Origin IGS: tagaaaaaagcctataaactttgcacaattacgaataaatccctaaatttgtatttagaaacaattaatacgcatacttatgatagacgttaaagaaacattaaacgaggccgaagagcgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acgctcttcggcctcgtttaatgtttctttaacgtctatcataagtatgcgtattaattgtttctaaatacaaatttagggatttattcgtaattgtgcaaagtttataggcttttttcta Mask Tandem Repeat Region ================================================ tagaaaaaagcctataaactttgcacaattacgaataaatccctaaatttgtatttagaaacaattaatacgcatacttatgatagacgttaaagaaacattaaacgaggccgaagagcgt Find is-nt database================================================ Query_seq: PI1685:PI1687|PI1685:PI1687:GAF domain-containing protein:ribosome recycling factor:->->:1602326..1602446 121 tagaaaaaagcctataaactttgcacaattacgaataaatccctaaatttgtatttagaaacaattaatacgcatacttatgatagacgttaaagaaacattaaacgaggccgaagagcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1685:PI1687|PI1685:PI1687:GAF domain-containing protein:ribosome recycling factor:->->:1602326..1602446 121 tagaaaaaagcctataaactttgcacaattacgaataaatccctaaatttgtatttagaaacaattaatacgcatacttatgatagacgttaaagaaacattaaacgaggccgaagagcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1685:PI1687|PI1685:PI1687:GAF domain-containing protein:ribosome recycling factor:->->:1602326..1602446 121 tagaaaaaagcctataaactttgcacaattacgaataaatccctaaatttgtatttagaaacaattaatacgcatacttatgatagacgttaaagaaacattaaacgaggccgaagagcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagaaaaaagcctataaactttgcacaattacgaataaatccctaaatttgtatttagaaacaattaatacgcatacttatgatagacgttaaagaaacattaaacgaggccgaagagcgt Predict ORF larger than 30AA ================================================ tagaaaaaagcctataaactttgcacaattacgaataaatccctaaatttgtatttagaaacaattaatacgcatacttatgatagacgttaaagaaacattaaacgaggccgaagagcgt 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================================================ tagaaaaaagcctataaactttgcacaattacgaataaatccctaaatttgtatttagaaacaattaatacgcatacttatgatagacgttaaagaaacattaaacgaggccgaagagcgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1685:PI1687|PI1685:PI1687:GAF domain-containing protein:ribosome recycling factor:->->:1602326..1602446 121 tagaaaaaagcctataaactttgcacaattacgaataaatccctaaatttgtatttagaaacaattaatacgcatacttatgatagacgttaaagaaacattaaacgaggccgaagagcgt Intra-Species Hit: Count: 1 Min: 1 Max: 121 Len: 121 Subject: pint_PI1685_PI1687|GAF domain-containing protein:ribosome recycling factor|POSITIVE:POSITIVE|[1602326,1602446]|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 tagaaaaaagcctataaactttgcacaattacgaataaatccctaaatttgtatttagaaacaattaatacgcatacttatgatagacgttaaagaaacattaaacgaggccgaagagcgt tagaaaaaagcctataaactttgcacaattacgaataaatccctaaatttgtatttagaaacaattaatacgcatacttatgatagacgttaaagaaacattaaacgaggccgaagagcgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAAAAAAGCCUAUAAACUUUGCACAAUUACGAAUAAAUCCCUAAAUUUGUAUUUAGAAACAAUUAAUACGCAUACUUAUGAUAGACGUUAAAGAAACAUUAAACGAGGCCGAAGAGCGU .........((((........(((........((.....)).((((((....)))))).............))).............((((.((......)).)))))))).......... (-10.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGCUCUUCGGCCUCGUUUAAUGUUUCUUUAACGUCUAUCAUAAGUAUGCGUAUUAAUUGUUUCUAAAUACAAAUUUAGGGAUUUAUUCGUAAUUGUGCAAAGUUUAUAGGCUUUUUUCUA .........(((((......(((((.....)))))....(((((...((((...(((..((..((((((....))))))..)))))..)))).)))))..........)))))........ (-18.