTCCGAGTTATGAGTGGAACG 17 173 0 CTTCGAGTAT 0.79111 -62 *** ***** ** Masking position 9 Map Score: 11.0079 Number of sites scoring better than the average of aligned sites = 1348 Number in coding regions = 1166 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 5 TGGACTTTTCTGCCGTGATTATAGACACTTTTGT 2 178 0 TGCCGTGTTG 0.993506 -161 ACAGAGCCGCCCTTCGGGGCGGTTTTTT 3 5 1 AGCCGCCTTG 0.90776 -138 TACGCCTGTGTGCCGTGTTAATGACAAAAGCAGA 4 45 1 TGCCGTGTAA 0.931699 -256 TTATCAGTTTTGCCGCACTTTGCGCGCTTTTCCC 4 151 1 TGCCGCATTG 0.9848 -150 TTTCGCCTGTTGCCGCCGTTGTCGATTTACTGGC 8 86 1 TGCCGCCTTG 0.985904 -199 ACCCACTTAATGCCGTGATTGCCAGTAAATCGAC 8 106 0 TGCCGTGTTA 0.977358 -179 TGATTATCAATGCCGTACTTTTCGTAAGGGTATG 8 176 0 TGCCGTATTG 0.983553 -109 CGATTGTTAATGCCGCGTAAGCAGTTGGTTCATT 8 235 0 TGCCGCGAAG 0.880527 -50 TCGAAAATAATGCCGTATTCTAGAGAAAAAAACC 10 22 0 TGCCGTATCA 0.817575 -54 CTATTTGTAATGCCGTGGTTGCTGCCAAAAACAA 11 37 1 TGCCGTGTTG 0.993506 -158 ******* ** * Masking position 4 Map Score: 9.96138 Number of sites scoring better than the average of aligned sites = 487 Number in coding regions = 469 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 TAAGCAACTTTTAGCTCACTTATTATTTACCATTTGA 3 69 0 TACTATTATT 0.643927 -74 GACCTGCTCCTCACCTGATTAATTTTTTCTTTCTGTT 3 116 0 TACTATTTTT 0.954823 -27 TTTACCCAATGGAAAACGATGATTTTTTTATCAGTTT 4 124 1 GAATATTTTT 0.56648 -177 CGCTTACCACTTATAAAGATTAATTATAAATATATAA 5 14 1 TAATAATTAT 0.694304 -85 TATAAATATATAATCAATTTTATTTTTAAACCAGTTA 5 38 1 TACTATTTTT 0.954823 -61 AAGTTATTGATTTTAACCTTGAATTATTATTGCTTGA 7 43 1 TTATAATTAT 0.360949 -258 CTAAAACTTTTAAGATGTTTCATTTATCGCTATAGAT 7 147 0 TAATATTTAT 0.828695 -154 CTTCTTATCCTCATCATTTTTCGTCGCGTCA 8 5 1 TACTATTTTT 0.954823 -280 TAAAATTATTTTAACATATTGATTTATAAATAATTTA 15 64 1 TACTATTTAT 0.908447 -112 TCAATAAATGTAAAATAAATAAATTATTTATAAATCA 15 83 0 TAATAATTAT 0.69418 -93 ATTTATTGACTGAGCTTTCTTATTTTTGTAAATTATG 15 111 1 TACTATTTTT 0.954823 -65 TTTTTCCTCTCTTAATTTTATATAGTAAA 15 157 0 TTCTAATTTT 0.711621 -19 AAACATTTAATGATCTAAATCAATTTTTTTGCTATTA 16 154 1 TACTAATTTT 0.908448 -95 TTTAGCCCCGTTATTTTCTCAATCTTAC 17 2 1 TACTATTTTC 0.728282 -233 ATAATGCATATTTAATTATTTATTTTTTAGGGTTTTT 17 66 0 TTATATTTTT 0.719168 -169 ATGATCTATGTCACAAAACTGATTTTTAACGTTTTTG 17 133 1 TAATATTTTT 0.911534 -102 * * * * ****** Masking position 10 Map Score: 10.1684 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 182 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 7 TATCTGGCCTACACGCTGCGATTTTGTAGGCC 1 57 1 ACCGCTGCAT 0.992589 -228 TATCAGGCCTACGCGCTGCGATTTTGTAGGCC 1 142 1 ACCGCTGCAT 0.992589 -143 TATCAGGCCTACACGCTGCGATTTTGTAGGCC 1 227 1 ACCGCTGCAT 0.992589 -58 GCACGGCGTCACACTTTGCTATGCCATAGCAT 2 224 1 ACCTTTGCAT 0.904115 -115 TTTTATCGCAACTCTCTACTGTTTCTCCATAC 2 292 1 ACCTCTACGT 0.836856 -47 GCTCCTGTTAACCCGCTATCATTACCGTTTTC 6 24 1 ACCGCTATAT 0.922925 -50 GTTATTAACCCTCTGTTATATGCCTTTAT 