AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00910_ecoli_reg_100.orf -o00910_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 cynT 108 carbonic anhydrase #2 cynS 30 cyanate aminohydrolase, cyanase #3 ylbE 266 orf, hypothetical protein #4 asnB 247 asparagine synthetase B #5 dadA 300 D-amino acid dehydrogenase subunit #6 narG 300 nitrate reductase 1, alpha subunit #7 narZ 81 cryptic nitrate reductase 2, alpha subunit #8 narU 300 nitrite extrusion protein 2 #9 gdhA 235 NADP-specific glutamate dehydrogenase #10 ansA 166 cytoplasmic L-asparaginase I #11 napF 300 ferredoxin-type protein: electron transfer #12 gcvT 300 aminomethyltransferase (T protein; tetrahydrofolate-dependent) of glycine cleavage system #13 ansB 175 periplasmic L-asparaginase II #14 metC 103 cystathionine beta-lyase (beta-cystathionase) #15 gltB 300 glutamate synthase, large subunit #16 nirB 261 nitrite reductase (NAD(P)H) subunit #17 tnaA 205 tryptophanase #18 asnA 151 asparagine synthetase A #19 glnA 300 glutamine synthetase #20 aspA 300 aspartate ammonia-lyase (aspartase) Motif number 1 TTCCCCTGCTCCAGTATTGCCAGCGCCT 3 249 0 CCCCGCCTTT 0.982976 -18 GAAAAAAATTCTCCGGCGACGCGGTTTTTAACAGGT 5 42 0 CTCCGCCGTT 0.992265 -259 GACATGACTCCTGCTCCAGGAATGAATTGGGAT 7 59 0 CTCCGCCGAT 0.992267 -23 AAGTTTTGCCACCCGGCTACCGTTATCAGTAGCAGA 9 35 0 ACCCGCCTAT 0.919157 -201 AGGTGCGCTCCCCCTGCCTCACGTATATACTTTTGC 10 114 1 CCCCGCCGAT 0.995137 -53 TTTGCCACGCTTCCCGCCACTCTTTTGATCCTGCTA 11 139 1 TTCCGCCTTT 0.801714 -162 CACTCTTTTGATCCTGCTACAGGTTTTACCCCGATC 11 156 1 ATCCGCCGTT 0.961931 -145 TTCCTCTCTTCCCCCGCTACGTGCATCTATTTCTAT 16 48 1 CCCCGCCGAT 0.995137 -214 TTTTTATACTCCTGCGTCCTGTTGCTTATGATTA 18 128 0 CTCCGCCGTG 0.963969 -24 AGCCGGTTAACCCCGGCTACCTGAATGGGTTGCGAA 20 39 1 CCCCGCCGAT 0.995135 -262 **** ** * * ** Masking position 7 Map Score: 16.0138 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 69 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 2 TGAAGCAGTGTTTTGCCTTCGTTTAGTTCGCTGATAAG 3 113 0 TTTGCCTTTT 0.964616 -154 GCGCTTCATCTTTCGCCCAACCTTCGAACAGACATGCG 3 211 0 TTTGCCCTTA 0.953295 -56 CGGAGAATTTTTTTCTTTGCGATTTCTTATTATCAGAG 5 63 1 TTTCTTTTTT 0.465361 -238 TTACCTCGTGTTTTGTCTTTTTTTCATTACCAATGTGT 8 257 1 TTTGTCTTTT 0.888003 -44 CTTCCCGCTGTTTCGCCCCATATTTCCTTATCCGCATA 10 71 1 TTTGCCCTTT 0.953295 -96 TTTCTGCTGGTTTGCTCTCTCATTAGAATTTAACACTA 11 33 0 TTTCTCTTTA 0.731567 -268 AAAAACGGGCTTTTGCTCACATTTCAAATGGTTATAAA 