AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -ifhlA_mthe_opreg_100.orf -g0.495 -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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH384 249 unknown #2 MTH387 24 conserved protein #3 MTH388 35 unknown #4 MTH393 41 NADH dehydrogenase (ubiquinone), subunit 1 related protein #5 MTH394 55 unknown #6 MTH397 40 formate hydrogenlyase, subunit 7 #7 MTH783 83 hydrogenase expression/formation protein HypA #8 MTH1072 67 hydrogenase expression/formation protein HypD #9 MTH1246 30 NADH dehydrogenase I, subunit N #10 MTH1251 147 conserved protein #11 MTH1552 139 formate dehydrogenase, alpha subunit homolog #12 MTH1553 71 tungsten formylmethanofuran dehydrogenase, subunit H #13 MTH1649 110 hydrogenase expression/formation protein HypC Motif number 1 ACTTACCGGTTTCTGTGAATATAATCACGAAAACG 1 56 1 TTCTTGAAAT 0.878008 -194 TTACTAAATCTTCTGTAGAGGGACCCTTCAGATAT 1 114 1 TTCTTAAGAC 0.886659 -136 ACAGAAACTTTTTTTTACTGATATCTGAAGGGTCC 1 134 0 TTTTTATAAC 0.983138 -116 AAAAAAAAGTTTCTGTAGAGAAACCTCCAGATATT 1 153 1 TTCTTAAAAC 0.980237 -97 AATTATGGCCTTTTTTACTAATATCTGGAGGTTTC 1 172 0 TTTTTATAAC 0.983122 -78 CTAACTCACCTTTTTTAAAAAGATTTATAT 1 230 1 TTTTTAAAAT 0.951018 -20 AAATCCCCTCTTTTCTGATTAAATCCCTTCCATTT 5 30 0 TTTTTGTAAC 0.967142 -26 AATTAACAATTTTTATATAGATAACTCTATTAATT 7 29 1 TTTTTAAAAC 0.985411 -55 TCTGACAAAATTTTATAATTAGAATTAATAGAGTT 7 51 0 TTTTTATAAT 0.943693 -33 TAATATAAAGTTTTCTATATAAATCGTAATAAAAT 10 73 0 TTTTTAAAAC 0.985411 -75 CTTCACCTCACTCTCTACTCATAACCTTTATCTGT 11 14 1 CTCTTATAAC 0.871014 -126 TCAGTGTCCTTTTTATGGTGAAACTTTATCATGAT 11 51 0 TTTTTGTAAT 0.8943 -89 CATATAATAATTTTCTACAAAAATCAAATAGAAAA 12 31 0 TTTTTAAAAC 0.985408 -41 **** ** * * * * Masking position 13 Map Score: 22.0466 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 33 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 2 ATTCCCACCCCATCATGTCCTGGAGGTT 1 8 1 CCCCATCATT 0.990767 -242 CATTTTCATTCCACATCATGTCTT 5 4 0 CCACATCATT 0.93297 -52 CTGATTAAATCCCTTCCATTTTCATTCCACA 5 20 0 CCCTTCCATT 0.981393 -36 TTCTTTACCTCAGCATTTGCTCTTTATT 6 23 0 CCTCAGCATT 0.927846 -18 ATCCTTTGGCCTCCTCCATATATATATGATC 8 12 1 CTCCTCCATT 0.963841 -56 GCAGCCTCTTCCCCTTCAAGTGTTTAATCAT 10 32 1 CCCCTTCAAT 0.986823 -116 CCTCTTCACCTCACTCTCTAC 11 1 1 CCTCTTCACT 0.953766 -139 ATTTAACAGTCCCCTTCATGTTATCTTCAGT 11 81 0 CCCCTTCATT 0.995798 -59 GCCTCAAGTTCCCTTCCATCTATTCTAAATT 11 109 0 CCCTTCCATT 0.981393 -31 TCAATAACCCTCTCCAAATTAATAGGATT 13 92 0 CCTCTCCAAT 0.969324 -19 ********* * Masking position 8 Map Score: 17.2858 Number of sites scoring better than the average of aligned sites = 321 Number in coding regions = 291 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 3 ATATAAATCTTTTTAAAAAAGGTGAG 1 234 0 ATCTTTTTAA 0.858158 -16 ACCAGTAATCATCTATATATTC 2 3 0 ATCTATATAT 0.925081 -22 TAATAGAGTTATCTATATAAAAATTGTTAA 7 31 0 ATCTATATAA 0.931946 -53 GGCCTCCTCCATATATATATGATCGTGATA 8 19 1 ATATATATAT 0.454487 -49 ACACTTAAAGATCTATTTATCACGATCATA 8 36 0 ATCTATTTAT 0.917426 -32 ATATAAAGTTTTCTATATAAATCGTAATAA 10 76 0 TTCTATATAA 0.764783 -72 TTATATAGAAAACTTTATATTATCATAAAT 10 86 1 AACTTTATAT 0.91877 -62 TCTACTCATAACCTTTATCTGTGCATCATG 11 27 1 ACCTTTATCT 0.927907 -113 TTTATGGTGAAACTTTATCATGATGCACAG 11 45 0 AACTTTATCA 0.725622 -95 ATCTTCAGTGTCCTTTTTATGGTGAAACTT 11 60 0 TCCTTTTTAT 0.625729 -80 CCACACACCTATATATATATTTTTCT 12 7 1 ACCTATATAT 0.954993 -65 TTTCCCACAAATCTTTATATGTGACGGATC 13 32 1 ATCTTTATAT 0.974802 -79 TATGTGACGGATCTTTATCTAAACATTAGT 