AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -icrp_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 AF0094 300 conserved hypothetical protein #2 AF0373 300 transcription initiation factor IID #3 AF0871 63 glycerol-3-phosphate dehydrogenase (NAD(P)+) (gpsA) #4 AF0883 71 argininosuccinate lyase (argH) #5 AF1008 300 A. fulgidus predicted coding region AF1008 #6 AF1009 263 A. fulgidus predicted coding region AF1009 #7 AF1010 31 ferredoxin (fdx-6) #8 AF1055 111 flagellin (flaB1-2) #9 AF1057 39 cytochrome C-type biogenesis protein (ccdA) #10 AF1058 293 A. fulgidus predicted coding region AF1058 #11 AF1316 48 threonine synthase (thrC-2) #12 AF1342 126 thymidine phosphorylase (deoA-2) #13 AF1427 23 A. fulgidus predicted coding region AF1427 #14 AF1428 143 A. fulgidus predicted coding region AF1428 #15 AF1429 73 A. fulgidus predicted coding region AF1429 #16 AF1608 59 spermidine/putrescine ABC transporter, ATP-binding protein (potA) #17 AF1720 182 acetolactate synthase, large subunit (ilvB-1) #18 AF1753 39 lysophospholipase #19 AF1755 115 conserved hypothetical protein #20 AF1756 162 conserved hypothetical protein #21 AF1758 300 A. fulgidus predicted coding region AF1758 #22 AF2106 39 conserved hypothetical protein #23 AF2127 104 transcriptional regulatory protein, LysR family #24 AF2232 87 ferric uptake regulation protein (fur) #25 AF2289 216 mevalonate kinase (mvk) Motif number 1 TTACAAAAACAAAATTTATTAAACTAAAATTCG 1 51 1 AAAATTATTA 0.619045 -250 TTTCGAAAACAAAAATTTTATAATACGCATGTT 1 150 1 AAAATTTTAA 0.67524 -151 ACACACGAAAGGAGTTTCGTAAATGTTGCTG 5 9 1 AAGGGTTTCA 0.62677 -292 GCATACATAAAAGAGGTTTTTGACAAAGGCAAT 6 114 0 AAGAGTTTTA 0.906233 -150 AACAGGTTATAAAATTTTTTAGAGGGTCAGCCT 6 224 0 AAAATTTTTA 0.957828 -40 AGCAATATATAAGAATTTTCTTATATGTTGAAA 8 48 0 AAGATTTTCA 0.828914 -64 GGGAGTTCATAAAATTTTTTGAAACATTGAATT 10 27 1 AAAATTTTTA 0.957828 -267 TTCTCACCTGAAAAGGTTTTAAAGCTGACGACA 12 21 0 AAAAGTTTTA 0.955839 -106 GGCTGACACGAAAGTTTTTTATACAAAATGGAT 16 25 1 AAAGTTTTTA 0.892018 -35 CTACAAAGGTAAGTAGTTTTTAAAACTTAGCTT 17 15 1 AAGTGTTTTA 0.609396 -168 TGGGCGAACCAAAACTTTTTAAAGCGCATGCTG 17 70 1 AAAATTTTTA 0.957828 -113 AAAAAAGATTAAAATTTTTCGCAG 18 2 0 AAAATTTTCA 0.915615 -38 TATAATTCTTAAAATGTTTTTAAAGTTGATCGC 20 16 0 AAAAGTTTTA 0.955839 -147 CACTTGAACTAAAAATTTTTCGAAACAGACCAT 20 91 0 AAAATTTTTA 0.957828 -72 CGTAAGGCTTATAAATTTTTGGACTCTTGCGCT 21 93 0 ATAATTTTTA 0.619045 -208 GAATTCGTTCAAAGATTTTCGAACGTTTTCGTT 21 125 1 AAAGTTTTCA 0.797835 -176 TGGTTTTAAAATTTTTTGAATTTTTATTAT 23 85 0 AAAATTTTTA 0.957828 -20 TTCTAAATCGAAATTGTTTTAAAACATCAGCTT 