Origin IGS: aaaactcctttccagtccatgtagttcttagatgattatagcaaagatagggcaaaaaaactagccctcaaaagctttatagtcagcttaaaacaccagaacttggtagcttgtcagattcaaaacagcaaaaaaggagccgcttttggctcctcctctg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cagaggaggagccaaaagcggctccttttttgctgttttgaatctgacaagctaccaagttctggtgttttaagctgactataaagcttttgagggctagtttttttgccctatctttgctataatcatctaagaactacatggactggaaaggagtttt Mask Tandem Repeat Region ================================================ aaaactcctttccagtccatgtagttcttagatgattatagcaaagatagggcaaaaaaactagccctcaaaagctttatagtcagcttaaaacaccagaacttggtagcttgtcagattcaaaacagcaaaaaaggagccgcttttggctcctcctctg Find is-nt database================================================ Query_seq: SSA_1730:SSA_1731|SSA_1730:SSA_1731:hypothetical protein:ATP-dependent Clp protease, proteolytic subunit, putative:<-<-:1716148..1716307 160 aaaactcctttccagtccatgtagttcttagatgattatagcaaagatagggcaaaaaaactagccctcaaaagctttatagtcagcttaaaacaccagaacttggtagcttgtcagattcaaaacagcaaaaaaggagccgcttttggctcctcctctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1730:SSA_1731|SSA_1730:SSA_1731:hypothetical protein:ATP-dependent Clp protease, proteolytic subunit, putative:<-<-:1716148..1716307 160 aaaactcctttccagtccatgtagttcttagatgattatagcaaagatagggcaaaaaaactagccctcaaaagctttatagtcagcttaaaacaccagaacttggtagcttgtcagattcaaaacagcaaaaaaggagccgcttttggctcctcctctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1730:SSA_1731|SSA_1730:SSA_1731:hypothetical protein:ATP-dependent Clp protease, proteolytic subunit, putative:<-<-:1716148..1716307 160 aaaactcctttccagtccatgtagttcttagatgattatagcaaagatagggcaaaaaaactagccctcaaaagctttatagtcagcttaaaacaccagaacttggtagcttgtcagattcaaaacagcaaaaaaggagccgcttttggctcctcctctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaactcctttccagtccatgtagttcttagatgattatagcaaagatagggcaaaaaaactagccctcaaaagctttatagtcagcttaaaacaccagaacttggtagcttgtcagattcaaaacagcaaaaaaggagccgcttttggctcctcctctg Predict ORF larger than 30AA ================================================ aaaactcctttccagtccatgtagttcttagatgattatagcaaagatagggcaaaaaaactagccctcaaaagctttatagtcagcttaaaacaccagaacttggtagcttgtcagattcaaaacagcaaaaaaggagccgcttttggctcctcctctg 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: 81 Start: 35 End: 64 ..................................CTAGTTTTTTTGCCCTATCTTTGCTATAAT................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaactcctttccagtccatgtagttcttagatgattatagcaaagatagggcaaaaaaactagccctcaaaagctttatagtcagcttaaaacaccagaacttggtagcttgtcagattcaaaacagcaaaaaaggagccgcttttggctcctcctctg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 53 HP_score: -2.1 Tail_Score: -4.15006 Start: 94 End: 108 Full_Region: ttgaatctgacaagc tacca agttc tggtg ttttaagctgactat .............................................................................................taccaagttctggtg.................................................... Find igs database================================================ Query_seq: SSA_1730:SSA_1731|SSA_1730:SSA_1731:hypothetical protein:ATP-dependent Clp protease, proteolytic subunit, putative:<-<-:1716148..1716307 160 aaaactcctttccagtccatgtagttcttagatgattatagcaaagatagggcaaaaaaactagccctcaaaagctttatagtcagcttaaaacaccagaacttggtagcttgtcagattcaaaacagcaaaaaaggagccgcttttggctcctcctctg Intra-Species Hit: Count: 1 Min: 1 Max: 160 Len: 160 Subject: NC_009009_SSA_1730_SSA_1731|hypothetical protein:ATP-dependent Clp protease, proteolytic subunit, putative|NEGATIVE:NEGATIVE|[1716148,1716307]|160 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 160 Query Start:1 Query End:160 Subject Strand: POSITIVE Subject Start: 1 Subject End: 160 aaaactcctttccagtccatgtagttcttagatgattatagcaaagatagggcnnnnnnnctagccctcaaaagctttatagtcagcttaaaacaccagaacttggtagcttgtcagattcaaaacagcaaaaaaggagccgcttttggctcctcctctg aaaactcctttccagtccatgtagttcttagatgattatagcaaagatagggcaaaaaaactagccctcaaaagctttatagtcagcttaaaacaccagaacttggtagcttgtcagattcaaaacagcaaaaaaggagccgcttttggctcctcctctg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAACUCCUUUCCAGUCCAUGUAGUUCUUAGAUGAUUAUAGCAAAGAUAGGGCAAAAAAACUAGCCCUCAAAAGCUUUAUAGUCAGCUUAAAACACCAGAACUUGGUAGCUUGUCAGAUUCAAAACAGCAAAAAAGGAGCCGCUUUUGGCUCCUCCUCUG ............(((....(((.(((......((((...(((......(((((..........)))))...(((((........))))).....(((((...))))).))).)))).......))).)))....((((((((....))))))))...))) (-35.