AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i017_ecoli_bsub_300.orf -o017_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -x5 -e 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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 asnS 168 asparagine tRNA synthetase #2 pncB 265 nicotinate phosphoribosyltransferase #3 glk 203 glucokinase #4 pgi 300 glucosephosphate isomerase #5 yqjJ 226 similar to glucose-6-phosphate 1-dehydrogenase (pentose phosphate) #6 pgi 111 glucose-6-phosphate isomerase #7 yugK 103 similar to NADH-dependent butanol dehydrogenase #8 yugJ 229 similar to NADH-dependent butanol dehydrogenase Motif number 1 CTGCATTTGCGAATTCTGCTTGTCTGATTGC 1 67 1 GATTCTGCTT 0.914504 -102 TATGTTACCTGGCATCTGCAATCAGACAAGC 1 84 0 GCATCTGCAA 0.742013 -85 GAAAAGATGAAGATTCTGCATAGCGCGATTT 2 66 0 AATTCTGCAT 0.962925 -200 TCACAGGACTGGCTCCTCCAACACCGTTACT 4 19 1 GCTCCTCCAA 0.93602 -282 CATTTTTTCAGCATTCTGCTTAAAAAAGGGC 5 112 1 GATTCTGCTT 0.914504 -115 GGTAAAAAACAGATTTTCCATTGTAACATAA 7 61 0 AATTTTCCAT 0.720801 -43 AGTAAAACCTCCAAATGATGCTGG 7 90 0 AAACCTCCAA 0.774759 -14 GTTTTGCAACCTCCTCCATGAATTATTAA 8 9 1 ACTCCTCCAT 0.960553 -221 ATGCATGTATAGATTCTCCAATATGTCACAA 8 52 0 AATTCTCCAA 0.949139 -178 ATCTATACATGCATTCTCCATATGAGGGAAG 8 69 1 GATTCTCCAT 0.97657 -161 TGTGGTGAGGACATTCTGCATAATAAAAAAT 8 193 1 AATTCTGCAT 0.962925 -37 GACATCTCCTCCTTAGATTTTTTA 8 216 0 ACTCCTCCTT 0.896453 -14 * ********* Masking position 7 Map Score: 10.2152 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 273 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 2 GAGCTAATCGGCTCCCTTTTTTTACCTTTAAT 1 21 1 GCCCCTTTTT 0.982865 -148 GAAATCTTTCGCTGCATTTGCGAATTCTGCTT 1 56 1 GCGCATTTCG 0.868168 -113 CATAGGTATCCCCCCATTTACGGGTGGACAAG 1 111 1 CCCCATTTCG 0.884383 -58 TTCAGGTACAAACGCCTTTATTGCTACATTTT 2 94 1 AAGCCTTTTT 0.770314 -172 CACACCATATGCCACCTTTCTGGTCGATGGCA 2 145 0 GCACCTTTTG 0.932099 -121 CAATTGCAGCGATGCCTTTTTGCAAGCTGGGC 3 46 0 GAGCCTTTTG 0.946866 -158 TTACAGGGAGCCTGCCTTTCCGGCGTTGTTGT 3 119 1 CCGCCTTTCG 0.955155 -85 ACCGCCCCGCTCACCCTTTATTTATAAATGTA 4 90 0 TCCCCTTTTT 0.881519 -211 TTAGCGCAGTGAAGCATTTATTAGCTGAACTA 4 170 0 GAGCATTTTT 0.791717 -131 TTTCGTGCTAGAAACATTTTTTCAGCATTCTG 5 98 1 GAACATTTTT 0.509061 -129 GCAAACATTTAAGCCCTTTTTTAAGCAGAATG 5 123 0 AACCCTTTTT 0.822889 -104 TAAAAGTACCTCACTTTATTCGAAGCTTTA 5 207 0 CCCACTTTTT 0.745388 -20 TGACTGGATTCCGCCCTTTGGGT 6 2 0 CCCCCTTTGG 0.916717 -110 TCCAGTCATTCCGCCCTTTCTTCTTGACTTGA 6 26 1 CCCCCTTTTT 0.979631 -86 ** ****** ** Masking position 7 Map Score: 9.63156 Number of sites scoring better than the average of aligned sites = 930 Number in coding regions = 735 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 3 TTTATTTTTTCCGACTATTAACAGAGAGAATATT 1 145 1 CCTTACAGGA 0.904866 -24 TATGCAGAATCTTCATCTTTTCAGGTACAAACGCCTTTA 2 75 1 CTTTTCAGCA 0.991811 -191 CACACAATTACTTTATCGTTTCAGCACCAATTGCAGCGA 