AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00190_aful_reg_300.orf -o00190_aful_300.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -x5 -e 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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 AF0140 123 ubiquinone/menaquinone biosynthesis methyltransferase (ubiE) #2 AF0190 135 cytochrome C oxidase, subunit II, putative #3 AF0191 23 A. fulgidus predicted coding region AF0191 #4 AF0192 300 A. fulgidus predicted coding region AF0192 #5 AF0681 145 succinate dehydrogenase, flavoprotein subunit A (sdhA) #6 AF1158 163 ATP synthase, subunit E, putative #7 AF1160 27 H+-transporting ATP synthase, subunit K (atpK-1) #8 AF1168 25 H+-transporting ATP synthase, subunit D (atpD) #9 AF1461 87 iron-sulfur cluster binding protein, putative #10 AF1462 136 A. fulgidus predicted coding region AF1462 #11 AF2046 26 cytochrome oxidase, subunit I, putative #12 AF2297 126 cytochrome oxidase, subunit I (cydA-2) #13 AF2298 34 conserved hypothetical protein #14 AF2300 60 deoxyhypusine synthase (dys1-2) #15 AF2301 278 conserved hypothetical protein #16 AF2350 300 ATP-dependent RNA helicase HepA, putative #17 AF2351 219 conserved hypothetical protein Motif number 1 GTGGTATAGAGAGCTGAACTTTTCAAAACCACTCGATC 2 16 1 GAAACTTTAA 0.775841 -120 AGGAAACTTAGAATAAAAAGTTTGGAATCTTTTGTTGC 2 68 0 GAAAAGTTAT 0.952456 -68 TTGGAACCGAGTAAAAAAATTTTTAAAATTTT 2 114 1 GTAAATTTAA 0.804513 -22 TACATCGCTGGATAAAGAAGTTTGAGGAAAAATTGCCC 4 31 0 GAGAAGTTGA 0.849337 -270 GGAACGACTCGAAATTAAAGTTTTGGGAATTGCAACCT 4 141 0 GAAAAGTTGA 0.939392 -160 TATTTTTAAGGAGCTTAAATCTTTGAGAGGAACGACTC 4 169 0 GAAAATTTAA 0.964655 -132 TGTGTTCACTAATATCAAATGTTTAAAAATCTTTCGCC 4 239 0 AAAAATTTAA 0.795967 -62 TAGTACGCACGAGAAAAAAGATTTTATATAACAAACCT 5 23 0 GAAAAGTTAA 0.984145 -123 CCTGTGTAAAAATAACAAAGCTTAAATACGATTTGTAA 6 98 1 AAAAAGTTAA 0.8987 -66 GCTTTCGAATGTCTTTAAAGTTTAGAGTTTGATCAGG 6 137 1 GTAAAGTTAT 0.752031 -27 AGCCCAATTAGACGGGGAAGTTTATAAAGAGAATGGAC 9 12 1 GAGAAGTTAA 0.957585 -76 TTCGATTATCGAAAGCAAATTTTTTAAACGATTTATTG 12 65 0 GAAAATTTAA 0.964641 -62 TTCGATAATCGAACGAAAAGATTAAATTTTATGTAGAT 12 90 1 GAAAAGTTAT 0.952589 -37 TTAAAATTAGGAAATTAATTATTTGACATTCGTATAAA 15 70 0 GAAATTTTAA 0.700173 -209 TTAAAATCTGGAATAAAAATTTTGATTAAGAGATAAAT 15 115 0 GAAAATTTTA 0.713604 -164 AACAGAGAACGAGTACAAAGCTGCTAAATTCTACGGGG 17 15 1 GAAAAGTGAA 0.880801 -205 ACTATATTTAAAATATGAAGATTTAATTTTGCTGGAGG 17 185 1 AAGAAGTTAT 0.51105 -35 ** **** ** * * Masking position 8 Map Score: 14.1461 Number of sites scoring better than the average of aligned sites = 406 Number in coding regions = 313 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 2 TCCTGGCATCTTTTTACCCAAAAAACATGC 1 60 0 TTTTTACCCA 0.942334 -64 TTTAAAAATTTTTTTACTCGGTTCCAACGA 2 111 0 TTTTTACTCG 0.97357 -25 CCTTTTTTCTCCGCTGAGATGGG 4 4 1 TTTTTCTCCG 0.861814 -297 AGATGGGCAATTTTTCCTCAAACTTCTTTA 4 27 1 TTTTTCCTCA 0.905979 -274 TGGCGAAAGATTTTTAAACATTTGATATTA 4 238 1 TTTTTAAACA 0.726245 -63 ATATAAAATCTTTTTTCTCGTGCGTACTAA 5 32 1 TTTTTTCTCG 0.868442 -114 AGCTTTGTTATTTTTACACAGGTAGAATTT 6 90 0 TTTTTACACA 0.930976 -74 GAAAGCAAATTTTTTAAACGATTTATTGTT 12 63 0 TTTTTAAACG 0.878809 -64 CGGTTCAGAATTTTTATACGAATGTCAAAT 15 58 1 TTTTTATACG 0.878838 -221 ATTTAGCAGCTTTGTACTCGTTCTCTGTTA 17 14 0 TTTGTACTCG 0.874006 -206 AGAGGTAGTATTTTTCCCCGTAGAATTTAG 17 38 0 TTTTTCCCCG 0.969393 -182 ********** Masking position 5 Map Score: 9.46963 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 63 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 3 GCTAAAATCCTTTCAGAGTTGCATCCTGTTTC 4 80 0 TTTGAGTTGC 0.65068 -221 TAGCAGTTCTTCTCACAGATGATGTCTGGATG 4 108 1 TCTCAGATGA 0.930635 -193 GGAGCTTAAATCTTTGAGAGGAACGACTCGAA 4 166 0 TCTGAGAGGA 0.95577 -135 GAAGTGAATTTTAAAGAGAGGCAACAGTTAGT 5 78 1 TTAGAGAGGC 0.749218 -68 CGGAAAATAATCGATGAGATAAAAAACGGT 6 9 0 TCGGAGATAA 0.651883 -155 GGTGTGTTTGAGGAGGTGAGATGAATG 7 8 1 TTGGAGGTGA 0.936009 -20 AAACAATTTTTAGAGGTGACAGGGA 8 8 1 TTTGAGGTGA 0.952198 -18 TCGCTGAGGTGCTATAAAAGCG 9 76 0 TCGGAGGTGC 0.905582 -12 AACAGGAGGCTCTTCCAGAGGAAACCGTATTT 10 32 0 TCTCAGAGGA 0.92422 -105 CCGATTGAGGTTTACGAGAAGACTTCGCAGAA 14 27 1 TTTGAGAAGA 0.754986 -34 TATTAAAGTCTTACACAGATGATATAAATCTT 15 13 1 TTACAGATGA 0.754229 -266 TTTAATTTGATTTGCCAGATGCTGATAAAATT 15 210 0 TTTCAGATGC 0.882021 -69 TGGTGAGATTTCGGTGAGGTGATAAC 16 285 1 TCGGAGGTGA 0.940715 -16 CTTTAACAGAGAACGAGTACAAA 17 2 1 TTTCAGAGAA 0.547006 -218 CTCCACTCGATTTCAAAGGGGAGTTTGTTTGC 17 127 0 TTTAAGGGGA 0.612843 -93 *** ******* Masking position 7 Map Score: 7.44653 Number of sites scoring better than the average of aligned sites = 980 Number in coding regions = 903 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 4 TTTTAAATTTTCGCTCCTTT 1 1 1 TTTTAAATTT 0.9091 -123 TAAAAAAATTTTTAAAATTTT 2 125 1 TTTAAAATTT 0.872306 -11 GTTGCCTCTCTTTAAAATTCACTTCGTATG 5 73 0 TTTAAAATTC 0.746019 -73 TAATCCTCGTTTTTAATTACAAATTCTACC 6 70 1 TTTTAATTAC 0.595592 -94 TTCGAATGTCTTTAAAGTTTAGAGTTTGAT 6 140 1 TTTAAAGTTT 0.754742 -24 GAACGAAAAGATTAAATTTTATGTAGATTA 12 100 1 ATTAAATTTT 0.700555 -27 AATTTCCTAATTTTAATTTTATTATTTATC 15 92 1 TTTTAATTTT 0.924934 -187 TTATTCCAGATTTTAATTTTCGTGCAAAAT 15 137 1 TTTTAATTTT 0.924934 -142 AATCTTCATATTTTAAATATAGTTTCCGTA 17 178 0 TTTTAAATAT 0.735456 -42 AAATATGAAGATTTAATTTTGCTGGAGGTG 17 195 1 ATTTAATTTT 0.774018 -25 ********** Masking position 5 Map Score: 3.82752 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 68 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 5 TTCAATGGGCGATTTAAGCAAAGGAGCGAA 1 20 0 GATTTAAGCA 0.985339 -104 AAAACCACTCGATCTAAGCATTAGTCTAGC 2 40 1 GATCTAAGCA 0.946953 -96 ACTCTGAAAGGATTTTAGCAGTTCTTCTCA 4 93 1 GATTTTAGCA 0.955033 -208 TCCTCTCAAAGATTTAAGCTCCTTAAAAAT 4 176 1 GATTTAAGCT 0.955033 -125 TTACAAATCGTATTTAAGCTTTGTTATTTT 6 106 0 TATTTAAGCT 0.829283 -58 TGATGAAAGCAGTTCTGCGAA 14 50 0 