11 104 0 TTTGCTCTTA 0.867002 -197 TGGTGTATTTTTTGGTTTTTTATTCTGTCGCGATTTTT 12 87 1 TTTGTTTTTT 0.7169 -214 GATGATCAATTTTACCTTATGGTTAACAGTCTGTTTCG 12 150 1 TTTCCTTTTA 0.749547 -151 AATCGTTCTCTTTTGCCTGAACTTACCACCGAAACAGA 12 179 0 TTTGCCTTTA 0.964616 -122 AGAAATGTGCTTTAGCGCAAAATTCTTTATTAAATGAC 15 98 0 TTTGCGCTTT 0.704458 -203 AACCCGCTCATTTTGTCTATTTTTTGCACAAACATGAA 16 85 1 TTTGTCTTTA 0.888003 -177 TTTTGCCTCGATTTCTTTTCTATTACCG 16 244 0 TTTGCCTTTT 0.964616 -18 TTCATTCTATTTTAGCCTTCTTTTTTAATGAATCAAAA 18 36 1 TTTGCCTTTA 0.964616 -116 TTGGCACAGATTTCGCTTTATCTTTTTTACGGCGACAC 19 211 1 TTTGCTTTTT 0.89698 -90 AGTGTCGGTTTTTACCCCTTAATTATTAATTTGTGAAA 20 162 0 TTTCCCCTTA 0.875245 -139 *** **** ** * Masking position 13 Map Score: 12.5 Number of sites scoring better than the average of aligned sites = 325 Number in coding regions = 263 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 3 CCATGTTTACATCAGTGGCGCAAGCCAATGC 3 18 1 ATCAGGGCGC 0.97132 -249 ATCTCCTGCCAGCGCATTGGCGGCCCGGCGT 3 150 0 AGCGCTTGGC 0.809355 -117 CGAAAGATGAAGCGCAGGCGCTGGCAATACT 3 234 1 AGCGCGGCGC 0.969968 -33 TCACCGCCAAATCGCTTGCGCACAGTGCTGC 4 162 1 ATCGCTGCGC 0.919992 -86 ATTTCTTATTATCAGAGTGCCACTAATCCGC 5 84 1 ATCAGGTGCC 0.757929 -217 ATCTACCGTTATCGGAGTGGCT 5 289 1 ATCGGGTGGC 0.981567 -12 ATGTCGATTTATCAGAGGGCCGACAGGCTCC 6 265 1 ATCAGGGGCC 0.881519 -36 AGAAAGCGTAACCGCGGGGGCAGAATGGGGA 8 161 0 ACCGCGGGGC 0.923869 -140 TGATAACGGTAGCCGGGTGGCAAAACTTTAG 9 43 1 AGCCGGTGGC 0.820531 -193 TCCGCATAGTATCAGGTGCGCTCCCCCTGCC 10 101 1 ATCAGTGCGC 0.888829 -66 TCCTCATTGAATAAGCGGGGCTGACAACTTT 12 276 0 ATAAGGGGGC 0.717154 -25 AGCATGAATATTCGCGGGCGCATCCTGAAGA 14 44 0 TTCGCGGCGC 0.816818 -60 AAGGGGGCGAATCGGAGGCGCGCGT 15 286 1 ATCGGGGCGC 0.989652 -15 TACATCAATAAGCGGGGTTGCTGAATCGTTA 16 206 1 AGCGGGTTGC 0.775858 -56 ATTGAATCTAATCGGTTTGGCTCTGGTGATG 17 27 0 ATCGGTTGGC 0.926311 -179 ***** ***** Masking position 11 Map Score: 12.307 Number of sites scoring better than the average of aligned sites = 1566 Number in coding regions = 1507 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 4 TGATAATAAGAAATCGCAAAGAAAAAAATTCTCC 5 64 0 AAAGCAAAGA 0.719997 -237 GGTAATGAAAAAAAGACAAAACACGAGGTAAGGC 8 254 0 AAAACAAAAC 0.786078 -47 GTATAGTCGAAAACTGCAAAAGCACATGACATAA 9 168 1 AAAGCAAAAA 0.94988 -68 CACATGACATAAACAACATAAGCACAATCGTATT 9 190 1 AAAACATAAA 0.79739 -46 AATGATATCGAAAGAGCAAAAGTATATACGTGAG 10 131 0 AAAGCAAAAA 0.94988 -36 GCGACCAAATAAACCGCATAATTAATAAGCCATT 