AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i320_mixed5_ecoli_hinf_reg_100.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 aspS 276 aspartate tRNA synthetase #2 hisS 110 histidine tRNA synthetase #3 ndk 148 nucleoside diphosphate kinase #4 HI0317 218 aspartyl-tRNA synthetase (aspS) #5 HI0366 101 fimbrial biogenesis and twitching motility protein, putative #6 HI0367 71 conserved hypothetical protein #7 HI0876 300 nucleoside diphosphate kinase (ndk) Motif number 1 AATGCGATTAGCCGATGGCGGAACGACAAATTTT 1 16 1 GCTGGCGGAC 0.944503 -261 TAAGAGCCTGGCCCGCGCTGGAACGCCTCGTTAC 1 126 0 GCCGCTGGAC 0.995534 -151 CGGGCCAGGCTCTTACGGTGCGGCAGAATTTCCA 1 145 1 TCCGGTGCGC 0.90191 -132 GTGACATACAGCTAACGCTGCGACTTGGTCACCT 1 208 1 GCCGCTGCAC 0.995676 -69 GCAGCAGGGGGCATCCGCCGGCAGCTAAGTTAAG 1 244 1 GCCGCCGGAG 0.981146 -33 GCGGGTTCAATCATACACGGGAAGCGAGGCGCTT 2 23 0 TCCACGGGAG 0.862493 -88 CCGCGCCATCTCGTACGCTGGTACAGACAACAAC 3 103 1 TCCGCTGGAC 0.993233 -46 GCTTGCCCCAGCTCCAACTGGAACCGAACCAATA 7 100 0 GCAACTGGAC 0.911951 -201 TGGAGCTGGGGCAAGCACTGCAACGGCATTTTTA 7 118 1 GCCACTGCAC 0.985007 -183 TGATTTATGGTCTGTTGGGGCAACAGGAATTGGT 7 226 1 TCTGGGGCAC 0.830975 -75 ** ****** ** Masking position 2 Map Score: 9.07609 Number of sites scoring better than the average of aligned sites = 1894 Number in coding regions = 1829 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 2 GGTGCGGCAGAATTTCCAGTATAATAGCCGCCTTTTTTCATTCA 1 161 1 AATTTAAGTT 0.955522 -116 TTGAGGGTTCATTTTTATATTCAGAAAGAGAATAAAC 2 84 1 ATTTTAAGTA 0.980566 -27 GAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATC 3 25 0 TTTTTAAGTT 0.955523 -124 TCCTTAACGTAATTTAATCTCAACAAGCGGCATAATATAACAAA 4 18 1 AATTTAAGTA 0.963594 -201 AATAAAGGCTTTTTTGTGCCATATCATCAGATTTTTTGTTATAT 4 52 0 TTTTTAAGTT 0.955522 -167 TTGCGACAGATTTTTGAGCATAATTAAAAGAGTACAAAGGATTT 4 181 1 TTTTTAAGTA 0.963594 -38 AATATGCTTTAATTTGTATGAAAACATAGGGGTATGTGAACTTG 5 33 0 AATTTAAGTA 0.963594 -69 TGGAGGCTAAATTTTAAAGTCCAATACTTGATTTGGCAATGCT 6 10 0 ATTTTAAGTT 0.976165 -62 TTTAGCCTCCATTTACCGCCTAATTATTTGATTAAATTT 6 43 1 ATTTAAAGTA 0.88832 -29 ***** * * * ** Masking position 13 Map Score: 5.58013 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 62 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 3 CACCTTTATAGCAAACTGGCGTAGAGTCTGAT 1 74 1 GAAATGGCGT 0.900152 -203 ATATAAAGTGGTAACGAGGCGTTCCAGCGCGG 1 116 1 GAACAGGCGT 0.971338 -161 ACAACTGAATGAAAAAAGGCGGCTATTATACT 1 178 0 GAAAAGGCGG 0.979823 -99 TCATACACGGGAAGCGAGGCGCTTCCCATCAC 2 15 0 GAGCAGGCGC 0.959175 -96 CAATGTTTCGGGAGCCATGCGGGTTCAATCAT 2 43 0 GAGCATGCGG 0.984178 -68 CATGGCTCCCGAAACATTGAGGGAAGCGTTGA 