| cis-Decoder: cDT-Libraries
Drosophila Peripheral nervous system cDT-library A cDT, is a short sequence element of 6 bp or greater that is a perfect match to sequences within CSBs that are present in two or more enhancers. A cDT-library represents a collection of cDTs that are shared by the various enhancers examined. All libraries were generated from readouts of the CSB-aligner. Making enhancer-type specific libraries requires two different CSB-libraries generated from functionally different enhancers, a library from the tissue of interest (e.g. neural), and a second library that serves as an 'out-group' (e.g. mesodermal). For the generation of a neural cDT-library, neural CSBs in both forward and reverse directions were copy/pasted into both upper and lower windows of CSB-aligner. The resulting cDTs from this alignment are listed in the 'Result of CSB alignment table' of the CSB-aligner output, in the column titled 'Motif.' Since this cDT list contains multiple copies of different cDTs, the extra copies are removed using the Java applet Puzzamatic 1.0, a freeware created by Ron Surratt. The cDT list that contains all unique cDTs is then alphabetized and sorted by size also using Puzzamatic 1.0. The cDTs, constituting a raw neural cDT-library, were then copy/pasted into a Microsoft Word document. A second CSB-alignment is then performed with the neural CSBs in the top window of CSB-aligner, and mesodermal CSBs in the lower window. The cDTs from this alignment were freed of extra copies as above. These cDTs constituted an unedited common neural/mesodermal cDT-library. The unedited neural and common cDT-libraries are combined and cDTs common to the two libraries (present in the first and second alignments) are both removed using the JavaScript program cDT-cleaner, thus leaving only the neural-specific sequences. Frequency of sequence matches for each cDT was assessed using cDT-cataloger and cDT-counter. For example the cDT AAACCG is annotated pns03-AAACCG to indicate that there was three hits on a Drosophila PNS CSB library. Drosophila Enhancer of split cDT-library pns03-AAACCG pns02-AAACGG pns02-AAAGTT pns04-AACCAC pns03-AACCAT pns03-AACCTG pns02-AACTTT pns03-AAGATC pns04-AAGCGC pns02-AAGCGG pns03-AAGCTG pns02-AAGGCA pns02-AAGTCG pns03-AATAGA pns02-AATCTC pns02-ACATGA pns08-ACCACC pns02-ACCATG pns02-ACCCCA