AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i056_ecoli_bsub_300.orf -o056_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 leuA 92 2-isopropylmalate synthase #2 leuL_leuO 482 leuL: leu operon leader peptide, leuO: probable transcriptional activator for leuABCD operon #3 ilvI 227 acetolactate synthase III, valine sensitive, large subunit #4 acnB 300 aconitate hydrase B #5 yeaU 81 putative tartrate dehydrogenase #6 ilvB 105 acetolactate synthase I,valine-sensitive, large subunit #7 ivbL 300 ilvB operon leader peptide #8 ilvM 300 acetolactate synthase II, valine insensitive, small subunit #9 ilvD 95 dihydroxyacid dehydratase #10 ilvC 149 ketol-acid reductoisomerase #11 ycnL 164 ycnL #12 mtlA 172 phosphotransferase system (PTS) mannitol-specific enzyme IIABC component #13 mtlD 52 mannitol-1-phosphate dehydrogenase #14 ycsA 107 similar to 3-isopropylmalate dehydrogenase #15 ilvD 288 dihydroxy-acid dehydratase #16 ypgR 59 similar to hypothetical proteins #17 bsaA 300 glutathione peroxidase #18 leuC 49 3-isopropylmalate dehydratase (large subunit) #19 ilvB 300 acetolactate synthase (acetohydroxy-acid synthase) (large subunit) #20 alsS 154 alpha-acetolactate synthase (pH6) Motif number 1 GCGCAATGGCGCGGGTTTTTTGTTTGACTGC 1 19 0 GCGGTTTTTT 0.969923 -74 GCGCCATTGCGCGGGTTTTTTTATGCCCGAA 1 38 1 GCGGTTTTTT 0.969923 -55 TATATGTTTTGCGATTTTTTTTGATATTGAT 2 179 0 GCGTTTTTTT 0.922168 -304 TCACGCTGGCGGGACGTTTTTATTGCGTCAG 2 397 1 GGGCGTTTTT 0.957874 -86 TAACGATTCAGCCACTTTTTTATGTTGCTTT 4 137 1 GCCCTTTTTT 0.807026 -164 GTTTGCGCCGGCGGGGTTTTGGAATCGTGTG 6 23 0 GCGGGTTTTG 0.953003 -83 CGCAAACCGGGCGGGGTTTTTCGTTTAAGCA 6 47 1 GCGGGTTTTT 0.981081 -59 CCCCGCCGGAGCGAGGTTTCGTCAGTCGCCT 7 145 0 GCGGGTTTCG 0.835073 -156 CCTCGCTCCGGCGGGGTTTTTTGTTATCTGC 7 160 1 GCGGGTTTTT 0.981081 -141 TTATCAGTAAGGGTGGTTTCGCTGTATCGTT 8 79 0 GGGGGTTTCG 0.754646 -222 ACAATGTCACGGGCTTTTTTTACTATCTCGC 14 43 1 GGGTTTTTTT 0.878008 -65 TGCATGATCTGCACCTTTTTTATCT 15 5 0 GCACTTTTTT 0.729995 -284 TGCAGATCATGCACCTTTTTTATGTGAATTC 15 23 1 GCACTTTTTT 0.729995 -266 GTTTATTTATGGGCTGTTTTTGCAAATAAGA 15 211 0 GGGTGTTTTT 0.920466 -78 CAATTCATATGGCTCGTTTTTTATCTTATCA 17 161 0 GGCCGTTTTT 0.803344 -140 GTGGGCGGAAGGGCTTTTTTTATTGAATAAT 19 218 1 GGGTTTTTTT 0.878008 -83 *** ******* Masking position 7 Map Score: 21.0479 Number of sites scoring better than the average of aligned sites = 693 Number in coding regions = 511 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 2 TAGAGCGCCTCGCTTCGGGCATAAAAAAAC 1 52 0 CGCTTCGGGC 0.737719 -41 GCAGAACTCACGCTGGCGGGACGTTTTTAT 2 390 1 CGCTGGCGGG 0.960261 -93 TGAAGAGAATCGCCTGCCGCACTATGACAA 4 261 1 CGCCTGCCGC 0.990161 -40 GCCCGGTTTGCGCCGGCGGGGTTTTGGAAT 6 29 0 CGCCGGCGGG 0.993622 -77 AAACGAAAAACCCCGCCCGGTTTGCGCCGG 