AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00010_aquae_reg_300.orf -o00010_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 timA 300 triose phophate isomerase #4 eno 300 enolase #5 aq_503 83 hypothetical protein #6 otnA' 30 polysaccharide biosynthesis protein (fragment) #7 lpdA 85 dihydrolipoamide dehydrogenase #8 pgi 33 glucose-6-phosphate isomerase #9 aq_759 152 hypothetical protein #10 gap 40 glyceraldehyde-3-phosphate dehydrogenase #11 ilvC 66 acetohydroxy acid isomeroreductase #12 efp 187 elongation factor P #13 fba 300 fructose-1,6-bisphosphate aldolase class II #14 metE 44 tetrahydropteroyltriglutamate methyltransferase #15 gpmA 220 phosphoglycerate mutase #16 murE 300 UDP-MurNac-tripeptide synthetase #17 era1 62 GTP-binding protein Era #18 aq_1996 38 hypothetical protein Motif number 1 CGTCCGAAAATTTACGGAGGTACGGGAAA 2 9 0 TTACGGAGGT 0.951572 -73 TAAATTGAAAATTAAGGAGGTGGGAGCCATG 3 264 0 ATAAGGAGGT 0.975679 -37 TAATTTGCCTTAAAAGGAGGAAGCGA 7 6 0 TAAAGGAGGA 0.952533 -80 TAAAACCCCTTTTCAGGAGGAGCTTC 7 70 1 TTCAGGAGGA 0.92521 -16 ATGTAAACCTTAATAGGAGGTGGGTAAG 9 135 1 TATAGGAGGT 0.906088 -18 ATAATAAATCCTTCAGGAGGTCACGC 11 51 1 CTCAGGAGGT 0.953836 -16 CCGGGCTCATAACCCGGAGGTCGCGGGTTCA 12 60 0 AACCGGAGGT 0.957912 -128 TAAGAAGTTCTAAAAGGAGGAGAAATCC 14 27 1 TAAAGGAGGA 0.952533 -18 ACCCAAAAGGAGGTCCCTGTGACT 15 4 1 CAAAGGAGGT 0.971029 -217 CTACCATGTAAAACAGGAGCTTCTCGAAATA 15 48 1 AACAGGAGCT 0.840139 -173 AAGAGTGAAGATAAAGGAGTTAAAATCCGCC 15 105 1 ATAAGGAGTT 0.823299 -116 GGAGTTCTTTATTCAGGAGTTTGAGTCTGAG 16 175 1 ATCAGGAGTT 0.809081 -126 GATAATATATTAGAAGGAGGGGTGGCCGAGC 16 231 1 TAAAGGAGGG 0.921698 -70 TTAAGTTTAGTAAACGGAGGTTTTT 17 48 1 TAACGGAGGT 0.966657 -15 GATAAACAAAAAGAAGGAGGTGGAAA 18 6 0 AAAAGGAGGT 0.983386 -33 ** ******** Masking position 8 Map Score: 21.6471 Number of sites scoring better than the average of aligned sites = 418 Number in coding regions = 314 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 2 ATTTTCGGACGAATAATTTTAACACAATAAGTTTA 2 29 1 GATTTTAACC 0.907743 -53 CGCGTAGGGGGAGAGTTTTGTAAGCATGACGTACA 3 225 1 GGTTTGTAAC 0.793419 -76 GGTTGCGGGGGCGGGATTTGAACCCGCGACCTCCG 12 42 1 GGTTTGAACC 0.991868 -146 GAGGAGATATTTTAACTCAAGTGGAGGG 12 170 0 GGTTTTAACC 0.991083 -18 AAGGAGCCAAGAGGCATTGTAGCCCTCTAAGGAGC 13 248 1 GGTTGTAGCC 0.951987 -53 GGAGGTCCCTGTGACTTTGAAACACTTTACTACCA 15 19 1 GGTTGAAACC 0.956267 -202 CACAAATTTGGGCGGATTTTAACTCCTTTATCTTC 15 111 0 GCTTTTAACC 0.935835 -110 GCCCAAATTTGTGGACTTGTAAACCTTGCAAAAGT 15 133 1 GGTTGTAAAC 0.963087 -88 AAGAAAAATAGAGCTCTTTGAACACCTTATTAAAA 16 112 1 GGTTTGAACC 0.991076 -189 GGACGAAGGCGGGGGATTTGAAATCCCTTGGCGGG 16 262 1 GGTTTGAAAC 0.967977 -39 GGGCGGGCCTGTAACCCGCCAAGGGAT 16 284 0 GGCTGTAACC 0.951502 -17 * * ******* * Masking position 8 Map Score: 10.7317 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 60 