AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00520_mjan_reg_300.orf -o00520_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -x5 -e 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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: MJ1101 27 glucose-1-phosphate thymidylyltransferase (strD) Input sequences: #1 MJ0210 86 succinyl-CoA synthetase, beta subunit #2 MJ0210.1 43 M. jannaschii predicted coding region MJ0210.1 #3 MJ1100 205 phosphomannomutase (pmmB) #4 MJ1334 214 UDP-glucose pyrophosphorylase (gtaB) Motif number 1 TAAACCTATAAATTTATCACCAAATT 1 7 1 TATAAATTTA 0.778346 -80 ATTATCATATAAAAAATTTGGTGATAAATT 1 21 0 AAAAAATTTG 0.880597 -66 TATGATAATTTTAAAATTTTGCATTAAAAA 1 42 1 TTAAAATTTT 0.925022 -45 AAAAAGAAATTTATCATTTAAGGTGATAGG 1 67 1 TTATCATTTA 0.772486 -20 CAAAATAATTTTTATTTTATAT 2 3 1 AAATAATTTT 0.958891 -41 ATTAAAAAATTATGGGAAATAAT 2 31 0 AAAAAATTAT 0.831865 -13 ATATTGTCATTAATCATTTTTGAAATCAAT 3 27 0 TAATCATTTT 0.922491 -179 CAATATATATAAAAACTTAATGTTTTAAAA 3 51 1 AAAAACTTAA 0.575559 -155 ACTTAATGTTTTAAAATTTTAATGTCTTTC 3 65 1 TTAAAATTTT 0.925022 -141 TTATTAATTTTAATACTTTTGAAAGACATT 3 85 0 TAATACTTTT 0.922491 -121 AAACATTTTGTAATAATTGAGGTATTAATG 3 148 0 TAATAATTGA 0.810886 -58 GATAATAATCAAAACATTTTGTAATAATTG 3 159 0 AAAACATTTT 0.899936 -47 ACCTTTGCTATAATCATTAAAGATAATAAT 3 180 0 TAATCATTAA 0.624723 -26 ATTAAAATTTTATTTCCATTT 4 2 1 TTAAAATTTT 0.925022 -213 AATAGCTTTTTTTAACTTTTCCTCATCTTC 4 55 1 TTTAACTTTT 0.501142 -160 ACTTTCCTCGAAATACTTTTTCATAATCAT 4 112 1 AAATACTTTT 0.907356 -103 TAGTAGGTATAAATAATTTGGTGATGATTA 4 135 0 AAATAATTTG 0.880841 -80 TATTAATACTATATAATTGTAACATAAATT 4 165 1 ATATAATTGT 0.706576 -50 ATTTTTATTAAATTAATTTATGTTACAATT 4 179 0 AATTAATTTA 0.743054 -36 ATTAATTTAATAAAAATTTACTAAAGGGAG 4 192 1 TAAAAATTTA 0.94217 -23 ********** Masking position 7 Map Score: 22.4661 Number of sites scoring better than the average of aligned sites = 3537 Number in coding regions = 2398 Number in noncoding regions = 1139 Number of orfs with sites within 600 bp upstream = 655 Fraction of orfs with sites within 600 bp upstream = 0.105204 Motif number 2 TTTAAAATTATCATATAAAAAATTTGGTGAT 1 26 0 TATATAAAAA 0.920432 -61 TTTTATATGATAATTTTAAAATTTTGCATTA 1 37 1 TATTTTAAAA 0.944154 -50 TTTTAAAATTTTGCATTAAAAAGAAATTTAT 1 50 1 TGCATTAAAA 0.943466 -37 GGAAATAATATAAAATAAAAATTATTTTG 2 9 0 TAAATAAAAA 0.762805 -35 CCCATGATATTGATTTCAAAAATGATTAATG 3 19 1 TATTTCAAAA 0.87927 -187 TAATGACAATATATATAAAAACTTAATGTTT 3 45 1 AATATAAAAA 0.868391 -161 TAAAAACTTAATGTTTTAAAATTTTAATGTC 3 60 1 AGTTTTAAAA 0.897817 -146 TACTTTTGAAAGACATTAAAATTTTAAAACA 3 71 0 AACATTAAAA 0.912788 -135 TGTTCCTTATTAATTTTAATACTTTTGAAAG 3 90 0 TATTTTAATA 0.906102 -116 GTCATATATAATGCATTAAAAAATGGAAATA 4 21 0 AGCATTAAAA 0.904939 -194 GCATTATATATGACTTCAATAGCTTTTTTTA 4 38 1 TACTTCAATA 0.773613 -177 TTAATATAGTAGGTATAAATAATTTGGTGAT 4 140 0 AGTATAAATA 0.773913 -75 TACAATTATATAGTATTAATATAGTAGGTAT 4 155 0 TGTATTAATA 0.920273 -60 