AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00350_ecoli_reg_300.orf -o00350_ecoli_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/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 surA 52 survival protein #2 imp 254 organic solvent tolerance #3 rpsB 300 30S ribosomal subunit protein S2 #4 tsf 257 protein chain elongation factor EF-Ts #5 pyrH 146 uridylate kinase #6 frr 291 ribosome releasing factor #7 yaeM 91 putative ATP-binding component of a transport system #8 yaeS 185 orf, hypothetical protein #9 cdsA 120 CDP-diglyceride synthetase #10 yaeT 29 orf, hypothetical protein #11 hlpA 121 histone-like protein, located in outer membrane or nucleoid #12 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #13 mhpA 76 3-(3-hydroxyphenyl)propionate hydroxylase #14 adhC 34 alcohol dehydrogenase class III; formaldehyde dehydrogenase, glutathione-dependent #15 yaiN 166 putative alpha helix chain #16 lnt 24 apolipoprotein N-acyltransferase, copper homeostasis protein, inner membrane #17 ybeX 89 putative transport protein #18 ybeZ 113 putative ATP-binding protein in pho regulon #19 yleA 145 orf, hypothetical protein #20 potF 300 periplasmic putrescine-binding protein; permease protein #21 ybjO 59 orf, hypothetical protein #22 ybjF 40 putative enzyme #23 ybjU 36 putative arylsulfatase #24 poxB 132 pyruvate oxidase #25 ybjW 137 putative prismane #26 ybjE 300 putative surface protein #27 aspC 184 aspartate aminotransferase #28 ompF 300 outer membrane protein 1a (Ia;b;F) #29 htrB 224 heat shock protein #30 adhE 300 CoA-linked acetaldehyde dehydrogenase and iron-dependent alcohol dehydrogenase; pyruvate-formate-lyase deactivase #31 ycjL 121 probable amidotransferase subunit #32 ycjC 26 orf, hypothetical protein #33 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #34 tynA 247 copper amine oxidase (tyramine oxidase) #35 maoC 284 putative aldehyde dehydrogenase #36 ydcH 72 orf, hypothetical protein #37 rimL 62 acetylation of N-terminal serine of 30S ribosomal subunit protein L7; acetyl transferase #38 msbB 119 suppressor of htrB, heat shock protein #39 yebA 78 orf, hypothetical protein #40 yebL 24 putative adhesin #41 hisL 255 his operon leader peptide #42 hisG 145 ATP phosphoribosyltransferase #43 wcaA 34 putative regulator #44 BIME92 24 BIME #45 wza 300 putative polysaccharide export protein #46 gatY 197 tagatose-bisphosphate aldolase 1 #47 BIME96 27 BIME #48 b2097 184 orf, hypothetical protein #49 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #50 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #51 cvpA 165 membrane protein required for colicin V production #52 folC 69 dihydrofolate:folylpolyglutamate synthetase; dihydrofolate synthetase #53 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #54 dedA 82 orf, hypothetical protein #55 usg 