AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00260_mgen_reg_100.orf -o00260_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 MG001 300 DNA polymerase III, subunit beta (dnaN) #2 MG003 84 DNA gyrase subunit B (gyrB) #3 MG254 175 DNA ligase #4 MG272 249 dihydrolipoamide acetyltransferase (pdhC) #5 MG377 46 conserved hypothetical protein #6 MG378 28 arginyl-tRNA synthetase (argS) #7 MG395 300 putative lipoprotein Motif number 1 TGTACATATGTAATTATTACTGCT 1 4 0 TAATTATTAT 0.660648 -297 TGTAAAATATCATTAATTTCTGTTATATATA 1 44 1 CATTAATTTT 0.931619 -257 TTTTAGAGAGTATTAATTATTACTATAATTA 1 85 1 TATTAATTAT 0.899664 -216 TTAATTATTACTATAATTAAGCATTTATGCT 1 97 1 CTATAATTAG 0.792727 -204 CATAAAAAGCTTATAATTAAGCATAAATGCT 1 116 0 TTATAATTAG 0.799455 -185 ACTAAAATGTCTATAATTTTGTTCATAAAAA 1 139 0 CTATAATTTG 0.858241 -162 TCTTTAATATCTATTATTTATTATAAGAACT 1 167 0 CTATTATTTT 0.853319 -134 ATTTCTATTTTTTTATTTTCTTTAATATCTA 1 185 0 TTTTATTTTT 0.837614 -116 AGGGTTATGATATTTATTTCTATTTTTTTAT 1 200 0 TATTTATTTT 0.837945 -101 TTTGATTAAGTATTAATTTCTGGGTTATCAA 1 230 0 TATTAATTTT 0.934144 -71 TTAATTAATATTTTCATTTTTGATTAAGTAT 1 248 0 TTTTCATTTT 0.916788 -53 AAAATGAAAATATTAATTAATAAAAGTGAAT 1 259 1 TATTAATTAT 0.899664 -42 AAAACCTTTCATTTTTAATGTGTTAT 2 6 1 CTTTCATTTT 0.91366 -79 TTTTAATGTGTTATAATTATTTGTTATGCCA 2 23 1 TTATAATTAT 0.913068 -62 GTTGTTACTTTAATATTTAGTATATTTTAAC 3 15 0 TAATATTTAT 0.496847 -161 TACAAAGAAGTTTTAATTTGGAGCAGATAAC 3 107 0 TTTTAATTTG 0.913708 -69 AGTTACCTAGCTTTATTTTTTAGAGCTAGGT 4 27 1 CTTTATTTTT 0.83205 -223 TCTTCCATCACTTTAATTTATGAAATGAGGT 4 58 0 CTTTAATTTT 0.96402 -192 AAACTGGCTTTTTTTATTTGTTATAGATCAC 4 191 1 TTTTTATTTT 0.910469 -59 ACTTATTAAATTTTAATTCCTATATGCGTGA 5 16 0 TTTTAATTCT 0.768569 -31 TACTTTAAATTATATTTAATGATGCAAA 6 9 0 TTATATTTAT 0.660101 -20 ATTTTTTTGGTTTTAATTTAGTTAGTTTACC 7 48 1 TTTTAATTTG 0.913705 -253 AGTAGTTCTATTTTCATTTTTAACTTTTTTG 7 88 1 TTTTCATTTT 0.916788 -213 GTTGCATTTGCTTTCATTAGTTTTTTCATTA 7 122 1 CTTTCATTAT 0.869948 -179 CTGATAAATTTAATTATTTTTATTCTGCTTA 7 181 0 TAATTATTTT 0.754887 -120 AAGATGAACTCAATTATTTTTGAAGCTAAAG 7 216 1 CAATTATTTT 0.747348 -85 ATTTCAAAACCTTTAATTAATGAAGTTAAGA 7 266 0 CTTTAATTAT 0.944248 -35 ********* * Masking position 7 Map Score: 35.1821 Number of sites scoring better than the average of aligned sites = 786 Number in coding regions = 658 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 2 ACAGAAATTAATGATATTTTACATATGTAC 1 37 0 ATGATATTTT 0.811639 -264 AATAGATACTATTATATATAACAGAAATTA 1 57 0 ATTATATATA 0.500901 -244 CTTTTTATGAACAAAATTATAGACATTTTA 1 138 1 ACAAAATTAT 0.478428 -163 ATCAAGGGTTATGATATTTATTTCTATTTT 1 205 0 ATGATATTTA 0.791681 -96 AGTGAATTGAATAAAATTTTGGGAAAAA 1 283 1 ATAAAATTTT 0.853376 -18 TTTGCCACAAACTAAATTTATGGCATAACA 2 44 0 ACTAAATTTA 0.936371 -41 