AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -irpoN_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 PH0359 300 443aa long hypothetical glutamine synthetase #2 PH0879 300 367aa long hypothetical hydrogenase expression/formation protein hypD #3 PH1353 66 679aa long hypothetical formate dehydrogenase #4 PH1354 28 196aa long hypothetical protein #5 PH1427 209 167aa long hypothetical protein #6 PH1428 259 121aa long hypothetical protein #7 PHS039 52 64aa long hypothetical protein #8 PH1429 288 147aa long hypothetical protein #9 PH1433 59 118aa long hypothetical protein #10 PH1437 45 427aa long hypothetical NADH-ubiquinone oxidoreductase subunit #11 PH1439 300 321aa long hypothetical NADH-ubiquinone oxidoreductase subunit #12 PH1454 265 241aa long hypothetical protein #13 PH1455 247 120aa long hypothetical protein #14 PH1456 82 174aa long hypothetical phaE product #15 PH1581 75 139aa long hypothetical protein #16 PH1815 24 284aa long hypothetical cobalt transport ATP-binding protein Motif number 1 TTCCATAAAGGAAGGCGAATA 1 1 0 GAAGGGAATA 0.72132 -300 CAGCAAGTAAGAGGGTTAGGAAGGCAAGTAA 1 100 0 GAGGGTAGGA 0.929037 -201 AGTTGATTTTGGAGGTGTGAAAAGGGAGGTT 2 136 1 GGAGGGTGAA 0.694455 -165 CTCAGCCCTTGGAGGTGAGTGA 2 289 1 GGAGGGAGTG 0.945571 -12 CAATGGTTGAGGAGGTTTGGAG 5 198 1 GGAGGTTGGA 0.882045 -12 ATTTGGTCTAGGCGGTGAAGATTGGAAAAGA 8 90 1 GGCGGGAAGA 0.722228 -199 ACACGGACTCGAAGACGTGGGTGGAATGAAC 8 150 1 GAAGAGTGGG 0.842224 -139 GGCCCTGGAGGAGGGAGAGGA 8 278 1 GAGGGGAGGA 0.984933 -11 TATCTCCTGAGGAGGGGAGGTAA 10 33 1 GGAGGGAGGT 0.936106 -13 GGAAGAAGGGTAGGGATGGTCCCGT 11 5 1 GAAGGTAGGG 0.958494 -296 CCGTCAGATGGAAGATGAGGGAACCAACTTT 11 32 1 GAAGAGAGGG 0.942808 -269 TCCTACTCCCGCGGGAGTGGGATCCCCTTTT 11 261 0 GCGGGGTGGG 0.796122 -40 GGATGCATTAGGGGGTGAGGAT 11 289 1 GGGGGGAGGA 0.984624 -12 TTTTAATGGCGAAGATGAAGACAGCACCGCT 12 202 0 GAAGAGAAGA 0.706396 -64 GTACAGGTATGAAAGCGAGGAGGAAGAGAAA 12 237 1 GAAAGGAGGA 0.853748 -29 TAACCCCGGCGAAGGATAGTACTGCATATAC 13 196 0 GAAGGTAGTA 0.783823 -52 GATGCTCCCAAGGAGAGGGGAGTA 16 9 1 CAAGGGAGGG 0.894461 -16 ***** ***** Masking position 4 Map Score: 16.4127 Number of sites scoring better than the average of aligned sites = 1292 Number in coding regions = 1179 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 2 CTTGACCTTCTAACCGATGTAAGAGCTGGTGATTAC 2 170 1 TACGGAGAGC 0.944947 -131 ATAGAAAAACTCGACGAGGAAAAAGCTAAGGAAATA 