Origin IGS: tttccttttccttttgactatctggctggcttatagtatagtaaagatagttgatattccaaaaatctaagctaattgattttacttgggtagaaaaagtttttgagggatttct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agaaatccctcaaaaactttttctacccaagtaaaatcaattagcttagatttttggaatatcaactatctttactatactataagccagccagatagtcaaaaggaaaaggaaa Mask Tandem Repeat Region ================================================ tttccttttccttttgactatctggctggcttatagtatagtaaagatagttgatattccaaaaatctaagctaattgattttacttgggtagaaaaagtttttgagggatttct Find is-nt database================================================ Query_seq: SSA_1134:SSA_1135|SSA_1134:SSA_1135:Xanthine phosphoribosyltransferase, putative:Na+-driven multidrug efflux pump, putative:->->:1160377..1160491 115 tttccttttccttttgactatctggctggcttatagtatagtaaagatagttgatattccaaaaatctaagctaattgattttacttgggtagaaaaagtttttgagggatttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1134:SSA_1135|SSA_1134:SSA_1135:Xanthine phosphoribosyltransferase, putative:Na+-driven multidrug efflux pump, putative:->->:1160377..1160491 115 tttccttttccttttgactatctggctggcttatagtatagtaaagatagttgatattccaaaaatctaagctaattgattttacttgggtagaaaaagtttttgagggatttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1134:SSA_1135|SSA_1134:SSA_1135:Xanthine phosphoribosyltransferase, putative:Na+-driven multidrug efflux pump, putative:->->:1160377..1160491 115 tttccttttccttttgactatctggctggcttatagtatagtaaagatagttgatattccaaaaatctaagctaattgattttacttgggtagaaaaagtttttgagggatttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttccttttccttttgactatctggctggcttatagtatagtaaagatagttgatattccaaaaatctaagctaattgattttacttgggtagaaaaagtttttgagggatttct Predict ORF larger than 30AA ================================================ tttccttttccttttgactatctggctggcttatagtatagtaaagatagttgatattccaaaaatctaagctaattgattttacttgggtagaaaaagtttttgagggatttct 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: 86 Start: 13 End: 42 ............TTTGACTATCTGGCTGGCTTATAGTATAGT......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttccttttccttttgactatctggctggcttatagtatagtaaagatagttgatattccaaaaatctaagctaattgattttacttgggtagaaaaagtttttgagggatttct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1134:SSA_1135|SSA_1134:SSA_1135:Xanthine phosphoribosyltransferase, putative:Na+-driven multidrug efflux pump, putative:->->:1160377..1160491 115 tttccttttccttttgactatctggctggcttatagtatagtaaagatagttgatattccaaaaatctaagctaattgattttacttgggtagaaaaagtttttgagggatttct Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: NC_009009_SSA_1134_SSA_1135|Xanthine phosphoribosyltransferase, putative:Na+-driven multidrug efflux pump, putative|POSITIVE:POSITIVE|[1160377,1160491]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 tttccttttccttttgactatctggctggcttatagtatagtaaagatagttgatattccaaaaatctaagctaattgattttacttgggtagaaaaagtttttgagggatttct tttccttttccttttgactatctggctggcttatagtatagtaaagatagttgatattccaaaaatctaagctaattgattttacttgggtagaaaaagtttttgagggatttct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCCUUUUCCUUUUGACUAUCUGGCUGGCUUAUAGUAUAGUAAAGAUAGUUGAUAUUCCAAAAAUCUAAGCUAAUUGAUUUUACUUGGGUAGAAAAAGUUUUUGAGGGAUUUCU ..((((((.....(..(((((((.((((((.....)).))))..)))))))..)..........(((((((.(((......)))))))))).............))))))..... (-23.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAAUCCCUCAAAAACUUUUUCUACCCAAGUAAAAUCAAUUAGCUUAGAUUUUUGGAAUAUCAACUAUCUUUACUAUACUAUAAGCCAGCCAGAUAGUCAAAAGGAAAAGGAAA ................((((((((..((((...(((((..........))))))))).......(((((((.....................)))))))....)))))))).... (-15.