AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02020_ecoli_reg_300.orf -o02020_ecoli_300.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 hyaA 300 hydrogenase-1 small subunit #17 appC 133 probable third cytochrome oxidase, subunit I #18 appA 184 phosphoanhydride phosphorylase; pH 2.5 acid phosphatase; periplasmic #19 torS 112 sensor protein torS (regulator TorR) #20 torR_torC 129 torR: response transcriptional regulator for torA (sensor TorS), torC: trimethylamine N-oxide reductase, cytochrome c-type subunit #21 phoP 168 transcriptional regulatory protein #22 ycfC 35 orf, hypothetical protein #23 ymfC 201 orf, hypothetical protein #24 narX 300 nitrate/nitrate sensor, histidine protein kinase acts on NarL regulator #25 narG 300 nitrate reductase 1, alpha subunit #26 ychK 73 orf, hypothetical protein #27 hnr 91 Hnr protein #28 fdnG 231 formate dehydrogenase-N, nitrate-inducible, alpha subunit #29 rstA 119 response transcriptional regulatory protein (RstB sensor) #30 uvrY 300 putative 2-component transcriptional regulator #31 fliF 214 flagellar biosynthesis; basal-body MS(membrane and supramembrane)-ring and collar protein #32 fliL 104 flagellar biosynthesis #33 fliO 62 flagellar biosynthesis #34 rcsA 289 positive regulator for ctr capsule biosynthesis, positive transcription factor #35 yedW 84 putative 2-component transcriptional regulator #36 b2074 300 putative membrane protein #37 yehU 221 putative 2-component sensor protein #38 narP 300 nitrate/nitrite response regulator (sensor NarQ) #39 ompC_yojN 600 ompC: outer membrane protein 1b (Ib;c), yojN: putative 2-component sensor protein #40 rcsC_atoS 214 rcsC: sensor for ctr capsule biosynthesis, probable histidine kinase acting on RcsB, atoS: sensor protein AtoS for response regulator AtoC #41 evgA 300 putative positive transcription regulator (sensor EvgS) #42 b2380 300 putative sensor protein #43 narQ 205 sensor for nitrate reductase system, protein histidine kinase (acts on NarP and narL) #44 glnB 60 regulatory protein P-II for glutamine synthetase #45 yfhG 164 putative alpha helix protein #46 yfhK 300 putative 2-component sensor protein #47 barA 56 sensor-regulator, activates OmpR by phophorylation #48 ygiX 151 putative 2-component transcriptional regulator #49 arcB 95 aerobic respiration sensor-response protein; histidine protein kinase/phosphatase, sensor for arcA #50 yhcC 300 orf, hypothetical protein #51 ompR 191 response