AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -inarL_ecoli_opreg_100.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 dmsA 300 anaerobic dimethyl sulfoxide reductase subunit A #2 narK 300 nitrite extrusion protein #3 narG 300 nitrate reductase 1, alpha subunit #4 fdnG 231 formate dehydrogenase-N, nitrate-inducible, alpha subunit #5 ccmC 41 heme exporter protein C #6 napF 300 ferredoxin-type protein: electron transfer #7 nirB 261 nitrite reductase (NAD(P)H) subunit #8 nirC 300 nitrite reductase activity #9 nrfA 300 periplasmic cytochrome c(552): plays a role in nitrite reduction #10 nrfB 38 formate-dependent nitrite reductase; a penta-haeme cytochrome c #11 nrfE 79 formate-dependent nitrite reductase; possible assembly function #12 frdA 294 fumarate reductase, anaerobic, flavoprotein subunit Motif number 1 GCGCCTGCGGGCGCTTTTTTTGTCTCCCTTTGA 1 4 1 CCGGGCGTGT 0.941106 -297 AACGAAAATCCCTGATGCGGTATTGGCTGCTGAGGTGAGT 1 229 1 CCGGCGGTGC 0.978859 -72 TGCCAGGCCGCCGATCGCTGTCGTTTTTACCAAACCACGG 1 271 0 CCAGCTGTAC 0.761926 -30 TATACTTCAGCCAATAGCCGAGAATACTGCCATTCCAGAA 2 31 0 CCAGCCGTGC 0.990932 -270 TGTTAATTATCCTAAAGGGGTATCTTAGGAATTTACTTTA 3 147 1 CCAGGGGGGA 0.936979 -154 AGGTCAATTTGCGAAGGCGGATTATTTTGTGGCAAACAGA 4 116 1 GCAGCGGTGT 0.989466 -116 GATGCATACCCCGATCGGGGTAAAACCTGTAGCAGGATCA 6 164 0 CCAGGGGTGT 0.989466 -137 GCCGGACGACGATAGTGCCGTCCGGCATGAGCAA 7 5 0 GAAGCCGTGA 0.853817 -257 TAAGTGTGCGGCTAACGCTGCGCGCATTGCACGCCTGTCG 8 79 1 GCAGCTGTGC 0.930598 -222 CGGAGCTGACCCAAAAGCCGAGCGGGTTATTTGCCGACAG 8 113 0 CCAGCCGTAT 0.92617 -188 GGTCAGCTCCGCCATGGCGGGCGCGTATGTGGGTCTTGGG 8 142 1 GCAGCGGTGT 0.989217 -159 GCGCCCATCACCAAAGGGCGTACGGATGGATCGAGCAAAT 8 207 0 CCAGGCGGGA 0.904044 -94 TTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTG 9 198 1 CAAGGGGTGT 0.939876 -103 CGCCATTGTTGCAATGGCGGTTTTTATTGTTTTTCACGAC 9 252 0 GCAGCGGTGT 0.989466 -49 ACGCAGGAATCAAACAGCGGTGGGCAGTGACTAAAAAAAG 12 47 1 CAAGCGGTGA 0.947634 -248 ** * **** *** Masking position 10 Map Score: 16.1524 Number of sites scoring better than the average of aligned sites = 990 Number in coding regions = 929 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 2 GAGGAGTAATTATTGTTCGGTATCAAAGGGAGACAA 1 30 0 TTTGTCTCAA 0.988507 -271 GCTAAAGGCAATTTGATGTAAATCAAACGATAAGAT 2 228 0 ATTGTGTCAA 0.941804 -73 TTTACTTTATTTTTCATCCCCATCACTCTTGATCGT 3 178 1 TTTCTCTCAC 0.827475 -123 TCCCCATCACTCTTGATCGTTATCAATTCCCACGCT 3 194 1 TTTGTCTCAA 0.988507 -107 TTTCTACCGCTATTGAGGTAGGTCAATTTGCGAAGG 4 97 1 TTTGGGTCAA 0.961587 -135 TTCTGAATCTTTTTGCGCGAAATCAAAAAGAACATC 