AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -irpoH_pyro_opreg_300.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 PH1703 42 235aa long hypothetical protein #10 PH1704 300 166aa long hypothetical intracellular proteinase #11 PH1804 83 441aa long hypothetical protein #12 PH1805 212 341aa long hypothetical 3-hydroxy-3-methylglutaryl coenzyme A reductase #13 PH1806 164 252aa long hypothetical protein #14 PH1830 100 334aa long hypothetical glyceraldehyde-3-phosphate dehydrogenase Motif number 1 GGTTTTTAATCTTTCTCCTTCTTTTCTCC 2 10 1 TCTTTCTCCT 0.970062 -21 CTTTCTCCTTCTTTTCTCCT 2 21 1 CTTTTCTCCT 0.974118 -10 CCCCCTCTCCCTTTTCTCTTCAACCTTTCT 3 34 1 CTTTTCTCTT 0.909488 -243 TTCTCTTCAACCTTTCTCCATATCTCTATG 3 47 1 CCTTTCTCCA 0.983671 -230 TATATACTCCATTTCCTCCACTTCCCCTTG 5 23 1 ATTTCCTCCA 0.763437 -59 CCCTTGAGAATTTTTCTTCTGTTCTGGGAA 5 47 1 TTTTTCTTCT 0.874949 -35 GTTGAAATTTCTTCAAGCTATTTCT 6 6 1 AATTTCTTCA 0.800863 -65 TTCTTCAAGCTATTTCTCCGCAAAAGATTT 6 19 1 TATTTCTCCG 0.799211 -52 TGTTTCTTTCTTTTTTAGTATTAT 7 5 1 TCTTTCTTTT 0.749362 -36 CAAATTCTTCCATTTCTCTTCTTACCTGGA 8 24 1 CATTTCTCTT 0.894246 -201 TTTGAGCATATATTTCTTCAGCTAAGAAAT 10 161 1 TATTTCTTCA 0.854817 -140 TTATTACATAATTTTCTTTAAAGGGTTTTG 10 264 0 ATTTTCTTTA 0.560618 -37 CTTTCTCTATTATTTCTTCAATATTCAAAT 12 20 0 TATTTCTTCA 0.854817 -193 CCCATTAGCTACTTTCTCTATTATTTCTTC 12 31 0 ACTTTCTCTA 0.855258 -182 TTCTCCAGGGCCTTCCTCCTTATTTCTGTA 12 114 0 CCTTCCTCCT 0.933595 -99 TATTCCGAGCCTTTTCTCCAGGGCCTTCCT 12 127 0 CTTTTCTCCA 0.974118 -86 TGGAATATTGCCTATCTCCTCAAAAACCTT 13 63 0 CCTATCTCCT 0.828719 -102 ********** Masking position 7 Map Score: 18.5508 Number of sites scoring better than the average of aligned sites = 1257 Number in coding regions = 1155 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 2 AAAAGAAGGAGAAAGATTAAAAACC 2 4 0 GAAAGTTAAA 0.80427 -27 AACTTCTCAAGAAAGCTTAAAAGTTAACTCCC 3 232 1 GAAAGTTAAA 0.80427 -45 AATCGAAAACTTTATATACTCCATTT 5 5 1 GAAAATTATA 0.931709 -77 ATTTCTCCGCAAAAGATTTATAATTCCTGGAA 6 30 1 AAAAGTTATA 0.967531 -41 TTCTTTATTGTAAAGGTTCATAAGCATCCATT 8 72 0 TAAAGTTATA 0.807542 -153 TGAGAAATCCGAAAAATTTATATAGTTTTTCC 8 172 1 GAAAATTATA 0.931486 -53 TTTTGAAATGAAAAGACTGATAGGAG 8 209 1 AAAAGCTATA 0.964442 -16 TTTATCAAAAACTTTATATTATTTTGAT 9 7 1 AAAAATTATA 0.9489 -36 ACAGAACTTAAAAAGGCTTATTAAATTATGAG 10 19 0 AAAAGCTATT 0.727372 -282 GTGCATCACCAAAAGGTTATTACATAATTTTC 10 278 0 AAAAGTTTTA 0.848372 -23 TGACGGTTGAAAAAAGTTGATAAAAGG 11 6 0 AAAAATTATA 0.948914 -78 CTATCTCCTCAAAAACCTTTTAAGTTATTATC 13 50 0 AAAAACTTTA 0.759066 -115 CCAAACGAACAAAAATCTTATAATCAAATTAT 13 90 1 AAAAACTATA 0.944106 -75 ATTATATATGAAAAATCAAATAGTTTGGAGAA 13 117 1 AAAAACAATA 0.624551 -48 ***** ** *** Masking position 4 Map Score: 14.4096 