TTTAATATTTAGTATATTTTAACTTGC 3 8 0 AGTATATTTT 0.722001 -168 AAGCTAGGTAACTATATTTTAAAAAAGTG 4 10 0 ACTATATTTT 0.918692 -240 AAAAAGTAAGACAAAATTTTTGTCTAACAA 4 144 1 ACAAAATTTT 0.842797 -106 GATCACTACTATTAAATTTAAACTTTAAGT 4 216 1 ATTAAATTTA 0.941788 -34 TTAGAAACTTATTAAATTTTAATTCCTATA 5 23 0 ATTAAATTTT 0.948251 -24 TACTTTAAATTATATTTAATGATGCAAA 6 11 0 ATTATATTTA 0.916391 -18 TTCTAACGGGATTAATTTTTTTGGTTTTAA 7 34 1 ATTAATTTTT 0.627211 -267 AGGTAAACTAACTAAATTAAAACCAAAAAA 7 50 0 ACTAAATTAA 0.718619 -251 AATAAAAATAATTAAATTTATCAGTGAAAA 7 188 1 ATTAAATTTA 0.941788 -113 ********** Masking position 4 Map Score: 14.9434 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 125 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 3 TGCTTAATTATAAGCTTTTTATGAACAAAA 1 124 1 TAAGCTTTTT 0.83324 -177 ATATAGTTACCTAGCTTTATTTTTTAGAGC 4 23 1 CTAGCTTTAT 0.94847 -227 AAAATTTTGTCTTACTTTTTACAGCAGCTG 4 134 0 CTTACTTTTT 0.643425 -116 AGTTTAGTTACTGGCTTTTTAGTTGTTAGA 4 166 0 CTGGCTTTTT 0.956947 -84 AGTAACTAAACTGGCTTTTTTTATTTGTTA 4 184 1 CTGGCTTTTT 0.956947 -66 AGAATTTGCATTGGCTTGATAACTACT 7 8 0 TTGGCTTGAT 0.766035 -293 TCTAACGGGATTAATTTTTTTGGTTTTAAT 7 35 1 TTAATTTTTT 0.659078 -266 ATTTTCATTTTTAACTTTTTTGATGGTTGC 7 97 1 TTAACTTTTT 0.932948 -204 TTTGCTTTCATTAGTTTTTTCATTAGCTTC 7 128 1 TTAGTTTTTT 0.857015 -173 AGTTTTTTCATTAGCTTCTTCTTTTTAATT 7 140 1 TTAGCTTCTT 0.96431 -161 AACTTAGGCTTTAGCTTCAAAAATAATTGA 7 225 0 TTAGCTTCAA 0.618772 -76 CAAGTGCTTCTTAACTTCATTAATTAAAGG 7 258 1 TTAACTTCAT 0.81883 -43 ********** Masking position 6 Map Score: 7.75424 Number of sites scoring better than the average of aligned sites = 467 Number in coding regions = 422 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 AAGAAATGCTGCCAATGCAAGTGCGAATGC 4 93 1 GCCAATGCAA 0.993787 -157 TAGTTATCAAGCCAATGCAAATTCTAACGG 7 13 1 GCCAATGCAA 0.993787 -288 ACTAATGAAAGCAAATGCAACCATCAAAAA 7 113 0 GCAAATGCAA 0.983232 -188 TAATGAAAAAACTAATGAAAGCAAATGCAA 7 123 0 ACTAATGAAA 0.897895 -178 AAAAGAAGAAGCTAATGAAAAAACTAATGA 7 135 0 GCTAATGAAA 0.978674 -166 ********** Masking position 5 Map Score: 6.43398 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 14 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 5 ACATATGTACATAGTACATATGTAAAATAT 1 24 1 ATAGTACATA 0.871841 -277 TATAGACATTTTAGTTCTTATAATAAATAA 1 155 1 TTAGTTCTTA 0.94426 -146 CTTATAATAAATAATAGATATTAAAGAAAA 1 171 1 ATAATAGATA 0.696871 -130 AACCCAGAAATTAATACTTAATCAAAAATG 1 235 1 TTAATACTTA 0.799268 -66 TGTGTTATAATTATTTGTTATGCCATAAAT 2 29 1 TTATTTGTTA 0.852324 -56 AAATCCTGACTTAGTTGATACCAATCAGGA 3 141 0 TTAGTTGATA 0.921103 -35 TACTGGCTTTTTAGTTGTTAGACAAAAATT 4 158 0 TTAGTTGTTA 0.966996 -92 CTGGCTTTTTTTATTTGTTATAGATCACTA 4 194 1 TTATTTGTTA 0.852324 -56 TTTAAATTTAATAGTAGTGATCTATAACAA 4 208 0 ATAGTAGTGA 0.846609 -42 ATCGTATTGATAGTACTTAAAGTTTAAAT 