AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -ifruR_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 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 PH1214 267 441aa long hypothetical cytoplasmic protein #6 PH1217 127 216aa long hypothetical alkyl hydroperoxide reductase #7 PH1218 82 410aa long hypothetical phosphoglycerate kinase #8 PH1390 56 301aa long hypothetical thiamin biosynthesis protein Motif number 1 ATTTCCGAAATTGATAAAGGTGGATCATATTTA 1 65 0 TTATAGGTGG 0.598931 -35 TCACAGAGATAAGATTTGGTAGGATCAGAGTTA 2 93 0 AAATGGTAGG 0.937351 -208 CTATAAATTTTAGTGAGGGGAGGCTTGAAGTCT 2 153 0 TATGGGGAGG 0.988298 -148 CTAGGTTTGCTAGATAAGGAAGGTTTTTGTCAA 2 205 0 TAATGGAAGG 0.928136 -96 TTGAGGTAACTTCTTGGGGGAGGGAAG 3 5 0 TTTTGGGAGG 0.973633 -96 AATAAGGGGAAATAGCAGGGATGGAGAGGGATC 3 75 1 AAAGGGGATG 0.955105 -26 AATGTTCCCAAAGATCAAGGAGGTTAG 4 5 0 AAATAGGAGG 0.963481 -85 TCATCATCGGTTCAGGAGGGATGAATCATGTCA 5 65 1 TTAGGGGATG 0.854982 -203 AAATTTGTCAAAGTTTTGGGAGTTATGAGGAGA 5 163 0 AATTGGGAGT 0.897711 -105 AGTCTAACATAAATGTAGGGAGGCGACTAACA 5 246 1 AATGGGGAGG 0.989883 -22 TAATGGAAACAAAATATGGGAGGAGATCGAA 6 107 1 AAATGGGAGG 0.995227 -21 ATATTATGCCAATATAGGGGAAGATAAGAATAG 7 23 0 AAATGGGAAG 0.942628 -60 GATAGGTAAATAATTTTGGGTGGATGC 8 40 1 TATTGGGTGG 0.959169 -17 ** ** ****** Masking position 9 Map Score: 16.684 Number of sites scoring better than the average of aligned sites = 583 Number in coding regions = 521 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 2 GATAAAGGTGGATCATATTTAAAATTAACGTGAA 1 52 0 GTATTTAAAA 0.944282 -48 ATCTTATCTCTGTGATTATTGAAATATCCTTAAC 2 111 1 TTATATGAAA 0.919214 -190 GAAGTAAATTGCTAAGCTTAGAAAAATCAAAGTA 2 237 1 GTAGTTGAAA 0.968558 -64 GGGACCGAGGGTTGTTGATAAAAACGTTGTCCGG 2 271 0 GTTTATAAAA 0.923674 -30 GATTTTAAACTATTTTATTCAAAAAATTTTATAA 4 36 0 TTTTTTAAAA 0.659927 -54 AATACTTAAAGTTTTTGTTAGAATCTCTTCTAGG 5 205 0 GTTTTTGAAT 0.692255 -63 TAACAAAAACTTTAAGTATTAAAAATCAGTCTAA 5 219 1 TTAGATAAAA 0.808836 -49 GGATAAGCTAGGTAAGATTCAAAAGAAGGAAAAA 6 12 0 GTAGTTAAAA 0.933081 -116 AACTATTCCTGATCATGATCGAAAAGTTTATAAG 6 54 1 GTATATGAAA 0.98097 -74 AACCATATTAGTTTATAATGGAAACAAAATATGG 6 92 1 GTATATGAAA 0.980966 -36 TATAGGGGAAGATAAGAATAGAAAGGAATGCAA 7 10 0 GTAGATGAAA 0.976962 -73 CTTAACCTTCGTTTTTTATTGAAATTTGGTGGTG 7 57 1 GTTTATGAAA 0.963817 -26 * * ** ** **** Masking position 12 Map Score: 13.9667 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 167 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 3 TATTAAAGTACCTCCCTATCTAGCAACCCA 2 44 1 CCTCCCTATC 0.97498 -257 AACCCAAGTTCCTCACCATCTTCCCTAACT 2 68 1 CCTCACCATC 0.995158 -233 TGACAAAAACCTTCCTTATCTAGCAAACCT 2 206 1 CTTCCTTATC 0.776986 -95 TCTGATCCCTCTCCATCCCTGCTATTT 3 84 0 CCTCTCCATC 0.991003 -17 TGGGGGACCGCTTCATCATCGGTTCAGGAG 5 53 1 CTTCATCATC 0.948383 -215 CCTAGCTTATCCTCACCTTCAACTATTCCT 6 34 1 CCTCACCTTC 0.986882 -94 GCATAATATTCTTAACCTTCGTTTTTTATT 7 47 1 CTTAACCTTC 0.870572 -36 AAATTATTTACCTATCCATTGTATTTAAAG 8 26 0 CCTATCCATT 0.737757 -31 ********** Masking position 3 Map Score: 8.50728 Number of sites scoring better than the average of aligned sites = 611 Number in coding