65 putative PTS system enzyme II A component #56 pdxB 98 erythronate-4-phosphate dehyrogenase #57 b2654 300 orf, hypothetical protein #58 b2657 171 putative enzyme #59 b2658 138 orf, hypothetical protein #60 b2659 230 orf, hypothetical protein #61 gabD 22 succinate-semialdehyde dehydrogenase, NADP-dependent activity #62 ygcA 56 putative enzyme #63 pepP 25 proline aminopeptidase P II #64 ygfB 161 orf, hypothetical protein #65 agaZ 248 putative tagatose 6-phosphate kinase 2 #66 BIME157 76 BIME #67 agaS 191 putative tagatose-6-phosphate aldose/ketose isomerase #68 agaB 166 PTS system, cytoplasmic, N-acetylgalactosamine-specific IIB component 1 (EIIB-AGA) #69 agaC 38 PTS system N-acetylgalactosamine-specific IIC component 1 #70 accB 300 acetylCoA carboxylase, BCCP subunit; carrier of biotin #71 yhdT 108 orf, hypothetical protein #72 yiaK 200 putative dehydrogenase #73 yiaM 117 orf, hypothetical protein #74 yiaY 189 putative oxidoreductase #75 selA 97 selenocysteine synthase: L-seryl-tRNA (Ser) selenium transferase #76 yibF 227 putative S-transferase #77 udp 298 uridine phosphorylase #78 yigN 140 putative alpha helix chain #79 ubiE 94 2-octaprenyl-6-methoxy-1,4-benzoquinone --> 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone #80 dnaB 82 replicative DNA helicase; part of primosome #81 alr 52 alanine racemase 1 #82 BIME213 26 BIME #83 tyrB 192 tyrosine aminotransferase, tyrosine repressible #84 sgaT 291 orf, hypothetical protein Motif number 1 AGATGGGCACAAAAAGAAGCCGCCCTCAGGCG 5 26 0 AAAAGAGCCG 0.814782 -121 TTCTTGAACGACAAAAACGCCGCTCAGTAGAT 7 12 1 AAAAAAGCCG 0.977654 -80 CAGAATAAAAAGCAAAACGCCGCCAGCCGATC 7 51 0 ACAAAAGCCG 0.948289 -41 AAGCCTATACAAAAAAAAGCCGTGTAAAACCA 8 119 0 AAAAAAGCCG 0.977654 -67 GGCGGCAACAGAAACAACGCCGCGATGACGAC 9 65 0 GAACAAGCCG 0.792462 -56 ATGTTAGTTAATCAAAACGCCGTCGTTAATCA 17 50 0 ACAAAAGCCG 0.948289 -40 AAAGAGAGAAAAAACAAGGCCCACCGGAACGG 18 23 0 AAACAAGCCC 0.77296 -91 GAAAACAATGCCGCGACATGCGC 21 47 0 AAACAAGCCG 0.929353 -13 GCTCTGGCGAACAAAATCGCCGCTGCGCGGTG 26 28 1 AAAAATGCCG 0.846617 -273 GTTGGTGGCGTCAAAATCGCCGAGGCGTTCCC 26 159 0 TAAAATGCCG 0.738856 -142 CATGCAGTTGTTAAAAAAGCCGCCTGGCTGGC 37 24 0 TAAAAAGCCG 0.957313 -39 CCGCACCAAATAAAAAAAGCCGGTACTGACTG 38 36 0 TAAAAAGCCG 0.957313 -84 CATAAAATATATAAAAAAGCCCTTGCTTTCTA 41 176 1 AAAAAAGCCC 0.918849 -80 CAACCGCGCAATAAAAAAGCCCCCGGAAGGTG 42 88 0 AAAAAAGCCC 0.918849 -58 AGTGAAAGGCAAAAAAACGGCCTCCCGATAGG 46 76 0 AAAAAAGGCC 0.677544 -122 CCGCGCATCAATAAAAATGGCGCTGAAAAAAT 51 59 0 AAAAAAGGCG 0.890338 -107 CTGCTAAAGCGTCAAAAGGCCGGATTTTCCGG 71 13 1 GCAAAAGCCG 0.841845 -96 TCCCCAGTAATAAAAAAGGCCGGAAAATCCGG 71 32 0 TAAAAAGCCG 0.957313 -77 CCTGAAAGTGTAAAAAAGGGCGGGCAGCTTAC 74 160 0 TAAAAAGGCG 0.806266 -30 TACGCAAAAATACAAAAGGCCGAACGCGTCGG 78 32 0 TCAAAAGCCG 0.903846 -109 * ***** **** Masking position 4 Map Score: 