AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i184_thi_operon_mjan_reg_100.orf -o184_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 RMJ07723 300 M_jannaschii_chromosome #2 RMJ03619 161 M_jannaschii_chromosome Motif number 1 ACAAACACAAAATAAAAATATTAAAAATAA 1 15 0 AATAAAAATA 0.721787 -286 GGATAACAAAACTATTAATATCAACAAACA 1 38 0 ACTATTAATA 0.895859 -263 TCAATTTTGAAATTTTGATAGGATAACAAA 1 58 0 AATTTTGATA 0.960867 -243 GGACATTTGGAATTTAGATACCAAAGGCAC 1 137 0 AATTTAGATA 0.964876 -164 GGACTTAAGCACTTTATATTGGACATTTGG 1 157 0 ACTTTATATT 0.810615 -144 TATTTAATAAACCTTAGATTTTTGTGTCTA 1 187 1 ACCTTAGATT 0.805831 -114 TGTAATATCTACTTTATATACTCTCACTAT 1 223 1 ACTTTATATA 0.961125 -78 ATATACTCTCACTATATATATGTGTTGATT 1 238 1 ACTATATATA 0.940415 -63 ATATTGAAGAAATTTAAATAACACTAAATT 1 276 0 AATTTAAATA 0.874544 -25 AACAACACCCAACAATTATAAACATGATAA 2 12 1 AACAATTATA 0.701623 -150 TATCATTATTAATTATGATAAATTATCTAT 2 69 0 AATTATGATA 0.920174 -93 TATCATAATTAATAATGATAATTAGCTTAA 2 79 1 AATAATGATA 0.880391 -83 AATTAGCTTAACCTTTTATATAGTTTTGTT 2 98 1 ACCTTTTATA 0.916669 -64 ********** Masking position 8 Map Score: 14.6747 Number of sites scoring better than the average of aligned sites = 1070 Number in coding regions = 700 Number in noncoding regions = 370 Number of orfs with sites within 600 bp upstream = 360 Fraction of orfs with sites within 600 bp upstream = 0.057822 Motif number 2 ACAAACACAAAATAAAAATATTAAAAATAAA 1 14 0 AATAAAATAT 0.9361 -287 TTGATAGGATAACAAAACTATTAATATCAAC 1 43 0 AACAAACTAT 0.939362 -258 TGAGTGTTTTAATAGGTCTTACGCAGTAATA 1 85 1 AATAGGCTTA 0.91425 -216 CTTACGCAGTAATAAATCTTTTCTATTGAAT 1 102 1 AATAAACTTT 0.978037 -199 AGGTTTATTAAATAGGACTTAAGCACTTTAT 1 170 0 AATAGGCTTA 0.914252 -131 AGTCCTATTTAATAAACCTTAGATTTTTGTG 1 182 1 AATAAACTTA 0.958647 -119 GTTGATTGACAATAAAATTTAGTGTTATTTA 1 261 1 AATAAATTTA 0.883691 -40 TAAACATGATAATAGGTATATGACTCACTAA 2 30 1 AATAGGATAT 0.870756 -132 TAAGGTAATGAATAGATAATTTATCATAATT 2 58 1 AATAGAAATT 0.72775 -104 ACTTTATTAAAACAAAACTATATAAAAGGTT 2 107 0 AACAAACTAT 0.939362 -55 GTTTTGTTTTAATAAAGTTATCGAGATGCAT 2 120 1 AATAAATTAT 0.936097 -42 CAGATTTGTAATAAAATAATAATGCATCTC 2 142 0 AATAAATAAT 0.766402 -20 ****** **** Masking position 4 Map Score: 12.7991 Number of sites scoring better than the average of aligned sites = 1330 Number in coding regions = 994 Number in noncoding regions = 336 Number of orfs with sites within 600 bp upstream = 297 Fraction of orfs with sites within 600 bp upstream = 0.0477032 Motif number 3 CACAAAATAAAAATATTAAAAATAAAAAA 1 10 0 AAATATTAAA 0.916441 -291 TAATATCAACAAACACAAAATAAAAATATT 1 23 0 AAACACAAAA 0.945733 -278 TATCCTATCAAAATTTCAAAATTGAGTGTT 1 63 1 AAATTTCAAA 0.77795 -238 AGACCTATTAAAACACTCAATTTTGAAATT 1 74 0 AAACACTCAA 0.961672 -227 CCAAAGGCACCAATATTCAATAGAAAAGAT 1 117 0 CAATATTCAA 0.830247 -184 TTTGGAATTTAGATACCAAAGGCACCAATA 1 132 0 AGATACCAAA 0.936509 -169 TTTGGTATCTAAATTCCAAATGTCCAATAT 1 142 1 AAATTCCAAA 0.905086 -159 ACAAACCCATAGACACAAAAATCTAAGGTT 1 196 0 AGACACAAAA 0.869938 -105 GAAATTTAAATAACACTAAATTTTATTGTC 1 268 0 TAACACTAAA 0.877737 -33 TAAATTTCTTCAATATTAAAG 1 290 1 CAATATTAAA 0.886479 -11 GAACAACACCCAACAATTATAAA 2 4 1 CAACACCCAA 0.958333 -158 ********** Masking position 3 Map Score: 11.6864 Number of sites scoring better than the average of aligned sites = 960 Number in coding regions = 804 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 4 TTTTTTATTTTTAATATTTTTATTT 1 6 1 TATTTTTAAT 0.9299 -295 TTATATTGGACATTTGGAATTTAGATACCA 1 144 0 CATTTGGAAT 0.935322 -157 TGTGTCTATGGGTTTGTAATATCTACTTTA 1 209 1 GGTTTGTAAT 0.955969 -92 CCTATTATCATGTTTATAATTGTTGGGTGT 2 16 0 TGTTTATAAT 0.779386 -146 AGCTAATTATCATTATTAATTATGATAAAT 2 76 0 CATTATTAAT 0.928583 -86 TATCGAGATGCATTATTATTTTATTACAAA 2 138 1 CATTATTATT 0.729675 -24 CAGATTTGTAATAAAATAATAA 2 150 0 GATTTGTAAT 0.969938 -12 ********** Masking position 8 Map Score: 2.54573 Number of sites scoring better than the average of aligned sites = 518 Number in coding regions = 410 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 5 ********** No masking Map Score: 7.55607e-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: 7.55607e-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 7 ********** No masking Map Score: 7.55607e-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