AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i216_Ribosomal_Operon_3_mjan_reg_100.orf -o216_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 RMJ13034 93 M_jannaschii_chromosome #2 RMJ09255 300 M_jannaschii_chromosome #3 RMJ01438 300 M_jannaschii_chromosome Motif number 1 AATTAAAAATTTTATTGTTTTCAGAAATTTTAGAATTATAC 1 12 0 TTATTTTATT 0.973584 -82 ATTGAAGAAATATAATATTTTATTAAGTGTTGTATAGTTTA 1 50 1 TTAATTTTTT 0.981344 -44 AAAGATTTTGTTTAACTTTTTCTAAAAGTTTCGTTTGTATC 2 141 1 TTAATTTTTT 0.981345 -160 TCGGCACCATTTTATTATTTTATTTTAGGTTGTTATATTTA 2 188 1 TTATTTTTTT 0.984255 -113 TTTAGGTTGTTATATTTATTTTTTTAGATTTATGGATTAAC 2 211 1 TTATTTTTTT 0.984255 -90 ATTTTTAAATAGTATTTATTTTTTAAATCTTAACTTAACAG 2 253 1 ATATTTTTTT 0.973584 -48 TCAAATTTTCATTATGAATTTTAATGACTTTTGCAAAAAAC 3 32 1 ATATTTTATT 0.956007 -269 TTTGCAAAAAACTATAGGTTTTTGTAGTATTTTAATATTCT 3 61 1 ATATTTTTTT 0.973581 -240 TAGTTTAAGCAGTAAGCATTTTATATGCTTTTTTAAAGAAT 3 97 0 ATAATTTATT 0.948151 -204 TTTATCTCTATATAATAATTTCTACTTAGTTTAAGCAGTAA 3 123 0 TTAATTTTTT 0.981345 -178 AATTTAGCTATGTAATACTTTTAGATTTCGTTTTAAAAAAG 3 260 1 TTAATTTAGT 0.85382 -41 * *** *** * ** Masking position 4 Map Score: 17.1892 Number of sites scoring better than the average of aligned sites = 690 Number in coding regions = 517 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 2 AGTATAATTCTAAAATTTCTGAAAACA 1 8 1 TTCTAAAATT 0.86554 -86 ATATTTCTTCAATTAAAAATTTTATTGTTT 1 33 0 AATTAAAAAT 0.836613 -61 GTTAAATGAAAACTAAAAGAGTTTTCATAG 2 81 0 AACTAAAAGA 0.923122 -220 GGGCTACAAAATCTGAAAGATTTTGTTTAA 2 126 1 ATCTGAAAGA 0.790961 -175 GTTTAACTTTTTCTAAAAGTTTCGTTTGTA 2 150 1 TTCTAAAAGT 0.910811 -151 AAATATAACAACCTAAAATAAAATAATAAA 2 198 0 ACCTAAAATA 0.773252 -103 TAATCCATAAATCTAAAAAAATAAATATAA 2 220 0 ATCTAAAAAA 0.959848 -81 AATAAATACTATTTAAAAATAGTTAATCCA 2 243 0 ATTTAAAAAT 0.9137 -58 TTAAGTTAAGATTTAAAAAATAAATACTAT 2 261 0 ATTTAAAAAA 0.934424 -40 TTGCAAAAGTCATTAAAATTCATAATGAAA 3 38 0 CATTAAAATT 0.606301 -263 TTTTAAAGAATATTAAAATACTACAAAAAC 3 78 0 TATTAAAATA 0.709011 -223 TTTTAATATTCTTTAAAAAAGCATATAAAA 3 90 1 CTTTAAAAAA 0.865018 -211 TTAAAACGAAATCTAAAAGTATTACATAGC 3 266 0 ATCTAAAAGT 0.95166 -35 TTAGATTTCGTTTTAAAAAAGAGGTGCAAT 3 280 1 TTTTAAAAAA 0.882131 -21 ********** Masking position 6 Map Score: 14.1073 Number of sites scoring better than the average of aligned sites = 1774 Number in coding regions = 1429 Number in noncoding regions = 345 Number of orfs with sites within 600 bp upstream = 276 Fraction of orfs with sites within 600 bp upstream = 0.0443302 Motif number 3 CTTCAATTAAAAATTTTATTGTTTTCAGAA 1 27 0 AAATTTTATT 0.855758 -67 AAGAAATATAATATTTTATTAAGTGTTGTA 1 54 1 ATATTTTATT 0.701317 -40 AAACTAAAAGAGTTTTCATAGCTGGAAAGC 2 72 0 AGTTTTCATA 0.921395 -229 AAACTCTTTTAGTTTTCATTTAACCGAAGC 2 87 1 AGTTTTCATT 0.970562 -214 AAAATCTTTCAGATTTTGTAGCCCGAAGCT 2 120 0 AGATTTTGTA 0.907954 -181 