AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i165_ecoli_bsub_300.orf -o165_ecoli_bsub_300.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) #6 ywiD 143 ywiD Motif number 1 AACATATTAATGGCTCTTAATGAAATCCGGCGA 1 11 0 TGGCCTTAAA 0.983144 -290 TTTATGCAGATGGGTATTAAGGAGTATTCCCCA 1 49 0 TGGGATTAAA 0.985909 -252 TGTTATGTGGTGGCTGTTAATTATCCTAAAGGG 1 133 1 TGGCGTTAAA 0.988369 -168 TCAAGAGTGATGGGGATGAAAAATAAAGTAAAT 1 177 0 TGGGATGAAA 0.980328 -124 TGAAACAGCGTGGGAATTGATAACGATCAAGAG 1 203 0 TGGGATTGAA 0.935883 -98 GAGCGTTACCTTGCCCTTAAACATTAGCAATGT 1 236 1 TTGCCTTAAA 0.835952 -65 GGGGGCAGAATGGGGATTAAGTAGCCAGATATG 3 144 0 TGGGATTAAA 0.985914 -157 ATGCACACATTGGTAATGAAAAAAAGACAAAAC 3 266 0 TGGTATGAAA 0.905194 -35 TTTGAATGAAAGGCAGCTAATGACCCAAGCGTC 5 33 1 AGGCGCTAAA 0.831262 -163 TTCATCATACAGGCTGTGAAATACATCACTGCT 6 67 1 AGGCGTGAAA 0.94388 -77 **** ***** * Masking position 10 Map Score: 8.79544 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 268 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 2 GTCTTAATTTACAGTCTGTTATGTGGTGGC 1 117 1 ACAGTCTGTT 0.929337 -184 ACGCTCTGAAACAGCGTGGGAATTGATAAC 1 212 0 ACAGCGTGGG 0.984624 -89 AGAAAGCGTAACCGCGGGGGCAGAATGGGG 3 162 0 ACCGCGGGGG 0.961576 -139 ATTGCGCCTTACCTCGTGTTTTGTCTTTTT 3 249 1 ACCTCGTGTT 0.929816 -52 ATAGAGCCGGTTTTTTTTGATC 5 3 1 AGAGCCGGTT 0.908625 -193 TGAAAAAAGCAGAGTGTGTGACATAGTTCA 5 109 1 AGAGTGTGTG 0.887265 -87 ATAAACAGAGACAGCGTGTTTCCTTGTGAA 5 135 0 ACAGCGTGTT 0.988037 -61 GATGTATTTCACAGCCTGTATGATGAATGT 6 64 0 ACAGCCTGTA 0.953052 -80 AGGAAAACCTCCTGTGCTAAGGATAG 6 128 0 ACCTCCTGTG 0.945074 -16 ********** Masking position 1 Map Score: 8.40629 Number of sites scoring better than the average of aligned sites = 1222 Number in coding regions = 1157 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 3 AAGGAGTATTCCCCATGGGTAACATATTAATGGCT 1 29 0 CCATGGTACT 0.821995 -272 GTTTAAATAACTACAGGTATAAAACGTCTTAATTT 1 92 1 CCAGGATAAC 0.986448 -209 GTTAATTATCCTAAAGGGGTATCTTAGGAATTTAC 1 148 1 CAAGGGTTCT 0.812586 -153 CGACAGGCTCCCACAGGAGAAAACCG 1 285 1 CCAGGGAAAC 0.976917 -16 CACGGTTGTACATCAGGCATCGATCTC 2 3 0 CCAGGATGAC 0.938198 -79 ATGACTCCTGCTCCAGGAATGAATTGGGATCTGAT 2 54 0 CCAGGATAAT 0.963956 -28 GATTCACGATCTGAAGGGTTGAAACATGACATACG 3 57 1 CAAGGTTAAC 0.920839 -244 AGCTAACCTTCAAACGGGGTTAATCTTTGAACGTA 3 88 0 CACGGGTAAC 0.971767 -213 CCCCATTCTGCCCCCGCGGTTACGCTTTCTTATCT 3 162 1 CCCGCGTACC 0.877295 -139 TGACATAGTTCACAAGGAAACACGCTGTCTCTGTT 5 127 1 CAAGGAAACC 0.898792 -69 TCACCTGACTCGGAAGGAGTGAACTCTC 5 178 1 CAAGGGTAAT 0.970544 -18 * **** ** ** * Masking position 1 Map Score: 6.3036 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 4 TATGTTACCCATGGGGAATACTCCTTAATA 1 38 1 ATGGGGAATA 0.947154 -263 TTTTATGCAGATGGGTATTAAGGAGTATTC 1 53 0 ATGGGTATTA 0.959268 -248 ATTATCCTAAAGGGGTATCTTAGGAATTTA 1 152 1 AGGGGTATCT 0.909828 -149 ATCAAGAGTGATGGGGATGAAAAATAAAGT 1 181 0 ATGGGGATGA 0.974932 -120 CCAGGAATGAATTGGGATCTGATGCCTTGT 2 47 0 