AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i054_aful_mthe_100.orf -o054_aful_mthe_100.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 Purged sequences: RAG47711 27 Archaeoglobus_fulgidus RAG47320 27 Archaeoglobus_fulgidus Input sequences: #1 RAG47710 69 Archaeoglobus_fulgidus #2 RAG09686 71 Archaeoglobus_fulgidus #3 RAG48909 68 Archaeoglobus_fulgidus #4 RAG02411 38 Archaeoglobus_fulgidus #5 RAG47340 36 Archaeoglobus_fulgidus #6 RAG02631 207 Archaeoglobus_fulgidus #7 RAG47453 272 Archaeoglobus_fulgidus #8 RAG17481 39 Archaeoglobus_fulgidus #9 RAG46689 78 Archaeoglobus_fulgidus #10 RTH01222 117 M.thermo #11 RTH00669 49 M.thermo #12 RTH02113 36 M.thermo #13 RTH01449 18 M.thermo #14 RTH01769 269 M.thermo #15 RTH00704 49 M.thermo #16 RTH02072 18 M.thermo #17 RTH01577 19 M.thermo #18 RTH00727 24 M.thermo #19 RTH01200 24 M.thermo #20 RTH00115 20 M.thermo #21 RTH01872 170 M.thermo #22 RTH00804 135 M.thermo #23 RTH00893 81 M.thermo #24 RTH00026 64 M.thermo Motif number 1 CTTATACCTTAAAATTTTTTACGGTAACCTTTTTG 1 32 0 AAATTTTAGT 0.883079 -38 TTCTTACCGCAAATGTATTTATGTTTTGGAGATGA 2 20 0 AAATTTTATT 0.959462 -52 AAAATTTTCAGAAAGTTTTTAATTTCACCTTCCGA 3 20 0 GAATTTTATT 0.933358 -49 CAAAAGTTTTTAGCTTGCCGTCATTT 5 2 1 AAATTTTATT 0.959462 -35 AATTTGAAAAGAATTCTTTTAGCTGGTGGGGCTGG 6 97 0 GAACTTTATG 0.8628 -111 AGTAGCCTTGAAAAATCTTTAGATTGGAGCGGACC 7 109 0 AAATTTTATT 0.959462 -164 CTCAGAAAACTCTTTATTTTGCCTCTTAAC 8 6 1 AAATTTTATT 0.959462 -34 GAAAACCCAGGAAGTTTTTTAACTTTTGTTTAATC 9 18 1 GAATTTTATT 0.933358 -61 GGAGAGGTTTAAATCTTTTGAGATTAAACAAAAGT 9 39 0 AAATTTGATT 0.726381 -40 AATTGGCAGCAAAACTTTATATGTGATGAAGCTTT 14 44 1 AAATTATATG 0.892667 -226 AAGTGGGTGAGTACCTTTATATGTTCTCGGTATAT 14 176 0 GTATTATATT 0.627954 -94 AAAGGCACTAAAAGCCTTTCAATTTCAATTTAATA 15 14 1 AAACTTCATT 0.66825 -36 TAAAAGCGTTTATAGGTGTAATCT 18 2 1 AAACTTTAGG 0.772276 -23 GTTGTCCATGAAATACTTATAAATTTTGGTGGCCA 21 40 1 AAACTATATT 0.91427 -131 ACTTCCGGAAAAATCCGTATACCTGCGGCAGGTGG 22 26 1 AAACTATATG 0.863214 -110 CAGGTGGGACATACACTTATAACTTATCCCATATT 22 54 1 ATACTATATT 0.683974 -82 TAAACTGATAATAAATATTTATGTTGAGGTGGTTA 23 12 0 ATATTTTATT 0.827683 -70 GATATCACCAAAAATTTATATGGGGACCTGTATT 23 58 0 AAATTATAGG 0.726328 -24 TTATTTGAAAGTATATATTTTATAGGAAATA 24 44 0 GAATTATATT 0.892667 -21 *** * **** ** Masking position 8 Map Score: 20.4582 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 69 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 2 TCAGACCAGCCCCACCAGCTAAAAGAATTCTTTTC 6 92 1 CCCACCTAAG 0.894735 -116 ACCAATGCCCCCCTACCCTTAAGGGCCCGTGGCTC 7 18 1 CCCTACTAGG 0.802883 -255 