AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -iflhCD_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 AF0154 139 conserved hypothetical protein #2 AF0155 62 A. fulgidus predicted coding region AF0155 #3 AF0157 99 molybdopterin oxidoreductase, iron-sulfur binding subunit #4 AF0162 241 A. fulgidus predicted coding region AF0162 #5 AF0163 157 A. fulgidus predicted coding region AF0163 #6 AF2089 111 conserved hypothetical protein Motif number 1 GCCTAAAATCGGTTTTGAAAATGCAATCAAA 1 77 0 GGTTTGAAAA 0.983526 -63 AAAATATAAGGGTTTTGGAAATTAACACCGT 3 26 0 GGTTTGGAAA 0.993388 -74 TAGCCAGAAAGGTTCTGGCAAGAGGAGGTGG 3 76 1 GGTTTGGCAA 0.95951 -24 TCTGGCAAGAGGAGGTGGAAA 3 89 1 GGAGTGGAAA 0.929519 -11 TTAATCTAAGGTTAACGGAAACATCC 4 6 0 GTTACGGAAA 0.927518 -236 AAATTTAAAAAGTAATGAAAAAACAAAAGTG 4 46 1 AGTATGAAAA 0.890338 -196 AAACAAAAGTGGTGGTTAAAATGACCAGCGA 4 66 1 GGTGTTAAAA 0.861704 -176 ATACAATCCAGTTACCGGAAAGTATTATGCT 4 118 1 GTTACGGAAA 0.927518 -124 AAGGACTATCAGTTCAGGAAAAGCAGGGCAG 4 157 1 AGTTAGGAAA 0.89264 -85 CAGATAAAGAGGTTGTGGAAACCATCAAAAA 4 185 1 GGTTTGGAAA 0.993388 -57 TGGTGGAGCTGGTAAAGAAAATCGATAAAGT 5 14 1 GGTAAGAAAA 0.918936 -144 TAATTAACTCGTTTACGGAAAATTTTAAACA 5 115 1 GTTTCGGAAA 0.949327 -43 TTGGATGGAGAGTGTTTAAAATTTTCCGTAA 5 127 0 AGTGTTAAAA 0.55367 -31 **** ****** Masking position 10 Map Score: 18.3422 Number of sites scoring better than the average of aligned sites = 959 Number in coding regions = 887 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 2 CCCATCACCACCCCAAACACTG 1 2 1 CCACACCACC 0.978309 -138 TTTAGGCCAACCAAAAACTTTTTAAATTTAG 1 101 1 CCAAAACTTT 0.894839 -39 GTGTTAATTTCCAAAACCCTTATATTTTATC 3 29 1 CCAAACCCTT 0.984971 -71 CCTCCTCTTGCCAGAACCTTTCTGGCTAACA 3 73 0 CCAAACCTTT 0.989837 -27 TTTCCACCTCCTCTTGCCAGAACC 3 86 0 CCACTCCTCT 0.991375 -14 GTCATTTTAACCACCACTTTTGTTTTTTCAT 4 60 0 CCACACTTTT 0.938373 -182 TTGATGGTTTCCACAACCTCTTTATCTGCCC 4 182 0 CCAAACCTCT 0.990612 -60 ACAGTAAATCCCATATCGATTTCTTTTCTCT 4 218 0 CCAATCGATT 0.85766 -24 ATTTTCTTTACCAGCTCCACCAATC 5 5 0 CCACTCCACC 0.96856 -153 CCAACTCCCTTAAAAGTAATT 6 1 1 CCACTCCCTT 0.986186 -111 *** ******* Masking position 3 Map Score: 15.3852 Number of sites scoring better than the average of aligned sites = 801 Number in coding regions = 750 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 3 TCACCACCCCAAACACTGTTACCTAACAGTG 1 15 1 AAACCTGTTA 0.958635 -125 TGTTAAATATAAACACTGTTAGGTAACAGTG 1 28 0 AAACCTGTTA 0.958635 -112 GCATTTTCAAAACCGATTTTAGGCCAACCAA 1 84 1 AACCATTTTA 0.83867 -56 AGGCCAACCAAAAACTTTTTAAATTTAGGCT 1 104 1 AAAATTTTTA 0.781523 -36 TTAATTTCCAAAACCCTTATATTTTATCAAG 3 32 1 AAACCTTATA 0.938378 -68 ATCAAGTAGTAAACATTGTTAGCCAGAAAGG 3 57 1 AAACTTGTTA 0.842166 -43 TTTAAATTTCTACCGCTTTTAATCTAAGGTT 4 24 0 TACCCTTTTA 0.954551 -218 AGGAGATAATTAACTCGTTTACGGAAAATTT 5 109 1 TAACCGTTTA 0.90614 -49 TACGCTATATTAAAGCTTTTAGCTAATGACC 6 31 1 TAAACTTTTA 0.887913 -81 TCAAGTTTAAAAACGCTTTTCAAAAGGTTGC 6 76 0 AAACCTTTTC 0.957584 -36 **** ****** Masking position 2 Map Score: 9.22406 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 177 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 4 CCAAACACTGTTACCTAACAGTGTTTATATTT 1 23 1 TCCTAACAGT 0.956094 -117 AGTTTTTGGTTGGCCTAAAATCGGTTTTGAAA 1 88 0 TCCTAAAATC 0.980707 -52 ATGTTTAGGATAGCCTAAATTTAAAAAGTTTT 1 114 0 TCCTAAATTT 0.851701 -26 CATCTACCTTTTCCCTAAAATCTTCGAATATG 2 18 0 TCCTAAAATC 0.980707 -45 CCGTTAACCTTAGATTAAAAGCGGTAGAAATT 4 19 1 TATTAAAAGC 0.868306 -223 TGTACTGGACTATCTTAAAAGTTGGAATAGAC 5 72 1 TCTTAAAAGT 0.969698 -86 CCAACTCCCTTAAAAGTAATTACGCTA 6 6 1 TCTTAAAAGT 0.969736 -106 ATTATGGTCATTAGCTAAAAGCTTTAATATAG 6 35 0 TGCTAAAAGC 0.961539 -77 * ********* Masking position 7 Map Score: 6.82432 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 149 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 GCATTTTTGATTGCATTTTCAAAACCGATTT 1 72 1 TTGCATTTCA 0.766569 -68 TTTTTCGTTTTTTTTACGGTGTT 3 3 1 TTTCGTTTTT 0.979657 -97 TTCATTACTTTTTAAATTTCTACCGCTTTTA 4 34 0 TTTAATTTCT 0.746377 -208 TAACCACCACTTTTGTTTTTTCATTACTTTT 4 53 0 TTTTGTTTTT 0.825206 -189 TATTCTCTTTTTTCTCTTTCTCTCGCTGGTC 4 88 0 TTTCTTTTCT 0.954441 -154 CGATTTCTTTTCTCTCTTTTTTGATGGTTTC 4 202 0 TCTCTTTTTT 0.777245 -40 GTAAATCCCATATCGATTTCTTTTCTCTCTT 4 215 0 TATCGTTTCT 0.960424 -27 AGTTTTACTTTATCGATTTTCTTTACCAGCT 5 20 0 TATCGTTTTC 0.824021 -138 GATTCTGGACTTTCAGTTTTACTTTATCGAT 5 34 0 TTTCATTTTA 0.90804 -124 AGCCGGATTTCGATTTCAAGTTTAAAAA 6 94 0 TTTCGTTTCA 0.975778 -18 ***** ***** Masking position 7 Map Score: 4.73878 Number of sites scoring better than the average of aligned sites = 443 Number in coding regions = 376 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 6 GGTAACAGTGTTTGGGGTGGTGATGGG 1 8 0 TTTGGGGTGG 0.936201 -132 GCATTATGCATTTTTGATTGCATTTTCAAA 1 65 1 TTTTTGATTG 0.92321 -75 TTTAAAAAGTTTTTGGTTGGCCTAAAATCG 1 97 0 TTTTGGTTGG 0.964385 -43 CGTTATGTTTAGGATAGCCTAAATTTA 1 123 0 TTTAGGATAG 0.950428 -17 TTTTCTCTCTTTTTTGATGGTTTCCACAAC 4 196 0 TTTTTGATGG 0.972663 -46 CCAGTACATATTTTGGATTCTGGACTTTCA 5 50 0 TTTTGGATTC 0.879434 -108 TATTCCAACTTTTAAGATAGTCCAGTACAT 5 71 0 TTTAAGATAG 0.747858 -87 GGTTTGGATCTTGGATGGAGAGTGTTTA 5 140 0 TCTTGGATGG 0.971944 -18 ********** Masking position 3 Map Score: 5.42944 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 200 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 7 GTAAGACAAAGGACTATCAGTTCAGGAAAA 4 149 1 GGACTATCAG 0.981658 -93 AATCGATATGGGATTTACTGTAAT 4 228 1 GGATTTACTG 0.936803 -14 TTTACTTTATCGATTTTCTTTACCAGCTCC 5 18 0 CGATTTTCTT 0.860093 -140 TTTGGATTCTGGACTTTCAGTTTTACTTTA 5 39 0 GGACTTTCAG 0.987128 -119 AATATGTACTGGACTATCTTAAAAGTTGGA 5 68 1 GGACTATCTT 0.971458 -90 ********** Masking position 5 Map Score: 1.11448 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 135 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 ATAGCCTAAATTTAAAAAGTTTTTGGTTGG 1 107 0 TTTAAAAAGT 0.976492 -33 ACCCTTATATTTTATCAAGTAGTAAACATT 3 44 1 TTTATCAAGT 0.850469 -56 GCGGTAGAAATTTAAAAAGTAATGAAAAAA 4 39 1 TTTAAAAAGT 0.976492 -203 TACTGGACTATCTTAAAAGTTGGAATAGAC 5 74 1 TCTTAAAAGT 0.880441 -84 AAGGCAACCTTTTGAAAAGCGTTTTTAAAC 6 73 1 TTTGAAAAGC 0.916504 -39 ********** Masking position 7 Map Score: 0.400896 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 34 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 9 ********** No masking Map Score: 1.72905e-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: 1.72905e-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: 1.72905e-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