GTAACATAAATTAATTTAATAAAAATTTACT 4 183 1 TAATTTAATA 0.728657 -32 * ********* Masking position 8 Map Score: 14.1166 Number of sites scoring better than the average of aligned sites = 2061 Number in coding regions = 1527 Number in noncoding regions = 534 Number of orfs with sites within 600 bp upstream = 378 Fraction of orfs with sites within 600 bp upstream = 0.0607131 Motif number 3 TATAAAAAATTTGGTGATAAATTTATAGGT 1 14 0 TTGGTGATAA 0.96703 -73 CCAAATTTTTTATATGATAATTTTAAAATT 1 30 1 TATATGATAA 0.796252 -57 TTTATCATTTAAGGTGATAGG 1 76 1 AAGGTGATAG 0.871881 -11 TGGGAAATAATATAAAATAAAAATTATTTT 2 12 0 TATAAAATAA 0.547813 -32 TAAAAAATTATGGGAAATAATATAAAATAA 2 22 0 TGGGAAATAA 0.803769 -22 ATCAAAACATTTTGTAATAATTGAGGTATT 3 152 0 TTTGTAATAA 0.792525 -54 ATAATCATTAAAGATAATAATCAAAACATT 3 171 0 AAGATAATAA 0.874694 -35 GATTATAGCAAAGGTGATTAA 3 195 1 AAGGTGATTA 0.850671 -11 GCATTAAAAAATGGAAATAAAATTTTAAT 4 10 0 ATGGAAATAA 0.884414 -205 AAATTCATTGAAGAAGATGAGGAAAAGTTA 4 67 0 AAGAAGATGA 0.770951 -148 TATAAATAATTTGGTGATGATTATGAAAAA 4 128 0 TTGGTGATGA 0.926535 -87 ********** Masking position 7 Map Score: 5.26239 Number of sites scoring better than the average of aligned sites = 1748 Number in coding regions = 1459 Number in noncoding regions = 289 Number of orfs with sites within 600 bp upstream = 290 Fraction of orfs with sites within 600 bp upstream = 0.0465789 Motif number 4 TTAAATGATAAATTTCTTTTTAATGCAAAA 1 58 0 AATTTCTTTT 0.892699 -29 TATAAAATAAAAATTATTTTG 2 2 0 AAATTATTTT 0.72762 -42 TTAAAATTTTAATGTCTTTCAAAAGTATTA 3 75 1 AATGTCTTTC 0.95371 -131 GGAACACTTGAACGTCTTCTTATAGAAGGC 3 115 1 AACGTCTTCT 0.953045 -91 GGTATTAATGAACGCCTTCTATAAGAAGAC 3 128 0 AACGCCTTCT 0.93178 -78 TCCATTTTTTAATGCATTATATATGACTTC 4 25 1 AATGCATTAT 0.792014 -190 CATCTTCTTCAATGAATTTTAGTTTCACAT 4 78 1 AATGAATTTT 0.849797 -137 TGATTATGAAAAAGTATTTCGAGGAAAGTG 4 111 0 AAAGTATTTC 0.873943 -104 ********** Masking position 2 Map Score: 1.98896 Number of sites scoring better than the average of aligned sites = 554 Number in coding regions = 479 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 5 AATTTTTATTTTATATTATTTCCCATAATT 2 17 1 TTATATTATT 0.80056 -27 TTAAGTTTTTATATATATTGTCATTAATCA 3 41 0 ATATATATTG 0.837145 -165 GAACGTCTTCTTATAGAAGGCGTTCATTAA 3 124 1 TTATAGAAGG 0.89767 -82 TATTGAAGTCATATATAATGCATTAAAAAA 4 29 0 ATATATAATG 0.961249 -186 TATAGTAGGTATAAATAATTTGGTGATGAT 4 137 0 ATAAATAATT 0.713685 -78 TATAGTATTAATATAGTAGGTATAAATAAT 4 148 0 ATATAGTAGG 0.939344 -67 TGTTACAATTATATAGTATTAATATAGTAG 4 159 0 ATATAGTATT 0.917645 -56 ********** Masking position 5 Map Score: 1.83941 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 264 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 6 ********** No masking Map Score: 3.7902e-13 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 7 ********** No masking Map Score: 3.7902e-13 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: 3.7902e-13 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