AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00240_ecoli_reg_100.orf -o00240_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 Purged sequences: BIME6 21 BIME Input sequences: #1 polB 74 DNA polymerase II #2 araB 300 L-ribulokinase #3 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #4 dnaE 36 DNA polymerase III, alpha subunit #5 dnaQ 64 DNA polymerase III, epsilon subunit #6 codB 152 cytosine permease/transport #7 dnaX 128 DNA polymerase III, tau and gamma subunits; DNA elongation factor III #8 ushA 217 UDP-sugar hydrolase (5'-nucleotidase) #9 leuS 234 leucine tRNA synthetase #10 trxB 300 thioredoxin reductase #11 cmk 172 cytidylate kinase #12 pyrD 110 dihydro-orotate dehydrogenase #13 pyrC 105 dihydro-orotase #14 pabC 119 4-amino-4-deoxychorismate lyase #15 tdk 300 thymidine kinase #16 pyrF 193 orotidine-5'-phosphate decarboxylase #17 holE 138 DNA polymerase III, theta subunit #18 dcd 91 2'-deoxycytidine 5'-triphosphate deaminase #19 udk 263 uridine/cytidine kinase #20 cdd 129 cytidine/deoxycytidine deaminase #21 rsuA 148 16S pseudouridylate 516 synthase #22 nrdA 300 ribonucleoside diphosphate reductase 1, alpha subunit, B1 #23 nrdB 21 ribonucleoside-diphosphate reductase 1, beta subunit, B2 #24 usg 65 putative PTS system enzyme II A component #25 pdxB 98 erythronate-4-phosphate dehyrogenase #26 upp 297 uracil phosphoribosyltransferase #27 ndk 148 nucleoside diphosphate kinase #28 nrdH 247 glutaredoxin-like protein; hydrogen donor #29 pyrG 227 CTP synthetase #30 lgt 150 phosphatidylglycerol-prolipoprotein diacylglyceryl transferase; a major membrane phospholipid #31 pnp 177 polynucleotide phosphorylase; cytidylate kinase activity #32 rpoA 25 RNA polymerase, alpha subunit #33 rpsD 33 30S ribosomal subunit protein S4 #34 rpsM 146 30S ribosomal subunit protein S13 #35 rpoH 244 RNA polymerase, sigma(32) factor; regulation of proteins induced at high temperatures #36 dfp 93 flavoprotein affecting synthesis of DNA and pantothenate metabolism #37 pyrE 94 orotate phosphoribosyltransferase #38 rph 126 RNase PH #39 gmk 251 guanylate kinase #40 rpoZ 54 RNA polymerase, omega subunit #41 dnaA 300 DNA biosynthesis; initiation of chromosome replication; can be transcription regulator #42 udp 298 uridine phosphorylase #43 polA 300 DNA polymerase I, 3' --> 5' polymerase, 5' --> 3' and 3' --> 5' exonuclease #44 rpoB 300 RNA polymerase, beta subunit #45 rpoC 76 RNA polymerase, beta prime subunit #46 cpdB 189 2':3'-cyclic-nucleotide 