AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -iflhCD_mjan_opreg_300.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 MJ0774 300 M. jannaschii predicted coding region MJ0774 #2 MJ0842 219 methyl coenzyme M reductase I, subunit beta (mcrB) Motif number 1 GAATGAAATTAAATATAATATATATA 1 1 0 AAATATAATA 0.891925 -300 TTCTATATGAAATATTGTTTGATTCATTAGATTTTT 1 67 1 AATATTTATA 0.862219 -234 ATCAAACAATAAAATTAAAAAATCTAATGAATCAAA 1 84 0 AAAATTAATA 0.964313 -217 TAATAAACTTTATAATAAAACATTTAAATTTAAGAA 1 132 1 TATAATAATA 0.80341 -169 ATTTAAATTTAAGAATAATTGATTCAATCTATCTTT 1 153 1 AAGAATTATA 0.908787 -148 TAGATTTCGAAAAATCGAAAGATAGATTGAATCAAT 1 170 0 AAAATCAATA 0.978589 -131 CTTTTGTCTTAAGAACGTTATATAGATTTCGAAAAA 1 192 0 AAGAACAATA 0.955206 -109 TTCTTAAGACAAAAGTTCGAAATCAATGGAAAATAT 1 213 1 AAAAGTAATA 0.949476 -88 CAATAAAATATAAATTAATTTATTTAAATTAATTAT 1 265 0 TAAATTTATA 0.715126 -36 ATTTTTTATTAAAAATAACAGTTATAGTGTGAAATT 2 11 0 AAAAATATTA 0.883639 -209 ATTTTTAATAAAAAATTTCAGATAGAAAATTTTATA 2 31 1 AAAAATAATA 0.988963 -189 TTTTTGGTGAAAAAATCCCTTATAAAATTTTCTATC 2 51 0 AAAAATTATA 0.969291 -169 TTAAAATTAAAATAACATAAAATCCAATAATTTTTG 2 81 0 AATAACAATA 0.951784 -139 ATTTACAGGCAAAGTTTTAAAATTAAAATAACATAA 2 97 0 AAAGTTAATA 0.892301 -123 TCATTTGAACAAAATCGTAACATTTATATAGTGGAT 2 142 0 AAAATCAATA 0.978482 -78 TGTTCAAATGAAAAACTGGATATATATAAACTGCGA 2 167 1 AAAAACAATA 0.985274 -53 ****** * ** * Masking position 13 Map Score: 23.0321 Number of sites scoring better than the average of aligned sites = 1080 Number in coding regions = 825 Number in noncoding regions = 255 Number of orfs with sites within 600 bp upstream = 232 Fraction of orfs with sites within 600 bp upstream = 0.0372631 Motif number 2 TATATATATTATATTTAATTTCATTCAAGT 1 11 1 ATATTTAATT 0.955297 -290 AGAATAAGTGATTATTATTTTCAGAAATAA 1 41 0 ATTATTATTT 0.742757 -260 GAATCAAACAATATTTCATATAGAATAAGT 1 62 0 ATATTTCATA 0.92313 -239 ATTCATTAGATTTTTTAATTTTATTGTTTG 1 88 1 TTTTTTAATT 0.821601 -213 GATTCATGAGATTTTTAATAAACTTTATAA 1 117 1 ATTTTTAATA 0.949492 -184 TTAAATTTAAATGTTTTATTATAAAGTTTA 1 135 0 ATGTTTTATT 0.778981 -166 GATTGAATCAATTATTCTTAAATTTAAATG 1 152 0 ATTATTCTTA 0.61868 -149 TATCTACAATATTTTCCATTGATTTCGAAC 1 227 0 ATTTTCCATT 0.870827 -74 TAATTAGTAGATAATTAATTTAAATAAATT 1 255 1 ATAATTAATT 0.883696 -46 AAATTAATTTATATTTTATTGCGGTGGAAA 1 280 1 ATATTTTATT 0.886669 -21 TATAACTGTTATTTTTAATAAAAAATTTCA 2 21 1 ATTTTTAATA 0.949492 -199 TATATATCCAGTTTTTCATTTGAACAAAAT 2 163 0 GTTTTTCATT 0.880888 -57 ********** Masking position 5 Map Score: 10.8376 Number of sites scoring better than the average of aligned sites = 1797 Number in coding regions = 1255 Number in noncoding regions = 542 Number of orfs with sites within 600 bp upstream = 417 Fraction of orfs with sites within 600 bp upstream = 0.0669772 Motif number 3 AATCAAACAATAAAATTAAAAAATCTAATGA 1 90 0 TAAAATTAAA 0.939393 -211 ATAAAACATTTAAATTTAAGAATAATTGATT 1 146 1 TAAATTTAGA 0.917301 -155 ATAGATTTCGAAAAATCGAAAGATAGATTGA 1 176 0 AAAAATCAAA 0.952279 -125 TCTTAAGACAAAAGTTCGAAATCAATGGAAA 1 214 1 AAAGTTCAAA 0.926264 -87 TCCACCGCAATAAAATATAAATTAATTTATT 1 277 0 TAAAATAAAA 0.792695 -24 TTTTTAATAAAAAATTTCAGATAGAAAATTT 2 32 1 AAAATTTAGA 0.917301 -188 TTTCAGATAGAAAATTTTATAAGGGATTTTT 2 46 1 AAAATTTATA 0.802627 -174 TAAAATAACATAAAATCCAATAATTTTTGGT 2 79 0 TAAAATCAAT 0.737386 -141 ATTTACAGGCAAAGTTTTAAAATTAAAATAA 2 102 0 AAAGTTTAAA 0.90704 -118 ACTTTGCCTGTAAATTCCAAATCCATCCACT 2 118 1 TAAATTCAAA 0.966904 -102 ******* *** Masking position 6 Map Score: 9.02657 Number of sites scoring better than the average of aligned sites = 1147 Number in coding regions = 753 Number in noncoding regions = 394 Number of orfs with sites within 600 bp upstream = 274 Fraction of orfs with sites within 600 bp upstream = 0.044009 Motif number 4 TCTATATGAAATATTGTTTGATTCATTAGAT 1 68 1 ATATGTTTGA 0.969182 -233 TTTTTTAATTTTATTGTTTGATTCATGAGAT 1 98 1 TTATGTTTGA 0.885825 -203 AAATTAATTTATATTTTATTGCGGTGGAAAC 1 280 1 ATATTTATTG 0.763588 -21 ATAAAATCCAATAATTTTTGGTGAAAAAATC 2 70 0 ATATTTTTGG 0.969182 -150 TAACATTTATATAGTGGATGGATTTGGAATT 2 130 0 ATATGGATGG 0.97639 -90 TCCCACATATTGGTTCGATATTAGTTA 2 203 0 ATATGGTTCG 0.956359 -17 *** ******* Masking position 5 Map Score: 0.382335 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 292 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 ********** No masking Map Score: -3.74156e-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: -3.74156e-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: -3.74156e-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