27.4678 Number of sites scoring better than the average of aligned sites = 406 Number in coding regions = 314 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 2 CGAAATGGATCGGAAGTCCGGCGCGCTTTATACCA 3 134 0 CGATCGCGCG 0.950105 -167 CGGCAAGCTCGAGAATTCCCGGGAGCTTACATCAG 4 55 1 GGATCGGGAG 0.748963 -203 TAGATCCTTGCGGATCGGCTGGCGGCGTTTTGCTT 7 39 1 CGAGCGGCGG 0.962144 -53 CTTCTGCCGCCCGCTATCCGGGGCGGCCTTCCCTG 15 14 1 CGCTCGGGCG 0.965769 -153 ATTTGACTGGCAGACGTCCCCGCCGTTGGTGATTA 17 21 1 CGATCCGCCG 0.780319 -69 CAAGGCCCACCGGAACGGCAGGCCTGAGAA 18 6 0 CGAGCGGCCT 0.918408 -108 AAATAGTAGCCAGGAATGCAGGGCGCATAGTGTAA 19 106 0 CGGTCGGGCG 0.989028 -40 TTTATATAGCGAGCAGTGCTGGCCGGGAGAAAGTT 20 171 1 GGCTCGGCCG 0.886988 -130 TTTGGCGGCAGGGATCTACCGCCAGAGAGGTA 25 8 0 GGATCGCCAG 0.47946 -130 CGCCAGAGCCCGGGGGTGCAGGGGGC 26 2 0 CGGTCGGGGG 0.973475 -299 GAGGCGTTCCCTGAAGGCCGGGGCAGCCCACATGG 26 135 0 CGAGCGGGCA 0.719658 -166 CAGAAATAAACGGGCATACGGCCCGGGGATCTCTG 33 196 1 CGGTCGCCCG 0.831579 -79 TATGCAGTTTGTGAACGTCAGGGCGCAGAGATCCC 33 221 0 GGAGCGGGCG 0.940376 -54 CTTTCCTAAGCCGCCAGCCAGGCGGCTTTTTTAAC 37 12 1 CGCGCGGCGG 0.496768 -51 TATTAAACGCCAGGGCGACAGAGCGGGCTATCTGT 39 31 0 CGGGCGAGCG 0.865766 -48 CCCCCGGAAGGTGATCTTCCGGGGGCTTTCTCATG 42 66 0 GGATCGGGGG 0.874861 -80 AGTTGCAAGTCAGGGTGCCAGACCGGCACCCTCAG 49 19 0 CGGGCGACCG 0.874413 -76 GCAGACTTTGCAGGATTTCGGCGGGAGTTGCAAGT 49 44 0 CGGTCGCGGG 0.912894 -51 GTTGCCCTGTCAGACTTGCAGGCAGACTTTGCAGG 49 65 0 CGATCGGCAG 0.926219 -30 GCGCCCCGAACAGGATGACAGGGCGTAAAATCGTG 51 133 1 CGGGCGGGCG 0.98807 -33 CACCTTCCTGCTGATTGACTGCGCTGCCTTCGTCT 64 13 1 CGAGCGCGCT 0.748042 -149 GCAAAATAGACCGGCGTCCCGGCCTGCTGGAATTT 70 182 1 CGGTCGGCCT 0.942772 -119 GTCAAAAGGCCGGATTTTCCGGCCTTTTTTATTAC 71 23 1 CGATCGGCCT 0.924512 -86 TAACATTACCCAGGCGTTCTGGCGTAGACGATTAT 73 15 0 CGGTCGGCGT 0.870803 -103 GATGGTTCTCCAGGTTTACGGGCAGGTGGTTAAAA 83 166 0 CGGTCGGCAG 0.944319 -27 * ** * * ***** Masking position 9 Map Score: 30.7259 Number of sites scoring better than the average of aligned sites = 1797 Number in coding regions = 1677 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 3 CGTTTGTCACGCGCAACGTTACCGATGATGGAACAAT 2 217 1 GCGCAATCTG 0.911128 -38 CGATACTTACGCGGAATCTTACCCTTATTTATCCATC 6 18 0 GCGGAATCTA 0.863699 -274 CAGGAAAAAGGCGCAAGCATTGCAATAAAGATGGGGA 18 56 0 GCGCAATCTA 0.986939 -58 TATAAAAGCATCGCAAGAATAACTTTAGCCAGGGTTT 20 140 0 TCGCAATCTA 0.810441 -161 GATTGATTTAGCGCAATTTTGGCGGCAGGGATCTACC 25 23 0 GCGCAATCCA 0.980432 -115 TGTAATTAAAGCGCAAGAATATCTTTAAATGAAAACG 26 203 1 GCGCAATCTA 0.986939 -98 AATTTTTAATGCGCAAATGTAGCGTAAAATGTGTGGA 29 81 0 GCGCAATCAA 0.905668 -144 GTCATTTAAAGCGCAGTAATGGCGATAATTTAGTCCA 31 91 1 GCGCAGTCTA 0.953018 -31 AGCCGGGTAAGCGCAATGCGCCCGGCAATCTATACAC 33 26 1 GCGCAAGCCA 0.958432 -249 TAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAA 38 53 0 GCGCAAGCCA 0.958432 -67 