AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00710_aquae_reg_300.orf -o00710_aquae_300.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 talC 28 transaldolase #2 hisS1 81 histidyl-tRNA synthetase #3 aspC4 80 aminotransferase (AspC family) #4 timA 300 triose phophate isomerase #5 aspC3 31 aminotransferase (AspC family) #6 aq_1137 29 putative protein #7 fba 300 fructose-1,6-bisphosphate aldolase class II #8 aq_1666 252 hypothetical protein #9 thrS 36 threonyl-tRNA synthetase #10 aq_1763 300 hypothetical protein #11 tktA 296 transketolase #12 aco 52 aconitase #13 aq_1791 40 putative protein #14 ntrC2 209 transcriptional regulator (NtrC family) #15 aspC1 260 aspartate aminotransferase #16 pepA 26 leucine aminopeptidase Motif number 1 TCCCATTTTTGGAGGTAAAGGAA 1 16 1 GGAGGTAAAG 0.871325 -13 GAAAATTTACGGAGGTACGGGAAA 2 5 0 GGAGGTACGG 0.981187 -77 AAACTTTAAAGGAGGTAGCGGA 3 69 1 GGAGGTAGCG 0.985751 -12 CTTTGACCGCGTAGGGGGAGAGTTTTGTAA 4 218 1 GTAGGGGGAG 0.828856 -83 TGAAAATTAAGGAGGTGGGAGCCATGCCTA 4 260 0 GGAGGTGGGA 0.990192 -41 GGAGGTGGGGGGAGGGAGGGGCTTTCTCAC 8 180 0 GGAGGGAGGG 0.993836 -73 ATCGGTGGAGGGAGGTGGGGGGAGGGAGGG 8 190 0 GGAGGTGGGG 0.997858 -63 GTTATGAAGGCGAGGTGGGGATTTCCTTCA 10 45 1 CGAGGTGGGG 0.986283 -256 AAAATTTTAAGGAGGTGGAAAATGTTACCG 10 140 0 GGAGGTGGAA 0.972791 -161 AACCCAAAAGGGAGGTGTGAGAATGGCAGA 10 275 1 GGAGGTGTGA 0.869276 -26 CTACGGATCCCGAGGTTGCGGGTTCGACTC 11 214 0 CGAGGTTGCG 0.771375 -83 CACACGAAACGGAGGTTCGGAA 13 29 1 GGAGGTTCGG 0.942796 -12 GCTGGCACTGGGAGAGAGGGCAAAAGAGCC 15 19 0 GGAGAGAGGG 0.961235 -242 AGAAGCTCGAGGAGATAGAGAAGGGTATCT 15 110 0 GGAGATAGAG 0.940521 -151 GATTGGAGTGGGAGAGAGGATAAGGAAGAT 15 199 0 GGAGAGAGGA 0.843101 -62 TAAAAAGGGAGGAGGTGGAGCCATGATTGG 15 223 0 GGAGGTGGAG 0.993975 -38 ********** Masking position 3 Map Score: 31.7372 Number of sites scoring better than the average of aligned sites = 365 Number in coding regions = 288 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 2 TTTTCGGACGAATAATTTTAACACAATAAGT 2 30 1 AATAATTTAA 0.936787 -52 ATTTTAACACAATAAGTTTACCACAAAAAAC 2 44 1 AATAATTTAC 0.811425 -38 TTTACCACAAAAAACCTTTAATATTTATCTT 2 60 1 AAAACTTTAA 0.902846 -22 ATAATCTTCTAAAAACTTTAAAGGAGGTAGC 3 57 1 AAAAATTTAA 0.968771 -24 AATCAAAGATAAAAATTTTACAAATGTATGC 7 126 0 AAAAATTTAC 0.902657 -175 TCATGATGCAATAAACTTTAATAGACTGAAA 