AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i103_ecoli_mtub_100.orf -o103_ecoli_mtub_100.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 = 0.58 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 feoA 300 ferrous iron transport protein A #2 ideR 132 ideR Motif number 1 AAGGTTATATCGCAGCGAAAATATAATTCG 1 80 0 CGCAGCGAAA 0.957275 -221 CCGCCGCTGGCGCGGCGGGCATACCGTCTG 2 35 0 CGCGGCGGGC 0.999578 -98 CCGCCGCGCCAGCGGCGGGCATACCGCTGC 2 47 1 AGCGGCGGGC 0.998381 -86 GCCGCCCCACCGCAGCGGTATGCCCGCCGC 2 58 0 CGCAGCGGTA 0.993051 -75 GCTGCGGTGGGGCGGCGGGCAACCATTTTC 2 72 1 GGCGGCGGGC 0.995989 -61 CAACCATTTTCGCAGCTGGCCAAGTAGACT 2 91 1 CGCAGCTGGC 0.991009 -42 ********** Masking position 5 Map Score: 15.8765 Number of sites scoring better than the average of aligned sites = 537 Number in coding regions = 523 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 2 TATTTATCATTTCATTAACAACTGAAACCT 1 14 1 TTCATTAACA 0.904222 -287 AACCTTGAGCCACATCAACATTGAGTCAGA 1 104 1 CACATCAACA 0.989775 -197 GATTATTATTCAAACCAACATTCGCACACA 1 132 1 CAAACCAACA 0.935152 -169 AGAAACCATTCTCATTATCATTGTGTTGTT 1 179 1 CTCATTATCA 0.9637 -122 GAGAGATTAAATAATCAACAACACAATGAT 1 195 0 ATAATCAACA 0.904222 -106 CCTTTGTTGGCAAATCATCTGGTCTCATGT 1 224 1 CAAATCATCT 0.898677 -77 CTACTTGTTTCTCATTAACTGGATAACTAC 1 275 0 CTCATTAACT 0.9637 -26 ********** Masking position 4 Map Score: 4.99829 Number of sites scoring better than the average of aligned sites = 1089 Number in coding regions = 981 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 3 CTTAATTAAACATTAGCCAGTCCGGGTAAT 1 42 1 CATTAGCCAG 0.986029 -259 GCGATATAACCTTGAGCCACATCAACATTG 1 97 1 CTTGAGCCAC 0.978052 -204 CCACATCAACATTGAGTCAGATTATTATTC 1 113 1 ATTGAGTCAG 0.950637 -188 CCCATGAGGTAGTTATCCAGTTAATGAGAA 1 267 1 AGTTATCCAG 0.911464 -34 AGCTGGACATCCTGAGCCAGGTAGCAGACG 2 11 1 CCTGAGCCAG 0.996578 -122 AGCTGAGTCTACTTGGCCAGCTGCGAAAAT 2 96 0 ACTTGGCCAG 0.978157 -37 ********** Masking position 3 Map Score: 4.86178 Number of sites scoring better than the average of aligned sites = 1135 Number in coding regions = 1079 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 4 GCTGGCGCGGCGGGCATACCGTCTGCTACC 2 30 0 CGGGCATACC 0.998817 -103 GCGCCAGCGGCGGGCATACCGCTGCGGTGG 2 52 1 CGGGCATACC 0.998817 -81 GGTGGGGCGGCGGGCAACCATTTTCGCAGC 2 77 1 CGGGCAACCA 0.993158 -56 ********** Masking position 6 Map Score: 4.22076 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 41 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 5 TATAACCTTGAGCCACATCAACATTGAGTC 1 101 1 AGCCACATCA 0.959744 -200 CGCTGTCAAACGCCCCATGAGGTAGTTATC 1 254 1 CGCCCCATGA 0.992927 -47 GTATGCCCGCCGCGCCAGCGGCGGGCATAC 2 41 1 CGCGCCAGCG 0.988984 -92 GGTTGCCCGCCGCCCCACCGCAGCGGTATG 2 66 0 CGCCCCACCG 0.997704 -67 ********** Masking position 7 Map Score: 1.6149 Number of sites scoring better than the average of aligned sites = 690 Number in coding regions = 617 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 CAATATTTATCATTTCATTAACAACT 1 5 1 ATTTATTTTC 0.96746 -296 GCTAATGTTTAATTAAGGTTTCAGTTGTTAAT 1 27 0 AATTAATTTC 0.983882 -274 CAGTCCGGGTAATTCACTATTCGAATTATATT 1 59 1 AATTCAATTC 0.893131 -242 TCACTATTCGAATTATATTTTCGCTGCGATAT 1 72 1 AATTATTTTC 0.977059 -229 GTTGTTGATTATTTAATCTCTCCTTTGTTGGC 1 203 1 ATTTAATCTC 0.950475 -98 ****** **** Masking position 4 Map Score: 0.210039 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 60 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 ********** No masking Map Score: -2.03625e-13 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: -2.03625e-13 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: -2.03625e-13 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