AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icynR_ecoli_bsub_100.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 cynR_cynT 108 cynR: cyn operon positive regulator, cynT: carbonic anhydrase #2 cynS 30 cyanate aminohydrolase, cyanase #3 cynX 32 cyanate transport #4 ycgK 192 similar to transcriptional regulator (LysR family) #5 gltC 146 transcriptional regulator (LysR family) #6 ytiB 93 similar to carbonic anhydrase #7 ytiA 219 similar to hypothetical proteins #8 alsR 154 transcriptional regulator (LysR family) #9 ywfK 146 alternate gene name: ipa-89d; similar to transcriptional regulator (LysR family) #10 ywbI 105 alternate gene name: ipa-24d; similar to transcriptional regulator (LysR family) #11 yybE 228 similar to transcriptional regulator (LysR family) Motif number 1 AAAGTCTCATTTATGATGAGTTCCATTGGATTTAC 1 71 1 TTAGATTTCA 0.903814 -38 ATTTTCATCATTTTTATATCTTGGACGAATCATAA 4 142 0 TTTTATTTGA 0.903244 -51 TTATATATTGTTTATATCGTTTTGAAAACCTACAA 5 74 0 TTTTATTTTA 0.919013 -73 CTATCTCATTTTGAGATTCTTTTGATCTAAATTAT 5 105 0 TTGGATTTTA 0.977561 -42 TAAACAAGGGTTGTGATATATTGAAGAGTAAAAAG 6 49 1 TTGGATTTGA 0.972859 -45 TCGTTGTCCCTTTCTATTCTTTTTACTCTTCAATA 6 67 0 TTTTATTTTA 0.919013 -27 ATCGTAATAATTACGTTTTATTTTATAACCTTACA 7 176 0 TTAGTTTTTA 0.810601 -44 AACGTAATTATTACGATTTATTGAAAGGAGATACC 7 194 1 TTAGATTTGA 0.970662 -26 CCTCACTCCTTATTATGCATTTTAAACGTAAAAT 8 10 1 TTATATTTTA 0.955816 -145 TTTAAATATCTTGTGATAAGTTTCACTATACACTC 8 45 1 TTGGATTTTA 0.977564 -110 AAATATATGGTTATGATTAGTTTTCTTTATTGTAC 9 99 0 TTAGATTTTC 0.863821 -48 CTTCTTATTCTTAATATATATTTTACCTATAGAGA 10 49 0 TTATATTTTA 0.955815 -57 CTTAGCACCGTTGATATATGTTGTATAATGCATAT 11 118 1 TTGTATTTGA 0.950692 -111 *** *** *** * Masking position 7 Map Score: 14.9011 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 75 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 2 CGTTAACCTCTGTCTGTCTCTGGAATGAGAG 1 7 1 CTCGTCTTTT 0.934964 -102 ATCTTCCCCCTCGGCAAATACCTTTTC 4 3 1 CTCCCCTGCA 0.953359 -190 AATTCCTCTCCCCCGATCAATTTCCGATA 5 5 1 CTCCCCCGTA 0.986332 -142 GTTTGTCTCACATCCATCTATCTCATTTTGAGATT 5 122 0 CTCATCTTTA 0.943436 -25 TTCTTATATCCTTCCCTCTGTTTCACATCGTAAAC 7 126 0 CTCCTCTTTA 0.992283 -94 CCTCACTCCTTATTATGCATTTTAA 8 1 1 CTCCTCCTTA 0.99066 -154 GTACTCATATCATCCGTCTTGGTAAAGAAGGGCTA 9 68 0 CTCGTCTGTA 0.974043 -79 GCGCTTCACCCTTTCTATAGACAAAAGG 10 88 0 CTCCCCTTTT 0.971028 -18 TTCCAATTATCATCTCTCCTTATTACATATAAGCA 11 168 0 CTCCTCCTTA 0.99066 -61 * ** **** * * * Masking position 3 Map Score: 9.07067 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 51 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 3 TGTATCGGGATGAAAAGGTATTTGCCGAGG 4 19 0 TGAAAAGGTA 0.875078 -174 TCGTAAATGATGATATGGATTATGTTAGCA 4 105 1 TGATATGGAT 0.608122 -88 GTAAAAAGAATAGAAAGGGACAACGAAC 6 76 1 TAGAAAGGGA 0.912164 -18 AACGTCTTTTTGGAAAGGTGGTTTACGATT 7 26 0 TGGAAAGGTG 0.960856 -194 GACAAAACGTTTGTAAGGTTATAAAATAAA 7 165 