Origin IGS: ttgaacaaaaaagcagactccggtctgttttttgttttcactctttggagagaagaggaagattgtgtgcaatggacaagaaaaaaacactgattttcatcagtgaattctct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agagaattcactgatgaaaatcagtgtttttttcttgtccattgcacacaatcttcctcttctctccaaagagtgaaaacaaaaaacagaccggagtctgcttttttgttcaa Mask Tandem Repeat Region ================================================ ttgaacaaaaaagcagactccggtctgttttttgttttcactctttggagagaagaggaagattgtgtgcaatggacaagaaaaaaacactgattttcatcagtgaattctct Find is-nt database================================================ Query_seq: SSA_0820:SSA_0822|SSA_0820:SSA_0822:Ribosomal protein S21, putative:Large conductance mechano-sensitive ion channel, putative:-><-:801566..801678 113 ttgaacaaaaaagcagactccggtctgttttttgttttcactctttggagagaagaggaagattgtgtgcaatggacaagaaaaaaacactgattttcatcagtgaattctct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0820:SSA_0822|SSA_0820:SSA_0822:Ribosomal protein S21, putative:Large conductance mechano-sensitive ion channel, putative:-><-:801566..801678 113 ttgaacaaaaaagcagactccggtctgttttttgttttcactctttggagagaagaggaagattgtgtgcaatggacaagaaaaaaacactgattttcatcagtgaattctct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0820:SSA_0822|SSA_0820:SSA_0822:Ribosomal protein S21, putative:Large conductance mechano-sensitive ion channel, putative:-><-:801566..801678 113 ttgaacaaaaaagcagactccggtctgttttttgttttcactctttggagagaagaggaagattgtgtgcaatggacaagaaaaaaacactgattttcatcagtgaattctct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgaacaaaaaagcagactccggtctgttttttgttttcactctttggagagaagaggaagattgtgtgcaatggacaagaaaaaaacactgattttcatcagtgaattctct Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 1 End: 90 M N K K A D S G L F F V F T L W R E E E D C V Q W T R K K H ....................... Protein_Len: 30 Strand: - Start: 1 End: 90 Q V F F C V G T Q K K N E S K P S F L F I T H L P C S F F M ....................... ttgaacaaaaaagcagactccggtctgttttttgttttcactctttggagagaagaggaagattgtgtgcaatggacaagaaaaaaacactgattttcatcagtgaattctct 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================================================ ttgaacaaaaaagcagactccggtctgttttttgttttcactctttggagagaagaggaagattgtgtgcaatggacaagaaaaaaacactgattttcatcagtgaattctct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0820:SSA_0822|SSA_0820:SSA_0822:Ribosomal protein S21, putative:Large conductance mechano-sensitive ion channel, putative:-><-:801566..801678 113 ttgaacaaaaaagcagactccggtctgttttttgttttcactctttggagagaagaggaagattgtgtgcaatggacaagaaaaaaacactgattttcatcagtgaattctct Intra-Species Hit: Count: 1 Min: 1 Max: 113 Len: 113 Subject: NC_009009_SSA_0820_SSA_0822|Ribosomal protein S21, putative:Large conductance mechano-sensitive ion channel, putative|POSITIVE:NEGATIVE|[801566,801678]|113 HSP 1 e-value: 2.0E-45 bit: 182.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 ttgaacaaaaaagcagactccggtctgttttttgttttcactctttggagagaagaggaagattgtgtgcaatggacaagnnnnnnncactgattttcatcagtgaattctct ttgaacaaaaaagcagactccggtctgttttttgttttcactctttggagagaagaggaagattgtgtgcaatggacaagaaaaaaacactgattttcatcagtgaattctct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAACAAAAAAGCAGACUCCGGUCUGUUUUUUGUUUUCACUCUUUGGAGAGAAGAGGAAGAUUGUGUGCAAUGGACAAGAAAAAAACACUGAUUUUCAUCAGUGAAUUCUCU ..((((((((((.(((((....)))))))))))))))...((((....)))).((((((..((((....))))..............(((((((....)))))))..)))))) (-31.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAGAAUUCACUGAUGAAAAUCAGUGUUUUUUUCUUGUCCAUUGCACACAAUCUUCCUCUUCUCUCCAAAGAGUGAAAACAAAAAACAGACCGGAGUCUGCUUUUUUGUUCAA ((((((..(((((((....)))))))...))))))...................(((((((.......))))).)).((((((((((((((....))))).)))))))))... (-30.