AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i102_Ferric_Transport_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 fecB 38 citrate-dependent iron transport, periplasmic protein #2 fecA 86 outer membrane receptor; citrate-dependent iron transport, outer membrane receptor #3 fecI 291 probable RNA polymerase sigma factor Motif number 1 AACAAAAATGATGATGGGGAAGGT 2 73 1 ATGATGGGGA 0.99844 -14 GATTTAGTGTATGATGGTGATTTTAAGGTG 3 16 0 ATGATGGTGA 0.993829 -276 ACTGCCCTAAAGGATGGGGATTTCGGTAAT 3 60 0 AGGATGGGGA 0.997343 -232 AGAATGACTCATGATGTGGTCTGCTATTAT 3 100 0 ATGATGTGGT 0.984551 -192 ********** Masking position 5 Map Score: 7.13905 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 17 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 2 CTTATTTCGATTGTCCTTTTTACCCTTCTCGTTC 2 22 1 TTGCCTTACC 0.991765 -65 AATCAGTAAGTTGGCAGCATTACCGAAATCCCCA 3 42 1 TTGCAGTACC 0.991765 -250 TCTGCTATTATTGACATCCTCACTGCCCTAAAGG 3 77 0 TTGCATTACT 0.983754 -215 ACCACATCATGAGTCATTCTGACCGACACATGCC 3 110 1 GAGCATTACC 0.989304 -182 TTGTTTCCAATAGACATTTTTAACATGTTGTTTT 3 192 0 TAGCATTAAC 0.978948 -100 TTATTTCCAATTGTAATGATAACCATTCTCATAT 3 228 1 TTGAATTACC 0.980684 -64 AATTATCACGTAGTCATATTAATATGAGAATGGT 3 249 0 TAGCATTATA 0.877922 -43 *** *** * *** Masking position 12 Map Score: 4.87722 Number of sites scoring better than the average of aligned sites = 500 Number in coding regions = 456 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 3 TACCTTATAACACTTAGAAAAACAACATGT 3 174 1 CACTTAGAAA 0.976721 -118 TTAAAAATGTCTATTGGAAACAATTTTATT 3 203 1 CTATTGGAAA 0.987214 -89 GTTATCATTACAATTGGAAATAAAATTGTT 3 221 0 CAATTGGAAA 0.992709 -71 ********** Masking position 8 Map Score: 1.1008 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 1 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 4 TGTGTTAACGCCCGGCTTGCCGGGCT 1 7 1 AACGCCCGGC 0.997984 -32 ATTCCAGCTAAAAGCCCGGCAAGCCGGGCG 1 19 0 AAAGCCCGGC 0.99843 -20 ********** Masking position 2 Map Score: 1.09855 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 23 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 GGACAATCGAAATAAGAATTATTTTCC 2 8 0 AATAAGAATT 0.862485 -79 CTATGAGTCGAACGAGAAGGGTAAAAAGGA 2 35 0 AACGAGAAGG 0.958527 -52 AGCTGAACACAACAAAAATGATGATGGGGA 2 63 1 AACAAAAATG 0.955328 -24 ATAAGGTAGGTATAAAATGGGATGGAGCCT 3 152 0 TATAAAATGG 0.860004 -140 TACAATTGGAAATAAAATTGTTTCCAATAG 3 213 0 AATAAAATTG 0.932548 -79 GTCATATTAATATGAGAATGGTTATCATTA 3 241 0 TATGAGAATG 0.94743 -51 ********** Masking position 5 Map Score: 0.682866 Number of sites scoring better than the average of aligned sites = 506 Number in coding regions = 377 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 6 GAGAAGGGTAAAAAGGACAATCGAAATAAG 2 22 0 AAAAGGACAA 0.94623 -65 TAGGGCAGTGAGGATGTCAATAATAGCAGA 3 81 1 AGGATGTCAA 0.926165 -211 TGTGTCGGTCAGAATGACTCATGATGTGGT 3 110 0 AGAATGACTC 0.935853 -182 CAACATGTTAAAAATGTCTATTGGAAACAA 3 196 1 AAAATGTCTA 0.962676 -96 TAGTCATATTAATATGAGAATGGTTATCAT 3 243 0 AATATGAGAA 0.885074 -49 TTCTCATATTAATATGACTACGTGATAATT 3 253 1 AATATGACTA 0.971088 -39 ********** Masking position 4 Map Score: 1.29023 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 202 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 7 ********** No masking Map Score: -3.17312e-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: -3.17312e-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: -3.17312e-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