AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i179_folate_biosynthesis_ecoli_reg_300.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 folC 69 dihydrofolate:folylpolyglutamate synthetase; dihydrofolate synthetase #2 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #3 dedA 82 orf, hypothetical protein #4 usg 65 putative PTS system enzyme II A component #5 pdxB 98 erythronate-4-phosphate dehyrogenase #6 holC 52 DNA polymerase III, chi subunit #7 BIME233 22 BIME #8 pepA 266 aminopeptidase A/I Motif number 1 TTATCCAAAGTTTCGGGCTGTTATGTTTTAA 2 39 1 TTCGGGCTGT 0.995405 -117 GCCTGAAATGTTCCGAGCATTATTCTCG 3 8 0 TTCGAGCATT 0.923505 -75 GCTCGGAACATTTCAGGCTGTAGCCAACGTA 3 21 1 TTCAGGCTGT 0.994456 -62 ACTCGTCATCTTTCAGGCTGTAACTACGTTG 3 45 0 TTCAGGCTGT 0.994456 -38 AGACGAGTTTTTACGGGCGTATTTAAA 8 7 0 TTCGGGCGTA 0.931588 -260 AACTCGTCTTTTGCAGGATTTTAGCTTGTTT 8 29 1 TTCAGGATTT 0.950662 -238 ACAGATAGAATTGCAAGCTTTCGTAACTCAT 8 207 0 TTCAAGCTTT 0.975917 -60 ** ******** Masking position 2 Map Score: 9.19686 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 455 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 2 GCAGAGCCAGTGGCCCTGCCCTTATCAGTTA 1 10 0 TGGCCTGCCT 0.99776 -60 GCAGGGCCACTGGCTCTGCCCTTTTGCTATTC 1 23 1 TGGCCTGCCT 0.998006 -47 ATTTGCCTATGCCTTGTACTCGTCA 3 68 0 TGCCATGCCT 0.99688 -15 TGTTCTGACGTGCCAATGCCGTAATAACGTTA 8 144 1 TGCCATGCCT 0.99688 -123 ATGTCCGCTGTTGCGATGACTTCGTGTTAATC 8 177 0 TTGCATGACT 0.884338 -90 TTCTATCTGTAGCCACCGCCGTTGTCTTTAAG 8 228 1 AGCCCCGCCT 0.97841 -39 **** ***** * Masking position 12 Map Score: 9.19332 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 152 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 3 AAAAGGGCAGAGCCAGTGGCCCTGCCCTTA 1 18 0 AGCCAGTGGC 0.940973 -52 GGAACATTTCAGGCTGTAGCCAACGTAGTT 3 25 1 AGGCTGTAGC 0.990222 -58 GTCATCTTTCAGGCTGTAACTACGTTGGCT 3 42 0 AGGCTGTAAC 0.966186 -41 GACGAGTACAAGGCATAGGCAAAT 3 69 1 AGGCATAGGC 0.813289 -14 TTCATGCTCTCTGCTGTAACATTGGCAGGG 4 18 1 CTGCTGTAAC 0.817086 -48 GCGTCAGGCAAGGCTGTTAT 7 13 1 AGGCTGTTAT 0.713989 -10 CGTAAAAACTCGTCTTTTGCAGGATTTTAG 8 23 1 CGTCTTTTGC 0.817086 -244 AACGTTATTACGGCATTGGCACGTCAGAAC 8 145 0 CGGCATTGGC 0.980146 -122 TAACTCATGTCCGCTGTTGCGATGACTTCG 8 185 0 CCGCTGTTGC 0.959125 -82 TTAAAGACAACGGCGGTGGCTACAGATAGA 8 229 0 CGGCGGTGGC 0.99035 -38 ********** Masking position 4 Map Score: 7.77686 Number of sites scoring better than the average of aligned sites = 3972 Number in coding regions = 3808 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 4 TGGTCGAACCGCGGAGTTACTTT 2 4 0 GCGGAGTTAC 0.984392 -152 GCTGTAGCCAACGTAGTTACAGCCTGAAAG 3 37 1 ACGTAGTTAC 0.978439 -46 TATACCTGATGCGTATTTAAATCCACCACA 6 20 1 GCGTATTTAA 0.968594 -33 GTTTTTACGGGCGTATTTAAA 8 2 0 GCGTATTTAA 0.968594 -265 TGCAAAAGACGAGTTTTTACGGGCGTATTT 8 14 0 GAGTTTTTAC 0.864486 -253 ATTATACTCAACGGATTCACCTCTCAGATT 8 113 1 ACGGATTCAC 0.918918 -154 