Origin IGS: tagatttaattaaaatgactagaaagtctgagatatgatcctatctcaggctttttctttatcattttgagtatttaaacattgctaatatgcctttgctttgataaaatagaaaagtatgtgaaataaacaggcaactgtttaaaggagaaatggagtttat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataaactccatttctcctttaaacagttgcctgtttatttcacatacttttctattttatcaaagcaaaggcatattagcaatgtttaaatactcaaaatgataaagaaaaagcctgagataggatcatatctcagactttctagtcattttaattaaatcta Mask Tandem Repeat Region ================================================ tagatttaattaaaatgactagaaagtctgagatatgatcctatctcaggctttttctttatcattttgagtatttaaacattgctaatatgcctttgctttgataaaatagaaaagtatgtgaaataaacaggcaactgtttaaaggagaaatggagtttat Find is-nt database================================================ Query_seq: SSA_0955:SSA_0956|SSA_0955:SSA_0956:Aminopeptidase N, putative:surface protein D:->->:961200..961362 163 tagatttaattaaaatgactagaaagtctgagatatgatcctatctcaggctttttctttatcattttgagtatttaaacattgctaatatgcctttgctttgataaaatagaaaagtatgtgaaataaacaggcaactgtttaaaggagaaatggagtttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0955:SSA_0956|SSA_0955:SSA_0956:Aminopeptidase N, putative:surface protein D:->->:961200..961362 163 tagatttaattaaaatgactagaaagtctgagatatgatcctatctcaggctttttctttatcattttgagtatttaaacattgctaatatgcctttgctttgataaaatagaaaagtatgtgaaataaacaggcaactgtttaaaggagaaatggagtttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0955:SSA_0956|SSA_0955:SSA_0956:Aminopeptidase N, putative:surface protein D:->->:961200..961362 163 tagatttaattaaaatgactagaaagtctgagatatgatcctatctcaggctttttctttatcattttgagtatttaaacattgctaatatgcctttgctttgataaaatagaaaagtatgtgaaataaacaggcaactgtttaaaggagaaatggagtttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagatttaattaaaatgactagaaagtctgagatatgatcctatctcaggctttttctttatcattttgagtatttaaacattgctaatatgcctttgctttgataaaatagaaaagtatgtgaaataaacaggcaactgtttaaaggagaaatggagtttat Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 65 End: 163 ................................................................ K S Y K F M A L I G K S Q Y F L F T H S I F L C S N L P S I S N M tagatttaattaaaatgactagaaagtctgagatatgatcctatctcaggctttttctttatcattttgagtatttaaacattgctaatatgcctttgctttgataaaatagaaaagtatgtgaaataaacaggcaactgtttaaaggagaaatggagtttat 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: 85 Start: 81 End: 110 ................................................................................ATTGCTAATATGCCTTTGCTTTGATAAAAT..................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagatttaattaaaatgactagaaagtctgagatatgatcctatctcaggctttttctttatcattttgagtatttaaacattgctaatatgcctttgctttgataaaatagaaaagtatgtgaaataaacaggcaactgtttaaaggagaaatggagtttat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 48 HP_score: -4.2 Tail_Score: -3.1434 Start: 16 End: 61 Full_Region: TAGATTTAATTAAAA TGACTAGAAAGTCTGAGATA TGATCC TATCTCAGGCTTTTTCTTTA TCATTTTGAGTATTT ...............TGACTAGAAAGTCTGAGATATGATCCTATCTCAGGCTTTTTCTTTA...................................................................................................... TransTerm Strand: - Conf: 68 HP_score: -6.2 Tail_Score: -4.05816 Start: 