AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i162_Precorrin-2_Biosynthesis_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 hemL 224 glutamate-1-semialdehyde aminotransferase (aminomutase) #2 hemB 136 5-aminolevulinate dehydratase = porphobilinogen synthase #3 b0370 84 orf, hypothetical protein #4 hemA 213 enzyme in alternate path of synthesis of 5-aminolevulinate #5 hemC 300 porphobilinogen deaminase = hydroxymethylbilane synthase Motif number 1 TAGAGTATAAAAGTTTTGTGCATTTGAAACA 1 92 0 AGTTTTGTGC 0.836241 -133 AAGCAGCCTGATGTTTGACGAGTATTTAACT 1 146 1 AGTTTGACGA 0.930947 -79 GTTTTACGAAAGTTGTCGCGATGTTGACAAG 2 91 0 ATTGTCGCGA 0.801262 -46 CAGGGTAGGGATGTTTTACGAAAGTTGTCGC 2 103 0 AGTTTTACGA 0.958304 -34 AAAACATATTATGTTTCGCGCTAACGATT 3 66 1 AGTTTCGCGC 0.994424 -19 AACCGTTACCACTTTTCGCGCCTGGTTTTTT 5 39 1 ATTTTCGCGC 0.968583 -262 CTGGTTTTTTTAGTTTCACGACGAAAAAATG 5 60 1 TGTTTCACGA 0.917006 -241 ATCCTGACAGGCGTTTCACGCCGTTGTAATA 5 186 0 GGTTTCACGC 0.958344 -115 ACCTCATTTTACGGTTTGCGCAGGCGTCTAC 5 227 1 AGGTTTGCGC 0.924182 -74 GCAGGCGTCTACGTTTCACCACAACACTGAC 5 246 1 AGTTTCACCA 0.900688 -55 * ********* Masking position 6 Map Score: 8.78358 Number of sites scoring better than the average of aligned sites = 838 Number in coding regions = 774 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 2 ATGACCAATAAGTGATCATTGG 1 1 0 AGGATCTTGG 0.864009 -224 AGAGAATGGAAGAGAGGCCAGGACATCTTTTT 2 58 0 AGGAGGCAGG 0.993903 -79 AGTATACCTGAAGCAGGGTAGGGATGTTTTAC 2 115 0 AACAGGTAGG 0.91471 -22 AGTGATGACAAGTCCTTGAGAT 4 1 1 AGGATGCAAG 0.94891 -213 AAATAATACCAACGTTGATAGGGTTAGTCTGC 4 183 0 AAGTTGTAGG 0.922162 -31 CAAACCGTAAAATGAGGTCTGGCAGTGGATCC 5 213 0 AAGAGGCTGG 0.974103 -88 TCCTTGCCAGAGTGATGTCAGTGTTGTGGTGA 5 261 0 AGGATGCAGT 0.948877 -40 TCACTCTGGCAAGGATGTTAGGATGGACCACG 5 278 1 AAGATGTAGG 0.985099 -23 ** **** **** Masking position 1 Map Score: 4.08888 Number of sites scoring better than the average of aligned sites = 452 Number in coding regions = 414 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 3 TTACTCGCACGTTCCATGAAAATCCTTTGCAA 1 53 1 GTTCTGAAAA 0.946385 -172 TTGAAACATTACGCTTTGCAAAGGATTTTCAT 1 68 0 ACGCTGCAAA 0.905088 -157 AAACTTTTATACTCTAAGAAATCAGGATTGCA 1 107 1 ACTCAGAAAT 0.860694 -118 AGGGTTCCTGATTCGTAGAAAAAGTGAATGGC 1 201 0 ATTCAGAAAA 0.977874 -24 ATAATTTTATATTCACTGAAAATATTTTTAAT 2 13 0 ATTCTGAAAA 0.982932 -124 TCAATTATCAATGCATAGAAAACATATTATGT 3 48 1 ATGCAGAAAA 0.967495 -37 AGCACCGTTTATTCTCTGTAAATTCCTTATTA 5 159 1 ATTCTGTAAA 0.934249 -142 **** ****** Masking position 10 Map Score: 1.87783 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 94 