ATTGGGATCT 0.876993 -35 CGGGGGCAGAATGGGGATTAAGTAGCCAGA 3 148 0 ATGGGGATTA 0.988549 -153 GAAAGAAAAAAGGAGGATTTCG 6 3 0 AGGAGGATTT 0.852658 -141 ********** Masking position 7 Map Score: 4.30606 Number of sites scoring better than the average of aligned sites = 321 Number in coding regions = 273 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 5 TGATAACGATCAAGAGTGATGGGGATGAAA 1 189 0 CAAGAGTGAT 0.96024 -112 CAGGCTCCCACAGGAGAAAACCG 1 288 1 CAGGAGAAAA 0.880671 -13 ACTCCTGCTCCAGGAATGAATTGGGATCTG 2 56 0 CAGGAATGAA 0.96024 -26 ATTCCTGGAGCAGGAGTCATGTC 2 69 1 CAGGAGTCAT 0.977943 -13 CCTGACTCGGAAGGAGTGAACTCTC 5 181 1 AAGGAGTGAA 0.96024 -15 TGAGCCTGTACAGCAGTGATGTATTTCACA 6 81 0 CAGCAGTGAT 0.972822 -63 ********** Masking position 5 Map Score: 2.80502 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 272 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 6 CATGGGTAACATATTAATGGCTCTTAATGAAA 1 19 0 AATTAAGGCT 0.856387 -282 AACAGCCACCACATAACAGACTGTAAATTAAG 1 119 0 AATAACGACT 0.821448 -182 CTGTTAATTATCCTAAAGGGGTATCTTAGGAA 1 146 1 TCTAAAGGGT 0.831935 -155 CAGATCGTGAATCTAAAGGGTTACATATTAAC 3 38 0 ACTAAAGGTT 0.889309 -263 TAGATTCACGATCTGAAGGGTTGAAACATGAC 3 55 1 ACTGAAGGTT 0.652434 -246 CAAGCTAACCTTCAAACGGGGTTAATCTTTGA 3 93 0 TCAAACGGGT 0.842931 -208 TACTAAATGTAACTAACAAGCTAACCTTCAAA 3 109 0 ACTAACAGCT 0.897097 -192 ATTTAGTAACACATATCTGGCTACTTAATCCC 3 133 1 AATATCGGCT 0.881202 -168 TCCTTAATTCTAATAACTGGCTATTGCGCCTT 3 227 1 TATAACGGCT 0.958775 -74 CAAAGATCAAAAAAAACCGGCTCTAT 5 5 0 AAAAACGGCT 0.958775 -191 AGTGACATTCATCATACAGGCTGTGAAATACA 6 60 1 ACATACGGCT 0.92479 -84 * ***** **** Masking position 12 Map Score: 3.75938 Number of sites scoring better than the average of aligned sites = 1353 Number in coding regions = 1250 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 7 AATTTACAGTCTGTTATGTGGTGGCTGTTA 1 122 1 CTGTTATGTG 0.948345 -179 TGTCGGCCCTCTGATAAATCGACATTGCTA 1 260 0 CTGATAAATC 0.921352 -41 ATTAAGTAGCCAGATATGTGTTACTAAATG 3 132 0 CAGATATGTG 0.914131 -169 CTTTTGATAAATGAGGTGTAACA 4 4 1 TTGATAAATG 0.887706 -22 ATTCACCCTCCTGATAAGTGACATTCATCA 6 44 1 CTGATAAGTG 0.988606 -100 ********** Masking position 5 Map Score: 0.308743 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 80 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 ACAGCGTGGGAATTGATAACGATCAAGAGTG 1 201 0 AATTGTAACG 0.942559 -100 GATAAATCGACATTGCTAATGTTTAAGGGCA 1 247 0 CATTGTAATG 0.746601 -54 CACATGCACACATTGGTAATGAAAAAAAGAC 3 271 0 CATTGTAATG 0.746601 -30 AGGGTGAATGCATTTATAATGAAAGAAAAAA 6 22 0 CATTTTAATG 0.729357 -122 ***** ***** Masking position 7 Map Score: 0.968982 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 33 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 ********** No masking Map Score: -9.70439e-14 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: -9.70439e-14 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: -9.70439e-14 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