GATGAAAGCA 0.849422 -11 TGGCAAATCAAATTAAAGCAATGCTTAAAT 15 225 1 AATTAAAGCA 0.733677 -54 ATACGCTGAGTATTTAAGCATTGCTTTAAT 15 236 0 TATTTAAGCA 0.938914 -43 TTTCCCCGTAGAATTTAGCAGCTTTGTACT 17 26 0 GAATTTAGCA 0.770013 -194 ********** Masking position 7 Map Score: 7.14624 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 98 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 TACATCGCTGGATAAAGAAGTTTGAGGAAA 4 39 0 GATAAAGAAG 0.77905 -262 TGATGATTTAGAAACAGGATGCAACTCTGA 4 70 1 GAAACAGGAT 0.95225 -231 AAAAAAAAAACGAACAGGAGGCTCTTCCAG 10 46 0 CGAACAGGAG 0.918562 -91 GGCGGACTGCGTTAAAGGAGGCTATCTCCT 10 115 1 GTTAAAGGAG 0.870234 -22 AAGAGAAAAAGAAAAAGGAGTACTACGAGG 12 20 0 GAAAAAGGAG 0.972524 -107 TTCATTCTCCCAAACAGGAGTTTGGTCGTC 16 79 0 CAAACAGGAG 0.9686 -222 AGTATATCAGGATACAGGATTATCTGGACG 16 188 1 GATACAGGAT 0.938708 -113 ********** Masking position 6 Map Score: 1.76785 Number of sites scoring better than the average of aligned sites = 316 Number in coding regions = 292 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 GGCTTAAGGATTCATTTATACCTTTCGTTTAC 1 92 0 TTCATTATAC 0.927942 -32 TATTCTAAGTTTCCTTAATATCGTTGGAACCG 2 91 1 TTCCTAATAC 0.950215 -45 CATACATGTGTTCACTAATATCAAATGTTTAA 4 251 0 TTCATAATAC 0.976942 -50 CGTAATACGTTTCTTTAATAACTCCGATGGCG 16 48 0 TTCTTAATAC 0.927938 -253 GGAGAATGAATTCAGTCATAGCAGAGTTACTT 16 99 1 TTCATCATAC 0.950215 -202 GAGGTTCGAGTTCACCAATACCGTAACCGTCC 16 213 0 TTCACAATAC 0.939365 -88 **** ***** * Masking position 8 Map Score: 1.13786 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 3 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 8 GAATTTACAGGCTGCATGTTTTTTGGGTAAA 1 47 1 GCTGCAGTTT 0.951574 -77 CGCTTGAAGTTTAGGTTTGTTA 5 2 1 GCTTGAGTTT 0.981983 -144 CAATTTACTCGCTTGACGGTTTTCCAAGGCG 10 88 1 GCTTGAGGTT 0.978348 -49 CGACAGAGCCGATTGAGGTTTACGAGAAGAC 14 19 1 GATTGAGTTT 0.893974 -42 TACAGGATTATCTGGACGGTTACGGTATTGG 16 200 1 TCTGGAGGTT 0.916608 -101 ATTTAATTTTGCTGGAGGTGTTGAG 17 205 1 GCTGGAGTGT 0.969075 -15 ****** **** Masking position 6 Map Score: 0.940869 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 103 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 9 AGGATGGTAAACGAAAGGTATAAATGAATC 1 86 1 ACGAAAGGTA 0.949958 -38 CGAAAGCCTTACAAATCGTATTTAAGCTTT 6 114 0 ACAAATCGTA 0.850708 -50 TAAAAGCGGGAAGAAAGGAAAATGTGCATC 9 54 0 AAGAAAGGAA 0.866138 -34 CAAAAAAAAAAAAAAACGAACAGGAGGCTC 10 52 0 AAAAAACGAA 0.887296 -85 ATAAAATTCCACAAAACGTAACTAAATCGA 15 188 0 ACAAAACGTA 0.958502 -91 GGAGTTATTAAAGAAACGTATTACGACGAC 16 55 1 AAGAAACGTA 0.958502 -246 ********** Masking position 5 Map Score: 0.0684158 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 30 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 10 ********** No masking Map Score: -2.0013e-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: -2.0013e-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: -2.0013e-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