AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i293_aful_mthe_300.orf -o293_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 Purged sequences: RTH00437 20 M.thermo Input sequences: #1 RAG50078 24 Archaeoglobus_fulgidus #2 RAG49761 216 Archaeoglobus_fulgidus #3 RAG50073 94 Archaeoglobus_fulgidus #4 RAG32214 35 Archaeoglobus_fulgidus #5 RAG50068 112 Archaeoglobus_fulgidus #6 RAG17083 76 Archaeoglobus_fulgidus #7 RTH01746 83 M.thermo #8 RTH01824 300 M.thermo #9 RTH00902 142 M.thermo #10 RTH00250 30 M.thermo #11 RTH00057 21 M.thermo #12 RTH01659 205 M.thermo #13 RTH01211 72 M.thermo #14 RTH00503 300 M.thermo #15 RTH00097 230 M.thermo Motif number 1 TGAAGCTGAGTGACAGAGTATCGTGAGATTTTCCGA 2 33 0 TAGGTTCTGA 0.889148 -184 ATGGAGTGTGAAATAGACTATCCGGGAAGCTTTGAA 2 65 0 AAGCTTCGGG 0.967558 -152 CAAGAGGCTAATAAGGTTTTTCATGAGTTTGATATT 2 177 0 AAGTTTCTGA 0.983115 -40 ATTTACCGCTAAAAGGCCTGTCTTGAAGTATTTAGC 5 59 0 AAGCTTCTGA 0.961592 -54 GGAGTAAGTTAAAAAGCTTGCCGTGAAAGAAAGTTT 6 25 1 AAGTTCCTGA 0.97331 -52 GTGATAATCTTTAATGCTTCTCATGGGCTTCTGAGG 8 127 0 TAGTTTCTGG 0.984916 -174 GGATCCGGGATCAGGGGTTCCCGTGATAATCTTTAA 8 149 0 TAGTTCCTGA 0.935455 -152 ATTTAAACTCAAAGAGGTTTCCCTGGGAACAGCGTT 8 249 1 AAGTTCCTGG 0.985788 -52 TTCCCTGGGAACAGCGTTTTTCAGGGGATAGGAGGT 8 267 1 AAGTTTCGGG 0.985788 -34 TTTAATCATCTCAATGGTTCTCATGGCCCTCCTGTG 14 23 0 TAGTTTCTGG 0.984916 -278 CTATTCCTTTAATTAGTTTTTCCGGGATCTGGATGG 15 138 0 ATGTTTCGGG 0.898096 -93 * * * ** ** *** Masking position 9 Map Score: 12.6542 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 55 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 2 GAATCAAAAAAAGAGGAAGGGCTT 1 4 0 AAGAGGAGGG 0.9269 -21 GGCGGTTTGTATGGGGGAGGGTACACTGGCG 3 70 0 ATGGGGAGGG 0.963629 -25 TTAACTTACTCCGGAAATGGGTGTTG 6 6 0 CCGGAATGGG 0.697409 -71 CGGGATTTAAAGGAAATAGGGGGTGCAGCTT 8 74 0 AGGAAAAGGG 0.936366 -227 TGGGCTTCTGAGGGAAAAGGATACCTCTAAG 8 109 0 AGGGAAAGGA 0.912618 -192 ATGGCGGATCCGGGATCAGGGGTTCCCGTGA 8 159 0 CGGGATAGGG 0.919586 -142 AGCGTTTTTCAGGGGATAGGAGGTTTTTTTA 8 279 1 AGGGGAAGGA 0.910959 -22 TCATAAATCTAGGAAGGTGGGTTAATC 10 14 1 AGGAAGTGGG 0.839997 -17 TACTCTATAATAGGATAAGGGAGTATTTAAA 12 71 0 TAGGATAGGG 0.713031 -135 TGGCCTCCTCCAGGGGGAGGAGGTTGACCTC 13 25 1 CAGGGGAGGA 0.791887 -48 AAGGAACTGGGAGGCCCTCCC 13 62 0 AAGGAATGGG 0.953539 -11 TATTTAAGAAAAGAGATAGAGAGCGCCTGAG 14 171 1 AAGAGAAGAG 0.656814 -130 GGTTAAATGATGGGTATGGGTTTAAGGAGT 15 10 1 ATGGGTTGGG 0.783831 -221 