AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -imetR_aful_opreg_300.orf -g0.49 -x5 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 = 0 Input sequences: #1 AF0003 300 A. fulgidus predicted coding region AF0003 #2 AF0004 266 RNase L inhibitor #3 AF0005 38 A. fulgidus predicted coding region AF0005 #4 AF0006 104 corrinoid methyltransferase protein (mtaC-1) #5 AF0008 73 oxalate/formate antiporter (oxlT-1) #6 AF1626 300 A. fulgidus predicted coding region AF1626 #7 AF1628 177 transposase, putative #8 AF2113 44 A. fulgidus predicted coding region AF2113 Motif number 1 GTCTCGCTTTCAATCCCATTT 1 1 0 CATCCCATTT 0.965587 -300 AATCCCATTTTGGTCTGATTTCAACCCGTCA 1 58 0 TGTCTGATTT 0.972807 -243 GTCTGCCTTTCAATCCCATTTTGGTCTGATT 1 69 0 CATCCCATTT 0.965587 -232 GTAGTGTACGTCGTCTGCCTTTCAATCCCAT 1 81 0 TGTCTGCCTT 0.811364 -220 AATCCCATTTTGGTCTGATTTCAACTGTTCC 1 126 0 TGTCTGATTT 0.972807 -175 TTCTTACTTTCAATCCCATTTTGGTCTGATT 1 137 0 CATCCCATTT 0.965587 -164 AATCCCATTTTGGTCTGATTTCAACTTGGGA 1 199 0 TGTCTGATTT 0.972807 -102 CATTGCCTTTCAATCCCATTTTGGTCTGATT 1 210 0 CATCCCATTT 0.965587 -91 AATCCCACTTTAGTCTGATTTCAAAAAACGC 2 69 0 TGTCTGATTT 0.970558 -198 TAAATTTACGTAATCCCACTTTAGTCTGATT 2 80 0 TATCCCACTT 0.962086 -187 TTTTGTTTCCTTGTCACACTTTCCACAAATA 2 109 0 TGTCACACTT 0.840863 -158 AAACTCTCGTCGGTCTGAGTTTTGTTTCCTT 2 128 0 CGTCTGAGTT 0.883947 -139 CATAACAAAATTATCTGACTTTTGATTAAAA 4 24 0 TATCTGACTT 0.948289 -81 ACAAAGTTCGTTATCCCAATTCGATTTTGCT 6 66 0 TATCCCAATT 0.829479 -235 * ********* Masking position 4 Map Score: 21.977 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 103 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 2 AGAAGAGCTTTAGGCGGTTTTAAACTCTCGT 2 149 0 TAGGGGTTTT 0.968983 -118 AATAAATTTGGTGGTGGATTTGCTGGAGAAG 2 175 0 GTGGGGATTT 0.903897 -92 GGTTTGGGCGTTTGGGGATTTTTAAACGGTT 2 217 0 TTTGGGATTT 0.906114 -50 CGGTTTGGTATTTAAGGTTTGGGCGTTTGGG 2 232 0 TTTAGGTTTG 0.926449 -35 TGGTTCTCGATGGGCGGTTTGGTATTTAAGG 2 246 0 TGGGGGTTTG 0.883373 -21 CAGAAAATCTTATAAGGATTGTCAAAAATTT 3 13 1 TATAGGATTG 0.770887 -26 ATTTTCTAATTTGGAGGTGTTTAG 4 91 1 TTGGGGTGTT 0.957445 -14 GTTAAGCTTAGTGATGGTTTGGGCAAATCAG 6 29 0 GTGAGGTTTG 0.924672 -272 GGAGAGCTGAGAGAGGGTTTTCAACGGCAAC 6 127 0 GAGAGGTTTT 0.922053 -174 AGGTAAATTTTAGAGGGAGGTTGATGGGCAA 6 180 0 TAGAGGAGGT 0.589389 -121 AGTTAACTTATTTAAGGTTTTTGGTTGGGGA 6 240 0 TTTAGGTTTT 0.94999 -61 AGTTATAGGGTGTTCCTTCAACCC 7 4 1 TATAGGTGTT 0.848161 -174 TTGTTTTTGATTTAGGGTTGTGTAGTTTTGT 7 105 0 TTTAGGTTGT 0.846483 -73 TTTTCGAATTTTGGTGGTTTTGTTTTTGATT 7 124 0 