AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i183_aful_mthe_300.orf -o183_aful_mthe_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 RAG49239 61 Archaeoglobus_fulgidus #2 RAG50184 33 Archaeoglobus_fulgidus #3 RAG50182 111 Archaeoglobus_fulgidus #4 RAG05245 60 Archaeoglobus_fulgidus #5 RAG05244 121 Archaeoglobus_fulgidus #6 RAG05258 41 Archaeoglobus_fulgidus #7 RAG05274 111 Archaeoglobus_fulgidus #8 RAG36611 300 Archaeoglobus_fulgidus #9 RTH02079 84 M.thermo #10 RTH01298 50 M.thermo Motif number 1 CTGATTGTGCAAAAAAATTGAAAA 1 1 0 AAAAATTAAA 0.789643 -61 ATCAGTGAGCAAAAGTTCTTAATCCTTGACGCAA 1 30 1 AAATTCTAAC 0.783673 -32 AATGTTATATATAATATTTGAAAATAAAATCAGA 3 41 0 AAAATTTAAA 0.972432 -71 AATATTATATATAACATTTCGACCAATATTCCTT 3 57 1 AAAATTTGAC 0.947769 -55 CTACTGCGTGAGAATATTTAAAGAATTCGAAGAA 4 30 0 AAAATTTAAA 0.972432 -31 TGTTATTATTACAATATTTCGAAATTCGTGAATA 5 51 0 AAAATTTGAA 0.946829 -71 AAAACCAAAGCTTTTTAATCATAAAGTTTA 6 7 1 AAGTTTTAAC 0.944026 -35 CAAGTTTAAAAACGCTTTTCAAAAGGTTGCCTTA 7 72 0 ACGTTTTAAA 0.72303 -40 CGAGCCTTAGATAGAATTTGAGGCTTTTGTTTGT 8 39 1 AAGATTTAGC 0.819203 -262 AGATAACTTCAAAGGATTTTGAAAGCATGAGCAA 8 117 0 AAGATTTGAA 0.928957 -184 TGCAAGCTGGAAAATTTTTAAAGATTGAAGTGAT 8 227 0 AAATTTTAAA 0.957519 -74 TGCAAAAATAAAAAGATTTAAATCGCTTCTACCA 8 257 1 AAAATTTAAC 0.972933 -44 GAGTAATAAAATAATTTTTGATTAGTGTTTATCT 9 43 1 AAATTTTATA 0.723048 -42 * ** **** ** * Masking position 1 Map Score: 10.8263 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 114 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 2 TTACTTTCCTCATAAAAAATTAAATT 2 18 0 TCCTCATAAA 0.973336 -16 TCCTCCTTAATTTTTACCCT 3 1 1 TCCTCCTTAA 0.974645 -111 AAAAAGCAGATACGCCTCAAAATGCGATGA 5 16 0 TACGCCTCAA 0.911501 -106 CAAAGCTTTTTAATCATAAAGTTTAGGAGG 6 16 1 TAATCATAAA 0.858944 -26 CCTTCTCCTCCTAAACTTTATGATT 6 27 0 TCCTCCTAAA 0.986249 -15 AGAGAAAGCTCATCCTCAAGCCTCACTCC 8 10 1 TCATCCTCAA 0.965969 -291 ATTATCACGTTACTCAACAAACAAAAGCCT 8 59 0 TACTCAACAA 0.876394 -242 ATTTTATTACTCCTACTTAAAATATACTCC 9 25 0 TCCTACTTAA 0.790285 -60 AGATAAACACTAATCAAAAATTATTTTATT 9 47 0 TAATCAAAAA 0.658035 -38 ********** Masking position 9 Map Score: 7.18981 Number of sites scoring better than the average of aligned sites = 1507 Number in coding regions = 1412 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 3 AATTTTTACCCTGATTTTGGCTTCTGATTTTAT 3 19 1 CTGATTTCTT 0.925654 -93 ATTTTGGCTTCTGATTTTATTTTCAAATATTAT 3 32 1 CTGATTTTTT 0.983526 -80 TGAGGCGTATCTGCTTTTTTTATTTATTCACGA 5 27 1 CTGCTTTTAT 0.783179 -95 AAGATGAATTATCTTTAGCTATATTT 5 106 0 ATGAATTTTT 0.79991 -16 TTTAATATAGCGTAATTACTTTTAAGGGAGTTG 7 12 0 CGTAATTTTT 0.794235 -100 AGCCGGATTTCGATTTCAAGTTTAAA 7 96 0 CGGATTTTTT 0.984775 -16 TGTAATAAACCGGAATTTCGTTAAGAGGCTGAT 8 187 0 CGGAATTTTA 0.924705 -114 AAAGATTGAAGTGATTTAACTTTGTAATAAACC 8 209 0 GTGATTTTTT 0.896637 -92 ACTATCACCTGCTTTTTGTTTGGTAGAAGCG 8 280 0 CTGCTTTTTT 0.962506 -21 TACCGTGACCCGGAATTATTTTACTCA 10 5 0 CGGAATTTTA 0.924705 -46 ******* *** Masking position 7 Map Score: 6.84147 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 140 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 TGTTATATATAATATTTGAAAATAAAATCAGA 3 41 0 AATATTTAAA 0.930496 -71 TATTATATATAACATTTCGACCAATATTCCTT 3 59 1 AACATTTGAC 0.937789 -53 ACTGCGTGAGAATATTTAAAGAATTCGAAGAA 4 30 0 AATATTTAAA 0.930496 -31 TTATTATTACAATATTTCGAAATTCGTGAATA 5 51 0 AATATTTGAA 0.926036 -71 GAGTAGAGGAAATCTATAAATATAGCTAAAGA 5 89 1 AATCTATAAA 0.648001 -33 AAAACCAAAGCTTTTTAATCATAAAGTTTA 