2 230 1 TCCGGAAAGC 0.981168 -71 TGCTTTTAAATATTCACTAAAAGAGCTAC 5 4 0 TACAAAGAGC 0.719136 -206 CAATTGTGTATCACCAAAACCAAAGATATTAAACCA 5 50 1 TCCAAAAAGA 0.584899 -160 TTTTTCTTCTTCAGAGAGAAGATAGCGTAGAAATCT 5 135 0 TCAGAATAGC 0.767539 -75 TATGCTGTATTCCTCATTGGAATAGCCGGATTGATA 6 31 1 TCCAGATAGC 0.988046 -229 GAGAGGGCAATTTACATTGACATAGCGATAGTTTAT 6 175 1 TTCAGATAGC 0.890147 -85 TTTTATGTAGTAATCATCGGTATAGCGATATCTTTT 8 115 0 TACAGATAGC 0.970454 -174 GCAACGGTTTTATTCACGGCAATAGCCGGAGCTGTA 8 232 1 TACAGATAGC 0.970454 -57 CTAGCCGATGTCGTCGTTGCAATAGCCTCTATAGAT 11 106 1 TCCGGATAGC 0.990143 -195 ACCGATAGGGTAGCCGTAGTGAAAGAAGGCAAGAAG 11 157 1 TACGGAAAGA 0.78963 -144 AAGAAGATTATCCTAACCGAAAAAGATCTGCTAAAA 11 187 1 TCAAGAAAGA 0.584898 -114 GTTTATTTAGTCTTAATAGCGATAGCAACGCTACTT 13 22 1 TCAAGATAGC 0.937442 -226 GTACTATCCTTCGCCGGGGTTATAGCATTTGCAAGG 13 205 1 TCCGGATAGC 0.990143 -43 ** ** * ***** Masking position 12 Map Score: 15.6208 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 173 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 3 ATTAGTGGGTAGAAGATTTCTTCGTCTAATGTTC 1 201 1 AGGTTCTTCG 0.667341 -100 TTTAATTTCAAGAACCTTTCCTGGGACGGCAAGA 2 88 0 AGCTTCCTGG 0.839895 -213 CCTCTGATAGGGTAGTTGCCCTGGATACCCTCAA 6 98 1 GGGTCCCTGG 0.989014 -162 ACCAAATTTTATTCCGTACCCTGGACTAAGAGCA 8 63 0 ATCTCCCTGG 0.654055 -226 CTACAGCTCCGGCTATTGCCGTGAATAAAACCGT 8 235 0 GGATCCGTGA 0.79234 -54 AGAAGGGTAGGGATGGTCCCGTCAGATGGAAGAT 11 14 1 GGGTCCGTCA 0.968121 -287 AGTTGGGAAAAGTTGGTTCCCTCATCTTCCATCT 11 37 0 AGGTCCCTCA 0.976629 -264 GAAATCAACTAGCCGATGTCGTCGTTGCAATAGC 11 98 1 AGGTTCGTCG 0.939269 -203 GGGATTTGCTAGCTGCTACCGTGGGAATGGCCGC 12 83 1 AGGTCCGTGG 0.99191 -183 CCGCTCCTATGGCCGCTTCCGTCATTGCAACGTC 12 163 0 GGGTCCGTCA 0.96844 -103 AAGCGGCCATAGGAGCGGCCCTGAGCGGTGCTGT 12 179 1 AGGGCCCTGA 0.912292 -87 TATCTACGGTAGTGGGTCCCCTGAAGACCCTGTA 13 64 0 AGGTCCCTGA 0.985037 -184 CCGTAGATAGACTAGTTGCCGTGGATATAATGAC 13 89 1 ACGTCCGTGG 0.928766 -159 ** * * ****** Masking position 12 Map Score: 10.6627 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 217 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 TGAGAAAACTTCCTCCCAAGCTTCAAGTATTTCCT 2 258 0 TCTCCAGCTA 0.978413 -43 TCACTCACCTCCAAGGGCTGAGAAAACTTCC 2 280 0 ACTCCAGGTA 0.933171 -21 CCAAAGATATTAAACCAAAGGTTGAACACTTTTAT 5 69 1 TAACCAGGTA 0.751496 -141 AATAGCGTTTTAAACCAATGGTTGAGGAGGTTTGG 5 183 1 TAACCAGGTA 0.751496 -27 CATAATAATCCAATTCATAATCCTCCTAGG 