AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i034_Pyruvate_Synthase_2_mjan_reg_300.orf -o034_mjan_300.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 RMJ01729 27 M_jannaschii_chromosome #2 RMJ01808 30 M_jannaschii_chromosome #3 RMJ00500 18 M_jannaschii_chromosome #4 RMJ03363 283 M_jannaschii_chromosome #5 RMJ02854 300 M_jannaschii_chromosome Motif number 1 CTTAAAAAATTATTTAAATAAAATTAT 1 10 0 ATTATTTAAA 0.964341 -18 AGCCGATTTGATTTTTAAACAGCTTTATTG 4 50 0 ATTTTTAAAC 0.822813 -234 ATCATTAACAATTATTAAAAGTAATATATA 4 238 0 ATTATTAAAA 0.981182 -46 GTCATTATCAATCATTAACAATTATTAAAA 4 248 0 ATCATTAACA 0.935887 -36 CCAAAAAGAAAGGATTAACATAATGGATGA 5 36 1 AGGATTAACA 0.903011 -265 ATAATGGATGATTTTTTAAATATCTCTGCT 5 55 1 ATTTTTTAAA 0.933449 -246 TAATTCATCTATTATTAAAAACTCTGTTAA 5 87 1 ATTATTAAAA 0.981182 -214 TACTTCTCGGATTTTTAACAGAGTTTTTAA 5 101 0 ATTTTTAACA 0.973189 -200 AATGTAAAGTATTATTAACATGATAGAGGA 5 146 0 ATTATTAACA 0.985913 -155 TATGTTAAGTATGTTTAACATTTTTGTATA 5 175 1 ATGTTTAACA 0.933035 -126 TATAATTCTAAGTATTTAAATATTTTTATG 5 215 0 AGTATTTAAA 0.903606 -86 TTTATTTCCAATTATTTATAATTCTAAGTA 5 231 0 ATTATTTATA 0.848857 -70 ********** Masking position 8 Map Score: 19.0674 Number of sites scoring better than the average of aligned sites = 674 Number in coding regions = 500 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 2 AAAATTATTTAAATAAAATTAT 1 3 0 AAATAAAATT 0.628455 -25 AATTTTATTTAAATAATTTTTTAAG 1 13 1 AAATAATTTT 0.937537 -15 GTTTCCACCTTAGTAATTTAGTGTTTATT 2 10 0 TAGTAATTTA 0.764279 -21 GAAAAAATAAAATTAATTTACATGGATTAC 4 163 0 AATTAATTTA 0.824721 -121 CAATTAACGAAAATAGTTTAGGCATAAGAA 4 190 0 AAATAGTTTA 0.874166 -94 CAATTATTAAAAGTAATATATAAAGTTTTG 4 230 0 AAGTAATATA 0.933802 -54 AAAATCCGAGAAGTAATTTACCCATCTTTT 5 116 1 AAGTAATTTA 0.968203 -185 ACATAATGTAAAGTATTATTAACATGATAG 5 150 0 AAGTATTATT 0.866013 -151 ACATTATGTTAAGTATGTTTAACATTTTTG 5 171 1 AAGTATGTTT 0.725389 -130 TATTTTTATGAAAAATTTTATATACAAAAA 5 195 0 AAAAATTTTA 0.601407 -106 CTAAGTATTTAAATATTTTTATGAAAAATT 5 208 0 AAATATTTTT 0.756757 -93 AAATAATTGGAAATAAAATAGGACTTTCGC 5 244 1 AAATAAAATA 0.730913 -57 TCGCATGAGGAAATATTTTATTATATAATA 5 270 1 AAATATTTTA 0.922589 -31 ********** Masking position 5 Map Score: 12.7072 Number of sites scoring better than the average of aligned sites = 1026 Number in coding regions = 725 Number in noncoding regions = 301 Number of orfs with sites within 600 bp upstream = 244 Fraction of orfs with sites within 600 bp upstream = 0.0391905 Motif number 3 ACCTTAGTAATTTAGTGTTTATT 2 4 0 TTTAGTGTTT 0.925417 -27 TTTAAACAGCTTTATTGTTGAATTACTGTC 4 37 0 TTTATTGTTG 0.972032 -247 