AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00740_ctra_reg_300.orf -o00740_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 truB 37 tRNA Pseudouridine Synthase #2 nusA 117 Transcription antitermination factor #3 rs1 244 S1 Ribosomal Protein #4 ribC 300 Riboflavin Synthase #5 ribD 41 Riboflavin Deaminase #6 ribA/ribB 109 GTP Cyclohydratase and DHBP Synthase Motif number 1 AAAAAGCAAAAAAAATAATGCTAACGGAGCAGAGCCCTA 2 63 0 AAAATCTGAG 0.890871 -55 CATTAAAATAAAAACCGTGGTATCTTGAGCGTCCTGCAG 4 67 0 AAAAGTAGAG 0.995164 -234 GCCCGTAGAGAAAACCTTTCTAAGAAGAGGTTCTTTTCA 4 128 0 AAAATTAGAG 0.987722 -173 TTATAATCAAAAAATAATTATACTCCGAGACCGCCCGTA 4 160 0 AAAATTAGAG 0.987722 -141 AGCAATCTTGAAAAACTAGATACACGAAAAAGCCCTCTC 4 228 0 AAAAGTAAAA 0.840165 -73 ACTCAACCTGAAAAATCAGATAGCGAGAGAGATGCAAGG 5 11 0 AAAAGTAGAG 0.995164 -31 GTTTTTGAGGAAAACTTAGCCAGTGGGAAACGTTCTTTG 6 67 0 AAAAGCAGAA 0.96384 -43 AGTTTTCCTCAAAAACGGGGTAGATTGAGA 6 90 1 AAAAGTAGAG 0.995164 -20 **** * ** *** Masking position 4 Map Score: 8.71574 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 46 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 CAAAAAGACAATCCTTCTGAACTCCA 1 5 1 AAGACAACTT 0.963859 -33 TAACACAATTCTTGATTGTGATT 4 2 1 AACACAACTT 0.989431 -299 AAAAAAAATCACCACAAATCACAATCAAGAAT 4 18 0 ACCACAACAC 0.985027 -283 GGTTCTTTTCAACACAAGACACAGGATTTTAT 4 107 0 AACACAACAC 0.987554 -194 CTAGGTCGTGACAACAATACTTTTTAGCAATC 4 260 0 ACAACAACTT 0.937335 -41 CGCAGAGTATAACACAAACCTCTACTTTCTGC 6 15 0 AACACAACTC 0.993291 -95 ******* *** Masking position 6 Map Score: 5.23744 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 27 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 GCATTATTTTTTTTGCTTTTTTTCCCTTAC 2 81 1 TTTTGCTTTT 0.955359 -37 CTGTCAATCCTTGAGATTTTCAAGGATATC 3 19 0 TTGAGATTTT 0.895005 -226 TAATTTTAGTTTTAGATTTTGTGTGTCGAA 3 89 0 TTTAGATTTT 0.95198 -156 GCAAGGGAAATCTTGCCTTTTTTAAGGTGA 3 174 1 TCTTGCCTTT 0.883587 -71 ACACTACTCTTTTTGACTTTGTAGTTTTTA 3 210 1 TTTTGACTTT 0.94956 -35 TAACACAATTCTTGATTGTGATTTGTGGT 4 10 1 TCTTGATTGT 0.894041 -291 TTGTGATTTGTGGTGATTTTTTTTCAAAAG 4 26 1 TGGTGATTTT 0.85278 -275 GATACCACGGTTTTTATTTTAATGGATAAA 4 82 1 TTTTTATTTT 0.79275 -219 TATAATTATTTTTTGATTATAAGTAACCGC 4 177 1 TTTTGATTAT 0.873447 -124 TTTTCGTGTATCTAGTTTTTCAAGATTGCT 4 237 1 TCTAGTTTTT 0.745573 -64 ********** Masking position 8 Map Score: 6.51249 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 253 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 TCTTATGTTTGCTCTTCACTAACGAAGATT 2 24 0 GCTCTTCACT 0.955961 -94 GAGCCCTAGAGCTCTGCTCTTATGTTTGCT 2 41 0 GCTCTGCTCT 0.988538 -77 GAGCTCTAGGGCTCTGCTCCGTTAGCATTA 2 57 1 GCTCTGCTCC 0.99488 -61 TTAATGATGTTCTCCTAAAAACTAC 3 230 0 GATGTTCTCC 0.950281 -15 ATAAGTAACCGCTGTTTGCCTTGATCAGAT 4 195 1 GCTGTTTGCC 0.953784 -106 TAATCCCCTCGCTGTGCGCAGAGTATAACA 6 33 0 GCTGTGCGCA 0.981411 -77 ********** Masking position 5 Map Score: 4.30935 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 126 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 ACGAAGATTATTAGTAAAGAGA 2 1 0 TTTAAAGAGA 0.982065 -117 GAAACTTTTTTTAATAAAGAGATGCATCTTAT 3 132 1 TTTAAAGAGA 0.982065 -113 AATCTTGCCTTTTTTAAGGTGAATATTTACAC 3 182 1 TTTAAGGTGA 0.918037 -63 GTGGTGATTTTTTTTCAAAAGTCGCCTAATAT 4 35 1 TTTCAAAAGT 0.872211 -266 AGAGAAAACCTTTCTAAGAAGAGGTTCTTTTC 4 129 0 TTTAAGAAGA 0.966517 -172 TTTTTCAAGATTGCTAAAAAGTATTGTTGTCA 4 252 1 TTTAAAAAGT 0.949155 -49 ** ******** Masking position 7 Map Score: 1.53619 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 83 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 CTCTTTACTAATAATCTTCGTTAGTGAAGA 2 12 1 ATAATCTTCG 0.943021 -106 TAATACTCCTCTTATGGGTAAG 2 106 0 ATACTCCTCT 0.973885 -12 AAAAATAATTATACTCCGAGACCGCCCGTA 4 160 0 ATACTCCGAG 0.961403 -141 GGTTTGTGTTATACTCTGCGCACAGCGAGG 6 27 1 ATACTCTGCG 0.982962 -83 TTCTTTGTCTATAATCCCCTCGCTGTGCGC 6 44 0 ATAATCCCCT 0.932945 -66 ********** Masking position 5 Map Score: 0.963057 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 43 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 TCCTTCTGAACTCCACTATCAATATT 1 22 1 CTCCTACAAT 0.991169 -16 TAGGGCTCTGCTCCGTTAGCATTATTTTTTTTG 2 63 1 CTCCTACATT 0.991169 -55 TTTGCTTTTTTTCCCTTACCCATAAGAGGAGTA 2 92 1 TTCCTACCAT 0.977628 -26 CCCCCTCCGATATCCTTGAAAATCTCA 3 5 1 CTCCTACCTT 0.994273 -240 **** ** **** Masking position 7 Map Score: 0.0134596 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 20 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: 6.20604e-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: 6.20604e-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: 6.20604e-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