Origin IGS: tgaggagcaataggggttatgtttataaaaaaagattctctactattaagaataatttcatataatgggattgcgatagtgattgttgcttcaattatggcaagcctttttggaatcatgatttttaatgaattgaatatgagacttttagataaatctcgtgagagaactttgcttgtaaacaaggcttatttgttctttattgatagaagtcgtgaacag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctgttcacgacttctatcaataaagaacaaataagccttgtttacaagcaaagttctctcacgagatttatctaaaagtctcatattcaattcattaaaaatcatgattccaaaaaggcttgccataattgaagcaacaatcactatcgcaatcccattatatgaaattattcttaatagtagagaatctttttttataaacataacccctattgctcctca Mask Tandem Repeat Region ================================================ tgaggagcaataggggttatgtttataaaaaaagattctctactattaagaataatttcatataatgggattgcgatagtgattgttgcttcaattatggcaagcctttttggaatcatgatttttaatgaattgaatatgagacttttagataaatctcgtgagagaactttgcttgtaaacaaggcttatttgttctttattgatagaagtcgtgaacag Find is-nt database================================================ Query_seq: FN0065:FN0066|FN0065:FN0066:Transcription accessory protein (S1 RNA binding domain):Two component system histidine kinase:->->:702245..702466 222 tgaggagcaataggggttatgtttataaaaaaagattctctactattaagaataatttcatataatgggattgcgatagtgattgttgcttcaattatggcaagcctttttggaatcatgatttttaatgaattgaatatgagacttttagataaatctcgtgagagaactttgcttgtaaacaaggcttatttgttctttattgatagaagtcgtgaacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0065:FN0066|FN0065:FN0066:Transcription accessory protein (S1 RNA binding domain):Two component system histidine kinase:->->:702245..702466 222 tgaggagcaataggggttatgtttataaaaaaagattctctactattaagaataatttcatataatgggattgcgatagtgattgttgcttcaattatggcaagcctttttggaatcatgatttttaatgaattgaatatgagacttttagataaatctcgtgagagaactttgcttgtaaacaaggcttatttgttctttattgatagaagtcgtgaacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0065:FN0066|FN0065:FN0066:Transcription accessory protein (S1 RNA binding domain):Two component system histidine kinase:->->:702245..702466 222 tgaggagcaataggggttatgtttataaaaaaagattctctactattaagaataatttcatataatgggattgcgatagtgattgttgcttcaattatggcaagcctttttggaatcatgatttttaatgaattgaatatgagacttttagataaatctcgtgagagaactttgcttgtaaacaaggcttatttgttctttattgatagaagtcgtgaacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaggagcaataggggttatgtttataaaaaaagattctctactattaagaataatttcatataatgggattgcgatagtgattgttgcttcaattatggcaagcctttttggaatcatgatttttaatgaattgaatatgagacttttagataaatctcgtgagagaactttgcttgtaaacaaggcttatttgttctttattgatagaagtcgtgaacag Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 10 End: 222 ......... M G V M F I K K D S L L L R I I S Y N G I A I V I V A S I M A S L F G I M I F N E L N M R L L D K S R E R T L L V N K A Protein_Len: 60 Strand: - Start: 3 End: 185 .. A I P T I N I F F S E R S N L I I E Y L P I A I T I T A E I I A L R K P I M I K L S N F I L S K S L D R S L V K S T F M ..................................... tgaggagcaataggggttatgtttataaaaaaagattctctactattaagaataatttcatataatgggattgcgatagtgattgttgcttcaattatggcaagcctttttggaatcatgatttttaatgaattgaatatgagacttttagataaatctcgtgagagaactttgcttgtaaacaaggcttatttgttctttattgatagaagtcgtgaacag 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================================================ tgaggagcaataggggttatgtttataaaaaaagattctctactattaagaataatttcatataatgggattgcgatagtgattgttgcttcaattatggcaagcctttttggaatcatgatttttaatgaattgaatatgagacttttagataaatctcgtgagagaactttgcttgtaaacaaggcttatttgttctttattgatagaagtcgtgaacag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 