AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02020_ecoli_reg_100.orf -o02020_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 yabB 300 orf, hypothetical protein #2 murC 53 L-alanine adding enzyme, UDP-N-acetyl-muramate:alanine ligase #3 ftsZ 60 cell division; forms circumferential ring; tubulin-like GTP-binding protein and GTPase #4 glnD 61 protein PII; uridylyltransferase acts on regulator of glnA #5 map 300 methionine aminopeptidase #6 yaiB 300 orf, hypothetical protein #7 phoA 31 alkaline phosphatase #8 phoB 189 positive response regulator for pho regulon, sensor is PhoR (or CreC) #9 phoR 57 positive and negative sensor protein for pho regulon #10 fimZ 242 fimbrial Z protein; probable signal transducer #11 ylcA 156 putative 2-component transcriptional regulator #12 citA 291 putative sensor-type protein #13 kdpB 22 ATPase of high-affinity potassium transport system, B chain #14 kdpA 300 ATPase of high-affinity potassium transport system, A chain #15 ompF 300 outer membrane protein 1a (Ia;b;F) #16 appA 184 phosphoanhydride phosphorylase; pH 2.5 acid phosphatase; periplasmic #17 torS 112 sensor protein torS (regulator TorR) #18 torR_torC 129 torR: response transcriptional regulator for torA (sensor TorS), torC: trimethylamine N-oxide reductase, cytochrome c-type subunit #19 phoP 168 transcriptional regulatory protein #20 narX 300 nitrate/nitrate sensor, histidine protein kinase acts on NarL regulator #21 narG 300 nitrate reductase 1, alpha subunit #22 ychK 73 orf, hypothetical protein #23 hnr 91 Hnr protein #24 fdnG 231 formate dehydrogenase-N, nitrate-inducible, alpha subunit #25 rstA 119 response transcriptional regulatory protein (RstB sensor) #26 uvrY 300 putative 2-component transcriptional regulator #27 rcsA 289 positive regulator for ctr capsule biosynthesis, positive transcription factor #28 yedW 84 putative 2-component transcriptional regulator #29 b2074 300 putative membrane protein #30 yehU 221 putative 2-component sensor protein #31 narP 300 nitrate/nitrite response regulator (sensor NarQ) #32 ompC_yojN 600 ompC: outer membrane protein 1b (Ib;c), yojN: putative 2-component sensor protein #33 rcsC_atoS 214 rcsC: sensor for ctr capsule biosynthesis, probable histidine kinase acting on RcsB, atoS: sensor protein AtoS for response regulator AtoC #34 evgA 300 putative positive transcription regulator (sensor EvgS) #35 b2380 300 putative sensor protein #36 narQ 205 