Origin IGS: atacagattaaagctcggttgccttatttctaggctactgagttttttatcttttcaataatcaaaaaagcccagacgacattgtctgagcgttcttctatattgtcgtttaaccaagttgagtttagcttttcagg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cctgaaaagctaaactcaacttggttaaacgacaatatagaagaacgctcagacaatgtcgtctgggcttttttgattattgaaaagataaaaaactcagtagcctagaaataaggcaaccgagctttaatctgtat Mask Tandem Repeat Region ================================================ atacagattaaagctcggttgccttatttctaggctactgagttttttatcttttcaataatcaaaaaagcccagacgacattgtctgagcgttcttctatattgtcgtttaaccaagttgagtttagcttttcagg Find is-nt database================================================ Query_seq: SMT_1020:SMT_1021|SMT_1020:SMT_1021:transcriptional regulator, TetR family:K05846 osmoprotectant transport system permease protein:-><-:956432..956568 137 atacagattaaagctcggttgccttatttctaggctactgagttttttatcttttcaataatcaaaaaagcccagacgacattgtctgagcgttcttctatattgtcgtttaaccaagttgagtttagcttttcagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1020:SMT_1021|SMT_1020:SMT_1021:transcriptional regulator, TetR family:K05846 osmoprotectant transport system permease protein:-><-:956432..956568 137 atacagattaaagctcggttgccttatttctaggctactgagttttttatcttttcaataatcaaaaaagcccagacgacattgtctgagcgttcttctatattgtcgtttaaccaagttgagtttagcttttcagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1020:SMT_1021|SMT_1020:SMT_1021:transcriptional regulator, TetR family:K05846 osmoprotectant transport system permease protein:-><-:956432..956568 137 atacagattaaagctcggttgccttatttctaggctactgagttttttatcttttcaataatcaaaaaagcccagacgacattgtctgagcgttcttctatattgtcgtttaaccaagttgagtttagcttttcagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atacagattaaagctcggttgccttatttctaggctactgagttttttatcttttcaataatcaaaaaagcccagacgacattgtctgagcgttcttctatattgtcgtttaaccaagttgagtttagcttttcagg Predict ORF larger than 30AA ================================================ atacagattaaagctcggttgccttatttctaggctactgagttttttatcttttcaataatcaaaaaagcccagacgacattgtctgagcgttcttctatattgtcgtttaaccaagttgagtttagcttttcagg 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================================================ atacagattaaagctcggttgccttatttctaggctactgagttttttatcttttcaataatcaaaaaagcccagacgacattgtctgagcgttcttctatattgtcgtttaaccaagttgagtttagcttttcagg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 90 HP_score: -8.0 Tail_Score: -5.37865 Start: 70 End: 91 Full_Region: acaatatagaagaac gctcagac aatgtc gtctgggc ttttttgattattga .....................................................................gctcagacaatgtcgtctgggc.............................................. Find igs database================================================ Query_seq: SMT_1020:SMT_1021|SMT_1020:SMT_1021:transcriptional regulator, TetR family:K05846 osmoprotectant transport system permease protein:-><-:956432..956568 137 atacagattaaagctcggttgccttatttctaggctactgagttttttatcttttcaataatcaaaaaagcccagacgacattgtctgagcgttcttctatattgtcgtttaaccaagttgagtttagcttttcagg Intra-Species Hit: Count: 1 Min: 1 Max: 137 Len: 137 Subject: smit_SMT_1020_SMT_1021|transcriptional regulator, TetR family:K05846 osmoprotectant transport system permease protein|POSITIVE:NEGATIVE|[956432,956568]|137 HSP 1 e-value: 3.0E-72 bit: 272.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 atacagattaaagctcggttgccttatttctaggctactgagttttttatcttttcaataatcaaaaaagcccagacgacattgtctgagcgttcttctatattgtcgtttaaccaagttgagtttagcttttcagg atacagattaaagctcggttgccttatttctaggctactgagttttttatcttttcaataatcaaaaaagcccagacgacattgtctgagcgttcttctatattgtcgtttaaccaagttgagtttagcttttcagg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUACAGAUUAAAGCUCGGUUGCCUUAUUUCUAGGCUACUGAGUUUUUUAUCUUUUCAAUAAUCAAAAAAGCCCAGACGACAUUGUCUGAGCGUUCUUCUAUAUUGUCGUUUAACCAAGUUGAGUUUAGCUUUUCAGG ....((((.((((((((((.((((.......)))).))))))))))..)))).............((((((..((((((((.(((..(((....)))..))).))))))))((((.....).)))..)))))).... (-33.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUGAAAAGCUAAACUCAACUUGGUUAAACGACAAUAUAGAAGAACGCUCAGACAAUGUCGUCUGGGCUUUUUUGAUUAUUGAAAAGAUAAAAAACUCAGUAGCCUAGAAAUAAGGCAACCGAGCUUUAAUCUGUAU .......