AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00252_ecoli_reg_100.orf -o00252_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 panD 273 aspartate 1-decarboxylase #2 pepD 260 aminoacyl-histidine dipeptidase (peptidase D) #3 asnB 247 asparagine synthetase B #4 aspC 184 aspartate aminotransferase #5 asnS 168 asparagine tRNA synthetase #6 ycfC 35 orf, hypothetical protein #7 ymfC 201 orf, hypothetical protein #8 dadA 300 D-amino acid dehydrogenase subunit #9 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #10 goaG 37 4-aminobutyrate aminotransferase #11 gadB 300 glutamate decarboxylase isozyme #12 ansA 166 cytoplasmic L-asparaginase I #13 aspS 276 aspartate tRNA synthetase #14 nadB 300 quinolinate synthetase, B protein #15 b2659 230 orf, hypothetical protein #16 gabD 22 succinate-semialdehyde dehydrogenase, NADP-dependent activity #17 alaS 128 alanyl-tRNA synthetase #18 ansB 175 periplasmic L-asparaginase II #19 argG 300 argininosuccinate synthetase #20 gadA 210 glutamate decarboxylase isozyme #21 asnA 151 asparagine synthetase A #22 argC 153 N-acetyl-gamma-glutamylphosphate reductase #23 argH 60 argininosuccinate lyase #24 dnaB 82 replicative DNA helicase; part of primosome #25 alr 52 alanine racemase 1 #26 aspA 300 aspartate ammonia-lyase (aspartase) #27 purA 103 adenylosuccinate synthetase Motif number 1 TTTGCGTACCGCGCCGAAGCGTGCCATGTATCG 1 129 0 GCGCAAGCGG 0.976686 -145 CCACTTTATCCCGCGTCAGGGAGAGGCAGTGCG 2 134 0 CCGCCAGGGG 0.994732 -127 CATATTGCCGCAGAGTCAGGGAGATGTGAGCCA 8 174 1 CAGACAGGGG 0.945881 -127 TGCAGTTTGTGAACGTCAGGGCGCAGAGATCCC 9 221 0 GAACCAGGGG 0.893337 -54 GAAATATGGGGCGAAACAGCGGGAAGAGGATTC 12 64 0 GCGACAGCGG 0.987134 -103 AAGTATATACGTGAGGCAGGGGGAGCGCACCTG 12 113 0 GTGACAGGGG 0.954402 -54 TGGTAACGAGGCGTTCCAGCGCGGGCCAGGCTC 13 124 1 GCGTCAGCGG 0.968119 -153 TTGGTCACCTGCGCAGCAGGGGGCATCCGCCGG 13 232 1 GCGCCAGGGG 0.996926 -45 TCTCGCCGCCCTGCGTCAGCGTGTTTAGCAACT 14 192 1 CTGCCAGCGG 0.973151 -109 ATATCGCCACCAGCTCCAGCGTGTCTTAACCGC 17 80 0 CAGCCAGCGG 0.981109 -49 GTAAAATAATGCGCTTAAGGGAGAGCAGGAGAA 19 148 0 GCGCAAGGGG 0.980379 -153 **** ***** * Masking position 8 Map Score: 16.1897 Number of sites scoring better than the average of aligned sites = 556 Number in coding regions = 510 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 2 TGTGACCTGCAATACTGTTTTGCGGGTGATC 2 224 1 AATCTGTTTT 0.687568 -37 ATCCTCACACCAGACCTTTTTTCACCAATCG 