Origin IGS: gacaccgtctccttttgttataaaataaattgattcgatattattataacatgtttctatgagtttgtaatcgctatcatcaattttatttcaaaaaaagaactacccgaaggcagttcaattaattc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaattaattgaactgccttcgggtagttctttttttgaaataaaattgatgatagcgattacaaactcatagaaacatgttataataatatcgaatcaatttattttataacaaaaggagacggtgtc Mask Tandem Repeat Region ================================================ gacaccgtctccttttgttataaaataaattgattcgatattattataacatgtttctatgagtttgtaatcgctatcatcaattttatttcaaaaaaagaactacccgaaggcagttcaattaattc Find is-nt database================================================ Query_seq: SSA_1621:SSA_1622|SSA_1621:SSA_1622:Amino acid transporter, putative:50S ribosomal protein L1, putative:<-<-:1624714..1624841 128 gacaccgtctccttttgttataaaataaattgattcgatattattataacatgtttctatgagtttgtaatcgctatcatcaattttatttcaaaaaaagaactacccgaaggcagttcaattaattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1621:SSA_1622|SSA_1621:SSA_1622:Amino acid transporter, putative:50S ribosomal protein L1, putative:<-<-:1624714..1624841 128 gacaccgtctccttttgttataaaataaattgattcgatattattataacatgtttctatgagtttgtaatcgctatcatcaattttatttcaaaaaaagaactacccgaaggcagttcaattaattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1621:SSA_1622|SSA_1621:SSA_1622:Amino acid transporter, putative:50S ribosomal protein L1, putative:<-<-:1624714..1624841 128 gacaccgtctccttttgttataaaataaattgattcgatattattataacatgtttctatgagtttgtaatcgctatcatcaattttatttcaaaaaaagaactacccgaaggcagttcaattaattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gacaccgtctccttttgttataaaataaattgattcgatattattataacatgtttctatgagtttgtaatcgctatcatcaattttatttcaaaaaaagaactacccgaaggcagttcaattaattc Predict ORF larger than 30AA ================================================ gacaccgtctccttttgttataaaataaattgattcgatattattataacatgtttctatgagtttgtaatcgctatcatcaattttatttcaaaaaaagaactacccgaaggcagttcaattaattc 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: 82 Start: 43 End: 72 ..........................................GATTACAAACTCATAGAAACATGTTATAAT........................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gacaccgtctccttttgttataaaataaattgattcgatattattataacatgtttctatgagtttgtaatcgctatcatcaattttatttcaaaaaaagaactacccgaaggcagttcaattaattc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1621:SSA_1622|SSA_1621:SSA_1622:Amino acid transporter, putative:50S ribosomal protein L1, putative:<-<-:1624714..1624841 128 gacaccgtctccttttgttataaaataaattgattcgatattattataacatgtttctatgagtttgtaatcgctatcatcaattttatttcaaaaaaagaactacccgaaggcagttcaattaattc Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: NC_009009_SSA_1621_SSA_1622|Amino acid transporter, putative:50S ribosomal protein L1, putative|NEGATIVE:NEGATIVE|[1624714,1624841]|128 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 gacaccgtctccttttgttataaaataaattgattcgatattattataacatgtttctatgagtttgtaatcgctatcatcaattttatttcnnnnnnngaactacccgaaggcagttcaattaattc gacaccgtctccttttgttataaaataaattgattcgatattattataacatgtttctatgagtttgtaatcgctatcatcaattttatttcaaaaaaagaactacccgaaggcagttcaattaattc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACACCGUCUCCUUUUGUUAUAAAAUAAAUUGAUUCGAUAUUAUUAUAACAUGUUUCUAUGAGUUUGUAAUCGCUAUCAUCAAUUUUAUUUCAAAAAAAGAACUACCCGAAGGCAGUUCAAUUAAUUC (((...)))...(((((..(((((((....((((.((((..(((.....((((....)))).....)))))))..))))...)))))))..)))))...(((((.((....)).)))))......... (-19.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUUAAUUGAACUGCCUUCGGGUAGUUCUUUUUUUGAAAUAAAAUUGAUGAUAGCGAUUACAAACUCAUAGAAACAUGUUAUAAUAAUAUCGAAUCAAUUUAUUUUAUAACAAAAGGAGACGGUGUC .........((((((((....))))))))......(((((((((.(((((((((...((((..(((............))).))))..))))..))))))))))))))..(((...(....)..))). (-28.