AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00251_rpxx_reg_100.orf -o00251_rpxx_100.ace -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -g0.29 -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 = 0.29 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RP091 174 ASPARTATE AMINOTRANSFERASE A (aatA) #2 RP325 107 GLUTAMYL-TRNA SYNTHETASE (gltX1) #3 RP623 114 GLUTAMYL-TRNA SYNTHETASE (gltX2) Motif number 1 GTTTAATTACTAAATTCATATTATTTACACTA 1 12 1 TAAATTAATT 0.910145 -163 TATGCTTTATTATAGTGTAAATAATATGAATT 1 24 0 TATAGTTAAT 0.880314 -151 TATTTAAAAATTTATTAAGATATGCTTTATTA 1 44 0 TTTATTAATA 0.708997 -131 ATAAAATTATTTTATTTAAAAATTTATTAAGA 1 56 0 TTTATTAAAA 0.859285 -119 ATAAAATAATTTTATTGAGATTAAAATTGCTG 1 73 1 TTTATTAATT 0.950915 -102 TGTATTATCGTTTATTATTAATGTTATTCTAA 1 103 1 TTTATTTAAT 0.93059 -72 CCGAATTCAGTATTTTAAGATTCTCAAAGCTC 1 148 1 TATTTTAATT 0.861692 -27 ATTTTTAGTTTATAGTAATAATTTGATATTAA 2 16 0 TATAGTAAAT 0.830761 -92 TGTAACACCGTATATTTTTAGTTTATAGTAAT 2 29 0 TATATTTAGT 0.957624 -79 ACTAATTTTATTAATTGCTATACGTGTGTGGC 2 81 0 TTAATTCATA 0.585399 -27 CTCAACAGTATATATTGCAAATTATTTTCCTA 3 17 1 TATATTCAAT 0.963966 -98 TATTGCAAATTATTTTCCTAGATACTCTAATC 3 29 1 TATTTTCAGA 0.592953 -86 CAGAACTTTTTAAATTATAATTTGATTAGAGT 3 52 0 TAAATTTATT 0.880469 -63 AAGTTCTGAGTATATTCTGAGTTATATATATT 3 76 1 TATATTTAGT 0.957628 -39 CTGAGTTATATATATTTAAAATAATAATAATA 3 92 1 TATATTAAAT 0.973661 -23 ****** * *** Masking position 10 Map Score: 18.2004 Number of sites scoring better than the average of aligned sites = 1483 Number in coding regions = 890 Number in noncoding regions = 593 Number of orfs with sites within 600 bp upstream = 265 Fraction of orfs with sites within 600 bp upstream = 0.0425634 Motif number 2 AAATAATATGAATTTAGTAATTAAACT 1 5 0 AATTTAATTA 0.771842 -170 TTTATTTAAAAATTTATTAAGATATGCTTTATT 1 45 0 AATTTAAGAT 0.827809 -130 TAAATTTTTAAATAAAATAATTTTATTGAGATT 1 62 1 AATAAAATTT 0.909261 -113 AATAAACGATAATACAGCAATTTTAATCTCAAT 1 86 0 AATACAATTT 0.967948 -89 TAAGAATCCGAATTCAGTATTTTAAGATTCTCA 1 141 1 AATTCATTTT 0.888727 -34 ATAAACTAAAAATATACGGTGTTACAATACAAG 2 35 1 AATATATGTT 0.970664 -73 ACGGTGTTACAATACAAGATTTCGTGGTTAAGC 2 50 1 AATACATTTC 0.831596 -58 TATAGCAATTAATAAAATTAGTTATTT 2 91 1 AATAAAAGTT 0.945825 -17 AATAATTTGCAATATATACTGTTGAGATTTTA 3 10 0 AATATATGTT 0.971681 -105 ATCAAATTATAATTTAAAAAGTTCTGAGTATAT 3 58 1 AATTTAAGTT 0.970642 -57 ****** **** Masking position 6 Map Score: 8.98254 Number of sites scoring better than the average of aligned sites = 542 Number in coding regions = 331 Number in noncoding regions = 211 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 3 GCTTTATTATAGTGTAAATAATATGAATTTAG 1 21 0 AGTTAAATAT 0.939758 -154 TATTTACACTATAATAAAGCATATCTTAATAA 1 33 1 ATATAAAGAT 0.964665 -142 AATAACATTAATAATAAACGATAATACAGCAA 1 99 0 ATATAAACAT 0.964665 -76 TATTAATGTTATTCTAAAGTATATAAGAATCC 1 118 1 ATTTAAAGAT 0.940969 -57 TAATAATTTGATATTAAACCAT 2 1 0 ATATAAACAT 0.969106 -107 AACAGTATATATTGCAAATTATTTTCCTAGAT 3 20 1 ATTCAAATAT 0.94818 -95 TACTCAGAACTTTTTAAATTATAATTTGATTA 3 56 0 TTTTAAATAT 0.916574 -59 AGTTATATATATTTAAAATAATAATAATAA 3 95 1 ATTAAAATAT 0.927058 -20 *** ***** ** Masking position 6 Map Score: 9.11614 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 186 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 4 AGTTTAATTACTAAATTCATATTATTTA 1 9 1 TACTAAATTC 0.95364 -166 AATCTTAAAATACTGAATTCGGATTCTTAT 1 140 0 TACTGAATTC 0.945333 -35 TATTTTAAGATTCTCAAAGCTCATTTT 1 158 1 TTCTCAAAGC 0.926016 -17 ATCAAATTATTACTATAAACTAAAAATATA 2 21 1 TACTATAAAC 0.934874 -87 TTTTCCTAGATACTCTAATCAAATTATAAT 3 41 1 TACTCTAATC 0.978875 -74 ACTCAGAATATACTCAGAACTTTTTAAATT 3 68 0 TACTCAGAAC 0.956656 -47 ********** Masking position 4 Map Score: 3.35049 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 53 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 ********** No masking Map Score: -1.60993e-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: -1.60993e-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: -1.60993e-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