AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00071_rpxx_reg_100.orf -o00071_rpxx_100.ace -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -g0.29 -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 = 0.29 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RP620 300 2-ACYLGLYCEROPHOSPHOETHANOLAMINE ACYLTRANSFERASE (aas) #2 RP738 300 POLY-BETA-HYDROXYBUTYRATE POLYMERASE (phbC1) Motif number 1 AATTTATATTAATATGTCAAATTTAGATAAATATTTA 1 10 0 AATATATAAT 0.944445 -291 TTGACATATTAATATAAATTGATAATATTTGTTGGGTT 1 28 1 AATATTTAAT 0.990708 -273 ATCTCTGTATAGTATTATCTACTTGGATCAGTTTTACG 1 91 1 AGTATTTGAT 0.924904 -210 AAAATCCAATAAAATTGGCTTTTTAAATTATTGAATAT 1 272 1 AAAATTTAAT 0.944445 -29 TTTTAGGGGAAATATCTTTTCATAAAATCTTGAAGTGC 2 35 0 AATATTTAAT 0.99079 -266 CTTTAGAGCATATATACTGTTATTACATTCTGAAGGTG 2 73 1 TATATTTAAT 0.944446 -228 CAAAAAGCTGAATATATTGTATTAAGTTCAGCACCTTC 2 104 0 AATATTTATT 0.944314 -197 TTTTGTCAAGAATTTAGTGTACTCAGATAGGATTTTAA 2 137 1 AATTTTTAAT 0.944441 -164 CTCGAGTATATCCTAATTAAATAAAGAATAGC 2 279 0 AGTATTTAAT 0.981382 -22 ***** * * * ** Masking position 13 Map Score: 8.35752 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 50 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 2 ATTGATAATATTTGTTGGGTTTAGGCTGCATT 1 45 1 TTTGTTGGTT 0.88393 -256 ATTATTAGTATTTAGTTGCGTTCGTGATATAG 1 174 1 TTTAGTTGTT 0.855064 -127 CAACGCCGCGTATTTTTGAACTATGTTTTGAA 1 222 1 TATTTTTGCT 0.903741 -79 TTTATCGTTCTGTCTTGGTATTTCAAAACATA 1 243 0 TGTCTTGGTT 0.836723 -58 AAAAGCCAATTTTATTGGATTTTATCGTTCTG 1 263 0 TTTATTGGTT 0.954186 -38 GCTTAACTTTTTTTTTTGTCCTTAGG 2 5 0 TTTTTTTGCT 0.955716 -296 GTAATAACAGTATATATGCTCTAAAGTTTTAG 2 67 0 TATATATGCT 0.872121 -234 TAAAAAGTTGTTTATTTGTACTCAAGTACTGT 2 172 1 TTTATTTGCT 0.980241 -129 TCAAATATTATGTATATGCTCTGTTCTTCATA 2 209 1 TGTATATGCT 0.913414 -92 ******** ** Masking position 3 Map Score: 3.68599 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 209 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 3 TCCGTGAATAAATTACAGAATGACAGACGTAAA 1 123 0 AATCAGAAGA 0.804634 -178 TGGCTTTTTAAATTATTGAATATC 1 287 1 AATTTGAAAT 0.916019 -14 TAAAATCTTGAAGTGCTTAACTTTTTTTTTTGT 2 18 0 AATCTTAATT 0.660865 -283 TTTCCCCTAAAACTTTAGAGCATATATACTGTT 2 61 1 AATTAGAGAT 0.836745 -240 TTCAGAATGTAATAACAGTATATATGCTCTAAA 2 74 0 AAACAGTAAT 0.683979 -227 TACTGTTATTACATTCTGAAGGTGCTGAACTTA 2 87 1 ACTCTGAAGT 0.501808 -214 ATTCTTGACAAAAAGCTGAATATATTGTATTAA 2 117 0 AAACTGAAAT 0.969515 -184 GCTTTTTGTCAAGAATTTAGTGTACTCAGATAG 2 134 1 AAATTTAGGT 0.810647 -167 ACAAATAAACAACTTTTTAAAATCCTATCTGAG 2 158 0 AATTTTAAAT 0.812857 -143 GCATATACATAATATTTGAGCGTCACAGTACTT 2 195 0 AAATTGAGGT 0.915046 -106 