Origin IGS: atatacctctatatactattttcacgcaaaccgtctgcctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttaggcagttttat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataaaactgcctaacacccgcttcaacctgacattgcggacgagccgcaaatgcaggttaagcgaatgttaggcagacggtttgcgtgaaaatagtatatagaggtatat Mask Tandem Repeat Region ================================================ atatacctctatatactattttcacgcaaaccgtctgcctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttaggcagttttat Find is-nt database================================================ Query_seq: TDE0267:TDE0268|TDE0267:TDE0268:HAM1 protein:hypothetical protein:<-<-:299199..299308 110 atatacctctatatactattttcacgcaaaccgtctgcctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttaggcagttttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0267:TDE0268|TDE0267:TDE0268:HAM1 protein:hypothetical protein:<-<-:299199..299308 110 atatacctctatatactattttcacgcaaaccgtctgcctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttaggcagttttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0267:TDE0268|TDE0267:TDE0268:HAM1 protein:hypothetical protein:<-<-:299199..299308 110 atatacctctatatactattttcacgcaaaccgtctgcctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttaggcagttttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atatacctctatatactattttcacgcaaaccgtctgcctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttaggcagttttat Predict ORF larger than 30AA ================================================ atatacctctatatactattttcacgcaaaccgtctgcctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttaggcagttttat 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================================================ atatacctctatatactattttcacgcaaaccgtctgcctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttaggcagttttat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 68 HP_score: -8.9 Tail_Score: -3.06009 Start: 45 End: 94 Full_Region: ACCGTCTGCCTAACA TTCGCTTAACCTGCATTTGCGG CTCGT CCGCAATGTCAGGTTGAAGCGGG TGTTAGGCAGTTTTA ............................................TTCGCTTAACCTGCATTTGCGGCTCGTCCGCAATGTCAGGTTGAAGCGGG................ Find igs database================================================ Query_seq: TDE0267:TDE0268|TDE0267:TDE0268:HAM1 protein:hypothetical protein:<-<-:299199..299308 110 atatacctctatatactattttcacgcaaaccgtctgcctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttaggcagttttat Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: NC_002967_TDE0267_TDE0268|HAM1 protein:hypothetical protein|NEGATIVE:NEGATIVE|[299199,299308]|110 HSP 1 e-value: 3.0E-56 bit: 218.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 atatacctctatatactattttcacgcaaaccgtctgcctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttaggcagttttat atatacctctatatactattttcacgcaaaccgtctgcctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttaggcagttttat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUACCUCUAUAUACUAUUUUCACGCAAACCGUCUGCCUAACAUUCGCUUAACCUGCAUUUGCGGCUCGUCCGCAAUGUCAGGUUGAAGCGGGUGUUAGGCAGUUUUAU ..................................(((((((((((((((((((((((((((.((((.....)))))))).))))))).))))))))))))))))...... (-46.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAACUGCCUAACACCCGCUUCAACCUGACAUUGCGGACGAGCCGCAAAUGCAGGUUAAGCGAAUGUUAGGCAGACGGUUUGCGUGAAAAUAGUAUAUAGAGGUAUAU ......((((((((((..(((((.((((((.((((((((.....)))).)))))))))))))))..))))))))))..................((((((....)))))) (-44.