AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00380_ecoli_reg_300.orf -o00380_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 caiC 58 probable crotonobetaine/carnitine-CoA ligase #2 caiB 35 l-carnitine dehydratase #3 caiA 30 probable carnitine operon oxidoreductase #4 caiT 300 probable carnitine transporter #5 surA 52 survival protein #6 imp 254 organic solvent tolerance #7 rpsB 300 30S ribosomal subunit protein S2 #8 tsf 257 protein chain elongation factor EF-Ts #9 pyrH 146 uridylate kinase #10 frr 291 ribosome releasing factor #11 yaeM 91 putative ATP-binding component of a transport system #12 yaeS 185 orf, hypothetical protein #13 cdsA 120 CDP-diglyceride synthetase #14 yaeT 29 orf, hypothetical protein #15 hlpA 121 histone-like protein, located in outer membrane or nucleoid #16 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #17 mhpA 76 3-(3-hydroxyphenyl)propionate hydroxylase #18 entC 300 isochorismate hydroxymutase 2, enterochelin biosynthesis #19 sdhC 300 succinate dehydrogenase, cytochrome b556 #20 potF 300 periplasmic putrescine-binding protein; permease protein #21 ybjO 59 orf, hypothetical protein #22 ybjF 40 putative enzyme #23 hemA 213 enzyme in alternate path of synthesis of 5-aminolevulinate #24 ycjL 121 probable amidotransferase subunit #25 ycjC 26 orf, hypothetical protein #26 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #27 tynA 247 copper amine oxidase (tyramine oxidase) #28 maoC_ydbO 284 maoC: putative aldehyde dehydrogenase, ydbO: orf, hypothetical protein #29 katE 182 catalase; hydroperoxidase HPII(III) #30 atoS 214 sensor protein AtoS for response regulator AtoC #31 atoD 195 acetyl-CoA:acetoacetyl-CoA transferase alpha subunit #32 atoB 30 acetyl-CoA acetyltransferase #33 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #34 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #35 cvpA 165 membrane protein required for colicin V production #36 folC 69 dihydrofolate:folylpolyglutamate synthetase; dihydrofolate synthetase #37 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #38 dedA 82 orf, hypothetical protein #39 usg 65 putative PTS system enzyme II A component #40 pdxB 98 erythronate-4-phosphate dehyrogenase #41 ygcA 56 putative enzyme #42 yqeF 251 putative acyltransferase #43 pepP 25 proline aminopeptidase P II #44 ygfB 161 orf, hypothetical protein #45 epd 284 D-erythrose 4-phosphate dehydrogenase #46 yggD 21 putative transcriptional regulator #47 cmtA 27 PTS system, mannitol-specific enzyme II component, cryptic #48 cmtB 300 PTS system, mannitol-specific enzyme II component, cryptic #49 accB 300 acetylCoA carboxylase, BCCP subunit; carrier of biotin #50 yhdT 108 orf, hypothetical protein #51 dam 106 DNA adenine methylase #52 damX 91 putative membrane protein; interferes with cell division #53 aroB 56 3-dehydroquinate synthase #54 aroK 199 