AlignACE version 2.2 July 7, 1998 alignACE -z/skink1/amcguire/genomes/ecoli.fna -a/home/amcguire/alignace/lib/ORF_ecoli.txt -b/home/amcguire/alignace/lib/bimes_ecoli.txt -k0 -l300 -jpurR.reg -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 = 179 Input sequences: #1 carA 300 bp carA 382 1-1149 CDS #2 codB 152 bp codB 419 1-1260 CDS #3 purE 117 bp purE 169 1-510 CDS #4 pyrD 110 bp pyrD 336 1-1011 CDS #5 pyrC 105 bp pyrC 348 1-1047 CDS #6 purB 3 bp purB 456 1-1371 CDS #7 prsA 150 bp prsA 315 1-948 CDS #8 purR 300 bp purR 341 1-1026 CDS #9 purT 133 bp purT 392 1-1179 CDS #10 purF 36 bp purF 505 1-1518 CDS #11 purC 66 bp purC 237 1-714 CDS #12 purM 297 bp purM 345 1-1038 CDS #13 guaB 161 bp guaB 488 1-1467 CDS #14 glyA 300 bp glyA 417 1-1254 CDS #15 glnB 60 bp glnB 112 1-339 CDS #16 purL 300 bp purL 1295 1-3888 CDS #17 gcvT 300 bp gcvT 364 1-1095 CDS #18 speA 8 bp speA 658 1-1977 CDS #19 purH 300 bp purH 529 1-1590 CDS #20 purA 103 bp purA 432 1-1299 CDS Motif number 1 TTCTTGCTGCGCAAGCGTTTTCCAGAACAGGT 1 67 1 GCAACGTTTC 0.674992 -234 TCTCCAGAATGCCGCCGTTTGCCAGAAATTCG 1 195 1 GCCGCGTTTC 0.853021 -106 AAGATAAAAAGCAATCGTTTTCGTGGGGAAAT 2 73 0 GCAACGTTTC 0.55631 -80 TCACAGCCACGCAACCGTTTTCCTTGCTCTCT 3 33 1 GCAACGTTTC 0.521975 -85 CAAAAAAAACGCAAACGTTTTCCGAACCTGTT 4 11 0 GCAACGTTTC 0.506858 -100 TCGTGCAAAGGAAAACGTTTCCGCTTATCCTT 5 41 1 GAAACGTTTC 0.520597 -65 GTGTGTAAAGGCAAACGTTTACCTTGCGATTT 8 243 1 GCAACGTTTC 0.529045 -58 AAAGACACACGCAAACGTTTTCGTTTATACTG 9 83 1 GCAACGTTTC 0.506858 -51 AAGCAGTCTCGCAAACGTTTGCTTTCCCTGTT 12 221 1 GCAACGTTTC 0.499998 -77 AGGGGTAGATGCAATCGGTTACGCTCTGTATA 13 95 1 GCAACGGTTC 0.672766 -67 AGGAATTTACGCAAACGATTACCTTCAGGCTA 14 169 0 GCAACGATTC 0.524826 -132 TTATTTCCACGCAAACGGTTTCGTCAGCGCAT 16 211 1 GCAACGGTTC 0.505823 -90 GGTCCCCAACGCAATCGTTCTCTTTTGCCTGA 17 197 0 GCAACGTTCC 0.912055 -104 CGAGCGTTGCGCAAACGTTTTCGTTACAATGC 19 180 1 GCAACGTTTC 0.506858 -121 **** ***** * Masking position 9 Map Score: 55.3955 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 6 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 2 TCTTCTTGCTGCGCAAGCGTTTTCCAGAAC 1 65 1 GCGCAAGCGT 0.907341 -236 GACGAATTTCTGGCAAACGGCGGCATTCTG 1 199 0 TGGCAAACGG 0.831813 -102 TGAAGATAAAAAGCAATCGTTTTCGTGGGG 2 77 0 AAGCAATCGT 0.934676 -76 TTTCACAGCCACGCAACCGTTTTCCTTGCT 