3 104 1 CAGCCTTTTT 0.860827 -144 GATGAAAACGCAGGCTGTTTTTGCAAGACGT 4 86 0 CAGCTGTTTT 0.90818 -99 GAGCTAATCGGCTCCCTTTTTTTACCTTTAA 5 21 1 GCTCCTTTTT 0.625626 -148 CTCCTGCTGAACGCCCTTTTTATCCAGCATA 8 130 0 ACGCCTTTTT 0.780916 -171 TATTCAACATGCGGCTTTTTTATGGTGAGCT 8 206 0 GCGCTTTTTT 0.82363 -95 ATCGATAAATCCTACTTTTTTAATGCGATCC 11 259 1 CCTCTTTTTT 0.938038 -42 AGTATAATAGCCGCCTTTTTTCATTCAGTTG 13 178 1 CCGCTTTTTT 0.956003 -99 GAGTAACCCAACGGCCTTTTTATTTCACCAC 14 129 1 ACGCCTTTTT 0.780916 -172 CGGATAAACACCTGCTATTTTAATATTTGTT 14 227 0 CCTCTATTTT 0.772311 -74 CGCTACATCCTGTTTTCAAAGG 16 7 0 CATCTGTTTT 0.873275 -16 AAGACGGCATAATACTTTTTTATGCCGTTTA 18 22 1 AATCTTTTTT 0.728238 -154 TACGATAATAAAGTCTGTTTTTAATATTATC 20 53 1 AAGCTGTTTT 0.759555 -158 GCGGATAAATCCTACTTTTTTATTGCCTTCA 20 169 1 CCTCTTTTTT 0.938038 -42 ATTGATGATTCATTCTATTTTAGCCTTCTTT 21 28 1 CATCTATTTT 0.652762 -124 TCTATTTTAGCCTTCTTTTTTAATGAATCAA 21 41 1 CCTCTTTTTT 0.938038 -111 TGACCTCGATCAGTCTGTTTTTTGT 27 5 0 CAGCTGTTTT 0.90818 -99 *** ******* Masking position 8 Map Score: 16.3668 Number of sites scoring better than the average of aligned sites = 532 Number in coding regions = 414 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 3 ACGTTTTTTATTTTTTCACCGCCAAATCGCTTG 3 147 1 TTTTCCCGCC 0.859634 -101 AGCACACCTCTTTGTTAAATGCCGAAAAAACAG 4 12 1 TTTTAATGCC 0.82051 -173 GTCCTGTTTTTTTTATACCTTCCAGAGCAATCT 4 52 1 TTATACTTCC 0.784772 -133 GGGGGATACCTATGTTACCTGGCATCTGCAATC 5 92 0 TTTTACTGGC 0.871388 -77 GAATTTCCAGTATAATAGCCGCCTTTTTTCATT 13 170 1 TTATACCGCC 0.946094 -107 AGATATCCCTTAACTTAGCTGCCGGCGGATGCC 13 253 0 TATTACTGCC 0.95648 -24 GTAGAAATGCCCATTTAACTGCCTGAAGAGTAA 14 102 1 CATTACTGCC 0.864489 -199 TTTAATGTTATATCTGCCCCGATAAAAC 15 6 1 TTATACTGCC 0.96913 -225 GTAAACTAAACATATTATCTGCCCCGTTTTATC 15 31 0 CTTTACTGCC 0.956137 -200 ACGCATACGGTATTTTACCTTCCCAGTCAAGAA 17 11 1 TTTTACTTCC 0.897143 -118 TTCCCACTTTTCAGTTACCAGCCCGGCGGTTAA 17 55 1 TATTACAGCC 0.845039 -74 AGCTCCAGCGTGTCTTAACCGCCGGGCTGGTAA 17 69 0 TTTTACCGCC 0.976735 -60 AATTCTTCGTTTTGTTACCTGCCTCTAACTTTG 18 52 1 TTTTACTGCC 0.986859 -124 AGGTTTCTCCTGTAATAGCAGCCGGTTAACCCC 26 20 1 TTATACAGCC 0.886227 -281 * * *** ***** Masking position 6 Map Score: 13.636 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 214 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 ACAATAAAGAGGTGGCTGACGATAGCGCGCCT 1 57 0 GGTGCGACGA 0.928472 -217 