AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -iflhCD_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 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 AAATTAATAA 0.818628 -300 TTCTATATGAAATATTGTTTGATTCATTAGATTTTT 1 67 1 AATATTATTA 0.779235 -234 ATCAAACAATAAAATTAAAAAATCTAATGAATCAAA 1 84 0 AAAATAATCA 0.960019 -217 AAGTTTATTAAAAATCTCATGAATCAAACAATAAAA 1 106 0 AAAACTAATA 0.717516 -195 AGATTTTTAATAAACTTTATAATAAAACATTTAAAT 1 125 1 TAAATTATAA 0.861256 -176 ATTTAAATTTAAGAATAATTGATTCAATCTATCTTT 1 153 1 AAGATTATTA 0.845162 -148 TAGATTTCGAAAAATCGAAAGATAGATTGAATCAAT 1 170 0 AAAACAATAA 0.978762 -131 CTTTTGTCTTAAGAACGTTATATAGATTTCGAAAAA 1 192 0 AAGACAATAA 0.920078 -109 TTCTTAAGACAAAAGTTCGAAATCAATGGAAAATAT 1 213 1 AAAATAATCA 0.978816 -88 CAATAAAATATAAATTAATTTATTTAAATTAATTAT 1 265 0 TAAATTATTA 0.747638 -36 ATTTTTTATTAAAAATAACAGTTATAGTGTGAAATT 2 11 0 AAAATATTAA 0.808979 -209 ATTTTTAATAAAAAATTTCAGATAGAAAATTTTATA 2 31 1 AAAATAATAA 0.98249 -189 TTTTTGGTGAAAAAATCCCTTATAAAATTTTCTATC 2 51 0 AAAATTATAA 0.966449 -169 TTAAAATTAAAATAACATAAAATCCAATAATTTTTG 2 81 0 AATACAATCA 0.859574 -139 ATTTACAGGCAAAGTTTTAAAATTAAAATAACATAA 2 97 0 AAAGTAATTA 0.835476 -123 TCATTTGAACAAAATCGTAACATTTATATAGTGGAT 2 142 0 AAAACAATTA 0.972133 -78 TGTTCAAATGAAAAACTGGATATATATAAACTGCGA 2 167 1 AAAACAATAA 0.978724 -53 TGGATATATATAAACTGCGATAACTAATATCGAACC 2 183 1 TAAATAAACA 0.586022 -37 **** * * *** * Masking position 2 Map Score: 22.3742 Number of sites scoring better than the average of aligned sites = 1720 Number in coding regions = 1277 Number in noncoding regions = 443 Number of orfs with sites within 600 bp upstream = 357 Fraction of orfs with sites within 600 bp upstream = 0.0573402 Motif number 2 ACTTGAATGAAATTAAATATAATATATATA 1 11 0 AATTAAATAT 0.909005 -290 TGAAAATAATAATCACTTATTCTATATGAA 1 48 1 AATCACTTAT 0.910279 -253 AAATCTAATGAATCAAACAATATTTCATAT 1 71 0 AATCAAACAA 0.958105 -230 CAAACAATAAAATTAAAAAATCTAATGAAT 1 88 0 AATTAAAAAA 0.68557 -213 AAATCTCATGAATCAAACAATAAAATTAAA 1 101 0 AATCAAACAA 0.958105 -200 TAAACTTTATAATAAAACATTTAAATTTAA 1 135 1 AATAAAACAT 0.921677 -166 AGATAGATTGAATCAATTATTCTTAAATTT 1 157 0 AATCAATTAT 0.959994 -144 AATTTATTTAAATTAATTATCTACTAATTA 1 255 0 AATTAATTAT 0.87131 -46 AATTAATTTAAATAAATTAATTTATATTTT 1 267 1 AATAAATTAA 0.905255 -34 TTTCCACCGCAATAAAATATAAATTAATTT 1 280 0 AATAAAATAT 0.941265 -21 TGTTATTTTTAATAAAAAATTTCAGATAGA 2 27 1 AATAAAAAAT 0.799047 -193 TTGGTGAAAAAATCCCTTATAAAATTTTCT 2 54 0 AATCCCTTAT 0.810951 -166 AATAACATAAAATCCAATAATTTTTGGTGA 2 77 0 AATCCAATAA 0.929418 -143 TTAAAATTAAAATAACATAAAATCCAATAA 2 87 0 AATAACATAA 0.85633 -133 GTAAATTCCAAATCCATCCACTATATAAAT 2 127 1 AATCCATCCA 0.470666 -93 ********** Masking position 2 Map Score: 20.945 Number of sites scoring better than the average of aligned sites = 1294 Number in coding regions = 996 Number in noncoding regions = 298 Number of orfs with sites within 600 bp upstream = 256 Fraction of orfs with sites within 600 bp upstream = 0.0411179 Motif number 3 CTATATGAAATATTGTTTGATTCATTAGAT 1 69 1 TATTGTTTGA 0.986849 -232 TTTTTAATTTTATTGTTTGATTCATGAGAT 1 99 1 TATTGTTTGA 0.986849 -202 AAAATCGAAAGATAGATTGAATCAATTATT 1 166 0 GATAGATTGA 0.945716 -135 AAATAACAGTTATAGTGTGAAATT 2 5 0 TATAGTGTGA 0.977787 -215 ********** Masking position 3 Map Score: 2.58762 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 13 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 TAAACTTGAATGAAATTAAATATAATATAT 1 14 0 TGAAATTAAA 0.893798 -287 TTTTCAGAAATAAACTTGAATGAAATTAAA 1 24 0 TAAACTTGAA 0.872793 -277 AATCAAACAATAAAATTAAAAAATCTAATG 1 91 0 TAAAATTAAA 0.921975 -210 CAATTATTCTTAAATTTAAATGTTTTATTA 1 144 0 TAAATTTAAA 0.945413 -157 AACGTTATATAGATTTCGAAAAATCGAAAG 1 185 0 AGATTTCGAA 0.61482 -116 TATTTTCCATTGATTTCGAACTTTTGTCTT 1 218 0 TGATTTCGAA 0.926266 -83 TAGTAGATAATTAATTTAAATAAATTAATT 1 259 1 TTAATTTAAA 0.75626 -42 TAAAATAACATAAAATCCAATAATTTTTGG 2 80 0 TAAAATCCAA 0.914405 -140 TATGTTATTTTAATTTTAAAACTTTGCCTG 2 98 1 TAATTTTAAA 0.910811 -122 ACTTTGCCTGTAAATTCCAAATCCATCCAC 2 118 1 TAAATTCCAA 0.939907 -102 CTGCGATAACTAATATCGAACCAATATGTG 2 197 1 TAATATCGAA 0.92338 -23 ********** Masking position 3 Map Score: 10.4165 Number of sites scoring better than the average of aligned sites = 972 Number in coding regions = 727 Number in noncoding regions = 245 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 5 ATTATCTACTAATTATCTACAATATTTTCC 1 240 0 AATTATCTAC 0.985588 -61 TATTTAAATTAATTATCTACTAATTATCTA 1 251 0 AATTATCTAC 0.985588 -50 TTCTATCTGAAATTTTTTATTAAAAATAAC 2 28 0 AATTTTTTAT 0.917544 -192 TCCCTTATAAAATTTTCTATCTGAAATTTT 2 42 0 AATTTTCTAT 0.977881 -178 ********** Masking position 6 Map Score: 3.04709 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 68 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 TATATATATTATATTTAATTTCA 1 4 1 ATATATTATA 0.849774 -297 ATTCTATATGAAATATTGTTTGATTCATTA 1 66 1 AAATATTGTT 0.840721 -235 TTAGATTTTTTAATTTTATTGTTTGATTCA 1 93 1 TAATTTTATT 0.657909 -208 GATTTTTAATAAACTTTATAATAAAACATT 1 126 1 AAACTTTATA 0.813658 -175 TCTTAAATTTAAATGTTTTATTATAAAGTT 1 137 0 AAATGTTTTA 0.746253 -164 GATAGATTGAATCAATTATTCTTAAATTTA 1 156 0 ATCAATTATT 0.466386 -145 AATCAATGGAAAATATTGTAGATAATTAGT 1 233 1 AAATATTGTA 0.869716 -68 AAATTAATTTATATTTTATTGCGGTGGAAA 1 280 1 ATATTTTATT 0.852994 -21 TTCACACTATAACTGTTATTTTTAATAAAA 2 14 1 AACTGTTATT 0.837808 -206 TTTCTATCTGAAATTTTTTATTAAAAATAA 2 29 0 AAATTTTTTA 0.838517 -191 TTCAGATAGAAAATTTTATAAGGGATTTTT 2 47 1 AAATTTTATA 0.954414 -173 TTTTTTCACCAAAAATTATTGGATTTTATG 2 72 1 AAAAATTATT 0.812642 -148 ACAAAATCGTAACATTTATATAGTGGATGG 2 140 0 AACATTTATA 0.789703 -80 ********** Masking position 6 Map Score: 10.227 Number of sites scoring better than the average of aligned sites = 2138 Number in coding regions = 1504 Number in noncoding regions = 634 Number of orfs with sites within 600 bp upstream = 470 Fraction of orfs with sites within 600 bp upstream = 0.0754899 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 Motif number 8 ********** 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 9 ********** 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