AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i162_Precorrin-2_Biosynthesis_ecoli_hinf_reg_100.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 hemA 213 enzyme in alternate path of synthesis of 5-aminolevulinate #4 hemC 300 porphobilinogen deaminase = hydroxymethylbilane synthase Motif number 1 GCAAAGGATTTTCATGGAACGTGCGAGTAA 1 53 0 TTCATGGAAC 0.831755 -172 ATGTTTCAAATGCACAAAACTTTTATACTC 1 91 1 TGCACAAAAC 0.845361 -134 GGGTTCCTGATTCGTAGAAAAAGTGAATGG 1 202 0 TTCGTAGAAA 0.715609 -23 CGCGACAACTTTCGTAAAACATCCCTACCC 2 102 1 TTCGTAAAAC 0.963153 -35 AAAAAAACCAGGCGCGAAAAGTGGTAACGG 4 41 0 GGCGCGAAAA 0.932551 -260 CCATTTTTTCGTCGTGAAACTAAAAAAACC 4 62 0 GTCGTGAAAC 0.985079 -239 TTATTACAACGGCGTGAAACGCCTGTCAGG 4 185 1 GGCGTGAAAC 0.988385 -116 CGTAGACGCCTGCGCAAACCGTAAAATGAG 4 229 0 TGCGCAAACC 0.866423 -72 TGTCAGTGTTGTGGTGAAACGTAGACGCCT 4 248 0 GTGGTGAAAC 0.905712 -53 ********** Masking position 8 Map Score: 5.57489 Number of sites scoring better than the average of aligned sites = 1771 Number in coding regions = 1684 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 2 CGTGCGAGTAAAATGCCGTCATCTTATTTGTATGACCAA 1 25 0 AAATGGCATT 0.755227 -200 TTGCACCAGTACAAGCAGCCTGATGTTTGACGAGTATTT 1 134 1 ACAAGGCTTG 0.864985 -91 AATAACATAGAATAGCAGCCATTCACTTTTTCTACGAAT 1 184 1 AATAGGCCTT 0.965082 -41 GTTTCTATTAAAAAGATGTCCTGGCCTCTCTTCCATTCT 2 49 1 AAAAGGCCTT 0.991098 -88 GATGTTTTACGAAAGTTGTCGCGATGTTGACAAGAAGAG 2 86 0 GAAAGGCGTG 0.977053 -51 GAACATAGACGATAGCGGACGGTAACGCTAGCATTAAGG 3 49 0 GATAGGCCGT 0.908427 -165 AGTAATTGCCGAAAGCCGTTAGATTCTGGCAATTAAGAC 3 93 0 GAAAGGTCTG 0.916772 -121 CAATTACTCCAAAAGGGGGCGCTCTCTTTTATTGATCTT 3 124 1 AAAAGGCCTT 0.9905 -90 CCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGT 3 169 1 GCAAGGCCTT 0.975599 -45 TTCACGACGAAAAAATGGTCTAAAACGTGATCAATTTAA 4 74 1 AAAAAGCCGG 0.818858 -227 GCAAACCGTAAAATGAGGTCTGGCAGTGGATCCTGACAG 4 207 0 AAATGGCGTG 0.918682 -94 ***** * * ** * Masking position 8 Map Score: 5.6384 Number of sites scoring better than the average of aligned sites = 611 Number in coding regions = 565 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 3 TACTCTAAGAAATCAGGATTGCACCAGTAC 1 116 1 AATCAGGATT 0.927776 -109 TTTTTCTACGAATCAGGAACCCTCC 1 210 1 AATCAGGAAC 0.969336 -15 TTTTTAATAGAAACAGCAATAATTTTATAT 2 33 0 AAACAGCAAT 0.938878 -104 TGCTTGCATCATACAGGATGCGTAAGATCA 3 156 0 ATACAGGATG 0.807392 -58 CTTTACGGTCAATCAGCAAGGTGTTAAATT 4 106 0 AATCAGCAAG 0.968681 -195 ACGCCGTTGTAATAAGGAATTTACAGAGAA 4 170 0 AATAAGGAAT 0.894135 -131 ********** Masking position 5 Map Score: 1.48019 Number of sites scoring better than the average of aligned sites = 536 Number in coding regions = 459 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 4 AAGTTGTCGCGATGTTGACAAGAAGAGAAT 2 83 0 GATGTTGACA 0.766343 -54 AGCGGACGGTAACGCTAGCATTAAGGGTTA 3 45 0 AACGCTAGCA 0.943934 -169 AAAGCCGTTAGATTCTGGCAATTAAGACAA 3 91 0 GATTCTGGCA 0.95927 -123 