AATATCAATTCGTTACAGGCGATACATGGCAC 1 110 1 CGTACGGCGA 0.945378 -164 CTGTCGTTAACGAAGCAGGCGATGCCTGCTTT 1 234 0 CGAGCGGCGA 0.946424 -40 GGGGAAAATAGGTTGCGCGAGATTATAGAGAT 2 56 1 GGTGCCGAGA 0.825692 -205 ACAAATACCAGGTTAACGGAGAAGGTT 3 231 1 GGTAAGGAGA 0.654991 -17 CCGCTATCAGGGTAACGGGAGATTTACAAAAT 4 130 0 GGTACGGAGA 0.955965 -55 GTTCCATTATGGTTACAGAAGGGAAGTCCGCT 4 157 0 GGTACGAAGG 0.798342 -28 CTTGTCCACCCGTAAATGGGGGGATACCTATG 5 111 0 CGTAAGGGGG 0.597201 -58 TATGCAACGTGGTGGCAGACGAGCAAACCAGT 7 31 0 GGTGCGACGA 0.928472 -171 TTAAAAACCGCGTCGCCGGAGAATTTTTTTCT 8 47 1 CGTGCGGAGA 0.981663 -254 TAAAAAATAATGTGGCCGACGATCTGTCGGCC 12 25 0 TGTGCGACGA 0.666641 -142 AGTATATACGTGAGGCAGGGGGAGCGCACCTG 12 113 0 TGAGCGGGGG 0.773113 -54 TGGTCACCTGCGCAGCAGGGGGCATCCGCCGG 13 233 1 CGCGCGGGGG 0.886303 -44 GTAGCGTTCACGTAACTGGAGGAATGAA 18 158 1 CGTACGGAGG 0.943304 -18 ATAAGCAACAGGACGCAGGAGTATAAAAA 21 133 1 GGAGCGGAGT 0.832344 -19 GTTTTGTTGGCCGGAGGCGCAGCTTTC 23 6 1 GTTGCGGAGG 0.757917 -55 AACCCATTCAGGTAGCCGGGGTTAACCGGCTG 26 38 0 GGTGCGGGGT 0.939842 -263 GGTATTCGGTCGATGCAGGGGATAATCGTCGG 26 249 1 CGAGCGGGGA 0.946424 -52 *** ** ***** Masking position 11 Map Score: 12.513 Number of sites scoring better than the average of aligned sites = 2157 Number in coding regions = 2051 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 5 GTGAAATACTGGTTTTTAGTGCGCCAGATCT 2 84 0 GGTTTTTGTG 0.841128 -177 AATTTTTAGCGGGTTTTATTGAATGTTTATA 3 53 0 GGGTTTTTTG 0.948048 -195 CTGCTTTGCGGCATTTTTTTAAACAAGCAAA 3 189 1 GCATTTTTTA 0.811878 -59 CCGTTAACCTGGTATTTGTTGCTTGTTGTGT 3 219 0 GGTATTTTTG 0.867757 -29 AGTAATAGTTGGAATTTTGTAAATCTCCCGT 4 117 1 GGAATTTGTA 0.733676 -68 ATGCTTTAGAGCAATTTTTTGTTAATGATTT 7 86 1 GCAATTTTTG 0.797987 -116 TTTTTTCTTTGCGATTTCTTATTATCAGAGT 8 71 1 GCGATTTTTA 0.727282 -230 AATAACATTAGGATTTTGTTATTTAAACACG 11 205 1 GGATTTTTTA 0.913011 -96 CTGCTGGGATTTGGTGTACCGAGACG 19 6 1 GGGATTTGTG 0.827279 -295 TTTCTGCTTAGGATTTTGTTATTTAAATTAA 20 115 1 GGATTTTTTA 0.913011 -96 AGGATTTTCTTATGCGGATTGA 21 2 1 GGATTTTTTA 0.913011 -150 AGTGAGTTAGGCTTTTTATTGAATGATTATT 21 73 1 GCTTTTTTTG 0.825499 -79 CATGTGTGTCGGTTTTTGTTGCTTAATCATA 21 105 1 GGTTTTTTTG 0.920031 -47 TACGGCTGGTGGGTTTTATTACGCTCAACGT 22 77 0 GGGTTTTTTA 0.919167 -77 ******* *** Masking position 6 Map Score: 10.1718 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 164 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 6 TTTAGTGTCTACTCATCTGACGGCATTTGCGTCA 