AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i110_aful_mthe_300.orf -o110_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 RAG48384 262 Archaeoglobus_fulgidus #2 RAG48385 39 Archaeoglobus_fulgidus #3 RAG50406 145 Archaeoglobus_fulgidus #4 RAG00797 148 Archaeoglobus_fulgidus #5 RAG00616 27 Archaeoglobus_fulgidus #6 RAG00615 143 Archaeoglobus_fulgidus #7 RAG07898 50 Archaeoglobus_fulgidus #8 RAG07804 89 Archaeoglobus_fulgidus Motif number 1 GATAAATCAAAAATTGGAAAAGCTTAAATAC 1 203 0 AAATGGAAAA 0.975004 -60 CACAATTTTTAAAACTTAAAAAATTTTCGAT 1 235 0 AAAATTAAAA 0.87548 -28 TCAAAAGGCGAATTAGTGAAACTCCATGAGG 4 33 1 AATTGTGAAA 0.944379 -116 TGTACATCATAGAAAGTGAAATTTTTCCTCA 4 59 0 AGAAGTGAAA 0.921334 -90 CTAATGCTATTAATTGGAAAAAAACCAAAAA 4 98 1 TAATGGAAAA 0.805861 -51 ATCACCAAAAAATAATGGAAAGT 5 3 0 AATATGGAAA 0.760642 -25 ATTGTTGAATAAATTGTGAAATAAAGAATTA 6 61 1 AAATGTGAAA 0.981442 -83 AAACTACGCAAAAAAGGAAAAGCTTATATGT 6 94 1 AAAAGGAAAA 0.961427 -50 CTTATATGTAATAATGTAAAATCACAAATGG 6 116 1 ATAAGTAAAA 0.756566 -28 GTAAAATCACAAATGGTGAAAAA 6 131 1 AAATGTGAAA 0.981442 -13 AAAGATTTTGAGTTTGTAAAATCT 7 4 0 AGTTGTAAAA 0.809855 -47 GACCGTCAAAAAATTTGGAAAGATTTTGAGT 7 22 0 AAATTGGAAA 0.939359 -29 TACAACGTTAAAATTTTAAAACTTTACTAAA 8 22 0 AAATTTAAAA 0.916688 -68 **** ****** Masking position 9 Map Score: 15.2108 Number of sites scoring better than the average of aligned sites = 364 Number in coding regions = 280 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 2 CCGTGCTTGTGTATGGGTTTATGCTCTAAA 1 51 0 GTATGGGTTT 0.892238 -212 TTGGATTTTATTTTAGGTTTAGCTTTGGCT 1 124 0 TTTTAGGTTT 0.956999 -139 AAACCAGGGTGTTTGGATTTTATTTTAGGT 1 136 0 GTTTGGATTT 0.920964 -127 AAACACCCTGGTTTTGGCTACACCATGCAT 1 152 1 GTTTTGGCTA 0.806099 -111 GCTTTTCCAATTTTTGATTTATCTATCGAA 1 211 1 TTTTTGATTT 0.933897 -52 ATCGAAAATTTTTTAAGTTTTAAAAATTGT 1 235 1 TTTTAAGTTT 0.737935 -28 CGTATGCTTTGTATTGATTAGTACGCACGA 3 88 1 GTATTGATTA 0.607449 -58 CGCTTGAAGTTTAGGTTTGTTATATAAA 3 128 0 GTTTAGGTTT 0.96266 -18 GATTTTGGTTATCCTAAAGTG 4 2 1 ATTTTGGTTA 0.803057 -147 GTATAAAACCTTTTTGGTTTTTTTCCAATT 4 109 0 TTTTTGGTTT 0.98006 -40 TTTCCATTATTTTTTGGTGATATAT 5 13 1 TTTTTGGTGA 0.782078 -15 TTTTTCACCATTTGTGATTTTACATTATTA 6 124 0 TTTGTGATTT 0.690241 -20 TTTGGAAAGATTTTGAGTTTGTAAAATCT 7 10 0 TTTTGAGTTT 0.815761 -41 ********** Masking position 2 Map Score: 10.8315 Number of sites scoring better than the average of aligned sites = 525 Number in coding regions = 395 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 3 AGGGTGTTTGGATTTTATTTTAGGTTTAGCTTTGGC 1 125 0 GATTATTTAT 0.875884 -138 AGGTTTAGCAGCATGTATTTAAGCTTTTCCAATTTT 1 189 1 GCTTATTAAT 0.988756 -74 CTCTATTAATCCCTCTATATAAACATTATACTAACT 3 28 1 CCTTATTAAT 0.9639 -118 ACTAACTGTTGCCTCTCTTTAAAATTCACTTCGTAT 3 57 1 GCTTCTTAAT 0.977266 -89 CGAGAAAAAAGATTTTATATAACAAACCTAAACTTC 3 115 1 GATTATTAAA 0.933866 -31 AACAATTCACGATTCTCTTCAAACTATACTAATTAT 6 31 0 GATTCTCAAA 0.850828 -113 CTTTATTTCACAATTTATTCAACAATTCACGATTCT 6 51 0 CATTATCAAT 0.918348 -93 AAAAGGAAAAGCTTATATGTAATAATGTAAAATCAC 6 105 1 GCTTATTAAT 0.988758 -39 CCTTCGCATAGCGTTTATACAACGTTAAAATTTTAA 8 34 0 