Origin IGS: ttttgtttgtgttactctaaattaattaatcatttaattcgccatcacacactgatactgcacttgcggtaggtttattgcctgttccgtttgccgttctcaatttgcaaaaagcggtgcaaagttacgtctttttagtggaatgaacaaatata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatatttgttcattccactaaaaagacgtaactttgcaccgctttttgcaaattgagaacggcaaacggaacaggcaataaacctaccgcaagtgcagtatcagtgtgtgatggcgaattaaatgattaattaatttagagtaacacaaacaaaa Mask Tandem Repeat Region ================================================ ttttgtttgtgttactctaaattaattaatcatttaattcgccatcacacactgatactgcacttgcggtaggtttattgcctgttccgtttgccgttctcaatttgcaaaaagcggtgcaaagttacgtctttttagtggaatgaacaaatata Find is-nt database================================================ Query_seq: PI0631:PI0632|PI0631:PI0632:50S ribosomal protein L25/general stress protein:NusB family protein (N utilization substance protein B):->->:578461..578615 155 ttttgtttgtgttactctaaattaattaatcatttaattcgccatcacacactgatactgcacttgcggtaggtttattgcctgttccgtttgccgttctcaatttgcaaaaagcggtgcaaagttacgtctttttagtggaatgaacaaatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0631:PI0632|PI0631:PI0632:50S ribosomal protein L25/general stress protein:NusB family protein (N utilization substance protein B):->->:578461..578615 155 ttttgtttgtgttactctaaattaattaatcatttaattcgccatcacacactgatactgcacttgcggtaggtttattgcctgttccgtttgccgttctcaatttgcaaaaagcggtgcaaagttacgtctttttagtggaatgaacaaatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0631:PI0632|PI0631:PI0632:50S ribosomal protein L25/general stress protein:NusB family protein (N utilization substance protein B):->->:578461..578615 155 ttttgtttgtgttactctaaattaattaatcatttaattcgccatcacacactgatactgcacttgcggtaggtttattgcctgttccgtttgccgttctcaatttgcaaaaagcggtgcaaagttacgtctttttagtggaatgaacaaatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttgtttgtgttactctaaattaattaatcatttaattcgccatcacacactgatactgcacttgcggtaggtttattgcctgttccgtttgccgttctcaatttgcaaaaagcggtgcaaagttacgtctttttagtggaatgaacaaatata Predict ORF larger than 30AA ================================================ ttttgtttgtgttactctaaattaattaatcatttaattcgccatcacacactgatactgcacttgcggtaggtttattgcctgttccgtttgccgttctcaatttgcaaaaagcggtgcaaagttacgtctttttagtggaatgaacaaatata 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================================================ ttttgtttgtgttactctaaattaattaatcatttaattcgccatcacacactgatactgcacttgcggtaggtttattgcctgttccgtttgccgttctcaatttgcaaaaagcggtgcaaagttacgtctttttagtggaatgaacaaatata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0631:PI0632|PI0631:PI0632:50S ribosomal protein L25/general stress protein:NusB family protein (N utilization substance protein B):->->:578461..578615 155 ttttgtttgtgttactctaaattaattaatcatttaattcgccatcacacactgatactgcacttgcggtaggtttattgcctgttccgtttgccgttctcaatttgcaaaaagcggtgcaaagttacgtctttttagtggaatgaacaaatata Intra-Species Hit: Count: 1 Min: 1 Max: 155 Len: 155 Subject: pint_PI0631_PI0632|50S ribosomal protein L25/general stress protein:NusB family protein (N utilization substance protein B)|POSITIVE:POSITIVE|[578461,578615]|155 HSP 1 e-value: 6.0E-83 bit: 307.0 Len: 155 Query Start:1 Query End:155 Subject Strand: POSITIVE Subject Start: 1 Subject End: 155 ttttgtttgtgttactctaaattaattaatcatttaattcgccatcacacactgatactgcacttgcggtaggtttattgcctgttccgtttgccgttctcaatttgcaaaaagcggtgcaaagttacgtctttttagtggaatgaacaaatata ttttgtttgtgttactctaaattaattaatcatttaattcgccatcacacactgatactgcacttgcggtaggtttattgcctgttccgtttgccgttctcaatttgcaaaaagcggtgcaaagttacgtctttttagtggaatgaacaaatata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUGUUUGUGUUACUCUAAAUUAAUUAAUCAUUUAAUUCGCCAUCACACACUGAUACUGCACUUGCGGUAGGUUUAUUGCCUGUUCCGUUUGCCGUUCUCAAUUUGCAAAAAGCGGUGCAAAGUUACGUCUUUUUAGUGGAAUGAACAAAUAUA .((((((..(.........((((((........))))))..........((((((((((((....))))))......(((((((((...(((((.(........).))))).))))).))))............))))))..)..)))))).... (-30.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAUUUGUUCAUUCCACUAAAAAGACGUAACUUUGCACCGCUUUUUGCAAAUUGAGAACGGCAAACGGAACAGGCAAUAAACCUACCGCAAGUGCAGUAUCAGUGUGUGAUGGCGAAUUAAAUGAUUAAUUAAUUUAGAGUAACACAAACAAAA ....