AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i280_hypothetical5_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 yeaG 300 orf, hypothetical protein #2 yeaH 112 orf, hypothetical protein Motif number 1 AAGACCAGGCTCGCCAGTAACGCTAAATTCATTTGGCT 1 10 0 TCGCCTGCTT 0.988984 -291 AATGGAAAACTTGCCTGCACGGCTTTCTTAATTTCAATG 1 91 0 TTGCCCGCTT 0.996928 -210 AGTTTTCCATTTGCCATCTACGCTTAATTTTGAAGGTGT 1 119 1 TTGCCCGCTT 0.997079 -182 AGCAACTCTCATGCCATTTTATCGACGATGAGAACAACG 1 169 0 ATGCCTTCAT 0.948905 -132 GGTATGCCGTCCTTTCGTTTTTTAGCACAGGT 1 279 0 ATGCCCTCTT 0.996242 -22 GCCGCTTCTCAGGCCCACGGTTCGCTGTCGTTGTAGGCC 2 39 0 AGGCCCTCTC 0.982109 -74 ACTGTATGCTACGCCTGTGTTGCCGCTTCTCAGGCCCAC 2 60 0 ACGCCTGCTC 0.987879 -53 ATGCCCCCCGTACTACATTTGCCAACTGT 2 94 0 ATGCCCACTT 0.990559 -19 ***** * ** ** Masking position 13 Map Score: 10.1842 Number of sites scoring better than the average of aligned sites = 503 Number in coding regions = 470 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 2 AGCGTTACTGGCGAGCCTGGTCTTTACATTA 1 25 1 GCGAGCCGGT 0.989774 -276 AGAAAGCCGTGCAGGCAAGTTTTCCATTTGC 1 102 1 GCAGGCAGTT 0.981344 -199 AGGTGTATCACCGGGCACGTTGTTCTCATCG 1 152 1 CCGGGCAGTT 0.988053 -149 AACATGTGTACCGGGCCAGGGTTG 2 4 0 CCGGGCCGGG 0.997601 -109 CGCTGTCGTTGTAGGCCCGGTAACATGTGTA 2 25 0 GTAGGCCGGT 0.993218 -88 ACAGCGAACCGTGGGCCTGAGAAGCGGCAAC 2 50 1 GTGGGCCGAG 0.989245 -63 CAACTGTATGCTACGCCTGTGTTGCCGCTTC 2 70 0 CTACGCCGTG 0.951617 -43 ******* *** Masking position 6 Map Score: 9.05298 Number of sites scoring better than the average of aligned sites = 1181 Number in coding regions = 1111 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 3 CTTAATTTCAATGGCATATCAACAACTCAT 1 74 0 ATGGCATATC 0.962222 -227 TTAAGCGTAGATGGCAAATGGAAAACTTGC 1 116 0 ATGGCAAATG 0.992278 -185 CGTCGATAAAATGGCATGAGAGTTGCTGTG 1 181 1 ATGGCATGAG 0.985415 -120 TTGCTGTGTTTTAGCAAGAGACGTCGTTCA 1 203 1 TTAGCAAGAG 0.9283 -98 TAGCATACAGTTGGCAAATGTAGTACGGGG 2 88 1 TTGGCAAATG 0.988973 -25 ********** Masking position 6 Map Score: 4.4358 Number of sites scoring better than the average of aligned sites = 406 Number in coding regions = 365 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 AGCCAAATGAATTTAGCGTTA 1 2 1 GCCAAATGAA 0.986652 -299 CATTAATTATGCAAAATTTATGGATGAGTT 1 51 1 GCAAAATTTA 0.942175 -250 AGCGTAGATGGCAAATGGAAAACTTGCCTG 1 113 0 GCAAATGGAA 0.928646 -188 TGATACACCTTCAAAATTAAGCGTAGATGG 1 132 0 TCAAAATTAA 0.823848 -169 CCCGGAAGAGGTAAACTGAACGACGTCTCT 1 219 0 GTAAACTGAA 0.93707 -82 TACTACATTTGCCAACTGTATGCTACGCCT 2 83 0 GCCAACTGTA 0.977329 -30 ********** Masking position 5 Map Score: 2.76484 Number of sites scoring better than the average of aligned sites = 668 Number in coding regions = 591 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 5 CAATGGCATATCAACAACTCATCCATAAAT 1 66 0 TCAACAACTC 0.972935 -235 AAAACTTGCCTGCACGGCTTTCTTAATTTC 1 95 0 TGCACGGCTT 0.954231 -206 ATCGACGATGAGAACAACGTGCCCGGTGAT 1 158 0 AGAACAACGT 0.951064 -143 TTGCTAAAACACAGCAACTCTCATGCCATT 1 190 0 ACAGCAACTC 0.875696 -111 AGAGGTAAACTGAACGACGTCTCTTGCTAA 1 213 0 TGAACGACGT 0.982763 -88 ACTATTCATATGAACGGCTCTTAACCTGTG 1 256 1 TGAACGGCTC 0.98897 -45 ********** Masking position 5 Map Score: 2.17718 Number of sites scoring better than the average of aligned sites = 640 Number in coding regions = 598 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 6 AACAACGTGCCCGGTGATACACCTTCAAAA 1 146 0 CCGGTGATAC 0.922724 -155 TTTACCTCTTCCGGGAGCCTCTACTATTCA 1 234 1 CCGGGAGCCT 0.993765 -67 CAACCCTGGCCCGGTACACATGTTACCGG 2 10 1 CCCGGTACAC 0.92949 -103 CGTTGTAGGCCCGGTAACATGTGTACCGGG 2 20 0 CCGGTAACAT 0.976368 -93 CGACAGCGAACCGTGGGCCTGAGAAGCGGC 2 48 1 CCGTGGGCCT 0.98232 -65 AAATGTAGTACGGGGGGCAT 2 103 1 CGGGGGGCAT 0.990034 -10 ********** Masking position 1 Map Score: 2.88955 Number of sites scoring better than the average of aligned sites = 1232 Number in coding regions = 1136 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 7 ********** No masking Map Score: 1.80068e-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: 1.80068e-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: 1.80068e-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