Origin IGS: attttctccaaatcaaattgataaccataataataaaatagggtaacaatttaagagacctatgtcaagcccccgtattgcctcaggttaaatctgaccgattcggcttaaatattttgccggt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 accggcaaaatatttaagccgaatcggtcagatttaacctgaggcaatacgggggcttgacataggtctcttaaattgttaccctattttattattatggttatcaatttgatttggagaaaat Mask Tandem Repeat Region ================================================ attttctccaaatcaaattgataaccataataataaaatagggtaacaatttaagagacctatgtcaagcccccgtattgcctcaggttaaatctgaccgattcggcttaaatattttgccggt Find is-nt database================================================ Query_seq: TDE1651:TDE1652|TDE1651:TDE1652:BioY family protein:ABC transporter, ATP-binding/permease protein:<-<-:1698823..1698946 124 attttctccaaatcaaattgataaccataataataaaatagggtaacaatttaagagacctatgtcaagcccccgtattgcctcaggttaaatctgaccgattcggcttaaatattttgccggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1651:TDE1652|TDE1651:TDE1652:BioY family protein:ABC transporter, ATP-binding/permease protein:<-<-:1698823..1698946 124 attttctccaaatcaaattgataaccataataataaaatagggtaacaatttaagagacctatgtcaagcccccgtattgcctcaggttaaatctgaccgattcggcttaaatattttgccggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1651:TDE1652|TDE1651:TDE1652:BioY family protein:ABC transporter, ATP-binding/permease protein:<-<-:1698823..1698946 124 attttctccaaatcaaattgataaccataataataaaatagggtaacaatttaagagacctatgtcaagcccccgtattgcctcaggttaaatctgaccgattcggcttaaatattttgccggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attttctccaaatcaaattgataaccataataataaaatagggtaacaatttaagagacctatgtcaagcccccgtattgcctcaggttaaatctgaccgattcggcttaaatattttgccggt Predict ORF larger than 30AA ================================================ attttctccaaatcaaattgataaccataataataaaatagggtaacaatttaagagacctatgtcaagcccccgtattgcctcaggttaaatctgaccgattcggcttaaatattttgccggt 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: 40 End: 69 .......................................CTTGACATAGGTCTCTTAAATTGTTACCCT....................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attttctccaaatcaaattgataaccataataataaaatagggtaacaatttaagagacctatgtcaagcccccgtattgcctcaggttaaatctgaccgattcggcttaaatattttgccggt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1651:TDE1652|TDE1651:TDE1652:BioY family protein:ABC transporter, ATP-binding/permease protein:<-<-:1698823..1698946 124 attttctccaaatcaaattgataaccataataataaaatagggtaacaatttaagagacctatgtcaagcccccgtattgcctcaggttaaatctgaccgattcggcttaaatattttgccggt Intra-Species Hit: Count: 1 Min: 1 Max: 124 Len: 124 Subject: NC_002967_TDE1651_TDE1652|BioY family protein:ABC transporter, ATP-binding/permease protein|NEGATIVE:NEGATIVE|[1698823,1698946]|124 HSP 1 e-value: 1.0E-64 bit: 246.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 attttctccaaatcaaattgataaccataataataaaatagggtaacaatttaagagacctatgtcaagcccccgtattgcctcaggttaaatctgaccgattcggcttaaatattttgccggt attttctccaaatcaaattgataaccataataataaaatagggtaacaatttaagagacctatgtcaagcccccgtattgcctcaggttaaatctgaccgattcggcttaaatattttgccggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUCUCCAAAUCAAAUUGAUAACCAUAAUAAUAAAAUAGGGUAACAAUUUAAGAGACCUAUGUCAAGCCCCCGUAUUGCCUCAGGUUAAAUCUGACCGAUUCGGCUUAAAUAUUUUGCCGGU ...........(((.....)))...................(((((..(((((((.(((....)))......(((.((((..((((((...)))))).)))).))))))))))...)))))... (-19.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCGGCAAAAUAUUUAAGCCGAAUCGGUCAGAUUUAACCUGAGGCAAUACGGGGGCUUGACAUAGGUCUCUUAAAUUGUUACCCUAUUUUAUUAUUAUGGUUAUCAAUUUGAUUUGGAGAAAAU ..((((...........))))....(((((((((((((((((((((((..(((((((((...)))))))))...))))))..............))).)))))