AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i013_Glycolysis___PPS_tpal_reg_300.orf -o013_tpal_300.ace -a/home/amcguire/alignace/lib/ORF_tpal.txt -z/skink1/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTP00193 63 AE000520 #2 RTP00194 66 AE000520 #3 RTP01039 60 AE000520 #4 RTP00195 72 AE000520 #5 RTP00196 111 AE000520 #6 RTP00024 300 AE000520 Motif number 1 GCAGCTAGCCGCGCAGGGTGGATTCGGCCTGGCGGAAAAGG 1 32 0 GCGGGTGGCG 0.993493 -32 CTACCCAGCCGTGAAAGACACTATCCAGCAGGGGTACGGTC 2 15 0 GTGAGTCACG 0.871654 -52 TTTCACGGCTGGGTAGCAGTGGGTACACGACTCTTTT 2 40 1 GGGGCTCAGC 0.795394 -27 TGTATTTCCTGCGGGGTAAGATGGACGATGGAGACCCCGGC 3 27 0 GCGGTGCGTG 0.904727 -34 TCGTTCTGCGCCTCAAACTCGTCTTCTGGCAAATACTG 4 45 0 GCGTCGCTCG 0.9194 -28 TCTTTTTAAGGTGAGTGTGCTCTTAGGTGCGCTCTTT 5 7 0 GTGTGTGGGG 0.966696 -105 TCGGCAGCGTGCGGTACAGGGGGTCGGTGTGCGGTATGGCA 5 49 0 GCGACTGGGG 0.993875 -63 CGAGAATTCAGCGACGCGCGGGTGTCGGCAGCGTGCGGTAC 5 73 0 GCGGCGCGCG 0.993964 -39 CCGTCACTGAGCGAGACATCCACTTCGACAGTGGGGTTTCC 6 12 0 GCGACTCGCG 0.99507 -289 AGCTTTGGCCGTGCGTGTGTTCCTTCAGGGGCGTCTACCgG 6 54 1 GTGTGTCAGG 0.938503 -247 CGCATTTCGAGCGCCTCGAACTCTCcGGTAGACGCCCCTGA 6 78 0 GCGTCTcGTG 0.987393 -223 CGCTCGAAATGCGTGATGGAGACAAGGAGCGCTATAACGGT 6 106 1 GCGATAGGGG 0.810519 -195 TCAGCAATGAGCGTGTTGACAGTTCCAACGGCCTTGAGAAC 6 153 0 GCGTTTCACG 0.964396 -148 CCCTGGTTGAGCGCATCCATACCTTCGAGCGTATCAGCAAT 6 186 0 GCGTCTCGGG 0.997798 -115 GATAGATCACGCGATGCGGAATCTGGACGGCACTGACAATA 6 230 1 GCGGCTGAGC 0.96066 -71 AAAGCTTGGTGCGAATGCTATGCTTGGCGTCTCCAT 6 275 1 GCGTGTGGGC 0.976842 -26 *** ** * ** * * Masking position 3 Map Score: 22.7609 Number of sites scoring better than the average of aligned sites = 1676 Number in coding regions = 1553 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 2 TTTCCGCCAGGCCGAATCCACCCTGCGCGG 1 35 1 GCCGAATCCA 0.938521 -29 ACCTGACCGTACCCCTGCTGGATAG 2 6 1 ACCGTACCCC 0.86557 -61 ACAGAAAGCCGGGGTCTCCATCGTCCATCT 3 20 1 GGGGTCTCCA 0.982261 -41 ATACTGAGCAGGGGTCTGGACAAAAGCATT 4 21 0 GGGGTCTGGA 0.87119 -52 GGGTCGGTGTGCGGTATGGCACTCTTTTTA 5 40 0 GCGGTATGGC 0.60794 -72 CATACCGCACACCGACCCCCTGTACCGCAC 5 52 1 ACCGACCCCC 0.943684 -60 ACCGCACGCTGCCGACACCCGCGCGTCGCT 5 75 1 GCCGACACCC 0.922957 -37 CCGAGAATTCAGCGACGCGCGGGTGTCGGC 5 85 0 AGCGACGCGC 0.825002 -27 CTTCGACAGTGGGGTTTCCC 6 1 0 GGGGTTTCCC 0.813621 -300 