3 66 0 CTTTTCAGCA 0.991811 -138 TGTTATGCCCCCAGGTATTTACAGTGTGAGAAAGAATTA 3 148 1 CCTTTCAGGA 0.932999 -56 GTGACTGGCGCTACAATCTTCCAAAGTCACAATTCTCAA 4 253 1 CTATTCAACA 0.74628 -48 GTTTCCTTCCTCCTACTAGAACCAGATACCTACA 5 6 1 CTTTATAGCA 0.878455 -221 AACCAGATACCTACAAGAATACAGGATCAAGCGGAAAAT 5 30 1 CTAATCAGCA 0.825698 -197 GCACGAAAGGATTGTTCTTTTCAGAGGCAAGATTCACAT 5 67 0 ATTTTCAGCA 0.913653 -160 AATGGAAAATCTGTTTTTTACCAGCATCATTTGGAGGTT 7 70 1 CTTTACAGCA 0.988056 -34 CTGGCCTGCCCTCGCTTATATCAGCTTCTTTCCCAGCAC 8 100 1 CTTTACAGCT 0.920887 -130 ** * ** *** ** Masking position 13 Map Score: 4.46299 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 295 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 4 TTAATAGTCGGAAAAAATAAACACTTGTCCACCCGTAAA 1 127 0 GAAAAACTGC 0.940218 -42 TTGCAAGCTGGGCAAACTAAGTATCTGACCCCGCATAAG 3 20 0 GGAAAATTGC 0.983241 -184 GTGCTGAAACGATAAAGTAATTGTGTGACCCAGATCGAT 3 78 1 GAAAAATTGC 0.980668 -126 TTTACAGTGTGAGAAAGAATTATTTTGACTTTAGCGGAG 3 165 1 GAAAAATTGC 0.885375 -39 GCCAGGAGTGGATGAAAAATCCGCATGACCCCATCGTTG 4 125 0 GAGAAACTGC 0.973839 -176 AGGATCAAGCGGAAAATGTGAATCTTGCCTCTGAAAAGA 5 52 1 GGAAATCTGC 0.88439 -175 AAAAAGGGGAAATAGCCGTTTGGCTGCTTCCCTT 7 6 1 GGGAAATTGC 0.983472 -98 AAATGATGCTGGTAAAAAACAGATTTTCCATTGTAACAT 7 63 0 GGAAAATTTC 0.695688 -41 ** *** * * ** * Masking position 6 Map Score: 6.59503 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 85 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 ATATTTACAGGGAGCCTGCCTTTCCGGCGT 3 115 1 GGAGCCTGCC 0.848163 -89 GCAACGCGCCTCTTCTGGCCTGCGCTAGCG 4 53 1 TCTTCTGGCC 0.852625 -248 GTTTCCTTCCTCCTACTAGA 5 1 1 GTTTCCTTCC 0.788127 -226 CGGAAAATGTGAATCTTGCCTCTGAAAAGA 5 61 1 GAATCTTGCC 0.913527 -166 GGAATGACTGGATTCCGCCCTTTGGGT 6 8 0 GATTCCGCCC 0.968443 -104 GGAATCCAGTCATTCCGCCCTTTCTTCTTG 6 22 1 CATTCCGCCC 0.816818 -90 GCTGCTGTCCCTCCATAACG 6 102 0 GCTGCTGTCC 0.968708 -10 TAGCCGTTTGGCTGCTTCCCTTTTTCTTTT 7 23 1 GCTGCTTCCC 0.968278 -81 CCATATGAGGGAAGCTGGCCTGCCCTCGCT 8 86 1 GAAGCTGGCC 0.948058 -144 GCTTATATCAGCTTCTTTCCCAGCACCTTG 8 113 1 GCTTCTTTCC 0.947139 -117 ********** Masking position 5 Map Score: 3.83026 Number of sites scoring better than the average of aligned sites = 1794 Number in coding regions = 1690 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 6 AAACACTTGTCCACCCGTAAATGGGGGGATA 1 117 0 CACCCGTAAA 0.81053 -52 GCGCAGTAGCGTCCTCGTACAGGAGCGTTTA 2 241 0 GCCTCGTACA 0.925727 -25 CTAAGTATCTGACCCCGCATAAGGAATAGAA 3 12 0 GCCCCGCATA 0.989026 -192 GAAAGGCAGGCTCCCTGTAAATATCGATCTG 3 108 0 CCCCTGTAAA 0.934646 -96 CGTTGACAACCGCCCCGCTCACCCTTTATTT 4 99 0 CCCCCGCTCA 0.966938 -202 TATTTTAGTACACCCCGTATATTTCCTTCAT 5 178 0 CCCCCGTATA 0.982705 -49 GCTGCTGTCCCTCCATAACGGTATAAT 6 95 0 GCCCTCCATA 0.811027 -17 AAGCTGGCCTGCCCTCGCTTATATCAGCTTC 8 97 1 GCCTCGCTTA 0.903232 -133 TCTTTCCCAGCACCTTGCAAAATAAAACCAT 8 126 1 CCCTTGCAAA 0.902046 -104 * ********* Masking position 