4 231 0 ATAGTACTTA 0.944218 -19 ACCTGAGTCAATAGTAGTTCTATTTTCATT 7 76 1 ATAGTAGTTC 0.846619 -225 ********** Masking position 3 Map Score: 7.62428 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 92 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 TTTTTTTATTTTCTTTAATATCTATTATTTA 1 178 0 TTCTTTAAAT 0.827356 -123 TATTAATTAATATTTTCATTTTTGATTAAGT 1 250 0 TATTTTCATT 0.862342 -51 ATATTTAGTATATTTTAACTTGC 3 3 0 TATTTTAATT 0.942067 -173 TCTGCGTTGTTACTTTAATATTTAGTATATT 3 20 0 TACTTTAAAT 0.901692 -156 CACTTTTTTAAAATATAGTTACCT 4 4 1 TTTTTTAAAT 0.750114 -246 TGTCTTCCATCACTTTAATTTATGAAATGAG 4 60 0 CACTTTAATT 0.815759 -190 CTAAACTGGCTTTTTTTATTTGTTATAGATC 4 189 1 TTTTTTTATT 0.543694 -61 GTATTGATAGTACTTAAAGTTTAAATTTAAT 4 226 0 TACTTAAATT 0.886879 -24 TTTTAGAAACTTATTAAATTTTAATTCCTAT 5 24 0 TTATTAAATT 0.566068 -23 TACTTTAAATTATATTTAATG 6 18 0 TACTTTAATT 0.959187 -11 ATAGTAGTTCTATTTTCATTTTTAACTTTTT 7 86 1 TATTTTCATT 0.862342 -215 AGAATAAAAATAATTAAATTTATCAGTGAAA 7 186 1 TAATTAAATT 0.712864 -115 ******** ** Masking position 8 Map Score: 7.37453 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 242 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 AATAAATATCATAACCCTTGATAACCCAGA 1 213 1 ATAACCCTTG 0.888517 -88 ATAACCCTTGATAACCCAGAAATTAATACT 1 223 1 ATAACCCAGA 0.883532 -78 AAAACCTTTCATTTTTAATG 2 1 1 AAAACCTTTC 0.902383 -84 ATGGTAGAACATAACCTTGCCAAGGTTAAG 3 60 1 ATAACCTTGC 0.936173 -116 ACTTCTTTGTAAAATCCTGATTGGTATCAA 3 127 1 AAAATCCTGA 0.928467 -49 ATAAATAAGAAAAATCCTGACTTAGTTGAT 3 152 0 AAAATCCTGA 0.928467 -24 AAAATATTTCAAAACCTTTAATTAATGAAG 7 272 0 AAAACCTTTA 0.917693 -29 ********** Masking position 4 Map Score: 1.55833 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 91 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 TAAATAAACAGTACAGAAGCTTTTGCCACAAACT 2 61 0 GTAAGAAGCT 0.973687 -24 CCTTGCCAAGGTTAAGATGCGGGTTCGATTCCCG 3 74 1 GTTAGATGCT 0.973687 -102 GTCTTACTTTTTACAGCAGCTGTTGCACTTAGCG 4 122 0 TTAAGCAGCT 0.861041 -128 ATTTTTAGAAACTTATTAAATTTTAA 5 31 0 TTTAGAAACT 0.87679 -16 AGTAGTTATCAAGCCAATGCAAATTCTA 7 5 1 GTTTCAAGCT 0.859636 -296 TTCTGCTTAGTTTTAGATGCAATTAAAAAGAAGA 7 156 0 TTTAGATGCT 0.958897 -145 AACTCAATTATTTTTGAAGCTAAAGCCTAAGTTT 7 222 1 TTTTGAAGCA 0.806977 -79 AATTAATGAAGTTAAGAAGCACTTGTTAAACTTA 7 249 0 GTTAGAAGCT 0.990204 -52 *** ****** * Masking position 2 Map Score: 0.924781 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 62 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 9 ********** No masking Map Score: -6.44162e-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 10 ********** No masking Map Score: -6.44162e-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 11 ********** No masking Map Score: -6.44162e-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