Origin IGS: aagcaaacttccttttgttagctaacaaataatagttagcgttagctaacatttatgtaaagtcatcgcccattcttataaacaaagacaggcgatgagccttttaacgctattcaattatacaagtta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taacttgtataattgaatagcgttaaaaggctcatcgcctgtctttgtttataagaatgggcgatgactttacataaatgttagctaacgctaactattatttgttagctaacaaaaggaagtttgctt Mask Tandem Repeat Region ================================================ aagcaaacttccttttgttagctaacaaataatagttagcgttagctaacatttatgtaaagtcatcgcccattcttataaacaaagacaggcgatgagccttttaacgctattcaattatacaagtta Find is-nt database================================================ Query_seq: TDE2626:TDE2627|TDE2626:TDE2627:ABC transporter, ATP-binding/permease protein:transcriptional regulator, TetR family:<-<-:2668493..2668621 129 aagcaaacttccttttgttagctaacaaataatagttagcgttagctaacatttatgtaaagtcatcgcccattcttataaacaaagacaggcgatgagccttttaacgctattcaattatacaagtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2626:TDE2627|TDE2626:TDE2627:ABC transporter, ATP-binding/permease protein:transcriptional regulator, TetR family:<-<-:2668493..2668621 129 aagcaaacttccttttgttagctaacaaataatagttagcgttagctaacatttatgtaaagtcatcgcccattcttataaacaaagacaggcgatgagccttttaacgctattcaattatacaagtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2626:TDE2627|TDE2626:TDE2627:ABC transporter, ATP-binding/permease protein:transcriptional regulator, TetR family:<-<-:2668493..2668621 129 aagcaaacttccttttgttagctaacaaataatagttagcgttagctaacatttatgtaaagtcatcgcccattcttataaacaaagacaggcgatgagccttttaacgctattcaattatacaagtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagcaaacttccttttgttagctaacaaataatagttagcgttagctaacatttatgtaaagtcatcgcccattcttataaacaaagacaggcgatgagccttttaacgctattcaattatacaagtta Predict ORF larger than 30AA ================================================ aagcaaacttccttttgttagctaacaaataatagttagcgttagctaacatttatgtaaagtcatcgcccattcttataaacaaagacaggcgatgagccttttaacgctattcaattatacaagtta 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================================================ aagcaaacttccttttgttagctaacaaataatagttagcgttagctaacatttatgtaaagtcatcgcccattcttataaacaaagacaggcgatgagccttttaacgctattcaattatacaagtta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -7.6 Tail_Score: -3.70444 Start: 35 End: 50 Full_Region: tgactttacataaat gttagc taac gctaac tattatttgttagct ..................................gttagctaacgctaac............................................................................... Find igs database================================================ Query_seq: TDE2626:TDE2627|TDE2626:TDE2627:ABC transporter, ATP-binding/permease protein:transcriptional regulator, TetR family:<-<-:2668493..2668621 129 aagcaaacttccttttgttagctaacaaataatagttagcgttagctaacatttatgtaaagtcatcgcccattcttataaacaaagacaggcgatgagccttttaacgctattcaattatacaagtta Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: NC_002967_TDE2626_TDE2627|ABC transporter, ATP-binding/permease protein:transcriptional regulator, TetR family|NEGATIVE:NEGATIVE|[2668493,2668621]|129 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 aagcaaacttccttttgttagctaacaaataatagttagcgttagctaacatttatgtaaagtcatcgcccattcttataaacaaagacaggcgatgagccttttaacgctattcaattatacaagtta aagcaaacttccttttgttagctaacaaataatagttagcgttagctaacatttatgtaaagtcatcgcccattcttataaacaaagacaggcgatgagccttttaacgctattcaattatacaagtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCAAACUUCCUUUUGUUAGCUAACAAAUAAUAGUUAGCGUUAGCUAACAUUUAUGUAAAGUCAUCGCCCAUUCUUAUAAACAAAGACAGGCGAUGAGCCUUUUAACGCUAUUCAAUUAUACAAGUUA .(((...........(((((((((((..............)))))))))))...........((((((((...((((.......))))..))))))))..........))).................. (-31.44) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACUUGUAUAAUUGAAUAGCGUUAAAAGGCUCAUCGCCUGUCUUUGUUUAUAAGAAUGGGCGAUGACUUUACAUAAAUGUUAGCUAACGCUAACUAUUAUUUGUUAGCUAACAAAAGGAAGUUUGCUU ..................((((....((((.((((((((((((((.......))).))))))))))))))).......