AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i165_Nitrate_Reductase_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 narG 300 nitrate reductase 1, alpha subunit #2 narZ 81 cryptic nitrate reductase 2, alpha subunit #3 narU 300 nitrite extrusion protein 2 Motif number 1 TCGCCGGATTTCATTAAGAGCCATTAATATGTT 1 11 1 TTTAAGGCCA 0.984161 -290 TGGGGAATACTCCTTAATACCCATCTGCATAAA 1 49 1 TTTAATCCCA 0.994425 -252 CCCTTTAGGATAATTAACAGCCACCACATAACA 1 133 0 TTTAACGCCA 0.971299 -168 ATTTACTTTATTTTTCATCCCCATCACTCTTGA 1 177 1 TTTCATCCCA 0.988695 -124 CTCTTGATCGTTATCAATTCCCACGCTGTTTCA 1 203 1 TTCAATCCCA 0.976621 -98 ACATTGCTAATGTTTAAGGGCAAGGTAACGCTC 1 236 0 TTTAAGGCAA 0.924541 -65 CATATCTGGCTACTTAATCCCCATTCTGCCCCC 3 144 1 TTTAATCCCA 0.994443 -157 ACCCAATTCATCCTTAATTCTAATAACTGGCTA 3 217 1 TTTAATCTAA 0.775519 -84 GTTTTGTCTTTTTTTCATTACCAATGTGTGCAT 3 266 1 TTTCATACCA 0.931108 -35 * ***** **** Masking position 7 Map Score: 11.5936 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 202 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 2 CTGCATAAAAATCTTAATAGTTTAAATAACTA 1 73 1 ATCTTATGTT 0.97864 -228 CTAAAGGGGTATCTTAGGAATTTACTTTATTT 1 158 1 ATCTTAGATT 0.918644 -143 ATCCCCATCACTCTTGATCGTTATCAATTCCC 1 193 1 CTCTTGTGTT 0.922959 -108 ATGAATTGGGATCTGATGCCTTGTCGGATGCG 2 39 0 ATCTGAGCTT 0.973817 -43 CAGATCGTGAATCTAAAGGGTTACATATTAAC 3 38 0 ATCTAAGGTT 0.956858 -263 TAGATTCACGATCTGAAGGGTTGAAACATGAC 3 55 1 ATCTGAGGTT 0.988781 -246 TTTGAAGGTTAGCTTGTTAGTTACATTTAGTA 3 109 1 AGCTTGTGTT 0.921495 -192 AGTAACACATATCTGGCTACTTAATCCCCATT 3 137 1 ATCTGGTCTT 0.958271 -164 ****** * *** Masking position 4 Map Score: 5.15387 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 132 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 3 ATTCCCCATGGGTAACATATTAATGGCTCT 1 27 0 GGTAACATAT 0.972442 -274 TTAAGGGCAAGGTAACGCTCTGAAACAGCG 1 226 0 GGTAACGCTC 0.943883 -75 GAATCTAAAGGGTTACATATTAACTATATT 3 32 0 GGTTACATAT 0.972442 -269 TTAGCTTGTTAGTTACATTTAGTAACACAT 3 117 1 AGTTACATTT 0.922622 -184 AGTTACATTTAGTAACACATATCTGGCTAC 3 127 1 AGTAACACAT 0.949365 -174 CTGCCCCCGCGGTTACGCTTTCTTATCTAT 3 169 1 GGTTACGCTT 0.978724 -132 ********** Masking position 5 Map Score: 3.97916 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 127 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 ATTAATATGTTACCCATGGGGAATACTCCTT 1 33 1 TCCCATGGGG 0.988073 -268 AAGATTTTTATGCAGATGGGTATTAAGGAGT 1 57 0 TCAGATGGGT 0.829697 -244 CTGTTAATTATCCTAAAGGGGTATCTTAGGA 1 146 1 TCTAAAGGGG 0.885089 -155 TCGTTATCAATTCCCACGCTGTTTCAGAGCG 1 210 1 TCCCACGCTG 0.906168 -91 AAATCGACATTGCTAATGTTTAAGGGCAAGG 1 244 0 TCTAATGTTT 0.592196 -57 CGGTTTTCTCCTGTGGGAGCCTGTCG 1 285 