4 154 0 TTTGGCTCAA 0.973671 -78 TATGCGGTTTATTTGGTCGCTCTCAATTTTCAGAGC 6 253 1 ATTGTCTCAA 0.959852 -48 CAACCCCGCTTATTGATGTAAATCAAATTCACCTTT 7 190 0 TTTGTGTCAA 0.983113 -72 AATCAACTTTTGTTGCTGACCTTCAAAAATTACCCT 9 44 0 TTTGTGTCAA 0.983113 -257 TTAGTCAGTATCTTCCTCTTTTTCAACAGCATGCAT 9 103 0 TTTCTCTCAA 0.95833 -198 * *** ** **** Masking position 4 Map Score: 11.2238 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 50 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 3 TGTTCGGTATCAAAGGGAGACAAAAAAAGCGCCC 1 19 0 CAAGGAGAAA 0.929071 -282 ATTTTTAACGGCAAGAGAGACAAAACAGCGAGC 4 10 0 GAAGGAGAAA 0.990211 -222 TAACCATTTGAAATGTGAGCAAAAGCCCGTTTTT 6 108 1 AATGGAGAAA 0.710706 -193 AAGAGTGGCGGGAAGCGTGGCAAAAACGGGCTTT 6 129 0 GAAGGTGAAA 0.94772 -172 ACGTAGCGGGGGAAGAGAGGAAAAGGCCGGACGA 7 36 0 GAAGGAGAAA 0.990211 -226 TAATAGAAAAGAAATCGAGGCAAAA 7 247 1 GAATGAGAAA 0.888523 -15 GTTCCGCCTCGCAAGGGGCGGAAAACACAATGGA 10 15 1 GAAGGGCAAA 0.944944 -24 CTCGCAACGCGACGGCGAGACAAATTTTACGCAG 12 19 1 GCGGGAGAAA 0.93672 -276 AACAGCGGTGGGCAGTGACTAAAAAAAGCACGAT 12 59 1 GCAGGACAAA 0.93788 -236 TTTTTAGTGCGCAAGAGGGCTAAATTATCACTGA 12 123 0 GAAGGGGAAA 0.986306 -172 TGAAGTACGTGGCTGTGGGATAAAAACAATCTGG 12 262 1 GCTGGGGAAA 0.926142 -33 * *** *** *** Masking position 12 Map Score: 9.82153 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 196 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 ATGAGATTTTTCACGGTGCTGTAAAATCCCTACCCT 2 130 0 TACGGCTAAA 0.9834 -171 GGTAACGCTCTGAAACAGCGTGGGAATTGATAACGA 3 210 0 TAACGCGGAA 0.787272 -91 TTTCAGAGCGTTACCTTGCCCTTAAACATTAGCAAT 3 231 1 TACTGCTAAA 0.694774 -70 CACCACTGCCTGACAGGCCAGTTAAAAAAATGCTAT 4 57 0 TACGCCTAAA 0.884676 -175 TTCAGGGGTATTACTGCGCGAGGAAACTAACAGTAA 4 192 0 TACGGCGAAA 0.987772 -40 AATTTAACACTAAAAGAGCAGGTAAAATTGTCTG 6 9 0 TAAGGCGAAA 0.982566 -292 CCTTCCATCATTAACGCGCTCTGAAAATTGAGAGCG 6 270 0 TAAGGCTAAA 0.732942 -31 ATCGAGCAAATTACCGAGCGTGAAAATCAGGATGAT 8 182 0 TACGGCGAAA 0.989111 -119 TTTAATCAATTGTAAGTGCATGTAAAATACCACTTT 9 143 0 TTAGGCGAAA 0.889669 -158 GTTGTACCTATAAAGGAGCAGTGGAATAGCGTTCGC 12 200 1 TAAGGCTGAA 0.941075 -95 * ** * ** * *** Masking position 15 Map Score: 7.39565 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 209 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 AAAAAAAGCGCCCGCAGGCGC 1 2 0 CCCGCAGGCG 0.988599 -299 AAACGAAAATCCCTGATGCGGTATTGGCTG 1 228 1 CCCTGATGCG 0.878144 -73 TATCAGAGGGCCGACAGGCTCCCACAGGAG 3 274 1 CCGACAGGCT 0.910705 -27 CCGACAGGCTCCCACAGGAGAAAACCG 3 284 1 CCCACAGGAG 0.962081 -17 ATAGTGCCGTCCGGCATGAGCAA 7 4 