13 49 1 ATCTTTATCT 0.953553 -62 ********** Masking position 6 Map Score: 15.576 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 78 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 4 ACAGAAGATTTAGTAATAAATTTTAAGGAT 1 100 0 TAGTAATAAA 0.915312 -150 CTTCAGATATCAGTAAAAAAAAGTTTCTGT 1 139 1 CAGTAAAAAA 0.905138 -111 CTCCAGATATTAGTAAAAAAGGCCATAATT 1 177 1 TAGTAAAAAA 0.873517 -73 AAAAAAGACCTCTTAATAAAATTATGGCCT 1 196 0 TCTTAATAAA 0.76663 -54 CCCCGTAAATAATCCTGAATGA 3 24 0 CCGTAAATAA 0.93195 -12 AATCACCTTCCGGTAATTAACAATTTTTAT 7 15 1 CGGTAATTAA 0.756934 -69 ATATATATGATCGTGATAAATAGATCTTTA 8 31 1 TCGTGATAAA 0.913693 -37 GAAGAGGCTGCCGTAATAACCCCATGAGTC 10 13 0 CCGTAATAAC 0.888238 -135 TCTATATAAATCGTAATAAAATAGGGGATC 10 65 0 TCGTAATAAA 0.971022 -83 CTTTATATTATCATAAATAATCATGTTAAT 10 98 1 TCATAAATAA 0.761745 -50 TCTTTAGTACCAATAATTAACATGATTATT 10 113 0 CAATAATTAA 0.690371 -35 TATCTGTGCATCATGATAAAGTTTCACCAT 11 42 1 TCATGATAAA 0.773478 -98 TAAAGTTTCACCATAAAAAGGACACTGAAG 11 58 1 CCATAAAAAG 0.620925 -82 ********** Masking position 6 Map Score: 9.08241 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 134 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 5 ACCGGTAAGTGGATGTGACTCCATAGGAAC 1 36 0 GGATGTGACT 0.846382 -214 GAATGAAAATGGAAGGGATTTAATCAGAAA 5 24 1 GGAAGGGATT 0.947718 -32 TAATCAGAAAAGAGGGGATTTA 5 44 1 AGAGGGGATT 0.889414 -12 TTAATTACCGGAAGGTGATTTTTC 7 5 0 GAAGGTGATT 0.899856 -79 ATATATATATGGAGGAGGCCAAAGGATT 8 9 0 GGAGGAGGCC 0.917681 -59 CACTTGAAGGGGAAGAGGCTGCCGTAATAA 10 24 0 GGAAGAGGCT 0.913239 -124 GTACTAAAGAGAAGGGAGCTATAAA 10 133 1 GAAGGGAGCT 0.945179 -15 AAGATAACATGAAGGGGACTGTTAAATTTA 11 85 1 GAAGGGGACT 0.989254 -55 AGAATAGATGGAAGGGAACTTGAGGCTGAA 11 114 1 GAAGGGAACT 0.940877 -26 CTATTAATTTGGAGAGGGTTATTGA 13 96 1 GGAGAGGGTT 0.897051 -15 ********** Masking position 3 Map Score: 9.64373 Number of sites scoring better than the average of aligned sites = 1117 Number in coding regions = 1046 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 6 TTACTAAATCTTCTGTAGAGGGACCCTTCA 1 114 1 TTCTGTAGAG 0.922642 -136 AAAAAAAAGTTTCTGTAGAGAAACCTCCAG 1 153 1 TTCTGTAGAG 0.922642 -97 GGCCATAATTTTATTAAGAGGTCTTTTTTA 1 197 1 TTATTAAGAG 0.745909 -53 GAACTTCAATCAATAAAGAGCAAATGCTGA 6 12 1 CAATAAAGAG 0.865915 -29 TTAACAATTTTTATATAGATAACTCTATTA 7 31 1 TTATATAGAT 0.582426 -53 AATTTTGTCAGACTAAAGAG 7 74 1 GACTAAAGAG 0.898351 -10 TAATTATTGGTACTAAAGAGAAGGGAGCTA 10 124 1 TACTAAAGAG 0.958143 -24 ATAAAAAGGACACTGAAGATAACATGAAGG 11 70 1 CACTGAAGAT 0.822489 -70 ********** Masking position 7 Map Score: 1.78493 Number of sites scoring better than the average of aligned sites = 329 Number in coding regions = 296 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 TAGGTCTAACTCACCTTTTTTAAAAAGATT 1 225 1 TCACCTTTTT 0.93426 -25 TCACCAGTAATCATCTATAT 2 15 0 TCACCAGTAA 0.975897 -10 CTCATCACCATTAACACCGGAATG 4 28 0 TCACCATTAA 0.980179 -14 AATTCCTCACCTGTTAGATTCCTCAT 9 15 0 TCACCTGTTA 0.955239 -16 TCTCTACTCATAACCTTTATCTGTGCATCA 11 25 1 TAACCTTTAT 0.804003 -115 TGATAAAGTTTCACCATAAAAAGGACACTG 11 55 1 TCACCATAAA 0.924274 -85 ********** Masking position 3 Map Score: 3.10476 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 96 Number in noncoding regions = 23 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: -1.39023e-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: -1.39023e-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: -1.39023e-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