AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00252_aquae_reg_100.orf -o00252_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 aspC4 80 aminotransferase (AspC family) #2 carA 300 carbamoyl phosphate synthetase small subunit #3 aspC3 31 aminotransferase (AspC family) #4 panD 300 aspartate 1-decarboxylase #5 purB 41 adenylosuccinate lyase #6 aq_598 99 putative protein #7 hisD 300 histidinol dehydrogenase #8 aq_1137 29 putative protein #9 purA 28 adenylosuccinate synthetase #10 aq_1292_alaS 68 aq_1292: hypothetical protein, alaS: alanyl-tRNA synthetase #11 icd 113 isocitrate dehydrogenase #12 aq_1515 25 putative protein #13 aq_1516 58 putative protein #14 aspS 104 aspartyl-tRNA synthetase #15 alr 252 alanine racemase #16 aspC1 260 aspartate aminotransferase #17 pepA 26 leucine aminopeptidase Motif number 1 CTTATCTTAAATAAAGGAGGAGAAAG 1 2 0 AAAGAGGAAA 0.917331 -79 TTCTAATGTACCGTGTGGAGTTAAAACTTCTTCCA 2 50 1 CGGGGAGAAA 0.960262 -251 TTCTAATGTACCGTGTGGAGTTAAAACAGGTTTGA 2 117 1 CGGGGAGAAA 0.960262 -184 TTCTAATGTACCGTGTGGAGTTAAAACAAGGTTTT 2 182 1 CGGGGAGAAA 0.960262 -119 TTCTAATGTACCGTGTGGAGTTAAAACGCAGATTG 2 247 1 CGGGGAGAAA 0.960262 -54 AAGTCTTCAAAAGAGTGAAGGAGAACCTGAGCGAG 4 37 0 AGGGAAGGAA 0.911098 -264 ACTCTTTGACGCGGAGGACGTTAAAGTCTTCAAAA 4 60 0 GGAGACGAAA 0.717488 -241 TACTTGAGGCAGATGAGAAGCTAAACTTCTACGGC 4 124 0 AAGGAAGAAA 0.936117 -177 TTTTCTATGAAAGCGTGGGGGAAAGTACTTCAGGC 4 200 0 AGGGGGGAAG 0.964936 -101 ATAGGATATCAGAAGGGAGGGAAAGGAAAGAAGGG 5 12 0 AAGGAGGAAG 0.95928 -30 TTTTACGTTCCAAAGAGAGGTGAAAAGGCTTACTC 7 178 1 CAGGAGGAAA 0.975942 -123 TTACTGCAAGGTAAACGAGGAAAAGAGAAACGATT 7 255 0 GAAGAGGAAG 0.91705 -46 AAGGAAAATTAAACGGGAGGTAAAAGT 14 3 0 AAGGAGGAAA 0.966371 -102 TGACGAAGCTCTGAAGGAAGCGGAGGGCTTCCTAG 15 25 0 CGAGAAGGAG 0.820777 -228 TTCTTGAGCTGTACACGAAGCTAAAGGGAAGTGAC 15 56 0 GAAGAAGAAA 0.873046 -197 ATTGCCGACAGCAGAGGAAGGGAAGTTCTTGAGCT 15 81 0 GAAGAAGAAG 0.849342 -172 CTGCTGTCGGCAATAAGGGGATAAATCATCCTAAG 15 102 1 CAAGGGGAAA 0.911765 -151 CTAAAAACGGAGAAGAGAGGAAGAAGGAGCTTATG 15 143 0 AAGGAGGGAA 0.919022 -110 GGCTGGCACTGGGAGAGAGGGCAAAAGAGCCCGCA 16 15 0 GGGGAGGAAA 0.984088 -246 TGATTGGAGTGGGAGAGAGGATAAGGAAGATCAGA 16 195 0 GGGGAGGAAG 0.980658 -66 TAAATTAAAAAGGGAGGAGGTGGAGCCATGATTGG 16 223 0 AGAGAGGGAG 0.864165 -38 * * * **** *** Masking position 14 Map Score: 32.793 Number of sites scoring better than the average of aligned sites = 853 Number in coding regions = 784 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 2 TCCGCTACCTCCTTTAAAGTTT 1 69 0 CGCTACCTCC 