AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iompR_ecoli_opreg_300.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 ompF 300 outer membrane protein 1a (Ia;b;F) #2 ompC 300 outer membrane protein 1b (Ib;c) #3 fadL 300 transport of long-chain fatty acids; sensitivity to phage T2 Motif number 1 ATAGATTAAAATTGCTGTAAATATCATCACG 1 29 1 ATGCTGTAAA 0.982716 -272 ACACCGTCATATTTCCATAGAGACGTGATGA 1 52 0 ATTCCATAGA 0.795781 -249 GTGTTCACAAAGTTCCTTAAATTTTACTTTT 1 79 1 ATTCCTTAAA 0.880881 -222 CTACCGTGAAAGTGCTACAAAGATAAAGATT 1 138 0 ATGCTACAAA 0.889309 -163 TCTCATCAATAGTTCCGTAAATTTTTATTGA 1 222 1 ATTCCGTAAA 0.982762 -79 GCCGTCAATAAGTTCTGTCAATAAAAATTTA 1 239 0 ATTCTGTCAA 0.962199 -62 GACACCTGCCACTGCCGTCAATAAGTTCTGT 1 252 0 ATGCCGTCAA 0.984787 -49 TTGACATTCAGTGCTGTCAAATACTTAAGA 2 10 1 ATGCTGTCAA 0.975957 -291 ATCAGTATGCAGTGGCATAAAAAAGCAAATA 2 254 1 ATGGCATAAA 0.79417 -47 TCCAGTTGTTAATTCTGCAAAATCGGATAAG 3 22 1 ATTCTGCAAA 0.938917 -279 * ********* Masking position 3 Map Score: 10.739 Number of sites scoring better than the average of aligned sites = 526 Number in coding regions = 460 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 2 ATGTAACCAAAAGTAAAATTTAAGGAACTTTGTGA 1 83 0 AATAAATAGG 0.965525 -218 AAGTTCTGTCAATAAAAATTTACGGAACTATTGAT 1 226 0 AAAAAATAGG 0.992645 -75 GGTGTCATAAAAAAAACCATGAGGGTAATAAATA 1 277 1 AAAACCTAGG 0.927425 -24 TCAAATACTTAAGAATAAGTTATTGATTTTAACCT 2 27 1 AAAAAATATG 0.973558 -274 AACATCAAGCAATAATAATTCAAGGTTAAAATCAA 2 49 0 AAAAAATAGG 0.992646 -252 AGTGGCATAAAAAAGCAAATAAAGGCATATAACAG 2 264 1 AAAGAATAGG 0.976487 -37 TAGTTTGTATAAAAATAAATCATTGAGGTT 3 281 1 AAAAAATATG 0.973559 -20 ** ** ** * * ** Masking position 12 Map Score: 6.43096 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 10 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 3 TAAATAGATTAAAATTGCTGTAAATATCATCACGTCTCT 1 26 1 AATGAAATTA 0.738771 -275 CAAAAAGAAAAAATATGTAACCAAAAGTAAAATTTAAGG 1 93 0 AATGCAAAGA 0.96642 -208 ACAAAGATAAAGATTTGGTTTCAAAAAGAAAAAATATGT 1 114 0 AATGCAAAAA 0.972138 -187 GTTTGAATGGAAAGATGCCTGCAGACACATAAAGACACC 1 179 1 AATGCAGAAA 0.937511 -122 GACGGCAGTGGCAGGTGTCATAAAAAAAACCATGAGGGT 1 264 1 GATGAAAAAA 0.954692 -37 ATTTATCGCTATAGATGTTTCAAAATGTAAATGCAAGGG 2 124 0 AATGAAAAGA 0.975858 -177 TAATCAGTATGCAGTGGCATAAAAAAGCAAATAAAGGCA 2 252 1 GAGGAAAAGA 0.783766 -49 GCAAAATCGGATAAGTGACCGAAATCACACTTAAAAATG 3 38 1 AATGAAATAA 0.931611 -263 AATCACACTTAAAAATGATCTAAAACAAAATTCACCCGA 3 60 1 AATGAAAAAA 0.980002 -241 TTCTTAGATCATATTTGAAAAAAGATAGAAACATACTTG 3 143 1 AATGAAGAAA 0.954692 -158 * * ** **** * * Masking position 13 Map Score: 