AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -icytR_mjan_opreg_100.orf -g0.314 -x5 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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ0667 91 thymidine phosphorylase (deoA) #2 MJ0703.1 125 M. jannaschii predicted coding region MJ0703.1 #3 MJ0704 95 M. jannaschii predicted coding region MJ0704 Motif number 1 GAAGTAATATTAAAGAAAATATATAAAGTT 1 25 1 TAAAGAAAAT 0.982402 -67 ATATATAAAGTTTAGAAAATATAAAAATTT 1 43 1 TTTAGAAAAT 0.943743 -49 ATTTAATAGATAAAGAAATTAGTGGTGATT 1 69 1 TAAAGAAATT 0.966978 -23 AGAAACATATTTAAAAGATGGTGTTATAGT 2 68 1 TTAAAAGATG 0.85994 -58 AAAAATAATAAAATAGTTCTATAC 2 112 0 ATAATAAAAT 0.820645 -14 TTAAAAAAATTATTATAACT 3 1 1 TTAAAAAAAT 0.9667 -95 GTAGGAGATTTTAATAAATGGATATCTATT 3 49 1 TTAATAAATG 0.926258 -47 GCATAAGCAATTAAGAGAATAGATATCCAT 3 66 0 TTAAGAGAAT 0.981138 -30 GTAAAGAAAAGCATAAGCAAT 3 85 0 TAAAGAAAAG 0.978744 -11 ********** Masking position 6 Map Score: 12.4412 Number of sites scoring better than the average of aligned sites = 1220 Number in coding regions = 1045 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 2 TATATATTTTCTTTAATATTACTTCTCATT 1 20 0 CTTTAATATT 0.933928 -72 TTTTCTAAACTTTATATATTTTCTTTAATA 1 32 0 TTTATATATT 0.975988 -60 ATCTATTAAATTTTTATATTTTCTAAACTT 1 50 0 TTTTTATATT 0.981553 -42 CACTAATTTCTTTATCTATTAAATTTTTAT 1 63 0 TTTATCTATT 0.926337 -29 TAAAAAGTAGTGTTTATTTTTTCATTAGAT 2 37 0 TGTTTATTTT 0.843775 -89 AACACCATCTTTTAAATATGTTTCTGTAAA 2 63 0 TTTAAATATG 0.915497 -63 TATAGAACTATTTTATTATTTTT 2 113 1 TTTTATTATT 0.917008 -13 CTACAAATAATGTGAATATTGTAGTTATAA 3 23 0 TGTGAATATT 0.931397 -73 ********** Masking position 7 Map Score: 6.93654 Number of sites scoring better than the average of aligned sites = 1117 Number in coding regions = 786 Number in noncoding regions = 331 Number of orfs with sites within 600 bp upstream = 299 Fraction of orfs with sites within 600 bp upstream = 0.0480244 Motif number 3 AAAGAAATTAGTGGTGATTTAA 1 80 1 GTGGTGATTA 0.956505 -12 TCATCAACTGATAGAACTTTA 2 1 0 ATAGAACTTA 0.899974 -125 TCTTTTAAATATGTTTCTGTAAAAAGTAGTG 2 55 0 ATGTTTCTTA 0.951028 -71 TATTTAAAAGATGGTGTTATAGTTGGATGAA 2 75 1 ATGGTGTTTA 0.971516 -51 AAATAATAAAATAGTTCTATACCTCAACTTC 2 103 0 ATAGTTCTTA 0.976967 -23 ATTTTAATAAATGGATATCTATTCTCTTAAT 3 56 1 ATGGATATTA 0.967596 -40 ******** ** Masking position 8 Map Score: 1.81557 Number of sites scoring better than the average of aligned sites = 360 Number in coding regions = 319 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 TATTTTCTTTAATATTACTTCTCATTGGTG 1 16 0 AATATTACTT 0.873812 -76 TTAAATCACCACTAATTTCTTTATCTA 1 75 0 ACCACTAATT 0.97722 -17 TGAAAAAATAAACACTACTTTTTACAGAAA 2 43 1 AACACTACTT 0.990952 -83 ATAGTTCTATACCTCAACTTCATCCAACTA 2 94 0 ACCTCAACTT 0.96367 -32 ********** Masking position 7 Map Score: 0.492897 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 88 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 ********** No masking Map Score: 5.92183e-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 6 ********** No masking Map Score: 5.92183e-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: 5.92183e-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