Origin IGS: tttctctcctgtaccgaaggcgtcagcctaacatccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcgtctttcatttatcttgtattaataatcttaattctttttccataacaaatgggcatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatgcccatttgttatggaaaaagaattaagattattaatacaagataaatgaaagacgcctaacacccgcttcaacctgacattgcctttgcggcaatgcaggttaagcggatgttaggctgacgccttcggtacaggagagaaa Mask Tandem Repeat Region ================================================ tttctctcctgtaccgaaggcgtcagcctaacatccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcgtctttcatttatcttgtattaataatcttaattctttttccataacaaatgggcatc Find is-nt database================================================ Query_seq: TDE0268:TDE0269|TDE0268:TDE0269:hypothetical protein:hypothetical protein:<-<-:300140..300285 146 tttctctcctgtaccgaaggcgtcagcctaacatccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcgtctttcatttatcttgtattaataatcttaattctttttccataacaaatgggcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0268:TDE0269|TDE0268:TDE0269:hypothetical protein:hypothetical protein:<-<-:300140..300285 146 tttctctcctgtaccgaaggcgtcagcctaacatccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcgtctttcatttatcttgtattaataatcttaattctttttccataacaaatgggcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0268:TDE0269|TDE0268:TDE0269:hypothetical protein:hypothetical protein:<-<-:300140..300285 146 tttctctcctgtaccgaaggcgtcagcctaacatccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcgtctttcatttatcttgtattaataatcttaattctttttccataacaaatgggcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttctctcctgtaccgaaggcgtcagcctaacatccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcgtctttcatttatcttgtattaataatcttaattctttttccataacaaatgggcatc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 44 End: 145 ........................................... M H C R K G N V R L K R V L G V F H L S C I N N L N S F S I T N G H . tttctctcctgtaccgaaggcgtcagcctaacatccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcgtctttcatttatcttgtattaataatcttaattctttttccataacaaatgggcatc 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================================================ tttctctcctgtaccgaaggcgtcagcctaacatccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcgtctttcatttatcttgtattaataatcttaattctttttccataacaaatgggcatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -16.2 Tail_Score: -3.07029 Start: 34 End: 80 Full_Region: GGCGTCAGCCTAACA TCCGCTTAACCTGCATTGCC GCAAA GGCAATGTCAGGTTGAAGCGGG TGTTAGGCGTCTTTC .................................TCCGCTTAACCTGCATTGCCGCAAAGGCAATGTCAGGTTGAAGCGGG.................................................................. Find igs database================================================ Query_seq: TDE0268:TDE0269|TDE0268:TDE0269:hypothetical protein:hypothetical protein:<-<-:300140..300285 146 tttctctcctgtaccgaaggcgtcagcctaacatccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcgtctttcatttatcttgtattaataatcttaattctttttccataacaaatgggcatc Intra-Species Hit: Count: 1 Min: 1 Max: 146 Len: 146 Subject: NC_002967_TDE0268_TDE0269|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[300140,300285]|146 HSP 1 e-value: 1.0E-77 bit: 289.0 Len: 146 Query Start:1 Query End:146 Subject Strand: POSITIVE Subject Start: 1 Subject End: 146 tttctctcctgtaccgaaggcgtcagcctaacatccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcgtctttcatttatcttgtattaataatcttaattctttttccataacaaatgggcatc tttctctcctgtaccgaaggcgtcagcctaacatccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcgtctttcatttatcttgtattaataatcttaattctttttccataacaaatgggcatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUCUCCUGUACCGAAGGCGUCAGCCUAACAUCCGCUUAACCUGCAUUGCCGCAAAGGCAAUGUCAGGUUGAAGCGGGUGUUAGGCGUCUUUCAUUUAUCUUGUAUUAAUAAUCUUAAUUCUUUUUCCAUAACAAAUGGGCAUC ...............(((((.....((((((((((((((((((((((((((((.....))))))).))))))).))))))))))))))..)))))................................(((((.....))))).... (-56.