AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i061_ecoli_bsub_300.orf -o061_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 yffG 205 putative oxidoreductase, Fe-S subunit #2 gltB 300 glutamate synthase, large subunit #3 gltA 146 glutamate synthase (large subunit) Motif number 1 ACGCGTCTTCTCCACAAAAAATC 1 2 1 CGCGTTTCCC 0.973925 -204 ATCATTAATGTTCCAGTTCGCTGAAACGCAAT 1 31 1 TTCCATTCCT 0.826216 -175 ACATGAACATTGCCGATTCCCCTGTAAGTCGG 1 127 1 TGCCGTTCCC 0.991565 -79 TCTAACGACTTCCCTTTTAGCCTTAAAGATAA 2 49 1 TCCCTTTACC 0.957872 -252 CCAATAAGCTTGCCATTTGACCTGTATCAGCT 2 139 1 TGCCATTGCC 0.964236 -162 TAATTGAGATCCCCTCTTCACCGTATTAACCG 2 238 1 CCCCTTTCCC 0.995589 -63 CCGATTCGCCCCCTTGTTGTCCTTTTCGCATC 2 269 0 CCCTTTTGCC 0.899156 -32 ACGCGCGCCTCCGATTCGCCCCCTTGTTGT 2 281 0 CTCCGTTCCC 0.989723 -20 AATTCCTCTCCCCCGATCAATTTC 3 133 0 TTCCTTCCCC 0.963027 -14 ***** *** ** Masking position 7 Map Score: 9.22915 Number of sites scoring better than the average of aligned sites = 744 Number in coding regions = 690 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 2 GTAACTATTTCGCTATAAACTGTGGCAGATCA 1 84 0 CGCTATAACG 0.962304 -122 TTGCCGATTCCCCTGTAAGTCGGGTAATAACA 1 136 1 CCCTGTAGTG 0.911142 -70 CTAACGACTTCCCTTTTAGCCTTAAAGATAAA 2 50 1 CCCTTTAGCT 0.912772 -251 GCCATTTGACCTGTATCAGCTTTCCCGATAAG 2 150 1 CTGTATAGCT 0.946131 -151 TATCAGCTTTCCCGATAAGTTGGAAATCCGCT 2 163 1 CCCGATAGTG 0.968991 -138 TGGAAGCTTTCTGGATGAGCAGCCTGCTCATC 2 194 1 CTGGATAGCG 0.966992 -107 CCCCTCTTCACCGTATTAACCGATGCGAAAAG 2 248 1 CCGTATAACG 0.973875 -53 AATCTAACAACTCTATAATCATTGTAGGTTTT 3 83 0 CTCTATATCT 0.876211 -64 ATTTTATGACCGGTATTATCGGAAATTGATCG 3 112 1 CGGTATATCG 0.92355 -35 ATTCCTCTCCCCCGATCAATTTCCGATAATAC 3 124 0 CCCGATAATT 0.839041 -23 ****** *** * Masking position 6 Map Score: 6.40742 Number of sites scoring better than the average of aligned sites = 1308 Number in coding regions = 1194 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 3 ACAACACTCATATAAAGAATAAGGTTTTTA 1 165 1 TATAAAGAAT 0.978614 -41 TTTTACAACCAAAAAAGAAGGTCGTT 1 190 1 AAAAAAGAAG 0.909418 -16 TCAGTCATTTAATAAAGAATTTTGCGCTAA 2 95 1 AATAAAGAAT 0.969636 -206 ATAATTTAGATCAAAAGAATCTCAAAATGA 3 33 0 TCAAAAGAAT 0.935006 -114 TTCAAAACGATATAAACAATATATAATTTA 3 55 0 TATAAACAAT 0.928551 -92 ********** Masking position 5 Map Score: 1.41882 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 59 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 4 CTGTAAGTCGGGTAATAACAACACTCATATAA 1 148 1 GGTATACAAC 0.989087 -58 TAAAGAATAAGGTTTTTACAACCAAAAAAGAA 1 177 1 GGTTTACAAC 0.967677 -29 AATCATTGTAGGTTTTCAAAACGATATAAACA 3 67 0 GGTTTAAAAC 0.96377 -80 CGATAATACCGGTCATAAAATCTAACAACTCT 3 101 0 GGTATAAATC 0.968196 -46 *** ** ***** Masking position 6 Map Score: 1.40506 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 21 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 AGCGAACTGGAACATTAATGATTTTTTGTG 1 23 0 AACATTAATG 0.90363 -183 TTAACACACCTTTATGACAGTCAGGA 2 7 1 CACCTTTATG 0.968864 -294 TCATTTAATAAAGAATTTTGCGCTAAAGCA 2 99 1 AAGAATTTTG 0.750661 -202 TGCGCTAAAGCACATTTCTGTACCAATAAG 2 117 1 CACATTTCTG 0.945778 -184 GTCAAATGGCAAGCTTATTGGTACAGAAAT 2 130 0 AAGCTTATTG 0.887679 -171 AATCCGCTGGAAGCTTTCTGGATGAGCAGC 2 187 1 AAGCTTTCTG 0.965269 -114 GCCTGCTCATCATATTTATGCAGTAATTGA 2 215 1 CATATTTATG 0.823066 -86 ********** Masking position 2 Map Score: 1.40621 Number of sites scoring better than the average of aligned sites = 416 Number in coding regions = 357 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 6 AATAATCCCATCACTGACTAAATTGCGTTT 1 54 0 TCACTGACTA 0.884481 -152 AGAGAAACAGTCAATTCCTGACTGTCATAA 2 22 0 TCAATTCCTG 0.979673 -279 AATTCTTTATTAAATGACTGAAATTAAAAT 2 86 0 TAAATGACTG 0.944433 -215 AGAGGGGATCTCAATTACTGCATAAATATG 2 225 0 TCAATTACTG 0.987976 -76 TCTCCCCCGATCAATTTCCGATAATACCGG 3 121 0 TCAATTTCCG 0.936098 -26 ********** Masking position 5 Map Score: 0.76487 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 215 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 ********** No masking Map Score: -1.36181e-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: -1.36181e-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: -1.36181e-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