AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00020_aquae_reg_300.orf -o00020_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 aq_142 300 putative protein #2 frdB1 35 fumarate reductase iron-sulfur subunit #3 frdA 295 fumarate reductase flavoprotein subunit #4 purB 41 adenylosuccinate lyase #5 aq_598 99 putative protein #6 frdB2 39 fumarate reductase iron-sulfur subunit #7 lpdA 85 dihydrolipoamide dehydrogenase #8 sucC1 67 succinyl-CoA ligase beta subunit #9 icd 113 isocitrate dehydrogenase #10 aq_1515 25 putative protein #11 aq_1516 58 putative protein #12 aq_1618 43 putative protein #13 sucC2 29 succinyl-CoA ligase beta subunit #14 aq_1666 252 hypothetical protein #15 thrS 36 threonyl-tRNA synthetase #16 aco 52 aconitase #17 aq_1791 40 putative protein #18 ntrC2 209 transcriptional regulator (NtrC family) #19 sucD1 53 succinyl-CoA ligase alpha subunit Motif number 1 AGTAATCTGGCTCTCCTCTCAAGTCTTTATG 1 120 0 CTCCCTCTCA 0.933653 -181 GCCTTACCTCCCATAGGGAATTT 1 288 0 CTTCCTCCCA 0.968038 -13 GGTATATAATCGTGCCTCCCACGATTAAGGA 3 216 0 CGTCCTCCCA 0.961354 -80 CCTTCTTTCCTTTCCCTCCCTTCTGATATCC 4 13 1 TTTCCTCCCT 0.913585 -29 GAAGCTCCTCCTGAAAAGGGGTT 7 73 0 AGCCCTCCTG 0.92648 -13 TCTCCTTCCTCCTGAAACTTAATT 8 54 0 CCTCCTCCTG 0.874546 -14 CGCTCTCCTCCGAAAGTAGAGTG 9 101 0 CTCCCTCCGA 0.979609 -13 TTATGACCTCCTTGTTAGGGAAT 10 13 0 ATGCCTCCTT 0.905003 -13 ACATCCACCTCCGAAAGTAAAAAA 13 16 0 TCCCCTCCGA 0.828422 -14 TCTCCCCTCTTTTCCCGCTTTT 14 2 1 CTCCCTCTTT 0.897306 -251 GAGGGGCTTTCTCACCTCTCTACTATTAAAT 14 164 0 CTCCCTCTCT 0.961049 -89 GAGGTGAGAAAGCCCCTCCCTCCCCCCACCT 14 177 1 AGCCCTCCCT 0.979782 -76 CCTCCCTCCCCCCACCTCCCTCCACCGATTT 14 191 1 CCCCCTCCCT 0.989391 -62 CCACCGATTTTTGGCCTCCCGCCCGGGAGGC 14 212 1 TTGCCTCCCG 0.924886 -41 TATTTTAGAAAGGGCCTCCCGGGCGGGAGGC 14 225 0 AGGCCTCCCG 0.941821 -28 ACTGACCTCCTTTCAAAACAAT 16 41 0 CTGCCTCCTT 0.967562 -12 TTCCGAACCTCCGTTTCGTGTGGT 17 27 0 CGACCTCCGT 0.858035 -14 TCATCACCTCCGTTAAGAATTTA 19 3 1 ATCCCTCCGT 0.964159 -51 *** ******* Masking position 7 Map Score: 27.375 Number of sites scoring better than the average of aligned sites = 671 Number in coding regions = 571 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 2 ACTCATCTCTTTTTAATTTACCACCTAAGT 3 138 0 TTTTAATTTA 0.879822 -158 ACAAAGCTCTCTTTATTGTATTTACACTTA 3 175 1 CTTTATTGTA 0.904719 -121 TTTAATTGCCTTTAATTTTAGCATTTTGAT 7 44 0 TTTAATTTTA 0.889262 -42 ACTTGATTTATTTTAATTAAAATAC 