GGTCTGTTGGGGGCAAAAATGGCATTATGCGTCCCCA 53 84 1 GGGCAATCTA 0.926176 -72 CGTTTTATCGGGGCAGATATAACATTAAA 60 3 0 GGGCAGTCTA 0.771062 -228 CTTTTCCGCAGCGCAAAAACTGCGTCAGGGAGGACGA 70 48 0 GCGCAACCCA 0.895845 -253 CCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATC 72 21 1 GCGCAAGCTA 0.972045 -180 TAAAAATGTTGCGCAATGTTAACTATAGTCAGCATGC 77 67 1 GCGCAATCTA 0.986939 -232 ****** * * ** Masking position 5 Map Score: 17.5919 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 158 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 4 CCTGTCATTCAATGCCGTGCCTAACACCAC 2 127 1 AATGCCGTGC 0.921494 -128 TGTGCGGTTTAATGCCGGGCAGATCACATC 4 223 1 AATGCCGGGC 0.964919 -35 GAACGACAAAAACGCCGCTCAGTAGATCCT 7 17 1 AACGCCGCTC 0.948967 -75 CAACAGAAACAACGCCGCGATGACGACGGG 9 62 0 AACGCCGCGA 0.86285 -59 TCAATATAAGATCGCCGGGCCACGCAAAGA 11 61 1 ATCGCCGGGC 0.950269 -61 CTGCCAGTCAAATGCCTGGCAAA 17 4 0 AATGCCTGGC 0.916754 -86 CTGGCTACATAATGCCGCGCATGTCGCGGC 21 31 1 AATGCCGCGC 0.973256 -29 GAAAACAATGCCGCGACATGCGCGGC 21 44 0 AATGCCGCGA 0.79618 -16 GGCGAACAAAATCGCCGCTGCGCGGTGCCC 26 33 1 ATCGCCGCTG 0.659853 -268 GCCTTCAGGGAACGCCTCGGCGATTTTGAC 26 152 1 AACGCCTCGG 0.850199 -149 ACTGGGCGAAATTGCCGCGCTTGTAAATAA 29 123 0 ATTGCCGCGC 0.940112 -102 TTGTGTATAGATTGCCGGGCGCATTGCGCT 33 35 0 ATTGCCGGGC 0.922267 -240 TTTGCCTATTAACGCCTTTCTATTAAGCAA 65 47 1 AACGCCTTTC 0.706002 -202 ACGGCGGTGAAACGCCTGTCACAATCACAC 70 256 1 AACGCCTGTC 0.849104 -45 TCTACGCCAGAACGCCTGGGTAATGTTATT 73 22 1 AACGCCTGGG 0.810948 -96 ATTTTTGCGTAGCGCCTCGCAGGAAATGCC 78 53 1 AGCGCCTCGC 0.787294 -88 CCTCGCAGGAAATGCCTTTCCAACTGGACG 78 67 1 AATGCCTTTC 0.598561 -74 TCTGTTGCTAATTGCCGTTCGCTCCTGAAC 83 100 1 ATTGCCGTTC 0.616324 -93 ********** Masking position 1 Map Score: 15.4731 Number of sites scoring better than the average of aligned sites = 1741 Number in coding regions = 1652 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 5 TTGGTTTCAAAAAGAAAAAATATGTAACCAAAAGTAA 28 102 0 AGAAAAAGAA 0.964319 -199 AAGTTCTGTCAATAAAAATTTACGGAACTATTGATGA 28 224 0 AAAAATAGAA 0.636719 -77 CCACTGCTAGATTGAAAAAATATTGAACATAAAGGTC 31 57 1 AGAAAAATAA 0.715828 -65 CACAAAACTTAGTGAAATAAAAGGGCAACTATTCGCC 34 30 0 AGAAAAAGCA 0.907661 -218 ATATTTTGAAATCGAAAACAAACGACAGGAT 46 177 1 AGAAAAAGCA 0.907661 -21 TAATAGGCAAAACGAAATGAAACGAAAGTTTTACGAA 65 21 0 AGAAAAAGAA 0.964319 -228 CTGATTCACAAAAGAAACATAATGAAAGTCACTGAAA 65 116 0 AGAAATAGAA 0.897451 -133 TCATGGTGAGATAAAAATAAAACGAAAGATAATGGTT 65 160 0 AAAAAAAGAA 0.844057 -89 CGCAGTATCAACTGAAACAAAACGAAAGATTAATATC 65 197 1 AGAAAAAGAA 0.964319 -52 CACAGATCAAAACGAAAGAAAAAGAAAGGCCTTACGG 66 43 0 AGAAAAAGAA 0.964319 -34 TGATCGTTGAAAGAAAAGATAAAGGAAGCAAAAGGGA 67 12 0 AAAAATAGAA 0.636719 -180 AATGGAGAAAAAAGAAATAAAACGAAATTTGTGATCG 67 43 0 AGAAAAAGAA 0.964319 -149 ATTAAAATCTATAGAAAAGAAACTGAAAGTTCAATGG 67 75 0 AGAAAAATAA 0.715828 -117 GACATCACCAAGTGAAATGAAACGAAAGGCAAGTGAA 