AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i216_Ribosomal_Operon_3_pyro_reg_300.orf -o216_pyro_300.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 = 0.42 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RPH01519 185 Pyrococcus_OT3 #2 RPH01554 37 Pyrococcus_OT3 #3 RPH01557 59 Pyrococcus_OT3 #4 RPH01559 70 Pyrococcus_OT3 #5 RPH01560 55 Pyrococcus_OT3 #6 RPH01561 233 Pyrococcus_OT3 #7 RPH01563 186 Pyrococcus_OT3 #8 RPH01564 300 Pyrococcus_OT3 Motif number 1 TTAACTTAAATTTAAACCTTGTGCATTTTTGGG 1 36 1 TTTAAATTTG 0.966703 -150 GGGCAATCCTTTTAGACGTTTTGAAAACTCACA 1 66 1 TTTAGATTTG 0.84541 -120 AATACTTCCTTAAAAAGGTTATGTAACTGAACA 1 137 0 TAAAAATTTG 0.957215 -49 CTTTATAAGATATTAAATTTTTGTAAAAAGGAA 3 13 0 TATTAATTTG 0.957257 -47 TTCCAGGAATTATAAATCTTTTGCGGAGAAATA 4 29 0 TATAAATTTG 0.960503 -42 TTTCTTTCTTTTTTAGTATTATTTTTAAGTAGA 5 13 1 TTTTAGTTTT 0.532992 -43 GCGGAAAAACTATATAAATTTTTCGGATTTCTC 6 173 0 TATATATTTT 0.639926 -61 ATCAAAATAATATAAAGTTTTTGATAAA 7 6 0 TATAAATTTG 0.955601 -181 GAAAGGAGGATTATTAGGTTTTGCTCTCTTCCT 7 67 1 TTATTATTTG 0.903789 -120 ATCCAAGGCCTAATAATGTTAAGCCTACTAATC 7 120 0 TAATAATTAG 0.644069 -67 TTAAAAAGGCTTATTAAATTATGAGAAGAGGCA 8 11 0 TTATTATTTG 0.903789 -290 TTAATAAGCCTTTTTAAGTTCTGTTTTTGGTTT 8 27 1 TTTTTATTTG 0.914375 -274 ATCATGGAGATTAAAACCTTATTACTTACATCA 8 233 1 TTAAAATTTT 0.809411 -68 ATAATTTTCTTTAAAGGGTTTTGATGTAAGTAA 8 254 0 TTAAAGTTTG 0.872724 -47 GAAAATTATGTAATAACCTTTTGGTGATGCACG 8 278 1 TAATAATTTG 0.95181 -23 ****** ** ** Masking position 9 Map Score: 13.6503 Number of sites scoring better than the average of aligned sites = 321 Number in coding regions = 199 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 2 AAAAGGATTGCCCAAAAATGCACAAGGTTT 1 49 0 CCCAAAAATG 0.926147 -137 TTAATACTTCCTTAAAAAGGTTATGTAACT 1 142 0 CTTAAAAAGG 0.983914 -44 AATTTAATATCTTATAAAGGTAATAAAAAC 3 27 1 CTTATAAAGG 0.906994 -33 AAAAATAATACTAAAAAAGAAAGAAACA 5 9 0 CTAAAAAAGA 0.838931 -47 TGGAAATCTACTTAAAAATAATACTAAAAA 5 22 0 CTTAAAAATA 0.878664 -34 GAGATTATGGCCAAATAAGGATTCAATGAA 6 132 0 CCAAATAAGG 0.937495 -102 GAGAGCAAAACCTAATAATCCTCCTTTCCT 7 65 0 CCTAATAATC 0.804293 -122 GAATCCAAGGCCTAATAATGTTAAGCCTAC 7 125 0 CCTAATAATG 0.953312 -62 AAAAACAGAACTTAAAAAGGCTTATTAAAT 8 25 0 CTTAAAAAGG 0.983914 -276 ********** Masking position 4 Map Score: 7.06249 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 218 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 3 TTAGACGTTTTGAAAACTCACAGAGGATAAAACT 1 77 1 TAAAACTCGA 0.979524 -109 CTCACAGAGGATAAAACTCCACAATTTCTTGAAT 1 93 1 AAAAACTCAA 