AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -irpoH_pyro_opreg_100.orf -g0.419 -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 = 0.419 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 PH0452 30 1127aa long hypothetical ATP-dependent protease La #2 PH0686 30 263aa long hypothetical ORFZ protein #3 PH1399 276 257aa long hypothetical peptidyl-prolyl cis-trans isomerase #4 PH1400 23 298aa long hypothetical protein #5 PH1402 81 207aa long hypothetical proteasome beta subunit precursor #6 PH1700 70 132aa long hypothetical protein #7 PH1701 40 428aa long hypothetical protein #8 PHS046 224 70aa long hypothetical archaeal histon #9 PH1804 83 441aa long hypothetical protein #10 PH1805 212 341aa long hypothetical 3-hydroxy-3-methylglutaryl coenzyme A reductase #11 PH1830 100 334aa long hypothetical glyceraldehyde-3-phosphate dehydrogenase Motif number 1 AGGAGAAAAGAAGGAGAAAGATTAAAAACC 2 11 0 AAGGAGAAAG 0.916558 -20 AGGAGAAAAGAAGGAGAAAG 2 21 0 AGGAGAAAAG 0.910304 -10 GAAAAGGGAGAGGGGGGAAGAGATCAGAGT 3 20 0 AGGGGGGAAG 0.979233 -257 AGAAAGGTTGAAGAGAAAAGGGAGAGGGGG 3 34 0 AAGAGAAAAG 0.715417 -243 CCATAGAGATATGGAGAAAGGTTGAAGAGA 3 48 0 ATGGAGAAAG 0.960409 -229 TGCTCAAAGCTTGGAAGAAGTTGTTTCCTA 3 119 0 TTGGAAGAAG 0.926409 -158 CAAGGGGAAGTGGAGGAAATGGAGTATATA 5 23 0 TGGAGGAAAT 0.889403 -59 GAGAAATAGCTTGAAGAAATTTCAAC 6 7 0 TTGAAGAAAT 0.84282 -64 AAGAAGAGAAATGGAAGAATTTGCCAATTT 8 17 0 ATGGAAGAAT 0.799754 -208 GATGCTATCCAGGTAAGAAGAGAAATGGAA 8 31 0 AGGTAAGAAG 0.69287 -194 ATTTTGACGGTTGAAAAAAGTTGATAAAAG 9 12 0 TTGAAAAAAG 0.871251 -72 AATTTGAATATTGAAGAAATAATAGAGAAA 10 19 1 TTGAAGAAAT 0.84282 -194 CTACAGAAATAAGGAGGAAGGCCCTGGAGA 10 113 1 AAGGAGGAAG 0.934369 -100 AGGAAGGCCCTGGAGAAAAGGCTCGGAATA 10 127 1 TGGAGAAAAG 0.910304 -86 ACGAGCTCATTGGAAGGAATATAGAGAAC 10 194 1 TGGAAGGAAT 0.92703 -19 GTAAGGGCGGTGGGGGGAAG 11 1 0 TGGGGGGAAG 0.979233 -100 TTAAAAGCCCAGGAAGATAGGTAAGGGCGG 11 21 0 AGGAAGATAG 0.81398 -80 TCTATCTTTTTTGGAGGTATCTCTTAACTA 11 68 0 TTGGAGGTAT 0.585539 -33 ********** Masking position 9 Map Score: 21.0358 Number of sites scoring better than the average of aligned sites = 2327 Number in coding regions = 2180 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 2 GAAGAGAAAAGGGAGAGGGGGGAAGAGATCAGA 3 22 0 GGGAGGGGGA 0.980553 -255 TATGGAGAAAGGTTGAAGAGAAAAGGGAGAGGG 3 36 0 GGGAAGAGAA 0.904629 -241 ACCTGGGAAGGGCCATAGAGATATGGAGAAAGG 3 57 0 GGATAGAGAA 0.933454 -220 GAGAAGTTAAGGCTATGAAGGCCAAGGATATAG 3 207 0 GGATGAAGGC 0.651409 -70 CTCCCCAAACGCCGATGGGGAGCGAACC 3 259 1 GCATGGGGAC 0.957412 -18 ATTCTCAAGGGGAAGTGGAGGAAATGGAGTATA 5 25 0 GGGTGGAGGA 0.98884 -57 TGCTATCCAGGTAAGAAGAGAAATGGAAGAATT 8 26 0 GTGAAGAGAA 0.651301 -199 AGAGAAAGTAGCTAATGGGGAGATTAAGTTTTA 10 42 1 GCATGGGGAA 0.975736 -171 TGAAAAGTACGTTAATGGGGACAAAAGGCTAGC 10 81 1 GTATGGGGAA 0.946943 -132 TAAGGAGGAAGGCCCTGGAGAAAAGGCTCGGAA 10 122 1 GGCTGGAGAA 0.953929 -91 CTTCCAATGAGCTCGTTGGGATCTATTGAATAA 10 177 0 GCGTTGGGAC 0.807381 -36 GATAGGTAAGGGCGGTGGGGGGAAG 11 3 0 GGGTGGGGGA 0.992998 -98 ** ******* * Masking position 10 Map Score: 10.46 Number of sites scoring better than the average of aligned sites = 641 Number in coding regions = 598 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 3 TTAATCTTTCTCCTTCTTTTCTCCT 2 16 1 TCCCTTTTCT 0.961897 -15 TCTTCCCCCCTCTCCCTTTTCTCTTCAACCTT 3 29 1 TCTCTTTTCT 0.978335 -248 CCTTCAATTTTCTCGCTTTTTTTGAGAACTAT 3 179 1 TCTCTTTTTT 0.987771 -98 GTCTCTCCTTTTTAGTATTTAAC 4 2 1 TCTCCTTTTT 0.986935 -22 TGTTTCTTTCTTTTTTAGTATTATTT 7 5 1 TCTCTTTTTT 0.987771 -36 ATTGGCAAATTCTTCCATTTCTCTTCTTACCT 8 19 1 TCTCATTTCT 