0.889941 -12 ACCACATAGCCCCTTCCTTCCATCTGCTCG 4 11 1 CCCTTCCTTC 0.992733 -290 ACTTCTACGGCACTCCCTTAAAGGAGTTCT 4 105 0 CACTCCCTTA 0.820869 -196 TCCCTTCTTTCCTTTCCCTCC 5 2 1 CCCTTCTTTC 0.885453 -40 TCTTTCCTTTCCCTCCCTTCTGATATCCTA 5 16 1 CCCTCCCTTC 0.996555 -26 CGCTCTCCTCCGAAAGTAGA 11 104 0 CGCTCTCCTC 0.895947 -10 CTTTCGTGCACACTCCCTCCACTATAATTA 14 79 1 CACTCCCTCC 0.981293 -26 GGAAGCCCTCCGCTTCCTTCAGAGCTTCGT 15 28 1 CGCTTCCTTC 0.979348 -225 AGAGCTTCGTCACTTCCCTTTAGCTTCGTG 15 48 1 CACTTCCCTT 0.594783 -205 TCAAGAACTTCCCTTCCTCTGCTGTCGGCA 15 84 1 CCCTTCCTCT 0.953146 -169 AGCTCCTTCTTCCTCTCTTCTCCGTTTTTA 15 147 1 TCCTCTCTTC 0.938942 -106 GGCTCTTTTGCCCTCTCTCCCAGTGCCAGC 16 19 1 CCCTCTCTCC 0.986995 -242 AAGGACATTCCCCTTTCTTCTCTGATCTTC 16 175 1 CCCTTTCTTC 0.977595 -86 ATCTTCCTTATCCTCTCTCCCACTCCAATC 16 199 1 TCCTCTCTCC 0.926634 -62 TGGCTCCACCTCCTCCCTTTTTAATTTAAA 16 230 1 TCCTCCCTTT 0.897216 -31 ********** Masking position 4 Map Score: 24.5045 Number of sites scoring better than the average of aligned sites = 703 Number in coding regions = 640 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 3 AAAGCTCTCGGTTCTTCTGAGAGTTCTGTTTCTAA 2 21 1 GTCTAGAGTT 0.978446 -280 TGTTTCTAATGTACCGTGTGGAGTTAAAACTTCTT 2 47 1 GTCCGGAGTT 0.997355 -254 TGTTTCTAATGTACCGTGTGGAGTTAAAACAGGTT 2 114 1 GTCCGGAGTT 0.997355 -187 AGTTTCTAATGTACCGTGTGGAGTTAAAACAAGGT 2 179 1 GTCCGGAGTT 0.997355 -122 GGTTTCTAATGTACCGTGTGGAGTTAAAACGCAGA 2 244 1 GTCCGGAGTT 0.997355 -57 CCTTAAAGGAGTTCTGCAAGGAGGAACTCTTTGAC 4 85 0 GTCTGGAGGA 0.969552 -216 CAACTTTTACGTTCCAAAGAGAGGTGAAAAGGCTT 7 174 1 GTCCAGAGGT 0.986969 -127 AATTAAACCTGTCGTAAACGGAGTAAGCCTTTTCA 7 198 0 GTGTGGAGTA 0.852749 -103 AAGCGGAGGGCTTCCTAGAAGAGGTTATCAGA 15 8 0 CTCCAGAGGT 0.907469 -245 AAAGGGGAATGTCCTTGGAGGAGTTCGCTAAGGCT 16 156 0 GTCTGGAGTT 0.993823 -105 ** ** ****** Masking position 12 Map Score: 19.1521 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 59 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 GAGAGTTCTGTTTCTAATGTACCGTGTGGAGTT 2 39 1 TTTCTATTCC 0.993959 -262 TTGATTATTGTTTCTAATGTACCGTGTGGAGTT 2 106 1 TTTCTATTCC 0.993959 -195 CTTGACGAAGTTTCTAATGTACCGTGTGGAGTT 2 171 1 TTTCTATTCC 0.993959 -130 TTGCAGATGGTTTCTAATGTACCGTGTGGAGTT 2 236 1 TTTCTATTCC 0.993959 -65 AGAAGTTTAGCTTCTCATCTGCCTCAAGTATGT 4 129 1 CTTCTATTCC 0.986062 -172 CTTTCCCTCCCTTCTGATATCCTATTCCCT 5 22 1 CTTCTATTCT 0.933026 -20 GTTGTAATCGTTTCTCTTTTCCTCGTTTACCTT 7 250 1 TTTCTTTTCT 0.820107 -51 AGTACCTGTTTCTCTAATATATCAATAACTATA 10 23 0 TCTCTATTTC 0.860743 -46 CACTTCTGTCTTTCTGATGTCCATAGGGAAAAT 