AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -iglpR_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 uhpC 300 Hexosphosphate Transport #2 CT565 90 hypothetical protein #3 CT569 61 predicted OMP [leader (16) peptide] #4 CT573 127 hypothetical protein #5 mutL 294 DNA Mismatch Repair #6 CT646 100 hypothetical protein Motif number 1 CTCTCTATTATTTCTTTTATTTGACACACC 1 9 1 TTTTCTTTAT 0.763342 -292 TATGCATTTGTATTTTTCTTAAGCTTCTAGAG 1 251 1 TTTTTTTTAA 0.92989 -50 TGGTTTTTTATGTTTATATTTAAATTATCTTT 2 12 1 TTTTATTTTA 0.904526 -79 CCATACCTGATTTTTTTCTTTTTATTAAATTA 2 66 0 TTTTTTTTTT 0.986562 -25 ATTGTTTTCTTTTTTTTGTTTTCTTCACAGTT 3 23 0 TTTTTTTTTT 0.986562 -39 TAAAAGCCGATTTTTTTGTTTTTTAACAAAAA 4 18 1 TTTTTTTTTT 0.986562 -110 AGAAAAGCCGTTTTTTTGTTAAAAAACAAAAA 4 30 0 TTTTTTTTAA 0.92989 -98 ACGGCTTTTCTTATTTTCTTTTGTAAAAATTG 4 51 1 TATTTTTTTT 0.956732 -77 TTGTAAAAATTGATTTTTTTTCTCAAATCAGT 4 71 1 TATTTTTTTC 0.791488 -57 TTTATACAATTCTTTTTTGTTTCTCTGTTGTT 4 106 1 TTTTTTGTTT 0.891711 -22 AGTAATTTGTTATTTTTATTTTTTTAGGAATT 5 17 0 TTTTTTTTTT 0.986562 -278 ATATTAAAAACGTTTTTATTAATTAACTTGTT 5 81 0 CTTTTTTTAA 0.743963 -214 ACGTTTTTAATATTTTGCTTTTAATAAAACAT 5 100 1 TTTTTGTTTT 0.891711 -195 CAAAAAGAATTAATTATGTTTTATTAAAAGCA 5 115 0 TATTATTTTT 0.836456 -180 CGTTGCCTTGCAATTTTTTTTAACAGGAGGTA 5 177 1 CATTTTTTTA 0.729921 -118 TTATAATTAATGTTTTTCTTGAAAAAGATGTT 6 25 1 TTTTTTTTGA 0.856628 -76 TTGAAAAAGATGTTTTTATTTTTTAAAATGAG 6 43 1 TTTTTTTTTT 0.986562 -58 TTAGCGTTTTTCTTTATCTTTTTAAAATGAAG 6 79 0 TTTTATTTTT 0.944387 -22 * ***** **** Masking position 5 Map Score: 29.3319 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 301 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 GAGAGTAAGGTGTGTCAAATAAAAGAAATAAT 1 17 0 TGTGTAAATA 0.87911 -284 ATACGTTTGCTGTGTAAAGAGAGGGAGTAGGG 1 82 0 TGTGTAAGAA 0.853528 -219 GCTTAATAGCTTTTAGAAGACAATACGTTTGC 1 104 0 TTTTAAAGAA 0.928044 -197 TTTTTTTCTTTTTATTAAATTAATCTCGTACT 2 56 0 TTTATAAATA 0.867547 -35 GCCGTTTTTTTGTTAAAAAACAAAAAAATCGG 4 24 0 TGTTAAAAAA 0.913 -104 AAAAATCAATTTTTACAAAAGAAAATAAGAAA 4 57 0 TTTTAAAAAA 0.934673 -71 AAGTAACTGATTTGAGAAAAAAAATCAATTTT 4 76 0 TTTGAAAAAA 0.889909 -52 AAAAAAGAATTGTATAAAGTAACTGATTTGAG 4 92 0 TGTATAAGTA 0.869472 -36 ATTTTTATTTTTTTAGGAATTATCGCG 5 6 0 TTTTAGAATA 0.687507 -289 AATTTAATATTGTTAGTAGTAATTTGTTATTT 5 34 0 TGTTATAGTA 0.726742 -261 AACGATCTGATTTAACAAGTTAATTAATAAAA 5 68 1 TTTAAAAGTA 0.891992 -227 ATATTTTGCTTTTAATAAAACATAATTAATTC 5 109 1 TTTAAAAAAA 0.8869 -186 CGGTACCTCCTGTTAAAAAAAATTGCAAGGCA 5 180 0 TGTTAAAAAA 0.916397 -115 