AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i210_tpal_bbur_300.orf -o210_tpal_bbur_300.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 RTP00665 147 AE000520 #2 RTP00669 175 AE000520 #3 RTP00670 49 AE000520 #4 RTP00971 174 AE000520 #5 RTP00672 21 AE000520 #6 RTP00676 38 AE000520 #7 RTP00677 40 AE000520 #8 RBB00551 17 3615 #9 RBB00524 163 3615 #10 RBB00511 49 3615 #11 RBB00462 198 3615 Motif number 1 GTAGGAACTGCTGCAGTGACGCGCGTGTCGTCTT 1 101 1 CAGTACGCGC 0.990258 -47 TAACACCGTGCATTAGATACATGCCAACACCTTC 2 42 1 CAGAACATGC 0.952483 -134 CTTCAGGAAACCACGGACGCACACGCTTGCACAC 2 72 1 CGGAGCACAC 0.980492 -104 AAAAAATACCCACGAGAGGCACGCCCATTGCAAC 2 126 1 CAGAGCACGC 0.997827 -50 TCTTTTCAGACAAAAGTTGCGCGCAGATCTCCTC 3 17 1 CAGTGCGCGC 0.996169 -33 CGCCCTTGAACGAAGATAGCACGCTCCCCCGGAT 4 90 1 CGATGCACGC 0.99038 -85 ATCTTGAGCACGAAGGATGCACGCAGCACCGTGT 6 13 1 CGGAGCACGC 0.997783 -26 CTCCAATGTGCAGTAATTACACGCGTA 7 4 0 CAATACACGC 0.976223 -37 * *** ****** Masking position 10 Map Score: 12.3566 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 11 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 2 TGTTGGCATGTATCTAATGCACGGTGTTATCGAAATGGT 2 32 0 TATATGTTTA 0.731914 -144 GAATTCCATTCGGGGTCTTTGATGCGGTTG 2 156 0 AATATGTTTT 0.97748 -20 GCTTTTTAATAATTAAATAGCGTTTAATTGCGTAAAATA 9 35 1 AATATTTATT 0.769317 -129 TTGCGTAAAATATTTTTTTTATGGTCTTTTTATTATTTT 9 62 1 TATTTGTTTT 0.92061 -102 GTCTTTTTATTATTTTATATTCTTTCTTTTTAATTGAAT 9 85 1 TATATTTTTT 0.958015 -79 CTTTCTTTTTAATTGAATTATATTTATTTTATAATATCA 9 106 1 AATATTTTTT 0.967588 -58 ATATTTATTTTATAATATCAATTGTAATTCAATATTATT 9 125 1 TATATTTATT 0.859472 -39 ATAAAATTAAAATGTCATAATATATTTATAA 11 3 0 AATATTTTAT 0.778453 -196 ATGACATTTTAATTTTATATTTGTTTTTTTAAACAATTT 11 24 1 AATATGTTTT 0.97748 -175 TTTTTTAAACAATTTAATAATTTATTATTAAAAATAACC 11 48 1 AATATTTATT 0.914897 -151 AAAAGCAATTTATCCTTTTCGGGTTATTTTTAATAATAA 11 69 0 TATTTGTTTT 0.92061 -130 GAAAAGGATAAATTGCTTTTGTTATTTTTAAGAAAAAAT 11 88 1 AATTTTTTTT 0.93723 -111 TAACTACTACGATAGATTATAATATTTTTTCTTAAAAAT 11 111 0 GATTTTTTTT 0.777219 -88 GCTTTGCTATAATGGTATAGGAGTTGCTTT 11 179 1 AATATGTCTT 0.890866 -20 *** ** * * *** Masking position 2 Map Score: 13.6276 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 50 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 3 AACTCTTGACAAAAAATACCCACGAGAGGC 2 116 1 AAAAAATACC 0.841264 -60 AAAAAGACCATAAAAAAAATATTTTACGCA 9 63 0 TAAAAAAAAT 0.677987 -101 TATAAAATAATAAAAAGACCATAAAAAAAA 9 74 0 TAAAAAGACC 0.915226 -90 ATAATTCAATTAAAAAGAAAGAATATAAAA 9 97 0 TAAAAAGAAA 0.891646 -67 AATTGATATTATAAAATAAATATAATTCAA 9 118 0 ATAAAATAAA 0.646528 -46 AAAACAAATATAAAATTAAAATGTCATAAT 11 21 0 TAAAATTAAA 