67 120 1 AGAAAAAGAA 0.964319 -72 AGTTTCGCATATTGAAATTTTAAGCCAAAAAAGCGAT 72 152 1 AGAAATAGCA 0.760938 -49 CAAAAAAGCGATCAAAAAAACAAGGAAGCCTGGG 72 177 1 AAAAAAAGAA 0.844057 -24 TATCCATCAGAGTGAAATAATTAGGAAAATATTTATA 76 90 1 AGAAAATGAA 0.684611 -138 * **** * * * ** Masking position 7 Map Score: 15.6687 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 48 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 GAACTATTTTGGGGGAGTTATCAAGCCTTA 4 6 0 GGGGTTCAAG 0.972554 -252 AGTGAAAAAGGGGGCCATATGCAGGCCCCCTAACC 4 180 0 GGGCTACAGG 0.810614 -78 TGTTGCCGCCGGTGGGGTTCGCCATTGTAACGCTG 9 87 1 GGGGTTCCAT 0.807574 -34 AAAGGGTGGCATTTCCCGTCATAATAAGG 23 5 1 GGGGTTCCGT 0.852904 -32 TACCTCTCTGGCGGTAGATCCCTGCCGCCAAAAT 25 10 1 GGGGGACCTG 0.698685 -128 GTGGGCTGAGGGCGCGTTTTACAGGGATGTTACCT 26 98 0 GGGCTTCAGG 0.868807 -203 TGAAAACGCAGGCTGTTTTTGCAAGACGTGAGATT 27 80 0 GGTGTTCAAG 0.651933 -105 GTCACTTCCAGGTGGCGTAAGCAAGATTACTCACT 30 104 0 GGGGTACAAG 0.958164 -197 GCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTAT 34 185 0 GGGGTACAGG 0.969365 -63 CCGCCTGGCTGGCGGCTTAGGAAAGT 37 2 0 GGGGTAAAAG 0.516846 -61 GTGATCTTCCGGGGGCTTTCTCATGCGTTCATGCA 42 56 0 GGGGTTCATG 0.962603 -90 GCAGGATTTCGGCGGGAGTTGCAAGTCAGGGTGCC 49 35 0 GGGGGTCAAG 0.885884 -60 CAGACTTGCAGGCAGACTTTGCAGGATTTCGGCGG 49 55 0 GGAGTTCAGG 0.721273 -40 GGTGGTTTACTCCAGAAATAGCAAA 55 51 0 GGGGTACCAG 0.935778 -15 TTTAATGCATGGAGGTTTTCCCATTCATCCTTAGA 58 128 0 GGGGTTCATT 0.827342 -44 CAACAGGTTAGGGGGAGTTAACATTAGAGAACAGA 60 115 0 GGGGTTCATT 0.827342 -116 GTCGTCAAAGGGAGGAATATTCATGATATGCTACC 64 135 0 GGGGTACATG 0.9433 -27 AGCGTCAAAAGGCCGGATTTTCCGGCCTTTTTTAT 71 20 1 GGCGTTCCGG 0.709308 -89 ** ** ** **** Masking position 2 Map Score: 11.3744 Number of sites scoring better than the average of aligned sites = 393 Number in coding regions = 356 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 CCGTGACCAAACTGCCTGCAACAATAACGC 6 79 0 ACTGCCTGCA 0.884153 -213 TTGCTGAAGTATCGCCTGATATCTGCTTTT 9 23 1 ATCGCCTGAT 0.734505 -98 TAACGGTTAAATAGCCCGATGAAAGGAATA 24 29 0 ATAGCCCGAT 0.828097 -104 TCTTGCAAAAACAGCCTGCGTTTTCATCAG 27 89 1 ACAGCCTGCG 0.794137 -96 AATACATACAATTGCCCGAATAGGTTGAAA 29 193 1 ATTGCCCGAA 0.86511 -32 TGCAAAGGGGATTGCCTGCACCTGCCAGGT 34 146 0 ATTGCCTGCA 0.893516 -102 CGTGCAACAGATAGCCCGCTCTGTCGCCCT 39 25 1 ATAGCCCGCT 0.825143 -54 TCCAGCACACATCGCCTGAAAGA 42 4 0 ATCGCCTGAA 0.829079 -142 TATTCTGTCAATAGCCTGCGGATGAAATCA 45 161 1 ATAGCCTGCG 0.809205 -140 ACGCATTGCCCGATGCCGCAAAGG 51 5 1 ATTGCCCGAT 0.78531 -161 TTAAAACATAACAGCCCGAAACTTTGGATA 53 40 0 ACAGCCCGAA 0.884822 -116 TACGTTGGCTACAGCCTGAAATGTTCCGAG 54 22 0 ACAGCCTGAA 0.911195 -61 CAACGTAGTTACAGCCTGAAAGATGACGAG 54 45 1 ACAGCCTGAA 0.911195 -38 GATTTATAAGAAAGCCTGAAGTGAGATATC 76 64 1 AAAGCCTGAA 0.736777 -164 AACAAATCACATTGCCTGAATCGGCTCATC 77 104 1 ATTGCCTGAA 0.895463 -195 CTCAATGCCTGCTCATCAAAAAA 79 