AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00561_ecoli_reg_100.orf -o00561_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 cdsA 120 CDP-diglyceride synthetase #4 hlpA 121 histone-like protein, located in outer membrane or nucleoid #5 prpB 238 putative phosphonomutase 2 #6 lacZ 122 beta-D-galactosidase #7 adhC 34 alcohol dehydrogenase class III; formaldehyde dehydrogenase, glutathione-dependent #8 yaiN 166 putative alpha helix chain #9 ddlA_yaiB 462 ddlA: D-alanine-D-alanine ligase A, yaiB: orf, hypothetical protein #10 phoA 31 alkaline phosphatase #11 ybaD 90 orf, hypothetical protein #12 ribH 88 riboflavin synthase, beta chain #13 thiL 77 thiamin-monophosphate kinase #14 lnt 24 apolipoprotein N-acyltransferase, copper homeostasis protein, inner membrane #15 ybeX 89 putative transport protein #16 ybeZ 113 putative ATP-binding protein in pho regulon #17 htrB 224 heat shock protein #18 adhE 300 CoA-linked acetaldehyde dehydrogenase and iron-dependent alcohol dehydrogenase; pyruvate-formate-lyase deactivase #19 cls 300 cardiolipin synthase, a major membrane phospholipid; novobiocin sensitivity #20 pgpB 169 non-essential phosphatidylglycerophosphate phosphatase, membrane bound #21 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #22 ydcH 72 orf, hypothetical protein #23 rimL 62 acetylation of N-terminal serine of 30S ribosomal subunit protein L7; acetyl transferase #24 msbB 119 suppressor of htrB, heat shock protein #25 pgsA 56 phosphatidylglycerophosphate synthetase = CDP-1,2-diacyl-sn-glycero-3-phosphate phosphatidyl transferase #26 uvrC 62 excinuclease ABC, subunit C; repair of UV damage to DNA #27 uvrY 300 putative 2-component transcriptional regulator #28 wcaA 34 putative regulator #29 BIME92 24 BIME #30 wza 300 putative polysaccharide export protein #31 glpT_glpA 272 glpT: sn-glycerol-3-phosphate permease, glpA: sn-glycerol-3-phosphate dehydrogenase (anaerobic), large subunit #32 pssA 110 phosphatidylserine synthase; phospholipid synthesis #33 plsC 233 1-acyl-sn-glycerol-3-phosphate acyltransferase #34 ebgA 147 evolved beta-D-galactosidase, alpha subunit; cryptic gene #35 glpD 189 sn-glycerol-3-phosphate dehydrogenase (aerobic) #36 ugpA 21 sn-glycerol 3-phosphate transport system, integral membrane protein #37 BIME167 47 BIME #38 ugpB 238 sn-glycerol 3-phosphate transport system; periplasmic binding protein #39 yiaY 189 putative oxidoreductase #40 secB 62 protein export; molecular chaperone; may bind to signel sequence #41 grxC 141 glutaredoxin 3 #42 rfaS 36 lipopolysaccharide core biosynthesis #43 