AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i165_Nitrate_Reductase_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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 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 0.983584 -290 TGGGGAATACTCCTTAATACCCATCTGCATAAA 1 49 1 TTTAATCCCA 0.994219 -252 CCCTTTAGGATAATTAACAGCCACCACATAACA 1 133 0 TTTAACGCCA 0.970262 -168 ATTTACTTTATTTTTCATCCCCATCACTCTTGA 1 177 1 TTTCATCCCA 0.988279 -124 CTCTTGATCGTTATCAATTCCCACGCTGTTTCA 1 203 1 TTCAATCCCA 0.975773 -98 ACATTGCTAATGTTTAAGGGCAAGGTAACGCTC 1 236 0 TTTAAGGCAA 0.921955 -65 CATATCTGGCTACTTAATCCCCATTCTGCCCCC 3 144 1 TTTAATCCCA 0.994237 -157 ACCCAATTCATCCTTAATTCTAATAACTGGCTA 3 217 1 TTTAATCTAA 0.76909 -84 GTTTTGTCTTTTTTTCATTACCAATGTGTGCAT 3 266 1 TTTCATACCA 0.928731 -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 TACTCCTTAATACCCATCTGCATAAAAATC 1 56 1 TACCCATCTG 0.946858 -245 TTCCTAAGATACCCCTTTAGGATAATTAAC 1 148 0 ACCCCTTTAG 0.988874 -153 TTATTTTTCATCCCCATCACTCTTGATCGT 1 184 1 TCCCCATCAC 0.922992 -117 GTTAATATGTAACCCTTTAGATTCACGATC 3 38 1 AACCCTTTAG 0.982616 -263 GTCATGTTTCAACCCTTCAGATCGTGAATC 3 57 0 AACCCTTCAG 0.988874 -244 TCAAAGATTAACCCCGTTTGAAGGTTAGCT 3 93 1 ACCCCGTTTG 0.965448 -208 ********** Masking position 7 Map Score: 5.07854 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 151 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 AGAGCCATTAATATGTTACCCATGGGGAAT 1 27 1 ATATGTTACC 0.971092 -274 CGCTGTTTCAGAGCGTTACCTTGCCCTTAA 1 226 1 GAGCGTTACC 0.941219 -75 AATATAGTTAATATGTAACCCTTTAGATTC 3 32 1 ATATGTAACC 0.971092 -269 ATGTGTTACTAAATGTAACTAACAAGCTAA 3 117 0 AAATGTAACT 0.919035 -184 GTAGCCAGATATGTGTTACTAAATGTAACT 3 127 0 ATGTGTTACT 0.946946 -174 ATAGATAAGAAAGCGTAACCGCGGGGGCAG 3 169 0 AAGCGTAACC 0.977674 -132 ********** Masking position 6 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 GACGTTTTATACCTGTAGTTATTTAAACTATTAA 1 86 0 ACGAGTATTT 0.919692 -215 GTCTTAATTTACAGTCTGTTATGTGGTGGCTGTT 1 117 1 AATTGTATGT 0.90461 -184 CTTGCCCTTAAACATTAGCAATGTCGATTTATCA 1 245 1 ACTAGCATGT 0.974214 -56 ATGAATTGGGATCTGATGCCTTGTCGGATGCGAC 2 37 0 ACGTGCTTGT 0.971109 -45 TCATTCCTGGAGCAGGAGTCATGTC 2 67 1 ACGAGTATGT 0.98879 -15 TTAATCTTTGAACGTATGTCATGTTTCAACCCTT 3 70 0 ACTTGTATGT 0.986499 -231 ATTGCGCCTTACCTCGTGTTTTGTCTTTTTTTCA 3 249 1 ACCTGTTTGT 0.949083 -52 * * * *** **** Masking position 1 Map Score: 2.51365 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 134 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 CAGCCACCACATAACAGACTGTAAATTAAG 1 119 0 ATAACAGACT 0.93898 -182 TATCAGAGGGCCGACAGGCTCCCACAGGAG 1 274 1 CCGACAGGCT 0.961535 -27 ACACGGTTGTACATCAGGCATCGATCTC 2 9 0 ACATCAGGCA 0.915993 -73 CTAAATGTAACTAACAAGCTAACCTTCAAA 3 109 0 CTAACAAGCT 0.927312 -192 TTAGTAACACATATCTGGCTACTTAATCCC 3 135 1 ATATCTGGCT 0.966186 -166 CTTAATTCTAATAACTGGCTATTGCGCCTT 3 229 1 ATAACTGGCT 0.981588 -72 ********** Masking position 5 Map Score: 2.33634 Number of sites scoring better than the average of aligned sites = 606 Number in coding regions = 546 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 6 TTAATATGTTACCCATGGGGAATACTCCTT 1 34 1 ACCCATGGGG 0.775066 -267 AACGCTCTGAAACAGCGTGGGAATTGATAA 1 213 0 AACAGCGTGG 0.977737 -88 CTTAAACATTAGCAATGTCGATTTATCAGA 1 251 1 AGCAATGTCG 0.911714 -50 CCTGATGTACAACCGTGTCGCATCCGACAA 2 21 1 AACCGTGTCG 0.977346 -61 AAGAAAGCGTAACCGCGGGGGCAGAATGGG 3 163 0 AACCGCGGGG 0.962759 -138 TTTTTTCATTACCAATGTGTGCATGTGAGG 3 275 1 ACCAATGTGT 0.843413 -26 ********** Masking position 1 Map Score: 1.69275 Number of sites scoring better than the average of aligned sites = 706 Number in coding regions = 663 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 7 TTGGGATCTGATGCCTTGTCGGATGCGACA 2 36 0 ATGCCTTGTC 0.969738 -46 CCTGGAGCAGGAGTCATGTC 2 72 1 GAGTCATGTC 0.97142 -10 TAAGTGTCTGGTCTTGTTGATAA 3 4 1 GTGTCTGGTC 0.986338 -297 CTTTGAACGTATGTCATGTTTCAACCCTTC 3 69 0 ATGTCATGTT 0.904878 -232 GCCTTACCTCGTGTTTTGTCTTTTTTTCAT 3 254 1 GTGTTTTGTC 0.968466 -47 ********** Masking position 9 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 8 CCTGCTCCAGGAATGAATTGGGATCTGATGC 2 52 0 GAATGAATGG 0.990843 -30 TAACCGCGGGGGCAGAATGGGGATTAAGTAG 3 153 0 GGCAGAATGG 0.989917 -148 AGTGCTGATTGAAAGAATAGATAAGAAAGCG 3 184 0 GAAAGAATGA 0.964583 -117 TTAGAATTAAGGATGAATTGGGTGAAGTGCT 3 209 0 GGATGAATGG 0.994061 -92 ******** ** Masking position 6 Map Score: 1.26514 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 30 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 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