TTGGGGTTTT 0.979956 -54 **** ****** Masking position 6 Map Score: 14.0776 Number of sites scoring better than the average of aligned sites = 611 Number in coding regions = 542 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 3 CCATTTTGGTCTGATTTCAACCCGTCAGGA 1 55 0 CTGATTTCAA 0.973843 -246 CCATTTTGGTCTGATTTCAACTGTTCCTTG 1 123 0 CTGATTTCAA 0.973843 -178 CCATTTTGGTCTGATTTCAACTTGGGAGCT 1 196 0 CTGATTTCAA 0.973843 -105 CCACTTTAGTCTGATTTCAAAAAACGCCGG 2 66 0 CTGATTTCAA 0.973843 -201 TCAGATAATTTTGTTATGAACTGATTCATA 4 37 1 TTGTTATGAA 0.820258 -68 AAGATAAAAGCTGTTATGAATCAGTTCATA 4 51 0 CTGTTATGAA 0.973334 -54 TAAATAAAGGCTGTTATGAACTGGTTCATA 5 23 0 CTGTTATGAA 0.973334 -51 ********** Masking position 9 Map Score: 11.9698 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 73 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 GCCTTTCAATCCCATTTTGGTCTGATTTCA 1 66 0 CCCATTTTGG 0.983511 -235 TACTTTCAATCCCATTTTGGTCTGATTTCA 1 134 0 CCCATTTTGG 0.983511 -167 GCCTTTCAATCCCATTTTGGTCTGATTTCA 1 207 0 CCCATTTTGG 0.983511 -94 TTTACGTAATCCCACTTTAGTCTGATTTCA 2 77 0 CCCACTTTAG 0.962566 -190 ATTGGGATAACGAACTTTGTCAAAGCCAAT 6 77 1 CGAACTTTGT 0.821455 -224 ATTAATTTTTCGAATTTTGGTGGTTTTGTT 7 131 0 CGAATTTTGG 0.964422 -47 ********** Masking position 6 Map Score: 8.57614 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 40 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 TAGAAAATCTTTTTCCTCTTGCCACGCTTG 1 260 0 TTTTCCTCTT 0.972427 -41 AGGAAAAAGATTTTCTAATTTTTTTATGAA 1 273 1 TTTTCTAATT 0.92774 -28 TGTTTTTTACTTTTCCTCTTTTTTCTGAAC 2 14 0 TTTTCCTCTT 0.972427 -253 AGAAGGCCTATTTTCTAATTTGGAGGTGTT 4 82 1 TTTTCTAATT 0.92774 -23 TTTTTTCTTATTTATGAACCAG 5 3 1 TTTTCTTATT 0.953697 -71 TTGTGTAGTTTTGTCCTGTTGAAGGGGAAG 7 89 0 TTGTCCTGTT 0.903541 -89 ATTGATTAATTTTTCGAATTTTGGTGGTTT 7 135 0 TTTTCGAATT 0.882769 -43 AATTGAGTTATTTTCCTGTTAAAAAATTTT 8 23 0 TTTTCCTGTT 0.972427 -22 ********** Masking position 4 Map Score: 8.56986 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 86 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 6 AAATGGGATTGAAAGCGAGACATTAACAC 1 9 1 TTGAAGCGAG 0.938274 -292 CAAAATGGGATTGAAAGGCAGACGACGTACA 1 77 1 TTGAAGGCAG 0.98841 -224 CAAAATGGGATTGAAAGGCAATGGCGACTTT 1 218 1 TTGAAGGCAA 0.991926 -83 AACGAACTTTGTCAAAGCCAATCAAACTCCA 6 85 1 GTCAAGCCAA 0.874228 -216 AGAGAGGGTTTTCAACGGCAACTAATGATAT 6 118 0 TTCAAGGCAA 0.981558 -183 TAGAGGGAGGTTGATGGGCAATAAAGACGGT 6 170 0 TTGATGGCAA 0.963178 -131 TTTTGTCCTGTTGAAGGGGAAGGTGGAAGAG 7 80 0 TTGAAGGGAA 0.981558 -98 ***** ***** Masking position 4 Map