8 6 1 ATTTATTTTA 0.95465 -62 TAAAACAACATTTTATTGTATTTTAATTAA 8 23 0 TTTTATTGTA 0.920075 -45 CCTCCTGAAACTTAATTTTAAAACAACATT 8 41 0 CTTAATTTTA 0.868841 -27 TTCGGACTCTTTTTGTTTTATAAGCTCGGA 11 31 1 TTTTGTTTTA 0.784903 -28 ACAAGTTATATTTTATTGTAATATTATTAT 14 61 1 TTTTATTGTA 0.920075 -192 CCTCTCTACTATTAAATTTATGCAATTGAA 14 151 0 ATTAAATTTA 0.664193 -102 CGCTATTTATTTTAGAAAGGGCCT 14 239 0 ATTTATTTTA 0.95465 -14 AGAGATTTATTTTAGGCTTAGCTT 15 23 0 ATTTATTTTA 0.95465 -14 AATTTTAAAACTTCATTTTAAAATTAGAAA 16 14 0 CTTCATTTTA 0.795321 -39 TGGTGGACTAATATATTTTA 17 1 0 ATATATTTTA 0.674465 -40 TTATTTTTAATTTAGCTTTTCAAG 18 196 0 TTTTAATTTA 0.879822 -14 ********** Masking position 10 Map Score: 14.5365 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 47 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 3 AAGGTTTAGTAATAGAATTTAAAAACGGGGAGA 1 163 1 AAAGTTTAAA 0.792167 -138 AGATTTACACAATAGACGTTTATGATCCGGAAG 1 193 1 AAAGGTTTAT 0.513907 -108 ATTAAGTATAAAGGAAAGTTTAAAGTACTAGAA 1 253 0 AAGAGTTTAA 0.77471 -48 AGTCTGGGGGATAAATTTTTCAAACGGAATT 2 9 0 ATAATTTCAA 0.808885 -27 AGTAGTATCAAAGAAATTATTAATCCGTAGAGC 3 82 0 AAAATATTAA 0.864444 -214 AACAATATTTTAAGATACAGCGT 3 283 0 AAAATTTTAA 0.954901 -13 ACCGAAAGGGATAAAATTTTTAATCGTGGGAG 5 10 0 ATAATTTTAA 0.893037 -90 CTCCTTATAGATTTTTTAAAAATAGTATT 5 81 0 ATGATTTTAA 0.838312 -19 AAGGCAAATTATTAGTATATCAAAATGCTAAAA 7 26 1 ATAGTATCAA 0.570053 -60 CTCCTCCTGAAAAGGGGTTTTAATTGCCTTTAA 7 59 0 AAGGTTTTAA 0.912982 -27 TTAATTTTAAAACAACATTTTATTGTATTTTAA 8 27 0 AAAATTTTAT 0.749774 -41 ACAAAAATCAAAAAGTGTTTTAAATTAACTTGA 9 41 1 AAAGTTTTAA 0.95645 -73 GTATTATATTATTAGTTTTTAAAGCTGGTGAGG 12 18 0 ATAGTTTAAA 0.66145 -26 GACTACTATCATAAGAGGATTAATAAAAGCGGG 14 24 0 ATAGGATTAA 0.535452 -229 GAGAACTTGCAAAAAAATTTCAATTGCATAAAT 14 133 1 AAAATTTCAA 0.891846 -120 CTAATTTTAAAATGAAGTTTTAAAATTGTTTTG 16 17 1 AAGATTTTAA 0.910033 -36 GAACTTTGTGAAAAAGGTTTTAAACAGTGAAAA 18 135 1 AAAATTTTAA 0.954893 -75 CACCTCCGTTAAGAATTTATTAAATAGGCGCTG 19 15 1 AAAATATTAA 0.864448 -39 ** ** ****** Masking position 10 Map Score: 14.6542 Number of sites scoring better than the average of aligned sites = 575 Number in coding regions = 486 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 4 ATACCTCTCGAAAAGGAAAAGTATGAGATAAAG 1 54 1 AAAAAAAAGA 0.924648 -247 TTTAGTAATAGAATTTAAAAACGGGGAGATTTA 1 167 1 GAATAAAAAG 0.825479 -134 CTTAGGTGGTAAATTAAAAAGAGATGAGTGAAG 3 139 1 AAATAAAAGG 0.951943 -157 