AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i005_Pyrimidine_Biosynthesis_aquae_reg_100.orf -o005_aquae_100.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RAA00099 19 Aquifex_aeolicus Input sequences: #1 RAA01271 17 Aquifex_aeolicus #2 RAA01272 300 Aquifex_aeolicus #3 RAA01579 17 Aquifex_aeolicus #4 RAA01580 66 Aquifex_aeolicus #5 RAA00098 128 Aquifex_aeolicus #6 RAA00102 23 Aquifex_aeolicus #7 RAA00105 46 Aquifex_aeolicus #8 RAA01637 35 Aquifex_aeolicus Motif number 1 TGAGAGTTCTGTTTCTAATGTACCGTGTGGAG 2 20 1 GTTTCTATTA 0.988477 -281 AATGGAAGAAGTTTTAACTCCACACGGTACAT 2 37 0 GTTTTAATCA 0.98767 -264 GTTGATTATTGTTTCTAATGTACCGTGTGGAG 2 87 1 GTTTCTATTA 0.988477 -214 TCTCAAACCTGTTTTAACTCCACACGGTACAT 2 104 0 GTTTTAATCA 0.98767 -197 GCTTGACGAAGTTTCTAATGTACCGTGTGGAG 2 152 1 GTTTCTATTA 0.988477 -149 TCAAAACCTTGTTTTAACTCCACACGGTACAT 2 169 0 GTTTTAATCA 0.98767 -132 GTTGCAGATGGTTTCTAATGTACCGTGTGGAG 2 217 1 GTTTCTATTA 0.988477 -84 TACAATCTGCGTTTTAACTCCACACGGTACAT 2 234 0 GTTTTAATCA 0.98767 -67 GCATATTAGAGTTTTTATTTTAATTTCTTTTT 2 265 0 GTTTTTATTA 0.989216 -36 AGCCCCTCCTGTTTAAAATGTAGTTCTCTATT 4 42 0 GTTTAAATTA 0.982047 -25 TTAAAACAACGGTTTAAGTGTATATAACGTCC 5 33 0 GGTTTAATTA 0.950133 -96 TTAAACCGTTGTTTTAATTTTGAGCTTCCTCA 5 48 1 GTTTTAATTG 0.9463 -81 AACTTTTTAAGCTTAAATTATATCTTTAGGTA 5 82 1 GCTTAAATTA 0.896131 -47 TCACCTCACTGTTTATACTATATACTTTAA 8 16 1 GTTTATATTA 0.97649 -20 ******* * ** Masking position 7 Map Score: 38.0796 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 35 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 2 TTTCTAATGTACCGTGTGGAGTTAAAACTTC 2 31 1 ACCGTGTGGG 0.999721 -270 TTTCTAATGTACCGTGTGGAGTTAAAACAGG 2 98 1 ACCGTGTGGG 0.999721 -203 TTTCTAATGTACCGTGTGGAGTTAAAACAAG 2 163 1 ACCGTGTGGG 0.999721 -138 TTTCTAATGTACCGTGTGGAGTTAAAACGCA 2 228 1 ACCGTGTGGG 0.999721 -73 TATAGTATAAACAGTGAGGTGAAGGAA 8 7 0 ACAGTGAGGG 0.995235 -29 ********* * Masking position 5 Map Score: 20.0556 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 2 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 3 CGGTTCTTCTGAGAGTTCTGTTTCTAATG 2 6 1 CTCAGAGTTT 0.988101 -295 CATTTCACAAAATCAAAGAGTTGTTGATTATTGT 2 65 1 ATCAGAGTTT 0.934874 -236 CCTCAAAAGTCCTCTCAAACCTGTTTTAACTCCA 2 114 0 CTCAAACCTT 0.982761 -187 ACATTAGAAACTTCGTCAAGCTTTACCTCAAAAG 2 139 0 CTCCAAGCTT 0.965357 -162 TCAAGTTCAGCTTCAAAACCTTGTTTTAACTCCA 2 179 0 CTCAACCTTT 0.960509 -122 CATTAGAAACCATCTGCAACATATTCAAGTTCAG 2 203 0 CTCCAACATT 0.910843 -98 CAGTTTTCCGCATATTAGAGTTTTTATTTTAATT 2 272 0 CTAAGAGTTT 0.878859 -29 TATTTAAAATATTCACTAACTTATAATTATTACC 4 12 0 ATCTAACTTT 0.783224 -55 TTTTGAGCTTCCTCATAAACTTTTTAAGCTTAAA 5 65 1 CTCAAACTTT 0.991499 -64 ATCAACACCTCCTTAAAGTTTTT 6 2 0 CCCAAAGTTT 0.960509 -22 * ** ****** * Masking position 12 Map Score: 9.57919 Number of sites scoring better than the average of aligned sites = 498 Number in coding regions = 464 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 TTAAAACAGGTTTGAGAGGACTTTTGAGGT 2 119 1 TTTGAGAGGA 0.818177 -182 TGAGAGGACTTTTGAGGTAAAGCTTGACGA 2 131 1 TTTGAGGTAA 0.934481 -170 TAACGTCCAATTTAAGGTCGTAAAGATCCC 5 11 0 TTTAAGGTCG 0.936906 -118 TTAAAAAGTTTATGAGGAAGCTCAAAATTA 5 62 0 TATGAGGAAG 0.939591 -67 AACAAATTCTTTTGTGGAGGTTGTAC 5 113 1 TTTGTGGAGG 0.960718 -16 AAAAACTTTAAGGAGGTGTTGAT 6 7 1 TTTAAGGAGG 0.98277 -17 TATACTTTTCTTTAAGGGAGGTGAAGT 7 30 1 TTTAAGGGAG 0.975098 -17 ********** Masking position 3 Map Score: 3.93227 Number of sites scoring better than the average of aligned sites = 486 Number in coding regions = 431 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 5 TTTAGCCCCTCCTGTTTAAAAT 4 55 0 TAGCCCCTCC 0.96656 -12 TTTAAGTGTATATAACGTCCAATTTAAGGT 5 23 0 TATAACGTCC 0.912595 -106 GTACAACCTCCACAAAAGAAT 5 118 0 TACAACCTCC 0.963913 -11 ATCAACACCTCCTTAAAGTTTT 6 12 0 CAACACCTCC 0.988217 -12 ACTTCACCTCCCTTAAAGAAA 7 36 0 CTTCACCTCC 0.991272 -11 TTCCTTCACCTCACTGTTTATAC 8 4 1 CTTCACCTCA 0.94615 -32 ********** Masking position 8 Map Score: 3.27772 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 263 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 6 CAACTCTTTGATTTTGTGAAATGGAAGAAG 2 58 0 ATTTTGTGAA 0.926035 -243 AGTTAAAACAAGGTTTTGAAGCTGAACTTG 2 182 1 AGGTTTTGAA 0.950899 -119 GTTAAAACGCAGATTGTAAAAAGAAATTAA 2 248 1 AGATTGTAAA 0.942676 -53 AATAATTATAAGTTAGTGAATATTTTAAAT 4 15 1 AGTTAGTGAA 0.962767 -52 GTCCAATTTAAGGTCGTAAAGATCCC 5 7 0 AGGTCGTAAA 0.963384 -122 ********** Masking position 4 Map Score: 0.0967669 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 232 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 ********** No masking Map Score: -9.28379e-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: -9.28379e-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: -9.28379e-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