Origin IGS: tagtatatatatctagaagaagaaaataaacattttaaggaatttgaaacgataagaatgtattcgtatgcgaaatcggtttaagattctttaaataccgggaggattttcaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attgaaaatcctcccggtatttaaagaatcttaaaccgatttcgcatacgaatacattcttatcgtttcaaattccttaaaatgtttattttcttcttctagatatatatacta Mask Tandem Repeat Region ================================================ tagtatatatatctagaagaagaaaataaacattttaaggaatttgaaacgataagaatgtattcgtatgcgaaatcggtttaagattctttaaataccgggaggattttcaat Find is-nt database================================================ Query_seq: TDE0876:TDE0877|TDE0876:TDE0877:hypothetical protein:hypothetical protein:<-->:898615..898728 114 tagtatatatatctagaagaagaaaataaacattttaaggaatttgaaacgataagaatgtattcgtatgcgaaatcggtttaagattctttaaataccgggaggattttcaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0876:TDE0877|TDE0876:TDE0877:hypothetical protein:hypothetical protein:<-->:898615..898728 114 tagtatatatatctagaagaagaaaataaacattttaaggaatttgaaacgataagaatgtattcgtatgcgaaatcggtttaagattctttaaataccgggaggattttcaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0876:TDE0877|TDE0876:TDE0877:hypothetical protein:hypothetical protein:<-->:898615..898728 114 tagtatatatatctagaagaagaaaataaacattttaaggaatttgaaacgataagaatgtattcgtatgcgaaatcggtttaagattctttaaataccgggaggattttcaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagtatatatatctagaagaagaaaataaacattttaaggaatttgaaacgataagaatgtattcgtatgcgaaatcggtttaagattctttaaataccgggaggattttcaat Predict ORF larger than 30AA ================================================ tagtatatatatctagaagaagaaaataaacattttaaggaatttgaaacgataagaatgtattcgtatgcgaaatcggtttaagattctttaaataccgggaggattttcaat 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================================================ tagtatatatatctagaagaagaaaataaacattttaaggaatttgaaacgataagaatgtattcgtatgcgaaatcggtttaagattctttaaataccgggaggattttcaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0876:TDE0877|TDE0876:TDE0877:hypothetical protein:hypothetical protein:<-->:898615..898728 114 tagtatatatatctagaagaagaaaataaacattttaaggaatttgaaacgataagaatgtattcgtatgcgaaatcggtttaagattctttaaataccgggaggattttcaat Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: NC_002967_TDE0876_TDE0877|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[898615,898728]|114 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 tagtatatatatctagaagaagaaaataaacattttaaggaatttgaaacgataagaatgtattcgtatgcgaaatcggtttaagattctttaaataccgggaggattttcaat tagtatatatatctagaagaagaaaataaacattttaaggaatttgaaacgataagaatgtattcgtatgcgaaatcggtttaagattctttaaataccgggaggattttcaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUAUAUAUAUCUAGAAGAAGAAAAUAAACAUUUUAAGGAAUUUGAAACGAUAAGAAUGUAUUCGUAUGCGAAAUCGGUUUAAGAUUCUUUAAAUACCGGGAGGAUUUUCAAU ..................(((((..........((((((((((((....((((.........((((....)))))))).....))))))))))))..((....)).)))))... (-20.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUGAAAAUCCUCCCGGUAUUUAAAGAAUCUUAAACCGAUUUCGCAUACGAAUACAUUCUUAUCGUUUCAAAUUCCUUAAAAUGUUUAUUUUCUUCUUCUAGAUAUAUAUACUA .((((((.......((((..((((......))))))))..((((....)))).............))))))............((.(((..(((......)))...))).)).. (-10.