AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -ifruR_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 PH0092 99 821aa long hypothetical phosphoenolpyruvate synthase #2 PH0198 300 168aa long hypothetical protein #3 PH0583 100 318aa long hypothetical protein #4 PH1150 89 236aa long hypothetical arylmalonate decarboxylase #5 PH1217 127 216aa long hypothetical alkyl hydroperoxide reductase #6 PH1218 82 410aa long hypothetical phosphoglycerate kinase #7 PH1390 56 301aa long hypothetical thiamin biosynthesis protein Motif number 1 TAAAACTTAGGGTGAGTTATGGACAT 1 5 1 ACTTAGGGTG 0.844827 -95 TTGGGTTGCTAGATAGGGAGGTACTTTAATAC 2 43 0 AGATAGGGAT 0.981486 -258 TAGGGAAGATGGTGAGGAACTTGGGTTGCTAG 2 63 0 GGTGAGGAAT 0.935054 -238 GTAGGATCAGAGTTAGGGAAGATGGTGAGGAA 2 76 0 AGTTAGGGAA 0.95664 -225 ATAATCACAGAGATAAGATTTGGTAGGATCAG 2 98 0 AGATAAGATG 0.765397 -203 TCTTAACTCCAGTTAAGGATATTTCAATAATC 2 124 0 AGTTAAGGAT 0.950613 -177 TATAAATTTTAGTGAGGGGAGGCTTGAAGTCT 2 153 0 AGTGAGGGGG 0.940468 -148 TAGGTTTGCTAGATAAGGAAGGTTTTTGTCAA 2 205 0 AGATAAGGAG 0.96921 -96 AAGTGAGGGACCGAGGGTTGTTG 2 288 0 AGTGAGGGAG 0.98925 -13 TAGCAGGGATGGAGAGGGATCAGA 3 87 1 GGAGAGGGAA 0.929039 -14 AATCCCTATTACATAGGGATTTTAAACTATTT 4 55 0 ACATAGGGAT 0.897983 -35 AATAGTTGAAGGTGAGGATAAGCTAGGTAAGA 5 29 0 GGTGAGGATG 0.886795 -99 ATATAGGGGAAGATAAGAATAGAAAGGAATGC 6 13 0 AGATAAGAAG 0.91768 -70 AAAAAACGAAGGTTAAGAATATTATGCCAATA 6 42 0 GGTTAAGAAT 0.848453 -41 TAAATACAATGGATAGGTAAATAATTTTGGGT 7 29 1 GGATAGGTAT 0.791847 -28 ********* * Masking position 5 Map Score: 15.8334 Number of sites scoring better than the average of aligned sites = 1420 Number in coding regions = 1328 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 2 GATAAAGGTGGATCATATTTAAAATTAACGTGAA 1 52 0 GTATTTAAAA 0.955373 -48 ATCTTATCTCTGTGATTATTGAAATATCCTTAAC 2 111 1 TTATATGAAA 0.926988 -190 GAAGTAAATTGCTAAGCTTAGAAAAATCAAAGTA 2 237 1 GTAGTTGAAA 0.972771 -64 GGGACCGAGGGTTGTTGATAAAAACGTTGTCCGG 2 271 0 GTTTATAAAA 0.934189 -30 GATTTTAAACTATTTTATTCAAAAAATTTTATAA 4 36 0 TTTTTTAAAA 0.626321 -54 GGATAAGCTAGGTAAGATTCAAAAGAAGGAAAAA 5 12 0 GTAGTTAAAA 0.938446 -116 AACTATTCCTGATCATGATCGAAAAGTTTATAAG 5 54 1 GTATATGAAA 0.98657 -74 AACCATATTAGTTTATAATGGAAACAAAATATGG 5 92 1 GTATATGAAA 0.986564 -36 TATAGGGGAAGATAAGAATAGAAAGGAATGCAA 6 10 0 GTAGATGAAA 0.981239 -73 CTTAACCTTCGTTTTTTATTGAAATTTGGTGGTG 6 57 1 GTTTATGAAA 0.970612 -26 * * ** ** **** Masking position 9 Map Score: 13.9516 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 129 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 3 AGCAAAAGGTTTATTAAATATATGAAACC 2 8 0 TTATTAATTA 0.909863 -293 ATACTCAAGGCTATAAATTTTAGTGAGGGGAG 2 164 0 CTATAAATTA 0.877145 -137 CTATTTCCCCTTATTAAGTCTTTAGGTACTAA 3 58 0 TTATTAATTT 0.958684 -43 TTTGGGAACATTATAAAATTTTTTGAATAAAA 4 26 1 TTATAAATTT 0.981597 -64 TACATAGGGATTTTAAACTATTTTATTCAAAA 4 46 0 TTTTAAATTT 0.917173 -44 TGGTTCGAACTTATAAACTTTTCGATCATGAT 5 65 0 TTATAAATTT 0.981597 -63 TTTGTTTCCATTATAAACTAATATGGTTCGAA 5 88 0 TTATAAATAT 0.917173 -40 ******* * ** Masking position 6 Map Score: 4.67138 