Origin IGS: ggtgagggatgaatttacataaaggaactttaaaaaacatttctaaagtccatttttagcggacaagttaatgaatttccttatattttgctccgatatttcacgaggccgcctattacaggcgtaatgaggta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tacctcattacgcctgtaataggcggcctcgtgaaatatcggagcaaaatataaggaaattcattaacttgtccgctaaaaatggactttagaaatgttttttaaagttcctttatgtaaattcatccctcacc Mask Tandem Repeat Region ================================================ ggtgagggatgaatttacataaaggaactttaaaaaacatttctaaagtccatttttagcggacaagttaatgaatttccttatattttgctccgatatttcacgaggccgcctattacaggcgtaatgaggta Find is-nt database================================================ Query_seq: TDE2451:TDE2452|TDE2451:TDE2452:S-adenosylmethionine:tRNA ribosyltransferase-isomerase:hypothetical protein:->->:2481016..2481149 134 ggtgagggatgaatttacataaaggaactttaaaaaacatttctaaagtccatttttagcggacaagttaatgaatttccttatattttgctccgatatttcacgaggccgcctattacaggcgtaatgaggta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2451:TDE2452|TDE2451:TDE2452:S-adenosylmethionine:tRNA ribosyltransferase-isomerase:hypothetical protein:->->:2481016..2481149 134 ggtgagggatgaatttacataaaggaactttaaaaaacatttctaaagtccatttttagcggacaagttaatgaatttccttatattttgctccgatatttcacgaggccgcctattacaggcgtaatgaggta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2451:TDE2452|TDE2451:TDE2452:S-adenosylmethionine:tRNA ribosyltransferase-isomerase:hypothetical protein:->->:2481016..2481149 134 ggtgagggatgaatttacataaaggaactttaaaaaacatttctaaagtccatttttagcggacaagttaatgaatttccttatattttgctccgatatttcacgaggccgcctattacaggcgtaatgaggta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggtgagggatgaatttacataaaggaactttaaaaaacatttctaaagtccatttttagcggacaagttaatgaatttccttatattttgctccgatatttcacgaggccgcctattacaggcgtaatgaggta Predict ORF larger than 30AA ================================================ ggtgagggatgaatttacataaaggaactttaaaaaacatttctaaagtccatttttagcggacaagttaatgaatttccttatattttgctccgatatttcacgaggccgcctattacaggcgtaatgaggta 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================================================ ggtgagggatgaatttacataaaggaactttaaaaaacatttctaaagtccatttttagcggacaagttaatgaatttccttatattttgctccgatatttcacgaggccgcctattacaggcgtaatgaggta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2451:TDE2452|TDE2451:TDE2452:S-adenosylmethionine:tRNA ribosyltransferase-isomerase:hypothetical protein:->->:2481016..2481149 134 ggtgagggatgaatttacataaaggaactttaaaaaacatttctaaagtccatttttagcggacaagttaatgaatttccttatattttgctccgatatttcacgaggccgcctattacaggcgtaatgaggta Intra-Species Hit: Count: 1 Min: 1 Max: 134 Len: 134 Subject: NC_002967_TDE2451_TDE2452|S-adenosylmethionine:tRNA ribosyltransferase-isomerase:hypothetical protein|POSITIVE:POSITIVE|[2481016,2481149]|134 HSP 1 e-value: 2.0E-70 bit: 266.0 Len: 134 Query Start:1 Query End:134 Subject Strand: POSITIVE Subject Start: 1 Subject End: 134 ggtgagggatgaatttacataaaggaactttaaaaaacatttctaaagtccatttttagcggacaagttaatgaatttccttatattttgctccgatatttcacgaggccgcctattacaggcgtaatgaggta ggtgagggatgaatttacataaaggaactttaaaaaacatttctaaagtccatttttagcggacaagttaatgaatttccttatattttgctccgatatttcacgaggccgcctattacaggcgtaatgaggta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUGAGGGAUGAAUUUACAUAAAGGAACUUUAAAAAACAUUUCUAAAGUCCAUUUUUAGCGGACAAGUUAAUGAAUUUCCUUAUAUUUUGCUCCGAUAUUUCACGAGGCCGCCUAUUACAGGCGUAAUGAGGUA .((((((((..............(((.(((((...........))))))))....(((((......))))).....)))))))).....((..((........))..)).(((((((((....))))).)))). (-26.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACCUCAUUACGCCUGUAAUAGGCGGCCUCGUGAAAUAUCGGAGCAAAAUAUAAGGAAAUUCAUUAACUUGUCCGCUAAAAAUGGACUUUAGAAAUGUUUUUUAAAGUUCCUUUAUGUAAAUUCAUCCCUCACC ..........((((((...)))))).....((((.....((((.(((..((....(.....)..))..)))))))....(((.(((((((((((.....))))))))))).)))...............)))). (-23.