AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -iglpR_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 MJ0085 134 iron transport periplasmic binding protein, putative (ceuE) #2 MJ0086 36 unspecified methyltransferase #3 MJ0087 23 hemin permease (hemU) #4 MJ0090 80 collagenase (prtC) #5 MJ0091 95 Na+/Ca+ exchanger protein, putative #6 MJ0956 145 M. jannaschii predicted coding region MJ0956 Motif number 1 CATAAAAATTATATAAAAAATAGAAAAAAG 1 11 0 ATATAAAAAA 0.961486 -124 TACATCAATATTCATAAAAATTATATAAAA 1 23 0 TTCATAAAAA 0.807483 -112 TTTCGGTAGTTTATCAAAAATAATCGTTAA 1 56 0 TTATCAAAAA 0.844521 -79 TATATATTAGATATTAAAAATTTTTGTTCA 1 88 1 ATATTAAAAA 0.991207 -47 AAATTATAAAAAATTAAAAA 2 1 0 AAATTAAAAA 0.985641 -36 TTTATCACCAAAATAAAAATTATAAAAAA 2 18 0 AAAATAAAAA 0.970194 -19 AATAATTCAAAAAATGTGATAG 3 3 1 TAATTCAAAA 0.864159 -21 TGACCTCATTATATAAAAAAGA 4 3 0 ATATAAAAAA 0.961486 -78 ATATAATTTAAAATTTAAAAAAATTTCTAA 4 61 1 AAATTTAAAA 0.940764 -20 TTCTGCAATAATATTTAAACTTAAGCAAAA 5 34 0 ATATTTAAAC 0.84664 -62 ATTGCAGAATATATTCAAAAACAAACTTTA 5 55 1 ATATTCAAAA 0.966518 -41 AATAAAACAAAAATTAAAAAGAT 6 4 0 AAATTAAAAA 0.985641 -142 TAAAAATAAAATAATAAAACAAAAATTAAA 6 16 0 ATAATAAAAC 0.918798 -130 AATGGATAAATTAATAAAAATAAAATAATA 6 30 0 TTAATAAAAA 0.952951 -116 TTATCCATTTAAATTAAAGAATAATAAAAA 6 51 1 AAATTAAAGA 0.879238 -95 AAATTAAAGAATAATAAAAACTTTTATATG 6 61 1 ATAATAAAAA 0.98208 -85 AAGTCTTTTGATAATTAAAATTTACTTAAA 6 92 1 ATAATTAAAA 0.926895 -54 AATTAAAATTTACTTAAAAAATAATATAGA 6 104 1 TACTTAAAAA 0.84006 -42 AAAACCCACTATATAAAAAAATCTATATTA 6 125 0 ATATAAAAAA 0.961486 -21 ********** Masking position 7 Map Score: 38.5685 Number of sites scoring better than the average of aligned sites = 2120 Number in coding regions = 1494 Number in noncoding regions = 626 Number of orfs with sites within 600 bp upstream = 447 Fraction of orfs with sites within 600 bp upstream = 0.0717957 Motif number 2 ATATTCATAAAAATTATATAAAAAATAGAA 1 16 0 AAATTATATA 0.959616 -119 AAACTACCGAAAAATATATATTAGATATTA 1 74 1 AAAATATATA 0.900622 -61 ATATGATATGAACAAAAATTTTTAATATCT 1 96 0 AACAAAAATT 0.684847 -39 AAATTATAAAAAATTAAAAA 2 1 0 AAATTAAAAA 0.859678 -36 TCACCAAAATAAAAATTATAAAAAATTAAA 2 13 0 AAAAATTATA 0.806399 -24 TTTAAATTTTAAATTATATTTGAAGTATAA 4 50 0 AAATTATATT 0.938813 -31 ATATAATTTAAAATTTAAAAAAATTTCTAA 4 61 1 AAATTTAAAA 0.805914 -20 GCTTAAGTTTAAATATTATTGCAGAATATA 5 38 1 AAATATTATT 0.879873 -58 TTCAAAAACAAACTTTAATTAATTTAGTAG 5 68 1 AACTTTAATT 0.848713 -28 AAAATAATAAAACAAAAATTAAAAAGAT 6 9 0 AACAAAAATT 0.684847 -137 AAATTAATAAAAATAAAATAATAAAACAAA 6 23 0 AAATAAAATA 0.93406 -123 TTATCCATTTAAATTAAAGAATAATAAAAA 6 51 1 AAATTAAAGA 0.78231 -95 GAATAATAAAAACTTTTATATGTAAGTCTT 6 69 1 AACTTTTATA 0.906934 -77 TTTTTTAAGTAAATTTTAATTATCAAAAGA 6 95 0 AAATTTTAAT 0.761837 -51 TTTACTTAAAAAATAATATAGATTTTTTTA 6 112 1 AAATAATATA 0.941582 -34 ********** Masking position 8 Map Score: 17.7711 Number of sites scoring better than the average of aligned sites = 2403 Number in coding regions = 1571 Number in noncoding regions = 832 Number of orfs with sites within 600 bp upstream = 541 Fraction of orfs with sites within 600 bp upstream = 0.0868937 Motif number 3 ACATCAATATTCATAAAAATTATATAAAAA 1 22 0 TCATAAAAAT 0.889719 -113 CGTTAAAAATACATCAATATTCATAAAAAT 1 32 0 ACATCAATAT 0.91041 -103 GATGTATTTTTAACGATTATTTTTGATAAA 1 47 1 TAACGATTAT 0.551238 -88 ATTGTCACCATTTTAGGCTATATG 1 121 0 TCACCATTTT 0.498947 -14 TTTATCACCAAAATAAAAATTATA 2 23 0 TCACCAAAAT 0.974601 -14 AAAATAGCAATAACCAATATGACCTCATTA 4 22 0 TAACCAATAT 0.970696 -59 AATTTTCAGTTCATCCATATTGTAT 5 6 0 TCATCCATAT 0.843374 -90 TATTTAAACTTAAGCAAAATTTTCAGTTCA 5 23 0 TAAGCAAAAT 0.883654 -73 TAAAATAATAAAACAAAAATTAAAAAGAT 6 10 0 AAACAAAAAT 0.768675 -136 ATGGATAAATTAATAAAAATAAAATAATAA 6 29 0 TAATAAAAAT 0.874444 -117 AGTCTTTTGATAATTAAAATTTACTTAAAA 6 93 1 TAATTAAAAT 0.733784 -53 CTATATAAAAAAATCTATATTATTTTTTAA 6 117 0 AAATCTATAT 0.527006 -29 ********** Masking position 3 Map Score: 6.41392 Number of sites scoring better than the average of aligned sites = 1851 Number in coding regions = 1563 Number in noncoding regions = 288 Number of orfs with sites within 600 bp upstream = 251 Fraction of orfs with sites within 600 bp upstream = 0.0403148 Motif number 4 ********** No masking Map Score: 2.29806e-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 5 ********** No masking Map Score: 2.29806e-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: 2.29806e-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