AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i147_Reductases_aful_reg_300.orf -o147_aful_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 RAG48295 148 Archaeoglobus_fulgidus #2 RAG03812 62 Archaeoglobus_fulgidus #3 RAG48297 99 Archaeoglobus_fulgidus #4 RAG00148 241 Archaeoglobus_fulgidus #5 RAG04000 157 Archaeoglobus_fulgidus #6 RAG48241 99 Archaeoglobus_fulgidus Motif number 1 CACTGTTAGGTAACAGTGTTTGGGGTGGTG 1 16 0 TAACAGTGTT 0.991101 -133 CACTGTTACCTAACAGTGTTTATATTTAAC 1 28 1 TAACAGTGTT 0.991101 -121 GTTGGCCTAAAATCGGTTTTGAAAATGCAA 1 82 0 AATCGGTTTT 0.828981 -67 ATCCTAAACATAACGGTGTTAAAA 1 135 1 TAACGGTGTT 0.994422 -14 TTCGTTTTTTTTACGGTGTTAATTTCCAAA 3 14 1 TTACGGTGTT 0.975574 -86 TGATAAAATATAAGGGTTTTGGAAATTAAC 3 31 0 TAAGGGTTTT 0.945479 -69 CCTTTCTGGCTAACAATGTTTACTACTTGA 3 58 0 TAACAATGTT 0.939301 -42 AAGAAATCGATATGGGATTTACTGTAAT 4 224 1 TATGGGATTT 0.668346 -18 AGTTTTACTTTATCGATTTTCTTTACCAGC 5 21 0 TATCGATTTT 0.853257 -137 GATTCTGGACTTTCAGTTTTACTTTATCGA 5 35 0 TTTCAGTTTT 0.854193 -123 TTTATAAATTTAACAGAGTTAAGGCAAAAG 6 11 1 TAACAGAGTT 0.961471 -89 TTTATTAACTTAACAGTGTTAATTAACCTA 6 42 1 TAACAGTGTT 0.991101 -58 ********** Masking position 9 Map Score: 21.94 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 133 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 2 ATAATGTTAAATATAAACACTGTTAGGTAACAGTGTTTGG 1 23 0 ATAAGTGGAA 0.933157 -126 TTTTTTTCATATTCGAAGATTTTAGGGAAAAGGTAGATGT 2 11 1 ATAATTGGAA 0.981296 -52 CTACTTGATAAAATATAAGGGTTTTGGAAATTAACACCGT 3 26 0 AAAGTTGGAA 0.874439 -74 AAACATTGTTAGCCAGAAAGGTTCTGGCAAGAGGAGGTGG 3 67 1 AGAATTGGAA 0.99626 -33 TTTGTCTTACAGCATAATACTTTCCGGTAACTGGATTGTA 4 119 0 AGAATTGGAA 0.996268 -123 TGTAAGACAAAGGACTATCAGTTCAGGAAAAGCAGGGCAG 4 148 1 AGACTTGGAA 0.984218 -94 AAAGCAGGGCAGATAAAGAGGTTGTGGAAACCATCAAAAA 4 176 1 AGAATTGGAA 0.996268 -66 GGATGGAGAGTGTTTAAAATTTTCCGTAAACGAGTTAATT 5 116 0 TGAATTGTAA 0.866353 -42 AACTTAACAGTGTTAATTAACCTATGGCAATTGAAGTCGA 6 48 1 TGTACTGGAA 0.836158 -52 ATTGAAGTCGAGCTTCACAAACTGCGGGAATGG 6 77 1 AGAACTGGAA 0.992394 -23 ** * * ** ** ** Masking position 13 Map Score: 11.6414 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 106 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 3 TACCTAACAGTGTTTATATTTAACATTATA 1 34 1 TGTTTATATT 0.648516 -115 CTAAAATCGGTTTTGAAAATGCAATCAAAA 1 76 0 TTTTGAAAAT 0.792866 -73 AACCAAAAACTTTTTAAATTTAGGCTATCC 1 109 1 TTTTTAAATT 0.947556 -40 TGTTTACTACTTGATAAAATATAAGGGTTT 3 42 0 TTGATAAAAT 0.737277 -58 TTTTCATTACTTTTTAAATTTCTACCGCTT 4 37 0 TTTTTAAATT 0.947556 -205 ACAAAAGTGGTGGTTAAAATGACCAGCGAG 4 68 1 TGGTTAAAAT 0.934192 -174 TCTATTCCAACTTTTAAGATAGTCCAGTAC 5 73 0 CTTTTAAGAT 0.848384 -85 GGATGGAGAGTGTTTAAAATTTTCCGTAAA 5 126 0 TGTTTAAAAT 0.927873 -32 TGCCTTAACTCTGTTAAATTTATAAA 6 7 0 CTGTTAAATT 0.934205 -93 TTAATTAACACTGTTAAGTTAATAAATCTT 6 38 0 CTGTTAAGTT 0.859325 -62 ********** Masking position 6 Map Score: 7.01591 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 79 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 4 GCAATCAACATCTACCTTTTCCCTAAAATCTTCG 2 24 0 TCTCTTCCCT 0.89202 -39 TTTTTCGTTTTTTTTACGGTGTTAA 3 2 1 TTTCTTTTTT 0.943377 -98 TTTCCACCTCCTCTTGCCAGAACC 3 86 0 TTTCCCCTCT 