regulator (sensor, EnvZ) affecting transcription of ompC and ompF: outer membrane protein synthesis #52 uhpT 137 hexose phosphate transport protein #53 uhpA 75 response regulator, positive activator of uhpT transcription (sensor, uhpB) #54 ilvB 105 acetolactate synthase I,valine-sensitive, large subunit #55 ivbL 300 ilvB operon leader peptide #56 glnL 181 histidine protein kinase sensor for GlnG regulator (nitrogen regulator II, NRII) #57 BIME194 68 BIME #58 glnA 300 glutamine synthetase #59 cpxR 146 transcriptional regulator in 2-component system #60 hydH 96 sensor kinase for HydG, hydrogenase 3 activity #61 yjdB 73 orf, hypothetical protein #62 yjdE 136 putative amino acid/amine transport protein, cryptic #63 adiY 300 putative ARAC-type regulatory protein #64 yjdH 180 putative 2-component sensor protein #65 frdA 294 fumarate reductase, anaerobic, flavoprotein subunit #66 creA 210 orf, hypothetical protein #67 arcA 95 negative response regulator of genes in aerobic pathways, (sensors, ArcB and CpxA) Motif number 1 CTTTTTTTACACCCCGCCCGCAGATTTTTG 14 129 1 ACCCCGCCCG 0.93403 -172 CTAAACATCCCCACCGCCCGGCCAAAAGAA 16 44 1 CCACCGCCCG 0.720831 -257 TTACCTCCCCTCCCCGCTGGTTTATTTAAT 21 84 1 TCCCCGCTGG 0.918485 -85 GTTATCAATTCCCACGCTGTTTCAGAGCGT 25 212 1 CCCACGCTGT 0.67944 -89 GCTATTGCCACCTGCGCCTGTCAGAATTAA 27 35 0 CCTGCGCCTG 0.547487 -57 GTCACAATACACCGCGCTGTTTTTACTTAC 29 85 0 ACCGCGCTGT 0.88554 -35 CCGCGTCTTTTCCCCGCTTTGTTGCGCTCA 32 32 1 TCCCCGCTTT 0.712045 -73 TGTGCAATCTTCCGCGCCGGTTTCTGCTGC 33 30 1 TCCGCGCCGG 0.913088 -33 GGCGGGGGAAACCCCGCTCTACCCTCACTC 36 84 0 ACCCCGCTCT 0.891771 -217 AGCGGGGTTTCCCCCGCCCTGGTAGTCTTA 36 96 1 CCCCCGCCCT 0.956343 -205 CTCCGGTTTCTCCGCGCTGTCCATGTCCAG 45 95 1 TCCGCGCTGT 0.858994 -70 GTTTATGTCTCCTCCGCTGTTTGAATGTAA 46 27 0 CCTCCGCTGT 0.808429 -274 AATCTGATAGACCGCGCCTTGAAAAGAGGC 50 281 0 ACCGCGCCTT 0.796678 -20 CGATTCCAAAACCCCGCCGGCGCAAACCGG 54 27 1 ACCCCGCCGG 0.965203 -79 TAAACGAAAAACCCCGCCCGGTTTGCGCCG 54 44 0 ACCCCGCCCG 0.93403 -62 ATAACAAAAAACCCCGCCGGAGCGAGGTTT 55 157 0 ACCCCGCCGG 0.965203 -144 CAGCGCTTACCCTGCGCTGTAACACAAAGG 60 22 0 CCTGCGCTGT 0.706173 -75 GCGGCCCCACCCCGCGCTTTTTTTTGCCTG 63 106 1 CCCGCGCTTT 0.83095 -195 TAGTCACTGCCCACCGCTGTTTGATTCCTG 65 50 0 CCACCGCTGT 0.738068 -245 ********** Masking position 5 Map Score: 19.8654 Number of sites scoring better than the average of aligned sites = 933 Number in coding regions = 842 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 