((((((.......((....))..((.((((((...((((..(..((.(((((..((.(((..(((...(((.......))).)))....))).)).))))).))..).))))((((((....))))))....)))))).))...)))))). (-28.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 468 120 72 89 42 pint:PI0093|5end_riboflavin_biosynthesis_protein_90489..90719_POSITIVE 370 98 54 83 28 pint:PI1625|5end_conserved_hypothetical_protein;_possible_phage_transposase_1549316..1549546_POSITIVE 370 98 54 83 28 pint:PI0332|5end_conserved_hypothetical_protein_312600..312830_POSITIVE 366 87 50 176 138 pint:PI1909|5end_DNA_gyrase,_B_subunit_1853223..1853453_POSITIVE 355 108 66 166 106 pint:PI0218|5end_conserved_hypothetical_protein_210770..211000_POSITIVE 337 89 47 213 158 pint:PI1811|5end_conserved_hypothetical_protein_1749518..1749748_POSITIVE 335 90 41 201 147 pint:PI0735|5end_ABC_transporter,_ATP-binding_/_permease_668793..669023_POSITIVE 331 99 52 180 124 pint:PI1610|5end_Na+/H+_anti-porter_1536942..1537172_POSITIVE 331 99 58 69 24 pint:PI0262|5end_conserved_hypothetical_protein_254685..254915_POSITIVE 326 100 58 62 25 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 325 126 82 67 7 pint:PI2158|5end_glycosyl_transferase,_group_2_family_protein_2104392..2104622_POSITIVE 325 100 54 218 169 pint:PI1497|5end_LuxS_protein,_autoinducer_AI-2_production_protein_1417571..1417801_POSITIVE 324 97 53 188 123 pint:PI1411|5end_conserved_hypothetical_protein_1331884..1332114_POSITIVE 321 95 53 176 132 pint:PI0743|5end_hypothetical_protein_672728..672958_POSITIVE 318 108 63 198 149 pint:PI0546|5end_hypothetical_protein_497799..498029_POSITIVE 316 100 52 161 101 pint:PI0529|5end_hypothetical_protein_483026..483256_POSITIVE 315 98 51 174 124 pint:PI1980|5end_conserved_hypothetical_protein_1937470..1937700_POSITIVE 315 130 81 157 102 pint:PI0839|5end_conserved_hypothetical_protein_773843..774073_POSITIVE 313 102 64 87 42 pint:PI1824|5end_ThiJ/PfpI_family_protein_1764479..1764709_POSITIVE 310 146 116 157 127 pint:PI1737|5end_glycyl-tRNA_synthetase_1657766..1657996_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 366 87 50 77 39 pint:PI1908|3end_transcriptional_regulator,_AraC_family_1853204..1853354_POSITIVE 355 108 66 110 50 pint:PI0217|3end_conserved_hypothetical_protein;_possible_lipoprotein_210794..210944_POSITIVE 338 132 93 46 1 pint:PI0094|3end_protoporphyrinogen_oxidase_90511..90661_POSITIVE 335 90 41 88 34 pint:PI0734|3end_ABC_transporter,_ATP-binding_/_permease_668760..668910_POSITIVE 331 99 58 69 24 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 330 100 58 143 103 pint:PI1388|3end_transcriptional_regulator,_LuxR_family_1310024..1310174_POSITIVE 321 95 53 117 73 pint:PI0742|3end_hypothetical_protein_672749..672899_POSITIVE 308 89 41 148 106 pint:PI1574|3end_conserved_hypothetical_protein_1501226..1501376_POSITIVE 304 98 53 141 92 pint:PI0489|3end_probable_cardiolipin_synthetase_449108..449258_POSITIVE 302 93 52 91 41 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 302 129 110 55 36 pint:PI0520|3end_hypothetical_protein_478951..479101_POSITIVE 301 135 92 113 69 pint:PI0968|3end_hypothetical_protein_896646..896796_POSITIVE 300 97 52 98 31 pint:PI0356|3end_hypothetical_protein_327288..327438_POSITIVE 300 120 72 140 84 pint:PI0355|3end_probable__N-acetylmuramoyl-L-alanine_amidase_326698..326848_POSITIVE 298 108 65 115 69 pint:PI1827|3end_peptidase,_M23/M37_family,_N-terminal_1768602..1768752_POSITIVE 295 117 80 138 97 pint:PI1514|3end_tRNA_nucleotidyltransferase/poly(A)_polymerase_1434072..1434222_POSITIVE 294 100 52 61 6 pint:PI0728|3end_integrase_661508..661658_POSITIVE 294 118 72 76 27 pint:PI0418|3end_hypothetical_protein_386856..387006_POSITIVE 293 109 61 147 104 pint:PI0336|3end_hypothetical_protein_314806..314956_POSITIVE 291 70 24 144 101 pint:PI0188|3end_phosphomethylpyrimidine_kinase_179670..179820_POSITIVE