AAACTAATTAAAGGAACAGAGATAACATGTT 15 100 1 AAGGAAAGAG 0.900159 -131 CGGGATCTGGATGGAGAAGGGAACATGTTAT 15 121 0 ATGGAGAGGG 0.964345 -110 AAACTAATTAAAGGAATAGAGATAACTAACT 15 155 1 AAGGAAAGAG 0.900159 -76 ****** **** Masking position 3 Map Score: 13.4216 Number of sites scoring better than the average of aligned sites = 1856 Number in coding regions = 1767 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 3 GGAGGGTACACTGGCGGTTCCTGCATAATGCA 3 54 0 CTGGCGGTCT 0.981345 -41 TTCGGGCGGTTTGTATGGGGGAGG 3 81 0 CGGGCGGTTT 0.969734 -14 CCATCATTTCCTGGAGGTATTCC 9 2 0 CTGGAGGTTC 0.965107 -141 CCCGCATAACTGGCTGTTCATATTCATGACC 12 10 1 CTGGCTGTCT 0.949057 -196 GTATTCCATACTGGCGGTGTATGTAACTCTAA 12 99 1 CTGGCGGTTT 0.965107 -107 CCTCCTCCCCCTGGAGGAGGCCAGTGCTATCC 13 16 0 CTGGAGGAGC 0.775013 -57 ACCTCCATTTCGGGAGGGCCTCCCAGTTCCTT 13 51 1 CGGGAGGGCC 0.968491 -22 TAACGCCCCACAGGAGGGCCATGAGAACCATT 14 15 1 CAGGAGGGCT 0.902138 -286 CTTTACTTCTCAGGCGCTCTCTATCTCTTTTC 14 178 0 CAGGCGCTTT 0.610909 -123 GTTCTCTATCCGGTATGTGCTTTACTCTTTAC 14 204 0 CGGTATGTCT 0.590886 -97 TGCTGCACACCGGGAGGGAGACC 14 288 1 CGGGAGGGGC 0.940667 -13 TTAGTTTTTCCGGGATCTGGATGGAGAAGGGA 15 130 0 CGGGATCTGT 0.687183 -101 AAGACATCTGCTGGATGTATGCTTTAAAGTTA 15 181 0 CTGGATGTTC 0.907365 -50 CTCAACTCTCCTTGATGTGCTTGATTTTAAGA 15 209 0 CTTGATGTCT 0.554925 -22 ******** * * Masking position 1 Map Score: 9.9426 Number of sites scoring better than the average of aligned sites = 718 Number in coding regions = 674 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 4 TAACTTGACAAAACGAATAGCCCTGATGGAGT 2 94 0 AAGAATAGCC 0.900939 -123 ATTGCATTATGCAGGAACCGCCAGTGTACCCT 3 52 1 GAGAACCGCC 0.978795 -43 ACCCTCCCCCATACAAACCGCCCGAA 3 79 1 AAAAACCGCC 0.993102 -16 AAATAGACTAATCGCCTAACAAGATA 4 20 0 AATAATCGCC 0.909158 -16 CTTCATCCACAGAGAAACCGCAGTTATTGTTC 8 45 0 AAAAACCGCA 0.941438 -256 TTAAAAAAACCTCCTATCCCCTGA 8 287 0 AAAAACCTCC 0.941438 -14 GTGGTCATGAATATGAACAGCCAGTTATGCGG 12 12 0 AAGAACAGCC 0.975468 -194 ATTTAGAGTTACATACACCGCCAGTATGGAAT 12 101 0 AAACACCGCC 0.974514 -105 * * ******** Masking position 7 Map Score: 5.73609 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 77 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 TTATCGGCCCAACCAGAACAACATCA 5 97 1 AACCAGAACA 0.713227 -16 CGCTGCTAACCAGCTGAACAATAACTGCGG 8 30 1 CAGCTGAACA 0.934651 -271 TCTGTGGATGAAGCTGCACCCCCTATTTCC 8 64 1 AAGCTGCACC 0.899913 -237 CCTTTTCCCTCAGAAGCCCATGAGAAGCAT 8 120 1 CAGAAGCCCA 0.907859 -181 