AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i064_aful_mthe_100.orf -o064_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: RAG48457 25 Archaeoglobus_fulgidus Input sequences: #1 RAG18763 209 Archaeoglobus_fulgidus #2 RAG15094 200 Archaeoglobus_fulgidus #3 RAG00432 102 Archaeoglobus_fulgidus #4 RAG22490 30 Archaeoglobus_fulgidus #5 RAG22489 109 Archaeoglobus_fulgidus #6 RAG50216 152 Archaeoglobus_fulgidus #7 RAG50214 54 Archaeoglobus_fulgidus #8 RAG32775 72 Archaeoglobus_fulgidus #9 RAG35275 48 Archaeoglobus_fulgidus #10 RTH01080 300 M.thermo #11 RTH02062 231 M.thermo #12 RTH02127 159 M.thermo #13 RTH01004 66 M.thermo #14 RTH01088 218 M.thermo #15 RTH00777 35 M.thermo #16 RTH00316 57 M.thermo #17 RTH00321 44 M.thermo #18 RTH01047 56 M.thermo #19 RTH02145 30 M.thermo #20 RTH00013 16 M.thermo #21 RTH00133 56 M.thermo #22 RTH01743 127 M.thermo #23 RTH00602 189 M.thermo #24 RTH00576 116 M.thermo #25 RTH00954 31 M.thermo #26 RTH00250 30 M.thermo #27 RTH00057 21 M.thermo #28 RTH01659 205 M.thermo Motif number 1 AAGCAATGTTCTGCATCCCGGGGATAAGAAGGCTA 1 94 0 CTGCCCGGGT 0.984959 -116 CTTTCCAAGCCTGTATCCAGCGGTAATTAAGGCGT 2 107 0 CTGTCCGGGA 0.995146 -94 AACCCCACCTTTTGCCTGCGGTATATAAGTTTG 3 80 0 CTTTCCGGGA 0.972559 -23 TTATAAATAGCTTTGTCCGGAGGTAGGGATTGATG 5 66 0 CTTTCCGGGA 0.972559 -44 GGGCGAGAGGCTGTGCCCAGGGGATGGCCCATGAT 11 14 1 CTGTCCGGGT 0.997132 -218 GTCACACTCTCCCCTGGATTATAGGTAAC 11 213 0 CACTCCCGGT 0.830015 -19 AGTGATGTTTCTGTAGCTGCAGGGTTACATCTGCA 12 51 0 CTGTCTCGGT 0.954267 -109 ACTGATGTTTCTGTAGCTACAGGGTTACAATCTTG 12 86 0 CTGTCTCGGT 0.954267 -74 AAGCTGTCTGCTGTCCCCTGAGTCTGGTCTTCGGC 14 166 0 CTGTCCGGTT 0.981675 -53 GAGGATGACCCTGTCCCCGGCGGATACATC 16 6 0 CTGTCCGGGT 0.997132 -52 CTCTCCAGTGACCTGAGTTAACCGAGATTG 25 6 1 CAGTCCGGTA 0.886841 -26 **** ** * ** * Masking position 7 Map Score: 17.4278 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 44 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 2 TATGCAGGCAAACTATTTATATGATTTCAATT 3 20 1 AACTTTTATT 0.812613 -83 GAAAAATTTTTAACTTTTTCTTTAA 6 138 0 AAATTTTAAT 0.947594 -15 ATCCCGAAGAAATTTTTTATATTGGCAAATGT 8 42 1 AATTTTTATT 0.613935 -31 GGCTTGAGAAAAAGGATTAATTAAGGTTGTTC 9 21 0 AAAGATTAAT 0.609525 -28 TAATGGACCAAAATTTTTAAATAATAAGTTTA 10 43 0 AAATTTTAAT 0.947594 -258 CTACCATTTGCAATTTTTATATTAATCTGTGG 10 104 0 CAATTTTATT 0.901033 -197 AACCATCAACCAATGTTTAAGTGAAAGCATAT 10 158 1 CAATTTTAAT 0.923019 -143 GCATATAAATAAATGTTTATATTACTGGAATT 10 184 1 AAATTTTATT 0.93209 -117 GGAATTCTTCAAATTATTAAATGATCCGGTGT 