1 166 0 ATCACTCGGC 0.940674 -108 ACAGAAGGGAAGTCCGCTATCAGGGTAACGGGAG 4 141 0 ATCCCTCAGG 0.679882 -44 TGAAAATATTATTCAACATGCGGCTTTTTTATGG 8 212 0 ATCACACGGC 0.924111 -89 TACGTCGACGAATCCTCTTCCCGCTGTTTCGCCC 12 55 1 ATCCCTCCGC 0.958462 -112 TATCAGGTGCGCTCCCCCTGCCTCACGTATATAC 12 110 1 GTCCCCCCTC 0.73734 -57 AAAATTTGTCGTTCCGCCATCGGCTAATCGCATT 13 16 0 GTCCCCCGGC 0.988949 -261 CAGCAGGGGGCATCCGCCGGCAGCTAAGTTAAGG 13 245 1 CTCCCCCAGC 0.930374 -32 GATAGATAATGATCCGTCTACAGCATGACAAACA 14 30 0 GTCCTCCAGC 0.7412 -271 CTGCCTGAAGAGTAACCCAACGGCCTTTTTATTT 14 120 1 ATAACCCGGC 0.739759 -181 TTCACCACCTAATCCTCCACCAGCCAGTAACTTC 14 152 1 ATCCCCCAGC 0.984633 -149 AAATAGAATGAATCATCAATCCGCATAAGAAAAT 21 14 0 ATCACACCGC 0.862552 -138 AACGTAAAACATTCACCTTACGGCTGGTGGGTTT 22 92 0 ATCACTCGGC 0.940674 -62 ATGCCGGAAAGCTGCGCCTCCGGCCAACAAAAC 23 10 0 GTGCCCCGGC 0.897285 -51 TTACGGTAGAAATCCTCAAGCAGCATATGATCTC 26 214 1 ATCCCACAGC 0.947586 -87 * *** ** **** Masking position 3 Map Score: 9.23917 Number of sites scoring better than the average of aligned sites = 871 Number in coding regions = 834 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 GTAAACAATAAAGAGGTGGCTGACGATAGCGCGC 1 59 0 AGGTGGCGAC 0.953223 -215 CCGTAGATAAACAGGCTGGGACACTTCAC 2 6 0 AACTGGGCAC 0.761677 -255 CGAGATTATAGAGATCTGGCGCACTAAAAACCAG 2 73 1 GGCTGGCCAC 0.981504 -188 GCGTCTTTTTACGCACTGCCTCTCCCTGACGCGG 2 123 1 AGCTGCCCTC 0.675766 -138 TTCACCGCCAAATCGCTTGCGCACAGTGCTGCTT 3 161 1 ATCTTGCCAC 0.584129 -87 CGCATATGCAACGTGGTGGCAGACGAGCAAACCA 7 33 0 AGGTGGCGAC 0.953223 -169 TTCAGAAGCGGATTAGTGGCACTCTGATAATAAG 8 88 0 GTGTGGCCTC 0.677162 -213 CTTTTTTATGGTGAGCTGGCTCACATCTCCCTGA 8 189 0 GGCTGGCCAC 0.969548 -112 GTCTTGTACTGAGTGGCCGACAGATCGTCGG 12 8 1 ATGTGGCGAC 0.882171 -159 GACGTAAAAAATAATGTGGCCGACGATCTGTCGG 12 27 0 AAGTGGCGAC 0.90219 -140 CCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGC 13 134 0 AACTGGCCGC 0.826862 -143 ATTATACTGGAAATTCTGCCGCACCGTAAGAGCC 13 152 0 AACTGCCCAC 0.844619 -125 TTAGTTATTCATTTCCTGTCTCACTTTGCCTTAA 15 152 1 ATCTGTCCAC 0.617967 -79 TTGACAAAATGTGGCGTGGATCACTATAATGCCT 19 52 0 GGGTGGACAC 0.845373 -249 CCCTGACGATACGTTCTGGAGGACAC 24 3 0 AGCTGGAGAC 0.848091 -80 GATTTCTACCGTAATCTGGATCACTTTAAGTGTC 26 194 0 GACTGGACAC 0.803095 -107 * * ***** *** Masking position 7 Map Score: 8.63176 Number of sites scoring better than the average of aligned sites = 1227 Number in coding regions = 1165 