40 HP_score: -2.9 Tail_Score: -2.50398 Start: 141 End: 160 Full_Region: gcaaagttctctcac gagattt atctaa aagtctc atattcaattcatta ............................................................................................................................................gagatttatctaaaagtctc.............................................................. Find igs database================================================ Query_seq: FN0065:FN0066|FN0065:FN0066:Transcription accessory protein (S1 RNA binding domain):Two component system histidine kinase:->->:702245..702466 222 tgaggagcaataggggttatgtttataaaaaaagattctctactattaagaataatttcatataatgggattgcgatagtgattgttgcttcaattatggcaagcctttttggaatcatgatttttaatgaattgaatatgagacttttagataaatctcgtgagagaactttgcttgtaaacaaggcttatttgttctttattgatagaagtcgtgaacag Intra-Species Hit: Count: 1 Min: 1 Max: 222 Len: 222 Subject: NC_003454_FN0065_FN0066|Transcription accessory protein (S1 RNA binding domain):Two component system histidine kinase|POSITIVE:POSITIVE|[702245,702466]|222 HSP 1 e-value: 1.0E-110 bit: 398.0 Len: 222 Query Start:1 Query End:222 Subject Strand: POSITIVE Subject Start: 1 Subject End: 222 tgaggagcaataggggttatgtttatnnnnnnngattctctactattaagaataatttcatataatgggattgcgatagtgattgttgcttcaattatggcaagcctttttggaatcatgatttttaatgaattgaatatgagacttttagataaatctcgtgagagaactttgcttgtaaacaaggcttatttgttctttattgatagaagtcgtgaacag tgaggagcaataggggttatgtttataaaaaaagattctctactattaagaataatttcatataatgggattgcgatagtgattgttgcttcaattatggcaagcctttttggaatcatgatttttaatgaattgaatatgagacttttagataaatctcgtgagagaactttgcttgtaaacaaggcttatttgttctttattgatagaagtcgtgaacag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGGAGCAAUAGGGGUUAUGUUUAUAAAAAAAGAUUCUCUACUAUUAAGAAUAAUUUCAUAUAAUGGGAUUGCGAUAGUGAUUGUUGCUUCAAUUAUGGCAAGCCUUUUUGGAAUCAUGAUUUUUAAUGAAUUGAAUAUGAGACUUUUAGAUAAAUCUCGUGAGAGAACUUUGCUUGUAAACAAGGCUUAUUUGUUCUUUAUUGAUAGAAGUCGUGAACAG ((((((((((...((((..(((((((((..((((.((((((..((((((((((.((((((......(((.((((.(((((((........)).))))).)))).)))...))))))....)))))))))).......(((((((.((......)).)))))))))))))))))..)))))))))..))))..))))))))))..(((....)))........ (-59.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUUCACGACUUCUAUCAAUAAAGAACAAAUAAGCCUUGUUUACAAGCAAAGUUCUCUCACGAGAUUUAUCUAAAAGUCUCAUAUUCAAUUCAUUAAAAAUCAUGAUUCCAAAAAGGCUUGCCAUAAUUGAAGCAACAAUCACUAUCGCAAUCCCAUUAUAUGAAAUUAUUCUUAAUAGUAGAGAAUCUUUUUUUAUAAACAUAACCCCUAUUGCUCCUCA .(((((..................))))).........((((((.(((.(((((((((((..(((((((......)))))))...((((..((((........)))).........((.((((.(((((((......))))...))).)))).)).......)))).............).)))))).)))).))).))))))................... (-32.07) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 236 114 75 162 122 NC_003454:FN0530|5end_hypothetical_protein_1186275..1186505_POSITIVE 236 114 75 162 122 NC_003454:FN0404|5end_hypothetical_protein_1042213..1042443_POSITIVE 236 114 75 162 122 NC_003454:FN0373|5end_hypothetical_protein_1002385..1002615_POSITIVE 236 114 75 162 122 NC_003454:FN1510|5end_hypothetical_protein_14311..14541_NEGATIVE 234 121 85 57 24 NC_003454:FN1547|5end_PTS_permease_for_N-acetylglucosamine_and_glucose_63270..63500_NEGATIVE 230 93 56 77 40 