15 212 1 TTTCTATTCA 0.948383 -41 TCCCCTTTCTTCTCTGATCTTCCTTATCCTCTC 16 183 1 TCTCTATTCC 0.986062 -78 ***** ** * ** Masking position 8 Map Score: 17.2294 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 17 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 GTTTTAACTCCACACGGTACATTAGAAACA 2 47 0 CACACGGTAC 0.998731 -254 GTTTTAACTCCACACGGTACATTAGAAACA 2 114 0 CACACGGTAC 0.998731 -187 GTTTTAACTCCACACGGTACATTAGAAACT 2 179 0 CACACGGTAC 0.998731 -122 GTTTTAACTCCACACGGTACATTAGAAACC 2 244 0 CACACGGTAC 0.998731 -57 ********** Masking position 4 Map Score: 12.2471 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 6 TATAATCTTCTAAAAACTTTAAAGGAGGTAGC 1 56 1 TAAACTTTAA 0.793397 -25 GAAATTAAAATAAAAACTCTAAT 2 288 1 TAAACTCTAA 0.928774 -13 TTCACTCTTTTGAAGACTTTAACGTCCTCCGC 4 53 1 TAAGCTTTAA 0.871149 -248 CCGAAAGGGATAAAATTTTTAATCGTGGGAG 6 10 0 TAAATTTTAA 0.909803 -90 TTTCTATGACTTTAAACATTAACCGAAAGGGA 6 32 0 TTAACATTAA 0.635159 -68 GAATATTGCCTAAAAGCTTTACCATGTAAAGT 7 66 0 TAAACTTTAC 0.818624 -235 AGTAGAAGTTTATAACCTCTAAGGGAAGTATT 7 138 0 TTAACTCTAA 0.747135 -163 CTTGCAGTAATTAAACCTTAAAATCCATATT 7 280 1 TAAACTTAAA 0.71726 -21 GTTTTATATATTAAATCATTAATTT 8 15 1 TAAACATTAA 0.88291 -15 TATCAAAATTTTACAATGAGCTGA 10 55 0 TAAATTTTAC 0.770995 -14 TCTCTAGAGGTAAAATCTTTAAGT 11 3 0 TAAACTTTAA 0.957971 -111 ATGTCCATAGGGAAAATTTTAAAATACTTGAG 15 228 1 GAAATTTTAA 0.622236 -25 CCTTTTTAATTTAAAATTTTAAGGAA 16 245 1 TAAATTTTAA 0.497508 -16 * *** ****** Masking position 4 Map Score: 12.2487 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 189 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 CTTTCTCCTCCTTTATTTAAGATAAGTG 1 5 1 CTCCTCTTTT 0.956041 -76 GCTCTCGGTTCTTCTGAGAGTTCTGTTTCTAATG 2 24 1 CTTCTAGTCT 0.835817 -277 GGAGTTAAAACTTCTTCCATTTCACAAAATCAAA 2 66 1 CTTCTCTTCA 0.950232 -235 ACATTAGAAACTTCGTCAAGCTTTACCTCAAAAG 2 157 0 CTTCGCGTTT 0.820089 -144 CCCTTCCTTCCATCTGCTCGCTCAGGTTCTCCTT 4 21 1 CATCTCGTCA 0.841431 -280 CGCTCAGGTTCTCCTTCACTCTTTTGAAGACTTT 4 39 1 CTCCTCTTTT 0.956041 -262 TCGGCTCCTCCAAGATTAATTAAGAATA 4 283 0 CTCCTCGTTA 0.985879 -18 CTCCTTATAGATTTTTTAAAAATA 6 86 0 CTCCTAGTTT 0.868283 -14 AGGTTATAAACTTCTACTTGGTCAACTTTTACGT 7 152 1 CTTCTCGTCA 0.98179 -149 AATCGTTTCTCTTTTCCTCGTTTACCTTGCAGTA 7 255 1 CTTTTCGTTA 0.683643 -46 GAATCATAAGCTCCTTCTTCCTCTCTTCTCCGTT 15 139 1 CTCCTCCTCT 0.918208 -114 TTCTTCCTCTCTTCTCCGTTTTTAGATTTGATAT 15 153 1 CTTCTCTTTA 0.931154 -100 CGCCTGCGGGCTCTTTTGCCCTCT 16 1 1 CGCCTCGTCT 0.926722 -260 CCTTAGCGAACTCCTCCAAGGACATTCCCCTTTC 16 158 1 CTCCTCGACA 0.900222 -103 ATGGCTCCACCTCCTCCCTTTTTAATTTAAAATT 16 229 1 CTCCTCTTTA 0.961126 -32 ***** * * *** Masking position 1 Map Score: 17.216 Number of sites scoring better than the average of aligned sites = 530 Number in coding regions = 486 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 8 GATAAGTGTAACTCTTACATACTGATATAATCTT 1 31 1 ACTACAACTG 0.886729 -50 ATTCAAGTTCAGCTTCAAAACCTTGTTTTAACTC 2 199 0 ATTAAACCTT 0.843844 -102 AAGGGAATAGACCTTTACATACTTGAGGCAGATG 4 144 0 ATTACAACTT 0.981147 -157 ACAGAATACTCACAAACTTGGAAATACTT 7 6 1 ACTACAACTT 0.967185 -295 GTGTCAAGTTAATTTAAAACACTTTTTGATTTTT 11 43 0 ATTAAAACTT 0.953141 -71 GTTTTAAATTAACTTGACACACTTCTTCAAAATG 11 57 1 ATTACAACTT 0.981147 -57 AAGGTATAAAAGGTTGACACAATTATACTCAAGA 14 48 0 ATTACAAATT 0.853203 -57 CATAGGGAAAATTTTAAAATACTTGAGGTA 15 233 1 ATTAAAACTT 0.953151 -20 * ** *** **** Masking position 7 Map Score: 4.39839 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 65 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 9 CTTTCTCCTCCTTTATTTAAGATAA 1 6 1 TCCTCCTTTA 0.951743 -75 TCCGCTACCTCCTTTAAAGTTTTTAG 1 65 0 ACCTCCTTTA 0.977557 -16 AATAATCAACAACTCTTTGATTTTGTGAAA 2 85 0 AACTCTTTGA 0.893555 -216 GTCCTCTCAAACCTGTTTTAACTCCACACG 2 128 0 ACCTGTTTTA 0.780503 -173 TGCAAGGAGGAACTCTTTGACGCGGAGGAC 4 76 0 AACTCTTTGA 0.893555 -225 CTCCTTGCAGAACTCCTTTAAGGGAGTGCC 4 97 1 AACTCCTTTA 0.924755 -204 GTTTCTCTTTTCCTCGTTTACCTTGCAGTA 7 259 1 TCCTCGTTTA 0.911564 -42 TTATGACCTCCTTGTTAGGGAATAA 12 11 0 ACCTCCTTGT 0.86911 -15 TCTGATAACCTCTTCTAGGAAGCCCTC 15 8 1 ACCTCTTCTA 0.851343 -245 CCACCTGTAATCCACGTTGAATCGTTTCGC 16 48 1 TCCACGTTGA 0.610527 -213 ********** Masking position 7 Map Score: 5.4178 Number of sites scoring better than the average of aligned sites = 596 Number in coding regions = 520 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 10 TGTAAAGGTCTATTCCCTTTTCCTTAGCCT 4 159 1 TATTCCCTTT 0.920248 -142 TAGAAAAGATTATACACTTATGATTTAAAC 4 228 1 TATACACTTA 0.758235 -73 TTAAAAATAGTATTCACTAACCATTCTATC 6 65 0 TATTCACTAA 0.878187 -35 CATTCGGGAATATTGCCTAAAAGCTTTACC 7 75 0 TATTGCCTAA 0.917702 -226 TTATTCCCTAACAAGGAGGTC 12 2 1 TATTCCCTAA 0.969249 -24 TAGGATGATTTATCCCCTTATTGCCGACAG 15 105 0 TATCCCCTTA 0.920159 -148 TATTTTAAAATTTTCCCTATGGACATCAGA 15 224 0 TTTTCCCTAT 0.674038 -29 TGGAAATGCCTATAGCCTTAGCGAACTCCT 16 143 1 TATAGCCTTA 0.829078 -118 ********** Masking position 3 Map Score: 2.48777 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 233 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 11 TTTTGAGGTAAAGCTTGACGAAGTTTCTAA 2 158 