regions = 564 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 4 AACCTTTTGCTTAAGTATTAAAGTACCTCC 2 29 1 TTAAGTATTA 0.975659 -272 AGGGGAGGCTTGAAGTCTTAACTCCAGTTA 2 141 0 TGAAGTCTTA 0.951204 -160 TCAATAGATGTTAAGTATTTCGGTTTAGTA 3 34 1 TTAAGTATTT 0.965489 -67 TTTCCCCTTATTAAGTCTTTAGGTACTAAA 3 57 0 TTAAGTCTTT 0.967949 -44 AACAAAAACTTTAAGTATTAAAAATCAGTC 5 220 1 TTAAGTATTA 0.975659 -48 ********** Masking position 6 Map Score: 4.91721 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 22 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 AAGGTGGATCATATTTAAAATTAACGTGAA 1 52 0 ATATTTAAAA 0.592215 -48 CGAATTTCCGAAATTGATAAAGGTGGATCA 1 71 0 AAATTGATAA 0.930468 -29 CCCCTCACTAAAATTTATAGCCTTGAGTAT 2 166 1 AAATTTATAG 0.796742 -135 ACCTAGAAGTAAATTGCTAAGCTTAGAAAA 2 232 1 AAATTGCTAA 0.736214 -69 GGACCGAGGGTTGTTGATAAAAACGTTGTC 2 274 0 TTGTTGATAA 0.765755 -27 TTATTCAAAAAATTTTATAATGTTCCCAAA 4 26 0 AATTTTATAA 0.822601 -64 TTGAATAAAATAGTTTAAAATCCCTATGTA 4 48 1 TAGTTTAAAA 0.821257 -42 GGAGCCCGCTTAATTTATAATTCCCCATAC 5 23 0 TAATTTATAA 0.927611 -245 CATGATCGAAAAGTTTATAAGTTCGAACCA 6 67 1 AAGTTTATAA 0.960315 -61 CGAACCATATTAGTTTATAATGGAAACAAA 6 90 1 TAGTTTATAA 0.942946 -38 ********** Masking position 5 Map Score: 4.36134 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 133 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 6 TAAAACTTAGGGTGAGTTATGGACATTG 1 8 1 TGGGTGAGTT 0.879151 -92 AGGATCAGAGTTAGGGAAGATGGTGAGGAAC 2 75 0 TAGGGAAGAT 0.963486 -226 AGAGATAAGATTTGGTAGGATCAGAGTTAGG 2 91 0 TTGGTAGGAT 0.738317 -210 TAACATCTATTGAGGTAACTTCTTGGGGGAG 3 16 0 TAGGTAACTT 0.77692 -85 AAAGACTTAATAAGGGGAAATAGCAGGGATG 3 67 1 TAGGGGAAAT 0.916689 -34 CTCCTTGATCTTTGGGAACATTATAAAATTT 4 16 1 TTGGGAACAT 0.918234 -74 ATAGGGATTTCTAGGTGACAGC 4 78 1 CAGGTGACAG 0.516219 -12 ATGTTATGGGTATGGGGAATTATAAATTAAG 5 14 1 TTGGGGAATT 0.655012 -254 CATCATCGGTTCAGGAGGGATGAATCATGTC 5 66 1 TAGGAGGGAT 0.787677 -202 TAAATGACACTATGGTGACATCATATGATAA 5 129 1 TTGGTGACAT 0.936942 -139 TTGGGAGTTATGAGGAGACATTTATCATATG 5 150 0 TAGGAGACAT 0.902207 -118 TGAGGATAAGCTAGGTAAGATTCAAAAGAAG 6 18 0 CAGGTAAGAT 0.827147 -110 AAACAAAATATGGGAGGAGATCGAA 6 113 1 TGGAGGAGAT 0.707759 -15 TATGCCAATATAGGGGAAGATAAGAATAGAA 7 21 0 TGGGGAAGAT 0.949462 -62 * ********* Masking position 4 Map Score: 8.52007 Number of sites scoring better than the average of aligned sites = 743 Number in coding regions = 674 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 7 GGAACTTGGGTTGCTAGATAGGGAGGTACT 2 50 0 TTGCTAGATA 0.947634 -251 ACTTCTAGGTTTGCTAGATAAGGAAGGTTT 2 212 0 TTGCTAGATA 0.947634 -89 GTAATAGGGATTTCTAGGTGACAGC 4 75 1 TTTCTAGGTG 0.904521 -15 CGCCCAGCTAATTCTAGATACAGACATTTT 5 99 1 ATTCTAGATA 0.911376 -169 AGGTGAGGATAAGCTAGGTAAGATTCAAAA 6 22 0 AAGCTAGGTA 0.908346 -106 ********** Masking position 5 Map Score: 1.29934 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 25 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: 2.10564e-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: 2.10564e-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: 2.10564e-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