AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -igcvA_ecoli_hinf_100.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 0.985117 -207 ACCGTAAGCCAAAAGTTCACCAGAACACGCAT 1 118 1 AAATTCACCA 0.897736 -183 TTGTTAAATTCATTTAACATCAAAGTTTAATA 1 276 1 CATAACATCA 0.832354 -25 ATTAAGAGCTAAAAAAATGTCAAAAA 4 5 0 AAAAATGTCA 0.783638 -296 TAAAAAACCAAAAAATACACCAGTTTCTATAC 4 77 0 AAATACACCA 0.956596 -224 ATCGCGACAGAATAAAAAACCAAAAAATACAC 4 89 0 AAAAAAACCA 0.88585 -212 CATAAGGTAAAATTGATCATCACATTAGCTTA 4 139 0 AATATCATCA 0.913053 -162 TTTCATGGTGAAATTATCACCACGAAACCCAG 4 245 0 AATATCACCA 0.933742 -56 AATCGGGATGAAAAAAACGCCACTCAATGAGA 5 14 1 AAAAACGCCA 0.982343 -287 ACTATATGCAAACACAACATCATACTTAAGTC 5 125 1 AAAAACATCA 0.985117 -176 TACCTCAAATAAAAAAACGTCACTTGTCCTTT 5 225 0 AAAAACGTCA 0.976446 -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 0.94605 -272 AACACAACAACACAACATCACAACCGTAAG 1 96 1 CACAACATCA 0.870801 -205 ATAGTGGCGGCACTTCCTGAGCCGGAACGA 1 164 0 CACTTCCTGA 0.952232 -137 GAAGTGCCGCCACTATAGGTATTTGCTGGT 1 178 1 CACTATAGGT 0.45903 -123 ACAATTAGATCACACTATGTAACCTATTAG 1 250 0 CACACTATGT 0.849757 -51 CACCCTGATCCTCTCCCGCAGAAGAGGAAT 2 18 0 CTCTCCCGCA 0.872331 -101 ATAAATTTTCCTCACCCTGATCCTCTCCCG 2 30 0 CTCACCCTGA 0.950196 -89 AAATTTATGCCTCACCCTCACTCTCTTCGT 2 52 1 CTCACCCTCA 0.927801 -67 ACTTTCTCATCACATCATCTTTGTATAGAA 4 55 1 CACATCATCT 0.904865 -246 AATTGATCATCACATTAGCTTATGGTTAAA 4 131 0 CACATTAGCT 0.510356 -170 GCATCGGAGCCACTCCCGGTCCCCAACGCA 4 216 0 CACTCCCGGT 0.959044 -85 TGGTGATAATTTCACCATGAAAAAGTTGTC 4 255 1 TTCACCATGA 0.591948 -46 AAAAAAACGCCACTCAATGAGAGCAGCGTT 5 24 1 CACTCAATGA 0.691209 -277 GTTACTCATTTACTTCCTGTATATTATTAA 5 67 0 TACTTCCTGT 0.65305 -234 TATATGCAAACACAACATCATACTTAAGTC 5 127 1 CACAACATCA 0.870801 -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 ATGTAACCTATTAGTTTTTTTAATCTGAGC 1 234 0 TTAGTTTTTT 0.937164 -67 TTTACTTTTTTGGAGATTGAT 3 2 1 TTACTTTTTT 0.96042 -22 TTTTTGACATTTTTTTAGCTCTTA 4 5 1 TGACATTTTT 0.927259 -296 GGTGTATTTTTTGGTTTTTTATTCTGTCGC 4 88 1 TTGGTTTTTT 0.935975 -213 GTCGCGATTTTTGCATTTTTTAACCATAAG 4 113 1 TTGCATTTTT 0.927259 -188 TCTCATTGAGTGGCGTTTTTTTCATCCCGA 5 16 0 TGGCGTTTTT 0.950805 -285 AAAGGACAAGTGACGTTTTTTTATTTGAGG 5 225 1 TGACGTTTTT 0.951733 -76 