AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i070_Threonine_Biosynthesis_aquae_reg_100.orf -o070_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 Input sequences: #1 RAA01286 26 Aquifex_aeolicus #2 RAA01288 17 Aquifex_aeolicus #3 RAA01290 30 Aquifex_aeolicus #4 RAA00243 300 Aquifex_aeolicus #5 RAA00732 168 Aquifex_aeolicus Motif number 1 GCTGTTGTATTTTCCCCTTTGTTTTTTAGCCTTTCT 4 9 0 TTTTTTTTTA 0.988645 -292 ACAGCTCTGTTTTATTGTTTTTGATTAAGTTTTTCCAA 4 42 1 TTTTTTTTAA 0.960294 -259 TGATTAAGTTTTTCCAATTCCTTCTTTATATCGTGCAA 4 63 1 TTTTTTTTTA 0.988604 -238 TTGTTTACTTTATATACTGGCTTATTGATGTAAGGCAA 4 104 0 TATTGTTTGA 0.915778 -197 GTCTTATTTATTTAGCTTTTGTTGTTTACTTTATATAC 4 125 0 TTTTTTTTTA 0.988643 -176 TTTTTGTCTTTATAGTAAGTCTTATTTATTTAGCTTTT 4 143 0 TATAGTTTTA 0.920119 -158 ATTATAGCAATATATCTTGATTTTTATAATTGCGGCAG 4 228 0 TATTGTTATA 0.831283 -73 CCTTTAACCCTTTGTCCTGTATCTTTTATACTTG 5 7 0 TTTTGTTTTA 0.991513 -162 TTCATAAGTATTTCTTAATAGTCCTTTAACCCTTTGTC 5 29 0 TTTATTTTTA 0.955728 -140 TTAAACTAATTTTTATATGTTTAATTTACCATTTTATC 5 95 0 TTTTGTTTTA 0.991503 -74 AAGAGAATTATCCTTTATTTTTAAAAGGGGGACA 5 145 0 ATTTTTTTAA 0.754608 -24 *** ** * **** Masking position 18 Map Score: 14.9805 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 124 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 2 AGAAAGGCTAAAAAACAAAGGGGAAAATACAACAGC 4 10 1 AAAAAAAAAA 0.991638 -291 TGGAAAAACTTAATCAAAAACAATAAAACAGAGCTGT 4 42 0 TAAAAAAAAA 0.986653 -259 TGCACGATATAAAGAAGGAATTGGAAAAACTTAATCA 4 63 0 AAAAGAAAAA 0.965166 -238 TATATAAAGTAAACAACAAAAGCTAAATAAATAAGAC 4 126 1 AAAAAAAAAA 0.991638 -175 AGACTTACTATAAAGACAAAAACAAAATAATGAGTGC 4 159 1 TAAAAAAAAA 0.986653 -142 GCTGCTGCCGCAATTATAAAAATCAAGATATATTGCT 4 224 1 CAAAAAAAAG 0.92011 -77 CAAGTATAAAAGATACAGGACAAAGGGTTAAAGG 5 8 1 AAAAACAAAA 0.983041 -161 ATAAAATGGTAAATTAAACATATAAAAATTAGTTTAA 5 96 1 AAAAACAAAA 0.983041 -73 GTCCCCCTTTTAAAAATAAAGGATAATTCTCTT 5 146 1 TAAAAAAAAT 0.929813 -23 *** * *** *** Masking position 10 Map Score: 12.0712 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 168 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 3 GTCTTTATAGTAAGTCTTATTTATTTAGCT 4 146 0 TAAGTCTTAT 0.90109 -155 CAATATATCTTGATTTTTATAATTGCGGCA 4 229 0 TGATTTTTAT 0.82044 -72 TATATTGCTATAATTTACAATAACCATTAT 4 252 1 TAATTTACAA 0.849992 -49 TCAAATAAGGTATTTTATAAATGTA 4 286 1 TATTTTATAA 0.688696 -15 CATTCATAAGTATTTCTTAATAGTCCTTTA 5 39 0 TATTTCTTAA 0.896078 -130 TAAAATGTCTTAATTTTCAAAAATGATAAA 5 71 1 TAATTTTCAA 0.953239 -98 AGACTTAAACTAATTTTTATATGTTTAATT 5 107 0 TAATTTTTAT 0.951353 -62 AAAATTAGTTTAAGTCTTAAGTCCTTGTCC 5 120 1 TAAGTCTTAA 0.930252 -49 GAATTATCCTTTATTTTTAAAAGGGGGACA 5 145 0 TTATTTTTAA 0.818568 -24 AAATAAAGGATAATTCTCTT 5 159 1 TAATTCTCTT 0.67976 -10 ********** Masking position 5 Map Score: 6.63584 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 145 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 CAAAGGGGAAAATACAACAGCTCTGTTTTA 4 26 1 AATACAACAG 0.809998 -275 AATCAAAAACAATAAAACAGAGCTGTTGTA 4 38 0 AATAAAACAG 0.953362 -263 GCCTTACATCAATAAGCCAGTATATAAAGT 4 106 1 AATAAGCCAG 0.972537 -195 AAGCTAAATAAATAAGACTTACTATAAAGA 4 145 1 AATAAGACTT 0.887868 -156 AAGACTTACTATAAAGACAAAAACAAAATA 4 158 1 ATAAAGACAA 0.636023 -143 GCAGCTACAGAAAAAGCTAGATCGTTTGGT 4 199 0 AAAAAGCTAG 0.659682 -102 TATAGAATCAAATAAGGTATTTTATAAATG 4 279 1 AATAAGGTAT 0.746395 -22 TTAAAGGACTATTAAGAAATACTTATGAAT 5 38 1 ATTAAGAAAT 0.739881 -131 ATTTTTGAAAATTAAGACATTTTATGCATT 5 65 0 ATTAAGACAT 0.962233 -104 TAAAATGGTAAATTAAACATATAAAAATTA 5 97 1 AATTAAACAT 0.690799 -72 ********** Masking position 1 Map Score: 2.53739 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 275 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 ********** No masking Map Score: 4.99812e-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: 4.99812e-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: 4.99812e-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