AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i293_ecoli_bsub_100.orf -o293_ecoli_bsub_100.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 pcnB 92 poly(A) polymerase I #2 yadB 36 putative tRNA synthetase #3 dksA 177 dnaK suppressor protein #4 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #5 dnaE 36 DNA polymerase III, alpha subunit #6 ldcC 98 lysine decarboxylase 2, constitutive #7 yaeR 29 orf, hypothetical protein #8 mesJ 64 cell cycle protein #9 ychF 116 putative GTP-binding protein #10 pth 277 peptidyl-tRNA hydrolase #11 prsA 150 phosphoribosylpyrophosphate synthetase #12 rplY 124 50S ribosomal subunit protein L25 #13 folP 44 7,8-dihydropteroate synthase #14 hflB 99 degrades sigma32, integral membrane peptidase, cell division protein #15 ftsJ 125 cell division protein #16 glmU 300 N-acetyl glucosamine-1-phosphate uridyltransferase #17 gcaD 192 UDP-N-acetylglucosamine pyrophosphorylase #18 prs 22 phosphoribosyl pyrophosphate synthetase #19 ctc 84 general stress protein #20 spoVC 106 thermosensitive mutant blocks spore coat formation (stage V sporulation) #21 yacA 103 similar to cell-cycle protein #22 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #23 pabB 166 para-aminobenzoate synthase (subunit A) #24 ybbP 160 alternate gene name: ybbQ; similar to hypothetical proteins #25 yyaF 126 similar to hypothetical proteins Motif number 1 GTTACTCGCCCGGAAGCCGCTCT 7 17 0 TCTCGCCCGG 0.937826 -13 TTTTACAGTAGCAATGCCCGGCACGTTACCG 8 34 0 GAATGCCCGG 0.818651 -31 TGTAATTGTGATCACGCCCGCACATAACCCA 10 88 0 ACACGCCCGC 0.985443 -190 ACCGAAACTCAGCTTGCCCGGC 11 2 0 ACTTGCCCGG 0.963244 -149 GCTCTTTAATACACCGCCTGGAAAGGATCAT 11 66 1 AACCGCCTGG 0.895217 -85 CCTGGAAAGGATCATGCCTGGCCCGCACAGT 11 82 1 ACATGCCTGG 0.842041 -69 TGAGTATAGAATCTCGCCCGCTTTTGCATAC 12 40 1 ACTCGCCCGC 0.978831 -85 CTTTCGTCTGAAATCTCCCGG 14 1 0 AATCTCCCGG 0.971076 -99 CTTAAGGCGTAACCCTCCCGCGGTTACGTCT 20 14 1 ACCCTCCCGC 0.945509 -93 CCTTAGTCACATAACTCCCGTCTTCATAAAC 20 75 0 AAACTCCCGT 0.828137 -32 AAAAAGCCAAAACTCCCGGTTCGCCGGGA 23 9 1 AAACTCCCGG 0.980061 -158 GAAATATAAAAAAACTCCCGGCGAACCGGGA 23 24 0 AAACTCCCGG 0.980061 -143 * ********* Masking position 7 Map Score: 14.4379 Number of sites scoring better than the average of aligned sites = 984 Number in coding regions = 899 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 2 TTCCCGCCTGTGGTAAACGTGATGGAACGG 2 17 0 CGCTGTACGT 0.980616 -20 CCAAACTTTACGGCCTGTCTCATTCTTACGATTGCGG 4 29 1 CGCTGCACTT 0.989475 -76 AATAATAACACGGCCTGCCGCAATCGTAAGAATGAGA 