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGCCCAUUUGUUAUGGAAAAAGAAUUAAGAUUAUUAAUACAAGAUAAAUGAAAGACGCCUAACACCCGCUUCAACCUGACAUUGCCUUUGCGGCAAUGCAGGUUAAGCGGAUGUUAGGCUGACGCCUUCGGUACAGGAGAGAAA ......((((((((.((.......(((....))).......)).))))))))......((((((((.((((((.((((((.(((((((.....))))))))))))))))))).))))))))......((((......))))..... (-53.34) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1055 60 11 151 102 NC_002967:TDE0268|5end_hypothetical_protein_300049..300279_NEGATIVE 848 50 1 141 92 NC_002967:TDE1839|5end_hypothetical_protein_1871221..1871451_NEGATIVE 777 90 41 224 172 NC_002967:TDE1797|5end_hypothetical_protein_1836272..1836502_NEGATIVE 774 80 31 195 143 NC_002967:TDE1823|5end_hypothetical_protein_1856990..1857220_NEGATIVE 730 90 41 196 143 NC_002967:TDE0267|5end_HAM1_protein_299108..299338_NEGATIVE 729 89 41 186 135 NC_002967:TDE1836|5end_hypothetical_protein_1869443..1869673_NEGATIVE 727 90 41 208 157 NC_002967:TDE1796|5end_hypothetical_protein_1835515..1835745_NEGATIVE 725 80 31 197 145 NC_002967:TDE1820|5end_hypothetical_protein_1854692..1854922_NEGATIVE 702 80 35 181 133 NC_002967:TDE1827|5end_hydrolase,_carbon-nitrogen_family_1860830..1861060_NEGATIVE 702 80 35 167 119 NC_002967:TDE1795|5end_funZ_protein,_putative_1834673..1834903_NEGATIVE 699 80 31 214 162 NC_002967:TDE1831|5end_hypothetical_protein_1865032..1865262_NEGATIVE 699 80 31 179 127 NC_002967:TDE1817|5end_hypothetical_protein_1852599..1852829_NEGATIVE 699 80 31 176 124 NC_002967:TDE1811|5end_hypothetical_protein_1847483..1847713_NEGATIVE 686 88 42 207 158 NC_002967:TDE1832|5end_hypothetical_protein_1865921..1866151_NEGATIVE 686 90 41 194 142 NC_002967:TDE1791|5end_hypothetical_protein_1828775..1829005_NEGATIVE 680 80 35 176 126 NC_002967:TDE1803|5end_hypothetical_protein_1839270..1839500_NEGATIVE 667 60 15 230 185 NC_002967:TDE1826|5end_hypothetical_protein_1859781..1860011_NEGATIVE 660 80 31 228 176 NC_002967:TDE1813|5end_hypothetical_protein_1848249..1848479_NEGATIVE 651 80 34 174 125 NC_002967:TDE1822|5end_hypothetical_protein_1855922..1856152_NEGATIVE 632 80 31 228 176 NC_002967:TDE1790|5end_hypothetical_protein_1828007..1828237_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 990 88 41 82 35 NC_002967:TDE1839|3end_hypothetical_protein_1870391..1870541_NEGATIVE 962 80 31 88 39 NC_002967:TDE1827|3end_hydrolase,_carbon-nitrogen_family_1859943..1860093_NEGATIVE 745 60 14 61 2 NC_002967:TDE1840|3end_hypothetical_protein_1871324..1871474_NEGATIVE 730 90 41 85 32 NC_002967:TDE0268|3end_hypothetical_protein_299219..299369_NEGATIVE 729 89 41 87 36 NC_002967:TDE1837|3end_hypothetical_protein_1869542..1869692_NEGATIVE 729 89 41 79 28 NC_002967:TDE1787|3end_hypothetical_protein_1826378..1826528_NEGATIVE 727 90 41 68 17 NC_002967:TDE1831|3end_hypothetical_protein_1864415..1864565_NEGATIVE 727 90 41 68 17 NC_002967:TDE1797|3end_hypothetical_protein_1835655..1835805_NEGATIVE 725 80 31 74 22 NC_002967:TDE1821|3end_hypothetical_protein_1854815..1854965_NEGATIVE 725 80 31 71 19 NC_002967:TDE1800|3end_hypothetical_protein_1837427..1837577_NEGATIVE 722 79 31 71 20 NC_002967:TDE0097|3end_hypothetical_protein_114801..114951_POSITIVE 702 80 35 77 29 NC_002967:TDE1828|3end_hypothetical_protein_1860934..1861084_NEGATIVE 702 80 35 74 26 NC_002967:TDE1796|3end_hypothetical_protein_1834766..1834916_NEGATIVE 699 80 31 88 36 NC_002967:TDE1843|3end_hypothetical_protein_1872199..1872349_NEGATIVE 699 80 31 74 22 NC_002967:TDE1832|3end_hypothetical_protein_1865172..1865322_NEGATIVE 699 80 31 79 27 NC_002967:TDE1812|3end_hypothetical_protein_1847580..1847730_NEGATIVE 699 80 31 88 36 NC_002967:TDE1780|3end_hypothetical_protein_1822183..1822333_NEGATIVE 695 80 31 105 53 NC_002967:TDE1815|3end_hypothetical_protein_1849458..1849608_NEGATIVE 688 80 34 83 34 NC_002967:TDE1811|3end_hypothetical_protein_1846773..1846923_NEGATIVE 686 90 41 58 6 NC_002967:TDE1814|3end_hypothetical_protein_1848429..1848579_NEGATIVE