AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00010_aquae_reg_100.orf -o00010_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 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 era1 62 GTP-binding protein Era #17 aq_1996 38 hypothetical protein Motif number 1 TTTCCCGTACCTCCGTAAATTTTCGGAC 2 9 1 ACCTCCGTAA 0.941076 -73 CATGGCTCCCACCTCCTTAATTTTCAATTT 3 264 1 ACCTCCTTAA 0.96936 -37 TCGCTTCCTCCTTTTAAGGCAAATT 7 6 1 TCCTCCTTTT 0.964234 -80 GAAGCTCCTCCTGAAAAGGGGTTTT 7 71 0 TCCTCCTGAA 0.893113 -15 CTTACCCACCTCCTATTAAGGTTTACA 9 136 0 ACCTCCTATT 0.929763 -17 GCGTGACCTCCTGAAGGATTTATTA 11 52 0 ACCTCCTGAA 0.962999 -15 TGAACCCGCGACCTCCGGGTTATGAGCCCG 12 60 1 ACCTCCGGGT 0.902557 -128 GGATTTCTCCTCCTTTTAGAACTTCTT 14 28 0 TCCTCCTTTT 0.964234 -17 AGTCACAGGGACCTCCTTTTGGGT 15 5 0 ACCTCCTTTT 0.988232 -216 TATTTCGAGAAGCTCCTGTTTTACATGGTA 15 49 0 AGCTCCTGTT 0.880188 -172 GGCGGATTTTAACTCCTTTATCTTCACTCT 15 106 0 AACTCCTTTA 0.793816 -115 AAAAACCTCCGTTTACTAAACTTA 16 49 0 ACCTCCGTTT 0.976954 -14 TTTCCACCTCCTTCTTTTTGTTTAT 17 6 1 ACCTCCTTCT 0.957088 -33 ********** Masking position 4 Map Score: 20.4921 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 258 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 2 TGTGGTAAACTTATTGTGTTAAAATTATTCGTCCGAAAA 2 30 0 TTATTTAATT 0.808262 -52 TCTATTTCTTTTAATTTCTTTGGATCTTTGACCGCGTAG 3 193 1 TTATTTATTT 0.575076 -108 CCTCCTTAATTTTCAATTTAAGTAGAATTAGATCTT 3 275 1 TTTTTAAATT 0.96997 -26 GATTATGTTGTAGGGAGAATTCTTAAGAGC 6 10 0 TTATTAAATT 0.953788 -21 AATTTTAGCATTTTGATATACTAATAATTTGCCTTAAAA 7 22 0 TTTTTAAATT 0.96997 -64 TTTTATAAAGTTTTATGATAAGAATTATTGCAAAAATTT 9 72 1 TTTGTAAATT 0.847195 -81 ATTTTATTATATTCCTTTTAAAAATTTTTGCAATAATTC 9 93 0 ATTTTAATTT 0.678962 -60 CCACCTCCTATTAAGGTTTACATATAATTTTATTATATT 9 119 0 TTATTAAATT 0.953788 -34 GATAAGATTTTTTCTATATATTAATAATTTGGCAACGCG 12 114 0 TTTTTAAATT 0.96997 -74 TATCTTTGATTTTCAGTCTATTAAAGTTTATTGCATCAT 13 146 1 TTTTTAATTT 0.912048 -155 CTATTCAAAATTATACCATATAAATTATT 13 282 1 TTACTAAATT 0.779888 -19 AATATGATATATTCTTTATAAAGAAAATTAAGTTTAGTA 16 21 1 ATTTTAAATT 0.868261 -42 CACCTCCTTCTTTTTGTTTATCTACAATTATAAT 17 15 1 TTTTTAAATT 0.96997 -24 *** * ** * *** Masking position 14 Map Score: 10.3037 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 12 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 3 CCGGGACAGTTTTCTTCAATTAATTTCTTAACTTT 3 154 1 TTTTCAATAT 0.865932 -147 TTCTTAACTTTCTGTTCTATTTCTTTTAATTTCTT 3 178 1 TTTTCTATCT 0.959539 -123 ATCCTGTCCTTTTCTTCTATGAAGTACCAAAGAGC 4 57 1 TTTTCTATAT 0.966474 -244 TTAATGCATGTGTATTATTTAAAGTAGGGAGATGT 5 28 1 TTTTATTTAT 0.767469 -56 TCTTTTCTCTTCTTTCCCCTTATAATTTTT 8 6 1 TTTTCTTTCT 0.924812 -28 CTAAAGAGGCTAAATTCTATTAATTGCG 9 4 0 TATTCTATAT 0.769531 -149 TACATATAATTTTATTATATTCCTTTTAAAAATTT 9 105 0 TTTTATATCT 0.839619 -48 CTCGTGGAACTATTTTATATAAACTT 10 2 0 TTTTATATAT 0.864198 -39 TATCTTACAATTTGTTCTTTATAATAAATCCTTCA 11 31 1 TTTTCTTTAT 0.937309 -36 CGAGATAAGATTTTTTCTATATATTAATAATTTGG 