AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i036_Acetate_Metabolism_tpal_reg_300.orf -o036_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 RTP00410 181 AE000520 #2 RTP00411 70 AE000520 #3 RTP00413 137 AE000520 #4 RTP00194 66 AE000520 #5 RTP01039 60 AE000520 #6 RTP00195 72 AE000520 #7 RTP00196 111 AE000520 Motif number 1 GCACCCAATCCTGGGCCTTCACCGGCTGAGGAAAGAACAC 1 36 1 CGCCCCGCGG 0.980557 -146 AAAGGTGTTACAGTACCAGCGCGTGTTCTTTCCTCAGCCG 1 58 0 CGCCCGGTCT 0.737978 -124 AGGGTAGCGTCGCAACGGACATGGGTTCGGGGATCTTTGT 1 149 0 CCCCTGGTCG 0.665881 -33 TCTGTTGATCCTGCACAGACCCCCGTCGTGC 2 50 1 CGCCCCGTGG 0.583613 -21 GCACCTGCTGCGCACCCAACTCCCGTGCTGCGCACAAATG 3 29 1 CCCCCCGTCG 0.995624 -109 CCACCGTCTACCCACACTTCACCGGCACAGCGCGCTAACT 3 85 1 CCACCCGCCG 0.996101 -53 ACCTGACCGTACCCCTGCTGGATAGTGTCTTT 4 3 1 CGCCCCGCGA 0.990362 -64 GAGTCGTGTACCCACTGCTACCCAGCCGTGAAAGACACTA 4 33 0 CCTACCGCGG 0.903651 -34 GCTAATGCTTTTGTCCAGACCCCTGCTCAGTATTTGCCAG 6 18 1 TGCCCCGCCG 0.986592 -55 TCGTTCTGCGCCTCAAACTCGTCTTCTGGCAAATACTG 6 45 0 CCCCCGCTCG 0.986745 -28 TGCCATACCGCACACCGACCCCCTGTACCGCACGCTGCCG 7 49 1 CCCCCCGTCG 0.999288 -63 CTGTACCGCACGCTGCCGACACCCGCGCGTCGCTGAATTC 7 71 1 CCCCCCGCCT 0.97443 -41 * * * * ** ** * * Masking position 10 Map Score: 31.488 Number of sites scoring better than the average of aligned sites = 560 Number in coding regions = 511 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 2 TGGGCCTTCACCGGCTGAGGAAAGAACACGC 1 47 1 CCGGCTGGGA 0.986713 -135 GCACGACGGGGGTCTGTGCAGGATCAACAG 2 51 0 GGGTCTGGCA 0.865975 -20 CCTATCAGCACCTGCTGCGCACCCAACTCCC 3 22 1 CCTGCTGGCA 0.998079 -116 ACCCAACTCCCGTGCTGCGCACAAATGCGCA 3 42 1 CGTGCTGGCA 0.997381 -96 GGAGAGTTAGCGCGCTGTGCCGGTGAAGTGT 3 98 0 CGCGCTGGCC 0.978542 -40 TGACCGTACCCCTGCTGGATAGTGTCTTTCA 4 14 1 CCTGCTGATA 0.972733 -53 AGTGTCTTTCACGGCTGGGTAGCAGTGGGTA 4 34 1 ACGGCTGGTA 0.935083 -33 TCCTGTATTTCCTGCGGGGTAAGATGGACGA 5 40 0 CCTGCGGGTA 0.988873 -21 TGTCCAGACCCCTGCTCAGTATTTGCCAGAA 6 29 1 CCTGCTCGTA 0.964339 -44 TCGTTCTGCGCCTCAAACTCGT 6 61 0 CGTTCTGGCC 0.961595 -12 GTGTCGGCAGCGTGCGGTACAGGGGGTCGGT 7 62 0 CGTGCGGACA 0.964126 -50 ******* *** Masking position 5 Map Score: 19.5368 Number of sites scoring better than the average of aligned sites = 688 Number in coding regions = 638 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 3 AGGCCCAGGATTGGGTGCGTTCATTTTTTA 1 24 0 TTGGGTGCGT 0.974617 -158 GCGTGCTGATGTGGTTGCACGTTACC 2 7 0 GTGGTTGCAC 0.97435 -64 AGCACGGGAGTTGGGTGCGCAGCAGGTGCT 3 28 0 TTGGGTGCGC 0.9971 -110 CCGGTGAAGTGTGGGTAGACGGTGGTATTC 3 80 0 GTGGGTAGAC 0.947408 -58 CTGGGTAGCAGTGGGTACACGACTCTTTT 4 48 1 GTGGGTACAC 0.987173 -19 GAGTGTGCTCTTAGGTGCGCTCTTT 7 6 0 TTAGGTGCGC 0.97807 -106 TCTTTTTAAGGTGAGTGTGCTCTTAGGTGC 7 18 