GCTTATCAAT 0.986334 -56 ** * *** *** * Masking position 8 Map Score: 6.42851 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 41 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 4 CTTTTACCTAACATATAAAACACCTCTTATA 1 18 1 ACTATAAAAC 0.867192 -245 TATATTTTTAGAGCATAAACCCATACACAAG 1 45 1 GACATAAACC 0.860361 -218 CCGCTAATTAGAAGCTAAACCAGTAGCCAAA 1 100 1 GAGCTAAACC 0.981411 -163 ACCAGTAGCCAAAGCTAAACCTAAAATAAAA 1 118 1 AAGCTAAACC 0.97068 -145 AATGCATGGTGTAGCCAAAACCAGGGTGTTT 1 152 0 GTGCCAAAAC 0.813084 -111 TTAAATACATGCTGCTAAACCTTCCTCCAAT 1 180 0 GCGCTAAACC 0.977552 -83 AGGATTGCAAAAGTATAAAACCTTTTTGGTT 4 120 0 AATATAAAAC 0.887846 -29 TGAAATAAAGAATTATAAAACTACGCAAAAA 6 77 1 AATATAAAAC 0.887845 -67 ACAACGTTAAAATTTTAAAACTTTACTAAAG 8 21 0 AATTTAAAAC 0.70639 -69 TAATACGGCCGCCAAAACTATTTTGTTC 8 72 0 GCGCCAAAAC 0.945304 -18 ** ******** Masking position 7 Map Score: 6.23217 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 172 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 ATGTTAGGTAAAAGAAGAAGG 1 2 0 AAAGAAGAAG 0.786182 -261 TTATGCTCTAAAAATATAAGAGGTGTTTTA 1 33 0 AAAATATAAG 0.5735 -230 TTTAAAACTTAAAAAATTTTCGATAGATAA 1 229 0 AAAAAATTTT 0.721314 -34 TTTAAGTTTTAAAAATTGTGAGCCCTC 1 246 1 AAAAATTGTG 0.720642 -17 CAAAAAAATTTTTTATATCCCT 2 3 1 AAAAAATTTT 0.721314 -37 TGAGCCTTAAAAAAAGGAGGGATATAAAA 2 21 0 AAAAAAGGAG 0.953221 -19 TAATAGAGTTAAACAAGGTGGTGTA 3 6 0 AAACAAGGTG 0.803528 -140 TACGCACGAGAAAAAAGATTTTATATAACA 3 109 1 AAAAAAGATT 0.88619 -37 GGAAAAAAACCAAAAAGGTTTTATACTTTT 4 113 1 CAAAAAGGTT 0.698988 -36 TTTAAAATAGGATTGCAAAAGTA 4 136 0 AAAATAGGAT 0.782048 -13 ATATATCACCAAAAAATAATGGAAAGT 5 8 0 AAAAAATAAT 0.792921 -20 ATTGTGAAATAAAGAATTATAAAACTACGC 6 73 1 AAAGAATTAT 0.703244 -71 AAAACTACGCAAAAAAGGAAAAGCTTATAT 6 93 1 AAAAAAGGAA 0.694711 -51 AAAAATTTGGAAAGATTTTGAGTTTGTAAA 7 15 0 AAAGATTTTG 0.405487 -36 TGAGACCGTCAAAAAATTTGGAAAGATTTT 7 26 0 AAAAAATTTG 0.879041 -25 AAGGGGGAACAAAATAGTTTTGGCGGCCGT 8 66 1 AAAATAGTTT 0.615563 -24 ********** Masking position 3 Map Score: 9.50154 Number of sites scoring better than the average of aligned sites = 992 Number in coding regions = 746 Number in noncoding regions = 246 Number of orfs with sites within 600 bp upstream = 244 Fraction of orfs with sites within 600 bp upstream = 0.0391905 Motif number 6 AGCTTAAATACATGCTGCTAAACCTTCCTCC 1 183 0 CATGTGCTAA 0.86111 -80 CACCTTGTTTAACTCTATTAATCCCTCTATA 3 16 1 AACTTATTAA 0.929119 -130 TCTATATAAACATTATACTAACTGTTGCCTC 3 41 1 CATTTACTAA 0.953386 -105 GTGGGAGTCTAATGCTATTAATTGGAAAAAA 4 90 1 AATGTATTAA 0.873594 -59 ATTCTCTTCAAACTATACTAATTATAAATTC 6 25 0 AACTTACTAA 0.97487 -119 AAAATTTTAAAACTTTACTAAAGCTCGGAGT 8 13 0 AACTTACTAA 0.97487 -77 **** ****** Masking position 6 Map Score: 1.11022 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 8 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 ********** No masking Map Score: -1.22681e-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 8 ********** No masking Map Score: -1.22681e-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: -1.22681e-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