2'-phosphodiesterase #47 nrdD 300 anaerobic ribonucleoside-triphosphate reductase #48 holC 52 DNA polymerase III, chi subunit #49 BIME233 22 BIME #50 pepA 266 aminopeptidase A/I #51 holD 102 DNA polymerase III, psi subunit #52 deoC 257 2-deoxyribose-5-phosphate aldolase #53 deoA 83 thymidine phosphorylase #54 deoB 51 phosphopentomutase #55 deoD 56 purine-nucleoside phosphorylase Motif number 1 ATGAATGAGTGCAAAAAGGTGGGGGAAAAATT 6 30 0 GCAAAAAGGG 0.94516 -123 GTTTCAAACAGCAAAAAGGGGGAATTTC 6 135 1 GCAAAAAGGG 0.94516 -18 AACAGGTTCGGAAAACGTTTGCGTTTTTTTT 12 10 1 GGAAAACGTG 0.715979 -101 TTCGTGCAAAGGAAAACGTTTCCGCTTATCCT 13 40 1 GGAAAACGTC 0.802366 -66 TTTGTGTCCGGCAAAAACATCCCTTCAGCCGG 13 71 1 GCAAAAACAC 0.663289 -35 TAAAAGCTAAGAAAAAAGGCCCGCAAGCGGAC 14 37 0 GAAAAAAGGC 0.834223 -83 ATCCCTCAAGGGAAAAAGATCCATGGCATACT 21 41 0 GGAAAAAGAC 0.917295 -108 AACTCAGGAAGGAAAAAGTGGCTTTCGCGCAC 22 119 0 GGAAAAAGTC 0.851905 -182 GAAAAGACGTGCAAAAAGGTTGTGTAAAGCAG 26 92 0 GCAAAAAGGG 0.94516 -206 GATTCACCAGGCAAAAAGAAACCCCGAAGACA 28 52 0 GCAAAAAGAC 0.94524 -196 AGATGTAGTTGAAAAAAGATTCAACCACACAA 28 148 0 GAAAAAAGAC 0.757836 -100 CCGTCAGCTTGAAAAAAGGGGCCACTCAGGCC 31 34 0 GAAAAAAGGC 0.834223 -144 CAACAAACCTGGAAAACGAGGCG 33 2 0 GGAAAACGAC 0.88672 -32 AAGCCGAGTGGCAAAAACGGAGTCTGCGAGGA 39 55 1 GCAAAAACGG 0.662945 -197 AAGCAGCTACGCAAAACGCAACAACTTTGCGC 39 135 1 GCAAAACGCC 0.740014 -117 ACAACTTTGCGCAAAAAGTGTGAGCAAGGGCT 39 155 1 GCAAAAAGTG 0.847536 -97 TCAAGATCCTGCAAAACGATCGGGACCGCGGA 41 153 0 GCAAAACGAG 0.883238 -148 GTCAGAAGAAGCAAAAAGACACTTTACCGAAG 42 251 0 GCAAAAAGAC 0.94524 -48 GCCTTACAGCGCAAAAAGGCTGGTGACTAAAA 44 42 0 GCAAAAAGGG 0.94516 -259 TTTGTTGACCGGAAAATGGAACACTTTCCGCA 44 212 0 GGAAAATGGC 0.620157 -89 GGAAAGCACCGGAAAACGAAACGAAAAAACCG 47 223 1 GGAAAACGAC 0.88672 -78 ********* * Masking position 6 Map Score: 23.3888 Number of sites scoring better than the average of aligned sites = 487 Number in coding regions = 423 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 2 TGTGCATTCAGCCTCGCCGTTCTGACGGGG 7 54 1 GCCTCGCCGT 0.877275 -75 GCGCGTATAATGCGCGCGGTTATGTTAACG 11 128 1 TGCGCGCGGT 0.940261 -45 CGAGGGCGCATTCGCGCCCTTTATTTTTCG 13 14 1 TTCGCGCCCT 0.735919 -92 GCAGGCTTTTTCTGCGCCGTCGTTGCCGGA 16 69 0 TCTGCGCCGT 0.722874 -125 ACGGGTAGAATGCTCGCCGTTTACCTGTTT 16 135 1 TGCTCGCCGT 0.927313 -59 GTTTACCTGTTTCGCGCCACTTCCGGTGCC 16 153 1 TTCGCGCCAC 0.841796 -41 ATTAACTCTGAGCGCGCGGCAACGCTATTC 19 204 1 AGCGCGCGGC 0.579823 -60 ACATCAAAAATGCGCGACGCATCGCAAATT 20 11 0 TGCGCGACGC 0.833316 -119 