sensor for nitrate reductase system, protein histidine kinase (acts on NarP and narL) #37 glnB 60 regulatory protein P-II for glutamine synthetase #38 yfhG 164 putative alpha helix protein #39 yfhK 300 putative 2-component sensor protein #40 barA 56 sensor-regulator, activates OmpR by phophorylation #41 ygiX 151 putative 2-component transcriptional regulator #42 arcB 95 aerobic respiration sensor-response protein; histidine protein kinase/phosphatase, sensor for arcA #43 yhcC 300 orf, hypothetical protein #44 ompR 191 response regulator (sensor, EnvZ) affecting transcription of ompC and ompF: outer membrane protein synthesis #45 uhpT 137 hexose phosphate transport protein #46 uhpA 75 response regulator, positive activator of uhpT transcription (sensor, uhpB) #47 ilvB 105 acetolactate synthase I,valine-sensitive, large subunit #48 glnL 181 histidine protein kinase sensor for GlnG regulator (nitrogen regulator II, NRII) #49 glnA 300 glutamine synthetase #50 cpxR 146 transcriptional regulator in 2-component system #51 hydH 96 sensor kinase for HydG, hydrogenase 3 activity #52 yjdB 73 orf, hypothetical protein #53 yjdE 136 putative amino acid/amine transport protein, cryptic #54 yjdH 180 putative 2-component sensor protein #55 frdA 294 fumarate reductase, anaerobic, flavoprotein subunit #56 creA 210 orf, hypothetical protein #57 arcA 95 negative response regulator of genes in aerobic pathways, (sensors, ArcB and CpxA) Motif number 1 TCACGCGATTACACCGCATTGCGGTATCAAC 10 9 0 ACACCGCTGG 0.727873 -234 AAACAAACGCACACCGCTGCGCGTCTGAATCAA 10 141 1 ACACCGCGGG 0.973875 -102 ATTAAATAAACCAGCGGGGAGGGGAGGTAAAGT 19 81 0 CCAGCGGGGG 0.928152 -88 TAGGGATTTTACAGCACCGTGAAAAATCTCATA 20 117 0 ACAGCACGGA 0.947747 -184 GTAAGTAAAAACAGCGCGGTGTATTGTGACGTT 25 85 1 ACAGCGCGGA 0.992398 -35 ACTAAGACTACCAGGGCGGGGGAAACCCCGCTC 29 95 0 CCAGGGCGGA 0.827923 -206 TAAGTATTTGACAGCACTGAATGTCAAAACAAA 32 305 0 ACAGCACGAG 0.674604 -296 GGAATATGATACACCGCCGAGAAATCATCACCT 33 59 0 ACACCGCGGA 0.978408 -156 CTGGACATGGACAGCGCGGAGAAACCGGAGCGT 38 92 0 ACAGCGCGGA 0.992398 -73 TTACATTCAAACAGCGGAGGAGACATAAACCCC 39 27 1 ACAGCGGGAA 0.862937 -274 CCTTTGTGTTACAGCGCAGGGTAAGCGCTGATA 51 22 1 ACAGCGCGGA 0.992398 -75 CAGGAATCAAACAGCGGTGGGCAGTGACTAAAA 55 50 1 ACAGCGGGGA 0.978408 -245 ******* * * * Masking position 3 Map Score: 10.1434 Number of sites scoring better than the average of aligned sites = 464 Number in coding regions = 439 