11 239 0 AAAGCATAAA 0.943411 -62 GCGACAGAATAAAAAACCAAAAAATACACCAGTT 12 84 0 AAAACCAAAA 0.545675 -217 TTATGGTTAAAAAATGCAAAAATCGCGACAGAAT 12 108 0 AAAGCAAAAC 0.939634 -193 CTCTATTTTAAGACGGCATAATACTTTTTTATGC 13 13 1 AGAGCATAAC 0.650082 -163 ACGAAGAATTAAACGGCATAAAAAAGTATTATGC 13 28 0 AAAGCATAAA 0.943411 -148 CATCCTGAAGAATTGGCATAAAGCAGAAAATTTT 14 21 0 AATGCATAAC 0.786405 -83 TTGTGCAAAAAATAGACAAAATGAGCGGGTTTAT 16 82 0 AATACAAAAA 0.546072 -180 TGACCTTTGCAAAAGGCAAAATTAAGATATAGCA 17 72 0 AAAGCAAAAA 0.94988 -134 ATGAATCATCAATCCGCATAAGAAAATCCT 18 7 0 AATGCATAAA 0.817608 -145 ATCATTCAATAAAAAGCCTAACTCACTTTTGATT 18 66 0 AAAGCCTAAC 0.786136 -86 *** ****** * Masking position 10 Map Score: 10.5015 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 170 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 5 CATTGGCGGCCCGGCGTGAAGCAGTGTTTTGCCT 3 133 0 CGGCGTAACG 0.96633 -134 TTATATTTTACGGGGGCCAAATTGCTGACAAAGT 4 24 0 CGGGGCAATG 0.884915 -224 GTTTAAAAAAATGCCGCAAAGCAGCACTGTGCGC 4 179 0 AGCCGCAACG 0.773466 -69 CTGGATAAAAAGGGCGTTCAGCAGGAGATACTAA 5 134 1 AGGCGTCACG 0.810584 -167 TCACGATCTGAAGGGTTGAAACATGACATACGTT 8 60 1 AGGGTTAACT 0.777828 -241 TAACCTTCAAACGGGGTTAATCTTTGAACGTATG 8 86 0 AGGGGTAACT 0.940693 -215 ATAAGGAAATATGGGGCGAAACAGCGGGAAGAGG 10 68 0 AGGGGCAACG 0.989298 -99 ATACCCCGATCGGGGTAAAACCTGTAGCAGGATC 11 165 0 CGGGTAAACG 0.911078 -136 AAGGACAACAAGGGGGCGAATCGGAGGCGCGCGT 15 277 1 AGGGGCAACG 0.989298 -24 ATTCAGGTAGCCGGGGTTAACCGGCTGCTATTAC 20 31 0 CGGGGTAACG 0.987119 -270 TTAATAATTAAGGGGTAAAAACCGACACTTAAAG 20 171 1 AGGGTAAACG 0.908122 -130 TCGGTCGATGCAGGGGATAATCGTCGGTCGAAAA 20 254 1 CGGGGAAACT 0.919691 -47 * ***** ** * * Masking position 10 Map Score: 7.9331 Number of sites scoring better than the average of aligned sites = 608 Number in coding regions = 544 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 6 AACAACATAAGCACAATCGTATTAATATAT 9 201 1 GCACAATCGT 0.951398 -35 ATGCCGGACGGCACTATCGTCGTCCGGCCT 16 17 1 GCACTATCGT 0.885679 -245 TCTATTTTTTGCACAAACATGAAATATCAG 16 100 1 GCACAAACAT 0.952316 -162 ATATATGCAAGCACCATCATTTACTAAAAC 17 124 0 GCACCATCAT 0.97633 -82 AAAGGTCATTGCACCAACATGGTGCTTAAT 19 81 1 GCACCAACAT 0.97633 -220 TGTGAATGTTGCACCAATATAGTGCTTCAA 19 118 0 GCACCAATAT 0.821623 -183 GTTATCATGCGCACCATCGTGCAAAAGGGC 19 158 0 GCACCATCGT 0.975863 -143 AAAAATAGTTGCGCAAACATCTTGAAATTT 20 106 0 GCGCAAACAT 0.841382 -195 ********** Masking position 6 Map Score: 