Origin IGS: tattgtctcctactaaataaaatagcagtgttattttatttagtatacataattcttttttgactgtcaagatagcaatgctatttttttttaaataatttaccgagtattattatcatatggtagaaaaaaatgaatttagaatgatatactgccggcaaatagtgaaaaatagagtattcctgtggatattattgagaatttatggtataaaaagaaaagaatatttagggtaagttatatggagggaacatatttt .........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 aaaatatgttccctccatataacttaccctaaatattcttttctttttataccataaattctcaataatatccacaggaatactctatttttcactatttgccggcagtatatcattctaaattcatttttttctaccatatgataataatactcggtaaattatttaaaaaaaaatagcattgctatcttgacagtcaaaaaagaattatgtatactaaataaaataacactgctattttatttagtaggagacaata Mask Tandem Repeat Region ================================================ tattgtctcctactaaataaaatagcagtgttattttatttagtatacataattcttttttgactgtcaagatagcaatgctatttttttttaaataatttaccgagtattattatcatatggtagaaaaaaatgaatttagaatgatatactgccggcaaatagtgaaaaatagagtattcctgtggatattattgagaatttatggtataaaaagaaaagaatatttagggtaagttatatggagggaacatatttt Find is-nt database================================================ Query_seq: TDE0274:TDE0275|TDE0274:TDE0275:ABC transporter, ATP-binding/permease protein:CAAX amino terminal protease family protein:<-->:306514..306772 259 tattgtctcctactaaataaaatagcagtgttattttatttagtatacataattcttttttgactgtcaagatagcaatgctatttttttttaaataatttaccgagtattattatcatatggtagaaaaaaatgaatttagaatgatatactgccggcaaatagtgaaaaatagagtattcctgtggatattattgagaatttatggtataaaaagaaaagaatatttagggtaagttatatggagggaacatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0274:TDE0275|TDE0274:TDE0275:ABC transporter, ATP-binding/permease protein:CAAX amino terminal protease family protein:<-->:306514..306772 259 tattgtctcctactaaataaaatagcagtgttattttatttagtatacataattcttttttgactgtcaagatagcaatgctatttttttttaaataatttaccgagtattattatcatatggtagaaaaaaatgaatttagaatgatatactgccggcaaatagtgaaaaatagagtattcctgtggatattattgagaatttatggtataaaaagaaaagaatatttagggtaagttatatggagggaacatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0274:TDE0275|TDE0274:TDE0275:ABC transporter, ATP-binding/permease protein:CAAX amino terminal protease family protein:<-->:306514..306772 259 tattgtctcctactaaataaaatagcagtgttattttatttagtatacataattcttttttgactgtcaagatagcaatgctatttttttttaaataatttaccgagtattattatcatatggtagaaaaaaatgaatttagaatgatatactgccggcaaatagtgaaaaatagagtattcctgtggatattattgagaatttatggtataaaaagaaaagaatatttagggtaagttatatggagggaacatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattgtctcctactaaataaaatagcagtgttattttatttagtatacataattcttttttgactgtcaagatagcaatgctatttttttttaaataatttaccgagtattattatcatatggtagaaaaaaatgaatttagaatgatatactgccggcaaatagtgaaaaatagagtattcctgtggatattattgagaatttatggtataaaaagaaaagaatatttagggtaagttatatggagggaacatatttt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 120 End: 233 ....................................................................................................................... M V E K N E F R M I Y C R Q I V K N R V F L W I L L R I Y G I K R K E Y L G .......................... Protein_Len: 30 Strand: - Start: 84 End: 173 ................................................................................... K K K F L K G L I I I M H Y F F I F K S H Y V A P L Y H F M ...................................................................................... tattgtctcctactaaataaaatagcagtgttattttatttagtatacataattcttttttgactgtcaagatagcaatgctatttttttttaaataatttaccgagtattattatcatatggtagaaaaaaatgaatttagaatgatatactgccggcaaatagtgaaaaatagagtattcctgtggatattattgagaatttatggtataaaaagaaaagaatatttagggtaagttatatggagggaacatatttt 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: 86 Start: 42 End: 71 .........................................CTTGACAGTCAAAAAAGAATTATGTATACT............................