AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i222_Ribosomal_Operon___Transcription_mjan_reg_300.orf -o222_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 RMJ00193 285 M_jannaschii_chromosome #2 RMJ10489 300 M_jannaschii_chromosome Motif number 1 ACTAAAATAAATTTTTATTAATTGAGATTATT 1 28 1 ATTTATTAAT 0.964588 -258 TCCAATAATGAACTTTAATAATCTCAATTAAT 1 44 0 ATTTAATAAT 0.979925 -242 CTATTTGTAAAACTTTGATATTAGAAATTTTA 1 113 0 ATTTGATATT 0.690395 -173 TCCATATTCTTATTTTAAAAATTTTCGTCCTT 1 151 0 TTTTAAAAAT 0.787329 -135 TAGTATTATTTTCTTTAATAAATAGATAACTA 1 225 0 TTTTAATAAA 0.830609 -61 TATTTAGGAATTATTTATTTATTTAGAGGTTT 2 32 0 TTTTATTTAT 0.842028 -269 TTTTGTTAATTGATTTATTGATTGTCTTGTTG 2 91 0 TTTTATTGAT 0.891867 -210 TAGGATTTTCAATTTTGTTAATTGATTTATTG 2 103 0 ATTTGTTAAT 0.926184 -198 AAAACCCTAATAATGTAATGATAGAATAACGA 2 134 1 TTGTAATGAT 0.906361 -167 TAATTATAGTTTGTTTAATAATATTCTATCGT 2 162 0 TTTTAATAAT 0.980371 -139 GTCTGTAGATAATTTTAATTATAGTTTGTTTA 2 177 0 ATTTAATTAT 0.912856 -124 TATATAAACATTTTGTGATAATAAAGCTTTAT 2 212 1 TTGTGATAAT 0.928333 -89 GTGATAATAAAGCTTTATTAAGTCAATTATCC 2 226 1 ATTTATTAAG 0.812358 -75 TGTAATAATTAGTTGTAATAATAGGATAATTG 2 249 0 ATGTAATAAT 0.972023 -52 TTTTTATCTTAGTTGTAATAATTAGTTGTAAT 2 262 0 ATGTAATAAT 0.972023 -39 * ********* Masking position 6 Map Score: 19.0044 Number of sites scoring better than the average of aligned sites = 895 Number in coding regions = 664 Number in noncoding regions = 231 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 2 ATTTTTATTAATTGAGATTATTAAAGTTCAT 1 38 1 ATTGAGATAT 0.939236 -248 AAATTTTTAAAATAAGAATATGGACGAAACT 1 159 1 AATAAGATAT 0.973353 -127 TATTAAAGAAAATAATACTATAAAAAGAATA 1 237 1 AATAATATAT 0.958162 -49 ATACTATAAAAAGAATAAAATTTAGCAGTTC 1 251 1 AAGAATAAAT 0.850222 -35 GGAATTTAGAAATGAGAGTATTTAGGAATTA 2 51 0 AATGAGATAT 0.967794 -250 AAACTTATACAACAAGACAATCAATAAATCA 2 82 1 AACAAGAAAT 0.943283 -219 CAATAAATCAATTAACAAAATTGAAAATCCT 2 103 1 ATTAACAAAT 0.835673 -198 CTAATAATGTAATGATAGAATAACGATAGAA 2 140 1 AATGATAAAT 0.957242 -161 ATGATAGAATAACGATAGAATATTATTAAAC 2 151 1 AACGATAAAT 0.895767 -150 ACAAACTATAATTAAAATTATCTACAGACTC 2 180 1 ATTAAAATAT 0.744585 -121 ATAAAGCTTTATTAAGTCAATTATCCTATTA 2 232 1 ATTAAGTAAT 0.559151 -69 AATTAGTTGTAATAATAGGATAATTGACTTA 2 244 0 AATAATAGAT 0.893335 -57 ******* *** Masking position 5 Map Score: 10.0564 Number of sites scoring better than the average of aligned sites = 765 Number in coding regions = 556 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 3 ATTAAATATTAACTACTAAAATAAATTTTTA 1 14 1 AACTCTAAAA 0.982792 -272 TAATAATCTCAATTAATAAAAATTTATTTTA 1 30 0 AATTATAAAA 0.903387 -256 GGATATATCAAACTGCGAAGTCCTATTCAAA 1 73 1 AACTCGAAGT 0.817268 -213 TTGCCATTAAAATTTCTAATATCAAAGTTTT 1 106 1 AATTCTAATA 0.895637 -180 GAAGGACGAAAATTTTTAAAATAAGAATATG 1 150 1 AATTTTAAAA 0.842164 -136 CACCATACAGAACTGCTAAATTTTATTCTTT 1 260 0 AACTCTAAAT 0.985479 -26 TTTTAAATTTAATTTCTAAGGGTT 2 4 0 AATTCTAAGG 0.895508 -297 TTAAATTTAAAACCTCTAAATAAATAAATAA 2 23 1 AACCCTAAAT 0.959228 -278 ATAAATAAATAATTCCTAAATACTCTCATTT 2 42 1 AATTCTAAAT 0.985512 -259 TAAATACTCTCATTTCTAAATTCCAAACTTA 2 58 1 CATTCTAAAT 0.92567 -243 ACAACAAGACAATCAATAAATCAATTAACAA 2 90 1 AATCATAAAT 0.794449 -211 ACAAAATTGAAAATCCTAAAACCCTAATAAT 2 117 1 AAATCTAAAA 0.916294 -184 **** ****** Masking position 8 Map Score: 13.1865 Number of sites scoring better than the average of aligned sites = 620 Number in coding regions = 504 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 4 CAAATTAAATATTAACTACTA 1 2 1 AAATTAAATA 0.890301 -284 TTAATAATCTCAATTAATAAAAATTTATTT 1 32 0 CAATTAATAA 0.628763 -254 AAAGTTTTACAAATAGAAAAAGAAGGACGA 1 129 1 AAATAGAAAA 0.971279 -157 TTTCTTTAATAAATAGATAACTATGTTTAT 1 218 0 AAATAGATAA 0.938696 -68 TCTATTTATTAAAGAAAATAATACTATAAA 1 231 1 AAAGAAAATA 0.735375 -55 ATAATACTATAAAAAGAATAAAATTTAGCA 1 248 1 AAAAAGAATA 0.707082 -38 CTTAGAAATTAAATTTAAAACCTCTAAATA 2 15 1 AAATTTAAAA 0.815707 -286 TAAAACCTCTAAATAAATAAATAATTCCTA 2 30 1 AAATAAATAA 0.922416 -271 TCAATTAACAAAATTGAAAATCCTAAAACC 2 110 1 AAATTGAAAA 0.958504 -191 ATTACAACTAAGATAAAAAATACTGCTGGT 2 275 1 AGATAAAAAA 0.845631 -26 ********** Masking position 7 Map Score: 7.15585 Number of sites scoring better than the average of aligned sites = 1749 Number in coding regions = 1274 Number in noncoding regions = 475 Number of orfs with sites within 600 bp upstream = 359 Fraction of orfs with sites within 600 bp upstream = 0.0576614 Motif number 5 ********** No masking Map Score: 1.21035e-12 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: 1.21035e-12 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: 1.21035e-12 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