AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i182_riboflafin_biosynthesis_mjan_reg_300.orf -o182_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 Purged sequences: RMJ07423 27 M_jannaschii_chromosome Input sequences: #1 RMJ04822 125 M_jannaschii_chromosome #2 RMJ03702 287 M_jannaschii_chromosome #3 RMJ08451 53 M_jannaschii_chromosome #4 RMJ14035 95 M_jannaschii_chromosome Motif number 1 ACTTAATAATTTTTTATTACGCA 1 4 1 TAATAATTTT 0.890156 -122 TTATTACGCATATTCCTTTTTTTAATCTCC 1 24 1 TATTCCTTTT 0.941386 -102 AAAATATTTATATGATTTTTAGATTTTAAA 1 70 1 TATGATTTTT 0.798757 -56 CAATATAAAATTATCTTTTTGGCTGAATAT 1 99 0 TTATCTTTTT 0.982841 -27 AACCTCATTTTTATAATTTTACAAATTTGG 2 17 1 TTATAATTTT 0.939849 -271 TAGTAATCATTTTTATTTTTATCTAAAAGG 2 73 1 TTTTATTTTT 0.979806 -215 AAAGAATCTTTTTTCCTTTTAGATAAAAAT 2 87 0 TTTTCCTTTT 0.968717 -201 CCTTAGTAAGTTATATATTTAAGCTTTTCC 2 147 1 TTATATATTT 0.856614 -141 GGTATTGATGTTTTCTTTTTTATGTGGGCA 2 250 1 TTTTCTTTTT 0.980175 -38 GCAGCATCGTTAATATTTTTC 2 277 1 TAATATTTTT 0.966795 -11 TTCACATTTTTTATACTTTTTTAAATGTTA 4 16 1 TTATACTTTT 0.972379 -80 TTTTAGATATTTATCTTTATACAAACTACA 4 48 0 TTATCTTTAT 0.859062 -48 AAGTTTTTTATGTTATTTTTAGATATTTAT 4 64 0 TGTTATTTTT 0.918939 -32 ********** Masking position 8 Map Score: 20.4241 Number of sites scoring better than the average of aligned sites = 1447 Number in coding regions = 1003 Number in noncoding regions = 444 Number of orfs with sites within 600 bp upstream = 365 Fraction of orfs with sites within 600 bp upstream = 0.0586251 Motif number 2 ACTTAATAATTTTTTATTACGCATATT 1 6 1 ATTTTTTTAT 0.804938 -120 ATTTTTTATTACGCATATTCCTTTTTTTAATC 1 19 1 ACATATTCCT 0.532716 -107 TTTAATCTCCAATTATTTTCCTCGATAAAATA 1 44 1 AAATTTTCCT 0.955371 -82 TTCCTCGATAAAATATTTATATGATTTTTAGA 1 61 1 AAATTTATAT 0.797683 -65 CACAATATAAAATTATCTTTTTGGCTGAATAT 1 99 0 AAATCTTTTT 0.76805 -27 AATCTCAACCTCATTTTTATAATTTTACAA 2 9 1 CCATTTTTAT 0.83207 -279 ATTTGGTAGTAATCATTTTTATTTTTATCTAA 2 67 1 AAATTTTTAT 0.977333 -221 AAAAGGAAAAAAGATTCTTTATTCCTAAATAA 2 97 1 AATTCTTTAT 0.92442 -191 TTACTAAGGAAAGAATTTTCCTTCCTATTATT 2 124 0 AAATTTTCCT 0.95512 -164 TTATATATTTAAGCTTTTCCATTAGGGGAATT 2 157 1 AATTTTCCAT 0.672835 -131 CTTACCTACTACCCATCTTCCTAATTCCCCTA 2 179 0 ACATCTTCCT 0.856211 -109 GTTTCACCTCAAACACTTTTATAGGAATTATC 2 210 0 AAACTTTTAT 0.845392 -78 TTTTACTTCAAAGGATTTTTGTTATTTCTATT 3 22 0 AAATTTTTGT 0.889822 -32 GGGCATTCACATTTTTTATACTTTTTTAA 4 8 1 CATTTTTTAT 0.834849 -88 ATTTTTAGATATTTATCTTTATACAAACTACA 4 48 0 ATATCTTTAT 0.841814 -48 ATTTCACCAAAAAGTTTTTTATGTTATTTTTA 4 73 0 AATTTTTTAT 0.952923 -23 ** ******** Masking position 8 Map Score: 13.7627 Number of sites scoring better than the average of aligned sites = 1921 Number in coding regions = 1464 Number in noncoding regions = 457 Number of orfs with sites within 600 bp upstream = 364 Fraction of orfs with sites within 600 bp upstream = 0.0584645 Motif number 3 TAAAATCTAAAAATCATATAAATATTTTATC 1 67 0 AAATCAATAA 0.83569 -59 AGATTTTAAATATTCAGCCAAAAAGATAATT 1 90 1 TATTCACCAA 0.926431 -36 ACCAAATTCAAATTAATCTAAAAACCACCAA 2 43 0 AATTAACTAA 0.959643 -245 ATCATTTTTATTTTTATCTAAAAGGAAAAAA 2 78 1 TTTTTACTAA 0.578459 -210 CCATCTTCCTAATTCCCCTAATGGAAAAGCT 2 168 0 AATTCCCTAA 0.975909 -120 TAGGTAAGATAATTCCTATAAAAGTGTTTGA 2 203 1 AATTCCATAA 0.929955 -85 AAATTAAACTAAATAGAAATAA 3 2 1 AATTAACTAA 0.959643 -52 AAATATCTAAAAATAACATAAAAAACTTTTT 4 66 1 AAATAAATAA 0.71121 -30 TATTTCACCAAAAAGTTTTTT 4 85 0 TATTTCCCAA 0.77826 -11 ****** **** Masking position 4 Map Score: 4.07367 Number of sites scoring better than the average of aligned sites = 853 Number in coding regions = 745 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 4 TTAATCTAAAAACCACCAAATTTGTAAAAT 2 32 0 AACCACCAAA 0.95036 -256 TAAAAATGATTACTACCAAATTCAAATTAA 2 58 0 TACTACCAAA 0.957836 -230 TTATCTTACCTACTACCCATCTTCCTAATT 2 185 0 TACTACCCAT 0.984976 -103 AAAACATCAATACCATCCATATGTTTCACC 2 234 0 TACCATCCAT 0.940997 -54 CAATACCACCTTTTACTTCAAAG 3 41 0 TACCACCTTT 0.942668 -13 TCTTTATACAAACTACATATAACATTTAAA 4 35 0 AACTACATAT 0.778483 -61 ********** Masking position 5 Map Score: 1.45776 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 162 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 ********** No masking Map Score: 1.48747e-12 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 6 ********** No masking Map Score: 1.48747e-12 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: 1.48747e-12 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