AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -inarL_aquae_opreg_300.orf -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 dmsB2 232 dimethylsulfoxide reductase chain B #2 rpmJ 60 ribosomal protein L36 #3 secY 44 preprotein translocase SecY #4 nirB 120 nitrite reductase (NAD(P)H) large subunit #5 fhp 133 flavohemoprotein #6 frdB1 35 fumarate reductase iron-sulfur subunit #7 frdA 295 fumarate reductase flavoprotein subunit #8 purB 41 adenylosuccinate lyase #9 aq_598 99 putative protein #10 aq_811 66 putative protein #11 lysR2 50 transcriptional regulator (LysR family) #12 fdoG 212 formate dehydrogenase alpha subunit #13 aq_1188 48 putative protein #14 fdx3 74 ferredoxin #15 dmsA 23 DMSO reductase chain A #16 aq_1809 21 putative protein #17 trxA2 168 thioredoxin #18 aq_1912 300 putative protein #19 rplI 70 ribosomal protein L09 Motif number 1 GAATGAAAGTAAGAAGGATGAGGAGCTGAAT 1 37 0 AAGAAGGAGA 0.792805 -196 TATCGGCTCTAAAAAGGGAGACACTATCCAG 1 126 0 AAAAAGGGGA 0.894477 -107 GATAAGTATTAAGGGGGAAAAGTCAATGCCG 1 180 0 AAGGGGGAAA 0.898002 -53 AGTTGAAAAAGGCAAGGACTTAGGT 2 5 1 GAAAAAGGAA 0.651014 -56 TGTTAAAACAGAACGGGGAGAATTTGGCACG 5 77 1 GAACGGGGGA 0.772772 -57 TAGTTTGAGTGAAGGAGGTGAAAAG 5 119 1 GAAGGAGGGA 0.947531 -15 TGGTAAATTAAAAAGAGATGAGTGAAGTTGA 7 145 1 AAAAGAGAGA 0.96082 -151 AGGATATCAGAAGGGAGGGAAAGGAAAGAAG 8 14 0 AAGGGAGGAA 0.898002 -28 AACATTAACCGAAAGGGATAAAATTTTTAAT 9 19 0 GAAAGGGAAA 0.874799 -81 GGTAGTTCACAAAAGAGATGATAAGAGAATA 11 17 0 AAAAGAGAGA 0.96082 -34 AAAAATTTAAAAAAAAGACAAAATTTTCAAA 12 143 0 AAAAAAGAAA 0.761449 -70 TCATGATTTGAAAGGGGAATAAACTAAAAAC 12 174 1 AAAGGGGATA 0.75441 -39 TTATTTTTAAAAGGGGGACAAGGACTTAAGA 17 25 1 AAGGGGGAAA 0.898002 -144 GTCCGAGGAAAAAGGAGAGGATGAAGA 18 7 0 AAAGGAGAGA 0.968653 -294 ATTCCAGTTAAAAAGAGAAGAGCGTTTGCCA 18 155 0 AAAAGAGAGA 0.96082 -146 TACTGGAAGAAAAAAAGGCGAGGGATTACTA 18 191 1 AAAAAAGGGA 0.881654 -110 AAACCTTCGCAAAGGAGGTAAAGG 19 57 1 AAAGGAGGAA 0.944877 -14 ******** ** Masking position 2 Map Score: 19.041 Number of sites scoring better than the average of aligned sites = 1200 Number in coding regions = 1084 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 2 TTAACAGTTCTTGGAAACTTTTCTCTGATT 5 53 0 TTGGAAACTT 0.615197 -81 AATTCCGTTTGAAAAATTTATCCCCCAG 6 9 1 TTGAAAAATT 0.867307 -27 CTCACAGAATTAGGAAAATACTTTTTGCTA 7 27 1 TAGGAAAATA 0.578412 -269 CTCCCACGATTAAAAATTTTATCCCTTT 9 9 1 ATTAAAAATT 0.588512 -91 TTTCTATGACTTTAAACATTAACCGAAAGG 9 34 0 TTTAAACATT 0.884951 -66 TTATAGATTTTTTAAAAATAGTATTCACTA 9 76 0 TTTAAAAATA 0.910952 -24 TTATGTGATATTTGAATATAAGGAATTTAT 12 49 1 TTTGAATATA 0.671773 -164 AAAATAGGCATATGAACATTTTTTTATTGT 12 102 0 TATGAACATT 0.725098 -111 AAAACAATATTTTAAAAATAGGCATATGAA 12 116 0 TTTAAAAATA 