ACTATAGCAGTTCCTTTTTTAACTCCTTCA 4 87 0 TTCCTTTTTT 0.795715 -197 TGATGTTGTATTTATTTTTGAGAATGACAC 4 115 0 TTTATTTTTG 0.972571 -169 GTAAATTAATTTTATTTTTTCTTATGCCTA 4 172 1 TTTATTTTTT 0.957183 -112 ACTATTTTCGTTAATTGCTTAAATCTCCAA 4 203 1 TTAATTGCTT 0.720356 -81 TTTGGATTTATTTAGTTCTGATTCTTAATT 5 11 0 TTTAGTTCTG 0.91916 -290 ATGTTAATCCTTTCTTTTTGGATTTATTTA 5 27 0 TTTCTTTTTG 0.952559 -274 ********** Masking position 6 Map Score: 6.19094 Number of sites scoring better than the average of aligned sites = 631 Number in coding regions = 462 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 4 ATAAATCTTAATCTCCCAGCTTTCAT 4 5 0 ATCCCAGCTT 0.88278 -279 TAAAAATCAAATCGGCTATTATATTGAAGGAG 4 63 1 ATCGCATTAT 0.931294 -221 TTAAACTGTCATTATCAATCATTAACAATTAT 4 253 0 ATTTCATCAT 0.925832 -31 TATTTAAAAAATCATCCATTATGTTAATCCTT 5 45 0 ATCTCATTAT 0.960372 -256 CTGCTTTTAATTCATCTATTATTAAAAACTCT 5 80 1 TTCTCATTAT 0.960626 -221 GGTAAATTACTTCTCGGATTTTTAACAGAGTT 5 106 0 TTCCGATTTT 0.747006 -195 CGAGAAGTAATTTACCCATCTTTTTCCTCTAT 5 122 1 TTTCCATCTT 0.895555 -179 ACCCATCTTTTTCCTCTATCATGTTAATAATA 5 135 1 TTCTCATCAT 0.969168 -166 GTCCTATTTTATTTCCAATTATTTATAATTCT 5 236 0 ATTCCATTAT 0.93991 -65 *** ** ***** Masking position 8 Map Score: 5.01839 Number of sites scoring better than the average of aligned sites = 636 Number in coding regions = 579 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 5 TTGTTGAATTACTGTCATAAATCTTAATCT 4 23 0 ACTGTCATAA 0.960368 -261 GAACTGCTATAGTGTCATTCTCAAAAATAA 4 104 1 AGTGTCATTC 0.981243 -180 CTCACCTTAAACTGTCATTATCAATCATTA 4 261 0 ACTGTCATTA 0.987612 -23 CATAATGTAAAGTATTATTAACATGATAGA 5 149 0 AGTATTATTA 0.908059 -152 TCAAAGAGTGTTATTATATAATAAAA 5 285 0 AGTGTTATTA 0.980967 -16 ********** Masking position 5 Map Score: 3.56183 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 21 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 TTAATTCACCTCAATAAT 3 9 0 TTAATTCACC 0.990883 -10 ATTTATGACAGTAATTCAACAATAAAGCTG 4 31 1 GTAATTCAAC 0.945213 -253 AAAAATAAAATTAATTTACATGGATTACAT 4 161 0 TTAATTTACA 0.850322 -123 CGTTAATTGCTTAAATCTCCAAAACTTTAT 4 211 1 TTAAATCTCC 0.868562 -73 ATCTCTGCTTTTAATTCATCTATTATTAAA 5 76 1 TTAATTCATC 0.954183 -225 AATCCGAGAAGTAATTTACCCATCTTTTTC 5 118 1 GTAATTTACC 0.968159 -183 ********** Masking position 6 Map Score: 4.16837 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 163 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 7 ********** No masking Map Score: -9.70439e-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: -9.70439e-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: -9.70439e-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