AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02060_mgen_reg_100.orf -o02060_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 MG040 158 lipoprotein, putative #2 MG062 300 PTS system, fructose-specific IIABC component (fruA) #3 MG069 300 PTS system, glucose-specific IIABC component (ptsG) #4 MG431 59 triosephosphate isomerase (tpiA) #5 MG432 85 conserved hypothetical protein Motif number 1 CTTTTTTGCAAAATAACTAACTAAATACTAG 1 22 0 AAAAACTAAC 0.957551 -137 AATCACAACTATAAAACTAATCCTTTTTTGC 1 44 0 ATAAACTAAT 0.91545 -115 TTATTTTTAGTAAAAAGAAATCAAAAGATAA 1 117 0 TAAAAGAAAT 0.795277 -42 AGTTTGTTCTAAAAAACAATTAGCTACAGCT 2 43 0 AAAAACAATT 0.936452 -258 TAACAGCATTTAACAACAAAATTGAATAAAA 2 106 1 TAAAACAAAA 0.904157 -195 AATTGAATAAAAATAAAAAACAGACCCTGAT 2 125 1 AAAAAAAAAC 0.741035 -176 ATAATAAATTTAACAACAAACTGGGAGCGTA 2 254 0 TAAAACAAAC 0.919304 -47 TGTTGCATGCAAACAACATATGCTCTTTTAG 3 12 1 AAAAACATAT 0.838582 -289 AAAATTCCAAAAACAACTAAAAGAGCATATG 3 28 0 AAAAACTAAA 0.949186 -273 CCTAGTCCAATTAGAACTAATAAAATTCCAA 3 49 0 TTAAACTAAT 0.800706 -252 TTTAAAGCTCAAAATAAAAATCCTAGTCCAA 3 70 0 AAATAAAAAT 0.655799 -231 AATTTCACTTAAAGAACAAAAGAAAGGTCAA 3 101 1 AAAAACAAAA 0.962155 -200 AAGAAAGGTCAAATTACTAATGATTTGACTT 3 120 1 AAATACTAAT 0.937576 -181 GATGAAAAAGAAACAACAAATTAGTTTTATT 3 190 1 AAAAACAAAT 0.986415 -111 CCTAGCATTAAAAAAACTATTGCAAGCAAAA 3 220 0 AAAAACTATT 0.91545 -81 TTTAAAACTACTAAATTTTATTAAC 3 286 0 AAATACTAAA 0.84022 -15 ACTAAGCTTAATATTACTAATAAGATAGTAA 5 17 1 ATATACTAAT 0.752969 -69 ATAAGATAGTAAATAAGAAATTATTAATTAC 5 36 1 AAAAAGAAAT 0.912807 -50 AGTTAAGAACAATTATTTTAATAA 5 72 0 TAAAACAATT 0.845396 -14 *** ******* Masking position 6 Map Score: 25.1124 Number of sites scoring better than the average of aligned sites = 696 Number in coding regions = 620 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 2 GGTATTTTAGCTAATTATTTTTAGTAAAAA 1 132 0 CTAATTATTT 0.944635 -27 AAAGCTGTAGCTAATTGTTTTTTAGAACAA 2 41 1 CTAATTGTTT 0.745484 -260 TTGCATATTTATAATAAATTTAACAACAAA 2 265 0 ATAATAAATT 0.658351 -36 CTAAAGCGCTAATTAGTTGCATATTTAT 2 283 0 CTAATTAGTT 0.948679 -18 CCAATTAGAACTAATAAAATTCCAAAAACA 3 44 0 CTAATAAAAT 0.847092 -257 ATTTTGAGCTTTAAAAATTTCACTTAAAGA 3 86 1 TTAAAAATTT 0.613095 -215 GGTCAAATTACTAATGATTTGACTTCCAAT 3 126 1 CTAATGATTT 0.884874 -175 AAAAATAAAACTAATTTGTTGTTTCTTTTT 3 194 0 CTAATTTGTT 0.681637 -107 AGCTGTTTGGTTAATAAAATTTAGTAGTTT 3 277 1 TTAATAAAAT 0.714909 -24 ATGAAAGATTTTATAAGTTTTCAAAAACC 4 41 0 TTTATAAGTT 0.631919 -19 CTTAATATTACTAATAAGATAGTAAATAAG 5 23 1 CTAATAAGAT 0.919628 -63 ATTTTGGTAATTAATAATTTCTTATTTACT 5 43 0 TTAATAATTT 0.937068 -43 AACAATTATTTTAATAATTTTGGTAATTAA 5 59 0 TTAATAATTT 0.937068 -27 ********** Masking position 4 Map Score: 8.78237 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 286 