AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00061_mjan_reg_300.orf -o00061_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 MJ1230 22 M. jannaschii predicted coding region MJ1230 #2 MJ1231 255 oxaloacetate decarboxylase alpha chain (oadA) #3 MJ1232 113 conserved hypothetical protein #4 MJ1545 77 conserved hypothetical protein Motif number 1 CATATATATCATTTCAATCAATACTACACTA 2 27 1 ATTTAATCAA 0.97942 -229 GGATAGAGATTTTTGTATTAATTAATTTAAA 2 71 1 TTTTTATTAA 0.874289 -185 ATAAAATTGAGTTTAAATTAATTAATACAAA 2 82 0 GTTTAATTAA 0.901472 -174 ATCTTAAATTTTCTTAATCAATTTTTGATGA 2 120 1 TTCTAATCAA 0.970741 -136 TAGTCTTATAATTTCAATCATAGTTACCCCT 2 150 0 ATTTAATCAT 0.970156 -106 GCTGTGCCTTTTTTAAATCAAAATAAATATT 2 221 1 TTTTAATCAA 0.983231 -35 TTCTGAATTAAATCGATAAGT 3 1 1 TTCTAATTAA 0.934074 -113 ATTGCCATAAATATTTATCATGGATGTCAAT 3 45 1 ATATTATCAT 0.767406 -69 ATACTAATGATTATAAATTATAATAGATTAT 3 74 0 TTATAATTAT 0.862153 -40 AGTATTTAAATCTTCTCTTTACAA 4 4 1 ATTTAATCTT 0.820599 -74 **** ****** Masking position 7 Map Score: 9.78723 Number of sites scoring better than the average of aligned sites = 859 Number in coding regions = 679 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 2 TTCAATCAATACTACACTACGGCTATAAACAAGGAT 2 39 1 ATATAGCTAT 0.732145 -217 ACGGCTATAAACAAGGATAGAGATTTTTGTATTAAT 2 57 1 AAATAGATTT 0.98227 -199 AAATTGATTAAGAAAATTTAAGATTTAGGAGATAAA 2 108 0 AAATTGATTT 0.953248 -148 GATTGAAATTATAAGACTATGGCTAACCAAATAACG 2 162 1 AAATAGCTAA 0.893875 -94 GGCTAACCAAATAACGGAACTGCATTGCCGTTTTAT 2 182 1 AAAAAGCATT 0.840371 -74 TCCCTCACAAATATTTATTTTGATTTAAAAAAGGCA 2 225 0 AATTTGATTT 0.882438 -31 TAAAATAAATATATACTTATCGATTTAATTCAGAA 3 10 0 AATTAGATTT 0.847843 -104 CATCCATGATAAATATTTATGGCAATAAAATAAATA 3 35 0 AATTAGCAAT 0.810622 -79 TAATGATTATAAATTATAATAGATTATTGACATCCA 3 65 0 AATAAGATTA 0.700966 -49 CCCCTTATTAAAAATACTAATGATTATAAATTATAA 3 82 0 AAATAGATTA 0.952915 -32 ATATCCGACAATAAACATAATGCATTTCAACAAAAT 4 34 1 AAATAGCATT 0.959448 -44 TATTATATAAAGTTTTTGATTTTGTTGAAATG 4 56 0 AAATTGATTT 0.951895 -22 * ** ** ***** Masking position 1 Map Score: 12.1783 Number of sites scoring better than the average of aligned sites = 1080 Number in coding regions = 935 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 3 TTAATTAATTTAAACTCAATTTTATCTCCT 2 88 1 TAAACTCAAT 0.833944 -168 CTTAAATTTTCTTAATCAATTTTTGATGAG 2 122 1 CTTAATCAAT 0.865033 -134 AAAGGCACAGCCAAATAAAACGGCAATGCA 2 202 0 CCAAATAAAA 0.887398 -54 TTTTTTAAATCAAAATAAATATTTGTGAGG 2 229 1 CAAAATAAAT 0.980216 -27 TTTATGGCAATAAAATAAATATATACTTAT 3 26 0 TAAAATAAAT 0.931108 -88 TATTGACATCCATGATAAATATTTATGGCA 3 47 0 CATGATAAAT 0.868947 -67 TGCATTTCAACAAAATCAAAAACTTTATAT 4 54 1 CAAAATCAAA 0.962998 -24 ********** Masking position 8 Map Score: 2.94198 Number of sites scoring better than the average of aligned sites = 681 Number in coding regions = 569 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 4 ATACTACACTACGGCTATAAACAAGGATAG 2 47 1 ACGGCTATAA 0.983002 -209 GCCAAATAAAACGGCAATGCAGTTCCGTTA 2 193 0 ACGGCAATGC 0.974755 -63 ATAAATATTTATGGCAATAAAATAAATATA 3 33 0 ATGGCAATAA 0.988296 -81 TTTATCATGGATGTCAATAATCTATTATAA 3 58 1 ATGTCAATAA 0.955064 -56 TTTACAATATCCGACAATAAACATAATGCA 4 28 1 CCGACAATAA 0.955699 -50 ********** Masking position 7 Map Score: 3.09136 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 57 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 ********** No masking Map Score: 8.764e-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: 8.764e-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: 8.764e-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