AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02020_aful_reg_300.orf -o02020_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 AF0448 104 signal-transducing histidine kinase, putative #2 AF1045 86 methyl-accepting chemotaxis protein (tlpC-2) #3 AF1049 102 type II secretion system protein (gspE-4) #4 AF1052 32 A. fulgidus predicted coding region AF1052 #5 AF1053 34 A. fulgidus predicted coding region AF1053 #6 AF1055 111 flagellin (flaB1-2) #7 AF1057 39 cytochrome C-type biogenesis protein (ccdA) #8 AF1058 293 A. fulgidus predicted coding region AF1058 #9 AF1473 98 response regulator #10 AF1475 109 mitochondrial benzodiazepine receptor/sensory transduction protein #11 AF2420 40 signal-transducing histidine kinase, putative #12 AF2421 58 leucyl-tRNA synthetase (leuS) #13 AF2425 85 methanol dehydrogenase regulatory protein (moxR) Motif number 1 TTTTTAGGATAAATTTAAACAAGTTACCCT 1 68 1 AAATTTAAAC 0.809432 -37 ATTTTCTCTATAAAGTAAAATTTCGAATAA 2 29 0 TAAAGTAAAA 0.631311 -58 GTAGATTGCGAAAATAAAAAATAAAATTTT 2 54 0 AAAATAAAAA 0.949476 -33 TGTAATCCCAAAAATGAAAGCAAAGGTTAA 3 31 1 AAAATGAAAG 0.856724 -72 TCACCTCTAAAAAATTAAAAATTTGGGGGA 5 11 0 AAAATTAAAA 0.96958 -24 TCAAGCATAAAAATTGAAAAAGAAATGTAT 7 19 0 AAATTGAAAA 0.908721 -21 TTCACTGGCCAAAAGAAAAAACATGGACTC 8 70 1 AAAAGAAAAA 0.904644 -224 AGAGTGCTGGAAATTTAAAAAGGGTGATTT 8 272 1 AAATTTAAAA 0.953199 -22 TATCCCATTCAAAATTAAATATTTTTCGTG 9 47 0 AAAATTAAAT 0.817681 -52 TGCTTTTTAAAAAAGAAAAATCGCTTTCAA 10 36 0 AAAAGAAAAA 0.904644 -74 AAGCACTCGTAAATTTAAAACCTCGCCAAA 10 61 1 AAATTTAAAA 0.953199 -49 GGGTATAGTTAAATTTAAAGTATAAAAGAT 10 90 0 AAATTTAAAG 0.88658 -20 GGGAAATTCAAAAATAAAAAACTTTTTGA 11 10 0 AAAATAAAAA 0.949476 -31 ********** Masking position 7 Map Score: 17.5102 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 125 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 2 TTACACTTCTGAATTTTCTTATTCGAAATTTT 2 10 1 TGAATTCTAT 0.981337 -77 TACTATCAACTGATGTTGCTATTAACCTTTGCT 3 49 0 TGATTTCTTT 0.849889 -54 TTTTCTAAGTTGAAATTTCCTTTACGTAATT 6 9 0 TGAATTCCTT 0.98284 -103 TCTTATATGTTGAAATTACCTTTTTCTAAGTTG 6 30 0 TGAATTCCTT 0.98284 -82 GCAATATATAAGAATTTTCTTATATGTTGAAAT 6 47 0 AGAATTCTAT 0.880933 -65 AAAAATTTTATGAACTCCCTTATCAAAAATACG 8 13 0 TGAATCCTAT 0.973984 -281 GGTTTCCCTCTGAAGTCCCTGAATGAGGAACCG 8 221 0 TGAATCCTAA 0.912334 -73 TCAAATCACCCTTTTTAAATTTC 8 281 0 TCAATCCCTT 0.840776 -13 TTTTTATTTTTGAATTTCCCTAATTGTGATA 11 20 1 TGAATTCCAA 0.958863 -21 ATCTGCTATTTGACGTTTCCCATAGCTCTAACC 13 26 1 TGACTTCCAT 0.951436 -60 **** ** ** ** Masking position 6 Map Score: 8.76741 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 