0.920126 -93 GTTATGTAACTGAACATTCGACAATAATTCAAGA 1 119 0 TAACATTCAA 0.825312 -67 ATAAAGGTAATAAAAACTCTGGGAGTTACT 3 40 1 TAAAACTCGA 0.979524 -20 GTTGAAATTTCTTCAAGCTATTTCTC 4 3 1 TAAATTTCAA 0.931221 -68 CGCAAAAGATTTATAATTCCTGGAACTATCAACT 4 37 1 TATAATTCGA 0.880759 -34 CTCCAATTATTTATAATTCATTGAATCCTTATTT 6 116 1 TATAATTCGA 0.880759 -118 ACATAGATGGTGAAAACTAAGGAATCCAAGGCCT 7 142 0 TAAAACTAAA 0.820521 -45 TTAAGTTGTTACAAATTTCGTTGAACTTTATCCC 8 65 1 AAAATTTCGA 0.828052 -236 CTCCCATTCCTCAAATTTCAAAAATGAGTATGGA 8 125 1 TAAATTTCAA 0.931221 -176 AAATATATGCTCAAAATTCCATACTCATTTTTGA 8 142 0 TAAAATTCAC 0.825312 -159 GTAATAAGGTTTTAATCTCCATGATTAAACAACA 8 224 0 TTAATCTCGA 0.663104 -77 ATTACTTACATCAAAACCCTTTAAAGAAAATTAT 8 253 1 TAAAACCCAA 0.85166 -48 AACCCTTTAAAGAAAATTATGTAATAACCTTTTG 8 267 1 AAAAATTAAA 0.524012 -34 * ******* ** Masking position 3 Map Score: 9.40465 Number of sites scoring better than the average of aligned sites = 416 Number in coding regions = 349 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 4 ACTCCACAATTTCTTGAATTATTGTCGAATGTT 1 108 1 TTCTTGATTT 0.929745 -78 TTTCTTTCTTTTTTAGTATTATTTTTAAGTAGA 5 13 1 TTTTAGATTT 0.838004 -43 AATGGAAGAATTTGCCAATTTATGGTC 6 5 0 TTTGCCATTT 0.895803 -229 AATTGGCAAATTCTTCCATTTCTCTTCTTACCT 6 18 1 TTCTTCATTT 0.962518 -216 CATGCTCAAATACTCCAATTATTTATAATTCAT 6 104 1 TACTCCATTT 0.936867 -130 CTATATAAATTTTTCGGATTTCTCATGCCTGCA 6 164 0 TTTTCGATTT 0.949907 -70 TTATTTTGATTTCTACTATTACTGGTGTTAGTA 7 29 1 TTCTACATTT 0.962518 -158 CTCTTCCTACTTGTCCTATTTATAGTTGGATTA 7 92 1 TTGTCCATTT 0.955721 -95 CCAAACAATCTTCTCCCATTCCTCAAATTTCAA 8 113 1 TTCTCCATTT 0.989489 -188 ****** *** * Masking position 8 Map Score: 7.27843 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 129 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 TAAGAATCACCATGCTAATATTTGC 1 6 1 ATCACCATGC 0.954465 -180 CAGAGGATAAAACTCCACAATTTCTTGAAT 1 97 1 AACTCCACAA 0.838294 -89 TGGAACTATCAACTCCACGTCAAA 4 57 1 AACTCCACGT 0.940538 -14 TTTTAAGTAGATTTCCATGAGCTATTCTTC 5 35 1 ATTTCCATGA 0.93625 -21 TTTGGCCATAATCTCTATGCAGGCATGAGA 6 147 1 ATCTCTATGC 0.918532 -87 GTTGAACTTTATCCCCATGTTTAATGATTC 8 84 1 ATCCCCATGT 0.932379 -217 ATATGCTCAAAATTCCATACTCATTTTTGA 8 142 0 AATTCCATAC 0.767037 -159 TAAGGTTTTAATCTCCATGATTAAACAACA 8 224 0 ATCTCCATGA 0.984665 -77 ********** Masking position 7 Map Score: 3.54373 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 282 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 CGACAATAATTCAAGAAATTGTGGAGTTTT 1 105 0 TCAAGAAATT 0.799912 -81 ACCTTTTTAAGGAAGTATTAAGGCAACCAA 