Origin IGS: tacccttcgttacgacgcaagcgtcggggtattaaactctccgcacgaataaaattatgcaaaaagaggattttaaaaagaagctctcacttctacaaaaaaaattaaagcggcttaatctcagcgaaatggttaaaatttccctcgatgtaaaatccgttattttagaaggcgatgtttcttcaatggaagaaagaatggaagcaggttatgcggctgcccgctgcgggtttaagggagttgtaaacgatttaactataaacggccgtggagaagaacct .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aggttcttctccacggccgtttatagttaaatcgtttacaactcccttaaacccgcagcgggcagccgcataacctgcttccattctttcttccattgaagaaacatcgccttctaaaataacggattttacatcgagggaaattttaaccatttcgctgagattaagccgctttaattttttttgtagaagtgagagcttctttttaaaatcctctttttgcataattttattcgtgcggagagtttaataccccgacgcttgcgtcgtaacgaagggta Mask Tandem Repeat Region ================================================ tacccttcgttacgacgcaagcgtcggggtattaaactctccgcacgaataaaattatgcaaaaagaggattttaaaaagaagctctcacttctacaaaaaaaattaaagcggcttaatctcagcgaaatggttaaaatttccctcgatgtaaaatccgttattttagaaggcgatgtttcttcaatggaagaaagaatggaagcaggttatgcggctgcccgctgcgggtttaagggagttgtaaacgatttaactataaacggccgtggagaagaacct Find is-nt database================================================ Query_seq: TDE0133:TDE0134|TDE0133:TDE0134:transcriptional regulator, GntR family:oxidoreductase, FAD-dependent:->->:153263..153543 281 tacccttcgttacgacgcaagcgtcggggtattaaactctccgcacgaataaaattatgcaaaaagaggattttaaaaagaagctctcacttctacaaaaaaaattaaagcggcttaatctcagcgaaatggttaaaatttccctcgatgtaaaatccgttattttagaaggcgatgtttcttcaatggaagaaagaatggaagcaggttatgcggctgcccgctgcgggtttaagggagttgtaaacgatttaactataaacggccgtggagaagaacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0133:TDE0134|TDE0133:TDE0134:transcriptional regulator, GntR family:oxidoreductase, FAD-dependent:->->:153263..153543 281 tacccttcgttacgacgcaagcgtcggggtattaaactctccgcacgaataaaattatgcaaaaagaggattttaaaaagaagctctcacttctacaaaaaaaattaaagcggcttaatctcagcgaaatggttaaaatttccctcgatgtaaaatccgttattttagaaggcgatgtttcttcaatggaagaaagaatggaagcaggttatgcggctgcccgctgcgggtttaagggagttgtaaacgatttaactataaacggccgtggagaagaacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0133:TDE0134|TDE0133:TDE0134:transcriptional regulator, GntR family:oxidoreductase, FAD-dependent:->->:153263..153543 281 tacccttcgttacgacgcaagcgtcggggtattaaactctccgcacgaataaaattatgcaaaaagaggattttaaaaagaagctctcacttctacaaaaaaaattaaagcggcttaatctcagcgaaatggttaaaatttccctcgatgtaaaatccgttattttagaaggcgatgtttcttcaatggaagaaagaatggaagcaggttatgcggctgcccgctgcgggtttaagggagttgtaaacgatttaactataaacggccgtggagaagaacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tacccttcgttacgacgcaagcgtcggggtattaaactctccgcacgaataaaattatgcaaaaagaggattttaaaaagaagctctcacttctacaaaaaaaattaaagcggcttaatctcagcgaaatggttaaaatttccctcgatgtaaaatccgttattttagaaggcgatgtttcttcaatggaagaaagaatggaagcaggttatgcggctgcccgctgcgggtttaagggagttgtaaacgatttaactataaacggccgtggagaagaacct Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 54 End: 281 ..................................................... M M Q K E D F K K K L S L L Q K K L K R L N L S E M V K I S L D V K S V I L E G D V S S M E E R M E A G Y A A A R C G F Protein_Len: 55 Strand: - Start: 35 End: 199 .................................. V R R V F L I I C F S S K L F F S E S R C F F N F R S L R L S I T L I E R S T F D T I K S P S T E E I S S L M .................................................................................. tacccttcgttacgacgcaagcgtcggggtattaaactctccgcacgaataaaattatgcaaaaagaggattttaaaaagaagctctcacttctacaaaaaaaattaaagcggcttaatctcagcgaaatggttaaaatttccctcgatgtaaaatccgttattttagaaggcgatgtttcttcaatggaagaaagaatggaagcaggttatgcggctgcccgctgcgggtttaagggagttgtaaacgatttaactataaacggccgtggagaagaacct 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: 82 Start: 70 End: 99 .....................................................................TTTGTAGAAGTGAGAGCTTCTTTTTAAAAT...................