shikimate kinase I #55 yrfD 68 orf, hypothetical protein #56 rpmH 300 50S ribosomal subunit protein L34 #57 yidC 223 60 KD inner-membrane protein #58 thdF 105 GTP-binding protein in thiophene and furan oxidation #59 tnaL 242 tryptophanase leader peptide #60 tnaA 205 tryptophanase #61 udp 298 uridine phosphorylase #62 yigN 140 putative alpha helix chain #63 ubiE 94 2-octaprenyl-6-methoxy-1,4-benzoquinone --> 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone #64 fadB 189 4-enzyme protein: 3-hydroxyacyl-CoA dehydrogenase; 3-hydroxybutyryl-CoA epimerase; delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase; enoyl-CoA hydratase #65 katG 300 catalase; hydroperoxidase HPI(I) #66 yjfG 175 putative ligase Motif number 1 TAGTTCGAGTTGCAGAAAGGCGGCAAGCTCGAG 8 35 1 TCAAAGGCGG 0.932424 -223 GATATAAAAGTGAAAAAGGGGGCCATATGCAGG 8 190 0 TAAAAGGGGC 0.736455 -68 AGATGGGCACAAAAAGAAGCCGCCCTCAGGCGG 9 25 0 AAAGAGCCGC 0.799766 -122 TTCTTGAACGACAAAAACGCCGCTCAGTAGATC 11 12 1 AAAAAGCCGC 0.939708 -80 CAGAATAAAAAGCAAAACGCCGCCAGCCGATCC 11 50 0 ACAAAGCCGC 0.955874 -42 GGCGGCAACAGAAACAACGCCGCGATGACGACG 13 64 0 GAAAAGCCGC 0.934107 -57 AGGGAGAGGGGGCAGAACGGCGCAGGACATCAC 18 93 1 GCAAAGGCGC 0.933989 -208 CCAACCTGGCTACATAATGCCGCGCATGTCGCG 21 26 1 TCAAAGCCGC 0.966265 -34 GAAAACAATGCCGCGACATGCGCG 21 46 0 AAAAAGCCGC 0.939708 -14 CGGCAATTACTCCAAAAGGGGGCGCTCTCTTTT 23 121 1 TCAAAGGGGC 0.795244 -93 TCATTCAAGTTGCATCAAGGCGGCAAGTGAGCG 26 67 1 TCACAGGCGG 0.779542 -208 GAAGTGTATATAAAGAATGTCGCCAGAAATAAA 26 173 1 TAAAAGTCGC 0.672796 -102 CCGCGCATCAATAAAAATGGCGCTGAAAAAATA 35 58 0 AAAAAGGCGC 0.917982 -108 ATCAAGGTAATAAAAAAGGTCGCCGAAGCACCT 48 16 0 TAAAAGTCGC 0.672796 -285 AGCGATAAATTCCAGCAGGCCGGGACGCCGGTC 49 190 0 TCACAGCCGG 0.831196 -111 CTGCTAAAGCGTCAAAAGGCCGGATTTTCCGGC 50 13 1 GCAAAGCCGG 0.929664 -96 TCCCCAGTAATAAAAAAGGCCGGAAAATCCGGC 50 31 0 TAAAAGCCGG 0.932546 -78 CCCTGATGGGTGAAGAAAGCGGGGATTGTACCT 50 79 0 TAAAAGCGGG 0.723027 -30 TAAAAAAGACAGCAAAATGCCGCCTGAATGATA 54 143 0 ACAAAGCCGC 0.955874 -57 ACCAGTGGAAACCAGCATGGCGCGCCGGGTGGA 56 85 0 ACACAGGCGC 0.799457 -216 CCATGGGTGATTAAAGAGGCCGGATTGTAATAA 56 199 0 TAAGAGCCGG 0.779872 -102 AGTTTTCGCTAAAATAAGGGCGGTCAGTTGACC 58 18 1 AAAAAGGCGG 0.882468 -88 CCCTACGAAAAGAAAAAAGGCGGTCAACTGACC 58 39 0 AAAAAGGCGG 0.882468 -67 GCATCTGACAGTCAGAATGCGGCTTCGTAAGCG 59 14 0 GCAAAGCGGC 0.788154 -229 TACGCAAAAATACAAAAGGCCGAACGCGTCGGC 62 31 0 TCAAAGCCGA 0.602225 -110 ATGCTGCCTCGAAATGAGGGCGGGAAAATAAGG 65 40 1 GAAGAGGCGG 0.636374 -261 * ** ** ***** Masking position 7 Map Score: 30.3337 Number of sites scoring better than the average of aligned sites = 1077 Number in coding regions = 943 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 2 AGTCTGTGTATACGAAATGGATCGGAAGTCCGGCGCGCTTTATA 7 137 0 TAAACGTCGC 0.948499 -164 CGGGATGAGCGAGCGAAGATAACGCATCTGCGGCGCGAAATATG 8 98 1 GAAACGTCGC 0.989993 -160 TAACACAAAAGCAGATATCAGGCGATACTTCAGCAAAAGCGACC 