AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i027_Fumarate_Hydratase_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 fumC 142 fumarase C= fumarate hydratase Class II; isozyme #2 fumA 198 fumarase A = fumarate hydratase Class I; aerobic isozyme #3 HI1398 234 fumarate hydratase, class II (fumC) Motif number 1 TTCGGGGCGGTTTTTTTACATGGCACGAAA 1 23 1 TTTTTTTACA 0.85936 -120 ATGTTTGGTCTTTCGTGCCATGTAAAAAAA 1 33 0 TTTCGTGCCA 0.949102 -110 TCTGTTTTGCTTTCGTTAAGCAACTTTTAG 1 92 0 TTTCGTTAAG 0.976491 -51 TGATTAATTTTTTCTTTCTGTTTTGCTTTC 1 108 0 TTTCTTTCTG 0.757828 -35 TAGTCTCAGTTTTTGTTAAAAAAGTGTGTA 2 99 1 TTTTGTTAAA 0.951204 -100 TACTGCCTGGTTTGGTTATGCTCTGGGCGG 2 167 0 TTTGGTTATG 0.836538 -32 TTTAGGGTTTTTTCGTTAAAATTTTACCCT 3 48 0 TTTCGTTAAA 0.972672 -187 TAAAAATCAGTTTTGTGACATAGATCATAA 3 131 0 TTTTGTGACA 0.930146 -104 TTTTTAACGTTTTTGTTACGTTCCACTCAT 3 155 1 TTTTGTTACG 0.971115 -80 GCGTTTTAATTTTCATTCAATTCATAGGAG 3 209 1 TTTCATTCAA 0.751939 -26 ********** Masking position 6 Map Score: 9.60937 Number of sites scoring better than the average of aligned sites = 554 Number in coding regions = 454 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 2 TGCCATGTAAAAAAACCGCCCCGAAGGGCGGCTCT 1 13 0 AAAAACGCAA 0.933268 -130 AATGGTAAATAATAAGTGAGCTAAAAGTTGCTTAA 1 72 1 AATAAGGGAA 0.974144 -71 ATTTCCACATTAAAACAGGGATTGATC 2 3 0 TAAAACGGGA 0.987006 -196 ATTCTTGCTTTAATAGTGGGATTAATTTCCACATT 2 27 0 TAATAGGGAA 0.938467 -172 CTTTTTTAACAAAAACTGAGACTAGTACGACTTTT 2 88 0 AAAAACGGAG 0.957426 -111 GTTTTTGTTAAAAAAGTGTGTAGGATATTGTTACT 2 107 1 AAAAAGGGGA 0.991515 -92 GTTGCCCTGTTAAAAGCGAGTAACAATATCCTACA 2 125 0 TAAAAGGGCA 0.972493 -74 AGATTGAGAAAATAACGGGGCTAAA 3 1 0 AATAACGGAA 0.968168 -234 ACATAGATCATAAAAGCGCGGTGGATTTTCAGACA 3 109 0 TAAAAGGGGA 0.989567 -126 ****** * * ** Masking position 5 Map Score: 9.51298 Number of sites scoring better than the average of aligned sites = 343 Number in coding regions = 264 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 3 CTCACTTATTATTTACCATTTGATAACAAAT 1 61 0 ATTTACCTTT 0.967856 -82 ATTTTCTCAATCTTACCCTATAAAAAGGGTA 3 23 1 TCTTACCTAT 0.931337 -212 TTCGTTAAAATTTTACCCTTTTTATAGGGTA 3 36 0 TTTTACCTTT 0.990006 -199 CAAAACTGATTTTTAACGTTTTTGTTACGTT 3 146 1 TTTTAACTTT 0.977762 -89 ACGCAAGTGATTTTAACACTTCCGAGTTATG 3 182 0 TTTTAACCTT 0.951938 -53 ******* *** Masking position 5 Map Score: 2.1358 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 84 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 4 GTCTTTCGTGCCATGTAAAAAAACCGCCCC 1 26 0 CCATGTAAAA 0.970435 -117 GGATTAATTTCCACATTAAAACAGGGATTG 2 14 0 CCACATTAAA 0.935387 -185 AAATTAATCCCACTATTAAAGCAAGAATCC 2 34 1 CACTATTAAA 0.947717 -165 TGTTCCGTTGCCCTGTTAAAAGCGAGTAAC 2 136 0 CCCTGTTAAA 0.98981 -63 CTCAATCTTACCCTATAAAAAGGGTAAAAT 3 28 1 CCCTATAAAA 0.991537 -207 AACGAAAAAACCCTAAAAAATAAATAATTA 3 61 1 CCCTAAAAAA 0.966563 -174 ********** Masking position 8 Map Score: 6.87181 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 60 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 5 CACGAAAGACCAAACATTTGTTATCAAATG 1 46 1 CAAACATTTG 0.780167 -97 AATAAGTGAGCTAAAAGTTGCTTAACGAAA 1 82 1 CTAAAAGTTG 0.954935 -61 CCTGGAGCCGCAAAAAGTCGTACTAGTCTC 2 76 1 CAAAAAGTCG 0.968419 -123 GGTGGATTTTCAGACATTTGTAATAATGCA 3 95 0 CAGACATTTG 0.9473 -140 ********** Masking position 6 Map Score: 0.082047 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 59 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 ********** No masking Map Score: -1.28365e-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: -1.28365e-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: -1.28365e-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