AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i216_Ribosomal_Operon_3_mjan_reg_300.orf -o216_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 RMJ13034 93 M_jannaschii_chromosome #2 RMJ09255 300 M_jannaschii_chromosome #3 RMJ01438 300 M_jannaschii_chromosome Motif number 1 TTTTCAGAAATTTTAGAATTATACT 1 6 0 TTTTAGAATT 0.960763 -88 CAATTAAAAATTTTATTGTTTTCAGAAATT 1 24 0 TTTTATTGTT 0.923063 -70 CTTAATAAAATATTATATTTCTTCAATTAA 1 47 0 TATTATATTT 0.810945 -47 TTATTAAGTGTTGTATAGTTTAATTTGGTG 1 69 1 TTGTATAGTT 0.851282 -25 ATGAAAACTCTTTTAGTTTTCATTTAACCG 2 83 1 TTTTAGTTTT 0.975177 -218 AAACAAAATCTTTCAGATTTTGTAGCCCGA 2 124 0 TTTCAGATTT 0.902763 -177 CTCGGCACCATTTTATTATTTTATTTTAGG 2 187 1 TTTTATTATT 0.917447 -114 TATTTTAGGTTGTTATATTTATTTTTTTAG 2 208 1 TGTTATATTT 0.864187 -93 ATATTTATTTTTTTAGATTTATGGATTAAC 2 222 1 TTTTAGATTT 0.981845 -79 TTTAAATAGTATTTATTTTTTAAATCTTAA 2 256 1 ATTTATTTTT 0.739779 -45 CTATAGGTTTTTGTAGTATTTTAATATTCT 3 72 1 TTGTAGTATT 0.860433 -229 TATGTAATACTTTTAGATTTCGTTTTAAAA 3 268 1 TTTTAGATTT 0.981845 -33 ********** Masking position 5 Map Score: 15.1136 Number of sites scoring better than the average of aligned sites = 1188 Number in coding regions = 832 Number in noncoding regions = 356 Number of orfs with sites within 600 bp upstream = 307 Fraction of orfs with sites within 600 bp upstream = 0.0493093 Motif number 2 ATATTTCTTCAATTAAAAATTTTATTGTTT 1 33 0 AATTAAAAAT 0.88652 -61 ATACAACACTTAATAAAATATTATATTTCT 1 55 0 TAATAAAATA 0.694736 -39 GATATCACCAAATTAAACTATACAACACTT 1 74 0 AATTAAACTA 0.753378 -20 CTTTCCATTTCATCAAAATAGGATGCATTG 2 38 0 CATCAAAATA 0.767999 -263 TAACAACCTAAAATAAAATAATAAAATGGT 2 193 0 AAATAAAATA 0.812712 -108 TAATCCATAAATCTAAAAAAATAAATATAA 2 220 0 ATCTAAAAAA 0.72975 -81 AATAAATACTATTTAAAAATAGTTAATCCA 2 243 0 ATTTAAAAAT 0.833729 -58 TTAAGTTAAGATTTAAAAAATAAATACTAT 2 261 0 ATTTAAAAAA 0.933462 -40 AAATTCACCATTAAAAACTGTTAAGTTA 2 283 0 CATTAAAAAC 0.835267 -18 TTGCAAAAGTCATTAAAATTCATAATGAAA 3 38 0 CATTAAAATT 0.881517 -263 TTTTAAAGAATATTAAAATACTACAAAAAC 3 78 0 TATTAAAATA 0.905451 -223 TTTTAATATTCTTTAAAAAAGCATATAAAA 3 90 1 CTTTAAAAAA 0.939401 -211 TTAGATTTCGTTTTAAAAAAGAGGTGCAAT 3 280 1 TTTTAAAAAA 0.879094 -21 ********** Masking position 5 Map Score: 9.4286 Number of sites scoring better than the average of aligned sites = 2454 Number in coding regions = 1888 Number in noncoding regions = 566 Number of orfs with sites within 600 bp upstream = 394 Fraction of orfs with sites within 600 bp upstream = 0.063283 Motif number 3 TAAGAGGCATTGCCGAGCGTAGCGAGG 2 5 1 AGCATTCCAG 0.994638 -296 TCAAAATAGGATGCATTGCCTCGCTACGCTCGG 2 23 0 AGCATTCCCG 0.992052 -278 ATGGAAAGCTACGCTTTCCAGCTATGAAAACTC 2 60 1 AGCTTTCACT 0.925071 -241 