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tattgtctcctactaaataaaatagcagtgttattttatttagtatacataattcttttttgactgtcaagatagcaatgctatttttttttaaataatttaccgagtattattatcatatggtagaaaaaaatgaatttagaatgatatactgccggcaaatagtgaaaaatagagtattcctgtggatattattgagaatttatggtataaaaagaaaagaatatttagggtaagttatatggagggaacatatttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -5.4 Tail_Score: -6.11644 Start: 73 End: 83 Full_Region: TTTTGACTGTCAAGA TAGC AAT GCTA TTTTTTTTTAAATAA ........................................................................TAGCAATGCTA................................................................................................................................................................................ Find igs database================================================ Query_seq: TDE0274:TDE0275|TDE0274:TDE0275:ABC transporter, ATP-binding/permease protein:CAAX amino terminal protease family protein:<-->:306514..306772 259 tattgtctcctactaaataaaatagcagtgttattttatttagtatacataattcttttttgactgtcaagatagcaatgctatttttttttaaataatttaccgagtattattatcatatggtagaaaaaaatgaatttagaatgatatactgccggcaaatagtgaaaaatagagtattcctgtggatattattgagaatttatggtataaaaagaaaagaatatttagggtaagttatatggagggaacatatttt Intra-Species Hit: Count: 1 Min: 1 Max: 259 Len: 259 Subject: NC_002967_TDE0274_TDE0275|ABC transporter, ATP-binding/permease protein:CAAX amino terminal protease family protein|NEGATIVE:POSITIVE|[306514,306772]|259 HSP 1 e-value: 1.0E-116 bit: 418.0 Len: 259 Query Start:1 Query End:259 Subject Strand: POSITIVE Subject Start: 1 Subject End: 259 tattgtctcctactaaataaaatagcagtgttattttatttagtatacataattcttttttgactgtcaagatagcaatgctannnnnnnnnaaataatttaccgagtattattatcatatggtagnnnnnnntgaatttagaatgatatactgccggcaaatagtgaaaaatagagtattcctgtggatattattgagaatttatggtataaaaagaaaagaatatttagggtaagttatatggagggaacatatttt tattgtctcctactaaataaaatagcagtgttattttatttagtatacataattcttttttgactgtcaagatagcaatgctatttttttttaaataatttaccgagtattattatcatatggtagaaaaaaatgaatttagaatgatatactgccggcaaatagtgaaaaatagagtattcctgtggatattattgagaatttatggtataaaaagaaaagaatatttagggtaagttatatggagggaacatatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUGUCUCCUACUAAAUAAAAUAGCAGUGUUAUUUUAUUUAGUAUACAUAAUUCUUUUUUGACUGUCAAGAUAGCAAUGCUAUUUUUUUUUAAAUAAUUUACCGAGUAUUAUUAUCAUAUGGUAGAAAAAAAUGAAUUUAGAAUGAUAUACUGCCGGCAAAUAGUGAAAAAUAGAGUAUUCCUGUGGAUAUUAUUGAGAAUUUAUGGUAUAAAAAGAAAAGAAUAUUUAGGGUAAGUUAUAUGGAGGGAACAUAUUUU ...(((..(((.(((...(((((((((.(((((((((...((((..................))))..))))))))).))))))))).......(((((((((((((((((.(((((....)))))......((((((((..((((((((.(..(.((..((((.(.........).)))))).)..)))))))))..))))))))................)))))))..)))))))))).))))))..)))...... (-53.97) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUAUGUUCCCUCCAUAUAACUUACCCUAAAUAUUCUUUUCUUUUUAUACCAUAAAUUCUCAAUAAUAUCCACAGGAAUACUCUAUUUUUCACUAUUUGCCGGCAGUAUAUCAUUCUAAAUUCAUUUUUUUCUACCAUAUGAUAAUAAUACUCGGUAAAUUAUUUAAAAAAAAAUAGCAUUGCUAUCUUGACAGUCAAAAAAGAAUUAUGUAUACUAAAUAAAAUAACACUGCUAUUUUAUUUAGUAGGAGACAAUA ............((((....................................(((((.((((............(((((........((((.....((((((((..((((((((((........................))))))....)))))))))))).....)))).....((((...)))))))))...........)))))))))..((((((((((((((.......))))))))))))))))))