AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -isoxS_mthe_opreg_100.orf -g0.495 -x5 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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH155 228 rubredoxin #2 MTH1009 300 glyceraldehyde 3-phosphate dehydrogenase Motif number 1 CTTTTTTAAGGACCTCCGGGTCCTGCAGATATT 1 15 1 GCTCCGGTCC 0.990951 -214 TTTATCAGCAGGTACCCTGCTCCTATGGCAGCC 1 100 1 GTCCCTGTCC 0.97249 -129 ATTATCAGATGTATGCCGGGTCTCTCAACACTA 1 143 1 GAGCCGGTCT 0.979082 -86 TATTTCCTTTAAATCCCGGGTCCTTAGAGGTAT 2 87 1 AACCCGGTCC 0.944952 -214 GGTCCTTAGAGGTATCCTTTTCCCTCAGAAGCC 2 105 1 GTTCCTTTCC 0.906567 -196 ATTATCACGGGAACCCCTGATCCCGGATCCGCC 2 155 1 GACCCTGTCC 0.98331 -146 AAAGTGCGGTGAATGGCGGATCCGGGATCAGGG 2 169 0 GAGGCGGTCC 0.993666 -132 TATCCCCTGAAAAACGCTGTTCCCAGGGAAACC 2 264 0 AACGCTGTCC 0.979452 -37 * * ***** *** Masking position 11 Map Score: 12.6379 Number of sites scoring better than the average of aligned sites = 329 Number in coding regions = 303 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 CACTATAAAGCTTTCGCAGTGAATTTTATAG 1 171 1 CTTCGCAGTG 0.941638 -58 TTGTTCAGCTGGTTAGCAGCGATCAGTAGCA 2 20 0 GTTAGCAGCG 0.957183 -281 AATAACTGCGGTTTCTCTGTGGATGAAGCTG 2 49 1 GTTCTCTGTG 0.981496 -252 CTTCTCATGGGCTTCTGAGGGAAAAGGATAC 2 116 0 GTTCTGAGGG 0.98873 -185 AATCTTTAATGCTTCTCATGGGCTTCTGAGG 2 127 0 GTTCTCATGG 0.985692 -174 AAGCATTAAAGATTATCACGGGAACCCCTGA 2 144 1 GTTATCACGG 0.965343 -157 ACTCAAAGAGGTTTCCCTGGGAACAGCGTTT 2 255 1 GTTCCCTGGG 0.98613 -46 TGGGAACAGCGTTTTTCAGGGGATAGGAGGT 2 272 1 GTTTTCAGGG 0.987976 -29 * ********* Masking position 4 Map Score: 8.65275 Number of sites scoring better than the average of aligned sites = 606 Number in coding regions = 570 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 3 TTAATCTCAAAAAAATAATATCTGCAGGACCCGG 1 30 0 AAAAAAATCG 0.995275 -199 ATCTGAAGCAAAGAATAATATACGTCCAGATTAA 1 60 0 AAGAAAATAG 0.947891 -169 ACCTGCTGATAAAAAGAAGATCTGAAGCAAAGAA 1 79 0 AAAAAAATCG 0.995275 -150 GCAGCCCATTAAACAAATTATCAGATGTATGCCG 1 127 1 AAACAAATCG 0.989575 -102 ATAATCCATTAAAAATAGTATCAGGTTAGGAATT 2 218 1 AAAAAAATCG 0.995277 -83 ***** * *** * Masking position 7 Map Score: 5.18072 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 8 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 ACCTCCGGGTCCTGCAGATATTATTTTTTT 1 26 1 CCTGCAGATA 0.983282 -203 ATTATTCTTTGCTTCAGATCTTCTTTTTAT 1 75 1 GCTTCAGATC 0.965729 -154 GAGCAGGGTACCTGCTGATAAAAAGAAGAT 1 92 0 CCTGCTGATA 0.99097 -137 GACCCGGCATACATCTGATAATTTGTTTAA 1 135 0 ACATCTGATA 0.867906 -94 AAAACTGATTGCTACTGATCGCTGCTAACC 2 11 1 GCTACTGATC 0.96755 -290 TCGCTGCTAACCAGCTGAACAATAACTGCG 2 29 1 CCAGCTGAAC 0.958013 -272 ********** Masking position 8 Map Score: 4.06472 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 257 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 AACTCTTTTTTAAGGACCTCCGGGTCC 1 8 1 TTTTAAGGAC 0.973181 -221 TGATAATTTGTTTAATGGGCTGCCATAGGA 1 120 0 TTTAATGGGC 0.961176 -109 TCGCAGTGAATTTTATAGATAATTTTAAAT 1 184 1 TTTTATAGAT 0.909886 -45 GGACCCGGGATTTAAAGGAAATAGGGGGTG 2 80 0 TTTAAAGGAA 0.901315 -221 TAATGGATTATTTTATATACTTATCTAAAA 2 199 0 TTTTATATAC 0.779311 -102 TGATACTATTTTTAATGGATTATTTTATAT 2 211 0 TTTAATGGAT 0.967789 -90 ********** Masking position 5 Map Score: 1.96594 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 181 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 6 TCTGCAGGACCCGGAGGTCCTTAAAAAAGA 1 14 0 CCGGAGGTCC 0.993758 -215 TTCTTTTTATCAGCAGGTACCCTGCTCCTA 1 95 1 CAGCAGGTAC 0.978045 -134 CACAGAGAAACCGCAGTTATTGTTCAGCTG 2 40 0 CCGCAGTTAT 0.800129 -261 TTAAAGGAAATAGGGGGTGCAGCTTCATCC 2 69 0 TAGGGGGTGC 0.966392 -232 TTCCTTTAAATCCCGGGTCCTTAGAGGTAT 2 90 1 TCCCGGGTCC 0.93162 -211 GATCCGGGATCAGGGGTTCCCGTGATAATC 2 154 0 CAGGGGTTCC 0.977492 -147 TTTCAGGGGATAGGAGGTTTTTTTAA 2 285 1 TAGGAGGTTT 0.814219 -16 ********** Masking position 8 Map Score: 2.18691 Number of sites scoring better than the average of aligned sites = 1358 Number in coding regions = 1271 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 7 ********** No masking Map Score: 4.00336e-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: 4.00336e-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: 4.00336e-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