AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i070_Threonine_Biosynthesis_mjan_reg_100.orf -o070_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 RMJ03213 300 M_jannaschii_chromosome #2 RMJ01903 20 M_jannaschii_chromosome #3 RMJ08949 251 M_jannaschii_chromosome #4 RMJ05083 300 M_jannaschii_chromosome Motif number 1 TAAGAAAAATTATATTTCACTATTTTTTCAAATAT 1 30 1 TATTTCATTT 0.78549 -271 TTTTTATTCTTTATACTAAAAATATTTGAAAAAAT 1 51 0 TTACTAATAT 0.911409 -250 CTTAAAGAAGTTTAATTATTTTTATTCTTTATACT 1 69 0 TTATTATTAT 0.81194 -232 TATTTTTAAATTTGATTAAAACTATTTAGGAAAAG 1 110 0 TTATTAATAT 0.963932 -191 AAATAGAACATTATATTCTCTTTTTAGCTTATGAA 1 140 1 TTATTCTTTT 0.782418 -161 TTTTTAGCTTATGAACTAAAAATATAAAAGGTTAA 1 160 1 ATACTAATAT 0.784355 -141 TGGAGCATCTTTTTATTAACCTTTTATATTTTTAG 1 175 0 TTATTAATTT 0.982749 -126 TTAGACCATGTATATTTAAAATTTTTCTTTATTGG 1 225 0 TATTTAATTT 0.90349 -76 TTAAATATACATGGTCTAAAATTTTGTGTGGTTAA 1 241 1 ATTCTAATTT 0.73146 -60 TTATAGGATTATTTTTTCATAATATTCATCACCAT 3 204 0 ATTTTCATAT 0.561785 -48 AAAATAATCCTATAATTAAAGTTTTTTGGTGTCAA 3 224 1 TAATTAATTT 0.963957 -28 ACCTAATATTTAGCATTAAAAATTTAGAATCTATA 4 32 0 TAATTAATTT 0.963932 -269 TTAAATCTTTATGCATTAAATATTTATAGCAATAC 4 65 0 ATATTAATTT 0.950411 -236 TGTAACCATGTATTATTAAATCTTTATGCATTAAA 4 80 0 TAATTAATTT 0.963883 -221 TTCTTTAAAATTTTATTAAGTTTTTGAAAAATGCT 4 138 0 TTATTAATTT 0.982735 -163 ACTTTTAGGCTTATATTAATTCTTTAAAATTTTAT 4 157 0 TTATTAATTT 0.982704 -144 ** ***** *** Masking position 7 Map Score: 19.2368 Number of sites scoring better than the average of aligned sites = 1181 Number in coding regions = 878 Number in noncoding regions = 303 Number of orfs with sites within 600 bp upstream = 276 Fraction of orfs with sites within 600 bp upstream = 0.0443302 Motif number 2 CTATTTAGGAAAAGCTTTCTCTTAAAGAAG 1 94 0 AAAGCTTTCT 0.878472 -207 AAGAGAATATAATGTTCTATTTTTAAATTT 1 132 0 AATGTTCTAT 0.889446 -169 TGTATATTTAAAATTTTTCTTTATTGGGGA 1 222 0 AAATTTTTCT 0.802541 -79 TACATGGTCTAAAATTTTGTGTGGTTAATC 1 248 1 AAAATTTTGT 0.68412 -53 TGGTTACTTCAAATCTCTATTAAAGTGGGG 3 27 1 AAATCTCTAT 0.916379 -225 TATTCCTGTGAAAGTCCTGTGGTATACCCA 3 79 0 AAAGTCCTGT 0.947578 -173 CACAGGAATAAATTTCTTATTGAACATAAT 3 99 1 AATTTCTTAT 0.771995 -153 TAGACATCATAATTCCTTATATTGAATTAT 3 136 1 AATTCCTTAT 0.717117 -116 CAGGACTTTCACAGTTTTATAATTCAATAT 3 154 0 ACAGTTTTAT 0.784315 -98 TAAAACTGTGAAAGTCCTGTGCCAATAGGG 3 165 1 AAAGTCCTGT 0.947578 -87 CCAATAGGGCGAAGCCCTATGGTGATGAAT 3 186 1 GAAGCCCTAT 0.779127 -66 