AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00710_aquae_reg_100.orf -o00710_aquae_100.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 tktA 296 transketolase #10 aco 52 aconitase #11 aq_1791 40 putative protein #12 ntrC2 209 transcriptional regulator (NtrC family) #13 aspC1 260 aspartate aminotransferase #14 pepA 26 leucine aminopeptidase Motif number 1 TTCCTTTACCTCCAAAAATGGGA 1 16 0 CTTTACCTCC 0.872821 -13 TTTCCCGTACCTCCGTAAATTTTC 2 5 1 CCGTACCTCC 0.989568 -77 TCCGCTACCTCCTTTAAAGTTT 3 69 0 CGCTACCTCC 0.987546 -12 TTACAAAACTCTCCCCCTACGCGGTCAAAG 4 218 0 CTCCCCCTAC 0.801704 -83 TAGGCATGGCTCCCACCTCCTTAATTTTCA 4 260 1 TCCCACCTCC 0.976772 -41 GTGAGAAAGCCCCTCCCTCCCCCCACCTCC 8 180 1 CCCTCCCTCC 0.996354 -73 CCCTCCCTCCCCCCACCTCCCTCCACCGAT 8 190 1 CCCCACCTCC 0.996707 -63 CCGATTTTTGGCCTCCCGCCCGGGAGGCCC 8 215 1 GCCTCCCGCC 0.925819 -38 GTCCCGGGCAGCCCACCACCTTTCTATAAA 9 86 0 GCCCACCACC 0.90315 -211 TTCCGAACCTCCGTTTCGTGTG 11 29 0 CCGAACCTCC 0.930302 -12 GGCTCTTTTGCCCTCTCTCCCAGTGCCAGC 13 19 1 CCCTCTCTCC 0.984737 -242 AGATAGAGAAGGGTATCTCCAGACCTTGTG 13 98 0 GGGTATCTCC 0.625549 -163 AGATACCCTTCTCTATCTCCTCGAGCTTCT 13 110 1 CTCTATCTCC 0.95759 -151 ATCTTCCTTATCCTCTCTCCCACTCCAATC 13 199 1 TCCTCTCTCC 0.89964 -62 CCAATCATGGCTCCACCTCCTCCCTTTTTA 13 223 1 CTCCACCTCC 0.988636 -38 ********** Masking position 7 Map Score: 25.3406 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 301 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 2 ACTTATTGTGTTAAAATTATTCGTCCGAAAA 2 30 0 TTAAAATTTT 0.970825 -52 GTTTTTTGTGGTAAACTTATTGTGTTAAAAT 2 44 0 GTAAACTTTT 0.812966 -38 AAGATAAATATTAAAGGTTTTTTGTGGTAAA 2 60 0 TTAAAGGTTT 0.781561 -22 GCTACCTCCTTTAAAGTTTTTAGAAGATTAT 3 57 0 TTAAAGTTTT 0.953835 -24 GCATACATTTGTAAAATTTTTATCTTTGATT 7 126 1 GTAAAATTTT 0.948976 -175 TTTCAGTCTATTAAAGTTTATTGCATCATGA 7 156 1 TTAAAGTTAT 0.704669 -145 ATATTTTATTGTAATATTATTATAACTGTCA 8 68 1 GTAATATTTT 0.68303 -185 ATTTATGCAATTGAAATTTTTTTGCAAGTTC 8 135 0 TTGAAATTTT 0.850978 -118 CCCCTTTAGGTAAAAATTTTTTTATTTTTAA 9 45 1 TAAAAATTTT 0.793568 -252 GGGCAAGGGATTAAAATTATTAACTTGGTAC 9 275 0 TTAAAATTTT 0.970825 -22 AAATGAAGTTTTAAAATTGTTTTGAAAGGAG 10 26 1 TTAAAATTTT 0.970825 -27 CCTTTTTAATTTAAAATTTTAAGGAA 13 245 1 TTAAAATTTA 0.792482 -16 ******** ** Masking position 4 Map Score: 9.46641 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 127 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 GCCCCTCCCTCCCCCCACCTCCCTCCACCG 8 188 1 CCCCCCACCT 0.952985 -65 CCCCCCACCTCCCTCCACCGATTTTTGGCC 8 198 1 CCCTCCACCG 0.952311 -55 GGCCTCCCGCCCGGGAGGCCCTTTCTAAAA 8 224 1 CCGGGAGGCC 0.922935 -29 GGTTCGAGTCCCGGGCAGCCCACCACCTTT 9 93 0 CCGGGCAGCC 