AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icynR_ecoli_bsub_300.orf -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 cynR_cynT 108 cynR: cyn operon positive regulator, cynT: carbonic anhydrase #2 cynS 30 cyanate aminohydrolase, cyanase #3 cynX 32 cyanate transport #4 ycgK 192 similar to transcriptional regulator (LysR family) #5 gltC 146 transcriptional regulator (LysR family) #6 ytiB 93 similar to carbonic anhydrase #7 ytiA 219 similar to hypothetical proteins #8 alsR 154 transcriptional regulator (LysR family) #9 ywfK 146 alternate gene name: ipa-89d; similar to transcriptional regulator (LysR family) #10 pta 269 phosphotransacetylase #11 ywbI 105 alternate gene name: ipa-24d; similar to transcriptional regulator (LysR family) #12 yybE 228 similar to transcriptional regulator (LysR family) Motif number 1 GTAAATCCAATGGAACTCATCATAAATGAGACTTT 1 71 0 TGAAATCAAA 0.830712 -38 TTATGATTCGTCCAAGATATAAAAATGATGAAAAT 4 142 1 TCAAATAAAA 0.902852 -51 TTGTAGGTTTTCAAAACGATATAAACAATATATAA 5 74 1 TAAAATATAA 0.885272 -73 ATAATTTAGATCAAAAGAATCTCAAAATGAGATAG 5 105 1 TAAAATCTAA 0.934834 -42 CTTTTTACTCTTCAATATATCACAACCCTTGTTTA 6 49 0 TCAAATCAAA 0.945289 -45 TATTGAAGAGTAAAAAGAATAGAAAGGGACAACGA 6 67 1 TAAAATAGAA 0.903084 -27 TGTAAGGTTATAAAATAAAACGTAATTATTACGAT 7 176 1 TAAAAACGAA 0.648326 -44 GGTATCTCCTTTCAATAAATCGTAATAATTACGTT 7 194 0 TCAAATCGAA 0.934432 -26 ATTTTACGTTTAAAATGCATAATAAGGAGTGAGG 8 10 0 TAAAATAAAA 0.918679 -145 GAGTGTATAGTGAAACTTATCACAAGATATTTAAA 8 45 0 TAAAATCAAA 0.95455 -110 GTACAATAAAGAAAACTAATCATAACCATATATTT 9 99 1 GAAAATCAAA 0.76812 -48 TCTCTATAGGTAAAATATATATTAAGAATAAGAAG 11 49 1 TAAAATATAA 0.885272 -57 ATATGCATTATACAACATATATCAACGGTGCTAAG 12 118 0 TCAAATATAA 0.863907 -111 * *** **** ** Masking position 9 Map Score: 12.1029 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 79 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 2 CATGCGCAACCATCAAAAGACGTTCACG 3 15 1 CATCAAAAGA 0.924995 -18 GATGTATCGGGATGAAAAGGTATTTGCCGA 4 21 0 GATGAAAAGG 0.975124 -172 TTTCGTAAATGATGATATGGATTATGTTAG 4 103 1 GATGATATGG 0.864497 -90 ATATAAAAATGATGAAAATGATAGGTTCAA 4 158 1 GATGAAAATG 0.844874 -35 ATATAATTTAGATCAAAAGAATCTCAAAAT 5 103 1 GATCAAAAGA 0.911818 -44 GTTTAAAATGCATAATAAGGAGTGAGG 8 8 0 CATAATAAGG 0.79127 -147 ATTACATATTAATCATAAGGCGAATCGATA 8 99 0 AATCATAAGG 0.719649 -56 TACCAAGACGGATGATATGAGTACAATAAA 9 79 1 GATGATATGA 0.742787 -68 TGAAGGCAATCATGAAAAGATAATGGGAGT 10 19 0 CATGAAAAGA 0.954878 -251 CGTATAACTCCATCAAAATAGAAGAACCTA 10 101 1 CATCAAAATA 0.631459 -169 TGCTCCACAACATGATGAGGGACCGATAAA 12 17 0 CATGATGAGG 0.851976 -212 TACATATAAGCATGAAAAGGATATTTTATA 12 150 0 CATGAAAAGG 0.979057 -79 ********** Masking position 5 Map Score: 10.7191 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 284 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 3 ATTCTTTTTACTCTTCAATATATCACAACC 6 57 0 CTCTTCAATA 0.677047 -37 GTTCGTTGTCCCTTTCTATTCTTTTTACTC 6 74 0 CCTTTCTATT 0.808694 -20 TCGTAAACCACCTTTCCAAAAAGACGTTCT 7 28 1 CCTTTCCAAA 0.820783 -192 GGGTATCTCCTTTCAATAAATCGTAATA 7 202 0 CCTTTCAATA 0.930366 -18 AATATGCATTCCTTTCCATAGGTTAATAAT 8 133 0 CCTTTCCATA 0.975333 -22 GCCTTTTTTGCGCTTCTGTATAGCCCTTCT 9 48 1 CGCTTCTGTA 0.934427 -99 TTCTGTATAGCCCTTCTTTACCAAGACGGA 9 61 1 CCCTTCTTTA 0.902042 -86 CCTTGAACATCCCTTCCGTATAACTCCATC 10 85 1 CCCTTCCGTA 0.975392 -185 TTCATTATAGCGCTTTCATAAAAAAATCTT 10 169 0 CGCTTTCATA 0.791561 -101 TAAAAGAAAGCGTTTTTGTAACTTTTTGAG 10 239 1 CGTTTTTGTA 0.578351 -31 ATTGATGCCTCCCTTATATACTTATTGTAC 11 11 1 CCCTTATATA 0.836159 -95 GCGCTTCACCCTTTCTATAGACAAAAGGA 11 87 0 CCTTTCTATA 0.973331 -19 ********** Masking position 5 Map Score: 9.2624 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 254 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 4 TTACGATTGTGGATGATTTAGTT 7 2 0 GGAGATTTAT 0.973089 -218 AACCTATAAGGGAAGATTGAGTCACTTAAATT 10 125 1 GGAGATTGAT 0.990742 -145 AATGAAAGTTGGCTGTTTGAATTTGATTGGAA 10 193 1 GGCGTTTGAT 0.97508 -77 AACTTTTTGAGGAGGTTTTATT 10 258 1 GGAGTTTTAT 0.973089 -12 AAGAAATAAAGGATGATTGTTTATGAATGGCA 12 48 0 GGAGATTGTT 0.963503 -181 ACAGACTCGAGGATGTTTGAATTCGTAAGAAA 12 74 0 GGAGTTTGAT 0.990742 -155 *** ****** * Masking position 7 Map Score: 5.7556 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 8 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 5 ATCTTCCCCCTCGGCAAATACC 4 3 1 CTTCCCCCTC 0.961477 -190 AATTCCTCTCCCCCGATCAATTTC 5 5 1 CCTCTCCCCC 0.976086 -142 TTCTTATATCCTTCCCTCTGTTTCACATCG 7 131 0 CTTCCCTCTG 0.846293 -89 CCTCACTCCTTATTATGCAT 8 1 1 CCTCACTCCT 0.973885 -154 AAACCCCACCCCTGTCATTAATG 9 134 0 CCCCACCCCT 0.918151 -13 TTATCTTCACTCCCATTATCTTTT 10 5 1 CTTCACTCCC 0.979993 -265 AAACCTTGAACATCCCTTCCGTATAACTCC 10 82 1 CATCCCTTCC 0.756572 -188 GCGCTTCACCCTTTCTATAGACA 11 93 0 CTTCACCCTT 0.928726 -13 TTCCAATTATCATCTCTCCTTATTACATAT 12 173 0 CATCTCTCCT 0.898692 -56 ********** Masking position 6 Map Score: 4.83361 Number of sites scoring better than the average of aligned sites = 401 Number in coding regions = 301 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 6 CGTTAACCTCTGTCTGTCTC 1 1 1 CGTTAACCTC 0.97827 -108 ATTGTCATAAGGTAAAAGTCTCATTTATGA 1 57 1 GGTAAAAGTC 0.85617 -52 CGTGAACGTCTTTTGATGGT 3 23 0 CGTGAACGTC 0.966453 -10 CATCCACAATCGTAAACCACCTTTCCAAAA 7 19 1 CGTAAACCAC 0.945766 -201 TGTTTCACATCGTAAACCTCATGGCATTTA 7 113 0 CGTAAACCTC 0.988235 -107 ACATCCCTTCCGTATAACTCCATCAAAATA 10 91 1 CGTATAACTC 0.894106 -179 GATGAGGGACCGATAAAGTCCCG 12 4 0 CGATAAAGTC 0.775045 -225 ********** Masking position 6 Map Score: 2.97041 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 205 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 7 CAGCCATGCGCAACCATCAAAAGACGTT 3 9 1 CGCAACCATC 0.848648 -24 GGCAGGCCTGAGGGTTTGTC 6 1 1 GGCAGGCCTG 0.984608 -93 TGAAGACAATGGCAGCTCTCGACCGAGGGC 9 17 1 GGCAGCTCTC 0.971236 -130 GCGCAAAAAAGGCAGCCCTCGGTCGAGAGC 9 31 0 GGCAGCCCTC 0.995478 -116 GTATAGTGAAGGCAATCATGAAAAGATAAT 10 25 0 GGCAATCATG 0.845256 -245 AAGTATATAAGGGAGGCATCAAT 11 4 0 GGGAGGCATC 0.933821 -102 GTTTATGAATGGCAGTGCTCCACAACATGA 12 32 0 GGCAGTGCTC 0.957392 -197 ********** Masking position 4 Map Score: 2.69197 Number of sites scoring better than the average of aligned sites = 505 Number in coding regions = 469 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 8 CTCTCATTCCAGAGACAGACAGAGGTTAAC 1 12 0 AGAGACAGAC 0.986428 -97 CTCTGGAATGAGAGGCAGACTACTCGCCGA 1 28 1 AGAGGCAGAC 0.957199 -81 TAGATGGATGTGAGACAAAC 5 137 1 TGAGACAAAC 0.891442 -10 CATAATAAAAAAAGACAAACCCTCAGGCCT 6 14 0 AAAGACAAAC 0.920212 -80 CAAAGAGTGTATAGTGAAACTTATCACAAG 