AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -imalT_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 MJ1022 80 alignment in /usr/local/projects/ARG/Intergenic/ARG_R428_orf1.nr #2 MJ1243 91 conserved hypothetical protein #3 MJ1245 148 M. jannaschii predicted coding region MJ1245 #4 MJ1246 300 succinyl-CoA synthetase, alpha subunit (sucD) #5 MJ1368 122 sulfate transport system permease protein (cysT) #6 MJ1569 300 cobalamin biosynthesis protein (cbiM) #7 MJ1631 300 glycogen phosphorylase (glgP) Motif number 1 CCAACATTAATTTTATTAATGGTGATTATT 1 17 1 TTTTATTAAT 0.715676 -64 TCAACAACTTTAATTTTAAAACTCAAAAGA 1 52 0 TAATTTTAAA 0.861462 -29 ATAATCTCCTCATTTTAAATAGAAGTTTT 2 73 0 TCATTTTAAA 0.72445 -19 TATCCTATTATTTAAAAATTTGAAA 3 6 1 TATTATTTAA 0.83935 -143 TATCGTATTATAATTTTCAAATTTTTAAAT 3 20 0 TAATTTTCAA 0.741037 -129 ATAATACGATAATTGTTAAAATTTCTTTTT 3 39 1 AATTGTTAAA 0.592111 -110 TTAAAATTTCTTTTTTTAATAACATATTAA 3 54 1 TTTTTTTAAT 0.847321 -95 TTTATATTCTATATTTTTAACAGTTAAATT 3 102 1 ATATTTTTAA 0.840303 -47 CACCCCCACCATTTTTTAAATAACTTAAAT 4 27 0 ATTTTTTAAA 0.806155 -274 TTCACAATTTATATATTTATAAGGCACTTT 4 221 0 ATATATTTAT 0.570719 -80 TTTAATAAATTTTTAATGAAAATATT 5 7 1 AAATTTTTAA 0.798852 -116 ATGTCATCAATTTTGTTTAACACAAATTTT 5 47 1 TTTTGTTTAA 0.875836 -76 TCAATCTTAATCATTTTTAAGGTAATTAAA 5 91 0 TCATTTTTAA 0.800949 -32 AACTTATTTTTATTTTTGTTTAA 6 4 1 TTATTTTTAT 0.875338 -297 TTATTTTTATTTTTGTTTAAGTATAAATCT 6 14 1 TTTTGTTTAA 0.875836 -287 TATTTTCAGATATTTTTCAATCCAGTGCAT 6 67 1 TATTTTTCAA 0.775859 -234 CTGAATCTTATATTTTTCAAATACTATATT 6 104 1 TATTTTTCAA 0.775859 -197 ATTTTAATGGAATTTTTAATATAGTATTTG 6 121 0 AATTTTTAAT 0.636091 -180 ATACTAAATATTATTTTAATGGAATTTTTA 6 133 0 TTATTTTAAT 0.82104 -168 TTTATGTAACATTTTTTTATATTAGCTCAA 6 184 1 ATTTTTTTAT 0.779954 -117 TTAGCTCAAGACATTTTTAATAAACTTTAA 6 205 1 ACATTTTTAA 0.626749 -96 ATTTAAACTTTTTTGTTTAAAGTTTATTAA 6 221 0 TTTTGTTTAA 0.875836 -80 ACCCTTTTGGTATTATTTAATTGTGTTATC 6 275 0 TATTATTTAA 0.83935 -26 TTATGTGGTTTATTTTTTAT 7 1 0 TATTTTTTAT 0.865062 -300 TTAATATCTATTTTATTTATGTGGTTTATT 7 17 0 TTTTATTTAT 0.793904 -284 TGAGGGATTGTAATGTTAATTAGTTTAGTC 7 69 1 TAATGTTAAT 0.615595 -232 ATTTTTCGTAATATATTTAATAATCATACT 7 107 1 ATATATTTAA 0.704633 -194 GTTGGCTGGATTATATTAAATAAACAGTAT 7 144 1 TTATATTAAA 0.788458 -157 TAAGTTCATATTATTTTTAAGGCATTACTT 7 194 1 TTATTTTTAA 0.926517 -107 TGAAGTTCTTTATTTTTTAAGTAATGCCTT 7 212 0 TATTTTTTAA 0.920078 -89 CATAATAAATTTTTATTAATTGAAAGACGC 7 247 0 TTTTATTAAT 0.715676 -54 ********** Masking position 6 Map Score: 32.9158 Number of sites scoring better than the average of aligned sites = 3857 Number in coding regions = 2779 Number in noncoding regions = 1078 Number of orfs with sites within 600 bp upstream = 610 Fraction of orfs with sites within 600 bp upstream = 0.0979762 Motif number 2 AATCTCCCAACATTAATTTTATTAATGGTGA 