0.97798 -204 GGGACTCGAACCCGGAACCTGCGGATTAAG 9 111 1 CCCGGAACCT 0.971489 -186 GGGTTCGACTCCCGCCAGCCCGGCCAATGT 9 195 0 CCCGCCAGCC 0.994879 -102 GGGAGTCGAACCCGCAACCTCGGGATCCGT 9 212 1 CCCGCAACCT 0.987146 -85 ACCGATAATTCCGTCAAGCCCCTTTTTCAT 12 72 1 CCGTCAAGCC 0.925159 -138 GGCAAAAGAGCCCGCAGGCG 13 1 0 CCCGCAGGCG 0.96476 -260 TCTCCCAGTGCCAGCCACCTGTAATCCACG 13 34 1 CCAGCCACCT 0.940779 -227 ********** Masking position 2 Map Score: 10.9058 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 161 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 TCTAAAAACTTTAAAGGAGGTAGCGGA 3 64 1 TTAAAGGAGG 0.668744 -17 GGTTGCATGTCCAAAAGAGCGTATAATGAG 4 30 1 CCAAAAGAGC 0.936441 -271 CGTATTTGAAGCCAAAGACGACGAAGAAGC 4 73 0 GCCAAAGACG 0.740926 -228 TTATTCAATTGCCAAGGAGCCAAGAGGCAT 7 235 1 GCCAAGGAGC 0.931656 -66 ATTGTAGCCCTCTAAGGAGCTATTCAAAAT 7 263 1 TCTAAGGAGC 0.764034 -38 AATAAAAGCGGGAAAAGAGGGGAGA 8 6 0 GGAAAAGAGG 0.96746 -247 ATGACTACTATCATAAGAGGATTAATAAAA 8 29 0 TCATAAGAGG 0.749022 -224 CAAAAGAAAAGGAAAAGGGGAGTTTTTA 9 9 0 GGAAAAGGGG 0.937535 -288 AAAATTTTTACCTAAAGGGGGTATTCCAAA 9 35 0 CCTAAAGGGG 0.744388 -262 AAAATTGTTTTGAAAGGAGGTCAGT 10 38 1 TGAAAGGAGG 0.889147 -15 GCGCAGGAATGAAAAAGGGGCTTGACGGAA 12 80 0 GAAAAAGGGG 0.790693 -130 CTTTGTAAAAGCAAAAGAGCGCAGGAATGA 12 98 0 GCAAAAGAGC 0.979745 -112 GGGAGAGAGGGCAAAAGAGCCCGCAGGCG 13 10 0 GCAAAAGAGC 0.979745 -251 ********** Masking position 5 Map Score: 9.1519 Number of sites scoring better than the average of aligned sites = 710 Number in coding regions = 639 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 5 TAGGAACCCTGCGCGCCTATGTCTGA 7 5 1 AACCCGCGCC 0.986541 -296 TCATGATATCAATCCATCACACAATCAAAGCA 7 181 1 AATCCTCACC 0.956694 -120 GAGGTGAGAAAGCCCCTCCCTCCCCCCACCTC 8 177 1 AGCCCTCCCC 0.96472 -76 AGTCCCGGGCAGCCCACCACCTTTCTATAAAC 9 85 0 AGCCCCCACT 0.877842 -212 GCGGATTAAGAGTCCGCCGCTCTGCCTATTGA 9 131 1 AGTCCCCGCC 0.995621 -166 CGGGATCCGTAGTCCCGCGCTCTATCCAGTTG 9 232 1 AGTCCGCGCC 0.995621 -65 TAATAATTTTAATCCCTTGCCCT 9 284 1 AATCCTTGCC 0.847107 -13 AAAATATATTAGTCCACCACACGAAACGGAGG 11 12 1 AGTCCCCACC 0.988873 -29 CCCCTTTTTCATTCCTGCGCTCTTTTGCTTTT 12 90 1 ATTCCGCGCC 0.972354 -120 ***** **** * Masking position 1 Map Score: 10.1668 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 72 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 AAACCTTTAATATTTATCTTT 2 71 1 TATTTATCTT 0.720666 -11 TTCAATTAATTTCTTAACTTTCTGTTCTAT 4 168 1 TTCTTAACTT 0.786227 -133 TGTTCTATTTCTTTTAATTTCTTTGGATCT 4 190 1 CTTTTAATTT 0.780279 -111 ACCTCCTTAATTTTCAATTTAAGTAGAATT 4 274 1 TTTTCAATTT 0.78028 -27 ATTTGTAAAATTTTTATCTTTGATTTTCAG 7 132 1 TTTTTATCTT 0.912265 -169 CGCTATTTATTTTAGAAAGGGCC 