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 806 110 61 201 152 NC_002967:TDE0876|5end_hypothetical_protein_898524..898754_NEGATIVE 254 103 70 224 184 NC_002967:TDE0890|5end_hypothetical_protein_905890..906120_POSITIVE 250 109 63 203 146 NC_002967:TDE1515|5end_permease_domain_protein_1561978..1562208_POSITIVE 230 106 61 144 101 NC_002967:TDE1287|5end_transcription-repair_coupling_factor_1322738..1322968_POSITIVE 229 109 63 158 119 NC_002967:TDE2582|5end_GGDEF_domain_protein_2611789..2612019_POSITIVE 229 102 62 229 192 NC_002967:TDE1161|5end_hypothetical_protein_1196041..1196271_NEGATIVE 227 102 72 231 200 NC_002967:TDE1425|5end_hypothetical_protein_1467548..1467778_POSITIVE 225 106 61 66 29 NC_002967:TDE1678|5end_ribosomal_protein_S6_1730483..1730713_NEGATIVE 223 105 70 144 108 NC_002967:TDE2404|5end_RNA_polymerase_sigma-54_factor,_putative_2430704..2430934_NEGATIVE 219 106 64 105 66 NC_002967:TDE2306|5end_hypothetical_protein_2344251..2344481_NEGATIVE 219 104 70 27 1 NC_002967:TDE1265|5end_1-hydroxy-2-methyl-2-(E)-butenyl_4-diphosphate_synthase_1300436..1300666_NEGATIVE 217 80 39 70 29 NC_002967:TDE0151|5end_integral_membrane_protein,_YeeE/YedE_family_173101..173331_NEGATIVE 216 105 70 52 15 NC_002967:TDE1549|5end_recombination_protein_RecR_1592140..1592370_POSITIVE 216 103 63 74 32 NC_002967:TDE1184|5end_hypothetical_protein_1211334..1211564_POSITIVE 214 90 50 211 174 NC_002967:TDE0667|5end_FeS_assembly_protein_SufB_704290..704520_POSITIVE 213 72 33 227 180 NC_002967:TDE1595|5end_cobalamin_biosynthesis_protein_CbiD_1646039..1646269_NEGATIVE 213 110 61 198 152 NC_002967:TDE0969|5end_hypothetical_protein_993260..993490_POSITIVE 212 104 63 97 62 NC_002967:TDE0137|5end_carbohydrate_kinase,_FGGY_family_156640..156870_POSITIVE 210 110 66 161 112 NC_002967:TDE2363|5end_high-affinity_branched_chain_amino_acid_ABC_transporter,_ATP-binding_protein_2398179..2398409_NEGATIVE 207 106 65 56 1 NC_002967:TDE1259|5end_amino_acid_carrier_family_protein_1293670..1293900_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 254 103 70 68 28 NC_002967:TDE0889|3end_hypothetical_protein_905814..905964_POSITIVE 243 110 61 129 83 NC_002967:TDE2577|3end_hypothetical_protein_2602490..2602640_NEGATIVE 230 106 61 143 100 NC_002967:TDE1286|3end_TPR_domain_protein_1322817..1322967_POSITIVE 230 110 62 92 45 NC_002967:TDE0626|3end_hypothetical_protein_659684..659834_POSITIVE 223 105 70 132 96 NC_002967:TDE2405|3end_hypothetical_protein_2430716..2430866_NEGATIVE 219 106 64 121 82 NC_002967:TDE2307|3end_seryl-tRNA_synthetase_2344235..2344385_NEGATIVE 218 106 63 151 97 NC_002967:TDE1514|3end_permease_domain_protein_1562009..1562159_POSITIVE 217 80 39 49 8 NC_002967:TDE0152|3end_amino_acid_permease_family_protein_173122..173272_NEGATIVE 215 110 70 79 32 NC_002967:TDE0886|3end_hypothetical_protein_904374..904524_POSITIVE 213 101 74 84 62 NC_002967:TDE0239|3end_glycine_reductase_complex_protein_GrdD_271828..271978_NEGATIVE 212 104 63 100 65 NC_002967:TDE0136|3end_hypothetical_protein_156723..156873_POSITIVE 207 105 64 121 79 NC_002967:TDE2328|3end_efflux_pump_component_MtrF_2366364..2366514_POSITIVE 203 102 63 37 5 NC_002967:TDE0398|3end_oligopeptide/dipeptide_ABC_transporter,_periplasmic_peptide-binding_protein_449436..449586_POSITIVE 202 69 26 64 18 NC_002967:TDE2013|3end_hypothetical_protein_2034359..2034509_NEGATIVE 200 105 62 36 7 NC_002967:TDE0158|3end_hypothetical_protein_185724..185874_NEGATIVE 199 109 61 145 92 NC_002967:TDE1716|3end_glyoxalase_family_protein_1770851..1771001_NEGATIVE 197 107 65 32 1 NC_002967:TDE0871|3end_hypothetical_protein_894657..894807_NEGATIVE 196 95 56 82 42 NC_002967:TDE2406|3end_TldD/PmbA_family_protein_2432047..2432197_NEGATIVE 196 108 63 151 103 NC_002967:TDE1073|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1104635..1104785_POSITIVE 195 59 20 43 5 NC_002967:TDE1747|3end_nicotinate_(nicotinamide)_nucleotide_adenylyltransferase_1800712..1800862_NEGATIVE