AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -iphoB_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 PH0024 36 284aa long hypothetical sugar transport membrane protein #2 PH0025 169 426aa long hypothetical protein #3 PH0164 300 160aa long hypothetical protein #4 PH0194 60 375aa long hypothetical multiple sugar-binding transport ATP-binding protein #5 PH0206 132 544aa long hypothetical protein #6 PH0207 206 428aa long hypothetical protein #7 PH0209 300 131aa long hypothetical protein #8 PH1037 129 142aa long hypothetical protein #9 PH1214 267 441aa long hypothetical cytoplasmic protein #10 PH1238 73 231aa long hypothetical protein #11 PH1239 59 237aa long hypothetical protein #12 PH1241 48 167aa long hypothetical protein #13 PH1605 300 425aa long hypothetical protein #14 PH1606 43 447aa long hypothetical protein #15 PH1607 25 249aa long hypothetical PHNP protein #16 PH1815 24 284aa long hypothetical cobalt transport ATP-binding protein Motif number 1 TAAATTTACCAATTAAAAATGTATCTTCCT 2 19 1 AATTAAAAAT 0.73909 -151 CTCTTCTTAAAAATAAAATTGCAT 4 47 0 TCTTAAAAAT 0.75865 -14 ATTCGGGGTATTTAAAAAGTGTTTCGGTTA 5 49 0 TTTAAAAAGT 0.655517 -84 GTACACTAAAATTGAAAAGTCCAATGTAAG 5 81 0 ATTGAAAAGT 0.851506 -52 CATGTTTACTTTTGTAAAGTTGTAGGTTAC 6 138 0 TTTGTAAAGT 0.567404 -69 GGAGCCTTGCTTATAAAAATTTGCTACTAA 7 28 1 TTATAAAAAT 0.646774 -273 GAACTAGTAAATTTAAAAGTATTAGTAGCA 7 49 0 ATTTAAAAGT 0.918129 -252 CCATAGTGTCATTTAAAAATGTCTGTATCT 9 114 0 ATTTAAAAAT 0.893124 -154 AAACTTTAAGTATTAAAAATCAGTCTAACA 9 225 1 TATTAAAAAT 0.789608 -43 AAACTAAAACTTTTAAAAATTGTTAAAAGC 10 23 1 TTTTAAAAAT 0.951361 -51 CTTTTAGGAGTTTTTAAAATAAAAGGTTAA 11 14 0 TTTTTAAAAT 0.739437 -46 GACGATCTTTGAAAAATAGAAAAGGGC 11 43 0 TTTGAAAAAT 0.901991 -17 ATTTAAAAATCAAGTGTTAA 12 1 1 ATTTAAAAAT 0.893124 -48 GGAGCTTAACCTTTAAAAGTTGCACATTAA 13 192 0 CTTTAAAAGT 0.793191 -109 AGCGATTTCGATTTAAAAATATAATGGAAA 14 13 0 ATTTAAAAAT 0.893124 -31 ********** Masking position 6 Map Score: 13.348 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 50 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 2 TAGGGCATAAGGGATCTTTGGTGAACCATCC 2 149 1 GGGATTGGTG 0.922515 -21 TTACAGTAACGGGCTTAGGGAGGAGTTCAGGGA 3 41 1 GGGCTAGAGG 0.979651 -260 GAGGAGTTCAGGGATAAGAAGGGACTTCTCTAT 3 60 1 GGGATAAGGG 0.881594 -241 ATTGGATTGATGGCGTTTTGAAGGTTATTCTAA 3 256 1 TGGCGTGAAG 0.720187 -45 ACAAAGGGGCTATTTAAGGAGCCTTGCTT 7 7 1 GGGCTTAAGG 0.949239 -294 ACATCAAGGAGGGCGAAGGAAAGGTTCTAATAC 7 190 1 GGGCGAAAAG 0.889002 -111 TCCCATGAACGGGATTAGCCAGGCTATTCCAAT 8 60 0 GGGATACAGG 0.919931 -70 