TCCTATAATTAAAGTTTTTTGGTGTCAAAC 3 231 1 AAAGTTTTTT 0.778099 -21 TTTATGCATTAAATATTTATAGCAATACCT 4 63 0 AAATATTTAT 0.598386 -238 ATGTATTATTAAATCTTTATGCATTAAATA 4 78 0 AAATCTTTAT 0.905943 -223 TTAATTCTTTAAAATTTTATTAAGTTTTTG 4 147 0 AAAATTTTAT 0.824827 -154 TATTCTTGCGAAAGTCCTATTAGGCACTTT 4 187 0 AAAGTCCTAT 0.975295 -114 ATAAACTGCAAAAGTCCTATTCAATGTTAT 4 270 1 AAAGTCCTAT 0.975295 -31 ********** Masking position 8 Map Score: 15.9563 Number of sites scoring better than the average of aligned sites = 1235 Number in coding regions = 923 Number in noncoding regions = 312 Number of orfs with sites within 600 bp upstream = 243 Fraction of orfs with sites within 600 bp upstream = 0.0390299 Motif number 3 AAAGTGGGGTTGCCTTTGGCAACCCCGCTCT 3 48 1 TGCCTTTGCA 0.951989 -204 GTATACCACAGGACTTTCACAGGAATAAATT 3 82 1 GGACTTTACA 0.991862 -170 GGAATTATGATGTCTATAGCATCATTATGTT 3 121 0 TGTCTATGCA 0.900158 -131 TATTGGCACAGGACTTTCACAGTTTTATAAT 3 161 0 GGACTTTACA 0.991862 -91 GTGCCTAATAGGACTTTCGCAAGAATACAAT 4 190 1 GGACTTTGCA 0.997234 -111 ACATTGAATAGGACTTTTGCAGTTTATAGAT 4 266 0 GGACTTTGCA 0.997234 -35 ******* *** Masking position 5 Map Score: 10.2983 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 26 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 4 TAAGAGGATGAAAACTAAGAAAAATTATATT 1 15 1 AAAATAAGAA 0.896436 -286 TTTATACTAAAAATATTTGAAAAAATAGTGA 1 46 0 AAATTTTGAA 0.937505 -255 TTTTAGTATAAAGAATAAAAATAATTAAACT 1 65 1 AAGATAAAAA 0.640261 -236 AGTTTTAATCAAATTTAAAAATAGAACATTA 1 122 1 AAATTAAAAA 0.806044 -179 CTTATGAACTAAAAATATAAAAGGTTAATAA 1 167 1 AAAATATAAA 0.922512 -134 CCAATAAAGAAAAATTTTAAATATACATGGT 1 225 1 AAAATTTAAA 0.940044 -76 TAACCACACAAAATTTTAGACCATGTATATT 1 244 0 AAATTTAGAC 0.529864 -57 ATTGAATTATAAAACTGTGAAAGTCCTGTGC 3 156 1 AAAATGTGAA 0.83796 -96 TATGGTGATGAATATTATGAAAAAATAATCC 3 203 1 AATATATGAA 0.641385 -49 TTGACACCAAAAAACTTTAATTATAGGATTA 3 228 0 AAAATTTAAT 0.606785 -24 TTTAGCATTAAAAATTTAGAATCTATAAATA 4 28 0 AAAATTAGAA 0.919351 -273 TTTATGCATTAAATATTTATAGCAATACCTA 4 62 0 AAATTTTATA 0.493106 -239 AAATTTTATTAAGTTTTTGAAAAATGCTACA 4 135 0 AAGTTTTGAA 0.813235 -166 AAAACTTAATAAAATTTTAAAGAATTAATAT 4 149 1 AAAATTTAAA 0.940044 -152 TAACCTTAACAAATCTATAAACTGCAAAAGT 4 254 1 AAATTATAAA 0.889734 -47 **** ****** Masking position 2 Map Score: 13.8616 Number of sites scoring better than the average of aligned sites = 1784 Number in coding regions = 1263 Number in noncoding regions = 521 Number of orfs with sites within 600 bp upstream = 376 