AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i113_bsub_mtub_300.orf -o113_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yflD 100 yflD #2 yflA 124 similar to aminoacid carrier protein #3 yrbD 300 similar to sodium/proton-dependent alanine carrier protein Motif number 1 AACTGGATCGGAAAAAAGGAGTGTAACA 1 9 0 GAAAAAAGGA 0.987116 -92 CGAAACGATAGAAAAAACGAACGTATCCAA 1 43 1 GAAAAAACGA 0.982239 -58 AACTTGGAACATAAAAAGGATGGCTTTTAT 2 38 0 ATAAAAAGGA 0.944173 -87 CAAGTTCTATGTCAAAAGGTTTATGTTTTT 2 62 1 GTCAAAAGGT 0.946005 -63 ATTCATAAACGAAAAAAGGGTGATGGG 2 108 1 GAAAAAAGGG 0.947091 -17 GTCAAACCGTATATAAAGGATAAAGCAATC 3 57 0 ATATAAAGGA 0.791203 -244 GCCTAGTTCAGTCAAACCGTATATAAAGGA 3 67 0 GTCAAACCGT 0.844669 -234 TGCCTCTGTAGAAAAACGCAGCGTAGTCGA 3 137 1 GAAAAACGCA 0.777939 -164 AAGGGAAAAAGAAAAAACGCGGCGTATCGA 3 163 0 GAAAAAACGC 0.928166 -138 CATATAATGTGACAAATCGATTGTAGAAAT 3 218 1 GACAAATCGA 0.926722 -83 AAGGATTTTGGTCTAATCGAACTATTTCTA 3 241 0 GTCTAATCGA 0.739145 -60 GAATACATGTATAAAAAGGATTTTGGTCTA 3 256 0 ATAAAAAGGA 0.944173 -45 ********** Masking position 5 Map Score: 14.4695 Number of sites scoring better than the average of aligned sites = 2456 Number in coding regions = 2110 Number in noncoding regions = 346 Number of orfs with sites within 600 bp upstream = 348 Fraction of orfs with sites within 600 bp upstream = 0.0558946 Motif number 2 CACTCCTTTTTTCCGATCCAGTTCGAGCGAAA 1 16 1 TTCCATCAGT 0.943062 -85 ACGTTCGTTTTTTCTATCGTTTCGCTCGAACT 1 35 0 TTTCATCTTT 0.981579 -66 ATTTTCACTTTTCTAATCTGCTGATTCGTGTT 1 76 0 TTCTATCGCT 0.895135 -25 GGTTTATGTTTTTCCATCTATGGGAAATGATT 2 79 1 TTTCATCATG 0.860278 -46 TCATCATTTGTTCCGTTCATCTTAT 3 4 0 TTCCTTCTCT 0.973935 -297 ATTGAAATGCTTTTCATCATTTGTTCCGTTCA 3 17 0 TTTTATCTTT 0.924174 -284 ATGAAAAGCATTTCAATCATTTTGTGATTGCT 3 32 1 TTTCATCTTT 0.981579 -269 TTTTTTCTTTTTCCCTTCCTCTTCTTATTGAT 3 176 1 TTCCTTCTCT 0.973935 -125 **** *** *** Masking position 7 Map Score: 5.91292 Number of sites scoring better than the average of aligned sites = 717 Number in coding regions = 613 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 3 TGGCTTTTATCAATCGCCATCCTGCAGACA 2 18 0 CAATCGCCAT 0.871957 -107 TGGCGATTGATAAAAGCCATCCTTTTTATG 2 29 1 TAAAAGCCAT 0.835217 -96 GATGGAAAAACATAAACCTTTTGACATAGA 2 67 0 CATAAACCTT 0.868757 -58 GTTTATGAATCATTTCCCATAGATGGAAAA 2 88 0 CATTTCCCAT 0.920695 -37 CCCATCACCCTTTTTTCGTTTA 2 113 0 CATCACCCTT 0.922164 -12 TTTGTGATTGCTTTATCCTTTATATACGGT 3 52 1 CTTTATCCTT 0.851368 -249 GCAATTGTTATAAAATCCTTCAGCAACAAA 3 99 0 TAAAATCCTT 0.82515 -202 GATTTTATAACAATTGCCATAAGTTTGCCT 3 112 1 CAATTGCCAT 0.920695 -189 GCGTTTTTTCTTTTTCCCTTCCTCTTCTTA 3 173 1 TTTTTCCCTT 0.571388 -128 TCGATTAGACCAAAATCCTTTTTATACATG 3 251 1 CAAAATCCTT 0.943584 -50 ********** Masking position 10 Map Score: 3.93517 Number of sites scoring better than the average of aligned sites = 1916 Number in coding regions = 1654 Number in noncoding regions = 262 Number of orfs with sites within 600 bp upstream = 263 Fraction of orfs with sites within 600 bp upstream = 0.0422422 Motif number 4 GTCTGCAGGATGGCGATTGATAAAAGCCATCCTT 2 19 1 TGGGATTGTA 0.99077 -106 TTCCCATAGATGGAAAAACATAAACCTTTTGACA 2 71 0 TGGAAAACTA 0.894974 -54 TTTCCATCTATGGGAAATGATTCATAAACGAAAA 2 89 1 TGGAAATGTA 0.985784 -36 TTCAATCATTTTGTGATTGCTTTATCCTTTATAT 3 43 1 TTGGATTGTA 0.95363 -258 GGCAAACTTATGGCAATTGTTATAAAATCCTTCA 3 107 0 TGGAATTGTA 0.992318 -194 AAATCGATTGTAGAAATAGTTCGATTAGACCAAA 3 231 1 TAGAATAGTA 0.924867 -70 *** ***** * * Masking position 6 Map Score: 1.96982 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 127 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 GCGTATCGACTACGCTGCGTTTTTCTACAG 3 142 0 TACGCTGCGT 0.99647 -159 GCGTAGTCGATACGCCGCGTTTTTTCTTTT 3 157 1 TACGCCGCGT 0.997615 -144 ********** Masking position 2 Map Score: 0.200344 Number of sites scoring better than the average of aligned sites = 2 Number in coding regions = 1 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 ********** No masking Map Score: 1.3033e-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 7 ********** No masking Map Score: 1.3033e-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 8 ********** No masking Map Score: 1.3033e-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