AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i210_tpal_bbur_100.orf -o210_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 RTP00665 147 AE000520 #2 RTP00669 175 AE000520 #3 RTP00670 49 AE000520 #4 RTP00971 174 AE000520 #5 RBB00524 163 3615 #6 RBB00511 49 3615 #7 RBB00462 198 3615 Motif number 1 TATTTAATTATTAAAAAGCCTAATGTTTTA 5 24 0 TTAAAAAGCC 0.858946 -140 TAAAAAGACCATAAAAAAAATATTTTACGC 5 64 0 ATAAAAAAAA 0.93844 -100 ATATAAAATAATAAAAAGACCATAAAAAAA 5 75 0 ATAAAAAGAC 0.952255 -89 TATAATTCAATTAAAAAGAAAGAATATAAA 5 98 0 TTAAAAAGAA 0.964218 -66 AATTGATATTATAAAATAAATATAATTCAA 5 118 0 ATAAAATAAA 0.873452 -46 AAAAACAAATATAAAATTAAAATGTCATAA 7 22 0 ATAAAATTAA 0.841009 -177 ATTAAATTGTTTAAAAAAACAAATATAAAA 7 36 0 TTAAAAAAAC 0.960285 -163 TAATTTATTATTAAAAATAACCCGAAAAGG 7 65 1 TTAAAAATAA 0.944674 -134 ATATTTTTTCTTAAAAATAACAAAAGCAAT 7 99 0 TTAAAAATAA 0.944674 -100 TTGCCATAATTTAAAATAACTACTACGATA 7 136 0 TTAAAATAAC 0.9163 -63 ********** Masking position 5 Map Score: 11.2926 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 51 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 2 GTAGGGTCTCCAAGATGGCTAATGAGCACTACGTGT 1 35 1 CAGAGATGAG 0.919147 -113 CATCATCGAGCAGGGGCCGCGACACGTAGTGCTCAT 1 56 0 CAGGCACACG 0.976918 -92 TGGTATGGTGCAAGACGACACGCGCGTCACTGCAGC 1 110 0 CAGAGGCGCG 0.991272 -38 TTCAGGAAACCACGGACGCACACGCTTGCACACACG 2 73 1 CAGGCACGCT 0.990552 -103 GAATTCCATTCGGGGTCTTTGATGCGGTTGCAATGG 2 150 0 CGGGCATGCG 0.985129 -26 AGTACAATCGAGGAGATCTGCGCGCAACTTTTGT 3 26 0 CGGGGGCGCG 0.987703 -24 AAAAGCGGCTCACCAAGATCAGTGCGTCCAATTTCT 4 32 1 CACAGGTGCG 0.902204 -143 TATCTTCGTTCAAGGGCGCAGGTGCTTACACAATAG 4 72 0 CAGGCGTGCT 0.986158 -103 CCCCGGATGTCAGGAGGAACCATGATAGTGTGCACA 4 116 1 CAGAGATGAT 0.829101 -59 GAGTCTCCTGCACGGTCCCTAACACT 4 159 1 CAGGCACACT 0.947721 -16 ** ** * ***** Masking position 1 Map Score: 7.56187 Number of sites scoring better than the average of aligned sites = 498 Number in coding regions = 144 Number in noncoding regions = 354 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 3 ACGTGTCGCGGCCCCTGCTCGATGATGTACCG 1 65 1 GCCCTGCCGA 0.94909 -83 GTGCAAGACGACACGCGCGTCACTGCAGCAGT 1 107 0 ACACCGCTCA 0.978553 -41 AACCACGGACGCACACGCTTGCACACACGCTC 2 80 1 GCACCGCTGC 0.759095 -96 ACACGCTTGCACACACGCTCCAAAAACTCTTG 2 92 1 ACACCGCCCA 0.993083 -84 CACGCCCATTGCAACCGCATCAAAGACCCCGA 2 145 1 GCAACGCTCA 0.970539 -31 TATTGTGTAAGCACCTGCGCCCTTGAACGAAG 4 73 1 GCACTGCCCC 0.99413 -102 AACGAAGATAGCACGCTCCCCCGGATGTCAGG 4 98 1 GCACCTCCCC 0.987829 -77 **** *** *** Masking position 8 Map Score: 6.82973 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 60 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 4 CAGTGCGTCCAATTTCTTCATCTATTGTGTAAGCAC 4 51 1 AATTCTTATT 0.98917 -124 AATAGCGTTTAATTGCGTAAAATATTTTTTTTATGG 5 50 1 AATTCTTATT 0.979012 -114 AATAATATTGAATTACAATTGATATTATAAAATAAA 5 128 0 AATTCATATT 0.893471 -36 ATAAAATTAAAATGTCATAATATATTTATAA 7 6 0 AATGCTTATT 0.927985 -193 TTTTTTAAACAATTTAATAATTTATTATTAAAAATA 7 48 1 AATTATTATT 0.903419 -151 GAAAAGGATAAATTGCTTTTGTTATTTTTAAGAAAA 7 88 1 AATTCTTATT 0.91354 -111 **** * * **** Masking position 13 Map Score: 4.75394 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 9 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 5 AGTTAATTAAATTTAAAACATTA 5 4 1 TAATTAAATT 0.941122 -160 GGCTTTTTAATAATTAAATAGCGTTTAATT 5 34 1 TAATTAAATA 0.930551 -130 AAAATAAATATAATTCAATTAAAAAGAAAG 5 106 0 TAATTCAATT 0.916684 -58 ACAATTGATATTATAAAATAAATATAATTC 5 120 0 TTATAAAATA 0.743245 -44 ATATCAATTGTAATTCAATATTATTTAGGA 5 139 1 TAATTCAATA 0.944956 -25 TAATAATAAATTATTAAATTGTTTAAAAAA 7 48 0 TTATTAAATT 0.910254 -151 TAATAATTTATTATTAAAAATAACCCGAAA 7 62 1 TTATTAAAAA 0.849919 -137 