AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i061_Glutamate_Synthase_pyro_reg_100.orf -o061_pyro_100.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 = 0.42 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RPH00254 247 Pyrococcus_OT3 #2 RPH01722 125 Pyrococcus_OT3 Motif number 1 AAAATGTCTAAAAATATTGGTAAGCACTTCT 1 25 0 AAAATATGGT 0.980545 -223 GATAGGTTGAAAACTTTTGGTTTTAAAAATG 1 50 0 AAACTTTGGT 0.990967 -198 AGAGGGTTTTAAACTAATGGTTTTAAAAACC 1 162 1 AAACTATGGT 0.987316 -86 TTTGTTCATTAAAATAATTTTATCCGTTATA 1 217 0 AAAATATTTT 0.498418 -31 AACTTATTGTAAACTATTGGTTGGATAATAA 2 37 0 AAACTATGGT 0.992656 -89 TTGTTTTTATAAACTTATTGTAAACTATTGG 2 48 0 AAACTTTTGT 0.965565 -78 CTAGGTTCTGAACATTTTGTTTTTATAAACT 2 64 0 AACATTTGTT 0.681164 -62 AAATGTTCAGAACCTAGTGTAATGTCCAAAA 2 78 1 AACCTATGTA 0.869962 -48 CGAGTTCGTGAACATTTTTGGACATTACACT 2 93 0 AACATTTTGG 0.803789 -33 ****** **** Masking position 5 Map Score: 13.8685 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 147 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 2 TTTTAGACATTTTTAAAACCAAAAGTTTTC 1 43 1 TTTTAAAACC 0.989558 -205 AAAACCAAAAGTTTTCAACCTATCCCCTTA 1 57 1 GTTTTCAACC 0.945884 -191 AAAACCATTAGTTTAAAACCCTCTAAAAGG 1 156 0 GTTTAAAACC 0.984218 -92 TTATAGCGGTTTTTAAAACCATTAGTTTAA 1 170 0 TTTTAAAACC 0.989558 -78 GTGTACCACCTTTGTTCATT 1 238 0 GTGTACCACC 0.947397 -10 CTTTTATTTATTATCCAACCAATAGTTTAC 2 30 1 TTATCCAACC 0.939933 -96 TACAATAAGTTTATAAAAACAAAATGTTCA 2 57 1 TTATAAAAAC 0.824493 -69 AAAACAAAATGTTCAGAACCTAGTGTAATG 2 72 1 GTTCAGAACC 0.947821 -54 ********** Masking position 8 Map Score: 9.83495 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 134 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 3 AATATTGGTAAGCACTTCTTAATGGTGAAGC 1 13 0 AGCATTCTTA 0.966198 -235 CAATATTTTTAGACATTTTTAAAACCAAAAG 1 37 1 AGACTTTTTA 0.963466 -211 TTTTAAAACCAAAAGTTTTCAACCTATCCCC 1 53 1 AAAATTTTCA 0.796858 -195 ATGTTGTCGGAGCATTTTCTACTCTACTCCA 1 99 1 AGCATTTCTA 0.966199 -149 AAGGAAAGGAAGCGTTTTTCATGCTTATCCT 1 129 0 AGCGTTTTCA 0.989927 -119 CTTTCCTTTTAGAGGGTTTTAAACTAATGGT 1 152 1 AGAGGTTTTA 0.956064 -96 CAGGGTTTATAGCGGTTTTTAAAACCATTAG 1 175 0 AGCGTTTTTA 0.993201 -73 **** ****** Masking position 1 Map Score: 5.58589 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 131 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 4 TTCCCTTTTGGGATAAGGGGATAGGTTGAA 1 70 0 GGATAAGGGG 0.986541 -178 TATAGGCCTGGAATTCAGGGTTTATAGCGG 1 191 0 GAATTCAGGG 0.985486 -57 TTATTTTAATGAACAAAGGTGGTACAC 1 231 1 GAACAAAGGT 0.861761 -17 ATAAATAAAAGGATGCGAGGAGTGTATCGA 2 11 0 GGATGCGAGG 0.963767 -115 AAATGTTCACGAACTCGGGGGTGTTCATT 2 107 1 GAACTCGGGG 0.99398 -19 ********** Masking position 3 Map Score: 1.46905 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 143 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 AGTTTTCAACCTATCCCCTTATCCCAAAAG 1 66 1 CTATCCCCTT 0.981736 -182 GCTCCGACAACATTCCCTTTTGGGATAAGG 1 82 0 CATTCCCTTT 0.98112 -166 AAAACGCTTCCTTTCCTTTTAGAGGGTTTT 1 142 1 CTTTCCTTTT 0.9834 -106 TACACTCCTCGCATCCTTTTATTTATTATC 2 15 1 GCATCCTTTT 0.948913 -111 ********** Masking position 4 Map Score: 0.284999 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 288 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 AGGATAAGCATGAAAAACGCTTCCTTTCCT 1 129 1 TGAAAAACGC 0.981675 -119 ACCATTAGTTTAAAACCCTCTAAAAGGAAA 1 153 0 TAAAACCCTC 0.96731 -95 CTAATGGTTTTAAAAACCGCTATAAACCCT 1 175 1 TAAAAACCGC 0.992785 -73 AATGAACACCCCCGAGTTCGTG 2 114 0 TGAACACCCC 0.985473 -12 ********** Masking position 4 Map Score: 1.24569 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 34 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 ********** No masking Map Score: 3.93231e-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: 3.93231e-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: 3.93231e-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