CTTAAGTATCCCAACCTGAATCTGGACAC 7 254 1 CCAACCACGG 0.96572 -19 AGATTTAAACCTCTCCGCATGACGGGATTGT 9 58 1 CTCTCCTAGG 0.92751 -21 ACGGTCTCATCCCTCAAACTGAGGGGTAAAGATAT 10 19 1 CCCTCATAGG 0.497478 -99 TGCTCTCTCCCTGCACCTGATTGAGAACT 10 99 0 CTCTCCCCTG 0.897518 -19 TATAAAGGTACTCACCCACTTCATGTTAATCCATA 14 190 1 CTCACCTCTG 0.911901 -80 CATATAATGTCCATCACTGACCCGGTCGTGGCCAC 21 68 0 CCATCAACGG 0.828802 -103 GGTGGGGCCTCCCACCCATATAATGTCCATCACTG 21 84 0 CCCACCAATG 0.965476 -87 GGTGGGAGGCCCCACCATACCCTCGCAGACTATCC 21 103 1 CCCACCCCCG 0.958259 -68 TATATAATGTCCATCACTGACCTGGGTACTCTGGA 21 135 0 CCATCAACGG 0.828662 -36 CTATACCCACCTATATAATGTCCATCACTG 21 151 0 CCCACCAATG 0.965476 -20 AAGTGTATGTCCCACCTGCCGCAGGTATACGGATT 22 37 0 CCCACCCCGG 0.992839 -99 ****** * * ** Masking position 1 Map Score: 10.2675 Number of sites scoring better than the average of aligned sites = 707 Number in coding regions = 665 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 3 CACTTCAATTCGGAAGGTGAAAT 3 2 1 ACTTCAATCG 0.782951 -67 AAAACCTAAACTTTCAAAGCTGGCAGATCTTT 6 15 0 CTTTCAAGCG 0.948237 -193 AGAGTGCAGAACATCAACGCTGCCGACACGGA 6 152 1 ACATCAAGCG 0.967092 -56 GGCCGTCGCTCTATCCATGCTGAGCCACGGGC 7 42 0 CTATCCAGCG 0.966449 -231 AGAGCGACGGCCTTCTAAGCCGTAGATCGCGG 7 62 1 CCTTCTAGCG 0.958248 -211 ATTGCCTGAGCCATCCACGCCGATTTTGGGAA 7 175 1 CCATCCAGCG 0.99321 -98 ACACTTGCCTCCAGCAATGCGGTCTGATAATC 7 222 1 CCAGCAAGCG 0.986477 -51 AGGGATGAGACCGTCCCGGCAG 10 1 0 CCGTCCCGCG 0.925886 -117 CGGAAGTGGGCCAGCAATTCAG 22 1 0 CCAGCAATCG 0.934917 -135 ******* ** * Masking position 5 Map Score: 7.45188 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 302 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 TTTTTAATTTCACCTTCCGAATTGAAGTG 3 10 0 CACCTTCCGA 0.880804 -59 CAAGTGTTAAAAACTGCCTGGATTCCCAAA 7 199 0 AAACTGCCTG 0.789275 -74 CAGTTTTTAACACTTGCCTCCAGCAATGCG 7 213 1 CACTTGCCTC 0.880366 -60 TGCCTCTTAACCTTTTCCTC 8 30 1 CCTTTTCCTC 0.573458 -10 AAAAGTTAAAAAACTTCCTGGGTTTTCAGA 9 15 0 AAACTTCCTG 0.800202 -64 AAAAACACCTTCAGCCAG 13 4 0 CACCTTCAGC 0.92207 -15 CTCTCATCTGCATCCATTATTCCT 14 5 1 CATCTGCATC 0.763465 -265 AGGTACTCACCCACTTCATGTTAATCCATA 14 195 1 CCACTTCATG 0.80132 -75 TGGTAAACACCTTCCTGA 16 2 0 CACCTTCCTG 0.980797 -17 AATTGCTGGCCCACTTCCGGAAAAATCCGT 22 14 1 CCACTTCCGG 0.938375 -122 GTGTATGTCCCACCTGCCGCAGGTATACGG 22 40 0 CACCTGCCGC 0.978104 -96 ********** Masking position 5 Map Score: 5.01161 Number of sites scoring better than the average of aligned sites = 1535 Number in coding regions = 1462 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 5 AAGATATTAACTCATATAATACATATTACA 10 47 1 CTCATATAAT 