4 46 0 CGCTGCACGT 0.993387 -59 TCCTTAATCATAGCCTGCTCAAACCGTGGCGATAAAA 6 51 0 TGCTGAACGT 0.909037 -48 GTGTTCCTCCTGGAAAATCCTTCCTTAATCAT 6 77 0 CTCTGAACTT 0.872733 -22 GTGACAACGTCACCTTGTTCCAGACGTTGCATCGCGC 11 31 1 CCCTGCACGT 0.946297 -120 ACTCTATATCCAGCATCTTTCAAACTTTCGTCTGAAA 14 19 0 CGCTCCACTT 0.924271 -81 CCTTAATTTTCTGCAGACAAAAGGCGTGACGATGGTC 16 139 1 CGCGAAACGT 0.946393 -162 GCGCTTTCGTCAGCGGGGATAATCCGTTATTGAACAA 16 183 1 CGCGGAACGT 0.991349 -118 TAAAAAAGGACCGCCGGCAAAAGGCTTATGTCAGCCC 17 41 0 CGCGGAACTT 0.986189 -152 ATGGTGCAAACTGCAGAGCCTATGCTTCTTCTTTGCT 21 11 1 CGCGATACTT 0.801507 -93 AAAGCATTTTCAGCTTGCCAATCCCTTTGA 25 4 0 CGCTGATCTT 0.909752 -123 * ** ** ** *** Masking position 17 Map Score: 10.9169 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 424 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 3 GCAAATACGCTTTTCCTCACACAGTTGTCAAGTGTTACG 3 51 1 TTTCTCTTTC 0.691795 -127 TCTGCTATTTATAGCGGCCTCATTTTTCCCCCGAACATG 3 117 1 ATGCGCTTCC 0.706195 -61 GTGTTCCTCCTGGAAAATCCTTCCTTAATC 6 79 0 TGTCTCAACC 0.739422 -20 GGCTTGTCATCGCCGCATTTGCCCGGTAACGT 8 4 1 TTTCTCTTGC 0.952608 -61 GTCGTTGTCTGCGGCATTTTTGCCGAGTGCCGT 9 5 1 TTTCGCTTGC 0.98047 -112 AGTTATTTCCATTTCTGCAATCTGTTAGCAATAACAGGT 9 57 1 ATTCGCTTGC 0.937967 -60 AATTATTACGTTATCTGCATTTGATACGCAGTTTTTTGT 10 188 1 TTTCGCTAGC 0.98047 -90 GCCCGCACAGTTTTCGGCAGATTCTTTCCACCAATGGAC 11 102 1 TTTCGCTTCC 0.98614 -49 AACAGGTAAGTGATCTGCTTTGCGTATGCAAAAGCGGGC 12 55 0 TGTCGCTAGC 0.926112 -70 ACTGCCTTAATTTTCTGCAGACAAAAGGCGTGACGATGG 16 135 1 TTTCGCAAGC 0.952445 -166 AATGGCGCTTTCGTCAGCGGGGATAATCCGTTATTGAAC 16 179 1 TCTCGCAACC 0.876345 -122 ATTGAACAATTTATCCTCTGTCCATTTCACGATGAAAAA 16 211 1 TTTCTCTTCA 0.713565 -90 TTATTGGCCTCCAATATCCCTTTTATCCA 17 174 0 TTTTGCTACC 0.76869 -19 TCCTTACCTCCTCCCACAGTAAGCACAACTATGT 22 74 0 ACTCTCTAGC 0.601857 -24 AAAAGTGAATTTCTCTTCCAAGAATAACATTCGTCGCAG 23 75 0 TTTCTCTACA 0.713563 -92 CAAAAAAGCATTTTCAGCTTGCCAATCCCTTTGA 25 6 0 TTTCGCATCC 0.965969 -121 AAATGCTTTTTTGTCAGCTTGTCTTTTCCAGTGAACCTC 25 32 1 TTTCGCTTCC 0.98614 -95 TCTTTCATCTCCTCTATATAAAACCGTCATTGTAT 25 102 0 ATTCTCAACC 0.773908 -25 ** ** ** ** ** Masking position 8 Map Score: 15.1883 Number of sites scoring better than the average of aligned sites = 1188 Number in coding regions = 1076 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 4 ATGTTCGGGGGAAAAATGAGGCCGCTATAA 3 125 0 GAAAAATGAG 0.88179 -53 CAAAAGTTCTGAAAAAGGGTCACTTCGGTG 6 15 1 GAAAAAGGGT 0.832509 -84 ACCGTGGCGATAAAAAAGGGCCACCGAAGT 6 36 0 TAAAAAAGGG 0.770861 -63 AAGTTTTGTTGAAATAAGGGTTGTAATTGT 