1 9 1 AAAAATTTTA 0.940846 -72 TTTATCACATCAACAACTTTAATTTTAAAAC 1 60 0 ATAAACTTTA 0.955176 -21 CGTTTTTTATTTGAGGAATTTTAGCATATTAAA 2 37 0 TTAAATTTTA 0.899346 -55 CGTATTATAATTTTCAAATTTTTAAATAATAGG 3 14 0 TTTAATTTTT 0.486525 -135 TGTTATTAAAAAAAGAAATTTTAACAATTATCG 3 45 0 AAAAATTTTA 0.933152 -104 AGGAAACTAAATGAAAAACTTTATATTCTATAT 3 83 1 ATAAACTTTA 0.955176 -66 TTAACAGTTAAATTGTAACTTTTCCACATAAGG 3 118 1 AATAACTTTT 0.67182 -31 CCACCATTTTTTAAATAACTTAAATCTTTCTGA 4 19 0 TTAAACTTAA 0.502899 -282 TAAAAGGGGATATATAAATTTTACGGTTTAATA 4 277 1 TAAAATTTTA 0.890691 -24 TTTAATAAATTTTTAATGAAAATA 5 2 1 TTAAATTTTT 0.744169 -121 AATTTTGTTTAACACAAATTTTATATAATTAGG 5 55 1 AAAAATTTTA 0.941009 -68 TTGAGATACTAAATATTATTTTAATGGAATTTT 6 135 0 AATTATTTTA 0.406333 -166 CAATTTTGTCAATTTTAATTTTATGTAACATTT 6 165 1 AATAATTTTA 0.838524 -136 CAAGACATTTTTAATAAACTTTAAACAAAAAAG 6 211 1 TTAAACTTTA 0.915823 -90 TTGATAATACTATTTAAACTTTTTTGTTTAAAG 6 229 0 TATAACTTTT 0.512688 -72 TTTAAATAGTATTATCAACATTAGATATGATGA 6 244 1 ATAAACATTA 0.718301 -57 TGCATGAATTAATATCTATTTTATTTATGTGGT 7 22 0 AAATATTTTA 0.742509 -279 TAGTATGATTATTAAATATATTACGAAAAATAA 7 105 0 ATATATATTA 0.274536 -196 CCTTAAAAATAATATGAACTTAATGAAATCAAT 7 183 0 AAAAACTTAA 0.71026 -118 TACTTAAAAAATAAAGAACTTCATTTTGGCGTC 7 219 1 ATAAACTTCA 0.693258 -82 AGGATTATTCATAATAAATTTTTATTAATTGAA 7 253 0 ATAAATTTTT 0.850649 -48 ** * ******* Masking position 11 Map Score: 17.0812 Number of sites scoring better than the average of aligned sites = 1756 Number in coding regions = 1315 Number in noncoding regions = 441 Number of orfs with sites within 600 bp upstream = 380 Fraction of orfs with sites within 600 bp upstream = 0.0610344 Motif number 3 AATCTCCCAACATTAATTTT 1 1 1 AATCTCCCAA 0.903432 -80 ATAATCTCCTCATTTTAAATAG 2 80 0 AATCTCCTCA 0.96588 -12 AATATCCCCCTTATGTGGAA 3 139 0 AATATCCCCC 0.972491 -10 ATCAATGTAGAATCTTCACAGGAATAAATC 4 159 1 AATCTTCACA 0.866219 -142 GTAAAATTTATATATCCCCTTTTACTTTTT 4 271 0 TATATCCCCT 0.85441 -30 TTTAAGTATAAATCTCCTCTACAGTATGGA 6 29 1 AATCTCCTCT 0.96588 -272 ATCCCTCAGAAATATTCACTGTTGCATGAA 7 47 0 AATATTCACT 0.71679 -254 TAATCTCCCCCAATTTTATTT 7 290 0 AATCTCCCCC 0.989064 -11 ********** Masking position 2 Map Score: 5.68261 Number of sites scoring better than the average of aligned sites = 422 Number in coding regions = 380 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 4 ATTCTTTTGAGTTTTAAAATTAAAGTTGTTG 1 50 1 GTTTAAAATT 0.516069 -31 AGTTTTTTGCGTTTTTTATTTGAGGAATTTT 2 48 0 GTTTTTATTT 0.96487 -44 AACAATTATCGTATTATAATTTTCAAATTTT 3 25 0 GTTTATAATT 0.902028 -124 AGAATATAAAGTTTTTCATTTAGTTTCCTTA 3 81 0 GTTTTCATTT 0.926682 -68 TTAAATCTTTCTGATTTATTTT 4 2 0 CTATTTATTT 0.719037 -299 ACATTTGATAGTATAATATTTTCATTAAAAA 5 20 0 GTTAATATTT 0.507421 -103 ATATAATTAGGTAATTTAATTACCTTAAAAA 5 77 1 GTATTTAATT 0.926095 -46 ATAATATTTAGTATCTCAATTTTGTCAATTT 