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 3 AAAAAACCTTTAATATTTATCTTT 2 68 1 TATATTCTTT 0.924037 -14 CTTTGAAGCTTCTTCGTCGTCTTTGGCTTCAAAT 3 66 1 TTTCTCCTTT 0.903993 -235 CTTAACTTTCTGTTCTATTTCTTTTAATTTCTTT 3 180 1 TTTCATCTTT 0.906185 -121 GAAATCCCTGTATTCCTCTCCTTTGAACCTTTCC 4 248 1 TTTCTCCTTT 0.903993 -53 TTTGATATACTAATAATTTGCCTTAAAAGGAGGA 7 16 0 TATATTCCTT 0.909149 -70 TGAAAAGGGGTTTTAATTGCCTTTAATTTTAGCA 7 51 0 TTTATTCTTT 0.959106 -35 TCTTTTCTCTTCTTTCCCCTTATAATTTTTC 8 8 1 TTTCTTCCTT 0.957174 -26 CATATAATTTTATTATATTCCTTTTAAAAATTTT 9 104 0 TTTAATCTTT 0.892916 -49 CTTGCAAAAGTCTTACTTTACCTTGAAAACTTAG 15 157 1 TTTATTCCTT 0.950725 -64 CCTTACAATCTCATCGATATCCTTTTTAATAAGG 16 136 0 TATCATCCTT 0.80474 -165 AAAGAATATATCATATTTTCCTTTTGG 17 4 0 TATATTCTTT 0.924037 -59 CGTTTACTAAACTTAATTTTCTTTATAAAGAATA 17 30 0 ATTATTCTTT 0.730933 -33 * *** ** **** Masking position 4 Map Score: 8.84344 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 293 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 4 ACGCCAAACTCCTCTTCAGGATACTCTCCG 4 139 0 CCTCTTCAGG 0.946632 -162 CTCCTTTGAACCTTTCCAGGTACTTTTCCA 4 265 1 CCTTTCCAGG 0.93738 -36 ATGTATTACACCTTTTCGGAGACAGCAGGT 5 59 1 CCTTTTCGGA 0.965659 -25 TCGCTTCCTCCTTTTAAGGCAAATTATTA 7 10 1 CCTTTTAAGG 0.925053 -76 AATTAAAACCCCTTTTCAGGAGGAGCTTC 7 67 1 CCTTTTCAGG 0.982605 -19 TTATTATATTCCTTTTAAAAATTTTTGCAA 9 99 0 CCTTTTAAAA 0.839062 -54 TTACCCACCTCCTATTAAGGTTTACATATA 9 132 0 CCTATTAAGG 0.899756 -21 GATTTCTCCTCCTTTTAGAACTTCTTATTT 14 24 0 CCTTTTAGAA 0.811362 -21 AGGGGAGTTGCATTTTAGGATCGAAATCGG 16 39 0 CATTTTAGGA 0.681667 -262 ********** Masking position 5 Map Score: 6.19481 Number of sites scoring better than the average of aligned sites = 436 Number in coding regions = 408 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 TTCCTTTACCTCCAAAAATGGGATT 1 14 0 CTTTACCTAA 0.962584 -15 AACACAATAAGTTTACCACAAAAAACCTTTAA 2 49 1 GTTTACCAAA 0.898367 -33 TCCTATTAAGGTTTACATATAATTTTATTATA 9 121 0 GTTTACATAA 0.864727 -32 AAGTTTATATAAAATAGTTCCACG 10 3 1 GTTTATATAA 0.827177 -38 ACAATTTGTTCTTTATAATAAATCCTTCAGGA 11 37 1 CTTTATAAAA 0.873758 -30 AAAAATAACGCTTTATCAATAACTTATTAGAC 13 36 1 CTTTATCAAA 0.941925 -265 ATTTTAACTCCTTTATCTTCACTCTTGGTATA 15 99 0 CTTTATCTAC 0.838194 -122 AAAAGTCTTACTTTACCTTGAAAACTTAGGTG 15 162 1 CTTTACCTAA 0.962584 -59 TAGTAGTACTCTTTATTTACAACGGTAACTAC 15 193 0 CTTTATTTAA 0.781085 -28 ATGATATATTCTTTATAAAGAAAATTAAGTTT 17 24 1 CTTTATAAAA 0.873758 -39 CCTTCTTTTTGTTTATCTACAATTATAAT 18 20 1 GTTTATCTAA 0.941219 -19 ******** ** Masking position 5 Map Score: 8.33173 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 87 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 ATCCCATTTTTGGAGGTAAAGGAA 1 15 1 TGGAGGTAAA 0.742681 -14 TCTTTGACCGCGTAGGGGGAGAGTTTTGTA 3 217 1 CGTAGGGGGA 0.909663 -84 TTGAAAATTAAGGAGGTGGGAGCCATGCCT 3 261 0 AGGAGGTGGG 0.963316 -40 ACGTACTCCATGGTGGGAGGGACTTTTGCG 