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 2 TGACGATGAGGGATTTTTTCTTACAGCTATTCATAAC 1 100 1 GTTTTTTTCC 0.955637 -201 TAATATCAGCGTTGTTTATTTTACGTCCAACGTGCGA 1 148 0 GGTTTATTCC 0.907299 -153 CATAATTTCTGGTGATTTTATGCCGCCAACTTTACTC 11 16 1 GGATTTTTCC 0.771127 -141 TGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAG 11 61 0 GATTTTTTCC 0.794252 -96 GCGTATTGCTGGTGTTTTTATTACTGGGTTATCTGGT 14 244 1 GGTTTTTTCG 0.948086 -57 TACCCTCATGGTTTTTTTTATGACACCTGCCACTGCC 15 267 0 GTTTTTTTCC 0.955634 -34 CGGTTAATACGCCGTTATTGTTTCCAGGGAGATTATT 22 12 0 GGTTATTTCG 0.746718 -62 GGTGTATTGTGACGTTTTTATATCTACC 25 102 1 GGTTTTTTCC 0.974372 -18 TCGTATATTAGCGGTTTTTATTGCAACTTTGAAACGT 26 228 0 GGTTTTTTCC 0.97523 -73 TCTATAGGGTGATTTTATTTTTGCCAGGCGATTTTGA 30 93 1 GTTTATTTCG 0.617268 -129 CCTCGCATTCGGTTTTTTTTACCCTTCTTTACACACT 32 167 0 GTTTTTTACC 0.64828 -434 TTAGTCCTCTGTTGTTTTTTTTGCACCTCATTTAAAT 34 11 0 GGTTTTTTCC 0.975232 -290 GTTGCTTTGAGGGGTTTATGTCTCCTCCGCTGTTTGA 39 33 0 GGTTTATTCC 0.907343 -268 TGCGTCATTCGTATTTTATGTAGCACGTCCCGAAGGG 39 160 0 GTTTTATTCG 0.713023 -141 TCTTGTGTCAGATTTTTTTATCTCCTGATGGATTTTA 43 115 0 GTTTTTTTCG 0.909016 -186 AGGTAAGCGCGTATTTTTTTTACCCGCCAGGACAAGA 46 47 1 GTTTTTTTCC 0.955636 -29 * ****** * * * Masking position 9 Map Score: 13.8766 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 67 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 3 CAAAAATCTGCGGGCGGGGTGTAAAAAAAG 14 129 0 CGGGCGGGGT 0.981483 -172 AAAAGTGATACCGGAAGGGTAGAATTCTGG 14 173 0 CCGGAAGGGT 0.748741 -128 TTTTAGGCCACTGGAGGTGCACTGTGAGTG 14 199 1 CTGGAGGTGC 0.794746 -102 GTTAAATTCACGGTCGGTGCACTTTAGGTG 17 74 0 CGGTCGGTGC 0.890897 -39 CGCTTTACATCGGTAAGGGTAGGGATTTTA 20 139 0 CGGTAAGGGT 0.63193 -162 GCCCCTTCCTCGGGAGGGGCTTTCCCGTTT 29 199 1 CGGGAGGGGC 0.986863 -102 AGTTCGGCCCCGGGCAGTGCTCGAAATCTT 38 48 1 CGGGCAGTGC 0.937325 -117 TCAGCCCCTTCGGGACGTGCTACATAAAAT 39 155 1 CGGGACGTGC 0.867321 -146 CCGGTTTGCGCCGGCGGGGTTTTGGAATCG 47 27 0 CCGGCGGGGT 0.934094 -79 CGGCGCAAACCGGGCGGGGTTTTTCGTTTA 47 44 1 CGGGCGGGGT 0.981483 -62 GCCGACTTTCCGGGAGGTGCTTAAACGAAA 47 65 0 CGGGAGGTGC 0.975306 -41 ********** Masking position 1 Map Score: 10.5416 Number of sites scoring better than the average of aligned sites = 331 Number in coding regions = 303 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 AAATCAATAACCTGAAGATATGTGCGACGAGCTT 8 87 1 CCTGAAGTTG 0.844397 -103 TGGTTTATGCCCTGATCAATGCGGAGGCGTTCTG 14 277 1 CCTGATCGGG 0.920414 -24 TCATTTAAAGCCTGAAGGAAGAGGTTTAC 20 