Origin IGS: tactattttatatcatgctgacttcagtcagataagcagcatgataccttttcctttccaaagatatacagtctctattataacaaaaaacaggcgcaaacgcacctgctgacagtgattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaatcactgtcagcaggtgcgtttgcgcctgttttttgttataatagagactgtatatctttggaaaggaaaaggtatcatgctgcttatctgactgaagtcagcatgatataaaatagta Mask Tandem Repeat Region ================================================ tactattttatatcatgctgacttcagtcagataagcagcatgataccttttcctttccaaagatatacagtctctattataacaaaaaacaggcgcaaacgcacctgctgacagtgattt Find is-nt database================================================ Query_seq: SSA_1561:SSA_1562|SSA_1561:SSA_1562:Ribonuclease III, putative:hypothetical protein:<-<-:1565974..1566094 121 tactattttatatcatgctgacttcagtcagataagcagcatgataccttttcctttccaaagatatacagtctctattataacaaaaaacaggcgcaaacgcacctgctgacagtgattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1561:SSA_1562|SSA_1561:SSA_1562:Ribonuclease III, putative:hypothetical protein:<-<-:1565974..1566094 121 tactattttatatcatgctgacttcagtcagataagcagcatgataccttttcctttccaaagatatacagtctctattataacaaaaaacaggcgcaaacgcacctgctgacagtgattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1561:SSA_1562|SSA_1561:SSA_1562:Ribonuclease III, putative:hypothetical protein:<-<-:1565974..1566094 121 tactattttatatcatgctgacttcagtcagataagcagcatgataccttttcctttccaaagatatacagtctctattataacaaaaaacaggcgcaaacgcacctgctgacagtgattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tactattttatatcatgctgacttcagtcagataagcagcatgataccttttcctttccaaagatatacagtctctattataacaaaaaacaggcgcaaacgcacctgctgacagtgattt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 5 End: 109 .... M L Y H A D F S Q I S S M I P F P F Q R Y T V S I I T K N R R K R T C ............ Protein_Len: 35 Strand: - Start: 11 End: 115 .......... I M S V E T L Y A A H Y R K R E L S I C D R N Y C F V P A F A G A S M ...... tactattttatatcatgctgacttcagtcagataagcagcatgataccttttcctttccaaagatatacagtctctattataacaaaaaacaggcgcaaacgcacctgctgacagtgattt 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================================================ tactattttatatcatgctgacttcagtcagataagcagcatgataccttttcctttccaaagatatacagtctctattataacaaaaaacaggcgcaaacgcacctgctgacagtgattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1561:SSA_1562|SSA_1561:SSA_1562:Ribonuclease III, putative:hypothetical protein:<-<-:1565974..1566094 121 tactattttatatcatgctgacttcagtcagataagcagcatgataccttttcctttccaaagatatacagtctctattataacaaaaaacaggcgcaaacgcacctgctgacagtgattt Intra-Species Hit: Count: 1 Min: 1 Max: 121 Len: 121 Subject: NC_009009_SSA_1561_SSA_1562|Ribonuclease III, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1565974,1566094]|121 HSP 1 e-value: 8.0E-63 bit: 240.0 Len: 121 Query Start:1 Query End:121 Subject Strand: POSITIVE Subject Start: 1 Subject End: 121 tactattttatatcatgctgacttcagtcagataagcagcatgataccttttcctttccaaagatatacagtctctattataacaaaaaacaggcgcaaacgcacctgctgacagtgattt tactattttatatcatgctgacttcagtcagataagcagcatgataccttttcctttccaaagatatacagtctctattataacaaaaaacaggcgcaaacgcacctgctgacagtgattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACUAUUUUAUAUCAUGCUGACUUCAGUCAGAUAAGCAGCAUGAUACCUUUUCCUUUCCAAAGAUAUACAGUCUCUAUUAUAACAAAAAACAGGCGCAAACGCACCUGCUGACAGUGAUUU ..........((((((((((...((.....))....)))))))))).....((((.((...((((.....))))................((((.((....)).))))..)).)).))... (-24.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUCACUGUCAGCAGGUGCGUUUGCGCCUGUUUUUUGUUAUAAUAGAGACUGUAUAUCUUUGGAAAGGAAAAGGUAUCAUGCUGCUUAUCUGACUGAAGUCAGCAUGAUAUAAAAUAGUA .....(((((..((((((((....))))))))(((((.((....((((((.......))))))..)).))))).((((((((((((((.........))).)))))))))))...))))). (-34.