AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00790_aful_reg_100.orf -o00790_aful_100.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 AF0006 104 corrinoid methyltransferase protein (mtaC-1) #2 AF0008 73 oxalate/formate antiporter (oxlT-1) #3 AF0714 73 N5,N10-methylenetetrahydromethanopterin dehydrogenase (mtd) #4 AF1232 63 conserved hypothetical protein #5 AF1415 203 chloride channel, putative #6 AF1935 49 N5,N10-methenyltetrahydromethanopterin cyclohydrolase (mch) #7 AF1936 35 conserved hypothetical protein #8 AF1937 112 cell division inhibitor (minD-2) #9 AF2073 49 formylmethanofuran:tetrahydromethanopterin formyltransferase (ftr-1) #10 AF2075 61 hydroxyethylthiazole kinase (thiM) #11 AF2079 33 A. fulgidus predicted coding region AF2079 #12 AF2081 111 A. fulgidus predicted coding region AF2081 #13 AF2207 300 formylmethanofuran:tetrahydromethanopterin formyltransferase (ftr-2) Motif number 1 GAAAATAGGCCTTCTAAAGATAAAAGCTGTTATG 1 63 0 CTAAAATAAA 0.932854 -42 GAACTGGTTCATAAATAAGAAAAAA 2 2 0 ATTAAAAAAA 0.897922 -72 TAAAAAGGAAATGTTAAATAAACTGAAGCATACA 3 33 1 ATAAAAAACT 0.81372 -41 GTTTTATGAAATAAAAAACAAAAA 5 1 0 ATAAAAAAAA 0.977308 -203 TGGTGACAGAATCTGAAAGAAAAATATATCATCA 5 159 1 ATAAAAAAAA 0.977308 -45 AAGATAAAAAATAAAAACTCCAATGTT 6 4 1 ATAAAAAAAA 0.977307 -46 TCATTGGAAATATACACGACAATATA 7 20 0 ATAAAATACA 0.896848 -16 ATAATGTCTTATTTTTAAAATAATTAAATTTTTT 8 87 0 ATTAAATAAT 0.642456 -26 TACTTTCCTCATAAAAAATTAAATTTGAGAGC 11 9 0 ATAAATAAAT 0.816118 -25 TATATATAATATTTGAAAATAAAATCAGAAGCCA 12 36 0 ATAAATAAAA 0.932554 -76 ATTCCGGTTTATTACAAAGTTAAATCACTTCAAT 13 204 1 ATAAATTAAA 0.898325 -97 AATTTTCCAGCTTGCAAAAATAAAAAGATTTAAA 13 245 1 CTAAAATAAA 0.932854 -56 TAAATCGCTTCTACCAAACAAAAAGCAGGTGATA 13 275 1 CTAAAAAAAA 0.956028 -26 ** *** ***** Masking position 7 Map Score: 14.0941 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 65 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 2 CAAAGAAGTAAACTTTGAAAGTTGGGCTGAG 5 34 0 AATTTGAAAG 0.989892 -170 TCGAAATGGCAATTTTGTAAGTTGGTGACAG 5 137 1 AATTTGTAAG 0.968699 -67 GTTGGTGACAGAATCTGAAAGAAAAATATAT 5 157 1 GATCTGAAAG 0.91793 -47 ACAGTCGCAGAATTTTTATAGTATCATGAAA 9 20 1 AATTTTATAG 0.775581 -30 ATAAAAAATTAAATTTGAGAGC 11 2 0 AATTTGAGAG 0.96298 -32 AAGCATGAGCAAGGTTGAAAGGCTTGCGGTG 13 98 0 AAGTTGAAAG 0.958127 -203 AACTTCAAAGGATTTTGAAAGCATGAGCAAG 13 116 0 GATTTGAAAG 0.979538 -185 GAAGTGATTTAACTTTGTAATAAACCGGAAT 13 204 0 AATTTGTAAT 0.752105 -97 CAAGCTGGAAAATTTTTAAAGATTGAAGTGA 13 228 0 AATTTTAAAG 0.950702 -73 ** ******** Masking position 6 Map Score: 8.51563 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 151 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 CCAAATCAAGTTATTTTAATCAAAAG 1 2 1 CAATAAGTTT 0.432289 -103 GGCCTTCTAAAGATAAAAGCTGTTATGAATCAGTT 1 55 0 AATAAAGTTA 0.957719 -50 GATGAGTGCTAAATAAAGGCTGTTATGAACTGGTT 2 27 0 AATAAGGTTA 0.767671 -47 CAATGAGATTAAAAAGGAAATGTTAAATAAACTGA 3 24 1 AAAAGAATTA 0.771549 -50 TCGTAGTCCCAGATACGAAAGATTATATATACCTT 4 22 1 AATAGAATTA 0.889854 -42 CCGTATTGATAAATACAAAGCTTTATCCTCCTACT 5 85 1 AATAAAATTA 0.92415 -119 AAGACCACTAACATTGGAGTTTTTATTTTTTATCT 6 12 0 AATTGAGTTA 0.862615 -38 ATATACACGACAATATAAGTACTTTC 7 2 0 CATAAAGTTT 0.81335 -34 AGTTCAGCAGCAATACAAAAAATTTAATTATTTTA 8 71 1 CATAAAATTT 0.700934 -42 TAATTATTTTAAAAATAAGACATTATCG 8 95 1 AAAAAAGTTA 0.904481 -18 GCTCTCAAATTTAATTTTTTATGAGGAAAGT 11 7 1 AATTAATTTA 0.51381 -27 TAAGAGGCTGATAAAGGAACATTTACGACTCCATT 13 164 0 AAAAGAATTA 0.771549 -137 AAATTTTTAAAGATTGAAGTGATTTAACTTTGTAA 13 215 0 AATTAAGTTT 0.798326 -86 CAGCTTGCAAAAATAAAAAGATTTAAATCGCTTCT 13 252 1 AATAAAATTA 0.924147 -49 * *** *** *** Masking position 3 Map Score: 6.8008 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 112 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 4 CATACAGCCAGCAGGTGATAAAA 3 61 1 GCAGGTGAAA 0.990811 -13 TGGGACTACGACAGGTGAGACA 4 1 0 ACAGGTGAAA 0.981206 -63 AATTTTGTAAGTTGGTGACAGAATCTGAAAGA 5 147 1 GTTGGTGAAA 0.927952 -57 TTGCTGGGGGAGTGATGATATATTTTTCTTTC 5 173 0 AGTGATGAAA 0.761359 -31 AGTGGTCTTTTGAGGTGGTAAA 6 38 1 TGAGGTGGAA 0.946835 -12 GAAGGCTGGTGGAATTAGGGATTTAA 8 5 1 GCTGGTGGAT 0.912143 -108 ATGCCGAGTAAGAGGTGAAAAA 12 100 1 AGAGGTGAAA 0.981206 -12 TTGAAAGGCTTGCGGTGAGATACAACATTATC 13 83 0 TGCGGTGAAA 0.930178 -218 CAAACAAAAAGCAGGTGATAGT 13 289 1 GCAGGTGAAT 0.971489 -12 ******** * * Masking position 6 Map Score: 5.4529 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 289 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 5 TTATGAATCAGTTCATAACAAAATTATCTG 1 38 0 GTTCATAACA 0.988393 -67 TTATGAACTGATTCATAACAGCTTTTATCT 1 50 1 ATTCATAACA 0.95539 -55 TTATGAACTGGTTCATAAATAAGAAAAAA 2 10 0 GTTCATAAAT 0.91911 -64 TTATGAACCAGTTCATAACAGCCTTTATTT 2 22 1 GTTCATAACA 0.988393 -52 TTGTTTTTTATTTCATAAAACTCAGCCCAA 5 14 1 TTTCATAAAA 0.88773 -190 ********** Masking position 5 Map Score: 4.27821 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 17 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 CCAAATCAAGTTATTTTAATCAAAAG 1 6 1 TCAAGTATTT 0.8406 -99 TAATCAAAAGTCAGATAATTTTGTTATGAAC 1 27 1 TCAGATATTT 0.954134 -78 GCTGTATGCTTCAGTTTATTTAACATTTCCT 3 38 0 TCAGTTATTT 0.837703 -36 TATTTTTCTTTCAGATTCTGTCACCAACTTA 5 154 0 TCAGATCTGT 0.809549 -50 ATTAGGGATTTAAAATGCTTTTCAGATGATT 8 24 1 TAAAATCTTT 0.684089 -89 AAAATGCTTTTCAGATGATTTCTCGCTCTTT 8 35 1 TCAGATATTT 0.954134 -78 TTTAAAATAATTAAATTTTTTGTATTGCTGC 8 77 0 TTAAATTTTT 0.759728 -36 TTTTCAATTTTTTTGCACAATCAG 10 4 1 TCAATTTTTT 0.835862 -58 GATTTTATTTTCAAATATTATATATAACATT 12 44 1 TCAAATTTAT 0.835865 -68 AACAAAAGCCTCAAATTCTATCTAAGGCTCG 13 39 0 TCAAATCTAT 0.860129 -262 AGAGATAACTTCAAAGGATTTTGAAAGCATG 13 122 0 TCAAAGATTT 0.812769 -179 TAGAAGCGATTTAAATCTTTTTATTTTTGCA 13 257 0 TTAAATTTTT 0.759733 -44 ****** **** Masking position 3 Map Score: 6.07914 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 127 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 CTGAAGCATACAGCCAGCAGGTGATAAAA 3 55 1 CAGCCAGCAG 0.93351 -19 AATTTTTGTGCTGCCAGCAGTAGGAGGATA 5 108 0 CTGCCAGCAG 0.919105 -96 TATCATCACTCCCCCAGCAAAAACGAAGC 5 185 1 CCCCCAGCAA 0.952061 -19 ATCCCTAATTCCACCAGCCTTC 8 3 0 CCACCAGCCT 0.98019 -110 GAAAGCTCATCCTCAAGCCTCACTCCGAGC 13 14 1 CCTCAAGCCT 0.943564 -287 TCAAGCCTCACTCCGAGCCTTAGATAGAAT 13 26 1 CTCCGAGCCT 0.928321 -275 TTGTATCTCACCGCAAGCCTTTCAACCTTG 13 90 1 CCGCAAGCCT 0.985152 -211 ********** Masking position 6 Map Score: 4.17167 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 278 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 ATTTTGTTATGAACTGATTCATAACAGCTT 1 44 1 GAACTGATTC 0.944363 -61 AGGCTGTTATGAACTGGTTCATAAATAAGA 2 16 0 GAACTGGTTC 0.73713 -58 CTCTGCTTAAGAGGGGATTCGCG 2 61 1 GAGGGGATTC 0.942943 -13 TTTAAAGATTGAAGTGATTTAACTTTGTAA 13 215 0 GAAGTGATTT 0.965221 -86 TTGTTTGGTAGAAGCGATTTAAATCTTTTT 13 266 0 GAAGCGATTT 0.937069 -35 ********** Masking position 8 Map Score: 0.224126 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 77 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 9 ********** No masking Map Score: -1.75261e-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 ********** No masking Map Score: -1.75261e-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: -1.75261e-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