((((((((((((............))))))))))))..........)))). (-35.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 922 110 61 201 152 NC_002967:TDE2626|5end_ABC_transporter,_ATP-binding/permease_protein_2668402..2668632_NEGATIVE 265 110 62 170 132 NC_002967:TDE1292|5end_TldD/PmbA_family_protein_1330621..1330851_NEGATIVE 261 99 57 184 140 NC_002967:TDE1658|5end_basic_membrane_protein,_putative_1708731..1708961_NEGATIVE 258 109 63 50 9 NC_002967:TDE0122|5end_dihydrouridine_synthase,_putative_141539..141769_NEGATIVE 253 110 61 69 34 NC_002967:TDE2736|5end_hypothetical_protein_2791812..2792042_NEGATIVE 250 109 66 179 140 NC_002967:TDE1165|5end_hypothetical_protein_1198390..1198620_NEGATIVE 249 116 78 90 36 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 249 101 61 144 100 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 245 74 38 229 196 NC_002967:TDE0554|5end_hypothetical_protein_590968..591198_NEGATIVE 244 74 36 75 33 NC_002967:TDE1487|5end_conserved_hypothetical_protein_TIGR01033_1530705..1530935_POSITIVE 242 74 34 124 78 NC_002967:TDE2029|5end_hydrolase,_TatD_family_2058002..2058232_NEGATIVE 239 114 89 214 186 NC_002967:TDE0865|5end_hypothetical_protein_887127..887357_POSITIVE 235 100 59 229 180 NC_002967:TDE2062|5end_hypothetical_protein_2088344..2088574_NEGATIVE 228 102 66 132 96 NC_002967:TDE1155|5end_hypothetical_protein_1191455..1191685_NEGATIVE 224 97 51 155 108 NC_002967:TDE2059|5end_hypothetical_protein_2086509..2086739_NEGATIVE 224 110 61 133 85 NC_002967:TDE1080|5end_dimethyladenosine_transferase_1111738..1111968_POSITIVE 221 105 62 76 37 NC_002967:TDE2660|5end_hypothetical_protein_2697517..2697747_NEGATIVE 221 106 61 71 17 NC_002967:TDE2065|5end_FeoA_family_protein_2091779..2092009_NEGATIVE 220 104 62 224 180 NC_002967:TDE2479|5end_hypothetical_protein_2503290..2503520_NEGATIVE 220 116 91 77 51 NC_002967:TDE0991|5end_ribosomal_protein_L28_1018065..1018295_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 274 117 71 65 4 NC_002967:TDE2089|3end_signal_recognition_particle_protein_2116232..2116382_NEGATIVE 261 99 57 84 40 NC_002967:TDE1659|3end_alanyl-tRNA_synthetase_1708831..1708981_NEGATIVE 258 110 63 45 5 NC_002967:TDE0123|3end_hypothetical_protein_141543..141693_NEGATIVE 256 106 65 82 40 NC_002967:TDE0362|3end_bacterial_Ig-like_domain_protein_407501..407651_NEGATIVE 249 46 1 85 47 NC_002967:TDE1803|3end_hypothetical_protein_1838395..1838545_NEGATIVE 249 101 61 117 73 NC_002967:TDE0572|3end_hypothetical_protein_604734..604884_POSITIVE 239 80 49 148 118 NC_002967:TDE1293|3end_TldD/PmbA_family_protein_1330621..1330771_NEGATIVE 236 77 36 131 91 NC_002967:TDE1245|3end_hypothetical_protein_1277905..1278055_NEGATIVE 235 100 59 143 94 NC_002967:TDE2063|3end_ferrous_iron_transport_protein_B_2088430..2088580_NEGATIVE 228 78 36 119 64 NC_002967:TDE0598|3end_3-oxoacyl-(acyl-carrier-protein)_reductase_637358..637508_NEGATIVE 224 110 61 120 72 NC_002967:TDE1079|3end_DNA-binding_protein/PTS_system,_IIA_component_1111805..1111955_POSITIVE 221 105 62 69 30 NC_002967:TDE2661|3end_hypothetical_protein_2697524..2697674_NEGATIVE 220 104 62 148 104 NC_002967:TDE2480|3end_heat_shock_protein_90_2503366..2503516_NEGATIVE 219 77 32 147 107 NC_002967:TDE1982|3end_hypothetical_protein_1992511..1992661_NEGATIVE 218 110 61 118 60 NC_002967:TDE1707|3end_hypothetical_protein_1762775..1762925_NEGATIVE 214 102 61 68 16 NC_002967:TDE2234|3end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2272310..2272460_NEGATIVE 214 80 31 148 103 NC_002967:TDE1123|3end_sigma_factor_regulatory_protein,_putative_1153737..1153887_NEGATIVE 213 99 65 47 1 NC_002967:TDE1863|3end_Holliday_junction_DNA_helicase_RuvA_1887974..1888124_NEGATIVE 212 72 34 139 103 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 212 104 66 56 27 NC_002967:TDE0773|3end_30S_ribosomal_protein_S3_810242..810392_POSITIVE