GCTTAATATGAAGAACAGAGCATATACATAATA 2 214 0 AAACAGAGAT 0.937304 -87 AAAAAGAGCTAAGAGCTTAATATGAAGAACAGA 2 228 0 AAACTTAAAT 0.926822 -73 TTAAATAAAGAATAGCATAATGAAGATAAACGT 2 262 0 AAACATAAGA 0.656925 -39 ** * ***** ** Masking position 1 Map Score: 4.31069 Number of sites scoring better than the average of aligned sites = 1037 Number in coding regions = 798 Number in noncoding regions = 239 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 4 ACGTCTGTCATTCTGTAATTTATTCACGGA 1 126 1 TTCTGTAATT 0.70447 -175 ATAATTAGTGTTTTTAACGAGATTCCGTGA 1 149 0 TTTTTAACGA 0.889727 -152 CGCCGCGTATTTTTGAACTATGTTTTGAAA 1 225 1 TTTTGAACTA 0.949618 -76 TTGAACTATGTTTTGAAATACCAAGACAGA 1 237 1 TTTTGAAATA 0.903597 -64 TAAAATTGGCTTTTTAAATTATTGAATATC 1 281 1 TTTTTAAATT 0.932344 -20 AATCTTGAAGTGCTTAACTTTTTTTTTTGT 2 18 0 TGCTTAACTT 0.918563 -283 ATTCTGAAGGTGCTGAACTTAATACAATAT 2 99 1 TGCTGAACTT 0.935575 -202 AATAAACAACTTTTTAAAATCCTATCTGAG 2 158 0 TTTTTAAAAT 0.712806 -143 CTCTTAGCTCTTTTTAACGTTTATCTTCAT 2 246 1 TTTTTAACGT 0.940524 -55 ********** Masking position 4 Map Score: 5.24011 Number of sites scoring better than the average of aligned sites = 407 Number in coding regions = 271 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 5 TAAATATTTATCTAAATTTGACA 1 4 1 ATATTTATCT 0.920406 -297 TAAATTTGACATATTAATATAAATTGATAA 1 23 1 ATATTAATAT 0.485507 -278 CTAATTATTAGTATTTAGTTGCGTTCGTGA 1 171 1 GTATTTAGTT 0.93634 -130 TGAATATATTGTATTAAGTTCAGCACCTTC 2 104 0 GTATTAAGTT 0.95417 -197 TTAATACAATATATTCAGCTTTTTGTCAAG 2 117 1 ATATTCAGCT 0.970549 -184 TCTGTTCTTCATATTAAGCTCTTAGCTCTT 2 228 1 ATATTAAGCT 0.971555 -73 ********** Masking position 5 Map Score: 3.4837 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 97 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 6 GCAGCCTAAACCCAACAAATATTATCAATT 1 44 0 CCCAACAAAT 0.798556 -257 CTGTGGATTGTCCACTATATCACGAACGCA 1 190 0 TCCACTATAT 0.945492 -111 CCTAAAACTTTAGAGCATATATACTGTTAT 2 66 1 TAGAGCATAT 0.950583 -235 CTGAACTTAATACAATATATTCAGCTTTTT 2 111 1 TACAATATAT 0.902781 -190 CCTATCTGAGTACACTAAATTCTTGACAAA 2 138 0 TACACTAAAT 0.862044 -163 ATATGAAGAACAGAGCATATACATAATATT 2 212 0 CAGAGCATAT 0.928286 -89 CTCGAGTATATCCTAATTAAA 2 290 0 TCGAGTATAT 0.950583 -11 ********** Masking position 4 Map Score: 1.8649 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 105 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 7 ********** No masking Map Score: 1.30983e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 ********** No masking Map Score: 1.30983e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 9 ********** No masking Map Score: 1.30983e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0