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 896 120 71 211 162 NC_009009:SSA_1561|5end_Ribonuclease_III,_putative_1565883..1566113_NEGATIVE 347 114 90 144 119 NC_009009:SSA_0037|5end_Phosphoribosylamine-glycine_ligase;_phosphoribosyl_glycinamide_synthetase_(GARS),_putative_44272..44502_POSITIVE 310 120 71 171 116 NC_009009:SSA_2160|5end_Deoxyuridinetriphosphatase,_putative_2160066..2160296_NEGATIVE 308 55 13 148 104 NC_009009:SSA_0511|5end_Propanediol_utilization_kinase,_putative_509610..509840_POSITIVE 287 54 12 215 176 NC_009009:SSA_1810|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1795396..1795626_NEGATIVE 273 54 11 154 121 NC_009009:SSA_0479|5end_CbiQ_protein,_putative_480425..480655_POSITIVE 272 118 92 47 20 NC_009009:SSA_0190|5end_hypothetical_protein_191481..191711_POSITIVE 271 59 13 142 88 NC_009009:SSA_1419|5end_hypothetical_protein_1429675..1429905_NEGATIVE 271 87 41 123 84 NC_009009:SSA_0874|5end_hypothetical_protein_867935..868165_POSITIVE 269 107 66 150 114 NC_009009:SSA_0856|5end_Glycosyltransferase_(vectorial_glycosyl_polymerization_(VGP)_family),_putative_843210..843440_POSITIVE 269 75 37 121 86 NC_009009:SSA_0343|5end_DNA-damage-inducible_protein_P,_putative_337525..337755_POSITIVE 259 37 6 210 175 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 259 78 38 137 106 NC_009009:SSA_0402|5end_Histidine_kinase,_putative_399144..399374_POSITIVE 258 52 16 143 106 NC_009009:SSA_0303|5end_surface_protein_C_296451..296681_POSITIVE 255 58 15 157 119 NC_009009:SSA_0765|5end_hypothetical_protein_745519..745749_POSITIVE 253 60 16 226 180 NC_009009:SSA_1504|5end_hypothetical_protein_1506947..1507177_NEGATIVE 252 120 87 225 190 NC_009009:SSA_0475|5end_CbiK_protein,_putative_477723..477953_POSITIVE 251 119 92 77 37 NC_009009:SSA_1544|5end_Conserved_uncharacterized_protein_1548796..1549026_NEGATIVE 250 120 74 163 106 NC_009009:SSA_0065|5end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67175..67405_POSITIVE 248 49 5 59 9 NC_009009:SSA_1728|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1714293..1714523_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 120 71 86 31 NC_009009:SSA_2161|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160151..2160301_NEGATIVE 306 48 3 130 91 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 284 74 35 146 105 NC_009009:SSA_1854|3end_Conserved_uncharacterized_protein_1849433..1849583_NEGATIVE 273 120 77 85 33 NC_009009:SSA_0867|3end_hypothetical_protein_860711..860861_POSITIVE 273 54 11 36 3 NC_009009:SSA_0478|3end_Cobalt_transport_protein_cbiN,_putative_480387..480537_POSITIVE 271 59 13 133 79 NC_009009:SSA_1420|3end_Homoserine_O-succinyltransferase,_putative_1429684..1429834_NEGATIVE 269 107 66 52 16 NC_009009:SSA_0855|3end_O-acetylhomoserine_sulfhydrylase,_putative_843192..843342_POSITIVE 264 49 1 142 77 NC_009009:SSA_0540|3end_Glycerol_uptake_facilitator_protein,_putative_535748..535898_POSITIVE 260 119 91 138 114 NC_009009:SSA_1786|3end_Conserved_uncharacterized_protein_1769996..1770146_NEGATIVE 260 75 35 53 3 NC_009009:SSA_1602|3end_Exoribonuclease,_VacB/Rnb_family,_putative_1607022..1607172_NEGATIVE 259 78 38 135 104 NC_009009:SSA_0401|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_399222..399372_POSITIVE 254 43 13 144 111 NC_009009:SSA_0510|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_509697..509847_POSITIVE 253 64 24 111 74 NC_009009:SSA_2101|3end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2104509..2104659_NEGATIVE 253 60 16 146 100 NC_009009:SSA_1505|3end_hypothetical_protein_1507027..1507177_NEGATIVE 251 119 92 61 21 NC_009009:SSA_1545|3end_Conserved_uncharacterized_protein_1548812..1548962_NEGATIVE 250 52 11 142 92 NC_009009:SSA_1594|3end_Metalloendopeptidase,_putative_1598457..1598607_NEGATIVE 246 109 62 115 52 NC_009009:SSA_1668|3end_NrdI_protein,_putative_1667738..1667888_NEGATIVE 238 120 87 77 39 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 238 60 13 115 54 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 237 119 89 55 20 NC_009009:SSA_0473|3end_Precorrin-6x_reductase,_putative_476331..476481_POSITIVE