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 8 TGACTGGATACTGCCTTCACGCAAAGCCACACGG 1 23 0 CTGCTCAGAA 0.984245 -251 GTTTACCGAGCAGCGTTCAGAGAAATATCAATTC 1 87 1 CAGCTCAAAA 0.894643 -187 CAGGCGATGCCTGCTTTGAGGAAATTCTCACGCA 1 217 0 CTGCTGAGAA 0.931357 -57 GAAGGGAAGTCCGCTATCAGGGTAACGGGAGATT 4 138 0 CCGCTCAGTA 0.938746 -47 TACCTGGCATCTGCAATCAGACAAGCAGAATTCG 5 76 0 CTGCTCAAAA 0.95867 -93 ACCCTATTGTTTGCCGTCATGAAAGATGCGCGTT 7 137 1 TTGCTCAGAA 0.93305 -65 CGCTCACTTGCCGCCTTGATGCAACTTGAATGAT 9 66 0 CCGCTGAGAA 0.936302 -209 AAGGTGTTGCCCGAACTCATAAAAATTAACAAAA 13 46 0 CCGATCAAAA 0.777363 -231 AATTATCCTGAAATCAAGCTAACGAAATATC 17 108 0 CTGATCAGTA 0.662775 -21 GGATAATGCGTAGCGTTCACGTAACTGGAGGAAT 18 149 1 TAGCTCAGAA 0.836103 -27 GCCTGGATTTCCGCTCTCACTGAATTTTTATGCA 19 244 0 CCGCTCATAA 0.884235 -57 TACTTTTTTATTGCCTTCAAATAAATTTAAGGAG 20 181 1 TTGCTCAAAA 0.836612 -30 **** *** * ** Masking position 9 Map Score: 5.05982 Number of sites scoring better than the average of aligned sites = 571 Number in coding regions = 524 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 9 ACCTCTTTATTGTTTACCGAGCAGCGTTCAG 1 76 1 TGTTTCCGAG 0.770809 -198 TGTCCCAGCCTGTTTATCTACGGCTTAAAAA 2 17 1 TGTTTTCTAC 0.628897 -244 CAAGTGTTTATTTTTTCCGACTATTAACAGA 5 139 1 TTTTTCCGAC 0.905145 -30 ACTACCCTATTGTTTGCCGTCATGAAAGATG 7 134 1 TGTTTCCGTC 0.962925 -68 TATGACTCCTGTTTCACGTCTATCAGATAT 9 255 0 TGTTTACGTC 0.955571 -20 GGCCACATTATTTTTTACGTCGACGAATCCT 12 40 1 TTTTTACGTC 0.887665 -127 GTAACTTCTCTTTTTCTCGCCGCCCTGCGTC 14 178 1 TTTTTTCGCC 0.742886 -123 CATTTACTGTTTTTTATCGACCAGATAATCT 15 87 1 TTTTTTCGAC 0.887665 -144 CGTTGTAAATTGTTTAACGTCAAATTTCCCA 18 106 1 TGTTTACGTC 0.955571 -70 GTAAGGTGAATGTTTTACGTTTAACCTGGCA 22 105 1 TGTTTACGTT 0.652666 -49 TGGTTTCGAATGTTTTTCGACCGACGATTAT 26 270 0 TGTTTTCGAC 0.955571 -31 ***** ***** Masking position 5 Map Score: 5.03563 Number of sites scoring better than the average of aligned sites = 397 Number in coding regions = 373 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 10 ACCTGGTATTTGTTGCTTGTTGTGTTTGCTT 3 213 0 TGTTGCTTTT 0.888251 -35 CGAAATCTTTCGCTGCATTTGCGAATTCTGC 5 55 1 CGCTGCATTG 0.834963 -114 TCTGCCACCACGTTGCATATGCGTTTGCGTC 7 44 1 CGTTGCATTG 0.911896 -158 CCCCCTAACCTGTTGCTTTAGTTATTCATTT 15 135 1 TGTTGCTTAG 0.954904 -96 GTTACTAATTTGTTGCTTTTGATCACAATAA 15 201 1 TGTTGCTTTG 0.975826 -30 ATTGAATGATTATTGCATGTGTGTCGGTTTT 21 90 1 TATTGCATTG 0.674887 -62 