AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -igcvA_ecoli_hinf_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 gcvA 300 positive regulator of gcv operon #2 gcvP 118 glycine decarboxylase, P protein of glycine cleavage system #3 gcvH 23 in glycine cleavage complex, carrier of aminomethyl moiety via covalently bound lipoyl cofactor #4 gcvT 300 aminomethyltransferase (T protein; tetrahydrofolate-dependent) of glycine cleavage system #5 HI1194 300 glycine cleavage system transcriptional activator (gcvA) Motif number 1 CAAACACAACAACACAACATCACAACCGTAAG 1 94 1 AAAAACATCA 0.98557 -207 ACCGTAAGCCAAAAGTTCACCAGAACACGCAT 1 118 1 AAATTCACCA 0.90058 -183 TTGTTAAATTCATTTAACATCAAAGTTTAATA 1 276 1 CATAACATCA 0.836686 -25 ATTAAGAGCTAAAAAAATGTCAAAAA 4 5 0 AAAAATGTCA 0.78891 -296 TAAAAAACCAAAAAATACACCAGTTTCTATAC 4 77 0 AAATACACCA 0.95788 -224 ATCGCGACAGAATAAAAAACCAAAAAATACAC 4 89 0 AAAAAAACCA 0.888984 -212 CATAAGGTAAAATTGATCATCACATTAGCTTA 4 139 0 AATATCATCA 0.915512 -162 TTTCATGGTGAAATTATCACCACGAAACCCAG 4 245 0 AATATCACCA 0.935657 -56 AATCGGGATGAAAAAAACGCCACTCAATGAGA 5 14 1 AAAAACGCCA 0.982879 -287 ACTATATGCAAACACAACATCATACTTAAGTC 5 125 1 AAAAACATCA 0.98557 -176 TACCTCAAATAAAAAAACGTCACTTGTCCTTT 5 225 0 AAAAACGTCA 0.977157 -76 ** * ******* Masking position 2 Map Score: 12.9346 Number of sites scoring better than the average of aligned sites = 496 Number in coding regions = 431 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 2 TACCTTTTTTCACTTCCTGTACATTTACCC 1 29 0 CACTTCCTGT 0.950098 -272 AACACAACAACACAACATCACAACCGTAAG 1 96 1 CACAACATCA 0.879777 -205 ATAGTGGCGGCACTTCCTGAGCCGGAACGA 1 164 0 CACTTCCTGA 0.955838 -137 GAAGTGCCGCCACTATAGGTATTTGCTGGT 1 178 1 CACTATAGGT 0.479515 -123 ACAATTAGATCACACTATGTAACCTATTAG 1 250 0 CACACTATGT 0.85996 -51 CACCCTGATCCTCTCCCGCAGAAGAGGAAT 2 18 0 CTCTCCCGCA 0.881216 -101 ATAAATTTTCCTCACCCTGATCCTCTCCCG 2 30 0 CTCACCCTGA 0.953948 -89 AAATTTATGCCTCACCCTCACTCTCTTCGT 2 52 1 CTCACCCTCA 0.933121 -67 ACTTTCTCATCACATCATCTTTGTATAGAA 4 55 1 CACATCATCT 0.911715 -246 AATTGATCATCACATTAGCTTATGGTTAAA 4 131 0 CACATTAGCT 0.530884 -170 GCATCGGAGCCACTCCCGGTCCCCAACGCA 4 216 0 CACTCCCGGT 0.962156 -85 TGGTGATAATTTCACCATGAAAAAGTTGTC 4 255 1 TTCACCATGA 0.611658 -46 AAAAAAACGCCACTCAATGAGAGCAGCGTT 5 24 1 CACTCAATGA 0.708485 -277 GTTACTCATTTACTTCCTGTATATTATTAA 5 67 0 TACTTCCTGT 0.671447 -234 TATATGCAAACACAACATCATACTTAAGTC 5 127 1 CACAACATCA 0.879777 -174 ********** Masking position 3 Map Score: 10.7795 Number of sites scoring better than the average of aligned sites = 2834 Number in coding regions = 2553 Number in noncoding regions = 281 Number of orfs with sites within 600 bp upstream = 302 Fraction of orfs with sites within 600 bp upstream = 0.0485063 Motif number 3 GCTCAGATTAAAAAAACTAATAGGTTACAT 1 234 1 AAAAAACTAA 0.941633 -67 ATCAATCTCCAAAAAAGTAAA 3 2 0 AAAAAAGTAA 0.9633 -22 TAAGAGCTAAAAAAATGTCAAAAA 4 5 0 AAAAATGTCA 0.932382 -296 GCGACAGAATAAAAAACCAAAAAATACACC 4 88 0 AAAAAACCAA 0.940523 -213 CTTATGGTTAAAAAATGCAAAAATCGCGAC 4 113 0 AAAAATGCAA 0.932382 -188 TCGGGATGAAAAAAACGCCACTCAATGAGA 5 16 1 AAAAACGCCA 0.954351 -285 CCTCAAATAAAAAAACGTCACTTGTCCTTT 