8 240 0 TATTTATTTT 0.733951 -13 GGTAAAAATTTTTTTATTTTTAAAAGGATT 9 53 1 TTTTTATTTT 0.917481 -244 GGGATTAAAATTATTAACTTGGTACGGGCT 9 270 0 TTATTAACTT 0.712763 -27 AGGTTTCTAATTTTAAAATGAAG 10 4 1 TTTCTAATTT 0.78028 -49 TTATTTTTAATTTAGCTTTTCAA 12 197 0 TTTTTAATTT 0.949641 -13 ACCTCCTCCCTTTTTAATTTAAAATTTTAA 13 237 1 TTTTTAATTT 0.949641 -24 ********** Masking position 6 Map Score: 6.29189 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 123 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 TACCTCCGTAAATTTTCGGACGAATAATTTT 2 18 1 ATTTTCGGAC 0.933053 -64 CCTCCTTTAAAGTTTTTAGAAGATTATATCA 3 53 0 ATTTTTAGAA 0.821155 -28 ATAAAGCGTTATTTTTCAGACATAGGCGCGC 7 21 0 ATTTTCAGAC 0.983512 -280 TTTATCAATAACTTATTAGACACCTAACCTT 7 47 1 ATTATTAGAC 0.880502 -254 TGTATGCTCAAGTTTGCAGAACTTGGGGTTA 7 102 0 ATTTGCAGAA 0.732936 -199 TCAAAGCATCACTTATTAGACCAATCCGCTT 7 205 1 ATTATTAGAC 0.880502 -96 CATTCTCCGTAGTTTTCAAACCATTGACAGT 8 92 0 ATTTTCAAAC 0.921545 -161 GTGTTATAATATTCTTCAGACGAGGGCTGCT 9 166 0 ATCTTCAGAC 0.933053 -131 CTTTCAAAACAATTTTAAAACTTCATTTTAA 10 23 0 ATTTTAAAAC 0.645031 -30 * ********* Masking position 3 Map Score: 2.60095 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 123 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 AGCCCCTCCCTCCCCCCACCTCCCTCCACCG 8 187 1 TCCCCCACCT 0.947405 -66 CCCACCTCCCTCCACCGATTTTTGGCCTCCC 8 201 1 TCCCCGATTT 0.969557 -52 GGATTAAGAGTCCGCCGCTCTGCCTATTGAG 9 133 1 TCCCCGCTCT 0.995313 -164 GGATCCGTAGTCCCGCGCTCTATCCAGTTGA 9 234 1 TCCGCGCTCT 0.991071 -63 CCTTTTTCATTCCTGCGCTCTTTTGCTTTTA 12 92 1 TCCGCGCTCT 0.991071 -118 TGGCTCCACCTCCTCCCTTTTTAATTTAAAA 13 230 1 TCCCCCTTTT 0.904216 -31 *** ******* Masking position 1 Map Score: 3.42147 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 41 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 GACACCTAACCTTCACGAAACGAATGTTAATT 7 65 1 CCACGAAACG 0.984666 -236 AGGGGGTATTCCAAAAGAAAAGGAAAAGGGGA 9 18 0 CAAAGAAAAG 0.857516 -279 TATTAGTCCACCACACGAAACGGAGGTTCGGA 11 18 1 CCACGAAACG 0.984728 -23 CCGCAAATCACGTAAAGAAACT 12 1 0 CAAAGAAACT 0.926779 -209 GAACTTTCTTCGGAACGAAGCGCCTTACCTTT 12 165 0 CAACGAAGCG 0.984701 -45 CGCTCGTATTCATAGCGAAACGATTCAACGTG 13 60 0 CAGCGAAACG 0.967184 -201 TAGGCATTTCCACAAAGAAGCTCGAGGAGATA 13 123 0 CAAAGAAGCT 0.894928 -138 * ********* Masking position 8 Map Score: 3.56816 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 26 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 TAAGGAGGTGGGAGCCATGCCTATGTACGT 4 253 0 GGAGCCATGC 0.995536 -48 TAGGAACCCTGCGCGCCTATGT 7 3 1 GGAACCCTGC 0.965129 -298 CAATTGCCAAGGAGCCAAGAGGCATTGTAG 7 240 1 GGAGCCAAGA 0.97603 -61 AGCCCTCTAAGGAGCTATTCAAAATTATAC 7 268 