GTGTGCCATAATCTCGCGGCCAGGCATACT 25 40 0 ATCTCGCGGC 0.63264 -59 CTTTTCCCCAGGCGCGCGGCGAAAGAAGAC 26 118 1 GGCGCGCGGC 0.558806 -180 CTCATTATAATCCGCGCCATCTCGTACGCT 27 92 1 TCCGCGCCAT 0.838664 -57 GACGCGTATCATCGCGCCGTATCTTCATTT 28 210 1 ATCGCGCCGT 0.90398 -38 GCGATTGAAATGCGCGCCGCAGGTTTCAGG 30 91 0 TGCGCGCCGC 0.988635 -60 GTTGCAGAGGTTCGCGCGGCTAATGAGAGG 31 113 1 TTCGCGCGGC 0.895605 -65 ACGTCACATGGCCGCGCCGTGTATAATAAG 39 187 1 GCCGCGCCGT 0.827692 -65 AATCGTGCCCGCCTCGCGGCAGGATCGTTT 41 37 1 GCCTCGCGGC 0.55268 -264 ********** Masking position 5 Map Score: 17.0468 Number of sites scoring better than the average of aligned sites = 1932 Number in coding regions = 1849 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 3 CCGCTAATCTTATGGATAAAAATGCTATGG 2 209 0 TATGGATAAA 0.819255 -92 GACCAGGTCTTGCGGATAAAGCGGTA 19 7 0 TGCGGATAAA 0.850587 -257 TGCATAACTTTGTGGATAACTCAGGAAGGA 22 138 0 TGTGGATAAC 0.951694 -163 CCCAGCTCTATGTGGGTAAAGCCTCTCATT 31 134 0 TGTGGGTAAA 0.947255 -44 AATGCAAGCTTGTGAATAAATTACGCACAA 35 105 0 TGTGAATAAA 0.719924 -140 GCATTGAACTTGTGGATAAAATCACGGTCT 35 130 1 TGTGGATAAA 0.975016 -115 TGGAAAGTCCTGTGGATAAATCGGGAAAAT 41 82 1 TGTGGATAAA 0.975016 -219 CATCACTTTTGGTGGGTAAATTTATGCAAC 42 177 1 GGTGGGTAAA 0.72374 -122 TTTTTTCTAATGTGGATAGATATGAATTAT 43 27 0 TGTGGATAGA 0.850587 -274 TGGATAACTTTGTGCATAAATTATTTACAT 43 156 0 TGTGCATAAA 0.792088 -145 CAAATCGTCATGTGGATAACTTTGTGCATA 43 168 0 TGTGGATAAC 0.951694 -133 TTTATCAGATTATGGGTAAAGGATGCCACA 43 267 0 TATGGGTAAA 0.675943 -34 GGTGCGGCGTTGTGGATAAGCGGATGGCGA 47 189 1 TGTGGATAAG 0.88023 -112 TCCCAATTTCTGTGGATAACCTGTTCTTAA 47 266 1 TGTGGATAAC 0.951694 -35 ********** Masking position 8 Map Score: 14.2658 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 29 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 4 AATAACACGGCCTGCCGCAATCGTAAGAAT 3 50 0 CCTGCCGCAA 0.971168 -55 AGCCCGCTATAATTGCGCAATAAATCCCCA 11 43 1 AATTGCGCAA 0.628754 -130 AGGGAATTGACCTGCGGCAAAAAAAACGCA 12 30 0 CCTGCGGCAA 0.738548 -81 GAGGGCTATTACTTGCGCAACAGGTTAAAG 15 83 1 ACTTGCGCAA 0.837863 -218 AAGGCGGATAATTTGCGCAACTGCGTTTAA 19 113 1 ATTTGCGCAA 0.763518 -151 TTTTGGAATTCTTTCCGCAATAGTTTCATG 22 266 0 CTTTCCGCAA 0.950981 -35 TGCGAGACTGCTTTACACAACCTTTTTGCA 26 85 1 CTTTACACAA 0.405641 -213 TAACCTTTACCCTGGCACAAGTCTTCTTTC 26 138 0 CCTGGCACAA 0.783344 -160 AACGCAACAACTTTGCGCAAAAAGTGTGAG 39 149 1 CTTTGCGCAA 0.950981 -103 TGTAAACGATCCTGCCGCGAGGCGGGCACG 41 40 0 CCTGCCGCGA 0.820474 -261 CTATAGTTAACATTGCGCAACATTTTTATA 42 65 0 CATTGCGCAA 0.910527 -234 TACTCATCACCATGACGCAAATGCGTTGCA 42 201 0 CATGACGCAA 0.783461 -98 AAATGGAACACTTTCCGCAATGCCTGTTGC 44 201 0 CTTTCCGCAA 0.950981 -100 TTTTCCGGTGCTTTCCGCAATCGCCATCCG 47 209 0 CTTTCCGCAA 0.950981 -92 AACAGCCTTGCCTGACGCAA 49 1 0 CCTGACGCAA 0.916941 -22 ********** Masking position 10 Map Score: 11.3039 Number of sites scoring better than the average of aligned sites = 464 Number in coding regions = 409 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 5 TTCAACACGTTGAAATCAGGTCAGGGAGAG 8 194 1 TGAAATCAGG 0.955003 -24 GTAGCCGTATTGAAAACAGGACCACTGGCT 9 212 1 TGAAAACAGG 0.97383 -23 CTTTATCTCCTTAAAACAGGCGTACCGTTA 11 153 0 TTAAAACAGG 0.812097 -20 ATAAAAGCTAAGAAAAAAGGCCCGCAAGCG 14 40 0 AGAAAAAAGG 0.643713 -80 AGCGCACTATTGAAATCAGGAGTGAGAAAA 29 99 0 TGAAATCAGG 0.955003 -129 GCCGTCAGCTTGAAAAAAGGGGCCACTCAG 31 37 0 TGAAAAAAGG 0.812097 -141 TTGAGTATCCTGAAAACGGGCTTTTCAGCA 34 94 1 TGAAAACGGG 0.949457 -53 TACCGGGAAGAGACAACGGGGTCTCTTTCC 35 55 0 AGACAACGGG 0.695069 -190 TTTCCAGGATTGAAAACTGGCCGTCGATTT 36 51 0 TGAAAACTGG 0.825422 -43 GGCATGATACTGAAATCAGGT 40 2 0 TGAAATCAGG 0.955003 -53 AGTCCTGTGGATAAATCGGGAAAATCTGTG 41 87 1 ATAAATCGGG 0.342196 -214 ACAGACAGGATGAAAACATGAGTTTTTCAC 43 240 0 TGAAAACATG 0.693733 -61 GCCTGAGAAATCAGGCTGATGGCTG 44 6 1 AGAAATCAGG 0.898707 -295 TTTGCGCCCCTGACAACAGGAGCGATTCGC 51 82 1 TGACAACAGG 0.915262 -21 ********** Masking position 5 Map Score: 11.7008 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 190 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 6 CACTGCGTCTTTTACTGGCTCTTCTCGCTAACC 2 37 1 TTTCGGTCTT 0.906625 -264 ATCGCAACTCTCTACTGTTTCTCCATACCCGTT 2 258 1 TCTCGTTCTC 0.747109 -43 GAAAGTCACTTTTTCAGGGTTGCGATGTAAAGA 8 13 1 TTTCGGTTGC 0.883257 -205 CGTTTCATCTCCCGGGTCGTTAACTGACTA 9 8 1 TCTCGGTCGT 0.955815 -227 GAACTCTCCTGGATTCCCGGTGTGCAA 12 94 0 TCTCGGTTCC 0.767879 -17 TCTCTTCTTCATGCTCTCTGCTGTAACA 24 6 1 TCTCTGTCTC 0.61118 -60 CCGAAGCCTGTCTTCGGGGTTTCTTTTTGCCTG 28 44 1 TCTCGGTTTC 0.946139 -204 CGCCTCGTTTTCCAGGTTTGTTGGAGAAAGA 33 9 1 TTTCGGTTGT 0.840542 -25 TCAATCGATATCTTCTGGCGCTTCAGTGGTAGC 35 212 0 TCTCGGGCTT 0.846487 -33 GCGCAAGAGATCTTCTGTTTCTCACAGATTTTC 41 106 0 TCTCGTTCTC 0.747109 -195 TCCCGATCGTTTTGCAGGATCTTGACTCGGGCA 41 160 1 TTTCGGTCTT 0.906625 -141 CACCCTTCATTCTGCAGGACTGCATAAAAGATG 42 130 0 TCTCGGCTGC 0.700126 -169 CTTTTGTAGATCTTCTGGATCGCTCGCAAATCG 43 191 0 TCTCGGTCGC 0.968798 -110 TTTCGTTTCGTTTTCCGGTGCTTTCCGCAATCG 47 216 0 TTTCGGGCTT 0.70798 -85 GGGAAAGGCGTTTTCCGGTTTTTTCGTTTCGTT 47 237 0 TTTCGGTTTT 0.843288 -64 