10 210 1 AAATATTAAT 0.772271 -91 ATGGTACTTACAATATTTATTTACCATCAGCG 11 162 1 CAATTTTATT 0.899947 -70 GTTGATGAGAAAATATTTAAATGGTTAACTTT 14 128 0 AAATTTTAAT 0.947464 -91 ATCCGTCAACTCTTTATTTCTGGTGATTC 19 8 1 AACTTTTATT 0.812613 -23 TATGTACAGTAAAGTTTTAAATAGTTCTTTAA 22 42 1 AAAGTTTAAT 0.892721 -86 ACCACCATGTCAAGATTTAAATACTCCCTTAT 28 56 1 CAAGTTTAAT 0.846573 -150 **** ***** * Masking position 9 Map Score: 12.7501 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 29 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 3 AGCAATGTTCTGCATCCCGGGGATAAGAAG 1 98 0 TGCATCCCGG 0.931395 -112 CTTTTCGTTCTGCATCATGGCTTTAGTGTT 2 32 0 TGCATCATGG 0.993074 -169 ACATGTAACCGGAATCATGGGCCATCCCCT 11 32 0 GGAATCATGG 0.955283 -200 TCCATGGATATGAATCATGGGATGGATTTG 24 45 1 TGAATCATGG 0.985801 -72 GGGATGGATTTGCATCATGGTTCCAGCCAT 24 63 1 TGCATCATGG 0.993074 -54 TCTGTGGTTATGCAACATGGCTGGAACCAT 24 79 0 TGCAACATGG 0.9675 -38 TATGTAACTCTAAATCATGGTTAACCAGTT 28 118 1 TAAATCATGG 0.900054 -88 ********** Masking position 4 Map Score: 8.96162 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 16 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 4 TTAACGAAAACACCTCAAACATACTACCA 1 10 0 CACCTCAAAC 0.948725 -200 CAATCTGGGACGCCTTAATTACCGCTGGAT 2 98 1 CGCCTTAATT 0.768683 -103 TGACGTTGACCACCCCAAGCTGGTTTTTAA 2 162 1 CACCCCAAGC 0.915458 -39 CCATTAGATGCCCCCTAATCCAAATTAAGG 10 69 1 CCCCCTAATC 0.957413 -232 ATCCGGTGTGCCCCCTAAATTCTTAAAAGG 10 233 1 CCCCCTAAAT 0.926129 -68 ACTAACCATTCGCCCTAACTTTTTCACTGG 10 278 1 CGCCCTAACT 0.815138 -23 AGACTACGGGCCCCCTACACACATCTCTAT 14 96 1 CCCCCTACAC 0.905653 -123 ATACTAAATGCCCCTTAATTAATAAAT 14 202 1 CCCCTTAATT 0.86409 -17 ACCCCTCCACCACCTCACCCCTACTGATTT 21 11 1 CACCTCACCC 0.811855 -46 ATTACGTCACCTCAAATGTCTGTGGTT 24 100 0 CACCTCAAAT 0.893335 -17 GACCACACAGCACCCCAAACCACCATGTCA 28 38 1 CACCCCAAAC 0.967336 -168 TATATCACCTTAATCTTTAACACCG 28 191 0 CACCTTAATC 0.92839 -15 ********** Masking position 7 Map Score: 9.02603 Number of sites scoring better than the average of aligned sites = 387 Number in coding regions = 357 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 TGCCTGCGGTATATAAGTTTGAATTCTTTT 3 71 0 ATATAAGTTT 0.928308 -32 ACAAAGCTATTTATAAGTGATTTATTATCA 5 85 1 TTATAAGTGA 0.76214 -25 AAGTGATTTATTATCAGTTTT 5 99 1 TTATCAGTTT 0.860682 -11 CTTTTTCTTTAAATAGGTTTCGAAAAGTTT 6 120 0 AAATAGGTTT 0.720159 -33 CGGGTGGTAAAAATAGGTTTTTGTGTTGTA 7 22 0 AAATAGGTTT 0.720159 -33 CTCAGTCTCCTTATAAGTGTGTATTAAACT 10 19 1 TTATAAGTGT 0.860683 -282 AATTTTTAAATAATAAGTTTAATACACACT 