10 110 0 GAAATAAGGG 0.942522 -168 AGAATCTGCCGAAAACTGTGCGGGCCAGGC 11 97 0 GAAAACTGTG 0.744269 -54 CGTTGGGATTGAAAACGGGTCATTCTACCG 15 26 1 GAAAACGGGT 0.735361 -100 CCTATTTGGTGATATATGGGAGATGGCGGT 15 52 0 GATATATGGG 0.663829 -74 GAATAAACAGGAAAACAGGGGGGTTTTATA 16 56 0 GAAAACAGGG 0.966164 -245 TTCATTGATCGAAATAAGAGCAAAAACATC 16 83 1 GAAATAAGAG 0.802443 -218 TTTTTCTATGGATAAAAGGGATATTGGAGG 17 166 1 GATAAAAGGG 0.912526 -27 TTTAAACCTCGAAAAATGGT 19 1 0 GAAAAATGGT 0.85705 -84 TGTTGTTAGTGAAAAAAGTGAATTTCTCTT 23 97 0 GAAAAAAGTG 0.898266 -70 AAGTAAAAAAGAAAATAGAGGAATGATACA 23 146 1 GAAAATAGAG 0.640317 -21 ********** Masking position 4 Map Score: 8.19544 Number of sites scoring better than the average of aligned sites = 622 Number in coding regions = 506 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 5 TAGCCGCTATTTTTTTGTCCTGAATGATGTTT 1 19 1 TTTTTGTCTG 0.96021 -74 TTCTTGTGTCGAGATTAAGTAAA 5 2 1 TCTGTGTCAG 0.772495 -35 CCCCTCTTCCTTATGTGTAAAGTATAGACAAC 10 50 1 TTTGTGTAAG 0.918621 -228 GTTCAGGCGTTTATTTGTAAAGTTTTGTTGAA 10 127 0 TTTTTGTAAG 0.958495 -151 TGATACGCAGTTTTTTGTCAAGCGGGGCCGCA 10 209 1 TTTTTGTCAG 0.96746 -69 GTTTTTTTGTCCTGAGTGTGTACA 10 264 0 TTTTTGTCTG 0.96021 -14 GTTATGGGTATTGTTTGTAATAGGACAACTAA 19 39 1 TTTTTGTATA 0.647589 -46 GAGATGGTTATTGTTTGTATTGGAATGATTTT 22 27 1 TTTTTGTATG 0.949353 -71 TTACTTGTTTTTAATTGTAAAGCAATGTTGTT 23 120 0 TTATTGTAAG 0.784505 -47 ** ****** ** Masking position 6 Map Score: 4.9593 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 57 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 AGTTTGGCGAACAAAAGATGGAACG 4 6 0 ACAAAAGATG 0.905581 -99 CAACGTAAGCAAAAAATACG 15 1 0 AAAAAATACG 0.859145 -125 TTTTCTGCAGACAAAAGGCGTGACGATGGT 16 145 1 ACAAAAGGCG 0.95775 -156 TCATTCTAGCACAAAAGACGTAACCGCGGG 20 30 0 ACAAAAGACG 0.984126 -77 CACGTAAAACACAAAATACGAAATGACTGA 24 122 1 ACAAAATACG 0.975264 -39 TGCTCTAGGTTCAAAATACGTTCATACAAT 25 79 1 TCAAAATACG 0.906777 -48 ********** Masking position 5 Map Score: 3.33128 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 18 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 7 TGTCAAACATCATTCAGGACAAAAAAATAG 1 25 0 CATTCAGGAC 0.992009 -68 GGTTAATTTACATTCTGGTCGCGTGCGCAA 3 25 1 CATTCTGGTC 0.919798 -153 GTTATGTACACACTCAGGACAAAAAAAC 10 260 1 CACTCAGGAC 0.986453 -18 ATGTGAACGCTATTCAGGACGGGTCACACG 16 14 0 TATTCAGGAC 0.959659 -287 TCTCAAATTACAGTCAGGACGCGT 16 287 1 CAGTCAGGAC 0.986453 -14 ********** Masking position 4 Map Score: 3.12965 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 27 