2 TGATTTCCGTGGCGCAGAAAAAAGCAAATGGCAC 8 59 0 GGCAAAAAAG 0.977029 -131 TTTCGCTATAGCGGCAAACAAACGCACACCGCTG 10 126 1 GGCAACAAAG 0.903084 -117 TGATTTTCCGGTGACAGAAAAATGACAAAATTGT 11 62 1 GACAAAAAAG 0.850314 -95 TACCTCAATAGCGGTAGAAAAACGCACCACTGCC 28 83 0 GGTAAAAAAG 0.820324 -149 GCGCTAAATAGCAACAAAAAAACGGGTTTATTGG 31 69 1 GACAAAAAAG 0.850314 -146 TTTATTGGCGGATAGAAAAAAACGAAAGCACAAA 31 95 1 GAGAAAAAAG 0.578746 -120 TCACCCTATAGATGCACAAAAAACGGGCAAAACT 37 71 0 GGCAAAAAAC 0.875963 -151 TCTTTGAACTCTTGCAGAAAAATGAGAATTCGTG 37 141 0 CGCAAAAAAG 0.899319 -81 TCAGTATGCAGTGGCATAAAAAAGCAAATAAAGG 39 555 1 GGCAAAAAAG 0.977029 -46 ATTTAAATGAGGTGCAAAAAAAACAACAGAGGAC 41 11 1 GGCAAAAAAC 0.875963 -290 AAATACGAATGACGCACAACAAGGTGCCTGCCGT 46 181 1 GGCAAACAAG 0.903084 -120 TCAGAGAATTGACGGAGAAAAAAGCCCATGCAGA 56 87 0 GGGAAAAAAG 0.911401 -95 TCGCTTTCACGGAGCATAAAAAGGGTTATCCAAA 58 50 1 GGCAAAAAAG 0.977029 -251 TGCGTCAGGGGGTGTAAAACAACGTAAAGTCATG 59 74 1 GGTAAACAAG 0.500053 -73 CATAAAAATTGCTGCAAACAAAAATGTCATACTT 63 67 1 GGCAACAAAA 0.58902 -234 GGATAAATAACAGGCAAAAAAAAGCGCGGGGTGG 63 112 0 CGCAAAAAAG 0.899319 -189 TGAATATAAACATGCATAAAAATAACGAGTTTTA 63 196 0 CGCAAAAAAA 0.578746 -105 GTACGTGGCTGTGGGATAAAAACAATCTGGAGGA 65 266 1 GGGAAAAAAA 0.612731 -29 * *** ***** * Masking position 8 Map Score: 14.0285 Number of sites scoring better than the average of aligned sites = 578 Number in coding regions = 503 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 3 AAGATTAAATTATCGCATTAAAAAAGCCGG 4 28 0 TATCGCATTA 0.576283 -34 TTCTGATTTATTTCGCTATAGCGGCAAACA 10 116 1 TTTCGCTATA 0.919784 -127 CTTTTTCTCCTTTCGCTATACATCCTAAGG 12 40 1 TTTCGCTATA 0.919784 -252 GCTGCAAAGATTTCGCAAAAATCTGCGGGC 14 144 0 TTTCGCAAAA 0.58752 -157 CAAACTAACGTTTCGCTACCGTGAAAGTGC 15 154 0 TTTCGCTACC 0.768747 -147 GGTCCATTTTTATCGCTAAAAGATAAATCC 16 79 1 TATCGCTAAA 0.806753 -222 AGACGGTAAGTATCGCTTTCAGTCTTATGA 17 13 1 TATCGCTTTC 0.745672 -121 GTCTTATGAATATCGCAATCGGCGAATACC 17 34 1 TATCGCAATC 0.80595 -100 CTCACTCACATATCGCAACATTTACTTTAC 34 108 1 TATCGCAACA 0.636703 -182 CTGGACGCTTTTTCGCTATCCTCAAAACTC 35 34 0 TTTCGCTATC 0.905561 -51 GCAAGCAGTCTATCGCTAACGCGTAGATAA 36 270 1 TATCGCTAAC 0.77775 -31 ATGTTTCATTTATCGCTATAGATGTTTCAA 39 440 0 TATCGCTATA 0.92576 -161 TAAGTAACTATTTCGCTATAAACTGTGGCA 43 108 1 TTTCGCTATA 0.919784 -98 TTGGCACAGATTTCGCTTTATCTTTTTTAC 58 211 1 TTTCGCTTTA 0.758443 -90 TCAGTATGATTATCGCTATAAGCATAGCCC 64 27 1 TATCGCTATA 0.92576 -154 ********** Masking position 3 Map