10 34 0 TAATAAGTTT 0.863714 -267 GTTTTTCCAGTTATCAGTTTATCACCCCGG 11 62 1 TTATCAGTTT 0.860682 -170 AAGTTAGAACTTATAAGTTATAAGGTGGTT 23 13 0 TTATAAGTTA 0.902394 -177 CCCTGACCGATTATAAGTTAGAACTTATAA 23 27 0 TTATAAGTTA 0.902394 -163 CAAACCTATTATATAGGTTTCCTGAAAGAG 23 66 1 ATATAGGTTT 0.878624 -124 CCTGAAAGAGATATAAGTTAATCTCCAGTG 23 86 1 ATATAAGTTA 0.870396 -104 ********** Masking position 3 Map Score: 9.11187 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 17 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 GTTATAGCCTTCTTATCCCCGGGATGCAGAA 1 90 1 TCTTATCCCG 0.943812 -120 CAAATGGTAGTCATATCCATGGGATGAATTC 10 126 1 TCATATCCAG 0.982386 -175 AGTTATCAGTTTATCACCCCGGCATTACAGG 11 70 1 TTATCACCCG 0.75542 -162 AGTTTATCTCCATGAAACTTTATA 12 4 1 TTATCTCCAG 0.952965 -156 AAGTCCCACGTCATATTCCAGGCTAGACTAC 14 72 1 TCATATTCCG 0.922473 -147 CTACTGATTTTTTTCTCCCGGAGCCATCCAG 21 31 1 TTTTCTCCCG 0.85919 -26 GATGAAATCATCATTTCCATGCAGTAAGATA 22 77 0 TCATTTCCAG 0.932248 -51 GTTTATCCGTTCATCTGCAGGATCTATCATT 23 119 0 TCATCTGCAG 0.922387 -71 ATCCCATGATTCATATCCATGGATTGATTAA 24 37 0 TCATATCCAG 0.982386 -80 AACTGGCTGTTCATATTCATGACCACACAGC 28 18 1 TCATATTCAG 0.916546 -188 ********* * Masking position 4 Map Score: 6.97656 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 220 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 7 TAAAAACCAGCTTGGGGTGGTCAACGTCAA 2 161 0 CTTGGGGTGG 0.714729 -40 CTTAAGGAGTGGGAAGAAAAGG 4 19 0 TAAGGAGTGG 0.815405 -12 TGTCCGGAGGTAGGGATTGATGGTTTCAAT 5 58 0 TAGGGATTGA 0.725305 -52 ATAGGTTTTTAAGGGAGTGGGAGGATAAAA 8 14 0 AAGGGAGTGG 0.941835 -59 TAATCCAAATTAAGGAATGACCACAGATTA 10 84 1 TAAGGAATGA 0.663021 -217 TAGTCATATCCATGGGATGAATTCCAACCA 10 133 1 CATGGGATGA 0.897782 -168 AAATTCTTAAAAGGGAATGGCTCCATAAAA 10 249 1 AAGGGAATGG 0.95153 -52 AGGCTGTGCCCAGGGGATGGCCCATGATTC 11 21 1 CAGGGGATGG 0.979153 -211 ATGTACATCAAAGGGAATGGTTAATAAACA 22 11 0 AAGGGAATGG 0.95153 -117 GATTCATATCCATGGATTGATTAATATTCA 24 31 0 CATGGATTGA 0.774679 -86 GGATATGAATCATGGGATGGATTTGCATCA 24 50 1 CATGGGATGG 0.959849 -67 ********** Masking position 8 Map Score: 6.50663 Number of sites scoring better than the average of aligned sites = 319 Number in coding regions = 296 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 CTCAGTTGCGAGGTAGTAGGGTGGTTGGATAATCCT 1 47 0 ATGGGTGGTT 0.990743 -163 ATGGCTTTAGTGTTAAAGCGGTGGGTTTTATAAGC 2 10 0 TTAGGTGGGT 0.844189 -191 GCCTTAAATTGGCCGGGTGGTAAAAATAGGTT 7 33 0 ATGGGTGGTA 0.944045 -22 TTTCACTTAAACATTGGTTGATGGTTGGAATTCATC 10 148 0 ATGGATGGTT 