AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i133_Transmembrane_Transport_7_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 yjcH 88 orf, hypothetical protein #2 BIME214 34 BIME #3 acs 300 acetyl-CoA synthetase Motif number 1 GGCAAGGGTTACCCGAGCGTTAACCTTCTCCCAT 1 15 1 ACCCATTAAC 0.989454 -74 GCCCCTATGTGTAACAAATAACCAC 3 2 1 CCCCAGTAAC 0.990639 -299 GTAACAAATAACCACACTGTGAATGTTGTCTTTA 3 21 1 ACCAATGAAT 0.885709 -280 CTGCATGTTCCTCAAAGAATTAATCAACTTTTGT 3 129 1 CTCAATTAAT 0.923173 -172 TGATCTGTCGCCCAAATACTAAACAAAACTGCCA 3 216 1 CCCAATAAAC 0.985968 -85 ACTGCCAATACCCCTACATTTAACGCTTATGCCA 3 243 1 CCCCATTAAC 0.997101 -58 ACGCTTATGCCACATATTATTAACATCCTACAAG 3 265 1 CACAATTAAC 0.977808 -36 **** * ***** Masking position 6 Map Score: 5.32221 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 152 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 2 ACGCTCGGGTAACCCTTGCCGAAT 1 4 0 AACCTTGCCG 0.992742 -85 CCCGAGCGTTAACCTTCTCCCATAAGGGAGC 1 26 1 AACCTCTCCC 0.982016 -63 CCCACAATTGCCCGATGCGAGTC 2 3 1 CACATTGCCC 0.972341 -32 AAACCGTTACCGACTCGCATCG 2 23 0 AACCTTACCG 0.988634 -12 GATTAAAGACAACATTCACAGTGTGGTTATT 3 27 0 AACATCACAG 0.896531 -274 GCTGACCTTCAAAAATTACCCTGCCGTTTAT 3 164 1 AAAATTACCC 0.904072 -137 CTTTTGCGTGATCTGTCGCCCAAATACTAAA 3 208 1 ATCTTCGCCC 0.918937 -93 **** ****** Masking position 6 Map Score: 3.77229 Number of sites scoring better than the average of aligned sites = 1304 Number in coding regions = 1179 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 3 GTGGTATTTTACATGCACTTACAATTGATT 3 54 0 ACATGCACTT 0.981688 -247 ATGCAGTTATGCATGCTGTTGAAAAAGAGG 3 105 0 GCATGCTGTT 0.987944 -196 TCTTTGAGGAACATGCAGTTATGCATGCTG 3 117 0 ACATGCAGTT 0.97537 -184 TCAAAAATTACCCTGCCGTTTATTTGCACA 3 172 1 CCCTGCCGTT 0.984587 -129 ********** Masking position 4 Map Score: 2.21941 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 122 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 AACAATCCCTACATTACCTCTGGAGAATCT 1 66 1 ACATTACCTC 0.958217 -23 TATGTGTAACAAATAACCACACTGTGAATG 3 16 1 AAATAACCAC 0.951432 -285 AAGTGCATGTAAAATACCACTTTAGAGTTA 3 64 1 AAAATACCAC 0.951431 -237 TCAACAGCATGCATAACTGCATGTTCCTCA 3 113 1 GCATAACTGC 0.926248 -188 GTTTATTTGCACAATTCTACTTTTGCGTGA 3 189 1 ACAATTCTAC 0.900898 -112 CAAATACTAAACAAAACTGCCAATACCCCT 3 228 1 ACAAAACTGC 0.975182 -73 ********** Masking position 3 Map Score: 1.84886 Number of sites scoring better than the average of aligned sites = 721 Number in coding regions = 666 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 5 CTGACTAACTCTAAAGTGGTATTTTACATG 3 69 0 CTAAAGTGGT 0.96562 -232 CATGCTGTTGAAAAAGAGGAAGATACTGAC 3 94 0 AAAAAGAGGA 0.946985 -207 AGGTCAGCAACAAAAGTTGATTAATTCTTT 3 142 0 CAAAAGTTGA 0.985012 -159 ACAGATCACGCAAAAGTAGAATTGTGCAAA 3 194 0 CAAAAGTAGA 0.985017 -107 ********** Masking position 5 Map Score: 0.970882 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 103 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 6 ********** No masking Map Score: -7.64954e-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: -7.64954e-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: -7.64954e-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