TTTATACAGACAACTGCACAATTTATCTAT 9 63 1 CAACTGCACA 0.860355 -80 GAATTTGTTTCTGAAGAACAGGTGAT 9 127 1 CTGAAGAACA 0.616906 -16 CATGACCACACAGCACCCCAAACCACCATG 12 35 1 CAGCACCCCA 0.856078 -171 GGAGGTCAACCTCCTCCCCCTGGAGGAGGC 13 27 0 CTCCTCCCCC 0.633332 -46 AACATGACCTCACATCCACCACAACGGCAA 14 57 1 CACATCCACC 0.746352 -244 AAATAATCTCCACATGAACATGGTAGTGGA 14 146 0 CACATGAACA 0.853254 -155 TCATAAACTTAAGATGCACATACACTGAGT 14 247 0 AAGATGCACA 0.902213 -54 TCAATATCACCTGCTGCACACCGGGAGGGA 14 277 1 CTGCTGCACA 0.958444 -24 TTTGTAGGATAACCTGCCCACCATAATTTC 15 40 1 AACCTGCCCA 0.91772 -191 ATGTCTTAAAATCAAGCACATCAAGGAGAG 15 206 1 ATCAAGCACA 0.654442 -25 ********** Masking position 9 Map Score: 7.26908 Number of sites scoring better than the average of aligned sites = 1237 Number in coding regions = 1174 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 6 ACAGAGTATCGTGAGATTTTCCGAGCCCGCAG 2 25 0 GTGAGATTCC 0.78435 -192 GTTTGTATGGGGGAGGGTACACTGGCGGTTCC 3 65 0 GGGAGGGCAC 0.921352 -30 CATCATTTCCTGGAGGTATTCC 9 1 0 TGGAGGTTCC 0.985276 -142 CCTCCCGAAATGGAGGTCAACCTCCTCCCCCT 13 36 0 TGGAGGTACC 0.966793 -37 CCTCCATTTCGGGAGGGCCTCCCAGTTCCTT 13 52 1 GGGAGGGTCC 0.995375 -21 GAGTTATTGAGGGGGGTTCTCTATCCGGTATG 14 219 0 GGGGGGTTCT 0.896732 -82 GCTGCACACCGGGAGGGAGACC 14 289 1 GGGAGGGACC 0.992049 -12 AATTATGGTGGGCAGGTTATCCTACAAACTCC 15 36 0 GGCAGGTTCC 0.979778 -195 ******* *** Masking position 5 Map Score: 5.03823 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 94 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 TGCTTTGAATGTTAAAAAGTTTGCTGTGCTA 3 19 0 GTTAAAAGTT 0.941546 -76 CGCCTAACAAGATAAAGCTTTGG 4 3 0 GATAAAGTTT 0.875032 -33 TGAAGTTGAGGTTAAAATTTTTTAGGTTGGG 5 22 1 GTTAAAATTT 0.942638 -91 TGGTTGGGCCGATAAAAATTTACCGCTAAAA 5 81 0 GATAAAATTT 0.963454 -32 TCCGGAGTAAGTTAAAAAGCTTGCCGTGAAA 6 22 1 GTTAAAAGCT 0.810542 -55 CAGTATGGCAGATAAAACTTTCTTTCACGGC 6 44 0 GATAAAATTT 0.963454 -33 TCTTTAGTCTGACAAAATTTTATAATTAGAA 7 12 1 GACAAAATTT 0.875032 -72 AAGGAACAGAGATAACATGTTCCCTTCTCCA 15 110 1 GATAACAGTT 0.872826 -121 ******* *** Masking position 5 Map Score: 4.02829 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 20 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 TTTTCATGAGTTTGATATTGAGATATTGCAGAAA 2 162 0 TTGATGAGAT 0.720347 -55 TGGATTTTGCTTGAAGTTGAGGTTAAAATTTTT 5 10 1 CTGATGAGGT 0.977213 -103 AAAAGCTTGCCGTGAAAGAAAGTTTTATCTGCCA 6 36 1 CTGAGAAGTT 0.734653 -41 GGGAAACCTCTTTGAGTTTAAATTCCTAACCTGA 8 238 0 TTGATAAATT 