AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -icspA_mgen_opreg_100.orf -g0.317 -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 = 0.317 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MG001 300 DNA polymerase III, subunit beta (dnaN) #2 MG003 84 DNA gyrase subunit B (gyrB) Motif number 1 AGCAGTAATAATTACATATGTACA 1 4 1 ATAATAATTA 0.888441 -297 TATATATAACAGAAATTAATGATATTTTACA 1 44 0 AAAATTAATG 0.960348 -257 AATTTCTGTTATATATAATAGTATCTATTTT 1 58 1 AATATAATAG 0.63252 -243 TTTAGAGAGTATTAATTATTACTATAATTAA 1 86 1 ATAATTATTA 0.945059 -215 AGCATAAATGCTTAATTATAGTAATAATTAA 1 97 0 CTAATTATAG 0.918547 -204 AGCATTTATGCTTAATTATAAGCTTTTTATG 1 116 1 CTAATTATAA 0.914619 -185 TTTTTATGAACAAAATTATAGACATTTTAGT 1 139 1 CAAATTATAG 0.943124 -162 AGTTCTTATAATAAATAATAGATATTAAAGA 1 167 1 AAAATAATAG 0.949511 -134 TAGATATTAAAGAAAATAAAAAAATAGAAAT 1 185 1 AAAAATAAAA 0.750976 -116 ATAAAAAAATAGAAATAAATATCATAACCCT 1 200 1 AAAATAAATA 0.911787 -101 TTGATAACCCAGAAATTAATACTTAATCAAA 1 230 1 AAAATTAATA 0.957131 -71 ATACTTAATCAAAAATGAAAATATTAATTAA 1 248 1 AAAATGAAAA 0.926703 -53 ATTCACTTTTATTAATTAATATTTTCATTTT 1 259 0 ATAATTAATA 0.938011 -42 ATAACACATTAAAAATGAAAGGTTTT 2 6 0 AAAATGAAAG 0.932043 -79 TGGCATAACAAATAATTATAACACATTAAAA 2 23 0 ATAATTATAA 0.962092 -62 * ********* Masking position 5 Map Score: 20.8071 Number of sites scoring better than the average of aligned sites = 514 Number in coding regions = 415 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 2 ACAGAAATTAATGATATTTTACATATGTAC 1 37 0 ATGATATTTT 0.918068 -264 GTTATATATAATAGTATCTATTTTAGAGAG 1 65 1 ATAGTATCTA 0.796258 -236 ATAGTAATAATTAATACTCTCTAAAATAGA 1 81 0 TTAATACTCT 0.798108 -220 TTTATTTTCTTTAATATCTATTATTTATTA 1 175 0 TTAATATCTA 0.918068 -126 ATCAAGGGTTATGATATTTATTTCTATTTT 1 205 0 ATGATATTTA 0.918068 -96 AACCCAGAAATTAATACTTAATCAAAAATG 1 235 1 TTAATACTTA 0.929639 -66 CTTTTATTAATTAATATTTTCATTTTTGAT 1 255 0 TTAATATTTT 0.926307 -46 AGTGAATTGAATAAAATTTTGGGAAAAA 1 283 1 ATAAAATTTT 0.831752 -18 ********** Masking position 6 Map Score: 4.71324 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 152 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 3 ATATGTACTATGTACATATGTAATTATTAC 1 15 0 TGTACATATG 0.983848 -286 ATATGTACATAGTACATATGTAAAATATCA 1 26 1 AGTACATATG 0.988691 -275 TCTATAATTTTGTTCATAAAAAGCTTATAA 1 131 0 TGTTCATAAA 0.929531 -170 TAGACATTTTAGTTCTTATAATAAATAATA 1 157 1 AGTTCTTATA 0.8917 -144 TAAATAAACAGTACAGAAGCTTTTGCCAC 2 66 0 AGTACAGAAG 0.964907 -19 ********** Masking position 3 Map Score: 2.68454 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 17 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 4 ATACTATTATATATAACAGAAATTAATGATA 1 51 0 ATATAACAAA 0.902724 -250 ATAACCCTTGATAACCCAGAAATTAATACTT 1 223 1 ATAACCCAAA 0.914435 -78 TTTTTCCCAAAATTTTATTCAA 1 289 0 TTTTCCCAAA 0.924879 -12 TAACAAATAATTATAACACATTAAAAATGAA 2 18 0 TTATAACAAT 0.809964 -67 TAATTATTTGTTATGCCATAAATTTAGTTTG 2 36 1 TTATGCCAAA 0.555477 -49 GTACAGAAGCTTTTGCCACAAACTAAATTTA 2 54 0 TTTTGCCAAA 0.809285 -31 ******** ** Masking position 8 Map Score: 2.05061 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 56 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 TGTACTATGTACATATGTAATTATTACTGC 1 12 0 ACATATGTAA 0.991664 -289 TGTACATAGTACATATGTAAAATATCATTA 1 29 1 ACATATGTAA 0.991664 -272 ********** Masking position 5 Map Score: 0.691765 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: -1.32571e-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: -1.32571e-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: -1.32571e-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