CATCCTGTATGATGCAAGCAGACTAACCCT 3 166 1 GATGCAAGCA 0.809805 -48 CAAGCAGACTAACCCTATCAACGTTGGTAT 3 180 1 AACCCTATCA 0.763382 -34 TCTGGCAGTGGATCCTGACAGGCGTTTCAC 4 198 0 GATCCTGACA 0.970977 -103 GTTTCACCACAACACTGACATCACTCTGGC 4 258 1 AACACTGACA 0.839973 -43 ACACTGACATCACTCTGGCAAGGATGTTAG 4 269 1 CACTCTGGCA 0.940646 -32 CCGTGGTCCATCCTAACATCCTTGCCAG 4 283 0 CATCCTAACA 0.898991 -18 ********** Masking position 2 Map Score: 1.90142 Number of sites scoring better than the average of aligned sites = 1940 Number in coding regions = 1800 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 5 GCCGTTAGATTCTGGCAATTAAGACAACTT 3 88 0 TCTGGCAATT 0.988415 -126 TCTAACGGCTTTCGGCAATTACTCCAAAAG 3 109 1 TTCGGCAATT 0.927002 -105 TAAAATGAGGTCTGGCAGTGGATCCTGACA 4 208 0 TCTGGCAGTG 0.987295 -93 CTGACATCACTCTGGCAAGGATGTTAGGAT 4 272 1 TCTGGCAAGG 0.985787 -29 ********** Masking position 7 Map Score: 0.64445 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 154 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 TGAATGGCTGCTATTCTATGTTATTCATAA 1 179 0 CTATTCTATG 0.933868 -46 AGAATAGCAGCCATTCACTTTTTCTACGAA 1 192 1 CCATTCACTT 0.960999 -33 CAATAATTTTATATTCACTGAAAATATTTT 2 17 0 ATATTCACTG 0.928286 -120 GGCCTCTCTTCCATTCTCTTCTTGTCAACA 2 71 1 CCATTCTCTT 0.972457 -66 GTAGCACCGTTTATTCTCTGTAAATTCCTT 4 157 1 TTATTCTCTG 0.948844 -144 ********** Masking position 5 Map Score: 0.434086 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 167 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 7 GAGTATTTAACTTGTTATGAATAACATAGA 1 165 1 CTTGTTATGA 0.947747 -60 CCATTCTCTTCTTGTCAACATCGCGACAAC 2 81 1 CTTGTCAACA 0.976115 -56 ATCTCAAGGACTTGTCATCACT 3 3 0 CTTGTCATCA 0.986313 -211 GCGTGAAACGCCTGTCAGGATCCACTGCCA 4 196 1 CCTGTCAGGA 0.972624 -105 ********** Masking position 5 Map Score: 0.115327 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 31 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 ********** No masking Map Score: -1.58918e-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 CCAATGATCACTTATTGGTCATACAAATAA 1 9 1 CATTATTGTC 0.920154 -216 AAATGCCGTCATCTTATTTGTATGACCAATAA 1 22 0 ATTTATTGTA 0.913953 -203 CTGCTATTCTATGTTATTCATAACAAGTTAAA 1 170 0 ATTTATTATA 0.897913 -55 TTCACTGAAAATATTTTTAATCT 2 2 0 ATTTTTTATC 0.933115 -135 AGGCCAGGACATCTTTTTAATAGAAACAGCAA 2 44 0 ATTTTTTATA 0.871048 -93 GGGGCGCTCTCTTTTATTGATCTTACGCATCC 3 139 1 CTTTATTATC 0.956403 -75 CGTTTTAGACCATTTTTTCGTCGTGAAACTAA 4 69 0 CATTTTTGTC 0.898483 -232 ** ***** *** Masking position 7 Map Score: 0.451971 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 172 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 10 ********** No masking Map Score: -1.58918e-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 11 ********** No masking Map Score: -1.58918e-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 12 ********** No masking Map Score: -1.58918e-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