0 CCGGCATGAG 0.914583 -258 GGGTTATTTGCCGACAGGCGTGCAATGCGC 8 100 0 CCGACAGGCG 0.990479 -201 GATCCCAAGACCCACATACGCGCCCGCCAT 8 155 0 CCCACATACG 0.907512 -146 GGGGCTTCATCCGAATTGCGCCATTGTTGC 9 280 0 CCGAATTGCG 0.740328 -21 GATAATTTAGCCCTCTTGCGCACTAAAAAA 12 128 1 CCCTCTTGCG 0.932234 -167 ********** Masking position 2 Map Score: 6.40107 Number of sites scoring better than the average of aligned sites = 1019 Number in coding regions = 961 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 6 TACACAATACGGTTTGTTACTGGAATCAATCG 1 169 1 GTTGTTACTG 0.955714 -132 TCTTTTTTCAGGGGTATTACTGCGCGAGGAAA 4 202 0 GGTATTACTG 0.955713 -30 CGCTGGATTACTGATTTTTGTTC 5 2 1 GTGATTACTG 0.955714 -40 TGATTCACCAGAGATATTTCTGCTGGTTTGCT 6 55 0 GGTATTTCTG 0.920372 -246 CTCCTTAATGGGTATATTGCTGATTTGTATAA 7 153 0 GTTATTGCTG 0.942336 -109 ACATCAATAAGCGGGGTTGCTGAATCGTTAAG 7 207 1 GGGGTTGCTG 0.985135 -55 AATTAATCAACTTTTGTTGCTGACCTTCAAAA 9 52 0 CTTGTTGCTG 0.791082 -249 GACAGTGTAGGTGCGGTTACTGTCGTGAAAAA 9 231 1 GGGGTTACTG 0.982105 -70 GCCAGAAAAGAGGTGGTTTCTGGACGTATTCC 11 11 1 AGGGTTTCTG 0.742508 -69 GCCCACCGCTGTTTGATTCCTGCGTAAAATTT 12 40 0 GTGATTCCTG 0.906731 -255 * * ******** Masking position 7 Map Score: 5.41861 Number of sites scoring better than the average of aligned sites = 571 Number in coding regions = 539 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 TACTTTCGAGTGAAAATCTACCTATCTCTT 1 81 1 TGAAAATCTA 0.847492 -220 TCGAATAATTTGAAAATCAAAGAGATAGGT 1 100 0 TGAAAATCAA 0.968758 -201 GGCAATTTGATGTAAATCAAACGATAAGAT 2 228 0 TGTAAATCAA 0.942084 -73 CATAACAGACTGTAAATTAAGACGTTTTAT 3 110 0 TGTAAATTAA 0.842049 -191 GTGATGGGGATGAAAAATAAAGTAAATTCC 3 174 0 TGAAAAATAA 0.762557 -127 TAACGCGCTCTGAAAATTGAGAGCGACCAA 6 265 0 TGAAAATTGA 0.729674 -36 CGCTTATTGATGTAAATCAAATTCACCTTT 7 190 0 TGTAAATCAA 0.942084 -72 TTACCGAGCGTGAAAATCAGGATGATCCCA 8 178 0 TGAAAATCAG 0.878716 -123 GTTACTGTCGTGAAAAACAATAAAAACCGC 9 246 1 TGAAAAACAA 0.907399 -55 ********** Masking position 5 Map Score: 7.275 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 140 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 ATTCGATGTATACAAGCCTATATAGCGAACTG 1 124 1 TAAAGCCTTA 0.645488 -177 CGACTCACCTCAGCAGCCAATACCGCATCAGG 1 239 0 CACAGCCATA 0.970705 -62 TATGGGTATACTTCAGCCAATAGCCGAGAATA 2 45 0 CTCAGCCATA 0.92957 -256 TTGCCTTTAGCTACAGACACTAAGGTGGCAGA 2 253 1 CTCAGACATA 0.907707 -48 CGGATTTCATTAAGAGCCATTAATATGTTACC 3 15 1 TAGAGCCATA 0.821033 -286 AGCCACCACATAACAGACTGTAAATTAAGACG 3 116 0 TACAGACTTA 0.939638 -185 TTAGGATAATTAACAGCCACCACATAACAGAC 3 130 0 TACAGCCACA 