AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -irpoN_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 MTH133 167 cobalt transport ATP-binding protein O #2 MTH151 75 methyl coenzyme M reductase system, component A2 homolog #3 MTH384 249 unknown #4 MTH387 24 conserved protein #5 MTH388 35 unknown #6 MTH393 41 NADH dehydrogenase (ubiquinone), subunit 1 related protein #7 MTH394 55 unknown #8 MTH397 40 formate hydrogenlyase, subunit 7 #9 MTH478 49 sulfate transport system permease protein #10 MTH479 136 conserved protein #11 MTH604 116 adhesion protein #12 MTH695 248 conserved protein #13 MTH783 83 hydrogenase expression/formation protein HypA #14 MTH1072 67 hydrogenase expression/formation protein HypD #15 MTH1246 30 NADH dehydrogenase I, subunit N #16 MTH1251 147 conserved protein #17 MTH1370 137 ABC transporter (ATP-binding protein) #18 MTH1552 139 formate dehydrogenase, alpha subunit homolog #19 MTH1553 71 tungsten formylmethanofuran dehydrogenase, subunit H #20 MTH1570 74 glutamine synthetase #21 MTH1571 300 molybdopterin biosynthesis protein MoeB homolog #22 MTH1649 110 hydrogenase expression/formation protein HypC #23 MTH1705 33 cobalt transport membrane protein #24 MTH1707 300 cobalamin biosynthesis protein M Motif number 1 CCTTTTTTAAAAAGATTTATAT 3 238 1 AAATTTATAT 0.966674 -12 TCACCAGTAATCATCTATATATTC 4 5 0 AATTCTATAT 0.685739 -20 CTATCTTAATAAATGTTTATATATTTTATGTT 11 19 1 AAATTTATAT 0.966625 -98 TTTATATTAACAATTATTATATGGTTGCGTTG 11 72 1 CAAATTATAT 0.923113 -45 CGGTAATTAACAATTTTTATATAGATAACTCT 13 25 1 CAATTTATAT 0.96784 -59 TTAGTCTGACAAAATTTTATAATTAGAATTAA 13 58 0 AAATTTATAA 0.804282 -26 ATTTATATAGAAAACTTTATATTATCATAAAT 16 84 1 AAATTTATAT 0.966683 -64 TCAATTCCTGAATTAATTATATGGGGGTCCTT 17 56 0 AATATTATAT 0.777059 -82 TCAAATAGAAAAATATATATATAGGTGTGTGG 19 11 0 AAATATATAT 0.822956 -61 TTTTTGTAGAAAATTATTATATGGACGGCGGC 19 43 1 AAAATTATAT 0.920425 -29 ACAAAAAATATATAAACCAGTAG 20 2 1 CAAAATATAT 0.659645 -73 ATGACCCCCTCATGATTTATATCAACACACAC 21 245 1 CATTTTATAT 0.900638 -56 TGTTTCCCACAAATCTTTATATGTGACGGATC 22 30 1 AAATTTATAT 0.966674 -81 TTAATGATTTATAATGATGTTTTT 24 3 1 AATTTTATAA 0.553112 -298 CGACAATGCACAAAGTTTATATATAGATTCCA 24 42 0 CAATTTATAT 0.96784 -259 ATAATCACTTCAACCTTTATATTATATGAATG 24 232 1 CAATTTATAT 0.96784 -69 TCACTATATCAAACATTCATATAATATAAAGG 24 245 0 AAATTCATAT 0.764945 -56 TTTTTAATTCCAATCACTATATCAAACATTCA 24 258 0 CAAACTATAT 0.749871 -43 *** ******* Masking position 10 Map Score: 22.9936 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 20 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 2 ATTCCCACCCCATCATGTCCTGGAGGTTCCT 3 8 1 CCCCCATTCT 0.9954 -242 CATTTTCATTCCACATCATGTCTT 7 1 0 CCACCATTTT 0.905071 -55 CTGATTAAATCCCTTCCATTTTCATTCCACATCA 7 17 0 CCCTCATTCA 0.871939 -39 TTCTTTACCTCAGCATTTGCTCTTTATTGAT 8 20 0 CCTCCATTCT 0.92944 -21 ATTTTTAAGACCCCGACTTTTTCTGAAG 9 32 1 CCCCCTTTCT 0.951946 -18 TAATAGGAACCTCCATCATATAATCATCC 12 230 1 CTCCCATTAT 0.921162 -19 ATCCTTTGGCCTCCTCCATATATATATGATCGTG 14 12 1 CTCCCATTTA 0.865176 -56 GCAGCCTCTTCCCCTTCAAGTGTTTAATCATCGG 16 32 1 CCCCCAATTT 0.934804 -116 ATTTAACAGTCCCCTTCATGTTATCTTCAGTGTC 18 78 0 CCCCCATTAT 0.980196 -62 GCCTCAAGTTCCCTTCCATCTATTCTAAATTTAA 18 106 0 CCCTCATTTT 0.965982 -34 AGAGGACCGCCCCAGACATCTGCTTTTCACTGAT 21 136 1 CCCACATTCT 0.939492 -165 TACAGGATGACCCCCTCATGATTTATATCAACAC 21 239 1 CCCCCATATT 0.934804 -62 TCAAACCCTCTTTCATGTTCTTGCATAATAC 21 280 0 CTCTCATTCT 0.902547 -21 TCTGGCACATCCCCACCATTTATTAAAAAGGTCC 24 92 0 CCCCCATTTT 0.993656 -209 GCTATTCGCCTCCTTAATCTTTTTTTAATTCCA 24 278 0 CTCCAATTTT 0.676597 -23 **** *** * ** Masking position 1 Map Score: 21.2783 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 219 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 TTGATTTCTGATACCTCCAGATGGTGGGCT 1 47 1 ATACCTCCAG 0.857422 -121 ATAAATTCATAGCCCACCATCTGGAGGTAT 1 57 0 AGCCCACCAT 0.672176 -111 GACTCCATAGGAACCTCCAGGACATGATGG 3 20 0 GAACCTCCAG 0.978051 -230 TCTGTAGAGGGACCCTTCAGATATCAGTAA 3 125 1 GACCCTTCAG 0.719896 -125 TTCTGTAGAGAAACCTCCAGATATTAGTAA 3 163 1 AAACCTCCAG 0.960593 -87 GGTCTTTAACCTCCATTAACTCAGAA 10 121 0 TAACCTCCAT 0.623767 -16 ATGACTCTCAGGTCCTTCATTAGAATCTAA 12 47 1 GGTCCTTCAT 0.786503 -202 CTCCTTTTCCAGTCCTTCAGCTTCCCTTTC 12 82 1 AGTCCTTCAG 0.841519 -167 GTTATAATAGGAACCTCCATCATATAATCA 12 226 1 GAACCTCCAT 0.944171 -23 AAGACCACCATTACACTTAAA 14 57 0 AGACCACCAT 0.855414 -11 TATATATAAAGGACCCCCATATAATTAATT 17 48 1 GGACCCCCAT 0.960579 -90 CGCTACAGCGGGACCTCCAGTGGCTGACTG 17 109 1 GGACCTCCAG 0.992883 -29 TGAGTCCCCCAGTCAGCCACTG 17 126 0 AGTCCCCCAG 0.936236 -12 CTTTCCCACAGGATCTCCAGTGATAGGCTC 21 179 1 GGATCTCCAG 0.88059 -122 ATAAGGCTGTGGTCCTACAGGATGACCCCC 21 224 1 GGTCCTACAG 0.793454 -77 ATACACCCTGAGACCCCCGGCAATGGTCAT 24 148 1 AGACCCCCGG 0.816655 -153 ********** Masking position 5 Map Score: 18.5715 Number of sites scoring better than the average of aligned sites = 1304 Number in coding regions = 1221 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 4 GGATTAAGCAGACTTAAATATAGAATACACATTAT 1 117 1 GACTAAAGAA 0.770677 -51 TGATCCCTTAAACGTTATGATAATAATGTGTATTC 1 139 0 AACTAAAATA 0.35615 -29 GGACCCTTCAGATATCAGTAAAAAAAAGTTTCTGT 3 134 1 GATTAAAAAA 0.956811 -116 GAAACCTCCAGATATTAGTAAAAAAGGCCATAATT 3 172 1 GATTAAAAAA 0.956799 -78 ACCTAAAAAAGACCTCTTAATAAAATTATGGCCTT 3 195 0 GACTTAAAAA 0.918957 -55 ATATAAATCTTTTTAAAAAAGGTGAGTTAG 3 230 0 AATTTAAAAA 0.778839 -20 AAATGGAAGGGATTTAATCAGAAAAGAGGGGATTT 7 30 1 GATTAAAAAA 0.956811 -26 AAAAGTCGGGGTCTTAAAAATAAAGTAGTATGTTA 9 18 0 GTCTAAAAAG 0.754291 -32 AAATTTAATAAATTTTAACATAAAATATATAAACA 11 32 0 AATTAAAAAA 0.84941 -85 GCTTAAAAATAATTTAATGAAAAAGGGAGTT 12 7 0 AATTAAAAAG 0.745449 -242 AATTAATAGAGTTATCTATATAAAAATTGTTAATT 13 29 0 GTTTTAAAAA 0.818288 -55 AACTCTATTAATTCTAATTATAAAATTTTGTCAGA 13 51 1 ATTTAAAAAA 0.647438 -33 ATTTTATTACGATTTATATAGAAAACTTTATATTA 16 73 1 GATTTAAAAA 0.932578 -75 CTCTTATATGGACCTATATATAAAGGACCCCCATA 17 34 1 GACTTAAAAG 0.854801 -104 ACAGATAAAGGTTATGAGTAGAGAGTGAGGTGAAG 18 14 0 GTTTAAAGAG 0.409309 -126 TTTTCTATTTGATTTTTGTAGAAAATTATTATATG 19 31 1 GATTTAAAAA 0.932575 -41 CATCTTTTCTGTTTTAAGGATAAAAAAGT 21 5 0 GTTTAAAAAA 0.878238 -296 AGAATACACTAATGTTTAGATAAAGATCCGTCACA 22 51 0 AATTTAAAAG 0.646441 -60 TCGACTTCACCAGAAAAAAATTAATTG 23 17 0 GACTAAAAAA 0.947812 -17 TAAAGACATGGACCTTTTTAATAAATGGTGGGGAT 24 83 1 GACTTATAAA 0.422424 -218 CTCAGGGTGCGATATTACCACAATATAAGGGAAAC 24 185 1 GATTAAAATA 0.726047 -116 *** * * * **** Masking position 5 Map Score: 20.3823 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 118 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 5 ATGAATTTATCCATTCATGATCTGTTTCATCGA 1 77 1 CCATCATGAT 0.875283 -91 CGCATAAAGTTATTATGTCAGTA 2 1 1 CGCTAAAGTT 0.843251 -75 ATTCCCACCCCATCATGTCCTGGAGGTTCCT 3 9 1 CCCTCATGTT 0.988789 -241 ATTTTCATTCCACATCATGTCTT 7 1 0 CACTCATGTT 0.971812 -55 ACCACCATTACACTTAAAGATCTATTTATCACG 14 42 0 CACTAAAGAT 0.881573 -26 CAGCCTCTTCCCCTTCAAGTGTTTAATCATCGG 16 33 1 CCCTCAAGTT 0.986224 -115 TTTAACAGTCCCCTTCATGTTATCTTCAGTGTC 18 78 0 CCCTCATGTT 0.988789 -62 ACAGGATGACCCCCTCATGATTTATATCAACAC 21 240 1 CCCTCATGAT 0.986224 -61 TGTCGCTGAACACATAAAGACATGGACCTTTTT 24 69 1 CACTAAAGAT 0.881573 -232 *** ****** * Masking position 7 Map Score: 7.04559 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 116 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 TTAGGTCTAACTCACCTTTTTTAAAAAGATTT 3 224 1 CTCACTTTTT 0.809205 -26 GGCTTCCATGTTCTCATTCAGGAT 5 3 1 CTTCCTTTCT 0.950587 -33 GATTAAATCCCTTCCATTTTCATTCCACATCA 7 17 0 CTTCCTTTCA 0.849174 -39 TAAATCCCCTCTTTTCTGATTAAAT 7 41 0 ATCCCTTTTT 0.91534 -15 TTTCAGGACGATCCCATGTTCTCATTCCTTCA 10 50 1 ATCCCTTTCT 0.92928 -87 AACTCCCTTTTTCATTAAATTATT 12 3 1 CTCCCTTTCA 0.922618 -246 AGTCCTTCAGCTTCCCTTTCTAAGTGGCTATG 12 92 1 CTTCCTTCTA 0.743687 -157 TAATCATCGGATCCCCTATTTTATTACGATTT 16 56 1 ATCCCTTTTT 0.91534 -92 TTTATAGCTCCCTTCTCTTTAGTACCAAT 16 129 0 CTCCCTTCTT 0.954535 -19 CTCAAGTTCCCTTCCATCTATTCTAAATTTAA 18 106 0 CTTCCTTATT 0.863107 -34 CGGAAGTAACTTTCCTTCTACTGGTTTATATA 20 19 0 TTTCCTTACT 0.569828 -56 AAAAACAAAAATCACGTTTCTTTAAATTGGAG 21 51 1 ATCACTTCTT 0.461437 -250 TCAAACCCTCTTTCATGTTCTTGCATAATAC 21 280 0 CTTTCTTTCT 0.579893 -21 AATCTTCGGTTTCCCTTATATTGTGGTAATAT 24 196 0 TTCCCTTATT 0.697717 -105 ***** * **** Masking position 7 Map Score: 7.73129 Number of sites scoring better than the average of aligned sites = 383 Number in coding regions = 340 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 CATGATCTGTTTCATCGATCCGATAGGATTAA 1 92 1 TTCATGACCG 0.986946 -76 CTAGTATATATTCATGGAGCCGGTGGCGA 2 57 1 TTCATGACCG 0.986947 -19 CGTGATTATATTCACAGAAACCGGTAAGTGGA 3 53 0 TTCACGAACC 0.888106 -197 TTCTCATTCCTTCACAGAACCGATATGTATAT 10 68 1 TTCACGACCG 0.995551 -69 ATAAAACCCCTTCCCTGAACCGAACTGTTTTT 21 86 1 TTCCCGACCG 0.987925 -215 ACATCTGCTTTTCACTGATCTGAAGAATCTTT 21 151 1 TTCACGACTG 0.971923 -150 ***** ** *** Masking position 8 Map Score: 4.85085 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 25 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 CTTAAACGTTATGATAATAATGTGTATTCTA 1 137 0 ATATAATAAT 0.759186 -31 CATAGTCGTTTTCGTGATTATATTCACAGAA 3 66 0 TTGTGATTAT 0.577641 -184 TACAGAAGATTTAGTAATAAATTTTAAGGAT 3 100 0 TTGTAATAAA 0.855717 -150 GTTTATGATAATAGAATCATTC 6 2 1 TTATGATAAT 0.8098 -40 AGTCGGGGTCTTAAAAATAAAGTAGTATGTT 9 19 0 TTAAAATAAA 0.506386 -31 CATCTGGAGCTTAAAAATAATTTAATGAAAA 12 19 0 TTAAAATAAT 0.616219 -230 TATATATATGATCGTGATAAATAGATCTTTA 14 30 1 ATGTGATAAA 0.839847 -38 TTCTATATAAATCGTAATAAAATAGGGGATC 16 65 0 ATGTAATAAA 0.791506 -83 AACATGATTATTTATGATAATATAAAGTTTT 16 94 0 TTATGATAAT 0.8098 -54 TTATCTGTGCATCATGATAAAGTTTCACCAT 18 41 1 ATATGATAAA 0.734521 -99 TTTCTTTAAATTGGAGATAATAAAACCCCTT 21 67 1 TTGAGATAAT 0.804935 -234 AGGGTGTATAATGGTAATAATCCTCCGCCTA 24 126 0 ATGTAATAAT 0.855936 -175 AAACCGAAGATTAGTAATAATCACTTCAACC 24 216 1 TTGTAATAAT 0.902749 -85 ** ******** Masking position 7 Map Score: 6.01986 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 75 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 9 TCATAGCCCACCATCTGGAGGTATCAGAAA 1 51 0 CCATCTGGAG 0.800703 -117 TCCTGGAGGTTCCTATGGAGTCACATCCAC 3 28 1 TCCTATGGAG 0.909413 -222 TATTACTAAATCTTCTGTAGAGGGACCCTT 3 112 1 TCTTCTGTAG 0.822366 -138 TTTTTTACTAATATCTGGAGGTTTCTCTAC 3 167 0 ATATCTGGAG 0.662394 -83 GACCCCGACTTTTTCTGAAG 9 40 1 TTTTCTGAAG 0.855257 -10 GACCTGAGAGTCATCTGGAGCTTAAAAATA 12 31 0 TCATCTGGAG 0.959022 -218 AGCGGTTGACTTTTATGGATCTTTAACGGA 12 166 0 TTTTATGGAT 0.5711 -83 GCGATAACATTTTTATCGAGTGCATCAATT 17 82 0 TTTTATCGAG 0.622599 -56 