AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -ifnr_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 MJ0020 300 asparaginase (ansA) #2 MJ0076 80 conserved hypothetical protein) #3 MJ0292 186 conserved hypothetical protein #4 MJ0649 172 NADH oxidase (nox) #5 MJ0792 300 M. jannaschii predicted coding region MJ0792 #6 MJ0792.1 68 M. jannaschii predicted coding region MJ0792.1 #7 MJ0793 60 M. jannaschii predicted coding region MJ0793 #8 MJ0794 48 M. jannaschii predicted coding region MJ0794 #9 MJ0795 79 M. jannaschii predicted coding region MJ0795 #10 MJ0965 38 uroporphyrin-III C-methyltransferase (cobA) #11 MJ1225 80 conserved hypothetical protein Motif number 1 AAGTTCCTTAATATATTTAAATTGCATTC 1 8 1 TTAAATATTA 0.496369 -293 TTAAAGCTACTTAATATATTTATGGCGGATGA 1 105 1 TTAAATATTA 0.496369 -196 TTTGCAAATATTAATTTATATATTTAAATATA 1 195 1 TTAATTATAA 0.931346 -106 TTTATATATTTAAATATAAAAATTTATATGAT 1 209 1 TAAAATAAAA 0.861309 -92 ATTAGGGTATAAAAATTATAAAAAGATAGCTA 1 240 0 AAAATTATAA 0.931617 -61 AAAATAAATCATAAAATATATATACTATCTTG 2 34 1 ATAAATATAA 0.951002 -47 AAAAGTTATACATCCAAGGGTT 3 1 1 AAAATTATAA 0.931619 -186 TATTATCACCAAAAGTTATAAATAAGATTTAT 3 135 1 AAAATTATAA 0.931619 -52 TAAAAATAGAATAAGATTATTAAATAATAAAA 4 22 0 ATAAATTATA 0.640256 -151 ATTACTAAAAATAACTTAAAAATAGAATAAGA 4 38 0 ATAATTAAAA 0.964689 -135 AAAATGAAATATAACATAATCAATA 5 4 0 ATAAATAATA 0.859886 -297 TTTTTTGATATAAAATTATAAAATAGTTAAAA 5 32 1 TAAATTATAA 0.880741 -269 TAAAACAATTATAACTTTAAAAAAGTAAATTA 5 65 0 ATAATTTAAA 0.887928 -236 AAAAATTCTAATAAGTTAAAAATTTTAACATA 5 102 1 ATAATTAAAA 0.964689 -199 GTTAAAAATTTTAACATATATAATTTACTATT 5 116 1 TTAAATATAA 0.913103 -185 TATTATGATTTAAAGTTAAATAGTAAATTATA 5 134 0 TAAATTAAAA 0.889487 -167 ACTTTAAATCATAATATATATAGAGGTTTTGT 5 150 1 ATAAATATAA 0.950804 -151 GCACCATACAAAAAATTAAAGAATAGTTGGCG 5 219 1 AAAATTAAAA 0.936823 -82 AAAAAATTATTAAAATTAAAAAAGAAAAACAT 6 13 0 TAAATTAAAA 0.889485 -56 TTTAATTTTAATAATTTTTTGATATTTTTTAG 6 25 1 ATAATTTTTA 0.678554 -44 AATAATGATGATAAAATAAATAATAACTTTAA 7 26 1 ATAAATAAAA 0.954876 -35 AAAATAAATAATAACTTTAACAATTGTGAAAC 7 38 1 ATAATTTAAA 0.887928 -23 ATTCTTACACATAATATTAATATTTCATTTAA 11 19 0 ATAAATTAAA 0.859883 -62 **** ***** * Masking position 7 Map Score: 33.7805 Number of sites scoring better than the average of aligned sites = 1567 Number in coding regions = 1007 Number in noncoding regions = 560 Number of orfs with sites within 600 bp upstream = 425 Fraction of orfs with sites within 600 bp upstream = 0.0682621 Motif number 2 TTCGCAGGAATAAAATCTTTAAAGGAAAGTTTAAC 1 45 0 TAAATTTAGG 0.777715 -256 GAGATTGTTATAGATTAGGGTATAAAAATTATAAA 1 250 0 TAATTGGAAA 0.778444 -51 TTAGATTTAGTATTATGGTGAAAGA 2 1 0 TATATTGAGA 0.681805 -80 ATACTAAATCTAAAATAAATCATAAAATATATATA 2 23 1 TAAATATAAA 0.902294 -58 AAAATATATATACTATCTTGTATAAAAGTATTACA 2 46 1 TATATTGAAA 0.901776 -35 ATTAGGAATTTATAATGATTAATAATGATAAATCT 3 159 0 TAAATTTAAA 0.976313 -28 TTCTAACTAATACAATAATTGTGAAATAAATTTCT 4 75 0 TAAATTTTAA 0.768008 -98 TATAAAATTATAAAATAGTTAAAAATAATTTACTT 5 40 1 TAAATTTAAA 0.976313 -261 TTTAACTTATTAGAATTTTTAATAATAAAACAATT 5 87 0 TAAATTTAAA 0.976313 -214 CCTCTATATATATTATGATTTAAAGTTAAATAGTA 5 141 0 TATATTTAAG 0.829187 -160 TTTGTATTATTACATTTGTGAAAAATGTGGAAAAT 5 177 1 TAATTTGAAA 0.81053 -124 TTTTAGGTGATATAATGGGTGATAATAC 6 51 1 TAAATGTAAA 0.971308 -18 ATAATGATGATAAAATAAATAATAACTTTAACAAT 7 27 1 TAAATATAAA 0.902294 -34 AAGTAACAAATACAATCATTGAAAAATCTAATAG 8 25 1 TAAATTTAAA 0.976313 -24 AAAGTTACTATAAAATGAGGGAAAAAG 9 63 1 TAAATGGAAA 0.958825 -17 TAAAATAAGTTATAGCTTCTAATAC 10 24 0 TAAATGTAAG 0.924883 -15 GAAATATTAATATTATGTGTAAGAATTCAAATTTA 11 25 1 TATATGTAAA 0.916402 -56 ** *** ** * ** Masking position 6 Map Score: 21.8788 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 302 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 3 TTTATTTTGCAAATATTAATTTATATATTTA 1 190 1 AAATATAATT 0.882473 -111 TCTTTCACCATAATACTAAATCTAAAATAAA 2 11 1 TAATATAAAT 0.944302 -70 TAATGATTAATAATGATAAATCTTATTTATA 3 151 0 TAATGTAAAT 0.682898 -36 TAAGATTATTAAATAATAAAAGAGGGGATAG 4 12 0 AAATATAAAA 0.891631 -161 AATATATTACTAAAAATAACTTAAAAATAGA 4 44 0 TAAAATAACT 0.884148 -129 ATTTTGACACAAAAATGAACTTAACCAAAAA 4 123 0 AAAAAGAACT 0.708198 -50 TTTTATATCAAAAAATGAAATATAACATAAT 5 16 0 AAAAAGAAAT 0.767721 -285 TATAACTTTAAAAAAGTAAATTATTTTTAAC 5 57 0 AAAAATAAAT 0.929755 -244 TTAGAATTTTTAATAATAAAACAATTATAAC 5 82 0 TAATATAAAA 0.866093 -219 ATTTAAAGTTAAATAGTAAATTATATATGTT 5 128 0 AAATATAAAT 0.955579 -173 GCACCATACAAAAAATTAAAGAATAGTTGGC 5 219 1 AAAAATAAAG 0.694409 -82 AAAAAATTATTAAAATTAAAAAAGAAAAACA 6 14 0 TAAAATAAAA 0.798412 -55 ATGATAAAATAAATAATAACTTTAACAATTG 7 33 1 AAATATAACT 0.94071 -28 TTCCCTCATTTTATAGTAACTTTAATACACT 9 55 0 TTATATAACT 0.516166 -25 TTATAGCTTCTAATACTAATTTTTATGGG 10 9 0 TAATATAATT 0.856998 -30 ACGTTAAATGAAATATTAATATTATGTGTAA 11 16 1 AAATATAATA 0.743945 -65 ***** ***** Masking position 8 Map Score: 12.5788 Number of sites scoring better than the average of aligned sites = 1125 Number in coding regions = 763 Number in noncoding regions = 362 Number of orfs with sites within 600 bp upstream = 321 Fraction of orfs with sites within 600 bp upstream = 0.051558 Motif number 4 TATATATTTAAATATAAAAATTTATATGAT 1 211 1 AATATAAAAA 0.544099 -90 AAAGATAGCTATCATATAAATTTTTATATT 1 221 0 ATCATATAAA 0.811114 -80 GGGTATAAAAATTATAAAAAGATAGCTATC 1 238 0 ATTATAAAAA 0.887578 -63 TCTAAAATAAATCATAAAATATATATACTA 2 31 1 ATCATAAAAT 0.682874 -50 TAAGCCTATTATCACCAAAAGTTATAAATA 3 129 1 ATCACCAAAA 0.859751 -58 ATCATTATTAATCATTATAAATTCCTAATA 3 165 1 ATCATTATAA 0.569427 -22 ATAGAATAAGATTATTAAATAATAAAAGAG 4 19 0 ATTATTAAAT 0.749694 -154 ATTACTAAAAATAACTTAAAAATAGAATAA 4 40 0 ATAACTTAAA 0.286801 -133 TTTCTAATATATTACTAAAAATAACTTAAA 4 50 0 ATTACTAAAA 0.868859 -123 CAAAATCATGATCATCAAAAAGGATAAAAA 4 148 1 ATCATCAAAA 0.927703 -25 TTGATATAAAATTATAAAATAGTTAAAAAT 5 36 1 ATTATAAAAT 0.623378 -265 TAATTGTTTTATTATTAAAAATTCTAATAA 5 86 1 ATTATTAAAA 0.932739 -215 TATATATATTATGATTTAAAGTTAAATAGT 