Score: 9.65014 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 106 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 4 ATGATTCTCAATTTGCCCGGGTGTGATACC 5 225 1 ATTTGCCCGG 0.881341 -76 GCCCATGCTTTTTCGCCAGGGAACCGTT 8 9 0 TTTCGCCAGG 0.735984 -181 TTCCTCCGCATGTTGCCCGGGCAATTCTAG 11 135 0 TGTTGCCCGG 0.853085 -22 CCTATTTTTCTTTTGGCCGGGCGGTGGGGA 16 51 0 TTTTGGCCGG 0.87663 -250 TTCTGAATCTTTTTGCGCGAAATCAAAAAG 28 160 0 TTTTGCGCGA 0.551241 -72 CATGAATGTTTTTTGCCCGTATTGTTCGGG 30 13 1 TTTTGCCCGT 0.944464 -288 GTGTTGTATAATTTGCCTGGAATTGTCTTA 34 140 0 ATTTGCCTGG 0.68102 -150 AACCAGGTAGTTTTGCCCGTTTTTTGTGCA 37 63 1 TTTTGCCCGT 0.944464 -159 GTGATTTTATTTTTGCCAGGCGATTTTGAG 37 101 1 TTTTGCCAGG 0.868304 -121 TAACTCGACGTTTCGCCCGATGGTTGATAT 46 239 0 TTTCGCCCGA 0.757753 -62 ATTTTCCAGGTTTTGCCTGGACGCTATCTC 52 52 1 TTTTGCCTGG 0.924821 -86 CGTGGAAACTTTTCGCCTGTCTCTGGCAGG 57 24 1 TTTCGCCTGT 0.673931 -45 TCTGCAATTATTTTGGCCGTGTCGCCGTAA 58 237 0 TTTTGGCCGT 0.73847 -64 ATGTCATACTTTTTGCGCGGCCCCACCCCG 63 90 1 TTTTGCGCGG 0.87663 -211 CCGCGCTTTTTTTTGCCTGTTATTTATCCT 63 117 1 TTTTGCCTGT 0.830174 -184 ********** Masking position 3 Map Score: 11.7382 Number of sites scoring better than the average of aligned sites = 540 Number in coding regions = 493 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 5 TAAGAAATCATAAGCCCTGCTCTGCGTCCG 9 23 0 TAAGCCCTGC 0.799519 -35 ACGCCGGTTATCACGCCTGCACTCACAGTG 14 218 0 TCACGCCTGC 0.820174 -83 ATGCGCCGCATCAGGCCTACGTTCGTTAAC 18 111 0 TCAGGCCTAC 0.898662 -74 GGCGATGCTGTCCGGCCTGCTTATTAAGAT 21 31 1 TCCGGCCTGC 0.956205 -138 ATTGCTCATTTAAAGCCTGAAGGAAGAGGT 24 277 1 TAAAGCCTGA 0.425255 -24 CGTTTCACAGTAAGCCCTACGATGAAATGT 30 107 0 TAAGCCCTAC 0.508365 -194 TTTCTGGTAGCAAAGCCTACCAGTAAGTCA 31 28 1 CAAAGCCTAC 0.62768 -187 TCGCAGACTACAAAGCCTGCGGATTGACAA 36 29 1 CAAAGCCTGC 0.866719 -272 TTTCCTCAAAAACGGCCTGCTGGTCATCAG 42 233 1 AACGGCCTGC 0.69886 -68 GATCAATCGTCCCGGCCTGCTTTTATCAAC 50 212 0 CCCGGCCTGC 0.959688 -89 GAAAAGAGGCCAAAGCCTGCCATTTTTAGC 50 261 0 CAAAGCCTGC 0.866719 -40 GGACGCTATCTCAGGCCTGATTTGCTGCTG 52 70 1 TCAGGCCTGA 0.481062 -68 ACTCACCTGCTCCGGCCTACCACATCATCA 56 16 0 TCCGGCCTAC 0.859565 -166 GCCACCGATCCCAGGCCTGCCAGAGACAGG 57 39 0 CCAGGCCTGC 0.953846 -30 ********** Masking position 8 Map Score: 6.36813 Number of sites scoring better than the average of aligned sites = 1099 Number in coding regions = 763 Number in noncoding regions = 336 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 6 