0.972281 -153 CAGGGTTACAATCTTGAGTGATGTTTCTGTAGCTGC 12 66 0 ATGGATGTTT 0.873529 -94 TGTGGAATTTATCTTGACTGATGTTTCTGTAGCTAC 12 101 0 ATGGATGTTT 0.873529 -59 TAGAACTTATAAGTTATAAGGTGGTTCC 23 3 0 ATAGGTGGTT 0.972281 -187 AGATCATAAATCTAGGAAGGTGGGTTAATC 26 10 1 ATGGGTGGGT 0.981243 -21 AGTATTTAAATCTTGACATGGTGGTTTGGGGTGCTG 28 45 0 TTAGGTGGTT 0.917248 -161 * * * ******* Masking position 12 Map Score: 4.93844 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 93 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 9 TACTCGCGACAGCCGTCGCGTTCCTTCTCA 1 190 0 AGCCGTCGCG 0.928144 -20 GCGGTAATTAAGGCGTCCCAGATTGGCTTT 2 93 0 AGGCGTCCCA 0.967078 -108 TTAAGAATTTAGGGGGCACACCGGATCATT 10 229 0 AGGGGGCACA 0.920825 -72 TTAATAAAAAAGCGGACCCGGGGGGATTTG 14 21 1 AGCGGACCCG 0.971489 -198 AGATGTGTGTAGGGGGCCCGTAGTCTAGCC 14 92 0 AGGGGGCCCG 0.993409 -127 GAGGGGTCCCGATCCATTTGA 27 11 0 AGGGGTCCCG 0.992972 -11 ********** Masking position 1 Map Score: 3.7216 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 10 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 CCATGATTCCGGTTACATGTGTTTTTCCAGT 11 42 1 GGTTACATTG 0.976382 -190 TGTTGCCATAGGTTACCTATAATCCAGGGGA 11 202 1 GGTTACCTTA 0.9644 -30 GTAGCTGCAGGGTTACATCTGCAGTAGTGCA 12 43 0 GGTTACATTG 0.976382 -117 ATATTTAAATGGTTAACTTTAAATAGAGATG 14 117 0 GGTTAACTTA 0.954632 -102 CTCGATGACTGGTTAAATTTATTTTACATTA 23 162 0 GGTTAAATTA 0.942343 -28 TCATTTAGAAGCTTACATATATA 24 3 0 GCTTACATTA 0.753535 -114 ACAATCTCGGTTAACTCAGGTCACTGGAG 25 13 0 GGTTAACTAG 0.86697 -19 ATATTTAACTGGTTAACCATGATTTAGAGTT 28 123 0 GGTTAACCTG 0.906183 -83 ATGGTTAACCAGTTAAATATGAATTTTTTGA 28 134 1 AGTTAAATTG 0.75892 -72 ******** ** Masking position 5 Map Score: 3.85504 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 33 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 11 CCTAACTTTTTCACTGGAGG 10 291 1 TCACTGGAGG 0.957352 -10 GCTGCACCGGTCAGTATAGAATCTGATTTT 11 125 1 TCAGTATAGA 0.796108 -107 TACAGAAACATCACTCAAGATTGTAACCCT 12 71 1 TCACTCAAGA 0.881382 -89 TACAGAAACATCAGTCAAGATAAATTCCAC 12 106 1 TCAGTCAAGA 0.881449 -54 GAGAAAAAAATCAGTAGGGGTGAGGTGGTG 21 18 0 TCAGTAGGGG 0.890009 -39 GATGATTTCATCAGTAGGGACCAGTTCCAG 22 96 1 TCAGTAGGGA 0.933053 -32 CTATCATTCTTCACTGGAGATTAACTTATA 23 97 0 TCACTGGAGA 0.973753 -93 TTAACTCAGGTCACTGGAGAG 25 2 0 TCACTGGAGA 0.973753 -30 ********** Masking position 3 Map Score: 3.3137 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 42 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 12 AGAACGAAAAGGTCAAGGTCTACTTCCTGA 2 51 1 