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 43 1 229 176 NC_009009:SSA_2181|5end_Conserved_uncharacterized_protein_2180083..2180313_NEGATIVE 289 40 5 56 29 NC_009009:SSA_0752|5end_hypothetical_protein_734171..734401_POSITIVE 284 110 65 157 111 NC_009009:SSA_1154|5end_hypothetical_protein_1182661..1182891_POSITIVE 280 31 1 99 72 NC_009009:SSA_1601|5end_VacB-like_protein,_putative_1607059..1607289_NEGATIVE 257 50 11 68 33 NC_009009:SSA_1442|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445941..1446171_NEGATIVE 249 42 1 222 175 NC_009009:SSA_1934|5end_Biotin_carboxyl_carrier_protein_of_acetyl-CoA_carboxylase,_putative_1921800..1922030_NEGATIVE 249 35 5 52 13 NC_009009:SSA_0878|5end_DNA_gyrase,_putative_871596..871826_POSITIVE 245 73 33 156 119 NC_009009:SSA_0668|5end_hypothetical_protein_650737..650967_POSITIVE 240 46 13 156 125 NC_009009:SSA_1584|5end_Ring-cleavage_extradiol_dioxygenase,_putative_1587030..1587260_NEGATIVE 239 94 56 176 133 NC_009009:SSA_1864|5end_Nicotinate_phosphoribosyltransferase_(NAPRTase),_subgroup_A,_putative_1860870..1861100_NEGATIVE 239 60 12 175 117 NC_009009:SSA_0033|5end_Phosphoribosylglycinamide_(GAR)_formyltransferase,_putative_38957..39187_POSITIVE 238 53 11 188 153 NC_009009:SSA_2275|5end_hypothetical_protein_2275590..2275820_NEGATIVE 235 68 22 69 18 NC_009009:SSA_2009|5end_Heat_shock_transcription_repressor_HrcA,_putative_2011132..2011362_NEGATIVE 231 105 70 212 172 NC_009009:SSA_1430|5end_Ribonuclease_Z,_putative_1438036..1438266_NEGATIVE 227 54 11 41 7 NC_009009:SSA_1972|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1968410..1968640_NEGATIVE 227 31 3 37 4 NC_009009:SSA_0190|5end_hypothetical_protein_191481..191711_POSITIVE 223 31 1 123 92 NC_009009:SSA_1928|5end_Acyl-CoA_dehydrogenase,_putative_1917010..1917240_NEGATIVE 222 30 2 121 96 NC_009009:SSA_1867|5end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1863096..1863326_NEGATIVE 222 54 12 223 172 NC_009009:SSA_1492|5end_hypothetical_protein_1498954..1499184_NEGATIVE 215 31 2 31 2 NC_009009:SSA_1683|5end_NrdI_protein,_putative_1677405..1677635_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 43 1 149 96 NC_009009:SSA_2182|3end_hypothetical_protein_2180163..2180313_NEGATIVE 289 40 5 54 27 NC_009009:SSA_0751|3end_Oligoendopeptidase_F,_putative_734249..734399_POSITIVE 280 31 1 136 109 NC_009009:SSA_1602|3end_Exoribonuclease,_VacB/Rnb_family,_putative_1607022..1607172_NEGATIVE 257 50 11 65 30 NC_009009:SSA_1443|3end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1445944..1446094_NEGATIVE 247 57 14 146 107 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 245 73 33 96 59 NC_009009:SSA_0667|3end_Transcriptional_regulator,_putative_650757..650907_POSITIVE 239 94 56 68 25 NC_009009:SSA_1865|3end_Thioredoxin_reductase,_putative_1860978..1861128_NEGATIVE 233 59 11 137 88 NC_009009:SSA_1595|3end_Tellurite_resistance,_putative_1600951..1601101_NEGATIVE 229 31 10 150 131 NC_009009:SSA_1615|3end_Alanine_dehydrogenase,_putative_1619318..1619468_POSITIVE 228 35 10 39 8 NC_009009:SSA_0877|3end_Phosphoglycolate_phosphatase,_putative_871663..871813_POSITIVE 227 54 11 44 10 NC_009009:SSA_1973|3end_Histidine_kinase,_putative_1968407..1968557_NEGATIVE 223 31 1 104 73 NC_009009:SSA_1929|3end_Macrophage_infectivity_potentiator_protein,_putative_1917029..1917179_NEGATIVE 223 54 12 58 6 NC_009009:SSA_0265|3end_ORFA,_transposon_ISSsa1_260007..260157_POSITIVE 223 46 2 149 102 NC_009009:SSA_0040|3end_Phosphoribosylaminoimidazole_carboxylase,_ATPase_subunit,_putative_47479..47629_POSITIVE 222 30 2 121 96 NC_009009:SSA_1868|3end_ABC-type_arginine/histidine_transport_system,_permease_component,_putative_1863096..1863246_NEGATIVE 219 38 3 147 95 NC_009009:SSA_1096|3end_Methyltransferase,_putative_1114099..1114249_POSITIVE 217 41 1 149 108 NC_009009:SSA_0032|3end_Phosphoribosylformylglycinamidine_cyclo-ligase,_putative_39040..39190_POSITIVE 215 60 18 137 91 NC_009009:SSA_0508|3end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_508064..508214_POSITIVE 214 86 52 66 26 NC_009009:SSA_1307|3end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1324921..1325071_NEGATIVE 214 36 5 62 30 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE