AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -iarcA_mjan_opreg_300.orf -g0.314 -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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ0030 300 coenzyme F420-reducing hydrogenase, delta subunit (frcD) #2 MJ0033 254 succinate dehydrogenase, flavoprotein subunit (sdhA) #3 MJ0720 194 3-isopropylmalate dehydrogenase 1 (leuB1) #4 MJ0792 300 M. jannaschii predicted coding region MJ0792 #5 MJ0792.1 68 M. jannaschii predicted coding region MJ0792.1 #6 MJ0793 60 M. jannaschii predicted coding region MJ0793 #7 MJ0794 48 M. jannaschii predicted coding region MJ0794 #8 MJ0795 79 M. jannaschii predicted coding region MJ0795 #9 MJ1411 300 glyceraldehyde-3-phosphate dehydrogenase, NADP-dependent (gapN) #10 MJ1596 226 3-isopropylmalate dehydrogenase 2 (leuB2) Motif number 1 TTATTAAAAATATTACTATTTTCTTGTTCTTT 2 120 1 TATTAATTTT 0.867955 -135 TTTCTTGTTCTTTTTTTATTTATACTATGCCA 2 139 1 TTTTTATTTA 0.928021 -116 ACTATGCCAATTTTTTCATTTAGGATTATTTT 2 162 1 TTTTTATTTA 0.928021 -93 TCATCAAAGCTATTTTGATTTATAAGTTTTAA 2 196 1 TATTTATTTA 0.915233 -59 ACCAAAATGATTTTAAAATTAAAAATAAAACT 3 17 1 TTTTAATTAA 0.958884 -178 AGTAATGCATTATAAGTATTTATATTTTGTGT 3 58 1 TATAAATTTA 0.915233 -137 TGTTGAGTATTTTAATCATTTTTGATATGGTT 3 97 1 TTTAAATTTT 0.752248 -98 TATGTGAAAGTATTTTTATTAATATTGCTATA 3 151 1 TATTTATTAA 0.883081 -44 TTTTTAACTATTTTATAATTTTATATCAAAAA 4 33 0 TTTTAATTTT 0.886984 -268 GTTATAATTGTTTTATTATTAAAAATTCTAAT 4 82 1 TTTTAATTAA 0.958884 -219 AAGTTAAAAATTTTAACATATATAATTTACTA 4 114 1 TTTTAATATA 0.672067 -187 AACATATATAATTTACTATTTAACTTTAAATC 4 128 1 ATTTAATTTA 0.791326 -173 CCTCTATATATATTATGATTTAAAGTTAAATA 4 144 0 TATTAATTTA 0.965427 -157 ATCAAAAAATTATTAAAATTAAAAAAGAAAAA 5 16 0 TATTAATTAA 0.951296 -53 TTAATTTGATTATTTAGATTAAAATCAGACCG 9 32 0 TATTTATTAA 0.883081 -269 AAATAAGAGCATTTAGAATTTATTAATTAGTT 9 96 0 ATTTAATTTA 0.791326 -205 TTATTAAGATTTTTAGGATTTTTAATTTTGTT 9 171 0 TTTTAATTTT 0.886984 -130 TATGTGTGCTTATAATTATTAAGATTTTTAGG 9 186 0 TATAAATTAA 0.883081 -115 ACACATAATATATAAACATTAAATGTTTGTTA 9 211 1 TATAAATTAA 0.883081 -90 TTATTGTTTCTATTTCTATTAAACGTTAATAA 10 22 0 TATTTATTAA 0.883081 -205 TAAAGATATTTTTAAGTATTAATACGGTATAT 10 54 0 TTTAAATTAA 0.900188 -173 AAGGAAGGCATTTAAATATTTATTGTCAAATA 10 127 0 TTTAAATTTA 0.928021 -100 ***** ***** Masking position 9 Map Score: 29.1897 Number of sites scoring better than the average of aligned sites = 887 Number in coding regions = 578 Number in noncoding regions = 309 Number of orfs with