0 GTGAGTGTGC 0.964023 -94 GGTACAGGGGGTCGGTGTGCGGTATGGCAC 7 48 0 GTCGGTGTGC 0.978783 -64 ********** Masking position 6 Map Score: 12.993 Number of sites scoring better than the average of aligned sites = 421 Number in coding regions = 375 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 4 GTACGTCTTCCCTAAAAGCGGCGATTATTT 1 108 0 CCTAAAAGCG 0.980527 -74 AACGTGCAACCACATCAGCACGCTCTTCAG 2 14 1 CACATCAGCA 0.966128 -57 AAAAGGACGCCCTATCAGCACCTGCTGCGC 3 12 1 CCTATCAGCA 0.966131 -126 CCGTGCTGCGCACAAATGCGCATAACTGCG 3 51 1 CACAAATGCG 0.954729 -87 CACAAATGCGCATAACTGCGAATACCACCG 3 61 1 CATAACTGCG 0.966126 -77 CAGGGGTCTGGACAAAAGCATTAGCGTACA 6 13 0 GACAAAAGCA 0.889097 -60 AAAGAGCGCACCTAAGAGCACACTCACCTT 7 11 1 CCTAAGAGCA 0.960725 -101 ********** Masking position 4 Map Score: 4.31328 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 163 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 AGTACCAGCGCGTGTTCTTTCCTCAGCCGG 1 57 0 CGTGTTCTTT 0.911087 -125 GACATCGGTACGTCTTCCCTAAAAGCGGCG 1 115 0 CGTCTTCCCT 0.668018 -67 ACATGGGTTCGGGGATCTTTGTCGCGGACA 1 141 0 GGGGATCTTT 0.956359 -41 GCACGACGGGGGTCTGTGCAGGATCAA 2 54 0 GGGGGTCTGT 0.991296 -17 GGTGCTGATAGGGCGTCCTTTTA 3 4 0 GGGCGTCCTT 0.980161 -134 GTGGGTAGACGGTGGTATTCGCAGTTATGC 3 70 0 GGTGGTATTC 0.726715 -68 TACAGAAAGCCGGGGTCTCCATCGTCCATC 5 19 1 CGGGGTCTCC 0.977888 -42 GTGCGGTACAGGGGGTCGGTGTGCGGTATG 7 52 0 GGGGGTCGGT 0.972264 -60 GCTGAATTCTCGGCGTCTTT 7 102 1 CGGCGTCTTT 0.986003 -10 ********** Masking position 6 Map Score: 7.70192 Number of sites scoring better than the average of aligned sites = 245 Number in coding regions = 209 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 CCGGTGAAGGCCCAGGATTGGGTGCGTTCA 1 31 0 CCCAGGATTG 0.905819 -151 TGTTACAGTACCAGCGCGTGTTCTTTCCTC 1 63 0 CCAGCGCGTG 0.630915 -119 ACCACATCAGCACGCTCTTCAGAAATCCTC 2 22 1 CACGCTCTTC 0.904089 -49 CTGCACAGACCCCCGTCGTGC 2 60 1 CCCCGTCGTG 0.987576 -11 TTGTGCGCAGCACGGGAGTTGGGTGCGCAG 3 36 0 CACGGGAGTT 0.86244 -102 CTGCGAATACCACCGTCTACCCACACTTCA 3 76 1 CACCGTCTAC 0.755141 -62 GCTAACTCTCCACCGTATTCAAAAAGAAAG 3 118 1 CACCGTATTC 0.860805 -20 CCCACTGCTACCCAGCCGTGAAAGACACTA 4 33 0 CCCAGCCGTG 0.913278 -34 ACGATGGAGACCCCGGCTTTCTGTATATTG 5 14 0 CCCCGGCTTT 0.971497 -47 GCTGCCGACACCCGCGCGTCGCTGAATTCT 7 82 1 CCCGCGCGTC 0.968217 -30 ********** Masking position 1 Map Score: 6.76919 Number of sites scoring better than the average of aligned sites = 936 Number in coding regions = 857 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 7 ********** No masking Map Score: -1.42576e-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: -1.42576e-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: -1.42576e-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