GGTCAAGGTC 0.9878 -150 AGCTTGGGGTGGTCAACGTCAATGAGGTAT 2 153 0 GGTCAACGTC 0.982357 -48 TATCCGCCGGGGACAGGGTCATCCTCCTTG 16 15 1 GGACAGGGTC 0.983893 -43 CAGGACAACATCGTCGGGTTCA 16 46 0 GGACAACATC 0.881607 -12 ACTTATAATCGGTCAGGGACCGGACTCCAA 23 39 1 GGTCAGGGAC 0.963764 -151 ********** Masking position 5 Map Score: 1.68484 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 30 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 13 GAAATTTCTTGGGCCACCGCGGGATAGATGAG 1 162 1 GGGCCACCGG 0.974698 -48 TTTGGATTAGGGGGCATCTAATGGACCAAAAT 10 61 0 GGGGCATAAT 0.923576 -240 AAGAATTTAGGGGGCACACCGGATCATTTAAT 10 225 0 GGGGCACCGG 0.990899 -76 CCGGAATCATGGGCCATCCCCTGGGCACAGCC 11 22 0 GGGCCATCCT 0.901164 -210 ATGTGTGTAGGGGGCCCGTAGTCTAGCCTGGA 14 88 0 GGGGCCCAGT 0.920212 -131 TATTAATTAAGGGGCATTTAGTATAAAGCTGT 14 194 0 GGGGCATAGT 0.977925 -25 TGTCATTGTTGGGGCATTCCGTGGAGCATTTC 18 21 1 GGGGCATCGT 0.991235 -36 GGCATTCCGTGGAGCATTTCAGGGCATATACC 18 33 1 GGAGCATCAG 0.771897 -24 ******* *** Masking position 5 Map Score: 3.61074 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 78 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 14 AAGGTCTACTTCCTGACGGTCATCTTGAAA 2 65 1 TCCTGACGGT 0.662565 -136 TCTTTGCCTGTAATGCCGGGGTGATAAACT 11 77 0 TAATGCCGGG 0.888417 -155 ATGTTTCTGTAGCTGCAGGGTTACATCTGC 12 52 0 AGCTGCAGGG 0.781627 -108 AACTGGAGGGGGTTGC 20 1 1 AACTGGAGGG 0.936329 -16 CGTTTCTGGATGGCTCCGGGAGA 21 44 0 TTCTGGATGG 0.764069 -13 AAAGATATCTTACTGCATGGAAATGATGAT 22 72 1 TACTGCATGG 0.898764 -56 ATCACCTCATGGCTGGAACTGGTCCC 22 112 0 TCATGGCTGG 0.888421 -16 TACATTAAGCTCCTGCAGGGTTTATCCGTT 23 139 0 TCCTGCAGGG 0.936453 -51 TGGTTATGCAACATGGCTGGAACCATGATG 24 75 0 ACATGGCTGG 0.824384 -42 CCCGCATAACTGGCTGTTCATATTCAT 28 8 1 AACTGGCTGT 0.784778 -198 GAGTATTCCATACTGGCGGTGTATGTAACT 28 97 1 TACTGGCGGT 0.921646 -109 ********** Masking position 4 Map Score: 2.65556 Number of sites scoring better than the average of aligned sites = 561 Number in coding regions = 517 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 15 TATGATTTTCGAACTTCGGAACGTGTGAAC 6 46 0 GAACTTCGGA 0.976609 -107 CACAACTTACGGACTTCACATTTATCACGG 12 133 1 GGACTTCACA 0.922226 -27 ATGATCCGGTGAACTTCAGAGTATATTATT 13 23 0 GAACTTCAGA 0.948798 -44 ATATGACGTGGGACTTCGGATCCCAAGGTC 14 58 0 GGACTTCGGA 0.989482 -161 CCCTGAGTCTGGTCTTCGGCTGACACGTTG 14 156 0 GGTCTTCGGC 0.927956 -63 ********** Masking position 5 Map Score: 0.910883 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 61 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