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 96 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 3 GTAGGTGAAGTTTATAAAACTG 1 1 1 GTAGTAAGTT 0.958623 -30 GAAAATTGAAGGGGTTGAAGTTAAAGGCCCCT 3 159 0 GGGGTAAGTT 0.988884 -118 TCGGCGTTTGGGGAGTTAACTTTTAAGCTTTC 3 242 0 GGGATAACTT 0.954641 -35 AGGAAATGGAGTATATAAAGTTTTCGATT 5 8 0 GTATTAAGTT 0.81616 -74 GGAAATCTACTTAAAAATAATA 7 29 0 GGAATTACTT 0.732148 -12 CATTAAACATGGGGATAAAGTTCAACGAAATT 10 78 0 GGGGTAAGTT 0.988884 -223 TTTCCATTTAGTAATTAAAATTATGATCTTAA 11 43 0 GTAATAAATT 0.667721 -41 ATTACTAAATGGAAATAAAGTTGGGGGTGATT 11 60 1 GGAATAAGTT 0.984563 -24 TAGCTAATGGGGAGATTAAGTTTTATCAGGTT 12 50 1 GGAGTAAGTT 0.987968 -163 AGAAAAGGCTCGGAATAAAGTTGCATCACATA 12 140 1 CGGATAAGTT 0.89947 -73 **** * ***** Masking position 6 Map Score: 8.72795 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 233 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 ACTCTGATCTCTTCCCCCCTCTCCCTTTTC 3 20 1 CTTCCCCCCT 0.954028 -257 CTCTATGGCCCTTCCCAGGTGAGTAGCTTG 3 70 1 CTTCCCAGGT 0.895921 -207 ACAGAATAGGCTTCCAAGCTACTCACCTGG 3 84 0 CTTCCAAGCT 0.901141 -193 GAAACAACTTCTTCCAAGCTTTGAGCATCA 3 122 1 CTTCCAAGCT 0.901141 -155 CTTTGAGCATCATCCAACCAGGGGCCTTTA 3 140 1 CATCCAACCA 0.630799 -137 GGTTCGCTCCCCATCGGCGTTTGGGG 3 261 0 CTCCCCATCG 0.951137 -16 ATTTCCTCCACTTCCCCTTGAGAATTTTTC 5 33 1 CTTCCCCTTG 0.84597 -49 AAAACTTAATCTCCCCATTAGCTACTTTCT 12 44 0 CTCCCCATTA 0.848561 -169 CTAGCCTTTTGTCCCCATTAACGTACTTTT 12 83 0 GTCCCCATTA 0.546331 -130 CTCTATATTCCTTCCAATGAGCTCGTTGGG 12 190 0 CTTCCAATGA 0.777275 -23 CTTCCCCCCACCGCCCTTAC 14 1 1 CTTCCCCCCA 0.96236 -100 GTTCCCACCGAATTCTATCT 14 91 0 GTTCCCACCG 0.905962 -10 ********** Masking position 5 Map Score: 6.05784 Number of sites scoring better than the average of aligned sites = 928 Number in coding regions = 849 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 5 CCAAGGATATAGTTCTCAAAAAAAGCGAGAA 3 188 0 ATTCTCAAAA 0.900711 -89 CATAGCCTTAACTTCTCAAGAAAGCTTAAAA 3 223 1 ATTCTCAAGA 0.490301 -54 GTTAAATACTAAAAAGGAGAGAC 4 9 0 ATACTAAAAA 0.766257 -15 ACTTAAAAATAATACTAAAAAAGAAAGAAAC 7 12 0 ATACTAAAAA 0.766257 -29 GGAAATCTACTTAAAAATAATACTAA 7 25 0 TTACTTAAAA 0.54442 -16 AACATGCTCAAATACTCCAATTATTTATAAT 8 102 1 ATACTCCAAT 0.811073 -123 CAGTAATAGTAGAAATCAAAATAATATAAAG 9 22 0 AAAATCAAAA 0.653889 -21 AACCAAAAACAGAACTTAAAAAGGCTTATTA 10 28 0 AAACTTAAAA 0.809352 -273 GAAATTTGTAACAACTTAAATGAGAAACCAA 10 53 0 AAACTTAAAT 0.611694 -248 ATCTTCTCCCATTCCTCAAATTTCAAAAATG 10 120 1 ATCCTCAAAT 0.802566 -181 ATTTCCATTTAGTAATTAAAATTATGATCTT 11 45 0 ATAATTAAAA 0.579355 -39 TTATTTCTTCAATATTCAAATTACCACCCC 12 10 0 ATATTCAAAT 0.59657 -203 AAGAAGGATAATAACTTAAAAGGTTTTTGAG 13 44 1 AAACTTAAAA 0.809352 -121 ATATTGCCTATCTCCTCAAAAACCTTTTAAG 13 58 0 TTCCTCAAAA 0.59381 -107 GGAGATAGGCAATATTCCAAACGAACAAAAA 13 74 1 ATATTCCAAA 0.640216 -91 ATTATATATGAAAAATCAAATAGTTTGGAGA 13 117 1 AAAATCAAAT 0.412125 -48 AGCCCTGATAAGTTCTCCAAACTATTTGATT 13 130 0 ATTCTCCAAA 0.802007 -35 TTGTCGGGATAATTTTTAAAAGCCCAGGAAG 14 35 0 ATTTTTAAAA 0.325337 -66 TAGTTAAGAGATACCTCCAAAAAAGATAGAA 14 68 1 AACCTCCAAA 0.698705 -33 * ********* Masking position 6 Map Score: 8.33375 Number of sites scoring better than the average of aligned sites = 638 Number in coding regions = 525 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 6 GTTGAAGAGAAAAGGGAGAGGGGGGAAGAG 3 28 0 AAAGGGAGAG 0.95409 -249 TAGTTCTCAAAAAAAGCGAGAAAATTGAAG 3 180 0 AAAAAGCGAG 0.975302 -97 TTAAATACTAAAAAGGAGAGAC 4 3 0 AAAAGGAGAG 0.98541 -21 AATAATACTAAAAAAGAAAGAAACA 7 6 0 AAAAAGAAAG 0.891666 -35 TAATGGGGACAAAAGGCTAGCTACAGAAAT 12 93 1 AAAAGGCTAG 0.981085 -120 GGCCCTGGAGAAAAGGCTCGGAATAAAGTT 12 132 1 AAAAGGCTCG 0.941038 -81 GATACCTCCAAAAAAGATAGAATTCGGTGG 14 77 1 AAAAAGATAG 0.954121 -24 ********** Masking position 3 Map Score: 6.26378 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 86 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 TCACCTGGGAAGGGCCATAGAGATATGGAG 3 62 0 AGGGCCATAG 0.943546 -215 TTGAAGTTAAAGGCCCCTGGTTGGATGATG 3 147 0 AGGCCCCTGG 0.987098 -130 TAAGGCTATGAAGGCCAAGGATATAGTTCT 3 203 0 AAGGCCAAGG 0.969676 -74 AATAAGGAGGAAGGCCCTGGAGAAAAGGCT 12 120 1 AAGGCCCTGG 0.994368 -93 ATTTGTCAGCCCCTAGCCCTGATAAG 13 149 0 CAGCCCCTAG 0.91937 -16 ATAATTTTTAAAAGCCCAGGAAGATAGGTA 14 28 0 AAAGCCCAGG 0.936061 -73 ********** Masking position 5 Map Score: 3.07968 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 277 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 CTTCAACCCCTTCAATTTTCTCGCTTTTTT 3 171 1 TTCAATTTTC 0.847686 -106 GTTGAAATTTCTTCAAGCTAT 6 2 1 TTGAAATTTC 0.880617 -69 TTTAAGTTGTTACAAATTTCGTTGAACTTT 10 64 1 TACAAATTTC 0.744856 -237 ATACTCATTTTTGAAATTTGAGGAATGGGA 10 126 0 TTGAAATTTG 0.915948 -175 AAAATGAGTATGGAATTTTGAGCATATATT 10 145 1 TGGAATTTTG 0.950656 -156 ATTATGATCTTAAAATTTTGACGGTTGAAA 11 26 0 TAAAATTTTG 0.612895 -58 GGGGTGGTAATTTGAATATTGAAG 12 5 1 TGGTAATTTG 0.64933 -208 AGGTACTCACTACAATTTTGGTCTAAGCGA 13 11 1 TACAATTTTG 0.863244 -154 TTTGTTCGTTTGGAATATTGCCTATCTCCT 13 73 0 TGGAATATTG 0.730526 -92 TCCAAACTATTTGATTTTTCATATATAATT 13 116 0 TTGATTTTTC 0.603106 -49 ********** Masking position 8 Map Score: 1.16239 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 121 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 9 ********** No masking Map Score: -2.49868e-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: -2.49868e-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 11 ********** No masking Map Score: -2.49868e-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