2 56 1 GAACTTGAGG 0.968901 -55 AACATTGAGGGAAGCGTTGAGGGTTCATTTTT 2 68 1 GAGCTTGAGG 0.962545 -43 ATGAGTTTTAGCAACAATCAGGGACAAAACAG 3 12 0 GAACATCAGG 0.847946 -137 ATAATTAGGCGGTAAATGGAGGCTAAATTTTA 6 38 0 GTAATGGAGG 0.759762 -34 * *** ****** Masking position 11 Map Score: 4.99788 Number of sites scoring better than the average of aligned sites = 1221 Number in coding regions = 1140 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 4 GGAACGACAAATTTTGTTAATTTTTATGAGTTCG 1 35 1 ATTTGTATTT 0.928184 -242 GCGTTGAGGGTTCATTTTTATATTCAGAAAGAGA 2 81 1 TTATTTAATT 0.643745 -30 TTGTCCCTGATTGTTGCTAAAACTCATTTTATTT 3 17 1 TTTTGTAACT 0.810839 -132 TGAAGGTAACATTTTTTTAAAATAAAATGAGTTT 3 36 0 ATTTTTAATA 0.642945 -113 TATCATCAGATTTTTTGTTATATTATGCCGCTTG 4 41 0 TTTTTTAATT 0.939761 -178 TTTATTTTGAATATTTATTACTTTTCTTTGCTTT 4 90 1 ATTTTTATTT 0.889974 -129 TTTCTTTGCTTTTTTGATTGATTTGTCAGCATAA 4 112 1 TTTTGTGTTT 0.817789 -107 ACCGCCTAATTATTTGATTAAATTT 6 57 1 TATTGTAATT 0.735613 -15 TCTTTTGCCGATATTGCTAATATTGGTTCGGTTC 7 80 1 ATTTGTAATT 0.961422 -221 CTGCAACGGCATTTTTATCGTATTTTGTAAAAAA 7 135 1 ATTTTTGATT 0.84372 -166 GCAACCAATTTTGTTTATAATTTTTTACAAAATA 7 155 0 TTTTTTATTT 0.889983 -146 TACTTCAATGATCTTGATAACATTAAATTAGCTA 7 270 0 ATTTGTAATT 0.961445 -31 ** *** * * *** Masking position 8 Map Score: 5.89194 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 204 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 5 AAAAATTAACAAAATTTGTCGTTCCGCCATC 1 29 0 AAAATTGTCG 0.955527 -248 ATTATACTGGAAATTCTGCCGCACCGTAAGA 1 155 0 AAATTCGCCG 0.92608 -122 AATATAACAAAAAATCTGATGATATGGCACA 4 51 1 AAAATCGATG 0.941487 -168 ATTATGCTCAAAAATCTGTCGCAATTATAGC 4 174 0 AAAATCGTCG 0.987462 -45 TTCAAAATCCTTTGTACTCTTTTA 4 205 0 AAAATCTTTG 0.894194 -14 AATACGATAAAAATGCCGTTGCAGTGCTTGC 7 128 0 AAATGCGTTG 0.897227 -173 AATTATAAACAAAATTGGTTGCATATTGATT 7 167 1 AAAATTGTTG 0.946785 -134 ****** **** Masking position 3 Map Score: 3.06359 Number of sites scoring better than the average of aligned sites = 327 Number in coding regions = 298 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 TTATGAGTTCGGGCAACACCTTTATAGCAA 1 58 1 GGGCAACACC 0.978637 -219 TTGGTCACCTGCGCAGCAGGGGGCATCCGC 1 232 1 GCGCAGCAGG 0.975899 -45 GCGCAGCAGGGGGCATCCGCCGGCAGCTAA 1 242 1 GGGCATCCGC 0.948444 -35 GGATTATAATGAGCAACAGGGCCGTTGACT 3 75 0 GAGCAACAGG 0.970551 -74 CCTTTTAATTGGGCAGGAAGAAATACTTAA 5 75 0 GGGCAGGAAG 0.961802 -27 GTTGGAGCTGGGGCAAGCACTGCAACGGCA 7 116 1 GGGCAAGCAC 0.933893 -185 TGGTCTGTTGGGGCAACAGGAATTGGTGTG 7 233 1 GGGCAACAGG 0.995327 -68 ********** Masking position 5 Map Score: 5.79441 Number of sites scoring