TCCCGTTCATGGGAGTATTGATGGCATCGGTAA 8 79 1 GGGAGAGATG 0.921419 -51 TAAATTAAGCGGGCTCCTGGGGGACCGCTTCAT 9 36 1 GGGCTCGGGG 0.947196 -232 AGAATTAGCTGGGCGATGACATGATTCATCCCT 9 81 0 GGGCGTCATG 0.930142 -187 TCAAAGTTTTGGGAGTTATGAGGAGACATTTAT 9 156 0 GGGAGTGAGG 0.980101 -112 AAATAGAAAAGGGCTTTTAGGAGTTTTTAAAAT 11 24 0 GGGCTTGGAG 0.966467 -36 AATAAATCTCGGGAGGTTGCGAG 12 36 1 GGGAGTCGAG 0.904786 -13 ***** * **** Masking position 3 Map Score: 11.298 Number of sites scoring better than the average of aligned sites = 358 Number in coding regions = 325 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 GTTAAATGGGCCTATCTCCTGGCGTATCAT 3 138 1 CCTATCTCCT 0.864334 -163 GAGAGTCCTAAACTTCTCCTCAAGCTCATG 3 177 0 AACTTCTCCT 0.902335 -124 GAAGACTAAAAACATTTCCTGGAAAAACAT 4 15 0 AACATTTCCT 0.776196 -46 ATTACCCCCGCATCTTTTCTAGATATTTTA 6 91 1 CATCTTTTCT 0.825128 -116 CAAGTATTAGAACCTTTCCTTCGCCCTCCT 7 196 0 AACCTTTCCT 0.946274 -105 GAACTCCAACCCTTTCTCCTGGTAGTGCAA 7 223 0 CCTTTCTCCT 0.901274 -78 TGACATGATTCATCCCTCCTGAACCGATGA 9 68 0 CATCCCTCCT 0.932978 -200 TCATATGATAAATGTCTCCTCATAACTCCC 9 149 1 AATGTCTCCT 0.796855 -119 TTTTTGTTAGAATCTCTTCTAGGATTTACA 9 198 0 AATCTCTTCT 0.825128 -70 AAAGCTGTAACACTTTTTCTGAAATTGGTG 10 48 1 CACTTTTTCT 0.647812 -26 CATCAGCATACACCCTTCCTGGGACTCTCA 13 77 1 CACCCTTCCT 0.911855 -224 TATTCACAGGACTCTTTCCTTT 15 3 0 ACTCTTTCCT 0.903484 -23 TACTCCCCTCTCCTTGGGAGCATC 16 11 0 CCCCTCTCCT 0.978119 -14 ********** Masking position 7 Map Score: 10.0037 Number of sites scoring better than the average of aligned sites = 910 Number in coding regions = 843 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 4 CCTCCCAGATAAAAAAGAAATAGAGAAA 1 2 0 AAAAAATAGA 0.890058 -35 CAGAAAAATAAATAAAGATTTAGGGCATAAGGGATCT 2 129 1 AAAAATTAGA 0.97307 -41 AGGATATCGGTGAAAAAATTTACAGTAACGGGCTTAG 3 22 1 TAAAATTAGA 0.958479 -279 ATGAGAAGACTAAAAACATTTCCTGGAAAAACATTGC 4 12 0 TAAAATTCGA 0.82803 -49 ATTTCCTTTCTTGAAATAATTTATGAAGCCCGGGGAG 6 17 1 TAAAATTTGA 0.891339 -190 TAAATTTACTAGTTCATAGTTAGGGAATGGTGAACTA 7 64 1 ATCAATTAGA 0.548491 -237 GGAATGGTGAACTAAATGGTTATGGAATTATCAAAGA 7 87 1 AAAAGTTAGA 0.850724 -214 TTATGGAATTATCAAAGATGTACGGGAAGCTGATATA 7 106 1 AAAAAGTAGA 0.871869 -195 GGAGTTCCTTACGAAAAAGTTACAGCAGTTGGAGATA 7 246 1 AAAAATTAGA 0.973069 -55 TCCCAAAACTTTGACAAATTTAATGTAAATCCTAGAA 9 175 1 TACAATTAGA 0.879369 -93 AAGAGATTCTAACAAAAACTTTAAGTATTAAAAATCA 9 210 1 AAAAATTTGA 0.927262 -58 TACTTGGTAAAGTAAAAATTTTGTGTAAATTTTTTCG 13 231 0 AAAAATTTGA 0.926973 -70 GCGATTTCGATTTAAAAATATAATGGAAAGG 14 5 0 TAAAAATAGA 0.838004 -39 * *** * *** * * Masking position 