TTCCTTCAGGGGCGTCTACCgGAGAGTTCG 6 73 1 GGCGTCTACC 0.967964 -228 ACGCATTTCGAGCGCCTCGAACTCTCcGGT 6 90 0 AGCGCCTCGA 0.921128 -211 ACCCTGGTTGAGCGCATCCATACCTTCGAG 6 198 0 AGCGCATCCA 0.855995 -103 TATTGTCAGTGCCGTCCAGATTCCGCATCG 6 241 0 GCCGTCCAGA 0.818229 -60 TGCTATGCTTGGCGTCTCCAT 6 290 1 GGCGTCTCCA 0.992659 -11 ********** Masking position 4 Map Score: 14.2813 Number of sites scoring better than the average of aligned sites = 1245 Number in coding regions = 1122 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 3 AAAGAGCGCACCTAAGAGCAC 5 1 1 AAAGAGCGCC 0.994706 -111 AGAGCGCACCTAAGAGCACACTCACCTTAAA 5 13 1 TAAGAGCACC 0.985441 -99 CTCACCTTAAAAAGAGTGCCATACCGCACAC 5 33 1 AAAGAGTGCA 0.869248 -79 GACGCCCCTGAAGGAACACACGCACGGCCAA 6 58 0 AAGGAACACC 0.97251 -243 TGATGGAGACAAGGAGCGCTATAACGGTAAG 6 119 1 AAGGAGCGCA 0.971822 -182 CCAACGGCCTTGAGAACACCCTTACCGTTAT 6 139 0 TGAGAACACC 0.893191 -162 CCAGGGTGAGATAGATCACGCGATGCGGAAT 6 221 1 ATAGATCACC 0.880314 -80 ********* * Masking position 5 Map Score: 3.46304 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 385 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 AGGGTGGATTCGGCCTGGCGGAAAAGGTAT 1 29 0 CGGCCTGGCG 0.934262 -35 AGACACTATCCAGCAGGGGTACGGTCAGGT 2 11 0 CAGCAGGGGT 0.989104 -56 CACTGCTACCCAGCCGTGAAAGACACTATC 2 31 0 CAGCCGTGAA 0.863387 -36 CACGGCTGGGTAGCAGTGGGTACACGACTC 2 43 1 TAGCAGTGGG 0.949112 -24 AATATACAGAAAGCCGGGGTCTCCATCGTC 3 15 1 AAGCCGGGGT 0.934405 -46 GGCAAATACTGAGCAGGGGTCTGGACAAAA 4 26 0 GAGCAGGGGT 0.929538 -47 ACATCCACTTCGACAGTGGGGTTTCCC 6 8 0 CGACAGTGGG 0.945545 -293 ACGGTAGCTTTGGCCGTGCGTGTGTTCCTT 6 49 1 TGGCCGTGCG 0.913234 -252 AGCGCTATAACGGTAAGGGTGTTCTCAAGG 6 133 1 CGGTAAGGGT 0.680436 -168 ACAGTTCCAACGGCCTTGAGAACACCCTTA 6 146 0 CGGCCTTGAG 0.917442 -155 TCGAGCGTATCAGCAATGAGCGTGTTGACA 6 173 0 CAGCAATGAG 0.895718 -128 TGGATGCGCTCAACCAGGGTGAGATAGATC 6 208 1 CAACCAGGGT 0.850676 -93 ********** Masking position 8 Map Score: 10.1547 Number of sites scoring better than the average of aligned sites = 1302 Number in coding regions = 1171 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 5 ********** No masking Map Score: 4.57179e-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: 4.57179e-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: 4.57179e-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