13 15 0 GTAGCGTCGC 0.961632 -106 CTGCTTTTGTGTTAATACCCGTCGTCATCGCGGCGTTGTTTCTG 13 45 1 GTAGCGCCGC 0.94109 -76 GCCACCCAGCGTTGTAACGTGTCGTTTTCGCATCTGGAAGCAGT 19 117 1 GAAGCGCCTC 0.788685 -184 AAAGTGGACTAAATTATCGCCATTACTGCGCTTTAAATG 24 93 0 GAAACGTCGC 0.989993 -29 AAAGAATGTCGCCAGAAATAAACGGGCATACGGCCCGGGGATCT 26 184 1 GAAACGTCGC 0.989993 -91 GAACATTTCAGGCTGTAGCCAACGTAGTTACAGCCTGAAAGATG 38 26 1 GTAACGTCGC 0.975289 -57 GCGAAACGTGGAATAAAAGGAATGTTTGTCCAGCCGAAGAAGAC 45 106 0 GAAATGTCGC 0.82209 -179 TAATTCACTGTTTTCAAAACACCGGTTTCCCTGCTCAATTGCTT 48 198 1 TAAACGCCGC 0.921365 -103 GACACTCTGGGGCAAAATAGACCGGCGTCCCGGCCTGCTGGAAT 49 171 1 GAAACGCCGC 0.98436 -130 GACTGCTAAAGCGTCAAAAGGCCGGATTTTCCGGCCTTTTTTAT 50 11 1 GAAGCGTCGG 0.813333 -98 ACGTTCAGCGTAAAAACATTACCGCTTTTACGGCTGT 54 4 0 TACACGTCGC 0.81126 -196 GCTTGAACAGGTTGGAGTGAAACGACAATGCGGCCCGAGTAGCG 57 47 0 GAGACGTCGC 0.926179 -177 TTTTCGTAGGGCGGATAAGCACCGCGCATCCGCCACACAAAGCA 58 61 1 GTAACGTCCC 0.755621 -45 AACAGGAGTGGTAACAATGAAGCGAAGCCGCATCTGACAGTCAG 59 32 0 GAAACGCCTC 0.854365 -211 AGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTAT 62 73 1 TAAGCGTCGC 0.921365 -68 TTAGCACATCGTTCATCCAGAGCGTGATTTCTGCCGAGCGTGAT 64 51 1 GTCACGTCGC 0.90207 -139 * ** * ** * * ** Masking position 14 Map Score: 20.1684 Number of sites scoring better than the average of aligned sites = 578 Number in coding regions = 531 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 GCGGGCGCTAGTCAGGCAAGCCGACTGACGCCACGCG 1 12 0 GTAGACGCTG 0.673558 -47 GTAACGTTGCGCGTGACAAACGGTCAGAGACTAACGT 6 202 0 GCTGACGCAG 0.979956 -53 GCAAAACGCCGCCAGCCGATCCGCAAGGATCTACTGA 11 35 0 GCAGACGAAG 0.789528 -57 GAGGGTTAGGGTGAGGGGAACAGCCAGCACTGGTGCG 18 23 1 GTAGACGCAG 0.909928 -278 TTTGTGAACAGCCTATACTGCCGCCAGGTCTCCGGAA 19 64 1 GCTATCGCAG 0.825186 -237 CCTCCGGTCTGCTTGCGGGTCAGACAGCGTCCTTTCT 19 183 0 GCTGGCGCAG 0.983448 -118 CTTTTATATAGCGAGCAGTGCTGGCCGGGAGAAAGTT 20 169 1 GCAGTCGCCG 0.967076 -132 AACCCTTAATGCTAGCGTTACCGTCCGCTATCGTCTA 23 46 1 GCAGTCGCCG 0.967076 -168 GGCGCATTGCGCTTACCCGGCTTACAGAACAAAAAGA 26 11 0 GCTAGCTCAG 0.491685 -264 TGGCAGGTGTGCCAGCTTTTCATACAGTGGATGCCCT 27 105 0 GCAGTCTCAG 0.774305 -143 TGGCACACCTGCCAAACAACCTGGCAGGTGCAGGCAA 27 128 1 GCAAACGCAG 0.933693 -120 GGAGTTGCAAGTCAGGGTGCCAGACCGGCACCCTCAG 33 19 0 GTAGGCGCCG 0.901888 -76 TGCAAAGTCTGCCTGCAAGTCTGACAGGGCAACTATT 33 67 1 GCTGGCGCAG 0.983448 -28 TGAAATCTTCGCAAGTATGCCTGGCCGCGAGATTATG 40 27 1 GCAGGCGCCG 0.985679 -72 AAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACT 42 140 0 GCTGACGCAG 0.979956 -112 TTTTCCCTGAGCAAATTTGCCAGACAGAGTAATCCAG 45 243 0 GCAAGCGCAG 0.944793 -42 CTAATAGACCGCTTGATAAGCGGCCTGACCTTTCTTG 52 14 0 GCTGACGCTG 0.908969 -78 TCCTGAATCCGCAAGGTGATCTGGTCGTACCAGATGA 64 156 0 GCAGACGTCG 0.737435 -34 ** ** * * * *** Masking position 11 Map Score: 20.1021 Number of sites scoring better than the average of aligned sites = 882 Number in coding regions = 843 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 CAATTGACCGCAGCCGGAAAACGGTAAAAG 6 66 0 CAGCCGGAAA 0.836429 -189 CCCCAAAGGGCACCCCGGAATATGTGCCGA 7 224 0 CACCCCGGAA 0.936815 -77 GGCTTGATAACTCCCCCAAAATAGTTCGAG 8 14 1 CTCCCCCAAA 0.701925 -244 CTGATGTAAGCTCCCGGGAATTCTCGAGCT 8 60 0 CTCCCGGGAA 0.883079 -198 GAGATGTGATCTGCCCGGCATTAAACCGCA 8 225 0 CTGCCCGGCA 0.898092 -33 CTTTTCAGCGCAGCCCCACAAGGGTTAGCT 9 67 0 CAGCCCCACA 0.583283 -80 CGTGACCAAACTGCCTGCAACAATAACGCC 10 78 0 CTGCCTGCAA 0.924659 -214 CCCCAGCCCTCACCCTGGAAGGGAGAGGGG 18 74 1 CACCCTGGAA 0.931822 -227 GTCTCCGGAACACCCTGCAATCCCGAGCCA 19 91 1 CACCCTGCAA 0.907968 -210 AGAGAACTTTCTCCCGGCCAGCACTGCTCG 20 180 0 CTCCCGGCCA 0.724848 -121 GCTGCGTTCGCTCCCCCGAATCACTTACCT 26 119 0 CTCCCCCGAA 0.814056 -156 CCTGCAAAGTCTGCCTGCAAGTCTGACAGG 33 65 1 CTGCCTGCAA 0.924659 -30 TAAAACATAACAGCCCGAAACTTTGGATAA 37 39 0 CAGCCCGAAA 0.908447 -117 ACGTTGGCTACAGCCTGAAATGTTCCGAGC 38 21 0 CAGCCTGAAA 0.901448 -62 AACGTAGTTACAGCCTGAAAGATGACGAGT 38 46 1 CAGCCTGAAA 0.901448 -37 AATAGCAAAGCTCCCTGCCAATGTTACAGC 39 30 0 CTCCCTGCCA 0.824966 -36 ATTATTACGCCAGCCTGGAATAAAGCTTCC 45 37 1 CAGCCTGGAA 0.94446 -248 GCACAAAATGCTGCCTCGAAATGAGGGCGG 65 33 1 CTGCCTCGAA 0.833922 -268 ********** Masking position 10 Map Score: 18.0825 Number of sites scoring better than the average of aligned sites = 898 Number in coding regions = 838 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 5 GATGGCGAGCACTGCCCGGGGCCAAAATGGCAAATA 10 147 1 ACCCGGGAAA 0.979354 -145 TACCGTAAACCCTGTCAGGGAATAAAAAACGC 12 164 1 CCTCGGGAAA 0.956297 -22 AATGGCGAACCCCACCGGCGGCAACAGAAACAACGC 13 77 0 CCCCGCGACA 0.921662 -44 GCAGACCACCAGCGTTACAATGGCGAACCC 13 101 0 ACCCGCGCAA 0.961339 -20 CAATCCCGAGCCACCCAGCGTTGTAACGTGTCGTTT 19 108 1 CCCCGCGTAA 0.909451 -193 GCAAAGCGGGACGTACAGGGGCTAAATCGGCTAAAC 29 33 0 ACACGGGAAA 0.879634 -150 GTAGGGATTTCCTTCCCGCGCATCAATAAAAATGGC 35 70 0 CCCCGCGCAA 0.975553 -96 CCTTTTCTGGTCCACCAGGGCCCAAAGTGGTAGCAT 44 107 1 TCCCGGGAAA 0.894747 -55 TTTTAGGGTACCGTCCGGCGGTAAAAATAAAATACT 48 257 0 CCCCGCGAAA 0.988599 -44 TCTAACATTGACACTCTGGGGCAAAATAGACCGGCG 49 162 1 ACTCGGGAAA 0.931672 -139 CATACGCTTTACAGACGGCGGTGAAACGCCTGTCAC 49 242 1 ACACGCGAAA 0.892755 -59 GCTTTCTTCACCCATCAGGGACAAAAA 50 92 1 CCTCGGGAAA 0.956297 -17 TAGATGAAACACGTTCAGCGTAAAAACATTACCGCT 54 22 0 ACTCGCGAAA 0.93951 -178 GTATAATCCTCCACCCGGCGCGCCATGCTGGTTTCC 56 76 1 CCCCGCGCAT 0.785086 -225 CGGGATCGTCACCACCAGGGTGTAAAGGGTGGCATT 57 161 0 ACCCGGGAAA 0.979354 -63 ** ** *** *** Masking position 8 Map Score: 15.4435 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 265 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 6 CGAAACAAAAATGTGATACCAATCACAGAATACAGC 4 145 1 AGTGATAACC 0.897425 -156 AAACCCTGTCAGGGAATAAAAAACGC 12 170 1 AGGAATAACC 0.435448 -16 CATAAGCGCAATGTGATGTCCTGCGCCGTTCTGCCC 18 102 0 AGTGATCTCC 0.950218 -199 