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 GTTACTCGCCCGGAAGCCGCTCTGGCAAG 7 10 0 CCGGAAGCGC 0.865705 -20 GCGTAGTTTACTGGTTGCGGCCCCGCTTGAC 10 225 0 CTGGTTGCGC 0.865294 -53 AGATCACTTACCTGTTGCTGGGTCGCCTGTA 12 78 1 CCTGTTGCGG 0.964646 -47 TGCTGGGTCGCCTGTAGCAGGATTAATTTAA 12 93 1 CCTGTAGCGG 0.797418 -32 AATACAGTCATCTGATGCGGGAAC 13 4 0 TCTGATGCGG 0.933033 -41 AATGGCGCTTTCGTCAGCGGGGATAATCCGT 16 179 1 TCGTCAGCGG 0.848107 -122 CTGACATAAGCCTTTTGCCGGCGGTCCTTTT 17 44 1 CCTTTTGCGG 0.948884 -149 AATAACCATCTCGGAAGCAGGCTGCCGA 22 8 0 TCGGAAGCGG 0.949713 -90 AGCGCGTTAGCCGCTTTGCTCTTT 24 4 1 GCGTTAGCGC 0.783674 -157 GCTTTGCTCTTTTTTTGCGGGCTGAGAGGGC 24 23 1 TTTTTTGCGG 0.663655 -138 ******** ** Masking position 8 Map Score: 3.42614 Number of sites scoring better than the average of aligned sites = 2340 Number in coding regions = 2047 Number in noncoding regions = 293 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 9 AGTAAGTAACTGGTTAATTTACATTCTGGT 3 14 1 TGGTTAATTT 0.800977 -164 CATAACCCACTGGGTGTTGTCTATACTTTA 10 67 0 TGGGTGTTGT 0.962162 -211 CAACACCCAGTGGGTTATGTGCGGGCGTGA 10 78 1 TGGGTTATGT 0.700869 -200 TGGTAGTTTTGATTGATGTA 12 1 1 TGGTAGTTTT 0.704061 -124 AAGCGTCAGGTGGATGTTTTTGCTCTTATT 16 95 0 TGGATGTTTT 0.801392 -206 CCTTGCTTTTTGGTTATTTT 17 1 0 TGGTTATTTT 0.916621 -192 CTTATCGTTATGGGTATTGTTTGTAATAGG 19 33 1 TGGGTATTGT 0.954663 -52 GCTTCCGAGATGGTTATTGTTTGTATTGGA 22 21 1 TGGTTATTGT 0.945762 -77 ********** Masking position 8 Map Score: 1.83907 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 181 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 10 GGTACAAATACAGTCATCTGATGCGGGAAC 13 11 0 CAGTCATCTG 0.878095 -34 GGTCATTCTACCGCCATCTCCCATATATCA 15 43 1 CCGCCATCTC 0.947578 -83 GCCCTTTCAGCAGTCCTTGCTTTTTGGTTA 17 15 0 CAGTCCTTGC 0.919973 -178 AGGCTTATGTCAGCCCTTTCAGCAGTCCTT 17 27 0 CAGCCCTTTC 0.980173 -166 TGAAATGTGCCAGCCCTCTCAGCCCGCAAA 24 36 0 CAGCCCTCTC 0.987296 -125 TCCAAGATTTCAGTCATTTCGTATTTTGTG 24 131 0 CAGTCATTTC 0.952368 -30 ********** Masking position 7 Map Score: 1.72563 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 110 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 GCTTTTCCTCACACAGTTGTCAAGTGTTAC 3 59 1 ACACAGTTGT 0.98138 -119 TGCATTTGATACGCAGTTTTTTGTCAAGCG 10 203 1 ACGCAGTTTT 0.965573 -75 TGCCTGGCCCGCACAGTTTTCGGCAGATTC 11 96 1 GCACAGTTTT 0.925206 -55 GAGTATCCTGACGCTGTTTTTAACACAGTT 14 52 1 ACGCTGTTTT 0.873726 -48 GCTGTTTTTAACACAGTTGTAATAAGAGGT 14 64 1 ACACAGTTGT 0.98138 -36 GTACTATTGAACATAGTTGTGCTTACTGTG 22 64 1 ACATAGTTGT 0.8915 -34 ********** Masking position 