AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00520_mjan_reg_100.orf -o00520_mjan_100.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 ATTTATCACCAAATTTTTTATATGATAATTT 1 22 1 AAATTTTTAT 0.987136 -65 GCAAAATTTTAAAATTATCATATAAAAAATT 1 33 0 AAAATTATAT 0.914307 -54 GATAATTTTAAAATTTTGCATTAAAAAGAAA 1 45 1 AAATTTTGAT 0.906837 -42 CATTAAAAAGAAATTTATCATTTAAGGTGAT 1 63 1 AAATTTATAT 0.925314 -24 CAAAATAATTTTTATTTTATATTAT 2 5 1 ATAATTTTAT 0.935214 -39 TATTTCCCATAATTTTTTAAT 2 33 1 AATTTTTTAT 0.953785 -11 TTTAAAACATTAAGTTTTTATATATATTGTC 3 49 0 TAAGTTTTAT 0.954182 -157 TTAATGTTTTAAAATTTTAATGTCTTTCAAA 3 67 1 AAAATTTTAT 0.98509 -139 GTGTTCCTTATTAATTTTAATACTTTTGAAA 3 91 0 TTAATTTTAT 0.86258 -115 ATTATTACAAAATGTTTTGATTATTATCTTT 3 161 1 AATGTTTTAT 0.936283 -45 AAATGGAAATAAAATTTTAAT 4 1 0 AAAATTTTAT 0.98509 -214 ATTTTATTTCCATTTTTTAATGCATTATATA 4 17 1 CATTTTTTAT 0.779879 -198 TTCCTCGAAATACTTTTTCATAATCATCACC 4 115 1 TACTTTTTAT 0.821853 -100 AATCATCACCAAATTATTTATACCTACTATA 4 136 1 AAATTATTAT 0.9253 -79 TTACAATTATATAGTATTAATATAGTAGGTA 4 156 0 ATAGTATTAT 0.686709 -59 CTCCCTTTAGTAAATTTTTATTAAATTAATT 4 191 0 TAAATTTTAT 0.961899 -24 ******** ** Masking position 5 Map Score: 26.1917 Number of sites scoring better than the average of aligned sites = 1511 Number in coding regions = 1028 Number in noncoding regions = 483 Number of orfs with sites within 600 bp upstream = 406 Fraction of orfs with sites within 600 bp upstream = 0.0652104 Motif number 2 TTGGTGATAAATTTATAGGTTTA 1 2 0 ATTTATATTT 0.810857 -85 TCACCAAATTTTTTATATGATAATTTTAAAAT 1 27 1 TTTTATAATA 0.789776 -60 TAAATTTCTTTTTAATGCAAAATTTTAAAATT 1 48 0 TTTAATGAAA 0.764056 -39 ATAATTTTTATTTTATATTATTTCCCATAATT 2 15 1 TTTTATAATT 0.835106 -29 ATATATTGTCATTAATCATTTTTGAAATCAAT 3 27 0 ATTAATCTTT 0.724397 -179 AACATTAAGTTTTTATATATATTGTCATTAAT 3 43 0 TTTTATATAT 0.792075 -163 TATATAAAAACTTAATGTTTTAAAATTTTAAT 3 56 1 CTTAATGTTA 0.844612 -150 GTTTTAAAATTTTAATGTCTTTCAAAAGTATT 3 72 1 TTTAATGTTT 0.979043 -134 CCTTATTAATTTTAATACTTTTGAAAGACATT 3 85 0 TTTAATATTT 0.974637 -121 GATTATTATCTTTAATGATTATAGCAAAGGTG 3 179 1 TTTAATGTAT 0.926231 -27 ATTTCCATTTTTTAATGCATTATATATGACTT 4 22 1 TTTAATGTTA 0.969384 -193 TATATATGACTTCAATAGCTTTTTTTAACTTT 4 42 1 TTCAATATTT 0.911655 -173 CCTCATCTTCTTCAATGAATTTTAGTTTCACA 4 75 1 TTCAATGTTT 0.926152 -140 TACCTACTATATTAATACTATATAATTGTAAC 4 156 1 ATTAATAATA 0.742677 -59 TTAGTAAATTTTTATTAAATTAATTTATGTTA 4 184 0 TTTATTATTA 0.704547 -31 ******* *** Masking position 6 Map Score: 14.007 Number of sites scoring better than the average of aligned sites = 2270 Number in coding regions = 1801 Number in noncoding regions = 469 Number of orfs with sites within 600 bp upstream = 398 Fraction of orfs with sites within 600 bp upstream = 0.0639255 Motif number 3 ATATAAAAAATTTGGTGATAAATTTATAGGTT 1 13 0 TTTGGTATAA 0.967091 -74 TAATGCAAAATTTTAAAATTATCATATAAAAA 1 36 0 TTTTAAATAT 0.908366 -51 TTAAAAAATTATGGGAAATAATATAAAATAAA 2 21 0 ATGGGAATAT 0.69531 -23 CATTAATCATTTTTGAAATCAATATCATGGGT 3 18 0 TTTTGAATAA 0.956307 -188 TTTTTATATATATTGTCATTAATCATTTTTGA 3 34 0 TATTGTATAA 0.886186 -172 CTTTCAAAAGTATTAAAATTAATAAGGAACAC 3 90 1 TATTAAATAA 0.778977 -116 AATCAAAACATTTTGTAATAATTGAGGTATTA 3 151 0 TTTTGTATAT 0.956316 -55 TACAAAATGTTTTGATTATTATCTTTAATGAT 3 166 1 TTTGATATAT 0.930085 -40 GATTATTATCTTTAATGATTATAGCAAAGGTG 3 179 1 TTTAATATAT 0.672991 -27 TGCATTAAAAAATGGAAATAAAATTTTAAT 4 9 0 AATGGAATAA 0.7007 -206 GTATAAATAATTTGGTGATGATTATGAAAAAG 4 127 0 TTTGGTATAT 0.967094 -88 TACTATATAATTGTAACATAAATTAATTTAAT 4 171 1 TTGTAAATAA 0.774548 -44 ****** ** ** Masking position 8 Map Score: 9.97846 Number of sites scoring better than the average of aligned sites = 1325 Number in coding regions = 1107 Number in noncoding regions = 218 Number of orfs with sites within 600 bp upstream = 211 Fraction of orfs with sites within 600 bp upstream = 0.0338901 Motif number 4 ********** 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 5 ********** 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 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