AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i105_tpal_bbur_100.orf -o105_tpal_bbur_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/synecho.fna -g0.40 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTP00321 174 AE000520 #2 RTP00320 147 AE000520 Motif number 1 GGCGCGCGTATGCACTGCTGGCAAATATAGC 1 10 0 TGCACCTGGC 0.988392 -165 GCAGTGCATACGCGCGCCTTGTGTAAAACTTT 1 24 1 CGCGCCTTGT 0.997874 -151 ACCTCTTTGTCGCGGTTTTTGTTTTCGACGTA 1 64 0 CGCGGTTTGT 0.975633 -111 TTCAGACACACGCACGTATGATCT 2 3 0 CGCACATGAT 0.937708 -145 ACAACAGTGCTGCACGATTTGTTTCAGACACA 2 25 0 TGCACTTTGT 0.988166 -123 GCTTGAATATCGCGCCGATTGCGCAGTGCTCT 2 87 0 CGCGCATTGC 0.992915 -61 CTACCGTAATGAACAACTTGTTGCTGCCTTC 2 127 0 TGAACCTTGT 0.960636 -21 ***** ***** Masking position 9 Map Score: 6.4717 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 61 Number in noncoding regions = 190 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 2 CAAAAACCGCGACAAAGAGGTAAGAAAAAAA 1 75 1 GACAAAGGGT 0.958367 -100 TGAAGAGGTAGGTAATGGGGTTGCTATTTTT 1 101 0 GGTAATGGGT 0.99739 -74 TGACTGTGCAGGTGAAGAGGTAGGTAATGGG 1 113 0 GGTGAAGGGT 0.993648 -62 CAGTCACAATGGTCATGTCGTCATGGGTAGT 1 138 1 GGTCATGCGT 0.984534 -37 TGTCGTCATGGGTAGTGCGATCCGCACTGAA 1 153 1 GGTAGTGGAT 0.970575 -22 ******* *** Masking position 11 Map Score: 2.28871 Number of sites scoring better than the average of aligned sites = 474 Number in coding regions = 134 Number in noncoding regions = 340 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 3 AGGCGCGCGTATGCACTGCTGGCAAATATA 1 13 0 ATGCACTGCT 0.933506 -162 ATGTCGTCATGGGTAGTGCGATCCGCACTG 1 152 1 GGGTAGTGCG 0.965833 -23 TTTCAGTGCGGATCGCACTA 1 165 0 TTTCAGTGCG 0.963322 -10 GAAACAAATCGTGCAGCACTGTTGTAAATA 2 32 1 GTGCAGCACT 0.969579 -116 CGCGCCGATTGCGCAGTGCTCTTAATGGAT 2 79 0 GCGCAGTGCT 0.991468 -69 GCAACAAGTTGTTCATTACGGTAG 2 134 1 GTTCATTACG 0.89873 -14 ********** Masking position 5 Map Score: 1.1999 Number of sites scoring better than the average of aligned sites = 822 Number in coding regions = 231 Number in noncoding regions = 591 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 TTTACACAAGGCGCGCGTATGCACTGCTGG 1 21 0 GCGCGCGTAT 0.958731 -154 GAAGAGGTAGGTAATGGGGTTGCTATTTTT 1 101 0 GTAATGGGGT 0.82011 -74 CATTGTGACTGTGCAGGTGAAGAGGTAGGT 1 119 0 GTGCAGGTGA 0.937352 -56 AGATCATACGTGCGTGTGTCTGAAACAAA 2 10 1 GTGCGTGTGT 0.980001 -138 AAATCGTGCAGCACTGTTGTAAATAACACG 2 37 1 GCACTGTTGT 0.893475 -111 GATACGATAAGTAATCGTGTTATTTACAAC 2 52 0 GTAATCGTGT 0.936634 -96 CGATTGCGCAGTGCTCTTAATGGATACGAT 2 74 0 GTGCTCTTAA 0.844324 -74 CTTCCAGGAGGTGCTTGAATATCGCGCCGA 2 101 0 GTGCTTGAAT 0.856501 -47 ********** Masking position 1 Map Score: 0.999091 Number of sites scoring better than the average of aligned sites = 1671 Number in coding regions = 464 Number in noncoding regions = 1207 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 5 TCTGTTTAAAGTTTTACACAAGGCGCGCGT 1 33 0 GTTTTACACA 0.959757 -142 AACAGAATACGTCGAAAACAAAAACCGCGA 1 57 1 GTCGAAAACA 0.982585 -118 ACGTGCGTGTGTCTGAAACAAATCGTGCAG 2 18 1 GTCTGAAACA 0.981837 -130 GTGCAGCACTGTTGTAAATAACACGATTAC 2 42 1 GTTGTAAATA 0.941507 -106 ********** Masking position 6 Map Score: 0.0350303 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 19 Number in noncoding regions = 62 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: -5.09159e-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: -5.09159e-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: -5.09159e-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