7 Map Score: 3.00053 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 46 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 12 GTTGCTTCTCCTTAACACGCACTAT 3 163 0 TTCTCCTTAA 0.871603 -15 GATTTAAATCACCTTAATATCTTAATA 9 100 0 ATCACCTTAA 0.926822 -17 TAAACGCCTGAACACCTTGACTTTCTAATA 10 146 1 AACACCTTGA 0.880305 -132 CGGTGACAACGTCACCTTGTTCCAGACGTT 11 29 1 GTCACCTTGT 0.888134 -122 TCTATACTCAATCGCCTTATACATCAATCA 12 20 0 ATCGCCTTAT 0.79356 -105 TTTAAACCGCTTCACCTTGAAAAAACTACA 16 252 0 TTCACCTTGA 0.952583 -49 ACTTCATGAAGTCTCCTTGAAATCAGAAGA 17 123 1 GTCTCCTTGA 0.920782 -70 GCGGGAGGGTTACGCCTTAAGCTA 20 5 0 TACGCCTTAA 0.79356 -102 ********** Masking position 7 Map Score: 1.05406 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 105 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 13 GTATTTGCGCACGCGACCAGAATGTAAATT 3 29 0 ACGCGACCAG 0.903262 -149 GACAATAATAACACGGCCTGCCGCAATCGT 4 56 0 ACACGGCCTG 0.985237 -49 GATACTCTTCCTGTCAAAATATA 4 92 0 ACTCTTCCTG 0.870439 -13 GCTCTTTAATACACCGCCTGGAAAGGATCA 11 66 1 ACACCGCCTG 0.949886 -85 GCGCGTGTGACCCGTCCTGAATAGCGTTC 16 10 1 ACCCGTCCTG 0.981119 -291 ACGCGTCCTGACTGTAATTT 16 291 0 ACGCGTCCTG 0.989651 -10 ********** Masking position 1 Map Score: 2.55758 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 98 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 14 TGTTCCTCCTGGAAAATCCTTCCTTAATCA 6 78 0 GGAAAATCCT 0.892681 -21 GTTGTAACAGGGAATACCCCTCTTCCTTAT 10 34 1 GGAATACCCC 0.828197 -244 TGCTGGATATAGAGTATCCTGACGCTGTTT 14 41 1 AGAGTATCCT 0.77002 -59 GTCACTCAAGGGATTAACCTCTTATTACAA 14 80 0 GGATTAACCT 0.934567 -20 GTTCAATAACGGATTATCCCCGCTGACGAA 16 188 0 GGATTATCCC 0.938748 -113 GGATAAACCTCCGAATTTAG 18 13 0 GGATAAACCT 0.901501 -10 TAGCTTAAGGCGTAACCCTCCCGCGGTT 20 9 1 GGCGTAACCC 0.918902 -98 GGCGAATCCTCCCTTAGTCA 20 97 0 GGCGAATCCT 0.913908 -10 ********** Masking position 6 Map Score: 0.55673 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 203 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 15 TAAGGAAGGATTTTCCAGGAGGAACAC 6 82 1 TTTTCCAGGA 0.826297 -17 TTAACTTTCCCATGGGGATAACTCA 15 111 0 TTTCCCATGG 0.931327 -15 AGTGCAAGAATTTTCTATTGAGTGCAACTA 17 96 0 TTTTCTATTG 0.888522 -97 TAGGATATATTTTTCTATGGATAAAAGGGA 17 157 1 TTTTCTATGG 0.959329 -36 ATTGGAATGATTTTCTATGGTACTATTGAA 22 45 1 TTTTCTATGG 0.959329 -53 TCAGCTTGTCTTTTCCAGTGAACCTCCTTA 25 45 1 TTTTCCAGTG 0.912205 -82 ********** Masking position 7 Map Score: 0.881623 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 69 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432