rfaQ 300 lipopolysaccharide core biosynthesis #44 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #45 yifM_2 241 orf, conceptual translation in SwissProt is fused with b4404 #46 pldA 146 outer membrane phospholipase A #47 cdh 106 CDP-diacylglycerol phosphotidylhydrolase #48 tpiA 107 triosephosphate isomerase #49 glpK 22 glycerol kinase #50 glpF 300 facilitated diffusion of glycerol #51 plsB_dgkA 110 plsB: glycerol-3-phosphate acyltransferase, dgkA: diacylglycerol kinase #52 melA 282 alpha-galactosidase #53 psd 96 phosphatidylserine decarboxylase; phospholipid synthesis #54 yjeQ 64 orf, hypothetical protein #55 mdoB 292 phosphoglycerol transferase I Motif number 1 GATATGTCCTAAAATGCCGCTCGCGTCGCAA 1 17 1 AAAAGCCGCT 0.954475 -284 GGCAACAGAAACAACGCCGCGATGACGACGG 3 63 0 ACAAGCCGCG 0.931142 -58 GATCAATATAAGATCGCCGGGCCACGCAAAG 4 59 1 AGATGCCGGG 0.916657 -63 TAATCGGCAGGGAAGGCCGCCCCGGATAGCG 8 25 0 GGAAGCCGCC 0.80873 -142 ACAATCTTTCAGAAGGCCGCGAATCCCCCGT 9 392 1 AGAAGCCGCG 0.985983 -71 GGTAAAAAAGAAAAGGCCGGCGATCATGGAA 13 41 0 AAAAGCCGGC 0.956914 -37 TTAGTTAATCAAAACGCCGTCGTTAATCACC 15 48 0 AAAAGCCGTC 0.685268 -42 ATGGGAAAGTAAAAATCCGCGGCATGATATA 17 30 1 AAAATCCGCG 0.806731 -195 AGACTGGGCGAAATTGCCGCGCTTGTAAATA 17 124 0 AAATGCCGCG 0.972194 -101 ATCATAACTGAAAACGCCAGTTCCAGGAAAA 20 122 0 AAAAGCCAGT 0.657198 -48 TTTTGTGTATAGATTGCCGGGCGCATTGCGC 21 36 0 AGATGCCGGG 0.916657 -239 GCAGTTGTTAAAAAAGCCGCCTGGCTGGCGG 23 22 0 AAAAGCCGCC 0.976299 -41 CACCAAATAAAAAAAGCCGGTACTGACTGCG 24 34 0 AAAAGCCGGT 0.918727 -86 ATTGGTAGCTAAAAAGCCAGGGGCGGTAGCG 30 100 1 AAAAGCCAGG 0.916833 -201 AGGGCATTGTTAAAAGCCGCTCTCTGGAAAA 33 159 0 TAAAGCCGCT 0.704545 -75 GAAAGTGTAAAAAAGGGCGGGCAGCTTACTG 39 158 0 AAAAGGCGGG 0.907284 -32 TCTTATGCCAAAAACGCCACGTGTTTACGTG 44 16 1 AAAAGCCACG 0.953372 -224 ATATAAAAGCAAAACGCCACGTAAACACGTG 44 33 0 AAAAGCCACG 0.953372 -207 AAAAAAGCTCAAATCGCCGCGGGTGGCAAAT 45 203 0 AAATGCCGCG 0.972194 -39 GAATAAAGGAAGATGGCCGCCCCGCAGGGCA 48 64 0 AGATGCCGCC 0.874527 -44 TCAGATGGAATAAATGGCGCGATAACGCTCA 50 138 1 TAAAGGCGCG 0.673658 -163 ACCGCGAAACGCCGCGTTTTAGCTGT 55 6 1 GAAAGCCGCG 0.954976 -287 AAAGGGCAGGAGAGAGCCGCGTCAGCCGGGT 55 38 0 AGAGGCCGCG 0.881781 -255 AGGAGCAGGGAAAAGGGCAGGAGAGAGCCGC 55 49 0 AAAAGGCAGG 0.624003 -244 **** ****** Masking position 3 Map Score: 29.4791 Number of sites scoring better than the average of aligned sites = 1003 Number in coding regions = 886 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 2 CAGTTTGCGACGCGAGCGGCATTTTAGGAC 1 22 0 CGCGAGCGGC 0.81372 -279 TTTCTGTTGCCGCCGGTGGGGTTCGCCATT 3 83 1 CGCCGGTGGG 0.738755 -38 CCCGGATAGCGGGCGGCAGAAGGAA 