282 1 CCTGAAGGGG 0.985184 -19 CAGTAATACCCCTGAAAAAAGAGGAAAGCA 24 212 1 CCTGAAAGGG 0.920502 -20 ATTATTATTGCTTGATGTTAGGTGCTTATTTCGC 32 365 1 CTTGATGGTG 0.76734 -236 TGATAGGTAACCTGAAGGCTGATGACCAGCAGGC 35 247 0 CCTGAAGGTG 0.972391 -54 AATAAAATAGCCTGATAGGATAGGCTGTTAGCA 38 10 0 CCTGATATGG 0.67951 -155 CGATAATCATACTGATGAGAGAGGGAAGGTC 54 8 0 ACTGATGGGG 0.862504 -173 AGGTACTTACCCTGAAGTACGTGGCTGTGGGATA 55 250 1 CCTGAAGGGG 0.98529 -45 TATCCAATTACCTGATGTCAGGTGCTCGTTGTTG 56 29 0 CCTGATGGTG 0.976667 -182 CCCTGACCTGCCTGATGCATGCTGCAAATTAACA 57 24 0 CCTGATGGTG 0.976653 -72 ******* * ** Masking position 5 Map Score: 7.41596 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 171 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 5 TCGGAAGTCCGGCGCGCTTTATACCACAAA 5 95 1 GGCGCGCTTT 0.714622 -206 AATAATTGTTGGCGCTGTGTACAGCATCAG 5 140 1 GGCGCTGTGT 0.854881 -161 AAAATCTGCGGGCGGGGTGTAAAAAAAGTA 14 127 0 GGCGGGGTGT 0.975645 -174 AAGTAAAAACAGCGCGGTGTATTGTGACGT 25 87 1 AGCGCGGTGT 0.697961 -33 GTGAGGGTAGAGCGGGGTTTCCCCCGCCCT 29 86 1 AGCGGGGTTT 0.876825 -215 CCCTTCCTCGGGAGGGGCTTTCCCGTTTCA 29 201 1 GGAGGGGCTT 0.839412 -100 ATGATTTCTCGGCGGTGTATCATATTCCAG 33 64 1 GGCGGTGTAT 0.764818 -151 GGTCACCTGAGGCGGAGCTTCGCCCCTTTG 33 150 1 GGCGGAGCTT 0.801984 -65 TATGGAATAAGGCGGTGCCTAACTCGACGT 39 258 0 GGCGGTGCCT 0.866904 -43 CTCTTTTCAAGGCGCGGTCTATCAGATT 43 283 1 GGCGCGGTCT 0.926137 -18 GGTTTGCGCCGGCGGGGTTTTGGAATCGTG 47 25 0 GGCGGGGTTT 0.982536 -81 GCGCAAACCGGGCGGGGTTTTTCGTTTAAG 47 46 1 GGCGGGGTTT 0.982536 -60 CGACTTTCCGGGAGGTGCTTAAACGAAAAA 47 63 0 GGAGGTGCTT 0.627693 -43 ********** Masking position 10 Map Score: 8.93284 Number of sites scoring better than the average of aligned sites = 618 Number in coding regions = 565 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 6 CATAAGATTAAATTATCGCATTAAAAAAGCCGGCATT 4 24 0 ATTGCTAAAA 0.431801 -38 TTATTGATTTCCGTGGCGCAGAAAAAAGCAAATGGCA 8 60 0 CTGGCGAAAA 0.856958 -130 TGATTTATTTCGCTATAGCGGCAAACAAACGCACACC 10 119 1 CTTGCGAACA 0.774427 -124 CCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAA 11 22 0 AGTGCGAAAA 0.668503 -135 GGAAGGGTAGAATTCTGGCTGCAAAGATTTCGCAAAA 14 154 0 ATTGCGAAGA 0.850771 -147 GCTGTTTTGTCTCTCTTGCCGTTAAAAATTAAGCTGA 24 15 1 CTTGCGTAAA 0.884005 -217 ATTGACCTACCTCAATAGCGGTAGAAAAACGCACCAC 24 87 0 CATGCGAAAA 0.794791 -145 GGCTGATTTTCATTTTTGCTGAATAAAGTCAATTTTT 26 67 1 CTTGCGAAAA 0.970039 -234 AATAAAATCACCCTATAGATGCACAAAAAACGGGCAA 30 75 0 CTTGAGAAAA 0.575301 -147 