AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00271_aful_reg_300.orf -o00271_aful_300.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 AF1446 63 A. fulgidus predicted coding region AF1446 #2 AF1448 114 transcriptional regulatory protein, AsnC family #3 AF1449 33 pyruvate formate-lyase 2 (pflD) #4 AF1451 88 thermosome, subunit beta (thsB) #5 AF1452 117 signal-transducing histidine kinase #6 AF1453 37 methionyl-tRNA synthetase (metS) #7 AF2113 44 A. fulgidus predicted coding region AF2113 Motif number 1 TTTCCCTCTTAAAAACTTTCACCAGTACACA 1 15 0 AAAAACTTCA 0.982983 -49 ATTACAAAGAAAAGACTGTCATTA 2 4 0 AAAGACTGCA 0.916852 -111 AGTTTACCTTATAAACTGACGTTGGAGAGCA 2 63 0 ATAAACTGCG 0.90306 -52 ACCTAATTAAAAAAGATTACGATTT 3 5 0 AAAAGATTCG 0.966886 -29 TAACAAATGCTTGCAATTTAAATTC 4 5 1 AAATGCTTCA 0.967088 -84 TTCGTGATAGAAAAGCTTATATAGAAATACC 4 33 1 AAAAGCTTTA 0.96328 -56 ATCCATTCCAAAAAACTGCCGCCAGCAAATA 5 44 0 AAAAACTGCG 0.98512 -74 ATAATCGGCCAAATGCTTTTATTTACAAAGA 5 84 1 AAATGCTTTA 0.892361 -34 GGAGGGAAAAGGTTGCGAGGGGTAAAT 6 21 0 AAAAGGTTCG 0.960848 -17 TTTTCCTGTTAAAAAATTTTGCACCTGACAA 7 12 0 AAAAAATTTG 0.837189 -33 ******** ** Masking position 7 Map Score: 11.9642 Number of sites scoring better than the average of aligned sites = 617 Number in coding regions = 546 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 2 CTGGTGAAAGTTTTTAAGAGGGAAAAATCCAAT 1 21 1 TTTTTAAGGA 0.991382 -43 AGGTAAACTTTATTTACAATGAAAGTGTTACAA 2 85 1 TATTTAAGAA 0.963859 -30 ATCGTAATCTTTTTTAATTAGGTTTTTAAGG 3 13 1 TTTTTATGGT 0.963467 -21 TATATAAGCTTTTCTATCACGAATTTAAATTGC 4 23 0 TTTCTAAGAA 0.949435 -66 TTTTTAATTTTTGTTTTGGTTACCTGTAAA 5 8 1 TTTTTGTGGT 0.937248 -110 TGGCGGCAGTTTTTTGGAATGGATTGCATCTGA 5 51 1 TTTTTGAGGA 0.984945 -67 CAAATGCTTTTATTTACAAAGATAGGCAATAGC 5 93 1 TATTTAAGAT 0.943267 -25 GGTGCAAAATTTTTTAACAGGAAAATAACTCAA 7 18 1 TTTTTAAGAA 0.977281 -27 ****** * *** Masking position 5 Map Score: 8.87177 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 74 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 3 CACCTTCGAAGTAATTGGATTTTTCCCTCT 1 37 0 GTAATTGGAT 0.951817 -27 CAATTACTTCGAAGGTGGAGCAGA 1 50 1 GAAGGTGGAG 0.98229 -14 TCTTTTCTTTGTAATTGAAGTAGCTGTCTT 2 20 1 GTAATTGAAG 0.951817 -95 CTTATAAACTGACGTTGGAGAGCATGCAGT 2 57 0 GACGTTGGAG 0.982289 -58 TCCTATTGCAGAAATTGGTGGATTGGTATT 4 58 0 GAAATTGGTG 0.978327 -31 ACCAATTTCTGCAATAGGAGGTGATGTGAA 4 69 1 GCAATAGGAG 0.963607 -20 ********** Masking position 7 Map Score: 4.4722 Number of sites scoring better than the average of aligned sites = 416 Number in coding regions = 372 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 AGTAATTGGATTTTTCCCTCTTAAAAACTT 1 28 0 TTTTTCCCTC 0.993065 -36 AGTAGCTGTCTTTATCCATACTGCATGCTC 2 38 1 TTTATCCATA 0.89473 -77 TCTATATAAGCTTTTCTATCACGAATTTAA 4 28 0 CTTTTCTATC 0.929315 -61 TAAAACGTTATTTACCCCTCGCAACCTTTT 6 12 1 TTTACCCCTC 0.978271 -26 CCCTCGCAACCTTTTCCCTCC 6 27 1 CTTTTCCCTC 0.993573 -11 ********** Masking position 3 Map Score: 3.96682 Number of sites scoring better than the average of aligned sites = 469 Number in coding regions = 435 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 TACTTCAATTACAAAGAAAAGACTGTCATT 2 12 0 ACAAAGAAAA 0.97042 -103 TGCAGTATGGATAAAGACAGCTACTTCAAT 2 33 0 ATAAAGACAG 0.965003 -82 AACTTTATTTACAATGAAAGTGTTACAATC 2 90 1 ACAATGAAAG 0.980983 -25 GCTTTTATTTACAAAGATAGGCAATAGCCT 5 98 1 ACAAAGATAG 0.986652 -20 ********** Masking position 4 Map Score: 2.1178 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 12 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 TTTATAAGGTAAACTTTATTTACAATGAAA 2 79 1 AAACTTTATT 0.959584 -36 CCTTAAAAACCTAATTAAAAAAGATT 3 18 0 AAACCTAATT 0.966267 -16 TCGTGATAGAAAAGCTTATATAGAAATACC 4 34 1 AAAGCTTATA 0.951657 -55 GGTTACCTGTAAAGCGTATTTGCTGGCGGC 5 28 1 AAAGCGTATT 0.966264 -90 GTAAAACGTTATTTACCCCTCGC 6 4 1 AAACGTTATT 0.972366 -34 ********** Masking position 3 Map Score: 2.60612 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 25 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 ********** No masking Map Score: -4.80737e-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: -4.80737e-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 9 ********** No masking Map Score: -4.80737e-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