8 6 0 GGGCGGCAGA 0.930195 -161 CGCCCGCTATCCGGGGCGGCCTTCCCTGCC 8 21 1 CCGGGGCGGC 0.833122 -146 AAGAGGAAAGGGGGGGGGGCTAATCGGCAG 8 46 0 GGGGGGGGGC 0.976022 -121 TGGCCCCGCAGGGGGGCGGATTTTAGCATA 12 47 0 GGGGGGCGGA 0.962593 -42 TATCCAGGCCGGTAGATTCACGGAAG 13 7 1 GGCCGGTAGA 0.80476 -71 AACGGAAGTGGGGCGCTGGCGCATGCAGCG 19 125 0 GGGCGCTGGC 0.631818 -176 TGGTCAGCGTCGGGGGTGGGGGTATAATGA 19 198 0 CGGGGGTGGG 0.80078 -103 AAAGCCGCCTGGCTGGCGGCTTAGGAAAGT 23 11 0 GGCTGGCGGC 0.895601 -52 AAAAAGCCAGGGGCGGTAGCGTGTCTGGAT 30 110 1 GGGCGGTAGC 0.947907 -191 TATGCCGGGGAGGGCGCTGTTTC 33 4 1 GCCGGGGAGG 0.472987 -230 TGTAAAAAAGGGCGGGCAGCTTACTGAGGA 39 154 0 GGCGGGCAGC 0.974719 -36 AACAATAAGTCGCTGGGGGCCTAATTGCAG 41 45 0 CGCTGGGGGC 0.588943 -97 TCATGTTGCAGGGCGGCAGCAAAATGGAGT 41 91 0 GGGCGGCAGC 0.97847 -51 GTTGAGCCTGGGGCGGTAGCGTGCTTTTTT 43 205 1 GGGCGGTAGC 0.947907 -96 TGGCATATCTGGGGGGCAGACCTGTATGAG 45 102 1 GGGGGGCAGA 0.936034 -140 CTCAAATCGCCGCGGGTGGCAAATACACAG 45 197 0 CGCGGGTGGC 0.907197 -45 CCGCCCCGCAGGGCAGCAGGTCTGTGAAAC 48 49 0 GGGCAGCAGG 0.720909 -59 CTGCTGCCCTGCGGGGCGGCCATCTTCCTT 48 60 1 GCGGGGCGGC 0.932648 -48 TTCCCAGAGGGGCGAGGGGACTCTCCGAGT 52 94 1 GGCGAGGGGA 0.622603 -189 ACTCTCCAAAGGCCAGCAGCGCCGC 54 50 1 GGCCAGCAGC 0.862674 -15 GCAGGGAAAAGGGCAGGAGAGAGCCGCGTC 55 46 0 GGGCAGGAGA 0.525122 -247 ********** Masking position 9 Map Score: 25.5829 Number of sites scoring better than the average of aligned sites = 2345 Number in coding regions = 2238 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 3 TTCCACACAACATACGAGCCGGAAGCATAAAGTGT 6 62 0 CCAGCCGGAG 0.983168 -61 CCTTCTGCCGCCCGCTATCCGGGGCGGCCTTCCCT 8 13 1 CCATCCGGGC 0.615965 -154 ACCGCATGGCCATTTAAGCCAGGAATAAATTAGCT 9 264 1 CTAGCCAGGA 0.879247 -199 CGCTGCTTCCCTTTCGAGCCGGGAGA 12 2 0 CCAGCCGGGG 0.995284 -87 CTAAAATCCGCCCCCCTGCGGGGCCATACTCGAAC 12 51 1 CCTGCGGGGC 0.860598 -38 ACTTTCCTAAGCCGCCAGCCAGGCGGCTTTTTTAA 23 11 1 GCAGCCAGGG 0.781376 -52 AAAACCGTAACCAGCCAGCCAGGCGTTTATCGC 26 40 1 CCAGCCAGGG 0.985217 -23 TCCGGTAAGCCGTTGGTGACGGGCGTGACCATAAC 27 138 1 CGTGACGGGG 0.516404 -163 AGCAAACCAGCTCATAAGCCGGGAGAACAACCT 28 12 1 CTAGCCGGGG 0.990795 -23 GTATTGGTAGCTAAAAAGCCAGGGGCGGTAGCGTG 30 98 1 CAAGCCAGGG 0.827048 -203 TCCGGCGTTCCTTGCAAGCGGGAGGAAACAGCGCC 33 23 0 CCAGCGGGAG 0.954616 -211 GTCCGGCAATCGTTTTTGCCGGACAGTGCTGCCGT 34 26 1 CTTGCCGGAA 0.711734 -122 AGATGGGGCACGGATAAGCGGGAAAATATAGAAGG 38 47 0 CTAGCGGGAA 0.696792 -192 ATTCAGGTAGCTGTTGAGCCTGGGGCGGTAGCGTG 43 193 1 CTAGCCTGGG 0.914817 -108 GTCTGCCCCCCAGATATGCCAGAAAAACTGGCTGG 45 88 0 CTTGCCAGAA 0.438064 -154 AGCCGACTCGCTTTTGCGCCAGGCGACGTAGTGGG 45 164 0 