AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -itrpR_mjan_opreg_100.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 MJ0233 71 M. jannaschii predicted coding region MJ0233 #2 MJ0918 70 indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase (trpC) #3 MJ0921 289 conserved hypothetical protein #4 MJ1036 300 M. jannaschii predicted coding region MJ1036 #5 MJ1037 62 tryptophan synthase beta subunit (trpB) #6 MJ1038 176 tryptophan synthase alpha subunit (trpA) #7 MJ1076 33 M. jannaschii predicted coding region MJ1076 #8 MJ1077 89 seryl-tRNA synthetase (serS) #9 MJ1078 273 M. jannaschii predicted coding region MJ1078 #10 MJ1393 247 conserved hypothetical protein Motif number 1 TAATTAAAGTATTTAAAAATATCTATTAGG 1 18 0 ATTTAAAAAT 0.924436 -54 TCCAAGTTTATTATAAAAATTCATAATTAA 1 41 0 TTATAAAAAT 0.913824 -31 AAGAATTGCTATTTAAAAAAGGTAGGATAA 2 33 0 ATTTAAAAAA 0.882546 -38 ATTATCACATTTAATAAAAAGAATTGCT 2 53 0 ATTTAATAAA 0.783455 -18 GTTTAATATTTATTAATAATGC 3 3 0 TATTAATAAT 0.877183 -287 TTGTAATAAGATATGAAAATAGTTTAATAT 3 24 0 ATATGAAAAT 0.747856 -266 TATTTGAATTTTATGAAAATTGTAATAAGA 3 43 0 TTATGAAAAT 0.853842 -247 AAAGATGATATTATAAAAAACTACAGAAAG 3 76 0 TTATAAAAAA 0.876914 -214 ACAATAATGATAATAAAAAATAATAAAATT 3 229 1 TAATAAAAAA 0.827639 -61 ATTTTGTTATTAAAAAATAATAACTAT 4 8 1 TATTAAAAAA 0.938405 -293 TATATAACTTAAATAAAAATAATAGTTATT 4 29 0 AAATAAAAAT 0.783813 -272 TTAAGTTATATATTAGAAAATCTAATAACT 4 47 1 TATTAGAAAA 0.836644 -254 ATTTTTGTTAATTTAAAAATTCAAATTGTA 4 201 0 ATTTAAAAAT 0.924436 -100 TTTTATCTTATATTAATAATATTCCAACAA 4 269 0 TATTAATAAT 0.877183 -32 CGAACAACCTTTTTAGAAAAGGTTGATCAA 6 138 0 TTTTAGAAAA 0.880432 -39 CTTTTTAGTAAAAGCTGCCCGA 6 165 0 TTTTAGTAAA 0.704949 -12 TTTATTGTGTTTTTAGAAATACAGTTTAAT 8 11 0 TTTTAGAAAT 0.917037 -79 GTTTTTATTGAATTGATAATTAGGTATTTA 8 46 0 AATTGATAAT 0.66621 -44 ATTGTTCTTTTATTTAAAATCTGTCCCTCT 9 20 0 TATTTAAAAT 0.702869 -254 CTAAATCAATTTTTGATAATATGTATAAAA 9 79 0 TTTTGATAAT 0.853842 -195 TTAGTGTTAATTTTAAAAAAACAAACATTT 9 114 1 TTTTAAAAAA 0.930659 -160 CTGCAAAAAATAATAAAAAATGTTTGTTTT 9 131 0 TAATAAAAAA 0.827639 -143 TGGAAAATCTTTTTAAAAATACCAACATTG 9 202 1 TTTTAAAAAT 0.956868 -72 ATTAAAAATATATTAAAAATGCATCTTTTA 9 241 0 TATTAAAAAT 0.957789 -33 AAAGATAATATATTAAAAATATATTAAAAA 9 252 0 TATTAAAAAT 0.957789 -22 CTAATAAAACATTTTAAAATAAGCAAAAAT 10 12 0 ATTTTAAAAT 0.439048 -236 TTTTATTAGGTATTGATAATTTTAATATCA 10 33 1 TATTGATAAT 0.797233 -215 AAGGTTTTCAATTTGAAAATAATAACAGCC 10 78 0 ATTTGAAAAT 0.884755 -170 TTTTTCAAAAATTTAGAAAAAGAACCCAAA 10 114 0 ATTTAGAAAA 0.789849 -134 TTTTCTAAATTTTTGAAAAATCAAAAATGT 