sites within 600 bp upstream = 256 Fraction of orfs with sites within 600 bp upstream = 0.0411179 Motif number 2 TGGAAGCTTAAATTAAACCCTTAAAAAACTTAAA 1 277 1 ATATAAAATT 0.891803 -24 ACCTTTTAGTAAAAGGTTCATCAAAACGGATGCACTGCCTC 2 31 0 AATTAAAAAT 0.836141 -224 TAGGATTACCAGTGCCTTATTAAAAATATTACTATTTTCTT 2 104 1 ATTTAAAATA 0.930718 -151 AAAAATTGGCATAGTATAAATAAAAAAAGAACAAGAAAATA 2 136 0 AATTAAAAAA 0.695809 -119 ATAAATCAAAATAGCTTTGATGAAAAAAATAATCCTAAATG 2 178 0 AATTAAAATA 0.95662 -77 TAAAAGTTTTATTTTTAATTTTAAAATCATTTTGGTGATTA 3 12 0 ATATAAAATT 0.889316 -183 CTTATAATGCATTACTTCCCTTAAAAGTTTTATTTTTAATT 3 33 0 ATTTAAAATT 0.967579 -162 ATTAATAAAAATACTTTCACATAAAAATGTTTTGTTGGTGA 3 133 0 AATAAAAATT 0.884459 -62 ATATAAAATTATAAAATAGTTAAAAATAATTTACTTTTTTA 4 39 1 AATTAAAATT 0.980107 -262 ATAATAAAACAATTATAACTTTAAAAAAGTAAATTATTTTT 4 60 0 ATATAAAATA 0.78697 -241 TAAATAGTAAATTATATATGTTAAAATTTTTAACTTATTAG 4 109 0 ATTTAAAATT 0.966661 -192 GTTTTGTATTATTACATTTGTGAAAAATGTGGAAAATAATA 4 175 1 ATTTAAAATG 0.781091 -126 AAAATTATTAAAATTAAAAAAGAAAAACATTT 5 2 0 AAAAAAAATT 0.677955 -67 TATATCACCTAAAAAATATCAAAAAATTATTAAAATTAAAA 5 24 0 AATAAAAATT 0.850921 -45 AATAATGATGATAAAATAAATAATAACTTTAACAATTGTGA 6 26 1 AATTATAATA 0.695808 -35 GAAGTAACAAATACAATCATTGAAAAATCTAATAG 7 24 1 AATTAAAATA 0.956695 -25 ACAAACCCTTAGAAATTAAATAAAAATCCTTTGAACTAATT 9 63 1 AATTAAAATT 0.980113 -238 TGGTTGATGGATTGTCTTGTTGAATATGTTTGAAATTTGAA 9 127 0 ATTTAATATT 0.627346 -174 CATCAACCAAACAACAAAATTAAAAATCCTAAAAATCTTAA 9 159 1 AAATAAAATA 0.858656 -142 TATAAACATTAAATGTTTGTTAAAAACATTTAAAATGAAAG 9 221 1 AATTAAAATT 0.900191 -80 AATTTTGAAGACAGTATAGTTTAAAGATATTTTTAAGTATT 10 66 0 AATTAAAGTT 0.804137 -161 ATTTATTGTCAAATATTTATTAATAAACTTTAATTAATTTT 10 101 0 AATTATAATT 0.76894 -126 TTCATAAGCTACTGGTTACTTCAAAATGTTTTTGAAAGACA 10 168 1 ATTTAAAATT 0.967579 -59 TGTTTTTGAAAGACACTATATAAAAAAGTTTTTGGTGCTGT 10 194 1 AATTAAAATT 0.979218 -33 * * * * **** ** Masking position 13 Map Score: 35.4025 Number of sites scoring better than the average of aligned sites = 916 Number in coding regions = 688 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 215 Fraction of orfs with sites within 600 bp upstream = 0.0345326 Motif number 3 TTTTTATCACCAAAAATAGGATACCCTC 2 237 0 CACCAAAAAA 0.98719 -18 TTAATCACCAAAATGATTTTAAAATT 3 6 1 CACCAAAATA 0.935323 -189 CAAAAAACAACACAAAATATAAATACTTATA 3 68 0 CACAAAATAA 0.965075 -127 TAAAATACTCAACAAAAAACAACACAAAATA 3 80 0 AACAAAAAAA 0.868378 -115 TGGTTTAAGTCACCAACAAAACATTTTTATG 3 124 1 CACCAACAAA 0.923983 -71 AAAATACTTTCACATAAAAATGTTTTGTTGG 3 136 0 CACATAAAAT 0.666503 -59 ACTTATCACCAAAAAGATTAATTATAG 3 178 0 CACCAAAAAA 0.98719 -17 CCCATTATATCACCTAAAAAATATCAAAAAA 5 39 0 CACCTAAAAA 0.957544 -30 AGTTGATACAAACCAAATATAACTGTTGGAA 8 20 0 AACCAAATAA 0.91386 -60 TCAACCAAACAACAAAATTAAAAATCCTAAA 9 161 1 AACAAAATTA 0.484557 -140 ATTATAAGCACACATAATATATAAACATTAA 9 202 1 CACATAATAA 0.889952 -99 ATGAAAGAGGCACAAATTATAAATTAGTTAC 9 255 1 CACAAATTAA 0.74623 -46 GATTCCACCAAATAAAAAGAATGTTG 9 285 0 CACCAAATAA 0.983198 -16 AGACAGCACCAAAAACTTTTTTATATA 10 210 0 CACCAAAAAT 0.935323 -17 ********* * Masking position 6 Map Score: 18.9936 Number of sites scoring better than the average of aligned sites = 406 Number in coding regions = 298 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 4 CTATATTCCATTGAATATTTATTCCTGCGA 1 188 0 TTGAATATTT 0.816241 -113 TTTATAAGTTTTAAATATCTGATGAGGGTA 2 214 1 TTAAATATCT 0.695924 -41 ATTACTTCCCTTAAAAGTTTTATTTTTAAT 3 34 0 TTAAAAGTTT 0.671572 -161 GTTGAGTATTTTAATCATTTTTGATATGGT 3 98 1 TTAATCATTT 0.703804 -97 TATAAAATTATAAAATAGTTAAAAATAATT 4 40 1 TAAAATAGTT 0.79131 -261 TTTAAAAAAGTAAATTATTTTTAACTATTT 4 52 0 TAAATTATTT 0.840627 -249 TTCTAATAAGTTAAAAATTTTAACATATAT 4 107 1 TTAAAAATTT 0.865007 -194 CAACTATTCTTTAATTTTTTGTATGGTGCC 4 218 0 TTAATTTTTT 0.600784 -83 TTTTTTAATTTTAATAATTTTTTGATATTT 5 22 1 TTAATAATTT 0.840629 -47 GTTAAAGTTATTATTTATTTTATCATCATT 6 29 0 TTATTTATTT 0.559686 -32 GATTTAAATAGTTGAAGTAACAA 7 4 1 TTAAATAGTT 0.930888 -45 GTTTGTTAATTTGATTATTTAGATTAAAAT 9 39 0 TTGATTATTT 0.785243 -262 TTAGAATTTATTAATTAGTTCAAAGGATTT 9 86 0 TTAATTAGTT 0.917269 -215 TATATAAACATTAAATGTTTGTTAAAAACA 9 219 1 TTAAATGTTT 0.878987 -82 CTCTTTCATTTTAAATGTTTTTAACAAACA 9 234 0 TTAAATGTTT 0.878987 -67 GCACAAATTATAAATTAGTTACAACATTCT 9 264 1 TAAATTAGTT 0.757356 -37 TTAATAAACTTTAATTAATTTTGAAGACAG 10 93 0 TTAATTAATT 0.631709 -134 ATATTTATTGTCAAATATTTATTAATAAAC 10 114 0 TCAAATATTT 0.742705 -113 AGGAAGGCATTTAAATATTTATTGTCAAAT 10 128 0 TTAAATATTT 0.957916 -99 AGACACTATATAAAAAAGTTTTTGGTGCTG 10 204 1 TAAAAAAGTT 0.516312 -23 ********** Masking position 1 Map Score: 16.4487 Number of sites scoring better than the average of aligned sites = 1110 Number in coding regions = 766 Number in noncoding regions = 344 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 5 CGCTACGCTCGGCAGTGCCTC 2 2 0 GGCAGTGCCT 0.996726 -253 AGCGTAGCGAGGCAGTGCATCCGTTTTGAT 2 23 1 GGCAGTGCAT 0.987118 -232 AATTAGGATTACCAGTGCCTTATTAAAAAT 2 101 1 ACCAGTGCCT 0.987118 -154 ATGGAGCTGAGCCAGTGCCTACACAACCAC 