AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i184_thi_operon_mjan_reg_300.orf -o184_mjan_300.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 TTATTTTTAATATTTTTATTTTGTGTTTGT 1 15 1 TATTTTTATT 0.723438 -286 TGTTTGTTGATATTAATAGTTTTGTTATCC 1 38 1 TATTAATAGT 0.897102 -263 TTTGTTATCCTATCAAAATTTCAAAATTGA 1 58 1 TATCAAAATT 0.961352 -243 GTGCCTTTGGTATCTAAATTCCAAATGTCC 1 137 1 TATCTAAATT 0.965283 -164 CCAAATGTCCAATATAAAGTGCTTAAGTCC 1 157 1 AATATAAAGT 0.812054 -144 TAGACACAAAAATCTAAGGTTTATTAAATA 1 187 0 AATCTAAGGT 0.807952 -114 ATAGTGAGAGTATATAAAGTAGATATTACA 1 223 0 TATATAAAGT 0.96161 -78 AATCAACACATATATATAGTGAGAGTATAT 1 238 0 TATATATAGT 0.941142 -63 AATTTAGTGTTATTTAAATTTCTTCAATAT 1 276 1 TATTTAAATT 0.874946 -25 TTATCATGTTTATAATTGTTGGGTGTTGTT 2 12 0 TATAATTGTT 0.704458 -150 ATAGATAATTTATCATAATTAATAATGATA 2 69 1 TATCATAATT 0.92115 -93 TTAAGCTAATTATCATTATTAATTATGATA 2 79 0 TATCATTATT 0.881789 -83 AACAAAACTATATAAAAGGTTAAGCTAATT 2 98 0 TATAAAAGGT 0.917703 -64 ********** Masking position 2 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 0.927723 -287 TTGATAGGATAACAAAACTATTAATATCAAC 1 43 0 AACAAACTAT 0.931381 -258 TGAGTGTTTTAATAGGTCTTACGCAGTAATA 1 85 1 AATAGGCTTA 0.903304 -216 CTTACGCAGTAATAAATCTTTTCTATTGAAT 1 102 1 AATAAACTTT 0.975031 -199 AGGTTTATTAAATAGGACTTAAGCACTTTAT 1 170 0 AATAGGCTTA 0.903306 -131 AGTCCTATTTAATAAACCTTAGATTTTTGTG 1 182 1 AATAAACTTA 0.953078 -119 GTTGATTGACAATAAAATTTAGTGTTATTTA 1 261 1 AATAAATTTA 0.869402 -40 TAAACATGATAATAGGTATATGACTCACTAA 2 30 1 AATAGGATAT 0.855138 -132 TAAGGTAATGAATAGATAATTTATCATAATT 2 58 1 AATAGAAATT 0.701215 -104 ACTTTATTAAAACAAAACTATATAAAAGGTT 2 107 0 AACAAACTAT 0.931381 -55 GTTTTGTTTTAATAAAGTTATCGAGATGCAT 2 120 1 AATAAATTAT 0.92772 -42 CAGATTTGTAATAAAATAATAATGCATCTC 2 142 0 AATAAATAAT 0.741927 -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 TAATATTTTTATTTTGTGTTTGTTGATATT 1 22 1 ATTTTGTGTT 0.974119 -279 AAATTTCAAAATTGAGTGTTTTAATAGGTC 1 73 1 ATTGAGTGTT 0.984878 -228 AATCTTTTCTATTGAATATTGGTGCCTTTG 1 116 1 ATTGAATATT 0.74056 -185 TATATTGGACATTTGGAATTTAGATACCAA 1 143 0 ATTTGGAATT 0.803294 -158 TGACAATAAAATTTAGTGTTATTTAAATTT 1 267 1 ATTTAGTGTT 0.981795 -34 GTTTATAATTGTTGGGTGTTGTTC 2 5 0 GTTGGGTGTT 0.9793 -157 CTTTTATATAGTTTTGTTTTAATAAAGTTA 2 110 1 GTTTTGTTTT 0.829155 -52 ********** Masking position 3 Map Score: 4.94466 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 211 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 CTATTAATATCAACAAACACAAAATAAAAA 1 27 0 CAACAAACAC 0.974471 -274 AATTTAGATACCAAAGGCACCAATATTCAA 1 127 0 CCAAAGGCAC 0.973079 -174 TATTACAAACCCATAGACACAAAAATCTAA 1 200 0 CCATAGACAC 0.990881 -101 ATTTTATTGTCAATCAACACATATATATAG 1 249 0 CAATCAACAC 0.963819 -52 ********** Masking position 3 Map Score: 0.21428 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 33 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 AAATAAAAATATTAAAAATAAAAAA 1 6 0 ATTAAAAATA 0.927254 -295 TGGTATCTAAATTCCAAATGTCCAATATAA 1 144 1 ATTCCAAATG 0.932865 -157 TAAAGTAGATATTACAAACCCATAGACACA 1 209 0 ATTACAAACC 0.954259 -92 ACACCCAACAATTATAAACATGATAATAGG 2 16 1 ATTATAAACA 0.772448 -146 ATTTATCATAATTAATAATGATAATTAGCT 2 76 1 ATTAATAATG 0.925891 -86 TTTGTAATAAAATAATAATGCATCTCGATA 2 138 0 AATAATAATG 0.721733 -24 TTATTATTTTATTACAAATCTG 2 150 1 ATTACAAATC 0.968753 -12 ********** Masking position 7 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 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 Motif number 8 ********** 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