AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00052_mjan_reg_100.orf -o00052_mjan_100.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 MJ0210 86 succinyl-CoA synthetase, beta subunit #2 MJ0210.1 43 M. jannaschii predicted coding region MJ0210.1 #3 MJ1334 214 UDP-glucose pyrophosphorylase (gtaB) Motif number 1 AAAAAATTTGGTGATAAATTTATAGGTTTA 1 10 0 GTATAAATTT 0.921673 -77 AAATTATCATATAAAAAATTTGGTGATAAAT 1 22 0 ATAAAAATTT 0.989949 -65 AATTTTTTATATGATAATTTTAAAATTTTGC 1 33 1 ATATAATTTT 0.95824 -54 TTTCTTTTTAATGCAAAATTTTAAAATTATC 1 45 0 ATCAAAATTT 0.963593 -42 ATCACCTTAAATGATAAATTTCTTTTTAATG 1 63 0 ATATAAATTT 0.988586 -24 CAAAATAATTTTTATTTTATAT 2 2 1 AAATAATTTT 0.614683 -42 TATGGGAAATAATATAAAATAAAAATTATTT 2 13 0 AAATAAAATA 0.84512 -31 ATTAAAAAATTATGGGAAATA 2 33 0 ATAAAAAATT 0.976307 -11 ATTAAAATTTTATTTCCATTT 3 1 1 ATAAAATTTT 0.963468 -214 TATATAATGCATTAAAAAATGGAAATAAAAT 3 17 0 ATAAAAAATG 0.876166 -198 TGCAAATGTGAAACTAAAATTCATTGAAGAA 3 82 0 AACTAAAATT 0.8317 -133 GGTGATGATTATGAAAAAGTATTTCGAGGAA 3 115 0 ATAAAAAGTA 0.844569 -100 TATAGTAGGTATAAATAATTTGGTGATGATT 3 136 0 ATAATAATTT 0.900151 -79 ATATAATTGTAACATAAATTAATTTAATAAA 3 175 1 AAATAAATTA 0.928842 -40 AAATTAATTTAATAAAAATTTACTAAAGGGA 3 190 1 AAAAAAATTT 0.980474 -25 ** ******** Masking position 7 Map Score: 26.0215 Number of sites scoring better than the average of aligned sites = 1856 Number in coding regions = 1318 Number in noncoding regions = 538 Number of orfs with sites within 600 bp upstream = 420 Fraction of orfs with sites within 600 bp upstream = 0.067459 Motif number 2 TAAACCTATAAATTTATCACCAAATT 1 7 1 TATAAATTTA 0.770028 -80 ATTTTAAAATTATCATATAAAAAATTTGGT 1 29 0 TATCATATAA 0.928506 -58 AAAAGAAATTTATCATTTAAGGTGATAGG 1 68 1 TATCATTTAA 0.840861 -19 ATAATTTTTATTTTATATTATTTCCCATAA 2 15 1 TTTTATATTA 0.649075 -29 ATTAAAAAATTATGGGAAATAA 2 32 0 TAAAAAATTA 0.742779 -12 ATTAAAATTTTATTTCCATTTT 3 3 1 TAAAATTTTA 0.476181 -212 GCTATTGAAGTCATATATAATGCATTAAAA 3 31 0 TCATATATAA 0.594382 -184 TCATAATCATCACCAAATTATTTATACCTA 3 132 1 CACCAAATTA 0.711693 -83 TATTTATACCTACTATATTAATACTATATA 3 150 1 TACTATATTA 0.748345 -65 ACTATATTAATACTATATAATTGTAACATA 3 161 1 TACTATATAA 0.884022 -54 AGTAAATTTTTATTAAATTAATTTATGTTA 3 184 0 TATTAAATTA 0.921838 -31 ********** Masking position 5 Map Score: 7.5335 Number of sites scoring better than the average of aligned sites = 1122 Number in coding regions = 757 Number in noncoding regions = 365 Number of orfs with sites within 600 bp upstream = 314 Fraction of orfs with sites within 600 bp upstream = 0.0504337 Motif number 3 TTTTAAAATTTTGCATTAAAAAGAAATTTA 1 50 1 TTGCATTAAA 0.969237 -37 AAAAGAAATTTATCATTTAAGGTGATAGG 1 68 1 TATCATTTAA 0.794591 -19 GTCATATATAATGCATTAAAAAATGGAAAT 3 22 0 ATGCATTAAA 0.9768 -193 TGAAACTAAAATTCATTGAAGAAGATGAGG 3 75 0 ATTCATTGAA 0.958434 -140 TTTAGTAAATTTTTATTAAATTAATTTATG 3 187 0 TTTTATTAAA 0.857789 -28 TTTAATAAAAATTTACTAAAGGGAGAGG 3 197 1 ATTTACTAAA 0.864378 -18 ********** Masking position 5 Map Score: 3.64933 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 359 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 4 ATATAAAAAATTTGGTGATAAATTTATAGG 1 15 0 TTTGGTGATA 0.893562 -72 ACCAAATTTTTTATATGATAATTTTAAAAT 1 29 1 TTATATGATA 0.896681 -58 ATTTATCATTTAAGGTGATAGG 1 75 1 TAAGGTGATA 0.91241 -12 TTATGGGAAATAATATAAAATAAAAATTAT 2 15 0 TAATATAAAA 0.644469 -29 ATTAAAAAATTATGGGAAATAATATAAAA 2 25 0 TTATGGGAAA 0.937963 -19 CATTGAAGAAGATGAGGAAAAGTTAAAAAA 3 62 0 GATGAGGAAA 0.857114 -153 AGGAAAGTGCAAATGTGAAACTAAAATTCA 3 90 0 AAATGTGAAA 0.791915 -125 GAAAAAGTATTTCGAGGAAAGTGCAAATGT 3 104 0 TTCGAGGAAA 0.846809 -111 ATTTGGTGATGATTATGAAAAAGTATTTCG 3 120 0 GATTATGAAA 0.885143 -95 TTTAGTAAATTTTTATTAAATTAATTTATG 3 187 0 TTTTATTAAA 0.570504 -28 ********** Masking position 8 Map Score: 2.88351 Number of sites scoring better than the average of aligned sites = 1921 Number in coding regions = 1609 Number in noncoding regions = 312 Number of orfs with sites within 600 bp upstream = 300 Fraction of orfs with sites within 600 bp upstream = 0.048185 Motif number 5 ********** No masking Map Score: 2.43208e-15 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: 2.43208e-15 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: 2.43208e-15 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