AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -irpoE_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 MJ0677 69 ethylene-inducible protein #2 MJ0678 62 conserved hypothetical protein #3 MJ0679 39 transketolase'' #4 MJ0680 23 pentose-5-phosphate-3-epimerase #5 MJ0681 156 transketolase' #6 MJ0682 26 conserved hypothetical protein #7 MJ0683 29 conserved hypothetical protein #8 MJ0684 68 aspartate aminotransferase (aspB2) Motif number 1 CATAACAAACTTTTATCAATGATTATGGAG 1 42 1 TTTTATCAAT 0.762219 -28 AATAATTTTATTTTATTTATTTTATTT 2 8 0 TTTTATTTAT 0.964775 -55 AATAAAATAAAATTATTATTCTATTTTCAA 2 21 1 AATTATTATT 0.917844 -42 TCAAATAAACTTTTATTGTTGGGATT 2 47 1 TTTTATTGTT 0.97232 -16 ATAATTAATTTATTATTTTTGTTT 3 5 0 TATTATTTTT 0.984368 -35 AAAATAATAAATTAATTATTTTGGGTGAAA 3 16 1 ATTAATTATT 0.505943 -24 AATTTTATTTTTTGGTGATTTA 4 3 1 TTTTATTTTT 0.986261 -21 ATTTACTATCTATTATTTTTAGGTGTAAGT 5 20 1 TATTATTTTT 0.984368 -137 TATGACTAACAATTATTTTAGCATAACATC 5 56 1 AATTATTTTA 0.686744 -101 ATTATGGATTTTTTGTTTTTGCTTTTTTTA 5 86 1 TTTTGTTTTT 0.907069 -71 TTTTTGCTTTTTTTATTAATTCATTGAGTA 5 101 1 TTTTATTAAT 0.95789 -56 TGAGTAATGATATTATTTTTTAAATCTTAA 5 125 1 TATTATTTTT 0.984368 -32 CCACGAAAAGTATTATTAATTAATAATAAT 8 20 1 TATTATTAAT 0.9501 -49 CACTAAAAGGAATTATTATTAATTAATAAT 8 31 0 AATTATTATT 0.917844 -38 TAATAATTCCTTTTAGTGTTTATAAATGGT 8 43 1 TTTTAGTGTT 0.826723 -26 ********** Masking position 3 Map Score: 27.2179 Number of sites scoring better than the average of aligned sites = 1858 Number in coding regions = 1229 Number in noncoding regions = 629 Number of orfs with sites within 600 bp upstream = 440 Fraction of orfs with sites within 600 bp upstream = 0.0706714 Motif number 2 TTAAACATATATAGTTGGAGACTATAATTTC 1 12 1 ATATTGGAGA 0.979514 -58 ATCAATGATTATGGAGGGAGAGTT 1 56 1 ATGAGGGAGA 0.970861 -14 TAAATTAATTATTTTGGGTGAAAAATC 3 23 1 ATTTGGGTGA 0.990652 -17 AATTTTATTTTTTGGTGATTTAA 4 8 1 TTTTTGGTGA 0.969265 -16 TAAAAACACATTAATGGTGATGCATA 6 10 1 ATTATGGTGA 0.992238 -17 TTTAGTGTTTATAAATGGTGATGTC 8 54 1 ATAATGGTGA 0.988915 -15 *** ******* Masking position 2 Map Score: 7.3886 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 171 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 AATTAATTATTTTGGGTGAAAAATC 3 25 1 TTTGGGTGAA 0.934559 -15 AATTTTATTTTTTGGTGATTTAA 4 10 1 TTTTGGTGAT 0.984291 -14 ATCTATTATTTTTAGGTGTAAGTTTTAAAT 5 27 1 TTTAGGTGTA 0.913711 -130 AAAAAATCCATAATGATGTTATGCTAAAAT 5 70 0 TAATGATGTT 0.813485 -87 TTAAATCTTAAAAAGGTGAAACT 5 144 1 AAAAGGTGAA 0.861482 -13 AAAAACACATTAATGGTGATGCATA 6 12 1 TAATGGTGAT 0.984291 -15 TAATAATTCCTTTTAGTGTTTATAAATGGT 8 43 1 TTTTAGTGTT 0.813485 -26 TAGTGTTTATAAATGGTGATGTC 8 56 1 AAATGGTGAT 0.958225 -13 ********** Masking position 7 Map Score: 5.2426 Number of sites scoring better than the average of aligned sites = 935 Number in coding regions = 719 Number in noncoding regions = 216 Number of orfs with sites within 600 bp upstream = 253 Fraction of orfs with sites within 600 bp upstream = 0.040636 Motif number 4 TAGAATAATAATTTTATTTTATTTATTTTA 2 14 0 ATTTTATTTT 0.941387 -49 TTAATTTATTATTTTTGTTT 3 1 0 ATTTTTGTTT 0.979397 -39 AATTTTATTTTTTGGTGATTT 4 2 1 ATTTTATTTT 0.941387 -22 ACTAACAATTATTTTAGCATAACATCATTA 5 60 1 ATTTTAGCAT 0.948448 -97 TGGATTTTTTGTTTTTGCTTTTTTTATTAA 5 90 1 GTTTTTGCTT 0.984119 -67 CCCTTATAAAGTTTTTGCTTAT 7 3 0 GTTTTTGCTT 0.984119 -27 ********** Masking position 5 Map Score: 6.95139 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 193 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 ATTAAACATATATAGTTGGAGA 1 1 1 ATTAAATATA 0.875932 -69 AAAAGTTTGTTATGAAATTATAGTCTCCAACT 1 24 0 TATAATTATA 0.828463 -46 AAATAAAATAAATAAAATAAAATT 2 3 1 ATAAAAAATA 0.861263 -60 TTTATTTGAAAATAGAATAATAATTTTATTTT 2 24 0 AATGATAATA 0.896666 -39 TCTATTTTCAAATAAACTTTTATTGTTGGGAT 2 40 1 AATAATTTTA 0.722275 -23 AAACAAAAATAATAAATTAATTATTTTGGGTG 3 11 1 AATAATAATT 0.519114 -29 TTACACCTAAAAATAATAGATAGTAAATAGAG 5 16 0 AAAAAAGATA 0.800587 -141 AAAAAAGCAAAAACAAAAAATCCATAATGATG 5 82 0 AAAAAAAATC 0.764817 -75 ATCATTACTCAATGAATTAATAAAAAAAGCAA 5 104 0 AATAATAATA 0.919768 -53 CCTTTTTAAGATTTAAAAAATAATATCATTAC 5 128 0 ATTAAAAATA 0.939703 -29 AAGGAATTATTATTAATTAATAATACTTTTCG 8 23 0 TATAATAATA 0.496822 -46 *** ** ***** Masking position 6 Map Score: 6.02166 Number of sites scoring better than the average of aligned sites = 2111 Number in coding regions = 1539 Number in noncoding regions = 572 Number of orfs with sites within 600 bp upstream = 390 Fraction of orfs with sites within 600 bp upstream = 0.0626405 Motif number 6 ********** No masking Map Score: -2.7468e-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: -2.7468e-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: -2.7468e-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