4 186 1 TGGTGGGAGG 0.736914 -115 AAAGGTTCAAAGGAGAGGAATACAGGGATT 4 250 0 AGGAGAGGAA 0.716388 -51 TATTATTTAAAGTAGGGAGATGTATTACAC 5 40 1 AGTAGGGAGA 0.926116 -44 GATTATGTTGTAGGGAGAATTCTTAAGA 6 13 0 TGTAGGGAGA 0.916849 -18 AAACCTTAATAGGAGGTGGGTAAG 9 139 1 AGGAGGTGGG 0.963316 -14 AAGATAATAATGTCGGGAGGTAGGTT 11 7 0 TGTCGGGAGG 0.743567 -60 TTAACTCAAGTGGAGGGGAAAGGGGACTTG 12 157 0 TGGAGGGGAA 0.976764 -31 AAGTTCTAAAAGGAGGAGAAATCC 14 31 1 AGGAGGAGAA 0.774209 -14 CTCACCCTTATGTAGGGGAGTTGCATTTTA 16 52 0 TGTAGGGGAG 0.939863 -249 TCGATGAGATTGTAAGGGAAGTGGAGTTCT 16 153 1 TGTAAGGGAA 0.457498 -148 ATATATTAGAAGGAGGGGTGGCCGAGCGGA 16 235 1 AGGAGGGGTG 0.906704 -66 GAGCGGACGAAGGCGGGGGATTTGAAATCC 16 258 1 AGGCGGGGGA 0.968239 -43 AACAAAAAGAAGGAGGTGGAAA 18 3 0 AGGAGGTGGA 0.964038 -36 ********** Masking position 2 Map Score: 17.9078 Number of sites scoring better than the average of aligned sites = 633 Number in coding regions = 534 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 7 AGAAAGTTAAGAAATTAATTGAAGAAAACTGTC 3 158 0 GAATTATGAA 0.983888 -143 AAGATCCAAAGAAATTAAAAGAAATAGAACAGA 3 188 0 GAATTAAGAA 0.970353 -113 CAGCTCTTTGGTACTTCATAGAAGAAAAGGACA 4 61 0 GACTTATGAA 0.957135 -240 AATGCGTTCTGTAATTTATAGAAATCCCTGTAT 4 228 1 GAATTATGAA 0.983888 -73 CGCAATTAATAGAATTTAGCCTCT 9 2 1 GAATTATGAA 0.983889 -151 TGGCTCCTTGGCAATTGAATAAAGCGGATTGGT 13 224 0 GAATTAAAAA 0.835073 -77 * **** ** *** Masking position 6 Map Score: 3.11725 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 64 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 ATGCAACCACGGAAACCTGGTCAGCAA 3 6 0 GGAAACCTGC 0.736129 -295 GAAGTGGGTAATGAACCTTGTCGTTTTTGGTC 3 119 0 ATGAACCTGC 0.853578 -182 TTAAGGAGGTGGGAGCCATGCCTATGTACGTC 3 252 0 GGGAGCCAGC 0.982683 -49 ATCCTAACATGGGAACCCAGTCGGGTATCCTG 4 31 1 GGGAACCCGC 0.982544 -270 GACCTGAGTGAGGAGGCAAGGGAAGATTTTAC 4 96 0 AGGAGGCAGG 0.905549 -205 CCTCCGGGTTATGAGCCCGGCGAGCTACCAGG 12 71 1 ATGAGCCCGG 0.9542 -117 TAGGAACCCTGCGCGCCTATGTC 13 2 1 AGGAACCCGG 0.982884 -299 TCAATTGCCAAGGAGCCAAGAGGCATTGTAGC 13 239 1 AGGAGCCAGG 0.98303 -62 ******** * * Masking position 4 Map Score: 2.71575 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 67 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 AAAGATAAATATTAAAGGTT 2 72 0 AAAGATAAAT 0.815094 -10 TTGGTACTTCATAGAAGAAAAGGACAGGAT 4 57 0 ATAGAAGAAA 0.705409 -244 TGCATTAAAAATAGGAAAAAAGCAA 5 6 0 ATAGGAAAAA 0.815046 -78 GATTTATTATAAAGAACAAATTGTAAGATA 11 31 0 AAAGAACAAA 0.820299 -36 TTATTAATATATAGAAAAAATCTTATCTCG 12 126 1 ATAGAAAAAA 0.900153 -62 ACTGAAAATCAAAGATAAAAATTTTACAAA 13 133 0 AAAGATAAAA 0.844503 -168 CATGCTCACGAAAGAAAAATAGAGCTCTTT 16 101 1 AAAGAAAAAT 0.933109 -200 CCAAAAGGAAAATATGATATATT 17 4 1 AAAGGAAAAT 0.872102 -59 TATTCTTTATAAAGAAAATTAAGTTTAGTA 17 30 1 AAAGAAAATT 0.687408 -33 ********** Masking position 3 Map Score: 1.66459 Number of