0.983333 -14 GGATGTTTCCGTTAACCTTAGATTAAAAG 4 6 1 TTTCTTCCTT 0.927306 -236 ACTTTTTAAATTTCTACCGCTTTTAATCTAAGGT 4 25 0 TTTTCCTTTT 0.762076 -217 CACTTTTGTTTTTTCATTACTTTTTAAATTTCTA 4 43 0 TTTCTTTTTT 0.943377 -199 ATATTCTCTTTTTTCTCTTTCTCTCGCTGGTCAT 4 86 0 TTTCCTCTCT 0.989495 -156 AACCTCTTTATCTGCCCTGCTTTTCCTGAACTGA 4 165 0 TCTCCTTTTT 0.953654 -77 TTTTTGATGGTTTCCACAACCTCTTTATCTGCCC 4 182 0 TTTCCACTCT 0.936905 -60 TATCGATTTCTTTTCTCTCTTTTTTGATGGTTTC 4 202 0 TTTCCTTTTT 0.97355 -40 TCCTCCTGCGTCTATTCCAACTTTTAAGATAGTC 5 79 0 TCTTCCCTTT 0.798223 -79 TAATAAATCTTTTGCCTTAACTCTGTTAAATTTA 6 15 0 TTTCTTCTCT 0.977084 -85 *** * ** **** Masking position 3 Map Score: 13.0624 Number of sites scoring better than the average of aligned sites = 811 Number in coding regions = 734 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 5 CCCATCACCACCCCAAACACTGTTACC 1 8 1 CCACCCCAAA 0.931025 -141 TTTGAAAATGCAATCAAAAATGCATAATGC 1 65 0 CAATCAAAAA 0.917074 -84 CGATTTTAGGCCAACCAAAAACTTTTTAAA 1 97 1 CCAACCAAAA 0.961401 -52 TAAATTTAGGCTATCCTAAACATAACGGTG 1 123 1 CTATCCTAAA 0.94634 -26 GTTGTGGAAACCATCAAAAAAGAGAGAAAA 4 196 1 CCATCAAAAA 0.970351 -46 TGAAAGTCCAGAATCCAAAATATGTACTGG 5 50 1 GAATCCAAAA 0.870291 -108 ATGTACTGGACTATCTTAAAAGTTGGAATA 5 71 1 CTATCTTAAA 0.73178 -87 TAAACACTCTCCATCCAAGATCCAAACC 5 140 1 CCATCCAAGA 0.969573 -18 ********** Masking position 3 Map Score: 5.46167 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 200 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 ACAGTGTTTGGGGTGGTGATGGG 1 4 0 GGGTGGTGAT 0.897496 -145 TTTAGGGAAAAGGTAGATGTTGATTGCTGA 2 31 1 AGGTAGATGT 0.800312 -32 AGGTTCTGGCAAGAGGAGGTGGAAA 3 85 1 AAGAGGAGGT 0.981513 -15 GAAAAAACAAAAGTGGTGGTTAAAATGACC 4 62 1 AAGTGGTGGT 0.981513 -180 AGGGCAGATAAAGAGGTTGTGGAAACCATC 4 181 1 AAGAGGTTGT 0.88331 -61 GATTGGTGGAGCTGGTAAAGAAA 5 4 1 TGGTGGAGCT 0.936133 -154 GAATAGACGCAGGAGGAGATAATTAACTCG 5 96 1 AGGAGGAGAT 0.966044 -62 ATGGCAATTGAAGTCGAGCTTCACAAACTG 6 71 1 AAGTCGAGCT 0.894629 -29 ********** Masking position 10 Map Score: 3.88999 Number of sites scoring better than the average of aligned sites = 1627 Number in coding regions = 1514 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 7 GATTTTAGGGAAAAGGTAGATGTTGATTGC 2 28 1 AAAAGGTAGA 0.801205 -35 ACCTTAGATTAAAAGCGGTAGAAATTTAAA 4 25 1 AAAAGCGGTA 0.969671 -217 TAGAAATTTAAAAAGTAATGAAAAAACAAA 4 43 1 AAAAGTAATG 0.809375 -199 ATGAAAAAACAAAAGTGGTGGTTAAAATGA 4 60 1 AAAAGTGGTG 0.952223 -182 TCAGTTCAGGAAAAGCAGGGCAGATAAAGA 4 165 1 AAAAGCAGGG 0.94381 -77 AAACCATCAAAAAAGAGAGAAAAGAAATCG 4 203 1 AAAAGAGAGA 0.889473 -39 GCTGGTAAAGAAAATCGATAAAGTAAAACT 5 21 1 AAAATCGATA 0.692405 -137 GGACTATCTTAAAAGTTGGAATAGACGCAG 5 78 1 AAAAGTTGGA 0.915954 -80 ********** Masking position 4 Map Score: 1.48141 Number of sites scoring better than the average of aligned sites = 580 Number in coding regions = 519 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 8 ********** No masking Map Score: -1.41155e-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: -1.41155e-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 10 ********** No masking Map Score: -1.41155e-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