AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -ilexA_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 MG070 110 ribosomal protein S2 (rpS2) #2 MG244 300 DNA helicase II, putative #3 MG298 202 P115 protein Motif number 1 AACCAAGGTTTTATGGCTTTTAGTTATTATC 1 23 0 TTATGCTTTT 0.989442 -88 AACCTTGGTTTTGTGGTTTTTAGCTTGTTTA 1 44 1 TTGTGTTTTT 0.892996 -67 GTTCTAATTGTTATCGCTATTGCATTAGGCT 2 52 0 TTATGCTATT 0.950362 -249 CAACTGATTTTTATTGGTTATTTTTGTTTTA 2 108 1 TTATGGTTAT 0.889136 -193 GTTTTTAAGCTAGTTGGTTTTGATTTTAAAG 2 202 0 TAGTGGTTTT 0.977554 -99 ATCAGGTTGATTGTTGGTTTTTAAGCTAGTT 2 218 0 TTGTGGTTTT 0.977554 -83 TTACCAGGCGTAATAGCTCTTGATGAAGTGG 2 258 1 TAATGCTCTT 0.941493 -43 TGTTATTAATTAATGAGTTTTTCCACTTCAT 2 280 0 TAATAGTTTT 0.832315 -21 CTTTTAAATGATATTGCTTTTCTAAAAGCAA 3 14 1 ATATGCTTTT 0.902209 -189 AAAATTACATTAATTGCTTTTAGAAAAGCAA 3 27 0 TAATGCTTTT 0.989445 -176 TTAAATAAACTAGTTACTATTAAAACATAGA 3 62 1 TAGTACTATT 0.693811 -141 TATTAAAACATAGAAGCTTTTTTAAATGAAG 3 79 1 TAGAGCTTTT 0.947151 -124 AATGAAGCGTTATTAGCTTATTTTTTAGTAA 3 103 1 TATTGCTTAT 0.734959 -100 AACATCCAAATTAAAGCTTTTTAGAACAA 3 184 1 TTAAGCTTTT 0.9462 -19 **** ****** Masking position 8 Map Score: 20.4948 Number of sites scoring better than the average of aligned sites = 408 Number in coding regions = 372 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 2 TTTTGTGGTTTTTAGCTTGTTTATAACAATAT 1 52 1 TTTCTTGTTT 0.95635 -59 CGCTTAATTTTTTCACTAATTTAGATAAGCCT 2 25 1 TTTCTAATTT 0.939468 -276 CGCTATTGCATTAGGCTTATCTAAATTAGTGA 2 37 0 TTACTTATCT 0.7271 -264 CCATAACAATTTTGATTAGTTTTTTACAACTG 2 82 1 TTTTTAGTTT 0.950301 -219 TTTTTATTGGTTATTTTTGTTTTAGTTCTGAA 2 115 1 TTATTTGTTT 0.950301 -186 GTATCTCTTGTAAAGCTTGTTTTTCAGAACTA 2 137 0 TAACTTGTTT 0.830304 -164 TTGTTGGTTTTTAAGCTAGTTGGTTTTGATTT 2 207 0 TTACTAGTTG 0.97851 -94 AATTTAAAAATTACATTAATTGCTTTTAGAAA 3 32 0 TTATTAATTG 0.883345 -171 TAGTAACTAGTTTATTTAATTTAAAAATTACA 3 49 0 TTTTTAATTT 0.875392 -154 TGAAGCGTTATTAGCTTATTTTTTAGTAACCT 3 105 1 TTATTATTTT 0.80457 -98 AACCTAATAATTAGCCTAGTTTAGTTTACTTC 3 132 1 TTACTAGTTT 0.987871 -71 TGTTATTAGATTATACTAGTTGAAGTAAACTA 3 153 0 TTACTAGTTG 0.97851 -50 *** ******* Masking position 7 Map Score: 15.5669 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 256 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 TCAATAAAACTCGATAATAAC 1 2 1 CAATAAAACT 0.964417 -109 CAATAAAACTCGATAATAACTAAAAGCCAT 1 12 1 CGATAATAAC 0.922442 -99 TAACTAAAAGCCATAAAACCTTGGTTTTGT 1 28 1 CCATAAAACC 0.968639 -83 AAGCTAAAAACCACAAAACCAAGGTTTTAT 1 40 0 CCACAAAACC 0.865615 -71 AGTAAAACTGCAATAATATTGTTATAAACA 1 69 0 CAATAATATT 0.731497 -42 TTACATTATGCAGTAAAACTGCAATAATAT 1 80 0 CAGTAAAACT 0.823095 -31 AATGCAATAGCGATAACAATTAGAACCATA 2 57 1 CGATAACAAT 0.921165 -244 ACAATTAGAACCATAACAATTTTGATTAGT 2 72 1 CCATAACAAT 0.944506 -229 CAAAAATAACCAATAAAAATCAGTTGTAAA 2 104 0 CAATAAAAAT 0.966645 -197 AGAACTAAAACAAAAATAACCAATAAAAAT 2 114 0 CAAAAATAAC 0.773947 -187 CTTTATGGTTCAAGAAAAACACACTTTAAA 2 179 1 CAAGAAAAAC 0.906311 -122 TAGTATAATCTAATAACAACATCCAAATTA 3 167 1 TAATAACAAC 0.732996 -36 ********** Masking position 5 Map Score: 10.3836 Number of sites scoring better than the average of aligned sites = 347 Number in coding regions = 315 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 TACTGCATAATGTAAAATTACACAGC 1 95 1 TGTAAAATTA 0.937226 -16 AAAAACACACTTTAAAATCAAAACCAACTA 2 193 1 TTTAAAATCA 0.913523 -108 CTATTACGCCTGGTAAATTAGCTGGATCAG 2 244 0 TGGTAAATTA 0.910592 -57 AAACTTTTAAATGATATTGCTTTT 3 5 1 TTTTAAATGA 0.973169 -198 TTAATGTAATTTTTAAATTAAATAAACTAG 3 45 1 TTTTAAATTA 0.971098 -158 ATAGAAGCTTTTTTAAATGAAGCGTTATTA 3 88 1 TTTTAAATGA 0.973169 -115 ********** Masking position 5 Map Score: 5.29293 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 88 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 ATAAAACTCGATAATAACTAAAAGCCATAA 1 14 1 ATAATAACTA 0.795682 -97 TTTTAGCTTGTTTATAACAATATTATTGCA 1 61 1 TTTATAACAA 0.878995 -50 AGCGATAACAATTAGAACCATAACAATTTT 2 65 1 ATTAGAACCA 0.965903 -236 AAGCTTGTTTTTCAGAACTAAAACAAAAAT 2 127 0 TTCAGAACTA 0.946447 -174 ACACTTTAAAATCAAAACCAACTAGCTTAA 2 199 1 ATCAAAACCA 0.931378 -102 ACCAACTAGCTTAAAAACCAACAATCAACC 2 215 1 TTAAAAACCA 0.919519 -86 ATTAAAGCTTTTTAGAACAA 3 193 1 TTTAGAACAA 0.942433 -10 ********** Masking position 6 Map Score: 4.12894 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 289 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 ********** No masking Map Score: 1.63668e-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 7 ********** No masking Map Score: 1.63668e-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: 1.63668e-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