127 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 3 CTCCTTAATCTCACAGGTGTTTTCATGGTC 1 20 1 TCACAGGTGT 0.949881 -85 CTATCCCTGCTCGGAGGGTAACTTGTTTAA 1 82 0 TCGGAGGGTA 0.969733 -23 ATAAGAAAATTCAGAAGTGTAA 2 3 0 TCAGAAGTGT 0.803558 -84 CAATCTACTTTCGGTGGTGTT 2 76 1 TCGGTGGTGT 0.955138 -11 TTTTAATTTTTTAGAGGTGATACC 5 21 1 TTAGAGGTGA 0.808448 -14 ATATTGCTAATCGCTGGTTTAGTTTGAGGA 6 73 1 TCGCTGGTTT 0.777989 -39 GAGGATGAGGTGAGAGGTGATGGG 6 98 1 TGAGAGGTGA 0.862261 -14 AAACATGGACTCGGCGGGATTTGAACCCGC 8 88 1 TCGGCGGGAT 0.77103 -206 CTTTTTGACCTCAGGGGTTATAAAGGTTTA 8 171 1 TCAGGGGTTA 0.854572 -123 TTCAGGGACTTCAGAGGGAAACCTTAATAT 8 231 1 TCAGAGGGAA 0.909813 -63 ATAGTGTCAATCGCAGGATAATCAGAGGTG 9 74 1 TCGCAGGATA 0.657762 -25 CGCAGGATAATCAGAGGTGTGAAG 9 85 1 TCAGAGGTGT 0.984137 -14 GGAAGAATGGTAGGAGGGTTAGAGCTATGG 13 45 0 TAGGAGGGTT 0.745194 -41 ********** Masking position 1 Map Score: 8.75728 Number of sites scoring better than the average of aligned sites = 852 Number in coding regions = 777 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 4 TCGGAGGGTAACTTGTTTAAATTTATCCTA 1 72 0 ACTTGTTTAA 0.774274 -33 TCCCCCAAATTTTTAATTTTTTAGAG 5 7 1 AAATTTTTAA 0.758155 -28 GAGTTCATAAAATTTTTTGAAACATTGAAT 8 29 1 AATTTTTTGA 0.91786 -265 GAGCCCTTGAACCTTTTTGACCTCAGGGGT 8 159 1 ACCTTTTTGA 0.965829 -135 TAAGACGTAAACCTTTATAACCCCTGAGGT 8 178 0 ACCTTTATAA 0.785909 -116 TCAAATCACCCTTTTTAAATTTCCAGCA 8 276 0 CCCTTTTTAA 0.859065 -18 AAGTTTTTGATTATGTTGGC 9 1 1 AAGTTTTTGA 0.834268 -98 AAGCGATTTTTCTTTTTTAAAAAGCACTCG 10 40 1 TCTTTTTTAA 0.72167 -70 AAAAATAAAAAACTTTTTGA 11 1 0 AACTTTTTGA 0.946593 -40 CCAAACGCCAAATTTTTTAATCCCATTTAT 12 27 1 AATTTTTTAA 0.911614 -32 ********** Masking position 6 Map Score: 6.63292 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 181 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 5 AAAATATCAACCTTTCGCAAGACCATGAAA 1 40 0 CCTTTCGCAA 0.962268 -65 TTTATTTTTTATTTTCGCAATCTACTTTCG 2 59 1 ATTTTCGCAA 0.732567 -28 CCTTTGGTCACAAGGTGCAG 3 1 1 CCTTTGGTCA 0.982844 -102 TTGAAATTTCCTTTACGTAATT 6 3 0 CTTTACGTAA 0.883825 -109 CATGTTTTTTCTTTTGGCCAGTGAACAACC 8 65 0 CTTTTGGCCA 0.982844 -229 CTTTATAACCCCTGAGGTCAAAAAGGTTCA 8 166 0 CCTGAGGTCA 0.884642 -128 CTTTTGGTCAATCAGGCCAA 12 1 1 CTTTTGGTCA 0.979356 -58 ********** Masking position 10 Map Score: 3.40533 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 135 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 GGCCGTGAGAGCGGCTGCGCTGAGGT 4 7 1 GAGAGCGGCT 0.992355 -26 AGCTCAGCGGGAGAGCGCCGCCTTCGCGAG 8 127 0 GAGAGCGCCG 0.986609 -167 AGTCTTGAAAGAGAGTGCTGGAAATTTAAA 8 261 1 GAGAGTGCTG 0.940724 -33 TAAGCAAAGTGGCTTTTAAGCTCG 