3 31 1 ACGCAACCGT 0.971156 -87 GGCAAAAAAAACGCAAACGTTTTCCGAACC 4 15 0 ACGCAAACGT 0.994289 -96 TTTCGTGCAAAGGAAAACGTTTCCGCTTAT 5 39 1 AGGAAAACGT 0.798622 -67 AGGTGTGTAAAGGCAAACGTTTACCTTGCG 8 241 1 AGGCAAACGT 0.985931 -60 ATAAAGACACACGCAAACGTTTTCGTTTAT 9 81 1 ACGCAAACGT 0.994289 -53 CTAACAGGGAAAGCAAACGTTTGCGAGACT 12 225 0 AAGCAAACGT 0.978056 -73 AAAGGGGTAGATGCAATCGGTTACGCTCTG 13 93 1 ATGCAATCGG 0.789715 -69 AAAGGAATTTACGCAAACGATTACCTTCAG 14 173 0 ACGCAAACGA 0.958078 -128 TTTTATTTCCACGCAAACGGTTTCGTCAGC 16 209 1 ACGCAAACGG 0.991684 -92 CCGGTCCCCAACGCAATCGTTCTCTTTTGC 17 201 0 ACGCAATCGT 0.982214 -100 CGCGAGCGTTGCGCAAACGTTTTCGTTACA 19 178 1 GCGCAAACGT 0.981209 -123 ATCCATTTTTAAGCAAACGGTGATTTTGAA 20 82 1 AAGCAAACGG 0.967273 -22 ********** Masking position 5 Map Score: 31.0898 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 147 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 3 CCATTTGGTCCACTTTTTTCTGCTCGTTTT 1 23 1 CACTTTTTTC 0.82371 -278 TTTTTCCCCCACCTTTTTGCACTCATTCAT 2 32 1 ACCTTTTTGC 0.973015 -121 GAAATTCCCCCTTTTTGCTGTTTGAAAC 2 135 0 CCCTTTTTGC 0.993177 -18 CAGGTCAATTCCCTTTTGGTCCGAACTCGC 4 46 1 CCCTTTTGGT 0.882625 -65 TGCGTAATATCACTTTTTGTGTGGTAATAA 8 29 0 CACTTTTTGT 0.929813 -272 TTACCACTTCCCCTTTTCGTCAAGATCGGC 8 112 1 CCCTTTTCGT 0.882625 -189 TCCACGCTTACACTATTTGCGTACTGGCCA 8 148 1 CACTATTTGC 0.871719 -153 GCTTTACACAACCTTTTTGCACGTCTTTTC 12 195 0 ACCTTTTTGC 0.973015 -103 TTGCATCTACCCCTTTTTGCAAAAAATGCT 13 79 0 CCCTTTTTGC 0.993177 -83 CCCGCTTTATACCTTTTTACGCACAGAGTT 19 65 1 ACCTTTTTAC 0.75905 -236 AGAGTTACAGCACTTTTTGCACTCAAAAAT 20 35 0 CACTTTTTGC 0.981645 -69 ********** Masking position 6 Map Score: 16.096 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 324 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 4 GTGCAAAAAGGTGGGGGAAAAATTATCGGTGT 2 22 0 GTGGGAAAAA 0.977576 -131 GAATTGACCTGCGGCAAAAAAAACGCAAACGT 4 25 0 GCGGAAAAAA 0.984651 -86 CACTTTTTGTGTGGTAATAAAAAAGGAGAAAA 8 17 0 GTGGATAAAA 0.945864 -284 TTTACACACTGTGATGAAAAAATCTCCCGTCA 8 61 1 GTGAAAAAAA 0.848377 -240 AAAAGGGGAAGTGGTAAAAACACTTATCATTA 8 97 0 GTGGAAAACA 0.936247 -204 CCCCAGGCGCGCGGCGAAAGAAGACTTGTGCC 12 164 0 GCGGAAAGAA 0.916757 -134 CGCGTTACTTGCGGTAGAAAAATAAAATTCGG 12 262 0 GCGGGAAAAA 0.972873 -36 CTCGACCAGAGTGGTTAATAAATATTGCCGCG 13 131 0 GTGGAATAAA 0.900322 -31 