0.890018 -206 ATATAGTTTTTCCGCCCATTTTGAAATGAAAA 8 191 1 TCCCCATTTT 0.830262 -34 CCTTTTATCAACTTTTTTCAACCGTCA 9 6 1 TATACTTTTT 0.544732 -78 TTAGCTACTTTCTCTATTATTTCTTCAATATT 10 25 0 TCTATTATTT 0.863751 -188 TCCAGGGCCTTCCTCCTTATTTCTGTAGCTAG 10 109 0 TCCCTTATTT 0.941365 -104 TGGAGGTATCTCTTAACTATTTTGTCGGGATA 11 55 0 TCTACTATTT 0.855673 -46 CCCACCGAATTCTATCTTTTTTGGAGGTATCT 11 76 0 TCTCTTTTTT 0.987771 -25 *** ******* Masking position 10 Map Score: 16.6117 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 257 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 4 GTAGGTGAAGTTTATAAAACTGGA 1 5 1 GTGAAGTTTA 0.881654 -26 ATTGAAGGGGTTGAAGTTAAAGGCCCCTGG 3 157 0 TTGAAGTTAA 0.750417 -120 CGCTTTTTTTGAGAACTATATCCTTGGCCT 3 192 1 GAGAACTATA 0.881667 -85 AAGCTTTCTTGAGAAGTTAAGGCTATGAAG 3 220 0 GAGAAGTTAA 0.966717 -57 CAAGAAAGCTTAAAAGTTAACTCCCCAAAC 3 239 1 TAAAAGTTAA 0.878371 -38 AATCGAAAACTTTATATACTCCAT 5 5 1 GAAAACTTTA 0.947938 -77 TCTGTTCTGGGAAAACTAAACCATCGGG 5 64 1 GAAAACTAAA 0.876994 -18 TGAGAAATCCGAAAAATTTATATAGTTTTT 8 172 1 GAAAAATTTA 0.778005 -53 TTCAACCTGATAAAACTTAATCTCCCCATT 10 55 0 TAAAACTTAA 0.878371 -158 ********** Masking position 5 Map Score: 4.30723 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 305 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 5 GAGATCAGAGTATTCCTGGG 3 1 0 TATTCCTGGG 0.880521 -276 TCTCTATGGCCCTTCCCAGGTGAGTAGCTT 3 69 1 CCTTCCCAGG 0.974262 -208 TACAGAATAGGCTTCCAAGCTACTCACCTG 3 85 0 GCTTCCAAGC 0.947798 -192 GGAAACAACTTCTTCCAAGCTTTGAGCATC 3 121 1 TCTTCCAAGC 0.98203 -156 ATATCCTTGGCCTTCATAGCCTTAACTTCT 3 209 1 CCTTCATAGC 0.884183 -68 GATGCAACTTTATTCCGAGCCTTTTCTCCA 10 137 0 TATTCCGAGC 0.884177 -76 TCTCTATATTCCTTCCAATGAGCTCGTTGG 10 191 0 CCTTCCAATG 0.876348 -22 CCCTTACCTATCTTCCTGGGCTTTTAAAAA 11 24 1 TCTTCCTGGG 0.969896 -77 ********** Masking position 4 Map Score: 4.29312 Number of sites scoring better than the average of aligned sites = 549 Number in coding regions = 517 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 TTTATAAAACTGGAATAAAA 1 21 1 TGGAATAAAA 0.933702 -10 AAGCCTATTCTGTAATAATAGGAAACAACT 3 101 1 TGTAATAATA 0.860251 -176 TGATAGTTCCAGGAATTATAAATCTTTTGC 6 38 0 AGGAATTATA 0.95767 -33 TAAGGATTCAATGAATTATAAATAATTGGA 8 117 0 ATGAATTATA 0.837958 -108 ATTTCCATTTAGTAATTAAAATTATGATCT 9 46 0 AGTAATTAAA 0.791327 -38 AATTACTAAATGGAAATAAAGTTGGGGGTG 9 59 1 TGGAAATAAA 0.716487 -25 TGAATATTGAAGAAATAATAGAGAAAGTAG 10 23 1 AGAAATAATA 0.777838 -190 TTGGGATCTATTGAATAATACCCTATGTGA 10 165 0 TTGAATAATA 0.837958 -48 ********** Masking position 5 Map Score: 1.42208 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 305 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 7 TTCCAGGAATTATAAATCTTTTGCGGAGAA 6 32 0 TATAAATCTT 0.785744 -39 GAAATCTACTTAAAAATAATACTAAAAAAG 7 20 0 TAAAAATAAT 0.880912 -21 TTCAATGAATTATAAATAATTGGAGTATTT 8 111 0 TATAAATAAT 0.850326 -114 GGAAAAACTATATAAATTTTTCGGATTTCT 8 174 0 TATAAATTTT 0.890586 -51 AATTATGATCTTAAAATTTTGACGGTTGAA 9 27 0 TTAAAATTTT 0.821757 -57 CATTTAGTAATTAAAATTATGATCTTAAAA 9 41 0 TTAAAATTAT 0.857222 -43 CCTGGGCTTTTAAAAATTATCCCGACAAAA 11 38 1 TAAAAATTAT 0.932432 -63 ********** Masking position 5 Map Score: 2.54187 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 49 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 8 ********** No masking Map Score: 1.67931e-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 9 ********** No masking Map Score: 1.67931e-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 10 ********** No masking Map Score: 1.67931e-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