12 121 0 TTTTCTATAT 0.966474 -67 ACCAATCCGCTTTATTCAATTGCCAAGGAGCCAAG 13 224 1 TTTTCAATCA 0.543485 -77 GAAAATATGATATATTCTTTATAAAGAAAATTAAG 16 18 1 TTTTCTTTAA 0.770105 -45 * * ****** * * Masking position 6 Map Score: 9.03122 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 202 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 4 ACGCCAAACTCCTCTTCAGGATACTCTCCG 4 139 0 CCTCTTCAGG 0.967388 -162 CTCCTTTGAACCTTTCCAGGTACTTTTCCA 4 265 1 CCTTTCCAGG 0.958242 -36 ATGTATTACACCTTTTCGGAGACAGCAGGT 5 59 1 CCTTTTCGGA 0.955681 -25 TCGCTTCCTCCTTTTAAGGCAAATTATTA 7 10 1 CCTTTTAAGG 0.904029 -76 AATTAAAACCCCTTTTCAGGAGGAGCTTC 7 67 1 CCTTTTCAGG 0.98516 -19 TTATTATATTCCTTTTAAAAATTTTTGCAA 9 99 0 CCTTTTAAAA 0.845913 -54 TTACCCACCTCCTATTAAGGTTTACATATA 9 132 0 CCTATTAAGG 0.920896 -21 GATTTCTCCTCCTTTTAGAACTTCTTATTT 14 24 0 CCTTTTAGAA 0.756676 -21 ********** Masking position 5 Map Score: 7.29516 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 257 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 5 ACTTATTGTGTTAAAATTATTCGTCCGAAAATT 2 28 0 TTAAAATACG 0.74384 -54 ACGAAGAAGCTTCAAAGGTAGCCCTCATTATAC 3 50 0 TTCAAAGTCC 0.812588 -251 CGTCTTTGGCTTCAAATACGTCCAGATAATCGT 3 83 1 TTCAAATCCC 0.961696 -218 AAGAGCTGCTGTAAAATCTTCCCTTGCCTCCTC 4 86 1 GTAAAATTCC 0.858949 -215 TTCTTTCCCCTTATAATTTTTCCC 8 20 1 TTATAATTCC 0.890313 -14 AATTTGTTCTTTATAATAAATCCTTCAGGAGGT 11 39 1 TTATAATACC 0.861759 -28 AGGTCGCGGGTTCAAATCCCGCCCCCGCAACCA 12 41 0 TTCAAATCCC 0.961696 -147 TCCACTTGAGTTAAAATATCTCCTC 12 173 1 TTAAAATTCC 0.966888 -15 AAGGAGCTATTCAAAATTATACCATATAAATTA 13 276 1 TCAAAATACC 0.823842 -25 GATAAAGGAGTTAAAATCCGCCCAAATTTGTGG 15 114 1 TTAAAATCCC 0.972423 -107 ******* * ** Masking position 6 Map Score: 4.78435 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 48 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 ATGCAACCACGGAAACCTGGTCAGCAA 3 7 0 GGAAACCTGT 0.858723 -294 GAAGTGGGTAATGAACCTTGTCGTTTTTGGT 3 120 0 ATGAACCTGT 0.891021 -181 TTAAGGAGGTGGGAGCCATGCCTATGTACGT 3 253 0 GGGAGCCAGC 0.967133 -48 ATCCTAACATGGGAACCCAGTCGGGTATCCT 4 31 1 GGGAACCCGT 0.975455 -270 CGCATTTAGAAGGAAACTCGCAAAAGTCCCT 4 203 0 AGGAAACTGC 0.922571 -98 AGCAAACCTGCTGTCTCCGAA 5 73 0 AGCAAACCGC 0.823716 -11 CCTCCGGGTTATGAGCCCGGCGAGCTACCAG 12 71 1 ATGAGCCCGC 0.958448 -117 CGCGGGGTGGAGCAGCCTGGTAGCTCGCCGG 12 87 0 AGCAGCCTGT 0.903798 -101 TAGGAACCCTGCGCGCCTATGT 13 2 1 AGGAACCCGC 0.990057 -299 TCAATTGCCAAGGAGCCAAGAGGCATTGTAG 13 239 1 AGGAGCCAGA 0.80321 -62 TTGTGGACTTGTAAACCTTGCAAAAGTCTTA 15 141 1 GTAAACCTGC 0.779158 -80 ******** ** Masking position 4 Map Score: 5.46658 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 145 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 ATCCCATTTTTGGAGGTAAAGGAA 1 15 1 TGAGGTAAAG 0.978173 -14 GAAATAGAACAGAAAGTTAAGAAATTAATTG 3 170 0 AGAAGTTAAG 0.874573 -131 CTACTTAAATTGAAAATTAAGGAGGTGGGAG 3 269 0 TGAAATTAAG 0.93661 -32 CTCACTCAGGTCAAAGTTAGGGTCGGAGAGT 4 116 1 TCAAGTTAGG 0.719906 -185 