AACCGTTTGCGTGGAAATAAAATCACCATCGT 16 199 0 GTGGATAAAA 0.945864 -102 ACATTAGCTTATGGTTAAAAAATGCAAAAATC 17 118 0 ATGGAAAAAA 0.848377 -183 TGTGGTTACCGTGGGCAAAATACAGAAATTAC 19 111 0 GTGGAAAATA 0.908327 -190 TCGTTACAATGCGGGCGAAAAATAAGGATGCC 19 200 1 GCGGGAAAAA 0.972873 -101 **** ****** Masking position 12 Map Score: 13.1542 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 232 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 5 TCAACTTAATGGCGGGATTTTTTATATTATT 1 149 0 GGCGGGATTT 0.949774 -152 TCTGGCAAACGGCGGCATTCTGGAGATATGG 1 190 0 GGCGGCATTT 0.992375 -111 CCAAAAAATCCGCCGCATTCTATTCATCTGA 2 104 0 CGCCGCATTT 0.978344 -49 ATAGTGTAAGCGTGGAATTTTGGCCGATCTT 8 133 0 CGTGGAATTT 0.69817 -168 TTATACTGCGCGCGGAATTAATCAGGGGATA 9 107 1 CGCGGAATTA 0.788762 -27 CTTTCTTCAAGGCGGCAATATTCTTTTCGTT 12 36 1 GGCGGCAATT 0.937789 -262 GTTAGAATTGCGCCGAATTTTATTTTTCTAC 12 250 1 CGCCGAATTT 0.917967 -48 TAAATATTGCCGCGGCATTATACAGAGCGTA 13 114 0 CGCGGCATTT 0.992375 -48 TTATCTGTTCATCGGCATTCTGG 16 3 0 ATCGGCATTT 0.736662 -298 CTCATAAATGAGCGGCATTTTGCGTAAACCT 16 118 1 AGCGGCATTT 0.972605 -183 GGGGGAAACGGGCGTCATTATAAAGAATCTG 16 243 0 GGCGTCATTT 0.903271 -58 CTTATTTTTCGCCCGCATTGTAACGAAAACG 19 195 0 GCCCGCATTT 0.840654 -106 ********* * Masking position 7 Map Score: 13.0926 Number of sites scoring better than the average of aligned sites = 1021 Number in coding regions = 938 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 6 TTCCTTGCTCTCTTTCCGTGCTATTCTCTG 3 52 1 TCTTTCCGTG 0.681755 -66 CGTTTGCGTTTTTTTTGCCGCAGGTCAATT 4 26 1 TTTTTTGCCG 0.86719 -85 CTGAAGGGATGTTTTTGCCGGACACAAAGG 5 69 0 GTTTTTGCCG 0.922696 -37 GCTCCGTGTCGTTTTTCCGGCGTACCGCAA 8 194 1 GTTTTTCCGG 0.739879 -107 TGCGTGTGTCTTTATTGCTGATGTTGATTT 9 66 0 TTTATTGCTG 0.642986 -68 CGTTTTAAAATCTTTTGCTGTCTGGTGTGC 11 21 0 TCTTTTGCTG 0.936699 -46 GCACAAGTCTTCTTTCGCCGCGCGCCTGGG 12 165 1 TCTTTCGCCG 0.943793 -133 GCAAACGTTTGCTTTCCCTGTTAGAATTGC 12 231 1 GCTTTCCCTG 0.93736 -67 AAAAATGCTTGCTATCCCCGAAGGGCGGGT 13 58 0 GCTATCCCCG 0.88737 -104 GCTATTCCTTGAAAAGGTCG 15 51 0 GCTATTCCTT 0.427022 -10 CGTCTTCTAAGCTTTCGGTGTACCCAAGGG 16 273 0 GCTTTCGGTG 0.853241 -28 GCAATCGTTCTCTTTTGCCTGAACTTACCA 17 189 0 TCTTTTGCCT 0.686959 -112 CTGCAATTTTTCTATTGCGG 19 1 0 TCTATTGCGG 0.733786 -300 TATAAAGCGGGCTTTTGCTGGGGAATGCAG 19 46 0 GCTTTTGCTG 0.964349 -255 CGTTAGCTGAGTTTTTCGCGAAAAATTCAG 