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 120 75 148 93 NC_002967:TDE1292|5end_TldD/PmbA_family_protein_1330621..1330851_NEGATIVE 297 130 87 62 24 NC_002967:TDE0078|5end_glycine_reductase_complex_selenoprotein_GrdB1_90076..90306_NEGATIVE 291 124 81 139 88 NC_002967:TDE0833|5end_lipoprotein,_putative_852992..853222_POSITIVE 287 124 91 77 47 NC_002967:TDE2731|5end_TIM-barrel_protein,_putative,_NifR3_family_2787372..2787602_POSITIVE 279 113 72 143 96 NC_002967:TDE1372|5end_hypothetical_protein_1416897..1417127_NEGATIVE 277 129 92 223 168 NC_002967:TDE1000|5end_3-hydroxyacid_dehydrogenase_family_protein_1026763..1026993_POSITIVE 274 130 92 75 36 NC_002967:TDE2476|5end_carbamate_kinase_2499450..2499680_NEGATIVE 274 123 88 219 172 NC_002967:TDE1550|5end_diphosphate--fructose-6-phosphate_1-phosphotransferase_1592747..1592977_POSITIVE 267 111 83 108 78 NC_002967:TDE0697|5end_hypothetical_protein_734372..734602_NEGATIVE 262 130 91 60 13 NC_002967:TDE1185|5end_lipoprotein,_putative_1212973..1213203_NEGATIVE 261 125 86 200 162 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 260 114 73 55 8 NC_002967:TDE1279|5end_phosphoribosylformylglycinamidine_synthase_II_1315115..1315345_NEGATIVE 257 114 73 117 79 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 253 117 76 126 83 NC_002967:TDE2353|5end_flagellar_hook-associated_protein_2389129..2389359_POSITIVE 251 117 73 152 109 NC_002967:TDE1165|5end_hypothetical_protein_1198390..1198620_NEGATIVE 250 117 77 205 154 NC_002967:TDE2384|5end_phosphoglycerate_mutase_family_protein_2413626..2413856_POSITIVE 249 123 86 167 125 NC_002967:TDE2635|5end_acetyltransferase,_GNAT_family_2675453..2675683_POSITIVE 249 130 86 69 16 NC_002967:TDE2467|5end_hypothetical_protein_2490930..2491160_NEGATIVE 246 130 86 187 154 NC_002967:TDE0868|5end_oxidoreductase,_FAD/FMN-binding_890385..890615_POSITIVE 246 84 45 146 95 NC_002967:TDE0675|5end_hypothetical_protein_713994..714224_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 120 75 148 93 NC_002967:TDE1293|3end_TldD/PmbA_family_protein_1330621..1330771_NEGATIVE 297 130 87 43 5 NC_002967:TDE0079|3end_DNA-binding_protein_90095..90245_NEGATIVE 294 124 82 111 75 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 291 124 81 142 91 NC_002967:TDE0832|3end_hypothetical_protein_853075..853225_POSITIVE 287 124 91 64 34 NC_002967:TDE2730|3end_hydrolase,_TatD_family_2787439..2787589_POSITIVE 284 126 88 72 32 NC_002967:TDE0759|3end_hypothetical_protein_799128..799278_NEGATIVE 267 124 87 57 19 NC_002967:TDE2543|3end_hypothetical_protein_2570753..2570903_NEGATIVE 262 130 91 48 1 NC_002967:TDE1186|3end_hypothetical_protein_1212985..1213135_NEGATIVE 261 125 86 68 30 NC_002967:TDE2104|3end_hypothetical_protein_2128525..2128675_NEGATIVE 259 114 76 122 83 NC_002967:TDE1403|3end_ABC_transporter,_ATP-binding_protein_1444500..1444650_NEGATIVE 257 114 73 115 77 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 253 117 76 103 60 NC_002967:TDE2352|3end_flagellar_hook-associated_protein_2389186..2389336_POSITIVE 251 126 86 109 55 NC_002967:TDE2548|3end_hypothetical_protein_2573064..2573214_NEGATIVE 251 117 73 148 105 NC_002967:TDE1166|3end_hypothetical_protein_1198394..1198544_NEGATIVE 249 123 86 145 103 NC_002967:TDE2634|3end_hypothetical_protein_2675511..2675661_POSITIVE 249 127 84 143 92 NC_002967:TDE2357|3end_iron_compound_ABC_transporter,_permease_protein_2393101..2393251_POSITIVE 246 130 86 122 89 NC_002967:TDE0867|3end_hypothetical_protein_890400..890550_POSITIVE 246 84 45 149 98 NC_002967:TDE0674|3end_hypothetical_protein_714077..714227_POSITIVE 245 111 79 134 96 NC_002967:TDE1054|3end_methyl-accepting_chemotaxis_protein_1082998..1083148_POSITIVE 244 130 88 120 72 NC_002967:TDE1848|3end_hypothetical_protein_1875897..1876047_NEGATIVE