ACTGATGCAAAGGGGATTGCCTGCACCTGCCAGGTT 27 145 0 AGGGATCTCC 0.940038 -103 AACGTTTGCGTAGGGATTTCCTTCCCGCGCATCAAT 35 79 0 TGGGATCTCC 0.93239 -87 CATATTTCCTTTGTGATAAAAATCACTTTTTTTAAA 42 166 1 TGTGATAACC 0.885006 -86 GCCACCTTCCTGCTGATTGACTGCGCTGCCTTCGTC 44 11 1 TCTGATCTCC 0.602363 -151 ATATAAATATTTGTGATCTACAACACGCCTTATCTA 48 71 0 TGTGATCACC 0.970239 -230 AATATCAATTATGTAATATGCATCACGATATGCGGT 48 113 1 AGTAATCACC 0.79912 -188 TTTTTATTACTGGGGATCGACAACCCCCATAAGGTA 50 48 1 TGGGATCACC 0.963998 -61 TCCGGGCGGGACGGGATCGTCACCACCAGGGTGTAA 57 172 0 AGGGATCACC 0.968193 -52 CCCCGAACGATTGTGATTCGATTCACATTTAAACAA 59 151 1 TGTGATATCC 0.79854 -92 AGGGTGATTTATGTGATTTGCATCACTTTTGGTGGG 61 157 1 AGTGATCACC 0.973726 -142 TAACATTTTTTCGTGATACTCATCACCATGACGCAA 61 211 0 TGTGATCACC 0.970239 -88 ATTAAGATCAATTTGATCTACATCTCTTTAACCAAC 65 173 1 ATTGATCACC 0.692873 -128 * ***** ** * * Masking position 6 Map Score: 11.7541 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 325 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 7 CTTCATATTTCGCGCCGCAGATGCGTTATCT 8 114 0 CGCGCGCAGA 0.899826 -144 ACCCTTGTGGGGCTGCGCTGAAAAGCGACGT 9 72 1 GGCTCGCTGA 0.772624 -75 ATCACTGAAGCCCTACGCTAACAAATAGCGC 12 34 0 CCCTCGCTAA 0.945868 -152 TTTCTTACACCGCGCCGATAAAAAATATGCA 20 210 1 CGCGCGATAA 0.490613 -91 AGCCAGATCCCGCTTCGGAGACTATTCTGGA 29 89 0 CGCTCGGAGA 0.942534 -94 TGCCTTCGCTGAGGGTGCCGGT 33 2 1 GCCTCGCTGA 0.772624 -93 GGAAGGAAATCCCTACGCAAACGTTTTCTTT 35 90 1 CCCTCGCAAA 0.966159 -76 ATAGTGTCGCCCCTTCGCAGACCATGGGTCT 44 50 0 CCCTCGCAGA 0.972954 -112 GCAAGGTTTTCCCTGAGCAAATTTGCCAGAC 45 255 0 CCCTAGCAAA 0.753969 -30 GCAGTTTTTGCGCTGCGGAAAAGGTGACATT 49 62 1 CGCTCGGAAA 0.928657 -239 CGTACATTTTCCCTGCGAAAAGGTGCGGAAA 56 125 1 CCCTCGAAAA 0.863059 -176 TGCTTATCCGCCCTACGAAAAGAAAAAAGGC 58 51 0 CCCTCGAAAA 0.863059 -55 AAATGTTAAACCCTTCGGTAAAGTGTCTTTT 61 239 1 CCCTCGGTAA 0.888475 -60 TCCTGCGAGGCGCTACGCAAAAATACAAAAG 62 46 0 CGCTCGCAAA 0.966159 -95 GATCTGATCACGCTCGGCAGAAATCACGCTC 64 70 0 CGCTGGCAGA 0.764461 -120 CTCAATGTTGCGCTCAGGTGAATCGCGCCAG 66 69 1 CGCTAGGTGA 0.518653 -107 **** ****** Masking position 11 Map Score: 11.8478 Number of sites scoring better than the average of aligned sites = 572 Number in coding regions = 532 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 8 TCCATTTCAATTAACCGCACTGCGGATTAC 5 27 0 TTAACCGCAC 0.958241 -26 TGCCCGGCATTAAACCGCACAGATATAAAA 8 214 0 TAAACCGCAC 0.915816 -44 TCTCTTTTCTTACACCGCGCCGATAAAAAA 20 205 1 TACACCGCGC 0.678224 -96 GTTGGTATTATTTCCCGCAGAC 23 202 1 TTTCCCGCAG 0.663472 -12 TGAACCTGACTAAACCGCCCACAGAGCGCG 27 191 1 TAAACCGCCC 0.925251 -57 TACCGCTACCTTAACCACACTCCATCGGTC 30 82 0 TTAACCACAC 0.503199 -133 ATAATCGTCATATACCGGACAAGACTAGTG 30 186 1 TATACCGGAC 0.702039 -29 GAGACGAGAGTTAACCGGACAAGTGTGCCA 40 62 0 TTAACCGGAC 0.863569 -37 CAGGTAAGGTTTCCCCGGACGATTTGCTGG 45 217 1 TTCCCCGGAC 0.662749 -68 TTGCTTTCATTAAACCGCACGAGTATTTTA 48 236 1 TAAACCGCAC 0.915816 -65 