Origin IGS: gaannnnnttaattaattaannnnntattaaaatcatgtagagcgcattaaccagctcttttcgacagatattaaaatcattcaaaatagagaggtttttagctattcg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgaatagctaaaaacctctctattttgaatgattttaatatctgtcgaaaagagctggttaatgcgctctacatgattttaatannnnnttaattaattaannnnnttc Mask Tandem Repeat Region ================================================ gaannnnnttaattaattaannnnntattaaaatcatgtagagcgcattaaccagctcttttcgacagatattaaaatcattcaaaatagagaggtttttagctattcg Find is-nt database================================================ Query_seq: SMT_1848:SMT_1849|SMT_1848:SMT_1849:K03458 nucleobase:cation symporter-2, NCS2 family:hypothetical protein:<-->:1813105..1813213 109 gaannnnnttaattaattaannnnntattaaaatcatgtagagcgcattaaccagctcttttcgacagatattaaaatcattcaaaatagagaggtttttagctattcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1848:SMT_1849|SMT_1848:SMT_1849:K03458 nucleobase:cation symporter-2, NCS2 family:hypothetical protein:<-->:1813105..1813213 109 gaannnnnttaattaattaannnnntattaaaatcatgtagagcgcattaaccagctcttttcgacagatattaaaatcattcaaaatagagaggtttttagctattcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1848:SMT_1849|SMT_1848:SMT_1849:K03458 nucleobase:cation symporter-2, NCS2 family:hypothetical protein:<-->:1813105..1813213 109 gaannnnnttaattaattaannnnntattaaaatcatgtagagcgcattaaccagctcttttcgacagatattaaaatcattcaaaatagagaggtttttagctattcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaannnnnttaattaattaannnnntattaaaatcatgtagagcgcattaaccagctcttttcgacagatattaaaatcattcaaaatagagaggtttttagctattcg Predict ORF larger than 30AA ================================================ gaannnnnttaattaattaannnnntattaaaatcatgtagagcgcattaaccagctcttttcgacagatattaaaatcattcaaaatagagaggtttttagctattcg 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================================================ gaannnnnttaattaattaannnnntattaaaatcatgtagagcgcattaaccagctcttttcgacagatattaaaatcattcaaaatagagaggtttttagctattcg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1848:SMT_1849|SMT_1848:SMT_1849:K03458 nucleobase:cation symporter-2, NCS2 family:hypothetical protein:<-->:1813105..1813213 109 gaannnnnttaattaattaannnnntattaaaatcatgtagagcgcattaaccagctcttttcgacagatattaaaatcattcaaaatagagaggtttttagctattcg Intra-Species Hit: Count: 1 Min: 9 Max: 109 Len: 101 Subject: smit_SMT_1848_SMT_1849|K03458 nucleobase:cation symporter-2, NCS2 family:hypothetical protein|NEGATIVE:POSITIVE|[1813105,1813213]|109 HSP 1 e-value: 6.0E-42 bit: 170.0 Len: 101 Query Start:9 Query End:109 Subject Strand: POSITIVE Subject Start: 9 Subject End: 109 ........ttaattaattaannnnntattaaaatcatgtagagcgcattaaccagctcttttcgacagatattaaaatcattcaaaatagagaggtttttagctattcg ........ttaattaattaannnnntattaaaatcatgtagagcgcattaaccagctcttttcgacagatattaaaatcattcaaaatagagaggtttttagctattcg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAUUAAUUAANNNNNUAUUAAAAUCAUGUAGAGCGCAUUAACCAGCUCUUUUCGACAGAUAUUAAAAUCAUUCAAAAUAGAGAGGUUUUUAGCUAUUCG .............................(...(((.....((((..(((((((.((..(((......)))..)).))).)))).))))....)))...). (-11.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAAUAGCUAAAAACCUCUCUAUUUUGAAUGAUUUUAAUAUCUGUCGAAAAGAGCUGGUUAAUGCGCUCUACAUGAUUUUAAUANNNNNUUAAUUAAUUAA .((...((....((((.((((.((((((..(((......)))..))))))))))..))))...))..))................................ (-15.