AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i194_tpal_bbur_300.orf -o194_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 RTP00762 73 AE000520 #2 RTP00763 58 AE000520 #3 RTP00764 108 AE000520 #4 RTP00766 42 AE000520 #5 RTP00767 126 AE000520 #6 RTP00768 96 AE000520 #7 RTP00769 125 AE000520 #8 RTP00770 34 AE000520 #9 RTP00771 204 AE000520 #10 RBB00291 300 3615 Motif number 1 TTTACAGAATCCGTTGCCGCTGCTTGCAGAAAA 1 31 1 CCGCCGCTGC 0.884328 -43 CCTATTCGTTCCGCACCTGCCTCTCTACGCAGC 2 33 0 CCCCTGCCTC 0.978039 -26 GCGTTCACCAGCGTGCCTGCCGCAAGACGCAGA 3 20 0 GCCCTGCCGC 0.995868 -89 ATTGCAGTCGTTCCGGGTCGTTTTCA 5 4 1 GCCGTTCCGG 0.969744 -123 GGCTATCGATCAAACCCTTACGCTGTGTGTCTC 5 85 1 CACCTTACGC 0.8872 -42 GGTGCTATCCTTTCGGCGCGAGACAC 5 111 0 GCCCTTTCGG 0.943716 -16 TCGGCGCGCCCCTTCTGGTGGGAACCCC 6 79 0 GCCCTTCTGG 0.979319 -18 GCATGGCCGTGCACACCCGCCGG 7 1 0 GCCCCGCCGG 0.993179 -125 ACGGCCATGCGCACTCCTTCTGCAAAAAAGATG 7 24 1 GCCCTTCTGC 0.988771 -102 CAACAGATTTCCCCGCCCTCCGCTTCTTTCAAA 9 22 0 CCCCCTCCGC 0.996648 -183 CACACAGAAACCCACCGTGCTGCTCGCCTTTGA 9 93 0 CCCGTGCTGC 0.966411 -112 TACCCGCGATCCTTTCCTCACCCGTGCCTACGA 9 144 0 CCCCTCACCC 0.870442 -61 CTTCTTCCGTCCTATCCCTACCCGCGATCCTTT 9 162 0 CCCCCTACCC 0.943734 -43 CTGCTACCTTCCAGTCCTGACGGGATTCAGCAA 10 46 0 CCCCTGACGG 0.989966 -255 ** ******** Masking position 2 Map Score: 22.161 Number of sites scoring better than the average of aligned sites = 1323 Number in coding regions = 376 Number in noncoding regions = 947 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 2 TCCGTTGCCGCTGCTTGCAGAAAAGGTTGG 1 40 1 CTGCTTGCAG 0.844626 -34 TCTGGGTCTGCGTCTTGCGGCAGGCACGCT 3 14 1 CGTCTTGCGG 0.932092 -95 CTGCGTTCACCAGCGTGCCTGCCGCAAGAC 3 25 0 CAGCGTGCCT 0.736959 -84 TTCCTCAAGTCATTTGGGGGAAAGGGGAG 4 24 1 CATTTGGGGG 0.62098 -19 TCGTTTTCACCTGTTGGGGGAGTATCTGTG 5 28 1 CTGTTGGGGG 0.957869 -99 AACCCTTACGCTGTGTGTCTCGCGCCGAAA 5 97 1 CTGTGTGTCT 0.563843 -30 CGTCTGGGCGGAGCAAGGCC 6 1 1 CGTCTGGGCG 0.937705 -96 CGGCGCGCCCCTTCTGGTGGGAACCCCCTT 6 76 0 CTTCTGGTGG 0.924712 -21 CCGGCGGGTGTGCACGGCCAT 7 2 1 CGGCGGGTGT 0.903478 -124 AGAAGGAGTGCGCATGGCCGTGCACACCCG 7 15 0 CGCATGGCCG 0.751016 -111 ATCATTGACACTGCTGGCCGT 8 2 0 CTGCTGGCCG 0.983129 -33 TTGAAAGAAGCGGAGGGCGGGGAAATCTGT 9 23 1 CGGAGGGCGG 0.954807 -182 GCGGGGAAATCTGTTGGTCGGTGATCGTAG 9 39 1 CTGTTGGTCG 0.949562 -166 ACCCACCGTGCTGCTCGCCTTTGACTCGGA 9 87 0 CTGCTCGCCT 0.814978 -118 CGGTGGGTTTCTGTGTGCGGGGATGTGGGG 9 109 1 CTGTGTGCGG 0.944349 -96 ********** Masking position 7 Map Score: 11.6518 Number of sites scoring better than the average of aligned sites = 3408 Number in coding regions = 990 Number in noncoding regions = 2418 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 3 TTTTCTGCAAGCAGCGGCAACGGATTCTGT 1 34 0 GCAGCGGCAA 0.99535 -40 TTACAAGCGCGCAGTGGTATTCTTGTCTCT 3 56 1 GCAGTGGTAT 0.983978 -53 ATACGCCAATGCAGTGGCCTTGCTCCGCCC 6 16 0 GCAGTGGCCT 0.984211 -81 ACGGCCAGCAGTGTCAATGATAAGTAC 8 8 1 GCAGTGTCAA 0.974355 -27 CTGGAAGGTAGCAGCGGTAAGCGATTTTTT 10 65 1 GCAGCGGTAA 0.989581 -236 ********** Masking position 3 Map Score: 5.93594 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 78 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 TTCGTTCCGCACCTGCCTCTCTACGCAGCAAGA 2 29 0 ACCTCCTTCA 0.982159 -30 GACTTGAGGAACCTGCCTTCCTTC 4 2 0 ACCTCCTCCT 0.984561 -41 CTCCCCTTTCCCCCAAATGACTTGAG 4 27 0 CCCTTCCCCA 0.728268 -16 TGCTCCACGTTCCAGTGTACCCGGTAGTG 7 107 0 ACGTCCATGA 0.865306 -19 CAATGACGTACTTATCATTGACACTGCT 8 17 0 ACGTCTTTCT 0.861441 -18 