AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -iglpR_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 AF0871 63 glycerol-3-phosphate dehydrogenase (NAD(P)+) (gpsA) #2 AF1008 300 A. fulgidus predicted coding region AF1008 #3 AF1009 263 A. fulgidus predicted coding region AF1009 #4 AF1010 31 ferredoxin (fdx-6) #5 AF1427 23 A. fulgidus predicted coding region AF1427 #6 AF1428 143 A. fulgidus predicted coding region AF1428 #7 AF1429 73 A. fulgidus predicted coding region AF1429 #8 AF1753 39 lysophospholipase #9 AF1755 115 conserved hypothetical protein #10 AF1756 162 conserved hypothetical protein #11 AF1758 300 A. fulgidus predicted coding region AF1758 Motif number 1 AGTATTTTTTGCTAATAAAGTTATTCTCGTAGAA 2 166 1 GCTAAATTAT 0.960453 -135 GTAAGCTAGCGCTGGAAAAACTTGGACTAGAACT 2 222 1 GCTAAACTTG 0.935068 -79 TTTTATGTATGCTGGGAAAGTTATAACCACAATA 3 135 1 GCTAAATTAT 0.960453 -129 ACCACAATAAGCTAACAAAATTATCTAAGTTTCT 3 160 1 GCTAAATTAT 0.960453 -104 GTGACAACAGGTTATAAAATTTTTTAGAGGGTCA 3 228 0 GTTAAATTTT 0.95814 -36 AGCGTTTAGCGTTATTTAAACTTTATTGGAGAAA 7 20 1 GTTTAACTTT 0.805692 -54 GATTTTTTCTGCTCATAAACCTTTCTCCAATAAA 7 41 0 GCTAAACTTT 0.985725 -33 TAAATGGTCTGTTTCGAAAAATTTTTAGTTCAAG 10 88 1 GTTAAAATTT 0.849553 -75 AATTCGTAAGGCTTATAAATTTTTGGACTCTTGC 11 96 0 GCTAAATTTT 0.981697 -205 CAACGAAAACGTTCGAAAATCTTTGAACGAATTC 11 125 0 GTTAAACTTT 0.967179 -176 *** *** **** Masking position 8 Map Score: 11.4495 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 56 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 2 AACTGCATTTGGACGGAGACA 1 2 1 ACTGCATTTG 0.889056 -62 CTTAACCAAAATTGCCTTTGTCAAAAACCT 3 104 1 ATTGCCTTTG 0.990428 -160 TCCACCTGAAATTGCGTCTGATTTCCTTTG 9 43 1 ATTGCGTCTG 0.956251 -73 ATTGCGTCTGATTTCCTTTGAAATTCTATC 9 53 1 ATTTCCTTTG 0.965785 -63 AAAGCCTTATTGAGTTTGAGAGGTAAAC 9 98 0 ATTGAGTTTG 0.950928 -18 GATTAATTGTATTTACTTTGAGACATATAA 10 44 0 ATTTACTTTG 0.88506 -119 ATCTTATATTGCTTTTGCTTTTCTGGA 11 8 1 ATTGCTTTTG 0.963023 -293 ********** Masking position 1 Map Score: 5.23791 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 86 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 3 TAAATGAAGTATTTTTTGCTAATAAAGTTA 2 159 1 ATTTTTTGCT 0.847082 -142 ATATCGTGATTTTTTCTGCTCATAAACCTT 7 52 0 TTTTTCTGCT 0.979026 -22 ATTTTAATCTTTTTTCTGCCAAGACCAGAC 8 20 1 TTTTTCTGCC 0.982569 -20 TTTCATTTTTCTGTCAGAATGAGCT 9 6 1 TTTTTCTGTC 0.938939 -110 TGAAGGACATTTTTATTGTTGGTTGCGGGA 10 138 1 TTTTATTGTT 0.601773 -25 ATTGCGCTTATTTTACTGCTGACAGACTGA 11 63 0 TTTTACTGCT 0.953065 -238 TATTGGCTGTAATTTCTGCCACCGCTGCTG 11 237 1 AATTTCTGCC 0.83582 -64 ********** Masking position 4 Map Score: 3.40855 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 273 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 CGTAAATGTTGCTGATCTGGATTCTATATTGCTC 2 28 1 GCTGTTGGAC 0.977355 -273 TAGCTTACAAGCTATTTTGTCTTCAGGACCTTCT 2 196 0 GCTATTGTCC 0.98351 -105 CCAGATACTCGCTTGTTTGTTGACCCCGATAGGG 3 54 0 GCTTTTGTTC 0.965527 -210 GTCAAAAACCTCTTTTATGTATGCTGGGAAAGTT 3 123 1 TCTTTTGTAC 0.911379 -141 GGTAAAAATCGCGGACATGTCCACCGGGTCATAA 6 26 0 GCGGCTGTCC 0.752653 -118 ATCCCGCCGGGCTTACATGTACGCCAAAACAGTG 6 94 1 GCTTCTGTAC 0.512019 -50 TGTCCTTCATGCTACTATGTCATCACTTGAACTA 10 113 0 GCTATTGTCC 0.979601 -50 TATTGCTTTTGCTTTTCTGGAACCAATGCTCATG 11 17 1 GCTTTTGGAC 0.981147 -284 **** * **** * Masking position 8 Map Score: 