7 6 1 TATCCATCTA 0.643485 -47 CAATTCATAATCCTCCTAGGGATCATACTCACTTC 7 21 1 TCTCCAGGTA 0.976522 -32 GCTTTGGCATTTCTCTCATTGATGATAATATTTGC 8 16 1 TCTCTATGTA 0.767764 -273 TAATATTTGCTGCTCTTATGGTTGCTCTTAGTCCA 8 41 1 TCTCTAGGTC 0.893422 -248 CTATGTTCATTCCACCCACGTCTTCGAGTCCGTGT 8 150 0 TCACCAGTTC 0.728247 -139 AAACCGTTGCTTCTCCAATGGTATCGTAACCTCTG 8 207 0 TCTCCAGGAC 0.875774 -82 TCCTCTCCCTCCTCCAGGGCCTTAGAAGAGCTAC 8 265 0 TCTCCGGCTA 0.877827 -24 GATATAATTGTTCTCCTAATGATTATATCCGCAAT 12 31 1 TCTCCATGTA 0.962869 -235 TTTAATAAATTTCACCCATGGTTAAGGACTTATTC 14 47 0 TCACCAGGTA 0.976376 -36 * **** * ** * * Masking position 5 Map Score: 10.1505 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 284 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 GGTGTGAAAAGGGAGGTTAGACTTGACCTT 2 149 1 GGGAGGTTAG 0.87314 -152 TCAGAGAGAAGATAGCGTAGAAATCTTAAA 5 131 0 GATAGCGTAG 0.913925 -79 TACAACCTCTGATAGGGTAGTTGCCCTGGA 6 93 1 GATAGGGTAG 0.984652 -167 CTCCTCAGGAGATAGGGATGACCTGCATTC 10 17 0 GATAGGGATG 0.926402 -29 CTATCTCCTGAGGAGGGGAGGTAA 10 32 1 AGGAGGGGAG 0.850881 -14 GGAAGAAGGGTAGGGATGGTCCCGTCAG 11 9 1 GGTAGGGATG 0.925025 -292 AAGCTGTACCGATAGGGTAGCCGTAGTGAA 11 150 1 GATAGGGTAG 0.984652 -151 TGCTCCCAAGGAGAGGGGAGTA 16 13 1 GAGAGGGGAG 0.981179 -12 ********** Masking position 4 Map Score: 5.76981 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 259 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 TATACCAAATATAAGTCTTTACTCATGAACAT 1 236 0 AAAGTCTTAC 0.852713 -65 TTTTAAAACCAAAAGTTTTCAACCTATCCC 2 9 0 AAAGTTTTAA 0.66494 -292 TTTTGGTTTTAAAAATGTCTAAAAATATTGGT 2 27 1 AAAATGTCAA 0.826818 -274 TTCACCATTAAGAAGTGCTTACCAATATTTTT 2 47 0 AAAGTGCTAC 0.920056 -254 ATAAATGTTAAAAATAAAAATA 3 55 0 AAAATGTTAA 0.917378 -12 AATTGAAAATAAAAGTGTTCAACCTTTGGTTT 5 80 0 AAAGTGTTAA 0.946728 -130 AAGATAGCGTAGAAATCTTAAAAGGGTTTTTT 5 121 0 AAAATCTTAA 0.866141 -89 TATGTAACTGAGAAGTGCATAAACTATCGCTA 6 197 0 AAAGTGCAAA 0.851248 -63 CATCAATGAGAGAAATGCCAAAGCTCTTT 8 8 0 AAAATGCCAA 0.846873 -281 AACTCGGGAAATAAATCCAGAAGTAAAAGGGG 11 237 1 AAAATCCAAA 0.675702 -64 ACTTATTCTTATAAATGTTTACCTTTGTCACA 14 23 0 AAAATGTTAC 0.861247 -60 ATTTATAAGAATAAGTCCTTAACCATGGGTGA 14 39 1 AAAGTCCTAA 0.923048 -44 * ******* ** Masking position 4 Map Score: 4.74775 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 77 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 GGTTCCATAAAGGAAGGCGAATA 1 4 0 