sites scoring better than the average of aligned sites = 517 Number in coding regions = 469 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 10 GTACTCCATGGTGGGAGGGACTTTTGCGAG 4 188 1 GTGGGAGGGA 0.956205 -113 ATTTAAAGTAGGGAGATGTATTACACCTTT 5 44 1 GGGAGATGTA 0.837313 -40 ATATGGTTGCGGGGGCGGGATTTGAACCCG 12 38 1 GGGGGCGGGA 0.967753 -150 ATTTGGCAACGCGGGGTGGAGCAGCCTGGT 12 97 0 GCGGGGTGGA 0.958721 -91 TTTAACTCAAGTGGAGGGGAAAGGGGACTT 12 158 0 GTGGAGGGGA 0.881174 -30 TGCTTTGATTGTGTGATGGATTGATATCAT 13 183 0 GTGTGATGGA 0.907043 -118 CCCTACATAAGGGTGAGGTACTACGTAGAA 16 65 1 GGGTGAGGTA 0.847933 -236 GAGATTGTAAGGGAAGTGGAGTTCTTTATT 16 158 1 GGGAAGTGGA 0.910007 -143 CTTCTGAGTACGGTGGTGGATAATATATTA 16 213 1 CGGTGGTGGA 0.894728 -88 AACAAAAAGAAGGAGGTGGAAA 18 3 0 AGGAGGTGGA 0.85151 -36 ********** Masking position 10 Map Score: 4.69929 Number of sites scoring better than the average of aligned sites = 401 Number in coding regions = 360 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 11 GAGCGTATAATGAGGGCTACCTTTGAAGCT 3 46 1 TGAGGGCTAC 0.966126 -255 TTATGAGCCCGGCGAGCTACCAGGCTGCTC 12 79 1 GGCGAGCTAC 0.979835 -109 ATAGCTCCTTAGAGGGCTACAATGCCTCTT 13 256 0 AGAGGGCTAC 0.966126 -45 CTTGGTATAGGGCGGTCTGCGTTTTTGAAT 15 78 0 GGCGGTCTGC 0.95648 -143 GAAATCCCTTGGCGGGTTACAGGCCCGCCC 16 281 1 GGCGGGTTAC 0.979982 -20 ********** Masking position 8 Map Score: 0.479896 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 28 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 12 TTTTCGGACGAATAATTTTAACACAATAAG 2 30 1 AATAATTTTA 0.690512 -52 TTTAATTGCCTTTAATTTTAGCATTTTGAT 7 44 0 TTTAATTTTA 0.65506 -42 TCTTTCCCCTTATAATTTTTCCC 8 21 1 TATAATTTTT 0.807905 -13 TAAAACTTTATAAAATTGTATTAAGACTTT 9 57 0 TAAAATTGTA 0.586713 -96 TACAATTTTATAAAGTTTTATGATAAGAAT 9 67 1 TAAAGTTTTA 0.553963 -86 GAATTATTGCAAAAATTTTTAAAAGGAATA 9 93 1 AAAAATTTTT 0.412169 -60 AAGGTTTACATATAATTTTATTATATTCCT 9 116 0 TATAATTTTA 0.742252 -37 CATACATTTGTAAAATTTTTATCTTTGATT 13 127 1 TAAAATTTTT 0.509976 -174 ATTTATATGGTATAATTTTGAATAGCTCCT 13 277 0 TATAATTTTG 0.800252 -24 ATTATAATTGTAGATAAACAAA 18 27 0 TATAATTGTA 0.836095 -12 ********** Masking position 6 Map Score: 2.1152 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 40 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 13 TTCCCATGTTAGGATACTGGGACGACTACA 4 16 0 AGGATACTGG 0.974912 -285 AGAAAAGGACAGGATACCCGACTGGGTTCC 4 42 0 AGGATACCCG 0.980378 -259 ACTCCTCTTCAGGATACTCTCCGACCCTAA 4 132 0 AGGATACTCT 0.96109 -169 CGCATTTAGAAGGAAACTCGCAAAAGTCCC 4 204 0 AGGAAACTCG 0.976314 -97 ********** Masking position 6 Map Score: 0.148903 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 25 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 14 ********** No masking Map Score: 9.04821e-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: 9.04821e-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