7 282 0 ACCTCTGTAT 0.970593 -19 CTTTCTATTTTCCCTCTGTAATT 16 2 0 TCCTCTGTAT 0.855384 -247 ** ****** ** Masking position 7 Map Score: 7.22421 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 149 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 AGATAAGACGCGTCAGCGTCGCATCAGGCG 1 32 0 CGTCAGCGTC 0.995579 -253 TGATAAGACGCGCCAGCGTCGCATCAGGCG 1 117 0 CGCCAGCGTC 0.997137 -168 TGATAAGACGCGCCAGCGTCGCATCAGGCG 1 202 0 CGCCAGCGTC 0.997137 -83 AGTAAATGTTCGTTAGCGTCAGCATAAAAT 11 78 0 CGTTAGCGTC 0.982662 -117 ********** Masking position 5 Map Score: 6.68561 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 116 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 ATCCGGTATGTAACGCCTGATGCGACGCTG 1 19 1 TAACGCCTGA 0.955459 -266 ATCCGGCATTCAACGCCTGATGCGACGCTG 1 104 1 CAACGCCTGA 0.988415 -181 ATCCGGCATTCAACGCCTGATGCGACGCTG 1 189 1 CAACGCCTGA 0.988415 -96 GCAGTGACGGCAATGTCTGATGCAATATGG 2 51 0 CAATGTCTGA 0.948291 -288 TTTTGCAGGAAAATGCCCGAGATGTGAAGC 8 145 0 AAATGCCCGA 0.898038 -140 GCATTATTACAAATGTCTGAAAATCCACCG 17 96 1 AAATGTCTGA 0.890582 -139 ********** Masking position 3 Map Score: 4.17613 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 140 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 10 TTCGGGGCGGTTTTTTTACATGGCACGAAA 3 23 1 TTTTTTTACA 0.60755 -120 ATCAGTGTCAGATTTTTACCCAATGGAAAA 4 110 1 GATTTTTACC 0.917396 -191 TAATCAATTTTATTTTTAAACCAGTTAGTC 5 48 1 TATTTTTAAA 0.663409 -51 ATAAGTTATTGATTTTAACCTTGAATTATT 7 41 1 GATTTTAACC 0.917347 -260 TCGACAGCACGATTTTTACACTCATCTCGT 8 50 0 GATTTTTACA 0.931036 -235 TCAGTAAAATTATTTTAACATATTGATTTA 15 60 1 TATTTTAACA 0.813221 -116 TTAACATATTGATTTATAAATAATTTATTT 15 74 1 GATTTATAAA 0.5778 -102 TAGGTTTATTGATTTAAAACAAAATTTAAT 16 101 1 GATTTAAAAC 0.518111 -148 ATGTTTTTCCTTTTTTAAAAAGTGAATTTA 16 130 0 TTTTTTAAAA 0.410418 -119 AACGAAATCTGTTTTTAACAATAGAAGGAA 16 223 1 GTTTTTAACA 0.827328 -26 TCACAAAACTGATTTTTAACGTTTTTGTTA 17 143 1 GATTTTTAAC 0.834072 -92 AAACGCAAGTGATTTTAACACTTCCGAGTT 17 185 0 GATTTTAACA 0.931019 -50 ********** Masking position 8 Map Score: 5.07143 Number of sites scoring better than the average of aligned sites = 504 Number in coding regions = 407 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 11 AAGCGCATCCGGCATTCAACGCCTGATGCGACGCT 1 98 1 GGCAAAGCTG 0.827445 -187 AAGCGCATCCGGCATTCAACGCCTGATGCGACGCT 1 183 1 GGCAAAGCTG 0.827445 -102 TTTTTTACATGGCACGAAAGACCAAACATTTGTTA 3 34 1 GGCAAAACAA 0.972479 -109 AGTTTTCGCAAGCTCGTAAAAGCAGTACAGTGCAC 4 213 1 AGCTAAACAG 0.910253 -88 AGTATTTGACAGCACTGAATGTCAA 7 1 0 AGCAAAGCAA 0.936389 -300 TGGCGAAATAAGCACCTAACATCAAGCAATAATAA 7 66 0 AGCAAAACAA 0.963412 -235 AGTATGCAGTGGCATAAAAAAGCAAATAAAGGCAT 7 257 1 GGCAAAACAA 0.972479 -44 CGAAAAGTACGGCATTGATAATCATTTTCAATATC 8 186 1 GGCAATACAT 0.599733 -99 TTACAAATAGAGCATAAAATACCATTCCGCATGTG 11 12 0 AGCAAAACAT 0.906011 -183 ATGCCGTGGTTGCTGCCAAAAACAAGAGAATAATT 11 