Origin IGS: aaaacgattcacttatcgacattggggctggaaaaatccagctccttttgaatggcttgactaaggtttttgtagtaaaatagaaagaaatactgcaaggaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttccttgcagtatttctttctattttactacaaaaaccttagtcaagccattcaaaaggagctggatttttccagccccaatgtcgataagtgaatcgtttt Mask Tandem Repeat Region ================================================ aaaacgattcacttatcgacattggggctggaaaaatccagctccttttgaatggcttgactaaggtttttgtagtaaaatagaaagaaatactgcaaggaa Find is-nt database================================================ Query_seq: SSA_1066:SSA_1067|SSA_1066:SSA_1067:ABC-type oligopeptide transport system, putative:hypothetical protein:->->:1086437..1086538 102 aaaacgattcacttatcgacattggggctggaaaaatccagctccttttgaatggcttgactaaggtttttgtagtaaaatagaaagaaatactgcaaggaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1066:SSA_1067|SSA_1066:SSA_1067:ABC-type oligopeptide transport system, putative:hypothetical protein:->->:1086437..1086538 102 aaaacgattcacttatcgacattggggctggaaaaatccagctccttttgaatggcttgactaaggtttttgtagtaaaatagaaagaaatactgcaaggaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1066:SSA_1067|SSA_1066:SSA_1067:ABC-type oligopeptide transport system, putative:hypothetical protein:->->:1086437..1086538 102 aaaacgattcacttatcgacattggggctggaaaaatccagctccttttgaatggcttgactaaggtttttgtagtaaaatagaaagaaatactgcaaggaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaacgattcacttatcgacattggggctggaaaaatccagctccttttgaatggcttgactaaggtttttgtagtaaaatagaaagaaatactgcaaggaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 2 End: 91 . F S E S I S M P A P F I W S R K F P K V L T K T T F Y F S M ........... aaaacgattcacttatcgacattggggctggaaaaatccagctccttttgaatggcttgactaaggtttttgtagtaaaatagaaagaaatactgcaaggaa 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================================================ aaaacgattcacttatcgacattggggctggaaaaatccagctccttttgaatggcttgactaaggtttttgtagtaaaatagaaagaaatactgcaaggaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1066:SSA_1067|SSA_1066:SSA_1067:ABC-type oligopeptide transport system, putative:hypothetical protein:->->:1086437..1086538 102 aaaacgattcacttatcgacattggggctggaaaaatccagctccttttgaatggcttgactaaggtttttgtagtaaaatagaaagaaatactgcaaggaa Intra-Species Hit: Count: 1 Min: 1 Max: 102 Len: 102 Subject: NC_009009_SSA_1066_SSA_1067|ABC-type oligopeptide transport system, putative:hypothetical protein|POSITIVE:POSITIVE|[1086437,1086538]|102 HSP 1 e-value: 2.0E-51 bit: 202.0 Len: 102 Query Start:1 Query End:102 Subject Strand: POSITIVE Subject Start: 1 Subject End: 102 aaaacgattcacttatcgacattggggctggaaaaatccagctccttttgaatggcttgactaaggtttttgtagtaaaatagaaagaaatactgcaaggaa aaaacgattcacttatcgacattggggctggaaaaatccagctccttttgaatggcttgactaaggtttttgtagtaaaatagaaagaaatactgcaaggaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAACGAUUCACUUAUCGACAUUGGGGCUGGAAAAAUCCAGCUCCUUUUGAAUGGCUUGACUAAGGUUUUUGUAGUAAAAUAGAAAGAAAUACUGCAAGGAA ...........(((((((((((((((((((((....))))))))).....))))..)))).)))).(((((((((((.............))))))))))). (-28.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCCUUGCAGUAUUUCUUUCUAUUUUACUACAAAAACCUUAGUCAAGCCAUUCAAAAGGAGCUGGAUUUUUCCAGCCCCAAUGUCGAUAAGUGAAUCGUUUU ....(((.((((.............)))).)))...........((((.(((((...((.((((((....)))))).))