6 Map Score: 9.34695 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 70 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 TTTAACGCCCTCCCAGATAAAAAAGAAA 1 19 0 CCTCCCAGAT 0.913211 -18 TCCCTGAACTCCTCCCTAAGCCCGTTACTG 3 44 0 CCTCCCTAAG 0.924469 -257 CTTAATTCGTCCTCTAAGGGGGGTGAAAG 5 114 1 CCTCTAAGGG 0.712712 -19 CTTCGGCGGTGCTCCCCGGGCTTCATAAAT 6 35 0 GCTCCCCGGG 0.946994 -172 CCGGGGAGCACCGCCGAAGGCGGAGTCAAT 6 46 1 CCGCCGAAGG 0.693115 -161 GGGTAATAACCCGCCCAAGTTCATTGACTC 6 68 0 CCGCCCAAGT 0.821287 -139 TTTCCTTCGCCCTCCTTGATGTCAATTACA 7 182 0 CCTCCTTGAT 0.68685 -119 TTCCTCTCTGGGGCTTGGACTA 7 289 0 CCTCTCTGGG 0.955218 -12 AATTAAGCGGGCTCCTGGGGGACCGCTTCA 9 38 1 GCTCCTGGGG 0.815665 -230 CAGCATACACCCTTCCTGGGACTCTCATTC 13 80 1 CCTTCCTGGG 0.87586 -221 TCTTATCTATCCTCTTTAGGGGAACCACCA 13 140 1 CCTCTTTAGG 0.677135 -161 TAAAGGTTAAGCTCCCAGATTGATCGAAAA 13 207 1 GCTCCCAGAT 0.827509 -94 GATGCTCCCAAGGAGAGGGGAGT 16 4 1 GCTCCCAAGG 0.958404 -21 ********** Masking position 2 Map Score: 7.11875 Number of sites scoring better than the average of aligned sites = 962 Number in coding regions = 881 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 6 TAAATTTACCAATTAAAAATGTATCTTCCT 2 19 1 AATTAAAAAT 0.429348 -151 TATCTGTTTTTAATGTAAATTAGGCATTAG 2 78 1 TAATGTAAAT 0.834913 -92 GCAAAAACAGAAAAATAAATAAAGATTTAG 2 122 1 AAAAATAAAT 0.431434 -48 CTAAGCCCGTTACTGTAAATTTTTTCACCG 3 29 0 TACTGTAAAT 0.541631 -272 TCAAGAAAGGAAATATAAAT 6 1 0 AAATATAAAT 0.87682 -206 ATGATGCCTCAAATGTAAAATATCTAGAAA 6 106 0 AAATGTAAAA 0.879412 -101 TTCGTCAATTAAATATAAATGTTTCGGCAT 6 179 0 AAATATAAAT 0.87682 -28 ATGAACTAGTAAATTTAAAAGTATTAGTAG 7 51 0 AAATTTAAAA 0.448842 -250 AAGTTGATGAAATTGTAATTGACATCAAGG 7 169 1 AATTGTAATT 0.460238 -132 GGGTATGGGGAATTATAAATTAAGCGGGCT 9 21 1 AATTATAAAT 0.780088 -247 TTGACAAATTTAATGTAAATCCTAGAAGAG 9 185 1 TAATGTAAAT 0.834913 -83 CTTCTTGAAAAAATGAAAAACGATAGAACC 13 42 0 AAATGAAAAA 0.598314 -259 ATGGATATATAATTGTAAAACTGTCAATTA 13 266 0 AATTGTAAAA 0.790837 -35 ********** Masking position 7 Map Score: 3.67971 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 119 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 7 GGATGGTTCACCAAAGATCCCTT 2 157 0 TGGTTCACCA 0.915755 -13 AAATCGGCTGAGGTTCCCCTCTTTCAAGGG 3 226 0 AGGTTCCCCT 0.948237 -75 CATAACCATTTAGTTCACCATTCCCTAACT 7 81 0 TAGTTCACCA 0.926504 -220 GCTTAATTTATAATTCCCCATACCCATAAC 9 16 0 TAATTCCCCA 0.855937 -252 GATGATGAAGCGGTCCCCCAGGAGCCCGCT 9 43 0 CGGTCCCCCA 0.949064 -225 ATAGAAATGGTGGTTCCCCTAAAGAGGATA 13 147 0 TGGTTCCCCT 0.982841 -154 ********** Masking position 4 Map