0.880798 -171 AGTTTCGATACCAGACTCGAACAAAAATCA 5 22 0 TACAGACTGA 0.764509 -20 AAACATGAAATATCAGACAATTCCGTGACTTA 7 114 1 TACAGACATT 0.770364 -148 AATCAAATGTTTACAGACACTATTAATAAGTG 8 53 1 TTCAGACATA 0.913168 -248 CAGACTTATCCATCAGACTATACTGTTGTACC 12 176 1 CACAGACTTA 0.935725 -119 ** ****** ** Masking position 5 Map Score: 4.16379 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 335 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 9 ATAGCGAACTGCTATAGAAATAATTACACAA 1 145 1 GCTATAAAAT 0.97029 -156 TTAAAAAAATGCTATAAAATTCAGCTTAATT 4 41 0 GCTATAAATT 0.854071 -191 TGACAGGCCAGTTAAAAAAATGCTATAAAAT 4 52 0 GTTAAAAAAT 0.786772 -180 TGAATCAATCGCTATATAAATATATTTATAA 6 80 1 GCTATAAAAT 0.97029 -221 ATTTCAAATGGTTATAAATATATTTATATAG 6 91 0 GTTATAATAT 0.786773 -210 TATCTTAGCGGCTATAAAAATGGCTTATTAA 6 221 1 GCTATAAAAT 0.97029 -80 AATGAGCGGGTTTATAGAAATAGATGCACGT 7 66 0 TTTATAAAAT 0.82485 -196 CTTAAGAAAATTTATACAAATCAGCAATATA 7 142 1 TTTATAAAAT 0.82485 -120 ****** **** Masking position 6 Map Score: 4.19378 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 6 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 TATCAATTCCCACGCTGTTTCAGAGCGTTA 3 214 1 CACGCTGTTT 0.902724 -87 AGAGCGTTACCTTGCCCTTAAACATTAGCA 3 235 1 CTTGCCCTTA 0.900732 -66 GCTCGCTGTTTTGTCTCTCTT 4 2 1 CTCGCTGTTT 0.876952 -230 TTTTGTCTCTCTTGCCGTTAAAAATTAAGC 4 19 1 CTTGCCGTTA 0.946257 -213 GACAATTTTACCTGCTCTTTTAGTGTTAAA 6 13 1 CCTGCTCTTT 0.890246 -288 CAAAAATTACCCTGCCGTTTATTTGCACAA 9 27 0 CCTGCCGTTT 0.950017 -274 CTTTGAGGAACATGCAGTTATGCATGCTGT 9 84 1 CATGCAGTTA 0.910517 -217 TGCAGTTATGCATGCTGTTGAAAAAGAGGA 9 96 1 CATGCTGTTG 0.895315 -205 TGGTATTTTACATGCACTTACAATTGATTA 9 147 1 CATGCACTTA 0.839842 -154 ********** Masking position 8 Map Score: 3.52267 Number of sites scoring better than the average of aligned sites = 513 Number in coding regions = 478 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 11 GAACAATAATTACTCCTCACTTACACGTAAT 1 48 1 TACTCCTCAT 0.967045 -253 CGGAAAGAGTTACTCCTTATTTGCCGTGTGG 2 79 1 TACTCCTTAT 0.984881 -222 CCATGGGGAATACTCCTTAATACCCATCTGC 3 46 1 TACTCCTTAT 0.984881 -255 CACCTTTATATACTCCTTAATGGGTATATTG 7 166 0 TACTCCTTAT 0.984881 -96 GCTATTCCACTGCTCCTTTATAGGTACAACA 12 199 0 TGCTCCTTTT 0.899184 -96 ********* * Masking position 7 Map Score: 3.05371 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 3 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 12 TGCTTTCCTCTTTTTTCAGGGGTATT 4 216 0 CCTCTTTTTT 0.915487 -16 CCCGTTTTTGCCACGCTTCCCGCCACTCTT 6 133 1 CCACGCTTCC 0.898522 -168 ACGCTTCCCGCCACTCTTTTGATCCTGCTA 