6 149 1 GTTCTCAATT 0.618593 -152 CCCTTTTGGTATTATTTAATTGTGTTATCAT 6 273 0 ATATTTAATT 0.45216 -28 TTTTATTTATGTGGTTTATTTTTTAT 7 6 0 GTGTTTATTT 0.921934 -295 GAATTAATATCTATTTTATTTATGTGGTTTA 7 19 0 CTTTTTATTT 0.831488 -282 TAGTTTAGTCGTAGTTTTATTTTTCGTAATA 7 89 1 GTGTTTTATT 0.487445 -212 TTTATTTTTCGTAATATATTTAATAATCATA 7 104 1 GTATATATTT 0.844442 -197 CCAAAATGAAGTTCTTTATTTTTTAAGTAAT 7 217 0 GTCTTTATTT 0.865177 -84 TCATTTTGGCGTCTTTCAATTAATAAAAATT 7 239 1 GTTTTCAATT 0.91748 -62 ** ******** Masking position 2 Map Score: 6.93758 Number of sites scoring better than the average of aligned sites = 577 Number in coding regions = 464 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 5 ATAATCACCATTAATAAAATTAATGTTGGG 1 16 0 TTAATAAAAT 0.648845 -65 ATGGTGATTATTAATATTCTTTTGAGTTTT 1 35 1 TTAATATTCT 0.913932 -46 TGGTGTTTCTTTAATATGCTAAAATTCCTC 2 28 1 TTAATATGCT 0.823712 -64 ATCCTATTATTTAAAAATTTGAAAATTATA 3 12 1 TTAAAAATTT 0.404952 -137 TTTAGTTTCCTTAATATGTTATTAAAAAAA 3 64 0 TTAATATGTT 0.837057 -85 AATGAAAAACTTTATATTCTATATTTTTAA 3 92 1 TTTATATTCT 0.620125 -57 ACTTTCACAATTTATATATTTATAAGGCAC 4 224 0 TTTATATATT 0.613154 -77 TTTAATAAATTTTTAATGAAA 5 2 1 TTAATAAATT 0.881699 -121 ATTTGATAGTATAATATTTTCATTAAAAAT 5 19 0 ATAATATTTT 0.738643 -104 CTAATCAATCTTAATCATTTTTAAGGTAAT 5 95 0 TTAATCATTT 0.50215 -28 TATGGACATTGTAATATTTTCAGATATTTT 6 53 1 GTAATATTTT 0.635295 -248 AATGGAATTTTTAATATAGTATTTGAAAAA 6 116 0 TTAATATAGT 0.686539 -185 TTCCATTAAAATAATATTTAGTATCTCAAT 6 139 1 ATAATATTTA 0.296158 -162 CAAGACATTTTTAATAAACTTTAAACAAAA 6 211 1 TTAATAAACT 0.871447 -90 CGTAATATATTTAATAATCATACTATGGAT 7 113 1 TTAATAATCA 0.537555 -188 TACTGTTTATTTAATATAATCCAGCCAACA 7 143 0 TTAATATAAT 0.711192 -158 AGGATTATTCATAATAAATTTTTATTAATT 7 256 0 ATAATAAATT 0.649534 -45 ********** Masking position 4 Map Score: 6.26342 Number of sites scoring better than the average of aligned sites = 1136 Number in coding regions = 858 Number in noncoding regions = 278 Number of orfs with sites within 600 bp upstream = 263 Fraction of orfs with sites within 600 bp upstream = 0.0422422 Motif number 6 AATATCCCCCTTATGTGGAAAAGTTA 3 133 0 CCCCTTATGT 0.958122 -16 TGGTCCAGCGCCCTATAGGCAACTGGAGTC 4 95 1 CCCTATAGGC 0.90988 -206 AATGACGATACCCTTTAGGCATCAAAGTGC 4 198 1 CCCTTTAGGC 0.986703 -103 ATTTATATATCCCCTTTTACTTTTTATATG 4 266 0 CCCCTTTTAC 0.873355 -35 AGTTTCACCCTTTTGGTATTATTTAAT 6 284 0 CCCTTTTGGT 0.970499 -17 ********** Masking position 6 Map Score: 0.596374 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 31 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 ********** No masking Map Score: 1.48036e-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 8 ********** No masking Map Score: 1.48036e-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: 1.48036e-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