CTCGCCAGGG 0.801808 -78 CACAGACCTGCTGCCCTGCGGGGCGGCCATCTTCC 48 53 1 CCTGCGGGGG 0.967102 -55 CCTTTATTCGCTTATAAGCGTGGAGAATTAAA 48 86 1 CTAGCGTGGG 0.794542 -22 TTTTCACCCTCTTCCCAGAGGGGCGAGGGGACTCT 52 83 1 CCAGAGGGGG 0.834964 -200 GAATGCTCAACCTGGAAGCCGGAGGTTTTCTGCAG 52 212 1 CGAGCCGGAG 0.919562 -71 TGAAGTTATTCAAGCAAGCCAGGAGATCTGC 52 262 1 CCAGCCAGGG 0.985217 -21 CCTGATCCGGCCTACATGCCGGATCCTGAAAAAAA 53 43 0 CCTGCCGGAC 0.825962 -54 AGGAGAGAGCCGCGTCAGCCGGGTAACAGCTAAAA 55 27 0 CTAGCCGGGA 0.95844 -266 * * ******* * Masking position 12 Map Score: 23.395 Number of sites scoring better than the average of aligned sites = 1249 Number in coding regions = 1154 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 4 TACCCGTCGTCATCGCGGCGTTGTTTCTGTT 3 60 1 CACGCGGCGT 0.956448 -61 GGCGAACCCCACCGGCGGCAACAGAAACAAC 3 79 0 ACGGCGGCAA 0.856449 -42 TGTTGCAATGAAACGCGGTGAAACATTGCCT 5 64 1 AACGCGGTGA 0.872331 -175 TAAAAAAGAAAAGGCCGGCGATCATGGAACG 13 39 0 AAGCCGGCGA 0.736816 -39 GTTAATCACCAACGGCGGGGACGTCTGCCAG 15 27 0 AAGGCGGGGA 0.865233 -63 GAAAGTAAAAATCCGCGGCATGATATAGCAA 17 34 1 ATCGCGGCAT 0.578445 -191 TGTTATTTACAAGCGCGGCAATTTCGCCCAG 17 121 1 AACGCGGCAA 0.973394 -104 CTTGAGGGGCAATCGCGCCGAAATATGCGTA 19 66 0 AACGCGCCGA 0.821707 -235 TGGCAAATAAAAACGCGGGAAAAGCACTGGT 19 224 0 AACGCGGGAA 0.867947 -77 CAAGTTGCATCAAGGCGGCAAGTGAGCGAAT 21 72 1 CAGGCGGCAA 0.956083 -203 GTTTTCTTAACATCGCGGCAACTCAAGAAAC 31 187 1 CACGCGGCAA 0.972854 -86 AGAAAGATGACAAGGCGGTGACGGCGTGGGT 38 95 0 CAGGCGGTGA 0.8026 -144 TTTCATGTTGCAGGGCGGCAGCAAAATGGAG 41 92 0 CAGGCGGCAG 0.788907 -50 CTAACATCGCCAGCGCGGCATTAAGATTACA 44 65 0 CACGCGGCAT 0.931773 -175 TGTATTTGCCACCCGCGGCGATTTGAGCTTT 45 200 1 ACCGCGGCGA 0.940452 -42 GTAACAGCTAAAACGCGGCGTTTCGCGGT 55 9 0 AACGCGGCGT 0.957299 -284 ** ******** Masking position 6 Map Score: 15.7683 Number of sites scoring better than the average of aligned sites = 1322 Number in coding regions = 1262 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 5 AGCGCACCGCAAAGTTAAGAA 5 2 1 GCGCACCGCA 0.933149 -237 GCGCAACGCAATTAATGTGA 6 1 1 GCGCAACGCA 0.990373 -122 AAAAATATTTGCGCAAAGTATTTCCTTTGT 9 93 0 GCGCAAAGTA 0.820315 -370 TTGATTACCAGCGAAACGTTTCTCTTATTT 9 126 1 GCGAAACGTT 0.722518 -337 CTGACAAAGCGTGCAACGTACTGGTGAAGA 9 350 0 GTGCAACGTA 0.845401 -113 TACAACAAAGGCGCAACGCTTTTGAGATAA 11 18 0 GCGCAACGCT 0.962302 -73 AGCTATAATGGCGAAAAGCGATGCTGAAAG 18 25 1 GCGAAAAGCG 0.718486 -276 AGCCGGGTAAGCGCAATGCGCCCGGCAATC 21 26 1 GCGCAATGCG 0.919682 -249 TAATTCGAAAGTGAAACGTGATTTCATGCG 31 91 1 GTGAAACGTG 0.494024 -182 AGGGTCCTCTGTGCAATGCAGACGACATAA 32 66 0 GTGCAATGCA 0.773176 -45 