AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i296_mixed11_pyro_reg_300.orf -o296_pyro_300.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 RPH00798 50 Pyrococcus_OT3 #2 RPH00797 116 Pyrococcus_OT3 #3 RPH01183 186 Pyrococcus_OT3 #4 RPH01184 211 Pyrococcus_OT3 Motif number 1 TTTTCATCACTGGAGAAATTA 1 40 0 TTTTCACACT 0.851785 -11 GTATCAACCCCCACTCCCAGT 2 1 1 GTATCACCCC 0.829883 -116 TAGTATGGATATTTTATCCCGTAAGGAACTT 2 47 0 ATTTTACCCG 0.881583 -70 TTTTCTCACCCCTGGGATTCTAT 2 104 0 TTCTCACCCT 0.98626 -13 AGAACTTAAGGTTTAATCCCTATAGAATGCT 3 41 0 GTTTAACCCT 0.966367 -146 GGTTGATGTTTGTAAAGCCCTCTTAAAAGGA 3 148 0 TGTAAACCCT 0.781886 -39 GATGCTCCCCCCGGTCTGGGTTG 3 174 0 TGCTCCCCCG 0.917737 -13 TGAGCATCATGGTTAATCCTGTTCATTAATG 4 23 0 GGTTAACCTG 0.849326 -189 TTAACCATGATGCTCATCCCTGATCCTCGAT 4 38 1 TGCTCACCCT 0.981381 -174 TAAAAACGCTTTTTTATCCTGGACTTTAACT 4 73 0 TTTTTACCTG 0.84207 -139 AAAAAAGCGTTTTTAAACCCGAAAATTGAAA 4 89 1 TTTTAACCCG 0.984016 -123 AAAAAAAGAGTTCTCAACCTTTGGTTTTCAA 4 114 0 TTCTCACCTT 0.9346 -98 TGATAAATATATTTAAGCCCCGCACCTTGAC 4 172 1 ATTTAACCCC 0.878363 -40 ****** **** Masking position 8 Map Score: 13.2836 Number of sites scoring better than the average of aligned sites = 873 Number in coding regions = 771 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 2 TGCTAGTATGGATATTTTATCCCGTAAGGAAC 2 49 0 GATTTTATCC 0.821431 -68 TCTCACCCCTGGGATTCTATTCTATGAAACAA 2 92 0 GGTTCTATTC 0.977205 -25 ATGCTTTCCTGGGCTTTTCTTTGTTGTATTAC 3 14 0 GGTTTTCTTT 0.977652 -173 GTGAAGATAGGGCGTTTACCTTTGAAATTATT 3 88 0 GGTTTACCTT 0.939177 -99 CCTCTTAAAAGGATTTTTATTTAACAGTATGA 3 129 0 GGTTTTATTT 0.987217 -58 TTTTTATCCTGGACTTTAACTCGTTATCGAGG 4 62 0 GGTTTAACTC 0.963688 -150 CTCAACCTTTGGTTTTCAATTTTCGGGTTTAA 4 101 0 GGTTCAATTT 0.964621 -111 CCCGCACCTTGACCTTTTATTTGGTGAAAAGT 4 190 1 GATTTTATTT 0.946439 -22 ** ******** Masking position 6 Map Score: 6.36376 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 177 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 3 ATGAAGGAAGTTAAAAAGATAAGGG 1 6 0 TTAAAAAGAT 0.964517 -45 TTGATAATAATTTCAAAGGTAAACGCCCTA 3 83 1 TTTCAAAGGT 0.949979 -104 TAAAGCCCTCTTAAAAGGATTTTTATTTAA 3 137 0 TTAAAAGGAT 0.908584 -50 TAAGAGGGCTTTACAAACATCAACCCAGAC 3 154 1 TTACAAACAT 0.957155 -33 ATTTTCGGGTTTAAAAACGCTTTTTTATCC 4 85 0 TTAAAAACGC 0.907105 -127 GAACTCTTTTTTTCAAAGACCAAGCTTTGA 4 132 1 TTTCAAAGAC 0.949979 -80 ********** Masking position 5 Map Score: 2.37988 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 135 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 4 TACTAGCAACTCTTAAATATTGTTTCATAG 2 73 1 TCTTAAATAT 0.836739 -44 TCTGCATTTTTGATAATAATTTCAAAGGTA 3 74 1 TGATAATAAT 0.846971 -113 TTTAACAGTATGACCAATATATGTGAAGAT 3 112 0 TGACCAATAT 0.898531 -75 TTGGTCATACTGTTAAATAAAAATCCTTTT 3 125 1 TGTTAAATAA 0.920609 -62 TGGTTAATCCTGTTCATTAATGGAGGTGAT 4 15 0 TGTTCATTAA 0.880726 -197 GACCAAGCTTTGATGATTATATATGATAAA 4 149 1 TGATGATTAT 0.923134 -63 TGATTATATATGATAAATATATTTAAGCCC 4 162 1 TGATAAATAT 0.971997 -50 ********** Masking position 6 Map Score: 1.12325 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 157 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 TTTAACTTCCTTCATTGGATAATTTCTCCA 1 21 1 TTCATTGGAT 0.976777 -30 ACTTAACAAATTCATTGGAACTGGGAGTGG 2 21 0 TTCATTGGAA 0.907851 -96 TAAATATTGTTTCATAGAATAGAATCCCAG 2 86 1 TTCATAGAAT 0.934476 -31 TGATAATAATTTCAAAGGTAAACGCCCTAT 3 84 1 TTCAAAGGTA 0.913004 -103 TAAAGCCCTCTTAAAAGGATTTTTATTTAA 3 137 0 TTAAAAGGAT 0.908887 -50 ********** Masking position 4 Map Score: 1.74331 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 249 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 6 ********** No masking Map Score: 7.69818e-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: 7.69818e-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: 7.69818e-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