AAACTCGTCTTTTGCAGGATTTTAGCTTGTTTC 50 28 1 TTTCGGTTTT 0.843288 -239 TTCATTCTCCTGGCTTGTCGCCAATAAA 52 240 0 TCTCGGTTGT 0.923011 -18 *** * ** **** Masking position 3 Map Score: 11.5994 Number of sites scoring better than the average of aligned sites = 380 Number in coding regions = 353 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 GTTACAGAATGCTTTTAATAAGCGGGGTTACCGGT 2 72 0 GCTTATAGCG 0.965388 -229 TGGCAGGCTCTGAAACGCTGGAAGGTGGAT 7 109 0 GGTTAACGCG 0.779981 -20 CTTAAATTTCCCGCTTTATAAGCCGATTAAATGAT 10 128 0 CCCTATAGCG 0.761574 -173 TGGCGTCGGCGCGTATAATGCGCGCGGTTATGTTA 11 120 1 GCTTATCGCC 0.937738 -53 GTCCGAACTCGCACATAATACGCCCCCGGTTTGCA 12 64 1 GCCTATCGCC 0.845689 -47 CAACTGCCTCGCTTGTTATAAGCGGGTAAATGACT 15 132 0 GCTTATAGCG 0.965394 -169 CCCCTGGCAGGCTTTTTCTGCGCCGTCGTTGCCGG 16 70 0 GCTTCTCGCG 0.929846 -124 TCTTAATCTCCTCATCATTCGCGGGCAAAAGTTA 17 115 0 CCCTATCGCG 0.923522 -24 AAGATCCATGGCATACTATTAGCAGAATAATCTAC 21 23 0 GCTCATAGCG 0.768611 -126 ATAATCCGCGCCATCTCGTACGCTGGTACAGACAA 27 98 1 CCTTGTCGCG 0.808078 -51 CCTGCGGCGCGCATTTCAATCGCTGTTCTCTTTCA 30 98 1 GCTTAACGCG 0.940368 -53 TGTGGGTAAAGCCTCTCATTAGCCGCGCGAACCTC 31 119 0 GCTTATAGCG 0.965402 -59 AGAGCAACGAGGTTATCATTCACTGTTTTATCAGA 35 157 0 GGTTATCACG 0.770596 -88 CGCCGGAAGTCCGTATAATGCGCAGCCACATTTGT 38 82 1 CCTTATCGCG 0.97076 -45 TTCCGCATTTGCCTGTCATTCACTGCAATAAAGAC 39 102 0 GCTTATCACG 0.937274 -150 CTACATACGAGCTTATTATACACGGCGCGGCCATG 39 193 0 GCTTATCACG 0.937273 -59 GCGCAGTTTAGGCTATGATCCGCGGTCCCGATCGT 41 135 1 GGTTATCGCG 0.959176 -166 ** * * ** *** * Masking position 13 Map Score: 17.4242 Number of sites scoring better than the average of aligned sites = 408 Number in coding regions = 374 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 8 GAGTTGCGATAAAAAGCGTCAGGTAGGATCCGCT 2 234 0 AAAACGCGGT 0.742383 -67 TGAAACCCAAAAAATCCGCCGCATTCTATTCATC 6 107 0 AAAACGCCAT 0.966818 -46 GATTTTTAGTACAACATGCCAGATATTCATTAAC 10 80 1 ACAATGCGAT 0.563589 -221 TAAATTCCCTACAATCCTGCCCATTGTCTGCCAA 10 261 1 ACAACTCCAT 0.66166 -40 GTAGAAAAATAAAATTCGGCGCAATTCTAACAGG 26 38 1 AAAACGCCAA 0.903423 -260 AAAAAAAATCGACGGATTATACCTCCT 26 281 0 AAAACGCGAT 0.9012 -17 CAACAGAGAGACAACCCGACGCGTATCATCGCGC 28 193 1 ACAACGCCGT 0.903661 -55 CTTGTCATTTAAAAAATGACACAAATGGCGCTTG 29 25 0 AAAATGCCAA 0.565162 -203 ACAGACAAAAAAAAGGCGACTCATCAGTCGCCTT 37 45 0 AAAACGCCAT 0.966806 -50 CAGCTCGCTGACAAGTCGACCCATCTGTCCATTG 44 268 0 ACAACGCCAT 0.967414 -33 TATAGACTTTAAAATGCGTCCCAACCCAATATGT 47 111 1 AAAACGCCAA 0.903423 -190 TAAATCCACCACAAGAAGCCCCATTT 