Origin IGS: agtatcataaaagtcagagaggttagcttggaaactagcctctttttccttttcaaaatggggattcttccttgaaaataatcagtaattgtgctaaaattaaaagaacattctaaaatattcggaatttaaagtaaggaaaaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtttttccttactttaaattccgaatattttagaatgttcttttaattttagcacaattactgattattttcaaggaagaatccccattttgaaaaggaaaaagaggctagtttccaagctaacctctctgacttttatgatact Mask Tandem Repeat Region ================================================ agtatcataaaagtcagagaggttagcttggaaactagcctctttttccttttcaaaatggggattcttccttgaaaataatcagtaattgtgctaaaattaaaagaacattctaaaatattcggaatttaaagtaaggaaaaac Find is-nt database================================================ Query_seq: SMT_1062:SMT_1063|SMT_1062:SMT_1063:hypothetical protein:preprotein translocase SecA subunit:->->:1000709..1000853 145 agtatcataaaagtcagagaggttagcttggaaactagcctctttttccttttcaaaatggggattcttccttgaaaataatcagtaattgtgctaaaattaaaagaacattctaaaatattcggaatttaaagtaaggaaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1062:SMT_1063|SMT_1062:SMT_1063:hypothetical protein:preprotein translocase SecA subunit:->->:1000709..1000853 145 agtatcataaaagtcagagaggttagcttggaaactagcctctttttccttttcaaaatggggattcttccttgaaaataatcagtaattgtgctaaaattaaaagaacattctaaaatattcggaatttaaagtaaggaaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1062:SMT_1063|SMT_1062:SMT_1063:hypothetical protein:preprotein translocase SecA subunit:->->:1000709..1000853 145 agtatcataaaagtcagagaggttagcttggaaactagcctctttttccttttcaaaatggggattcttccttgaaaataatcagtaattgtgctaaaattaaaagaacattctaaaatattcggaatttaaagtaaggaaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtatcataaaagtcagagaggttagcttggaaactagcctctttttccttttcaaaatggggattcttccttgaaaataatcagtaattgtgctaaaattaaaagaacattctaaaatattcggaatttaaagtaaggaaaaac Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: - Start: 3 End: 128 .. I M F T L S T L K S V L R K K R K L I P I R G Q F Y D T I T S F N F S C E L I N P M ................. agtatcataaaagtcagagaggttagcttggaaactagcctctttttccttttcaaaatggggattcttccttgaaaataatcagtaattgtgctaaaattaaaagaacattctaaaatattcggaatttaaagtaaggaaaaac 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: 88 Start: 71 End: 100 ......................................................................CTTGAAAATAATCAGTAATTGTGCTAAAAT............................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtatcataaaagtcagagaggttagcttggaaactagcctctttttccttttcaaaatggggattcttccttgaaaataatcagtaattgtgctaaaattaaaagaacattctaaaatattcggaatttaaagtaaggaaaaac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1062:SMT_1063|SMT_1062:SMT_1063:hypothetical protein:preprotein translocase SecA subunit:->->:1000709..1000853 145 agtatcataaaagtcagagaggttagcttggaaactagcctctttttccttttcaaaatggggattcttccttgaaaataatcagtaattgtgctaaaattaaaagaacattctaaaatattcggaatttaaagtaaggaaaaac Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: smit_SMT_1062_SMT_1063|hypothetical protein:preprotein translocase SecA subunit|POSITIVE:POSITIVE|[1000709,1000853]|145 HSP 1 e-value: 5.0E-77 bit: 287.