0.671547 -178 ATTAAATTGTTTAAAAAAACAAATATAAAA 11 36 0 TTAAAAAAAC 0.880239 -163 AATTTATTATTAAAAATAACCCGAAAAGGA 11 66 1 TAAAAATAAC 0.977944 -133 TATTTTTTCTTAAAAATAACAAAAGCAATT 11 98 0 TAAAAATAAC 0.977944 -101 TTGCCATAATTTAAAATAACTACTACGATA 11 136 0 TTAAAATAAC 0.952555 -63 ********** Masking position 5 Map Score: 6.94586 Number of sites scoring better than the average of aligned sites = 401 Number in coding regions = 122 Number in noncoding regions = 279 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 4 CGCTCCAAAAACTCTTGACAAAAAATACCC 2 107 1 ACTCTTGACA 0.982633 -69 TATCATGGTTCCTCCTGACATCCGGGGGAG 4 113 0 CCTCCTGACA 0.992466 -62 CTTAACCTCTTAACAAT 8 3 0 CCTCTTAACA 0.982645 -15 CTCTAACAAACCTCTTGCCATAATTTAAAA 11 150 0 CCTCTTGCCA 0.992478 -49 ********** Masking position 6 Map Score: 3.41218 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 3 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 5 CCCTCTGCTTTATCCGCATCACGG 1 2 1 CCTGCTTATC 0.842663 -146 CGTGTCGCGGCCCCTGCTCGATGATGTACCGCA 1 66 1 CCTGCCGATG 0.997219 -82 ACCGATGCGTGATGGTATGGTGCA 1 134 0 CCTGCTGATG 0.989884 -14 TGGCATGTATCTAATGCACGGTGTTATCGAAAT 2 35 0 CTTGCCGGTG 0.991516 -141 AGCACCTGCGCCCTTGAACGAAGATAGCACGCT 4 82 1 CCTGACGAAG 0.952921 -93 CAGAAGGAGTCTCCTGCACGGTCCCTAACACT 4 153 1 CTTGCCGGTC 0.980125 -22 TCATCTTGAGCACGAAGGATGCACGCA 6 5 1 CTAGCCGAAG 0.940045 -34 ** *** ***** Masking position 6 Map Score: 3.49955 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 72 Number in noncoding regions = 178 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 CTCATTAGCCATCTTGGAGACCCTACCCGTGA 1 29 0 ATCGGAGACC 0.99414 -119 AGTACAATCGAGGAGATCTGCGCGCAAC 3 32 0 ATCGGAGATC 0.99134 -18 GGACGCACTGATCTTGGTGAGCCGCTTTTTCT 4 29 0 ATCGGTGAGC 0.994384 -146 TCCTCCTGACATCCGGGGGAGCGTGCTATCTT 4 102 0 ATCGGGGAGC 0.996204 -73 *** ******* Masking position 10 Map Score: 1.71603 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 5 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 GCTTTATCCGCATCACGGGTAGGGTCTCCA 1 17 1 CATCACGGGT 0.965658 -131 CAAGCGTGTGCGTCCGTGGTTTCCTGAAGG 2 71 0 CGTCCGTGGT 0.977877 -105 GAATTCCATTCGGGGTCTTTGATGCG 2 160 0 CATTCGGGGT 0.986901 -16 TTCCTCCTGACATCCGGGGGAGCGTGCTAT 4 105 0 CATCCGGGGG 0.991932 -70 ********** Masking position 3 Map Score: 0.335272 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 38 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 ********** No masking Map Score: 2.29038e-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: 2.29038e-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 10 ********** No masking Map Score: 2.29038e-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