AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00280_aquae_reg_100.orf -o00280_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 aq_037 112 putative protein #2 aq_194 53 putative protein #3 aldH2 300 aldehyde dehydrogenase #4 gsa 24 glutamate-1-semialdehyde aminotransferase Motif number 1 ATGGTGCCCGAAAAGGTAGAGGAATACATAAGGG 1 46 1 AAAGGTGGAA 0.996251 -67 AGAGGAATACATAAGGGAAAAGAAACTCTACATT 1 63 1 AAAGGGAGAA 0.981885 -50 CGAAGTTCGGATGCGGTAAGGGAATATGCGGTTC 3 28 1 AGCGGTGGAA 0.982121 -273 CCGTCTATTAAAACGGTGCAGGAACCGCATATTC 3 49 0 AACGGTGGAA 0.994435 -252 CAGTACCCAGTCAAGGAAGCGGAATGAAAAGAAA 3 102 1 TAAGGAGGAA 0.978609 -199 ACACCCTGTTAAAAGGGCATGGATTGAACTTCAG 3 164 1 AAAGGGGGAT 0.994529 -137 TTTCCTCTTTTGAAGGGTTCGGATTTTTACTCAG 3 252 0 TAAGGGGGAT 0.98751 -49 * ***** **** Masking position 13 Map Score: 9.02671 Number of sites scoring better than the average of aligned sites = 397 Number in coding regions = 362 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 2 CTGCATGGTGCCCGAAAAGGTAGAGGAATA 1 42 1 CCCGAAAAGG 0.93253 -71 TACTGACAGCTCCTCACAGGATTTCCGTCT 3 77 0 TCCTCACAGG 0.985338 -224 CATTCCGCTTCCTTGACTGGGTACTGACAG 3 98 0 CCTTGACTGG 0.950897 -203 TTCGGGAATTCCCTCGATGGTTATTATTTC 3 132 0 CCCTCGATGG 0.860537 -169 GCTGGCAGTATCCGCACTGGGGAACCTGAA 3 193 0 TCCGCACTGG 0.994227 -108 CCACTATTTGTCCGGGCTGGCAGTATCCGC 3 208 0 TCCGGGCTGG 0.99032 -93 ********** Masking position 2 Map Score: 6.18507 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 166 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 3 AAATCTGATTATAGGTCCGGAGATT 1 98 0 CTGATATAGG 0.943511 -15 TACAAGCTTACTTTTTAAAGGCTATTATAAA 2 16 0 CTTTTAAAGG 0.798052 -38 GGATTTCCGTCTATTAAAACGGTGCAGGAAC 3 58 0 CTATTAAACG 0.930361 -243 GAAGAACACCCTGTTAAAAGGGCATGGATTG 3 159 1 CTGTTAAAGG 0.972721 -142 ACTATTTCCTCTTTTGAAGGGTTCGGATTTT 3 259 0 CTTTTAAGGG 0.943071 -42 ***** ***** Masking position 5 Map Score: 3.69372 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 99 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 4 ACTCTTACCCTCCGAAACTCTCTTCC 1 7 0 TCCGAAACTC 0.990804 -106 ACATTAAATCTCCGGACCTATAATCAGATT 1 92 1 TCCGGACCTA 0.964168 -21 CCTTACCGCATCCGAACTTCGTCCCGGTAA 3 19 0 TCCGAACTTC 0.990804 -282 GTTTTAATAGACGGAAATCCTGTGAGGAGC 3 69 1 ACGGAAATCC 0.879878 -232 AGGGTGTTCTTCGGGAATTCCCTCGATGGT 3 141 0 TCGGGAATTC 0.967417 -160 TGAGTAAAAATCCGAACCCTTCAAAAGAGG 3 253 1 TCCGAACCCT 0.964174 -48 ********** Masking position 6 Map Score: 4.00418 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 290 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 TTTTCGGGCACCATGCAGTAAATACTCTTA 1 30 0 CCATGCAGTA 0.951927 -83 TAAAAAGTAAGCTTGTAGAAATATTATTAA 2 30 1 GCTTGTAGAA 0.930371 -24 CCTGTGAGGAGCTGTCAGTACCCAGTCAAG 3 87 1 GCTGTCAGTA 0.98421 -214 ATTTGTCCGGGCTGGCAGTATCCGCACTGG 3 203 0 GCTGGCAGTA 0.995978 -98 AAGTGCATAGGCTTCCACTATTTGTCCGGG 3 222 0 GCTTCCACTA 0.960483 -79 ********** Masking position 7 Map Score: 1.87246 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 62 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 CTTATGTATTCCTCTACCTTTTCGGGCACCAT 1 46 0 CCCTCCTTTT 0.982766 -67 TGTAGAGTTTCTTTTCCCTTATGTATTCCTCT 1 63 0 CTTTCCTTAT 0.958203 -50 ACCGCATATTCCCTTACCGCATCCGAACTTCG 3 28 0 CCTTCCGCAT 0.979005 -273 ATATGCGGTTCCTGCACCGTTTTAATAGACGG 3 51 1 CCGCCCGTTT 0.955151 -250 GAAGTTCAATCCATGCCCTTTTAACAGGGTGT 3 164 0 CCTGCCTTTT 0.982766 -137 ATGACACTTACTATTTCCTCTTTTGAAGGGTT 3 267 0 CTTTCCTCTT 0.972574 -34 ** ** ****** Masking position 12 Map Score: 1.30068 Number of sites scoring better than the average of aligned sites = 754 Number in coding regions = 703 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 7 TGTAGAGTTTCTTTTCCCTTATGTATTCCT 1 65 0 CTTTTCCCTT 0.983741 -48 CAGGAACCGCATATTCCCTTACCGCATCCG 3 35 0 ATATTCCCTT 0.974454 -266 GAAGTTCAATCCATGCCCTTTTAACAGGGT 3 166 0 CCATGCCCTT 0.989775 -135 TAGTGGAAGCCTATGCACTTCTGAGTAAAA 3 232 1 CTATGCACTT 0.976285 -69 ATGACACTTACTATTTCCTCTTTTGAAGGG 3 269 0 CTATTTCCTC 0.945007 -32 ********** Masking position 4 Map Score: 3.41092 Number of sites scoring better than the average of aligned sites = 395 Number in coding regions = 373 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 8 ********** No masking Map Score: -8.99385e-14 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: -8.99385e-14 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 10 ********** No masking Map Score: -8.99385e-14 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