AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i103_Ferrous_Iron_Transporter_aful_reg_100.orf -o103_aful_100.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RAG48446 108 Archaeoglobus_fulgidus #2 RAG06372 16 Archaeoglobus_fulgidus #3 RAG06597 204 Archaeoglobus_fulgidus Motif number 1 TTTTTTAATACAGAAAATTAAAGTTATTAA 1 32 0 CAGAAAATTA 0.915001 -77 AGGTTTTGGTCAAAAAATTCAAAACCGATT 1 60 0 CAAAAAATTC 0.982554 -49 AAAGAGTAGCCAGAAAAGAGGTGATTTGTA 3 11 0 CAGAAAAGAG 0.927125 -194 TTAATTACAGGAAAAAAGAGTAGCCAGAAA 3 25 0 GAAAAAAGAG 0.887788 -180 GGAAATAAATCGAAAAGTTCTTAATTACAG 3 45 0 CGAAAAGTTC 0.959633 -160 TGTTATCCTCCGAGAAATTCGGAAATAAAT 3 65 0 CGAGAAATTC 0.920194 -140 CAAAAAATTGCGAAAAAGTGTTATCCTCCG 3 83 0 CGAAAAAGTG 0.984627 -122 CTTTTGGTAACAAAAAATTGCGAAAAAGTG 3 93 0 CAAAAAATTG 0.989119 -112 TTTTTTGTTACCAAAAGTAAATTATATAGC 3 106 1 CCAAAAGTAA 0.766355 -99 CTCCGGAATGGCAAAAATTGTAATGCTATA 3 130 0 GCAAAAATTG 0.942898 -75 ********** Masking position 5 Map Score: 10.9609 Number of sites scoring better than the average of aligned sites = 618 Number in coding regions = 485 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 2 TAATACAGAAAATTAAAGTTATTAACAACT 1 27 0 AATTAAAGTT 0.96218 -82 AACCTAAATTATTTAAAGGTTTTGGTCAAA 1 76 0 ATTTAAAGGT 0.897864 -33 ACCTTTAAATAATTTAGGTTAGCCTAAAAA 1 86 1 AATTTAGGTT 0.97331 -23 TGGTTTTTAGGCTAACCTAAATT 1 96 0 TTTTTAGGCT 0.952469 -13 GGTTGTCCTAAATTAAAGCTCCGGAATGGC 3 148 0 AATTAAAGCT 0.973828 -57 ACCTAAATGTTATTAAAGCTTTCGGTTGTC 3 171 0 TATTAAAGCT 0.952965 -34 GCTTTAATAACATTTAGGTTAACCTAAGAG 3 182 1 CATTTAGGTT 0.976029 -23 CGTCTCTTAGGTTAACCTAAATG 3 192 0 CTCTTAGGTT 0.871361 -13 ********** Masking position 6 Map Score: 8.79162 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 183 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 3 AAATTAAAGTTATTAACAACTTAGCCCTAA 1 18 0 TATTAACAAC 0.885415 -91 TAATTTTCTGTATTAAAAAATCGGTTTTGA 1 42 1 TATTAAAAAA 0.934079 -67 TTGGTCAAAAAATTCAAAACCGATTTTTTA 1 55 0 AATTCAAAAC 0.97877 -54 TGCAATCTTCAAAAAA 2 2 0 TCTTCAAAAA 0.898597 -15 TTTTTCCTGTAATTAAGAACTTTTCGATTT 3 39 1 AATTAAGAAC 0.948762 -166 ATTCGGAAATAAATCGAAAAGTTCTTAATT 3 49 0 AAATCGAAAA 0.842082 -156 TCCTCCGAGAAATTCGGAAATAAATCGAAA 3 60 0 AATTCGGAAA 0.955059 -145 ********** Masking position 8 Map Score: 3.40561 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 154 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 4 ********** No masking Map Score: 1.3033e-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 5 ********** No masking Map Score: 1.3033e-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 6 ********** No masking Map Score: 1.3033e-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