AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i319_ecoli_bsub_100.orf -o319_ecoli_bsub_100.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 yheE 179 putative general secretion pathway for protein export (GSP) #3 comGB 52 probably part of the DNA transport machinery #4 comGA 300 late competence gene Motif number 1 CTCGCAAATTTCTTGTCTTTCGCTGCAACGAAATA 1 79 1 TTTGTCTCTG 0.83457 -124 GATTCCGAGGTTTTTTATTTCGTTGCAGCGAAAGA 1 94 0 TTTTTATTTG 0.872346 -109 ATCTGCTTTCCCGTTTCGTTTTTTGCCCCTCGCCT 1 126 1 CGTTTCTTTG 0.991085 -77 CTGTTTCGCTCCTTGATTTGGTTGG 1 188 0 CGTTTCTTTG 0.991085 -15 AGAACTTCCTGTTTTAATTATTGATTATCCTTA 2 9 1 CGTTTTTTTG 0.97749 -171 TTCATTATGCTGTTTTCGCTTATTGACCAGTATCT 4 68 0 TTTTTCTTTG 0.977863 -233 ACCATGTCTGCTTTTTTATTTATAGGGAAAATTAT 4 126 1 CTTTTTTTAG 0.943338 -175 AGTTGAAAGTCTTTTTTCTTGCCAGAAAGAATTGG 4 179 1 CTTTTTTCAG 0.890565 -122 CACAAAATCACGTTTTCCCTGTTTGATTACCTTTT 4 234 1 CTTTTCTTTG 0.992635 -67 * ***** * *** Masking position 6 Map Score: 7.99317 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 TGTTCTAATAAAATAGATTGGGTGGGTTGTATA 2 151 0 AAAAGATGGT 0.987356 -29 CCAGGTTATTAAAGAGGCTCGGTGAA 3 37 1 AAAAGGTGGT 0.984761 -16 AAATGGAATCTAGCAGGCATGGTGACCATGTCT 4 102 1 TAGAGGAGGT 0.961708 -199 ATAAATAAAAAAGCAGACATGGTCACCATGCCT 4 116 0 AAGAGAAGGT 0.991921 -185 TTTTCTTGCCAGAAAGAATTGGTTTTTCAGCAT 4 192 1 AGAAGATGGT 0.966163 -109 ATTGTAGAAAAAGAAGAAAAGGTAATCAAACAG 4 252 0 AAGAGAAGGT 0.991922 -49 *** *** * *** Masking position 5 Map Score: 5.10198 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 40 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 3 CGCGGGCGGATAATCTCCCCTTCCCCAACTTTC 1 36 1 TAATCCCCTC 0.860722 -167 AAAAACCTCGGAATCTGCTTTCCCGTTTCGTTT 1 114 1 GAATCGTTTC 0.893528 -89 TCGCCTGTGCTGATGGCGTTTGCCAAAGTAGCG 1 155 1 TGATGCTTTC 0.973401 -48 TTTCGCTCCTTGATTTGGTTGGCGCTACTTTGG 1 177 0 TGATTGTTGC 0.834216 -26 TAAATAGTATTAATGCCGCTTGCATGAATCAAG 2 106 0 TAATGCCTTC 0.907978 -74 CATGCCTGCTAGATTCCATTTTCATTATGCTGT 4 90 0 AGATTCTTTC 0.952174 -211 TTGCCAGAAAGAATTGGTTTTTCAGCATATAAC 4 197 1 GAATTGTTTC 0.895441 -104 ACATCTCACAAAATCACGTTTTCCCTGTTTGAT 4 228 1 AAATCCTTTC 0.924454 -73 TTTCCCTGTTTGATTACCTTTTCTTCTTTTTCT 4 247 1 TGATTCTTTC 0.981944 -54 TTTGATTCCCTCTCCTTTCAACGCA 4 286 0 TGATTCTCTC 0.958989 -15 ***** * *** * Masking position 4 Map Score: 5.48934 Number of sites scoring better than the average of aligned sites = 616 Number in coding regions = 555 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 4 CGGATAATCTCCCCTTCCCCAACTTTCTTC 1 42 1 CCCCTTCCCC 0.984255 -161 ACCTCGGAATCTGCTTTCCCGTTTCGTTTT 