46 1 TGCTAAACAA 0.660272 -149 AATAGGATCTAGATCACAAAATCAGTAAAATTATT 15 39 1 AGATAAACAG 0.421209 -137 ACCAAAATTGAGCAAATAATAGCAAAAAAATTGAT 16 172 0 AGCAAAACAA 0.963412 -77 **** ** * *** Masking position 8 Map Score: 4.37976 Number of sites scoring better than the average of aligned sites = 442 Number in coding regions = 380 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 12 ACAGTAGAGAGTTGCGATAAAAAGCGTCAG 2 284 0 GTTGCGATAA 0.957516 -55 CACTGATCATGTTATGAAAAAAAATAACAA 4 87 0 GTTATGAAAA 0.764732 -214 CTTTTACGAGCTTGCGAAAACTGTAAACGC 4 205 0 CTTGCGAAAA 0.967065 -96 AAACCATACCCTTACGAAAAGTACGGCATT 8 172 1 CTTACGAAAA 0.870333 -113 AAAAGTCTCCTTGTGTTAAGAAAGTCTGT 13 12 0 CTTGTGTTAA 0.769875 -19 ACGAATCACATTTGTGATAATCAATTGGAG 14 47 1 TTTGTGATAA 0.781526 -25 ATCCTATTTTCTTGTGATAATATTTCATAT 15 17 0 CTTGTGATAA 0.949157 -159 ATGTGTTTGAGTTGCGAAAATTTCATCAAA 16 50 0 GTTGCGAAAA 0.957262 -199 ********** Masking position 9 Map Score: 3.32801 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 69 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 13 CCCACCATTCAGAGAAGAAACCAATTGTCC 2 23 1 AGAGAAGAAA 0.911724 -316 AGCAAAACAGAAAGAAAAAATTAATCAGGT 3 111 1 AAAGAAAAAA 0.911116 -32 TGACAAAAGCAGATAAAAAAGTTGTTATTT 4 66 1 AGATAAAAAA 0.825474 -235 GCCGTATTCTAGAGAAAAAAACCAATCGAA 10 15 0 AGAGAAAAAA 0.960032 -61 TAATTTACAAAAATAAGAAAGCTCAGTCAA 15 116 0 AAATAAGAAA 0.464642 -60 TAAAATTAAGAGAGGAAAAA 15 166 1 AGAGGAAAAA 0.944758 -10 AATTACAGAGGGAAAATAGAAAGTGA 16 7 1 AGAGGGAAAA 0.78102 -242 ACTTTTTAAAAAAGGAAAAACATTTAATGA 16 137 1 AAAGGAAAAA 0.879495 -112 AGCAAATAATAGCAAAAAAATTGATTTAGA 16 167 0 AGCAAAAAAA 0.535604 -82 GTAAAATTTTAACGAAAAAACCCTAAAAAA 17 51 1 AACGAAAAAA 0.815074 -184 ********** Masking position 8 Map Score: 3.62656 Number of sites scoring better than the average of aligned sites = 406 Number in coding regions = 315 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 14 TTAATCGACAGCACGATTTTTACACTCATC 8 54 0 GCACGATTTT 0.927575 -231 TCAATAGGCTGGATTTTACATAATAAA 12 8 1 GCTGGATTTT 0.983969 -51 TTTTTTATGGGCTGGATTTTTATTATGTAA 12 26 0 GCTGGATTTT 0.983969 -33 GCTATTATTTGCTCAATTTTGGTTATAGAC 16 184 1 GCTCAATTTT 0.889801 -65 ATAAAAGCGCGGTGGATTTTCAGACATTTG 17 105 0 GGTGGATTTT 0.945746 -130 ********** Masking position 6 Map Score: 1.60272 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 84 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 15 AACCCAACCGGTAACCCCGCTTATTAAAAG 2 104 1 GTAACCCCGC 0.951932 -235 TCTTGCTCCTGTTAACCCGCTATCATTACC 6 20 1 GTTAACCCGC 0.984373 -54 AGGACTCCTGTTAAACCCGCTGGAGGAAAA 6 51 0 TTAAACCCGC 0.94158 -23 CTGCATACTGATTAACCCTCATTAATCAGT 7 236 0 ATTAACCCTC 0.947574 -65 GTTATTAACCCTCTGTTATATGC 7 288 0 ATTAACCCTC 0.947574 -13 ********** Masking position 4 Map Score: 0.406675 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 121 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274