AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i013_ecoli_bsub_300.orf -o013_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 GCAATCAGACAAGCAGAATTCGCAAATGCAG 1 67 0 AAGCAGAATC 0.916316 -102 GCTTGTCTGATTGCAGATGCCAGGTAACATA 1 84 1 TTGCAGATGC 0.746467 -85 AAATCGCGCTATGCAGAATCTTCATCTTTTC 2 66 1 ATGCAGAATT 0.963751 -200 AGTAACGGTGTTGGAGGAGCCAGTCCTGTGA 4 19 0 TTGGAGGAGC 0.937408 -282 GCCCTTTTTTAAGCAGAATGCTGAAAAAATG 5 112 0 AAGCAGAATC 0.916316 -115 TTATGTTACAATGGAAAATCTGTTTTTTACC 7 61 1 ATGGAAAATT 0.725485 -43 CCAGCATCATTTGGAGGTTTTACT 7 90 1 TTGGAGGTTT 0.778816 -14 TTAATAATTCATGGAGGAGGTTGCAAAAC 8 9 0 ATGGAGGAGT 0.96143 -221 TTGTGACATATTGGAGAATCTATACATGCAT 8 52 1 TTGGAGAATT 0.950257 -178 CTTCCCTCATATGGAGAATGCATGTATAGAT 8 69 0 ATGGAGAATC 0.977099 -161 ATTTTTTATTATGCAGAATGTCCTCACCACA 8 193 0 ATGCAGAATT 0.963751 -37 TAAAAAATCTAAGGAGGAGATGTC 8 216 1 AAGGAGGAGT 0.898605 -14 ********* * Masking position 5 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 TCCTTATGCGGGGTCAGATACTTAGTTTGCC 3 18 1 GGGTCAGATC 0.823255 -186 AACGCCGGAAAGGCAGGCTCCCTGTAAATAT 3 115 0 AGGCAGGCTC 0.94694 -89 GCGCTAGCGCAGGCCAGAAGAGGCGCGTTGC 4 53 0 AGGCCAGAAA 0.851872 -248 TTCTAGTAGGAGGAAGGAAAC 5 1 0 AGGAAGGAAC 0.940015 -226 TTCTTTTCAGAGGCAAGATTCACATTTTCCG 5 61 0 AGGCAAGATC 0.953283 -166 ACCCAAAGGGCGGAATCCAGTCATTCC 6 7 1 AGGGCGGAAC 0.979109 -105 TCAAGAAGAAAGGGCGGAATGACTGGATTCC 6 22 0 AGGGCGGAAG 0.858533 -90 CCGTTATGGAGGGACAGCAGC 6 101 1 GGGACAGCAC 0.949155 -11 AAAAAGAAAAAGGGAAGCAGCCAAACGGCTA 7 23 0 AGGGAAGCAC 0.961001 -81 AAGCGAGGGCAGGCCAGCTTCCCTCATATGG 8 86 0 AGGCCAGCTC 0.973187 -144 GCAAGGTGCTGGGAAAGAAGCTGATATAAGC 8 113 0 GGGAAAGAAC 0.913007 -117 ********* * Masking position 7 Map Score: 8.92444 Number of sites scoring better than the average of aligned sites = 799 Number in coding regions = 732 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 3 GCTAATCGGCTCCCTTTTTTTACCTTTAAT 1 23 1 TCCCTTTTTT 0.98261 -146 CGCCCCGCTCACCCTTTATTTATAAATGTA 4 90 0 ACCCTTTATT 0.841567 -211 ACTAAAACCATCACATTTTTCTGTGACTGG 4 231 1 TCACATTTTT 0.883993 -70 GAGGCAAGATTCACATTTTCCGCTTGATCC 5 53 0 TCACATTTTC 0.788349 -174 AAACATTTAAGCCCTTTTTTAAGCAGAATG 5 123 0 GCCCTTTTTT 0.96506 -104 TAAAAGTACCTCACTTTATTCGAAGCTTTA 5 207 0 TCACTTTATT 0.926736 -20 CAGTCATTCCGCCCTTTCTTCTTGACTTGA 6 28 1 GCCCTTTCTT 0.894722 -84 GTTTCATCTTTCACTTTATATGAACTTATC 6 65 0 TCACTTTATA 0.693894 -47 AACGGCTATTTCCCCTTTTT 7 1 0 TCCCCTTTTT 0.937532 -103 TTTGGCTGCTTCCCTTTTTCTTTTTTGTCA 7 29 1 TCCCTTTTTC 0.96506 -75 ********** Masking position 6 Map Score: 8.57386 