AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00271_mjan_reg_100.orf -o00271_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MJ1263 130 methionyl-tRNA synthetase (metS) #2 MJ1388 300 adenosylhomocysteinase (ahcY) Motif number 1 TGTCTTTCAAAAAAGGTATTAAAGTTTATTAA 1 5 1 TCAAAAATAA 0.969594 -126 ATAGAAGGCATTCAAATTTCCTTAATAAACTTTAATAC 1 26 0 TAATTCATAA 0.937478 -105 TATTTTGTAATAACTATTAATGTATTAATGAACGCCTT 1 67 0 TCATAAATAA 0.972929 -64 TAATAGTGTCTTTCAAAATATTTTGTAATAACTATTAA 1 85 0 TCAATATTAA 0.735894 -46 CACTTAAAAATTAAGATTAATTAAGTAAGTAAATAAGT 2 18 1 TAATAAATAA 0.983835 -283 TGTCCTTCTTTGGAAACTACAAGATTAAAATCAGACCG 2 116 1 TAATACATAA 0.976849 -185 ATCAGACCGATTCAGAATAAAAATTTAAGGTTTATTTT 2 145 1 TAATAATTAA 0.963894 -156 AATTCAAATATATAAATTAAATTAATAAAAAGAAAATA 2 177 0 TAATAAATAA 0.986917 -124 TTTATATATTTGAATTTATAAATAATAAAAGCTTTTCT 2 199 1 TATATAATAA 0.756966 -102 AAAGCTTTTCTTCACTAAAAAATAGTAATTTATATATC 2 226 1 TATAAAATAA 0.906098 -75 AATTTATATATCTCTGCTACCCTACTAATTTTTAAAAT 2 252 1 TCGTACATAA 0.87863 -49 CTACTAATTTTTAAAATTAATTCTTTAAGGTGAAATGA 2 273 1 TAATAATTAA 0.933114 -28 * * * *** * *** Masking position 17 Map Score: 14.1427 Number of sites scoring better than the average of aligned sites = 588 Number in coding regions = 397 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 2 CTTTAATACCTTTTTTGAAAGACA 1 5 0 TTTTTTGAAA 0.870482 -126 TTTATTAAGGAAATTTGAATGCCTTCTATA 1 35 1 AAATTTGAAT 0.916856 -96 TATTACAAAATATTTTGAAAGACACTATTA 1 93 1 TATTTTGAAA 0.93921 -38 CTTACTTAATTAATCTTAATTTTTAAGTGT 2 17 0 TAATCTTAAT 0.875327 -284 AAATAAGTTATGTTGTGAATGATTGTCCTA 2 48 1 TGTTGTGAAT 0.887416 -253 CAAATCAGTCTGATTTTAATAGGACAATCA 2 67 0 TGATTTTAAT 0.954591 -234 AAAATCAGACTGATTTGGAATGGAAACATT 2 80 1 TGATTTGGAA 0.864005 -221 TGAATCGGTCTGATTTTAATCTTGTAGTTT 2 129 0 TGATTTTAAT 0.954591 -172 CTTAAATTTTTATTCTGAATCGGTCTGATT 2 144 0 TATTCTGAAT 0.918482 -157 TTTAATTTATATATTTGAATTTATAAATAA 2 194 1 ATATTTGAAT 0.827503 -107 CTTAAAGAATTAATTTTAAAAATTAGTAGG 2 272 0 TAATTTTAAA 0.905904 -29 ********** Masking position 9 Map Score: 11.8009 Number of sites scoring better than the average of aligned sites = 792 Number in coding regions = 536 Number in noncoding regions = 256 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 3 GTTATTACAAAATATTTTGAAAGACACTAT 1 91 1 AATATTTTGA 0.694046 -40 GAAAGACACTATTAGTCAAAAGGAGGGAGA 1 109 1 ATTAGTCAAA 0.874643 -22 TACTTACTTAATTAATCTTAATTTTTAAGT 2 19 0 ATTAATCTTA 0.933533 -282 TAATAGGACAATCATTCACAACATAACTTA 2 51 0 ATCATTCACA 0.775737 -250 TCCATTCCAAATCAGTCTGATTTTAATAGG 2 74 0 ATCAGTCTGA 0.970133 -227 TTTATTCTGAATCGGTCTGATTTTAATCTT 2 136 0 ATCGGTCTGA 0.871365 -165 ACCTTAAATTTTTATTCTGAATCGGTCTGA 2 146 0 TTTATTCTGA 0.84166 -155 TTTTCTTTTTATTAATTTAATTTATATATT 2 179 1 ATTAATTTAA 0.80681 -122 AAAAGCTTTTATTATTTATAAATTCAAATA 2 205 0 ATTATTTATA 0.779442 -96 ACCTTAAAGAATTAATTTTAAAAATTAGTA 2 274 0 ATTAATTTTA 0.856994 -27 ********** Masking position 6 Map Score: 2.57174 Number of sites scoring better than the average of aligned sites = 525 Number in coding regions = 389 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 4 TGTCTTTCAAAAAAGGTATTAAAGTT 1 7 1 TCAAAAAAGG 0.96883 -124 GAATGCCTTCTATAAGAAGGCGTTCATTAA 1 51 1 TATAAGAAGG 0.969325 -80 CACTATTAGTCAAAAGGAGGGAGAGG 1 115 1 CAAAAGGAGG 0.986379 -16 CTTGTAGTTTCCAAAGAAGGACACCAGCTA 2 109 0 CCAAAGAAGG 0.994637 -192 ********** Masking position 5 Map Score: 2.06617 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 88 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 TGTAATAACTATTAATGTATTAATGAACGC 1 70 0 ATTAATGTAT 0.922629 -61 TATAAATTAAATTAATAAAAAGAAAATAAA 2 175 0 ATTAATAAAA 0.780082 -126 TATTAATTTAATTTATATATTTGAATTTAT 2 188 1 ATTTATATAT 0.597417 -113 ATATATTTGAATTTATAAATAATAAAAGCT 2 202 1 ATTTATAAAT 0.499522 -99 AAAAATAGTAATTTATATATCTCTGCTACC 2 243 1 ATTTATATAT 0.597417 -58 ********** Masking position 5 Map Score: 4.88036 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 115 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 6 ********** No masking Map Score: 9.48026e-14 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: 9.48026e-14 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: 9.48026e-14 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