AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -icspA_ctra_opreg_300.orf -g0.413 -x5 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 = 0.413 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 CT191 146 hypothetical protein #2 CT192 26 hypothetical protein #3 tgt 126 Queuine tRNA Ribosyl Transferase #4 mgtE 300 Mg++ Transporter (CBS Domain) Motif number 1 ACTACCCATTTTAAGAATCCAAGGATTTAC 1 18 1 TTAAGAATCC 0.888805 -129 GTTGCGAACTAAAAAAGTCAAAGTATTAGC 1 59 0 AAAAAAGTCA 0.86479 -88 CGCAACAAGTATAAGAGCCTTCTTCCTGAG 1 83 1 ATAAGAGCCT 0.962216 -64 AAAAAGAATCTCATAATCGCG 2 16 0 AAAAGAATCT 0.9601 -11 AGACATAGTGAAAAAAGCCCGAAGAAAACC 3 31 0 AAAAAAGCCC 0.907002 -96 TATCTGTTTGTAAAGTATCTTTTTATAGTG 4 63 1 TAAAGTATCT 0.676204 -238 AGACTCTTAAACAAGAGTCCTTCACTATAA 4 85 0 ACAAGAGTCC 0.955121 -216 GGACTCTTGTTTAAGAGTCTCGGAAGACTT 4 95 1 TTAAGAGTCT 0.978412 -206 ACGAAAACGACAAAAAGTCTTCCGAGACTC 4 109 0 CAAAAAGTCT 0.91654 -192 TCGTTTTCGTAAAAAAGTCTCTTAATAGAT 4 129 1 AAAAAAGTCT 0.972745 -172 TAGACGACTTTTAAGAGTCTTTATATAAAG 4 208 1 TTAAGAGTCT 0.978412 -93 ********** Masking position 4 Map Score: 13.6294 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 289 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 2 AGAAGGCTCAGGAAGAAGGCTCTTATACTT 1 89 0 GGAAGAAGGC 0.941579 -58 GAGCCTTCTGCGAAGGAAGGTGTGCTTGCG 1 110 1 CGAAGGAAGG 0.98461 -37 TTGCGCATATCGAAGGAGCGTT 1 135 1 CGAAGGAGCG 0.973139 -12 TGGGTGAGTCCGAAGACAAAGGTTTTCTTC 3 11 1 CGAAGACAAA 0.873548 -116 GAAAAAAGCCCGAAGAAAACCTTTGTCTTC 3 22 0 CGAAGAAAAC 0.978603 -105 TAAAGAGAGAGGGAGAAAAGACATAGTGAA 3 49 0 GGGAGAAAAG 0.949351 -78 CAGAAGAAACGAAGCTTACAG 4 2 1 AGAAGAAACG 0.920981 -299 ATATAAAGAACGGAGAAGGGCGTGAAAGAG 4 230 1 CGGAGAAGGG 0.981403 -71 AAAATAGAAACGAAGAAAAATTGGATGTTG 4 261 1 CGAAGAAAAA 0.967285 -40 ********** Masking position 4 Map Score: 10.2657 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 228 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 3 CTTTTCTCCCTCTCTCTTTAGAATGATTCATG 3 59 1 TCTCTTTTAA 0.986001 -68 TGAATTTTATTATTTTTTTAGAATTCGCTTAG 3 89 1 TATTTTTTAA 0.965408 -38 TGCCTAAGTGTATCTGTTTGTAAAGTATCTTT 4 53 1 TATCTTTTGA 0.947507 -248 GTTTGTAAAGTATCTTTTTATAGTGAAGGACT 4 68 1 TATCTTTTAA 0.983174 -233 AGTGAAGGACTCTTGTTTAAGAGTCTCGGAAG 4 89 1 TCTTGTTAAA 0.819904 -212 TACCTCAGACTATCTATTAAGAGACTTTTTTA 4 138 0 TATCTTTAAA 0.943425 -163 CCTTCTCCGTTCTTTATATAAAGACTCTTAAA 4 217 0 TCTTTTATAA 0.862251 -84 ***** **** * Masking position 12 Map Score: 3.51426 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 99 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 4 AGTCAAAGTATTAGCGCTAAGTTCTAGTAAAT 1 42 0 TTAGCGCAAT 0.988383 -105 GGTATTAGATTTGGCGAGACTTTAGACCGAAT 4 166 1 TTGGCGAACT 0.992249 -135 AAGTCGTCTATTAGCGACACATTCGGTCTAAA 4 186 0 TTAGCGAACT 0.995445 -115 TTTCCGGAAGTTAGCGCAACATCCAATTTTTC 4 275 0 TTAGCGCACT 0.997042 -26 ******* ** * Masking position 9 Map Score: 3.24571 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 5 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 5 ATGAATCATTCTAAAGAGAGAGGGAGAAAAG 3 59 0 CTAAAAGAGA 0.976736 -68 TAAGCGAATTCTAAAAAAATAATAAAATTCA 3 89 0 CTAAAAAATA 0.935142 -38 AAGATACTTTACAAACAGATACACTTAGGCA 4 53 0 ACAAAAGATA 0.934154 -248 GTCCTTCACTATAAAAAGATACTTTACAAAC 4 68 0 ATAAAAGATA 0.969224 -233 AAAAAAGTCTCTTAATAGATAGTCTGAGGTA 4 139 1 CTTAAAGATA 0.958321 -162 CGTGAAAGAGCAAAATAGAAACGAAGAAAAA 4 250 1 CAAAAAGAAA 0.895942 -51 ***** ***** Masking position 5 Map Score: 2.2675 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 74 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 6 ********** No masking Map Score: -7.36532e-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: -7.36532e-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: -7.36532e-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