AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i319_ecoli_bsub_300.orf -o319_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -x5 -e 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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ppdD 202 prelipin peptidase dependent protein #2 nadC 87 quinolinate phosphoribosyltransferase #3 yheE 179 putative general secretion pathway for protein export (GSP) #4 comGB 52 probably part of the DNA transport machinery #5 comGA 300 late competence gene Motif number 1 TATTTCGTTGCAGCGAAAGACAAGAAATTTGCGAG 1 79 0 CAGAGACAAA 0.782494 -124 TCTTTCGCTGCAACGAAATAAAAAACCTCGGAATC 1 94 1 CAAATAAAAA 0.829736 -109 AGGCGAGGGGCAAAAAACGAAACGGGAAAGCAGAT 1 126 0 CAAAGAAACG 0.987543 -77 CCAACCAAATCAAGGAGCGAAACAG 1 188 1 CAAAGAAACG 0.987543 -15 TAAGGATAATCAATAATTAAAACAGGAAGTTCT 3 9 0 CAAAAAAACG 0.968728 -171 AGATACTGGTCAATAAGCGAAAACAGCATAATGAA 5 68 1 CAAAGAAAAA 0.969231 -233 ATAATTTTCCCTATAAATAAAAAAGCAGACATGGT 5 126 0 CTAAAAAAAG 0.922314 -175 CCAATTCTTTCTGGCAAGAAAAAAGACTTTCAACT 5 179 0 CTGAAAAAAG 0.853012 -122 AAAAGGTAATCAAACAGGGAAAACGTGATTTTGTG 5 234 0 CAAAGAAAAG 0.989703 -67 *** * ***** * Masking position 6 Map Score: 7.05975 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 219 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 2 GAAAGTTGGGGAAGGGGAGATTATCCGCCCGC 1 37 0 GAAGGGGATT 0.83161 -166 AAACGAAACGGGAAAGCAGATTCCGAGGTTTT 1 115 0 GGAAACGATT 0.888577 -88 CGCTACTTTGGCAAACGCCATCAGCACAGGCG 1 156 0 GCAAAGCATC 0.966276 -47 CCAAAGTAGCGCCAACCAAATCAAGGAGCGAA 1 177 1 GCCAACAATC 0.797627 -26 CTTGATTCATGCAAGCGGCATTAATACTATTT 3 106 1 GCAAGGCATT 0.885436 -74 ACAGCATAATGAAAATGGAATCTAGCAGGCAT 5 90 1 GAAAAGAATC 0.977507 -211 GTTATATGCTGAAAAACCAATTCTTTCTGGCA 5 198 0 GAAAACAATT 0.923611 -103 ATCAAACAGGGAAAACGTGATTTTGTGAGATG 5 229 0 GAAAAGGATT 0.963912 -72 AGAAAAAGAAGAAAAGGTAATCAAACAGGGAA 5 248 0 GAAAAGAATC 0.977466 -53 TGCGTTGAAAGGAGAGGGAATCAAA 5 286 1 GGAGAGAATC 0.926331 -15 ***** * **** Masking position 10 Map Score: 5.66731 Number of sites scoring better than the average of aligned sites = 791 Number in coding regions = 714 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 3 CTACTCTGAACCGGGTATTAGCACCACATA 2 25 0 CCGGGTATTA 0.975885 -63 AAAAGTCTGGTTGTTAAAGGATCAAG 4 7 1 CTGGTTGTTA 0.94726 -46 AGGATCAAGCCAGGTTATTAAAGAGGCTCG 4 28 1 CAGGTTATTA 0.965346 -25 TGCAACAATACCGGTCATTTGGTCATTTTC 5 15 0 CCGGTCATTT 0.977239 -286 GAGAAAGATACTGGTCAATAAGCGAAAACA 5 63 1 CTGGTCAATA 0.950138 -238 TGAATGTACCCCTGTCATTATAATTTTCCC 5 150 0 CCTGTCATTA 0.964187 -151 ********** Masking position 9 Map Score: 2.92875 Number of sites scoring better than the average of aligned sites = 402 Number in coding regions = 360 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 4 GCAGATTCCGAGGTTTTTTATTTCGTTGCA 1 102 0 AGGTTTTTTA 0.852577 -101 CTTTCCCGTTTCGTTTTTTGCCCCTCGCCT 1 131 1 TCGTTTTTTG 0.85922 -72 GTTAGCTATCTGGAGTTTTAAC 2 76 1 TGGAGTTTTA 0.920507 -12 AGAACTTCCTGTTTTAATTATTGATT 3 7 1 TCCTGTTTTA 0.951081 -173 ATTTTCATTATGCTGTTTTCGCTTATTGAC 5 76 0 TGCTGTTTTC 0.906829 -225 CCTGCTAGATTCCATTTTCATTATGCTGTT 5 89 0 TCCATTTTCA 0.804376 -212 TGACCATGTCTGCTTTTTTATTTATAGGGA 5 124 1 TGCTTTTTTA 0.969944 -177 CAGAAAGAATTGGTTTTTCAGCATATAACA 5 201 1 TGGTTTTTCA 0.948116 -100 ********** Masking position 6 Map