82 0 AATGCCTGCT 0.542852 -13 ********** Masking position 1 Map Score: 9.49615 Number of sites scoring better than the average of aligned sites = 450 Number in coding regions = 402 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 8 CTAACCCTTGTGGGGCTGCGCTGAAAAGCGAC 5 69 1 TGGGCTGCGT 0.684535 -78 ACCAGACTTACGCCCCCGCGATACTTACGCGG 6 41 0 CGCCCCGCGT 0.938311 -251 CCGGTTGCTGCGCGCTGGCCGTGACCAAACTG 6 95 0 CGCGTGGCCT 0.776002 -197 GTTCTTTGCGTGGCCCGGCGATCTTATATTGA 11 61 0 TGGCCGGCGT 0.925826 -61 GCCCGCTATCCGGGGCGGCCTTCCCTGCCGAT 15 22 1 CGGGCGGCCT 0.944232 -145 GACTGGCAGACGTCCCCGCCGTTGGTGATTAA 17 25 1 CGTCCCGCCT 0.775253 -65 CGAACAAAATCGCCGCTGCGCGGTGCCCTCGA 26 35 1 CGCCCTGCGG 0.928225 -266 CCATGTGGGCTGCCCCGGCCTTCAGGGAACGC 26 135 1 TGCCCGGCCT 0.979756 -166 CTTCAGGGAACGCCTCGGCGATTTTGACGCCA 26 154 1 CGCCCGGCGT 0.984572 -147 TTATGACACCTGCCACTGCCGTCAATAAGTTC 28 255 0 TGCCCTGCCT 0.97334 -46 TCCTTCAAGCCGCCTCTGCCTTGGCTGCGTTC 33 140 0 CGCCCTGCCT 0.990265 -135 AACGGGCATACGGCCCGGGGATCTCTGCGCCC 33 204 1 CGGCCGGGGT 0.849999 -71 GGCAACTATTCGCCGTTGCCCTTCATTCACCG 34 12 0 CGCCTTGCCT 0.918993 -236 CCCGCTCTGTCGCCCTGGCGTTTAATAATTTA 39 39 1 CGCCTGGCGT 0.876831 -40 GACACGCTACCGCCCCTGGCTTTTTAGCTACC 45 103 0 CGCCCTGGCT 0.944154 -198 GCAGAGCCAGTGGCCCTGCCCTTATCAGTTA 52 10 0 TGGCCTGCCT 0.952132 -60 GCAGGGCCACTGGCTCTGCCCTTTTGCTATTC 52 23 1 TGGCCTGCCT 0.952157 -47 ATTTGCCTATGCCTTGTACTCGTCA 54 68 0 TGCCATGCCT 0.617084 -15 TGCTGATTGACTGCGCTGCCTTCGTCTTTAGA 64 21 1 CTGCCTGCCT 0.677519 -141 AATAGACCGGCGTCCCGGCCTGCTGGAATTTA 70 186 1 CGTCCGGCCG 0.795915 -115 AAAGGCCGAACGCGTCGGCCTTCAGACAGGAG 78 18 0 CGCGCGGCCT 0.968809 -123 ATAAAGGTCGTGCCTCTGGCGGATGTACGTTT 83 54 1 TGCCCTGGCG 0.620615 -139 **** ***** * Masking position 8 Map Score: 24.5365 Number of sites scoring better than the average of aligned sites = 1625 Number in coding regions = 1556 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 9 TTCTTACGATTGCGGCAGGCCGTGTTATTATT 12 51 1 TGCGGCAGCG 0.9437 -54 TCATTCAAGTTGCATCAAGGCGGCAAGTGAGC 33 67 1 TGCATCAGGG 0.945907 -208 TTTATGCCTTTGCGGCATCGGGCAATGCGT 51 9 0 TGCGGCACGG 0.935194 -157 GAGAGTAGCTTGCGTCAATGGGCAAGGTGGGC 65 83 0 TGCGTCATGG 0.952196 -166 CAGTTGATACTGCGTCATGGTGAGATAAAAAT 65 179 0 TGCGTCAGGG 0.994425 -70 GCGCAAAAACTGCGTCAGGGAGGACGAGGTCG 70 43 0 TGCGTCAGGG 0.994425 -258 TAACGTGAGATGGGTCAGGAGGACATATCGCG 75 13 0 TGGGTCAGAG 0.855658 -85 GCAACGCATTTGCGTCATGGTGATGAGTATCA 77 202 1 TGCGTCAGGG 0.994425 -97 GGTAAGTTGTTGCGTCAGGAGGCGTT 78 125 1 TGCGTCAGAG 0.976076 -16 ******* ** * Masking position 7 Map Score: 7.81395 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 101 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 TAGTGTTAATCCTGTCCGAATAGCGTCAGT 2 155 0 CCTGTCCGAA 0.902716 -100 TGCTTTTTATTCTGTCTCAACTCTGGATGT 7 69 1 TCTGTCTCAA 0.719946 -23 AACTTTACGGCCTGTCTCATTCTTACGATT 12 32 1 CCTGTCTCAT 