24 16 0 AAATGTTTTA 0.777478 -72 TTCTAGAAGAAAAATGTTTTTTACTAAGATGTG 24 54 1 AAAAGTTTTA 0.955839 -34 **** ***** * Masking position 7 Map Score: 22.4224 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 74 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 2 TTTGTAAACGTTTGAATTATTCCCCCTAAACCAA 1 225 1 TTTATATTCC 0.905807 -76 ACTGCGGAGATTTTCAGAACTCTCCATTTTTGAG 2 169 1 TTTCGACTCC 0.975242 -132 ACTCTCCATTTTTGAGGTTCTCGCTTTTACCTAC 2 187 1 TTTAGTCTCC 0.931245 -114 GGTTCTCGCTTTTACCTACTTCTCAATCGTGATT 2 202 1 TTTCTCTTCC 0.722434 -99 AGGTTTTATTCCCGTATTCCCTCCACAATCT 5 280 0 ATTCGATTCC 0.897434 -21 TTTCAAAAAATTTTATGAACTCCCTTATCAAAAA 10 17 0 TTTAGACTCC 0.971432 -277 CCTTTTTAAATTTCCAGCACTCTCTTTCAAGACT 10 261 0 TTTCGACTCC 0.975242 -33 CTGAAAGAATATTAACTTTTTCTCGCTATCGTGA 12 88 0 ATTATTTTCC 0.576601 -39 CCAGAGAACTTTTTCATCACTCCCACCACCAGCA 17 98 0 TTTCTACTCC 0.946893 -85 TTACCCTGTGTTTCACGAACTCACCCCCGACTTT 21 192 0 TTTAGACTCC 0.971432 -109 TTATTTAATAATTTAGGGATTCGCATTGCCTCAA 23 41 1 ATTAGATTCC 0.883087 -64 CACAAAATTCTTTAAGTTTTTCCCGTAGTCTAAT 25 191 1 TTTATTTTCC 0.792979 -26 *** * * **** * Masking position 11 Map Score: 9.96245 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 137 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 GTAGGCAACAGCGCAGGAAACGAGGGGCAGAA 2 77 0 GCGCAGGAAG 0.927341 -224 AGAATCTTTCGCCAAGTAAAGGCTGACCCTCT 6 205 1 GCCAAGTAAG 0.664696 -59 TTCAAATCCCGCCGAGTCCATGTTTTTTCTTT 10 81 0 GCCGAGTCAG 0.962476 -213 CCTTCGCGAGGCGGAGGCCGCGGGTTCAAATC 10 105 0 GCGGAGGCGG 0.994129 -189 CCTCCGCCTCGCGAAGGCGGCGCTCTCCCGCT 10 120 1 GCGAAGGCGG 0.982823 -174 GTTTTGGTTCGCCCAGGCAAGGTAATTGCACT 17 53 0 GCCCAGGCAG 0.971669 -130 CGACCCCGCAGCGGAGGCTGGGAGGATGGAGG 25 102 0 GCGGAGGCGG 0.994129 -115 AGCCTCCGCTGCGGGGTCGGAGGTGTAGACGG 25 115 1 GCGGGGTCGG 0.946181 -102 ******** * * Masking position 6 Map Score: 5.99592 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 169 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 4 GCACTCAGTTTGTGCAGAGGTTATTAATTCT 4 51 0 TTTTCAGAGT 0.961082 -21 CTAGTCCAAGTTTTTCCAGCGCTAGCTTACAAG 5 219 0 TTTTCAGCGT 0.960327 -82 AAAGTTAATATTCTTTCAGAGTTTTTGAAGTTC 12 103 1 TTCTCAGAGT 0.984417 -24 GTTTCATGCAGCGTTTAGCGTTATT 15 3 1 TTCTCAGCGT 0.984108 -71 TTTCCTACAAAGGTAAGTAGTTTT 17 2 1 TTCTCAAAGT 0.961082 -181 GCCTTACGAATTCGTTCAAAGATTTTCGAACGT 21 118 1 TTCTCAAAGT 0.960333 -183 CGGTTCTTGCTGCGTTCTCGTTCTAT 21 285 0 TTCTCTGCGT 0.957752 -16 AGAAAAATGTTTTTTACTAAGATGTGAAATTGA 24 61 1 TTTTCTAAGT 0.779432 -27 *** * ***** * Masking position 5 Map Score: 5.47231 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 57 