48 37 1 ACAAAGCCAT 0.700548 -16 CGCATCCGGCAAAAGCCGCCTCATACTCTTTTCC 53 47 1 AAAACGCCAT 0.966806 -37 **** ** * *** Masking position 4 Map Score: 8.69547 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 126 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 9 GTCCATATTGCATCAGACATTGCCGTCAC 2 10 1 GCATCAGACA 0.7051 -291 GCGATAAAAAGCGTCAGGTAGGATCCGCTA 2 233 0 GCGTCAGGTA 0.934655 -68 AGACAAGTCTGCGTCCGGTGAAGATAAATC 8 142 0 GCGTCCGGTG 0.826296 -76 CTTATCCTTTGTGTCCGGCAAAAACATCCC 13 64 1 GTGTCCGGCA 0.951544 -42 GTCAGACAAGGTGTCCGGGAAAGTCAATGG 22 84 0 GTGTCCGGGA 0.790584 -217 TCTTTTAACGGTATCCGGCAACCAGCCAGG 30 28 1 GTATCCGGCA 0.924891 -123 AAGCGTGATAGCAACAGGCATTGCGGAAAG 44 191 1 GCAACAGGCA 0.793848 -110 ATTTAAATACGCATCAGGTATACACCGCAG 48 12 0 GCATCAGGTA 0.899692 -41 TTGCGTCAGGCAAGGCTGTTAT 49 3 1 GCGTCAGGCA 0.9776 -20 AGGCGTAGACGCATCCGGCAAAAGCCGCCT 53 38 1 GCATCCGGCA 0.9776 -46 ********** Masking position 5 Map Score: 5.87134 Number of sites scoring better than the average of aligned sites = 1239 Number in coding regions = 745 Number in noncoding regions = 494 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 10 ATCAGACATTGCCGTCACTGCGTCTTTTACTGGC 2 22 1 GCACTGCGTC 0.890316 -279 CTGCCAGCCCGCTATAATTGCGCAATAAATCCCC 11 38 1 GCATTGCGCA 0.885807 -135 ATAACCGCGCGCATTATACGCGCCGACGCCACAA 11 117 0 GCTACGCGCC 0.830631 -56 GTCCGAACTCGCACATAATACGCCCCCGGTTTGC 12 64 1 GCAATACGCC 0.562354 -47 AAAAATAAAGGGCGCGAATGCGCCCTCGTGA 13 8 0 GGAATGCGCC 0.498557 -98 TTTTTTCTTAGCTTTTATTCCGACTTGTTCCGTA 14 52 1 GCATTCCGAC 0.693645 -68 CTAAGTCCATGCTCTTATTGCGACTGTTCTACTT 15 22 0 GCATTGCGAC 0.90281 -279 CCCCTGGCAGGCTTTTTCTGCGCCGTCGTTGCCG 16 71 0 GCTCTGCGCC 0.966688 -123 ACGCAGTTGCGCAAATTATCCGCCTTTACGTCAC 19 105 0 GCTATCCGCC 0.762 -159 GAAGGAAAAAGTGGCTTTCGCGCACCTTAGGTCA 22 110 0 GTTTCGCGCA 0.217516 -191 TGCTTTCCCTGTTAGAATTGCGCCGAATTTTATT 26 45 0 GTATTGCGCC 0.914614 -253 ACGCGGTCAAGCGCCATTTGTGTCATTTTTTAAA 29 18 1 GCTTTGTGTC 0.33095 -210 AATGACAAGCGCTTGATTTGCGTCAAAAACATTT 29 50 1 GCTTTGCGTC 0.773046 -178 AATAAATTACGCACAAAATGTGACATAGAGATGA 35 87 0 GCAATGTGAC 0.409953 -158 TTCAGTGGTAGCAACAACTGTGCCAGAGCTTAAG 35 190 0 GCACTGTGCC 0.898231 -55 CCAATATGCGGCGTAAATCGTGCCCGCCTCGCGG 41 22 1 GCATCGTGCC 0.743342 -279 GCGGATCATAGCCTAAACTGCGCAAGAGATCTTC 41 124 0 GCACTGCGCA 0.898232 -177 GCTGACTATAGTTAACATTGCGCAACATTTTTAT 42 66 0 GTATTGCGCA 0.609273 -233 GCAGCGGATTGTGCTAACTCCGACGGGAGCAAAT 45 51 1 GTACTCCGAC 0.341187 -26 TAGCAAATTCGTCGATACCGCGCCAACATATGGC 51 46 0 GTACCGCGCC 0.820193 -57 