GTTAATCTTAACGTTATTACGGCATTGGCA 8 154 0 ACGTTATTAC 0.878608 -113 ********** Masking position 9 Map Score: 4.0659 Number of sites scoring better than the average of aligned sites = 599 Number in coding regions = 545 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 5 AACTCCGCGGTTCGACCACTTTTTTATCCA 2 16 1 TTCGACCACT 0.982015 -140 AATGGCATTATGCGTCCCCAAAGATAAAAC 2 101 1 TGCGTCCCCA 0.930493 -55 CTGAACCTGGTTCGATGCCAGTTTTATCTT 2 121 0 TTCGATGCCA 0.963698 -35 TAGCGACGATTTCGACGACTCAAGAGAATA 8 78 0 TTCGACGACT 0.987589 -189 TGTCCGCTGTTGCGATGACTTCGTGTTAAT 8 178 0 TGCGATGACT 0.974312 -89 ********** Masking position 1 Map Score: 1.95135 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 149 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 CAGGCATACTTGCGAAGATTTCAGGTATAA 5 20 0 TGCGAAGATT 0.907434 -79 TCGAAATCGTCGCTAAGATAATTATACTCA 8 93 1 CGCTAAGATA 0.971844 -174 ACGGATTCACCTCTCAGATTTTGTTCTGAC 8 123 1 CTCTCAGATT 0.957815 -144 GCCGTAATAACGTTAAGATTAACACGAAGT 8 161 1 CGTTAAGATT 0.980545 -106 CCGCCGTTGTCTTTAAGATTCAGGAGCGTA 8 243 1 CTTTAAGATT 0.95721 -24 ********** Masking position 6 Map Score: 1.34677 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 144 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 CCAGTGGCCCTGCCCTTATCAGTTA 1 4 0 TGCCCTTTCG 0.916367 -66 TCTGCCCTTTTGCTATTCTCACCGTAACGAAT 1 37 1 TGCTATTTCC 0.958911 -33 GGACGCATAATGCCATTTTTGCCCCCAACAGA 2 86 0 TGCCATTTTC 0.988651 -70 CCTGGTTCGATGCCAGTTTTATCTTTGGGGAC 2 114 0 TGCCAGTTTT 0.896792 -42 CAAAGCTCCCTGCCAATGTTACAGCAGAGAGC 4 23 0 TGCCAATTTC 0.974291 -43 CGGACAAGTGTGCCATAATCTCGCGGCCAGGC 5 45 0 TGCCATATCC 0.969918 -54 TGTTCTGACGTGCCAATGCCGTAATAACGTTA 8 144 1 TGCCAATCCT 0.8501 -123 TACGAAAGCTTGCAATTCTATCTGTAGCCACC 8 213 1 TGCAATTTAC 0.81725 -54 ******* ** * Masking position 1 Map Score: 2.08599 Number of sites scoring better than the average of aligned sites = 875 Number in coding regions = 813 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 8 TAGGGACCTTTCTGTCTGAACCTGGTTCG 2 137 0 TTCTGTCTGA 0.965556 -19 CTACGTTGGCTACAGCCTGAAATGTTCCGA 3 23 0 TACAGCCTGA 0.951093 -60 CCAACGTAGTTACAGCCTGAAAGATGACGA 3 44 1 TACAGCCTGA 0.951093 -39 TACGTATCCTTATACCTGAAATCTTCGCA 5 10 1 TTATACCTGA 0.960116 -89 ATCTTCGCAAGTATGCCTGGCCGCGAGATT 5 31 1 GTATGCCTGG 0.924488 -68 GCTGCGGTGTATACCTGATGCGTATTTA 6 9 1 GTATACCTGA 0.941899 -44 AAGCTTGCAATTCTATCTGTAGCCACCGCC 8 218 1 TTCTATCTGT 0.770049 -49 ********** Masking position 8 Map Score: 3.19316 Number of sites scoring better than the average of aligned sites = 1234 Number in coding regions = 1085 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 9 ********** No masking Map Score: 1.06825e-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 10 ********** No masking Map Score: 1.06825e-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 11 ********** No masking Map Score: 1.06825e-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