GGATAAGTGTAAATACAATAAAGAGAGCTTTGT 3 175 0 AAATAATAAG 0.864851 -121 AGAAGGGAGGGAAAGGAAAGAAGGGA 4 4 0 GAAAAAAGAG 0.713291 -38 CTATTTTTAAAAAATCTATAAGGAG 5 85 1 AAAATATAAG 0.583728 -15 TCAAAATGCTAAAATTAAAGGCAATTAAAACCC 7 45 1 AAAAAAAGGA 0.806637 -41 ATTTTAATTAAAATACAATAAAATGTTGTTTTA 8 20 1 AAATAATAAA 0.719273 -48 TTTATAACAAAAATCAAAAAGTGTTTTAAATTA 9 35 1 AAATAAAAGG 0.951943 -79 ACACTTCTTCAAAATGAATAAAATTACACTCTA 9 75 1 AAAAAATAAA 0.798557 -39 CCGAGCTTATAAAACAAAAAGAGTCCGAAAGAA 11 27 0 AAAAAAAAGG 0.968402 -32 ACCAGCTTTAAAAACTAATAATATAATACGAG 12 22 1 AAAAAATAAA 0.798557 -22 ATCCACCTCCGAAAGTAAAAAAATGTT 13 5 0 GAAAAAAAAA 0.745553 -25 TCAATTGCATAAATTTAATAGTAGAGAGGTGAG 14 152 1 AAATAATAGA 0.836765 -101 GGCCCTTTCTAAAATAAATAGCG 14 240 1 AAAAAATAGG 0.951943 -13 AAGAGCGCAGGAATGAAAAAGGGGCTTGACGGA 18 81 0 GAATAAAAGG 0.904427 -129 TAGGCTTTGTAAAAGCAAAAGAGCGCAGGAATG 18 99 0 AAAAAAAAGG 0.968402 -111 TTAAACAGTGAAAAGGTAAGGCGCTTCGTTCCG 18 154 1 AAAATAAGGG 0.596065 -56 **** ***** * Masking position 8 Map Score: 18.4875 Number of sites scoring better than the average of aligned sites = 840 Number in coding regions = 749 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 5 AAAAATACCTCTCGAAAAGGAAAAGTATGA 1 50 1 CTCGAAAAGG 0.967152 -251 AAAGGAATATCCTGAAACGGGAACGATGTT 1 83 1 CCTGAAACGG 0.983531 -218 TTAAACATTAACCGAAAGGGATAAAATTTT 5 23 0 ACCGAAAGGG 0.879343 -77 TAATAATTTGCCTTAAAAGGAGGAAGCGA 7 10 0 CCTTAAAAGG 0.896297 -76 GAAGCTCCTCCTGAAAAGGGGTTTTAATT 7 67 0 CCTGAAAAGG 0.988368 -19 TAGTCCACCACACGAAACGGAGGTTCGGAA 17 21 1 CACGAAACGG 0.918281 -20 GGTTTTAAACAGTGAAAAGGTAAGGCGCTT 18 150 1 AGTGAAAAGG 0.852409 -60 GAAGAAAGTTCTTGAAAAGCTAAATTAAAA 18 186 1 CTTGAAAAGC 0.832558 -24 ********** Masking position 5 Map Score: 5.26215 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 256 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 6 CCTCTCGAAAAGGAAAAGTATGAGATAAAGG 1 57 1 AGGAAAGTAT 0.825476 -244 TATGAGATAAAGGAATATCCTGAAACGGGAA 1 75 1 AGGATATCCT 0.734403 -226 TCACAGAATTAGGAAAATACTTTTTGCTACG 3 28 1 AGGAAATACT 0.963744 -268 CCCACGATTAAGGAAAAAACAAGGATAAGTG 3 199 0 AGGAAAAACA 0.868917 -97 CCTGTTTACAAGGTATATAATCGTGCCTCCC 3 227 0 AGGATATAAT 0.919211 -69 CCTTGTAAACAGGCAAATAAAGAACAGCAGG 3 245 1 AGGAAATAAA 0.876365 -51 ATTAACCGAAAGGGATAAAATTTTTAATCGT 5 16 0 AGGATAAAAT 0.919218 -84 CCTCCTTTTAAGGCAAATTATTAGTATATCA 7 17 1 AGGAAATTAT 0.928242 -69 AAATCTCTAGAGGTAAAATCTTTAAGT 9 7 0 