AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i216_Ribosomal_Operon_3_ecoli_reg_100.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #2 rplS 41 50S ribosomal subunit protein L19 #3 trmD 30 tRNA methyltransferase; tRNA (guanine-7-)-methyltransferase #4 rpsP 248 30S ribosomal subunit protein S16 #5 ffh 91 GTP-binding export factor binds to signal sequence, GTP and RNA Motif number 1 AATGAGACAGGCCGTAAAGTTTGGCGAACAAAAGA 1 18 0 GCCGTAAGGC 0.880287 -87 AACACGGCCTGCCGCAATCGTAAGAATGAGACAGG 1 42 0 GCCGCAACGA 0.984359 -63 GCCCCCGAGATATCAGTTTACCCAG 2 1 1 GCCCCCGGCA 0.959641 -41 CCATTTTGGCACCGGGATGTGCTCGTCATCCTCAC 4 28 1 ACCGGGAGCG 0.873291 -221 GCGCGCAGTCACCGGAGCGTACACGCAGTACGTGA 4 59 0 ACCGGAGGCG 0.987247 -190 CCAGTTTGGTGCCGGAGTGCGCGCAGTCACCGGAG 4 77 0 GCCGGAGGCA 0.994322 -172 GCTGTAAAAGGCCGTCGGCGGTGCAGCCAGTTTGG 4 103 0 GCCGTCGCCA 0.967719 -146 ACGGCCTTTTACAGCAGAGTTAGCAACTGTTGATT 4 123 1 ACAGCAGGCA 0.928175 -126 TTAATATGACACCGGACTCCGTTCCTCGATGGGGT 4 194 1 ACCGGACCCC 0.964764 -55 GAATAAAACAACCGGACCCCATCGAGGAACGGAGT 4 209 0 ACCGGACCGA 0.970235 -40 GAAACGGTTGGCCGCAATCGCGACACATCATCAGT 5 49 0 GCCGCAACCA 0.991935 -43 AACCGTTTCCACCCCAGGCGAGAGACA 5 75 1 ACCCCAGCGA 0.951868 -17 ******* * ** Masking position 2 Map Score: 11.4077 Number of sites scoring better than the average of aligned sites = 4798 Number in coding regions = 4545 Number in noncoding regions = 253 Number of orfs with sites within 600 bp upstream = 215 Fraction of orfs with sites within 600 bp upstream = 0.0345326 Motif number 2 AAGAATGAGACAGGCCGTAAAGTTTGGCGA 1 26 0 CAGGCCGTAA 0.76518 -79 ACGATTGCGGCAGGCCGTGTTATTATTGTC 1 56 1 CAGGCCGTGT 0.954677 -49 ATTTTGGCACCGGGATGTGCTCGTCATCCT 4 30 1 CGGGATGTGC 0.936373 -219 GTCATCCTCACGTACTGCGTGTACGCTCCG 4 52 1 CGTACTGCGT 0.914541 -197 GCGCAGTCACCGGAGCGTACACGCAGTACG 4 62 0 CGGAGCGTAC 0.953339 -187 AGTTTGGTGCCGGAGTGCGCGCAGTCACCG 4 80 0 CGGAGTGCGC 0.983938 -169 CGGCACCAAACTGGCTGCACCGCCGACGGC 4 98 1 CTGGCTGCAC 0.936372 -151 AATATGACACCGGACTCCGTTCCTCGATGG 4 196 1 CGGACTCCGT 0.970802 -53 ATAAAACAACCGGACCCCATCGAGGAACGG 4 212 0 CGGACCCCAT 0.956116 -37 ********** Masking position 1 Map Score: 6.49513 Number of sites scoring better than the average of aligned sites = 4495 Number in coding regions = 4266 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 3 CGTTCCATCTTTTGTTCGCCAAACTTTAC 1 8 1 TCTTGTTCGC 0.961392 -97 CCTGTCTCATTCTTACGATTGCGGCAGGCCGT 1 42 1 TCTCGATTGC 0.988389 -63 CGGCAGGCCGTGTTATTATTGTCGTTTCTTAT 1 63 1 TGTTTATTGT 0.702493 -42 TCGGCCTGGCTTGTTTGCCATTTTGGCA 4 7 1 TGGTGTTTGC 0.946615 -242 GCGTGTACGCTCCGGTGACTGCGCGCACTCCG 4 68 1 TCCTGACTGC 0.924769 -181 AGAGTTAGCAACTGTTGATTGCAATTCCCGCA 4 138 1 ACTTGATTGC 0.982155 -111 CGAAAATTTTACTCATTTTTGCGGGAATTGCA 4 157 0 ACTTTTTTGC 0.887013 -92 ACTGATGATGTGTCGCGATTGCGGCCAACCGT 5 49 1 TGTCGATTGC 0.981256 -43 *** ******* Masking position 11 Map Score: 3.2401 Number of sites scoring better than the average of aligned sites = 1042 Number in coding regions = 971 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 4 CGTTCCATCTTTTGTTCGCCAAACTT 1 7 1 ATCTTTTGTT 0.856727 -98 GTCGTTTCTTATATTTTGACAGGAAGAGTA 1 83 1 ATATTTTGAC 0.881048 -22 AATTTAATCTCTTATCCTGGGTAAAC 2 26 0 ATCTCTTATC 0.915456 -16 AGCGCCGTCTTTTACCGTTTATCCGG 3 15 0 GTCTTTTACC 0.978846 -16 CACATCATCAGTATTTTGCCGCAGTATAAC 5 31 0 GTATTTTGCC 0.978846 -61 TGTCTCTCGCCTGGGGTGGAA 5 81 0 GTCTCTCGCC 0.976461 -11 ********** Masking position 6 Map Score: 0.951662 Number of sites scoring better than the average of aligned sites = 825 Number in coding regions = 734 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 5 CCCCGAGATATCAGTTTACCCAGGATAAGA 2 13 1 TCAGTTTACC 0.832689 -29 GCCGTCTTTTACCGTTTATCCGGTGGT 3 8 0 ACCGTTTATC 0.942796 -23 ACGAGCACATCCCGGTGCCAAAATGGCAAA 4 24 0 CCCGGTGCCA 0.951855 -225 ATTGCAATCAACAGTTGCTAACTCTGCTGT 4 133 0 ACAGTTGCTA 0.895989 -116 GACACCGGACTCCGTTCCTCGATGGGGTCC 4 201 1 TCCGTTCCTC 0.972188 -48 GAATAAAACAACCGGACCCCATCGAGGAAC 4 214 0 ACCGGACCCC 0.949541 -35 ATTGCGGCCAACCGTTTCCACCCCAGGCGA 5 66 1 ACCGTTTCCA 0.983718 -26 ********** Masking position 4 Map Score: 1.17285 Number of sites scoring better than the average of aligned sites = 2138 Number in coding regions = 2036 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 6 ********** No masking Map Score: -3.30951e-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: -3.30951e-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 8 ********** No masking Map Score: -3.30951e-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