AGTTTGCGACGCGAGCGGCATTTTAGGACAT 1 20 0 GCGAGCGGCT 0.78809 -281 TGGGAATAAGGGGTGAGGCTGGC 1 288 1 GGGTGAGGCG 0.943394 -13 TGTGCCTGTCGCCTGAGGCCGTAATCATCGT 3 25 0 GCCTGAGGCG 0.95599 -36 ACTTATTGACGGCAGTGGCAGGTGTCATAAA 15 257 1 GGCAGTGGCG 0.595764 -44 ACGAACGTAGGCCTGATGCGGCGCATTAGCA 18 115 1 GCCTGATGCG 0.836812 -70 CCCCTTCCTCGGGAGGGGCTTTCCCGTTTCA 36 200 1 GGGAGGGGCT 0.827366 -101 TCCATCGGTCACCTGAGGCGGAGCTTCGCCC 40 144 1 ACCTGAGGCG 0.551385 -71 GTAGCGCGAGGCTTTCAGGGTTGT 40 201 0 GCGCGAGGCT 0.853375 -14 ACAGGGAGAAGGGAGATGCTTCATTGCAAAG 41 270 1 GGGAGATGCT 0.578995 -31 TTCGAGCACTGCCCGGGGCCGAACTGACAAA 45 42 0 GCCCGGGGCG 0.884842 -123 ATGAATACCTGCGTGAGGCATGCATTGTAAA 52 103 0 GCGTGAGGCT 0.931204 -35 CCGACTTTCCGGGAGGTGCTTAAACGAAAAA 54 63 0 GGGAGGTGCT 0.530821 -43 TTCGTCAGTCGCCTGCGGCTGGTAACCGCAA 55 128 0 GCCTGCGGCG 0.903289 -173 AAAAAGCGCGGGGTGGGGCCGCGCAAAAAGT 63 97 0 GGGTGGGGCG 0.932021 -204 TCCCTGACCTGCCTGATGCATGCTGCAAATT 67 28 0 GCCTGATGCT 0.737202 -68 ********* * Masking position 5 Map Score: 6.07309 Number of sites scoring better than the average of aligned sites = 905 Number in coding regions = 848 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 7 GATGAAGCCGGCGAATGCCGGCTTTTTTA 4 8 1 CCGCGAAGCC 0.812505 -54 CCGTATAATTCACGCGATTACACCGCATTGCG 10 19 0 CAGCGATACA 0.404887 -224 ATTTTGCCAATAAGCGATTGCCATCTGATCCC 11 97 1 TAGCGATGCC 0.71735 -60 AATATCGCAATCGGCGAATACCTCTGGTCGTA 17 42 1 TCGCGAAACC 0.944532 -92 AGGAAATTTATCTGCGCTAACAAGAAAATTAC 42 87 1 TCGCGCTACA 0.865407 -214 CTCCGGTTTCTCCGCGCTGTCCATGTCCAGAC 45 95 1 TCGCGCTTCC 0.865899 -70 TTTTTCATCCCTGCGATAACCGTATTTGCTG 48 131 0 CCGCGATACC 0.964298 -21 TTAGCTCAATTCGGCGATGACCTGGATCAATC 50 234 0 TCGCGATACC 0.973533 -67 GTAAAAAAAATACGCGCTTACCTTAACGATAA 53 38 0 TAGCGCTACC 0.910051 -38 CAAAACCCCGCCGGCGCAAACCGGGCGGGGTT 54 33 1 CCGCGCAACC 0.945281 -73 GTATACGTGTTCCGCGCAGAACGCGCAATTTC 55 68 0 TCGCGCAAAC 0.607777 -233 CCATCTTTTATCAGCGCTTACCCTGCGCTGTA 60 31 0 TCGCGCTACC 0.980702 -66 AATAACGGCATCAGCGATAACCCGGTCGATAA 62 38 1 TCGCGATACC 0.973533 -99 ** ***** *** Masking position 5 Map Score: 8.9654 Number of sites scoring better than the average of aligned sites = 583 Number in coding regions = 557 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 TCTGATGCTGTACACAGCGCCAACAATTATTGGTG 5 136 0 TACACGCAAA 0.390125 -165 TTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCT 11 56 0 TTCTGCCGAA 0.536853 -101 AAGGGTAGAATTCTGGCTGCAAAGATTTCGCAAAA 14 154 0 TTCTGGCAAA 0.909343 -147 