AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i225_Glutamyl_tRNA_synthase_mjan_reg_100.orf -o225_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 RMJ14632 144 M_jannaschii_chromosome #2 RMJ06354 111 M_jannaschii_chromosome #3 RMJ02789 36 M_jannaschii_chromosome #4 RMJ02161 56 M_jannaschii_chromosome Motif number 1 ATGAAACTTTATTAAATTTTCACGTGCATT 1 76 0 ATTAAATTTT 0.944646 -69 GGAGGTGTAAATTAAAATTTA 1 134 1 ATTAAAATTT 0.922428 -11 TAACTTATACATTAAAAAATTTATGTTATG 2 40 1 ATTAAAAAAT 0.94267 -72 GTTATGTTATATTATATATTATTTTTTAAT 2 64 1 ATTATATATT 0.615235 -48 TAAATGGCAAATTAAAAAATAATATATAAT 2 74 0 ATTAAAAAAT 0.94267 -38 TAAATATATGATTATATAAATGGCAAATTA 2 90 0 ATTATATAAA 0.7117 -22 ATTAAATATATGATTATATA 2 102 0 ATTAAATATA 0.976073 -10 AATTCTATTCAAAATAATTTTTTATG 3 7 1 ATTCAAAATA 0.926308 -30 CAAAAAATAAATAAATATAAGTCAATATT 4 10 1 AATAAATATA 0.86877 -47 AATAAATATAAGTCAATATTATAACCAAAA 4 20 1 AGTCAATATT 0.862775 -37 ********** Masking position 6 Map Score: 12.7058 Number of sites scoring better than the average of aligned sites = 1348 Number in coding regions = 964 Number in noncoding regions = 384 Number of orfs with sites within 600 bp upstream = 354 Fraction of orfs with sites within 600 bp upstream = 0.0568583 Motif number 2 TTCCACCTTATTTTGGTCTTTTTAAAAC 1 9 0 TTTTGGTCTT 0.958756 -136 GAGGTGTTAGTTTTGATGAAACTTTATTAA 1 91 0 TTTTGATGAA 0.926804 -54 GAATCCAACATTTTGGTGATTTT 2 4 0 TTTTGGTGAT 0.996995 -108 AAATAATTTTTTATGGTGATGATTT 3 22 1 TTATGGTGAT 0.994407 -15 CCGTAAATTTTTTTGGTTATAATATTGACT 4 30 0 TTTTGGTTAT 0.984514 -27 CCAAAAAAATTTACGGTGATGAG 4 44 1 TTACGGTGAT 0.984852 -13 ********** Masking position 7 Map Score: 10.0497 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 156 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 3 CATGTTTCCACCTTATTTTGGTCTTTTTAAA 1 13 0 CTTATTTTGG 0.881574 -132 AGCGAGGAGGTGTTAGTTTTGATGAAACTTT 1 96 0 TTTAGTTTTG 0.972459 -49 TTTTTTAATGTATAAGTTATGTGGGGAATCC 2 28 0 TTAAGTTATG 0.924825 -84 CATTAAAAAATTTATGTTATGTTATATTATA 2 49 1 TTATGTTATG 0.932053 -63 TTATATTATATATTATTTTTTAATTTGCCAT 2 70 1 TTTATTTTTT 0.800897 -42 TATTCAAAATAATTTTTTATGGTGATGATTT 3 16 1 ATTTTTTATG 0.907097 -21 CTTATATTTATTTATTTTTTG 4 1 0 TTATTTTTTG 0.957366 -56 CATCACCGTAAATTTTTTTGGTTATAATATT 4 34 0 ATTTTTTTGG 0.898725 -23 * ********* Masking position 7 Map Score: 4.03093 Number of sites scoring better than the average of aligned sites = 839 Number in coding regions = 665 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 4 AAGACCAAAATAAGGTGGAAACATGAACGAT 1 19 1 TAAGGTGAAA 0.974761 -126 ACATGAACGATGACGTTAAAATGAAGTGTGG 1 39 1 TGACGTTAAA 0.952801 -106 GTTTGGAAATGCACGTGAAAATTTAATAAAG 1 69 1 GCACGTGAAA 0.988833 -76 GCGTAAGCGAGGAGGTGTTAGTTTTGATGAA 1 101 0 GGAGGTGTAG 0.979313 -44 GCTTACGCTCGGAGGTGTAAATTAAAATTTA 1 124 1 GGAGGTGAAA 0.997116 -21 ******* *** Masking position 6 Map Score: 2.46665 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 61 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 5 TTAACGTCATCGTTCATGTTTCCACCTTAT 1 28 0 CGTTCATGTT 0.939236 -117 TCCAAACCACACTTCATTTTAACGTCATCG 1 46 0 ACTTCATTTT 0.903919 -99 TAAATTTTCACGTGCATTTCCAAACCACAC 1 64 0 CGTGCATTTC 0.92853 -81 ATGAAACTTTATTAAATTTTCACGTGCATT 1 76 0 ATTAAATTTT 0.757036 -69 TGTGGGGAATCCAACATTTTGGTGATTTT 2 10 0 CCAACATTTT 0.930351 -102 TATAACATAACATAAATTTTTTAATGTATA 2 45 0 CATAAATTTT 0.919493 -67 CTCATCACCGTAAATTTTTTTGGTTATA 4 39 0 CGTAAATTTT 0.978439 -18 ********** Masking position 6 Map Score: 2.16688 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 297 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 6 ********** No masking Map Score: -4.94948e-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 7 ********** No masking Map Score: -4.94948e-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 8 ********** No masking Map Score: -4.94948e-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