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 145 agtatcataaaagtcagagaggttagcttggaaactagcctctttttccttttcaaaatggggattcttccttgaaaataatcagtaattgtgctaaaattaaaagaacattctaaaatattcggaatttaaagtaaggaaaaac agtatcataaaagtcagagaggttagcttggaaactagcctctttttccttttcaaaatggggattcttccttgaaaataatcagtaattgtgctaaaattaaaagaacattctaaaatattcggaatttaaagtaaggaaaaac Inter-species Hit: Count: 3 Min: 1 Max: 145 Len: 145 Subject: NC_008533_SPD_1512_SPD_1514|preprotein translocase, SecA subunit:ABC transporter, ATP-binding protein|NEGATIVE:NEGATIVE|[1536436,1536880]|445 HSP 1 e-value: 3.0E-72 bit: 272.0 Len: 145 Query Start:1 Query End:145 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 145 agtatcataaaagtcagagaggttagcttggaaactagcctctttttccttttcaaaatggggattcttccttgaaaataatcagtaattgtgctaaaattaaaagaacattctaaaatattcggaatttaaagtaaggaaaaac agtatcataaaagtcagagaggttagcttggaaactaacctctttttccttttcaaaatggggattcttccttgaaaataatcagtaattgtgctaaaattaaaggaacattctaaaatattcggaatttaaagtaaggaaaaac Subject: NC_003098_spr1544_spr1545|translocase:hypothetical protein|NEGATIVE:NEGATIVE|[1528905,1529049]|145 HSP 1 e-value: 3.0E-72 bit: 272.0 Len: 145 Query Start:1 Query End:145 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 145 agtatcataaaagtcagagaggttagcttggaaactagcctctttttccttttcaaaatggggattcttccttgaaaataatcagtaattgtgctaaaattaaaagaacattctaaaatattcggaatttaaagtaaggaaaaac agtatcataaaagtcagagaggttagcttggaaactaacctctttttccttttcaaaatggggattcttccttgaaaataatcagtaattgtgctaaaattaaaggaacattctaaaatattcggaatttaaagtaaggaaaaac Subject: NC_003028_SP_1702_SP_1703|translocase:hypothetical protein|NEGATIVE:NEGATIVE|[1609146,1609290]|145 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 141 Query Start:5 Query End:145 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 141 ....tcataaaagtcagagaggttagcttggaaactagcctctttttccttttcaaaatggggattcttccttgaaaataatcagtaattgtgctaaaattaaaagaacattctaaaatattcggaatttaaagtaaggaaaaac ....tcataaaagtcggagaggttagcttgaaaactaacctctttttccttttcaaaatggggattcttccttgaaaataatcagtaattgtgctaaaattaaaggaacattctaaaatattcggaatttaaagtaaggaaaaac Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAUCAUAAAAGUCAGAGAGGUUAGCUUGGAAACUAGCCUCUUUUUCCUUUUCAAAAUGGGGAUUCUUCCUUGAAAAUAAUCAGUAAUUGUGCUAAAAUUAAAAGAACAUUCUAAAAUAUUCGGAAUUUAAAGUAAGGAAAAAC ...............(((((((((((........))))))))))).(((((........)))))...(((((((.........((((....)))).(((((....(((.(((....))).)))..)))))....))))))).... (-25.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUUCCUUACUUUAAAUUCCGAAUAUUUUAGAAUGUUCUUUUAAUUUUAGCACAAUUACUGAUUAUUUUCAAGGAAGAAUCCCCAUUUUGAAAAGGAAAAAGAGGCUAGUUUCCAAGCUAACCUCUCUGACUUUUAUGAUACU ((((((((((............(((((((....)))))))........((((........))))........))))))))))....(((...(((((...(.(((((.(((((....))))).))))).)..)))))..)))... (-26.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 40 1 157 117 smit:SMT_1602|5end_hypothetical_protein_1592385..1592615_POSITIVE 302 40 1 169 129 smit:SMT_1488|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1467157..1467387_POSITIVE 298 40 10 205 176 smit:SMT_1138|5end_hypothetical_protein_1079547..1079777_NEGATIVE 298 40 10 182 153 smit:SMT_833|5end_hypothetical_protein_predicted_by_Glimmer/Critica_775362..775592_NEGATIVE 298 40 10 166 137 smit:SMT_130|5end_capsular_polysaccharide_biosynthesis_protein_80995..81225_POSITIVE 275 40 1 144 104 smit:SMT_1200|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1163235..1163465_NEGATIVE 