Origin IGS: tattttctccatgcccgcaggggcaacctaactaccgcttaacctgcattcgcgggcttgacccgcaatgtcaggttgaagcgggtgttatgcgccattataatatataattttcaatcaatttgtatatatgcaaataaaacaaatagtgttaaatttatacatttcctaaatatagagagccatcatactatattgtaatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaattacaatatagtatgatggctctctatatttaggaaatgtataaatttaacactatttgttttatttgcatatatacaaattgattgaaaattatatattataatggcgcataacacccgcttcaacctgacattgcgggtcaagcccgcgaatgcaggttaagcggtagttaggttgcccctgcgggcatggagaaaata Mask Tandem Repeat Region ================================================ tattttctccatgcccgcaggggcaacctaactaccgcttaacctgcattcgcgggcttgacccgcaatgtcaggttgaagcgggtgttatgcgccattataatatataattttcaatcaatttgtatatatgcaaataaaacaaatagtgttaaatttatacatttcctaaatatagagagccatcatactatattgtaatttt Find is-nt database================================================ Query_seq: TDE1803:TDE1804|TDE1803:TDE1804:hypothetical protein:hypothetical protein:<-<-:1839361..1839565 205 tattttctccatgcccgcaggggcaacctaactaccgcttaacctgcattcgcgggcttgacccgcaatgtcaggttgaagcgggtgttatgcgccattataatatataattttcaatcaatttgtatatatgcaaataaaacaaatagtgttaaatttatacatttcctaaatatagagagccatcatactatattgtaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1803:TDE1804|TDE1803:TDE1804:hypothetical protein:hypothetical protein:<-<-:1839361..1839565 205 tattttctccatgcccgcaggggcaacctaactaccgcttaacctgcattcgcgggcttgacccgcaatgtcaggttgaagcgggtgttatgcgccattataatatataattttcaatcaatttgtatatatgcaaataaaacaaatagtgttaaatttatacatttcctaaatatagagagccatcatactatattgtaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1803:TDE1804|TDE1803:TDE1804:hypothetical protein:hypothetical protein:<-<-:1839361..1839565 205 tattttctccatgcccgcaggggcaacctaactaccgcttaacctgcattcgcgggcttgacccgcaatgtcaggttgaagcgggtgttatgcgccattataatatataattttcaatcaatttgtatatatgcaaataaaacaaatagtgttaaatttatacatttcctaaatatagagagccatcatactatattgtaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattttctccatgcccgcaggggcaacctaactaccgcttaacctgcattcgcgggcttgacccgcaatgtcaggttgaagcgggtgttatgcgccattataatatataattttcaatcaatttgtatatatgcaaataaaacaaatagtgttaaatttatacatttcctaaatatagagagccatcatactatattgtaatttt Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 58 End: 198 ......................................................... M T R N V R L K R V L C A I I I Y N F Q S I C I Y A N K T N S V K F I H F L N I E S H H T I L ....... tattttctccatgcccgcaggggcaacctaactaccgcttaacctgcattcgcgggcttgacccgcaatgtcaggttgaagcgggtgttatgcgccattataatatataattttcaatcaatttgtatatatgcaaataaaacaaatagtgttaaatttatacatttcctaaatatagagagccatcatactatattgtaatttt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 75 End: 104 ..........................................................................GTTGAAGCGGGTGTTATGCGCCATTATAAT..................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tattttctccatgcccgcaggggcaacctaactaccgcttaacctgcattcgcgggcttgacccgcaatgtcaggttgaagcgggtgttatgcgccattataatatataattttcaatcaatttgtatatatgcaaataaaacaaatagtgttaaatttatacatttcctaaatatagagagccatcatactatattgtaatttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 84 HP_score: -11.4 Tail_Score: -3.31799 Start: 32 End: 87 Full_Region: GCAGGGGCAACCTAA CTACCGCTTAACCTGCATTCGCGGG CTTGA CCCGCAATGTCAGGTTGAAGCGGGTG TTATGCGCCATTATA ...............................CTACCGCTTAACCTGCATTCGCGGGCTTGACCCGCAATGTCAGGTTGAAGCGGGTG...................................................................................................................... TransTerm Strand: - Conf: 87 HP_score: -12.1 Tail_Score: -3.17723 Start: 32 End: 87 Full_Region: tataatggcgcataa cacccgcttcaacctgacattgcgggt caa gcccgcgaatgcaggttaagcggtag ttaggttgcccctgc ...............................cacccgcttcaacctgacattgcgggtcaagcccgcgaatgcaggttaagcggtag...................................................................................................................... TransTerm Strand: + Conf: 95 HP_score: -12.6 Tail_Score: -3.224 Start: 34 End: 85 Full_Region: AGGGGCAACCTAACT ACCGCTTAACCTGCATTCGCGGG CTTGA CCCGCAATGTCAGGTTGAAGCGGG TGTTATGCGCCATTA .................................ACCGCTTAACCTGCATTCGCGGGCTTGACCCGCAATGTCAGGTTGAAGCGGG........................................................................................................................ TransTerm Strand: + Conf: 100 HP_score: -16.1 Tail_Score: -2.53119 Start: 35 End: 84 Full_Region: GGGGCAACCTAACTA CCGCTTAACCTGCATTCGCGGG CTTGA CCCGCAATGTCAGGTTGAAGCGG GTGTTATGCGCCATT ..................................CCGCTTAACCTGCATTCGCGGGCTTGACCCGCAATGTCAGGTTGAAGCGG......................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -16.8 Tail_Score: -2.78712 Start: 35 End: 84 Full_Region: aatggcgcataacac ccgcttcaacctgacattgcgggt caa gcccgcgaatgcaggttaagcgg tagttaggttgcccc ..................................ccgcttcaacctgacattgcgggtcaagcccgcgaatgcaggttaagcgg......................................................................................................................... Find igs database================================================ Query_seq: TDE1803:TDE1804|TDE1803:TDE1804:hypothetical protein:hypothetical protein:<-<-:1839361..1839565 205 tattttctccatgcccgcaggggcaacctaactaccgcttaacctgcattcgcgggcttgacccgcaatgtcaggttgaagcgggtgttatgcgccattataatatataattttcaatcaatttgtatatatgcaaataaaacaaatagtgttaaatttatacatttcctaaatatagagagccatcatactatattgtaatttt Intra-Species Hit: Count: 1 Min: 1 Max: 205 Len: 205 Subject: NC_002967_TDE1803_TDE1804|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1839361,1839565]|205 HSP 1 e-value: 1.0E-112 bit: 406.0 Len: 205 Query Start:1 Query End:205 Subject Strand: POSITIVE Subject Start: 1 Subject End: 205 tattttctccatgcccgcaggggcaacctaactaccgcttaacctgcattcgcgggcttgacccgcaatgtcaggttgaagcgggtgttatgcgccattataatatataattttcaatcaatttgtatatatgcaaataaaacaaatagtgttaaatttatacatttcctaaatatagagagccatcatactatattgtaatttt tattttctccatgcccgcaggggcaacctaactaccgcttaacctgcattcgcgggcttgacccgcaatgtcaggttgaagcgggtgttatgcgccattataatatataattttcaatcaatttgtatatatgcaaataaaacaaatagtgttaaatttatacatttcctaaatatagagagccatcatactatattgtaatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUUUCUCCAUGCCCGCAGGGGCAACCUAACUACCGCUUAACCUGCAUUCGCGGGCUUGACCCGCAAUGUCAGGUUGAAGCGGGUGUUAUGCGCCAUUAUAAUAUAUAAUUUUCAAUCAAUUUGUAUAUAUGCAAAUAAAACAAAUAGUGUUAAAUUUAUACAUUUCCUAAAUAUAGAGAGCCAUCAUACUAUAUUGUAAUUUU ...........(((((....)))))...((((..((((((((((((((((.(((((.....))))))))).))))))).)))))..))))......(((((((((((.............(((((((....)))))))..........((((.......))))..((((((....))).))).........)))))))))))... (-55.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUACAAUAUAGUAUGAUGGCUCUCUAUAUUUAGGAAAUGUAUAAAUUUAACACUAUUUGUUUUAUUUGCAUAUAUACAAAUUGAUUGAAAAUUAUAUAUUAUAAUGGCGCAUAACACCCGCUUCAACCUGACAUUGCGGGUCAAGCCCGCGAAUGCAGGUUAAGCGGUAGUUAGGUUGCCCCUGCGGGCAUGGAGAAAAUA ........................(((((((.(.((((.(((((((((.(((......((((((..(((......))).))))))......))).))))))))).....(((((.((((..((((((.((((((.(((((((((.....))))).))))))))))))))))..)))).).)))))))).)...)))))))..... (-59.