GTATTTTATTTTTACCGCCGGACGGTACCC 48 258 1 TTTACCGCCG 0.801563 -43 TGACAGGCGTTTCACCGCCGTCTGTAAAGC 49 247 0 TTCACCGCCG 0.742006 -54 AAAGGCCGGATTTTCCGGCCTTTTTTATTA 50 27 1 TTTTCCGGCC 0.60326 -82 CGTTTGTTTATAAACTGCCCAA 55 3 0 TAAACTGCCC 0.353324 -66 TTTACCGCGCTTTTCCGCACCTTTTCGCAG 56 137 0 TTTTCCGCAC 0.828904 -164 TCTTTCCTTATTTACCGCGCTTTTCCGCAC 56 147 0 TTTACCGCGC 0.861961 -154 TGCGCGGTGCTTATCCGCCCTACGAAAAGA 58 59 0 TTATCCGCCC 0.875321 -47 ACGCAACAACTTACCCGCACAAAATAGAAT 62 110 0 TTACCCGCAC 0.927239 -31 ATAACCTTATTTTCCCGCCCTCATTTCGAG 65 47 0 TTTCCCGCCC 0.919258 -254 ********** Masking position 1 Map Score: 9.71627 Number of sites scoring better than the average of aligned sites = 1059 Number in coding regions = 963 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 9 ACAATTGACCGCAGCCGGAAAACGGTAAAAGCACCT 6 61 0 GCGGGACGGT 0.61839 -194 ATTCCGGGGTGCCCTTTGGGGTCGGTAATATGGGAT 7 233 1 GCCTGGCGGT 0.966381 -68 CGTTATCTTCGCTCGCTCATCCCGGTCACTTACTGA 8 86 0 GCCTCTCGGT 0.796104 -172 TCAAAAAGGAGCCGCCTGAGGGCGGCTTCTTTTTGT 9 14 1 GCGTGGCGGC 0.976321 -133 ATTGTTGCAGGCAGTTTGGTCACGGCCAGCGCGCAG 10 84 1 GCGTGTCGGC 0.965917 -208 GATATAGTCTGCGCCATCTGATCGTAAGTAGTTGGC 12 62 1 GCCTCGCGTA 0.448783 -124 TTCTGTTGCCGCCGGTGGGGTTCGCCATTGTAACGC 13 84 1 GCGGGGCGCC 0.780196 -37 AGCCGGGTAAGCGCAATGCGCCCGGCAATCTATACA 26 26 1 GCCTGGCGGC 0.978739 -249 TCAGATATATGCAGTTTGTGAACGTCAGGGCGCAGA 26 227 0 GCGTGGCGTC 0.956108 -48 GTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGT 27 194 0 GCCTGGCGGT 0.966443 -54 AGTCTCCGAAGCGGGATCTGGCTGGTGGTCTATAGT 29 97 1 GCGTCGTGGT 0.644836 -86 GGTATCCGCTGATTCGTTACGGTGAGAATAGCA 36 47 0 GCGTCTCGGT 0.901669 -23 CCAATCAGTCGCAGTTTGCGACAGGTAAGGTTTCCC 45 196 1 GCGTGGAGGT 0.863098 -89 TGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCA 51 50 1 GCGTGTCGGA 0.833878 -57 GTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTA 57 121 1 GCGGGTCGGT 0.867874 -103 AATGGTCCGGGCGGGACGGGATCGTCACCACCAGGG 57 177 0 GCGCGGCGTC 0.746589 -47 ATGAAGCGAAGCCGCATCTGACAGTCAGAATGCGGC 59 24 0 GCGTCGAGTC 0.507636 -219 TTTCTGCCGAGCGTGATCAGATCGGCATTTCTTTAA 64 78 1 GCTTCGCGGC 0.784379 -112 ** * ** * **** Masking position 14 Map Score: 11.7767 Number of sites scoring better than the average of aligned sites = 1191 Number in coding regions = 1151 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 10 CCACGTAATCCGCAGTGCGGTTAATTGAAATG 5 23 1 CCGTGCGGTT 0.871883 -30 CATCATCGGTAACGTTGCGCGTGACAAACGGT 6 215 0 ACTTGCGCGT 0.937804 -40 TCACTTTTATATCTGTGCGGTTTAATGCCGGG 8 210 1 ACGTGCGGTT 0.7728 -48 CGCTCAGTAGATCCTTGCGGATCGGCTGGCGG 11 32 1 ACTTGCGGAT 0.829445 -60 CGCAGGACATCACATTGCGCTTATGCGAATCC 18 113 1 CCTTGCGCTT 0.934406 -188 TTCCTCCGGTCTGCTTGCGGGTCAGACAGCGT 19 190 0 CGTTGCGGGT 0.676202 -111 GAAAGTTAACCTCTGTGCCCGTAGTCCCCAGG 19 248 1 CCGTGCCCGT 0.751648 -53 GATTGCCGGGCGCATTGCGCTTACCCGGCTTA 26 24 0 CCTTGCGCTT 0.934406 -251 CTGTACGTCCCGCTTTGCGTGTATTTCATAAC 