AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i263_tpal_bbur_100.orf -o263_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 RTP00501 73 AE000520 #2 RTP00500 127 AE000520 #3 RTP00498 117 AE000520 #4 RBB00736 178 3615 #5 RBB00735 61 3615 #6 RBB00734 56 3615 #7 RBB00725 54 3615 #8 RBB00716 39 3615 Motif number 1 GCTGGCAAAATTTTTAATGTCCTCTGAACC 1 49 0 TTTTTAATGT 0.924957 -25 TTTGCTTAATTTTATATTTTTTTGTCTAGG 4 37 1 TTTATATTTT 0.915341 -142 TTTGTCTAGGTTTTTATCTTAATAATTAAA 4 57 1 TTTTTATCTT 0.911992 -122 TACAACTTATTTTATAATTTTAATTATTAA 4 75 0 TTTATAATTT 0.926065 -104 TTGTGGCTAATTTTTAAATTAGCTGCCTTA 4 114 1 TTTTTAAATT 0.974994 -65 TATAGCTCTTTTTTTAAATTACTCATGTAA 4 141 0 TTTTTAAATT 0.974994 -38 CATCTATATGTTTATATATTTTTCAAATAT 5 29 0 TTTATATATT 0.915338 -33 TAATGCTTGACTTTTCTTTTTTATTAAATT 6 13 1 CTTTTCTTTT 0.843044 -44 CTTTTCTTTTTTATTAAATTTACAATGTTT 6 23 1 TTATTAAATT 0.805883 -34 AATCTCCAATCTTTTCAATTAAAA 7 5 0 CTTTTCAATT 0.861542 -50 CTTTCTCCAATTTTTCAATTAAAACCAAAA 7 34 0 TTTTTCAATT 0.95168 -21 TAAAATTGATTTTTATTGTGGGCTTTTTA 8 10 1 TTTTTATTGT 0.914087 -30 TATTGTGGGCTTTTTATTTTTAAGAC 8 24 1 TTTTTATTTT 0.971163 -16 ********** Masking position 5 Map Score: 18.8981 Number of sites scoring better than the average of aligned sites = 370 Number in coding regions = 105 Number in noncoding regions = 265 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 2 GGAAGTGGCGCTTGCGCGCTACGGACTTT 2 5 1 GGGCCGCGCC 0.999267 -123 CTCCGCACAAGCGCCTGCAGCGTCCTTGTCGAAAA 2 37 0 GGCCGGCGTC 0.996086 -91 CGGAGTATGCGCGGCAGAGGCGTACCTTCTCCATC 2 67 1 GGGCGGCGTC 0.998873 -61 GACGGGGAAGGAGGAAGCTGCGCACCGCA 2 109 1 GGGAGGCGCC 0.995447 -19 CGGATGTTGAGGTGCTCTTGCGTGCTGAGGCAGAA 3 59 0 GTGCCGCGTC 0.99674 -59 CTCAACATCCGGTTCACTGGCACTCACTATTTCGT 3 83 1 GTTCCGCACC 0.934351 -35 * *** * **** * Masking position 10 Map Score: 7.98029 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 39 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 3 ATGTATTTGACTCTGCAAGTCG 1 1 1 ATTATTTGCT 0.947123 -73 ATAACAATTAATTGGCCTGTTGTGTTTT 4 7 1 ATAATTGGCT 0.780743 -172 TTGGCCTGTTGTGTTTTTGCTTAATTTTATAT 4 22 1 GTTTTTTGTT 0.946238 -157 TTAATTTTATATTTTTTTGTCTAGGTTTTTAT 4 42 1 ATTTTTTGCT 0.980541 -137 TTTTTTGTCTAGGTTTTTATCTTAATAATTAA 4 54 1 AGTTTTTACT 0.901176 -125 AACTTATTTTATAATTTTAATTATTAAGATAA 4 70 0 ATATTTTATT 0.711893 -109 TTGTATAATGATGTTTGTGGCTAATTTTTAAA 4 100 1 ATTTTGTGCT 0.904667 -79 AAAAAGAGCTATAATTTGGTTTTAAGGAGGA 4 158 1 ATATTTGGTT 0.862213 -21 