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tacccttcgttacgacgcaagcgtcggggtattaaactctccgcacgaataaaattatgcaaaaagaggattttaaaaagaagctctcacttctacaaaaaaaattaaagcggcttaatctcagcgaaatggttaaaatttccctcgatgtaaaatccgttattttagaaggcgatgtttcttcaatggaagaaagaatggaagcaggttatgcggctgcccgctgcgggtttaagggagttgtaaacgatttaactataaacggccgtggagaagaacct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0133:TDE0134|TDE0133:TDE0134:transcriptional regulator, GntR family:oxidoreductase, FAD-dependent:->->:153263..153543 281 tacccttcgttacgacgcaagcgtcggggtattaaactctccgcacgaataaaattatgcaaaaagaggattttaaaaagaagctctcacttctacaaaaaaaattaaagcggcttaatctcagcgaaatggttaaaatttccctcgatgtaaaatccgttattttagaaggcgatgtttcttcaatggaagaaagaatggaagcaggttatgcggctgcccgctgcgggtttaagggagttgtaaacgatttaactataaacggccgtggagaagaacct Intra-Species Hit: Count: 1 Min: 1 Max: 281 Len: 281 Subject: NC_002967_TDE0133_TDE0134|transcriptional regulator, GntR family:oxidoreductase, FAD-dependent|POSITIVE:POSITIVE|[153263,153543]|281 HSP 1 e-value: 1.0E-143 bit: 509.0 Len: 281 Query Start:1 Query End:281 Subject Strand: POSITIVE Subject Start: 1 Subject End: 281 tacccttcgttacgacgcaagcgtcggggtattaaactctccgcacgaataaaattatgcaaaaagaggattttaaaaagaagctctcacttctacnnnnnnnnttaaagcggcttaatctcagcgaaatggttaaaatttccctcgatgtaaaatccgttattttagaaggcgatgtttcttcaatggaagaaagaatggaagcaggttatgcggctgcccgctgcgggtttaagggagttgtaaacgatttaactataaacggccgtggagaagaacct tacccttcgttacgacgcaagcgtcggggtattaaactctccgcacgaataaaattatgcaaaaagaggattttaaaaagaagctctcacttctacaaaaaaaattaaagcggcttaatctcagcgaaatggttaaaatttccctcgatgtaaaatccgttattttagaaggcgatgtttcttcaatggaagaaagaatggaagcaggttatgcggctgcccgctgcgggtttaagggagttgtaaacgatttaactataaacggccgtggagaagaacct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACCCUUCGUUACGACGCAAGCGUCGGGGUAUUAAACUCUCCGCACGAAUAAAAUUAUGCAAAAAGAGGAUUUUAAAAAGAAGCUCUCACUUCUACAAAAAAAAUUAAAGCGGCUUAAUCUCAGCGAAAUGGUUAAAAUUUCCCUCGAUGUAAAAUCCGUUAUUUUAGAAGGCGAUGUUUCUUCAAUGGAAGAAAGAAUGGAAGCAGGUUAUGCGGCUGCCCGCUGCGGGUUUAAGGGAGUUGUAAACGAUUUAACUAUAAACGGCCGUGGAGAAGAACCU (((((.......(((((....))))))))))......(((((.......(((((((...(.....)..)))))))...(((((......)))))...............((((((.......((..((((.(((.....((((((..(......((((((......((..(((..(.(((((((....))))))).)..((..(((.....)))..)))))..)))))))))..)))))).....))).))))..))......)))))))))))....... (-66.23) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUUCUUCUCCACGGCCGUUUAUAGUUAAAUCGUUUACAACUCCCUUAAACCCGCAGCGGGCAGCCGCAUAACCUGCUUCCAUUCUUUCUUCCAUUGAAGAAACAUCGCCUUCUAAAAUAACGGAUUUUACAUCGAGGGAAAUUUUAACCAUUUCGCUGAGAUUAAGCCGCUUUAAUUUUUUUUGUAGAAGUGAGAGCUUCUUUUUAAAAUCCUCUUUUUGCAUAAUUUUAUUCGUGCGGAGAGUUUAAUACCCCGACGCUUGCGUCGUAACGAAGGGUA (((..........((((.((((.((((.((((.(((......((((((......((.((((....)))).................(((((((....)))))))....))....((((((.....))))))....))))))......))).)))).))))))))...))))..........(((((.((((((....))))))...))))).)))(((((((((..(......)..))))))))).....((((((((((....))))).......))))) (-65.21) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 807 50 1 202 152 NC_002967:TDE2691|5end_hypothetical_protein_2728838..2729068_POSITIVE 704 50 1 202 152 NC_002967:TDE0830|5end_hypothetical_protein_852025..852255_NEGATIVE 677 53 11 177 132 NC_002967:TDE0713|5end_transcription_antitermination_protein,_NusG_family_747109..747339_POSITIVE 658 54 13 187 145 NC_002967:TDE0017|5end_hypothetical_protein_22936..23166_NEGATIVE 520 36 1 229 193 NC_002967:TDE0580|5end_hypothetical_protein_615338..615568_POSITIVE 504 26 1 231 206 NC_002967:TDE1051|5end_hypothetical_protein_1078496..1078726_NEGATIVE 374 235 199 168 122 NC_002967:TDE2399|5end_ribonuclease_P_protein_component_2426160..2426390_NEGATIVE 364 47 3 51 9 NC_002967:TDE1736|5end_ferredoxin,_2(4Fe-4S)_1789908..1790138_POSITIVE 362 237 198 190 145 NC_002967:TDE2069|5end_endoribonuclease_L-PSP,_putative_2096632..2096862_POSITIVE 357 230 181 57 3 NC_002967:TDE0875|5end_ribosomal_large_subunit_pseudouridine_synthase_B_897489..897719_POSITIVE 354 240 199 53 1 NC_002967:TDE0852|5end_50S_ribosomal_protein_L13_875019..875249_POSITIVE 351 243 204 222 175 NC_002967:TDE0808|5end_acetyltransferase,_GNAT_family_829650..829880_NEGATIVE 350 43 4 69 27 NC_002967:TDE0071|5end_peptidase,_U32_family_78602..78832_POSITIVE 342 41 2 198 165 NC_002967:TDE1194|5end_hypothetical_protein_1224973..1225203_POSITIVE 340 243 203 82 41 NC_002967:TDE2233|5end_iron_compound_ABC_transporter,_permease_protein,_putative_2272310..2272540_NEGATIVE 340 232 199 166 124 NC_002967:TDE0991|5end_ribosomal_protein_L28_1018065..1018295_NEGATIVE 338 249 212 53 7 NC_002967:TDE2180|5end_tRNA_modification_GTPase_2212008..2212238_NEGATIVE 332 240 194 220 171 NC_002967:TDE2419|5end_hypothetical_protein_2444769..2444999_NEGATIVE 332 56 26 57 26 NC_002967:TDE1692|5end_hypothetical_protein_1748293..1748523_POSITIVE 327 221 186 62 28 NC_002967:TDE0851|5end_hypothetical_protein_874997..875227_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1004 50 1 109 60 NC_002967:TDE0710|3end_hypothetical_protein_745667..745817_POSITIVE 1004 50 1 62 13 NC_002967:TDE0333|3end_MATE_efflux_family_protein_373083..373233_POSITIVE 928 50 1 86 37 NC_002967:TDE2499|3end_hypothetical_protein_2523191..2523341_NEGATIVE 928 50 1 52 3 NC_002967:TDE2140|3end_protease_II_2173083..2173233_NEGATIVE 892 50 1 144 95 NC_002967:TDE2459|3end_hypothetical_protein_2485764..2485914_NEGATIVE 807 50 1 132 82 NC_002967:TDE2689|3end_hypothetical_protein_2728848..2728998_POSITIVE 806 53 12 42 1 NC_002967:TDE1052|3end_rubredoxin_1078712..1078862_NEGATIVE 781 52 13 57 18 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 704 50 1 132 82 NC_002967:TDE0831|3end_hypothetical_protein_852095..852245_NEGATIVE 658 54 13 50 8 NC_002967:TDE0018|3end_LysM_domain_protein_23073..23223_NEGATIVE 558 50 2 68 12 NC_002967:TDE2429|3end_hypothetical_protein_2456628..2456778_NEGATIVE 404 259 211 114 58 NC_002967:TDE0353|3end_lipase/acylhydrolase,_GDSL_family_396743..396893_NEGATIVE 385 242 203 87 45 NC_002967:TDE1811|3end_hypothetical_protein_1846773..1846923_NEGATIVE 382 250 203 140 93 NC_002967:TDE0742|3end_hypothetical_protein_778450..778600_NEGATIVE 364 47 3 61 19 NC_002967:TDE1735|3end_hypothetical_protein_1789998..1790148_POSITIVE 362 237 198 73 28 NC_002967:TDE2068|3end_antigen,_putative_2096595..2096745_POSITIVE 358 30 3 74 52 NC_002967:TDE0202|3end_hypothetical_protein_235870..236020_NEGATIVE 352 250 201 140 99 NC_002967:TDE0616|3end_hypothetical_protein_650079..650229_POSITIVE 345 250 201 120 57 NC_002967:TDE1848|3end_hypothetical_protein_1875897..1876047_NEGATIVE 341 229 199 148 110 NC_002967:TDE2400|3end_50S_ribosomal_protein_L34_2426172..2426322_NEGATIVE