1 118 1 CTGCTTTCCC 0.874323 -85 TCGTTTTTTGCCCCTCGCCTGTGCTGATGG 1 141 1 CCCCTCGCCT 0.99518 -62 AGTATTAATGCCGCTTGCATGAATCAAGCA 2 104 0 CCGCTTGCAT 0.966276 -76 CAGACATGGTCACCATGCCTGCTAGATTCC 4 106 0 CACCATGCCT 0.888866 -195 ACTGAATGTACCCCTGTCATTATAATTTTC 4 152 0 CCCCTGTCAT 0.95113 -149 TTTGATTCCCTCTCCTTTCAACGCAT 4 285 0 TCCCTCTCCT 0.944539 -16 ********** Masking position 4 Map Score: 2.34787 Number of sites scoring better than the average of aligned sites = 613 Number in coding regions = 481 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 5 TTATACTAACGTCAATATACAACCCACCCA 2 136 1 GTCAATATAC 0.977141 -44 AAAGATACTGGTCAATAAGCGAAAACAGCA 4 66 1 GTCAATAAGC 0.969187 -235 AGATTCCATTTTCATTATGCTGTTTTCGCT 4 83 0 TTCATTATGC 0.967821 -218 AGCAGACATGGTCACCATGCCTGCTAGATT 4 108 0 GTCACCATGC 0.964733 -193 ATGTACCCCTGTCATTATAATTTTCCCTAT 4 147 0 GTCATTATAA 0.823097 -154 CTTCTTTTTCTACAATATGCGTTGAAAGGA 4 269 1 TACAATATGC 0.914031 -32 ********** Masking position 4 Map Score: 1.43658 Number of sites scoring better than the average of aligned sites = 556 Number in coding regions = 505 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 6 ATTTGCGAGGCGTTACGAAGAAAGTTGGGGAAG 1 55 0 CGTTCGGAAA 0.994637 -148 TTTTTTATTTCGTTGCAGCGAAAGACAAGAAAT 1 86 0 CGTTCAGAAA 0.987997 -117 ATTAGGCGATCTTTCCGTTGAGAAAGATACTGG 4 44 1 CTTTCGGAGA 0.980542 -257 GACAGGGGTACATTCAGTTGAAAGTCTTTTTTC 4 164 1 CATTAGGAAA 0.953959 -137 CTACAATATGCGTTGAAAGGAGAGGGAATCAAA 4 278 1 CGTTAAGAGA 0.975273 -23 **** ** **** Masking position 4 Map Score: 0.264806 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 81 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 TTATTTCGTTGCAGCGAAAGACAAGAAATT 1 85 0 GCAGCGAAAG 0.968761 -118 ACCAAATCAAGGAGCGAAACAG 1 191 1 GGAGCGAAAC 0.876666 -12 AAAAGTCTGGTTGTTAAAGGATCAAGCCA 3 10 1 GTTGTTAAAG 0.932956 -43 ATCAAGCCAGGTTATTAAAGAGGCTCGGTG 3 31 1 GTTATTAAAG 0.644301 -22 CGATCTTTCCGTTGAGAAAGATACTGGTCA 4 50 1 GTTGAGAAAG 0.978012 -251 GATGTTATATGCTGAAAAACCAATTCTTTC 4 203 0 GCTGAAAAAC 0.874805 -98 AACGCATATTGTAGAAAAAGAAGAAAAGGT 4 262 0 GTAGAAAAAG 0.938942 -39 ********** Masking position 7 Map Score: 0.297465 Number of sites scoring better than the average of aligned sites = 1390 Number in coding regions = 1254 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 8 ********** No masking Map Score: 1.20325e-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: 1.20325e-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 10 ********** No masking Map Score: 1.20325e-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