29 51 1 CCTTGCGTGT 0.839098 -132 GAGAAGAGAGAACATTGCGGTAACACGCTTTT 30 111 0 ACTTGCGGTA 0.821491 -104 CAGAAATTTGCACAGTGCGCAATTTTCTGCAT 31 28 1 CCGTGCGCAA 0.750273 -168 ACGCATTGCCCGATGCCGCAAAG 35 2 1 CCTTGCCCGA 0.803716 -164 GCAACGATAAACCATTGCGGGAGATAACCTTG 51 12 0 ACTTGCGGGA 0.906938 -95 GCAATGGTTTATCGTTGCGGGAGTTGCCTGAA 51 26 1 ACTTGCGGGA 0.906938 -81 ATCCAGGACGATCCTTGCGCTTTACCCATCAG 56 41 1 ACTTGCGCTT 0.876849 -260 GACTATAGTTAACATTGCGCAACATTTTTATA 61 65 0 ACTTGCGCAA 0.758648 -234 TGCAACAAATCACATTGCCTGAATCGGCTCAT 61 101 1 CCTTGCCTGA 0.414467 -198 ACGACCAGATCACCTTGCGGATTCAGGAGACT 64 165 1 CCTTGCGGAT 0.906804 -25 * * ******** Masking position 6 Map Score: 12.215 Number of sites scoring better than the average of aligned sites = 736 Number in coding regions = 677 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 11 CCTTCATATTTCGCGCCGCAGATGCGTTAT 8 116 0 TCGCGCCGCA 0.741871 -142 TTGGTCACGGCCAGCGCGCAGCAACCGGAG 10 99 1 CCAGCGCGCA 0.784867 -193 TAAGAATGAGACAGGCCGTAAAGTTTGGCG 16 27 0 ACAGGCCGTA 0.803568 -78 GAACTTTCTCCCGGCCAGCACTGCTCGCTA 20 177 0 CCGGCCAGCA 0.449768 -124 GCAGAGATCCCCGGGCCGTATGCCCGTTTA 26 202 0 CCGGGCCGTA 0.922235 -73 TTTGTGAACGTCAGGGCGCAGAGATCCCCG 26 219 0 TCAGGGCGCA 0.957894 -56 GTCATCCTGTTCGGGGCGCATTCTAACAGA 35 122 0 TCGGGGCGCA 0.957054 -44 GAACAGGATGACAGGGCGTAAAATCGTGGG 35 140 1 ACAGGGCGTA 0.713056 -26 TCGGAACATTTCAGGCTGTAGCCAACGTAG 38 23 1 TCAGGCTGTA 0.78425 -60 TCGTCATCTTTCAGGCTGTAACTACGTTGG 38 44 0 TCAGGCTGTA 0.78425 -39 ACAAGAAAGGTCAGGCCGCTTATCAAGCGG 52 13 1 TCAGGCCGCT 0.762159 -79 GATTTATCATTCAGGCGGCATTTTGCTGTC 54 139 1 TCAGGCGGCA 0.813904 -61 GCTTTACCCATCAGCCCGTATAATCCTCCA 56 59 1 TCAGCCCGTA 0.815351 -242 AGTCCGCTACTCGGGCCGCATTGTCGTTTC 57 43 1 TCGGGCCGCA 0.973462 -181 ATCGTCACCACCAGGGTGTAAAGGGTGGCA 57 163 0 CCAGGGTGTA 0.594179 -61 TCACAATCGTTCGGGGAGCAATATTAAATG 59 137 0 TCGGGGAGCA 0.75588 -106 ********** Masking position 8 Map Score: 9.42082 Number of sites scoring better than the average of aligned sites = 983 Number in coding regions = 888 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 12 GATGCTGTACACAGCGCCAACAATTATTGG 7 87 1 ACAGCGCCAA 0.702305 -214 AGACTGGACGGAAGCGACAATCTCACTTTG 7 176 1 GAAGCGACAA 0.408886 -125 GCGGTTTAATGCCGGGCAGATCACATCTCC 8 226 1 GCCGGGCAGA 0.829329 -32 ATATAAGATCGCCGGGCCACGCAAAGAACT 15 64 1 GCCGGGCCAC 0.896668 -58 CGCGCACAGTACAGCGCAACTTATTTTGTT 17 23 0 ACAGCGCAAC 0.815526 -54 CTTTTCTTACACCGCGCCGATAAAAAATAT 20 208 1 ACCGCGCCGA 0.500966 -93 TCGGTGAATGAAGGGCAACGGCGAATAGT 27 10 1 GAAGGGCAAC 0.882286 -238 TAGTGAAATAAAAGGGCAACTATTCGCCGT 27 28 0 AAAGGGCAAC 0.733673 -220 TTTATTACTGAAAGGGCCGCTGTTTTGGTC 29 146 0 AAAGGGCCGC 0.714429 -37 TGCAAGTCTGACAGGGCAACTATTT 33 80 1 ACAGGGCAAC 0.882286 -15 ACTGATAAGGGCAGGGCCACTGGCTCTGCC 36 13 1 GCAGGGCCAC 0.95106 -57 GAGAATAGCAAAAGGGCAGAGCCAGTGGCC 36 27 0 AAAGGGCAGA 0.595151 -43 AAGCAATTGAGCAGGGAAACCGGTGTTTTG 48 212 