7 156 0 ATAAATTTAA 0.752303 -145 AGAACTTGCAAAAAAATTTCAATTGCATAAA 8 134 1 AAAAATTTCA 0.834537 -119 ATTTCAATTGCATAAATTTAATAGTAGAGAG 8 149 1 CATAATTTAA 0.824035 -104 AACAACGGGAAAAACGTTTAAATCCCTCATC 10 92 1 AAAACTTTAA 0.902846 -209 TATCTGTAAACAAAATTTTAAGGAGGTGGAA 10 150 0 CAAAATTTAA 0.909158 -151 TTAAAAATAAAAAAATTTTTACCTAAAGGGG 11 45 0 AAAAATTTTA 0.765614 -252 GTACCAAGTTAATAATTTTAATCCCTTGCCC 11 275 1 AATAATTTAA 0.936787 -22 CTCCTTTCAAAACAATTTTAAAACTTCATTT 12 26 0 AACAATTTAA 0.869743 -27 CTTTTTAATTTAAAATTTTAAGGAA 15 246 1 TAAAATTTAA 0.759524 -15 ***** ***** Masking position 4 Map Score: 12.8627 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 85 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 3 AAGCTTCAAAGGTAGCCCTCATTATACGCT 4 47 0 GGTAGCCCTC 0.97672 -254 TTAAGGAGGTGGGAGCCATGCCTATGTACG 4 254 0 GGGAGCCATG 0.979851 -47 TAGGAACCCTGCGCGCCTATG 7 2 1 AGGAACCCTG 0.898334 -299 TCAATTGCCAAGGAGCCAAGAGGCATTGTA 7 239 1 AGGAGCCAAG 0.918851 -62 CAAGAGGCATTGTAGCCCTCTAAGGAGCTA 7 255 1 TGTAGCCCTC 0.949132 -46 TCGAGTCCCGGGCAGCCCACCACCTTTCTA 11 90 0 GGCAGCCCAC 0.959685 -207 CTATTGAGCTAGCAGCCCTCGTCTGAAGAA 11 156 1 AGCAGCCCTC 0.976391 -141 AGGGAGGAGGTGGAGCCATGATTGGAGTGG 15 218 0 TGGAGCCATG 0.955724 -43 ********** Masking position 4 Map Score: 6.22477 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 140 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 4 CTCATTATACGCTCTTTTGGACATGCAACC 4 30 0 GCTCTTTTGG 0.971894 -271 TCTCCCCTCTTTTCCCGCTTTTATT 8 6 1 CCTCTTTTCC 0.968927 -247 TTCTCACACCTCCCTTTTGGGTTTTCTCTA 10 268 0 TCCCTTTTGG 0.932457 -33 TAAAAACTCCCCTTTTCCTTTTCTTTTG 11 9 1 CCCCTTTTCC 0.980182 -288 TTTGGAATACCCCCTTTAGGTAAAAATTTT 11 35 1 CCCCTTTAGG 0.928111 -262 TTCCGTCAAGCCCCTTTTTCATTCCTGCGC 14 80 1 CCCCTTTTTC 0.947735 -130 TCATTCCTGCGCTCTTTTGCTTTTACAAAG 14 98 1 GCTCTTTTGC 0.982535 -112 CGCCTGCGGGCTCTTTTGCCCTCTCTCCC 15 10 1 GCTCTTTTGC 0.982535 -251 ********** Masking position 5 Map Score: 8.53183 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 118 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 TATTTTAGGCTTAGCTTATCTTTTTCAAT 9 10 0 TTAGCTTATC 0.79368 -27 TTCCCCGACGTTTGCCTTTCTATGAGTTAG 10 192 1 TTTGCCTTTC 0.940608 -109 AAACTCCCCTTTTCCTTTTCTTTTGGAATA 11 14 1 TTTCCTTTTC 0.913702 -283 ATTTGCGGAGTTATCCTTTCAATATTCGGA 14 25 1 TTATCCTTTC 0.941716 -185 