ACTTTCTTTGAACTCTTGCAGAAAAATGAGAATTCGT 30 142 0 ATTGCGAAAT 0.552158 -80 ATTAATTGCTGTTAAAAGCATTGGGTA 31 1 1 AATGCGTAAA 0.360927 -300 GTACAAGCGCCATTTTGCTGTACAAATAACCTACAA 32 10 1 CTTGCGAAAA 0.970039 -591 TTTCGCTATAAACTGTGGCAGATCAAATAATCCCATC 36 118 1 ATTGCGTAAA 0.825207 -88 GTTATGTGTTACGTTTAGCAGATCAAAAGACAGGCGA 37 17 1 ATTGCGTAAA 0.825207 -44 AAAAAATAAAATTTAGTGCTGTACAGAGCGCGTTACA 41 80 1 ATGGCGAAGA 0.51337 -72 CGTCATTACCAATTAAGGCAGTATAAAATGCTGGTTT 43 57 0 ATAGCGAAAA 0.576384 -244 AGAATCAATAATGTTTCGCCGAATAAATTGTATACTT 44 37 1 ATTGCGAAAA 0.952502 -155 ATTGTTGCGAACCTTTGGGAGTACAAACA 44 173 1 ATTGGGAAAA 0.695944 -19 ATGCTTCGCGCTTTTTATCCGTAAAAAGCTATAATGC 48 120 1 CTTTCGAAAA 0.562844 -62 ATTATTTTGGCCGTGTCGCCGTAAAAAAGATAAAGCG 49 224 0 CTTGCGAAAA 0.970039 -77 CTGCTCATCCCTTTCTGACAGCAGAAATCATGCCATC 51 58 0 CTTACGAAAA 0.562845 -39 GAATGATTGGCTATATAGGGGAAGAGACTCTGGCAAC 54 87 0 CTTGGGAAGA 0.512262 -94 * * * ** * * *** Masking position 15 Map Score: 8.25021 Number of sites scoring better than the average of aligned sites = 628 Number in coding regions = 563 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 7 TGTTTGCCGCTATAGCGAAATAAATCAGAA 10 116 0 TATAGCGAAA 0.953254 -127 CCTTAGGATGTATAGCGAAAGGAGAAAAAG 12 40 0 TATAGCGAAA 0.953254 -252 GCACTTTCACGGTAGCGAAACGTTAGTTTG 15 154 1 GGTAGCGAAA 0.853423 -147 GGAGGGGAGGTAAAGTGAAAAAATAAAAAG 19 67 0 TAAAGTGAAA 0.642297 -102 AGGATACTCCTGCAGCGAAATATTTGTTTT 27 75 1 TGCAGCGAAA 0.796961 -215 GAGTTTTGAGGATAGCGAAAAAGCGTCCAG 28 34 1 GATAGCGAAA 0.876197 -51 TGTATGGACATGTAGTGAAAACTACAACCT 31 194 0 TGTAGTGAAA 0.787622 -107 TTGAAACATCTATAGCGATAAATGAAACAT 32 440 1 TATAGCGATA 0.819175 -161 TGCCACAGTTTATAGCGAAATAGTTACTTA 36 108 0 TATAGCGAAA 0.953254 -98 TTGCCGGATATGAAGTGAAAAGGTGAGATG 45 13 0 TGAAGTGAAA 0.596316 -125 GTAAAAAAGATAAAGCGAAATCTGTGCCAA 49 211 0 TAAAGCGAAA 0.890519 -90 GGGCTATGCTTATAGCGATAATCATACTGA 54 27 0 TATAGCGATA 0.819175 -154 ********** Masking position 4 Map Score: 7.01095 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 112 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 ATCGGAAGTCCGGCGCGCTTTATACCACAA 5 94 1 CGGCGCGCTT 0.940196 -207 TTTTTACACCCCGCCCGCAGATTTTTGCGA 14 132 1 CCGCCCGCAG 0.753158 -169 CGATGCTGTCCGGCCTGCTTATTAAGATTA 19 33 1 CGGCCTGCTT 0.920471 -136 TTTACCTCCCCTCCCCGCTGGTTTATTTAA 19 83 1 CTCCCCGCTG 0.833356 -86 GGGAGCCTGTCGGCCCTCTGATAAATCGAC 21 267 0 CGGCCCTCTG 0.909099 -34 CGTCACAATACACCGCGCTGTTTTTACTTA 25 86 0 CACCGCGCTG 0.689117 -34 