6 43 0 CCCCGCCCGG 0.869504 -63 TTCGTTTAAGCACCTCCCGGAAAGTCGGCC 6 66 1 CACCTCCCGG 0.880545 -40 TTTCGTCAGTCGCCTGCGGCTGGTAACCGC 7 130 0 CGCCTGCGGC 0.994242 -171 CGAAACCTCGCTCCGGCGGGGTTTTTTGTT 7 155 1 CTCCGGCGGG 0.945954 -146 TGTTAGCCAGCGCCTTCGGCATCCATGGCC 8 124 1 CGCCTTCGGC 0.950699 -177 CGCCAGGCGGCACCAGCGGCCAGACGTTCT 8 250 0 CACCAGCGGC 0.875921 -51 CCGCTGGTGCCGCCTGGCGCCAGTAATTCA 8 261 1 CGCCTGGCGC 0.959969 -40 ********** Masking position 3 Map Score: 13.711 Number of sites scoring better than the average of aligned sites = 1806 Number in coding regions = 1712 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 3 GTCTGGTTTATTCTGCATTTTTTATTGAATG 3 39 1 TTCTGCTTTT 0.654959 -189 CTTTTCACCTTTCCTCCTGTTTATTCTTATT 3 202 1 TTCCTCTGTT 0.913749 -26 TTTAAACTACCGCCTCTTTATACTCGGATTC 4 13 0 CGCCTCTTAT 0.495589 -288 AATCCTGCTATTCTGCCCGTTGCGGTACTGG 4 195 1 TTCTGCCGTT 0.785234 -106 GCAGGCGATTCTCTTCACGCTCCTGTGAGAC 4 247 0 CTCTTCCGCT 0.696046 -54 GAGAATCGCCTGCCGCACTATGACAATGAGA 4 265 1 TGCCGCCTAT 0.675393 -36 GACGGTTCTCCTCGCTCTCATTGTCATA 4 283 0 CTCCTCCTCT 0.876686 -18 TAACCCCGATTTCCTCATGTTAGCCAGCGCC 8 107 1 TTCCTCTGTT 0.913749 -194 GGTGATTCCTCGTGATGTTGTGCTTC 10 134 0 TTCCTCTGAT 0.808421 -16 AGGGTATTCCTCACTTTCTATTCCATC 11 148 0 TTCCTCCTTT 0.961038 -17 CAGAGAATGATGCTTCCCTTTGACTCTATGT 12 102 0 TGCTTCCTTT 0.80079 -71 CGATCAAATCTTCTTCGCTTTAGCGGAGA 13 9 0 TTCTTCCTTT 0.897279 -44 CTTTTATTTCCTCCCTCTACCTAGAGCT 18 32 0 TTCCTCCTCT 0.939206 -18 TTTAGTTCCTCCTTTTGGATTTTCAT 19 285 0 TTCCTCTTTT 0.920934 -16 ****** **** Masking position 11 Map Score: 7.38184 Number of sites scoring better than the average of aligned sites = 458 Number in coding regions = 385 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 4 TGATCAATAATATTCACCAAATCAATATCAAAAAAAATCGC 2 159 1 TATCAAAAAA 0.877562 -324 AGCATAAATTTTTGCATCTAATCAACGAGGAAAAAGGGGAC 2 255 0 TTTCAAAAGA 0.843189 -228 TCCGTTTTTGTATCCAGTAACTCTAAAAGCATATCGCATTC 2 436 1 TATCAATAAA 0.877567 -47 TGTTAATCTGTTTACAAAAAAGCAACATAAAAAAGTGGCTG 4 145 0 TTTCAAAAAA 0.962663 -156 AATGGAAAATTTTTCAGCAAGGGAAAATTGAGGGGTTGATC 7 208 0 TTTCAAAAAA 0.962666 -93 AGCAACTGTTTTTTCAGGAACGATACAGCGAAACCACCCTT 8 61 1 TTTCAATAAA 0.962666 -240 TTTCGGATATTTTTCAACAATATTCGAAATAATTTTTATAA 15 59 0 TTTCAATCAA 0.843198 -230 ATGGGCTGTTTTTGCAAATAAGATAAATACAGGCCGCCCTC 15 193 0 TTTCAATAAA 0.962666 -96 AGTAAAATGATTTTCAAAGATGTAAGAGGGAATTGTAATGT 17 111 1 TTTCAAAAAA 0.962666 -190 TGGAGGTCAATTTCCAAAGAGTGTATAGTGAAACTTATCAC 20 78 1 TTTCAATAAA 0.962663 -77 *** ** * ** * * Masking position 10 Map Score: 4.69373 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 14 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 ATTAAATATATAAATTAATTATTAAATAAGCACA 2 104 0 TAATTAATTA 0.925727 -379 ATATTATTGATCAATTAATGTTAAGAATTAATGC 