26 End: 51 Full_Region: aatgataaagaaaaa gcctgagata ggatca tatctcagac tttctagtcatttta .........................gcctgagataggatcatatctcagac................................................................................................................ Find igs database================================================ Query_seq: SSA_0955:SSA_0956|SSA_0955:SSA_0956:Aminopeptidase N, putative:surface protein D:->->:961200..961362 163 tagatttaattaaaatgactagaaagtctgagatatgatcctatctcaggctttttctttatcattttgagtatttaaacattgctaatatgcctttgctttgataaaatagaaaagtatgtgaaataaacaggcaactgtttaaaggagaaatggagtttat Intra-Species Hit: Count: 1 Min: 1 Max: 163 Len: 163 Subject: NC_009009_SSA_0955_SSA_0956|Aminopeptidase N, putative:surface protein D|POSITIVE:POSITIVE|[961200,961362]|163 HSP 1 e-value: 1.0E-87 bit: 323.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 1 Subject End: 163 tagatttaattaaaatgactagaaagtctgagatatgatcctatctcaggctttttctttatcattttgagtatttaaacattgctaatatgcctttgctttgataaaatagaaaagtatgtgaaataaacaggcaactgtttaaaggagaaatggagtttat tagatttaattaaaatgactagaaagtctgagatatgatcctatctcaggctttttctttatcattttgagtatttaaacattgctaatatgcctttgctttgataaaatagaaaagtatgtgaaataaacaggcaactgtttaaaggagaaatggagtttat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAUUUAAUUAAAAUGACUAGAAAGUCUGAGAUAUGAUCCUAUCUCAGGCUUUUUCUUUAUCAUUUUGAGUAUUUAAACAUUGCUAAUAUGCCUUUGCUUUGAUAAAAUAGAAAAGUAUGUGAAAUAAACAGGCAACUGUUUAAAGGAGAAAUGGAGUUUAU (((((....(((((((((..(((((((((((((((......)))))))))))..))))...)))))))))..)))))..((((.((.((((((.(((.((.(......).))))).))))))....(((((((....)))))))....)).))))........ (-41.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAACUCCAUUUCUCCUUUAAACAGUUGCCUGUUUAUUUCACAUACUUUUCUAUUUUAUCAAAGCAAAGGCAUAUUAGCAAUGUUUAAAUACUCAAAAUGAUAAAGAAAAAGCCUGAGAUAGGAUCAUAUCUCAGACUUUCUAGUCAUUUUAAUUAAAUCUA ...................(((((((....))))))).........................(((((...((......))..)))))........((((((((..((((..((.((((((((......)))))))).)))))).))))))))........... (-28.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 53 13 141 92 NC_009009:SSA_1132|5end_TatC,_sec-independent_protein_translocase,_putative_1158645..1158875_POSITIVE 260 64 26 86 41 NC_009009:SSA_0105|5end_Uridine_kinase,_putative_106761..106991_POSITIVE 256 69 26 48 1 NC_009009:SSA_0658|5end_Conserved_uncharacterized_protein_642126..642356_POSITIVE 240 100 52 199 137 NC_009009:SSA_0269|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262550..262780_POSITIVE 239 58 18 179 135 NC_009009:SSA_1376|5end_Transport_protein,_putative_1396111..1396341_NEGATIVE 239 60 17 202 162 NC_009009:SSA_1258|5end_Purine_nucleoside_phosphorylase,_family_1,_putative_1284652..1284882_NEGATIVE 239 54 19 71 37 NC_009009:SSA_0346|5end_hypothetical_protein_339448..339678_POSITIVE 237 67 27 174 130 NC_009009:SSA_0893|5end_ATP-binding_cassette_transporter-like_protein,_putative_884527..884757_POSITIVE 235 60 11 225 167 NC_009009:SSA_1923|5end_NADPH-q_uinone_reductase_(modulator_of_drug_activity_B),_putative_1912698..1912928_NEGATIVE 235 55 16 230 192 