AGGAAAATCT 0.923609 -107 CACCTCCGAAAGTAAAAAAATGTT 13 4 0 AGTAAAAAAT 0.692391 -26 CCCGGGCGGGAGGCCAAAAATCGGTGGAGGG 14 208 0 AGGCAAAAAT 0.843257 -45 *** ******* Masking position 7 Map Score: 4.42726 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 318 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 ACAAGCTCCTGCTTAATTTTTCTTGCCACT 1 224 0 GCTTAATTTT 0.91919 -77 TAGTCTGGGGGATAAATTTTTCAAACGGAA 2 13 0 GATAAATTTT 0.904022 -23 AACCGAAAGGGATAAAATTTTTAATCGTGG 5 14 0 GATAAAATTT 0.544796 -86 ACTTGATTTATTTTAATTAAAATA 8 5 1 GATTTATTTT 0.95164 -63 TCCTCCTGAAACTTAATTTTAAAACAACAT 8 42 0 ACTTAATTTT 0.788491 -26 AGTGTAATTTTATTCATTTTGAAGAAGTGT 9 75 0 TATTCATTTT 0.75182 -39 TCATAAACAAGTTATATTTTATTGTAATAT 14 55 1 GTTATATTTT 0.675286 -198 CGCTATTTATTTTAGAAAGGGCC 14 240 0 TATTTATTTT 0.818234 -13 AGAGATTTATTTTAGGCTTAGCT 15 24 0 GATTTATTTT 0.95164 -13 CAATTTTAAAACTTCATTTTAAAATTAGAA 16 15 0 ACTTCATTTT 0.755537 -38 GTGGTGGACTAATATATTTTA 17 2 0 AATATATTTT 0.789563 -39 ********** Masking position 6 Map Score: 3.00926 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 71 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 CTTTTCGAGAGGTATTTTTAATAACAGCTCCATC 1 35 0 GATTTTATAA 0.9561 -266 CTATAGAAGGGGAAGGTTTAGTAATAGAATTTAA 1 151 1 GAGGTTATAA 0.932617 -150 CCTCCCATAGGGAATTTTTATTAAGTATAAAGGA 1 271 0 GATTTTATAA 0.956099 -30 TTTACCTCTAGAGATTTATAACAAAAATCAAAAA 9 21 1 GATTTTACAA 0.870153 -93 ATCCTCTTATGATAGTAGTCATAAACAAGTTATA 14 37 1 GAGTATCTAA 0.862711 -216 TCAAACCATTGACAGTTATAATAATATTACAATA 14 74 0 GAGTTTATAA 0.978252 -179 AAATTTTTTTGCAAGTTCTCCTAACTTCTTCATT 14 119 0 GAGTTTCTAA 0.968019 -134 * **** ** *** Masking position 4 Map Score: 0.794947 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 = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 AAATTGGGTTTATTCGTAGCAAAAAGTATT 3 43 0 TATTCGTAGC 0.885678 -253 GTTTTTTCCTTAATCGTGGGAGGCACGATT 3 210 1 TAATCGTGGG 0.987305 -86 ACAAGGTATATAATCGTGCCTCCCACGATT 3 221 0 TAATCGTGCC 0.966681 -75 ATAAAATTTTTAATCGTGGGAG 5 3 0 TAATCGTGGG 0.987305 -97 ********** Masking position 4 Map Score: 0.0984175 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 12 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 ********** No masking Map Score: 2.94408e-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: 2.94408e-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: 2.94408e-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