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 5 ACATTTAAAGTCGAATTTTTAATTACAAAA 1 29 1 TCGAATTTTT 0.951531 -272 AAAGTCCTCATCGAATTTTAGTTTAATAAA 1 65 0 TCGAATTTTA 0.829669 -236 TCGGAGCCAACCGAATTGTTCAGAAAGTCC 1 88 0 CCGAATTGTT 0.928937 -213 TCGATTAATTCCGAATTGTTCGGAGCCAAC 1 107 0 CCGAATTGTT 0.928937 -194 TCGGAATTAATCGAATTTTTAATATATTTT 1 123 1 TCGAATTTTT 0.951531 -178 TTGTAAACGTTTGAATTATTCCCCCTAAAC 1 226 1 TTGAATTATT 0.563806 -75 ACATTTCTTTTTCAATTTTTATGCTTGAG 9 21 1 TTCAATTTTT 0.632189 -19 TTTTGAAACATTGAATTGTATTGGTTGTTC 10 43 1 TTGAATTGTA 0.560267 -251 TTCGTGTCAGCCCAATTTTTTATCTA 16 7 0 CCCAATTTTT 0.813957 -53 GAACTCACCCCCGACTTTTTGAGTGCATTC 21 180 0 CCGACTTTTT 0.775657 -121 TTAAAATTTTTTGAATTTTTATTATCCGTG 23 80 0 TTGAATTTTT 0.878237 -25 ********** Masking position 4 Map Score: 6.15336 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 79 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 6 CTCAAGCATAAAAATTGAAAAAGA 9 26 0 AGCATAAAAA 0.853973 -14 TTCACTGGCCAAAAGAAAAAACATGGACTC 10 70 1 AAAAGAAAAA 0.832049 -224 CACCTAAAAATAAAAAAAATAGA 13 8 0 AAAATAAAAA 0.493807 -16 AAGGTTTATGAGCAGAAAAAATCACGATAT 15 52 1 AGCAGAAAAA 0.967425 -22 CCTTTAGAAAAGAAGTAAAAGCTGTACTAC 17 145 0 AGAAGTAAAA 0.826892 -38 GTCTGGTCTTGGCAGAAAAAAGATTAAAAT 18 20 0 GGCAGAAAAA 0.935554 -20 AGCTCATTCTGACAGAAAAATGAAA 19 6 0 GACAGAAAAA 0.82632 -110 TCAGTCTGTCAGCAGTAAAATAAGCGCAAT 21 63 1 AGCAGTAAAA 0.903707 -238 AGTTATTTCTAGAAGAAAAATGTTTTTTAC 24 48 1 AGAAGAAAAA 0.93795 -40 ********** Masking position 4 Map Score: 5.78982 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 141 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 7 CCGAATTGTTCGGAGCCAACCGAATTGTTCA 1 96 0 CGGAGCAACC 0.963354 -205 AGGGATAAAACGTAGGCAACAGCGCAGGAAA 2 89 0 CGTAGCAACA 0.96237 -212 AAAATCTCCGCAGTGTCAACACCCTTTTCGG 2 152 0 CAGTGCAACA 0.954436 -149 TGCATTTGGACGGAGACAATATAAACGTTAG 3 14 1 CGGAGCAATA 0.956818 -50 CTTGCCCTATCGGGGTCAACAAACAAGCGAG 6 50 1 CGGGGCAACA 0.971924 -214 TAACTACTTTCAGTGACAACAGGTTATAAAA 6 243 0 CAGTGCAACA 0.954436 -21 AATTTTTAAACATAAACAACATTATCTATAA 12 52 1 CATAACAACA 0.720655 -75 GTAGCTCCCGCAACCAACAATAAAAATGT 20 144 0 CGCAACAACA 0.809892 -19 AAGAGTAGTCCAGAGCCAATAAAAGCCTTCC 22 14 1 CAGAGCAATA 0.91856 -26 ***** ***** Masking position 8 Map Score: 4.8961 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 143 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 8 CTTAACTTTGATTTATTTTGTTAATCACGA 2 228 0 ATTTATTTTG 0.607117 -73 TGCCATCCCTCTTAACTTTGATTTATTTTG 2 238 0 CTTAACTTTG 0.708118 -63 ATACCATATAAATACCTTTGCCATCCCTCT 2 256 0 AATACCTTTG 0.715407 -45 