AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -icspA_mthe_opreg_300.orf -g0.495 -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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH1492 51 5'-nucleotidase #2 MTH1493 78 cation transporting P-type ATPase related protein #3 MTH1494 266 conserved protein #4 MTH1495 194 ornithine cyclodeaminase Motif number 1 GGTTAAAACCTGTAAGGGGGGTGTTT 1 1 1 GGTAACTAAG 0.803633 -51 CTAGATTATGCTCAGTTCAGCCATAAAACACCCC 1 28 0 TGTATCCCAT 0.97738 -24 CATAGTATAAGGATCCTTCCAGTCATCTGTGATGAT 3 34 0 GGTCTCTCAT 0.992472 -233 CGTCCTGGTGGGGTACATGCTATCAGCTCCATATCA 3 82 0 GGTCTCTCAG 0.98472 -185 TCCATCCTTGTGAGGAGTTCATTCATATACGTCCTG 3 111 0 TGGATCTCAT 0.953818 -156 GACCTTGTCCGGCTAACTATCCTCATCCTCTCGAAG 3 153 0 GGTATTTCAT 0.988814 -114 CAGTTGTATCTGTTCAGTATCCTCATTATCTCTGAG 3 228 0 TGTATTTCAT 0.966635 -39 TTAAAACCACGGATGAGTACTGTCATGGCTGTCCCG 4 105 0 GGTATCTCAT 0.996306 -90 TCAGGGTCAATCTACCAATCTTTAAATAT 4 176 0 GGTATTCAAT 0.89483 -19 ** * * * * **** Masking position 15 Map Score: 8.05377 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 180 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 2 TAAAACACCCCCCTTACAGGTTTTAACC 1 9 0 CCCTTACAGG 0.74819 -43 GGTATTAAGATTTTGAGAGGATACAGTGGC 2 37 0 TTTTGAGAGG 0.864196 -42 TCATATACGTCCTGGTGGGGTACATGCTAT 3 95 0 CCTGGTGGGG 0.936975 -172 CATGGTCCATCCTTGTGAGGAGTTCATTCA 3 122 0 CCTTGTGAGG 0.98683 -145 TGGACCATGTCTTCGAGAGGATGAGGATAG 3 143 1 CTTCGAGAGG 0.967988 -124 TTTTAAGGGACCTTGTCCGGCTAACTATCC 3 167 0 CCTTGTCCGG 0.974591 -100 TCCTCATTATCTCTGAGAGGTGGTGGTCTA 3 215 0 CTCTGAGAGG 0.972534 -52 GCCATGACTGCCTCGAGGGTGGAGTTTCCG 4 62 1 CCTCGAGGGT 0.920609 -133 CCCGGCGGTCCATGGACCGGAAACTCCACC 4 79 0 CATGGACCGG 0.861992 -116 GCCGGGACAGCCATGACAGTACTCATCCGT 4 103 1 CCATGACAGT 0.823328 -92 ********** Masking position 9 Map Score: 8.25506 Number of sites scoring better than the average of aligned sites = 2249 Number in coding regions = 2179 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 3 TTATCGGCGGCAGGGTGCCTCCAG 3 4 0 CAGGGTGCTC 0.984972 -263 CTCATAGTATAAGGATCCTTCCAGTCATCTG 3 41 0 AAGGATCCTC 0.942149 -226 CTCTCGAAGACATGGTCCATCCTTGTGAGGA 3 131 0 CATGGTCCTC 0.899571 -136 GTTAGCCGGACAAGGTCCCTTAAAAGAGAAG 3 172 1 CAAGGTCCTT 0.634648 -95 GTTTCCGGTCCATGGACCGCCGGGACAGCCA 4 85 1 CATGGACCCC 0.967671 -110 TCAGGGTCAATCTACCAATCTT 4 183 0 CAGGGTCATC 0.988594 -12 ******** ** Masking position 2 Map Score: 5.47252 Number of sites scoring better than the average of aligned sites = 560 Number in coding regions = 538 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 GATGTTTATGGGTCTCGCTTACAGGTGCC 2 10 1 GGGTCTCGCT 0.935104 -69 ATCGGCGGCAGGGTGCCTCCAG 3 3 0 GGGTGCCTCC 0.96479 -264 CATAGTATAAGGATCCTTCCAGTCATCTGT 3 40 0 GGATCCTTCC 0.913894 -227 CGTCCTGGTGGGGTACATGCTATCAGCTCC 3 88 0 GGGTACATGC 0.907196 -179 CTCGAAGACATGGTCCATCCTTGTGAGGAG 3 130 0 TGGTCCATCC 0.988471 -137 TGAGAGGTGGTGGTCTATCTCTTCGATCTC 3 202 0 TGGTCTATCT 0.939039 -65 TCAGGGTCAATCTACCAATCTTT 4 182 0 GGGTCAATCT 0.9696 -13 ********** Masking position 4 Map Score: 3.8608 Number of sites scoring better than the average of aligned sites = 618 Number in coding regions = 589 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 GTGTTTTATGGCTGAACTGAGCATAATCTA 1 31 1 GCTGAACTGA 0.986126 -21 AAGAGAAGAGATCGAAGAGATAGACCACCA 3 195 1 ATCGAAGAGA 0.930561 -72 TAATGAGGATACTGAACAGATACAACTGAA 3 236 1 ACTGAACAGA 0.972786 -31 TATATTTCAAGTTGAAGTGAGATATAAGTC 4 14 1 GTTGAAGTGA 0.979069 -181 AGCTATTAAGGTTGATCAGACTTATATCTC 4 32 0 GTTGATCAGA 0.963488 -163 ********** Masking position 5 Map Score: 2.19702 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 78 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 ATTCATATACGTCCTGGTGGGGTACATGCT 3 97 0 GTCCTGGTGG 0.990071 -170 CCTCGAGGCAGTCATGGCAGCTATTAAGGT 4 50 0 GTCATGGCAG 0.994008 -145 TGTCATGGCTGTCCCGGCGGTCCATGGACC 4 91 0 GTCCCGGCGG 0.995237 -104 CGCCGGGACAGCCATGACAGTACTCATCCG 4 102 1 GCCATGACAG 0.960783 -93 ********** Masking position 6 Map Score: 1.89354 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 171 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 ********** No masking Map Score: 1.24588e-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: 1.24588e-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 9 ********** No masking Map Score: 1.24588e-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