271 55 16 47 5 smit:SMT_1612|5end_K06024_segregation_and_condensation_protein_B_1600052..1600282_POSITIVE 260 53 13 106 60 smit:SMT_108|5end_hypothetical_protein_53488..53718_POSITIVE 259 74 32 66 27 smit:SMT_1644|5end_3-isopropylmalate_dehydrogenase_1630704..1630934_POSITIVE 257 58 14 164 110 smit:SMT_236|5end_ribosomal_small_subunit_pseudouridine_synthase_A_174625..174855_POSITIVE 253 95 61 56 23 smit:SMT_1447|5end_hypothetical_protein_1430476..1430706_NEGATIVE 252 50 2 51 9 smit:SMT_1262|5end_ribosomal_protein_L11_methyltransferase_1227152..1227382_POSITIVE 251 40 1 154 114 smit:SMT_1782|5end_hypothetical_protein_1759520..1759750_POSITIVE 251 40 1 211 171 smit:SMT_1379|5end_thymidylate_kinase_1357438..1357668_NEGATIVE 251 96 58 119 90 smit:SMT_347|5end_hypothetical_protein_286210..286440_NEGATIVE 247 40 10 156 127 smit:SMT_1963|5end_ribonuclease_BN,_putative_1896462..1896692_NEGATIVE 247 40 10 191 162 smit:SMT_1810|5end_hypothetical_protein_1785219..1785449_POSITIVE 247 54 15 83 43 smit:SMT_771|5end_spermidine/putrescine_transport_system_permease_protein_PotB_682183..682413_NEGATIVE 247 40 10 143 114 smit:SMT_483|5end_transcriptional_activator_TipA,_putative_418827..419057_POSITIVE 247 40 10 225 196 smit:SMT_443|5end_hydroxyethylthiazole_kinase_382555..382785_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 290 43 1 130 87 smit:SMT_1084|3end_hypothetical_protein_1021326..1021476_NEGATIVE 277 57 15 100 53 smit:SMT_459|3end_hypothetical_protein_397690..397840_POSITIVE 266 60 11 102 51 smit:SMT_297|3end_ABC_transporter_substrate-binding_protein_-_oligopeptide_transport_240606..240756_POSITIVE 259 74 32 54 15 smit:SMT_1643|3end_2-isopropylmalate_synthase_1630772..1630922_POSITIVE 247 54 15 123 83 smit:SMT_772|3end_spermidine/putrescine_ABC_transporter,_ATP-binding_protein_682143..682293_NEGATIVE 242 60 12 118 63 smit:SMT_1066|3end_holo-(acyl_carrier_protein)_synthase_1005859..1006009_POSITIVE 239 44 1 48 12 smit:SMT_750|3end_3-phosphoshikimate_1-carboxyvinyltransferase_653964..654114_NEGATIVE 236 73 34 47 3 smit:SMT_1387|3end_hypothetical_protein_1365237..1365387_POSITIVE 236 45 9 75 38 smit:SMT_1062|3end_hypothetical_protein_1000648..1000798_POSITIVE 236 58 13 150 116 smit:SMT_269|3end_phospho-N-acetylmuramoyl-pentapeptide-transferas_e_208785..208935_POSITIVE 228 40 12 27 1 smit:SMT_834|3end_hypothetical_protein_775517..775667_NEGATIVE 228 48 2 88 42 smit:SMT_317|3end_K03625_N_utilization_substance_protein_B_257475..257625_NEGATIVE 226 60 16 98 50 smit:SMT_1534|3end_signal_peptidase_I_1517912..1518062_POSITIVE 225 72 39 47 16 smit:SMT_978|3end_hypothetical_protein_925765..925915_NEGATIVE 223 49 1 96 49 smit:SMT_1531|3end_hypothetical_protein_1515449..1515599_NEGATIVE 223 38 10 76 37 smit:SMT_964|3end_cadmium_resistance_transporter,_putative_909891..910041_NEGATIVE 222 50 1 100 52 smit:SMT_1380|3end_pyrroline-5-carboxylate_reductase_1357667..1357817_NEGATIVE 220 40 14 26 1 smit:SMT_698|3end_uracil_permease_609769..609919_POSITIVE 220 45 1 87 47 smit:SMT_90|3end_DNA_polymerase_III_beta_subunit_22593..22743_POSITIVE 219 42 2 111 67 smit:SMT_1169|3end_phosphorylase,_Pnp/UDP_family_1116586..1116736_NEGATIVE