ATTCGTTTCGTGAAGGTTAGGTGTCTAATAA 13 59 0 TGAGGTTAGG 0.935376 -242 CTGTTTTACATGGTAGTAAAGTGTTTCAAAG 15 33 0 TGTAGTAAAG 0.809276 -188 ATACCAAGAGTGAAGATAAAGGAGTTAAAAT 15 100 1 TGAGATAAAG 0.959287 -121 ACCTAAGTTTTCAAGGTAAAGTAAGACTTTT 15 162 0 TCAGGTAAAG 0.91438 -59 TAGTTACCGTTGTAAATAAAGAGTACTACTA 15 194 1 TGAAATAAAG 0.946115 -27 TTCTTTATAAAGAAAATTAAGTTTAGTAAAC 16 32 1 AGAAATTAAG 0.785687 -31 ATTATAATTGTAGATAAACAAAAAGAAGG 17 20 0 TGAGATAAAC 0.733451 -19 ** ******** Masking position 9 Map Score: 5.96153 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 344 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 AGGTTCATTACCCACTTCACACCGGGACAG 3 133 1 CCCACTTCAC 0.847192 -168 ACAAAACTCTCCCCCTACGCGGTCAAAGAT 3 216 0 CCCCCTACGC 0.972553 -85 CTCGCAAAAGTCCCTCCCACCATGGAGTAC 4 188 0 TCCCTCCCAC 0.961874 -113 TAAGACTTTGTCCCATACACTATTTTGCTA 9 36 0 TCCCATACAC 0.884525 -117 GGTTCAAATCCCGCCCCCGCAACCATATCA 12 36 0 CCGCCCCCGC 0.944312 -152 ACCAGGCTGCTCCACCCCGCGTTGCCAAAT 12 97 1 TCCACCCCGC 0.983767 -91 AAGTCCCCTTTCCCCTCCACTTGAGTTAAA 12 158 1 TCCCCTCCAC 0.98627 -30 ATGATATCAATCCATCACACAATCAAAGCA 13 183 1 TCCATCACAC 0.833871 -118 CACTTATTAGACCAATCCGCTTTATTCAAT 13 214 1 ACCAATCCGC 0.760073 -87 ********** Masking position 8 Map Score: 3.97688 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 284 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 AAGCTTCAAAGGTAGCCCTCATTATACGCT 3 47 0 GGTAGCCCTC 0.980828 -254 TACCTTGTAGTCGTCCCAGTATCCT 4 6 1 TGTAGTCGTC 0.958241 -295 TAGAAATCCCTGTATTCCTCTCCTTTGAAC 4 246 1 TGTATTCCTC 0.93933 -55 CAAGAGGCATTGTAGCCCTCTAAGGAGCTA 13 255 1 TGTAGCCCTC 0.988665 -46 TCCTGATAGTAGTACTCTTTATTTACA 15 204 0 AGTAGTACTC 0.859699 -17 ********** Masking position 4 Map Score: 0.819481 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 69 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 TTCCTTTACCTCCAAAAATGGGATTATA 1 11 0 ACCTCCAAAA 0.886722 -18 CAATAAGTTTACCACAAAAAACCTTTAATAT 2 53 1 ACCACAAAAA 0.864155 -29 TGGACATGCAACCACGGAAACCTGGTCAGCA 3 12 0 ACCACGAAAC 0.932844 -289 TTTAGAAGGAAACTCGCAAAAGTCCCTCCCA 4 199 0 AACTCGAAAA 0.805148 -102 ATACTATCTTACTATGGAAAAGTACCTGGAA 4 278 0 ACTATGAAAA 0.893768 -23 TTATCATAAAACTTTATAAAATTGTATTAAG 9 62 0 ACTTTAAAAA 0.70807 -91 GGTCCCTGTGACTTTGAAACACTTTACTACC 15 22 1 ACTTTGAACA 0.719791 -199 ACACTTTACTACCATGTAAAACAGGAGCTTC 15 40 1 ACCATGAAAA 0.967551 -181 GGACTTGTAAACCTTGCAAAAGTCTTACTTT 15 145 1 ACCTTGAAAA 0.977606 -76 GTCTTACTTTACCTTGAAAACTTAGGTGTAG 15 166 1 ACCTTGAAAC 0.94942 -55 ****** **** Masking position 8 Map Score: 4.52098 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 330 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 11 ********** No masking Map Score: -7.08111e-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 12 ********** No masking Map Score: -7.08111e-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 13 ********** No masking Map Score: -7.08111e-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