AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -inarL_ecoli_opreg_300.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 yhfC 270 putative transport #8 nirB 261 nitrite reductase (NAD(P)H) subunit #9 nirC 300 nitrite reductase activity #10 nrfA 300 periplasmic cytochrome c(552): plays a role in nitrite reduction #11 nrfB 38 formate-dependent nitrite reductase; a penta-haeme cytochrome c #12 nrfE 79 formate-dependent nitrite reductase; possible assembly function #13 frdA 294 fumarate reductase, anaerobic, flavoprotein subunit Motif number 1 CAAAAAAAGCGCCCGCAGGCGC 1 2 0 GCCCGAGGCG 0.958421 -299 TGCCAGGCCGCCGATCGCTGTCGTTTTTAC 1 281 0 GCCGACGCTG 0.94828 -20 GTATACTTCAGCCAATAGCCGAGAATACTGC 2 41 0 GCCAAAGCCG 0.781512 -260 TTATCAGAGGGCCGACAGGCTCCCACAGGAG 3 273 1 GCCGAAGGCT 0.933234 -28 CAAAAGAGTGGCGGGAAGCGTGGCAAAAACG 6 135 0 GCGGGAGCGT 0.886133 -166 CAGGTTTTACCCCGATCGGGGTATGCATCTT 6 175 1 CCCGACGGGG 0.878517 -126 AGCGGGATATGCCGCGAGCGGGCGATTTTAG 7 219 0 GCCGCAGCGG 0.939064 -52 TTGCTCATGCCGGACGGCACTATCGTCGT 8 9 1 GCCGGCGGCA 0.886711 -253 AGAGGAAAAGGCCGGACGACGATAGTGCCGT 8 24 0 GCCGGCGACG 0.917312 -238 AGAAATAGATGCACGTAGCGGGGGAAGAGAG 8 51 0 GCACGAGCGG 0.69663 -211 GGCGTGCAATGCGCGCAGCGTTAGCCGCACA 9 83 0 GCGCGAGCGT 0.744439 -218 CGGGTTATTTGCCGACAGGCGTGCAATGCGC 9 100 0 GCCGAAGGCG 0.977661 -201 TGACCCAAAAGCCGAGCGGGTTATTTGCCGA 9 116 0 GCCGACGGGT 0.967464 -185 GCTCCGCCATGGCGGGCGCGTATGTGGGTCT 9 147 1 GGCGGCGCGT 0.789286 -154 CCCTTGCGAGGCGGAACGGGG 11 1 0 GCGGACGGGG 0.960556 -38 TTTAGTCACTGCCCACCGCTGTTTGATTCCT 13 51 0 GCCCACGCTG 0.872856 -244 ***** ***** Masking position 8 Map Score: 13.4383 Number of sites scoring better than the average of aligned sites = 3561 Number in coding regions = 3229 Number in noncoding regions = 332 Number of orfs with sites within 600 bp upstream = 206 Fraction of orfs with sites within 600 bp upstream = 0.0330871 Motif number 2 GGAGTAATTATTGTTCGGTATCAAAGGGAGACAA 1 30 0 TTGCGATCAA 0.983935 -271 ATCTTATCGTTTGATTTACATCAAATTGCCTTTA 2 228 1 TTGTTATCAA 0.57396 -73 CCCATCACTCTTGATCGTTATCAATTCCCACGCT 3 196 1 TTGCGATCAA 0.869117 -105 CCTTCGCAAATTGACCTACCTCAATAGCGGTAGA 4 99 0 TTGCTCTCAA 0.88438 -133 CTGAATCTTTTTGCGCGAAATCAAAAAGAACATC 4 154 0 TTGCGATCAA 0.741382 -78 TGCGGTTTATTTGGTCGCTCTCAATTTTCAGAGC 6 255 1 TTGCGCTCAA 0.879247 -46 AAAGGTGAATTTGATTTACATCAATAAGCGGGGT 8 190 1 TTGTTATCAA 0.57396 -72 ACTGTGAATGTTGTCTTTAATCAATTGTAAGTGC 10 160 0 TTGTTATCAA 0.956958 -141 *** ** ***** Masking position 13 Map Score: 9.6879 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 33 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 GTATCAAAGGGAGACAAAAAAAGCGCCCGCAGGCGC 1 11 0 GGACAAAACC 0.796044 -290 TTTAGCTACAGACACTAAGGTGGCAGACATCGAAAC 2 258 1 GCACAAGGCG 0.809559 -43 AACGGCAAGAGAGACAAAACAGCGAGC 4 2 0 