ACGAAGCGCCTTACCTTTTCACTGTTTAAA 14 153 0 TTACCTTTTC 0.960534 -57 TATTTTTAATTTAGCTTTTCAAGAACTTTC 14 189 0 TTAGCTTTTC 0.948795 -21 GCGGGCTCTTTTGCCCTCTCTCCCAGTGCC 15 16 1 TTGCCCTCTC 0.908263 -245 TCCAAGGACATTCCCCTTTCTTCTCTGATC 15 172 1 TTCCCCTTTC 0.9459 -89 CTGATCTTCCTTATCCTCTCTCCCACTCCA 15 196 1 TTATCCTCTC 0.901473 -65 ********** Masking position 7 Map Score: 6.033 Number of sites scoring better than the average of aligned sites = 469 Number in coding regions = 440 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 6 TCAGACATAGGCGCGCAGGGTTCCTA 7 5 0 GCGGCGGGTT 0.89043 -296 AGAACTTGGGGTTAGCGGAAATTAACATTCGT 7 84 0 GTTGCGAAAT 0.774023 -217 GTATGCTCAAGTTTGCAGAACTTGGGGTTAGC 7 100 0 GTTGCGAACT 0.912672 -201 TGCTTTGATTGTGTGATGGATTGATATCATGA 7 181 0 GTGGAGGATT 0.886884 -120 GAATGAAGAAGTTAGGAGAACTTGCAAAAAAA 8 118 1 GTTGGGAACT 0.843406 -135 GAGGTGGGGGGAGGGAGGGGCTTTCTCACCTC 8 177 0 GAGGAGGGCT 0.90604 -76 TCAATAGGCAGAGCGGCGGACTCTTAATCCGC 11 131 0 GAGGGGGACT 0.977654 -166 CATTGGCCGGGCTGGCGGGAGTCGAACCCGCA 11 196 1 GCTGCGGAGT 0.899204 -101 CAACTGGATAGAGCGCGGGACTACGGATCCCG 11 232 0 GAGGCGGACT 0.988358 -65 CCTCCGTTTCGTGTGGTGGACTAATATATTTT 13 12 0 GTGGGGGACT 0.981785 -29 TGAAAAAGGGGCTTGACGGAATTATCGGTAGT 14 69 0 GCTGAGGAAT 0.832901 -141 AAAAGCAAAAGAGCGCAGGAATGAAAAAGGGG 14 90 0 GAGGCGGAAT 0.965306 -120 *** ** ***** Masking position 12 Map Score: 8.4292 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 185 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 TCTCCTCCTTTATTTAAGATAAGTGTAACTCT 3 14 1 TATAAGATAA 0.858099 -67 CTTTAAAGTTTTTAGAAGATTATATCAGTATG 3 48 0 TTTAAGATTA 0.835769 -33 ATTCTACTTAAATTGAAAATTAAGGAGGTGGG 4 271 0 AATAAAATTA 0.827308 -30 CGCGCCTATGTCTGAAAAATAACGCTTTATCA 7 22 1 TCTAAAATAA 0.779271 -279 ATAGACTGAAAATCAAAGATAAAAATTTTACA 7 135 0 AATAAGATAA 0.780968 -166 TCTAAGGAGCTATTCAAAATTATACCATATAA 7 273 1 TATAAAATTA 0.890411 -28 CGGGAGGCCCTTTCTAAAATAAATAGCG 8 235 1 TTTAAAATAA 0.90615 -18 TTATCGTTCTTTTATAAAATTATATACCTAAC 10 217 0 TTTAAAATTA 0.890413 -84 AACAGAATCCTTTTAAAAATAAAAAAATTTTT 11 56 0 TTTAAAATAA 0.90615 -241 TTAAAACTTCATTTTAAAATTAGAAACCT 12 8 0 ATTAAAATTA 0.827308 -45 TGAAAAGCTAAATTAAAAATAA 14 198 1 AATAAAATAA 0.850587 -12 *** ******* Masking position 6 Map Score: 5.44862 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 45 