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 251 119 71 128 88 pint:PI0654|5end_K+-dependent_Na+/Ca+_exchanger_related-protein_596283..596513_POSITIVE 250 120 81 85 37 pint:PI2148|5end_ribonuclease_III_2094505..2094735_POSITIVE 250 120 73 131 82 pint:PI0094|5end_protoporphyrinogen_oxidase_89571..89801_POSITIVE 250 120 73 57 8 pint:PI0091|5end_hypothetical_protein_89497..89727_POSITIVE 246 120 71 140 95 pint:PI1938|5end_hypothetical_protein_1891854..1892084_POSITIVE 243 120 71 86 32 pint:PI1607|5end_ABC-related_lipoprotein_releasing_system,_ATP-binding_protein_1535125..1535355_POSITIVE 243 120 71 60 6 pint:PI1606|5end_conserved_hypothetical_protein_1535099..1535329_POSITIVE 241 120 81 59 15 pint:PI0787|5end_glycosyltransferase_724136..724366_POSITIVE 230 119 71 70 25 pint:PI0752|5end_conserved_hypothetical_protein_681882..682112_POSITIVE 228 118 72 193 155 pint:PI0785|5end_hypothetical_protein_723744..723974_POSITIVE 226 110 61 222 180 pint:PI1469|5end_hypothetical_protein_1395016..1395246_POSITIVE 224 120 77 156 111 pint:PI2171|5end_conserved_hypothetical_protein_2112735..2112965_POSITIVE 222 120 71 99 48 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 221 120 71 169 116 pint:PI1623|5end_hypothetical_protein_1547163..1547393_POSITIVE 219 120 85 224 193 pint:PI0807|5end_hydrolase,_haloacid_dehalogenase-like_hydrolase_744407..744637_POSITIVE 219 120 72 41 2 pint:PI0283|5end_Zn-dependent_peptidase_267554..267784_POSITIVE 217 120 86 154 126 pint:PI2170|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_2112238..2112468_POSITIVE 217 120 87 32 3 pint:PI1131|5end_folylpolyglutamate_synthase_1057124..1057354_POSITIVE 213 119 85 123 85 pint:PI0553|5end_recombination_protein_503344..503574_POSITIVE 211 102 61 54 11 pint:PI0761|5end_hypothetical_protein_696173..696403_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 120 71 145 99 pint:PI1798|3end__elongation_factor_Ts_1732824..1732974_POSITIVE 250 120 73 131 82 pint:PI0092|3end_regulatory_protein_RecX_89651..89801_POSITIVE 243 120 71 59 5 pint:PI1605|3end_conserved_hypothetical_protein_1535178..1535328_POSITIVE 237 45 4 73 30 pint:PI0429|3end_hypothetical_protein_399602..399752_POSITIVE 224 120 77 129 84 pint:PI2170|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_2112788..2112938_POSITIVE 220 120 73 106 55 pint:PI0027|3end_aminopeptidase_C_31756..31906_POSITIVE 219 120 71 91 41 pint:PI1136|3end_conserved_hypothetical_protein_1062541..1062691_POSITIVE 219 120 85 131 100 pint:PI0806|3end_heavy_metal_efflux_pump_744394..744544_POSITIVE 217 120 79 87 40 pint:PI0375|3end_hypothetical_protein_346082..346232_POSITIVE 215 120 71 147 96 pint:PI1943|3end_hypothetical_protein_1902206..1902356_POSITIVE 215 120 79 131 85 pint:PI0197|3end_acetate_kinase_189827..189977_POSITIVE 211 102 61 149 106 pint:PI0761|3end_hypothetical_protein_696348..696498_POSITIVE 210 119 80 127 91 pint:PI1045|3end_cytidine/deoxycytidylate_deaminase_family_protein_965648..965798_POSITIVE 208 117 79 103 54 pint:PI1727|3end__ATP-dependent_Clp_protease,_ATP-binding_subunit_1646989..1647139_POSITIVE 206 119 71 122 64 pint:PI0100|3end_LPS_biosynthesis_protein_(lipopolysaccharide_biosynthesis_protein)_96726..96876_POSITIVE 203 120 75 107 51 pint:PI1176|3end_endonuclease_III_1098819..1098969_POSITIVE 202 120 79 140 90 pint:PI0736|3end_transcriptional_regulator,_TetR_family_671271..671421_POSITIVE 201 120 80 127 73 pint:PI1801|3end_30S_ribosomal_protein_S9_1734412..1734562_POSITIVE 199 116 74 78 37 pint:PI1166|3end_hypothetical_protein_1089537..1089687_POSITIVE 194 119 71 51 1 pint:PI1551|3end_HesA/MoeB/ThiF_family_protein_1468580..1468730_POSITIVE