10 5 1 CAAAGTGGCT 0.923299 -105 AAGCTCGATTGAAAGCGATTTTTCTTTTTT 10 28 1 GAAAGCGATT 0.875326 -82 GGAAAGTGGCTAATAAATGGG 12 48 0 GAAAGTGGCT 0.981309 -11 ********** Masking position 4 Map Score: 2.75939 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 266 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 TCCTTAATCTCACAGGTGTTTTCATGGTCT 1 21 1 CACAGGTGTT 0.974985 -84 AATCTACTTTCGGTGGTGTT 2 77 1 CGGTGGTGTT 0.879254 -10 AGCGGCTGCGCTGAGGTATTACG 4 20 1 CTGAGGTATT 0.931696 -13 TTTAATTTTTTAGAGGTGATACC 5 22 1 TAGAGGTGAT 0.866839 -13 AGGATGAGGTGAGAGGTGATGGG 6 99 1 GAGAGGTGAT 0.906087 -13 CCTTTTTGACCTCAGGGGTTATAAAGGTTT 8 170 1 CTCAGGGGTT 0.851303 -124 AGGTTTACGTCTTAGGTGTGAGTTATACGG 8 194 1 CTTAGGTGTG 0.813852 -100 GTTGGCGGAGCAGCGGTAATCACACGAAAA 9 25 1 CAGCGGTAAT 0.753017 -74 GCAGGATAATCAGAGGTGTGAAG 9 86 1 CAGAGGTGTG 0.98171 -13 ********** Masking position 5 Map Score: 2.85881 Number of sites scoring better than the average of aligned sites = 733 Number in coding regions = 674 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 8 TAATACCTCAGCGCAGCCGCTCTCACGGCC 4 11 0 GCGCAGCCGC 0.801166 -22 CCTTCGCGAGGCGGAGGCCGCGGGTTCAAA 8 107 0 GCGGAGGCCG 0.983526 -187 CCTCCGCCTCGCGAAGGCGGCGCTCTCCCG 8 120 1 GCGAAGGCGG 0.986667 -174 AGGGCTCGTAGCTCAGCGGGAGAGCGCCGC 8 136 0 GCTCAGCGGG 0.957768 -158 GATTATGTTGGCGGAGCAGCGGTAATCACA 9 19 1 GCGGAGCAGC 0.907699 -80 ********** Masking position 5 Map Score: 1.3151 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 94 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 TCCTAAAAAAATATCAACCTTTCGCAAGACCAT 1 44 0 ATATAATTTC 0.932949 -61 TTTTCTCTATAAAGTAAAATTTCGAATAAGAAA 2 25 0 AAAGAATTTC 0.955599 -62 CGAAAATAAAAAATAAAATTTTCTCTATAAAGT 2 43 0 AAATAATTTC 0.980412 -44 ACCTCTAAAAAATTAAAAATTTGGGGGA 5 6 0 AATTAATTTG 0.79232 -29 ACCTTTTTCTAAGTTGAAATTTCCTTTACGTAA 6 13 0 AAGTGATTTC 0.882745 -99 ATTTAAATATACATTTCTTTTTCAATT 7 5 1 AAATTATTTC 0.899698 -35 CAACCAATACAATTCAATGTTTCAAAAAATTTT 8 37 0 AATTAATTTC 0.963312 -257 TTTCAAGACTATATTAAGGTTTCCCTCTGAAGT 8 238 0 ATATAATTTC 0.932949 -56 TCCCATTCAAAATTAAATATTTTTCGTGTGATT 9 42 0 AATTAATTTT 0.720205 -57 AGCTCGATTGAAAGCGATTTTTCTTTTTTAAAA 10 29 1 AAAGGATTTC 0.913193 -81 **** ** **** Masking position 7 Map Score: 6.83467 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 85 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 10 ********** No masking Map Score: -3.08843e-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 11 ********** No masking Map Score: -3.08843e-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: -3.08843e-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