Score: 3.36622 Number of sites scoring better than the average of aligned sites = 562 Number in coding regions = 438 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 5 ATCTCCCCTTCCCCAACTTTCTTCGTAACGCCT 1 48 1 CCCACTTCTT 0.841721 -155 AATCTGCTTTCCCGTTTCGTTTTTTGCCCCTCG 1 125 1 CCCTTCGTTT 0.890541 -78 TATACAACCCACCCAATCTATTTTATTAGAACA 3 151 1 ACCATCTTTT 0.981848 -29 TTCACCGAGCCTCTTTAATAACCTGG 4 37 0 ACCACCTTTT 0.981483 -16 AGACATGGTCACCATGCCTGCTAGATTCCATTT 5 102 0 ACCTCCTCTA 0.937776 -199 AGGCATGGTGACCATGTCTGCTTTTTTATTTAT 5 116 1 ACCTTCTCTT 0.988479 -185 ATGCTGAAAAACCAATTCTTTCTGGCAAGAAAA 5 192 0 ACCATCTTCT 0.934927 -109 CTGTTTGATTACCTTTTCTTCTTTTTCTACAAT 5 252 1 ACCTTCTCTT 0.988479 -49 *** * *** *** Masking position 3 Map Score: 4.71182 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 180 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 CTTCCCCAACTTTCTTCGTAACGCCTCGCAAAT 1 55 1 TTTCTTCAAG 0.969972 -148 GAGTAGCATGTTTCTACCTTATGATTCGTTAGC 2 49 1 TTTCTACTAG 0.986697 -39 CCAGTATCTTTCTCAACGGAAAGATCGCCTAAT 5 44 0 TCTCAACAAG 0.970941 -257 GAAAAAAGACTTTCAACTGAATGTACCCCTGTC 5 164 0 TTTCAACAAG 0.986697 -137 TTTTCTTCTTTTTCTACAATATGCGTTGAAAGG 5 265 1 TTTCTACTAG 0.986696 -36 ******* ** * Masking position 3 Map Score: 1.8952 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 20 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 TGATTATCCTTAATCATAAAAATAATGTATGTA 3 32 1 TAATAAAAAT 0.943652 -148 ATTTAATTAATAAATACATACATTATTTTTATG 3 46 0 TAAAAATAAT 0.943652 -134 ATGTATTTATTAATTAAATACATATTACTAATA 3 60 1 TAATAATAAT 0.982174 -120 AAATACATATTACTAATATAAATAAATTTTGCT 3 75 1 TACTAATAAT 0.961271 -105 ATGTATGTTCTAATAAAATAGATTGGGTGGGTT 3 156 0 TAATAATAAT 0.982173 -24 **** * *** ** Masking position 6 Map Score: 1.15033 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 8 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 TGCTACTCTGAACCGGGTATTAGCACCACA 2 27 0 AACCGGGTAT 0.934712 -61 ATCCTTTAACAACCAGACTTTT 4 3 0 AACCAGACTT 0.953188 -50 CCTCTTTAATAACCTGGCTTGATCCTTTAA 4 24 0 AACCTGGCTT 0.945499 -29 AATGCAACAATACCGGTCATTTGGTCATTT 5 17 0 TACCGGTCAT 0.92585 -284 AAATGGAATCTAGCAGGCATGGTGACCATG 5 102 1 TAGCAGGCAT 0.959871 -199 ATAAATAAAAAAGCAGACATGGTCACCATG 5 119 0 AAGCAGACAT 0.952032 -182 ********** Masking position 2 Map Score: 1.42793 Number of sites scoring better than the average of aligned sites = 654 Number in coding regions = 567 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 9 CGGATAATCTCCCCTTCCCCAACTTTCTTC 1 42 1 CCCCTTCCCC 0.961177 -161 TTCTTCGTAACGCCTCGCAAATTTCTTGTC 1 66 1 CGCCTCGCAA 0.936352 -137 TCGTTTTTTGCCCCTCGCCTGTGCTGATGG 1 141 1 CCCCTCGCCT 0.996996 -62 AGTATTAATGCCGCTTGCATGAATCAAGCA 3 104 0 CCGCTTGCAT 0.955521 -76 ACTGAATGTACCCCTGTCATTATAATTTTC 5 152 0 CCCCTGTCAT 0.972185 -149 TTTGATTCCCTCTCCTTTCAACGCAT 5 285 0 TCCCTCTCCT 0.957969 -16 ********** Masking position 5 Map Score: 1.05448 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 272 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 10 ********** No masking Map Score: -9.56801e-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 11 ********** No masking Map Score: -9.56801e-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 12 ********** No masking Map Score: -9.56801e-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