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1111 60 11 151 102 NC_002967:TDE1803|5end_hypothetical_protein_1839270..1839500_NEGATIVE 807 90 41 182 135 NC_002967:TDE1836|5end_hypothetical_protein_1869443..1869673_NEGATIVE 807 90 41 219 172 NC_002967:TDE1831|5end_hypothetical_protein_1865032..1865262_NEGATIVE 807 90 41 186 139 NC_002967:TDE1827|5end_hydrolase,_carbon-nitrogen_family_1860830..1861060_NEGATIVE 807 90 41 200 153 NC_002967:TDE1823|5end_hypothetical_protein_1856990..1857220_NEGATIVE 807 90 41 184 137 NC_002967:TDE1817|5end_hypothetical_protein_1852599..1852829_NEGATIVE 807 90 41 181 134 NC_002967:TDE1811|5end_hypothetical_protein_1847483..1847713_NEGATIVE 807 90 41 219 172 NC_002967:TDE1797|5end_hypothetical_protein_1836272..1836502_NEGATIVE 807 90 41 172 125 NC_002967:TDE1795|5end_funZ_protein,_putative_1834673..1834903_NEGATIVE 807 90 41 190 143 NC_002967:TDE0267|5end_HAM1_protein_299108..299338_NEGATIVE 798 90 42 179 133 NC_002967:TDE1839|5end_hypothetical_protein_1871221..1871451_NEGATIVE 798 90 42 204 158 NC_002967:TDE1832|5end_hypothetical_protein_1865921..1866151_NEGATIVE 798 90 42 202 156 NC_002967:TDE1820|5end_hypothetical_protein_1854692..1854922_NEGATIVE 765 90 41 189 142 NC_002967:TDE1791|5end_hypothetical_protein_1828775..1829005_NEGATIVE 751 90 41 203 157 NC_002967:TDE1796|5end_hypothetical_protein_1835515..1835745_NEGATIVE 745 88 41 231 186 NC_002967:TDE1813|5end_hypothetical_protein_1848249..1848479_NEGATIVE 730 90 41 179 132 NC_002967:TDE1822|5end_hypothetical_protein_1855922..1856152_NEGATIVE 710 88 41 231 186 NC_002967:TDE1790|5end_hypothetical_protein_1828007..1828237_NEGATIVE 666 80 35 229 186 NC_002967:TDE1799|5end_hypothetical_protein_1837264..1837494_NEGATIVE 613 67 21 166 114 NC_002967:TDE1781|5end_hypothetical_protein_1823260..1823490_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 807 90 41 93 46 NC_002967:TDE1843|3end_hypothetical_protein_1872199..1872349_NEGATIVE 807 90 41 83 36 NC_002967:TDE1837|3end_hypothetical_protein_1869542..1869692_NEGATIVE 807 90 41 79 32 NC_002967:TDE1832|3end_hypothetical_protein_1865172..1865322_NEGATIVE 807 90 41 82 35 NC_002967:TDE1828|3end_hypothetical_protein_1860934..1861084_NEGATIVE 807 90 41 84 37 NC_002967:TDE1812|3end_hypothetical_protein_1847580..1847730_NEGATIVE 807 90 41 79 32 NC_002967:TDE1796|3end_hypothetical_protein_1834766..1834916_NEGATIVE 807 90 41 75 28 NC_002967:TDE1787|3end_hypothetical_protein_1826378..1826528_NEGATIVE 807 90 41 93 46 NC_002967:TDE1780|3end_hypothetical_protein_1822183..1822333_NEGATIVE 807 90 41 79 32 NC_002967:TDE0268|3end_hypothetical_protein_299219..299369_NEGATIVE 798 90 42 76 30 NC_002967:TDE1840|3end_hypothetical_protein_1871324..1871474_NEGATIVE 798 90 42 83 37 NC_002967:TDE1836|3end_hypothetical_protein_1868514..1868664_NEGATIVE 798 90 42 79 33 NC_002967:TDE1821|3end_hypothetical_protein_1854815..1854965_NEGATIVE 798 90 42 79 33 NC_002967:TDE1810|3end_hypothetical_protein_1845924..1846074_NEGATIVE 798 90 42 84 38 NC_002967:TDE1808|3end_hypothetical_protein_1844084..1844234_NEGATIVE 798 90 42 76 30 NC_002967:TDE1800|3end_hypothetical_protein_1837427..1837577_NEGATIVE 791 90 41 88 41 NC_002967:TDE1811|3end_hypothetical_protein_1846773..1846923_NEGATIVE 788 90 41 88 41 NC_002967:TDE1806|3end_hypothetical_protein_1843190..1843340_NEGATIVE 780 90 41 93 46 NC_002967:TDE1793|3end_hydrolase,_carbon-nitrogen_family_1829957..1830107_NEGATIVE 779 90 41 82 35 NC_002967:TDE1776|3end_hypothetical_protein_1818414..1818564_NEGATIVE 777 90 41 84 37 NC_002967:TDE1789|3end_hypothetical_protein_1827338..1827488_NEGATIVE