AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -isoxS_ctra_opreg_100.orf -g0.413 -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 = 0.413 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 zwf 300 Glucose-6-P Dehyrogenase #2 sodM 131 Superoxide Dismutase (Mn) #3 nfo 172 Endonuclease IV #4 fumC 52 Fumarate Hydratase Motif number 1 AAAAAGATTTCTCTCTCATAAAACA 1 6 0 CTCTCTCATA 0.932876 -295 GTATTGTGGGCTCTCTCTTAAAAAATTAAC 1 57 1 CTCTCTCTTA 0.952185 -244 AAAATTAACACTCTATACTAGGTTGTATCT 1 78 1 CTCTATACTA 0.862275 -223 CTCTAGGAAGCTCTTTCCTGCTTTATACAA 1 193 1 CTCTTTCCTG 0.948209 -108 TCGCCACCTTCTCTATTTTCTACAGGCTAG 2 83 0 CTCTATTTTC 0.929913 -49 AAAATAAGGTTACTATCCTCGCCACCTTCT 2 101 0 TACTATCCTC 0.898005 -31 CACTCTCCTCTTTTTTTGTC 3 1 1 CACTCTCCTC 0.984106 -172 CAATAACTACCACTATTCTCGCTATTTATA 3 91 1 CACTATTCTC 0.941605 -82 TCTGGCAATCTTCTATCATGAATGACTAGA 3 140 1 TTCTATCATG 0.756539 -33 AGCCCGTTCTCTATCTAGTCATTCATGA 3 155 0 CTCTATCTAG 0.802624 -18 ATGCTCTCTTCCCCTATGATTCT 4 40 0 CTCTCTTCCC 0.901448 -13 ********** Masking position 6 Map Score: 8.76591 Number of sites scoring better than the average of aligned sites = 573 Number in coding regions = 573 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 2 TTAGGCACATATTCGTTTTTTTGGTATTGTGG 1 34 1 ATTCTTTTTT 0.886944 -267 CCTAGTATAGAGTGTTAATTTTTTAAGAGAGA 1 68 0 AGTGTATTTT 0.98113 -233 GTGGGGCCAAAGTCTTTAATTTCTTCCAAGAT 1 104 0 AGTCTTATTT 0.934815 -197 CTCCCTGTATCGTGGTTATTTTTGGTGCTACA 1 150 1 CGTGTTTTTT 0.979778 -151 TTCGGATAGACGTCCTTCCTTTGTTAAATTGT 1 219 0 CGTCTTCTTT 0.9122 -82 AGCTCTTGACAGTGAATATTTTATTGATAATC 2 34 1 AGTGATTTTT 0.939853 -98 AATAACGGCTAGTGATATTTTTCTGATAATGC 3 60 1 AGTGTATTTT 0.98113 -113 TAGCGAGAATAGTGGTAGTTATTGCATTATCA 3 83 0 AGTGTATTAT 0.891265 -90 TCCTTCATGAAGTCGTTTTTTCTATTTTT 4 8 0 AGTCTTTTTC 0.949231 -45 **** ** **** Masking position 3 Map Score: 7.12391 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 90 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 3 ACGAATATGTGCCTAAAAAGATTTCTCTCT 1 20 0 GCCTAAAAAG 0.979455 -281 AGCCCACAATACCAAAAAAACGAATATGTG 1 39 0 ACCAAAAAAA 0.973157 -262 GTGGGCTCTCTCTTAAAAAATTAACACTCT 1 62 1 TCTTAAAAAA 0.750367 -239 CTCCTGTAGCACCAAAAATAACCACGATAC 1 156 0 ACCAAAAATA 0.866611 -145 CAAACCCAACACAAACAAAGTTTTCGGATA 1 243 0 ACAAACAAAG 0.806444 -58 AGCCATCCTAAAAAATAAGGTTACT 2 117 0 TCCTAAAAAA 0.951053 -15 GGCTTAAAAGACAAAAAAAGAGGAGAGTG 3 10 0 ACAAAAAAAG 0.940072 -163 GGTATAAAGGGCCTAAAAAGGCTTAAAAGA 3 29 0 GCCTAAAAAG 0.979455 -144 ********** Masking position 5 Map Score: 6.84148 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 152 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 4 GTTATTTTTGGTGCTACAGGAGACTTGACC 1 164 1 GTGCTACAGG 0.985516 -137 AGGAAAGAGCTTCCTAGAGGTCAAGTCTCC 1 182 0 TTCCTAGAGG 0.987791 -119 TGTGTTGGGTTTGCTAGGCGACCTAAGTCT 1 260 1 TTGCTAGGCG 0.965655 -41 CCTTCTCTATTTTCTACAGGCTAGCTAGAT 2 77 0 TTTCTACAGG 0.974358 -55 TGATAGAAGATTGCCAGAGGTTCTTGATTA 3 128 0 TTGCCAGAGG 0.99001 -45 ********** Masking position 6 Map Score: 2.92632 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 68 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 5 TAGGTTGTATCTTGGAAGAAATTAAAGACT 1 96 1 CTTGGAAGAA 0.870588 -205 AACCACGATACAGGGAGGACAGGCTGGTAA 1 137 0 CAGGGAGGAC 0.988624 -164 TTGTATAAAGCAGGAAAGAGCTTCCTAGAG 1 193 0 CAGGAAAGAG 0.958891 -108 CAATTTAACAAAGGAAGGACGTCTATCCGA 1 220 1 AAGGAAGGAC 0.943665 -81 CCTAAAAAGGCTTAAAAGACAAAAAAAGAG 3 18 0 CTTAAAAGAC 0.793287 -155 AATCTTCTATCATGAATGACTAGATAGAGA 3 146 1 CATGAATGAC 0.964179 -27 AAAACGACTTCATGAAGGAAGAATCATAGG 4 21 1 CATGAAGGAA 0.973072 -32 ********** Masking position 6 Map Score: 4.04417 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 191 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: -1.70998e-12 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: -1.70998e-12 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: -1.70998e-12 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