0.76594 -71 TTCAATTCCCCTTAATATTATCTTGAAG 11 32 0 CCCTTAATAT 0.735473 -18 TCTCCCGTAAAAAAAGTTCGCTG 12 24 0 CCCGTAAAAA 0.896564 -13 AAAGCTTCATCACATATAAAGTTTTGCTGC 14 49 0 CACATATAAA 0.79548 -221 TAAATCACCTTTATTAAATTGAAATTG 15 33 0 CCTTTATTAA 0.752933 -17 GGGCCTCCCACCCATATAATGTCCATCACT 21 85 0 CCCATATAAT 0.974 -86 CTATACCCACCTATATAATGTCCATCACT 21 152 0 CCTATATAAT 0.932239 -19 TATAACTTATCCCATATTAATATCTATAGT 22 71 1 CCCATATTAA 0.963301 -65 TATATGGGGACCTGTATTAATGTTGAACCT 23 46 0 CCTGTATTAA 0.824989 -36 AATACAGGTCCCCATATAAATTTTTGGTGA 23 58 1 CCCATATAAA 0.97803 -24 TGACATATTTCCTATAAAATATATACTTTC 24 39 1 CCTATAAAAT 0.845731 -26 ********** Masking position 6 Map Score: 7.76638 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 61 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 CATCAACGCTGCCGACACGGAAAAAGCTTA 6 163 1 GCCGACACGG 0.978658 -45 TTAGATTGGAGCGGACCCGGCGGGATTTGA 7 96 0 GCGGACCCGG 0.991201 -177 GAGGGATGAGACCGTCCCGGCAG 10 4 0 ACCGTCCCGG 0.97893 -114 CGTCTTACTGGATGATCCGGGATAATTCAG 14 107 1 GATGATCCGG 0.8679 -163 AATGTCCATCACTGACCCGGTCGTGGCCAC 21 68 0 ACTGACCCGG 0.99421 -103 AATGTCCATCACTGACCTGGGTACTCTGGA 21 135 0 ACTGACCTGG 0.964295 -36 ********** Masking position 4 Map Score: 4.99159 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 31 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 AAAAAATTTTAAGGTATAAGTTAATTAATT 1 47 1 AAGGTATAAG 0.81945 -23 ATTCAAAATGAAGGGAAAAGGGGGTAGC 4 21 1 AAGGGAAAAG 0.933177 -18 TCGTCCTGTCTAGGGAAAAGTAAAAAAAGA 6 47 0 TAGGGAAAAG 0.687641 -161 ATCTTAGAGAAAGGAATCAGACCAGCCCCA 6 76 1 AAGGAATCAG 0.893509 -132 CGCTGCCGACACGGAAAAAGCTTAAAAGAT 6 169 1 ACGGAAAAAG 0.91403 -39 TTAAAAAGGGAAGGAATAATGGATGCAGAT 14 16 0 AAGGAATAAT 0.919963 -254 CCAGGAAAACAAGGATTAATAGAAATTAAA 14 76 0 AAGGATTAAT 0.593573 -194 ACTGGATGATCCGGGATAATTCAGAATACG 14 113 1 CCGGGATAAT 0.815384 -157 TGGCCCACTTCCGGAAAAATCCGTATACCT 22 20 1 CCGGAAAAAT 0.706193 -116 AGATATTAATATGGGATAAGTTATAAGTGT 22 66 0 ATGGGATAAG 0.896596 -70 CTTATAAATGGAATCATTCTGATACGC 22 119 0 ATGGAATCAT 0.617568 -17 ********** Masking position 9 Map Score: 2.66617 Number of sites scoring better than the average of aligned sites = 384 Number in coding regions = 348 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 8 AATTAAAGATCTGCCAGCTTTGAA 6 1 1 ATTAAAGTCC 0.966172 -207 CAGCTTTGAAAGTTTAGGTTTTTCTTTTTTTACT 6 25 1 ATTTAGGTTC 0.92019 -183 AGGTTGGGATACTTAAGGATTATCAGACCGCATT 7 237 0 ATTAAGGTTC 0.978932 -36 ATCTCAAAAGATTTAAACCTCTCCGCATGACGGG 9 50 1 ATTAAACTCC 0.769342 -29 AAAGAAATCTATTTAAGGATACTTCAAGATAATA 11 11 1 ATTAAGGTAT 0.72378 -39 GCTTCATCACATATAAAGTTTTGCTGCCAATTAA 