..))))))))).......... (-24.43) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 975 110 61 201 152 NC_002967:TDE1651|5end_BioY_family_protein_1698732..1698962_NEGATIVE 447 101 68 195 164 NC_002967:TDE2323|5end_mechanosensitive_ion_channel_family_protein_2359084..2359314_NEGATIVE 374 103 61 185 140 NC_002967:TDE0968|5end_translation_elongation_factor_P_993126..993356_NEGATIVE 308 106 61 136 83 NC_002967:TDE1681|5end_V-type_ATP_synthase_subunit_D_1733537..1733767_NEGATIVE 305 120 72 221 171 NC_002967:TDE1818|5end_hypothetical_protein_1853791..1854021_NEGATIVE 305 89 41 128 67 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 303 107 63 131 86 NC_002967:TDE2094|5end_hypothetical_protein_2121319..2121549_NEGATIVE 303 90 42 66 29 NC_002967:TDE1441|5end_dTDP-glucose_4,6-dehydratase_1486247..1486477_POSITIVE 303 99 62 189 153 NC_002967:TDE1114|5end_transcriptional_regulator,_TetR_family_1148905..1149135_NEGATIVE 291 107 66 43 2 NC_002967:TDE2748|5end_acetyltransferase,_GNAT_family_2805108..2805338_POSITIVE 284 108 61 158 109 NC_002967:TDE0292|5end_hypothetical_protein_322014..322244_NEGATIVE 283 106 70 45 7 NC_002967:TDE0549|5end_TfoX_N-terminal_domain_family_protein_587317..587547_NEGATIVE 283 107 61 230 184 NC_002967:TDE0018|5end_LysM_domain_protein_23573..23803_NEGATIVE 280 107 69 46 5 NC_002967:TDE1750|5end_hypothetical_protein_1803825..1804055_NEGATIVE 275 120 71 188 138 NC_002967:TDE2430|5end_bacteriocin_ABC_transporter,_bacteriocin-binding_protein,_putative_2459173..2459403_NEGATIVE 275 107 64 70 29 NC_002967:TDE0693|5end_phosphomethylpyrimidine_kinase_729942..730172_POSITIVE 270 110 72 164 125 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 269 80 40 47 9 NC_002967:TDE2060|5end_hypothetical_protein_2086521..2086751_POSITIVE 269 84 42 69 26 NC_002967:TDE1974|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_1988910..1989140_NEGATIVE 268 116 71 152 102 NC_002967:TDE1078|5end_metallo-beta-lactamase_family_protein_1109739..1109969_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 308 106 61 125 72 NC_002967:TDE1682|3end_V-type_ATP_synthase_subunit_B_1733548..1733698_NEGATIVE 306 109 61 140 92 NC_002967:TDE0019|3end_formate--tetrahydrofolate_ligase_23665..23815_NEGATIVE 305 89 41 126 65 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 303 90 42 47 10 NC_002967:TDE1440|3end_glucose-1-phosphate_thymidylyltransferase_1486308..1486458_POSITIVE 303 99 62 56 20 NC_002967:TDE1115|3end_DNA-binding_protein,_putative_1149038..1149188_NEGATIVE 290 90 41 111 36 NC_002967:TDE0362|3end_bacterial_Ig-like_domain_protein_407501..407651_NEGATIVE 278 120 73 135 79 NC_002967:TDE2517|3end_DNA_repair_protein_RadA_2542454..2542604_NEGATIVE 273 99 51 51 1 NC_002967:TDE2588|3end_integrase_domain_protein_2624778..2624928_POSITIVE 265 86 41 132 94 NC_002967:TDE1665|3end_hypothetical_protein_1718908..1719058_NEGATIVE 256 110 68 65 13 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 255 120 72 49 7 NC_002967:TDE0592|3end_acetyl-CoA_carboxylase,_biotin_carboxyl_carrier_protein_631363..631513_NEGATIVE 255 120 72 135 81 NC_002967:TDE0377|3end_hypothetical_protein_431885..432035_NEGATIVE 254 101 63 98 51 NC_002967:TDE0479|3end_hydroxylamine_reductase_535029..535179_NEGATIVE 252 89 54 64 25 NC_002967:TDE2119|3end_glycine_reductase_complex_selenoprotein_GrdB2_2151398..2151548_NEGATIVE 252 119 73 64 4 NC_002967:TDE2037|3end_ATP:guanido_phosphotransferase_domain_protein_2066647..2066797_NEGATIVE 252 107 74 82 45 NC_002967:TDE0352|3end_ribose_5-phosphate_isomerase_B_396739..396889_POSITIVE 250 107 68 135 99 NC_002967:TDE0136|3end_hypothetical_protein_156723..156873_POSITIVE 249 110 67 137 94 NC_002967:TDE1930|3end_hypothetical_protein_1947432..1947582_NEGATIVE 248 109 63 52 7 NC_002967:TDE1049|3end_elongation_factor_EF-2_1077454..1077604_POSITIVE 248 120 72 121 75 NC_002967:TDE0923|3end_ABC_transporter,_ATP-binding/permease_protein_943920..944070_NEGATIVE