10 124 1 TTTTGAAAAA 0.899784 -124 ********** Masking position 4 Map Score: 41.0493 Number of sites scoring better than the average of aligned sites = 2449 Number in coding regions = 1835 Number in noncoding regions = 614 Number of orfs with sites within 600 bp upstream = 400 Fraction of orfs with sites within 600 bp upstream = 0.0642467 Motif number 2 AGATATTTTTAAATACTTTAATTATGAATTTTTATAA 1 24 1 AAATAAAATA 0.846091 -48 AGGTAGGATAAAATAAAATAATAGTATAAGCTC 2 7 0 AAATAAAGTT 0.952996 -64 TAAGATATGAAAATAGTTTAATATTTATTAATAATGC 3 11 0 AAATAAATTA 0.933477 -279 TAATGTTTTAAACTACAAAAAAGTTCTATTTGGAACT 3 154 1 AACTAAATTT 0.695393 -136 AATGATAATAAAAAATAATAAAATTTACCTCTGCGAA 3 234 1 AAAAAAATTA 0.957794 -56 TTTGTTATTAAAAAATAATAACTATTATTTTTATTTA 4 13 1 AAAAAAAATA 0.867981 -288 AAATGACTATAAATATGAGAATAGTCAGAAATTAACA 4 79 1 AAATAAAGTA 0.952996 -222 AAATTAACATTAATAACCAAAGTTTTAGCTTTTGTAT 4 107 1 TAATAAATTA 0.856789 -194 TTGTTAATTTAAAAATTCAAATTGTATAATTAATTAA 4 190 0 AAAAAAAGTT 0.952323 -111 AAATTAACAAAAATAAAATAATGTGAATGATATTAAC 4 217 1 AAATAAATGA 0.695393 -84 TTAATATAAGATAAAATATAAAATTTAG 4 283 1 ATAAAAATTA 0.605502 -18 TCAATTCAATAAAAACAATAAGAGTGTTATTGGTGAT 8 60 1 AAAAAAAGTT 0.952996 -30 AGATTTTAAATAAAAGAACAATAGTTTCTTTTGTTAT 9 28 1 TAAAAAAGTT 0.842708 -246 TGTTAATTTTAAAAAAACAAACATTTTTTATTATTTT 9 118 1 AAAAAAATTT 0.957737 -156 AAATCTTTTTAAAAATACCAACATTGATTTAGAATTA 9 206 1 AAAAAAATTA 0.957814 -68 TGAAAGATAATATATTAAAAATATATTAAAAATG 9 250 0 TAATAAAATT 0.637078 -24 TTGATAATTTTAATATCAAAAGGTTTATATATCGGCT 10 45 1 TAATAAATTA 0.857134 -203 AAAAGAACCCAAAAAGTCCAAGGTTTTCAATTTGAAA 10 90 0 AAAAAAATTT 0.952802 -158 TAAATTTTTGAAAAATCAAAAATGTCTAAAAAATGTT 10 129 1 AAAAAAAGTT 0.952993 -119 CATTTGTGTGAAATAGGGGAACATTCTTAAGTAGGTA 10 207 0 AAATAAATTT 0.957814 -41 ***** ** ** * Masking position 10 Map Score: 24.9775 Number of sites scoring better than the average of aligned sites = 822 Number in coding regions = 577 Number in noncoding regions = 245 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 3 AAATATCTATTAGGTGATAAT 1 1 0 TAGGTGTAAT 0.959692 -71 GCATTATTAATAAATATTAAACTATTTTCAT 3 11 1 TAAATATAAA 0.436684 -279 TGGATGTACAAAGGTGTTAAAGTTCCAAATA 3 180 0 AAGGTGTAAA 0.772341 -110 CTATACAATAATGATAATAAAAAATAATAAA 3 225 1 ATGATATAAA 0.513724 -65 ATTTTGTTATTAAAAAATAATAAC 4 4 1 TTGTTATAAA 0.631208 -297 ACTTTGGTTATTAATGTTAATTTCTGACTAT 4 99 0 TTAATGTAAT 0.620351 -202 GAAATAGTATTTGGTAGTAATACTTATACGT 5 18 0 TTGGTATAAT 0.962686 -45 TTTTAACCTTTTGGTGATAAT 7 23 1 TTGGTGTAAT 0.969093 -11 AATTGATAATTAGGTATTTATGTTTTTTATT 8 35 0 TAGGTATTAT 0.675826 -55 