AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -ifis_aful_opreg_300.orf -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 AF0421 25 A. fulgidus predicted coding region AF0421 #2 AF0422 138 uroporphyrin-III C-methyltransferase (cysG-1) #3 AF1485 87 queuine tRNA-ribosyltransferase (tgtB) #4 AF1664 147 ribonucleotide reductase (nrd) Motif number 1 CTGTTTTTTCTTAACCTCAGGTCA 1 12 0 TTTTTCTTAA 0.930399 -14 AATTTCGAAATTTGCGCTTTCTGGTTTAAGC 2 62 1 TTTGGCTTTC 0.925143 -77 CGCTTTCTGGTTTAAGCTTACCTAAAAATAT 2 76 1 TTTAGCTTAC 0.941777 -63 CGAGAAGTTTTTTAACCTTCCCACAACTCCC 2 114 1 TTTACCTTCC 0.98194 -25 TCACAAAATCTTTTATTTTCAAATAGCAACA 3 18 0 TTTTTTTTCA 0.840474 -70 CTTAAAAGATTATTCCCTTTCGGTGACCTCA 3 46 0 TATTCCTTTC 0.889471 -42 GGAATAATCTTTTAAGTTTTCTGTCAATTTA 3 61 1 TTTAGTTTTC 0.764479 -27 GAATAGAAAAATTTTTCTTACAGCATCTCAA 4 57 0 ATTTTCTTAC 0.827599 -91 TAAGAAAAATTTTTCTATTCAATTTTTCCTT 4 68 1 TTTTTATTCA 0.749236 -80 TTCTATTCAATTTTTCCTTCAATAGATGCTC 4 80 1 TTTTCCTTCA 0.977792 -68 GATAAAACAATTTTGCCTGCCCTTCGAGAGC 4 107 0 TTTTCCTGCC 0.959073 -41 GGCAAAATTGTTTTATCTTTCTTATCTACCA 4 121 1 TTTTTCTTTC 0.981807 -27 **** ****** Masking position 8 Map Score: 12.134 Number of sites scoring better than the average of aligned sites = 1155 Number in coding regions = 1002 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 2 CGCAAATTTCGAAATTCTTATATATTGCCTAA 2 46 0 GAAATTTATA 0.948992 -93 TCTGCAATCGAGAAGTTTTTTAACCTTCCCAC 2 106 1 AGAATTTTTA 0.966935 -33 GGTGACCTCACAAAATCTTTTATTTTCAAATA 3 24 0 CAAATTTTTA 0.962533 -64 ACCGAAAGGGAATAATCTTTTAAGTTTTCTGT 3 53 1 AATATTTTTA 0.946754 -35 TGTCTTCTTGAAAAGTATTAAAGTTAATGTCA 4 18 1 AAAATTTAAA 0.913564 -130 TGCTGTAAGAAAAATTTTTCTATTCAATTTTT 4 63 1 AAAATTTCTA 0.97717 -85 AAGGGCAGGCAAAATTGTTTTATCTTTCTTAT 4 114 1 AAAATTTTTA 0.989176 -34 **** * ***** Masking position 4 Map Score: 6.20873 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 39 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 3 CAAGTCCCCCTCTTTTTAGGCAATATATAA 2 31 1 TCTTTTTAGG 0.985081 -108 CGATTGCAGATATTTTTAGGTAAGCTTAAA 2 86 0 TATTTTTAGG 0.911842 -53 AAGGGAATAATCTTTTAAGTTTTCTGTCAA 3 58 1 TCTTTTAAGT 0.943737 -30 AAGTTTTCTGTCAATTTAGTTCGA 3 74 1 TCAATTTAGT 0.912953 -14 GAAAAATTTTTCTATTCAATTTTTCCTTCA 4 71 1 TCTATTCAAT 0.893937 -77 TTCGAGAGCATCTATTGAAGGAAAAATTGA 4 86 0 TCTATTGAAG 0.929839 -62 ********** Masking position 5 Map Score: 2.28136 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 115 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 CCTAAAAAGAGGGGGACTTGCAATTACAGG 2 21 0 GGGGGACTTG 0.998271 -118 AAGGGGGAGTTGTGGGAAGGTT 2 127 0 GGGGGAGTTG 0.998278 -12 ********** Masking position 6 Map Score: 0.852606 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 12 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 ********** No masking Map Score: 2.36911e-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: 2.36911e-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 7 ********** No masking Map Score: 2.36911e-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