AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i321_mixed6_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 xpaC 119 xpaC #2 yaaO 81 similar to lysine decarboxylase #3 yaaQ 73 similar to hypothetical proteins #4 metS 300 methionyl-tRNA synthetase #5 yabD 78 similar to hypothetical proteins Motif number 1 ACCTGAAAAGGTCTTTTTTTGTACTC 1 7 1 AAAGGTCTTT 0.787126 -113 AAAGAAGATGAAACTTGTTTAAGGATTGAA 1 47 1 AAACTTGTTT 0.542776 -73 AGACACATTCAAAGGATTGTTTTC 2 68 1 AAAGGATTGT 0.933095 -14 TCTTGATTTAAAAGGATTTTTAGTAGGATA 4 22 0 AAAGGATTTT 0.970748 -279 CTTTCGAACCAAAGTTTTTTATTTCATTTG 4 52 1 AAAGTTTTTT 0.895945 -249 TATTTTCATTAAAGATTTTTAATTTTAATT 4 120 1 AAAGATTTTT 0.826805 -181 TGATAAACAAAAGGTGTTTCACGTGTAAC 5 10 1 AAAGGTGTTT 0.951161 -69 TCGAAACACAAAAGGTGTTCGACGAATTGT 5 38 0 AAAGGTGTTC 0.975438 -41 TTTCGACAAGAAAGGAGTTTTTCACTT 5 62 1 AAAGGAGTTT 0.918313 -17 ********** Masking position 3 Map Score: 15.1711 Number of sites scoring better than the average of aligned sites = 403 Number in coding regions = 304 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 2 TTTCATCTTCTTTTTATTATTAAGAGTACAAAA 1 27 0 TTTTTTTTAA 0.967689 -93 ATACTCAGTTTTATTATTATTATCTACTACGTT 1 75 0 TTTTTTTTAT 0.942467 -45 CGAACCAAAGTTTTTTATTTCATTTGATTATAT 4 56 1 TTTTATTCAT 0.883681 -245 CGAACAGACTTTTTTTATTTTCATTAAAGATTT 4 105 1 TTTTATTTCA 0.983807 -196 TCATTAAAGATTTTTAATTTTAATTATTCTTTT 4 125 1 TTTTATTTAA 0.984079 -176 TTAATTTTAATTATTCTTTTTCAGGGCGTATGT 4 138 1 TTTTTTTTCA 0.969575 -163 TATGTATATATTCTTGATCTTAAAGGCTAAGAT 4 166 1 TTTTATTTAA 0.984113 -135 TATATGAATATTATTTATATTTATCCTTTATCT 4 207 0 TTTTATTTTA 0.938579 -94 GGGCGGGAGCTTTTTGACATTCTGATTAGGAGG 4 271 1 TTTTACTTCT 0.881606 -30 ** ** ** **** Masking position 5 Map Score: 10.0387 Number of sites scoring better than the average of aligned sites = 619 Number in coding regions = 459 Number in noncoding regions = 160 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261 Motif number 3 TTGAACGTAGTAGATAATAATAATAAAACT 1 72 1 TAGATAATAA 0.947654 -48 GAGATAATCGACTCCTGTGT 1 110 0 GAGATAATCG 0.901963 -10 TCAGAGGCACGATATAATAAGGTGTAAGAA 2 39 1 GATATAATAA 0.97194 -43 CCCAATAGTTGATATAATAATGTAAACGAG 3 18 1 GATATAATAA 0.97194 -56 ATAATCAAATGAAATAAAAAACTTTGGTTC 4 57 0 GAAATAAAAA 0.833844 -244 AATTTTGTCGTATATAATCAAATGAAATAA 4 70 0 TATATAATCA 0.918593 -231 AGGATAAATATAAATAATATTCATATATGA 4 213 1 TAAATAATAT 0.742761 -88 ********** Masking position 6 Map Score: 3.87769 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 146 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 4 CTCCTTTAGATTGGAAACAACGTGATCTCG 3 44 0 TTGGAAACAA 0.926389 -30 AATCAAGACTTTCGAACCAAAGTTTTTTAT 4 44 1 TTCGAACCAA 0.950752 -257 TTTGATTATATACGACAAAATTCGACACGA 4 78 1 TACGACAAAA 0.932333 -223 TACGACAAAATTCGACACGAACAGACTTTT 4 88 1 TTCGACACGA 0.991005 -213 CCTTTTGTGTTTCGACAAGAAAGGAGTTTT 5 53 1 TTCGACAAGA 0.979974 -26 ********** Masking position 5 Map Score: 1.80464 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 76 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 TTGAATGTGTCTTCTTACACCTTATTATATC 2 49 0 CTTCTACACC 0.978742 -33 CTTGAAACCTCCTAATCAGAA 4 290 0 CTTGAACCTC 0.94755 -11 AATTGTTACACGTGAAACACCTTTTGTTTAT 5 13 0 CGTGAACACC 0.983963 -66 TGTAACAATTCGTCGAACACCTTTTGTGTTT 5 34 1 CGTCAACACC 0.994246 -45 **** ****** Masking position 7 Map Score: 0.00801745 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 29 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 ********** No masking Map Score: -7.36532e-13 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 7 ********** No masking Map Score: -7.36532e-13 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: -7.36532e-13 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