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 795 70 21 169 120 smit:SMT_1848|5end_K03458_nucleobase:cation_symporter-2,_NCS2_family_1813014..1813244_NEGATIVE 275 90 43 107 59 smit:SMT_2016|5end_tyrosine_recombinase_1933425..1933655_NEGATIVE 273 89 44 178 133 smit:SMT_271|5end_autoinducer-2_production_protein_211736..211966_NEGATIVE 242 97 52 205 155 smit:SMT_1739|5end_hypothetical_protein_1721263..1721493_POSITIVE 236 60 32 202 172 smit:SMT_2002|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1924405..1924635_NEGATIVE 236 60 32 202 172 smit:SMT_1942|5end_zinc_metalloprotease_ZmpB,_truncated_1877882..1878112_POSITIVE 236 60 32 223 193 smit:SMT_1885|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1840057..1840287_NEGATIVE 233 67 24 96 47 smit:SMT_1785|5end_phenylalanyl-tRNA_synthetase_beta_chain_1763277..1763507_NEGATIVE 222 63 27 83 45 smit:SMT_1622|5end_K03499_trk_system_potassium_uptake_protein_TrkA_1608243..1608473_POSITIVE 217 73 32 135 91 smit:SMT_1473|5end_hypothetical_protein_1454320..1454550_POSITIVE 216 57 32 112 76 smit:SMT_476|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_414134..414364_NEGATIVE 213 63 44 27 7 smit:SMT_1132|5end_glutamate--cysteine_ligase,_putative,_truncated_1068108..1068338_NEGATIVE 212 76 32 71 22 smit:SMT_1382|5end_glutamate_5-kinase_1360744..1360974_NEGATIVE 207 55 26 228 196 smit:SMT_1685|5end_phenylalanyl-tRNA_synthetase_alpha_chain_1668845..1669075_NEGATIVE 205 57 25 56 14 smit:SMT_346|5end_K01992_ABC-2_type_transport_system_permease_protein_284720..284950_POSITIVE 203 66 23 154 111 smit:SMT_1881|5end_hypothetical_protein_1837351..1837581_POSITIVE 203 61 29 225 187 smit:SMT_261|5end_ImpB/MucB/SamB_family_protein_200160..200390_POSITIVE 203 66 23 154 111 smit:SMT_73|5end_peptidase,_M16_family_950..1180_NEGATIVE 199 98 62 50 19 smit:SMT_1920|5end_ABC_transporter,_ATP-binding_protein_1863125..1863355_NEGATIVE 199 77 33 210 158 smit:SMT_1662|5end_histidine_protein_kinase_1652357..1652587_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 273 89 44 83 38 smit:SMT_272|3end_hypothetical_protein_211831..211981_NEGATIVE 233 67 24 138 89 smit:SMT_1786|3end_phenylalanyl-tRNA_synthetase_beta_chain_1763235..1763385_NEGATIVE 222 64 36 150 124 smit:SMT_862|3end_hypothetical_protein_predicted_by_Glimmer/Critica_809191..809341_POSITIVE 212 69 24 146 89 smit:SMT_2112|3end_transcription-repair_coupling_factor_2000373..2000523_NEGATIVE 206 58 31 123 92 smit:SMT_2141|3end_hypothetical_protein_2018960..2019110_NEGATIVE 205 57 25 59 17 smit:SMT_345|3end_K01990_ABC-2_type_transport_system_ATP-binding_protein_284803..284953_POSITIVE 200 60 26 53 18 smit:SMT_1806|3end_aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase_1781644..1781794_POSITIVE 199 58 32 70 42 smit:SMT_1951|3end_ABC_transporter,_ATP-binding_protein_1885141..1885291_NEGATIVE 199 58 37 144 119 smit:SMT_870|3end_hypothetical_protein_817700..817850_NEGATIVE 199 57 30 149 128 smit:SMT_602|3end_5'-methylthioadenosine_nucleosidase_/_S-adenosylhomocysteine_nucleosidase_517964..518114_POSITIVE 198 61 28 59 25 smit:SMT_2024|3end_hypothetical_protein_1940690..1940840_POSITIVE 198 61 28 48 14 smit:SMT_2002|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1924145..1924295_NEGATIVE 198 61 28 59 25 smit:SMT_1981|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912868..1913018_POSITIVE 198 61 28 64 30 smit:SMT_1971|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1903526..1903676_POSITIVE 198 61 28 48 14 smit:SMT_1966|3end_DNA_polymerase_III_alpha_subunit_1898328..1898478_POSITIVE 198 61 28 59 25 smit:SMT_1942|3end_zinc_metalloprotease_ZmpB,_truncated_1878384..1878534_POSITIVE 198 61 28 48 14 smit:SMT_1927|3end_cell_division_protein_FtsH_1868408..1868558_NEGATIVE 198 61 28 59 25 smit:SMT_1926|3end_mevalonate_kinase_1868062..1868212_POSITIVE 198 61 28 59 25 smit:SMT_1887|3end_LicC_protein_1841740..1841890_POSITIVE 198 61 28 48 14 smit:SMT_1885|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1839830..1839980_NEGATIVE