19 242 1 GTTTTTCGCG 0.677822 -59 ********** Masking position 5 Map Score: 8.47127 Number of sites scoring better than the average of aligned sites = 3045 Number in coding regions = 2860 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 7 ACCGATAATTTTTCCCCCACCTTTTTGCAC 2 24 1 TTTCCCCCAC 0.980204 -129 TAAAAAATATATTTCCCCACGAAAACGATT 2 63 1 ATTTCCCCAC 0.792267 -90 CGGCAGATTCTTTCCACCAATGGACGCATG 7 116 1 TTTCCACCAA 0.832761 -35 TTCTCCTTTTTTATTACCACACAAAAAGTG 8 19 1 TTATTACCAC 0.673512 -282 ACGGGAGATTTTTTCATCACAGTGTGTAAA 8 61 0 TTTTCATCAC 0.630801 -240 ATGATAAGTGTTTTTACCACTTCCCCTTTT 8 99 1 TTTTTACCAC 0.865329 -202 TTTGCACGTCTTTTCCCCAGGCGCGCGGCG 12 180 0 TTTTCCCCAG 0.807147 -118 GAATTTTATTTTTCTACCGCAAGTAACGCG 12 264 1 TTTCTACCGC 0.832297 -34 ATGACGCCCGTTTCCCCCCCTTGGGTACAC 16 256 1 TTTCCCCCCC 0.911709 -45 TTGCCTGAACTTACCACCGAAACAGACTGT 17 175 0 TTACCACCGA 0.471939 -126 CATGGTGAAATTATCACCACGAAACCCAGC 17 244 0 TTATCACCAC 0.892796 -57 AATTTCTGTATTTTGCCCACGGTAACCACA 19 113 1 TTTTGCCCAC 0.905511 -188 CATCCTTATTTTTCGCCCGCATTGTAACGA 19 200 0 TTTCGCCCGC 0.88098 -101 ********** Masking position 2 Map Score: 5.57133 Number of sites scoring better than the average of aligned sites = 1153 Number in coding regions = 1002 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 8 GCACAACTCTCGGCTTTAGAGGGCACAGAGAATAGCA 3 70 0 CGCTAGGACA 0.939541 -48 TTTAATACACCGCCTGGAAAGGATCATGCCTGGCCCG 7 70 1 CGCGAGGCAT 0.989769 -81 TTCCCCTTTTCGTCAAGATCGGCCAAAATTCCACGCT 8 119 1 CGCGAGGAAA 0.990504 -182 CGACACGGAGCGTCAGGAAGGGGTCAATGGCCAGTAC 8 168 0 CGCGAGGCAA 0.992124 -133 GGCAATATCTCGACCAGAGTGGTTAATAAATATTGCC 13 134 0 CGCGAGGAAT 0.987671 -28 CCAACAGGACCGCCTATAAAGGCCAAAAATTTTATTG 14 252 1 CGCTAGGAAA 0.980584 -49 ACTCAGCTAACGCCCCTAACGGGGCATCCTTATTTTT 19 217 0 CGCTAGGCAT 0.979096 -84 ** * ** ** *** Masking position 8 Map Score: 5.48625 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 38 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 9 GACCAAAAGGGAATTGACCTGCGGCAAAAAAAACG 4 32 0 GAATGACCTC 0.865006 -79 GTTGTCACCGAAACTCAGCTTGCCCGGC 7 4 0 AAATCAGCTC 0.984272 -147 TTTCGGTGACAACGTCACCTTGTTCCAGACGTTGC 7 26 1 AACTCACCTC 0.974287 -125 TCCAGACCCTAACTTCAGCTCCTGCAAAATCGCAA 8 266 0 AACTCAGCTC 0.968344 -35 TTCCATCCGAAAACTAACCTTTACCCTGGCACAAG 12 137 1 AAATAACCTC 0.909541 -161 