11 Map Score: 3.85146 Number of sites scoring better than the average of aligned sites = 606 Number in coding regions = 539 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 7 TTATAGAGTCTGGTGTTCAGTCTATTCCTGT 2 30 1 TGGTGTCAGT 0.96788 -236 AGGTGCGCAGTAGCGTCCTCG 2 255 0 AGGTGGCAGT 0.979331 -11 TTTTGACTTTAGCGGAGCAGTTGAAGA 3 187 1 AGCGGGCAGT 0.98082 -17 ATAAAGGGTGAGCGGGGCGGTTGTCAACGAT 4 101 1 AGCGGGCGGT 0.97689 -200 CATCCACTCCTGGCGGTCAGTAGTTCAGCTA 4 150 1 TGGCGTCAGT 0.946454 -151 CCATCTGGTATGCTGATCGGTGAGAGCTGAT 8 153 1 TGCTGTCGGT 0.961511 -77 ***** ***** Masking position 11 Map Score: 2.31983 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 212 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 GCATAACAACAACGCCGGAAAGGCAGGCTCC 3 125 0 AACGCCGGAA 0.948788 -79 TACCTGCGCTAGCGCAGGCCAGAAGAGGCGC 4 58 0 AGCGCAGGCA 0.988795 -243 GGCCTGCGCTAGCGCAGGTAGTACATTTATA 4 69 1 AGCGCAGGAG 0.988797 -232 TGAACTACTGACCGCCAGGAGTGGATGAAAA 4 146 0 ACCGCCAGAG 0.860256 -155 GTAAACCCTTAGCGCAGTGAAGCATTTATTA 4 179 0 AGCGCAGTAA 0.953696 -122 TGATGGTTTTAGTGCCGTTAGCGTAATGTTG 4 213 0 AGTGCCGTAG 0.805956 -88 GGAAGATTGTAGCGCCAGTCACAGAAAAATG 4 244 0 AGCGCCAGCA 0.969717 -57 GATATAAGCGAGGGCAGGCCAGCTTCCCTCA 8 91 0 AGGGCAGGCA 0.944345 -139 ******** ** Masking position 1 Map Score: 4.4241 Number of sites scoring better than the average of aligned sites = 1419 Number in coding regions = 1370 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 9 CACCCGTAAATGGGGGGATACCTATGTTAC 1 107 0 TGGGGGGATA 0.971782 -62 CCCCCATTTACGGGTGGACAAGTGTTTATT 1 121 1 CGGGTGGACA 0.905584 -48 ATTCCTTATGCGGGGTCAGATACTTAGTTT 3 16 1 CGGGGTCAGA 0.974025 -188 AAATATCGATCTGGGTCACACAATTACTTT 3 91 0 CTGGGTCACA 0.85915 -113 TGTAAATACCTGGGGGCATAACAACAACGC 3 141 0 TGGGGGCATA 0.982463 -63 TTGTCAACGATGGGGTCATGCGGATTTTTC 4 121 1 TGGGGTCATG 0.925381 -180 TATACCGTTATGGAGGGACAGCAGC 6 97 1 TGGAGGGACA 0.858097 -15 CTGATATAAGCGAGGGCAGGCCAGCTTCCC 8 94 0 CGAGGGCAGG 0.858487 -136 ********** Masking position 8 Map Score: 1.74189 Number of sites scoring better than the average of aligned sites = 566 Number in coding regions = 489 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 10 AGAAAGAATTATTTTGACTTTAGCGGAGCA 3 176 1 ATTTTGACTT 0.93108 -28 GATTTTGAGAATTGTGACTTTGGAAGATTG 4 266 0 ATTGTGACTT 0.981721 -35 CAGATTTTCCATTGTAACATAAGTTGACAA 7 53 0 ATTGTAACAT 0.930391 -51 ACAGTTATAGATTGTGACATATTGGAGAAT 8 41 1 ATTGTGACAT 0.981668 -189 ********** Masking position 5 Map Score: 0.813099 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 10 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 ********** No masking Map Score: -5.2337e-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 12 ********** No masking Map Score: -5.2337e-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 13 ********** No masking Map Score: -5.2337e-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