AAAATCTGAAAGATTTTGTTTAACTTTTTC 2 133 1 AGATTTTGTT 0.965211 -168 CTTTTTCTAAAAGTTTCGTTTGTATCCCTC 2 156 1 AAGTTTCGTT 0.744309 -145 ATTTTTAAATAGTATTTATTTTTTAAATCT 2 253 1 AGTATTTATT 0.767248 -48 TTAACTTAACAGTTTTTAATGGTGAATTT 2 282 1 AGTTTTTAAT 0.767258 -19 AAGGCGTTCAAATTTTCATTATGAATTTTA 3 25 1 AATTTTCATT 0.890906 -276 AAAAACTATAGGTTTTTGTAGTATTTTAAT 3 67 1 GGTTTTTGTA 0.668025 -234 TAATACTTTTAGATTTCGTTTTAAAAAAGA 3 272 1 AGATTTCGTT 0.969825 -29 ********** Masking position 5 Map Score: 11.2435 Number of sites scoring better than the average of aligned sites = 806 Number in coding regions = 665 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 4 TAAGAGGCATTGCCGAGCGTAGCG 2 5 1 AGGCATTGCC 0.97882 -296 TCAAAATAGGATGCATTGCCTCGCTACGCT 2 26 0 ATGCATTGCC 0.982169 -275 ATGGAAAGCTACGCTTTCCAGCTATGAAAA 2 60 1 ACGCTTTCCA 0.969469 -241 ACGCCTTCCAAAGGAAGGCG 3 1 1 ACGCCTTCCA 0.988585 -300 GAAAATTTGAACGCCTTCCTTTGGAAGGCG 3 12 0 ACGCCTTCCT 0.98001 -289 ATGAGCAGAAATGCATTTCCTATCCATAGG 3 167 1 ATGCATTTCC 0.952819 -134 ********** Masking position 6 Map Score: 5.32847 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 18 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 GGCATTGCCGAGCGTAGCGAGGCAATGCAT 2 16 1 AGCGTAGCGA 0.988748 -285 ATAGCTGGAAAGCGTAGCTTTCCATTTCAT 2 55 0 AGCGTAGCTT 0.982704 -246 TTTTCATTTAACCGAAGCGTTAGCTTCGGG 2 99 1 ACCGAAGCGT 0.988725 -202 GATTTTGTAGCCCGAAGCTAACGCTTCGGT 2 109 0 CCCGAAGCTA 0.970874 -192 ********** Masking position 6 Map Score: 1.10705 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 4 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 TAATTCTAAAATTTCTGAAAACAATAAAATT 1 15 1 ATTTCTAAAA 0.867578 -79 AAAATATTATATTTCTTCAATTAAAAATTTT 1 40 0 ATTTCTCAAT 0.94559 -54 GATATCACCAAATTAAACTATA 1 82 0 ATATCACAAA 0.903451 -12 GTAGCTTTCCATTTCATCAAAATAGGATGCA 2 41 0 ATTTCACAAA 0.967255 -260 GTTAATCCATAAATCTAAAAAAATAAATATA 2 221 0 AAATCTAAAA 0.648181 -80 AAATTCACCATTAAAAACTGTT 2 289 0 AATTCACATT 0.642202 -12 AGAATATTAAAATACTACAAAAACCTATAGT 3 71 0 AATACTCAAA 0.823612 -230 CTATATAATAATTTCTACTTAGTTTAAGCAG 3 126 0 ATTTCTCTTA 0.867232 -175 TAGGAAATGCATTTCTGCTCATAAGTTTATC 3 158 0 ATTTCTCTCA 0.845898 -143 ****** **** Masking position 1 Map Score: 1.46685 Number of sites scoring better than the average of aligned sites = 1178 Number in coding regions = 1050 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 7 TGTATAGTTTAATTTGGTGATATC 1 80 1 AATTTGGTGA 0.882775 -14 ATAAAATAATAAAATGGTGCCGAGGGAGGG 2 181 0 AAAATGGTGC 0.975185 -120 GACGTCCATTAAGTTGGGGCTTTCAGCCCC 3 219 1 AAGTTGGGGC 0.984345 -82 AATTGGACATTAATTGGGGCTGAAAGCCCC 3 234 0 TAATTGGGGC 0.970221 -67 TCGTTTTAAAAAAGAGGTGCAATT 3 287 1 AAAGAGGTGC 0.946534 -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 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 Motif number 10 ********** 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