pns02-ACCCTC pns02-ACCGCT pns02-ACGCGC pns02-ACGGCA pns02-ACTGTC pns02-AGAACC pns06-AGCACG pns02-AGCAGG pns03-AGCCAC pns02-AGCGGC pns02-AGCGGT pns03-AGCGTG pns02-AGGAGG pns02-AGGCGC pns02-AGGGCG pns03-AGGTGA pns03-AGTAGG pns02-ATACAC pns02-ATAGGA pns03-ATCTAA pns03-ATGCTC pns02-ATGGTA pns03-ATGGTT pns03-CAAACG pns03-CAACCC pns02-CAAGCG pns02-CAAGGG pns03-CAAGTC pns03-CACGCT pns03-CACGTC pns05-CAGCAC pns03-CAGCTT pns02-CAGGTC pns03-CAGGTT pns02-CATATG pns02-CATCCG pns02-CATGCA pns02-CATGGT pns03-CCCTAA pns02-CCCTTG pns02-CCGCTA pns02-CCGCTT pns03-CCGTGC pns02-CCGTTT pns03-CCTACT pns02-CCTCCT pns02-CCTGCT pns03-CCTGTC pns02-CCTTGC pns02-CGACTT pns02-CGAGCC pns03-CGCACC pns02-CGCCAG pns02-CGCCCT pns03-CGCCTC pns03-CGCGAG pns03-CGCTAA pns02-CGCTTG pns02-CGGATG pns02-CGGTAA pns03-CGGTTT pns02-CGTCCA pns06-CGTGCC pns06-CGTGCT pns02-CGTTAC pns03-CGTTTG pns02-CTAAAG pns02-CTCAAC pns02-CTCGAG pns03-CTCGCG pns02-CTGGCG pns02-CTGTTC pns02-CTTCCC pns02-CTTTAG pns05-GAAAGC pns02-GAACAG pns02-GAATCC pns03-GACAGG pns02-GACAGT pns02-GACCTG pns03-GACGTG pns03-GACTTG pns02-GAGATT pns03-GAGCAT pns02-GAGCCA pns03-GAGGCG pns02-GAGGGT pns03-GAGTCA pns02-GATAAC pns03-GATCTT pns03-GCAAAC pns02-GCAAGG pns05-GCACGC pns03-GCACGG pns02-GCATGA pns04-GCATGC pns02-GCCGCT pns02-GCGATA pns02-GCGCCC pns02-GCGCCT pns02-GCGCGT pns04-GCGCTT pns02-GCGTCC pns05-GCGTGC pns02-GCTACC pns02-GCTCGA pns03-GCTTCC pns05-GCTTTC pns03-GGAAGC pns02-GGACAA pns02-GGACGC pns02-GGAGGA pns02-GGATCC pns02-GGATTC pns06-GGCACG pns02-GGCGGA pns03-GGCTAA pns02-GGCTCG pns02-GGGAAG pns02-GGGCGC pns03-GGGTTG pns05-GGTAAA pns02-GGTAGC pns02-GGTCAA pns03-GGTGCG pns08-GGTGGT pns02-GGTTCT pns02-GTAACA pns02-GTAACG pns03-GTAGGA pns02-GTCCTA pns02-GTGCGA pns05-GTGCTG pns03-GTGGCT pns02-GTGGGA pns04-GTGGTT pns02-GTGTAT pns02-GTTATC pns02-GTTGAG pns03-GTTTGA pns03-GTTTGC pns02-TAAAGA pns02-TACCAT pns05-TAGCCA pns02-TAGCGG pns02-TAGGAC pns02-TATCGC pns03-TCAAAC pns03-TCACCT pns02-TCATGC pns02-TCATGT pns02-TCCCAC pns02-TCCGCC pns03-TCCTAC pns02-TCCTAT pns02-TCCTCC pns02-TCGACA pns02-TCGAGC pns02-TCGCAC pns03-TCTATT pns02-TCTTTA pns03-TGACTC pns04-TGAGAA pns02-TGCATG pns02-TGCCGT pns02-TGCCTT pns02-TGGACG pns05-TGGCTA pns02-TGGCTC pns02-TGGGGT pns02-TGGTAA pns02-TGTCGA pns02-TGTTAC pns02-TTACCA pns02-TTACCG pns03-TTAGAT pns03-TTAGCC pns03-TTAGCG pns03-TTAGGG pns04-TTCTCA pns02-TTGACC