Origin IGS: agaaaaattcttctagtattagctagaagaatttttttaatctcaagtaaaaatcagcatcgccgatacaaaaagctcagcaaagaaagcaataactgatgaatgaggtgactcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagagtcacctcattcatcagttattgctttctttgctgagctttttgtatcggcgatgctgatttttacttgagattaaaaaaattcttctagctaatactagaagaatttttct Mask Tandem Repeat Region ================================================ agaaaaattcttctagtattagctagaagaatttttttaatctcaagtaaaaatcagcatcgccgatacaaaaagctcagcaaagaaagcaataactgatgaatgaggtgactcta Find is-nt database================================================ Query_seq: SSA_1792:SSA_1793|SSA_1792:SSA_1793:Preprotein translocase subunit YidC, putative:Histidine kinase (sensor protein), putative:-><-:1775100..1775215 116 agaaaaattcttctagtattagctagaagaatttttttaatctcaagtaaaaatcagcatcgccgatacaaaaagctcagcaaagaaagcaataactgatgaatgaggtgactcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1792:SSA_1793|SSA_1792:SSA_1793:Preprotein translocase subunit YidC, putative:Histidine kinase (sensor protein), putative:-><-:1775100..1775215 116 agaaaaattcttctagtattagctagaagaatttttttaatctcaagtaaaaatcagcatcgccgatacaaaaagctcagcaaagaaagcaataactgatgaatgaggtgactcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1792:SSA_1793|SSA_1792:SSA_1793:Preprotein translocase subunit YidC, putative:Histidine kinase (sensor protein), putative:-><-:1775100..1775215 116 agaaaaattcttctagtattagctagaagaatttttttaatctcaagtaaaaatcagcatcgccgatacaaaaagctcagcaaagaaagcaataactgatgaatgaggtgactcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaaaaattcttctagtattagctagaagaatttttttaatctcaagtaaaaatcagcatcgccgatacaaaaagctcagcaaagaaagcaataactgatgaatgaggtgactcta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 7 End: 96 ...... M L L V L A R R I F L I S S K N Q H R R Y K K L S K E S N N .................... agaaaaattcttctagtattagctagaagaatttttttaatctcaagtaaaaatcagcatcgccgatacaaaaagctcagcaaagaaagcaataactgatgaatgaggtgactcta 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================================================ agaaaaattcttctagtattagctagaagaatttttttaatctcaagtaaaaatcagcatcgccgatacaaaaagctcagcaaagaaagcaataactgatgaatgaggtgactcta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 77 HP_score: -5.5 Tail_Score: -4.87893 Start: 54 End: 66 Full_Region: gctgagctttttgta tcggc gat gctga tttttacttgagatt .....................................................tcggcgatgctga.................................................. Find igs database================================================ Query_seq: SSA_1792:SSA_1793|SSA_1792:SSA_1793:Preprotein translocase subunit YidC, putative:Histidine kinase (sensor protein), putative:-><-:1775100..1775215 116 agaaaaattcttctagtattagctagaagaatttttttaatctcaagtaaaaatcagcatcgccgatacaaaaagctcagcaaagaaagcaataactgatgaatgaggtgactcta Intra-Species Hit: Count: 1 Min: 1 Max: 116 Len: 116 Subject: NC_009009_SSA_1792_SSA_1793|Preprotein translocase subunit YidC, putative:Histidine kinase (sensor protein), putative|POSITIVE:NEGATIVE|[1775100,1775215]|116 HSP 1 e-value: 3.0E-47 bit: 188.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 agaaaaattcttctagtattagctagaagaannnnnnnaatctcaagtaaaaatcagcatcgccgatacaaaaagctcagcaaagaaagcaataactgatgaatgaggtgactcta agaaaaattcttctagtattagctagaagaatttttttaatctcaagtaaaaatcagcatcgccgatacaaaaagctcagcaaagaaagcaataactgatgaatgaggtgactcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAAAAUUCUUCUAGUAUUAGCUAGAAGAAUUUUUUUAAUCUCAAGUAAAAAUCAGCAUCGCCGAUACAAAAAGCUCAGCAAAGAAAGCAAUAACUGAUGAAUGAGGUGACUCUA (((((((((((((((((....)))))))))))))))))..............(((((....((...........))...((.......)).....)))))....(((....))).. (-28.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAGUCACCUCAUUCAUCAGUUAUUGCUUUCUUUGCUGAGCUUUUUGUAUCGGCGAUGCUGAUUUUUACUUGAGAUUAAAAAAAUUCUUCUAGCUAAUACUAGAAGAAUUUUUCU .........((((...((((((...........(((((((((.....)).))))))).)))))).......)))).....((((((((((((((......)))))))))))))).. (-29.