GGACAAAGGG 0.88253 -230 ACATCTGTTTGCCACAAAATAATCCGCCTTCGCAAA 4 123 0 GCACAAAACG 0.979579 -109 GTATTACTGCGCGAGGAAACTAACAGTAAAATTCTG 4 185 0 GGAGAAAACG 0.966739 -47 ATTAGAATTTAACACTAAAAGAGCAGGTAAAATTGT 6 14 0 ACACAAAACG 0.922093 -287 ATTCTAATGAGAGAGCAAACCAGCAGAAATATCTCT 6 42 1 GGAGAAAACG 0.966739 -259 AAAATTGAGAGCGACCAAATAAACCGCATAATTAAT 6 247 0 GGACAAAACG 0.977407 -54 TAACAAACAGAGCAGAAAAAAAGCAAGTGAAGAGAT 7 21 1 ACAGAAAACA 0.662401 -250 ATTTAAACAGATCACAAAATCACCTAAAATCGCCCG 7 196 1 ACACAAAACA 0.744923 -75 AGCGGGGGAAGAGAGGAAAAGGCCGGACGACGATAG 8 30 0 GGAGAAAGCG 0.962431 -232 GTGCAAAAAATAGACAAAATGAGCGGGTTTATAGAA 8 78 0 TGACAAAACG 0.822809 -184 ATTTTCTTAAGTCACGGAATTGTCTGATATTTCATG 8 117 0 GCACGAAGCG 0.809557 -145 TTGCACGCCTGTCGGCAAATAACCCGCTCGGCTTTT 9 105 1 GCGGAAAACG 0.764178 -196 TACGGATGGATCGAGCAAATTACCGAGCGTGAAAAT 9 191 0 TGAGAAAACA 0.434965 -110 GGTCGCGCCCATCACCAAAGGGCGTACGGATGGATC 9 215 0 ACACAAAGGA 0.3365 -86 GCCAGAAAAGAGGTGGTTTCTGGACG 12 1 1 GCAGAAAGTG 0.584835 -79 TAACAACAACGCCAGAAAACCGACTTCAGGAAGGAA 12 39 0 GCAGAAAGCT 0.633576 -41 GCGGTGGGCAGTGACTAAAAAAAGCACGATCTGATG 13 63 1 GGACAAAAGA 0.677754 -232 GATTAATTTAATTACTAAACCATCAGATCGTGCTTT 13 83 0 ATACAAAACG 0.482558 -212 * *** *** * * * Masking position 8 Map Score: 12.1413 Number of sites scoring better than the average of aligned sites = 1478 Number in coding regions = 1312 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 4 AGTATACCCATACCCGGAAAGAGTTACTCCTTATTT 2 65 1 TACCGAAGGA 0.768824 -236 ATTCCTAAGATACCCCTTTAGGATAATTAACAGCCA 3 143 0 TACCTTAGAA 0.762993 -158 TGGGAATTGATAACGATCAAGAGTGATGGGGATGAA 3 190 0 TACGTAAGGA 0.727056 -111 GAGCGTTACCTTGCCCTTAAACATTAGCAATGTCGA 3 236 1 TTCCTAAAAA 0.853313 -65 TTTGTCTCTCTTGCCGTTAAAAATTAAGCTGAATTT 4 20 1 TTCCTAAAAA 0.881704 -212 CGCGCAGTAATACCCCTGAAAAAAGAGGAAAGCA 4 208 1 TACCTAAAAA 0.959005 -24 CATTAGAATTTAACACTAAAAGAGCAGGTAAAATTG 6 15 0 TACATAAAAA 0.644833 -286 AGATTCTAAATAGCCTTCAAGAACAAGGCCATCCCT 7 53 1 TACCTAAGAA 0.980081 -218 ATCAGCAATATACCCATTAAGGAGTATATAAAGGTG 8 161 1 TACCTAAGAA 0.973379 -101 AACATTTGATTATCCTTTAAAAAATAAAAACAAAAA 9 28 0 TACCTAAAAA 0.940568 -273 CTTTTGTTGCTGACCTTCAAAAATTACCCTGCCGTT 10 38 0 TGCCTAAAAA 0.814729 -263 AGATACTGACTAACTCTAAAGTGGTATTTTACATGC 10 126 1 TACTTAAGGA 0.664772 -175 TATACTGTTGTACCTATAAAGGAGCAGTGGAATAGC 13 194 1 TACTTAAGAA 0.873111 -101 TTTCAGGTACTTACCCTGAAGTACGTGGCTGTGGGA 13 246 1 TTCCTAAGAT 0.610363 -49 ** ** * *** * * Masking position 10 Map Score: 8.1612 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 133 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 5 AAGAGATAGGTAGATTTTCACTCGAAAGTA 1 81 0 TAGATTTTCA 0.866701 -220 ACCTATCTCTTTGATTTTCAAATTATTCGA 1 100 1 TTGATTTTCA 0.973177 -201 ATCTTATCGTTTGATTTACATCAAATTGCC 2 228 1 TTGATTTACA 0.95008 -73 ATAAAACGTCTTAATTTACAGTCTGTTATG 