AAATGAAAATCAGCCCGCTGAATATGTAAC 26 52 0 CAGCCCGCTG 0.767847 -249 CCCGTTTCAGCGTCCCGCTGAAATCGTCGG 29 222 1 CGTCCCGCTG 0.961422 -79 TCCTCAAAAACGGCCTGCTGGTCATCAGCC 35 235 1 CGGCCTGCTG 0.968585 -66 TCAATCGTCCCGGCCTGCTTTTATCAACTG 43 210 0 CGGCCTGCTT 0.920471 -91 GCTTGAACAACATCGCGCTTATCGTTAAGG 46 20 1 CATCGCGCTT 0.53767 -56 ********** Masking position 4 Map Score: 5.59763 Number of sites scoring better than the average of aligned sites = 835 Number in coding regions = 806 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 9 GATTTCTTAACTGGAGTATCTTAC 9 44 1 CTGGAGTATC 0.760403 -14 TATACATCCTAAGGAGTATTTCGGCGTGAA 12 56 1 AAGGAGTATT 0.738437 -236 GTTTTTATTACTGGGTTATCTGGTTTATGC 14 257 1 CTGGGTTATC 0.546431 -44 CACGGCAAATAAGGAGTAACTCTTTCCGGG 20 177 1 AAGGAGTAAC 0.820187 -124 GATGGGTATTAAGGAGTATTCCCCATGGGT 21 44 0 AAGGAGTATT 0.738437 -257 AATTATCCTAAAGGGGTATCTTAGGAATTT 21 151 1 AAGGGGTATC 0.95444 -150 CCTCTTTTTTCAGGGGTATTACTGCGCGAG 24 206 0 CAGGGGTATT 0.816413 -26 ATGTTATCCTAAGGATTATCCGAAAAATAA 27 27 1 AAGGATTATC 0.754629 -263 TATTTCGCTGCAGGAGTATCCTGGAAGATG 27 67 0 CAGGAGTATC 0.927335 -223 ATATTCAGGTAAGGGGAATTATCGTTACGC 27 252 1 AAGGGGAATT 0.422908 -38 CATACATAAAATGGGGTAACATTCACGCGC 31 218 1 ATGGGGTAAC 0.645896 -83 ACCCGACTTACAGGGGAATCGGCAATGTTC 36 66 1 CAGGGGAATC 0.768124 -140 AGAAGTTGTTAAGGACTATCTTGTTAAATG 41 43 0 AAGGACTATC 0.58079 -109 AAGGCAGGATAAGGGTTAACACACCTTTAT 43 15 0 AAGGGTTAAC 0.6339 -286 GTATTCATTTCAGGAGTAACCC 45 126 1 CAGGAGTAAC 0.817124 -12 GGAGCATAAAAAGGGTTATCCAAAGGTCAT 49 60 1 AAGGGTTATC 0.831803 -241 ********** Masking position 8 Map Score: 6.17628 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 251 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 10 AAAAGCCGGCATTCGCCGGCTTCATC 4 6 0 ATTCCCGGCT 0.944018 -56 AACACCAGCAATACGCCGGTTATCACGCCTG 14 229 0 ATACCCGGTT 0.568975 -72 GCTTATTAAGATTATCCGCTTTTTATTTTTT 19 49 1 ATTACCGCTT 0.814053 -120 ATAACGGCGTATTAACCGCCTGAGTAGCACT 22 31 1 ATTACCGCCT 0.962013 -43 TTGCCACAAAATAATCCGCCTTCGCAAATTG 24 120 0 ATAACCGCCT 0.919789 -112 CTGGAATATGATACACCGCCGAGAAATCATC 33 63 0 ATACCCGCCG 0.721519 -152 GAGTGTTGTTATTACCCGACTTACAGGGGAA 36 53 1 ATTACCGACT 0.873553 -153 CCAGTGGCTCATTCACCGACTTATGTCAGCC 39 130 1 ATTCCCGACT 0.882139 -171 AGCCGGGAATTACCCGGCTTTGTTATGGA 39 282 0 ATTACCGGCT 0.939634 -19 CTCCCTTTGAATTACCCGCCTCATCAGAGAT 54 127 1 ATTACCGCCT 0.962013 -54 **** ****** Masking position 2 Map Score: 4.21298 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 