0.720799 -73 GATACTCTTCCTGTCAAAATATAAGAAAC 12 86 0 CCTGTCAAAA 0.668802 -19 GATTTAATATCCCGTCTGAAAAACGAAAAT 36 44 1 CCCGTCTGAA 0.872087 -29 CCTCTTTAAACCTGTCTGAACCGTTATCAA 42 117 0 CCTGTCTGAA 0.975439 -29 GCCTGAAAGACCAGTCTGAATTATTCTGTC 45 140 1 CCAGTCTGAA 0.82143 -161 AAATAGTTGCCCTGTCAGACTTGCAGGCAG 49 75 0 CCTGTCAGAC 0.877131 -20 TAGGGACCTTTCTGTCTGAACCTGGTTCGA 53 136 0 TCTGTCTGAA 0.834022 -20 TTATTCATTTCCTGTCTCACTTTGCCTTAA 60 156 1 CCTGTCTCAC 0.875648 -75 CGGTGAAACGCCTGTCACAATCACACTAAA 70 260 1 CCTGTCACAA 0.91333 -41 TAGGGTTTCGCCTGTCAGCAGACAAATAAC 76 32 0 CCTGTCAGCA 0.764641 -196 TTCTCTTCTCCTGTCTGAAGGCCGACGCG 78 10 1 CCTGTCTGAA 0.975439 -131 ********** Masking position 5 Map Score: 7.91133 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 94 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 11 GGAGATGTGATCTGCCCGGCATTAAACCGC 4 226 0 TCTGCCCGGC 0.739119 -32 TGTACGTCGCTTTTCAGCGCAGCCCCACAA 5 76 0 TTTTCAGCGC 0.825272 -71 ATGCCGTGGTTTTACACGGCTTTTTTTTGT 8 113 1 TTTACACGGC 0.861652 -73 AAAGAGAACTTTCTCCCGGCCAGCACTGCT 20 182 0 TTCTCCCGGC 0.875265 -119 GTTCTCTTTTCTTACACCGCGCCGATAAAA 20 203 1 CTTACACCGC 0.83456 -98 AAAATCCCTTTTATCCCCGCGTTAAGCGTC 25 78 1 TTATCCCCGC 0.840766 -60 GTTAAGCAAATCATCACCGCACTGACTATA 30 224 1 TCATCACCGC 0.536728 -77 GCGCATTGCGCTTACCCGGCTTACAGAACA 33 17 0 CTTACCCGGC 0.812284 -258 TGTACATCTATTTTCAGGGCATCCACTGTA 34 90 1 TTTTCAGGGC 0.735859 -158 AGCGGCGCAACTTGCCCCGCACCAAATAAA 38 54 0 CTTGCCCCGC 0.877914 -66 TAGCCCCCTCCTTTCCCCGCTCATTCATTA 41 132 1 CTTTCCCCGC 0.939853 -124 AGGTTGTTCTCCCGGCTTATGAGCTG 43 19 0 TTCTCCCGGC 0.875265 -16 GACGCCTGCATTCGCACCGCCCC 44 12 1 TTCGCACCGC 0.79011 -13 GCCACGTATGTTTACACCGCATCCGGCATA 46 19 1 TTTACACCGC 0.913489 -179 CGCGGTCAAGTTTTCACCGCAAAGGTATTT 48 77 0 TTTTCACCGC 0.95743 -108 GTTGAATATTTTTTCAGCGCCATTTTTATT 51 52 1 TTTTCAGCGC 0.825272 -114 TGTGACAGGCGTTTCACCGCCGTCTGTAAA 70 249 0 GTTTCACCGC 0.753179 -52 ATACTGATATTTTTCCTCGCACAAAGGACT 76 204 1 TTTTCCTCGC 0.633553 -24 GCCCTAGATTTCTACCCGGCTTAACTACTC 79 19 0 TCTACCCGGC 0.742961 -76 ********** Masking position 5 Map Score: 9.74836 Number of sites scoring better than the average of aligned sites = 1000 Number in coding regions = 863 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 12 CGGAAGTCCGGCGCGCTTTATACCACAAATACGTC 3 124 0 GGCGTTTCCA 0.961469 -177 GTGCCGATACGTGTGTGTTGTTACACAAAGTGAGA 3 196 0 GGTGTTTACA 0.685177 -105 GACAACTTTTGTTCGTTTGTTAACGAACTTTCAGA 20 265 1 GTCGTGTACG 0.674695 -36 CTACCGGGTCGGGCGCGAGGTAACATCCCTGTAAA 26 81 1 GGCGAGTACA 0.802753 -220 TGTGGGCTGAGGGCGCGTTTTACAGGGATGTTACC 26 99 0 GGCGTTTCAG 0.617951 -202 CGCCCACAGAGCGCGGTTGCTAACAAGAACACAAC 34 206 1 GGCGTGTACA 0.972327 -42 TAACAGGGAGTGCGTATGTTTCCAGAATACCGAG 36 10 1 GGCGTGTCCA 0.966561 -63 CTTTTTTATTGCGCGGTTGATAACGGTTCAGACAG 42 101 1 GGCGTGTACG 0.966561 -45 GTAGCAAAGTGCGCGTGTTTTTATGCCGGATGCGG 46 35 0 