AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i106_Potassium_Transport_kdp_operon_mtub_reg_100.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 = 0.66 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 kdpD_kdpA 325 kdpD: kdpD, kdpA: kdpA Motif number 1 TTCGCGGCGCTGCTGTTTCCGGAGAAGTTCTG 1 9 0 TGCTGTCGGG 0.978471 -317 GCGCTAATGGCGTTCCTATTCGCGGCGCTGCTGT 1 27 0 CGTTCTTCGG 0.861125 -299 ATCGTCGGGTTGGTGATCGCGGTGGCGCTAATGG 1 51 0 TGGTGTCGGG 0.997411 -275 ATCACCAACCCGACGATGTTGTCGACCGTAGTCA 1 68 1 CGACGTTGTG 0.824348 -258 GCCGGCCGAATGGCGATGACTACGGTCGACAACA 1 84 0 TGGCGTCTAG 0.937186 -242 GCCATTCGGCCGGCGCTCGCGTGAGTTCGACTGT 1 104 1 CGGCGTCGTA 0.859356 -222 TCATTCGCCGCGACGAAATCGGGGAAACAACAGT 1 133 0 CGACGACGGG 0.563865 -193 GCCTGCTCTACGTCCGTGGCTGTGAACGGATCAT 1 163 0 CGTCCTCTGG 0.957151 -163 CTGACCGTGATGGCCTTTGCCGGGCTTTGCCTGC 1 191 0 TGGCCTCCGG 0.994835 -135 GACTTGGTGTTGGTGCTGACCGTGATGGCCTTTG 1 206 0 TGGTGTCCGG 0.994954 -120 AGGACTCACATGGCCGACTTGGTGTTGGTGCTGA 1 221 0 TGGCCATGGG 0.954284 -105 ATGTGAGTCCTCTCGATTCTTGTGCACCGGCATC 1 244 1 TCTCGTTTGG 0.741834 -82 ATCTGATGCGCTGCGATGCCGGTGCACAAGAATC 1 258 0 CTGCGTCGGG 0.984232 -68 CCCAGCAGGATGGTAGTTGCCGGGCCCCCCAGGA 1 294 1 TGGTATCCGG 0.939526 -32 GGTCGTGTTCCTGGGGGGCCCGGCAA 1 310 0 TCGTGTTGGG 0.956736 -16 ***** * *** * Masking position 14 Map Score: 22.1231 Number of sites scoring better than the average of aligned sites = 44280 Number in coding regions = 42312 Number in noncoding regions = 1968 Number of orfs with sites within 600 bp upstream = 980 Fraction of orfs with sites within 600 bp upstream = 0.157404 Motif number 2 CAGAACTTCTCCGGAAACAGCAGCGCCGCGAA 1 11 1 CCGGACAGCA 0.993017 -315 AACAGCAGCGCCGCGAATAGGAACGCCATTAG 1 26 1 CCGCATAGGA 0.962783 -300 GCGAATAGGAACGCCATTAGCGCCACCGCGAT 1 38 1 ACGCATAGCG 0.960715 -288 ATTAGCGCCACCGCGATCACCAACCCGACGAT 1 53 1 CCGCACACCA 0.880452 -273 AGTCGAACTCACGCGAGCGCCGGCCGAATGGC 1 104 0 ACGCACGCCG 0.915174 -222 AGGCAAAGCCCGGCAAAGGCCATCACGGTCAG 1 193 1 CGGCAGGCCA 0.908938 -133 AAGGCCATCACGGTCAGCACCAACACCAAGTC 1 208 1 CGGTACACCA 0.972818 -118 TTCTTGTGCACCGGCATCGCAGCGCATCAGAT 1 260 1 CCGGACGCAG 0.921801 -66 CTGGGGGGCCCGGCAACTACCATCCTGCTGGG 1 294 0 CGGCATACCA 0.98184 -32 **** * ***** Masking position 6 Map Score: 12.4741 Number of sites scoring better than the average of aligned sites = 15208 Number in coding regions = 14536 Number in noncoding regions = 672 Number of orfs with sites within 600 bp upstream = 484 Fraction of orfs with sites within 600 bp upstream = 0.0777385 Motif number 3 TCCGGAAACAGCAGCGCCGCGAATAGGAACGCCATTA 1 20 1 GCACGCGCAG 0.98441 -306 ACGGTCGACAACATCGTCGGGTTGGTGATCGCGGTGG 1 60 0 ACACGCGGGG 0.993649 -266 ACTCACGCGAGCGCCGGCCGAATGGCGATGACTACGG 1 93 0 GCGCGCCGGG 0.996973 -233 CGGATCATTCGCCGCGACGAAATCGGGGAAACAACAG 1 134 0 GCCCGCGAGG 0.99558 -192 TCCGTTCACAGCCACGGACGTAGAGCAGGCAAAGCCC 1 167 1 GCCCGACGGA 0.977211 -159 CGTAGAGCAGGCAAAGCCCGGCAAAGGCCATCACGGT 1 185 1 GCAAGCCGAG 0.979146 -141 CAGCACCAACACCAAGTCGGCCATGTGAGTCCTCTCG 1 222 1 ACCAGCGGGG 0.989748 -104 CGATTCTTGTGCACCGGCATCGCAGCGCATCAGATAG 1 257 1 GCACGCATGG 0.947884 -69 GCATCAGATAGCCCAGCAGGATGGTAGTTGCCGGGCC 1 283 1 GCCAGAGGTG 0.918462 -43 GATGGTAGTTGCCGGGCCCCCCAGGAACACGACC 1 302 1 GCCGGCCCGA 0.944134 -24 *** ** *** * * Masking position 2 Map Score: 11.7073 Number of sites scoring better than the average of aligned sites = 16122 Number in coding regions = 15135 Number in noncoding regions = 987 Number of orfs with sites within 600 bp upstream = 690 Fraction of orfs with sites within 600 bp upstream = 0.110826 Motif number 4 ACCGCGATCACCAACCCGACGATGTTGTCGA 1 62 1 CCAACCCACG 0.985673 -264 GGCCGAATGGCGATGACTACGGTCGACAACA 1 84 0 CGATGACACG 0.837791 -242 CACGCGAGCGCCGGCCGAATGGCGATGACTA 1 96 0 CCGGCCGATG 0.97615 -230 CCGATTTCGTCGCGGCGAATGATCCGTTCAC 1 145 1 CGCGGCGATG 0.948578 -181 CCGGGCTTTGCCTGCTCTACGTCCGTGGCTG 1 175 0 CCTGCTCACG 0.68929 -151 GCAGGCAAAGCCCGGCAAAGGCCATCACGGT 1 191 1 CCCGGCAAGG 0.94064 -135 ACGGTCAGCACCAACACCAAGTCGGCCATGT 1 217 1 CCAACACAAG 0.89188 -109 ATCAGATAGCCCAGCAGGATGGTAGTTGCCG 1 285 1 CCAGCAGATG 0.985993 -41 GCCGGGCCCCCCAGGAACACGACC 1 312 1 CCAGGAAACG 0.979791 -14 ******* *** Masking position 9 Map Score: 4.97371 Number of sites scoring better than the average of aligned sites = 9145 Number in coding regions = 8564 Number in noncoding regions = 581 Number of orfs with sites within 600 bp upstream = 494 Fraction of orfs with sites within 600 bp upstream = 0.0793447 Motif number 5 ********** No masking Map Score: 2.43208e-15 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: 2.43208e-15 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: 2.43208e-15 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