CTTAACCAAAATTGCCTTTGTCAAAAACCT 6 104 1 ATTGCCTTTG 0.935915 -160 CTAAGTTGAAATTTCCTTTACGTAATT 8 8 0 ATTTCCTTTA 0.680271 -104 ATATGTTGAAATTACCTTTTTCTAAGTTGA 8 29 0 ATTACCTTTT 0.843161 -83 TTAAATATACATTTCTTTTTCAATTTTTAT 9 13 1 ATTTCTTTTT 0.542701 -27 CTGAAAGAATATTAACTTTTTCTCGCTATC 12 92 0 ATTAACTTTT 0.634231 -35 TTAAAAACTACTTACCTTTGTAGGAAA 17 8 0 CTTACCTTTG 0.882652 -175 ATTGCGTCTGATTTCCTTTGAAATTCTATC 19 53 1 ATTTCCTTTG 0.955953 -63 GATTAATTGTATTTACTTTGAGACATATAA 20 44 0 ATTTACTTTG 0.875002 -119 ATCTTATATTGCTTTTGCTTTTCTGGA 21 8 1 ATTGCTTTTG 0.763252 -293 ********** Masking position 7 Map Score: 5.29049 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 165 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 9 TCGAATTTTTAATTACAAAAACAAAATTTA 1 39 1 AATTACAAAA 0.857326 -262 CTATGATTAGAATTACAAAAAGCTAACGTT 3 37 0 AATTACAAAA 0.857326 -27 TCCGTTATGGAATTTCTACAAGTATAAACT 5 88 0 AATTTCTACA 0.704116 -213 AAAATTATTAAACGAATGCAAG 7 3 1 AATTATTAAA 0.576615 -29 AGAAAAAGGTAATTTCAACATATAAGAAAA 8 36 1 AATTTCAACA 0.806664 -76 GAGTGCTGGAAATTTAAAAAGGGTGATTTG 10 273 1 AATTTAAAAA 0.584919 -21 TTCAGGTGAGAATTTTTAAACATAAACAAC 12 42 1 AATTTTTAAA 0.76514 -85 TGAACTTCAAAAACTCTGAAAG 12 115 0 AACTTCAAAA 0.878883 -12 AGCTGGATAGAATTTCAAAGGAAATCAGAC 19 58 0 AATTTCAAAG 0.677088 -58 AACTGCGATCAACTTTAAAAACATTTTAAG 20 12 1 AACTTTAAAA 0.742503 -151 CGAATCCCTAAATTATTAAATAACTGACGG 23 34 0 AATTATTAAA 0.576615 -71 CGGATAATAAAAATTCAAAAAATTTTAAAA 23 82 1 AAATTCAAAA 0.646194 -23 AAATTCAAAAAATTTTAAAACCA 23 92 1 AATTTTAAAA 0.851013 -13 TTCTAGAAATAACTTCTAAATCGAAATTGT 24 32 0 AACTTCTAAA 0.8054 -56 ********** Masking position 8 Map Score: 5.53358 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 120 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 10 CGAAAACAAAAATTTTATAATACGCATGTTAG 1 153 1 AATTTTATAA 0.582033 -148 CTACGAGAATAACTTTATTAGCAAAAAATACT 5 166 0 AACTTTATAC 0.963028 -135 AAACTTAGATAATTTTGTTAGCTTATTGTGGT 6 160 0 AATTTTGTAC 0.801897 -104 CCCTCTAAAAAATTTTATAACCTGTTGTCACT 6 231 1 AATTTTATAC 0.951003 -33 TGTTTCAAAAAATTTTATGAACTCCCTTATCA 10 21 0 AATTTTATAC 0.951004 -273 GAGCCCTTGAACCTTTTTGACCTCAGGGGTTA 10 159 1 ACCTTTTTAC 0.712682 -135 TAAGACGTAAACCTTTATAACCCCTGAGGTCA 10 176 0 ACCTTTATAC 0.909066 -118 TTTTCCAGAGAACTTTTTCATCACTCCCACCA 17 104 0 AACTTTTTAC 0.866005 -79 AACTGCGATCAACTTTAAAAACATTTTAAGAA 20 12 1 AACTTTAAAC 0.853712 -151 AAGAGTCCAAAAATTTATAAGCCTTACGAATT 21 98 1 AAATTTATAC 0.801177 -203 AATTTTTTGAATTTTTATTATCCGTGACAGAT 23 74 0 ATTTTTATAC 0.731984 -31 AAATTCAAAAAATTTTAAAACCA 23 92 1 AATTTTAAAC 0.812994 -13 ******** * * Masking position 10 Map