AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i067_2_1_1_13_aful_reg_300.orf -o067_aful_300.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RAG29671 300 Archaeoglobus_fulgidus #2 RAG49483 266 Archaeoglobus_fulgidus #3 RAG49462 38 Archaeoglobus_fulgidus #4 RAG29645 104 Archaeoglobus_fulgidus Motif number 1 GTCTCGCTTTCAATCCCATTT 1 1 0 CATCCCATTT 0.977602 -300 AATCCCATTTTGGTCTGATTTCAACCCGTCA 1 58 0 TGTCTGATTT 0.987517 -243 GTCTGCCTTTCAATCCCATTTTGGTCTGATT 1 69 0 CATCCCATTT 0.977602 -232 GTAGTGTACGTCGTCTGCCTTTCAATCCCAT 1 81 0 TGTCTGCCTT 0.912053 -220 AATCCCATTTTGGTCTGATTTCAACTGTTCC 1 126 0 TGTCTGATTT 0.987517 -175 TTCTTACTTTCAATCCCATTTTGGTCTGATT 1 137 0 CATCCCATTT 0.977602 -164 AATCCCATTTTGGTCTGATTTCAACTTGGGA 1 199 0 TGTCTGATTT 0.987517 -102 CATTGCCTTTCAATCCCATTTTGGTCTGATT 1 210 0 CATCCCATTT 0.977602 -91 AATCCCACTTTAGTCTGATTTCAAAAAACGC 2 69 0 TGTCTGATTT 0.982264 -198 TAAATTTACGTAATCCCACTTTAGTCTGATT 2 80 0 TATCCCACTT 0.97239 -187 TTTTGTTTCCTTGTCACACTTTCCACAAATA 2 109 0 TGTCACACTT 0.910254 -158 AAACTCTCGTCGGTCTGAGTTTTGTTTCCTT 2 128 0 CGTCTGAGTT 0.950068 -139 CATAACAAAATTATCTGACTTTTGATTAAAA 4 24 0 TATCTGACTT 0.972222 -81 * ********* Masking position 4 Map Score: 28.7473 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 69 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 2 TGTTAATGTCTCGCTTTCAATCCCATTT 1 9 0 TCGCTTTCAA 0.973942 -292 CCATTTTGGTCTGATTTCAACCCGTCAGGA 1 55 0 CTGATTTCAA 0.987051 -246 GTACGTCGTCTGCCTTTCAATCCCATTTTG 1 77 0 TGCCTTTCAA 0.966846 -224 CCATTTTGGTCTGATTTCAACTGTTCCTTG 1 123 0 CTGATTTCAA 0.987051 -178 TGAGATGTTCTTACTTTCAATCCCATTTTG 1 145 0 TTACTTTCAA 0.94072 -156 CCATTTTGGTCTGATTTCAACTTGGGAGCT 1 196 0 CTGATTTCAA 0.987051 -105 AAGTCGCCATTGCCTTTCAATCCCATTTTG 1 218 0 TGCCTTTCAA 0.966846 -83 CCACTTTAGTCTGATTTCAAAAAACGCCGG 2 66 0 CTGATTTCAA 0.987051 -201 ********** Masking position 9 Map Score: 15.3626 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 142 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 3 GCCTTTCAATCCCATTTTGGTCTGATTTCA 1 66 0 CCCATTTTGG 0.991235 -235 TACTTTCAATCCCATTTTGGTCTGATTTCA 1 134 0 CCCATTTTGG 0.991235 -167 GCCTTTCAATCCCATTTTGGTCTGATTTCA 1 207 0 CCCATTTTGG 0.991235 -94 AAAGGCAATGGCGACTTTTGCATAGGTGGC 1 231 1 GCGACTTTTG 0.977101 -70 GTTTTTGCCGGCGTTTTTTGAAATCAGACT 2 59 1 GCGTTTTTTG 0.863617 -208 TTTACGTAATCCCACTTTAGTCTGATTTCA 2 77 0 CCCACTTTAG 0.973323 -190 TCTCGTCGGTCTGAGTTTTGTTTCCTTGTC 2 125 0 CTGAGTTTTG 0.911428 -142 ACAAAATTATCTGACTTTTGATTAAAATAA 4 21 0 CTGACTTTTG 0.965014 -84 ********** Masking position 6 Map Score: 11.2614 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 136 