ACAGTGCACCTCCAGTGGCCTAAAAGTGATACCGG 14 189 0 TCCAGCCAAA 0.818786 -112 GCGCACTCCTGTAGGCGAAGAGAGAAAAATA 17 113 0 TCCTGGCAAA 0.965925 -21 CGCGCATCTTTCATGACGGCAAACAATAGGGTAGT 23 134 0 TCATGGCAAA 0.584341 -68 TGAGTCTTGTTCCACTTTGCCAATAACGCCGTCCA 31 169 1 TCCACGCAAA 0.74344 -46 TCCAGGATACTCCTGCAGCGAAATATTTGTTTTAA 34 72 1 TCCTGCGAAA 0.58892 -218 TAGTCTGCGATCCTGCCAGCAAATATTC 36 4 0 TCCTGGCAAA 0.965922 -297 TCATTAATGTTCCAGTTCGCTGAAACGCAATTTAG 43 160 0 TCCAGGCGAA 0.911686 -46 CAACACGGTTTACTGGCAGCAAATACGGTTATCGC 48 115 1 TACTGGCAAA 0.862202 -37 GGTCTTGTCCTGGCGGGTAAAAAAAATACGCG 53 54 0 TCCTGGGAAA 0.864341 -22 TGGAAAATTTTTCAGCAAGGGAAAATTGAGGGGTT 55 212 0 TTCAGGGAAA 0.615401 -89 AGAGATGGGCTACAGATAGCTGACAAACTTCACGT 56 55 0 TACAGGCGAA 0.695017 -127 GAGTTTACGATTCAGGCTGCAAACATGCGTCAGGG 59 49 1 TTCAGGCAAA 0.876813 -98 GCTCATCCCTTTCTGACAGCAGAAATCATGCCATC 60 58 0 TTCTGGCGAA 0.837561 -39 ACATGTACTCCTGAGTGCGAATAAAAGACCAGT 63 278 0 TCCTGGCAAA 0.965925 -23 ***** ** ** * Masking position 13 Map Score: 7.294 Number of sites scoring better than the average of aligned sites = 565 Number in coding regions = 511 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 9 GTTCATCCTGACCAGTGCCGCTGTTCATAT 20 59 0 ACCAGTGCCG 0.948864 -71 ACCTCGTATCAGTGCCGGATGGCGATG 21 8 1 ATCAGTGCCG 0.891723 -161 AGACGAGCAAACCAGTAGCGCTCGAAGGAG 23 17 0 ACCAGTAGCG 0.970645 -185 ATGTTAACCGAGCAGTAGCGAT 26 62 1 AGCAGTAGCG 0.970645 -12 ATGACTAACTATCAGTAGCGTTATCCCTAT 30 265 1 ATCAGTAGCG 0.936207 -36 TTAGCCGATAAGCAGTAGCGACACAGGAAG 32 75 1 AGCAGTAGCG 0.970645 -30 CTGCAGCAGTGGCGCAGCAGAAAC 33 49 0 AGCAGTGGCG 0.98129 -14 CATAATAGTAACCAGTGGCTCATTCACCGA 46 119 1 ACCAGTGGCT 0.85416 -182 ********** Masking position 4 Map Score: 5.6389 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 116 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 CCACAATTTCCCACTGAAAGGAGTTTACGG 1 251 0 CCACTGAAAG 0.82899 -50 GCCAAACGTGCCACTGAAGGTTTTCTATAA 5 185 0 CCACTGAAGG 0.826046 -116 GCGCACTCCTGTAGGCGAAGAGAGA 17 119 0 CTCCTGTAGG 0.705082 -15 AATAACCCCTGTAGAATTATGGTTT 20 6 1 CCCCTGTAGA 0.80372 -124 GCTCATTTAAAGCCTGAAGGAAGAGGTTTA 24 280 1 AGCCTGAAGG 0.575141 -21 TCCTAAGATACCCCTTTAGGATAATTAACA 25 147 0 CCCCTTTAGG 0.534932 -154 CGCAGTAATACCCCTGAAAAAAGAGGAAAG 28 210 1 CCCCTGAAAA 0.872286 -22 ATAGTAAGTCCGCCTGAAAAATCGCGAGAG 34 178 1 CGCCTGAAAA 0.660679 -112 TCTACCCTCACTCCTGAAAGTATGCCTTCA 36 67 0 CTCCTGAAAG 0.799509 -234 TTTTCGTACAACCCTGAAAGCCTCGCGCTA 40 194 1 ACCCTGAAAG 0.82899 -21 