4 265 1 GCCAGTGCCT 0.996726 -36 ********** Masking position 6 Map Score: 4.93997 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 1 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 TGTGCAACACACGTTATAGTTAAAGATGAAG 1 73 1 ACTTATAGTT 0.965367 -228 CTTCACATGAACCTTTTAGTAAAAGGTTCAT 2 51 0 ACTTTTAGTA 0.697428 -204 TATTGATTATGTTATATTTCATTTTTTGA 4 9 1 ATTTATATTT 0.76443 -292 ATTTTTAACTATTTTATAATTTTATATCAAA 4 35 0 ATTTATAATT 0.647918 -266 TATCATCATTATTGTATAGTATAGTGTT 6 8 0 ATGTATAGTA 0.905495 -53 ACTTTAATACACTGTATAGTTGATACAAACC 8 37 0 ACGTATAGTT 0.97289 -43 TTTTTCCCTCATTTTATAGTAACTTTAATAC 8 58 0 ATTTATAGTA 0.881548 -22 AAGTATTAATACGGTATATTTATTGTTTCTA 10 42 0 ACGTATATTT 0.8914 -185 AATTTTGAAGACAGTATAGTTTAAAGATATT 10 76 0 ACGTATAGTT 0.97289 -151 ** ******** Masking position 5 Map Score: 4.76441 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 71 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 AATATTTATTCCTGCGAAAGTCCTGTTATG 1 175 0 CCTGCGAAAG 0.962046 -126 TGGAATATAGACATCCAAAGATGTCAAAGT 1 208 1 ACATCCAAAG 0.935389 -93 AAGATGTCAAAGTTCCAAAGTGCATATATA 1 225 1 AGTTCCAAAG 0.930771 -76 GCATATATAAACTGCGAAAGTCCTGTTTCT 1 246 1 ACTGCGAAAG 0.962077 -55 TTTAATTTAAGCTTCCAAAGAAACAGGACT 1 264 0 GCTTCCAAAG 0.971716 -37 CTTATGAACACCTTCCAAAGGAAGGCATTT 10 146 0 CCTTCCAAAG 0.982667 -81 ********** Masking position 7 Map Score: 3.6956 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 42 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 CTATAATCTCTTTTGTCTCTTCATCTTTAAC 1 91 0 TTTGTCTCTT 0.952683 -210 GAAAGTCCTGTTATGCCTCTCGGGTCCCTTT 1 159 0 TTTGCCTCTC 0.97931 -142 CTTTTTCCCTCATTTTATAGTAA 8 67 0 TTTCCCTCAT 0.956379 -13 AATTTATAATTTGTGCCTCTTTCATTTTAAA 9 249 0 TTTGCCTCTT 0.990571 -52 TTTTATCCCTCTTATTAACGTTT 10 3 1 TTTCCCTCTT 0.986326 -224 ** ******** Masking position 4 Map Score: 2.35081 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 72 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 TAGGATTATTTTTTTCATCAAAGCTATTTT 2 182 1 TTTTTCATCA 0.774376 -73 TTTTTATCACCAAAAATAGGAT 2 243 0 TTTATCACCA 0.980769 -12 TTAATCACCAAAATGATTTT 3 1 1 TTAATCACCA 0.95687 -194 TGATATGGTTTAAGTCACCAACAAAACATT 3 119 1 TAAGTCACCA 0.7792 -76 ACTTATCACCAAAAAGATTAA 3 184 0 CTTATCACCA 0.940091 -11 TATCACCCATTATATCACCTAAAAAATATC 5 45 0 TATATCACCT 0.821616 -24 TATTATTTATTTTATCATCATTATTGTATA 6 21 0 TTTATCATCA 0.93294 -40 ********** Masking position 7 Map Score: 2.63657 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 61 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 