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 803 120 71 211 162 NC_009009:SSA_1621|5end_Amino_acid_transporter,_putative_1624623..1624853_NEGATIVE 248 116 72 149 96 NC_009009:SSA_0469|5end_Precorrin-6B_methylase_2,putative_472310..472540_POSITIVE 242 68 39 147 118 NC_009009:SSA_0664|5end_Conserved_uncharacterized_protein_649086..649316_NEGATIVE 226 90 50 209 177 NC_009009:SSA_0711|5end_hypothetical_protein_696631..696861_NEGATIVE 216 91 58 86 52 NC_009009:SSA_0448|5end_Excinuclease_ATPase_subunit_A,_putative_446480..446710_POSITIVE 210 119 88 163 128 NC_009009:SSA_2203|5end_30S_ribosomal_protein_S2,_putative_2204205..2204435_NEGATIVE 210 78 32 186 131 NC_009009:SSA_0839|5end_hypothetical_protein_826751..826981_POSITIVE 206 113 71 134 81 NC_009009:SSA_1243|5end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1268204..1268434_NEGATIVE 206 108 62 151 108 NC_009009:SSA_0419|5end_Alpha-galactosidase,_putative_416213..416443_POSITIVE 206 93 56 90 60 NC_009009:SSA_0389|5end_hypothetical_protein_384172..384402_POSITIVE 200 118 73 50 5 NC_009009:SSA_1149|5end_Glycosyl_hydrolase,_family_1,_putative_1178399..1178629_POSITIVE 199 42 7 127 98 NC_009009:SSA_1386|5end_NADPH-dependent_FMN_reductase,_putative_1402800..1403030_POSITIVE 199 95 59 106 64 NC_009009:SSA_1084|5end_Conserved_uncharacterized_protein_1101675..1101905_POSITIVE 198 119 96 150 128 NC_009009:SSA_1881|5end_hypothetical_protein_1875964..1876194_NEGATIVE 198 120 82 182 141 NC_009009:SSA_1258|5end_Purine_nucleoside_phosphorylase,_family_1,_putative_1284652..1284882_NEGATIVE 195 115 73 134 85 NC_009009:SSA_1313|5end_hypothetical_protein_1330548..1330778_NEGATIVE 193 81 44 132 88 NC_009009:SSA_0153|5end_hypothetical_protein_148677..148907_POSITIVE 190 100 54 177 129 NC_009009:SSA_1321|5end_Ferrochelatase,_putative_1338343..1338573_NEGATIVE 188 50 9 121 73 NC_009009:SSA_1915|5end_hypothetical_protein_1905440..1905670_NEGATIVE 187 116 100 30 9 NC_009009:SSA_1949|5end_AliA_protein,_putative_1944373..1944603_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 242 68 39 79 50 NC_009009:SSA_0665|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes_(MutT/NUDIX_family)_649154..649304_NEGATIVE 226 90 50 79 47 NC_009009:SSA_0712|3end_P-type_ATPase-metal_cation_transport_(calcium_efflux),_putative_696761..696911_NEGATIVE 226 38 1 114 68 NC_009009:SSA_0452|3end_Nitrogen_utilization_substance_protein_B,_putative_452060..452210_POSITIVE 221 120 89 46 7 NC_009009:SSA_0921|3end_Zn-dependeant_threonine_dehydrogenase,_putative_932164..932314_POSITIVE 206 93 56 86 56 NC_009009:SSA_0388|3end_Mismatch_repair_ATPase_(MutS_family),_putative_384248..384398_POSITIVE 199 42 7 41 12 NC_009009:SSA_1385|3end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_1402794..1402944_POSITIVE 199 95 59 103 61 NC_009009:SSA_1083|3end_Conserved_uncharacterized_protein_1101752..1101902_POSITIVE 193 81 44 106 62 NC_009009:SSA_0152|3end_hypothetical_protein_148731..148881_POSITIVE 187 118 75 44 4 NC_009009:SSA_1148|3end_Beta-glucosides_PTS,_EIIC,_putative_1178473..1178623_POSITIVE 187 82 50 49 18 NC_009009:SSA_0975|3end_2-isopropylmalate_synthase,_putative_982769..982919_POSITIVE 186 80 31 126 78 NC_009009:SSA_2260|3end_DNA_mismatch_repair_protein_hexA,_putative_2255601..2255751_NEGATIVE 183 119 75 53 5 NC_009009:SSA_1990|3end_Zn-porter_lipoprotein,_putative_1985402..1985552_NEGATIVE 182 38 3 47 16 NC_009009:SSA_1822|3end_hypothetical_protein_1810871..1811021_NEGATIVE 179 81 55 147 116 NC_009009:SSA_2360|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase,_putative_2362658..2362808_NEGATIVE 177 120 73 151 104 NC_009009:SSA_1752|3end_Phosphotransferase_system,_trehalose-specific_IIBC_component,_putative_1739812..1739962_NEGATIVE 176 13 2 104 93 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 175 48 9 52 13 NC_009009:SSA_2245|3end_RecA_protein,_putative_2239961..2240111_NEGATIVE 172 119 82 78 36 NC_009009:SSA_1542|3end_Peptidase,_U32_family,_putative_1546825..1546975_NEGATIVE 172 118 73 84 35 NC_009009:SSA_1225|3end_Branched-chain_amino_acid_aminotransferase,_putative_1247589..1247739_NEGATIVE 171 21 1 78 56 NC_009009:SSA_2181|3end_Conserved_uncharacterized_protein_2179148..2179298_NEGATIVE