AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i165_ecoli_bsub_100.orf -o165_ecoli_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -x5 -e 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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 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 #4 narJ 25 nitrate reductase (protein J) #5 narG 195 nitrate reductase (alpha subunit) Motif number 1 TCGCCGGATTTCATTAAGAGCCATTAATATGTT 1 11 1 TTTAAGGCCA 0.977618 -290 TGGGGAATACTCCTTAATACCCATCTGCATAAA 1 49 1 TTTAATCCCA 0.992091 -252 CCCTTTAGGATAATTAACAGCCACCACATAACA 1 133 0 TTTAACGCCA 0.959615 -168 ATTTACTTTATTTTTCATCCCCATCACTCTTGA 1 177 1 TTTCATCCCA 0.983977 -124 CTCTTGATCGTTATCAATTCCCACGCTGTTTCA 1 203 1 TTCAATCCCA 0.967044 -98 ACATTGCTAATGTTTAAGGGCAAGGTAACGCTC 1 236 0 TTTAAGGCAA 0.895907 -65 CATATCTGGCTACTTAATCCCCATTCTGCCCCC 3 144 1 TTTAATCCCA 0.992104 -157 ACCCAATTCATCCTTAATTCTAATAACTGGCTA 3 217 1 TTTAATCTAA 0.708076 -84 GTTTTGTCTTTTTTTCATTACCAATGTGTGCAT 3 266 1 TTTCATACCA 0.904718 -35 * ***** **** Masking position 7 Map Score: 9.17588 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 AAGGAGTATTCCCCATGGGTAACATATTAATGGCT 1 29 0 CCATGGTACT 0.83123 -272 GTTTAAATAACTACAGGTATAAAACGTCTTAATTT 1 92 1 CCAGGATAAC 0.987283 -209 GTTAATTATCCTAAAGGGGTATCTTAGGAATTTAC 1 148 1 CAAGGGTTCT 0.822203 -153 CGACAGGCTCCCACAGGAGAAAACCG 1 285 1 CCAGGGAAAC 0.978326 -16 CACGGTTGTACATCAGGCATCGATCTC 2 3 0 CCAGGATGAC 0.94183 -79 ATGACTCCTGCTCCAGGAATGAATTGGGATCTGAT 2 54 0 CCAGGATAAT 0.966129 -28 GATTCACGATCTGAAGGGTTGAAACATGACATACG 3 57 1 CAAGGTTAAC 0.925411 -244 AGCTAACCTTCAAACGGGGTTAATCTTTGAACGTA 3 88 0 CACGGGTAAC 0.973482 -213 CCCCATTCTGCCCCCGCGGTTACGCTTTCTTATCT 3 162 1 CCCGCGTACC 0.884065 -139 TGACATAGTTCACAAGGAAACACGCTGTCTCTGTT 5 127 1 CAAGGAAACC 0.904506 -69 TCACCTGACTCGGAAGGAGTGAACTCTC 5 178 1 CAAGGGTAAT 0.972331 -18 * **** ** ** * Masking position 1 Map Score: 7.90747 Number of sites scoring better than the average of aligned sites = 1052 Number in coding regions = 952 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 3 GAGTATTCCCCATGGGTAACATATTAATGGCTCT 1 27 0 CAGGTACATT 0.90721 -274 AATTATCCTAAAGGGGTATCTTAGGAATTTACTT 1 151 1 AAGGTTCTTG 0.929121 -150 ACGCTGTTTCAGAGCGTTACCTTGCCCTTAAACA 1 225 1 AGGGTACCTG 0.990776 -76 TCGTGAATCTAAAGGGTTACATATTAACTATATT 3 32 0 AAGGTACATT 0.976659 -269 TTAATCTTTGAACGTATGTCATGTTTCAACCCTT 3 70 0 AAGATTCATT 0.682746 -231 AATAGATAAGAAAGCGTAACCGCGGGGGCAGAAT 3 166 0 AAGGTACCGG 0.967897 -135 AAAAAAGCAGAGTGTGTGACATAGTTCACAAGGA 5 111 1 AGGGTACATG 0.985469 -85 AAACAGAGACAGCGTGTTTCCTTGTGAACTATGT 5 129 0 AGGGTTCCTG 0.982531 -67 CCTGACTCGGAAGGAGTGAACTCTC 5 181 1 AAGGTAACTT 0.866795 -15 ** * ** **** * Masking position 7 Map Score: 5.41325 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 220 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 4 TCGCCGGATTTCATTAAGAGC 1 2 1 CGCCGGATTT 0.957734 -299 CTTAATTTACAGTCTGTTATGTGGTGGCTG 1 119 1 AGTCTGTTAT 0.878872 -182 GGGATTAAGTAGCCAGATATGTGTTACTAA 3 135 0 AGCCAGATAT 0.97899 -166 AAGGCGCAATAGCCAGTTATTAGAATTAAG 3 229 0 AGCCAGTTAT 0.985244 -72 ATAGAGCCGGTTTTTTTTGATCTT 5 5 1 AGCCGGTTTT 0.986316 -191 ********** Masking position 8 Map Score: 2.50827 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 254 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 TATCAATTCCCACGCTGTTTCAGAGCGTTA 1 214 1 CACGCTGTTT 0.988272 -87 CCCCCGCGGTTACGCTTTCTTATCTATTCT 3 172 1 TACGCTTTCT 0.901544 -129 GTCCTGCCTGAACGCAGCCTTCCTTCTCCT 5 63 1 AACGCAGCCT 0.940044 -133 CTATGTCACACACTCTGCTTTTTTCACAAA 5 105 0 CACTCTGCTT 0.945742 -91 CACAAGGAAACACGCTGTCTCTGTTTATAG 5 137 1 CACGCTGTCT 0.99476 -59 ********** Masking position 2 Map Score: 1.64141 Number of sites scoring better than the average of aligned sites = 512 Number in coding regions = 494 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 ATATTAATGGCTCTTAATGAAATCCGGCGA 1 10 0 CTCTTATGAA 0.870673 -291 AACTATTAAGATTTTTATGCAGATGGGTATT 1 64 0 ATTTTATGCA 0.739181 -237 ATTAAGGATGAATTGGGTGAAGTGCTGATTG 3 204 0 AATTGGTGAA 0.886993 -97 TTTTCATTACCAATGTGTGCATGTGAGGAAC 3 277 1 CAATGGTGCA 0.801361 -24 CTTTTGATAAATGAGGTGTAA 4 1 1 CTTTTATAAA 0.709594 -25 TTTTTTTGATCTTTGAATGAAAGGCAGCTAA 5 22 1 CTTTGATGAA 0.971994 -174 CTTCCTTCTCCTTTGTGTGAACATTTTGTGA 5 81 1 CTTTGGTGAA 0.982159 -115 TTTGTGTGAACATTTTGTGAAAAAAGCAGAG 5 92 1 CATTTGTGAA 0.95582 -104 ***** ***** Masking position 11 Map Score: 1.6363 Number of sites scoring better than the average of aligned sites = 429 Number in coding regions = 366 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 7 ********** No masking Map Score: 6.2771e-13 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 8 ********** No masking Map Score: 6.2771e-13 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 9 ********** No masking Map Score: 6.2771e-13 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