109 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 11 AGAGAATATATTTCATAACTTTTATTTATAATAAAGGTT 6 89 1 TTTTTATTAT 0.916835 -212 CAGCGAAACGTTTCTCTTATTTAAATAATTACCCACACA 6 149 0 TTTTTAATAT 0.763391 -152 TCACATAGAGTTAGTGGTTTTTTATTTATTTAATGATTT 12 99 1 TTTTTATTAT 0.916835 -193 ATTTAATGATTTTAAGTTTTTTAATTAATGTAATTACGA 12 126 1 TTTTTATTAT 0.916835 -166 GACTCGCAGGTTTAAGTGATTTAATTGATTTAATGAATA 12 168 1 TTTTTATTAT 0.916834 -124 CTTATTAAGATTATCCGCTTTTTATTTTTTCACTTTACC 19 50 1 TTTTTATTTT 0.520392 -119 TGATTGATTTTTTAGTTGTTTTTCTTGATGAGAAGCTGA 31 108 1 TTTTTCTTAT 0.835344 -193 GTCGTTCGCTTTGGCATCATTTTCATTATAAAGACGGAA 31 154 0 TTTTTCATAT 0.597544 -147 TTTACCCTTCTTTACACACTTTTCATTATTCTGTGCTAC 32 148 0 TTTTTCATAT 0.597544 -453 TACTAAAACTTTTAAGATGTTTCATTTATCGCTATAGAT 32 447 0 TTTTTATTAT 0.916835 -154 CCTGATTTTATTGTTGACATTTCATTTATGCCGACTATT 34 139 1 TTTTTATTAT 0.916835 -162 GAAGCTCAGATTTTCTTATTTTTATTGAGAAAATGAGAT 34 209 1 TTTTTATTAG 0.616587 -92 TGTCCAGCGTTTTAGAACATTTTATTAATGACGTTAAAT 35 27 1 TTTTTATTAT 0.916835 -274 TGCATGAAATTTCGGTAATTTTGATTGATTATGCAGTTG 43 177 1 TTTTTATTAT 0.916835 -124 ** *** *** ** Masking position 10 Map Score: 5.61772 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 25 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 12 CATTTTAAAACGGTGATGACGATGAGGGATT 1 84 1 CGTGATGACG 0.98156 -217 GTAAAAAACCCGATGTTTACGGCTAATATCA 1 177 0 CGTGTTTACG 0.782135 -124 ATGAGGCCGACGATGATTACGGCCTCAGGCG 3 16 1 CGTGATTACG 0.935699 -45 CCATCAGCGTCGGTGATACCGACAATATATA 5 271 0 CGTGATACCG 0.875691 -30 TCCGGTAAGCCGTTGGTGACGGGCGTGACCA 26 138 1 CGTGGTGACG 0.981215 -163 TTGAGCGTAGCGTTGGTAACGCTACCAGGCG 31 245 0 CGTGGTAACG 0.933942 -56 TACCAGATTTAGCTGGTGACGAACGTGAGCT 44 119 1 AGTGGTGACG 0.836766 -73 CACGGTGATGATGTGGTAGGCCG 48 3 1 CGTGATGATG 0.839481 -179 ACCGGGTTATCGCTGATGCCGTTATTAATAT 53 33 0 CGTGATGCCG 0.963064 -104 ** ******** Masking position 7 Map Score: 4.0593 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 357 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 13 ATTTGTGCCTGTCGCCTGAGGCCGTAATCATCGT 3 25 0 GCGCCTGACG 0.985204 -36 TAGAAAATTCGACGTCTGATGCTGTACACAGCGC 5 151 0 GCGTCTGACG 0.956184 -150 ATAAGCGATTGCCATCTGATCCCGCTACTCTAGA 11 106 1 GCATCTGACG 0.957015 -51 TTTTTTTTATGACACCTGCCACTGCCGTCAATAA 15 259 0 GCACCTGCCG 0.982466 -42 GCATGCTATTGCCACCTGCGCCTGTCAGAATTAA 23 35 0 GCACCTGCCG 0.982466 -57 CACTCCATCGGTCACCTGAGGCGGAGCTTCGCCC 33 141 1 GCACCTGACG 0.985493 -74 TGGAGAGCGACTCACCTGCTCCGGCCTACCACAT 