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 154 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 4 GGAGCCTGCCTTTCCGGCGTTGTTGTTATGC 3 125 1 TTCCGGCGTT 0.96248 -79 GCGCCTCTTCTGGCCTGCGCTAGCGCAGGTA 4 58 1 TGCCTGCGCT 0.991881 -243 TATAAATGTACTACCTGCGCTAGCGCAGGCC 4 69 0 CTCCTGCGCT 0.991884 -232 TTTTCATCCACTCCTGGCGGTCAGTAGTTCA 4 146 1 CTCTGGCGGT 0.894998 -155 TAATAAATGCTTCACTGCGCTAAGGGTTTAC 4 179 1 TTACTGCGCT 0.966122 -122 CAACATTACGCTAACGGCACTAAAACCATCA 4 213 1 CTACGGCACT 0.851873 -88 CATTTTTCTGTGACTGGCGCTACAATCTTCC 4 244 1 TGCTGGCGCT 0.977943 -57 TGAGGGAAGCTGGCCTGCCCTCGCTTATATC 8 91 1 TGCCTGCCCT 0.959172 -139 ** ******** Masking position 11 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 5 TCCACCCGTAAATGGGGGGATACCTATGTT 1 109 0 AATGGGGGGA 0.953901 -60 TCCCCCCATTTACGGGTGGACAAGTGTTTA 1 119 1 TACGGGTGGA 0.939801 -50 TCGATGGCATTACGCGGTGTATGTTATAAA 2 124 0 TACGCGGTGT 0.949711 -142 AAAGGTGGCATATGGTGTGATCGGGGTTCA 2 158 1 TATGGTGTGA 0.881876 -108 TTCTATTCCTTATGCGGGGTCAGATACTTA 3 12 1 TATGCGGGGT 0.969969 -192 GAAGGAAATATACGGGGTGTACTAAAATAA 5 180 1 TACGGGGTGT 0.978145 -47 ATTATACCGTTATGGAGGGACAGCAGC 6 95 1 TATGGAGGGA 0.939096 -17 ********** Masking position 2 Map Score: 3.69934 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 95 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 ACAAGTGTTTATTTTTTCCGACTATTAACA 1 138 1 ATTTTTTCCG 0.944887 -31 CAGAATCTTCATCTTTTCAGGTACAAACGC 2 79 1 ATCTTTTCAG 0.982878 -187 CAATTACTTTATCGTTTCAGCACCAATTGC 3 71 0 ATCGTTTCAG 0.94642 -133 ACCCAGATCGATATTTACAGGGAGCCTGCC 3 105 1 ATATTTACAG 0.841003 -99 GGCAAGATTCACATTTTCCGCTTGATCCTG 5 51 0 ACATTTTCCG 0.840646 -176 GAAAGGATTGTTCTTTTCAGAGGCAAGATT 5 72 0 TTCTTTTCAG 0.922587 -155 TGCTAGAAACATTTTTTCAGCATTCTGCTT 5 103 1 ATTTTTTCAG 0.962233 -124 ********** Masking position 5 Map Score: 3.68478 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 164 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 GCGTCCTCGTACAGGAGCGTTTAGTACAATAA 2 232 0 ACAGGGCTTT 0.944487 -34 CACCAATTGCAGCGATGCCTTTTTGCAAGCTG 3 49 0 AGCGAGCTTT 0.982543 -155 TTTTGACTTTAGCGGAGCAGTTGAAGA 3 187 1 AGCGGGCGTT 0.99262 -17 GCAGGCCAGAAGAGGCGCGTTGCCCAAGTAAC 4 44 0 AGAGGGCTTG 0.964337 -257 ATAAAGGGTGAGCGGGGCGGTTGTCAACGATG 4 101 1 AGCGGGCGTT 0.99262 -200 CCCTTAGCGCAGTGAAGCATTTATTAGCTGAA 4 173 0 AGTGAGCTTT 0.934432 -128 ***** ** *** Masking position 11 Map Score: 2.96583 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 159 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 8 AATTCGCAAATGCAGCGAAAGATTTCGGAA 1 52 0 TGCAGCGAAA 0.867056 -117 CACCCGTAAATGGGGGGATACCTATGTTAC 