AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i025_1_2_1_2_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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 fdhD 193 affects formate dehydrogenase-N #2 fdhF 197 selenopolypeptide subunit of formate dehydrogenase H #3 yjcQ 140 putative enzyme #4 yjcR 300 putative membrane protein Motif number 1 AACTCCCACTCCCTGCACACGCAGCAAGCGAATGTAAAT 1 44 0 CCGCACGGCC 0.998424 -150 TACCGCGTGACAGCCATCACGCGGCAGACATT 2 4 0 CGCCACGGCC 0.997735 -194 CACGTCAAAACTGACGACAGCCTGTTTTTCGTCAGAGTT 2 54 1 CGCCAGCGTT 0.872983 -144 TGAGCGCGCTCAACTCCCTGCCATTACCGGTGGTC 3 7 1 CCCCTCCGCT 0.973345 -134 CTGCCATTACCGGTGGTCAGGCTGCTGGCGTTCTTTCAT 3 28 1 CGGCAGGGCC 0.995376 -113 GTTAAGCGAGCGGCGACCAGGTCGCGTGCCGCAGACCGT 3 72 1 CGGCAGGGCC 0.995376 -69 GACCGTGCAACTCTGGGTAGGCTGCCTGCTGGTGATTCT 3 105 1 CCGTAGGGCC 0.969947 -36 ACAGTTCTCTCTCGCATGGCGATGCAACTCAAAAAAACA 4 23 1 CCCGGCGGCT 0.95677 -278 GGATAATAAGCGCCGATCACCGGGATTGCCGGAGATAAT 4 100 0 CCGCACCGAC 0.969947 -201 CTTATTTTGACGCTCATCACGAGGCGAGTTATTCAGCGG 4 167 1 CCCCACGGCT 0.997491 -134 GCCCTTTTTGCTCTCTACGCCATGCTGTTCTGGCTGGCA 4 245 1 CCCCGCCGCT 0.990059 -56 * * * **** ** * Masking position 1 Map Score: 16.6646 Number of sites scoring better than the average of aligned sites = 1370 Number in coding regions = 1313 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 2 AAGCGAATGTAAATGGGACGTGACAATGTCGA 1 26 0 AAAGGACGTG 0.703428 -168 ATTTACATTCGCTTGCTGCGTGTGCAGGGAGT 1 44 1 GCTGCGCGTG 0.926748 -150 AATGTCTGCCGCGTGATGGCTGTCA 2 4 1 GTCGCGCGTG 0.984134 -194 TGACGAAACGAAATACCGCGTGACAGCCATCA 2 24 0 AAAACGCGTG 0.961351 -174 CGTCAAAACTGACGACAGCCTGTTTTTCGTCA 2 56 1 GACACGCCTG 0.992272 -142 AGTTTTGAATAAATAGTGCCCGTAATATCAGG 2 89 1 AAAAGGCCCG 0.865987 -109 GCATACTGTAGTCGAGAGCGCGTATGCGTGAT 2 154 1 GTCAGGCGCG 0.883578 -44 TGATTTGATTAACTGGAGCGAGACCG 2 182 1 AACGGGCGAG 0.909347 -16 ATGAAAGAACGCCAGCAGCCTGACCACCGGTA 3 35 0 GCCGCGCCTG 0.992311 -106 ACGGTCTGCGGCACGCGACCTGGTCGCCGCTC 3 79 0 GCAGCACCTG 0.915603 -62 GCAACTCTGGGTAGGCTGCCTGCTGGTGATTC 3 111 1 GTAGCGCCTG 0.983445 -30 TGCAACTCAAAAAAACAGCCTGGATAATTCCC 4 45 1 AAAACGCCTG 0.97051 -256 AAATAATTCCGACAAATGCCAGATTGATATTT 4 208 0 GACAAGCCAG 0.887529 -93 AAATAGATTAGAAAAATGCCAGCCAGAACAGC 4 268 0 GAAAAGCCAG 0.851005 -33 *** ** ***** Masking position 9 Map Score: 15.9151 Number of sites scoring better than the average of aligned sites = 5484 Number in coding regions = 5135 Number in noncoding regions = 349 Number of orfs with sites within 600 bp upstream = 240 Fraction of orfs with sites within 600 bp upstream = 0.038548 Motif number 3 GGATTGCTCCTTGTTTCGACATTGTCACGTCCCA 1 11 1 TGTTCGCATG 0.973204 -183 GAGTTATTTTTCTTTGCGGAAGGGGCCGCAAAGG 1 78 1 TTTTCGAAGG 