AGGAAGGCGA 0.919164 -297 TAAGAGGGTTAGGAAGGCAAGTAAACTTAG 1 94 0 AGGAAGGCAA 0.979866 -207 CTCCAAAAAGAGGAAAGAAA 4 1 0 AGGAAAGAAA 0.81266 -28 CTTCTCTCTGAAGAAGAAAAAATAAGGAAG 5 150 1 AAGAAGAAAA 0.806666 -60 AGAAAAAATAAGGAAGTAAAATAGCGTTTT 5 164 1 AGGAAGTAAA 0.847201 -46 GGAAGAAGGGTAGGGATGGTCC 11 3 1 AAGAAGGGTA 0.69209 -298 GCGAAGGGATTGGAAGGAAATCAACTAGCC 11 82 1 TGGAAGGAAA 0.874787 -219 GCCGTAGTGAAAGAAGGCAAGAAGATTATC 11 169 1 AAGAAGGCAA 0.954063 -132 CGGGGGCCTGAAGCAGGAAAAACAGTATCG 12 134 0 AAGCAGGAAA 0.815461 -132 GAAAGCGAGGAGGAAGAGAAACCTGGTTG 12 247 1 AGGAAGAGAA 0.868058 -19 ********** Masking position 5 Map Score: 5.00569 Number of sites scoring better than the average of aligned sites = 581 Number in coding regions = 540 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 8 CTTTATGGAACCCTGTTAATGATAATTTCT 1 22 1 CCCTGTTAAT 0.950074 -279 GCCTTCCTAACCCTCTTACTTGCTGGGGCT 1 106 1 CCCTCTTACT 0.940392 -195 CTTTAAAAAACCCTTTTAAGATTTCTACGC 5 117 1 CCCTTTTAAG 0.939194 -93 GAGTGGGATCCCCTTTTACTTCTGGATTTA 11 248 0 CCCTTTTACT 0.972238 -53 TACCTGTACGTCCTTTTAATGGCGAAGATG 12 216 0 TCCTTTTAAT 0.934528 -50 GGATTTTTCCTTTTAATAAATTTCACC 14 66 0 TCCTTTTAAT 0.934528 -17 ********** Masking position 6 Map Score: 2.85504 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 49 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 AGACTAATCCTGGGACCTACAACCTCTGATA 6 76 1 TGGGACCACA 0.865996 -184 AATCCTCCTAGGGATCATACTCACTTCAGCA 7 29 1 GGGATCAACT 0.935341 -24 TGGAAGATGAGGGAACCAACTTTTCCCAACT 11 40 1 GGGAACCACT 0.989419 -261 GAAGTAAAAGGGGATCCCACTCCCGCGGGAG 11 256 1 GGGATCCACT 0.989419 -45 CACCCCCTAATGCATCCTACTCCCGCGGGAG 11 275 0 TGCATCCACT 0.878712 -26 AGGGTCTTCAGGGGACCCACTACCGTAGATA 13 67 1 GGGGACCACT 0.987265 -181 ******* *** Masking position 9 Map Score: 1.79467 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 32 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 10 AGACGAAGAAATCTTCTACCCACTAATATAC 1 197 0 ATCTTCTACC 0.981735 -104 CACCTCCAAAATCAACTATCCCGATGTTTCC 2 122 0 ATCAACTACC 0.963206 -179 GTTAGACTTGACCTTCTAACCGATGTAAGAG 2 164 1 ACCTTCTACC 0.960338 -137 TTGGAAGGAAATCAACTAGCCGATGTCGTCG 11 91 1 ATCAACTACC 0.963204 -210 GGTTAGGATAATCTTCTTGCCTTCTTTCACT 11 174 0 ATCTTCTTCC 0.942319 -127 ******** ** Masking position 7 Map Score: 0.678159 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 6 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 11 