1 TTGTAAGGTT 0.647374 -55 TTACGATTTATTGAAAGGAGATACCC 7 204 1 TTGAAAGGAG 0.914553 -16 TTAAAATGCATAATAAGGAGTGAGG 8 6 0 TAATAAGGAG 0.824199 -149 TATTAACCTATGGAAAGGAATGCATATTGA 8 135 1 TGGAAAGGAA 0.967215 -20 CTTTTGTCTATAGAAAGGGTGAAGCGC 10 89 1 TAGAAAGGGT 0.912164 -17 CATATAAGCATGAAAAGGATATTTTATATG 11 148 0 TGAAAAGGAT 0.930333 -81 TGCTTATATGTAATAAGGAGAGATGATAAT 11 168 1 TAATAAGGAG 0.824199 -61 AGATGATAATTGGAATGGGAACAACTTGAA 11 188 1 TGGAATGGGA 0.845015 -41 ********** Masking position 5 Map Score: 8.12362 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 359 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 4 TCGCAACCTATAAGTAAATCCAATGGAA 1 91 0 CCTATGTAAA 0.969147 -18 CCTTATTTTTAAACCATCAGGAG 2 2 1 CTTATTTAAA 0.950777 -29 GATTATTCTTCCTATTCTTAAATGCCATGAGG 7 95 1 CCTATTTAAA 0.974412 -125 ATCGATTCGCCTTATGATTAATATGTAATACG 8 100 1 CTTATTTAAT 0.940208 -55 AAACCCCACCCCTGTCATTAATGAAATATATG 9 125 0 CCTGTTTAAT 0.937935 -22 ATAAGGTCTCTCTATAGGTAAAATATATATTA 10 41 1 TCTATGTAAA 0.754828 -65 AGGAATACTTCTTATTCTTAATATATATTTTA 10 59 0 CTTATTTAAT 0.940208 -47 CCTTTTCATGCTTATATGTAATAAGGAGAGAT 11 160 1 CTTATGTAAT 0.928428 -69 CCGGGCCAGTGTTTAAAAATATTCAAG 11 212 0 CCAGTTTAAA 0.745874 -17 ***** ***** Masking position 5 Map Score: 6.12565 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 52 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 GCCTCTCATTCCAGAGACAGACAGAGGTTAAC 1 12 0 CCAGAGACAC 0.795797 -97 ATAAGTAAATCCAATGGAACTCATCATAAATG 1 78 0 CCAATGGAAC 0.794145 -31 GCGCAACCATCAAAAGACGTTCACG 3 18 1 CAAAAGACGC 0.958188 -15 GTTCAAATTACAAATGAAACACCGTTTTCTAA 4 60 0 CAAATGAAAC 0.905742 -133 TAATTTAGATCAAAAGAATCTCAAAATGAGAT 5 106 1 CAAAAGAATC 0.791798 -41 GTCATAATAAAAAAAGACAAACCCTCAGGCCT 6 14 0 AAAAAGACAC 0.950639 -80 CCACCTTTCCAAAAAGACGTTCTGTATGTATT 7 35 1 AAAAAGACGC 0.880833 -185 ATAATAAACCCAAAATACATACAGAACGTCTT 7 48 0 CAAAATACAC 0.929484 -172 TCAATATGCATTCCTTTCCATAG 8 142 0 CAATATGCAC 0.659876 -13 TAAAATTGAAGACAATGGCAGCT 9 2 1 AAAATTGAAC 0.44214 -145 CAGAAGCGCAAAAAAGGCAGCCCTCGGTCGAG 9 34 0 AAAAAGGCAC 0.957099 -113 TTTCTATAGACAAAAGGAATACTTCTTATTCT 10 73 0 CAAAAGGAAC 0.969049 -33 ********* * Masking position 3 Map Score: 5.24649 Number of sites scoring better than the average of aligned sites = 753 Number in coding regions = 653 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 6 GACAAACCCTCAGGCCTGCC 6 1 0 CAGGCCTGCC 0.990019 -93 GCCCTCGGTCGAGAGCTGCCATTGTCTTCA 9 17 0 GAGAGCTGCC 0.986371 -130 GCTCTCGACCGAGGGCTGCCTTTTTTGCGC 9 31 1 GAGGGCTGCC 0.997004 -116 ATTGATGCCTCCCTTATATACTT 10 4 1 GATGCCTCCC 0.950002 -102 TCATGTTGTGGAGCACTGCCATTCATAAAC 11 32 1 GAGCACTGCC 0.979489 -197 ********** Masking position 7 Map Score: 3.47035 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 50 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 7 CTGATGGTTTAAAAATAAGG 2 1 0 AAAAATAAGG 0.901771 -30 CATCATTTACGAAAAGAAGGAGCTGGTTCA 4 87 0 GAAAAGAAGG 