1 107 0 TGGGGGGATA 0.975971 -62 CTATTCCTTATGCGGGGTCAGATACTTAGT 3 14 1 TGCGGGGTCA 0.944836 -190 TGTAAATACCTGGGGGCATAACAACAACGC 3 141 0 TGGGGGCATA 0.903028 -63 TATACCGTTATGGAGGGACAGCAGC 6 97 1 TGGAGGGACA 0.96537 -15 CTCCAAATGATGCTGGTAAAAAACAGATTT 7 76 0 TGCTGGTAAA 0.839965 -28 TTTTGCAAGGTGCTGGGAAAGAAGCTGATA 8 118 0 TGCTGGGAAA 0.971369 -112 ********** Masking position 10 Map Score: 1.32759 Number of sites scoring better than the average of aligned sites = 278 Number in coding regions = 232 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 9 GATTGCAGATGCCAGGTAACATAGGTATCC 1 92 1 GCCAGGTAAC 0.852211 -77 ATAGGTATCCCCCCATTTACGGGTGGACAA 1 112 1 CCCCATTTAC 0.847905 -57 ATTTATTGAACCCCGATCACACCATATGCC 2 164 0 CCCCGATCAC 0.972324 -102 AGGCGCGTTGCCCAAGTAACGGTGTTGGAG 4 34 0 CCCAAGTAAC 0.961298 -267 TTGACAACCGCCCCGCTCACCCTTTATTTA 4 98 0 CCCCGCTCAC 0.981157 -203 AAGATTGTAGCGCCAGTCACAGAAAAATGT 4 243 0 CGCCAGTCAC 0.966873 -58 CTACAATCTTCCAAAGTCACAATTCTCAAA 4 263 1 CCAAAGTCAC 0.905076 -38 ********** Masking position 9 Map Score: 0.882213 Number of sites scoring better than the average of aligned sites = 433 Number in coding regions = 385 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 10 GAAATCTTTCGCTGCATTTGCGAATTCTGC 1 56 1 GCTGCATTTG 0.984106 -113 CGCCTTTATTGCTACATTTTTATAACATAC 2 106 1 GCTACATTTT 0.935219 -160 AAAAGGCATCGCTGCAATTGGTGCTGAAAC 3 58 1 GCTGCAATTG 0.938558 -146 CCGTATATTTCCTTCATTTTAAATCTAAAA 5 165 0 CCTTCATTTT 0.893206 -62 TTTATTCGAAGCTTTATTTTAGTACACCCC 5 193 0 GCTTTATTTT 0.849468 -34 TTTTTTACCAGCATCATTTGGAGGTTTTAC 7 83 1 GCATCATTTG 0.933995 -21 ********** Masking position 6 Map Score: 0.74033 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 237 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 11 CCTTTAGCATCTTTTATAGAGTCTGGTGTT 2 17 1 CTTTTATAGA 0.700227 -249 ATTTACGCAACAGGAATAGACTGAACACCA 2 40 0 CAGGAATAGA 0.958349 -226 TTCATCTTTTCAGGTACAAACGCCTTTATT 2 86 1 CAGGTACAAA 0.872617 -180 GACCCCGCATAAGGAATAGAAC 3 3 0 AAGGAATAGA 0.719843 -201 GCAGGTAGTACATTTATAAATAAAGGGTGA 4 82 1 CATTTATAAA 0.748826 -219 ATTGTAGCGCCAGTCACAGAAAAATGTGAT 4 240 0 CAGTCACAGA 0.873488 -61 ATTATTAAAACAGTTATAGATTGTGACATA 8 32 1 CAGTTATAGA 0.970884 -198 ATGGAGAATGCATGTATAGATTCTCCAATA 8 60 0 CATGTATAGA 0.953862 -170 ********** Masking position 6 Map Score: 0.817626 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 325 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 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 Motif number 14 ********** 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