6 145 1 CCACTCTTTT 0.861796 -156 CCGGCCTTTTCCTCTCTTCCCCCGCTACGT 7 40 1 CCTCTCTTCC 0.977123 -222 CCGCTACGTGCATCTATTTCTATAAACCCG 7 61 1 CATCTATTTC 0.683515 -201 TTTTGCCTCGATTTCTTTTCTATTA 7 247 0 CCTCGATTTC 0.91633 -15 TCAGTATCTTCCTCTTTTTCAACAGCATGC 9 105 0 CCTCTTTTTC 0.965172 -196 CCAGAAACCACCTCTTTTCTGGC 11 4 0 CCTCTTTTCT 0.913925 -76 ********** Masking position 7 Map Score: 2.80966 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 213 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 13 TTTTTTTGTCTCCCTTTGATACCGAACAAT 1 25 1 TCCCTTTGAT 0.930042 -276 AATCTACCTATCTCTTTGATTTTCAAATTA 1 95 1 TCTCTTTGAT 0.871242 -206 AGACACCTCTGATACTCGTTTCG 2 288 0 CACCTCTGAT 0.76692 -13 GAGCCTGTCGGCCCTCTGATAAATCGACAT 3 265 0 GCCCTCTGAT 0.977672 -36 CTGCTGGTTTGCTCTCTCATTAGAATTTAA 6 38 0 GCTCTCTCAT 0.76405 -263 CCAGCAGAAATATCTCTGGTGAATCAATCG 6 61 1 TATCTCTGGT 0.701937 -240 CCATCCGTACGCCCTTTGGTGATGGGCGCG 8 218 1 GCCCTTTGGT 0.96558 -83 TGATGGGCGCGACCTTTGGTATCGCCTTAA 8 237 1 GACCTTTGGT 0.901904 -64 ACTGCCCACCGCTGTTTGATTCCTGCGTAA 12 45 0 GCTGTTTGAT 0.715522 -250 ********** Masking position 5 Map Score: 1.89681 Number of sites scoring better than the average of aligned sites = 388 Number in coding regions = 341 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 14 CAGCGATCGGCGGCCTGGCA 1 291 1 CGGCCTGGCA 0.977519 -10 CAAAATAATCCGCCTTCGCAAATTGACCTA 4 115 0 CGCCTTCGCA 0.97794 -117 GGGTCAGCTCCGCCATGGCGGGCGCGTATG 8 141 1 CGCCATGGCG 0.499805 -160 CAATAAAAACCGCCATTGCAACAATGGCGC 9 263 1 CGCCATTGCA 0.915605 -38 CCCCGTTCCGCCTCGCAAGGGGCGGAA 10 8 1 CCGCCTCGCA 0.941746 -31 AAATTTGTCTCGCCGTCGCGTTGCGAGTAG 12 16 0 CGCCGTCGCG 0.919829 -279 ********** Masking position 6 Map Score: 1.2659 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 412 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 15 TGGCTGCTGAGGTGAGTCGCCGTGGTTTGG 1 252 1 GGTGAGTCGC 0.940735 -49 CAGTATTCTCGGCTATTGGCTGAAGTATAC 2 42 1 GGCTATTGGC 0.917046 -259 TTTGCCGTGTGGTTAGTCGCTTTACATCGG 2 98 1 GGTTAGTCGC 0.959332 -203 AAGCCGAGCGGGTTATTTGCCGACAGGCGT 8 109 0 GGTTATTTGC 0.980486 -192 TTTCACGCTCGGTAATTTGCTCGATCCATC 8 193 1 GGTAATTTGC 0.925331 -108 TACGCCCTTTGGTGATGGGCGCGACCTTTG 8 225 1 GGTGATGGGC 0.88159 -76 TTACCCTGCCGTTTATTTGCACAATTCTAC 9 21 0 GTTTATTTGC 0.848739 -280 TTCACAGTGTGGTTATTTGTTACACATAGG 9 186 1 GGTTATTTGT 0.848739 -115 ********** Masking position 5 Map Score: 2.43517 Number of sites scoring better than the average of aligned sites = 378 Number in coding regions = 352 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727