0.908571 -116 ACGCGGTATTTCGTTTCGTCACGTCAAAACTGAC 2 35 1 TGTTCGCAGT 0.954448 -163 ACGACAGCCTGTTTTTCGTCAGAGTTTTGAATAA 2 67 1 GTTTCGCAAG 0.850784 -131 AGAGTTGCACGGTCTGCGGCACGCGACCTGGTCG 3 85 0 GTCTCGCAGC 0.988446 -56 TTTTTTTGAGTTGCATCGCCATGCGAGAGAGAAC 4 26 0 TGCACGCAGC 0.968558 -275 CCCGTCTTCATGGTTTCGGGATGCTCATTATCTC 4 74 1 TGTTCGGAGC 0.952251 -227 GGATGCTCATTATCTCCGGCAATCCCGGTGATCG 4 92 1 TTCTCGCATC 0.985062 -209 CCAGCTGGTTTTTCTGCGCCATTGCCAGCCTTAT 4 138 1 TTCTCGCATG 0.98164 -163 CCCTTTTTGCTCTCTACGCCATGCTGTTCTGGCT 4 246 1 TTCTCGCAGC 0.995066 -55 * *** ** ** ** Masking position 11 Map Score: 10.7663 Number of sites scoring better than the average of aligned sites = 962 Number in coding regions = 910 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 4 TGTGCAGGGAGTGGGAGTTATTTTTCTTTGCGGAAG 1 64 1 GTGGGTTTTC 0.98531 -130 ATACCATAATGTTGGTGTGTGTGTTCTTATCTGGTT 1 160 1 GTGGGTGTGC 0.977078 -34 GAGCGCGTATGCGTGATTTGATTAACTGGAGCGAGA 2 169 1 GCTGTTTTTC 0.89691 -29 TGGTCAGGCTGCTGGCGTTCTTTCATGAAGAGTTAA 3 41 1 GCGGGTTTTT 0.969598 -100 TAGGCTGCCTGCTGGTGATTCTGATCTCG 3 122 1 GCGGGATTGC 0.995493 -19 CACCGGGATTGCCGGAGATAATGAGCATCCCGAAAC 4 86 0 GCGGGATTGC 0.9954 -215 TATTATCCCAGCTGGTTTTTCTGCGCCATTGCCAGC 4 131 1 GCGGTTTTGC 0.992833 -170 ** ** *** ** * Masking position 12 Map Score: 5.62758 Number of sites scoring better than the average of aligned sites = 776 Number in coding regions = 742 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 AAGAACACACACACCAACATTATGGTATTC 1 158 0 ACACCAACAT 0.69259 -36 GTCAAAACTGACGACAGCCTGTTTTTCGTC 2 57 1 ACGACAGCCT 0.874729 -141 TCATGAAAGAACGCCAGCAGCCTGACCACC 3 39 0 ACGCCAGCAG 0.992254 -102 GAGATCAGAATCACCAGCAGGCAGCCTACC 3 120 0 TCACCAGCAG 0.920599 -21 TTTAATATGCCAACAGTTCTCTCTCG 4 7 1 ATGCCAACAG 0.953989 -294 GGCGCTTATTATCCCAGCTGGTTTTTCTGC 4 125 1 ATCCCAGCTG 0.938483 -176 TTCTGCGCCATTGCCAGCCTTATTTTGACG 4 149 1 TTGCCAGCCT 0.970385 -152 AGATTGATATTTGCCCGCTGAATAACTCGC 4 190 0 TTGCCCGCTG 0.896932 -111 ATTCCGACAAATGCCAGATTGATATTTGCC 4 205 0 ATGCCAGATT 0.803841 -96 GATTAGAAAAATGCCAGCCAGAACAGCATG 4 265 0 ATGCCAGCCA 0.9565 -36 ********** Masking position 5 Map Score: 8.10439 Number of sites scoring better than the average of aligned sites = 5262 Number in coding regions = 5044 Number in noncoding regions = 218 Number of orfs with sites within 600 bp upstream = 182 Fraction of orfs with sites within 600 bp upstream = 0.0292323 Motif number 6 ********** No masking Map Score: 6.20604e-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 7 ********** No masking Map Score: 6.20604e-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 8 ********** No masking Map Score: 6.20604e-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