AAGAGTGTTATTGGTGATAAA 8 79 1 TTGGTGTAAA 0.95969 -11 TTTAGATAAATTAGTGTTAATTTTAAAAAAA 9 104 1 TTAGTGTAAT 0.850403 -170 AATGTTTTATTAGGTATTGATAATTTTAATA 10 29 1 TAGGTATGAT 0.755494 -219 TATAAACCTTTTGATATTAAAATTATCAATA 10 43 0 TTGATATAAA 0.849195 -205 CATTCTTAAGTAGGTAGTAATAATGTAATGT 10 192 0 TAGGTATAAT 0.951434 -56 ****** **** Masking position 10 Map Score: 9.08295 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 405 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 4 TAAAAAAGGTAGGATAAAATAAAATAATAG 2 20 0 AGGATAAAAT 0.941333 -51 GAACGTTCGTAGACTAAAATTTATCATTGC 3 110 1 AGACTAAAAT 0.871304 -180 ATAATAAAAAATAATAAAATTTACCTCTGC 3 238 1 ATAATAAAAT 0.658432 -52 AATTATACAAAAGCTAAAACTTTGGTTATT 4 118 0 AAGCTAAAAC 0.894996 -183 TAAATTAACAAAAATAAAATAATGTGAATG 4 216 1 AAAATAAAAT 0.902786 -85 TTATTAATATAAGATAAAATATAAAATTTA 4 280 1 AAGATAAAAT 0.965911 -21 ACTATTTCAGAAGCTAAAATTATCTTTTTG 5 41 1 AAGCTAAAAT 0.973319 -22 TGAAAGATAATATATTAAAAATA 9 261 0 AAGATAATAT 0.817076 -13 ATTTTAAAATAAGCAAAAATA 10 2 0 AAGCAAAAAT 0.85187 -246 ********** Masking position 6 Map Score: 6.68558 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 209 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 AAACTACAGAAAGTCCTATTTGAATTTTAT 3 59 0 AAGTCCTATT 0.981973 -231 TAGTCTACGAACGTTCTATCAAAGATGATA 3 96 0 ACGTTCTATC 0.91236 -194 AACTACAAAAAAGTTCTATTTGGAACTTTA 3 164 1 AAGTTCTATT 0.963469 -126 ATATACAATTACGTCCTATACAATAATGAT 3 210 1 ACGTCCTATA 0.962379 -80 ACCTCTGCGAAAGTCCTATTTAAATATCAC 3 260 1 AAGTCCTATT 0.981973 -30 ATTTTTATTTAAGTTATATATTAGAAAATC 4 39 1 AAGTTATATA 0.704794 -262 CAATAGGGCGAAGTCCTATGGTGTCTTGAC 6 85 0 AAGTCCTATG 0.969653 -92 ********** Masking position 8 Map Score: 6.28919 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 30 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 6 TAGACTAAAATTTATCATTGCACAAAAAAG 3 119 1 TTTATCATTG 0.878715 -171 AGAGGTAAATTTTATTATTTTTTATTATCA 3 236 0 TTTATTATTT 0.850813 -54 AAAAATAATAGTTATTATTTTTTAATAACA 4 15 0 GTTATTATTT 0.93486 -286 TAAAACTTTGGTTATTAATGTTAATTTCTG 4 104 0 GTTATTAATG 0.890012 -197 TTCACATTATTTTATTTTTGTTAATTTAAA 4 214 0 TTTATTTTTG 0.668808 -87 TTTAAATCCGGTTTTTGTTGGAATATTATT 4 255 1 GTTTTTGTTG 0.903354 -46 GGTATTTATGTTTTTTATTGTGTTTTTAGA 8 24 0 TTTTTTATTG 0.869178 -66 CACTCTTATTGTTTTTATTGAATTGATAAT 8 56 0 GTTTTTATTG 0.943565 -34 CAATAAGAGTGTTATTGGTGATAAA 8 75 1 GTTATTGGTG 0.791765 -15 ACAAACATTTTTTATTATTTTTTGCAGTAG 9 134 1 TTTATTATTT 0.850813 -140 CTAATTAAAAGTTATCGTTGGAAAATCTTT 9 184 1 GTTATCGTTG 0.910656 -90 TATATCGGCTGTTATTATTTTCAAATTGAA 10 72 1 GTTATTATTT 0.93486 -176 AAAGTCCAAGGTTTTCAATTTGAAAATAAT 10 85 0 GTTTTCAATT 0.429057 -163 ********** Masking position 5 Map Score: 11.644 Number of sites scoring better than the average of aligned sites = 523 Number in coding regions = 459 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 7 GTAGGATAAAATAAAATAATAGTATAAGCT 2 12 0 ATAAAATAAT 0.723032 -59 TTTTTGTAGTTTAAAACATTAGGTCACTTT 3 145 0 TTAAAACATT 0.869861 -145 TTATTTTTTAATAACAAAAT 4 1 0 ATAACAAAAT 0.56464 -300 TATACAAAAGCTAAAACTTTGGTTATTAAT 4 115 0 CTAAAACTTT 0.696159 -186 GAATATAGCCCTAACTCATTTATGCCCATG 4 152 0 CTAACTCATT 0.780494 -149 ATTAACAAAAATAAAATAATGTGAATGATA 4 219 1 ATAAAATAAT 0.723032 -82 CACCAAAAGGTTAAAAAATTAAAGAAAT 7 9 0 TTAAAAAATT 0.653496 -25 ACTAATTTATCTAAATCAATTTTTGATAAT 9 89 0 CTAAATCAAT 0.881691 -185 GGATTGAGATATAAAACATTACTACTGCAA 9 155 0 ATAAAACATT 0.948074 -119 TCTTTTAATTCTAAATCAATGTTGGTATTT 9 218 0 CTAAATCAAT 0.881691 -56 TCAATACCTAATAAAACATTTTAAAATAAG 10 19 0 ATAAAACATT 0.948074 -229 TTCCGTTTGTATAAATAATTTATGGAACAT 10 161 0 ATAAATAATT 0.727663 -87 ********** Masking position 4 Map Score: 5.1676 Number of sites scoring better than the average of aligned sites = 636 Number in coding regions = 546 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 8 TAAAACATTAGGTCACTTTTTTGTGCAATGAT 3 132 0 GGCATTTTTT 0.95203 -158 TTAAGATTTTGATCAACCTTTTCTAAAAAGGT 6 130 1 GACACCTTTT 0.950857 -47 AAAGCTGCCCGAACAACCTTTTTAGAAAAGGT 6 145 0 GACACCTTTT 0.950855 -32 AAGGTTGTTCGGGCAGCTTTTACTAAAAAG 6 157 1 GGCACTTTTA 0.951107 -20 GGACTTAGAGGGACAGATTTTAAATAAAAGAA 9 14 1 GGCAATTTTA 0.896197 -260 TTATATCGTTGGGCATAATTTTATACATATTA 9 61 1 GGCAAATTTT 0.763763 -213 AGTTATCGTTGGAAAATCTTTTTAAAAATACC 9 193 1 GGAATCTTTT 0.755265 -81 ATAATTTATGGAACATTTTTTAGACATTTTTG 10 145 0 GACATTTTTA 0.891275 -103 TGAAATAGGGGAACATTCTTAAGTAGGTAGTA 10 204 0 GACATCTTAA 0.672145 -44 ** ** ****** Masking position 5 Map Score: 1.42587 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 88 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 ATAACTTCACCTCCAAGTTTATT 1 59 0 ACTTCACCTC 0.992133 -13 AAAATAATAAAATTTACCTCTGCGAAAGTC 3 245 1 AATTTACCTC 0.944291 -45 AACTTCACCTCATGCATTTGT 10 237 0 ACTTCACCTC 0.992133 -11 ********** Masking position 6 Map Score: 0.186965 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 1 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 ********** No masking Map Score: -1.30497e-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: -1.30497e-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: -1.30497e-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