ACAATTCTTACGCCTGTAGGATTAGTAAGA 41 65 1 CGCCTGTAGG 0.843425 -236 ATTGCCGATTCCCCTGTAAGTCGGGTAATA 43 62 0 CCCCTGTAAG 0.950714 -144 GAGACATAAACCCCTCAAAGCAACGTATAA 46 46 1 CCCCTCAAAG 0.739822 -255 TATTATGTCAACACTGAAAGTATACGTGTT 55 89 0 ACACTGAAAG 0.42713 -212 TCCATTGTCTCCCCTGTAAAGCTGTGCTTG 55 243 1 CCCCTGTAAA 0.806955 -58 TTTTAAATTGCCCCTAAAAGGCGTTATCAT 58 180 0 CCCCTAAAAG 0.657363 -121 ********** Masking position 5 Map Score: 6.84954 Number of sites scoring better than the average of aligned sites = 435 Number in coding regions = 364 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 11 ACATTAATTAAAAAACTTAAAATCATTAAATAAATAAAAAACCACT 12 111 0 AAAAAAAATA 0.900031 -181 CGGGGTGTAAAAAAAGTATAAAAATGGCAAAAGCCATGATTTAACT 14 99 0 AAAAAAAAAA 0.742959 -202 CAGGTGTCATAAAAAAAACCATGAGGGTAATAAATA 15 275 1 AAAAAAAATA 0.900031 -26 AGGTAAAGTGAAAAAATAAAAAGCGGATAATCTTAATAAGCAGGCC 21 44 0 AAAAAAAATA 0.900031 -125 ACACTATTTTAATAATTAAGACAGGGAGAAATAAAA 21 143 1 AATAAAAAAA 0.437317 -26 CCATCTGCATAAAAATCTTAATAGTTTAAATAACTACAGGTATAAA 25 69 1 AAAAAAAATA 0.900031 -232 AAGTTGCAATAAAAACCGCTAATATACGAATGACTAACTATCAGTA 30 236 1 AAAAAAAATA 0.900031 -65 CCAGTAAGTCAATAAGACAAAGGCGCTAAATAGCAACAAAAAAACG 31 47 1 AATAAAAATA 0.707673 -168 TCTCATCAAGAAAAACAACTAAAAAATCAATCACAATACTTGTGCA 38 95 0 AAAAAAAATA 0.900031 -206 AATAACCTACAAAAAGCCCAACAAAAATAATTGCAAATAAACAAAG 39 35 1 AAAAAAAATA 0.900031 -566 CTATTTCACAAATAATTAACATCCGCATAATTTCCAGCAATCTTTG 39 76 0 AATAAAAATA 0.707673 -525 CATTCTCCCCAAAAATGCAGAATAATCCAACACGAATATGATACTA 39 481 0 AAAAAAAACA 0.757295 -120 TATCCTGTAAAAAAATATGTACATGAGAAATTACTATAAAAATTTG 63 141 1 AAAAAAAATA 0.900031 -160 CTTGCGCACTAAAAAAATCGATCTCGTCAAATTTCAGACTTATCCA 65 142 1 AAAAAAAAAA 0.742959 -153 CTACTAAGAAAAAAACACTGAATGCTAAAACAGCAAAAAATGCTAT 66 63 0 AAAAAAAACA 0.757295 -148 ***** * *** * Masking position 11 Map Score: 6.03923 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 29 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 12 ATAATTTAATCTTATGGGTGGCGCACA 4 45 1 CTTATGGGGC 0.983245 -17 CTTATTTTTGCTTATTGATGGTTTATTTACAT 14 20 1 CTTATTGGGT 0.745433 -281 ATTGACAGAACTTATTGACGGCAGTGGCAGGT 15 248 1 CTTATTGGGC 0.967605 -53 ACACCGGGCGCTTATGGTCGGCAAGCGACGTC 16 245 0 CTTATGGGGC 0.983245 -56 CTCGTGGCTGATTATGGACGGCGTTATTGGCA 31 186 0 ATTATGGGGC 0.851921 -29 TGACCCTTTCCTTATTTATGGCCCCTTCCTCG 36 179 1 CTTATTTGGC 0.769346 -122 GAAATAGTTACTTATTCTGGGCACATGAACAT 43 90 0 CTTATTCGGC 0.831752 -116 ACCTTAAGTTCTTAAGGTTGGCTTTTATGTTT 61 27 0 