8 54 0 ATAGTGAAAC 0.735945 -101 TATTTTACCTATAGAGAGACCTTATGTACA 11 36 0 ATAGAGAGAC 0.955145 -70 CACCCTTTCTATAGACAAAAGGAATACTTC 11 80 0 ATAGACAAAA 0.809063 -26 AGATAATAATATAAACAGACTCGAGGATGT 12 90 0 ATAAACAGAC 0.870484 -139 ********** Masking position 7 Map Score: 2.50964 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 160 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 9 TTTTTATATCTTGGACGAATCATAACAGAAAT 4 135 0 TTGACGAATA 0.930886 -58 CTTTTTTTATTATGACGAATAAACAAGGGTTG 6 30 1 TAGACGAATA 0.984793 -64 CATTTAAGAATAGGAAGAATAATCTAACCGAG 7 87 0 TAGAAGAATA 0.969149 -133 GGGAAGGATATAAGAAGATTGACAAAACGTTT 7 145 1 TAGAAGATTA 0.931816 -75 AAAACGTAATTATTACGATTTATTGAAAGGAG 7 192 1 TATACGATTA 0.931608 -28 GATTAATATGTAATACGAATTATTAACCTATG 8 115 1 TATACGAATA 0.920034 -40 GTAAAATATATATTAAGAATAAGAAGTATTCC 11 58 1 TATAAGAATA 0.938299 -48 ** ******* * Masking position 5 Map Score: 5.22065 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 20 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 TCGCCGATTGTCATAAGGTAAAAGTCTCATT 1 51 1 TCATAAGGAA 0.906865 -58 TCGCAACCTATAAGTAAATCCAATGGAA 1 91 0 CTATAAGTAA 0.9442 -18 TTCAGCCTCCATAGGTTGAACCTATCATT 4 174 0 CCATAGGTGA 0.937096 -19 TACATATTAATCATAAGGCGAATCGATATTG 8 96 0 TCATAAGGGA 0.846482 -59 GCATTCCTTTCCATAGGTTAATAATTCGTAT 8 127 0 CCATAGGTAA 0.96338 -28 ATAGAAGAACCTATAAGGGAAGATTGAGTCA 10 118 1 CTATAAGGAA 0.96408 -152 TATGAAAGCGCTATAATGAAAGTTGGCTGTT 10 179 1 CTATAATGAA 0.749823 -91 TAAGGTCTCTCTATAGGTAAAATATATATTA 11 42 1 CTATAGGTAA 0.943136 -64 ******** ** Masking position 5 Map Score: 3.53941 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 64 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 CCTCTGTCTGTCTCTGGAATGAGAGGCAGACTAC 1 17 1 TTCTGGAAGA 0.950553 -92 ATGACCGGTATTATCGGAAATTGATCGGGGGAGA 5 17 0 TATCGGAAGA 0.972877 -130 TTATTACGATTTATTGAAAGGAGATACCC 7 201 1 TATTGAAAGA 0.938181 -19 CACTATACACTCTTTGGAAATTGACCTCCAATAT 8 68 1 TTTTGGAAGA 0.98132 -87 TGTTTGAATTTGATTGGAAGAAGAGTATGCTAGT 10 206 1 TATTGGAAGA 0.989908 -64 GGAGAGATGATAATTGGAATGGGAACAACTTGAA 12 184 1 TATTGGAAGA 0.989909 -45 * ******* ** Masking position 8 Map Score: 3.25109 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 2 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 12 GGTAAAAGTCTCATTTATGATGAGTTCCAT 1 67 1 TCATTTATGA 0.873995 -42 ATCCATATCATCATTTACGAAAAGAAGGAG 4 95 0 TCATTTACGA 0.886781 -98 GTTAGCAATTTCTGTTATGATTCGTCCAAG 4 128 1 TCTGTTATGA 0.866728 -65 GGGTTTGTCTTTTTTTATTATGACGAATAA 6 22 1 TTTTTTATTA 0.710684 -72 ACCATATATTTCATTAATGACAGGGGTGGG 9 123 1 TCATTAATGA 0.456961 -24 AAAATAAGATTTTTTTATGAAAGCGCTATA 10 164 1 TTTTTTATGA 0.925691 -106 AAAAACGCTTTCTTTTACTAGCATACTCTT 10 226 0 TCTTTTACTA 0.799164 -44 TAAAGGATGATTGTTTATGAATGGCAGTGC 12 44 0 TTGTTTATGA 0.81876 -185 TCATCCTTTATTTCTTACGAATTCAAACAT 12 64 1 TTTCTTACGA 0.732118 -165 ********** Masking position 5 Map Score: 1.79829 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 139 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 13 ********** No masking Map Score: -9.4259e-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: -9.4259e-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 15 ********** No masking Map Score: -9.4259e-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