0.383266 -63 GGAATACCTCCAGGAAATGATGGTAACTAACTTG 9 11 1 CGGATATGGT 0.808647 -132 ACTTGAATCATCTGACCTAAAGGTTTATACAGAC 9 40 1 TTGATAAGGT 0.949949 -103 GTATTTAAATCTTGACATGGTGGTTTGGGGTGCT 12 46 0 CTGATGTGGT 0.970205 -160 ACTGGTTAACCATGATTTAGAGTTACATACACCG 12 113 0 CTGATGAGTT 0.958449 -93 ATATGAATTTTTTGAATTTATGTTAAATCCAGCT 12 150 1 TTGATATGTT 0.88574 -56 GGGAGGCCCTCCCGAAATGGAGGTCAACCTCCTC 13 41 0 CCGATGAGGT 0.871198 -32 TTGTGGTGGATGTGAGGTCATGTTTAATCATCTC 14 47 0 TTGATATGTT 0.88574 -254 TCTCGGGCACCTTGCCGTTGTGGTGGATGTGAGG 14 64 0 CTGCTGTGGT 0.904324 -237 GATAAAATGGAATGAAATTATGGTGGGCAGGTTA 15 49 0 ATGATATGGT 0.749499 -182 CTGCTGGATGTATGCTTTAAAGTTAGTTATCTCT 15 172 0 TTGCTAAGTT 0.747686 -59 * *** * ***** Masking position 14 Map Score: 8.07813 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 294 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 TACTCTGTCACTCAGCTTCAAAGCTTCCCGGA 2 49 1 CTCAGTCAAA 0.95487 -168 TCTGCAATATCTCAATATCAAACTCATGAAAA 2 164 1 CTCAATCAAA 0.962474 -53 AAATTTTAACCTCAACTTCAAGCAAAATCCA 5 10 0 CTCAATCAAG 0.980294 -103 TGTGATATATCTCAGAAACAAGGTCATCATAG 9 89 0 CTCAGACAAG 0.881651 -54 TGAGATATATCACAGTATCAGAATTTGTTTCT 9 107 1 CACAGTCAGA 0.8005 -36 CACCCCAAACCACCATGTCAAGATTTAAATAC 12 48 1 CACCATCAAG 0.905273 -158 CTGGATTTAACATAAATTCAAAAAATTCATAT 12 150 0 CATAATCAAA 0.803912 -56 TCACATCCACCACAACGGCAAGGTGCCCGAGA 14 66 1 CACAAGCAAG 0.915719 -235 CAGCAGATGTCTTAAAATCAAGCACATCAAGG 15 200 1 CTTAATCAAG 0.901615 -31 ***** ***** Masking position 10 Map Score: 3.46806 Number of sites scoring better than the average of aligned sites = 358 Number in coding regions = 335 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 10 AGACTAATCGCCTAACAAGATAAAGCTTTG 4 12 0 CCTAACAAGA 0.92099 -24 TAGCGCATCACCCAACCTAAAAAATTTTAA 5 33 0 CCCAACCTAA 0.974116 -80 TTTTTATCGGCCCAACCAGAACAACATCA 5 94 1 CCCAACCAGA 0.983382 -19 AGTTTAAATTCCTAACCTGATACTATTTTT 8 228 0 CCTAACCTGA 0.974116 -73 GGATAACCTGCCCACCATAATTTCATTCCA 15 46 1 CCCACCATAA 0.882688 -185 ********** Masking position 4 Map Score: 0.646198 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 56 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 ********** No masking Map Score: 6.10599e-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 12 ********** No masking Map Score: 6.10599e-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 13 ********** No masking Map Score: 6.10599e-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