Score: 6.31265 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 44 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 11 GATTATAATCGCGGGAGTGATGATTAGGGA 2 115 0 GCGGGAGTGA 0.971831 -186 TCAAAGTTAAGAGGGATGGCAAAGGTATTT 2 247 1 GAGGGATGGC 0.921975 -54 ATAGATTGTGGAGGGAATACGGGAATAAAA 5 278 1 GAGGGAATAC 0.687985 -23 GGCGGAGGCCGCGGGTTCAAATCCCGCCGA 10 98 0 GCGGGTTCAA 0.602969 -196 TCGTAGCTCAGCGGGAGAGCGCCGCCTTCG 10 131 0 GCGGGAGAGC 0.943574 -163 TGTAAGCCCGGCGGGATGGACATCTCCAAA 14 81 0 GCGGGATGGA 0.935724 -63 CATGCTGGTGGTGGGAGTGATGAAAAAGTT 17 96 1 GTGGGAGTGA 0.842203 -87 ATTGTTGGTTGCGGGAGCTAC 20 152 1 GCGGGAGCTA 0.865686 -11 TCGTTCACACGAGGGAGCACTAC 25 4 0 GAGGGAGCAC 0.94509 -213 TGGAGGAGCTGAGGGATTACGAGGTCGTTG 25 66 0 GAGGGATTAC 0.878855 -151 ********** Masking position 5 Map Score: 2.32669 Number of sites scoring better than the average of aligned sites = 485 Number in coding regions = 460 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 12 ********** No masking Map Score: -1.31284e-11 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 13 GAGGATGAGGTGAGAGGTGATGGG 8 98 1 TGAGAGGTGA 0.955227 -14 TTTAAAACCTTTTCAGGTGAGAATTTTTAA 12 31 1 TTTCAGGTGA 0.931346 -96 TCTAAAGGAGTTAGAGGTGGTTTTAA 17 167 1 TTAGAGGTGG 0.955228 -16 TCAGACGCAATTTCAGGTGGAATTCTGAAG 19 34 0 TTTCAGGTGG 0.955228 -82 TTATTGAGTTTGAGAGGTAAACACCGAAGA 19 90 0 TGAGAGGTAA 0.76746 -26 CGGAGATTCTTGTCAGGTGGTTTCAA 23 7 0 TGTCAGGTGG 0.971055 -98 ********** Masking position 5 Map Score: 0.501751 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 112 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 14 TATCGGATATTTAACTTTTGTGAAGTGTCGC 1 271 0 TTAACTTTTT 0.766306 -30 TCTACAAGTATAAACTTTTGTTCCACCATTC 5 73 0 TAAACTTTTT 0.95413 -228 CAACAGGTTATAAAATTTTTTAGAGGGTCAG 6 227 0 TAAAATTTTT 0.837344 -37 AGGGAGTTCATAAAATTTTTTGAAACATTGA 10 26 1 TAAAATTTTT 0.837344 -268 TACGAGCCCTTGAACCTTTTTGACCTCAGGG 10 156 1 TGAACCTTTT 0.848524 -138 ACCTAAGACGTAAACCTTTATAACCCCTGAG 10 180 0 TAAACCTTTT 0.928714 -114 TAGCGTTATTTAAACTTTATTGGAGAAAGGT 15 26 1 TAAACTTTAT 0.7255 -48 TTTCTGCTCATAAACCTTTCTCCAATAAAGT 15 39 0 TAAACCTTTT 0.928713 -35 TGTACTACAATGAACTCTTTTCCAGAGAACT 17 122 0 TGAACTCTTT 0.627469 -61 CGAAAAATTTTAATCTTTTTTCTGCCAAGAC 18 14 1 TAATCTTTTT 0.7255 -26 TGGTTTTAAAATTTTTTGAATTTTTAT 23 88 0 TAAAATTTTT 0.837344 -17 ********* * Masking position 3 Map Score: 6.26177 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 38 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 15 ********** No masking Map Score: -1.31284e-11 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