GTATTGTTAATCGCAACGCATGAATAAACA 33 127 0 TCGCAACGCA 0.853397 -107 GGTCAGATAAGCGAAACGCATCCGACATTA 37 17 0 GCGAAACGCA 0.970465 -31 CTTAAATACTGCGCAATGTAATGCCAACGT 40 18 0 GCGCAATGTA 0.867403 -45 GTTTCGCGCGGCGCTACGCAAACCCGAATC 51 66 0 GCGCTACGCA 0.904012 -45 ACCGCGAAACGCCGCGTTTTAGC 55 4 1 GCGAAACGCC 0.872651 -289 ********** Masking position 3 Map Score: 12.9129 Number of sites scoring better than the average of aligned sites = 1255 Number in coding regions = 1126 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 6 GGCATACCGAGGTAAAAAACCCGATGTTTA 1 189 0 GGTAAAAAAC 0.911322 -112 GTCAGTTCAGGGTAAAATAGATTTCCGTTA 11 50 1 GGTAAAATAG 0.790334 -41 TGCCTCAGCAGGTAAAAAAGAAAAGGCCGG 13 52 0 GGTAAAAAAG 0.952579 -26 TTCTCGTTATGGCAAAATAAGCCAATACAG 20 35 0 GGCAAAATAA 0.399043 -135 CCATGCAGTTGTTAAAAAAGCCGCCTGGCT 23 27 0 GTTAAAAAAG 0.550112 -36 TTTCGGATAAGGCAAAAATCAATCTGGTGA 24 90 0 GGCAAAAATC 0.527055 -30 GAACAATACGGGCAAAAAACATTCATGAT 27 10 0 GGCAAAAAAC 0.912832 -291 ATGGCTAAATGGTAAAAAACGAACTTCAGA 31 20 0 GGTAAAAAAC 0.911322 -253 AGCACTGTCCGGCAAAAACGATTGCCGGAC 34 26 0 GGCAAAAACG 0.763509 -122 CTCCTGAAAGTGTAAAAAAGGGCGGGCAGC 39 164 0 TGTAAAAAAG 0.550112 -26 GAAATTTCAGGGTAAAAAAACAGGAGCTAA 41 119 1 GGTAAAAAAA 0.776414 -23 CGACGTAGTGGGTAAAAAAGCTTATATCTC 45 146 0 GGTAAAAAAG 0.952579 -96 GGTGCGTTTTGGCAAAAAAGCTCAAATCGC 45 217 0 GGCAAAAAAG 0.953422 -25 TGAGGTACAGGGAAAAAAAG 47 97 1 GGAAAAAAAG 0.759998 -10 ********** Masking position 5 Map Score: 10.1157 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 189 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 TTTAAAATGACTCACTATTTTCCACAGCAAATATA 1 58 0 CCCTTTTCCC 0.990264 -243 TGACTGGCTTGACAAGCTTTTCCTCAGCTCCGTAA 1 222 1 GCATTTTCCC 0.668111 -79 CCCACTTTGCCCCACAATTTCCCACTGAAAGGAGT 1 257 0 CCCTTTCCCC 0.975474 -44 CTCTCGCTCTTCCTCAATATGGTAA 7 20 0 CCCTCTTCCC 0.982604 -15 CCGATTAGCCCCCCCCCCTTTCCTCTTTGTTTTCC 8 49 1 CCCCTTTCCC 0.928051 -118 TTTGAGATAACGCACTTTCTTCACCAGTACGTTGC 9 333 1 CCCTCTTCAC 0.942621 -130 GCGGCAATTTCGCCCAGTCTTCAGCCACAAATTTT 17 135 1 CCCTCTTCAC 0.942621 -90 TGTATGTATTGTCGCATTTTTTCGCCCGCAACCAA 17 168 0 GCCTTTTTCC 0.873492 -57 AAATCGAATACCCACCATTTTTAACGTTTCAAAGT 27 205 1 CCCTTTTTAC 0.842843 -96 CGTGCCCCATCTCCCATTTTCCCTCACCCACGCCG 38 70 1 CCCTTTCCCC 0.975474 -169 GTAAGCTGCCCGCCCTTTTTTACACTTTCAGGAGT 39 160 1 CCCTTTTACC 0.879488 -30 ATACACAGCCGACTCGCTTTTGCGCCAGGCGACGT 45 170 0 GCCTTTTGCC 0.801985 -72 ATTACGGTTTGCCACACTTTTCATCCTTCTCCTGG 50 27 1 GCCTTTTCAC 0.917195 -274 CGTGCTCCCACTCGCAGTCATCCTCCCTCACTCCT 52 47 0 CCCTCATCCC 0.828565 -236 TGCGAGTGGGAGCACGGTTTTCACCCTCTTCCCAG 52 66 1 ACCTTTTCAC 0.679748 -217 