2 138 0 TAATTAATTA 0.925718 -345 CTCTATTTTTTTAATTAATCCTAAAATAGAGAGC 3 94 0 TAATTAATTA 0.92573 -134 TACAGAGGATTAAATTGATAATAAATCGGCTGAA 3 149 0 TAATTGATTA 0.960757 -79 CCTCTACGCTTAAATAGATCTTAATGAAGAGGGT 11 17 0 TAATAGATTA 0.885212 -148 CTTTTTATTTTTAAAAAATTGTCACAGTCATGTG 12 21 1 TAAAAAATTA 0.554449 -152 GGTTTCACAGTAAAATGATTTTCAAAGATGTAAG 17 103 1 TAAATGATTA 0.885478 -198 ACGAGCCATATGAATTGATAATGAACTGACGCTC 17 175 1 TAATTGATTA 0.960757 -126 TTATGAGTTCTTAATTGATGTTTACATTTTGAAT 17 224 1 TAATTGATTA 0.960755 -77 * ******* * * Masking position 8 Map Score: 4.64479 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 9 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 ACAAAAAACCCGCGCCATTGCGCGGGTTTT 1 27 1 CGCGCCATTG 0.970241 -66 TTTTGCAACGCGTGCATTTTGTCCCCTTTT 2 235 1 CGTGCATTTT 0.846954 -248 CCGCGCAGAACGCGCAATTTCGGCACGAAT 7 59 0 CGCGCAATTT 0.928162 -242 CGGTGCGTGCCGTCCCATTTTTTGTAT 9 8 0 CGTCCCATTT 0.966346 -88 CGGCACGCACCGTCCCATTTACGAGACAGA 9 26 1 CGTCCCATTT 0.966346 -70 ATATTCACAACGTCACATTGCAATTTTTGC 10 36 0 CGTCACATTG 0.852259 -114 AAAAAAAGCCCGTGACATTGTGTCACGGGT 14 34 0 CGTGACATTG 0.852259 -74 GGAATTTTCACGCCAATTTTCAATCTATCT 17 12 1 CGCCAATTTT 0.713472 -289 AACGCACTGACACGCCTTTTGGTTTCACAG 17 83 1 CACGCCTTTT 0.73209 -218 AAAGCCTTTTCGCCCCTTTTAGCTATCGCA 19 170 1 CGCCCCTTTT 0.969018 -131 ********** Masking position 8 Map Score: 5.48863 Number of sites scoring better than the average of aligned sites = 633 Number in coding regions = 566 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 7 TAATGTTTTTGTTGCGAAAACAATCTAATC 2 32 1 GTTGCGAAAA 0.875205 -451 AAATGCACGCGTTGCAAAACCTATCCTGAT 2 224 0 GTTGCAAAAC 0.935508 -259 TCGTTGATTAGATGCAAAAATTTATGCTGA 2 268 1 GATGCAAAAA 0.958445 -215 TAATTTTACGGATGCAGAACTCACGCTGGC 2 377 1 GATGCAGAAC 0.810042 -106 AGAGTTACTGGATACAAAAACGGATGTCAA 2 430 0 GATACAAAAA 0.866807 -53 TGTTAATCTGTTTACAAAAAAGCAACATAA 4 156 0 TTTACAAAAA 0.62221 -145 ATTCAGAAATGTTGGAGAAATTATC 8 286 1 GTTGGAGAAA 0.652792 -15 CGATGTTGACGTTGCAAAAATTGCAATGTG 10 23 1 GTTGCAAAAA 0.971227 -127 GTCGCTGTAAGATACAAAAATATGTTCAGA 12 129 0 GATACAAAAA 0.866807 -44 ATTTATCTTATTTGCAAAAACAGCCCATAA 15 206 1 TTTGCAAAAA 0.853726 -83 ********** Masking position 3 Map Score: 4.74595 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 381 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 8 TATGATTAGATTGTTTTCGCAACAAAAACA 2 35 0 TTGTTTTCGC 0.86575 -448 GGTCTAGAGATTGTTTCCCTCCGTAAAAAC 4 102 0 TTGTTTCCCT 0.911705 -199 AAATTTTCCATTGTCTCCCCTGTAAAGCTG 7 237 1 TTGTCTCCCC 0.969117 -64 ATCCACTTACTTGTCTCCGTCTCTAAAATC 11 50 0 TTGTCTCCGT 0.918327 -115 GAGTTTTCTGTTGTTTCCCCCTCAACACGT 17 44 0 TTGTTTCCCC 0.974261 -257 TCATGGATATTTCTATCCGCTTTAGTAACG 19 94 0 TTCTATCCGC 0.864433 -207 GAAAAGGCTTTTCTTTCCGCGGTACCACCC 19 151 0 