Score: 6.74585 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 116 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 AGCGAGACATTAACACAATTTATTGGGCAT 1 24 1 TAACACAATT 0.916884 -277 CTACCGAGTCCAACACAAGTTTATGAGATG 1 168 0 CAACACAAGT 0.788479 -133 TCTACATTCATAAAAAAATTAGAAAATCTT 1 279 0 TAAAAAAATT 0.908921 -22 AGGAAAAGTAAAAAACAATTGCTGCGATAA 2 27 1 AAAAACAATT 0.630529 -240 ACACTTTCCACAAATAAATTTACGTAATCC 2 95 0 CAAATAAATT 0.847659 -172 GTAAAAAATTTTTGACAATCC 3 28 0 TAAAAAATTT 0.69097 -11 CCAAATCAAGTTATTTTAATC 4 2 1 CAAATCAAGT 0.75681 -103 AATCAGTTCATAACAAAATTATCTGACTTT 4 33 0 TAACAAAATT 0.900762 -72 AGATGAGTGCTAAATAAAGGCTGTTATGAA 5 33 0 TAAATAAAGG 0.50303 -41 ATGGTTTGGGCAAATCAGTTTTATTTTCGT 6 17 0 CAAATCAGTT 0.700928 -284 CCAAAAACCTTAAATAAGTTAACTATTTCT 6 247 1 TAAATAAGTT 0.724229 -54 TAACTATTTCTAACAAAATGTTAGAAAAAC 6 266 1 TAACAAAATG 0.724872 -35 ATTTTCCTGTTAAAAAATTTTGCACCTGAC 8 14 0 TAAAAAATTT 0.69097 -31 AACAGGAAAATAACTCAATTAT 8 33 1 TAACTCAATT 0.893349 -12 ********** Masking position 7 Map Score: 6.83165 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 103 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 8 GGATTTGCTGGAGAAGAGCTTTAGGCGGTT 2 161 0 GAGAAGAGCT 0.991916 -106 GCCTTCTAAAGATAAAAGCTGTTATGAATC 4 59 0 GATAAAAGCT 0.865115 -46 CTTAAGCAGAGATGAGTGCTAAATAAAGGC 5 42 0 GATGAGTGCT 0.94851 -32 AAAGCCGCTGGAGGAGAGCTGAGAGAGGGT 6 140 0 GAGGAGAGCT 0.990265 -161 AAGAGATTGTTAGAAGTGCTATGTGAGGTA 6 206 0 TAGAAGTGCT 0.956934 -95 AAGGGGAAGGTGGAAGAGCTCGTTGTTCGC 7 68 0 TGGAAGAGCT 0.938115 -110 ********** Masking position 5 Map Score: 4.61767 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 256 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 GTGTGACAAGGAAACAAAACTCAGACCGAC 2 121 1 GAAACAAAAC 0.923462 -146 AAGTTTACGAAAATAAAACTGATTTGCCC 6 10 1 AAAATAAAAC 0.914506 -291 TGATTTGCCCAAACCATCACTAAGCTTAAC 6 30 1 AAACCATCAC 0.86373 -271 AAATGTTAGAAAAACATAACGAGGTGGAGT 6 281 1 AAAACATAAC 0.944623 -20 TCAACAGGACAAAACTACACAACCCTAAAT 7 97 1 AAAACTACAC 0.907669 -81 CCCTAAATCAAAAACAAAACCACCAAAATT 7 119 1 AAAACAAAAC 0.975132 -59 TTTTAACAGGAAAATAACTCAATTAT 8 29 1 AAAATAACTC 0.728388 -16 ********** Masking position 3 Map Score: 2.42819 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 60 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 10 ********** No masking Map Score: 3.09329e-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: 3.09329e-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: 3.09329e-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