0.910952 -97 AAAATATTGTTTTGAAAATTTTGTCTTTTT 12 133 1 TTTGAAAATT 0.942441 -80 ACTTTTTAAATATACAATTCACGT 13 5 1 TTTAAATATA 0.67631 -44 TGAATTAAAATATAAAAATTCCTTAATAAT 14 29 0 TATAAAAATT 0.854062 -46 TTGTCCCCCTTTTAAAAATAAAGGATAATT 17 16 0 TTTAAAAATA 0.910952 -153 AAATTAAACATATAAAAATTAGTTTAAGTC 17 54 0 TATAAAAATT 0.854062 -115 TTTTATCATTTTTGAAAATTAAGACATTTT 17 88 1 TTTGAAAATT 0.942441 -81 AGTAGTATAATTTAAACCTTCGCAAAGGAG 19 44 1 TTTAAACCTT 0.657612 -27 ********** Masking position 5 Map Score: 13.4712 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 165 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 ATGAAAGTAAGAAGGATGAGGAGCTGAATGA 1 35 0 GAAGGAGAGG 0.880993 -198 TAAGTATTAAGGGGGAAAAGTCAATGCCGTT 1 178 0 GGGGGAAAGT 0.924765 -55 AGTATCCTCAGGAGGATAGAGAGTATAAGGA 1 209 0 GGAGGAAGAG 0.961864 -24 AAGTTCTCTCGGAGGTAGAAGA 3 2 0 GGAGGTGAAG 0.976848 -43 TTTGAGTGAAGGAGGTGAAAAG 5 122 1 GGAGGTAAAA 0.783433 -12 TTTTAGTCTGGGGGATAAATTTTTCAAACG 6 16 0 GGGGGAAAAT 0.898957 -20 ATATCAGAAGGGAGGGAAAGGAAAGAAGGGA 8 11 0 GGAGGGAAGG 0.962645 -31 ACTCTTTTCTGGAGGAAGAGGTA 14 62 1 GGAGGAGAGG 0.991181 -13 TAAAAACTCTGGAGGTGGGAT 16 11 1 GGAGGTGGAT 0.74636 -11 ATTTTTAAAAGGGGGACAAGGACTTAAGACT 17 27 1 GGGGGAAAGG 0.982357 -142 AGGAAAAAGGAGAGGATGAAGA 18 2 0 AGAGGAGAAG 0.853738 -299 ACGCCGAGTCCGAGGAAAAAGGAGAGGATGA 18 14 0 CGAGGAAAAG 0.894625 -287 CCTTCGCAAAGGAGGTAAAGG 19 60 1 GGAGGTAAGG 0.98282 -11 ****** **** Masking position 5 Map Score: 17.0262 Number of sites scoring better than the average of aligned sites = 577 Number in coding regions = 512 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 4 AAGCGTCTCCACAATCAGAGAAAAGTTTCCAAG 5 41 1 AATAGAGAAA 0.84212 -93 ATGCTCTCACAGAATTAGGAAAATACTTTTTGC 7 22 1 AATAGGAAAA 0.787291 -274 TAGAAGTAGTAGTATCAAAGAAATTATTAATCC 7 89 0 AATAAAGAAA 0.898213 -207 CGTGCCTCCCACGATTAAGGAAAAAACAAGGAT 7 204 0 AATAAGGAAA 0.896311 -92 CTCCCACGATTAAAAATTTTATCCCTTT 9 6 1 AATAAAAATT 0.788931 -94 CACAAAAGAGATGATAAGAGAATATAAGCT 11 8 0 AATAGAGAAT 0.871683 -43 TTTTCATTGAATAATTAAATAAATAAGTTATGT 12 22 1 AATAAATAAA 0.496324 -191 GTGATATTTGAATATAAGGAATTTATTAACATG 12 53 1 AATAGGAATT 0.68878 -160 GCATTGATACACAATAAAAAAATGTTCATATGC 12 92 1 AATAAAAAAT 0.888409 -121 CCCCTTTCAAATCATGAAAAAATTTAAAAAAAA 12 158 0 AATAAAAAAT 0.888409 -55 AAGATAACGTAGTATAAAAAATT 13 36 1 AATAAAAATT 0.78893 -13 CCCTTGTAAAATTATTAAGGAATTTTTATATTT 14 19 1 AATAAGGAAT 0.916723 -56 CCCCCTTTTAAAAATAAAGGATAATTCTCTT 17 9 0 AATAAGGATA 0.80231 -160 TTAATTTTCAAAAATGATAAAATGGTAAATTAA 17 77 0 AATATAAAAT 0.479743 -92 GGGTTAAAGGACTATTAAGAAATACTTATGAAT 17 122 0 AATAAGAAAT 0.886347 -47 CAAGTATAAAAGATACAGGACAAAG 17 154 0 AATAAAGATA 0.805562 -15 * ** ******* Masking position 7 Map Score: 13.9042 Number of sites scoring better than the average of aligned sites = 343 Number in coding regions = 308 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 AACTCTTGCAAAAAACGTGCCAAAAAGTTCC 4 81 0 AAAACGTGCC 0.995712 -40 ACTAATTGCAAAAAGCGTGCCAAATTCTCCC 5 92 0 AAAACGTGCC 0.995712 -42 TACAAGGTATATAATCGTGCCTCCCACGATT 7 221 0 ATAACGTGCC 0.989236 -75 ACTCAAAAAGAAAAACGTTCCGAGAATGCCT 18 93 0 AAAACGTTCC 0.983176 -208 **** ****** Masking position 4 Map Score: 3.70351 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 3 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 AGAAATTATTAATCCGTAGAGCATCAAACCAAA 7 71 0 AATCCTAAGA 0.926549 -225 CCTTTCGGTTAATGTTTAAAGTCATAGAAATGA 9 34 1 AATGTTAAGC 0.872456 -66 GAAATGATAGAATGGTTAGTGAATACTATTTTT 9 60 1 AATGGTATGA 0.93583 -40 ATTGTGTATCAATGCATATTGCATGTTAATAAA 12 74 0 AATGCTATGA 0.9654 -139 AAAAACTAAGAATGCTTAAAGGAG 12 199 1 AATGCTAAGA 0.98705 -14 ATACAGGACAAAGGGTTAAAGGACTATTAAGAA 17 134 0 AAGGGTAAGA 0.913651 -35 ACGTTCCGAGAATGCCTAGAGCATTTAACAAAA 18 77 0 AATGCTAAGA 0.98705 -224 ATTATAAACTAATGTCTAAAGGAAGTAGTATAA 19 21 1 AATGTTAAGA 0.962622 -50 ***** ** ** * Masking position 8 Map Score: 5.1184 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 24 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 7 AGACTTTAACGAGTTTTATTATCA 1 4 0 GAGTTTTTTA 0.921974 -229 TCGGTTTTACGACTTTCCTTATCGGCTCTAA 1 145 0 GACTTTCTTA 0.865215 -88 CTGAGTATCCTCAGGAGGATAGA 1 220 0 GAGTATCTCA 0.911299 -13 ACCTCCGAGAGAACTTTATTATATTAAAATC 3 17 1 GAACTTTTTA 0.805821 -28 TTTTTTGCAAGAGTTTCCTCAGGAGGAGTGA 4 97 1 GAGTTTCTCA 0.951422 -24 AATTCTGTGAGAGCATCCTTACTAAAT 7 7 0 GAGCATCTTA 0.911299 -289 ACAATAAAGAGAGCTTTGTCAACTTCACTCA 7 163 0 GAGCTTTTCA 0.951422 -133 TTTTTCGAACATTTTCATTGAATAATT 12 7 1 GAACATTTCA 0.737025 -206 AAATTATCAAGACTTTTGTTAAATGCTCTAG 18 64 1 GACTTTTTTA 0.832944 -237 ******* *** Masking position 6 Map Score: 3.68673 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 184 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 TAAGGAGAAGTAAAATTTACTGGTACATAGA 1 95 1 TAAAATTACT 0.842066 -138 TTTATTATATTAAAATCTTTTAAC 3 31 1 TAAAATTTTT 0.83515 -14 ATTTTGTAGCTACATTTTTGTT 5 2 0 TACATTTTGT 0.731893 -132 ACGCTTTGCGTACAATTTTGTAGCTACATTT 5 16 0 TACAATTTGT 0.884769 -118 GTCTGGGGGATAAATTTTTCAAACGGAATT 6 10 0 TAAATTTTCA 0.653904 -26 CGCTGTATCTTAAAATATTGTT 7 284 1 TAAAATTTGT 0.956802 -12 CCGAAAGGGATAAAATTTTTAATCGTGGGAG 9 11 0 TAAAATTTTA 0.616918 -89 GTTCTCTATTTAAAATATTCACTAACTTATA 10 21 0 TAAAATTTCA 0.841725 -46 CCCTCCTGTTTAAAATGTAGTTCTCTATTTA 10 40 0 TAAAATTAGT 0.887346 -27 TGCCTATTTTTAAAATATTGTTTTGAAAATT 12 122 1 TAAAATTTGT 0.956802 -91 ATATTGTTTTGAAAATTTTGTCTTTTTTTTA 12 136 1 GAAAATTTGT 0.791808 -77 TGCGAAGGTTTAAATTATACTACTTCCTTTA 19 37 0 TAAATTTACT 0.65465 -34 ****** **** Masking position 4 Map Score: 7.17838 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 45 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 9 TGAAAGTAAGAAGGATGAGGAGCTGAATGAA 1 34 0 AAGGATAGGA 0.863069 -199 TTCCCGAGGTAAGGAGAAGTAAAATTTACTG 1 86 1 AAGGAGAGTA 0.979674 -147 TAGAGAGTATAAGGATAAGTATTAAGGGGGA 1 193 0 AAGGATAGTA 0.967972 -40 AGAGTTTCCTCAGGAGGAGTGAAAG 4 106 1 CAGGAGAGTG 0.915894 -15 TGAACTCTAGAAGTAGTAGTATCAAAGAAAT 7 98 0 AAGTAGAGTA 0.843311 -198 TAAATTAAAAAGAGATGAGTGAAGTTGACAA 7 148 1 AGAGATAGTG 0.670712 -148 AGGAAAAAACAAGGATAAGTGTAAATACAAT 7 189 0 AAGGATAGTG 0.970365 -107 AAAAAAGGCGAGGGATTACTACCAGATTACA 18 201 1 AGGGATACTA 0.851942 -100 TGAGAATATTAAGAAGTACTGTGGATCGGGA 18 273 0 AAGAAGACTG 0.733283 -28 TAATGTCTAAAGGAAGTAGTATAATTTAAAC 19 30 1 AGGAAGAGTA 0.87109 -41 ****** **** Masking position 5 Map Score: 3.83937 Number of sites scoring better than the average of aligned sites = 515 Number in coding regions = 474 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 10 CTTAGGTTATACTAAGATATTCCGCTATTG 2 29 1 ACTAAGATAT 0.890329 -32 TAAAATATTCACTAACTTATAATTATTACC 10 12 0 ACTAACTTAT 0.892757 -55 TCTTTTGTGAACTACCATATGGAAAAGAG 11 32 1 ACTACCATAT 0.978708 -19 AATTTTTTATACTACGTTATCTTGACGTGA 13 29 0 ACTACGTTAT 0.927885 -20 AAAGACGGGCTACCATATTCCTT 15 6 0 GCTACCATAT 0.943844 -18 GCGAGGGATTACTACCAGATTACACTTCTA 18 208 1 ACTACCAGAT 0.943844 -93 ********** Masking position 4 Map Score: 2.00824 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 15 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 11 TTGAAAAAGGCAAGGACTTAGGTTATACTA 2 13 1 CAAGGACTTA 0.970913 -48 ACAACCTCTGTAAGGACTTACAAAACATAA 4 45 1 TAAGGACTTA 0.900495 -76 TATTTGAATATAAGGAATTTATTAACATGC 12 57 1 TAAGGAATTT 0.93138 -156 GTAAAATTATTAAGGAATTTTTATATTTTA 14 24 1 TAAGGAATTT 0.93138 -51 AAAAGGGGGACAAGGACTTAAGACTTAAAC 17 33 1 CAAGGACTTA 0.970913 -136 ********** Masking position 6 Map Score: 3.51762 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 41 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 12 CTCGGGTCTTGGTTTCCCGAGGTAAGGAGA 1 73 1 GGTTTCCCGA 0.992787 -160 GCCGTTAATCGGTTTTACGACTTTCCTTAT 1 154 0 GGTTTTACGA 0.957258 -79 CGATCTGAAAGGTTTTCCGAAATTATCAAG 18 45 1 GGTTTTCCGA 0.988887 -256 TACACTTCTAGCTTTCCTGAGCTCGGCGGT 18 228 1 GCTTTCCTGA 0.928178 -73 ********** Masking position 5 Map Score: 0.0455295 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 34 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 13 ********** No masking Map Score: 3.64041e-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 14 ********** No masking Map Score: 3.64041e-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: 3.64041e-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