Origin IGS: ttaattaannnnnggtttagatgttgttttcatatagtcttcctagaaatgagataaccagggcagatagggtagtgatgatgctatttacccagggattagggtggcaaaaaaggccactgtaatgatagagaaccmaggctcytagactaaaaaccagatagattttgg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccaaaatctatctggtttttagtctargagcctkggttctctatcattacagtggccttttttgccaccctaatccctgggtaaatagcatcatcactaccctatctgccctggttatctcatttctaggaagactatatgaaaacaacatctaaaccnnnnnttaattaa Mask Tandem Repeat Region ================================================ ttaattaannnnnggtttagatgttgttttcatatagtcttcctagaaatgagataaccagggcagatagggtagtgatgatgctatttacccagggattagggtggcaaaaaaggccactgtaatgatagagaaccmaggctcytagactaaaaaccagatagattttgg Find is-nt database================================================ Query_seq: SMT_1791:SMT_1792|SMT_1791:SMT_1792:hypothetical protein:K03307 solute:Na+ symporter, SSS family:-><-:1766494..1766664 171 ttaattaannnnnggtttagatgttgttttcatatagtcttcctagaaatgagataaccagggcagatagggtagtgatgatgctatttacccagggattagggtggcaaaaaaggccactgtaatgatagagaaccmaggctcytagactaaaaaccagatagattttgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1791:SMT_1792|SMT_1791:SMT_1792:hypothetical protein:K03307 solute:Na+ symporter, SSS family:-><-:1766494..1766664 171 ttaattaannnnnggtttagatgttgttttcatatagtcttcctagaaatgagataaccagggcagatagggtagtgatgatgctatttacccagggattagggtggcaaaaaaggccactgtaatgatagagaaccmaggctcytagactaaaaaccagatagattttgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1791:SMT_1792|SMT_1791:SMT_1792:hypothetical protein:K03307 solute:Na+ symporter, SSS family:-><-:1766494..1766664 171 ttaattaannnnnggtttagatgttgttttcatatagtcttcctagaaatgagataaccagggcagatagggtagtgatgatgctatttacccagggattagggtggcaaaaaaggccactgtaatgatagagaaccmaggctcytagactaaaaaccagatagattttgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaattaannnnnggtttagatgttgttttcatatagtcttcctagaaatgagataaccagggcagatagggtagtgatgatgctatttacccagggattagggtggcaaaaaaggccactgtaatgatagagaaccmaggctcytagactaaaaaccagatagattttgg Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 21 End: 122 .................... M L F S Y S L P R N E I T R A D R V V M M L F T Q G L G W Q K R P L ................................................. Protein_Len: 49 Strand: - Start: 20 End: 166 ................... I N N E Y L R G L F S I V L A S L T T I I S N V W P N P H C F L G S Y H Y L V X A X L S F V L Y M ..... ttaattaannnnnggtttagatgttgttttcatatagtcttcctagaaatgagataaccagggcagatagggtagtgatgatgctatttacccagggattagggtggcaaaaaaggccactgtaatgatagagaaccmaggctcytagactaaaaaccagatagattttgg 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================================================ ttaattaannnnnggtttagatgttgttttcatatagtcttcctagaaatgagataaccagggcagatagggtagtgatgatgctatttacccagggattagggtggcaaaaaaggccactgtaatgatagagaaccmaggctcytagactaaaaaccagatagattttgg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1791:SMT_1792|SMT_1791:SMT_1792:hypothetical protein:K03307 solute:Na+ symporter, SSS family:-><-:1766494..1766664 171 ttaattaannnnnggtttagatgttgttttcatatagtcttcctagaaatgagataaccagggcagatagggtagtgatgatgctatttacccagggattagggtggcaaaaaaggccactgtaatgatagagaaccmaggctcytagactaaaaaccagatagattttgg Intra-Species Hit: Count: 1 Min: 16 Max: 171 Len: 156 Subject: smit_SMT_1791_SMT_1792|hypothetical protein:K03307 solute:Na+ symporter, SSS family|POSITIVE:NEGATIVE|[1766494,1766664]|171 HSP 1 e-value: 7.0E-82 bit: 304.0 Len: 156 Query Start:16 Query End:171 Subject Strand: POSITIVE Subject Start: 16 Subject End: 171 ...............tttagatgttgttttcatatagtcttcctagaaatgagataaccagggcagatagggtagtgatgatgctatttacccagggattagggtggcaaaaaaggccactgtaatgatagagaaccmaggctcytagactaaaaaccagatagattttgg ...............tttagatgttgttttcatatagtcttcctagaaatgagataaccagggcagatagggtagtgatgatgctatttacccagggattagggtggcaaaaaaggccactgtaatgatagagaaccmaggctcytagactaaaaaccagatagattttgg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAGAUGUUGUUUUCAUAUAGUCUUCCUAGAAAUGAGAUAACCAGGGCAGAUAGGGUAGUGAUGAUGCUAUUUACCCAGGGAUUAGGGUGGCAAAAAAGGCCACUGUAAUGAUAGAGAACCMAGGCUCYUAGACUAAAAACCAGAUAGAUUUUGG ...................((((((.(((.(...........((.(((.((((((.((.......)).)))))).))).)).((((.((((((.......)))))).))))..........).))).....))))))....(((((.....))))) (-36.