TTCTTTCCGC 0.954502 -150 ********** Masking position 6 Map Score: 2.90353 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 50 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 AAATAAGCACATTTAATCCATTTTGTAGATGATT 2 81 0 ATTTACTTTT 0.798671 -402 CAACGCGTGCATTTTGTCCCCTTTTTCCTCGTTG 2 240 1 ATTTTCCTTT 0.882189 -243 AACTTACAGCAATTTCTCTATTTTTTTAATTAAT 3 109 0 AATTTCTTTT 0.79867 -119 GTAATGGAGGATTTTATCGTTTCTTTTCACCTTT 3 180 1 ATTTTCTTCT 0.923795 -48 GGTAGTTTAAATTTTGACTAATCTTGGGATTCGT 4 33 1 ATTTTCATCT 0.792993 -268 TAGGATGGTGATGTTGTCAATTTTGATGGTCAGG 5 45 1 ATGTTCTTTT 0.854642 -37 TTCGGCACGAATTTTGACGTATTTAGTGCATAGT 7 37 0 ATTTTCATTT 0.899082 -264 TGTTCAACACATTTTCACATTTTTTATCATCCAC 11 74 0 ATTTTCTTTT 0.965745 -91 ATTGGATTTTATTTTGACAATTTTCAGTTTATTT 15 234 0 ATTTTCTTTT 0.965745 -55 GGTGCTGATTATTTTACCTTTTTTAAATCGCAAT 17 256 0 ATTTTCTTTT 0.965745 -45 ***** * **** Masking position 4 Map Score: 5.15136 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 56 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 GCATCTAATCAACGAGGAAAAAGGGGACAA 2 253 0 AACGAGGAAA 0.96416 -230 TAAGAATAAACAGGAGGAAAGGTGAAAAGA 3 201 0 CAGGAGGAAA 0.966828 -27 TGACAATGAGAGCGAGGAGAACCGTC 4 285 1 AGCGAGGAGA 0.838306 -16 CGCTGGCTAACATGAGGAAATCGGGGTTAT 8 106 0 CATGAGGAAA 0.907821 -195 AGCACAACATCACGAGGAATCACC 10 136 1 CACGAGGAAT 0.890392 -14 TGGAATAGAAAGTGAGGAATACCCT 11 150 1 AGTGAGGAAT 0.782863 -15 CTCTAGGTAGAGGGAGGAAATAAAAG 18 34 1 AGGGAGGAAA 0.966828 -16 ATGATCTTTAAAGGATGAAAATCCAAAAGG 19 271 1 AAGGATGAAA 0.77599 -30 GAAAATCCAAAAGGAGGAACTAAA 19 287 1 AAGGAGGAAC 0.915773 -14 ********** Masking position 5 Map Score: 2.91773 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 102 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 11 CCGATGAAAAGCGTCGGTAGTTAAGCAGAAATT 2 308 1 GCGCGGGTTA 0.881749 -175 AGCTAATTGTGCTGCGGTGGTTAAAGTAAGCGA 2 345 0 GCTCGGGTTA 0.681869 -138 TAAATCAGCTCCAGATGAATGCGATATGCT 2 463 0 GCTCAGGAAT 0.637927 -20 TAAGTTGTGGGATTCAGCCGATTTATTATCAAT 3 137 1 GATCAGGATT 0.899045 -91 CGAGTATAAAGAGGCGGTAGTTTAAATTTTGAC 4 18 1 GAGCGGGTTT 0.951544 -283 GGGATTCGTTGAGAAAGGTGATTATCACCATGC 4 58 1 GAGAAGGATT 0.860491 -243 ACGCTCCTGTGAGACAGCAGTTTGTAGGGTAAA 4 229 0 GAGCAGGTTT 0.963955 -72 TTGTCATAGTGCGGCAGGCGATTCTCTTCACGC 4 258 0 GCGCAGGATT 0.982935 -43 GCTCCAGTCCTTTTCTTCTGGGC 6 93 0 GCTCAGCTTT 0.817316 -13 GTTGGTTATCGAGTAAGACGATTTTC 8 4 0 GAGAAGGATT 0.860491 -297 AACGATATGAGCGTCAGTTCATTATCAATTCAT 17 184 0 GCGCAGCATT 0.947455 -117 AAATATCCATGAGACGGCCGATTAACAGGCCGT 19 112 1 GAGCGGGATT 0.957894 -189 CTGATTGTGGGCGGAAGGGCTTTTTTTATTGAA 19 212 1 GCGAAGCTTT 0.756021 -89 *** *** **** Masking position 7 Map Score: 9.48314 Number of sites scoring better than the average of aligned sites = 1265 Number in coding regions = 