TTATTTCAAATTAGTTTTTCTAATACCTCA 5 250 0 TTAGTTTTTC 0.798443 -51 ********** Masking position 6 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 GAGCCGGAACGAAAAGTTTTATCGGAATGC 1 146 0 GAAAAGTTTT 0.924077 -155 AAGCTCAACGGACAATTTATAATGGCTCAG 1 210 1 GACAATTTAT 0.944843 -91 TCAGGGTGAGGAAAATTTATGCCTCACCCT 2 40 1 GAAAATTTAT 0.869445 -79 TTTTTGACATTTTTTTAGCTCTTAA 4 6 1 GACATTTTTT 0.893462 -295 ATTTGAATAAGACAATATTAAGAGCTAAAA 4 23 0 GACAATATTA 0.862506 -278 AAGCGGGGCTGACAACTTTTTCATGGTGAA 4 265 0 GACAACTTTT 0.944777 -36 GTCTATAATGGACAAGATTTATTTCAAATT 5 268 0 GACAAGATTT 0.92021 -33 CATTATAGACGAAAATTTTATAA 5 288 1 GAAAATTTTA 0.852751 -13 ********** Masking position 4 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 GAACTTTTGGCTTACGGTTGTGATGTTGTG 1 106 0 CTTACGGTTG 0.930971 -195 ATAGTGTGATCTAATTGTTAAATTCATTTA 1 262 1 CTAATTGTTA 0.953684 -39 ATCACATTAGCTTATGGTTAAAAAATGCAA 4 123 0 CTTATGGTTA 0.98518 -178 TCAATTTTACCTTATGGTTAACAGTCTGTT 4 155 1 CTTATGGTTA 0.98518 -146 AAATGAGTAACAAATTGTTACTCAAGTTCG 5 86 1 CAAATTGTTA 0.862228 -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 6 CTTTTTTCACTTCCTGTACATTTACCCTGT 1 26 0 TTCCTGTACA 0.968605 -275 GTGGCGGCACTTCCTGAGCCGGAACGAAAA 1 161 0 TTCCTGAGCC 0.9702 -140 GAGCGATGGTTCCTGAAACGTGCAGTGAA 2 100 0 TTCCTGAAAC 0.944638 -19 CGTTCTCTTTTGCCTGAACTTACCACCGAA 4 184 0 TGCCTGAACT 0.954646 -117 ACTCATTTACTTCCTGTATATTATTAAACC 5 64 0 TTCCTGTATA 0.855329 -237 CAAGTTCGGTTTCCCGAACTATATGCAAAC 5 108 1 TTCCCGAACT 0.954644 -193 ********** Masking position 1 Map Score: 1.89259 Number of sites scoring better than the average of aligned sites = 325 Number in coding regions = 292 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 CCTATTAGTTTTTTTAATCTGAGCCATTAT 1 228 0 TTTTTAATCT 0.88723 -73 GTGCAGTGAATTGTGAACCTCTCTCCTTAC 2 80 0 TTGTGAACCT 0.839911 -39 ATTTTTTGGTTTTTTATTCTGTCGCGATTT 4 93 1 TTTTTATTCT 0.660014 -208 ATTTTTGCATTTTTTAACCATAAGCTAATG 4 119 1 TTTTTAACCA 0.944132 -182 CCGAAACAGACTGTTAACCATAAGGTAAAA 4 159 0 CTGTTAACCA 0.936751 -142 ATGAGAGCAGCGTTTAACCAAATCGGTTTA 5 40 1 CGTTTAACCA 0.734784 -261 GAGTAACAATTTGTTACTCATTTACTTCCT 5 79 0 TTGTTACTCA 0.930601 -222 GAGTAACAAATTGTTACTCAAGTTCGGTTT 5 90 1 TTGTTACTCA 0.930601 -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