7.41865 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 168 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 ATTTTATGCTGGATAAAAAGGGCGTTCAGCAG 5 126 1 GATAAAAGGG 0.972003 -175 TTCAGATCGTGAATCTAAAGGGTTACATATTA 8 40 0 GATCAAAGGG 0.982259 -261 GATATGAATGATATCGAAAGAGCAAAAGTATA 10 139 0 AATCAAAGAG 0.654071 -28 ACCTGTAGCAGGATCAAAAGAGTGGCGGGAAG 11 148 0 GATCAAAGAG 0.955834 -153 CATCATCTTTGTATAGAAACTGGTGTATTTTT 12 67 1 GATAAAACTG 0.807766 -234 ACATCCAGACGTATAAAAACAGGAATCCCGAC 14 82 1 GATAAAACAG 0.857571 -22 CCATTAAGGAGTATATAAAGGTGAATTTGATT 16 174 1 GATAAAAGGT 0.752059 -88 AGATCACATTGAATCTAATCGGTTTGGCTCTG 17 33 0 GATCAATCGG 0.775602 -173 CTTTTTTAATGAATCAAAAGTGAGTTAGGCTT 18 55 1 GATCAAAGTG 0.937901 -97 CTTTCACGGAGCATAAAAAGGGTTATCCAAAG 19 53 1 GATAAAAGGG 0.972003 -248 * *** ****** Masking position 7 Map Score: 4.6925 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 72 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 CCGATTGTCATAAGGTAAAAGTCTCATTTA 1 46 0 TAAGGTAAAA 0.906927 -63 CGAACTAAACGAAGGCAAAACACTGCTTCA 3 121 1 GAAGGCAAAA 0.968119 -146 CACTAAAAGAGCAGGTAAAATTGTCTG 11 8 0 GCAGGTAAAA 0.927265 -293 CTGTTAACCATAAGGTAAAATTGATCATCA 12 149 0 TAAGGTAAAA 0.906927 -152 GGTGGTAAGTTCAGGCAAAAGAGAACGATT 12 187 1 TCAGGCAAAA 0.940445 -114 AAAGTTAGAGGCAGGTAACAAAACGAAGAA 13 54 0 GCAGGTAACA 0.748657 -122 ATTTTATCTTTAAGGCTAAAAGGGAAGTCG 15 54 0 TAAGGCTAAA 0.858152 -247 GACCTTTGCAAAAGGCAAAATTAAGATATA 17 75 0 AAAGGCAAAA 0.853348 -131 CATTAAAAAAGAAGGCTAAAATAGAATGAA 18 36 0 GAAGGCTAAA 0.905624 -116 ********** Masking position 3 Map Score: 5.10148 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 244 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 9 TTTCACCAATCGACAATCACCATTACGTTTTTT 4 123 1 CACAACCCAT 0.882596 -125 CGCCGGATTTCATTAAGAGCCATTAATATGTTA 6 12 1 CTTAAACCAT 0.805112 -289 GGGGAATACTCCTTAATACCCATCTGCATAAAA 6 50 1 CTTAAACCAT 0.805112 -251 ATATCTGGCTACTTAATCCCCATTCTGCCCCCG 8 145 1 ATTAACCCAT 0.937575 -156 ATCTCTGGTGAATCAATCGCTATATAAATATAT 11 72 1 ATCAACCTAT 0.659446 -229 GAGAGCGACCAAATAAACCGCATAATTAATAAG 11 244 0 AATAACGCAT 0.771888 -57 CAAAACGAAGAATTAAACGGCATAAAAAAGTAT 13 33 0 ATTAACGCAT 0.904921 -143 TTAGCCTTAAAGATAAAATCCATTTTAATTTCA 15 65 1 AATAAACCAT 0.51529 -236 CCAGATATATATGCAAGCACCATCATTTACTAA 17 127 0 AGCAACCCAT 0.761434 -79 ATATCTGGCGAATTAATCGGTATAGCAGATGTA 17 152 1 ATTAACGTAT 0.546323 -54 TAGAATGAATCATCAATCCGCATAAGAAAATCC 18 12 0 CTCAACGCAT 0.930552 -140 TCAATGGAAACATTAAGCACCATGTTGGTGCAA 19 89 0 CTTAACCCAT 0.954024 -212 CGGTAGAAATCCTCAAGCAGCATATGATCTCGG 20 217 1 CTCAACGCAT 0.930552 -84 * **** * **** Masking position 6 Map Score: 5.41185 Number of sites scoring better than the average of aligned sites = 437 Number in coding regions = 399 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 10 CCTTATTTTTAAACCATCAGGAGTT 2 4 1 TATTTTTACC 0.935354 -27 TCACACCAGACCTTTTTTCACCAATCGACAAT 4 108 1 CCTTTTTACC 0.901973 -140 TTACGTTTTTTATTTTTTCACCGCCAAATCGC 4 145 1 TATTTTTACC 0.935354 -103 GAATTTACTTTATTTTTCATCCCCATCACTCT 6 175 1 TATTTTTTCC 0.647692 -126 GAACGTATGTCATGTTTCAACCCTTCAGATCG 8 63 0 CATGTTTACC 0.881184 -238 ATTAATAAGCCATTTTTATAGCCGCTAAGATA 11 221 0 CATTTTTAGC 0.903705 -80 TTTTTGACATTTTTTTAGCTCTTAATATT 12 8 1 CATTTTTAGC 0.903705 -293 GCGATTTTTGCATTTTTTAACCATAAGCTAAT 12 116 1 CATTTTTACC 0.975236 -185 TTTAATTCTTCGTTTTGTTACCTGCCTCTAAC 13 49 1 CGTTTTGACC 0.761274 -127 CGCTAAAGCACATTTCTGTACCAATAAGCTTG 15 119 1 CATTTCTACC 0.881184 -182 TGGTTTCGAATGTTTTTCGACCGACGATTATC 20 269 0 TGTTTTTACC 0.861522 -32 ******* *** Masking position 5 Map Score: 6.04548 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 125 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 11 GGATTAGTGGCACTCTGATAATAAGAAATCG 5 82 0 CCTCTGATAA 0.9835 -219 AGCCACTCCGATAACGGTAGATAC 5 287 0 CCTCCGATAA 0.964098 -14 GGCAAGGTAACGCTCTGAAACAGCGTGGGAA 6 220 0 CCTCTGAAAC 0.949345 -81 AGCCTGTCGGCCCTCTGATAAATCGACATTG 6 263 0 CCTCTGATAA 0.9835 -38 ATCATTAACGCGCTCTGAAAATTGAGAGCGA 11 269 0 CCTCTGAAAA 0.976526 -32 * ********* Masking position 4 Map Score: 1.47902 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 12 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 Motif number 12 GTCATCTCCTGCCAGCGCATTGGCGGCCCG 3 154 0 GCCAGCGCAT 0.979271 -113 ACAGACATGCGCCCACGCACGCCCCTTTCA 3 192 0 GCCCACGCAC 0.895927 -75 TATTGCCAGCGCCTGCGCTTCATCTTTCGC 3 233 0 GCCTGCGCTT 0.965348 -34 CCGCCAAATCGCTTGCGCACAGTGCTGCTT 4 165 1 GCTTGCGCAC 0.876975 -83 GGAGATGTGAGCCAGCTCACCATAAAAAAG 5 193 1 GCCAGCTCAC 0.951999 -108 AGACAATTTTACCTGCTCTTTTAGTGTTAA 11 12 1 ACCTGCTCTT 0.736297 -289 TTCAGGATGCGCCCGCGAATATTCATGCTA 14 46 1 GCCCGCGAAT 0.912531 -58 TGGATGAGCAGCCTGCTCATCATATTTATG 15 205 1 GCCTGCTCAT 0.9782 -96 ATTTCTATAAACCCGCTCATTTTGTCTATT 16 76 1 ACCCGCTCAT 0.914306 -186 ********** Masking position 6 Map Score: 4.27836 Number of sites scoring better than the average of aligned