AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00052_mgen_reg_100.orf -o00052_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 MG062 300 PTS system, fructose-specific IIABC component (fruA) #2 MG063 94 1-phosphofructokinase (fruK) #3 MG069 300 PTS system, glucose-specific IIABC component (ptsG) #4 MG109 59 serine/threonine protein kinase, putative #5 MG115 24 conserved hypothetical protein #6 MG211 189 conserved hypothetical protein #7 MG452 52 conserved hypothetical protein Motif number 1 TGAAATTGTCTTTCATTGTTAACAGCATTT 1 87 1 TTTCATTGTT 0.842592 -214 TTTTATTCAATTTTGTTGTTAAATGCTGTT 1 107 0 TTTTGTTGTT 0.993045 -194 AGGGTCTGTTTTTTATTTTTATTCAATTTT 1 123 0 TTTTATTTTT 0.862539 -178 TACGCTCCCAGTTTGTTGTTAAATTTATTA 1 254 1 GTTTGTTGTT 0.964141 -47 CAATTGATTATTATGTTGATTTAAACAAGC 2 22 1 TTATGTTGAT 0.829871 -73 CTAAAAGAGCATATGTTGTTTGCATGCAAC 3 13 0 ATATGTTGTT 0.911269 -288 CATATGCTCTTTTAGTTGTTTTTGGAATTT 3 28 1 TTTAGTTGTT 0.969687 -273 TTGACCTTTCTTTTGTTCTTTAAGTGAAAT 3 102 0 TTTTGTTCTT 0.948685 -199 AATAAAACTAATTTGTTGTTTCTTTTTCAT 3 191 0 ATTTGTTGTT 0.969687 -110 AACAAATTAGTTTTATTTTTGCTTGCAATA 3 204 1 TTTTATTTTT 0.862539 -97 GTTAATAAAATTTAGTAGTTTTAAA 3 286 1 TTTAGTAGTT 0.772944 -15 CTGTGCTATCTTTTGTTTTTCTCTTAACCG 6 130 0 TTTTGTTTTT 0.969247 -60 TTGTTTAAATTATGTTGTTAATTTTAAAT 7 10 1 TTATGTTGTT 0.978649 -43 ********** Masking position 6 Map Score: 19.8779 Number of sites scoring better than the average of aligned sites = 493 Number in coding regions = 437 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 2 TTAGACTAATTTTAAAAGCTGTAGCTAATT 1 27 1 TTTAAAAGCT 0.98116 -274 CAATTTTGTTGTTAAATGCTGTTAACAATG 1 100 0 GTTAAATGCT 0.79619 -201 TAAAACACTATTTTTTTGCTTGTTTAAATC 2 39 0 TTTTTTTGCT 0.796374 -56 AAAATAGTGTTTTAATACCTGGTGGTAAGG 2 55 1 TTTAATACCT 0.889866 -40 TTTTTGGAATTTTATTAGTTCTAATTGGAC 3 46 1 TTTATTAGTT 0.671778 -255 TAAGTGAAATTTTTAAAGCTCAAAATAAAA 3 82 0 TTTTAAAGCT 0.984099 -219 GCAATAGTTTTTTTAATGCTAGGAATAGGT 3 228 1 TTTTAATGCT 0.961015 -73 CCCACCCCTATTTAAAAGCTTTTCAATTTG 4 40 0 TTTAAAAGCT 0.98116 -20 TAAATCATCATTTTTAACTTCAATCTTAGG 6 13 0 TTTTTAACTT 0.703996 -177 TTTTAAACTTTTTTAAAGCTAGCTCTAAAT 6 38 0 TTTTAAAGCT 0.984099 -152 AGTGATATCCTTTTAAACTTTTTTAAAGCT 6 48 0 TTTTAAACTT 0.856548 -142 ********** Masking position 3 Map Score: 12.3288 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 346 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 TAAGACAGAATTTACATTAGAC 1 1 1 TAAACAAATT 0.910994 -300 AGAATTTACATTAGACTAATTTTAAAAGCTGT 1 17 1 TTAACTATTT 0.944363 -284 CAGTTTGTTCTAAAAAACAATTAGCTACAGCT 1 43 0 TAAAAAAATT 0.822471 -258 AGTTGCATATTTATAATAAATTTAACAACAAA 1 265 0 TTAAATAATT 0.884833 -36 TAAATCAACATAATAATCAATTGCGCAAGCGT 2 13 0 TAAAATAATT 0.928723 -82 CACCAGGTATTAAAACACTATTTTTTTGCTTG 2 47 0 TAAACATATT 0.696347 -48 AAGGTCAAATTACTAATGATTTGACTTCCAAT 3 124 1 TACAATATTT 0.691065 -177 ATAACTCACTTAAAAATGAAGTTCCTAGAGGG 3 154 1 TAAAATAAGT 0.691072 -147 CAAGCAAAAATAAAACTAATTTGTTGTTTCTT 3 197 0 TAAACTATTT 0.966428 -104 CTTTTCAATTTGATACTTATTTTCAACAATAT 4 20 0 TGAACTATTT 0.884337 -40 TGATATCCTTTTAAACTTTTTTAAAGCTAGCT 6 44 0 TTAACTTTTT 0.791797 -146 CCAGCTTATCTTAAACTTATTTAAAATTAACA 7 26 0 TTAACTATTT 0.944361 -27 *** *** **** Masking position 5 Map