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 81 46 170 133 NC_009009:SSA_1050|5end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064888..1065118_POSITIVE 290 99 54 74 19 NC_009009:SSA_1957|5end_Glycosyl_transferase_N-acetylglucosaminyltransferase,_putative_1954670..1954900_NEGATIVE 280 90 41 76 11 NC_009009:SSA_0879|5end_Cell_division_regulator,_negative_regulator_of_FtsZ_septation_ring_formation,_putative_873632..873862_POSITIVE 276 90 42 173 130 NC_009009:SSA_0714|5end_hypothetical_protein_700042..700272_POSITIVE 260 109 62 223 172 NC_009009:SSA_0915|5end_hypothetical_protein_927542..927772_POSITIVE 260 93 53 49 9 NC_009009:SSA_0253|5end_CAAX_amino_terminal_protease_family_protein,_putative_246289..246519_POSITIVE 252 106 62 57 7 NC_009009:SSA_0626|5end_hypothetical_protein_616089..616319_POSITIVE 247 90 41 178 130 NC_009009:SSA_0239|5end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_232961..233191_POSITIVE 245 90 43 176 124 NC_009009:SSA_0875|5end_Rod_shape_determining_protein_(cell-cycle_protein),_putative_868928..869158_POSITIVE 243 99 51 62 13 NC_009009:SSA_1106|5end_IgA-specific_metalloendopeptidase_1125974..1126204_POSITIVE 241 100 51 73 28 NC_009009:SSA_2087|5end_Conserved_uncharacterized_protein_2092657..2092887_NEGATIVE 238 109 62 68 8 NC_009009:SSA_2338|5end_Conserved_uncharacterized_protein_2339272..2339502_POSITIVE 237 86 41 79 33 NC_009009:SSA_0069|5end_Hypothetical_protein,_possibly_membrane-associated_73037..73267_POSITIVE 236 89 53 52 6 NC_009009:SSA_0956|5end_surface_protein_D_961223..961453_POSITIVE 234 98 52 189 146 NC_009009:SSA_1491|5end_Methionine_aminopeptidase_A,_putative_1497637..1497867_NEGATIVE 232 91 52 178 136 NC_009009:SSA_0760|5end_Acetylornithine_aminotransferase,_putative_742581..742811_POSITIVE 228 98 54 154 109 NC_009009:SSA_1101|5end_Multidrug_resistance_efflux_pump/hemolysin_secretion_transmembrane_protein,_putative_1121911..1122141_POSITIVE 227 77 37 68 22 NC_009009:SSA_0964|5end_DEAD_RNA_helicase,_putative_974114..974344_NEGATIVE 225 90 41 56 7 NC_009009:SSA_1015|5end_4-hydroxybenzoate_octaprenyltransferase,_putative_1018703..1018933_POSITIVE 225 79 31 137 90 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 311 43 1 96 53 NC_009009:SSA_1792|3end_Preprotein_translocase_subunit_YidC,_putative_1775039..1775189_POSITIVE 290 99 54 83 28 NC_009009:SSA_1958|3end_Adapter_protein_mecA,_putative_1954661..1954811_NEGATIVE 288 82 41 86 43 NC_009009:SSA_0812|3end_hypothetical_protein_794434..794584_POSITIVE 276 90 42 79 36 NC_009009:SSA_0713|3end_1-acyl-sn-glycerol-3-phosphate_acyltransferase,_putative_700028..700178_POSITIVE 252 106 62 70 20 NC_009009:SSA_0625|3end_Phosphopantetheine_adenylyltransferase_616182..616332_POSITIVE 238 109 62 75 15 NC_009009:SSA_2337|3end_hypothetical_protein_2339359..2339509_POSITIVE 237 37 1 86 41 NC_009009:SSA_0690|3end_Recombinational_DNA_repair_protein_(RecF_pathway),_putative_675108..675258_POSITIVE 235 110 62 108 47 NC_009009:SSA_0192|3end_Acetate_kinase,_putative_194182..194332_POSITIVE 231 98 58 35 1 NC_009009:SSA_1414|3end_hypothetical_protein_1424942..1425092_NEGATIVE 227 77 37 147 101 NC_009009:SSA_0965|3end_Oxidoreductase,_putative_974035..974185_NEGATIVE 225 90 41 71 22 NC_009009:SSA_1014|3end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1018798..1018948_POSITIVE 225 79 31 127 80 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 225 65 21 134 84 NC_009009:SSA_0221|3end_PTS_system,_mannose-specific_IIC_component,_putative_217295..217445_POSITIVE 222 108 64 57 6 NC_009009:SSA_2339|3end_Microcin_C7_resistance_protein,_putative_2341489..2341639_POSITIVE 222 67 21 57 8 NC_009009:SSA_2278|3end_Ukp_protein,_putative_2280410..2280560_NEGATIVE 222 99 55 69 24 NC_009009:SSA_1867|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1862353..1862503_NEGATIVE 219 79 31 149 93 NC_009009:SSA_0839|3end_hypothetical_protein_827013..827163_POSITIVE 218 98 51 72 29 NC_009009:SSA_2088|3end_Carbohydrate_isomerase,_AraD/FucA_family,_putative_2092766..2092916_NEGATIVE 218 64 24 124 92 NC_009009:SSA_0815|3end_hypothetical_protein_797411..797561_POSITIVE 218 46 1 117 62 NC_009009:SSA_0594|3end_Transcriptional_regulator,_AraC_family,_putative_586513..586663_POSITIVE