AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i110_Amino_Acid_Transport_1_aful_reg_100.orf -o110_aful_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 Input sequences: #1 RAG48384 262 Archaeoglobus_fulgidus #2 RAG48385 39 Archaeoglobus_fulgidus #3 RAG50406 145 Archaeoglobus_fulgidus #4 RAG00797 148 Archaeoglobus_fulgidus #5 RAG07898 50 Archaeoglobus_fulgidus #6 RAG07804 89 Archaeoglobus_fulgidus Motif number 1 TTTAGAGCATAAACCCATACACAAGCACGGA 1 51 1 AAACCATACA 0.77979 -212 AGCCAAAGCTAAACCTAAAATAAAATCCAAA 1 124 1 AAACTAAAAT 0.971665 -139 ACCTAAAATAAAATCCAAACACCCTGGTTTT 1 136 1 AAACCAAACA 0.968327 -127 AAAAATTGGAAAAGCTTAAATACATGCTGCT 1 195 0 AAACTTAAAT 0.946769 -68 TTCGATAGATAAATCAAAAATTGGAAAAGCT 1 210 0 AAACAAAAAT 0.937178 -53 CACAATTTTTAAAACTTAAAAAATTTTCGAT 1 235 0 AAACTTAAAA 0.946769 -28 TTTATATAACAAACCTAAACTTCAAGCG 3 128 1 AAACTAAACT 0.950424 -18 GCACTTTAGGATAACCAAAATC 4 2 0 ATACCAAAAT 0.863652 -147 TAATTGGAAAAAAACCAAAAAGGTTTTATAC 4 108 1 AAACCAAAAA 0.982042 -41 TAGGATTGCAAAAGTATAAAACCTTTTTGGT 4 121 0 AAATATAAAA 0.63073 -28 AGATTTTACAAACTCAAAATCTTTCCAAAT 5 10 1 AAATCAAAAT 0.923502 -41 TACAACGTTAAAATTTTAAAACTTTACTAAA 6 22 0 AAATTTAAAA 0.797007 -68 *** ******* Masking position 3 Map Score: 14.3218 Number of sites scoring better than the average of aligned sites = 364 Number in coding regions = 229 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 2 TTTAAAACTTAAAAAATTTTCGATAGATAA 1 229 0 AAAAAATTTT 0.903903 -34 GGAGGGATATAAAAAATTTTTTTG 2 5 0 AAAAAATTTT 0.903903 -35 CGCACGAGAAAAAAGATTTTATATAACAAA 3 111 1 AAAAGATTTT 0.89711 -35 ACTCCATGAGGAAAAATTTCACTTTCTATG 4 53 1 GAAAAATTTC 0.893547 -96 AAAAAAACCAAAAAGGTTTTATACTTTTGC 4 115 1 AAAAGGTTTT 0.887742 -34 AAAAAATTTGGAAAGATTTTGAGTTTGTAA 5 16 0 GAAAGATTTT 0.948047 -35 TGAGACCGTCAAAAAATTTGGAAAGATTTT 5 26 0 AAAAAATTTG 0.919816 -25 CCGAGCTTTAGTAAAGTTTTAAAATTTTAA 6 16 1 GTAAAGTTTT 0.894128 -74 TTATACAACGTTAAAATTTTAAAACTTTAC 6 26 0 TTAAAATTTT 0.750177 -64 AGGGGGAACAAAATAGTTTTGGCGGCCGTA 6 67 1 AAATAGTTTT 0.836754 -23 ********** Masking position 7 Map Score: 12.2052 Number of sites scoring better than the average of aligned sites = 245 Number in coding regions = 113 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 3 ATTTAAGCTTTTCCAATTTTTGATTTATCTATC 1 205 1 TCCATTTTGA 0.941161 -58 GAGGGCTCACAATTTTTAAAACTTAAAAA 1 244 0 TACATTTTAA 0.94638 -19 TTTTATATCCCTCCTTTTTTTAAGGCTCA 2 21 1 CCCTTTTTAA 0.967597 -19 TACACCACCTTGTTTAACTCTATTAAT 3 5 1 CACTTTTTAA 0.949561 -141 ACTCTATTAATCCCTCTATATAAACATTATACT 3 27 1 TCCCTTATAA 0.964603 -119 TACTAACTGTTGCCTCTCTTTAAAATTCACTTC 3 56 1 TCCCTTTTAA 0.977638 -90 AGGAAAAATTTCACTTTCTATGATGTACAGTGG 4 61 1 TACTTTATGA 0.921477 -88 TTTAAAATTTTAACGTTGTATAAACGCTATGCG 6 33 