3.37102 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 105 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 CGTTTATATTGTCTCCGTCCAAATGCAGTT 1 8 0 GCTGTCCAAA 0.988268 -56 ACGCTATAAAGACAGCGTCAAAATTTGACGAGG 2 123 1 GCAGTCAAAA 0.967659 -178 ACCCCGATAGGGCAAGGTTCGAAGCACCGCAGA 3 33 0 GCAGTTCGAA 0.972779 -231 AACCAAAATTGCCTTTGTCAAAAACCTCTTTTA 3 107 1 GCTGTCAAAA 0.958296 -157 GCGCAATAGCGCAAGAGTCCAAAAATTTATAAG 11 86 1 GAAGTCCAAA 0.981518 -215 TAAGCCTTACGAATTCGTTCAAAGATTTTCGAA 11 115 1 GATGTTCAAA 0.9518 -186 ATAAACCAACGAAAACGTTCGAAAATCTTTGAA 11 132 0 GAAGTTCGAA 0.945363 -169 * ** ******* Masking position 12 Map Score: 3.30044 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 30 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 GATTCTATATTGCTCGTAAAAAAAGAGAATG 2 47 1 TCTCGTAAAA 0.955372 -254 CAAAAGTTTATACTTGTAGAAATTCCATAAC 2 84 1 TCTTGTAGAA 0.975472 -217 TTCATTTATTTCCTCGTCAAATTTTGACGCT 2 136 0 TCTCGTCAAA 0.946848 -165 AATAAAGTTATTCTCGTAGAAGGTCCTGAAG 2 179 1 TCTCGTAGAA 0.905056 -122 GGTCAGCCTTTACTTGGCGAAAGATTCTTGG 3 202 0 TCTTGGCGAA 0.964951 -62 TATTTAAACTTTATTGGAGAAAGGTTTATGA 7 32 1 TATTGGAGAA 0.833121 -42 * ********* Masking position 4 Map Score: 1.84152 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 122 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 AATAGCTTGTAAGCTAGCGCTGGAAAAACT 2 214 1 AAGCTAGCGC 0.838547 -87 CGGTGCTTCGAACCTTGCCCTATCGGGGTC 3 37 1 AACCTTGCCC 0.911229 -227 GCACGCCAAGAATCTTTCGCCAAGTAAAGG 3 197 1 AATCTTTCGC 0.987798 -67 TCTGCTCATAAACCTTTCTCCAATAAAGTT 7 38 0 AACCTTTCTC 0.876021 -36 AAAAGATTAAAATTTTTCGCAG 8 3 0 AATTTTTCGC 0.94876 -37 AAATACAATTAATCTTTGGCAAGAGTATTA 10 60 1 AATCTTTGGC 0.930548 -103 TTGAACTAAAAATTTTTCGAAACAGACCAT 10 91 0 AATTTTTCGA 0.674022 -72 AAATTTTTGGACTCTTGCGCTATTGCGCTT 11 84 0 ACTCTTGCGC 0.9547 -217 ********** Masking position 1 Map Score: 2.23521 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 173 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 8 AACTGCATTTGGACGGAGACAATA 1 5 1 GCATTTGGAC 0.880528 -59 CGCAAATCTTGCATTCGTTTAATAATTTT 4 10 0 GCATTCGTTT 0.975375 -22 TCTAACATGAGCATTGGTTCCAGAAAAGCA 11 26 0 GCATTGGTTC 0.97083 -275 TAAGCCTTACGAATTCGTTCAAAGATTTTC 11 115 1 GAATTCGTTC 0.944636 -186 CTTTTTGAGTGCATTCGGTTTAATTTGTAT 11 166 0 GCATTCGGTT 0.977147 -135 ********** Masking position 5 Map Score: 0.465268 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 22 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 9 ACGAAACTCCTTTCGTGTGT 2 1 0 TTTCGTGTGT 0.889579 -300 TTAACCAAAATTGCCTTTGTCAAAAACCTC 3 105 1 TTGCCTTTGT 0.95131 -159 CCACCTGAAATTGCGTCTGATTTCCTTTGA 9 44 1 TTGCGTCTGA 0.887596 -72 TTGCGTCTGATTTCCTTTGAAATTCTATCC 9 54 1 TTTCCTTTGA 0.95223 -62 AAAGCCTTATTGAGTTTGAGAGGTAAACA 9 97 0 TTGAGTTTGA 0.90935 -19 ATTAATTGTATTTACTTTGAGACATATAAT 10 43 0 TTTACTTTGA 0.886257 -120 TTTCGAACGTTTTCGTTGGTTTATTATACA 11 141 1 TTTCGTTGGT 0.874279 -160 GTGCATTCGGTTTAATTTGTATAATAAACC 11 158 0 TTTAATTTGT 0.662291 -143 ********** Masking position 6 Map Score: 1.26544 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 93 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 ********** No masking Map Score: 2.17669e-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: 2.17669e-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: 2.17669e-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