AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i254_soj_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 gidB 63 glucose-inhibited division; chromosome replication? #2 gidA 300 glucose-inhibited division; chromosome replication? #3 HI0486 139 glucose-inhibited division protein (gidB) #4 HI0582 300 glucose inhibited division protein (gidA) Motif number 1 ATCATTAACTGTGAATGATCGGTGATCCTG 2 68 0 GTGAATGATC 0.818453 -233 ATCATTCACAGTTAATGATCCTTTCCAGGT 2 79 1 GTTAATGATC 0.939418 -222 AGGATCCGGCTTTTAAGATCAACAACCTGG 2 103 0 TTTTAAGATC 0.963023 -198 TGTGATCTCTTATTAGGATCGCACTGCCCT 2 143 0 TATTAGGATC 0.942232 -158 AGATCTGTTCTATTGTGATCTCTTATTAGG 2 156 0 TATTGTGATC 0.872668 -145 GATCTATTTATTTAGAGATCTGTTCTATTG 2 171 0 TTTAGAGATC 0.936503 -130 GATCTCTAAATAAATAGATCTTCTTTTTAA 2 181 1 TAAATAGATC 0.745976 -120 GATCATTTTCTTTAAAAATCTTGTGTGTAA 4 38 0 TTTAAAAATC 0.692244 -263 GATTTTTAAAGAAAATGATCGCATTTTCAC 4 48 1 GAAAATGATC 0.71933 -253 TTTCACAAGATTTTTGGATCCTATAACACC 4 72 1 TTTTTGGATC 0.885744 -229 CACCTGTTTCCATAAGGATCGAATAAGGTT 4 98 1 CATAAGGATC 0.807836 -203 TTATTGTTATTATTAAGATCTTTTTTGGTT 4 134 0 TATTAAGATC 0.958077 -167 TCTTTTTATATATAAAGATCTTATTATTGT 4 157 0 TATAAAGATC 0.973957 -144 TATTGATCCTTTGAAAGATCAGGTTTGTAT 4 201 0 TTGAAAGATC 0.925108 -100 AAAGAATGGATCTATTGATCCTTTGAAAGA 4 213 0 TCTATTGATC 0.782036 -88 ATAACGCCAATTTTTTGATCAGAATAAATA 4 272 1 TTTTTTGATC 0.903828 -29 ********** Masking position 8 Map Score: 17.4425 Number of sites scoring better than the average of aligned sites = 544 Number in coding regions = 482 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 2 CAGTTTTTGAGTTGTGTATAACCCCTCATTC 2 17 1 GTTTGTATAA 0.924269 -284 ATAAATAGATCTTCTTTTTAATACCCAGGAT 2 190 1 CTTTTTTTAA 0.86134 -111 TTTCCTTAATGTTTTTAGTAATTTGATGAAT 3 68 0 GTTTTAGTAA 0.979575 -72 ATTTACCGCACTTTTAAGTAAAATAGCGTAA 3 98 1 CTTTAAGTAA 0.89961 -42 AAATAAAGTTGTTAATAACTTTCCATTT 4 8 1 GTTTTAATAA 0.941904 -293 CTTTAAAAATCTTGTGTGTAAAATGGAAAGT 4 28 0 CTTTGTGTAA 0.956897 -273 ATCTTTTTTGGTTGTGAGTAACCTTATTCGA 4 116 0 GTTTGAGTAA 0.983034 -185 TCTTATTATTGTTATTATTAAGATCTTTTTT 4 138 0 GTTTTATTAA 0.941896 -163 *** ******* Masking position 10 Map Score: 7.29703 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 97 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 3 ATTAAAAATGCCTGGTAAGCACCCGCTTACC 1 14 1 CCTGGAAGCA 0.985799 -50 TGATGCGTTGCCTGGTAAGCGGGTGCTTACC 1 27 0 CCTGGAAGCG 0.988932 -37 CGCATCAAGAACAGGTAATCACC 1 51 1 ACAGGAATCA 0.731882 -13 GATCGGTGATCCTGGACCGTATAAGCTGGGA 2 51 0 CCTGGCCGTA 0.981962 -250 AGATCAACAACCTGGAAAGGATCATTAACTG 2 87 0 CCTGGAAGGA 0.962816 -214 CTTGTTATCCACAGGGCAGTGCGATCCTAAT 2 131 1 ACAGGCAGTG 0.945463 -170 GACCTGGGATCCTGGGTATTAAAAAGAAGAT 2 198 0 CCTGGTATTA 0.875852 -103 TGGATTGAAGCCCGGGCCGTGGATTCTACTC 2 249 0 CCCGGCCGTG 0.838414 -52 ATGGTGTAAAACTGGACATTGATTCGGTAAA 3 35 1 ACTGGCATTG 0.939516 -105 ***** ***** Masking position 2 Map Score: 6.83901 Number of sites scoring better than the average of aligned sites = 1418 Number in coding regions = 1315 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 4 TATTGTGATCTCTTATTAGGATCGCACTGC 2 146 0 TCTTATTAGG 0.904257 -155 AAAAAGAAGATCTATTTATTTAGAGATCTG 2 179 0 TCTATTTATT 0.937011 -122 AATAAATAGATCTTCTTTTTAATACCCAGG 2 189 1 TCTTCTTTTT 0.798064 -112 GGAGGTGCATTCAATTTATGGTGTAAAACT 3 18 1 TCAATTTATG 0.729393 -122 ATTTCCTTAATGTTTTTAGTAATTTGATGA 3 70 0 TGTTTTTAGT 0.751836 -70 ATTATTAAGATCTTTTTTGGTTGTGAGTAA 4 126 0 TCTTTTTTGG 0.931688 -175 TATATAAAGATCTTATTATTGTTATTATTA 4 149 0 TCTTATTATT 0.912144 -152 AAATAAGATCTCTTTTTATATATAAAGATC 4 167 0 TCTTTTTATA 0.890179 -134 ATAGATCCATTCTTTTTTTGTCAGGTGTTT 4 228 1 TCTTTTTTTG 0.950388 -73 ATCTATCTCTATTTATTCTGATCAAAA 4 284 0 TCTATTTATT 0.937011 -17 ********** Masking position 6 Map Score: 7.48962 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 244 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 5 CTGGTAAGCGGGTGCTTACCAGGCATTTTT 1 17 0 GGTGCTTACC 0.896494 -47 GGTGATTACCTGTTCTTGAT 1 54 0 GGTGATTACC 0.635324 -10 GGTGATTGCCTCGCATAACG 2 291 0 GGTGATTGCC 0.896494 -10 ********** Masking position 6 Map Score: 3.13167 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 28 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 ********** No masking Map Score: -1.24812e-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: -1.24812e-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: -1.24812e-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