1205 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 12 AATGTGTGGGCTCTCTATTTTAGGATTAATTA 3 85 1 CTTCTATTTA 0.968221 -143 TTACAGCAATTTCTCTATTTTTTTAATTAATC 3 108 0 TTTCTATTTT 0.645156 -120 ACCTTTCCTCCTGTTTATTCTTATTACCCC 3 208 1 CTTTTATTTT 0.78249 -20 AATTCCTTTTCAGTCAATTATAGGATGGTGAT 5 25 1 CATCAATTTA 0.66 -57 TCTATTCCATCTGTCTATTATACCAGAGTCCC 11 127 0 CTTCTATTTA 0.968221 -38 GTATTCCTCACTTTCTATTCCATCTGTCTATT 11 140 0 CTTCTATTCA 0.864017 -25 AACCAGGAGCCTTTTTATTTTTAAAAAATTGT 12 11 1 CTTTTATTTT 0.78249 -162 GTCCTCTTTACTTTCAATTGTATAGGGACTGT 12 60 1 CTTCAATTTA 0.932413 -113 ATCGTAAGCGCTTTCTATTATACTAGATTGCG 14 71 0 CTTCTATTTA 0.968221 -37 CTCCTAAATTCTTTCAATTGTTTGATTGGATT 15 260 0 CTTCAATTTT 0.904059 -29 ** ****** ** Masking position 7 Map Score: 4.68097 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 39 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 CCAACGGTTAGGGATGGTTCGACAATGGCA 8 32 1 GGGATGGTTC 0.891056 -269 TGTTTTTTCAGGAACGATACAGCGAAACCA 8 67 1 GGAACGATAC 0.768051 -234 ACATGAAGCAGGTATGGCCCATCACTGTTC 8 203 0 GGTATGGCCC 0.837081 -98 TACAAAAAATGGGACGGCACGCACCGTCCC 9 12 1 GGGACGGCAC 0.98586 -84 TCTCGTAAATGGGACGGTGCGTGCCGTCCC 9 22 0 GGGACGGTGC 0.9769 -74 TGGTGGTGGCGGAACGGTACTTAGGCATAC 9 73 0 GGAACGGTAC 0.961539 -23 AGGGACAGCCCTCGATGTTGA 10 2 1 GGGACAGCCC 0.897318 -148 ********** Masking position 4 Map Score: 0.324467 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 190 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 14 AGTCCTTTTCTTCTGGGCCGACTTTCCGGG 6 81 0 TTCTGGGCCG 0.978899 -25 AAATTGCGCGTTCTGCGCGGAACACGTATA 7 69 1 TTCTGCGCGG 0.988423 -232 TTCAGTTTATTTATGGGCTGTTTTTGCAAA 15 216 0 TTATGGGCTG 0.887364 -73 CTATCGCAGTTACTGCGCGGCTGATTGTGG 19 192 1 TACTGCGCGG 0.962893 -109 GCGCGGCTGATTGTGGGCGGAAGGGCTTTT 19 206 1 TTGTGGGCGG 0.978899 -95 ********** Masking position 4 Map Score: 0.00168777 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 163 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 15 GAATTATATGTTTTGCGATTTTTTTTGATAT 2 183 0 TTTTGCGTTT 0.667896 -300 GGTGGTTAAAGTAAGCGATATTAATTTCTGC 2 332 0 GTAAGCGTAT 0.914973 -151 AGCTCCAGATGAATGCGATATGCTTTTAGAG 2 456 0 GAATGCGTAT 0.866356 -27 ATCGATCACAGTTTGCGTTTT 7 1 0 GTTTGCGTTT 0.953519 -300 AACACTGAAAGTATACGTGTTCCGCGCAGAA 7 79 0 GTATACGGTT 0.671454 -222 TTCGGTTCGCGTTTGCGAGATTGAATTCACT 10 97 0 GTTTGCGGAT 0.932131 -53 TATAGGGACTGTAAGCGTTTTAACATAGAGT 12 80 1 GTAAGCGTTT 0.929863 -93 TATTATACTAGATTGCGAGATAGTAAAAAAA 14 57 0 GATTGCGGAT 0.812738 -51 CCCTGTTATCGTAAGCGCTTTCTATTATACT 14 79 0 GTAAGCGTTT 0.929863 -29 ******* *** Masking position 11 Map Score: 1.06978 Number of sites scoring better than the average of aligned sites = 357 Number in coding regions = 323 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405