TACTCTCTTTCGCCCTTTTTCTCGCCTCT 55 274 1 CCCTTTCTCC 0.878208 -19 * * * ****** * Masking position 3 Map Score: 13.2435 Number of sites scoring better than the average of aligned sites = 420 Number in coding regions = 366 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 8 ACGTAAAATAAACAACGCTGATATTAGCCGTAAACAT 1 159 1 AACCGTGTTG 0.824146 -142 CCGAGGTAAAAAACCCGATGTTTACGGCTAATATCAG 1 176 0 AAACGTGTAG 0.965589 -125 TTGATAATTAAAAGCCTATATTTTGTGTGGGTAATTA 9 159 0 AAACTTATTG 0.571324 -304 TATAATGGCGAAAAGCGATGCTGAAAGGTGTCAGCTT 18 28 1 AAACGTGTAG 0.965589 -273 ACAAACAGCGTAACTCGTTATTGTTTGC 19 2 0 TAACGTATTG 0.56384 -299 AAAACGCGGGAAAAGCACTGGTCAGCGTCGGGGGTGG 19 209 0 AAACATGTAG 0.648907 -92 CCAAATAAAAAAAGCCGGTACTGACTGCGTACCGGCT 24 26 0 AAACGTATAG 0.858774 -94 AACGATCCGGTAAGCCGTTGGTGACGGGCGTGACCAT 27 133 1 TAACGTGTAG 0.819159 -168 AGTTGCAATAAAAACCGCTAATATACGAATGACTAAC 27 237 1 AAACGTATTG 0.888991 -64 CCGTGGAAGAAAAAACGCTGCTGACGG 45 1 0 AAACGTGTAG 0.965589 -241 GATAATTATCAAACCCGGTGGTTTCTCGCGACCGGGT 47 20 1 AAACGTGTTC 0.743266 -87 TCATCGGCACAAAGGCTTTGCTTTTTG 48 1 0 AAACTTGTTG 0.860143 -107 GTGTACCGTTAAATCCGATGATTCGGGTTTGCGTAGC 51 47 1 AAACGTGTCG 0.940793 -64 GGGAAATTCTGTGGTATCCGCTCATGTTTC 51 91 0 AAACTTGTTG 0.860143 -20 GTAACAGCTAAAACGCGGCGTTTCGCGGT 55 3 0 AAACGCGTCG 0.668339 -290 AGTGTCAAAAAAATGCGATGTTGTTAGGAATTAGTTT 55 136 0 AAACGTGTTG 0.973653 -157 *** ** ** * * * Masking position 12 Map Score: 10.6423 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 213 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 9 TGGGGGTCGCTTTTGCTGAAGTATCGC 3 8 1 CGCTTTTGCT 0.960042 -113 AAAGGCGCAACGCTTTTGAGATAAAGGATC 11 12 0 CGCTTTTGAG 0.698204 -79 TGTATTGTCGCATTTTTTCGCCCGCAACCA 17 169 0 CATTTTTTCG 0.477208 -56 TTTTTAAAAACGCTTTTGCGTCAAACTGAT 26 14 0 CGCTTTTGCG 0.969861 -49 GGCTGATTTTCATTTTTGCTGAATAAAGTC 27 67 1 CATTTTTGCT 0.754978 -234 GGTGGGTATTCGATTTTTCTCTCGTTTTTG 27 191 0 CGATTTTTCT 0.641859 -110 GTCCGGCAATCGTTTTTGCCGGACAGTGCT 34 26 1 CGTTTTTGCC 0.872185 -122 CCGTCAGCAGCGTTTTTTCTTCCACGGTCA 45 11 1 CGTTTTTTCT 0.830381 -231 ACAGCCGACTCGCTTTTGCGCCAGGCGACG 45 171 0 CGCTTTTGCG 0.969861 -71 TTATTTGTCACGATTTTGCGTTACCCTTGC 47 60 1 CGATTTTGCG 0.915919 -47 CGATATTTCTCGTTTTTGCTCGTTAACGAT 50 199 1 CGTTTTTGCT 0.956853 -102 CGAAACGCCGCGTTTTAGCTGTTACCCGGC 55 15 1 CGTTTTAGCT 0.719783 -278 ********** Masking position 5 Map Score: 7.72173 Number of sites scoring better than the average of aligned sites = 430 Number in coding regions = 394 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 10 GGGAATAAGGGGTGAGGCTGGC 1 289 1 GGGAGCTGGC 0.928782 -12 