((((((.......))))))......(((((..((((((.((((((((......))))))))))))))...)))))...((((.(((..(((.((.(((((....).)))).)).))).))).)))).... (-34.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 130 84 104 44 smit:SMT_1860|5end_hypothetical_protein_1823609..1823839_NEGATIVE 292 100 52 197 145 smit:SMT_991|5end_hypothetical_protein_934425..934655_NEGATIVE 285 54 11 95 45 smit:SMT_1538|5end_two-component_response_regulator_YvqC_1523301..1523531_NEGATIVE 270 109 61 91 29 smit:SMT_912|5end_fructokinase_863620..863850_NEGATIVE 261 116 73 87 34 smit:SMT_2016|5end_tyrosine_recombinase_1933425..1933655_NEGATIVE 255 99 51 74 26 smit:SMT_1496|5end_conserved_hypothetical_protein_TIGR00150_1480999..1481229_POSITIVE 253 44 3 173 123 smit:SMT_772|5end_spermidine/putrescine_ABC_transporter,_ATP-binding_protein_683300..683530_NEGATIVE 251 109 69 158 107 smit:SMT_896|5end_hypothetical_protein_844003..844233_NEGATIVE 243 130 82 224 169 smit:SMT_732|5end_K07467_phage_replication_initiation_protein_639409..639639_NEGATIVE 243 115 77 98 68 smit:SMT_323|5end_amino_acid_transport_ATP-binding_protein_261872..262102_NEGATIVE 242 129 84 177 125 smit:SMT_1645|5end_hypothetical_protein_1631738..1631968_POSITIVE 242 99 70 63 18 smit:SMT_411|5end_thymidylate_synthase_355496..355726_POSITIVE 241 107 72 190 146 smit:SMT_1393|5end_hypothetical_protein_1369106..1369336_POSITIVE 241 116 72 98 55 smit:SMT_1007|5end_radical_SAM_domain_protein_947035..947265_POSITIVE 240 46 12 190 149 smit:SMT_1647|5end_3-isopropylmalate_dehydratase_small_subunit_1633403..1633633_POSITIVE 239 99 69 180 140 smit:SMT_1768|5end_hydrolase,_alpha/beta_fold_family_1744959..1745189_NEGATIVE 239 121 81 175 137 smit:SMT_1692|5end_hypothetical_protein_1675169..1675399_POSITIVE 239 109 64 215 176 smit:SMT_534|5end_hypothetical_protein_predicted_by_Glimmer/Critica_453571..453801_POSITIVE 239 109 64 215 176 smit:SMT_531|5end_hypothetical_protein_predicted_by_Glimmer/Critica_452672..452902_POSITIVE 239 109 64 215 176 smit:SMT_527|5end_hypothetical_protein_predicted_by_Glimmer/Critica_451502..451732_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 59 11 95 46 smit:SMT_1020|3end_transcriptional_regulator,_TetR_family_956371..956521_POSITIVE 292 100 52 93 41 smit:SMT_992|3end_hypothetical_protein_934529..934679_NEGATIVE 285 54 11 81 31 smit:SMT_1539|3end_sensor_histidine_kinase,_putative_1523315..1523465_NEGATIVE 254 119 71 129 76 smit:SMT_1041|3end_K07586_hypothetical_protein_984164..984314_POSITIVE 251 109 69 146 95 smit:SMT_897|3end_serine_O-acetyltransferase_844015..844165_NEGATIVE 251 55 11 51 5 smit:SMT_625|3end_50S_ribosomal_protein_L27_530400..530550_POSITIVE 243 115 77 58 28 smit:SMT_324|3end_K02029_polar_amino_acid_transport_system_permease_protein_261912..262062_NEGATIVE 241 116 72 105 62 smit:SMT_1006|3end_6-pyruvoyl_tetrahydrobiopterin_synthase,_putative_947122..947272_POSITIVE 239 109 64 101 62 smit:SMT_533|3end_RNA_binding_protein_453537..453687_POSITIVE 239 109 64 101 62 smit:SMT_530|3end_RNA_binding_protein_452638..452788_POSITIVE 239 109 64 101 62 smit:SMT_526|3end_RNA_binding_protein_451468..451618_POSITIVE 239 109 64 101 62 smit:SMT_510|3end_hypothetical_protein_439357..439507_POSITIVE 232 56 12 70 32 smit:SMT_2033|3end_hydrolase,_haloacid_dehalogenase-like_family_1946739..1946889_POSITIVE 232 130 86 124 67 smit:SMT_1305|3end_glycerol_kinase_1269805..1269955_POSITIVE 231 34 4 85 54 smit:SMT_2044|3end_transcriptional_activator_TipA,_putative_1955274..1955424_NEGATIVE 231 34 4 85 54 smit:SMT_2026|3end_K03466_DNA_segregation_ATPase_FtsK/SpoIIIE,_S-DNA-T_family_1941905..1942055_NEGATIVE 231 34 4 85 54 smit:SMT_2016|3end_tyrosine_recombinase_1933021..1933171_NEGATIVE 231 34 4 85 54 smit:SMT_2006|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1926803..1926953_POSITIVE 231 34 4 95 64 smit:SMT_2001|3end_membrane_protease_protein_family_1923889..1924039_POSITIVE 231 34 4 95 64 smit:SMT_1985|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1914407..1914557_NEGATIVE