pns02-TTGTCC pns05-TTTACC pns03-AAAAACT pns02-AAAACCA pns02-AAAAGGG pns02-AAAATAG pns02-AAACCAC pns02-AAACCGC pns02-AAAGGAT pns02-AAAGTAG pns03-AACAACA pns03-AACACGC pns02-AACAGCA pns03-AACCACC pns02-AAGATCA pns02-AAGCGAC pns03-AAGCGCA pns02-AAGCGTG pns02-AAGTAAC pns02-AATAGAG pns04-AATTAGC pns02-AATTTAG pns03-ACAACAC pns03-ACAAGAT pns02-ACACGTC pns03-ACAGATG pns03-ACAGGTA pns06-ACCACCA pns03-ACCCCTA pns02-ACGCAAT pns02-ACGCCTC pns03-ACGGAAG pns05-ACGTGTG pns02-AGATGAT pns02-AGATTAC pns03-AGATTAT pns02-AGCACGC pns04-AGCCAAA pns02-AGCCACA pns03-AGCGTCA pns08-AGCTGCA pns02-AGGACAC pns02-AGTAGGA pns02-AGTGGGC pns02-AGTGTGC pns03-AGTTTTT pns02-ATAAAAG pns03-ATAATCT pns02-ATCATCT pns02-ATCCTTT pns02-ATCTAAT pns03-ATCTTGT pns02-ATGATGC pns02-ATGATTA pns02-ATGCTGC pns02-ATGGTTA pns02-ATTAGAT pns03-ATTAGCA pns02-ATTGCGT pns03-ATTTGCC pns02-CAAAAAC pns03-CAAACAA pns02-CAACCTG pns02-CAAGTGC pns02-CAATCTA pns05-CACACGT pns05-CACCACC pns02-CACGCAA pns02-CACGCTT pns02-CACTTGC pns02-CAGACCC pns03-CAGCACG pns02-CAGGTTG pns02-CAGTGTC pns03-CATCTGT pns02-CATGCTC pns02-CATGTAA pns02-CATTGCG pns02-CCACAGA pns02-CCACCCC pns02-CCCTTTT pns02-CCGTGCC pns02-CCTGTCA pns02-CCTTGAA pns02-CCTTTTA pns02-CGCAATG pns02-CGCGAGC pns02-CGCTTTC pns02-CGTGCCC pns03-CGTGCTG pns02-CGTTAAG pns02-CGTTGAA pns02-CGTTTGA pns02-CTAAATT pns02-CTACTTT pns02-CTATTTT pns02-CTCTATT pns02-CTGCCAC pns02-CTGTCAC pns02-CTTAAAA pns02-CTTAACG pns03-CTTCCGT pns05-CTTTCAA pns02-CTTTCTC pns02-CTTTTAC pns02-CTTTTAT pns02-CTTTTGC pns02-GAAAAAC pns02-GAAAGCG pns03-GAATTGA pns03-GACAACA pns02-GACACTG pns02-GACGTGT pns02-GAGAAAG pns02-GAGCATG pns02-GAGCCGA pns02-GAGGCGT pns03-GCAAAAA pns02-GCAAAAG pns02-GCAAACA pns02-GCAAGTG pns02-GCAATAA pns02-GCACACT pns02-GCACGCC pns02-GCACTTG pns02-GCAGCAC pns02-GCAGCAT pns02-GCAGGAC pns02-GCATCAT pns02-GCCCACT pns02-GCGAAAC pns02-GCGCACC pns02-GCGGTTT pns02-GCGTGCC pns02-GCGTGCT pns03-GCGTGTT pns04-GCTAATT pns02-GCTCGCG pns06-GCTGCAA pns02-GGAATTA pns03-GGCAAAT pns02-GGCACGC pns02-GGCACGG pns02-GGCGTGC pns02-GGGCACG pns02-GGGGTGG pns02-GGGTCTG pns03-GGTAAAA pns02-GGTGCGC pns05-GGTGGTG pns03-GGTGGTT pns02-GTAAAAG pns02-GTAATCT pns02-GTCAAAC pns03-GTCAATA pns02-GTCCTGC pns02-GTCGCTT pns02-GTGACAG pns03-GTGAGAA pns02-GTGCTGC pns02-GTGGCAG pns02-GTGGTTT pns02-GTGTCCT pns02-GTGTTAA pns03-GTGTTGT pns02-GTTACTT pns02-GTTCAAC