...... (-37.06) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 720 110 61 201 152 NC_002967:TDE0274|5end_ABC_transporter,_ATP-binding/permease_protein_306423..306653_NEGATIVE 501 70 21 164 115 NC_002967:TDE0339|5end_transcriptional_regulator,_TetR_family_377871..378101_POSITIVE 417 70 21 181 132 NC_002967:TDE0284|5end_hypothetical_protein_313428..313658_NEGATIVE 339 70 21 201 155 NC_002967:TDE0258|5end_methlytransferase,_UbiE/COQ5_family_292884..293114_NEGATIVE 318 90 51 102 63 NC_002967:TDE1690|5end_hypothetical_protein_1747200..1747430_NEGATIVE 290 189 141 65 12 NC_002967:TDE0899|5end_ABC_transporter,_permease_protein,_putative_916481..916711_POSITIVE 251 195 152 197 154 NC_002967:TDE0566|5end_hypothetical_protein_597185..597415_POSITIVE 227 111 71 160 125 NC_002967:TDE2409|5end_hypothetical_protein_2436006..2436236_NEGATIVE 225 100 55 114 66 NC_002967:TDE2085|5end_uridylate_kinase_2114182..2114412_POSITIVE 223 214 180 212 180 NC_002967:TDE2235|5end_methylaspartate_ammonia-lyase_2274588..2274818_NEGATIVE 223 192 152 73 28 NC_002967:TDE0454|5end_hypothetical_protein_511243..511473_NEGATIVE 220 200 152 47 4 NC_002967:TDE1678|5end_ribosomal_protein_S6_1730483..1730713_NEGATIVE 217 106 61 181 142 NC_002967:TDE0900|5end_ABC_transporter,_ATP-binding_protein_917188..917418_POSITIVE 215 186 151 227 192 NC_002967:TDE1354|5end_hypothetical_protein_1394886..1395116_POSITIVE 215 119 79 57 15 NC_002967:TDE0655|5end_response_regulator_690921..691151_POSITIVE 213 196 155 84 46 NC_002967:TDE1247|5end_hypothetical_protein_1281623..1281853_POSITIVE 208 189 141 122 66 NC_002967:TDE2637|5end_hypothetical_protein_2677316..2677546_NEGATIVE 208 209 172 135 90 NC_002967:TDE2541|5end_hypothetical_protein_2568165..2568395_POSITIVE 208 67 22 109 59 NC_002967:TDE0728|5end_FAD-binding_protein,_putative_767206..767436_POSITIVE 207 190 152 225 193 NC_002967:TDE0808|5end_acetyltransferase,_GNAT_family_829650..829880_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 501 70 21 77 28 NC_002967:TDE0338|3end_methyl-accepting_chemotaxis_protein-like_protein_377864..378014_POSITIVE 290 189 141 61 8 NC_002967:TDE0898|3end_hypothetical_protein_916557..916707_POSITIVE 230 194 151 118 76 NC_002967:TDE0361|3end_transporter,_putative_407442..407592_POSITIVE 227 111 71 133 98 NC_002967:TDE2410|3end_hemolysin_2436033..2436183_NEGATIVE 226 185 152 149 119 NC_002967:TDE0565|3end_hypothetical_protein_597230..597380_POSITIVE 225 100 55 81 33 NC_002967:TDE2084|3end_RNA_methyltransferase,_TrmH_family_2114229..2114379_POSITIVE 223 214 180 140 108 NC_002967:TDE2236|3end_methylaspartate_mutase,_E_subunit_2274660..2274810_NEGATIVE 220 185 152 57 13 NC_002967:TDE0296|3end_formiminotransferase,_putative_326842..326992_NEGATIVE 219 166 131 69 39 NC_002967:TDE0316|3end_ABC_transporter,_ATP-binding/permease_protein_348870..349020_NEGATIVE 217 166 141 90 71 NC_002967:TDE0113|3end_Tpl_protein_133609..133759_POSITIVE 208 67 22 103 53 NC_002967:TDE0727|3end_iron-sulfur_cluster-binding_protein_767280..767430_POSITIVE 206 105 62 62 18 NC_002967:TDE0648|3end_protein-glutamate_methylesterase_683998..684148_POSITIVE 206 188 141 142 95 NC_002967:TDE0014|3end_hypothetical_protein_19487..19637_POSITIVE 205 117 77 135 97 NC_002967:TDE1623|3end_hypothetical_protein_1671018..1671168_NEGATIVE 205 160 142 29 10 NC_002967:TDE0935|3end_hypothetical_protein_959661..959811_NEGATIVE 205 199 152 82 31 NC_002967:TDE0919|3end_hypothetical_protein_939125..939275_POSITIVE 205 191 152 117 73 NC_002967:TDE0141|3end_hypothetical_protein_164065..164215_POSITIVE 203 180 134 52 5 NC_002967:TDE2043|3end_signal_recognition_particle-docking_protein_FtsY_2072180..2072330_NEGATIVE 203 186 142 81 28 NC_002967:TDE1609|3end_hypothetical_protein_1659227..1659377_POSITIVE 203 212 172 142 98 NC_002967:TDE1355|3end_hypothetical_protein_1395527..1395677_POSITIVE