1 TACTTTATAA 0.953966 -57 * ** ** ***** Masking position 13 Map Score: 4.93935 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 39 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 GAGGTGTTCTGCAGTGGCTCCGTGCTTGTGT 1 69 0 GCAGTGGCTC 0.961306 -194 TTTGGCTACTGGTTTAGCTTCTAATTAGCGG 1 100 0 GGTTTAGCTC 0.98985 -163 TTTAGGTTTAGCTTTGGCTACTGGTTTAGCT 1 112 0 GCTTTGGCTC 0.996537 -151 AAACACCCTGGTTTTGGCTACACCATGCATT 1 152 1 GTTTTGGCTC 0.994659 -111 ATTGGAGGAAGGTTTAGCAGCATGTATTTAA 1 180 1 GGTTTAGCAC 0.967303 -83 GAACAAAATAGTTTTGGCGGCCGTATTA 6 72 1 GTTTTGGCGC 0.98824 -18 ********* * Masking position 5 Map Score: 7.51736 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 80 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 AACCCATACACAAGCACGGAGCCACTGCAGA 1 62 1 CAAGCAGGAG 0.977397 -201 GGTGTAGCCAAAACCAGGGTGTTTGGATTTT 1 145 0 AAACCAGGTG 0.982687 -118 ACCTTCCTCCAATGCATGGTGTAGCCAAAAC 1 162 0 AATGCAGGTG 0.985291 -101 GAAAAGCTTAAATACATGCTGCTAAACCTTC 1 187 0 AATACAGCTG 0.891189 -76 TGAGCCTTAAAAAAAGGAGGGATATAAAA 2 21 0 AAAAAAGGAG 0.907025 -19 TTAATAGAGTTAAACAAGGTGGTGTA 3 6 0 TAAACAGGTG 0.960255 -140 AAACTTTACTAAAGCTCGGAGTCT 6 4 0 AAAGCTGGAG 0.960864 -86 ****** **** Masking position 2 Map Score: 4.01905 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 267 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 GCAGAACACCTCCCGCTAATTAGAAGCTAAAC 1 88 1 TCCCCTATTA 0.976032 -175 ATTTTTTATATCCCTCCTTTTTTTAAGGCTCA 2 18 1 TCCCCCTTTT 0.923581 -22 ACTCTATTAATCCCTCTATATAAACATTATAC 3 27 1 TCCCCTTATA 0.989418 -119 TACTAACTGTTGCCTCTCTTTAAAATTCACTT 3 56 1 TGCCCTTTTA 0.968474 -90 AGCATTAGACTCCCACTGTACATCATAGAAAG 4 74 0 TCCCCTTACA 0.987264 -75 ACTATTTTGTTCCCCCTTCGCATAGCGTTTAT 6 52 0 TCCCCTCGCA 0.967047 -38 **** ** **** Masking position 1 Map Score: 1.54634 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 123 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 TTCTGCAGTGGCTCCGTGCTTGTGTATGGG 1 64 0 GCTCCGTGCT 0.962356 -199 GGTTTTGGCTACACCATGCATTGGAGGAAG 1 161 1 ACACCATGCA 0.935635 -102 ACAAACCTAAACTTCAAGCG 3 136 1 ACTTCAAGCG 0.940317 -10 AATTAGTGAAACTCCATGAGGAAAAATTTC 4 43 1 ACTCCATGAG 0.967101 -106 AGACTCCGAGCTTTAGTAAAGT 6 3 1 ACTCCGAGCT 0.974006 -87 CGTTGTATAAACGCTATGCGAAGGGGGAAC 6 46 1 ACGCTATGCG 0.929787 -44 ********** Masking position 8 Map Score: 0.478749 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 269 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 ********** No masking Map Score: -2.95996e-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 9 ********** No masking Map Score: -2.95996e-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 10 ********** No masking Map Score: -2.95996e-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