............))))).)))). (-17.78) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 59 13 119 73 NC_009009:SSA_0607|5end_ABC_transporter,_permease_component,_putative_596926..597156_NEGATIVE 311 70 24 202 156 NC_009009:SSA_1492|5end_hypothetical_protein_1498954..1499184_NEGATIVE 291 63 23 210 165 NC_009009:SSA_0242|5end_hypothetical_protein_234978..235208_POSITIVE 291 70 24 206 152 NC_009009:SSA_0210|5end_hypothetical_protein_207757..207987_POSITIVE 281 70 23 164 106 NC_009009:SSA_1673|5end_hypothetical_protein_1670353..1670583_POSITIVE 280 66 21 210 168 NC_009009:SSA_1897|5end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894450..1894680_NEGATIVE 279 69 23 152 111 NC_009009:SSA_2330|5end_Acetyltransferase,_putative_2333655..2333885_NEGATIVE 279 70 24 123 67 NC_009009:SSA_1672|5end_hypothetical_protein_1670389..1670619_NEGATIVE 278 61 25 76 37 NC_009009:SSA_0093|5end_V-type_sodium_ATPase,_subunit_D,_putative_94286..94516_POSITIVE 277 69 23 49 3 NC_009009:SSA_0271|5end_Glycosylhydrolase,_family_35,_putative_264235..264465_POSITIVE 275 64 25 48 13 NC_009009:SSA_2270|5end_Aspartyl-tRNA_synthetase,_putative_2272068..2272298_NEGATIVE 275 46 11 77 46 NC_009009:SSA_0005|5end_GTP-binding_protein,_putative_3821..4051_POSITIVE 274 66 23 201 151 NC_009009:SSA_0928|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_936679..936909_POSITIVE 274 60 18 192 143 NC_009009:SSA_0487|5end_Delta-aminolevulinic_acid_dehydratase,_putative_487349..487579_POSITIVE 272 70 26 229 182 NC_009009:SSA_2366|5end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368869..2369099_NEGATIVE 272 69 24 57 9 NC_009009:SSA_1890|5end_Acetyltransferase,_putative_1888145..1888375_NEGATIVE 270 67 25 178 130 NC_009009:SSA_2055|5end_hypothetical_protein_2058160..2058390_NEGATIVE 270 72 35 140 107 NC_009009:SSA_1441|5end_Phosphoribosyl-AMP_cyclohydrolase,_putative_1445183..1445413_NEGATIVE 270 69 22 79 27 NC_009009:SSA_1017|5end_hypothetical_protein_1022072..1022302_POSITIVE 270 58 13 207 163 NC_009009:SSA_0030|5end_Phosphoribosylformylglycinamidine_synthase,_putative_32610..32840_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 60 12 75 26 NC_009009:SSA_1066|3end_ABC-type_oligopeptide_transport_system,_putative_1086376..1086526_POSITIVE 347 69 24 69 22 NC_009009:SSA_2094|3end_Conserved_uncharacterized_protein_2097990..2098140_NEGATIVE 340 59 13 144 98 NC_009009:SSA_0608|3end_Macrolide-efflux_protein,_putative_596901..597051_NEGATIVE 299 58 18 121 64 NC_009009:SSA_1341|3end_Carbamoyl-phosphate_synthase_large_chain,_putative_1356648..1356798_NEGATIVE 281 70 23 68 10 NC_009009:SSA_1671|3end_hypothetical_protein_1670337..1670487_POSITIVE 279 69 23 111 70 NC_009009:SSA_2331|3end_D-alanine_transfer_protein,_putative_2333696..2333846_NEGATIVE 278 61 25 79 40 NC_009009:SSA_0092|3end_V-type_sodium_ATPase,_subunit_B,_putative_94369..94519_POSITIVE 277 69 23 48 2 NC_009009:SSA_0270|3end_Phosphotransferase_system_(PTS)_cellobiose-specific,_IIC_component,_putative_264314..264464_POSITIVE 272 69 24 56 8 NC_009009:SSA_1891|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888146..1888296_NEGATIVE 270 77 38 151 111 NC_009009:SSA_2068|3end_Superfamily_I_DNA_and_RNA_helicases,_putative_2070931..2071081_NEGATIVE 270 55 11 96 39 NC_009009:SSA_1535|3end_hypothetical_protein_1542457..1542607_NEGATIVE 270 72 35 140 107 NC_009009:SSA_1442|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445183..1445333_NEGATIVE 270 69 22 92 40 NC_009009:SSA_1016|3end_Phosphoenolpyruvate_synthase,_putative_1022165..1022315_POSITIVE 269 68 26 150 108 NC_009009:SSA_2045|3end_Reductase,_putative_2048427..2048577_NEGATIVE 267 58 12 76 23 NC_009009:SSA_1968|3end_Ketol-acid_reductoisomerase,_putative_1963659..1963809_NEGATIVE 265 57 11 84 39 NC_009009:SSA_0886|3end_Enolase,_putative_881057..881207_POSITIVE 258 62 21 74 33 NC_009009:SSA_1079|3end_hypothetical_protein_1097448..1097598_POSITIVE 251 44 4 91 59 NC_009009:SSA_0831|3end_Nucleotide_sugar_synthetase-like_protein,_putative_816755..816905_POSITIVE 250 68 24 74 30 NC_009009:SSA_0125|3end_50S_ribosomal_protein_L30,_putative_117192..117342_POSITIVE 249 48 3 59 9 NC_009009:SSA_1285|3end_hypothetical_protein_1304993..1305143_NEGATIVE