TCAGTGTCCTTTTTATGGTGAAACTTTATC 18 56 0 TTTTATGGTG 0.775362 -84 AAAGATGAATTCTTCTGAAAAAACAAAAAT 21 33 1 TCTTCTGAAA 0.531452 -268 TCTGGGGCGGTCCTCTGGAGCCATTCTGAA 21 122 0 TCCTCTGGAG 0.961925 -179 CAATTAATTTTTTTCTGGTGAAGTCGA 23 17 1 TTTTCTGGTG 0.896758 -17 ATGTTTTTAATTTTATGGAATCTATATATA 24 27 1 TTTTATGGAA 0.70128 -274 ********** Masking position 6 Map Score: 3.54925 Number of sites scoring better than the average of aligned sites = 621 Number in coding regions = 531 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 10 AGGTATCAGAAATCAAAAAACCGATGTGAG 1 33 0 AATCAAAAAA 0.936198 -135 GAAGGGATTTAATCAGAAAAGAGGGGATTT 7 35 1 AATCAGAAAA 0.923683 -21 TGAACTTCAATCAATAAAGAGCAAATGC 8 9 1 AATCAATAAA 0.822597 -32 TTGTTAATATAAACGATAAAATTTAATAAA 11 55 0 AAACGATAAA 0.647848 -62 TACAAAAATCAAATAGAAAAATATATATAT 19 21 0 AAATAGAAAA 0.659221 -51 TTTATCCTTAAAACAGAAAAGATGAATTCT 21 16 1 AAACAGAAAA 0.907612 -285 TCTTCTGAAAAAACAAAAATCACGTTTCTT 21 43 1 AAACAAAAAT 0.652478 -258 GCCATTCTGAAATCGAAAAACAGTTCGGTT 21 103 0 AATCGAAAAA 0.877637 -198 TAGTGATTGGAATTAAAAAAAGATTAAGGA 24 271 1 AATTAAAAAA 0.74289 -30 ********** Masking position 8 Map Score: 1.74293 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 65 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 11 CCCCATCATGTCCTGGAGGTTCCTATGGAG 3 18 1 TCCTGGAGGT 0.72313 -232 ATTCACAGAAACCGGTAAGTGGATGTGACT 3 46 0 ACCGGTAAGT 0.513374 -204 CCGTAAATAATCCTGAATGAGAACATGGAA 5 14 0 TCCTGAATGA 0.896121 -22 CACCATTAACACCGGAATGATTCTATTATC 6 17 0 ACCGGAATGA 0.887138 -25 AAAGAGCAAATGCTGAGGTAAAGAA 8 26 1 TGCTGAGGTA 0.544555 -15 CATGGGATCGTCCTGAAAGATAAAGAAGGA 10 38 0 TCCTGAAAGA 0.896121 -99 CTAATGAAGGACCTGAGAGTCATCTGGAGC 12 40 0 ACCTGAGAGT 0.705497 -209 TAGAAAGGGAAGCTGAAGGACTGGAAAAGG 12 84 0 AGCTGAAGGA 0.908553 -165 ATTGTTAATTACCGGAAGGTGATTTTTC 13 9 0 ACCGGAAGGT 0.929739 -75 GTGCATCAATTCCTGAATTAATTATATGGG 17 63 0 TCCTGAATTA 0.61041 -75 GCTTAACTTCACCGGAAGTAACTTTCCTTC 20 33 0 ACCGGAAGTA 0.851919 -42 TCACTGGAGATCCTGTGGGAAAGATTCTTC 21 172 0 TCCTGTGGGA 0.880925 -129 GAGGGGGTCATCCTGTAGGACCACAGCCTT 21 226 0 TCCTGTAGGA 0.905513 -75 TCGCACCCTGAGCGGAGGGATGACCATTGC 24 167 0 AGCGGAGGGA 0.857112 -134 ********** Masking position 3 Map Score: 7.27519 Number of sites scoring better than the average of aligned sites = 1559 Number in coding regions = 1478 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 12 ********** No masking Map Score: 1.18193e-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: 1.18193e-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 14 ********** No masking Map Score: 1.18193e-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