Origin IGS: aaagaagtttgattgcttctttcttttttgatggtgaagtaataatccagatatttgtaacaacgatggatacatgatataattttgtacatctatcattaaaaggaatgaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttcattccttttaatgatagatgtacaaaattatatcatgtatccatcgttgttacaaatatctggattattacttcaccatcaaaaaagaaagaagcaatcaaacttcttt Mask Tandem Repeat Region ================================================ aaagaagtttgattgcttctttcttttttgatggtgaagtaataatccagatatttgtaacaacgatggatacatgatataattttgtacatctatcattaaaaggaatgaaaa Find is-nt database================================================ Query_seq: SSA_1157:SSA_1158|SSA_1157:SSA_1158:PvaA-like protein, putative:hypothetical protein:->->:1186279..1186392 114 aaagaagtttgattgcttctttcttttttgatggtgaagtaataatccagatatttgtaacaacgatggatacatgatataattttgtacatctatcattaaaaggaatgaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1157:SSA_1158|SSA_1157:SSA_1158:PvaA-like protein, putative:hypothetical protein:->->:1186279..1186392 114 aaagaagtttgattgcttctttcttttttgatggtgaagtaataatccagatatttgtaacaacgatggatacatgatataattttgtacatctatcattaaaaggaatgaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1157:SSA_1158|SSA_1157:SSA_1158:PvaA-like protein, putative:hypothetical protein:->->:1186279..1186392 114 aaagaagtttgattgcttctttcttttttgatggtgaagtaataatccagatatttgtaacaacgatggatacatgatataattttgtacatctatcattaaaaggaatgaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagaagtttgattgcttctttcttttttgatggtgaagtaataatccagatatttgtaacaacgatggatacatgatataattttgtacatctatcattaaaaggaatgaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 3 End: 92 .. S T Q N S R E K K I T F Y Y D L Y K Y C R H I C S I I K Y M ...................... Protein_Len: 36 Strand: - Start: 2 End: 109 . L L K I A E K K K S P S T I I W I N T V V I S V H Y L K T C R D N F P M ..... Protein_Len: 33 Strand: - Start: 1 End: 99 F F N S Q K K R K Q H H L L L G S I Q L L S P Y M I Y N Q V D I M ............... aaagaagtttgattgcttctttcttttttgatggtgaagtaataatccagatatttgtaacaacgatggatacatgatataattttgtacatctatcattaaaaggaatgaaaa 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: 87 Start: 54 End: 83 .....................................................TTTGTAACAACGATGGATACATGATATAAT............................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaagaagtttgattgcttctttcttttttgatggtgaagtaataatccagatatttgtaacaacgatggatacatgatataattttgtacatctatcattaaaaggaatgaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1157:SSA_1158|SSA_1157:SSA_1158:PvaA-like protein, putative:hypothetical protein:->->:1186279..1186392 114 aaagaagtttgattgcttctttcttttttgatggtgaagtaataatccagatatttgtaacaacgatggatacatgatataattttgtacatctatcattaaaaggaatgaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: NC_009009_SSA_1157_SSA_1158|PvaA-like protein, putative:hypothetical protein|POSITIVE:POSITIVE|[1186279,1186392]|114 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 aaagaagtttgattgcttctttcttttttgatggtgaagtaataatccagatatttgtaacaacgatggatacatgatataattttgtacatctatcattaaaaggaatgaaaa aaagaagtttgattgcttctttcttttttgatggtgaagtaataatccagatatttgtaacaacgatggatacatgatataattttgtacatctatcattaaaaggaatgaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGAAGUUUGAUUGCUUCUUUCUUUUUUGAUGGUGAAGUAAUAAUCCAGAUAUUUGUAACAACGAUGGAUACAUGAUAUAAUUUUGUACAUCUAUCAUUAAAAGGAAUGAAAA ((((((((......)))))))).((((((((((((((.(((.(((.....(((((((((.((....))..)))).)))))....)))))).)).))))))))))))........ (-21.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCAUUCCUUUUAAUGAUAGAUGUACAAAAUUAUAUCAUGUAUCCAUCGUUGUUACAAAUAUCUGGAUUAUUACUUCACCAUCAAAAAAGAAAGAAGCAAUCAAACUUCUUU .........(((((..((((.((((((......))))))....(((((..(((......)))...)))))............)))).))))).((((((........)))))). (-14.