AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i233_protein_modification____ecoli_hinf_reg_300.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 yeaZ 57 orf, hypothetical protein #2 b1808 83 putative enzyme #3 holD 102 DNA polymerase III, psi subunit #4 HI0011 105 DNA polymerase III, psi subunit (holD) #5 HI0387 300 ATP-dependent helicase (dinG) Motif number 1 GACATAATCCCTGTTCAAATCAACAGGGGG 2 60 1 CTGTTCAAAT 0.878332 -24 TGTGGGTTATTGGTTAAAATTACGCACCAT 4 22 1 TGGTTAAAAT 0.874336 -84 AAAAACGTTGCTTGAAAAATAGTGTTAATT 4 74 0 CTTGAAAAAT 0.943463 -32 CAAGCAACGTTTTTAAAAATTCACTT 4 90 1 TTTTAAAAAT 0.949611 -16 AATTTTAGATGTTTTAAAATGAATAAAATC 5 71 0 GTTTTAAAAT 0.901272 -230 GCTAAAAGTGCGGTAAAAATTTTAGATGTT 5 88 0 CGGTAAAAAT 0.979854 -213 CAATGAGAAAGGTTAAAAATGATTTGTCAT 5 140 0 GGTTAAAAAT 0.961311 -161 CATAACCGTTCTTTAAAAATAGCCTCTATG 5 188 1 CTTTAAAAAT 0.98453 -113 CGGTTATTTACTTTAAAAATATGTTTTACT 5 279 1 CTTTAAAAAT 0.98453 -22 ********** Masking position 7 Map Score: 11.3629 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 142 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 2 GGTATGATGCGCGCCTTTTTATTGATCTAA 1 26 1 GCGCCTTTTT 0.920556 -32 ACTGGCGAAAGCGCCCTCATCCTGACATAA 2 37 1 GCGCCCTCAT 0.971525 -47 GCTATAATCGCCGCCAGTATCAATTGAGGA 3 18 0 CCGCCAGTAT 0.986152 -85 CGTCGATACCGCGCCAACATATGGCTATAA 3 41 0 GCGCCAACAT 0.978846 -62 GTTGTCAGGGGCGCAAATATAGCAAATTCG 3 69 0 GCGCAAATAT 0.964004 -34 TTAAAATTACGCACCATTTTAGCAAAGATT 4 35 1 GCACCATTTT 0.916602 -71 AAAATTTTTACCGCACTTTTAGCCTGACTA 5 95 1 CCGCACTTTT 0.893193 -206 TAATCTTAAGCCACCAGTATTTTTATTCTT 5 218 1 CCACCAGTAT 0.933436 -83 AAGTAAATAACCGCAAAGATTGTCGCATAG 5 262 0 CCGCAAAGAT 0.869328 -39 ********** Masking position 10 Map Score: 8.35179 Number of sites scoring better than the average of aligned sites = 2554 Number in coding regions = 2381 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 3 TAGATCAATAAAAAGGCGCGCATCATACCA 1 25 0 AAAAGGCGCG 0.934457 -33 TCGCCAGTTGAAGTGGTGACGGCGACCTCA 2 15 0 AAGTGGTGAC 0.864722 -69 TCACCACTTCAACTGGCGAAAGCGCCCTCA 2 26 1 AACTGGCGAA 0.90996 -58 TGTTCAAATCAACAGGGGGTAGT 2 71 1 AACAGGGGGT 0.887096 -13 CCTCAATTGATACTGGCGGCGATTATAGCC 3 19 1 TACTGGCGGC 0.966203 -84 CGCCCCTGACAACAGGAGCGATTCGCT 3 86 1 AACAGGAGCG 0.940079 -17 ATCTTTGCTAAAATGGTGCGTAATTTTAAC 4 34 0 AAATGGTGCG 0.957459 -72 TTATCCCAAAAACTGGTTCTAGAATACACG 5 14 0 AACTGGTTCT 0.810658 -287 AGAATAAAAATACTGGTGGCTTAAGATTAC 5 217 0 TACTGGTGGC 0.959472 -84 ********** Masking position 2 Map Score: 2.55192 Number of sites scoring better than the average of aligned sites = 3884 Number in coding regions = 3710 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 4 ATCAATAAAAAGGCGCGCATCATACCATAC 1 22 0 AGGCGCGCAT 0.827212 -36 ATGTCAGGATGAGGGCGCTTTCGCCAGTTG 2 35 0 GAGGGCGCTT 0.867755 -49 AGCCATATGTTGGCGCGGTATCGACGAATT 3 45 1 TGGCGCGGTA 0.947445 -58 TCCTGTTGTCAGGGGCGCAAATATAGCAAA 3 73 0 AGGGGCGCAA 0.985746 -30 CCCTGACAACAGGAGCGATTCGCT 3 89 1 AGGAGCGATT 0.891836 -14 TTTGCTAAAATGGTGCGTAATTTTAACCAA 4 31 0 TGGTGCGTAA 0.887316 -75 GTCAGGCTAAAAGTGCGGTAAAAATTTTAG 5 93 0 AAGTGCGGTA 0.925962 -208 ********** Masking position 5 Map Score: 1.69605 Number of sites scoring better than the average of aligned sites = 1673 Number in coding regions = 1553 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 5 CGTGCTTAGATCAATAAAAAGGCGCGCATCA 1 30 0 TCAATAAAAG 0.787953 -28 CTTTTATTAATCTTTGCTAAAATGGTGCGTA 4 42 0 TCTTTGCAAA 0.889415 -64 AAAAACTGGTTCTAGAATACACGGTT 5 6 0 TCTAGAAACA 0.869472 -295 AAGCAAGCTATCTATGAAAAACTCAATAAGA 5 42 1 TCTATGAAAA 0.978463 -259 TAGATTTTACTCAATGAGAAAGGTTAAAAAT 5 150 0 TCAATGAAAA 0.966547 -151 TTGAGTAAAATCTATTCAAAACATAACCGTT 5 167 1 TCTATTCAAA 0.894662 -134 ACGCTAAATATCAAGAATAAAAATACTGGTG 5 229 0 TCAAGAAAAA 0.887595 -72 ATTTAGCGTTTCTATGCGACAATCTTTGCGG 5 251 1 TCTATGCACA 0.962532 -50 ******* *** Masking position 9 Map Score: 3.62104 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 197 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 6 ********** No masking Map Score: -1.31207e-12 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: -1.31207e-12 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: -1.31207e-12 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