TGTCGGTTTTTGTTGCTTAATCATAAGCAAC 21 111 1 TGTTGCTTAT 0.806561 -41 TCCTGCGTCCTGTTGCTTATGATTAAGCAAC 21 122 0 TGTTGCTTTG 0.975826 -30 CGAGATCATATGCTGCTTGAGGATTTCTACC 26 218 0 TGCTGCTTAG 0.911896 -83 ******** ** Masking position 4 Map Score: 4.29992 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 241 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 11 TTGCGTACCGCGCCGAAGCGTGCCATGTAT 1 131 0 CGCCGAAGCG 0.875395 -143 TACTGTTTTGCGGGTGATCGACAAGGAGAC 2 236 1 CGGGTGATCG 0.963202 -25 AAAAATTCTCCGGCGACGCGGTTTTTAACA 8 45 0 CGGCGACGCG 0.928683 -256 TTCTGTAAGCCGGGTAAGCGCAATGCGCCC 9 19 1 CGGGTAAGCG 0.97117 -256 GTAAGTGATTCGGGGGAGCGAACGCAGCCA 9 121 1 CGGGGGAGCG 0.985133 -154 TGACTCTTCACGGTTAATCGGAAA 10 5 0 CGGTTAATCG 0.824549 -33 TACGTGAGGCAGGGGGAGCGCACCTGATAC 12 109 0 AGGGGGAGCG 0.866902 -58 GTTCCGCCATCGGCTAATCGCATTAAGGT 13 10 0 CGGCTAATCG 0.95106 -267 CATATGATCTCGGGTATTCGGTCGATGCAG 26 237 1 CGGGTATTCG 0.850455 -64 ********** Masking position 9 Map Score: 5.66355 Number of sites scoring better than the average of aligned sites = 465 Number in coding regions = 431 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 12 AGGCGATGCCTGCTTTGAGGAAATTCTCACG 1 219 0 TGCTTGAGGA 0.829023 -55 CCTGCAATACTGTTTTGCGGGTGATCGACAA 2 229 1 TGTTTGCGGG 0.831814 -32 CGCACAGTGCTGCTTTGCGGCATTTTTTTAA 3 180 1 TGCTTGCGGC 0.983756 -68 GTTTGCGTCCTGCGATACGGATGCTTTAGAG 7 66 1 TGCGTACGGA 0.853643 -136 GTTATTAGGCTATAATGCGGCAATTCATAAT 7 168 1 TATATGCGGC 0.640094 -34 ACATCTCCCTGACTCTGCGGCAATATGGCGT 8 170 0 GACTTGCGGC 0.778271 -131 GCGCACCTGATACTATGCGGATAAGGAAATA 12 91 0 TACTTGCGGA 0.964352 -76 GCCAGGCTCTTACGGTGCGGCAGAATTTCCA 13 148 1 TACGTGCGGC 0.933057 -129 CAAAAACAGATGCGTTACGGA 14 1 0 TGCGTACGGA 0.853203 -300 CATAGCATCATGTTGTGCGGATAAACACCTG 14 244 0 TGTTTGCGGA 0.95489 -57 CACAACATGATGCTATGCTGACCAAACCATG 14 258 1 TGCTTGCTGA 0.829075 -43 ATGCCTTGCTTCCATTGCGGATAAATCCTAC 20 153 1 TCCATGCGGA 0.861232 -58 AGGATTTTCTTATGCGGATTGATGATTC 21 8 1 TCTTTGCGGA 0.865723 -144 **** ****** Masking position 6 Map Score: 6.7285 Number of sites scoring better than the average of aligned sites = 708 Number in coding regions = 666 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 13 TATAATCTCGCGCAACCTATTTTCCCCTCGAACA 2 49 0 CGCACATTTC 0.977999 -212 CACATGAGTCCGCGTCTTTTTACGCACTGCCTCT 2 112 1 CGCTCTTTCG 0.822939 -149 CAATAAAACCCGCTAAAAATTATCGATTCATCAA 3 63 1 CGCAAATTTC 0.884853 -185 