48 21 0 CCACCTGCCG 0.89061 -161 AAAGCAGTCTCCTGAACAGGTTGCACCATT 48 162 0 GCTCCTGAAG 0.767448 -20 ATGGATTAGCGACGTCTGATGACGTAATTTCTGC 50 105 1 GCGTCTGAAG 0.811221 -42 * ******* * * Masking position 7 Map Score: 4.94585 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 186 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 14 TGGGAATAAGGGGTGAGGCTGGC 1 288 1 GGGTGAGGCT 0.794275 -13 ATCGGACGCAGAGCAGGGCTTATGATTTCT 9 21 1 GAGCAGGGCT 0.695427 -37 AAAAATCTGCGGGCGGGGTGTAAAAAAAGT 14 128 0 GGGCGGGGTG 0.713555 -173 AGTGAGGGTAGAGCGGGGTTTCCCCCGCCC 29 85 1 GAGCGGGGTT 0.78076 -216 CCCCTTCCTCGGGAGGGGCTTTCCCGTTTC 29 200 1 GGGAGGGGCT 0.974454 -101 TATTTCAAAGGGGCGAAGCTCCGCCTCAGG 33 155 0 GGGCGAAGCT 0.794275 -60 GTAGCGCGAGGCTTTCAGGGTTG 33 202 0 GCGCGAGGCT 0.896359 -13 ACAGGGAGAAGGGAGATGCTTCATTGCAAA 34 270 1 GGGAGATGCT 0.8867 -31 GTTCGGCCCCGGGCAGTGCTCGAAATCTTC 38 49 1 GGGCAGTGCT 0.84127 -116 TACGCCCACTGGGATAGGCTTTAAGTCTGG 38 140 1 GGGATAGGCT 0.787344 -25 CAGCCCCTTCGGGACGTGCTACATAAAATA 39 156 1 GGGACGTGCT 0.652134 -145 TTAACGATAAGCGCGATGTTGTTCAAGCCT 46 18 0 GCGCGATGTT 0.44094 -58 GGCGCAAACCGGGCGGGGTTTTTCGTTTAA 47 45 1 GGGCGGGGTT 0.951557 -61 CCGACTTTCCGGGAGGTGCTTAAACGAAAA 47 64 0 GGGAGGTGCT 0.941359 -42 AGCCCATGCAGAGATGGGCTACAGATAGCT 48 69 0 GAGATGGGCT 0.579273 -113 GAAGATTCCGGGGCTATGCTTATAGCGATA 54 37 0 GGGCTATGCT 0.787344 -144 ********** Masking position 3 Map Score: 6.99981 Number of sites scoring better than the average of aligned sites = 530 Number in coding regions = 480 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 15 TATTTTCCACAGCAAATATAAAGTGTCAGTT 1 47 0 AGCAAAATAA 0.949948 -254 ACCATCAATAAGCAAAAATAAGTGGTCGGAT 14 11 0 AGCAAAATAA 0.949948 -290 TGATATTTACAGCAATTTTAATCTATTTATA 15 24 0 AGCAATTTAA 0.56692 -277 GATCTTAATGAGCAAATATGAACAGCGGCAC 18 44 1 AGCAAAATGA 0.922403 -86 GACTTTATTCAGCAAAAATGAAAATCAGCCC 26 66 0 AGCAAAATGA 0.922403 -235 AAAATCGCCTGGCAAAAATAAAATCACCCTA 30 97 0 GGCAAAATAA 0.781381 -125 CAAAAAGCCCAACAAAAATAATTGCAAATAA 32 44 1 AACAAAATAA 0.599269 -557 CCTAACATCAAGCAATAATAATTCAAGGTTA 32 356 0 AGCAATATAA 0.824842 -245 ACACAAGATAAGCAAAAGTGATTTATGTGAT 43 144 1 AGCAAAGTGA 0.735265 -157 CCCTTAATCCAGCAAACATAAAAGCCAACCT 52 14 1 AGCAAAATAA 0.949948 -60 ATGCTCGCAAAGCAAAATTAAGCCAACCTTA 52 53 0 AGCAAATTAA 0.840659 -21 ****** **** Masking position 5 Map Score: 3.47956 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 27 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548