AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i070_Threonine_Biosynthesis_aquae_reg_300.orf -o070_aquae_300.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 CCCTTTGTTTTTTAGCCTTTCT 4 1 0 TTTAGCTTTT 0.99167 -300 GCTGTTGTATTTTCCCCTTTGTTTTTTAGCCT 4 15 0 TTTCCCTTTT 0.892825 -286 ACAGCTCTGTTTTATTGTTTTTGATTAAGTTT 4 42 1 TTTATTTTTT 0.953818 -259 TTGTTTTTGATTAAGTTTTTCCAATTCCTTCT 4 56 1 TTAAGTTTTC 0.872143 -245 GCTTTTGTTGTTTACTTTATATACTGGCTTAT 4 117 0 TTTACTTATT 0.710542 -184 GTCTTATTTATTTAGCTTTTGTTGTTTACTTT 4 131 0 TTTAGCTTTT 0.99167 -170 ATTATTTTGTTTTTGTCTTTATAGTAAGTCTT 4 158 0 TTTTGTTTTT 0.856779 -143 CACCAAACGATCTAGCTTTTTCTGTAGCTGCT 4 198 1 TCTAGCTTTC 0.844963 -103 CCCTTTGTCCTGTATCTTTTATACTTG 5 6 0 TGTATCTTTT 0.873392 -163 TAATAGTCCTTTAACCCTTTGTCCTGTATCTT 5 20 0 TTAACCTTTT 0.956671 -149 TTATGCATTCATAAGTATTTCTTAATAGTCCT 5 42 0 ATAAGTTTTT 0.812979 -127 AATTTACCATTTTATCATTTTTGAAAATTAAG 5 79 0 TTTATCTTTT 0.977647 -90 AGTTTAAGTCTTAAGTCCTTGTCCCCCTTTTA 5 126 1 TTAAGTCTTT 0.774069 -43 AAGAGAATTATCCTTTATTTTTAAAAGG 5 151 0 ATTATCTTTT 0.891389 -18 ****** *** * Masking position 10 Map Score: 14.9572 Number of sites scoring better than the average of aligned sites = 705 Number in coding regions = 646 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 2 CCCCTTTGTTTTTTAGCCTTTCT 4 4 0 TTTTAGCCTT 0.97429 -297 AGCTGTTGTATTTTCCCCTTTGTTTTTTAG 4 18 0 TTTTCCCCTT 0.848731 -283 ATTGTTTTTGATTAAGTTTTTCCAATTCCT 4 55 1 ATTAAGTTTT 0.887859 -246 AGTCTTATTTATTTAGCTTTTGTTGTTTAC 4 134 0 ATTTAGCTTT 0.945051 -167 TTGTCTTTATAGTAAGTCTTATTTATTTAG 4 148 0 AGTAAGTCTT 0.826312 -153 CATTATTTTGTTTTTGTCTTTATAGTAAGT 4 161 0 TTTTTGTCTT 0.886495 -140 TCACCAAACGATCTAGCTTTTTCTGTAGCT 4 197 1 ATCTAGCTTT 0.730648 -104 CCCTTTGTCCTGTATCTTTTATACTTG 5 8 0 TGTATCTTTT 0.48781 -161 TTAATAGTCCTTTAACCCTTTGTCCTGTAT 5 23 0 TTTAACCCTT 0.965302 -146 ATTAAGACATTTTATGCATTCATAAGTATT 5 55 0 TTTATGCATT 0.838915 -114 TATATGTTTAATTTACCATTTTATCATTTT 5 90 0 ATTTACCATT 0.825822 -79 TAAAAATTAGTTTAAGTCTTAAGTCCTTGT 5 118 1 TTTAAGTCTT 0.945785 -51 AAGAGAATTATCCTTTATTTTTAAAA 5 153 0 ATTATCCTTT 0.867523 -16 ********** Masking position 9 Map Score: 11.2181 Number of sites scoring better than the average of aligned sites = 1187 Number in coding regions = 1096 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 3 CAACATTTGCCTTACATCAATAAGCCAGTAT 4 98 1 CTTACACAAT 0.932339 -203 TGCTGCCGCAATTATAAAAATCAAGATATAT 4 226 1 ATTATAAAAT 0.907678 -75 GTTATTGTAAATTATAGCAATATATCTTGAT 4 245 0 ATTATACAAT 0.971737 -56 CAAATAAGGTATTTTATAAATGTA 4 287 1 ATTTTAAAAT 0.916485 -14 TTAATTTACCATTTTATCATTTTTGAAAATT 5 82 0 ATTTTACATT 0.854548 -87 GTAAATTAAACATATAAAAATTAGTTTAAGT 5 104 1 CATATAAAAT 0.884505 -65 CCTTGTCCCCCTTTTAAAAATAAAGGATAAT 5 142 1 CTTTTAAAAT 0.928359 -27 ****** **** Masking position 6 Map Score: 4.90694 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 71 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 AAAACAGAGCTGTTGTATTTTCCCCTTTGT 4 25 0 TGTTGTATTT 0.941991 -276 ACAACAGCTCTGTTTTATTGTTTTTGATTA 4 39 1 TGTTTTATTG 0.972612 -262 CTTTATATACTGGCTTATTGATGTAAGGCA 4 105 0 TGGCTTATTG 0.929555 -196 TAGCTTTTGTTGTTTACTTTATATACTGGC 4 121 0 TGTTTACTTT 0.875996 -180 CTTTATAGTAAGTCTTATTTATTTAGCTTT 4 144 0 AGTCTTATTT 0.92973 -157 ATGCATAAAATGTCTTAATTTTCAAAAATG 5 66 1 TGTCTTAATT 0.92973 -103 AATTTTTATATGTTTAATTTACCATTTTAT 5 96 0 TGTTTAATTT 0.958258 -73 ********** Masking position 9 Map Score: 4.49714 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 59 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 AAAAACTATTTTCTCACGTATA 1 15 0 AAACTATTTT 0.732876 -12 TAAACAACAAAAGCTAAATAAATAAGACTT 4 135 1 AAGCTAAATA 0.826165 -166 TATAAAAATCAAGATATATTGCTATAATTT 4 238 1 AAGATATATT 0.891184 -63 AGAATCAAATAAGGTATTTTATAAATGTA 4 282 1 AAGGTATTTT 0.941505 -19 TTTGAAAATTAAGACATTTTATGCATTCAT 5 62 0 AAGACATTTT 0.829606 -107 AAATGATAAAATGGTAAATTAAACATATAA 5 91 1 ATGGTAAATT 0.765414 -78 CTTAAGACTTAAACTAATTTTTATATGTTT 5 111 0 AAACTAATTT 0.853652 -58 ********** Masking position 6 Map Score: 0.991124 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 179 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 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 Motif number 8 ********** 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