TTAGGAAGGCAAGTAAACTTAGTTTATATA 1 86 0 AAGTAAACTT 0.669631 -215 CTTGAAATTAAAGGAAACATCGGGATAGTT 2 110 1 AAGGAAACAT 0.957193 -191 TAAATGTTAAAAATAAAAATATTATTCGCA 3 46 0 AAATAAAAAT 0.635275 -21 AATACAGCATAGAGAAACATCGACATCAAA 6 12 0 AGAGAAACAT 0.934788 -248 GCGAGGAGGAAGAGAAACCTGGTTG 12 251 1 AGAGAAACCT 0.791973 -15 TATTAAGACTAAATAAACATTAACGCTCA 13 10 0 AAATAAACAT 0.898428 -238 TATAGGGCTAAAAGAACCATTAATCCCACT 13 132 0 AAAGAACCAT 0.802388 -116 TTTGTGACAAAGGTAAACATTTATAAGAAT 14 21 1 AGGTAAACAT 0.903635 -62 AATTTATTAAAAGGAAAAATCC 14 71 1 AAGGAAAAAT 0.815012 -12 ********** Masking position 5 Map Score: 1.65674 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 123 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 12 ATTTCTTCGTCTAATGTTCAATGTTCATGA 1 216 1 CTAATGTTCA 0.816995 -85 TAAGTCTTTACTCATGAACATTGAACATTA 1 227 0 CTCATGAACA 0.719338 -74 TCATCCGCTTTTAGTGAACAATATACCAAA 1 259 0 TTAGTGAACA 0.831534 -42 GAATAGTTATCTAATGATCATCCGCTTTTA 1 276 0 CTAATGATCA 0.941383 -25 CTAGTGAATAGTTATCTAAT 1 291 0 CTAGTGAATA 0.916456 -10 GATGTAAGAGCTGGTGATTACGTTATAGTT 2 185 1 CTGGTGATTA 0.789577 -116 GTAGCTCTTTTAGTGAATATTTAAAAGCA 5 10 1 TTAGTGAATA 0.75581 -200 CATAATCCTCCTAGGGATCATACTCACTTC 7 26 1 CTAGGGATCA 0.842299 -27 AATTGTTCTCCTAATGATTATATCCGCAAT 12 36 1 CTAATGATTA 0.909673 -230 TGAGCGTTAATGTTTATTTAGTCTTA 13 7 1 TTAATGTTTA 0.441307 -241 ********** Masking position 2 Map Score: 1.29759 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 65 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 13 CACTAAAAGCGGATGATCATTAGATAACTA 1 273 1 GGATGATCAT 0.829906 -28 TAGTTGCCCTGGATACCCTCAACACACTAG 6 110 1 GGATACCCTC 0.814849 -150 CTGCTCTTATGGTTGCTCTTAGTCCAGGGT 8 50 1 GGTTGCTCTT 0.940509 -239 CAGGAGATAGGGATGACCTGCATTCTTTAC 10 12 0 GGATGACCTG 0.891439 -34 TTTTCGGTTAGGATAATCTTCTTGCCTTCT 11 180 0 GGATAATCTT 0.901958 -121 CGCGGGAGTGGGATCCCCTTTTACTTCTGG 11 253 0 GGATCCCCTT 0.923206 -48 CAACCAGGTTTCTCTTCCTCCTCGCT 12 250 0 GGTTTCTCTT 0.751827 -16 TACTACAAGAGGATGATCTTCCTTGACGTT 13 160 1 GGATGATCTT 0.964572 -88 ********** Masking position 4 Map Score: 0.664868 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 154 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 14 ********** No masking Map Score: 2.29749e-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 15 ********** No masking Map Score: 2.29749e-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