Origin IGS: ttgttttatctttatttatcaagcctctgggttgtcgctctaacatccgcttaacctgcatttgcggcttgtcctgtttgtcggcgttgaagcggatgttaggcggatttat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataaatccgcctaacatccgcttcaacgccgacaaacaggacaagccgcaaatgcaggttaagcggatgttagagcgacaacccagaggcttgataaataaagataaaacaa Mask Tandem Repeat Region ================================================ ttgttttatctttatttatcaagcctctgggttgtcgctctaacatccgcttaacctgcatttgcggcttgtcctgtttgtcggcgttgaagcggatgttaggcggatttat Find is-nt database================================================ Query_seq: TDE0279:TDE0280|TDE0279:TDE0280:hypothetical protein:PIN domain protein:<-<-:309873..309984 112 ttgttttatctttatttatcaagcctctgggttgtcgctctaacatccgcttaacctgcatttgcggcttgtcctgtttgtcggcgttgaagcggatgttaggcggatttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0279:TDE0280|TDE0279:TDE0280:hypothetical protein:PIN domain protein:<-<-:309873..309984 112 ttgttttatctttatttatcaagcctctgggttgtcgctctaacatccgcttaacctgcatttgcggcttgtcctgtttgtcggcgttgaagcggatgttaggcggatttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0279:TDE0280|TDE0279:TDE0280:hypothetical protein:PIN domain protein:<-<-:309873..309984 112 ttgttttatctttatttatcaagcctctgggttgtcgctctaacatccgcttaacctgcatttgcggcttgtcctgtttgtcggcgttgaagcggatgttaggcggatttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgttttatctttatttatcaagcctctgggttgtcgctctaacatccgcttaacctgcatttgcggcttgtcctgtttgtcggcgttgaagcggatgttaggcggatttat Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 18 End: 110 ................. M K P L G C R S N I R L T C I C G L S C L S A L K R M L G G F .. Protein_Len: 37 Strand: - Start: 2 End: 112 . T K D K N I L G R P Q R E L M R K V Q M Q P K D Q K D A N F R I N P P N M ttgttttatctttatttatcaagcctctgggttgtcgctctaacatccgcttaacctgcatttgcggcttgtcctgtttgtcggcgttgaagcggatgttaggcggatttat Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgttttatctttatttatcaagcctctgggttgtcgctctaacatccgcttaacctgcatttgcggcttgtcctgtttgtcggcgttgaagcggatgttaggcggatttat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0279:TDE0280|TDE0279:TDE0280:hypothetical protein:PIN domain protein:<-<-:309873..309984 112 ttgttttatctttatttatcaagcctctgggttgtcgctctaacatccgcttaacctgcatttgcggcttgtcctgtttgtcggcgttgaagcggatgttaggcggatttat Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_002967_TDE0279_TDE0280|hypothetical protein:PIN domain protein|NEGATIVE:NEGATIVE|[309873,309984]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 ttgttttatctttatttatcaagcctctgggttgtcgctctaacatccgcttaacctgcatttgcggcttgtcctgtttgtcggcgttgaagcggatgttaggcggatttat ttgttttatctttatttatcaagcctctgggttgtcgctctaacatccgcttaacctgcatttgcggcttgtcctgtttgtcggcgttgaagcggatgttaggcggatttat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUUUUAUCUUUAUUUAUCAAGCCUCUGGGUUGUCGCUCUAACAUCCGCUUAACCUGCAUUUGCGGCUUGUCCUGUUUGUCGGCGUUGAAGCGGAUGUUAGGCGGAUUUAU .....................((((....)))).((((.(((((((((((((((((((((...((((......)))).)).))).)))).))))))))))))))))...... (-38.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAUCCGCCUAACAUCCGCUUCAACGCCGACAAACAGGACAAGCCGCAAAUGCAGGUUAAGCGGAUGUUAGAGCGACAACCCAGAGGCUUGAUAAAUAAAGAUAAAACAA .......((((((((((((((((.....((........))...((((((....)).))))))))))))))))).))).(((((....)).)))................... (-32.