10 GAAGTTAGAAAAATGTTATAAGCCTCGAGG 1 121 1 AAATGTTATA 0.542314 -180 AGAACAAGAAAATAGTAATATTTTTAATAA 2 120 0 AATAGTAATA 0.225335 -135 AAATAATCCTAAATGAAAAAATTGGCATAG 2 163 0 AAATGAAAAA 0.775713 -92 AATGATTTTAAAATTAAAAATAAAACTTTT 3 22 1 AAATTAAAAA 0.779281 -173 TTATATCAAAAAATGAAATATAACATAATC 4 15 0 AAATGAAATA 0.937312 -286 TATTATTAAAAATTCTAATAAGTTAAAAAT 4 95 1 AATTCTAATA 0.514189 -206 GTTAAATAGTAAATTATATATGTTAAAATT 4 122 0 AAATTATATA 0.670718 -179 TTATGATTTAAAGTTAAATAGTAAATTATA 4 134 0 AAGTTAAATA 0.674365 -167 CATTTTTCACAAATGTAATAATACAAAACC 4 174 0 AAATGTAATA 0.898776 -127 ACCATACAAAAAATTAAAGAATAGTTGGCG 4 221 1 AAATTAAAGA 0.792158 -80 TTTCTTTTTTAATTTTAATAATTTTTTGAT 5 18 1 AATTTTAATA 0.677047 -51 TAATGATGATAAAATAAATAATAACTTTAA 6 28 1 AAAATAAATA 0.683724 -33 AATCATTGAAAAATCTAATAG 7 38 1 AAATCTAATA 0.820654 -11 TAGTTGATACAAACCAAATATAACTGTTGG 8 22 0 AAACCAAATA 0.478432 -58 ATTTTATAGTAACTTTAATACACTGTATAG 8 49 0 AACTTTAATA 0.551534 -31 AAACCCTTAGAAATTAAATAAAAATCCTTT 9 65 1 AAATTAAATA 0.938453 -236 CCAAACAACAAAATTAAAAATCCTAAAAAT 9 165 1 AAATTAAAAA 0.779281 -136 AAAACATTTAAAATGAAAGAGGCACAAATT 9 243 1 AAATGAAAGA 0.788742 -58 ACTGTCTTCAAAATTAATTAAAGTTTATTA 10 92 1 AAATTAATTA 0.521858 -135 ********** Masking position 2 Map Score: 11.422 Number of sites scoring better than the average of aligned sites = 1299 Number in coding regions = 946 Number in noncoding regions = 353 Number of orfs with sites within 600 bp upstream = 283 Fraction of orfs with sites within 600 bp upstream = 0.0454545 Motif number 11 CTGAAGTCATAATGAGAGCTTATGATATAT 1 35 1 AATGAGAGCT 0.6136 -266 CATGTGAAGGAAATAGAGCATAGGAAAGAA 2 73 1 AAATAGAGCA 0.957194 -182 GTATAAATAAAAAAAGAACAAGAAAATAGT 2 134 0 AAAAAGAACA 0.791776 -121 CAAAAAGATTAATTATAGCAATATTAATAA 3 166 0 AATTATAGCA 0.90029 -29 TCAAAAAATGAAATATAACATAATCAATA 4 10 0 AAATATAACA 0.666577 -291 ATATCACCTAAAAAATATCAAAAAATTATT 5 34 0 AAAAATATCA 0.554809 -35 TAACTGTTGGAATTAGTGCAG 8 2 0 AATTAGTGCA 0.89697 -78 AGAATTTATTAATTAGTTCAAAGGATTTTT 9 84 0 AATTAGTTCA 0.703697 -217 GAAATTTGAAAATAAGAGCATTTAGAATTT 9 107 0 AATAAGAGCA 0.944974 -194 ********** Masking position 5 Map Score: 0.480257 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 256 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 12 ********** No masking Map Score: -2.86816e-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: -2.86816e-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: -2.86816e-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