0 TCTCCTGTGG 0.947489 -16 ATGCCTGATGTACAACCGTGTCGCATCCGAC 2 18 1 TCAACCGTGT 0.88506 -64 CAAGCTAACCTTCAAACGGGGTTAATCTTTG 3 94 0 TCAAACGGGG 0.975726 -207 ATCCCCATTCTGCCCCCGCGGTTACGCTTTC 3 160 1 TCCCCCGCGG 0.975476 -141 TTTTTTTCATTACCAATGTGTGCATGTGAGG 3 274 1 TCCAATGTGT 0.945495 -27 * ********* Masking position 1 Map Score: 4.44346 Number of sites scoring better than the average of aligned sites = 1368 Number in coding regions = 1270 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 5 TGTCGCATCCGACAAGGCATCAGATCCCAA 2 36 1 GACAAGGCAT 0.96841 -46 GACATGACTCCTGCTCCAGG 2 72 0 GACATGACTC 0.970164 -10 TTATCAACAAGACCAGACACTTA 3 4 0 GACCAGACAC 0.985728 -297 GAAGGGTTGAAACATGACATACGTTCAAAG 3 69 1 AACATGACAT 0.900994 -232 ATGAAAAAAAGACAAAACACGAGGTAAGGC 3 254 0 GACAAAACAC 0.967084 -47 ********** Masking position 2 Map Score: 1.51578 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 94 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 AAGGAGTATTCCCCATGGGTAACATATTAA 1 34 0 CCCCATGGGT 0.912408 -267 TTATCAATTCCCACGCTGTTTCAGAGCGTT 1 213 1 CCACGCTGTT 0.977075 -88 TTGTCGGATGCGACACGGTTGTACATCAGG 2 21 0 CGACACGGTT 0.965516 -61 CCCATTCTGCCCCCGCGGTTACGCTTTCTT 3 163 1 CCCCGCGGTT 0.98251 -138 TTGCGCCTTACCTCGTGTTTTGTCTTTTTT 3 250 1 CCTCGTGTTT 0.914909 -51 ********** Masking position 10 Map Score: 1.08588 Number of sites scoring better than the average of aligned sites = 463 Number in coding regions = 429 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 GGCATCAGATCCCAATTCATTCCTGGAGCA 2 51 1 CCCAATTCAT 0.992116 -31 GCTACTTAATCCCCATTCTGCCCCCGCGGT 3 152 1 CCCCATTCTG 0.980711 -149 CAGCACTTCACCCAATTCATCCTTAATTCT 3 208 1 CCCAATTCAT 0.992116 -93 ********** Masking position 5 Map Score: 0.773494 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 19 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 TAAGGAGTATTCCCCATGGGTAACATATTA 1 35 0 TCCCCATGGG 0.953843 -266 ACGCTCTGAAACAGCGTGGGAATTGATAAC 1 212 0 ACAGCGTGGG 0.98012 -89 TCAAAGATTAACCCCGTTTGAAGGTTAGCT 3 93 1 ACCCCGTTTG 0.967732 -208 AGAAAGCGTAACCGCGGGGGCAGAATGGGG 3 162 0 ACCGCGGGGG 0.784462 -139 ATTGCGCCTTACCTCGTGTTTTGTCTTTTT 3 249 1 ACCTCGTGTT 0.905578 -52 ********** Masking position 5 Map Score: 0.226773 Number of sites scoring better than the average of aligned sites = 465 Number in coding regions = 441 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 ********** No masking Map Score: -1.4826e-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 10 ********** No masking Map Score: -1.4826e-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 11 ********** No masking Map Score: -1.4826e-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