AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ilacI_ecoli_hinf_300.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 lacA 65 thiogalactoside acetyltransferase #2 lacY 51 galactoside permease (M protein) #3 lacZ 122 beta-D-galactosidase #4 lacI 76 transcriptional repressor of the lac operon #5 mhpR 76 transcriptional regulator for mhp operon Motif number 1 TTGGTCGGATAAGGCGCTCGCGCCGCATCCGAC 1 20 0 AAGCTCGCGC 0.990037 -46 AATGGATTTCCTTACGCGAAATACGGG 2 35 0 GATCTTACGC 0.97096 -17 AACTCACATTAATTGCGTTGCGC 3 1 0 AATGTTGCGC 0.997387 -122 TCCTGTGTGAAATTGTTATCCGCTCACAATTCC 3 93 0 AATTATCCGC 0.927589 -30 CCATACCGCGAAAGGTTTTGCGCCATTCGATGG 4 13 0 AAGTTTGCGC 0.994014 -64 ACCCTGAATTGACTCTCTTCCGGGCGCTATCAT 4 47 0 GATCTTCCGG 0.937867 -30 ACTCGGACAAAATGTCGTTGCGCGCACAGTACA 5 25 1 AAGGTTGCGC 0.997334 -52 GTTTTTAACAAAATAAGTTGCGCTGTACTGTGC 5 48 0 AATGTTGCGC 0.997386 -29 ** * ******* Masking position 2 Map Score: 12.1452 Number of sites scoring better than the average of aligned sites = 627 Number in coding regions = 564 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 2 CAATGTCGGATGCGGCGCGAGCGCCTTATC 1 16 1 TGCGGCGCGA 0.965633 -50 AATGGATTTCCTTACGCGAAATACGGG 2 35 0 TTCCTTACGC 0.977348 -17 TCACATTAATTGCGTTGCGC 3 1 0 TGCGTTGCGC 0.99466 -122 AATGGCGCAAAACCTTTCGCGGTATGGCAT 4 19 1 AACCTTTCGC 0.891082 -58 ATTGACTCTCTTCCGGGCGCTATCATGCCA 4 43 0 TTCCGGGCGC 0.982664 -34 TTCAGTACCTCACGACTCGGACAAA 5 6 1 TACCTCACGA 0.925318 -71 AGTTGCGCTGTACTGTGCGCGCAACGACAT 5 36 0 TACTGTGCGC 0.982278 -41 TTTAACAAAATAAGTTGCGCTGTACTGTGC 5 48 0 TAAGTTGCGC 0.961669 -29 ********** Masking position 8 Map Score: 7.29862 Number of sites scoring better than the average of aligned sites = 3007 Number in coding regions = 2815 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 3 CGCGCCGCATCCGACATTGATTGC 1 2 0 CCGCATTGTG 0.969532 -64 TGCGATCACTCCGTTATGATATGTTGGTCGGAT 1 43 0 CCGTATGATG 0.976679 -23 GAAATACGGGCAGACATGGCCTGCCCGGTTATT 2 12 0 CAGCATGGTG 0.680374 -40 CATAAAGTGTAAAGCCTGGGGTGCCTAATGAGT 3 39 0 AAACCTGGTG 0.86082 -84 ATACGAGCCGGAAGCATAAAGTGTAAAGCCTGG 3 53 0 GAACATAATG 0.768163 -70 GAAAGGTTTTGCGCCATTCGATGGTG 4 4 0 GCGCATTCTG 0.957321 -73 AAAACCTTTCGCGGTATGGCATGATAGCGCCCG 4 27 1 GCGTATGGTG 0.985111 -50 ATTCACCACCCTGAATTGACTCTCTTCC 4 59 0 CCACCTGATG 0.966041 -18 *** ***** ** Masking position 7 Map Score: 4.43397 Number of sites scoring better than the average of aligned sites = 1577 Number in coding regions = 1460 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 4 ATAAGGCGCTCGCGCCGCATCCGACATTGA 1 15 0 CGCGCCGCAT 0.964139 -51 TTATGATATGTTGGTCGGATAAGGCGCTCG 1 33 0 TTGGTCGGAT 0.94075 -33 CAGACATGGCCTGCCCGGTTATTA 2 5 0 CTGCCCGGTT 0.987031 -47 CAGGCCATGTCTGCCCGTATTTCGCGTAAG 2 22 1 CTGCCCGTAT 0.992671 -30 TTTATGCTTCCGGCTCGTATGTTGTGTGGA 3 66 1 CGGCTCGTAT 0.992751 -57 CAGTACCTCACGACTCGGACAAAATGTCGT 5 13 1 CGACTCGGAC 0.955813 -64 ********** Masking position 6 Map Score: 3.4435 Number of sites scoring better than the average of aligned sites = 1147 Number in coding regions = 1054 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 5 ********** No masking Map Score: -1.88842e-14 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 6 ********** No masking Map Score: -1.88842e-14 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: -1.88842e-14 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