NC_003454:FN0984|5end_Tetracenomycin_polyketide_synthesis_O-methyltransferase_tcmP_1637295..1637525_NEGATIVE 226 114 71 162 120 NC_003454:FN1338|5end_hypothetical_protein_1991763..1991993_NEGATIVE 218 110 88 25 8 NC_003454:FN1326|5end_Undecaprenyl_pyrophosphate_synthetase_1981890..1982120_NEGATIVE 216 109 71 62 19 NC_003454:FN0007|5end_glucose-inhibited_division_protein_A_645938..646168_POSITIVE 214 76 36 111 62 NC_003454:FN1792|5end_hypothetical_protein_273264..273494_NEGATIVE 212 127 97 170 139 NC_003454:FN0104|5end_Acetyltransferase_739896..740126_NEGATIVE 211 111 71 62 22 NC_003454:FN1723|5end_glucose-inhibited_division_protein_A_222645..222875_NEGATIVE 208 118 73 154 104 NC_003454:FN0925|5end_hypothetical_protein_1579921..1580151_POSITIVE 207 120 78 216 163 NC_003454:FN0054|5end_tyrosyl-tRNA_synthetase_690836..691066_POSITIVE 205 107 64 175 119 NC_003454:FN1351|5end_15_kDa_lipoprotein_precursor_2003372..2003602_NEGATIVE 204 108 62 169 125 NC_003454:FN2104|5end_hypothetical_protein_614237..614467_POSITIVE 202 98 56 46 1 NC_003454:FN0863|5end_hypothetical_protein_1522574..1522804_NEGATIVE 201 105 68 184 132 NC_003454:FN0909|5end_DNA_repair_protein_radC_1567654..1567884_NEGATIVE 200 108 70 100 66 NC_003454:FN0715|5end_hypothetical_protein_1373104..1373334_POSITIVE 198 106 65 89 48 NC_003454:FN1422|5end_NA+/H+_antiporter_NHAC_2088426..2088656_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 105 67 74 38 NC_003454:FN0935|3end_hypothetical_protein_1587558..1587708_NEGATIVE 258 110 70 151 110 NC_003454:FN0934|3end_chorismate_synthase_1587593..1587743_POSITIVE 245 207 164 95 50 NC_003454:FN0065|3end_Transcription_accessory_protein_(S1_RNA_binding_domain)_702184..702334_POSITIVE 230 93 56 57 20 NC_003454:FN0985|3end_Phosphoribosylglycinamide_formyltransferase_1637315..1637465_NEGATIVE 217 202 183 104 85 NC_003454:FN0317|3end_tryptophan_synthase_subunit_beta_953819..953969_NEGATIVE 215 98 55 58 12 NC_003454:FN0864|3end_hypothetical_protein_1522562..1522712_NEGATIVE 211 111 71 53 13 NC_003454:FN1724|3end_Potassium_uptake_protein_KtrA_222654..222804_NEGATIVE 208 118 73 115 65 NC_003454:FN0924|3end_hypothetical_protein_1579962..1580112_POSITIVE 204 108 62 61 17 NC_003454:FN2103|3end_RecA_protein_614209..614359_POSITIVE 195 34 3 54 21 NC_003454:FN0212|3end_hypothetical_protein_837583..837733_NEGATIVE 193 111 71 84 37 NC_003454:FN1088|3end_NADH_oxidase_1733095..1733245_POSITIVE 190 119 74 80 17 NC_003454:FN1377|3end_CITG_protein_2026131..2026281_POSITIVE 187 110 67 70 17 NC_003454:FN1641|3end_SSU_ribosomal_protein_S19P_138552..138702_NEGATIVE 184 130 82 53 10 NC_003454:FN1259|3end_Uracil-DNA_glycosylase_1915756..1915906_POSITIVE 184 117 71 128 77 NC_003454:FN0398|3end_Dipeptide_transport_system_permease_protein_dppC_1037707..1037857_POSITIVE 183 115 89 59 31 NC_003454:FN1091|3end_Sigma_factor_sigB_regulation_protein_rsbU_1737338..1737488_POSITIVE 181 121 81 55 7 NC_003454:FN1352|3end_ABC_transporter_ATP-binding_protein_2003506..2003656_NEGATIVE 180 107 63 78 33 NC_003454:FN0514|3end_hypothetical_protein_1163912..1164062_POSITIVE 180 217 185 118 79 NC_003454:FN0140|3end_Transposase_772179..772329_NEGATIVE 180 79 33 77 34 NC_003454:FN1710|3end_Integral_membrane_protein,_YGGT_family_206347..206497_POSITIVE