GGCGTTTATG 0.662861 -163 TGGTCGTTACGGGCGAGTTTTTCCATCTTTTGGAT 48 155 0 GGCGTTTCCA 0.961469 -30 ATCCTGTTCGGGGCGCATTCTAACAGAAAAAGAAA 51 114 0 GGCGTTTACA 0.968084 -52 AGTTTCGTATGAGCGATTTTTGACAGTTGCCTCTC 57 115 1 GGCGTTTACA 0.968084 -186 * *** ** * *** Masking position 11 Map Score: 5.80424 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 115 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 13 ATAAAAGGGATTTTTCATGCAACTTTAAGG 25 62 0 TTTTTCATGC 0.814397 -76 ATACACTTCATCCTTCAAGCCGCCTCTGCC 33 152 0 TCCTTCAAGC 0.803363 -123 TCTTTCAGGCGATGTGTGCT 42 1 1 TCTTTCAGGC 0.965801 -145 TTCAGACTGGTCTTTCAGGCATCCAGACAC 45 130 0 TCTTTCAGGC 0.965801 -171 CTTTTAATTCCTTCATGACAGGTAATGT 48 9 1 TCCTTCATGA 0.718406 -176 GTACTCGTCATCTTTCAGGCTGTAACTACG 54 48 0 TCTTTCAGGC 0.965801 -35 TCTCTTCTTCATGCTCTCTGCTGT 55 5 1 TTCTTCATGC 0.804057 -61 AGCTATTCCTTGAGGCTATGTCTGTC 73 102 0 TCCTTGAGGC 0.77375 -16 AATCGGCTCATCTTTTATGCAGTCCTGCAG 77 122 1 TCTTTTATGC 0.607476 -177 AAGTTGATGTTCTTTCATGCTCTTATAAAG 83 30 1 TCTTTCATGC 0.946564 -163 CTGACACTATTTTTTCAGGAAGGCAATGAC 84 64 1 TTTTTCAGGA 0.518766 -228 ********** Masking position 7 Map Score: 3.64654 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 158 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 14 CATATTACCGACCCCAAAGGGCACCCCGGAAT 3 233 0 ACCCCAGGGC 0.914678 -68 TTGATAACTCCCCCAAAATAGTTCGAGTTGCA 4 17 1 CCCCAATAGT 0.540198 -241 CAAAAAGGAGCCGCCTGAGGGCGGCTTCTTTT 5 15 1 CCGCCAGGGC 0.892032 -132 TTCAGCGCAGCCCCACAAGGGTTAGCTGAATT 5 62 0 CCCCAAGGGT 0.902919 -85 TCAATGCATACCCCCCTATAGTATATAACACT 15 115 0 CCCCCATAGT 0.894244 -52 ATATAGAATACCCCCCTATAGTATATTGC 15 148 1 CCCCCATAGT 0.894244 -19 CAGGATTTTTACCCCTAAGGGCTGATAACGCT 19 47 1 ACCCCAGGGC 0.914678 -99 CTGACTAAACCGCCCACAGAGCGCGGTTGCTA 34 196 1 CGCCCAGAGC 0.727139 -52 CATGAGAAAGCCCCCGGAAGATCACCTTCCGG 42 66 1 CCCCCAAGAT 0.71009 -80 AATAAAAAAGCCCCCGGAAGGTGATCTTCCGG 42 79 0 CCCCCAAGGT 0.971537 -67 GCCTTCACTTCCCCCGTAAGGCCTTTCTTTTT 66 30 1 CCCCCAAGGC 0.975335 -47 GGATCGACAACCCCCATAAGGTACAATCCCCG 71 61 1 CCCCCAAGGT 0.971537 -48 ***** ***** Masking position 8 Map Score: 5.05864 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 51 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 15 GCATTAAACCGCACAGATATAAAAGTGAAAAAG 4 205 0 GCCGATTAAA 0.89067 -53 GCTAAGTATAGCCCTGATTAAACATATTACGGG 6 209 0 GCCGATAAAC 0.963511 -83 TGAGACTATAGCTCGGATTAAAAAACGGTATTT 20 108 0 GCCGATAAAA 0.975149 -193 TTCTTACACCGCGCCGATAAAAAATATGCACGT 20 211 1 GCCGATAAAA 0.975149 -90 AAACATTAATGCACTGATAAATAATGATTTATA 35 148 0 GCCGATAATA 0.89067 -137 TGTTATATCTGCCCCGATAAAACGGGGCAGATA 60 16 1 GCCGATAAAC 0.963511 -215 ACCGCTGCACAGATCAAAACGAAAGAAAA 66 58 0 GCCGATAAAA 0.975149 -19 ** * *** **** Masking position 7 Map Score: 3.2333 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 38 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678