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCAAAAUCUAUCUGGUUUUUAGUCUARGAGCCUKGGUUCUCUAUCAUUACAGUGGCCUUUUUUGCCACCCUAAUCCCUGGGUAAAUAGCAUCAUCACUACCCUAUCUGCCCUGGUUAUCUCAUUUCUAGGAAGACUAUAUGAAAACAACAUCUAAA ..............(((((((((((..((((....)))).(((..((((..(((((.......)))))..)))).((.(((((.((((.............)))).))))).))............)))..)))))....)))))).......... (-30.32) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 868 70 21 143 94 smit:SMT_1174|5end_acylneuraminate_cytidylyltransferase_1126321..1126551_NEGATIVE 318 64 28 180 146 smit:SMT_769|5end_spermidine/putrescine-binding_periplasmic_protein_680589..680819_NEGATIVE 312 90 41 217 166 smit:SMT_484|5end_hypothetical_protein_420180..420410_NEGATIVE 291 95 51 228 169 smit:SMT_1519|5end_DNA-binding_response_regulator_VncR_1499662..1499892_NEGATIVE 283 90 42 175 130 smit:SMT_950|5end_UDP-glucose_4-epimerase_898696..898926_NEGATIVE 283 80 32 158 108 smit:SMT_788|5end_hypothetical_protein_700319..700549_NEGATIVE 281 50 1 126 77 smit:SMT_1209|5end_choline_binding_protein_PcpA_1170972..1171202_NEGATIVE 277 85 42 56 5 smit:SMT_866|5end_50S_ribosomal_protein_L11_816234..816464_NEGATIVE 275 84 43 188 143 smit:SMT_1900|5end_K03710_GntR_family_transcriptional_regulator_1850208..1850438_POSITIVE 275 76 40 222 185 smit:SMT_853|5end_ATP-dependent_endopeptidase_clp_ATP-binding_subunit_ClpX_799285..799515_NEGATIVE 273 70 21 79 29 smit:SMT_1617|5end_K02015_iron_complex_transport_system_permease_protein_1604500..1604730_NEGATIVE 272 78 31 185 133 smit:SMT_1790|5end_hypothetical_protein_1765644..1765874_POSITIVE 270 83 46 107 68 smit:SMT_76|5end_DNA_repair_and_genetic_recombination_protein_2677..2907_POSITIVE 267 88 46 40 1 smit:SMT_1978|5end_hypothetical_protein_1909566..1909796_NEGATIVE 267 118 76 59 5 smit:SMT_1742|5end_sodium-dependent_phosphate_transporter_1723553..1723783_POSITIVE 266 129 86 87 42 smit:SMT_229|5end_mechanosensitive_ion_channel_165623..165853_NEGATIVE 263 57 21 131 98 smit:SMT_1922|5end_exonuclease_RexA_1865998..1866228_NEGATIVE 261 69 21 88 41 smit:SMT_2107|5end_tyrosine_recombinase_1998537..1998767_NEGATIVE 260 81 43 188 148 smit:SMT_1065|5end_phospho-2-dehydro-3-deoxyheptonate_aldolase_1004341..1004571_POSITIVE 258 109 64 119 71 smit:SMT_1571|5end_CAAX_amino_terminal_protease_family_protein_1563780..1564010_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 804 60 11 149 100 smit:SMT_1175|3end_K03307_solute:Na+_symporter,_SSS_family_1126305..1126455_NEGATIVE 324 119 77 47 4 smit:SMT_964|3end_cadmium_resistance_transporter,_putative_909891..910041_NEGATIVE 295 108 68 150 101 smit:SMT_1981|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912868..1913018_POSITIVE 291 95 51 85 26 smit:SMT_1520|3end_K02004_1499805..1499955_NEGATIVE 283 80 32 145 95 smit:SMT_789|3end_hypothetical_protein_700332..700482_NEGATIVE 281 50 1 139 90 smit:SMT_1210|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1170959..1171109_NEGATIVE 273 70 21 89 39 smit:SMT_1618|3end_K02015_iron_complex_transport_system_permease_protein_1604490..1604640_NEGATIVE 272 56 19 143 102 smit:SMT_580|3end_K04094_glucose_inhibited_division_protein_Gid_498034..498184_POSITIVE 270 83 46 104 65 smit:SMT_75|3end_hypothetical_protein_2754..2904_POSITIVE 262 85 47 77 33 smit:SMT_2035|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1947384..1947534_POSITIVE 261 79 41 151 117 smit:SMT_485|3end_hypothetical_protein_420229..420379_NEGATIVE 252 129 82 70 15 smit:SMT_1871|3end_modification_methylase,_HemK_family_1829803..1829953_NEGATIVE 248 70 21 120 66 smit:SMT_1326|3end_X-prolyl_dipeptidyl_peptidase_1303359..1303509_POSITIVE 246 90 45 54 9 smit:SMT_1626|3end_undecaprenyl-diphosphatase_1615183..1615333_NEGATIVE 244 89 43 96 44 smit:SMT_1826|3end_ATP_synthase_beta_chain_1797622..1797772_POSITIVE 243 50 5 89 47 smit:SMT_983|3end_GTP_pyrophosphokinase_929684..929834_NEGATIVE 242 67 24 69 26 smit:SMT_775|3end_alpha-acetolactate_decarboxylase_685241..685391_NEGATIVE 240 116 79 60 22 smit:SMT_1879|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1836567..1836717_NEGATIVE 239 89 47 61 12 smit:SMT_308|3end_trans-2-enoyl-ACP_reductase_II_250493..250643_POSITIVE 238 64 21 150 111 smit:SMT_1875|3end_hypothetical_protein_1833422..1833572_POSITIVE