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 25 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 4 CAATGTCCATAACTCACCCTAAGTTTTA 1 5 0 AACTACCAAT 0.706381 -95 TTTAAATATGATCCACCTTTATCAATTTCGGAAA 1 63 1 ATCCCCTATA 0.881405 -37 CCTAACTCTGATCCTACCAAATCTTATCTCTGTG 2 91 1 ATCCACCATT 0.983191 -210 TAAGACTTCAAGCCTCCCCTCACTAAAATTTATA 2 151 1 AGCCCCCCAT 0.925704 -150 CCTTGACAAAAACCTTCCTTATCTAGCAAACCTA 2 203 1 AACCTCCATT 0.912908 -98 CTTCCCTCCCCCAAGAAGTTACCTCAATA 3 6 1 CTCCCCAAAT 0.839703 -95 CTAACCTCCTTGATCTTTGGGAACAT 4 3 1 AACCCCTATT 0.963617 -87 TTCGATCTCCTCCCATATTTTGTTTCCATT 5 108 0 CTCCCCCATT 0.987587 -20 TTCTATTCTTATCTTCCCCTATATTGGCATAATA 6 21 1 ATCTCCCATT 0.969639 -62 GCTTTATCCCACTCACTTTAAATACAATG 7 6 1 ATCCACTCTT 0.863652 -51 GCATCCACCCAAAATTATTTACCTAT 7 41 0 ATCCCCCAAT 0.991885 -16 **** *** ** * Masking position 7 Map Score: 8.43578 Number of sites scoring better than the average of aligned sites = 396 Number in coding regions = 337 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 5 GGTTTATTAAATATATGAAACC 2 1 0 ATATATAACC 0.939974 -300 GTACCTCCCTATCTAGCAACCCAAGTTCCTCA 2 51 1 ATCTAGAACC 0.99597 -250 AACCTTCCTTATCTAGCAAACCTAGAAGTAAA 2 213 1 ATCTAGAACC 0.99597 -88 GCTGTCACCTAGAAATCCCTATTACATA 4 72 0 ACCTAGAACC 0.993149 -18 ****** ** ** Masking position 5 Map Score: 1.60109 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 10 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 CATAACTCACCCTAAGTTTTA 1 2 0 CCTAAGTTTT 0.648882 -98 CATTGGAGAACTAAGGTATTCACGTTAATT 1 34 1 CTAAGGTATT 0.727551 -66 AAACCTTTTGCTTAAGTATTAAAGTACCTC 2 28 1 CTTAAGTATT 0.977844 -273 CTTAACTCCAGTTAAGGATATTTCAATAAT 2 125 0 GTTAAGGATA 0.848691 -176 CTTAACTGGAGTTAAGACTTCAAGCCTCCC 2 139 1 GTTAAGACTT 0.864431 -162 AATTTATAGCCTTGAGTATTCCAACTCCTT 2 177 1 CTTGAGTATT 0.902006 -124 CTCAATAGATGTTAAGTATTTCGGTTTAGT 3 33 1 GTTAAGTATT 0.972701 -68 ATTTCCCCTTATTAAGTCTTTAGGTACTAA 3 58 0 ATTAAGTCTT 0.769458 -43 ATCCCTATTACATAGGGATTTTAAACTATT 4 56 0 CATAGGGATT 0.628823 -34 AAAAACGAAGGTTAAGAATATTATGCCAAT 6 43 0 GTTAAGAATA 0.783837 -40 ********** Masking position 9 Map Score: 1.78093 Number of sites scoring better than the average of aligned sites = 425 Number in coding regions = 382 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 7 GGTGAGTTATGGACATTGGAGAACTAAGGTA 1 21 1 GGACTTGGAG 0.985581 -79 TATCAATTTCGGAAATTCGAGCCTGGAG 1 82 1 GGAATTCGAG 0.977201 -18 AAGATGGTGAGGAACTTGGGTTGCTAGATAG 2 59 0 GGAATTGGGT 0.944332 -242 TCAGAGTTAGGGAAGATGGTGAGGAACTTGG 2 71 0 GGAAATGGTG 0.969866 -230 CTTAATAAGGGGAAATAGCAGGGATGGAGAG 3 72 1 GGAATAGCAG 0.913601 -29 GTTTTTTATTGAAATTTGGTGGTGAA 6 67 1 GAAATTGGTG 0.952791 -16 **** ****** Masking position 3 Map Score: 0.740221 Number of sites scoring better than the average of aligned sites = 325 Number in coding regions = 303 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: 1.37435e-13 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: 1.37435e-13 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: 1.37435e-13 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