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 57 12 71 30 NC_009009:SSA_0255|5end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_247946..248176_NEGATIVE 275 57 18 151 102 NC_009009:SSA_1062|5end_50S_ribosomal_protein_L27,_putative_1078284..1078514_POSITIVE 268 57 13 168 117 NC_009009:SSA_2220|5end_Galactosyltransferase,_putative_2221439..2221669_NEGATIVE 267 59 15 168 121 NC_009009:SSA_1222|5end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_1245454..1245684_NEGATIVE 264 60 15 208 147 NC_009009:SSA_2313|5end_hypothetical_protein_2315848..2316078_NEGATIVE 263 38 5 198 164 NC_009009:SSA_2087|5end_Conserved_uncharacterized_protein_2092657..2092887_NEGATIVE 259 51 11 124 75 NC_009009:SSA_0088|5end_V-type_sodium_ATPase,_subunit_C,_putative_88930..89160_POSITIVE 247 46 13 103 64 NC_009009:SSA_2176|5end_hypothetical_protein_2175159..2175389_NEGATIVE 247 60 12 210 138 NC_009009:SSA_1728|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1714293..1714523_NEGATIVE 246 81 46 177 132 NC_009009:SSA_1503|5end_Ferredoxin,_putative_1506209..1506439_POSITIVE 239 105 61 179 133 NC_009009:SSA_0158|5end_hypothetical_protein_153801..154031_POSITIVE 238 60 18 145 98 NC_009009:SSA_0726|5end_FmtA-like_protein,_putative_710905..711135_POSITIVE 237 63 21 49 1 NC_009009:SSA_1591|5end_Dipeptidase,_putative_1595451..1595681_NEGATIVE 237 80 32 52 5 NC_009009:SSA_0841|5end_hypothetical_protein_826935..827165_POSITIVE 237 51 14 156 115 NC_009009:SSA_0799|5end_hypothetical_protein_781970..782200_NEGATIVE 237 49 9 63 22 NC_009009:SSA_0357|5end_Thioredoxin,_putative_350763..350993_POSITIVE 236 59 12 175 126 NC_009009:SSA_2322|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_2327044..2327274_POSITIVE 236 84 46 214 172 NC_009009:SSA_0689|5end_Penicillin-binding_protein_2B,_putative_672262..672492_POSITIVE 235 45 11 174 148 NC_009009:SSA_0031|5end_Glutamine_phosphoribosylpyrophosphate_amidotransferase,_putative_36439..36669_POSITIVE 234 78 33 201 142 NC_009009:SSA_2016|5end_Phosphoglycerate_mutase,_putative_2016293..2016523_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 269 49 10 119 83 NC_009009:SSA_0218|3end_Sugar-binding_periplasmic_protein,_putative_215226..215376_POSITIVE 266 59 12 143 83 NC_009009:SSA_0166|3end_hypothetical_protein_165146..165296_POSITIVE 263 38 5 89 55 NC_009009:SSA_2088|3end_Carbohydrate_isomerase,_AraD/FucA_family,_putative_2092766..2092916_NEGATIVE 259 79 31 81 26 NC_009009:SSA_1828|3end_Glycerol_uptake_facilitator_protein,_putative_1818791..1818941_POSITIVE 259 51 11 113 64 NC_009009:SSA_0087|3end_V-type_sodium_ATPase,_subunit_E,_putative_88999..89149_POSITIVE 253 71 31 49 1 NC_009009:SSA_0292|3end_Transcriptional_regulator,_AraC_family_(arabinose_operon_control),_putative_287262..287412_POSITIVE 247 79 37 143 90 NC_009009:SSA_2269|3end_hypothetical_protein_2269392..2269542_NEGATIVE 246 49 1 95 47 NC_009009:SSA_0394|3end_hypothetical_protein_390931..391081_POSITIVE 244 36 2 87 51 NC_009009:SSA_0820|3end_Ribosomal_protein_S21,_putative_801505..801655_POSITIVE 240 103 64 101 63 NC_009009:SSA_0851|3end_Cation_efflux_family_protein,_putative_837644..837794_NEGATIVE 239 56 13 151 101 NC_009009:SSA_2221|3end_Cps9E,_putative_2221455..2221605_NEGATIVE 237 80 32 50 3 NC_009009:SSA_0839|3end_hypothetical_protein_827013..827163_POSITIVE 237 51 14 137 96 NC_009009:SSA_0800|3end_Glutamine_amidotransferase,_putative_781989..782139_NEGATIVE 237 58 18 63 22 NC_009009:SSA_0631|3end_Tryptophan_synthase_beta_chain,_putative_621133..621283_POSITIVE 235 45 11 79 53 NC_009009:SSA_0030|3end_Phosphoribosylformylglycinamidine_synthase,_putative_36424..36574_POSITIVE 234 50 9 66 26 NC_009009:SSA_0589|3end_Acetylornithine_deacetylase/succinyl-diaminopimelate_desuccinylase_(M20/M25/M40_family_peptidase),_putative_582207..582357_POSITIVE 234 43 13 43 18 NC_009009:SSA_0546|3end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_541963..542113_POSITIVE 234 55 17 42 3 NC_009009:SSA_0503|3end_Peptide_ABC_transporter,_ATP-binding_protein,_putative_503102..503252_POSITIVE 232 54 11 130 80 NC_009009:SSA_1436|3end_hypothetical_protein_1442199..1442349_NEGATIVE 230 81 45 50 18 NC_009009:SSA_0209|3end_Glutamyl_aminopeptidase,_putative_206572..206722_NEGATIVE