AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i222_Ribosomal_Operon___Transcription_mjan_reg_100.orf -o222_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 RMJ00193 285 M_jannaschii_chromosome #2 RMJ10489 300 M_jannaschii_chromosome Motif number 1 TAATAATCTCAATTAATAAAAATTTATTTT 1 31 0 AATTAATAAA 0.97428 -255 TATTAATTGAGATTATTAAAGTTCATTATT 1 43 1 GATTATTAAA 0.939445 -243 GAAGGACGAAAATTTTTAAAATAAGAATAT 1 150 1 AATTTTTAAA 0.867313 -136 ATAGTTATCTATTTATTAAAGAAAATAATA 1 224 1 ATTTATTAAA 0.875571 -62 AAAACCTCTAAATAAATAAATAATTCCTAA 2 31 1 AATAAATAAA 0.894541 -270 ACAACAAGACAATCAATAAATCAATTAACA 2 90 1 AATCAATAAA 0.929221 -211 TCAATAAATCAATTAACAAAATTGAAAATC 2 102 1 AATTAACAAA 0.916637 -199 ATCGTTATTCTATCATTACATTATTAGGGT 2 137 0 TATCATTACA 0.906838 -164 AACGATAGAATATTATTAAACAAACTATAA 2 161 1 TATTATTAAA 0.976233 -140 TTAAACAAACTATAATTAAAATTATCTACA 2 176 1 TATAATTAAA 0.878969 -125 AATAAAGCTTTATTATCACAAAATGTTTAT 2 215 0 TATTATCACA 0.890908 -86 AGGATAATTGACTTAATAAAGCTTTATTAT 2 229 0 ACTTAATAAA 0.856627 -72 TCAATTATCCTATTATTACAACTAATTATT 2 248 1 TATTATTACA 0.965509 -53 TATTACAACTAATTATTACAACTAAGATAA 2 261 1 AATTATTACA 0.977794 -40 ********** Masking position 8 Map Score: 19.9096 Number of sites scoring better than the average of aligned sites = 778 Number in coding regions = 569 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 2 ATTTTTATTAATTGAGATTATTAAAGTTCAT 1 38 1 ATTGAGATAT 0.928487 -248 AAATTTTTAAAATAAGAATATGGACGAAACT 1 159 1 AATAAGATAT 0.968363 -127 TATTAAAGAAAATAATACTATAAAAAGAATA 1 237 1 AATAATATAT 0.950475 -49 ATACTATAAAAAGAATAAAATTTAGCAGTTC 1 251 1 AAGAATAAAT 0.826291 -35 GGAATTTAGAAATGAGAGTATTTAGGAATTA 2 51 0 AATGAGATAT 0.961804 -250 AAACTTATACAACAAGACAATCAATAAATCA 2 82 1 AACAAGAAAT 0.933081 -219 CAATAAATCAATTAACAAAATTGAAAATCCT 2 103 1 ATTAACAAAT 0.810567 -198 CTAATAATGTAATGATAGAATAACGATAGAA 2 140 1 AATGATAAAT 0.949396 -161 ATGATAGAATAACGATAGAATATTATTAAAC 2 151 1 AACGATAAAT 0.878071 -150 ACAAACTATAATTAAAATTATCTACAGACTC 2 180 1 ATTAAAATAT 0.709832 -121 ATAAAGCTTTATTAAGTCAATTATCCTATTA 2 232 1 ATTAAGTAAT 0.545568 -69 AATTAGTTGTAATAATAGGATAATTGACTTA 2 244 0 AATAATAGAT 0.875283 -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 0.976197 -272 TAATAATCTCAATTAATAAAAATTTATTTTA 1 30 0 AATTATAAAA 0.870693 -256 GGATATATCAAACTGCGAAGTCCTATTCAAA 1 73 1 AACTCGAAGT 0.762539 -213 TTGCCATTAAAATTTCTAATATCAAAGTTTT 1 106 1 AATTCTAATA 0.860453 -180 GAAGGACGAAAATTTTTAAAATAAGAATATG 1 150 1 AATTTTAAAA 0.793015 -136 CACCATACAGAACTGCTAAATTTTATTCTTT 1 260 0 AACTCTAAAT 0.979893 -26 TTTTAAATTTAATTTCTAAGGGTT 2 4 0 AATTCTAAGG 0.860215 -297 TTAAATTTAAAACCTCTAAATAAATAAATAA 2 23 1 AACCCTAAAT 0.944108 -278 ATAAATAAATAATTCCTAAATACTCTCATTT 2 42 1 AATTCTAAAT 0.980531 -259 TAAATACTCTCATTTCTAAATTCCAAACTTA 2 58 1 CATTCTAAAT 0.899436 -243 ACAACAAGACAATCAATAAATCAATTAACAA 2 90 1 AATCATAAAT 0.735336 -211 ACAAAATTGAAAATCCTAAAACCCTAATAAT 2 117 1 AAATCTAAAA 0.887126 -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 0.916089 -284 TTAATAATCTCAATTAATAAAAATTTATTT 1 32 0 CAATTAATAA 0.695086 -254 AAAGTTTTACAAATAGAAAAAGAAGGACGA 1 129 1 AAATAGAAAA 0.978507 -157 TTTCTTTAATAAATAGATAACTATGTTTAT 1 218 0 AAATAGATAA 0.953732 -68 TCTATTTATTAAAGAAAATAATACTATAAA 1 231 1 AAAGAAAATA 0.789077 -55 ATAATACTATAAAAAGAATAAAATTTAGCA 1 248 1 AAAAAGAATA 0.764689 -38 CTTAGAAATTAAATTTAAAACCTCTAAATA 2 15 1 AAATTTAAAA 0.856291 -286 TAAAACCTCTAAATAAATAAATAATTCCTA 2 30 1 AAATAAATAA 0.941179 -271 TCAATTAACAAAATTGAAAATCCTAAAACC 2 110 1 AAATTGAAAA 0.968843 -191 ATTACAACTAAGATAAAAAATACTGCTGGT 2 275 1 AGATAAAAAA 0.880591 -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 CAAATTAAATATTAACTACTAAA 1 4 1 ATTAAATATT 0.728687 -282 TAACTACTAAAATAAATTTTTATTAATTGA 1 23 1 AATAAATTTT 0.923743 -263 AATTGAGATTATTAAAGTTCATTATTGGAT 1 47 1 ATTAAAGTTC 0.912107 -239 AAAGATTGCCATTAAAATTTCTAATATCAA 1 101 1 ATTAAAATTT 0.955564 -185 AATTTCTAATATCAAAGTTTTACAAATAGA 1 116 1 ATCAAAGTTT 0.912107 -170 CTATAAAAAGAATAAAATTTAGCAGTTCTG 1 254 1 AATAAAATTT 0.945751 -32 AACCCTTAGAAATTAAATTTAAAACCTCTA 2 11 1 AATTAAATTT 0.733381 -290 GATAATTTTAATTATAGTTTGTTTAATAAT 2 172 0 ATTATAGTTT 0.875014 -129 ATTTTGTGATAATAAAGCTTTATTAAGTCA 2 221 1 AATAAAGCTT 0.905427 -80 ********** Masking position 6 Map Score: 7.29911 Number of sites scoring better than the average of aligned sites = 703 Number in coding regions = 474 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 216 Fraction of orfs with sites within 600 bp upstream = 0.0346932 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 Motif number 8 ********** 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