ACGCCTTCCAAAGGAAGGCGTTC 3 1 1 AGCCTTCAAG 0.982506 -300 TTTAAGCAGTAAGCATTTTATATGCTTTTTTAA 3 102 0 AGCATTTAAT 0.90607 -199 ATGAGCAGAAATGCATTTCCTATCCATAGGGCT 3 167 1 AGCATTCCAT 0.988988 -134 CGAAATCTAAAAGTATTACATAGCTAAATTGGA 3 257 0 AGTATTCAAG 0.952205 -44 * ***** ** ** Masking position 1 Map Score: 5.65759 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 42 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 TAAGAGGCATTGCCGAGCGTAGCGAGGC 2 7 1 GCATTCCGGC 0.982509 -294 AAAATAGGATGCATTGCCTCGCTACGCTCGGC 2 22 0 GCATTCCTGC 0.993453 -279 GGAAAGCGTAGCTTTCCATTTCATCAAAATAG 2 47 0 GCTTTCATTC 0.976983 -254 GGAAAGCTACGCTTTCCAGCTATGAAAACTCT 2 62 1 GCTTTCAGTA 0.847699 -239 GAGCAGAAATGCATTTCCTATCCATAGGGCTC 3 169 1 GCATTCCTTC 0.992194 -132 AAATCTAAAAGTATTACATAGCTAAATTGGAC 3 256 0 GTATTCATGC 0.951265 -45 ***** *** ** Masking position 5 Map Score: 4.70217 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 29 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 TTTCTGAAAACAATAAAATTTTTAATTGAA 1 26 1 CAATAAAATT 0.682059 -68 CGCTTTCCAGCTATGAAAACTCTTTTAGTT 2 71 1 CTATGAAAAC 0.908861 -230 CGCTTCGGTTAAATGAAAACTAAAAGAGTT 2 88 0 AAATGAAAAC 0.922186 -213 TAGCTTCGGGCTACAAAATCTGAAAGATTT 2 119 1 CTACAAAATC 0.936203 -182 AGAAAAAGTTAAACAAAATCTTTCAGATTT 2 134 0 AAACAAAATC 0.945768 -167 TAACAACCTAAAATAAAATAATAAAATGGT 2 193 0 AAATAAAATA 0.649378 -108 AAAAAAATAAATATAACAACCTAAAATAAA 2 206 0 ATATAACAAC 0.72554 -95 AAGATTTAAAAAATAAATACTATTTAAAAA 2 254 0 AAATAAATAC 0.710593 -47 AAATTCACCATTAAAAACTGTTAAGTTA 2 283 0 CATTAAAAAC 0.73987 -18 TATTAAAATACTACAAAAACCTATAGTTTT 3 68 0 CTACAAAAAC 0.936203 -233 TTAAAAAAGCATATAAAATGCTTACTGCTT 3 102 1 ATATAAAATG 0.66598 -199 CTCTTTTTTAAAACGAAATCTAAAAGTATT 3 273 0 AAACGAAATC 0.906972 -28 ********** Masking position 6 Map Score: 6.79233 Number of sites scoring better than the average of aligned sites = 1120 Number in coding regions = 915 Number in noncoding regions = 205 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 6 TGTATAGTTTAATTTGGTGATATC 1 80 1 AATTTGGTGA 0.877858 -14 ATAAAATAATAAAATGGTGCCGAGGGAGGG 2 181 0 AAAATGGTGC 0.974031 -120 GACGTCCATTAAGTTGGGGCTTTCAGCCCC 3 219 1 AAGTTGGGGC 0.983609 -82 AATTGGACATTAATTGGGGCTGAAAGCCCC 3 234 0 TAATTGGGGC 0.968842 -67 TCGTTTTAAAAAAGAGGTGCAATT 3 287 1 AAAGAGGTGC 0.944122 -14 ********** Masking position 2 Map Score: 0.271557 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 75 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 ********** No masking Map Score: 1.5301e-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: 1.5301e-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 9 ********** No masking Map Score: 1.5301e-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