CTTAAGGGGC 0.948835 -47 ACCTTAAGAACTTAAGGTTGGCTTAATTTTGC 61 41 1 CTTAAGGGGC 0.948835 -33 ******* *** Masking position 4 Map Score: 4.35089 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 29 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 GACTCACTATTTTCCACAGCAAATATAAAGTG 1 53 0 TTTACAGCAA 0.92482 -248 GACGTGATGATATTTACAGCAATTTTAATCTA 15 30 0 TATACAGCAA 0.773753 -271 ACCGGGCGCTTATGGTCGGCAAGCGACGTCCC 16 243 0 TATTCGGCAA 0.711775 -58 TCAGCTTAATTTTTAACGGCAAGAGAGACAAA 28 20 0 TTTACGGCAA 0.951502 -212 AAAAATTGACTTTATTCAGCAAAAATGAAAAT 30 72 0 TTTTCAGCAA 0.847812 -229 TACCCAATGCTTTTAACAGCAATTAAT 38 6 0 TTTACAGCAA 0.924828 -295 TTGTAGGTTATTTGTACAGCAAAATGGCGCTT 39 15 0 TTTACAGCAA 0.924828 -586 AAGTATACAATTTATTCGGCGAAACATTATTG 51 42 0 TTTTCGGCGA 0.792526 -150 AGGCGAAAAGTTTCCACGGCAACTAAAACAC 57 10 0 TTTACGGCAA 0.951494 -59 CGCTTTATCTTTTTTACGGCGACACGGCCAAA 58 224 1 TTTACGGCGA 0.894024 -77 *** ******* Masking position 3 Map Score: 5.08141 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 97 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 14 ATAGAAAATTCGACGTCTGATGCTGTACAC 5 156 0 CGACGTCTGA 0.931501 -145 AAGCCCTGCTCTGCGTCCGATGAGCAAGGC 9 12 0 CTGCGTCCGA 0.908393 -46 AAGTGAACGACCGCGTCTGATTTTCTGATT 10 94 1 CCGCGTCTGA 0.986415 -149 GCACACCGCTGCGCGTCTGAATCAAGAAAA 10 149 1 GCGCGTCTGA 0.933152 -94 ATGGCTGGACCCGCGTCTGAAAAGTTAACG 18 88 1 CCGCGTCTGA 0.986415 -97 GTTCGCAAAACTGCGTCTAAAGTTAAACCG 37 36 0 CTGCGTCTAA 0.806956 -186 CATGGATTAGCGACGTCTGATGACGTAATT 59 104 1 CGACGTCTGA 0.931501 -43 ********** Masking position 10 Map Score: 1.13856 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 121 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 15 TGGCCTAAAAGTGATACCGGAAGGGTAGAATTC 14 176 0 GTGAACGGAG 0.902845 -125 TCTCCTCCTTGCGACACCGGCAGGACACCGGGC 16 268 0 GCGAACGGAG 0.989561 -33 ATAAGCAGTAGCGACACAGGAAGACCGCAACAC 32 82 1 GCGAACGGAG 0.989561 -23 TTTGTAGTCTGCGATCCTGCCAGCAAATATTC 36 10 0 GCGACCGCAG 0.959804 -291 ACGCAGTTTTGCGAACCAGGTAGTTTTGCCCGT 37 50 1 GCGACCGGAG 0.978874 -172 CAACCATCGGGCGAAACGTCGAGTTAGGCACCG 46 243 1 GCGAACTCAG 0.82726 -58 CTTTTTTACGGCGACACGGCCAAAATAATTGCA 58 232 1 GCGAACGCAA 0.905832 -69 CTAAAGCAAAGCGATACCGGGAAATGGTTATAT 63 240 0 GCGAACGGAA 0.94915 -61 GCCAACTAAATCGAAACAGGAAGTACAAAAGTC 67 57 0 TCGAACGGAG 0.902845 -39 **** ** ** ** Masking position 4 Map Score: 6.57156 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 107 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432