TTTTCGCGAAAAACTCAGCTAACGCCCCTAACGGG 19 231 0 AAATCAGCTC 0.984272 -70 TTTTCGCGAAAAATTCAGCTAACGCTCTCTGTAAT 19 254 1 AAATCAGCTC 0.984272 -47 TTTGCACTCAAAAATGACCTCGATCAGTCTGTTTT 20 15 0 AAATGACCTC 0.96482 -89 TTTTCAAAATCACCGTTTGCTTAAAAATGG 20 84 0 AAATCACCGC 0.947675 -20 *** ****** * Masking position 7 Map Score: 7.00492 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 66 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 Motif number 10 AATATGCAAATAAAGTGAGTGAATATTCTCT 1 270 1 TAAAGGAGTG 0.926375 -31 GCACGAAAAATAAAGGGCGCGAATGCGCCCT 5 16 0 TAAAGGCGCG 0.989612 -90 GGCGGTGTATTAAAGAGCGCGATGCAACGTC 7 53 0 TAAAGGCGCG 0.989612 -98 TTTTCGTTTATACTGCGCGCGGAATTAATCA 9 100 1 TACTGGCGCG 0.959812 -34 CGCGGCATTATACAGAGCGTAACCGATTGCA 13 104 0 TACAGGCGTA 0.878408 -58 CTTTGGAGAATAAAGAGCTTGCAACCGGAAA 14 131 0 TAAAGGCTTG 0.85679 -170 ATTTGACTATTACAGAGAGCGTTAGCTGAAT 19 266 0 TACAGGAGCG 0.969119 -35 ***** ***** Masking position 2 Map Score: 4.50079 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 265 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 11 GCTTAATGCCTGTAAAACATGCATGAGCCACA 1 116 1 TGAAAAATGC 0.942185 -185 CACACTGTGATGAAAAAATCTCCCGTCATTTA 8 65 1 TGAAAATCTC 0.82997 -236 TACCCCTTTTTGCAAAAAATGCTTGCTATCCC 13 70 0 TGAAAAATGC 0.942185 -92 TGTGATGAAGTGAAAAATTTGCATCACAAACC 14 85 1 TGAAAATTGC 0.980978 -216 GCTATTCCTTGAAAAGGTCGCCTGTCTTTTG 15 40 0 TGAAAGTCGC 0.92096 -21 GGTTAAAAAATGCAAAAATCGCGACAGAATAA 17 106 0 TGAAAATCGC 0.982416 -195 AATTTCACCATGAAAAAGTTGTCAGCCCCGCT 17 262 1 TGAAAATTGT 0.818364 -39 CCGCAATAGAAAAATTGCAGAAAAATGA 19 7 1 TAAAAATTGC 0.818364 -294 CCATTGAAAGAGAAAAATTCGCGAGCGTTGCG 19 159 1 AGAAAATCGC 0.887154 -142 CATTTTTGAGTGCAAAAAGTGCTGTAACTCTG 20 34 1 TGAAAAGTGC 0.93196 -70 ** **** **** Masking position 6 Map Score: 7.94143 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 271 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 12 TTTAGCGCCCATATCTCCAGAATGCCGCCG 1 182 1 ATATCTCCAG 0.891773 -119 GCGTCTTAAAACTCCTGTGGTGCACAA 3 101 0 AAAACTCCTG 0.949798 -17 GAACTCTCCTGGATTCCCGGT 4 100 0 AACTCTCCTG 0.966959 -11 TGTGATGAAAAAATCTCCCGTCATTTATAA 8 70 1 AAATCTCCCG 0.940836 -231 AACGAATATCCCCTGATTAATTCCG 9 119 0 ATATCCCCTG 0.957402 -15 CTTTATCACTCCTGGGTGTGAATT 11 53 0 ATCACTCCTG 0.907212 -14 GGTAAATCCCCTGGATTTGACTA 19 288 0 AAATCCCCTG 0.966959 -13 ********** Masking position 1 Map Score: 3.92162 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 69 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 13 ATATTAATTCACAATGATGACGTAAATCAA 1 245 0 ACAATGATGA 0.814279 -56 AAAACCCGCAACTTTGCTGATTTCACAGCC 3 11 1 ACTTTGCTGA 0.845401 -107 ATTTTTACACACTGTGATGAAAAAATCTCC 8 58 1 ACTGTGATGA 0.981341 -243 TTTCAGAAAGAATGTGATGAAGTGAAAAAT 14 73 1 AATGTGATGA 0.962215 -228 ATACAAAGATGATGTGATGAGAAAGTCAAT 17 51 0 GATGTGATGA 0.886823 -250 ACCATAAGCTAATGTGATGATCAATTTTAC 17 135 1 AATGTGATGA 0.962215 -166 TACAGAAATTACATTGATGATTGTGGATAA 19 93 0 ACATTGATGA 0.885454 -208 ********** Masking position 10 Map Score: 1.94619 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 132 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 14 TTTGCTGATTTCACAGCCACGCAACCGTTTTC 3 23 1 TCCAGCCCGC 0.987006 -95 GAAAGGATCATGCCTGGCCCGCACAGTTTTCG 7 86 1 TGCTGGCCGC 0.940381 -65 GAGAAGAACCTCAGGCATGCGTCCATTGGT 7 131 0 CCCAGGCTGC 0.982525 -20 CACGTCTTTTCCCCAGGCGCGCGGCGAAAGAA 12 174 0 CCCAGGCCGC 0.99517 -124 TCTTTATTCTCCAAAGCCTTGCGTAGCCTGAA 14 146 1 CCAAGCCTGC 0.921102 -155 ATGAAAAAGTTGTCAGCCCCGCTTATTCAATG 17 271 1 TGCAGCCCGC 0.983006 -30 AAAACGTTTGCGCAACGCTCGCGAATTTTTCT 19 169 0 CGAACGCCGC 0.891649 -132 ** ***** *** Masking position 8 Map Score: 2.10887 Number of sites scoring better than the average of aligned sites = 728 Number in coding regions = 707 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 15 AAGTCAACTTAATGGCGGGATTTTTTATAT 1 153 0 AATGGCGGGA 0.812627 -148 AAACAGCAAAAAGGGGGAATTTC 2 140 1 AAGGGGGAAT 0.856293 -13 ACGAAAAATAAAGGGCGCGAATGCGCCCTC 5 15 0 AAGGGCGCGA 0.984894 -91 CGGTGTATTAAAGAGCGCGATGCAACGTCT 7 52 0 AAGAGCGCGA 0.850666 -99 TCTTGACGAAAAGGGGAAGTGGTAAAAACA 8 107 0 AAGGGGAAGT 0.702225 -194 GAGCGTCAGGAAGGGGTCAATGGCCAGTAC 8 168 0 AAGGGGTCAA 0.842565 -133 TCCTTTCTTCAAGGCGGCAATATTCTTTTC 12 34 1 AAGGCGGCAA 0.778728 -264 GCTATCCCCGAAGGGCGGGTTACTATCGAC 13 48 0 AAGGGCGGGT 0.957406 -114 TTTTTGCAAAAAGGGGTAGATGCAATCGGT 13 84 1 AAGGGGTAGA 0.901804 -78 CGGTGTACCCAAGGGGGGGAAACGGGCGTC 16 258 0 AAGGGGGGGA 0.986547 -43 ********** Masking position 2 Map Score: 3.86515 Number of sites scoring better than the average of aligned sites = 410 Number in coding regions = 331 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918