AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i135_Transmembrane_Transport_9_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 cydA 300 cytochrome d terminal oxidase, polypeptide subunit I #2 ybgE 127 orf, hypothetical protein #3 ybgC 149 orf, hypothetical protein #4 tolA 64 membrane spanning protein, required for outer membrane integrity #5 tolB 132 periplasmic protein involved in the tonb-independent uptake of group A colicins #6 pal 34 peptidoglycan-associated lipoprotein Motif number 1 AACCCCGTTAGAAAGGGTCACACGCATGCCCC 1 244 0 GAAGGTCACA 0.883519 -57 TACCCCAAACGAACAGGCAAGAAGCGTTCCCA 2 47 0 GACAGCAAGA 0.981399 -81 AATCAGGCAAAGCCGGTCAAGAAGACATCTG 2 107 1 AGCGGCAAGA 0.944267 -21 TATGGGCCTGGAGCGGCCCATAATTTTTTAAA 3 23 0 GACGGCCATA 0.982727 -127 GCTTGAAAGAGAGCGGGTAACAGGCGAACAGT 4 28 1 GACGGTAACA 0.985775 -37 TTGACCGTCCGAACAGTCAACATCGCGA 5 7 0 GACAGCAACA 0.985775 -126 TTGACTGTTCGGACGGTCAACATCAGGCACCG 5 19 1 GGCGGCAACA 0.994205 -114 TATCGTGGGCCATCGGTCCAGATAAGGGAGAT 5 108 1 CACGGCCAGA 0.977511 -25 ** *** ***** Masking position 10 Map Score: 7.83715 Number of sites scoring better than the average of aligned sites = 347 Number in coding regions = 318 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 2 CAATTTGATCGAGAACAATTTATCT 1 5 0 GGAACAATTT 0.989243 -296 TTTTTCGACGGTGATCAATTTATAGCTAAAT 1 50 0 GGATCAATTT 0.975613 -251 ATATATACGTGGGATCAATTTGAGTTTTTAT 1 132 1 GGATCAATTT 0.975613 -169 AGAAATTTGTTTGAACACTTTCATCATACCA 1 210 0 TGAACACTTT 0.975276 -91 CATGGATTCTGGGAACGCTTCTTGCCTGTTC 2 38 1 GGAACGCTTC 0.967679 -90 GCGCTGGCGCTTGAACACGTCGAATCAGGCA 2 85 1 TGAACACGTC 0.890918 -43 CGGGTAACAGGCGAACAGTTTTTGGAAACCG 4 41 1 GGAACAGTTT 0.981799 -24 * ********* Masking position 4 Map Score: 6.08382 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 193 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 ACAATAAACAGGTTTTTGTTGAAGCAAATT 1 85 0 GGTTTTTGTT 0.861198 -216 ACAAAAACCTGTTTATTGTAAGGATTTTGC 1 96 1 GTTTATTGTA 0.882658 -205 TTGCCTGTTCGTTTGGGGTAATCACCGCGC 2 59 1 GTTTGGGGTA 0.965285 -69 GCGCGATTGAGGTTTGGGAATGAGGGCAAG 3 74 0 GGTTTGGGAA 0.970084 -76 CAGGCGAACAGTTTTTGGAAACCGAGA 4 48 1 GTTTTTGGAA 0.956963 -17 GTTGCCACGGGGTTCTGGTAGTTTTGTGTA 5 51 1 GGTTCTGGTA 0.965285 -82 GGTTCTGGTAGTTTTGTGTATTTTAGTTTG 5 61 1 GTTTTGTGTA 0.967623 -72 ********** Masking position 4 Map Score: 3.84705 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 214 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 ACGGCGTAAAGAAAGGTTGCAAACATGTTAATA 1 160 0 GAAAGGCAAA 0.990341 -141 CATACCATGTGAATGCACACAAAAACGGCGTAA 1 184 0 GAATGACAAA 0.978313 -117 ATGGTATGATGAAAGTGTTCAAACAAATTTCTA 1 209 1 GAAAGTCAAA 0.951565 -92 AGCGTTCCCAGAATCCATGCGAAATACCACATT 2 24 0 GAATCGCGAA 0.945266 -104 TGAGGTTTGGGAATGAGGGCAAGTTAAGGGAGC 3 64 0 GAATGGCAAG 0.988991 -86 TCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGA 4 22 1 GAAAGGCGGG 0.934575 -43 TAATTTAGCAGAATGTTAACAAACTAAAATACA 5 77 0 GAATGACAAA 0.978313 -56 ***** ***** Masking position 3 Map Score: 4.33878 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 241 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 AATTGGCTGAAAGGCGGTAATTTAGCTATA 1 31 1 AAGGCGGTAA 0.968513 -270 GTAAGGATTTTGCGGCGTAATATATACGTG 1 113 1 TGCGGCGTAA 0.723867 -188 TGCACACAAAAACGGCGTAAAGAAAGGTTG 1 174 0 AACGGCGTAA 0.952743 -127 TCCGAGAGTGAACCCCGTTAGAAAGGGTCA 1 256 0 AACCCCGTTA 0.933024 -45 TTCAAGCGCCAGCGCGGTGATTACCCCAAA 2 70 0 AGCGCGGTGA 0.955005 -58 GAATCAGGCAAAGCCGGTCAAGAAGACATC 2 106 1 AAGCCGGTCA 0.933202 -22 GGGCCGCTCCAGGCCCATAAATTTTTACGC 3 36 1 AGGCCCATAA 0.766062 -114 TTTACATCCCGGTAATGCAACAAAA 3 135 0 ATCCCGGTAA 0.932989 -15 GCTTGAAAGAGAGCGGGTAACAGGCGAACA 4 28 1 GAGCGGGTAA 0.824871 -37 AAACTACCAGAACCCCGTGGCAACCGGTGC 5 45 0 AACCCCGTGG 0.88799 -88 ********** Masking position 8 Map Score: 2.99272 Number of sites scoring better than the average of aligned sites = 1895 Number in coding regions = 1737 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 6 AATTGATCACCGTCGAAAAATGCAAATTTGCTT 1 61 1 CGTCGAAATC 0.984307 -240 GTATATATTACGCCGCAAAATCCTTACAATAAA 1 107 0 CGCCGAAATC 0.985437 -194 CGCTTGAACACGTCGAATCAGGCAAAGCCGGTC 2 92 1 CGTCGACAGC 0.996864 -36 AAAAATTATGGGCCGCTCCAGGCCCATAAATTT 3 27 1 GGCCGTCAGC 0.960122 -123 TGATGTTGACCGTCCGAACAGTCAACATCGCGA 5 11 0 CGTCCACAGC 0.989063 -122 ***** * *** * Masking position 10 Map Score: 0.49753 Number of sites scoring better than the average of aligned sites = 716 Number in coding regions = 374 Number in noncoding regions = 342 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 7 ********** No masking Map Score: -1.41155e-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: -1.41155e-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 9 ********** No masking Map Score: -1.41155e-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