5 142 0 ATGATTTAAA 0.555076 -159 ATATCAAAAAATTATTAAAATTAAAAAAGA 6 20 0 ATTATTAAAA 0.932739 -49 TCACCTAAAAAATATCAAAAAATTATTAAA 6 31 0 AATATCAAAA 0.605759 -38 CACCCATTATATCACCTAAAAAATATCAAA 6 42 0 ATCACCTAAA 0.725597 -27 TGTTACTTCAACTATTTAAATC 8 3 0 ACTATTTAAA 0.431382 -46 AACAAATACAATCATTGAAAAATCTAATAG 8 29 1 ATCATTGAAA 0.733775 -20 ********** Masking position 4 Map Score: 10.8819 Number of sites scoring better than the average of aligned sites = 1340 Number in coding regions = 1051 Number in noncoding regions = 289 Number of orfs with sites within 600 bp upstream = 266 Fraction of orfs with sites within 600 bp upstream = 0.0427241 Motif number 5 ATTCCTGCGAAGTCCTATTGAGGTAAGTAT 1 69 1 AGTCCTATTG 0.94314 -232 CAAGGGTTTTGCTCCTATTGATATGCTCTC 3 25 1 GCTCCTATTG 0.985669 -162 CATGGGGAAAACCCCTATTGGGATACCCGA 3 93 0 ACCCCTATTG 0.985669 -94 TTTGTATGGTGCCCCTATTATTTTCCACAT 5 201 0 GCCCCTATTA 0.964 -100 ********** Masking position 6 Map Score: 0.573448 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 17 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 TATCATATAAATTTTTATATTTAAATATAT 1 212 0 ATTTTTATAT 0.673849 -89 TCTTTTTATAATTTTTATACCCTAATCTAT 1 246 1 ATTTTTATAC 0.891659 -55 ACCGTGTAATACTTTTATACAAGATAGTAT 2 55 0 ACTTTTATAC 0.954672 -26 AGACAACCTCACTTTAATAAAGATTTGAGA 3 51 0 ACTTTAATAA 0.965458 -136 AACAATTATAACTTTAAAAAAGTAAATTAT 5 64 0 ACTTTAAAAA 0.852313 -237 TTCTTTTTTAATTTTAATAATTTTTTGATA 6 19 1 ATTTTAATAA 0.915348 -50 ATAAATAATAACTTTAACAATTGTGAAACC 7 41 1 ACTTTAACAA 0.895902 -20 TTTTATAGTAACTTTAATACACTGTATAGT 9 48 0 ACTTTAATAC 0.97122 -32 ********** Masking position 7 Map Score: 5.58633 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 81 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 TAAATATATTAAGTAGCTTTAAGTATATATACTT 1 93 0 AAACTTAAGT 0.890763 -208 CCTAATCTATAACAATCTCTAAGAATCAGTTTTT 1 266 1 AAACTTAAGA 0.764652 -35 TAATGATAAATCTTATTTATAACTTTTGGTGATA 3 138 0 TCATTTAACT 0.807457 -49 AAAGTTTTTATAGAACTTCTAACTAATACAATAA 4 92 0 TAATTTAACT 0.957217 -81 TATATCAAAAAATGAAATATAACATAATCAATA 5 10 0 AAAATTAACA 0.821514 -291 TAAAAAAGTAAATTATTTTTAACTATTTTATAAT 5 46 0 AAATTTAACT 0.963561 -255 TTTAATAATAAAACAATTATAACTTTAAAAAAGT 5 71 0 AAATTTAACT 0.963751 -230 TTATATATGTTAAAATTTTTAACTTATTAGAATT 5 105 0 TAATTTAACT 0.957217 -196 ATAAAATAAATAATAACTTTAACAATTGTGAAAC 7 36 1 TAACTTAACA 0.919828 -25 AGTTGATACAAACCAAATATAACTGTTGGAATTA 9 17 0 AAAATTAACT 0.920416 -63 AAATTAGTATTAGAAGCTATAACTTATTTTA 10 18 1 TAACTTAACT 0.966448 -21 ** * ** ***** Masking position 5 Map Score: 10.7131 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 261 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 8 ********** No masking Map Score: -4.73059e-14 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 9 ********** No masking Map Score: -4.73059e-14 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 10 ********** No masking Map Score: -4.73059e-14 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