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1039 80 31 171 122 NC_002967:TDE0267|5end_HAM1_protein_299108..299338_NEGATIVE 1034 100 51 183 134 NC_002967:TDE1836|5end_hypothetical_protein_1869443..1869673_NEGATIVE 1034 100 51 187 138 NC_002967:TDE1827|5end_hydrolase,_carbon-nitrogen_family_1860830..1861060_NEGATIVE 1034 100 51 182 133 NC_002967:TDE1811|5end_hypothetical_protein_1847483..1847713_NEGATIVE 1014 100 53 203 156 NC_002967:TDE1820|5end_hypothetical_protein_1854692..1854922_NEGATIVE 978 100 51 204 156 NC_002967:TDE1796|5end_hypothetical_protein_1835515..1835745_NEGATIVE 958 100 51 220 171 NC_002967:TDE1831|5end_hypothetical_protein_1865032..1865262_NEGATIVE 958 100 51 201 152 NC_002967:TDE1823|5end_hypothetical_protein_1856990..1857220_NEGATIVE 958 100 51 185 136 NC_002967:TDE1817|5end_hypothetical_protein_1852599..1852829_NEGATIVE 958 100 51 220 171 NC_002967:TDE1797|5end_hypothetical_protein_1836272..1836502_NEGATIVE 958 100 51 173 124 NC_002967:TDE1795|5end_funZ_protein,_putative_1834673..1834903_NEGATIVE 938 100 53 180 133 NC_002967:TDE1839|5end_hypothetical_protein_1871221..1871451_NEGATIVE 938 100 53 205 158 NC_002967:TDE1832|5end_hypothetical_protein_1865921..1866151_NEGATIVE 911 90 41 224 175 NC_002967:TDE1790|5end_hypothetical_protein_1828007..1828237_NEGATIVE 881 100 51 180 131 NC_002967:TDE1822|5end_hypothetical_protein_1855922..1856152_NEGATIVE 877 100 51 190 141 NC_002967:TDE1791|5end_hypothetical_protein_1828775..1829005_NEGATIVE 860 90 41 230 181 NC_002967:TDE1799|5end_hypothetical_protein_1837264..1837494_NEGATIVE 831 90 41 224 175 NC_002967:TDE1813|5end_hypothetical_protein_1848249..1848479_NEGATIVE 821 99 51 181 131 NC_002967:TDE1803|5end_hypothetical_protein_1839270..1839500_NEGATIVE 764 100 51 194 144 NC_002967:TDE0262|5end_hypothetical_protein_296300..296530_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1034 100 51 84 35 NC_002967:TDE1837|3end_hypothetical_protein_1869542..1869692_NEGATIVE 1034 100 51 83 34 NC_002967:TDE1828|3end_hypothetical_protein_1860934..1861084_NEGATIVE 1034 100 51 85 36 NC_002967:TDE1812|3end_hypothetical_protein_1847580..1847730_NEGATIVE 1034 100 51 76 27 NC_002967:TDE1787|3end_hypothetical_protein_1826378..1826528_NEGATIVE 1034 100 51 94 45 NC_002967:TDE1780|3end_hypothetical_protein_1822183..1822333_NEGATIVE 1015 100 51 89 40 NC_002967:TDE1806|3end_hypothetical_protein_1843190..1843340_NEGATIVE 1014 100 53 80 33 NC_002967:TDE1821|3end_hypothetical_protein_1854815..1854965_NEGATIVE 1014 100 53 85 38 NC_002967:TDE1808|3end_hypothetical_protein_1844084..1844234_NEGATIVE 1006 100 51 83 34 NC_002967:TDE1776|3end_hypothetical_protein_1818414..1818564_NEGATIVE 983 100 51 111 62 NC_002967:TDE1815|3end_hypothetical_protein_1849458..1849608_NEGATIVE 978 100 51 64 16 NC_002967:TDE1831|3end_hypothetical_protein_1864415..1864565_NEGATIVE 978 100 51 64 16 NC_002967:TDE1797|3end_hypothetical_protein_1835655..1835805_NEGATIVE 968 100 51 89 40 NC_002967:TDE1811|3end_hypothetical_protein_1846773..1846923_NEGATIVE 958 100 51 94 45 NC_002967:TDE1843|3end_hypothetical_protein_1872199..1872349_NEGATIVE 958 100 51 80 31 NC_002967:TDE1832|3end_hypothetical_protein_1865172..1865322_NEGATIVE 958 100 51 80 31 NC_002967:TDE1796|3end_hypothetical_protein_1834766..1834916_NEGATIVE 938 100 53 77 30 NC_002967:TDE1840|3end_hypothetical_protein_1871324..1871474_NEGATIVE 938 100 53 84 37 NC_002967:TDE1836|3end_hypothetical_protein_1868514..1868664_NEGATIVE 938 100 53 80 33 NC_002967:TDE1810|3end_hypothetical_protein_1845924..1846074_NEGATIVE 938 100 53 77 30 NC_002967:TDE1800|3end_hypothetical_protein_1837427..1837577_NEGATIVE