AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i210_trans4_aquae_reg_100.orf -o210_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: RAA01489 30 Aquifex_aeolicus Input sequences: #1 RAA00853 79 Aquifex_aeolicus #2 RAA00925 58 Aquifex_aeolicus #3 RAA00927 105 Aquifex_aeolicus #4 RAA00958 300 Aquifex_aeolicus #5 RAA01180 38 Aquifex_aeolicus #6 RAA01137 30 Aquifex_aeolicus Motif number 1 AACAACTTATGAGTTTTCCACAATTCTCCAC 4 11 0 GAGTTTCCAC 0.975807 -290 GAAAACTCATAAGTTGTTCATATAACGACAC 4 24 1 AAGTTTTCAT 0.987044 -277 ATAACTTAAGAAGTTTTCCACATTTATCCAC 4 104 0 AAGTTTCCAC 0.994856 -197 AAAACTTCTTAAGTTATTCATACTACGAAAC 4 118 1 AAGTTTTCAT 0.987044 -183 TGAACAACTTAAGTTATTTATAATTCGTAAG 4 166 0 AAGTTTTTAT 0.869382 -135 TAAATAACTTAAGTTGTTCATGTGGAAAAGT 4 177 1 AAGTTTTCAT 0.987044 -124 AACTTTCCACAACTTTTCCACATGAACAACT 4 188 0 AACTTTCCAC 0.969707 -113 TTTTCCCGAAAAACTTTCCACAACTTTTCCA 4 199 0 AAACTTCCAC 0.942448 -102 ATTGATTTTCAAGCTTTTCCCGAAAAACTTT 4 213 0 AAGCTTTCCC 0.941204 -88 ATGGGTTTTGAAATTTGTCACATGAAAATAG 4 242 1 AAATTGTCAC 0.879966 -59 ***** ***** Masking position 5 Map Score: 16.0518 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 320 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 2 TTCAAGAATAAGGAGTGGAAG 1 2 0 AGGAGTGGAA 0.952239 -78 GTGGAGAATTGTGGAAAACTCATAAG 4 7 1 AATTGTGGAA 0.988897 -294 CTTACGTTAAAAATGTGGATAAATGTGGAA 4 90 1 AAATGTGGAT 0.969218 -211 AAATGTGGATAAATGTGGAAAACTTCTTAA 4 100 1 AAATGTGGAA 0.992226 -201 CTTAAGTTGTTCATGTGGAAAAGTTGTGGA 4 184 1 TCATGTGGAA 0.948637 -117 CATGTGGAAAAGTTGTGGAAAGTTTTTCGG 4 195 1 AGTTGTGGAA 0.989707 -106 ********** Masking position 6 Map Score: 7.82214 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 47 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 3 ACATGTATGAAAAGAAATTACATTCAAGAATA 1 22 0 AAAAAATTCA 0.886745 -58 TGTTTAGACGACATGAATACTAGGATAAAATA 1 51 1 ACAGAATATA 0.948542 -29 AGAATTGAGCAAATAAATATTATAAGGAATTT 2 11 0 AAAAAATATA 0.973864 -48 AAAGAAATAATAACCATCGAGG 3 1 1 AAAAAATATA 0.974206 -105 CAATCTACTCAAAAGAAAACCACGGTGTATAA 4 54 1 AAAGAAAACA 0.925479 -247 TTTTGTATTAATAAGAATAATAATAGGCGGCT 4 271 0 ATAGAATATA 0.92558 -30 AAGAAAGAAAATTTAAACCATTTCG 5 4 1 AAAAAAATTA 0.835031 -35 ACCTCCTAAAAGGTATATTATATGCTTCAA 6 11 0 AAAGTATATA 0.91477 -20 *** ***** ** Masking position 7 Map Score: 4.14239 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 83 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 4 ACCTCCGTCTTTTCTTAGAATTGAGCAAAT 2 29 0 TTTCTTAGAA 0.933753 -30 GAGTAGATTGTGTCGTTATATGAACAACTT 4 34 0 TGTCGTTATA 0.922991 -267 TATAAACTACTTACGTTAAAAATGTGGATA 4 81 1 TTACGTTAAA 0.935289 -220 CACCGGATTGTTTCGTAGTATGAATAACTT 4 128 0 TTTCGTAGTA 0.957196 -173 AACAATCCGGTGACTTAAAACTTACGAATT 4 146 1 TGACTTAAAA 0.883128 -155 ATTTAAACCATTTCGTAAAATAATCCTT 5 21 1 TTTCGTAAAA 0.980275 -18 ********** Masking position 6 Map Score: 2.20916 Number of sites scoring better than the average of aligned sites = 355 Number in coding regions = 329 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 5 TTAACAGGGTGTTCTTCGGGAATTCCCTCG 3 28 0 GTTCTTCGGG 0.986313 -78 GGCATGGATTGAACTTCAGGTTCCCCAGTG 3 61 1 GAACTTCAGG 0.955446 -45 AATAACTTAAGTTGTTCATGTGGAAAAGTT 4 179 1 GTTGTTCATG 0.954438 -122 GTTGTGGAAAGTTTTTCGGGAAAAGCTTGA 4 206 1 GTTTTTCGGG 0.985241 -95 AAAACCCATTGATTTTCAAGCTTTTCCCGA 4 221 0 GATTTTCAAG 0.952977 -80 AATAGGCGGCTATTTTCATGTGACAAATTT 4 252 0 TATTTTCATG 0.846829 -49 ********** Masking position 5 Map Score: 2.9963 Number of sites scoring better than the average of aligned sites = 367 Number in coding regions = 341 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 AGCAAATAAATATTATAAGGAATTT 2 6 0 TATTATAAGG 0.928261 -53 AAGAACACCCTGTTAAAAGGGCATGGATTG 3 42 1 TGTTAAAAGG 0.95959 -64 CGACACAATCTACTCAAAAGAAAACCACGG 4 49 1 TACTCAAAAG 0.875539 -252 TTAATAAGAATAATAATAGGCGGCTATTTT 4 266 0 TAATAATAGG 0.917951 -35 ATTTATTTTGTATTAATAAGAATAATAATA 4 278 0 TATTAATAAG 0.90523 -23 ACCTCCTAAAAGGTATATTATAT 6 18 0 TCCTAAAAGG 0.962451 -13 ********** Masking position 4 Map Score: 0.388165 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 190 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 7 ********** No masking Map Score: 2.65333e-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: 2.65333e-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: 2.65333e-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