TCACTCATTAGGCACCCCAGGCTTTACACTTT 6 37 1 GGACCCAGGC 0.91311 -86 CTAATCGGCAGGGAAGGCCGCCCCGGATAGCG 8 25 0 GGAAGCCGCC 0.550353 -142 ACCAACGGCGGGGACGTCTGCCAGTCAAATGC 15 19 0 GGACGCTGCC 0.942906 -71 AAGGCCCACCGGAACGGCAGGCCTGAGAA 16 8 0 GGACGCAGGC 0.958345 -106 CGCATATTTCGGCGCGATTGCCCCTCAAGCCA 19 68 1 GGGCGTTGCC 0.622496 -233 GCTGGCGCATGCAGCGTCAGGCTAGCCGACGT 19 109 0 GCGCGCAGGC 0.978752 -192 ATTCGGGGGAGCGAACGCAGCCAAGGCAGAGG 21 128 1 GCAACCAGCC 0.731392 -147 CATCCTTCAAGCCGCCTCTGCCTTGGCTGCGT 21 142 0 GCGCCCTGCC 0.938579 -133 GGGGCGGTGCGAATGCAGGCGTCG 29 5 0 GCAATCAGGC 0.4803 -20 CAGACACGCTACCGCCCCTGGCTTTTTAGCTA 30 105 0 ACGCCCTGGC 0.625064 -196 AAAGCACGCTACCGCCCCAGGCTCAACAGCTA 43 200 0 ACGCCCAGGC 0.651359 -101 CCACCACTCAGCAGAGCCAGCCACAGTGTGGG 45 48 0 GCGAGCAGCC 0.921536 -194 AGCTCAAATCGCCGCGGGTGGCAAATACACAG 45 197 0 GCGCGGTGGC 0.693698 -45 GCGGCACGCCTTGCAGATTACGGT 50 3 1 GGACGCTTGC 0.473427 -298 TGATATTCCAGGAAAGAGAGCCATCC 52 5 0 GGAAGGAGCC 0.458323 -278 GCGGCGCTGCTGGCCTTTGGAGAG 54 51 0 GGGCTCTGGC 0.83542 -14 GCAGGAGAGAGCCGCGTCAGCCGGGTAACAGC 55 32 0 GCGCGCAGCC 0.973693 -261 ** *** ***** Masking position 12 Map Score: 10.7406 Number of sites scoring better than the average of aligned sites = 2878 Number in coding regions = 2757 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 11 TGAAATTGTTATCCGCTCACAATTCCACAC 6 89 0 ATCCGCTCAC 0.817227 -34 AACAAAAAATATTTGCGCAAAGTATTTCCT 9 97 0 ATTTGCGCAA 0.688117 -366 TTTACGCTACATTTGCGCATTAAAAATTAT 17 90 1 ATTTGCGCAT 0.874001 -135 GCTCATCGGGATTCGCTCACTTGCCGCCTT 21 83 0 ATTCGCTCAC 0.92094 -192 AATTGTTTGATTTCGCGCATATTCGCTCAT 31 62 1 TTTCGCGCAT 0.844645 -211 TTTCGCGCATATTCGCTCATAATTCGAAAG 31 72 1 ATTCGCTCAT 0.959178 -201 TTTTTCTGTAATTCGAGCATGTCATGTTAC 38 163 1 ATTCGAGCAT 0.780911 -76 AAACGCGTGAATTCGCGCATTCGGTACAAC 38 205 1 ATTCGCGCAT 0.952362 -34 ATCTTCCTTTATTCGCTTATAAGCGTGGAG 48 81 1 ATTCGCTTAT 0.652172 -27 TTGTTAGATCATTCGCGCAACAAATTTATT 50 91 0 ATTCGCGCAA 0.931434 -210 ATTCTGTGGTATCCGCTCATGTTTCGCGCG 51 86 0 ATCCGCTCAT 0.900937 -25 ********** Masking position 9 Map Score: 6.56442 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 203 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 12 AAACATTGCCTGAAACGTTAACTGAAACGCA 5 84 1 TGAAACGTTA 0.953155 -155 TGACAGCTGTTGAAAAGATTAACTTT 10 6 0 TGAAAAGATA 0.725239 -26 GGGCTTACTGTGAAACGATCCGGTAAGCCGT 27 120 1 TGAAACGATC 0.809295 -181 ATTGCAACTTTGAAACGTTAAAAATGGTGGG 27 215 0 TGAAACGTTA 0.953155 -86 GTAAGGTACTGGAAATGTTGACCACTTAATC 32 11 1 GGAAATGTTA 0.826041 -100 GAACGCCGGATGAAACGTTAAGTCGTCATCC 33 48 1 TGAAACGTTA 0.953155 -186 TTCAACCCCCGGAAACGATAAAAATTCCCTT 33 88 1 