1 151 1 GGAAGTATTA 0.848685 -35 AGAAATAGCTTGAAGAAATTTCAAC 4 6 0 TGAAGAAATT 0.954118 -65 AAATCTTTTGCGGAGAAATAGCTTGAAGAA 4 19 0 CGGAGAAATA 0.872449 -52 GAAGAGAAATGGAAGAATTTGCCAATTTAT 6 15 0 GGAAGAATTT 0.929443 -219 TATAAATAATTGGAGTATTTGAGCATGTTC 6 101 0 TGGAGTATTT 0.736636 -133 ATTTCTTAGCTGAAGAAATATATGCTCAAA 8 161 0 TGAAGAAATA 0.944068 -140 ATTTCTTCAGCTAAGAAATTAATTTTACAC 8 172 1 CTAAGAAATT 0.797703 -129 GGGTTTTGATGTAAGTAATAAGGTTTTAAT 8 242 0 GTAAGTAATA 0.709772 -59 ********** Masking position 4 Map Score: 2.38338 Number of sites scoring better than the average of aligned sites = 517 Number in coding regions = 477 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 AACCTTTTTAAGGAAGTATTAAGGCAACCA 1 150 1 AGGAAGTATT 0.786945 -36 GGGTCTTAAAGTAAGATTAACTTGAAGGT 2 10 1 AGTAAGATTA 0.804164 -28 AAAGACTGATAGGAGGTGTTGGTA 6 220 1 AGGAGGTGTT 0.967549 -14 TAATGAGGAAAGGAGGATTATTAGGTTTTG 7 60 1 AGGAGGATTA 0.972947 -127 TAGTTGGATTAGTAGGCTTAACATTATTAG 7 114 1 AGTAGGCTTA 0.910827 -73 AGAACCCAACAGGAGGTGTAAAATTAATTT 8 187 0 AGGAGGTGTA 0.982342 -114 ********** Masking position 4 Map Score: 0.727073 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 258 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 ********** No masking Map Score: -3.14527e-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: -3.14527e-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 ATTTAAACCTTGTGCATTTTTGGGCAATCCT 1 45 1 TGTGCTTTTT 0.654125 -141 TTTTCCTTTTTACAAAAATTT 3 1 1 TTTTCTTTTT 0.882123 -59 TGTTTCTTTCTTTTTTAGTAT 5 1 1 TGTTTTTTCT 0.872128 -55 TATTTGAGCATGTTCTTTATTGTAAAGGTTC 6 85 0 TGTTCTTATT 0.713612 -149 CCTATCAGTCTTTTCATTTCAAAATGGGCGG 6 202 0 TTTTCTTTCA 0.771163 -32 CTTTATATTATTTTGATTTCTACTATTACTG 7 22 1 TTTTGTTTCT 0.97046 -165 GATTATTAGGTTTTGCTCTCTTCCTACTTGT 7 75 1 TTTTGTCTCT 0.860854 -112 TAATAAGCCTTTTTAAGTTCTGTTTTTGGTT 8 28 1 TTTTAGTTCT 0.661082 -273 TAAGTTCTGTTTTTGGTTTCTCATTTAAGTT 8 41 1 TTTTGTTTCT 0.97046 -260 TTACACCTCCTGTTGGGTTCTACAAGAATGT 8 196 1 TGTTGGTTCT 0.944198 -105 TCTACAAGAATGTTGTTTAATCATGGAGATT 8 214 1 TGTTGTTAAT 0.54986 -87 ***** ***** Masking position 3 Map Score: 2.32891 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 346 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 11 ********** No masking Map Score: -3.14527e-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 12 ********** No masking Map Score: -3.14527e-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 13 ********** No masking Map Score: -3.14527e-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