AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00450_ctra_reg_300.orf -o00450_ctra_300.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -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 = 0.41 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 rl31 75 L31 Ribosomal Protein #2 pfrA 187 Peptide Chain Releasing Factor (RF-1) #3 rl19 25 L19 Ribosomal Protein #4 rnhB_2 63 Ribonuclease HII #5 fusA 41 Elongation Factor G #6 rs7 49 S7 Ribosomal Protein #7 rs12 259 S12 Ribosomal Protein Motif number 1 GTGTTCGCCCCGCTTTTCTCTAGATAACAG 2 26 0 CGCTTTTCTC 0.975973 -162 GCGAACACCCCGCTTTTTTTGTTTTAATAA 2 48 1 CGCTTTTTTT 0.983399 -140 TTTAATAAGTCTCTCTTTTTGAATCTGACT 2 70 1 CTCTCTTTTT 0.935578 -118 CCAATGTACACTCTGGTCTTTGTTAGAGAG 2 138 1 CTCTGGTCTT 0.968098 -50 TAATGCCGCTCTCTTTTCTTTA 4 3 0 CTCTTTTCTT 0.988661 -61 AAGCCCTTTCTGCTGTTCTCAACGTCAAGA 4 32 1 TGCTGTTCTC 0.819538 -32 CTCTTCGTATTTCTTTTCTTTAGGTTTAGG 6 19 0 TTCTTTTCTT 0.952253 -31 GATACAAGTCTTGTTTTCAAGTTTTTG 7 8 1 GTCTTGTTTT 0.932311 -252 AAGGATTTAACTCTTTTTTTATTAATTATT 7 72 1 CTCTTTTTTT 0.98204 -188 TTTTAGGGAAGGCTTGTTTTAAGAAAATCT 7 101 1 GGCTTGTTTT 0.937195 -159 ********** Masking position 4 Map Score: 14.9462 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 260 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 AATCACTATCTTAGTATGTGAAAATCTCACATA 1 40 0 TTAGTGGAAA 0.877008 -36 TGGCAATCAATTTTTGGGGAACACTAGACTTTA 2 108 0 TTTTTGAACA 0.869189 -80 CACTCTGGTCTTTGTTAGAGAGATACTAGAGTA 2 146 1 TTTGTGGAGA 0.994248 -42 AAAAAGAATTTTTAGGTGAAATACA 3 9 1 TTTTTGGAAA 0.939111 -17 ACGTTTAACATTCGTGTGTGAGAGGCAAAAAAG 5 15 1 TTCGTGGAGA 0.978816 -27 AAGAAAACATTTTATCAGCAAGGATTTAACTCT 7 53 1 TTTATGAAGG 0.946319 -207 TTATTAATTATTTTTAGGGAAGGCTTGTTTTAA 7 90 1 TTTTTGAAGG 0.978045 -170 TAAGAATATCTTTGTTTGCAAGGGGTTATTTCT 7 191 0 TTTGTGAAGG 0.991304 -69 TATTTCCCTGTTTGTAAGAGAGGTTGAATCGAG 7 229 1 TTTGTGGAGG 0.995554 -31 ***** * **** Masking position 5 Map Score: 10.6155 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 135 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 ACAACCCCAAAATCACTATCTTAGTATGTGA 1 52 0 AATCCTATCT 0.809483 -24 TTTCACCTAAAAATTCTTTTT 3 1 0 AAATCTTTTT 0.699513 -25 GAGCGGCATTAAGCCCTTTCTGCTGTTCTCA 4 22 1 AAGCCTTTCT 0.940515 -42 ATAAAGGCAATCTCTTGACGTTG 4 51 0 AAAGCAATCT 0.880853 -13 ATAAACTCAACCTCTTCGTATTT 6 37 0 AAACCAACCT 0.854636 -13 CTTGCTGATAAAATGTTTTCTTCGAATACTG 7 44 0 AAATTTTTCT 0.915879 -216 AAAAAGAGTTAAATCCTTGCTGATAAAATGT 7 59 0 AAATCTTGCT 0.887276 -201 ATTTCCTCCAAAAGATTTTCTTAAAACAAGC 7 112 0 AAAGTTTTCT 0.944808 -148 TTTTATTAAAAAACATTTCCTCCAAAAGATT 7 126 0 AAACTTTCCT 0.931577 -134 AGAGATCGATAAACTCTTACTAGACCTAGAA 7 164 1 AAACCTTACT 0.931443 -96 CCTTGCAAACAAAGATATTCTTATTCTATAT 7 201 1 AAAGTATTCT 0.872107 -59 **** ****** Masking position 2 Map Score: 6.88264 Number of sites scoring better than the average of aligned sites = 527 Number in coding regions = 527 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 AACCCCAAAATCACTATCTTAGTATGTGAA 1 51 0 TCACTATCTT 0.857855 -25 GAACGACTTCTTCTGCCTTTAC 2 176 0 ACGACTTCTT 0.798955 -12 GGGCTTAATGCCGCTCTCTTTTCTTTA 4 8 0 CCGCTCTCTT 0.954999 -56 ATAAAGGCAATCTCTTGACGTTGAGA 4 48 0 GCAATCTCTT 0.963119 -16 ATAAACTCAACCTCTTCGTATTTCTT 6 34 0 TCAACCTCTT 0.985917 -16 TAAGAGTTTATCGATCTCTATAACAATTTT 7 153 0 TCGATCTCTA 0.945067 -107 TCTTCTCGATTCAACCTCTCTTACAAACAG 7 236 0 TCAACCTCTC 0.962403 -24 ********** Masking position 7 Map Score: 2.23144 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 188 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 ACCCCGCTTTTTTTGTTTTAATAAGTCTCTCTT 2 54 1 TTTTTTAATA 0.953807 -134 TGGCAATCAATTTTTGGGGAACACTAGACTTTA 2 108 0 TTTTGGAACA 0.900875 -80 AAAAAGAATTTTTAGGTGAAATACA 3 11 1 TTTAGTAATA 0.819989 -15 GTTTTCAAGTTTTTGAACTAACAGTATTCGAAG 7 23 1 TTTTAAAACA 0.831831 -237 TGATAAAATGTTTTCTTCGAATACTGTTAGTTC 7 37 0 TTTTTTAATA 0.946185 -223 ATTTAACTCTTTTTTTATTAATTATTTTTAGGG 7 76 1 TTTTTAAATT 0.828973 -184 CTCCAAAAGATTTTCTTAAAACAAGCCTTCCCT 7 105 0 TTTTTTAACA 0.941254 -155 AGGAAATGTTTTTTAATAAAATTGTTATAGAGA 7 136 1 TTTTATAATT 0.856592 -124 **** ** **** Masking position 10 Map Score: 0.959032 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 132 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: 1.80068e-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: 1.80068e-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: 1.80068e-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