1 AAGCTTGACG 0.908317 -143 AAGTCTTCAAAAGAGTGAAGGAGAACCTGA 4 42 0 AAGAGTGAAG 0.817016 -259 AGACCTTTACATACTTGAGGCAGATGAGAA 4 140 0 ATACTTGAGG 0.839601 -161 TTTTCTATGAAAGCGTGGGGGAAAGTACTT 4 205 0 AAGCGTGGGG 0.96388 -96 ATTCTTAATTAATCTTGGAGGAGCCGA 4 284 1 AATCTTGGAG 0.560472 -17 CAACAACGGGAAAAGCGACGTAATTAAACC 7 224 0 AAAAGCGACG 0.580836 -77 TTTGTTTTATAAGCTCGGAGACCTGAG 13 42 1 AAGCTCGGAG 0.874995 -17 AAGGAAAATTAAACGGGAGGTAAAAGT 14 8 0 AAACGGGAGG 0.892894 -97 AAATTTTAAAATACTTGAGGTA 15 241 1 ATACTTGAGG 0.839601 -12 TTCCACAAAGAAGCTCGAGGAGATAGAGAA 16 118 0 AAGCTCGAGG 0.95224 -143 AGGTGGAGCCATGATTGGAGTGGGAGAGAG 16 211 0 ATGATTGGAG 0.529932 -50 TTTTAAATTAAAAAGGGAGGAGGTGGAGCC 16 231 0 AAAAGGGAGG 0.728914 -30 ********** Masking position 1 Map Score: 2.79109 Number of sites scoring better than the average of aligned sites = 532 Number in coding regions = 486 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 12 TTGAGAGGACTTTTGAGGTAAAGCTTGACG 2 148 1 TTTTGAGGTA 0.850146 -153 ACCTTTACATACTTGAGGCAGATGAGAAGC 4 138 0 ACTTGAGGCA 0.97457 -163 GGGGGAAAGTACTTCAGGCACTTTGCGAAG 4 189 0 ACTTCAGGCA 0.880489 -112 GTTATAAATCTCTAGAGGTAAAATCTTTAA 11 13 0 TCTAGAGGTA 0.930039 -101 GGAAAATTAAACGGGAGGTAAAAGT 14 6 0 ACGGGAGGTA 0.9356 -99 ATTTTAAAATACTTGAGGTA 15 243 1 ACTTGAGGTA 0.982744 -10 CGTCACAAGGTCTGGAGATACCCTTCTCTA 16 95 1 TCTGGAGATA 0.824662 -166 ********** Masking position 6 Map Score: 1.35677 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 130 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 13 AGTCTTCAAAAGAGTGAAGGAGAACCTGAG 4 41 0 AGAGTGAAGG 0.949769 -260 TTTCTATGAAAGCGTGGGGGAAAGTACTTC 4 204 0 AGCGTGGGGG 0.983575 -97 TTCTTAATTAATCTTGGAGGAGCCGA 4 285 1 ATCTTGGAGG 0.673294 -16 AAAATTTTTAATCGTGGGAG 6 1 0 ATCGTGGGAG 0.878209 -99 GAAATTAATTATAGTGGAGGGAGTGTGCAC 14 84 0 ATAGTGGAGG 0.966214 -21 AAAACGGAGAAGAGAGGAAGAAGGAGCTTA 15 145 0 AGAGAGGAAG 0.928135 -108 GCTGGCACTGGGAGAGAGGGCAAAAGAGCC 16 19 0 GGAGAGAGGG 0.857476 -242 GCTCGAGGAGATAGAGAAGGGTATCTCCAG 16 106 0 ATAGAGAAGG 0.846425 -155 AGCCATGATTGGAGTGGGAGAGAGGATAAG 16 205 0 GGAGTGGGAG 0.898044 -56 TAAATTAAAAAGGGAGGAGGTGGAGCCATG 16 228 0 AGGGAGGAGG 0.933705 -33 ********** Masking position 6 Map Score: 6.48823 Number of sites scoring better than the average of aligned sites = 459 Number in coding regions = 426 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 14 ********** No masking Map Score: -5.74586e-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: -5.74586e-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