AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -icspA_mthe_opreg_100.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 Motif number 1 GGTTAAAACCTGTAAGGGGGGTGTTTTAT 1 10 1 CTGTAAGGGG 0.953248 -42 TGTTTTATGGCTGAACTGAGCATAATCTAG 1 32 1 CTGAACTGAG 0.94158 -20 TATTAAGATTTTGAGAGGATACAGTGGCAC 2 35 0 TTGAGAGGAT 0.979141 -44 TTCCAGTCATCTGTGATGATTATCGGCGGC 3 24 0 CTGTGATGAT 0.952281 -243 TCACAGATGACTGGAAGGATCCTTATACTA 3 38 1 CTGGAAGGAT 0.969788 -229 TGGTCCATCCTTGTGAGGAGTTCATTCATA 3 120 0 TTGTGAGGAG 0.975165 -147 GACCATGTCTTCGAGAGGATGAGGATAGTT 3 145 1 TCGAGAGGAT 0.907315 -122 GACAAGGTCCCTTAAAAGAGAAGAGATCGA 3 180 1 CTTAAAAGAG 0.768742 -87 CTCATTATCTCTGAGAGGTGGTGGTCTATC 3 213 0 CTGAGAGGTG 0.976647 -54 AATGAGGATACTGAACAGATACAACTGAAG 3 237 1 CTGAACAGAT 0.911177 -30 ********** Masking position 8 Map Score: 10.9686 Number of sites scoring better than the average of aligned sites = 1718 Number in coding regions = 1620 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 2 AGGTGCCACTGTATCCTCTCAAAATCTTAA 2 33 1 GTATCCTCTC 0.916787 -46 CTGGAGGCACCCTGCCGCCGATAATC 3 7 1 GCACCCTGCC 0.990823 -260 CATAGTATAAGGATCCTTCCAGTCATCTGT 3 40 0 GGATCCTTCC 0.934004 -227 CATGCTATCAGCTCCATATCAATTTCTATC 3 73 0 GCTCCATATC 0.917853 -194 TCACAAGGATGGACCATGTCTTCGAGAGGA 3 134 1 GGACCATGTC 0.994903 -133 CTCTTTTAAGGGACCTTGTCCGGCTAACTA 3 170 0 GGACCTTGTC 0.987223 -97 GAGAGGTGGTGGTCTATCTCTTCGATCTCT 3 201 0 GGTCTATCTC 0.883206 -66 ********** Masking position 7 Map Score: 4.97831 Number of sites scoring better than the average of aligned sites = 1120 Number in coding regions = 1087 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 TGTAAGGGGGGTGTTTTATGGCTGAACTGAG 1 21 1 GTTTTTATGG 0.985627 -31 GATGTTTATGGGTCTCGCTTA 2 1 1 GAGTTTATGG 0.995504 -78 ACCAATATATGTTTTTTATGGTATTAAGATT 2 55 0 GTTTTTATGG 0.985627 -24 AGTCATCTGTGATGATTATCGGCGGCAGGGT 3 19 0 GAGATTATCG 0.950279 -248 ACCCCACCAGGACGTATATGAATGAACTCCT 3 104 1 GAGTATATGA 0.928033 -163 ** ******** Masking position 7 Map Score: 3.17615 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 115 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 4 GGTTAAAACCTGTAAGGGGGGTGTTT 1 7 1 AACCTGTAAG 0.953966 -45 GATACAGTGGCACCTGTAAGCGAGACCCAT 2 18 0 CACCTGTAAG 0.992553 -61 CTGGAGGCACCCTGCCGCCGATAATCA 3 8 1 CACCCTGCCG 0.948984 -259 GCATGTACCCCACCAGGACGTATATGAATG 3 98 1 CACCAGGACG 0.99273 -169 ATGAACTCCTCACAAGGATGGACCATGTCT 3 125 1 CACAAGGATG 0.888483 -142 GATAGACCACCACCTCTCAGAGATAATGAG 3 213 1 CACCTCTCAG 0.969264 -54 ********** Masking position 2 Map Score: 3.07435 Number of sites scoring better than the average of aligned sites = 657 Number in coding regions = 621 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 5 CTAGATTATGCTCAGTTCAGCC 1 40 0 AGATTATGCT 0.908954 -12 TATGGTATTAAGATTTTGAGAGGATACAGT 2 40 0 AGATTTTGAG 0.977464 -39 CATAAAAAACATATATTGGTCCG 2 66 1 ATATATTGGT 0.676877 -13 AAGGATCCTTATACTATGAGTGATAGAAAT 3 52 1 ATACTATGAG 0.874066 -215 TATGAGTGATAGAAATTGATATGGAGCTGA 3 66 1 AGAAATTGAT 0.863946 -201 CATGTCTTCGAGAGGATGAGGATAGTTAGC 3 148 1 AGAGGATGAG 0.937205 -119 CACCTCTCAGAGATAATGAGGATACTGAAC 3 223 1 AGATAATGAG 0.982602 -44 ********** Masking position 3 Map Score: 1.13136 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 380 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 6 ATTATGCTCAGTTCAGCCATAAAACACCCC 1 28 0 GTTCAGCCAT 0.993627 -24 ATAAGGATCCTTCCAGTCATCTGTGATGAT 3 34 0 TTCCAGTCAT 0.975151 -233 CTTGTGAGGAGTTCATTCATATACGTCCTG 3 111 0 GTTCATTCAT 0.984877 -156 CGAAGACATGGTCCATCCTTGTGAGGAGTT 3 128 0 GTCCATCCTT 0.984053 -139 ********** Masking position 5 Map Score: 2.35427 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 120 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 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 Motif number 8 ********** 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 9 ********** 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