Score: 1.97924 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 70 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 8 GCCAGGAGATAGGCCCATTTAACATCCTCTGGATC 3 126 0 AGGCCTAAAT 0.930199 -175 ATAGACGTTGAGGCCCTTGAAAGAGGGGAACCTCA 3 213 1 AGGCCTAAAG 0.985439 -88 AAAATTGAAAAGTCCAATGTAAGTTATTCGGGGTA 5 69 0 AGTCCTAATT 0.846284 -64 GAATTAAGAAAGTACACTAAAATTGAAAAGTCCAA 5 87 0 AGTACTAATG 0.846284 -46 TTTATAAGCAAGGCTCCTTAAATAGCCCCTTTGT 7 10 0 AGGCTTAAAG 0.95686 -291 ACCAGGGGCAAGTACATTGGAAAAGTTGATGAAAT 7 147 1 AGTACTAAAG 0.871513 -154 GGGATTAGCCAGGCTATTCCAATTGACCAGGCAAT 8 48 0 AGGCTTAATG 0.947377 -82 GGCATCGGTAAGGCCCTATGAAGAGATCGTGAGCG 8 101 1 AGGCCAAAAG 0.923827 -29 ATTAAAAATCAGTCTAACATAAATGTAGGGAGGCG 9 236 1 AGTCTCAATG 0.70878 -32 ***** * ** ** Masking position 11 Map Score: 1.28025 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 249 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 TAATAGATTTGAATTTTAGGAAGATACATTT 2 35 0 GAATTTAGGA 0.980262 -135 TAGTAGGCATGAGCTTGAGGAGAAGTTTAGG 3 170 1 GAGTTGAGGA 0.929194 -131 AGCTTGAGGAGAAGTTTAGGACTCTCTTCGG 3 181 1 GAATTTAGGA 0.980262 -120 AAGTAAACATGAAAATCAGGAAATGCCGAAA 6 157 1 GAAATCAGGA 0.953118 -50 TGGGATGAAAATTAGGAGGTATCTAGT 8 7 1 GAAATTAGGA 0.971956 -123 *** ******* Masking position 6 Map Score: 1.09401 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 70 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 CCCTTATGCCCTAAATCTTTATTTATTTTT 2 132 0 CTAAATCTTT 0.696236 -38 TAATATCTAACCGAAACACTTTTTAAATAC 5 42 1 CCGAAACACT 0.805291 -91 CATTTGTAACCTACAACTTTACAAAAGTAA 6 133 1 CTACAACTTT 0.827325 -74 TCAGGAAATGCCGAAACATTTATATTTAAT 6 172 1 CCGAAACATT 0.915083 -35 AAATTTGCTACTAATACTTTTAAATTTACT 7 44 1 CTAATACTTT 0.696236 -257 TCTCCAACTGCTGTAACTTTTTCGTAAGGA 7 251 0 CTGTAACTTT 0.884243 -50 TTCCCCATACCCATAACATTAA 9 3 0 CCATAACATT 0.839166 -265 CTCATAACTCCCAAAACTTTGACAAATTTA 9 167 1 CCAAAACTTT 0.951323 -101 GAGATTCTAACAAAAACTTTAAGTATTAAA 9 212 1 CAAAAACTTT 0.789251 -56 AAGTTGAAAACTAAAACTTTTAAAAATTGT 10 16 1 CTAAAACTTT 0.947476 -58 TTGTTAAAAGCTGTAACACTTTTTCTGAAA 10 42 1 CTGTAACACT 0.633507 -32 ********** Masking position 10 Map Score: 6.12528 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 124 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 11 ********** No masking Map Score: -5.29822e-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 12 ********** No masking Map Score: -5.29822e-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 13 ********** No masking Map Score: -5.29822e-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