AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i012_Glycogen_Biosynthesis_mjan_reg_100.orf -o012_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 RMJ06822 167 M_jannaschii_chromosome #2 RMJ10722 300 M_jannaschii_chromosome Motif number 1 ACTATATTTAAAAATCTAAATGATGATATT 1 11 0 AAAATCTAAA 0.943531 -157 ATTTTTAAATATAGTATAAATCTTAGAAAG 1 26 1 ATAGTATAAA 0.963609 -142 AAATCTTAGAAAGGTATAAAAACTATCTAA 1 43 1 AAGGTATAAA 0.806882 -125 TTTAAATTAGATAATATAAAAACATTGTGA 1 80 1 ATAATATAAA 0.982205 -88 TATGTACATCATAATATAATATTTATTGTT 1 112 1 ATAATATAAT 0.888215 -56 ATTTATTGTTAAAATCTGAAATTGAAATTG 1 132 1 AAAATCTGAA 0.884916 -36 ATAAAAAATAAACCACATAAAT 2 3 1 AAAAAATAAA 0.977633 -298 AACCACATAAATAAAATAGATATTAATTCA 2 21 1 ATAAAATAGA 0.864428 -280 AATATATTACGAAAAATAAAACTACGACTA 2 94 0 GAAAAATAAA 0.864428 -207 CCAACAATCCATAGTATGATTATTAAATAT 2 119 0 ATAGTATGAT 0.695715 -182 GCTGGATTATATTAAATAAACAGTATGGCA 2 148 1 ATTAAATAAA 0.822503 -153 TGCCTTAAAAATAATATGAACTTAATGAAA 2 188 0 ATAATATGAA 0.963457 -113 GGCATTACTTAAAAAATAAAGAACTTCATT 2 214 1 AAAAAATAAA 0.977633 -87 AATAATCCTAAAAAAATAAAATTGGGGGAG 2 277 1 AAAAAATAAA 0.977633 -24 ********** Masking position 7 Map Score: 20.9164 Number of sites scoring better than the average of aligned sites = 1658 Number in coding regions = 1234 Number in noncoding regions = 424 Number of orfs with sites within 600 bp upstream = 330 Fraction of orfs with sites within 600 bp upstream = 0.0530035 Motif number 2 ATTTATACTATATTTAAAAATCTAAATGATG 1 16 0 TATTTAAAAT 0.759645 -152 AATGTTTTTATATTATCTAATTTAAAGTATC 1 75 0 TATTATTAAT 0.843535 -93 ATGATGTACATATATCACAATGTTTTTATAT 1 93 0 TATATCCAAT 0.784579 -75 TCAATTTCAGATTTTAACAATAAATATTATA 1 126 0 ATTTTACAAT 0.673319 -42 AATTACCCCTTTAAAGCAATTTCAATTTCA 1 148 0 TTTAAACAAT 0.887045 -20 ATAAAATAGATATTAATTCATGCAACAGTGA 2 31 1 TATTAATCAT 0.753637 -270 CGTAGTTTTATTTTTCGTAATATATTTAATA 2 98 1 TTTTTCTAAT 0.956557 -203 TTTCGTAATATATTTAATAATCATACTATGG 2 110 1 TATTTATAAT 0.957355 -191 ATACTGTTTATTTAATATAATCCAGCCAACA 2 143 0 TTTAATTAAT 0.766726 -158 AAGTAATGCCTTAAAAATAATATGAACTTAA 2 193 0 TTAAAATAAT 0.741389 -108 GTTCTTTATTTTTTAAGTAATGCCTTAAAAA 2 207 0 TTTTAATAAT 0.96804 -94 TCATAATAAATTTTTATTAATTGAAAGACGC 2 247 0 TTTTTATAAT 0.971026 -54 TTTTTTAGGATTATTCATAATAAATTTTTAT 2 261 0 TTATTCTAAT 0.818116 -40 ****** **** Masking position 10 Map Score: 9.81767 Number of sites scoring better than the average of aligned sites = 2233 Number in coding regions = 1657 Number in noncoding regions = 576 Number of orfs with sites within 600 bp upstream = 416 Fraction of orfs with sites within 600 bp upstream = 0.0668166 Motif number 3 AATATCATCATTTAGATTTTTAAATA 1 7 1 ATCATTTAGA 0.486378 -161 ATTTATGTGGTTTATTTTTTAT 2 3 0 TTTATTTTTT 0.669809 -298 AATATCTATTTTATTTATGTGGTTTATTTT 2 15 0 TTATTTATGT 0.788963 -286 GTAATGTTAATTAGTTTAGTCGTAGTTTTA 2 78 1 TTAGTTTAGT 0.712503 -223 AGTCGTAGTTTTATTTTTCGTAATATATTT 2 95 1 TTATTTTTCG 0.344035 -206 TGCCATACTGTTTATTTAATATAATCCAGC 2 148 0 TTTATTTAAT 0.642859 -153 AGAGATTGATTTCATTAAGTTCATATTATT 2 179 1 TTCATTAAGT 0.926819 -122 AGTTCATATTATTTTTAAGGCATTACTTAA 2 196 1 ATTTTTAAGG 0.711651 -105 AAGTTCTTTATTTTTTAAGTAATGCCTTAA 2 210 0 TTTTTTAAGT 0.928165 -91 AATAAAGAACTTCATTTTGGCGTCTTTCAA 2 228 1 TTCATTTTGG 0.897622 -73 ATAATAAATTTTTATTAATTGAAAGACGCC 2 246 0 TTTATTAATT 0.732644 -55 TTAATAAAAATTTATTATGAATAATCCTAA 2 258 1 TTTATTATGA 0.782216 -43 CCCAATTTTATTTTTTTAGGATTATTCATA 2 273 0 TTTTTTTAGG 0.933327 -28 ********** Masking position 5 Map Score: 3.04758 Number of sites scoring better than the average of aligned sites = 2426 Number in coding regions = 1985 Number in noncoding regions = 441 Number of orfs with sites within 600 bp upstream = 357 Fraction of orfs with sites within 600 bp upstream = 0.0573402 Motif number 4 ********** No masking Map Score: 5.06917e-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: 5.06917e-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: 5.06917e-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