0 GCAGGGAAAC 0.85672 -89 CACCTTTTCCGCAGCGCAAAAACTGCGTCA 49 58 0 GCAGCGCAAA 0.870725 -243 ATTCCAGCAGGCCGGGACGCCGGTCTATTT 49 185 0 GCCGGGACGC 0.708003 -116 TGGAACGCAGGCAGCGAAGAGCACCAACTC 54 102 0 GCAGCGAAGA 0.653021 -98 GCACCTTTTCGCAGGGAAAATGTACGACCT 56 121 0 GCAGGGAAAA 0.770024 -180 TGGTAACAATGAAGCGAAGCCGCATCTGAC 59 38 0 GAAGCGAAGC 0.552627 -205 GATGGCTACAGAAGGGCAAA 60 1 0 GAAGGGCAAA 0.807585 -205 ********** Masking position 6 Map Score: 10.6904 Number of sites scoring better than the average of aligned sites = 2388 Number in coding regions = 2278 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 13 AGTACACGTTTGGTTAGGGGGCCTGCATAT 8 169 1 TGGTTAGGGG 0.83779 -89 CCCCTTTGGGGAGAGGGTTAGGGTGAGG 18 9 1 GGGAGAGGGT 0.955469 -292 GAGAGGGTTAGGGTGAGGGGAACAGCCAGC 18 21 1 GGGTGAGGGG 0.993196 -280 GTGAGGGCTGGGGTGAGGGTTAATGTTCGC 18 57 0 GGGTGAGGGT 0.980128 -244 CTCCCTTCCAGGGTGAGGGCTGGGGTGAGG 18 69 0 GGGTGAGGGC 0.976446 -232 CACCCTGGAAGGGAGAGGGGGCAGAACGGC 18 84 1 GGGAGAGGGG 0.984496 -217 CTCTATTGGTGGGTTAGTGGTTGCAAACCT 42 102 1 GGGTTAGTGG 0.83779 -150 ********** Masking position 6 Map Score: 4.84167 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 37 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 14 GTTGAGACAGAATAAAAAGCAAAACGCCGCCAG 11 57 0 AAAAAGCAAA 0.914819 -35 TTGGCTTTATCACATAGAGCAAATATGCATAAA 20 67 1 CAAAAGCAAA 0.970387 -234 AATCGCGAATCATAAAAAGCAAAGGATCTTTTA 28 220 0 CAAAAGCAAA 0.970387 -65 CGCATTCTAACAGAAAAAGAAAACGTTTGCGTA 35 103 0 CAAAAGAAAA 0.762612 -63 TGGTTTACTCCAGAAATAGCAAAGCTCCCTGCC 39 41 0 CAAAAGCAAA 0.970387 -25 ATTAGCGTAAAAAAGACAGCAAAATGCCGCCTG 54 150 0 AAAAAGCAAA 0.914819 -50 GCGCATCCGCCACACAAAGCAACAGGAACATC 58 84 1 CAAAAGCAAC 0.884477 -22 AGGCAAAATTAAGATATAGCAAACAAATAGATC 60 60 0 AAAAAGCAAA 0.914819 -146 TCGGTTTAGTCAGAAGAAGCAAAAAGACACTTT 61 258 0 CAAGAGCAAA 0.884477 -41 ** * * ****** Masking position 8 Map Score: 4.62617 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 17 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 15 GGCTTGCCTGACTAGCGCCCGCCCAATAACAA 1 27 1 ATAGCGCCCC 0.880254 -32 GGATATCAGGGCTATCTCCCACAATATAAAGG 6 32 1 GTATCTCCCC 0.963341 -223 TAAGGCTTGATAACTCCCCCAAAATAGTTC 8 9 1 GTAACTCCCC 0.963341 -249 TGGTCTATAAGGGCTCTCCCCCTTCATATTTC 8 134 0 GGCTCTCCCC 0.846696 -124 TTATAACCAGACTTACGCCCCCGCGATACTTA 10 46 0 ATTACGCCCC 0.657964 -246 GAATAACGCCCACATGCTGTTCT 19 288 0 ATAACGCCCC 0.858905 -13 ATCAATAAAAGAGAGCGCCCCCTTTTGGAGTA 23 128 0 GGAGCGCCCC 0.918968 -86 CCTTGGCTGCGTTCGCTCCCCCGAATCACTTA 26 122 0 GTCGCTCCCC 0.939433 -153 TCAAGGTTATCTCCCGCAATGGTTTAT 51 6 1 GTATCTCCCC 0.963341 -101 CAGCGCTTCAGGCAACTCCCGCAACGATAAAC 51 32 0 GCAACTCCCC 0.859938 -75 TATCAGCCTTGTTTTCTCCCTCATTACTTGAA 65 74 1 GTTTCTCCCC 0.89252 -227 * ******** * Masking position 6 Map Score: 3.9419 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 256 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665