TAAAAAACTCTGTTTATAATTAATGTTTTTCT 6 12 1 TGTTTTAATA 0.678029 -89 TAAAAACATCTTTTTCAAGAAAAACATTAATT 6 29 0 TTTTTAAGAA 0.863533 -72 GAGCGCTCATTTTAAAAAATAAAAACATCTTT 6 48 0 TTTAAAAATA 0.902411 -53 TTTCTTTATCTTTTTAAAATGAAGAGCGCTCA 6 71 0 TTTTTAAATA 0.919161 -30 ***** **** * Masking position 8 Map Score: 18.1033 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 448 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 CAGCAAACGTATTGTCTTCTAAAAGCTATT 1 102 1 ATTGTCTTCT 0.917106 -199 CATTTAGCTTAATAGCTTTTAGAAGACAAT 1 112 0 AATAGCTTTT 0.918389 -189 AGACGAAAGTATCAGCTTCTAAGACCTCGT 1 218 0 ATCAGCTTCT 0.940202 -83 TTATATTTAAATTATCTTTTGATAATTGTT 2 25 1 ATTATCTTTT 0.968922 -66 AAACAAAAAAATCGGCTTTTATATGAAA 4 9 0 ATCGGCTTTT 0.967926 -119 TTAACAAAAAAACGGCTTTTCTTATTTTCT 4 40 1 AACGGCTTTT 0.931226 -88 GGCTTTTCTTATTTTCTTTTGTAAAAATTG 4 53 1 ATTTTCTTTT 0.866241 -75 AAAAGAATTAATTATGTTTTATTAAAAGCA 5 115 0 ATTATGTTTT 0.801559 -180 AAAAAATAAAAACATCTTTTTCAAGAAAAA 6 37 0 AACATCTTTT 0.938223 -64 AGCGTTTTTCTTTATCTTTTTAAAATGAAG 6 79 0 TTTATCTTTT 0.814447 -22 ********** Masking position 7 Map Score: 9.67805 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 216 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 TCTTCACAGTTTCCCTCCTGTAG 3 4 0 TTCCCTCCTG 0.995786 -58 GGAGGTAACGGTACCTCCTGTTAAAAAAAA 5 190 0 GTACCTCCTG 0.988964 -105 GGAGGTACCGTTACCTCCTGCGCGAAAGGC 5 202 1 TTACCTCCTG 0.993497 -93 ACTTCACGCTTTCTCTCGTGCTGTCTCTCA 5 236 1 TTCTCTCGTG 0.956874 -59 ********** Masking position 6 Map Score: 3.46914 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 12 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 TAGCTTTTAGAAGACAATACGTTTGCTGTG 1 100 0 AAGACAATAC 0.869678 -201 TAAGCTTCTAGAGCAAACACACTTGAATCG 1 270 1 GAGCAAACAC 0.964517 -31 CACTTGAATCGAGCTAACACCT 1 289 1 GAGCTAACAC 0.849381 -12 ATTTAATAAAAAGAAAAAAATCAGGTATGG 2 68 1 AAGAAAAAAA 0.901513 -23 GGAAACTGTGAAGAAAACAAAAAAAAGAAA 3 20 1 AAGAAAACAA 0.97106 -42 AAACAAAAAAAAGAAAACAATCCATTACGT 3 34 1 AAGAAAACAA 0.97106 -28 ATTTTTACAAAAGAAAATAAGAAAAGCCGT 4 51 0 AAGAAAATAA 0.901513 -77 TAACTGATTTGAGAAAAAAAATCAATTTTT 4 75 0 GAGAAAAAAA 0.921782 -53 TATTCAGTGAGAGACAGCACGAGAGAAAGC 5 243 0 GAGACAGCAC 0.880354 -52 ********** Masking position 6 Map Score: 7.77299 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 139 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: 2.65333e-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: 2.65333e-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: 2.65333e-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