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGAGGAGGAGCCAAAAGCGGCUCCUUUUUUGCUGUUUUGAAUCUGACAAGCUACCAAGUUCUGGUGUUUUAAGCUGACUAUAAAGCUUUUGAGGGCUAGUUUUUUUGCCCUAUCUUUGCUAUAAUCAUCUAAGAACUACAUGGACUGGAAAGGAGUUUU (((((((((((((......))))))))))))).((((........)))).....(((.((((((..(((((.((.(((.(((..(((.....(((((..........)))))......)))))).))).)).)))))..)).)))))))........... (-47.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 895 110 61 201 152 NC_009009:SSA_1730|5end_hypothetical_protein_1716057..1716287_NEGATIVE 308 130 82 66 15 NC_009009:SSA_1897|5end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894450..1894680_NEGATIVE 302 159 114 202 146 NC_009009:SSA_0931|5end_hypothetical_protein_940281..940511_POSITIVE 297 99 51 213 174 NC_009009:SSA_1076|5end_hypothetical_protein_1094227..1094457_POSITIVE 286 129 85 178 134 NC_009009:SSA_1451|5end_Exonuclease_RexA,_putative_1456418..1456648_NEGATIVE 283 68 35 140 109 NC_009009:SSA_0065|5end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67175..67405_POSITIVE 282 150 102 54 5 NC_009009:SSA_0831|5end_Nucleotide_sugar_synthetase-like_protein,_putative_815671..815901_POSITIVE 280 150 103 191 146 NC_009009:SSA_1438|5end_Acetyltransferase,_putative_1443612..1443842_NEGATIVE 279 159 116 177 130 NC_009009:SSA_2160|5end_Deoxyuridinetriphosphatase,_putative_2160066..2160296_NEGATIVE 279 160 111 231 172 NC_009009:SSA_0279|5end_Sugar-binding_transcriptional_repressor_(DeoR),_putative_272319..272549_POSITIVE 277 160 130 210 183 NC_009009:SSA_2339|5end_Microcin_C7_resistance_protein,_putative_2340456..2340686_POSITIVE 277 107 61 55 12 NC_009009:SSA_1452|5end_Second_subunit_of_major_exonuclease,_putative_1459696..1459926_NEGATIVE 277 150 101 225 177 NC_009009:SSA_0403|5end_CAAX_amino_terminal_protease_family,_putative_400475..400705_POSITIVE 276 150 101 48 6 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 275 148 103 63 15 NC_009009:SSA_1161|5end_hypothetical_protein_1187383..1187613_POSITIVE 275 160 136 222 188 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 274 159 111 212 160 NC_009009:SSA_2393|5end_Transcriptional_regulator,_XRE_family,_putative_204056..204286_POSITIVE 273 157 113 68 17 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 271 109 62 187 144 NC_009009:SSA_1840|5end_RNA_binding_protein,_putative_1834422..1834652_NEGATIVE 271 130 82 68 12 NC_009009:SSA_0373|5end_Dihydroorotate_dehydrogenase,_putative_362062..362292_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 160 111 59 11 NC_009009:SSA_0597|3end_hypothetical_protein_588563..588713_POSITIVE 308 130 82 73 22 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 302 159 114 104 48 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 300 151 111 84 40 NC_009009:SSA_1482|3end_Pullulanase,_putative_1486949..1487099_NEGATIVE 296 157 111 83 31 NC_009009:SSA_2191|3end_Conserved_uncharacterized_protein_2193082..2193232_POSITIVE 279 159 116 92 45 NC_009009:SSA_2161|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160151..2160301_NEGATIVE 279 159 127 144 112 NC_009009:SSA_1985|3end_hypothetical_protein_1979623..1979773_NEGATIVE 278 54 12 85 42 NC_009009:SSA_1244|3end_hypothetical_protein_1268465..1268615_NEGATIVE 277 160 130 66 39 NC_009009:SSA_2338|3end_Conserved_uncharacterized_protein_2340392..2340542_POSITIVE 276 150 101 55 13 NC_009009:SSA_1651|3end_hypothetical_protein_1649587..1649737_NEGATIVE 273 157 113 75 24 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 272 108 63 57 21 NC_009009:SSA_0380|3end_Enzyme_of_poly-gamma-glutamate_biosynthesis_(capsule_formation),_putative_372378..372528_POSITIVE 270 158 113 63 20 NC_009009:SSA_0834|3end_Accessory_secretory_protein_Asp2,_putative_821119..821269_POSITIVE 266 150 102 73 20 NC_009009:SSA_0965|3end_Oxidoreductase,_putative_974035..974185_NEGATIVE 266 157 111 64 14 NC_009009:SSA_0157|3end_hypothetical_protein_153877..154027_POSITIVE 265 120 74 92 50 NC_009009:SSA_1343|3end_Aspartate_carbamoyltransferase,_putative_1361042..1361192_NEGATIVE 265 158 115 55 8 NC_009009:SSA_0281|3end_hypothetical_protein_273963..274113_POSITIVE 262 150 101 86 35 NC_009009:SSA_1832|3end_hypothetical_protein_1822614..1822764_POSITIVE 262 60 13 74 20 NC_009009:SSA_1023|3end_Von_Willebrand_factor-binding_protein_precursor,_putative_1041166..1041316_POSITIVE 261 160 111 111 63 NC_009009:SSA_2167|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165644..2165794_NEGATIVE