Fraction of orfs with sites within 600 bp upstream = 0.0603919 Motif number 5 TTTTATTCTTTATACTAAAAATATTTGAAAA 1 54 0 TATCTAAAAA 0.819169 -247 TTTTAGTTCATAAGCTAAAAAGAGAATATAA 1 150 0 TAACTAAAAA 0.956179 -151 TTTTAGCTTATGAACTAAAAATATAAAAGGT 1 161 1 TGACTAAAAA 0.903683 -140 AATAAAAAGATGCTCCAATAACTCCTAACTC 1 193 1 TGCCCAATAA 0.848213 -108 TTTGTGTGGTTAATCTTATCAATTATAAAAT 1 263 1 TAACTTATCA 0.743703 -38 AACTTACACCAAAAATTATTTTATA 1 286 0 TACCCAAAAA 0.966332 -15 TATGAAAAAATAATCCTATAATTAAAGTTTT 3 218 1 TAACCTATAA 0.914981 -34 AGTTTGACACCAAAAAACTTTAATTA 3 236 0 GACCCAAAAA 0.856851 -16 AGAATTAATATAAGCCTAAAAGTGCCTAATA 4 169 1 TAACCTAAAA 0.959625 -132 AGATATCAAGTAACCTTAACAAATCTATAAA 4 244 1 TAACTTAACA 0.865021 -57 *** ******* Masking position 8 Map Score: 6.47996 Number of sites scoring better than the average of aligned sites = 465 Number in coding regions = 393 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 6 GGGCATAACCCCATATTGGTTAC 3 4 1 CATAACCCCA 0.956369 -248 GGTTGCCAAAGGCAACCCCACTTTAATAGA 3 42 0 GGCAACCCCA 0.994701 -210 GGTTGCCTTTGGCAACCCCGCTCTTGGGTA 3 55 1 GGCAACCCCG 0.995089 -197 AAAGTCCTGTGGTATACCCAAGAGCGGGGT 3 69 0 GGTATACCCA 0.910138 -183 CTAATTGAATGATAACACCGTTAGATATCA 4 222 1 GATAACACCG 0.941056 -79 ********** Masking position 4 Map Score: 1.42206 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 13 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 GAAGTTTAATTATTTTTATTCTTTATACTA 1 68 0 TATTTTTATT 0.576417 -233 TTTTATTAACCTTTTATATTTTTAGTTCAT 1 170 0 CTTTTATATT 0.850148 -131 AATTTTAGACCATGTATATTTAAAATTTTT 1 234 0 CATGTATATT 0.899243 -67 ACCAAAAATTATTTTATAATTGATAAGATT 1 274 0 ATTTTATAAT 0.743671 -27 GATTTCCCTCATTTTTAATT 2 2 0 CATTTTTAAT 0.94372 -19 GACTTTCACAGTTTTATAATTCAATATAAG 3 151 0 GTTTTATAAT 0.712931 -101 ATAGATTCTAAATTTTTAATGCTAAATATT 4 33 1 AATTTTTAAT 0.820543 -268 ACTATGTAACCATGTATTATTAAATCTTTA 4 89 0 CATGTATTAT 0.728728 -212 TACATAGTGGCATGTTTAATAATATGTAGC 4 111 1 CATGTTTAAT 0.932575 -190 ********** Masking position 5 Map Score: 2.51921 Number of sites scoring better than the average of aligned sites = 669 Number in coding regions = 555 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 8 ********** No masking Map Score: 3.79592e-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 9 ********** No masking Map Score: 3.79592e-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 10 ********** No masking Map Score: 3.79592e-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