CCTCTTGCCATAATTTAAAATAACTACTAC 7 140 0 TAATTTAAAA 0.700475 -59 ********** Masking position 7 Map Score: 5.42349 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 53 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 ACTGGCCAGTACTGGGATAGAAAAAGCGGC 4 10 1 TACTGGATAG 0.96993 -165 TGCGCCCTTGAACGAAGATAGCACGCTCCCC 4 88 1 AACGAGATAG 0.976745 -87 TGTCAGGAGGAACCATGATAGTGTGCACAAC 4 123 1 AACCAGATAG 0.987228 -52 TTAAAATAACTACTACGATAGATTATAATAT 7 125 0 TACTAGATAG 0.986226 -74 GCAACTCCTATACCATTATAGCAAAGCTCTA 7 175 0 TACCATATAG 0.955003 -24 ***** ***** Masking position 8 Map Score: 1.95823 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 10 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 GTCGATGTGGTGTCGGGATTTTT 2 1 0 TGCGATTTTT 0.984335 -175 GGGTATTTTTTGTCAAGAGTTTTTGGAGCGTGT 2 104 0 TGCGAGTTTT 0.992986 -72 TGTTGACATTATTTTTGCTAAGTGTT 6 4 1 TGCTATTTTT 0.940528 -46 GTGTTAACCTTGACTTAAGGTTTAGTTT 6 32 1 TGCAAGGTTT 0.974647 -18 TTTTAAATTATGGCAAGAGGTTTGTTAGAGCTT 7 150 1 TGCGAGGTTT 0.9935 -49 ** * ******* Masking position 8 Map Score: 1.7795 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 3 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 TCAGGAAACCACGGACGCACACGCTTGCAC 2 74 1 ACGGACGCAC 0.956048 -102 ACGCACACGCTTGCACACACGCTCCAAAAA 2 88 1 TTGCACACAC 0.966201 -88 CAGACAAAAGTTGCGCGCAGATCTCCTCGA 3 23 1 TTGCGCGCAG 0.804211 -27 GATGAAGAAATTGGACGCACTGATCTTGGT 4 43 0 TTGGACGCAC 0.990799 -132 ATCTTCGTTCAAGGGCGCAGGTGCTTACAC 4 77 0 AAGGGCGCAG 0.927519 -98 TGAACGAAGATAGCACGCTCCCCCGGATGT 4 96 1 TAGCACGCTC 0.924339 -79 ACTCCTTCTGTTGTGCACACTATCATGGTT 4 133 0 TTGTGCACAC 0.884977 -42 ********** Masking position 6 Map Score: 4.03155 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 40 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 9 ********** No masking Map Score: 3.03645e-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 CGTCTTGCACCATACCATCACGCATCGGT 1 129 1 CATACCATCA 0.861781 -19 GCATTAGATACATGCCAACACCTTCAGGAA 2 51 1 CATGCCAACA 0.95908 -125 TCCAAAAACTCTTGACAAAAAATACCCACG 2 110 1 CTTGACAAAA 0.936174 -66 TAGCAAAAATAATGTCAACA 6 1 0 AATGTCAACA 0.773204 -49 AAGGTTAACACTTAGCAAAAATAATGTCAA 6 13 0 CTTAGCAAAA 0.738174 -37 AAGTGTTAACCTTGACTTAAGGTTTAGTTT 6 30 1 CTTGACTTAA 0.652389 -20 ATAAAATTAAAATGTCATAATATATTTATA 7 12 0 AATGTCATAA 0.770371 -187 TTTTCTTAAAAATAACAAAAGCAATTTATC 7 94 0 AATAACAAAA 0.659985 -105 TAACAAACCTCTTGCCATAATTTAAAATAA 7 147 0 CTTGCCATAA 0.949291 -52 ********** Masking position 3 Map Score: 1.01794 Number of sites scoring better than the average of aligned sites = 896 Number in coding regions = 266 Number in noncoding regions = 630 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 11 ********** No masking Map Score: 3.03645e-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 12 ********** No masking Map Score: 3.03645e-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 13 GCTTTATCCGCATCACGGGTAGGGTCTCCAAGA 1 17 1 CAACGGTAGG 0.970147 -131 GGCTAATGAGCACTACGTGTCGCGGCCCCTGCT 1 51 1 CAACGGTCGC 0.992315 -97 TGCACCATACCATCACGCATCGGT 1 134 1 CAACGATCGG 0.956515 -14 CGAAATGGTCGATGTGGTGTCGGGATTTTT 2 8 0 GATGGGTCGG 0.951253 -168 CCGTGGTTTCCTGAAGGTGTTGGCATGTATCTA 2 55 0 CTAGGGTTGG 0.970365 -121 GTGTGCACAACAGAAGGAGTCTCCTGCACGGTC 4 143 1 CAAGGGTCTC 0.956497 -32 TGCTATAATGGTATAGGAGTTGCTTT 7 183 1 GTAGGGTTGC 0.91319 -16 ** *** ***** Masking position 10 Map Score: 0.18134 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 58 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 ********** No masking Map Score: 3.03645e-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 15 ********** No masking Map Score: 3.03645e-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