AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00150_aquae_reg_300.orf -o00150_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 aq_260 300 hypothetical protein #2 aq_1510 113 putative protein #3 carB2 26 carbamoyl-phosphate synthase large subunit Motif number 1 AACAACTTATGAGTTTTCCACAATTCTCCA 1 12 0 GAGTTTTCCA 0.946451 -289 GAAAACTCATAAGTTGTTCATATAACGACA 1 24 1 AAGTTGTTCA 0.992431 -277 TTTTTAACGTAAGTAGTTTATACACCGTGG 1 73 0 AAGTAGTTTA 0.802879 -228 ATAACTTAAGAAGTTTTCCACATTTATCCA 1 105 0 AAGTTTTCCA 0.990381 -196 AAAACTTCTTAAGTTATTCATACTACGAAA 1 118 1 AAGTTATTCA 0.983107 -183 TGAACAACTTAAGTTATTTATAATTCGTAA 1 167 0 AAGTTATTTA 0.927783 -134 TAAATAACTTAAGTTGTTCATGTGGAAAAG 1 177 1 AAGTTGTTCA 0.992431 -124 AACTTTCCACAACTTTTCCACATGAACAAC 1 189 0 AACTTTTCCA 0.923216 -112 AAGTTGTGGAAAGTTTTTCGGGAAAAGCTT 1 204 1 AAGTTTTTCG 0.96934 -97 ATGGGTTTTGAAATTTGTCACATGAAAATA 1 242 1 AAATTTGTCA 0.834138 -59 CATTTTGAAGAAGTGTGTCAAGTTAATTTA 2 44 1 AAGTGTGTCA 0.960779 -70 AAAAATCAAAAAGTGTTTTAAATTAACTTG 2 62 0 AAGTGTTTTA 0.939771 -52 ********** Masking position 2 Map Score: 22.1729 Number of sites scoring better than the average of aligned sites = 592 Number in coding regions = 553 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 2 GTGGAGAATTGTGGAAAACTCATAAGTT 1 9 1 TTGTGGAAAA 0.973567 -292 TTGTGTCGTTATATGAACAACTTATGAGTT 1 27 0 ATATGAACAA 0.919554 -274 TACGTTAAAAATGTGGATAAATGTGGAAAA 1 92 1 ATGTGGATAA 0.989521 -209 ATGTGGATAAATGTGGAAAACTTCTTAAGT 1 102 1 ATGTGGAAAA 0.991575 -199 TTGTTTCGTAGTATGAATAACTTAAGAAGT 1 121 0 GTATGAATAA 0.871499 -180 TAAGTTGTTCATGTGGAAAAGTTGTGGAAA 1 186 1 ATGTGGAAAA 0.991575 -115 TGTGGAAAAGTTGTGGAAAGTTTTTCGGGA 1 197 1 TTGTGGAAAG 0.885874 -104 GGCTATTTTCATGTGACAAATTTCAAAACC 1 245 0 ATGTGACAAA 0.939055 -56 TTTTGTATTAATAAGAATAATAATAGGCGG 1 273 0 ATAAGAATAA 0.782653 -28 CACTTCTTCAAAATGAATAAAATTACACTC 2 29 0 AAATGAATAA 0.782654 -85 ********** Masking position 9 Map Score: 14.2117 Number of sites scoring better than the average of aligned sites = 365 Number in coding regions = 323 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 3 ACATTTATCCACATTTTTAACGTAAGTAGTT 1 85 0 ACATTTTAAC 0.954347 -216 TTATAATTCGTAAGTTTTAAGTCACCGGATT 1 149 0 TAAGTTTAAG 0.910641 -152 CAAAACCCATTGATTTTCAAGCTTTTCCCGA 1 221 0 TGATTTTAAG 0.972791 -80 GTAATTTTATTCATTTTGAAGAAGTGTGTCA 2 33 1 TCATTTTAAG 0.972791 -81 TGTGTCAAGTTAATTTAAAACACTTTTTGAT 2 57 1 TAATTTAAAC 0.916452 -57 TTACCTCTAGAGATTTATAACAAAAATCAAA 2 82 0 AGATTTAAAC 0.90093 -32 TCTAGAGGTAAAATCTTTAAGT 2 102 1 AAATCTTAAG 0.886703 -12 ******* *** Masking position 3 Map Score: 3.11635 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 169 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 4 CTCATAAGTTGTTCATATAACGACACAATC 1 29 1 GTTCATATAA 0.899398 -272 AACGTAAGTAGTTTATACACCGTGGTTTTC 1 68 0 GTTTATACAC 0.910648 -233 AGTTTTCCACATTTATCCACATTTTTAACG 1 94 0 ATTTATCCAC 0.911293 -207 TTCTTAAGTTATTCATACTACGAAACAATC 1 123 1 ATTCATACTA 0.951811 -178 TATTATTCTTATTAATACAAAATAAATAGT 1 281 1 ATTAATACAA 0.931066 -20 CTCACTGTTTATACTATATACTTTAA 3 7 1 GTTTATACTA 0.966185 -20 ********** Masking position 5 Map Score: 2.77574 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 74 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 TTTTCTTTTGAGTAGATTGTGTCGTTATAT 1 43 0 AGTAGATTGT 0.991162 -258 TTTTAACGTAAGTAGTTTATACACCGTGGT 1 72 0 AGTAGTTTAT 0.905461 -229 ATTAATACAAAATAAATAGT 1 291 1 AATAAATAGT 0.642568 -10 CTCCTCCGAAAGTAGAGTGTAATTTTATTC 2 15 1 AGTAGAGTGT 0.989682 -99 TTCATTTTGAAGAAGTGTGTCAAGTTAATT 2 42 1 AGAAGTGTGT 0.926985 -72 TTAAAGTATATAGTATAAACAGTG 3 13 0 AGTATATAGT 0.908238 -14 ********** Masking position 4 Map Score: 3.02434 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 83 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 ATTGTGTCGTTATATGAACAACTTATGAGT 1 28 0 TATATGAACA 0.86478 -273 ACAATCTACTCAAAAGAAAACCACGGTGTA 1 53 1 CAAAAGAAAA 0.936194 -248 ACAACTTTTCCACATGAACAACTTAAGTTA 1 181 0 CACATGAACA 0.985777 -120 TGAAATTTGTCACATGAAAATAGCCGCCTA 1 250 1 CACATGAAAA 0.984663 -51 ACACTTCTTCAAAATGAATAAAATTACACT 2 30 0 AAAATGAATA 0.912639 -84 ATTTATAACAAAAATCAAAAAGTGTTTTAA 2 71 0 AAAATCAAAA 0.858202 -43 ********** Masking position 4 Map Score: 2.43086 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 96 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 ********** No masking Map Score: 9.48026e-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 8 ********** No masking Map Score: 9.48026e-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: 9.48026e-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