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 40 6 182 141 NC_009009:SSA_1872|5end_Cell_division_protein,_putative_1869186..1869416_NEGATIVE 244 49 11 46 10 NC_009009:SSA_1535|5end_hypothetical_protein_1543188..1543418_NEGATIVE 238 70 46 137 115 NC_009009:SSA_0475|5end_CbiK_protein,_putative_477723..477953_POSITIVE 230 49 3 129 81 NC_009009:SSA_1972|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1968410..1968640_NEGATIVE 223 41 12 123 96 NC_009009:SSA_1868|5end_ABC-type_arginine/histidine_transport_system,_permease_component,_putative_1863902..1864132_NEGATIVE 221 41 1 157 116 NC_009009:SSA_2082|5end_Carbohydrate_kinase,_FGGY_family,_putative_2086874..2087104_NEGATIVE 221 66 23 226 185 NC_009009:SSA_1788|5end_Integral_membrane_protein,_possible_receptor,_putative_1772339..1772569_NEGATIVE 217 49 6 130 94 NC_009009:SSA_1051|5end_Spermidine/putrescine_ABC_transporter,_spermidine/putrescine-binding_protein,_putative_1065658..1065888_POSITIVE 216 60 16 145 103 NC_009009:SSA_2239|5end_Conserved_uncharacterized_cytosolic_protein_2237233..2237463_NEGATIVE 214 47 12 84 51 NC_009009:SSA_2105|5end_hypothetical_protein_2107802..2108032_NEGATIVE 214 68 26 230 189 NC_009009:SSA_0080|5end_Superfamily_I_DNA_and_RNA_helicases,_putative_83785..84015_POSITIVE 210 54 11 218 174 NC_009009:SSA_1937|5end_Malonyl-CoA:ACP_transacylase,_putative_1924771..1925001_NEGATIVE 210 88 46 138 101 NC_009009:SSA_1596|5end_hypothetical_protein_1603034..1603264_NEGATIVE 208 50 1 170 120 NC_009009:SSA_1955|5end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1952602..1952832_NEGATIVE 204 58 12 134 90 NC_009009:SSA_2310|5end_hypothetical_protein_2313418..2313648_NEGATIVE 204 49 6 207 159 NC_009009:SSA_1161|5end_hypothetical_protein_1187383..1187613_POSITIVE 200 50 12 144 90 NC_009009:SSA_1050|5end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064888..1065118_POSITIVE 197 36 3 124 78 NC_009009:SSA_0705|5end_hypothetical_protein_690950..691180_NEGATIVE 197 53 12 220 172 NC_009009:SSA_0365|5end_Small-conductance_mechanosensitive_efflux_channel,_putative_356621..356851_POSITIVE 194 35 4 61 28 NC_009009:SSA_0638|5end_Tryptophan_synthase_alpha_chain,_putative_626935..627165_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 238 70 46 123 101 NC_009009:SSA_0474|3end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_477789..477939_POSITIVE 230 49 3 132 84 NC_009009:SSA_1973|3end_Histidine_kinase,_putative_1968407..1968557_NEGATIVE 221 41 1 81 40 NC_009009:SSA_2083|3end_hypothetical_protein_2086950..2087100_NEGATIVE 221 69 21 145 99 NC_009009:SSA_0436|3end_Imidazolonepropionase,_putative_440214..440364_POSITIVE 217 49 6 133 97 NC_009009:SSA_1050|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1065741..1065891_POSITIVE 216 60 16 120 78 NC_009009:SSA_2240|3end_Holliday_junction_resolvase,_putative_2237258..2237408_NEGATIVE 208 50 1 128 78 NC_009009:SSA_1956|3end_ABC-type_Fe-S_cluster_assembly_transporter,_ATPase_component,_putative_1952644..1952794_NEGATIVE 204 58 12 121 77 NC_009009:SSA_2311|3end_Nitric_oxide_reductase_NorD_/_Von_Willebrand_factor_type_A_(vWA)_domain_protein,_putative_2313431..2313581_NEGATIVE 204 39 13 148 119 NC_009009:SSA_1962|3end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_1960930..1961080_POSITIVE 201 47 5 81 44 NC_009009:SSA_1210|3end_GTP_pyrophosphokinase,_putative_1233984..1234134_NEGATIVE 200 50 12 147 93 NC_009009:SSA_1049|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064971..1065121_POSITIVE 197 50 4 110 69 NC_009009:SSA_1535|3end_hypothetical_protein_1542457..1542607_NEGATIVE 195 48 12 126 93 NC_009009:SSA_0243|3end_Cyclo-nucleotide_phosphodiesterase,_putative_235824..235974_NEGATIVE 194 47 2 57 10 NC_009009:SSA_2025|3end_Conserved_hypothetical_GTPase_protein_2031012..2031162_POSITIVE 194 35 4 68 35 NC_009009:SSA_0637|3end_Tryptophan_synthase_beta_chain,_putative_627022..627172_POSITIVE 194 39 9 148 113 NC_009009:SSA_0333|3end_Mevalonate_kinase,_putative_327953..328103_POSITIVE 193 50 18 128 95 NC_009009:SSA_0146|3end_DNA_repair_ATPase,_putative_142159..142309_POSITIVE 191 49 9 43 1 NC_009009:SSA_1454|3end_hypothetical_protein_1460255..1460405_NEGATIVE 189 32 8 148 127 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 186 110 82 49 21 NC_009009:SSA_1796|3end_Transcription_elongation_factor_GreA,_putative_1777825..1777975_NEGATIVE