6.53648 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 87 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 TTTACTTTTGGTTACATATTTTTTCTTTTT 1 101 1 GTTACATATT 0.939735 -200 TTTACATTTTGAAACATCTATAGCGATAAA 2 132 1 GAAACATCTA 0.899865 -169 AGCGATAAATGAAACATCTTAAAAGTTTTA 2 153 1 GAAACATCTT 0.97742 -148 AAAAGTTTTAGTATCATATTCGTGTTGGAT 2 173 1 GTATCATATT 0.881541 -128 AAAAAAGATAGAAACATACTTGCAACATTC 3 160 1 GAAACATACT 0.929111 -141 TAGGGTCTGAGGTACATCTTAGAAATCAGA 3 221 0 GGTACATCTT 0.916983 -80 GTTACAGCACGTAACATAGTTTGTATAAAA 3 265 1 GTAACATAGT 0.929111 -36 ********** Masking position 6 Map Score: 2.96645 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 125 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 5 ATGCAGAATAATCCAACACGAATATGATAC 2 183 0 ATCCAACACG 0.94438 -118 TTTGCAGAATTAACAACTGGAGCAGCACTT 3 13 0 TAACAACTGG 0.872614 -288 AAGAAACGCGATCCAGCTGGCAAAATTTGG 3 118 0 ATCCAGCTGG 0.987631 -183 ACTTGCAACATTCCAGCTGGTCCGACCTAT 3 177 1 TTCCAGCTGG 0.991336 -124 CGCGCTCCTGTTACAGCACGTAACATAGTT 3 256 1 TTACAGCACG 0.96052 -45 ********** Masking position 5 Map Score: 1.13815 Number of sites scoring better than the average of aligned sites = 670 Number in coding regions = 648 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 TATAAGGAAATCATATAAATAGATTAAAAT 1 11 1 TCATATAAAT 0.835169 -290 GTGGCAGGTGTCATAAAAAAAACCATGAGG 1 271 1 TCATAAAAAA 0.835495 -30 GCTGTCAAATACTTAAGAATAAGTTATTGA 2 23 1 ACTTAAGAAT 0.863624 -278 TCCGCAATAATCTTAAAAAGTTCCCTTGCA 2 102 1 TCTTAAAAAG 0.945324 -199 AAATGAAACATCTTAAAAGTTTTAGTATCA 2 159 1 TCTTAAAAGT 0.92095 -142 CCGAAATCACACTTAAAAATGATCTAAAAC 3 56 1 ACTTAAAAAT 0.952022 -245 CTGAGGTACATCTTAGAAATCAGACCAGTG 3 215 0 TCTTAGAAAT 0.94497 -86 ********** Masking position 5 Map Score: 1.63042 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 95 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 7 TACGGAACTATTGATGAGAGTTTGGTGTCT 1 211 0 TTGATGAGAG 0.947498 -90 CCGTAAATTTTTATTGACAGAACTTATTGA 1 236 1 TTATTGACAG 0.968505 -65 TTGACAGAACTTATTGACGGCAGTGGCAGG 1 249 1 TTATTGACGG 0.979419 -52 TGCCGACTGATTAATGAGGGTTAATCAGTA 2 231 1 TTAATGAGGG 0.97942 -70 ********** Masking position 5 Map Score: 0.382977 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 46 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 ********** No masking Map Score: -6.79689e-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 9 ********** No masking Map Score: -6.79689e-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 10 ********** No masking Map Score: -6.79689e-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