1 GGAGCTATTC 0.869509 -33 AACTTTCTTCGGAACGAAGCGCCTTACCTT 12 166 0 GGAACGAAGC 0.920402 -44 GGGAGGAGGTGGAGCCATGATTGGAGTGGG 13 217 0 GGAGCCATGA 0.987007 -44 ********** Masking position 3 Map Score: 3.78623 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 18 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 AAACTCTCCCCCTACGCGGTCAAAGATCCA 4 213 0 CCTACGCGGT 0.937021 -88 TAGGAACCCTGCGCGCCTATGTCTGAA 7 8 1 CCTGCGCGCC 0.991892 -293 GATTAAGAGTCCGCCGCTCTGCCTATTGAG 9 134 1 CCGCCGCTCT 0.965046 -163 GATCCGTAGTCCCGCGCTCTATCCAGTTGA 9 235 1 CCCGCGCTCT 0.989515 -62 CTTTTTCATTCCTGCGCTCTTTTGCTTTTA 12 93 1 CCTGCGCTCT 0.99537 -117 CGCCTGCGGGCTCTTTTGCCCT 13 3 1 CCTGCGGGCT 0.987279 -258 ********** Masking position 5 Map Score: 5.39522 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 4 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 12 TCCGTGGTTGCATGTCCAAAAGAGCGTATAA 4 25 1 CATGTCCAAA 0.795251 -276 CCCGGGAGGCCCTTTCTAAAATAAATAGCG 8 233 1 CCTTTCTAAA 0.954846 -20 TAAACAGAATCCTTTTAAAAATAAAAAAATT 9 59 0 CCTTTTAAAA 0.932036 -238 CAGCCCACCACCTTTCTATAAACAGAATCCT 9 77 0 CCTTTCTAAA 0.954846 -220 TTTAAAACTTCATTTTAAAATTAGAAACCT 10 10 0 CATTTTAAAT 0.628823 -43 ACTGACCTCCTTTCAAAACAATTTTAAAA 10 34 0 CCTTTCAAAC 0.928106 -19 GCGGAGTTATCCTTTCAATATTCGGAATTAT 12 29 1 CCTTTCAAAT 0.938878 -181 TGTTTAAAACCTTTTTCACAAAGTTCGGATA 12 130 0 CTTTTTCAAA 0.785745 -80 TTTAATTTAGCTTTTCAAGAACTTTCTTCGG 12 184 0 CTTTTCAAAA 0.929868 -26 AGGCTATAGGCATTTCCACAAAGAAGCTCGA 13 130 0 CATTTCCAAA 0.949042 -131 ******** ** Masking position 5 Map Score: 4.51995 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 269 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 13 CTTTCTCCTCCTTTATTTAA 3 1 1 CTTTCTCCTC 0.979117 -80 CTCCCACCTCCTTAATTTTCAATTTAAGTA 4 269 1 CTTAATTTTC 0.473302 -32 TCCCGCTTTTATTAATCCTCTTATGATAGT 8 23 1 ATTAATCCTC 0.732754 -230 CTCCTAACTTCTTCATTCTCCGTAGTTTTC 8 106 0 CTTCATTCTC 0.908216 -147 GCGGCGGACTCTTAATCCGCAGGTTCCGGG 9 121 0 CTTAATCCGC 0.86728 -176 ATACCCTTCTCTATCTCCTCGAGCTTCTTT 13 112 1 CTATCTCCTC 0.936774 -149 GGACATTCCCCTTTCTTCTCTGATCTTCCT 13 177 1 CTTTCTTCTC 0.9389 -84 CTCTGATCTTCCTTATCCTCTCTCCCACTC 13 194 1 CCTTATCCTC 0.946812 -67 AATCATGGCTCCACCTCCTCCCTTTTTAAT 13 225 1 CCACCTCCTC 0.857227 -36 ********** Masking position 6 Map Score: 3.15916 Number of sites scoring better than the average of aligned sites = 762 Number in coding regions = 703 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 14 ********** No masking Map Score: -1.14154e-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 15 ********** No masking Map Score: -1.14154e-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