5 225 0 AAAAACGTCA 0.955215 -76 TGAGGTATTAGAAAAACTAATTTGAAATAA 5 250 1 GAAAAACTAA 0.810787 -51 ********** Masking position 5 Map Score: 6.74221 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 257 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 4 GCATTCCGATAAAACTTTTCGTTCCGGCTC 1 146 1 AAAACTTTTC 0.930087 -155 CTGAGCCATTATAAATTGTCCGTTGAGCTT 1 210 0 ATAAATTGTC 0.949401 -91 AGGGTGAGGCATAAATTTTCCTCACCCTGA 2 40 0 ATAAATTTTC 0.879333 -79 TTAAGAGCTAAAAAAATGTCAAAAA 4 6 0 AAAAAATGTC 0.901828 -295 TTTTAGCTCTTAATATTGTCTTATTCAAAT 4 23 1 TAATATTGTC 0.872961 -278 TTCACCATGAAAAAGTTGTCAGCCCCGCTT 4 265 1 AAAAGTTGTC 0.949339 -36 AATTTGAAATAAATCTTGTCCATTATAGAC 5 268 1 AAATCTTGTC 0.926653 -33 TTATAAAATTTTCGTCTATAATG 5 288 0 TAAAATTTTC 0.860909 -13 ********** Masking position 3 Map Score: 5.52989 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 176 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 5 ATTTACCCTGTCTGTCCATAGTGATT 1 7 0 TCTGTCCATA 0.883235 -294 TTTTTCACTTCCTGTACATTTACCCTGTCT 1 24 0 CCTGTACATT 0.963586 -277 TTCTCTTTTGCCTGAACTTACCACCGAAAC 4 182 0 CCTGAACTTA 0.826232 -119 CTTGTCCTCATTGAATAAGC 4 291 0 CTTGTCCTCA 0.919135 -10 TCATTTACTTCCTGTATATTATTAAACCGA 5 62 0 CCTGTATATT 0.747657 -239 CTTTCCTACCCTTTTCCTTACAATACAACC 5 199 0 CTTTTCCTTA 0.826954 -102 AAAAACGTCACTTGTCCTTTCCTACCCTTT 5 215 0 CTTGTCCTTT 0.977166 -86 TGAAATAAATCTTGTCCATTATAGACGAAA 5 272 1 CTTGTCCATT 0.977162 -29 ********** Masking position 3 Map Score: 2.94961 Number of sites scoring better than the average of aligned sites = 526 Number in coding regions = 463 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 6 GAACTTTTGGCTTACGGTTGTGATGTTGTG 1 106 0 CTTACGGTTG 0.927578 -195 ATAGTGTGATCTAATTGTTAAATTCATTTA 1 262 1 CTAATTGTTA 0.951348 -39 ATCACATTAGCTTATGGTTAAAAAATGCAA 4 123 0 CTTATGGTTA 0.984407 -178 TCAATTTTACCTTATGGTTAACAGTCTGTT 4 155 1 CTTATGGTTA 0.984407 -146 AAATGAGTAACAAATTGTTACTCAAGTTCG 5 86 1 CAAATTGTTA 0.855976 -215 ********** Masking position 4 Map Score: 2.0894 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 54 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 CCTATTAGTTTTTTTAATCTGAGCCATTAT 1 228 0 TTTTTAATCT 0.895662 -73 GTGCAGTGAATTGTGAACCTCTCTCCTTAC 2 80 0 TTGTGAACCT 0.851243 -39 ATTTTTTGGTTTTTTATTCTGTCGCGATTT 4 93 1 TTTTTATTCT 0.679303 -208 ATTTTTGCATTTTTTAACCATAAGCTAATG 4 119 1 TTTTTAACCA 0.947153 -182 CCGAAACAGACTGTTAACCATAAGGTAAAA 4 159 0 CTGTTAACCA 0.939945 -142 ATGAGAGCAGCGTTTAACCAAATCGGTTTA 5 40 1 CGTTTAACCA 0.748993 -261 GAGTAACAATTTGTTACTCATTTACTTCCT 5 79 0 TTGTTACTCA 0.935974 -222 GAGTAACAAATTGTTACTCAAGTTCGGTTT 5 90 1 TTGTTACTCA 0.935974 -211 ********** Masking position 6 Map Score: 1.39126 Number of sites scoring better than the average of aligned sites = 388 Number in coding regions = 312 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 8 ********** No masking Map Score: -1.26944e-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 9 ********** No masking Map Score: -1.26944e-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 10 ********** No masking Map Score: -1.26944e-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