AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i036_Acetate_Metabolism_tpal_reg_100.orf -o036_tpal_100.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 RTP00413 137 AE000520 #2 RTP00194 66 AE000520 #3 RTP01039 60 AE000520 #4 RTP00195 72 AE000520 #5 RTP00196 111 AE000520 Motif number 1 GCCCTATCAGCACCTGCTGCGCACCCAACTCCCG 1 20 1 CACCGCTCAC 0.9987 -118 GCACCCAACTCCCGTGCTGCGCACAAATGCGCAT 1 40 1 CCCGGCTCAC 0.995728 -98 CTGCGAATACCACCGTCTACCCACACTTCACCGG 1 76 1 CACCTCTCAC 0.985317 -62 ACCCACACTTCACCGGCACAGCGCGCTAACTCTC 1 94 1 CACCGCACGC 0.994241 -44 CCTGACCGTACCCCTGCTGGATAGTGTCTTTCAC 2 12 1 CCCCGCTTAG 0.994465 -55 AGTCGTGTACCCACTGCTACCCAGCCGTGAAAGA 2 38 0 CCACGCTCAG 0.982338 -29 ACGATGGAGACCCCGGCTTTCTGTATATTGTTG 3 10 0 CCCCGCTTGT 0.988053 -51 TTTGTCCAGACCCCTGCTCAGTATTTGCCAGAAG 4 27 1 CCCCGCTTAT 0.991461 -46 GCACACCGACCCCCTGTACCGCACGCTGCCGACA 5 58 1 CCCCGTACAC 0.980269 -54 ACGCTGCCGACACCCGCGCGTCGCTGAATTCTCG 5 80 1 CACCGCGCGC 0.993161 -32 **** *** *** Masking position 1 Map Score: 22.0504 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 342 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 2 GGGAGTTGGGTGCGCAGCAGGTGCTGATAGG 1 22 0 TGCCAGCAGG 0.998553 -116 TGCGCATTTGTGCGCAGCACGGGAGTTGGGT 1 42 0 TGCCAGCACG 0.997175 -96 ACACTTCACCGGCACAGCGCGCTAACTCTCC 1 98 1 GGCCAGCGCG 0.982833 -40 TGAAAGACACTATCCAGCAGGGGTACGGTCA 2 14 0 TATCAGCAGG 0.992098 -53 TACCCACTGCTACCCAGCCGTGAAAGACACT 2 34 0 TACCAGCCGT 0.900822 -33 CAACAATATACAGAAAGCCGGGGTCTC 3 7 1 TATCAGAAAG 0.770515 -54 TCGTCCATCTTACCCCGCAGGAAATACAGGA 3 40 1 TACCCGCAGG 0.9948 -21 TTCTGGCAAATACTGAGCAGGGGTCTGGACA 4 29 0 TACGAGCAGG 0.98294 -44 ACGAGTTTGAGGCGCAGAACGA 4 61 1 GGCCAGAACG 0.975995 -12 ACCGACCCCCTGTACCGCACGCTGCCGACAC 5 62 1 TGTCCGCACG 0.985709 -50 *** ******* Masking position 7 Map Score: 20.5337 Number of sites scoring better than the average of aligned sites = 643 Number in coding regions = 595 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 3 CAGCACCTGCTGCGCACCCAACTCCCGTGC 1 27 1 TGCGCACCCA 0.991275 -111 ACTCCCGTGCTGCGCACAAATGCGCATAAC 1 47 1 TGCGCACAAA 0.986438 -91 TGCGCACAAATGCGCATAACTGCGAATACC 1 57 1 TGCGCATAAC 0.957272 -81 TGCGCATAACTGCGAATACCACCGTCTACC 1 67 1 TGCGAATACC 0.811859 -71 TCACCGGCACAGCGCGCTAACTCTCCACCG 1 103 1 AGCGCGCTAA 0.901699 -35 ACCTGACCGTACCCCTGCTGGATAG 2 6 1 ACCGTACCCC 0.866427 -61 TCGTTCTGCGCCTCAAACTCGTCTTC 4 57 0 TGCGCCTCAA 0.884573 -16 AAAGAGCGCACCTAAGAGCACACT 5 5 1 AGCGCACCTA 0.972472 -107 CGCACCTAAGAGCACACTCACCTTAAAAAG 5 17 1 AGCACACTCA 0.87079 -95 AGAGTGCCATACCGCACACCGACCCCCTGT 5 45 1 ACCGCACACC 0.976589 -67 ********** Masking position 3 Map Score: 10.358 Number of sites scoring better than the average of aligned sites = 2467 Number in coding regions = 2288 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 4 GGACGCCCTATCAGCACCTGCTGCGCACCC 1 16 1 TCAGCACCTG 0.950191 -122 GCGCGCTAACTCTCCACCGTATTCAAAAAG 1 114 1 TCTCCACCGT 0.988575 -24 AAAGCCGGGGTCTCCATCGTCCATCTTACC 3 24 1 TCTCCATCGT 0.975018 -37 TCGTTCTGCGCCTCAAACTCGTCT 4 59 0 TCTGCGCCTC 0.975105 -14 CGCGCGGGTGTCGGCAGCGTGCGGTACAGG 5 70 0 TCGGCAGCGT 0.977187 -42 CGCTGAATTCTCGGCGTCTTT 5 101 1 TCGGCGTCTT 0.976296 -11 ********** Masking position 1 Map Score: 4.14323 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 209 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 5 GGTGCTGATAGGGCGTCCTTTTA 1 4 0 GGGCGTCCTT 0.989272 -134 CCCTGCTGGATAGTGTCTTTCACGGCTGGG 2 23 1 TAGTGTCTTT 0.896302 -44 CCGGGGTCTCCATCGTCCATCTTACCCCGC 3 28 1 CATCGTCCAT 0.954593 -33 ACAAAAGCATTAGCGTACATG 4 2 0 TAGCGTACAT 0.931464 -71 GCTGAATTCTCGGCGTCTTT 5 102 1 CGGCGTCTTT 0.986897 -10 ********** Masking position 6 Map Score: 0.467089 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 187 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 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 Motif number 8 ********** 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