AACAGATTTCCCCGCCCTCCGCTTCTTTCAAAA 9 21 0 CCCGCCTCGT 0.866681 -184 GATATCATCTACCTTCTTTTCTACGATCACCGA 9 56 0 ACCTCTTTCA 0.923968 -149 CTTTCCTCACCCGTGCCTACGAAATCTCCCCAC 9 133 0 CCGTCCTCGA 0.950916 -72 TCCGTCCTATCCCTACCCGCGATCCTTTCCTCA 9 157 0 CCCTCCCCGT 0.964237 -48 TACCGCTGCTACCTTCCAGTCCTGACGGGATTC 10 51 0 ACCTCCATCT 0.945641 -250 CCTAAGACTTACGTACTCATCAAAAAAATCGCT 10 84 0 ACGTCTCTCA 0.815723 -217 TAACTTTTTACCTCCCTATGCTTTAATAAGTA 10 279 0 ACCTCCTTGT 0.975452 -22 **** *** ** * Masking position 2 Map Score: 8.77708 Number of sites scoring better than the average of aligned sites = 853 Number in coding regions = 241 Number in noncoding regions = 612 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 CTGCCTCTCTACGCAGCAAGAGTTTTATCC 2 20 0 ACGCAGCAAG 0.982915 -39 ACCAGCGTGCCTGCCGCAAGACGCAGACCC 3 17 0 CTGCCGCAAG 0.931062 -92 TGTGTGTCTCGCGCCGAAAGGATAGCACC 5 108 1 GCGCCGAAAG 0.974687 -19 CGTCTGGGCGGAGCAAGGCCACTGCAT 6 8 1 GCGGAGCAAG 0.985681 -89 AGATGAGCGCGCACAGCACGATCACCCAAT 7 52 1 GCACAGCACG 0.974687 -74 AGTCAAAGGCGAGCAGCACGGTGGGTTTCT 9 91 1 GAGCAGCACG 0.979464 -114 ********** Masking position 8 Map Score: 3.58387 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 26 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 6 ATCTGCGTTCACCAGCGTGCCTGCCGCAAG 3 27 0 ACCAGCGTGC 0.848601 -82 AACGCAGATTACAAGCGCGCAGTGGTATTC 3 48 1 ACAAGCGCGC 0.992134 -61 TCCCACCAGAAGGGGCGCGCCGA 6 84 1 AGGGGCGCGC 0.951234 -13 GTGCGCATGGCCGTGCACACCCGCCGG 7 8 0 CCGTGCACAC 0.86649 -118 GTGTGCACGGCCATGCGCACTCCTTCTGCA 7 18 1 CCATGCGCAC 0.974197 -108 TGCAAAAAAGATGAGCGCGCACAGCACGAT 7 44 1 ATGAGCGCGC 0.957255 -82 ACCCAATCTCTCATGCGCGCATAGTACGTG 7 75 1 TCATGCGCGC 0.976686 -51 CGCGCATAGTACGTGCGCACTACCGGGTAC 7 90 1 ACGTGCGCAC 0.990405 -36 AAATCTCCCCACATCCCCGCACACAGAAAC 9 115 0 ACATCCCCGC 0.830388 -90 ********** Masking position 6 Map Score: 7.6476 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 12 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 CGTCCTATTCGTTCCGCACCTG 2 47 0 TCCTATTCGT 0.828085 -12 TGATCTGGGTCTGCGTCTTGCGGCAGGCA 3 10 1 TCTGCGTCTT 0.874101 -99 TTGCAGTCGTTCCGGGTCGTTTTCACCTGT 5 12 1 TCCGGGTCGT 0.988066 -115 TTCCCCGCCCTCCGCTTCTTTCAAAACGCA 9 17 0 TCCGCTTCTT 0.962848 -188 GTAGATGATATCCGAGTCAAAGGCGAGCAG 9 77 1 TCCGAGTCAA 0.853752 -128 TTCTCTCCGATTCCTAGGACCCGTA 10 6 1 TCCGATTCCT 0.973778 -295 TACTTGATAGTACGGGTCCTAGGAATCGGA 10 16 0 TACGGGTCCT 0.914817 -285 ********** Masking position 7 Map Score: 1.15905 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 80 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 TGTAAACCGTCGTACACCTGACCGAG 1 7 0 CGTACACCTG 0.956252 -67 TTGTAATCTGCGTTCACCAGCGTGCCTGCC 3 32 0 CGTTCACCAG 0.941664 -77 TGGTGAATTGCAGACACAGGATTTTGCACA 3 86 1 CAGACACAGG 0.827133 -23 GCGCACAGCACGATCACCCAATCTCTCATG 7 60 1 CGATCACCCA 0.920534 -66 TTCTTTTCTACGATCACCGACCAACAGATT 9 46 0 CGATCACCGA 0.968802 -159 CCCACATCCCCGCACACAGAAACCCACCGT 9 108 0 CGCACACAGA 0.906587 -97 TTCCTTACCGGTCACATGTGCTTCTTCC 9 187 0 CGGTCACATG 0.955188 -18 ********** Masking position 6 Map Score: 0.556895 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 81 Number in noncoding regions = 189 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 ********** No masking Map Score: -6.37056e-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 10 ********** No masking Map Score: -6.37056e-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 11 ********** No masking Map Score: -6.37056e-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