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 3 AACTAATCCTTTTTTGCAAAATAACTAACT 1 31 0 TTTTTGCAAA 0.927132 -128 TGTGATTTACTTTTTGGTATCTCTATAAAA 1 68 1 TTTTTGGTAT 0.939632 -91 TAGCTAATTATTTTTAGTAAAAAGAAATCA 1 125 0 TTTTTAGTAA 0.913009 -34 TATGACGGTATTTTAGCTAATTATTTTTAG 1 138 0 TTTTAGCTAA 0.645847 -21 AGCTAATTGTTTTTTAGAACAAACTGAATC 2 49 1 TTTTTAGAAC 0.785934 -252 CTTTTAGTTGTTTTTGGAATTTTATTAGTT 3 36 1 TTTTTGGAAT 0.939504 -265 TTTAAGTGAGTTATTGGAAGTCAAATCATT 3 138 0 TTATTGGAAG 0.78444 -163 AAGAAAATGGTTTTTGAAAACTTATAAAAT 4 33 1 TTTTTGAAAA 0.792577 -27 ATTTACTATCTTATTAGTAATATTAAGCTT 5 20 0 TTATTAGTAA 0.761056 -66 TATTTTAATAATTTTGGTAATTAATAATTT 5 53 0 ATTTTGGTAA 0.856776 -33 ********** Masking position 4 Map Score: 5.13082 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 246 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 AAAAAGTAGTATCAAACATTTTTTTATCTTTT 1 94 1 ATCAAACATT 0.983399 -65 AACAAACTGAATCAAAGAATTTGAAATTGTCT 2 66 1 ATCAAAGATT 0.9834 -235 GCTGTTAACAATGAAAGACAATTTCAAATTCT 2 81 0 ATGAAAGAAT 0.884241 -220 CCGTAGAACGATCTAACACCTTAGCAGGGTGT 2 205 1 ATCTAACATT 0.935957 -96 AATTTTATTAACCAAACAGCTTAGGAAGGGAA 3 266 0 ACCAAACATT 0.955871 -35 ATGAAAGATTTTATAAGTTTTC 4 48 0 ATGAAAGATT 0.968714 -12 ******** ** Masking position 6 Map Score: 2.14452 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 27 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 TTAGTAAAAAGAAATCAAAAGATAAAAAAA 1 112 0 GAAATCAAAA 0.781243 -47 ATTAGCTACAGCTTTTAAAATTAGTCTAAT 2 26 0 GCTTTTAAAA 0.940618 -275 ATTGTTAACAGCATTTAACAACAAAATTGA 2 101 1 GCATTTAACA 0.935026 -200 TATGTTGTTTGCATGCAACAT 3 2 0 GCATGCAACA 0.960184 -299 TTTATTTTGAGCTTTAAAAATTTCACTTAA 3 83 1 GCTTTAAAAA 0.94054 -218 AAAAACTATTGCAAGCAAAAATAAAACTAA 3 210 0 GCAAGCAAAA 0.939726 -91 CCTATTCCTAGCATTAAAAAAACTATTGCA 3 227 0 GCATTAAAAA 0.962137 -74 GATTTTATAAGTTTTCAAAAACCATTTTCT 4 34 0 GTTTTCAAAA 0.857914 -26 ********** Masking position 7 Map Score: 4.68231 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 182 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 CGAACCCACGCACCGTAGAACGATCTAACACC 2 193 1 CACCGTAGAG 0.987638 -108 AACGATCTAACACCTTAGCAGGGTGTCCTCTT 2 211 1 CACCTTAGAG 0.994388 -90 TCCTCTTAACCACTTGAGTACGCTCCCAGTTT 2 236 1 CACTTGAGAG 0.978866 -65 TCCAATAACTCACTTAAAAATGAAGTTCCTAG 3 150 1 CACTTAAAAG 0.854918 -151 ATTAACCAAACAGCTTAGGAAGGGAAACAAGT 3 260 0 CAGCTTAGAG 0.980223 -41 ******** * * Masking position 7 Map Score: 0.224024 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 3 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 ********** No masking Map Score: 1.73616e-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: 1.73616e-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: 1.73616e-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