sites = 1259 Number in coding regions = 1208 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 13 AAAATATAAACATTCAATAAAACCCGCTAA 4 49 1 CATTCAATAA 0.95053 -199 TTGTTAGTTACATTTAGTAACACATATCTG 8 122 1 CATTTAGTAA 0.817119 -179 CTTGTCCTCATTGAATAAGCGGGGCTGA 12 283 0 CATTGAATAA 0.877567 -18 TAATTTCAGTCATTTAATAAAGAATTTTGC 15 90 1 CATTTAATAA 0.924354 -211 CAAGCACCATCATTTACTAAAACAAGTAAA 17 117 0 CATTTACTAA 0.817119 -89 ATGCAATAATCATTCAATAAAAAGCCTAAC 18 78 0 CATTCAATAA 0.95053 -74 AACCGACACACATGCAATAATCATTCAATA 18 89 0 CATGCAATAA 0.855329 -63 ********** Masking position 6 Map Score: 1.61629 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 24 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 14 CAATGCGCTGGCAGGAGATGACCGGACCCA 3 162 1 GCAGGAGATG 0.950316 -105 AAACCGCGTCGCCGGAGAATTTTTTTCTTT 5 51 1 GCCGGAGAAT 0.790845 -250 AGGGCGTTCAGCAGGAGATACTAAAGACGC 5 144 1 GCAGGAGATA 0.951253 -157 ACAGGCTCCCACAGGAGAAAACCG 6 287 1 ACAGGAGAAA 0.865427 -14 CATTCCTGGAGCAGGAGTCATGTC 7 68 1 GCAGGAGTCA 0.783418 -14 TATACGTGAGGCAGGGGGAGCGCACCTGAT 10 111 0 GCAGGGGGAG 0.873348 -56 GATGCACGTAGCGGGGGAAGAGAGGAAAAG 16 45 0 GCGGGGGAAG 0.858474 -217 GCAACAGGACGCAGGAGTATAAAAA 18 137 1 GCAGGAGTAT 0.836442 -15 GGCTGCTATTACAGGAGAAACCTTTGCGCT 20 13 0 ACAGGAGAAA 0.865427 -288 TTCGGTCGATGCAGGGGATAATCGTCGGTC 20 253 1 GCAGGGGATA 0.932859 -48 ********** Masking position 2 Map Score: 3.07998 Number of sites scoring better than the average of aligned sites = 607 Number in coding regions = 556 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 15 TGTGCGCAAGCGATTTGGCGGTGAAAAAATAAA 4 153 0 CTTTGCGGTG 0.97535 -95 CAACAAATACCAGGTTAACGGAGAAGGTT 4 229 1 CGTTACGGAG 0.931696 -19 CAACATGCGGCTTTTTTATGGTGAGCTGGCTCA 5 200 0 CTTTATGGTG 0.958161 -101 AATTTACAGTCTGTTATGTGGTGGCTGTTAATT 6 122 1 CTTAGTGGTG 0.777347 -179 ATTTTCAGAGCGCGTTAATGATGGAAGGTCAAT 11 278 1 CGTTATGATG 0.587559 -23 CTCCGATGCTGGGTTTCGTGGTGATAATTTCAC 12 237 1 GTTTGTGGTG 0.762633 -64 GGGCTGACAACTTTTTCATGGTGAAATTATCAC 12 257 0 CTTTATGGTG 0.958161 -44 CTCTGCAATACTTGTTTGCGGAGGATGT 19 6 0 CGTTGCGGAG 0.936622 -295 CCTTTGTGATCGCTTTCACGGAGCATAAAAAGG 19 41 1 CTTTACGGAG 0.950383 -260 TTCGCTTTATCTTTTTTACGGCGACACGGCCAA 19 222 1 CTTTACGGCG 0.918284 -79 * *** ****** Masking position 5 Map Score: 2.86212 Number of sites scoring better than the average of aligned sites = 539 Number in coding regions = 508 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159