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 4 CTGATTTCTTAGAGTATAAAAGTTTTGTGC 1 102 0 AGAGTATAAA 0.83843 -123 TATGAATAACATAGAATAGCAGCCATTCAC 1 180 1 ATAGAATAGC 0.858724 -45 TCGTAGAAAAAGTGAATGGCTGCTATTCTA 1 191 0 AGTGAATGGC 0.945824 -34 AAATATTTTCAGTGAATATAAAATTATTGC 2 18 1 AGTGAATATA 0.864742 -119 GTTGACAAGAAGAGAATGGAAGAGAGGCCA 2 70 0 AGAGAATGGA 0.97518 -67 AGGAATTTACAGAGAATAAACGGTGCTACA 5 156 0 AGAGAATAAA 0.954616 -145 ********** Masking position 6 Map Score: 0.507491 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 141 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 TCATACAAATAAGATGACGGCATTTTACTCGC 1 29 1 AAGAGAGGCA 0.930415 -196 GTTATAACCCTTAATGCTAGCGTTACCGTCCG 4 41 1 TTAAGCAGCG 0.943296 -173 AACTTGAACATAGACGATAGCGGACGGTAACG 4 61 0 TAGAGAAGCG 0.978467 -153 CGAAAGCCGTTAGATTCTGGCAATTAAGACAA 4 91 0 TAGATCGGCA 0.876814 -123 GTAAGATCAATAAAAGAGAGCGCCCCCTTTTG 4 133 0 TAAAGAAGCG 0.946702 -81 CGCATCCTGTATGATGCAAGCAGACTAACCCT 4 164 1 ATGAGCAGCA 0.912047 -50 GTGAAACTAAAAAAACCAGGCGCGAAAAGTGG 5 47 0 AAAACCGGCG 0.868004 -254 TGGTGAAACGTAGACGCCTGCGCAAACCGTAA 5 235 0 TAGAGCTGCG 0.972477 -66 **** ** **** Masking position 4 Map Score: 0.944594 Number of sites scoring better than the average of aligned sites = 1608 Number in coding regions = 1521 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 6 CATTCTCTTCTTGTCAACATCGCGACAACT 2 82 1 TTGTCAACAT 0.920675 -55 TTGTCATCCCTCCTCAGGGA 3 1 1 TTGTCATCCC 0.985707 -84 TCTCAAGGACTTGTCATCACT 4 2 0 TTGTCATCAC 0.991248 -212 CACCACAACACTGACATCACTCTGGCAAGG 5 262 1 CTGACATCAC 0.963898 -39 ********** Masking position 6 Map Score: 0.471559 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 26 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 ACTCTAAGAAATCAGGATTGCACCAGTACA 1 117 1 ATCAGGATTG 0.938203 -108 CTCGTCAAACATCAGGCTGCTTGTACTGGT 1 138 0 ATCAGGCTGC 0.969716 -87 TTTTCTACGAATCAGGAACCCTCC 1 211 1 ATCAGGAACC 0.959452 -14 GCTTGCATCATACAGGATGCGTAAGATCAA 4 155 0 TACAGGATGC 0.867841 -59 TTTACGGTCAATCAGCAAGGTGTTAAATTG 5 105 0 ATCAGCAAGG 0.868871 -196 TGAAACGCCTGTCAGGATCCACTGCCAGAC 5 199 1 GTCAGGATCC 0.978305 -102 TGGCAAGGATGTTAGGATGGACCACGG 5 284 1 GTTAGGATGG 0.894956 -17 ********** Masking position 4 Map Score: 0.891114 Number of sites scoring better than the average of aligned sites = 1198 Number in coding regions = 1073 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 8 ********** No masking Map Score: 1.35957e-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: 1.35957e-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: 1.35957e-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