AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i074_ecoli_bsub_300.orf -o074_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 yusL 267 similar to 3-hydroxyacyl-CoA dehydrogenase #2 yusM 300 similar to proline dehydrogenase Motif number 1 AAGCAGCCGTGGGAAGCAGC 1 1 1 AAGCAGCCGT 0.990868 -267 CCGTGGGAAGCAGCTGCATTATGATTGTCC 1 17 1 CAGCTGCATT 0.942248 -251 GACAAGTCAAAATCAGCAGTATAAAAAACA 1 54 0 AATCAGCAGT 0.952845 -214 TGTCCGTTTTCCGCCGCCGTAATGCTGAGT 1 80 1 CCGCCGCCGT 0.994152 -188 TGCCGGTCCGACTCAGCATTACGGCGGCGG 1 90 0 ACTCAGCATT 0.866501 -178 AATCCGTCTTCAGCGGCAGTCAGCGCGGCG 1 134 0 CAGCGGCAGT 0.986627 -134 GCATTTCATGGCGCAGCAGTGCCAGGATCA 2 80 0 GCGCAGCAGT 0.978421 -221 GCAATCTCAAATGCCGCCTTCCGTTATTTC 2 173 0 ATGCCGCCTT 0.935004 -128 AATGGATAATCAGCAGCAATCTCAAATGCC 2 188 0 CAGCAGCAAT 0.9632 -113 CCGACTCCCTCCCGCCGTCATCTTCAAA 2 283 0 CTCCCGCCGT 0.939125 -18 ********** Masking position 10 Map Score: 13.4967 Number of sites scoring better than the average of aligned sites = 2172 Number in coding regions = 2093 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 2 CTCAGCATTACGGCGGCGGAAAACGGACAAGTC 1 76 0 CGCGGCGAAA 0.991882 -192 GCAGTCAGCGCGGCGAGCGTAAAGGGAGATGCC 1 116 0 CGCGAGGAAA 0.987672 -152 AATCCGTCTTCAGCGGCAGTCAGCGCGGCGAGC 1 131 0 CACGGCGCAG 0.942385 -137 GAAGGGAATGGTACGAGAGAAAAAAAATCCGTC 1 156 0 GTCGAGGAAA 0.84932 -112 TTCCCTTCACCTCCGGGCTTAAGTTGCCCGACT 1 181 1 CTCGGGTAAG 0.97922 -87 TGCATGTGTCCGACGCGGTCGAGTTCTTGCTTT 2 41 1 CGCGCGTGAG 0.97734 -260 CCTGGCACTGCTGCGCCATGAAATGCGCTTTTT 2 84 1 CTCGCCTAAA 0.936531 -217 GCGCTTTTTTCATCGCGAGCAAATTCCAGTTCA 2 108 1 CACGCGGAAA 0.983871 -193 TTGAAGATGACGGCGGGAGGGAGTCGG 2 284 1 CGCGGGGGAG 0.994226 -17 ** **** * *** Masking position 12 Map Score: 8.26167 Number of sites scoring better than the average of aligned sites = 1503 Number in coding regions = 1439 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 3 CAGCTGCTTCCCACGGCTGCTT 1 3 0 CCACGGCTGC 0.866168 -265 GACAATCATAATGCAGCTGCTTCCCACGGC 1 16 0 ATGCAGCTGC 0.859865 -252 TTTTATACTGCTGATTTTGACTTGTCCGTT 1 58 1 CTGATTTTGA 0.483775 -210 CTCAGCATTACGGCGGCGGAAAACGGACAA 1 79 0 CGGCGGCGGA 0.991711 -189 CGCCGTAATGCTGAGTCGGACCGGCATCTC 1 94 1 CTGAGTCGGA 0.921565 -174 TGAGTCGGACCGGCATCTCCCTTTACGCTC 1 105 1 CGGCATCTCC 0.878909 -163 GCCGCGCTGACTGCCGCTGAAGACGGATTT 1 135 1 CTGCCGCTGA 0.977803 -133 AAGAACTCGACCGCGTCGGACACATGCATC 2 39 0 CCGCGTCGGA 0.977369 -262 GATCCTGGCACTGCTGCGCCATGAAATGCG 2 81 1 CTGCTGCGCC 0.939947 -220 TAACGGAAGGCGGCATTTGAGATTGCTGCT 2 177 1 CGGCATTTGA 0.833817 -124 GCATTTGAGATTGCTGCTGATTATCCATTG 2 189 1 TTGCTGCTGA 0.867745 -112 ********** Masking position 3 Map Score: 6.58337 Number of sites scoring better than the average of aligned sites = 10549 Number in coding regions = 10145 Number in noncoding regions = 404 Number of orfs with sites within 600 bp upstream = 331 Fraction of orfs with sites within 600 bp upstream = 0.0531642 Motif number 4 GCTGCATTATGATTGTCCCATGTTATGTTTTTT 1 29 1 GATTCCATGT 0.989995 -239 TTATACTGCTGATTTTGACTTGTCCGTTTTCCG 1 60 1 GATTGATTGT 0.946573 -208 TTGAGATACAAATGATCCTTTGTCGAAATAACG 2 149 1 AATTCCTTGT 0.984223 -152 GATTGCTGCTGATTATCCATTGTGATCCTCCTT 2 197 1 GATTCCTTGT 0.996938 -104 TATCCATTGTGATCCTCCTTTGGTTTCTGTTCA 2 210 1 GATTCCTTGG 0.993228 -91 *** *** **** Masking position 6 Map Score: 3.18056 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 49 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 CGGCGGCGGAAAACGGACAAGTCAAAATCA 1 69 0 AAACGGACAA 0.892886 -199 CGTAATGCTGAGTCGGACCGGCATCTCCCT 1 97 1 AGTCGGACCG 0.995832 -171 AGCCTATAAAAGTCGGGCAACTTAAGCCCG 1 194 0 AGTCGGGCAA 0.984727 -74 TAGCTATTGAAGTCGAACCGGAAATCTTTT 1 245 1 AGTCGAACCG 0.97863 -23 AACTCGACCGCGTCGGACACATGCATCATG 2 36 0 CGTCGGACAC 0.981881 -265 ********** Masking position 5 Map Score: 2.09603 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 172 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 ********** No masking Map Score: 1.67221e-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: 1.67221e-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: 1.67221e-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