14 42 0 AATAAAGTTC 0.895741 -228 GATTAATAGAAATTAAAGCTTCATCACATATAAA 14 59 0 ATTAAAGTTT 0.842136 -211 TACCGAGAACATATAAAGGTACTCACCCACTTCA 14 179 1 AATAAAGTAC 0.75876 -91 CAATAATCCAAGTTATGGATTAACATGAAGTGGG 14 204 0 ATTATGGTTC 0.855162 -66 CCCCATGGACAGTTAAAGGTTGTCCATGAAATAC 21 22 1 ATTAAAGTTC 0.971931 -149 ATTTATTATCAGTTTAGGTTCAACATTAATACAG 23 31 1 ATTTAGGTCC 0.904854 -51 * ****** ** * Masking position 1 Map Score: 5.5236 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 98 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 9 TTAAAATTTTCAGAAAGTTTTTAATTTCACC 3 26 0 CAGAAAGTTT 0.870698 -43 AAGCAATCAACCGCAATCTTTTAAGCTTTTT 6 183 0 CCGCAATTTT 0.862128 -25 TCTGAAAACCCAGGAAGTTTTTTAACTTTTG 9 15 1 CAGGAAGTTT 0.908929 -64 GAGACGACCCCAGCGAACTTTTTTTACGGGA 12 14 1 CAGCGAATTT 0.921055 -23 TTTTAATTGGCAGCAAAACTTTATATGTGAT 14 40 1 CAGCAAACTT 0.929889 -230 AATCTGTATCCAGCAAGTTTTATATACCGAG 14 155 1 CAGCAAGTTT 0.983687 -115 TGGTCATAGACACCAATTTTTT 19 13 1 CACCAATTTT 0.932398 -12 CGGTCGTGGCCACCAAAATTTATAAGTATTT 21 50 0 CACCAAATTT 0.962595 -121 GATATCACCAAAAATTTATATGGGGA 23 66 0 CACCAAAATT 0.821801 -16 ******* *** Masking position 6 Map Score: 4.45744 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 171 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 10 GCACTCAGTTTGTGCAGAGGTT 2 60 0 GCATCATTTG 0.974554 -12 ACCCCCTTTTCCCTTCATTTTGAATAATATAA 4 14 0 CCCTCATTTG 0.9834 -25 TTTTTAGCTTGCCGTCATTTTTCTTCTGTA 5 17 1 GCCTCATTTT 0.946047 -20 TGCTAGTAACGGCATCAATTTGAAAAGAATTC 6 116 0 GGCTCATTTG 0.9834 -92 AATATCTTTACCCCTCAGTTTGAGGGATGAGA 10 23 0 CCCTCATTTG 0.9834 -95 CTTATAAATGGAATCATTCTGATACGCTCAT 22 115 0 GGATCATCTG 0.879801 -21 *** *** **** Masking position 7 Map Score: 2.32989 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 33 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 11 ATCCATGCTGAGCCACGGGCCCTTAAGGGT 7 32 0 AGCCACGGGC 0.954982 -241 GCATGGATAGAGCGACGGCCTTCTAAGCCG 7 54 1 AGCGACGGCC 0.986335 -219 GATTTTTCAAGGCTACTACCATTCAGCAGC 7 127 1 GGCTACTACC 0.917104 -146 TGGGAGACGACCCCAGCGAACT 12 3 1 GGAGACGACC 0.967886 -34 AAATTTTGGTGGCCACGACCGGGTCAGTGA 21 60 1 GGCCACGACC 0.977835 -111 ********** Masking position 5 Map Score: 0.441671 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 44 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 12 ********** No masking Map Score: 3.36387e-13 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: 3.36387e-13 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 14 ********** No masking Map Score: 3.36387e-13 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