ATTTGGCTTTTGGTCTTGATATTTGA 5 5 1 GGTTTTGGCT 0.928346 -57 TACTTATCCCATCTATATGTTTATATATTTTT 5 36 0 ATTATATGTT 0.587146 -26 AAAAGATTGGAGATTTTTGGTTTTAATTGAAA 7 20 1 AGTTTTTGTT 0.962825 -35 TTTTATTGTGGGCTTTTTATTTTTAAGAC 8 21 1 GGTTTTTATT 0.761697 -19 ** ****** ** Masking position 6 Map Score: 8.19551 Number of sites scoring better than the average of aligned sites = 1303 Number in coding regions = 369 Number in noncoding regions = 934 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 CCCGTCGGGAATGGATGGAGAAGGTACGCCT 2 84 0 ATGATGGAGA 0.939033 -44 GTTTGGAATAAAACTTGGTGATTTTCTCATG 3 26 0 AAATTGGTGA 0.95743 -92 TGAGGCAGAAAAGTTTGGAATAAAACTTGGT 3 38 0 AAGTTGGAAT 0.906634 -80 TTTAATTGAAAAGATTGGAGATTTTTGGTTT 7 12 1 AAGTTGGAGA 0.994038 -43 TTTTAATTGAAAAATTGGAGAAAGT 7 40 1 AAATTGGAGA 0.986666 -15 *** ******* Masking position 6 Map Score: 1.82517 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 47 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 5 TAGAGACGACTTGCAGAGTCAAATACAT 1 9 0 TTGCAGAGTC 0.870586 -65 TCTGAACCGAGCTCAGCGTAGAGACGACTT 1 27 0 GCTCAGCGTA 0.958858 -47 GCTGAGCTCGGTTCAGAGGACATTAAAAAT 1 40 1 GTTCAGAGGA 0.922254 -34 TGGCGCTTGCGCGCTACGGACTTTTCGACA 2 16 1 GCGCTACGGA 0.866641 -112 GCACAAGCGCCTGCAGCGTCCTTGTCGAAA 2 38 0 CTGCAGCGTC 0.95143 -90 GCAGGCGCTTGTGCGGAGTATGCGCGGCAG 2 54 1 GTGCGGAGTA 0.969218 -74 TGCGGAGTATGCGCGGCAGAGGCGTACCTT 2 65 1 GCGCGGCAGA 0.91968 -63 TGCGGTGCGCAGCTTCCTCCTTCCCC 2 112 0 GCGCAGCTTC 0.944493 -16 GTGCTCTTGCGTGCTGAGGCAGAAAAGTTT 3 53 0 GTGCTGAGGC 0.971214 -65 ********** Masking position 4 Map Score: 5.39541 Number of sites scoring better than the average of aligned sites = 1040 Number in coding regions = 296 Number in noncoding regions = 744 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 GGAAGTGGCGCTTGCGCGCTACGGACTT 2 9 1 CGCTTGCGCG 0.977712 -119 GAAGGTACGCCTCTGCCGCGCATACTCCGC 2 66 0 CTCTGCCGCG 0.959267 -62 ACCTTCTCCATCCATTCCCGACGGGGAAGG 2 90 1 TCCATTCCCG 0.970139 -38 CGCAGCTTCCTCCTTCCCCGTCGGGAATGG 2 101 0 TCCTTCCCCG 0.986303 -27 TTTTCTCATGCCCATTCGCGTTGCG 3 6 0 CCCATTCGCG 0.99064 -112 ********** Masking position 7 Map Score: 1.45182 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 58 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 ********** No masking Map Score: -1.78814e-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: -1.78814e-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: -1.78814e-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