pns02-GTTGAAC pns02-GTTTCGC pns02-GTTTGAC pns02-GTTTTTC pns02-GTTTTTG pns02-TAAAAGG pns02-TAACCAT pns02-TAATCAT pns02-TAATTCC pns03-TACCTGT pns02-TAGAGCA pns02-TAGATTG pns03-TAGGGGT pns03-TATTGAC pns02-TATTGCA pns02-TCAAACG pns02-TCAACGA pns03-TCAATAA pns03-TCAATTC pns02-TCCATCA pns02-TCCTACT pns02-TCGGCTC pns02-TCGTTGA pns02-TCTGTGG pns02-TCTTAAA pns02-TGACAGG pns03-TGACGCT pns02-TGATCTT pns02-TGATGGA pns03-TGCAAAA pns02-TGCAATA pns08-TGCAGCT pns02-TGCGAAA pns03-TGCGCTT pns03-TGCTAAT pns02-TGCTCTA pns02-TGCTGTT pns02-TGGCTAA pns06-TGGTGGT pns02-TGGTTTT pns02-TGTGGCT pns03-TGTTGTC pns03-TGTTGTT pns02-TGTTTGC pns02-TTAACAC pns02-TTACATG pns02-TTAGCCA pns03-TTATTGA pns02-TTATTGC pns02-TTCAACG pns02-TTCAAGG pns03-TTCTCAC pns05-TTGAAAG pns06-TTGCAGC pns02-TTGCCAA pns02-TTGCGTG pns02-TTGGCAA pns03-TTGTTTG pns02-TTTAAGA pns02-TTTCGCA pns04-TTTGGCT pns02-TTTTAAG pns03-TTTTACC pns03-TTTTGCA pns03-TTTTTGC pns02-AAAACTGG pns02-AAACACGC pns02-AAAGCGCA pns02-AAATGCAT pns02-AAATTAGC pns02-AAATTTGT pns02-AACAAGAT pns02-AACACGCG pns02-AAGCGCAA pns02-AAGTGCAT pns02-AATAAATC pns02-AATATTGA pns02-AATCAAAA pns02-AATTAGCC pns03-AATTCATA pns02-AATTCTCA pns02-AATTGACA pns02-AATTTGCC pns02-ACAAATTT pns02-ACAACAAC pns03-ACAGCTGC pns02-ACAGGAAA pns02-ACAGGTAA pns02-ACCCCTAA pns02-ACGCTCGC pns02-ACGGAAGC pns02-ACTTTCAA pns03-AGCACGTG pns02-AGCGTCAA pns02-AGGCAAAT pns02-ATCAATTC pns02-ATCACATA pns02-ATCTTGTT pns02-ATGAAGCG pns02-ATGCACTT pns02-ATGCATTT pns02-ATGCTAAT pns02-ATTAGCAT pns03-ATTGAAAA pns03-ATTGCAGC pns02-ATTGTTTG pns02-ATTTCCTG pns02-ATTTGACA pns02-ATTTGCCT pns02-ATTTTAGC pns02-CAAACAAT pns02-CAAATGCA pns02-CAACAACA pns02-CAATTAGC pns02-CACAACAA pns03-CACGTGCT pns07-CAGCTGCA pns02-CAGGAAAT pns02-CAGGTAAA pns02-CATTTGGC pns02-CCAGGTGA pns02-CCAGTTTT pns02-CGCGTGTT pns02-CGCTTCAT pns02-CGGCAAAC pns02-CGTCAACA pns02-CGTCACAC pns02-CGTGCCAC pns02-CTAATTGA pns02-CTATTAAC pns02-CTCGCGAG pns02-CTCGTTAA pns02-CTTGAAAG pns02-CTTTCAAG pns02-GAATTGAT pns02-GATGACAA pns02-GATTTATT pns04-GCACGTGC pns03-GCAGCTGT pns02-GCCAAATG pns02-GCGAGCGT pns02-GCGCTAAA pns02-GCGTGTTT pns02-GCTAAAAT pns02-GCTAATTG pns02-GCTAATTT pns02-GCTGACAA pns03-GCTGCAAT pns02-GCTTATTA pns02-GCTTCCGT pns03-GCTTTCAA pns02-GGCAAATT pns02-GGCAATTA pns02-GGCTAATT pns02-GTCACACA pns02-GTGAGAAA pns02-GTGGCACG pns02-GTGTGACG pns02-GTTAATAG pns02-GTTGTTGT pns02-GTTTGCCG