GGAAACGATA 0.935438 -146 ATGAAACGATGAGCAATCTGTA 38 2 1 TGAAACGATA 0.953161 -237 GGAAATGATTAATTAAGTTTT 39 1 1 GGAAATGATA 0.826045 -189 TGGTTAATGAAATGTTGATTTTATGCTT 46 8 1 TGAAATGTTA 0.869588 -139 ********* * Masking position 5 Map Score: 5.23848 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 51 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 13 TGTTGCAATCTTCTGCTGACAAAGCGTGCAA 9 364 0 TTCTGCGACA 0.939717 -99 GCCCGTTTATTTCTGGCGACATTCTTTATAT 21 180 0 TTCTGGGACA 0.972326 -95 AATCTCGGTATTCTGGAAACATACGCACTCC 22 17 0 TTCTGGAACA 0.858634 -56 GCAAAAATCAATCTGGTGATAGTGTAGCGGC 24 78 0 ATCTGGGATA 0.792434 -42 TTATCCCTATTTCTGGAGATATTCCT 27 285 1 TTCTGGGATA 0.93213 -16 TGTTATAAGCTTCTGGGGACACTCCATTTTG 41 71 1 TTCTGGGACA 0.972326 -71 GTGGTTATACTTCTGCTAATAATTTTCTCTG 44 207 1 TTCTGCAATA 0.512994 -33 TTGATAATTATCCTGGGGAAA 47 1 0 TCCTGGGAAA 0.804736 -106 TTCATCCTTCTCCTGGTGACATAATCCACAT 50 46 1 TCCTGGGACA 0.937917 -255 TGGCAGGCGAATCTGCAGAAAACCTCCGGCT 52 228 0 ATCTGCGAAA 0.541725 -55 ****** **** Masking position 4 Map Score: 4.50869 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 174 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 14 TCCTTTTGAAAGCGCATTGTTATGAGTTTA 19 271 0 AGCGCATTGT 0.976576 -30 AAGCCGGGTAAGCGCAATGCGCCCGGCAAT 21 25 1 AGCGCAATGC 0.836324 -250 TCTCTGGAAAAGCGTATTGTTAATCGCAAC 33 140 0 AGCGTATTGT 0.803425 -94 AAATCAGGTTAGGGCATTGTTAAAAGCCGC 33 170 0 AGGGCATTGT 0.926999 -64 ATTTAAAAAAAGCACATTGTTTAATGAATA 39 60 1 AGCACATTGT 0.942184 -130 TCTAATAAAAAGCACATTGTATTCATTAAA 39 79 0 AGCACATTGT 0.942184 -111 CCTTAAATACTGCGCAATGTAATGCCAACG 40 19 0 TGCGCAATGT 0.775156 -44 GGTAGCCTCCAGGCCATTGTTTTGTCGTTC 53 77 0 AGGCCATTGT 0.744351 -20 CTTTTTGAGAAGCACAATGTAATGGCGTCG 55 191 0 AGCACAATGT 0.895271 -102 ********** Masking position 6 Map Score: 3.77516 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 175 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 15 AAGCCAGTCACAAGGCATACCGAGGTAAAAAA 1 200 0 CAAGGCACCG 0.983049 -101 GGCTAATCGGCAGGGAAGGCCGCCCCGGATAG 8 27 0 CAGGGAGCCG 0.941671 -140 CCGGTAGATTCACGGAAGACCGTTCCATGATC 13 19 1 CACGGAACCG 0.977853 -59 AGAGAAAAAACAAGGCCCACCGGAACGGCAGG 16 19 0 CAAGGCACCG 0.983049 -95 GCCCGTCACCAACGGCTTACCGGATCGTTTCA 27 130 0 AACGGCACCG 0.886628 -171 CTCCCGCTTGCAAGGAACGCCGGATGAAACGT 33 34 1 CAAGGAGCCG 0.972854 -200 GGAGATGGGGCACGGATAAGCGGGAAAATATA 38 52 0 CACGGAAGCG 0.879628 -187 CCGTAATCTGCAAGGCGTGCCGC 50 2 0 CAAGGCGCCG 0.982712 -299 ****** **** Masking position 2 Map Score: 5.39767 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 97 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863