AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -intrC_ctra_opreg_100.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 glnP 206 ABC Amino Acid Transporter Permease #2 CT466 293 hypothetical protein #3 atoC 42 2-component regulatory system-ATPase Motif number 1 TCTTTTATCGAAAAAATTTTATACGACTTCT 1 96 0 AAAAATTTTA 0.855077 -111 TTTCCTAATTAAAATCTTTTATCGAAAAAAT 1 110 0 AAAACTTTTA 0.92117 -97 TTCTTATAAAAAAAGCCTTTCCTAATTAAAA 1 127 0 AAAACCTTTC 0.983369 -80 CTTTTTTTATAAGAACCTTTCGTTCAATATA 1 143 1 AAGACCTTTC 0.940026 -64 TTTGTTAAGGAAAATACGCTCAGCAGAGGTA 2 12 0 AAAAACGCTC 0.949053 -282 CCTTAACAAAAAAACCTTCTCTCCCCTATAC 2 33 1 AAAACTTCTC 0.98592 -261 CTGTCAGGGGAAAAAACTCTATTTCTTCTTC 2 86 1 AAAAACTCTA 0.958011 -208 CGGTAGACTCAAAATCTACTCTTAGCAGTAA 2 164 1 AAAACTACTC 0.926302 -130 TATCAAATGCAAAACACTCACCTCTGAAAAA 3 18 1 AAAAACTCAC 0.917056 -25 **** ****** Masking position 4 Map Score: 9.85073 Number of sites scoring better than the average of aligned sites = 457 Number in coding regions = 457 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 GTATTGTCGGCTTACAAGATAGTTTATTAGG 1 16 0 CTACAAGATA 0.982669 -191 TGTCATTAGTATCACAAGAAATGTATGTAAC 1 174 0 ATACAAGAAA 0.984401 -33 TGTGATACTAATGACAGGATAGGGGATA 1 189 1 ATACAGGATA 0.970719 -18 GTTTTTTCCCCTGACAGGAAATATCCTTAAG 2 72 0 CTACAGGAAA 0.993682 -222 GTCTGAAAACAGAAGAAGAAATAGAGTTTTT 2 97 0 AGAGAAGAAA 0.890874 -197 TTCGCGTTCTCTTTCAAGAAAAGGGTCCTAC 2 259 0 CTTCAAGAAA 0.96436 -35 AAAGAGAACGCGAACAGGCAACTCTTTT 2 276 1 CGACAGGCAA 0.970228 -18 ** ******** Masking position 6 Map Score: 6.57031 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 81 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 TATCTTGTAAGCCGACAATACTTTTGGAGG 1 26 1 GCCGACAATA 0.98703 -181 ATTTTATATGGCCTCCAAAAGTATTGTCGG 1 37 0 GCCTCCAAAA 0.965974 -170 ATTCCGCCACGCCGGCATAACCATCTAGGT 2 126 0 GCCGGCATAA 0.995205 -168 GAGTCCAATCGCCGGCATTAATCACATTTC 2 206 1 GCCGGCATTA 0.995205 -88 ********** Masking position 7 Map Score: 3.6955 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 15 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 TATCCCCTATCCTGTCATTAG 1 196 0 TTCCCCTATC 0.983957 -11 AAAAACCTTCTCTCCCCTATACTTTGTCCTC 2 42 1 TTCCCCTATA 0.982702 -252 CCCTATACTTTGTCCTCTTAAGGATATTTCC 2 56 1 TTCCTCTTAA 0.953468 -238 AATAGAGTTTTTTCCCCTGACAGGAAATATC 2 78 0 TTCCCCTGAC 0.992698 -216 TGCAAAACACTCACCTCTGAAAAACCCC 3 25 1 TACCTCTGAA 0.944406 -18 * ********* Masking position 8 Map Score: 1.93886 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 59 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 TTTTATACGACTTCTGTTTCGAAAAAAAAT 1 81 0 CTTCTGTTTC 0.992261 -126 ACAAAAAAACCTTCTCTCCCCTATACTTTG 2 38 1 CTTCTCTCCC 0.977836 -256 TCTATTTCTTCTTCTGTTTTCAGACCTAGA 2 103 1 CTTCTGTTTT 0.969945 -191 GCCTGTTCGCGTTCTCTTTCAAGAAAAGGG 2 265 0 GTTCTCTTTC 0.979521 -29 ********** Masking position 5 Map Score: 1.27928 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 73 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 CTTACAAGATAGTTTATTAGGATGAT 1 7 0 AGTTTATTAG 0.829831 -200 ACTCGTGTACATTTTATATGGCCTCCAAAA 1 47 0 ATTTTATATG 0.879025 -160 CGAGTTTTTATTTTTTTTCGAAACAGAAGT 1 72 1 TTTTTTTTCG 0.818935 -135 TATCGAAAAAATTTTATACGACTTCTGTTT 1 92 0 ATTTTATACG 0.951949 -115 CGATAAAAGATTTTAATTAGGAAAGGCTTT 1 117 1 TTTTAATTAG 0.819152 -90 GGAAAGGCTTTTTTTATAAGAACCTTTCGT 1 136 1 TTTTTATAAG 0.967088 -71 GAGAAGGTTTTTTTGTTAAGGAAAATACGC 2 24 0 TTTTGTTAAG 0.878871 -270 AGTGTTTTGCATTTGATAACTGCTC 3 6 0 ATTTGATAAC 0.76637 -37 ********** Masking position 4 Map Score: 1.96935 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 204 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: 2.36911e-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: 2.36911e-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: 2.36911e-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