CGACGAATTTGCTATATTTGCGCCCCTGACAACA 51 66 1 GCTTTGCGCC 0.962268 -37 TTTGGGCGGAGCGTTGACTCCGCCTTTGTTATGT 55 15 1 GCACTCCGCC 0.936766 -42 ** ******** Masking position 12 Map Score: 13.0649 Number of sites scoring better than the average of aligned sites = 2728 Number in coding regions = 2570 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 11 CAAACTTTACGGCCTGTCTCATTCTTACGA 3 30 1 GGCCTGTCTC 0.768523 -75 ATAATAACACGGCCTGCCGCAATCGTAAGA 3 52 0 GGCCTGCCGC 0.977788 -53 AAAGGGAATTGACCTGCGGCAAAAAAAACG 12 32 0 GACCTGCGGC 0.97465 -79 TATCATTGAGGGCCTGTGGCTG 15 289 1 GGCCTGTGGC 0.981359 -12 TGGCGACCAGGTCTTGCGGATAAAGCGGTA 19 11 0 GTCTTGCGGA 0.541129 -253 GGCGAAAGAAGACTTGTGCCAGGGTAAAGG 26 135 1 GACTTGTGCC 0.635837 -163 ACCCGAACATGACCTGTGCCACAAACTTTC 29 148 0 GACCTGTGCC 0.887758 -80 GAGCGCCTGAAACCTGCGGCGCGCATTTCA 30 86 1 AACCTGCGGC 0.842322 -65 AGTGTAAACGATCCTGCCGCGAGGCGGGCA 41 42 0 ATCCTGCCGC 0.794072 -259 GTTCTGGAAAGTCCTGTGGATAAATCGGGA 41 78 1 GTCCTGTGGA 0.821797 -223 CAGAACGGACGTCCTGTCGCAGTATATTAA 44 138 0 GTCCTGTCGC 0.959933 -163 TCATTCTCCTGGCTTGTCGCCAATAAAATT 52 237 0 GGCTTGTCGC 0.893491 -21 ********** Masking position 5 Map Score: 6.03025 Number of sites scoring better than the average of aligned sites = 781 Number in coding regions = 748 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 12 CTTCAGATTCCGGTTTACTTAATCT 4 22 0 CGATTCGGTT 0.636262 -15 ATCATTGTCATCTTTCGGGCTGGTCTTCTG 11 9 1 CTCTTCGGGC 0.783271 -164 CTCTATGCTCCGGCTGAAGGGATGTTTTTGCC 13 80 0 CGCTGAGGGA 0.704138 -26 TATAAAAGGTCCGCTTGCGGGCCTTTTTTCTT 14 29 1 CGCTTCGGGC 0.980533 -91 CCTGTAAAAACGGAGGTCGGGCATTGACCCGA 21 114 0 CGAGGCGGGC 0.872968 -35 CGAAAAGACCCTGCTTGAGGGTGACGCACGAA 41 211 0 CGCTTAGGGT 0.892444 -90 GCCTGTTTATCAGATTATGGGTAAAGGATGCC 43 270 0 CGATTTGGGT 0.680502 -31 AGAAATCAGGCTGATGGCTGGTGACTTTTTAG 44 16 1 CGATGCTGGT 0.736824 -285 AAACAGGTCACTGCTGTCGGGTTAAAACCCGG 45 20 1 CGCTGCGGGT 0.988533 -57 TTAGCACAATCCGCTGCCGGGTTTTAACCCGA 45 36 0 CGCTGCGGGT 0.988532 -41 GCAGAGCGTACGGATGACGGGCGCTACAGCGA 47 22 0 CGATGCGGGC 0.973327 -279 ACGCCTTATCCGGCCTACGGGTAGATACGTCT 53 12 0 CGCCTCGGGT 0.910255 -72 * **** ***** Masking position 1 Map Score: 5.60083 Number of sites scoring better than the average of aligned sites = 655 Number in coding regions = 613 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 13 TACTGTTTCTCCATACCCGTTTTTTTGGATG 2 270 1 CCAACCCGTT 0.623822 -31 TGATGAATAAACGCCCCTGTTAATGAATATC 10 101 0 ACGCCCTGTT 0.962382 -200 CAAACGTTTTCCGAACCTGTT 12 1 0 CCGACCTGTT 0.971101 -110 CGCACATAATACGCCCCCGGTTTGCACACCG 12 73 1 ACGCCCCGGT 0.751091 -38 ATAACAGTTTACGAACCCGTTGTGGCTTTAT 20 82 0 ACGACCCGTT 0.942355 -48 GTATGTCGTACCTGTTTTTGGAATTC 22 285 0 TCGACCTGTT 0.919058 -16 TCAATAGTCAACGGCCCTGTTGCTCATTATA 27 70 1 ACGCCCTGTT 0.962382 -79 AGACGTTCCTGTTTATAAAAGGA 38 3 1 ACGTCCTGTT 0.919058 -124 AATGTCCGTGCCTGTTTATCAGATTA 43 285 0 CCGGCCTGTT 0.924738 -16 ATCCACAACGCCGCACCTTTTTCGTGGGGAG 47 175 0 CCGACCTTTT 0.725855 -126 AGCGAATCGCTCCTGTTGTCAGGGGCG 51 86 0 TCGTCCTGTT 0.831637 -17 *** ******* Masking position 11 Map Score: 5.67261 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 165 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 14 TGACTGTATAAAACCACAGCCAA 1 4 1 CTGTATAAAA 0.808 -71 TCTATAATCACGGCAGAAAAGTCCACATTG 2 149 1 CGGCAGAAAA 0.891588 -152 GAAAAATTATCGGTGTAAAAACAGTGG 6 8 0 CGGTGTAAAA 0.548195 -145 CCCCTTTTTGCTGTTTGAAACCCAAAAAAT 6 126 0 CTGTTTGAAA 0.323106 -27 AATTGACCTGCGGCAAAAAAAACGCAAACG 12 26 0 CGGCAAAAAA 0.78495 -85 CGGAACAAGTCGGAATAAAAGCTAAGAAAA 14 54 0 CGGAATAAAA 0.614953 -66 AGGTTATGCTCTGTAAAAAAGTTATTACAA 17 26 0 CTGTAAAAAA 0.485305 -113 ATTTCTTGAACGGCATAATAGGTTAGATAA 22 19 0 CGGCATAATA 0.598612 -282 TACAGGTAGTCTGCATGAAACTATTGCGGA 22 253 1 CTGCATGAAA 0.843428 -48 GCGTTACTTGCGGTAGAAAAATAAAATTCG 26 26 1 CGGTAGAAAA 0.79523 -272 TTTTTTTTGTCTGTAGAAAAGTAAGATGAG 37 65 1 CTGTAGAAAA 0.679946 -30 TTGAAATCTCCGGCTTGAAACAAATGTGGC 38 106 0 CGGCTTGAAA 0.648856 -21 TTCTGCAGGACTGCATAAAAGATGAGCCGA 42 124 0 CTGCATAAAA 0.899112 -175 TTATTTTTAACTGCATGAAAAACAAAGACA 43 86 1 CTGCATGAAA 0.843428 -215 GCATCACCTTCGGCATAAAAGGAAAAGAAG 52 11 0 CGGCATAAAA 0.942167 -247 ********** Masking position 8 Map Score: 5.14524 Number of sites scoring better than the average of aligned sites = 491 Number in coding regions = 423 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 15 CCCTTACGAAGCCTTGCATAATCCTTCTGAG 15 176 0 GCTTGCATAA 0.951571 -125 TATGTTTCACGCGTTGCATAATTAATGAGAT 20 40 1 GCTTGCATAA 0.951571 -90 GGCGTTGCCTCATAATCATGTA 20 118 0 GCTTGCCTCA 0.964674 -12 ACAAGCGCTTGATTTGCGTCAAAAACATTTA 29 54 1 GATTGCGTCA 0.772415 -174 TGATTTATGTGATTTGCATCACTTTTGGTGG 42 161 1 GATTGCATCA 0.902744 -138 TGACGCAAATGCGTTGCATAAATTTACCCAC 42 188 0 GCTTGCATAA 0.951571 -111 TATATATAGTGCTTTGCATCAAGGATGTTTG 47 84 0 GCTTGCATCA 0.975951 -217 ATAACAGCCTTGCCTGACGCAA 49 6 0 GCTTGCCTGA 0.88579 -17 ** ******** Masking position 11 Map Score: 4.38114 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 35 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617