NC_009009:SSA_0708|5end_hypothetical_protein_694144..694374_POSITIVE 232 88 49 82 41 NC_009009:SSA_1538|5end_hypothetical_protein_1544482..1544712_POSITIVE 232 56 21 225 191 NC_009009:SSA_1314|5end_Fe-S-cluster_oxidoreductase,_putative_1331240..1331470_NEGATIVE 228 69 27 118 72 NC_009009:SSA_1992|5end_Fructose-bisphosphate_aldolase,_putative_1989972..1990202_NEGATIVE 221 70 41 126 88 NC_009009:SSA_0271|5end_Glycosylhydrolase,_family_35,_putative_264235..264465_POSITIVE 221 52 21 190 155 NC_009009:SSA_0033|5end_Phosphoribosylglycinamide_(GAR)_formyltransferase,_putative_38957..39187_POSITIVE 218 54 20 213 174 NC_009009:SSA_2373|5end_DNA_replication_and_repair_protein_recF,_putative_2374208..2374438_POSITIVE 216 60 14 228 166 NC_009009:SSA_0517|5end_Sensor_histidine_kinase,_putative_515060..515290_POSITIVE 215 59 15 127 90 NC_009009:SSA_0745|5end_hypothetical_protein_727035..727265_NEGATIVE 214 81 47 68 34 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 214 56 19 49 13 NC_009009:SSA_0136|5end_ABC_transporter,_Zn_porter,_putative_131014..131244_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 427 70 21 81 35 NC_009009:SSA_0955|3end_Aminopeptidase_N,_putative_961139..961289_POSITIVE 303 59 21 92 56 NC_009009:SSA_0395|3end_6-phospho-beta-glucosidase,_putative_392580..392730_POSITIVE 286 61 24 80 46 NC_009009:SSA_0224|3end_hypothetical_protein_218518..218668_POSITIVE 265 70 21 115 60 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 262 62 25 94 59 NC_009009:SSA_1535|3end_hypothetical_protein_1542457..1542607_NEGATIVE 260 64 26 60 15 NC_009009:SSA_0104|3end_Queuine_tRNA-ribosyltransferase,_putative_106815..106965_POSITIVE 250 56 14 50 13 NC_009009:SSA_2201|3end_hypothetical_protein_2202237..2202387_POSITIVE 248 60 14 64 21 NC_009009:SSA_0708|3end_hypothetical_protein_694757..694907_POSITIVE 247 69 21 98 57 NC_009009:SSA_1127|3end_H2O-forming_NADH_dehydrogenase,_putative_1153187..1153337_POSITIVE 242 55 20 61 29 NC_009009:SSA_1110|3end_hypothetical_protein_1136185..1136335_POSITIVE 240 59 15 85 38 NC_009009:SSA_1349|3end_Transcriptional_regulator,_biotin_repressor_family,_putative_1366513..1366663_POSITIVE 237 67 27 145 101 NC_009009:SSA_0892|3end_ATP-binding_cassette_lipoprotein,_putative_884578..884728_POSITIVE 235 56 15 74 36 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 235 55 16 47 9 NC_009009:SSA_0707|3end_Lactose_phosphotransferase_system_transcriptional_repressor,_putative_694041..694191_POSITIVE 232 56 21 57 23 NC_009009:SSA_1315|3end_hypothetical_protein_1331408..1331558_NEGATIVE 231 57 28 29 2 NC_009009:SSA_0396|3end_hypothetical_protein_392648..392798_NEGATIVE 229 56 13 80 38 NC_009009:SSA_1205|3end_Bta,_putative_1230057..1230207_POSITIVE 221 58 19 149 98 NC_009009:SSA_1664|3end_Phosphatidylethanolamine_N-methyltransferase,_putative_1664449..1664599_NEGATIVE 221 70 41 125 87 NC_009009:SSA_0270|3end_Phosphotransferase_system_(PTS)_cellobiose-specific,_IIC_component,_putative_264314..264464_POSITIVE 220 53 15 73 40 NC_009009:SSA_2271|3end_hypothetical_protein_2272238..2272388_NEGATIVE