AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i348_weak9_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 csrA 234 carbon storage regulator; controls glycogen synthesis, gluconeogenesis, cell size and surface properties #2 alaS 128 alanyl-tRNA synthetase #3 oraA 68 regulator, OraA protein #4 recA 79 DNA strand exchange and renaturation, DNA-dependent ATPase, DNA- and ATP-dependent coprotease #5 ygaD 144 orf, hypothetical protein #6 mltB 255 membrane-bound lytic murein transglycosylase B Motif number 1 GAAGCGAGTCCACGGCATTGCCTGACGCTT 1 14 0 CACGGCATTG 0.987608 -221 GGACTCGCTTCACGGCATTCGCATTAACGC 1 33 1 CACGGCATTC 0.987673 -202 TCTAAGCAGTCATGGCATTACATTCTGTTA 1 117 0 CATGGCATTA 0.960721 -118 CTCTCTGTATCCCGGCATTATCCATCATAT 1 182 0 CCCGGCATTA 0.997124 -53 ACGCATACGGTATTTTACCTTCCCA 2 6 1 TACGGTATTT 0.828601 -123 ATATTGACTATCCGGTATTACCCGGCATGA 4 49 1 TCCGGTATTA 0.968829 -31 TCCGGTATTACCCGGCATGACAGGAGTAAA 4 59 1 CCCGGCATGA 0.990725 -21 TGCTATCTTGTCCGGCATAAATTTTTGACT 5 112 1 TCCGGCATAA 0.965766 -33 ********** Masking position 7 Map Score: 11.7271 Number of sites scoring better than the average of aligned sites = 625 Number in coding regions = 557 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 2 GTTTGTCATTGCTTACTTTTTGGCGTTATATG 1 155 1 GCACTTTTTG 0.940606 -80 GGCCGCAGATGCGACCCTTGTGTATCAAACAA 3 16 0 GCCCCTTGTG 0.994907 -53 GGTCGCATCTGCGGCCCTTTTGCTTTTTTAAG 3 32 1 GCCCCTTTTG 0.998132 -37 GGAAGCTCACGCCCCCCTCTTGTAAATAG 5 8 0 GCCCCTCTTG 0.997747 -137 GGGGGCGTGAGCTTCCCTCTGGCTAATCAGCT 5 24 1 GCCCCTCTGG 0.993863 -121 CATTCCCCTCGCTATCCTTTTATTCAAACTTT 6 127 0 GCTCCTTTTA 0.940606 -129 ** ******** Masking position 8 Map Score: 6.71689 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 71 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 3 AAACTTAGGTTTAACAGAATGTAATGCCAT 1 106 1 TTAACAGAAT 0.89252 -129 TCTTTGCTCCTTGAAAGATTAAAAGAGTCG 1 215 0 TTGAAAGATT 0.984578 -20 TCTAATCAGATTGAAAGATTTAAAAGTGTT 6 59 1 TTGAAAGATT 0.984578 -197 AACTTTCAAATTAAAATATTTATCTTTCAT 6 103 0 TTAAAATATT 0.862657 -153 ATATTTTAATTTGAAAGTTTGAATAAAAGG 6 114 1 TTGAAAGTTT 0.940299 -142 AGGGGTCCATTTAACAGATTCAACCAGGGG 6 235 0 TTAACAGATT 0.971148 -21 ********** Masking position 6 Map Score: 5.53292 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 25 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 GCATTCGCATTAACGCTATCGACAACGATA 1 47 1 TAACGCTATC 0.940563 -188 ATCCATCATATAACGCCAAAAAGTAAGCAA 1 163 0 TAACGCCAAA 0.882715 -72 GCTAACGAAATATCGCCACCAGCTCCAGCG 2 92 0 TATCGCCACC 0.970926 -37 TATCCTGAAATCAAGCTAACGAAATATCGC 2 106 0 TCAAGCTAAC 0.800699 -23 AGAGGGAAGCTCACGCCCCCCTCTTGTAAA 5 14 0 TCACGCCCCC 0.987945 -131 CGTAAAATTGCAACGCCAACACCATCTTCC 5 73 1 CAACGCCAAC 0.970465 -72 AACTCATTCCCCTCGCTATCCTTTTATTCA 6 133 0 CCTCGCTATC 0.838774 -123 TGGTAAAGCATCACGCCCCGCACAAGGAAG 6 199 0 TCACGCCCCG 0.940317 -57 ********** Masking position 5 Map Score: 3.76923 Number of sites scoring better than the average of aligned sites = 2316 Number in coding regions = 2210 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 5 TTTTACCTTCCCAGTCAAGAAAACTTATCT 2 23 1 CCAGTCAAGA 0.97781 -106 TACCAGCCCGGCGGTTAAGACACGCTGGAG 2 70 1 GCGGTTAAGA 0.891684 -59 CCCTTGTGTATCAAACAAGACGA 3 4 0 TCAAACAAGA 0.895308 -65 CGAGGAGGATTCAGAAAAAAGCTGATTAGC 5 45 0 TCAGAAAAAA 0.701332 -100 AAAATTTATGCCGGACAAGATAGCACTTTC 5 107 0 CCGGACAAGA 0.976115 -38 ACAACCTCTGTCAGTCAAAAATTTATGCCG 5 124 0 TCAGTCAAAA 0.951841 -21 CTTTCATTTTGCGATCAAAATAACACTTTT 6 80 0 GCGATCAAAA 0.875446 -176 ********** Masking position 7 Map Score: 1.38415 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 293 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 6 ********** No masking Map Score: -1.69577e-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 7 ********** No masking Map Score: -1.69577e-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 8 ********** No masking Map Score: -1.69577e-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