pns02-TAATAAGC pns02-TAATTGCC pns03-TAGCCAAA pns02-TATCTTAA pns03-TATGAATT pns02-TATGTGAT pns02-TCAATATT pns02-TCAATTAG pns02-TCACCTGG pns02-TGAGAATT pns02-TGCAAAAA pns07-TGCAGCTG pns02-TGCATTTG pns02-TGCGCTTT pns02-TGTAATAA pns02-TGTCAAAT pns02-TGTCAATT pns02-TGTGTGAC pns02-TGTTGACG pns02-TGTTGTTG pns02-TTAACGAG pns02-TTAAGATA pns02-TTACCTGT pns02-TTAGGGGT pns02-TTATTACA pns03-TTGAAAAA pns03-TTGAAAGC pns02-TTGAAAGT pns02-TTGACGCT pns02-TTGCGCTT pns02-TTGTCAGC pns02-TTGTCATC pns02-TTGTTGTG pns02-TTTACCTG pns02-TTTAGCGC pns02-TTTCCTGT pns02-TTTCTCAC pns02-TTTGCAAA pns03-TTTGGCTA pns03-TTTTCAAT pns02-TTTTGATT pns03-TTTTTCAA pns02-TTTTTGCA pns02-AAAATCAAT pns02-AAAATTCAT pns02-AAATGCAGG pns02-AAATGGCAG pns02-AAGTGTTGT pns02-AATCTTTGC pns02-AATTCATAA pns02-AATTTATTG pns02-ACAACACTT pns02-ACATCTGCC pns02-ACGTGTGGC pns02-AGCATTTAA pns02-ATCATAAAT pns02-ATGAATTTT pns02-ATGACAAAC pns02-ATTGAAAAA pns02-ATTGATTTT pns02-ATTTATGAT pns02-CAACATGTG pns02-CAACCCCTA pns02-CAATAAATT pns02-CACATGTTG pns02-CACGTCAAC pns02-CACGTGCTG pns02-CAGCACGTG pns02-CAGCAGCTG pns06-CAGCTGCAA pns02-CAGCTGCCG pns03-CAGCTGCTG pns04-CCACCACCA pns02-CCTGCATTT pns03-CGCGTGGCA pns02-CGGCAGCTG pns02-CGTGCAAAA pns02-CTGCCATTT pns02-CTTCCGTGC pns02-GCAAAGATT pns02-GCACGGAAG pns04-GCAGCTGCA pns02-GCAGGTGTA pns02-GCCACACGT pns02-GGCAGATGT pns02-GTTGACGTG pns02-GTTTGTCAT pns02-TACACCTGC pns02-TAGCAACAA pns02-TAGGGGTTG pns04-TGCAGCTGC pns03-TGCCACGCG pns04-TGGTGGTGG pns02-TTAAATGCT pns02-TTATGAATT pns05-TTGCAGCTG pns02-TTGTTGCTA pns02-TTTTGCACG pns02-TTTTTCAAT pns02-AAATTGAAAA pns02-AATTTTTCAA pns03-ACCACCACCA pns02-AGCACGTGCC pns02-ATAGCCAAAA pns02-CAACAATAGG pns02-CACCAAATGG pns02-CCATTTGGTG pns02-CCTATTGTTG pns02-GCACACGTGC pns02-GCACGTGTGC pns03-GCAGCTGCAA pns02-GCGCATGCGC pns02-GGCAAAACAA pns02-GGCACGTGCT pns02-TCGCGTGGCA pns02-TGAAATTTCA pns02-TGCCACGCGA pns03-TGGTGGTGGT pns02-TTGAAAAATT pns03-TTGCAGCTGC pns02-TTGTTTTGCC pns02-TTTAATTAAA pns02-TTTTCAATTT pns02-TTTTGGCTAT pns02-AACCACCACCA pns02-AGATTATCATC pns02-AGTGTCAATAA pns02-GATGATAATCT pns02-GCAGCTGCAAA pns02-GCTTTCAATTA pns02-GGCAGCTGCAA pns02-TAATTGAAAGC pns02-TGGTGGTGGTT pns02-TTATTGACACT pns02-TTGCAGCTGCC pns02-TTTGCAGCTGC pns02-AAATTGCAGCTG pns02-CAGCTGCAATTTContact information Discover multispecies conserved sequences using EvoPrinter. 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