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 GCGAGACATTAACACAATTTATTGGGCATG 1 25 1 AACACAATTT 0.957013 -276 TACCGAGTCCAACACAAGTTTATGAGATGT 1 167 0 AACACAAGTT 0.920305 -134 TGGCAAGAGGAAAAAGATTTTCTAATTTTT 1 266 1 AAAAAGATTT 0.868803 -35 CTACATTCATAAAAAAATTAGAAAATCTTT 1 278 0 AAAAAAATTA 0.932113 -23 GGAAAAGTAAAAAACAATTGCTGCGATAAT 2 28 1 AAAACAATTG 0.927115 -239 AACGCCGGCAAAAACGATTATCGCAGCAAT 2 44 0 AAAACGATTA 0.885781 -223 CACTTTCCACAAATAAATTTACGTAATCCC 2 94 0 AAATAAATTT 0.865785 -173 GTAAAAAATTTTTGACAATCCT 3 27 0 AAAAAATTTT 0.780427 -12 CCAAATCAAGTTATTTTAATCA 4 3 1 AAATCAAGTT 0.74886 -102 ATCAGTTCATAACAAAATTATCTGACTTTT 4 32 0 AACAAAATTA 0.907259 -73 ********** Masking position 2 Map Score: 8.5191 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 99 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 5 ACCCGTCAGGACATGCCCAATAAATTGTGT 1 36 0 ACATGCCCAA 0.929524 -265 TGTTCCTTGACAACGCCCCAGTAGTGTACG 1 102 0 CAACGCCCCA 0.979155 -199 CGAGAGTTTAAAACCGCCTAAAGCTCTTCT 2 150 1 AAACCGCCTA 0.958468 -117 TCCAGCAAATCCACCACCAAATTTATTCAT 2 179 1 CCACCACCAA 0.957664 -88 AAAAATCCCCAAACGCCCAAACCTTAAATA 2 225 1 AAACGCCCAA 0.988263 -42 CTTAAATACCAAACCGCCCATCGAGAACCA 2 247 1 AAACCGCCCA 0.984362 -20 CTAAACACCTCCAAATTAGAAAAT 4 91 0 ACACCTCCAA 0.971111 -14 ********** Masking position 3 Map Score: 5.92932 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 162 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 ATTGAAAGTAAGAACATCTCATAAACTTGT 1 154 1 AGAACATCTC 0.976093 -147 TAAAAAAATTAGAAAATCTTTTTCCTCTTG 1 269 0 AGAAAATCTT 0.983217 -32 GATTTGCTGGAGAAGAGCTTTAGGCGGTTT 2 160 0 AGAAGAGCTT 0.981538 -107 ATCAGAAAATCTTATAAGGATTG 3 4 1 AGAAAATCTT 0.983217 -35 GAACTGATTCATAACAGCTTTTATCTTTAG 4 54 1 ATAACAGCTT 0.949363 -51 ********** Masking position 6 Map Score: 4.19754 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 82 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 ACATTAACACAATTTATTGGGCATGTCCTG 1 30 1 AATTTATTGG 0.967984 -271 GGATTACGTAAATTTATTTGTGGAAAGTGT 2 95 1 AATTTATTTG 0.852802 -172 TTTGGTGGTGGATTTGCTGGAGAAGAGCTT 2 170 0 GATTTGCTGG 0.962677 -97 TTAATGAATAAATTTGGTGGTGGATTTGCT 2 182 0 AATTTGGTGG 0.990599 -85 CCTATTTTCTAATTTGGAGGTGTTTAG 4 88 1 AATTTGGAGG 0.969722 -17 ********** Masking position 5 Map Score: 2.00162 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 58 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 ********** No masking Map Score: 1.77168e-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: 1.77168e-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: 1.77168e-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