3 110 1 TTAATTTACA 0.861832 -191 GGAATTTACTTTATTTTTCATCCCCATCAC 3 174 1 TTATTTTTCA 0.789811 -127 TTGGTCGCTCTCAATTTTCAGAGCGCGTTA 6 265 1 TCAATTTTCA 0.75951 -36 AAAGGTGAATTTGATTTACATCAATAAGCG 8 190 1 TTGATTTACA 0.95008 -72 TGGGATCATCCTGATTTTCACGCTCGGTAA 9 178 1 CTGATTTTCA 0.894482 -123 GCGGTTTTTATTGTTTTTCACGACAGTAAC 10 246 0 TTGTTTTTCA 0.919777 -55 ********** Masking position 5 Map Score: 6.4225 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 6 CGATTGATTCCAGTAACAAACCGTATTGTGTA 1 169 0 CAGAACAACC 0.959099 -132 TTTCCTCGCGCAGTAATACCCCTGAAAAAAGA 4 202 1 CAGAATACCC 0.966717 -30 GAACAAAAATCAGTAATCCAGCG 5 2 0 CAGAATCAGC 0.956736 -40 AGCAAACCAGCAGAAATATCTCTGGTGAATCA 6 55 1 CAGAATACTC 0.847694 -246 ACAAACAGAGCAGAAAAAAAGCAAGTGAAGAG 7 23 1 CAGAAAAAGC 0.773808 -248 TTATACAAATCAGCAATATACCCATTAAGGAG 8 153 1 CAGAATAACC 0.947954 -109 CTTAACGATTCAGCAACCCCGCTTATTGATGT 8 207 0 CAGAACCCGC 0.978449 -55 TTTTTCACGACAGTAACCGCACCTACACTGTC 10 231 0 CAGAACCCAC 0.952719 -70 GGAATACGTCCAGAAACCACCTCTTTTCTGGC 12 11 0 CAGAACCCCT 0.83897 -69 AAATTTTACGCAGGAATCAAACAGCGGTGGGC 13 40 1 CAGAATCAAC 0.907533 -255 *** **** *** Masking position 6 Map Score: 6.42253 Number of sites scoring better than the average of aligned sites = 405 Number in coding regions = 382 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 CTGAGGTGAGTCGCCGTGGTTTGGTAAAAA 1 258 1 TCGCCGTGGT 0.960773 -43 AGGCCGCCGATCGCTGTCGTTTTTACCAAA 1 277 0 TCGCTGTCGT 0.798791 -24 CTCTGATAAATCGACATTGCTAATGTTTAA 3 252 0 TCGACATTGC 0.842664 -49 ACAAAATAATCCGCCTTCGCAAATTGACCT 4 116 0 CCGCCTTCGC 0.965067 -116 ACATACGCGCCCGCCATGGCGGAGCTGACC 9 142 0 CCGCCATGGC 0.984285 -159 ACAATAAAAACCGCCATTGCAACAATGGCG 10 262 1 CCGCCATTGC 0.983057 -39 CATCCGAATTGCGCCATTGTTGCAATGGCG 10 273 0 GCGCCATTGT 0.894328 -28 AAAATTTGTCTCGCCGTCGCGTTGCGAGTA 13 17 0 TCGCCGTCGC 0.98304 -278 ********** Masking position 7 Map Score: 4.1914 Number of sites scoring better than the average of aligned sites = 1237 Number in coding regions = 1197 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 8 TTGTGTAATTATTTCTATAGCAGTTCGCTAT 1 145 0 ATTTTATAGC 0.964603 -156 AATTAAGCTGAATTTTATAGCATTTTTTTAA 4 41 1 AATTTATAGC 0.830033 -191 ATTTTATAGCATTTTTTTAACTGGCCTGTCA 4 52 1 ATTTTTTAAC 0.754831 -180 TTATAAATATATTTATATAGCGATTGATTCA 6 80 0 ATTTTATAGC 0.964603 -221 CTATATAAATATATTTATAACCATTTGAAAT 6 91 1 ATATTATAAC 0.754832 -210 TTAATAAGCCATTTTTATAGCCGCTAAGATA 6 221 0 ATTTTATAGC 0.964603 -80 ACGTGCATCTATTTCTATAAACCCGCTCATT 8 66 1 ATTTTATAAA 0.797142 -196 TATATTGCTGATTTGTATAAATTTTCTTAAG 8 142 0 ATTTTATAAA 0.797142 -120 **** ****** Masking position 9 Map Score: 3.4355 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 9 AGACACTAAGGTGGCAGACATCGAAACGAG 2 267 1 GTGGCAGACA 0.972895 -34 GGATTATTTTGTGGCAAACAGATGTTCTTT 4 134 1 