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 CTAAAAACTTTAAAGGAGGTAGCGGA 3 65 1 TAAAGGAGGT 0.890868 -16 CCAAAGACGACGAAGAAGCTTCAAAGGTAG 4 62 0 CGAAGAAGCT 0.945036 -239 GAACAGAAAGTTAAGAAATTAATTGAAGAA 4 165 0 TTAAGAAATT 0.65626 -136 GTCAAAGATCCAAAGAAATTAAAAGAAATA 4 195 0 CAAAGAAATT 0.64223 -106 AAATTGAAAATTAAGGAGGTGGGAGCCATG 4 264 0 TTAAGGAGGT 0.909561 -37 TTGTAGCCCTCTAAGGAGCTATTCAAAATT 7 264 1 CTAAGGAGCT 0.935194 -37 CTACGGAGAATGAAGAAGTTAGGAGAACTT 8 111 1 TGAAGAAGTT 0.852981 -142 AAACAAAATTTTAAGGAGGTGGAAAATGTT 10 144 0 TTAAGGAGGT 0.909561 -157 AATAAAGCTTTTAAGAAGCTTTATCGTTCT 10 239 0 TTAAGAAGCT 0.938053 -62 GCAAATCACGTAAAGAAACT 14 1 0 TAAAGAAACT 0.798566 -209 CGCTTCGTTCCGAAGAAAGTTCTTGAAAAG 14 175 1 CGAAGAAAGT 0.817424 -35 GGCATTTCCACAAAGAAGCTCGAGGAGATA 15 123 0 CAAAGAAGCT 0.934375 -138 ********** Masking position 4 Map Score: 10.5533 Number of sites scoring better than the average of aligned sites = 498 Number in coding regions = 433 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 9 GGATCTTTGACCGCGTAGGGGGAGAGTTTT 4 214 1 CCGCGTAGGG 0.895698 -87 TCAGACATAGGCGCGCAGGGTTCCTA 7 7 0 GCGCGCAGGG 0.985023 -294 GAGGTGGGGGGAGGGAGGGGCTTTCTCACC 8 179 0 GAGGGAGGGG 0.850528 -74 AAAGGGCCTCCCGGGCGGGAGGCCAAAAAT 8 218 0 CCGGGCGGGA 0.984251 -35 GGTTCGAGTCCCGGGCAGCCCACCACCTTT 11 93 0 CCGGGCAGCC 0.861241 -204 CATTGGCCGGGCTGGCGGGAGTCGAACCCG 11 196 1 GCTGGCGGGA 0.934383 -101 CAACTGGATAGAGCGCGGGACTACGGATCC 11 234 0 GAGCGCGGGA 0.980911 -63 AAAAGCAAAAGAGCGCAGGAATGAAAAAGG 14 92 0 GAGCGCAGGA 0.975949 -118 GGGCAAAAGAGCCCGCAGGCG 15 2 0 GCCCGCAGGC 0.658858 -259 ********** Masking position 5 Map Score: 5.26597 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 123 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 10 AAAGATAAATATTAAAGGTTTTTTGTG 2 65 0 AATATTAAAG 0.558521 -17 GTGAGTTTTATATATTAAATCATTAATTT 6 11 1 TATATTAAAT 0.779039 -19 AGGTTAGGTGTCTAATAAGTTATTGATAAA 7 47 0 TCTAATAAGT 0.84461 -254 TGATTTTCAGTCTATTAAAGTTTATTGCAT 7 152 1 TCTATTAAAG 0.937923 -149 AGCGGATTGGTCTAATAAGTGATGCTTTGA 7 205 0 TCTAATAAGT 0.84461 -96 TCACCTCTCTACTATTAAATTTATGCAATT 8 154 0 ACTATTAAAT 0.849464 -99 CCTCATCAAATCTATTAAATCTCTCGGTAA 10 116 1 TCTATTAAAT 0.939078 -185 TTGGGTTTTCTCTAATAAAGCTTTTAAGAA 10 252 0 TCTAATAAAG 0.904013 -49 ********** Masking position 4 Map Score: 2.55048 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 