better than the average of aligned sites = 584 Number in coding regions = 549 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 CTCGTTACCACTTTATATCGGGCCTGAAAT 1 104 0 CTTTATATCG 0.820989 -173 TTTTACCTCTGTAAATTGTTCTGTTGTT 3 131 0 CTGTAAATTG 0.856557 -18 AAAATAAAGGCTTTTTTGTGCCATATCATC 4 68 0 CTTTTTTGTG 0.821027 -151 ACAAAAAAGCCTTTATTTTGAATATTTATT 4 79 1 CTTTATTTTG 0.945269 -140 ATATTTATTACTTTTCTTTGCTTTTTTGAT 4 100 1 CTTTTCTTTG 0.910163 -119 CCTTTGTACTCTTTTAATTATGCTCAAAAA 4 191 0 CTTTTAATTA 0.715215 -28 ACTTAATATGCTTTAATTTGTATGAAAACA 5 51 0 CTTTAATTTG 0.957427 -51 TTTTCCTCCTTTTAATTGGGCAGGAAGA 5 84 0 CTTTTAATTG 0.957367 -18 ********** Masking position 4 Map Score: 2.83667 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 105 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 8 GATATAAAGTGGTAACGAGGCGTTCCAGCGC 1 115 1 GGAACGAGGC 0.989091 -162 GCGTTCCAGCGCGGGCCAGGCTCTTACGGTG 1 134 1 GCGGCCAGGC 0.925969 -143 GTGACATACAGCTAACGCTGCGACTTGGTCA 1 208 1 GCAACGCTGC 0.93483 -69 ATCATACACGGGAAGCGAGGCGCTTCCCATC 2 17 0 GGAGCGAGGC 0.994675 -94 TCAATGTTTCGGGAGCCATGCGGGTTCAATC 2 45 0 GGAGCCATGC 0.984927 -66 AAACATTGAGGGAAGCGTTGAGGGTTCATTT 2 67 1 GGAGCGTTGA 0.912549 -44 GAATTAATTTGTGAACGATGAAAATCTTCAA 7 48 0 GTAACGATGA 0.796942 -253 ** ******** Masking position 6 Map Score: 2.24148 Number of sites scoring better than the average of aligned sites = 1139 Number in coding regions = 1069 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 9 CTTAATGCGATTAGCCGATGGCGGAACGAC 1 13 1 TTAGCCGATG 0.751184 -264 TTTTACCTCTGTAAATTGTTC 3 138 0 TTTACCTCTG 0.843088 -11 TTTGTTATATTATGCCGCTTGTTGAGATTA 4 32 0 TATGCCGCTT 0.902206 -187 TCTCTCTTGGTTTTCCGCTATAATTGCGAC 4 158 1 TTTTCCGCTA 0.956065 -61 TTTTCCTCCTTTTAATTGGG 5 92 0 TTTTCCTCCT 0.884527 -10 ACTTTAAAATTTAGCCTCCATTTACCGCCT 6 34 1 TTAGCCTCCA 0.793365 -38 TTAGCCTCCATTTACCGCCTAATTATTTGA 6 44 1 TTTACCGCCT 0.942234 -28 GAAAGGTTCATTTTCTGCTTGTGC 7 5 0 TTTTCTGCTT 0.735299 -296 TAATTCATCTTTTGCCGATATTGCTAATAT 7 73 1 TTTGCCGATA 0.898479 -228 ********** Masking position 1 Map Score: 1.09752 Number of sites scoring better than the average of aligned sites = 3489 Number in coding regions = 3255 Number in noncoding regions = 234 Number of orfs with sites within 600 bp upstream = 262 Fraction of orfs with sites within 600 bp upstream = 0.0420816 Motif number 10 ********** No masking Map Score: -3.62844e-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: -3.62844e-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 12 ********** No masking Map Score: -3.62844e-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