GTGGCAAACA 0.95803 -98 GGCGGGAAGCGTGGCAAAAACGGGCTTTTG 6 127 0 GTGGCAAAAA 0.935554 -174 GATCAAAAGAGTGGCGGGAAGCGTGGCAAA 6 139 0 GTGGCGGGAA 0.967487 -162 GTTACACATAGGGGCGAGCAATGTCATGAC 10 204 1 GGGGCGAGCA 0.961043 -97 CGCCTCGCAAGGGGCGGAAAACACAATGGA 11 19 1 GGGGCGGAAA 0.967487 -20 ********** Masking position 10 Map Score: 3.01881 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 178 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 ATTCGATGTATACAAGCCTATATAGCGAACTG 1 124 1 TAAAGCCTTA 0.599943 -177 CGACTCACCTCAGCAGCCAATACCGCATCAGG 1 239 0 CACAGCCATA 0.964631 -62 TATGGGTATACTTCAGCCAATAGCCGAGAATA 2 45 0 CTCAGCCATA 0.915708 -256 TTGCCTTTAGCTACAGACACTAAGGTGGCAGA 2 253 1 CTCAGACATA 0.890051 -48 CGGATTTCATTAAGAGCCATTAATATGTTACC 3 15 1 TAGAGCCATA 0.790625 -286 AGCCACCACATAACAGACTGTAAATTAAGACG 3 116 0 TACAGACTTA 0.927604 -185 TTAGGATAATTAACAGCCACCACATAACAGAC 3 130 0 TACAGCCACA 0.858796 -171 AGTTTCGATACCAGACTCGAACAAAAATCA 5 22 0 TACAGACTGA 0.727678 -20 AAACATGAAATATCAGACAATTCCGTGACTTA 8 114 1 TACAGACATT 0.734131 -148 AATCAAATGTTTACAGACACTATTAATAAGTG 9 53 1 TTCAGACATA 0.896438 -248 CAGACTTATCCATCAGACTATACTGTTGTACC 13 176 1 CACAGACTTA 0.922975 -119 ** ****** ** Masking position 5 Map Score: 3.12029 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 11 TTTACATCGGTAAGGGTAGGGATTTTACAG 2 118 1 TAAGGGTAGG 0.86851 -183 ATAGTTTAAATAACTACAGGTATAAAACGT 3 89 1 TAACTACAGG 0.761795 -212 TGCTAATGTTTAAGGGCAAGGTAACGCTCT 3 235 0 TAAGGGCAAG 0.95235 -66 GCTTAATTTTTAACGGCAAGAGAGACAAAA 4 19 0 TAACGGCAAG 0.95235 -213 TTTAACACTAAAAGAGCAGGTAAAATTGTC 6 13 0 AAAGAGCAGG 0.8058 -288 TTGTGCAAATAAACGGCAGGGTAATTTTTG 10 27 1 AAACGGCAGG 0.955857 -274 ACAGCATGCATAACTGCATGTTCCTCAAAG 10 84 0 TAACTGCATG 0.906341 -217 TAATCAATTGTAAGTGCATGTAAAATACCA 10 147 0 TAAGTGCATG 0.906341 -154 ********** Masking position 3 Map Score: 1.94737 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 268 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 12 TATTGTTCGGTATCAAAGGGAGACAAAAAA 1 26 0 TATCAAAGGG 0.863574 -275 TCGAAACGAGTATCAGAGGTGTCT 2 287 1 TATCAGAGGT 0.959397 -14 TCCCACGCTGTTTCAGAGCGTTACCTTGCC 3 221 1 TTTCAGAGCG 0.964046 -80 AATGTCGATTTATCAGAGGGCCGACAGGCT 3 264 1 TATCAGAGGG 0.97992 -37 TTTCCTCTTTTTTCAGGGGTATTACTGCGC 4 209 0 TTTCAGGGGT 0.904461 -23 CGCTCTCAATTTTCAGAGCGCGTTAATGAT 6 270 1 TTTCAGAGCG 0.964046 -31 TAAATTGCATTTTAAGAGGTGATTTTGATC 7 146 0 TTTAAGAGGT 0.79963 -125 ********** Masking position 5 Map Score: 4.05891 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 73 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 ********** No masking Map Score: 1.17483e-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: 1.17483e-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: 1.17483e-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