Score: 7.76723 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 188 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 4 GGATATTTAATGGCGGAAGCGGTGGGATTC 1 164 1 TGGCGGAAGC 0.836766 -137 TAATAATCAATTGCGCAAGCGTAA 2 5 0 TTGCGCAAGC 0.984203 -90 AACACTATTTTTTTGCTTGTTTAAATCAAC 2 36 0 TTTTGCTTGT 0.769677 -59 ATGTTGCATGCAAACAACATA 3 2 1 TGTTGCATGC 0.886366 -299 TTAGTTTTATTTTTGCTTGCAATAGTTTTT 3 210 1 TTTTGCTTGC 0.94435 -91 AATGATGATTTAGAGCTAGCTTTAAAAAAG 6 31 1 TAGAGCTAGC 0.876124 -159 ATTCATGGCGTTGTGCTAACCTGCGTACTT 6 80 0 TTGTGCTAAC 0.861662 -110 CCGCATCCCTTTGCGCAAGTGGTATTCATG 6 103 0 TTGCGCAAGT 0.924632 -87 AGTTTCGCAGTTTAGCTAGCCATTAAG 6 173 1 TTTAGCTAGC 0.945404 -17 ********** Masking position 1 Map Score: 4.34837 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 80 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 TGTTTTTTATTTTTATTCAATTTTGTTGTT 1 117 0 TTTTATTCAA 0.76144 -184 TATTATGTTGATTTAAACAAGCAAAAAAAT 2 30 1 ATTTAAACAA 0.939014 -65 TGTTGTTTCTTTTTCATCAACTCCCTCTAG 3 178 0 TTTTCATCAA 0.912016 -123 TTGATACTTATTTTCAACAATATCACCTAT 4 13 0 TTTTCAACAA 0.959574 -47 ATTGAAAAGCTTTTAAATAGGGGTGGG 4 43 1 TTTTAAATAG 0.74824 -17 TAACAACATAATTTAAACAA 7 1 0 ATTTAAACAA 0.939014 -52 ATGTTGTTAATTTTAAATAAGTTTAAGATA 7 22 1 TTTTAAATAA 0.905592 -31 ********** Masking position 9 Map Score: 3.33473 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 304 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 6 ATATTTAATGGCGGAAGCGGTGGGATTCGAA 1 166 1 GCGGAAGGGT 0.989646 -135 AGGACACCCTGCTAAGGTGTTAGATCGTTCT 1 209 0 GCTAAGGGTT 0.859242 -92 CTGGGAGCGTACTCAAGTGGTTAAGAGGACA 1 234 0 ACTCAAGGGT 0.946207 -67 ATAATCAATTGCGCAAGCGTAA 2 2 0 GCGCAAGGTA 0.965582 -93 GCATCCCTTTGCGCAAGTGGTATTCATGGCG 6 100 0 GCGCAAGGGT 0.997037 -90 CACAGAAAAAGCGCAGGAAGTTTCGCAGTTT 6 155 1 GCGCAGGAGT 0.977356 -35 ******* *** Masking position 5 Map Score: 2.73958 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 6 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 AAAAAACAATTAGCTACAGCTTTTAAAATTAG 1 32 0 TACTCAGCTT 0.970829 -269 AATATGCAACTAATTAGCGCTTTAG 1 286 1 TATTGCGCTT 0.981641 -15 CTAGGATTTTTATTTTGAGCTTTAAAAATTTC 3 75 1 TATTGAGCTT 0.984656 -226 AAATCATTAGTAATTTGACCTTTCTTTTGTTC 3 114 0 TATTGACCTT 0.97119 -187 TTTCGCAGTTTAGCTAGCCATTAAG 6 175 1 TACTGCCATT 0.871745 -15 TATCTCCAGCTTATCTTAAACT 7 41 0 TACTCAGCTT 0.946957 -12 ** ** ****** Masking position 5 Map Score: 2.1082 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 18 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 TGATGATTTAGAGCTAGCTTTAAAAAAGTT 6 33 1 GAGCTAGCTT 0.896307 -157 CGTACTTCCAGTGATATCCTTTTAAACTTT 6 57 0 GTGATATCCT 0.962843 -133 TCATGGCGTTGTGCTAACCTGCGTACTTCC 6 78 0 GTGCTAACCT 0.983336 -112 CGCTTTTTCTGTGCTATCTTTTGTTTTTCT 6 138 0 GTGCTATCTT 0.983035 -52 ********** Masking position 5 Map Score: 0.471534 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 13 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 ********** No masking Map Score: 2.69539e-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 10 ********** No masking Map Score: 2.69539e-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 11 ********** No masking Map Score: 2.69539e-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