AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00561_mgen_reg_100.orf -o00561_mgen_100.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.32 -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 = 0.32 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MG039 158 conserved hypothetical protein #2 MG109 59 serine/threonine protein kinase, putative #3 MG211 189 conserved hypothetical protein #4 MG431 59 triosephosphate isomerase (tpiA) #5 MG432_MG433 85 MG432: conserved hypothetical protein, MG433: elongation factor Ts (tsf) #6 MG437 68 M. genitalium predicted coding region MG437 Motif number 1 TGACGGTATTTTAGCTAATTATTTTTAGTAAAAA 1 14 1 TTAGTATTTT 0.939997 -145 TTTTTTATCTTTTGATTTCTTTTTACTAAAAATA 1 33 0 TTTGTTCTTT 0.936186 -126 TAAAAAAATGTTTGATACTACTTTTTATAGAGAT 1 60 1 TTTGTATATT 0.892046 -99 TGATTTACTTTTTGGTATCTCTATAAAAAGTAGT 1 76 0 TTTGTACTTT 0.982001 -83 AAAGGATTAGTTTTATAGTTGTGATTTACTTTTT 1 97 0 TTTTTATTTA 0.874632 -62 CTTCTAGTATTTAGTTAGTTATTTTGCAAAAAAG 1 127 0 TTAGTATTTT 0.939997 -32 AGCTTTTCAATTTGATACTTATTTTCAACAATAT 2 20 0 TTTGTATTTT 0.989043 -40 TAAATCATCATTTTTAACTTCAATCTTAGGCA 3 9 0 TTTTAATTAT 0.782162 -181 AGTGATATCCTTTTAAACTTTTTTAAAGCTAGCT 3 44 0 TTTTAATTTT 0.874632 -146 CTGTGCTATCTTTTGTTTTTCTCTTAACCGCATC 3 126 0 TTTTTTTTTT 0.874632 -64 GAAAATGGTTTTTGAAAACTTATAAAATCTTTCA 4 35 1 TTTGAACTAA 0.669972 -25 TAATTTCTTATTTACTATCTTATTAGTAATATTA 5 25 0 TTTATACTAT 0.812352 -61 TTTTAATAATTTTGGTAATTAATAATTTCTTATT 5 47 0 TTTGTATTAA 0.925925 -39 GATGAATTGTTTTGCTTTTTCATTCAT 6 4 0 TTTGTTTTAT 0.925927 -65 TATTCATTGCTTTATTAGTTGTATT 6 54 1 TTTATATTTT 0.932913 -15 **** ** ** * * Masking position 2 Map Score: 17.506 Number of sites scoring better than the average of aligned sites = 679 Number in coding regions = 598 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 2 GTATTTTAGCTAATTATTTTTAGTAAAAAGA 1 19 1 TAATTTTTTT 0.914473 -140 TTTTATCTTTTGATTTCTTTTTACTAAAAAT 1 34 0 TGATTCTTTT 0.927618 -125 AAATGTTTGATACTACTTTTTATAGAGATAC 1 65 1 TACTATTTTT 0.818503 -94 ACTATAAAACTAATCCTTTTTTGCAAAATAA 1 112 1 TAATCTTTTT 0.821378 -47 TAATTAATCTTCTAGTATTTA 1 148 0 TAATTATCTT 0.84542 -11 CACCCCTATTTAAAAGCTTTTCAATTTGATA 2 37 0 TAAAACTTTT 0.859141 -23 AAGCTAGCTCTAAATCATCATTTTTAACTTC 3 22 0 TAAATATCAT 0.611126 -168 GATATCCTTTTAAACTTTTTTAAAGCTAGCT 3 44 0 TAAACTTTTT 0.683393 -146 GCTTTTTCTGTGCTATCTTTTGTTTTTCTCT 3 136 0 TGCTACTTTT 0.843853 -54 CTTTTCCAACTAATTGATCATTAAG 4 5 0 TAATTATCAT 0.769971 -55 AAATGGTTTTTGAAAACTTATAAAATCTTTC 4 37 1 TGAAACTTAT 0.73658 -23 ATGAAAGATTTTATAAGTTTTC 4 48 0 TGAAAATTTT 0.660953 -12 ATTTCTTATTTACTATCTTATTAGTAATATT 5 26 0 TACTACTTAT 0.815418 -60 TGGTAATTAATAATTTCTTATTTACTATCTT 5 38 0 TAATTCTTAT 0.912862 -48 ATTATTAAAATAATTGTTCTTAACT 5 71 1 TAATTTTCTT 0.888975 -15 TGAATTGTTTTGCTTTTTCATTCAT 6 5 0 TGCTTTTCAT 0.670793 -64 ***** ***** Masking position 8 Map Score: 12.2261 Number of sites scoring better than the average of aligned sites = 747 Number in coding regions = 671 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 3 TTTACTTTTTGGTATCTCTATAAAAAGTAG 1 77 0 GGTATCTCTA 0.927958 -82 CTTTTTTAAAGCTAGCTCTAAATCATCATT 3 31 0 GCTAGCTCTA 0.985876 -159 AGTTTAAAAGGATATCACTGGAAGTACGCA 3 59 1 GATATCACTG 0.927035 -131 AAGTACGCAGGTTAGCACAACGCCATGAAT 3 80 1 GTTAGCACAA 0.962556 -110 AAAAACAAAAGATAGCACAGAAAAAGCGCA 3 140 1 GATAGCACAG 0.974073 -50 CTTAATGGCTAGCTAAACTGCGAAACT 3 173 0 GCTAGCTAAA 0.914883 -17 ********** Masking position 4 Map Score: 2.17095 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 33 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 4 TCACTGGAAGTACGCAGGTTAGCACAACGC 3 73 1 TACGCAGGTT 0.925597 -117 CGAAACTTCCTGCGCTTTTTCTGTGCTATC 3 150 0 TGCGCTTTTT 0.981926 -40 CGCAGGAAGTTTCGCAGTTTAGCTAGCCAT 3 166 1 TTCGCAGTTT 0.985871 -24 GATGAATTGTTTTGCTTTTTCATTCAT 6 8 0 TTTGCTTTTT 0.946662 -61 AATACTGAAGTTCGCTTTTTGATGAATTGT 6 28 0 TTCGCTTTTT 0.989319 -41 ********** Masking position 9 Map Score: 3.4443 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 20 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 CTTTTTACTAAAAATAATTAGCTAAAATACC 1 18 0 AAAATATTAG 0.777417 -141 AAATCACAACTATAAAACTAATCCTTTTTTG 1 104 1 TATAAACTAA 0.656841 -55 CCTTTTTTGCAAAATAACTAACTAAATACTA 1 126 1 AAAATACTAA 0.964244 -33 TATTTTCAACAATATCACCTATCT 2 4 0 AATATACCTA 0.80805 -56 CAACGCCATGAATACCACTTGCGCAAAGGGA 3 97 1 AATACACTTG 0.857944 -93 CACTAAGCTTAATATTACTAATAAGATAGTA 5 16 1 AATATACTAA 0.977423 -70 ATTAATTACCAAAATTATTAAAATAATTGTT 5 58 1 AAAATATTAA 0.859947 -28 AATACAACTAATAAAGCAATG 6 58 0 AATACACTAA 0.966814 -11 ***** ***** Masking position 7 Map Score: 2.57069 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 214 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 ********** No masking Map Score: 1.49457e-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 7 ********** No masking Map Score: 1.49457e-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: 1.49457e-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