6 9 1 AGCTTTTAAC 0.676994 -33 GTTATAAGGCAACCTTTTGAAAAGCGTTTTTA 7 68 1 AACCTTTGAA 0.945839 -44 TCTCACCGCAAGCCTTTCAACCTTGCTCATGC 8 95 1 AGCCTTTAAC 0.916231 -206 ATAACTTCAAAGGATTTTGAAAGCATGAGCAA 8 117 0 AGGATTTGAA 0.84068 -184 AAATCACTTCAATCTTTAAAAATTTTCCAGCT 8 225 1 AATCTTTAAA 0.935501 -76 CAAAAATAAAAAGATTTAAATCGCTTCTACCA 8 259 1 AAGATTTAAC 0.893898 -42 ******* ** * Masking position 10 Map Score: 6.19972 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 180 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 5 TTTTCAATTTTTTTGCACAATC 1 3 1 TTCAATTTTT 0.944442 -59 GCTCTCAAATTTAATTTTTTATGAGGAAA 2 10 1 TTTAATTTTT 0.724511 -24 TTACGCTATATTAAAGCTTTTAGCTAATGA 7 30 1 TTAAAGCTTT 0.934755 -82 GGATTTCGATTTCAAGTTTAAAAACGCTTT 7 88 0 TTCAAGTTTA 0.835107 -24 CCGCAAGCCTTTCAACCTTGCTCATGCTTT 8 100 1 TTCAACCTTG 0.929496 -201 GTTAAATCACTTCAATCTTTAAAAATTTTC 8 222 1 TTCAATCTTT 0.977523 -79 TTTAAAAATTTTCCAGCTTGCAAAAATAAA 8 239 1 TTCCAGCTTG 0.903723 -62 TAGAAGCGATTTAAATCTTTTTATTTTTGC 8 258 0 TTAAATCTTT 0.922262 -43 ********** Masking position 5 Map Score: 4.3586 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 217 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 6 ACCCTGATTTTGGCTTCTGATTTTATTTTC 3 26 1 TGGCTTCTGA 0.976865 -86 ATTCGAAGAATGGCTACTGAGGCAAATCA 4 10 0 TGGCTACTGA 0.990707 -51 TCTATAAATATAGCTAAAGATAATTCATCT 5 101 1 TAGCTAAAGA 0.946368 -21 TTAAAGCTTTTAGCTAATGACCATAATAGT 7 40 1 TAGCTAATGA 0.978059 -72 ********** Masking position 5 Map Score: 1.79759 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 15 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 AACTTTTGCTCACTGATTGTGCAAAAAAAT 1 17 0 CACTGATTGT 0.929842 -45 ATTTCCTCTACTCTTATTGTTATTATTACA 5 72 0 CTCTTATTGT 0.965741 -50 TGCCTTATAACTATTATGGTCATTAGCTAA 7 49 0 CTATTATGGT 0.924076 -63 GAAGTTATCTCTCTGATGGACTCAATGGAG 8 141 1 CTCTGATGGA 0.985625 -160 GTTAACCCTCTAATGGAGTATATTTTA 9 8 1 CTCTAATGGA 0.961741 -77 ********** Masking position 6 Map Score: 1.44323 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 75 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 TTTTTCACCTCTTACTCGGCATT 3 99 0 TTCACCTCTT 0.870761 -13 CCTTCTCCTCCTAAACTTTATG 6 30 0 TTCTCCTCCT 0.987843 -12 AGAGAAAGCTCATCCTCAAGCCTCAC 8 7 1 AGCTCATCCT 0.940747 -294 CTTTCAACCTTGCTCATGCTTTCAAAATCC 8 108 1 TGCTCATGCT 0.953104 -193 ACTATCACCTGCTTTTTGTTTGG 8 288 0 ATCACCTGCT 0.940435 -13 ATTATTTTATTACTCCTACTTAAAATATAC 9 28 0 TACTCCTACT 0.890044 -57 ********** Masking position 7 Map Score: 0.643698 Number of sites scoring better than the average of aligned sites = 876 Number in coding regions = 819 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 9 GGATTAAGAACTTTTGCTCACTGATTGTGC 1 25 0 CTTTTGCTCA 0.931166 -37 TTACTTTCCTCATAAAAAATTA 2 22 0 ACTTTCCTCA 0.983101 -12 TGATTTGCCTCAGTAGCCATTC 4 3 1 ATTTGCCTCA 0.931166 -58 CAACATTATCACGTTACTCAACAAACAAAA 8 63 0 ACGTTACTCA 0.944266 -238 AAGCCTTTCAACCTTGCTCATGCTTTCAAA 8 104 1 ACCTTGCTCA 0.963245 -197 ACCCGGAATTATTTTACTCA 10 1 0 ATTTTACTCA 0.959868 -50 ********** Masking position 4 Map Score: 2.84039 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 97 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 ********** No masking Map Score: 9.97192e-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 11 ********** No masking Map Score: 9.97192e-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 12 ********** No masking Map Score: 9.97192e-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