0.951317 -106 ATTATGACGAATAAACAAGGGTTGTGATAT 6 38 1 ATAAACAAGG 0.858248 -56 CCCAAAATACATACAGAACGTCTTTTTGGA 7 42 0 ATACAGAACG 0.870431 -178 TTACGATGTGAAACAGAGGGAAGGATATAA 7 128 1 AAACAGAGGG 0.880813 -92 ATTACATATTAATCATAAGGCGAATCGATA 8 99 0 AATCATAAGG 0.717346 -56 AAGAAGGGCTATACAGAAGCGCAAAAAAGG 9 49 0 ATACAGAAGC 0.870431 -98 ATCCGTCTTGGTAAAGAAGGGCTATACAGA 9 62 0 GTAAAGAAGG 0.966226 -85 TGTACAATAAGTATATAAGGGAGGCATCAA 10 12 0 GTATATAAGG 0.815696 -94 TATACTTATTGTACATAAGGTCTCTCTATA 10 27 1 GTACATAAGG 0.966226 -79 ********** Masking position 5 Map Score: 4.85662 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 256 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 8 TTCTGTTATGATTCGTCCAAGATATAAAAA 4 137 1 ATTCGTCCAA 0.832702 -56 ACCCTTGTTTATTCGTCATAATAAAAAAAG 6 30 0 ATTCGTCATA 0.953297 -64 GTCCCTTTCTATTCTTTTTACTCTTCAATA 6 67 0 ATTCTTTTTA 0.755963 -27 CGGTTAGATTATTCTTCCTATTCTTAAATG 7 89 1 ATTCTTCCTA 0.941419 -131 ACGTTTTGTCAATCTTCTTATATCCTTCCC 7 145 0 AATCTTCTTA 0.882998 -75 CCTTTCAATAAATCGTAATAATTACGTTTT 7 192 0 AATCGTAATA 0.596017 -28 TCCAATATCGATTCGCCTTATGATTAATAT 8 94 1 ATTCGCCTTA 0.916408 -61 TAGGTTAATAATTCGTATTACATATTAATC 8 115 0 ATTCGTATTA 0.914763 -40 GACAAAAGGAATACTTCTTATTCTTAATAT 10 67 0 ATACTTCTTA 0.790128 -39 ********** Masking position 1 Map Score: 3.40708 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 128 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 9 CTTCTTTTCGTAAATGATGATATGGATTAT 4 98 1 TAAATGATGA 0.975013 -95 CCAAGATATAAAAATGATGAAAATGATAGG 4 153 1 AAAATGATGA 0.975016 -40 AGTGCTCCACAACATGATGAGGGACCGATA 11 19 0 AACATGATGA 0.958144 -210 TCGTAAGAAATAAAGGATGATTGTTTATGA 11 54 0 TAAAGGATGA 0.958141 -175 ********** Masking position 4 Map Score: 0.935647 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 37 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 ********** No masking Map Score: -4.59421e-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 11 GATTTACTTATAGGTTGCGA 1 99 1 TAGGTTGCGA 0.885692 -10 ACGTCTTTTGATGGTTGCGCATGGCTG 3 8 0 ATGGTTGCGC 0.915698 -25 AATGAGATAGATGGATGTGAGACAAAC 5 130 1 ATGGATGTGA 0.82208 -17 CGAATAAACAAGGGTTGTGATATATTGAAG 6 45 1 AGGGTTGTGA 0.968882 -49 TTTGGAAAGGTGGTTTACGATTGTGGATGA 7 18 0 TGGTTTACGA 0.883476 -202 AAATGCCATGAGGTTTACGATGTGAAACAG 7 114 1 AGGTTTACGA 0.92407 -106 AATGAAATATATGGTTATGATTAGTTTTCT 9 108 0 ATGGTTATGA 0.942046 -39 TAAAGGATGATTGTTTATGAATGGCAGTGC 11 44 0 TTGTTTATGA 0.798416 -185 ********** Masking position 6 Map Score: 2.39958 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 376 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 12 ********** No masking Map Score: -4.59421e-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 13 ********** No masking Map Score: -4.59421e-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 14 ********** No masking Map Score: -4.59421e-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