CCCGCTGTTTCGCCCCATATTTCCTTATCCGCAT 12 74 1 CGCCCATTCC 0.852317 -93 TCCGTAACGCATCTGTTTTTGTTTGTCATGC 14 8 1 CGCTCTTTTG 0.904839 -293 GTTACGTGAACGCTACGCATTATCCCTTAGCTCT 18 140 0 CGCACATTTC 0.977999 -36 TAGTGATCCACGCCACATTTTGTCAACGTTTATT 19 60 1 CGCACTTTTC 0.977998 -241 CCAGCGCAAAGGTTTCTCCTGTAATAGC 26 5 1 CGCAATTTTC 0.884839 -296 AAACGCGATTCGCAACCCATTCAGGTAGCCGGGG 26 49 0 CGCACATTAG 0.843557 -252 AAGATGTTTGCGCAACTATTTTTGGTAGTAATCC 26 113 1 CGCACTTTTG 0.967785 -188 *** ** *** ** Masking position 10 Map Score: 4.73075 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 183 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 14 GTTTTTAGTGCGCCAGATCTCTATAATCTCG 2 73 0 CGCCAATCTC 0.94084 -188 ATTTTACGGGGGCCAAATTGCTGACAAAGTG 3 23 0 GGCCAATTGC 0.962255 -225 ATTTTTTCACCGCCAAATCGCTTGCGCACAG 3 156 1 CGCCAATCGC 0.962198 -92 TTTTGCAAGACGTGAGATTGCTCTGGAAGGT 4 68 0 CGTGAATTGC 0.777007 -117 ATACTAAAGACGCCATATTGCCGCAGAGTCA 8 161 1 CGCCAATTGC 0.986567 -140 CGCTGTTTCGCCCCATATTTCCTTATCCGCA 12 76 1 CCCCAATTTC 0.829928 -91 TCAGACTCTACGCCAGTTTGCTATAAAGGTG 13 74 0 CGCCATTTGC 0.963116 -203 GTATAATAGCCGCCTTTTTTCATTCAGTTGT 13 179 1 CGCCTTTTTC 0.653935 -98 GTTTACTAACGGTCATTTTGCAGTGAAGCCA 15 58 1 GGTCATTTGC 0.666763 -173 TGGAGCTGGTGGCGATATTTCGTTAGCTTGA 17 95 1 GGCGAATTTC 0.773921 -34 AATTGTTTAACGTCAAATTTCCCATACAGAG 18 113 1 CGTCAATTTC 0.91015 -63 TAGTGATCCACGCCACATTTTGTCAACGTTT 19 60 1 CGCCAATTTT 0.767035 -241 ***** ***** Masking position 8 Map Score: 7.88517 Number of sites scoring better than the average of aligned sites = 914 Number in coding regions = 852 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 15 TTTGCGTCAGCAGTTTGCGTACCGCGCCGA 1 145 0 CAGTTTGCGT 0.913132 -129 TCATCTGACGGCATTTGCGTCAGCAGTTTG 1 158 0 GCATTTGCGT 0.903834 -116 GTTGCTTGTTGTGTTTGCTTGTTTAAAAAA 3 203 0 GTGTTTGCTT 0.86889 -45 ATCTTTCGCTGCATTTGCGAATTCTGCTTG 5 59 1 GCATTTGCGA 0.748113 -110 CGTTGCATATGCGTTTGCGTCCTGCGATAC 7 54 1 GCGTTTGCGT 0.979478 -148 GACTCTACGCCAGTTTGCTATAAAGGTGTT 13 72 0 CAGTTTGCTA 0.628352 -205 AGGTAAAATACCGTATGCGT 17 1 0 CCGTATGCGT 0.85864 -128 TCCTTGATAAGTGTTTGCTTTAATTACCTA 25 27 0 GTGTTTGCTT 0.86889 -26 TTCAAAATCACCGTTTGCTTAAAAATGGAT 27 82 0 CCGTTTGCTT 0.951486 -22 ********** Masking position 6 Map Score: 3.66004 Number of sites scoring better than the average of aligned sites = 555 Number in coding regions = 504 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331