60 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 GGAGGTGGGAGCCATGCCTATGTACGTCATG 4 249 0 GCATGCCTAT 0.990803 -52 TTAGAGGGCTACAATGCCTCTTGGCTCCTTG 7 247 0 ACATGCCTCT 0.930119 -54 AAAAAGATAAGCTAAGCCTAAAATAAATCTC 9 15 1 GCAAGCCTAA 0.934402 -22 AGAGTCCGCCGCTCTGCCTATTGAGCTAGCA 11 139 1 GCCTGCCTAT 0.975242 -158 TTTTGCTTTTACAAAGCCTATCCGAACTTTG 14 112 1 ACAAGCCTAT 0.951243 -98 CTTCTTTGTGGAAATGCCTATAGCCTTAGCG 15 135 1 GAATGCCTAT 0.943393 -126 ** ******** Masking position 9 Map Score: 1.93985 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 17 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 12 TTTCCCGTACCTCCGTAAATTT 2 1 1 TTTCCCGCCT 0.892052 -81 CTTTCTCCTCCTTTATTTAAGATA 3 3 1 TTCTCCTTTT 0.728698 -78 TGCTGACCAGGTTTCCGTGGTTGCATGTCCAA 4 12 1 GTTTCCGGTT 0.884584 -289 TCTCCCCTCTTTTCCCGCTTTTATTAATCCTC 8 11 1 TTTCCCGTTT 0.936819 -242 AACTTCTTCATTCTCCGTAGTTTTCAAACCAT 8 99 0 TTCTCCGGTT 0.964026 -154 TTTTTGCAAGTTCTCCTAACTTCTTCATTCTC 8 116 0 TTCTCCTCTT 0.888254 -137 TTTAAACGTTTTTCCCGTTGTTGTGTCGACCG 10 82 0 TTTCCCGGTT 0.981934 -219 TTTAATTTGTTTCCCCGACGTTTGCCTTTCTA 10 182 1 TTCCCCGGTT 0.986476 -119 AAACTCCCCTTTTCCTTTTCTTTTGGAATACC 11 14 1 TTTCCTTCTT 0.55953 -283 CGGGACTACGGATCCCGAGGTTGCGGGTTCGA 11 217 0 GATCCCGGTT 0.72607 -80 TCCAAGGACATTCCCCTTTCTTCTCTGATCTT 15 172 1 TTCCCCTCTT 0.955821 -89 ******* *** Masking position 12 Map Score: 5.87005 Number of sites scoring better than the average of aligned sites = 521 Number in coding regions = 477 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 13 TTCATAACCTGGGTTTATCCTACAGACGAGA 10 22 0 GGGTTTTCCT 0.97474 -279 AAGGCGAGGTGGGGATTTCCTTCACCGTCAA 10 51 1 GGGGATTCCT 0.988304 -250 TTACCTAAAGGGGGTATTCCAAAAGAAAAGG 11 27 0 GGGGTATCCA 0.919496 -270 CGTGATTTGCGGAGTTATCCTTTCAATATTC 14 21 1 GGAGTTTCCT 0.932311 -189 AGATAGAGAAGGGTATCTCCAGACCTTGTGA 15 97 0 GGGTATTCCA 0.95487 -164 GAGAAGAAAGGGGAATGTCCTTGGAGGAGTT 15 166 0 GGGAATTCCT 0.9562 -95 ****** **** Masking position 8 Map Score: 2.61956 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 121 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 14 ********** No masking Map Score: -3.31523e-13 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 15 ********** No masking Map Score: -3.31523e-13 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