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1024 70 21 161 112 NC_002967:TDE0279|5end_hypothetical_protein_309782..310012_NEGATIVE 820 100 51 192 143 NC_002967:TDE0262|5end_hypothetical_protein_296300..296530_NEGATIVE 761 90 41 189 141 NC_002967:TDE1823|5end_hypothetical_protein_1856990..1857220_NEGATIVE 720 70 23 154 103 NC_002967:TDE1781|5end_hypothetical_protein_1823260..1823490_NEGATIVE 713 77 33 220 172 NC_002967:TDE1799|5end_hypothetical_protein_1837264..1837494_NEGATIVE 712 90 41 168 120 NC_002967:TDE1839|5end_hypothetical_protein_1871221..1871451_NEGATIVE 712 90 41 191 143 NC_002967:TDE1820|5end_hypothetical_protein_1854692..1854922_NEGATIVE 710 90 41 168 120 NC_002967:TDE1822|5end_hypothetical_protein_1855922..1856152_NEGATIVE 705 103 66 175 138 NC_002967:TDE0276|5end_HD_domain_protein_308029..308259_NEGATIVE 704 100 51 181 133 NC_002967:TDE1836|5end_hypothetical_protein_1869443..1869673_NEGATIVE 704 100 51 218 170 NC_002967:TDE1831|5end_hypothetical_protein_1865032..1865262_NEGATIVE 704 100 51 185 137 NC_002967:TDE1827|5end_hydrolase,_carbon-nitrogen_family_1860830..1861060_NEGATIVE 704 100 51 183 135 NC_002967:TDE1817|5end_hypothetical_protein_1852599..1852829_NEGATIVE 704 100 51 180 132 NC_002967:TDE1811|5end_hypothetical_protein_1847483..1847713_NEGATIVE 704 100 51 218 170 NC_002967:TDE1797|5end_hypothetical_protein_1836272..1836502_NEGATIVE 704 100 51 171 123 NC_002967:TDE1795|5end_funZ_protein,_putative_1834673..1834903_NEGATIVE 704 100 51 189 141 NC_002967:TDE0267|5end_HAM1_protein_299108..299338_NEGATIVE 675 100 54 203 158 NC_002967:TDE1832|5end_hypothetical_protein_1865921..1866151_NEGATIVE 653 100 51 182 134 NC_002967:TDE1825|5end_hypothetical_protein_1858344..1858574_NEGATIVE 648 100 51 202 155 NC_002967:TDE1796|5end_hypothetical_protein_1835515..1835745_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 820 100 51 92 43 NC_002967:TDE0263|3end_spermidine_N1-acetyltransferase,_putative_296400..296550_NEGATIVE 742 90 41 66 18 NC_002967:TDE0097|3end_hypothetical_protein_114801..114951_POSITIVE 720 70 23 110 59 NC_002967:TDE1782|3end_hypothetical_protein_1823304..1823454_NEGATIVE 713 77 33 57 9 NC_002967:TDE1800|3end_hypothetical_protein_1837427..1837577_NEGATIVE 712 90 41 65 17 NC_002967:TDE1840|3end_hypothetical_protein_1871324..1871474_NEGATIVE 712 90 41 68 20 NC_002967:TDE1821|3end_hypothetical_protein_1854815..1854965_NEGATIVE 705 103 66 95 58 NC_002967:TDE0277|3end_hypothetical_protein_308109..308259_NEGATIVE 704 100 51 92 44 NC_002967:TDE1843|3end_hypothetical_protein_1872199..1872349_NEGATIVE 704 100 51 82 34 NC_002967:TDE1837|3end_hypothetical_protein_1869542..1869692_NEGATIVE 704 100 51 78 30 NC_002967:TDE1832|3end_hypothetical_protein_1865172..1865322_NEGATIVE 704 100 51 81 33 NC_002967:TDE1828|3end_hypothetical_protein_1860934..1861084_NEGATIVE 704 100 51 83 35 NC_002967:TDE1812|3end_hypothetical_protein_1847580..1847730_NEGATIVE 704 100 51 78 30 NC_002967:TDE1796|3end_hypothetical_protein_1834766..1834916_NEGATIVE 704 100 51 74 26 NC_002967:TDE1787|3end_hypothetical_protein_1826378..1826528_NEGATIVE 704 100 51 92 44 NC_002967:TDE1780|3end_hypothetical_protein_1822183..1822333_NEGATIVE 704 100 51 78 30 NC_002967:TDE0268|3end_hypothetical_protein_299219..299369_NEGATIVE 686 90 41 73 25 NC_002967:TDE1789|3end_hypothetical_protein_1827338..1827488_NEGATIVE 685 100 51 87 39 NC_002967:TDE1806|3end_hypothetical_protein_1843190..1843340_NEGATIVE 677 100 51 92 44 NC_002967:TDE1793|3end_hydrolase,_carbon-nitrogen_family_1829957..1830107_NEGATIVE 676 100 51 81 33 NC_002967:TDE1776|3end_hypothetical_protein_1818414..1818564_NEGATIVE